Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 34 of 135
Found at i:13130584 original size:33 final size:31
Alignment explanation
Indices: 13130537--13130597 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
13130527 CACGTGTCCC
* *
13130537 ATTTTTGGTTTATTTCTACATTTGGTCCTTTTT
1 ATTTTTGATCTATTT-TA-ATTTGGTCCTTTTT
*
13130570 ATTTTTGATCTATTTTAATTTTGTCCTT
1 ATTTTTGATCTATTTTAATTTGGTCCTT
13130598 AAATCAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 10 0.40
32 2 0.08
33 13 0.52
ACGTcount: A:0.15, C:0.11, G:0.10, T:0.64
Consensus pattern (31 bp):
ATTTTTGATCTATTTTAATTTGGTCCTTTTT
Found at i:13130987 original size:29 final size:28
Alignment explanation
Indices: 13130769--13130986 Score: 181
Period size: 29 Copynumber: 7.5 Consensus size: 28
13130759 CAAGCTTTTT
*
13130769 AAAAATTACATTTTGACCCCTCGAACTTTCC
1 AAAAATTACATTTT-ACCCCT-AAAC-TTCC
* * *
13130800 AAAAGTTACATTTTGACCTCTAAACTTTC
1 AAAAATTACATTTT-ACCCCTAAACTTCC
* * *
13130829 TAAAATTGCATTTTGA-CCCTAAACTTATC
1 AAAAATTACATTTT-ACCCCTAAACTT-CC
13130858 AAAAATTACATTTTACCCCTAAACTTCC
1 AAAAATTACATTTTACCCCTAAACTTCC
** * *
13130886 AAAAACCACATTTTTAACCCTAAATTTTCC
1 AAAAATTACA-TTTTACCCCTAAA-CTTCC
* * *
13130916 AAAAATGACCATTTTACACCTAAACATCC
1 AAAAATTA-CATTTTACCCCTAAACTTCC
*
13130945 -AAAATTACCATTTTACCCCTAGA-TGTCC
1 AAAAATTA-CATTTTACCCCTAAACT-TCC
13130973 AAAAATTACATTTT
1 AAAAATTACATTTT
13130987 TGAGCTCGAG
Statistics
Matches: 155, Mismatches: 25, Indels: 17
0.79 0.13 0.09
Matches are distributed among these distances:
28 48 0.31
29 62 0.40
30 24 0.15
31 21 0.14
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAAATTACATTTTACCCCTAAACTTCC
Found at i:13131062 original size:28 final size:29
Alignment explanation
Indices: 13130913--13131097 Score: 94
Period size: 29 Copynumber: 6.3 Consensus size: 29
13130903 CCCTAAATTT
* * * *
13130913 TCCAAAAATGACCATTTTACACCT-AAACA
1 TCCAAAAATTACCATTTTGC-CCTCGAATA
* * *
13130942 TCC-AAAATTACCATTTTACCC-CTAGATG
1 TCCAAAAATTACCATTTTGCCCTCGA-ATA
** * *
13130970 TCCAAAAATTA-CATTTTTGAGCTCGAGTTT
1 TCCAAAAATTACCA-TTTTGCCCTCGA-ATA
* *
13131000 TCCAAAAAAATTACCATTTTACCCTCGAATT
1 TCC--AAAAATTACCATTTTGCCCTCGAATA
* *
13131031 TCC-AGAATTACCATTTTGCCC-CTAAGTA
1 TCCAAAAATTACCATTTTGCCCTCGAA-TA
* ***
13131059 TCCAAAAATTACTATTTTGCCCTCGGGCA
1 TCCAAAAATTACCATTTTGCCCTCGAATA
13131088 TCCAAAAATT
1 TCCAAAAATT
13131098 GCATTTTTTT
Statistics
Matches: 121, Mismatches: 24, Indels: 22
0.72 0.14 0.13
Matches are distributed among these distances:
27 6 0.05
28 41 0.34
29 42 0.35
30 8 0.07
31 5 0.04
32 17 0.14
33 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTGCCCTCGAATA
Found at i:13131069 original size:29 final size:29
Alignment explanation
Indices: 13130857--13131076 Score: 107
Period size: 28 Copynumber: 7.6 Consensus size: 29
13130847 CTAAACTTAT
*
13130857 CAAAAATTA-CATTTTACCCCTAAACT-TC
1 CAAAAATTACCATTTTACCCCT-AAGTATC
** * * *
13130885 CAAAAACCA-CATTTTTAACCCTAAATTTTC
1 CAAAAATTACCA-TTTTACCCCT-AAGTATC
* * **
13130915 CAAAAATGACCATTTTACACCTAAACATC
1 CAAAAATTACCATTTTACCCCTAAGTATC
*
13130944 C-AAAATTACCATTTTACCCCT-AGATGTC
1 CAAAAATTACCATTTTACCCCTAAG-TATC
* * * *
13130972 CAAAAATTA-CATTTTTGAGCTC-GAGTTTTC
1 CAAAAATTACCA-TTTT-ACCCCTAAG-TATC
* *
13131002 CAAAAAAATTACCATTTTACCCTCGAA-TTTC
1 C--AAAAATTACCATTTTACCC-CTAAGTATC
* *
13131033 C-AGAATTACCATTTTGCCCCTAAGTATC
1 CAAAAATTACCATTTTACCCCTAAGTATC
*
13131061 CAAAAATTACTATTTT
1 CAAAAATTACCATTTT
13131077 GCCCTCGGGC
Statistics
Matches: 148, Mismatches: 29, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
27 4 0.03
28 52 0.35
29 41 0.28
30 26 0.18
31 9 0.06
32 13 0.09
33 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCTAAGTATC
Found at i:13134378 original size:29 final size:28
Alignment explanation
Indices: 13134320--13134380 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
13134310 CTCATTTTGA
13134320 TACTTAAATTTTTTTTTTGTCATAAGTGG
1 TACTTAAATTTTTTTTTTGTCA-AAGTGG
13134349 TACTTAAATTATATTTTTTT-TC-AAGTTGG
1 TACTTAAATT-T-TTTTTTTGTCAAAG-TGG
13134378 TAC
1 TAC
13134381 CTTCATTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
28 3 0.10
29 16 0.55
30 3 0.10
31 7 0.24
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.54
Consensus pattern (28 bp):
TACTTAAATTTTTTTTTTGTCAAAGTGG
Found at i:13138105 original size:21 final size:20
Alignment explanation
Indices: 13138052--13138106 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
13138042 TTCGACCGTT
13138052 ATTTGATAACTTAAAATAATTA
1 ATTTG-TAA-TTAAAATAATTA
* *
13138074 TTTTCTCAATTAAAATAATTAA
1 ATTTGT-AATTAAAATAATT-A
13138096 ATTTGTAATTA
1 ATTTGTAATTA
13138107 TTTAATTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (20 bp):
ATTTGTAATTAAAATAATTA
Found at i:13153886 original size:22 final size:22
Alignment explanation
Indices: 13153858--13153899 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
13153848 ATCTTTTAGA
13153858 ATTTATAT-ATATATATATTTGC
1 ATTTATATAAT-TATATATTTGC
13153880 ATTTATATAATTATATATTT
1 ATTTATATAATTATATATTT
13153900 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTATATAATTATATATTTGC
Found at i:13158315 original size:2 final size:2
Alignment explanation
Indices: 13158310--13158334 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13158300 AAAAAAAAAA
13158310 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13158335 GGTTACCGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13159073 original size:25 final size:25
Alignment explanation
Indices: 13159040--13159088 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
13159030 TATTTATTTT
*
13159040 TATTTTTTAACTTATAAAAAAATTA
1 TATTATTTAACTTATAAAAAAATTA
* *
13159065 TATTATTTAATTTCTAAAAAAATT
1 TATTATTTAACTTATAAAAAAATT
13159089 CTAAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
TATTATTTAACTTATAAAAAAATTA
Found at i:13169645 original size:6 final size:6
Alignment explanation
Indices: 13169634--13169693 Score: 120
Period size: 6 Copynumber: 10.0 Consensus size: 6
13169624 AGATTTAGGT
13169634 GGACTG GGACTG GGACTG GGACTG GGACTG GGACTG GGACTG GGACTG
1 GGACTG GGACTG GGACTG GGACTG GGACTG GGACTG GGACTG GGACTG
13169682 GGACTG GGACTG
1 GGACTG GGACTG
13169694 AAATTTGAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (6 bp):
GGACTG
Found at i:13170216 original size:16 final size:18
Alignment explanation
Indices: 13170177--13170210 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13170167 TAAGTTTATA
13170177 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
13170194 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
13170211 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:13170331 original size:25 final size:25
Alignment explanation
Indices: 13170303--13170355 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
13170293 ATTATATAAA
13170303 AAAATTTAATAAATA-ATAAATATAT
1 AAAA-TTAATAAATATATAAATATAT
* * *
13170328 AAAATTATTAAATATTTAAATATTT
1 AAAATTAATAAATATATAAATATAT
13170353 AAA
1 AAA
13170356 TAAAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAATTAATAAATATATAAATATAT
Found at i:13174864 original size:6 final size:6
Alignment explanation
Indices: 13174855--13174893 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
13174845 TATATCTTAA
*
13174855 GTTTGT GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTT
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTT
13174894 ATTTCCTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (6 bp):
GTTTGG
Found at i:13189339 original size:23 final size:25
Alignment explanation
Indices: 13189313--13189358 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
13189303 CCAATTAGGG
13189313 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
13189336 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
13189359 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:13190444 original size:14 final size:14
Alignment explanation
Indices: 13190419--13190452 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
13190409 TTACTTTAGC
13190419 CATTTT-TTATTTT
1 CATTTTATTATTTT
*
13190432 TATTTTATTATTTT
1 CATTTTATTATTTT
13190446 CATTTTA
1 CATTTTA
13190453 AATTTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
