Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 159 of 290
Found at i:54286544 original size:9 final size:8
Alignment explanation
Indices: 54286527--54286593 Score: 55
Period size: 9 Copynumber: 7.8 Consensus size: 8
54286517 GGCCTCTCCA
54286527 TTTTTTCT
1 TTTTTTCT
54286535 TTTTTCTCT
1 TTTTT-TCT
*
54286544 TTTTTTAT
1 TTTTTTCT
54286552 TTTTATT-T
1 TTTT-TTCT
*
54286560 TTTTCTCTTT
1 TTTT-T-TCT
54286570 TTATTTTCT
1 TT-TTTTCT
54286579 TTTTTTCCT
1 TTTTTT-CT
54286588 TTTTTT
1 TTTTTT
54286594 TGAAATAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
8 21 0.42
9 23 0.46
10 4 0.08
11 2 0.04
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTCT
Found at i:54286554 original size:22 final size:21
Alignment explanation
Indices: 54286529--54286593 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 21
54286519 CCTCTCCATT
54286529 TTTTCTTTTTTCTCTTTTTTTA
1 TTTTCTTTTTT-TCTTTTTTTA
* *
54286551 TTTTTATTTTTTTCTCTTTTTA
1 -TTTTCTTTTTTTCTTTTTTTA
54286573 TTTTCTTTTTTTCCTTTTTTT
1 TTTTCTTTTTTT-CTTTTTTT
54286594 TGAAATAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 11 0.30
22 16 0.43
23 10 0.27
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTCTTTTTTTCTTTTTTTA
Found at i:54292264 original size:22 final size:21
Alignment explanation
Indices: 54292234--54292280 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
54292224 TACAAATTAA
54292234 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
54292256 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
54292277 ATCT
1 ATCT
54292281 AAGATTGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:54292286 original size:19 final size:19
Alignment explanation
Indices: 54292251--54292348 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
54292241 AGATTACAAG
54292251 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
*
54292272 ATCATATCTAAGATTGTAT
1 ATCATATCTAAGATTGCAT
54292291 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
54292308 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
54292327 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
54292346 ATC
1 ATC
54292349 CTTAAAGATT
Statistics
Matches: 74, Mismatches: 1, Indels: 6
0.91 0.01 0.07
Matches are distributed among these distances:
17 17 0.23
19 48 0.65
20 1 0.01
21 8 0.11
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:54292315 original size:36 final size:37
Alignment explanation
Indices: 54292251--54292348 Score: 144
Period size: 36 Copynumber: 2.6 Consensus size: 37
54292241 AGATTACAAG
*
54292251 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGTAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATTGCAT
54292291 ATCATATCTAAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
54292327 ATCATATCTAAGATTGCATATC
1 ATCATATCTAAGATTG-ATATC
54292349 CTTAAAGATT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
36 35 0.64
38 11 0.20
39 1 0.02
40 8 0.15
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
Found at i:54293200 original size:15 final size:16
Alignment explanation
Indices: 54293182--54293212 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54293172 AGTGTATTTT
54293182 ATTTTTT-TTTTGTCA
1 ATTTTTTGTTTTGTCA
54293197 ATTTTTTGTTTTGTCA
1 ATTTTTTGTTTTGTCA
54293213 TTAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.13, C:0.06, G:0.10, T:0.71
Consensus pattern (16 bp):
ATTTTTTGTTTTGTCA
Found at i:54293765 original size:11 final size:11
Alignment explanation
Indices: 54293734--54293773 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
54293724 TTAGGTTAGG
54293734 TTTTCTTTCTC
1 TTTTCTTTCTC
*
54293745 TTTTCCTTCTC
1 TTTTCTTTCTC
*
54293756 TTTTTTTTCT-
1 TTTTCTTTCTC
54293766 TTTTCTTT
1 TTTTCTTT
54293774 TCATTTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTTTCTC
Found at i:54293780 original size:20 final size:20
Alignment explanation
Indices: 54293743--54293781 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54293733 GTTTTCTTTC
*
54293743 TCTTTTCCTTCTCTTTTTTT
1 TCTTTTCCTTCTCATTTTTT
* *
54293763 TCTTTTTCTTTTCATTTTT
1 TCTTTTCCTTCTCATTTTT
54293782 AGTTTAGGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (20 bp):
TCTTTTCCTTCTCATTTTTT
Found at i:54293824 original size:26 final size:26
Alignment explanation
Indices: 54293765--54293824 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
54293755 CTTTTTTTTC
* **
54293765 TTTTTCTTTTCATTTTTAGTTTAGGT
1 TTTTTCTTTTCATTTTTAGGTTAAAT
*
54293791 TTTCTCTTTTC-TTTTTAGGTTAAAT
1 TTTTTCTTTTCATTTTTAGGTTAAAT
54293816 TTTATTCTT
1 TTT-TTCTT
54293825 GTAGTTTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.13, C:0.10, G:0.08, T:0.68
Consensus pattern (26 bp):
TTTTTCTTTTCATTTTTAGGTTAAAT
Found at i:54297136 original size:18 final size:18
Alignment explanation
Indices: 54297109--54297145 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54297099 CAAATGAATC
* *
54297109 ATTTCCATTTTCATTTTT
1 ATTTCAATTTCCATTTTT
54297127 ATTTCAATTTCCATTTTT
1 ATTTCAATTTCCATTTTT
54297145 A
1 A
54297146 GAAACCTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTCAATTTCCATTTTT
Found at i:54301119 original size:2 final size:2
Alignment explanation
Indices: 54301112--54301154 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
54301102 TCTTACCCTT
54301112 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
54301154 T
1 T
54301155 TGTCTTTCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:54305535 original size:14 final size:14
Alignment explanation
Indices: 54305516--54305547 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
54305506 TTCAACTAGA
54305516 TCTACGGAGGACAT
1 TCTACGGAGGACAT
54305530 TCTACGGAGGACAT
1 TCTACGGAGGACAT
54305544 TCTA
1 TCTA
54305548 GTAAGTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (14 bp):
TCTACGGAGGACAT
Found at i:54306137 original size:5 final size:5
Alignment explanation
Indices: 54306127--54306154 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
54306117 CTGTATGTTC
54306127 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
54306155 CAAAAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:54315896 original size:35 final size:35
Alignment explanation
Indices: 54315857--54315928 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
54315847 TTTTGATACT
54315857 ATTATGGTGCTAGTAAGCAAACTCTTAAAGTATGC
1 ATTATGGTGCTAGTAAGCAAACTCTTAAAGTATGC
*
54315892 ATTATGGTGCTAGTAAGCAAATTCTTAAAGTATGC
1 ATTATGGTGCTAGTAAGCAAACTCTTAAAGTATGC
54315927 AT
1 AT
54315929 ACTCCATTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (35 bp):
ATTATGGTGCTAGTAAGCAAACTCTTAAAGTATGC
Found at i:54321905 original size:21 final size:21
Alignment explanation
Indices: 54321881--54321931 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
54321871 TAATTCAATA
*
54321881 TTTAGGGTTTTGAGTTTAAAG
1 TTTAGGGTTTGGAGTTTAAAG
** *
54321902 TTTAATGTTTGGAGTTTAGAG
1 TTTAGGGTTTGGAGTTTAAAG
54321923 TTTAGGGTT
1 TTTAGGGTT
54321932 AAAATTCAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTTGGAGTTTAAAG
Found at i:54322174 original size:21 final size:20
Alignment explanation
Indices: 54322124--54322174 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
54322114 ACTCGGAACC
54322124 TTGAACTC-AAACCCAAACT
1 TTGAACTCTAAACCCAAACT
**
54322143 TTG-GGTCCTAAACCCTAAACT
1 TTGAACT-CTAAACCC-AAACT
54322164 TTGAACTCTAA
1 TTGAACTCTAA
54322175 TATTGAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
18 1 0.04
19 4 0.17
20 6 0.25
21 12 0.50
22 1 0.04
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.27
Consensus pattern (20 bp):
TTGAACTCTAAACCCAAACT
Found at i:54323232 original size:127 final size:127
Alignment explanation
Indices: 54323006--54323495 Score: 944
Period size: 127 Copynumber: 3.9 Consensus size: 127
54322996 TAGCCTTAAG
54323006 AGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
1 AGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
54323071 GAATTCTTTAAATACCGAACATTGCCCTTATTTTGAAAATTTTTTGAGAGTGAACTGGTAAA
66 GAATTCTTTAAATACCGAACATTGCCCTTATTTTGAAAATTTTTTGAGAGTGAACTGGTAAA
54323133 AGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
1 AGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
54323198 GAATTCTTTAAATACCGAACATTGCCCTTATTTTGAAAATTTTTTGAGAGTGAACTGGTAAA
66 GAATTCTTTAAATACCGAACATTGCCCTTATTTTGAAAATTTTTTGAGAGTGAACTGGTAAA
54323260 AGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
1 AGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
54323325 GAATTCTTTAAATACCGAACATTGCCCTTATTTTGAAAATTTTTTGAGAGTGAACTGGTAAA
66 GAATTCTTTAAATACCGAACATTGCCCTTATTTTGAAAATTTTTTGAGAGTGAACTGGTAAA
54323387 AGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
1 AGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
** * *
54323452 GAATTCTTTAAATACCGAACATTATCTTTATTTTGAAAAATTTT
66 GAATTCTTTAAATACCGAACATTGCCCTTATTTTGAAAATTTTT
54323496 GACAGAAGAT
Statistics
Matches: 359, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 359 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (127 bp):
AGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
GAATTCTTTAAATACCGAACATTGCCCTTATTTTGAAAATTTTTTGAGAGTGAACTGGTAAA
Found at i:54323620 original size:13 final size:14
Alignment explanation
Indices: 54323599--54323649 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
54323589 CCAACCATAT
*
54323599 ATAAATAATAAATA
1 ATAATTAATAAATA
54323613 ATAA-TAAT-AATA
1 ATAATTAATAAATA
* *
54323625 GTAATTAATAGA-A
1 ATAATTAATAAATA
54323638 ATAATTAATAAA
1 ATAATTAATAAA
54323650 ACAACAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 7 0.23
13 19 0.61
14 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (14 bp):
ATAATTAATAAATA
Found at i:54323984 original size:14 final size:14
Alignment explanation
Indices: 54323965--54323995 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
54323955 ATATATTTAC
*
54323965 ATAATAAATATATA
1 ATAATAAATAAATA
54323979 ATAATAAATAAATA
1 ATAATAAATAAATA
54323993 ATA
1 ATA
54323996 TAATAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATAAATAAATA
Found at i:54323996 original size:19 final size:18
Alignment explanation
Indices: 54323967--54324003 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
54323957 ATATTTACAT
54323967 AATAAATATATAATAATA
1 AATAAATATATAATAATA
54323985 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
54324004 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Found at i:54324339 original size:11 final size:11
Alignment explanation
Indices: 54324319--54324361 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
54324309 GTGTTCTCTA
54324319 AAAAATTCCTCC
1 AAAAA-TCCTCC
*
54324331 AAAAATCCTCT
1 AAAAATCCTCC
54324342 AAAAATCCTCTC
1 AAAAATCCTC-C
*
54324354 CAAAATCC
1 AAAAATCC
54324362 CCCCTCATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 15 0.56
12 12 0.44
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATCCTCC
