Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 7 of 182
Found at i:2492283 original size:2 final size:2
Alignment explanation
Indices: 2492276--2492305 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2492266 CTGATCATTA
2492276 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
2492306 CATTGTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2498550 original size:26 final size:26
Alignment explanation
Indices: 2498505--2498561 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2498495 ATCTCTTTCC
*
2498505 TTTTCCTTTTTATTTATTTTTCTTTT
1 TTTTCCTTTTTATTTATTTTACTTTT
*
2498531 TTTTCCTCTTTTA-TTCTTTTACTTTT
1 TTTTCCT-TTTTATTTATTTTACTTTT
*
2498557 GTTTC
1 TTTTC
2498562 TTTATTTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTTCCTTTTTATTTATTTTACTTTT
Found at i:2501327 original size:34 final size:35
Alignment explanation
Indices: 2501275--2501344 Score: 106
Period size: 34 Copynumber: 2.0 Consensus size: 35
2501265 GATATAAACC
*
2501275 ATTAAAATGATATAATTATATTTTTATT-TTTTAA
1 ATTAAAATAATATAATTATATTTTTATTATTTTAA
* *
2501309 ATTAAATTAATATGATTATATTTTTATTATTTTAA
1 ATTAAAATAATATAATTATATTTTTATTATTTTAA
2501344 A
1 A
2501345 AATTACAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 25 0.78
35 7 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (35 bp):
ATTAAAATAATATAATTATATTTTTATTATTTTAA
Found at i:2511677 original size:24 final size:24
Alignment explanation
Indices: 2511650--2511702 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
2511640 AAAAAGCCTC
2511650 TGAAACAAATAAACAAAATTTAAT
1 TGAAACAAATAAACAAAATTTAAT
*
2511674 TGAAACAAATAAACAGAATTTAAT
1 TGAAACAAATAAACAAAATTTAAT
2511698 TGAAA
1 TGAAA
2511703 GATTATTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.25
Consensus pattern (24 bp):
TGAAACAAATAAACAAAATTTAAT
Found at i:2512264 original size:19 final size:20
Alignment explanation
Indices: 2512230--2512279 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2512220 TTTCCATTCC
* *
2512230 AACAATCATCACAAGC-AAA
1 AACAATCCTCAGAAGCGAAA
*
2512249 AACAATTCTCAGAAGCGAAA
1 AACAATCCTCAGAAGCGAAA
*
2512269 CACAATCCTCA
1 AACAATCCTCA
2512280 AATAAAGCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.50, C:0.28, G:0.08, T:0.14
Consensus pattern (20 bp):
AACAATCCTCAGAAGCGAAA
Found at i:2515776 original size:116 final size:116
Alignment explanation
Indices: 2515559--2515778 Score: 273
Period size: 116 Copynumber: 1.9 Consensus size: 116
2515549 TGTGCAGGGA
* * * * *
2515559 AATCCAAATGCACCCTAGTTCTAAATGCTCTTGTTTCTAATCAACTGGTAAAATGTTATTTTTGG
1 AATCCAAATGCACCCTAGTTCCAAATGCTCTGGTTTCTAATCAACAGGTAAAATGCTATTTTAGG
* * * *
2515624 GTACTTTGGCATTAGAGCAACTGTATCTCTAGGTTTTTACGGGTGGTGAGC
66 ATACTGTGGCATTACAGCAACTGTATCTATAGGTTTTTACGGGTGGTGAGC
* *
2515675 AATCCAAATGCACCTTAGTTCCAAATGCT-TAGGTTTC-AGCTCAACAGGTAAAATGCTATTTCT
1 AATCCAAATGCACCCTAGTTCCAAATGCTCT-GGTTTCTA-ATCAACAGGTAAAATGCTATTT-T
* * *
2515738 AGGATACTGTGGCATTACAGCCACTGTTTCTATAGTTTTTT
63 AGGATACTGTGGCATTACAGCAACTGTATCTATAGGTTTTT
2515779 TTTGGATGAA
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
115 2 0.02
116 51 0.59
117 34 0.39
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (116 bp):
AATCCAAATGCACCCTAGTTCCAAATGCTCTGGTTTCTAATCAACAGGTAAAATGCTATTTTAGG
ATACTGTGGCATTACAGCAACTGTATCTATAGGTTTTTACGGGTGGTGAGC
Found at i:2518055 original size:29 final size:28
Alignment explanation
Indices: 2517997--2518056 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
2517987 CAGTAATTTT
* * *
2517997 ATAATCACTTTTTGTTTTTCTAAATTAA
1 ATAATCACTTTTTGTTTATATAAACTAA
2518025 ATAATCACTTTTTGTTTATATATAACTAA
1 ATAATCACTTTTTGTTTATATA-AACTAA
2518054 ATA
1 ATA
2518057 GTATGTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (28 bp):
ATAATCACTTTTTGTTTATATAAACTAA
Found at i:2522102 original size:18 final size:18
Alignment explanation
Indices: 2522061--2522104 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2522051 CGCAACCGTG
*
2522061 ATAGGGAACGCGATCGAG
1 ATAGGGAACGCGATCGAC
* * *
2522079 ACAGGGATCGGGATCGAC
1 ATAGGGAACGCGATCGAC
2522097 ATAGGGAA
1 ATAGGGAA
2522105 GACAAAGACA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.39, T:0.11
Consensus pattern (18 bp):
ATAGGGAACGCGATCGAC
Found at i:2536035 original size:30 final size:30
Alignment explanation
Indices: 2535999--2536062 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
2535989 CCACCAAGAG
* * *
2535999 CTCCAGGTGGTGGCGGAGGTGGTGCTCTTC
1 CTCCAGGAGGTGGCGGAGGAGGTGCTCCTC
* *
2536029 CTCCAGGAGGTGGTGGCGGAGGTGCTCCTC
1 CTCCAGGAGGTGGCGGAGGAGGTGCTCCTC
2536059 CTCC
1 CTCC
2536063 TCCTGGAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.08, C:0.28, G:0.41, T:0.23
Consensus pattern (30 bp):
CTCCAGGAGGTGGCGGAGGAGGTGCTCCTC
Found at i:2536040 original size:33 final size:33
Alignment explanation
Indices: 2536003--2536109 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
2535993 CAAGAGCTCC
*
2536003 AGGTGGTGGCGGAGGTGGTGCTCTTCCTCCAGG
1 AGGTGGTGGCGGAGGTGGTGCTCCTCCTCCAGG
* * *
2536036 AGGTGGTGGCGGAGGTGCTCCTCCTCCTCCTGG
1 AGGTGGTGGCGGAGGTGGTGCTCCTCCTCCAGG
* * * ** *
2536069 AGGTGGTGGTGGCGGTGGTGGTCCAACTCCAAG
1 AGGTGGTGGCGGAGGTGGTGCTCCTCCTCCAGG
2536102 AGGTGGTG
1 AGGTGGTG
2536110 TTGGTTCAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.10, C:0.21, G:0.45, T:0.23
Consensus pattern (33 bp):
AGGTGGTGGCGGAGGTGGTGCTCCTCCTCCAGG
Found at i:2536114 original size:24 final size:24
Alignment explanation
Indices: 2536079--2536137 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
2536069 AGGTGGTGGT
2536079 GGCGGTGGTGGTCCAACTCCAAGA
1 GGCGGTGGTGGTCCAACTCCAAGA
* * *
2536103 GGTGGTGTTGGTTCAACTCCAAGA
1 GGCGGTGGTGGTCCAACTCCAAGA
2536127 GGCGGTGGTGG
1 GGCGGTGGTGG
2536138 AGGTGGTGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.42, T:0.22
Consensus pattern (24 bp):
GGCGGTGGTGGTCCAACTCCAAGA
Found at i:2536469 original size:114 final size:111
Alignment explanation
Indices: 2536351--2536587 Score: 242
Period size: 114 Copynumber: 2.1 Consensus size: 111
2536341 AGGGTGGTGG
* *
2536351 AGGTGGAGGAGGTG-AGACACTAGACATCAAGGGGGGTGATAAAGGTGGGGCACTAGACACCAAT
1 AGGTGGAGGAAGTGAAG-CACTAGACATCAA-GAGGG-GA-AAAGGTGGGGCACTAGACACCAAT
*
2536415 GGGGGTGGTGGAGATGGAGGTGGGGCACTAGTTGAAAAAGTGGTTGATGA
62 GGGGGTGGTGGAGATGGAGGTGGGGCACTAGTCGAAAAAGTGGTTGATGA
* ** ** * * ****
2536465 AGGTGAAGGAGGAAGTGAAGCACTAGACATCAATAGGGGAGGAGGTGGGGTGCTGGATATTGTTG
1 AGGT---GGAGGAAGTGAAGCACTAGACATCAAGAGGGGAAAAGGTGGGGCACTAGACACCAATG
** *
2536530 GGGGTGGTGGAGATGGAGGTGGGGCACTAGTCGTCAAAGTGGTTGGTGA
63 GGGGTGGTGGAGATGGAGGTGGGGCACTAGTCGAAAAAGTGGTTGATGA
*
2536579 AGGAGGAGG
1 AGGTGGAGG
2536588 TAGGGTGCTA
Statistics
Matches: 101, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
111 5 0.05
114 67 0.66
115 2 0.02
116 3 0.03
117 22 0.22
118 2 0.02
ACGTcount: A:0.27, C:0.08, G:0.46, T:0.19
Consensus pattern (111 bp):
AGGTGGAGGAAGTGAAGCACTAGACATCAAGAGGGGAAAAGGTGGGGCACTAGACACCAATGGGG
GTGGTGGAGATGGAGGTGGGGCACTAGTCGAAAAAGTGGTTGATGA
Found at i:2536594 original size:78 final size:80
Alignment explanation
Indices: 2536502--2536662 Score: 227
Period size: 78 Copynumber: 2.0 Consensus size: 80
2536492 CATCAATAGG
* * * * *
2536502 GGAGGAGGTGGGGTGCTGGATATTGTTGGGGGTGGTGGAGA-T-GGAGGTGGGGCACTAGTCGTC
1 GGAGGAGGTAGGGTGCTAGATATTGATGGGGATGGTGGAGATTAGGAGGTGGGGCACTAGTCATC
2536565 AAAGTGGTTGGTGAA
66 AAAGTGGTTGGTGAA
* *
2536580 GGAGGAGGTAGGGTGCTAGATATTGATGGGGATGGTGGAGATTGAGGAGTTGGGGCCCTAGTCAT
1 GGAGGAGGTAGGGTGCTAGATATTGATGGGGATGGTGGAGATT-AGGAGGTGGGGCACTAGTCAT
*
2536645 CGAAGTGGTTGGTGAA
65 CAAAGTGGTTGGTGAA
2536661 GG
1 GG
2536663 TGAAGGTGAA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
78 37 0.51
79 1 0.01
81 34 0.47
ACGTcount: A:0.20, C:0.07, G:0.49, T:0.24
Consensus pattern (80 bp):
GGAGGAGGTAGGGTGCTAGATATTGATGGGGATGGTGGAGATTAGGAGGTGGGGCACTAGTCATC
AAAGTGGTTGGTGAA
Found at i:2536666 original size:6 final size:6
