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 11 of 126
Found at i:3747609 original size:41 final size:41
Alignment explanation
Indices: 3747548--3747627 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
3747538 ACACTTAAAA
* *
3747548 ATATTAAAACAAATATTAAAATAACAAACAAATTAAAAACG
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG
* * *
3747589 ATATTAAAACAATTCGTAAAACAACAAACAAATTGAAAA
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAA
3747628 TACAATAAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (41 bp):
ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG
Found at i:3748322 original size:24 final size:23
Alignment explanation
Indices: 3748283--3748328 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
3748273 TATTACAAGC
3748283 AAAAAAAATTAGTATTAAAAATA
1 AAAAAAAATTAGTATTAAAAATA
* *
3748306 AAAATAAAATTATTATTATAAAT
1 AAAA-AAAATTAGTATTAAAAAT
3748329 TCGGGCCGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAAAAATTAGTATTAAAAATA
Found at i:3757227 original size:30 final size:28
Alignment explanation
Indices: 3757186--3757383 Score: 138
Period size: 29 Copynumber: 6.8 Consensus size: 28
3757176 TTGGGCACTC
*
3757186 GGGGAAAAATGGTAATTTTGGGAAGATTT
1 GGGGTAAAATGGTAATTTT-GGAAGATTT
*
3757215 GGGGTCAAAATGG-AATTTTTGGGAG-TTT
1 GGGGT-AAAATGGTAA-TTTTGGAAGATTT
* *
3757243 AGGGGTAAAATGGTAATTTTGGAAAAATT
1 -GGGGTAAAATGGTAATTTTGGAAGATTT
* *
3757272 GAGGTCAAAAAT-GAAATTTTGGAAG-TTT
1 GGGGT--AAAATGGTAATTTTGGAAGATTT
* *
3757300 GGGGGTAAAATGGTAACTTTTGGAAAAATT
1 -GGGGTAAAATGGTAA-TTTTGGAAGATTT
* * *
3757330 AGGGTAAAAAATGG-AACTTTGGAA-AGTTC
1 GGGGT--AAAATGGTAATTTTGGAAGA-TTT
3757359 GAGGGTAAAATGGTAACTTTTGGAA
1 G-GGGTAAAATGGTAA-TTTTGGAA
3757384 AAATCGGGGT
Statistics
Matches: 133, Mismatches: 19, Indels: 33
0.72 0.10 0.18
Matches are distributed among these distances:
27 5 0.04
28 34 0.26
29 56 0.42
30 31 0.23
31 7 0.05
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.30
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGAAGATTT
Found at i:3757262 original size:58 final size:58
Alignment explanation
Indices: 3757186--3757674 Score: 340
Period size: 59 Copynumber: 8.3 Consensus size: 58
3757176 TTGGGCACTC
* * * *
3757186 GGGGAAAAATGGTAATTTTGGGAAGATTTGGGGTC-AAAATGGAATTTTTGGGAGTTTA
1 GGGGTAAAATGGTAATTTT-GGAAAAATTGGGGTCAAAAATGGAATTTTTGGAAGTTTA
* * *
3757244 GGGGTAAAATGGTAATTTTGGAAAAATTGAGGTCAAAAAT-GAAATTTTGGAAGTTTG
1 GGGGTAAAATGGTAATTTTGGAAAAATTGGGGTCAAAAATGGAATTTTTGGAAGTTTA
* * * *
3757301 GGGGTAAAATGGTAACTTTTGGAAAAATTAGGGTAAAAAATGGAA-CTTTGGAAAG-TTC
1 GGGGTAAAATGGTAA-TTTTGGAAAAATTGGGGTCAAAAATGGAATTTTTGG-AAGTTTA
* * * *
3757359 GAGGGTAAAATGGTAACTTTTGGAAAAATCGGGGTCAAAAATAGAATTCTTGGAAGTCTA
1 G-GGGTAAAATGGTAA-TTTTGGAAAAATTGGGGTCAAAAATGGAATTTTTGGAAGTTTA
* * *** * *
3757419 AGGGTAAAATAGTAATTTTTGGAAAAATCAAGGTTAAAAATGGAA-TTTTGGAAAGTTTG
1 GGGGTAAAATGGTAA-TTTTGGAAAAATTGGGGTCAAAAATGGAATTTTTGG-AAGTTTA
* * ** ** *
3757478 GGGGTAAAAAAT-GAAATTTTTAGAAAAATCAGGGTTTAAAATGGAATTTTTGGAAGCTTA
1 GGGGT--AAAATGGTAA-TTTTGGAAAAATTGGGGTCAAAAATGGAATTTTTGGAAGTTTA
* * * * * **
3757538 AGGGTAAAAAT-GTAATTTTTGG-AAAGTTAAGGGT-TAAAATAGAA-TTTTGGAAAAAATTA
1 GGGGT-AAAATGGTAA-TTTTGGAAAAATT-GGGGTCAAAAATGGAATTTTTGG--AAGTTTA
** * *
3757597 GGGGTTAAAAT-GTAATTTTGGAAAGTTTAGGGGT-TAAAATGTG-ATTTTTGGAAAGTTTG
1 GGGG-TAAAATGGTAATTTTGGAAAAATT-GGGGTCAAAAATG-GAATTTTTGG-AAGTTTA
3757656 GGGGTCAAAAT-GTAATTTT
1 GGGGT-AAAATGGTAATTTT
3757675 TGGATAATTT
Statistics
Matches: 359, Mismatches: 53, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
57 47 0.13
58 78 0.22
59 171 0.48
60 52 0.14
61 11 0.03
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGAAAAATTGGGGTCAAAAATGGAATTTTTGGAAGTTTA
Found at i:3757393 original size:29 final size:30
Alignment explanation
Indices: 3757184--3757472 Score: 124
Period size: 29 Copynumber: 9.9 Consensus size: 30
3757174 TTTTGGGCAC
* *
3757184 TCGGGG-AAAAATGGTAA-TTTTGGGAAGAT
1 TCGGGGTAAAAATGGTAACTTTT-GGAAAAA
* * * * ***
3757213 TTGGGGTCAAAATGG-AATTTTTGGGAGTT
1 TCGGGGTAAAAATGGTAACTTTTGGAAAAA
*
3757242 TAGGGGT-AAAATGGTAA-TTTTGGAAAAA
1 TCGGGGTAAAAATGGTAACTTTTGGAAAAA
* * * ***
3757270 TTGAGGTCAAAAAT-G-AAATTTTGGAAGTT
1 TCGGGGT-AAAAATGGTAACTTTTGGAAAAA
*
3757299 TGGGGGT-AAAATGGTAACTTTTGGAAAAA
1 TCGGGGTAAAAATGGTAACTTTTGGAAAAA
** **
3757328 TTAGGGTAAAAAATGG-AAC-TTTGGAAAGT
1 TCGGGGT-AAAAATGGTAACTTTTGGAAAAA
3757357 TCGAGGGT-AAAATGGTAACTTTTGGAAAAA
1 TCG-GGGTAAAAATGGTAACTTTTGGAAAAA
* ***
3757387 TCGGGGTCAAAAATAG-AA-TTCTTGGAAGTC
1 TCGGGGT-AAAAATGGTAACTT-TTGGAAAAA
** * *
3757417 TAAGGGT-AAAATAGTAATTTTTGGAAAAA
1 TCGGGGTAAAAATGGTAACTTTTGGAAAAA
* *
3757446 TCAAGGTTAAAAATGG-AA-TTTTGGAAA
1 TC-GGGGTAAAAATGGTAACTTTTGGAAA
3757473 GTTTGGGGGT
Statistics
Matches: 200, Mismatches: 40, Indels: 40
0.71 0.14 0.14
Matches are distributed among these distances:
27 5 0.03
28 36 0.18
29 85 0.43
30 55 0.28
31 19 0.09
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (30 bp):
TCGGGGTAAAAATGGTAACTTTTGGAAAAA
Found at i:3757485 original size:29 final size:29
Alignment explanation
Indices: 3757186--3757688 Score: 264
Period size: 30 Copynumber: 17.1 Consensus size: 29
3757176 TTGGGCACTC
*
3757186 GGGG-AAAAATGGTAATTTTGGGAAGATTT-
1 GGGGTAAAAATGG-AATTTTGGAAAG-TTTA
* *
3757215 GGGGTCAAAATGGAATTTTTGG-GAGTTTA
1 GGGGTAAAAATGGAA-TTTTGGAAAGTTTA
**
3757244 GGGGT-AAAATGGTAATTTTGGAAAAATT-
1 GGGGTAAAAATGG-AATTTTGGAAAGTTTA
* * *
3757272 GAGGTCAAAAATGAAATTTTGG-AAGTTTG
1 GGGGT-AAAAATGGAATTTTGGAAAGTTTA
**
3757301 GGGGT-AAAATGGTAACTTTTGGAAAAATTA
1 GGGGTAAAAATGG-AA-TTTTGGAAAGTTTA
* *
3757331 -GGGTAAAAAATGGAACTTTGGAAAG-TTC
1 GGGGT-AAAAATGGAATTTTGGAAAGTTTA
** *
3757359 GAGGGT-AAAATGGTAACTTTTGGAAA-AATC
1 G-GGGTAAAAATGG-AA-TTTTGGAAAGTTTA
* *
3757389 GGGGTCAAAAATAGAATTCTTGG-AAGTCTA
1 GGGGT-AAAAATGGAATT-TTGGAAAGTTTA
* * ** *
3757419 AGGGT-AAAATAGTAATTTTTGGAAAAATCA
1 GGGGTAAAAAT-GGAA-TTTTGGAAAGTTTA
* * *
3757449 AGGTTAAAAATGGAATTTTGGAAAGTTTG
1 GGGGTAAAAATGGAATTTTGGAAAGTTTA
* * ** *
3757478 GGGGTAAAAAATGAAATTTTTAGAAAAATCA
1 GGGGT-AAAAATGGAA-TTTTGGAAAGTTTA
* * *
3757509 GGGTTTAAAATGGAATTTTTGG-AAGCTTA
1 GGGGTAAAAATGGAA-TTTTGGAAAGTTTA
* *
3757538 AGGGTAAAAATGTAATTTTTGGAAAG-TTA
1 GGGGTAAAAATGGAA-TTTTGGAAAGTTTA
* * * **
3757567 AGGGTTAAAATAGAATTTTGGAAAAAATTA
1 GGGGTAAAAATGGAATTTTGG-AAAGTTTA
* *
3757597 GGGGTTAAAATGTAATTTTGGAAAGTTTA
1 GGGGTAAAAATGGAATTTTGGAAAGTTTA
* * *
3757626 GGGGTTAAAATGTGATTTTTGGAAAGTTTG
1 GGGGTAAAAATG-GAATTTTGGAAAGTTTA
* *
3757656 GGGGTCAAAATGTAATTTTTGGATAA-TTTA
1 GGGGTAAAAATGGAA-TTTTGGA-AAGTTTA
3757686 GGG
1 GGG
3757689 ACCTTTAAGG
Statistics
Matches: 369, Mismatches: 71, Indels: 67
0.73 0.14 0.13
Matches are distributed among these distances:
27 6 0.02
28 46 0.12
29 136 0.37
30 148 0.40
31 33 0.09
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTGGAAAGTTTA
Found at i:3759509 original size:17 final size:17
Alignment explanation
Indices: 3759486--3759560 Score: 114
Period size: 17 Copynumber: 4.4 Consensus size: 17
3759476 ACCTTTATTT
*
3759486 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
3759503 TTTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
* *
3759520 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
3759537 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
3759554 ATTTAAA
1 ATTTAAA
3759561 ATGAGTTTAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:3759569 original size:11 final size:11
Alignment explanation
Indices: 3759506--3759562 Score: 71
Period size: 11 Copynumber: 5.1 Consensus size: 11
3759496 ATAATAATTT
3759506 TAAATTTAAAA
1 TAAATTTAAAA
*
3759517 TAAATTTAAACT
1 TAAATTTAAA-A
*
3759529 TAAA-TTAAATT
1 TAAATTTAAA-A
3759540 TAAATTTAAAA
1 TAAATTTAAAA
3759551 TAAATTTAAAA
1 TAAATTTAAAA
3759562 T
1 T
3759563 GAGTTTAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
11 32 0.78
12 9 0.22
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:3761764 original size:2 final size:2
Alignment explanation
Indices: 3761759--3761796 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3761749 AAACTCATAC
3761759 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
3761797 TATGTTTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3764460 original size:6 final size:6
Alignment explanation
Indices: 3764435--3764501 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
3764425 TTTAAATTAT
* * *
3764435 TTTAAA TTT-TA TTTAGA TTTAAA TTT--A TCTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
3764480 TTTAAA TTT-AA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
3764502 AATAATATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
4 4 0.08
5 14 0.29
6 29 0.59
7 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:3764471 original size:17 final size:17
Alignment explanation
Indices: 3764435--3764490 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
3764425 TTTAAATTAT
*
3764435 TTTAAATTTTATTTAGA
1 TTTAAATTTTATTTAAA
3764452 TTTAAA-TTTATCTTAAA
1 TTTAAATTTTAT-TTAAA
* *
3764469 TTT-ACTTTAAATTTAAA
1 TTTAAATTT-TATTTAAA
3764486 TTTAA
1 TTTAA
3764491 TTAAATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 6 0.19
17 23 0.72
18 3 0.09
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTAAATTTTATTTAAA
Found at i:3764471 original size:28 final size:29
Alignment explanation
Indices: 3764419--3764498 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 29
3764409 GACTTTGATT
* *
3764419 TTTAAGTTTAAA-TTATTTTAAATTTTA-
1 TTTAAATTTAAATTTATATTAAATTTTAC
* *
3764446 TTTAGATTTAAATTTATCTTAAA-TTTAC
1 TTTAAATTTAAATTTATATTAAATTTTAC
3764474 TTTAAATTTAAATTTA-ATTAAATTT
1 TTTAAATTTAAATTTATATTAAATTT
3764499 AAAAATAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 19 0.42
28 26 0.58
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (29 bp):
TTTAAATTTAAATTTATATTAAATTTTAC
Found at i:3764492 original size:11 final size:11
Alignment explanation
Indices: 3764445--3764501 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
3764435 TTTAAATTTT
3764445 ATTTAGATTTAA
1 ATTTA-ATTTAA
3764457 ATTT-ATCTTAA
1 ATTTAAT-TTAA
*
3764468 ATTTACTTTAA
1 ATTTAATTTAA
3764479 ATTTAAATTT-A
1 ATTT-AATTTAA
*
3764490 ATTAAATTTAA
1 ATTTAATTTAA
3764501 A
1 A
3764502 AATAATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.18
11 22 0.58
12 9 0.24
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (11 bp):
ATTTAATTTAA
Found at i:3764494 original size:16 final size:17
Alignment explanation
Indices: 3764464--3764501 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
3764454 TAAATTTATC
*
3764464 TTAAATTTACTTTAAAT
1 TTAAATTTACATTAAAT
3764481 TTAAATTTA-ATTAAAT
1 TTAAATTTACATTAAAT
3764497 TTAAA
1 TTAAA
3764502 AATAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATTTACATTAAAT
Found at i:3766319 original size:162 final size:162
Alignment explanation
Indices: 3766045--3766413 Score: 530
Period size: 162 Copynumber: 2.3 Consensus size: 162
3766035 CGTTTTTAAT
* **
3766045 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCTTTTTTTGGCTTATTTATTCA
1 TTAATCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATTCA
*
3766110 TTTAGTCCCTGACATTTTGAATTTATTTTAATTTAATCCCTAAATCAAC-CTTTATTTAATTGCA
66 TTTAGTCCCTGACATTTTGAATTTATTTTAATTTAATCCCTAAATCAACTC-TTATTTAATTACA
*
3766174 AAATTAGCCCAACAATTTTTCAAGGTTTATAAA
130 AAATTAGCCCAACAATTTTTCAAGGTTTACAAA
*
3766207 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATTCA
1 TTAATCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATTCA
* * *
3766272 TTTAGTCCCTGAGATTTTGAATTTGTTTTAATTTAAT-CCTCAAATCAACTCTTATTTAATTATA
66 TTTAGTCCCTGACATTTTGAATTTATTTTAATTTAATCCCT-AAATCAACTCTTATTTAATTACA
* * *
3766336 AAATTGGCCCAAGAATTTTTCAAGGTTTACAAT
130 AAATTAGCCCAACAATTTTTCAAGGTTTACAAA
* * * **
3766369 TTAATCCCTTGACTGCTGGA-TGC-CTGTGGGGCTGCCACGTGTCAC
