Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 176 of 193
Found at i:54879497 original size:17 final size:17
Alignment explanation
Indices: 54879460--54879507 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
54879450 ATATATTTTT
*
54879460 TTTTGA-ATTTTTATTAC
1 TTTTGATATTTTT-TTAA
*
54879477 TTTTTATATTTTTTTAA
1 TTTTGATATTTTTTTAA
*
54879494 TTTTGGTATTTTTT
1 TTTTGATATTTTTT
54879508 GTTTTTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (17 bp):
TTTTGATATTTTTTTAA
Found at i:54879532 original size:24 final size:24
Alignment explanation
Indices: 54879485--54879534 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
54879475 ACTTTTTATA
* * *
54879485 TTTTTTTAATTTTGGTATTTTTTG
1 TTTTTATAATTTTGGAATTATTTG
*
54879509 TTTTTATAATTTTTGAATTATTTG
1 TTTTTATAATTTTGGAATTATTTG
54879533 TT
1 TT
54879535 GATATGAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (24 bp):
TTTTTATAATTTTGGAATTATTTG
Found at i:54880080 original size:21 final size:21
Alignment explanation
Indices: 54880046--54880085 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54880036 AATTTTTTTG
* * *
54880046 GAATCGAGTGAAATGAAATTC
1 GAATCGAATCAAATCAAATTC
54880067 GAATCGAATCAAATCAAAT
1 GAATCGAATCAAATCAAAT
54880086 ATTTTTATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.23
Consensus pattern (21 bp):
GAATCGAATCAAATCAAATTC
Found at i:54883322 original size:2 final size:2
Alignment explanation
Indices: 54883315--54883342 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54883305 CCCTAAACTT
54883315 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
54883343 GGGGAATTAC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54890260 original size:6 final size:6
Alignment explanation
Indices: 54890246--54890302 Score: 98
Period size: 6 Copynumber: 9.7 Consensus size: 6
54890236 AAAGAAAGTT
*
54890246 GAAGAA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
54890294 G-AGGA GAAG
1 GAAGGA GAAG
54890303 AGGAGTTTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
5 5 0.10
6 44 0.90
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:54890975 original size:3 final size:3
Alignment explanation
Indices: 54890967--54890995 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54890957 CTGCCTCATC
54890967 CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
54890996 ATCACTATTT
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:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (3 bp):
CTG
Found at i:54891347 original size:12 final size:12
Alignment explanation
Indices: 54891308--54891348 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
54891298 CTTCTCATCT
*
54891308 TCATCCTCAACA
1 TCATCATCAACA
*
54891320 TCAACATCAACA
1 TCATCATCAACA
*
54891332 TCATCATCATCA
1 TCATCATCAACA
54891344 TCATC
1 TCATC
54891349 CTAATTCTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (12 bp):
TCATCATCAACA
Found at i:54892225 original size:2 final size:2
Alignment explanation
Indices: 54892218--54892280 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
54892208 GTGATAACCC
54892218 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
54892260 CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C
54892281 CTTTGTCTTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:54896865 original size:48 final size:48
Alignment explanation
Indices: 54896794--54896893 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
54896784 TTTATCCGTG
54896794 TGAAGCTTGGGGTGTAGATGAACAGGTGACTTTTGTTCTTGCTGCTAT
1 TGAAGCTTGGGGTGTAGATGAACAGGTGACTTTTGTTCTTGCTGCTAT
54896842 TGAAGCTTGGGGTGTAGATGAACAGGTGACTTTTGTTCTTGCTGCTAT
1 TGAAGCTTGGGGTGTAGATGAACAGGTGACTTTTGTTCTTGCTGCTAT
54896890 TGAA
1 TGAA
54896894 TAAGCAGTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.20, C:0.12, G:0.31, T:0.37
Consensus pattern (48 bp):
TGAAGCTTGGGGTGTAGATGAACAGGTGACTTTTGTTCTTGCTGCTAT
Found at i:54897202 original size:7 final size:8
Alignment explanation
Indices: 54897186--54897211 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
54897176 TTTGTTGTCA
54897186 TTTTGTTT
1 TTTTGTTT
54897194 TTTTGTTT
1 TTTTGTTT
54897202 TTTTGTTT
1 TTTTGTTT
54897210 TT
1 TT
54897212 CCCTTGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTGTTT
Found at i:54899173 original size:16 final size:16
Alignment explanation
Indices: 54899131--54899173 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
54899121 AAATTCAAAC
*
54899131 ATTTTATTGAAATAAT
1 ATTTTATTTAAATAAT
*
54899147 ATTTTAATTAAGATAAT
1 ATTTTATTTAA-ATAAT
54899164 -TTTTATTTAA
1 ATTTTATTTAA
54899174 CAAATTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTTTATTTAAATAAT
Found at i:54911141 original size:14 final size:16
Alignment explanation
Indices: 54911107--54911146 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
54911097 AAAAGCAGCT
54911107 GAAGAAGAAATACAAG
1 GAAGAAGAAATACAAG
*
54911123 GAAGAAGAAA-AC-GG
1 GAAGAAGAAATACAAG
54911137 GAAGAAGAAA
1 GAAGAAGAAA
54911147 GAGTTGTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 10 0.43
ACGTcount: A:0.62, C:0.05, G:0.30, T:0.03
Consensus pattern (16 bp):
GAAGAAGAAATACAAG
Found at i:54913109 original size:22 final size:19
Alignment explanation
Indices: 54913070--54913115 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 19
54913060 ATATTTTTAA
54913070 TTTTTTATAATTTTATGAT
1 TTTTTTATAATTTTATGAT
54913089 TTTTTTAATAATTATTTATGAT
1 TTTTTT-ATAA-T-TTTATGAT
54913111 TTTTT
1 TTTTT
54913116 AATCATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.25
20 4 0.17
21 1 0.04
22 13 0.54
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTTTATAATTTTATGAT
Found at i:54915076 original size:28 final size:28
Alignment explanation
Indices: 54915040--54915093 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
54915030 ATTCTAAATT
*
54915040 TTCATAAAATTCTTAAAAAAT-TATAAGA
1 TTCATAAAATTC-CAAAAAATATATAAGA
54915068 TTCATAAAATTCCAAAAAATATATAA
1 TTCATAAAATTCCAAAAAATATATAA
54915094 AAAAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (28 bp):
TTCATAAAATTCCAAAAAATATATAAGA
Found at i:54918087 original size:19 final size:19
Alignment explanation
Indices: 54918063--54918099 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54918053 TTAATTTTTT
* *
54918063 ATATAATTTTTTCTAAAAA
1 ATATAATTATATCTAAAAA
54918082 ATATAATTATATCTAAAA
1 ATATAATTATATCTAAAA
54918100 TATTAAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAATTATATCTAAAAA
Found at i:54935072 original size:62 final size:63
Alignment explanation
Indices: 54934954--54935080 Score: 247
Period size: 62 Copynumber: 2.0 Consensus size: 63
54934944 AAATGACATG
54934954 AATTTTTGTGTAATGAAATTTATTTTGTTTCAGATTTTTAAATTTTCTTCAATATCCATTCTT
1 AATTTTTGTGTAATGAAATTTATTTTGTTTCAGATTTTTAAATTTTCTTCAATATCCATTCTT
54935017 AATTTTTGTGTAATGAAATTTATTTTG-TTCAGATTTTTAAATTTTCTTCAATATCCATTCTT
1 AATTTTTGTGTAATGAAATTTATTTTGTTTCAGATTTTTAAATTTTCTTCAATATCCATTCTT
54935079 AA
1 AA
54935081 ACATAACAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 37 0.58
63 27 0.42
ACGTcount: A:0.28, C:0.09, G:0.08, T:0.54
Consensus pattern (63 bp):
AATTTTTGTGTAATGAAATTTATTTTGTTTCAGATTTTTAAATTTTCTTCAATATCCATTCTT
Found at i:54938215 original size:15 final size:15
Alignment explanation
Indices: 54938195--54938241 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
54938185 TTTATTTATT
54938195 TTATATTTTAATCAC
1 TTATATTTTAATCAC
* *
54938210 TTATA-TTTAA-AATG
1 TTATATTTTAATCA-C
54938224 TTATATTTTAATCAC
1 TTATATTTTAATCAC
54938239 TTA
1 TTA
54938242 CATTAACGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
13 1 0.04
14 10 0.40
15 13 0.52
16 1 0.04
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (15 bp):
TTATATTTTAATCAC
Found at i:54938430 original size:28 final size:25
Alignment explanation
Indices: 54938388--54938450 Score: 83
Period size: 24 Copynumber: 2.4 Consensus size: 25
54938378 AGCAATTTAA
54938388 TTTTTTTTCTGTTATGTTTTTTAACTTTC
1 TTTTTTTTCTGTTAT-TTTTTT---TTTC
54938417 TTTTTTTTCT-TTATTTTTTTTTTC
1 TTTTTTTTCTGTTATTTTTTTTTTC
54938441 TTTTTTTTCT
1 TTTTTTTTCT
54938451 CTTTCTGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
24 14 0.41
27 6 0.18
28 4 0.12
29 10 0.29
ACGTcount: A:0.06, C:0.10, G:0.03, T:0.81
Consensus pattern (25 bp):
TTTTTTTTCTGTTATTTTTTTTTTC
Found at i:54938438 original size:15 final size:14
Alignment explanation
Indices: 54938417--54938448 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
