Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 157 of 172
Found at i:51419284 original size:42 final size:41
Alignment explanation
Indices: 51419194--51419290 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 41
51419184 AACATAATGT
* * *
51419194 TTAATAATAATTTATAAAATTTTAAAATTATACATGATAATA
1 TTAATAATAATGTAT-AAATTTTAAAATTATAAATAATAATA
51419236 TGTAATATATAATGTAT-AATTTTAAAA-TATAAAATAATATATA
1 T-TAATA-ATAATGTATAAATTTTAAAATTAT-AAATAATA-ATA
51419279 TTAATAAATAAT
1 TTAAT-AATAAT
51419291 ATAATATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
41 3 0.06
42 26 0.55
43 10 0.21
44 8 0.17
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (41 bp):
TTAATAATAATGTATAAATTTTAAAATTATAAATAATAATA
Found at i:51419304 original size:20 final size:21
Alignment explanation
Indices: 51419264--51419304 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
51419254 ATTTTAAAAT
51419264 ATAAAATAATATATATTAATAA
1 ATAAAATAATATATA-TAATAA
*
51419286 ATAATATAATATATA-AATA
1 ATAAAATAATATATATAATA
51419305 TACTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
22 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAAAATAATATATATAATAA
Found at i:51419339 original size:24 final size:23
Alignment explanation
Indices: 51419312--51419388 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 23
51419302 ATATACTTGA
51419312 AAATAACAAAAATAATATACAAAT
1 AAATAACAAAAATAATATA-AAAT
*** *
51419336 AAATAA-AATTTTATATGTATAAAT
1 AAATAACAAAAATA-ATATA-AAAT
*
51419360 AAATAACAAATAAT-ATTTAAAAT
1 AAATAACAAA-AATAATATAAAAT
51419383 AAATAA
1 AAATAA
51419389 ATTTAAAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
23 14 0.34
24 24 0.59
25 2 0.05
26 1 0.02
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (23 bp):
AAATAACAAAAATAATATAAAAT
Found at i:51419394 original size:15 final size:15
Alignment explanation
Indices: 51419367--51419400 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
51419357 AATAAATAAC
51419367 AAATAATATTTAAAA
1 AAATAATATTTAAAA
51419382 TAAATAA-ATTTAAAA
1 -AAATAATATTTAAAA
51419397 AAAT
1 AAAT
51419401 GATTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 8 0.44
16 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAATATTTAAAA
Found at i:51422163 original size:43 final size:43
Alignment explanation
Indices: 51422115--51422196 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
51422105 CACCGCTCAT
* * *
51422115 GACTTTTAGCGGCGTTTATCCCACAAATGCCGTTAAAAGCTAG
1 GACTTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAAGCTAG
*
51422158 GACTTTTAGCGGTGCTTATCCCACAAACGCCGCTAAAAG
1 GACTTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAAG
51422197 TCATGATCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (43 bp):
GACTTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAAGCTAG
Found at i:51423792 original size:17 final size:17
Alignment explanation
Indices: 51423772--51423809 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
51423762 AGTGCTTCAC
* *
51423772 TGATGCAAGTGTTATAG
1 TGATGAAAGTGTTACAG
51423789 TGATGAAAGTGTTACAG
1 TGATGAAAGTGTTACAG
51423806 TGAT
1 TGAT
51423810 ATATGTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (17 bp):
TGATGAAAGTGTTACAG
Found at i:51423817 original size:17 final size:17
Alignment explanation
Indices: 51423797--51423832 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
51423787 AGTGATGAAA
*
51423797 GTGTTACAGTGATATAT
1 GTGTTACAGTAATATAT
*
51423814 GTGTTTCAGTAATATAT
1 GTGTTACAGTAATATAT
51423831 GT
1 GT
51423833 AAATTAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (17 bp):
GTGTTACAGTAATATAT
Found at i:51429586 original size:20 final size:20
Alignment explanation
Indices: 51429561--51429600 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
51429551 GATCTTGCAG
*
51429561 GGGATCATATAAGCATCAAA
1 GGGATCACATAAGCATCAAA
51429581 GGGATCACATAAGCATCAAA
1 GGGATCACATAAGCATCAAA
51429601 TCAGCCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.17
Consensus pattern (20 bp):
GGGATCACATAAGCATCAAA
Found at i:51433746 original size:21 final size:22
Alignment explanation
Indices: 51433717--51433763 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
51433707 CAGAAGGAGT
*
51433717 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51433739 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51433760 GAGT
1 GAGT
51433764 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:51436836 original size:21 final size:22
Alignment explanation
Indices: 51436807--51436853 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
51436797 CAGAAGGAGT
*
51436807 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51436829 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51436850 GAGT
1 GAGT
51436854 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:51440046 original size:21 final size:22
Alignment explanation
Indices: 51440017--51440063 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
51440007 CAGAAGGAGT
*
51440017 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51440039 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51440060 GAGT