1 TTAATCCTTTGACTGTTTGACTGCAC-CAGGGGCTGCCACGTGTCAC
3766414 CAACTCTTTG
Statistics
Matches: 186, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
160 1 0.01
161 24 0.13
162 160 0.86
163 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (162 bp):
TTAATCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATTCA
TTTAGTCCCTGACATTTTGAATTTATTTTAATTTAATCCCTAAATCAACTCTTATTTAATTACAA
AATTAGCCCAACAATTTTTCAAGGTTTACAAA
Found at i:3766487 original size:29 final size:30
Alignment explanation
Indices: 3766442--3766653 Score: 201
Period size: 29 Copynumber: 7.2 Consensus size: 30
3766432 GTTTATTGGT
*
3766442 CCCCGAAACTTCCAAAATTACCA-TTTTAC
1 CCCCGAACCTTCCAAAATTACCATTTTTAC
* *
3766471 CCCCGAACCTTCTAAAATT-CCATTTTTAA
1 CCCCGAACCTTCCAAAATTACCATTTTTAC
* *
3766500 CCCCAAAACTTCCAAAAATTACCA-TTTTAC
1 CCCCGAACCTTCC-AAAATTACCATTTTTAC
*
3766530 CCCCGAACCTTCCAAAATT-CCATTTTTAA
1 CCCCGAACCTTCCAAAATTACCATTTTTAC
*
3766559 CCCCG-A-TTTCACCAAAAATTACCA-TTTTAC
1 CCCCGAACCTT--CC-AAAATTACCATTTTTAC
* * *
3766589 CCCCAAACTTTCCAAAATT-CCATTTTTAA
1 CCCCGAACCTTCCAAAATTACCATTTTTAC
*
3766618 CCCCG-A-TTTCACCAAAATTACCATTTTTAC
1 CCCCGAACCTT--CCAAAATTACCATTTTTAC
3766648 CCCCGA
1 CCCCGA
3766654 GTATCCAAAA
Statistics
Matches: 152, Mismatches: 16, Indels: 28
0.78 0.08 0.14
Matches are distributed among these distances:
27 5 0.03
28 11 0.07
29 73 0.48
30 53 0.35
31 7 0.05
32 3 0.02
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.30
Consensus pattern (30 bp):
CCCCGAACCTTCCAAAATTACCATTTTTAC
Found at i:3766538 original size:59 final size:57
Alignment explanation
Indices: 3766448--3766653 Score: 279
Period size: 59 Copynumber: 3.5 Consensus size: 57
3766438 TGGTCCCCGA
*
3766448 AACTTCC-AAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCC
1 AACTTCCAAAAATTACCATTTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCCC
3766504 AAAACTTCCAAAAATTACCATTTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCCC
1 --AACTTCCAAAAATTACCATTTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCCC
* * * *
3766563 GATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCC
1 AACTT--CCAAAAATTACCATTTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCCC
* * *
3766622 GATTTCACCAAAATTACCATTTTTACCCCCGA
1 AACTTC-CAAAAATTACCA-TTTTACCCCCGA
3766654 GTATCCAAAA
Statistics
Matches: 136, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
57 4 0.03
58 18 0.13
59 114 0.84
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.31
Consensus pattern (57 bp):
AACTTCCAAAAATTACCATTTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCCC
Found at i:3766649 original size:118 final size:117
Alignment explanation
Indices: 3766455--3766687 Score: 310
Period size: 118 Copynumber: 2.0 Consensus size: 117
3766445 CGAAACTTCC
* *
3766455 AAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATT
1 AAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCC-AAACTTCCAAAAATT
* *
3766520 ACCATTTTACCCCCGAACCT-TCCAAAA-TTCCATTTTTAACCCCGATTTCACCA
65 ACCATTTTACCCCCG-A-CTATCCAAAAGTCCCATTTTCAACCCCGATTTCACCA
* * * *
3766573 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCC-GATTTCACCAAAATT
1 AAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCCAAACTTC-CAAAAATT
* *
3766637 ACCATTTTTACCCCCGAGTATCCAAAAGTCCCGTTTTCAACCCCGATTTCA
65 ACCA-TTTTACCCCCGACTATCCAAAAGTCCCATTTTCAACCCCGATTTCA
3766688 TCGTTTCTTA
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
116 5 0.05
117 19 0.19
118 77 0.76
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.31
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCCAAACTTCCAAAAATTA
CCATTTTACCCCCGACTATCCAAAAGTCCCATTTTCAACCCCGATTTCACCA
Found at i:3766679 original size:59 final size:57
Alignment explanation
Indices: 3766455--3766687 Score: 274
Period size: 59 Copynumber: 3.9 Consensus size: 57
3766445 CGAAACTTCC
* * *
3766455 AAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCAAAACTT--CCA
1 AAAATTACCATTTTACCCCCG-A-CTTCCAAAATTCCATTTTTAACCCC--GATTTCACCA
3766514 AAAATTACCATTTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCG-A-CTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
*
3766573 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC-
1 AAAATTACCATTTTACCCCC-GAC-TTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * * *
3766631 AAAATTACCATTTTTACCCCCGAGTATCCAAAAGTCCCGTTTTCAACCCCGATTTCA
1 AAAATTACCA-TTTTACCCCCGACT-TCCAAAA-TTCCATTTTTAACCCCGATTTCA
3766688 TCGTTTCTTA
Statistics
Matches: 158, Mismatches: 9, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
57 4 0.03
58 19 0.12
59 135 0.85
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.31
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCCGACTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:3770153 original size:31 final size:25
Alignment explanation
Indices: 3770134--3770181 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3770124 ATTCAACTAT
** *
3770134 ATATATATTTTGAAAATAAAAAATA
1 ATATATAAATTGAAAATAAAAATTA
3770159 ATATATAAATTGAAAATAAAAAT
1 ATATATAAATTGAAAATAAAAAT
3770182 AACAAAATTA
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:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (25 bp):
ATATATAAATTGAAAATAAAAATTA
Found at i:3770239 original size:26 final size:26
Alignment explanation
Indices: 3770210--3770259 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3770200 TTCAAAATTT
*
3770210 TCAAAATAAATAAATATGTTTAAAAA
1 TCAAAATAAATAAATATGGTTAAAAA
* *
3770236 TCAATATAAATAAATTTGGTTAAA
1 TCAAAATAAATAAATATGGTTAAA
3770260 TTTTTAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (26 bp):
TCAAAATAAATAAATATGGTTAAAAA
Found at i:3770655 original size:26 final size:25
Alignment explanation
Indices: 3770606--3770655 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3770596 TCTCTTAAAA
* **
3770606 TTTTAATTTTTTTCAAATTTTTAAT
1 TTTTAATTTTTTTAAAATGATTAAT
3770631 TTTTAATTTTTTTAAGAATGATTAA
1 TTTTAATTTTTTTAA-AATGATTAA
3770656 AAATGAGTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (25 bp):
TTTTAATTTTTTTAAAATGATTAAT
Found at i:3790672 original size:23 final size:22
Alignment explanation
Indices: 3790635--3790678 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
3790625 ATTTTTAATT
3790635 ATAAAAATATATTTAATATTAA
1 ATAAAAATATATTTAATATTAA
*
3790657 ATAAAATTACTATTTAATATTA
1 ATAAAAATA-TATTTAATATTA
3790679 TATTTCCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAAAAATATATTTAATATTAA
Found at i:3795883 original size:19 final size:20
Alignment explanation
Indices: 3795859--3795909 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
3795849 AAAAATTCAA
*
3795859 AAAATTTATTTAGAAAA-TT
1 AAAATTTATTTAAAAAAGTT
**
3795878 AAAATTTA-AAAAAAAAGTT
1 AAAATTTATTTAAAAAAGTT
3795897 AAAATTTATTTAA
1 AAAATTTATTTAA
3795910 TTGCTAACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 5 0.20
19 18 0.72
20 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
AAAATTTATTTAAAAAAGTT
Found at i:3797242 original size:6 final size:6
Alignment explanation
Indices: 3797221--3797310 Score: 89
Period size: 6 Copynumber: 15.0 Consensus size: 6
3797211 TTAAATTGGT
*
3797221 TTTAAA TTT-TA TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
* *
3797269 TTTAAA TTT-AC CTTAAA TTTAAA TTTAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
3797311 ACAAATGTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
4 2 0.03
5 9 0.13
6 47 0.67
7 6 0.09
8 6 0.09
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:3797243 original size:17 final size:16
Alignment explanation
Indices: 3797221--3797310 Score: 94
Period size: 17 Copynumber: 5.4 Consensus size: 16
3797211 TTAAATTGGT
3797221 TTTAAATTTTATTTAAA
1 TTTAAA-TTTATTTAAA
3797238 TTTAAATTTATCTTAAA
1 TTTAAATTTAT-TTAAA
*
3797255 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
3797269 TTTAAATTTACCTTAAA
1 TTTAAATTTA-TTTAAA
3797286 TTTAAATTTAAATTTAAA
1 TTTAAATTT--ATTTAAA
3797304 TTATAAA
1 TT-TAAA
3797311 ACAAATGTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.17
15 2 0.03
16 7 0.11
17 31 0.49
18 7 0.11
19 5 0.08
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:3797253 original size:11 final size:11
Alignment explanation
Indices: 3797239--3797289 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
3797229 TTATTTAAAT
3797239 TTAAATTTATC
1 TTAAATTTATC
**
3797250 TTAAATTTAAA
1 TTAAATTTATC
*
3797261 TTTAA-TTAT-
1 TTAAATTTATC
*
3797270 TTAAATTTACC
1 TTAAATTTATC
3797281 TTAAATTTA
1 TTAAATTTA
3797290 AATTTAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 4 0.12
10 6 0.19
11 22 0.69
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (11 bp):
TTAAATTTATC
Found at i:3797275 original size:37 final size:38
Alignment explanation
Indices: 3797229--3797307 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 38
3797219 GTTTTAAATT
*
3797229 TTATTTAAATTTAAATT-TATCTTAAATTTAAATTT-AA
1 TTATTTAAATTTAAATTAAAT-TTAAATTTAAATTTAAA
**
3797266 TTATTTAAATTTACCTTAAATTTAAATTTAAATTTAAA
1 TTATTTAAATTTAAATTAAATTTAAATTTAAATTTAAA
3797304 TTAT
1 TTAT
3797308 AAAACAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 29 0.78
38 8 0.22
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (38 bp):
TTATTTAAATTTAAATTAAATTTAAATTTAAATTTAAA
Found at i:3797423 original size:30 final size:29
Alignment explanation
Indices: 3797389--3797455 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 29
3797379 ATTACAATGG
3797389 CCCAAATTGAGCCCAAATTTTAAAAAATAA
1 CCCAAATTGAGCCCAAATTTT-AAAAATAA
* *
3797419 CCCAAATTGAGCCCAAATTTTACAATTAA
1 CCCAAATTGAGCCCAAATTTTAAAAATAA
3797448 CCCAAATT
1 CCCAAATT
3797456 ACAATGACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 14 0.40
30 21 0.60
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.25
Consensus pattern (29 bp):
CCCAAATTGAGCCCAAATTTTAAAAATAA
Found at i:3799317 original size:59 final size:59
Alignment explanation
Indices: 3799184--3799556 Score: 433
Period size: 58 Copynumber: 6.4 Consensus size: 59
3799174 CCCGAAACTT
* *
3799184 CCAAAAATTACCATTTTACCCTCGAACCTTTTAAAATTCCA-TTTTAACCCCGATTTTA
1 CCAAAAATTACCATTTTACCCTCGAACCTTTTAAAATTCCATTTTTAACCTCGATTTCA
* * * *
3799242 CCAAAAATTATCATTTTACCCTTGAACCTTTTAAAATTCCATTTTTAACCTCGGTTTTA
1 CCAAAAATTACCATTTTACCCTCGAACCTTTTAAAATTCCATTTTTAACCTCGATTTCA
* *
3799301 TCAAAAATTACCATTTTACCCTCGAA-CTTTCTAAAATTCC-TTTTTAAACC-CTAATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACCTTT-TAAAATTCCATTTTT-AACCTC-GATTTCA
* * * * *
3799360 CTAAAATTTACCATTTTACCC-CTGAATCTTCTAAAATTCCA-TTTTAACC-CTAGTTTCA
1 CCAAAAATTACCATTTTACCCTC-GAACCTTTTAAAATTCCATTTTTAACCTCGA-TTTCA
* * * *
3799418 CCAAAAATTACCGTTTTACCC-CCAAACTTTCCAAAATTCCATTTTTAAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACCTTT-TAAAATTCCATTTTT-AACCTCGATTTCA
* *
3799478 CCAAAAATTACCATTTTACCCTCAAACCTTCTAAAATTCCATTTTTAATCCT-GATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACCTTTTAAAATTCCATTTTTAA-CCTCGATTTCA
3799537 CC-AAAATTACCATTTTACCC
1 CCAAAAATTACCATTTTACCC
3799557 CCTTGGTATC
Statistics
Matches: 273, Mismatches: 28, Indels: 28
0.83 0.09 0.09
Matches are distributed among these distances:
57 6 0.02
58 106 0.39
59 104 0.38
60 49 0.18
61 8 0.03
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.38
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCTCGAACCTTTTAAAATTCCATTTTTAACCTCGATTTCA
Found at i:3799363 original size:29 final size:28
Alignment explanation
Indices: 3799331--3799468 Score: 86
Period size: 29 Copynumber: 4.7 Consensus size: 28
3799321 CTCGAACTTT
*
3799331 CTAAAATTCCTTTTTAAACCCTAATTTC
1 CTAAAATTCCATTTTAAACCCTAATTTC
*
3799359 ACTAAAATTTACCATTTT-ACCCCTGAATCTT-
1 -CTAAAA-TT-CCATTTTAAACCCT-AAT-TTC
*
3799390 CTAAAATTCCATTTT-AACCCTAGTTTCAC
1 CTAAAATTCCATTTTAAACCCTAATTT--C
* * ** *
3799419 CAAAAATTACCGTTTTACCCCCAAACTTTC
1 CTAAAATT-CCATTTTAAACCCTAA-TTTC