54938407 TTTAACTTTC
54938417 TTTTTTTTCTTTATT
1 TTTTTTTTCTTT-TT
54938432 TTTTTTTTCTTTTT
1 TTTTTTTTCTTTTT
54938446 TTT
1 TTT
54938449 CTCTTTCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTTTTCTTTTT
Found at i:54938447 original size:11 final size:11
Alignment explanation
Indices: 54938413--54938465 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
54938403 GTTTTTTAAC
54938413 TTTCTTTTTTTT
1 TTTC-TTTTTTT
*
54938425 CTTTATTTTTTT
1 -TTTCTTTTTTT
54938437 TTTCTTTTTTT
1 TTTCTTTTTTT
* * *
54938448 TCTCTTTCTGT
1 TTTCTTTTTTT
54938459 TTTCTTT
1 TTTCTTT
54938466 CCTTCTCCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 24 0.71
12 7 0.21
13 3 0.09
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:54938461 original size:24 final size:24
Alignment explanation
Indices: 54938413--54938461 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
54938403 GTTTTTTAAC
* *
54938413 TTTCTTTTTTTTCTTTATTTTTTT
1 TTTCTTTTTTTTCTTTATCTGTTT
54938437 TTTCTTTTTTTTCTCTT-TCTGTTT
1 TTTCTTTTTTTTCT-TTATCTGTTT
54938461 T
1 T
54938462 CTTTCCTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (24 bp):
TTTCTTTTTTTTCTTTATCTGTTT
Found at i:54942685 original size:35 final size:35
Alignment explanation
Indices: 54942611--54942686 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
54942601 TTTTTTTAAG
* *
54942611 ATTTAAGATTTAGTATATATTGTTAGAAAGTTATG
1 ATTTAAGATTTAGTATATATTGTTAGAAAGATATA
* *
54942646 ATTTAAGATTTAG-AGTTTATTGATTA-AATGATATA
1 ATTTAAGATTTAGTA-TATATTG-TTAGAAAGATATA
54942681 ATTTAA
1 ATTTAA
54942687 AGTTTAAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 1 0.03
35 31 0.89
36 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.46
Consensus pattern (35 bp):
ATTTAAGATTTAGTATATATTGTTAGAAAGATATA
Found at i:54944708 original size:4 final size:4
Alignment explanation
Indices: 54944658--54944688 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
54944648 GCAATAACAT
54944658 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
54944689 TATGTGTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:54949384 original size:43 final size:44
Alignment explanation
Indices: 54949290--54949386 Score: 178
Period size: 44 Copynumber: 2.2 Consensus size: 44
54949280 GTTATGAATA
54949290 AATAATTTGATGTTTTAAATAAAAAAATTGAAAGAATTTGACCC
1 AATAATTTGATGTTTTAAATAAAAAAATTGAAAGAATTTGACCC
54949334 AATAATTTGATGTTTTAAATAAAAAAATTGAAAGAATTTGACCC
1 AATAATTTGATGTTTTAAATAAAAAAATTGAAAGAATTTGACCC
*
54949378 GA-AATTTGA
1 AATAATTTGA
54949387 ATGTAAAATG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 7 0.13
44 45 0.87
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (44 bp):
AATAATTTGATGTTTTAAATAAAAAAATTGAAAGAATTTGACCC
Found at i:54950483 original size:10 final size:10
Alignment explanation
Indices: 54950413--54950485 Score: 62
Period size: 10 Copynumber: 7.2 Consensus size: 10
54950403 AACAAAATGG
54950413 ATATTATAAA
1 ATATTATAAA
*
54950423 ATCTTATAAA
1 ATATTATAAA
54950433 AT-TT-TAAA
1 ATATTATAAA
54950441 ATATTTAACTAAA
1 ATA-TT-A-TAAA
*
54950454 ATATGTAAAAA
1 ATAT-TATAAA
*
54950465 ATAAT-TAAA
1 ATATTATAAA
54950474 ATATTATAAA
1 ATATTATAAA
54950484 AT
1 AT
54950486 CTTAAATGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
8 6 0.12
9 9 0.18
10 20 0.39
11 6 0.12
12 2 0.04
13 8 0.16
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (10 bp):
ATATTATAAA
Found at i:54950673 original size:15 final size:15
Alignment explanation
Indices: 54950637--54950678 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
54950627 TATAAAATCT
*
54950637 TATAAAAATAAAATA
1 TATAAAATTAAAATA
*
54950652 AAT-AAATTAAAATA
1 TATAAAATTAAAATA
54950666 TATAAAATTAAAA
1 TATAAAATTAAAA
54950679 GAGAGGTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TATAAAATTAAAATA
Found at i:54952999 original size:17 final size:18
Alignment explanation
Indices: 54952977--54953010 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54952967 TTGATTTGGA
54952977 GATTTGG-GGGAAAAAAG
1 GATTTGGAGGGAAAAAAG
54952994 GATTTGGAGGGAAAAAA
1 GATTTGGAGGGAAAAAA
54953011 CATAAAAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (18 bp):
GATTTGGAGGGAAAAAAG
Found at i:54953960 original size:57 final size:58
Alignment explanation
Indices: 54953885--54954137 Score: 282
Period size: 57 Copynumber: 4.3 Consensus size: 58
54953875 TGGATACTCG
* * * * *
54953885 GGGGCAAAATGGTAATTTTAGTTGGAAT-TGGGTTAAAAATGAGG-TTTTAGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATG-GGATTTTAGAAGTTTA
* * *
54953942 GGGGTAAAATAGTAATTTTTGGTGAAATCGGGGTT-AAAATGGGGTTTTTAGAAG-TTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-GGGATTTTAGAAGTTTA
* * * * *
54953999 GAGGGCAAAATGATAA-TTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTAG-AAGTTTA
* *
54954058 GGGGTAAAATGGTAATTTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGATAGTTTG
1 GGGGTAAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTAGA-AGTTTA
54954118 GGGGTAAAATGGTAATTTTT
1 GGGGTAAAATGGTAATTTTT
54954138 AGACAGTCTA
Statistics
Matches: 166, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
57 59 0.36
58 46 0.28
59 8 0.05
60 53 0.32
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTAGAAGTTTA
Found at i:54954046 original size:29 final size:29
Alignment explanation
Indices: 54954014--54954109 Score: 99
Period size: 29 Copynumber: 3.2 Consensus size: 29
54954004 CAAAATGATA
54954014 ATTTTGGTAAAATCGGGGTTAAAAATGGG
1 ATTTTGGTAAAATCGGGGTTAAAAATGGG
* *
54954043 ATTTTGG-AAAGTTCAGGGG-T-AAAATGGTA
1 ATTTTGGTAAA-ATC-GGGGTTAAAAATGG-G
*
54954072 ATTTTTTGGTGAAATCGGGGTTAAAAATGGG
1 A--TTTTGGTAAAATCGGGGTTAAAAATGGG
54954103 ATTTTGG
1 ATTTTGG
54954110 ATAGTTTGGG
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
28 10 0.19
29 17 0.31
30 8 0.15
31 10 0.19
32 9 0.17
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.34
Consensus pattern (29 bp):
ATTTTGGTAAAATCGGGGTTAAAAATGGG
Found at i:54954100 original size:60 final size:59
Alignment explanation
Indices: 54953885--54954137 Score: 277
Period size: 60 Copynumber: 4.3 Consensus size: 59
54953875 TGGATACTCG
* * * * * * *
54953885 GGGGCAAAATGGTAATTTTAGTTGGAAT-TGGGTTAAAAATGAGG-TTTTAG-AAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATG-GGATTTTGGAAAGTTCA
* * *
54953942 GGGGTAAAATAGTAATTTTTGGTGAAATCGGGGTT-AAAATGGGGTTTT-TAGAAGTTC-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGA-AAGTTCA
* * *
54953999 GAGGGCAAAATGATAA-TTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
* **
54954058 GGGGTAAAATGGTAATTTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGATAGTTTG
1 GGGGTAAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
54954118 GGGGTAAAATGGTAATTTTT
1 GGGGTAAAATGGTAATTTTT
54954138 AGACAGTCTA
Statistics
Matches: 166, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
56 2 0.01
57 52 0.31
58 51 0.31
59 7 0.04
60 54 0.33
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
Found at i:54954120 original size:29 final size:29
Alignment explanation
Indices: 54954028--54954126 Score: 69
Period size: 29 Copynumber: 3.3 Consensus size: 29
54954018 TGGTAAAATC
*
54954028 GGGGTTAAAAATGGGATTTTGGAAAGTTCA
1 GGGGTTAAAAATGGGATTTTGGATAGTT-A
* ** *
54954058 GGGG-T-AAAATGGTAATTTTTTGG-TGAAATC
1 GGGGTTAAAAATGG-GA--TTTTGGAT-AGTTA
*
54954088 GGGGTTAAAAATGGGATTTTGGATAGTTT
1 GGGGTTAAAAATGGGATTTTGGATAGTTA
*
54954117 GGGGGTAAAA
1 GGGGTTAAAA
54954127 TGGTAATTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
28 7 0.13
29 19 0.37
30 9 0.17
31 10 0.19
32 7 0.13
ACGTcount: A:0.31, C:0.02, G:0.34, T:0.32
Consensus pattern (29 bp):
GGGGTTAAAAATGGGATTTTGGATAGTTA
Found at i:54955997 original size:6 final size:6
Alignment explanation
Indices: 54955983--54956039 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
54955973 GACTTTTTAA
* * * *
54955983 TTAATT TTAAAT TTAAAT TCAAA- TTAAAT TTAAAC TT-AAT TAAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
54956029 TTAAAC TTAAA
1 TTAAAT TTAAA
54956040 AGAAAAGTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 7 0.17
6 34 0.83
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:54956001 original size:17 final size:17
Alignment explanation
Indices: 54955983--54956038 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
54955973 GACTTTTTAA
54955983 TTAATTTTAAATTTAAA-
1 TTAA-TTTAAATTTAAAC
*
54956000 TTCAAATTAAATTTAAAC
1 TT-AATTTAAATTTAAAC
*
54956018 TTAATTAAAATTTAAAC
1 TTAATTTAAATTTAAAC
54956035 TTAA
1 TTAA
