Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 103 of 163
Found at i:29362296 original size:60 final size:57
Alignment explanation
Indices: 29362192--29362425 Score: 197
Period size: 60 Copynumber: 4.0 Consensus size: 57
29362182 GGAGCTCCTT
** *
29362192 AAACTATCCAAAAATT-GTATTTTGACCCCTAAACTTCAAAAAATTCCATTTTTATCCCTA
1 AAACT-TCCAAAAATTACAATTTT-ACCCC-AAACTTCCAAAAATTCCATTTTTA-CCCTA
* *
29362252 AAACTTCCAAAAATTACAATTTTACCCTCAAACTTCCAAAAAATTCTATTTTTAACCCCA
1 AAACTTCCAAAAATTACAATTTTACCC-CAAACTTCC-AAAAATTCCATTTTT-ACCCTA
* ** *
29362312 AAACTTTTC-AAAATTAC-ATTTCTACCCTTGAACTTCCAAAAATTCCATTTTGA-CCTCA
1 AAAC-TTCCAAAAATTACAATTT-TACCC-CAAACTTCCAAAAATTCCATTTTTACCCT-A
* * * * * *
29362370 AAATTTCCCAAAATTACATTTTTACCCCAAAATTTCAAAAATTTCATTTTTGACCC
1 AAACTTCCAAAAATTACAATTTTACCCCAAACTTCCAAAAATTCCATTTTT-ACCC
29362426 CGATACTTTC
Statistics
Matches: 143, Mismatches: 20, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
57 23 0.16
58 19 0.13
59 43 0.30
60 54 0.38
61 4 0.03
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (57 bp):
AAACTTCCAAAAATTACAATTTTACCCCAAACTTCCAAAAATTCCATTTTTACCCTA
Found at i:29362645 original size:146 final size:146
Alignment explanation
Indices: 29362474--29362743 Score: 368
Period size: 146 Copynumber: 1.8 Consensus size: 146
29362464 GAAAATTTAG
* * * ** *
29362474 TTTTTGATCTCAATTTTTCTAAAAATTA-CTGTTTTACCCTC-AAGTGTCTAAAATATCATTTTT
1 TTTTTGATCCCAATTCTTCCAAAAATTATC-GTTTTACCCTCTAA-CATCTAAAATATCATTTCT
* * *
29362537 AACCCTAAAT-TTTCCTAAATTTACCATTTT-GCCCTCGAGAGTCTAAAATTACTATTTTACCAA
64 AACCCTAAATCTTTCC-AAAATTACCATTTTGGCCC-CAAGAGTCCAAAATTACTATTTTACCAA
29362600 CGGGCATCTAAAAAGTCCCA
127 CGGGCATCTAAAAAGTCCCA
* *
29362620 TTTTTGATCCCGATTCTTCCAAAAATTATCGTTTTACCCTCTAACATCTAAAATGTCATTTCTAA
1 TTTTTGATCCCAATTCTTCCAAAAATTATCGTTTTACCCTCTAACATCTAAAATATCATTTCTAA
*
29362685 CCTTAAATCTTTCCAAAATTACCATTTTGGCCCCAAGAGTCCAAAATTACTATTTTACC
66 CCCTAAATCTTTCCAAAATTACCATTTTGGCCCCAAGAGTCCAAAATTACTATTTTACC
29362744 CCAGGATATC
Statistics
Matches: 108, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
146 96 0.89
147 12 0.11
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (146 bp):
TTTTTGATCCCAATTCTTCCAAAAATTATCGTTTTACCCTCTAACATCTAAAATATCATTTCTAA
CCCTAAATCTTTCCAAAATTACCATTTTGGCCCCAAGAGTCCAAAATTACTATTTTACCAACGGG
CATCTAAAAAGTCCCA
Found at i:29362755 original size:28 final size:28
Alignment explanation
Indices: 29362696--29362757 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
29362686 CTTAAATCTT
* *
29362696 TCCAAAATTACCATTTTGGCCCCAAGAG
1 TCCAAAATTACCATTTTGACCCCAAGAA
* *
29362724 TCCAAAATTACTATTTT-ACCCCAGGATA
1 TCCAAAATTACCATTTTGACCCCAAGA-A
29362752 TCCAAA
1 TCCAAA
29362758 GGTCCCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.27
Consensus pattern (28 bp):
TCCAAAATTACCATTTTGACCCCAAGAA
Found at i:29375470 original size:11 final size:11
Alignment explanation
Indices: 29375454--29375555 Score: 66
Period size: 11 Copynumber: 9.1 Consensus size: 11
29375444 TACTTTGAGA
*
29375454 TTAAATTTATT
1 TTAAATTTAAT
29375465 TTAAATTTAAAT
1 TTAAATTT-AAT
** *
29375477 TTATCTTAAAT
1 TTAAATTTAAT
* *
29375488 TTAAATGTATT
1 TTAAATTTAAT
29375499 TTAAATTTAAT
1 TTAAATTTAAT
*
29375510 TTAAGTTTGAAT
1 TTAAATTT-AAT
*
29375522 TT-AGTTTAAAT
1 TTAAATTT-AAT
29375533 TT-AATATT-AT
1 TTAAAT-TTAAT
29375543 TATAAATTTAAT
1 T-TAAATTTAAT
29375555 T
1 T
29375556 AATCAAAAAG
Statistics
Matches: 71, Mismatches: 14, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
10 3 0.04
11 48 0.68
12 20 0.28
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:29375474 original size:17 final size:17
Alignment explanation
Indices: 29375454--29375512 Score: 93
Period size: 17 Copynumber: 3.5 Consensus size: 17
29375444 TACTTTGAGA
29375454 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
*
29375471 TTAAATTTATCTTAAAT
1 TTAAATTTATTTTAAAT
*
29375488 TTAAATGTATTTTAAAT
1 TTAAATTTATTTTAAAT
29375505 TT-AATTTA
1 TTAAATTTA
29375513 AGTTTGAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
16 5 0.13
17 33 0.87
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:29375503 original size:45 final size:45
Alignment explanation
Indices: 29375454--29375555 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 45
29375444 TACTTTGAGA
*
29375454 TTAAATTTATTTTAAATTTAAATTTA-TCTTAAATTTAA-ATGTATT
1 TTAAATTTAATTTAAATTTAAATTTAGT-TTAAATTTAATAT-TATT
* *
29375499 TTAAATTTAATTTAAGTTTGAATTTAGTTTAAATTTAATATTATT
1 TTAAATTTAATTTAAATTTAAATTTAGTTTAAATTTAATATTATT
*
29375544 ATAAATTTAATT
1 TTAAATTTAATT
29375556 AATCAAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
45 48 0.94
46 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (45 bp):
TTAAATTTAATTTAAATTTAAATTTAGTTTAAATTTAATATTATT
Found at i:29375523 original size:34 final size:32
Alignment explanation
Indices: 29375437--29375524 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 32
29375427 CCAAACCATT
*
29375437 TTTAATTTACTTTGAGA-TTAAATTTATTTTAAA
1 TTTAATTTA-TTTGA-ATTTAAATGTATTTTAAA
*
29375470 TTTAAATTTATCTTAAATTTAAATGTATTTTAAA
1 TTT-AATTTAT-TTGAATTTAAATGTATTTTAAA
29375504 TTTAATTTAAGTTTGAATTTA
1 TTTAATTT-A-TTTGAATTTA
29375525 GTTTAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
33 10 0.21
34 36 0.77
35 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (32 bp):
TTTAATTTATTTGAATTTAAATGTATTTTAAA
Found at i:29375536 original size:28 final size:29
Alignment explanation
Indices: 29375470--29375537 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
29375460 TTATTTTAAA
*
29375470 TTTAAATTT-ATCTTAAATTTAAATGTAT
1 TTTAAATTTAATCTTAAATTTAAATGTAG
* * *
29375498 TTTAAATTTAAT-TTAAGTTTGAATTTAG
1 TTTAAATTTAATCTTAAATTTAAATGTAG
29375526 TTTAAATTTAAT
1 TTTAAATTTAAT
29375538 ATTATTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.54
Consensus pattern (29 bp):
TTTAAATTTAATCTTAAATTTAAATGTAG
Found at i:29376316 original size:3 final size:3
Alignment explanation
Indices: 29376308--29376338 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
29376298 CATTAATGAG
29376308 TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29376339 TTAAAAGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:29376405 original size:9 final size:10
Alignment explanation
Indices: 29376308--29376408 Score: 51
Period size: 9 Copynumber: 10.6 Consensus size: 10
29376298 CATTAATGAG
29376308 TAATAA-TAA
1 TAATAATTAA
29376317 TAATAA-TAA
1 TAATAATTAA
29376326 TAATAA--AA
1 TAATAATTAA
29376334 TAAT-ATTAA
1 TAATAATTAA
*
29376343 -AAGGGAATT-A
1 TAA--TAATTAA
29376353 -AATAATTTAA
1 TAATAA-TTAA
29376363 TAA-ATATTAA
1 TAATA-ATTAA
** *
29376373 TAATGTTTTAG
1 TAAT-AATTAA
29376384 TAATAATTAA
1 TAATAATTAA
29376394 TAATAA-TAA
1 TAATAATTAA
29376403 TAATAA
1 TAATAA
29376409 AGAAATCAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
7 1 0.01
8 10 0.14
9 28 0.38
10 21 0.29
11 13 0.18
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (10 bp):
TAATAATTAA
Found at i:29377638 original size:59 final size:58
Alignment explanation
Indices: 29377543--29377683 Score: 140
Period size: 59 Copynumber: 2.4 Consensus size: 58
29377533 CCCTAAATTG
* * * * * * *
29377543 TCCAAAAATTATATTTTGACTCCTAAACTTCTAAAAATTTCATTTTTGAC-CCCAAAACT
1 TCCAAAAATTACATTTTTACCCCCAAACATCCAAAAATTCCATTTTT-ACTCCCAAAA-T
* **
29377602 TCCAAAAATTACATTTTTACCCCCGAACATCCAAAAATTCCATTTTTACTCTGAAAAT
1 TCCAAAAATTACATTTTTACCCCCAAACATCCAAAAATTCCATTTTTACTCCCAAAAT
* *
29377660 TCTAAAAATTCCATTTTTGACCCC
1 TCCAAAAATTACATTTTT-ACCCC
29377684 GACACTTTCA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 19 0.28
59 49 0.72
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (58 bp):
TCCAAAAATTACATTTTTACCCCCAAACATCCAAAAATTCCATTTTTACTCCCAAAAT
Found at i:29377696 original size:29 final size:29
Alignment explanation
Indices: 29377543--29377714 Score: 134
Period size: 29 Copynumber: 5.9 Consensus size: 29
29377533 CCCTAAATTG
** * * *
29377543 TCCAAAAATTATATTTTGACTCCTAAACT
1 TCCAAAAATTCCATTTTTACCCCGAAACT
* * *
29377572 TCTAAAAATTTCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTT-ACCCCGAAACT
* *
29377602 TCCAAAAATTACATTTTTACCCCCG-AACA
1 TCCAAAAATTCCATTTTTA-CCCCGAAACT
* * *
29377631 TCCAAAAATTCCATTTTTACTCTGAAAAT
1 TCCAAAAATTCCATTTTTACCCCGAAACT
* *
29377660 TCTAAAAATTCCATTTTTGACCCCGACACT
1 TCCAAAAATTCCATTTTT-ACCCCGAAACT
* *
29377690 TTC-AAAATTACCA-TCTTACCCCGAA
1 TCCAAAAATT-CCATTTTTACCCCGAA
29377715 TGTCTGAAAA
Statistics
Matches: 114, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
28 10 0.09
29 64 0.56
30 40 0.35
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCCGAAACT
Found at i:29377995 original size:146 final size:145
Alignment explanation
Indices: 29377737--29378002 Score: 360
Period size: 146 Copynumber: 1.8 Consensus size: 145
29377727 TCATTTTTGA
** * **
29377737 TCCCGATTTTTCTAAAAATTACCGTTTTACCCTCAAGTGTCTAAAATGTCATTTTAACCCCAAAT
1 TCCCGATTTTTCTAAAAATTACCACTTTACCCGCAAGCATCTAAAATGTCATTTTAACCCCAAAT
* *** * *
29377802 TTTCTGAAAATTACCATTTTGCCTTTGAGAGTCTAAAATTACTATTTTACCCTCGAGCATCTAAA
66 TTTCTCAAAATTACCATTTTGCCTCCAAGAGTCCAAAATTACCATTTTACCCTCGAGCATCTAAA
29377867 AAGTCTCGTTTTTAT
131 AAGTCTCGTTTTTAT
29377882 TCCCGATTCTTTC-AAAAATTACCACTTTACCCGC-AGACATCTAAAATGTCATTTTTAACCCCA
1 TCCCGATT-TTTCTAAAAATTACCACTTTACCCGCAAG-CATCTAAAATGTCA-TTTTAACCCCA
29377945 AATCTTTC-CAAAATTACCATTTTGGCC-CCAAGAGTCCAAAATTACCATTTTACCCTCG
63 AAT-TTTCTCAAAATTACCATTTT-GCCTCCAAGAGTCCAAAATTACCATTTTACCCTCG
29378003 GATATCCAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
144 2 0.02
145 38 0.36
146 58 0.55
147 7 0.07
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (145 bp):
TCCCGATTTTTCTAAAAATTACCACTTTACCCGCAAGCATCTAAAATGTCATTTTAACCCCAAAT
TTTCTCAAAATTACCATTTTGCCTCCAAGAGTCCAAAATTACCATTTTACCCTCGAGCATCTAAA
AAGTCTCGTTTTTAT
Found at i:29382770 original size:67 final size:66
Alignment explanation
Indices: 29382693--29382905 Score: 177
Period size: 67 Copynumber: 3.1 Consensus size: 66
29382683 TTGATTCATA
*
29382693 CAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAAATATTTATATTAATTAATTTTA
1 CAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAAATA-TTATATTAATTAATTTCA
29382758 GT
65 GT
* * * * * * *
29382760 CAAAATATTAAAGACATGAAAATTAATATTCTTTTGGAA---A-TAATATAATTAATATATGAAT
1 CAAAATATT--A-A-TTG--TA-T-ATATT-TTATCGAATTTATTAATATAAATATTATATTAA-
*
29382821 TTGA-TTCA-T
56 TTAATTTCAGT
*
29382830 ACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAATAGTTATATTAATTAATTTC
1 -CAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAAATA-TTATATTAATTAATTTC
29382895 AGT
64 AGT
29382898 CAAAATAT
1 CAAAATAT
29382906 AAAAGACATC
Statistics
Matches: 110, Mismatches: 18, Indels: 36
0.67 0.11 0.22
Matches are distributed among these distances:
62 5 0.05
63 5 0.05
64 1 0.01
65 2 0.02
66 13 0.12
67 30 0.27
68 2 0.02
69 2 0.02
70 2 0.02
71 21 0.19
72 13 0.12
73 2 0.02
74 1 0.01
75 5 0.05
76 6 0.05
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (66 bp):
CAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAAATATTATATTAATTAATTTCAG
T
Found at i:29382830 original size:138 final size:138
Alignment explanation
Indices: 29382673--29383355 Score: 968
Period size: 138 Copynumber: 5.0 Consensus size: 138
29382663 AATAGTGAAC
* * *
29382673 ATATATAAAATTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAAAT
1 ATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAAT
* * *
29382738 ATTTATATTAATTAATTTTAGTCAAAATATTAAAGACATGAAAATTAATATTCTTTTGGAAATAA
66 AGTTATATTAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGAA
29382803 TATAATTA
131 TATAATTA
29382811 ATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAAT
1 ATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAAT
* * * *
29382876 AGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATCAAAATTAATATTCTTTTAGAAACAA
66 AGTTATATTAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGAA
*
29382941 TATAAGTA
131 TATAATTA
* *
29382949 ATATATGAATTTGATTCATATAAAATATTAATTATATATATTTTACCGAATTTATTAATATAAAC
1 ATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAA-
** * *
29383014 TA-TTATATTAA-T--TTCGA-TCAAAATATAAAAGACATGGAAATTAATATTCCTTTAGG-AAG
65 TAGTTATATTAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATT-CTTTTGGAAAG
29383073 AATATAATTA
129 AATATAATTA
* * * * * * *
29383083 ATATAAGAATTTGATTCAGACAAAATTTTAATTATTTATATTTTACTGGATTTATTAATATAAAT
1 ATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAAT
* *
29383148 AGTTATATTAATTAA-TTTAGGTCAAAATATAGAAGACATAGAAAATTAATATTCTTTTGCAAAG
66 AGTTATATTAATTAATTTTA-GTCAAAATATAAAAGACAT-GAAAATTAATATTCTTTTGGAAAG
29383212 AATATAATTA
129 AATATAATTA
* *
29383222 ATATATTAATTTGATTCATACAAAATATTAATTGTATATAATTTACCGAATTTATTAATATAAAT
1 ATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAAT
* * * * *
29383287 ATTTATATTAATTAA-TTTCGATCAAAAAATAAAAGACATAAAAATTAATATTCTTTTAGAAAGA
66 AGTTATATTAATTAATTTTAG-TCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGA
29383351 ATATA
130 ATATA
29383356 TTTCTTTTTT
Statistics
Matches: 485, Mismatches: 49, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
133 2 0.00
134 106 0.22
135 9 0.02
136 2 0.00
137 1 0.00
138 249 0.51
139 116 0.24
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (138 bp):
ATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAAT
AGTTATATTAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGAA
TATAATTA
Found at i:29382837 original size:71 final size:69
Alignment explanation
Indices: 29382760--29382979 Score: 163
Period size: 71 Copynumber: 3.2 Consensus size: 69
29382750 TAATTTTAGT
29382760 CAAAATATTAAAGACATGAAAATTAATATTCTTTTGGAAATAATATAATTAATATATGAATTTGA
1 CAAAATATTAAAGACAT-AAAATTAATATTCTTTT-GAAATAATATAATTAATATATGAATTTGA
29382825 TTCATA
64 TTCATA
* * ** * *
29382831 CAAAATATTAATTG-TATATATTTTACCGA-ATT-TATT-AATATAA-ATAGTT-ATAT-T-AA-
1 CAAAATATTAA-AGACATA-AAATTA---ATATTCTTTTGAA-ATAATATAATTAATATATGAAT
*
29382887 TTAATTTCAGT-
60 TTGA-TTCA-TA
* * *
29382898 CAAAATATAAAAGACATCAAAATTAATATTCTTTTAGAAACAATATAAGTAATATATGAATTTGA
1 CAAAATATTAAAGACAT-AAAATTAATATTCTTTT-GAAATAATATAATTAATATATGAATTTGA
29382963 TTCATA
64 TTCATA
*
29382969 TAAAATATTAA
1 CAAAATATTAA
29382980 TTATATATAT
Statistics
Matches: 110, Mismatches: 19, Indels: 40
0.65 0.11 0.24
Matches are distributed among these distances:
64 1 0.01
65 3 0.03
66 7 0.06
67 25 0.23
68 9 0.08
69 8 0.07
70 10 0.09
71 36 0.33
72 7 0.06
73 3 0.03
74 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (69 bp):
CAAAATATTAAAGACATAAAATTAATATTCTTTTGAAATAATATAATTAATATATGAATTTGATT
CATA
Found at i:29383174 original size:272 final size:273
Alignment explanation
Indices: 29382673--29383355 Score: 971
Period size: 272 Copynumber: 2.5 Consensus size: 273
29382663 AATAGTGAAC
* *
29382673 ATATATAAAATTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAAAT
1 ATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAAT
** * * *
29382738 ATTTATATTAATTAATTTTAGTCAAAATATTAAAGACATGAAAATTAATATT-CTTTTGGAAATA
66 ATTTATATTAA-T--TTCGA-TCAAAATATAAAAGACATGAAAATTAATATTCCTTTAGG-AAGA
* * *
29382802 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
126 ATATAATTAATATAAGAATTTGATTCAGACAAAATATTAATTATATATATTTTACCGAATTTATT
29382867 AATATAAATAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACAT-CAAAATTAATATTCTT
191 AATATAAATAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATACAAAATTAATATTCTT
29382931 TTAG-AAACAATATAAGTA
