Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 130 of 144
Found at i:32203229 original size:6 final size:6
Alignment explanation
Indices: 32203168--32203268 Score: 85
Period size: 6 Copynumber: 16.8 Consensus size: 6
32203158 CCGGTTTCGA
* * * * * *
32203168 CTCCGG CTCCAG CTCCGG CTCCGG CTCCGG CTCCGG CTCCTG CTCCTG
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG
* * * * * * *
32203216 CTCCTG CTCGTG CTCCTA CTCCTA CTCCTA CTCCTA CCCCTA CTCCTG
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG
32203264 CTCCT
1 CTCCT
32203269 ACTACAGCTT
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 86 1.00
ACGTcount: A:0.06, C:0.50, G:0.17, T:0.27
Consensus pattern (6 bp):
CTCCTG
Found at i:32207535 original size:23 final size:22
Alignment explanation
Indices: 32207491--32207535 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
32207481 GATGCCATTT
*
32207491 CTCCCGCTGCATAAGCCTGAAA
1 CTCCCGCTGCATAAGCCGGAAA
* *
32207513 CTCCTCGCTGCATTATCCGGAAA
1 CTCC-CGCTGCATAAGCCGGAAA
32207536 TCCAGTTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (22 bp):
CTCCCGCTGCATAAGCCGGAAA
Found at i:32221326 original size:8 final size:7
Alignment explanation
Indices: 32221278--32221332 Score: 65
Period size: 7 Copynumber: 7.9 Consensus size: 7
32221268 ATACAGGGGC
*
32221278 TTAATAT
1 TTAAAAT
32221285 TTAAAAT
1 TTAAAAT
32221292 TTAAAAT
1 TTAAAAT
32221299 TTAAAAT
1 TTAAAAT
* *
32221306 ATAAAAA
1 TTAAAAT
* *
32221313 CTAAATT
1 TTAAAAT
32221320 TTAAAAT
1 TTAAAAT
32221327 TTAAAA
1 TTAAAA
32221333 GGTACAGGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (7 bp):
TTAAAAT
Found at i:32232677 original size:6 final size:6
Alignment explanation
Indices: 32232666--32232700 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
32232656 GGCTGAGAAA
* *
32232666 GTGGTG GTGGTG GTGGCG GTGGCG GTGGCG GTGGC
1 GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGC
32232701 CGGATAACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.11, G:0.66, T:0.23
Consensus pattern (6 bp):
GTGGCG
Found at i:32235950 original size:19 final size:20
Alignment explanation
Indices: 32235914--32235953 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
32235904 CAAAATAGAT
32235914 TAAATGTTATTTTGTGAATA
1 TAAATGTTATTTTGTGAATA
32235934 TAAAT-TTATTGTT-TGAATA
1 TAAATGTTATT-TTGTGAATA
32235953 T
1 T
32235954 GAAAGAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (20 bp):
TAAATGTTATTTTGTGAATA
Found at i:32240807 original size:16 final size:17
Alignment explanation
Indices: 32240783--32240823 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
32240773 TATTAATAAT
32240783 AAAATATTA-TAGGCCC
1 AAAATATTAGTAGGCCC
*
32240799 AATATATTATGTAGGCCC
1 AAAATATTA-GTAGGCCC
32240817 AAAATAT
1 AAAATAT
32240824 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 8 0.38
18 13 0.62
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (17 bp):
AAAATATTAGTAGGCCC
Found at i:32242036 original size:14 final size:14
Alignment explanation
Indices: 32242014--32242075 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
32242004 GTCATTTCAC
*
32242014 TATTATATTTTTAT
1 TATTTTATTTTTAT
*
32242028 TATTTTATTATTAT
1 TATTTTATTTTTAT
*
32242042 TATTTTAATATTATAT
1 TATTTT-AT-TTTTAT
*
32242058 AATTCTTA-TTTTAT
1 TATT-TTATTTTTAT
32242072 TATT
1 TATT
32242076 AATTTTACTA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
14 26 0.68
15 2 0.05
16 8 0.21
17 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTATTTTTAT
Found at i:32242048 original size:22 final size:22
Alignment explanation
Indices: 32242014--32242076 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
32242004 GTCATTTCAC
*
32242014 TATTA-TATTTTTATTATTTTAT
1 TATTATTA-TTTTATTATTATAT
*
32242036 TATTATTATTTTAATATTATAT
1 TATTATTATTTTATTATTATAT
* *
32242058 AATTCTTATTTTATTATTA
1 TATTATTATTTTATTATTA
32242077 ATTTTACTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 33 0.94
23 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTATTATTTTATTATTATAT
Found at i:32245963 original size:7 final size:7
Alignment explanation
Indices: 32245930--32245954 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32245920 ATCTGGTTTG
32245930 TTTTGTT
1 TTTTGTT
32245937 TTTTGTT
1 TTTTGTT
32245944 TTTTGTT
1 TTTTGTT
32245951 TTTT
1 TTTT
32245955 TTTGTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:32254566 original size:389 final size:388
Alignment explanation
Indices: 32254001--32254780 Score: 1276
Period size: 389 Copynumber: 2.0 Consensus size: 388
32253991 CTTGTTTTTT
* * *
32254001 AAATGGATCTTATTTTTTGTCTAAGCTCATTTTTCTGACCTATTTTTTTGCCTAAATTCTCTCAC
1 AAATGAATCTTATTTTTTGCCTAAACTCATTTTTCTGACCTATTTTTTTGCCTAAATTCTCTCAC
* * *
32254066 TTTTTTCACGATCCTTCAGGTCGGATGATCTGACTCATGAATAGATCTTGTCCCATACAAACGTG
66 TTTTTTCACGATCCTTCAGGTCGGATGATCCGACTCATGAACAGATATTGTCCCATACAAACGTG
* *
32254131 CAACCAATACAAAGCAAACCGTACAAAAAGGATTGAAATGTGGATAACTCAAATACTGTAATCTC
131 CAACCAATACAAAGCAAACCGTAAAAAAAGGATTGAAATGTGGATAACTCAAACACTGTAATCTC
*
32254196 ATCTTAAAATGTTAGATTGTGATATAAAATTTGGCGAATTAAATGCCCTTTAAAGCAAACCATAA
196 ATCTTAAAATGTTAGATTGTGATATAAAATTTGGCGAATTAAACGCCCTTTAAAGCAAACCATAA
*
32254261 AAACACCAAAACATGAAAAGGTTAGCCAAGTGTTGATTGGGTGACAGAAAAAGTTGAGTGAAGAA
261 AAACACCAAAACATGAAAAGGTTAGCCAAGTGTTGATTGGGTGACAGAAAAAGTTGAGTGAAAAA
*
32254326 TGAAGAGATGAGGGACTGCTAAGGAAAATCCGCAATAACTCTATGAAATAAGCTGAATTCTCG
326 TGAAGAGATGAGGGACTGCTAAGGAAAATCCGCAATAACTCTATGAAATAAGCTGAATTCCCG
* ** * *
32254389 AAATGAATCTTATTTTTTTGCCTAAACTTATTTTT-TAGATTTATTTTTTTGCTTAAATTCTCTT
1 AAATGAATCTTA-TTTTTTGCCTAAACTCATTTTTCT-GACCTATTTTTTTGCCTAAATTCTCTC
* * * * *
32254453 ACTTTTTTGACGATCCTTCGGGTTGGATGGTCCGA-TCTATGAACAGGTATTGTCCCATACAAAC
64 ACTTTTTTCACGATCCTTCAGGTCGGATGATCCGACTC-ATGAACAGATATTGTCCCATACAAAC
* * *
32254517 GTGCAATCAATACAAAGCAAACTGTAAAAAAAGGATTGAAATGTGGATAACTCTAACACTGTAAT
128 GTGCAACCAATACAAAGCAAACCGTAAAAAAAGGATTGAAATGTGGATAACTCAAACACTGTAAT
* *
32254582 CTCATTTTAAAATGTTAGATTGTGATATAAAATTTGGTGAATTAAACGCCCTTTAAAGCAAACCA
193 CTCATCTTAAAATGTTAGATTGTGATATAAAATTTGGCGAATTAAACGCCCTTTAAAGCAAACCA
32254647 TAAAAACACCAAAACATGAAAAGGTTAGCCAAGTGTTGATTGGGTGACAGAAAAAGTTGAGTGAA
258 TAAAAACACCAAAACATGAAAAGGTTAGCCAAGTGTTGATTGGGTGACAGAAAAAGTTGAGTGAA
*
32254712 AAATGAAGAGATGAGGGACTGCTAAGGAAAATCCGCAATAACTTTATGAAATAAGCTGAATTCCC
323 AAATGAAGAGATGAGGGACTGCTAAGGAAAATCCGCAATAACTCTATGAAATAAGCTGAATTCCC
32254777 G
388 G
32254778 AAA
1 AAA
32254781 CGACATCGTT
Statistics
Matches: 362, Mismatches: 27, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
388 14 0.04
389 348 0.96
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (388 bp):
AAATGAATCTTATTTTTTGCCTAAACTCATTTTTCTGACCTATTTTTTTGCCTAAATTCTCTCAC
TTTTTTCACGATCCTTCAGGTCGGATGATCCGACTCATGAACAGATATTGTCCCATACAAACGTG
CAACCAATACAAAGCAAACCGTAAAAAAAGGATTGAAATGTGGATAACTCAAACACTGTAATCTC
ATCTTAAAATGTTAGATTGTGATATAAAATTTGGCGAATTAAACGCCCTTTAAAGCAAACCATAA
AAACACCAAAACATGAAAAGGTTAGCCAAGTGTTGATTGGGTGACAGAAAAAGTTGAGTGAAAAA
TGAAGAGATGAGGGACTGCTAAGGAAAATCCGCAATAACTCTATGAAATAAGCTGAATTCCCG
Found at i:32266223 original size:28 final size:26
Alignment explanation
Indices: 32266173--32266224 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
32266163 TTCAATTAAA
* *
32266173 AATAAAAAAATTTAAATTCTCCTTTG
1 AATAAAAAAAATTAAAATCTCCTTTG
32266199 AATAAAATAAAATTAAAATCATCCTT
1 AATAAAA-AAAATTAAAATC-TCCTT
32266225 CTTTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 10 0.45
28 5 0.23
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (26 bp):
AATAAAAAAAATTAAAATCTCCTTTG
Found at i:32266993 original size:16 final size:16
Alignment explanation
Indices: 32266968--32266998 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32266958 TTATAGAAAA
32266968 TTTATATACTTTTAAT
1 TTTATATACTTTTAAT
*
32266984 TTTATGTACTTTTAA
1 TTTATATACTTTTAA
32266999 ATAATAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTATATACTTTTAAT
Found at i:32267570 original size:16 final size:15
Alignment explanation
Indices: 32267555--32267600 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
32267545 TTATAATTAT
32267555 TAATTTAAAATTTTA
1 TAATTTAAAATTTTA
32267570 TAAATTATAAAATATTTA
1 T-AATT-TAAAAT-TTTA
32267588 -AA-TTAAAATTTTA
1 TAATTTAAAATTTTA
32267601 ATTTTTTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 4 0.14
14 6 0.21
15 2 0.07
16 6 0.21
17 6 0.21
18 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTTAAAATTTTA
Found at i:32275781 original size:15 final size:16
Alignment explanation