54956039 AAGAAAAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 30 0.88
18 4 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATTTAAATTTAAAC
Found at i:54956032 original size:23 final size:23
Alignment explanation
Indices: 54955981--54956039 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
54955971 TGGACTTTTT
* * *
54955981 AATTAATTTTAAATTTAAATTCA
1 AATTAAATTTAAACTTAAATTAA
54956004 AATTAAATTTAAACTT-AATTAA
1 AATTAAATTTAAACTTAAATTAA
*
54956026 AATTTAAACTTAAA
1 AA-TTAAATTTAAA
54956040 AGAAAAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTAAATTTAAACTTAAATTAA
Found at i:54956052 original size:19 final size:18
Alignment explanation
Indices: 54956008--54956058 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
54955998 AATTCAAATT
**
54956008 AAATTTAAACTT-AATTA
1 AAATTTAAACTTAAAAGA
54956025 AAATTTAAACTTAAAAGA
1 AAATTTAAACTTAAAAGA
54956043 AAAGTTTAAACTTAAA
1 AAA-TTTAAACTTAAA
54956059 CTAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.40
18 6 0.20
19 12 0.40
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (18 bp):
AAATTTAAACTTAAAAGA
Found at i:54956266 original size:2 final size:2
Alignment explanation
Indices: 54956261--54956303 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
54956251 TTTTTTAGAT
54956261 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
54956303 T
1 T
54956304 TAAAATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54957888 original size:31 final size:29
Alignment explanation
Indices: 54957853--54957918 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
54957843 CAATATTATG
* * *
54957853 CATGAACATTGATTTAATGTGCAATTATATA
1 CATGAACATTAATTT--GGTGCAATTATACA
*
54957884 CATGAACTTTAATTTGGTGCAATTATACA
1 CATGAACATTAATTTGGTGCAATTATACA
54957913 CATGAA
1 CATGAA
54957919 TTTCTAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 18 0.58
31 13 0.42
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (29 bp):
CATGAACATTAATTTGGTGCAATTATACA
Found at i:54957903 original size:29 final size:29
Alignment explanation
Indices: 54957871--54957959 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
54957861 TTGATTTAAT
54957871 GTGCAATTATATACATGAACTTTAATTTG
1 GTGCAATTATATACATGAACTTTAATTTG
* *
54957900 GTGCAATTATACACATGAATTTCTAATTGTG
1 GTGCAATTATATACATGAACTT-TAATT-TG
* *
54957931 GTTCACA-TGTATACATGAAACTTTAATTT
1 GTGCA-ATTATATACATG-AACTTTAATTT
54957960 TGATTTAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 20 0.40
30 6 0.12
31 19 0.38
32 5 0.10
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (29 bp):
GTGCAATTATATACATGAACTTTAATTTG
Found at i:54957948 original size:31 final size:27
Alignment explanation
Indices: 54957871--54957959 Score: 79
Period size: 31 Copynumber: 3.0 Consensus size: 27
54957861 TTGATTTAAT
54957871 GTGCAATTATATACATGAACTTTAATTTG
1 GTGCAA-T-TATACATGAACTTTAATTTG
*
54957900 GTGCAATTATACACATGAATTTCTAATTGTG
1 GTGCAATTAT--ACATGAACTT-TAATT-TG
*
54957931 GTTCACATGTATACATGAAACTTTAATTT
1 GTGCA-AT-TATACATG-AACTTTAATTT
54957960 TGATTTAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
27 3 0.06
28 1 0.02
29 15 0.30
30 6 0.12
31 16 0.32
32 6 0.12
33 3 0.06
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (27 bp):
GTGCAATTATACATGAACTTTAATTTG
Found at i:54958341 original size:41 final size:40
Alignment explanation
Indices: 54958296--54958470 Score: 179
Period size: 41 Copynumber: 4.3 Consensus size: 40
54958286 ATAAGCGGCA
* * * * **
54958296 TTAGTGGCGTTTTCTAATAAATGTCGCTAATGCTCTAAATT
1 TTAGCGGCGTTTCCTCATAAA-GCCGCTAATGCTCTAACCT
* * * *
54958337 TTAGTGGCGTTTCCTTATAAACGCCGCCAATGCTCTGACCT
1 TTAGCGGCGTTTCCTCATAAA-GCCGCTAATGCTCTAACCT
*
54958378 TTAGCGGCGTTTCCTCATAAAGCCACTAATGCTCTAACCT
1 TTAGCGGCGTTTCCTCATAAAGCCGCTAATGCTCTAACCT
* * * *
54958418 TTAGCGGCGTTTCCTCATAAACACCGTTAATGCTCTGACAT
1 TTAGCGGCGTTTCCTCATAAA-GCCGCTAATGCTCTAACCT
*
54958459 TTAACGGCGTTT
1 TTAGCGGCGTTT
54958471 TTCCTACAAA
Statistics
Matches: 114, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
40 37 0.32
41 77 0.68
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (40 bp):
TTAGCGGCGTTTCCTCATAAAGCCGCTAATGCTCTAACCT
Found at i:54958414 original size:81 final size:81
Alignment explanation
Indices: 54958322--54958470 Score: 217
Period size: 81 Copynumber: 1.8 Consensus size: 81
54958312 ATAAATGTCG
* * * * * *
54958322 CTAATGCTCTAAATTTTAGTGGCGTTTCCTTATAAACGCCGCCAATGCTCTGACCTTTAGCGGCG
1 CTAATGCTCTAAACTTTAGCGGCGTTTCCTCATAAACACCGCCAATGCTCTGACATTTAACGGCG
54958387 TTTCCTCATAAAGCCA
66 TTTCCTCATAAAGCCA
* **
54958403 CTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAACACCGTTAATGCTCTGACATTTAACGGCG
1 CTAATGCTCTAAACTTTAGCGGCGTTTCCTCATAAACACCGCCAATGCTCTGACATTTAACGGCG
54958468 TTT
66 TTT
54958471 TTCCTACAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 59 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (81 bp):
CTAATGCTCTAAACTTTAGCGGCGTTTCCTCATAAACACCGCCAATGCTCTGACATTTAACGGCG
TTTCCTCATAAAGCCA
Found at i:54958420 original size:40 final size:41
Alignment explanation
Indices: 54958322--54958511 Score: 179
Period size: 41 Copynumber: 4.7 Consensus size: 41
54958312 ATAAATGTCG
** * * *
54958322 CTAATGCTCTAAATTTTAGTGGCGTTTCCTTATAAACGCCG
1 CTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAACGCCA
* *
54958363 CCAATGCTCTGACCTTTAGCGGCGTTTCCTCATAAA-GCCA
1 CTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAACGCCA
* *
54958403 CTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAACACCG
1 CTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAACGCCA
* * * * * *
54958444 TTAATGCTCTGACATTTAACGGCGTTTTTCCT-ACAAATGCCA
1 CTAATGCTCTAACCTTTAGCGGCG--TTTCCTCATAAACGCCA
* * *
54958486 CTATTGCT-TTACCTTTTGCGGCGTTT
1 CTAATGCTCTAACCTTTAGCGGCGTTT
54958512 TTGGAAAAAC
Statistics
Matches: 121, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
39 3 0.02
40 37 0.31
41 63 0.52
42 12 0.10
43 6 0.05
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (41 bp):
CTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAACGCCA
Found at i:54958508 original size:41 final size:40
Alignment explanation
Indices: 54958463--54958559 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 40
54958453 TGACATTTAA
* * * **
54958463 CGGCGTTTTTCCTACAAATGCCACTATTGCTTTACCTTTTG
1 CGGCGTTTTT-CGAAAAACGCCACTATTGCCCTACCTTTTG
* *
54958504 CGGCGTTTTTGGAAAAACGCCAGTATTGCCCTACCTTTTG
1 CGGCGTTTTTCGAAAAACGCCACTATTGCCCTACCTTTTG
*
54958544 CGGCGTTTAT-GAAAAA
1 CGGCGTTTTTCGAAAAA
54958560 ACACCGCTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 6 0.12
40 32 0.67
41 10 0.21
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (40 bp):
CGGCGTTTTTCGAAAAACGCCACTATTGCCCTACCTTTTG
Found at i:54958583 original size:40 final size:41
Alignment explanation
Indices: 54958486--54958583 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
54958476 ACAAATGCCA
* * *
54958486 CTATTGCTTTACCTTTTGCGGCGTTTTTGGAAAAACGCCAG
1 CTATTGCTTTACCTTTTGCGGCGTTTATGAAAAAACACCAG
**
54958527 -TATTGCCCTACCTTTTGCGGCGTTTATGAAAAAACACC-G
1 CTATTGCTTTACCTTTTGCGGCGTTTATGAAAAAACACCAG
* *
54958566 CTATTGATTTACTTTTTG
1 CTATTGCTTTACCTTTTG
54958584 TGCCGTTTTC
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.02
40 46 0.98
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (41 bp):
CTATTGCTTTACCTTTTGCGGCGTTTATGAAAAAACACCAG
Found at i:54961057 original size:3 final size:3
Alignment explanation
Indices: 54961051--54961079 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54961041 TTGTGTTTAA
54961051 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54961080 GGGAAAAAGG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54961372 original size:2 final size:2
Alignment explanation
Indices: 54961365--54961424 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
54961355 AGGAGAGGGT
54961365 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
54961407 GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
54961425 TTTTTTAAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:54961933 original size:30 final size:31
Alignment explanation
Indices: 54961885--54961942 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
54961875 TGCTTATAGG
* *
54961885 TCCCTAAACTATTCAAAAATTATATTTTTGA
1 TCCCAAAACTATTAAAAAATTATATTTTTGA
54961916 TCCCAAAACT-TTAAAAAATTATATTTT
1 TCCCAAAACTATTAAAAAATTATATTTT
54961943 AACCCTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (31 bp):
TCCCAAAACTATTAAAAAATTATATTTTTGA