Found at i:54324446 original size:18 final size:18
Alignment explanation
Indices: 54324423--54324495 Score: 69
Period size: 18 Copynumber: 4.0 Consensus size: 18
54324413 ATAACAAGTA
54324423 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
*
54324441 GGGTGATAGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
* * *
54324459 ACGGT-TTAGTAGGGT-GTGG
1 -GGGTGAT-GGA-GGTAGTGG
54324478 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
54324496 ATGGTTTAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
17 3 0.07
18 27 0.64
19 9 0.21
20 3 0.07
ACGTcount: A:0.18, C:0.01, G:0.56, T:0.25
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:54324490 original size:37 final size:37
Alignment explanation
Indices: 54324432--54324511 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 37
54324422 AGGGTGATGG
54324432 AGGTAGTGGGGGTGATAGAGGTAGTGGACGGTTTAGTA
1 AGGT-GTGGGGGTGATAGAGGTAGTGGACGGTTTAGTA
* * *
54324470 GGGTGTGGGGGTGATGGAGGTAGTGGATGGTTTAGTA
1 AGGTGTGGGGGTGATAGAGGTAGTGGACGGTTTAGTA
54324507 AGGTG
1 AGGTG
54324512 ATGGAGTTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 35 0.92
38 3 0.08
ACGTcount: A:0.20, C:0.01, G:0.51, T:0.28
Consensus pattern (37 bp):
AGGTGTGGGGGTGATAGAGGTAGTGGACGGTTTAGTA
Found at i:54324540 original size:29 final size:29
Alignment explanation
Indices: 54324477--54324540 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
54324467 GTAGGGTGTG
54324477 GGGGTGATGGAGGTAGTGGATGGTTTAGT
1 GGGGTGATGGAGGTAGTGGATGGTTTAGT
** * *
54324506 AAGGTGATGGAGTTAGT-GTTCGGTTTAGT
1 GGGGTGATGGAGGTAGTGGAT-GGTTTAGT
54324535 GGGGTG
1 GGGGTG
54324541 TTTAATTTGG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.17, C:0.02, G:0.48, T:0.33
Consensus pattern (29 bp):
GGGGTGATGGAGGTAGTGGATGGTTTAGT
Found at i:54326933 original size:39 final size:39
Alignment explanation
Indices: 54326886--54327079 Score: 257
Period size: 39 Copynumber: 5.0 Consensus size: 39
54326876 GTGTGAAATA
* * *
54326886 TATATCCGGGCTAATTCCCGAAGGCGTTTGTACTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
54326925 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* **
54326964 TATATCCGGGCTAAGTCCCGAATGCATTCATGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* *
54327003 TATATCTGGGCTAAGTCCCGAAGGC-TTTGTGCTGGTAT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* * *
54327041 TATATCCGGGCTTAAAGTCCCGCATGC-TTTGTGGTGGTG
1 TATATCCGGGC-T-AAGTCCCGAAGGCATTTGTGCTGGTG
54327080 ATTGAATTTG
Statistics
Matches: 137, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
38 20 0.15
39 96 0.70
40 21 0.15
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (39 bp):
TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
Found at i:54330461 original size:49 final size:49
Alignment explanation
Indices: 54330337--54330461 Score: 144
Period size: 49 Copynumber: 2.6 Consensus size: 49
54330327 ATGAAAGTTG
* * * * *
54330337 AACATGTGACCACATAACTACTGTCAACTGGGCTCTCGAGTTATACTCC
1 AACACGTGACCGCATAACCACTGTCAAATGGGCTCCCGAGTTATACTCC
* ** *
54330386 AACATGTGATTGCATAACCAATGTCAAATGGGCTCCCGAGTTATACTCC
1 AACACGTGACCGCATAACCACTGTCAAATGGGCTCCCGAGTTATACTCC
*
54330435 AATC-CGTGACCGCATAACCACCGTCAA
1 AA-CACGTGACCGCATAACCACTGTCAA
54330462 CTAGAAGCCC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
49 62 0.98
50 1 0.02
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (49 bp):
AACACGTGACCGCATAACCACTGTCAAATGGGCTCCCGAGTTATACTCC
Found at i:54344425 original size:18 final size:18
Alignment explanation
Indices: 54344402--54344444 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
54344392 GTGAAATGGT
* *
54344402 AAAAAAAAAATAAAAATG
1 AAAAAAAAAAGAAAAAAG
54344420 AAAAAAAAAAGAAAAAAG
1 AAAAAAAAAAGAAAAAAG
54344438 AAAAAAA
1 AAAAAAA
54344445 CCAATTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.88, C:0.00, G:0.07, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAAAG
Found at i:54348812 original size:16 final size:16
Alignment explanation
Indices: 54348791--54348824 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
54348781 TTGTAACGCC
*
54348791 CCAAAAATCTTGAAAT
1 CCAAAAATCCTGAAAT
54348807 CCAAAAATCCTGAAAT
1 CCAAAAATCCTGAAAT
54348823 CC
1 CC
54348825 CAGAATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.26, G:0.06, T:0.21
Consensus pattern (16 bp):
CCAAAAATCCTGAAAT
Found at i:54349301 original size:16 final size:16
Alignment explanation
Indices: 54349280--54349314 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
54349270 TTGTAATGCC
54349280 CCAAAAAT-CTCGAAAT
1 CCAAAAATCCT-GAAAT
54349296 CCAAAAATCCTGAAAT
1 CCAAAAATCCTGAAAT
54349312 CCA
1 CCA
54349315 GAATTTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.49, C:0.29, G:0.06, T:0.17
Consensus pattern (16 bp):
CCAAAAATCCTGAAAT
Found at i:54349318 original size:488 final size:488
Alignment explanation
Indices: 54348373--54349323 Score: 1823
Period size: 488 Copynumber: 1.9 Consensus size: 488
54348363 GGTGTTAAGG
54348373 TTTGGACGTAAAGGAAAGCTAAGCCTAAGGTTCATCGGGCCATATCGGGTTGCAATACGGATTGG
1 TTTGGACGTAAAGGAAAGCTAAGCCTAAGGTTCATCGGGCCATATCGGGTTGCAATACGGATTGG
54348438 GCCAGTCGCTTATCAACTGGAATTACCTCCTGAACTAGGCCAGATCCACGACGTGTTCCATGTTT
66 GCCAGTCGCTTATCAACTGGAATTACCTCCTGAACTAGGCCAGATCCACGACGTGTTCCATGTTT
54348503 CTATGCTGAGACGGTATCGCTTAGATCCTTCCCATTTCGTGGTGATTGAAGAAATCGAGGTCAAA
131 CTATGCTGAGACGGTATCGCTTAGATCCTTCCCATTTCGTGGTGATTGAAGAAATCGAGGTCAAA
54348568 CCAGACCTAACTTTCGAGGAAGAGCCCATACAAATAATTGGTCATAATGTTAAGGTACTGAGAAG
196 CCAGACCTAACTTTCGAGGAAGAGCCCATACAAATAATTGGTCATAATGTTAAGGTACTGAGAAG
*
54348633 AAAGTCTGTTCCATTAGTCAAAGTGCTTTGGTGTAATCACAAGTTGAGGAGGCTACTTGGGAACT
261 AAAGTCTGTTCCATTAGTCAAAGTGCTTTGGTGTAATCACAAGTTGAGGAGGCTACTTGGGAACC
*
54348698 TGAGGAAGCTGTGTAACGTCAACATCCTCAACTGTTTGAATCAGGTGAATTTTGAGGATGAAATT
326 TGAGGAAGCTGTGCAACGTCAACATCCTCAACTGTTTGAATCAGGTGAATTTTGAGGATGAAATT
*
54348763 TCTTTTAGGGACGTAGAGTTGTAACGCCCCAAAAATCTTGAAATCCAAAAATCCTGAAATCCCAG
391 TCTTTTAGGGACGTAGAGTTGTAACGCCCCAAAAATCTCGAAATCCAAAAATCCTGAAATCCCAG
54348828 AATTTTCTTTATTTTTGATTTTGATAAAAATTA
456 AATTTTCTTTATTTTTGATTTTGATAAAAATTA
* *
54348861 TTTGGACGTAAAGGAAAGCTAAGCCTAAGGTTCATTGGGCCATATCGGGTTGCAATGCGGATTGG
1 TTTGGACGTAAAGGAAAGCTAAGCCTAAGGTTCATCGGGCCATATCGGGTTGCAATACGGATTGG
54348926 GCCAGTCGCTTATCAACTGGAATTACCTCCTGAACTAGGCCAGATCCACGACGTGTTCCATGTTT
66 GCCAGTCGCTTATCAACTGGAATTACCTCCTGAACTAGGCCAGATCCACGACGTGTTCCATGTTT
54348991 CTATGCTGAGACGGTATCGCTTAGATCCTTCCCATTTCGTGGTGATTGAAGAAATCGAGGTCAAA
131 CTATGCTGAGACGGTATCGCTTAGATCCTTCCCATTTCGTGGTGATTGAAGAAATCGAGGTCAAA
*
54349056 CCAGACCTAACTTTCGAGGAAGAGCCCATACAAATAATTGGTCGTAATGTTAAGGTACTGAGAAG
196 CCAGACCTAACTTTCGAGGAAGAGCCCATACAAATAATTGGTCATAATGTTAAGGTACTGAGAAG
54349121 AAAGTCTGTTCCATTAGTCAAAGTGCTTTGGTGTAATCACAAGGTTGAGGAGGCTACTTGGGAAC
261 AAAGTCTGTTCCATTAGTCAAAGTGCTTTGGTGTAATCACAA-GTTGAGGAGGCTACTTGGGAAC
54349186 CTGAGGAAGCTGTGCAACGTCAACATCCTCAACTGTTTGAATCAGGTGAATTTTGAGGATGAAAT
325 CTGAGGAAGCTGTGCAACGTCAACATCCTCAACTGTTTGAATCAGGTGAATTTTGAGGATGAAAT
*
54349251 TTCTTTTAGGGACGTAGAGTTGTAATGCCCCAAAAATCTCGAAATCCAAAAATCCTGAAAT-CCA
390 TTCTTTTAGGGACGTAGAGTTGTAACGCCCCAAAAATCTCGAAATCCAAAAATCCTGAAATCCCA
54349315 GAATTTTCT
455 GAATTTTCT
54349324 AATGTAAGTG
Statistics
Matches: 455, Mismatches: 7, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
488 311 0.68
489 144 0.32
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (488 bp):
TTTGGACGTAAAGGAAAGCTAAGCCTAAGGTTCATCGGGCCATATCGGGTTGCAATACGGATTGG
GCCAGTCGCTTATCAACTGGAATTACCTCCTGAACTAGGCCAGATCCACGACGTGTTCCATGTTT
CTATGCTGAGACGGTATCGCTTAGATCCTTCCCATTTCGTGGTGATTGAAGAAATCGAGGTCAAA
CCAGACCTAACTTTCGAGGAAGAGCCCATACAAATAATTGGTCATAATGTTAAGGTACTGAGAAG
AAAGTCTGTTCCATTAGTCAAAGTGCTTTGGTGTAATCACAAGTTGAGGAGGCTACTTGGGAACC
TGAGGAAGCTGTGCAACGTCAACATCCTCAACTGTTTGAATCAGGTGAATTTTGAGGATGAAATT
TCTTTTAGGGACGTAGAGTTGTAACGCCCCAAAAATCTCGAAATCCAAAAATCCTGAAATCCCAG
AATTTTCTTTATTTTTGATTTTGATAAAAATTA
Found at i:54349694 original size:16 final size:16
Alignment explanation
Indices: 54349673--54349707 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54349663 ATGTATCGGC
* *
54349673 AAAAGCTGAAATGCTG
1 AAAAGCCGAAATGCCG
54349689 AAAAGCCGAAATGCCG
1 AAAAGCCGAAATGCCG
54349705 AAA
1 AAA
54349708 TGTCAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (16 bp):
AAAAGCCGAAATGCCG
Found at i:54350046 original size:28 final size:29
Alignment explanation
Indices: 54349936--54350050 Score: 128
Period size: 29 Copynumber: 4.0 Consensus size: 29
54349926 GTGAGCATGA
* * *
54349936 ATATGAATGTGA-CTGGGACTAACGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
**
54349964 ATAAAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
54349993 ATAT-ACAGGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATGTGATTTGGGCCTAATGGGCC
* *
54350022 ATATGAATATGA-TTGGGCTTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
54350050 A
1 A
54350051 GATACAGGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
28 27 0.36
29 46 0.62
30 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.27
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:54350048 original size:57 final size:58
Alignment explanation
Indices: 54349949--54350059 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 58
54349939 TGAATGTGAC
* *
54349949 TGGGACTAACGGGCCATAAAAATGTGATTTGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGACTAACGGGCCATAAAAATATGATTTGGGCCTAATGGGCCAGATACAGGTGATT
* * ** *
54350007 TGGGCCTAATGGGCCATATGAATATGA-TTGGGCTTAATGGGCCAGATACAGGT
1 TGGGACTAACGGGCCATAAAAATATGATTTGGGCCTAATGGGCCAGATACAGGT
54350060 ATGTGAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 24 0.52
58 22 0.48
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (58 bp):
TGGGACTAACGGGCCATAAAAATATGATTTGGGCCTAATGGGCCAGATACAGGTGATT
Found at i:54374268 original size:39 final size:40
Alignment explanation
Indices: 54374173--54374434 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
54374163 TTGAATGATG
*
54374173 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
54374211 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
54374252 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
54374291 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
54374330 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
54374369 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
54374408 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
54374435 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:54388492 original size:6 final size:6
Alignment explanation
Indices: 54388474--54388558 Score: 50
Period size: 6 Copynumber: 13.8 Consensus size: 6
54388464 AAGAAGCATT
* * * *
54388474 ATCAGA A-CTAGA ATCAGA ATTAAA ATCAGA ATTAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* *
54388523 ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAG
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAG
54388559 TATTAGGTAA
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
5 4 0.07
6 47 0.80
7 6 0.10
8 2 0.03
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:54388525 original size:25 final size:25
Alignment explanation
Indices: 54388488--54388558 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
54388478 GAACTAGAAT
* * *
54388488 CAGAATTAAAATCAGAATTAGGTGA
1 CAGAATCAAAATCAGAATCAGGTAA
* *
54388513 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAAAATCAGAATCAGGTAA
54388538 CAGAATCAAAATCAGAATCAG
1 CAGAATCAAAATCAGAATCAG
54388559 TATTAGGTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (25 bp):
CAGAATCAAAATCAGAATCAGGTAA
Found at i:54388683 original size:27 final size:27
Alignment explanation
Indices: 54388654--54388818 Score: 240
Period size: 27 Copynumber: 6.1 Consensus size: 27
54388644 GGGCAAAATG
* * * *
54388654 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
54388681 GTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
54388708 GTAATTCTACCATACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* **
54388735 GTAATTCTACCCTACAGGGGTATTTTG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
54388762 GTAATTCTATCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
54388789 GTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
54388816 GTA
1 GTA
54388819 CTTTTTTTAC
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 124 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:54388864 original size:27 final size:27
Alignment explanation
Indices: 54388832--54389068 Score: 312
Period size: 27 Copynumber: 8.7 Consensus size: 27
54388822 TTTTTACATT
54388832 GAGGGTAAAATGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
* *
54388859 GAGGGTAAGACGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
54388886 GAGGGTAAAACGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
* * * * *
54388913 AAAGGTAAAATAGTAATTCTATAAATT
1 GAGGGTAAAATGGTAATTCTGTAAATC
* * *
54388940 GAGGGTAAAACGATAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
54388967 GAGGGTAAAATGGTAATTTTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
* *
54388994 GAGGGTAAAAATAGTAATTCTATAAATC
1 GAGGGT-AAAATGGTAATTCTGTAAATC
* *
54389022 GAGGGTAAAACGATAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
54389049 GAGAGTAAAATGGTAATTCT
1 GAGGGTAAAATGGTAATTCT
54389069 ATCTTACAGG
Statistics
Matches: 180, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
27 156 0.87
28 24 0.13
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (27 bp):
GAGGGTAAAATGGTAATTCTGTAAATC
Found at i:54388938 original size:81 final size:81
Alignment explanation
Indices: 54388835--54389068 Score: 360
Period size: 81 Copynumber: 2.9 Consensus size: 81
54388825 TTACATTGAG
* * * * *
54388835 GGTAAAATGGTAATTCTGTAAATCGAGGGTAAGACGGTAATTCTGTAAATCGAGGGTAAAACGGT
1 GGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGGT
54388900 AATTCTGTAAATCAAA
66 AATTCTGTAAATCAAA
* *
54388916 GGTAAAATAGTAATTCTATAAATTGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAATGGT
1 GGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGGT
* * *
54388981 AATTTTGTAAATCGAG
66 AATTCTGTAAATCAAA
*
54388997 GGTAAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGAGTAAAATGG
1 GGT-AAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGG
54389062 TAATTCT
65 TAATTCT
54389069 ATCTTACAGG
Statistics
Matches: 138, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
81 74 0.54
82 64 0.46
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (81 bp):
GGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGGT
AATTCTGTAAATCAAA
Found at i:54389110 original size:27 final size:27
Alignment explanation
Indices: 54389080--54389229 Score: 169
Period size: 27 Copynumber: 5.6 Consensus size: 27
54389070 TCTTACAGGA
54389080 GTATTTCAGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* *
54389107 GTATTTCAGTAATTTTGCAAA-CTGGGG
1 GTATTTCAGTAATTTTACAAATC-GAGG
*
54389134 GTATTTCTGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* ** * *
54389161 ATATTTGGGTAATTTTATAAATCGGGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * *
54389188 GTACTTT-GGTAATTTTACAAGTTGAGG
1 GTA-TTTCAGTAATTTTACAAATCGAGG
54389215 GTATTTCAGTAATTT
1 GTATTTCAGTAATTT
54389230 GGTAAACTAA
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
26 4 0.04
27 95 0.92
28 4 0.04
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAATCGAGG
Found at i:54389166 original size:81 final size:82
Alignment explanation
Indices: 54389076--54389229 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 82
54389066 TCTATCTTAC
* *
54389076 AGGAGTATTTCAGTAATTTTACAAATCGAGGGTA-TTTCAGTAATTTTGCAAACTGGGGGTATTT
1 AGGAGTATTTCAGTAATTTTACAAATCGAGGGTACTTT-AGTAATTTTACAAACTGAGGGTATTT
*
54389140 CTGTAATTTTACAAATCG
65 CAGTAATTTTACAAATCG
** * * * **
54389158 AGGA-TATTTGGGTAATTTTATAAATCGGGGGTACTTTGGTAATTTTACAAGTTGAGGGTATTTC
1 AGGAGTATTTCAGTAATTTTACAAATCGAGGGTACTTTAGTAATTTTACAAACTGAGGGTATTTC
54389222 AGTAATTT
66 AGTAATTT
54389230 GGTAAACTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
81 54 0.89
82 7 0.11
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (82 bp):
AGGAGTATTTCAGTAATTTTACAAATCGAGGGTACTTTAGTAATTTTACAAACTGAGGGTATTTC
AGTAATTTTACAAATCG
Found at i:54390653 original size:672 final size:672
Alignment explanation
Indices: 54389365--54390713 Score: 2689
Period size: 672 Copynumber: 2.0 Consensus size: 672
54389355 TCCATTATCA
*
54389365 GAGTTCAAATTCAACACCAACTCTTGCCACTCCTTGTTAGCAAAATAAATGCTCTTCACTTGCCA
1 GAGTACAAATTCAACACCAACTCTTGCCACTCCTTGTTAGCAAAATAAATGCTCTTCACTTGCCA
54389430 TGAGTTTCGAACCCTGGACCTCCTTGCCACCTCTATAACGCAACCTTCCTGCCTCTTCTGTGGCG
66 TGAGTTTCGAACCCTGGACCTCCTTGCCACCTCTATAACGCAACCTTCCTGCCTCTTCTGTGGCG
54389495 CTACTTTGCCACTAGACCACAAGGCTTTTTGTGTCACAATTTCTCCAACAATATTCTTAAGGCCT
131 CTACTTTGCCACTAGACCACAAGGCTTTTTGTGTCACAATTTCTCCAACAATATTCTTAAGGCCT
54389560 ACCTACTACACCCAGGGTTTGATTCACCTTAAACCAAATTTTTTTGCTAGAGTCCAGGTTTAAAC
196 ACCTACTACACCCAGGGTTTGATTCACCTTAAACCAAATTTTTTTGCTAGAGTCCAGGTTTAAAC
54389625 CCAGGACTTCTCCAACACTTCTCAACACACTTAACCACTAAAACAAGCCTTCATTAGCGAAATTT
261 CCAGGACTTCTCCAACACTTCTCAACACACTTAACCACTAAAACAAGCCTTCATTAGCGAAATTT
54389690 ACACGCACAACAAAATATTATAAGCTGCCTTTAACCGCTCCAATGCTCAAGGCCCAAAACTTCTA
326 ACACGCACAACAAAATATTATAAGCTGCCTTTAACCGCTCCAATGCTCAAGGCCCAAAACTTCTA
54389755 GGCCCAAATTCAGGGTGTTACAACTGAACTCTTTAGTCTCGCACTAATGAGCTCATTCAACATAA
391 GGCCCAAATTCAGGGTGTTACAACTGAACTCTTTAGTCTCGCACTAATGAGCTCATTCAACATAA
54389820 ATCTCGTGAAATTTTGTTATAAAATACCACATTGGTAAGGGGGTTGAGGTCGTAAAGCCTCTAAC
456 ATCTCGTGAAATTTTGTTATAAAATACCACATTGGTAAGGGGGTTGAGGTCGTAAAGCCTCTAAC
54389885 TCAACTCTTATATATACACACATGTAACTTAACATAATATCACGCAGTTATATCACTCACTTTAA
521 TCAACTCTTATATATACACACATGTAACTTAACATAATATCACGCAGTTATATCACTCACTTTAA
54389950 ACAAATTAACATACATATTTAAGCTAGACAAACTTTCCGATTATCTTATTCAAACAAATGCACAT
586 ACAAATTAACATACATATTTAAGCTAGACAAACTTTCCGATTATCTTATTCAAACAAATGCACAT
54390015 ATATATACATTCCATAAATTTT
651 ATATATACATTCCATAAATTTT
54390037 GAGTACAAATTCAACACCAACTCTTGCCACTCCTTGTTAGCAAAATAAATGCTCTTCACTTGCCA
1 GAGTACAAATTCAACACCAACTCTTGCCACTCCTTGTTAGCAAAATAAATGCTCTTCACTTGCCA
54390102 TGAGTTTCGAACCCTGGACCTCCTTGCCACCTCTATAACGCAACCTTCCTGCCTCTTCTGTGGCG
66 TGAGTTTCGAACCCTGGACCTCCTTGCCACCTCTATAACGCAACCTTCCTGCCTCTTCTGTGGCG
54390167 CTACTTTGCCACTAGACCACAAGGCTTTTTGTGTCACAATTTCTCCAACAATATTCTTAAGGCCT
131 CTACTTTGCCACTAGACCACAAGGCTTTTTGTGTCACAATTTCTCCAACAATATTCTTAAGGCCT
54390232 ACCTACTACACCCAGGGTTTGATTCACCTTAAACCAAATTTTTTTGCTAGAGTCCAGGTTTAAAC
196 ACCTACTACACCCAGGGTTTGATTCACCTTAAACCAAATTTTTTTGCTAGAGTCCAGGTTTAAAC
54390297 CCAGGACTTCTCCAACACTTCTCAACACACTTAACCACTAAAACAAGCCTTCATTAGCGAAATTT
261 CCAGGACTTCTCCAACACTTCTCAACACACTTAACCACTAAAACAAGCCTTCATTAGCGAAATTT
54390362 ACACGCACAACAAAATATTATAAGCTGCCTTTAACCGCTCCAATGCTCAAGGCCCAAAACTTCTA
326 ACACGCACAACAAAATATTATAAGCTGCCTTTAACCGCTCCAATGCTCAAGGCCCAAAACTTCTA
54390427 GGCCCAAATTCAGGGTGTTACAACTGAACTCTTTAGTCTCGCACTAATGAGCTCATTCAACATAA
391 GGCCCAAATTCAGGGTGTTACAACTGAACTCTTTAGTCTCGCACTAATGAGCTCATTCAACATAA
54390492 ATCTCGTGAAATTTTGTTATAAAATACCACATTGGTAAGGGGGTTGAGGTCGTAAAGCCTCTAAC
456 ATCTCGTGAAATTTTGTTATAAAATACCACATTGGTAAGGGGGTTGAGGTCGTAAAGCCTCTAAC
54390557 TCAACTCTTATATATACACACATGTAACTTAACATAATATCACGCAGTTATATCACTCACTTTAA
521 TCAACTCTTATATATACACACATGTAACTTAACATAATATCACGCAGTTATATCACTCACTTTAA
54390622 ACAAATTAACATACATATTTAAGCTAGACAAACTTTCCGATTATCTTATTCAAACAAATGCACAT
586 ACAAATTAACATACATATTTAAGCTAGACAAACTTTCCGATTATCTTATTCAAACAAATGCACAT
54390687 ATATATACATTCCATAAATTTT
651 ATATATACATTCCATAAATTTT
54390709 GAGTA
1 GAGTA
54390714 AGCTTACTTA
Statistics
Matches: 676, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
672 676 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (672 bp):
GAGTACAAATTCAACACCAACTCTTGCCACTCCTTGTTAGCAAAATAAATGCTCTTCACTTGCCA
TGAGTTTCGAACCCTGGACCTCCTTGCCACCTCTATAACGCAACCTTCCTGCCTCTTCTGTGGCG
CTACTTTGCCACTAGACCACAAGGCTTTTTGTGTCACAATTTCTCCAACAATATTCTTAAGGCCT
ACCTACTACACCCAGGGTTTGATTCACCTTAAACCAAATTTTTTTGCTAGAGTCCAGGTTTAAAC
CCAGGACTTCTCCAACACTTCTCAACACACTTAACCACTAAAACAAGCCTTCATTAGCGAAATTT
ACACGCACAACAAAATATTATAAGCTGCCTTTAACCGCTCCAATGCTCAAGGCCCAAAACTTCTA
GGCCCAAATTCAGGGTGTTACAACTGAACTCTTTAGTCTCGCACTAATGAGCTCATTCAACATAA
ATCTCGTGAAATTTTGTTATAAAATACCACATTGGTAAGGGGGTTGAGGTCGTAAAGCCTCTAAC
TCAACTCTTATATATACACACATGTAACTTAACATAATATCACGCAGTTATATCACTCACTTTAA
ACAAATTAACATACATATTTAAGCTAGACAAACTTTCCGATTATCTTATTCAAACAAATGCACAT
ATATATACATTCCATAAATTTT
Found at i:54393201 original size:42 final size:42
Alignment explanation
Indices: 54393152--54393280 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 42
54393142 AATACTGTAC
* * *
54393152 CAATGCCATATCCTAGATATGGTCTTACATGTAATCTCGTAA
1 CAATGCCATATCCCAGATATGGTCTTACACGTAATCTCATAA
* * * * *
54393194 CGATGCCAATAGCCCAGCTATGGTGTTACACG-AAGTCTCATAT
1 CAATGCC-ATATCCCAGATATGGTCTTACACGTAA-TCTCATAA
* *
54393237 CAATGCCATATCCCATATATGGTCTTACACGTTATCTCAATAA
1 CAATGCCATATCCCAGATATGGTCTTACACGTAATCTC-ATAA
54393280 C
1 C
54393281 CCTAATGTCA
Statistics
Matches: 68, Mismatches: 15, Indels: 7
0.76 0.17 0.08
Matches are distributed among these distances:
42 32 0.47
43 36 0.53
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
CAATGCCATATCCCAGATATGGTCTTACACGTAATCTCATAA
Found at i:54406404 original size:40 final size:40
Alignment explanation
Indices: 54406360--54406621 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
54406350 GCTCCTCGTT
* *
54406360 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
54406400 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54406440 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54406479 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54406518 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
54406557 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
