Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014009.1 Corchorus capsularis cultivar CVL-1 contig14030, whole genome shotgun sequence
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: 71977
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:14343 original size:140 final size:140
Alignment explanation
Indices: 14091--14372 Score: 564
Period size: 140 Copynumber: 2.0 Consensus size: 140
14081 CATACTTTAA
14091 ATAAGTTCTAAAAATCAACTTCACAGTATTTGAGGACATAAATGAGTTTATCTTTTAAAAACAGG
1 ATAAGTTCTAAAAATCAACTTCACAGTATTTGAGGACATAAATGAGTTTATCTTTTAAAAACAGG
14156 GAGCAGCGCATAACAAGACCTTGAAACTGTGTAACTCAAACTGCTCAGTCCATAACAGAGACAGC
66 GAGCAGCGCATAACAAGACCTTGAAACTGTGTAACTCAAACTGCTCAGTCCATAACAGAGACAGC
14221 ATTAAAGTAC
131 ATTAAAGTAC
14231 ATAAGTTCTAAAAATCAACTTCACAGTATTTGAGGACATAAATGAGTTTATCTTTTAAAAACAGG
1 ATAAGTTCTAAAAATCAACTTCACAGTATTTGAGGACATAAATGAGTTTATCTTTTAAAAACAGG
14296 GAGCAGCGCATAACAAGACCTTGAAACTGTGTAACTCAAACTGCTCAGTCCATAACAGAGACAGC
66 GAGCAGCGCATAACAAGACCTTGAAACTGTGTAACTCAAACTGCTCAGTCCATAACAGAGACAGC
14361 ATTAAAGTAC
131 ATTAAAGTAC
14371 AT
1 AT
14373 GAGACTAAAG
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 142 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.25
Consensus pattern (140 bp):
ATAAGTTCTAAAAATCAACTTCACAGTATTTGAGGACATAAATGAGTTTATCTTTTAAAAACAGG
GAGCAGCGCATAACAAGACCTTGAAACTGTGTAACTCAAACTGCTCAGTCCATAACAGAGACAGC
ATTAAAGTAC
Found at i:19395 original size:45 final size:45
Alignment explanation
Indices: 19344--19433 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
19334 TAATAAAATA
*
19344 GTGGAATTACTAAAAGATCTCTACCCCGAATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCACTACCCCGAATTAATGATGAGCTGG
* *
19389 GTGGAATTACTAAAAGATCACTATCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCACTACCCCGAATTAATGATGAGCTGG
19434 AGAAGTAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCACTACCCCGAATTAATGATGAGCTGG
Found at i:19813 original size:2 final size:2
Alignment explanation
Indices: 19806--19899 Score: 57
Period size: 2 Copynumber: 51.5 Consensus size: 2
19796 TTTTAATTGA
* * *
19806 AT AT AT AT AA AT AT AT AT A- AT AT AT AT AA AT GA- AG A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
*
19845 AGT TT AT AT AT AT -T AT -T AT -T AT -T AT -T AT -T AT AT -T AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19881 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
19900 CTACATACAT
Statistics
Matches: 73, Mismatches: 6, Indels: 26
0.70 0.06 0.25
Matches are distributed among these distances:
1 11 0.15
2 60 0.82
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20218 original size:165 final size:166
Alignment explanation
Indices: 19977--20418 Score: 529
Period size: 165 Copynumber: 2.7 Consensus size: 166
19967 ATGAGGAGTG
* * * * *
19977 AGAGAACTAATTTTTTTCATCTTTTCCCACTTGACAGATTACTTAAATGTCCCAACTATTGATTC
1 AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
* ** *
20042 TTGAAGGGATTAAATAACTAGGCTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGAAAT
66 TTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGAAAT
* * * * *
20107 TACTAAAAGA-TCTCTACCAAGGCTT-ACT-TTTGGAGTT
131 TAATAAAAGATTC-CCACCAAGGATTGA-TGATT--AGCT
* * *
20144 AGAGAA-T-TTTTTTTTTGTCTTTTCCTATTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
1 AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
* * * * *
20207 TTTAGGGGATTAAATAAGTAATCTTTTTGGTCATTTCTCAA-TGAACTTGAATAGAGTGGTGGAA
66 TTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTG-ACTTGAATAGAGTAGTGAAA
*
20271 TTAATAAAAGATTCCCATCAAGGATTGATGATTAGCT
130 TTAATAAAAGATTCCCACCAAGGATTGATGATTAGCT
* * *
20308 AGAGAACTAATCTTTTTCGTCTTTAT-CTACTTGGTAGATTACTTAAATGTCCTAACTTTTAATT
1 AGAGAACTAATTTTTTTCGTCTTT-TCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATT
* *
20372 ATTGAGGAGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGAC
65 CTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGAC
20419 AAATGACTCA
Statistics
Matches: 234, Mismatches: 33, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
164 11 0.05
165 122 0.52
166 92 0.39
167 9 0.04
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (166 bp):
AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
TTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGAAAT
TAATAAAAGATTCCCACCAAGGATTGATGATTAGCT
Found at i:27937 original size:91 final size:91
Alignment explanation
Indices: 27782--27961 Score: 315
Period size: 91 Copynumber: 2.0 Consensus size: 91
27772 AAACATTACA
*
27782 TAACAATTACTCAAATTGATTTTGGAGTCACTTAACCTGGCTGGAGCAGTTGGGAACTTGGGGAA
1 TAACAATTACTCAAATTGATTTTGGAGTCAATTAACCTGGCTGGAGCAGTTGGGAACTTGGGGAA
27847 TCCATAGTAATTGATTTCAAAGTCTT
66 TCCATAGTAATTGATTTCAAAGTCTT
* * *
27873 TAACAATTACTGAAATTGATTTTGGAGTCAATTAACCTGGCTGGGGTAGTTGGGAACTTGGGGAA
1 TAACAATTACTCAAATTGATTTTGGAGTCAATTAACCTGGCTGGAGCAGTTGGGAACTTGGGGAA
*
27938 TCGATAGTAATTGATTTCAAAGTC
66 TCCATAGTAATTGATTTCAAAGTC
27962 CATGGTTTCA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (91 bp):
TAACAATTACTCAAATTGATTTTGGAGTCAATTAACCTGGCTGGAGCAGTTGGGAACTTGGGGAA