Found at i:54961952 original size:29 final size:31
Alignment explanation
Indices: 54961886--54961965 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 31
54961876 GCTTATAGGT
*
54961886 CCCT-AAACTATTCAAAAATTATATTTTTGAT
1 CCCTAAAACT-TTCAAAAATTATATTTTTGAA
*
54961917 CCC-AAAACTTTAAAAAATTATA-TTTT-AA
1 CCCTAAAACTTTCAAAAATTATATTTTTGAA
*
54961945 CCCTAAAACTTCCAAAAATTA
1 CCCTAAAACTTTCAAAAATTA
54961966 CCATTTTACC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
28 4 0.09
29 19 0.44
30 12 0.28
31 8 0.19
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (31 bp):
CCCTAAAACTTTCAAAAATTATATTTTTGAA
Found at i:54961972 original size:30 final size:28
Alignment explanation
Indices: 54961930--54962119 Score: 91
Period size: 29 Copynumber: 6.5 Consensus size: 28
54961920 AAAACTTTAA
*
54961930 AAAATTA-TATTTTAACCCTAAAACTTCC
1 AAAATTACCATTTT-ACCCTAAAACTTCC
**
54961958 AAAAATTACCATTTTACCCCCAAACTTTCC
1 -AAAATTACCATTTTACCCTAAAAC-TTCC
* * *** **
54961988 AAAATT-TCATTTTTAATCCCGATTTCACCC
1 AAAATTACCA-TTTT-A-CCCTAAAACTTCC
** *
54962018 AAAATTACCATTTTACCCTTGAACTTTTC
1 AAAATTACCATTTTACCCTAAAAC-TTCC
**
54962047 AAAATT-CCATTTTTGACCCTAAAACTTTTA
1 AAAATTACCA-TTTT-ACCCTAAAAC-TTCC
**
54962077 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTACCCTAAAAC-TTCC
*
54962106 AAAA-TCCCATTTTA
1 AAAATTACCATTTTA
54962120 ACCCCGATTT
Statistics
Matches: 123, Mismatches: 28, Indels: 21
0.72 0.16 0.12
Matches are distributed among these distances:
28 18 0.15
29 52 0.42
30 44 0.36
31 9 0.07
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTAAAACTTCC
Found at i:54962108 original size:118 final size:117
Alignment explanation
Indices: 54961939--54962181 Score: 348
Period size: 118 Copynumber: 2.1 Consensus size: 117
54961929 AAAAATTATA
**
54961939 TTTTAACCCTAAAACTTCCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTTCATTTTTAA
1 TTTTAACCCTAAAACTTCCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCA-TTTTAA
* * *
54962004 TCCCGATTTCACCCAAAA-TTACCATTTTACCCTTGAACTTTTCAAAAT-TCCAT
65 CCCCGATTTCA-CCAAAAGTTACCATTTTACCCCTGAACTTTCCAAAATCT-CAT
* **
54962057 TTTTGACCCTAAAACTTTTAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTAAC
1 TTTTAACCCTAAAACTTCCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTAAC
* *
54962122 CCCGATTTCACCAAAAGTTACCATTTTTCCCCTGAGCTTTCCAAAATCTCA-
66 CCCGATTTCACCAAAAGTTACCATTTTACCCCTGAACTTTCCAAAATCTCAT
54962173 TTTTAACCC
1 TTTTAACCC
54962182 CAATTTCATA
Statistics
Matches: 112, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
116 14 0.12
117 44 0.39
118 54 0.48
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (117 bp):
TTTTAACCCTAAAACTTCCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTAAC
CCCGATTTCACCAAAAGTTACCATTTTACCCCTGAACTTTCCAAAATCTCAT
Found at i:54962148 original size:30 final size:29
Alignment explanation
Indices: 54962077--54962215 Score: 78
Period size: 28 Copynumber: 4.8 Consensus size: 29
54962067 AAAACTTTTA
* *
54962077 AAAATTACCATTTTACCCCCAAACTTT--CC
1 AAAATTACCATTTTAACCCC-GA-TTTCACC
*
54962106 AAAA-TCCCATTTTAACCCCGATTTCACC
1 AAAATTACCATTTTAACCCCGATTTCACC
*
54962134 AAAAGTTACCATTTT-TCCCCTGAGCTTT--CC
1 AAAA-TTACCATTTTAACCCC-GA--TTTCACC
* **
54962164 AAAA-T-CTCATTTTAACCCCAATTTCATAA
1 AAAATTAC-CATTTTAACCCCGATTTCA-CC
54962193 AAAATTACCATTTTTAACCCCGA
1 AAAATTACCA-TTTTAACCCCGA
54962216 ATTTTTCTGA
Statistics
Matches: 85, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
26 6 0.07
27 2 0.02
28 27 0.32
29 16 0.19
30 19 0.22
31 12 0.14
32 3 0.04
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTAACCCCGATTTCACC
Found at i:54962207 original size:58 final size:59
Alignment explanation
Indices: 54961956--54962206 Score: 244
Period size: 59 Copynumber: 4.3 Consensus size: 59
54961946 CCTAAAACTT
* * *
54961956 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTTCATTTTTAATCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCTCATTTTTAACCCCAATTTCA
* *** * * *
54962015 CCCAAAATTACCATTTTACCCTTGAACTTTTCAAAAT-TCCATTTTTGACCCTAAAACTTT--
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCT-CATTTTTAACCC--CAA-TTTCA
* * *
54962075 -TAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCA-TTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCTCATTTTTAACCCCAATTTCA
* * ** *
54962132 CCAAAAGTTACCATTTTTCCCCTGAGCTTTCCAAAATCTCA-TTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCTCATTTTTAACCCCAATTTCA
**
54962190 TAAAAAATTACCATTTT
1 CCAAAAATTACCATTTT
54962207 TAACCCCGAA
Statistics
Matches: 154, Mismatches: 30, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
55 3 0.02
56 1 0.01
58 72 0.47
59 74 0.48
61 1 0.01
62 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCTCATTTTTAACCCCAATTTCA
Found at i:54972831 original size:17 final size:15
Alignment explanation
Indices: 54972811--54972840 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54972801 ATGCTTTATA
54972811 TATATACACTCCTAT
1 TATATACACTCCTAT
54972826 TATATACACTCCTAT
1 TATATACACTCCTAT
54972841 CTTCCGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATACACTCCTAT
Found at i:54975296 original size:19 final size:19
Alignment explanation
Indices: 54975272--54975311 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
54975262 ATTAATGATT
54975272 TTAATTAATATCTATT-TTA
1 TTAATTAATATC-ATTATTA
54975291 TTAATTAATATCATTATTA
1 TTAATTAATATCATTATTA
54975310 TT
1 TT
54975312 TTATATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATTAATATCATTATTA
Found at i:54975390 original size:3 final size:3
Alignment explanation
Indices: 54975382--54975423 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
54975372 TCTATACTAA
54975382 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54975424 TTCAAATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54975854 original size:19 final size:20
Alignment explanation
Indices: 54975804--54975855 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
54975794 ATATTAATAT
*
54975804 ATATTTATATATATATATAAT
1 ATATTTAT-TATATATATAAC
* *
54975825 ATTTTTCATTATATA-ATTAC
1 ATATTT-ATTATATATATAAC
54975845 ATATTTATTAT
1 ATATTTATTAT
54975856 TTTGTTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.19
20 8 0.31
21 11 0.42
22 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTATTATATATATAAC
Found at i:54978048 original size:21 final size:21
Alignment explanation
Indices: 54978024--54978075 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
54978014 TGAGATAATA
54978024 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* * *
54978045 CTACTGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
54978066 CTACCGATAC
1 CTACCGATAC
54978076 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:54987332 original size:51 final size:53
Alignment explanation
Indices: 54987252--54987359 Score: 127
Period size: 51 Copynumber: 2.1 Consensus size: 53
54987242 TGTCATTTTC
* *
54987252 TTTTTCATTTTGGAGAAAATCGCATTCA-TTTCAAAATGATT-TCATTTCTCCA
1 TTTTTCATTTTGGAGAAAATCGAATTCATTTTC-AAATGATTCTCATTTATCCA
*
54987304 TTTTT-ATTTTGGAGAAAA-C-AATAATCATTTTCAAATGTTTCTCATTTATCCA
1 TTTTTCATTTTGGAGAAAATCGAAT--TCATTTTCAAATGATTCTCATTTATCCA
54987356 TTTT
1 TTTT
54987360 CACCATTTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
49 2 0.04
50 1 0.02
51 23 0.47
52 23 0.47
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (53 bp):
TTTTTCATTTTGGAGAAAATCGAATTCATTTTCAAATGATTCTCATTTATCCA
Found at i:54989354 original size:29 final size:27
Alignment explanation
Indices: 54989279--54989367 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 27
54989269 TGCTGAAAAT
* *
54989279 TTAATATATTTTAATTATATTTAATCAT-
1 TTAA-ATAATTTAATTATA-TTAATTATA
*
54989307 TTAAATAATATTACTTTATATTAATTATA
1 TTAAATAAT-TTA-ATTATATTAATTATA
54989336 TTAAATACAATTTAATTAT-TTAATTA-A
1 TTAAAT--AATTTAATTATATTAATTATA
54989363 TTAAA
1 TTAAA
54989368 AATAAAATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
27 10 0.19
28 21 0.40
29 15 0.29
30 3 0.06
31 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAAATAATTTAATTATATTAATTATA
Found at i:54991910 original size:16 final size:16
Alignment explanation
Indices: 54991889--54991919 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
54991879 AGGATCATTA
54991889 TATATACATATTATAT
1 TATATACATATTATAT
54991905 TATATACATATTATA
1 TATATACATATTATA
54991920 AGGTATCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATACATATTATAT
Found at i:54998715 original size:43 final size:43
