Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 91 of 135
Found at i:28454107 original size:20 final size:20
Alignment explanation
Indices: 28454082--28454128 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
28454072 ATGGGGAAGC
28454082 AAAAGAAAATAAAAAAAAAT
1 AAAAGAAAATAAAAAAAAAT
* *
28454102 AAAAGAAAGTTAAAAAAAAT
1 AAAAGAAAATAAAAAAAAAT
28454122 AAAAGAA
1 AAAAGAA
28454129 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.11
Consensus pattern (20 bp):
AAAAGAAAATAAAAAAAAAT
Found at i:28454115 original size:11 final size:10
Alignment explanation
Indices: 28454082--28454128 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
28454072 ATGGGGAAGC
28454082 AAAAGAAAAT
1 AAAAGAAAAT
*
28454092 AAAAAAAAAT
1 AAAAGAAAAT
*
28454102 AAAAGAAAGTT
1 AAAAGAAA-AT
28454113 AAAA-AAAAT
1 AAAAGAAAAT
28454122 AAAAGAA
1 AAAAGAA
28454129 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 5 0.16
10 21 0.68
11 5 0.16
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.11
Consensus pattern (10 bp):
AAAAGAAAAT
Found at i:28455654 original size:29 final size:30
Alignment explanation
Indices: 28455621--28455684 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
28455611 AAATTTAATA
* *
28455621 TATACAATTGTACA-AAATCAAAGTTCATG
1 TATACAATTGCACATAAACCAAAGTTCATG
*
28455650 TATACAATTGCACATTAAACCATAGTTCATG
1 TATACAATTGCACA-TAAACCAAAGTTCATG
28455681 TATA
1 TATA
28455685 GTTTTGATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 13 0.43
31 17 0.57
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (30 bp):
TATACAATTGCACATAAACCAAAGTTCATG
Found at i:28462711 original size:31 final size:30
Alignment explanation
Indices: 28462658--28462720 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
28462648 TGCTCCATTT
28462658 ATTAAAAATGATAAAGTAATTTTTATACATTAA
1 ATTAAAAA-GATAAAGTAATTTTT-TA-ATTAA
* *
28462691 ATTAAAAA-ATAAATTGATTTTTTAATTAA
1 ATTAAAAAGATAAAGTAATTTTTTAATTAA
28462720 A
1 A
28462721 AATTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 6 0.21
30 2 0.07
31 12 0.43
33 8 0.29
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (30 bp):
ATTAAAAAGATAAAGTAATTTTTTAATTAA
Found at i:28462826 original size:16 final size:16
Alignment explanation
Indices: 28462805--28462842 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
28462795 TTTGGTTCGT
*
28462805 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGC
28462821 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGC
28462837 TGTAAT
1 TGTAAT
28462843 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.03, G:0.32, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAGAGC
Found at i:28463124 original size:58 final size:59
Alignment explanation
Indices: 28463014--28463141 Score: 156
Period size: 58 Copynumber: 2.2 Consensus size: 59
28463004 TTTTAATGAT
* * *
28463014 TATTATTAAATATAATTTAGAATAAAAATATTAATTAATTTAATTATATTTTAACAT-AA
1 TATTATTAAATACAATTTA-AATAAAAATAATAATTAATTTAATAATATTTTAACATAAA
*
28463073 TAATTATTAAATACAATTT-AAT-AAAATAAT-ATATAATTTAATAATATTTTTAATATAAA
1 T-ATTATTAAATACAATTTAAATAAAAATAATAAT-TAATTTAATAATA-TTTTAACATAAA
28463132 TATTATTAAA
1 TATTATTAAA
28463142 ATATGAATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
56 2 0.03
57 19 0.31
58 20 0.33
59 4 0.07
60 16 0.26
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (59 bp):
TATTATTAAATACAATTTAAATAAAAATAATAATTAATTTAATAATATTTTAACATAAA
Found at i:28463161 original size:25 final size:25
Alignment explanation
Indices: 28463128--28463183 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
28463118 ATTTTTAATA
* *
28463128 TAAATATTATTAAAATATGA-ATTAG
1 TAAAAATTA-TAAAATATAATATTAG
*
28463153 TAAAAATTATAATATATAATATTAG
1 TAAAAATTATAAAATATAATATTAG
28463178 -AAAAAT
1 TAAAAAT
28463184 AATATATAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (25 bp):
TAAAAATTATAAAATATAATATTAG
Found at i:28474618 original size:5 final size:5
Alignment explanation
Indices: 28474608--28474632 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28474598 TGGTTTTCTA
28474608 TTGTT TTGTT TTGTT TTGTT TTGTT
1 TTGTT TTGTT TTGTT TTGTT TTGTT
28474633 ATATTATAAT
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:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TTGTT
Found at i:28474888 original size:20 final size:21
Alignment explanation
Indices: 28474859--28474900 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
28474849 TAATGTCACG
28474859 TTAATAATTTT-ATTCTGAATT
1 TTAATAATTTTCATT-TGAATT
28474880 TTAAT-ATTTTCATTTGAATT
1 TTAATAATTTTCATTTGAATT
28474900 T
1 T
28474901 AATTTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (21 bp):
TTAATAATTTTCATTTGAATT
Found at i:28476359 original size:28 final size:28
Alignment explanation
Indices: 28476292--28476360 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
28476282 GTCTAAGGAT
*
28476292 AGCTCGGTTAAAGCTTTAATTCACTTAC
1 AGCTCGGTTAGAGCTTTAATTCACTTAC
* **
28476320 AGCTCGAG-TAGAGCTTTAGTTTGCTTAC
1 AGCTCG-GTTAGAGCTTTAATTCACTTAC
*
28476348 ATCTCGGTTAGAG
1 AGCTCGGTTAGAG
28476361 TGTAAAGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.03
28 32 0.94
29 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (28 bp):
AGCTCGGTTAGAGCTTTAATTCACTTAC
Found at i:28476386 original size:55 final size:55
Alignment explanation
Indices: 28476320--28476427 Score: 135
Period size: 55 Copynumber: 2.0 Consensus size: 55
28476310 ATTCACTTAC
* * *
28476320 AGCTCGAGTAGAGCTTTAGTTTGCTTACATCTCGGTTAGAGTGTAAAGCTATTAT
1 AGCTCGAGTAGAGCTTCAGATTGCTTACATCTCGGTTAAAGTGTAAAGCTATTAT
* * * ** *
28476375 AGCTCGGGTAGATCTTCGGATTGCTTATGTCTCGGTTAAAGTGTAATGCTATT
1 AGCTCGAGTAGAGCTTCAGATTGCTTACATCTCGGTTAAAGTGTAAAGCTATT
28476428 TCAGATCAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (55 bp):
AGCTCGAGTAGAGCTTCAGATTGCTTACATCTCGGTTAAAGTGTAAAGCTATTAT
Found at i:28481137 original size:35 final size:35
Alignment explanation
Indices: 28481056--28481144 Score: 117
Period size: 35 Copynumber: 2.5 Consensus size: 35
28481046 ATTGATGTTC
* *
28481056 TGATTCGCATGTAAAGTATGCTATTATTCTGATTA
1 TGATTCGCATGTTAAGCATGCTATTATTCTGATTA
* *
28481091 TGACTCGCATGTTAAGCATGGC-ATTATTCTGATTT
1 TGATTCGCATGTTAAGCAT-GCTATTATTCTGATTA
*
28481126 TGATTCACATGTTAAGCAT
1 TGATTCGCATGTTAAGCAT
28481145 ACCACTGTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 45 0.96
36 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (35 bp):
TGATTCGCATGTTAAGCATGCTATTATTCTGATTA
Found at i:28481202 original size:46 final size:46
Alignment explanation
Indices: 28481126--28481277 Score: 218
Period size: 46 Copynumber: 3.3 Consensus size: 46
28481116 ATTCTGATTT
* *
28481126 TGATTCACATGTTAAGCATACCACTGTATTAAACCGTAATAAGAT-
1 TGATTCGCATGTTAAGCATGCCACTGTATTAAACCGTAATAAGATA
* * *
28481171 TCGATTTGCGTGTTAAGCATGCCACTGTATTAAATCGTAATAAGATA
1 T-GATTCGCATGTTAAGCATGCCACTGTATTAAACCGTAATAAGATA
* *
28481218 TGATTCGCATGTTAAACATGCCACTGTATTAAACCGTAATAAGATC
1 TGATTCGCATGTTAAGCATGCCACTGTATTAAACCGTAATAAGATA
28481264 TGATTCGCAT-TTAA
1 TGATTCGCATGTTAA
28481278 AGTTTGCCTA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
45 5 0.05
46 89 0.94
47 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (46 bp):
TGATTCGCATGTTAAGCATGCCACTGTATTAAACCGTAATAAGATA
Found at i:28484880 original size:13 final size:13
Alignment explanation
Indices: 28484862--28484886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28484852 AATGGCTGCC
28484862 TTTTCTTTCTTCT
1 TTTTCTTTCTTCT
28484875 TTTTCTTTCTTC
1 TTTTCTTTCTTC
28484887 ATCATGGTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTCTTCT
Found at i:28487448 original size:86 final size:86
Alignment explanation
Indices: 28487346--28487504 Score: 223
Period size: 86 Copynumber: 1.8 Consensus size: 86
28487336 ATTCCTGAAC
** * * *
28487346 AAAAATAGTCACAAAGACGTCCTTAAGAAAAGAA-AACCACGAAGGCT-TCCATAAGCAAAGATA
1 AAAAATAACCACAAAGACGTCCATAAGAAAA-AATAACCAC-AAAGATGTCCATAAGCAAAGATA
*
28487409 ACCATAAAGGCGTCCATAAGAAA
64 ACCACAAAGGCGTCCATAAGAAA
*
28487432 AAAAATAACCACAAAGAGGTCCATAAGAAAAAATAACCACAAAGATGTCCATAAGCAAAGATAAC
1 AAAAATAACCACAAAGACGTCCATAAGAAAAAATAACCACAAAGATGTCCATAAGCAAAGATAAC
28487497 CACAAAGG
66 CACAAAGG
28487505 AATCCATTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
85 6 0.09
86 58 0.91
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.13
Consensus pattern (86 bp):
AAAAATAACCACAAAGACGTCCATAAGAAAAAATAACCACAAAGATGTCCATAAGCAAAGATAAC
CACAAAGGCGTCCATAAGAAA
Found at i:28487457 original size:58 final size:56
Alignment explanation
Indices: 28487355--28487537 Score: 185
Period size: 58 Copynumber: 3.3 Consensus size: 56
28487345 CAAAAATAGT
* * **
28487355 CACAAAGACGTCCTTAAGAAAAGAA-AACCACGAAGGCTTCCATAAGCAAAGATAAC
1 CACAAAGACGTCCATAAGAAAA-AATAACCACAAAGGAATCCATAAGCAAAGATAAC
* * * * *
28487411 CATAAAGGCGTCCATAAGAAAAAAAATAACCACAAA-GAGGTCCATAAGAAAAAATAAC
1 CACAAAGACGTCCATAAG--AAAAAATAACCACAAAGGA-ATCCATAAGCAAAGATAAC
* * * *
28487469 CACAAAGATGTCCATAAGCAAAGATAACCACAAAGGAATCCAT--TCAAAGATAAC
1 CACAAAGACGTCCATAAGAAAAAATAACCACAAAGGAATCCATAAGCAAAGATAAC
28487523 CACAAAGACGTCCAT
1 CACAAAGACGTCCAT
28487538 TTAAATATAG
Statistics
Matches: 104, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
54 22 0.21
56 34 0.33
57 5 0.05
58 43 0.41
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.13
Consensus pattern (56 bp):
CACAAAGACGTCCATAAGAAAAAATAACCACAAAGGAATCCATAAGCAAAGATAAC
Found at i:28487510 original size:28 final size:28
Alignment explanation
Indices: 28487355--28487537 Score: 144
Period size: 28 Copynumber: 6.5 Consensus size: 28
28487345 CAAAAATAGT
* *
28487355 CACAAA-GACGTCCTTAAGAAAAGAAAAC
1 CACAAAGGA-GTCCATAAGAAAAGATAAC
* ** *
28487383 CACGAAGGCTTCCATAAGCAAAGATAAC
1 CACAAAGGAGTCCATAAGAAAAGATAAC
* * *
28487411 CATAAAGGCGTCCATAAGAAAAAAAATAAC
1 CACAAAGGAGTCCATAAG--AAAAGATAAC
*
28487441 CACAAA-GAGGTCCATAAGAAAAAATAAC
1 CACAAAGGA-GTCCATAAGAAAAGATAAC
*
28487469 CACAAA-GATGTCCATAAGCAAAGATAAC
1 CACAAAGGA-GTCCATAAGAAAAGATAAC
* **
28487497 CACAAAGGAATCCAT--TCAAAGATAAC
1 CACAAAGGAGTCCATAAGAAAAGATAAC
28487523 CACAAA-GACGTCCAT
1 CACAAAGGA-GTCCAT
28487538 TTAAATATAG
Statistics
Matches: 130, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
25 2 0.02
26 21 0.16
28 81 0.62
29 4 0.03
30 22 0.17
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.13
Consensus pattern (28 bp):
CACAAAGGAGTCCATAAGAAAAGATAAC
Found at i:28487551 original size:26 final size:26
Alignment explanation
Indices: 28487436--28487565 Score: 93
Period size: 26 Copynumber: 4.9 Consensus size: 26
28487426 AAGAAAAAAA
* ** *
28487436 ATAACCACAAAGAGGTCCATAAGAAAAA
1 ATAACCACAAAGACGTCCAT--TTAAAG
* **
28487464 ATAACCACAAAGATGTCCATAAGCAAAG
1 ATAACCACAAAGACGTCCAT--TTAAAG
* *
28487492 ATAACCACAAAGGA-ATCCATTCAAAG
1 ATAACCACAAA-GACGTCCATTTAAAG
*
28487518 ATAACCACAAAGACGTCCATTTAAAT
1 ATAACCACAAAGACGTCCATTTAAAG
* *
28487544 ATAGCCACAAAGGCGTCC-TTTA
1 ATAACCACAAAGACGTCCATTTA
28487566 CAGAATTAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
25 6 0.07
26 41 0.46
28 41 0.46
29 2 0.02
ACGTcount: A:0.48, C:0.22, G:0.13, T:0.17
Consensus pattern (26 bp):
ATAACCACAAAGACGTCCATTTAAAG
Found at i:28487639 original size:29 final size:28
Alignment explanation
Indices: 28487545--28487785 Score: 158
Period size: 29 Copynumber: 8.7 Consensus size: 28
28487535 CATTTAAATA
28487545 TAGCCACAAAGGCGTC-CTTT-ACAGAAT
1 TAGCCACAAAGGC-TCACTTTAACAGAAT
* ** *
28487572 TAGCCACAGAGGCTCACGATAATAGAAT
1 TAGCCACAAAGGCTCACTTTAACAGAAT
* ** * *
28487600 CAATCATAAAGGCCTCACTTTAACAGATT
1 TAGCCACAAAGG-CTCACTTTAACAGAAT
*
28487629 TAGCCACAAAGG----C-GTAACAGAA-
1 TAGCCACAAAGGCTCACTTTAACAGAAT
* * *
28487651 TCGACCATAAAAGCTCACTTTAACAGAAT
1 TAG-CCACAAAGGCTCACTTTAACAGAAT
* * * *
28487680 TAACCACAAAGGCTTCCCTTTAATAGAAG
1 TAGCCACAAAGGC-TCACTTTAACAGAAT
* *