1 GAGT
51440064 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:51443256 original size:21 final size:22
Alignment explanation
Indices: 51443227--51443273 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
51443217 CAGAAGGAGT
*
51443227 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51443249 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51443270 GAGT
1 GAGT
51443274 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:51446466 original size:21 final size:22
Alignment explanation
Indices: 51446437--51446483 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
51446427 CAGAAGGAGT
*
51446437 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51446459 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51446480 GAGT
1 GAGT
51446484 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:51449676 original size:21 final size:22
Alignment explanation
Indices: 51449647--51449693 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
51449637 CAGAAGGAGT
*
51449647 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51449669 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
51449690 GAGT
1 GAGT
51449694 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:51463090 original size:21 final size:20
Alignment explanation
Indices: 51463050--51463091 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
51463040 TATTAGAAAT
*
51463050 ACTATAATTTAATGAAATTA
1 ACTATAATTTAATAAAATTA
*
51463070 ACTATTATTTAATTAAAATTA
1 ACTATAATTTAA-TAAAATTA
51463091 A
1 A
51463092 AATTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (20 bp):
ACTATAATTTAATAAAATTA
Found at i:51479301 original size:38 final size:39
Alignment explanation
Indices: 51479250--51479323 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
51479240 TAATTTGAAA
*
51479250 ATTTTTCAAAAAT-A-TTTAAAAGTTATAAAATAAAACTT
1 ATTTTTCAAAAATAAGTTTAAAAATTA-AAAATAAAACTT
51479288 ATTTTATC-AAAATAAGTTTAAAAATTAAAAATAAAA
1 ATTTT-TCAAAAATAAGTTTAAAAATTAAAAATAAAA
51479324 AATTAATATG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
38 10 0.31
39 12 0.38
40 10 0.31
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (39 bp):
ATTTTTCAAAAATAAGTTTAAAAATTAAAAATAAAACTT
Found at i:51487151 original size:18 final size:18
Alignment explanation
Indices: 51487117--51487176 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
51487107 TTTTATTCTT
*
51487117 TTAAAATAATAATTATATA
1 TTAAAA-AATTATTATATA
51487136 TTAAAAAATTATTATAGT-
1 TTAAAAAATTATTATA-TA
*
51487154 GT-AAAAATTA-TATATA
1 TTAAAAAATTATTATATA
51487170 CTTAAAA
1 -TTAAAA
51487177 TATAGAGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
15 1 0.03
16 4 0.12
17 9 0.26
18 13 0.38
19 7 0.21
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (18 bp):
TTAAAAAATTATTATATA
Found at i:51487175 original size:17 final size:16
Alignment explanation
Indices: 51487130--51487176 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
51487120 AAATAATAAT
51487130 TATATATTAAAAAATTA
1 TATATATT-AAAAATTA
51487147 T-TATAGTGTAAAAATTA
1 TATATA-T-TAAAAATTA
51487164 TATATACTTAAAA
1 TATATA-TTAAAA
51487177 TATAGAGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.15
17 16 0.62
18 6 0.23
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (16 bp):
TATATATTAAAAATTA
Found at i:51487435 original size:18 final size:18
Alignment explanation
Indices: 51487412--51487449 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
51487402 AAATAAAATT
51487412 ATGCATAATAAA-ATTAAA
1 ATGCATAA-AAATATTAAA
51487430 ATGCATAAAAATATTAAA
1 ATGCATAAAAATATTAAA
51487448 AT
1 AT
51487450 AAAATTTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
ATGCATAAAAATATTAAA
Found at i:51490020 original size:18 final size:18
Alignment explanation
Indices: 51489979--51490021 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
51489969 TTTATTTTTT
* * *
51489979 AAAAATTTTTAAATTTAT
1 AAAAATTTTAAAATTAAA
*
51489997 ATAAATTTTAAAATTAAA
1 AAAAATTTTAAAATTAAA
51490015 AAAAATT
1 AAAAATT
51490022 ATATCTTTCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAAATTTTAAAATTAAA
Found at i:51490074 original size:19 final size:19
Alignment explanation
Indices: 51490039--51490095 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
51490029 TCAAAAAAAA
*
51490039 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
51490057 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
* *
51490076 GA-AAATTATATTGAATTTT
1 TATAAA-TATTTTGAATTTT
51490095 T
1 T
51490096 TTAGAGACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 10 0.30
19 23 0.70
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:51490213 original size:23 final size:23
Alignment explanation
Indices: 51490179--51490241 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
51490169 AAATTGTAAA
51490179 ATTCAACTTAACTCAAACT-ACTT-
1 ATTCAA-TTAACTCAAA-TAACTTG
* *
51490202 ATTTAATTTAACTTAAATAACTTG
1 ATTCAA-TTAACTCAAATAACTTG
51490226 ATTCAATTAACTCAAA
1 ATTCAATTAACTCAAA
51490242 ATTTGAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 27 0.82
