Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 102 of 171
Found at i:32861870 original size:3 final size:3
Alignment explanation
Indices: 32861864--32861892 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
32861854 CATCATCATC
32861864 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
32861893 CGGTAGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:32862351 original size:28 final size:27
Alignment explanation
Indices: 32862274--32862351 Score: 75
Period size: 30 Copynumber: 2.7 Consensus size: 27
32862264 CAAATGATTT
* *
32862274 TAAAATTATTAAATTATTTTTTAAATA
1 TAAAATTATTAAATAATTTTTGAAATA
* *
32862301 TAAAAGTATTAAAAGTATTTTTTTGAAATAA
1 TAAAATTATT-AAA-TA-ATTTTTGAAAT-A
*
32862332 TAAAATTACTAAATAATTTT
1 TAAAATTATTAAATAATTTT
32862352 AATTTTCAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
27 9 0.22
28 7 0.17
29 3 0.08
30 12 0.30
31 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (27 bp):
TAAAATTATTAAATAATTTTTGAAATA
Found at i:32862351 original size:30 final size:28
Alignment explanation
Indices: 32862274--32862351 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 28
32862264 CAAATGATTT
*
32862274 TAAAATTATTAAATTA-TTTTTTAAATA
1 TAAAATTATTAAATAATTTTTTTAAATA
*
32862301 TAAAAGTATTAAA-AGTATTTTTTTGAAATAA
1 TAAAATTATTAAATA--ATTTTTTT-AAAT-A
*
32862332 TAAAATTACTAAATAATTTT
1 TAAAATTATTAAATAATTTT
32862352 AATTTTCAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
27 12 0.29
28 1 0.02
29 6 0.15
30 9 0.22
31 12 0.29
32 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (28 bp):
TAAAATTATTAAATAATTTTTTTAAATA
Found at i:32863185 original size:30 final size:28
Alignment explanation
Indices: 32863145--32863224 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 28
32863135 ATTGAAAATT
*
32863145 AAAATTATTTAATAATTTTATTATTTCAA
1 AAAATAATTTAATAATTTTA-TATTTCAA
*
32863174 AATAATAATTTAAATAATTTTATATTTTAA
1 AA-AATAATTT-AATAATTTTATATTTCAA
32863204 AAAATAATTTTAATAATTTTA
1 AAAATAA-TTTAATAATTTTA
32863225 AAATCATTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
29 17 0.37
30 19 0.41
31 10 0.22
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (28 bp):
AAAATAATTTAATAATTTTATATTTCAA
Found at i:32863210 original size:20 final size:22
Alignment explanation
Indices: 32863185--32863227 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
32863175 ATAATAATTT
32863185 AAATAATTTT-AT-ATTTTAAA
1 AAATAATTTTAATAATTTTAAA
32863205 AAATAATTTTAATAATTTTAAA
1 AAATAATTTTAATAATTTTAAA
32863227 A
1 A
32863228 TCATTTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATAATTTTAATAATTTTAAA
Found at i:32863218 original size:29 final size:31
Alignment explanation
Indices: 32863152--32863224 Score: 114
Period size: 29 Copynumber: 2.4 Consensus size: 31
32863142 ATTAAAATTA
32863152 TTTAATAATTTTATTATTTCAAAATAATAAT
1 TTTAATAATTTTATTATTTCAAAATAATAAT
* *
32863183 TTAAATAATTTTA-TATTTTAAAA-AATAAT
1 TTTAATAATTTTATTATTTCAAAATAATAAT
32863212 TTTAATAATTTTA
1 TTTAATAATTTTA
32863225 AAATCATTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 18 0.46
30 9 0.23
31 12 0.31
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTAATAATTTTATTATTTCAAAATAATAAT
Found at i:32863228 original size:20 final size:20
Alignment explanation
Indices: 32863176--32863233 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
32863166 TATTTCAAAA
32863176 TAATAA-TTT-AAATAATTT
1 TAATAATTTTAAAATAATTT
32863194 T-AT-ATTTTAAAAAATAATTT
1 TAATAATTTT--AAAATAATTT
*
32863214 TAATAATTTTAAAATCATTT
1 TAATAATTTTAAAATAATTT
32863234 GCTAAGGTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 1 0.03
17 5 0.15
18 1 0.03
20 19 0.58
21 2 0.06
22 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAATTTTAAAATAATTT
Found at i:32869577 original size:42 final size:42
Alignment explanation
Indices: 32869507--32869655 Score: 156
Period size: 42 Copynumber: 3.5 Consensus size: 42
32869497 AGAATTTGTA
* * * * * *
32869507 TAAATGGATGACTCGTGACTCGAAATGAGCATGAAAATATGAT
1 TAAA-GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGAT
* * * *
32869550 CAAAGGAAAACTCATGTCTCGAGATGAGAATGAGATTTTGAT
1 TAAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGAT
*
32869592 TAAAGGAAGACTCATGTCTC-AGGATGAGAATGAGAATATAAT
1 TAAAGGAAGACTCATGTCTCGA-GATGAGAATGAGAATATGAT
* *
32869634 TAAAGGAAGACTTATGACTCGA
1 TAAAGGAAGACTCATGTCTCGA
32869656 TAGGGCATAA
Statistics
Matches: 87, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 82 0.94
43 4 0.05
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.25
Consensus pattern (42 bp):
TAAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGAT
Found at i:32892628 original size:14 final size:16
Alignment explanation
Indices: 32892588--32892628 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
32892578 TTATTTTTTT
32892588 AATTAAATTGGAATTCAA
1 AATTAAATT--AATTCAA
32892606 AATTAAATTAATT-AA
1 AATTAAATTAATTCAA
32892621 AA-TAAATT
1 AATTAAATT
32892629 TGGGTTGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.26
15 4 0.17
16 4 0.17
18 9 0.39
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (16 bp):
AATTAAATTAATTCAA
Found at i:32893799 original size:35 final size:35
Alignment explanation
Indices: 32893753--32893823 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
32893743 GAAGTTAATC
32893753 ACTATGTCACGATAGAGACTACTCTACATCGCAAA
1 ACTATGTCACGATAGAGACTACTCTACATCGCAAA
32893788 ACTATGTCACGATAGAGACTACTCTACATCGCAAA
1 ACTATGTCACGATAGAGACTACTCTACATCGCAAA
32893823 A
1 A
32893824 AAGGGACCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (35 bp):
ACTATGTCACGATAGAGACTACTCTACATCGCAAA
Found at i:32899334 original size:16 final size:16
Alignment explanation
Indices: 32899310--32899343 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
32899300 CTTTAGGGAT
*
32899310 TTGGTTTGGGTTTGGG
1 TTGGATTGGGTTTGGG
*
32899326 TTGGATTGGTTTTGGG
1 TTGGATTGGGTTTGGG
32899342 TT
1 TT
32899344 TAAGTTGGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.44, T:0.53
Consensus pattern (16 bp):
TTGGATTGGGTTTGGG
Found at i:32899350 original size:22 final size:21
Alignment explanation
Indices: 32899310--32899351 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
32899300 CTTTAGGGAT
**
32899310 TTGGTTTGGGTTTGGGTTGGA
1 TTGGTTTGGGTTTAAGTTGGA
32899331 TTGGTTTTGGGTTTAAGTTGG
1 TTGG-TTTGGGTTTAAGTTGG
32899352 CTTGCACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (21 bp):
TTGGTTTGGGTTTAAGTTGGA
Found at i:32906392 original size:2 final size:2
Alignment explanation
Indices: 32906385--32906430 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
32906375 AATTGCAGAA
*
32906385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32906427 AT AT
1 AT AT
32906431 TAAATCTTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32909192 original size:40 final size:40
Alignment explanation
Indices: 32909137--32909216 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
32909127 AAATTTGTGA
*
32909137 TTTTGAACTAAATTTGTGATTTCCTAAGCACAGATTTTAG
1 TTTTGAACTAAATTTGTGATTTCCCAAGCACAGATTTTAG
* *
32909177 TTTTGAACTGAATTTGTGATTTCCCATGCACAGATTTTAG
1 TTTTGAACTAAATTTGTGATTTCCCAAGCACAGATTTTAG
32909217 CTAATTGGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (40 bp):
TTTTGAACTAAATTTGTGATTTCCCAAGCACAGATTTTAG
Found at i:32913624 original size:18 final size:18
Alignment explanation
Indices: 32913601--32913649 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
32913591 AAAATGCAAG
32913601 AAATGATGTTAACACTTC
1 AAATGATGTTAACACTTC
*
32913619 AAATGATGTTCAA-ATTTC
1 AAATGATGTT-AACACTTC
*
32913637 GAATGATG-TAACA
1 AAATGATGTTAACA
32913650 TTGATGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 2 0.07
17 2 0.07
18 21 0.78
19 2 0.07
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (18 bp):
AAATGATGTTAACACTTC
Found at i:32914151 original size:41 final size:40
Alignment explanation
Indices: 32914106--32914231 Score: 103
Period size: 41 Copynumber: 3.3 Consensus size: 40
32914096 TCAATAGTTG
32914106 TTTATGTTTAGTTTTGGAATATTGAATTTATGTTCTACTTA
1 TTTATGTTT-GTTTTGGAATATTGAATTTATGTTCTACTTA
*** *
32914147 TTTATG--TG---T--AAT-TT-AATTTAT-CAATAGTTA
1 TTTATGTTTGTTTTGGAATATTGAATTTATGTTCTACTTA
32914177 TTTATGTTTGGTTCTTGG-ATATTGAATTTATGTTCTACTTA
1 TTTATGTTT-GTT-TTGGAATATTGAATTTATGTTCTACTTA
32914218 TTTATGTGTTGTTT
1 TTTATGT-TTGTTT
32914232 ATGTTTGGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 27
0.65 0.08 0.27
Matches are distributed among these distances:
30 11 0.17
31 7 0.11
32 3 0.05
33 4 0.06
35 1 0.02
37 1 0.02
38 3 0.05
39 3 0.05
40 8 0.12
41 21 0.33
42 2 0.03
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (40 bp):
TTTATGTTTGTTTTGGAATATTGAATTTATGTTCTACTTA
Found at i:32914199 original size:71 final size:71
Alignment explanation
Indices: 32914092--32914226 Score: 236
Period size: 71 Copynumber: 1.9 Consensus size: 71
32914082 CTAAACTAGT
*
32914092 TTTATCAATAGTTGTTTATGTTTAGTTTTGGAATATTGAATTTATGTTCTACTTATTTATGTGTA
1 TTTATCAATAGTTATTTATGTTTAGTTTTGGAATATTGAATTTATGTTCTACTTATTTATGTGTA
32914157 ATTTAA
66 ATTTAA
*
32914163 TTTATCAATAGTTATTTATGTTTGGTTCTTGG-ATATTGAATTTATGTTCTACTTATTTATGTGT
1 TTTATCAATAGTTATTTATGTTTAGTT-TTGGAATATTGAATTTATGTTCTACTTATTTATGTGT
32914227 TGTTTATGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
71 57 0.93
72 4 0.07
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (71 bp):
TTTATCAATAGTTATTTATGTTTAGTTTTGGAATATTGAATTTATGTTCTACTTATTTATGTGTA
ATTTAA
Found at i:32914236 original size:52 final size:52
Alignment explanation
Indices: 32914177--32914326 Score: 175
Period size: 49 Copynumber: 2.9 Consensus size: 52
32914167 TCAATAGTTA
32914177 TTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTATGTGTTG
1 TTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTATGTGTTG
* * * * ** *
32914229 TTTATGTTTGGTTCTTGGAT-CT--ACTTAT-TTGTAATCTAATCAAT-AGTTG