Indices: 32275758--32275793 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
32275748 TGTTTTTTTA
32275758 AAAAT-TTTAAAAG-T
1 AAAATATTTAAAAGAT
32275772 AAAATATTTAAAAGAT
1 AAAATATTTAAAAGAT
32275788 AAAATA
1 AAAATA
32275794 AAAAGAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 8 0.40
16 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAATATTTAAAAGAT
Found at i:32275807 original size:15 final size:15
Alignment explanation
Indices: 32275787--32275821 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
32275777 ATTTAAAAGA
32275787 TAAAATAAAAAGAAT
1 TAAAATAAAAAGAAT
32275802 TAAAATAAAAAGAAT
1 TAAAATAAAAAGAAT
32275817 TAAAA
1 TAAAA
32275822 AAATCTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (15 bp):
TAAAATAAAAAGAAT
Found at i:32282674 original size:31 final size:30
Alignment explanation
Indices: 32282639--32282696 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
32282629 TTAATTAGTA
*
32282639 TTCAATCAATTTATTTTTCTTATAAAAATTC
1 TTCAAT-AATTTAATTTTCTTATAAAAATTC
*
32282670 TTCAATTATTTAATTTTCTTATAAAAA
1 TTCAATAATTTAATTTTCTTATAAAAA
32282697 AAAAGTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (30 bp):
TTCAATAATTTAATTTTCTTATAAAAATTC
Found at i:32283464 original size:21 final size:21
Alignment explanation
Indices: 32283423--32283470 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
32283413 TAAAGCAATA
* *
32283423 AATTTAAGTTTAAAAATAGAT
1 AATTTAAGTTAAAAAAGAGAT
32283444 AATTTAA-TTAAAATAAGAGAT
1 AATTTAAGTTAAAA-AAGAGAT
32283465 -ATTTAA
1 AATTTAA
32283471 AGGATAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (21 bp):
AATTTAAGTTAAAAAAGAGAT
Found at i:32284582 original size:21 final size:22
Alignment explanation
Indices: 32284545--32284585 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
32284535 TTCAACAGTC
*
32284545 TTGATTAGGACATACAAAAGTA
1 TTGATTAGGAAATACAAAAGTA
32284567 TTGATTA-GAAATACAAAAG
1 TTGATTAGGAAATACAAAAG
32284586 AGATTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (22 bp):
TTGATTAGGAAATACAAAAGTA
Found at i:32284591 original size:22 final size:21
Alignment explanation
Indices: 32284545--32284600 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
32284535 TTCAACAGTC
* *
32284545 TTGATTAGGACATACAAAAGTA
1 TTGATTA-GAAATACAAAAGGA
32284567 TTGATTAGAAATACAAAAGAGA
1 TTGATTAGAAATACAAAAG-GA
*
32284589 TTGAATA-AAATA
1 TTGATTAGAAATA
32284601 AAACGAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (21 bp):
TTGATTAGAAATACAAAAGGA
Found at i:32294194 original size:14 final size:14
Alignment explanation
Indices: 32294166--32294206 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
32294156 TAGAGTCCGA
32294166 TATAAAAAATA-AT
1 TATAAAAAATATAT
32294179 TATAAAAAATATAT
1 TATAAAAAATATAT
*
32294193 TATAAAAAGTATAT
1 TATAAAAAATATAT
32294207 GACAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
TATAAAAAATATAT
Found at i:32298931 original size:89 final size:89
Alignment explanation
Indices: 32298780--32298957 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
32298770 TGGGGGTGTG
32298780 ACTTAAGTTACGACTATGTTAAGATAAACGCAGAATATACAACATAAAAGACATTGTTGCAGAGA
1 ACTTAAGTTACGACTATGTTAAGATAAACGCAGAATATACAACATAAAAGACATTGTTGCAGAGA
32298845 GTTACATTATCCTGGTCAGGTGCA
66 GTTACATTATCCTGGTCAGGTGCA
32298869 ACTTAAGTTACGACTATGTTAAGATAAACGCAGAATATACAACATAAAAGACATTGTTGCAGAGA
1 ACTTAAGTTACGACTATGTTAAGATAAACGCAGAATATACAACATAAAAGACATTGTTGCAGAGA
32298934 GTTACATTATCCTGGTCAGGTGCA
66 GTTACATTATCCTGGTCAGGTGCA
32298958 TTAGATTGTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (89 bp):
ACTTAAGTTACGACTATGTTAAGATAAACGCAGAATATACAACATAAAAGACATTGTTGCAGAGA
GTTACATTATCCTGGTCAGGTGCA
Found at i:32321277 original size:33 final size:34
Alignment explanation
Indices: 32321203--32321281 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 34
32321193 CCCAACTGAG
*
32321203 GGGAATCTCTTTTTAATAGTAATGCAATGAAGACA
1 GGGAATCTCTTCTTAATAGTAATGCAAT-AAGACA
*
32321238 GCGAATCTCTTCTTAATAGTAATGCAAT-AGACA
1 GGGAATCTCTTCTTAATAGTAATGCAATAAGACA
32321271 GGGAATCTCTT
1 GGGAATCTCTT
32321282 TTTATTAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 15 0.37
35 26 0.63
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (34 bp):
GGGAATCTCTTCTTAATAGTAATGCAATAAGACA
Found at i:32322343 original size:3 final size:3
Alignment explanation
Indices: 32322335--32322363 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
32322325 TTAAGAGAGA
32322335 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
32322364 TATATTTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:32323622 original size:21 final size:21
Alignment explanation
Indices: 32323598--32323637 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
32323588 ACATTTTCTA
32323598 AAGTTAAAA-GTCAAAACTATT
1 AAGTTAAAAGGT-AAAACTATT
32323619 AAGTTAAAAGGTAAAACTA
1 AAGTTAAAAGGTAAAACTA
32323638 AGTTATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.25
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTATT
Found at i:32325176 original size:29 final size:30
Alignment explanation
Indices: 32325116--32325178 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
32325106 AATTTGTGAG
* * * *
32325116 AATTGAATCAAATCACAATTTCATGTATAA
1 AATTGAATAAAATCAAAATATCATGTACAA
32325146 AATTGAATAAAAT-AAAATATCATGTACAA
1 AATTGAATAAAATCAAAATATCATGTACAA
32325175 AATT
1 AATT
32325179 ACACAATTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (30 bp):
AATTGAATAAAATCAAAATATCATGTACAA
Found at i:32336431 original size:3 final size:3
Alignment explanation
Indices: 32336423--32336453 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
32336413 TTTAACCCTA
32336423 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
32336454 CAGCTCACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:32343877 original size:357 final size:366
Alignment explanation
Indices: 32343297--32343974 Score: 998
Period size: 357 Copynumber: 1.9 Consensus size: 366
32343287 TTATTCTTTT
* *
32343297 AAATATTAATTTTATTATAGTTTTTATCACATTTATTAATTTTTTTATATAATATTTAGAACTAC
1 AAATATTAATTTTATTATAATTTTTATCACATTTATTAATTTTTTTATATAATATTTAAAACTAC
** * *
32343362 TCATAAAAAAAATATATTTTAACATACTAAAGGTTACGTTCCTCTGCACTGATAATAATATTAAT
66 TCATAAAAAAAATATATTTTAACATACT-AAGGTTACAATCCACTGCACTAATAATAATATTAAT
* * *
32343427 ATCAATCGAATTAAAATTCAATCAAAATTTTTATTTTTTAGTTTTAAAAATTATTATTTGCTCTT
130 ATCAATCAAATTAAAATTCAATCAAAATTTTTATTTTTTA----TAAAAATTATGATTTGCTCGT
* * *
32343492 CTAATGTTCTCTCTTCAGGATCTTCATGTAATGAATAGTTTAATGTTATAAAAGATTGATTTAAT
191 CTAATCTACTCTCTTCAGGATCTTCATGTAATGAATAGTTTAATATTATAAAAGATTGATTTAAT
** * *
32343557 TTTTATAAATTTAGATATTGCAGAATTAAATAATATTTGAATTGAAATATTTTCATTTTTAAATA
256 TTTTATAAATTTAGATATTAAAAAATTAAATAATATTTGAATTGAAATATTTCCATTTTTAAATA
32343622 TTATTTATCATATTTCATGTAATTTAATATTAATATTATTTTTTAA
321 TTATTTATCATATTTCATGTAATTTAATATTAATATTATTTTTTAA
* * * * *
32343668 AAATATTAATTTTATTATAATTTTTATCATATTTGTTGA-TTTTTTATATAATATTTAAAATTAT
1 AAATATTAATTTTATTATAATTTTTATCACATTTATTAATTTTTTTATATAATATTTAAAACTAC
* * * *
32343732 TTATAATAAAAATATGTTTT-A-ATA-T-A-TTTA-AATCCAC-GCACTAATAATAATATTAATA
66 TCATAAAAAAAATATATTTTAACATACTAAGGTTACAATCCACTGCACTAATAATAATATTAATA
*
32343790 TCAATCAAATTAAAATTTAAT-AAATATTTTTATTTTTTA-AAAAATTATGATTTGCTCGTCTAA
131 TCAATCAAATTAAAATTCAATCAAA-ATTTTTATTTTTTATAAAAATTATGATTTGCTCGTCTAA
32343853 TCTACTCTCTTCAGGATCTTCATGTAATGAATAGTTTAATATTATAAAAGATTGATTTAATTTTT
195 TCTACTCTCTTCAGGATCTTCATGTAATGAATAGTTTAATATTATAAAAGATTGATTTAATTTTT
32343918 ATAAATTTAGATATTAAAAAATTAAATAATATTTGAATTGAAATATTTCCATTTTTA
260 ATAAATTTAGATATTAAAAAATTAAATAATATTTGAATTGAAATATTTCCATTTTTA
32343975 TTCATATCAG
Statistics
Matches: 280, Mismatches: 26, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
357 137 0.49
361 3 0.01
362 53 0.19
363 4 0.01
364 3 0.01
365 1 0.00
367 1 0.00
368 3 0.01
369 1 0.00
370 39 0.14
371 35 0.12
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.47
Consensus pattern (366 bp):
AAATATTAATTTTATTATAATTTTTATCACATTTATTAATTTTTTTATATAATATTTAAAACTAC
TCATAAAAAAAATATATTTTAACATACTAAGGTTACAATCCACTGCACTAATAATAATATTAATA
TCAATCAAATTAAAATTCAATCAAAATTTTTATTTTTTATAAAAATTATGATTTGCTCGTCTAAT
CTACTCTCTTCAGGATCTTCATGTAATGAATAGTTTAATATTATAAAAGATTGATTTAATTTTTA
TAAATTTAGATATTAAAAAATTAAATAATATTTGAATTGAAATATTTCCATTTTTAAATATTATT
TATCATATTTCATGTAATTTAATATTAATATTATTTTTTAA
Found at i:32346846 original size:18 final size:19
Alignment explanation
Indices: 32346808--32346847 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
32346798 TGCTACCACC
*
32346808 AAAAAAAGAAAAAAACTAG
1 AAAAAAAGAAAAAAACAAG
*
32346827 AAAAAAA-AAAAAGACAAG