256 TT-GCAAACAATATAAGTA
* * *
29382949 ATATATGAATTTGATTCATATAAAATATTAATTATATATATTTTACCGAATTTATTAATATAAAC
1 ATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAA-
*
29383014 TA-TTATATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCCTTTAGGAAGAATAT
65 TATTTATATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCCTTTAGGAAGAATAT
* * * *
29383078 AATTAATATAAGAATTTGATTCAGACAAAATTTTAATTATTTATATTTTACTGGATTTATTAATA
130 AATTAATATAAGAATTTGATTCAGACAAAATATTAATTATATATATTTTACCGAATTTATTAATA
* *
29383143 TAAATAGTTATATTAATTAATTT-AGGTCAAAATATAGAAGACATAGAAAATTAATATTCTTTTG
195 TAAATAGTTATATTAATTAATTTCA-GTCAAAATATAAAAGACATACAAAATTAATATTCTTTTG
* *
29383207 CAAAGAATATAATTA
259 CAAACAATATAAGTA
* *
29383222 ATATATTAATTTGATTCATACAAAATATTAATTGTATATAATTTACCGAATTTATTAATATAAAT
1 ATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAAT
* * * *
29383287 ATTTATATTAATTAATTTCGATCAAAAAATAAAAGACATAAAAATTAATATTCTTTTAGAAAGAA
66 A-TT-TA-T-ATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCCTTTAGGAAGAA
29383352 TATA
127 TATA
29383356 TTTCTTTTTT
Statistics
Matches: 366, Mismatches: 31, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
271 1 0.00
272 138 0.38
273 98 0.27
274 1 0.00
275 3 0.01
276 69 0.19
277 56 0.15
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (273 bp):
ATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAAT
ATTTATATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCCTTTAGGAAGAATATA
ATTAATATAAGAATTTGATTCAGACAAAATATTAATTATATATATTTTACCGAATTTATTAATAT
AAATAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATACAAAATTAATATTCTTTTGCA
AACAATATAAGTA
Found at i:29383461 original size:75 final size:75
Alignment explanation
Indices: 29383334--29383481 Score: 178
Period size: 75 Copynumber: 2.0 Consensus size: 75
29383324 ATAAAAATTA
* * * *
29383334 ATATTCTTTTAGAAAGAATATATTTCTTTTTTCTAACTTTTCATATGTCTTCTCTATTAATCAGT
1 ATATTCTTTTAGAAAGAAAATATTTCTTTTTTCTAACTTTTCATATGCCTTCTCTATTAATAAGA
29383399 GAATAATCCT
66 GAATAATCCT
* *
29383409 ATATTCTTTT-GAAAAGAAAATAATTT-TATTTTT-TAA-TTTTCCATTTGCCTTCTCTGTTAAT
1 ATATTCTTTTAG-AAAGAAAAT-ATTTCT-TTTTTCTAACTTTT-CATATGCCTTCTCTATTAAT
29383470 AAGAGAATAATC
62 AAGAGAATAATC
29383482 TTGGTTTTCT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
74 5 0.08
75 49 0.78
76 9 0.14
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (75 bp):
ATATTCTTTTAGAAAGAAAATATTTCTTTTTTCTAACTTTTCATATGCCTTCTCTATTAATAAGA
GAATAATCCT
Found at i:29383709 original size:18 final size:17
Alignment explanation
Indices: 29383684--29383717 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29383674 GACAAGGGCA
*
29383684 AAGGAAAGGCTAAGGAT
1 AAGGAAAGCCTAAGGAT
29383701 AAGGCAAAGCCTAAGGA
1 AAGG-AAAGCCTAAGGA
29383718 CAATGGCAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.12, G:0.32, T:0.09
Consensus pattern (17 bp):
AAGGAAAGCCTAAGGAT
Found at i:29386513 original size:22 final size:21
Alignment explanation
Indices: 29386472--29386514 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
29386462 CATAAAGCAT
*
29386472 AACACAACTCAATGCCATACA
1 AACACAACTCAATGCAATACA
*
29386493 AACACATACTTAATGCAATACA
1 AACACA-ACTCAATGCAATACA
29386515 CTCATACTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.49, C:0.28, G:0.05, T:0.19
Consensus pattern (21 bp):
AACACAACTCAATGCAATACA
Found at i:29398408 original size:12 final size:12
Alignment explanation
Indices: 29398387--29398430 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
29398377 CTTCTCTTCA
29398387 TTCTTC-TTCTC
1 TTCTTCATTCTC
*
29398398 TTCCTCATTCTC
1 TTCTTCATTCTC
*
29398410 TTCTTCCTTCTC
1 TTCTTCATTCTC
29398422 TTCTTCATT
1 TTCTTCATT
29398431 TTCCTTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 5 0.18
12 23 0.82
ACGTcount: A:0.05, C:0.36, G:0.00, T:0.59
Consensus pattern (12 bp):
TTCTTCATTCTC
Found at i:29413830 original size:180 final size:180
Alignment explanation
Indices: 29413522--29413883 Score: 652
Period size: 180 Copynumber: 2.0 Consensus size: 180
29413512 CGAGAACAAG
29413522 AAAAGGGCTAGATGAGGAAATGAAAAAAGAATTCTTTGAAGAATTGATTGATTGAATCGGCGAGC
1 AAAAGGGCTAGATGAGGAAATGAAAAAAGAATTCTTTGAAGAATTGATTGATTGAATCGGCGAGC
*
29413587 ACATCGATGTCTCATCCTTGGAAGGGGAAGTTGAAAGCTTTGTGAAAATCAAGATTTAGCCCCAA
66 ACATCGATGTCTCATCCTTGGAAGGGGAAGTTGAAAGCTTTGTGAAAATCAAGATTGAGCCCCAA
*
29413652 TCCAATGAAGAATCAATCCCTATAGAGGAAGATGACGATTTTCATAAAGA
131 TCCAATGAAGAATAAATCCCTATAGAGGAAGATGACGATTTTCATAAAGA
* *
29413702 AAAAGGGCTAGATGAGGAAATGAAAAAAGAATTCTTTGAAGAATTGTTTGATTGAATCGGTGAGC
1 AAAAGGGCTAGATGAGGAAATGAAAAAAGAATTCTTTGAAGAATTGATTGATTGAATCGGCGAGC
* * **
29413767 ACATTGATGTTTCATCCTTGGAAGGGGAAGTTGAAAGCTTTGTGAAAATTGAGATTGAGCCCCAA
66 ACATCGATGTCTCATCCTTGGAAGGGGAAGTTGAAAGCTTTGTGAAAATCAAGATTGAGCCCCAA
29413832 TCCAATGAAGAATAAATCCCTATAGAGGAAGATGACGATTTTCATAAAGA
131 TCCAATGAAGAATAAATCCCTATAGAGGAAGATGACGATTTTCATAAAGA
29413882 AA
1 AA
29413884 TTTTAGATCT
Statistics
Matches: 174, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
180 174 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.25
Consensus pattern (180 bp):
AAAAGGGCTAGATGAGGAAATGAAAAAAGAATTCTTTGAAGAATTGATTGATTGAATCGGCGAGC
ACATCGATGTCTCATCCTTGGAAGGGGAAGTTGAAAGCTTTGTGAAAATCAAGATTGAGCCCCAA
TCCAATGAAGAATAAATCCCTATAGAGGAAGATGACGATTTTCATAAAGA
Found at i:29421025 original size:38 final size:38
Alignment explanation
Indices: 29420960--29421059 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 38
29420950 GCAGCTACAT
*
29420960 TCTTGGGTGCAA-TTGAAGAATACTTTAT-CCAGCGATAG
1 TCTTGGGTGCAATTTGAAGAATA-TTTATGCAAG-GATAG
* *
29420998 TTTTGGATGCAATTTGAAGAATATTTATGCAAGGATAG
1 TCTTGGGTGCAATTTGAAGAATATTTATGCAAGGATAG
29421036 TCTTGGGTGC-ATTTCGAA-AATATT
1 TCTTGGGTGCAATTT-GAAGAATATT
29421060 CCTGTAGTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
37 10 0.19
38 31 0.57
39 13 0.24
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (38 bp):
TCTTGGGTGCAATTTGAAGAATATTTATGCAAGGATAG
Found at i:29422360 original size:159 final size:159
Alignment explanation
Indices: 29422071--29422368 Score: 384
Period size: 159 Copynumber: 1.9 Consensus size: 159
29422061 CTTCATAACA
* * *
29422071 TGTAATGCTCACACAAGCTATGAATTGGGCCTACTCACACAAGTTGTGGGTCGAGTTATTAGGCT
1 TGTAATGCTCACACAAGCTATGAATTGGGCCTACTCACACAAGCTGTGGGTAGAGATATTAGGCT
* *
29422136 ACACGATGCTGCTCACACGAGTCGTGAAGAATTCGCAATAAATGTCGGATCTCAACCATCAATAG
66 ACACGATGCTGCTCACACGAGTCATGAAGAATTCGCAATAAATGTCAGATCTCAACCATCAATAG
*
29422201 GATATCTAAAGACTAGCACCTATATAGCC
131 GACATCTAAAGACTAGCACCTATATAGCC
* * * ** * * *
29422230 TGTAATGCTGACACGAGCTGTGAATTGGGCCTGTTCACACGAGCTGTGGGTAGAGATGTTGGGCT
1 TGTAATGCTCACACAAGCTATGAATTGGGCCTACTCACACAAGCTGTGGGTAGAGATATTAGGCT
* * * * * *
29422295 ACACGATGCTTCTCATACGAG-CTATGGAGAA-TCTGCAATAAATGTCAGATCTTAGCCATCGAT
66 ACACGATGCTGCTCACACGAGTC-ATGAAGAATTC-GCAATAAATGTCAGATCTCAACCATCAAT
29422358 AGGACATCTAA
129 AGGACATCTAA
29422369 GACCAACGCA
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
158 3 0.03
159 114 0.97
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (159 bp):
TGTAATGCTCACACAAGCTATGAATTGGGCCTACTCACACAAGCTGTGGGTAGAGATATTAGGCT
ACACGATGCTGCTCACACGAGTCATGAAGAATTCGCAATAAATGTCAGATCTCAACCATCAATAG
GACATCTAAAGACTAGCACCTATATAGCC
Found at i:29423917 original size:26 final size:26
Alignment explanation
Indices: 29423875--29423928 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
29423865 ATTCTAGGTG
29423875 CAATTCTAAACACGTTCATGCAGCGA
1 CAATTCTAAACACGTTCATGCAGCGA
* * *
29423901 CAATTCTATACATGTTCATGCAGTGA
1 CAATTCTAAACACGTTCATGCAGCGA
29423927 CA
1 CA
29423929 TTCCTAGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (26 bp):
CAATTCTAAACACGTTCATGCAGCGA
Found at i:29424075 original size:36 final size:36
Alignment explanation
Indices: 29423998--29424125 Score: 123
Period size: 36 Copynumber: 3.5 Consensus size: 36
29423988 TATTTATACA
* * * ** *
29423998 ACGACAGTCTTGGTGCATTTTGGAAATATTCCTGCG
1 ACGACAGTTTTGGTGCAATTTGGAAGTGCTCATGCG
* *
29424034 GCGACAATTTTGGTGCAATTTGGAAGTGCTCATGCG
1 ACGACAGTTTTGGTGCAATTTGGAAGTGCTCATGCG
* *
29424070 ACGACAGTTTTGGGTGCAATCTAGAAGTGCTCATGC-
1 ACGACAGTTTT-GGTGCAATTTGGAAGTGCTCATGCG
*
29424106 AGCGACATGTTTGGGTGCAA
1 A-CGACA-GTTTTGGTGCAA
29424126 ATATAGATTA
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
36 38 0.50
37 34 0.45
38 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (36 bp):
ACGACAGTTTTGGTGCAATTTGGAAGTGCTCATGCG
Found at i:29424097 original size:37 final size:36
Alignment explanation
Indices: 29424030--29424125 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 36
29424020 GAAATATTCC
* * *
29424030 TGCGGCGACAATTTT-GGTGCAATTTGGAAGTGCTCA
1 TGCGACGAC-ATTTTGGGTGCAATCTAGAAGTGCTCA
29424066 TGCGACGACAGTTTTGGGTGCAATCTAGAAGTGCTCA
1 TGCGACGACA-TTTTGGGTGCAATCTAGAAGTGCTCA
29424103 TGC-AGCGACATGTTTGGGTGCAA
1 TGCGA-CGACAT-TTTGGGTGCAA
29424126 ATATAGATTA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
35 1 0.02
36 14 0.26
37 38 0.72
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (36 bp):
TGCGACGACATTTTGGGTGCAATCTAGAAGTGCTCA
Found at i:29441346 original size:16 final size:17
Alignment explanation
Indices: 29441313--29441353 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
29441303 GAAGCAGAAT
*
29441313 AAGAAGAAGGTCAAGAG
1 AAGAAGAAGGTAAAGAG
29441330 AAGAAGAAGG-AAAGAG
1 AAGAAGAAGGTAAAGAG
*
29441346 AGGAAGAA
1 AAGAAGAA
29441354 TTTGAGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.59, C:0.02, G:0.37, T:0.02
Consensus pattern (17 bp):
AAGAAGAAGGTAAAGAG
Found at i:29442095 original size:34 final size:34
Alignment explanation
Indices: 29442057--29442122 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
29442047 CTATAGTATA
*
29442057 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
* *
29442091 ATTGTCGCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
29442123 CCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:29442096 original size:17 final size:17
Alignment explanation
Indices: 29442065--29442122 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
29442055 TAATTGTCCC
* *
29442065 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
29442082 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
29442099 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
29442116 TGCATTT
1 TGCATTT
29442123 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:29442690 original size:18 final size:16
Alignment explanation
Indices: 29442663--29442709 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
29442653 CAATCACTTG
29442663 AAAAAGAAAAATGAGAA
1 AAAAAGAAAAATGA-AA
29442680 AAAACAGAAAAATGAAA
1 AAAA-AGAAAAATGAAA
*
29442697 AAGAAAAAAAAAT
1 AA-AAAGAAAAAT
29442710 TTAAATGCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (16 bp):
AAAAAGAAAAATGAAA
Found at i:29442697 original size:24 final size:24
Alignment explanation
Indices: 29442662--29442707 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
29442652 TCAATCACTT
* *
29442662 GAAAAAGAAAAATGAGAAAAAACA
1 GAAAAAGAAAAAAGAAAAAAAACA
29442686 GAAAAATG-AAAAAGAAAAAAAA
1 GAAAAA-GAAAAAAGAAAAAAAA
29442708 ATTTAAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.04
Consensus pattern (24 bp):
GAAAAAGAAAAAAGAAAAAAAACA
Found at i:29446248 original size:138 final size:137
Alignment explanation
Indices: 29446077--29446493 Score: 590
Period size: 138 Copynumber: 3.0 Consensus size: 137
29446067 ACATAGATAA
* * * *
29446077 AATTAATATATGAATTCGATTCATACAAAATATTACTTGTAGATATTTTATCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATAAAAAATATTAATTGTAGATATTTTA-CTAATTTATTAATA
* * *
29446142 TAGACCGTTATATTAATTAATTTTGGTAAAAATATAAAAGACAT-AGAAATTAATATTCTTTTGG
65 TAAACAGTTATATTAATTAATTTTGGTAAAAATATAAAAGACATGA-AAATTAATATTCTTTTGA
29446206 AAAGAATAT
129 AAAGAATAT
* * *
29446215 AATTAGTATATGAATTTAATTCATAAAAAATATTAATTGTATATATTTTACTTAATTTATTAATA
1 AATTAATATATGAATTTGATTCATAAAAAATATTAATTGTAGATATTTTAC-TAATTTATTAATA
* * *
29446280 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACGTGAAAATTAATATTCTTTTGCA
65 TAAACAGTTATATTAATTAATTTTGGTAAAAATATAAAAGACATGAAAATTAATATTCTTTTG-A
*
29446345 AAA-AAAAT
129 AAAGAATAT
*
29446353 AATTAATATATGAATTTGATTCATAAAAAATATTAATCGTATG-TATTTTACCTAA-TTATTAAT
1 AATTAATATATGAATTTGATTCATAAAAAATATTAATTGTA-GATATTTTA-CTAATTTATTAAT
* * *
29446416 ATAAATAGTTATATTAATTAATTTTAGTGAAAATATAAAAGACATGAAAATTAATATTCTTTTGA
64 ATAAACAGTTATATTAATTAATTTTGGTAAAAATATAAAAGACATGAAAATTAATATTCTTTTGA
29446481 AAAGAATAT
129 AAAGAATAT
29446490 AATT
1 AATT
29446494 CATTTTTTAA
Statistics
Matches: 249, Mismatches: 24, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
136 4 0.02
137 76 0.31
138 164 0.66
139 5 0.02
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (137 bp):
AATTAATATATGAATTTGATTCATAAAAAATATTAATTGTAGATATTTTACTAATTTATTAATAT
AAACAGTTATATTAATTAATTTTGGTAAAAATATAAAAGACATGAAAATTAATATTCTTTTGAAA
AGAATAT
Found at i:29451294 original size:103 final size:103
Alignment explanation
Indices: 29451157--29451355 Score: 317
Period size: 103 Copynumber: 1.9 Consensus size: 103
29451147 ATCACAGACT
* * *
29451157 TATGTTCCTAGATGATGTTTAAAGGTTAGCTGATTTAAGATCGCAACTTAAATCTCTTTGAGTTA
1 TATGTTCCCAGATGATGTTTAAAGGATAGCTGATTTAAGATCGCAACCTAAATCTCTTTGAGTTA
29451222 GCTAATTTAAGATCGCAACTCCTACACAGCTCCAAGCC
66 GCTAATTTAAGATCGCAACTCCTACACAGCTCCAAGCC
* * *
29451260 TATGTTCCCAGTTGATGTTTAAAGGATAGTTGATTTAAGATTGCAACCTAAATCTCTTTGAGTTA
1 TATGTTCCCAGATGATGTTTAAAGGATAGCTGATTTAAGATCGCAACCTAAATCTCTTTGAGTTA
* * *
29451325 GCTGATTTAAGATTGCAACTCCTACTCAGCT
66 GCTAATTTAAGATCGCAACTCCTACACAGCT
29451356 TGCGGACCTA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 87 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (103 bp):
TATGTTCCCAGATGATGTTTAAAGGATAGCTGATTTAAGATCGCAACCTAAATCTCTTTGAGTTA
GCTAATTTAAGATCGCAACTCCTACACAGCTCCAAGCC
Found at i:29455700 original size:10 final size:10
Alignment explanation
Indices: 29455685--29455711 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
29455675 GCTTCGGCCC
29455685 TATAAGGCGA
1 TATAAGGCGA
29455695 TATAAGGCGA
1 TATAAGGCGA
29455705 TATAAGG
1 TATAAGG
29455712 TAGTGTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.30, T:0.22
Consensus pattern (10 bp):
TATAAGGCGA
Found at i:29484197 original size:21 final size:21
Alignment explanation
Indices: 29484173--29484223 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
29484163 GACTTCTATT
29484173 GATACAAGTGACAATTCTACC
1 GATACAAGTGACAATTCTACC
*
29484194 GATACAAGTGACTATTCTACC
1 GATACAAGTGACAATTCTACC
* *
29484215 CAAACAAGT
1 GATACAAGT
29484224 CTTACTTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (21 bp):
GATACAAGTGACAATTCTACC
Found at i:29485048 original size:25 final size:25
Alignment explanation
Indices: 29484939--29485060 Score: 93
Period size: 25 Copynumber: 4.9 Consensus size: 25
29484929 TCAAATGAGC
* *
29484939 CCAGACA-AAATATCGCTCATACGAG
1 CCAGACAGAATTA-CGCTCTTACGAG
* * *
29484964 CCAAACAGAACTACGCTCTTACTAG
1 CCAGACAGAATTACGCTCTTACGAG
* * * * * **
29484989 CGATATATAATTTCGCTCTTATAAG
1 CCAGACAGAATTACGCTCTTACGAG
*
29485014 CTAGACAGAATTACGCTCTTACGAG
1 CCAGACAGAATTACGCTCTTACGAG
* *
29485039 CCAGATAGAAGTACGCTCTTAC
1 CCAGACAGAATTACGCTCTTAC
29485061 AAGTCAGAAT
Statistics
Matches: 74, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
25 70 0.95
26 4 0.05
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (25 bp):
CCAGACAGAATTACGCTCTTACGAG
Found at i:29485068 original size:25 final size:24