1 TTTATGTTTGGTTCTTGGATATTGAATTTATGTTCT-A-CTTATTTATGTGTTG
*
32914278 TTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTATTTATTTATGTG
1 TTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTATGTG
32914327 CTAATCTTAG
Statistics
Matches: 76, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
48 3 0.04
49 30 0.39
50 7 0.09
51 6 0.08
52 27 0.36
53 3 0.04
ACGTcount: A:0.19, C:0.07, G:0.18, T:0.56
Consensus pattern (52 bp):
TTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTATGTGTTG
Found at i:32914356 original size:74 final size:74
Alignment explanation
Indices: 32914267--32914447 Score: 269
Period size: 74 Copynumber: 2.4 Consensus size: 74
32914257 TTGTAATCTA
*
32914267 ATCAATAGTTGTTTATGTTTGGTTCTTGGATATTGAA-TT-TA-TGTTCTATTTATTTATGTGCT
1 ATCAATAGTTGTTTATGTTTGGTT-TTGGATATTGAATTTATATTGTTCTACTTATTTATGTG-T
32914329 AATCTTAGTTTT
64 -ATCTTAGTTTT
32914341 ATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATATTGTTCTACTTATTTATGTGTA
1 ATCAATAGTTGTTTATGTTTGG-TTTTGGATATTGAATTTATATTGTTCTACTTATTTATGTGTA
*
32914406 TTTTAGTTTT
65 TCTTAGTTTT
* *
32914416 ATCAATAGTTGTTTATATTTGATTTTGGATAT
1 ATCAATAGTTGTTTATGTTTGGTTTTGGATAT
32914448 AAAAATTTTC
Statistics
Matches: 99, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
74 44 0.44
75 34 0.34
76 3 0.03
77 18 0.18
ACGTcount: A:0.23, C:0.05, G:0.16, T:0.56
Consensus pattern (74 bp):
ATCAATAGTTGTTTATGTTTGGTTTTGGATATTGAATTTATATTGTTCTACTTATTTATGTGTAT
CTTAGTTTT
Found at i:32916244 original size:21 final size:21
Alignment explanation
Indices: 32916164--32916244 Score: 53
Period size: 21 Copynumber: 3.9 Consensus size: 21
32916154 TATTTAAATA
* *
32916164 TAAATATTTAATGATT-ATATT
1 TAAATAATTAAT-ATTAATTTT
* *
32916185 TAAATATTTAAAATATAA--TT
1 TAAATAATTAATAT-TAATTTT
* *
32916205 TATATAATCTAAT-TAAATTTT
1 TAAATAAT-TAATATTAATTTT
32916226 TAAATAATTAATATTAATT
1 TAAATAATTAATATTAATT
32916245 ACTTAGAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
19 2 0.04
20 15 0.32
21 29 0.62
22 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (21 bp):
TAAATAATTAATATTAATTTT
Found at i:32916518 original size:13 final size:13
Alignment explanation
Indices: 32916464--32916527 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
32916454 CTTTAACCAA
*
32916464 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
* *
32916477 ACTTCTCAAAAGA
1 ACTTTTCAAAAGC
**
32916490 ACTTTTCCATCA-C
1 ACTTTT-CAAAAGC
32916503 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
32916516 ACTTTTCAAAAG
1 ACTTTTCAAAAG
32916528 TAATGCTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 3 0.07
13 35 0.85
14 3 0.07
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:32919200 original size:22 final size:22
Alignment explanation
Indices: 32919145--32919200 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
32919135 CGGGTGATTT
* *
32919145 TTCTAGTGCTTCAAGTAGATCC
1 TTCTAGTGCTTTAAGTACATCC
* *
32919167 TTTTAGTGCTTTAGGTACATCC
1 TTCTAGTGCTTTAAGTACATCC
32919189 TTCTAGTGCTTT
1 TTCTAGTGCTTT
32919201 GCACAGCAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.45
Consensus pattern (22 bp):
TTCTAGTGCTTTAAGTACATCC
Found at i:32920140 original size:23 final size:26
Alignment explanation
Indices: 32920076--32920132 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
32920066 CAGTGAGGTG
**
32920076 GTAGAGAGGAGAAATTGGTGGTGGTT
1 GTAGAGAGGAGAGGTTGGTGGTGGTT
32920102 GTAGAGAGGAGAGGTTGGTGGTGGTT
1 GTAGAGAGGAGAGGTTGGTGGTGGTT
32920128 GTAGA
1 GTAGA
32920133 AGTCGGTTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.49, T:0.26
Consensus pattern (26 bp):
GTAGAGAGGAGAGGTTGGTGGTGGTT
Found at i:32920746 original size:37 final size:37
Alignment explanation
Indices: 32920705--32920784 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
32920695 ATATAATATG
*
32920705 TATTTAATAAAATTTATATACAAATTATTTACCACTC
1 TATTTAATAAAATTTATAAACAAATTATTTACCACTC
* * * *
32920742 TATTTATTATATTTTATAAACAAGTTATTTACCACTC
1 TATTTAATAAAATTTATAAACAAATTATTTACCACTC
32920779 TATTTA
1 TATTTA
32920785 TTATCATTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.47
Consensus pattern (37 bp):
TATTTAATAAAATTTATAAACAAATTATTTACCACTC
Found at i:32920785 original size:37 final size:37
Alignment explanation
Indices: 32920717--32920788 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
32920707 TTTAATAAAA
*
32920717 TTTATATACAAATTATTTACCACTCTATTTATTATAT
1 TTTATAAACAAATTATTTACCACTCTATTTATTATAT
*
32920754 TTTATAAACAAGTTATTTACCACTCTATTTATTAT
1 TTTATAAACAAATTATTTACCACTCTATTTATTAT
32920789 CATTGTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.50
Consensus pattern (37 bp):
TTTATAAACAAATTATTTACCACTCTATTTATTATAT
Found at i:32921509 original size:22 final size:20
Alignment explanation
Indices: 32921466--32921509 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
32921456 TAAAAAAATA
*
32921466 AAATAAAATAAACTTTGAGC
1 AAATAAAATAAACTTAGAGC
*
32921486 AAATACAAATAATCTTCAGAGC
1 AAATA-AAATAAACTT-AGAGC
32921508 AA
1 AA
32921510 TTTTCAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (20 bp):
AAATAAAATAAACTTAGAGC
Found at i:32923276 original size:15 final size:16
Alignment explanation
Indices: 32923246--32923283 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
32923236 AGACAGACAC
*
32923246 AAGAACAAGCAAACAAG
1 AAGAA-AAGCAAACAAA
32923263 AAGAAAAG-AAACAAA
1 AAGAAAAGCAAACAAA
32923278 AAGAAA
1 AAGAAA
32923284 TAATTGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 3 0.15
17 5 0.25
ACGTcount: A:0.74, C:0.11, G:0.16, T:0.00
Consensus pattern (16 bp):
AAGAAAAGCAAACAAA
Found at i:32925789 original size:24 final size:24
Alignment explanation
Indices: 32925753--32925888 Score: 146
Period size: 24 Copynumber: 5.7 Consensus size: 24
32925743 TATCTGAGTG
*
32925753 GCTGACGAGCATAAACGTATAGTA
1 GCTGACGAGCATAAACGTACAGTA
* * * *
32925777 GCTAACGAGCATAAATGTACCGTG
1 GCTGACGAGCATAAACGTACAGTA
* * *
32925801 GCTGACGAGCATAAACATACAATG
1 GCTGACGAGCATAAACGTACAGTA
*
32925825 GCTGACGAGCATAAACGTACATTA
1 GCTGACGAGCATAAACGTACAGTA
* * *
32925849 ACTGACGAGCATAAACGTACATTC
1 GCTGACGAGCATAAACGTACAGTA
* *
32925873 GCTGGCGAGCGTAAAC
1 GCTGACGAGCATAAAC
32925889 ACACTAAACT
Statistics
Matches: 94, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 94 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (24 bp):
GCTGACGAGCATAAACGTACAGTA
Found at i:32925882 original size:72 final size:72
Alignment explanation
Indices: 32925751--32925889 Score: 188
Period size: 72 Copynumber: 1.9 Consensus size: 72
32925741 TTTATCTGAG
* * * * *
32925751 TGGCTGACGAGCATAAACGTATAGTAGCTAACGAGCATAAATGTACCGTGGCTGACGAGCATAAA
1 TGGCTGACGAGCATAAACGTACAGTAACTAACGAGCATAAACGTACAGTCGCTGACGAGCATAAA
32925816 CATACAA
66 CATACAA
* * * * *
32925823 TGGCTGACGAGCATAAACGTACATTAACTGACGAGCATAAACGTACATTCGCTGGCGAGCGTAAA
1 TGGCTGACGAGCATAAACGTACAGTAACTAACGAGCATAAACGTACAGTCGCTGACGAGCATAAA
32925888 CA
66 CA
32925890 CACTAAACTT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (72 bp):
TGGCTGACGAGCATAAACGTACAGTAACTAACGAGCATAAACGTACAGTCGCTGACGAGCATAAA
CATACAA
Found at i:32927522 original size:40 final size:40
Alignment explanation
Indices: 32927477--32927624 Score: 190
Period size: 40 Copynumber: 3.7 Consensus size: 40
32927467 CAACATCGCG
*
32927477 GCTCATAACCTGCTAAGCCGTTGCTTGAGTTTTAACACCA
1 GCTCATAACCTGCTAAGCCGTAGCTTGAGTTTTAACACCA
* * * * *
32927517 GCTCATAGCCTGCTAAGTCGTAGCTTGAATTTCAACATC-
1 GCTCATAACCTGCTAAGCCGTAGCTTGAGTTTTAACACCA
* *
32927556 GACTCATAGCCTGCTAAGCCGTAGCTTGAGTTTTAACACTA
1 G-CTCATAACCTGCTAAGCCGTAGCTTGAGTTTTAACACCA
**
32927597 GCTCATAACCTGCTAAGCCAAAGCTTGA
1 GCTCATAACCTGCTAAGCCGTAGCTTGA
32927625 ATTTATTCAA
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
39 1 0.01
40 90 0.98
41 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (40 bp):
GCTCATAACCTGCTAAGCCGTAGCTTGAGTTTTAACACCA
Found at i:32927592 original size:80 final size:81
Alignment explanation
Indices: 32927457--32927628 Score: 256
Period size: 80 Copynumber: 2.1 Consensus size: 81
32927447 CCATGACTTG
* *
32927457 GCTTGAATTTCAACATCGCGGCTCATAACCTGCTAAGCCGTTGCTTGAGTTTTAACACCAGCTCA
1 GCTTGAATTTCAACATC-CGACTCATAACCTGCTAAGCCGTAGCTTGAGTTTTAACACCAGCTCA
* * **
32927522 TAGCCTGCTAAGTCGTA
65 TAACCTGCTAAGCCAAA
* *
32927539 GCTTGAATTTCAACAT-CGACTCATAGCCTGCTAAGCCGTAGCTTGAGTTTTAACACTAGCTCAT
1 GCTTGAATTTCAACATCCGACTCATAACCTGCTAAGCCGTAGCTTGAGTTTTAACACCAGCTCAT
32927603 AACCTGCTAAGCCAAA
66 AACCTGCTAAGCCAAA
32927619 GCTTGAATTT
1 GCTTGAATTT
32927629 ATTCAAACAT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 66 0.80
82 16 0.20
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (81 bp):
GCTTGAATTTCAACATCCGACTCATAACCTGCTAAGCCGTAGCTTGAGTTTTAACACCAGCTCAT
AACCTGCTAAGCCAAA
Found at i:32932763 original size:8 final size:8
Alignment explanation
Indices: 32932752--32932776 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
32932742 ATTTTAGCCC
32932752 TTTAAAAT
1 TTTAAAAT
32932760 TTTAAAAT
1 TTTAAAAT
32932768 TTTAAAAT
1 TTTAAAAT
32932776 T
1 T
32932777 AGTAAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAAAT
Found at i:32933296 original size:17 final size:20
Alignment explanation
Indices: 32933260--32933297 Score: 55
Period size: 17 Copynumber: 2.0 Consensus size: 20
32933250 TGGTAATTTT
32933260 TTAATTAAATTGAGACTCAA
1 TTAATTAAATTGAGACTCAA
32933280 TTAA-TAAA-TGA-ACTCAA
1 TTAATTAAATTGAGACTCAA
32933297 T
1 T
32933298 AAAACATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 4 0.22
20 4 0.22
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (20 bp):
TTAATTAAATTGAGACTCAA
Found at i:32935529 original size:86 final size:84
Alignment explanation
Indices: 32935471--32935639 Score: 239
Period size: 86 Copynumber: 2.0 Consensus size: 84
32935461 ATGAAAATGG
*
32935471 TTTATCAAATAAAAATAAAATAATAATTTTTTGAAAGTAAAACAAAATATTTTAATTTTCTTGAA
1 TTTATCAAATAAAAATAAAATAATAATTTTTTGAAAGTAAAACAAAATATTTTAATTTTATTG--