28487709 TAGCCATAAAGGCTC-CATTTAACATAAT
1 TAGCCACAAAGGCTCAC-TTTAACAGAAT
* * *
28487737 CAGCCACAAAAGCTTCACTTTAACAAAAT
1 TAGCCACAAAGGC-TCACTTTAACAGAAT
*
28487766 TAGCCACAAAGGTTCACTTT
1 TAGCCACAAAGGCTCACTTT
28487786 TTCGAGAAAT
Statistics
Matches: 158, Mismatches: 42, Indels: 27
0.70 0.19 0.12
Matches are distributed among these distances:
22 2 0.01
23 14 0.09
24 1 0.01
26 2 0.01
27 16 0.10
28 56 0.35
29 66 0.42
30 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (28 bp):
TAGCCACAAAGGCTCACTTTAACAGAAT
Found at i:28487675 original size:51 final size:52
Alignment explanation
Indices: 28487595--28487692 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 52
28487585 TCACGATAAT
* * * *
28487595 AGAATCAATCATAAAGGCCTCACTTTAACAGATTTAGCCACAAAGGCGTAAC
1 AGAATCAACCATAAAAGCCTCACTTTAACAGAATTAACCACAAAGGCGTAAC
*
28487647 AGAATCGACCATAAAAG-CTCACTTTAACAGAATTAACCACAAAGGC
1 AGAATCAACCATAAAAGCCTCACTTTAACAGAATTAACCACAAAGGC
28487693 TTCCCTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 27 0.66
52 14 0.34
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.19
Consensus pattern (52 bp):
AGAATCAACCATAAAAGCCTCACTTTAACAGAATTAACCACAAAGGCGTAAC
Found at i:28487731 original size:57 final size:57
Alignment explanation
Indices: 28487655--28487785 Score: 147
Period size: 57 Copynumber: 2.3 Consensus size: 57
28487645 ACAGAATCGA
* * * * * *
28487655 CCATAAAAGCTCACTTTAACAGAATTAACCACAAAGGCTTCCCTTTAATAGAAGTAG
1 CCATAAAGGCTCACTTTAACAGAATCAACCACAAAAGCTTCACTTTAACAAAAGTAG
* * *
28487712 CCATAAAGGCTC-CATTTAACATAATCAGCCACAAAAGCTTCACTTTAACAAAATTAG
1 CCATAAAGGCTCAC-TTTAACAGAATCAACCACAAAAGCTTCACTTTAACAAAAGTAG
* *
28487769 CCACAAAGGTTCACTTT
1 CCATAAAGGCTCACTTT
28487786 TTCGAGAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
56 1 0.02
57 59 0.97
58 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (57 bp):
CCATAAAGGCTCACTTTAACAGAATCAACCACAAAAGCTTCACTTTAACAAAAGTAG
Found at i:28487951 original size:56 final size:56
Alignment explanation
Indices: 28487890--28488103 Score: 288
Period size: 56 Copynumber: 3.8 Consensus size: 56
28487880 TCATCTTCTT
* * *
28487890 CCATATGATGCCATAGCCATCATGACCAGGTCTTACGCTATATGATCTTCATTTTC
1 CCATATGATGCCATAGCCACCATGACCAGGTCTTACACTATATGGTCTTCATTTTC
** * * * *
28487946 CCATATGATATCATAGCTACCATAACCAAGTCTTACGCTATATGGTCTTCA-TTTC
1 CCATATGATGCCATAGCCACCATGACCAGGTCTTACACTATATGGTCTTCATTTTC
* *
28488001 TCCATATGATGCCATAGCCACCATGA-CATTGTCTTACACTATATGGTCTTCATTTCC
1 -CCATATGATGCCATAGCCACCATGACCA-GGTCTTACACTATATGGTCTTCATTTTC
*
28488058 CCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGT
1 CCATATGATGCCATAGCCACCATGACCAGGTCTTACACTATATGGT
28488104 TTGCGATTGC
Statistics
Matches: 138, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
55 6 0.04
56 128 0.93
57 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.33
Consensus pattern (56 bp):
CCATATGATGCCATAGCCACCATGACCAGGTCTTACACTATATGGTCTTCATTTTC
Found at i:28491435 original size:20 final size:20
Alignment explanation
Indices: 28491410--28491496 Score: 75
Period size: 20 Copynumber: 4.0 Consensus size: 20
28491400 ATCGTAAAAG
*
28491410 GTGAAAAAGTTGAATTGGTT
1 GTGAAAAAGTTAAATTGGTT
* *
28491430 GTGAAAAAGTTAAATAAATCGTAAAAG
1 GTGAAAAAGTTAAAT---TGGT----T
*
28491457 GTGAAAAAGTTGAATTGGTT
1 GTGAAAAAGTTAAATTGGTT
28491477 GTGAAAAAGTTAAATTGGTT
1 GTGAAAAAGTTAAATTGGTT
28491497 AATTAGAAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
20 33 0.62
23 3 0.06
24 3 0.06
27 14 0.26
ACGTcount: A:0.43, C:0.01, G:0.25, T:0.31
Consensus pattern (20 bp):
GTGAAAAAGTTAAATTGGTT
Found at i:28491455 original size:47 final size:47
Alignment explanation
Indices: 28491397--28491491 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
28491387 TAAAAAAGAT
28491397 TAAATCGTAAAAGGTGAAAAAGTTGAATTGGTTGTGAAAAAGTTAAA
1 TAAATCGTAAAAGGTGAAAAAGTTGAATTGGTTGTGAAAAAGTTAAA
28491444 TAAATCGTAAAAGGTGAAAAAGTTGAATTGGTTGTGAAAAAGTTAAA
1 TAAATCGTAAAAGGTGAAAAAGTTGAATTGGTTGTGAAAAAGTTAAA
28491491 T
1 T
28491492 TGGTTAATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.28
Consensus pattern (47 bp):
TAAATCGTAAAAGGTGAAAAAGTTGAATTGGTTGTGAAAAAGTTAAA
Found at i:28504989 original size:38 final size:39
Alignment explanation
Indices: 28504947--28505021 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
28504937 TTTCTATTAA
* *
28504947 AAATAATAAATATATAA-TATTCAAAATTAAAAAATTTC
1 AAATAATAAATAAATAATTATACAAAATTAAAAAATTTC
* *
28504985 AAATAATAATTAAATAATTATACAATATTAAAAAATT
1 AAATAATAAATAAATAATTATACAAAATTAAAAAATT
28505022 ATATGTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 15 0.47
39 17 0.53
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (39 bp):
AAATAATAAATAAATAATTATACAAAATTAAAAAATTTC
Found at i:28508252 original size:31 final size:31
Alignment explanation
Indices: 28508217--28508281 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
28508207 TTTTTTTTAT
28508217 TTAGACCCTTTAAAAATTTAAAAATTTTAAA
1 TTAGACCCTTTAAAAATTTAAAAATTTTAAA
28508248 TTAGACCCTTTAAAAATTTAAAAATTTTAAA
1 TTAGACCCTTTAAAAATTTAAAAATTTTAAA
28508279 TTA
1 TTA
28508282 ATAAAGGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (31 bp):
TTAGACCCTTTAAAAATTTAAAAATTTTAAA
Found at i:28508293 original size:31 final size:31
Alignment explanation
Indices: 28508227--28508293 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
28508217 TTAGACCCTT
*****
28508227 TAAAAATTTAAAAATTTTAAATTAGACCCTT
1 TAAAAATTTAAAAATTTTAAATTAGAAAAGG
28508258 TAAAAATTTAAAAATTTTAAATTA-ATAAAGG
1 TAAAAATTTAAAAATTTTAAATTAGA-AAAGG
28508289 TAAAA
1 TAAAA
28508294 TTGTACTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (31 bp):
TAAAAATTTAAAAATTTTAAATTAGAAAAGG
Found at i:28512686 original size:29 final size:30
Alignment explanation
Indices: 28512449--28512711 Score: 227
Period size: 29 Copynumber: 8.9 Consensus size: 30
28512439 AAAAATTGTA
* *
28512449 TTTTGACCCCTAAACTTCCAAAAATTCCAT
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
** *
28512479 TTTTGACCCTAAAACTTCCAAAACTTACA-
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
* * *
28512508 TTTT-CCCCCCAAACTT-CAAACAATTCCA-
1 TTTTGACCCCGAAACTTCCAAA-AATTACAT
* ** * *
28512536 TTTTAACCTGGAAATTTTCAAAAATTACAT
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
* *
28512566 TTTTGA-CTCAAAACTTCCAAAAATTACAT
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
* *
28512595 TTTT-ACCCCTAAAATTCCAAAAATTACAT
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
*
28512624 TTTTGACCCCGAAACTTCCAAAAAATACAT
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
* * *
28512654 TTTT-ACTCTC-AAACTTCTAAAAGTTACATT
1 TTTTGAC-CCCGAAACTTCCAAAAATTACA-T
* * *
28512684 TTTTTACCTCGAAACTTGCAAAAATTAC
1 TTTTGACCCCGAAACTTCCAAAAATTAC
28512712 CACTTTACCC
Statistics
Matches: 190, Mismatches: 33, Indels: 19
0.79 0.14 0.08
Matches are distributed among these distances:
27 4 0.02
28 19 0.10
29 81 0.43
30 70 0.37
31 16 0.08
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (30 bp):
TTTTGACCCCGAAACTTCCAAAAATTACAT
Found at i:28518560 original size:7 final size:6
Alignment explanation
Indices: 28518542--28518635 Score: 97
Period size: 6 Copynumber: 15.7 Consensus size: 6
28518532 TTCAATGAAT
* *
28518542 AAAAAG -AAAAG AAAAA- AGAAAA- AAAAGG AGAAAG AAAAAGG AAAAAG
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAA-G AAAAAG
*
28518589 AAGAAGG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA- AGAAAAG AAAA
1 AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAA
28518636 GGAGAGTTCG
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
5 10 0.13
6 53 0.71
7 12 0.16
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:28518564 original size:13 final size:13
Alignment explanation
Indices: 28518542--28518635 Score: 104
Period size: 13 Copynumber: 7.2 Consensus size: 13
28518532 TTCAATGAAT
28518542 AAAAAG-AAAAGA
1 AAAAAGAAAAAGA
*
28518554 AAAAAGAAAAAAA
1 AAAAAGAAAAAGA
*
28518567 AGGAGAAAGAAAAAGG
1 A--A-AAAGAAAAAGA
* *
28518583 AAAAAGAAGAAGG
1 AAAAAGAAAAAGA
28518596 AAAAAGAAAAAG-
1 AAAAAGAAAAAGA
28518608 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
28518621 AAAAAG-AAAAGA
1 AAAAAGAAAAAGA
28518633 AAA
1 AAA
28518636 GGAGAGTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
12 27 0.38
13 33 0.46
14 1 0.01
15 1 0.01
16 10 0.14
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:28518573 original size:19 final size:19
Alignment explanation
Indices: 28518550--28518635 Score: 70
Period size: 19 Copynumber: 4.4 Consensus size: 19
28518540 ATAAAAAGAA
28518550 AAGAAAAAAGAAAAAAAAGGAG
1 AAGAAAAAAG-AAAAAAA--AG
* *
28518572 AAAGAAAAAGGAAAAAGAAG
1 -AAGAAAAAAGAAAAAAAAG
*
28518592 AAGGAAAAAGAAAAAGAAA-
1 AAGAAAAAAGAAAAA-AAAG
28518611 AAG-AAAAAGAAAAAAGAA-
1 AAGAAAAAAGAAAAAA-AAG
28518629 AAGAAAA
1 AAGAAAA
28518636 GGAGAGTTCG
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.02
18 16 0.29
19 19 0.35
20 4 0.07
22 6 0.11
23 9 0.16
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAGAAAAAAAAG
Found at i:28520015 original size:100 final size:99
Alignment explanation
Indices: 28519872--28520058 Score: 234
Period size: 100 Copynumber: 1.9 Consensus size: 99
28519862 GCAACGACAA
*
28519872 ATCCAGTACCGCAAAAATACAAAAGGGAAAGGTGATGACCGCAAC-GATGAACCTTACACCTCAG
1 ATCCAGTACCGCAAAAATACAAAAGGGAAAGGTGAAGACCGCAACAGA--AACCTTACACCTCAG
*
28519936 AGACATGACAGGAAAGATCTAAGATCGCAATGGTGG
64 AGACACGACAGGAAAGATCTAAGATCGCAATGGTGG
* * * * ** *
28519972 ATCCAGTACCGCAAAGATACAAAAGGGAAGGGTTTAAG-TCGCAACAGCAAACCTTGTACCTTAG
1 ATCCAGTACCGCAAAAATACAAAAGGGAAAGG-TGAAGACCGCAACAG-AAACCTTACACCTCAG
*
28520036 AGACACGACGGGAAAGATCTAAG
64 AGACACGACAGGAAAGATCTAAG
28520059 GCCACAACAG
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
100 69 0.93
101 4 0.05
102 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.16
Consensus pattern (99 bp):
ATCCAGTACCGCAAAAATACAAAAGGGAAAGGTGAAGACCGCAACAGAAACCTTACACCTCAGAG
ACACGACAGGAAAGATCTAAGATCGCAATGGTGG
Found at i:28520074 original size:100 final size:99
Alignment explanation
Indices: 28519847--28520081 Score: 224
Period size: 100 Copynumber: 2.4 Consensus size: 99
28519837 AACATGATGA
* ** *
28519847 GAAAGATCTAAGACCGCAAC-GACAAATCCAGTACCGCAAAAATACAAAAGGGAAAGGTGATGAC
1 GAAAGATCTAAGACCACAACAG-CGGATCCAGTACCGCAAAAATACAAAAGGGAAAGGTGAAGAC
*
28519911 CGCAACGATGAACCTTACACCTCAGAGACATGACAG
65 CGCAACGA-GAACCTTACACCTCAGAGACACGACAG
* * ** * * * * *
28519947 GAAAGATCTAAGATCGCAATGGTGGATCCAGTACCGCAAAGATACAAAAGGGAAGGGTTTAAG-T
1 GAAAGATCTAAGACCACAACAGCGGATCCAGTACCGCAAAAATACAAAAGGGAAAGG-TGAAGAC
** * *
28520011 CGCAAC-AGCAAACCTTGTACCTTAGAGACACGACGG
65 CGCAACGAG--AACCTTACACCTCAGAGACACGACAG
* *
28520047 GAAAGATCTAAGGCCACAACAGCGGATCCAATACC
1 GAAAGATCTAAGACCACAACAGCGGATCCAGTACC
28520082 ACGAAGACAT
Statistics
Matches: 109, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
98 1 0.01
99 1 0.01
100 103 0.94
101 4 0.04
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (99 bp):
GAAAGATCTAAGACCACAACAGCGGATCCAGTACCGCAAAAATACAAAAGGGAAAGGTGAAGACC
GCAACGAGAACCTTACACCTCAGAGACACGACAG
Found at i:28520437 original size:38 final size:38
Alignment explanation
Indices: 28520395--28520554 Score: 101
Period size: 39 Copynumber: 4.1 Consensus size: 38
28520385 GATTCAAGAA
**
28520395 GGGCAAAATGAAG-ATTCTGATCTCTTGTCCCGAGCCAG
1 GGGCAAAATGAAGCATT-TGATCTCTTACCCCGAGCCAG
* * **
28520433 GGGCAGATTGAAGCCATTTGATCTCTTACCCCGAGCTTG
1 GGGCAAAATGAAG-CATTTGATCTCTTACCCCGAGCCAG
* * * * * *
28520472 GGGCAGATCAT-CATCAATTAATCTCTTACCCCGAGCTAG
1 GGGCA-A-AATGAAGCATTTGATCTCTTACCCCGAGCCAG
* * * *
28520511 GGGC-AAATTACAGCCATTTAATCTTTTACCCCGAGCCTG
1 GGGCAAAATGA-AG-CATTTGATCTCTTACCCCGAGCCAG
28520550 GGGCA
1 GGGCA
28520555 GATCATCATC
Statistics
Matches: 93, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
36 2 0.02
37 1 0.01
38 12 0.13
