Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 104 of 126
Found at i:31405095 original size:11 final size:11
Alignment explanation
Indices: 31405017--31405102 Score: 72
Period size: 11 Copynumber: 8.0 Consensus size: 11
31405007 TAAATTGATT
*
31405017 TTAAATTT-AT
1 TTAAATTTAAA
31405027 TTAAATTTAAA
1 TTAAATTTAAA
* *
31405038 TTTACTTTAAA
1 TTAAATTTAAA
31405049 TTTAAATTT-AA
1 -TTAAATTTAAA
31405060 TT--ATTTAAA
1 TTAAATTTAAA
* *
31405069 TTTACTTTAAA
1 TTAAATTTAAA
31405080 TTTAAATTTAAA
1 -TTAAATTTAAA
*
31405092 TTAAAATTAAA
1 TTAAATTTAAA
31405103 ATACTAAACA
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 10 0.16
11 28 0.46
12 15 0.25
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:31405095 original size:17 final size:17
Alignment explanation
Indices: 31405006--31405102 Score: 94
Period size: 17 Copynumber: 5.9 Consensus size: 17
31404996 TAATTTGGAG
* *
31405006 TTAAATTGATTTTAAAT
1 TTAAATTAAATTTAAAT
*
31405023 TT-ATTTAAATTTAAAT
1 TTAAATTAAATTTAAAT
**
31405039 TTACTTTAAATTTAAAT
1 TTAAATTAAATTTAAAT
31405056 TT-AATT--ATTTAAAT
1 TTAAATTAAATTTAAAT
**
31405070 TTACTTTAAATTTAAAT
1 TTAAATTAAATTTAAAT
*
31405087 TTAAATTAAAATTAAA
1 TTAAATTAAATTTAAA
31405103 ATACTAAACA
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
14 10 0.15
15 2 0.03
16 15 0.23
17 38 0.58
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (17 bp):
TTAAATTAAATTTAAAT
Found at i:31406166 original size:20 final size:21
Alignment explanation
Indices: 31406129--31406167 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31406119 AGCAAAACAA
*
31406129 TTTCAAAAAAATGGAAAAGAG
1 TTTCAAAAAAATGAAAAAGAG
*
31406150 TTTCAAAATAAT-AAAAAG
1 TTTCAAAAAAATGAAAAAG
31406168 GATTGTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.59, C:0.05, G:0.13, T:0.23
Consensus pattern (21 bp):
TTTCAAAAAAATGAAAAAGAG
Found at i:31406246 original size:14 final size:15
Alignment explanation
Indices: 31406222--31406250 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31406212 ATGTTTTGGA
31406222 AAATCCCAGATCTGG
1 AAATCCCAGATCTGG
31406237 AAAT-CCAGATCTGG
1 AAATCCCAGATCTGG
31406251 GTTTGGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (15 bp):
AAATCCCAGATCTGG
Found at i:31407067 original size:30 final size:30
Alignment explanation
Indices: 31407026--31407406 Score: 523
Period size: 30 Copynumber: 12.7 Consensus size: 30
31407016 CCCTAAATTG
*
31407026 TCCAGAAATTACATTTTGACCTCAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
* *
31407057 TCCAAAATTACATTTTAACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
31407087 TCCAAAATTACATTTTAACCCCAACACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
31407117 TCCTAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
31407147 TCTAAAATTACATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
31407177 TCCAAAATTACATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
31407207 TCCAAAATTATATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
31407237 ACCAAAATTACATTTTGACCCCGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
31407267 TCCAAAATTACATTTTGACCCCAAAAATTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * *
31407297 TCCACAATTACATTTTGACCTCGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
31407327 TCCAAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * *
31407357 TCTAAAATTATATTTTGACCCCGAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
31407386 TCAAAAATTACCATTTT-ACCC
1 TCCAAAATTA-CATTTTGACCC
31407407 TTAAACTTCC
Statistics
Matches: 313, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
29 15 0.05
30 294 0.94
31 4 0.01
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:31407450 original size:59 final size:58
Alignment explanation
Indices: 31407387--31407587 Score: 165
Period size: 59 Copynumber: 3.4 Consensus size: 58
31407377 CCGAAACTTT
*
31407387 CAAAAATTACCATTTTACCCTTAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCTTAAACTT-CCTAAATTCCATTTTTAACCCCGATTTCAC
* * * * * * * * ** * **
31407446 CAAAACTTATCGTTTT-GCCTTCGAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGC
1 CAAAAATTACCATTTTACCCTT-AAAC-TTCCTAAATTCCATTTTTAACCCCGATTTCAC
* * * *
31407505 CAAAATTTACCATTTTATTCCC-CAAACTTTCTAAATTCCATTTTTAGCCCCGATTTCA-
1 CAAAAATTACCATTTTA--CCCTTAAACTTCCTAAATTCCATTTTTAACCCCGATTTCAC
*
31407563 CAAAAATTACCATTTTACCCCTAAA
1 CAAAAATTACCATTTTACCCTTAAA
31407588 AACCCAAATT
Statistics
Matches: 104, Mismatches: 32, Indels: 14
0.69 0.21 0.09
Matches are distributed among these distances:
56 3 0.03
57 3 0.03
58 20 0.19
59 71 0.68
60 5 0.05
62 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.04, T:0.38
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCTTAAACTTCCTAAATTCCATTTTTAACCCCGATTTCAC
Found at i:31413429 original size:28 final size:28
Alignment explanation
Indices: 31413354--31413430 Score: 136
Period size: 28 Copynumber: 2.8 Consensus size: 28
31413344 AGACTTCTTT
*
31413354 TATTTTATTTTAATTAGAACAGATCATC
1 TATTTTATTTTAATTAGAATAGATCATC
31413382 TATTTTATTTTAATTAGAATAGATCATC
1 TATTTTATTTTAATTAGAATAGATCATC
*
31413410 TATTTAATTTTAATTAGAATA
1 TATTTTATTTTAATTAGAATA
31413431 AGGTGTTTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (28 bp):
TATTTTATTTTAATTAGAATAGATCATC
Found at i:31416461 original size:41 final size:41
Alignment explanation
Indices: 31416400--31416495 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
31416390 TTGTTCAAAG
*
31416400 AGAATTCTTGTCAAGATGGAGATTGTTAAAATTGGGTGACT
1 AGAATTCTTGTTAAGATGGAGATTGTTAAAATTGGGTGACT
* *
31416441 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGATGGAGATTGTTAAAATTGGGTGACT
*
31416482 AAAATTCTTGTTAA
1 AGAATTCTTGTTAA
31416496 AGTAAAATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAGATGGAGATTGTTAAAATTGGGTGACT
Found at i:31418432 original size:6 final size:6
Alignment explanation
Indices: 31418412--31418453 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
31418402 TTAAATGGGT
* *
31418412 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
31418454 CACTTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
TTTAAA
Found at i:31418432 original size:17 final size:17
Alignment explanation
Indices: 31418412--31418525 Score: 87
Period size: 17 Copynumber: 7.1 Consensus size: 17
31418402 TTAAATGGGT
31418412 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
31418429 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
31418446 TTTAAATTCA-CTT--A
1 TTTAAATTTATTTTAAA
* *
31418460 TTTAGATTTACTTTAAA
1 TTTAAATTTATTTTAAA
* * *
31418477 TTTAAGTTTA-ATCAAA
1 TTTAAATTTATTTTAAA
* * *
31418493 TTTAAAATAATATTAAA
1 TTTAAATTTATTTTAAA
*
31418510 -CTAAATTT-TTTTAAA
1 TTTAAATTTATTTTAAA
31418525 T
1 T
31418526 CAAAGTCCAT
Statistics
Matches: 75, Mismatches: 17, Indels: 11
0.73 0.17 0.11
Matches are distributed among these distances:
14 9 0.12
15 8 0.11
16 18 0.24
17 40 0.53
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:31419222 original size:3 final size:3
Alignment explanation
Indices: 31419216--31419266 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
31419206 CAACAACAAC
31419216 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31419264 AAT
1 AAT
31419267 TACAGCATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31419346 original size:15 final size:14
Alignment explanation
Indices: 31419314--31419351 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
31419304 CTTAATGAAA
31419314 TATTAAT-AATAAT
1 TATTAATAAATAAT
*
31419327 TATTATTAAATAATT
1 TATTAATAAATAA-T
31419342 TATTAATAAA
1 TATTAATAAA
31419352 AAAGAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 6 0.29
14 5 0.24
15 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTAATAAATAAT
Found at i:31420365 original size:162 final size:162
Alignment explanation
Indices: 31420098--31420404 Score: 542
Period size: 162 Copynumber: 1.9 Consensus size: 162
31420088 AATTTTAATT
31420098 GGTTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGGTT
1 GGTTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGGTT
* * *
31420163 TATTTATGTATCTAGTCCCTGTCATTTTCAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGC
66 TATTTATGTATCTAGTCCCTGTCATTTTCAATTTGTTTTAATTTAAACCTCAAACCAACTTCTGC
31420228 TTAATTACAAAATTGACTCGGGAATCTTTTGA
131 TTAATTACAAAATTGACTCGGGAATCTTTTGA
* * *
31420260 GGTTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCGACGTGTCACTTTTTGGTT
1 GGTTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGGTT
* *
31420325 TATTTATGTATCTAGTCCCTGTCATTTTTAATTTGTTTTAATTTAAACCTCAAACCAACTTCTGT
66 TATTTATGTATCTAGTCCCTGTCATTTTCAATTTGTTTTAATTTAAACCTCAAACCAACTTCTGC
31420390 TTAATTACAAAATTG
131 TTAATTACAAAATTG
31420405 GCCTAAGAAT
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 137 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (162 bp):
GGTTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGGTT
TATTTATGTATCTAGTCCCTGTCATTTTCAATTTGTTTTAATTTAAACCTCAAACCAACTTCTGC
TTAATTACAAAATTGACTCGGGAATCTTTTGA
Found at i:31420435 original size:162 final size:162
Alignment explanation
Indices: 31420105--31420445 Score: 515
Period size: 162 Copynumber: 2.1 Consensus size: 162
31420095 ATTGGTTTTT
31420105 AAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGGTTTATTTAT
1 AAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGGTTTATTTAT
* * *
31420170 GTATCTAGTCCCTGTCATTTTCAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCTTAATTA
66 GTATCTAGTCCCTGTCATTTTCAATTTGTTTTAATTTAAACCTCAAACCAACTTCTGCTTAATTA
** * * **
31420235 CAAAATTGACTCGGGAATCTTTTGAGGTTTTT
131 CAAAATTGACTCAAGAATCTTTTAAGATTTAC
* * *
31420267 AAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCGACGTGTCACTTTTTGGTTTATTTAT
1 AAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGGTTTATTTAT
* *
31420332 GTATCTAGTCCCTGTCATTTTTAATTTGTTTTAATTTAAACCTCAAACCAACTTCTGTTTAATTA
66 GTATCTAGTCCCTGTCATTTTCAATTTGTTTTAATTTAAACCTCAAACCAACTTCTGCTTAATTA
*
31420397 CAAAATTGGC-CTAAGAAT-TTTTCAAGATTTAC
131 CAAAATTGACTC-AAGAATCTTTT-AAGATTTAC
31420429 AAATTAGTCCTTTGACT
1 AAATTAGTCCTTTGACT
31420446 TCTGGATGCC
Statistics
Matches: 162, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
161 5 0.03
162 157 0.97
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (162 bp):
AAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGGTTTATTTAT
GTATCTAGTCCCTGTCATTTTCAATTTGTTTTAATTTAAACCTCAAACCAACTTCTGCTTAATTA
CAAAATTGACTCAAGAATCTTTTAAGATTTAC
Found at i:31420584 original size:59 final size:59
Alignment explanation
Indices: 31420516--31421005 Score: 621
Period size: 59 Copynumber: 8.4 Consensus size: 59
31420506 CCTGGATGGT
* *
31420516 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
31420575 CCAAAAATTACCATTTTACTCTTAAACTTTCCAAAATTCCATTTTCAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
31420634 CCCAAAATTACCATTTTACCCCTAAACTTTCCAACATTCCATTTTCAATCCCGGTTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
31420693 CCAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
31420752 CCAAAAATTACCATTTTACTCCTAAAC-TTCCAAAATTCTATTTTTAATCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
31420810 CCAAAAACTACCATTTTA-CCCTCGAACTTCCCAAAATTCCATTTTTAACCCCGGTTTCA
1 CCAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
31420869 CC--AAATTACCATCTTACCCCTAAACTTTTCAAAATTCCA-TTTTAATCTCGATTTAA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * * ** *
31420925 CCAAAAATTACTATTTTACCCTTGAATTTTCTAAAATTCTTTTTTTAACCCCGATTTTA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
31420984 TCGAAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
31421006 CGCGAGTCCA
Statistics
Matches: 369, Mismatches: 56, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
56 15 0.04
57 30 0.08
58 80 0.22
59 244 0.66
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.36
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:31421046 original size:28 final size:29