3799449 C-AAAATTCCATTTTTAAACC
1 CTAAAATTCCA-TTTTAAACC
3799469 TCGATTTCAC
Statistics
Matches: 85, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 14 0.16
29 28 0.33
30 21 0.25
31 13 0.15
32 5 0.06
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (28 bp):
CTAAAATTCCATTTTAAACCCTAATTTC
Found at i:3799396 original size:30 final size:28
Alignment explanation
Indices: 3799159--3799410 Score: 115
Period size: 29 Copynumber: 8.6 Consensus size: 28
3799149 AAATTTTAGG
* * * * *
3799159 AAATTACATTCTAACCCCGAAACTTCCAA
1 AAATTCCATTTTAACCCTGAATCTT-CTA
* *
3799188 AAATTACCATTTT-ACCCTCGAACCTTTTA
1 AAATT-CCATTTTAACCCT-GAATCTTCTA
* * *
3799217 AAATTCCATTTTAACCCCG-ATTTTACCAA
1 AAATTCCATTTTAACCCTGAATCTT--CTA
* * *
3799246 AAATTATCATTTT-ACCCTTGAACCTTTTA
1 AAATT-CCATTTTAACCC-TGAATCTTCTA
** * *
3799275 AAATTCCATTTTTAA-CCTCGGTTTTATCAA
1 AAATTCCA-TTTTAACCCT-GAATCT-TCTA
3799305 AAATTACCATTTT-ACCCTCGAA-CTTTCTA
1 AAATT-CCATTTTAACCCT-GAATC-TTCTA
*
3799334 AAATTCCTTTTTAAACCCT-AAT-TTCACTA
1 AAATTCCATTTT-AACCCTGAATCTT--CTA
*
3799363 AAATTTACCATTTTACCCCTGAATCTTCTA
1 AAA-TT-CCATTTTAACCCTGAATCTTCTA
3799393 AAATTCCATTTTAACCCT
1 AAATTCCATTTTAACCCT
3799411 AGTTTCACCA
Statistics
Matches: 167, Mismatches: 32, Indels: 49
0.67 0.13 0.20
Matches are distributed among these distances:
27 5 0.03
28 31 0.19
29 60 0.36
30 54 0.32
31 15 0.09
32 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (28 bp):
AAATTCCATTTTAACCCTGAATCTTCTA
Found at i:3799482 original size:30 final size:31
Alignment explanation
Indices: 3799448--3799552 Score: 89
Period size: 30 Copynumber: 3.5 Consensus size: 31
3799438 CCCAAACTTT
3799448 CCAAAATT-CCATTTTTAAACCTCGATTTCA
1 CCAAAATTACCATTTTTAAACCTCGATTTCA
* * *
3799478 CCAAAAATTACCA-TTTT-ACCCTCAAACCTT--
1 CC-AAAATTACCATTTTTAAACCTC-GA-TTTCA
* *
3799508 CTAAAATT-CCATTTTTAATCCT-GATTTCA
1 CCAAAATTACCATTTTTAAACCTCGATTTCA
3799537 CCAAAATTACCATTTT
1 CCAAAATTACCATTTT
3799553 ACCCCCTTGG
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
27 2 0.03
28 4 0.07
29 17 0.29
30 19 0.33
31 11 0.19
32 5 0.09
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.37
Consensus pattern (31 bp):
CCAAAATTACCATTTTTAAACCTCGATTTCA
Found at i:3799489 original size:118 final size:116
Alignment explanation
Indices: 3799184--3799558 Score: 456
Period size: 118 Copynumber: 3.2 Consensus size: 116
3799174 CCCGAAACTT
* * * *
3799184 CCAAAAATTACCATTTTACCCTCGAACCTTT-TAAAATTCCA-TTTTAACCCCGATTTTACCAAA
1 CCAAAAATTACCATTTTACCC-CCAAACTTTCTAAAATTCCATTTTTAAACCCGATTTCACCAAA
* * * *
3799247 AATTATCATTTTACCCTTGAACCTTTTAAAATTCCATTTTTAACCTCGGTTTTA
65 AATTACCATTTTACCCCTGAACCTTCTAAAATTCCATTTTTAACCT--GTTTCA
* * * * *
3799301 TCAAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCC-TTTTTAAACCCTAATTTCACTAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAAACCC-GATTTCACCAAA
* *
3799365 ATTTACCATTTTACCCCTGAATCTTCTAAAATTCCA-TTTTAACCCTAGTTTCA
65 AATTACCATTTTACCCCTGAACCTTCTAAAATTCCATTTTTAA-CCT-GTTTCA
* *
3799418 CCAAAAATTACCGTTTTACCCCCAAACTTTCCAAAATTCCATTTTTAAACCTCGATTTCACCAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAAACC-CGATTTCACCAAA
*
3799483 AATTACCATTTTA-CCCTCAAACCTTCTAAAATTCCATTTTTAATCCTGATTTCA
65 AATTACCATTTTACCCCT-GAACCTTCTAAAATTCCATTTTTAA-CCTG-TTTCA
3799537 CC-AAAATTACCATTTTACCCCC
1 CCAAAAATTACCATTTTACCCCC
3799559 TTGGTATCCA
Statistics
Matches: 221, Mismatches: 28, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
116 5 0.02
117 88 0.40
118 111 0.50
119 17 0.08
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (116 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAAACCCGATTTCACCAAAA
ATTACCATTTTACCCCTGAACCTTCTAAAATTCCATTTTTAACCTGTTTCA
Found at i:3799581 original size:59 final size:59
Alignment explanation
Indices: 3799184--3799558 Score: 354
Period size: 59 Copynumber: 6.4 Consensus size: 59
3799174 CCCGAAACTT
* * ** * *
3799184 CCAAAAATTACCATTTTACCCTCGAACCTTTTAAAATTCCA-TTTT-AACCCCGATTTTA
1 CCAAAAATTACCATTTTACCC-CCAAACTTCCAAAATTCCATTTTTAAACCTCGATTTCA
* ** * ** * *
3799242 CCAAAAATTATCATTTTACCCTTGAACCTTTTAAAATTCCATTTTT-AACCTCGGTTTTA
1 CCAAAAATTACCATTTTACCC-CCAAACTTCCAAAATTCCATTTTTAAACCTCGATTTCA
* * * * *
3799301 TCAAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCC-TTTTTAAACC-CTAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAAC-TTCCAAAATTCCATTTTTAAACCTC-GATTTCA
* * * * * * *
3799360 CTAAAATTTACCATTTTACCCCTGAATCTTCTAAAATTCCA-TTTTAACCCTAG-TTTCA
1 CCAAAAATTACCATTTTACCCC-CAAACTTCCAAAATTCCATTTTTAAACCTCGATTTCA
*
3799418 CCAAAAATTACCGTTTTACCCCCAAACTTTCCAAAATTCCATTTTTAAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAAC-TTCCAAAATTCCATTTTTAAACCTCGATTTCA
* * *
3799478 CCAAAAATTACCATTTTACCCTCAAACCTTCTAAAATTCCATTTTTAATCCT-GATTTCA
1 CCAAAAATTACCATTTTACCCCCAAA-CTTCCAAAATTCCATTTTTAAACCTCGATTTCA
3799537 CC-AAAATTACCATTTTACCCCC
1 CCAAAAATTACCATTTTACCCCC
3799559 TTGGTATCCA
Statistics
Matches: 270, Mismatches: 36, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
57 3 0.01
58 103 0.38
59 110 0.41
60 53 0.20
61 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTCCAAAATTCCATTTTTAAACCTCGATTTCA
Found at i:3811697 original size:38 final size:37
Alignment explanation
Indices: 3811646--3811773 Score: 109
Period size: 38 Copynumber: 3.4 Consensus size: 37
3811636 CATATCCTCT
3811646 TGAAATTGAAGTAAAGCTGGATATCACGTCTTTATCTC
1 TGAAATTGAAGTAAAG-TGGATATCACGTCTTTATCTC
* ** * *
3811684 TGAAATTGAAGTAAGAGT-AAGCTCAAC-TC-CTATCCGC
1 TGAAATTGAAGTAA-AGTGGATATC-ACGTCTTTAT-CTC
*
3811721 TTGAAATTGAAGTAAAGTTGGATAACACGTCTTTATCTC
1 -TGAAATTGAAGTAAAG-TGGATATCACGTCTTTATCTC
* *
3811760 CGGAATTGAAGTAA
1 TGAAATTGAAGTAA
3811774 GAGCAACGTC
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
36 3 0.04
37 9 0.13
38 46 0.67
39 8 0.12
40 3 0.04
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (37 bp):
TGAAATTGAAGTAAAGTGGATATCACGTCTTTATCTC
Found at i:3811873 original size:106 final size:107
Alignment explanation
Indices: 3811683--3811882 Score: 312
Period size: 106 Copynumber: 1.9 Consensus size: 107
3811673 GTCTTTATCT
* *
3811683 CTGAAATTGAAGTAAGAGTAAGCTCAACTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACA
1 CTGAAATTGAAGTAAGAGCAAGATCAACTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACA
* *
3811748 CGTCTTTATCTCCGGAATTGAAGTAAGAGCAACGTCATCCGC
66 AGTCTTTATCTCCGAAATTGAAGTAAGAGCAACGTCATCCGC
** * *
3811790 CTGAAATTGAAGTAAGAGCAAGATC-TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACA
1 CTGAAATTGAAGTAAGAGCAAGATCAACTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACA
*
3811854 AGTCTTTATCTCTGAAATTGAAGTAAGAG
66 AGTCTTTATCTCCGAAATTGAAGTAAGAG
3811883 TAAGATCAAC
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
106 61 0.73
107 23 0.27
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (107 bp):
CTGAAATTGAAGTAAGAGCAAGATCAACTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACA
AGTCTTTATCTCCGAAATTGAAGTAAGAGCAACGTCATCCGC
Found at i:3811917 original size:76 final size:76
Alignment explanation
Indices: 3811790--3812705 Score: 1024
Period size: 76 Copynumber: 12.2 Consensus size: 76
3811780 CGTCATCCGC
*
3811790 CTGAAATTGAAGTAAGAGCAAGATC-TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACA
1 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
3811854 AGTCTTTATCT
66 AGTCTTTATCT
* ** * *
3811865 CTGAAATTGAAGTAAGAGTAAGATCAACTCCTATCCACTTGAAATTGAAGTAGAGTTGGATAACA
1 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
*
3811930 CGTCTTTATCT
66 AGTCTTTATCT
* * * * *
3811941 CTGAAATCGAAGTAGGAGCAAGAGCTTTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACA
1 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
* *
3812006 CGCCTTTATCT
66 AGTCTTTATCT
* * *
3812017 CCGAAATTGAAGTAAGAGCAACG-TCA--TCC---GC-C-TGAAATTGAAGT-AAG--AGA-AA-
1 CTGAAATTGAAGTAAGAGCAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAAC
* *
3812069 GA-TCTTTCCTATCCG
65 AAGTC-TT--TAT-CT
*** ** * * * *
3812084 CTTGAAATTGAAGTAA-AGTTGGATAACACGTCTTTAT-CTC-CGAAATTGAAGT-AAG--AG-C
1 C-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTATCCTCTTGAAATTGAAGTAAAGTTGGAT
* ***
3812142 AAC--GTCATCCGC-
62 AACAAGTCTTTATCT
* *
3812154 CTGAAATTGAAGTAAGAGCAAGATC-TTTCCTATCCTCTTGAAATTGAAGTAGAGTTAGATAACA
1 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
3812218 AGTCTTTATCT
66 AGTCTTTATCT
* * **
3812229 CTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATTA
1 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
3812294 AGTCTTTATCT
66 AGTCTTTATCT
* * *
3812305 CTGAAATTGAGGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
1 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
3812370 AGTCTTTATCT
66 AGTCTTTATCT
* * * *
3812381 TTGAAATTGAGGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
1 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
*
3812446 AGTCTTTATCC
66 AGTCTTTATCT
* * * *
3812457 CTGAAATCGAAGTAAGAGCAAGATCATTTCCAATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
1 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
3812522 AGTCTTTATCT
66 AGTCTTTATCT
*
3812533 CTGAAATTGAAGTAAGAGCAAGATCATTTCAC-ATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
1 CTGAAATTGAAGTAAGAGCAAGATCATTTC-CTATCCTCTTGAAATTGAAGTAAAGTTGGATAAC
3812597 AAGTCTTTATCT
65 AAGTCTTTATCT
* * *
3812609 CTGAAATTGAAGTAAGAGCAAGATCGTTTTCC-GTCCTCTTGAAATTGAAGTAAAGTTGGATAGC
1 CTGAAATTGAAGTAAGAGCAAGATC-ATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAAC
3812673 AAGTCTTTATCTCT
65 AAGTCTTTA--TCT
*
3812687 CTAAAATTGAAGTAAGAGC
1 CTGAAATTGAAGTAAGAGC
3812706 TAGACGAAGC
Statistics
Matches: 733, Mismatches: 73, Indels: 67
0.84 0.08 0.08
Matches are distributed among these distances:
63 1 0.00
64 2 0.00
65 2 0.00
66 9 0.01
67 10 0.01
68 28 0.04
69 30 0.04
70 7 0.01
71 6 0.01
72 3 0.00
74 10 0.01
75 70 0.10
76 528 0.72
77 6 0.01
78 21 0.03
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (76 bp):
CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
AGTCTTTATCT
Found at i:3812054 original size:31 final size:32
Alignment explanation
Indices: 3812019--3812174 Score: 113
Period size: 31 Copynumber: 4.6 Consensus size: 32
3812009 CTTTATCTCC
3812019 GAAATTGAAGTAAGAGCAACGTC-ATCCGCCT
1 GAAATTGAAGTAAGAGCAACGTCTATCCGCCT
* * *
3812050 GAAATTGAAGTAAGAGAAAGATCTTTCCTATCCGCTT
1 GAAATTGAAGTAAGAG-CA-A-C-GT-CTATCCGCCT
** *
3812087 GAAATTGAAGTAAAGTTGGATAACACGTCTTTAT-CTCC-
1 GAAATTGAAGT-AA----GAGCA-ACGTC--TATCCGCCT
3812125 GAAATTGAAGTAAGAGCAACGTC-ATCCGCCT
1 GAAATTGAAGTAAGAGCAACGTCTATCCGCCT
3812156 GAAATTGAAGTAAGAGCAA
1 GAAATTGAAGTAAGAGCAA
3812175 GATCTTTCCT
Statistics
Matches: 99, Mismatches: 11, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
29 2 0.02
30 3 0.03
31 35 0.35
32 6 0.06
33 4 0.04
34 1 0.01
35 1 0.01
36 1 0.01
37 20 0.20
38 14 0.14
39 3 0.03
40 4 0.04
41 3 0.03
42 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (32 bp):
GAAATTGAAGTAAGAGCAACGTCTATCCGCCT
Found at i:3812083 original size:37 final size:36
Alignment explanation
Indices: 3812042--3812281 Score: 119
Period size: 38 Copynumber: 6.6 Consensus size: 36
3812032 GAGCAACGTC
3812042 ATCCGCCTGAAATTGAAGTAAGAGAAAGATCTTTCCT
1 ATCCGCCTGAAATTGAAGTAAGAGAAAGATCTTT-CT
* * *
3812079 ATCCGCTTGAAATTGAAGTAAAGTTGGATAACA-CGTCTT-T
1 ATCCGCCTGAAATTGAAGT-AAG--AGA-AAGATC-T-TTCT
* * *
3812119 AT-CTCC-GAAATTGAAGTAAGAG-CA-A-C-GTC-
1 ATCCGCCTGAAATTGAAGTAAGAGAAAGATCTTTCT
*
3812148 ATCCGCCTGAAATTGAAGTAAGAGCAAGATCTTTCCT
1 ATCCGCCTGAAATTGAAGTAAGAGAAAGATCTTT-CT
* * *
3812185 ATCCTCTTGAAATTGAAGTAGAGTTAGATAACAAGTC-TT-T
1 ATCCGCCTGAAATTGAAGTA-AG--AGA-AA-GA-TCTTTCT
* *
3812225 AT-C-TCTGAAATTGAAGTAAGAGCAAGATCTTTTCCT
1 ATCCGCCTGAAATTGAAGTAAGAGAAAGATC-TTT-CT
* *
3812261 ATCCTCTTGAAATTGAAGTAA
1 ATCCGCCTGAAATTGAAGTAA
3812282 AGCTGGATAT
Statistics
Matches: 155, Mismatches: 21, Indels: 53