39 73 0.78
40 4 0.04
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (38 bp):
GGGCAAAATGAAGCATTTGATCTCTTACCCCGAGCCAG
Found at i:28520466 original size:39 final size:38
Alignment explanation
Indices: 28520414--28520597 Score: 147
Period size: 39 Copynumber: 4.7 Consensus size: 38
28520404 GAAGATTCTG
** *
28520414 ATCTCTTGTCCCGAGCCAGGGGCAGATTGAAGCCATTTG
1 ATCTCTTACCCCGAGCCAGGGGCAGATT-AAGCCATTTA
** * * *
28520453 ATCTCTTACCCCGAGCTTGGGGCAGATCATCA-TCAATTA
1 ATCTCTTACCCCGAGCCAGGGGCAGAT--TAAGCCATTTA
* *
28520492 ATCTCTTACCCCGAGCTAGGGGCAAATTACAGCCATTTA
1 ATCTCTTACCCCGAGCCAGGGGCAGATTA-AGCCATTTA
* * * * * *
28520531 ATCTTTTACCCCGAGCCTGGGGCAGATCATCA-TCAATCA
1 ATCTCTTACCCCGAGCCAGGGGCAGAT--TAAGCCATTTA
*
28520570 ATCTCTTACCCAGAGCCAGGGGCAGATT
1 ATCTCTTACCCCGAGCCAGGGGCAGATT
28520598 GCAACCATCC
Statistics
Matches: 115, Mismatches: 24, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
37 2 0.02
38 1 0.01
39 108 0.94
40 2 0.02
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCCAGGGGCAGATTAAGCCATTTA
Found at i:28520505 original size:78 final size:78
Alignment explanation
Indices: 28520414--28520661 Score: 304
Period size: 78 Copynumber: 3.2 Consensus size: 78
28520404 GAAGATTCTG
** *
28520414 ATCTCTTGTCCCGAGCCAGGGGCAGATTGAAGCCATTTGATCTCTTACCCCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCAGGGGCAGATTGAAGCCATTTGATCTTTTACCCCGAGCTTGGGGCAGA
*
28520479 TCATCATCAATTA
66 TCATCATCAATCA
* * * *
28520492 ATCTCTTACCCCGAGCTAGGGGCAAATT-ACAGCCATTTAATCTTTTACCCCGAGCCTGGGGCAG
1 ATCTCTTACCCCGAGCCAGGGGCAGATTGA-AGCCATTTGATCTTTTACCCCGAGCTTGGGGCAG
28520556 ATCATCATCAATCA
65 ATCATCATCAATCA
* ** * * * *
28520570 ATCTCTTACCCAGAGCCAGGGGCAGATTGCAA-CCATCCGACCTTTTACTCCGATCTTGGAGCAG
1 ATCTCTTACCCCGAGCCAGGGGCAGATTG-AAGCCATTTGATCTTTTACCCCGAGCTTGGGGCAG
*
28520634 ATCATCATCAACCA
65 ATCATCATCAATCA
28520648 ATCT-TCTACCCCGA
1 ATCTCT-TACCCCGA
28520662 TCACAGGGCG
Statistics
Matches: 145, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
77 2 0.01
78 141 0.97
79 1 0.01
80 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCAGGGGCAGATTGAAGCCATTTGATCTTTTACCCCGAGCTTGGGGCAGA
TCATCATCAATCA
Found at i:28521019 original size:49 final size:49
Alignment explanation
Indices: 28520859--28521029 Score: 193
Period size: 49 Copynumber: 3.5 Consensus size: 49
28520849 GACCAAATTC
* * **
28520859 ATCTTCCTGATGAGATACAGAGAAGTGAATTGAAACAAGTAAGGCAACT
1 ATCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGTAAGACGGCT
* * ** * * * *
28520908 ATCTTCCTGATGAGACACTGAGAAGC-AGGTCAAAGCAA-TAAAATGGTT
1 ATCTTCCTGATGAGATACAGAGAAGCGAATTGAAA-CAAGTAAGACGGCT
* *
28520956 AGCTTCCTGCTGAGATACAGAGAAGCGAATTGAAACAAGTAAGACGGCT
1 ATCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGTAAGACGGCT
28521005 ATCTTCCTGATGAGATACAGAGAAG
1 ATCTTCCTGATGAGATACAGAGAAG
28521030 TATGCCAACT
Statistics
Matches: 95, Mismatches: 24, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
48 34 0.36
49 61 0.64
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (49 bp):
ATCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGTAAGACGGCT
Found at i:28521315 original size:201 final size:201
Alignment explanation
Indices: 28520966--28521337 Score: 602
Period size: 201 Copynumber: 1.9 Consensus size: 201
28520956 AGCTTCCTGC
*
28520966 TGAGATACAGAGAAGCGAATTGAAACAAGTAAGACGGCTATCTTCCTGATGAGATACAGAGAAGT
1 TGAGATACAGAGAAGCGAATTGAAACAAGTAAGACGGCTATCTTCCTGATGAGATACAAAGAAGT
* * *
28521031 ATGCCAACTCGAGGCTCAATACCAGCAAATCTTCAAATCCCAGCTTCCTAATGAGATACTGAGAA
66 ATGCCAACTCGAGGCTCAATACCAGCAAATCTTCAAACCCCAACTTCCTAATGAGACACTGAGAA
* * *
28521096 GCAGGTCGTAGCAATAAAATGGTTAGCTTCCTCATGAGATATTGGGAAGTGGACCAAATTCGTGT
131 GCAGGTCGAAGAAATAAAATGATTAGCTTCCTCATGAGATATTGGGAAGTGGACCAAATTCGTGT
28521161 TCCTAG
196 TCCTAG
* * *
28521167 TGAGATACAGAGAAGCGAATTGAAACAAGTGAGGCAG-TCATCTTCCTGATGAGATACAAAGAAG
1 TGAGATACAGAGAAGCGAATTGAAACAAGTAAGACGGCT-ATCTTCCTGATGAGATACAAAGAAG
* * *
28521231 TATGCCAACTCGAGGCTCAATACGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGA
65 TATGCCAACTCGAGGCTCAATACCAGCAAATCTTCAAACCCCAACTTCCTAATGAGACACTGAGA
*
28521296 AGCAGGTCGAAGAAATAAAATGATTAGCTTCCTGATGAGATA
130 AGCAGGTCGAAGAAATAAAATGATTAGCTTCCTCATGAGATA
28521338 CAGAGAAGCG
Statistics
Matches: 156, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
200 1 0.01
201 155 0.99
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (201 bp):
TGAGATACAGAGAAGCGAATTGAAACAAGTAAGACGGCTATCTTCCTGATGAGATACAAAGAAGT
ATGCCAACTCGAGGCTCAATACCAGCAAATCTTCAAACCCCAACTTCCTAATGAGACACTGAGAA
GCAGGTCGAAGAAATAAAATGATTAGCTTCCTCATGAGATATTGGGAAGTGGACCAAATTCGTGT
TCCTAG
Found at i:28521445 original size:164 final size:164
Alignment explanation
Indices: 28521167--28521511 Score: 584
Period size: 164 Copynumber: 2.1 Consensus size: 164
28521157 GTGTTCCTAG
* *
28521167 TGAGATACAGAGAAGCGAATTGAAACAAGTGAGGCAGTCATCTTCCTGATGAGATACAAAGAAGT
1 TGAGATACAGAGAAGCGAATGGAAACAAGTAAGGCAGTCATCTTCCTGATGAGATACAAAGAAGT
28521232 ATGCCAACTCGAGGCTCAATACGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAA
66 ATGCCAACTCGAGGCTCAATACGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAA
*
28521297 GCAGGTCGAAGAAATAAAATGATTAGCTTCCTGA
131 GCAGGTCGAAGAAATAAAATGATTAGCTCCCTGA
* *
28521331 TGAGATACAGAGAAGCGAATGGAAACAAGTAAGGC-GGCTATCTTCCTGATGAGATACAGAGAAG
1 TGAGATACAGAGAAGCGAATGGAAACAAGTAAGGCAGTC-ATCTTCCTGATGAGATACAAAGAAG
* *
28521395 TATGCCAACTCGAGGCTCAATACGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGA
65 TATGCCAACTCGAGGCTCAATACGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGA
* *
28521460 AGCAGGTCGAAGCAATAAAATGGTTAGCTCCCTGA
130 AGCAGGTCGAAGAAATAAAATGATTAGCTCCCTGA
*
28521495 TGAGATACTGAGAAGCG
1 TGAGATACAGAGAAGCG
28521512 GACCAAATTC
Statistics
Matches: 170, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
163 2 0.01
164 168 0.99
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (164 bp):
TGAGATACAGAGAAGCGAATGGAAACAAGTAAGGCAGTCATCTTCCTGATGAGATACAAAGAAGT
ATGCCAACTCGAGGCTCAATACGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAA
GCAGGTCGAAGAAATAAAATGATTAGCTCCCTGA
Found at i:28521580 original size:365 final size:365
Alignment explanation
Indices: 28520910--28521585 Score: 1131
Period size: 365 Copynumber: 1.9 Consensus size: 365
28520900 AGGCAACTAT
* * *
28520910 CTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAAATGGTTAGCTTCCTGCTGAGATACA
1 CTTCCTGATGAGACACTGAGAAGCAGGTCAAAGAAATAAAATGATTAGCTTCCTGATGAGATACA
*
28520975 GAGAAGCGAATTGAAACAAGTAAGACGGCTATCTTCCTGATGAGATACAGAGAAGTATGCCAACT
66 GAGAAGCGAATGGAAACAAGTAAGACGGCTATCTTCCTGATGAGATACAGAGAAGTATGCCAACT
* *
28521040 CGAGGCTCAATACCAGCAAATCTTCAAATCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGT
131 CGAGGCTCAATACCAGCAAATCTTCAAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGA
* * * * *
28521105 AGCAATAAAATGGTTAGCTTCCTCATGAGATATTGGGAAGTGGACCAAATTCGTGTTCCTAGTGA
196 AGCAATAAAATGGTTAGCTCCCTCATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTAGTGA
* ** *
28521170 GATACAGAGAAGCGAATTGAAACAAGTGAGGCAGTCATCTTCCTGATGAGATACAAAGAAGTATG
261 GATACAAAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACAAAGAAGTATG
28521235 CCAACTCGAGGCTCAATACGAGCAAATCTTCGAACCCCAA
326 CCAACTCGAGGCTCAATACGAGCAAATCTTCGAACCCCAA
*
28521275 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGAAATAAAATGATTAGCTTCCTGATGAGATACA
1 CTTCCTGATGAGACACTGAGAAGCAGGTCAAAGAAATAAAATGATTAGCTTCCTGATGAGATACA
*
28521340 GAGAAGCGAATGGAAACAAGTAAGGCGGCTATCTTCCTGATGAGATACAGAGAAGTATGCCAACT
66 GAGAAGCGAATGGAAACAAGTAAGACGGCTATCTTCCTGATGAGATACAGAGAAGTATGCCAACT
* * *
28521405 CGAGGCTCAATACGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGA
131 CGAGGCTCAATACCAGCAAATCTTCAAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGA
*
28521470 AGCAATAAAATGGTTAGCTCCCTGATGAGATACTGAGAAGCGGACCAAATTCGTCTTCC-AGATG
196 AGCAATAAAATGGTTAGCTCCCTCATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTAG-TG
28521534 AGATACAAAGAAGCGAATTGAAACAAACGACGC-GATCATCTTCCTGATGAGA
260 AGATACAAAGAAGCGAATTGAAACAAACGACGCAG-TCATCTTCCTGATGAGA
28521586 CACTGAGAAG
Statistics
Matches: 288, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
364 3 0.01
365 285 0.99
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.21
Consensus pattern (365 bp):
CTTCCTGATGAGACACTGAGAAGCAGGTCAAAGAAATAAAATGATTAGCTTCCTGATGAGATACA
GAGAAGCGAATGGAAACAAGTAAGACGGCTATCTTCCTGATGAGATACAGAGAAGTATGCCAACT
CGAGGCTCAATACCAGCAAATCTTCAAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGA
AGCAATAAAATGGTTAGCTCCCTCATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTAGTGA
GATACAAAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACAAAGAAGTATG
CCAACTCGAGGCTCAATACGAGCAAATCTTCGAACCCCAA
Found at i:28522034 original size:17 final size:17
Alignment explanation
Indices: 28522012--28522046 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28522002 TTGAGTTTGG
28522012 ATTTATCTTAAAATTAA
1 ATTTATCTTAAAATTAA
* *
28522029 ATTTATTTTTAAATTAA
1 ATTTATCTTAAAATTAA
28522046 A
1 A
28522047 ATTAAATCAA
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTATCTTAAAATTAA
Found at i:28523789 original size:29 final size:29
Alignment explanation
Indices: 28523747--28523970 Score: 143
Period size: 29 Copynumber: 7.7 Consensus size: 29
28523737 TAAGCTGTCC
** **
28523747 AAAAATTGTATTTTGACCCCCGAACTTCT
1 AAAAATTCCATTTTGACCCCAAAACTTCT
*
28523776 AAAAATTCCATTTTAACCCCAAAACTTCT
1 AAAAATTCCATTTTGACCCCAAAACTTCT
* * * *
28523805 AAAACTTACAGTTTTG-CCCTCGAAACTTCC
1 AAAAATTCCA-TTTTGACCC-CAAAACTTCT
* * ***
28523835 AAAAATTACATTTTTACCCTTGAACTTC-
1 AAAAATTCCATTTTGACCCCAAAACTTCT
* *
28523863 CAAAATTCCATTTTTTACCCCAAAACTT-T
1 AAAAATTCCA-TTTTGACCCCAAAACTTCT
** * **
28523892 CAAAAATTATATTTTTACCCTTAAACTTCT
1 -AAAAATTCCATTTTGACCCCAAAACTTCT
* *
28523922 AAAAGTTTCATTTTTGACCCCAAAACTTGC-
1 AAAAATTCCA-TTTTGACCCCAAAACTT-CT
28523952 AAAAATTACCATTTT-ACCC
1 AAAAATT-CCATTTTGACCC
28523971 TCGAATGTCA
Statistics
Matches: 152, Mismatches: 33, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
28 8 0.05
29 85 0.56
30 56 0.37
31 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAAATTCCATTTTGACCCCAAAACTTCT
Found at i:28523900 original size:58 final size:59
Alignment explanation
Indices: 28523757--28523971 Score: 220
Period size: 59 Copynumber: 3.7 Consensus size: 59
28523747 AAAAATTGTA
** * * * ** * * * *
28523757 TTTTGACCCCCGAACTTCTAAAAATTCCATTTTAACCCCAAAACTTCTAAAACTTACAG
1 TTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCTTAAACTTCCAAAAGTTCCAT
* *
28523816 TTTTG-CCCTCGAAACTTCCAAAAATTACATTTTTACCCTTGAACTTCCAAAA-TTCCAT
1 TTTTGACCC-CAAAACTTCCAAAAATTACATTTTTACCCTTAAACTTCCAAAAGTTCCAT
* * * * *
28523874 TTTTTACCCCAAAACTTTCAAAAATTATATTTTTACCCTTAAACTTCTAAAAGTTTCAT
1 TTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCTTAAACTTCCAAAAGTTCCAT
*
28523933 TTTTGACCCCAAAACTTGCAAAAATTACCA-TTTTACCCT
1 TTTTGACCCCAAAACTTCCAAAAATTA-CATTTTTACCCT
28523972 CGAATGTCAA
Statistics
Matches: 131, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
58 49 0.37
59 81 0.62
60 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (59 bp):
TTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCTTAAACTTCCAAAAGTTCCAT
Found at i:28525290 original size:24 final size:25
Alignment explanation
Indices: 28525258--28525304 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28525248 TAAATAATTA
28525258 TAAAAG-AAAAAAAAGAAAGAAAAG
1 TAAAAGAAAAAAAAAGAAAGAAAAG
* *
28525282 TAAAGGAAAAAAAAATAAAGAAA
1 TAAAAGAAAAAAAAAGAAAGAAA
28525305 GGATATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (25 bp):
TAAAAGAAAAAAAAAGAAAGAAAAG
Found at i:28541536 original size:49 final size:49
Alignment explanation
Indices: 28541407--28541739 Score: 207
Period size: 49 Copynumber: 6.8 Consensus size: 49
28541397 TCATTACCAT
* * *