54406598 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54406622 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:54407718 original size:14 final size:14
Alignment explanation
Indices: 54407699--54407725 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54407689 AGGATGAGCA
54407699 TTTTTTTTTCTTTG
1 TTTTTTTTTCTTTG
54407713 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
54407726 CTAGTTTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.04, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTCTTTG
Found at i:54413645 original size:10 final size:10
Alignment explanation
Indices: 54413632--54413656 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54413622 GAAAAAGAGA
54413632 AAAAGTGAAG
1 AAAAGTGAAG
54413642 AAAAGTGAAG
1 AAAAGTGAAG
54413652 AAAAG
1 AAAAG
54413657 AAAGGAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (10 bp):
AAAAGTGAAG
Found at i:54417370 original size:14 final size:15
Alignment explanation
Indices: 54417351--54417380 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
54417341 ATATTTAACT
54417351 TGTTCTTAATT-ATG
1 TGTTCTTAATTCATG
54417365 TGTTCTTAATTCATG
1 TGTTCTTAATTCATG
54417380 T
1 T
54417381 TTTAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (15 bp):
TGTTCTTAATTCATG
Found at i:54441922 original size:14 final size:15
Alignment explanation
Indices: 54441903--54441932 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
54441893 ATATTTAACT
54441903 TGTTCTTAATT-ATG
1 TGTTCTTAATTCATG
54441917 TGTTCTTAATTCATG
1 TGTTCTTAATTCATG
54441932 T
1 T
54441933 TTTAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (15 bp):
TGTTCTTAATTCATG
Found at i:54451280 original size:30 final size:30
Alignment explanation
Indices: 54451240--54451297 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
54451230 CACGGCCATG
*
54451240 ACACATGGGCATATGGTAT-ACCCGTGTGTC
1 ACACACGGGCATATGG-ATCACCCGTGTGTC
*
54451270 ACACACGGGCATGTGGATCACCCGTGTG
1 ACACACGGGCATATGGATCACCCGTGTG
54451298 GAAGTGCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.22
Consensus pattern (30 bp):
ACACACGGGCATATGGATCACCCGTGTGTC
Found at i:54471402 original size:15 final size:15
Alignment explanation
Indices: 54471384--54471414 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54471374 CTCAGTCTAA
54471384 GAAATCTAAAGAGAT
1 GAAATCTAAAGAGAT
*
54471399 GAAATCTAATGAGAT
1 GAAATCTAAAGAGAT
54471414 G
1 G
54471415 GATTCTCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (15 bp):
GAAATCTAAAGAGAT
Found at i:54479332 original size:48 final size:48
Alignment explanation
Indices: 54479260--54479476 Score: 181
Period size: 48 Copynumber: 4.5 Consensus size: 48
54479250 CATTTGGGTG
* * * *
54479260 ATATGTGCGCTAGTGTAAGACCATGTCTAGGACATGGCAT-TGACCACA
1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAG-CCACA
* * * * *
54479308 TTATGTGTGCCAGTGTAAGGCCATGTTTGGGACATGGCGTCAGCCACA
1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAGCCACA
* *** *
54479356 ATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGAAATCAG-CATTA
1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAGCCA-CA
* * * * *
54479404 ATATGTGA-TTAGTGTAAGACCATGTCTAGGACATGGCATC-GACCTCG
1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAG-CCACA
* * *
54479451 ACATGTGAGCCAGTGTAAGAACATGT
1 ATATGTGAGCTAGTGTAAGACCATGT
54479477 TTGGAACAAG
Statistics
Matches: 134, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
46 1 0.01
47 37 0.28
48 95 0.71
49 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (48 bp):
ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAGCCACA
Found at i:54487396 original size:29 final size:29
Alignment explanation
Indices: 54487335--54487424 Score: 128
Period size: 29 Copynumber: 3.1 Consensus size: 29
54487325 CACATACCTG
*
54487335 TATATGGCCCACTAGGCCC-AATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
*
54487363 TATATCGCCCATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* * *
54487392 TATATGGCCCATCAGGCCCAATTTACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
54487421 TATA
1 TATA
54487425 GTCATGCTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
28 17 0.31
29 38 0.69
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.29
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:54488750 original size:59 final size:58
Alignment explanation
Indices: 54488642--54488754 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 58
54488632 ACATGCATAT
* **
54488642 GGCCCACTAGGCCCAATCTTATTCAAATGGCCCATCTGGCCCAGTTCATATTATTATG
1 GGCCCACTAGGCCCAATCTCATTCAAATGGCCCATCTGGCCCAAATCATATTATTATG
* *
54488700 GGCCCACTAGGTCCAAT-TCACCTTCATATGGCCCAT-TAGGCCCAAATCATATTAT
1 GGCCCACTAGGCCCAATCTCA--TTCAAATGGCCCATCT-GGCCCAAATCATATTAT
54488755 ACTCATGCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
57 2 0.04
58 17 0.36
59 28 0.60
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (58 bp):
GGCCCACTAGGCCCAATCTCATTCAAATGGCCCATCTGGCCCAAATCATATTATTATG
Found at i:54488858 original size:19 final size:19
Alignment explanation
Indices: 54488825--54488871 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
54488815 TGGGCCCAAC
*
54488825 AGCCCA-TCTGTCCCATTT
1 AGCCCATTCTGGCCCATTT
54488843 AGCCCATTCTGGCCCATTT
1 AGCCCATTCTGGCCCATTT
* *
54488862 GGCCAATTCT
1 AGCCCATTCT
54488872 CAACCCAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.17, C:0.36, G:0.15, T:0.32
Consensus pattern (19 bp):
AGCCCATTCTGGCCCATTT
Found at i:54488999 original size:24 final size:24
Alignment explanation
Indices: 54488972--54489018 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
54488962 CCCAACTTTC
*
54488972 GACTTTTTAGCATTTTGGCTTTTT
1 GACTTTTTAGCATTTCGGCTTTTT
*
54488996 GACTTTTTGGCATTTCGGCTTTT
1 GACTTTTTAGCATTTCGGCTTTT
54489019 GCCGATTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.11, C:0.15, G:0.19, T:0.55
Consensus pattern (24 bp):
GACTTTTTAGCATTTCGGCTTTTT
Found at i:54492236 original size:39 final size:40
Alignment explanation
Indices: 54492141--54492402 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
54492131 TTGAATGATG
*
54492141 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
54492179 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
54492220 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
54492259 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
54492298 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
54492337 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
54492376 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
54492403 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:54499410 original size:29 final size:30
Alignment explanation
Indices: 54499342--54499450 Score: 111
Period size: 29 Copynumber: 3.8 Consensus size: 30
54499332 ACCCCTATAT
* *
54499342 ACATGCATATGGCCCA-CTAGGCCCAA-TC
1 ACATTCATATGGCTCATCTAGGCCCAATTC
** *
54499370 TTATTCAAATGGCTCATCT-GGCCCAATTC
1 ACATTCATATGGCTCATCTAGGCCCAATTC
* *
54499399 ACATTCTTATGGCCCA-CTAGGCCCAATTC
1 ACATTCATATGGCTCATCTAGGCCCAATTC
*
54499428 ACCTTCATATGGCTCAT-TAGGCC
1 ACATTCATATGGCTCATCTAGGCC
54499451 AAAATCATAT
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
28 20 0.31
29 44 0.69
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.28
Consensus pattern (30 bp):
ACATTCATATGGCTCATCTAGGCCCAATTC
Found at i:54499548 original size:17 final size:17
Alignment explanation
Indices: 54499526--54499582 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
54499516 GTCTATTATT
54499526 GGCCCAACAGCCCATCA
1 GGCCCAACAGCCCATCA
* *
54499543 GGCCCAATAGACCATCA
1 GGCCCAACAGCCCATCA
54499560 GGCCCAACAGCCCATCA
1 GGCCCAACAGCCCATCA
54499577 GGCCCA
1 GGCCCA
54499583 TTTAGCCCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.30, C:0.44, G:0.19, T:0.07
Consensus pattern (17 bp):
GGCCCAACAGCCCATCA
Found at i:54499602 original size:19 final size:19
Alignment explanation
Indices: 54499578--54499614 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54499568 AGCCCATCAG
*
54499578 GCCCATTTAGCCCATTCTA
1 GCCCATTTAGCCAATTCTA
*
54499597 GCCCATTTGGCCAATTCT
1 GCCCATTTAGCCAATTCT
54499615 CAACCCAAGT
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:0.19, C:0.35, G:0.14, T:0.32
Consensus pattern (19 bp):
GCCCATTTAGCCAATTCTA
Found at i:54521657 original size:50 final size:51
Alignment explanation
Indices: 54521532--54521872 Score: 322
Period size: 50 Copynumber: 6.7 Consensus size: 51
54521522 CCAAAGCTAG
* * * *
54521532 CTGGTACGCATAGTAGACTGCACTTAGTACTACACATGTGACC-AAC-AAT
1 CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACGTAT
* * * * *
54521581 CCGGTACATGTAGTAGCCTACACTTAGTTCTACACACGTGACCTAACGT-T
1 CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACGTAT
* * * *
54521631 CTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAA-GTTGT
1 CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCT-AACG-TAT
* * * * *
54521682 CGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGATCTAAC-TAT
1 CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACGTAT
* * *
54521732 CTGGTACACGTAGTAGCCTACACTTAGTACTACACATGTGA-TTGAA-GTTGT
1 CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCT-AACG-TAT
* * * * *
54521783 CGGGTACACATAGTAGCCTACACTTAGTACTACACATGCGACGTAAC-TAT
1 CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACGTAT
*
54521833 CTGGTACACGTAATAGCCTGCACTTAGTACCATACACATG
1 CTGGTACACGTAGTAGCCTGCACTTAGTA-C-TACACATG
54521873 ACCTAAAACC
Statistics
Matches: 239, Mismatches: 39, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
49 38 0.16
50 110 0.46
51 81 0.34
52 10 0.04
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (51 bp):
CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACGTAT
Found at i:54521715 original size:101 final size:101
Alignment explanation
Indices: 54521591--54521862 Score: 429
Period size: 101 Copynumber: 2.7 Consensus size: 101
54521581 CCGGTACATG
* * * *
54521591 TAGTAGCCTACACTTAGTTCTACACACGTGACCTAACGT-TCTGATACACGTAGTAGCCTGCACT
1 TAGTAGCCTACACTTAGTACTACACATGCGACCTAAC-TATCTGGTACACGTAGTAGCCTGCACT
*
54521655 TAGTACTACACACGTGATTGAAGTTGTCGGGTACGCA
65 TAGTACTACACACGTGATTGAAGTTGTCGGGTACACA
* * *
54521692 TAGTAGCCTGCACTTAGTACTACACATGCGATCTAACTATCTGGTACACGTAGTAGCCTACACTT
1 TAGTAGCCTACACTTAGTACTACACATGCGACCTAACTATCTGGTACACGTAGTAGCCTGCACTT
*
54521757 AGTACTACACATGTGATTGAAGTTGTCGGGTACACA
66 AGTACTACACACGTGATTGAAGTTGTCGGGTACACA
* *
54521793 TAGTAGCCTACACTTAGTACTACACATGCGACGTAACTATCTGGTACACGTAATAGCCTGCACTT
1 TAGTAGCCTACACTTAGTACTACACATGCGACCTAACTATCTGGTACACGTAGTAGCCTGCACTT
54521858 AGTAC
66 AGTAC
54521863 CATACACATG
Statistics
Matches: 156, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
100 1 0.01
101 155 0.99
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (101 bp):
TAGTAGCCTACACTTAGTACTACACATGCGACCTAACTATCTGGTACACGTAGTAGCCTGCACTT
AGTACTACACACGTGATTGAAGTTGTCGGGTACACA
Found at i:54522848 original size:24 final size:24