CATTTTATTATTTT
Found at i:13193368 original size:23 final size:22
Alignment explanation
Indices: 13193342--13193415 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 22
13193332 ACACTAGCGC
13193342 GCTCTCTGATTAGCAC-CGTATGT
1 GCTCTCTGATTAGCACTCG--TGT
13193365 GCTCTCTGTTATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCAC-TCGTGT
* *
13193390 GCTCTTTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCAC-TCGTGT
13193413 GCT
1 GCT
13193416 TAGTACTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
23 25 0.56
25 18 0.40
27 2 0.04
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.42
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTCGTGT
Found at i:13193459 original size:22 final size:22
Alignment explanation
Indices: 13193424--13193478 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
13193414 CTTAGTACTT
*
13193424 TGTGTACTCTCTGTTCAGCACTA
1 TGTGTGCT-TCTGTTCAGCACTA
*
13193447 TGTGTGCTTCTGTTCAGCACTG
1 TGTGTGCTTCTGTTCAGCACTA
13193469 TGTGTGCTTC
1 TGTGTGCTTC
13193479 GTTTCCCCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 23 0.77
23 7 0.23
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.42
Consensus pattern (22 bp):
TGTGTGCTTCTGTTCAGCACTA
Found at i:13195895 original size:11 final size:10
Alignment explanation
Indices: 13195879--13195920 Score: 57
Period size: 11 Copynumber: 3.9 Consensus size: 10
13195869 AATTAGTATA
13195879 TTTATTTTCAT
1 TTTATTTT-AT
13195890 TTTATTTTAT
1 TTTATTTTAT
13195900 TTTATTTTTATT
1 TTTA-TTTTA-T
13195912 TTTATTTTA
1 TTTATTTTA
13195921 ATTATGCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.21
11 18 0.62
12 5 0.17
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:13195898 original size:5 final size:5
Alignment explanation
Indices: 13195879--13195920 Score: 57
Period size: 5 Copynumber: 7.8 Consensus size: 5
13195869 AATTAGTATA
13195879 TTTAT TTTCAT TTTAT TTTAT TTTATT TTTATT TTTAT TTTA
1 TTTAT TTT-AT TTTAT TTTAT TTTA-T TTTA-T TTTAT TTTA
13195921 ATTATGCACT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 19 0.54
6 16 0.46
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:13195908 original size:6 final size:6
Alignment explanation
Indices: 13195879--13195919 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
13195869 AATTAGTATA
*
13195879 TTTATT TTCA-T TTTA-T TTTA-T TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TT
13195920 AATTATGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 14 0.44
6 18 0.56
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:13197942 original size:23 final size:25
Alignment explanation
Indices: 13197916--13197961 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
13197906 CCAATTAGGG
13197916 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
13197939 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
13197962 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:13201665 original size:53 final size:53
Alignment explanation
Indices: 13201585--13201685 Score: 184
Period size: 53 Copynumber: 1.9 Consensus size: 53
13201575 TGGAATGTTC
*
13201585 TATCAACTGTTATGGCTTTACGTAACGGGTTGCAATTACACAAGACCACAATT
1 TATCAACTGTTATGGCGTTACGTAACGGGTTGCAATTACACAAGACCACAATT
*
13201638 TATCAACTGTTATGGCGTTACGTAACGGGTTGCAATTACACAATACCA
1 TATCAACTGTTATGGCGTTACGTAACGGGTTGCAATTACACAAGACCA
13201686 TTGTGCTGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (53 bp):
TATCAACTGTTATGGCGTTACGTAACGGGTTGCAATTACACAAGACCACAATT
Found at i:13211051 original size:28 final size:29
Alignment explanation
Indices: 13211018--13211092 Score: 116
Period size: 28 Copynumber: 2.6 Consensus size: 29
13211008 TGCCTCAGAT
13211018 TACATTTTAGTCACTTATGTTTGAAA-TG
1 TACATTTTAGTCACTTATGTTTGAAATTG
* *
13211046 TACATTTTAGTTACTTATGTTTGAAATTT
1 TACATTTTAGTCACTTATGTTTGAAATTG
*
13211075 TACGTTTTAGTCACTTAT
1 TACATTTTAGTCACTTAT
13211093 ATTATCATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 25 0.60
29 17 0.40
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.51
Consensus pattern (29 bp):
TACATTTTAGTCACTTATGTTTGAAATTG
Found at i:13211253 original size:18 final size:18
Alignment explanation
Indices: 13211230--13211272 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
13211220 TTTTTAGTTG
13211230 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
13211248 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
13211266 TAATTAA
1 TAATTAA
13211273 AAATTTGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:13229240 original size:27 final size:27
Alignment explanation
Indices: 13229210--13229274 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
13229200 AAAAAATAAG
13229210 AAAATTAAAAATTGATATAAA-CTTA-TT
1 AAAATTAAAAATT-A-ATAAAGCTTATTT
13229237 AAAA-TATAAAATTAATAAAGCTTATTT
1 AAAATTA-AAAATTAATAAAGCTTATTT
13229264 AAAATTAAAAA
1 AAAATTAAAAA
13229275 ACGTGTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
25 5 0.15
26 7 0.21
27 20 0.59
28 2 0.06
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (27 bp):
AAAATTAAAAATTAATAAAGCTTATTT
Found at i:13231362 original size:3 final size:3
Alignment explanation
Indices: 13231354--13231392 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
13231344 CTTGGAATAA
13231354 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13231393 TAGATCCTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:13234481 original size:2 final size:2
Alignment explanation
Indices: 13234474--13234500 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13234464 ATTTCTCAAA
13234474 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
13234501 ATAAAATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:13245384 original size:16 final size:18
Alignment explanation
Indices: 13245365--13245402 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
13245355 TTAATTCAAA
13245365 AAAAATATTTT-T-AAAT
1 AAAAATATTTTATAAAAT
*
13245381 AAAAGTATTTTATAAAAT
1 AAAAATATTTTATAAAAT
13245399 AAAA
1 AAAA
13245403 TCCAAACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 1 0.05
18 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAAATATTTTATAAAAT
Found at i:13245398 original size:18 final size:16
Alignment explanation
Indices: 13245362--13245403 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
13245352 AATTTAATTC
13245362 AAAA-AAAATATTTTT
1 AAAATAAAATATTTTT
13245377 -AAATAAAAGTATTTTAT
1 AAAATAAAA-TATTTT-T
13245394 AAAATAAAAT
1 AAAATAAAAT
13245404 CCAAACAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.13
15 4 0.17
16 6 0.26
17 2 0.09
18 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AAAATAAAATATTTTT
Found at i:13259592 original size:88 final size:88
Alignment explanation
Indices: 13259387--13259592 Score: 240
Period size: 88 Copynumber: 2.3 Consensus size: 88
13259377 AATTAGGGTG
* * *
13259387 GTTCAAGTACCCAATTGAGTGCAAAAAACATCATGGGCTTAATTAATTTTTTTGAAAAATTTTGA
1 GTTCAAGTACCCAATTGAGTGCAAAAAA-ATCAGGGGCTTAATTAATTTTTGTGAAAAAGTTTGA
*
13259452 GGATCATTTTTATGCATTTTGAAA
65 GGATCATTTTTATACATTTTGAAA
* * * **
13259476 GTTTAAGTACCCAATTGAGTGCAGAAAAATGTAGGGGCTTAATTGCTTTTTGTG-AAAAGTTTGA
1 GTTCAAGTACCCAATTGAGTGCAAAAAAAT-CAGGGGCTTAATTAATTTTTGTGAAAAAGTTTGA
13259540 GGA-C-TTTTTGGATACATTTT-AATA
65 GGATCATTTTT--ATACATTTTGAA-A
* *
13259564 GTTCAAATACCCAATTGAATGCAAAAAAA
1 GTTCAAGTACCCAATTGAGTGCAAAAAAA
13259593 AAATAGAAAT
Statistics
Matches: 100, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
86 5 0.05
87 3 0.03
88 48 0.48
89 44 0.44
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (88 bp):
GTTCAAGTACCCAATTGAGTGCAAAAAAATCAGGGGCTTAATTAATTTTTGTGAAAAAGTTTGAG
GATCATTTTTATACATTTTGAAA
Found at i:13268150 original size:59 final size:59
Alignment explanation
Indices: 13268085--13268201 Score: 225
Period size: 59 Copynumber: 2.0 Consensus size: 59
13268075 GAATAAATTC
13268085 AAAGTTTCAATTTTTATTTTCTTTCAAAAGGTTTCAGTCTTTCATACGTTTATTTACCA
1 AAAGTTTCAATTTTTATTTTCTTTCAAAAGGTTTCAGTCTTTCATACGTTTATTTACCA
*
13268144 AAAGTTTCAATTTTTATTTTCTTTCAAAAGGTTTCAGTCTTTCATATGTTTATTTACC
1 AAAGTTTCAATTTTTATTTTCTTTCAAAAGGTTTCAGTCTTTCATACGTTTATTTACC
13268202 GAAATTTTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (59 bp):
