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 38 of 163
Found at i:10056694 original size:35 final size:33
Alignment explanation
Indices: 10056643--10056740 Score: 97
Period size: 35 Copynumber: 2.7 Consensus size: 33
10056633 GAATATAAAT
*
10056643 AACATAAAAATGAATAACAAATAAATAAATAAATAA
1 AACA-AAAAATAAATAA-AAATAAAT-AATAAATAA
*
10056679 AACAAAAAATAAATAAAAATTAAATACTAAATAA
1 AACAAAAAATAAATAAAAA-TAAATAATAAATAA
*
10056713 AATAATATAAATAATATAAAAAATAAAT
1 AACAA-A-AAATAA-AT-AAAAATAAAT
10056741 GGGACCAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
34 15 0.28
35 17 0.31
36 10 0.19
37 7 0.13
38 5 0.09
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.22
Consensus pattern (33 bp):
AACAAAAAATAAATAAAAATAAATAATAAATAA
Found at i:10056758 original size:4 final size:4
Alignment explanation
Indices: 10056580--10056740 Score: 79
Period size: 4 Copynumber: 40.0 Consensus size: 4
10056570 CATTAAAAAC
* * *
10056580 AAAT AAAT AAAAT ACAT AAA- AAA- CAAT AAAT AAAT AAGATT AAAT AAAGG
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-A-T AAAT AAA-T
* * * *
10056630 CAAG AATAT AAAT AACAT -AA- AAAT GAAT -AAC AAAT AAAT AAAT AAAT
1 AAAT AA-AT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
10056677 AAA- ACAAA AAAT AAAT AAA- AATT AAAT -ACT AAAT AAAAT AATAT AAAT
1 AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT AAAT
10056725 AATAT AAA- AAAT AAAT
1 AA-AT AAAT AAAT AAAT
10056741 GGGACCAAAT
Statistics
Matches: 123, Mismatches: 16, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
3 18 0.15
4 76 0.62
5 26 0.21
6 3 0.02
ACGTcount: A:0.71, C:0.04, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:10056850 original size:30 final size:30
Alignment explanation
Indices: 10056815--10056871 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
10056805 CAAAATTAAA
*
10056815 TAAAGG-ACTAAATT-GAAAACACAAATACAT
1 TAAAGGTAC-AAATTAG-AAACAAAAATACAT
10056845 TAAAGGTACAAATTAGAAACAAAAATA
1 TAAAGGTACAAATTAGAAACAAAAATA
10056872 AAATAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.19
Consensus pattern (30 bp):
TAAAGGTACAAATTAGAAACAAAAATACAT
Found at i:10063737 original size:58 final size:58
Alignment explanation
Indices: 10063628--10063737 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
10063618 ATATCCATGG
* *
10063628 ATATTAAATCTTTAATTTCTCATATCTGAATCCAAAAAAAAAATGCCAAAAAAAACCC
1 ATATTAAATCTTTAATTTCTCATATCTGAATCCAAAAAAAAAACGCAAAAAAAAACCC
* * * *
10063686 ATATTAAATTTTTATTTTC-CTATATCTGAA-CCCAAAAAAAAACGCTAAAAAA
1 ATATTAAATCTTTAATTTCTC-ATATCTGAATCCAAAAAAAAAACGCAAAAAAA
10063738 GAATCCAGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
57 20 0.43
58 26 0.57
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (58 bp):
ATATTAAATCTTTAATTTCTCATATCTGAATCCAAAAAAAAAACGCAAAAAAAAACCC
Found at i:10065467 original size:15 final size:16
Alignment explanation
Indices: 10065442--10065479 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
10065432 ATGAAAATTG
*
10065442 AATAAAAGGCA-AAAA
1 AATAAATGGCATAAAA
*
10065457 TATAAATGGCATAAAA
1 AATAAATGGCATAAAA
10065473 AATAAAT
1 AATAAAT
10065480 AAAATACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (16 bp):
AATAAATGGCATAAAA
Found at i:10065481 original size:4 final size:4
Alignment explanation
Indices: 10065467--10065616 Score: 87
Period size: 4 Copynumber: 36.8 Consensus size: 4
10065457 TATAAATGGC
* * **
10065467 ATAA A-AA ATAA ATAAA ATAC ATAA AAAA ATAA GATTAA ATAA AGGCA
1 ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA -A-TAA ATAA A-TAA
* * *
10065514 AGAA TATAA ATAA CATAA A-AA ATGA AT-A ACAA ATAA ATAA ATAA ATAA
1 ATAA -ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * *
10065562 A-ACA ATAA ATAA ATAA A-AA TTAA AT-A CTAA ATAA GATAA TATAA ACAA
1 ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA -ATAA -ATAA ATAA
10065610 ATAA ATA
1 ATAA ATA
10065617 GGACCAAATG
Statistics
Matches: 114, Mismatches: 18, Indels: 28
0.71 0.11 0.17
Matches are distributed among these distances:
3 13 0.11
4 74 0.65
5 24 0.21
6 3 0.03
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:10065521 original size:61 final size:64
Alignment explanation
Indices: 10065427--10065563 Score: 172
Period size: 61 Copynumber: 2.2 Consensus size: 64
10065417 CAAAAACTAT
* ** *
10065427 AAAAAATGAAAATTGAATAAAAGGCAAAAATATAAATGGCATAAAAAATAAAT-A-AAATACATA
1 AAAAAAT-AAAATTAAATAAAAGGCAAAAATATAAATAACATAAAAAATAAATAACAAATAAATA
* * *
10065490 AAAAAATAAGATTAAAT-AAAGGCAAGAATATAAATAACATAAAAAATGAATAACAAATAAATA
1 AAAAAATAAAATTAAATAAAAGGCAAAAATATAAATAACATAAAAAATAAATAACAAATAAATA
*
10065553 AATAAATAAAA
1 AAAAAATAAAA
10065564 CAATAAATAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
61 30 0.48
62 9 0.14
63 24 0.38
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.19
Consensus pattern (64 bp):
AAAAAATAAAATTAAATAAAAGGCAAAAATATAAATAACATAAAAAATAAATAACAAATAAATA
Found at i:10065753 original size:5 final size:5
Alignment explanation
Indices: 10065736--10065781 Score: 65
Period size: 5 Copynumber: 8.8 Consensus size: 5
10065726 GTACAAATTA
*
10065736 AAAAT AGAAAT AAAAT AAAAT AAAACT AAATT AAAAT AAAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAA
10065782 ATTACAGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 28 0.76
6 9 0.24
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:10065757 original size:16 final size:15
Alignment explanation
Indices: 10065736--10065781 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
10065726 GTACAAATTA
10065736 AAAATAGAAATAAAAT
1 AAAATA-AAATAAAAT
*
10065752 AAAATAAAACTAAATT
1 AAAATAAAA-TAAAAT
10065768 AAAATAAAATAAAA
1 AAAATAAAATAAAA
10065782 ATTACAGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:10065782 original size:11 final size:11
Alignment explanation
Indices: 10065734--10065783 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
10065724 AGGTACAAAT
10065734 TAAAAATAGAAA
1 TAAAAATA-AAA
10065746 T-AAAATAAAA
1 TAAAAATAAAA
*
10065756 TAAAACT-AAA
1 TAAAAATAAAA
*
10065766 TTAAAATAAAA
1 TAAAAATAAAA
10065777 TAAAAAT
1 TAAAAAT
10065784 TACAGGGACC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 12 0.38
11 19 0.59
12 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:10068209 original size:5 final size:5
Alignment explanation
Indices: 10068201--10068225 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10068191 ATCTATAAAT
10068201 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
10068226 CCTAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:10071707 original size:17 final size:17
Alignment explanation
Indices: 10071685--10071719 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10071675 ATTATTGTTT
* *
10071685 ACGTTTTATCTTTATCA
1 ACGTTTCATCTTCATCA
10071702 ACGTTTCATCTTCATCA
1 ACGTTTCATCTTCATCA
10071719 A
1 A
10071720 TAGTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.46
Consensus pattern (17 bp):
ACGTTTCATCTTCATCA
Found at i:10072515 original size:22 final size:22
Alignment explanation
Indices: 10072490--10072534 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
10072480 TTTTATTGGA
*
10072490 TAGTGTATATTCATGTTCTTTC
1 TAGTGGATATTCATGTTCTTTC
10072512 TAGTGGATATTCATGTTCTTTC
1 TAGTGGATATTCATGTTCTTTC
10072534 T
1 T
10072535 CTCTTGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (22 bp):
TAGTGGATATTCATGTTCTTTC
Found at i:10080929 original size:55 final size:55
Alignment explanation
Indices: 10080850--10080981 Score: 165
Period size: 55 Copynumber: 2.4 Consensus size: 55
10080840 ATTTGGATTG
* * * * * *
10080850 AATCGATTGTTATGCTGGAATATTGCTTCATTTGAATCGATTGTTTTTATGTTTA
1 AATCAATTGTCATGTTGAAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
* * *
10080905 AATCAATTGTCATGTTGAAATATTGCTACTTTTGAATTGATTGTTTATATTTTTA
1 AATCAATTGTCATGTTGAAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
* *
10080960 AATCAATTATCATATTGAAATA
1 AATCAATTGTCATGTTGAAATA
10080982 CTTTTATGTA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (55 bp):
AATCAATTGTCATGTTGAAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
Found at i:10083145 original size:30 final size:28
Alignment explanation
Indices: 10083101--10083196 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 28
10083091 CCCCGAGCTT
10083101 TTCCAAAATTACATTTTTTACCCTAAAAC
1 TTCCAAAATTACA-TTTTTACCCTAAAAC
* * **
10083130 TTCCAAATATGACATTTATACCCTCGAAC
1 TTCCAAA-ATTACATTTTTACCCTAAAAC
* *
10083159 TTCCAAAAATTCCAATTTTGACCCTAAAAC
1 TTCC-AAAATTAC-ATTTTTACCCTAAAAC
10083189 TTCCAAAA
1 TTCCAAAA
10083197 ATTATCAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
29 30 0.56
30 24 0.44
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (28 bp):
TTCCAAAATTACATTTTTACCCTAAAAC
Found at i:10083197 original size:30 final size:29
Alignment explanation
Indices: 10083101--10083207 Score: 110
Period size: 30 Copynumber: 3.6 Consensus size: 29
10083091 CCCCGAGCTT
*
10083101 TTCC-AAAATTACATTTTTTACCCTAAAAC
1 TTCCAAAAATTACA-ATTTTACCCTAAAAC
* * **
10083130 TTCCAAATATGAC-ATTTATACCCTCGAAC
1 TTCCAAAAATTACAATTT-TACCCTAAAAC
*
10083159 TTCCAAAAATTCCAATTTTGACCCTAAAAC
1 TTCCAAAAATTACAATTTT-ACCCTAAAAC
10083189 TTCCAAAAATTATCAATTT
1 TTCCAAAAATTA-CAATTT
10083208 ATCCTCGGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
28 3 0.05
29 24 0.39
30 29 0.47
31 6 0.10
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATTACAATTTTACCCTAAAAC
Found at i:10083214 original size:59 final size:57
Alignment explanation
Indices: 10083101--10083242 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 57
10083091 CCCCGAGCTT
* * *
10083101 TTCC-AAAATTACATTTTTTACCCTAAAACTTCCAAATATGACATTTATACCCTCGAA
1 TTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATGACATTTATA-CCTCGAA
* * *
10083158 CTTCCAAAAATTCCAATTTTGACCCTAAAACTTCCAAAAATTATCAATTTAT-CCTCGGA
1 -TTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATGA-C-ATTTATACCTCGAA
*
10083217 TGTCCAAAAAACTCCATTTTTGACCC
1 T-TCC-AAAAATTCCATTTTTGACCC
10083243 GAAACTTTTC
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
58 5 0.07
59 41 0.58
60 19 0.27