Alignment explanation
Indices: 54522816--54522865 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
54522806 GATTACCAAA
54522816 ATGCCCCTAACTTAAAAATATTCT
1 ATGCCCCTAACTTAAAAATATTCT
54522840 ATGCCCCTAACTTAAAAATATTCT
1 ATGCCCCTAACTTAAAAATATTCT
54522864 AT
1 AT
54522866 TTCACCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (24 bp):
ATGCCCCTAACTTAAAAATATTCT
Found at i:54524054 original size:53 final size:53
Alignment explanation
Indices: 54523976--54524080 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
54523966 CTTGAGTAAG
54523976 AGAGCTTAAATTATGATGTGATTAGATCATGTTTTAAGCAAATTAAAATCATA
1 AGAGCTTAAATTATGATGTGATTAGATCATGTTTTAAGCAAATTAAAATCATA
*
54524029 AGAGCTTAAATTATGATTTGATTAGATCATGTTTTAAGCAAATTAAAATCAT
1 AGAGCTTAAATTATGATGTGATTAGATCATGTTTTAAGCAAATTAAAATCAT
54524081 GCTCTTTCTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (53 bp):
AGAGCTTAAATTATGATGTGATTAGATCATGTTTTAAGCAAATTAAAATCATA
Found at i:54524305 original size:39 final size:39
Alignment explanation
Indices: 54524210--54524588 Score: 561
Period size: 39 Copynumber: 9.6 Consensus size: 39
54524200 TTGAATGATG
*
54524210 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
54524248 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
54524289 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
54524328 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
54524367 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
54524406 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
54524445 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
54524484 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
54524523 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
54524562 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
54524589 AACGAGTAGC
Statistics
Matches: 319, Mismatches: 15, Indels: 11
0.92 0.04 0.03
Matches are distributed among these distances:
39 249 0.78
40 58 0.18
41 11 0.03
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:54528693 original size:26 final size:26
Alignment explanation
Indices: 54528664--54528731 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 26
54528654 CAGCATGGCT
*
54528664 ACCAGAACAGATATTGTGACAAAATC
1 ACCAGAACAGATATTGTGACAAAACC
* * * *
54528690 ACCAGATACAAATATTGTGGCAGAGCC
1 ACCAGA-ACAGATATTGTGACAAAACC
*
54528717 ACCAAAACAGATATT
1 ACCAGAACAGATATT
54528732 CGTGGCATGG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 14 0.41
27 20 0.59
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (26 bp):
ACCAGAACAGATATTGTGACAAAACC
Found at i:54528764 original size:28 final size:27
Alignment explanation
Indices: 54528689--54528778 Score: 112
Period size: 28 Copynumber: 3.3 Consensus size: 27
54528679 GTGACAAAAT
*
54528689 CACCAGATACAAATATTGTGGCA-GAGC
1 CACCAGAAACAAATATTGTGGCATG-GC
*
54528716 CACCA-AAACAGATATTCGTGGCATGGC
1 CACCAGAAACAAATATT-GTGGCATGGC
*
54528743 CACCAGAAACAAATAATTGTGGCATAGC
1 CACCAGAAACAAAT-ATTGTGGCATGGC
54528771 CACCAGAA
1 CACCAGAA
54528779 TGCTTCCTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
26 9 0.16
27 18 0.33
28 25 0.45
29 3 0.05
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (27 bp):
CACCAGAAACAAATATTGTGGCATGGC
Found at i:54539918 original size:24 final size:24
Alignment explanation
Indices: 54539889--54540010 Score: 92
Period size: 25 Copynumber: 4.9 Consensus size: 24
54539879 AATATACGTA
54539889 TTATATATTTTTATAATTAT-TTAC
1 TTATATATTTTTAT-ATTATATTAC
54539913 TTATAT-TTTATTATATTATATTAC
1 TTATATATTT-TTATATTATATTAC
*
54539937 TTCATAT-TTTTCTACTATCATATTA-
1 TT-ATATATTTT-TA-TATTATATTAC
* * *
54539962 ATATATATTTTAACATATATCATTAC
1 TTATATATTTTTATAT-TAT-ATTAC
54539988 TTAT-TATTTATTATATTTATATT
1 TTATATATTT-TTATA-TTATATT
54540011 TTACCACATA
Statistics
Matches: 79, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
23 10 0.13
24 24 0.30
25 26 0.33
26 18 0.23
27 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATATATTTTTATATTATATTAC
Found at i:54540047 original size:87 final size:89
Alignment explanation
Indices: 54539940--54540102 Score: 197
Period size: 87 Copynumber: 1.8 Consensus size: 89
54539930 ATATTACTTC
* * *
54539940 ATATTTTTCTACTATCATATTAATATATATTTTAAC-ATATATCATTACTTATTATTTATTA-TA
1 ATATTTTTATACTATCATATTAATATAGATTTTAACAATATATCATTACATATTA-TTATTACTA
54540003 TT-TATATTTTACCACATAATATTT
65 TTATATATTTTACCACATAATATTT
* * * * * * *
54540027 ATATTTTTATATTATTATATTATTTTGGATTTTAACAATATATTATTTCATATTATTATTATCTA
1 ATATTTTTATACTATCATATTAATATAGATTTTAACAATATATCATTACATATTATTATTA-CTA
54540092 TTATATATTTT
65 TTATATATTTT
54540103 TTCATGTATA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
87 35 0.56
88 15 0.24
89 4 0.06
90 8 0.13
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (89 bp):
ATATTTTTATACTATCATATTAATATAGATTTTAACAATATATCATTACATATTATTATTACTAT
TATATATTTTACCACATAATATTT
Found at i:54540059 original size:47 final size:50
Alignment explanation
Indices: 54539978--54540102 Score: 127
Period size: 47 Copynumber: 2.5 Consensus size: 50
54539968 ATTTTAACAT
* * *
54539978 ATATCATTACTTATTATT-TATTATATTTATATTTTACCACATA-A-TATTT-
1 ATATTATTA-TTATTATTATATTAT-TTTAGATTTTAACA-ATATATTATTTC
* *
54540027 ATATTTTTA-TATTATTATATTATTTTGGATTTTAACAATATATTATTTC
1 ATATTATTATTATTATTATATTATTTTAGATTTTAACAATATATTATTTC
54540076 ATATTATTATTATCTATTATA-TATTTT
1 ATATTATTATTAT-TATTATATTATTTT
54540103 TTCATGTATA
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
46 3 0.05
47 19 0.30
48 11 0.17
49 15 0.23
50 9 0.14
51 7 0.11
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (50 bp):
ATATTATTATTATTATTATATTATTTTAGATTTTAACAATATATTATTTC
Found at i:54540086 original size:16 final size:16
Alignment explanation
Indices: 54540067--54540141 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 16
54540057 TTTAACAATA
54540067 TATTATTTCATATTAT
1 TATTATTTCATATTAT
54540083 TATTA--TC-TATTAT
1 TATTATTTCATATTAT
* *
54540096 ATATTTTTTCATGTATAT
1 -TATTATTTCATAT-TAT
* *
54540114 CATTA-TTCACATTAT
1 TATTATTTCATATTAT
54540129 TA-T-TTTCATATTA
1 TATTATTTCATATTA
54540142 ATAAAATATT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
13 6 0.13
14 15 0.33
15 4 0.09
16 12 0.27
17 5 0.11
18 3 0.07
ACGTcount: A:0.31, C:0.09, G:0.01, T:0.59
Consensus pattern (16 bp):
TATTATTTCATATTAT
Found at i:54559420 original size:40 final size:40
Alignment explanation
Indices: 54559376--54559637 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
54559366 GCTCCTCGTT
* *
54559376 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
54559416 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54559456 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54559495 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54559534 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
54559573 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
54559614 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54559638 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:54563467 original size:206 final size:205
Alignment explanation
Indices: 54563103--54563658 Score: 781
Period size: 206 Copynumber: 2.7 Consensus size: 205
54563093 GCAGATCTGG
* *
54563103 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAGGAATAAATCGAAGACATAGCT
1 CTGAAGC-AGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAA-ACATAGCT
* * *
54563168 GATTTGGGTTTCACGTGCTTACGATAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
64 GATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * * **
54563233 AGAACAAATCAAAGTTCGGCGTCTCCATATTTGACGGAGAGCATATACATAGCAGATCTGGCCTT
129 AGAACAAATCGAAGTTCGGCGTCTCCATATTGGACGGAGAGCAAACACATAGCAGATCTAACCTT
* *
54563298 CAGATGTTTATA
194 CAGATGATTAGA
*
54563310 CTGAAGCATATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAATCATAGCTG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAA-CATAGCTG
* * * * * *
54563375 ACTTAGCTTTCATGTGCTTATGCTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAAA
65 ATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* *
54563440 GAACAAATCGAAGTTTGGCGTCTCCATATTGGACGGAGGGCAAACACATAGCAGATCTAACCTTC
130 GAACAAATCGAAGTTCGGCGTCTCCATATTGGACGGAGAGCAAACACATAGCAGATCTAACCTTC
54563505 AGATGATTAGA
195 AGATGATTAGA
* * * *
54563516 CTGAAGCAGATCCAAGAT-AGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGGCATAGCT
1 CTGAAGCAGATCCAAGATGA-TTTGGCATCCTTGTGTTTACAAGGAACAAATCGAA-ACATAGCT
* ** * *
54563580 GATTTGGTTTTTGCGTGCTAACGCTGAAGCAAATCTAAGATGATTTGGCAACTCTGTATTGTCAG
64 GATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
54563645 AGAACAAATCGAAG
129 AGAACAAATCGAAG
54563659 AAGCAGATTT
Statistics
Matches: 308, Mismatches: 38, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
205 2 0.01
206 299 0.97
207 7 0.02
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (205 bp):
CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAACATAGCTGA
TTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
AACAAATCGAAGTTCGGCGTCTCCATATTGGACGGAGAGCAAACACATAGCAGATCTAACCTTCA
GATGATTAGA
Found at i:54575526 original size:46 final size:46
Alignment explanation
Indices: 54575459--54575676 Score: 409
Period size: 46 Copynumber: 4.7 Consensus size: 46
54575449 AACCCGCCCC
* * *
54575459 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54575505 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54575551 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54575597 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54575643 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54575677 TGCTCAACCA
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 169 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:54577179 original size:26 final size:25
Alignment explanation
Indices: 54577117--54577183 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
54577107 TAAATATACG
*
54577117 TATT-ATATATATTTTATTATATTA
1 TATTAATATATATTTTATTATATCA
*
54577141 TATTACT-TCATATTTT-TCTACTATCA
1 TATTAATAT-ATATTTTAT-TA-TATCA
54577167 TATTAATATATATTTTA
1 TATTAATATATATTTTA
54577184 ACATATATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
24 6 0.18
25 10 0.29
26 17 0.50
27 1 0.03
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTAATATATATTTTATTATATCA
Found at i:54577218 original size:41 final size:40
Alignment explanation
Indices: 54577173--54577311 Score: 97
Period size: 46 Copynumber: 3.2 Consensus size: 40
54577163 ATCATATTAA
54577173 TATATATTTTAACATATATCATTACTTATTATTTATTATA-
1 TATATATTTTAACATATAT-ATTACTTATTATTTATTATAT
*
54577213 T-TATATTTTACCACATA-ATATTTATATTATTATATTATTATAT
1 TATATATTTTA--ACATATATA-TTA-CTTATTAT-TTATTATAT
* * *
54577256 TATTTTGCATTTTAACAATATATTATTTCATATTA-TTATTATCTAT
1 TA-TAT--ATTTTAAC-ATATA-TATTACTTATTATTTATTA--TAT
54577302 TATATATTTT
1 TATATATTTT
54577312 TTCATGTATA
Statistics
Matches: 78, Mismatches: 6, Indels: 27
0.70 0.05 0.24