24 5 0.15
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (23 bp):
ATTCAATTAACTCAAATAACTTG
Found at i:51496587 original size:33 final size:33
Alignment explanation
Indices: 51496545--51496609 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
51496535 TTGAACTGAA
51496545 CCTTACTAATTAAGTGCTTTTATGATTTAATCC
1 CCTTACTAATTAAGTGCTTTTATGATTTAATCC
*
51496578 CCTTGCTAATTAAGTGCTTTTATGATTTAATC
1 CCTTACTAATTAAGTGCTTTTATGATTTAATC
51496610 TTGTCAGGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (33 bp):
CCTTACTAATTAAGTGCTTTTATGATTTAATCC
Found at i:51501517 original size:52 final size:52
Alignment explanation
Indices: 51501401--51501554 Score: 168
Period size: 52 Copynumber: 2.9 Consensus size: 52
51501391 ACATAACATG
* * * *
51501401 CCGATGCCATATCTCAGATATGGTCTTATACGGAATCACATTATCACATCACA
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGAA-CACATAATCACATCACA
* * ***
51501454 CTGATGCCATAGCCCAGCTATGGTCTTATACGGGA-ACATGAATCACATTGTA
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGAACACAT-AATCACATCACA
* *
51501506 CCGATGCCATAGCCCAACTATGGTCTTATACGAAAGCACAT-ATCACATC
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGAA-CACATAATCACATC
51501555 TTTTCAGTCA
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
51 4 0.05
52 46 0.55
53 30 0.36
54 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (52 bp):
CCGATGCCATAGCCCAGCTATGGTCTTATACGGAACACATAATCACATCACA
Found at i:51506907 original size:25 final size:26
Alignment explanation
Indices: 51506860--51506912 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
51506850 TATCTTATCA
51506860 AATATGCTAACTTAATTCAATC-ATC
1 AATATGCTAACTTAATTCAATCAATC
*
51506885 AATATGCTAA-TTAATTTCTATCAATC
1 AATATGCTAACTTAA-TTCAATCAATC
51506911 AA
1 AA
51506913 CCAATTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 4 0.16
25 16 0.64
26 5 0.20
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (26 bp):
AATATGCTAACTTAATTCAATCAATC
Found at i:51507811 original size:26 final size:26
Alignment explanation
Indices: 51507779--51507839 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
51507769 ATAAGAGCCA
* **
51507779 TAATCAGGAAGTTCACAAAGAATTTT
1 TAATCAGGAAGCTCACAAAGAACCTT
*
51507805 TAATCAGGAAGCTCACGAAGAACCTT
1 TAATCAGGAAGCTCACAAAGAACCTT
51507831 TAATCAGGA
1 TAATCAGGA
51507840 GCTTGGGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAACCTT
Found at i:51513973 original size:21 final size:21
Alignment explanation
Indices: 51513944--51513983 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51513934 TTGATTTTTT
*
51513944 TTCACGATGAAAATCTTGAAA
1 TTCAAGATGAAAATCTTGAAA
*
51513965 TTCAAGATGAAAATGTTGA
1 TTCAAGATGAAAATCTTGA
51513984 TGTGGCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (21 bp):
TTCAAGATGAAAATCTTGAAA
Found at i:51520415 original size:20 final size:21
Alignment explanation
Indices: 51520377--51520418 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
51520367 ATTATTCCCG
*
51520377 AGCTATTTTTAGGGCCCCGTA
1 AGCTATTTTTAAGGCCCCGTA
*
51520398 AGCTCTTTTTAAGG-CCCGTA
1 AGCTATTTTTAAGGCCCCGTA
51520418 A
1 A
51520419 ATGTTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (21 bp):
AGCTATTTTTAAGGCCCCGTA
Found at i:51521691 original size:34 final size:34
Alignment explanation
Indices: 51521653--51521757 Score: 173
Period size: 34 Copynumber: 3.2 Consensus size: 34
51521643 TAGATGCAAC
51521653 TTAACAAGCAAATGCCTCTAAAATAATAACAAAA
1 TTAACAAGCAAATGCCTCTAAAATAATAACAAAA
51521687 TTAACAAGCAAATGCCTCTAAAATAATAACAAAA
1 TTAACAAGCAAATGCCTCTAAAATAATAACAAAA
*
51521721 TT---AA-CAAATGCCTCTAAAATAATAATAAAA
1 TTAACAAGCAAATGCCTCTAAAATAATAACAAAA
51521751 TTAACAA
1 TTAACAA
51521758 TAAAATAAGT
Statistics
Matches: 67, Mismatches: 1, Indels: 7
0.89 0.01 0.09
Matches are distributed among these distances:
30 27 0.40
31 2 0.03
33 2 0.03
34 36 0.54
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.23
Consensus pattern (34 bp):
TTAACAAGCAAATGCCTCTAAAATAATAACAAAA
Found at i:51521729 original size:30 final size:30
Alignment explanation
Indices: 51521661--51521757 Score: 149
Period size: 30 Copynumber: 3.1 Consensus size: 30
51521651 ACTTAACAAG
51521661 CAAATGCCTCTAAAATAATAACAAAATTAACAA
1 CAAATGCCTCTAAAATAATAACAAAATT---AA
51521694 GCAAATGCCTCTAAAATAATAACAAAATTAA
1 -CAAATGCCTCTAAAATAATAACAAAATTAA
*
51521725 CAAATGCCTCTAAAATAATAATAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
51521755 CAA
1 CAA
51521758 TAAAATAAGT
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
30 32 0.52
31 2 0.03
34 28 0.45
ACGTcount: A:0.57, C:0.16, G:0.04, T:0.23
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:51521812 original size:22 final size:22
Alignment explanation
Indices: 51521787--51521829 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
51521777 TATCTAAACA
51521787 ATAATAACAAAATAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
* * *
51521809 ATAATCATAAAATGGTAGCAA
1 ATAATAACAAAATAGTAGCAA
51521830 AATAGGACGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:51526859 original size:15 final size:15