* *
32935536 AATGCTTTTATACATAACATA
64 AATGCTATTATACATAAAATA
* *
32935557 TTTATCAAATAAAAATAAAATAATAATTTTTTGAAAGTAAAACAAAATATTTTAAAATTTCTTGA
1 TTTATCAAATAAAAATAAAATAATAATTTTTTGAAAGTAAAACAAAATATTTT-AATTTTATTG-
*
32935622 AAATGCTTTTATACATAA
64 -AATGCTATTATACATAA
32935640 TACACGAAAT
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 53 0.65
87 28 0.35
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (84 bp):
TTTATCAAATAAAAATAAAATAATAATTTTTTGAAAGTAAAACAAAATATTTTAATTTTATTGAA
TGCTATTATACATAAAATA
Found at i:32936283 original size:8 final size:9
Alignment explanation
Indices: 32936252--32936280 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
32936242 CTTTTACTAA
32936252 TTTAAAATT
1 TTTAAAATT
32936261 TTTAAAATT
1 TTTAAAATT
32936270 TTTAAAATT
1 TTTAAAATT
32936279 TT
1 TT
32936281 AAAGGGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAAAATT
Found at i:32936413 original size:15 final size:17
Alignment explanation
Indices: 32936392--32936432 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
32936382 TAATCATTTA
32936392 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
32936408 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
32936424 AAAATTATA
1 AAAATTATA
32936433 TTTTTGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:32939366 original size:15 final size:16
Alignment explanation
Indices: 32939336--32939367 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
32939326 GTTTTAAATA
32939336 TTAATGGGTATTGGGT
1 TTAATGGGTATTGGGT
32939352 TTAATGGGT-TTGGGT
1 TTAATGGGTATTGGGT
32939367 T
1 T
32939368 GAACAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.47
Consensus pattern (16 bp):
TTAATGGGTATTGGGT
Found at i:32939401 original size:47 final size:47
Alignment explanation
Indices: 32939329--32939452 Score: 167
Period size: 47 Copynumber: 2.6 Consensus size: 47
32939319 AAATTGTGTT
* *
32939329 TTAAATATTAATGGGTATTGGGTTTAATGGGTTTGGGTTGAACAATA
1 TTAAATTTTAATGGGTATTGAGTTTAATGGGTTTGGGTTGAACAATA
* * * *
32939376 TTAAATTTTAATCGGTATTGTGTTTAATGGGTTTGGGTTTAGCAATA
1 TTAAATTTTAATGGGTATTGAGTTTAATGGGTTTGGGTTGAACAATA
* *
32939423 TTAAGTTTTAATGGGCATTTGAGTTTAATG
1 TTAAATTTTAATGGGTA-TTGAGTTTAATG
32939453 TTTAAATTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 56 0.84
48 11 0.16
ACGTcount: A:0.27, C:0.03, G:0.25, T:0.44
Consensus pattern (47 bp):
TTAAATTTTAATGGGTATTGAGTTTAATGGGTTTGGGTTGAACAATA
Found at i:32941515 original size:27 final size:27
Alignment explanation
Indices: 32941477--32941531 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
32941467 TTAGTGGTAA
32941477 GGTGTTAGTGTACCCTAGGTCTTGTGT
1 GGTGTTAGTGTACCCTAGGTCTTGTGT
32941504 GGTGTTAGTGTACCCTAGGTCTTGTGT
1 GGTGTTAGTGTACCCTAGGTCTTGTGT
32941531 G
1 G
32941532 CAAATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.11, C:0.15, G:0.35, T:0.40
Consensus pattern (27 bp):
GGTGTTAGTGTACCCTAGGTCTTGTGT
Found at i:32941790 original size:24 final size:22
Alignment explanation
Indices: 32941732--32941782 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
32941722 TTTGTGTTCC
32941732 CTTCCTTTTTTCTATATTTTCT
1 CTTCCTTTTTTCTATATTTTCT
32941754 CTTCCTTTTTTCTATATTTTCT
1 CTTCCTTTTTTCTATATTTTCT
32941776 -TT-CTTTT
1 CTTCCTTTT
32941783 ATTTTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 5 0.17
21 2 0.07
22 22 0.76
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.71
Consensus pattern (22 bp):
CTTCCTTTTTTCTATATTTTCT
Found at i:32943988 original size:23 final size:23
Alignment explanation
Indices: 32943958--32944128 Score: 172
Period size: 23 Copynumber: 7.5 Consensus size: 23
32943948 ACGCTAGCGC
*
32943958 GCTTACTGTTTCGCATTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
32943981 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
32944004 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
32944027 GCTTACTGTTTCGCA-TCTTGTGT
1 GCTTACTGTTTCGCACT-TTGTGT
* * *
32944050 GCCTACTGATTT-GCGCTATGTG-
1 GCTTACTG-TTTCGCACTTTGTGT
* * * *
32944072 CCCTACTGATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* * *
32944094 GCCTACTGGATT-GCACTGTGTGT
1 GCTTACT-GTTTCGCACTTTGTGT
*
32944117 GCTTACTATTTC
1 GCTTACTGTTTC
32944129 CCCAGCACTT
Statistics
Matches: 130, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.08
22 16 0.12
23 100 0.77
24 4 0.03
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.44
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTTGTGT
Found at i:32944084 original size:21 final size:20
Alignment explanation
Indices: 32944047--32944115 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
32944037 TCGCATCTTG
*
32944047 TGTGCCTACTGATTTGCGCTA
1 TGTGCCTACTGA-TTGCACTA
*
32944068 TGTGCCCTACTGATTGCACTGTG
1 TGTG-CCTACTGATTGCAC--TA
*
32944091 TGTGCCTACTGGATTGCACTG
1 TGTGCCTACT-GATTGCACTA
32944112 TGTG
1 TGTG
32944116 TGCTTACTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 15 0.36
22 14 0.33
23 13 0.31
ACGTcount: A:0.13, C:0.23, G:0.28, T:0.36
Consensus pattern (20 bp):
TGTGCCTACTGATTGCACTA
Found at i:32944942 original size:49 final size:49
Alignment explanation
Indices: 32944838--32944942 Score: 113
Period size: 49 Copynumber: 2.1 Consensus size: 49
32944828 CCATTTGGGG
* * * * *
32944838 CACATGATCGTGTGAAATCATGCAGGCCATATGGGTAGATCGTGTAGGG
1 CACACGATCGTGTGAAATCATACAGACCATATGGGTAGACCGTGTAGGC
* * * *
32944887 CTCACGATCGTGTGAAATCATACAGATCGTGTGGGTAGACCGTGT-GGAC
1 CACACGATCGTGTGAAATCATACAGACCATATGGGTAGACCGTGTAGG-C
32944936 CACACGA
1 CACACGA
32944943 GCTAGCTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
48 2 0.04
49 43 0.96
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (49 bp):
CACACGATCGTGTGAAATCATACAGACCATATGGGTAGACCGTGTAGGC
Found at i:32944993 original size:26 final size:26
Alignment explanation
Indices: 32944964--32945017 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
32944954 GGGTCGTGTA
* *
32944964 GGCCACACGACCATGTGGGCCTTGTG
1 GGCCACACAACAATGTGGGCCTTGTG
*
32944990 GGCCACACAACAATGTGGGCCTTTTG
1 GGCCACACAACAATGTGGGCCTTGTG
32945016 GG
1 GG
32945018 TCAATTTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.28, G:0.33, T:0.20
Consensus pattern (26 bp):
GGCCACACAACAATGTGGGCCTTGTG
Found at i:32945147 original size:13 final size:13
Alignment explanation
Indices: 32945129--32945182 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
32945119 ACTTTAGCAT
32945129 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
32945142 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
* * *
32945155 TG-TGGTGGAGAAG
1 TGCT-TTTGAAAAG
32945168 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
32945181 TG
1 TG
32945183 TGGTTTAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
12 1 0.03
13 29 0.94
14 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:32945491 original size:14 final size:14
Alignment explanation
Indices: 32945454--32945495 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
32945444 CTATATTTTA
32945454 AATATTTAAATA-T
1 AATATTTAAATATT
32945467 AATCA-TTAAATATT
1 AAT-ATTTAAATATT
*
32945481 TATATTTAAATATT
1 AATATTTAAATATT
32945495 A
1 A
32945496 GCACAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:32947395 original size:72 final size:72
Alignment explanation
Indices: 32947187--32947370 Score: 289
Period size: 72 Copynumber: 2.6 Consensus size: 72
32947177 AACAAATTTT
* * * *
32947187 ATATCC-AAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTATACATAAATAAGTAGAACAT
32947251 AAATTCA
66 AAATTCA
*
32947258 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTTGATTATACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTATACATAAATAAGTAGAACAT
32947323 AAATTCA
66 AAATTCA
* * *
32947330 ATATCTAAAAACCAAACATAAATAATTATTGATAAAACTAG
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
32947371 TTTAGCATTG
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
71 6 0.06
72 97 0.94
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (72 bp):
ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTATACATAAATAAGTAGAACAT
AAATTCA
Found at i:32948995 original size:4 final size:4
Alignment explanation
Indices: 32948986--32949027 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
32948976 AATTAGATGA
32948986 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
32949028 TTGACAGTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:32955500 original size:20 final size:20
Alignment explanation
Indices: 32955450--32955500 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
32955440 AGCATGTTTT
32955450 AGTATCGATACCATAGTCAA
1 AGTATCGATACCATAGTCAA
* *
32955470 AGTACCGATACC-TAGTTGAA
1 AGTATCGATACCATAG-TCAA
*
32955490 AGTATCAATAC
1 AGTATCGATAC
32955501 TTCAACCACG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (20 bp):
AGTATCGATACCATAGTCAA
Found at i:32957611 original size:10 final size:10
Alignment explanation
Indices: 32957596--32957624 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
32957586 ATATTTTAAC
32957596 ATAAAAATAT
1 ATAAAAATAT
32957606 ATAAAAATAT
1 ATAAAAATAT
32957616 -TAAAAATAT
1 ATAAAAATAT
32957625 TTTTTATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:32962994 original size:42 final size:41
Alignment explanation
Indices: 32962914--32963017 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 41
32962904 TTCAATCTAC
* * *
32962914 CCCTCTAGATTA-GGGTAAAAGATTGGGTCGCTTTAATTTG
1 CCCTCTAGATTAGGGGTAAAAGACTGGATCGCTTCAATTTG
* *
32962954 CCCATCTGGATTAGGGGTAAAAGACTGGATGGCTTCAATTTG
1 CCC-TCTAGATTAGGGGTAAAAGACTGGATCGCTTCAATTTG
*
32962996 TCCCTTTAGATTAGGGGTAAAA
1 -CCCTCTAGATTAGGGGTAAAA
32963018 AATTGCATGG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 3 0.06
41 8 0.15
42 40 0.74
43 3 0.06
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (41 bp):
CCCTCTAGATTAGGGGTAAAAGACTGGATCGCTTCAATTTG
Found at i:32963054 original size:45 final size:43