Matches are distributed among these distances:
39 10 0.13
40 6 0.08
41 12 0.15
42 8 0.10
43 6 0.08
44 6 0.08
45 6 0.08
46 13 0.17
47 9 0.12
48 2 0.03
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (40 bp):
TATATATTTTAACATATATATTACTTATTATTTATTATAT
Found at i:54577247 original size:8 final size:8
Alignment explanation
Indices: 54577234--54577259 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
54577224 CACATAATAT
54577234 TTATATTA
1 TTATATTA
54577242 TTATATTA
1 TTATATTA
54577250 TTATATTA
1 TTATATTA
54577258 TT
1 TT
54577260 TTGCATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTATATTA
Found at i:54577295 original size:16 final size:16
Alignment explanation
Indices: 54577276--54577350 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 16
54577266 TTTAACAATA
54577276 TATTATTTCATATTAT
1 TATTATTTCATATTAT
54577292 TATTA--TC-TATTAT
1 TATTATTTCATATTAT
* *
54577305 ATATTTTTTCATGTATAT
1 -TATTATTTCATAT-TAT
* *
54577323 CATTA-TTCACATTAT
1 TATTATTTCATATTAT
54577338 TA-T-TTTCATATTA
1 TATTATTTCATATTA
54577351 ATAAAATATT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
13 6 0.13
14 15 0.33
15 4 0.09
16 12 0.27
17 5 0.11
18 3 0.07
ACGTcount: A:0.31, C:0.09, G:0.01, T:0.59
Consensus pattern (16 bp):
TATTATTTCATATTAT
Found at i:54583436 original size:419 final size:420
Alignment explanation
Indices: 54582637--54583467 Score: 1157
Period size: 419 Copynumber: 2.0 Consensus size: 420
54582627 CGACCACGAC
* * * * *
54582637 CCATACCATTTCCACCTTTGGCCTGACCACGGCCTCTCGGTGGCTGTTGACCACCCTTCGACGGT
1 CCATACCATTTCCACCTCTGACCTGACCACGACCTCTCGGTGGCTGATGACCACCCCTCGACGGT
* * * * *
54582702 TGAACATTACCCAAACCTGTAGCTTGCATCTAGTCGGGCCTCCGTAGACTATCTCTAATTTGGTA
66 TGAACATTACCCAAACCTGTAGCTTCCATCTACTCGGGCCTCCGTAGACAATCTCTAATTCGATA
* * *
54582767 CTCTAATGATCCATACCTCAAACATGCCCCAATCCATTTCTAGCACTCACCATGATGGCGTCTCC
131 CTCTAATGATCCACACCTCAAACATGCCCCAATCCATTTCCAGCACTCACCATGATGGCATCTCC
* * * * * *
54582832 CACAATCCGCACAGGGTTGTGGTCCAATAGCAGTAACAGGGGCCCCAACTCTGATTGGCCCATCA
196 CACAATCCACACAGGGTTGCGGTCCAATAGCAGCAACAGGGACCCCAACTCTGACTGACCCATCA
* * *
54582897 ACTCTAGCCTTTTTCTTAGGCCTCATAAATGAACTTGAAGGTTCTGAGTCCCTTTTGTTCCTACC
261 ACTCTAGCCTTTTTCTTAGGCCTCATAAATGAACTTGAAGGCTCTGAATCCCTCTTGTTCCTACC
* * * *
54582962 TCTTTCTTTCTCATGATTCTGTCGTTCTGTATGTTTCACTTTTTCAGCAATCTTCACCTTATCCA
326 TCTTTCTTTCTCATGATTCTGTCATTCTATACGTTTCACTTCTTCAGCAATCTTCACCTTATCCA
54583027 CTAAAGCAGCAAAATCT-ACTCAGGCCTAA
391 CTAAAGCAGCAAAATCTCACTCAGGCCTAA
*
54583056 CCATACCATTTCCACCTCTGACCTGAGCACGACCTCTCGGTGGCTGATGACCACCCCTCGACGGT
1 CCATACCATTTCCACCTCTGACCTGACCACGACCTCTCGGTGGCTGATGACCACCCCTCGACGGT
* * * * * ** *
54583121 TGTACATTATCCAAACCTGTAGCTTCCATCTACTCGGGCGTCTGTGGACAATCTCTGGTTCGATG
66 TGAACATTACCCAAACCTGTAGCTTCCATCTACTCGGGCCTCCGTAGACAATCTCTAATTCGATA
* ** **
54583186 CTCTAATGATCCACATCTCAAACATGCCCCAATCTGTTTCCAGCACTTGCCATGATGGCATCTCC
131 CTCTAATGATCCACACCTCAAACATGCCCCAATCCATTTCCAGCACTCACCATGATGGCATCTCC
* ** * *
54583251 CACAATCCATACA-GGTCTGCGGTCCTGTAGTAGCAACAGGGACCTCAACTCTGACTGACCCATC
196 CACAATCCACACAGGGT-TGCGGTCCAATAGCAGCAACAGGGACCCCAACTCTGACTGACCCATC
* * *
54583315 AACTTTGGCCTTTTTCTTAGGCCTCATAAATGAACTTG-AGGCCTCTGAATCCCTCTTGTTTCTA
260 AACTCTAGCCTTTTTCTTAGGCCTCATAAATGAACTTGAAGG-CTCTGAATCCCTCTTGTTCCTA
**
54583379 CCTCTTTCTTTCTCATGATTCTGTCATTCTATACGCTTT-ACTTCTTCAGTGATCTTCACCTTAT
324 CCTCTTTCTTTCTCATGATTCTGTCATTCTATACG-TTTCACTTCTTCAGCAATCTTCACCTTAT
54583443 CCACTAAAGCAGCAAAATCTCACTC
388 CCACTAAAGCAGCAAAATCTCACTC
54583468 TCTTTGCGGA
Statistics
Matches: 358, Mismatches: 50, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
418 6 0.02
419 345 0.96
420 7 0.02
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (420 bp):
CCATACCATTTCCACCTCTGACCTGACCACGACCTCTCGGTGGCTGATGACCACCCCTCGACGGT
TGAACATTACCCAAACCTGTAGCTTCCATCTACTCGGGCCTCCGTAGACAATCTCTAATTCGATA
CTCTAATGATCCACACCTCAAACATGCCCCAATCCATTTCCAGCACTCACCATGATGGCATCTCC
CACAATCCACACAGGGTTGCGGTCCAATAGCAGCAACAGGGACCCCAACTCTGACTGACCCATCA
ACTCTAGCCTTTTTCTTAGGCCTCATAAATGAACTTGAAGGCTCTGAATCCCTCTTGTTCCTACC
TCTTTCTTTCTCATGATTCTGTCATTCTATACGTTTCACTTCTTCAGCAATCTTCACCTTATCCA
CTAAAGCAGCAAAATCTCACTCAGGCCTAA
Found at i:54587922 original size:49 final size:48
Alignment explanation
Indices: 54587862--54587992 Score: 154
Period size: 49 Copynumber: 2.7 Consensus size: 48
54587852 ACATCAAAGT
* * * *
54587862 CGATGTCATGTCCCAGATACGTCTTACACTGACTTTCATTTATCGAGGC
1 CGATGCCATGTCCCAGACA-GTCTTACACTGACTCTCATCTATCGAGGC
* * * *
54587911 CGATGCCATGTCCCAGACAGATCTTACACTGTCTCTCGTCTATCGATGT
1 CGATGCCATGTCCCAGACAG-TCTTACACTGACTCTCATCTATCGAGGC
*
54587960 CGATGCCATGTGCCAGACAGGTCTTACACTGAC
1 CGATGCCATGTCCCAGACA-GTCTTACACTGAC
54587993 ACACAACATG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 1 0.01
49 68 0.97
50 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACAGTCTTACACTGACTCTCATCTATCGAGGC
Found at i:54588150 original size:46 final size:46
Alignment explanation
Indices: 54588050--54588173 Score: 150
Period size: 46 Copynumber: 2.7 Consensus size: 46
54588040 TATATCCCGA
54588050 GGCCGATGCATGTCCTAGACATGTCTTACACTAGCTCTCGTCTCAAT
1 GGCCGATGCATGTCCTAGACATGTCTTACACTAGCTCTC-TCTCAAT
* *
54588097 -GCTGATGCATGTTCC-AGACATGTCTTACACTTGCT-T-TCAT-AATGT
1 GGCCGATGCATG-TCCTAGACATGTCTTACACTAGCTCTCTC-TCAA--T
54588142 GGCCGATGCATGTCCTAGACATGTCTTACACT
1 GGCCGATGCATGTCCTAGACATGTCTTACACT
54588174 GGCACATATA
Statistics
Matches: 68, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
43 4 0.06
44 1 0.01
45 5 0.07
46 55 0.81
47 3 0.04
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (46 bp):
GGCCGATGCATGTCCTAGACATGTCTTACACTAGCTCTCTCTCAAT
Found at i:54600467 original size:73 final size:72
Alignment explanation
Indices: 54600293--54600582 Score: 370
Period size: 73 Copynumber: 4.0 Consensus size: 72
54600283 GCTTTATCAT
* *
54600293 ATAACTGGAGGCCT-AGCCTCTTTTAATTACTGGGGCA-AAGGCCCTTTTAATAACTGGGGCATA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAA-GCCCTTTTAATAACTGGGGCATA
* *
54600356 AGCCCTTTTG
63 AGCCTTTTTA
* * *
54600366 ATAACTGGGACATAAGCCCTTTTAATAACTGGGGCATAAGCCCATTTAATAACTGGAGGCCT-AG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGG-GGCATAAG
54600430 CCTATTTTA
65 CCT-TTTTA
* * * *
54600439 ATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCTTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAG-
54600504 CCTTTTTA
65 CCTTTTTA
** *
54600512 ATAGTTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGC
*
54600577 CCTTTT
66 CTTTTT
54600583 GCACTTCCTG
Statistics
Matches: 191, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
72 50 0.26
73 138 0.72
74 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (72 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGC
CTTTTTA
Found at i:54600583 original size:24 final size:24
Alignment explanation
Indices: 54600293--54600582 Score: 379
Period size: 24 Copynumber: 12.0 Consensus size: 24
54600283 GCTTTATCAT
*
54600293 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
54600318 ATTACTGGGGCA-AAGGCCCTTTTA
1 ATAACTGGGGCATAA-GCCCTTTTA
*
54600342 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
54600366 ATAACTGGGACATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
54600390 ATAACTGGGGCATAAGCCCATTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
54600414 ATAACTGGAGGCCT-AGCCTATTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
54600439 ATAACTGGGGCAAAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
54600463 ATAACTGGGGCATAAGCCTTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
54600487 ATAACTGGGGCATAAGCCCTTTTTA
1 ATAACTGGGGCATAAGCCC-TTTTA
**
54600512 ATAGTTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
54600536 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
54600560 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
54600583 GCACTTCCTG
Statistics
Matches: 234, Mismatches: 24, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
24 181 0.77
25 53 0.23
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:54600583 original size:97 final size:96
Alignment explanation
Indices: 54600314--54600583 Score: 400
Period size: 97 Copynumber: 2.8 Consensus size: 96
54600304 CCTAGCCTCT
* *
54600314 TTTAATTACTGGGGCA-AAGGCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGACA
1 TTTAATAACTGGGGCATAA-GCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCA
*
54600378 TAAGCCCTTTTAATAACTGGGGCATAAGCCCA
65 TAAGCCCTTTTGATAACTGGGGCATAAGCCCA
* * *
54600410 TTTAATAACTGGAGGCCT-AGCCTATTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGC
1 TTTAATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGC
* *
54600474 ATAAGCCTTTTTGATAACTGGGGCATAAGCCCTT
64 ATAAGCCCTTTTGATAACTGGGGCATAAGCCC-A
**
54600508 TTTAATAGTTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAT
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAT
54600573 AAGCCCTTTTG
66 AAGCCCTTTTG
54600584 CACTTCCTGT
Statistics
Matches: 155, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
96 14 0.09
97 127 0.82
98 14 0.09
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (96 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAT
AAGCCCTTTTGATAACTGGGGCATAAGCCCA
Found at i:54600653 original size:16 final size:15
Alignment explanation
Indices: 54600632--54600683 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
54600622 TTATGAATAC
54600632 ATCATGTACATATCAT
1 ATCATGT-CATATCAT
54600648 ATCATGTGCATATCAT
1 ATCATGT-CATATCAT
*
54600664 A-CATGTCATGTTCAT
1 ATCATGTCAT-ATCAT
54600679 ATCAT
1 ATCAT
54600684 ACATACCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 3 0.09
15 10 0.31
16 19 0.59
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (15 bp):
ATCATGTCATATCAT
Found at i:54600674 original size:20 final size:20
Alignment explanation
Indices: 54600649--54600687 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54600639 ACATATCATA
54600649 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
*
54600669 TCATGTTCATATCATACAT
1 TCATGTGCATATCATACAT
54600688 ACCATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:54600763 original size:25 final size:25
Alignment explanation
Indices: 54600731--54600778 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
54600721 ATATATAAAC
* * *
54600731 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
54600756 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
54600779 CATAAAATTA
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:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:54608416 original size:24 final size:24
Alignment explanation
Indices: 54608364--54608533 Score: 243
Period size: 24 Copynumber: 7.0 Consensus size: 24
54608354 GCTTTATCAT
* *
54608364 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
*
54608389 ATAACTGGGGCAAAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54608413 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