Alignment explanation
Indices: 51526835--51526868 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
51526825 AACAATTACG
* *
51526835 ATAATGCGAGTAAAA
1 ATAATACGAGCAAAA
51526850 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
51526865 ATAA
1 ATAA
51526869 CAAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.18
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:51527889 original size:9 final size:9
Alignment explanation
Indices: 51527872--51527907 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
51527862 TTCTATAAAC
51527872 AACAAAAAA
1 AACAAAAAA
51527881 CAA-AAAAAA
1 -AACAAAAAA
51527890 AACAAAAAA
1 AACAAAAAA
51527899 AACAAAAAA
1 AACAAAAAA
51527908 GTCCTCTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 2 0.08
9 21 0.84
10 2 0.08
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (9 bp):
AACAAAAAA
Found at i:51527907 original size:11 final size:11
Alignment explanation
Indices: 51527875--51527900 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
51527865 TATAAACAAC
51527875 AAAAAACAAAA
1 AAAAAACAAAA
51527886 AAAAAACAAAA
1 AAAAAACAAAA
51527897 AAAA
1 AAAA
51527901 CAAAAAAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:51528260 original size:16 final size:16
Alignment explanation
Indices: 51528222--51528262 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
51528212 TTCGTTTATC
*
51528222 AAAAATAAAAAACAAT
1 AAAAATAAAAAACAAA
* *
51528238 AATAATAAAAAATAAA
1 AAAAATAAAAAACAAA
51528254 AAAAATAAA
1 AAAAATAAA
51528263 GGTAAAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAATAAAAAACAAA
Found at i:51532967 original size:43 final size:43
Alignment explanation
Indices: 51532919--51533065 Score: 188
Period size: 43 Copynumber: 3.4 Consensus size: 43
51532909 CCAAATATGA
* * * *
51532919 TCTTACATGTTATCACATATCGATGCCACTGTCCTAGACAGGG
1 TCTTACACGTAATCACATATCGATGCCAATGTCCTAGACATGG
* *
51532962 TCTTACACGAAATCACATAACGATGCCAATGTCCTAGACATGG
1 TCTTACACGTAATCACATATCGATGCCAATGTCCTAGACATGG
* * *
51533005 TCTTACACGTAATCACA-ATACAATGCCAATGTCCCAGACATGT
1 TCTTACACGTAATCACATAT-CGATGCCAATGTCCTAGACATGG
*
51533048 TCTTACATGTAATCACAT
1 TCTTACACGTAATCACAT
51533066 CTCGGTAATC
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.01
43 89 0.99
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (43 bp):
TCTTACACGTAATCACATATCGATGCCAATGTCCTAGACATGG
Found at i:51542383 original size:40 final size:40
Alignment explanation
Indices: 51542306--51542392 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
51542296 AATTCATTAC
* * *
51542306 TTTAGTAATTTCACAGTTCAATGCAATACACATAACAATA
1 TTTAGTAACTTCACAATTCAATGCAATACACAAAACAATA
** * *
51542346 TTTAGTAACTTCACAATTCAATTTAATGCTCAAAACAATA
1 TTTAGTAACTTCACAATTCAATGCAATACACAAAACAATA
*
51542386 TTCAGTA
1 TTTAGTA
51542393 TTCCATAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (40 bp):
TTTAGTAACTTCACAATTCAATGCAATACACAAAACAATA
Found at i:51543111 original size:16 final size:15
Alignment explanation
Indices: 51543090--51543120 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
51543080 AACTTGAATT
51543090 TTTCCTTTCTTCTTTC
1 TTTCCTTT-TTCTTTC
51543106 TTTCCTTTTTCTTTC
1 TTTCCTTTTTCTTTC
51543121 CTGCTCTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCCTTTTTCTTTC
Found at i:51543515 original size:25 final size:23
Alignment explanation
Indices: 51543471--51543531 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
51543461 ATTTTAATTT
*
51543471 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
51543495 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
51543519 ATATAAATTATAT
1 AT-TTAATTATAT
51543532 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:51543520 original size:35 final size:34
Alignment explanation
Indices: 51543479--51543558 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 34
51543469 TTATTTAATA
* *
51543479 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTAT-ATTTAAATATCATAAATT
*
51543513 CATATAATATAAATTATATTTAAATATCATTAATT
1 -ATATAATATAAATTATATTTAAATATCATAAATT
51543548 ATATAAT-TAAA
1 ATATAATATAAA
51543559 ACAAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 25 0.61
36 5 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (34 bp):
ATATAATATAAATTATATTTAAATATCATAAATT
Found at i:51545886 original size:14 final size:12
Alignment explanation
Indices: 51545847--51545883 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
51545837 TTTCAAATCT
51545847 CTATTCTCTCTC
1 CTATTCTCTCTC
51545859 CTATTCTCTCTC
1 CTATTCTCTCTC
51545871 CTATTCTC-CTC
1 CTATTCTCTCTC
51545882 CT
1 CT
51545884 CCTCTTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.08, C:0.43, G:0.00, T:0.49
Consensus pattern (12 bp):
CTATTCTCTCTC
Found at i:51545929 original size:3 final size:3
Alignment explanation
Indices: 51545921--51545945 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
51545911 CTTTCATTCA
51545921 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
51545946 CCATGTCCTC
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:51555941 original size:21 final size:20