61 6 0.08
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (57 bp):
TTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATGACATTTATACCTCGAA
Found at i:10083280 original size:59 final size:58
Alignment explanation
Indices: 10083189--10083329 Score: 137
Period size: 59 Copynumber: 2.4 Consensus size: 58
10083179 ACCCTAAAAC
* * * *
10083189 TTCCAAAAATTATCAATTTATCCTCG-GATGTCCAAAAAACTCCATTTTTGA-CCCGAAACTT
1 TTCCAAAAATTACCATTTTACCCCCGAG-TGTCC-AAAAACTCCATTTTTGATCCCG--A-TT
* * *
10083250 TT-C-AAAATTACCATTTTACCCCCGAGTGTCCAAGAATTCCGTTTTTGATCCCGATT
1 TTCCAAAAATTACCATTTTACCCCCGAGTGTCCAAAAACTCCATTTTTGATCCCGATT
10083306 TTCCTAAAAATTACCATTTTACCC
1 TTCC-AAAAATTACCATTTTACCC
10083330 TCGAATATCT
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
56 4 0.06
57 2 0.03
58 14 0.21
59 44 0.65
60 2 0.03
61 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (58 bp):
TTCCAAAAATTACCATTTTACCCCCGAGTGTCCAAAAACTCCATTTTTGATCCCGATT
Found at i:10085379 original size:55 final size:55
Alignment explanation
Indices: 10085285--10085416 Score: 183
Period size: 55 Copynumber: 2.4 Consensus size: 55
10085275 GTCATAAAAG
* * * * *
10085285 TATTTCAACATGACAATTGATTTAAATATATAAACAATCGATTCAAAAGAAGCAA
1 TATTTCAACATGACAATCGATTTAAACAAAAAAACAATCGATTAAAAAGAAGCAA
* *
10085340 TATTCCAACATGACAATCGATTTAAACAAAAAAATAATCGATTAAAAAGAAGCAA
1 TATTTCAACATGACAATCGATTTAAACAAAAAAACAATCGATTAAAAAGAAGCAA
* *
10085395 TATTTCAGCATAACAATCGATT
1 TATTTCAACATGACAATCGATT
10085417 CAATCCAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.27
Consensus pattern (55 bp):
TATTTCAACATGACAATCGATTTAAACAAAAAAACAATCGATTAAAAAGAAGCAA
Found at i:10086236 original size:20 final size:19
Alignment explanation
Indices: 10086198--10086240 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
10086188 AATATTTATT
*
10086198 TAATATTTTAATTAAAATAA
1 TAATATTTTAATAAAAAT-A
10086218 TAATATTTT-ATAAACAATA
1 TAATATTTTAATAAA-AATA
10086237 TAAT
1 TAAT
10086241 TATATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTTTAATAAAAATA
Found at i:10086739 original size:13 final size:14
Alignment explanation
Indices: 10086721--10086767 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
10086711 CATAAAAAAC
10086721 AAATAAATAA-AAT
1 AAATAAATAACAAT
*
10086734 ACATAAA-AACAAT
1 AAATAAATAACAAT
* *
10086747 AAATAAATAAGATT
1 AAATAAATAACAAT
10086761 AAATAAA
1 AAATAAA
10086768 AGCAAGAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 2 0.07
13 15 0.54
14 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAATAACAAT
Found at i:10086768 original size:26 final size:24
Alignment explanation
Indices: 10086712--10086822 Score: 64
Period size: 26 Copynumber: 4.3 Consensus size: 24
10086702 AATAAATGGC
*
10086712 ATAAAAAACAAATAAATAAAATAC
1 ATAAAAAACAAATAAATAAAATAA
* *
10086736 ATAAAAACAATAAATAAATAAGATTAA
1 AT-AAAA-AACAAATAAATAA-AATAA
* *
10086763 ATAAAAGCAA-GAATACAAAAAACATAA
1 ATAAAA--AACAAATA-AATAAA-ATAA
*
10086790 AAAATGAATAACAAATAAAT-AAATAA
1 ATAA--AA-AACAAATAAATAAAATAA
10086816 ATAAAAA
1 ATAAAAA
10086823 TTAACTACTA
Statistics
Matches: 67, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
23 1 0.01
24 4 0.06
25 4 0.06
26 28 0.42
27 20 0.30
28 4 0.06
29 6 0.09
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (24 bp):
ATAAAAAACAAATAAATAAAATAA
Found at i:10086827 original size:26 final size:27
Alignment explanation
Indices: 10086798--10086865 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
10086788 AAAAAATGAA
10086798 TAACAAATAAATAAATA-AATAAAAAT
1 TAACAAATAAATAAATATAATAAAAAT
* * *
10086824 TAACTACTAAATAAA-ATAATATAAAT
1 TAACAAATAAATAAATATAATAAAAAT
*
10086850 TATATAAA-AAATAAAT
1 TA-ACAAATAAATAAAT
10086866 GGGACCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
25 1 0.03
26 30 0.91
27 2 0.06
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (27 bp):
TAACAAATAAATAAATATAATAAAAAT
Found at i:10086883 original size:4 final size:4
Alignment explanation
Indices: 10086712--10086865 Score: 52
Period size: 4 Copynumber: 37.5 Consensus size: 4
10086702 AATAAATGGC
* * *
10086712 ATAA A-AA ACAA ATAA ATAAA ATAC ATAA AAACA ATAA ATAA ATAA GATTAA
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATA-A ATAA ATAA ATAA -A-TAA
* * * * *
10086763 ATAA A-AGCA AGAA TACAA AAAA CATAA A-AA ATGA AT-A ACAA ATAA
1 ATAA ATA--A ATAA -ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA
* * * *
10086808 ATAA ATAA ATAA A-AA TTAA CT-A CTAA ATAAA ATAA TATAA ATTAT ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA -ATAA A-TAA ATAA
10086857 A-AA ATAA AT
1 ATAA ATAA AT
10086866 GGGACCAAAT
Statistics
Matches: 116, Mismatches: 16, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
3 17 0.15
4 67 0.58
5 28 0.24
6 4 0.03
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:10087003 original size:5 final size:5
Alignment explanation
Indices: 10086987--10087031 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
10086977 TACAAATTAG
* *
10086987 AAATA GAAATA AAATA AAATA AAACTA AATTC AAATA AAATA AAA
1 AAATA -AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA AAA
10087032 ATTATAAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:10087015 original size:16 final size:15
Alignment explanation
Indices: 10086987--10087031 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
10086977 TACAAATTAG
10086987 AAATAGAAATAAAATA
1 AAATA-AAATAAAATA
* *
10087003 AAATAAAACTAAATTC
1 AAATAAAA-TAAAATA
10087019 AAATAAAATAAAA
1 AAATAAAATAAAA
10087032 ATTATAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAAAATAAAATA
Found at i:10088839 original size:25 final size:24
Alignment explanation
Indices: 10088794--10088841 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
10088784 AAATCCAAAT
*
10088794 GAAAAAAAAAATTATAGAAATGGA
1 GAAAAAAAAAATTATAAAAATGGA
10088818 GAAAAGAAAAACATTA-AAAAATGG
1 GAAAA-AAAAA-ATTATAAAAATGG
10088842 TTATAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.17, T:0.15
Consensus pattern (24 bp):
GAAAAAAAAAATTATAAAAATGGA
Found at i:10094538 original size:4 final size:4
Alignment explanation
Indices: 10094529--10094691 Score: 67
Period size: 4 Copynumber: 40.0 Consensus size: 4
10094519 CATTAAAAAC
*
10094529 AAAT AAAT AAAAT ACAT AAA- AAA- ACAAT AAAT AAAT AAGATT AAAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AA-A-T AAAT
* * * * *
10094575 AAAGG CAAG AATAT AAAT AACAT -AA- AAAT GAAT -AAC AAAT AAAT AAAT
1 AAA-T AAAT AA-AT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
10094623 AAAT AAA- ACAA- AAATT AAAT AAA- AATT AAAT -ACT AAAT AAAAT AATAT
1 AAAT AAAT A-AAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT
10094671 AAAT AATAT AAA- AAAGT AAAT
1 AAAT AA-AT AAAT AAA-T AAAT
10094692 GGGACCAAAT
Statistics
Matches: 125, Mismatches: 13, Indels: 42
0.69 0.07 0.23
Matches are distributed among these distances:
3 19 0.15
4 71 0.57
5 32 0.26
6 3 0.02
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:10094547 original size:9 final size:9
Alignment explanation
Indices: 10094529--10094691 Score: 50
Period size: 9 Copynumber: 16.9 Consensus size: 9
10094519 CATTAAAAAC
10094529 AAATAAATA
1 AAATAAATA
*
10094538 AAATACATA
1 AAATAAATA
*
10094547 AAA-AAACAA
1 AAATAAA-TA
10094556 TAAATAAATA
1 -AAATAAATA
*
10094566 AGATTAAATA
1 A-AATAAATA
10094576 AAGGCA-AGAATA
1 AA---ATA-AATA
10094588 TAAATAACATAA
1 -AAATAA-AT-A
*
10094600 AAATGAATAA
1 AAATAAAT-A
10094610 CAAATAAAT-
1 -AAATAAATA
10094619 AAATAAATA
1 AAATAAATA
*
10094628 AAA-CAA-A
1 AAATAAATA
*
10094635 AATTAAATAA
1 AAATAAAT-A
10094645 AAATTAAATA
1 AAA-TAAATA
10094655 CTAAATAAAATA
1 --AAAT-AAATA
*
10094667 ATATAAATA
1 AAATAAATA
*
10094676 ATATAAA-A
1 AAATAAATA
*
10094684 AAGTAAAT
1 AAATAAAT
10094692 GGGACCAAAT
Statistics
Matches: 117, Mismatches: 15, Indels: 44
0.66 0.09 0.25
Matches are distributed among these distances:
7 3 0.03
8 20 0.17
9 29 0.25
10 25 0.21
11 25 0.21
12 13 0.11
13 2 0.02
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (9 bp):
AAATAAATA
Found at i:10094610 original size:15 final size:15
Alignment explanation
Indices: 10094587--10094654 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
10094577 AGGCAAGAAT
10094587 ATAAATAACATAAAA
1 ATAAATAACATAAAA
*
10094602 ATGAATAACA-AATAA
1 ATAAATAACATAA-AA
10094617 ATAAATAA-ATAAAA
1 ATAAATAACATAAAA
*
10094631 CAAAAATTAA-ATAAAA
1 -ATAAA-TAACATAAAA
10094647 ATTAAATA
1 A-TAAATA
10094655 CTAAATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.11
15 27 0.61
16 12 0.27
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.22
Consensus pattern (15 bp):
ATAAATAACATAAAA
Found at i:10094614 original size:11 final size:10
Alignment explanation
Indices: 10094584--10094676 Score: 53
Period size: 11 Copynumber: 8.5 Consensus size: 10
10094574 TAAAGGCAAG
*
10094584 AATATAAATA
1 AATAAAAATA
*
10094594 ACATAAAAATG
1 A-ATAAAAATA
10094605 AATAACAAATA
1 AATAA-AAATA
10094616 AATAAATAAATAA
1 AAT-AA-AAAT-A
*
10094629 AACAAAAATTA
1 AATAAAAA-TA
10094640 AATAAAAATTA
1 AATAAAAA-TA
*
10094651 AATACTAAATA
1 AATA-AAAATA
*
10094662 AA-ATAATATA
1 AATA-AAAATA
10094672 AATAA
1 AATAA
10094677 TATAAAAAAG
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
10 13 0.20
11 38 0.58
12 12 0.18
13 3 0.05
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (10 bp):
AATAAAAATA
Found at i:10094628 original size:34 final size:34
Alignment explanation
Indices: 10094587--10094667 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
10094577 AGGCAAGAAT
* *
10094587 ATAAATAACATAAAAA-TGAATAACAAA-TAAATAA
1 ATAAATAAAATAAAAATTAAATAA-AAATTAAAT-A
*
10094621 ATAAATAAAACAAAAATTAAATAAAAATTAAATA
1 ATAAATAAAATAAAAATTAAATAAAAATTAAATA
*
10094655 CTAAATAAAATAA
1 ATAAATAAAATAA
10094668 TATAAATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 29 0.73
35 11 0.28
ACGTcount: A:0.72, C:0.05, G:0.01, T:0.22
Consensus pattern (34 bp):
ATAAATAAAATAAAAATTAAATAAAAATTAAATA
Found at i:10094859 original size:6 final size:5
Alignment explanation
Indices: 10094819--10094857 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