Alignment explanation
Indices: 31420982--31421046 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
31420972 ACCCCGATTT
*
31420982 TATCGAAAATTACCATTTTGCCCCCGCGA
1 TATCAAAAATTACCATTTTGCCCCCGCGA
* *
31421011 -GTCCAAAATTACCATTTTGCCCCCG-GA
1 TATCAAAAATTACCATTTTGCCCCCGCGA
31421038 TATCAAAAA
1 TATCAAAAA
31421047 GTCTCATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.26
Consensus pattern (29 bp):
TATCAAAAATTACCATTTTGCCCCCGCGA
Found at i:31427797 original size:2 final size:2
Alignment explanation
Indices: 31427792--31427869 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
31427782 CAAAAAAGTA
31427792 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
31427834 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
31427870 TATGTTTAAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31433692 original size:25 final size:25
Alignment explanation
Indices: 31433646--31433693 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
31433636 AACACACCAA
*
31433646 TCATGTTATCAATTAATTATCATAG
1 TCATGTTATCAATTAATCATCATAG
*
31433671 TCATTTTATCTAATT-ATCATCAT
1 TCATGTTATC-AATTAATCATCAT
31433694 TATCTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (25 bp):
TCATGTTATCAATTAATCATCATAG
Found at i:31434336 original size:3 final size:3
Alignment explanation
Indices: 31434328--31434359 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
31434318 TCAAATCTAA
31434328 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
31434360 TAAAAAGATT
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:31438300 original size:23 final size:23
Alignment explanation
Indices: 31438270--31438326 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
31438260 TGACGTGGCA
*
31438270 TCCAGTCAGCAGCTTTTAGAAGG
1 TCCAGTCAGCAGCTTCTAGAAGG
*
31438293 TCCAGTCAACAGCTTCTAGAAGG
1 TCCAGTCAGCAGCTTCTAGAAGG
31438316 TCCAGTCAGCA
1 TCCAGTCAGCA
31438327 AGGATGGACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
TCCAGTCAGCAGCTTCTAGAAGG
Found at i:31446155 original size:24 final size:26
Alignment explanation
Indices: 31446119--31446166 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
31446109 GAAGAAATGT
31446119 AAATGTGATATATGA-A-ATTATGAG
1 AAATGTGATATATGAGAGATTATGAG
31446143 AAATGATGA-ATATGAGAGATTATG
1 AAATG-TGATATATGAGAGATTATG
31446167 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGTGATATATGAGAGATTATGAG
Found at i:31446293 original size:22 final size:22
Alignment explanation
Indices: 31446265--31446323 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
31446255 TCTGTTTCCC
*
31446265 CAGCACTGGGTGTGCTTTTGTT
1 CAGCACTGGGTGTGCTTCTGTT
31446287 CAGCACTGGGTGTGCTTCTGTT
1 CAGCACTGGGTGTGCTTCTGTT
*
31446309 CAGCACTGTGTGTGC
1 CAGCACTGGGTGTGC
31446324 CTACTATTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.10, C:0.22, G:0.32, T:0.36
Consensus pattern (22 bp):
CAGCACTGGGTGTGCTTCTGTT
Found at i:31446375 original size:25 final size:25
Alignment explanation
Indices: 31446333--31446380 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31446323 CCTACTATTT
*
31446333 CCCAGCACTTACGTGCTTCTGTTTC
1 CCCAGCACTTACGCGCTTCTGTTTC
* *
31446358 CCCAGCACTTATGCGCTTTTGTT
1 CCCAGCACTTACGCGCTTCTGTT
31446381 AAGTACTTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.12, C:0.33, G:0.17, T:0.38
Consensus pattern (25 bp):
CCCAGCACTTACGCGCTTCTGTTTC
Found at i:31450713 original size:18 final size:19
Alignment explanation
Indices: 31450680--31450719 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
31450670 GAATTCACAT
31450680 ATTTTATTTTCTAATT-TA
1 ATTTTATTTTCTAATTATA
31450698 ATTTTATTTTAC-AATTATA
1 ATTTTATTTT-CTAATTATA
31450717 ATT
1 ATT
31450720 CAATTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTATTTTCTAATTATA
Found at i:31453915 original size:43 final size:43
Alignment explanation
Indices: 31453868--31453954 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
31453858 CTCTTTTACC
*
31453868 TCCCTAACAGAAGTCCTATGTGGTAGTCCAAATGAATTTTAAA
1 TCCCTAACAGAAGTCCTACGTGGTAGTCCAAATGAATTTTAAA
*
31453911 TCCCTAACGGAAGTCCTACGTGGTAGTCCAAATGAATTTTAAA
1 TCCCTAACAGAAGTCCTACGTGGTAGTCCAAATGAATTTTAAA
31453954 T
1 T
31453955 GACAATTTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (43 bp):
TCCCTAACAGAAGTCCTACGTGGTAGTCCAAATGAATTTTAAA
Found at i:31453986 original size:44 final size:43
Alignment explanation
Indices: 31453871--31453987 Score: 155
Period size: 43 Copynumber: 2.7 Consensus size: 43
31453861 TTTTACCTCC
* *
31453871 CTAACAGAAGTCCTATGTGGTAGTCCAAATGAATTTTAAATCC
1 CTAACGGAAGTCCTATGTGGTAGTCCAAATGAATTTTAAATCA
* *
31453914 CTAACGGAAGTCCTACGTGGTAGTCCAAATGAATTTTAAATGA
1 CTAACGGAAGTCCTATGTGGTAGTCCAAATGAATTTTAAATCA
* *
31453957 C-AATTTGGATGTCCTATGTGGTAGTCCAAAT
1 CTAA--CGGAAGTCCTATGTGGTAGTCCAAAT
31453988 TAAATTTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 2 0.03
43 40 0.62
44 23 0.35
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (43 bp):
CTAACGGAAGTCCTATGTGGTAGTCCAAATGAATTTTAAATCA
Found at i:31455381 original size:18 final size:19
Alignment explanation
Indices: 31455358--31455396 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
31455348 GTAATAAAGC
*
31455358 ATGTATAATAAAA-TTAAA
1 ATGTATAAAAAAATTTAAA
31455376 ATGTATAAAAAAATTTAAA
1 ATGTATAAAAAAATTTAAA
31455395 AT
1 AT
31455397 AAAACTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
ATGTATAAAAAAATTTAAA
Found at i:31457119 original size:113 final size:113
Alignment explanation
Indices: 31456983--31457212 Score: 399
Period size: 113 Copynumber: 2.0 Consensus size: 113
31456973 CCATTAACCC
* *
31456983 AAAGAAACTAAATGGGAAGAAGATATTGGAACCAAAGATATTGAATTTTTTGGTTAATGGGTTTT
1 AAAGAAACTAAATGGGAAGAAGATATTAGAACCAAAGATATTGAATCTTTTGGTTAATGGGTTTT
* *
31457048 AAAGATTCAAGCTTTGAGATAGATTTGTAACTAAAGATATTGGAATCA
66 AAAGATTCAAGCTTTGAGAGAGATTTGTAACAAAAGATATTGGAATCA
*
31457096 AAAGAAACTTAACT-GGAAGAAGATATTAGAACCAAAGATATTGAATCTTTTGGTTAATGGGTTT
1 AAAGAAAC-TAAATGGGAAGAAGATATTAGAACCAAAGATATTGAATCTTTTGGTTAATGGGTTT
31457160 TAAAGATTCAAGCTTTGAGAGAGATTTGTAACAAAAGATATTGGAATCA
65 TAAAGATTCAAGCTTTGAGAGAGATTTGTAACAAAAGATATTGGAATCA
31457209 AAAG
1 AAAG
31457213 GGAAAAAGAT
Statistics
Matches: 111, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
113 107 0.96
114 4 0.04
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (113 bp):
AAAGAAACTAAATGGGAAGAAGATATTAGAACCAAAGATATTGAATCTTTTGGTTAATGGGTTTT
AAAGATTCAAGCTTTGAGAGAGATTTGTAACAAAAGATATTGGAATCA
Found at i:31459212 original size:36 final size:35
Alignment explanation
Indices: 31459172--31459239 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
31459162 TATTAAAACT
*
31459172 ATACATTAA-CTTTTATTTTATTTAATTTGTAATGTA
1 ATACA-TAATCTTTTATTTT-TTTAATTTATAATGTA
* *
31459208 ATACATAATTTTTTATTTTTTTATTTTATAAT
1 ATACATAATCTTTTATTTTTTTAATTTATAAT
31459240 TGTATATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 14 0.50
36 14 0.50
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.60
Consensus pattern (35 bp):
ATACATAATCTTTTATTTTTTTAATTTATAATGTA
Found at i:31460311 original size:23 final size:24
Alignment explanation
Indices: 31460285--31460331 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31460275 GTTAATTATG
*
31460285 ATGATTATT-CAAACAT-ATTACAC
1 ATGATAATTACAAA-ATAATTACAC
31460308 ATGATAATTACAAAATAATTACAC
1 ATGATAATTACAAAATAATTACAC
31460332 TTAAATTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (24 bp):
ATGATAATTACAAAATAATTACAC
Found at i:31461398 original size:60 final size:56
Alignment explanation
Indices: 31461331--31461787 Score: 348
Period size: 60 Copynumber: 7.8 Consensus size: 56
31461321 TGTTGATCAT
* *
31461331 TGCATGGCCGACATCCCCCTTTTAATCTGATAAAAAATCAAATTTTTTTGTGTTGGCCA
1 TGCATGACCGACA--CCCCTTTTTATCTGATAAAAAATC-AATTTTTTTGTGTTGGCCA
* * * *
31461390 TGCAATGGCCGACACTCCCTTTTTGT-TAGATAAAAAATTTAATTTTTTTGGTGTTGGCTA
1 TGC-ATGACCGACAC-CCCTTTTTATCT-GATAAAAAA-TCAATTTTTTT-GTGTTGGCCA
* *
31461450 TGTCATGACTGACACCCCTATTTATCTGATAAAAAAAATCAATTTTTTTGTGTTGGCCA
1 TG-CATGACCGACACCCCTTTTTATCTGAT--AAAAAATCAATTTTTTTGTGTTGGCCA
* * * * * * *
31461509 TGCAATGACCAACACTCCTTTTT-TCTTAGATAAAAT--TTTTTTTTGGTGTTGGTCA
1 TGC-ATGACCGACACCCCTTTTTATCTGATAAAAAATCAATTTTTTT-GTGTTGGCCA
* * * **
31461564 TTGCATGATCGACATCCCTTTTTATCTGAATAAAAAATTAAATTTTTGGGTGTTGGCCA
1 -TGCATGACCGACACCCCTTTTTATCTG-ATAAAAAA-TCAATTTTTTTGTGTTGGCCA
* * *
31461623 TCCCATGACCGACATCCCTTTTTTATCTGGTAAAAAAATCAATTTTTTTGGTGTTGGCCA
1 T-GCATGACCGACA-CCCCTTTTTATCTGAT-AAAAAATCAATTTTTTT-GTGTTGGCCA
* * * * *
31461683 TGCAATGGCTGACACCCCCTTTTTTGTCAGATAAAAAATTCGAA-TTTTTGGTGTTGGCCA
1 TGC-ATGACCGACA-CCCC-TTTTTATCTGATAAAAAA-TC-AATTTTTTTGTGTTGGCCA
** *
31461743 TTGCATGGTCGACAGCCCCTTTTTTATCTGGTAAAAAATCAATTT
1 -TGCATGACCGACA-CCCC-TTTTTATCTGATAAAAAATCAATTT
31461788 GGCCAACACA
Statistics
Matches: 318, Mismatches: 53, Indels: 54
0.75 0.12 0.13
Matches are distributed among these distances:
54 7 0.02
55 24 0.08
56 12 0.04
57 6 0.02
58 11 0.03
59 99 0.31
60 131 0.41
61 26 0.08
62 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (56 bp):
TGCATGACCGACACCCCTTTTTATCTGATAAAAAATCAATTTTTTTGTGTTGGCCA
Found at i:31461618 original size:114 final size:115
Alignment explanation
Indices: 31461316--31461743 Score: 377
Period size: 119 Copynumber: 3.6 Consensus size: 115
31461306 CAAAAAAAAA
* * * *
31461316 TTTGGTGTTGATCATTGCATGGCCGACATCCCCCTTTTAATCTGATAAAAAATCAAATTTTTTTG
1 TTTGGTGTTGGTCATTGCAT-GACGACAT--CCCTTTTTATCTGATAAAAAATTAAATTTTTTTG
* * *
31461381 TGTTGGCCATGCAATGGCCGACACTCCCTTTTTGTTAGATAAAAAATTTAATTTT
63 TGTTGGCCATGCAATGACCGACACTCCTTTTTTCTTAGAT-AAAAATTT-ATTTT
* * * *
31461436 TTTGGTGTTGG-C-TATGTCATGACTGACACCCCTATTTATCTGATAAAAAAAATCAATTTTTTT
1 TTTGGTGTTGGTCAT-TG-CATGAC-GACATCCCTTTTTATCTGAT-AAAAAATTAAATTTTTTT
*
31461499 GTGTTGGCCATGCAATGACCAACACTCCTTTTTTCTTAGAT-AAAA-TT-TTTT
62 GTGTTGGCCATGCAATGACCGACACTCCTTTTTTCTTAGATAAAAATTTATTTT
**
31461550 TTTGGTGTTGGTCATTGCATGATCGACATCCCTTTTTATCTGAATAAAAAATTAAATTTTTGGGT
1 TTTGGTGTTGGTCATTGCATGA-CGACATCCCTTTTTATCTG-ATAAAAAATTAAATTTTTTTGT
* * * * * **
31461615 GTTGGCCATCCCATGACCGACA-TCCCTTTTTTATCTGGTAAAAAAATCAATTTT
64 GTTGGCCATGCAATGACCGACACT-CCTTTTTTCT-TAG-ATAAAAATTTATTTT
* * * * * *
31461669 TTTGGTGTTGGCCA-TGCAATGGCTGACACCCCCTTTTTTGTCAGATAAAAAATTCGAA-TTTTT
1 TTTGGTGTTGGTCATTGC-ATGAC-GACA-TCCC-TTTTTATCTGATAAAAAATT-AAATTTTTT
*
31461732 GGTGTTGGCCAT
61 TGTGTTGGCCAT
31461744 TGCATGGTCG
Statistics
Matches: 256, Mismatches: 33, Indels: 38
0.78 0.10 0.12
Matches are distributed among these distances:
113 1 0.00
114 80 0.31
115 8 0.03
116 4 0.02
117 8 0.03
118 18 0.07
119 81 0.32
120 46 0.18
121 10 0.04
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (115 bp):
TTTGGTGTTGGTCATTGCATGACGACATCCCTTTTTATCTGATAAAAAATTAAATTTTTTTGTGT
TGGCCATGCAATGACCGACACTCCTTTTTTCTTAGATAAAAATTTATTTT
Found at i:31461960 original size:60 final size:57
Alignment explanation
Indices: 31461800--31462163 Score: 259
Period size: 59 Copynumber: 6.1 Consensus size: 57
31461790 CCAACACAAA
**
31461800 AAAAAAATTTCAAATTTTTTATCTGACAAAAAGAGGGTGTCGGTTATGGCATGACCAACAC
1 AAAAAAATTT-AAATTTTTTATCTGA-AAAAA-AGGGTGTCGGCCAT-GCATGACCAACAC
** * * *
31461861 CCAAAAATTT-AATTTTTTATTCAGATAAAAAGGAGTGTCGGCCATACAATG-CCAACAC
1 AAAAAAATTTAAATTTTTTA-TCTGAAAAAAAGG-GTGTCGGCCATGC-ATGACCAACAC
*
31461919 TAAAAAAATTTGAAATTTTTTTATCTGAAAAAAAAGGTGTCGGCCATTGCATGACCAACAC
1 -AAAAAAATTT-AAA-TTTTTTATCTGAAAAAAAGGGTGTCGGCCA-TGCATGACCAACAC
* * * * ** * **
31461980 AAAAAAATTTGATTTTTTTATCAGATAAATAAGGGTGTCGATCATGGAATGGTCAACAC
1 AAAAAAATTTAAATTTTTTATCTGA-AAAAAAGGGTGTCGGCCAT-GCATGACCAACAC
* *** *
31462039 TAAAAAAA-TTAAATTTTTTATCTGACAAAAAAAAGGTGTCAATCATTGCATGGCCAACAC
1 -AAAAAAATTTAAATTTTTTATCTG--AAAAAAAGGGTGTCGGCCA-TGCATGACCAACAC
** * * *
31462099 CCAAAAATTT-GATTTTTTATCAGAGTAAAAAGGGAATGTCGGCCATGCAATGACCAACATC
1 AAAAAAATTTAAATTTTTTATCTGA-AAAAAAGGG--TGTCGGCCATGC-ATGACCAACA-C