Alignment explanation
Indices: 32962903--32963157 Score: 193
Period size: 45 Copynumber: 5.8 Consensus size: 43
32962893 TTGTGTATGA
* * * *
32962903 CTTCAATCTACCCCTCTAGATTA-GGGTAAAAGATTG--GGTCG
1 CTTCAATCT-TCCCTCTTGACTAGGGGTAAAAGATTGATGGTAG
* * * *
32962944 CTTTAAT-TTGCCCATCTGGATTAGGGGTAAAAGACTGGAT-G--G
1 CTTCAATCTT-CCC-TCTTGACTAGGGGTAAAAGA-TTGATGGTAG
* * * *
32962986 CTTCAATTTGTCCCT-TTAGATTAGGGGTAAAAAATTGCATGGTGG
1 CTTCAATCT-TCCCTCTT-GACTAGGGGTAAAAGATTG-ATGGTAG
* * *
32963031 CTTCAATCTACCTCTCTTAATTAGGGGTAAAAGATTAGATGGTAG
1 CTTCAATCTTCC-CTCTTGACTAGGGGTAAAAGATT-GATGGTAG
**
32963076 CTTCAATCTTCCCCTCTTGACTAAAGGTAAAAGATTGGATGGTAG
1 CTTCAATCTT-CCCTCTTGACTAGGGGTAAAAGATT-GATGGTAG
32963121 CTTCAATCTGTCCCTCTTGACTAGGGGTAAAAGATTG
1 CTTCAATCT-TCCCTCTTGACTAGGGGTAAAAGATTG
32963158 GATGAGGTGA
Statistics
Matches: 175, Mismatches: 21, Indels: 33
0.76 0.09 0.14
Matches are distributed among these distances:
40 4 0.02
41 17 0.10
42 35 0.20
43 7 0.04
44 5 0.03
45 101 0.58
46 6 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (43 bp):
CTTCAATCTTCCCTCTTGACTAGGGGTAAAAGATTGATGGTAG
Found at i:32963158 original size:45 final size:44
Alignment explanation
Indices: 32962965--32963161 Score: 213
Period size: 45 Copynumber: 4.5 Consensus size: 44
32962955 CCATCTGGAT
* * *
32962965 TAGGGGTAAAAGACTGGAT-G--GCTTCAATTTGTCCCT-TTAGAT
1 TAGGGGTAAAAGATTGGATGGTAGCTTCAATCT-TCCCTCTT-GAC
* * * * * *
32963007 TAGGGGTAAAAAATTGCATGGTGGCTTCAATCTACCTCTCTTAAT
1 TAGGGGTAAAAGATTGGATGGTAGCTTCAATCTTCC-CTCTTGAC
*
32963052 TAGGGGTAAAAGATTAGATGGTAGCTTCAATCTTCCCCTCTTGAC
1 TAGGGGTAAAAGATTGGATGGTAGCTTCAATCTT-CCCTCTTGAC
**
32963097 TAAAGGTAAAAGATTGGATGGTAGCTTCAATCTGTCCCTCTTGAC
1 TAGGGGTAAAAGATTGGATGGTAGCTTCAATCT-TCCCTCTTGAC
32963142 TAGGGGTAAAAGATTGGATG
1 TAGGGGTAAAAGATTGGATG
32963162 AGGTGATGTA
Statistics
Matches: 130, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
42 16 0.12
43 1 0.01
44 2 0.02
45 106 0.82
46 5 0.04
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (44 bp):
TAGGGGTAAAAGATTGGATGGTAGCTTCAATCTTCCCTCTTGAC
Found at i:32963330 original size:49 final size:49
Alignment explanation
Indices: 32963273--32963415 Score: 128
Period size: 49 Copynumber: 2.9 Consensus size: 49
32963263 ATCGTTGCGA
* * *
32963273 CTTCAATCTATCTCTCCTA-ATCTTCACGGTATGAGATTCGCTGTTGTGG
1 CTTCAATCTATCCCTCC-ACATCTTCACGGTATAAGATTCGCCGTTGTGG
* * * * * *
32963322 CTTCAATCTTTCCCTCCACATTTTTAGGGTTTAAGGTTCGCCGTTGTGG
1 CTTCAATCTATCCCTCCACATCTTCACGGTATAAGATTCGCCGTTGTGG
* * * * *
32963371 CTTCAATCTTTCCCTTCACATC-CCTAGGGTATAAGGTTCGCCGTT
1 CTTCAATCTATCCCTCCACATCTTC-ACGGTATAAGATTCGCCGTT
32963416 TCATATCTCT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.01
49 77 0.99
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.38
Consensus pattern (49 bp):
CTTCAATCTATCCCTCCACATCTTCACGGTATAAGATTCGCCGTTGTGG
Found at i:32963490 original size:49 final size:49
Alignment explanation
Indices: 32963417--32963905 Score: 453
Period size: 49 Copynumber: 10.0 Consensus size: 49
32963407 TTCGCCGTTT
* * **
32963417 CATATCTCTAGGGTATAAGATTTGTTGTTGCGGCTTCAGTCTTTCCCTC
1 CATATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTC
* * * *
32963466 CATATCTCTAGGGTACAAGGTTTGTCGTTGCAGCTTCAACCTTTCCCTC
1 CATATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTC
* ** * * *
32963515 CATATCTCTAGGGTATGAGATTCACCATTGCGGCTTCAATCTCTCCCTC
1 CATATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTC
* * * *
32963564 CATATCTCTAAGGTACAAGGTTCGTCGTTGCGGCTTTAACCTTTCCCTC
1 CATATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTC
* * * * *
32963613 CATATCTCTAGGGTATGAGATTCGGT-GTTGCGGCTTTAACCTCTCCTTT
1 CATATCTCTAGGGTATAAGATTC-GTCGTTGCGGCTTCAACCTTTCCCTC
* * * *
32963662 AATATCTCTAAGGTATAAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTC
1 CATATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTC
* ** * *
32963711 CATATCTTTAGGGTATGAA-ATTTATCGTTGCGGCTTCAATCTCTCCCTC
1 CATATCTCTAGGGTAT-AAGATTCGTCGTTGCGGCTTCAACCTTTCCCTC
* * * * ** * *
32963760 TAGATCTCTATGGTATAAGGTTCACCGTTGCGACTTCAACCTGTCCCTC
1 CATATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTC
* ** * * * * *
32963809 CATATCTCTAGGGTATGAGATTCGTCGTTATGGCTTTAATCTCTCACTT
1 CATATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTC
* * * * *
32963858 CACATCTTTAGGGTATCAA-ATTTGTCGTTACGGCTTCAATCTTTCCCT
1 CATATCTCTAGGGTAT-AAGATTCGTCGTTGCGGCTTCAACCTTTCCCT
32963906 TTACATCTTT
Statistics
Matches: 351, Mismatches: 84, Indels: 10
0.79 0.19 0.02
Matches are distributed among these distances:
48 4 0.01
49 342 0.97
50 5 0.01
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (49 bp):
CATATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTC
Found at i:32963528 original size:128 final size:128
Alignment explanation
Indices: 32963300--32963530 Score: 300
Period size: 128 Copynumber: 1.8 Consensus size: 128
32963290 TAATCTTCAC
* * * * **
32963300 GGTATGAGATTCGCTGTTGTGGCTTCAATCTTTCCCTCCACATTTTTAGGGTTTAAGGTTCGCCG
1 GGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTCCACATCTCTAGGGTACAAGGTTCGCCG
** * *
32963365 TTGTGGCTTCAATCTTTCCCTTCACATCCCTAGGGTATAAGGTTCGCCGTTTCATATCTCTAG
66 TTGCAGCTTCAACCTTTCCCTCCACATCCCTAGGGTATAAGGTTCGCCGTTTCATATCTCTAG
* * * * * *
32963428 GGTATAAGATTTGTTGTTGCGGCTTCAGTCTTTCCCTCCATATCTCTAGGGTACAAGGTTTGTCG
1 GGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTCCACATCTCTAGGGTACAAGGTTCGCCG
* *
32963493 TTGCAGCTTCAACCTTTCCCTCCATATCTCTAGGGTAT
66 TTGCAGCTTCAACCTTTCCCTCCACATCCCTAGGGTAT
32963531 GAGATTCACC
Statistics
Matches: 85, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
128 85 1.00
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (128 bp):
GGTATAAGATTCGCTGTTGCGGCTTCAATCTTTCCCTCCACATCTCTAGGGTACAAGGTTCGCCG
TTGCAGCTTCAACCTTTCCCTCCACATCCCTAGGGTATAAGGTTCGCCGTTTCATATCTCTAG
Found at i:32963591 original size:98 final size:98
Alignment explanation
Indices: 32963417--32963853 Score: 545
Period size: 98 Copynumber: 4.5 Consensus size: 98
32963407 TTCGCCGTTT
* ** * * * *
32963417 CATATCTCTAGGGTATAAGATTTGTTGTTGCGGCTTCAGTCTTTCCCTCCATATCTCTAGGGTAC
1 CATATCTCTAGGGTATGAGATTCATCGTTGCGGCTTCAATCTCTCCCTCCATATCTCTAAGGTAC
*
32963482 AAGGTTTGTCGTTGCAGCTTCAACCTTTCCCTC
66 AAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTC
* *
32963515 CATATCTCTAGGGTATGAGATTCACCATTGCGGCTTCAATCTCTCCCTCCATATCTCTAAGGTAC
1 CATATCTCTAGGGTATGAGATTCATCGTTGCGGCTTCAATCTCTCCCTCCATATCTCTAAGGTAC
* *
32963580 AAGGTTCGTCGTTGCGGCTTTAACCTTTCCCTC
66 AAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTC
* * * * **
32963613 CATATCTCTAGGGTATGAGATTCGGT-GTTGCGGCTTTAACCTCTCCTTTAATATCTCTAAGGTA
1 CATATCTCTAGGGTATGAGATTC-ATCGTTGCGGCTTCAATCTCTCCCTCCATATCTCTAAGGTA
*
32963677 TAAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTC
65 CAAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTC
* * * * * * *
32963711 CATATCTTTAGGGTATGAAATTTATCGTTGCGGCTTCAATCTCTCCCTCTAGATCTCTATGGTAT
1 CATATCTCTAGGGTATGAGATTCATCGTTGCGGCTTCAATCTCTCCCTCCATATCTCTAAGGTAC
** *
32963776 AAGGTTCACCGTTGC-GACTTCAACCTGTCCCTC
66 AAGGTTCGTCGTTGCAG-CTTCAACCTTTCCCTC
* ** *
32963809 CATATCTCTAGGGTATGAGATTCGTCGTTATGGCTTTAATCTCTC
1 CATATCTCTAGGGTATGAGATTCATCGTTGCGGCTTCAATCTCTC
32963854 ACTTCACATC
Statistics
Matches: 292, Mismatches: 44, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
97 2 0.01
98 290 0.99
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (98 bp):
CATATCTCTAGGGTATGAGATTCATCGTTGCGGCTTCAATCTCTCCCTCCATATCTCTAAGGTAC
AAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTC
Found at i:32963873 original size:98 final size:97
Alignment explanation
Indices: 32963417--32963905 Score: 525
Period size: 98 Copynumber: 5.0 Consensus size: 97
32963407 TTCGCCGTTT
* * * * * * * *
32963417 CATATCTCTAGGGTATAAGATTTGTTGTTGCGGCTTCAGTCTTTCCCTCCATATCTCTAGGGTAC
1 CATATCTCTAGGGTATGAGATTCGTCGTTGCGGCTTCAATCTCT-CCTTCATATCTCTAAGGTAT
*
32963482 AAGGTTTGTCGTTGCAGCTTCAACCTTTCCCTC
65 AAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTC
** * * *
32963515 CATATCTCTAGGGTATGAGATTCACCATTGCGGCTTCAATCTCTCCCTCCATATCTCTAAGGTAC
1 CATATCTCTAGGGTATGAGATTCGTCGTTGCGGCTTCAATCTCT-CCTTCATATCTCTAAGGTAT
* *
32963580 AAGGTTCGTCGTTGCGGCTTTAACCTTTCCCTC
65 AAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTC
* * *
32963613 CATATCTCTAGGGTATGAGATTCGGT-GTTGCGGCTTTAACCTCTCCTTTAATATCTCTAAGGTA
1 CATATCTCTAGGGTATGAGATTC-GTCGTTGCGGCTTCAATCTCTCC-TTCATATCTCTAAGGTA
32963677 TAAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTC
64 TAAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTC
* * ** * * *
32963711 CATATCTTTAGGGTATGAAATTTATCGTTGCGGCTTCAATCTCTCCCTCTAGATCTCTATGGTAT
1 CATATCTCTAGGGTATGAGATTCGTCGTTGCGGCTTCAATCTCTCCTTC-ATATCTCTAAGGTAT
** *
32963776 AAGGTTCACCGTTGC-GACTTCAACCTGTCCCTC
65 AAGGTTCGTCGTTGCAG-CTTCAACCTTTCCCTC
** * * * *
32963809 CATATCTCTAGGGTATGAGATTCGTCGTTATGGCTTTAATCTCTCACTTCACATCTTTAGGGTAT
1 CATATCTCTAGGGTATGAGATTCGTCGTTGCGGCTTCAATCTCTC-CTTCATATCTCTAAGGTAT
* * * * *
32963874 CAA-ATTTGTCGTTACGGCTTCAATCTTTCCCT
65 -AAGGTTCGTCGTTGCAGCTTCAACCTTTCCCT
32963906 TTACATCTTT
Statistics
Matches: 330, Mismatches: 53, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
97 5 0.02
98 319 0.97
99 6 0.02
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (97 bp):
CATATCTCTAGGGTATGAGATTCGTCGTTGCGGCTTCAATCTCTCCTTCATATCTCTAAGGTATA
AGGTTCGTCGTTGCAGCTTCAACCTTTCCCTC
Found at i:32963917 original size:196 final size:195
Alignment explanation
Indices: 32963417--32963905 Score: 615
Period size: 196 Copynumber: 2.5 Consensus size: 195
32963407 TTCGCCGTTT
* * * * * *
32963417 CATATCTCTAGGGTATAAGATTTGTTGTTGCGGCTTCAGTCTTTCCCTCCATATCTCTAGGGTA-
1 CATATCTCTAGGGTATGAGATTCG-TGTTGCGGCTTTAATCTCT-CCTTCATATCTCTAGGGTAT
* *
32963481 CAAGGTTTGTCGTTGCAGCTTCAACCTTTCCCTCCATATCTCTAGGGTATGAGATTCACCATTGC
64 CAAGGTTTGTCGTTGCAGCTTCAACCTTTCCCTCCATATCTTTAGGGTATGAAATTCACCATTGC