10094809 TTAGAAACAG
* *
10094819 AAATA AAATA AAATA AAACTA AATTC AAATA AAATA AAA
1 AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA AAA
10094858 ATTATAGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:10100984 original size:17 final size:16
Alignment explanation
Indices: 10100964--10101055 Score: 116
Period size: 17 Copynumber: 5.7 Consensus size: 16
10100954 TAAGTTTAAA
*
10100964 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
10100981 TTAAATTTAAATTTAT
1 TTAAATTTAAATTTAT
*
10100997 CTGAAATTTAAATTTAT
1 -TTAAATTTAAATTTAT
10101014 TT--ATTTAAATTTATT
1 TTAAATTTAAATTTA-T
*
10101029 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAT
10101045 TTAAATTTAAA
1 TTAAATTTAAA
10101056 ATGATATTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.16
15 3 0.04
16 17 0.25
17 36 0.54
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:10100995 original size:6 final size:6
Alignment explanation
Indices: 10100952--10101055 Score: 78
Period size: 6 Copynumber: 18.0 Consensus size: 6
10100942 TTTGATTTTT
* * *
10100952 TTTAAG TTTAAA -TTAAT TTTAAA TTT-TA TTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
10100996 TCTGAAA TTTAAA TTTATTTA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
10101045 -TTAAA TTTAAA
1 TTTAAA TTTAAA
10101056 ATGATATTAA
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
4 4 0.05
5 17 0.22
6 49 0.64
7 2 0.03
8 5 0.06
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:10101046 original size:11 final size:11
Alignment explanation
Indices: 10100952--10101055 Score: 68
Period size: 11 Copynumber: 9.0 Consensus size: 11
10100942 TTTGATTTTT
10100952 TTTAAGTTTAAA
1 TTTAA-TTTAAA
10100964 -TTAATTTTAAA
1 TTTAA-TTTAAA
*
10100975 TTTTATTTAAA
1 TTTAATTTAAA
**
10100986 TTTAAATTTATC
1 TTT-AATTTAAA
**
10100998 TGAAATTTAAA
1 TTTAATTTAAA
10101009 TTTATTTATTTAAA
1 TTTA---ATTTAAA
*
10101023 TTTATTTTAAA
1 TTTAATTTAAA
10101034 TTTAAATTT-AA
1 TTT-AATTTAAA
*
10101045 TTAAATTTAAA
1 TTTAATTTAAA
10101056 ATGATATTAA
Statistics
Matches: 71, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
10 5 0.07
11 42 0.59
12 13 0.18
14 11 0.15
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:10101057 original size:17 final size:16
Alignment explanation
Indices: 10100952--10101055 Score: 97
Period size: 17 Copynumber: 6.4 Consensus size: 16
10100942 TTTGATTTTT
* *
10100952 TTTAAGTTTAAATTAAT
1 TTTAAATTT-AATTAAA
*
10100969 TTTAAATTTTATTTAAA
1 TTTAAA-TTTAATTAAA
10100986 TTTAAATTT-ATCTGAAA
1 TTTAAATTTAAT-T-AAA
*
10101003 TTTAAATTT-ATT-TA
1 TTTAAATTTAATTAAA
*
10101017 TTTAAATTTATTTTAAA
1 TTTAAATTTA-ATTAAA
10101034 TTTAAATTTAATTAAA
1 TTTAAATTTAATTAAA
10101050 TTTAAA
1 TTTAAA
10101056 ATGATATTAA
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 18 0.25
17 41 0.56
18 3 0.04
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:10101064 original size:17 final size:16
Alignment explanation
Indices: 10101029--10101071 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
10101019 TAAATTTATT
* *
10101029 TTAAATTTAAATTTAA
1 TTAAATTTAAAATGAA
10101045 TTAAATTTAAAATGATA
1 TTAAATTTAAAATGA-A
*
10101062 TTAAAATTAA
1 TTAAATTTAA
10101072 TAAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TTAAATTTAAAATGAA
Found at i:10101457 original size:26 final size:26
Alignment explanation
Indices: 10101415--10101476 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
10101405 GTAAAGGGGT
* * *
10101415 TACAAACCCAGTTCTTGAAATTTGAA
1 TACAAACCCAGTACTTGAAATCTAAA
10101441 TACAAATCCC-GTACTTGAAATCTAAA
1 TACAAA-CCCAGTACTTGAAATCTAAA
*
10101467 TACAAGCCCA
1 TACAAACCCA
10101477 ATTCCCAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 3 0.10
26 24 0.80
27 3 0.10
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (26 bp):
TACAAACCCAGTACTTGAAATCTAAA
Found at i:10101864 original size:3 final size:3
Alignment explanation
Indices: 10101856--10101880 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10101846 TTAGTAATTT
10101856 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
10101881 TTGTAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:10102138 original size:21 final size:21
Alignment explanation
Indices: 10102114--10102153 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10102104 CGAAAAACAA
10102114 GTTTGATTGTTAAA-AAAAATG
1 GTTTG-TTGTTAAATAAAAATG
*
10102135 GTTTGTTTTTAAATAAAAA
1 GTTTGTTGTTAAATAAAAA
10102154 AGGGGAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (21 bp):
GTTTGTTGTTAAATAAAAATG
Found at i:10103094 original size:58 final size:59
Alignment explanation
Indices: 10102981--10103097 Score: 173
Period size: 58 Copynumber: 2.0 Consensus size: 59
10102971 AAACTTTTAA
* * *
10102981 AAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCTTTTTTCAACCCCAATTTCATC
1 AAAATTACCATTTTACCCCCAAACTATCCAAAAGTCCTGTTTTCAACCCCAATTTCATC
* * *
10103040 AAAATTACCATTTTACCCCC-GAGTATCCAAAAGTCCTGTTTTCAACCCCGATTTCATC
1 AAAATTACCATTTTACCCCCAAACTATCCAAAAGTCCTGTTTTCAACCCCAATTTCATC
10103098 GTTTCTTCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
58 32 0.62
59 20 0.38
ACGTcount: A:0.31, C:0.32, G:0.04, T:0.32
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACTATCCAAAAGTCCTGTTTTCAACCCCAATTTCATC
Found at i:10105092 original size:56 final size:56
Alignment explanation
Indices: 10104986--10105093 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
10104976 ATAGCCATGG
* *
10104986 ATATTAAATCTTTAATTTCTCATATCTGAATAAAAAAAAATGCCAAAAAAAAACCC
1 ATATTAAATCTTTAATTTCCCATATCTGAACAAAAAAAAATGCCAAAAAAAAACCC
* * * *
10105042 ATATTAAATTTTTATTTTCCCATATCTGAACCCAAAAGAAAATGCTAAAAAA
1 ATATTAAATCTTTAATTTCCCATATCTGAA--CAAAAAAAAATGCCAAAAAA
10105094 GAATCCAGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 27 0.61
58 17 0.39
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.31
Consensus pattern (56 bp):
ATATTAAATCTTTAATTTCCCATATCTGAACAAAAAAAAATGCCAAAAAAAAACCC
Found at i:10106854 original size:4 final size:4
Alignment explanation
Indices: 10106839--10106980 Score: 85
Period size: 4 Copynumber: 34.8 Consensus size: 4
10106829 TATAAATGGC
* * * **
10106839 ATAA AAAA ATAA ATAA ATAC ATAA AAAA ATAA ATAA GATTAA ATAA AGGCA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA -A-TAA ATAA A-TAA
* * *
10106890 AGAA TATAA ATAA CATAA A-AA ATGA AT-A ACAA ATAA ATAA ATAA ATAA
1 ATAA -ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * *
10106938 ATAA A-AA TTAA AT-A CTAA GTAA GATAA TATAA ACAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA -ATAA -ATAA ATAA ATAA ATA
10106981 GGACCAAATG
Statistics
Matches: 107, Mismatches: 21, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
3 9 0.08
4 77 0.72
5 18 0.17
6 3 0.03
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:10106888 original size:65 final size:63
Alignment explanation
Indices: 10106818--10106937 Score: 161
Period size: 65 Copynumber: 1.9 Consensus size: 63
10106808 AAATTGAACA
**
10106818 AAAGGCAAAAATATAAATGGCATAAAAAAATAAATAA-ATACATAAAAAAATAAATAAGATTAAA
1 AAAGGCAAAAATATAAATAACAT-AAAAAATAAATAACA-A-ATAAAAAAATAAATAAGATTAAA
10106882 T
63 T
* * *
10106883 AAAGGCAAGAATATAAATAACATAAAAAATGAATAACAAATAAATAAATAAATAA
1 AAAGGCAAAAATATAAATAACATAAAAAATAAATAACAAATAAAAAAATAAATAA
10106938 ATAAAAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
63 15 0.31
64 13 0.27
65 21 0.43
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.19
Consensus pattern (63 bp):
AAAGGCAAAAATATAAATAACATAAAAAATAAATAACAAATAAAAAAATAAATAAGATTAAAT
Found at i:10106923 original size:11 final size:11
Alignment explanation
Indices: 10106897--10106951 Score: 65
Period size: 11 Copynumber: 4.8 Consensus size: 11
10106887 GCAAGAATAT
10106897 AAATAACATAAA
1 AAATAA-ATAAA
* *
10106909 AAATGAATAAC
1 AAATAAATAAA
10106920 AAATAAATAAA
1 AAATAAATAAA
10106931 TAAATAAATAAA
1 -AAATAAATAAA
*
10106943 AATTAAATA
1 AAATAAATA
10106952 CTAAGTAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
11 21 0.57
12 16 0.43
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:10106923 original size:23 final size:22
Alignment explanation
Indices: 10106892--10106951 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
10106882 TAAAGGCAAG
* *
10106892 AATATAAATAACATAAA-AAATG
1 AATAAAAATAA-ATAAATAAATA
10106914 AATAACAAATAAATAAATAAATA
1 AATAA-AAATAAATAAATAAATA
10106937 AATAAAAATTAAATA
1 AATAAAAA-TAAATA
10106952 CTAAGTAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 12 0.36
23 21 0.64
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (22 bp):
AATAAAAATAAATAAATAAATA
Found at i:10107111 original size:30 final size:30
Alignment explanation
Indices: 10107055--10107111 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
10107045 CAAAATTAAA
* *
10107055 TAAAGGACTAAATTGAAAACACAAATACAT
1 TAAAGGACTAAATTAAAAAAACAAATACAT
*
10107085 TAAAGGTAC-AAATTAAAAAAAGAAATA
1 TAAAGG-ACTAAATTAAAAAAACAAATA
10107112 AAATAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 21 0.91
31 2 0.09
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (30 bp):
TAAAGGACTAAATTAAAAAAACAAATACAT
Found at i:10107117 original size:5 final size:5
Alignment explanation
Indices: 10107107--10107145 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
10107097 TTAAAAAAAG
* *
10107107 AAATA AAATA AAATTA AACTA AATTA AAATA AAATA AAA
1 AAATA AAATA AAA-TA AAATA AAATA AAATA AAATA AAA
10107146 ATTACAGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:10108174 original size:46 final size:46
Alignment explanation
Indices: 10108103--10108197 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
10108093 TGTAATTGGG
10108103 TTTAGGGTAATAGGGTAGTTAGGCTAAAATGCAAATGGATTTTGTA
1 TTTAGGGTAATAGGGTAGTTAGGCTAAAATGCAAATGGATTTTGTA
*
10108149 TTTAGGGTAATAGGGTAGTTGGGCTAAAATGCAAATGGATTTTGTA
1 TTTAGGGTAATAGGGTAGTTAGGCTAAAATGCAAATGGATTTTGTA
10108195 TTT
1 TTT
10108198 GGACTTTGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.37
Consensus pattern (46 bp):
TTTAGGGTAATAGGGTAGTTAGGCTAAAATGCAAATGGATTTTGTA
Found at i:10109618 original size:5 final size:5
Alignment explanation