31462160 AAAA
1 AAAA
31462164 TTTTTTTTGT
Statistics
Matches: 239, Mismatches: 43, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
57 1 0.00
58 30 0.13
59 90 0.38
60 77 0.32
61 34 0.14
62 7 0.03
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (57 bp):
AAAAAAATTTAAATTTTTTATCTGAAAAAAAGGGTGTCGGCCATGCATGACCAACAC
Found at i:31461971 original size:119 final size:117
Alignment explanation
Indices: 31461800--31462157 Score: 427
Period size: 119 Copynumber: 3.0 Consensus size: 117
31461790 CCAACACAAA
* * *
31461800 AAAAAAATTTCAAATTTTTTATCTGACAAAAAGAGGGTGTCGGTTATGGCATGACCAACACCCAA
1 AAAAAAATTT-AAATTTTTTATCTGA-AAAAA-AAGGTGTCGGTCATTGCATGACCAACACCCAA
* *
31461865 AAATTTAATTTTTTATTCAGATAAAAAGGAGTGTCGGCCATACAATGCCAACACT
63 AAATTTGATTTTTTATTCAGATAAAAAGGAGTGTCGGCCATGCAATGCCAACACT
* **
31461920 AAAAAAATTTGAAATTTTTTTATCTGAAAAAAAAGGTGTCGGCCATTGCATGACCAACACAAAAA
1 AAAAAAATTT-AAA-TTTTTTATCTGAAAAAAAAGGTGTCGGTCATTGCATGACCAACACCCAAA
** * *
31461985 AATTTGATTTTTT-TATCAGATAAATAAGG-GTGTCGATCATGGAATGGTCAACACT
64 AATTTGATTTTTTAT-TCAGATAAA-AAGGAGTGTCGGCCATGCAAT-GCCAACACT
** *
31462040 AAAAAAA-TTAAATTTTTTATCTGACAAAAAAAAGGTGTCAATCATTGCATGGCCAACACCCAAA
1 AAAAAAATTTAAATTTTTTATCTG--AAAAAAAAGGTGTCGGTCATTGCATGACCAACACCCAAA
*
31462104 AATTTGATTTTTTA-TCAGAGTAAAAAGGGAATGTCGGCCATGCAATGACCAACA
64 AATTTGATTTTTTATTCAGA-TAAAAA-GGAGTGTCGGCCATGCAATG-CCAACA
31462158 TCAAAATTTT
Statistics
Matches: 203, Mismatches: 24, Indels: 22
0.82 0.10 0.09
Matches are distributed among these distances:
117 11 0.05
118 11 0.05
119 115 0.57
120 54 0.27
121 12 0.06
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (117 bp):
AAAAAAATTTAAATTTTTTATCTGAAAAAAAAGGTGTCGGTCATTGCATGACCAACACCCAAAAA
TTTGATTTTTTATTCAGATAAAAAGGAGTGTCGGCCATGCAATGCCAACACT
Found at i:31462183 original size:54 final size:54
Alignment explanation
Indices: 31462111--31462224 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
31462101 AAAAATTTGA
* *
31462111 TTTTTTATCAGAGTAAAAAGGGAA-TGTCGGCCATGCAATGACCAACATCAAAATT
1 TTTTTTATCAGAGTAAAAA--GAAGTGTCAGCCATGCAATGACCAACACCAAAATT
* * *
31462166 TTTTTTGTCAGA-TAAAAAGAAGGTGTCAGCTATGCAATGGCCAACACCAAAATT
1 TTTTTTATCAGAGTAAAAAGAA-GTGTCAGCCATGCAATGACCAACACCAAAATT
31462220 TTTTT
1 TTTTT
31462225 CTCAAATTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
52 3 0.06
54 38 0.73
55 11 0.21
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (54 bp):
TTTTTTATCAGAGTAAAAAGAAGTGTCAGCCATGCAATGACCAACACCAAAATT
Found at i:31480546 original size:2 final size:2
Alignment explanation
Indices: 31480541--31480573 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31480531 GATTCTACAA
31480541 TC TC TC 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 TC TC TC T
31480574 ATTTTTGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31482678 original size:23 final size:22
Alignment explanation
Indices: 31482637--31482697 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
31482627 AAATTTTATT
**
31482637 AAAATTATTAAATGTTAAATTAGA
1 AAAATTATTAAA-AATAAATTA-A
31482661 AAAATTATTAAAAATAAATTAA
1 AAAATTATTAAAAATAAATTAA
*
31482683 AATAACT-TTAAAAAT
1 AA-AATTATTAAAAAT
31482698 TAAAAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 11 0.33
23 10 0.30
24 12 0.36
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (22 bp):
AAAATTATTAAAAATAAATTAA
Found at i:31482701 original size:23 final size:24
Alignment explanation
Indices: 31482637--31482701 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
31482627 AAATTTTATT
* **
31482637 AAAATTATTAAATGTTAAATTAGA
1 AAAACTATTAAAAATTAAATTAGA
*
31482661 AAAATTATTAAAAA-TAAATTA-A
1 AAAACTATTAAAAATTAAATTAGA
31482683 AATAACT-TTAAAAATTAAA
1 AA-AACTATTAAAAATTAAA
31482702 AAATTACTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 10 0.28
23 14 0.39
24 12 0.33
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (24 bp):
AAAACTATTAAAAATTAAATTAGA
Found at i:31482994 original size:28 final size:28
Alignment explanation
Indices: 31482928--31482983 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
31482918 GCCCGAATTT
*
31482928 AATTTAAATAATAAAAATATTATTATTAA
1 AATTT-AATTATAAAAATATTATTATTAA
*
31482957 AATTTAATTATAAAAATA-TATTTTTAA
1 AATTTAATTATAAAAATATTATTATTAA
31482984 TTATTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.32
28 12 0.48
29 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AATTTAATTATAAAAATATTATTATTAA
Found at i:31483544 original size:58 final size:57
Alignment explanation
Indices: 31483454--31483775 Score: 364
Period size: 58 Copynumber: 5.5 Consensus size: 57
31483444 GGCCATGCAG
** * *
31483454 AAAAAAAATTCAAAATTTTTTAGTATTAGCCATCAAATGGCCGACACCTCCTTTTCTCGA
1 AAAAAAAATT--AAATTTTTGGGTGTTGGCCATCAAATGGCCGACACC-CCTTTTCTCGA
* **
31483514 AAAAGAAATTGTATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCTTGTT-TCAGA
1 AAAAAAAATTAAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCTT-TTCTC-GA
** *
31483572 AAAAAAAATTAAAATTTTTTTGTGTTGGCCATCAAATGGCCGACACCCTTTTTTCTCG-
1 AAAAAAAATT-AAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCC-CTTTTCTCGA
* * *
31483630 -AAAAAATTTACATTTTTGGGTGTTGGCCATCAAATGACCGACACTCCCTTTTCTCGA
1 AAAAAAAATTAAATTTTTGGGTGTTGGCCATCAAATGGCCGACAC-CCCTTTTCTCGA
* * *
31483687 AAAAAAAATTACATTTTTGGGTGTTGACCATCAAATGGTCGACACCCCTTGTT-TCAGA
1 AAAAAAAATTAAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCTT-TTCTC-GA
*
31483745 AAAAAAAATTCAAAATTTTGGGTGTTGGCCA
1 AAAAAAAATT-AAATTTTTGGGTGTTGGCCA
31483776 ACACCCACTA
Statistics
Matches: 225, Mismatches: 26, Indels: 23
0.82 0.09 0.08
Matches are distributed among these distances:
56 39 0.17
57 23 0.10
58 97 0.43
59 53 0.24
60 13 0.06
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (57 bp):
AAAAAAAATTAAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCTTTTCTCGA
Found at i:31483736 original size:115 final size:116
Alignment explanation
Indices: 31483454--31483775 Score: 354
Period size: 115 Copynumber: 2.8 Consensus size: 116
31483444 GGCCATGCAG
** *
31483454 AAAAAAAATTCAAAATTTTTTAGTATT-AGCCATCAAATGGCCGACACCTCC--TTTTCTCGAAA
1 AAAAAAAATT-AAAATTTTTGGGTGTTGA-CCATCAAATGGCCGACACC-CCTTTTTTCTCG-AA
** *
31483516 AAGAAATTGTATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCTTGTTTCAGA
62 AA-AAATTACATTTTTGGGTGTTGGCCATCAAATGACCGACACCCCTTGTTTCAGA
** *
31483572 AAAAAAAATTAAAATTTTTTTGTGTTGGCCATCAAATGGCCGACA-CCCTTTTTTCTCGAAAAAA
1 AAAAAAAATTAAAATTTTTGGGTGTTGACCATCAAATGGCCGACACCCCTTTTTTCTCGAAAAAA
*
31483636 TTTACATTTTTGGGTGTTGGCCATCAAATGACCGACACTCCCTT-TTCTC-GA
66 ATTACATTTTTGGGTGTTGGCCATCAAATGACCGACAC-CCCTTGTT-TCAGA
* * * *
31483687 AAAAAAAATT-ACATTTTTGGGTGTTGACCATCAAATGGTCGACACCCCTTGTTTC-AGAAAAAA
1 AAAAAAAATTAAAATTTTTGGGTGTTGACCATCAAATGGCCGACACCCCTTTTTTCTCG--AAAA
* *
31483750 AAATTCAAAATTTTGGGTGTTGGCCA
64 AAATT-ACATTTTTGGGTGTTGGCCA
31483776 ACACCCACTA
Statistics
Matches: 178, Mismatches: 17, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
114 30 0.17
115 61 0.34
116 20 0.11
117 57 0.32
118 10 0.06
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (116 bp):
AAAAAAAATTAAAATTTTTGGGTGTTGACCATCAAATGGCCGACACCCCTTTTTTCTCGAAAAAA
ATTACATTTTTGGGTGTTGGCCATCAAATGACCGACACCCCTTGTTTCAGA
Found at i:31483843 original size:37 final size:38
Alignment explanation
Indices: 31483792--31483863 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
31483782 ACTATTCTCA
31483792 AGAAAAAAATTTCAAATTTGTTTT-GTGTTGACCATTTG
1 AGAAAAAAATTTCAAATTT-TTTTCGTGTTGACCATTTG
*
31483830 AGAAAAAAA-TTCAAATTTTTTTCGTGTTGGCCAT
1 AGAAAAAAATTTCAAATTTTTTTCGTGTTGACCAT
31483864 CAACTTCTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 4 0.12
37 19 0.59
38 9 0.28
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (38 bp):
AGAAAAAAATTTCAAATTTTTTTCGTGTTGACCATTTG
Found at i:31487573 original size:12 final size:12
Alignment explanation
Indices: 31487531--31487578 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
31487521 ATTTGTGTAA
*
31487531 AAATTAATTTGA
1 AAATTAATTTGG
31487543 AAATTAATTTAAGTTG
1 AAATTAATTT--G--G
31487559 AAATTAATTTGG
1 AAATTAATTTGG
31487571 AAATTAAT
1 AAATTAAT
31487579 GAACATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
AAATTAATTTGG
Found at i:31487911 original size:89 final size:89
Alignment explanation
Indices: 31487709--31488152 Score: 635
Period size: 89 Copynumber: 5.1 Consensus size: 89
31487699 AAAAAGATAG
* * * * *
31487709 TTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTAT-TAATTTT-
* *
31487774 ATA--TTTAAAGTACAAACTATTATTA
64 ATATCTTTAAA-TAAAAATTATTATTA
*
31487799 TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
31487864 ATCTTTAAATAAAAATTATTATTA
66 ATCTTTAAATAAAAATTATTATTA
*
31487888 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
31487953 ATCTTTAAATAAAAATTATTATTA
66 ATCTTTAAATAAAAATTATTATTA
*
31487977 -T-TT-TATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
31488039 ATCTTTAAAT--AAA--A--ATTA
66 ATCTTTAAATAAAAATTATTATTA
* *
31488057 TTATTATATTACAATTTTTATCATATTTTAA-ATGTTGATTTGATAATACATTATTTATTAATTT
1 TTATTATATTACAATTTTTATCATA---TAATGTGTTGATTTGACAATACATTATTTATTAATTT
31488121 TATATCTTTAAATAAAAATTATTATTA
63 TATATCTTTAAATAAAAATTATTATTA
31488148 -TATTA
1 TTATTA
31488153 CAATTTTTAT
Statistics
Matches: 325, Mismatches: 15, Indels: 28
0.88 0.04 0.08
Matches are distributed among these distances:
80 4 0.01
81 1 0.00
82 3 0.01
83 18 0.06
84 3 0.01
85 44 0.14
86 70 0.22
87 5 0.02
88 4 0.01
89 107 0.33
90 62 0.19
91 4 0.01
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (89 bp):
TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
ATCTTTAAATAAAAATTATTATTA
Found at i:31488004 original size:175 final size:168
Alignment explanation
Indices: 31487709--31488167 Score: 658
Period size: 175 Copynumber: 2.7 Consensus size: 168
31487699 AAAAAGATAG
* * * * * *
31487709 TTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTAT-TAATTTT-
31487774 ATA--TTTAAAGTACAAACTATTATTATTATTATATTATAATTTTTATCATATAATGTGTTGATT
64 ATATCTTTAAA-TA-AAA--ATTATTATTATT-TATTATAATTTTTATCATATAATGTGTTGATT
31487837 TGACAATACATTATTTATTAATTTTATATCTTTAAATAAAAATTATTATTA
124 TGACAATACATTATTTATTAATTTTATATCTTTAAAT--AAA--A--ATTA
31487888 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTATTAATTTTAT
31487953 ATCTTTAAATAAAAATTATTATTATTTTATTATAATTTTTATCATATAATGTGTTGATTTGACAA
66 ATCTTTAAATAAAAATTATTATTA-TTTATTATAATTTTTATCATATAATGTGTTGATTTGACAA
31488018 TACATTATTTATTAATTTTATATCTTTAAATAAAAATTA
130 TACATTATTTATTAATTTTATATCTTTAAATAAAAATTA
*
31488057 TTATTATATTACAATTTTTATCATATTTTAA-ATGTTGATTTGATAATACATTATTTATTAATTT
1 TTATTATATTACAATTTTTATCATA---TAATGTGTTGATTTGATAATACATTATTTATTAATTT
*
31488121 TATATCTTTAAATAAAAATTATTATTA--TATTACAATTTTTATCATAT
63 TATATCTTTAAATAAAAATTATTATTATTTATTATAATTTTTATCATAT
31488168 TTTAAATTTA
Statistics
Matches: 266, Mismatches: 8, Indels: 23
0.90 0.03 0.08
Matches are distributed among these distances:
168 19 0.07
169 29 0.11
171 60 0.23
172 3 0.01
173 3 0.01
175 79 0.30
176 2 0.01
177 6 0.02
178 8 0.03
179 57 0.21
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (168 bp):
TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTATTAATTTTAT
ATCTTTAAATAAAAATTATTATTATTTATTATAATTTTTATCATATAATGTGTTGATTTGACAAT
ACATTATTTATTAATTTTATATCTTTAAATAAAAATTA
Found at i:31488020 original size:86 final size:85
Alignment explanation
Indices: 31487709--31488167 Score: 635
Period size: 86 Copynumber: 5.3 Consensus size: 85
31487699 AAAAAGATAG
* * * * *
31487709 TTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATT-TATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTAT-TAATTTT-
31487774 ATA--TTTAAAGTACAAACTATTATTA
63 ATATCTTTAAA-TA-AAA--ATTATTA
*
31487799 TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
1 TTATT-TATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
31487864 ATCTTTAAATAAAAATTATTATTA
65 ATCTTTAAAT-AAAA--ATTATTA
*