0.68 0.09 0.23
Matches are distributed among these distances:
29 3 0.02
30 3 0.02
31 16 0.10
32 5 0.03
33 3 0.02
34 5 0.03
35 4 0.03
36 4 0.03
37 42 0.27
38 43 0.28
39 3 0.02
40 11 0.07
41 6 0.04
42 5 0.03
43 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (36 bp):
ATCCGCCTGAAATTGAAGTAAGAGAAAGATCTTTCT
Found at i:3812087 original size:106 final size:106
Alignment explanation
Indices: 3811941--3812249 Score: 519
Period size: 106 Copynumber: 2.9 Consensus size: 106
3811931 GTCTTTATCT
* * *
3811941 CTGAAATCGAAGTAGGAGCAAGAGCTTTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACA
1 CTGAAATTGAAGTAAGAGCAAGATC-TTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACA
*
3812006 CGCCTTTATCTCCGAAATTGAAGTAAGAGCAACGTCATCCGC
65 CGTCTTTATCTCCGAAATTGAAGTAAGAGCAACGTCATCCGC
*
3812048 CTGAAATTGAAGTAAGAGAAAGATCTTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACAC
1 CTGAAATTGAAGTAAGAGCAAGATCTTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACAC
3812113 GTCTTTATCTCCGAAATTGAAGTAAGAGCAACGTCATCCGC
66 GTCTTTATCTCCGAAATTGAAGTAAGAGCAACGTCATCCGC
* * * *
3812154 CTGAAATTGAAGTAAGAGCAAGATCTTTCCTATCCTCTTGAAATTGAAGTAGAGTTAGATAACAA
1 CTGAAATTGAAGTAAGAGCAAGATCTTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACAC
*
3812219 GTCTTTATCTCTGAAATTGAAGTAAGAGCAA
66 GTCTTTATCTCCGAAATTGAAGTAAGAGCAA
3812250 GATCTTTTCC
Statistics
Matches: 191, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
106 170 0.89
107 21 0.11
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (106 bp):
CTGAAATTGAAGTAAGAGCAAGATCTTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACAC
GTCTTTATCTCCGAAATTGAAGTAAGAGCAACGTCATCCGC
Found at i:3812090 original size:258 final size:257
Alignment explanation
Indices: 3811638--3812553 Score: 934
Period size: 258 Copynumber: 3.6 Consensus size: 257
3811628 GATCATTTCA
* *
3811638 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGTA
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCACGTCTTTATCTCTGAAATCGAAGTAAGAGCA
** ** * * *
3811703 AGCTCAACTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACACGTCTTTATCTCCGGAATTG
66 AGAGCATTTCCTATCCGCTTGAAATTGAAGTAAAGCTGGATAACACGCCTTTATCTCCGAAATTG
3811768 AAGTAAGAGCAACGTCATCCGCCTGAAATTGAAGTAAGAGCAAGATCTTTCCTATCCTCTTGAAA
131 AAGTAAGAGCAACGTCATCCGCCTGAAATTGAAGTAAGAGCAAGATCTTTCCTATCCTCTTGAAA
*
3811833 TTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGTAAGATCAACTCC
196 TTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAG-AAGATCAACTCC
* * * * *
3811896 TATCCACTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATCGAAGTAGGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCACGTCTTTATCTCTGAAATCGAAGTAAGAGCA
* *
3811961 AGAGCTTTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACACGCCTTTATCTCCGAAATTG
66 AGAGCATTTCCTATCCGCTTGAAATTGAAGTAAAGCTGGATAACACGCCTTTATCTCCGAAATTG
* *
3812026 AAGTAAGAGCAACGTCATCCGCCTGAAATTGAAGTAAGAGAAAGATCTTTCCTATCCGCTTGAAA
131 AAGTAAGAGCAACGTCATCCGCCTGAAATTGAAGTAAGAGCAAGATCTTTCCTATCCTCTTGAAA
* *
3812091 TTGAAGTAAAGTTGGATAACACGTCTTTATCTCCGAAATTGAAGT-A-AG-AG--CAACGT-C
196 TTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGAAGATCAAC-TCC
* * * * ** * *
3812148 -ATCCGCCTGAAATTGAAGTAAGAGC--AAGATC-TTTC-CTATCCTCTTGAAATTGAAGT-AGA
1 TATCCTCTTGAAATTGAAGTAA-AGCTGGATATCACGTCTTTAT-CTC-TGAAATCGAAGTAAGA
* * * ** * * ** ***
3812207 GTTAGATAACAAGTCTTTAT-CTC-TGAAATTGAAGTAAGAGCAAGAT--CTTTTCC--TATCCT
63 G-CA-AGAGCATTTC-CTATCCGCTTGAAATTGAAGTAA-AGCTGGATAAC-ACGCCTTTAT-CT
* * * *** *
3812266 CTTGAAATTGAAGTAA-AGCTGGATATTAAGTCTTTATCTCTGAAATTGAGGTAAGAGCAAGATC
122 C-CGAAATTGAAGTAAGAGC-----A--ACGTCATCCGC-CTGAAATTGAAGTAAGAGCAAGATC
* * * *
3812330 ATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTTTGAAATTGAGGTA
178 -TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
**
3812395 AGAGCAAGATCATTTCC
242 AGAG-AAGATCAACTCC
* *
3812412 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCCCTGAAATCGAAGTAAGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCACGTCTTTATCTCTGAAATCGAAGTAAGAGCA
* * * * * * *
3812477 AGATCATTTCCAATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTG
66 AGAGCATTTCCTATCCGCTTGAAATTGAAGTAAAGCTGGATAACACGCCTTTATCTCCGAAATTG
3812542 AAGTAAGAGCAA
131 AAGTAAGAGCAA
3812554 GATCATTTCA
Statistics
Matches: 534, Mismatches: 84, Indels: 78
0.77 0.12 0.11
Matches are distributed among these distances:
248 6 0.01
249 15 0.03
250 44 0.08
251 30 0.06
252 10 0.02
253 1 0.00
254 3 0.01
256 8 0.01
257 24 0.04
258 277 0.52
259 1 0.00
260 3 0.01
262 3 0.01
263 1 0.00
264 8 0.01
265 34 0.06
266 45 0.08
267 15 0.03
268 6 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (257 bp):
TATCCTCTTGAAATTGAAGTAAAGCTGGATATCACGTCTTTATCTCTGAAATCGAAGTAAGAGCA
AGAGCATTTCCTATCCGCTTGAAATTGAAGTAAAGCTGGATAACACGCCTTTATCTCCGAAATTG
AAGTAAGAGCAACGTCATCCGCCTGAAATTGAAGTAAGAGCAAGATCTTTCCTATCCTCTTGAAA
TTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGAAGATCAACTCC
Found at i:3812380 original size:364 final size:368
Alignment explanation
Indices: 3811681--3812777 Score: 1286
Period size: 364 Copynumber: 2.9 Consensus size: 368
3811671 ACGTCTTTAT
* *
3811681 CTCTGAAATTGAAGTAAGAGTAAGCTCAACTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAA
1 CTCTGAAATTGAAGTAAGAGAAAGATCAACTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAA
*
3811746 CACGTCTTTATCTCCGGAATTGAAGTAAGAGCAACGTCATCCGCCTGAAATTGAAGTAAGAGCAA
66 CACGTCTTTATCTCCGAAATTGAAGTAAGAGCAACGTCATCCGCCTGAAATTGAAGTAAGAGCAA
3811811 GATCTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
131 GATCTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
* *** * * *
3811876 GTAAGAGTAAGATCAACTCCTATCCACTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCT
196 GTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCT
* * * * *
3811941 CTGAAATCGAAGTAGGAGCAAGAGCTTTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAACA
261 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
* * *
3812006 CGCCTTTATCTCCGAAATTGAAGTAAGAGCAACG-TCA-TCC-G
326 AGTCTTTATCTCCGAAATTGAAGTAAGAGCAA-GATCATTCCTC
**
3812047 C-CTGAAATTGAAGTAAGAGAAAGATC-TTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAA
1 CTCTGAAATTGAAGTAAGAGAAAGATCAACTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAA
3812110 CACGTCTTTATCTCCGAAATTGAAGTAAGAGCAACGTCATCCGCCTGAAATTGAAGTAAGAGCAA
66 CACGTCTTTATCTCCGAAATTGAAGTAAGAGCAACGTCATCCGCCTGAAATTGAAGTAAGAGCAA
*
3812175 GATCTTTCCTATCCTCTTGAAATTGAAGTAGAGTTAGATAACAAGTCTTTATCTCTGAAATTGAA
131 GATCTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
* **
3812240 GTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATTAAGTCTTTATCT
196 GTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCT
* * *
3812305 CTGAAATTGAGGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
261 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
** *
3812370 AGTCTTTATCTTTGAAATTGAGGTAAGAGCAAGATCATTTCCTATC
326 AGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGATCA-TTCC--TC
** * * * * ***
3812416 CTCTTGAAATTGAAGTAA-AGCTGGATATCAAGTCTTTATCC-C-TGAAATCGAAGTAAGAGCAA
1 CTC-TGAAATTGAAGTAAGAG--AAAGATCAACTC-CTATCCGCTTGAAATTGAAGTAA-AGTTG
** ** * * ***
3812478 GAT--CATTTC-CAATCCTCTTGAAATTGAAGTAA-AGCTGGATATCAAGTCTTTATCTCTGAAA
61 GATAACACGTCTTTAT-CTC-CGAAATTGAAGTAAGAGC---A-A-C--GTCATCCGC-CTGAAA
3812539 TTGAAGTAAGAGCAAGATCATTTCAC-ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCT
116 TTGAAGTAAGAGCAAGATC-TTTC-CTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCT
*
3812603 TTATCTCTGAAATTGAAGTAAGAGCAAGATCGTTTTCC-GTCCTCTTGAAATTGAAGTAAAGTTG
179 TTATCTCTGAAATTGAAGTAAGAGCAAGATC-TTTTCCTATCCTCTTGAAATTGAAGTAAAGTTG
* *
3812667 GATAGCAAGTCTTTATCTCTCTAAAATTGAAGTAAGAGCTAGACGAAGCATCAAATATCACTTCC
243 GATAACAAGTCTTTA--TCTCTGAAATTGAAGT-A-AG--AG-C-AAG-ATC----AT---TTCC
*
3812732 TATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTC
292 TATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTC
3812778 TCTGAAGAGC
Statistics
Matches: 630, Mismatches: 59, Indels: 54
0.85 0.08 0.07
Matches are distributed among these distances:
363 1 0.00
364 305 0.48
365 23 0.04
366 4 0.01
369 1 0.00
370 5 0.01
371 24 0.04
372 30 0.05
373 8 0.01
374 6 0.01
375 1 0.00
376 1 0.00
378 5 0.01
379 25 0.04
380 109 0.17
381 7 0.01
382 14 0.02
383 1 0.00
384 2 0.00
386 2 0.00
387 1 0.00
388 3 0.00
389 3 0.00
393 2 0.00
396 47 0.07
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (368 bp):
CTCTGAAATTGAAGTAAGAGAAAGATCAACTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATAA
CACGTCTTTATCTCCGAAATTGAAGTAAGAGCAACGTCATCCGCCTGAAATTGAAGTAAGAGCAA
GATCTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCT
CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACA
AGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGATCATTCCTC
Found at i:3812614 original size:38 final size:37
Alignment explanation
Indices: 3812192--3812706 Score: 239
Period size: 38 Copynumber: 13.5 Consensus size: 37
3812182 CCTATCCTCT
* *
3812192 TGAAATTGAAGTAGAGTTAGATAACAAGTCTTTATCTC
1 TGAAATTGAAGTAGAGCTGGAT-ACAAGTCTTTATCTC
** *** *
3812230 TGAAATTGAAGTAAGAGCAAGAT-CTTTTC-CTATCCTC
1 TGAAATTGAAGT-AGAGCTGGATACAAGTCTTTAT-CTC
* *
3812267 TTGAAATTGAAGTAAAGCTGGATATTAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGCTGGATA-CAAGTCTTTATCTC
* ** ** *
3812306 TGAAATTGAGGTAAGAGCAAGAT-CATTTC-CTATCCTC
1 TGAAATTGAAGT-AGAGCTGGATACAAGTCTTTAT-CTC
* *
3812343 TTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTT
1 -TGAAATTGAAGTAGAGCTGGATA-CAAGTCTTTATCTC
* ** ** *
3812382 TGAAATTGAGGTAAGAGCAAGAT-CATTTC-CTATCCTC
1 TGAAATTGAAGT-AGAGCTGGATACAAGTCTTTAT-CTC
* *
3812419 TTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCCC
1 -TGAAATTGAAGTAGAGCTGGATA-CAAGTCTTTATCTC
* ** ** **
3812458 TGAAATCGAAGTAAGAGCAAGAT-CATTTC-CAATCCTC
1 TGAAATTGAAGT-AGAGCTGGATACAAGTCTTTAT-CTC
*
3812495 TTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGCTGGATA-CAAGTCTTTATCTC
** ** **
3812534 TGAAATTGAAGTAAGAGCAAGAT-CATTTC-ACATCCTC
1 TGAAATTGAAGT-AGAGCTGGATACAAGTCTTTAT-CTC
*
3812571 TTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGCTGGAT-ACAAGTCTTTATCTC
** *
3812610 TGAAATTGAAGTAAGAGCAAGAT-C--GT-TTTCCGTCCTC
1 TGAAATTGAAGT-AGAGCTGGATACAAGTCTTT--AT-CTC
* *
3812647 TTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCTC
1 -TGAAATTGAAGTAGAGCTGGATA-CAAGTCTTTA--TCTC
*
3812688 TAAAATTGAAGTAAGAGCT
1 TGAAATTGAAGT-AGAGCT
3812707 AGACGAAGCA
Statistics
Matches: 345, Mismatches: 89, Indels: 83
0.67 0.17 0.16
Matches are distributed among these distances:
34 3 0.01
35 2 0.01
36 14 0.04
37 76 0.22
38 138 0.40
39 75 0.22
40 24 0.07
41 9 0.03
42 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (37 bp):
TGAAATTGAAGTAGAGCTGGATACAAGTCTTTATCTC
Found at i:3813094 original size:6 final size:6
Alignment explanation
Indices: 3813073--3813162 Score: 80
Period size: 6 Copynumber: 15.0 Consensus size: 6
3813063 TTAAATTGAT
*
3813073 TTTAAA TTT-TA TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
* * *
3813121 TTTATA TTT-AC CTTAAA TTTAAA TTTAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
3813163 ACAAATGTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
4 2 0.03
5 8 0.12
6 47 0.69
7 6 0.09
8 5 0.07
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:3813095 original size:17 final size:16
Alignment explanation
Indices: 3813073--3813162 Score: 85
Period size: 17 Copynumber: 5.4 Consensus size: 16
3813063 TTAAATTGAT
3813073 TTTAAATTTTATTTAAA
1 TTTAAA-TTTATTTAAA
3813090 TTTAAATTTATCTTAAA
1 TTTAAATTTAT-TTAAA
*
3813107 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
* *
3813121 TTTATATTTACCTTAAA
1 TTTAAATTTA-TTTAAA
3813138 TTTAAATTTAAATTTAAA
1 TTTAAATTT--ATTTAAA
3813156 TTATAAA
1 TT-TAAA
3813163 ACAAATGTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