Indices: 10109608--10109632 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10109598 ATCTATAAAT
10109608 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
10109633 CCTAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:10118748 original size:17 final size:17
Alignment explanation
Indices: 10118726--10118759 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10118716 ATTATTGTTT
* *
10118726 ACGTTTTATCTTTATCA
1 ACGTTTCATCTTCATCA
10118743 ACGTTTCATCTTCATCA
1 ACGTTTCATCTTCATCA
10118760 GTAGTTTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (17 bp):
ACGTTTCATCTTCATCA
Found at i:10119554 original size:22 final size:22
Alignment explanation
Indices: 10119529--10119570 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
10119519 TTTTATTGGA
*
10119529 TAGTGTATATTCATGTTCTTTC
1 TAGTGGATATTCATGTTCTTTC
10119551 TAGTGGATATTCATGTTCTT
1 TAGTGGATATTCATGTTCTT
10119571 CCTCTCTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.52
Consensus pattern (22 bp):
TAGTGGATATTCATGTTCTTTC
Found at i:10128794 original size:59 final size:58
Alignment explanation
Indices: 10128683--10128795 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 58
10128673 TGTGTGGCAC
* *
10128683 CCATTTCAATCATGAATTTAGAAGAATCAATTTTTGAAGTTTCTAGTATGTGTGCTAT
1 CCATTTCAATCAAGAATTTAGAAGAATCAATTTTTGAAGTTTCTAGAATGTGTGCTAT
10128741 CCATTTCAATCAAGTAATTTAGAAGAAAAT-AATTTTTGAAGTTTCTA-AATGTGTG
1 CCATTTCAATCAAG-AATTTAGAAG--AATCAATTTTTGAAGTTTCTAGAATGTGTG
10128796 GGTTTTTAGC
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
58 13 0.26
59 17 0.34
60 17 0.34
61 3 0.06
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (58 bp):
CCATTTCAATCAAGAATTTAGAAGAATCAATTTTTGAAGTTTCTAGAATGTGTGCTAT
Found at i:10129441 original size:22 final size:22
Alignment explanation
Indices: 10129416--10129457 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
10129406 TTTTATTGGA
*
10129416 TAGTGTATATTCATGTTCTTTC
1 TAGTGGATATTCATGTTCTTTC
10129438 TAGTGGATATTCATGTTCTT
1 TAGTGGATATTCATGTTCTT
10129458 CCCTCTCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.52
Consensus pattern (22 bp):
TAGTGGATATTCATGTTCTTTC
Found at i:10138647 original size:59 final size:57
Alignment explanation
Indices: 10138583--10138695 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 57
10138573 TGTGTGGCAC
*
10138583 CCATTTCAATCATGAAATTTAGAAG-AATCAATTTTTGAAGTTTCTAGTATGTGTGCTAT
1 CCATTTCAATCAAGAAATTTAGAAGAAAT-AATTTTTGAAGTTTCTA--ATGTGTGCTAT
*
10138642 CCATTTCAATCAAGTAATTTAGAAGAAAATAATTTTTGAAGTTTCTAATGTGTG
1 CCATTTCAATCAAGAAATTTAGAAG-AAATAATTTTTGAAGTTTCTAATGTGTG
10138696 GGTTTTAGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
58 7 0.14
59 23 0.46
60 17 0.34
61 3 0.06
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (57 bp):
CCATTTCAATCAAGAAATTTAGAAGAAATAATTTTTGAAGTTTCTAATGTGTGCTAT
Found at i:10139983 original size:55 final size:55
Alignment explanation
Indices: 10139907--10140038 Score: 165
Period size: 55 Copynumber: 2.4 Consensus size: 55
10139897 ATTTGGATTG
* * * * *
10139907 AATCGATTGTTATGCTGGAATATTGCTTCATTTGAATCGATTGTTTTTATGTTTA
1 AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
* * *
10139962 AATCAATTGTCATGTTGGAATATTGCTACTTTTGAATTGATTGTTTATATTTTTA
1 AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
* * *
10140017 AATCAATTATCATATTGAAATA
1 AATCAATTGTCATGTTGGAATA
10140039 CTTTTATGTA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (55 bp):
AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
Found at i:10142245 original size:58 final size:59
Alignment explanation
Indices: 10142122--10142390 Score: 257
Period size: 59 Copynumber: 4.5 Consensus size: 59
10142112 GTAAGTCCTT
* * * * * * *
10142122 AAACTATCCAAAAATTA-TATTTTGACCCCCGAGCT-TCTCCAAAATTACATTTTTTACCCTA
1 AAACT-TCCAAAAATTACCATTTT-ACCCTCGAACTGTC-CAAAAATTCCATTTTTGACCC-G
10142183 AAACTTCCAAAAATTA-CATTTTTACCCTCGAACT-TCCAAAAATTCCA-TTTTGACCCTG
1 AAACTTCCAAAAATTACCA-TTTTACCCTCGAACTGTCCAAAAATTCCATTTTTGACCC-G
* *
10142241 AAACTTCCAAAAATTATCATTTTACCCTCGAA-TGTCCAAAAAACTCCATTTTTGACCCG
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTGTCC-AAAAATTCCATTTTTGACCCG
** * * *
10142300 AAACTTTTAAAAATTACCATTTTACCCTCG-AGTGTCCAAGAATTCCGTTTTTGATCCCG
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTGTCCAAAAATTCCATTTTTGA-CCCG
**
10142359 -ATTTTCCTAAAAATTACCATTTTACCCTCGAA
1 AAACTTCC-AAAAATTACCATTTTACCCTCGAA
10142391 TATCTAAAAT
Statistics
Matches: 181, Mismatches: 18, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
57 1 0.01
58 59 0.33
59 79 0.44
60 33 0.18
61 9 0.05
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCTCGAACTGTCCAAAAATTCCATTTTTGACCCG
Found at i:10142278 original size:29 final size:28
Alignment explanation
Indices: 10142123--10142330 Score: 154
Period size: 29 Copynumber: 7.0 Consensus size: 28
10142113 TAAGTCCTTA
* *
10142123 AACTATCCAAAAATTATATTTTGACCCCCG
1 AACT-TCCAAAAATTACATTTT-ACCCTCG
* * **
10142153 AGCTTCTCCAAAATTACATTTTTTACCCTAA
1 AACTTC-CAAAAATTACA--TTTTACCCTCG
10142184 AACTTCCAAAAATTACATTTTTACCCTCG
1 AACTTCCAAAAATTACA-TTTTACCCTCG
*
10142213 AACTTCCAAAAATTCCATTTTGACCCT-G
1 AACTTCCAAAAATTACATTTT-ACCCTCG
10142241 AAACTTCCAAAAATTATCATTTTACCCTCG
1 -AACTTCCAAAAATTA-CATTTTACCCTCG
* *
10142271 AA-TGTCCAAAAAACTCCATTTTTGA-CC-CG
1 AACT-TCC-AAAAATTACA-TTTT-ACCCTCG
**
10142300 AAACTTTTAAAAATTACCATTTTACCCTCG
1 -AACTTCCAAAAATTA-CATTTTACCCTCG
10142330 A
1 A
10142331 GTGTCCAAGA
Statistics
Matches: 144, Mismatches: 18, Indels: 33
0.74 0.09 0.17
Matches are distributed among these distances:
28 7 0.05
29 74 0.51
30 48 0.33
31 11 0.08
32 4 0.03
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.33
Consensus pattern (28 bp):
AACTTCCAAAAATTACATTTTACCCTCG
Found at i:10142283 original size:59 final size:58
Alignment explanation
Indices: 10142162--10142391 Score: 261
Period size: 59 Copynumber: 3.9 Consensus size: 58
10142152 GAGCTTCTCC
* * *
10142162 AAAATTACATTTTTTACCCTAAAACTTCCAAAAATTA-CATTTTTACCCTCGAACT-TCCA
1 AAAATTCCATTTTTGACCC-GAAACTTCCAAAAATTACCA-TTTTACCCTCGAA-TGTCCA
*
10142221 AAAATTCCA-TTTTGACCCTGAAACTTCCAAAAATTATCATTTTACCCTCGAATGTCCAA
1 AAAATTCCATTTTTGACCC-GAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCC-A
* ** *
10142280 AAAACTCCATTTTTGACCCGAAACTTTTAAAAATTACCATTTTACCCTCGAGTGTCCA
1 AAAATTCCATTTTTGACCCGAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCCA
* * **
10142338 AGAATTCCGTTTTTGATCCCG-ATTTTCCTAAAAATTACCATTTTACCCTCGAAT
1 AAAATTCCATTTTTGA-CCCGAAACTTCC-AAAAATTACCATTTTACCCTCGAAT
10142392 ATCTAAAATG
Statistics
Matches: 149, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
57 1 0.01
58 58 0.39
59 81 0.54
60 9 0.06
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCCGAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCCA
Found at i:10142343 original size:29 final size:30
Alignment explanation
Indices: 10142191--10142475 Score: 86
Period size: 29 Copynumber: 9.7 Consensus size: 30
10142181 TAAAACTTCC
*
10142191 AAAAATTA-CATTTTTACCCTCGAACT-TCC-
1 AAAAATTACCA-TTTTACCCTCG-AGTGTCCT
*
10142220 AAAAATT-CCATTTTGACCCT-GAAACT-TCC-
1 AAAAATTACCATTTT-ACCCTCG--AGTGTCCT
* * *
10142249 AAAAATTATCATTTTACCCTCGAATGTCCA
1 AAAAATTACCATTTTACCCTCGAGTGTCCT
* *** **
10142279 AAAAACT-CCATTTTTGA-CC-CGAAACTTTT
1 AAAAATTACCA-TTTT-ACCCTCGAGTGTCCT
10142308 AAAAATTACCATTTTACCCTCGAGTGTCC-
1 AAAAATTACCATTTTACCCTCGAGTGTCCT
* * * * *
10142337 AAGAATT-CCGTTTTTGATCC-CGATTTTCCT
1 AAAAATTACC-ATTTT-ACCCTCGAGTGTCCT
* *
10142367 AAAAATTACCATTTTACCCTCGAATAT-CT
1 AAAAATTACCATTTTACCCTCGAGTGTCCT
** * * *
10142396 -AAAATGT--CATTTTAACCCTAAAATTTTCT
1 AAAAAT-TACCATTTT-ACCCTCGAGTGTCCT
* * *
10142425 CAAAAATTACCATTTTGCCCTTGAGAGT-CT
1 -AAAAATTACCATTTTACCCTCGAGTGTCCT
*
10142455 -AAAATTACCATTTTGCCCTCG
1 AAAAATTACCATTTTACCCTCG
10142476 GGTATCCAAA
Statistics
Matches: 197, Mismatches: 35, Indels: 49
0.70 0.12 0.17
Matches are distributed among these distances:
27 6 0.03
28 44 0.22
29 80 0.41
30 47 0.24
31 14 0.07
32 6 0.03
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.35
Consensus pattern (30 bp):
AAAAATTACCATTTTACCCTCGAGTGTCCT
Found at i:10144443 original size:55 final size:55
Alignment explanation
Indices: 10144340--10144453 Score: 149
Period size: 55 Copynumber: 2.1 Consensus size: 55
10144330 GTCATAAAAG
* * * * *
10144340 TATTTCAACATGACAATTGATTTAAATATATAAACAATCAATTCAAAAGAAGCAA
1 TATTCCAACATGAAAATTGATTTAAACATAAAAACAATCAATTAAAAAGAAGCAA
**
10144395 TATTCCAACATGAAAATTGATTTAAACA-AAAAACTAATTGATTAAAAAGAAGCAA
1 TATTCCAACATGAAAATTGATTTAAACATAAAAAC-AATCAATTAAAAAGAAGCAA
10144450 TATT
1 TATT
10144454 TCAGCATAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 5 0.10
55 46 0.90
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.29
Consensus pattern (55 bp):
TATTCCAACATGAAAATTGATTTAAACATAAAAACAATCAATTAAAAAGAAGCAA
Found at i:10145291 original size:20 final size:19
Alignment explanation
Indices: 10145253--10145295 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
10145243 AATATTTATT
*
10145253 TAATATTTTAATTAAAATAA
1 TAATATTTTAATAAAAAT-A
10145273 TAATATTTT-ATAAACAATA
1 TAATATTTTAATAAA-AATA
10145292 TAAT
1 TAAT
10145296 TATATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTTTAATAAAAATA
Found at i:10145786 original size:13 final size:14
Alignment explanation
Indices: 10145768--10145814 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
10145758 CATAAAAAAC
10145768 AAATAAATAA-AAT
1 AAATAAATAACAAT
*
10145781 ACATAAA-AACAAT
1 AAATAAATAACAAT
* *
10145794 AAATAAATAAGATT
1 AAATAAATAACAAT
10145808 AAATAAA
1 AAATAAA
10145815 AGCAAGAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 2 0.07
13 15 0.54
14 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAATAACAAT
Found at i:10145815 original size:26 final size:24
Alignment explanation
Indices: 10145759--10145869 Score: 64
Period size: 26 Copynumber: 4.3 Consensus size: 24
10145749 AATAAATGGC
*
10145759 ATAAAAAACAAATAAATAAAATAC
1 ATAAAAAACAAATAAATAAAATAA
* *
10145783 ATAAAAACAATAAATAAATAAGATTAA
1 AT-AAAA-AACAAATAAATAA-AATAA
* *