Alignment explanation
Indices: 29485002--29485068 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
29484992 TATATAATTT
* *
29485002 CGCTCTTATAAGCTAGACAGAATTA
1 CGCTCTTACAAGC-AGACAGAAGTA
* *
29485027 CGCTCTTACGAGCCAGATAGAAGTA
1 CGCTCTTACAAG-CAGACAGAAGTA
29485052 CGCTCTTACAAGTCAGA
1 CGCTCTTACAAG-CAGA
29485069 ATCAAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 34 0.97
26 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (24 bp):
CGCTCTTACAAGCAGACAGAAGTA
Found at i:29490446 original size:7 final size:7
Alignment explanation
Indices: 29490436--29490495 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
29490426 AAAAAGAAAA
29490436 GAAAATG
1 GAAAATG
29490443 G-AAATG
1 GAAAATG
*
29490449 GGAAATG
1 GAAAATG
*
29490456 GGAAATG
1 GAAAATG
*
29490463 GGAAATG
1 GAAAATG
*
29490470 GGAAATG
1 GAAAATG
*
29490477 GAAAGAAG
1 GAAA-ATG
29490485 GAAAA-G
1 GAAAATG
29490491 GAAAA
1 GAAAA
29490496 AGTGAAATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
6 12 0.24
7 31 0.63
8 6 0.12
ACGTcount: A:0.53, C:0.00, G:0.37, T:0.10
Consensus pattern (7 bp):
GAAAATG
Found at i:29490459 original size:14 final size:14
Alignment explanation
Indices: 29490438--29490477 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
29490428 AAAGAAAAGA
29490438 AAAT-GGAAATGGG
1 AAATGGGAAATGGG
29490451 AAATGGGAAATGGG
1 AAATGGGAAATGGG
29490465 AAATGGGAAATGG
1 AAATGGGAAATGG
29490478 AAAGAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.15
14 22 0.85
ACGTcount: A:0.45, C:0.00, G:0.40, T:0.15
Consensus pattern (14 bp):
AAATGGGAAATGGG
Found at i:29490466 original size:21 final size:20
Alignment explanation
Indices: 29490438--29490477 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
29490428 AAAGAAAAGA
29490438 AAATGGAAATGGGAAATGGG
1 AAATGGAAATGGGAAATGGG
29490458 AAATGGGAAATGGGAAATGG
1 AAAT-GGAAATGGGAAATGG
29490478 AAAGAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.45, C:0.00, G:0.40, T:0.15
Consensus pattern (20 bp):
AAATGGAAATGGGAAATGGG
Found at i:29491956 original size:16 final size:16
Alignment explanation
Indices: 29491892--29491965 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
29491882 AACCAATTTC
*
29491892 AAAAAAATTCAAACCC
1 AAAAAAATTCAAACCT
* * *
29491908 AGAAAAATACGAATCC-
1 AAAAAAATTC-AAACCT
** * *
29491924 AAAAAGGTTCGAGCCT
1 AAAAAAATTCAAACCT
29491940 AAAAAAATTCAAACCT
1 AAAAAAATTCAAACCT
29491956 AAAAAAATTC
1 AAAAAAATTC
29491966 GAGCCAAACT
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
15 3 0.07
16 36 0.84
17 4 0.09
ACGTcount: A:0.57, C:0.19, G:0.08, T:0.16
Consensus pattern (16 bp):
AAAAAAATTCAAACCT
Found at i:29497698 original size:18 final size:18
Alignment explanation
Indices: 29497675--29497709 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29497665 ACTGAACATA
29497675 TTTTATAACTAT-TTTCTC
1 TTTTATAA-TATGTTTCTC
29497693 TTTTATAATATGTTTCT
1 TTTTATAATATGTTTCT
29497710 TAAGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTATAATATGTTTCTC
Found at i:29501276 original size:22 final size:21
Alignment explanation
Indices: 29501250--29501327 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 21
29501240 ATATTTAAAT
*
29501250 AATAACAACAAAATAGTAGCA
1 AATAACAACAAAATGGTAGCA
* *
29501271 ATATAATAGCAAAATGGT-GTCAA
1 A-ATAACAACAAAATGGTAG-C-A
*
29501294 AATAACATCAAAATGGTAGCA
1 AATAACAACAAAATGGTAGCA
*
29501315 AACAACAACAAAA
1 AATAACAACAAAA
29501328 CAACAATGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
21 14 0.30
22 29 0.63
23 3 0.07
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.17
Consensus pattern (21 bp):
AATAACAACAAAATGGTAGCA
Found at i:29504583 original size:29 final size:30
Alignment explanation
Indices: 29504549--29504617 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 30
29504539 TCGAAATTAA
*
29504549 ATTATTTTTAAAGA-TTAAATTAAATTTTT
1 ATTATTTTTAAAGAGTTAAAATAAATTTTT
* *
29504578 ATTATTTTT-TAGAGTTAAAATATATTTTT
1 ATTATTTTTAAAGAGTTAAAATAAATTTTT
* *
29504607 ATAATTATTAA
1 ATTATTTTTAA
29504618 TTTAAAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (30 bp):
ATTATTTTTAAAGAGTTAAAATAAATTTTT
Found at i:29506069 original size:17 final size:17
Alignment explanation
Indices: 29506022--29506111 Score: 58
Period size: 18 Copynumber: 5.0 Consensus size: 17
29506012 TTATCGCAAA
*
29506022 ATTTTTAATTAATAATT
1 ATTTTTAATTTATAATT
* *
29506039 -TTAAATTAAGTTATAATT
1 ATT--TTTAATTTATAATT
29506057 ATTTTTAATTTATCATAATT
1 ATTTTTAA-TT-T-ATAATT
*
29506077 -TTTATTAAATTATAATT
1 ATTT-TTAATTTATAATT
*
29506094 ATTTTTAAATGTATAATT
1 ATTTTT-AATTTATAATT
29506112 TTTCAATGTC
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
16 2 0.04
17 12 0.21
18 25 0.45
19 7 0.12
20 10 0.18
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTTAATTTATAATT
Found at i:29506076 original size:20 final size:17
Alignment explanation
Indices: 29506051--29506103 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
29506041 AAATTAAGTT
29506051 ATAATTATTTTTAATTTATC
1 ATAATTATTTTTAA---ATC
*
29506071 ATAATT-TTTATTAAATT
1 ATAATTATTT-TTAAATC
29506088 ATAATTATTTTTAAAT
1 ATAATTATTTTTAAAT
29506104 GTATAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 14 0.47
18 3 0.10
19 3 0.10
20 10 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
ATAATTATTTTTAAATC
Found at i:29506090 original size:37 final size:35
Alignment explanation
Indices: 29506022--29506101 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 35
29506012 TTATCGCAAA
*
29506022 ATTTTTAATTAATAATTTTAAATTAAGTTATAATT
1 ATTTTTAATTAATAATTTTAAATTAAATTATAATT
*
29506057 ATTTTTAATTTATCATAATTTT-TATTAAATTATAATT
1 ATTTTTAA-TTA--ATAATTTTAAATTAAATTATAATT
29506094 ATTTTTAA
1 ATTTTTAA
29506102 ATGTATAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 8 0.20
36 3 0.08
37 21 0.52
38 8 0.20
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (35 bp):
ATTTTTAATTAATAATTTTAAATTAAATTATAATT
Found at i:29510434 original size:15 final size:15
Alignment explanation
Indices: 29510414--29510465 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 15
29510404 TTAGATATTG
29510414 AAATTTAATATTTTT
1 AAATTTAATATTTTT
29510429 AAATTTAAT-TTTTT
1 AAATTTAATATTTTT
* *
29510443 ATATTTAA-ATTTTC
1 AAATTTAATATTTTT
*
29510457 AAGTTTAAT
1 AAATTTAAT
29510466 TGTTAAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 22 0.71
15 9 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
AAATTTAATATTTTT
Found at i:29511009 original size:14 final size:15
Alignment explanation
Indices: 29510982--29511024 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
29510972 CAAAGAATAG
29510982 AAGAAAACAAGACAA
1 AAGAAAACAAGACAA
29510997 AAGAAAA-AAGACAA
1 AAGAAAACAAGACAA
*
29511011 AA-ACAACAAGACAA
1 AAGAAAACAAGACAA
29511025 CGGGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 3 0.12
14 16 0.62
15 7 0.27
ACGTcount: A:0.74, C:0.14, G:0.12, T:0.00
Consensus pattern (15 bp):
AAGAAAACAAGACAA
Found at i:29511198 original size:2 final size:2
Alignment explanation
Indices: 29511160--29511186 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29511150 TCTCTCTCTC
29511160 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
29511187 TCATACATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29512130 original size:26 final size:27
Alignment explanation
Indices: 29512076--29512146 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
29512066 TGTTTTTCCC
** * *
29512076 TTTTAAATTTTACCCATTTATTCTGTT
1 TTTTAAATTAAACCCTTTTATTATGTT
*
29512103 TTTTAAATTAAATCCTTTTATTAT-TT
1 TTTTAAATTAAACCCTTTTATTATGTT
*
29512129 TTTTAAATTTAACCCTTT
1 TTTTAAATTAAACCCTTT
29512147 AATTTTTGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 18 0.49
27 19 0.51
ACGTcount: A:0.27, C:0.13, G:0.01, T:0.59
Consensus pattern (27 bp):
TTTTAAATTAAACCCTTTTATTATGTT
Found at i:29512175 original size:29 final size:28
Alignment explanation
Indices: 29512129--29512190 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
29512119 TTTATTATTT
*
29512129 TTTTAAATTTAACCCTTTAATTTTTGTTTC
1 TTTTAAAATTAACCCTTT--TTTTTGTTTC
*
29512159 TTTTAAAATT-ACCCTTTTTTTTGTTTT
1 TTTTAAAATTAACCCTTTTTTTTGTTTC
29512186 TTTTA
1 TTTTA
29512191 TTTTTAATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 14 0.47
29 7 0.23
30 9 0.30
ACGTcount: A:0.21, C:0.11, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTAAAATTAACCCTTTTTTTTGTTTC
Found at i:29515011 original size:24 final size:24
Alignment explanation
Indices: 29514979--29515024 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
29514969 TACAAGTACC
29514979 CAGACTACCGATACTT-CTATGAA
1 CAGACTACCGATACTTACTATGAA
29515002 CAGATCTACCGATACTTACTATG
1 CAGA-CTACCGATACTTACTATG
29515025 CAACTACTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 12 0.57
25 5 0.24
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (24 bp):
CAGACTACCGATACTTACTATGAA
Found at i:29515708 original size:42 final size:43
Alignment explanation
Indices: 29515658--29515836 Score: 222
Period size: 42 Copynumber: 4.2 Consensus size: 43
29515648 TCTTCTTTTT
* *
29515658 TTTAAACATAATCTCACGCTCATTCCGAGACATTAGTCTTCC-
1 TTTAAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCCA
* *
29515700 TTTAAACATAATCTCATTCTCATCCCGAGACATGAGTCTTCC-
1 TTTAAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCCA
* * *
29515742 TTTAAACATAATCTCATTCTCATTCCGAGTCACGAGTCTTCCA
1 TTTAAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCCA
* *
29515785 TTTATACA-AATTCTCATGCTCAATT-TGAGACATGAGTCTTCCA
1 TTTAAACATAA-TCTCATGCTC-ATTCCGAGACATGAGTCTTCCA
*
29515828 TTTATACAT
1 TTTAAACAT
29515837 CAAGTGTTTC
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
42 79 0.65
43 39 0.32
44 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (43 bp):
TTTAAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCCA
Found at i:29521177 original size:15 final size:14
Alignment explanation
Indices: 29521151--29521189 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
29521141 TCACCCAAAA
*
29521151 AAAAGAAGAAAAGG
1 AAAAGAAAAAAAGG
29521165 AATAAGAAAAAAAGG
1 AA-AAGAAAAAAAGG
29521180 AAAAGAAAAA
1 AAAAGAAAAA
29521190 GAAAAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAAAGG
Found at i:29522502 original size:99 final size:99
Alignment explanation
Indices: 29522393--29522686 Score: 314
Period size: 98 Copynumber: 3.0 Consensus size: 99
29522383 GAAAGCTATG
* ** *
29522393 ACAC-CAAATCCTATATCCTTGAAGTTACAAG-GATCAAAGTAAAACAAGTAGCGGATCTCAATC
1 ACACTCAAATCCTATATCCTTGAAGTTGC-AGTGATCGGATTAAAACAAGTAGCGGATCTCAATC
*
29522456 TCCACTGAAGTTGTAGTGGAATGGAGTAAAGTCACA
65 TCC-CTGAAGTTGTAGTGGAATGGAGTGAAGTCACA
* * * * * *
29522492 AC-CTCAAATCCTATATCCCTGAAGTTGCAGTAGATCGGATTAAAA-AACTAACAGACCTTAATC
1 ACACTCAAATCCTATATCCTTGAAGTTGCAGT-GATCGGATTAAAACAAGTAGCGGATCTCAATC
* * *
29522555 TCCCTGAAGTTATAGTGGAATGGAGTGAAGTTACC
65 TCCCTGAAGTTGTAGTGGAATGGAGTGAAGTCACA
* * *
29522590 ACACT-AAATCCTATCTTCTTGAAGTTGCAGTGAAGCGGATTAAAACTACAGTAGCGGATCTCAA
1 ACACTCAAATCCTATATCCTTGAAGTTGCAGTG-ATCGGATTAAAAC-A-AGTAGCGGATCTCAA
29522654 TCTCTCC-GACA-TTGTAGTGGAATGGAGTGAAGT
63 TCTC-CCTGA-AGTTGTAGTGGAATGGAGTGAAGT
29522687 TACATCACCA
Statistics
Matches: 161, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
97 1 0.01
98 67 0.42
99 42 0.26
100 11 0.07
101 37 0.23
102 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (99 bp):
ACACTCAAATCCTATATCCTTGAAGTTGCAGTGATCGGATTAAAACAAGTAGCGGATCTCAATCT
CCCTGAAGTTGTAGTGGAATGGAGTGAAGTCACA
Found at i:29522873 original size:82 final size:80
Alignment explanation
Indices: 29522693--29522876 Score: 233
Period size: 82 Copynumber: 2.3 Consensus size: 80
29522683 AAGTTACATC
* * * *
29522693 ACCATCTAATCTTTTACCCCAACCAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCAAACTA
1 ACCATCTAATCTTTTACCCTAACCAGAGAGAAGACTGAAGACCATCCAATCTTTTACCCAAACTA
29522758 GAGGAAAGATTAAAG
66 GAGGAAAGATTAAAG
* * *
29522773 ACCATCCAATCTTTTACCCTAACCAGAGAGAAGACTGAAGACACCATCCAATCTTTTACCCTAAT
1 ACCATCTAATCTTTTACCCTAACCAGAGAGAAGACTGAAG--ACCATCCAATCTTTTACCCAAAC
** *
29522838 TAGAGGGCAGATTGAAG
64 TAGAGGAAAGATTAAAG
* * *
29522855 ACCATTTAGTCTTATACCCTAA
1 ACCATCTAATCTTTTACCCTAA
29522877 ATTTAGAAGG
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 35 0.40
82 53 0.60
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (80 bp):
ACCATCTAATCTTTTACCCTAACCAGAGAGAAGACTGAAGACCATCCAATCTTTTACCCAAACTA
GAGGAAAGATTAAAG
Found at i:29522876 original size:40 final size:40
Alignment explanation
Indices: 29522693--29522859 Score: 208
Period size: 40 Copynumber: 4.1 Consensus size: 40
29522683 AAGTTACATC
* * * *
29522693 ACCATCTAATCTTTTACCCCAACCAGAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTAACTAGAGGGAAGATTGAAG
* * *
29522733 ACCATCCAATCTTTTACCCAAACTAGAGGAAAGATTAAAG
1 ACCATCCAATCTTTTACCCTAACTAGAGGGAAGATTGAAG
* * *
29522773 ACCATCCAATCTTTTACCCTAACCAGAGAGAAGACTGAAG
1 ACCATCCAATCTTTTACCCTAACTAGAGGGAAGATTGAAG
* *
29522813 ACACCATCCAATCTTTTACCCTAATTAGAGGGCAGATTGAAG
1 --ACCATCCAATCTTTTACCCTAACTAGAGGGAAGATTGAAG
29522855 ACCAT
1 ACCAT
29522860 TTAGTCTTAT
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 73 0.68
42 35 0.32
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.23
Consensus pattern (40 bp):
ACCATCCAATCTTTTACCCTAACTAGAGGGAAGATTGAAG
Found at i:29523004 original size:93 final size:94
Alignment explanation
Indices: 29522891--29523131 Score: 285
Period size: 93 Copynumber: 2.6 Consensus size: 94
29522881 AGAAGGTCAA
* * * * *
29522891 ATTGAAGCCAT-ATTATCCAATCTTATACCTCAAATCTAGAATGGCAAATTGAAGCCATCCTATC
1 ATTGAAGCCATCACTATCCAATCTTATACCTCAAATCCAAAAAGGCAGATTGAAGCCATCC-ATC
* *
29522955 CAATCTTATACCTCAAATCT-AGGGGGCAG
65 CAATCTTATACCTCAAATCTAAAGAGGCAG
* * * ** *
29522984 ATTGAAGCTATC-CTATCCAATCTTATACC-CTAAATCCAAAAAGGTAGATTAAAGTTATCCATT
1 ATTGAAGCCATCACTATCCAATCTTATACCTC-AAATCCAAAAAGGCAGATTGAAGCCATCCATC
* *
29523047 TAATCTTATACCTCAAATCTAAAGAGGTAG
65 CAATCTTATACCTCAAATCTAAAGAGGCAG
*
29523077 ATTGAAGCCATCAC-ATCCAATCTTATACCTCAAATCCAAAAGGGCAGATTGAAGC
1 ATTGAAGCCATCACTATCCAATCTTATACCTCAAATCCAAAAAGGCAGATTGAAGC
29523132 TACCAGATTA
Statistics
Matches: 123, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
92 22 0.18
93 99 0.80
94 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (94 bp):
ATTGAAGCCATCACTATCCAATCTTATACCTCAAATCCAAAAAGGCAGATTGAAGCCATCCATCC
AATCTTATACCTCAAATCTAAAGAGGCAG
Found at i:29523005 original size:46 final size:46
Alignment explanation
Indices: 29522864--29523133 Score: 251
Period size: 47 Copynumber: 5.8 Consensus size: 46
29522854 GACCATTTAG
* * * * **
29522864 TCTTATACC-CTAAATTTAGAAGGTCAAATTGAAGCCATATTATCCAA
1 TCTTATACCTC-AAATCTAAAAGG-CAGATTGAAGCTATCCTATCCAA
* * *
29522911 TCTTATACCTCAAATCTAGAATGGCAAATTGAAGCCATCCTATCCAA
1 TCTTATACCTCAAATCTA-AAAGGCAGATTGAAGCTATCCTATCCAA
***
29522958 TCTTATACCTCAAATCTAGGGGGCAGATTGAAGCTATCCTATCCAA
1 TCTTATACCTCAAATCTAAAAGGCAGATTGAAGCTATCCTATCCAA
* * * * **
29523004 TCTTATACC-CTAAATCCAAAAAGGTAGATTAAAGTTATCC-ATTTAA
1 TCTTATACCTC-AAAT-CTAAAAGGCAGATTGAAGCTATCCTATCCAA
* *
29523050 TCTTATACCTCAAATCTAAAGAGGTAGATTGAAGCCATCAC-ATCCAA
1 TCTTATACCTCAAATCTAAA-AGGCAGATTGAAGCTATC-CTATCCAA
*
29523097 TCTTATACCTCAAATCCAAAAGGGCAGATTGAAGCTA
1 TCTTATACCTCAAATCTAAAA-GGCAGATTGAAGCTA
29523134 CCAGATTAAA
Statistics
Matches: 187, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
45 5 0.03
46 69 0.37
47 109 0.58
48 4 0.02