14 10 0.16
15 2 0.03
16 7 0.11
17 30 0.49
18 7 0.11
19 5 0.08
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:3813130 original size:37 final size:38
Alignment explanation
Indices: 3813081--3813159 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
3813071 ATTTTAAATT
*
3813081 TTATTTAAATTTAAATT-TATCTTAAATTTAAATTT-AA
1 TTATTTAAATTTAAATTAAAT-TTAAATTTAAATTTAAA
* **
3813118 TTATTTATATTTACCTTAAATTTAAATTTAAATTTAAA
1 TTATTTAAATTTAAATTAAATTTAAATTTAAATTTAAA
3813156 TTAT
1 TTAT
3813160 AAAACAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 28 0.78
38 8 0.22
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (38 bp):
TTATTTAAATTTAAATTAAATTTAAATTTAAATTTAAA
Found at i:3815121 original size:59 final size:58
Alignment explanation
Indices: 3815050--3815358 Score: 370
Period size: 59 Copynumber: 5.3 Consensus size: 58
3815040 CGAAACTTCT
3815050 AAAAATTACCATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCCTAATTTCACC
1 AAAAATTACCATTTTACCC-CGAACCTTCTAAAATTCCATTTTTAACCCTAATTTCACC
* * * * *
3815109 AAAAATTACCATTTTACCCCCAAACCTTTTAAAATTCCA-TTTTAACCGTAATTTTATC
1 AAAAATTACCATTTTA-CCCCGAACCTTCTAAAATTCCATTTTTAACCCTAATTTCACC
* * *** *
3815167 GAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGGTTTCACT
1 AAAAATTACCATTTTA-CCCCGAACCTTCTAAAATTCCATTTTTAACCCTAATTTCACC
* *
3815226 AAAATTTACCATTTTACCCCTGAATCTTCTAAAATTCCATTTTTAAACCCTAATTTCACC
1 AAAAATTACCATTTTACCCC-GAACCTTCTAAAATTCCATTTTT-AACCCTAATTTCACC
* * * ** *
3815286 AAAAATTACCATTTTACCCCTAAACCTTTTAAAATTCCATTCTTAACCCCGATTTTACC
1 AAAAATTACCATTTTACCCC-GAACCTTCTAAAATTCCATTTTTAACCCTAATTTCACC
*
3815345 -AAAATTACAATTTT
1 AAAAATTACCATTTT
3815359 TCCCTCGGGT
Statistics
Matches: 213, Mismatches: 33, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
58 68 0.32
59 92 0.43
60 53 0.25
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCGAACCTTCTAAAATTCCATTTTTAACCCTAATTTCACC
Found at i:3815200 original size:117 final size:119
Alignment explanation
Indices: 3815050--3815358 Score: 401
Period size: 117 Copynumber: 2.6 Consensus size: 119
3815040 CGAAACTTCT
* * **
3815050 AAAAATTACCATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCCTAATTTCACCAAAAAT
1 AAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
* * * *
3815115 TACCATTTTACCCCCAAACCTTTTAAAATTCCA-TTTT-AACCGTAATTTTATC
66 TACCATTTTACCCCCAAACCTTCTAAAATTCCATTTTTAAACCCTAATTTCACC
* * * *
3815167 GAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGGTTTCACTAAAATT
1 AAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
** *
3815232 TACCATTTTACCCCTGAATCTTCTAAAATTCCATTTTTAAACCCTAATTTCACC
66 TACCATTTTACCCCCAAACCTTCTAAAATTCCATTTTTAAACCCTAATTTCACC
** * *
3815286 AAAAATTACCATTTTACCCCTAAACCTTT-TAAAATTCCATTCTTAACCCCGATTTTACC-AAAA
1 AAAAATTACCATTTTACCCCCGAA-CTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
*
3815349 TTACAATTTT
65 TTACCATTTT
3815359 TCCCTCGGGT
Statistics
Matches: 165, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
117 86 0.52
118 16 0.10
119 59 0.36
120 4 0.02
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37
Consensus pattern (119 bp):
AAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
TACCATTTTACCCCCAAACCTTCTAAAATTCCATTTTTAAACCCTAATTTCACC
Found at i:3815269 original size:29 final size:29
Alignment explanation
Indices: 3815045--3815335 Score: 131
Period size: 30 Copynumber: 9.8 Consensus size: 29
3815035 GATCCCGAAA
*
3815045 CTTCTAAAAATTACCATTTTA-CCCTCGAAC
1 CTTCT-AAAATTACCATTTTACCCCT-GAAT
*
3815075 CTTCTAAAATT-CCATTTTTAACCCT-AAT
1 CTTCTAAAATTACCA-TTTTACCCCTGAAT
* ** *
3815103 -TTCACCAAAAATTACCATTTTACCCCCAAAC
1 CTT---CTAAAATTACCATTTTACCCCTGAAT
* * *
3815134 CTTTTAAAATT-CCATTTTAACCGT-AATT
1 CTTCTAAAATTACCATTTTACCCCTGAA-T
* * *
3815162 TTATCGAAAATTACCATTTTACCCCCGAA-
1 CT-TCTAAAATTACCATTTTACCCCTGAAT
* **
3815191 CTTTCTAAAATT-CCATTTTTAACCCCGGTTT
1 C-TTCTAAAATTACCA-TTTT-ACCCCTGAAT
*
3815222 C-ACTAAAATTTACCATTTTACCCCTGAAT
1 CTTCTAAAA-TTACCATTTTACCCCTGAAT
*
3815251 CTTCTAAAATT-CCATTTTTAAACCCT-AAT
1 CTTCTAAAATTACCA-TTTT-ACCCCTGAAT
* * *
3815280 -TTCACCAAAAATTACCATTTTACCCCTAAAC
1 CTT---CTAAAATTACCATTTTACCCCTGAAT
*
3815311 CTTTTAAAATT-CCATTCTTAACCCC
1 CTTCTAAAATTACCATT-TT-ACCCC
3815336 GATTTTACCA
Statistics
Matches: 199, Mismatches: 33, Indels: 58
0.69 0.11 0.20
Matches are distributed among these distances:
27 4 0.02
28 29 0.15
29 67 0.34
30 68 0.34
31 24 0.12
32 7 0.04
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (29 bp):
CTTCTAAAATTACCATTTTACCCCTGAAT
Found at i:3817075 original size:18 final size:19
Alignment explanation
Indices: 3817052--3817088 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3817042 ACAACATTTT
*
3817052 TATT-AAATTATTTTAGAA
1 TATTAAAATTATTTGAGAA
3817070 TATTAAAATTATTTGAGAA
1 TATTAAAATTATTTGAGAA
3817089 CATGACAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
TATTAAAATTATTTGAGAA
Found at i:3823038 original size:14 final size:16
Alignment explanation
Indices: 3823013--3823053 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
3823003 TTAATGAGGT
*
3823013 ATTTGATTGTTGTGTT-
1 ATTTG-TTGTTGAGTTG
3823029 ATTT-TTGTTGAGTTG
1 ATTTGTTGTTGAGTTG
3823044 ATTTGTTGTT
1 ATTTGTTGTT
3823054 TTTGTAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 9 0.41
15 4 0.18
16 9 0.41
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.63
Consensus pattern (16 bp):
ATTTGTTGTTGAGTTG
Found at i:3831416 original size:31 final size:32
Alignment explanation
Indices: 3831345--3831434 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 32
3831335 TAACGAAGGT
*
3831345 TAAATAACACG-AAATAAAATAATTAAGCAGA
1 TAAATAATACGAAAATAAAATAATTAAGCAGA
* *
3831376 TAAATAATACTAAAATAAAA-AATTAA-TAGAA
1 TAAATAATACGAAAATAAAATAATTAAGCAG-A
3831407 TATAA-AATACGAAAA-AAATGATAATTAA
1 TA-AATAATACGAAAATAAA--ATAATTAA
3831435 AACTAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
30 5 0.10
31 27 0.55
32 11 0.22
33 6 0.12
ACGTcount: A:0.64, C:0.06, G:0.07, T:0.23
Consensus pattern (32 bp):
TAAATAATACGAAAATAAAATAATTAAGCAGA
Found at i:3831587 original size:30 final size:29
Alignment explanation
Indices: 3831509--3831851 Score: 171
Period size: 29 Copynumber: 11.7 Consensus size: 29
3831499 ATGTCCGGGA
* *
3831509 GTAAAATGGTAA-TTTTGGATACTTT-GGGG
1 GTAAAATGG-AATTTTTGGA-AATTTCGAGG
3831538 GTAAAATGGTAATTTTTTGGAAATTTCGAGG
1 GTAAAATGG-AA-TTTTTGGAAATTTCGAGG
* * *
3831569 TTAAAAATGGAATTTTTGGATA-TTCGGGG
1 GT-AAAATGGAATTTTTGGAAATTTCGAGG
* *
3831598 GTAAAATAGTAATTTTTGAAAAGTTT--AGG
1 GTAAAAT-GGAATTTTTGGAAA-TTTCGAGG
* * *
3831627 GTCAAAATTGGAATTTTTGGACATAT-GGGG
1 GT-AAAA-TGGAATTTTTGGAAATTTCGAGG
* *
3831657 GTAAAATGGTAATTTTT-AAAAGTTTC-AAG
1 GTAAAATGG-AATTTTTGGAAA-TTTCGAGG
* *
3831686 GTCAAAATGGAATTTTTAGACA-TTCGAGG
1 GT-AAAATGGAATTTTTGGAAATTTCGAGG
3831715 GTAAAATGGTAATTTTT-GAAAGGTTT-G-GG
1 GTAAAATGG-AATTTTTGGAAA--TTTCGAGG
* * *
3831744 GTTAAAATGGAATTTTTAGATA-TCCGAGG
1 G-TAAAATGGAATTTTTGGAAATTTCGAGG
* * *
3831773 GTAAAATGGTAA--TTTAGAAGTTTCG-TG
1 GTAAAATGG-AATTTTTGGAAATTTCGAGG
* * *
3831800 ATCAAAAAAGGAATTTTTGGAAGTTTCGA-G
1 GT--AAAATGGAATTTTTGGAAATTTCGAGG
*
3831830 GTCAAAATGGAATTTTTTGAAA
1 GT-AAAATGGAATTTTTGGAAA
3831852 GTTTGGGGGT
Statistics
Matches: 245, Mismatches: 38, Indels: 62
0.71 0.11 0.18
Matches are distributed among these distances:
27 9 0.04
28 37 0.15
29 107 0.44
30 67 0.27
31 18 0.07
32 7 0.03
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
GTAAAATGGAATTTTTGGAAATTTCGAGG
Found at i:3831647 original size:59 final size:58
Alignment explanation
Indices: 3831511--3831787 Score: 310
Period size: 58 Copynumber: 4.7 Consensus size: 58
3831501 GTCCGGGAGT
* * * *
3831511 AAAATGGTAA-TTTTGGATACTTTGGGGGTAAAATGGTAATTTTTTGGAAA-TTTCGAGGTTA
1 AAAATGG-AATTTTTGGATA-TTCGGGGGTAAAATGGTAA-TTTTTGAAAAGTTT--AGGGTC
*
3831572 AAAATGGAATTTTTGGATATTCGGGGGTAAAATAGTAATTTTTGAAAAGTTTAGGGTC
1 AAAATGGAATTTTTGGATATTCGGGGGTAAAATGGTAATTTTTGAAAAGTTTAGGGTC
* *
3831630 AAAATTGGAATTTTTGGACATAT-GGGGGTAAAATGGTAATTTTT-AAAAGTTTCAAGGTC
1 AAAA-TGGAATTTTTGGATAT-TCGGGGGTAAAATGGTAATTTTTGAAAAGTTT-AGGGTC
* * * * * *
3831689 AAAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGAAAGGTTTGGGGTT
1 AAAATGGAATTTTTGGATATTCGGGGGTAAAATGGTAATTTTTGAAAAGTTTAGGGTC
* * *
3831747 AAAATGGAATTTTTAGATATCCGAGGGTAAAATGGTAATTT
1 AAAATGGAATTTTTGGATATTCGGGGGTAAAATGGTAATTT
3831788 AGAAGTTTCG
Statistics
Matches: 193, Mismatches: 16, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
57 1 0.01
58 93 0.48
59 60 0.31
60 23 0.12
61 16 0.08
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAATGGAATTTTTGGATATTCGGGGGTAAAATGGTAATTTTTGAAAAGTTTAGGGTC
Found at i:3831854 original size:30 final size:30
Alignment explanation
Indices: 3831540--3831867 Score: 140
Period size: 30 Copynumber: 11.2 Consensus size: 30
3831530 CTTTGGGGGT
*
3831540 AAAATGGTAATTTTTTGGAAA-TTTCGAGGTTA
1 AAAATGG-AATTTTTT-GAAAGTTTCGAGG-TC
* * *
3831572 AAAATGGAATTTTTGGATA--TTCGGGGGT-
1 AAAATGGAATTTTTTGAAAGTTTC-GAGGTC
* *
3831600 AAAATAGTAA-TTTTTGAAAAGTTTAG-GGTC
1 AAAAT-GGAATTTTTTG-AAAGTTTCGAGGTC
* * * * *
3831630 AAAATTGGAATTTTTGGACA-TATGGGGGT-
1 AAAA-TGGAATTTTTTGAAAGTTTCGAGGTC
* *
3831659 AAAATGGTAA-TTTTTAAAAGTTTCAAGGTC
1 AAAATGG-AATTTTTTGAAAGTTTCGAGGTC
* *
3831689 AAAATGGAATTTTTAGACA--TTCGAGGGT-
1 AAAATGGAATTTTTTGAAAGTTTCGA-GGTC
* *
3831717 AAAATGGTAA-TTTTTGAAAGGTTT-GGGGTT
1 AAAATGG-AATTTTTTGAAA-GTTTCGAGGTC
* * *
3831747 AAAATGGAATTTTTAGATA--TCCGAGGGT-
1 AAAATGGAATTTTTTGAAAGTTTCGA-GGTC
* * *
3831775 AAAATGGTAA--TTTAG-AAGTTTCGTGATC
1 AAAATGG-AATTTTTTGAAAGTTTCGAGGTC
* *
3831803 AAAAAAGGAA-TTTTTGGAAGTTTCGAGGTC
1 -AAAATGGAATTTTTTGAAAGTTTCGAGGTC
* *
3831833 AAAATGGAATTTTTTGAAAGTTTGGGGGTC
1 AAAATGGAATTTTTTGAAAGTTTCGAGGTC
3831863 AAAAT
1 AAAAT
3831868 ATAGTTTTTG
Statistics
Matches: 224, Mismatches: 42, Indels: 62
0.68 0.13 0.19
Matches are distributed among these distances:
26 1 0.00
27 8 0.04
28 50 0.22
29 61 0.27
30 80 0.36
31 17 0.08
32 7 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTTGAAAGTTTCGAGGTC
Found at i:3831861 original size:116 final size:114
Alignment explanation
Indices: 3831536--3831867 Score: 314
Period size: 116 Copynumber: 2.8 Consensus size: 114
3831526 GATACTTTGG
* * * * * * *
3831536 GGGTAAAATGGTAATTTTTTGGAAA-TTTCGAGGTTAAAAATGGAATTTTTGGATATTCGGGGGT
1 GGGTAAAATGGTAA--TTTT-AAAAGTTTCAAGATCAAAAA-GGAATTTTTAGACATTCGAGGGT
* * * * *
3831600 AAAATAGTAATTTTTGAAAAGTTTAGGGTCAAAATTGGAATTTTTGGACATATGG
62 AAAATGGTAATTTTTG-AAAGTTTGGGGTCAAAA-TGGAATTTTTAGACATACGA
* *
3831655 GGGTAAAATGGTAATTTTTAAAAGTTTCAAGGTCAAAATGGAATTTTTAGACATTCGAGGGTAAA
1 GGGTAAAATGGTAA-TTTTAAAAGTTTCAAGATCAAAAAGGAATTTTTAGACATTCGAGGGTAAA
* * *
3831720 ATGGTAATTTTTGAAAGGTTTGGGGTTAAAATGGAATTTTTAGATATCCGA
65 ATGGTAATTTTTGAAA-GTTTGGGGTCAAAATGGAATTTTTAGACATACGA
* ** *
3831771 GGGTAAAATGGTAA-TTTAGAAGTTTCGTGATCAAAAAAGGAATTTTTGGA-AGTTTCGA-GGTC
1 GGGTAAAATGGTAATTTTAAAAGTTTCAAGATC-AAAAAGGAATTTTTAGACA--TTCGAGGGT-
3831833 AAAATGG-AATTTTTTGAAAGTTTGGGGGTCAAAAT
62 AAAATGGTAA-TTTTTGAAAGTTT-GGGGTCAAAAT
3831868 ATAGTTTTTG
Statistics
Matches: 183, Mismatches: 22, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
114 15 0.08
115 24 0.13
116 63 0.34
117 50 0.27
118 17 0.09
119 14 0.08
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (114 bp):
GGGTAAAATGGTAATTTTAAAAGTTTCAAGATCAAAAAGGAATTTTTAGACATTCGAGGGTAAAA
TGGTAATTTTTGAAAGTTTGGGGTCAAAATGGAATTTTTAGACATACGA
Found at i:3833684 original size:17 final size:17
Alignment explanation
Indices: 3833658--3833746 Score: 97
Period size: 17 Copynumber: 5.2 Consensus size: 17
3833648 TTTTTTAATT
*
3833658 AATTTTAATTTAAAATA
1 AATTTAAATTTAAAATA
* *
3833675 AATTTGAATTTAAAGTA
1 AATTTAAATTTAAAATA
* *
3833692 AATTTAAACTCAAAATA
1 AATTTAAATTTAAAATA
*
3833709 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