10145810 ATAAAAGCAA-GAATACAAAAAACATAA
1 ATAAAA--AACAAATA-AATAAA-ATAA
*
10145837 AAAATGAATAACAAATAAAT-AAATAA
1 ATAA--AA-AACAAATAAATAAAATAA
10145863 ATAAAAA
1 ATAAAAA
10145870 TTAACTACTA
Statistics
Matches: 67, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
23 1 0.01
24 4 0.06
25 4 0.06
26 28 0.42
27 20 0.30
28 4 0.06
29 6 0.09
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (24 bp):
ATAAAAAACAAATAAATAAAATAA
Found at i:10145874 original size:26 final size:27
Alignment explanation
Indices: 10145845--10145912 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
10145835 AAAAAATGAA
10145845 TAACAAATAAATAAATA-AATAAAAAT
1 TAACAAATAAATAAATATAATAAAAAT
* * *
10145871 TAACTACTAAATAAA-ATAATATAAAT
1 TAACAAATAAATAAATATAATAAAAAT
*
10145897 TATATAAA-AAATAAAT
1 TA-ACAAATAAATAAAT
10145913 GGGACCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
25 1 0.03
26 30 0.91
27 2 0.06
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (27 bp):
TAACAAATAAATAAATATAATAAAAAT
Found at i:10145930 original size:4 final size:4
Alignment explanation
Indices: 10145759--10145912 Score: 52
Period size: 4 Copynumber: 37.5 Consensus size: 4
10145749 AATAAATGGC
* * *
10145759 ATAA A-AA ACAA ATAA ATAAA ATAC ATAA AAACA ATAA ATAA ATAA GATTAA
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATA-A ATAA ATAA ATAA -A-TAA
* * * * *
10145810 ATAA A-AGCA AGAA TACAA AAAA CATAA A-AA ATGA AT-A ACAA ATAA
1 ATAA ATA--A ATAA -ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA
* * * *
10145855 ATAA ATAA ATAA A-AA TTAA CT-A CTAA ATAAA ATAA TATAA ATTAT ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA -ATAA A-TAA ATAA
10145904 A-AA ATAA AT
1 ATAA ATAA AT
10145913 GGGACCAAAT
Statistics
Matches: 116, Mismatches: 16, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
3 17 0.15
4 67 0.58
5 28 0.24
6 4 0.03
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:10146049 original size:5 final size:5
Alignment explanation
Indices: 10146033--10146077 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
10146023 TACAAATTAG
* *
10146033 AAATA GAAATA AAATA AAATA AAACTA AATTC AAATA AAATA AAA
1 AAATA -AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA AAA
10146078 ATTATAAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:10146061 original size:16 final size:15
Alignment explanation
Indices: 10146033--10146077 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
10146023 TACAAATTAG
10146033 AAATAGAAATAAAATA
1 AAATA-AAATAAAATA
* *
10146049 AAATAAAACTAAATTC
1 AAATAAAA-TAAAATA
10146065 AAATAAAATAAAA
1 AAATAAAATAAAA
10146078 ATTATAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAAAATAAAATA
Found at i:10152243 original size:58 final size:58
Alignment explanation
Indices: 10152165--10152297 Score: 203
Period size: 58 Copynumber: 2.3 Consensus size: 58
10152155 ACTCATCAAC
* * * * *
10152165 AAACTAAACCCAAGTATTTTTAAACCCACATATAATTTTATTCTTCAAAACCACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACTCAT
*
10152223 AAACTAAATCCAAATATTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACTCAT
*
10152281 AAATTAAACCCAAATAT
1 AAACTAAACCCAAATAT
10152298 AATTTTATTC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 67 1.00
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.32
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACTCAT
Found at i:10152301 original size:42 final size:42
Alignment explanation
Indices: 10152242--10152325 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
10152232 CCAAATATTT
*
10152242 TTAAACCCAAATATAATTTCATTCTTAAAAAACACTCATAAA
1 TTAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAA
* *
10152284 TTAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAA
1 TTAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAA
10152326 CAACTCCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (42 bp):
TTAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAA
Found at i:10155098 original size:59 final size:58
Alignment explanation
Indices: 10155044--10155256 Score: 211
Period size: 59 Copynumber: 3.6 Consensus size: 58
10155034 GAACTTCTCC
10155044 AAATCACATTTTTGACCCTAAAA-TTCCAAAAATTACATTTTTGACCCCAAAACTTCCAA
1 AAATC-CATTTTTGACCCTAAAACTTCCAAAAATTACATTTTT-ACCCCAAAACTTCCAA
* * * ***
10155103 AAATTCCATTTTTGACCCCAAAACTTCCAAAATTTTCATTTTTACCCTTGAACTTCCAAA
1 AAA-TCCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTTACCCCAAAACTTCC-AA
* * *
10155163 AAATCCATTTTTGACCCTAAAACTTTCAAAAATTACCA-TTTTACCCTC--GAGTGTCCAA
1 AAATCCATTTTTGACCCTAAAACTTCCAAAAATTA-CATTTTTACCC-CAAAACT-TCCAA
* * *
10155221 AAACTCCATTTTTTACCC-GAAACTTTCAAAAATTAC
1 AAA-TCCATTTTTGACCCTAAAACTTCCAAAAATTAC
10155257 CAAATTACCC
Statistics
Matches: 132, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
57 1 0.01
58 23 0.17
59 82 0.62
60 26 0.20
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (58 bp):
AAATCCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAA
Found at i:10155208 original size:29 final size:30
Alignment explanation
Indices: 10155050--10155254 Score: 206
Period size: 30 Copynumber: 7.0 Consensus size: 30
10155040 CTCCAAATCA
*
10155050 CATTTTTGACCCTAAAA-TTCCAAAAATTA
1 CATTTTTGACCCTAAAACTTCCAAAAATTC
*
10155079 CATTTTTGACCCCAAAACTTCCAAAAATTC
1 CATTTTTGACCCTAAAACTTCCAAAAATTC
* * *
10155109 CATTTTTGACCCCAAAACTTCCAAAATTTT
1 CATTTTTGACCCTAAAACTTCCAAAAATTC
** *
10155139 CATTTTT-ACCCTTGAACTTCCAAAAAATC
1 CATTTTTGACCCTAAAACTTCCAAAAATTC
*
10155168 CATTTTTGACCCTAAAACTTTCAAAAATTAC
1 CATTTTTGACCCTAAAACTTCCAAAAATT-C
** * *
10155199 CA-TTTT-ACCCT-CGAGTGTCCAAAAACTC
1 CATTTTTGACCCTAAAACT-TCCAAAAATTC
* * *
10155227 CATTTTTTACCC-GAAACTTTCAAAAATT
1 CATTTTTGACCCTAAAACTTCCAAAAATT
10155255 ACCAAATTAC
Statistics
Matches: 145, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
28 5 0.03
29 64 0.44
30 73 0.50
31 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (30 bp):
CATTTTTGACCCTAAAACTTCCAAAAATTC
Found at i:10155252 original size:58 final size:58
Alignment explanation
Indices: 10155098--10155293 Score: 234
Period size: 59 Copynumber: 3.3 Consensus size: 58
10155088 CCCCAAAACT
* ** * *
10155098 TCCAAAAATTCCATTTTTGACCCCAAAAC-TTCCAAAATTTTCATTTTTACCCTTGAACT-
1 TCCAAAAATTCCATTTTTGA-CCCAAAACTTTCAAAAATTACCA-TTTTACCCTCG-AGTG
*
10155157 TCCAAAAAATCCATTTTTGACCCTAAAACTTTCAAAAATTACCATTTTACCCTCGAGTG
1 TCCAAAAATTCCATTTTTGACCC-AAAACTTTCAAAAATTACCATTTTACCCTCGAGTG
* * * ** *
10155216 TCCAAAAACTCCATTTTTTACCCGAAACTTTCAAAAATTACCAAATTACCCTCGGGTG
1 TCCAAAAATTCCATTTTTGACCCAAAACTTTCAAAAATTACCATTTTACCCTCGAGTG
10155274 TCCAAAAATTCCATTTTTGA
1 TCCAAAAATTCCATTTTTGA
10155294 TCCTGATTTT
Statistics
Matches: 120, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
58 54 0.45
59 55 0.46
60 11 0.09
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTGACCCAAAACTTTCAAAAATTACCATTTTACCCTCGAGTG
Found at i:10155400 original size:28 final size:28
Alignment explanation
Indices: 10155364--10155425 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
10155354 CCAAATTTTC
*
10155364 CCAAAATTACCATTTTGTCCTTGAG-AGT
1 CCAAAATTACCATTTTGCCCTTGAGTA-T
10155392 CCAAAATTACCATTTTGCCCTTGAGTAT
1 CCAAAATTACCATTTTGCCCTTGAGTAT
10155420 CCAAAA
1 CCAAAA
10155426 AGTTTCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCTTGAGTAT
Found at i:10160092 original size:7 final size:7
Alignment explanation
Indices: 10160075--10160152 Score: 52
Period size: 7 Copynumber: 10.3 Consensus size: 7
10160065 TTCAATGAAT
10160075 AAAAGAA
1 AAAAGAA
10160082 AAGAA-AA
1 AA-AAGAA
10160089 AAGAAGAA
1 AA-AAGAA
*
10160097 GAAAGAGA
1 AAAAGA-A
10160105 AAAAGAAA
1 AAAAG-AA
10160113 AATATAGAA
1 AA-A-AGAA
10160122 AACAA-AA
1 AA-AAGAA
*
10160129 AAGAGAAA
1 AAAAG-AA
10160137 AAAAGAA
1 AAAAGAA
10160144 AAAAGAA
1 AAAAGAA
10160151 AA
1 AA
10160153 GGAGAGGTCG
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
6 1 0.02
7 28 0.48
8 20 0.34
9 7 0.12
10 2 0.03
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (7 bp):
AAAAGAA
Found at i:10160123 original size:16 final size:16
Alignment explanation
Indices: 10160075--10160146 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
10160065 TTCAATGAAT
*
10160075 AAAAG-AAAAGA-AAA
1 AAAAGAAAAAGAGAGA
*
10160089 AAGAAGAAGAA-AGAGA
1 AA-AAGAAAAAGAGAGA
* *
10160105 AAAAGAAAAATATAGA
1 AAAAGAAAAAGAGAGA
*
10160121 AAACA-AAAAAGAGAAA
1 AAA-AGAAAAAGAGAGA
10160137 AAAAGAAAAA
1 AAAAGAAAAA
10160147 AGAAAAGGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
14 2 0.04
15 12 0.27
16 30 0.67
17 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAGAGAGA
Found at i:10161207 original size:50 final size:50
Alignment explanation
Indices: 10161151--10161315 Score: 154
Period size: 50 Copynumber: 3.3 Consensus size: 50
10161141 AAAGACAAAA
* ** *
10161151 GGGAAAGGTCTAAGTCATAACGGCGGATCGTGTACCTCAAAAAACACGAC
1 GGGAAAGATCTAAGTCGCAACGGCGGATCATGTACCTCAAAAAACACGAC
* * * * * * *
10161201 GGGAAAGATCTAAGACCGCAACAGCGGATCCA-ATACCACAAAAAGATA-AAA
1 GGGAAAGATCTAAG-TCGCAACGGCGGAT-CATGTACCTCAAAAA-ACACGAC
* * *
10161252 GGGAAAGGTCTAAGTCGCAACGGCGGACCATGTACCTCAAAAGACACGAC
1 GGGAAAGATCTAAGTCGCAACGGCGGATCATGTACCTCAAAAAACACGAC
*
10161302 GGAAAAGATCTAAG
1 GGGAAAGATCTAAG
10161316 ACCGCAATAG
Statistics
Matches: 87, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
49 4 0.05
50 46 0.53
51 34 0.39
52 3 0.03
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.13
Consensus pattern (50 bp):
GGGAAAGATCTAAGTCGCAACGGCGGATCATGTACCTCAAAAAACACGAC
Found at i:10161243 original size:51 final size:51
Alignment explanation
Indices: 10161173--10161338 Score: 176
Period size: 51 Copynumber: 3.3 Consensus size: 51
10161163 AGTCATAACG
**
10161173 GCGGATCGTGTACCTCAAAAAACACGACGGGAAAGATCTAAGACCGCAACA
1 GCGGATCCAGTACCTCAAAAAACACGACGGGAAAGATCTAAGACCGCAACA
* * * * * * * *
10161224 GCGGATCCAATACCACAAAAAGATA-AAAGGGAAAGGTCTAAG-TCGCAACG
1 GCGGATCCAGTACCTCAAAAA-ACACGACGGGAAAGATCTAAGACCGCAACA
* * *
10161274 GCGGA-CCATGTACCTCAAAAGACACGACGGAAAAGATCTAAGACCGCAATA
1 GCGGATCCA-GTACCTCAAAAAACACGACGGGAAAGATCTAAGACCGCAACA
10161325 GCGGATCCAGTACC