Alignment explanation
Indices: 2536655--2536680 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2536645 CGAAGTGGTT
2536655 GGTGAA GGTGAA GGTGAA GGTGAA GG
1 GGTGAA GGTGAA GGTGAA GGTGAA GG
2536681 AGAAATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.15
Consensus pattern (6 bp):
GGTGAA
Found at i:2537051 original size:216 final size:215
Alignment explanation
Indices: 2536741--2537233 Score: 582
Period size: 216 Copynumber: 2.3 Consensus size: 215
2536731 GTAGAGATGG
* ** * *
2536741 AGGAGGTAGGGCATTAGTTGTCAAAGTGGTTGGTGAAGGTGAAGGAGGAATTGAAGCACTAGATA
1 AGGAGGTAGGGCACTAGTAATCAAAGTGGTTGGTGAAGGTGAA-GAGGAAGTGGAGCACTAGATA
* * * * * *
2536806 TCGATGGGGGAAGAGGTTGGATTCTAGATATTGATGGGGGTGGTGGAGACGAAAGAGGTGGGGCA
65 CCGATAGGGGAAGAGGTGGGATGCTAGATATTGATAGGGGTGGTGGAGACGAAAGAGGTGGGCCA
*** * *
2536871 CTAGTCGTTGCGGAGAGCGGTGAAGGTGGAGGAGGAAGTAGGGAAGTAGACATCAAT-GTGAG-A
130 CTAGTCGTCAAGGAGAGCGGTGAAGGTGGAGAAGGAAGCAGGGAAGTAGACATCAATAG-G-GCA
* *
2536934 GGTGGAGATGGTAGTGGAGGTGA
193 GGTGGAGATGGTAGTAGAAGTGA
* *
2536957 AGGAGGTGGGGCACTAGTCATCAAAGTGGTTGGTGAAGGTGAAAGAGGAAGTGGAGCACTAGATA
1 AGGAGGTAGGGCACTAGTAATCAAAGTGGTTGGTGAAGGTG-AAGAGGAAGTGGAGCACTAGATA
* * * *
2537022 CCGATAGGGG-AGAAGGTGGGGTGCTAGATATTGATAGGGGTGGTGGAGATGGAGGAGGTGGGCC
65 CCGATAGGGGAAG-AGGTGGGATGCTAGATATTGATAGGGGTGGTGGAGACGAAAGAGGTGGGCC
* * * *
2537086 ACTAGTCGTCAAGGAGGGTGGTGAAGGTGGAGAAGGAAGCGGGGCAGTAGACATCAATAGGGCAG
129 ACTAGTCGTCAAGGAGAGCGGTGAAGGTGGAGAAGGAAGCAGGGAAGTAGACATCAATAGGGCAG
*
2537151 GTGGAGATGGTGGTAGAAGTGA
194 GTGGAGATGGTAGTAGAAGTGA
* * ** * * *
2537173 AGGAGGTAGAGCACTAGTAACCAAAAAGGGTGGTGAAGGTG--GAGAAAGTGGGGCACTAGAT
1 AGGAGGTAGGGCACTAGTAATCAAAGTGGTTGGTGAAGGTGAAGAGGAAGTGGAGCACTAGAT
2537234 GTTGATGGGA
Statistics
Matches: 236, Mismatches: 37, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
213 18 0.08
215 3 0.01
216 212 0.90
217 3 0.01
ACGTcount: A:0.29, C:0.08, G:0.44, T:0.19
Consensus pattern (215 bp):
AGGAGGTAGGGCACTAGTAATCAAAGTGGTTGGTGAAGGTGAAGAGGAAGTGGAGCACTAGATAC
CGATAGGGGAAGAGGTGGGATGCTAGATATTGATAGGGGTGGTGGAGACGAAAGAGGTGGGCCAC
TAGTCGTCAAGGAGAGCGGTGAAGGTGGAGAAGGAAGCAGGGAAGTAGACATCAATAGGGCAGGT
GGAGATGGTAGTAGAAGTGA
Found at i:2537293 original size:84 final size:84
Alignment explanation
Indices: 2537196--2537429 Score: 231
Period size: 84 Copynumber: 2.8 Consensus size: 84
2537186 CTAGTAACCA
* * * ** * *
2537196 AAAAGGGTGGTGAAGGTGGAGAAAGTGGGGCACTAGATGTTGATGGGAGTTGTGGAGCTGGAGGA
1 AAAAGGGTGGTGAAGGTGAAGGAAGTGGGGCACTACACATTGATGGGAGTGGTGGAGATGGAGGA
*
2537261 GATAG-GGCAATATTAGTCG
66 GA-AGAGGCAATAGTAGTCG
* * * *
2537280 AAGAGGGTGGTGAAGGTGAAGGAAGTGGAGTACTACACATTGATGGGGGTGGTGGAGATGGAGGA
1 AAAAGGGTGGTGAAGGTGAAGGAAGTGGGGCACTACACATTGATGGGAGTGGTGGAGATGGAGGA
* * *
2537345 GACGAGGCAGTAGTAGTTG
66 GAAGAGGCAATAGTAGTCG
* * * * * *
2537364 AAAAGGGTGGTGAGGGTGCAGGAAGTGGGGCAATA-ATCATTGAAGAGG-GTGGTGAAGGTGGAG
1 AAAAGGGTGGTGAAGGTGAAGGAAGTGGGGCACTACA-CATTGATG-GGAGTGGTGGAGATGGAG
2537427 GAG
64 GAG
2537430 GAAGTGGGGA
Statistics
Matches: 123, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
83 2 0.02
84 119 0.97
85 2 0.02
ACGTcount: A:0.29, C:0.06, G:0.46, T:0.19
Consensus pattern (84 bp):
AAAAGGGTGGTGAAGGTGAAGGAAGTGGGGCACTACACATTGATGGGAGTGGTGGAGATGGAGGA
GAAGAGGCAATAGTAGTCG
Found at i:2537452 original size:45 final size:45
Alignment explanation
Indices: 2537353--2537466 Score: 128
Period size: 45 Copynumber: 2.6 Consensus size: 45
2537343 GAGACGAGGC
* * *
2537353 AGTAGTAGTTGAAAAGGGTGGTG-A-GGGTGCAGGAAGTGGGGCA
1 AGTAGTCGTTGAAGAGGGTGGTGAAGGGGAGCAGGAAGTGGGGCA
* * *
2537396 A-TAATCATTGAAGAGGGTGGTGAAGGTGGAGGAGGAAGTGGGG-A
1 AGTAGTCGTTGAAGAGGGTGGTGAAGG-GGAGCAGGAAGTGGGGCA
*
2537440 AGTAGTCGTTGAAGAGGTTGGTGAAGG
1 AGTAGTCGTTGAAGAGGGTGGTGAAGG
2537467 CGAAGAAGGA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
42 17 0.29
43 2 0.03
44 3 0.05
45 36 0.62
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (45 bp):
AGTAGTCGTTGAAGAGGGTGGTGAAGGGGAGCAGGAAGTGGGGCA
Found at i:2537477 original size:45 final size:45
Alignment explanation
Indices: 2537383--2537477 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
2537373 GTGAGGGTGC
* * *
2537383 AGGAAGTGGGGCAATAATCATTGAAGAGGGTGGTGAAGGTGGAGG
1 AGGAAGTGGGGCAATAATCATTGAAGAGGGTGGTGAAGGCGAAGA
* * *
2537428 AGGAAGTGGGG-AAGTAGTCGTTGAAGAGGTTGGTGAAGGCGAAGA
1 AGGAAGTGGGGCAA-TAATCATTGAAGAGGGTGGTGAAGGCGAAGA
2537473 AGGAA
1 AGGAA
2537478 TCAGGGCACT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 2 0.05
45 41 0.95
ACGTcount: A:0.33, C:0.04, G:0.46, T:0.17
Consensus pattern (45 bp):
AGGAAGTGGGGCAATAATCATTGAAGAGGGTGGTGAAGGCGAAGA
Found at i:2537746 original size:6 final size:6
Alignment explanation
Indices: 2537710--2537748 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
2537700 ATGAGGGTGA
* * *
2537710 TGGAGT TGGAGG AGGAGG AGGAGG TGGAGG TGGAGG TGG
1 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGG
2537749 GACATTAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.21, C:0.00, G:0.64, T:0.15
Consensus pattern (6 bp):
TGGAGG
Found at i:2539739 original size:21 final size:21
Alignment explanation
Indices: 2539712--2539776 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
2539702 GTCGTAATCC
*
2539712 ACCTTTCCATCCAGCGCATCG
1 ACCTTTCCATCCAGCGCATCA
* *
2539733 ACTTTTCCATCCAGCACATCA
1 ACCTTTCCATCCAGCGCATCA
*
2539754 ACCTTTCCCTCCAGCGCATCA
1 ACCTTTCCATCCAGCGCATCA
2539775 AC
1 AC
2539777 TGCATTGCTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.23, C:0.43, G:0.09, T:0.25
Consensus pattern (21 bp):
ACCTTTCCATCCAGCGCATCA
Found at i:2554651 original size:23 final size:25
Alignment explanation
Indices: 2554616--2554666 Score: 88
Period size: 23 Copynumber: 2.1 Consensus size: 25
2554606 TAAATTTAAT
2554616 AAAATATATTTAAAATTTTATAAAA
1 AAAATATATTTAAAATTTTATAAAA
2554641 AAAAT-TA-TTAAAATTTTATAAAA
1 AAAATATATTTAAAATTTTATAAAA
2554664 AAA
1 AAA
2554667 TCATAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 19 0.73
24 2 0.08
25 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAATATATTTAAAATTTTATAAAA
Found at i:2554676 original size:23 final size:23
Alignment explanation
Indices: 2554627--2554675 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
2554617 AAATATATTT
* *
2554627 AAAATTTTATAAAAAAAATTATT
1 AAAATTTTATAAAAAAAATCATA
2554650 AAAATTTTAT-AAAAAAATCATA
1 AAAATTTTATAAAAAAAATCATA
2554672 AAAA
1 AAAA
2554676 AATTATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATTTTATAAAAAAAATCATA
Found at i:2554681 original size:22 final size:23
Alignment explanation
Indices: 2554633--2554681 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
2554623 ATTTAAAATT
* * **
2554633 TTATAAAAAAAATTATTAAAATT
1 TTATAAAAAAAATCATAAAAAAA
2554656 TTAT-AAAAAAATCATAAAAAAA
1 TTATAAAAAAAATCATAAAAAAA
2554678 TTAT
1 TTAT
2554682 TTAAAAAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TTATAAAAAAAATCATAAAAAAA
Found at i:2555296 original size:15 final size:14
Alignment explanation
Indices: 2555252--2555298 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
2555242 AATACGTTTT
2555252 TTTAATTTTAAATA
1 TTTAATTTTAAATA
*
2555266 TATT--TTTTGAATA
1 T-TTAATTTTAAATA
2555279 TTTAATTTTAAATAA
1 TTTAATTTTAAAT-A
2555294 TTTAA
1 TTTAA
2555299 ATAAGTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
12 2 0.07
13 9 0.33
14 8 0.30
15 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTTAATTTTAAATA
Found at i:2556423 original size:26 final size:26
Alignment explanation
Indices: 2556387--2556446 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
2556377 ATTATTTTGT
2556387 AAGTT-TAAGGGTCAATTTAAAATGA
1 AAGTTATAAGGGTCAATTTAAAATGA
*
2556412 GAGTTATAAGGGTCAATTTAAAATGA
1 AAGTTATAAGGGTCAATTTAAAATGA
*
2556438 AAATTATAA
1 AAGTTATAA
2556447 TTTGAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 4 0.13
26 27 0.87