Alignment explanation
Indices: 51555915--51555953 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
51555905 TTGATAACTT
51555915 GAATTTTGAAATTACATTTTA
1 GAATTTTGAAATT-CATTTTA
51555936 GAATTTTGAAATTCATTT
1 GAATTTTGAAATTCATTT
51555954 ATTATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (20 bp):
GAATTTTGAAATTCATTTTA
Found at i:51557475 original size:17 final size:17
Alignment explanation
Indices: 51557453--51557491 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
51557443 CCTAAAGGTG
*
51557453 ATTTTA-TCTTCTTTATT
1 ATTTTACTCTTATTT-TT
51557470 ATTTTACTCTTATTTTT
1 ATTTTACTCTTATTTTT
51557487 ATTTT
1 ATTTT
51557492 TATTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTACTCTTATTTTT
Found at i:51557578 original size:13 final size:13
Alignment explanation
Indices: 51557543--51557571 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
51557533 TATATACATC
51557543 ATAATAAAAATAT
1 ATAATAAAAATAT
51557556 ATAATAAAAATAT
1 ATAATAAAAATAT
51557569 ATA
1 ATA
51557572 TACAAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATAAAAATAT
Found at i:51557585 original size:15 final size:14
Alignment explanation
Indices: 51557543--51557595 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
51557533 TATATACATC
51557543 ATAAT-AAAAATAT
1 ATAATAAAAAATAT
51557556 ATAATAAAAATATAT
1 ATAATAAAAA-ATAT
51557571 ATACA-AAACAAATAT
1 ATA-ATAAA-AAATAT
51557586 A-AA-AAAAAAT
1 ATAATAAAAAAT
51557596 TTACCTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.11
13 9 0.25
14 5 0.14
15 15 0.42
16 3 0.08
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (14 bp):
ATAATAAAAAATAT
Found at i:51557697 original size:11 final size:11
Alignment explanation
Indices: 51557681--51557715 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
51557671 CCCTTCCCCC
51557681 CTCCCTTCTCT
1 CTCCCTTCTCT
51557692 CTCCCTTCTCT
1 CTCCCTTCTCT
51557703 CTTCCC-TCTCT
1 C-TCCCTTCTCT
51557714 CT
1 CT
51557716 TCTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:51558266 original size:11 final size:11
Alignment explanation
Indices: 51558242--51558284 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
51558232 TTCTAATACG
*
51558242 TATATATATTA
1 TATATATTTTA
*
51558253 TATGTATTTTA
1 TATATATTTTA
* *
51558264 TATATATTATG
1 TATATATTTTA
51558275 TATATATTTT
1 TATATATTTT
51558285 TTAATGCCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATATTTTA
Found at i:51558412 original size:28 final size:25
Alignment explanation
Indices: 51558342--51558412 Score: 63
Period size: 29 Copynumber: 2.6 Consensus size: 25
51558332 TTATATCATC
*
51558342 TTATGTATATATT-CTTAAATACTA
1 TTATGTATATATTATTTAAATACTA
*
51558366 TTATATACATATATATATTTAAAATACCATA
1 TTATGT--ATATAT-TATTT-AAATA-C-TA
51558397 TTATGTATATATTATT
1 TTATGTATATATTATT
51558413 ATTACAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
24 5 0.14
26 6 0.16
27 1 0.03
28 6 0.16
29 11 0.30
30 1 0.03
31 7 0.19
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (25 bp):
TTATGTATATATTATTTAAATACTA
Found at i:51560779 original size:23 final size:22
Alignment explanation
Indices: 51560751--51560819 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
51560741 AAACGTAATA
51560751 TCTTTATATATTAAAATATATTT
1 TCTTTATAT-TTAAAATATATTT
*
51560774 TCTTTA-ATTTGAAAATATATTA
1 TCTTTATATTT-AAAATATATTT
* *
51560796 TATATATATTCTAAAATATATTT
1 TCTTTATATT-TAAAATATATTT
51560819 T
1 T
51560820 GTTAGAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 2 0.05
22 16 0.41
23 20 0.51
24 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (22 bp):
TCTTTATATTTAAAATATATTT
Found at i:51572295 original size:18 final size:17
Alignment explanation
Indices: 51572248--51572298 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
51572238 TGCATTTCTT
*
51572248 TAAAAATTTATAAAATTA
1 TAAAAATAT-TAAAATTA
51572266 TAAAACATTATTAAAATATA
1 TAAAA-A-TATTAAAAT-TA
51572286 TAAAAATATTAAA
1 TAAAAATATTAAA
51572299 TAAATTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 12 0.41
19 8 0.28
20 9 0.31
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATATTAAAATTA
Found at i:51572972 original size:17 final size:17
Alignment explanation
Indices: 51572935--51572982 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
51572925 TAACTTTTAA
51572935 ATAATTTTTAT-TTTTG
1 ATAATTTTTATATTTTG
51572951 A-AATTTTTATATTTT-
1 ATAATTTTTATATTTTG
*
51572966 ATTAATTTTTAAATTTT
1 A-TAATTTTTATATTTT
51572983 CTAATAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.36
16 5 0.18
17 13 0.46
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
ATAATTTTTATATTTTG
Found at i:51575898 original size:22 final size:22
Alignment explanation
Indices: 51575865--51575919 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
51575855 TATGAAAATA
*
51575865 ATACTATGTATAA-AAGTATATAT
1 ATACTA-GTATAATAA-AATATAT
*
51575888 ATACTCGTATAATAAAATATAT
1 ATACTAGTATAATAAAATATAT
51575910 ATACTAGTAT
1 ATACTAGTAT
51575920 TAACAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (22 bp):
ATACTAGTATAATAAAATATAT