1 AAAAAAAGAAAAAAACAAG
32346845 AAA
1 AAA
32346848 TTGGTCGGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.82, C:0.05, G:0.10, T:0.03
Consensus pattern (19 bp):
AAAAAAAGAAAAAAACAAG
Found at i:32360007 original size:21 final size:21
Alignment explanation
Indices: 32359978--32360062 Score: 108
Period size: 21 Copynumber: 4.3 Consensus size: 21
32359968 TAGTAGGTTT
*
32359978 TGTGTCGGTGTTTTCAGGCTC
1 TGTGCCGGTGTTTTCAGGCTC
32359999 TGTGCCGGTGTTTTCAGGCTC
1 TGTGCCGGTGTTTTCAGGCTC
32360020 TGTGCCGG-G----CAGGCTC
1 TGTGCCGGTGTTTTCAGGCTC
* *
32360036 TGTGCCGGTGTTTTCAAGCTT
1 TGTGCCGGTGTTTTCAGGCTC
32360057 TGTGCC
1 TGTGCC
32360063 TAGTAGGTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
16 15 0.27
17 1 0.02
20 1 0.02
21 39 0.70
ACGTcount: A:0.06, C:0.24, G:0.34, T:0.36
Consensus pattern (21 bp):
TGTGCCGGTGTTTTCAGGCTC
Found at i:32360033 original size:37 final size:37
Alignment explanation
Indices: 32359992--32360062 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
32359982 TCGGTGTTTT
*
32359992 CAGGCTCTGTGCCGGTGTTTTCAGGCTCTGTGCCGGG
1 CAGGCTCTGTGCCGGTGTTTTCAAGCTCTGTGCCGGG
*
32360029 CAGGCTCTGTGCCGGTGTTTTCAAGCTTTGTGCC
1 CAGGCTCTGTGCCGGTGTTTTCAAGCTCTGTGCC
32360063 TAGTAGGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.07, C:0.27, G:0.34, T:0.32
Consensus pattern (37 bp):
CAGGCTCTGTGCCGGTGTTTTCAAGCTCTGTGCCGGG
Found at i:32360034 original size:16 final size:16
Alignment explanation
Indices: 32360013--32360043 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
32360003 CCGGTGTTTT
32360013 CAGGCTCTGTGCCGGG
1 CAGGCTCTGTGCCGGG
32360029 CAGGCTCTGTGCCGG
1 CAGGCTCTGTGCCGG
32360044 TGTTTTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.32, G:0.42, T:0.19
Consensus pattern (16 bp):
CAGGCTCTGTGCCGGG
Found at i:32360077 original size:37 final size:37
Alignment explanation
Indices: 32359992--32360083 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 37
32359982 TCGGTGTTTT
* *
32359992 CAGGCTCTGTGCCGGTGTTTTCAGGCTCTGTGCCGGG
1 CAGGCTCTGTGCCGGTGTTTTCAAGCTCTGTGCCGAG
* *
32360029 CAGGCTCTGTGCCGGTGTTTTCAAGCTTTGTGCCTAG
1 CAGGCTCTGTGCCGGTGTTTTCAAGCTCTGTGCCGAG
* * *
32360066 TAGGTTTTGTGCCGGTGT
1 CAGGCTCTGTGCCGGTGT
32360084 ATTCGGGCTA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.08, C:0.23, G:0.35, T:0.35
Consensus pattern (37 bp):
CAGGCTCTGTGCCGGTGTTTTCAAGCTCTGTGCCGAG
Found at i:32360100 original size:37 final size:37
Alignment explanation
Indices: 32359999--32360107 Score: 92
Period size: 37 Copynumber: 2.9 Consensus size: 37
32359989 TTTCAGGCTC
* * * * ** * *
32359999 TGTGCCGGTGTTTTCAGGCTCTGTGCCGGGCAGGCTC
1 TGTGCCGGTGTATTCAAGCTATATGCCTAGCAGGTTT
* * * *
32360036 TGTGCCGGTGTTTTCAAGCTTTGTGCCTAGTAGGTTT
1 TGTGCCGGTGTATTCAAGCTATATGCCTAGCAGGTTT
**
32360073 TGTGCCGGTGTATTCGGGCTATATGCCTAGCAGGT
1 TGTGCCGGTGTATTCAAGCTATATGCCTAGCAGGT
32360108 GATCCAATAA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.10, C:0.21, G:0.34, T:0.35
Consensus pattern (37 bp):
TGTGCCGGTGTATTCAAGCTATATGCCTAGCAGGTTT
Found at i:32361358 original size:3 final size:3
Alignment explanation
Indices: 32361350--32361387 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
32361340 TAATGCTTAA
32361350 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
32361388 AGCTTTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:32363398 original size:23 final size:23
Alignment explanation
Indices: 32363368--32363484 Score: 123
Period size: 23 Copynumber: 5.1 Consensus size: 23
32363358 ACGCTAGCGC
32363368 GCTTACCG-TTCAGCACTGTGTGT
1 GCTTACCGTTTC-GCACTGTGTGT
32363391 GCTTACCG-TTCAGCACTGTGTGT
1 GCTTACCGTTTC-GCACTGTGTGT
* *
32363414 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACCGTTTCGCACTGTGTGT
* * *
32363437 GATTACTGTTTCGCACTTTGTGT
1 GCTTACCGTTTCGCACTGTGTGT
* *
32363460 GCCTACTGTTTCGCACT-TCGTGT
1 GCTTACCGTTTCGCACTGT-GTGT
32363483 GC
1 GC
32363485 CAACTGATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
22 1 0.01
23 83 0.95
24 3 0.03
ACGTcount: A:0.11, C:0.25, G:0.24, T:0.40
Consensus pattern (23 bp):
GCTTACCGTTTCGCACTGTGTGT
Found at i:32363485 original size:23 final size:23
Alignment explanation
Indices: 32363380--32363538 Score: 137
Period size: 23 Copynumber: 7.0 Consensus size: 23
32363370 TTACCGTTCA
* * *
32363380 GCACTGTGTGTGCTTACCG-TTC
1 GCACTTTGTGTGCCTACTGTTTC
* *
32363402 AGCACTGTGTGTGCTTACTGTTTC
1 -GCACTTTGTGTGCCTACTGTTTC
**
32363426 GCACTTTGTGTGATTACTGTTTC
1 GCACTTTGTGTGCCTACTGTTTC
32363449 GCACTTTGTGTGCCTACTGTTTC
1 GCACTTTGTGTGCCTACTGTTTC
* *
32363472 GCACTTCGTGTGCCAACTGATTT-
1 GCACTTTGTGTGCCTACTG-TTTC
* * * *
32363495 GCGCTATGTGCG-CTACTGATT-
1 GCACTTTGTGTGCCTACTGTTTC
* *
32363516 GCACTGTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCCTACTGTTTC
32363539 CCCAGCACTT
Statistics
Matches: 114, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
21 11 0.10
22 12 0.11
23 85 0.75
24 6 0.05
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (23 bp):
GCACTTTGTGTGCCTACTGTTTC
Found at i:32364862 original size:14 final size:14
Alignment explanation
Indices: 32364832--32364880 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
32364822 TTGAGAAATC
*
32364832 TTTTTAAAAAGTG-
1 TTTTGAAAAAGTGA
*
32364845 TTTTGAAAAAATGA
1 TTTTGAAAAAGTGA
32364859 TTTT-AAAAAGT-A
1 TTTTGAAAAAGTGA
32364871 CTTTTGAAAA
1 -TTTTGAAAA
32364881 GATTGGTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 1 0.03
13 21 0.70
14 8 0.27
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (14 bp):
TTTTGAAAAAGTGA
Found at i:32365662 original size:5 final size:5
Alignment explanation
Indices: 32365652--32365680 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
32365642 AAGATGACGC
32365652 CACTG CACTG CACTG CACTG CACTG CACT
1 CACTG CACTG CACTG CACTG CACTG CACT
32365681 CACGTGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.41, G:0.17, T:0.21
Consensus pattern (5 bp):
CACTG
Found at i:32366840 original size:3 final size:3
Alignment explanation
Indices: 32366832--32366863 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
32366822 TATGGCTGAC
32366832 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
32366864 GCCGTCGCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:32370686 original size:3 final size:3
Alignment explanation
Indices: 32370680--32370705 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
32370670 TCTTCATAAT
32370680 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
32370706 CACTGCTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:32372825 original size:2 final size:2
Alignment explanation
Indices: 32372818--32372863 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
32372808 AAACGTAATA
32372818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32372860 AT AT
1 AT AT
32372864 TAAGCTAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32377483 original size:6 final size:6
Alignment explanation
Indices: 32377472--32377534 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
32377462 TGATCAAAAT
*
32377472 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
* *
32377520 TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGA
32377535 TATGAATTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.21
Consensus pattern (6 bp):
TGAAAG
Found at i:32384403 original size:14 final size:16
Alignment explanation
Indices: 32384375--32384406 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
32384365 TTTTAATAAT
32384375 TTTTTTACAATATTTA
1 TTTTTTACAATATTTA
*
32384391 TTTTTTACAATTTTTA
1 TTTTTTACAATATTTA
32384407 AATATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTTACAATATTTA
Found at i:32385032 original size:19 final size:20
Alignment explanation
Indices: 32385003--32385044 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
32384993 TAAAATTAAA
*
32385003 AAAATAATAAAAATTCTTGG
1 AAAATAATAAAAACTCTTGG
*
32385023 AAAA-AATAAAAGCTCTTGG
1 AAAATAATAAAAACTCTTGG
32385042 AAA
1 AAA
32385045 TAAGCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.57, C:0.07, G:0.12, T:0.24
Consensus pattern (20 bp):
AAAATAATAAAAACTCTTGG
Found at i:32394296 original size:15 final size:16
Alignment explanation
Indices: 32394276--32394308 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
32394266 GCCCGGTCGG
*
32394276 TCCATTCTCCATT-TC
1 TCCATTCCCCATTCTC
32394291 TCCATTCCCCATTCTC
1 TCCATTCCCCATTCTC
32394307 TC
1 TC
32394309 TTTTCTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.12, C:0.45, G:0.00, T:0.42
Consensus pattern (16 bp):