54608437 ATAACTGGGGCATAAGCCCTTTTTA
1 ATAACTGGGGCATAAGCCC-TTTTG
** *
54608462 ATAGTTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTG
54608486 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54608510 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54608534 CACTTCCTGT
Statistics
Matches: 133, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
24 100 0.75
25 33 0.25
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:54608462 original size:73 final size:73
Alignment explanation
Indices: 54608384--54608532 Score: 262
Period size: 73 Copynumber: 2.0 Consensus size: 73
54608374 GCCTAGCCTC
*
54608384 TTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCA
1 TTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCA
54608449 TAAGCCCT
66 TAAGCCCT
** *
54608457 TTTTAATAGTTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCA
1 TTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCA
54608522 TAAGCCCT
66 TAAGCCCT
54608530 TTT
1 TTT
54608533 GCACTTCCTG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (73 bp):
TTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCA
TAAGCCCT
Found at i:54608490 original size:49 final size:48
Alignment explanation
Indices: 54608364--54608532 Score: 250
Period size: 49 Copynumber: 3.5 Consensus size: 48
54608354 GCTTTATCAT
* *
54608364 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTG
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTG
* *
54608413 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTTA
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC-TTTTG
**
54608462 ATAGTTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTG
54608510 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
54608533 GCACTTCCTG
Statistics
Matches: 108, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
48 52 0.48
49 56 0.52
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTG
Found at i:54608603 original size:16 final size:16
Alignment explanation
Indices: 54608582--54608614 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54608572 TTATGAATAC
54608582 ATCATGTGCATATCAT
1 ATCATGTGCATATCAT
54608598 ATCATGTGCATATCAT
1 ATCATGTGCATATCAT
54608614 A
1 A
54608615 CATACCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (16 bp):
ATCATGTGCATATCAT
Found at i:54614233 original size:44 final size:42
Alignment explanation
Indices: 54614179--54614335 Score: 161
Period size: 43 Copynumber: 3.7 Consensus size: 42
54614169 TTCTGATATG
**
54614179 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGGCTT
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGAATT
** * *
54614221 ATGATTTACGTGTAAGACCATGTCTGGGACATCAGTATCGTATT
1 -TGATTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGAATT
* * * * *
54614265 TGATTTCGTGTAAGACCCTATTTGGGACAGTGGCATCAATATT
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGA-ATT
* * *
54614308 TGATTACATGTAAGACCATGTTTGGGAC
1 TGATTTCGTGTAAGACCATGTCTGGGAC
54614336 GTTGCCATTG
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
42 24 0.26
43 39 0.41
44 31 0.33
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGAATT
Found at i:54614293 original size:42 final size:43
Alignment explanation
Indices: 54614179--54614281 Score: 145
Period size: 44 Copynumber: 2.4 Consensus size: 43
54614169 TTCTGATATG
** *
54614179 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGGCTTA
1 TGATTTCGTGTAAGACCATGTCTGGGACATCAGCATCGGATTA
* *
54614222 TGATTTACGTGTAAGACCATGTCTGGGACATCAGTATCGTATT-
1 TGATTT-CGTGTAAGACCATGTCTGGGACATCAGCATCGGATTA
54614265 TGATTTCGTGTAAGACC
1 TGATTTCGTGTAAGACC
54614282 CTATTTGGGA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
42 11 0.20
43 12 0.22
44 31 0.57
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (43 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATCAGCATCGGATTA
Found at i:54618098 original size:28 final size:29
Alignment explanation
Indices: 54618042--54618098 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
54618032 GAATGTTTCC
* *
54618042 ATTGATGAACCTTGTGATTTTAGATGTTA
1 ATTGATGAACCTTGAGATATTAGATGTTA
* *
54618071 ATTGATGAA-TTTGAGATATTAGTTGTTA
1 ATTGATGAACCTTGAGATATTAGATGTTA
54618099 TTTAAAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.46
Consensus pattern (29 bp):
ATTGATGAACCTTGAGATATTAGATGTTA
Found at i:54621166 original size:109 final size:109
Alignment explanation
Indices: 54620975--54621296 Score: 608
Period size: 109 Copynumber: 3.0 Consensus size: 109
54620965 CACTTTGGTG
54620975 AAGAAAAATATTTTGTTTGAAGAGGGTGATTAAAAACTAAGATTTTAAACCAAGTAAACTAAATA
1 AAGAAAAATATTTTGTTTGAAGAGGGTGATTAAAAACTAAGATTTTAAACCAAGTAAACTAAATA
54621040 AATAAATCTCAAATGTATGATTTCAAAATATGATTTAATAAATA
66 AATAAATCTCAAATGTATGATTTCAAAATATGATTTAATAAATA
54621084 AAGAAAAATATTTTGTTTGAAGAGGGTGATTAAAAACTAAGATTTTAAACCAAGTAAACTAAATA
1 AAGAAAAATATTTTGTTTGAAGAGGGTGATTAAAAACTAAGATTTTAAACCAAGTAAACTAAATA
54621149 AATAAATCTCAAATGTATGATTTCAAAATATGATTTAATAAATA
66 AATAAATCTCAAATGTATGATTTCAAAATATGATTTAATAAATA
* *
54621193 AAGAAAAATATTTTGTTTGAAGAGGGTGATTAAAAACTAAGATTTTAAACTAAGTAAACTGAATA
1 AAGAAAAATATTTTGTTTGAAGAGGGTGATTAAAAACTAAGATTTTAAACCAAGTAAACTAAATA
* *
54621258 AATAAATCTCAAATGCACGATTTCAAAATATGATTTAAT
66 AATAAATCTCAAATGTATGATTTCAAAATATGATTTAAT
54621297 CAAGATGACA
Statistics
Matches: 209, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 209 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (109 bp):
AAGAAAAATATTTTGTTTGAAGAGGGTGATTAAAAACTAAGATTTTAAACCAAGTAAACTAAATA
AATAAATCTCAAATGTATGATTTCAAAATATGATTTAATAAATA
Found at i:54622912 original size:6 final size:6
Alignment explanation
Indices: 54622882--54622969 Score: 56
Period size: 6 Copynumber: 14.3 Consensus size: 6
54622872 AACAAACATT
* * * *
54622882 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATTAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* *
54622931 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
54622970 GTGAATGCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
5 4 0.06
6 50 0.81
7 6 0.10
8 2 0.03
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:54622936 original size:25 final size:25
Alignment explanation
Indices: 54622903--54622969 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
54622893 AATCAAAATG
* *
54622903 AGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGGTAAC
*
54622928 AGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
*
54622953 AGAATCAAAATCAGAAT
1 AGAATCAGAATCAGAAT
54622970 GTGAATGCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.19
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTAAC
Found at i:54623103 original size:27 final size:28
Alignment explanation
Indices: 54623066--54623126 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
54623056 GCTACACACC
* *
54623066 ACAGA-ATTTGTAGCATGGCTGCCAG-A
1 ACAGATATTTGTAGCATAGCTACCAGAA
* *
54623092 ACAGATATTTGTGGCATAGCTACTAGAA
1 ACAGATATTTGTAGCATAGCTACCAGAA
54623120 ACAGATA
1 ACAGATA
54623127 ATGTGGCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 5 0.17
27 16 0.55
28 8 0.28
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (28 bp):
ACAGATATTTGTAGCATAGCTACCAGAA
Found at i:54623252 original size:22 final size:22
Alignment explanation
Indices: 54623227--54623290 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
54623217 CCCACAATAA
*
54623227 TGGCACATAGCCATAATCAGGT
1 TGGCACAAAGCCATAATCAGGT
*
54623249 TGGCACAAAGCCAT-ATGTAGGT
1 TGGCACAAAGCCATAAT-CAGGT
*
54623271 TGGCGCAAAGCCATAATCAG
1 TGGCACAAAGCCATAATCAG
54623291 AATAATTGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TGGCACAAAGCCATAATCAGGT
Found at i:54625491 original size:27 final size:28
Alignment explanation
Indices: 54625407--54625504 Score: 162
Period size: 28 Copynumber: 3.5 Consensus size: 28
54625397 TAAATTGTAC
*
54625407 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
54625435 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
54625463 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
54625490 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54625505 GACTTAATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
27 24 0.36
28 43 0.64
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTTGATTATAT
Found at i:54625515 original size:27 final size:27
Alignment explanation
Indices: 54625407--54625517 Score: 125
Period size: 28 Copynumber: 4.0 Consensus size: 27
54625397 TAAATTGTAC
* *
54625407 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
54625435 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
54625463 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
54625490 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
54625517 A
1 A
54625518 CGTTTGAATC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
27 30 0.39
28 46 0.61
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:54627230 original size:27 final size:27
Alignment explanation
Indices: 54627200--54627304 Score: 147
Period size: 27 Copynumber: 3.9 Consensus size: 27
54627190 GGCAAAATGG
* * *
54627200 TAATTTTACCCCACAAGGGTATCTCGA
1 TAATTCTACCCTACAAGGGTATTTCGA
*
54627227 TAATTCTACCCTACAAGGGTATTTCGG
1 TAATTCTACCCTACAAGGGTATTTCGA
* *
54627254 TATTTCTACGCTACAAGGGTATTTCGA
1 TAATTCTACCCTACAAGGGTATTTCGA
*
54627281 TAATTCTACCCTACAGGGGTATTT
1 TAATTCTACCCTACAAGGGTATTT
54627305 TAGTAATTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (27 bp):
TAATTCTACCCTACAAGGGTATTTCGA
Found at i:54627245 original size:54 final size:54
Alignment explanation
Indices: 54627187--54627295 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
54627177 TTAACACCCT
54627187 AAGGGCAAAAT-GGTAATTT-TACCCCACAAGGGTATCTCGATAATTCTACCCTAC
1 AAGGG-AAAATCGGT-ATTTCTACCCCACAAGGGTATCTCGATAATTCTACCCTAC
* ** * * *
54627241 AAGGGTATTTCGGTATTTCTACGCTACAAGGGTATTTCGATAATTCTACCCTAC
1 AAGGGAAAATCGGTATTTCTACCCCACAAGGGTATCTCGATAATTCTACCCTAC
54627295 A
1 A
54627296 GGGGTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 6 0.13
54 41 0.87
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (54 bp):
AAGGGAAAATCGGTATTTCTACCCCACAAGGGTATCTCGATAATTCTACCCTAC
Found at i:54630887 original size:28 final size:28
Alignment explanation
Indices: 54630855--54630909 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
54630845 CAGTACAGTC
* *
54630855 TGGGCCTTAGCCCTATACAGTAATAGTG
1 TGGGCCTAAGCCCAATACAGTAATAGTG
* *
54630883 TGGGCCTAAGCCCAATGCAGTATTAGT
1 TGGGCCTAAGCCCAATACAGTAATAGT
54630910 ACAGTGTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (28 bp):
TGGGCCTAAGCCCAATACAGTAATAGTG
Found at i:54631098 original size:27 final size:26
Alignment explanation
Indices: 54631068--54631151 Score: 114
Period size: 27 Copynumber: 3.2 Consensus size: 26
54631058 TACTAGAAAT
*
54631068 AGTAAATGTGGCAAAGCCACCAGTATC
1 AGTAAATGTGGCATAGCCACCAGTA-C
*
54631095 AGTAATTGTGGCATAGCCACCAGTAAC