28541407 GAAGACATGAAGGGGAAGATTTAAGCCGCAACGGCGAATCC-GGTACCACA
1 GAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTTGTACCTCA
* * * *
28541457 -AAGATAATGGACGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCA
1 GAAG--CATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCA
** * *
28541507 GAAGCATGAAGGGAAAGATTTAAGCCGCAACAACGAATCTAGTA-C-CA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCA
* * * * * * *
28541554 TGAAG-ATACAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTATATCTCA
1 -GAAGCAT--GAAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCA
* * * * *
28541605 GAAGCGA-GAAGTGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCAC-
1 GAAGC-ATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCA
* * * * ** *
28541653 GAAG-ATACAAAGGGAAAGGTTTAAGTCACAACTACGAGCCTTGTACCTCA
1 GAAGCAT--GAAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCA
* * *
28541703 G-AGACATGAAAGGAAAAATTTAAGCCGCAACAGCGAA
1 GAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAA
28541740 TTTAGTACCA
Statistics
Matches: 210, Mismatches: 57, Indels: 33
0.70 0.19 0.11
Matches are distributed among these distances:
46 1 0.00
47 4 0.02
48 9 0.04
49 147 0.70
50 41 0.20
51 7 0.03
52 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (49 bp):
GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCA
Found at i:28541607 original size:98 final size:99
Alignment explanation
Indices: 28541407--28541749 Score: 410
Period size: 98 Copynumber: 3.5 Consensus size: 99
28541397 TCATTACCAT
* * ** * * *
28541407 GAAGACATGAAGGGGAAGATTTAAGCCGCAACGGCGAATCCGGTACCACAAAGATA-ATGGACGG
1 GAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCTAGTACCACGAAGATACA--AAGGG
* * *
28541471 AAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCA
64 AAAGGTTTAAGTCGCAATGACGAACCTTGTACCTCA
* *
28541507 GAAG-CATGAAGGGAAAGATTTAAGCCGCAACAACGAATCTAGTACCATGAAGATACAAAGGGAA
1 GAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCTAGTACCACGAAGATACAAAGGGAA
* *
28541571 AGGTTTAAGTCGCAATGACGAACCTTATATCTCA
66 AGGTTTAAGTCGCAATGACGAACCTTGTACCTCA
* * *
28541605 GAAG-CGA-GAAGTGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCACGAAGATACAAAGGGA
1 GAAGAC-ATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCTAGTACCACGAAGATACAAAGGGA
* *
28541668 AAGGTTTAAGTCACAACT-ACGAGCCTTGTACCTCA
65 AAGGTTTAAGTCGCAA-TGACGAACCTTGTACCTCA
* * *
28541703 G-AGACATGAAAGGAAAAATTTAAGCCGCAACAGCGAATTTAGTACCA
1 GAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCTAGTACCA
28541750 TGCAAACACG
Statistics
Matches: 209, Mismatches: 29, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
97 3 0.01
98 155 0.74
99 46 0.22
100 5 0.02
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (99 bp):
GAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCTAGTACCACGAAGATACAAAGGGAA
AGGTTTAAGTCGCAATGACGAACCTTGTACCTCA
Found at i:28546673 original size:18 final size:18
Alignment explanation
Indices: 28546650--28546717 Score: 59
Period size: 20 Copynumber: 3.7 Consensus size: 18
28546640 ATGAAAGAAT
28546650 TAATAAAATAAAAAAACA
1 TAATAAAATAAAAAAACA
* *
28546668 TAATAAAATGATAAAAATCT
1 TAATAAAAT-A-AAAAAACA
* *
28546688 TAAAAAAATAAAAGTAA-A
1 TAATAAAATAAAA-AAACA
28546706 -AATAAAATAAAA
1 TAATAAAATAAAA
28546718 TGACTTAGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
17 11 0.28
18 12 0.30
19 3 0.08
20 14 0.35
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
TAATAAAATAAAAAAACA
Found at i:28546821 original size:2 final size:2
Alignment explanation
Indices: 28546814--28546838 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28546804 ATTCAAAGTA
28546814 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28546839 AAAAGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28548550 original size:42 final size:42
Alignment explanation
Indices: 28548491--28548927 Score: 382
Period size: 40 Copynumber: 10.9 Consensus size: 42
28548481 GAGATGGTAG
*
28548491 CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGATGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
*
28548533 CTTCAATCTGCCCCATGATCGGGATAAGAGATTGGATGATGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
** * **
28548575 CTTCAAGATGCCCTATGATTAGGGTAAGAGATTGGATG--G-
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* *
28548614 CTTCAATCTGCCCTATGGTC-GGGTAAGAGATTGGATGATGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* *
28548655 CTTCAATTTGCCCCATGATCGGGGTAAGAGATT--A-GATGG
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* *
28548694 CTTCAATCTACCCCGTGATCGGGGTAAGAGATTGG-TG-TGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* ** *
28548734 CTTCAATCTACCCTC-TGATTAGGGTAAAAGATTGGAT-A---
1 CTTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGATGATGT
* *
28548772 CTTTAATCTGCCCCATGATCAGGGTAAGAGATTGG-TG-TGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * ** * *** *
28548812 ATTCAATATGCTTTC-TAATTAAGGTAAAAGATTGGATGAT-T
1 CTTCAATCTGC-CCCATGATCGGGGTAAGAGATTGGATGATGT
**
28548853 -TT--ATCTGCCCCATGATCTAGGTAAGAGATTGG-TGCA--T
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG-ATGT
* * *
28548890 CTTCAATCAGCCCCATGGTCGGGGTAGGAGATTGGATG
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG
28548928 CCTTCACTCT
Statistics
Matches: 323, Mismatches: 48, Indels: 49
0.77 0.11 0.12
Matches are distributed among these distances:
37 6 0.02
38 70 0.22
39 50 0.15
40 86 0.27
41 26 0.08
42 85 0.26
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (42 bp):
CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
Found at i:28548667 original size:80 final size:79
Alignment explanation
Indices: 28548512--28548939 Score: 400
Period size: 78 Copynumber: 5.4 Consensus size: 79
28548502 CCCATGATCG
28548512 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC-GGGATAAGAGATTGGATGATGTC
1 GGGTAAGAGATTGGATG--G-CTTCAATCTGCCCCATGATCAGGG-TAAGAGATTGG-TG-TGTC
*
28548576 TTCAAGATGCCCTATGATTA
60 TTCAATATGCCCTATGATTA
* *
28548596 GGGTAAGAGATTGGATGGCTTCAATCTGCCCTATGGTC-GGGTAAGAGATTGGATGATGTCTTCA
1 GGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGG-TG-TGTCTTCA
* * **
28548660 ATTTGCCCCATGATCG
64 ATATGCCCTATGATTA
* * * *
28548676 GGGTAAGAGATTAGATGGCTTCAATCTACCCCGTGATCGGGGTAAGAGATTGGTGTGTCTTCAAT
1 GGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGTGTGTCTTCAAT
* * *
28548741 CTACCCTCTGATTA
66 ATGCCCTATGATTA
* * * *
28548755 GGGTAAAAGATTGGAT-ACTTTAATCTGCCCCATGATCAGGGTAAGAGATTGGTGTGTATTCAAT
1 GGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGTGTGTCTTCAAT
** * *
28548819 ATGCTTTCTAATTA
66 ATGCCCTATGATTA
* * * ** **
28548833 AGGTAAAAGATTGGAT-GATTTTATCTGCCCCATGATCTA-GGTAAGAGATTGGTGCATCTTCAA
1 GGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATC-AGGGTAAGAGATTGGTGTGTCTTCAA
* * **
28548896 TCA-GCCCCATGGTCG
65 T-ATGCCCTATGATTA
* * *
28548911 GGGTAGGAGATTGGATGCCTTCACTCTGC
1 GGGTAAGAGATTGGATGGCTTCAATCTGC
28548940 TCTACTGCAG
Statistics
Matches: 286, Mismatches: 54, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
78 123 0.43
79 41 0.14
80 69 0.24
81 35 0.12
82 1 0.00
84 17 0.06
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (79 bp):
GGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGTGTGTCTTCAAT
ATGCCCTATGATTA
Found at i:28549170 original size:49 final size:49
Alignment explanation
Indices: 28549113--28549711 Score: 367
Period size: 49 Copynumber: 12.2 Consensus size: 49
28549103 CGACCACAAT
* *
28549113 CTTTCCCTTCACATCTCTA-GGT-CATAGGGTTCGTCGTTGCAGCTTCGAC
1 CTTTCCCTTCACATCTCTATGGTACA-A-GATTCGTCGTTGCAGCTTCAAC
* * * *
28549162 CTTTCCCTTCACGTCTCTATGGTACAAGATTCGCCGTTGCAACTTCAAT
1 CTTTCCCTTCACATCTCTATGGTACAAGATTCGTCGTTGCAGCTTCAAC
* * * * * * *
28549211 CTTTCCCATCATATCTCTAAGGTACAAGGTTTG-CTATTGCGGCTTCAAC
1 CTTTCCCTTCACATCTCTATGGTACAAGATTCGTC-GTTGCAGCTTCAAC
* * * *
28549260 CTTTCCCTCCACATCTCCATGGTACAAGATTCGTCGTTAC-GACTTCAAT
1 CTTTCCCTTCACATCTCTATGGTACAAGATTCGTCGTTGCAG-CTTCAAC
* * * * * *
28549309 CTTTCCCATCACATCTCTAAT-GTACAAGGTTTGCCATTGCGGCTTCAAC
1 CTTTCCCTTCACATCTCT-ATGGTACAAGATTCGTCGTTGCAGCTTCAAC
* * * * *
28549358 CTTTCCCTCCATATCTCCATGGTACAAGATTCG-CTGTTAC-GACTTCAAT
1 CTTTCCCTTCACATCTCTATGGTACAAGATTCGTC-GTTGCAG-CTTCAAC
* * * * * * * * *
28549407 CTTTCCCATCACATCTCTAAGGTACAAGGTTTGCCATTGCGGCTTCCAT
1 CTTTCCCTTCACATCTCTATGGTACAAGATTCGTCGTTGCAGCTTCAAC
* * * * *
28549456 ATTTCCCTCCATATCTCCATGGTACAAGATTCG-CTGTTGC-GACTTCAAT
1 CTTTCCCTTCACATCTCTATGGTACAAGATTCGTC-GTTGCAG-CTTCAAC
* * * * * * * * *
28549505 ATTTCCCATCACGTCTTTAAGGTACAAGGTTTGCCGTTGCGGCTTCAAC
1 CTTTCCCTTCACATCTCTATGGTACAAGATTCGTCGTTGCAGCTTCAAC
* * * * *
28549554 CTTTCCCTCCATATCTCCATGGTATAAGATTCG-CTGTTGC-GACTTCAAT
1 CTTTCCCTTCACATCTCTATGGTACAAGATTCGTC-GTTGCAG-CTTCAAC
* * * * * *
28549603 CTTTCTCATCACGTCTCTAAGGTACAAGGTTTGTCGTTGC-GACTTCAAC
1 CTTTCCCTTCACATCTCTATGGTACAAGATTCGTCGTTGCAG-CTTCAAC
* * * * * * * * *
28549652 ATTTCCCTCCATATCTCTAAGGTACTAGATTTGTAGTTGCGGCTTCAAT
1 CTTTCCCTTCACATCTCTATGGTACAAGATTCGTCGTTGCAGCTTCAAC
28549701 CTTTCCCTTCA
1 CTTTCCCTTCA
28549712 AACCTGTAGG
Statistics
Matches: 421, Mismatches: 109, Indels: 40
0.74 0.19 0.07
Matches are distributed among these distances:
48 10 0.02
49 395 0.94
50 14 0.03
51 2 0.00
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.35
Consensus pattern (49 bp):
CTTTCCCTTCACATCTCTATGGTACAAGATTCGTCGTTGCAGCTTCAAC
Found at i:28549266 original size:98 final size:98
Alignment explanation
Indices: 28549109--28549707 Score: 801
Period size: 98 Copynumber: 6.1 Consensus size: 98
28549099 ATCACGACCA
* * * * * * *
28549109 CAATCTTTCCCTTCACATCTCT-AGGT-CATAGGGTTCGTCGTTGCAGCTTCGACCTTTCCCTTC
1 CAATCTTTCCCATCACATCTCTAAGGTACA-A-GGTTTGCCATTGCGGCTTCAACCTTTCCCTCC
** * * *
28549172 ACGTCTCTATGGTACAAGATTCGCCGTTGCAACTT
64 ATATCTCCATGGTACAAGATTCGCTGTTGCGACTT
* * *
28549207 CAATCTTTCCCATCATATCTCTAAGGTACAAGGTTTGCTATTGCGGCTTCAACCTTTCCCTCCAC
1 CAATCTTTCCCATCACATCTCTAAGGTACAAGGTTTGCCATTGCGGCTTCAACCTTTCCCTCCAT
*
28549272 ATCTCCATGGTACAAGATTCG-TCGTTACGACTT
66 ATCTCCATGGTACAAGATTCGCT-GTTGCGACTT
*
28549305 CAATCTTTCCCATCACATCTCTAATGTACAAGGTTTGCCATTGCGGCTTCAACCTTTCCCTCCAT
1 CAATCTTTCCCATCACATCTCTAAGGTACAAGGTTTGCCATTGCGGCTTCAACCTTTCCCTCCAT
*
28549370 ATCTCCATGGTACAAGATTCGCTGTTACGACTT
66 ATCTCCATGGTACAAGATTCGCTGTTGCGACTT
* **
28549403 CAATCTTTCCCATCACATCTCTAAGGTACAAGGTTTGCCATTGCGGCTTCCATATTTCCCTCCAT
1 CAATCTTTCCCATCACATCTCTAAGGTACAAGGTTTGCCATTGCGGCTTCAACCTTTCCCTCCAT
28549468 ATCTCCATGGTACAAGATTCGCTGTTGCGACTT
66 ATCTCCATGGTACAAGATTCGCTGTTGCGACTT
* * * *
28549501 CAATATTTCCCATCACGTCTTTAAGGTACAAGGTTTGCCGTTGCGGCTTCAACCTTTCCCTCCAT
1 CAATCTTTCCCATCACATCTCTAAGGTACAAGGTTTGCCATTGCGGCTTCAACCTTTCCCTCCAT
*
28549566 ATCTCCATGGTATAAGATTCGCTGTTGCGACTT
66 ATCTCCATGGTACAAGATTCGCTGTTGCGACTT
* * * * * *
28549599 CAATCTTTCTCATCACGTCTCTAAGGTACAAGGTTTGTCGTTGCGACTTCAACATTTCCCTCCAT
1 CAATCTTTCCCATCACATCTCTAAGGTACAAGGTTTGCCATTGCGGCTTCAACCTTTCCCTCCAT
* * * * *
28549664 ATCTCTAAGGTACTAGATTTG-TAGTTGCGGCTT
66 ATCTCCATGGTACAAGATTCGCT-GTTGCGACTT
28549697 CAATCTTTCCC
1 CAATCTTTCCC
28549708 TTCAAACCTG
Statistics
Matches: 452, Mismatches: 44, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
97 1 0.00
98 443 0.98
99 6 0.01
100 2 0.00
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.35
Consensus pattern (98 bp):
CAATCTTTCCCATCACATCTCTAAGGTACAAGGTTTGCCATTGCGGCTTCAACCTTTCCCTCCAT
ATCTCCATGGTACAAGATTCGCTGTTGCGACTT
Found at i:28551527 original size:5 final size:5
Alignment explanation
Indices: 28551517--28551564 Score: 73
Period size: 5 Copynumber: 9.8 Consensus size: 5
28551507 TTTTCTTCCT
28551517 TTTTC TTTTC TTCTTC TTTTC TTTTC TTTTC TTTTC TTTT- TTTT- TTTT
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
28551565 AAAAAAAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.19
5 29 0.69
6 5 0.12