Found at i:51576096 original size:3 final size:3
Alignment explanation
Indices: 51576034--51576087 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
51576024 AAGTACCTAT
* *
51576034 TAA TAA TAT TATA TAA -ATA TAA TAA TAA TAA TAA TAA TAA TAA CAA
1 TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
51576080 CAA TAA TA
1 TAA TAA TA
51576088 GCAATAATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 1 0.02
3 40 0.91
4 3 0.07
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:51576096 original size:12 final size:12
Alignment explanation
Indices: 51576054--51576096 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
51576044 ATATAAATAT
*
51576054 AATAATAATAAT
1 AATAATAATAAC
51576066 AATAATAATAAC
1 AATAATAATAAC
* *
51576078 AACAATAATAGC
1 AATAATAATAAC
51576090 AATAATA
1 AATAATA
51576097 GTAAAAATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:51576184 original size:18 final size:17
Alignment explanation
Indices: 51576141--51576186 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
51576131 AGGTAAGGAA
51576141 AATA-AAATA-AAATAT
1 AATAGAAATATAAATAT
* *
51576156 ATTAGATATATAAATAT
1 AATAGAAATATAAATAT
51576173 AATAGTAAATATAA
1 AATAG-AAATATAA
51576187 TAATGTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 3 0.12
16 4 0.17
17 10 0.42
18 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (17 bp):
AATAGAAATATAAATAT
Found at i:51576267 original size:3 final size:3
Alignment explanation
Indices: 51576259--51576352 Score: 66
Period size: 3 Copynumber: 30.3 Consensus size: 3
51576249 AATATTTATA
* * *
51576259 AAT AAT AAT AGT AAT AAT AAT AAT AAT ATT AAGT -AT AGT -AT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT -AAT
* * * *
51576304 AAT ATGT ACAT AAC AGT AAT AAT AAT AAGT AAC AAT AAT AAT AAT AAT
1 AAT A-AT A-AT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
51576352 A
1 A
51576353 TAGAAATTCA
Statistics
Matches: 70, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
2 2 0.03
3 58 0.83
4 10 0.14
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:51576412 original size:16 final size:16
Alignment explanation
Indices: 51576377--51576409 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
51576367 AACTAAACAT
*
51576377 AATATAATAATATTAA
1 AATAAAATAATATTAA
51576393 AATAAAATAAT-TTAA
1 AATAAAATAATATTAA
51576408 AA
1 AA
51576410 ATACTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAATAATATTAA
Found at i:51576974 original size:20 final size:20
Alignment explanation
Indices: 51576949--51576994 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
51576939 CATTTGGTGA
51576949 GGAGAGAAAGAAA-AAAAAAG
1 GGAGAG-AAGAAAGAAAAAAG
* *
51576969 GGAGAGAAGAAAGAGAGAAG
1 GGAGAGAAGAAAGAAAAAAG
51576989 GGAGAG
1 GGAGAG
51576995 GGAGGAGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (20 bp):
GGAGAGAAGAAAGAAAAAAG
Found at i:51578406 original size:14 final size:15
Alignment explanation
Indices: 51578382--51578410 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
51578372 TTTTTTTTTT
51578382 GAAAGGCAGAAATTG
1 GAAAGGCAGAAATTG
51578397 GAAA-GCAGAAATTG
1 GAAAGGCAGAAATTG
51578411 AAAATACCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.07, G:0.31, T:0.14
Consensus pattern (15 bp):
GAAAGGCAGAAATTG
Found at i:51578492 original size:73 final size:73
Alignment explanation
Indices: 51578402--51578540 Score: 242
Period size: 73 Copynumber: 1.9 Consensus size: 73
51578392 AATTGGAAAG
*
51578402 CAGAAATTGAAAATACCTCAGCGTGCCCTGACGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 CAGAAATTGAAAATACCTCAGCGCGCCCTGACGCTCAACTCACCTCTCGCAATATGAGTTGATTT
51578467 TTGAAAAA
66 TTGAAAAA
* * *
51578475 CAGAAATTGAAATTACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 CAGAAATTGAAAATACCTCAGCGCGCCCTGACGCTCAACTCACCTCTCGCAATATGAGTTGATTT
51578540 T
66 T
51578541 CTTTCTTTCT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (73 bp):
CAGAAATTGAAAATACCTCAGCGCGCCCTGACGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TTGAAAAA
Found at i:51578506 original size:178 final size:178
Alignment explanation
Indices: 51578229--51578577 Score: 603
Period size: 178 Copynumber: 2.0 Consensus size: 178
51578219 AAAGCATACT
* * *
51578229 TTGAAAATACCTCAACATGTGACCCGAGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTGAT
1 TTGAAAATACCTCAACA-GTGACCCGACGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAA
* *
51578294 AAACAGGAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
65 AAACAGAAATTGAAATTACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
51578359 TTTTCTTTCTTTCTTTTTTTTTTGAAAGGCAGAAATTGGAAAGCAGAAA
130 TTTTCTTTCTTTCTTTTTTTTTTGAAAGGCAGAAATTGGAAAGCAGAAA
*
51578408 TTGAAAATACCTCAGC-GTG-CCCTGACGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
1 TTGAAAATACCTCAACAGTGACCC-GACGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGA
51578471 AAAACAGAAATTGAAATTACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
64 AAAACAGAAATTGAAATTACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
51578536 ATTTTCTTTCTTTCTTTTTTTTTTGAAAGGCAGAAATTGGAA