* * *
3833726 AATTCAAACTTAAAGTA
1 AATTTAAATTTAAAATA
3833743 AATT
1 AATT
3833747 AAAAAAAATA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 59 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:3840258 original size:89 final size:89
Alignment explanation
Indices: 3840095--3840360 Score: 410
Period size: 89 Copynumber: 3.0 Consensus size: 89
3840085 GCATATGTCT
* * * *
3840095 GGTTACATGTAAGA-TATTACAGTTAATTATTATCGGATG-TGACCTTATTAGCTGATTGAATAT
1 GGTTACATGTAA-ACTATTAAAGTTAATTCTTATTGGATGTTGACCTTATTAGCGGATTGAATAT
*
3840158 ACTATGACATTGTATTTCATTTCTC
65 AGTATGACATTGTATTTCATTTCTC
*
3840183 GGTTACATGTAAACTATTAAAGTTAATTCTTATTGGATGTTGACCTTATTAGCGGATTGAATGTA
1 GGTTACATGTAAACTATTAAAGTTAATTCTTATTGGATGTTGACCTTATTAGCGGATTGAATATA
3840248 GTATGACATTGTATTTCATTTCTC
66 GTATGACATTGTATTTCATTTCTC
* * *
3840272 GGTTACATGTAAACTGTTAAAGTTAATTCTTATTGGATCTTAACCTTATTAGCGGATTGAATATA
1 GGTTACATGTAAACTATTAAAGTTAATTCTTATTGGATGTTGACCTTATTAGCGGATTGAATATA
* *
3840337 GTATGACATTGTGTTTCCTTTCTC
66 GTATGACATTGTATTTCATTTCTC
3840361 AAGGAAAATA
Statistics
Matches: 164, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
87 1 0.01
88 34 0.21
89 129 0.79
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (89 bp):
GGTTACATGTAAACTATTAAAGTTAATTCTTATTGGATGTTGACCTTATTAGCGGATTGAATATA
GTATGACATTGTATTTCATTTCTC
Found at i:3848643 original size:14 final size:16
Alignment explanation
Indices: 3848616--3848648 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3848606 GGGGCTACTG
3848616 TTATGGTAGTTTG-CT
1 TTATGGTAGTTTGCCT
3848631 TTATGGT-GTTTGCCT
1 TTATGGTAGTTTGCCT
3848646 TTA
1 TTA
3848649 GGCTTAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.12, C:0.09, G:0.24, T:0.55
Consensus pattern (16 bp):
TTATGGTAGTTTGCCT
Found at i:3850296 original size:22 final size:23
Alignment explanation
Indices: 3850251--3850301 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
3850241 TCAACCAAAA
** *
3850251 TTTTATTTTAATATTTATACATT
1 TTTTATTTTAATATGCACACATT
3850274 TTTTATTTTAATATGCACA-ATT
1 TTTTATTTTAATATGCACACATT
*
3850296 TATTAT
1 TTTTAT
3850302 CTCCACAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTATTTTAATATGCACACATT
Found at i:3850443 original size:22 final size:23
Alignment explanation
Indices: 3850416--3850474 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
3850406 TGCAATTAGT
*
3850416 ATTGTTAATTTGATG-TATTTATG
1 ATTGTTAATTTCATGTTA-TTATG
3850439 -TTGTTAATTTCATGTTATTATG
1 ATTGTTAATTTCATGTTATTATG
3850461 ATTAGTTAATTTCA
1 ATT-GTTAATTTCA
3850475 AATCATACGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 18 0.56
23 4 0.12
24 10 0.31
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (23 bp):
ATTGTTAATTTCATGTTATTATG
Found at i:3853100 original size:17 final size:18
Alignment explanation
Indices: 3853069--3853102 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3853059 AATTTAACTT
3853069 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
3853087 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
3853103 TTATATACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:3855798 original size:15 final size:15
Alignment explanation
Indices: 3855778--3855825 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
3855768 AAGTTTAGAA
3855778 TTTAGTTTTTTTATT
1 TTTAGTTTTTTTATT
*** *
3855793 TTTAGTTTTAGGA-A
1 TTTAGTTTTTTTATT
3855807 TTTAGTTTTTTTATT
1 TTTAGTTTTTTTATT
3855822 TTTA
1 TTTA
3855826 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (15 bp):
TTTAGTTTTTTTATT
Found at i:3855810 original size:29 final size:28
Alignment explanation
Indices: 3855771--3855840 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 28
3855761 ATATCGAAAG
3855771 TTTAGAATTTAGTTTTTTTATTTTTAGT
1 TTTAGAATTTAGTTTTTTTATTTTTAGT
*
3855799 TTTAGGAATTTAGTTTTTTTATTTTTATAT
1 TTTA-GAATTTAGTTTTTTTATTTTTA-GT
*
3855829 TTTAAAATTTAG
1 TTTAGAATTTAG
3855841 GTTTAACTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 4 0.11
29 29 0.76
30 5 0.13
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (28 bp):
TTTAGAATTTAGTTTTTTTATTTTTAGT
Found at i:3863912 original size:3 final size:3
Alignment explanation
Indices: 3863904--3863932 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3863894 TCCACTTGCC
3863904 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3863933 TTCAATCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3865452 original size:14 final size:13
Alignment explanation
Indices: 3865429--3865500 Score: 55
Period size: 13 Copynumber: 5.6 Consensus size: 13
3865419 ATTTAATTGT
3865429 TAATATATATTAA
1 TAATATATATTAA
3865442 TAATCATATATT-A
1 TAAT-ATATATTAA
3865455 T-AT-TATATT-A
1 TAATATATATTAA
*
3865465 TATTATATTATT-A
1 TAATATA-TATTAA
*
3865478 TATTATACTATGTAA
1 TAATATA-TAT-TAA
3865493 TAATATAT
1 TAATATAT
3865501 TATCTATTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
10 8 0.16
11 1 0.02
12 4 0.08
13 21 0.42
14 9 0.18
15 7 0.14
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (13 bp):
TAATATATATTAA
Found at i:3865458 original size:5 final size:5
Alignment explanation
Indices: 3865448--3865503 Score: 62
Period size: 5 Copynumber: 11.6 Consensus size: 5
3865438 TTAATAATCA
* * * *
3865448 TATAT TATAT TATAT TATAT TATA- T-TAT TATAT TATAC TATGT AATAA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
3865496 TATAT TAT
1 TATAT TAT
3865504 CTATTATAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 37 0.90
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:3865698 original size:21 final size:21
Alignment explanation
Indices: 3865655--3865696 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3865645 TGAAGTATTA
**
3865655 ATTATTATATATGTTTTGTTT
1 ATTATTATATATGTAATGTTT
3865676 ATTATTATATTATGTAATGTT
1 ATTATTATA-TATGTAATGTT
3865697 ATATCATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (21 bp):
ATTATTATATATGTAATGTTT
Found at i:3866557 original size:15 final size:15
Alignment explanation
Indices: 3866537--3866566 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3866527 TAGATTTAGG
*
3866537 TTTTTTTAACTCGAA
1 TTTTTTGAACTCGAA
3866552 TTTTTTGAACTCGAA
1 TTTTTTGAACTCGAA
3866567 ATACATGAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (15 bp):
TTTTTTGAACTCGAA
Found at i:3870694 original size:16 final size:16
Alignment explanation
Indices: 3870673--3870723 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 16
3870663 AAATTATTTT
3870673 TTAAAATATAAAATTA
1 TTAAAATATAAAATTA
* *
3870689 TTAAAAT-T--AGTTT
1 TTAAAATATAAAATTA
3870702 TTAAAATAATAAAATTA
1 TTAAAAT-ATAAAATTA
3870719 TTAAA
1 TTAAA
3870724 TAATTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
13 10 0.37
15 2 0.07
16 7 0.26
17 8 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TTAAAATATAAAATTA
Found at i:3870697 original size:29 final size:30
Alignment explanation
Indices: 3870655--3870723 Score: 122
Period size: 29 Copynumber: 2.3 Consensus size: 30
3870645 ATAATTTTAC
*
3870655 AATTATTAAAATTATTTTTTAAAAT-ATAA
1 AATTATTAAAATTAGTTTTTAAAATAATAA
3870684 AATTATTAAAATTAGTTTTTAAAATAATAA
1 AATTATTAAAATTAGTTTTTAAAATAATAA
3870714 AATTATTAAA
1 AATTATTAAA
3870724 TAATTTTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 24 0.63
30 14 0.37
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (30 bp):
AATTATTAAAATTAGTTTTTAAAATAATAA
Found at i:3871992 original size:16 final size:16
Alignment explanation
Indices: 3871951--3871994 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3871941 ATTATATATC
3871951 TAAATATGTTAAAAAAT
1 TAAATATGTT-AAAAAT
3871968 T-AATA---TAAAAAT
1 TAAATATGTTAAAAAT
3871980 TAAATATGTTAAAAA
1 TAAATATGTTAAAAA
3871995 AAGCAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 9
0.72 0.00 0.28
Matches are distributed among these distances:
12 7 0.30
13 5 0.22
16 10 0.43
17 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (16 bp):
TAAATATGTTAAAAAT
Found at i:3889680 original size:45 final size:45
Alignment explanation
Indices: 3889616--3889742 Score: 182
Period size: 45 Copynumber: 2.8 Consensus size: 45
3889606 TCAAAGGGGA
* * * *
3889616 ACCATATTTTTCTTTTAATTTAGACCACTTTAATTTGTGACTTTT
1 ACCATAATTTTCTTTTAATTTGGACCACTTTGATTTGTAACTTTT
** *
3889661 ACCATAATTTTCTTTTAATTTGGGTCACTGTGATTTGTAACTTTT
1 ACCATAATTTTCTTTTAATTTGGACCACTTTGATTTGTAACTTTT
*
3889706 ACTATAATTTTCTTTTAATTTGGACCACTTTGATTTG
1 ACCATAATTTTCTTTTAATTTGGACCACTTTGATTTG
3889743 ATATAAATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (45 bp):
ACCATAATTTTCTTTTAATTTGGACCACTTTGATTTGTAACTTTT
Found at i:3891667 original size:183 final size:182
Alignment explanation
Indices: 3891359--3891730 Score: 627
Period size: 183 Copynumber: 2.0 Consensus size: 182
3891349 ACGAATTGGA
*
3891359 GTGGTCCCCTCAAGTCATTGCAAGTCTCATCTCCATATTTGCAGGAACTACCTGATTCAATTGGC
1 GTGGTCCACTCAAGTCATTGCAAGTCTCATCTCCATATTTGCAGGAACTACCTGATTCAATTGGC
* * ** *
3891424 AATCTTAGATCTATGGAGATATTGGATCTTCGCTTTAGTAATTTGAAAGGGCCAATTCCAGCATC
66 AATCTTAGATCTATGGAGATACTGAATCTTCGCGGTAGTAATTTAAAAGGGCCAATTCCAGCATC
* *
3891489 TCTCGTAAACCTCACACAACTTGAATATCTACATCTTTCCTATAACAACTTTG
131 TC-CGGAAACCTCACACAACTCGAATATCTACATCTTTCCTATAACAACTTTG
3891542 GTGGTCCACTCAAGTCATTGCAAGTCTCATCTCCATATTTGCAGGAACTACCTGATTCAATTGGC
1 GTGGTCCACTCAAGTCATTGCAAGTCTCATCTCCATATTTGCAGGAACTACCTGATTCAATTGGC
*
3891607 AATCTTAGATCTCTGGAGATACTGAATCTTCGCGGTAGTAATTTAAAAGGGCCAATTCCAGCATC
66 AATCTTAGATCTATGGAGATACTGAATCTTCGCGGTAGTAATTTAAAAGGGCCAATTCCAGCATC
* *
3891672 TCCGGAAACCTCACACAACTCGAATATCTAGATCTTTCCTATAATAACTTTG
131 TCCGGAAACCTCACACAACTCGAATATCTACATCTTTCCTATAACAACTTTG
*
3891724 GTTGTCC
1 GTGGTCC
3891731 TATTCTATGT
Statistics
Matches: 177, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
182 52 0.29
183 125 0.71
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (182 bp):
GTGGTCCACTCAAGTCATTGCAAGTCTCATCTCCATATTTGCAGGAACTACCTGATTCAATTGGC
AATCTTAGATCTATGGAGATACTGAATCTTCGCGGTAGTAATTTAAAAGGGCCAATTCCAGCATC
TCCGGAAACCTCACACAACTCGAATATCTACATCTTTCCTATAACAACTTTG
Found at i:3899524 original size:14 final size:15
Alignment explanation
Indices: 3899492--3899526 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3899482 TACTAAAAAT
*
3899492 AAATAAATTTAGTCA
1 AAATAAAATTAGTCA
3899507 AAATAAAATTAG-CA
1 AAATAAAATTAGTCA
3899521 AAATAA
1 AAATAA
3899527 CAACTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
AAATAAAATTAGTCA
Found at i:3899545 original size:43 final size:41
Alignment explanation
Indices: 3899493--3899574 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 41
3899483 ACTAAAAATA
*
3899493 AATAAATTTAGTCAAAAT-AAAATTAGCAAAATAACAACTTAT
1 AATAAATTTAGTCAAAATAAAAATAAG--AAATAACAACTTAT
*
3899535 AATATAATTTAGTTAAAATAAAAATAAGAAATAACAACTT
1 AATA-AATTTAGTCAAAATAAAAATAAGAAATAACAACTT
3899575 TGACCAAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
42 16 0.44
43 13 0.36
44 7 0.19
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (41 bp):
AATAAATTTAGTCAAAATAAAAATAAGAAATAACAACTTAT
Found at i:3912821 original size:60 final size:58
Alignment explanation
Indices: 3912682--3912850 Score: 225
Period size: 60 Copynumber: 2.9 Consensus size: 58
3912672 TTAATATAAC
* * * *
3912682 ATTTGGTATTTGAAGTTGATATTTTTTT-TAATTTGGTACCTAAATTTTTTTGACCCA
1 ATTTGGTATTTGAACTTGACATTTTTTTCTAATTTGGTACCTAAATTTATTGGACCCA
3912739 A-TTGGATATTTGAACTTGACATTTTTTTCTAATTTGGTACCTAAACGTTTATTGGACCCA
1 ATTTGG-TATTTGAACTTGACATTTTTTTCTAATTTGGTACCTAAA--TTTATTGGACCCA
** *
3912799 ATTTGGTACCTGAACTTGACATTTTTTTCCTAATTCGGTACCTAAATTTATT
1 ATTTGGTATTTGAACTTGACATTTTTTT-CTAATTTGGTACCTAAATTTATT
3912851 AAATATTATA
Statistics
Matches: 99, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
56 4 0.04
57 21 0.21
58 16 0.16
59 6 0.06
60 32 0.32
61 20 0.20
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (58 bp):
ATTTGGTATTTGAACTTGACATTTTTTTCTAATTTGGTACCTAAATTTATTGGACCCA