TCCATTCCCCATTCTC
Found at i:32397285 original size:24 final size:24
Alignment explanation
Indices: 32397252--32397298 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
32397242 TGTGGCATAC
* *
32397252 ATACACACACATGCATGCATACAT
1 ATACACACACATACATACATACAT
*
32397276 ATACATACACATACATACATACA
1 ATACACACACATACATACATACA
32397299 CACACACATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.04, T:0.21
Consensus pattern (24 bp):
ATACACACACATACATACATACAT
Found at i:32397295 original size:14 final size:14
Alignment explanation
Indices: 32397247--32397304 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
32397237 TTTCTTGTGG
32397247 CATACATACACACA
1 CATACATACACACA
* * *
32397261 CATGCATGCATACA
1 CATACATACACACA
* *
32397275 TATACATACACATA
1 CATACATACACACA
32397289 CATACATACACACA
1 CATACATACACACA
32397303 CA
1 CA
32397305 CATTTCTTTA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (14 bp):
CATACATACACACA
Found at i:32398149 original size:20 final size:19
Alignment explanation
Indices: 32398085--32398148 Score: 85
Period size: 20 Copynumber: 3.4 Consensus size: 19
32398075 TAAAATTTGA
*
32398085 AATTTTTATAAA-TATTTT
1 AATTTTTAAAAATTATTTT
* *
32398103 TATTTTTAAAAATTAATTTA
1 AATTTTTAAAAATT-ATTTT
32398123 AATTTTTAAAAATTATTTT
1 AATTTTTAAAAATTATTTT
32398142 AATTTTT
1 AATTTTT
32398149 TTTTATAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 10 0.26
19 12 0.31
20 17 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTTTAAAAATTATTTT
Found at i:32402257 original size:21 final size:21
Alignment explanation
Indices: 32402232--32402286 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
32402222 CAAAAGACAA
*
32402232 CTACCGATATAACTCTTGGTT
1 CTACCGATACAACTCTTGGTT
32402253 CTACCGATACAACTCTTGGTT
1 CTACCGATACAACTCTTGGTT
32402274 CTACCGATACAAC
1 CTACCGATACAAC
32402287 CAAAACTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (21 bp):
CTACCGATACAACTCTTGGTT
Found at i:32402877 original size:24 final size:24
Alignment explanation
Indices: 32402845--32402890 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
32402835 TTTTCAATCA
32402845 TTTTTTTAAGTGTTGTAACTTTAT
1 TTTTTTTAAGTGTTGTAACTTTAT
32402869 TTTTTTTAAGTGTTGTAACTTT
1 TTTTTTTAAGTGTTGTAACTTT
32402891 GTGTGAGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.04, G:0.13, T:0.63
Consensus pattern (24 bp):
TTTTTTTAAGTGTTGTAACTTTAT
Found at i:32404491 original size:13 final size:13
Alignment explanation
Indices: 32404431--32404494 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
32404421 TAATTTATTT
*
32404431 ACCTTGAATCATAA
1 ACCTTAAATC-TAA
* *
32404445 ACCTTTAACCGTAA
1 ACCTTAAATC-TAA
*
32404459 ACCTTAAA-CTCGA
1 ACCTTAAATCT-AA
32404472 ACC-TAAATCTAA
1 ACCTTAAATCTAA
32404484 ACCTTAAATCT
1 ACCTTAAATCT
32404495 TATACTCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
12 9 0.22
13 14 0.34
14 18 0.44
ACGTcount: A:0.41, C:0.27, G:0.05, T:0.28
Consensus pattern (13 bp):
ACCTTAAATCTAA
Found at i:32407551 original size:21 final size:21
Alignment explanation
Indices: 32407527--32407588 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
32407517 CAACACTCAC
32407527 AACATTATTTCCTGAATAGAA
1 AACATTATTTCCTGAATAGAA
**
32407548 AACAAAACTTT--TGAAATAGAA
1 AACATTA-TTTCCTG-AATAGAA
32407569 ACAGCATTATTTCCTGAATA
1 A-A-CATTATTTCCTGAATA
32407589 TGAACACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
20 2 0.06
21 13 0.42
22 7 0.23
23 7 0.23
24 2 0.06
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.31
Consensus pattern (21 bp):
AACATTATTTCCTGAATAGAA
Found at i:32408338 original size:2 final size:2
Alignment explanation
Indices: 32408331--32408364 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
32408321 AAAAACAAGA
32408331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32408365 TAGTGTTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32415262 original size:30 final size:31
Alignment explanation
Indices: 32415222--32415285 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
32415212 CTTTATCCAC
32415222 TTTTTTAAAATCATAAAAAT-T-TAATTTAA
1 TTTTTTAAAATCATAAAAATATATAATTTAA
*
32415251 TTTTTTAAAAATTATAAAAATATATAATTTAA
1 TTTTTT-AAAATCATAAAAATATATAATTTAA
32415283 TTT
1 TTT
32415286 CTATCTCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 6 0.19
30 13 0.42
31 1 0.03
32 11 0.35
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (31 bp):
TTTTTTAAAATCATAAAAATATATAATTTAA
Found at i:32419086 original size:30 final size:31
Alignment explanation
Indices: 32419025--32419086 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
32419015 ATAAAATTTT
* * *
32419025 AAATTAAATTTGATTCTTTCAAAAATTATAA
1 AAATTAAATTTAACTCTTTCAAAAATAATAA
*
32419056 AAATTTAATTTAACTCTTT-AAAAATAATAA
1 AAATTAAATTTAACTCTTTCAAAAATAATAA
32419086 A
1 A
32419087 TATATAAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (31 bp):
AAATTAAATTTAACTCTTTCAAAAATAATAA
Found at i:32420770 original size:12 final size:12
Alignment explanation
Indices: 32420755--32420846 Score: 53
Period size: 12 Copynumber: 7.8 Consensus size: 12
32420745 TTTTTTACTG
*
32420755 TTTTCGTTGCTA
1 TTTTTGTTGCTA
*
32420767 -TTTTGGTGCTA
1 TTTTTGTTGCTA
* *
32420778 TTTTTATTGTTA
1 TTTTTGTTGCTA
*
32420790 TTTTTGTTTCTA
1 TTTTTGTTGCTA
**
32420802 TTTTT-TCTATTA
1 TTTTTGT-TGCTA
* *
32420814 TTTTTGTTACTG
1 TTTTTGTTGCTA
* *
32420826 TTTTGGTTGTTA
1 TTTTTGTTGCTA
*
32420838 TTTTGGTTG
1 TTTTTGTTG
32420847 TTTGAATGTT
Statistics
Matches: 61, Mismatches: 16, Indels: 6
0.73 0.19 0.07
Matches are distributed among these distances:
11 10 0.16
12 50 0.82
13 1 0.02
ACGTcount: A:0.10, C:0.07, G:0.16, T:0.67
Consensus pattern (12 bp):
TTTTTGTTGCTA
Found at i:32420830 original size:35 final size:35
Alignment explanation
Indices: 32420743--32420842 Score: 100
Period size: 36 Copynumber: 2.8 Consensus size: 35
32420733 CTATTTTGGG
32420743 TTTTTT-TTACTGTTTTCGTTGCTATTTTGGTGCTAT
1 TTTTTTGTTACTGTTTT-GTTGCTATTTT-GTGCTAT
* *
32420779 TTTTATTGTTA-T-TTTTGTTTCTATTTT-TTCTAT
1 TTTT-TTGTTACTGTTTTGTTGCTATTTTGTGCTAT
*
32420812 TATTTTTGTTACTGTTTTGGTTGTTATTTTG
1 T-TTTTTGTTACTGTTTT-GTTGCTATTTTG
32420843 GTTGTTTGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
33 12 0.23
34 4 0.08
35 14 0.26
36 17 0.32
37 3 0.06
38 3 0.06
ACGTcount: A:0.10, C:0.07, G:0.14, T:0.69
Consensus pattern (35 bp):
TTTTTTGTTACTGTTTTGTTGCTATTTTGTGCTAT
Found at i:32420838 original size:24 final size:23
Alignment explanation
Indices: 32420670--32420841 Score: 90
Period size: 22 Copynumber: 7.7 Consensus size: 23
32420660 TATATTGTTG
* **
32420670 TTTTGG-TGCTATTTTTTTGTTA
1 TTTTGGTTGTTATTTTTTTACTA
* *
32420692 TTTTGGTTGCTA-TTTTTTACTG
1 TTTTGGTTGTTATTTTTTTACTA
* *
32420714 TTTTGG-TGTTGTGTTTTTACTA
1 TTTTGGTTGTTATTTTTTTACTA
*
32420736 TTTTGG--G-T-TTTTTTTACTG
1 TTTTGGTTGTTATTTTTTTACTA
* * ** *
32420755 TTTTCGTTGCTATTTTGGTGCTA
1 TTTTGGTTGTTATTTTTTTACTA
** *
32420778 TTTTTATTGTTATTTTTGTTTCTA
1 TTTTGGTTGTTATTTTT-TTACTA
* * *
32420802 TTTT-TTCTATTATTTTTGTTACTG
1 TTTTGGT-TGTTATTTTT-TTACTA
32420826 TTTTGGTTGTTATTTT
1 TTTTGGTTGTTATTTT
32420842 GGTTGTTTGA
Statistics
Matches: 115, Mismatches: 26, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
19 14 0.12
20 1 0.01
21 5 0.04
22 34 0.30
23 26 0.23
24 34 0.30
25 1 0.01
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.67
Consensus pattern (23 bp):
TTTTGGTTGTTATTTTTTTACTA
Found at i:32420842 original size:23 final size:23
Alignment explanation
Indices: 32420690--32420842 Score: 88
Period size: 24 Copynumber: 6.8 Consensus size: 23
32420680 ATTTTTTTGT
*
32420690 TATTTTGGTTGCTATTTT-TTAC
1 TATTTTGGTTGTTATTTTGTTAC
* *
32420712 TGTTTTGG-TGTTGTGTTT-TTAC
1 TATTTTGGTTGTTAT-TTTGTTAC
32420734 TATTTTGG--GTT-TTTT-TTAC
1 TATTTTGGTTGTTATTTTGTTAC
* * * * *
32420753 TGTTTTCGTTGCTATTTTGGTGC
1 TATTTTGGTTGTTATTTTGTTAC
** *
32420776 TATTTTTATTGTTATTTTTGTTTC
1 TATTTTGGTTGTTA-TTTTGTTAC
* *
32420800 TATTTT-TTCTATTATTTTTGTTAC
1 TATTTTGGT-TGTTA-TTTTGTTAC
*
32420824 TGTTTTGGTTGTTATTTTG
1 TATTTTGGTTGTTATTTTG
32420843 GTTGTTTGAA
Statistics
Matches: 102, Mismatches: 21, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.13
20 1 0.01
21 9 0.09
22 25 0.25
23 18 0.18
24 35 0.34
25 1 0.01
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.67
Consensus pattern (23 bp):
TATTTTGGTTGTTATTTTGTTAC
Found at i:32430924 original size:31 final size:28
Alignment explanation
Indices: 32430846--32430925 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 28
32430836 TGTGTAATTA
32430846 TATACATG-AACTTTAATTTGGTGCAAT