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:28551621 original size:16 final size:15
Alignment explanation
Indices: 28551602--28551656 Score: 78
Period size: 16 Copynumber: 3.7 Consensus size: 15
28551592 TCATCTTGAC
28551602 TTTCTTTTTTCTTCCT
1 TTTCTTTTTTCTT-CT
28551618 TTTCTTTTCTTCTTCT
1 TTTCTTTT-TTCTTCT
28551634 TTTCTTTTTTCTT-T
1 TTTCTTTTTTCTTCT
28551648 TTT-TTTTTT
1 TTTCTTTTTT
28551657 TAAAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.16
14 4 0.11
15 5 0.13
16 18 0.47
17 5 0.13
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTTTTTTCTTCT
Found at i:28551657 original size:7 final size:7
Alignment explanation
Indices: 28551602--28551656 Score: 67
Period size: 7 Copynumber: 7.4 Consensus size: 7
28551592 TCATCTTGAC
28551602 TTTCTTT
1 TTTCTTT
28551609 TTTCTTCCT
1 TTTCTT--T
28551618 TTTCTTT
1 TTTCTTT
28551625 TCTTCTTCT
1 T-TTCTT-T
28551634 TTTCTTT
1 TTTCTTT
28551641 TTTCTTT
1 TTTCTTT
28551648 TTT-TTT
1 TTTCTTT
28551654 TTT
1 TTT
28551657 TAAAAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
6 6 0.14
7 19 0.43
8 10 0.23
9 9 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTCTTT
Found at i:28551682 original size:93 final size:95
Alignment explanation
Indices: 28551471--28551737 Score: 405
Period size: 93 Copynumber: 2.8 Consensus size: 95
28551461 ATAGATTTTC
28551471 AAGATGCCCTTTGCGGGTTTTCATCTTGACTTTCTTTTTTCTTCCTTTTTCTTTTCTTCTTCTTT
1 AAGATGCCCTTTGCGGGTTTTCATCTTGACTTTCTTTTTTCTTCC-TTTTCTTTTCTTCTTCTTT
28551536 TCTTTTCTTTTCTTTTCTTTTTTTTTTTTAAAAAAA
65 TC--TT-TTTTC--TTCTTTTTTTTTTTTAAAAAAA
28551572 AAGATGCCCTTTGCGGGTTTTCATCTTGACTTTCTTTTTTCTTCCTTTTCTTTTCTTCTTCTTTT
1 AAGATGCCCTTTGCGGGTTTTCATCTTGACTTTCTTTTTTCTTCCTTTTCTTTTCTTCTTCTTTT
28551637 CTTTTTTC-T-TTTTTTTTTTTTAAAAAAA
66 CTTTTTTCTTCTTTTTTTTTTTTAAAAAAA
* * *
28551665 AAGATGCCCTTTGCGGGTTTTCATCTTAACTTT-TTCTTTCTTTTCTTTTCTTTTCTTCTTCTTC
1 AAGATGCCCTTTGCGGGTTTTCATCTTGACTTTCTTTTTTC-TTCCTTTTCTTTTCTTCTTCTT-
*
28551729 TTTTTTTTT
64 TTCTTTTTT
28551738 GATCTCCTCT
Statistics
Matches: 160, Mismatches: 4, Indels: 11
0.91 0.02 0.06
Matches are distributed among these distances:
92 6 0.04
93 72 0.45
94 9 0.06
97 5 0.03
98 2 0.01
100 21 0.13
101 45 0.28
ACGTcount: A:0.11, C:0.19, G:0.07, T:0.62
Consensus pattern (95 bp):
AAGATGCCCTTTGCGGGTTTTCATCTTGACTTTCTTTTTTCTTCCTTTTCTTTTCTTCTTCTTTT
CTTTTTTCTTCTTTTTTTTTTTTAAAAAAA
Found at i:28551713 original size:14 final size:13
Alignment explanation
Indices: 28551696--28551735 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
28551686 CATCTTAACT
28551696 TTTTCTTTCTTTTC
1 TTTTCTTT-TTTTC
*
28551710 TTTTCTTTTCTTC
1 TTTTCTTTTTTTC
28551723 TTCTTCTTTTTTT
1 TT-TTCTTTTTTT
28551736 TTGATCTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:28551737 original size:19 final size:19
Alignment explanation
Indices: 28551695--28551737 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28551685 TCATCTTAAC
28551695 TTTTTCTTTCTTTTCTTTT
1 TTTTTCTTTCTTTTCTTTT
*
28551714 CTTTTC-TTCTTCTTCTTTT
1 TTTTTCTTTCTT-TTCTTTT
28551733 TTTTT
1 TTTTT
28551738 GATCTCCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTCTTTCTTTTCTTTT
Found at i:28557587 original size:9 final size:9
Alignment explanation
Indices: 28557575--28557599 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28557565 TAATTTTGTG
28557575 TATTTATTT
1 TATTTATTT
28557584 TATTTATTT
1 TATTTATTT
28557593 TATTTAT
1 TATTTAT
28557600 GTTTGGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TATTTATTT
Found at i:28559166 original size:95 final size:95
Alignment explanation
Indices: 28558985--28559253 Score: 299
Period size: 95 Copynumber: 2.8 Consensus size: 95
28558975 AAAACAATGT
*
28558985 TTAAGATCCTGCATATATTGTGAATTCTTCATAGCTCATGTGAGTAGCATCGTGTAAC-AGTTAA
1 TTAAGATCCTGCATATGTTGTGAATTCTTCATAGCTCATGTGAGTAGCATCGTGTAACGA-TTAA
* * * * *
28559049 TATCCTGATTTATTGGGTACCTTACTGATGG
65 TGTCCCGATTTACTGGGTACCTTACCGATGA
* *
28559080 TTAAGATCCTGCATATGTTGTGGATTCTTCATAGCTCATGTGAGCAGCATCGTGTAACGATTAAT
1 TTAAGATCCTGCATATGTTGTGAATTCTTCATAGCTCATGTGAGTAGCATCGTGTAACGATTAAT
*
28559145 GTCCCGATTTACTGGAG-ACCTTTCCGATGA
66 GTCCCGATTTACTGG-GTACCTTACCGATGA
* * * *** * ** ** *
28559175 CTAAGATTCTGCATGTGTTACAAATTCTTCACAGCTTGTGTGAGTAGCATTATGTAACGATTAGT
1 TTAAGATCCTGCATATGTTGTGAATTCTTCATAGCTCATGTGAGTAGCATCGTGTAACGATTAAT
* *
28559240 GTCTCAATTTACTG
66 GTCCCGATTTACTG
28559254 AATACCTTGT
Statistics
Matches: 147, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
95 145 0.99
96 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.36
Consensus pattern (95 bp):
TTAAGATCCTGCATATGTTGTGAATTCTTCATAGCTCATGTGAGTAGCATCGTGTAACGATTAAT
GTCCCGATTTACTGGGTACCTTACCGATGA
Found at i:28559261 original size:95 final size:95
Alignment explanation
Indices: 28559103--28559302 Score: 240
Period size: 95 Copynumber: 2.1 Consensus size: 95
28559093 TATGTTGTGG
* * * *
28559103 ATTCTTCATAGCTCATGTGAGCAGCATCGTGTAACGATTAATGTCCCGATTTACTGGAGACCTT-
1 ATTCTTCACAGCTCATGTGAGCAGCATCATGTAACGATTAATGTCCCAATTTACTGAAGACCTTG
*
28559167 TCCGATGACTAAGATTCTGCATGTGTTACAA
66 T-CGATGACTAAGATTCTACATGTGTTACAA
** * * * * *
28559198 ATTCTTCACAGCTTGTGTGAGTAGCATTATGTAACGATTAGTGTCTCAATTTACTGAATACCTTG
1 ATTCTTCACAGCTCATGTGAGCAGCATCATGTAACGATTAATGTCCCAATTTACTGAAGACCTTG
* * * *
28559263 TCGATGGCTAAGATTCTATATGTGTTGCGA
66 TCGATGACTAAGATTCTACATGTGTTACAA
28559293 ATTCTTCACA
1 ATTCTTCACA
28559303 ATTCATGTTT
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
95 87 0.99
96 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (95 bp):
ATTCTTCACAGCTCATGTGAGCAGCATCATGTAACGATTAATGTCCCAATTTACTGAAGACCTTG
TCGATGACTAAGATTCTACATGTGTTACAA
Found at i:28559360 original size:25 final size:25
Alignment explanation
Indices: 28559327--28559378 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
28559317 CATCATTATT
*
28559327 TTTTGATTCACAGCTCGTGTGAGCA
1 TTTTCATTCACAGCTCGTGTGAGCA
* *
28559352 TTTTCATTCACATCTTGTGTGAGCA
1 TTTTCATTCACAGCTCGTGTGAGCA
28559377 TT
1 TT
28559379 ACTATCCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (25 bp):
TTTTCATTCACAGCTCGTGTGAGCA
Found at i:28561382 original size:28 final size:29
Alignment explanation
Indices: 28561345--28561413 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
28561335 ACAGAGACAA
* * * *
28561345 CCACAAAGGCTTTCCTTTGAG-AGGTTCG
1 CCACAAAGGCTTACCTTTCAGTAGATTAG
*
28561373 CCACAAAGGCTTACCTTTCCGTAGATTAG
1 CCACAAAGGCTTACCTTTCAGTAGATTAG
28561402 CCACAAAGGCTT
1 CCACAAAGGCTT
28561414 CTTTTTAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 18 0.51
29 17 0.49
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (29 bp):
CCACAAAGGCTTACCTTTCAGTAGATTAG
Found at i:28563154 original size:17 final size:17
Alignment explanation
Indices: 28563132--28563165 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28563122 TACATATGCA
*
28563132 TACATGCATTTCATTTT
1 TACATGCATTTAATTTT
28563149 TACATGCATTTAATTTT
1 TACATGCATTTAATTTT
28563166 AAGAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (17 bp):
TACATGCATTTAATTTT
Found at i:28565028 original size:22 final size:22
Alignment explanation
Indices: 28564984--28565030 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
28564974 ATTTTCTGCC
*
28564984 TCATTTGACAAATATCTTAAAT
1 TCATTTGACAAACATCTTAAAT
* *
28565006 TCATTTGACAAACATTTTCAAT
1 TCATTTGACAAACATCTTAAAT
28565028 TCA
1 TCA
28565031 CACATTACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40
Consensus pattern (22 bp):
TCATTTGACAAACATCTTAAAT
Found at i:28565122 original size:28 final size:28
Alignment explanation
Indices: 28565064--28565122 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
28565054 AATTCATTTG
* * **
28565064 TTCTTGTTCAATTTGACAAATATTTTTA
1 TTCTTGTCCAAATTGACAAATATTTCCA
28565092 TTCTTGTCCAAATTGACAAA-ATGTTCCA
1 TTCTTGTCCAAATTGACAAATAT-TTCCA
28565120 TTC
1 TTC
28565123 ATTCATACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (28 bp):
TTCTTGTCCAAATTGACAAATATTTCCA
Found at i:28566387 original size:22 final size:22
Alignment explanation
Indices: 28566360--28566443 Score: 107
Period size: 22 Copynumber: 3.8 Consensus size: 22
28566350 GCAATAATAG
* * *
28566360 GCACACAAAGTGCTAAACAAAA
1 GCACACACAGTGCTGAACAGAA
*
28566382 GCACACGC-GATGCTGAACAGAA
1 GCACACACAG-TGCTGAACAGAA
*
28566404 GCACACACAGTGCTGAACAGAG
1 GCACACACAGTGCTGAACAGAA
28566426 GCACACACAGTGCTGAAC
1 GCACACACAGTGCTGAAC
28566444 CGAGGGCACG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
21 1 0.02
22 52 0.96
23 1 0.02
ACGTcount: A:0.40, C:0.27, G:0.23, T:0.10
Consensus pattern (22 bp):
GCACACACAGTGCTGAACAGAA
Found at i:28570196 original size:45 final size:44
Alignment explanation
Indices: 28570128--28570438 Score: 303
Period size: 45 Copynumber: 7.0 Consensus size: 44
28570118 TACAACACCG
28570128 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGATACGA
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGATAC-A
* * * * ** *
28570173 TCTAATCTTTTACCCCTAATCAAGA-GGGAAAATTGAAGCCACCG
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGATA-CA
*
28570217 TCCAATCTTTTACCCCTAGCCAAGAGGGGCAGATTGAAGCCAT-CA
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAG--ATACA
* *
28570262 TCCAAT-TGTTTACCCCTAGTCAAGAGGGGCAAATTGAATATACCA
1 TCCAATCT-TTTACCCCTAGTCAAGAGGGGCAGATTGAAGATA-CA
* *
28570307 TCCAATCTTTTACCTCTAGTCAAGAGGGGCAGATTTAAGGCAT-CA
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAA-G-ATACA
* * * **
28570352 TCCAATCTCTTACCCCGA-TC-ATA-GGGCAGATTGAAGCCACCA
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGATA-CA
** *
28570394 TCCAATCTTTTACCATTAAGTCAAGAGGGGCAGATTGAAGTTACA
1 TCCAATCTTTTACCCCT-AGTCAAGAGGGGCAGATTGAAGATACA
28570439 ATCTCACAGA
Statistics
Matches: 214, Mismatches: 36, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.00
42 26 0.12
43 5 0.02
44 39 0.18
45 126 0.59
46 15 0.07
47 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (44 bp):
TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGATACA
Found at i:28570351 original size:90 final size:88
Alignment explanation
Indices: 28570123--28570433 Score: 378
Period size: 90 Copynumber: 3.5 Consensus size: 88
28570113 GAAGTTACAA
* *
28570123 CACCGTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAA-G-ATACGATCTAATCTTTTAC
1 CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGGCAT-C-ATCCAATCTTTTAC
*
28570186 CCCTAATCAAGAGGGAAAATTGAAGC
64 CCCT-ATCAAGAGGGCAAATTGAAGC
* * *
28570212 CACCGTCCAATCTTTTACCCCTAGCCAAGAGGGGCAGATTGAAGCCATCATCCAAT-TGTTTACC
1 CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGGCATCATCCAATCT-TTTACC
**
28570276 CCTAGTCAAGAGGGGCAAATTGAATA
65 CCTA-TCAAGA-GGGCAAATTGAAGC
* * * *
28570302 TACCATCCAATCTTTTACCTCTAGTCAAGAGGGGCAGATTTAAGGCATCATCCAATCTCTTACCC
1 CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGGCATCATCCAATCTTTTACCC
* * *
28570367 CGATC-ATAGGGCAGATTGAAGC
66 CTATCAAGAGGGCAAATTGAAGC
**
28570389 CACCATCCAATCTTTTACCATTAAGTCAAGAGGGGCAGATTGAAG
1 CACCATCCAATCTTTTACCCCT-AGTCAAGAGGGGCAGATTGAAG
28570434 TTACAATCTC
Statistics
Matches: 193, Mismatches: 22, Indels: 15
0.84 0.10 0.07
Matches are distributed among these distances:
87 30 0.16
88 25 0.13
89 65 0.34
90 70 0.36
91 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (88 bp):
CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGGCATCATCCAATCTTTTACCC
CTATCAAGAGGGCAAATTGAAGC
Found at i:28570884 original size:17 final size:17
Alignment explanation
Indices: 28570862--28570897 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28570852 GCCCAAGGAT
* *
28570862 AAAATAAACCAAAATAA
1 AAAATAAAACAAAACAA
28570879 AAAATAAAACAAAACAA
1 AAAATAAAACAAAACAA
28570896 AA
1 AA
28570898 GTCCATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (17 bp):
AAAATAAAACAAAACAA
Found at i:28573185 original size:85 final size:85
Alignment explanation