AAAGTTTCAATTTTTATTTTCTTTCAAAAGGTTTCAGTCTTTCATACGTTTATTTACCA
Found at i:13270943 original size:2 final size:2
Alignment explanation
Indices: 13270936--13270982 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
13270926 TGAATTTAAC
13270936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13270978 AT AT A
1 AT AT A
13270983 AAAGTTGGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13274470 original size:16 final size:17
Alignment explanation
Indices: 13274444--13274475 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13274434 ACAAAACTTT
13274444 TAAAAATATAAAAAAAC
1 TAAAAATATAAAAAAAC
13274461 TAAAAA-ATAAAAAAA
1 TAAAAATATAAAAAAA
13274476 AACCCAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (17 bp):
TAAAAATATAAAAAAAC
Found at i:13274484 original size:18 final size:18
Alignment explanation
Indices: 13274445--13274484 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13274435 CAAAACTTTT
* *
13274445 AAAAATATAAAAAAACTA
1 AAAAATAAAAAAAAACCA
13274463 AAAAATAAAAAAAAACCCA
1 AAAAATAAAAAAAAA-CCA
13274482 AAA
1 AAA
13274485 CATCTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (18 bp):
AAAAATAAAAAAAAACCA
Found at i:13274587 original size:10 final size:9
Alignment explanation
Indices: 13274564--13274597 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
13274554 CAGAGCTTCA
*
13274564 AAAAATTTT
1 AAAAATTTC
13274573 AAAAATTTC
1 AAAAATTTC
13274582 ATAAAATTTC
1 A-AAAATTTC
13274592 AAAAAT
1 AAAAAT
13274598 GTGTTTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAAATTTC
Found at i:13274587 original size:19 final size:19
Alignment explanation
Indices: 13274560--13274597 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
13274550 TATTCAGAGC
*
13274560 TTCAAAAAATTTTAAAAAT
1 TTCAAAAAATTTCAAAAAT
*
13274579 TTCATAAAATTTCAAAAAT
1 TTCAAAAAATTTCAAAAAT
13274598 GTGTTTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
TTCAAAAAATTTCAAAAAT
Found at i:13275750 original size:29 final size:28
Alignment explanation
Indices: 13275716--13275819 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 28
13275706 ATTTAAAATT
* *
13275716 TTATAAAAATGTATAAAATTCTTAAAAAC
1 TTATAAAAATATATAAAATT-ATAAAAAC
*
13275745 TTATAAAAAT-TATTGAAAATTAT-AAAAG
1 TTATAAAAATATA-T-AAAATTATAAAAAC
*
13275773 TTATTAAAAATAT-TAAAATTGATATAAAC
1 TTA-TAAAAATATATAAAATT-ATAAAAAC
*
13275802 TTATATAAATATATAAAA
1 TTATAAAAATATATAAAA
13275820 AAAAGTCATA
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
27 6 0.10
28 20 0.32
29 30 0.48
30 7 0.11
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.37
Consensus pattern (28 bp):
TTATAAAAATATATAAAATTATAAAAAC
Found at i:13275753 original size:10 final size:9
Alignment explanation
Indices: 13275614--13275820 Score: 84
Period size: 10 Copynumber: 21.4 Consensus size: 9
13275604 AAATATCAGG
13275614 AAAATTAT-
1 AAAATTATA
13275622 AAAATTCATAAA
1 AAAATT-AT--A
13275634 AAAATTATA
1 AAAATTATA
*
13275643 ACAAA-AATA
1 A-AAATTATA
* *
13275652 AAAAATCTA
1 AAAATTATA
*
13275661 ATAAATTTTA
1 A-AAATTATA
13275671 ATAAATTAT-
1 A-AAATTATA
*
13275680 AAAATTTTA
1 AAAATTATA
13275689 TAAAATTAATTA
1 -AAAATT-A-TA
13275701 AATATATT-TA
1 AA-A-ATTATA
*
13275711 AAATTTTATA
1 AAA-ATTATA
13275721 AAAATGTAT-
1 AAAAT-TATA
*
13275730 AAAATTCTTA
1 AAAATT-ATA
13275740 AAAACTTATA
1 AAAA-TTATA
*
13275750 AAAATTATTG
1 AAAATTA-TA
13275760 AAAATTATA
1 AAAATTATA
*
13275769 AAAGTTATTA
1 AAAATTA-TA
*
13275779 AAAA-TATT
1 AAAATTATA
13275787 AAAATTGATA
1 AAAATT-ATA
*
13275797 TAAACTTATA
1 -AAAATTATA
*
13275807 TAAATATATA
1 AAAAT-TATA
13275817 AAAA
1 AAAA
13275821 AAAGTCATAA
Statistics
Matches: 153, Mismatches: 22, Indels: 46
0.69 0.10 0.21
Matches are distributed among these distances:
8 21 0.14
9 39 0.25
10 70 0.46
11 11 0.07
12 9 0.06
13 3 0.02
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
AAAATTATA
Found at i:13275800 original size:11 final size:10
Alignment explanation
Indices: 13275677--13275819 Score: 88
Period size: 10 Copynumber: 14.7 Consensus size: 10
13275667 TTTAATAAAT
*
13275677 TATAAAATTT
1 TATAAAATTA
13275687 TATAAAATTA
1 TATAAAATTA
*
13275697 -ATTAAATATA
1 TATAAAAT-TA
* *
13275707 TTTAAAATTT
1 TATAAAATTA
* *
13275717 TATAAAAATG
1 TATAAAATTA
*
13275727 TATAAAATTC
1 TATAAAATTA
13275737 T-TAAAAACTTA
1 TAT-AAAA-TTA
13275748 TA-AAAATTA
1 TATAAAATTA
13275757 T-TGAAAATTA
1 TAT-AAAATTA
*
13275767 TA-AAAGTTA
1 TATAAAATTA
*
13275776 T-TAAAAATA
1 TATAAAATTA
13275785 T-TAAAATTGA
1 TATAAAATT-A
*
13275795 TATAAACTTA
1 TATAAAATTA
13275805 TAT-AAA-TA
1 TATAAAATTA
13275813 TATAAAA
1 TATAAAA
13275820 AAAAGTCATA
Statistics
Matches: 104, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
8 5 0.05
9 35 0.34
10 50 0.48
11 14 0.13
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (10 bp):
TATAAAATTA
Found at i:13275812 original size:28 final size:26
Alignment explanation
Indices: 13275673--13275819 Score: 96
Period size: 29 Copynumber: 5.1 Consensus size: 26
13275663 AAATTTTAAT
* *
13275673 AAATTATAAAATTTTATAAAATTAATTA
1 AAATTATAAAA-CTTATAAAAAT-ATTA
* * *
13275701 AATATATTTAAAATTTTATAAAAATGTATA
1 AA-AT-TATAAAA-CTTATAAAAATAT-TA
*
13275731 AAATTCTTAAAAACTTATAAAAATTATTGA
1 AAATT-AT-AAAACTTATAAAAA-TATT-A
*
13275761 AAATTATAAAAGTTATTAAAAATATTA
1 AAATTATAAAACTTA-TAAAAATATTA
*
13275788 AAATTGATATAAACTTATATAAATATATA
1 AAATT-ATA-AAACTTATAAAAATAT-TA
13275817 AAA
1 AAA
13275820 AAAAGTCATA
Statistics
Matches: 99, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
27 6 0.06
28 25 0.25
29 35 0.35
30 33 0.33
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (26 bp):
AAATTATAAAACTTATAAAAATATTA
Found at i:13276234 original size:16 final size:16
Alignment explanation
Indices: 13276205--13276246 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
13276195 TTAGTTTAGT
13276205 TTAATAAAAT-AAAAGA
1 TTAA-AAAATAAAAAGA
*
13276221 TTAAAAAATAAAAAATA
1 TTAAAAAAT-AAAAAGA
13276238 TTAAAAAAT
1 TTAAAAAAT
13276247 CGGTTCAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 4 0.17
17 14 0.61
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
TTAAAAAATAAAAAGA
Found at i:13276490 original size:20 final size:20
Alignment explanation
Indices: 13276445--13276490 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
13276435 ATTTTTTAAG
*
13276445 ATTTTTATACGTTTTTATGA
1 ATTTTTAAACGTTTTTATGA
* * *
13276465 AATTTTAAATGTTTTTATTA
1 ATTTTTAAACGTTTTTATGA
13276485 ATTTTT
1 ATTTTT
13276491 TATAATATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (20 bp):
ATTTTTAAACGTTTTTATGA
Found at i:13280253 original size:30 final size:30
Alignment explanation
Indices: 13280206--13280263 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
13280196 AGAAATTTTA
*
13280206 GATTAAATTAAATTTTTATTATTT-TTAAAG
1 GATTAAAATAAATTTTTATT-TTTATTAAAG
13280236 GATTAAAATATAA-TTTTATTTTTATTAA
1 GATTAAAATA-AATTTTTATTTTTATTAA
13280264 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 20 0.80
31 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
GATTAAAATAAATTTTTATTTTTATTAAAG
Found at i:13284577 original size:20 final size:20
Alignment explanation
Indices: 13284552--13284616 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
13284542 GACAGATAAC
* *
13284552 GCCACAAGGGCTAGCAGAAT
1 GCCACAAAGGCTAACAGAAT
13284572 GCCACAAAGGCTAACAGAAT
1 GCCACAAAGGCTAACAGAAT
*
13284592 GTCACAAAGGCTAACAGAAT
1 GCCACAAAGGCTAACAGAAT
13284612 GCCAC
1 GCCAC
13284617 CTAGGTACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (20 bp):
GCCACAAAGGCTAACAGAAT
Found at i:13286515 original size:12 final size:12
Alignment explanation
Indices: 13286463--13286521 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
13286453 TCAAATAACC
*
13286463 AAAATAACAACA
1 AAAACAACAACA
* *
13286475 AAAACAGCAGCA
1 AAAACAACAACA
* *
13286487 AAAACAATAA-T
1 AAAACAACAACA
13286498 AAAACAACAA-A
1 AAAACAACAACA
13286509 AACAACAACAACA
1 AA-AACAACAACA
13286522 TCAAAATAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
11 11 0.31
12 24 0.67
13 1 0.03
ACGTcount: A:0.71, C:0.20, G:0.03, T:0.05
Consensus pattern (12 bp):
AAAACAACAACA
Found at i:13286571 original size:14 final size:14
Alignment explanation