1 GCGGATCCAGTACC
10161339 GAAAAAAGAC
Statistics
Matches: 89, Mismatches: 21, Indels: 10
0.74 0.17 0.08
Matches are distributed among these distances:
49 5 0.06
50 33 0.37
51 46 0.52
52 5 0.06
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.12
Consensus pattern (51 bp):
GCGGATCCAGTACCTCAAAAAACACGACGGGAAAGATCTAAGACCGCAACA
Found at i:10161311 original size:101 final size:101
Alignment explanation
Indices: 10161136--10161363 Score: 350
Period size: 101 Copynumber: 2.3 Consensus size: 101
10161126 CTCAGTACCA
* * *
10161136 CACAAAAAGACAAAAGGGAAAGGTCTAAGTCATAACGGCGGATCGTGTACCTCAAAAAACACGAC
1 CACAAAAAGACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACCTCAAAAAACACGAC
*
10161201 GGGAAAGATCTAAGACCGCAACAGCGGATCCAATAC
66 GGAAAAGATCTAAGACCGCAACAGCGGATCCAATAC
* * *
10161237 CACAAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCATGTACCTCAAAAGACACGAC
1 CACAAAAAGACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACCTCAAAAAACACGAC
* *
10161302 GGAAAAGATCTAAGACCGCAATAGCGGATCCAGTAC
66 GGAAAAGATCTAAGACCGCAACAGCGGATCCAATAC
*
10161338 CGA-AAAAAGACAAAAGGGAAAAGTCT
1 C-ACAAAAAGACAAAAGGGAAAGGTCT
10161364 TTATCTCTCT
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
101 114 0.99
102 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (101 bp):
CACAAAAAGACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACCTCAAAAAACACGAC
GGAAAAGATCTAAGACCGCAACAGCGGATCCAATAC
Found at i:10161628 original size:77 final size:76
Alignment explanation
Indices: 10161488--10161632 Score: 184
Period size: 77 Copynumber: 1.9 Consensus size: 76
10161478 GTCATCAACC
* * * * *
10161488 AATCTCTTACCCCGAGCCTGGGTAAATTGAAGCCATTTGATCTTTTACACCGAGCTTGAGGCAGA
1 AATCTCTTACCCCAAGCCTGCGCAAATTGAAGCCACTTAATCTTTTACACCGAGCTTGAGGCAGA
10161553 TCACCACACCA
66 TCACCACACCA
* * * *
10161564 AATCTCTTACCCCAAGCCTAGCGCAAATTGTAGCTACTTAATCTTTTAC-CCTGATCTTGGGGCA
1 AATCTCTTACCCCAAGCCT-GCGCAAATTGAAGCCACTTAATCTTTTACACC-GAGCTTGAGGCA
10161628 GATCA
64 GATCA
10161633 TTGTCAACCA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
76 20 0.34
77 38 0.66
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (76 bp):
AATCTCTTACCCCAAGCCTGCGCAAATTGAAGCCACTTAATCTTTTACACCGAGCTTGAGGCAGA
TCACCACACCA
Found at i:10162116 original size:207 final size:207
Alignment explanation
Indices: 10161761--10162556 Score: 1173
Period size: 207 Copynumber: 3.9 Consensus size: 207
10161751 AATCTTCAAA
* * * * *
10161761 CCCCAGCTTCCTGATGAGATACTTAAAAGCAGGTAGAAGCAATAAAGTGGTTAGCTTCTTGATGA
1 CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
* * *
10161826 GATACTGAGAAGTGGATCGAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTG
66 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCG
* *
10161891 ATGC-AGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAGCCCACGCTCGATATGAG
131 ATGCGA-TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAG
10161955 CAAGTCTTTGGAC
195 CAAGTCTTTGGAC
*
10161968 CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGA
1 CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
* * * * *
10162033 CATACTAAGAAGTGGACCAAATTTGTTTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCG
66 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCG
* **
10162098 ATACGATCATCTTCCTGATGAGATACTGAGAAGAAGAATAAATCAAACCCACGCTCGATATGAGC
131 ATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGC
*
10162163 AAGTCTTCGGAC
196 AAGTCTTTGGAC
*
10162175 CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGA
1 CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
*
10162240 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTG
66 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCG
* * * *
10162305 AGGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
131 ATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGC
* * *
10162370 AAAT-TTTTGAA
196 AAGTCTTTGGAC
* * * * * *
10162381 CCTCAGCTTCCTGATGAGATATTGAGAAGCAGATCAAAGCAATAAAATGGTTAGCTTCCTTATAA
1 CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
* * *
10162446 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTGGAACAAACG
66 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCG
* * * * * *
10162511 ACGCGGTCATCTTTCTGATTAGACACTGAGAAGAAGACCAAGTCAA
131 ATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
10162557 TGAAACCAGA
Statistics
Matches: 534, Mismatches: 54, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
206 163 0.31
207 370 0.69
208 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (207 bp):
CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCG
ATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGC
AAGTCTTTGGAC
Found at i:10162937 original size:6 final size:6
Alignment explanation
Indices: 10162915--10162996 Score: 51
Period size: 6 Copynumber: 13.5 Consensus size: 6
10162905 GTTCAAGTTG
* * * * * * *
10162915 ATTTAA ATTTAT TTTTAA ATTTAA ATTTATC TTGTTAA GTTTAA ATGT-G
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTA-A AT-TTAA ATTTAA ATTTAA
*
10162964 CTTTAA ATTTAA ATTTAA A-TTAGA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTA-A ATTTAA ATT
10162997 GATATTAAAT
Statistics
Matches: 56, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
5 5 0.09
6 43 0.77
7 5 0.09
8 3 0.05
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:10163003 original size:18 final size:17
Alignment explanation
Indices: 10162966--10163007 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
10162956 TAAATGTGCT
*
10162966 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTGAAA
*
10162983 TTAGAATTTAAATTGATA
1 TTA-AATTTAAATTGAAA
10163001 TTAAATT
1 TTAAATT
10163008 AAAAAACCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (17 bp):
TTAAATTTAAATTGAAA
Found at i:10165094 original size:30 final size:30
Alignment explanation
Indices: 10165051--10165312 Score: 206
Period size: 30 Copynumber: 8.9 Consensus size: 30
10165041 TTGACCCCCG
* *
10165051 AACTTCTCTAAAATTACATTTTTAACCAC-AA
1 AACTTC-CAAAAATTACATTTTT-ACCCCTAA
**
10165082 AACTTCCAAAAATTACATTTTTA-CCCTTG
1 AACTTCCAAAAATTACATTTTTACCCCTAA
* *
10165111 AACTTCCAAAAATTCCAATTTTACCCCTAA
1 AACTTCCAAAAATTACATTTTTACCCCTAA
*
10165141 AACTTCC---AATTACATTTTCGACCCC-AA
1 AACTTCCAAAAATTACATTTT-TACCCCTAA
* *
10165168 AACTTCCAAAAATTATATTTTTA-CCCTCA
1 AACTTCCAAAAATTACATTTTTACCCCTAA
* *
10165197 AACTTCAAAAAATT-CTAATTTTT-CCCTCAAA
1 AACTTCCAAAAATTAC--ATTTTTACCC-CTAA
* * * **
10165228 AATTTCCAAAAATTCCATTTTAACCCC-CG
1 AACTTCCAAAAATTACATTTTTACCCCTAA
*
10165257 AACTTCCAAAAATTCCATTTTTGA-CCCTAA
1 AACTTCCAAAAATTACATTTTT-ACCCCTAA
*
10165287 AACTTTCAAAAATTACCA-TTTTACCC
1 AACTTCCAAAAATTA-CATTTTTACCC
10165313 TCGAGTGTCC
Statistics
Matches: 185, Mismatches: 29, Indels: 35
0.74 0.12 0.14
Matches are distributed among these distances:
27 18 0.10
28 10 0.05
29 61 0.33
30 70 0.38
31 25 0.14
32 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.34
Consensus pattern (30 bp):
AACTTCCAAAAATTACATTTTTACCCCTAA
Found at i:10165240 original size:31 final size:30
Alignment explanation
Indices: 10165020--10165314 Score: 179
Period size: 30 Copynumber: 10.0 Consensus size: 30
10165010 GTAAGTCCTT
* * * *
10165020 AAACTATCCAAAAATTGTAATTTGACCC-CC
1 AAACT-TCCAAAAATTCTATTTTTACCCTCA
* * * *
10165050 GAACTTCTCTAAAATTAC-ATTTTTAACCACA
1 AAACTTC-CAAAAATT-CTATTTTTACCCTCA
*
10165081 AAACTTCCAAAAATTAC-ATTTTTACCCT-T
1 AAACTTCCAAAAATT-CTATTTTTACCCTCA
* * *
10165110 GAACTTCCAAAAATTCCAATTTTACCC-CTA
1 AAACTTCCAAAAATTCTATTTTTACCCTC-A
*
10165140 AAACTTCC---AATTAC-ATTTTCGACCC-CA
1 AAACTTCCAAAAATT-CTATTTT-TACCCTCA
*
10165167 AAACTTCCAAAAATTATATTTTTACCCTC-
1 AAACTTCCAAAAATTCTATTTTTACCCTCA
*
10165196 AAACTTCAAAAAATTCTAATTTTT-CCCTCAA
1 AAACTTCCAAAAATTCT-ATTTTTACCCTC-A
* * * *
10165227 AAATTTCCAAAAATTCCATTTTAACCC-CC
1 AAACTTCCAAAAATTCTATTTTTACCCTCA
* *
10165256 GAACTTCCAAAAATTCCATTTTTGACCCT-A
1 AAACTTCCAAAAATTCTATTTTT-ACCCTCA
* *
10165286 AAACTTTCAAAAATTACCA-TTTTACCCTC
1 AAACTTCCAAAAATT-CTATTTTTACCCTC
10165315 GAGTGTCCAA
Statistics
Matches: 211, Mismatches: 33, Indels: 42
0.74 0.12 0.15
Matches are distributed among these distances:
27 17 0.08
28 7 0.03
29 74 0.35
30 86 0.41
31 27 0.13
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTCTATTTTTACCCTCA
Found at i:10165313 original size:29 final size:28
Alignment explanation
Indices: 10165080--10165358 Score: 190
Period size: 29 Copynumber: 9.6 Consensus size: 28
10165070 TTTTAACCAC
*
10165080 AAAACTTCCAAAAATTACATTTTTACCCT
1 AAAACTTCCAAAAATTCCA-TTTTACCCT
**
10165109 TGAACTTCCAAAAATTCCAATTTTACCCCT
1 AAAACTTCCAAAAATTCC-ATTTTA-CCCT
* *
10165139 AAAACTTCC---AATTACATTTTCGACCCC
1 AAAACTTCCAAAAATTCCATTTT--ACCCT
**
10165166 AAAACTTCCAAAAATTATATTTTTACCCT
1 AAAACTTCCAAAAATTCCA-TTTTACCCT
* * * *
10165195 CAAACTTCAAAAAATTCTAATTTTTCCCT
1 AAAACTTCCAAAAATTC-CATTTTACCCT
* *
10165224 CAAAAATTTCCAAAAATTCCATTTTAACCCC
1 --AAAACTTCCAAAAATTCCATTTT-ACCCT
**
10165255 CGAACTTCCAAAAATTCCATTTTTGACCCT
1 AAAACTTCCAAAAATTCCA-TTTT-ACCCT
*
10165285 AAAACTTTCAAAAATTACCATTTTACCCT
1 AAAACTTCCAAAAATT-CCATTTTACCCT
** * *
10165314 -CGAGTGTCCAAAAACTCCATTTTTGACCC-
1 AAAACT-TCCAAAAATTCCA-TTTT-ACCCT
*
10165343 AAAACTTTCAAAAATT
1 AAAACTTCCAAAAATT
10165359 ACTAAATTAC
Statistics
Matches: 194, Mismatches: 38, Indels: 36
0.72 0.14 0.13
Matches are distributed among these distances:
26 5 0.03
27 17 0.09
28 6 0.03
29 87 0.45
30 55 0.28
31 24 0.12
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAACTTCCAAAAATTCCATTTTACCCT
Found at i:10165324 original size:59 final size:58
Alignment explanation
Indices: 10165148--10165397 Score: 213
Period size: 59 Copynumber: 4.2 Consensus size: 58
10165138 TAAAACTTCC
* * * * * *
10165148 AATTACATTTTCGACCCCAAAACTTCCAAAAATTA-TATTTTTACCCTCAAACTTCAAAA
1 AATTCCATTTTTGACCCTAAAACTTTCAAAAATTACCA-TTTTACCCTC-GACTTCAAAA
* * * *
10165207 AATTCTAATTTTT--CCCTCAAAAATTTCCAAAAATT-CCATTTTAACCCCCGAACTTCCAAA
1 AATTC-CATTTTTGACCCT-AAAACTTT-CAAAAATTACCATTTT-ACCCTCG-ACTTCAAAA
* *
10165267 AATTCCATTTTTGACCCTAAAACTTTCAAAAATTACCATTTTACCCTCGAGTGTCCAAA