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.29
Consensus pattern (46 bp):
TCTTATACCTCAAATCTAAAAGGCAGATTGAAGCTATCCTATCCAA
Found at i:29523166 original size:47 final size:46
Alignment explanation
Indices: 29522905--29523176 Score: 217
Period size: 47 Copynumber: 5.8 Consensus size: 46
29522895 AAGCCATATT
* * * * * *
29522905 ATCCAATCTTATACCTCAAATCTAGAATGGCAAATTGAAGCCATCC
1 ATCCAATCTTATACCCCAAATCCAAAAGGGCAGATTGAAGCTATCC
* * **
29522951 TATCCAATCTTATACCTCAAAT-CTAGGGGGCAGATTGAAGCTATCC
1 -ATCCAATCTTATACCCCAAATCCAAAAGGGCAGATTGAAGCTATCC
* * * * *
29522997 TATCCAATCTTATACCCTAAATCCAAAAAGGTAGATTAAAGTTATCC
1 -ATCCAATCTTATACCCCAAATCCAAAAGGGCAGATTGAAGCTATCC
** * * * *
29523044 ATTTAATCTTATACCTCAAAT-CTAAAGAGGTAGATTGAAGCCATCAC
1 ATCCAATCTTATACCCCAAATCCAAAAG-GGCAGATTGAAGCTATC-C
*
29523091 ATCCAATCTTATACCTCAAATCCAAAAGGGCAGATTGAAGCTA-CC
1 ATCCAATCTTATACCCCAAATCCAAAAGGGCAGATTGAAGCTATCC
** * * *
29523136 AGATTAAATCGTATACCCCTAAATCCAAAGGGGCCGATTGA
1 --ATCCAATCTTATACCCC-AAATCCAAAAGGGCAGATTGA
29523177 GGTCACGACA
Statistics
Matches: 181, Mismatches: 37, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
45 5 0.03
46 68 0.38
47 84 0.46
48 24 0.13
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (46 bp):
ATCCAATCTTATACCCCAAATCCAAAAGGGCAGATTGAAGCTATCC
Found at i:29523434 original size:23 final size:23
Alignment explanation
Indices: 29523402--29523445 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
29523392 CCGGCCCATG
29523402 AAAATTAAAACAAAAAAATAAAAC
1 AAAATTAAAAC-AAAAAATAAAAC
*
29523426 AAAA-TAAAACACAAAATAAA
1 AAAATTAAAACAAAAAATAAA
29523446 GATCCATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 6 0.32
24 4 0.21
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (23 bp):
AAAATTAAAACAAAAAATAAAAC
Found at i:29523747 original size:14 final size:14
Alignment explanation
Indices: 29523711--29523749 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 14
29523701 TTAGATCTGC
29523711 AAAGAACAAAAGAAA
1 AAAG-ACAAAAGAAA
29523726 ACAAGACAAAAGAAA
1 A-AAGACAAAAGAAA
29523741 AAAGACAAA
1 AAAGACAAA
29523750 CAACGGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 12 0.52
16 3 0.13
ACGTcount: A:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAGACAAAAGAAA
Found at i:29537262 original size:26 final size:27
Alignment explanation
Indices: 29537233--29537287 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
29537223 AAACACCAGT
29537233 TTAC-TGATAAGT-GAAAGCCTTTGTGG
1 TTACTTGATAAGTAG-AAGCCTTTGTGG
*
29537259 TTACTTTGATATGTAGAAGCCTTTGTGG
1 TTAC-TTGATAAGTAGAAGCCTTTGTGG
29537287 T
1 T
29537288 GGCTTTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 4 0.16
28 20 0.80
29 1 0.04
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (27 bp):
TTACTTGATAAGTAGAAGCCTTTGTGG
Found at i:29537293 original size:28 final size:28
Alignment explanation
Indices: 29537247--29537300 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
29537237 TGATAAGTGA
*
29537247 AAGCCTTTGTGGTTACTTTGATATGTAG
1 AAGCCTTTGTGGTGACTTTGATATGTAG
* *
29537275 AAGCCTTTGTGGTGGCTTTGTTATGT
1 AAGCCTTTGTGGTGACTTTGATATGT
29537301 GTGTGAGCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.44
Consensus pattern (28 bp):
AAGCCTTTGTGGTGACTTTGATATGTAG
Found at i:29540628 original size:29 final size:29
Alignment explanation
Indices: 29540590--29540703 Score: 120
Period size: 29 Copynumber: 3.9 Consensus size: 29
29540580 AAAAAAATTA
* * * *
29540590 TGGCATAACTGTAAAATCTCGAAAACCAG
1 TGGCAAAACTATAAAATCTAGAAAAACAG
*
29540619 TGGCAAAACTATAAAATCTAAAAAAAACAG
1 TGGCAAAACTATAAAATCT-AGAAAAACAG
** * * * *
29540649 CAGCAAAACTCTAAAATTTAGAAAATCAA
1 TGGCAAAACTATAAAATCTAGAAAAACAG
29540678 TGGCAAAACTATAAAATCTAGAAAAA
1 TGGCAAAACTATAAAATCTAGAAAAA
29540704 TAATGGTAGA
Statistics
Matches: 67, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
29 45 0.67
30 22 0.33
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (29 bp):
TGGCAAAACTATAAAATCTAGAAAAACAG
Found at i:29540708 original size:29 final size:29
Alignment explanation
Indices: 29540582--29540709 Score: 109
Period size: 29 Copynumber: 4.4 Consensus size: 29
29540572 AAAATTTGAA
* * * *
29540582 AAAAATTATGGCATAACTGTAAAATCTCG
1 AAAAATAATGGCAAAACTATAAAATCTAG
** *
29540611 AAAACCAGTGGCAAAACTATAAAATCTA-
1 AAAAATAATGGCAAAACTATAAAATCTAG
* * *
29540639 AAAAA-AACAGCAGCAAAACTCTAAAATTTAG
1 AAAAATAA-TG--GCAAAACTATAAAATCTAG
29540670 -AAAATCAATGGCAAAACTATAAAATCTAG
1 AAAAAT-AATGGCAAAACTATAAAATCTAG
29540699 AAAAATAATGG
1 AAAAATAATGG
29540710 TAGAACTGTG
Statistics
Matches: 77, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
27 1 0.01
28 5 0.06
29 43 0.56
30 25 0.32
31 1 0.01
32 2 0.03
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.20
Consensus pattern (29 bp):
AAAAATAATGGCAAAACTATAAAATCTAG
Found at i:29540716 original size:29 final size:28
Alignment explanation
Indices: 29540653--29540739 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 28
29540643 AAACAGCAGC
* * *
29540653 AAAACTCTAAAATTTAGAAAATCAATGGC
1 AAAACTATAAAATCTAGAAAAT-AATGGT
29540682 AAAACTATAAAATCTAGAAAAATAATGGT
1 AAAACTATAAAATCTAG-AAAATAATGGT
* * * *
29540711 AGAACTGTGAAATCT-GTAAAATAGTGGT
1 AAAACTATAAAATCTAG-AAAATAATGGT
29540739 A
1 A
29540740 CACGGTTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 12 0.24
29 32 0.65
30 5 0.10
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (28 bp):
AAAACTATAAAATCTAGAAAATAATGGT
Found at i:29541134 original size:19 final size:20
Alignment explanation
Indices: 29541092--29541129 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
29541082 AAAAATGAGG
*
29541092 AATAATAAATAT-AATTAGA
1 AATAAAAAATATAAATTAGA
29541111 AATAAAAAATATAAATTAG
1 AATAAAAAATATAAATTAG
29541130 GATAAGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AATAAAAAATATAAATTAGA
Found at i:29542233 original size:3 final size:3
Alignment explanation
Indices: 29542219--29542253 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
29542209 AAATAAAACG
*
29542219 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
29542254 CAATCGTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:29543517 original size:29 final size:30
Alignment explanation
Indices: 29543485--29543616 Score: 133
Period size: 29 Copynumber: 4.4 Consensus size: 30
29543475 ATAGTGATAG
*
29543485 AACTATAAAATCT-GCAAAACTAGTGGCAA
1 AACTATAAAATCTAGAAAAACTAGTGGCAA
* *
29543514 AACTATAAAATCTAGAAAAAAATAGTGGCAG
1 AACTATAAAATCTAG-AAAAACTAGTGGCAA
* *
29543545 AATTCTAAAATCTAG-AAAACTAGTGGCAA
1 AACTATAAAATCTAGAAAAACTAGTGGCAA
* * * * * * *
29543574 AATTGTAAAATTTGGAAAAATTAGTGACAG
1 AACTATAAAATCTAGAAAAACTAGTGGCAA
29543604 AACTATAAAATCT
1 AACTATAAAATCT
29543617 GTAAAACGGT
Statistics
Matches: 84, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
29 37 0.44
30 22 0.26
31 25 0.30
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.24
Consensus pattern (30 bp):
AACTATAAAATCTAGAAAAACTAGTGGCAA
Found at i:29543543 original size:31 final size:30
Alignment explanation
Indices: 29543441--29543616 Score: 122
Period size: 29 Copynumber: 5.8 Consensus size: 30
29543431 ATTTTTTAAG
* * *
29543441 AATAGTGACAAAATTGTAAAATCTGAAAAAAAA
1 AATAGTGACAAAACTATAAAATCT---AGAAAA
* * *
29543474 AATAGTGATAGAACTATAAAATCT-GCAAA
1 AATAGTGACAAAACTATAAAATCTAGAAAA
* *
29543503 ACTAGTGGCAAAACTATAAAATCTAGAAAAA
1 AATAGTGACAAAACTATAAAATCTAG-AAAA
* * * *
29543534 AATAGTGGCAGAATTCTAAAATCTAG-AAA
1 AATAGTGACAAAACTATAAAATCTAGAAAA
* * * * * *
29543563 ACTAGTGGCAAAATTGTAAAATTTGGAAAA
1 AATAGTGACAAAACTATAAAATCTAGAAAA
* *
29543593 ATTAGTGACAGAACTATAAAATCT
1 AATAGTGACAAAACTATAAAATCT
29543617 GTAAAACGGT
Statistics
Matches: 114, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
29 47 0.41
30 22 0.19
31 25 0.22
33 20 0.18
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.24
Consensus pattern (30 bp):
AATAGTGACAAAACTATAAAATCTAGAAAA
Found at i:29543564 original size:60 final size:59
Alignment explanation
Indices: 29543469--29543623 Score: 195
Period size: 60 Copynumber: 2.6 Consensus size: 59
29543459 AAATCTGAAA
*
29543469 AAAAAAATAGTGATAGAACTATAAAATCTGCAAAACTAGTGGCAAAACTATAAAATCTAG
1 AAAAAAATAGTGACAGAACTATAAAATCTGCAAAACTAGTGGCAAAACTATAAAAT-TAG
* * * * * *
29543529 AAAAAAATAGTGGCAGAATTCTAAAATCTAG-AAAACTAGTGGCAAAATTGTAAAATTTG
1 AAAAAAATAGTGACAGAACTATAAAATCT-GCAAAACTAGTGGCAAAACTATAAAATTAG
* * *
29543588 GAAAAATTAGTGACAGAACTATAAAATCTGTAAAAC
1 AAAAAAATAGTGACAGAACTATAAAATCTGCAAAAC
29543624 GGTGGTACAC
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
58 1 0.01
59 31 0.38
60 48 0.59
61 1 0.01
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.23
Consensus pattern (59 bp):
AAAAAAATAGTGACAGAACTATAAAATCTGCAAAACTAGTGGCAAAACTATAAAATTAG
Found at i:29544054 original size:27 final size:26
Alignment explanation
Indices: 29544014--29544070 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
29544004 AAGAAAGATA
29544014 AATTCTATTAGGATTTGAAAAGGAGT
1 AATTCTATTAGGATTTGAAAAGGAGT
* *
29544040 AATTCTAGTTAGGATTTTAAAAGGATT
1 AATTCTA-TTAGGATTTGAAAAGGAGT
29544067 AATT
1 AATT
29544071 TAGGATAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (26 bp):
AATTCTATTAGGATTTGAAAAGGAGT
Found at i:29550018 original size:179 final size:179
Alignment explanation
Indices: 29549705--29550054 Score: 452
Period size: 179 Copynumber: 2.0 Consensus size: 179
29549695 ATTTTTATTT
* * * * *
29549705 TAGAGGCTATAGCCCCCTGATTAAAATTTTACTTCTTCCATCGAAATGGGTATAACAAACGATTT
1 TAGAGGCTATAGCCCCCTAATTAAAATTTTACTTCTTCCATCAAAATGGGCACAACAAACAATTT
* * * * *
29549770 TTGCTTTATTTTCATGGTTTCTTTATACGGTAGGTTCTTTAGCATATTGTAGCTTGCCAGTCCCA
66 ATGATTTATTTTCATGGTTTCTTTATACAGTAGGTTATTTAGCATATTGTAGCTTGCCAGTCACA
*
29549835 TGGTATTCTATATTTCTTAAGTCA-AGTTATATTTATATTAATTTCATTG
131 TGGTATTCTATATTCCTTAAGTCATA-TTATATTTATATTAATTTCATTG
* * * * * *
29549884 TAGAGGTTGTAGCCCCCTAATTAAAATTTTATTTCTTTCATCAAAATGGGCACGACATACAATTT
1 TAGAGGCTATAGCCCCCTAATTAAAATTTTACTTCTTCCATCAAAATGGGCACAACAAACAATTT
* * * *** *
29549949 ATGATTTGTTTTCATGTTTTCTTTGTACAGTAGGTTATTTTTTATATTGTCA-CTTGCCGGTCAC
66 ATGATTTATTTTCATGGTTTCTTTATACAGTAGGTTATTTAGCATATTGT-AGCTTGCCAGTCAC
29550013 ATGGTATTCTATATTCCTTAAGTCATATTATATTTATATTAA
130 ATGGTATTCTATATTCCTTAAGTCATATTATATTTATATTAA
29550055 ATTAAAATTT
Statistics
Matches: 145, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
179 143 0.99
180 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.44
Consensus pattern (179 bp):
TAGAGGCTATAGCCCCCTAATTAAAATTTTACTTCTTCCATCAAAATGGGCACAACAAACAATTT
ATGATTTATTTTCATGGTTTCTTTATACAGTAGGTTATTTAGCATATTGTAGCTTGCCAGTCACA
TGGTATTCTATATTCCTTAAGTCATATTATATTTATATTAATTTCATTG
Found at i:29550488 original size:219 final size:217
Alignment explanation
Indices: 29550039--29550614 Score: 610
Period size: 219 Copynumber: 2.6 Consensus size: 217
29550029 CTTAAGTCAT
* * * *
29550039 ATTATATTTATATTAAATTAAAATTTTATAAATTTTAAAAGAGTATAATGATAAAATATTCATTT
1 ATTATATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTT
* * * * * * * * * *
29550104 AAGAGTTGCAGCCCCTAATTAAAAATTTATATATGTTATA-GAAATTGACACGATATATTATTAT
66 AAGGGTTGTAGCCCCTAATTAAAATTTTATTTATGTTA-ACGAAATGGACAAGAAAGATAATTTT
* * *
29550168 T-TTTTATTTTCACAGTTTTTTTGTACGATAGGTTCTTTGGTATATTGTCAGTTGCCAATCACAT
130 TGTTTTATTTTCACAGTGTTTTTGTACGATAGATTCTTTGGTACATTGTCAGTT-CCAATCACAT
* * *
29550232 GCTCTTACATATTTTTTAGGTTAA
194 GCTATTACATATTTTTAAAGTTAA
* *
29550256 ATTAAATTTATATTAACTTAAAATTTTATAAGTTTTAAAAGAGTGTAATGAGAAAATTTTCATTT
1 ATTATATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTT
* * * * *
29550321 AGGGGTTGTAGCCCCTTAATTAAAATTTTATTTCTGTGAACGAAATGGTCAAGACAGATAATTTT
66 AAGGGTTGTAGCCCC-TAATTAAAATTTTATTTATGTTAACGAAATGGACAAGAAAGATAATTTT
**
29550386 TGTTTTATTTTCAC-GATGTTTTTGTACGATAGATTCTTTTTTACATTGTCACGTAT-CAATC-C
130 TGTTTTATTTTCACAG-TGTTTTTGTACGATAGATTCTTTGGTACATTGTCA-GT-TCCAATCAC
* * *
29550448 TATGGTATTCCGGT-TTTTTAAAGTTAA
192 -ATGCTATTAC-ATATTTTTAAAGTTAA
* * * * *
29550475 ATTATATTTATATTAACTTAAAACTTTAAAAATTTTAAAAGACTGTAAAGAGAAAATTTTTATTT
1 ATTATATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCA-TT
* * * * * *
29550540 TAAGGGTTGTTA--CCCTGATTAAAATTTTATTTTTGTTATCAAAATGGGCATGAAAGATAATTT
65 TAAGGGTTG-TAGCCCCTAATTAAAATTTTATTTATGTTAACGAAATGGACAAGAAAGATAATTT
*
29550603 TTGTTTCATTTT
129 TTGTTTTATTTT
29550615 TAACGTTTCT
Statistics
Matches: 301, Mismatches: 48, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
217 72 0.24
218 90 0.30
219 123 0.41
220 13 0.04
221 3 0.01
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (217 bp):
ATTATATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTT
AAGGGTTGTAGCCCCTAATTAAAATTTTATTTATGTTAACGAAATGGACAAGAAAGATAATTTTT
GTTTTATTTTCACAGTGTTTTTGTACGATAGATTCTTTGGTACATTGTCAGTTCCAATCACATGC
TATTACATATTTTTAAAGTTAA
Found at i:29550897 original size:17 final size:18
Alignment explanation
Indices: 29550866--29550903 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
29550856 AAGTAAAATT
*
29550866 AAATTTATATTAATTGTA
1 AAATTTATATAAATTGTA
*
29550884 AAATTT-TATAAATTTTA
1 AAATTTATATAAATTGTA
29550901 AAA
1 AAA
29550904 GAGTGTAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAATTTATATAAATTGTA
Found at i:29551461 original size:215 final size:213
Alignment explanation
Indices: 29551061--29552661 Score: 1128
Period size: 216 Copynumber: 7.4 Consensus size: 213
29551051 GTCTCATGAT
* * * * * ** *
29551061 ATTTATATTAA-TTCAAAATTTTATAAATTTTAAAAAATTTTAATGATAAATTTTTCATTTTTGA
1 ATTTATATTAACTT-AAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTTTCATTTAGGG
** * * * * * * *
29551125 CCTACAACCCCCTAATTAAAATATTT-TTTCT-ACAATCGAAATGAGCACGATAGAAATTTTTAT
65 GTTGC-ATCCCCTAATTAAAAT-TTTATTTCTGTC-ATCGAATTGGGCAGGACAGAAATTTTT-T
* * *
29551188 TTTATTCTTTC--GATTTCTTTGTAAGGTAAGTTTTTTGGTATATTGTCATTTGTCAATCACATG
126 TTTA-T-TTTCAAGATTTCTTTGTACGGT-AGGTTTTTGGTATATTGTCACTTGTCAATCACATG
* *
29551251 TTATTCTTTTTTTTTAAGTTAAATTAA
188 TTATTC-TATTTTTTAAGTCAAATTAA
* * * * * *
29551278 ATTTACATTAACTTAAAATTTGATAAATTTTGAAAGAGTGTAATAAAAAAAATTTCATTTAGTGG
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTTTCATTTAGGGG
* * * * * * *
29551343 TTGCATCCCTTTATTTAAAAATTTATTCCTGTCATCGAATTGGGCATGACAGATAGTTTTTTTTA
66 TTGCATCCC-CTAATTAAAATTTTATTTCTGTCATCGAATTGGGCAGGACAGAAATTTTTTTTTA
* * * * * *
29551408 TTTTCATGGTTTCTTTATACGGTAGGTTTTTGGTGTATTGTCACTAGTCAATCACATGTTATTCC
130 TTTTCAAGATTTCTTTGTACGGTAGGTTTTTGGTATATTGTCACTTGTCAATCACATGTTATTCT
* * *
29551473 ATATTTTAAGCCAAATTGA
195 ATTTTTTAAGTCAAATTAA
* * *
29551492 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAAAATGTGAA-GATAAAATTTTCATTTAGGG
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGT-AATGAAAAAATTTTCATTTAGGG
* * * * * ** * *
29551556 GCTGCAATCCCCTAATT-AAATTTTTTTTCTATCTTTGAAATT-ATCAGGACGGACATTTTTTTT
65 GTTGC-ATCCCCTAATTAAAATTTTATTTCTGTCATCG-AATTGGGCAGGACAGAAATTTTTTTT
* * *
29551619 TATTTTCACGATTTCTTTGTACGGTAGATTATTTGGTATATTGTCACTTGTCAGTC-CAATGGTA
128 TATTTTCAAGATTTCTTTGTACGGTAGGTT-TTTGGTATATTGTCACTTGTCAATCAC-AT-GT-
* * * * *
29551683 TTTTTTATTTCTTAAATCAAATTAT
189 TATTCTATTTTTTAAGTCAAATTAA
* * * *
29551708 ATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTTTAATCAGAAAATTTT-ATTTTA---
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTTTCA-TTTAGGG
** * * * * * * * * ** *
29551769 G--GC--CTACAAATTAAATCTTTTTTTTTTTTGTTATCGAAATGGACA-CAGTGGATATTTTTG
65 GTTGCATCCCCTAATTAAA---ATTTTATTTCTGTCATCGAATTGGGCAGGA-CAGAAATTTTT-
* * * * * *