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (26 bp):
AAGTTATAAGGGTCAATTTAAAATGA
Found at i:2556613 original size:2 final size:2
Alignment explanation
Indices: 2556608--2556638 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2556598 GGAGTATGAA
2556608 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
2556639 GTTTCTAAAA
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:2570407 original size:54 final size:53
Alignment explanation
Indices: 2570304--2570421 Score: 173
Period size: 54 Copynumber: 2.2 Consensus size: 53
2570294 TCATACACCC
*** *
2570304 AATGTCCAATATAGTGCATGAAATTCACTCACCAGGGTTCTCTGTATAAAAGT
1 AATGTCCAATATAGTGCATGAAATTCACTCACCAACATTCTCTGCATAAAAGT
*
2570357 AATGTCCAATATAGTGCATGTAATTTCACTCACCAACATTCTCTGCATAAAAGT
1 AATGTCCAATATAGTGCATG-AAATTCACTCACCAACATTCTCTGCATAAAAGT
*
2570411 AATATCCAATA
1 AATGTCCAATA
2570422 GAGCCAAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 20 0.34
54 38 0.66
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (53 bp):
AATGTCCAATATAGTGCATGAAATTCACTCACCAACATTCTCTGCATAAAAGT
Found at i:2576485 original size:2 final size:2
Alignment explanation
Indices: 2576478--2576504 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2576468 ATTCAATACT
2576478 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2576505 TCCATACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2580900 original size:21 final size:21
Alignment explanation
Indices: 2580875--2580922 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2580865 CTTTACACGA
*
2580875 CTAAA-CCTTAAACTCTAAACT
1 CTAAATCC-TAAACTCTAAACC
*
2580896 CTAAATCCTAAACTTTAAACC
1 CTAAATCCTAAACTCTAAACC
2580917 CTAAAT
1 CTAAAT
2580923 TAACACCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (21 bp):
CTAAATCCTAAACTCTAAACC
Found at i:2582556 original size:24 final size:24
Alignment explanation
Indices: 2582527--2582576 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2582517 AAATTAAAAG
2582527 CTATAGATGTAAAAATTACTTTTA
1 CTATAGATGTAAAAATTACTTTTA
2582551 CTATAGATGTAAAAATTACTTTTA
1 CTATAGATGTAAAAATTACTTTTA
2582575 CT
1 CT
2582577 GCTCTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (24 bp):
CTATAGATGTAAAAATTACTTTTA
Found at i:2585377 original size:19 final size:19
Alignment explanation
Indices: 2585353--2585389 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2585343 CCATATTCGA
2585353 CACTCAT-CTGTGCATCCAT
1 CACTCATGCTG-GCATCCAT
2585372 CACTCATGCTGGCATCCA
1 CACTCATGCTGGCATCCA
2585390 AATAACATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.22, C:0.38, G:0.14, T:0.27
Consensus pattern (19 bp):
CACTCATGCTGGCATCCAT
Found at i:2595770 original size:13 final size:13
Alignment explanation
Indices: 2595752--2595787 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2595742 TTTCGCTTAT
2595752 TTATTTTATACTA
1 TTATTTTATACTA
*
2595765 TTATTTTATATTA
1 TTATTTTATACTA
*
2595778 ATATTTTATA
1 TTATTTTATA
2595788 ACAATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTTATACTA
Found at i:2596532 original size:15 final size:15
Alignment explanation
Indices: 2596512--2596570 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
2596502 ATAGCCCCCA
2596512 CCGCCACCTCCATAT
1 CCGCCACCTCCATAT
*
2596527 CCGCCACCGCC--A-
1 CCGCCACCTCCATAT
* *
2596539 CTGCCACCTCCATAC
1 CCGCCACCTCCATAT
* *
2596554 CCGCCGCCACCATAT
1 CCGCCACCTCCATAT
2596569 CC
1 CC
2596571 ACTATTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
12 9 0.26
13 1 0.03
14 1 0.03
15 23 0.68
ACGTcount: A:0.19, C:0.58, G:0.10, T:0.14
Consensus pattern (15 bp):
CCGCCACCTCCATAT
Found at i:2596572 original size:27 final size:27
Alignment explanation
Indices: 2596509--2596565 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
2596499 GTCATAGCCC
* * *
2596509 CCACCGCCACCTCCATATCCGCCACCG
1 CCACTGCCACCTCCATACCCGCCACCA
*
2596536 CCACTGCCACCTCCATACCCGCCGCCA
1 CCACTGCCACCTCCATACCCGCCACCA
2596563 CCA
1 CCA
2596566 TATCCACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.60, G:0.11, T:0.11
Consensus pattern (27 bp):
CCACTGCCACCTCCATACCCGCCACCA
Found at i:2608752 original size:17 final size:19
Alignment explanation
Indices: 2608721--2608762 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2608711 TATATTTAGA
*
2608721 TTATTTTTAATTTAATA-T
1 TTATTTTTAATTTAAAATT
*
2608739 TTATTTTTTA-TTAAAATT
1 TTATTTTTAATTTAAAATT
2608757 TTATTT
1 TTATTT
2608763 ATAGACATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTTTTAATTTAAAATT
Found at i:2613175 original size:29 final size:29
Alignment explanation
Indices: 2613133--2613192 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
2613123 ACAATTCAGT
2613133 AATTCTATCCTTATTAAGCTTCGACTCCA
1 AATTCTATCCTTATTAAGCTTCGACTCCA
2613162 AATTCTATCCTTATTAAGCTTCGACTCCA
1 AATTCTATCCTTATTAAGCTTCGACTCCA
2613191 AA
1 AA
2613193 CCTCACCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (29 bp):
AATTCTATCCTTATTAAGCTTCGACTCCA
Found at i:2615216 original size:244 final size:247
Alignment explanation
Indices: 2614777--2615274 Score: 822
Period size: 244 Copynumber: 2.0 Consensus size: 247
2614767 CTGTGTTGAG
* *
2614777 CCTAGATGGAATTTGATTAATGTTTGTCAGAAATATGAAAATCTATACTTCAGTCTCTTTTTTTT
1 CCTAGATGGAATTTGATTAATGTTTGCCAGAAATAAGAAAATCTATACTTCAGTCTC------TT
* * *
2614842 TTTCTTTTTTTGTTCAATGAACTTGTATTCTTCATTCAATACCCAAAATGTTTTATTTTGATGGG
60 TATCTTTTTTTGTTCAACGAACTTGTATTCTTCATTCAATACCCAAAATGTTGTATTTTGATGGG
* * *
2614907 AGGCTTCACAGAATCTCTTATTGCTTGTACCTAAGGTTGAAGCATAGCTGTTTTAGCTTAATACT
125 AGGCATCACAGAATCTCTTATTGCTTGTACCTAAGGTTGAAGCATAGCCGTTTTAGCTAAATACT
*
2614972 TGAGTTCCTAGCTTGAC-TGAGGAGTTGGAAGATCATCTACTAATCAATAGCTAATAT
190 TGAGTTCCTAGCTTGACTTGAAGAGTTGGAAGATCATCTACTAATCAATAGCTAATAT
*
2615029 CCTAGATGGAATTTGATTAATGTTTGCCAGAAATAAGAAAATCTATTCTTCAGTCTC-TTAT-TT
1 CCTAGATGGAATTTGATTAATGTTTGCCAGAAATAAGAAAATCTATACTTCAGTCTCTTTATCTT
2615092 TTTTTGTTCAACGAACTTGTATTCTTCATTCAATACCCAAAATGTTGTATTTTGATGGGAGGCAT
66 TTTTTGTTCAACGAACTTGTATTCTTCATTCAATACCCAAAATGTTGTATTTTGATGGGAGGCAT
2615157 CACAGAATCTCTTATTGCTTGTACCTAAGGTTGAAGCATAGCCGTTTTAGCTAAATACTTGAGTT
131 CACAGAATCTCTTATTGCTTGTACCTAAGGTTGAAGCATAGCCGTTTTAGCTAAATACTTGAGTT
*
2615222 CCTAGCTTGACTTGAAGAGTTGGAAGATCATCTACTATTCAATAGCTAATAT
196 CCTAGCTTGACTTGAAGAGTTGGAAGATCATCTACTAATCAATAGCTAATAT
2615274 C
1 C
2615275 TTTTGAAATA
Statistics
Matches: 234, Mismatches: 11, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
244 138 0.59
245 42 0.18
252 54 0.23
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (247 bp):
CCTAGATGGAATTTGATTAATGTTTGCCAGAAATAAGAAAATCTATACTTCAGTCTCTTTATCTT
TTTTTGTTCAACGAACTTGTATTCTTCATTCAATACCCAAAATGTTGTATTTTGATGGGAGGCAT
CACAGAATCTCTTATTGCTTGTACCTAAGGTTGAAGCATAGCCGTTTTAGCTAAATACTTGAGTT
CCTAGCTTGACTTGAAGAGTTGGAAGATCATCTACTAATCAATAGCTAATAT
Found at i:2622410 original size:4 final size:4
Alignment explanation
Indices: 2622401--2622457 Score: 62
Period size: 4 Copynumber: 14.2 Consensus size: 4
2622391 TTTCTTGGTC
* ** *
2622401 GTAT GTAT GTAT GTAT G-AT GTAT GCAT GCGT GTAT GTAT CTAT GTAAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT-AT
2622449 GTAT GTAT G
1 GTAT GTAT G
2622458 GAAAAAATTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
3 3 0.07
4 38 0.84
5 4 0.09
ACGTcount: A:0.25, C:0.05, G:0.26, T:0.44
Consensus pattern (4 bp):
GTAT
Found at i:2623970 original size:18 final size:18
Alignment explanation
Indices: 2623944--2623986 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2623934 TAATAAGTTT
* * *
2623944 TTAAATAAATAAATTTAA
1 TTAATTAAAAAAATTAAA
2623962 TTAATTAAAAAAATTAAA
1 TTAATTAAAAAAATTAAA
2623980 TTAATTA
1 TTAATTA
2623987 CACTTTGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAATTAAAAAAATTAAA
Found at i:2623970 original size:22 final size:22
Alignment explanation
Indices: 2623944--2623986 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2623934 TAATAAGTTT
*
2623944 TTAAATAAA-TAAATTTAATTAA