Found at i:3915805 original size:14 final size:13
Alignment explanation
Indices: 3915786--3915860 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 13
3915776 GTTTATATAT
3915786 TTATTTAATAATTA
1 TTATTTAATAA-TA
*
3915800 TTATTTAAT--TT
1 TTATTTAATAATA
3915811 TTATTTTAA-AATA
1 TTA-TTTAATAATA
3915824 TTATTATAATTTAATA
1 TTATT-TAA--TAATA
*
3915840 TT-TTTAATTACTA
1 TTATTTAA-TAATA
3915853 TTATTTAA
1 TTATTTAA
3915861 AAAAATATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
11 4 0.08
12 7 0.14
13 14 0.28
14 17 0.34
15 2 0.04
16 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTTAATAATA
Found at i:3915844 original size:27 final size:26
Alignment explanation
Indices: 3915789--3915860 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 26
3915779 TATATATTTA
*
3915789 TTTAATAATTATTATTTAATTTTTAT
1 TTTAATAATTATTATTTAATTTATAT
3915815 TTTAA-AA-TATTATTATAATTTAATATT
1 TTTAATAATTATTATT-TAATTT-ATA-T
* *
3915842 TTTAATTACTATTATTTAA
1 TTTAATAATTATTATTTAA
3915861 AAAAATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
24 7 0.18
25 8 0.21
26 7 0.18
27 6 0.15
28 4 0.10
29 7 0.18
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTAATAATTATTATTTAATTTATAT
Found at i:3916445 original size:30 final size:28
Alignment explanation
Indices: 3916404--3916460 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
3916394 TACTTTAATT
3916404 TGATCAATTTTAATTTCTATATTTTTTAAC
1 TGATCAATTTTAATTT-TAT-TTTTTTAAC
*
3916434 TGATCACTTTTAATTTTATTTTTTTAA
1 TGATCAATTTTAATTTTATTTTTTTAA
3916461 AATTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 8 0.31
29 3 0.12
30 15 0.58
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (28 bp):
TGATCAATTTTAATTTTATTTTTTTAAC
Found at i:3924225 original size:60 final size:60
Alignment explanation
Indices: 3924132--3924254 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
3924122 AAATTAGTCC
3924132 ATGCGTCAAATAGATGCTCTAGATTTCCATGTTTATGACATGCTTCCCTATCTTGTGGTT
1 ATGCGTCAAATAGATGCTCTAGATTTCCATGTTTATGACATGCTTCCCTATCTTGTGGTT
3924192 ATGCGTCAAATAGATGCTCTAGATTTCCATGTTTATGACATGCTTCCCTATCTTGTGGTT
1 ATGCGTCAAATAGATGCTCTAGATTTCCATGTTTATGACATGCTTCCCTATCTTGTGGTT
3924252 ATG
1 ATG
3924255 TTACATGAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.40
Consensus pattern (60 bp):
ATGCGTCAAATAGATGCTCTAGATTTCCATGTTTATGACATGCTTCCCTATCTTGTGGTT
Found at i:3930515 original size:20 final size:21
Alignment explanation
Indices: 3930490--3930529 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3930480 TATTTCAAAA
*
3930490 TTTAAAAATTA-TATAACATG
1 TTTAAAAATGATTATAACATG
3930510 TTTAAAAATGATTATAACAT
1 TTTAAAAATGATTATAACAT
3930530 TTTCAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (21 bp):
TTTAAAAATGATTATAACATG
Found at i:3935244 original size:20 final size:20
Alignment explanation
Indices: 3935219--3935258 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3935209 CTCAATATTT
3935219 ACACATTATGCAATTTGGTC
1 ACACATTATGCAATTTGGTC
3935239 ACACATTATGCAATTTGGTC
1 ACACATTATGCAATTTGGTC
3935259 TTTCTTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (20 bp):
ACACATTATGCAATTTGGTC
Found at i:3941805 original size:15 final size:15
Alignment explanation
Indices: 3941785--3941813 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3941775 GTGATTGACA
3941785 AGGTTAAAGAAAAAC
1 AGGTTAAAGAAAAAC
3941800 AGGTTAAAGAAAAA
1 AGGTTAAAGAAAAA
3941814 GTTATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.03, G:0.21, T:0.14
Consensus pattern (15 bp):
AGGTTAAAGAAAAAC
Found at i:3942674 original size:26 final size:26
Alignment explanation
Indices: 3942632--3942694 Score: 110
Period size: 25 Copynumber: 2.5 Consensus size: 26
3942622 AAACTAAAGT
3942632 ATGCTATTTTAACTTTTTAGAACTCC
1 ATGCTATTTTAACTTTTTAGAACTCC
3942658 ATGC-ATTTTAACTTTTTAGAACTCC
1 ATGCTATTTTAACTTTTTAGAACTCC
*
3942683 ATGCTATCTTAA
1 ATGCTATTTTAA
3942695 AACTTTCTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 25 0.71
26 10 0.29
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (26 bp):
ATGCTATTTTAACTTTTTAGAACTCC
Found at i:3952467 original size:23 final size:23
Alignment explanation
Indices: 3952434--3952477 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3952424 AACATTCAAA
3952434 ATATTTATAAAAATTTCAAAATT
1 ATATTTATAAAAATTTCAAAATT
* *
3952457 ATATTTTTAAAAATTTTAAAA
1 ATATTTATAAAAATTTCAAAA
3952478 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTTATAAAAATTTCAAAATT
Found at i:3954289 original size:16 final size:16
Alignment explanation
Indices: 3954245--3954289 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3954235 TTTGAAAAGC
3954245 TCAAAAATATTTTATT
1 TCAAAAATATTTTATT
*
3954261 T-AACAATACTTTTATT
1 TCAAAAATA-TTTTATT
*
3954277 TCAAAAATGTTTT
1 TCAAAAATATTTT
3954290 TTATCTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 6 0.25
16 13 0.54
17 5 0.21
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (16 bp):
TCAAAAATATTTTATT
Found at i:3959771 original size:99 final size:99
Alignment explanation
Indices: 3959600--3959795 Score: 374
Period size: 99 Copynumber: 2.0 Consensus size: 99
3959590 TTCAACTAGA
*
3959600 GGTGGTAATTATGTTGGTTTGGGTTCAAGTTGAATTTAGGCTGTTTGAGAGTTCTTTATTTTTCT
1 GGTGGTAATTATGTTGGTTTGCGTTCAAGTTGAATTTAGGCTGTTTGAGAGTTCTTTATTTTTCT
3959665 GGATTGGATTTATTTTGTATTCAGGTTCTTTCCG
66 GGATTGGATTTATTTTGTATTCAGGTTCTTTCCG
3959699 GGTGGTAATTATGTTGGTTTGCGTTCAAGTTGAATTTAGGCTGTTTGAGAGTTCTTTATTTTTCT
1 GGTGGTAATTATGTTGGTTTGCGTTCAAGTTGAATTTAGGCTGTTTGAGAGTTCTTTATTTTTCT
*
3959764 GGATTGGATTTATTTTGTATTCAGGTTTTTTC
66 GGATTGGATTTATTTTGTATTCAGGTTCTTTC
3959796 GGGGGCTGGA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.16, C:0.08, G:0.26, T:0.51
Consensus pattern (99 bp):
GGTGGTAATTATGTTGGTTTGCGTTCAAGTTGAATTTAGGCTGTTTGAGAGTTCTTTATTTTTCT
GGATTGGATTTATTTTGTATTCAGGTTCTTTCCG
Found at i:3966173 original size:16 final size:17
Alignment explanation
Indices: 3966152--3966185 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3966142 TATTGTTTGA
3966152 TAAAAAA-TACTTATTT
1 TAAAAAATTACTTATTT
*
3966168 TAAAAAATTATTTATTT
1 TAAAAAATTACTTATTT
3966185 T
1 T
3966186 TTAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAAAAATTACTTATTT
Found at i:3966298 original size:26 final size:25
Alignment explanation
Indices: 3966254--3966318 Score: 62
Period size: 27 Copynumber: 2.6 Consensus size: 25
3966244 ATAATTTGAA
3966254 TATTTTAATTTTTTGAAAA-AAAAT
1 TATTTTAATTTTTTGAAAATAAAAT
3966278 TATTTTAATATTTTCAT-AAAATAAAAT
1 TATTTTAAT-TTTT--TGAAAATAAAAT
* * *
3966305 CAATTTATTTTTTT
1 TATTTTAATTTTTT
3966319 CTACATTGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
24 10 0.29
25 4 0.12
26 8 0.24
27 12 0.35
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (25 bp):
TATTTTAATTTTTTGAAAATAAAAT
Found at i:3966856 original size:23 final size:23
Alignment explanation
Indices: 3966810--3966873 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
3966800 GCCATAAGAC
**
3966810 AAAAACGTGCCACAAGTTAAAGG
1 AAAAACGTGCCACAAGGCAAAGG
* *
3966833 AAAAATGTGCCACAAGGCAGAGG
1 AAAAACGTGCCACAAGGCAAAGG
* *
3966856 AAAAGCATGCCACGAAGG
1 AAAAACGTGCCAC-AAGG
3966874 TAGATAAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 29 0.88
24 4 0.12
ACGTcount: A:0.45, C:0.19, G:0.27, T:0.09
Consensus pattern (23 bp):
AAAAACGTGCCACAAGGCAAAGG
Found at i:3967299 original size:18 final size:18
Alignment explanation
Indices: 3967270--3967323 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
3967260 TTTAATATGC
*
3967270 CATAATTATATTTTACTAAA
1 CATAA-TATATTATA-TAAA
3967290 -ATAATATATTATATAAA
1 CATAATATATTATATAAA
*
3967307 CTTAATATATTAATATA
1 CATAATATATT-ATATA
3967324 TCATATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.13
18 17 0.57
19 9 0.30
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
CATAATATATTATATAAA
Found at i:3967515 original size:30 final size:29
Alignment explanation
Indices: 3967464--3967520 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
3967454 AATAGTTGAA
**
3967464 ATTAAATTTTAAAATTTTAAAAATAAAAAT
1 ATTAAATTTTAAAATAAT-AAAATAAAAAT
3967494 ATTAAATTCTTAAAA-AATAAAATAAAA
1 ATTAAATT-TTAAAATAATAAAATAAAA
3967521 TGAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.38
30 9 0.38
31 6 0.25
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
ATTAAATTTTAAAATAATAAAATAAAAAT
Found at i:3971071 original size:2 final size:2
Alignment explanation
Indices: 3971064--3971088 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3971054 TCAATTAATT
3971064 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 T
3971089 TATTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3972824 original size:3 final size:3
Alignment explanation
Indices: 3972816--3972843 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3972806 TTGTAGTTTC
3972816 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
3972844 AAGTGAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3979962 original size:12 final size:12
Alignment explanation
Indices: 3979945--3979969 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3979935 CAGAGAGGTC
3979945 TCCTGTGCTGGG
1 TCCTGTGCTGGG
3979957 TCCTGTGCTGGG
1 TCCTGTGCTGGG
3979969 T
1 T
3979970 TCTTGAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.40, T:0.36
Consensus pattern (12 bp):
TCCTGTGCTGGG
Found at i:3983245 original size:35 final size:35
Alignment explanation
Indices: 3983195--3983271 Score: 104
Period size: 34 Copynumber: 2.2 Consensus size: 35
3983185 AAAATGTATT
*
3983195 ATAAAAATTAAATTCATGAATATTATC-TTTTATTTA
1 ATAAAAATTAAATTCAT-AA-ATTATCATTATATTTA
3983231 ATAAAAA-TAAATTCATAAATTATCATTATATTTA
1 ATAAAAATTAAATTCATAAATTATCATTATATTTA
*
3983265 AAAAAAA
1 ATAAAAA
3983272 ATACTTGGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 6 0.16
34 16 0.42
35 9 0.24
36 7 0.18
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (35 bp):
ATAAAAATTAAATTCATAAATTATCATTATATTTA
Found at i:3983270 original size:33 final size:34
Alignment explanation
Indices: 3983197--3983270 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 34
3983187 AATGTATTAT
* *
3983197 AAAAATTAAATTCATGAATATTATCTTTTATTTA
1 AAAAAATAAATTCATGAATATTATCTTATATTTA
3983231 ATAAAAATAAATTCAT-AA-ATTATCATTATATTTA
1 A-AAAAATAAATTCATGAATATTATC-TTATATTTA
3983265 AAAAAA
1 AAAAAA
3983271 AATACTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
33 11 0.31
34 12 0.33
35 13 0.36
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (34 bp):
AAAAAATAAATTCATGAATATTATCTTATATTTA
Found at i:3984954 original size:137 final size:136
Alignment explanation
Indices: 3984795--3985199 Score: 455
Period size: 137 Copynumber: 3.0 Consensus size: 136
3984785 TGATCTTTCA
* *
3984795 AAGC-AATCGAGACATCTTAACAATGCATACATAGATGCATTTAAAACTTGTATCAGTTCCTAAA
1 AAGCTAATCGAGACA-CTTAACAAAGCATACATAGATGCATTTAAAACTCGTATCAGTTCCTAAA
* * *
3984859 CTCAAAAGAAAGAGAAAATCAAATGATACACAAGTATACTCATTAATAAAAATAAATTCA-AAAC
65 CTCAAAAGAAAGAGAAAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCACAAA-
3984923 ACAAAGAG
129 ACAAAGAG
* * * *
3984931 AAGCTAATTGAGACACCTTAACAAAG--TACACAGATGCA-TTAGAAACTCATATCCA-CTCCTA
1 AAGCTAATCGAGACA-CTTAACAAAGCATACATAGATGCATTTA-AAACTCGTAT-CAGTTCCTA
* * *
3984992 AACTTACGAAAGAAAGCGGAAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCAC
63 AAC-T-CAAAAGAAAGAGAAAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCAC
*
3985057 AAAAGAAAGAG
126 AAAACAAAGAG
* * * * * *
3985068 AAGCTAATCAAGACATTTTACAAAGCATGCATAGATGCATTGAAAGCTCGTATCAGTTCCTAAAC
1 AAGCTAATCGAGACACTTAACAAAGCATACATAGATGCATTTAAAACTCGTATCAGTTCCTAAAC
* * * * *
3985133 ACACGAAAGAAAGCA-AAAATCAAAGGGCACACAAGCATACTTATTAATAAAAATAAATTCATAA
66 TCA--AAAGAAAG-AGAAAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCACAA
3985197 AAC
128 AAC
3985200 CTCTATCTCC
Statistics