Indices: 13286534--13286574 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
13286524 AAAATAATAA
13286534 AAAAATACCAAAA-
1 AAAAATACCAAAAT
* *
13286547 CAACA-ACCAAAAT
1 AAAAATACCAAAAT
13286560 AAAAATACCAAAAT
1 AAAAATACCAAAAT
13286574 A
1 A
13286575 GTAAAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
12 7 0.32
13 6 0.27
14 9 0.41
ACGTcount: A:0.71, C:0.20, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAATACCAAAAT
Found at i:13286610 original size:30 final size:32
Alignment explanation
Indices: 13286569--13286630 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
13286559 TAAAAATACC
* *
13286569 AAAATAGTAAAAAA-A-ACCAAAATATCAATT
1 AAAACAGTAAAAAACACACCAAAATAGCAATT
13286599 AAAACAGTAAAAAACAGCACCAAAATAGCAAT
1 AAAACAGTAAAAAACA-CACCAAAATAGCAAT
13286631 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 13 0.48
31 1 0.04
33 13 0.48
ACGTcount: A:0.65, C:0.15, G:0.06, T:0.15
Consensus pattern (32 bp):
AAAACAGTAAAAAACACACCAAAATAGCAATT
Found at i:13289656 original size:102 final size:102
Alignment explanation
Indices: 13289480--13289679 Score: 355
Period size: 102 Copynumber: 2.0 Consensus size: 102
13289470 TCATTCCAGT
* * *
13289480 GGATGCAGACAATGGATTAAACACCAATAATATTCCTATAAAAAAGAGGACTGGTACTCCGCTGC
1 GGATGCAGACAATGGAATAAACACCAACAACATTCCTATAAAAAAGAGGACTGGTACTCCGCTGC
13289545 AATTTCTTCAGGAAGATTCCACTGAAATGTTTCTCCC
66 AATTTCTTCAGGAAGATTCCACTGAAATGTTTCTCCC
* *
13289582 GGATGGAGACAATGGAATAAACACCAACAACATTCCTATAGAAAAGAGGACTGGTACTCCGCTGC
1 GGATGCAGACAATGGAATAAACACCAACAACATTCCTATAAAAAAGAGGACTGGTACTCCGCTGC
13289647 AATTTCTTCAGGAAGATTCCACTGAAATGTTTC
66 AATTTCTTCAGGAAGATTCCACTGAAATGTTTC
13289680 GGGGAGATCC
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 93 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (102 bp):
GGATGCAGACAATGGAATAAACACCAACAACATTCCTATAAAAAAGAGGACTGGTACTCCGCTGC
AATTTCTTCAGGAAGATTCCACTGAAATGTTTCTCCC
Found at i:13291421 original size:31 final size:31
Alignment explanation
Indices: 13291386--13291458 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
13291376 AACAATCTAG
*
13291386 TGACTTAAATAAAAATTTTC-AACTAGTTCAA
1 TGACTTAAATAAAAACTTTCGAA-TAGTTCAA
* *
13291417 TGACTTAAATGAAAACTTTCGAATAGTTTAA
1 TGACTTAAATAAAAACTTTCGAATAGTTCAA
*
13291448 TAACCTTAAAT
1 TGA-CTTAAAT
13291459 GTATTTTGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 27 0.75
32 9 0.25
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCGAATAGTTCAA
Found at i:13293451 original size:2 final size:2
Alignment explanation
Indices: 13293444--13293480 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
13293434 TTTGTGTATA
*
13293444 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
13293481 TCTTTTGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:13296400 original size:27 final size:25
Alignment explanation
Indices: 13296370--13296423 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
13296360 TAAAATATAA
13296370 AATTTGAAATTTTTTATAAATATTTTG
1 AATTT-AAATTTTTTATAAAT-TTTTG
* * *
13296397 AATTTTAATTTTTTTTGAATTTTTG
1 AATTTAAATTTTTTATAAATTTTTG
13296422 AA
1 AA
13296424 AATTATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.29
26 12 0.50
27 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (25 bp):
AATTTAAATTTTTTATAAATTTTTG
Found at i:13301903 original size:16 final size:17
Alignment explanation
Indices: 13301871--13301903 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13301861 AAAACAATAT
13301871 TTTAAAAAATCTAAATG
1 TTTAAAAAATCTAAATG
*
13301888 TTTAATAAAT-TAAATG
1 TTTAAAAAATCTAAATG
13301904 ACAAATGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (17 bp):
TTTAAAAAATCTAAATG
Found at i:13307932 original size:20 final size:19
Alignment explanation
Indices: 13307907--13307944 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
13307897 AATTCTCTAA
*
13307907 AAATAAAATATTAAAATATT
1 AAATAAAAT-TCAAAATATT
13307927 AAATAAAATTCAAAATAT
1 AAATAAAATTCAAAATAT
13307945 GAATATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATAAAATTCAAAATATT
Found at i:13308257 original size:19 final size:19
Alignment explanation
Indices: 13308235--13308285 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
13308225 TCTTCTGAAT
*
13308235 TTTTATATATTTATTTATG
1 TTTTATATATTTATTAATG
*
13308254 TTTTTTATATTT-TTAATG
1 TTTTATATATTTATTAATG
*
13308272 TGTTTATACATTTA
1 T-TTTATATATTTA
13308286 ATAAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTTATATATTTATTAATG
Found at i:13310045 original size:22 final size:21
Alignment explanation
Indices: 13310027--13310069 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
13310017 TAAAAATTAT
*
13310027 AATAT-TTTTTTTTATAAATA
1 AATATATTATTTTTATAAATA
13310047 AATATATTATTTTTATAATATA
1 AATATATTATTTTTATAA-ATA
13310069 A
1 A
13310070 GGCACGGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATATATTATTTTTATAAATA
Found at i:13310996 original size:13 final size:13
Alignment explanation
Indices: 13310978--13311007 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13310968 TATTTTGTAG
*
13310978 TACAAATTGTAAT
1 TACAAATCGTAAT
13310991 TACAAATCGTAAT
1 TACAAATCGTAAT
13311004 TACA
1 TACA
13311008 CGATTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (13 bp):
TACAAATCGTAAT
Found at i:13327531 original size:2 final size:2
Alignment explanation
Indices: 13327524--13327548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13327514 CTAGCTTAAG
13327524 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13327549 GGGGCGAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13327773 original size:2 final size:2
Alignment explanation
Indices: 13327766--13327794 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13327756 GTTTCACCCC
13327766 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13327795 TCTAATTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13333219 original size:101 final size:103
Alignment explanation
Indices: 13333063--13333271 Score: 298
Period size: 103 Copynumber: 2.0 Consensus size: 103
13333053 CCAAACTTAG
* * * * *
13333063 AACATCCATTAGAAAGAAAATCTAAACTTAAAACACTCATCAATTCATT-AAAAAAACCAAAAAC
1 AACACCCATTAGAAAGAAAATCCAAACATAAAACACCCATCAATCCATTAAAAAAAACCAAAAAC
*
13333127 TTAATATCACAAATAAAATCC-TAAAAAGTAACATATCA
66 TTAACATCACAAATAAAA-CCTTAAAAAGTAACATATCA
* * *
13333165 AACACCCATTAGAAA-AAAATCCAGACATATAACACCCATCAATCCATTTAAAAAAAATCAAAAA
1 AACACCCATTAGAAAGAAAATCCAAACATAAAACACCCATCAATCCA-TTAAAAAAAACCAAAAA
13333229 CTTAACATCACAAATAAAACCTTAAAAAGTAACATATCA
65 CTTAACATCACAAATAAAACCTTAAAAAGTAACATATCA
13333268 AACA
1 AACA
13333272 TCCAAACTTA
Statistics
Matches: 95, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
101 25 0.26
102 18 0.19
103 52 0.55
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (103 bp):
AACACCCATTAGAAAGAAAATCCAAACATAAAACACCCATCAATCCATTAAAAAAAACCAAAAAC
TTAACATCACAAATAAAACCTTAAAAAGTAACATATCA
Found at i:13333337 original size:86 final size:88
Alignment explanation
Indices: 13333195--13333357 Score: 249
Period size: 86 Copynumber: 1.9 Consensus size: 88
13333185 CCAGACATAT
* *
13333195 AACACCCATCAATCCATTTAAAAAAAATCAAAAACTTAACATCACAAATAAAACCTTAAAAAGTA
1 AACACACATCAATCCATTTAAAAAAAATCAAAAACTGAACATCACAAATAAAACCTTAAAAAGTA
13333260 ACATATCAAACATCCAAACTTAG
66 ACATATCAAACATCCAAACTTAG
* * * * *
13333283 AACACACATCAATCCA-TTAAAAAAACT-AGAAACTGAGCTTCACAAATAAAACCTTAAAAATTA
1 AACACACATCAATCCATTTAAAAAAAATCAAAAACTGAACATCACAAATAAAACCTTAAAAAGTA
13333346 ACATATCAAACA
66 ACATATCAAACA
13333358 AAACCATCAT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
86 43 0.63
87 10 0.15
88 15 0.22
ACGTcount: A:0.55, C:0.22, G:0.03, T:0.20
Consensus pattern (88 bp):
AACACACATCAATCCATTTAAAAAAAATCAAAAACTGAACATCACAAATAAAACCTTAAAAAGTA
ACATATCAAACATCCAAACTTAG
Found at i:13333843 original size:22 final size:20
Alignment explanation
Indices: 13333814--13333859 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
13333804 GGAGAGGAAA
* *
13333814 GAAAAAATTAAATGGAAATGG
1 GAAAAAAATAAAAGGAAA-GG
*
13333835 GAAAAAAATAAAAGGGAAGG
1 GAAAAAAATAAAAGGAAAGG
13333855 GAAAA
1 GAAAA
13333860 CGGGAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (20 bp):
GAAAAAAATAAAAGGAAAGG
Found at i:13333886 original size:20 final size:21