Alignment explanation
Indices: 54998625--54998715 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
54998615 GGCTTTTTCG
* * * *
54998625 ATGATATATTGTGTGTGTCAGTATAATTTCTTTGACTTTTCCG
1 ATGATATATTGTGTGTGTCAGTATAATTGCTTAGACTTATCCA
*
54998668 ATGATATATTGTGTGTGTCAGTATAATTGCTTCAG-CTTATCTA
1 ATGATATATTGTGTGTGTCAGTATAATTGCTT-AGACTTATCCA
54998711 ATGAT
1 ATGAT
54998716 GCGCTATATG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 41 0.98
44 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (43 bp):
ATGATATATTGTGTGTGTCAGTATAATTGCTTAGACTTATCCA
Found at i:55003267 original size:22 final size:23
Alignment explanation
Indices: 55003231--55003273 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
55003221 ACTTCACATG
* *
55003231 TCATATTAATGAAC-AATACCCA
1 TCATATAAATAAACAAATACCCA
55003253 TCATATAAATAAACAAATACC
1 TCATATAAATAAACAAATACC
55003274 ACATTCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.51, C:0.21, G:0.02, T:0.26
Consensus pattern (23 bp):
TCATATAAATAAACAAATACCCA
Found at i:55005126 original size:39 final size:39
Alignment explanation
Indices: 55005083--55005162 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
55005073 AAACTTAAGG
* *
55005083 TAACTAAGGCCTATTTATAGGCTGAAAATTTGTAGCATA
1 TAACTAAGGCCTATTTATAGACTGAAAATTCGTAGCATA
55005122 TAACTAAGGCCTATTTATAGACTGAAAATTCGTAGCATA
1 TAACTAAGGCCTATTTATAGACTGAAAATTCGTAGCATA
55005161 TA
1 TA
55005163 TTACTACAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (39 bp):
TAACTAAGGCCTATTTATAGACTGAAAATTCGTAGCATA
Found at i:55010632 original size:22 final size:21
Alignment explanation
Indices: 55010605--55010645 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
55010595 TTTTAAGGTA
55010605 AAATTTTATATTTT-ATTTTTAT
1 AAATTTT-T-TTTTAATTTTTAT
55010627 AAATTTTTTTTTAATTTTT
1 AAATTTTTTTTTAATTTTT
55010646 CTCATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
AAATTTTTTTTTAATTTTTAT
Found at i:55030844 original size:6 final size:6
Alignment explanation
Indices: 55030836--55030873 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
55030826 AGAACCTCCA
* *
55030836 CCACCA CCACCT CCACCT CCACCT CCACCC CCACCT CC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CC
55030874 CACCACTCCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.18, C:0.71, G:0.00, T:0.11
Consensus pattern (6 bp):
CCACCT
Found at i:55030849 original size:15 final size:15
Alignment explanation
Indices: 55030829--55030858 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55030819 CTCCATTAGA
55030829 ACCTCCACCACCACC
1 ACCTCCACCACCACC
*
55030844 ACCTCCACCTCCACC
1 ACCTCCACCACCACC
55030859 TCCACCCCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.67, G:0.00, T:0.10
Consensus pattern (15 bp):
ACCTCCACCACCACC
Found at i:55030851 original size:12 final size:12
Alignment explanation
Indices: 55030836--55030879 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
55030826 AGAACCTCCA
55030836 CCACCACCACCT
1 CCACCACCACCT
*
55030848 CCACCTCCACCT
1 CCACCACCACCT
*
55030860 CCACCCCCACCT
1 CCACCACCACCT
55030872 CCCACCAC
1 -CCACCAC
55030880 TCCGCCTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 22 0.79
13 6 0.21
ACGTcount: A:0.20, C:0.70, G:0.00, T:0.09
Consensus pattern (12 bp):
CCACCACCACCT
Found at i:55030863 original size:18 final size:18
Alignment explanation
Indices: 55030836--55030879 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
55030826 AGAACCTCCA
*
55030836 CCACCACCACCTCCACCT
1 CCACCACCACCCCCACCT
*
55030854 CCACCTCCACCCCCACCT
1 CCACCACCACCCCCACCT
55030872 CCCACCAC
1 -CCACCAC
55030880 TCCGCCTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.20, C:0.70, G:0.00, T:0.09
Consensus pattern (18 bp):
CCACCACCACCCCCACCT
Found at i:55030974 original size:6 final size:6
Alignment explanation
Indices: 55030965--55030999 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
55030955 ACCTCCTTCT
*
55030965 CCTCCA CCTCCA CCTCCG CCTCCA CCTCCA CCTCC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCC
55031000 TCCACTGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.11, C:0.69, G:0.03, T:0.17
Consensus pattern (6 bp):
CCTCCA
Found at i:55030988 original size:18 final size:18
Alignment explanation
Indices: 55030965--55030999 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
55030955 ACCTCCTTCT
55030965 CCTCCACCTCCACCTCCG
1 CCTCCACCTCCACCTCCG
55030983 CCTCCACCTCCACCTCC
1 CCTCCACCTCCACCTCC
55031000 TCCACTGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.69, G:0.03, T:0.17
Consensus pattern (18 bp):
CCTCCACCTCCACCTCCG
Found at i:55031342 original size:6 final size:6
Alignment explanation
Indices: 55031298--55031338 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
55031288 ATAACTACTG
*
55031298 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCA CCACC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACC
55031339 ACCAATACCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.20, C:0.68, G:0.00, T:0.12
Consensus pattern (6 bp):
CCACCT
Found at i:55038769 original size:23 final size:23
Alignment explanation
Indices: 55038743--55038788 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
55038733 TTTGCCTCAG
*
55038743 GTTATATTTAAGTCACTTATGTT
1 GTTACATTTAAGTCACTTATGTT
* *
55038766 GTTACGTTTTAGTCACTTATGTT
1 GTTACATTTAAGTCACTTATGTT
55038789 AATATTTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (23 bp):
GTTACATTTAAGTCACTTATGTT
Found at i:55046851 original size:21 final size:21
Alignment explanation
Indices: 55046810--55046851 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
55046800 CTTATACCAG
* *
55046810 TCCCCAGCTAGTACAGTGAAA
1 TCCCCAGCTAGGACAGGGAAA
55046831 TCCCCAGC-AGGACTAGGGAAA
1 TCCCCAGCTAGGAC-AGGGAAA
55046852 GGTACAGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.33, C:0.29, G:0.24, T:0.14
Consensus pattern (21 bp):
TCCCCAGCTAGGACAGGGAAA
Found at i:55053748 original size:46 final size:45
Alignment explanation
Indices: 55053686--55053784 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 45
55053676 TCTAACATTT
55053686 TATTT-AAACTTAAAAATCTAATTGCCAAAAAATCTTAAAAAAACTA
1 TATTTAAAACTTAAAAATCTAATTGCCAAAAAATC-TAAAAAAA-TA
** *
55053732 TATTTAAAACTT-AAAATCTAATTGTTAAAATATCTAAAAAAATA
1 TATTTAAAACTTAAAAATCTAATTGCCAAAAAATCTAAAAAAATA
55053776 TAATTTAAA
1 T-ATTTAAA
55053785 CCTAAACTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
44 3 0.06
45 15 0.31
46 24 0.50
47 6 0.12
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (45 bp):
TATTTAAAACTTAAAAATCTAATTGCCAAAAAATCTAAAAAAATA
Found at i:55084377 original size:22 final size:22
Alignment explanation
Indices: 55084351--55084403 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
55084341 TTGTTGTTGC
***
55084351 CATTTTGTTATTGTTTTGCTAT
1 CATTTTGTTATTACATTGCTAT
*
55084373 CATTTTGCTATTACATTGCTAT
1 CATTTTGTTATTACATTGCTAT
*
55084395 TATTTTGTT
1 CATTTTGTT
55084404 GTTATTGTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.60
Consensus pattern (22 bp):
CATTTTGTTATTACATTGCTAT
Found at i:55087111 original size:13 final size:13
Alignment explanation
Indices: 55087093--55087119 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55087083 ATATGTCATA
55087093 TTCGGATAACTAT
1 TTCGGATAACTAT
55087106 TTCGGATAACTAT
1 TTCGGATAACTAT
55087119 T
1 T
55087120 GTAATAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTCGGATAACTAT
Found at i:55091677 original size:21 final size:21
Alignment explanation
Indices: 55091649--55091698 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
55091639 CTCTCCCCCA
*
55091649 TTTC-CCTTCCCCCTTCCTTC
1 TTTCTCCTTCCCCCTTCCTCC
* * *
55091669 TTTCTCCTTTCTCCTTTCTCC
1 TTTCTCCTTCCCCCTTCCTCC
55091690 TTTCTCCTT
1 TTTCTCCTT
55091699 TCTCGTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTCTCCTTCCCCCTTCCTCC
Found at i:55091678 original size:7 final size:7
Alignment explanation
Indices: 55091668--55091702 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
55091658 CCCCTTCCTT
55091668 CTTTCTC
1 CTTTCTC
55091675 CTTTCTC
1 CTTTCTC
55091682 CTTTCTC
1 CTTTCTC
55091689 CTTTCTC
1 CTTTCTC
55091696 CTTTCTC
1 CTTTCTC
55091703 GTTTTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (7 bp):
CTTTCTC
Found at i:55091788 original size:14 final size:14
Alignment explanation
Indices: 55091755--55091795 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
55091745 CAGGGACGAT
55091755 CCTTTCTTCTTTCC
1 CCTTTCTTCTTTCC