TCCATAGTAATTGATTTCAAAGTCTT
Found at i:30919 original size:3 final size:3
Alignment explanation
Indices: 30913--30942 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
30903 ATTATATTAT
*
30913 ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30943 TTACACCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:44474 original size:38 final size:38
Alignment explanation
Indices: 44423--44496 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
44413 TTTAGATTTG
44423 GTATAATTTTCCAGCTGAAGGCATCCCAACTATTTTTA
1 GTATAATTTTCCAGCTGAAGGCATCCCAACTATTTTTA
*
44461 GTATAATTTTCCAGCTGAAGGCATCCCAAGTATTTT
1 GTATAATTTTCCAGCTGAAGGCATCCCAACTATTTT
44497 AATATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (38 bp):
GTATAATTTTCCAGCTGAAGGCATCCCAACTATTTTTA
Found at i:52036 original size:38 final size:37
Alignment explanation
Indices: 51972--52067 Score: 147
Period size: 38 Copynumber: 2.6 Consensus size: 37
51962 AATTTGACTT
51972 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
** *
52009 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCCTTTTGTC
*
52047 TTTGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
52068 GGGCTTAGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 19 0.37
38 33 0.63
ACGTcount: A:0.14, C:0.20, G:0.11, T:0.55
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
Found at i:52153 original size:22 final size:22
Alignment explanation
Indices: 52125--52177 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
52115 TGGTCCAATT
52125 TCAAAATTTCA-AA-GTGAGGTTA
1 TCAAAATTTCATAATGTGA--TTA
*
52147 TCAAAATTACATAATGTGATTA
1 TCAAAATTTCATAATGTGATTA
52169 TCAAAATTT
1 TCAAAATTT
52178 GGACAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 21 0.78
23 2 0.07
24 4 0.15
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAATGTGATTA
Found at i:52212 original size:22 final size:22
Alignment explanation
Indices: 52184--52228 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
52174 ATTTGGACAA
*
52184 CAAAATTT-GATAGAGAGGTTAT
1 CAAAATTTCG-TAAAGAGGTTAT
52206 CAAAATTTCGTAAAGAGGTTAT
1 CAAAATTTCGTAAAGAGGTTAT
52228 C
1 C
52229 GAATTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (22 bp):
CAAAATTTCGTAAAGAGGTTAT
Found at i:52401 original size:23 final size:23
Alignment explanation
Indices: 52328--52493 Score: 80
Period size: 22 Copynumber: 7.3 Consensus size: 23
52318 TCAGGGAGGA
*
52328 TATCAAAAATTTCATATGAAGGT
1 TATCAAAAATTTCATAAGAAGGT
* *
52351 TAT-TAAAATTTCAT-AGTTTA-GT
1 TATCAAAAATTTCATAAG--AAGGT
* *
52373 TTTCAAAAATTTCATAAGAGGGT
1 TATCAAAAATTTCATAAGAAGGT
* *
52396 TATC-AAAATTTCAT-AGTATGT
1 TATCAAAAATTTCATAAGAAGGT
* * * *
52417 AAGATC-AAAATTTCATAGGGAGAT
1 --TATCAAAAATTTCATAAGAAGGT
*
52441 TAAC-AAAATTTCATAATG-AGGT
1 TATCAAAAATTTCATAA-GAAGGT
* * *
52463 TATCAAAAA-ATCATAGGGAGGT
1 TATCAAAAATTTCATAAGAAGGT
52485 TATACAAAA
1 TAT-CAAAA
52494 TTTGTAGTTA
Statistics
Matches: 108, Mismatches: 23, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
21 6 0.06
22 55 0.51
23 42 0.39
24 5 0.05
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (23 bp):
TATCAAAAATTTCATAAGAAGGT
Found at i:52427 original size:45 final size:44
Alignment explanation
Indices: 52328--52455 Score: 129
Period size: 45 Copynumber: 2.9 Consensus size: 44
52318 TCAGGGAGGA
* * *
52328 TATCAAAAATTTCATATGAAGGTTATTAAAATTTCATAGTTTAG
1 TATCAAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTTTAG
*
52372 TTTTCAAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAAG
1 -TATCAAAAATTTCATAAGAGGGTTATCAAAATTTCATAGT-T-T-AG
*
52420 -ATC-AAAATTTCAT-AG-GGAGATTAACAAAATTTCATA
1 TATCAAAAATTTCATAAGAGG-G-TTATCAAAATTTCATA
52456 ATGAGGTTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
43 2 0.03
44 3 0.04
45 61 0.85
46 3 0.04
47 1 0.01
48 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (44 bp):
TATCAAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTTTAG
Found at i:52450 original size:22 final size:22
Alignment explanation
Indices: 52378--52606 Score: 114
Period size: 22 Copynumber: 10.5 Consensus size: 22
52368 TTAGTTTTCA
* *
52378 AAAATTTCATA-AGAGGGTTATC
1 AAAATTTCATAGGGA-GGTTAAC
* * *
52400 AAAATTTCATA-GTATGTAAGATC
1 AAAATTTCATAGGGAGGTTA-A-C
*
52423 AAAATTTCATAGGGAGATTAAC
1 AAAATTTCATAGGGAGGTTAAC
** *
52445 AAAATTTCATAATGAGGTTATC
1 AAAATTTCATAGGGAGGTTAAC
**
52467 AAAAAATCATAGGGAGGTTATAC
1 AAAATTTCATAGGGAGGTTA-AC
* *
52490 AAAA-TT--T--GTA-GTTATC
1 AAAATTTCATAGGGAGGTTAAC
* * *
52506 AAGATTTCATAAGGAGGTTATC
1 AAAATTTCATAGGGAGGTTAAC
* * *
52528 AAAATTTTATAGGGAGATTTATC
1 AAAATTTCATAGGGAG-GTTAAC
* * *
52551 AAAATTTTATAGGAAGGTTTATC
1 AAAATTTCATAGGGAGG-TTAAC
* * *
52574 AAAATTCCATAGCGAGGTTATC
1 AAAATTTCATAGGGAGGTTAAC
*
52596 ACAATTTCATA
1 AAAATTTCATA
52607 ATGTGATTAT
Statistics
Matches: 160, Mismatches: 35, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.03
17 6 0.04
18 2 0.01
19 1 0.01
20 1 0.01
21 5 0.03
22 81 0.51
23 56 0.35
24 4 0.03
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (22 bp):
AAAATTTCATAGGGAGGTTAAC