129 ATTTTCTTTCTTTCTTTTTTTTTTGAAAGGCAGAAATTGGAA
51578578 TTTTTTTGAA
Statistics
Matches: 162, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
176 3 0.02
177 34 0.21
178 110 0.68
179 15 0.09
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (178 bp):
TTGAAAATACCTCAACAGTGACCCGACGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAA
AACAGAAATTGAAATTACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTCTTTCTTTCTTTTTTTTTTGAAAGGCAGAAATTGGAAAGCAGAAA
Found at i:51578581 original size:25 final size:24
Alignment explanation
Indices: 51578553--51578603 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
51578543 TTCTTTCTTT
* *
51578553 TTTTTTTGAAAGGCAGAAATTGGAA
1 TTTTTTTGAAA-ACAGAAATTGAAA
51578578 TTTTTTTGAAAACAGAAATTGAAA
1 TTTTTTTGAAAACAGAAATTGAAA
51578602 TT
1 TT
51578604 ACCTCAACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (24 bp):
TTTTTTTGAAAACAGAAATTGAAA
Found at i:51578880 original size:72 final size:71
Alignment explanation
Indices: 51578743--51578966 Score: 279
Period size: 72 Copynumber: 3.1 Consensus size: 71
51578733 TTGATTTTTT
* * *
51578743 TTTTTGAAAGATAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCATCTCTCGCA
1 TTTTTGAAA-ACAGAAATTGAAAATACCTCA--ACGTG-TCCTGAGGCTCAACTCAT-TCTCGCA
51578807 ATATGAGTTGA
61 ATATGAGTTGA
* * *
51578818 TTTTTGAAAACATAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATAT
1 TTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCATT-CTCGCAATAT
51578883 GAGTTGA
65 GAGTTGA
* * * *
51578890 ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCA-TTCTCGCAATAT
*
51578955 GAGTCGA
65 GAGTTGA
51578962 TTTTT
1 TTTTT
51578967 TTTTTAAAAA
Statistics
Matches: 131, Mismatches: 15, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
71 2 0.02
72 100 0.76
73 1 0.01
74 19 0.15
75 9 0.07
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (71 bp):
TTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCATTCTCGCAATATG
AGTTGA
Found at i:51579003 original size:33 final size:31
Alignment explanation
Indices: 51578959--51579022 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
51578949 CAATATGAGT
* *
51578959 CGATTTTTTTTTTAAAAACAGAAATTGAAAA
1 CGATTTTTTTTTGAAAAACAGAAATTCAAAA
51578990 CGATTGTTGTTTTTGAAAAACAGAAATTCAAAA
1 CGATT-TT-TTTTTGAAAAACAGAAATTCAAAA
51579023 TACCTCAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.17
32 2 0.07
33 22 0.76
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (31 bp):
CGATTTTTTTTTGAAAAACAGAAATTCAAAA
Found at i:51579118 original size:72 final size:72
Alignment explanation
Indices: 51579000--51579160 Score: 234
Period size: 72 Copynumber: 2.2 Consensus size: 72
51578990 CGATTGTTGT
* *
51579000 TTTTGAAAA-ACAGAAATTCAAAATACCTCAGCATGTCTTAAGGCTCAACTCATTTCTCGCAATC
1 TTTTGAAAATA-A-AAATTCAAAATACCTCAACATGTCTTAAGGCTCAACTCATTTCTCGCAATA
51579064 TGAGTTGAA
64 TGAGTTGAA
* * * *
51579073 TTTTGAAAATAAAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
1 TTTTGAAAATAAAAATTCAAAATACCTCAACATGTCTTAAGGCTCAACTCATTTCTCGCAATATG
51579138 AGTTGAA
66 AGTTGAA
*
51579145 TTTTGAAAATAGAAAT
1 TTTTGAAAATAAAAAT
51579161 AAAAATTTCA
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
72 69 0.86
73 10 0.12
74 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (72 bp):
TTTTGAAAATAAAAATTCAAAATACCTCAACATGTCTTAAGGCTCAACTCATTTCTCGCAATATG
AGTTGAA
Found at i:51588415 original size:29 final size:30
Alignment explanation
Indices: 51588356--51588413 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
51588346 TCCGAGCCTT
*
51588356 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
51588386 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
51588414 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:51593129 original size:17 final size:19
Alignment explanation
Indices: 51593088--51593129 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
51593078 CTAGTAATGT
51593088 TAAA-ATATATATAATATA
1 TAAATATATATATAATATA
*
51593106 TACATATATATATAA-A-A
1 TAAATATATATATAATATA
51593123 TAAATAT
1 TAAATAT
51593130 TGAAAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 7 0.33
18 4 0.19
19 10 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATATATATATAATATA
Found at i:51593472 original size:9 final size:9
Alignment explanation
Indices: 51593443--51593482 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
51593433 AAATATAATA
*
51593443 AATAATAAT
1 AATAACAAT
*
51593452 AATAATAAT
1 AATAACAAT
51593461 AATAACAAT
1 AATAACAAT
*
51593470 AATAGCAAT
1 AATAACAAT
51593479 AATA
1 AATA
51593483 GTAAAAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (9 bp):
AATAACAAT
Found at i:51593482 original size:3 final size:3
Alignment explanation
Indices: 51593419--51593473 Score: 58
Period size: 3 Copynumber: 17.7 Consensus size: 3
51593409 AAGTACCTAT
*
51593419 TAA TAA TAT TATA TAA -ATA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA
*
51593466 CAA TAA TA
1 TAA TAA TA
51593474 GCAATAATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 1 0.02
3 37 0.84
4 6 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:51593653 original size:3 final size:3