Alignment explanation
Indices: 13333863--13333907 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
13333853 GGGAAAACGG
* *
13333863 GAAAAGAAAAT-AATAAAAGA
1 GAAAAGAAAATGAAGAAAAAA
*
13333883 GAAAGGAAAATGAAGAAAAAA
1 GAAAAGAAAATGAAGAAAAAA
13333904 GAAA
1 GAAA
13333908 TGACATCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (21 bp):
GAAAAGAAAATGAAGAAAAAA
Found at i:13336055 original size:52 final size:51
Alignment explanation
Indices: 13335968--13336212 Score: 240
Period size: 52 Copynumber: 4.7 Consensus size: 51
13335958 ATTTCACTTC
* * ** *
13335968 ATTCATATACTCATGATGACACATAGCCA-CTGGACCTTATAAACCACGAGGG
1 ATTCATATACTCACGATGACACATAGTCATC-GGACCTT-TAAACCATAAAGG
* * * *
13336020 ATTCCTATACTCACGATGACACAAAGTCATCGGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCT-TTAAACCATAAAGG
* * * *
13336072 ATCCATATACTCACGATGACCCTTTGTCATCGGACCTTTAAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTTTAAA-CCATAAAGG
* * * *
13336124 ATCTCATATACTCACGATGACACTTAGTCATCGGAACTCATAATCCATAAAGG
1 AT-TCATATACTCACGATGACACATAGTCATCGGACCT-TTAAACCATAAAGG
* * * *
13336177 ATTCATTTACTCACGATGACACTTAATCATCAGACC
1 ATTCATATACTCACGATGACACATAGTCATCGGACC
13336213 CTTTTTCATT
Statistics
Matches: 161, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
51 4 0.02
52 110 0.68
53 44 0.27
54 3 0.02
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCTTTAAACCATAAAGG
Found at i:13337097 original size:21 final size:22
Alignment explanation
Indices: 13337073--13337119 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
13337063 ACTTTCTTTA
13337073 TTAA-CTTAATTAA-TCATATTT
1 TTAACCTTAA-TAATTCATATTT
*
13337094 TTAACCTTAATAATTCTTATTT
1 TTAACCTTAATAATTCATATTT
13337116 TTAA
1 TTAA
13337120 TCAATATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAACCTTAATAATTCATATTT
Found at i:13355196 original size:17 final size:17
Alignment explanation
Indices: 13355170--13355212 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
13355160 AGAAAACAGT
*
13355170 AGTTACAAGAATATGAAA
1 AGTTA-AAGAAGATGAAA
13355188 AGTTAAAGAAGATGAAA
1 AGTTAAAGAAGATGAAA
*
13355205 GGTTAAAG
1 AGTTAAAG
13355213 GTCAAGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.23, T:0.21
Consensus pattern (17 bp):
AGTTAAAGAAGATGAAA
Found at i:13356484 original size:16 final size:17
Alignment explanation
Indices: 13356445--13356485 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
13356435 ATAATAAAAA
13356445 TATAATTTTATTATTTT
1 TATAATTTTATTATTTT
*
13356462 AAT-ATTTTA-TATTTT
1 TATAATTTTATTATTTT
13356477 TATAATTTT
1 TATAATTTT
13356486 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 8 0.38
16 11 0.52
17 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATAATTTTATTATTTT
Found at i:13356961 original size:19 final size:20
Alignment explanation
Indices: 13356928--13356968 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
13356918 TTTATATATT
13356928 TTTTATAATTTTTTTGAAAA
1 TTTTATAATTTTTTTGAAAA
*
13356948 TTTTATAATTTTTTTAAAAA
1 TTTTATAATTTTTTTGAAAA
13356968 T
1 T
13356969 ATAAATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTATAATTTTTTTGAAAA
Found at i:13357052 original size:21 final size:20
Alignment explanation
Indices: 13356958--13357045 Score: 90
Period size: 20 Copynumber: 4.2 Consensus size: 20
13356948 TTTTATAATT
13356958 TTTTTAAAAATATAAATTTTGAAA
1 TTTTTAAAAAT-T--ATTTTG-AA
* *
13356982 TTTTTATAAA-TATTTGGAA
1 TTTTTAAAAATTATTTTGAA
*
13357001 -TTTTAAAAACTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
13357020 TTTTTAAAAATTATTTTGAAA
1 TTTTTAAAAATTATTTTG-AA
13357041 TTTTT
1 TTTTT
13357046 TGTAATTTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
18 8 0.14
19 10 0.18
20 21 0.38
21 7 0.12
22 1 0.02
24 9 0.16
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:13367532 original size:21 final size:22
Alignment explanation
Indices: 13367468--13367532 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
13367458 TCTCATATTT
13367468 TTTTTGGAAAATTTATAATT-TA-
1 TTTTT-GAAAA-TTATAATTATAC
**
13367490 TTTTTGAAAATTATAAAAATAC
1 TTTTTGAAAATTATAATTATAC
13367512 TTTTT-AAAATTATAATTATAC
1 TTTTTGAAAATTATAATTATAC
13367533 AAAGAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.16
21 21 0.57
22 10 0.27
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTTTGAAAATTATAATTATAC
Found at i:13367786 original size:14 final size:15
Alignment explanation
Indices: 13367762--13367790 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13367752 TAAAAACTTT
13367762 TTTTATTTAAAAATA
1 TTTTATTTAAAAATA
13367777 TTTT-TTTAAAAATA
1 TTTTATTTAAAAATA
13367791 GAGATAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTATTTAAAAATA
Found at i:13387282 original size:21 final size:21
Alignment explanation
Indices: 13387234--13387284 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
13387224 AATCTAGAAT
*
13387234 TCTTTTATCAAAAAGATTCAA
1 TCTTTTTTCAAAAAGATTCAA
13387255 TCTTTTTTCAAAAAGATTCAA
1 TCTTTTTTCAAAAAGATTCAA
13387276 TCTTTTTTC
1 TCTTTTTTC
13387285 GCACCAGCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (21 bp):
TCTTTTTTCAAAAAGATTCAA
Found at i:13393285 original size:3 final size:3
Alignment explanation
Indices: 13393277--13393326 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
13393267 TACATCCCAA
13393277 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13393323 AAT A
1 AAT A
13393327 GAATATTCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:13394503 original size:15 final size:15
Alignment explanation
Indices: 13394485--13394514 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13394475 TGGTTCATTT
13394485 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
13394500 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
13394515 AATTTGGGTT
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:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:13394524 original size:21 final size:22
Alignment explanation
Indices: 13394498--13394544 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
13394488 TTGGTTCAAA
*
13394498 TGGGTTTGGTTTAAATGA-ATT
1 TGGGTTTGGTTTAAATAAGATT
13394519 TGGGTTTGGTTTAAATAAGATT
1 TGGGTTTGGTTTAAATAAGATT
13394541 TGGG
1 TGGG
13394545 CTTAATGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (22 bp):
TGGGTTTGGTTTAAATAAGATT
Found at i:13397081 original size:24 final size:26
Alignment explanation
Indices: 13397048--13397102 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
13397038 GTATAAAAGC
*
13397048 AAAATGAATTATTATATT-AAAAA-TT
1 AAAATGAATTATAAT-TTAAAAAATTT
13397073 AAAAT-AATTATAATTTAAAAAATTT
1 AAAATGAATTATAATTTAAAAAATTT
13397098 AAAAT
1 AAAAT
13397103 TATTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 2 0.07
24 13 0.48
25 12 0.44
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAATGAATTATAATTTAAAAAATTT
Found at i:13406723 original size:93 final size:95
Alignment explanation
Indices: 13406624--13406807 Score: 255
Period size: 93 Copynumber: 1.9 Consensus size: 95
13406614 TGATGTTAAG
* * *
13406624 GTTTAAGATTTGGGTTTAAAGGTTTAAGGGTTTGAGGTTATGTAGTATGAGTTTA-TG-ATTCAA
1 GTTTAAGATTCGAGTTTAAAGGTTTAAGGGTTTGAGATTATGTAGTATGAGTTTAGTGTATTCAA
13406687 GGTTTAAGGGTTTGAGGTTATGGGGTACGA
66 GGTTTAAGGGTTTGAGGTTATGGGGTACGA
* * *
13406717 GTTTAAGGTTCGAGTTTAAAGGTTTAAGGGTTTGAGATTATGTGGTATGAGTTTAGGGTTTGTGT
1 GTTTAAGATTCGAGTTTAAAGGTTTAAGGGTTTGAGATTATGTAGTATGAGTTTA--G--TGTAT
*
13406782 TTAAGGTTTAAGGGTTTGAGGTTATG
62 TCAAGGTTTAAGGGTTTGAGGTTATG
13406808 AGATATGAGT
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
93 50 0.64
98 2 0.03
99 26 0.33
ACGTcount: A:0.23, C:0.02, G:0.34, T:0.41
Consensus pattern (95 bp):
GTTTAAGATTCGAGTTTAAAGGTTTAAGGGTTTGAGATTATGTAGTATGAGTTTAGTGTATTCAA
GGTTTAAGGGTTTGAGGTTATGGGGTACGA
Found at i:13406744 original size:50 final size:49
Alignment explanation
Indices: 13406637--13406825 Score: 212
Period size: 50 Copynumber: 3.9 Consensus size: 49
13406627 TAAGATTTGG
13406637 GTTTAAAGGTTTAAGGGTTTGAGGTTATGTA-GTATGAGTTT-A---T-GA
1 GTTT-AAGGTTTAAGGGTTTGAGGTTATG-AGGTATGAGTTTAAGGTTCGA
* * *
13406682 -TTCAAGGTTTAAGGGTTTGAGGTTATGGGGTACGAGTTTAAGGTTCGA
1 GTTTAAGGTTTAAGGGTTTGAGGTTATGAGGTATGAGTTTAAGGTTCGA
* * * * *