31487888 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTATTAATTTTAT
1 TTATT-TATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
31487953 ATCTTTAAATAAAAATTATTA
65 ATCTTTAAATAAAAATTATTA
*
31487974 TTATTTTATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
1 TTA-TTTATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
31488039 ATCTTTAAATAAAAATTATTA
65 ATCTTTAAATAAAAATTATTA
* *
31488060 TTA--TATTACAATTTTTATCATATTTTAA-ATGTTGATTTGATAATACATTATTTATTAATTTT
1 TTATTTATTACAATTTTTATCATA---TAATGTGTTGATTTGACAATACATTATTTATTAATTTT
31488122 ATATCTTTAAATAAAAATTATTA
63 ATATCTTTAAATAAAAATTATTA
31488145 TTA--TATTACAATTTTTATCATAT
1 TTATTTATTACAATTTTTATCATAT
31488168 TTTAAATTTA
Statistics
Matches: 348, Mismatches: 14, Indels: 22
0.91 0.04 0.06
Matches are distributed among these distances:
82 1 0.00
83 18 0.05
85 77 0.22
86 94 0.27
87 2 0.01
88 7 0.02
89 91 0.26
90 58 0.17
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (85 bp):
TTATTTATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTATA
TCTTTAAATAAAAATTATTA
Found at i:31488288 original size:22 final size:21
Alignment explanation
Indices: 31488276--31488317 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
31488266 CACCTCACTT
*
31488276 AAACCAATATTCCAGCTCAGCA
1 AAACCAAAATTCCAGCTCA-CA
31488298 AAACCAAAATTCCAGCTCAC
1 AAACCAAAATTCCAGCTCAC
31488318 CAACGTCCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.43, C:0.33, G:0.07, T:0.17
Consensus pattern (21 bp):
AAACCAAAATTCCAGCTCACA
Found at i:31490500 original size:30 final size:30
Alignment explanation
Indices: 31490438--31490503 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
31490428 TCCCTTTACT
* *
31490438 TTTTAAATTTAATTTGTAATTTGGTTTTTA
1 TTTTAAATTTAATTTGTAATTTGCTTTATA
31490468 TTTTAAATTTAATTT-TGAATTT-CTTATATA
1 TTTTAAATTTAATTTGT-AATTTGCTT-TATA
31490498 TTTTAA
1 TTTTAA
31490504 TTTTTCTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTGTAATTTGCTTTATA
Found at i:31491475 original size:60 final size:59
Alignment explanation
Indices: 31491349--31491726 Score: 365
Period size: 60 Copynumber: 6.2 Consensus size: 59
31491339 AGGAGAAGTT
* *
31491349 GGTGTCGGCCATTTGATGGCCAACACGAAAAAAATTTGAAATTGTTTTCTCGAGAAAAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTT-AAATTTTTTTCTCGAGAAAA-GG
* *
31491410 GGTGTCGACCATTTGATGGTCAACACCAAAAAAATTTAAATTTTTTTTCTCGAGAAAAGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAA-TTTTTTTCTCGAGAAAAGG
* * **
31491470 GGTGTCGACCATTTGATGGCCAACACC-CAAAAA-TGCAATTTTTTT-TCGAGAAAATGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAA-GG
* *
31491527 GGTGTCGGCCATTTGATGGCCAACACCAAAAAATAAAAAAATTTAAATTTTTTTCTCAAGAATAG
1 GGTGTCGGCCATTTGATGGCCAACACC-------AAAAAAATTTAAATTTTTTTCTCGAGAA-AA
31491592 GG
58 GG
* * * * ** * *
31491594 GGTATCGGCCTTTTGATGGCCAACACC--CAAAATTGCACTTTTTTTTTTTCGAAAAAAGAG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATT-TA-AATTTTTTTCTCGAGAAAAG-G
* *
31491654 GGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTGAATTTTTTT-TCTGA-AACAAGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTCTC-GAGAA-AAGG
*
31491713 TGTGTCGGCCATTT
1 GGTGTCGGCCATTT
31491727 TCGTATATCA
Statistics
Matches: 264, Mismatches: 33, Indels: 42
0.78 0.10 0.12
Matches are distributed among these distances:
56 9 0.03
57 35 0.13
58 9 0.03
59 26 0.10
60 81 0.31
61 50 0.19
62 5 0.02
65 5 0.02
66 10 0.04
67 33 0.12
68 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (59 bp):
GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAGG
Found at i:31491659 original size:184 final size:184
Alignment explanation
Indices: 31491376--31491726 Score: 451
Period size: 184 Copynumber: 1.9 Consensus size: 184
31491366 GGCCAACACG
* * *
31491376 AAAAAAATTTGAAATTGTTTTCTCGAGAAAAGGGGGTGTCGACCATTTGATGGTCAACACCAAAA
1 AAAAAAATTTGAAATTGTTTTCTCAAGAAAAGGGGGTATCGACCATTTGATGGCCAACACC-AAA
* * *
31491441 AAATTTAAATTTTTTTTCTCGAGAAAAGGGGTGTCGACCATTTGATGGCCAACACCCAAAAA-TG
65 AAATTCAAATTTTTTTTCTCGAAAAAAGGGGTGTCGACCATTTGATGGCCAACACCAAAAAATTG
31491505 CAATTTTTTTTC-GAGAA-AATGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAAT
130 -AATTTTTTTTCTGA-AACAA-GGGGTGTCGGCCATTTGATGGCCAACACCAAAAAAT
* * * * *
31491561 AAAAAAATTT-AAATTTTTTTCTCAAGAATAGGGGGTATCGGCCTTTTGATGGCCAACACC-CAA
1 AAAAAAATTTGAAATTGTTTTCTCAAGAAAAGGGGGTATCGACCATTTGATGGCCAACACCAAAA
** * *
31491624 AATTGCACTTTTTTTTTTTCGAAAAAAGAGGGTGTCGGCCATTTGATGGCCAACACCAAAAAATT
66 AATT-CAAATTTTTTTTCTCGAAAAAAG-GGGTGTCGACCATTTGATGGCCAACACCAAAAAA--
*
31491689 TTGAATTTTTTTTCTGAAACAAGGTGTGTCGGCCATTT
127 TTGAATTTTTTTTCTGAAACAAGGGGTGTCGGCCATTT
31491727 TCGTATATCA
Statistics
Matches: 143, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
182 6 0.04
183 18 0.13
184 75 0.52
185 10 0.07
186 28 0.20
187 6 0.04
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (184 bp):
AAAAAAATTTGAAATTGTTTTCTCAAGAAAAGGGGGTATCGACCATTTGATGGCCAACACCAAAA
AATTCAAATTTTTTTTCTCGAAAAAAGGGGTGTCGACCATTTGATGGCCAACACCAAAAAATTGA
ATTTTTTTTCTGAAACAAGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAAT
Found at i:31492008 original size:19 final size:19
Alignment explanation
Indices: 31491987--31492034 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
31491977 AATCTATATT
31491987 TTTTATAATTTTT-TTATA
1 TTTTATAATTTTTATTATA
31492005 TTTTATAAATTTTTATTA-A
1 TTTTAT-AATTTTTATTATA
31492024 TTTTATAATTT
1 TTTTATAATTT
31492035 AAATTTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 11 0.39
19 14 0.50
20 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATAATTTTTATTATA
Found at i:31495126 original size:93 final size:93
Alignment explanation
Indices: 31494962--31495141 Score: 270
Period size: 93 Copynumber: 1.9 Consensus size: 93
31494952 GTATTTATTG
* * * *
31494962 ACCAAGATAGCTTTTCTTGTAAAGGTTCATGGACACTGGACTTAAATATTGACTCTTCTAGCGGT
1 ACCAAGATAGCTTGTCTTGTAAAGGCTCATAGACACTGGACTTAAATATTGACTCTTCTAGCAGT
** *
31495027 TGTTTATTATGCATGTATGTGATTGTTA
66 CATTTATTATGCATGGATGTGATTGTTA
* *
31495055 ACCAAGATAGCTTGTCTTGTAGAGGCTCATAGACACTGGACTTAAATATTGACTCTTCTAGTAGT
1 ACCAAGATAGCTTGTCTTGTAAAGGCTCATAGACACTGGACTTAAATATTGACTCTTCTAGCAGT
*
31495120 CATTTATTGTGCATGGATGTGA
66 CATTTATTATGCATGGATGTGA
31495142 GTCCATCTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (93 bp):
ACCAAGATAGCTTGTCTTGTAAAGGCTCATAGACACTGGACTTAAATATTGACTCTTCTAGCAGT
CATTTATTATGCATGGATGTGATTGTTA
Found at i:31502007 original size:28 final size:29
Alignment explanation
Indices: 31501960--31502020 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
31501950 TTTAGTTATT
*
31501960 TTTTTTGAATTATTTTTATTCTTAGAAAA
1 TTTTTTGAATTATTTATATTCTTAGAAAA
* *
31501989 TTTTTTGAATT-TTTATATTTTTATAAAA
1 TTTTTTGAATTATTTATATTCTTAGAAAA
31502017 TTTT
1 TTTT
31502021 AGGTAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (29 bp):
TTTTTTGAATTATTTATATTCTTAGAAAA
Found at i:31525933 original size:4 final size:4
Alignment explanation
Indices: 31525924--31525953 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
31525914 GATTGTGTAG
31525924 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
31525954 AGAATGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:31527188 original size:81 final size:81
Alignment explanation
Indices: 31527075--31527236 Score: 281
Period size: 81 Copynumber: 2.0 Consensus size: 81
31527065 TCAAAGCAAT
*
31527075 GGTACTGCAATAATGAAGCACATCCATCAACAAAAAAGTTGATCTATTGCATTGATCTAGAACTA
1 GGTACTGCAATAATGAAGCACATCCATCAACAAAAAAGGTGATCTATTGCATTGATCTAGAACTA
31527140 AAGAACCATCAATCCA
66 AAGAACCATCAATCCA
*
31527156 GGTACTGCAATAATGAAGCACAAT-CATTAACAAAAAAGGTGATCTATTGCATTGATCTAGAACT
1 GGTACTGCAATAATGAAGCAC-ATCCATCAACAAAAAAGGTGATCTATTGCATTGATCTAGAACT
*
31527220 AAAGAACCATCAGTCCA
65 AAAGAACCATCAATCCA
31527237 CTTAAATTTG
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
81 75 0.97
82 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (81 bp):
GGTACTGCAATAATGAAGCACATCCATCAACAAAAAAGGTGATCTATTGCATTGATCTAGAACTA
AAGAACCATCAATCCA
Found at i:31534297 original size:25 final size:26
Alignment explanation
Indices: 31534245--31534306 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
31534235 TTATATAAGC
** *
31534245 TTATAAACATATAAAAAATTTAATATA
1 TTATAAA-ATATAAAAAATCAAACATA
31534272 TTATAAAA-ATAAAAAATCAAACATA
1 TTATAAAATATAAAAAATCAAACATA
31534297 TTA-AAAATAT
1 TTATAAAATAT
31534307 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 4 0.13
25 19 0.61
26 1 0.03
27 7 0.23
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (26 bp):
TTATAAAATATAAAAAATCAAACATA
Found at i:31534622 original size:7 final size:7
Alignment explanation
Indices: 31534580--31534610 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
31534570 TAATTTATTC
31534580 TTTTTAA
1 TTTTTAA
31534587 TTTTTAA
1 TTTTTAA
31534594 TTTTTAA
1 TTTTTAA
31534601 TTTTTAA
1 TTTTTAA
31534608 TTT
1 TTT
31534611 CAGTTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:31534897 original size:10 final size:10
Alignment explanation
Indices: 31534884--31535249 Score: 88
Period size: 10 Copynumber: 37.2 Consensus size: 10
31534874 TTTTTTTATA
*
31534884 TTTTATATTT
1 TTTTATAATT
*
31534894 TTTTCA-AAAT
1 TTTT-ATAATT
*
31534904 TTTTATAAAT
1 TTTTATAATT
*
31534914 TTTTATAAGT
1 TTTTATAATT
*
31534924 TTTTATGATT
1 TTTTATAATT
* *
31534934 TTTTCTATTT
1 TTTTATAATT
*
31534944 TTTTCTAATT
1 TTTTATAATT
*
31534954 TTATATAATT
1 TTTTATAATT
*
31534964 TTTAAT-ATT
1 TTTTATAATT
31534973 TTAATTAT-A-T
1 TT--TTATAATT
31534983 TTTTAGTAA-T
1 TTTTA-TAATT
* * **
31534993 TCTAATAGGT
1 TTTTATAATT
31535003 TTTTATAA-T
1 TTTTATAATT
* *
31535012 ATTTATAATA
1 TTTTATAATT
*
31535022 TTTTATGA-T
1 TTTTATAATT
*
31535031 TTTTATAAGT
1 TTTTATAATT
*
31535041 TTTTATTCATT
1 TTTTA-TAATT
*
31535052 TTATAT-ATGT
1 TTTTATAAT-T
31535062 TTTT-T--TT
1 TTTTATAATT
*
31535069 TTAAATTATAAGT
1 TT---TTATAATT
* *
31535082 TTATATAA-A
1 TTTTATAATT
*
31535091 TTTCAT--TT
1 TTTTATAATT
*
31535099 TTTAATAACTGT
1 TTTTATAA-T-T
**
31535111 TTAAATAATT
1 TTTTATAATT
* * *
31535121 TATCATAAGT
1 TTTTATAATT
* *
31535131 TCTTATGATT
1 TTTTATAATT
* *
31535141 ATTTATAAGT
1 TTTTATAATT
*
31535151 TTTTATAA-C
1 TTTTATAATT
*
31535160 ATTTATAATT
1 TTTTATAATT
*
31535170 TTTTATGA-T
1 TTTTATAATT
*
31535179 TTTTATAAGT
1 TTTTATAATT
* *
31535189 TTTTGTGATTT
1 TTTTAT-AATT
31535200 TTTTATAA-T
1 TTTTATAATT
31535209 TTTTATAA-T
1 TTTTATAATT
*
31535218 ATTT-TAA-T
1 TTTTATAATT
*
31535226 ATTTATAATTT
1 TTTTATAA-TT
31535237 TTTTATAAGTT
1 TTTTATAA-TT
31535248 TT
1 TT
31535250 CTTAGAAAAT
Statistics
Matches: 263, Mismatches: 65, Indels: 55
0.69 0.17 0.14
Matches are distributed among these distances:
7 3 0.01
8 17 0.06
9 62 0.24
10 136 0.52
11 34 0.13
12 8 0.03
13 3 0.01
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (10 bp):
TTTTATAATT
Found at i:31534907 original size:20 final size:20
Alignment explanation
Indices: 31534871--31534937 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
31534861 AATAAGCAAC
*
31534871 TATTTTTTT-TATA-TTTTA
1 TATTTTTTTATAAATTTTTA
31534889 TATTTTTTTCA-AAATTTTTA
1 TATTTTTTT-ATAAATTTTTA
** *
31534909 TAAATTTTTATAAGTTTTTA
1 TATTTTTTTATAAATTTTTA
31534929 TGATTTTTT
1 T-ATTTTTT
31534938 CTATTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
18 9 0.24
19 3 0.08
20 21 0.55
21 5 0.13
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (20 bp):
TATTTTTTTATAAATTTTTA
Found at i:31534934 original size:19 final size:19
Alignment explanation
Indices: 31534903--31535249 Score: 120
Period size: 20 Copynumber: 18.2 Consensus size: 19
31534893 TTTTTCAAAA
31534903 TTTTTATAAATTTTTATAAG
1 TTTTTAT-AATTTTTATAAG
* * **
31534923 TTTTTATGATTTTTTCTATT
1 TTTTTAT-AATTTTTATAAG
*
31534943 TTTTTCTAATTTTATATAA-
1 TTTTTATAATTTT-TATAAG
*
31534962 TTTTTA-ATATTTTAATTATA-
1 TTTTTATA-ATTTTTA-TA-AG
* * *
31534982 TTTTTAGTAATTCTAATAGG
1 TTTTTA-TAATTTTTATAAG
*
31535002 TTTTTATAATATTTATAA-
1 TTTTTATAATTTTTATAAG
*