Indices: 28573038--28573197 Score: 209
Period size: 85 Copynumber: 1.9 Consensus size: 85
28573028 CTTTTGGTCC
** * * *
28573038 ACTTCTCTGTATCTCATCAGGAAGATGACCATTTCATTGTCTTGATCCACTTCTTTGCATCTCAT
1 ACTTCTCTGTATCTCATCAAAAAGATGACCATTTCATTGTCTTGACCCACTTCTCTACATCTCAT
*
28573103 TAGGAAGATGGACTTGGCCT
66 CAGGAAGATGGACTTGGCCT
*
28573123 ACTTCTCTGTATCTCATCAAAAAGATGATCGC-TTT-ATTG-CTTTGACCCACTTCTCTATATCT
1 ACTTCTCTGTATCTCATCAAAAAGATGA-C-CATTTCATTGTC-TTGACCCACTTCTCTACATCT
28573185 CATCAGGAAGATG
63 CATCAGGAAGATG
28573198 AGGGCTTGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
84 1 0.02
85 59 0.91
86 4 0.06
87 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (85 bp):
ACTTCTCTGTATCTCATCAAAAAGATGACCATTTCATTGTCTTGACCCACTTCTCTACATCTCAT
CAGGAAGATGGACTTGGCCT
Found at i:28573345 original size:48 final size:49
Alignment explanation
Indices: 28573247--28573355 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 49
28573237 AATTTGGTCT
* *
28573247 ACTTC-TCTGTATCTCATCAGGAAGATGACCGCCTCATTATTTTAATCC
1 ACTTCTTCTGTATCTCATCAGGAAGATGACCGCCTCATTACTTTAACCC
** * * * *
28573295 ACTTCTTC-GTATCTCATCAGGAAGATGATTGCTTTATTGCTTTGACCC
1 ACTTCTTCTGTATCTCATCAGGAAGATGACCGCCTCATTACTTTAACCC
28573343 ACTTC-TCTGTATC
1 ACTTCTTCTGTATC
28573356 ATTAGGAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
47 2 0.04
48 47 0.92
49 2 0.04
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.39
Consensus pattern (49 bp):
ACTTCTTCTGTATCTCATCAGGAAGATGACCGCCTCATTACTTTAACCC
Found at i:28573685 original size:85 final size:85
Alignment explanation
Indices: 28573540--28573709 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 85
28573530 TCGCTTCATC
* * * * *
28573540 GATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATAACCGTCTCATTATTTTAATCCACTTCTC
1 GATTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCGTCTCATTACTTTAACCCACTTCTC
*
28573605 TATATCTCATGAGAAAGATG
66 TATATCTCATCAGAAAGATG
* * * * *
28573625 GATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACTG-CTTTATTGCTTTGACCCACTTCT
1 GATTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCGTC-TCATTACTTTAACCCACTTCT
* *
28573689 CTGTATCTCATCAGGAAGATG
65 CTATATCTCATCAGAAAGATG
28573710 AGGGTTTGAA
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
84 1 0.01
85 70 0.99
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCGTCTCATTACTTTAACCCACTTCTC
TATATCTCATCAGAAAGATG
Found at i:28573741 original size:209 final size:209
Alignment explanation
Indices: 28573381--28573991 Score: 956
Period size: 209 Copynumber: 2.9 Consensus size: 209
28573371 GTTTGATTGA
* * *
28573381 TTTAATCCACTTCTCTAAATCTCATCAGAAAGGCGGATTTGGTCCACTTCTCTATATCTCATCAA
1 TTTAATCCACTTCTCTATATCTCATCAGAAAGACGGATTTGGTCCACTTCTCTATATCTCATCAG
* * * *
28573446 GAAGATGATTGTTTTATTGTTTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTGAA
66 GAAGATGACTGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAA
*
28573511 GTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTTCTTTGTATCTCATCAGGAAGAT
131 GTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGAT
**
28573576 AACCGTCTCATTAT
196 AACCACCTCATTAT
* *
28573590 TTTAATCCACTTCTCTATATCTCATGAGAAAGATGGATTTGGTCCACTTCTCTATATCTCATCAG
1 TTTAATCCACTTCTCTATATCTCATCAGAAAGACGGATTTGGTCCACTTCTCTATATCTCATCAG
*
28573655 GAAGATGACTGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGAGGGTTTGAA
66 GAAGATGACTGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAA
*
28573720 GTTTCACTCACATTGAGCTTCGCTTCATCAATTTGGTCTACTTCTTTGTATCTCATCAAGAA-AT
131 GTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGAT
* *
28573784 GACCACCTTATTAT
196 AACCACCTCATTAT
* * * * *
28573798 TTTAATCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGTATCTCATCAG
1 TTTAATCCACTTCTCTATATCTCATCAGAAAGACGGATTTGGTCCACTTCTCTATATCTCATCAG
* * * *
28573863 GAAGATGACTGCTTTATTGCTTCGA-CCTCTTCTTTGTATCTCATCGGGAAGATGGGGGTTTGAA
66 GAAGATGACTGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAA
* * *
28573927 GTTTCACTAACATTGAGCTTTGCTTCATCGATTTGGTCTACTTCTTTGTAACTCATCAAGAAGAT
131 GTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGAT
28573992 GACTACTTCA
Statistics
Matches: 369, Mismatches: 32, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
207 93 0.25
208 96 0.26
209 180 0.49
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (209 bp):
TTTAATCCACTTCTCTATATCTCATCAGAAAGACGGATTTGGTCCACTTCTCTATATCTCATCAG
GAAGATGACTGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAA
GTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGAT
AACCACCTCATTAT
Found at i:28582222 original size:57 final size:57
Alignment explanation
Indices: 28582180--28582298 Score: 139
Period size: 57 Copynumber: 2.1 Consensus size: 57
28582170 TTTAGAGAAT
* **
28582180 TTTGAGTTAAAATGTAATTTTAGAAAAATTTAAGGGTCAAATGTAATTTTAGGAAAG
1 TTTGAGTCAAAACATAATTTTAGAAAAATTTAAGGGTCAAATGTAATTTTAGGAAAG
* * * * * * *
28582237 TTTGGGTCAAAACATGATTTTAGAAAAGTTTAGGGGTCAAAATGTGATTTTGGGTAAG
1 TTTGAGTCAAAACATAATTTTAGAAAAATTTAAGGGTC-AAATGTAATTTTAGGAAAG
28582295 TTTG
1 TTTG
28582299 GGGTTAAAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
57 31 0.61
58 20 0.39
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (57 bp):
TTTGAGTCAAAACATAATTTTAGAAAAATTTAAGGGTCAAATGTAATTTTAGGAAAG
Found at i:28582296 original size:30 final size:30
Alignment explanation
Indices: 28582188--28582397 Score: 141
Period size: 29 Copynumber: 7.2 Consensus size: 30
28582178 ATTTTGAGTT
* * * *
28582188 AAAATGTAATTTTAGAAAAATTTAAGGGTC
1 AAAATGTAATTTTGGGAAAGTTTAGGGGTC
*
28582218 -AAATGTAATTTTAGGAAAGTTT--GGGTC
1 AAAATGTAATTTTGGGAAAGTTTAGGGGTC
** * * *
28582245 AAAACATGATTTTAGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTGGGAAAGTTTAGGGGTC
* * *
28582275 AAAATGTGATTTTGGGTAAGTTT-GGGGTT
1 AAAATGTAATTTTGGGAAAGTTTAGGGGTC
*
28582304 AAAAT-TCAATTTTGGGAAAGTTTAAGGGT-
1 AAAATGT-AATTTTGGGAAAGTTTAGGGGTC
** * * *
28582333 GGAATCTAAATTTTTGGG-AAGTTTATGAGTC
1 AAAATGT-AA-TTTTGGGAAAGTTTAGGGGTC
*
28582364 -AAATTTGAATTTT-GGAAAGTTTAGGGGTC
1 AAAATGT-AATTTTGGGAAAGTTTAGGGGTC
28582393 AAAAT
1 AAAAT
28582398 ATAGTTTTTA
Statistics
Matches: 145, Mismatches: 25, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
27 5 0.03
28 21 0.14
29 62 0.43
30 50 0.34
31 7 0.05
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTGGGAAAGTTTAGGGGTC
Found at i:28582406 original size:59 final size:60
Alignment explanation
Indices: 28582261--28582406 Score: 138
Period size: 59 Copynumber: 2.5 Consensus size: 60
28582251 TGATTTTAGA
* * * *
28582261 AAAGTTTAGGGGTCAAAATGT-GATTTTGGGTAAGTTTGGGGTTAAAATTCAATTTTGGG
1 AAAGTTTAGGGGTCAAAATATAGTTTTTGGGTAAGTTTGGAGTCAAAATTCAATTTTGGG
* ** * * * * *
28582320 AAAGTTTAAGGGT-GGAATCTAAATTTTTGGG-AAGTTTATGAGTCAAATTTGAATTTT-GG
1 AAAGTTTAGGGGTCAAAATAT-AGTTTTTGGGTAAGTTT-GGAGTCAAAATTCAATTTTGGG
28582379 AAAGTTTAGGGGTCAAAATATAGTTTTT
1 AAAGTTTAGGGGTCAAAATATAGTTTTT
28582407 AAACAAAATA
Statistics
Matches: 67, Mismatches: 16, Indels: 8
0.74 0.18 0.09
Matches are distributed among these distances:
58 4 0.06
59 38 0.57
60 25 0.37
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (60 bp):
AAAGTTTAGGGGTCAAAATATAGTTTTTGGGTAAGTTTGGAGTCAAAATTCAATTTTGGG
Found at i:28583444 original size:13 final size:13
Alignment explanation
Indices: 28583428--28583461 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28583418 AATGTTTAGT
28583428 AATAAATAATAGC
1 AATAAATAATAGC
* *
28583441 AATAAATGATAGT
1 AATAAATAATAGC
28583454 AATAAATA
1 AATAAATA
28583462 TATTAATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (13 bp):
AATAAATAATAGC
Found at i:28585609 original size:23 final size:20
Alignment explanation
Indices: 28585582--28585626 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 20
28585572 CATGTTGGTA
28585582 TATTTTACTCCTTTAAATTTATT
1 TATTTTA-T-CTTTAAA-TTATT
28585605 TA-TTTATCTTTAAATTATT
1 TATTTTATCTTTAAATTATT
28585624 TAT
1 TAT
28585627 ATGCTACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.33
20 7 0.33
21 1 0.05
22 4 0.19
23 2 0.10
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTATCTTTAAATTATT
Found at i:28585742 original size:3 final size:3
Alignment explanation
Indices: 28585719--28585819 Score: 98
Period size: 3 Copynumber: 33.3 Consensus size: 3
28585709 CATAGTCCCC
* *
28585719 ATT ATC ATT ATT CATTT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT
1 ATT ATT ATT ATT -A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
28585766 TTT ATT ATT ATT ATT ATT ATT ATT -TT GTT AAT GTT ACT ATT -TAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
28585810 ATT ATT ATT A
1 ATT ATT ATT A
28585820 GTAATATTAA
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
2 3 0.04
3 72 0.90
4 3 0.04
5 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:28590599 original size:47 final size:46
Alignment explanation
Indices: 28590490--28590600 Score: 141
Period size: 47 Copynumber: 2.4 Consensus size: 46
28590480 AAGGTGGAAG
* *
28590490 TTATTGGCAGTTTATCTGTGATTTAGTGGCTTGTCCACGATATTGA
1 TTATTGGCAGTTTATTTGTGATTTAGTGGCTTGTCCACAATATTGA
* * * * *
28590536 TTATTGGCAATATATTTGTGATTTTGGTGGCTTGTCCACAATTTTTA
1 TTATTGGCAGTTTATTTGTGA-TTTAGTGGCTTGTCCACAATATTGA
*
28590583 TTATTGACAGTTTATTTG
1 TTATTGGCAGTTTATTTG
28590601 CATTACTGTG
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 18 0.33
47 36 0.67
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.48
Consensus pattern (46 bp):
TTATTGGCAGTTTATTTGTGATTTAGTGGCTTGTCCACAATATTGA
Found at i:28591765 original size:98 final size:98
Alignment explanation
Indices: 28591591--28591772 Score: 328
Period size: 98 Copynumber: 1.9 Consensus size: 98
28591581 GTGCGTCATG
* * *
28591591 AGTTAACCCATATCTTAATAAGTTCAAGATTCGTTTGCTTGATAAAGAGAATAATCACTCATTTC
1 AGTTAACCCATATCTTAACAAGTTCAAGATTCGTTCGCTTGATAAAGAGAAGAATCACTCATTTC
28591656 ACTATATACTAGTTCAAATTCTATTTCTTCACA
66 ACTATATACTAGTTCAAATTCTATTTCTTCACA
*
28591689 AGTTCACCCATATCTTAACAAGTTCAAGATTCGTTCGCTTGATAAAGAGAAGAATCACTCATTTC
1 AGTTAACCCATATCTTAACAAGTTCAAGATTCGTTCGCTTGATAAAGAGAAGAATCACTCATTTC
28591754 ACTATATACTAGTTCAAAT
66 ACTATATACTAGTTCAAAT
28591773 CCACAAGATA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 80 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (98 bp):
AGTTAACCCATATCTTAACAAGTTCAAGATTCGTTCGCTTGATAAAGAGAAGAATCACTCATTTC
ACTATATACTAGTTCAAATTCTATTTCTTCACA
Found at i:28596807 original size:20 final size:22
Alignment explanation
Indices: 28596782--28596841 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
28596772 TCTAAAAAAT
*
28596782 AAAAATAC-ATAA-ATATTTTA
1 AAAAATACAATAATAAATTTTA
28596802 AAAAATACAATAATAAATTTTA
1 AAAAATACAATAATAAATTTTA
* *
28596824 AAAATATATAAAAATAAA
1 AAAA-ATACAATAATAAA
28596842 AAATATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.24
21 4 0.12
22 11 0.32
23 11 0.32
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAATACAATAATAAATTTTA
Found at i:28596828 original size:21 final size:19
Alignment explanation
Indices: 28596781--28596838 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
28596771 TTCTAAAAAA
*
28596781 TAAAAATACATAAATATTT
1 TAAAAATACATAAAAATTT
28596800 TAAAAAATACAATAATAAATTT
1 T-AAAAATAC-ATAA-AAATTT
*
28596822 TAAAAATATATAAAAAT
1 TAAAAATACATAAAAAT
28596839 AAAAAATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 5 0.15
20 12 0.35
21 11 0.32
22 6 0.18
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAATACATAAAAATTT
Found at i:28596841 original size:16 final size:17
Alignment explanation
Indices: 28596822--28596897 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 17
28596812 TAATAAATTT
28596822 TAAAAATATAT-AAAAA
1 TAAAAATATATAAAAAA
28596838 TAAAAAATATTATTGACAAAAAA
1 T-AAAAATA-TA-T---AAAAAA
* *
28596861 TAATAATATAT-AAAAT
1 TAAAAATATATAAAAAA
*
28596877 TTAAAATATATAAAAAA
1 TAAAAATATATAAAAAA