1 TTAAAAAAATTAAA-TTAATTAA
2623966 TTAAAAAAATTAAATTAATTA
1 TTAAAAAAATTAAATTAATTA
2623987 CACTTTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAAAAATTAAATTAATTAA
Found at i:2627458 original size:17 final size:16
Alignment explanation
Indices: 2627428--2627465 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2627418 ATTTTTTTAA
2627428 TTTT-TATAAATATAT
1 TTTTATATAAATATAT
*
2627443 TTATTATATAATTATAT
1 TT-TTATATAAATATAT
2627460 TTTTAT
1 TTTTAT
2627466 TCTCAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 6 0.30
17 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTATATAAATATAT
Found at i:2627987 original size:19 final size:19
Alignment explanation
Indices: 2627932--2627989 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
2627922 TTTTAAAAAA
*
2627932 TAAAA-AATAAAAATACTT
1 TAAAATAATAAAAATATTT
**
2627950 TAAAATAATATAATTTATTT
1 TAAAATAATA-AAAATATTT
2627970 T-AAATATATAAAAATATTT
1 TAAAATA-ATAAAAATATTT
2627989 T
1 T
2627990 CATAAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.16
19 17 0.53
20 10 0.31
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAATAATAAAAATATTT
Found at i:2638243 original size:35 final size:35
Alignment explanation
Indices: 2638204--2638271 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
2638194 AAACCCACAA
*
2638204 AATCTGGCACTACAAATGAATGTTGTAAAAGAACC
1 AATCTAGCACTACAAATGAATGTTGTAAAAGAACC
* * *
2638239 AATCTAGCGCTATAATTGAATGTTGTAAAAGAA
1 AATCTAGCACTACAAATGAATGTTGTAAAAGAA
2638272 TCAAATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (35 bp):
AATCTAGCACTACAAATGAATGTTGTAAAAGAACC
Found at i:2640401 original size:14 final size:14
Alignment explanation
Indices: 2640382--2640413 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2640372 GCCATTTGGT
2640382 CATTTTGGGGACTC
1 CATTTTGGGGACTC
2640396 CATTTTGGGGACTC
1 CATTTTGGGGACTC
2640410 CATT
1 CATT
2640414 GTCACCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (14 bp):
CATTTTGGGGACTC
Found at i:2641529 original size:23 final size:22
Alignment explanation
Indices: 2641503--2641547 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
2641493 ATTTTAAATG
2641503 CAATGTAAATAAATAATAT-AAAA
1 CAAT-TAAA-AAATAATATGAAAA
*
2641526 CAATTAAAATATAATATGAAAA
1 CAATTAAAAAATAATATGAAAA
2641548 AGGAAACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 8 0.40
23 4 0.20
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (22 bp):
CAATTAAAAAATAATATGAAAA
Found at i:2642361 original size:45 final size:45
Alignment explanation
Indices: 2642270--2642361 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 45
2642260 CCGAGGATCA
* *
2642270 AATTAAAGAGCTCAAATTTCAATACACTTTTGAGTTTAAAAGTTT
1 AATTAAAGAGCTCAAATTTCAATACACTGTTGACTTTAAAAGTTT
2642315 AATTAAAGAGCTCAAATTTCAATACAC-GTTGATTCTTTAAAA-TTT
1 AATTAAAGAGCTCAAATTTCAATACACTGTTGA--CTTTAAAAGTTT
2642360 AA
1 AA
2642362 AATAAAACTC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 4 0.09
45 32 0.74
46 7 0.16
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (45 bp):
AATTAAAGAGCTCAAATTTCAATACACTGTTGACTTTAAAAGTTT
Found at i:2648411 original size:12 final size:12
Alignment explanation
Indices: 2648394--2648418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2648384 AAAAAAGAGG
2648394 ATATATATAAAT
1 ATATATATAAAT
2648406 ATATATATAAAT
1 ATATATATAAAT
2648418 A
1 A
2648419 GGAATCCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:2653783 original size:13 final size:14
Alignment explanation
Indices: 2653767--2653808 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
2653757 TTTCAATTTT
2653767 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
2653780 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
2653795 ATTTTAAATAATAT
1 ATTTT-AATAATAT
2653809 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:2653793 original size:16 final size:16
Alignment explanation
Indices: 2653771--2653807 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2653761 AATTTTATTT
2653771 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
2653788 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
2653803 TAATA
1 TAATA
2653808 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:2653860 original size:15 final size:15
Alignment explanation
Indices: 2653840--2653896 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
2653830 ATTCAATATT
2653840 AATATTTTAATAATA
1 AATATTTTAATAATA
*
2653855 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
2653874 AATATATTAATAATA
1 AATATTTTAATAATA
2653889 AATATTTT
1 AATATTTT
2653897 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:2655874 original size:23 final size:23
Alignment explanation
Indices: 2655801--2655953 Score: 152
Period size: 23 Copynumber: 6.6 Consensus size: 23
2655791 TATACGAAAC
* *
2655801 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
2655823 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
2655844 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
2655870 AAACAGAGAGTACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
2655893 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
2655916 AATCAGAGAGCACACACAA-TGCT
1 AAACAGAGAGCACACA-AAGTGCT
2655939 AATAACAGAGAGCAC
1 -A-AACAGAGAGCAC
2655954 GAGACGTGGT
Statistics
Matches: 111, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
21 17 0.15
23 61 0.55
24 3 0.03
25 24 0.22
26 6 0.05
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:2655900 original size:46 final size:47
Alignment explanation
Indices: 2655849--2655974 Score: 159
Period size: 46 Copynumber: 2.7 Consensus size: 47
2655839 GTGCTGGGCA
*
2655849 ACAGAGAGCACACACAGTGCTAAACAGAGAGTACACA-AAGTGCTAAT
1 ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACACAA-TGCTAAT
* *
2655896 -CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAATGCTAAT
1 ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACACAATGCTAAT
* *
2655942 AACAGAGAGCACGAGAC-GTGGTAAACAGAGAGC
1 -ACAGAGAGCAC-ACACAGTGCTAAACAGAGAGC
2655975 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
46 40 0.59
47 2 0.03
48 24 0.35
49 2 0.03
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (47 bp):
ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACACAATGCTAAT
Found at i:2655923 original size:69 final size:67
Alignment explanation
Indices: 2655801--2655950 Score: 187
Period size: 69 Copynumber: 2.1 Consensus size: 67
2655791 TATACGAAAC
* *
2655801 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACACAA
2655866 TGCT-
63 TGCTA
*
2655870 AAACAGAGAGTACACAAAGTGCTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACACA
2655934 ATGCTA
62 ATGCTA
2655940 ATAACAGAGAG
1 A-AACAGAGAG
2655951 CACGAGACGT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
68 2 0.03
69 32 0.44
70 11 0.15
71 20 0.28
72 7 0.10
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACACAATGC
TA
Found at i:2658231 original size:7 final size:7
Alignment explanation
Indices: 2658216--2658276 Score: 65
Period size: 7 Copynumber: 9.0 Consensus size: 7
2658206 TTCCCTTCCC
*
2658216 CCTTCCT
1 CCTTTCT
2658223 CCTTTCT
1 CCTTTCT
2658230 CCTTTCT
1 CCTTTCT
*
2658237 CTTTTCT
1 CCTTTCT
2658244 CCTTTC-
1 CCTTTCT
*
2658250 CC-TTCC
1 CCTTTCT
2658256 CCTTTTCT
1 CC-TTTCT
2658264 CCTTTC-
1 CCTTTCT
2658270 CCTTTCT
1 CCTTTCT
2658277 TGTTTTCAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 3 0.07
6 10 0.22
7 28 0.61
8 5 0.11
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (7 bp):
CCTTTCT
Found at i:2658260 original size:20 final size:20
Alignment explanation
Indices: 2658200--2658273 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
2658190 GAAGCCTCTC
* *
2658200 CTCCATTTCCCTTCCCCCTTC
1 CTCC-TTTCCCTTCCCCTTTT
* *
2658221 CTCCTTTCTCCTTTCTCTTTT
1 CTCCTTTC-CCTTCCCCTTTT
2658242 CTCCTTTCCCTTCCCCTTTT
1 CTCCTTTCCCTTCCCCTTTT
2658262 CTCCTTTCCCTT
1 CTCCTTTCCCTT