* ** * * *
32963546 GGCTTCAATCTCTCCCTCCATATCTCTAAGGTACAAGGTTCGTCGTTGCGGCTTTAACCTTTCCC
129 GGCTTCAATCTCTCCCTCCAGATCTCTAAGGTACAAGGTTCACCGTTGCGACTTCAACCTGTCCC
32963611 TC
194 TC
* * *
32963613 CATATCTCTAGGGTATGAGATTCGGTGTTGCGGCTTTAACCTCTCCTTTAATATCTCTAAGGTAT
1 CATATCTCTAGGGTATGAGATTC-GTGTTGCGGCTTTAATCTCTCC-TTCATATCTCTAGGGTAT
* * * *
32963678 -AAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTCCATATCTTTAGGGTATGAAATTTATCGTTGC
64 CAAGGTTTGTCGTTGCAGCTTCAACCTTTCCCTCCATATCTTTAGGGTATGAAATTCACCATTGC
* * *
32963742 GGCTTCAATCTCTCCCTCTAGATCTCTATGGTATAAGGTTCACCGTTGCGACTTCAACCTGTCCC
129 GGCTTCAATCTCTCCCTCCAGATCTCTAAGGTACAAGGTTCACCGTTGCGACTTCAACCTGTCCC
32963807 TC
194 TC
** * *
32963809 CATATCTCTAGGGTATGAGATTCGTCGTTATGGCTTTAATCTCTCACTTCACATCTTTAGGGTAT
1 CATATCTCTAGGGTATGAGATTCGT-GTTGCGGCTTTAATCTCTC-CTTCATATCTCTAGGGTAT
* * * *
32963874 CAA-ATTTGTCGTTACGGCTTCAATCTTTCCCT
64 CAAGGTTTGTCGTTGCAGCTTCAACCTTTCCCT
32963906 TTACATCTTT
Statistics
Matches: 251, Mismatches: 36, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
195 4 0.02
196 243 0.97
197 4 0.02
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (195 bp):
CATATCTCTAGGGTATGAGATTCGTGTTGCGGCTTTAATCTCTCCTTCATATCTCTAGGGTATCA
AGGTTTGTCGTTGCAGCTTCAACCTTTCCCTCCATATCTTTAGGGTATGAAATTCACCATTGCGG
CTTCAATCTCTCCCTCCAGATCTCTAAGGTACAAGGTTCACCGTTGCGACTTCAACCTGTCCCTC
Found at i:32963923 original size:147 final size:148
Alignment explanation
Indices: 32963417--32963905 Score: 520
Period size: 147 Copynumber: 3.3 Consensus size: 148
32963407 TTCGCCGTTT
* *
32963417 CATATCTCTAGGGTAT-AAGATTTGTTGTTGCGGCTTCAGTCTTTCCCTCCATATCTCTAGGGTA
1 CATATCTCTAGGGTATCAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTCCATATCTCTAGGGTA
* * * * ** *
32963481 CAAGGTTTGTCGTTGC-AGCTTCAACCTTTCCCTCCATATCTCTAGGGTATGAGATTCACCATTG
66 TAAGGTTCGCCGTTGCGA-CTTCAACCTCTCCCTCCATATCTCTAGGGTATGAGATTCGTCGTTG
32963545 CGGCTTCAATCTCTCCCTC
130 CGGCTTCAATCTCTCCCTC
* * * * *
32963564 CATATCTCTAAGGTA-CAAGGTTCGTCGTTGCGGCTTTAACCTTTCCCTCCATATCTCTAGGGTA
1 CATATCTCTAGGGTATCAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTCCATATCTCTAGGGTA
* * ** * * * ** * * *
32963628 TGAGATTCGGTGTTGCGGCTTTAACCTCTCCTTTAATATCTCTAAGGTATAAGGTTCGTCGTTGC
66 TAAGGTTCGCCGTTGCGACTTCAACCTCTCCCTCCATATCTCTAGGGTATGAGATTCGTCGTTGC
* * *
32963693 AGCTTCAACCTTTCCCTC
131 GGCTTCAATCTCTCCCTC
* * * * * * *
32963711 CATATCTTTAGGGTATGAA-ATTTATCGTTGCGGCTTCAATCTCTCCCTCTAGATCTCTATGGTA
1 CATATCTCTAGGGTATCAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTCCATATCTCTAGGGTA
* * **
32963775 TAAGGTTCACCGTTGCGACTTCAACCTGTCCCTCCATATCTCTAGGGTATGAGATTCGTCGTTAT
66 TAAGGTTCGCCGTTGCGACTTCAACCTCTCCCTCCATATCTCTAGGGTATGAGATTCGTCGTTGC
* * *
32963840 GGCTTTAATCTCTCACTT
131 GGCTTCAATCTCTCCCTC
* * *
32963858 CACATCTTTAGGGTATCAA-ATTTGTCGTTACGGCTTCAATCTTTCCCT
1 CATATCTCTAGGGTATCAAGATTTGTCGTTGCGGCTTCAATCTTTCCCT
32963906 TTACATCTTT
Statistics
Matches: 272, Mismatches: 67, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
147 270 0.99
148 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (148 bp):
CATATCTCTAGGGTATCAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTCCATATCTCTAGGGTA
TAAGGTTCGCCGTTGCGACTTCAACCTCTCCCTCCATATCTCTAGGGTATGAGATTCGTCGTTGC
GGCTTCAATCTCTCCCTC
Found at i:32969311 original size:15 final size:16
Alignment explanation
Indices: 32969291--32969334 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
32969281 TTTAAAATTG
32969291 TTTTTCTTTTTCATT-
1 TTTTTCTTTTTCATTA
*
32969306 TTTTTCCTTTTT-TTTA
1 TTTTT-CTTTTTCATTA
32969322 TTTTTCTTTTTCA
1 TTTTTCTTTTTCA
32969335 AGTGACTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTCTTTTTCATTA
Found at i:32969930 original size:17 final size:17
Alignment explanation
Indices: 32969881--32969938 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
32969871 ATATATATGG
**
32969881 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* ** *
32969898 AGATGCAGCGAGAATAA
1 AAATGCAATGACAATAA
32969915 AAATGCAATGACAATAA
1 AAATGCAATGACAATAA
*
32969932 TAATGCA
1 AAATGCA
32969939 GGGACAATTA
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:32976553 original size:27 final size:28
Alignment explanation
Indices: 32976510--32976564 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
32976500 GCACATATAT
* * *
32976510 CAATAATATAATGACAAAT-ATACAATA
1 CAATAATAAAATAACAAATCAAACAATA
32976537 CAATAATAAAATAACAAATCAAACAATA
1 CAATAATAAAATAACAAATCAAACAATA
32976565 TTAATTTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.22
Consensus pattern (28 bp):
CAATAATAAAATAACAAATCAAACAATA
Found at i:32979016 original size:59 final size:59
Alignment explanation
Indices: 32978924--32979042 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 59
32978914 ACAACTGTTG
* *
32978924 AATCATTCTCTCGTCGAATTCATTTTTCAAATCCTTAATGGATATTCCCTTCCATGATC
1 AATCACTCTCTCGTCGAATTCATTCTTCAAATCCTTAATGGATATTCCCTTCCATGATC
*
32978983 AATCACTCTCTCGTCGAATTCATTCTTCAAATCCTTAATGGATATTCCCTTTCATGATC
1 AATCACTCTCTCGTCGAATTCATTCTTCAAATCCTTAATGGATATTCCCTTCCATGATC
32979042 A
1 A
32979043 TAATGTCAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.39
Consensus pattern (59 bp):
AATCACTCTCTCGTCGAATTCATTCTTCAAATCCTTAATGGATATTCCCTTCCATGATC
Found at i:32979381 original size:16 final size:16
Alignment explanation
Indices: 32979360--32979393 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
32979350 CAATATTAAG
32979360 TATTTTTATTATCTTT
1 TATTTTTATTATCTTT
32979376 TATTTTTATTATCTTT
1 TATTTTTATTATCTTT
32979392 TA
1 TA
32979394 CGATAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTATTATCTTT
Found at i:32980725 original size:12 final size:12
Alignment explanation
Indices: 32980710--32980751 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
32980700 ATAAAACAGT
32980710 AGCAAAAATAAC
1 AGCAAAAATAAC
*
32980722 AGC-AAAACAAC
1 AGCAAAAATAAC
* *
32980733 AACAAAAATAAT
1 AGCAAAAATAAC
32980745 AGCAAAA
1 AGCAAAA
32980752 GCAGCATCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.69, C:0.17, G:0.07, T:0.07
Consensus pattern (12 bp):
AGCAAAAATAAC
Found at i:32980774 original size:23 final size:22
Alignment explanation
Indices: 32980754--32980819 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 22
32980744 TAGCAAAAGC
*
32980754 AGCATCAAAACAGTAAAAAAAT
1 AGCACCAAAACAGTAAAAAAAT
** *
32980776 AATACCAAAACAGCAAAAAATAT
1 AGCACCAAAACAGTAAAAAA-AT
32980799 AGCACCAAAACAGTAAAAAAA
1 AGCACCAAAACAGTAAAAAAA
32980820 CTAAAAACAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 17 0.47
23 19 0.53
ACGTcount: A:0.65, C:0.17, G:0.08, T:0.11
Consensus pattern (22 bp):
AGCACCAAAACAGTAAAAAAAT
Found at i:32982754 original size:19 final size:19
Alignment explanation
Indices: 32982691--32982754 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
32982681 TATAACATTC
32982691 AAAT-TATATATAAACATA
1 AAATATATATATAAACATA
* * *
32982709 AAATAGATATGAAAAATATCA
1 AAATATATAT-ATAAACAT-A
* *
32982730 ATATATATATATAACCATA
1 AAATATATATATAAACATA
32982749 AAATAT
1 AAATAT
32982755 TTTAATCGAA
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
18 4 0.12
19 10 0.29
20 11 0.32
21 9 0.26
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (19 bp):
AAATATATATATAAACATA
Found at i:32984144 original size:29 final size:30
Alignment explanation
Indices: 32984086--32984176 Score: 107
Period size: 29 Copynumber: 3.1 Consensus size: 30
32984076 TTAAGGTTGA
*
32984086 AAAGGATCCAAAATTATTTTTTTCAGTTTTT
1 AAAGGATCCAAAATT-TTTTTTTCAATTTTT
32984117 AAAGGATCC-AAATTTTTTTTTCAATTTTT
1 AAAGGATCCAAAATTTTTTTTTCAATTTTT
** *
32984146 -AAGGGGCCTAAAA-TTTTTTTTCAACTTTT
1 AAAGGATCC-AAAATTTTTTTTTCAATTTTT
32984175 AA
1 AA
32984177 GGGACTCAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
28 6 0.11
29 29 0.55
30 9 0.17
31 9 0.17
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (30 bp):
AAAGGATCCAAAATTTTTTTTTCAATTTTT
Found at i:32984187 original size:29 final size:29
Alignment explanation
Indices: 32984102--32984187 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
32984092 TCCAAAATTA
* * *
32984102 TTTTTTTCAGTTTTTAAAGGA-TCCAAATT
1 TTTTTTTCAATTTTTAAGGGACT-CAAAAT
*
32984131 TTTTTTTCAATTTTTAAGGGGC-CTAAAAT
1 TTTTTTTCAATTTTTAAGGGACTC-AAAAT
*
32984160 TTTTTTTCAACTTTTAAGGGACTCAAAA
1 TTTTTTTCAATTTTTAAGGGACTCAAAA
32984188 CCCCAATTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.02
29 46 0.96
30 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (29 bp):
TTTTTTTCAATTTTTAAGGGACTCAAAAT
Found at i:32984836 original size:2 final size:2
Alignment explanation
Indices: 32984829--32984864 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32984819 TATTTTTAGA
32984829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32984865 TCAATTCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32991291 original size:2 final size:2
Alignment explanation
Indices: 32991286--32991356 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
32991276 ATAATTCTAT
32991286 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32991328 TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32991357 TTTTAAATTT
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 65 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32991357 original size:10 final size:10
Alignment explanation
Indices: 32991260--32991357 Score: 71
Period size: 12 Copynumber: 9.5 Consensus size: 10
32991250 TATTTTTTAA
*
32991260 ATATTAAATT
1 ATATTATATT
32991270 AT-TTATA-T
1 ATATTATATT
*
32991278 A-ATTCTATT
1 ATATTATATT
32991287 ATA-TATA-T
1 ATATTATATT
32991295 ATATATATATAT
1 ATAT-TATAT-T
32991307 ATATATATATAT
1 ATAT-TATAT-T
32991319 ATATATATATAT
1 ATAT-TATAT-T
32991331 ATATATATATAT
1 ATAT-TATAT-T
32991343 ATATTATATT
1 ATATTATATT
32991353 ATATT
1 ATATT
32991358 TTTAAATTTG
Statistics
Matches: 78, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
8 10 0.13