13406730 GTTTAAAGGTTTAAGGGTTTGAGATTATGTGGTATGAGTTTAGGGTTTGT
1 GTTT-AAGGTTTAAGGGTTTGAGGTTATGAGGTATGAGTTTAAGGTTCGA
* *
13406780 GTTTAAGGTTTAAGGGTTTGAGGTTATGAGATATGAGTTCAAGGTT
1 GTTTAAGGTTTAAGGGTTTGAGGTTATGAGGTATGAGTTTAAGGTT
13406826 TTGGTTCAAG
Statistics
Matches: 121, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
43 33 0.27
44 3 0.02
47 1 0.01
48 2 0.02
49 39 0.32
50 43 0.36
ACGTcount: A:0.24, C:0.02, G:0.33, T:0.40
Consensus pattern (49 bp):
GTTTAAGGTTTAAGGGTTTGAGGTTATGAGGTATGAGTTTAAGGTTCGA
Found at i:13410027 original size:1 final size:1
Alignment explanation
Indices: 13410021--13410045 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
13410011 TTTGAACGTT
13410021 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
13410046 GCGTCTCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:13427340 original size:15 final size:16
Alignment explanation
Indices: 13427320--13427353 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
13427310 AACCTTTTAA
13427320 AAATTATGAAAAT-AT
1 AAATTATGAAAATAAT
*
13427335 AAATTATTAAAATAAT
1 AAATTATGAAAATAAT
13427351 AAA
1 AAA
13427354 ATTACATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATGAAAATAAT
Found at i:13431116 original size:27 final size:26
Alignment explanation
Indices: 13431086--13431137 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
13431076 GCCTTGTCAC
*
13431086 AATAAGTAATTTAATCCAGTTTACCTA
1 AATAAGTAATTTAAT-CAATTTACCTA
13431113 AATAAGTAATTTAATCAATTTACCT
1 AATAAGTAATTTAATCAATTTACCT
13431138 CTCGATTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (26 bp):
AATAAGTAATTTAATCAATTTACCTA
Found at i:13433228 original size:30 final size:31
Alignment explanation
Indices: 13433173--13433231 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
13433163 TTTAGTTTCA
*
13433173 TCAATTTTAGTTTTTATATTTTTTGAATTAG
1 TCAATTTTAATTTTTATATTTTTTGAATTAG
13433204 TCAATTTTAATTTTTATA-TTTTTGAATT
1 TCAATTTTAATTTTTATATTTTTTGAATT
13433232 CTAAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (31 bp):
TCAATTTTAATTTTTATATTTTTTGAATTAG
Found at i:13433240 original size:30 final size:31
Alignment explanation
Indices: 13433175--13433242 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
13433165 TAGTTTCATC
* * *
13433175 AATTTTAGTTTTTATATTTTTTGAATTAGTC
1 AATTTTAATTTTTATATTTTTTGAATTACTA
13433206 AATTTTAATTTTTATA-TTTTTGAATT-CTAA
1 AATTTTAATTTTTATATTTTTTGAATTACT-A
13433236 AATTTTA
1 AATTTTA
13433243 GTCTTGACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 17 0.52
31 15 0.45
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (31 bp):
AATTTTAATTTTTATATTTTTTGAATTACTA
Found at i:13433830 original size:17 final size:17
Alignment explanation
Indices: 13433800--13433833 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
13433790 AAGTGGATTC
13433800 CTCCAAAAATAAAATTT
1 CTCCAAAAATAAAATTT
13433817 CTCCATAAAA-AAAATTT
1 CTCCA-AAAATAAAATTT
13433834 TAGTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (17 bp):
CTCCAAAAATAAAATTT
Found at i:13440419 original size:14 final size:15
Alignment explanation
Indices: 13440400--13440438 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
13440390 TCTTTTGACT
13440400 AAAAATGATTTTC-A
1 AAAAATGATTTTCTA
*
13440414 AAAAAT-ATTTTCTG
1 AAAAATGATTTTCTA
13440428 AAAAATGATTT
1 AAAAATGATTT
13440439 ACTTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 6 0.27
14 12 0.55
15 4 0.18
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (15 bp):
AAAAATGATTTTCTA
Found at i:13442590 original size:25 final size:25
Alignment explanation
Indices: 13442562--13442616 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
13442552 AAAACAAAAA
13442562 TGTTTGAAGGTTTCGAAA-ATTACCT
1 TGTTTGAAGGTTTC-AAAGATTACCT
*
13442587 TGTTTGAGGGTTTCAAAGATTACCT
1 TGTTTGAAGGTTTCAAAGATTACCT
13442612 TGTTT
1 TGTTT
13442617 TTCGGGTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 3 0.11
25 25 0.89
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.44
Consensus pattern (25 bp):
TGTTTGAAGGTTTCAAAGATTACCT
Found at i:13449112 original size:19 final size:19
Alignment explanation
Indices: 13449088--13449126 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
13449078 CTTACACAAT
*
13449088 TTTCAGGCTTTGTGCCTAG
1 TTTCAGGCTATGTGCCTAG
13449107 TTTCAGGCTATGTGCCTAG
1 TTTCAGGCTATGTGCCTAG
13449126 T
1 T
13449127 AGGCTTCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.26, T:0.41
Consensus pattern (19 bp):
TTTCAGGCTATGTGCCTAG
Found at i:13449155 original size:37 final size:35
Alignment explanation
Indices: 13449091--13449169 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 35
13449081 ACACAATTTT
* * *
13449091 CAGGCTTTGTGCCTAGTTTCAGGCTATGTGCCTAG
1 CAGGCTTCGTGCCGAGTTTCAGGCTATGAGCCTAG
* *
13449126 TAGGCTTCGTGCCGATGTATTCAGGCTATGAGCTTAG
1 CAGGCTTCGTGCCGA-GT-TTCAGGCTATGAGCCTAG
13449163 CAGGCTT
1 CAGGCTT
13449170 TATGACAGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 12 0.33
36 2 0.06
37 22 0.61
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (35 bp):
CAGGCTTCGTGCCGAGTTTCAGGCTATGAGCCTAG
Found at i:13451409 original size:27 final size:28
Alignment explanation
Indices: 13451368--13451422 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
13451358 AAATAAATTT
* *
13451368 TATAAAAATTATTAAATTTTAATAAAAA
1 TATAAAAACTATTAAAATTTAATAAAAA
*
13451396 TATAAAAACT-TTAAAATTTATTAAAAA
1 TATAAAAACTATTAAAATTTAATAAAAA
13451423 ATCAAACTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
TATAAAAACTATTAAAATTTAATAAAAA
Found at i:13451470 original size:36 final size:36
Alignment explanation
Indices: 13451417--13451488 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
13451407 TAAAATTTAT
13451417 TAAAAAATCAAACTTTTTTATAAAAATCATAAAAAA
1 TAAAAAATCAAACTTTTTTATAAAAATCATAAAAAA
* *
13451453 TAAAAAAT-AAATTTTTTTTATAGAAATCATAAAAAA
1 TAAAAAATCAAA-CTTTTTTATAAAAATCATAAAAAA
13451489 ATTATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 3 0.09
36 30 0.91
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.33
Consensus pattern (36 bp):
TAAAAAATCAAACTTTTTTATAAAAATCATAAAAAA
Found at i:13451772 original size:10 final size:9
Alignment explanation
Indices: 13451732--13451845 Score: 67
Period size: 9 Copynumber: 12.7 Consensus size: 9
13451722 CTTTATAAGA
13451732 TTTTATAAGT
1 TTTTATAA-T
13451742 TTTTAT-AT
1 TTTTATAAT
*
13451750 TTCTAT-AT
1 TTTTATAAT
13451758 ATTTTATAAT
1 -TTTTATAAT
*
13451768 TTTTTTACGAT
1 TTTTATA--AT
*
13451779 TTTTATAAA
1 TTTTATAAT
*
13451788 TTTTACAA-
1 TTTTATAAT
*
13451796 TTTTACAATT
1 TTTTATAA-T
*
13451806 TTTTACAAT
1 TTTTATAAT
*
13451815 TTTTAT-TT
1 TTTTATAAT
*
13451823 TTTTCT-AT
1 TTTTATAAT
*
13451831 TTTAATAAT
1 TTTTATAAT
13451840 TTTTAT
1 TTTTAT
13451846 TAAAAATTAA
Statistics
Matches: 84, Mismatches: 13, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
8 27 0.32
9 33 0.39
10 16 0.19
11 8 0.10
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:13451785 original size:29 final size:28
Alignment explanation
Indices: 13451725--13451799 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
13451715 CTTACGACTT
* *
13451725 TATAAGATTTTATAA-GTTTTTATATTTC
1 TATAA-ATTTTATAATTTTTTTAGATTTC
* *
13451753 TATATATTTTATAATTTTTTTACGATTTT
1 TATAAATTTTATAATTTTTTTA-GATTTC
*
13451782 TATAAATTTTACAATTTT
1 TATAAATTTTATAATTTT
13451800 ACAATTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
27 9 0.23
28 10 0.26
29 20 0.51
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (28 bp):
TATAAATTTTATAATTTTTTTAGATTTC
Found at i:13451792 original size:56 final size:58
Alignment explanation
Indices: 13451684--13451792 Score: 143
Period size: 56 Copynumber: 1.9 Consensus size: 58
13451674 TTTTTACGAA
* * *
13451684 TTTTATTTTTCTTTATATTCTGTATAGTTTTCTTACGACTTTATAAGATTTTATAAGT
1 TTTTATATTTCTATATATTCTGTATAATTTTCTTACGACTTTATAAGATTTTATAAGT
* *
13451742 TTTTATATTTCTATATATT-T-TATAATTTTTTTACGATTTTTATAA-ATTTTA
1 TTTTATATTTCTATATATTCTGTATAATTTTCTTACGA-CTTTATAAGATTTTA
13451793 CAATTTTACA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
56 20 0.44
57 8 0.18
58 17 0.38
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (58 bp):
TTTTATATTTCTATATATTCTGTATAATTTTCTTACGACTTTATAAGATTTTATAAGT