Found at i:52595 original size:45 final size:45
Alignment explanation
Indices: 52499--52623 Score: 128
Period size: 45 Copynumber: 2.8 Consensus size: 45
52489 CAAAATTTGT
* ** *
52499 AGTTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAG
1 AGTTATCAAAATTTCATAAGGAGGTTATCAAAATTCCATAGCGAG
* *
52544 ATTTATCAAAATTTTAT-AGGAAGGTTTATCAAAATTCCATAGCGAG
1 AGTTATCAAAATTTCATAAGG-AGG-TTATCAAAATTCCATAGCGAG
* * * *
52590 -GTTATCACAATTTCATAATGTGATTATCAAAATT
1 AGTTATCAAAATTTCATAAGGAGGTTATCAAAATT
52624 TCAGAGTGTG
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
44 14 0.22
45 31 0.48
46 20 0.31
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (45 bp):
AGTTATCAAAATTTCATAAGGAGGTTATCAAAATTCCATAGCGAG
Found at i:52616 original size:22 final size:22
Alignment explanation
Indices: 52591--52650 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
52581 CATAGCGAGG
52591 TTATCACAATTTCATAATGTGA
1 TTATCACAATTTCATAATGTGA
* * *
52613 TTATCAAAATTTCAGAGTGTGA
1 TTATCACAATTTCATAATGTGA
*
52635 TTACTGACAA-TTCATA
1 TTA-TCACAATTTCATA
52651 TGGAGGTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (22 bp):
TTATCACAATTTCATAATGTGA
Found at i:52798 original size:21 final size:22
Alignment explanation
Indices: 52760--52807 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
52750 TTCCTTAGGG
** *
52760 AGGTTAACAAAATTTTATAAGA
1 AGGTTAACAAAAAATTATAAAA
52782 AGGTTAA-AAAAAATTATAAAA
1 AGGTTAACAAAAAATTATAAAA
52803 AGGTT
1 AGGTT
52808 CTCGAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.29
Consensus pattern (22 bp):
AGGTTAACAAAAAATTATAAAA
Found at i:52913 original size:60 final size:61
Alignment explanation
Indices: 52835--52984 Score: 230
Period size: 60 Copynumber: 2.4 Consensus size: 61
52825 TCGTTATTGA
*
52835 AATTTCACAGGAAGGTTATCAAAATTTCATAAGGACGTTATAAAAAATAGTGTAATTATCAT
1 AATTT-ACAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
*
52897 AATTT-CAGGAAGGTTATCAAAATTTTATAAGGACGTCATAAAAAATAGTGTAATTATCAT
1 AATTTACAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
* * *
52957 AATTTAATAGGAAGATTATCACAATTTC
1 AATTT-ACAGGAAGGTTATCAAAATTTC
52985 GTATGAATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
60 58 0.73
62 22 0.28
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.33
Consensus pattern (61 bp):
AATTTACAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
Found at i:53146 original size:38 final size:37
Alignment explanation
Indices: 53074--53169 Score: 129
Period size: 38 Copynumber: 2.6 Consensus size: 37
53064 AATTTGCCTT
*
53074 TTTGTTTCCAACGTCCTATTTAATTTGGCCTTTTGTC
1 TTTGTTTCCAACGTCATATTTAATTTGGCCTTTTGTC
* * *
53111 TTTGTTTCCAATCGTTATATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAA-CGTCATATTTAATTTGGCCTTTTGTC
* *
53149 TTTGTCTCCAACGTCTTATTT
1 TTTGTTTCCAACGTCATATTT
53170 GGGTTTAGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 19 0.37
38 32 0.63
ACGTcount: A:0.15, C:0.19, G:0.11, T:0.55
Consensus pattern (37 bp):
TTTGTTTCCAACGTCATATTTAATTTGGCCTTTTGTC
Found at i:53643 original size:19 final size:20
Alignment explanation
Indices: 53607--53644 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
53597 CAACAGTATT
53607 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
53627 TTTT-AATTTCAAT-TTTTA
1 TTTTGAATTT-AATATTTTA
53645 ACTGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:53838 original size:22 final size:21
Alignment explanation
Indices: 53811--53939 Score: 132
Period size: 22 Copynumber: 5.9 Consensus size: 21
53801 GTCTCTACGT
*
53811 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* *
53832 TGGTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
53855 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
53877 GGTTATCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* *
53899 AGTTTTCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* *
53921 AGTTTTCAAAATTTCATAG
1 GGTTATCAAAATTTCATAG
53940 TATCAAGTTA
Statistics
Matches: 93, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
21 3 0.03
22 86 0.92
23 4 0.04
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:53880 original size:44 final size:43
Alignment explanation
Indices: 53811--54933 Score: 213
Period size: 44 Copynumber: 25.4 Consensus size: 43
53801 GTCTCTACGT
* *
53811 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCAT-AGATGGTTATCAAAATTTCAT-ATGGA
* *
53855 GGTTATCAAAATTCCATAGTGTGGTTATCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAG-ATGGTTATCAAAATTTCATATGGA
* * * * **
53899 AGTTTTCAAAATTTCATATGGA-AGTTTTCAAAATTTCATAGTATCA
1 GGTTATCAAAATTTCATA--GATGGTTATCAAAATTTCATA-T-GGA
* * * * ** *
53945 AGTTATTAAAATTTCTTAGGTTGGTTATTGAAATTTCATA-GTGT
1 GGTTATCAAAATTTCATA-GATGGTTATCAAAATTTCATATG-GA
* *
53989 GGTTAATCATCACAATTTTATAGAAAGGTTATCAAAGTGATTATCAAAATGTCATAGCGA
1 GGTT-ATCA--A-AATTTCATAG-ATGGTTATCAAA---ATT-TC---A--T-AT-G-GA
* *
54049 GATTAT-AAGAATTTCATAGTATGGTTAACAAAATTTCAT-TAGGA
1 GGTTATCAA-AATTTCATAG-ATGGTTATCAAAATTTCATAT-GGA
* * * * *
54093 GGTTA-CTAATATTTCATGGGGA-GGTTTTCAAAATTTTATA-GTGT
1 GGTTATC-AAAATTTCAT--AGATGGTTATCAAAATTTCATATG-GA