29551829 TTGTATTTTCACA-ATTTCTTTTTACGGTGGGTTCTTTGGTTTATTGTCGCTTGTTAATCACATG
125 TTTTATTTTCA-AGATTTCTTTGTACGGTAGGTT-TTTGGTATATTGTCACTTGTCAATCACATG
* * *
29551893 GTATTCCATATTTTTCAAGTTAAATT-A
188 TTATT-C-TATTTTTTAAGTCAAATTAA
* * *
29551920 ATTTATATTAACTTAAAATTTTTAAATTCTTAAATTTTGAAAGAGTGTAATGATAAAATTTTTAT
1 ATTTATATTAACTTAAAA-TTTT--A----TAAATTTTAAAAGAGTGTAATGAAAAAATTTTCAT
* * * *
29551985 TTAGGGGTTGAAACCCTCTAATTAAAAATTTATTTCT-TCATCGAATTGGGCAGGATAGAAAATT
59 TTAGGGGTTGCATCCC-CTAATTAAAATTTTATTTCTGTCATCGAATTGGGCAGGACAG-AAATT
* * * *
29552049 TTGTTTT-CTTTCAAGGTTTCTTTGTACGGTAGGTTTTTCGGTATATTGTCACTTTTCAATCACA
122 TTTTTTTATTTTCAAGATTTCTTTGTACGGTAGGTTTTT-GGTATATTGTCACTTGTCAATCACA
* *
29552113 TGTTCTTACATATTTTTTAAGTCAAATTAC
186 TGTTATT-C-TATTTTTTAAGTCAAATTAA
*
29552143 ATTTATATTAACTTAAAATTTTAT-AATTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAGGGG
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTTTCATTTAGGGG
* * * * * *
29552207 TTGTAGCCCCTAATTAAAATTTTATTTCTGTGAAT-GAAATGGTCAAGACAGACAATTTTTATTT
66 TTGCATCCCCTAATTAAAATTTTATTTCTGT-CATCGAATTGGGCAGGACAGA-AATTTTT-TTT
* * * * * * * *
29552271 TATTTTCACAGTTTTTTTTGTACGATAGGTTTTTTGTTATATTCTCACTTATCAATC-CTACGAT
128 TATTTTCA-AGATTTCTTTGTACGGTAGG-TTTTTGGTATATTGTCACTTGTCAATCAC-ATGTT
* * *
29552335 ATTCCATTTTTTAAGTTAAATTAT
190 ATTCTATTTTTTAAGTCAAATTAA
* *
29552359 ATTTATATTAACTTAAAATTTTAAAAATTTTAAAAGATTGTAAT-AAGAAAATTTTCATTTTAGG
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAA-AAAATTTTCA-TTTAGG
* * * * * * *
29552423 GGCTGC-TACCCCTAATTAAAATTTTATTTTTTTTATCGAAAT-GGCTA-G--A-TAATTTTTGT
64 GGTTGCAT-CCCCTAATTAAAATTTTATTTCTGTCATCGAATTGGGC-AGGACAGAAATTTTTTT
** * * * * *
29552482 TT-TTTT-ACCATTTCTTTGTACGGTAGGTTATTTGATATATTGTCACTTGTCAGTCTCGTGATA
127 TTATTTTCAAGATTTCTTTGTACGGTAGGTT-TTTGGTATATTGTCACTTGTCAATCACATGTTA
* * * *
29552545 TTCCGTATATCTTAAGTCAATTTAT
191 TT-C-TATTTTTTAAGTCAAATTAA
* * * * * * *
29552570 ATTTATATTAATTTCAAATTTAATATATTTTAACAGCGTGTAATGAGAAAATTTTCATTTAGGGG
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTTTCATTTAGGGG
* * * *
29552635 CTGCAGCCTCTTATTAAAATTTTATTT
66 TTGCATCCCCTAATTAAAATTTTATTT
29552662 TGTAATAAAA
Statistics
Matches: 1096, Mismatches: 221, Indels: 141
0.75 0.15 0.10
Matches are distributed among these distances:
208 8 0.01
209 44 0.04
210 34 0.03
211 74 0.07
212 45 0.04
213 132 0.12
214 127 0.12
215 115 0.10
216 139 0.13
217 122 0.11
218 83 0.08
219 37 0.03
220 2 0.00
221 4 0.00
222 71 0.06
223 35 0.03
224 15 0.01
226 1 0.00
227 8 0.01
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (213 bp):
ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTTTCATTTAGGGG
TTGCATCCCCTAATTAAAATTTTATTTCTGTCATCGAATTGGGCAGGACAGAAATTTTTTTTTAT
TTTCAAGATTTCTTTGTACGGTAGGTTTTTGGTATATTGTCACTTGTCAATCACATGTTATTCTA
TTTTTTAAGTCAAATTAA
Found at i:29552071 original size:435 final size:426
Alignment explanation
Indices: 29551061--29552629 Score: 1024
Period size: 427 Copynumber: 3.6 Consensus size: 426
29551051 GTCTCATGAT
* * * **
29551061 ATTTATATTAA-TTCAAAATTTTATAAATTTT-AAAAAATTTTAATGATAAATTTTTCATTTTTG
1 ATTTATATTAACTT-AAAATTTTATAAATTTTAAAAAAATGTGAA-GATAAAATTTTCATTTAGG
** * * * * * * *
29551124 ACCTACAACCCCCTAATTAAAATATTTTTTCTA-CAATCGAAATGAGCACGATAGAAATTTTTAT
64 GGCTGCAAACCCCTAATTAAAAT-TTATTTCTATC-ATCGAAATTAGCAGGA-AGAAAATTTTGT
* * *
29551188 TTTATTCTTTC--GATTTCTTTGTAAGGTA-AGTTTTTTGGTATATTGTCATTTGTCAATCACAT
126 TTTA--CTTTCAAGATTTCTTTGTACGGTAGA-TTTTTCGGTATATTGTCACTTGTCAATCACAT
* * * * * * * * * *
29551250 GTTATT-CTTTTTTTTTAAGTTAAATTAAATTTACATTAACTTAAAATTTGATAAATTTTGAAAG
188 GGTATTACATATTTCTTAAATCAAATTACATTTATATTAACTTAAAATTTTAT-AATTTTAAAAG
* * * * * * * * ** * ** *
29551314 AGTGTAATAAAAAAAATTTCATTTAGTGGTTGCATCCCTTTATTTAAA---AATTTATTCCTGTC
252 AGTGTAATCAGAAAATTTTCATTT--TAG--GCCT-AC--AAATTAAATCTTTTTTTTTTTTGTT
* * * ** ***
29551376 ATCGAATTGGGCA-TGACAGATAGTTTTT-TT-TATTTTCATGGTTTCTTTATACGGTAGGTTTT
310 ATCGAAATGGACACAG-TGGATA-TTTTTGTTGTATTTTCACAATTTCTTTATACGGTAGGTTTT
*
29551438 TGGTGTATTGTCACTAGTCAATCACATGTTATTCCATATTTTAAGCCAAATTGA
373 TGGTGTATTGTCACTAGTCAATCACATGGTATTCCATATTTTAAGCCAAATTGA
29551492 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAAAATGTGAAGATAAAATTTTCATTTAGGGG
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAAAATGTGAAGATAAAATTTTCATTTAGGGG
* * * * * * * * * * *
29551557 CTGCAATCCCCTAATTAAATTTTTTTTCTATCTTTGAAATTATCAGGACGGACATTTTTTTTTAT
66 CTGCAAACCCCTAATTAAAATTTATTTCTATCATCGAAATTAGCAGGAAGAAAATTTTGTTTTAC
* *
29551622 TTTCACGATTTCTTTGTACGGTAGATTATTT-GGTATATTGTCACTTGTCAGTC-CAATGGTATT
131 TTTCAAGATTTCTTTGTACGGTAGATT-TTTCGGTATATTGTCACTTGTCAATCAC-ATGGTATT
*** * * *
29551685 TTTTATTTCTTAAATCAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTTTA
194 ACATATTTCTTAAATCAAATTACATTTATATTAACTTAAAATTTTAT-AATTTTAAAAGAGTGTA
29551750 ATCAGAAAATTTT-ATTTTAGGCCTACAAATTAAATCTTTTTTTTTTTTGTTATCGAAATGGACA
258 ATCAGAAAATTTTCATTTTAGGCCTACAAATTAAATCTTTTTTTTTTTTGTTATCGAAATGGACA
* * * *
29551814 CAGTGGATATTTTTGTTGTATTTTCACAATTTCTTTTTACGGTGGGTTCTTTGGTTTATTGTCGC
323 CAGTGGATATTTTTGTTGTATTTTCACAATTTCTTTATACGGTAGGTT-TTTGGTGTATTGTCAC
* * **
29551879 TTGTTAATCACATGGTATTCCATATTTTTCAAGTTAAATT-A
387 TAGTCAATCACATGGTATTCCATA-TTTT-AAGCCAAATTGA
*
29551920 ATTTATATTAACTTAAAATTTT-TAAATTCTTAAATTTTGAAAGA-GTGTAATGATAAAATTTTT
1 ATTTATATTAACTTAAAATTTTATAAATT-TTAAA-----AAA-ATGTG-AA-GATAAAATTTTC
* *
29551983 ATTTAGGGGTTG-AAACCCTCTAATTAAAAATTTATTTCT-TCATCG-AATTGGGCAGGATAGAA
57 ATTTAGGGGCTGCAAACCC-CTAATT-AAAATTTATTTCTATCATCGAAATT-AGCAGGA-AGAA
* * *
29552045 AATTTTGTTTT-CTTTCAAGGTTTCTTTGTACGGTAGGTTTTTCGGTATATTGTCACTTTTCAAT
118 AATTTTGTTTTACTTTCAAGATTTCTTTGTACGGTAGATTTTTCGGTATATTGTCACTTGTCAAT
* * * *
29552109 CACATGTTCTTACATATTTTTTAAGTCAAATTACATTTATATTAACTTAAAATTTTATAATTTTA
183 CACATGGTATTACATATTTCTTAAATCAAATTACATTTATATTAACTTAAAATTTTATAATTTTA
* * * * * * * *
29552174 AAAGAGTGTAATGAGAAAATTTTCATTTAGGGGTTGTAGCC-CCTAATTAAA-ATTTTATTTCTG
248 AAAGAGTGTAATCAGAAAATTTTCATTT-----TAG--GCCTACAAATTAAATCTTTTTTTTTTT
* * ** * * * * * * *
29552237 TG-AAT-GAAATGGTCA-AGACAGACAATTTTTATTTTATTTTCACAGTTTTTTTTGTACGATAG
306 TGTTATCGAAATGGACACAG-TGGA-TATTTTTGTTGTATTTTCACA-ATTTCTTTATACGGTAG
* * * * * * **
29552299 GTTTTTTGTTATATTCTCACTTA-TCAATC-CTACGATATTCCATTTTTTAAGTTAAATT-A
368 G-TTTTTGGTGTATTGTCAC-TAGTCAATCAC-ATGGTATTCCATATTTTAAGCCAAATTGA
* * * * *
29552358 TATTTATATTAACTTAAAATTTTAAAAATTTTAAAAGATTGT-AATAAGAAAATTTTCATTTTAG
1 -ATTTATATTAACTTAAAATTTTATAAATTTTAAAAAAATGTGAA-GATAAAATTTTCA-TTTAG
* * * * * * *
29552422 GGGCTGC-TACCCCTAATTAAAATTTTATTTTTTTTATCGAAA-TGGCTA-G-A-TAATTTTTGT
63 GGGCTGCAAACCCCTAATTAAAA-TTTATTTCTATCATCGAAATTAGC-AGGAAGAAAATTTTGT
** * * * * * *
29552482 TTT--TTT-ACCATTTCTTTGTACGGTAGGTTATTT-GATATATTGTCACTTGTCAGTCTCGTGA
126 TTTACTTTCAAGATTTCTTTGTACGGTAGATT-TTTCGGTATATTGTCACTTGTCAATCACATGG
* * * * * * * * * * *
29552543 TATTCCGTATATCTTAAGTCAATTTATATTTATATTAATTTCAAATTTAATATATTTTAACAGCG
190 TATTACATATTTCTTAAATCAAATTACATTTATATTAACTTAAAATTTTATA-ATTTTAAAAGAG
*
29552608 TGTAATGAGAAAATTTTCATTT
254 TGTAATCAGAAAATTTTCATTT
29552630 AGGGGCTGCA
Statistics
Matches: 922, Mismatches: 158, Indels: 119
0.77 0.13 0.10
Matches are distributed among these distances:
422 6 0.01
424 6 0.01
425 28 0.03
426 26 0.03
427 131 0.14
428 71 0.08
429 79 0.09
430 88 0.10
431 67 0.07
432 43 0.05
433 27 0.03
434 49 0.05
435 131 0.14
436 23 0.02
437 2 0.00
438 22 0.02
439 52 0.06
440 57 0.06
441 11 0.01
442 3 0.00
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (426 bp):
ATTTATATTAACTTAAAATTTTATAAATTTTAAAAAAATGTGAAGATAAAATTTTCATTTAGGGG
CTGCAAACCCCTAATTAAAATTTATTTCTATCATCGAAATTAGCAGGAAGAAAATTTTGTTTTAC
TTTCAAGATTTCTTTGTACGGTAGATTTTTCGGTATATTGTCACTTGTCAATCACATGGTATTAC
ATATTTCTTAAATCAAATTACATTTATATTAACTTAAAATTTTATAATTTTAAAAGAGTGTAATC
AGAAAATTTTCATTTTAGGCCTACAAATTAAATCTTTTTTTTTTTTGTTATCGAAATGGACACAG
TGGATATTTTTGTTGTATTTTCACAATTTCTTTATACGGTAGGTTTTTGGTGTATTGTCACTAGT
CAATCACATGGTATTCCATATTTTAAGCCAAATTGA
Found at i:29552808 original size:181 final size:183
Alignment explanation
Indices: 29552498--29552844 Score: 457
Period size: 181 Copynumber: 1.9 Consensus size: 183
29552488 ACCATTTCTT
* * ** * *
29552498 TGTACGGTAGGTTATTTGATATATTGTCACTTGTCAGTCTCGTGATATTCCGTATATCTTAAGTC
1 TGTACAGTAGGTTATTTGATATATTGTCACTTGTCAATAACATGATATTCCATATATCTTAAGTC
* * * * * * *
29552563 AATTTATATTTATATTAATTTCAAATTTAATATATTTTAACAGCGTGTAATGAGAAAATTTTCAT
66 AAATTAAATTTATATTAACTTAAAATTTAATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCAT
* * * *
29552628 TTAGGGGCTGCAG-CCTCTTATT-AAAATTTTATTTTGTAATAAAAATGGACA
131 TGAGGAGCTGCAGTCCCCTAATTAAAAATTTTATTTTGTAATAAAAATGGACA
* * * *
29552679 TGTACAGTAGGTTATTTGGTATATTGTTACTTGTCAATAACATGTTATTCCATA-ATTTTTAAGT
1 TGTACAGTAGGTTATTTGATATATTGTCACTTGTCAATAACATGATATTCCATATA-TCTTAAGT
*
29552743 CAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCA
65 CAAATTAAATTTATATTAACTTAAAATTTAATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCA
*
29552808 TTGAGGAGTTGCAGTCCCCTAATTAAAAATTTTATTT
130 TTGAGGAGCTGCAGTCCCCTAATTAAAAATTTTATTT
29552845 CTGTCATCGA
Statistics
Matches: 140, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
180 1 0.01
181 120 0.86
182 7 0.05
183 12 0.09
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.43
Consensus pattern (183 bp):
TGTACAGTAGGTTATTTGATATATTGTCACTTGTCAATAACATGATATTCCATATATCTTAAGTC
AAATTAAATTTATATTAACTTAAAATTTAATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCAT
TGAGGAGCTGCAGTCCCCTAATTAAAAATTTTATTTTGTAATAAAAATGGACA
Found at i:29553607 original size:218 final size:216
Alignment explanation
Indices: 29552679--29553932 Score: 982
Period size: 218 Copynumber: 5.8 Consensus size: 216
29552669 AAAATGGACA
* * * * * * * *
29552679 TGTACAGTAGGTTATTTGGTATATTGTTACTTGTCAATAACATGTTATTCCATAATTTTTAAGTC
1 TGTACGGTAGGTTCTTTGATATATTGTCACTTATCAATCATATG-TATTCCATATTTTTTAAGTC
29552744 AAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCAT
65 AAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCAT
** * ** * * * * *
29552809 TGAGGAGTTGCAGTCCCCTAATTAAAAATTTTATTTCTGTCATCGAAATGTTCACAACAGACAAT
130 TTTGGGGTTATAG-CCTCT-ATTTAAAATTTTATTTCTGTCATCGAAATG-GCACGACAGATAAT
* * *
29552874 TTTTATTTTATTTTCATGGTTTCTT
192 TTTTGTTTTATTTTCACGATTTCTT
* ** * * * *
29552899 TTTACGGTAGGTAATTTGGTATA-T-TCACTTATCAATCTTATGGTATT-CTTAATTTCTTAAGT
1 TGTACGGTAGGTTCTTTGATATATTGTCACTTATCAATCATAT-GTATTCCAT-ATTTTTTAAGT
* * * * * *
29552961 CAAATTATATGTATATAAATTTAAAATTTTATAAATTTT-AAAGAGTTTAATGAAAAAATTTTCA
64 CAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCA
* *** * * * * * * *
29553025 TTTTCGGCCAACAATTCC-CTAATTAAAATATTT-TTTCTATAATCGAAATGAGCACGATAGA-C
129 TTTTGGGGTTA-TA-GCCTCTATTTAAAAT-TTTATTTCTGTCATCGAAATG-GCACGACAGATA
29553087 ATTTTTGTTTTATTTTCACGATTTCTT
190 ATTTTTGTTTTATTTTCACGATTTCTT
* * *
29553114 TGTATGGTAGGTTCTTTGATATATTGTCACTTATCAATCACATGTCATTCC-TTTTTTTTAAGGT
1 TGTACGGTAGGTTCTTTGATATATTGTCACTTATCAATCATATGT-ATTCCATATTTTTTAA-GT
* * * * *
29553178 TAAATTAAATTTATATTAATTTAAAA-TTTAAAAAGTTTTGAAAGAGTGTAATGAGAAAATTTTT
64 CAAATTAAATTTATATTAACTTAAAATTTTATAAA-TTTTAAAAGAGTGTAATGAGAAAATTTTC
* * * * * * *
29553242 ATTTAGTGGCTGCAT-CCCTCTATTTAAAAATTTATTTCTGTCATCGAATTGGGCACGGCAGATA
128 ATTTTG-GGGT-TATAGCCTCTATTTAAAATTTTATTTCTGTCATCGAAAT-GGCACGACAGATA
* *
29553306 ATTTTTGTTTTCTTTTCACGGTTTCTT
190 ATTTTTGTTTTATTTTCACGATTTCTT
* * * *
29553333 TGTATGGTAGGTTCTTTGATATATTATCACTTGTCAATCATATGCTATTACATATTTTTTAAGTC
1 TGTACGGTAGGTTCTTTGATATATTGTCACTTATCAATCATATG-TATTCCATATTTTTTAAGTC
* * * * *
29553398 AAATTAAATTTATACTAACTTAAAATATTATAAATTTTAAAAGAGTTTAATAAGAAAATTGTCAT
65 AAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCAT
* * *
29553463 TTTGGGGTTATAGCCTCTATTTAAAATTTTATATT-TGTGATCAAAATGGCCACGACAAATAATT
130 TTTGGGGTTATAGCCTCTATTTAAAATTTTAT-TTCTGTCATCGAAATGG-CACGACAGATAATT
*
29553527 TTTGTTTTATTTTCACGATTTTTT
193 TTTGTTTTATTTTCACGATTTCTT
* * ** * * * * * * *
29553551 TGAACGATAAATTTTTTGGTATATTGTCACGTATCAGTCTTACGATATTCCATA---TTTAAGTT
1 TGTACGGTAGGTTCTTTGATATATTGTCACTTATCAATCATATG-TATTCCATATTTTTTAAGTC
* * * *
29553613 AAATTAAATTTATATTAACTTAAAATTTTATAAGTTTTAAATGAGTGTAATGAGAAAAATTTCTT
65 AAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCAT
* * * * ** *
29553678 TTTAGGGGTTGCT-GCGTCCTAATT-AAATTTTATTTCTGTTAT-GAAAATGGGCACGATTGACA
130 TTT-GGGGTT-ATAGCCT-CTATTTAAAATTTTATTTCTGTCATCG-AAAT-GGCACGACAGATA
* * * * *
29553740 ATTTTTATTTCATTTTTAC-CTTTTTT
190 ATTTTTGTTTTATTTTCACGATTTCTT
* * * * * * * * * *
29553766 TGTATGGCAGGTTATTTGGTATATTG-CAAATTGTCAGTC-TCATGATATTTCATATATCTTAAG
1 TGTACGGTAGGTTCTTTGATATATTGTC-ACTTATCAATCAT-ATG-TATTCCATATTTTTTAAG
* * * * * * *
29553829 TCAATTTATATTTATATTAATTTAAAATTTTATAAATTTTAATAGAGTGTGATGTGAAAATTTTT
63 TCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTC
* * * * *
29553894 ATTTTAAGGGCTACAGCCCCTTAATTAAAATTTTATTTC
128 ATTTT-GGGGTTATAGCCTC-TATTTAAAATTTTATTTC
29553933 GATTATGTTC
Statistics
Matches: 827, Mismatches: 169, Indels: 77
0.77 0.16 0.07
Matches are distributed among these distances:
214 2 0.00
215 154 0.19
216 96 0.12
217 98 0.12
218 296 0.36
219 144 0.17
220 37 0.04
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (216 bp):
TGTACGGTAGGTTCTTTGATATATTGTCACTTATCAATCATATGTATTCCATATTTTTTAAGTCA
AATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATT
TTGGGGTTATAGCCTCTATTTAAAATTTTATTTCTGTCATCGAAATGGCACGACAGATAATTTTT
GTTTTATTTTCACGATTTCTT
Found at i:29553766 original size:215 final size:218
Alignment explanation
Indices: 29553390--29553929 Score: 508
Period size: 215 Copynumber: 2.5 Consensus size: 218
29553380 TTACATATTT
* * * * *
29553390 TTTAAGTCAAATTAAATTTATACTAACTTAAAATATTATAAATTTTAAAAGAGTTTAATAAG-AA
1 TTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAATGAGTGTAATGAGAAA
*
29553454 AATTGTCATTTTGGGGTTATAGCCTCTATTTAAAATTTTATATTTGTGATCAAAATGGCCACGAC
66 AATTGTCATTTTGGGGTTATAGCCTCTAATTAAAATTTTATATTTGTGATCAAAATGGCCACGAC
* * * * * *
29553519 AAATAATTTTTGTTTTATTTTCACGATTTTTTTGAACGATAAATTTTTTGGTATATTGTC-ACGT
131 AAACAATTTTTATTTCATTTTCACGATTTTTTTGAACGACAAATTATTTGGTATATTG-CAAAGT
*
29553583 ATCAGTCTTACGATA-TTC-CATA
195 ATCAGTCTCACGATATTTCACATA
* *
29553605 TTTAAGTTAAATTAAATTTATATTAACTTAAAATTTTATAAGTTTTAAATGAGTGTAATGAGAAA
1 TTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAATGAGTGTAATGAGAAA
* * * * * *
29553670 AATT-TCTTTTTAGGGGTTGCT-GCGTCCTAATT-AAATTTTAT-TTCTGTTATGAAAATGGGCA
66 AATTGTCATTTT-GGGGTT-ATAGCCT-CTAATTAAAATTTTATATT-TGTGATCAAAATGGCCA
*** * * * * * **
29553731 CGATTGACAATTTTTATTTCATTTTTAC-CTTTTTTTGTATGGCAGGTTATTTGGTATATTGCAA
127 CGACAAACAATTTTTATTTCATTTTCACGATTTTTTTGAACGACAAATTATTTGGTATATTGCAA
* * * *
29553795 ATTGTCAGTCTCATGATATTTCATATA
192 AGTATCAGTCTCACGATATTTCACATA
* * * * *
29553822 TCTTAAGTCAATTTATATTTATATTAATTTAAAATTTTATAAATTTT-AATAGAGTGTGATGTG-
1 T-TTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAT-GAGTGTAATGAGA
* * * * * *
29553885 AAAATTTTTATTTTAAGGGCTACAGCCCCTTAATTAAAATTTTAT
64 AAAATTGTCATTTT-GGGGTTATAGCCTC-TAATTAAAATTTTAT
29553930 TTCGATTATG
Statistics
Matches: 261, Mismatches: 50, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
214 1 0.00
215 102 0.39
216 62 0.24
217 20 0.08
218 67 0.26
219 9 0.03
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (218 bp):
TTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAATGAGTGTAATGAGAAA
AATTGTCATTTTGGGGTTATAGCCTCTAATTAAAATTTTATATTTGTGATCAAAATGGCCACGAC