1 AGTAAATGTGGCATAGCCACCAGT-AC
**
54631122 AGTAAATGTGGCATAGTAACCAGTAC
1 AGTAAATGTGGCATAGCCACCAGTAC
54631148 AGTA
1 AGTA
54631152 CTTCCTCCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
26 6 0.12
27 44 0.86
28 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (26 bp):
AGTAAATGTGGCATAGCCACCAGTAC
Found at i:54631342 original size:27 final size:25
Alignment explanation
Indices: 54631284--54631346 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
54631274 AAAGCATAAT
*
54631284 CGTCATTTGACCCTACAGGGCATCA
1 CGTCATTTTACCCTACAGGGCATCA
* *
54631309 CGATCATTTTACCCTACACTGGCATTA
1 CG-TCATTTTACCCTACA-GGGCATCA
54631336 CAGTCATTTTA
1 C-GTCATTTTA
54631347 TAATCTAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 2 0.06
26 14 0.44
27 15 0.47
28 1 0.03
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (25 bp):
CGTCATTTTACCCTACAGGGCATCA
Found at i:54636127 original size:29 final size:30
Alignment explanation
Indices: 54636070--54636127 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
54636060 ATTTTGAAAA
* * *
54636070 TATTTACAAAAAGAGGCATCTAATTTTTAT
1 TATTTACAAAAAGAGGCAACCAAATTTTAT
54636100 TATTTACAAAAAGA-GCAACCAAATTTTA
1 TATTTACAAAAAGAGGCAACCAAATTTTA
54636128 AAAAGAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (30 bp):
TATTTACAAAAAGAGGCAACCAAATTTTAT
Found at i:54646817 original size:38 final size:38
Alignment explanation
Indices: 54646774--54646849 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
54646764 TTCATCCTTT
54646774 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
*
54646812 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGGGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
54646850 GGAGTTCTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:54648132 original size:40 final size:40
Alignment explanation
Indices: 54648038--54648182 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
54648028 TACTCGAATG
*
54648038 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* * *
54648079 ACATCCGGACTAAGAT-CCAAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
54648119 ATATCCGGGCTAAGTCCCGAAGGCATTTTTGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
54648159 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
54648183 CTTGTGCGAG
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 61 0.68
41 27 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:54661487 original size:46 final size:46
Alignment explanation
Indices: 54661437--54661690 Score: 232
Period size: 46 Copynumber: 5.5 Consensus size: 46
54661427 TGTGTGTGCT
* * *
54661437 AGTGTAAGATATGTCTGGGACATGCATCGGCCAC-ATTATG-AGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGTA-AGCC
* * * * *
54661483 AGTGTAAGACCATGTCTGGGACATGGTATCGGCATTGAGACG-AGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA-AGCC
* * **
54661531 AGTGTAAGACATGTTTGGGACATGCAACACCCTCGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCC
* **
54661577 AGTTTAAGACATGTCTGGGACATGCATCGGATTCGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCC
* * * *
54661623 AGTGTAAGACATGTCTGGGACATGCATCAG-CTATGACATGT--GCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTAAGCC
*
54661667 AGTGTAAGACATGTCTGGAACATG
1 AGTGTAAGACATGTCTGGGACATG
54661691 GCATTGCCAT
Statistics
Matches: 172, Mismatches: 31, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
44 25 0.15
45 1 0.01
46 95 0.55
47 27 0.16
48 23 0.13
49 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCC
Found at i:54665250 original size:43 final size:42
Alignment explanation
Indices: 54665154--54665324 Score: 155
Period size: 43 Copynumber: 4.0 Consensus size: 42
54665144 ATAGGATTTC
* * ** *
54665154 CATATGTGATTTTGTGTAAGAAAACATCTGGGACGTTGGCAT
1 CATATTTGATTTCGTGTAAGACCACATCTGGGACATTGGCAT
** * **
54665196 CAGCTTATGATTTATGTGTAAGACCATGTCTGGGACATTGGCAT
1 CATATT-TGATTT-CGTGTAAGACCACATCTGGGACATTGGCAT
* * *
54665240 CATATTTGATTTCCTGTAAGACC-CTATTTGGGACAATGGCAT
1 CATATTTGATTTCGTGTAAGACCAC-ATCTGGGACATTGGCAT
* * *
54665282 CGATATTTGATTACATGTAAGACCACATCTGGGACGTTGGCAT
1 C-ATATTTGATTTCGTGTAAGACCACATCTGGGACATTGGCAT
54665325 TGTATGAGCT
Statistics
Matches: 103, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
42 27 0.26
43 46 0.45
44 30 0.29
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (42 bp):
CATATTTGATTTCGTGTAAGACCACATCTGGGACATTGGCAT
Found at i:54666194 original size:34 final size:34
Alignment explanation
Indices: 54666151--54666217 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
54666141 CATAAACATA
54666151 TTCATTTCATGTCTATTCGGCAACCAAGATCTAT
1 TTCATTTCATGTCTATTCGGCAACCAAGATCTAT
*
54666185 TTCATTTCATGTCTATTCGGCAACCATGATCTA
1 TTCATTTCATGTCTATTCGGCAACCAAGATCTA
54666218 CTAGTACATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (34 bp):
TTCATTTCATGTCTATTCGGCAACCAAGATCTAT
Found at i:54666480 original size:10 final size:10
Alignment explanation
Indices: 54666467--54666497 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
54666457 AAAAATATGT
54666467 ATATATATAC
1 ATATATATAC
*
54666477 ATATATATAA
1 ATATATATAC
54666487 ATATATATAC
1 ATATATATAC
54666497 A
1 A
54666498 GGTACCGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATATATAC
Found at i:54669908 original size:54 final size:54
Alignment explanation
Indices: 54669014--54669915 Score: 1741
Period size: 54 Copynumber: 16.7 Consensus size: 54
54669004 AAATTAGGGA
* * * * * *
54669014 TATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACTAGGGG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
*
54669068 TATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669122 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669176 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669230 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669284 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669338 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669392 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669446 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669500 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669554 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669608 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669662 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669716 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669770 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669824 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
54669878 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAA
1 TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAA
54669916 ACTAAAGTAT
Statistics
Matches: 842, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 842 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (54 bp):
TATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGTG
Found at i:54673860 original size:29 final size:29
Alignment explanation
Indices: 54673799--54673890 Score: 141
Period size: 29 Copynumber: 3.2 Consensus size: 29
54673789 CACATACCTG
*
54673799 TATATGGCCCACTAGGCCC-AATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
54673827 TATATGGCCCATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* * *
54673856 TATATAGCCCATCAGGCCCAATTCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
54673885 TATATG
1 TATATG
54673891 TATGCTCACA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
28 18 0.31
29 40 0.69
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:54689553 original size:46 final size:46
Alignment explanation
Indices: 54689503--54689678 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
54689493 TGGTTAAGCA
54689503 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
54689549 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
54689594 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* **
54689642 CCCGAGGTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54689679 GCGAGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54689659 original size:93 final size:93
Alignment explanation
Indices: 54689500--54689670 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
54689490 GGATGGTTAA
* *
54689500 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
54689565 TGAGTCTGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* **
54689593 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGGTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54689658 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
54689671 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:54692093 original size:38 final size:38
Alignment explanation
Indices: 54692042--54692119 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
54692032 AGCAGAATGT
*
54692042 GGGTCCTAAATCTCAGAATACTTCTCCAGCCAGTGTAG
1 GGGTCCTAAATCTCAGAATACTTCTCCAACCAGTGTAG
*
54692080 GGGTCCTAAATCTCAGAATACTTCTGCAACCAGTGTAG
1 GGGTCCTAAATCTCAGAATACTTCTCCAACCAGTGTAG
54692118 GG
1 GG
54692120 AACTCGAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (38 bp):
GGGTCCTAAATCTCAGAATACTTCTCCAACCAGTGTAG
Found at i:54694930 original size:46 final size:46
Alignment explanation
Indices: 54694880--54695055 Score: 173
Period size: 46 Copynumber: 3.8 Consensus size: 46
54694870 TGGTTGAGCA
54694880 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * * *
54694926 TCCGAACTCGTTGAGTTGAGTTCAAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54694971 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54695019 -CCCAAGCTTGTTGAGTTGAGTCCGAGTTCACATATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54695056 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 16, Indels: 20
0.74 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 7 0.07
46 56 0.54
47 27 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54695047 original size:93 final size:93
Alignment explanation
Indices: 54694877--54695047 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
54694867 GGATGGTTGA
* *
54694877 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT
*
54694942 TGAGTTCAAGTTCGTGAAATGTAACTAG
66 TGAGTCCAAGTTCGTGAAATGTAACTAG
*
54694970 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTTGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTGAG
*
54695034 TTGAGTCCGAGTTC
65 TTGAGTCCAAGTTC
54695048 ACATATGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 4 0.06
93 68 0.94
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT
TGAGTCCAAGTTCGTGAAATGTAACTAG
Found at i:54698385 original size:12 final size:12
Alignment explanation
Indices: 54698370--54698400 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54698360 CTCCAGTTTT
*
54698370 CACACAGCCTAG
1 CACACAGCCTAA
54698382 CACACAGCCTAA
1 CACACAGCCTAA
54698394 CACACAG
1 CACACAG
54698401 GTGTATGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.39, C:0.42, G:0.13, T:0.06
Consensus pattern (12 bp):
CACACAGCCTAA
Done.