2658274 TCTTGTTTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 26 0.57
21 20 0.43
ACGTcount: A:0.01, C:0.49, G:0.00, T:0.50
Consensus pattern (20 bp):
CTCCTTTCCCTTCCCCTTTT
Found at i:2660491 original size:22 final size:22
Alignment explanation
Indices: 2660463--2660506 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2660453 AAGTACTAAA
2660463 CATCAGCTAACTAGGTATGATT
1 CATCAGCTAACTAGGTATGATT
*
2660485 CATCAGCTAATTAGGTATGATT
1 CATCAGCTAACTAGGTATGATT
2660507 ATTAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (22 bp):
CATCAGCTAACTAGGTATGATT
Found at i:2671471 original size:2 final size:2
Alignment explanation
Indices: 2671464--2671500 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2671454 ACAAAGTTTC
2671464 AT AT AT 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 AT AT AT A
2671501 ACTCTTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2671650 original size:5 final size:6
Alignment explanation
Indices: 2671634--2671659 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2671624 AATTTAAGGT
2671634 GAAAAA GAAAAA GAAAAA GAAAAA GA
1 GAAAAA GAAAAA GAAAAA GAAAAA GA
2671660 GTGAGCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:2673158 original size:2 final size:2
Alignment explanation
Indices: 2673151--2673176 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2673141 ACAATTAGTA
2673151 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
2673177 TTAAAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2681082 original size:26 final size:26
Alignment explanation
Indices: 2681044--2681095 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2681034 TTTAGTTTTG
*
2681044 ATTTCTTTATTATA-TTTAAATTTGAA
1 ATTTATTTATTATACTTT-AATTTGAA
*
2681070 ATTTATTTTTTATACTTTAATTTGAA
1 ATTTATTTATTATACTTTAATTTGAA
2681096 TATAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (26 bp):
ATTTATTTATTATACTTTAATTTGAA
Found at i:2681103 original size:26 final size:26
Alignment explanation
Indices: 2681053--2681114 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
2681043 GATTTCTTTA
*
2681053 TTATATTTAAATTTGAAATTTATTTT
1 TTATATTTAAATTTGAAATTAATTTT
2681079 TTATACTTT-AATTTG-AATATAATTTTAT
1 TTATA-TTTAAATTTGAAAT-TAA-TTT-T
2681107 TTATATTT
1 TTATATTT
2681115 TTATAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 3 0.10
26 13 0.42
27 9 0.29
28 6 0.19
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (26 bp):
TTATATTTAAATTTGAAATTAATTTT
Found at i:2682074 original size:18 final size:20
Alignment explanation
Indices: 2682051--2682089 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2682041 ATTTATTCAT
2682051 TTTTAAA-AT-GAATAAATA
1 TTTTAAAGATAGAATAAATA
2682069 TTTTAAAGATACGAATAAATA
1 TTTTAAAGATA-GAATAAATA
2682090 GTTAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
21 9 0.50
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (20 bp):
TTTTAAAGATAGAATAAATA
Found at i:2685206 original size:4 final size:4
Alignment explanation
Indices: 2685197--2685228 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
2685187 AAATAAACGG
2685197 GAAA GAAA GAAA GAAA GAAA GGAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA -GAAA GAAA GAA
2685229 GGAGTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:2685230 original size:12 final size:12
Alignment explanation
Indices: 2685197--2685231 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
2685187 AAATAAACGG
*
2685197 GAAAGAAAGAAA
1 GAAAGAAGGAAA
2685209 GAAAGAAAGGAAA
1 GAAAG-AAGGAAA
2685222 GAAAGAAGGA
1 GAAAGAAGGA
2685232 GTAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (12 bp):
GAAAGAAGGAAA
Found at i:2685531 original size:23 final size:22
Alignment explanation
Indices: 2685493--2685580 Score: 61
Period size: 23 Copynumber: 3.6 Consensus size: 22
2685483 ATTTACTAAA
2685493 CAATAACAACATTAAATAACAAAT
1 CAATAA-AA-ATTAAATAACAAAT
*
2685517 CAATTAAAAATTAAATTAAACAAAA
1 CAA-TAAAAATTAAA-T-AACAAAT
*
2685542 CAA-AAAACTTAAAATAATCAAAT
1 CAATAAAAATT-AAATAA-CAAAT
*
2685565 TAACTAACAAATTAAA
1 CAA-TAA-AAATTAAA
2685581 ATATTTTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
22 2 0.04
23 19 0.37
24 9 0.18
25 17 0.33
26 4 0.08
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (22 bp):
CAATAAAAATTAAATAACAAAT
Found at i:2685810 original size:23 final size:22
Alignment explanation
Indices: 2685786--2685832 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
2685776 TTTCTTCTTC
2685786 TTCTTCTCCTTCTTCTTTTTTTCT
1 TTCTT-TCCTTC-TCTTTTTTTCT
*
2685810 TTCTTTCTTTCTC-TTTTTTCT
1 TTCTTTCCTTCTCTTTTTTTCT
2685831 TT
1 TT
2685833 TTTTTTCCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 2 0.09
23 5 0.23
24 5 0.23
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (22 bp):
TTCTTTCCTTCTCTTTTTTTCT
Found at i:2685827 original size:22 final size:19
Alignment explanation
Indices: 2685798--2685839 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
2685788 CTTCTCCTTC
2685798 TTCT-TTTTTTCTTTCTTTCT
1 TTCTCTTTTTTCTTT-TTT-T
2685818 TTCTCTTTTTTCTTTTTTT
1 TTCTCTTTTTTCTTTTTTT
2685837 TTC
1 TTC
2685840 CCCTTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 10 0.48
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTCTCTTTTTTCTTTTTTT
Found at i:2686947 original size:26 final size:26
Alignment explanation
Indices: 2686911--2686960 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
2686901 CGCGATATAT
2686911 TGTCGGCGTATCAACAAGCCCAAAAC
1 TGTCGGCGTATCAACAAGCCCAAAAC
*
2686937 TGTCGGCGTATCAACAAGCTCAAA
1 TGTCGGCGTATCAACAAGCCCAAA
2686961 TCAGACGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (26 bp):
TGTCGGCGTATCAACAAGCCCAAAAC
Found at i:2686969 original size:26 final size:26
Alignment explanation
Indices: 2686914--2686970 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
2686904 GATATATTGT
* *
2686914 CGGCGTATCAACAAGCCCAAAACTGT
1 CGGCGTATCAACAAGCCCAAAACAGA
* *
2686940 CGGCGTATCAACAAGCTCAAATCAGA
1 CGGCGTATCAACAAGCCCAAAACAGA
2686966 CGGCG
1 CGGCG
2686971 ATCGATGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (26 bp):
CGGCGTATCAACAAGCCCAAAACAGA
Found at i:2690772 original size:20 final size:22
Alignment explanation
Indices: 2690726--2690772 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
2690716 GATGGTTTCA
2690726 TAATGATAATTGATTAAGTGAT
1 TAATGATAATTGATTAAGTGAT
* * *
2690748 AAATG-TAA-TGATTTAGTGGT
1 TAATGATAATTGATTAAGTGAT
2690768 TAATG
1 TAATG
2690773 CTCCTCCAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 14 0.67
21 3 0.14
22 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.40
Consensus pattern (22 bp):
TAATGATAATTGATTAAGTGAT
Found at i:2695108 original size:53 final size:55
Alignment explanation
Indices: 2695011--2695116 Score: 171
Period size: 53 Copynumber: 2.0 Consensus size: 55
2695001 AGATAGAACT
*
2695011 ACAATAACCATAACTATTACAAGGAATCTATGTACCTCTAATAAGAATGAGGCAA
1 ACAATAACCATAACTATTACAAGGAATCTACGTACCTCTAATAAGAATGAGGCAA
* *
2695066 ACAATAACTATAACTATTAC-TGG-ATCTACGTACCTCTAATAAGAATGAGGC
1 ACAATAACCATAACTATTACAAGGAATCTACGTACCTCTAATAAGAATGAGGC
2695117 TTTATCTCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
53 27 0.56
54 2 0.04
55 19 0.40
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.25
Consensus pattern (55 bp):
ACAATAACCATAACTATTACAAGGAATCTACGTACCTCTAATAAGAATGAGGCAA
Found at i:2701156 original size:28 final size:28
Alignment explanation
Indices: 2701116--2701173 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
2701106 TGTAGGTTGG
*
2701116 TTTTATAATCTATGCTTAGGATTTGTGA
1 TTTTATAATCTATGCTTAAGATTTGTGA
2701144 TTTTATAATCTATGCTTAAGATTTGTGA
1 TTTTATAATCTATGCTTAAGATTTGTGA
2701172 TT
1 TT
2701174 GTCCATTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.52
Consensus pattern (28 bp):
TTTTATAATCTATGCTTAAGATTTGTGA
Found at i:2703326 original size:15 final size:16
Alignment explanation