AAACAATTTTTATTTCATTTTCACGATTTTTTTGAACGACAAATTATTTGGTATATTGCAAAGTA
TCAGTCTCACGATATTTCACATA
Found at i:29554653 original size:219 final size:217
Alignment explanation
Indices: 29553940--29556297 Score: 1554
Period size: 219 Copynumber: 10.8 Consensus size: 217
29553930 TTCGATTATG
* * ** * *
29553940 TTCACGGTTTCTTTGTACGGTAGGTTCTTTGGTGTATTGCCACTAGTCAATCACATGTTATTCCA
1 TTCAAGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCACATGCTATTCCA
* * *
29554005 TA-TTGTTATGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAAAGTGTAATG
66 TATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATG
* * * * * * * *
29554069 ATAAAATTTTTATTT-GGGTGCTGCAGCCCCCTAATT---AATTTTTTTTTGTCATCGAAATT-G
131 AGAAAATTTTCATTTAGGG-GTTACAG-CCCCTAATTAAAAATTTATTTCTATAATCG-AATTGG
* * * *
29554129 TCACGACT-GA-CATTTTTATTTTATT
193 GCAAGA-TAGATAATTTTTGTTTT-TT
* * * * ** * *
29554154 TTCACA-GTTTTTTTGCACGATAGGTTATTTGGTATATGGTCACTTGTCAGTC-CAATGGTATTC
1 TTCA-AGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCAC-ATGCTATTC
* * * * * *
29554217 CTTATTTCTTAAATCAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTTTAA
64 CATATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAA
* ** * ** * * * *
29554282 TCAGAAAATTTTCATTTTA-GGCCTACA------AA-TACATTTTTTTTTCTGTTATCGAAATGA
129 TGAGAAAATTTTCA-TTTAGGGGTTACAGCCCCTAATTAAAAATTTATTTCTATAATCGAATTG-
* * *
29554339 GG-ACGGTAGA-CATTTTTGTTTTATT
192 GGCAAGATAGATAATTTTTGTTTT-TT
* * * ** * * ** * *
29554364 TTCACGATTTCTTTTTACGGCGGGTTCTTTGGTTTATTGTGGCTTGTTAATCACATGTTATTCCA
1 TTCAAGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCACATGCTATTCCA
* * * * * *
29554429 TATTTTTCAAGTTAAATTAAATTTATATTAACTTAAAAATTGATAAATTTTGAAAGACTGTAATG
66 TATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATG
* * * * * *
29554494 AGAAAATTTTTATTTAGGAGTTGCAGCCGCTTAATTAAAAATTTGTTTCT-TCATCGAATTGGGC
131 AGAAAATTTTCATTTAGGGGTTACAGCC-CCTAATTAAAAATTTATTTCTATAATCGAATTGGGC
29554558 AAGATAGATAATTTTTGTTGTTTT
195 AAGATAGATAATTTTTGTT-TTTT
* * * * * * * **
29554582 TACAAGGTTTTTTTTGTAGGGTAGGTTCTTTGGTATATTGTCACTTTTCAATCACATACTCTTAA
1 TTCAAGG-TTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCACATGCTATTCC
*
29554647 ATATTTTTTAAGTCAAATTAAATTTATATTAACTTAATATTTTAT-AATGTTTAAAAGAGTGTAA
65 ATATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAAT-TTTAAAAGAGTGTAA
** *
29554711 TGAGAAAATTTTCATTTAGGGGTTGTAGCACCCTAATTAAAAATTTATTTCTATGAAT-GAAATG
129 TGAGAAAATTTTCATTTAGGGGTTACAGC-CCCTAATTAAAAATTTATTTCTAT-AATCGAATTG
* * *
29554775 GTCAAGACAGATAAATTTTGTTTTATT
192 GGCAAGATAGATAATTTTTGTTTT-TT
* * * * * * * * *
29554802 TTCATGGTTTTTTTTTGTACGATAGGTTCTTTGTTATATTCTCACTTATCAGTC-CTACGGTATT
1 TTCAAGG--TTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCAC-ATGCTATT
* * * * *
29554866 CCGGT-TTTTTTAAGTTAAATTATATTTATATTAACTTAAAATTTTAAAAATTTTAAAA-ATATG
63 CC-ATATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGA-GTG
* * ** * * * *
29554929 TAATGAGAAAATTTTCATTTTAGGGGTTATTA-CCCTTGTTTAAAATTTTATTTTTGT-TTCCG-
126 TAATGAGAAAATTTTCA-TTTAGGGGTTA-CAGCCCCTAATTAAAAATTTATTTCTATAAT-CGA
** *
29554991 ATATGGGCACTATAGATAATTCTTGTTTCATTT
188 AT-TGGGCAAGATAGATAATTTTTGTTT--TTT
** * * * * * *
29555024 TT-ACCGTTTCTTTGTATGGTAGGTTATTTGGTATATTGTCACTTGTCAGTCTCATGGTATTCCA
1 TTCAAGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCACATGCTATTCCA
* * * * * * * * * * * *
29555088 TATATCTTAACTCAATTTATATTTATATTAGCTTCAAATTTAATAAATTTTAATAGTGTATAAAG
66 TATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATG
* * * * * ** **
29555153 AGAAAATTTTCATTTAGGGGCTACAGCTCCCTAATTAAAATTTTATTTTTGTAATAGAAAAGAAC
131 AGAAAATTTTCATTTAGGGGTTACAGC-CCCTAATTAAAAATTTATTTCTATAATCGAATTGGGC
* * *
29555218 ATGGTAGACAATTTTTGTTTTATT
195 AAGATAGATAATTTTTGTTTT-TT
* * ** *
29555242 TTCACGGTTTGTTTGTATTGTAGGTTCTTTGGTATATTATCACTTGTCAATCAAATGTTATTCCA
1 TTCAAGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCACATG------C-
29555307 TATTCCATATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAG
59 TATTCCATATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAG
* * * * * *
29555372 TGTAATGAAAAAAATTCTT-ATTTAGAGGTTGCAATCCCCTAATTAAAATTTTTATTTCTATCAT
124 TGTAATG-AGAAAATT-TTCATTTAGGGGTTAC-AGCCCCTAATTAAAA-ATTTATTTCTATAAT
* ** * * * *
29555436 CAAAATT-CTCACA-ACAAACAATTTTT-ATTTTT
185 C-GAATTGGGCA-AGATAGATAATTTTTGTTTTTT
* * * * * * * *
29555468 TTCATGGTTTCTTTTTACGTTAGGTTATTTGGTATA-T-TCACTTGTCAGTCTCATGGTATTCCT
1 TTCAAGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCACATGCTATTCCA
* * * * * *
29555531 TATTTCTTAAGTCAAGTTATATTTATATTAATTTAAAATTTTATAACTTTTAAAAGAGTTTAATG
66 TATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATG
* ** *** * * ** *
29555596 AGAAATTTTTCATTTTCGACCTACATCCCCCTAATTAAAATAGTT-TTTCTATAATCGAAAAGAG
131 AGAAAATTTTCATTTAGGGGTTACA-GCCCCTAATTAAAA-ATTTATTTCTATAATCGAATTGGG
* * *
29555660 CACGATAGA-CATTCTTGTTTTATT
194 CAAGATAGATAATTTTTGTTTT-TT
* * * * * *
29555684 TTCACGATTTCTTTGTACGGTAGATTCTTTGGTATATTTTCACTTGTCAATTACATGTTATTCCA
1 TTCAAGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCACATGCTATTCCA
* * * * *
29555749 TATTTTTCAAGTTAAATTTAATTTATATTAACTTAAAATTTGATAAATTTTGAAAGAGTGTAATG
66 TATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATG
* * *
29555814 AGAAAATTTTCATTTAGGGGCTACAGCCCTCTATTTCAAAATTTATTTCTATCAA-C-AAGTTGG
131 AGAAAATTTTCATTTAGGGGTTACAGCCC-CTAATTAAAAATTTATTTCTAT-AATCGAA-TTGG
* * *
29555877 GCACGACAAATAATTTTTGTTTTTTTTT
193 GCAAGATAGATAATTTTTG---TTTTTT
* * * *
29555905 TTCACGGTTTCTTTGTATGGTAGGTCCTTTGGTATATTATCACTTGTCAATCACATGCTATTACA
1 TTCAAGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCACATGCTATTCCA
* * * * *
29555970 TATTTTTTAAGTCAAATTAAATTTATATTAACTTAATATATTATAAAATTTAAAAGAGTTTAATA
66 TATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATG
* ** ** * * * * * * *
29556035 AGAAAATTGTC-TTTTTGGGTTGTAGCCCCCTCATT---AATTT-TTTTTGTGATCAAAATGGTC
131 AGAAAATTTTCATTTAGGGGTTACAG-CCCCTAATTAAAAATTTATTTCTATAATCGAATTGGGC
*
29556095 ACA-ATAGACAATTTTTGTTTTATT
195 A-AGATAGATAATTTTTGTTTT-TT
* * **** ** * * * * ** * * *
29556119 TTCACGGTTT-TTTGAAAAAAAAATTCTTTGGTATATTGTCACTTATTAGTCTTACGATATTCCC
1 TTCAAGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCACATGCTATTCCA
* * * * *
29556183 T-TTTTTTAAGTTAAATTATATTTATACTAACTTAAAGTTTTATAAATTTTAAATGAGTGTAATG
66 TATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATG
* * * * * *
29556247 AGAAAATTTTCATTTTAGTGATTGCTGCGCCCTGATTAAAATTTTATTTCT
131 AGAAAATTTTCA-TTTAGGGGTTACAGC-CCCTAATTAAAAATTTATTTCT
29556298 GTTATGGGAA
Statistics
Matches: 1672, Mismatches: 379, Indels: 182
0.75 0.17 0.08
Matches are distributed among these distances:
207 1 0.00
208 2 0.00
209 8 0.00
210 146 0.09
211 2 0.00
212 63 0.04
213 43 0.03
214 86 0.05
215 90 0.05
216 89 0.05
217 104 0.06
218 169 0.10
219 345 0.21
220 52 0.03
221 277 0.17
222 23 0.01
223 3 0.00
224 15 0.01
225 1 0.00
226 91 0.05
227 32 0.02
228 28 0.02
229 2 0.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (217 bp):
TTCAAGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTATCACTTGTCAATCACATGCTATTCCA
TATTTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATG
AGAAAATTTTCATTTAGGGGTTACAGCCCCTAATTAAAAATTTATTTCTATAATCGAATTGGGCA
AGATAGATAATTTTTGTTTTTT
Found at i:29570280 original size:18 final size:18
Alignment explanation
Indices: 29570259--29570304 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
29570249 GCAGAACCTG
29570259 AGGAGAAGAAGGAA-AATA
1 AGGAGAAGAAGGAAGAA-A
*
29570277 AGGA-AGAGAAGGAAGAAG
1 AGGAGA-AGAAGGAAGAAA
29570295 AGGAGAAGAA
1 AGGAGAAGAA
29570305 TAAAGAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 1 0.04
18 20 0.83
19 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (18 bp):
AGGAGAAGAAGGAAGAAA
Found at i:29570298 original size:27 final size:28
Alignment explanation
Indices: 29570262--29570319 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
29570252 GAACCTGAGG
* *
29570262 AGAAGAAGGAAAATAAGGAAGAGAAGGA
1 AGAAGAAGGAAAAGAAGAAAGAGAAGGA
* *
29570290 AGAAG-AGGAGAAGAATAAAGAGAAGGA
1 AGAAGAAGGAAAAGAAGAAAGAGAAGGA
29570317 AGA
1 AGA
29570320 TGCCCCAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.03
Consensus pattern (28 bp):
AGAAGAAGGAAAAGAAGAAAGAGAAGGA
Found at i:29575520 original size:17 final size:17
Alignment explanation
Indices: 29575482--29575517 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29575472 ACTACAATGC
*
29575482 AAATGCATTGACAAATA
1 AAATGCAGTGACAAATA
29575499 AAATGCAGTGAC-AATA
1 AAATGCAGTGACAAATA
29575515 AAA
1 AAA
29575518 ATGTTATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.19
Consensus pattern (17 bp):
AAATGCAGTGACAAATA
Found at i:29586966 original size:26 final size:26
Alignment explanation
Indices: 29586935--29587007 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
29586925 CCTTGTTAAC
29586935 TGATTTGTGATTGAATTGTTATCAAT
1 TGATTTGTGATTGAATTGTTATCAAT
* * ****
29586961 TGATTTCTGACTGAACCAATATCAAT
1 TGATTTGTGATTGAATTGTTATCAAT
*
29586987 CG-TTATGTGATTGAATTGTTA
1 TGATT-TGTGATTGAATTGTTA
29587008 ACTAACGTGA
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
25 2 0.06
26 31 0.94
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.44
Consensus pattern (26 bp):
TGATTTGTGATTGAATTGTTATCAAT
Found at i:29600796 original size:19 final size:19
Alignment explanation
Indices: 29600772--29600812 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
29600762 CGATTTGTTC
* *
29600772 AAAGGATAAGAAACAGAAG
1 AAAGGAAAAGAAAAAGAAG
29600791 AAAGGAAAAGAAAAAGAAG
1 AAAGGAAAAGAAAAAGAAG
29600810 AAA
1 AAA
29600813 CAGCATGACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (19 bp):
AAAGGAAAAGAAAAAGAAG
Found at i:29601567 original size:6 final size:6
Alignment explanation
Indices: 29601540--29601586 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
29601530 TCAGTCACTT
*
29601540 GAAAAA TAAAAA -AAAATGA GAAAAA GAAGAAA GAAAAA GAAAAA GAA
1 GAAAAA GAAAAA GAAAA--A GAAAAA GAA-AAA GAAAAA GAAAAA GAA
29601587 TAAATTGCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
5 4 0.11
6 21 0.58
7 7 0.19
8 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:29601576 original size:12 final size:12
Alignment explanation
Indices: 29601540--29601586 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
29601530 TCAGTCACTT
*
29601540 GAAAAATAAAAA
1 GAAAAAGAAAAA
29601552 -AAAATGAGAAAAA
1 GAAAA--AGAAAAA
29601565 GAAGAAAGAAAAA
1 GAA-AAAGAAAAA
29601578 GAAAAAGAA
1 GAAAAAGAA
29601587 TAAATTGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
11 4 0.13
12 6 0.20
13 16 0.53
14 2 0.07
15 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (12 bp):
GAAAAAGAAAAA
Found at i:29602994 original size:7 final size:7
Alignment explanation
Indices: 29602982--29603012 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
29602972 AAATATTCAG
29602982 CACTCAA
1 CACTCAA
29602989 CACTCAA
1 CACTCAA
29602996 CACTCAA
1 CACTCAA
29603003 CACTCAA
1 CACTCAA
29603010 CAC
1 CAC
29603013 AATTGATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.45, G:0.00, T:0.13
Consensus pattern (7 bp):
CACTCAA
Found at i:29605251 original size:12 final size:12
Alignment explanation
Indices: 29605210--29605251 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
29605200 CACGACAAAG
*
29605210 TCTTCCTCTTTC
1 TCTTCTTCTTTC
*
29605222 TCGTCTTCTTT-
1 TCTTCTTCTTTC
29605233 TCTTTCTTCTTTC
1 TC-TTCTTCTTTC
29605246 TCTTCT
1 TCTTCT
29605252 AGCTTCTCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (12 bp):
TCTTCTTCTTTC
Found at i:29611339 original size:18 final size:18
Alignment explanation
Indices: 29611313--29611368 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
29611303 TGCAATCTAC
*
29611313 TGTGGCTGCATAC-GAGCA
1 TGTGACTGCAT-CTGAGCA
*
29611331 TGTGACTGCATCTGAGTA
1 TGTGACTGCATCTGAGCA
*
29611349 TGTGACTGCATCTGATCA
1 TGTGACTGCATCTGAGCA
29611367 TG
1 TG
29611369 ATGTGCTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 1 0.03
18 32 0.97
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (18 bp):
TGTGACTGCATCTGAGCA
Found at i:29616869 original size:39 final size:39
Alignment explanation
Indices: 29616808--29616886 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
29616798 GAAAGTTATC
*
29616808 AAATTACTAAATTAGCAGTGACACTGTAAACACTGCAAT
1 AAATTACTAAATTAGCAATGACACTGTAAACACTGCAAT
* *
29616847 AAATTACTGAATTGGCAATGACACTGTAAACACTGCAAT
1 AAATTACTAAATTAGCAATGACACTGTAAACACTGCAAT
29616886 A
1 A
29616887 CTACACTGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (39 bp):
AAATTACTAAATTAGCAATGACACTGTAAACACTGCAAT
Found at i:29617830 original size:217 final size:214
Alignment explanation
Indices: 29617409--29618293 Score: 782
Period size: 208 Copynumber: 4.1 Consensus size: 214
29617399 AGGTTATTCA
** * *
29617409 GTATATTGTCACTTGTCAATGTCATGATATTTCACATATCTTAAGT-AAATTTATATTTATATTA
1 GTATATTGTCACTTGTCAATCACATGATATTTCATAT-TCTTAAGTCAAA-TTAAATTTATATTA
* * * * *
29617473 ATTTAAAATTTTATAAATTTTAAAAGAATGTAATGTGAAAATATTCATTTTAGGAGCTGCAACCT
64 ACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAAGG-G-TGC-ACC-
* *
29617538 CCTAATTAAAA-TTTTATTTTTGTAATCGAAATAGGCACGGTTGACAATTTTTGTTTTATTTTCA
125 CCTAATTAAAATTTTTATTTCTGTAATCGAAATAGGCACGGTAGAC-ATTTTTGTTTTATTTTCA
*
29617602 GGGTTTCTTTATATGGTAGGTTCTTAT-
189 CGGTTTCTTTATATGGTAGGTT-TT-TG
* * * * *
29617629 GTGTATTGTCACTAGTCAATCACATGTTATTTTATATTTTTAAGTCAAATTAAATTTATATTAAC
1 GTATATTGTCACTTGTCAATCACATGATATTTCATATTCTTAAGTCAAATTAAATTTATATTAAC
* *
29617694 TTAAAATTTTATAAATTTTTAAAA-AGTGTAATGATAAAATTTTTATTTAAGGGTTGCAGCCCCT
66 TTAAAATTTTATAAA-TTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAAGGG-TGCA-CCCCT
* * * ** *
29617758 AATTAAAATTTTTATTTCTGTCATCGAAATTGTCACGACAGACATTTTTATTTTATTTTCACGGT
128 AATTAAAATTTTTATTTCTGTAATCGAAATAGGCACGGTAGACATTTTTGTTTTATTTTCACGGT
29617823 TTCTTTATATGGTAGGTTATTTG
193 TTCTTTATATGGTAGGTT-TTTG
* * * * * *
29617846 GTATATTGTCACTTGTCAGTCCCATGATATTCCTTATTTCTTAAGTCAAATTATATTTATATTTA
1 GTATATTGTCACTTGTCAATCACATGATATTTCATA-TTCTTAAGTCAAATTAAATTTATATTAA
* * * * ** *
29617911 TTTAAAATTTTAT-AATTTTAAAAGAGTTTAATGAGAATATTTTCATTTTA--G-GC-CTACAAA
65 CTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAAGGGTGCACCCCTAA
* * * *
29617971 TT--AATTTTT-TTTCTGTTATCGAAATGGGCACGGTAGACATTTTTGTTTTATTGTCACGATTT
130 TTAAAATTTTTATTTCTGTAATCGAAATAGGCACGGTAGACATTTTTGTTTTATTTTCACGGTTT
* *
29618033 CTTTGTACGGTAGGTTTTTTG
195 CTTTATATGGTAGG-TTTTTG
* ** * * * * *
29618054 GTTTATTGTTGCTTGTCAATCACATGTTATTCCATATTTTTCATGTTAAATTAAATTTATATTAA
1 GTATATTGTCACTTGTCAATCACATGATATTTCATATTCTT-AAGTCAAATTAAATTTATATTAA
** * * *
29618119 CTTAAAATTTGGTAGATTTTGAAAGAGTGTAATGAGAAAATTTTTATTT-A----GCAACCCCTT
65 CTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAAGGGTGC-ACCCC-T
* * * * * ** * * * *
29618179 AATTAAAA-ATTTATTTCT-TCATCGAATTGGGCGCAATAGATAATTTTTATTTTTTTTTTCAAG
128 AATTAAAATTTTTATTTCTGTAATCGAAATAGGCACGGTAGA-CATTTTT-GTTTTATTTTCACG
* * * *
29618242 GTTTTTTTTGTACGGTAGGTTCTTTA
191 G-TTTCTTTATATGGTAGGTT-TTTG
*
29618268 GTATATTGTCACTTTTCAATCACATG
1 GTATATTGTCACTTGTCAATCACATG
29618294 CTCTTACATA
Statistics
Matches: 547, Mismatches: 98, Indels: 46
0.79 0.14 0.07
Matches are distributed among these distances:
207 6 0.01
208 120 0.22
209 41 0.07
210 4 0.01
211 26 0.05
212 13 0.02
213 14 0.03
214 41 0.07
215 1 0.00
216 9 0.02
217 103 0.19
218 70 0.13
219 58 0.11
220 41 0.07
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.46
Consensus pattern (214 bp):