1 AATTCCATTTTTGACCCTAAAACTTTCAAAAATTACCATTTTACCCTCGACT-TCAAAA
* * ** **
10165326 AACTCCATTTTTGACCC-AAAACTTTCAAAAATTACTAAATTACCCTCGGGTGTCAAAA
1 AATTCCATTTTTGACCCTAAAACTTTCAAAAATTACCATTTTACCCTCGACT-TCAAAA
*
10165384 AATTCCGTTTTTGA
1 AATTCCATTTTTGA
10165398 TCCTGATTTT
Statistics
Matches: 159, Mismatches: 22, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
58 53 0.33
59 56 0.35
60 46 0.29
61 4 0.03
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (58 bp):
AATTCCATTTTTGACCCTAAAACTTTCAAAAATTACCATTTTACCCTCGACTTCAAAA
Found at i:10165369 original size:58 final size:59
Alignment explanation
Indices: 10165261--10165397 Score: 204
Period size: 58 Copynumber: 2.3 Consensus size: 59
10165251 CCCCCGAACT
**
10165261 TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACCATTTTACCCTCGAGTG
1 TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACCAAATTACCCTCGAGTG
* * *
10165320 TCCAAAAACTCCATTTTTGACCC-AAAACTTTCAAAAATTACTAAATTACCCTCGGGTG
1 TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACCAAATTACCCTCGAGTG
* *
10165378 TCAAAAAATTCCGTTTTTGA
1 TCCAAAAATTCCATTTTTGA
10165398 TCCTGATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 48 0.69
59 22 0.31
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACCAAATTACCCTCGAGTG
Found at i:10165604 original size:21 final size:20
Alignment explanation
Indices: 10165575--10165624 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
10165565 TTCCTCATCA
10165575 ATATT-TGCATTTAT-TCTTC
1 ATATTCTGCATTTATAT-TTC
*
10165594 ATTATTCTGCACTTATATTTC
1 A-TATTCTGCATTTATATTTC
10165615 ATATTC-GCAT
1 ATATTCTGCAT
10165625 ACCATTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 4 0.15
20 9 0.35
21 12 0.46
22 1 0.04
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (20 bp):
ATATTCTGCATTTATATTTC
Found at i:10167216 original size:4 final size:4
Alignment explanation
Indices: 10167202--10167309 Score: 64
Period size: 4 Copynumber: 26.8 Consensus size: 4
10167192 TATAAATGGC
* **
10167202 ATAA A-AA ATAA ATAAA ATAC ATAA A-AA ATAA ATAA GATTAA ATAA AGGCA
1 ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA -A-TAA ATAA A-TAA
* * *
10167252 AGAA TATAA ATAA CATAA A-AA ATGA AT-A ACAA ATAA ATAA ATAA ATAA
1 ATAA -ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
*
10167300 A-AA TTAA ATA
1 ATAA ATAA ATA
10167310 CTAAGTAAGA
Statistics
Matches: 82, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
3 13 0.16
4 51 0.62
5 15 0.18
6 3 0.04
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:10167218 original size:11 final size:11
Alignment explanation
Indices: 10167202--10167300 Score: 55
Period size: 11 Copynumber: 9.1 Consensus size: 11
10167192 TATAAATGGC
10167202 ATAAAAAATAA
1 ATAAAAAATAA
*
10167213 AT--AAAATAC
1 ATAAAAAATAA
10167222 ATAAAAAATAA
1 ATAAAAAATAA
* *
10167233 AT-AAGATTAA
1 ATAAAAAATAA
* *
10167243 ATAAAGGCAA-GA
1 ATAAA--AAATAA
*
10167255 AT-ATAAATAA
1 ATAAAAAATAA
*
10167265 CATAAAAAATGA
1 -ATAAAAAATAA
*
10167277 ATAACAAATAA
1 ATAAAAAATAA
10167288 ATAAATAAATAA
1 ATAAA-AAATAA
10167300 A
1 A
10167301 AATTAAATAC
Statistics
Matches: 64, Mismatches: 15, Indels: 17
0.67 0.16 0.18
Matches are distributed among these distances:
9 10 0.16
10 9 0.14
11 28 0.44
12 16 0.25
13 1 0.02
ACGTcount: A:0.71, C:0.04, G:0.05, T:0.20
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:10167252 original size:64 final size:64
Alignment explanation
Indices: 10167157--10167309 Score: 179
Period size: 64 Copynumber: 2.4 Consensus size: 64
10167147 AAAATATAAA
**
10167157 AAATGAAA-AAATAAAAATTGAACA-AAAGGCAAAAATATAAATGGCATAAAAAATAAATAAAAT
1 AAAT-AAATAAATAAAAATT-AA-ATAAAGGCAAAAATATAAATAACATAAAAAATAAATAAAA-
10167220 ACAT
62 A-AT
* * * *
10167224 AAA-AAATAAAT-AAGATTAAATAAAGGCAAGAATATAAATAACATAAAAAATGAATAACAAAT
1 AAATAAATAAATAAAAATTAAATAAAGGCAAAAATATAAATAACATAAAAAATAAATAAAAAAT
10167286 AAATAAATAAATAAAAATTAAATA
1 AAATAAATAAATAAAAATTAAATA
10167310 CTAAGTAAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
62 5 0.07
63 10 0.13
64 45 0.60
65 8 0.11
66 4 0.05
67 3 0.04
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.20
Consensus pattern (64 bp):
AAATAAATAAATAAAAATTAAATAAAGGCAAAAATATAAATAACATAAAAAATAAATAAAAAAT
Found at i:10167298 original size:19 final size:19
Alignment explanation
Indices: 10167257--10167309 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
10167247 AGGCAAGAAT
10167257 ATAAATAAC--ATAAA-AA
1 ATAAATAACAAATAAATAA
*
10167273 ATGAATAACAAATAAATAA
1 ATAAATAACAAATAAATAA
10167292 ATAAATAA-AAATTAAATA
1 ATAAATAACAAA-TAAATA
10167310 CTAAGTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 8 0.26
18 8 0.26
19 15 0.48
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (19 bp):
ATAAATAACAAATAAATAA
Found at i:10169271 original size:7 final size:6
Alignment explanation
Indices: 10169241--10169270 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
10169231 ATGGAAACAA
10169241 AAATGG AAATGG AAATGG AAATGAG AAATG
1 AAATGG AAATGG AAATGG AAATG-G AAATG
10169271 ATTTATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:10169924 original size:5 final size:5
Alignment explanation
Indices: 10169914--10169938 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10169904 ATCTATAAAT
10169914 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
10169939 CCTAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:10170904 original size:6 final size:6
Alignment explanation
Indices: 10170882--10170942 Score: 74
Period size: 6 Copynumber: 10.5 Consensus size: 6
10170872 GTTTAACTTG
* *
10170882 ATTTAA ATTT-- ATCTTAA ATTTAA ATTT-G CTTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
10170928 ATTTAA ATTTAA ATT
1 ATTTAA ATTTAA ATT
10170943 GATATTAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
4 2 0.04
5 5 0.11
6 38 0.81
7 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:10170904 original size:17 final size:17
Alignment explanation
Indices: 10170882--10170953 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
10170872 GTTTAACTTG
10170882 ATTTAAATTTATCTTAA
1 ATTTAAATTTATCTTAA
*
10170899 ATTTAAATTT-GCTTTAA
1 ATTTAAATTTATC-TTAA
10170916 ATTTAAATTTAAAT-TTAA
1 ATTTAAATTT--ATCTTAA
* *
10170934 ATTTAAATTGATATTAA
1 ATTTAAATTTATCTTAA
10170951 ATT
1 ATT
10170954 AAAAAACCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 3 0.06
17 31 0.66
18 13 0.28
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTATCTTAA
Found at i:10171373 original size:58 final size:58
Alignment explanation
Indices: 10171307--10171439 Score: 221
Period size: 58 Copynumber: 2.3 Consensus size: 58
10171297 ACTCATCAAC
* * *
10171307 AAACTAAACCCAAGTATTTTTAAACCCACATATAATTTTATTCTTCAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAAAACACTCAT
*
10171365 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAAAACACTTAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAAAACACTCAT
*
10171423 AAATTAAACCCAAATAT
1 AAACTAAACCCAAATAT
10171440 AAATTTATTC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 70 1.00
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.32
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAAAACACTCAT
Found at i:10171460 original size:42 final size:42
Alignment explanation
Indices: 10171384--10171467 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
10171374 CCAAATATTT
* *
10171384 TTAAACCCAAATATAATTTCATTCTTCAAAAACACTTATAAA
1 TTAAACCCAAATATAATTTCATTCCTCAAAAACACTCATAAA
10171426 TTAAACCCAAATATAAATTT-ATTCCT-AAATAACACTCATAAA
1 TTAAACCCAAATAT-AATTTCATTCCTCAAA-AACACTCATAAA
10171468 CAACTCCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 3 0.08
42 30 0.79
43 5 0.13
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (42 bp):
TTAAACCCAAATATAATTTCATTCCTCAAAAACACTCATAAA
Found at i:10174181 original size:29 final size:30
Alignment explanation
Indices: 10174148--10174245 Score: 119
Period size: 30 Copynumber: 3.3 Consensus size: 30
10174138 CTAAACTATC
*
10174148 CAAAAATTACA-TTTTAACCCCAAAACTTT
1 CAAAAATTACATTTTTGACCCCAAAACTTT
* * *
10174177 CAAAAATTCCATTTTTGACCCTAAAACTTC
1 CAAAAATTACATTTTTGACCCCAAAACTTT
* *
10174207 CAAAAATTCCATTTTTGA-CCCGAAACTTT
1 CAAAAATTACATTTTTGACCCCAAAACTTT
*
10174236 CACAAATTAC
1 CAAAAATTAC
10174246 CAAATTACCC
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 26 0.44
30 33 0.56
ACGTcount: A:0.40, C:0.26, G:0.03, T:0.32
Consensus pattern (30 bp):
CAAAAATTACATTTTTGACCCCAAAACTTT
Found at i:10174222 original size:30 final size:30
Alignment explanation
Indices: 10174136--10174227 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
10174126 CCTTGTAAGT
* *
10174136 CCCT-AAACTATCCAAAAATTACA-TTTTAA
1 CCCTAAAACT-TCCAAAAATTCCATTTTTGA
* *
10174165 CCCCAAAACTTTCAAAAATTCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTGA
10174195 CCCTAAAACTTCCAAAAATTCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTGA
10174225 CCC
1 CCC
10174228 GAAACTTTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 14 0.25
30 41 0.75
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (30 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTGA
Found at i:10174411 original size:28 final size:28
Alignment explanation
Indices: 10174353--10174414 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
10174343 CCAAATTTTC
**
10174353 CCAAAATTACCATTTTGTCCTCGAGAGT
1 CCAAAATTACCATTTTACCCTCGAGAGT
*
10174381 CCAAAATTACCATTTTACCCTTGAGTA-T
1 CCAAAATTACCATTTTACCCTCGAG-AGT
10174409 CCAAAA
1 CCAAAA
10174415 AGTCTCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.31
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCTCGAGAGT
Found at i:10179493 original size:7 final size:7
Alignment explanation
Indices: 10179476--10179554 Score: 52
Period size: 7 Copynumber: 10.3 Consensus size: 7
10179466 TTCAATGAAT
10179476 AAAAGAA
1 AAAAGAA
10179483 AAGAA-AA
1 AA-AAGAA
10179490 AAGAAGAA
1 AA-AAGAA
*
10179498 GAAAGAGA
1 AAAAGA-A
10179506 AAAAGAA
1 AAAAGAA
*
10179513 AAAATATA
1 AAAAGA-A
*
10179521 GAAAATAAA
1 -AAAA-GAA
10179530 AAAGAGAAA
1 AAA-AG-AA
10179539 AAAAGAA
1 AAAAGAA
10179546 AAAAGAA