** *
55091769 AGTTTCTCCTTTCC
1 CCTTTCTTCTTTCC
55091783 CCTTTCTTCTTTC
1 CCTTTCTTCTTTC
55091796 GGTAAGCATT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.02, T:0.56
Consensus pattern (14 bp):
CCTTTCTTCTTTCC
Found at i:55094324 original size:20 final size:21
Alignment explanation
Indices: 55094286--55094330 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
55094276 TCCAAATATC
55094286 AAAAAATATTAATTTTTTC-G
1 AAAAAATATTAATTTTTTCAG
*
55094306 AAAAAATAATTCA-TTTTTCAG
1 AAAAAAT-ATTAATTTTTTCAG
55094327 AAAA
1 AAAA
55094331 TGATTTCTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (21 bp):
AAAAAATATTAATTTTTTCAG
Found at i:55101458 original size:19 final size:20
Alignment explanation
Indices: 55101426--55101463 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
55101416 ATCACGTAAA
*
55101426 TTTTTATTTATTTTATCTAT
1 TTTTTATATATTTTATCTAT
*
55101446 TTTTTATAT-TTTTTTCTA
1 TTTTTATATATTTTATCTA
55101464 ATCAAACAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTATATATTTTATCTAT
Found at i:55102635 original size:28 final size:29
Alignment explanation
Indices: 55102574--55102636 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
55102564 AGTAACGATT
*
55102574 TAATAGTTTAAGTATTAATTCTGATAAAAA
1 TAATA-TTTAAGTACTAATTCTGATAAAAA
*
55102604 -AATATTTAGGTACTAATT-TGA-AAAAA
1 TAATATTTAAGTACTAATTCTGATAAAAA
55102630 CTAATAT
1 -TAATAT
55102637 AATTTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 5 0.17
27 3 0.10
28 17 0.59
29 4 0.14
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (29 bp):
TAATATTTAAGTACTAATTCTGATAAAAA
Found at i:55106549 original size:65 final size:64
Alignment explanation
Indices: 55106441--55106569 Score: 213
Period size: 65 Copynumber: 2.0 Consensus size: 64
55106431 GAATATCTAG
* *
55106441 TTTGATTGTGTAGCTTCAAAAAAAAAAGGTTAGGCATATTAATTGAAAAATACATTATATTTAA
1 TTTGATTGCGTAGCTTCAAAAAAAAAAGGTTACGCATATTAATTGAAAAATACATTATATTTAA
* *
55106505 TTTGATTGCGTATCTTCAGAAAAAAAAAGTTTACGCATATTAATTGAAAAATACATTATATTTAA
1 TTTGATTGCGTAGCTTCA-AAAAAAAAAGGTTACGCATATTAATTGAAAAATACATTATATTTAA
55106570 CATATAATTA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
64 16 0.27
65 44 0.73
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.36
Consensus pattern (64 bp):
TTTGATTGCGTAGCTTCAAAAAAAAAAGGTTACGCATATTAATTGAAAAATACATTATATTTAA
Found at i:55106852 original size:19 final size:19
Alignment explanation
Indices: 55106828--55106865 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55106818 CTTTTCTTTT
55106828 AAAATAATTAAACATATAA
1 AAAATAATTAAACATATAA
55106847 AAAATAATTAAACATATAA
1 AAAATAATTAAACATATAA
55106866 TACACGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAATAATTAAACATATAA
Found at i:55108544 original size:17 final size:17
Alignment explanation
Indices: 55108522--55108563 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
55108512 TTTCCTTGAC
* *
55108522 CTTTAATCTTTCATCTT
1 CTTTAACCTTTCATATT
55108539 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
55108556 CTTGTAAC
1 CTT-TAAC
55108564 TATTTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.21, C:0.24, G:0.02, T:0.52
Consensus pattern (17 bp):
CTTTAACCTTTCATATT
Found at i:55112888 original size:180 final size:180
Alignment explanation
Indices: 55112572--55112932 Score: 677
Period size: 180 Copynumber: 2.0 Consensus size: 180
55112562 AAAAAACAAA
55112572 TCATAATATATATAATTGACTTGTAACAAGAACGTTCACAAGACACCTGATATTGATTATGAAGA
1 TCATAATATATATAATTGACTTGTAACAAGAACGTTCACAAGACACCTGATATTGATTATGAAGA
* *
55112637 GACATACTCTCTTGTGGTGGATGCAACTACTTTTAGGTTCTTGATTAGTCTGGCAATAGGAGAAT
66 GACATACTCTCTTGTGGTGGATGCAACTACTTTTAGGTTCTTGATTAGTCTGGCAATAAGAGAAG
55112702 GGCTTGATTTACGCCTAATGGATGTAGTTACAGCCTATTTATATGGCCAC
131 GGCTTGATTTACGCCTAATGGATGTAGTTACAGCCTATTTATATGGCCAC
*
55112752 TCATAATATATATAATTGACTTGTAACAAGAACGTTCACAAGACACTTGATATTGATTATGAAGA
1 TCATAATATATATAATTGACTTGTAACAAGAACGTTCACAAGACACCTGATATTGATTATGAAGA
*
55112817 GACATACTCTCTTGTGGTGGATGCAACTACTTTTAGGTTCTTGATTAGTCTGGTAATAAGAGAAG
66 GACATACTCTCTTGTGGTGGATGCAACTACTTTTAGGTTCTTGATTAGTCTGGCAATAAGAGAAG
*
55112882 GGCTTGATTTTCGCCTAATGGATGTAGTTACAGCCTATTTATATGGCCAC
131 GGCTTGATTTACGCCTAATGGATGTAGTTACAGCCTATTTATATGGCCAC
55112932 T
1 T
55112933 TGATAATAAC
Statistics
Matches: 176, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
180 176 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (180 bp):
TCATAATATATATAATTGACTTGTAACAAGAACGTTCACAAGACACCTGATATTGATTATGAAGA
GACATACTCTCTTGTGGTGGATGCAACTACTTTTAGGTTCTTGATTAGTCTGGCAATAAGAGAAG
GGCTTGATTTACGCCTAATGGATGTAGTTACAGCCTATTTATATGGCCAC
Found at i:55122618 original size:154 final size:154
Alignment explanation
Indices: 55122411--55122724 Score: 619
Period size: 154 Copynumber: 2.0 Consensus size: 154
55122401 TATCTAGCTC
55122411 ATTATTGAAGATCATATCATTTAGAAAAATATATATTGGAGATTGGATTGGATCAGATCACCCTT
1 ATTATTGAAGATCATATCATTTAGAAAAATATATATTGGAGATTGGATTGGATCAGATCACCCTT
55122476 ATCTAATACCTTCAATCATATGGATATTAGATTGATTTAGAACATTGCATTCTTAGCTACCAAGA
66 ATCTAATACCTTCAATCATATGGATATTAGATTGATTTAGAACATTGCATTCTTAGCTACCAAGA
55122541 GTCCTTGTTTACTGCTTATTTATT
131 GTCCTTGTTTACTGCTTATTTATT
*
55122565 ATTATTGAAGATCATATCATTTAGAAAAATATATATTGGAGATTGGATTGGATCGGATCACCCTT
1 ATTATTGAAGATCATATCATTTAGAAAAATATATATTGGAGATTGGATTGGATCAGATCACCCTT
55122630 ATCTAATACCTTCAATCATATGGATATTAGATTGATTTAGAACATTGCATTCTTAGCTACCAAGA
66 ATCTAATACCTTCAATCATATGGATATTAGATTGATTTAGAACATTGCATTCTTAGCTACCAAGA
55122695 GTCCTTGTTTACTGCTTATTTATT
131 GTCCTTGTTTACTGCTTATTTATT
55122719 ATTATT
1 ATTATT
55122725 CTGTTGTATT
Statistics
Matches: 159, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 159 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (154 bp):
ATTATTGAAGATCATATCATTTAGAAAAATATATATTGGAGATTGGATTGGATCAGATCACCCTT
ATCTAATACCTTCAATCATATGGATATTAGATTGATTTAGAACATTGCATTCTTAGCTACCAAGA
GTCCTTGTTTACTGCTTATTTATT
Found at i:55123447 original size:31 final size:31
Alignment explanation
Indices: 55123406--55123469 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
55123396 TCAAGGCTGA
*
55123406 AAGGGACTTAAAAT-TTTTTTTATCAACTTTT
1 AAGGGACTTAAAATAATTTTTT-TCAACTTTT
*
55123437 AAGGGGCTTAAAATAATTTTTTTCAACTTTT
1 AAGGGACTTAAAATAATTTTTTTCAACTTTT
55123468 AA
1 AA
55123470 AGAATTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (31 bp):
AAGGGACTTAAAATAATTTTTTTCAACTTTT
Found at i:55138560 original size:30 final size:31
Alignment explanation
Indices: 55138519--55138580 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
55138509 TTAGTACCTG
*
55138519 TATTATTTTTATCAATTTGACCCTTGTACTT
1 TATTATTTTTATCAATTTGACCCCTGTACTT
* *
55138550 TATT-TTTTTATCAGTTTGGCCCCTGTACTT
1 TATTATTTTTATCAATTTGACCCCTGTACTT
55138580 T
1 T
55138581 CGTTCTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.18, C:0.18, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATTTTTATCAATTTGACCCCTGTACTT
Found at i:55139210 original size:17 final size:17
Alignment explanation
Indices: 55139185--55139218 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55139175 TAAGTAATAC
*
55139185 TTCAAAAAATTTAAAAA
1 TTCAAAAAATCTAAAAA
*
55139202 TTCATAAAATCTAAAAA
1 TTCAAAAAATCTAAAAA
55139219 AAAACAATCT
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:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (17 bp):
TTCAAAAAATCTAAAAA
Found at i:55139426 original size:9 final size:8
Alignment explanation
Indices: 55139406--55139444 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
55139396 AAATAAACAA
*
55139406 AATTTTAA
1 AATTTTAT
55139414 AATTTTAT
1 AATTTTAT
*
55139422 GAATTTTTT
1 -AATTTTAT
55139431 AATTTTAT
1 AATTTTAT
55139439 AATTTT
1 AATTTT
55139445 TTTATGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (8 bp):
AATTTTAT
Found at i:55139426 original size:17 final size:16
Alignment explanation
Indices: 55139406--55139444 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
55139396 AAATAAACAA
55139406 AATTTTAAAATTTTAT
1 AATTTTAAAATTTTAT
**
55139422 GAATTTTTTAATTTTAT
1 -AATTTTAAAATTTTAT
55139439 AATTTT
1 AATTTT
55139445 TTTATGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
AATTTTAAAATTTTAT
Found at i:55139448 original size:17 final size:17
Alignment explanation
Indices: 55139414--55139446 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
55139404 AAAATTTTAA
55139414 AATTTTATGAATTTTTT
1 AATTTTATGAATTTTTT
55139431 AATTTTAT-AATTTTTT
1 AATTTTATGAATTTTTT
55139447 TATGTTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