9 9 0.12
10 13 0.17
11 5 0.06
12 41 0.53
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (10 bp):
ATATTATATT
Found at i:32992319 original size:26 final size:28
Alignment explanation
Indices: 32992276--32992327 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
32992266 TTTATATATA
*
32992276 TAATTTTTAATGTAAAAATATATTTTTT
1 TAATTTTTAATATAAAAATATATTTTTT
*
32992304 TAATTTTTAA-AT-AAAATATGTTTT
1 TAATTTTTAATATAAAAATATATTTT
32992328 ATGAATTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
27 1 0.05
28 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
TAATTTTTAATATAAAAATATATTTTTT
Found at i:32996543 original size:2 final size:2
Alignment explanation
Indices: 32996536--32996575 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
32996526 ACAGACAGAC
32996536 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
32996576 CTGATGAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:32997105 original size:20 final size:21
Alignment explanation
Indices: 32997076--32997138 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 21
32997066 ATAAATGTCT
* *
32997076 TATAAATAAATATTAA-TAAT
1 TATAGATAAATATTAATTAAA
**
32997096 TATATTTAAATA-TAATTAAA
1 TATAGATAAATATTAATTAAA
*
32997116 TATAGATAAATATT-AGTAAA
1 TATAGATAAATATTAATTAAA
32997136 TAT
1 TAT
32997139 CGAGTTTAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.09
20 31 0.89
21 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
TATAGATAAATATTAATTAAA
Found at i:32997193 original size:21 final size:21
Alignment explanation
Indices: 32997169--32997229 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
32997159 TTATTTTGAA
*
32997169 TTTAGAGTTTAAAATTTAGGG
1 TTTAGAGTTTAAAATTTAGAG
* * *
32997190 TTTAAAGTTTTAAATCTAGAG
1 TTTAGAGTTTAAAATTTAGAG
*
32997211 TTTAGAGTTTTAATATTTA
1 TTTAGAG-TTTAAAATTTA
32997230 TTTATGTTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (21 bp):
TTTAGAGTTTAAAATTTAGAG
Found at i:33003306 original size:13 final size:14
Alignment explanation
Indices: 33003288--33003317 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
33003278 GTCAATGCAA
33003288 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
33003301 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
33003315 TCA
1 TCA
33003318 ATGTACTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:33004840 original size:14 final size:15
Alignment explanation
Indices: 33004821--33004851 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
33004811 TTTATCGTAA
33004821 TTTTTTTCTT-CTTT
1 TTTTTTTCTTCCTTT
33004835 TTTTTTTCTTCCTTT
1 TTTTTTTCTTCCTTT
33004850 TT
1 TT
33004852 CTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTCCTTT
Found at i:33010332 original size:21 final size:24
Alignment explanation
Indices: 33010306--33010355 Score: 79
Period size: 21 Copynumber: 2.2 Consensus size: 24
33010296 TAAAAGCTAT
33010306 TTACAAAATCA-AT-TTCT-AAGA
1 TTACAAAATCATATCTTCTAAAGA
33010327 TTACAAAATCATATCTTCTAAAGA
1 TTACAAAATCATATCTTCTAAAGA
33010351 TTACA
1 TTACA
33010356 TATCAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.42
22 2 0.08
23 4 0.15
24 9 0.35
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (24 bp):
TTACAAAATCATATCTTCTAAAGA
Found at i:33025774 original size:24 final size:24
Alignment explanation
Indices: 33025741--33025800 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
33025731 TGCATAGTAG
*
33025741 GTATCGGTAGTTCTGCTCATAGAA
1 GTATCGGTAGTTCTGCCCATAGAA
*
33025765 GTATCAGTAGTTCTGCCCATAGAA
1 GTATCGGTAGTTCTGCCCATAGAA
33025789 GTATCGGTAGTT
1 GTATCGGTAGTT
33025801 TGTGTACTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (24 bp):
GTATCGGTAGTTCTGCCCATAGAA
Found at i:33028285 original size:16 final size:18
Alignment explanation
Indices: 33028250--33028287 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
33028240 TTTCCTTCTT
*
33028250 TTATATTTATTAATATTA
1 TTATATTTATTAATAATA
33028268 TTATA-TTA-TAATAATA
1 TTATATTTATTAATAATA
33028284 TTAT
1 TTAT
33028288 TAATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 3 0.16
18 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATATTTATTAATAATA
Found at i:33028782 original size:23 final size:23
Alignment explanation
Indices: 33028751--33029098 Score: 455
Period size: 23 Copynumber: 15.2 Consensus size: 23
33028741 TAATTCTTTT
*
33028751 AGCATAAATCACATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* * *
33028774 ATCATAAATCATATTAATATTT-
1 AGCACAAATCACATTAATATTTA
*
33028796 AGCAAAAATCACATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* * * *
33028819 AACATAAATAATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* * *
33028842 AGCAGAAATCATATTAATATTTG
1 AGCACAAATCACATTAATATTTA
*
33028865 AGCACAAATCATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* *
33028888 AGTACAAATCACATTAATATTTG
1 AGCACAAATCACATTAATATTTA
*
33028911 AGCACAAATCATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
*
33028934 AGCACAAATCACATTAATATTTG
1 AGCACAAATCACATTAATATTTA
*
33028957 AGTACAAATCACATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* * *
33028980 AGCATAAATCAGATTAATATTCA
1 AGCACAAATCACATTAATATTTA
* *
33029003 AGCATAAATCACATTAATATTTG
1 AGCACAAATCACATTAATATTTA
* *
33029026 AGCGCAAATCATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
*
33029049 AGCACAAATCACATTAATATTTG
1 AGCACAAATCACATTAATATTTA
33029072 AGCACAAATCACATTAATATTTA
1 AGCACAAATCACATTAATATTTA
33029095 AGCA
1 AGCA
33029099 TAGATATAAG
Statistics
Matches: 284, Mismatches: 40, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
22 19 0.07
23 265 0.93
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (23 bp):
AGCACAAATCACATTAATATTTA
Found at i:33032423 original size:36 final size:36
Alignment explanation
Indices: 33032274--33032412 Score: 215
Period size: 36 Copynumber: 3.9 Consensus size: 36
33032264 AATATAATCA
* * *
33032274 GTCACATGGTATGAAGAATACACCCACATATTTTCT
1 GTCACATGGCATGAAGAACATACCCACATATTTTCT
**
33032310 GTCACATGGCATGAAGAACATATTCACATATTTTCT
1 GTCACATGGCATGAAGAACATACCCACATATTTTCT
* *
33032346 GTCACATGTCATGAAGAACATACTCACATATTTTCT
1 GTCACATGGCATGAAGAACATACCCACATATTTTCT
33032382 GTCACATGGCATGAAGAACATACCCACATAT
1 GTCACATGGCATGAAGAACATACCCACATAT
33032413 CCACCTTCAC
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (36 bp):
GTCACATGGCATGAAGAACATACCCACATATTTTCT
Found at i:33032543 original size:23 final size:23
Alignment explanation
Indices: 33032493--33032800 Score: 393
Period size: 23 Copynumber: 13.3 Consensus size: 23
33032483 ATCTTAATTC
33032493 TTTAAGCACAAATCACATTAAATA
1 TTTAAGCACAAATCACATT-AATA
* * *
33032517 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
33032540 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
33032563 TTTGAGCACAAACCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
33032586 TTTGAGCGCAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
33032609 TTTAAGCAAAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
33032632 TTTGAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
33032655 TTTAAACATAAATCACATTGATA
1 TTTAAGCACAAATCACATTAATA
*
33032678 TTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
33032701 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
33032724 TTTGAG-AGCAAATCATATTAATA
1 TTTAAGCA-CAAATCACATTAATA
* *
33032747 TTTAAGCAGAAATCGCATTAATA
1 TTTAAGCACAAATCACATTAATA
*
33032770 TTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
33032793 TTTAAGCA
1 TTTAAGCA
33032801 TAGATATAAG
Statistics
Matches: 245, Mismatches: 37, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
22 1 0.00
23 227 0.93
24 17 0.07
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:33032584 original size:46 final size:46
Alignment explanation
Indices: 33032497--33032802 Score: 443
Period size: 46 Copynumber: 6.6 Consensus size: 46
33032487 TAATTCTTTA
* * *
33032497 AGCACAAATCACATTAAATATTTAATCATAAATCATATTAATATTTA
1 AGCACAAATCACATT-AATATTTAAGCATAAATCACATTAATATTTG
* * * *
33032544 AGCACAAATCATATTAATATTTGAGCACAAACCACATTAATATTTG
1 AGCACAAATCACATTAATATTTAAGCATAAATCACATTAATATTTG
* * *
33032590 AGCGCAAATCATATTAATATTTAAGCAAAAATCACATTAATATTTG
1 AGCACAAATCACATTAATATTTAAGCATAAATCACATTAATATTTG
* * *
33032636 AGCATAAATCACATTAATATTTAAACATAAATCACATTGATATTTG
1 AGCACAAATCACATTAATATTTAAGCATAAATCACATTAATATTTG
33032682 AGCACAAATCACATTAATATTTAAGCATAAATCACATTAATATTTG
1 AGCACAAATCACATTAATATTTAAGCATAAATCACATTAATATTTG
* * *
33032728 AG-AGCAAATCATATTAATATTTAAGCAGAAATCGCATTAATATTTG
1 AGCA-CAAATCACATTAATATTTAAGCATAAATCACATTAATATTTG
33032774 AGCACAAATCACATTAATATTTAAGCATA
1 AGCACAAATCACATTAATATTTAAGCATA
33032803 GATATAAGAA
Statistics
Matches: 232, Mismatches: 25, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
45 1 0.00
46 216 0.93
47 15 0.06
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.33
Consensus pattern (46 bp):
AGCACAAATCACATTAATATTTAAGCATAAATCACATTAATATTTG
Found at i:33033665 original size:70 final size:67
Alignment explanation
Indices: 33033572--33033704 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
33033562 TCCGAATAAG
* * * *
33033572 AAAAGGCAAAACTATGTCGTTTTGATAAATGTTTACCCTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGCAAAACTATGTCATTTTGATAAATATTTACCC-AT-T-AAGTTAAAAGGCAAAACCATT
33033637 AAGTT
63 AAGTT
* *
33033642 AAAAGGTAAAATTATGTCATTTTGATAAATATTTACCCATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGGCAAAACTATGTCATTTTGATAAATATTTACCCATTAAGTTAAAAGGCAAAACCATTA
33033705 TATTGTTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 21 0.37
68 1 0.02
69 1 0.02
70 34 0.60
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (67 bp):
AAAAGGCAAAACTATGTCATTTTGATAAATATTTACCCATTAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:33034719 original size:23 final size:23
Alignment explanation
Indices: 33034688--33034731 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
33034678 AGACCCATGA