31535020 TATTTTATGATTTTTATAAG
1 T-TTTTATAATTTTTATAAG
* *
31535040 TTTTTATTCATTTTATATATG
1 TTTTTA-TAATTTT-TATAAG
31535061 -TTTT-T--TTTTTA-AA-
1 TTTTTATAATTTTTATAAG
*
31535074 ---TTATAAGTTTATATAA-
1 TTTTTATAA-TTTTTATAAG
* *
31535090 ATTTCAT--TTTTTAATAACTG
1 TTTTTATAATTTTT-ATAA--G
** *
31535110 TTTAAATAATTTATCATAAG
1 TTTTTATAATTT-TTATAAG
* *
31535130 TTCTTATGATTATTTATAAG
1 TTTTTATAATT-TTTATAAG
** *
31535150 TTTTTATAACATTTATAAT
1 TTTTTATAATTTTTATAAG
*
31535169 TTTTTATGATTTTTATAAG
1 TTTTTATAATTTTTATAAG
* *
31535188 TTTTTGTGATTTTTTTATAA-
1 TTTTTAT-A-ATTTTTATAAG
*
31535208 TTTTTATAATATTT-TAA-
1 TTTTTATAATTTTTATAAG
*
31535225 TATTTATAATTTTTTTATAAG
1 TTTTTATAA--TTTTTATAAG
31535246 TTTT
1 TTTT
31535250 CTTAGAAAAT
Statistics
Matches: 242, Mismatches: 52, Indels: 65
0.67 0.14 0.18
Matches are distributed among these distances:
11 2 0.01
12 1 0.00
14 1 0.00
15 7 0.03
16 10 0.04
17 15 0.06
18 8 0.03
19 81 0.33
20 84 0.35
21 24 0.10
22 8 0.03
23 1 0.00
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAG
Found at i:31534965 original size:20 final size:19
Alignment explanation
Indices: 31534903--31535249 Score: 111
Period size: 19 Copynumber: 17.7 Consensus size: 19
31534893 TTTTTCAAAA
*
31534903 TTTTTATAAATTTTTATAAG
1 TTTTTAT-AATTTTTATAAT
* * *
31534923 TTTTTATGATTTTTTCTATT
1 TTTTTAT-AATTTTTATAAT
*
31534943 TTTTTCTAATTTTATATAAT
1 TTTTTATAATTTT-TATAAT
* * *
31534963 TTTTAAT-ATTTTAATTAT
1 TTTTTATAATTTTTATAAT
* * **
31534981 ATTTTTAGTAATTCTAATAGG
1 -TTTTTA-TAATTTTTATAAT
*
31535002 TTTTTATAATATTTATAAT
1 TTTTTATAATTTTTATAAT
* * *
31535021 ATTTTATGATTTTTATAAG
1 TTTTTATAATTTTTATAAT
*
31535040 TTTTTATTCA-TTTTATATAT
1 TTTTTA-TAATTTTTATA-AT
* *
31535060 GTTTTT-T-TTTTAAATTATAAG
1 -TTTTTATAATTT---TTATAAT
* * *
31535081 TTTATATAAATTTCAT--T
1 TTTTTATAATTTTTATAAT
* *
31535098 TTTTAATAACTGTTTAAATAAT
1 TTTTTATAA-T-TTT-TATAAT
* * * *
31535120 TTATCATAAGTTCTTATGAT
1 TTTTTATAA-TTTTTATAAT
*
31535140 TATTTATAAGTTTTTATAA-
1 TTTTTATAA-TTTTTATAAT
** *
31535159 CATTTATAATTTTTTATGA-
1 TTTTTATAA-TTTTTATAAT
* *
31535178 TTTTTATAAGTTTTTGTGATT
1 TTTTTATAA-TTTTTAT-AAT
31535199 TTTTTATAATTTTTATAA-
1 TTTTTATAATTTTTATAAT
* *
31535217 TATTT-TAATATTTATAATT
1 TTTTTATAATTTTTATAA-T
31535236 TTTTTATAAGTTTT
1 TTTTTATAA-TTTT
31535250 CTTAGAAAAT
Statistics
Matches: 236, Mismatches: 67, Indels: 47
0.67 0.19 0.13
Matches are distributed among these distances:
17 18 0.08
18 8 0.03
19 93 0.39
20 73 0.31
21 28 0.12
22 16 0.07
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAT
Found at i:31535192 original size:11 final size:9
Alignment explanation
Indices: 31535142--31535238 Score: 79
Period size: 9 Copynumber: 10.3 Consensus size: 9
31535132 CTTATGATTA
31535142 TTTATAAGTT
1 TTTATAA-TT
**
31535152 TTTATAACA
1 TTTATAATT
31535161 TTTATAATTT
1 TTTATAA-TT
*
31535171 TTTATGATT
1 TTTATAATT
31535180 TTTATAAGTT
1 TTTATAA-TT
* *
31535190 TTTGTGATTTT
1 TTTAT-A-ATT
31535201 TTTATAATT
1 TTTATAATT
*
31535210 TTTATAATA
1 TTTATAATT
*
31535219 TTT-TAATA
1 TTTATAATT
31535227 TTTATAATT
1 TTTATAATT
31535236 TTT
1 TTT
31535239 TTATAAGTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
8 8 0.11
9 35 0.50
10 20 0.29
11 7 0.10
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (9 bp):
TTTATAATT
Found at i:31535198 original size:58 final size:58
Alignment explanation
Indices: 31535125--31535249 Score: 148
Period size: 58 Copynumber: 2.2 Consensus size: 58
31535115 ATAATTTATC
* *
31535125 ATAAGTTCTTATGA-TTATTTATAAGTTTTTATAACATTTATAAT-TTT-TTATGATTTTT
1 ATAAGTTTTTATGATTTATTTATAA-TTTTTATAACATTT-TAATATTTATAAT-ATTTTT
* * * *
31535183 ATAAGTTTTTGTGATTTTTTTATAATTTTTATAATATTTTAATATTTATAATTTTTTT
1 ATAAGTTTTTATGATTTATTTATAATTTTTATAACATTTTAATATTTATAATATTTTT
31535241 ATAAGTTTT
1 ATAAGTTTT
31535250 CTTAGAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
57 4 0.07
58 42 0.72
59 12 0.21
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (58 bp):
ATAAGTTTTTATGATTTATTTATAATTTTTATAACATTTTAATATTTATAATATTTTT
Found at i:31535230 original size:17 final size:16
Alignment explanation
Indices: 31535200--31535238 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
31535190 TTTGTGATTT
*
31535200 TTTTATAATTTTTATAA
1 TTTT-TAATATTTATAA
31535217 TATTTTAATATTTATAA
1 T-TTTTAATATTTATAA
31535234 TTTTT
1 TTTTT
31535239 TTATAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 13 0.65
18 3 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTAATATTTATAA
Found at i:31535241 original size:11 final size:11
Alignment explanation
Indices: 31535161--31535249 Score: 51
Period size: 11 Copynumber: 8.0 Consensus size: 11
31535151 TTTTATAACA
31535161 TTTATAA-TTT
1 TTTATAATTTT
*
31535171 TTTATGA--TT
1 TTTATAATTTT
*
31535180 TTTATAA-GTT
1 TTTATAATTTT
* *
31535190 TTTGTGATTTT
1 TTTATAATTTT
31535201 TTTATAATTTT
1 TTTATAATTTT
* *
31535212 TATAATATTTTAAT
1 T-TTATAATTT--T
31535226 ATTTATAATTTT
1 -TTTATAATTTT
31535238 TTTATAAGTTTT
1 TTTATAA-TTTT
31535250 CTTAGAAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
9 8 0.13
10 13 0.21
11 19 0.31
12 12 0.20
14 8 0.13
15 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (11 bp):
TTTATAATTTT
Found at i:31535633 original size:11 final size:10
Alignment explanation
Indices: 31535596--31535667 Score: 54
Period size: 8 Copynumber: 8.0 Consensus size: 10
31535586 TGCATAAATA
31535596 ATTTTATAAT
1 ATTTTATAAT
*
31535606 -TTTTAAAAT
1 ATTTTATAAT
31535615 ATTTTTATAAT
1 A-TTTTATAAT
*
31535626 ATATT-T-AT
1 ATTTTATAAT
31535634 ATTTT-TAAT
1 ATTTTATAAT
31535643 A-TTTAT-AT
1 ATTTTATAAT
31535651 -TTTTATAA-
1 ATTTTATAAT
31535659 ATTTT-TAAT
1 ATTTTATAAT
31535668 GATATTTCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
8 20 0.40
9 18 0.36
10 3 0.06
11 9 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTATAAT
Found at i:31535644 original size:17 final size:16
Alignment explanation
Indices: 31535598--31535655 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 16
31535588 CATAAATAAT
31535598 TTTATAATTTTTAAA-A
1 TTTAT-ATTTTTAAATA
31535614 --TAT-TTTTATAATATA
1 TTTATATTTT-TAA-ATA
31535629 TTTATATTTTT-AATA
1 TTTATATTTTTAAATA
31535644 TTTATATTTTTA
1 TTTATATTTTTA
31535656 TAAATTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
12 4 0.11
13 3 0.09
14 4 0.11
15 15 0.43
16 1 0.03
17 4 0.11
18 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTATATTTTTAAATA
Found at i:31535646 original size:15 final size:15
Alignment explanation
Indices: 31535626--31535655 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31535616 TTTTTATAAT
31535626 ATATTTATATTTTTA
1 ATATTTATATTTTTA
31535641 ATATTTATATTTTTA
1 ATATTTATATTTTTA
31535656 TAAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATTTATATTTTTA
Found at i:31536351 original size:16 final size:18
Alignment explanation
Indices: 31536332--31536369 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
31536322 ATTTTAATTA
31536332 ATAATAATATT-AT-AAT
1 ATAATAATATTAATAAAT
31536348 ATAATAATATTAATAAAT
1 ATAATAATATTAATAAAT
31536366 ATAA
1 ATAA
31536370 AAGAAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
17 2 0.10
18 7 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATAATATTAATAAAT
Found at i:31539690 original size:18 final size:18
Alignment explanation
Indices: 31539667--31539702 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31539657 GCTTCTGCAG
* *
31539667 CTCGAGGTTGTGGTAGTA
1 CTCGAGGTGGTGCTAGTA
31539685 CTCGAGGTGGTGCTAGTA
1 CTCGAGGTGGTGCTAGTA
31539703 ACAGAGGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.14, G:0.39, T:0.31
Consensus pattern (18 bp):
CTCGAGGTGGTGCTAGTA
Found at i:31541609 original size:23 final size:22
Alignment explanation
Indices: 31541583--31541703 Score: 143
Period size: 23 Copynumber: 5.2 Consensus size: 22
31541573 ACACTAGCGC
31541583 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACT-TGTGT
* * *
31541606 GCTCTCTGTTTAGCACATCTCGT
1 GCTCTCTGATTAGCACTTGT-GT
*
31541629 GCTCTCTGTTATTAGCACTATGTAT
1 GCTCTCTG--ATTAGCACT-TGTGT
31541654 GCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTT-GTGT
31541677 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCAC-TTGTGT
31541700 GCTC
1 GCTC
31541704 AGTACTTTGT
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
22 3 0.04
23 61 0.73
24 2 0.02
25 16 0.19
26 2 0.02
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.40
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTGTGT
Found at i:31541657 original size:48 final size:46
Alignment explanation
Indices: 31541583--31541703 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 46
31541573 ACACTAGCGC
* *
31541583 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACATC-TCGT
1 GCTCTCTGATTAGCACTATGTGTGCTCTCTGATTAGCACATCGT-GT
* *
31541629 GCTCTCTGTTATTAGCACTATGTATGCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTATGTGTGCTCTCTGATTAGCACATCGTGT
*
31541677 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTATGTGTGCTC
31541704 AGTACTTTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
46 25 0.38
48 40 0.61
49 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTATGTGTGCTCTCTGATTAGCACATCGTGT
Found at i:31541732 original size:39 final size:39
Alignment explanation
Indices: 31541668--31541742 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
31541658 TCTGATTAGC
*
31541668 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
31541707 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
31541743 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:31541737 original size:23 final size:23
Alignment explanation
Indices: 31541702--31541795 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
31541692 CTTTGTGTGC
*
31541702 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
31541725 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
31541748 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
31541773 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
31541795 T
1 T
31541796 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:31546501 original size:31 final size:31
Alignment explanation
Indices: 31546466--31546539 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
31546456 TCTTTCACCA
31546466 TTTTTCTTCAAAATTCAAGAATAATATATGG
1 TTTTTCTTCAAAATTCAAGAATAATATATGG
*
31546497 TTTTTCTTCAAAATTCAAGCATAATATATGG
1 TTTTTCTTCAAAATTCAAGAATAATATATGG
31546528 TTTTTCTTCAAA
1 TTTTTCTTCAAA
31546540 TTTTTCATAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (31 bp):
TTTTTCTTCAAAATTCAAGAATAATATATGG
Found at i:31553529 original size:22 final size:22
Alignment explanation
Indices: 31553491--31553534 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
31553481 CAGCAAATAA
*
31553491 TTTTAAAATTATTAAAATTATTT
1 TTTTAAAATTA-TAAAAATATTT
31553514 TTTTAAAA-TATAAAAATATTT
1 TTTTAAAATTATAAAAATATTT
31553535 AAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 2 0.10
23 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAAATTATAAAAATATTT
Found at i:31553553 original size:29 final size:31
Alignment explanation
Indices: 31553494--31553562 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 31
31553484 CAAATAATTT
*
31553494 TAAAATTA-TTAAAATTATTTTTTTAAAATA
1 TAAAATTATTTAAAATTATTTTTTCAAAATA
*
31553524 TAAAAATATTTAAAA-TA-TTTTTCAAAATA
1 TAAAATTATTTAAAATTATTTTTTCAAAATA
31553553 TAAAATTATT
1 TAAAATTATT
31553563 AAATAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 20 0.57
30 9 0.26
31 6 0.17
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (31 bp):
TAAAATTATTTAAAATTATTTTTTCAAAATA
Found at i:31553571 original size:28 final size:28
Alignment explanation
Indices: 31553494--31553572 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 28
31553484 CAAATAATTT
* *
31553494 TAAAATTATTAAAATTATTTTTTTAAAATA
1 TAAAATTATT-AAA-TAATTTTTCAAAATA
*
31553524 TAAAAATATTTAAA-ATATTTTTCAAAATA