* * *
54137 GGTTATCAAAATTTCATATGAAGGTTATAAAAGTCTCAATTTCATAAGGA
1 GGTTATCAAAATTTCATA-GATGGTTAT-CAA-----AATTTCATATGGA
* * *
54187 -G-TACCAAAATTTCATAGAAGGTTATC-AAATCTCATA--GA
1 GGTTATCAAAATTTCATAGATGGTTATCAAAATTTCATATGGA
* * *
54225 TTGATTATCGAAATTTCATGGAGATCAGATTATCAAAATTT-ATA-GGAA
1 --GGTTATCAAAATTTCAT--AGAT--GGTTATCAAAATTTCATATGG-A
* *
54273 GATTATCAAAATTTCATAG-TGTTGTTATCAAAATTTCA-AAGCGA
1 GGTTATCAAAATTTCATAGATG--GTTATCAAAATTTCATATG-GA
* *
54317 GATTATCAAAATTACATA-ATGTGATTATCAAAATTTCATA--GA
1 GGTTATCAAAATTTCATAGATG-G-TTATCAAAATTTCATATGGA
** * *
54359 GG-GGTCAACAATTT-ATAAAGA-GGTTATCAAATTTTCAAAATGTGA
1 GGTTATCAA-AATTTCAT--AGATGGTTATCAAAATTTC-ATATG-GA
* *
54404 --TTA-CAAAAATTTCATAG-TGGTATTTACCAAA--T--TA-GGAA
1 GGTTATC-AAAATTTCATAGATGGT-TAT-CAAAATTTCATATGG-A
* * * * *
54442 GGTTATTAAACTTTTATTACG--GAGTAATCTAAATTTCA-AT-GA
1 GGTTATCAAAATTTCA-TA-GATG-GTTATCAAAATTTCATATGGA
* ** * * *
54484 GGATATCAAAATTTCAGGGA-GGATATCACAATTTCATA-AGA
1 GGTTATCAAAATTTCATAGATGGTTATCAAAATTTCATATGGA
* * *
54525 GGGTTATCAAAATTTCATA-ATATGTAGATCAAAATTTCATAGGGA
1 -GGTTATCAAAATTTCATAGAT-GGT-TATCAAAATTTCATATGGA
* ** *
54570 GGTTAAC-AAATTTCATA-ATAAGGTTATCAAAAAATCATAGGGA
1 GGTTATCAAAATTTCATAGAT--GGTTATCAAAATTTCATATGGA
* * * *
54613 GGTTATCAAAATTT--T---TAGTTATCAAGATTTCATAAGAA
1 GGTTATCAAAATTTCATAGATGGTTATCAAAATTTCATATGGA
* * *
54651 AGTTATCAAAATTTTATAGGGA-GGTTTATCAAAATTTTATA-GGAA
1 GGTTATCAAAATTTCATA--GATGG-TTATCAAAATTTCATATGG-A
* *
54696 GATTTATCAAAATTTCATAGCGA-GGTTATCACAAA-CTCATAGTGTGA
1 G-GTTATCAAAATTTCATA--GATGGTTATCA-AAATTTCATA-TG-GA
*
54743 --TTATCAAAATTTCAGAG-TGTGATTA-CTAACAA-TTCATATGGA
1 GGTTATCAAAATTTCATAGATG-G-TTATC-AA-AATTTCATATGGA
* * * ** * *
54785 GGTTTTTAAATTTTTGTA-ACGTGGTTATCAATATATCATATGGA
1 GGTTATCAAAATTTCATAGA--TGGTTATCAAAATTTCATATGGA
* *
54829 GGTTATCAACATCTCATAG-TGTTGCTTATCAAAATTTCAT-TGGGA
1 GGTTATCAAAATTTCATAGATG--G-TTATCAAAATTTCATAT-GGA
* * * * * *
54874 AGTCATCAAAATTTCATATTGA-GGTTTTTAAAATTTCTTAGGGA
1 GGTTATCAAAATTTCATA--GATGGTTATCAAAATTTCATATGGA
*
54918 GGTTAACAAAATTTCA
1 GGTTATCAAAATTTCA
54934 CAAGAAGGTT
Statistics
Matches: 795, Mismatches: 153, Indels: 262
0.66 0.13 0.22
Matches are distributed among these distances:
37 1 0.00
38 33 0.04
39 1 0.00
40 36 0.05
41 28 0.04
42 67 0.08
43 75 0.09
44 286 0.36
45 80 0.10
46 82 0.10
47 22 0.03
48 31 0.04
49 2 0.00
50 9 0.01
51 4 0.01
52 4 0.01
53 3 0.00
55 1 0.00
56 20 0.03
57 1 0.00
58 2 0.00
59 2 0.00
60 5 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGATGGTTATCAAAATTTCATATGGA
Found at i:53915 original size:66 final size:66
Alignment explanation
Indices: 53809--53940 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 66
53799 TTGTCTCTAC
* * *
53809 GTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGA-GGAGGTTATCAAAATTCCATA
1 GTGGTTATCAAAATTTCATAAGATAGTTATTAAAATTTCAT-ATGGAAGTTATCAAAATTCCATA
53873 GT
65 GT
* * *
53875 GTGGTTATCAAAATTTCATATGGA-AGTT-TTCAAAATTTCATATGGAAGTTTTCAAAATTTCAT
1 GTGGTTATCAAAATTTCATA-AGATAGTTATT-AAAATTTCATATGGAAGTTATCAAAATTCCAT
53938 AGT
64 AGT
53941 ATCAAGTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
65 3 0.05
66 52 0.91
67 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (66 bp):
GTGGTTATCAAAATTTCATAAGATAGTTATTAAAATTTCATATGGAAGTTATCAAAATTCCATAG
T
Found at i:53991 original size:22 final size:22
Alignment explanation
Indices: 53810--53993 Score: 87
Period size: 22 Copynumber: 8.3 Consensus size: 22
53800 TGTCTCTACG
* * *
53810 TGGTTATCAAAATTTCATAAGA
1 TGGTTATTAAAATTTCATAGGT
*
53832 TGGTTATTATAATTTCATGAGG-
1 TGGTTATTAAAATTTCAT-AGGT
* * *
53854 AGGTTATCAAAATTCCATA-GT
1 TGGTTATTAAAATTTCATAGGT
*
53875 GTGGTTATCAAAATTTCATATGG-
1 -TGGTTATTAAAATTTCATA-GGT
**
53898 AAGTT-TTCAAAATTTCATATGG-
1 TGGTTATT-AAAATTTCATA-GGT
**
53920 AAGTT-TTCAAAATTTCATA-GT
1 TGGTTATT-AAAATTTCATAGGT
* *
53941 ATCAAGTTATTAAAATTTCTTAGGT
1 -T--GGTTATTAAAATTTCATAGGT
*
53966 TGGTTATTGAAATTTCATA-GT
1 TGGTTATTAAAATTTCATAGGT
53987 GTGGTTA
1 -TGGTTA
53994 ATCATCACAA
Statistics
Matches: 132, Mismatches: 17, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
20 2 0.02
21 4 0.03
22 104 0.79
23 2 0.02
24 16 0.12
25 4 0.03
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGT
Found at i:54164 original size:22 final size:22
Alignment explanation
Indices: 54058--54356 Score: 86
Period size: 22 Copynumber: 13.4 Consensus size: 22
54048 AGATTATAAG
* *
54058 AATTTCATA-GTATGGTTAACAA
1 AATTTCATATG-AAGGTTATCAA
*
54080 AATTTCAT-TAGGAGGTTA-CTAA
1 AATTTCATAT-GAAGGTTATC-AA
* ** * *
54102 TATTTCATGGGGAGGTTTTCAA
1 AATTTCATATGAAGGTTATCAA
* *
54124 AATTTTATAGTG-TGGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
54146 AATTTCATATGAAGGTTAT-AA
1 AATTTCATATGAAGGTTATCAA
* * *
54167 AAGTCTCAATTTCAT-AAGGAGTACCAA
1 AA-TTTC-A--T-ATGAAGG-TTATCAA
54194 AATTTCATA-GAAGGTTATC-A
1 AATTTCATATGAAGGTTATCAA
* * * *
54214 AATCTCATA-GATTGATTATCGA
1 AATTTCATATGA-AGGTTATCAA
*
54236 AATTTCATGGA-GATCAGATTATCAA
1 AATTTCAT--ATGA--AGGTTATCAA
* *
54261 AATTT-ATAGGAAGATTATCAA
1 AATTTCATATGAAGGTTATCAA