33034688 ATTGTGTT-GTTAGAATTAGATTGG
1 ATTGTGTTGGTT-GAATT-GATTGG
33034712 ATTG-GTTGGTTGAATTGATT
1 ATTGTGTTGGTTGAATTGATT
33034732 AGATCGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.48
Consensus pattern (23 bp):
ATTGTGTTGGTTGAATTGATTGG
Found at i:33035228 original size:23 final size:25
Alignment explanation
Indices: 33035202--33035260 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 25
33035192 GAAAACAATT
*
33035202 AAAAAAAGAAATTCAAGA-ATAAA-
1 AAAAAAAGAAATTCAAAACATAAAC
33035225 AAAATAAAG--ATTCAAAACATAAAC
1 AAAA-AAAGAAATTCAAAACATAAAC
*
33035249 AAATAAAGAAAT
1 AAAAAAAGAAAT
33035261 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
22 7 0.24
23 13 0.45
24 7 0.24
25 2 0.07
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.15
Consensus pattern (25 bp):
AAAAAAAGAAATTCAAAACATAAAC
Found at i:33044908 original size:13 final size:13
Alignment explanation
Indices: 33044890--33044914 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33044880 GTTAACAAGG
33044890 TGAAGGTTCACAT
1 TGAAGGTTCACAT
33044903 TGAAGGTTCACA
1 TGAAGGTTCACA
33044915 CTTCGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (13 bp):
TGAAGGTTCACAT
Found at i:33047467 original size:16 final size:15
Alignment explanation
Indices: 33047433--33047472 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
33047423 TCTTAAAAAG
*
33047433 AAAGAAAAA-TGTTA
1 AAAGAAAAATTGTAA
33047447 AAAGAAAAATTTGTAA
1 AAAGAAAAA-TTGTAA
33047463 AAAGAAAAAT
1 AAAGAAAAAT
33047473 ATTTTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 9 0.39
15 1 0.04
16 13 0.57
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (15 bp):
AAAGAAAAATTGTAA
Found at i:33048151 original size:2 final size:2
Alignment explanation
Indices: 33048144--33048171 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33048134 TTAATTGGTA
33048144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33048172 GTTTTTACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33051660 original size:10 final size:10
Alignment explanation
Indices: 33051645--33051678 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
33051635 TGTCAGAAGA
33051645 GTTTTATTTT
1 GTTTTATTTT
33051655 GTTTTATTTT
1 GTTTTATTTT
33051665 GATTTTGATTTT
1 G-TTTT-ATTTT
33051677 GT
1 GT
33051679 GTTAACTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 11 0.50
11 5 0.23
12 6 0.27
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.74
Consensus pattern (10 bp):
GTTTTATTTT
Found at i:33053926 original size:26 final size:26
Alignment explanation
Indices: 33053897--33053968 Score: 126
Period size: 26 Copynumber: 2.8 Consensus size: 26
33053887 AATGTCGCTG
33053897 CATGAGCATGTCCAGAATTGTCACTA
1 CATGAGCATGTCCAGAATTGTCACTA
* *
33053923 CATGAACATGTCCAGAATTGTCACTG
1 CATGAGCATGTCCAGAATTGTCACTA
33053949 CATGAGCATGTCCAGAATTG
1 CATGAGCATGTCCAGAATTG
33053969 CGCCCAGATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (26 bp):
CATGAGCATGTCCAGAATTGTCACTA
Found at i:33057502 original size:17 final size:18
Alignment explanation
Indices: 33057482--33057515 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33057472 AATTGCGCAG
33057482 ACAAAG-TAAATGTGATA
1 ACAAAGATAAATGTGATA
*
33057499 ACAAAGATAATTGTGAT
1 ACAAAGATAAATGTGAT
33057516 TGCAACTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (18 bp):
ACAAAGATAAATGTGATA
Found at i:33082653 original size:364 final size:364
Alignment explanation
Indices: 33081984--33082708 Score: 1378
Period size: 364 Copynumber: 2.0 Consensus size: 364
33081974 GCAATTATTA
* *
33081984 TCTTAGAACGCGCTCAGCGATTCAACGACAATCTATAGATCTGTGAAGAACATACTAGAACTGCG
1 TCTTAGAACGCGCTCAGCGATACAACGACAATCTACAGATCTGTGAAGAACATACTAGAACTGCG
33082049 TGAGTGCACAGTTGTATTCTAACTAATTTTGATAATTGTAAAAACCATATCTAGATCTGGGAGAG
66 TGAGTGCACAGTTGTATTCTAACTAATTTTGATAATTGTAAAAACCATATCTAGATCTGGGAGAG
33082114 AAGGCTGAATCTTGAAACATTTTAGAGGTTATAAATAGACAAACAAGGAAGGAAAGAGATCATCA
131 AAGGCTGAATCTTGAAACATTTTAGAGGTTATAAATAGACAAACAAGGAAGGAAAGAGATCATCA
33082179 AGAGCTAAGGGATTTAATTTTGAAAATTCTGTGTGAACTGGAGATTTGAGCTGGAAATCGGGGAG
196 AGAGCTAAGGGATTTAATTTTGAAAATTCTGTGTGAACTGGAGATTTGAGCTGGAAATCGGGGAG
* *
33082244 CTGATGAAGCAAGTCTGCAACTACTTCTAACGAGAGGTGCTAGATTTCGAGTAAGAGGAACAATT
261 CTGATGAAGCAAGTCTGCAACTACTTCTAACGAGAGGTGCTAGATTTCGAGCAAGAGAAACAATT
*
33082309 AGGGAGTAGACGTAGTAGTCTAGAGATAGTAAGCTTCAT
326 AGGGAGTAGACGTAATAGTCTAGAGATAGTAAGCTTCAT
*
33082348 TCTTAGAACGCGCTCAGCGATACAACGACAATCTGCAGATCTGTGAAGAACATACTAGAACTGCG
1 TCTTAGAACGCGCTCAGCGATACAACGACAATCTACAGATCTGTGAAGAACATACTAGAACTGCG
33082413 TGAGTGCACAGTTGTATTCTAACTAATTTTGATAATTGTAAAAACCATATCTAGATCTGGGAGAG
66 TGAGTGCACAGTTGTATTCTAACTAATTTTGATAATTGTAAAAACCATATCTAGATCTGGGAGAG
33082478 AAGGCTGAATCTTGAAACATTTTAGAGGTTATAAATAGACAAACAAGGAAGGAAAGAGATCATCA
131 AAGGCTGAATCTTGAAACATTTTAGAGGTTATAAATAGACAAACAAGGAAGGAAAGAGATCATCA
33082543 AGAGCTAAGGGATTTAATTTTGAAAATTCTGTGTGAACTGGAGATTTGAGCTGGAAATCGGGGAG
196 AGAGCTAAGGGATTTAATTTTGAAAATTCTGTGTGAACTGGAGATTTGAGCTGGAAATCGGGGAG
* *
33082608 CTGATGAAGCAAGTCTGCAACTGCTTCTAATGAGAGGTGCTAGATTTCGAGCAAGAGAAACAATT
261 CTGATGAAGCAAGTCTGCAACTACTTCTAACGAGAGGTGCTAGATTTCGAGCAAGAGAAACAATT
33082673 AGGGAGTAGACGTAATAGTCTAGAGATAGTAAGCTT
326 AGGGAGTAGACGTAATAGTCTAGAGATAGTAAGCTT
33082709 TAATTATTCT
Statistics
Matches: 353, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
364 353 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.26
Consensus pattern (364 bp):
TCTTAGAACGCGCTCAGCGATACAACGACAATCTACAGATCTGTGAAGAACATACTAGAACTGCG
TGAGTGCACAGTTGTATTCTAACTAATTTTGATAATTGTAAAAACCATATCTAGATCTGGGAGAG
AAGGCTGAATCTTGAAACATTTTAGAGGTTATAAATAGACAAACAAGGAAGGAAAGAGATCATCA
AGAGCTAAGGGATTTAATTTTGAAAATTCTGTGTGAACTGGAGATTTGAGCTGGAAATCGGGGAG
CTGATGAAGCAAGTCTGCAACTACTTCTAACGAGAGGTGCTAGATTTCGAGCAAGAGAAACAATT
AGGGAGTAGACGTAATAGTCTAGAGATAGTAAGCTTCAT
Found at i:33084162 original size:12 final size:12
Alignment explanation
Indices: 33084145--33084178 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
33084135 ATCCTGTTTT
33084145 CCTTCTTCTTCC
1 CCTTCTTCTTCC
* *
33084157 CCTTCTCCTTCT
1 CCTTCTTCTTCC
33084169 CCTTCTTCTT
1 CCTTCTTCTT
33084179 GGCTGTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (12 bp):
CCTTCTTCTTCC
Found at i:33090960 original size:452 final size:452
Alignment explanation
Indices: 33090116--33091471 Score: 2705
Period size: 452 Copynumber: 3.0 Consensus size: 452
33090106 TTGGGCGATT
33090116 AAAAAGATAAATGCTGATTGGTTGGTTTCAAGAGAGAAAAGGATGATGGATTTAAATGAGATAGA
1 AAAAAGATAAATGCTGATTGGTTGGTTTCAAGAGAGAAAAGGATGATGGATTTAAATGAGATAGA
33090181 GAAGTTTCAATTGCAGGCATACGAAAATGATAGGATTTATAAAGAAAAAATGAAAAGGTGGCATG
66 GAAGTTTCAATTGCAGGCATACGAAAATGATAGGATTTATAAAGAAAAAATGAAAAGGTGGCATG
33090246 ACAGTATTTTTTTATCTATGCATTTTGAACCAGGACAACAAGTTTTGCTGTTTGATTTGAAGCTT
131 ACAGTATTTTTTTATCTATGCATTTTGAACCAGGACAACAAGTTTTGCTGTTTGATTTGAAGCTT
33090311 AAATTATTTCCAGGGAAGTTGAAATCTAAGTGGACAGGGCCATTTGAGGTAGTGTTTGCCTATCC
196 AAATTATTTCCAGGGAAGTTGAAATCTAAGTGGACAGGGCCATTTGAGGTAGTGTTTGCCTATCC
33090376 ACAAGGTGTTGTTGATATAAAAAATGTCACGACAAGTAATGTGTTCAAAGTCAATGGATAGCGTC
261 ACAAGGTGTTGTTGATATAAAAAATGTCACGACAAGTAATGTGTTCAAAGTCAATGGATAGCGTC
33090441 TAAAGCGCTATTACAATGATCCGATGTTGTAGTAGAATTTTGCTATTATATTAAGTGATGTCAGA
326 TAAAGCGCTATTACAATGATCCGATGTTGTAGTAGAATTTTGCTATTATATTAAGTGATGTCAGA
33090506 AGAGTTTGAATTTGTTTTGTTTTTATTTCATTTTTGTGTTAACTTTGATTTTGAATTTTTGA
391 AGAGTTTGAATTTGTTTTGTTTTTATTTCATTTTTGTGTTAACTTTGATTTTGAATTTTTGA
33090568 AAAAAGATAAATGCTGATTGGTTGGTTTCAAGAGAGAAAAGGATGATGGATTTAAATGAGATAGA
1 AAAAAGATAAATGCTGATTGGTTGGTTTCAAGAGAGAAAAGGATGATGGATTTAAATGAGATAGA
33090633 GAAGTTTCAATTGCAGGCATACGAAAATGATAGGATTTATAAAGAAAAAATGAAAAGGTGGCATG
66 GAAGTTTCAATTGCAGGCATACGAAAATGATAGGATTTATAAAGAAAAAATGAAAAGGTGGCATG
33090698 ACAGTATTTTTTTATCTATGCATTTTGAACCAGGACAACAAGTTTTGCTGTTTGATTTGAAGCTT
131 ACAGTATTTTTTTATCTATGCATTTTGAACCAGGACAACAAGTTTTGCTGTTTGATTTGAAGCTT
33090763 AAATTATTTCCAGGGAAGTTGAAATCTAAGTGGACAGGGCCATTTGAGGTAGTGTTTGCCTATCC
196 AAATTATTTCCAGGGAAGTTGAAATCTAAGTGGACAGGGCCATTTGAGGTAGTGTTTGCCTATCC
33090828 ACAAGGTGTTGTTGATATAAAAAATGTCACGACAAGTAATGTGTTCAAAGTCAATGGATAGCGTC
261 ACAAGGTGTTGTTGATATAAAAAATGTCACGACAAGTAATGTGTTCAAAGTCAATGGATAGCGTC
33090893 TAAAGCGCTATTACAATGATCCGATGTTGTAGTAGAATTTTGCTATTATATTAAGTGATGTCAGA
326 TAAAGCGCTATTACAATGATCCGATGTTGTAGTAGAATTTTGCTATTATATTAAGTGATGTCAGA
33090958 AGAGTTTGAATTTGTTTTGTTTTTATTTCATTTTTGTGTTAACTTTGATTTTGAATTTTTGA
391 AGAGTTTGAATTTGTTTTGTTTTTATTTCATTTTTGTGTTAACTTTGATTTTGAATTTTTGA
33091020 AAAAAGATAAATGCTGATTGGTTGGTTTCAAGAGAGAAAAGGATGATGGATTTAAATGAGATAGA
1 AAAAAGATAAATGCTGATTGGTTGGTTTCAAGAGAGAAAAGGATGATGGATTTAAATGAGATAGA
33091085 GAAGTTTCAATTGCAGGCATACGAAAATGATAGGATTTATAAAG-AAAAATGAAAAGGTGGCATG
66 GAAGTTTCAATTGCAGGCATACGAAAATGATAGGATTTATAAAGAAAAAATGAAAAGGTGGCATG
33091149 ACAGTATTTTTTTATCTATGCATTTTGAACCAGGACAACAAGTTTTGCTGTTTGATTTGAAGCTT
131 ACAGTATTTTTTTATCTATGCATTTTGAACCAGGACAACAAGTTTTGCTGTTTGATTTGAAGCTT
33091214 AAATTATTTCCAGGGAAGTTGAAATCTAAGTGGACAGGGCCATTTGAGGTAGTGTTTGCCTATCC
196 AAATTATTTCCAGGGAAGTTGAAATCTAAGTGGACAGGGCCATTTGAGGTAGTGTTTGCCTATCC
33091279 ACAAGGTGTTGTTGATATAAAAAATGTCACGACAAGTAATGTGTTCAAAGTCAATGGATAGCGTC
261 ACAAGGTGTTGTTGATATAAAAAATGTCACGACAAGTAATGTGTTCAAAGTCAATGGATAGCGTC
33091344 TAAAGCGCTATTACAATGATCCGATGTTGTAGTAGAATTTTGCTATTATATTAAGTGATGTCAGA
326 TAAAGCGCTATTACAATGATCCGATGTTGTAGTAGAATTTTGCTATTATATTAAGTGATGTCAGA
33091409 AGAGTTTGAATTTGTTTTGTTTTTATTTCATTTTTGTGTTAACTTTGATTTTGAATTTTTGA
391 AGAGTTTGAATTTGTTTTGTTTTTATTTCATTTTTGTGTTAACTTTGATTTTGAATTTTTGA
33091471 A
1 A
33091472 TTAGCTGTAG
Statistics
Matches: 904, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
451 343 0.38
452 561 0.62
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (452 bp):
AAAAAGATAAATGCTGATTGGTTGGTTTCAAGAGAGAAAAGGATGATGGATTTAAATGAGATAGA
GAAGTTTCAATTGCAGGCATACGAAAATGATAGGATTTATAAAGAAAAAATGAAAAGGTGGCATG