Indices: 2703301--2703334 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2703291 AAAATGTAAT
2703301 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
2703317 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
2703332 TTT
1 TTT
2703335 TAATGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:2710136 original size:21 final size:21
Alignment explanation
Indices: 2710111--2710174 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
2710101 GTTATATTGG
*
2710111 TGTTGC-ATTTATTGTTGTTTT
1 TGTTGCTATTT-TTGTCGTTTT
2710132 TGTTGCTATTTTTGTCG-TTT
1 TGTTGCTATTTTTGTCGTTTT
* * *
2710152 GGATGCTATTTTTATGCGTTTT
1 TGTTGCTATTTTTGT-CGTTTT
2710174 T
1 T
2710175 ACTGTTGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 15 0.43
21 13 0.37
22 7 0.20
ACGTcount: A:0.09, C:0.08, G:0.20, T:0.62
Consensus pattern (21 bp):
TGTTGCTATTTTTGTCGTTTT
Found at i:2720890 original size:19 final size:19
Alignment explanation
Indices: 2720854--2720891 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2720844 CATTAACAGA
*
2720854 AACCAAATTAATCTAAATT
1 AACCAAATTAATCAAAATT
2720873 AACCAAAATTAA-CAAAATT
1 AACC-AAATTAATCAAAATT
2720892 GGTAACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (19 bp):
AACCAAATTAATCAAAATT
Found at i:2734218 original size:6 final size:6
Alignment explanation
Indices: 2734207--2734231 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2734197 AGTGTCTCTT
2734207 GGAAGA GGAAGA GGAAGA GGAAGA G
1 GGAAGA GGAAGA GGAAGA GGAAGA G
2734232 TCTTGAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GGAAGA
Found at i:2738046 original size:2 final size:2
Alignment explanation
Indices: 2738039--2738078 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2738029 AGGGACGAAT
2738039 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2738079 TATATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2741991 original size:17 final size:16
Alignment explanation
Indices: 2741969--2742002 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2741959 ACATTTTTAA
2741969 TAATATCTGTTTATTTT
1 TAATAT-TGTTTATTTT
*
2741986 TAATATTTTTTATTTT
1 TAATATTGTTTATTTT
2742002 T
1 T
2742003 TAAGATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (16 bp):
TAATATTGTTTATTTT
Found at i:2741999 original size:16 final size:17
Alignment explanation
Indices: 2741978--2742012 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2741968 ATAATATCTG
*
2741978 TTTA-TTTTTAATATTT
1 TTTATTTTTTAAGATTT
2741994 TTTATTTTTTAAGATTT
1 TTTATTTTTTAAGATTT
2742011 TT
1 TT
2742013 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTATTTTTTAAGATTT
Found at i:2747090 original size:10 final size:11
Alignment explanation
Indices: 2747067--2747091 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2747057 TTATCAATTA
2747067 TTTAATATTTT
1 TTTAATATTTT
2747078 TTTAATATTTT
1 TTTAATATTTT
2747089 TTT
1 TTT
2747092 CGTGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTAATATTTT
Found at i:2750018 original size:12 final size:12
Alignment explanation
Indices: 2750001--2750033 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
2749991 CTCGATTTGA
2750001 AGGAGGAGGAAG
1 AGGAGGAGGAAG
2750013 AGGAGGAGGAAG
1 AGGAGGAGGAAG
2750025 AGGAGGAGG
1 AGGAGGAGG
2750034 TGGTGGCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (12 bp):
AGGAGGAGGAAG
Found at i:2769781 original size:20 final size:21
Alignment explanation
Indices: 2769751--2769793 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
2769741 AAGATTTGTG
2769751 AAAATTATATAAAAAATATAA
1 AAAATTATATAAAAAATATAA
*
2769772 AAAATT-TATACAAAATATAA
1 AAAATTATATAAAAAATATAA
2769792 AA
1 AA
2769794 TATACAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATTATATAAAAAATATAA
Found at i:2769950 original size:28 final size:29
Alignment explanation
Indices: 2769910--2769983 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
2769900 AACGTTATAT
*
2769910 AAAAAGATA-AAAATTTAAT-AGAA-TTAA
1 AAAAATATATAAAATTTAATGA-AATTTAA
2769937 AAAAATATATAAAATTTAATGAAATTTAA
1 AAAAATATATAAAATTTAATGAAATTTAA
*
2769966 AAATATAATATATAAATT
1 AAAAAT-ATATA-AAATT
2769984 ACATAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 8 0.20
28 12 0.30
29 10 0.25
30 5 0.12
31 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAAATATATAAAATTTAATGAAATTTAA
Found at i:2769967 original size:27 final size:27
Alignment explanation
Indices: 2769907--2769973 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
2769897 AAAAACGTTA
*
2769907 TATAAAAAGATAAAAATTTAATAGAAT
1 TATAAAAATATAAAAATTTAATAGAAT
*
2769934 TAAAAAAATATATAAAATTTAAT-GAAAT
1 TATAAAAATATA-AAAATTTAATAG-AAT
2769962 T-TAAAAATATAA
1 TATAAAAATATAA
2769974 TATATAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.03
27 20 0.57
28 14 0.40
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (27 bp):
TATAAAAATATAAAAATTTAATAGAAT
Found at i:2770014 original size:21 final size:24
Alignment explanation
Indices: 2769970--2770014 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 24
2769960 ATTTAAAAAT
2769970 ATAATATATAAATTACATAAAATAG
1 ATAATATATAAA-TACATAAAATAG
2769995 ATAAT-TATAAA-ACA-AAAATA
1 ATAATATATAAATACATAAAATA
2770015 ACTCAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.30
22 3 0.15
24 6 0.30
25 5 0.25
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (24 bp):
ATAATATATAAATACATAAAATAG
Found at i:2770460 original size:15 final size:17
Alignment explanation
Indices: 2770435--2770473 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
2770425 TATTTTAATT
2770435 ATTTATTTTAATT-TTA
1 ATTTATTTTAATTGTTA
2770451 ATTT-TTTTAATTGTTAA
1 ATTTATTTTAATTGTT-A
2770468 ATTTAT
1 ATTTAT
2770474 ATTTTTTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.40
16 6 0.30
17 5 0.25
18 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTATTTTAATTGTTA
Found at i:2770467 original size:16 final size:16
Alignment explanation
Indices: 2770421--2770473 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 16
2770411 ACCTTTAAAA
2770421 AATTTATTTTAA--TT
1 AATTTATTTTAATTTT
2770435 -ATTTATTTTAATTTT
1 AATTTATTTTAATTTT
2770450 AATTT-TTTTAATTGTT
1 AATTTATTTTAATT-TT
2770466 AAATTTAT
1 -AATTTAT
2770474 ATTTTTTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 11 0.33
15 10 0.30
16 6 0.18
17 5 0.15
18 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
AATTTATTTTAATTTT
Found at i:2770472 original size:28 final size:30
Alignment explanation
Indices: 2770421--2770478 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
2770411 ACCTTTAAAA
* *
2770421 AATTTATTTTAATTATTTATTTTA-ATTTT
1 AATTTATTTTAATTATTAAATTTATATTTT
*
2770450 AATTT-TTTTAATTGTTAAATTTATATTTT
1 AATTTATTTTAATTATTAAATTTATATTTT
2770479 TTGTCAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (30 bp):
AATTTATTTTAATTATTAAATTTATATTTT
Found at i:2770546 original size:15 final size:15
Alignment explanation
Indices: 2770526--2770556 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2770516 GTTAATTTTG
2770526 CTATCATGGCATACA
1 CTATCATGGCATACA
2770541 CTATCATGGCATACA
1 CTATCATGGCATACA
2770556 C
1 C
2770557 GTAAATTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (15 bp):
CTATCATGGCATACA
Found at i:2776555 original size:14 final size:15
Alignment explanation
Indices: 2776522--2776569 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2776512 AAATTTAAGT
**
2776522 TTAATAATTAATACTA
1 TTAA-AATTAATTTTA
2776538 TTAAAATT-ATTTTA
1 TTAAAATTAATTTTA
*
2776552 TTAAATTTAATTTTA
1 TTAAAATTAATTTTA
2776567 TTA
1 TTA
2776570 CAACATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 11 0.39
15 13 0.46
16 4 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAAAATTAATTTTA
Found at i:2776564 original size:15 final size:14
Alignment explanation
Indices: 2776536--2776569 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2776526 TAATTAATAC
2776536 TATTAAAATTATTT
1 TATTAAAATTATTT
*
2776550 TATTAAATTTAATTT