1 TATACATGAAACTTTAATTTGGTGCAAT
* * *
32430873 TATACACGTAAAACTCTAATTGTGGTTCAAAT
1 TATACA--TGAAACTTTAATT-TGGTGC-AAT
32430905 CTATACATGAAACTTTAATTT
1 -TATACATGAAACTTTAATTT
32430926 TGATTTAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 6 0.14
29 1 0.02
30 10 0.24
31 16 0.38
32 3 0.07
33 6 0.14
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (28 bp):
TATACATGAAACTTTAATTTGGTGCAAT
Found at i:32431110 original size:29 final size:30
Alignment explanation
Indices: 32431068--32431147 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
32431058 GAATTGGATC
*
32431068 AAATCAAAATTTCATGTATAAAATTACACA-
1 AAATC-AAAGTTCATGTATAAAATTACACAT
* *
32431098 AAATCAAAGTTCATGTATACAATTGCACATT
1 AAATCAAAGTTCATGTATAAAATTACACA-T
* *
32431129 AAACCATAGTTCATGTATA
1 AAATCAAAGTTCATGTATA
32431148 GTTTTGGGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 21 0.49
30 5 0.12
31 17 0.40
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTACACAT
Found at i:32434591 original size:18 final size:18
Alignment explanation
Indices: 32434546--32434606 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
32434536 CTATATAAAC
* *
32434546 AAATAATTTAAAAATAAT
1 AAATAATTAAAAAATTAT
32434564 AAA-AATTTAAAAAATTAT
1 AAATAA-TTAAAAAATTAT
32434582 AAATAATTAATAAAAATTA-
1 AAATAATT-A-AAAAATTAT
32434601 AAATAA
1 AAATAA
32434607 ATACATGTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
17 2 0.05
18 18 0.49
19 9 0.24
20 8 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAATTAAAAAATTAT
Found at i:32434599 original size:10 final size:10
Alignment explanation
Indices: 32434554--32434601 Score: 57
Period size: 9 Copynumber: 5.0 Consensus size: 10
32434544 ACAAATAATT
32434554 TAAAAA-TAA
1 TAAAAATTAA
*
32434563 TAAAAATTTA
1 TAAAAATTAA
32434573 -AAAAATT-A
1 TAAAAATTAA
32434581 TAAATAATTAA
1 TAAA-AATTAA
32434592 TAAAAATTAA
1 TAAAAATTAA
32434602 AATAAATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
8 1 0.03
9 16 0.47
10 12 0.35
11 5 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:32438714 original size:30 final size:29
Alignment explanation
Indices: 32438638--32438746 Score: 87
Period size: 31 Copynumber: 3.7 Consensus size: 29
32438628 ACACTTGTTC
**
32438638 TTAATTTGGTA-TATAAACTTA-TTTTGGT
1 TTAATTTGGTACT-TAAACTTACTTTTTTT
* * **
32438666 TCAACTTGGTACCCAAACTTGACTTTTTTT
1 TTAATTTGGTACTTAAACTT-ACTTTTTTT
* *
32438696 TTAATTTGGTACTTAAACTTAACACTTTTTC
1 TTAATTTGGTACTTAAACTT-AC-TTTTTTT
*
32438727 TTAAGTTGGTACTTAAACTT
1 TTAATTTGGTACTTAAACTT
32438747 TTGGGGGATT
Statistics
Matches: 63, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
28 15 0.24
29 1 0.02
30 23 0.37
31 24 0.38
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.48
Consensus pattern (29 bp):
TTAATTTGGTACTTAAACTTACTTTTTTT
Found at i:32441261 original size:6 final size:6
Alignment explanation
Indices: 32441250--32441277 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
32441240 AACTTCAAAA
32441250 ACATAT ACATAT ACATAT ACATAT ACAT
1 ACATAT ACATAT ACATAT ACATAT ACAT
32441278 GCATATATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:32466469 original size:14 final size:14
Alignment explanation
Indices: 32466450--32466480 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
32466440 AGAATAAATC
32466450 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
32466464 TTTAATTAATTAAA
1 TTTAATTAAATAAA
32466478 TTT
1 TTT
32466481 TTAAACCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:32488149 original size:20 final size:19
Alignment explanation
Indices: 32488107--32488151 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
32488097 TTTTCTCATA
*
32488107 ATTTTTATTTAAAAAATAC
1 ATTTTTATTTAAAAAACAC
* *
32488126 ATTTTTAATTTAAAATACAT
1 ATTTTT-ATTTAAAAAACAC
32488146 ATTTTT
1 ATTTTT
32488152 GTTTTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTTATTTAAAAAACAC
Found at i:32489347 original size:16 final size:16
Alignment explanation
Indices: 32489326--32489385 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
32489316 TTTGGTTCGC
32489326 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGT
*
32489342 TGTAATAGAATAGAGT
1 TGTAATGGAATAGAGT
*
32489358 TGTAATGGAATAGAGA
1 TGTAATGGAATAGAGT
32489374 TGTAATGGAATA
1 TGTAATGGAATA
32489386 TGACTGTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:32489393 original size:16 final size:16
Alignment explanation
Indices: 32489324--32489395 Score: 92
Period size: 16 Copynumber: 4.5 Consensus size: 16
32489314 CGTTTGGTTC
32489324 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
32489340 GTTGTAATAGAATAGA
1 GCTGTAATGGAATAGA
*
32489356 GTTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
32489372 GATGTAATGGAATATGA
1 GCTGTAATGGAATA-GA
32489389 -CTGTAAT
1 GCTGTAAT
32489396 CAGTAATTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
16 48 0.96
17 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.28, T:0.31
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:32489473 original size:49 final size:51
Alignment explanation
Indices: 32489377--32489475 Score: 141
Period size: 49 Copynumber: 2.0 Consensus size: 51
32489367 ATAGAGATGT
32489377 AATGGAATATGACTGTAATCAGTAATTCAGTTGTTTGGTTGAATGGAATGG
1 AATGGAATATGACTGTAATCAGTAATTCAGTTGTTTGGTTGAATGGAATGG
* **
32489428 AATGGAATA-GAACTGTAAT-AGTATTTTTG-TGTTTGGTTGAATGGAATG
1 AATGGAATATG-ACTGTAATCAGTAATTCAGTTGTTTGGTTGAATGGAATG
32489476 ATGCTGCAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
49 19 0.43
50 8 0.18
51 17 0.39
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.37
Consensus pattern (51 bp):
AATGGAATATGACTGTAATCAGTAATTCAGTTGTTTGGTTGAATGGAATGG
Found at i:32489623 original size:58 final size:59
Alignment explanation
Indices: 32489561--32489722 Score: 197
Period size: 58 Copynumber: 2.8 Consensus size: 59
32489551 TTGTTATAAA
* *
32489561 ATTTTAATA-AGATTATTATTAAATATAATTTACTAAAAATAATAAATAATTTAATTA-T
1 ATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACT
* * *
32489619 ATTTTAACATAATTATTATTAAATATAATTAAAT-AAAATAATATATAATTTAATAACGT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAAC-T
* * *
32489678 -TTTTAATATAATTATTATTAAAATATAAATTAGTAAAAATTATAA
1 ATTTTAATATAATTATTATT-AAATATAATTTAATAAAAATAATAA
32489723 TATATAACTT
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
57 20 0.23
58 47 0.53
59 13 0.15
60 8 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (59 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACT
Found at i:32492796 original size:2 final size:2
Alignment explanation
Indices: 32492789--32492819 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32492779 GTTAATATCC
32492789 AT AT AT 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 AT AT AT A
32492820 CATGGATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32513195 original size:19 final size:19
Alignment explanation
Indices: 32513155--32513209 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
32513145 TAATAATTTT
*
32513155 ATTAAAAGTATAAAAATCAA
1 ATTAAAA-TATAAATATCAA
*
32513175 ATTAAAATATAAATATTAA
1 ATTAAAATATAAATATCAA
*
32513194 ATCT-AAATTTAAATAT
1 AT-TAAAATATAAATAT
32513210 AATATATGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 23 0.74
20 8 0.26
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
ATTAAAATATAAATATCAA
Found at i:32513200 original size:13 final size:12
Alignment explanation
Indices: 32513173--32513211 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
32513163 TATAAAAATC
*
32513173 AAATTAAAATAT
1 AAATTTAAATAT
*
32513185 AAATATTAAATCT
1 AAAT-TTAAATAT
32513198 AAATTTAAATAT
1 AAATTTAAATAT
32513210 AA
1 AA
32513212 TATATGGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATTTAAATAT
Found at i:32513201 original size:25 final size:25
Alignment explanation
Indices: 32513168--32513216 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
32513158 AAAAGTATAA
32513168 AAATCAAATTAAAATATAA-ATATT
1 AAATCAAATTAAAATATAATATATT
*
32513192 AAATCTAAATTTAAATATAATATAT
1 AAATC-AAATTAAAATATAATATAT
32513217 GGATCATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 13 0.59
26 4 0.18
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
AAATCAAATTAAAATATAATATATT
Found at i:32513659 original size:15 final size:17
Alignment explanation
Indices: 32513628--32513659 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32513618 TTAACTTGAG
32513628 ATCAATATAGATATTTA
1 ATCAATATAGATATTTA
32513645 ATCAATA-AG-TATTTA
1 ATCAATATAGATATTTA
32513660 TTAAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