28596894 TAAA
1 TAAA
28596898 TATTTTTGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
16 14 0.30
17 14 0.30
18 2 0.04
19 1 0.02
20 1 0.02
21 2 0.04
22 6 0.13
23 6 0.13
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (17 bp):
TAAAAATATATAAAAAA
Found at i:28596896 original size:23 final size:23
Alignment explanation
Indices: 28596857--28596902 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
28596847 TTATTGACAA
* *
28596857 AAAATAATAATATATAAA-ATTT
1 AAAATAATAAAAAATAAATATTT
28596879 AAAATATATAAAAAATAAATATTT
1 AAAATA-ATAAAAAATAAATATTT
28596903 TTGAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 10 0.50
24 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAATAATAAAAAATAAATATTT
Found at i:28597273 original size:29 final size:29
Alignment explanation
Indices: 28597241--28597306 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
28597231 AATTAATAAG
28597241 GATAAAA-TTACATTTTAACCCCTTAAAA-T
1 GATAAAATTTA-A-TTTAACCCCTTAAAACT
**
28597270 GATAAAAATTTAATTTAACCTTTTAAAACT
1 GAT-AAAATTTAATTTAACCCCTTAAAACT
28597300 GATAAAA
1 GATAAAA
28597307 ATATAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 20 0.62
30 9 0.28
31 3 0.09
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (29 bp):
GATAAAATTTAATTTAACCCCTTAAAACT
Found at i:28597680 original size:39 final size:38
Alignment explanation
Indices: 28597609--28597689 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 38
28597599 ATTTGTTGCA
*
28597609 TTTTTTGTGAAAATATTTATTTATTTTATATAT-TATT
1 TTTTTTGTCAAAATATTTATTTATTTTATATATATATT
*
28597646 GTTTTTTGTCAACAATAATTTTTTTATTTT-TATATATATT
1 -TTTTTTGTCAA-AAT-ATTTATTTATTTTATATATATATT
28597686 TTTT
1 TTTT
28597690 GAAATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
38 10 0.26
39 12 0.32
40 16 0.42
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (38 bp):
TTTTTTGTCAAAATATTTATTTATTTTATATATATATT
Found at i:28597713 original size:31 final size:29
Alignment explanation
Indices: 28597665--28597731 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
28597655 CAACAATAAT
* *
28597665 TTTTTTATTTTTATATATATTTTTTGAAA
1 TTTTTTATTTTTATATATATTTCTTAAAA
*
28597694 TTTTTTATGTATTTTTATATATTTCTTAAAA
1 TTTTTTAT-T-TTTATATATATTTCTTAAAA
*
28597725 ATTTTTA
1 TTTTTTA
28597732 GAATTAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 8 0.25
30 1 0.03
31 23 0.72
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTTTATTTTTATATATATTTCTTAAAA
Found at i:28597717 original size:21 final size:21
Alignment explanation
Indices: 28597663--28597717 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
28597653 GTCAACAATA
28597663 ATTTTTT-TATTTTTATATAT
1 ATTTTTTATATTTTTATATAT
* *
28597683 ATTTTTTGAAATTTTT-TATGT
1 ATTTTTT-ATATTTTTATATAT
28597704 ATTTTTATATATTT
1 ATTTTT-TATATTT
28597718 CTTAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 7 0.24
21 15 0.52
22 7 0.24
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
ATTTTTTATATTTTTATATAT
Found at i:28603486 original size:3 final size:3
Alignment explanation
Indices: 28603478--28603512 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28603468 AAGTAGTGGA
28603478 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28603513 AATTTGTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28604971 original size:9 final size:9
Alignment explanation
Indices: 28604954--28604989 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
28604944 ACCCATCATC
*
28604954 TCTCCCTTT
1 TCTCTCTTT
28604963 TCTCTCTTT
1 TCTCTCTTT
28604972 TCTCTCTTT
1 TCTCTCTTT
28604981 TCTCTCTTT
1 TCTCTCTTT
28604990 CTGACGAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (9 bp):
TCTCTCTTT
Found at i:28611201 original size:562 final size:561
Alignment explanation
Indices: 28609304--28611549 Score: 3918
Period size: 561 Copynumber: 4.0 Consensus size: 561
28609294 GTGTAATAAA
28609304 TACCTTGTATTGATGGATTGGAAAAACACACTTGAATTGAATTAAATACAATTATTTTCTTTTAT
1 TACCTTGTATTGATGGATTGGAAAAACACACTTGAATTGAATTAAATACAATTATTTTCTTTTAT
* *
28609369 TTCTTCCACCGTATGTAGCTTTTGGAAAAGCTTTCTGGCTTTTTATTTCATTTTCTCATTTTGGC
66 TTCTTCCATCGTATGTAGCTTTTGGAAAAGCTTTCTGGCTTTTTATTTCATTTTCTTATTTTGGC
* *
28609434 TCAATTGCTTTTTAAGTTCTTTCTCCTTTTCACGTATCACCATTACATTCAAATCCACTTTTAAA
131 TCAATTGCTTTGTAAGTTCTTTCTCCTTTTCACCTATCACCATTACATTCAAATCCACTTTTAAA
*
28609499 CCCTAATTGAGTATGATTAATTTCATGCTCATCTAATTCCCATTTAGTCTTAGGTTGGTCATCAT
196 CCCTAATTGAGTATGATTAATTTCATGCTCATCTAATTCCCATTTAGTCTTAGGCTGGTCATCAT
* *
28609564 TTCGATAGAAAATCGTGAGATATGAACTTGTACTAAAACCTTACAATACGATATTCATTATCTCT
261 TTCGATCGAAAATCGTGAGATATGAACCTGTACTAAAACCTTACAATACGATATTCATTATCTCT
* * *
28609629 TCGAATTATGGGATAATCACAATCGTCCCTTAAAGTTAATTCAATTTCAATTCAAAAAGCGCGCG
326 CCGAATTATGGGATAGTCACAATCATCCCTTAAAGTTAATTCAATTTCAATTCAAAAAGCGCGCG
* * *
28609694 TTAGGTTGGAGTTGTTTGACGTACAGTTGGGAAAACGAGATGGTTGTTTGTCGAGTTCGAATTCC
391 TTGGGTTAGAGTTGTTTGACGTACAGTTGGGAAAACGAGATGGTTGTCTGTCGAGTTCGAATTCC
* *
28609759 CACGAACAAATTGGCGCATTTCAATTGGAAAAAGCTAGTTGGATTCCATCAAGGGAGATAGTAAT
456 CACGAACAAATTGGCGTATTTCAATTGGAAAAAGCTAGTTGGATTCCATCAAGGGAGATAGTGAT
* *
28609824 TGAATTTAAATGACCCACGCAGTTGGGGCCGTTATTCGAGT
521 TGAATTTAAACGACCCACGCGGTTGGGGCCGTTATTCGAGT
* *
28609865 TACTTTGTATTGATAGATTGGAAAAACACACTTGAATTGAATTAAATACAATTATTTTCTTTTAT
1 TACCTTGTATTGATGGATTGGAAAAACACACTTGAATTGAATTAAATACAATTATTTTCTTTTAT
*
28609930 TTCTTCCATCGTATGTAGCTTTTGGAAAAGCTTTCTGACTTTTTATTTCATTTTCTTATTTTGGC
66 TTCTTCCATCGTATGTAGCTTTTGGAAAAGCTTTCTGGCTTTTTATTTCATTTTCTTATTTTGGC
* *
28609995 TCAATTGCTTTCTAGGTTCTTTCTCCTTTTCACCTATCACCATTACATTCAAATCCACTTTTAAA
131 TCAATTGCTTTGTAAGTTCTTTCTCCTTTTCACCTATCACCATTACATTCAAATCCACTTTTAAA
28610060 CCCTAATTGAGTATGATTAATTTCATGCTCATCTAATTCCCATTTAGTCTTAGGCTGGTCATCAT
196 CCCTAATTGAGTATGATTAATTTCATGCTCATCTAATTCCCATTTAGTCTTAGGCTGGTCATCAT
28610125 TTCGATCGAAAATCGTGAGATATGAACCTGTACTAAAACCTTACAATACGATATTCATTATCTCT
261 TTCGATCGAAAATCGTGAGATATGAACCTGTACTAAAACCTTACAATACGATATTCATTATCTCT
* *
28610190 TCGAATTATGGGATAGTCACAATCACCCCTTAAAGTTAATTCAATTTCAATTCAAAAAGCGCGCG
326 CCGAATTATGGGATAGTCACAATCATCCCTTAAAGTTAATTCAATTTCAATTCAAAAAGCGCGCG
* * * *
28610255 TTGGGTTGGAGTTATTTGACGTACAGTTGGGAAAACGAGATGGTTGTTTGTCAAGTTCGAACTT-
391 TTGGGTTAGAGTTGTTTGACGTACAGTTGGGAAAACGAGATGGTTGTCTGTCGAGTTCGAA-TTC
* * **
28610319 CCACGAACAAATTGGTGTATTTCAATTGGAAAAAGCTATTTGGATTTTATCAAGGGAGATAGTGA
455 CCACGAACAAATTGGCGTATTTCAATTGGAAAAAGCTAGTTGGATTCCATCAAGGGAGATAGTGA
28610384 TTGAATTTAAACGACCCACGCGGTTGGGGCCGTTATTCGAGT
520 TTGAATTTAAACGACCCACGCGGTTGGGGCCGTTATTCGAGT
28610426 TACCTTGTATTGATGGATTGGAAAAACACACTTGAATTGAATTAAATACAATTATTTTCTTTTAT
1 TACCTTGTATTGATGGATTGGAAAAACACACTTGAATTGAATTAAATACAATTATTTTCTTTTAT
* * * *
28610491 TTCTTCTATCGTATGTAGCTTTTGGAAAAGCTTTCTAGTTTTTTATTTCATTTTCTTATTTTGGT
66 TTCTTCCATCGTATGTAGCTTTTGGAAAAGCTTTCTGGCTTTTTATTTCATTTTCTTATTTTGGC
* **
28610556 TCTATTGCTTTGTAAGTTCTTTCTCCTTTTCACCTATCACCATTACATTCAAATATACTTTTAAA
131 TCAATTGCTTTGTAAGTTCTTTCTCCTTTTCACCTATCACCATTACATTCAAATCCACTTTTAAA
*
28610621 CCCTAATTGAGTATGATTAATTTCATGCTCATCTAATTCCCATTTAGTCTTAGGCTGGTCGTCAT
196 CCCTAATTGAGTATGATTAATTTCATGCTCATCTAATTCCCATTTAGTCTTAGGCTGGTCATCAT
* *
28610686 TTTGATCGAAAATCGTGAGATATGAACCTGTACTAAAACCTTACAATATGATATTCATTATCTCT
261 TTCGATCGAAAATCGTGAGATATGAACCTGTACTAAAACCTTACAATACGATATTCATTATCTCT
* **
28610751 CCGGATTATGGGATAGTCACAATCATCCCTTAAAGTTAATTCAATTTCAATTCAAAAAGCATGCG
326 CCGAATTATGGGATAGTCACAATCATCCCTTAAAGTTAATTCAATTTCAATTCAAAAAGCGCGCG
28610816 TTGGGTTAGAGTTGTTTGACGTACAGTTGGGAAAACGAGATGGTTGTCTGTCGAGTTCGAATTCC
391 TTGGGTTAGAGTTGTTTGACGTACAGTTGGGAAAACGAGATGGTTGTCTGTCGAGTTCGAATTCC
* *
28610881 CACGAACAAATTGGCGTATTTCAATTGGAAAAAAACTGGTTGGATTCCATCAAGGGAGATAGTGA
456 CACGAACAAATTGGCGTATTTCAATTGG-AAAAAGCTAGTTGGATTCCATCAAGGGAGATAGTGA
*
28610946 TTGAATTTAAACGACCCACGCGGTTGGGGCCATTATTCGAGT
520 TTGAATTTAAACGACCCACGCGGTTGGGGCCGTTATTCGAGT
28610988 TACCTTGTATTGATGGATTGGAAAAACACACTTGAATTGAATTAAATACAATTATTTTCTTTTAT
1 TACCTTGTATTGATGGATTGGAAAAACACACTTGAATTGAATTAAATACAATTATTTTCTTTTAT
* *
28611053 TTCTTCTATCGTATATAGCTTTTGGAAAAGCTTTCTGGCTTTTTATTTCATTTTCTTATTTTGGC
66 TTCTTCCATCGTATGTAGCTTTTGGAAAAGCTTTCTGGCTTTTTATTTCATTTTCTTATTTTGGC
28611118 TCAATTGCTTTGTAAGTTCTTTCTCCTTTTCACCTATCACCATTACATTCAAATCCACTTTTAAA
131 TCAATTGCTTTGTAAGTTCTTTCTCCTTTTCACCTATCACCATTACATTCAAATCCACTTTTAAA
*
28611183 CCCTAATTGAGTATGATTAATTTCATGCTCATCTAATTCCCATTTAGTCTTAGGCCGGTCATCAT
196 CCCTAATTGAGTATGATTAATTTCATGCTCATCTAATTCCCATTTAGTCTTAGGCTGGTCATCAT
*
28611248 TTCGATCTAAAATCGTGAGATATGAACCTGTACTAAAACCTTACAATACGATATTCATTATCTCT
261 TTCGATCGAAAATCGTGAGATATGAACCTGTACTAAAACCTTACAATACGATATTCATTATCTCT
* * * * *
28611313 CCGGATTATGGGTTAGTCACAATCGTCCCTTAAAATTAATTCAATTTCAATTCAAAAAGCGTGCG
326 CCGAATTATGGGATAGTCACAATCATCCCTTAAAGTTAATTCAATTTCAATTCAAAAAGCGCGCG
*
28611378 TTGGGTTAGAGTTGTTTGACGTACAGTTGGGAAAACGAAATGGTTGTCTGTCGAGTTCGAATTCC
391 TTGGGTTAGAGTTGTTTGACGTACAGTTGGGAAAACGAGATGGTTGTCTGTCGAGTTCGAATTCC
*
28611443 TACGAACAAATTGGCGTATTTCAATTGGAAAAAGCTAGTTGGATTCCATCAAGGGAGATAGTGAT
456 CACGAACAAATTGGCGTATTTCAATTGGAAAAAGCTAGTTGGATTCCATCAAGGGAGATAGTGAT
* *
28611508 TGAATTTAAACGACCCACGTGATTGGGGCCGTTATTCGAGT
521 TGAATTTAAACGACCCACGCGGTTGGGGCCGTTATTCGAGT
28611549 T
1 T
28611550 GGGCTTTTCT
Statistics
Matches: 1603, Mismatches: 79, Indels: 6
0.95 0.05 0.00
Matches are distributed among these distances:
560 2 0.00
561 1062 0.66
562 539 0.34
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (561 bp):
TACCTTGTATTGATGGATTGGAAAAACACACTTGAATTGAATTAAATACAATTATTTTCTTTTAT
TTCTTCCATCGTATGTAGCTTTTGGAAAAGCTTTCTGGCTTTTTATTTCATTTTCTTATTTTGGC
TCAATTGCTTTGTAAGTTCTTTCTCCTTTTCACCTATCACCATTACATTCAAATCCACTTTTAAA
CCCTAATTGAGTATGATTAATTTCATGCTCATCTAATTCCCATTTAGTCTTAGGCTGGTCATCAT
TTCGATCGAAAATCGTGAGATATGAACCTGTACTAAAACCTTACAATACGATATTCATTATCTCT
CCGAATTATGGGATAGTCACAATCATCCCTTAAAGTTAATTCAATTTCAATTCAAAAAGCGCGCG
TTGGGTTAGAGTTGTTTGACGTACAGTTGGGAAAACGAGATGGTTGTCTGTCGAGTTCGAATTCC
CACGAACAAATTGGCGTATTTCAATTGGAAAAAGCTAGTTGGATTCCATCAAGGGAGATAGTGAT
TGAATTTAAACGACCCACGCGGTTGGGGCCGTTATTCGAGT
Found at i:28612604 original size:31 final size:30
Alignment explanation
Indices: 28612568--28612668 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 30
28612558 ATATTAAAAT
*
28612568 CTTTAATTTAATGTGTAATTATATACATG-AA
1 CTTTAATTT-A-GTATAATTATATACATGAAA
* *
28612599 TTTTAATTTAGTATAATTGTATACATGAAA
1 CTTTAATTTAGTATAATTATATACATGAAA
* * * *
28612629 CTTTAATTGTGGT-TCAAATGTATACTTGAAA
1 CTTTAATT-TAGTAT-AATTATATACATGAAA
28612660 CTTTAATTT
1 CTTTAATTT
28612669 TGATTTAATC
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
29 15 0.25
30 12 0.20
31 33 0.55
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (30 bp):
CTTTAATTTAGTATAATTATATACATGAAA
Found at i:28612621 original size:29 final size:32
Alignment explanation
Indices: 28612568--28612636 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 32
28612558 ATATTAAAAT
*
28612568 CTTTAATTTAATGTGTAATTATATACATG-AA
1 CTTTAATTTAATGTATAATTATATACATGAAA
* *
28612599 TTTTAATTT-A-GTATAATTGTATACATGAAA
1 CTTTAATTTAATGTATAATTATATACATGAAA
28612629 CTTTAATT
1 CTTTAATT
28612637 GTGGTTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 15 0.45
30 10 0.30
31 8 0.24
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.48
Consensus pattern (32 bp):
CTTTAATTTAATGTATAATTATATACATGAAA
Found at i:28612683 original size:31 final size:31
Alignment explanation
Indices: 28612616--28612683 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
28612606 TTAGTATAAT
* *
28612616 TGTATACATGAAACTTTAATTGTGGTTCAAA
1 TGTATACATGAAACTTTAATTGTGATTCTAA
* *
28612647 TGTATACTTGAAACTTTAATTTTGATT-TAA
1 TGTATACATGAAACTTTAATTGTGATTCTAA
28612677 TCGTATA
1 T-GTATA
28612684 TACTTAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (31 bp):
TGTATACATGAAACTTTAATTGTGATTCTAA