1 TATTAAAATT-ATTT
2776565 TATTA
1 TATTA
2776570 CAACATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTAAAATTATTT
Found at i:2801393 original size:13 final size:12
Alignment explanation
Indices: 2801377--2801419 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
2801367 TAAACCAAAA
2801377 TTTTCAAAAATAC
1 TTTTC-AAAATAC
2801390 TTTTCAAAATCAC
1 TTTTCAAAAT-AC
*
2801403 TTTTCCAAAACAC
1 TTTT-CAAAATAC
2801416 TTTT
1 TTTT
2801420 AAAGTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 5 0.19
13 17 0.63
14 5 0.19
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTTCAAAATAC
Found at i:2804382 original size:14 final size:15
Alignment explanation
Indices: 2804365--2804393 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2804355 TTGATAGTTG
2804365 TTAAAGTAT-ATTTT
1 TTAAAGTATAATTTT
2804379 TTAAAGTATAATTTT
1 TTAAAGTATAATTTT
2804394 AATTGAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
TTAAAGTATAATTTT
Found at i:2806954 original size:10 final size:10
Alignment explanation
Indices: 2806918--2806959 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
2806908 CATTAACTCA
2806918 ATTA-AAATT
1 ATTATAAATT
*
2806927 ATTATATATAT
1 ATTATAAAT-T
2806938 ATATATAAATT
1 AT-TATAAATT
2806949 ATTATAAATT
1 ATTATAAATT
2806959 A
1 A
2806960 GTAATATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 12 0.43
11 6 0.21
12 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTATAAATT
Found at i:2807202 original size:22 final size:22
Alignment explanation
Indices: 2807174--2807218 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
2807164 TTTTTAAATA
*
2807174 TATATAAAATATATATTT-TTAT
1 TATAT-AAATACATATTTATTAT
2807196 TATATAAATACATATTTATTAT
1 TATATAAATACATATTTATTAT
2807218 T
1 T
2807219 TGATTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATATAAATACATATTTATTAT
Found at i:2807232 original size:27 final size:25
Alignment explanation
Indices: 2807161--2807232 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
2807151 TTAATTTCAA
*
2807161 ATATTTTTAAATATATATAA-A-ATAT
1 ATATTTTT-ATTATATA-AATACATAT
2807186 ATATTTTTATTATATAAATACATAT
1 ATATTTTTATTATATAAATACATAT
* *
2807211 TTATTATTTGATTTTATAAATA
1 ATATT-TTT-ATTATATAAATA
2807233 AAAGATTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.05
24 8 0.20
25 16 0.40
26 3 0.08
27 11 0.28
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
ATATTTTTATTATATAAATACATAT
Found at i:2812389 original size:19 final size:19
Alignment explanation
Indices: 2812351--2812389 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2812341 CACTGATGGT
* *
2812351 GACACTAACAAGCTAAGAA
1 GACAATAACAACCTAAGAA
*
2812370 GACAATAACAACCTATGAA
1 GACAATAACAACCTAAGAA
2812389 G
1 G
2812390 CAAGCATCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (19 bp):
GACAATAACAACCTAAGAA
Found at i:2813430 original size:31 final size:31
Alignment explanation
Indices: 2813395--2813531 Score: 106
Period size: 31 Copynumber: 4.5 Consensus size: 31
2813385 TTAATATAAT
*
2813395 ATTTGGTACCTAAACTTAACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
**
2813426 ATTTGGTACCTAAA-TT---TTTTTTGTCC-A
1 ATTTGGTACCTAAACTTGACACTTTT-TCCTA
* *
2813453 ATTTGGTA-TTCAAACTTGATACTTTTTCCTA
1 ATTTGGTACCT-AAACTTGACACTTTTTCCTA
* * * **
2813484 ATTTGATACTTAAACTTGACATTTTTTTTTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
* *
2813515 AGTTGGTACATAAACTT
1 ATTTGGTACCTAAACTT
2813532 TTGGGATCCA
Statistics
Matches: 85, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.01
27 16 0.19
28 5 0.06
30 5 0.06
31 56 0.66
32 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.47
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTA
Found at i:2813521 original size:89 final size:89
Alignment explanation
Indices: 2813395--2813583 Score: 213
Period size: 89 Copynumber: 2.1 Consensus size: 89
2813385 TTAATATAAT
* * * * **
2813395 ATTTGGTACCTAAACTTAACACTTTTTCCTAATTTGGTACCTAAATTTTTTTTG-TCCAATTTGG
1 ATTTGATACCTAAACTTAACACTTTTTCCTAAGTTGGTACATAAA-CTTTTGGGATCCAATTTGG
*
2813459 TA-TTCAAACTTGA-TACTTTTTCCTA
65 TACCT-AAACTTGACT-CTTTTTCCTA
* * * **
2813484 ATTTGATACTTAAACTTGACATTTTTTTTTAAGTTGGTACATAAACTTTTGGGATCCAATTTGGT
1 ATTTGATACCTAAACTTAACACTTTTTCCTAAGTTGGTACATAAACTTTTGGGATCCAATTTGGT
*
2813549 ACCTGAACTTGACTCTTTTTCCTA
66 ACCTAAACTTGACTCTTTTTCCTA
2813573 ATTTGATACCT
1 ATTTGATACCT
2813584 TTTTTTAATA
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
88 5 0.06
89 76 0.92
90 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (89 bp):
ATTTGATACCTAAACTTAACACTTTTTCCTAAGTTGGTACATAAACTTTTGGGATCCAATTTGGT
ACCTAAACTTGACTCTTTTTCCTA
Found at i:2814803 original size:30 final size:30
Alignment explanation
Indices: 2814769--2814862 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 30
2814759 TTTACGGTAT
2814769 AAAATAACAAATATGAAAAAACTGTTATTA
1 AAAATAACAAATATGAAAAAACTGTTATTA
* * * **
2814799 AAAATAACAATTGTGAAGAAAA-TGCCTGGT-
1 AAAATAACAAATATGAA-AAAACTG-TTATTA
**
2814829 AAGTTAACAAATATGAAAAAACTGTTATTA
1 AAAATAACAAATATGAAAAAACTGTTATTA
2814859 AAAA
1 AAAA
2814863 ACTCTAGAAG
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
29 6 0.13
30 34 0.74
31 6 0.13
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (30 bp):
AAAATAACAAATATGAAAAAACTGTTATTA
Found at i:2815383 original size:10 final size:10
Alignment explanation
Indices: 2815347--2815388 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
2815337 CATTAACTCA
2815347 ATTA-AAATT
1 ATTATAAATT
*
2815356 ATTATATATAT
1 ATTATAAAT-T
2815367 ATATATAAATT
1 AT-TATAAATT
2815378 ATTATAAATT
1 ATTATAAATT
2815388 A
1 A
2815389 GTAATATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 12 0.43
11 6 0.21
12 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTATAAATT
Found at i:2816587 original size:81 final size:81
Alignment explanation
Indices: 2816484--2816670 Score: 268
Period size: 81 Copynumber: 2.3 Consensus size: 81
2816474 AATTAAGAAT
* * * * * * *
2816484 ATATAATTTATCAAGTTAAATATATGTTTAAAAAGAATATGATAGACGAAAA-TTTCAAAAGAGT
1 ATATGATTTATCTAGTTAAATATATGTTTAAAAAGAATACGATAGACAAAAATTTTAAAAAAAAT
2816548 TTAGATAAAATTTATAC
66 TT-GATAAAATTTATAC
*
2816565 ATATGATTTATCTAGTTAAATATATGTTTAAAAATAATACGATAGACAAAAATTTTAAAAAAAAT
1 ATATGATTTATCTAGTTAAATATATGTTTAAAAAGAATACGATAGACAAAAATTTTAAAAAAAAT
2816630 TTGATAAAATTTATAC
66 TTGATAAAATTTATAC
* *
2816646 ATATGATCTATCTATTTAAATATAT
1 ATATGATTTATCTAGTTAAATATAT
2816671 ATTTGAATAA
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 84 0.88
82 11 0.12
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (81 bp):
ATATGATTTATCTAGTTAAATATATGTTTAAAAAGAATACGATAGACAAAAATTTTAAAAAAAAT
TTGATAAAATTTATAC
Found at i:2850155 original size:19 final size:19
Alignment explanation
Indices: 2850128--2850168 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2850118 GTTTTCTTTT
2850128 GTTCAAC-TTAAATATTTAA
1 GTTCAACTTTAAAT-TTTAA
*
2850147 GTTCGACTTTAAATTTTAA
1 GTTCAACTTTAAATTTTAA
2850166 GTT
1 GTT
2850169 GGTATATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (19 bp):
GTTCAACTTTAAATTTTAA
Found at i:2862148 original size:75 final size:75
Alignment explanation
Indices: 2862025--2862174 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
2862015 GTCGGCTAAT
2862025 TTACTTTATTGATTTAAATAAATTATAAATAATCAACTTGAATCATTAGGGAAGCGCAGGAGTAC
1 TTACTTTATTGATTTAAATAAATTATAAATAATCAACTTGAATCATTAGGGAAGCGCAGGAGTAC
2862090 ATCAGAACAA
66 ATCAGAACAA
2862100 TTACTTTATTGATTTAAATAAATTATAAATAATCAACTTGAATCATTAGGGAAGCGCAGGAGTAC
1 TTACTTTATTGATTTAAATAAATTATAAATAATCAACTTGAATCATTAGGGAAGCGCAGGAGTAC
2862165 ATCAGAACAA
66 ATCAGAACAA
2862175 CGAAGATAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Consensus pattern (75 bp):
TTACTTTATTGATTTAAATAAATTATAAATAATCAACTTGAATCATTAGGGAAGCGCAGGAGTAC
ATCAGAACAA
Found at i:2869770 original size:30 final size:30
Alignment explanation
Indices: 2869734--2869815 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