ATCAATATAGATATTTA
Found at i:32514834 original size:19 final size:18
Alignment explanation
Indices: 32514812--32514875 Score: 51
Period size: 20 Copynumber: 3.4 Consensus size: 18
32514802 AGTTTAATTT
32514812 TTAATATTGAAATATTTTA
1 TTAATATT-AAATATTTTA
*
32514831 TTAAT-TT-AATATTTTTT
1 TTAATATTAAATA-TTTTA
* *
32514848 TTAAAATTTAAATATAGTTA
1 TTAATA-TTAAATAT-TTTA
32514868 TTAATATT
1 TTAATATT
32514876 TAAAAAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
16 4 0.11
17 8 0.23
18 2 0.06
19 10 0.29
20 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TTAATATTAAATATTTTA
Found at i:32518850 original size:362 final size:362
Alignment explanation
Indices: 32518184--32519433 Score: 1817
Period size: 362 Copynumber: 3.5 Consensus size: 362
32518174 ATATCGAAAA
* * * * * *
32518184 AACGGCTAATAGCATGTTTTAACAAAATCAAAATAACCTCAATAATGGTAGTCAACACAGATTGG
1 AACGGCTAATAGCATGCTTTAACCAAATAAAAATAACATCAACAATGGTAGCCAACACAGATTGG
* * * * * * * *
32518249 GTTGAGTGTCATTTGATAAATGGTTTGTAATTATCATTTTTAACCACCTATTAAAAACTAATAGT
66 GCTGAGTGTCATTTGATAAATGATCTGTAATTACCATTTTTAGCCATCTATTAAAAGCTAATAGC
* * * * *
32518314 CGTTACTCTGGACTATCATAAAGTTAATAGCATGTCACAGTCTTTCTTCGTGTAAAATGTCAATT
131 CGTTACTCTAGACTATCATAAGGTTAATAGCATATCATAGTATTTCTTCGTGTAAAATGTCAATT
* * *
32518379 ATAGTCTAATCAACATGTTAAGTTTGCAAATTTTAACGAAAATATTAATAATTTTAATGATGGGA
196 ATAGTCTAATCAACATGTTAAGTTTGCAAATTTT-ATGAAAATACTAATAATTTTAATGATTGGA
*
32518444 CTGTGATTTTTGAATTAGAAAAGCAAGAGGGCTTAAGTTTTAATCATTTAGGTACAGAGACTAAA
260 CTGTGATTTTTAAATTAGAAAAGCAAGAGGGCTTAAGTTTTAATCATTTAGGTACAGAGACTAAA
*
32518509 TTTTAAATATTATCTAAGTATAAAGACCAAAAACATAT
325 TTTTAAATATTATCTAAGTATAAGGACCAAAAACATAT
* * * *
32518547 AACGGCTAGTAGCATGCTTTAACCAAATAAAAATAACATCAACAATGGTAACCAAAACAAATTGG
1 AACGGCTAATAGCATGCTTTAACCAAATAAAAATAACATCAACAATGGTAGCCAACACAGATTGG
* * *
32518612 GTTGAGTGTCATTTGATAAATGATCTGTAATTACCATTTTTAGCCATTTATTAAAAGCTAAT-GA
66 GCTGAGTGTCATTTGATAAATGATCTGTAATTACCATTTTTAGCCATCTATTAAAAGCTAATAGC
* * *
32518676 CGTTACTCTAGACTATCATAAGGTTAATAGCATATCATAGTATTTCTTCATATAAAACGTCAATT
131 CGTTACTCTAGACTATCATAAGGTTAATAGCATATCATAGTATTTCTTCGTGTAAAATGTCAATT
*
32518741 ATAGTCTAATCAACATGTTAAGTTTACAAATTTTGATGAAAATACTAATAATTTTAATGATTGGA
196 ATAGTCTAATCAACATGTTAAGTTTGCAAATTTT-ATGAAAATACTAATAATTTTAATGATTGGA
* * *
32518806 CTATGATTTTTAAATTAAAAAAGCAAGAGGGCTTAAGTTTTAATCATTTAGGTATAGAGACTAAA
260 CTGTGATTTTTAAATTAGAAAAGCAAGAGGGCTTAAGTTTTAATCATTTAGGTACAGAGACTAAA
*
32518871 TTTTAAATATTAT-TCAAGTATAAGGACCAAAAA-TTAT
325 TTTTAAATATTATCT-AAGTATAAGGACCAAAAACATAT
* *
32518908 AATGGCTAATAGCATGCTTTAACCAAATAAAAATAACATCAACAATGGTAGCCAACGCAGATTGG
1 AACGGCTAATAGCATGCTTTAACCAAATAAAAATAACATCAACAATGGTAGCCAACACAGATTGG
* * *
32518973 GCTGAGTGTCATTCGATAAATGATCTGTAATTACTATTTTTAGCCATTTATTAAAAGCTAATAGC
66 GCTGAGTGTCATTTGATAAATGATCTGTAATTACCATTTTTAGCCATCTATTAAAAGCTAATAGC
* *
32519038 CGTTACTCTGGACTATCATAAGGTTAATAGCATATCATAGTATTTCTTTGTGTAAAATGTCAATT
131 CGTTACTCTAGACTATCATAAGGTTAATAGCATATCATAGTATTTCTTCGTGTAAAATGTCAATT
*
32519103 ATAGTCTAATCAACATGTTAATTTTGCAAAATTTTATGAAAATACTAATAATTTTAATGA-TGAG
196 ATAGTCTAATCAACATGTTAAGTTTGC-AAATTTTATGAAAATACTAATAATTTTAATGATTG-G
* * * *
32519167 ACTGTGATTTTTAATTTAGAAAAGTAAGAGGGCTTAAGTTTTAACCATTTAGGTACAAAGACTAA
259 ACTGTGATTTTTAAATTAGAAAAGCAAGAGGGCTTAAGTTTTAATCATTTAGGTACAGAGACTAA
*
32519232 ATTTTAAATATTAACTAAGTATAAGGACC-AAAACATAT
324 ATTTTAAATATTATCTAAGTATAAGGACCAAAAACATAT
* * * **
32519270 AATGGCTAATAGCATGCTCTAACCAAATAAAAATAACATCAACAATGGTAGCCAACGCAGATTAA
1 AACGGCTAATAGCATGCTTTAACCAAATAAAAATAACATCAACAATGGTAGCCAACACAGATTGG
* * ** *
32519335 GCTAAGTGTTATTTGATAAATGATCTGTAATTACCATTTTTATTCATCTATTAAAAGTTAATAGC
66 GCTGAGTGTCATTTGATAAATGATCTGTAATTACCATTTTTAGCCATCTATTAAAAGCTAATAGC
* * * * *
32519400 CGTTATTTTAAATTACCATAAGGTTAATAGCATA
131 CGTTACTCTAGACTATCATAAGGTTAATAGCATA
32519434 CCACAACTTT
Statistics
Matches: 801, Mismatches: 80, Indels: 13
0.90 0.09 0.01
Matches are distributed among these distances:
361 128 0.16
362 555 0.69
363 118 0.15
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (362 bp):
AACGGCTAATAGCATGCTTTAACCAAATAAAAATAACATCAACAATGGTAGCCAACACAGATTGG
GCTGAGTGTCATTTGATAAATGATCTGTAATTACCATTTTTAGCCATCTATTAAAAGCTAATAGC
CGTTACTCTAGACTATCATAAGGTTAATAGCATATCATAGTATTTCTTCGTGTAAAATGTCAATT
ATAGTCTAATCAACATGTTAAGTTTGCAAATTTTATGAAAATACTAATAATTTTAATGATTGGAC
TGTGATTTTTAAATTAGAAAAGCAAGAGGGCTTAAGTTTTAATCATTTAGGTACAGAGACTAAAT
TTTAAATATTATCTAAGTATAAGGACCAAAAACATAT
Found at i:32527930 original size:70 final size:71
Alignment explanation
Indices: 32527814--32527966 Score: 245
Period size: 70 Copynumber: 2.2 Consensus size: 71
32527804 CAACTATTGG
* * *
32527814 TTCTACCGATACAACCAATACTTTTATCGGTAGAACAAACTCCAGTGAG-CAAGAAGTTGTGGCT
1 TTCTACCGATACAACCAAGACTTCTATCGGTAGAACAAACTCCAGTGAGAAAAGAAGTTGTGGCT
32527878 TGGGAC
66 TGGGAC
* *
32527884 TTTTACCGATACAACCAAGACTTCTATCGGTAGAACAAACTTCAGTGAGAAAAGAAGTTGTGGCT
1 TTCTACCGATACAACCAAGACTTCTATCGGTAGAACAAACTCCAGTGAGAAAAGAAGTTGTGGCT
32527949 TGGGAC
66 TGGGAC
*
32527955 TTCTACTGATAC
1 TTCTACCGATAC
32527967 CTTGGCTAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
70 45 0.60
71 30 0.40
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (71 bp):
TTCTACCGATACAACCAAGACTTCTATCGGTAGAACAAACTCCAGTGAGAAAAGAAGTTGTGGCT
TGGGAC
Found at i:32528946 original size:26 final size:28
Alignment explanation
Indices: 32528913--32528964 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
32528903 TTTCGATATT
32528913 TAATTTAATCCT-TAA-AAATAAAAAAA
1 TAATTTAATCCTATAATAAATAAAAAAA
*
32528939 TAATTTAATCCTATAATAAATCAAAA
1 TAATTTAATCCTATAATAAATAAAAA
32528965 TTGCAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 12 0.52
27 3 0.13
28 8 0.35
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.33
Consensus pattern (28 bp):
TAATTTAATCCTATAATAAATAAAAAAA
Found at i:32549664 original size:36 final size:36
Alignment explanation
Indices: 32549624--32549695 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
32549614 ATTTGATTTA
* *
32549624 TGCAAACATCCGCCCAAATTAAGAGGGAAAAGAAAC
1 TGCAAACATCCACCCAAATTAAGAAGGAAAAGAAAC
32549660 TGCAAACATCCACCCAAATTAAGAAGGAAAAGAAAC
1 TGCAAACATCCACCCAAATTAAGAAGGAAAAGAAAC
32549696 CCAGACTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (36 bp):
TGCAAACATCCACCCAAATTAAGAAGGAAAAGAAAC
Found at i:32553593 original size:21 final size:22
Alignment explanation
Indices: 32553560--32553602 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
32553550 TTAATGAAAA
32553560 AATTAACTTTTAAAAATTAATT
1 AATTAACTTTTAAAAATTAATT
32553582 AATTAA-TTTTAAAAATTAATT
1 AATTAACTTTTAAAAATTAATT
32553603 TATCTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTAACTTTTAAAAATTAATT
Found at i:32553600 original size:13 final size:13
Alignment explanation
Indices: 32553557--32553603 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
32553547 AAATTAATGA
32553557 AAAAATTAACTTTT
1 AAAAATTAA-TTTT
32553571 AAAAATTAA--TT
1 AAAAATTAATTTT
32553582 ---AATTAATTTT
1 AAAAATTAATTTT
32553592 AAAAATTAATTT
1 AAAAATTAATTT
32553604 ATCTTGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
8 6 0.21
10 2 0.07
11 2 0.07
13 9 0.32
14 9 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAAATTAATTTT
Found at i:32554410 original size:18 final size:18
Alignment explanation
Indices: 32554387--32554429 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
32554377 AAATAGGTTT
32554387 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
32554405 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
32554423 TTAATTA
1 TTAATTA
32554430 CACATCTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:32555001 original size:24 final size:23
Alignment explanation
Indices: 32554950--32555001 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
32554940 AAAGTAGATA
* *
32554950 AAAAAACGTGCCATAAGGCAAAG
1 AAAAAACGTGCCAAAAGACAAAG
* *
32554973 GAAAAACGTGCCACAAAGACAAAT
1 AAAAAACGTGCCA-AAAGACAAAG
32554997 AAAAA
1 AAAAA
32555002 CTAGAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.58, C:0.17, G:0.17, T:0.08
Consensus pattern (23 bp):
AAAAAACGTGCCAAAAGACAAAG
Found at i:32555002 original size:23 final size:23
Alignment explanation
Indices: 32554951--32554995 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
32554941 AAGTAGATAA
* *
32554951 AAAAACGTGCCATAAGGCAAAGG
1 AAAAACGTGCCAAAAGACAAAGG
32554974 AAAAACGTGCCACAAAGACAAA
1 AAAAACGTGCCA-AAAGACAAA
32554996 TAAAAACTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.53, C:0.20, G:0.20, T:0.07
Consensus pattern (23 bp):