GTATATTGTCACTTGTCAATCACATGATATTTCATATTCTTAAGTCAAATTAAATTTATATTAAC
TTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAAGGGTGCACCCCTAAT
TAAAATTTTTATTTCTGTAATCGAAATAGGCACGGTAGACATTTTTGTTTTATTTTCACGGTTTC
TTTATATGGTAGGTTTTTG
Found at i:29621153 original size:217 final size:218
Alignment explanation
Indices: 29620648--29621170 Score: 576
Period size: 217 Copynumber: 2.4 Consensus size: 218
29620638 TGTACAATAG
* * *
29620648 GTTCTTTGATATATTGTCACTTATCAATCCTACGATATTCCATTTTTTTTAAGTTAAATTATATT
1 GTTCTTTGATATATTGTCACTTATCAAT-CTATGATATTCCATATTTTTTAAGTCAAATTATATT
* * *
29620713 TATATTAATTTAAAATTTTATAAATTTTAAAAGAGTCTAATAAGAAAATTTTCATTTTAAGGGTT
65 TATATTAATCTAAAATTTTATAAATTTTAAAAGAGTCTAATAAGAAAATTTTCAATTTAAGGGCT
* * * * *
29620778 GTTACCCCTTGATTAAAATTTTATTTCTGTTATCGAAATGGGCATGACAGATATTTTTTGCTTCA
130 GTCACCCCTTAATTAAAATTTTATTTCTGTAATCGAAATGGGCACGACAGATAATTTTTGCTT-A
* * * *
29620843 TTTTTTAACGTTTCTTTGTAGGTAT
194 TATTTTAACGATCCTTTGTAGGTAA
* * * * * * * * *
29620868 TTTATTTGATATATTGTCACTTATTAGTCTCATGGTATTCCAAATATCTTAAGTCAACTTATATT
1 GTTCTTTGATATATTGTCACTTATCAATCT-ATGATATTCCATATTTTTTAAGTCAAATTATATT
* *
29620933 TATATTAATCTAAAATTTTAT-AATTTTAAAAGAGTGTAATGAGAAAATTTTCAATTT-AGAGGC
65 TATATTAATCTAAAATTTTATAAATTTTAAAAGAGTCTAATAAGAAAATTTTCAATTTAAG-GGC
* **
29620996 TG-CAGCCCC-TAATTAAAATTTTACTTT-TGTAATCGAAATGGGTACGGTAGATAATTTTTG-T
129 TGTCA-CCCCTTAATTAAAATTTTA-TTTCTGTAATCGAAATGGGCACGACAGATAATTTTTGCT
* *
29621057 T-TATTTTCACGGATCCTTTTTACGGTAA
192 TATATTTTAAC-GATCCTTTGTA-GGTAA
* * * * *
29621085 GTTCTTTGGTGTATTGTCACTTGTCAATCATATGCTATTCCATATTTTTTAAGTCAAATTAAATT
1 GTTCTTTGATATATTGTCACTTATCAATC-TATGATATTCCATATTTTTTAAGTCAAATTATATT
29621150 TATATTAA-CTTAAAATTTTAT
65 TATATTAATC-TAAAATTTTAT
29621171 CAAGGCTGCG
Statistics
Matches: 251, Mismatches: 44, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
215 7 0.03
216 9 0.04
217 75 0.30
218 44 0.18
219 46 0.18
220 70 0.28
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (218 bp):
GTTCTTTGATATATTGTCACTTATCAATCTATGATATTCCATATTTTTTAAGTCAAATTATATTT
ATATTAATCTAAAATTTTATAAATTTTAAAAGAGTCTAATAAGAAAATTTTCAATTTAAGGGCTG
TCACCCCTTAATTAAAATTTTATTTCTGTAATCGAAATGGGCACGACAGATAATTTTTGCTTATA
TTTTAACGATCCTTTGTAGGTAA
Found at i:29621681 original size:589 final size:592
Alignment explanation
Indices: 29620691--29621758 Score: 1290
Period size: 589 Copynumber: 1.8 Consensus size: 592
29620681 GATATTCCAT
*
29620691 TTTTTTTAAGTTAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTCTAATAA
1 TTTTTTTAAGTCAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTCTAATAA
** * * * *
29620756 GAAAATTTTCATTTTAAGGGTTGTTACCCCTTGATTAAAATTTTATTTCTGTTATCGAAATGGGC
66 GAAAATTTTCATTTTAAGGG-TACTACACCTTAATTAAAATTTTATTTCTGTAATCAAAATGGGC
* * *
29620821 ATGACAGATATTTTTTGCTTCATTTTTTAACGTTTCTTTGTAGGTATTTTATTTGATATATTGTC
130 ACGACAGATATTTTTTGCTT-ATTTTTTAACGTTTCTTTGTACGTAGTTTATTTGATATATTGTC
* * * * * *
29620886 ACTTATTAGTCTCATGGTATTCCAAATATCTTAAGTCAACTTATATTTATATTAATCTAAAATTT
194 ACTTATCAATCACATGGTATTCCAAATATCTTAAGTCAAATTAAATTTATATCAATCTAAAATTT
* *
29620951 TATAATTTTAAAAGAGTGTAATGAGAAAATTTTCAATTTAGAGGCTGCAGCCCCTAATTAAAATT
259 TATAATTTTAAAAGAGTGTAATGAGAAAATTTTCAATTTAGAGGCTGCACCCCCTAATTAAAAAT
* * * **
29621016 TTACTTTTGTAATCGAAATGGGTACGGTAGATAATTTTTGTTTATTTTCACGGATCCTTTTTACG
324 TTACTTTTGTAATAGAAATAGGCACGACAGATAATTTTTGTTTATTTTCACGGATCCTTTTTACG
* *
29621081 GTAAGTTCTTTGGTGTATTGTCACTTGTCAATCAT-ATGCTATTCCATATTTTTTAAGTCAAATT
389 ATAAGTTCTTTGGTATATTGTCACTTGTCAATC-TCATGCTATTCCATATTTTTTAAGTCAAATT
29621145 AAATTTATATTAACTTAAAATTTTATCAAGGCTGCGGCTCCCTAATTAAAATTTTTATTTTTGTC
453 -AATTTATATTAACTTAAAATTTTATCAAGGCTGCGGCTCCCTAATTAAAATTTTTATTTTTGTC
29621210 ATCGAAATGGTCACAACATATATTTTTTGTTTACTTTCACGGTTTCTTTGTATCTCCATTTGTTA
517 ATCGAAATGGTCACAACATATATTTTTTGTTTACTTTCACGGTTTCTTTGTATCTCCATTTGTTA
29621275 GTTTCATGGTA
582 GTTTCATGGTA
* * *
29621286 TTTTTTTAAGTCAAATTATATTTATGTTAATTTAAAATTTTATAAATTTTAAAAGAGTGTAATGA
1 TTTTTTTAAGTCAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTCTAATAA
* *
29621351 GAAAATTTTTATTTT-A-GG-ACTACAACCTTAAATT-AAATTTT-TTTC-GTAATCAAAATTGG
66 GAAAATTTTCATTTTAAGGGTACTAC-ACCTT-AATTAAAATTTTATTTCTGTAATCAAAATGGG
** * * *
29621410 CACGGTAGATA-TTTTTG-TT-TTATTTTCACGATTTCTTTGTACCGTAGGTTT-TTTGGTATGT
129 CACGACAGATATTTTTTGCTTATT-TTTTAACG-TTTCTTTGTA-CGTA-GTTTATTTGATATAT
* ** * ** * *
29621471 TGTCACTT-TCAATCACTTTTTATTTCTTAT-TTTTCAAGTTAAATTAAATTTATATCAA-CTTA
190 TGTCACTTATCAATCACATGGTATTCCAAATATCTT-AAGTCAAATTAAATTTATATCAATC-TA
* * * *
29621533 AAATTTTATAAATTTTAAATGAGTGTAATGAGAAAATTTT-TATTTAGGGGTTGCAACCCCCTAA
253 AAATTTTAT-AATTTTAAAAGAGTGTAATGAGAAAATTTTCAATTTAGAGGCTGC-ACCCCCTAA
* * * * * * * *
29621597 TTAAAAATTTAGTTTTTTCATAGAAATAGGCATGACAGATCATTTTTGTTTTTTTTCAC-TATTT
316 TTAAAAATTTACTTTTGTAATAGAAATAGGCACGACAGATAATTTTTGTTTATTTTCACGGA-TC
* * * **
29621661 CTTTGTT-TGAT-AGATTCTTTGGTATATTGTTACTTGTCAATCTCTTTTTATTCCATATTTTTT
380 CTTT-TTACGATAAG-TTCTTTGGTATATTGTCACTTGTCAATCTCATGCTATTCCATATTTTTT
* * *
29621724 AAGTTAAATTAATTTCTATTGACTTAAAATTTTAT
443 AAGTCAAATTAATTTATATTAACTTAAAATTTTAT
29621759 AAATTTTAAA
Statistics
Matches: 396, Mismatches: 63, Indels: 35
0.80 0.13 0.07
Matches are distributed among these distances:
586 2 0.01
587 11 0.03
588 93 0.23
589 167 0.42
590 24 0.06
591 7 0.02
592 11 0.03
593 5 0.01
594 1 0.00
595 75 0.19
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (592 bp):
TTTTTTTAAGTCAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTCTAATAA
GAAAATTTTCATTTTAAGGGTACTACACCTTAATTAAAATTTTATTTCTGTAATCAAAATGGGCA
CGACAGATATTTTTTGCTTATTTTTTAACGTTTCTTTGTACGTAGTTTATTTGATATATTGTCAC
TTATCAATCACATGGTATTCCAAATATCTTAAGTCAAATTAAATTTATATCAATCTAAAATTTTA
TAATTTTAAAAGAGTGTAATGAGAAAATTTTCAATTTAGAGGCTGCACCCCCTAATTAAAAATTT
ACTTTTGTAATAGAAATAGGCACGACAGATAATTTTTGTTTATTTTCACGGATCCTTTTTACGAT
AAGTTCTTTGGTATATTGTCACTTGTCAATCTCATGCTATTCCATATTTTTTAAGTCAAATTAAT
TTATATTAACTTAAAATTTTATCAAGGCTGCGGCTCCCTAATTAAAATTTTTATTTTTGTCATCG
AAATGGTCACAACATATATTTTTTGTTTACTTTCACGGTTTCTTTGTATCTCCATTTGTTAGTTT
CATGGTA
Found at i:29621764 original size:217 final size:214
Alignment explanation
Indices: 29621287--29622047 Score: 748
Period size: 217 Copynumber: 3.5 Consensus size: 214
29621277 TTCATGGTAT
* * * *
29621287 TTTTTTAAGTCAAATTATATTTATGTTAATTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAG
1 TTTTTCAAGTTAAATTA-ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAG
* * * * *
29621352 AAAATTTTTATTTTA-GGACTACAA--CCTTAAATT--AAATTT-TTTTCGTAATCA-AAATTGG
65 AAAATTTTTA-TTTAGGGGCTGCAACCCCCT-AATTAAAAATTTATTTT-TTAAT-AGAAATAGG
* * * * *
29621410 CACGGTAGATATTTTTGTTTTATTTTCACGATTTCTTTGTACCGTAGGTTTTTTGGTATGTTGTC
126 CATGATAGATATTTTTGTTTTATTTTCACTATTTCTTTGTA-CGTAGGTTCTTTGGTATATTGTC
29621475 ACTT-TCAATCACTTTTTATTTCTTA
190 ACTTGTCAATCACTTTTTA-TTCTTA
* *
29621500 TTTTTCAAGTTAAATTAAATTTATATCAACTTAAAATTTTATAAATTTTAAATGAGTGTAATGAG
1 TTTTTCAAGTTAAATT-AATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAG
* *
29621565 AAAATTTTTATTTAGGGGTTGCAACCCCCTAATTAAAAATTTAGTTTTTTCATAGAAATAGGCAT
65 AAAATTTTTATTTAGGGGCTGCAACCCCCTAATTAAAAATTTA-TTTTTTAATAGAAATAGGCAT
* ** * *
29621630 GACAGATCATTTTTGTTTT-TTTTCACTATTTCTTTGTTTGATAGATTCTTTGGTATATTGTTAC
129 GATAGAT-ATTTTTGTTTTATTTTCACTATTTCTTTGTACG-TAGGTTCTTTGGTATATTGTCAC
* *
29621694 TTGTCAATCTCTTTTTATTCCATA
192 TTGTCAATCACTTTTTATT-CTTA
* * * *
29621718 TTTTTTAAGTTAAATTAATTTCTATTGACTTAAAATTTTATAAATTTTAAAAGTGTGTAATGAGA
1 TTTTTCAAGTTAAATTAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGA
* * * * *
29621783 ATAA-TTTTATTTAGGGGCTGCAGCCCCCTAATTAAAATTTTATTTCTTTGATAGAAATGGGTAT
66 A-AATTTTTATTTAGGGGCTGCAACCCCCTAATTAAAAATTTATTT-TTTAATAGAAATAGGCAT
* * * *
29621847 GATAGAAAATTTTTGTTTTATTTTCA-TGATTTCTTTATACGGTAGGTTCTTTCGTATATTATCA
129 GATAG-ATATTTTTGTTTTATTTTCACT-ATTTCTTTGTAC-GTAGGTTCTTTGGTATATTGTCA
* * * **
29621911 CTTGTCAGTCCCATGGTATT-TTA
191 CTTGTCAATCACTTTTTATTCTTA
* * * * **
29621934 TGTTTCAAATT--A-T-ATTTATATTAAATTAAAATTTTATAAATTTTAAAAGTGTACAATGAG-
1 TTTTTCAAGTTAAATTAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGA
* *
29621994 AAATTTTTCAATTTACGGG-TAGCAACCCCCTAATTAAAATTTTATTTTTATAAT
66 AAATTTTT--ATTTAGGGGCT-GCAACCCCCTAATTAAAAATTTATTTTT-TAAT
29622048 CAAAATTATT
Statistics
Matches: 461, Mismatches: 63, Indels: 48
0.81 0.11 0.08
Matches are distributed among these distances:
210 2 0.00
211 5 0.01
212 49 0.11
213 110 0.24
214 6 0.01
215 3 0.01
216 21 0.05
217 167 0.36
218 97 0.21
219 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.47
Consensus pattern (214 bp):
TTTTTCAAGTTAAATTAATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGA
AAATTTTTATTTAGGGGCTGCAACCCCCTAATTAAAAATTTATTTTTTAATAGAAATAGGCATGA
TAGATATTTTTGTTTTATTTTCACTATTTCTTTGTACGTAGGTTCTTTGGTATATTGTCACTTGT
CAATCACTTTTTATTCTTA
Found at i:29623496 original size:219 final size:217
Alignment explanation
Indices: 29623109--29624088 Score: 928
Period size: 219 Copynumber: 4.5 Consensus size: 217
29623099 TAGCTGTAGG
* * *
29623109 CCCCTAATTAAAATTTTATTTATGTGATCGAAATGG--TTACAATAGACAATTTTTGTTTTATTT
1 CCCCTAATTAAAATTTTATTTCTGTCATCGAAATGGCATGAC-A-A-AC-ATTTTTGTTTTATTT
* * * * * * * *
29623172 TCACGGTTTTTTTGTATGATAGGTTATTTGGTATATTTTCACTTGTTC-GTCCCATGATATTCCT
62 TCACGGTTTCTTTGTATGGTAGGTTCTTTGGTATATTGTCACTTGATCAATCCCATGGTATTCCA
* * * *
29623236 TATTTTTTAAGTTAAATTATATTTATATTAACTTT-AAATTTTAT-AATTGTTAAAACAATGTAA
127 TATTTCTTAAGTCAAATTATATTTATATTAA-TTTAAAATTTTATAAATT-TTAAAAGAGTGTAA
*
29623299 TGAGAAAATTTTTATTTTAGGGGTTGCA
190 TGAGAAAATTTTCATTTTAGGGGTTGCA
* * * *
29623327 GTTCCCTGATTAAAATTTTATTTCTGTCATCGAAATGCGCATGACAAACATTTTTATTTTACTTT
1 --CCCCTAATTAAAATTTTATTTCTGTCATCGAAATG-GCATGACAAACATTTTTGTTTTATTTT
* * *
29623392 CATGGTTTCTTTGTATGGTAGGTTGTTTGGTATATTGTCAC-TGATCAAACCCATGGTATTCCAT
63 CACGGTTTCTTTGTATGGTAGGTTCTTTGGTATATTGTCACTTGATCAATCCCATGGTATTCCAT
29623456 ATTTCTTAAGTCAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTGTAATGA
128 ATTTCTTAAGTCAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTGTAATGA
* *
29623521 GAAAAGTTTCCATTTTACGGGTTGCAA
193 GAAAA-TTTTCATTTTAGGGGTTGC-A
* * * * * * ** * *
29623548 CCCCTAATT-AATTTTTTTTTTTGTAATTGAAATGGGCACGTTAGACAATTTTGTTTTATTTTCA
1 CCCCTAATTAAAATTTTATTTCTGTCATCGAAAT-GGCATGACAAACATTTTTGTTTTATTTTCA
** * * * * *
29623612 TTGTTTGTTTGTATGGTAGGTTGTTTGGTATTTTGTCACTTGTCAATTCAATTCCATGTTATTCC
65 CGGTTTCTTTGTATGGTAGGTTCTTTGGTATATTGTCACTTG---A-TCAATCCCATGGTATTCC
* * * * * *
29623677 ATATTTTTTAAATCAAATTAAATTTCTATTAACTTAAAATTTTATAAATCTTAAAAGAGTGTGTA
126 ATATTTCTTAAGTCAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGA--GTGTA
* * **
29623742 ATGAAAAAAATTTCATTTTAGGGGCAGCAA
189 ATGAGAAAATTTTCATTTTAGGGGTTGC-A
* * * *
29623772 CCCTTTAATTAAAATTTTATTTCTGCCATCGAAACGGACATGACATACACTTTTTGTTTTATTTT
1 CCC-CTAATTAAAATTTTATTTCTGTCATCGAAATGG-CATGACAAACA-TTTTTGTTTTATTTT
* * * * * *
29623837 CACGGTTTCTTTGTACGGTAGATTCTTTGATATATTGTCACTTG-T-TAGCCTCATAGTATTCCA
63 CACGGTTTCTTTGTATGGTAGGTTCTTTGGTATATTGTCACTTGATCAATCC-CATGGTATTCCA
*
29623900 TATTTCTTAAGTTAAATTATATTTATATTAATTTGAAAA-TTTATAAATTTT---AG-GTGTAAT
127 TATTTCTTAAGTCAAATTATATTTATATTAATTT-AAAATTTTATAAATTTTAAAAGAGTGTAAT
** * *
29623960 GTTAAAATTTTCA-TTCAGGGGATGCAA
191 GAGAAAATTTTCATTTTAGGGGTTGC-A
* * * *
29623987 CCCCCTGATTAAAATTTTATTTCTTTCATCAAAATGGGCATGACAAACAATTTTTTTTTTTATTT
1 -CCCCTAATTAAAATTTTATTTCTGTCATCGAAAT-GGCATGACAAAC-A-TTTTTGTTTTATTT
* * *
29624052 TCACAGTTTCTTTGTACGGTAGGTTCTTTGATATATT
62 TCACGGTTTCTTTGTATGGTAGGTTCTTTGGTATATT
29624089 TGTTTGAAAA
Statistics
Matches: 629, Mismatches: 106, Indels: 54
0.80 0.13 0.07
Matches are distributed among these distances:
215 45 0.07
216 71 0.11
218 84 0.13
219 132 0.21
220 53 0.08
221 5 0.01
222 52 0.08
223 74 0.12
224 19 0.03
225 20 0.03
226 24 0.04
227 50 0.08
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (217 bp):
CCCCTAATTAAAATTTTATTTCTGTCATCGAAATGGCATGACAAACATTTTTGTTTTATTTTCAC
GGTTTCTTTGTATGGTAGGTTCTTTGGTATATTGTCACTTGATCAATCCCATGGTATTCCATATT
TCTTAAGTCAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAGAA
AATTTTCATTTTAGGGGTTGCA
Found at i:29623904 original size:445 final size:437
Alignment explanation
Indices: 29623151--29623951 Score: 1058
Period size: 445 Copynumber: 1.8 Consensus size: 437
29623141 ATGGTTACAA
*
29623151 TAGACAATTTTTGTTTTATTTTCACGGTTTTTTTGTATGATAGGTTATTTGGTATATTTTCACTT
1 TAGACAATTTTTGTTTTATTTTCACGGTTTGTTTGTATGATAGGTTATTTGGTATATTTTCACTT
* * * * * *
29623216 GTTCGTCCCATGATATTCCTTATTTTTTAAGTTAAATTATATTTATATTAACTTTAAATTTTATA
66 GTTCATCCCATGATATTCCATATTTTTTAAATCAAATTAAATTTATATTAACTTAAAATTTTATA
* * * * * ** * *
29623281 ATTGTTAAAACAATGTAATGAGAAAATTTTTATTTTAGGGGTTGCAGTTCCCTGATTAAAATTTT
131 AATCTTAAAACAATGTAATGAAAAAAATTTCATTTTAGGGGCAGCAG-ACCCTAATTAAAATTTT
* * * *
29623346 ATTTCTGTCATCGAAATGCGCATGACAAACATTTTTATTTTACTTTCATGGTTTCTTTGTATGGT
195 ATTTCTGCCATCGAAACGCGCATGACAAACATTTTTATTTTACTTTCACGGTTTCTTTGTACGGT
* * * *
29623411 AGGTTGTTTGGTATATTGTCACTGATCAAACCCATGGTATTCCATATTTCTTAAGTCAAATTATA
260 AGATTCTTTGATATATTGTCACTGATCAAACCCATAGTATTCCATATTTCTTAAGTCAAATTATA
29623476 TTTATATTAATTT-AAAATTTTATAAATTTTAAAAGAGTGTAATGAGAAAAGTTTCCATTTTACG
325 TTTATATTAATTTGAAAA-TTTATAAATTTTAAAAGAGTGTAATGAGAAAAGTTTCCATTTTACG
29623540 GGTTGCAACCCCTAATTAATTTTTTTTTTTGTAATTGAAATGGGCACGT
389 GGTTGCAACCCCTAATTAATTTTTTTTTTTGTAATTGAAATGGGCACGT
** * *
29623589 TAGACAA-TTTTGTTTTATTTTCATTGTTTGTTTGTATGGTAGGTTGTTTGGTAT-TTTGTCACT
1 TAGACAATTTTTGTTTTATTTTCACGGTTTGTTTGTATGATAGGTTATTTGGTATATTT-TCACT
* * *
29623652 TGTCAATTCAATTCCATGTTATTCCATATTTTTTAAATCAAATTAAATTTCTATTAACTTAAAAT
65 TG----TTC-ATCCCATGATATTCCATATTTTTTAAATCAAATTAAATTTATATTAACTTAAAAT
* *
29623717 TTTATAAATCTTAAAAGAGTGTGTAATGAAAAAAATTTCATTTTAGGGGCAGCA-ACCCTTTAAT
125 TTTATAAATCTTAAAACA--ATGTAATGAAAAAAATTTCATTTTAGGGGCAGCAGACCC--TAAT
* * *
29623781 TAAAATTTTATTTCTGCCATCGAAACG-GACATGACATACACTTTTTGTTTTATTTTCACGGTTT
186 TAAAATTTTATTTCTGCCATCGAAACGCG-CATGACAAACA-TTTTTATTTTACTTTCACGGTTT
* *
29623845 CTTTGTACGGTAGATTCTTTGATATATTGTCACTTG-T-TAGCCTCATAGTATTCCATATTTCTT
249 CTTTGTACGGTAGATTCTTTGATATATTGTCAC-TGATCAAACC-CATAGTATTCCATATTTCTT
*
29623908 AAGTTAAATTATATTTATATTAATTTGAAAATTTATAAATTTTA
312 AAGTCAAATTATATTTATATTAATTTGAAAATTTATAAATTTTA
29623952 GGTGTAATGT
Statistics
Matches: 309, Mismatches: 39, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
436 3 0.01
437 49 0.16
438 7 0.02
441 3 0.01
442 64 0.21
443 1 0.00
444 69 0.22
445 107 0.35
446 6 0.02
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.46
Consensus pattern (437 bp):
TAGACAATTTTTGTTTTATTTTCACGGTTTGTTTGTATGATAGGTTATTTGGTATATTTTCACTT
GTTCATCCCATGATATTCCATATTTTTTAAATCAAATTAAATTTATATTAACTTAAAATTTTATA
AATCTTAAAACAATGTAATGAAAAAAATTTCATTTTAGGGGCAGCAGACCCTAATTAAAATTTTA
TTTCTGCCATCGAAACGCGCATGACAAACATTTTTATTTTACTTTCACGGTTTCTTTGTACGGTA
GATTCTTTGATATATTGTCACTGATCAAACCCATAGTATTCCATATTTCTTAAGTCAAATTATAT
TTATATTAATTTGAAAATTTATAAATTTTAAAAGAGTGTAATGAGAAAAGTTTCCATTTTACGGG
TTGCAACCCCTAATTAATTTTTTTTTTTGTAATTGAAATGGGCACGT
Found at i:29625041 original size:49 final size:48
Alignment explanation
Indices: 29624983--29625077 Score: 154
Period size: 49 Copynumber: 2.0 Consensus size: 48
29624973 GATCTTGTTT
* *
29624983 ATTTATATTGTTTTGTTCAGATCTTGTGTTTTACATAAAATAATTATTA
1 ATTTATATTGTTTTGTTCAGATATTGTGGTTTACA-AAAATAATTATTA
*
29625032 ATTTATATTGTTTTGTTCAGATATTGTGGTTTACAAAAATATTTAT
1 ATTTATATTGTTTTGTTCAGATATTGTGGTTTACAAAAATAATTAT