Found at i:13451825 original size:18 final size:18
Alignment explanation
Indices: 13451768--13451844 Score: 61
Period size: 17 Copynumber: 4.4 Consensus size: 18
13451758 ATTTTATAAT
*
13451768 TTTTTTACGATTTTTATA
1 TTTTTTACAATTTTTATA
** *
13451786 AATTTTACAA-TTTTACAA
1 TTTTTTACAATTTTTA-TA
13451804 TTTTTTACAATTTTTAT-
1 TTTTTTACAATTTTTATA
* *
13451821 TTTTTT-CTATTTTAATA
1 TTTTTTACAATTTTTATA
*
13451838 ATTTTTA
1 TTTTTTA
13451845 TTAAAAATTA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
16 8 0.18
17 16 0.36
18 16 0.36
19 5 0.11
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTTTTACAATTTTTATA
Found at i:13452036 original size:31 final size:31
Alignment explanation
Indices: 13451970--13452046 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
13451960 AAATTCTTAT
* * *
13451970 TTGGTACCTGAACTTGACACTTTTTCCTAAT
1 TTGGTACCTAAACTTAACACTTTTTCCTAAG
**
13452001 TTGGTACCTAAACTTAACACTTTTTTTTAAG
1 TTGGTACCTAAACTTAACACTTTTTCCTAAG
*
13452032 TTGGTACTTAAACTT
1 TTGGTACCTAAACTT
13452047 TTTGGGGCCC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (31 bp):
TTGGTACCTAAACTTAACACTTTTTCCTAAG
Found at i:13452348 original size:60 final size:58
Alignment explanation
Indices: 13452267--13452438 Score: 179
Period size: 60 Copynumber: 2.9 Consensus size: 58
13452257 AATTGAATCT
* * * * *
13452267 AAAAAAAGATTAGGTATCAAATTAGGAAAAAATGCCAAGTTCAAGTGTCAAATTGGGCCC
1 AAAAAAAGTTTAAGTA-CAAATTAGGAAAAAATGTCAAGTTCAAGTATCAAATTAGG-CC
* * * *
13452327 AAAAAAAGTTTAAGTACCAAATTAGGAAAAAGTGTCAAGTTTAGGTATCAAATTAGGTC
1 AAAAAAAGTTTAAGTA-CAAATTAGGAAAAAATGTCAAGTTCAAGTATCAAATTAGGCC
*
13452386 AAAAAAA-TTTAGATGT-CAAATTA-AAAAAAAGTGTCAAGTTCAAGTATCAAATT
1 AAAAAAAGTTTA-A-GTACAAATTAGGAAAAAA-TGTCAAGTTCAAGTATCAAATT
13452439 TTATATTACG
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
57 5 0.05
58 31 0.33
59 9 0.09
60 50 0.53
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.26
Consensus pattern (58 bp):
AAAAAAAGTTTAAGTACAAATTAGGAAAAAATGTCAAGTTCAAGTATCAAATTAGGCC
Found at i:13453543 original size:13 final size:13
Alignment explanation
Indices: 13453525--13453573 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
13453515 ATTTGATTTC
13453525 AATTAAAATTATA
1 AATTAAAATTATA
*
13453538 AATTAAAATAATA
1 AATTAAAATTATA
* *
13453551 AATATAAATTTATC
1 AAT-TAAAATTATA
13453565 AATTAAAAT
1 AATTAAAAT
13453574 ATTATTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATTAAAATTATA
Found at i:13454355 original size:13 final size:13
Alignment explanation
Indices: 13454337--13454385 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 13
13454327 ATTATTAATA
13454337 TTTTTAAAATTAT
1 TTTTTAAAATTAT
13454350 TTTTTAAAATTTAAGT
1 TTTTTAAAA-TT-A-T
13454366 TTATTATAAAATTAT
1 TT-TT-TAAAATTAT
13454381 TTTTT
1 TTTTT
13454386 TAATTACACG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.32
14 4 0.13
15 4 0.13
16 4 0.13
17 4 0.13
18 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTTTAAAATTAT
Found at i:13462636 original size:177 final size:177
Alignment explanation
Indices: 13462091--13462625 Score: 953
Period size: 177 Copynumber: 3.0 Consensus size: 177
13462081 GCTTTTTCAT
*
13462091 CTTCATCTCCACCATCTTCTGAATCAAGACCAGCTGCGGCCCCTTTTACTTCTGTACTCTCTTGT
1 CTTCATCTCCACCATCTACTGAATCAAGACCAGCTGCGGCCCCTTTTACTTCTGTACTCTCTTGT
*
13462156 CCCTGATAAGTATCTCCTTTTACAGGCATCTCAATTACTGTATCAGACTTGAGACTTCTTTTTTC
66 CCCTGATCAGTATCTCCTTTTACAGGCATCTCAATTACTGTATCAGACTTGAGACTTCTTTTTTC
* *
13462221 CTCGTCCCTTGGAACTTCTGTTTCTCCAGGACCATTGGTTTCAGGTA
131 CTCGTCCCTTGGAACTTCTGTTTCTCCAGTACCATTGATTTCAGGTA
* * * *
13462268 CTTCATCTCCACCATCTACTGAATCGAGAACAGCTGCGGCCTCTTTTATTTCTGTACTCTCTTGT
1 CTTCATCTCCACCATCTACTGAATCAAGACCAGCTGCGGCCCCTTTTACTTCTGTACTCTCTTGT
13462333 CCCTGATCAGTATCTCCTTTTACAGGCATCTCAATTACTGTATCAGACTTGAGACTTCTTTTTTC
66 CCCTGATCAGTATCTCCTTTTACAGGCATCTCAATTACTGTATCAGACTTGAGACTTCTTTTTTC
* *
13462398 CTTGTCCCTTGGAACTTCTGTTTCTCCAGTACCATTGATGTCAGGTA
131 CTCGTCCCTTGGAACTTCTGTTTCTCCAGTACCATTGATTTCAGGTA
* * *
13462445 CTTCATCTCCACCATCTACTGAACCAAGACCAGCTGCAGCCCCTTTTACTTCTGTAGTCTCTTGT
1 CTTCATCTCCACCATCTACTGAATCAAGACCAGCTGCGGCCCCTTTTACTTCTGTACTCTCTTGT
13462510 CCCTGATCAGTATCTCCTTTTACAGGCATCTCAATTACTGTATCAGACTTGAGACTTCTTTTTTC
66 CCCTGATCAGTATCTCCTTTTACAGGCATCTCAATTACTGTATCAGACTTGAGACTTCTTTTTTC
13462575 CTCGTCCCTTGGAACTTCTGTTTCTCCAGTACCATTGATTTCAGGTA
131 CTCGTCCCTTGGAACTTCTGTTTCTCCAGTACCATTGATTTCAGGTA
13462622 CTTC
1 CTTC
13462626 CTTCCCACCA
Statistics
Matches: 339, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
177 339 1.00
ACGTcount: A:0.19, C:0.29, G:0.14, T:0.38
Consensus pattern (177 bp):
CTTCATCTCCACCATCTACTGAATCAAGACCAGCTGCGGCCCCTTTTACTTCTGTACTCTCTTGT
CCCTGATCAGTATCTCCTTTTACAGGCATCTCAATTACTGTATCAGACTTGAGACTTCTTTTTTC
CTCGTCCCTTGGAACTTCTGTTTCTCCAGTACCATTGATTTCAGGTA
Found at i:13472007 original size:20 final size:21
Alignment explanation
Indices: 13471966--13472012 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
13471956 AGTAATGTGA
*
13471966 TTTAAAAAATATTAAATGTTT
1 TTTAAAAAATAGTAAATGTTT
13471987 TTTAAAAATATAGT-AAT-TTT
1 TTTAAAAA-ATAGTAAATGTTT
13472007 TTTAAA
1 TTTAAA
13472013 TGTTGTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 11 0.46
22 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TTTAAAAAATAGTAAATGTTT
Found at i:13473922 original size:24 final size:24
Alignment explanation
Indices: 13473870--13473922 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
13473860 TTTATGTATC
*
13473870 ATTATATTAAATTATTTAAATATT
1 ATTATATTAAATTATTAAAATATT
*
13473894 ATTATATTAAATT-TTAAAATCTT
1 ATTATATTAAATTATTAAAATATT
13473917 ACTTAT
1 A-TTAT
13473923 TATATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTATATTAAATTATTAAAATATT
Found at i:13473923 original size:22 final size:23
Alignment explanation
Indices: 13473872--13473929 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
13473862 TATGTATCAT
* *
13473872 TATATTAAATTATTTAAATATTAT
1 TATATTAAATT-TTAAAATATTAC
*
13473896 TATATTAAATTTTAAAATCTTAC
1 TATATTAAATTTTAAAATATTAC
*
13473919 T-TATTATATTT
1 TATATTAAATTT
13473930 GATTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 9 0.30
23 10 0.33
24 11 0.37
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (23 bp):
TATATTAAATTTTAAAATATTAC
Found at i:13474503 original size:3 final size:3
Alignment explanation
Indices: 13474495--13474545 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
13474485 TTTTCAACTG
13474495 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13474543 TAA
1 TAA
13474546 AGTAGGCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:13480810 original size:20 final size:20
Alignment explanation
Indices: 13480773--13480838 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 20
13480763 TACAAAATAG
* *
13480773 TCAAAATAAATTTCAAAAAT
1 TCAAAATAATTTTTAAAAAT
*
13480793 TGAAAATAATTTTT-AAAAT
1 TCAAAATAATTTTTAAAAAT
* *
13480812 TCAAAAT-GTTTATAAAAAT
1 TCAAAATAATTTTTAAAAAT
13480831 TCTAAAAT
1 TC-AAAAT
13480839 TTGTAAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 4 0.11
19 18 0.47
20 16 0.42
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (20 bp):
TCAAAATAATTTTTAAAAAT
Found at i:13482652 original size:16 final size:16
Alignment explanation
Indices: 13482613--13482656 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
13482603 CAAATCAAAT
13482613 AAATTATTAAAAATAAA
1 AAATTA-TAAAAATAAA
*
13482630 AAA-TATAAATATAAA
1 AAATTATAAAAATAAA
13482645 AAATTATAAAAA
1 AAATTATAAAAA
13482657 CTAATTCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 12 0.50
16 9 0.38
17 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATTATAAAAATAAA
Found at i:13483322 original size:9 final size:8
Alignment explanation
Indices: 13483301--13483398 Score: 53
Period size: 8 Copynumber: 11.8 Consensus size: 8
13483291 TTGTAATTTA
13483301 TTTATAATT
1 TTTA-AATT
13483310 TTTAAATT
1 TTTAAATT
*
13483318 GTTTATATT
1 -TTTAAATT
13483327 TTT-AATT
1 TTTAAATT
*
13483334 TTTGAATT
1 TTTAAATT
*
13483342 TTAAAGAGTT
1 TTTAA-A-TT
13483352 TTT--ATT
1 TTTAAATT
13483358 TTTCATAATT
1 TTT-A-AATT
13483368 TTT--ATT
1 TTTAAATT
13483374 TTTAGAATTTT
1 TTTA-AA--TT
13483385 TTTAAATT
1 TTTAAATT