AAAAACGTGCCAAAAGACAAAGG
Found at i:32556056 original size:29 final size:28
Alignment explanation
Indices: 32556018--32556078 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
32556008 TCATTCATTT
*
32556018 AATCCTATTTAACAATAAACA-AAATAAC
1 AATCCTATTTAACAA-AAAAATAAATAAC
**
32556046 AATCCATATTTGTCAAAAAAATAAATAAC
1 AATCC-TATTTAACAAAAAAATAAATAAC
32556075 AATC
1 AATC
32556079 ATACATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (28 bp):
AATCCTATTTAACAAAAAAATAAATAAC
Found at i:32565747 original size:7 final size:7
Alignment explanation
Indices: 32565735--32565767 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
32565725 AGATGATTTG
32565735 ATAAAAA
1 ATAAAAA
32565742 ATAAAAA
1 ATAAAAA
32565749 ATAAAAA
1 ATAAAAA
*
32565756 A-ATAAA
1 ATAAAAA
32565762 ATAAAA
1 ATAAAA
32565768 TGCTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:32575851 original size:14 final size:14
Alignment explanation
Indices: 32575814--32575855 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
32575804 TTATATTTTA
32575814 AATATTTAAATA-T
1 AATATTTAAATATT
32575827 AATCA-TTAAATATT
1 AAT-ATTTAAATATT
*
32575841 TATATTTAAATATT
1 AATATTTAAATATT
32575855 A
1 A
32575856 GCACAGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:32576385 original size:21 final size:21
Alignment explanation
Indices: 32576361--32576432 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 21
32576351 ATAAATAAGT
32576361 AGAACATAAATTCAATATCCA
1 AGAACATAAATTCAATATCCA
***
32576382 AGAACCA-AACATTTGCACATAAATA
1 AGAA-CATAA-A-TT-CA-ATATCCA
32576407 AGAACATAAATTCAATATCCA
1 AGAACATAAATTCAATATCCA
32576428 AGAAC
1 AGAAC
32576433 CAAACATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 15 0.38
22 5 0.13
23 4 0.10
24 5 0.13
25 10 0.26
ACGTcount: A:0.53, C:0.19, G:0.07, T:0.21
Consensus pattern (21 bp):
AGAACATAAATTCAATATCCA
Found at i:32576392 original size:26 final size:26
Alignment explanation
Indices: 32576363--32576442 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
32576353 AAATAAGTAG
32576363 AACATAAATTCAATATCCAAGAACCA
1 AACATAAATTCAATATCCAAGAACCA
* *
32576389 AACAT---TTGCACATA---AATAA-GA
1 AACATAAATT-CA-ATATCCAAGAACCA
32576410 -ACATAAATTCAATATCCAAGAACCA
1 AACATAAATTCAATATCCAAGAACCA
32576435 AACATAAA
1 AACATAAA
32576443 CAACTATTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 20
0.62 0.06 0.31
Matches are distributed among these distances:
20 4 0.10
21 4 0.10
22 6 0.15
23 4 0.10
24 6 0.15
25 4 0.10
26 12 0.30
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (26 bp):
AACATAAATTCAATATCCAAGAACCA
Found at i:32576464 original size:46 final size:46
Alignment explanation
Indices: 32576347--32576444 Score: 142
Period size: 46 Copynumber: 2.1 Consensus size: 46
32576337 AAACTAAAAT
**
32576347 ACACATAAATAAGTAGAACATAAATTCAATATCCAAGAACCAAACATTT
1 ACACATAAAT-A--AGAACATAAATTCAATATCCAAGAACCAAACATAA
*
32576396 GCACATAAATAAGAACATAAATTCAATATCCAAGAACCAAACATAA
1 ACACATAAATAAGAACATAAATTCAATATCCAAGAACCAAACATAA
32576442 ACA
1 ACA
32576445 ACTATTGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
46 35 0.78
48 1 0.02
49 9 0.20
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (46 bp):
ACACATAAATAAGAACATAAATTCAATATCCAAGAACCAAACATAA
Found at i:32576993 original size:18 final size:18
Alignment explanation
Indices: 32576964--32577015 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
32576954 CGTTTCCATC
*
32576964 AATGTTAACATCATTT-G
1 AATGTTAACATCATTTAA
*
32576981 AATTTTGAACATCATTTAA
1 AATGTT-AACATCATTTAA
32577000 AATGTTAACATCATTT
1 AATGTTAACATCATTT
32577016 CCTGCATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.17
18 20 0.67
19 5 0.17
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (18 bp):
AATGTTAACATCATTTAA
Found at i:32581137 original size:15 final size:17
Alignment explanation
Indices: 32581095--32581132 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
32581085 CTCCACCTTG
*
32581095 ACAAGAATTCTCTACGA
1 ACAAGAATTCTCAACGA
32581112 ACAAGAATTCTCAACGA
1 ACAAGAATTCTCAACGA
32581129 ACAA
1 ACAA
32581133 ATTCTTCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.24, G:0.11, T:0.18
Consensus pattern (17 bp):
ACAAGAATTCTCAACGA
Found at i:32584103 original size:27 final size:28
Alignment explanation
Indices: 32584065--32584118 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
32584055 TAAGGTTGAA
32584065 ATACCTTATTCTAATTAAAATAAAATAG
1 ATACCTTATTCTAATTAAAATAAAATAG
32584093 ATACC-TATTCTAATTAAAATAAAATA
1 ATACCTTATTCTAATTAAAATAAAATA
32584119 AAAGAAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (28 bp):
ATACCTTATTCTAATTAAAATAAAATAG
Found at i:32584189 original size:17 final size:18
Alignment explanation
Indices: 32584151--32584191 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
32584141 CTTTACTTTT
* *
32584151 ATTTTATTTTACCACTGA
1 ATTTTATTTTAACACAGA
32584169 ATTTTATTTTAACA-AGA
1 ATTTTATTTTAACACAGA
32584186 ATTTTA
1 ATTTTA
32584192 GTCACCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTTATTTTAACACAGA
Found at i:32584607 original size:65 final size:65
Alignment explanation
Indices: 32584531--32584659 Score: 197
Period size: 65 Copynumber: 2.0 Consensus size: 65
32584521 GTAAATTGGA
*
32584531 CCCCACACTTGTAAGCACGTTGGTGGAAAGAT-GAAAACCCGAGACGCACACATTCAATCTTCCA
1 CCCCACACTTGTAAGCACGTTGGTAGAAAGATAG-AAACCCGAGACGCACACATTCAATCTTCCA
32584595 C
65 C
* * * *
32584596 CCCCACACTTGTAAGCGCGTTGGTAGAAAGATAGAGACCCGAGATGCACACATTCCATCTTCCA
1 CCCCACACTTGTAAGCACGTTGGTAGAAAGATAGAAACCCGAGACGCACACATTCAATCTTCCA
32584660 TGCAACGAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 57 0.98
66 1 0.02
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.19
Consensus pattern (65 bp):
CCCCACACTTGTAAGCACGTTGGTAGAAAGATAGAAACCCGAGACGCACACATTCAATCTTCCAC
Found at i:32585938 original size:6 final size:6
Alignment explanation
Indices: 32585927--32585958 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
32585917 AATGAGGAAT
32585927 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA
32585959 CCACAGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:32596715 original size:31 final size:32
Alignment explanation
Indices: 32596669--32596734 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
32596659 TAATAGAAAT
*
32596669 AAAATTATACTTTAATTTCTTAAAAATGATAA
1 AAAATTATAATTTAATTTCTTAAAAATGATAA
* *
32596701 AAAATT-TAATTTAATTTTTTAAAAATTATAA
1 AAAATTATAATTTAATTTCTTAAAAATGATAA
32596732 AAA
1 AAA
32596735 TATAGATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (32 bp):
AAAATTATAATTTAATTTCTTAAAAATGATAA
Found at i:32598182 original size:17 final size:18
Alignment explanation
Indices: 32598153--32598199 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
32598143 CACTGGTGCA
*
32598153 GGTGGGAGGAGGTCCGGT
1 GGTGGGAGGAGGTCCAGT
32598171 GGTGGG-GGAGGTCCAGT
1 GGTGGGAGGAGGTCCAGT
* *
32598188 GGGGGGCGGAGG
1 GGTGGGAGGAGG
32598200 GAGAGGGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.11, C:0.11, G:0.66, T:0.13
Consensus pattern (18 bp):
GGTGGGAGGAGGTCCAGT
Found at i:32608292 original size:31 final size:31
Alignment explanation
Indices: 32608252--32608348 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
32608242 ATTTCAAAAA
* * *
32608252 AATTAAATATAATAATAAATAAAATTTTAAT
1 AATTTAATATAATGATAAATAAAATTTAAAT
* *
32608283 AATTTAATATAATGATAAATGATATTTAAAT
1 AATTTAATATAATGATAAATAAAATTTAAAT
* * *
32608314 AATTTAATATATTGATATATAAAATATAAAGT
1 AATTTAATATAATGATAAATAAAATTTAAA-T
32608346 AAT
1 AAT
32608349 GCAATTTTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 51 0.93
32 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (31 bp):
AATTTAATATAATGATAAATAAAATTTAAAT
Found at i:32612231 original size:3 final size:3
Alignment explanation
Indices: 32612223--32612247 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
32612213 GAACACAAAG
32612223 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
32612248 GTAGCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:32618495 original size:3 final size:3
Alignment explanation
Indices: 32618477--32618515 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
32618467 ATATGTTTTT
*
32618477 ATA AAA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
32618516 AACATTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:32619451 original size:11 final size:11
Alignment explanation
Indices: 32619430--32619458 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
32619420 TTTAAGTATA
32619430 AATTT-TTTTT
1 AATTTATTTTT
32619440 AATTTATTTTT