ACAGTATTTTTTTATCTATGCATTTTGAACCAGGACAACAAGTTTTGCTGTTTGATTTGAAGCTT
AAATTATTTCCAGGGAAGTTGAAATCTAAGTGGACAGGGCCATTTGAGGTAGTGTTTGCCTATCC
ACAAGGTGTTGTTGATATAAAAAATGTCACGACAAGTAATGTGTTCAAAGTCAATGGATAGCGTC
TAAAGCGCTATTACAATGATCCGATGTTGTAGTAGAATTTTGCTATTATATTAAGTGATGTCAGA
AGAGTTTGAATTTGTTTTGTTTTTATTTCATTTTTGTGTTAACTTTGATTTTGAATTTTTGA
Found at i:33093829 original size:16 final size:15
Alignment explanation
Indices: 33093795--33093834 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
33093785 GCGTAAAAAG
*
33093795 AAAGAAAAA-TGTTA
1 AAAGAAAAATTGTAA
33093809 AAAGAAAAATTTGTAA
1 AAAGAAAAA-TTGTAA
33093825 AAAGAAAAAT
1 AAAGAAAAAT
33093835 ATTTTTTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 9 0.39
15 1 0.04
16 13 0.57
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (15 bp):
AAAGAAAAATTGTAA
Found at i:33097024 original size:15 final size:16
Alignment explanation
Indices: 33097004--33097033 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33096994 TCATAAATTT
33097004 TTTTCTT-CTTTTTCA
1 TTTTCTTCCTTTTTCA
33097019 TTTTCTTCCTTTTTC
1 TTTTCTTCCTTTTTC
33097034 TCATTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTCTTCCTTTTTCA
Found at i:33097045 original size:15 final size:16
Alignment explanation
Indices: 33097002--33097048 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
33096992 TATCATAAAT
*
33097002 TTTTTTCTTCTTTTTCA
1 TTTTTTCTT-TTTCTCA
33097019 TTTTCTTCCTTTTTCTCA
1 TTTT-TT-CTTTTTCTCA
33097037 -TTTTTCTTTTTC
1 TTTTTTCTTTTTC
33097049 AAGTGACTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 7 0.26
16 2 0.07
17 7 0.26
18 8 0.30
19 3 0.11
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTCTTTTTCTCA
Found at i:33097653 original size:20 final size:19
Alignment explanation
Indices: 33097630--33097669 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
33097620 AACAAAAAAA
33097630 CAATGACAAAAATAAAAATG
1 CAATGAC-AAAATAAAAATG
*
33097650 CAATGTCAAAATAAAAATG
1 CAATGACAAAATAAAAATG
33097669 C
1 C
33097670 CTGAAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.17
Consensus pattern (19 bp):
CAATGACAAAATAAAAATG
Found at i:33113364 original size:17 final size:18
Alignment explanation
Indices: 33113344--33113386 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
33113334 CCCAAATGAA
* *
33113344 AGAAAAGGAGGAG-GAAG
1 AGAAAAAGAAGAGAGAAG
33113361 AGAAAAAAGAAGAGAGAAG
1 AG-AAAAAGAAGAGAGAAG
33113380 AGAAAAA
1 AGAAAAA
33113387 CCTGTCGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
19 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAAGAGAGAAG
Found at i:33136636 original size:26 final size:26
Alignment explanation
Indices: 33136598--33136652 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
33136588 AATTCTGGGT
33136598 ACAATTCTAGACACGTTCATGCAA-CG
1 ACAATTCTAGACACGTTCATG-AAGCG
* *
33136624 ACAATTCTGGACATGTTCATGAAGCG
1 ACAATTCTAGACACGTTCATGAAGCG
33136650 ACA
1 ACA
33136653 TTCCTAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (26 bp):
ACAATTCTAGACACGTTCATGAAGCG
Found at i:33167772 original size:21 final size:21
Alignment explanation
Indices: 33167746--33167786 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33167736 TTCACATGTT
33167746 TTCTTACTCATGATTCTTTTG
1 TTCTTACTCATGATTCTTTTG
**
33167767 TTCTTACTCATTTTTCTTTT
1 TTCTTACTCATGATTCTTTT
33167787 CTTTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.20, G:0.05, T:0.63
Consensus pattern (21 bp):
TTCTTACTCATGATTCTTTTG
Found at i:33178842 original size:22 final size:20
Alignment explanation
Indices: 33178798--33178842 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
33178788 GATTGACTCC
*
33178798 AAGGAAAAAAAAGAAAGAGA
1 AAGGAAAAAAAAGAAACAGA
*
33178818 AAGGACAAGAAAAAGAAACATA
1 AAGGA-AA-AAAAAGAAACAGA
33178840 AAG
1 AAG
33178843 AGGAGCGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 2 0.10
22 14 0.67
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.02
Consensus pattern (20 bp):
AAGGAAAAAAAAGAAACAGA
Found at i:33178968 original size:17 final size:17
Alignment explanation
Indices: 33178943--33178976 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33178933 ATGCATGTCA
33178943 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
* *
33178960 TTTAGTTGTCGTTGCAT
1 TTTAATTGTCATTGCAT
33178977 ATTACTTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:33184856 original size:3 final size:3
Alignment explanation
Indices: 33184850--33184893 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
33184840 TCATCATTTC
33184850 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
33184894 CATGTGATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:33186109 original size:18 final size:18
Alignment explanation
Indices: 33186086--33186127 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
33186076 TGAGCAAACT
33186086 TTTCTTTGC-TCTCTCTTC
1 TTTCTTTGCTTCT-TCTTC
*
33186104 TTTCTTTTCTTCTTCTTC
1 TTTCTTTGCTTCTTCTTC
33186122 -TTCTTT
1 TTTCTTT
33186128 TTTTTACTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 13 0.59
19 3 0.14
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTCTTTGCTTCTTCTTC
Found at i:33189483 original size:21 final size:21
Alignment explanation
Indices: 33189459--33189510 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
33189449 AGGAAAAGAC
*
33189459 GAGAAAGGTAAAGAAGAGAAG
1 GAGAAAGGTAAAGAAGAAAAG
*
33189480 GAGAAAGGTGAAGAAGAAAAG
1 GAGAAAGGTAAAGAAGAAAAG
*
33189501 GA-AATGGTAA
1 GAGAAAGGTAA
33189511 GGAGAAGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.08
Consensus pattern (21 bp):
GAGAAAGGTAAAGAAGAAAAG
Found at i:33189486 original size:15 final size:14
Alignment explanation
Indices: 33189439--33189486 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
33189429 CTGACAGAAG
33189439 AAGAAGGAGAAGGAA
1 AAGAA-GAGAAGGAA
* *
33189454 AAGACGAGAAAGGTA
1 AAGAAGAG-AAGGAA
33189469 AAGAAGAGAAGGAGA
1 AAGAAGAGAAGGA-A
33189484 AAG
1 AAG
33189487 GTGAAGAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.58, C:0.02, G:0.38, T:0.02
Consensus pattern (14 bp):
AAGAAGAGAAGGAA
Found at i:33192140 original size:24 final size:24
Alignment explanation
Indices: 33192115--33192161 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
33192105 AACTATTCAT
33192115 TTTATGTTA-ATTTGC-TCTGACAA
1 TTTATGTTATATTTGCGT-TGACAA
*
33192138 TTTATTTTATATTTGCGTTGACAA
1 TTTATGTTATATTTGCGTTGACAA
33192162 ATTAACTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.51
Consensus pattern (24 bp):
TTTATGTTATATTTGCGTTGACAA
Found at i:33195272 original size:24 final size:24
Alignment explanation
Indices: 33195244--33195290 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
33195234 TTTAGACATA
33195244 GATTTCTATTTGAAAATTTATTTC
1 GATTTCTATTTGAAAATTTATTTC
33195268 GATTTCTATTTGAAAATTTATTT
1 GATTTCTATTTGAAAATTTATTT
33195291 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
GATTTCTATTTGAAAATTTATTTC
Found at i:33195668 original size:12 final size:12
Alignment explanation
Indices: 33195653--33195694 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
33195643 CATAGATTTC
33195653 TATTTGAAAATT
1 TATTTGAAAATT
* *
33195665 TATTT-AGATTT
1 TATTTGAAAATT
33195676 CTATTTGAAAATT
1 -TATTTGAAAATT
33195689 TATTTG
1 TATTTG
33195695 CTTTCTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 4 0.17
12 16 0.67
13 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (12 bp):
TATTTGAAAATT
Found at i:33195673 original size:24 final size:24
Alignment explanation
Indices: 33195645--33195693 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
33195635 TATTTAGACA
33195645 TAGATTTCTATTTGAAAATTTATT
1 TAGATTTCTATTTGAAAATTTATT
33195669 TAGATTTCTATTTGAAAATTTATT
1 TAGATTTCTATTTGAAAATTTATT
33195693 T
1 T
33195694 GCTTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (24 bp):
TAGATTTCTATTTGAAAATTTATT
Found at i:33230839 original size:8 final size:8
Alignment explanation
Indices: 33230826--33230856 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
33230816 ATTACAAACC
*
33230826 CAAAATTT
1 CAAAATAT
33230834 CAAAATAT
1 CAAAATAT
33230842 CAAAATAT
1 CAAAATAT
33230850 CAAAATA
1 CAAAATA
33230857 AAATTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (8 bp):
CAAAATAT
Found at i:33241398 original size:16 final size:17
Alignment explanation
Indices: 33241373--33241405 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
33241363 ATAATTTTAT
*
33241373 TTTTATTAA-TTTAAAA
1 TTTTAATAATTTTAAAA
33241389 TTTTAATAATTTTAAAA
1 TTTTAATAATTTTAAAA
33241406 GATCTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAATAATTTTAAAA
Found at i:33243174 original size:32 final size:32
Alignment explanation
Indices: 33243113--33243174 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
33243103 AGGAGATTTT
* *
33243113 AAATCAATTTGAATAGAATCAAATTAAATTAA
1 AAATCAATTTGAATAGAATAAAATCAAATTAA
*
33243145 AAATCAATTTG-ATTGAAATAAAATCAAATT
1 AAATCAATTTGAATAG-AATAAAATCAAATT
33243175 GAGATATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (32 bp):
AAATCAATTTGAATAGAATAAAATCAAATTAA
Found at i:33246721 original size:20 final size:19
Alignment explanation
Indices: 33246696--33246735 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
33246686 ACCATCTCCG
33246696 TCCAACCCAACACACCAATA
1 TCCAACCCAACACA-CAATA
*
33246716 TCCAACCCTACACACAATA
1 TCCAACCCAACACACAATA
33246735 T
1 T
33246736 AGTGTCGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (19 bp):
TCCAACCCAACACACAATA
Found at i:33247190 original size:20 final size:19
Alignment explanation
Indices: 33247165--33247204 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
33247155 ACCATCTCCG
33247165 TCCAACCCAACACACCAATA
1 TCCAACCCAACACA-CAATA
*
33247185 TCCAACCCTACACACAATA
1 TCCAACCCAACACACAATA
33247204 T
1 T
33247205 AGTGTCGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (19 bp):
TCCAACCCAACACACAATA
Done.