AATTTTATGAATTTTTT
Found at i:55139586 original size:18 final size:19
Alignment explanation
Indices: 55139565--55139614 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
55139555 TCTTTTTTAC
55139565 TTTTTATTTTTAATA-ATT
1 TTTTTATTTTTAATATATT
**
55139583 TTTTGCTTTTT-ATATATT
1 TTTTTATTTTTAATATATT
55139601 TTTTAATATTTTTA
1 TTTT--TATTTTTA
55139615 GTATTTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
17 3 0.12
18 16 0.67
20 5 0.21
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTTATTTTTAATATATT
Found at i:55140042 original size:27 final size:27
Alignment explanation
Indices: 55140004--55140060 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
55139994 AAATACCTGA
*
55140004 CACCAGTGGAGGAACACCAAGTGGCGG
1 CACCAATGGAGGAACACCAAGTGGCGG
* *
55140031 CACCAATGGAGGAATATCAAGTGGCGG
1 CACCAATGGAGGAACACCAAGTGGCGG
55140058 CAC
1 CAC
55140061 TAAGGGGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.33, T:0.11
Consensus pattern (27 bp):
CACCAATGGAGGAACACCAAGTGGCGG
Found at i:55140286 original size:19 final size:18
Alignment explanation
Indices: 55140262--55140304 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
55140252 GAAAAAAAGA
55140262 AAGAAGAAGGAAGAAGGAG
1 AAGAAGAAGGAAGAAGG-G
*
55140281 AAGAAG-GGGAAGAAGGG
1 AAGAAGAAGGAAGAAGGG
55140298 AA-AAGAA
1 AAGAAGAA
55140305 AAAAAGGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 3 0.14
17 3 0.14
18 9 0.43
19 6 0.29
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (18 bp):
AAGAAGAAGGAAGAAGGG
Found at i:55140814 original size:95 final size:94
Alignment explanation
Indices: 55140653--55141104 Score: 732
Period size: 95 Copynumber: 4.8 Consensus size: 94
55140643 TTAATTTTGC
*
55140653 TAGTTAGTAATTTTATTTTGTTG-T--TAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTA
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTG
* ***
55140715 ATTTAAAATTTCATAATGTTT-AAATTTT
66 ATTTAAAATTTAATAATGTTTAAAAAAAT
* *
55140743 GCTAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAAGTAAAAAACATTGTTTATATTTAT
1 --TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTAT
55140808 TGATTTAAAATTTAATAATGTTTAAAAAAAT
64 TGATTTAAAATTTAATAATGTTTAAAAAAAT
* *
55140839 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAGTTAGTAAAAAACATTGTTCATATTTT
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTA---AGTAAAAAATATTGTTCATATTTA
55140904 TTGATTTAAAATTTAATAATGTTTAAAAAAAT
63 TTGATTTAAAATTTAATAATGTTTAAAAAAAT
55140936 TAGTTAGTAATTTTATTTTGTTGTTAGTAAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
1 TAGTTAGTAATTTTATTTTGTTGTTAGT-AGTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
55141001 GATTTAAAATTTAATAATGTTTAAAAAAAT
65 GATTTAAAATTTAATAATGTTTAAAAAAAT
55141031 TAGTTAGTAATTTTATTTTGTTGTTAGTAAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
1 TAGTTAGTAATTTTATTTTGTTGTTAGT-AGTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
55141096 GATTTAAAA
65 GATTTAAAA
55141105 AAATAATATA
Statistics
Matches: 341, Mismatches: 11, Indels: 13
0.93 0.03 0.04
Matches are distributed among these distances:
92 23 0.07
93 1 0.00
94 38 0.11
95 183 0.54
96 4 0.01
97 82 0.24
98 10 0.03
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.48
Consensus pattern (94 bp):
TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTG
ATTTAAAATTTAATAATGTTTAAAAAAAT
Found at i:55140974 original size:192 final size:190
Alignment explanation
Indices: 55140653--55141104 Score: 722
Period size: 192 Copynumber: 2.4 Consensus size: 190
55140643 TTAATTTTGC
55140653 TAGTTAGTAATTTTATTTTGTTG-T--TAGTAGTAGTA--AGTAAAAAATATTGTTCATATTTAT
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAGTAGTAAAAAATATTGTTCATATTTAT
* * ***
55140713 TAATTTAAAATTTCATAATGTTTAAATTTTGCTAGTTAGTAATTTTATTTTGTTGTTAGTAGTAG
66 TGATTTAAAATTTAATAATGTTTAAAAAAT-CTAGTTAGTAATTTTATTTTGTTGTTAGTAGTAG
*
55140778 TAGTAAGTAAAAAACATTGTTTATATTTATTGATTTAAAATTTAATAATGTTTAAAAAAAT
130 TAGTAAGTAAAAAACATTGTTCATATTTATTGATTTAAAATTTAATAATGTTTAAAAAAAT
* *
55140839 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAGTTAGTAAAAAACATTGTTCATATTTT
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAG-TAGTAAAAAATATTGTTCATATTTA
55140904 TTGATTTAAAATTTAATAATGTTTAAAAAAAT-TAGTTAGTAATTTTATTTTGTTGTTAGTAAGT
65 TTGATTTAAAATTTAATAATGTTT-AAAAAATCTAGTTAGTAATTTTATTTTGTTGTTAGT-AGT
*
55140968 AGTAGTAAGTAAAAAATATTGTTCATATTTATTGATTTAAAATTTAATAATGTTTAAAAAAAT
128 AGTAGTAAGTAAAAAACATTGTTCATATTTATTGATTTAAAATTTAATAATGTTTAAAAAAAT
55141031 TAGTTAGTAATTTTATTTTGTTGTTAGTA--AGTAGTAGTAAGTAAAAAATATTGTTCATATTTA
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAGT-AGTAAAAAATATTGTTCATATTTA
55141094 TTGATTTAAAA
65 TTGATTTAAAA
55141105 AAATAATATA
Statistics
Matches: 246, Mismatches: 11, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
186 23 0.09
187 1 0.00
189 12 0.05
190 41 0.17
191 28 0.11
192 137 0.56
193 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.48
Consensus pattern (190 bp):
TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAGTAGTAAAAAATATTGTTCATATTTAT
TGATTTAAAATTTAATAATGTTTAAAAAATCTAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGT
AGTAAGTAAAAAACATTGTTCATATTTATTGATTTAAAATTTAATAATGTTTAAAAAAAT
Found at i:55143266 original size:12 final size:12
Alignment explanation
Indices: 55143224--55143263 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
55143214 CCAGAACAAC
55143224 AAGAAGAGGAGG
1 AAGAAGAGGAGG
*
55143236 AAGAAGAGAAGG
1 AAGAAGAGGAGG
*
55143248 AAGAGGAGGAGG
1 AAGAAGAGGAGG
55143260 AAGA
1 AAGA
55143264 GGAAGAGGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (12 bp):
AAGAAGAGGAGG
Found at i:55143398 original size:21 final size:21
Alignment explanation
Indices: 55143372--55143418 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
55143362 ACGAGCCACC
*
55143372 GCAATACTTTACTCCTCCCGG
1 GCAATACTCTACTCCTCCCGG
*
55143393 GCAATACTCTACTCCTCCGGG
1 GCAATACTCTACTCCTCCCGG
55143414 GCAAT
1 GCAAT
55143419 TGGACCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCCGG
Found at i:55145968 original size:4 final size:4
Alignment explanation
Indices: 55145949--55146009 Score: 61
Period size: 4 Copynumber: 15.0 Consensus size: 4
55145939 ACACATTACT
* * *
55145949 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC TTTC TTTC TTTC TTTCC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTT-C
*
55145998 TCTC TTTC TTTC
1 TTTC TTTC TTTC
55146010 CCCTTTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
3 3 0.06
4 38 0.81
5 6 0.13
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:55145982 original size:17 final size:15
Alignment explanation
Indices: 55145949--55146010 Score: 66
Period size: 13 Copynumber: 4.6 Consensus size: 15
55145939 ACACATTACT
55145949 TTTCTTTCCTTCTTC
1 TTTCTTTCCTTCTTC
55145964 TTTCTTTCC-TC-TC
1 TTTCTTTCCTTCTTC
*
55145977 CTTCTTT-C-T-TTC
1 TTTCTTTCCTTCTTC
55145989 TTTCTTTCC-TC-TC
1 TTTCTTTCCTTCTTC
55146002 TTTCTTTCC
1 TTTCTTTCC
55146011 CCTTTTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 10 0.24
13 21 0.50
14 2 0.05
15 9 0.21
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTCTTTCCTTCTTC
Found at i:55145995 original size:25 final size:25
Alignment explanation
Indices: 55145961--55146009 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
55145951 TCTTTCCTTC
55145961 TTCTTTCTTTCCTCTCCTTCTTTCT
1 TTCTTTCTTTCCTCTCCTTCTTTCT
*
55145986 TTCTTTCTTTCCTCTCTTTCTTTC
1 TTCTTTCTTTCCTCTCCTTCTTTC
55146010 CCCTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (25 bp):
TTCTTTCTTTCCTCTCCTTCTTTCT
Found at i:55146882 original size:31 final size:31
Alignment explanation
Indices: 55146847--55146909 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
55146837 TGAGCTACAT
*
55146847 AGAAAAAATTTGGGTTTCATATATACAACTC
1 AGAAAAAATTTGAGTTTCATATATACAACTC
55146878 AGAAAAAATTTGAGTTTCATATATACAACTC
1 AGAAAAAATTTGAGTTTCATATATACAACTC
55146909 A
1 A
55146910 ATAATTCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (31 bp):
AGAAAAAATTTGAGTTTCATATATACAACTC
Found at i:55147354 original size:10 final size:10
Alignment explanation
Indices: 55147325--55147406 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 10
55147315 TTAATAAACC
55147325 ATATT-TAAA
1 ATATTATAAA
55147334 ATATT-TAAA
1 ATATTATAAA
*
55147343 ATTTTATAAA
1 ATATTATAAA
*
55147353 ATCTTAT-AA
1 ATATTATAAA
55147362 ATATTCATAAA
1 ATATT-ATAAA
55147373 A-ACTTATAAA
1 ATA-TTATAAA