1 AATTTATTTTT
32619451 AATTTATT
1 AATTTATT
32619459 AAGAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
AATTTATTTTT
Found at i:32632052 original size:15 final size:17
Alignment explanation
Indices: 32632016--32632058 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
32632006 ATAATAAAAA
32632016 TATAA-TTTTATTATTT
1 TATAATTTTTATTATTT
32632032 TAATAATTTTTA-TA-TT
1 T-ATAATTTTTATTATTT
32632048 TATAATTTTTA
1 TATAATTTTTA
32632059 AGAGATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.40
16 4 0.16
17 6 0.24
18 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATAATTTTTATTATTT
Found at i:32638574 original size:26 final size:27
Alignment explanation
Indices: 32638544--32638604 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 27
32638534 CTTCAATAAC
32638544 TTAATATATTAATATTTTATT-AAAAA
1 TTAATATATTAATATTTTATTAAAAAA
*
32638570 TTAATATATTAGTATTTTATTAAAAAA
1 TTAATATATTAATATTTTATTAAAAAA
32638597 TTAATATA
1 TTAATATA
32638605 AATGGAAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 20 0.61
27 13 0.39
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
TTAATATATTAATATTTTATTAAAAAA
Found at i:32639815 original size:24 final size:24
Alignment explanation
Indices: 32639788--32639882 Score: 66
Period size: 24 Copynumber: 3.8 Consensus size: 24
32639778 TTTATTTTTA
32639788 TTTATATATTTATTTTTTTGAATT
1 TTTATATATTTATTTTTTTGAATT
* *
32639812 TTTATAAATTACCTATATTTTT-ATATT
1 TTTATATATT---TATTTTTTTGA-ATT
* * * *
32639839 TTAAAAATGTTTACTTTTTTGAATT
1 TT-TATATATTTATTTTTTTGAATT
* *
32639864 TATATATTTTTATTTTTTT
1 TTTATATATTTATTTTTTT
32639883 AAAATAATTA
Statistics
Matches: 52, Mismatches: 13, Indels: 12
0.68 0.17 0.16
Matches are distributed among these distances:
24 22 0.42
25 11 0.21
26 2 0.04
27 13 0.25
28 4 0.08
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (24 bp):
TTTATATATTTATTTTTTTGAATT
Found at i:32654182 original size:30 final size:30
Alignment explanation
Indices: 32654138--32654205 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
32654128 AAATTTTAAA
* *
32654138 TTAATAAA-AATAAAA-TTATATTTTAATATT
1 TTAA-AAATAATAAAATTTAAATTTAAAT-TT
32654168 TTAAAAATAATAAAATTTAAATTTAAATTT
1 TTAAAAATAATAAAATTTAAATTTAAATTT
32654198 TTAAAAAT
1 TTAAAAAT
32654206 TTATATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 3 0.09
30 21 0.62
31 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TTAAAAATAATAAAATTTAAATTTAAATTT
Found at i:32654205 original size:16 final size:16
Alignment explanation
Indices: 32654186--32654216 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32654176 AATAAAATTT
32654186 AAATTTAAATTTTTAA
1 AAATTTAAATTTTTAA
*
32654202 AAATTTATATTTTTA
1 AAATTTAAATTTTTA
32654217 TTATTATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATTTAAATTTTTAA
Found at i:32661161 original size:43 final size:43
Alignment explanation
Indices: 32661100--32661200 Score: 202
Period size: 43 Copynumber: 2.3 Consensus size: 43
32661090 AAAAATTTAA
32661100 TGAGGGCATCTTCCTATGGAATCCTATTACAGGTAAGGTTGAT
1 TGAGGGCATCTTCCTATGGAATCCTATTACAGGTAAGGTTGAT
32661143 TGAGGGCATCTTCCTATGGAATCCTATTACAGGTAAGGTTGAT
1 TGAGGGCATCTTCCTATGGAATCCTATTACAGGTAAGGTTGAT
32661186 TGAGGGCATCTTCCT
1 TGAGGGCATCTTCCT
32661201 TTTTCTAATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (43 bp):
TGAGGGCATCTTCCTATGGAATCCTATTACAGGTAAGGTTGAT
Found at i:32674867 original size:7 final size:7
Alignment explanation
Indices: 32674857--32674881 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32674847 TGGAACTTTG
32674857 ATTTGGA
1 ATTTGGA
32674864 ATTTGGA
1 ATTTGGA
32674871 ATTTGGA
1 ATTTGGA
32674878 ATTT
1 ATTT
32674882 ATTTGTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (7 bp):
ATTTGGA
Found at i:32676289 original size:30 final size:29
Alignment explanation
Indices: 32676255--32676316 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
32676245 ATAGAAATTG
*
32676255 ATTTAATTAGTTAATAATATTATAAAAACA
1 ATTTAATTAATTAATAATATTATAAAAA-A
32676285 ATTTAATTAATTAATAATATTATAAAAAA
1 ATTTAATTAATTAATAATATTATAAAAAA
32676314 ATT
1 ATT
32676317 AACTTCTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (29 bp):
ATTTAATTAATTAATAATATTATAAAAAA
Found at i:32676562 original size:3 final size:3
Alignment explanation
Indices: 32676554--32676579 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
32676544 TGTAATTCAA
32676554 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
32676580 CAACGCCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:32690651 original size:60 final size:60
Alignment explanation
Indices: 32690587--32690721 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
32690577 AATTTAATCC
* * * *
32690587 TAAA-TAAAAAATATTCAACAAATTTATC-TTTCAATATTTATAAAATTTATTATTTTAATT
1 TAAATTAAAAAAT-TTCAACAAATTTAACATTT-AAAATTTACAAAATTTATAATTTTAATT
* **
32690647 TAAATTCAAAAATTTCATTAAATTTAACATTTAAAATTTACAAAATTTATAATTTTAATTT
1 TAAATTAAAAAATTTCAACAAATTTAACATTTAAAATTTACAAAATTTATAATTTTAA-TT
*
32690708 TAATTCTAAAAAAT
1 TAAAT-TAAAAAAT
32690722 CAATAAACTT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
60 39 0.63
61 16 0.26
62 7 0.11
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (60 bp):
TAAATTAAAAAATTTCAACAAATTTAACATTTAAAATTTACAAAATTTATAATTTTAATT
Found at i:32690734 original size:60 final size:60
Alignment explanation
Indices: 32690622--32690734 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
32690612 ATCTTTCAAT
* * * * *
32690622 ATTTATAAAATTTATTATTTTAATTTAAATTCAAAAATTTCATTAAATTTAACATTTAAA
1 ATTTACAAAATTTATAATTTTAATTTAAATTCAAAAATATCAATAAACTTAACATTTAAA
*
32690682 ATTTACAAAATTTATAATTTTAATTTTAATTCTAAAAA-ATCAATAAACTTAAC
1 ATTTACAAAATTTATAATTTTAATTTAAATTC-AAAAATATCAATAAACTTAAC
32690735 TCTCGATCCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 41 0.89
61 5 0.11
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (60 bp):
ATTTACAAAATTTATAATTTTAATTTAAATTCAAAAATATCAATAAACTTAACATTTAAA
Found at i:32691013 original size:4 final size:4
Alignment explanation
Indices: 32691004--32691029 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
32690994 TTAAATAGAG
32691004 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
32691030 ATCTTCCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:32708205 original size:22 final size:22
Alignment explanation
Indices: 32708179--32708232 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
32708169 ATATCCAAAC
*
32708179 AATAACAACAAAATAATAGCAA
1 AATAACAACAAAATAATAACAA
* * * *
32708201 TATAATAGCAAAATGATAACAA
1 AATAACAACAAAATAATAACAA
*
32708223 AACAACAACA
1 AATAACAACA
32708233 TAACATAAAA
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.65, C:0.15, G:0.06, T:0.15
Consensus pattern (22 bp):
AATAACAACAAAATAATAACAA
Found at i:32708245 original size:21 final size:21
Alignment explanation
Indices: 32708216--32708258 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
32708206 TAGCAAAATG
*
32708216 ATAACAAAACAACAACATAAC
1 ATAAAAAAACAACAACATAAC
* *
32708237 ATAAAAAAATAGCAACATAAC
1 ATAAAAAAACAACAACATAAC
32708258 A
1 A
32708259 ATAGTAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.67, C:0.19, G:0.02, T:0.12
Consensus pattern (21 bp):
ATAAAAAAACAACAACATAAC
Found at i:32708401 original size:18 final size:16
Alignment explanation
Indices: 32708347--32708401 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
32708337 GTTTTTTAAA
*
32708347 TAAACCTTATTTTTAAT
1 TAAACTTTATTTTT-AT
32708364 TCAAA-TTTATTTTT-T
1 T-AAACTTTATTTTTAT
32708379 TAAACTTATATTTTTACT
1 TAAACTT-TATTTTTA-T
32708397 TAAAC
1 TAAAC
32708402 CCTTAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 7 0.22
17 9 0.28
18 9 0.28
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAACTTTATTTTTAT
Found at i:32709703 original size:60 final size:61
Alignment explanation
Indices: 32709611--32709749 Score: 185
Period size: 60 Copynumber: 2.3 Consensus size: 61
32709601 TCAGATAGAT
* *
32709611 TTTTTTTGTGTTGGCCATGCAATGGTCGACACCTCC-TTTTTGTCAAAT-AAAAAATTCAAA
1 TTTTTTGGTGTTGGCCATGCAATGGCCGACACC-CCTTTTTTGTCAAATAAAAAAATTCAAA
* * *
32709671 TTTTTTGGTGTTTGCCATTGC-ATGGCCGACACCCCTTTTTTGTCAGATAAAAAAATTTAAA
1 TTTTTTGGTGTTGGCCA-TGCAATGGCCGACACCCCTTTTTTGTCAAATAAAAAAATTCAAA
*
32709732 TTTTTTGGTGTCGGCCAT
1 TTTTTTGGTGTTGGCCAT
32709750 AGCCCTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
59 2 0.03
60 38 0.55
61 29 0.42
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.40
Consensus pattern (61 bp):
TTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTGTCAAATAAAAAAATTCAAA
Done.