**
54282 AATTTCATAGTG-TTGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
* * *
54304 AATTTCA-AAGCGAGATTATCAA
1 AATTTCATATG-AAGGTTATCAA
* * *
54326 AATTACATAATG-TGATTATCAA
1 AATTTCAT-ATGAAGGTTATCAA
54348 AATTTCATA
1 AATTTCATA
54357 GAGGGGTCAA
Statistics
Matches: 212, Mismatches: 38, Indels: 55
0.70 0.12 0.18
Matches are distributed among these distances:
20 12 0.06
21 33 0.16
22 122 0.58
23 8 0.04
24 7 0.03
25 19 0.09
26 7 0.03
27 4 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:54263 original size:25 final size:22
Alignment explanation
Indices: 54191--54357 Score: 123
Period size: 22 Copynumber: 7.6 Consensus size: 22
54181 TAAGGAGTAC
*
54191 CAAAATTTCATA-GAAGGTTAT
1 CAAAATTTCATAGGAAGATTAT
* *
54212 C-AAATCTCATA-GATTGATTAT
1 CAAAATTTCATAGGA-AGATTAT
* *
54233 CGAAATTTCATGGAGATCAGATTAT
1 CAAAATTTCATAG-GA--AGATTAT
54258 CAAAATTT-ATAGGAAGATTAT
1 CAAAATTTCATAGGAAGATTAT
**
54279 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAG-GAAGATTAT
*
54301 CAAAATTTCAAAGCG-AGATTAT
1 CAAAATTTCATAG-GAAGATTAT
* * *
54323 CAAAATTACATAATG-TGATTAT
1 CAAAATTTCAT-AGGAAGATTAT
54345 CAAAATTTCATAG
1 CAAAATTTCATAG
54358 AGGGGTCAAC
Statistics
Matches: 117, Mismatches: 20, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
20 11 0.09
21 24 0.21
22 59 0.50
23 5 0.04
24 5 0.04
25 13 0.11
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGATTAT
Found at i:54497 original size:20 final size:20
Alignment explanation
Indices: 54472--54541 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
54462 GGAGTAATCT
*
54472 AAATTTCAATGAGGATATCA
1 AAATTTCAAAGAGGATATCA
**
54492 AAATTTCAGGGAGGATATCA
1 AAATTTCAAAGAGGATATCA
* *
54512 CAATTTCATAAGAGGGTTATCA
1 AAATTTCA-AAGA-GGATATCA
54534 AAATTTCA
1 AAATTTCA
54542 TAATATGTAG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 25 0.61
21 2 0.05
22 14 0.34
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (20 bp):
AAATTTCAAAGAGGATATCA
Found at i:54538 original size:22 final size:22
Alignment explanation
Indices: 54507--54756 Score: 103
Period size: 22 Copynumber: 11.6 Consensus size: 22
54497 TCAGGGAGGA
*
54507 TATCACAATTTCATAAGAGGGT
1 TATCAAAATTTCATAAGAGGGT
* *
54529 TATCAAAATTTCATAATA-TGT
1 TATCAAAATTTCATAAGAGGGT
* *
54550 AGATCAAAATTTCAT-AGGGAGGT
1 -TATCAAAATTTCATAAGAG-GGT
* * *
54573 TAAC-AAATTTCATAATAAGGT
1 TATCAAAATTTCATAAGAGGGT
** *
54594 TATCAAAAAATCAT-AGGGAGGT
1 TATCAAAATTTCATAAGAG-GGT
*
54616 TATCAAAATTT--T--TA--GT
1 TATCAAAATTTCATAAGAGGGT
* **
54632 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATAAGAGGGT
* * *
54654 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATA-AGAGGGT
* * **
54677 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAAG-AGGGT
*
54700 TATCAAAATTTCAT-AGCGAGGT
1 TATCAAAATTTCATAAGAG-GGT
* * *
54722 TATCACAAA-CTCAT-AGTGTGAT
1 TATCA-AAATTTCATAAGAG-GGT
54744 TATCAAAATTTCA
1 TATCAAAATTTCA
54757 GAGTGTGATT
Statistics
Matches: 170, Mismatches: 41, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
16 12 0.07
18 1 0.01
20 2 0.01
21 23 0.14
22 92 0.54
23 40 0.24
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
TATCAAAATTTCATAAGAGGGT
Found at i:54582 original size:21 final size:21
Alignment explanation
Indices: 54482--54933 Score: 98
Period size: 22 Copynumber: 20.8 Consensus size: 21
54472 AAATTTCAAT
*
54482 GAGGATATCAAAATTTC--AGG
1 GAGGTTATC-AAATTTCATAGG
* *
54502 GAGGATATCACAATTTCATA-A
1 GAGGTTATCA-AATTTCATAGG
*
54523 GAGGGTTATCAAAATTTCATA-A
1 GA-GGTTATC-AAATTTCATAGG
* * *
54545 TATGTAGATCAAAATTTCATAGG
1 GAGGT-TATC-AAATTTCATAGG
* **
54568 GAGGTTAACAAATTTCATAAT
1 GAGGTTATCAAATTTCATAGG
* **
54589 AAGGTTATCAAAAAATCATAGG
1 GAGGTTATC-AAATTTCATAGG
54611 GAGGTTATCAAAATTT--T---
1 GAGGTTATC-AAATTTCATAGG
* *
54628 TA-GTTATCAAGATTTCATAAG
1 GAGGTTATCAA-ATTTCATAGG
* * *
54649 AAAGTTATCAAAATTTTATAGG
1 GAGGTTATC-AAATTTCATAGG
*
54671 GAGGTTTATCAAAATTTTATAGG
1 GAGG-TTATC-AAATTTCATAGG
* * *
54694 AAGATTTATCAAAATTTCATAGC
1 GAG-GTTATC-AAATTTCATAGG
** *
54717 GAGGTTATCACAAACTCATAGT
1 GAGGTTATCA-AATTTCATAGG
* * * *
54739 GTGATTATCAAAATTTCAGAGT
1 GAGGTTATC-AAATTTCATAGG
* * * *
54761 GTGATTA-CTAACAATTCATATG
1 GAGGTTATC-AA-ATTTCATAGG
* * ** **
54783 GAGGTTTTTAAATTTTTGTAAC
1 GAGGTTATCAAA-TTTCATAGG
* * *
54805 GTGGTTATCAATATATCATATG
1 GAGGTTATCAA-ATTTCATAGG
*
54827 GAGGTTATCAACATCTCATAGTG
1 GAGGTTATCAA-ATTTCATAG-G
** * *
54850 TTGCTTATCAAAATTTCATTGG
1 GAGGTTATC-AAATTTCATAGG
* * **
54872 GAAGTCATCAAAATTTCATATT
1 GAGGTTATC-AAATTTCATAGG
* * *
54894 GAGGTTTTTAAAATTTCTTAGG
1 GAGG-TTATCAAATTTCATAGG
*
54916 GAGGTTAACAAAATTTCA
1 GAGGTTATC-AAATTTCA
54934 CAAGAAGGTT
Statistics
Matches: 313, Mismatches: 91, Indels: 54
0.68 0.20 0.12
Matches are distributed among these distances:
15 2 0.01
16 10 0.03
17 1 0.00
18 1 0.00
19 1 0.00
20 16 0.05
21 29 0.09
22 189 0.60
23 62 0.20
24 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (21 bp):
GAGGTTATCAAATTTCATAGG
Found at i:54608 original size:65 final size:64
Alignment explanation
Indices: 54488--54608 Score: 163
Period size: 65 Copynumber: 1.9 Consensus size: 64