1 TAAAATTA-TTAAATA-ATTTTTCAAAATA
31553553 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATAATTTT
31553573 AATTTTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
28 11 0.26
29 19 0.45
30 10 0.24
31 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAAATTATTAAATAATTTTTCAAAATA
Found at i:31555328 original size:48 final size:48
Alignment explanation
Indices: 31555253--31555353 Score: 184
Period size: 48 Copynumber: 2.1 Consensus size: 48
31555243 ATAAGGCAAC
*
31555253 ATTTTATTTTGGCTTTAAAAGGAGCAGCTGATATACAAAAAGATTAGA
1 ATTTTATTTTGACTTTAAAAGGAGCAGCTGATATACAAAAAGATTAGA
*
31555301 ATTTTATTTTGACTTTAAAAGGGGCAGCTGATATACAAAAAGATTAGA
1 ATTTTATTTTGACTTTAAAAGGAGCAGCTGATATACAAAAAGATTAGA
31555349 ATTTT
1 ATTTT
31555354 TAAATGAAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.36
Consensus pattern (48 bp):
ATTTTATTTTGACTTTAAAAGGAGCAGCTGATATACAAAAAGATTAGA
Found at i:31563192 original size:18 final size:18
Alignment explanation
Indices: 31563171--31563210 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
31563161 ATTCTAAATC
31563171 TTCTAGCTCAT-TGTCACA
1 TTCTAGCTCATCT-TCACA
*
31563189 TTCTAGTTCATCTTCACA
1 TTCTAGCTCATCTTCACA
31563207 TTCT
1 TTCT
31563211 GGTTCTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.20, C:0.28, G:0.07, T:0.45
Consensus pattern (18 bp):
TTCTAGCTCATCTTCACA
Found at i:31563270 original size:165 final size:165
Alignment explanation
Indices: 31563077--31563594 Score: 876
Period size: 165 Copynumber: 3.1 Consensus size: 165
31563067 TCTCCCGTAA
* * * *
31563077 ATTCTAATAATTCTAAAGATTCTGGTTTAGGTCATGGGGGTTCTATTTCCTCTACAACTTCTAGT
1 ATTCTAACAATTCTAAGGATTCTGGTTTAGGTCATGGGGATTCTATTTCCTCTAAAACTTCTAGT
31563142 TCTTTATCAGGTTCTAGCCATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTCACA
66 TCTTTATCAGGTTCTAGCCATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTCACA
*
31563207 TTCTGGTTCTTGGAAGGGTTCCAGCTCATTAGGAG
131 TTCTGGTTCTTGGAAGGGTTCTAGCTCATTAGGAG
* * *
31563242 ATTCTAACAATTCTAAGGATTTTGGTTTAGGTCATGGGGATTCTA-GTCCTTCTAAAACTTCTAA
1 ATTCTAACAATTCTAAGGATTCTGGTTTAGGTCATGGGGATTCTATTTCC-TCTAAAACTTCTAG
* *
31563306 TTCTTTATCAGGTTCTAGTCATTCTAAATCTTCTAACTCATTGTCACATTCTAGTTCATCTTCAC
65 TTCTTTATCAGGTTCTAGCCATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTCAC
31563371 ATTCTGGTTCTTGGAAGGGTTCTAGCTCATTAGGAG
130 ATTCTGGTTCTTGGAAGGGTTCTAGCTCATTAGGAG
* *
31563407 ATTCTAACAATTCTAAGGATTCTGGTTTAGGTCATGAGAATTCTATTTCCTCTAAAACTTCTAGT
1 ATTCTAACAATTCTAAGGATTCTGGTTTAGGTCATGGGGATTCTATTTCCTCTAAAACTTCTAGT
*
31563472 TCTTTATCAGGTTCTAGCAATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTCACA
66 TCTTTATCAGGTTCTAGCCATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTCACA
* * *
31563537 TTCTGGTTCTTGGAAGGGTTCTAACTCACTCGGAG
131 TTCTGGTTCTTGGAAGGGTTCTAGCTCATTAGGAG
31563572 ATTCTAACAATTCTAAGGATTCT
1 ATTCTAACAATTCTAAGGATTCT
31563595 AGTTCTGCTA
Statistics
Matches: 330, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
164 3 0.01
165 324 0.98
166 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (165 bp):
ATTCTAACAATTCTAAGGATTCTGGTTTAGGTCATGGGGATTCTATTTCCTCTAAAACTTCTAGT
TCTTTATCAGGTTCTAGCCATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTCACA
TTCTGGTTCTTGGAAGGGTTCTAGCTCATTAGGAG
Found at i:31563358 original size:36 final size:36
Alignment explanation
Indices: 31563281--31563360 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
31563271 GGTCATGGGG
* * * *
31563281 ATTCTAGTCCTTCTAAAACTTCTAATTCTTTATCAG
1 ATTCTAGTCATTCTAAAACTTCTAACTCATTATCAC
* * *
31563317 GTTCTAGTCATTCTAAATCTTCTAACTCATTGTCAC
1 ATTCTAGTCATTCTAAAACTTCTAACTCATTATCAC
31563353 ATTCTAGT
1 ATTCTAGT
31563361 TCATCTTCAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (36 bp):
ATTCTAGTCATTCTAAAACTTCTAACTCATTATCAC
Found at i:31563522 original size:18 final size:18
Alignment explanation
Indices: 31563501--31563540 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
31563491 ATTCTAAATC
31563501 TTCTAGCTCAT-TGTCACA
1 TTCTAGCTCATCT-TCACA
*
31563519 TTCTAGTTCATCTTCACA
1 TTCTAGCTCATCTTCACA
31563537 TTCT
1 TTCT
31563541 GGTTCTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.20, C:0.28, G:0.07, T:0.45
Consensus pattern (18 bp):
TTCTAGCTCATCTTCACA
Found at i:31564015 original size:18 final size:18
Alignment explanation
Indices: 31563994--31564051 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
31563984 AGCTTCTGGC
31563994 TCATCTTCACATTCCAGT
1 TCATCTTCACATTCCAGT
* *
31564012 TCATATTCACATTCTAGT
1 TCATCTTCACATTCCAGT
*
31564030 TCTTCTTCACATTCCAGT
1 TCATCTTCACATTCCAGT
31564048 TCAT
1 TCAT
31564052 TTAAGCATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.22, C:0.29, G:0.05, T:0.43
Consensus pattern (18 bp):
TCATCTTCACATTCCAGT
Found at i:31564037 original size:36 final size:36
Alignment explanation
Indices: 31563997--31564068 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
31563987 TTCTGGCTCA
* *
31563997 TCTTCACATTCCAGTTCATATTCA-CATTCTAGTTCT
1 TCTTCACATTCCAGTTCAT-TTAAGCATTCAAGTTCT
31564033 TCTTCACATTCCAGTTCATTTAAGCATTCAAGTTCT
1 TCTTCACATTCCAGTTCATTTAAGCATTCAAGTTCT
31564069 GGTTCTTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 3 0.09
36 30 0.91
ACGTcount: A:0.24, C:0.26, G:0.07, T:0.43
Consensus pattern (36 bp):
TCTTCACATTCCAGTTCATTTAAGCATTCAAGTTCT
Found at i:31564550 original size:192 final size:190
Alignment explanation
Indices: 31564333--31564902 Score: 619
Period size: 192 Copynumber: 3.0 Consensus size: 190
31564323 TAGTGCTACT
** * *
31564333 ACAAACTCGGGTTCCAACAATTCTAAGGATTCTGGTTCTACTACAACTTCTCAGTCTTCATTAAA
1 ACAAACTTAGGTTCCAACAATTCTAAGGATTCTGATTCTACTAC-GCTTCTCAGTCTTCATTAAA
** *
31564398 TCATAAGGCTTCTAATTCCTCTGCAAGTTCTAGTTCTTTATCAAGTTCTAGCAATTATAAGGCTT
65 TCATGGGGCTTCTAATTCCTCTACAAGTTCTAGTTCTTTATCAAGTTCTAGCAATTATAAGGCTT
* * *
31564463 CAGGCTTATCCACAAATTCCAGTTCATCTTTACATTCTGGCTCTAGTGCTGCTAACTCATCC
130 CAGGCTCATCCTCAAATTCCAGTTCATCTTTACATTCTGGTTCTAGTGCT-CTAACTCATCC
*
31564525 ACAAACTTAGGTTCCAACCATTCTAAGGATTCTGATTCTA-TGACGGCTTCTCAGTCTTCATTAA
1 ACAAACTTAGGTTCCAACAATTCTAAGGATTCTGATTCTACT-AC-GCTTCTCAGTCTTCATTAA
* * * * ** * *
31564589 ATCATGGGGCTACTAGTTCCTCCACAAGTTCTCA-TTCTTTATCAAGTTCAAATAGTTCTAAGGC
64 ATCATGGGGCTTCTAATTCCTCTACAAGTTCT-AGTTCTTTATCAAGTTCTAGCAATTATAAGGC
** * * * * * *
31564653 TTTTGGCTCATCTTCACATTCCAGTTC-T-TTTAAGTATTCTGGTTCTGGTGCATCTAAATCTTC
128 TTCAGGCTCATCCTCAAATTCCAGTTCATCTTT-A-CATTCTGGTTCTAGTGC-TCTAACTCATC
31564716 C
190 C
* * * * * * *
31564717 ACAAACATAGGTTCCAACAATTCTAAGGATTCTAATTCTGCTGCGGTTACTCAGTCTACAGTAAA
1 ACAAACTTAGGTTCCAACAATTCTAAGGATTCTGATTCTACTACGCTT-CTCAGTCTTCATTAAA
* * **
31564782 TCATGGGGCTTCTAATTCCTCTTCAAGTTCTGGTTCTTTATCCGGTTCTAGCAATTATAAGGCTT
65 TCATGGGGCTTCTAATTCCTCTACAAGTTCTAGTTCTTTATCAAGTTCTAGCAATTATAAGGCTT
* * * * *
31564847 CTAGG-TCATCCTCAAATTCTATTTCATCTTCACATTCCGGTTCTAATGCTACTAAC
130 C-AGGCTCATCCTCAAATTCCAGTTCATCTTTACATTCTGGTTCTAGTGCT-CTAAC
31564903 CATAAGGCTT
Statistics
Matches: 306, Mismatches: 60, Indels: 24
0.78 0.15 0.06
Matches are distributed among these distances:
190 3 0.01
191 7 0.02
192 287 0.94
193 7 0.02
194 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.36
Consensus pattern (190 bp):
ACAAACTTAGGTTCCAACAATTCTAAGGATTCTGATTCTACTACGCTTCTCAGTCTTCATTAAAT
CATGGGGCTTCTAATTCCTCTACAAGTTCTAGTTCTTTATCAAGTTCTAGCAATTATAAGGCTTC
AGGCTCATCCTCAAATTCCAGTTCATCTTTACATTCTGGTTCTAGTGCTCTAACTCATCC
Found at i:31565220 original size:210 final size:210
Alignment explanation
Indices: 31564907--31565392 Score: 541
Period size: 210 Copynumber: 2.3 Consensus size: 210
31564897 ACTAACCATA
* * * * * *
31564907 AGGCTTTTAATTCCTCTGCAAGTTCTGGCTCTTTATCAGGTTCTAGTAATCATAAGGCTTTAGGT
1 AGGCTTCTAATTCCTCTACAAGTTCTGGTTCTTTATCAGGTTCTAGTAATAATAAGGCTTTTGGC
* * * * * *
31564972 TTATCCTCAAATTCCAGTTCAGCTTCACATTTTGGTTCTTTTAAGCAT-TCTGGTTCTAGTG-TT
66 TCATCCTCAAAATCCAATTCAGCTTCACATTCTGGTTCTTCTAAGAATGT-TGGTTCTAGTGCTT
* * * * *
31565035 GCTAACTCATCTACAA-ATTCTAGTTCCAACAATTCTAAAGATT-TTGATTCTACTACGGCTTCT
130 -CTAACTCATCAACAATA-CCTAGTTCCAACAATTCTAAAGATTCTAG-TCCTACTACGACTTCT
*
31565098 CAGTCTTCATTA-AATCATG
192 AAGTCTTCATTAGAA-CATG
* * * * **
31565117 GGGCTTCTAATTCTTCTACCAGTTCTGGTTCTTTATCAGGTTCTAGCAATTTTAAGGCTTTTGGC
1 AGGCTTCTAATTCCTCTACAAGTTCTGGTTCTTTATCAGGTTCTAGTAATAATAAGGCTTTTGGC
* ** * * *
31565182 TCATCCTCAAAATCTAATTCATTTTTACATTCTGGTTCTTCTAAGAATGTTGGTTTTGGTGCTTC
66 TCATCCTCAAAATCCAATTCAGCTTCACATTCTGGTTCTTCTAAGAATGTTGGTTCTAGTGCTTC
* *
31565247 TAACTCATCAACAATACCTGGTTCCAACAATTCTAAGGATTCTAGTCCTACTACGACTTCTAAGT
131 TAACTCATCAACAATACCTAGTTCCAACAATTCTAAAGATTCTAGTCCTACTACGACTTCTAAGT
*
31565312 CTTCATTAGGACATG
196 CTTCATTAGAACATG
* ** * * *
31565327 AAGCTTCTGGTTCCTCTACAAGTTCTGGTTCTTTGTCAGGTTCTAGTAATACTAAGGCTTCTGGC
1 AGGCTTCTAATTCCTCTACAAGTTCTGGTTCTTTATCAGGTTCTAGTAATAATAAGGCTTTTGGC
31565392 T
66 T
31565393 TGTCATCACA
Statistics
Matches: 228, Mismatches: 43, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
210 221 0.97
211 7 0.03
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (210 bp):
AGGCTTCTAATTCCTCTACAAGTTCTGGTTCTTTATCAGGTTCTAGTAATAATAAGGCTTTTGGC
TCATCCTCAAAATCCAATTCAGCTTCACATTCTGGTTCTTCTAAGAATGTTGGTTCTAGTGCTTC
TAACTCATCAACAATACCTAGTTCCAACAATTCTAAAGATTCTAGTCCTACTACGACTTCTAAGT
CTTCATTAGAACATG
Found at i:31565499 original size:18 final size:18
Alignment explanation
Indices: 31565455--31565504 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
31565445 TTTCTCTTTG
* *
31565455 TCACATTCAAGTTCAGCT
1 TCACATTCTAGTTCAGAT
*
31565473 TCACATTCTAGTTCATAT
1 TCACATTCTAGTTCAGAT
*
31565491 TCACATTCTGGTTC
1 TCACATTCTAGTTC
31565505 CTTTAAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (18 bp):
TCACATTCTAGTTCAGAT
Found at i:31565516 original size:18 final size:18
Alignment explanation
Indices: 31565495--31565529 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31565485 TCATATTCAC
*
31565495 ATTCTGGTTCCTTTAAGA
1 ATTCAGGTTCCTTTAAGA
*
31565513 ATTCAGGTTCTTTTAAG
1 ATTCAGGTTCCTTTAAG
31565530 GGTTCTGGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (18 bp):
ATTCAGGTTCCTTTAAGA
Found at i:31567792 original size:213 final size:213
Alignment explanation
Indices: 31567425--31568698 Score: 2217
Period size: 213 Copynumber: 6.0 Consensus size: 213
31567415 TCTAAAGCAA
* * *
31567425 CTAGTACTAAAGATACAGGTACTTTCACAGGCACTAGTACTTTTGTGACAAATGGTCCTACAACT
1 CTAGTACTAAAGATACAGGTACTTCCACAGGCACTAGTACTTCTGTGACAAATGGTCCTACAGCT
31567490 TTTGCTCCTTCTTCGAGCCCTTCCACAGGCGTTAGTTCTTCCACAACTAATAGCCATAAGGGATT
66 TTTGCTCCTTCTTCGAGCCCTTCCACAGGCGTTAGTTCTTCCACAACTAATAGCCATAAGGGATT
31567555 TGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGTTCGTATACAACTTCTGGTCACTCTTCCG
131 TGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGTTCGTATACAACTTCTGGTCACTCTTCCG
*
31567620 TAAGTCATAGTTCTAGTC
196 CAAGTCATAGTTCTAGTC
* * * *
31567638 CTAGTACTAAAGATACAGGTACTTCCACAGGCACTAGTACTTCTATGACAAATGGTCTTAAAACT
1 CTAGTACTAAAGATACAGGTACTTCCACAGGCACTAGTACTTCTGTGACAAATGGTCCTACAGCT
* *
31567703 TTTGCTCCTTCTTTGAGCCCTTCCACAGGCGTTAGTTCTTCCACAACTAATAGCCATAAGGGCTT
66 TTTGCTCCTTCTTCGAGCCCTTCCACAGGCGTTAGTTCTTCCACAACTAATAGCCATAAGGGATT
* *
31567768 TGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGTTTGTATACAACTTCTGGTCACTCTTTCG
131 TGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGTTCGTATACAACTTCTGGTCACTCTTCCG
31567833 CAAGTCATAGTTCTAGTC
196 CAAGTCATAGTTCTAGTC
31567851 CTAGTACTAAAGATA-AGAGTACTTCCACAGGCACTAGTACTTCTGTGACAAATGGTCCTACAGC
1 CTAGTACTAAAGATACAG-GTACTTCCACAGGCACTAGTACTTCTGTGACAAATGGTCCTACAGC
*
31567915 TTTTGCTCCTTCTTCGAGCCCTTCCACAGGCATTAGTTCTTCCACAACTAATAGCCATAAGGGAT
65 TTTTGCTCCTTCTTCGAGCCCTTCCACAGGCGTTAGTTCTTCCACAACTAATAGCCATAAGGGAT
* *
31567980 TTGACCATACAAGTTCAAGCAATTTCGCTCACTCTGGTTCGTATACAACTTCTTGTCACTCTTCC
130 TTGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGTTCGTATACAACTTCTGGTCACTCTTCC
31568045 GCAAGTCATAGTTCTAGTC