1 AAAAGAA
10179553 AA
1 AA
10179555 GGAGAGGTCG
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
7 30 0.51
8 17 0.29
9 11 0.19
10 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:10179511 original size:15 final size:15
Alignment explanation
Indices: 10179476--10179551 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 15
10179466 TTCAATGAAT
10179476 AAAAGAAAAGAA-A-A
1 AAAAGAAAA-AAGAGA
*
10179490 AAGAAGAAGAAAGAGA
1 AA-AAGAAAAAAGAGA
* *
10179506 AAAAGAAAAAATATA
1 AAAAGAAAAAAGAGA
*
10179521 GAAAATAAAAAAGAGAAA
1 -AAAAGAAAAAAGAG--A
10179539 AAAAGAAAAAAGA
1 AAAAGAAAAAAGA
10179552 AAAGGAGAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
14 4 0.08
15 17 0.35
16 14 0.29
17 12 0.25
18 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (15 bp):
AAAAGAAAAAAGAGA
Found at i:10179523 original size:17 final size:17
Alignment explanation
Indices: 10179487--10179551 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
10179477 AAAGAAAAGA
10179487 AAAAAGAAGAAGAA-AGAG
1 AAAAAGAA-AA-AAGAGAG
* *
10179505 AAAAAGAAAAAATATAG
1 AAAAAGAAAAAAGAGAG
* *
10179522 -AAAATAAAAAAGAGAA
1 AAAAAGAAAAAAGAGAG
10179538 AAAAAGAAAAAAGA
1 AAAAAGAAAAAAGA
10179552 AAAGGAGAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 14 0.36
17 17 0.44
18 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAAAAGAGAG
Found at i:10179559 original size:23 final size:22
Alignment explanation
Indices: 10179476--10179555 Score: 83
Period size: 25 Copynumber: 3.5 Consensus size: 22
10179466 TTCAATGAAT
10179476 AAAAGAAAAGAAAAAAGAAGAA
1 AAAAGAAAAGAAAAAAGAAGAA
*
10179498 GAAAGAGAAAAAGAAAAAATATAGAA
1 -AAA-AG-AAAAGAAAAAAGA-AGAA
10179524 AATAA-AAAAGAGAAAAA-AAGAA
1 AA-AAGAAAAGA-AAAAAGAAGAA
10179546 AAAAGAAAAG
1 AAAAGAAAAG
10179556 GAGAGGTCGC
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
21 2 0.04
22 11 0.22
23 10 0.20
24 7 0.14
25 15 0.30
26 5 0.10
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (22 bp):
AAAAGAAAAGAAAAAAGAAGAA
Found at i:10182467 original size:60 final size:61
Alignment explanation
Indices: 10182374--10182533 Score: 252
Period size: 60 Copynumber: 2.7 Consensus size: 61
10182364 ATAAATATGG
** * *
10182374 GTACCAAATTGAATCTAAAAAAAGTTTAGGTACCAAATTAGG-AAAAAATGCCAAGTTCAA
1 GTACCAAATTGGGTCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGCCAAATTCAA
* *
10182434 GTACCAAATTGGGTCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGTCAAATTCAG
1 GTACCAAATTGGGTCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGCCAAATTCAA
10182495 GTACCAAATTGGGT-CAAAAAAAGTTTAGGTACCAAATTA
1 GTACCAAATTGGGTCCAAAAAAAGTTTAGGTACCAAATTA
10182534 AAAATAAGTG
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 64 0.69
61 29 0.31
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (61 bp):
GTACCAAATTGGGTCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGCCAAATTCAA
Found at i:10182501 original size:32 final size:31
Alignment explanation
Indices: 10182401--10182504 Score: 94
Period size: 31 Copynumber: 3.4 Consensus size: 31
10182391 AAAAAAGTTT
*
10182401 AGGTACCAAATTAGG-AAAAAATGCCAAGTTC
1 AGGTACCAAATTAGGAAAAAAATGTCAA-TTC
* *
10182432 AAGTACCAAATTGGGTCCAAAAAAA-GT---TT-
1 AGGTACCAAATTAGG---AAAAAAATGTCAATTC
10182461 AGGTACCAAATTAGGAAAAAAATGTCAAATTC
1 AGGTACCAAATTAGGAAAAAAATGTC-AATTC
10182493 AGGTACCAAATT
1 AGGTACCAAATT
10182505 GGGTCAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
26 7 0.12
27 2 0.03
29 13 0.22
30 2 0.03
31 15 0.26
32 12 0.21
34 1 0.02
35 6 0.10
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.22
Consensus pattern (31 bp):
AGGTACCAAATTAGGAAAAAAATGTCAATTC
Found at i:10182514 original size:32 final size:31
Alignment explanation
Indices: 10182395--10182533 Score: 112
Period size: 32 Copynumber: 4.6 Consensus size: 31
10182385 AATCTAAAAA
*
10182395 AAGTTTAGGTACCAAATTAGG-AAAAAATGCC
1 AAGTTCAGGTACCAAATTAGGTAAAAAATG-C
* * *
10182426 AAGTTCAAGTACCAAATTGGGTCCAAAAA---
1 AAGTTCAGGTACCAAATTAGGT-AAAAAATGC
* *
10182455 AAGTTTAGGTACCAAATTAGGAAAAAAATGTC
1 AAGTTCAGGTACCAAATTAGGTAAAAAATG-C
* * *
10182487 AAATTCAGGTACCAAATTGGGTCAAAAA---
1 AAGTTCAGGTACCAAATTAGGTAAAAAATGC
*
10182515 AAGTTTAGGTACCAAATTA
1 AAGTTCAGGTACCAAATTA
10182534 AAAATAAGTG
Statistics
Matches: 85, Mismatches: 17, Indels: 15
0.73 0.15 0.13
Matches are distributed among these distances:
28 21 0.25
29 18 0.21
31 18 0.21
32 23 0.27
33 5 0.06
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (31 bp):
AAGTTCAGGTACCAAATTAGGTAAAAAATGC
Found at i:10182996 original size:17 final size:17
Alignment explanation
Indices: 10182974--10183007 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10182964 ATTATTGTTT
* *
10182974 ACGTTTTATCTTTATCA
1 ACGTTTCATCTTCATCA
10182991 ACGTTTCATCTTCATCA
1 ACGTTTCATCTTCATCA
10183008 GTAGTTTGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (17 bp):
ACGTTTCATCTTCATCA
Found at i:10183805 original size:22 final size:22
Alignment explanation
Indices: 10183780--10183824 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
10183770 TTTTATTGGA
10183780 TAGTGGATATTCATGTTCTTTC
1 TAGTGGATATTCATGTTCTTTC
10183802 TAGTGGATATTCATGTTCTTTC
1 TAGTGGATATTCATGTTCTTTC
10183824 T
1 T
10183825 CTCTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (22 bp):
TAGTGGATATTCATGTTCTTTC
Found at i:10188489 original size:25 final size:24
Alignment explanation
Indices: 10188450--10188506 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
10188440 AATCGATTCA
**
10188450 ATCCAAAATTGACC-AATTCGCGATC
1 ATCCAAAATCAACCAAATT-GC-ATC
*
10188475 ATCCAAAATCAACCAAATTTCATC
1 ATCCAAAATCAACCAAATTGCATC
10188499 ATCCAAAA
1 ATCCAAAA
10188507 ACAAGTCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 11 0.39
25 13 0.46
26 4 0.14
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (24 bp):
ATCCAAAATCAACCAAATTGCATC
Found at i:10189757 original size:24 final size:24
Alignment explanation
Indices: 10189733--10189788 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
10189723 TAAAAGGCAA
*
10189733 AAATATAAATAGCATTAAAAACAAAT
1 AAATA-AAATA-CATAAAAAACAAAT
*
10189759 AAATAAAATACATAAAAAAC-ATT
1 AAATAAAATACATAAAAAACAAAT
10189782 AAATAAA
1 AAATAAA
10189789 TAAGATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.32
24 9 0.32
25 5 0.18
26 5 0.18
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (24 bp):
AAATAAAATACATAAAAAACAAAT
Found at i:10189764 original size:4 final size:4
Alignment explanation
Indices: 10189755--10189875 Score: 68
Period size: 4 Copynumber: 28.8 Consensus size: 4
10189745 CATTAAAAAC
* * *
10189755 AAAT AAAT AAAAT ACAT AAAA AACATT AAAT AAAT AAGATT AAAT AAAGG
1 AAAT AAAT -AAAT AAAT AAAT AA-A-T AAAT AAAT AA-A-T AAAT AAA-T
* * * *
10189805 CAAG AATAT AAAT AACAT AAA- AAAT GAAT -AAC AAAT AAAT AAAT AAAT
1 AAAT AA-AT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
10189853 AAAT AAA- ACAAA AAAT AAAT AAA
1 AAAT AAAT A-AAT AAAT AAAT AAA
10189876 AATTAATTGA
Statistics
Matches: 93, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
3 6 0.06
4 64 0.69
5 18 0.19
6 5 0.05
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:10189773 original size:9 final size:9
Alignment explanation
Indices: 10189755--10189876 Score: 55
Period size: 9 Copynumber: 14.3 Consensus size: 9
10189745 CATTAAAAAC
10189755 AAATAAATA
1 AAATAAATA
*
10189764 AAATACATA
1 AAATAAATA
*
10189773 AAA-AACATT
1 AAATAA-ATA
10189782 AAATAAATA
1 AAATAAATA
*
10189791 AGATTAAATA
1 A-AATAAATA
*** *
10189801 AAGGCAAGA
1 AAATAAATA
*
10189810 ATATAAATA
1 AAATAAATA
*
10189819 ACAT-AA-A
1 AAATAAATA
*
10189826 AAATGAAT-
1 AAATAAATA
*
10189834 -AACAAAT-
1 AAATAAATA
10189841 AAATAAAT-
1 AAATAAATA
10189849 AAATAAATA
1 AAATAAATA
*
10189858 AAA-CAA-A
1 AAATAAATA
10189865 AAATAAATA
1 AAATAAATA
10189874 AAA
1 AAA
10189877 ATTAATTGAA
Statistics
Matches: 83, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
7 13 0.16
8 23 0.28
9 37 0.45
10 10 0.12
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (9 bp):
AAATAAATA
Found at i:10189796 original size:14 final size:13
Alignment explanation
Indices: 10189755--10189802 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
10189745 CATTAAAAAC
*
10189755 AAATAAATAAAAT
1 AAATAAATAAATT
* *
10189768 ACATAAAAAACATT
1 AAATAAATAA-ATT
10189782 AAATAAATAAGATT
1 AAATAAATAA-ATT
10189796 AAATAAA
1 AAATAAA
10189803 GGCAAGAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 8 0.29
14 20 0.71
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (13 bp):
AAATAAATAAATT
Found at i:10189840 original size:23 final size:23
Alignment explanation
Indices: 10189814--10189875 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
10189804 GCAAGAATAT
*
10189814 AAATAACATAAA-AAATGAATAAC
1 AAATAA-ATAAATAAATAAATAAC
10189837 AAATAAATAAATAAATAAATAAAAC
1 AAATAAATAAATAAATAAAT--AAC
10189862 AAA-AAATAAATAAA
1 AAATAAATAAATAAA
10189876 AATTAATTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
22 5 0.14
23 13 0.37
24 11 0.31
25 6 0.17
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.18
Consensus pattern (23 bp):
AAATAAATAAATAAATAAATAAC
Found at i:10191336 original size:23 final size:22
Alignment explanation
Indices: 10191305--10191352 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
10191295 TTGTCAACTC
10191305 CAAACCCTA-AAACTAAAACCAAG
1 CAAACCCTATAAA--AAAACCAAG
* *
10191328 CAAAGCCTATAAAAAAATCAAG
1 CAAACCCTATAAAAAAACCAAG
10191350 CAA
1 CAA
10191353 CCAAAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
23 8 0.36
24 3 0.14
ACGTcount: A:0.58, C:0.25, G:0.06, T:0.10
Consensus pattern (22 bp):
CAAACCCTATAAAAAAACCAAG
Found at i:10196784 original size:14 final size:14
Alignment explanation
Indices: 10196751--10196783 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
10196741 AGAATATCTG
10196751 ATTTTTTATTTACT
1 ATTTTTTATTTACT
10196765 ATTTTTTA-TTA-T
1 ATTTTTTATTTACT
10196777 ATTTTTT
1 ATTTTTT
10196784 TGCTTCTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 3 0.16
14 8 0.42
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
ATTTTTTATTTACT
Done.