54478 CAATGAGGAT
* * **
54488 ATCAAAATTTCAGGGAGGATATCACAATTTCATAAGAGGGTTATCAAAATTTCATAATATGTAG
1 ATCAAAATTTCAGGGAGGATAACACAATTTCATAAGAAGGTTATCAAAAAATCATAATATGTAG
* *
54552 ATCAAAATTTCATAGGGAGGTTAACA-AATTTCATAATAAGGTTATCAAAAAATCATA
1 ATCAAAATTTC--AGGGAGGATAACACAATTTCATAAGAAGGTTATCAAAAAATCATA
54609 GGGAGGTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
64 11 0.22
65 27 0.55
66 11 0.22
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (64 bp):
ATCAAAATTTCAGGGAGGATAACACAATTTCATAAGAAGGTTATCAAAAAATCATAATATGTAG
Found at i:54670 original size:60 final size:60
Alignment explanation
Indices: 54571--54688 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
54561 TCATAGGGAG
* *
54571 GTTAACAAATTTCATAATAAGGTTATCAAAAAATCATAGGGAGG-TTATCAAAATTTTTA
1 GTTAACAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAATTTTTA
* ** *
54630 GTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTT
1 GTTAACAA-ATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAATTTT
54689 ATAGGAAGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 7 0.14
60 31 0.61
61 13 0.25
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (60 bp):
GTTAACAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAATTTTTA
Found at i:54683 original size:23 final size:23
Alignment explanation
Indices: 54653--54726 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
54643 CATAAGAAAG
54653 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
54676 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
54699 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
54721 TTATCA
1 TTATCA
54727 CAAACTCATA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
22 6 0.13
23 39 0.87
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:54725 original size:45 final size:44
Alignment explanation
Indices: 54487--54726 Score: 131
Period size: 43 Copynumber: 5.6 Consensus size: 44
54477 TCAATGAGGA
* * * **
54487 TATCAAAATTTC--AGGGAGGATATCACAATTTCATAAGAGGGT
1 TATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAAAGT
** * * * * *
54529 TATCAAAATTTCATA-ATATGTAGATCAAAATTTCATAGGGAGGT
1 TATCAAAATTTCATAGCGAGGT-TATCAAAATTTCATAAGAAAGT
* *** ** * * *
54573 TAAC-AAATTTCATAATAAGGTTATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAAAGT
* *
54616 TATCAAAATTT--T---TA-GTTATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAAAGT
* * * * *
54654 TATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGCGAGG-TTATCAAAATTTCATAAGAA-AGT
54700 TATCAAAATTTCATAGCGAGGTTATCA
1 TATCAAAATTTCATAGCGAGGTTATCA
54727 CAAACTCATA
Statistics
Matches: 154, Mismatches: 31, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
38 29 0.19
39 1 0.01
40 1 0.01
42 13 0.08
43 35 0.23
44 31 0.20
45 23 0.15
46 21 0.14
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (44 bp):
TATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAAAGT
Found at i:54761 original size:22 final size:22
Alignment explanation
Indices: 54653--54767 Score: 81
Period size: 23 Copynumber: 5.1 Consensus size: 22
54643 CATAAGAAAG
* * * *
54653 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGTG-TGA
* *
54676 TTATCAAAATTTTATAG-GAAGA
1 TTATCAAAATTTCATAGTG-TGA
* * *
54698 TTTATCAAAATTTCATAGCGAGG
1 -TTATCAAAATTTCATAGTGTGA
*
54721 TTATCACAAA-CTCATAGTGTGA
1 TTATCA-AAATTTCATAGTGTGA
*
54743 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
54765 TTA
1 TTA
54768 CTAACAATTC
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
21 3 0.04
22 36 0.46
23 38 0.49
24 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:60350 original size:20 final size:19
Alignment explanation
Indices: 60325--60362 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
60315 CTAAATAATA
60325 TTTTAATTATTCCATTATTT
1 TTTTAATTATTCC-TTATTT
60345 TTTTAATTATTCCTTATT
1 TTTTAATTATTCCTTATT
60363 AAATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTAATTATTCCTTATTT
Found at i:60457 original size:22 final size:22
Alignment explanation
Indices: 60429--60534 Score: 92
Period size: 22 Copynumber: 4.7 Consensus size: 22
60419 TGTCTCTATG
60429 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
60451 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
60474 -GGTTATCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
* *
60493 TGTGATTACCAAAATTTCATAGGA
1 TG-G-TTATCAAAATTTCATAAGA
*
60517 TCAGGTTATTAAAATTTC
1 T--GGTTATCAAAATTTC
60535 TTACGTTGGT
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
20 2 0.03
21 1 0.02
22 45 0.68
23 4 0.06
24 12 0.18
25 1 0.02
26 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:60509 original size:44 final size:44
Alignment explanation
Indices: 60430--60534 Score: 108
Period size: 44 Copynumber: 2.3 Consensus size: 44
60420 GTCTCTATGT
** *
60430 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-A
1 GGTTATCAAAATTTCATAAGATGGTTACCAAAATTTCAT-AGGAA
60474 GGTTATCAAAATTTCAT-AG-TGTGATTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAAGATG-G-TTACCAAAATTTCATAGGA--A
*
60520 GGTTATTAAAATTTC
1 GGTTATCAAAATTTC