195 GCAAGTCATAGTTCTAGTC
** * *
31568064 CTAGTACTAAAGATATGGGTACTTCCACAGGCACTAGTACTTCTATGACAAATGCTCCTACAGCT
1 CTAGTACTAAAGATACAGGTACTTCCACAGGCACTAGTACTTCTGTGACAAATGGTCCTACAGCT
*
31568129 TTTGCTCCTTCTTCGAGCCCTTCCACAGGCGTTAGTTCTTCCACAACTAATAGCCATAAGAGATT
66 TTTGCTCCTTCTTCGAGCCCTTCCACAGGCGTTAGTTCTTCCACAACTAATAGCCATAAGGGATT
*
31568194 TGATCATACAAGTTCAAGCAATTTTGCTCACTCTGGTTCGTATACAACTTCTGGTCACTCTTCCG
131 TGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGTTCGTATACAACTTCTGGTCACTCTTCCG
31568259 CAAGTCATAGTTCTAGTC
196 CAAGTCATAGTTCTAGTC
* * *
31568277 CTAGTACTAAAGATACGGGTACTTCCACAGGAACTAGTACTTCTGTGACAAATGGTCCTATAGCT
1 CTAGTACTAAAGATACAGGTACTTCCACAGGCACTAGTACTTCTGTGACAAATGGTCCTACAGCT
* *
31568342 TTTGCTCCTTCTTCGAACCCTTCCACAGGCGTTAGTTCTTCCACAACTAATAGCCATAAGAGATT
66 TTTGCTCCTTCTTCGAGCCCTTCCACAGGCGTTAGTTCTTCCACAACTAATAGCCATAAGGGATT
*
31568407 TGATCATACAAGTTCAAGCAATTTTGCTCACTCTGGTTCGTATACAACTTCTGGTCACTCTTCCG
131 TGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGTTCGTATACAACTTCTGGTCACTCTTCCG
31568472 CAAGTCATAGTTCTAGTC
196 CAAGTCATAGTTCTAGTC
* *
31568490 CTAGTACTAAAGATACGGGTACTTCCACAGGAACTAGTACTTCTGTGACAAATGGTCCTACAGCT
1 CTAGTACTAAAGATACAGGTACTTCCACAGGCACTAGTACTTCTGTGACAAATGGTCCTACAGCT
** *
31568555 TTTGCTCCTTCTTCGAGCCCTTCCACAGGAATTAGTTCTTCCACAACTAATACCCATAAGGGATT
66 TTTGCTCCTTCTTCGAGCCCTTCCACAGGCGTTAGTTCTTCCACAACTAATAGCCATAAGGGATT
* * *
31568620 TGATCATACAAGTTCAAGTAATTTCGCTCACTCTGGTTCGTATACAACTTCTGATCACACTTCCG
131 TGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGTTCGTATACAACTTCTGGTCACTCTTCCG
31568685 CAAGTCATAGTTCT
196 CAAGTCATAGTTCT
31568699 GGTTCATCTA
Statistics
Matches: 1014, Mismatches: 45, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
212 2 0.00
213 1011 1.00
214 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (213 bp):
CTAGTACTAAAGATACAGGTACTTCCACAGGCACTAGTACTTCTGTGACAAATGGTCCTACAGCT
TTTGCTCCTTCTTCGAGCCCTTCCACAGGCGTTAGTTCTTCCACAACTAATAGCCATAAGGGATT
TGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGTTCGTATACAACTTCTGGTCACTCTTCCG
CAAGTCATAGTTCTAGTC
Found at i:31569010 original size:18 final size:18
Alignment explanation
Indices: 31568987--31569031 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
31568977 AAAATCTGGC
*
31568987 TCTTCTACACATACAGGT
1 TCTTCTACACACACAGGT
* *
31569005 TCTTCTAAACACACTGGT
1 TCTTCTACACACACAGGT
*
31569023 TCCTCTACA
1 TCTTCTACA
31569032 ACCTCTAGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (18 bp):
TCTTCTACACACACAGGT
Found at i:31569183 original size:198 final size:198
Alignment explanation
Indices: 31568843--31570160 Score: 1866
Period size: 198 Copynumber: 6.7 Consensus size: 198
31568833 TGAGTCCGGC
* * * * * ** * *
31568843 TCCAAAACTTCAGGCTCTTCCACAAACATTGGTTCTACTATGACTGATGGCCATATAGCTACCGG
1 TCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGCAACTACTGG
* * * *
31568908 TTCTATTTCGAGCCACTCTTCAGGTTCTACTTCTCATAAGAGTAATAGTCACACAACTTCTACTC
66 TTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGCTC
* * * * *
31568973 AAACAAAATCTGGCTCTTCTACACATACAGGTTCTTCTAAACACACTGGTTCCTCTACAACCTCT
131 ATACAAAATCTGGCTCTTCTACACACACAGGTTCTTCTAAACACATTGGTTCTTCCACAACCTCT
*
31569038 AGT
196 GGT
* * * *
31569041 TCCAAAACTTCAGGCTCTTCCACAAACACTGGTTCTGCTACGACTAATGGCCATACAACTACTGG
1 TCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGCAACTACTGG
* * *
31569106 TTCTATTTCGAGCCACTCTTTAGGTTCTAATTCTCATAAGACTAATAGTCACATGACTTCTGCTC
66 TTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGCTC
* * *
31569171 ATACAGAATCTGGCTCTTCTACACACACAGGTTCTTCAAAACACATTGGTTCTTCTACAACCTCT
131 ATACAAAATCTGGCTCTTCTACACACACAGGTTCTTCTAAACACATTGGTTCTTCCACAACCTCT
31569236 GGT
196 GGT
* * *
31569239 TCCAAAACTTTGGGCTCTTCCACAAACACTGGTTCTGCTACGACTAATGGCCATGCAACTACTGG
1 TCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGCAACTACTGG
* * *
31569304 TTCTATTTCGAGCCACTCTTCAGGTTGTAATTCTCATAAGACTAATAGTCACACGACTTCTGGTC
66 TTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGCTC
* * *
31569369 ATACAGAATCTGGGTCTTCTACACACACAGGTTCTTCCAAACACATTGGTTCTTCCACAACCTCT
131 ATACAAAATCTGGCTCTTCTACACACACAGGTTCTTCTAAACACATTGGTTCTTCCACAACCTCT
31569434 GGT
196 GGT
* * * * *
31569437 TCTAAAACTTCGGGCTCTTCTACAAGCACTGGTTCTGCTACAACGGATAGCCATGCAACTACTGG
1 TCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGCAACTACTGG
* * *
31569502 TTCTATTTCAAGCCACTCTTCAGATTCTAGTTCTCATAAGACTAATAGTCACATGACTTCTGCTC
66 TTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGCTC
* * *
31569567 ATACAAAATTTGGCTCTTCTAAACACACAGGTTCTTCCAAACACATTGGTTCTTCCACAACCTCT
131 ATACAAAATCTGGCTCTTCTACACACACAGGTTCTTCTAAACACATTGGTTCTTCCACAACCTCT
31569632 GGT
196 GGT
* * * *
31569635 TCTAAAACTTCGGGCTCTTCCACAAGCACTGGTTTTGTTACAACTGATGGCCATGCAACTACTGG
1 TCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGCAACTACTGG
* *
31569700 TTCTATTTCAAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGGTC
66 TTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGCTC
* *
31569765 ATACAGAATCTGGCTCTTCTACACACAGAGGTTCTT-TCAAACACATTGGTTCTTCCACAACCTC
131 ATACAAAATCTGGCTCTTCTACACACACAGGTTCTTCT-AAACACATTGGTTCTTCCACAACCTC
31569829 TGGT
195 TGGT
* * *
31569833 TCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGGTGGCCATTCAACTATTGG
1 TCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGCAACTACTGG
* *
31569898 TTCTATTTCAAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGGTC
66 TTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGCTC
*
31569963 ATACAAAATCTGGCTCTTCT------ACA-------C---ACACA--GGTTCTTCCACAATCTCT
131 ATACAAAATCTGGCTCTTCTACACACACAGGTTCTTCTAAACACATTGGTTCTTCCACAACCTCT
31570010 GGT
196 GGT
*
31570013 TCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGCAACTACTAG
1 TCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGCAACTACTGG
* *
31570078 TTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTGATAGTCAGA-GCACTTCTGCT
66 TTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACG-ACTTCTGCT
* *
31570142 CCTACAAAATCTTGCTCTT
130 CATACAAAATCTGGCTCTT
31570161 GCACTTGCAC
Statistics
Matches: 1036, Mismatches: 81, Indels: 24
0.91 0.07 0.02
Matches are distributed among these distances:
179 1 0.00
180 156 0.15
182 5 0.00
192 2 0.00
198 872 0.84
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (198 bp):
TCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGCAACTACTGG
TTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGCTC
ATACAAAATCTGGCTCTTCTACACACACAGGTTCTTCTAAACACATTGGTTCTTCCACAACCTCT
GGT
Found at i:31569206 original size:18 final size:18
Alignment explanation
Indices: 31569185--31569229 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
31569175 AGAATCTGGC
31569185 TCTTCTACACACACAGGT
1 TCTTCTACACACACAGGT
* * **
31569203 TCTTCAAAACACATTGGT
1 TCTTCTACACACACAGGT
31569221 TCTTCTACA
1 TCTTCTACA
31569230 ACCTCTGGTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (18 bp):
TCTTCTACACACACAGGT
Found at i:31569412 original size:18 final size:18
Alignment explanation
Indices: 31569391--31569425 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31569381 GGTCTTCTAC
31569391 ACACACAGGTTCTTCCAA
1 ACACACAGGTTCTTCCAA
**
31569409 ACACATTGGTTCTTCCA
1 ACACACAGGTTCTTCCA
31569426 CAACCTCTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.29
Consensus pattern (18 bp):
ACACACAGGTTCTTCCAA
Found at i:31569637 original size:18 final size:18
Alignment explanation
Indices: 31569576--31569623 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
31569566 CATACAAAAT
* *
31569576 TTGGCTCTTCTAAACACA
1 TTGGTTCTTCCAAACACA
**
31569594 CAGGTTCTTCCAAACACA
1 TTGGTTCTTCCAAACACA
31569612 TTGGTTCTTCCA
1 TTGGTTCTTCCA
31569624 CAACCTCTGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (18 bp):
TTGGTTCTTCCAAACACA
Found at i:31570114 original size:180 final size:180
Alignment explanation
Indices: 31569812--31570160 Score: 583
Period size: 180 Copynumber: 1.9 Consensus size: 180
31569802 CAAACACATT
31569812 GGTTCTTCCACAACCTCTGGTTCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGAC
1 GGTTCTTCCACAACCTCTGGTTCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGAC
* * * *
31569877 TGGTGGCCATTCAACTATTGGTTCTATTTCAAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTA
66 TGATGGCCATGCAACTACTAGTTCTATTTCAAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTA
*
31569942 ATAGTCACA-CGACTTCTGGTCATACAAAATCTGGCTCTTCTACACACACA
131 ATAGTCACAGC-ACTTCTGCTCATACAAAATCTGGCTCTTCTACACACACA
*
31569992 GGTTCTTCCACAATCTCTGGTTCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGAC
1 GGTTCTTCCACAACCTCTGGTTCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGAC
* *
31570057 TGATGGCCATGCAACTACTAGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTG
66 TGATGGCCATGCAACTACTAGTTCTATTTCAAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTA
* * *
31570122 ATAGTCAGAGCACTTCTGCTCCTACAAAATCTTGCTCTT
131 ATAGTCACAGCACTTCTGCTCATACAAAATCTGGCTCTT
31570161 GCACTTGCAC
Statistics
Matches: 157, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
180 156 0.99
181 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (180 bp):
GGTTCTTCCACAACCTCTGGTTCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACGAC
TGATGGCCATGCAACTACTAGTTCTATTTCAAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTA
ATAGTCACAGCACTTCTGCTCATACAAAATCTGGCTCTTCTACACACACA
Found at i:31570306 original size:153 final size:153
Alignment explanation
Indices: 31570026--31570313 Score: 479
Period size: 153 Copynumber: 1.9 Consensus size: 153
31570016 AAAACTTCGG
* *
31570026 GCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGCAACTACTAGTTCTATTTCGAGC
1 GCTCTTCCACAAGCACTGGTTCTACTACGACTGATGGCCATACAACTACTAGTTCTATTTCGAGC
* * * *
31570091 CACTCTTCAGGTTCTAGTTCTCATAAGACTGATAGTCAGAGCACTTCTGCTCCTACAAAATCTTG
66 CACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACAGCACTTCTGCTCATACAAAATCTGG
31570156 CTCTTGCACTTGCACACCCATCA
131 CTCTTGCACTTGCACACCCATCA
* *
31570179 GCTCTTCCACAAGCACTGGTTCTACTATGACTGATGGCCATACAACTACTGGTTCTATTTCGAGC
1 GCTCTTCCACAAGCACTGGTTCTACTACGACTGATGGCCATACAACTACTAGTTCTATTTCGAGC
*
31570244 CACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACATG-ACTTCTGCTCATACAGAATCTG
66 CACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACA-GCACTTCTGCTCATACAAAATCTG
31570308 GCTCTT
130 GCTCTT
31570314 CTACCCACAC
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
153 124 0.99
154 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.31
Consensus pattern (153 bp):
GCTCTTCCACAAGCACTGGTTCTACTACGACTGATGGCCATACAACTACTAGTTCTATTTCGAGC
CACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACAGCACTTCTGCTCATACAAAATCTGG
CTCTTGCACTTGCACACCCATCA
Found at i:31570526 original size:198 final size:198
Alignment explanation
Indices: 31570179--31570759 Score: 835
Period size: 198 Copynumber: 2.9 Consensus size: 198
31570169 ACACCCATCA
*
31570179 GCTCTTCCACAAGCACTGGTTCTACTATGACTGATGGCCATACAACTACTGGTTCTATTTCGAGC
1 GCTCTTCCACAAGCACTGGTTCTACTATGACTAATGGCCATACAACTACTGGTTCTATTTCGAGC
* *
31570244 CACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACATGACTTCTGCTCATACAGAATCTGG
66 CACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGCTCATACAAAATCTGG
* * *
31570309 CTCTTCTACCCACACAGGTTCTTCCAAACACATTGGTTCTTCTACAACCTCTGGTTCCAAAACTT
131 CTCTTCTACACATACAGGTTCTTCCAAACACACTGGTTCTTCTACAACCTCTGGTTCCAAAACTT
31570374 CAG
196 CAG
* ** * *
31570377 GCTCCTCCACAAGCACTGGTTCTGGTACGACTAATGGCCATACAACTACTGGTTCTATTTCAAGC
1 GCTCTTCCACAAGCACTGGTTCTACTATGACTAATGGCCATACAACTACTGGTTCTATTTCGAGC
* * * *
31570442 CACTCTTCAGGTTCTACTTCTCACAAGAGTAATAGTCACACGACTTCTGCCCATACAAAATCTGG
66 CACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGCTCATACAAAATCTGG
*
31570507 CTCTTCTACACATACAGGTTCTTCCAAACACACTGGTTCTTCCACAACCTCTGGTTCCAAAACTT
131 CTCTTCTACACATACAGGTTCTTCCAAACACACTGGTTCTTCTACAACCTCTGGTTCCAAAACTT
31570572 CAG
196 CAG
* * *