2869724 AATACTTAAA
**
2869734 ACCTCATATTTCACATTATTAAAAGTATTG
1 ACCTCATATCCCACATTATTAAAAGTATTG
2869764 ACCTCATATCCCACATTATTAAAAGTATTG
1 ACCTCATATCCCACATTATTAAAAGTATTG
*
2869794 ACCTCATATCCCACATTGTTAA
1 ACCTCATATCCCACATTATTAA
2869816 TTTACATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (30 bp):
ACCTCATATCCCACATTATTAAAAGTATTG
Found at i:2871077 original size:2 final size:2
Alignment explanation
Indices: 2871070--2871103 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2871060 TGGTGATCTG
2871070 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2871104 GTTTCTCTTG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2880402 original size:14 final size:17
Alignment explanation
Indices: 2880355--2880396 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2880345 TAAAGTAAAT
* *
2880355 ATTATTATTTATTATTAA
1 ATTA-TATTTAATAATAA
2880373 ATTATATTTAATAATAA
1 ATTATATTTAATAATAA
2880390 A-TATATT
1 ATTATATT
2880397 AAAATATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 6 0.27
17 12 0.55
18 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATATTTAATAATAA
Found at i:2884186 original size:6 final size:6
Alignment explanation
Indices: 2884139--2884167 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2884129 TGCTGAAGAT
2884139 AAGAAA AAGAAA AAGAAA AAGAAA AAGAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAA
2884168 GTTCCTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:2890884 original size:6 final size:6
Alignment explanation
Indices: 2890875--2890906 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2890865 GACAAGAGGA
2890875 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GA
1 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GA
2890907 ATGAAGAAAA
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:0.34, C:0.00, G:0.50, T:0.16
Consensus pattern (6 bp):
GAGAGT
Found at i:2891351 original size:24 final size:24
Alignment explanation
Indices: 2891306--2891351 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2891296 TAATGAGATC
**
2891306 TATAATTTAAAATTAATTAATATG
1 TATAATTTAAAATTAAAAAATATG
2891330 TATAATATTAAAA-TAAAAAATA
1 TATAAT-TTAAAATTAAAAAATA
2891352 GATTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
TATAATTTAAAATTAAAAAATATG
Found at i:2897758 original size:38 final size:39
Alignment explanation
Indices: 2897697--2897770 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
2897687 CATAGTAATT
2897697 TTTTATTTTAAATTTTTAGATA-T-TTTGATAAAATGAA
1 TTTTATTTTAAATTTTTAGATATTATTTGATAAAATGAA
*
2897734 TTTTGTTTTATAATTTTT-GAATATTATTTGATAAAAT
1 TTTTATTTTA-AATTTTTAG-ATATTATTTGATAAAAT
2897771 ATTAGTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
37 10 0.31
38 10 0.31
39 1 0.03
40 11 0.34
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (39 bp):
TTTTATTTTAAATTTTTAGATATTATTTGATAAAATGAA
Found at i:2906748 original size:25 final size:25
Alignment explanation
Indices: 2906720--2906772 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
2906710 TAAGATAACT
2906720 ATATAAAAAAATTAATAAATA-TAAA
1 ATAT-AAAAAATTAATAAATATTAAA
* *
2906745 ATATATAAAATTATTAAATATTAAA
1 ATATAAAAAATTAATAAATATTAAA
2906770 ATA
1 ATA
2906773 ATATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
ATATAAAAAATTAATAAATATTAAA
Found at i:2906752 original size:9 final size:9
Alignment explanation
Indices: 2906738--2906782 Score: 51
Period size: 8 Copynumber: 5.3 Consensus size: 9
2906728 AAATTAATAA
2906738 ATATAAAAT
1 ATATAAAAT
2906747 ATATAAAAT
1 ATATAAAAT
*
2906756 -TATTAAAT
1 ATATAAAAT
2906764 AT-TAAAAT
1 ATATAAAAT
*
2906772 A-ATATAAT
1 ATATAAAAT
2906780 ATA
1 ATA
2906783 ATTTTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
8 19 0.63
9 11 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
ATATAAAAT
Found at i:2906762 original size:24 final size:26
Alignment explanation
Indices: 2906727--2906778 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
2906717 ACTATATAAA
2906727 AAAATTAATAAATA-TAAAAT-ATAT
1 AAAATTAATAAATATTAAAATAATAT
*
2906751 AAAATTATTAAATATTAAAATAATAT
1 AAAATTAATAAATATTAAAATAATAT
2906777 AA
1 AA
2906779 TATAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 13 0.52
25 6 0.24
26 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAATTAATAAATATTAAAATAATAT
Found at i:2908621 original size:76 final size:76
Alignment explanation
Indices: 2908495--2908652 Score: 316
Period size: 76 Copynumber: 2.1 Consensus size: 76
2908485 TAACCATGCT
2908495 ATTTAACATGAACCAATAGATTAGCTTCCCTTGTCAAAAATAACAGACATAAAACATTAAATGTG
1 ATTTAACATGAACCAATAGATTAGCTTCCCTTGTCAAAAATAACAGACATAAAACATTAAATGTG
2908560 TTCTTCGAAAG
66 TTCTTCGAAAG
2908571 ATTTAACATGAACCAATAGATTAGCTTCCCTTGTCAAAAATAACAGACATAAAACATTAAATGTG
1 ATTTAACATGAACCAATAGATTAGCTTCCCTTGTCAAAAATAACAGACATAAAACATTAAATGTG
2908636 TTCTTCGAAAG
66 TTCTTCGAAAG
2908647 ATTTAA
1 ATTTAA
2908653 GCCATATTGC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 82 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.30
Consensus pattern (76 bp):
ATTTAACATGAACCAATAGATTAGCTTCCCTTGTCAAAAATAACAGACATAAAACATTAAATGTG
TTCTTCGAAAG
Found at i:2918419 original size:2 final size:2
Alignment explanation
Indices: 2918412--2918438 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2918402 TTGTAGGGCA
2918412 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2918439 GCATTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2932010 original size:95 final size:93
Alignment explanation
Indices: 2931820--2932070 Score: 342
Period size: 95 Copynumber: 2.7 Consensus size: 93
2931810 TACCAAAAAA
* *
2931820 AATATAATATCATAATTTAAAGATATAATTAAAATATTTTAAAATTTAAAAACTAATTTAAATTA
1 AATATAATATCATAATTTAAAGATATAATTAAAATGTTTTAAAATTTAAAAATTAATTTAAATTA
** * * *
2931885 AATGATTTGATAACAAAACAACTTAATT
66 AACCACTAGATAACAAAAAAACTTAATT
2931913 AATATAATATTCATAATTTAAAGATATAATTAAAATGTTTTAAAATTTTAAAAATTAATTTAAAT
1 AATATAATA-TCATAATTTAAAGATATAATTAAAATGTTTTAAAA-TTTAAAAATTAATTTAAAT
* **
2931978 TAAACCACTAGATAACAAAAAAATTTGGTT
64 TAAACCACTAGATAACAAAAAAACTTAATT
* * *
2932008 AATATAATATCTATAATTTAGAA-ATATAATTGAAACGTTTCAAAATTTAAAAATTAATTTAAA
1 AATATAATATC-ATAATTTA-AAGATATAATTAAAATGTTTTAAAATTTAAAAATTAATTTAAA
2932071 ATGATGTCTA
Statistics
Matches: 141, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
93 9 0.06
94 54 0.38
95 76 0.54
96 2 0.01
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (93 bp):
AATATAATATCATAATTTAAAGATATAATTAAAATGTTTTAAAATTTAAAAATTAATTTAAATTA
AACCACTAGATAACAAAAAAACTTAATT
Found at i:2932414 original size:18 final size:18
Alignment explanation
Indices: 2932393--2932461 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
2932383 GATTTTTAAA
2932393 ATTTTAGTATTTTTTTAT
1 ATTTTAGTATTTTTTTAT
* *
2932411 ATTTTATGT-TGTTTTTGT
1 ATTTTA-GTATTTTTTTAT
* *
2932429 ATTTTA-AAATTTTTTAT
1 ATTTTAGTATTTTTTTAT
* *
2932446 -TTTTAATACTTTTTTA
1 ATTTTAGTATTTTTTTA
2932462 AATGTTTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
16 5 0.12
17 14 0.35
18 19 0.47
19 2 0.05
ACGTcount: A:0.23, C:0.01, G:0.06, T:0.70
Consensus pattern (18 bp):
ATTTTAGTATTTTTTTAT
Found at i:2932500 original size:22 final size:22
Alignment explanation
Indices: 2932458--2932499 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
2932448 TTAATACTTT
2932458 TTTAAATGTTTAAATTTTTTTG
1 TTTAAATGTTTAAATTTTTTTG
2932480 TTTAAAT-TTTAAATTTTTTT
1 TTTAAATGTTTAAATTTTTTT
2932500 TAAAGATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTTAAATGTTTAAATTTTTTTG
Found at i:2932995 original size:15 final size:14
Alignment explanation
Indices: 2932975--2933004 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2932965 TCAAATTTTA
2932975 ATATTTTAATATAAT
1 ATATTTTAAT-TAAT
2932990 ATATTTTAATTAAT
1 ATATTTTAATTAAT
2933004 A
1 A
2933005 CACACAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATTTTAATTAAT
Done.