60535 TTACGTTGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
42 2 0.04
43 6 0.12
44 29 0.56
46 15 0.29
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAAGATGGTTACCAAAATTTCATAGGAA
Found at i:60628 original size:22 final size:21
Alignment explanation
Indices: 60600--60729 Score: 84
Period size: 22 Copynumber: 6.0 Consensus size: 21
60590 TGTTATCAAA
*
60600 GAGGTTATCAAAATGTCATAG
1 GAGGTTATCAAAATTTCATAG
*
60621 CGAGGTTAT-AAGAATTTCATAAT
1 -GAGGTTATCAA-AATTTCAT-AG
* *
60644 GTGGTTAACAAAATTTCATTAG
1 GAGGTTATCAAAATTTCA-TAG
* *
60666 GAGGTTA-CTAATATTTCATGGG
1 GAGGTTATC-AAAATTTCAT-AG
* * *
60688 GATGTTATTAAAATTTTATAG
1 GAGGTTATCAAAATTTCATAG
* *
60709 TGTGGTTATCAAATTTTCATA
1 -GAGGTTATCAAAATTTCATA
60730 TGAAAGTTAT
Statistics
Matches: 82, Mismatches: 18, Indels: 16
0.71 0.16 0.14
Matches are distributed among these distances:
21 5 0.06
22 73 0.89
23 4 0.05
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (21 bp):
GAGGTTATCAAAATTTCATAG
Found at i:61078 original size:22 final size:22
Alignment explanation
Indices: 61052--61235 Score: 94
Period size: 22 Copynumber: 8.3 Consensus size: 22
61042 TTATCCAATC
*
61052 TCATAGAGTGATTATCGAAATT
1 TCATAGAGTGATTATCAAAATT
61074 TCATAGAGATCGGATTATCAAAATT
1 TCATAGAG-T--GATTATCAAAATT
*
61099 TCATAGCATTG-TTATCAAAATT
1 TCATAG-AGTGATTATCAAAATT
* *
61121 TCAAAGCGATG-TTA-CAAAATT
1 TCATAGAG-TGATTATCAAAATT
*
61142 ACATA-ATGTGATTAT-AAGAATT
1 TCATAGA-GTGATTATCAA-AATT
* * * * *
61164 TCATAAAGGGGTCAACAAAATT
1 TCATAGAGTGATTATCAAAATT
* * * * *
61186 TTATAAAGAGGTTATCAAATTT
1 TCATAGAGTGATTATCAAAATT
*
61208 TCA-AAATGTGATTA-CAAAAATT
1 TCATAGA-GTGATTATC-AAAATT
61230 TCATAG
1 TCATAG
61236 TGGTATTTCT
Statistics
Matches: 125, Mismatches: 23, Indels: 27
0.71 0.13 0.15
Matches are distributed among these distances:
20 2 0.02
21 20 0.16
22 77 0.62
23 6 0.05
25 19 0.15
26 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
TCATAGAGTGATTATCAAAATT
Found at i:61303 original size:22 final size:22
Alignment explanation
Indices: 61240--61659 Score: 108
Period size: 22 Copynumber: 19.4 Consensus size: 22
61230 TCATAGTGGT
*
61240 ATTTC-TACGGAGGTTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
* * * *
61261 ATGTCAT-AGTATGTAGATCAAA
1 ATTTCATAAGGAGGT-TATCAAA
* *
61283 ATTTCATAATGAGGTTGTCAAGA
1 ATTTCATAAGGAGGTTATCAA-A
* *
61306 A-ATCATAGGGAGGTTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
* *
61327 A-TT--T--GTA-GTTATCAAC
1 ATTTCATAAGGAGGTTATCAAA
* *
61343 ATTTCATAAGAAAGTTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
* *
61365 ATTTTATAGGGAGGTTTATCAAA
1 ATTTCATAAGGAGG-TTATCAAA
61388 ATTTCA-AAGTGTA--TTA-CTAACA
1 ATTTCATAAG-G-AGGTTATC-AA-A
* * *
61410 A-TTCATATGGAGGTTTTTAAA
1 ATTTCATAAGGAGGTTATCAAA
* * * * *
61431 TTTTCATAACGTGGTTGTCAAT
1 ATTTCATAAGGAGGTTATCAAA
* * *
61453 ATATCATATGGAGGTTATCAAC
1 ATTTCATAAGGAGGTTATCAAA
* *
61475 ATCTCAT-AGTGTTGGTTATCAAA
1 ATTTCATAAG-G-AGGTTATCAAA
*
61498 ATTTCAT-TGGTTA-GTTATCAAA
1 ATTTCATAAGG--AGGTTATCAAA
* *** *
61520 ATTTTATGTTGA-GATATTCAAA
1 ATTTCATAAGGAGGTTA-TCAAA
* * * *
61542 ATTCCTTAGGGAGGTTAACAAA
1 ATTTCATAAGGAGGTTATCAAA
* **
61564 ATTTCATAAGAAGGTTAAAAAA
1 ATTTCATAAGGAGGTTATCAAA
** * *
61586 ATTT-ATAAAAAGGTTCTCGAA
1 ATTTCATAAGGAGGTTATCAAA
* * * * *
61607 ATTCCAT-AGTATCGTTGTTAAA
1 ATTTCATAAGGA-GGTTATCAAA
*
61629 ATTTCAT-AGGAAGATTATCAAA
1 ATTTCATAAGG-AGGTTATCAAA
61651 ATTTCATAA
1 ATTTCATAA
61660 TGGGATCATA
Statistics
Matches: 285, Mismatches: 84, Indels: 58
0.67 0.20 0.14
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
20 2 0.01
21 46 0.16
22 177 0.62
23 44 0.15
24 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATTTCATAAGGAGGTTATCAAA
Found at i:61495 original size:23 final size:22
Alignment explanation
Indices: 61465--61521 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
61455 ATCATATGGA
*
61465 GGTTATCAACATCTCATAGTGTT
1 GGTTATCAAAATCTCATAG-GTT
* *
61488 GGTTATCAAAATTTCATTGGTT
1 GGTTATCAAAATCTCATAGGTT
*
61510 AGTTATCAAAAT
1 GGTTATCAAAAT
61522 TTTATGTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (22 bp):
GGTTATCAAAATCTCATAGGTT
Found at i:61786 original size:2 final size:2
Alignment explanation
Indices: 61779--61803 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61769 CTAAAACTAG
61779 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
61804 TTGACAGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62293 original size:28 final size:28
Alignment explanation
Indices: 62253--62310 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
62243 ATCATGACCA
62253 GAAGAAACAATATCCAAATTTCTTGAAG
1 GAAGAAACAATATCCAAATTTCTTGAAG
62281 GAAGAAACAATATCCAAATTTCTTGAAG
1 GAAGAAACAATATCCAAATTTCTTGAAG
62309 GA
1 GA
62311 TTCATGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.24
Consensus pattern (28 bp):
GAAGAAACAATATCCAAATTTCTTGAAG
Found at i:62861 original size:22 final size:22
Alignment explanation
Indices: 62833--62879 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
62823 GAGTAATAAT
62833 ATTAGAAAGTATAAGATTGAAA
1 ATTAGAAAGTATAAGATTGAAA