13483393 TTTAAA
1 TTTAAA
13483399 ATTTATTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 27
0.69 0.05 0.26
Matches are distributed among these distances:
6 11 0.15
7 7 0.10
8 22 0.31
9 13 0.18
10 12 0.17
11 6 0.08
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (8 bp):
TTTAAATT
Found at i:13483385 original size:31 final size:31
Alignment explanation
Indices: 13483300--13483385 Score: 79
Period size: 32 Copynumber: 2.7 Consensus size: 31
13483290 CTTGTAATTT
*
13483300 ATTTATAATTTTTA-AATTGTTTATATTTTTA
1 ATTTTTAATTTTTAGAATT-TTTATATTTTTA
* *
13483331 ATTTTTGAATTTTAAAGAGTTTTTAT-TTTTCATA
1 ATTTTT-AATTTT-TAGAATTTTTATATTTT--TA
13483365 ATTTTT-ATTTTTAGAATTTTT
1 ATTTTTAATTTTTAGAATTTTT
13483386 TTAAATTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
31 13 0.29
32 15 0.33
33 6 0.13
34 11 0.24
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (31 bp):
ATTTTTAATTTTTAGAATTTTTATATTTTTA
Found at i:13491031 original size:45 final size:43
Alignment explanation
Indices: 13490976--13491065 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 43
13490966 ACAAATTTTT
*
13490976 AATTTGTATATAAAATTTTGATTTTTTAAAAAAATTATATTTATA
1 AATTTGTATATAAAATTTTGAGTTTTT--AAAAATTATATTTATA
* ** * *
13491021 AATTTTTATATATTATTTTTAGTTTTTAAAATTTATATTTATA
1 AATTTGTATATAAAATTTTGAGTTTTTAAAAATTATATTTATA
13491064 AA
1 AA
13491066 CCACAGGAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 17 0.44
45 22 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (43 bp):
AATTTGTATATAAAATTTTGAGTTTTTAAAAATTATATTTATA
Found at i:13491368 original size:31 final size:31
Alignment explanation
Indices: 13491310--13491368 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
13491300 AAACTTTTTA
* *
13491310 ATTTTTTTGAATTATTTATATATTATATATG
1 ATTTTTTTGAATTATTTAAATAGTATATATG
*
13491341 ATTTTTTTTACATT-TTTAAATAGTATAT
1 ATTTTTTTGA-ATTATTTAAATAGTATAT
13491369 TATATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (31 bp):
ATTTTTTTGAATTATTTAAATAGTATATATG
Found at i:13506652 original size:20 final size:20
Alignment explanation
Indices: 13506616--13506653 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13506606 ATTTATGATT
*
13506616 CCTTATTTCTATCTCATTAG
1 CCTTATTTCAATCTCATTAG
*
13506636 CCTTATTTCAATTTCATT
1 CCTTATTTCAATCTCATT
13506654 TCGTATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (20 bp):
CCTTATTTCAATCTCATTAG
Found at i:13506910 original size:16 final size:16
Alignment explanation
Indices: 13506884--13506923 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
13506874 ATTCTATTAT
*
13506884 ATATTTATATATTCTA
1 ATATATATATATTCTA
*
13506900 TTATATATATATTCTA
1 ATATATATATATTCTA
13506916 ATATATAT
1 ATATATAT
13506924 TAGAATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATATATATATTCTA
Found at i:13513816 original size:81 final size:81
Alignment explanation
Indices: 13513681--13513913 Score: 372
Period size: 81 Copynumber: 3.0 Consensus size: 81
13513671 CTTTAGAAAG
13513681 TGTTTGGAGTTAACATGAATATATATATGTATTAGATAGATTTGTTTGGGATTTCATATCCAGCG
1 TGTTTGGAGTTAACATGAATATATATATGTATTAGATAGATTTGTTTGGGATTTCATATCCAGCG
13513746 CCTGGTTTTTAAAATA
66 CCTGGTTTTTAAAATA
13513762 TGTTTGGAGTTAACATGAATATATATATGTATTAGATAGATTTGTTTGGGATTTCATATCCAGCG
1 TGTTTGGAGTTAACATGAATATATATATGTATTAGATAGATTTGTTTGGGATTTCATATCCAGCG
13513827 CCTGGTTTTTAAAATA
66 CCTGGTTTTTAAAATA
* * *
13513843 TGTTTGGAGTTATCAT-AA-ATATA-A---ATTGGATAGATTTGTTTGGGATTTCATAAT-CATC
1 TGTTTGGAGTTAACATGAATATATATATGTATTAGATAGATTTGTTTGGGATTTCAT-ATCCAGC
*
13513901 GCATGGTTTTTAA
65 GCCTGGTTTTTAA
13513914 GTTGGTCAAT
Statistics
Matches: 147, Mismatches: 4, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
75 41 0.28
76 2 0.01
78 1 0.01
79 5 0.03
80 2 0.01
81 96 0.65
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (81 bp):
TGTTTGGAGTTAACATGAATATATATATGTATTAGATAGATTTGTTTGGGATTTCATATCCAGCG
CCTGGTTTTTAAAATA
Found at i:13516605 original size:51 final size:51
Alignment explanation
Indices: 13516545--13516714 Score: 225
Period size: 51 Copynumber: 3.3 Consensus size: 51
13516535 TGTGGAAGAC
*
13516545 AAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACT
1 AAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAGGTCCGATGACT
* * *
13516596 AAGTGTCATCGTGAGTAAATGAATCATTTGCGAATTAAAGGTCTGATGACT
1 AAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAGGTCCGATGACT
* * * * * *
13516647 AAGTGTTATCATGAATAAATGAATCCATGAAGAATTAAAGGTCCGATGAC-
1 AAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAGGTCCGATGACT
*
13516697 AATATGTCATCGTGAGTA
1 AA-GTGTCATCGTGAGTA
13516715 TTAAATGAAA
Statistics
Matches: 101, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
50 2 0.02
51 99 0.98
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (51 bp):
AAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAGGTCCGATGACT
Found at i:13524156 original size:24 final size:23
Alignment explanation
Indices: 13524129--13524175 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
13524119 ATGGCTAAAG
13524129 AAAAAAGTCAGACCATCAACCTAT
1 AAAAAAGTC-GACCATCAACCTAT
13524153 AAAAAAGTCGACCATCAACCTAT
1 AAAAAAGTCGACCATCAACCTAT
13524176 TTATAGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.49, C:0.26, G:0.09, T:0.17
Consensus pattern (23 bp):
AAAAAAGTCGACCATCAACCTAT
Found at i:13532648 original size:2 final size:2
Alignment explanation
Indices: 13532641--13532673 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13532631 ATATCTTATC
13532641 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
13532674 ATCATTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:13534807 original size:19 final size:19
Alignment explanation
Indices: 13534783--13534819 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13534773 GTTTTAGGAC
13534783 TTTGAATCAAATTAGTTAA
1 TTTGAATCAAATTAGTTAA
**
13534802 TTTGAATTGAATTAGTTA
1 TTTGAATCAAATTAGTTA
13534820 TTTATATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.46
Consensus pattern (19 bp):
TTTGAATCAAATTAGTTAA
Found at i:13537857 original size:27 final size:27
Alignment explanation
Indices: 13537807--13537858 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
13537797 AAATTAATTA
*
13537807 AAAATATTAAAATATATTTACTTTTAT
1 AAAATATGAAAATATATTTACTTTTAT
* * *
13537834 AAAATATGAAAGTATTTTTGCTTTT
1 AAAATATGAAAATATATTTACTTTT
13537859 GCATATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (27 bp):
AAAATATGAAAATATATTTACTTTTAT
Found at i:13538076 original size:2 final size:2
Alignment explanation
Indices: 13538069--13538103 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13538059 TTAGGCTATT
13538069 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
13538104 CTATAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13538341 original size:29 final size:29
Alignment explanation
Indices: 13538288--13538344 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
13538278 TGGTTCAATC
*
13538288 AAATATATATATAATGACATATTAATATG
1 AAATATATATAGAATGACATATTAATATG
* * *
13538317 AAATATATATAGACTGTCATGTTAATAT
1 AAATATATATAGAATGACATATTAATAT
13538345 TGTTAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (29 bp):
AAATATATATAGAATGACATATTAATATG
Found at i:13540200 original size:20 final size:19
Alignment explanation
Indices: 13540161--13540216 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
13540151 CTTTAATAAA
*
13540161 ATTTATAAATATAA-TTTT
1 ATTTATAAAAATAATTTTT
13540179 ATTTATTAAAAATAATTTTT
1 ATTTA-TAAAAATAATTTTT
13540199 ATTTAATAAAATATAATT
1 ATTT-ATAAAA-ATAATT
13540217 AATATAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 5 0.15
19 8 0.24
20 13 0.39
21 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTATAAAAATAATTTTT
Found at i:13540216 original size:21 final size:21
Alignment explanation
Indices: 13540167--13540216 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
13540157 TAAAATTTAT
*
13540167 AAATATAA-TTTTATTTATTA
1 AAATATAATTTTTATTTAATA
13540187 AAA-ATAATTTTTATTTAATA
1 AAATATAATTTTTATTTAATA
13540207 AAATATAATT
1 AAATATAATT
13540217 AATATAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 17 0.63
21 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATATAATTTTTATTTAATA
Done.