55147383 A-A-TATAAAA
1 ATATTAT-AAA
55147392 ATATT-TAAA
1 ATATTATAAA
*
55147401 AAATTA
1 ATATTA
55147407 GAAATTATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
8 3 0.05
9 30 0.49
10 22 0.36
11 6 0.10
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATTATAAA
Found at i:55163004 original size:69 final size:69
Alignment explanation
Indices: 55162893--55163048 Score: 242
Period size: 69 Copynumber: 2.3 Consensus size: 69
55162883 TTTTTGCAGT
* * *
55162893 CGGAAATTACTCTGAATTTTAATTATTGCTTGCTTTTCCTTCATACAATTCCTTCTTAACTGCCA
1 CGGAAATGACACTGAATTTTAATTATTGCTTGCTTTTCCTTCATAAAATTCCTTCTTAACTGCCA
55162958 ACCA
66 ACCA
* *
55162962 CGGAAATGAGACTGAATTTTAATTATTGCTTG-TTTCTTCTTCATAAAATTCCTTCTTAACTGCC
1 CGGAAATGACACTGAATTTTAATTATTGCTTGCTTT-TCCTTCATAAAATTCCTTCTTAACTGCC
55163026 AACCA
65 AACCA
*
55163031 CGGAAATGACTCTGAATT
1 CGGAAATGACACTGAATT
55163049 CTGGTTGCAG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
68 3 0.04
69 76 0.96
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (69 bp):
CGGAAATGACACTGAATTTTAATTATTGCTTGCTTTTCCTTCATAAAATTCCTTCTTAACTGCCA
ACCA
Found at i:55171743 original size:19 final size:21
Alignment explanation
Indices: 55171709--55171755 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
55171699 TAAGTAATTT
55171709 TAAATATTGTATAAAAAATAG
1 TAAATATTGTATAAAAAATAG
55171730 TAAATA-TG-ATAAAAAATA-
1 TAAATATTGTATAAAAAATAG
*
55171748 TTAATATT
1 TAAATATT
55171756 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.21
19 11 0.46
20 2 0.08
21 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (21 bp):
TAAATATTGTATAAAAAATAG
Found at i:55173396 original size:72 final size:72
Alignment explanation
Indices: 55173308--55173444 Score: 220
Period size: 72 Copynumber: 1.9 Consensus size: 72
55173298 CAAGGTTGAC
* * * *
55173308 TTTAATACTATATTTAAATTGTTTATATAACTTTTAAAATACTCGACATGAAATCGAGCAATCAA
1 TTTAATACTATATTTAAACTGTTTATACAACTTTTAAAACACTCAACATGAAATCGAGCAATCAA
55173373 GGGTCAT
66 GGGTCAT
* *
55173380 TTTAATATTATGTTTAAACTGTTTATACAACTTTTAAAACACTCAACATGAAATCGAGCAATCAA
1 TTTAATACTATATTTAAACTGTTTATACAACTTTTAAAACACTCAACATGAAATCGAGCAATCAA
55173445 ATGTTACTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.36
Consensus pattern (72 bp):
TTTAATACTATATTTAAACTGTTTATACAACTTTTAAAACACTCAACATGAAATCGAGCAATCAA
GGGTCAT
Found at i:55193629 original size:14 final size:16
Alignment explanation
Indices: 55193591--55193622 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
55193581 CCCTAATTAG
55193591 AAAAGCAAATGAAAGA
1 AAAAGCAAATGAAAGA
55193607 AAAAG-AAA-GAAAGA
1 AAAAGCAAATGAAAGA
55193621 AA
1 AA
55193623 GAAAAAGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (16 bp):
AAAAGCAAATGAAAGA
Found at i:55210350 original size:23 final size:23
Alignment explanation
Indices: 55210318--55210368 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 23
55210308 TTTATATCTT
55210318 ATTATTAAAT-ATTAAGAAGTTA
1 ATTATTAAATAATTAAGAAGTTA
55210340 ATTATGTAAATAAAATTAAGAAGTTA
1 ATTAT-TAAAT--AATTAAGAAGTTA
55210366 ATT
1 ATT
55210369 CAAATAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.20
23 5 0.20
26 15 0.60
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (23 bp):
ATTATTAAATAATTAAGAAGTTA
Found at i:55213514 original size:2 final size:2
Alignment explanation
Indices: 55213507--55213557 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
55213497 CAAGTGTTAA
55213507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55213549 AT AT AT AT A
1 AT AT AT AT A
55213558 GAAAGTTATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55222443 original size:18 final size:19
Alignment explanation
Indices: 55222419--55222496 Score: 65
Period size: 18 Copynumber: 4.2 Consensus size: 19
55222409 AAAATTAGAA
**
55222419 AAAAATTATAAAAAATCGT
1 AAAAATTATAAAAAATAAT
*
55222438 -AAAATTTTATAAAAATAAT
1 AAAAATTATA-AAAAATAAT
*
55222457 AAAAATTATAAAATAT-AT
1 AAAAATTATAAAAAATAAT
*
55222475 AAATAAATA-AAAAAAT-AT
1 AAA-AATTATAAAAAATAAT
55222493 AAAA
1 AAAA
55222497 TTTTATAGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 1 0.02
18 24 0.49
19 16 0.33
20 8 0.16
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (19 bp):
AAAAATTATAAAAAATAAT
Found at i:55222496 original size:8 final size:8
Alignment explanation
Indices: 55222445--55222496 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 8
55222435 CGTAAAATTT
55222445 TATAAAAA
1 TATAAAAA
55222453 TAATAAAAA
1 T-ATAAAAA
55222462 TTATAAAATA
1 -TATAAAA-A
55222472 TATAAATAAA
1 TAT-AA-AAA
*
55222482 TAAAAAAA
1 TATAAAAA
55222490 TATAAAA
1 TATAAAA
55222497 TTTTATAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 10 0.27
9 18 0.49
10 7 0.19
11 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
TATAAAAA
Found at i:55222566 original size:10 final size:10
Alignment explanation
Indices: 55222419--55222566 Score: 59
Period size: 10 Copynumber: 15.6 Consensus size: 10
55222409 AAAATTAGAA
55222419 AAAAAT-TAT
1 AAAAATATAT
*
55222428 AAAAA-ATCGT
1 AAAAATAT-AT
* *
55222438 AAAATTTTAT
1 AAAAATATAT
55222448 AAAAATA-AT
1 AAAAATATAT
55222457 AAAAAT-TAT
1 AAAAATATAT
55222466 -AAAATATAT
1 AAAAATATAT
55222475 AAATAA-ATA-
1 AAA-AATATAT
55222484 AAAAA-ATAT
1 AAAAATATAT
*
55222493 -AAAAT-TTT
1 AAAAATATAT
* ** * *
55222501 ATAGTTGTAG
1 AAAAATATAT
*
55222511 AAAATTATA-
1 AAAAATATAT
55222520 AAAAATATAT
1 AAAAATATAT
55222530 AAATAA-ATAT
1 AAA-AATATAT
* * *
55222540 AAAATTCGTAA
1 AAAAAT-ATAT
55222551 AAAAATATAT
1 AAAAATATAT
55222561 AAAAAT
1 AAAAAT
55222567 TAACATACTA
Statistics
Matches: 102, Mismatches: 22, Indels: 29
0.67 0.14 0.19
Matches are distributed among these distances:
8 16 0.16
9 33 0.32
10 41 0.40
11 12 0.12
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (10 bp):
AAAAATATAT
Found at i:55226264 original size:37 final size:37
Alignment explanation
Indices: 55226214--55226284 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
55226204 GTTCGAGTCA
*
55226214 ACTCGAATAATTTGAATAAC-AGATTGGTGTAAATTTG
1 ACTCGAATAATTTGAAT-ACTAAATTGGTGTAAATTTG
55226251 ACTCGAATAATTTGAATACTAAATTGGTGTAAAT
1 ACTCGAATAATTTGAATACTAAATTGGTGTAAAT
55226285 ACTTCTTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 2 0.06
37 30 0.94
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.35
Consensus pattern (37 bp):
ACTCGAATAATTTGAATACTAAATTGGTGTAAATTTG
Found at i:55226439 original size:25 final size:24
Alignment explanation
Indices: 55226394--55226442 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
55226384 AAAATTCAAA
*
55226394 ATATTTATAAAAAATCCAAAATTT
1 ATATTTATAAAAAATACAAAATTT
* *
55226418 ATATTTTTAAAAAATTATAAAATTT
1 ATATTTATAAAAAA-TACAAAATTT
55226443 TTAGAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATTTATAAAAAATACAAAATTT
Found at i:55226444 original size:19 final size:19
Alignment explanation
Indices: 55226420--55226457 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55226410 CAAAATTTAT
55226420 ATTTTTAAAAAATTATAAA
1 ATTTTTAAAAAATTATAAA
* *
55226439 ATTTTTAGAAAATTCTAAA
1 ATTTTTAAAAAATTATAAA
55226458 GATAATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
ATTTTTAAAAAATTATAAA
Found at i:55226564 original size:3 final size:3
Alignment explanation
Indices: 55226556--55226580 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55226546 CTAAAGTATC
55226556 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
55226581 ACTTTGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55227232 original size:29 final size:29
Alignment explanation
Indices: 55227175--55227233 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
55227165 ATATGTATAA
*
55227175 AATTATTTAATATTATAAATAAAACATAT
1 AATTATTTAATATTATAAATAAAAAATAT
55227204 AATTATATTAAT-TTATAAA-AATAAAATAT
1 AATTAT-TTAATATTATAAATAA-AAAATAT
55227233 A
1 A
55227234 TCTAATTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 2 0.07
29 20 0.74
30 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AATTATTTAATATTATAAATAAAAAATAT
Found at i:55227241 original size:24 final size:25
Alignment explanation
Indices: 55227193--55227241 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
55227183 AATATTATAA
*
55227193 ATAAAACATATAATTATATTAATTT
1 ATAAAACATATAAATATATTAATTT
55227218 ATAAAA-ATA-AAATATATCTAATTT
1 ATAAAACATATAAATATAT-TAATTT
55227242 GTACTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 9 0.41
25 6 0.27
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAAAACATATAAATATATTAATTT
Done.