62855 ATTAGAAAGTATAAGATTGAAA
1 ATTAGAAAGTATAAGATTGAAA
62877 ATT
1 ATT
62880 CCAAGATCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (22 bp):
ATTAGAAAGTATAAGATTGAAA
Found at i:63938 original size:12 final size:12
Alignment explanation
Indices: 63921--63956 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
63911 AAGAACATCA
*
63921 AAGGATTCCCAC
1 AAGGATTTCCAC
63933 AAGGATTTCCAC
1 AAGGATTTCCAC
63945 AAGGATTTCCAC
1 AAGGATTTCCAC
63957 CTACTTGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (12 bp):
AAGGATTTCCAC
Found at i:64069 original size:9 final size:9
Alignment explanation
Indices: 64052--64082 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
64042 CACTAATTCT
64052 ATCACCATA
1 ATCACCATA
*
64061 ATTACCATA
1 ATCACCATA
64070 ATCACCATA
1 ATCACCATA
64079 ATCA
1 ATCA
64083 TCGTCCTGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (9 bp):
ATCACCATA
Found at i:65800 original size:2 final size:2
Alignment explanation
Indices: 65793--65818 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65783 AATCAAGGTA
65793 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
65819 CTTTATACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67247 original size:27 final size:26
Alignment explanation
Indices: 67201--67251 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
67191 CTAATTCACT
* * *
67201 ATTAAAATTTAAATATTAAAATAAAAA
1 ATTAAAAATTAAACAAT-AAATAAAAA
67228 ATTAAAAATTAAACAATAAATAAA
1 ATTAAAAATTAAACAATAAATAAA
67252 GATTATTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (26 bp):
ATTAAAAATTAAACAATAAATAAAAA
Found at i:71742 original size:439 final size:439
Alignment explanation
Indices: 70841--71846 Score: 1260
Period size: 439 Copynumber: 2.3 Consensus size: 439
70831 GTTGGCTTTT
* *
70841 ATTTTTGTATT-TTTTTTCTTCTATTTGTCTGATTAAGGTGATTCAAGTGTCTATTAAAA-GTAA
1 ATTTTTGT-TTATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAA
* * * *
70904 TTTCATGATCTACAATTTTCATGAAGAACTCAAAAGCCAATTTTAATGTTTTGATTCTAAAAAAT
65 TTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAAAT
* ** * * * *
70969 GCTTCTGAAATTTTGTGGTTTTGATTATCAGTCAATTTAATTTCGTATAATTTTTTGTCCACATG
130 GCTTCTGAAATTTGGTCATTTCGATTATCAGTCAATTTAATATCATATAATTTTTCGTCCACATG
* * * * * *
71034 TCCGATTGAAGTCATTGAAGTGTCAGTTAAAATGTTATTGCATGATTTACGACTTTCATGAAGGA
195 TCCGATTAAAGTCATTCAAGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAA
* * *
71099 TCAGAAAGCTAAATTTGATCTGCGAGTTTCATGAAGAGTTCAAAAGAGAATTTTTATGCTTCGAG
260 CCAGAAAGCTAAATTTGATCTACGAGTTTCATGAAGAGTTCAAAAGAGAATTTTTATGCTTCAAG
* * * *
71164 ATCTCCATTAACAAACATTTTCTTATTTGAATTATTTATCAAATGACCATAATATTTTTCTACTT
325 ATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCATAATACTTTTCAACTT
* *
71229 TATACTACTTAGTCCTTTACAAATTCTATCTTAATCTAACGTTTAAGATTT
390 TATACTACTTAGTCATTTACAAATTCTATCTTAATCT-ACGTTTAAGATTC
* * *
71280 ATTTTTTTTTA-TTTTTTTTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAAT
1 ATTTTTGTTTATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAAT
* * *
71344 TTCATGATCTACAACTTTCATGAAGGTCTCAAAAGCAAATTTTTATGTTTTAATTCAAAAAAATG
66 TTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAAATG
* * *
71409 CTTCCT-AAATTTGGTCATTTCGATTGGT-GGTCTATTTAATATCATATAA-TTTTCGATCCACA
131 CTT-CTGAAATTTGGTCATTTCGATT-ATCAGTCAATTTAATATCATATAATTTTTCG-TCCACA
* * * *
71471 TTTCCGATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGTATGATCTACGACTTTCATGAAG
193 TGTCCGATTAAAGTCATTCAAGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAG
* * * * **
71536 AACCATAAAG-TTAATTTGATCTACGAGTTTCA-GAAGGGTTTAAAAGAGAATTTTTATTTTTCA
258 AACCAGAAAGCTAAATTTGATCTACGAGTTTCATGAAGAGTTCAAAAGAGAATTTTTATGCTTCA
* * * * *
71599 AGATATCCATTAAGAAATATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCAAT
323 AGATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCATAATACTTTTCAAC
* *
71664 TTTATGCTACTTAGTCATTTACAAATTCTATCTT-AT-T-CGATTTAACGCTTC
388 TTTATACTACTTAGTCATTTACAAATTCTATCTTAATCTACG-TTTAA-GATTC
* * ** *
71715 ATTTCTTGTTTATTTTCTTTGTTCTATTTGTCCAATTAAGGTAATTCGGGTGTTTATTAAAAGGT
1 ATTT-TTGTTTATTTT-TTT-TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGT
* * * * * *
71780 AATTTTATGATCTACAACTTTCATTAAAGACTCAAAAGCTAATTTTCATGTTTCAATTCTAAAAA
63 AATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAA
71845 AT
128 AT
71847 ACTTTTGTTA
Statistics
Matches: 487, Mismatches: 69, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
433 2 0.00
434 5 0.01
435 8 0.02
436 8 0.02
437 117 0.24
438 73 0.15
439 271 0.56
440 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (439 bp):
ATTTTTGTTTATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAAT
TTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAAATG
CTTCTGAAATTTGGTCATTTCGATTATCAGTCAATTTAATATCATATAATTTTTCGTCCACATGT
CCGATTAAAGTCATTCAAGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAAC
CAGAAAGCTAAATTTGATCTACGAGTTTCATGAAGAGTTCAAAAGAGAATTTTTATGCTTCAAGA
TATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCATAATACTTTTCAACTTT
ATACTACTTAGTCATTTACAAATTCTATCTTAATCTACGTTTAAGATTC
Done.