Matches: 223, Mismatches: 33, Indels: 24
0.80 0.12 0.09
Matches are distributed among these distances:
134 3 0.01
135 27 0.12
136 16 0.07
137 92 0.41
138 83 0.37
139 2 0.01
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.21
Consensus pattern (136 bp):
AAGCTAATCGAGACACTTAACAAAGCATACATAGATGCATTTAAAACTCGTATCAGTTCCTAAAC
TCAAAAGAAAGAGAAAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCACAAAAC
AAAGAG
Found at i:3988830 original size:21 final size:19
Alignment explanation
Indices: 3988804--3988851 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
3988794 ATTAGACCCA
3988804 TCATCATCCATTAAATCATCT
1 TCATCATCCATT--ATCATCT
*
3988825 TCATCAAATTCATTATCATCT
1 TCATC--ATCCATTATCATCT
3988846 TCATCA
1 TCATCA
3988852 CTGTCTGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
21 17 0.71
23 6 0.25
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (19 bp):
TCATCATCCATTATCATCT
Found at i:3991922 original size:91 final size:91
Alignment explanation
Indices: 3991767--3991950 Score: 368
Period size: 91 Copynumber: 2.0 Consensus size: 91
3991757 GAATATAGGG
3991767 TTTTCTTTGGTAAAATCACTTTTTCAGTTTCTTTCCATTTCGGAATTGAATAAATTAATTTTTCT
1 TTTTCTTTGGTAAAATCACTTTTTCAGTTTCTTTCCATTTCGGAATTGAATAAATTAATTTTTCT
3991832 TAAAAATAAATTAGAGTAATCTAATT
66 TAAAAATAAATTAGAGTAATCTAATT
3991858 TTTTCTTTGGTAAAATCACTTTTTCAGTTTCTTTCCATTTCGGAATTGAATAAATTAATTTTTCT
1 TTTTCTTTGGTAAAATCACTTTTTCAGTTTCTTTCCATTTCGGAATTGAATAAATTAATTTTTCT
3991923 TAAAAATAAATTAGAGTAATCTAATT
66 TAAAAATAAATTAGAGTAATCTAATT
3991949 TT
1 TT
3991951 ATTAATTTCA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.48
Consensus pattern (91 bp):
TTTTCTTTGGTAAAATCACTTTTTCAGTTTCTTTCCATTTCGGAATTGAATAAATTAATTTTTCT
TAAAAATAAATTAGAGTAATCTAATT
Found at i:4006525 original size:24 final size:26
Alignment explanation
Indices: 4006463--4006528 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 26
4006453 AATTTTAAAT
4006463 ATTAATATAAATTA-TTTAAATTTACA
1 ATTAA-ATAAATTATTTTAAATTTACA
* *
4006489 TTTTAAT-AA-TATTTTAAA-TTA-A
1 ATTAAATAAATTATTTTAAATTTACA
4006511 ATTAAATAAATTATTTTA
1 ATTAAATAAATTATTTTA
4006529 CAAATAGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
22 6 0.18
23 7 0.21
24 15 0.45
25 2 0.06
26 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTAAATAAATTATTTTAAATTTACA
Found at i:4007602 original size:13 final size:13
Alignment explanation
Indices: 4007584--4007610 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4007574 TTATGAGGAT
4007584 TCGTCAAAAGGGC
1 TCGTCAAAAGGGC
4007597 TCGTCAAAAGGGC
1 TCGTCAAAAGGGC
4007610 T
1 T
4007611 TGCAAAGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.30, T:0.19
Consensus pattern (13 bp):
TCGTCAAAAGGGC
Found at i:4010855 original size:7 final size:7
Alignment explanation
Indices: 4010843--4010867 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4010833 AAGGCATCAT
4010843 TAATAAA
1 TAATAAA
4010850 TAATAAA
1 TAATAAA
4010857 TAATAAA
1 TAATAAA
4010864 TAAT
1 TAAT
4010868 TATTCTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TAATAAA
Found at i:4014447 original size:20 final size:18
Alignment explanation
Indices: 4014414--4014452 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
4014404 GAAAAATATA
4014414 AATTTAACTAATAATTAT
1 AATTTAACTAATAATTAT
4014432 AATTTATACATAATAATTAT
1 AATTTA-AC-TAATAATTAT
4014452 A
1 A
4014453 TTATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAACTAATAATTAT
Found at i:4017647 original size:18 final size:18
Alignment explanation
Indices: 4017626--4017660 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4017616 TCAAAAAACT
4017626 TAAA-TTTTTTTCTTTGTA
1 TAAACTTTTTTT-TTTGTA
4017644 TAAACTTTTTTTTTTGT
1 TAAACTTTTTTTTTTGT
4017661 CTTCTTGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.69
Consensus pattern (18 bp):
TAAACTTTTTTTTTTGTA
Found at i:4023712 original size:46 final size:44
Alignment explanation
Indices: 4023644--4023768 Score: 128
Period size: 44 Copynumber: 2.8 Consensus size: 44
4023634 ATCCCCTTAA
* *
4023644 ATGGAATCTG-CTTTAGGTTGTGGATTACACAACAAATATC-TCGCAG
1 ATGGAATCTGCCTCT-GGCTGTGGA-TACACAACAAATA-CAT-GCAG
* ** *
4023690 ATGGAATCTGCCTCTGGCTGTGGGTACGTAACAAATACATGCTG
1 ATGGAATCTGCCTCTGGCTGTGGATACACAACAAATACATGCAG
* *
4023734 ATAGAATCTGCCTCTGGCTGTGGATGCACAACAAA
1 ATGGAATCTGCCTCTGGCTGTGGATACACAACAAA
4023769 ATTTGCAGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
44 34 0.52
45 12 0.18
46 17 0.26
47 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
ATGGAATCTGCCTCTGGCTGTGGATACACAACAAATACATGCAG
Found at i:4028534 original size:17 final size:18
Alignment explanation
Indices: 4028502--4028535 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4028492 AGAAGTACTG
*
4028502 ATAATTATACATTTAAAA
1 ATAATTAGACATTTAAAA
4028520 ATAATTAGA-ATTTAAA
1 ATAATTAGACATTTAAA
4028536 TTTCATTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAATTAGACATTTAAAA
Found at i:4030353 original size:75 final size:74
Alignment explanation
Indices: 4030198--4030361 Score: 175
Period size: 75 Copynumber: 2.2 Consensus size: 74
4030188 AATCTTACTG
* * * *
4030198 AACTTGATCTTTCATCAAATAAATTTAATGGCGTAATCAACTCAGTTATGCTTTCAAAGTTAGAG
1 AACTTGATCTTTCATCAAATAAATTTAACGGCGTAATCAACTCAGATATGCTTTCAAAGCTAAAG
* *
4030263 AATCTTTTA
66 AAGCTTTGA
** * * * * * *
4030272 ACACTTGATCTTTCATCAAATAGTTTTAGCGGTGTCATCAAGTTAGATGTGCTTTCAAAGCTAAA
1 A-ACTTGATCTTTCATCAAATAAATTTAACGGCGTAATCAACTCAGATATGCTTTCAAAGCTAAA
4030337 GAAGCTTATGA
65 GAAGCTT-TGA
*
4030348 AACTTGATATTTCA
1 AACTTGATCTTTCA
4030362 AACAACACAT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
74 1 0.01
75 69 0.95
76 3 0.04
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (74 bp):
AACTTGATCTTTCATCAAATAAATTTAACGGCGTAATCAACTCAGATATGCTTTCAAAGCTAAAG
AAGCTTTGA
Found at i:4033016 original size:22 final size:22
Alignment explanation
Indices: 4032988--4033033 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
4032978 AACAAGCCAC
4032988 CTAAGGTTTGTTCTAGACATTT
1 CTAAGGTTTGTTCTAGACATTT
4033010 CTAAGGTTTGTTCTAGACATTT
1 CTAAGGTTTGTTCTAGACATTT
4033032 CT
1 CT
4033034 GCCATTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (22 bp):
CTAAGGTTTGTTCTAGACATTT
Found at i:4033075 original size:92 final size:92
Alignment explanation
Indices: 4032918--4033104 Score: 347
Period size: 92 Copynumber: 2.0 Consensus size: 92
4032908 AACAAGCCAC
4032918 CTAAGGCTTGTTCTAGACATTTCTACCATTATCATCCATCAAGCCAAATTAACCACAATTAACAA
1 CTAAGGCTTGTTCTAGACATTTCTACCATTATCATCCATCAAGCCAAATTAACCACAATTAACAA
*
4032983 GCCACCTAAGGTTTGTTCTAGACATTT
66 GCCACCTAAGGCTTGTTCTAGACATTT
* *
4033010 CTAAGGTTTGTTCTAGACATTTCTGCCATTATCATCCATCAAGCCAAATTAACCACAATTAACAA
1 CTAAGGCTTGTTCTAGACATTTCTACCATTATCATCCATCAAGCCAAATTAACCACAATTAACAA
4033075 GCCACCTAAGGCTTGTTCTAGACATTT
66 GCCACCTAAGGCTTGTTCTAGACATTT
4033102 CTA
1 CTA
4033105 CCAATTTTAA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (92 bp):
CTAAGGCTTGTTCTAGACATTTCTACCATTATCATCCATCAAGCCAAATTAACCACAATTAACAA
GCCACCTAAGGCTTGTTCTAGACATTT
Found at i:4036489 original size:12 final size:12
Alignment explanation
Indices: 4036472--4036496 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4036462 TCATCAATTG
4036472 ATATTTGTGATA
1 ATATTTGTGATA
4036484 ATATTTGTGATA
1 ATATTTGTGATA
4036496 A
1 A
4036497 ATCTTTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (12 bp):
ATATTTGTGATA
Found at i:4041992 original size:24 final size:24
Alignment explanation
Indices: 4041959--4042021 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
4041949 AGAAATAATC
* *
4041959 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
*
4041983 TTTCATTTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
4042007 TTTAAGTCAAACTCT
1 TTTCAGTTAAACTCT
4042022 TATTAGTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.13, G:0.08, T:0.54
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:4043631 original size:19 final size:19
Alignment explanation
Indices: 4043607--4043649 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4043597 AAACCTAAAT
4043607 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
4043626 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
4043645 TAAAT
1 TAAAT
4043650 CCTAATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:4048596 original size:21 final size:21
Alignment explanation
Indices: 4048570--4048609 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4048560 ATAGATGCCT
*
4048570 CAGTTTTCTTTTGAAAATCCA
1 CAGTTTGCTTTTGAAAATCCA
4048591 CAGTTTGCTTTTGAAAATC
1 CAGTTTGCTTTTGAAAATC
4048610 TATAAATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
CAGTTTGCTTTTGAAAATCCA
Found at i:4048619 original size:21 final size:21
Alignment explanation
Indices: 4048577--4048628 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
4048567 CCTCAGTTTT
**
4048577 CTTTTGAAAATCCACAGTTTG
1 CTTTTGAAAATCCACAAATTG
* *
4048598 CTTTTGAAAATCTATAAATTG
1 CTTTTGAAAATCCACAAATTG
*
4048619 CTGTT-AAAAT
1 CTTTTGAAAAT
4048629 TAAAGAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (21 bp):
CTTTTGAAAATCCACAAATTG
Found at i:4049974 original size:22 final size:22
Alignment explanation
Indices: 4049932--4049991 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
4049922 CAATCTGAGG
* *
4049932 AAAAATAGAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
4049953 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATAGAATT
*
4049975 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
4049992 AGAAAGTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.30
22 22 0.67
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:4050537 original size:7 final size:6
Alignment explanation
Indices: 4050484--4050537 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
4050474 CCCATTTTTA
* *
4050484 AAATTT AAATCT AAATTT --ATTT AAATTT -ATTTT AAA-TT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
4050528 AAACTTT AAA
1 AAA-TTT AAA
4050538 AGTCCTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
4 4 0.10
5 9 0.23
6 20 0.51
7 6 0.15
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:4052394 original size:30 final size:28
Alignment explanation
Indices: 4052338--4052769 Score: 171
Period size: 29 Copynumber: 14.9 Consensus size: 28
4052328 CCCTAAAGGT
* *
4052338 CCCTAAACTATCCAAAAAT-CATATTTTGA
1 CCCT-AACTTTCCAAAATTACAT-TTTTGA
* *
4052367 CCCTTAATCTTTTCCAAAATTCCATTTTTAA
1 CCC-TAA-C-TTTCCAAAATTACATTTTTGA
* * *
4052398 CCCTAAACTTTCTGAAAATTATATTTTT-T
1 CCCT-AACTTTC-CAAAATTACATTTTTGA
* *
4052427 CCGTCGAACTTTCCAAAATTCCATTTTTGA
1 CC--CTAACTTTCCAAAATTACATTTTTGA
*
4052457 TCCCTAATTTTCCAAAAATTACATTTTTG-
1 -CCCTAACTTTCC-AAAATTACATTTTTGA
*
4052486 CTCCTAAACTTTCCAAAATTCCATTTTTGA
1 C-CCT-AACTTTCCAAAATTACATTTTTGA
***
4052516 CCCCTAA-TTTTTGAAATTACATTTTT-A
1 -CCCTAACTTTCCAAAATTACATTTTTGA
*
4052543 CCCTTAAAC-TTCCAAAAGTTTCATTTTTGA
1 CCC-T-AACTTTCCAAAA-TTACATTTTTGA
** *
4052573 --CT--CTGACAAAAATTACATTTTT-A
1 CCCTAACTTTCCAAAATTACATTTTTGA
* **
4052596 CCCCTAAACTTTCAAAAATCCCA-TTTTGA
1 -CCCT-AACTTTCCAAAATTACATTTTTGA
* *
4052625 CCCTAAAACTTTCAAAAATTATATTTTT--
1 CCCT--AACTTTCCAAAATTACATTTTTGA
* *
4052653 CCCTCGAAC-TTCCAAAAATATTATTTTTGA
1 CCCT--AACTTTCCAAAATTA-CATTTTTGA
*
4052683 CCCCGAACTTTCCAAAAATTACCA-TTTT-A
1 -CCCTAACTTTCC-AAAATTA-CATTTTTGA
* * * *
4052712 CCCCTAAATGTCTAAAAATT-CTAATTTTGA
1 -CCCTAACTTTC-CAAAATTAC-ATTTTTGA
4052742 CCCTAAACTTTCCAAAAATTAGCATTTT
1 CCCT-AACTTTCC-AAAATTA-CATTTT
4052770 ACCCTCGAAT
Statistics
Matches: 307, Mismatches: 52, Indels: 86
0.69 0.12 0.19
Matches are distributed among these distances:
23 1 0.00
24 10 0.03
25 5 0.02
26 5 0.02
27 13 0.04
28 47 0.15
29 113 0.37
30 72 0.23
31 37 0.12
32 4 0.01
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.39
Consensus pattern (28 bp):
CCCTAACTTTCCAAAATTACATTTTTGA
Done.