31570575 GCTCTTCCACAAACACTGGTTCTACTATAACTAATGGCCATACAGCTACTGGTTCTACTTT-GAG
1 GCTCTTCCACAAGCACTGGTTCTACTATGACTAATGGCCATACAACTACTGGTTCTA-TTTCGAG
* * * * * * * *
31570639 TCACTCTTCAGGTTTTAGTTCTCATGAGACTAATAGTCATACAAATTTTTCTCATACAAAATCTG
65 CCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGCTCATACAAAATCTG
* * * *
31570704 GCTCTTCCACACACT-CCGATTCTTCCAAACACACAGGTTCTT-TCACAACCTCTGGT
130 GCTCTTCTACACA-TACAGGTTCTTCCAAACACACTGGTTCTTCT-ACAACCTCTGGT
31570760 CACTCTTCCC
Statistics
Matches: 339, Mismatches: 41, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
198 335 0.99
199 4 0.01
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (198 bp):
GCTCTTCCACAAGCACTGGTTCTACTATGACTAATGGCCATACAACTACTGGTTCTATTTCGAGC
CACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACTTCTGCTCATACAAAATCTGG
CTCTTCTACACATACAGGTTCTTCCAAACACACTGGTTCTTCTACAACCTCTGGTTCCAAAACTT
CAG
Found at i:31570544 original size:18 final size:18
Alignment explanation
Indices: 31570523--31570563 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
31570513 TACACATACA
31570523 GGTTCTTCCA-AACACACT
1 GGTTCTTCCACAAC-CACT
*
31570541 GGTTCTTCCACAACCTCT
1 GGTTCTTCCACAACCACT
31570559 GGTTC
1 GGTTC
31570564 CAAAACTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.20, C:0.34, G:0.15, T:0.32
Consensus pattern (18 bp):
GGTTCTTCCACAACCACT
Found at i:31580225 original size:43 final size:44
Alignment explanation
Indices: 31580154--31580323 Score: 188
Period size: 43 Copynumber: 3.9 Consensus size: 44
31580144 TTCCTTTAAT
31580154 CATAATCTCATGCTCATCTCGAGACATGAGTCTTCC-TTTCTTA
1 CATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTCTTA
* *
31580197 CATAATCTCATGTTCAT-TCTGAGTCATGAGTCTTCCATTTAC--A
1 CATAATCTCATGCTCATCTC-GAGACATGAGTCTTCCATTT-CTTA
* * * * * * *
31580240 CATAAACTTATGCTTATCCCGAGTCACGAGTATTCCATTT-TATA
1 CATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTCT-TA
*
31580284 CATAATCTCATACTCATCTCGAGACATGAGTCTTCCATTT
1 CATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTT
31580324 ATACACCAAG
Statistics
Matches: 103, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
42 2 0.02
43 63 0.61
44 37 0.36
45 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.37
Consensus pattern (44 bp):
CATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTCTTA
Found at i:31580312 original size:87 final size:85
Alignment explanation
Indices: 31580131--31580324 Score: 214
Period size: 87 Copynumber: 2.3 Consensus size: 85
31580121 TATGCTCAAC
** * * * *
31580131 CGAGACAAAAGTCTTCC-TTTAATCATAATCTCATGCTCATCTCGAGACATGAGTCTTCCTTTCT
1 CGAGACATGAGTCTTCCATTTAATCATAAACTCATGCTCATCCCGAGACACGAGTATTCCTTTCT
**
31580195 TACATAATCTCATGTTCATT
66 TACATAATCTCATACTCATT
* * * *
31580215 CTGAGTCATGAGTCTTCCATTTACA-CATAAACTTATGCTTATCCCGAGTCACGAGTATTCCATT
1 C-GAGACATGAGTCTTCCATTTA-ATCATAAACTCATGCTCATCCCGAGACACGAGTATTCC-TT
31580279 T-TATACATAATCTCATACTCATCT
63 TCT-TACATAATCTCATACTCAT-T
31580303 CGAGACATGAGTCTTCCATTTA
1 CGAGACATGAGTCTTCCATTTA
31580325 TACACCAAGT
Statistics
Matches: 91, Mismatches: 13, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
84 1 0.01
85 13 0.14
86 34 0.37
87 41 0.45
88 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (85 bp):
CGAGACATGAGTCTTCCATTTAATCATAAACTCATGCTCATCCCGAGACACGAGTATTCCTTTCT
TACATAATCTCATACTCATT
Found at i:31587369 original size:2 final size:2
Alignment explanation
Indices: 31587362--31587390 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31587352 TGGATATTAA
31587362 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 A
31587391 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31587395 original size:2 final size:2
Alignment explanation
Indices: 31587390--31587415 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31587380 ATATATATAT
31587390 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
31587416 TATGATCCTA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31587642 original size:19 final size:19
Alignment explanation
Indices: 31587620--31587664 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31587610 TTATATTAGG
31587620 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
31587639 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
31587658 ATTTAAT
1 ATTTAAT
31587665 TTATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:31588485 original size:15 final size:16
Alignment explanation
Indices: 31588467--31588496 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31588457 CTTCTCTATT
31588467 TTCTATTT-CTTTTAA
1 TTCTATTTACTTTTAA
31588482 TTCTATTTACTTTTA
1 TTCTATTTACTTTTA
31588497 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (16 bp):
TTCTATTTACTTTTAA
Found at i:31588489 original size:22 final size:22
Alignment explanation
Indices: 31588438--31588522 Score: 66
Period size: 22 Copynumber: 3.8 Consensus size: 22
31588428 TTATTTTATG
* * *
31588438 CTATTTATTTTTACTTTGACTTCT
1 CTATTTACTTTTACTTTTA-AT-T
*
31588462 CTATTTTCTATTT-CTTTTAATT
1 CTATTTACT-TTTACTTTTAATT
*
31588484 CTATTTACTTTTATTTTTAATT
1 CTATTTACTTTTACTTTTAATT
* *
31588506 CTGTTT-CTTTTATTTTT
1 CTATTTACTTTTACTTTT
31588523 CCTTAGATCG
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
21 14 0.27
22 22 0.42
23 1 0.02
24 12 0.23
25 3 0.06
ACGTcount: A:0.16, C:0.13, G:0.02, T:0.68
Consensus pattern (22 bp):
CTATTTACTTTTACTTTTAATT
Found at i:31588515 original size:21 final size:22
Alignment explanation
Indices: 31588476--31588522 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
31588466 TTTCTATTTC
31588476 TTTTAATTCTATTTACTTTTAT
1 TTTTAATTCTATTTACTTTTAT
*
31588498 TTTTAATTCTGTTT-CTTTTAT
1 TTTTAATTCTATTTACTTTTAT
31588519 TTTT
1 TTTT
31588523 CCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTAATTCTATTTACTTTTAT
Found at i:31590296 original size:29 final size:29
Alignment explanation
Indices: 31590263--31590335 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
31590253 TAGGGTTTTC
31590263 ATTAAAATAATATAAATCTA-AAATTAATTT
1 ATTAAAATAATATAAAT-TATAAATT-ATTT
*
31590293 -TT-AAATAGTATAAATTATAAATTATTT
1 ATTAAAATAATATAAATTATAAATTATTT
*
31590320 ATCAAAATAATATAAA
1 ATTAAAATAATATAAA
31590336 AAAATTACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 6 0.16
28 18 0.49
29 13 0.35
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (29 bp):
ATTAAAATAATATAAATTATAAATTATTT
Found at i:31592828 original size:10 final size:10
Alignment explanation
Indices: 31592813--31592845 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
31592803 TGAATTTTTT
*
31592813 TTTTTTTAAA
1 TTTTTTAAAA
31592823 TTTTTTAAAA
1 TTTTTTAAAA
31592833 -TTTTTAAAA
1 TTTTTTAAAA
31592842 TTTT
1 TTTT
31592846 AAATTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:31592855 original size:16 final size:17
Alignment explanation
Indices: 31592825--31592857 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31592815 TTTTTAAATT
*
31592825 TTTTAAAATTTTTAAAA
1 TTTTAAAATTATTAAAA
31592842 TTTT-AAATTATTAAAA
1 TTTTAAAATTATTAAAA
31592858 ATAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAAAATTATTAAAA
Found at i:31598270 original size:17 final size:18
Alignment explanation
Indices: 31598248--31598285 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
31598238 ACCATTTATA
*
31598248 TTTATATATTT-TAGAAT
1 TTTATAAATTTATAGAAT
*
31598265 TTTATAAATTTATTGAAT
1 TTTATAAATTTATAGAAT
31598283 TTT
1 TTT
31598286 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTATAAATTTATAGAAT
Found at i:31599514 original size:28 final size:28
Alignment explanation
Indices: 31599470--31599524 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
31599460 GGGGATTAAG
31599470 TTTTTTTTTAAAGAATAGATATATCATA
1 TTTTTTTTTAAAGAATAGATATATCATA
31599498 TTTTTTTTTACAA-AATAGATATATCAT
1 TTTTTTTTTA-AAGAATAGATATATCAT
31599525 GTTTGTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (28 bp):
TTTTTTTTTAAAGAATAGATATATCATA
Found at i:31599823 original size:18 final size:18
Alignment explanation
Indices: 31599797--31599835 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31599787 AAAAATATTG
*
31599797 ATTTTAATTT-TTGAAAAT
1 ATTTAAATTTATT-AAAAT
31599815 ATTTAAATTTATTAAAAT
1 ATTTAAATTTATTAAAAT
31599833 ATT
1 ATT
31599836 AATATCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTAAATTTATTAAAAT
Found at i:31600516 original size:23 final size:23
Alignment explanation
Indices: 31600489--31600546 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
31600479 TGATTTAAAG
31600489 AAATATTTATATTTATATAAT-TA
1 AAATATTTATATTT-TATAATATA
* * *
31600512 AAATATTCATGTTTTATACTATA
1 AAATATTTATATTTTATAATATA
*
31600535 ATATATTTATAT
1 AAATATTTATAT
31600547 AAACATTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (23 bp):
AAATATTTATATTTTATAATATA
Found at i:31600607 original size:22 final size:19
Alignment explanation
Indices: 31600565--31600610 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 19
31600555 TCAAAAATAT
31600565 ATTTAAAATATTTTTTAAA
1 ATTTAAAATATTTTTTAAA
31600584 ATTTAATAATATTATTGTTAAA
1 ATTTAA-AATATT-TT-TTAAA
31600606 ATTTA
1 ATTTA
31600611 TTAGTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.25
20 6 0.25
21 2 0.08
22 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTTAAAATATTTTTTAAA
Found at i:31600746 original size:17 final size:17
Alignment explanation
Indices: 31600726--31600760 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31600716 TATTTTAAAA
31600726 ATTAAAATAAAAATATT
1 ATTAAAATAAAAATATT
* *
31600743 ATTAATATAATAATATT
1 ATTAAAATAAAAATATT
31600760 A
1 A
31600761 GGTGAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAAAATAAAAATATT
Found at i:31601664 original size:33 final size:33
Alignment explanation
Indices: 31601627--31601697 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
31601617 TGCTGTCGTT
31601627 CTCTTACATCGGTGTCATTAATGGATCTACTAA
1 CTCTTACATCGGTGTCATTAATGGATCTACTAA
31601660 CTCTTACATCGGTGTCATTAATGGATCTACTAA
1 CTCTTACATCGGTGTCATTAATGGATCTACTAA
*
31601693 ATCTT
1 CTCTT
31601698 TGCATGATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (33 bp):
CTCTTACATCGGTGTCATTAATGGATCTACTAA
Found at i:31606252 original size:21 final size:20
Alignment explanation
Indices: 31606208--31606270 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
31606198 AATATATCTT
*
31606208 TATTATATATTTTTTAAATT
1 TATTATATATTTTTTAAATA
31606228 TATTATTATATTTTTTGAAA-A
1 TATTA-TATATTTTTT-AAATA
31606249 TATTA-ATGA-TTTTT-AATA
1 TATTATAT-ATTTTTTAAATA
31606267 TATT
1 TATT
31606271 TTTAAATTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 2 0.05
18 5 0.13
19 7 0.18
20 6 0.16
21 15 0.39
22 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TATTATATATTTTTTAAATA
Found at i:31614888 original size:25 final size:25
Alignment explanation
Indices: 31614860--31614910 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
31614850 ATGAACTTGT
31614860 CCCATTGCTCCCTGCATAACATTTA
1 CCCATTGCTCCCTGCATAACATTTA
31614885 CCCATTGCTCCCTGCATAACATTTA
1 CCCATTGCTCCCTGCATAACATTTA
31614910 C
1 C
31614911 AGGAGGCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.37, G:0.08, T:0.31
Consensus pattern (25 bp):
CCCATTGCTCCCTGCATAACATTTA
Found at i:31626664 original size:23 final size:22
Alignment explanation
Indices: 31626584--31626707 Score: 97
Period size: 23 Copynumber: 5.5 Consensus size: 22
31626574 GCTGGGGAAA
*
31626584 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
*
31626606 CCAGTAGGCAAACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * * *
31626629 TAGTAGGCCCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
*
31626652 CAGTAGGCACACA-AGGTGCGAAA
1 CAGTAGGCACACACA-GTGC-AAT
* * *
31626675 CAGTAAGCACACAAAGTGCGAAA
1 CAGTAGGCACACACAGTGC-AAT
*
31626698 CAGTAAGCAC
1 CAGTAGGCAC
31626708 GCTAGAGTTC
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
22 15 0.18
23 69 0.81
24 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Done.