29625078 ATTTATGTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 10 0.23
49 33 0.77
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.53
Consensus pattern (48 bp):
ATTTATATTGTTTTGTTCAGATATTGTGGTTTACAAAAATAATTATTA
Found at i:29625362 original size:77 final size:77
Alignment explanation
Indices: 29625213--29625579 Score: 441
Period size: 77 Copynumber: 4.8 Consensus size: 77
29625203 TTAAAAAATG
* * * * * *
29625213 AATAATTCTGTTTCGAGATTTGA-TGCTGCCATTCAACAGAATT-ATTTTGATTTTATTTTCAAC
1 AATAATTCTATTTCAAGATTT-ATTCCTACCGTTCAACAGAATTGATTTTGATTTTATTTTCAAA
*
29625276 CAATAATTAATTA
65 CAAGAATTAATTA
* ** *** *
29625289 AATAATTCTATTTCAGGATTTATTTATGTTGTTCAATAGAATTGATTTTGATTTTATTTTCAAAC
1 AATAATTCTATTTCAAGATTTATTCCTACCGTTCAACAGAATTGATTTTGATTTTATTTTCAAAC
29625354 AAGAATTAATTA
66 AAGAATTAATTA
* * *** * * *
29625366 AATAATTCTATTTAAACATTTATTCCTGTTGTTCAACAGAATTAATTTTGATTTTGTTTCCAAAC
1 AATAATTCTATTTCAAGATTTATTCCTACCGTTCAACAGAATTGATTTTGATTTTATTTTCAAAC
*
29625431 AAGATTTAATTA
66 AAGAATTAATTA
* * * * * *
29625443 AATAATTCTGTTTCAGGATTTATTCCTACCGTTTAATAGAATTGATTTTGGTTTTATTTCCAAAC
1 AATAATTCTATTTCAAGATTTATTCCTACCGTTCAACAGAATTGATTTTGATTTTATTTTCAAAC
29625508 AAGAATTAATTA
66 AAGAATTAATTA
*
29625520 AATAATTCTATTTCAAGATTTATTCCTACCGTTCAACAGAATTGATTTCGATTTTATTTT
1 AATAATTCTATTTCAAGATTTATTCCTACCGTTCAACAGAATTGATTTTGATTTTATTTT
29625580 AGAATTTTAA
Statistics
Matches: 248, Mismatches: 41, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
75 1 0.00
76 32 0.13
77 215 0.87
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (77 bp):
AATAATTCTATTTCAAGATTTATTCCTACCGTTCAACAGAATTGATTTTGATTTTATTTTCAAAC
AAGAATTAATTA
Found at i:29633840 original size:15 final size:15
Alignment explanation
Indices: 29633817--29633862 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
29633807 TCATCCAATT
*
29633817 AAGGTAATTATAGA-C
1 AAGGAAATTATA-ATC
29633832 AAGGAAATTATAATC
1 AAGGAAATTATAATC
29633847 AAGGAAATTATAATC
1 AAGGAAATTATAATC
29633862 A
1 A
29633863 GCAGCAGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 1 0.03
15 28 0.97
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (15 bp):
AAGGAAATTATAATC
Found at i:29644561 original size:12 final size:12
Alignment explanation
Indices: 29644541--29644573 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
29644531 TGGAAGAAGT
29644541 GGAAGAAGAGGAA
1 GGAA-AAGAGGAA
29644554 GGAAAAGAGGAA
1 GGAAAAGAGGAA
29644566 GGAAAAGA
1 GGAAAAGA
29644574 AGATGAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
GGAAAAGAGGAA
Found at i:29645149 original size:3 final size:3
Alignment explanation
Indices: 29645141--29645193 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
29645131 CCCAAATATA
29645141 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
29645189 GTC AT
1 ATC AT
29645194 TATTATTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:29645211 original size:3 final size:3
Alignment explanation
Indices: 29645205--29645269 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
29645195 ATTATTATTA
* * * *
29645205 TTG TTG TTG TTG TTG TTA TTG TTT TTG TTG TTG TTA TTT TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
*
29645253 TTG TTG TTG TTA TTG TT
1 TTG TTG TTG TTG TTG TT
29645270 ATTTTAGGGT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.05, C:0.00, G:0.25, T:0.71
Consensus pattern (3 bp):
TTG
Found at i:29645225 original size:18 final size:18
Alignment explanation
Indices: 29645202--29645269 Score: 100
Period size: 18 Copynumber: 3.8 Consensus size: 18
29645192 ATTATTATTA
29645202 TTATTGTTGTTGTTGTTG
1 TTATTGTTGTTGTTGTTG
*
29645220 TTATTGTTTTTGTTGTTG
1 TTATTGTTGTTGTTGTTG
*
29645238 TTATTTTTGTTGTTGTTG
1 TTATTGTTGTTGTTGTTG
* *
29645256 TTGTTGTTATTGTT
1 TTATTGTTGTTGTT
29645270 ATTTTAGGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.06, C:0.00, G:0.24, T:0.71
Consensus pattern (18 bp):
TTATTGTTGTTGTTGTTG
Found at i:29645270 original size:6 final size:6
Alignment explanation
Indices: 29645196--29645272 Score: 73
Period size: 6 Copynumber: 12.8 Consensus size: 6
29645186 ATCGTCATTA
* * * * * *
29645196 TTATTA TTATTG TTGTTG TTGTTG TTATTG TTTTTG TTGTTG TTATTT
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
* * *
29645244 TTGTTG TTGTTG TTGTTG TTATTG TTATT
1 TTATTG TTATTG TTATTG TTATTG TTATT
29645273 TTAGGGTTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.09, C:0.00, G:0.21, T:0.70
Consensus pattern (6 bp):
TTATTG
Found at i:29645841 original size:148 final size:149
Alignment explanation
Indices: 29645639--29646026 Score: 498
Period size: 150 Copynumber: 2.6 Consensus size: 149
29645629 TTTCTTTAAA
**
29645639 AAAG-AAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTT
1 AAAGAAAAAAGTTTAAATTTTTAAA-AAA-AATTGATTTTTTTAACTATTTCGAAATAAAAGTTT
* * * * * * *
29645703 GGATTTTTAAGTAAAATAGTGATTTTC-TTTAAAAAGGAGAGAAAATTTATATTTTTAAAAATAA
64 AGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAGAAAGAAAATTTAGATTTTTAAAAACAA
*
29645767 AAATAAG-TTTTTAGTTATTTT
129 AAATAAGTTTTTTAG-GATTTT
* *
29645788 AAAGAAAAAATTTTAAATTTTTAAATAAAATTGATTTTTTTAACTATTTCGAAATAAAAGTTTAG
1 AAAGAAAAAAGTTTAAATTTTTAAAAAAAATTGATTTTTTTAACTATTTCGAAATAAAAGTTTAG
* *
29645853 ATTTTTAAGTAAAGTAATGATTTTCATTAAAAAAAGAAAGAAAGTTTAGATTTTTAAAAACAAAA
66 ATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAGAAAGAAAATTTAGATTTTTAAAAACAAAA
**
29645918 ATTTGTTTTTTAGGATTTT
131 ATAAGTTTTTTAGGATTTT
*
29645937 AAA-AAAAAAGTTTAAATTTTTAAAAAAAAAAATT-TTTTTTTTAACTATTTCGAAATAAAAGTT
1 AAAGAAAAAAGTTTAAATTTTT---AAAAAAAATTGATTTTTTTAACTATTTCGAAATAAAAGTT
* ***
29646000 TTGATTGAGAAGTAAAGTAGTGATTTT
63 TAGATTTTTAAGTAAAGTAGTGATTTT
29646027 GTTTTAATCA
Statistics
Matches: 209, Mismatches: 24, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
148 74 0.35
149 50 0.24
150 76 0.36
151 9 0.04
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (149 bp):
AAAGAAAAAAGTTTAAATTTTTAAAAAAAATTGATTTTTTTAACTATTTCGAAATAAAAGTTTAG
ATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAGAAAGAAAATTTAGATTTTTAAAAACAAAA
ATAAGTTTTTTAGGATTTT
Found at i:29645997 original size:51 final size:50
Alignment explanation
Indices: 29645893--29646000 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
29645883 AAAAAGAAAG
* * * *
29645893 AAAGTTTAGATTTTTAAAAACAAAAATTTGTTTTTTAGGATTTTAAAAAA
1 AAAGTTTAAATTTTTAAAAAAAAAAATTTGTTTTTTACGATTTCAAAAAA
* * * *
29645943 AAAGTTTAAATTTTTAAAAAAAAAAATTTTTTTTTTAACTATTTCGAAATA
1 AAAGTTTAAATTTTTAAAAAAAAAAATTTGTTTTTT-ACGATTTCAAAAAA
29645994 AAAGTTT
1 AAAGTTT
29646001 TGATTGAGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 33 0.67
51 16 0.33
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (50 bp):
AAAGTTTAAATTTTTAAAAAAAAAAATTTGTTTTTTACGATTTCAAAAAA
Found at i:29646062 original size:150 final size:144
Alignment explanation
Indices: 29645638--29646060 Score: 424
Period size: 148 Copynumber: 2.8 Consensus size: 144
29645628 TTTTCTTTAA
* **
29645638 AAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTT
1 AAAA-AAAAAGTTTAAATTTTTAAAAAAAAATTT--TTTTTTTAACTATTTCGAAATAAAAGTTT
* * * * *
29645703 GGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAGGAGAGAAAATTT-ATATTTTTAAAAATAA
63 AGATTTTTAAGTAAAGTAGTGATTTTTTTTAAAAA--A-AGAAATTTTGAT-TTTTTAAAAACAA
*
29645767 AAATAAGTTTTTAGTTATTTT
124 AAATAAGTTTTTAGTGATTTT
* * *
29645788 AAAGAAAAAATTTTAAATTTTT-AAATAAAATTGATTTTTTTAACTATTTCGAAATAAAAGTTTA
1 AAA-AAAAAAGTTTAAATTTTTAAAAAAAAATT-TTTTTTTTAACTATTTCGAAATAAAAGTTTA
* ** *
29645852 GATTTTTAAGTAAAGTAATGATTTTCATTAAAAAAAGAAAGAAAGTTTAGA-TTTTTAAAAACAA
64 GATTTTTAAGTAAAGTAGTGATTTT--TT-TTAAAA-AAAGAAA-TTTTGATTTTTTAAAAACAA
**
29645916 AAATTTGTTTTTTAG-GATTTT
124 AAATAAG-TTTTTAGTGATTTT
*
29645937 AAAAAAAAAGTTTAAATTTTTAAAAAAAAAAATTTTTTTTTTAACTATTTCGAAATAAAAGTTTT
1 AAAAAAAAAGTTTAAATTTTT--AAAAAAAAATTTTTTTTTTAACTATTTCGAAATAAAAGTTTA
*** *
29646002 GATTGAGAAGTAAAGTAGTGATTTTGTTTTAATCAAAA-AAATTTTGATTTTTTTAAAAA
64 GATTTTTAAGTAAAGTAGTGATTTT-TTTTAA-AAAAAGAAATTTTGA-TTTTTTAAAAA
29646061 AAAGAAAAAA
Statistics
Matches: 227, Mismatches: 31, Indels: 32
0.78 0.11 0.11
Matches are distributed among these distances:
146 5 0.02
147 3 0.01
148 84 0.37
149 39 0.17
150 80 0.35
151 15 0.07
152 1 0.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (144 bp):
AAAAAAAAAGTTTAAATTTTTAAAAAAAAATTTTTTTTTTAACTATTTCGAAATAAAAGTTTAGA
TTTTTAAGTAAAGTAGTGATTTTTTTTAAAAAAAGAAATTTTGATTTTTTAAAAACAAAAATAAG
TTTTTAGTGATTTT
Found at i:29647452 original size:240 final size:239
Alignment explanation
Indices: 29647029--29647508 Score: 741
Period size: 240 Copynumber: 2.0 Consensus size: 239
29647019 AAAATAATAA
** * *
29647029 TAATGATAAAAGATTGAATAAGTTGTAAATGAATTTTAATATTTTTCTTAATTCATTAGTAACTA
1 TAATGATAAAAGATCAAATAAGTTGTAAATGAATTTTAATATTTCTCTTAATTCATTAATAACTA
29647094 TCAGGGTTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTAAAGGTATTTTACTAGAA
66 TCAGGG-TTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTAAAGGTATTTTACTAGAA
*
29647159 TTATTTAAGTATCTTTTAGGTTTCTCATTAGAAGTAAAAATCGCTAATTTAAGTTTTAAATTAGA
130 TTATTTAAGTATCTTTTAGGGTTCTCATTAGAAGTAAAAATCGCTAATTTAAGTTTTAAATTAGA
*
29647224 TAAGTTTGGTGAACATGTCTTAGTCAAGTTAAAAGTAAATCGGAG
195 TAAGTTTGGTGAACACGTCTTAGTCAAGTTAAAAGTAAATCGGAG
* *
29647269 TAATGATAAAAGATCAAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAATATTTT
1 TAATGATAAAAGATCAAATAAGTTGTAAATGAATTTTAATATTTCTCTTAATTCATTAATA---A
* * * *
29647334 TTTTTA-GG-TTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTTACTAG
63 CTATCAGGGTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTAAAGGTATTTTACTAG
* * *
29647397 AATTATTTAAGTAT-TCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATT
128 AATTATTTAAGTATCT-TTTAGGGTTCTCATTAGAAGTAAAAATCGCTAATTTAAGTTTTAAATT
* *
29647461 AGATAAGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATTGGAG
192 AGATAAGTTTGGTGAACACGTCTTAGTCAAGTTAAAAGTAAATCGGAG
29647509 GCATTTTTTA
Statistics
Matches: 219, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
239 1 0.00
240 213 0.97
242 2 0.01
243 3 0.01
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (239 bp):
TAATGATAAAAGATCAAATAAGTTGTAAATGAATTTTAATATTTCTCTTAATTCATTAATAACTA
TCAGGGTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTAAAGGTATTTTACTAGAAT
TATTTAAGTATCTTTTAGGGTTCTCATTAGAAGTAAAAATCGCTAATTTAAGTTTTAAATTAGAT
AAGTTTGGTGAACACGTCTTAGTCAAGTTAAAAGTAAATCGGAG
Found at i:29650719 original size:12 final size:12
Alignment explanation
Indices: 29650696--29650744 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
29650686 GAAATGGTTA
29650696 TCATTCACTCAT
1 TCATTCACTCAT
* *
29650708 TTATTCATTCAT
1 TCATTCACTCAT
*
29650720 TCATTCACTCAC
1 TCATTCACTCAT
*
29650732 TCATTCGCTCAT
1 TCATTCACTCAT
29650744 T
1 T
29650745 TGTTTATTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.22, C:0.31, G:0.02, T:0.45
Consensus pattern (12 bp):
TCATTCACTCAT
Found at i:29658888 original size:13 final size:13
Alignment explanation
Indices: 29658870--29658906 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
29658860 AAGTAGAAAA
29658870 AGAAAAAAATAAT
1 AGAAAAAAATAAT
29658883 AGAAAAAAATAAT
1 AGAAAAAAATAAT
29658896 AGAAAAAAATA
1 AGAAAAAAATA
29658907 GAAAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (13 bp):
AGAAAAAAATAAT
Found at i:29658901 original size:10 final size:10
Alignment explanation
Indices: 29658843--29658910 Score: 59
Period size: 10 Copynumber: 6.5 Consensus size: 10
29658833 GTTTAAATCA
29658843 AGAAAAAAAT
1 AGAAAAAAAT
*
29658853 ACAAAAAAAGT
1 AGAAAAAAA-T
29658864 AGAAAAAGAA-
1 AGAAAAA-AAT
*
29658874 A-AAAATAAT
1 AGAAAAAAAT
29658883 AGAAAAAAATAAT
1 AG--AAAAA-AAT
29658896 AGAAAAAAAT
1 AGAAAAAAAT
29658906 AGAAA
1 AGAAA
29658911 GAGAGAGCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
8 2 0.04
9 5 0.11
10 17 0.36
11 12 0.26
12 6 0.13
13 5 0.11
ACGTcount: A:0.78, C:0.01, G:0.10, T:0.10
Consensus pattern (10 bp):
AGAAAAAAAT
Found at i:29659411 original size:42 final size:42
Alignment explanation
Indices: 29659311--29659600 Score: 318
Period size: 42 Copynumber: 6.9 Consensus size: 42
29659301 AAGGAAAACA
* *
29659311 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* ** * * * *
29659353 TTTATCACAGTCAGAGGCCTAAGTGTAGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTC-CATTTACTT
* *
29659395 TTCATTACATTTAGAGG-CCAAGATGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAAG-TGTGGAGGTCCATTTACTT
*
29659437 TTCATTGCATTTAGAGGCCC-AGATTTGGAGGTCCATTTAC-T
1 TTCATTGCATTTAGAGGCCCAAG-TGTGGAGGTCCATTTACTT
*
29659478 TTCATTGCATTTAGAGGCCCATGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * ** *
29659520 TTCGTTGCGTTCGGAGGCCCATGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * ** *
29659562 TTCATTGCAATTAGAGGCCTAAGCATAGAGGTCCATTTA
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTA
29659601 TTTATTTATT
Statistics
Matches: 207, Mismatches: 35, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
41 42 0.20
42 162 0.78
43 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
Found at i:29659963 original size:3 final size:3
Alignment explanation
Indices: 29659943--29659987 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
29659933 AAGGTCTCAA
* *
29659943 ATT ATC ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29659988 GTTGTTGTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:29660587 original size:30 final size:32
Alignment explanation
Indices: 29660547--29660608 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
29660537 TTTAGAAAAG
* *
29660547 TTTAAGTATTT-AAA-CAAAGTTTTGATTTTT
1 TTTAACTATTTCAAATCAAAGTTTGGATTTTT
*
29660577 TTTAACTATTTCAAATCGAAGTTTGGATTTTT
1 TTTAACTATTTCAAATCAAAGTTTGGATTTTT
29660609 AAATAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 10 0.37
31 3 0.11
32 14 0.52
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (32 bp):
TTTAACTATTTCAAATCAAAGTTTGGATTTTT
Found at i:29660588 original size:139 final size:141
Alignment explanation
Indices: 29660422--29660762 Score: 349
Period size: 138 Copynumber: 2.4 Consensus size: 141
29660412 GATTTTGGGA
* * *
29660422 AAAGTTTTTGTTTTTTTTAAACAATTTCGAAATAAAAGCTTTGATTTTTAAGTAAAA-TAGTGTT
1 AAAG-TTTTGTTTTTTTT-AACTATTTC-AAATAAAAG-TTTGATTTTTAAATAAAACT-GTGAT
* * *
29660486 TTTCTTTAAAAAA-AAAGAAAGTTTAGA-TTTTAAAAA-ATAAA-A-ATTTGTT-T-TTTT-AGA
61 TTTCATTAAAAAAGAAA-AAA-TTTAGATTTTTAAAAATAAAAATATATTTGTTATATTTTAAAA
*
29660543 AAAGTTTAAGTATTTAAAC
124 AAAGTTTAAAT-TTTAAAC
**
29660562 AAAGTTTTGATTTTTTTTAACTATTTCAAATCGAAGTTTGGATTTTTAAATAAAACTGTGATTTT
1 AAAGTTTTG-TTTTTTTTAACTATTTCAAATAAAAGTTT-GATTTTTAAATAAAACTGTGATTTT
* * *
29660627 CATTAAAAAAGATAAAATTTATATTTTTAAAAATAAAAATATATTTTTTAGTGATTTTAAAAAAA
64 CATTAAAAAAGAAAAAATTTAGATTTTTAAAAATAAAAATATATTTGTTA-T-ATTTT-AAAAAA
29660692 AGTTTAAATTTTAAAC
126 AGTTTAAATTTTAAAC
* *
29660708 AAAGTTTTTTATTTTTTTAACTATTTCAAAATAAAAGTTTTGATTTTGAAATAAA
1 AAAGTTTTGT-TTTTTTTAACTATTTC-AAATAAAAG-TTTGATTTTTAAATAAA
29660763 GTAGAGATTT
Statistics
Matches: 168, Mismatches: 16, Indels: 27
0.80 0.08 0.13
Matches are distributed among these distances:
137 8 0.05
138 49 0.29
139 20 0.12
140 13 0.08
141 6 0.04
143 1 0.01
145 5 0.03
146 31 0.18
147 32 0.19
148 3 0.02
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (141 bp):
AAAGTTTTGTTTTTTTTAACTATTTCAAATAAAAGTTTGATTTTTAAATAAAACTGTGATTTTCA
TTAAAAAAGAAAAAATTTAGATTTTTAAAAATAAAAATATATTTGTTATATTTTAAAAAAAGTTT
AAATTTTAAAC
Done.