Found at i:28612848 original size:29 final size:30
Alignment explanation
Indices: 28612806--28612864 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
28612796 GAATTGGATC
* *
28612806 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAAGTTCATATATAAAATTACACA
* *
28612836 AAATC-AAAGTTCATATATACAATTGCACA
1 AAATCAAAAGTTCATATATAAAATTACACA
28612865 TCAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATATATAAAATTACACA
Found at i:28614253 original size:32 final size:32
Alignment explanation
Indices: 28614208--28614268 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
28614198 TTAAACTTTT
28614208 TTTTTGTCCAATTTGATACTCAAACTTGACAC
1 TTTTTGTCCAATTTGATACTCAAACTTGACAC
* *
28614240 TTTTT-TCCTAATTTGGTACTTAAACTTGA
1 TTTTTGTCC-AATTTGATACTCAAACTTGA
28614269 TTTTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (32 bp):
TTTTTGTCCAATTTGATACTCAAACTTGACAC
Found at i:28616010 original size:24 final size:22
Alignment explanation
Indices: 28615977--28616043 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 22
28615967 ATACAGTACG
28615977 TTTAAT-TTATTTTTATATTACA
1 TTTAATATTATTTTTATATTA-A
* *
28615999 TTATAATATTATTATAATATTTAA
1 TT-TAATATTATTTTTATA-TTAA
28616023 TTT--TATTATTTTTATATTAA
1 TTTAATATTATTTTTATATTAA
28616043 T
1 T
28616044 AGAAGTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 5 0.13
21 11 0.29
22 2 0.05
23 5 0.13
24 12 0.32
25 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTAATATTATTTTTATATTAA
Found at i:28616988 original size:19 final size:20
Alignment explanation
Indices: 28616951--28617003 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
28616941 AAAAATATTT
28616951 AAAATTATAAAAATATTCAAA
1 AAAATTAT-AAAATATTCAAA
* *
28616972 AAAATTATAAAA-CTTCATA
1 AAAATTATAAAATATTCAAA
28616991 AAAATT-TAAAATA
1 AAAATTATAAAATA
28617004 ATTAACATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 4 0.14
21 8 0.29
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATTATAAAATATTCAAA
Found at i:28617001 original size:29 final size:29
Alignment explanation
Indices: 28616940--28617007 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
28616930 TATGCCATAC
*
28616940 TAAAAATATT-TAAAATTATAAAAATATT
1 TAAAAAAATTATAAAATTATAAAAATATT
*
28616968 CAAAAAAATTATAAAACTTCAT-AAAA-ATT
1 TAAAAAAATTATAAAA-TT-ATAAAAATATT
*
28616997 TAAAATAATTA
1 TAAAAAAATTA
28617008 ACATGAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 8 0.24
29 17 0.52
30 6 0.18
31 2 0.06
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (29 bp):
TAAAAAAATTATAAAATTATAAAAATATT
Found at i:28617088 original size:25 final size:23
Alignment explanation
Indices: 28617060--28617105 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
28617050 AAATTTTGAG
28617060 AGTTAAATTTAATTAAAAAAATAAA
1 AGTTAAA-TTAA-TAAAAAAATAAA
*
28617085 AGTTAAATTGATAAAAAAATA
1 AGTTAAATTAATAAAAAAATA
28617106 TAATCATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (23 bp):
AGTTAAATTAATAAAAAAATAAA
Found at i:28617108 original size:25 final size:25
Alignment explanation
Indices: 28617060--28617108 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28617050 AAATTTTGAG
*
28617060 AGTTAAATTTAATTAAAAAAATAAA
1 AGTTAAATTTAATAAAAAAAATAAA
*
28617085 AGTTAAA-TTGATAAAAAAATATAA
1 AGTTAAATTTAATAAAAAAA-ATAA
28617109 TCATTGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (25 bp):
AGTTAAATTTAATAAAAAAAATAAA
Found at i:28632195 original size:20 final size:20
Alignment explanation
Indices: 28632166--28632209 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28632156 GTGGTGGCTA
*
28632166 GAAAAGGGAGAAGAATAG-GT
1 GAAAAGGGAG-AGAAAAGAGT
*
28632186 GAAAATGGAGAGAAAAGAGT
1 GAAAAGGGAGAGAAAAGAGT
28632206 GAAA
1 GAAA
28632210 TGGGTGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.36, T:0.09
Consensus pattern (20 bp):
GAAAAGGGAGAGAAAAGAGT
Found at i:28632309 original size:39 final size:39
Alignment explanation
Indices: 28632251--28632329 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
28632241 AGGGGTGGTG
28632251 AGTGAGAAGAAGGCCTGGTCAACATGGACTAGGTTCTAT
1 AGTGAGAAGAAGGCCTGGTCAACATGGACTAGGTTCTAT
* *
28632290 AGTGAGAAGAAGGCTTGGTCAACATGGATTAGGTTCTAT
1 AGTGAGAAGAAGGCCTGGTCAACATGGACTAGGTTCTAT
28632329 A
1 A
28632330 AACCTTTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (39 bp):
AGTGAGAAGAAGGCCTGGTCAACATGGACTAGGTTCTAT
Found at i:28636196 original size:13 final size:14
Alignment explanation
Indices: 28636169--28636197 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28636159 AGGCTTTCCA
28636169 AAGGATTTACCATG
1 AAGGATTTACCATG
28636183 AAGGATTT-CCATG
1 AAGGATTTACCATG
28636196 AA
1 AA
28636198 ATCCATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (14 bp):
AAGGATTTACCATG
Found at i:28640241 original size:17 final size:19
Alignment explanation
Indices: 28640214--28640252 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
28640204 GATATGGGAC
*
28640214 AAAAATGAGAA-TGATGTG
1 AAAAATGAGAATTGAAGTG
28640232 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAATTGAAGTG
28640250 AAA
1 AAA
28640253 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (19 bp):
AAAAATGAGAATTGAAGTG
Found at i:28643295 original size:16 final size:17
Alignment explanation
Indices: 28643261--28643295 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
28643251 AAATGTAGAG
28643261 TTAAAAAAAAAGCAGAA
1 TTAAAAAAAAAGCAGAA
28643278 TTAAAAAAAAAGCA-AA
1 TTAAAAAAAAAGCAGAA
28643294 TT
1 TT
28643296 GTTATCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (17 bp):
TTAAAAAAAAAGCAGAA
Found at i:28644691 original size:27 final size:27
Alignment explanation
Indices: 28644660--28644722 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
28644650 CTCATGGATG
28644660 AAATTAAAGAAGAGGGTGTGATGAATA
1 AAATTAAAGAAGAGGGTGTGATGAATA
*
28644687 AAATTAAAGAAGAGGGTGTGATGAATG
1 AAATTAAAGAAGAGGGTGTGATGAATA
*
28644714 AAATGAAAG
1 AAATTAAAG
28644723 GGACTTCTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (27 bp):
AAATTAAAGAAGAGGGTGTGATGAATA
Found at i:28654510 original size:22 final size:23
Alignment explanation
Indices: 28654460--28654510 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
28654450 TTGTGTTGCT
*
28654460 ACGAGAGACCAAAGAAGTTAGTAC
1 ACGAGAGACCAAAGAAATTAG-AC
28654484 ACGAGAGACCAAA-AAATTA-AC
1 ACGAGAGACCAAAGAAATTAGAC
28654505 AGCGAG
1 A-CGAG
28654511 TCAAAGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 3 0.12
22 4 0.16
23 5 0.20
24 13 0.52
ACGTcount: A:0.49, C:0.18, G:0.24, T:0.10
Consensus pattern (23 bp):
ACGAGAGACCAAAGAAATTAGAC
Found at i:28655256 original size:14 final size:14
Alignment explanation
Indices: 28655237--28655290 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
28655227 ATATAGCTTG
28655237 TTAAAATTATTTTA
1 TTAAAATTATTTTA
*
28655251 TTAAAATTAGGTTTA
1 TTAAAATTA-TTTTA
* *
28655266 -TGAAATTATTATA
1 TTAAAATTATTTTA
*
28655279 TTAAATTTATTT
1 TTAAAATTATTT
28655291 ACTAGCTACT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
13 3 0.10
14 24 0.77
15 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (14 bp):
TTAAAATTATTTTA
Found at i:28658336 original size:87 final size:86
Alignment explanation
Indices: 28658189--28658355 Score: 246
Period size: 87 Copynumber: 1.9 Consensus size: 86
28658179 ACATTTAAGT
* *
28658189 TCGGTGAATTCATCAAGTCCGTCACAATAAGACCACCCAAACTTTGGGATATGAATTCATTAAGA
1 TCGGTGAATTCATCAAGTCCATCACAATAAGACCACCCAAACTTTGGGATATGAACTCATTAAGA
28658254 GTAATAAACTCAACCTCTTATG
66 GTAA-AAACTCAACCTCTTATG
* * *
28658276 TCGGTGAATTCATCAAGTCCATCTCAATAGGACCACTCAAA-TCTTGGGATATGAACTCATTAAG
1 TCGGTGAATTCATCAAGTCCATCACAATAAGACCACCCAAACT-TTGGGATATGAACTCATTAAG
* *
28658340 AGTGAGAACTCAACCT
65 AGTAAAAACTCAACCT
28658356 TATGCATGTA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
86 11 0.15
87 61 0.85
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (86 bp):
TCGGTGAATTCATCAAGTCCATCACAATAAGACCACCCAAACTTTGGGATATGAACTCATTAAGA
GTAAAAACTCAACCTCTTATG
Found at i:28662123 original size:16 final size:17
Alignment explanation
Indices: 28662094--28662128 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28662084 GTACTTAGTT
28662094 TATCATTTACTTTTCAG
1 TATCATTTACTTTTCAG
*
28662111 TATCATTTA-TTTTTAG
1 TATCATTTACTTTTCAG
28662127 TA
1 TA
28662129 CTTGGTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (17 bp):
TATCATTTACTTTTCAG
Found at i:28665325 original size:23 final size:23
Alignment explanation
Indices: 28665282--28665368 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
28665272 TAATGTTCAC
*
28665282 GAACATGTTCATTTAAC-TTAATT
1 GAACATGTTCA-TGAACATTAATT
* **
28665305 GAACATGTTCACGAACATTAAAC
1 GAACATGTTCATGAACATTAATT
*
28665328 AAACATGTTCATGAACATATAATT
1 GAACATGTTCATGAACAT-TAATT
* *
28665352 GAACATTTTAATGAACA
1 GAACATGTTCATGAACA
28665369 ATGTTAATGA
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.61
24 17 0.33
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (23 bp):
GAACATGTTCATGAACATTAATT
Found at i:28667427 original size:24 final size:25
Alignment explanation
Indices: 28667392--28667441 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
28667382 TGGCTCGTAT
28667392 TCTTCTTCCAATTAAACTCTG-TTA
1 TCTTCTTCCAATTAAACTCTGATTA
28667416 TCTT-TTCTCAATTAAACTCTGATTA
1 TCTTCTTC-CAATTAAACTCTGATTA
28667441 T
1 T
28667442 TCCAAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 3 0.12
24 17 0.71
25 4 0.17
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (25 bp):
TCTTCTTCCAATTAAACTCTGATTA
Found at i:28668383 original size:24 final size:25
Alignment explanation
Indices: 28668356--28668406 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
28668346 TTAAACTCTG
*
28668356 TTTATTTGTTTCAATTAAATT-TTA
1 TTTATTTGTTTCAATCAAATTCTTA
*
28668380 TTTATTTGTTTGAATCAAATTCTTA
1 TTTATTTGTTTCAATCAAATTCTTA
28668405 TT
1 TT
28668407 ACTCTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (25 bp):
TTTATTTGTTTCAATCAAATTCTTA
Found at i:28669307 original size:31 final size:30
Alignment explanation
Indices: 28669263--28669322 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
28669253 AAACATAAAT
28669263 TAAAAAATAGTTATTTATATATATT-TTTTA
1 TAAAAAATAGTTATTTATAT-TATTATTTTA
*
28669293 TAAAATATAAGTTATTTATATTATTATTTT
1 TAAAAAAT-AGTTATTTATATTATTATTTT
28669323 GAAATTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
TAAAAAATAGTTATTTATATTATTATTTTA
Found at i:28669334 original size:27 final size:31
Alignment explanation
Indices: 28669263--28669321 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
28669253 AAACATAAAT
* *
28669263 TAAAAAAT-AGTTATTTATATATATTTTTTA
1 TAAAATATAAGTTATTTATATATATTATTTA
28669293 TAAAATATAAGTTATTTATAT-TATTATTT
1 TAAAATATAAGTTATTTATATATATTATTT
28669322 TGAAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (31 bp):
TAAAATATAAGTTATTTATATATATTATTTA
Found at i:28669339 original size:27 final size:27
Alignment explanation
Indices: 28669277--28669339 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
28669267 AAATAGTTAT
28669277 TTATATATATTTTTTATAAAATATAAG
1 TTATATATATTTTTTATAAAATATAAG
* * *
28669304 TTATTTATATTATTATTTTGAAAT-TAA-
1 TTATATATATT-TT-TTATAAAATATAAG
28669331 TTATATATA
1 TTATATATA
28669340 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 18 0.60
28 5 0.17
29 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (27 bp):
TTATATATATTTTTTATAAAATATAAG
Found at i:28669533 original size:28 final size:28
Alignment explanation
Indices: 28669480--28669533 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
28669470 TGCTTTTTAA
*
28669480 TTTTTTATATATTTATATATTTTTTAGT
1 TTTTTTATATATTTATATATATTTTAGT
*
28669508 TTTTTTATA-ATTTTTTATATATTTTA
1 TTTTTTATATA-TTTATATATATTTTA
28669534 ATTGCATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (28 bp):
TTTTTTATATATTTATATATATTTTAGT
Done.