Alignment explanation
Indices: 51593645--51594024 Score: 218
Period size: 3 Copynumber: 124.3 Consensus size: 3
51593635 AATATTTATA
* *
51593645 AAT AAT AAT AGT AAT -GT 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 AAT AAT
* * * * *
51593692 AAT AAT ATT AAGT -AT AGT -AT AAAT AAT ATGT ACAT AAC AGT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT -AAT AAT A-AT A-AT AAT AAT AAT AAT
* *
51593739 AAT AAGT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAGT -AT AGT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
* * *
51593785 -AT AAAT AAT ATGT ACAT AAC AGT AAT AAT AAT AAGT AAT AAT AAT AAT
1 AAT -AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
51593833 AAT AAT AAT -AT AGA- AATT CAA- AA- AAGT AA- ACAT AAT -AT AAT
1 AAT AAT AAT AAT A-AT AA-T -AAT AAT AA-T AAT A-AT AAT AAT AAT
* * * *
51593874 GAT ATT AA- AAT AA- AAT -AT ACACT AAT ATT TAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT -AAT AAT AAT AAT
* * *
51593919 AA- ATAT AAT AAT AAT AAT AAT GAT AAT AAT AAT ATT AAGT -AT AGT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
* * * *
51593964 -AT AAAT AAT ATGT ACAT AAC AAT AAT AAT AAT AAGT AAC AAC AAT AAT
1 AAT -AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
51594012 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
51594025 TAGAAATTCA
Statistics
Matches: 293, Mismatches: 47, Indels: 74
0.71 0.11 0.18
Matches are distributed among these distances:
2 24 0.08
3 226 0.77
4 39 0.13
5 4 0.01
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:51593784 original size:75 final size:75
Alignment explanation
Indices: 51593661--51593842 Score: 339
Period size: 75 Copynumber: 2.4 Consensus size: 75
51593651 AATAGTAATG
*
51593661 TAATAATAA-TAATAATAATAATAATAATAATAATAATATTAAGTATAGTATAAATAATATGTAC
1 TAATAATAAGTAATAATAATAATAATAATAATAATAATAATAAGTATAGTATAAATAATATGTAC
51593725 ATAACAGTAA
66 ATAACAGTAA
*
51593735 TAATAATAAGTAACAATAATAATAATAATAATAATAATAATAAGTATAGTATAAATAATATGTAC
1 TAATAATAAGTAATAATAATAATAATAATAATAATAATAATAAGTATAGTATAAATAATATGTAC
51593800 ATAACAGTAA
66 ATAACAGTAA
51593810 TAATAATAAGTAATAATAATAATAATAATAATA
1 TAATAATAAGTAATAATAATAATAATAATAATA
51593843 TAGAAATTCA
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 9 0.09
75 95 0.91
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (75 bp):
TAATAATAAGTAATAATAATAATAATAATAATAATAATAATAAGTATAGTATAAATAATATGTAC
ATAACAGTAA
Found at i:51594009 original size:22 final size:23
Alignment explanation
Indices: 51593967--51594019 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
51593957 GTATAGTATA
* *
51593967 AATAATATGTACATAACAATAAT
1 AATAATAAGTACACAACAATAAT
51593990 AATAATAAGTA-ACAACAATAAT
1 AATAATAAGTACACAACAATAAT
51594012 AATAATAA
1 AATAATAA
51594020 TAATATAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (23 bp):
AATAATAAGTACACAACAATAAT
Found at i:51594069 original size:179 final size:176
Alignment explanation
Indices: 51593732--51594074 Score: 533
Period size: 179 Copynumber: 1.9 Consensus size: 176
51593722 TACATAACAG
*
51593732 TAATAATAATAAGTAACAATAATAATAATAATAATAATAATAATAAGTATAGTATAAATAATATG
1 TAATAATAATAAATAACAATAATAATAATAATAATAATAATAATAAGTATAGTATAAATAATATG
* * *
51593797 TACATAACAGTAATAATAATAAGTAATAATAATAATAATAATAATATAGAAATTCAAAAAAGTAA
66 TACATAACAATAATAATAATAAGTAACAATAATAATAATAATAATATAGAAATTCAAAAAACTAA
51593862 ACATAATATAATGATATTAAAATAAAATATACACTAATATTTATAAA
131 ACATAATATAATGATATT-AAATAAAATATACACTAATATTTATAAA
* * *
51593909 TAATAATAATAAATATAATAATAATAATAATGATAATAATAATATTAAGTATAGTATAAATAATA
1 TAATAATAAT-AA-ATAACAATAATAATAATAATAATAATAATAATAAGTATAGTATAAATAATA
51593974 TGTACATAACAATAATAATAATAAGTAACAACAATAATAATAATAATAATATAGAAATTCAAAAA
64 TGTACATAACAATAATAATAATAAGT---AACAATAATAATAATAATAATATAGAAATTC--AAA
*
51594039 AAACTAAACATAATATAATAATATTAAAATAAAATA
124 AAACTAAACATAATATAATGATATT-AAATAAAATA
51594075 ATTTAAAAAA
Statistics
Matches: 151, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
177 10 0.07
178 2 0.01
179 72 0.48
182 30 0.20
184 37 0.25
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (176 bp):
TAATAATAATAAATAACAATAATAATAATAATAATAATAATAATAAGTATAGTATAAATAATATG
TACATAACAATAATAATAATAAGTAACAATAATAATAATAATAATATAGAAATTCAAAAAACTAA
ACATAATATAATGATATTAAATAAAATATACACTAATATTTATAAA
Found at i:51594083 original size:16 final size:16
Alignment explanation
Indices: 51594050--51594082 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
51594040 AACTAAACAT
*
51594050 AATATAATAATATTAA
1 AATAAAATAATATTAA
51594066 AATAAAATAAT-TTAA
1 AATAAAATAATATTAA
51594081 AA
1 AA
51594083 AATACTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAATAATATTAA
Found at i:51595446 original size:20 final size:19
Alignment explanation
Indices: 51595423--51595461 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
51595413 TTTAGATTAA
51595423 TTAAAT-AAATATTAGTTTAT
1 TTAAATCAAAT-TTA-TTTAT
51595443 TTAAATCAAATTTATTTAT
1 TTAAATCAAATTTATTTAT
51595462 ATTTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
TTAAATCAAATTTATTTAT
Found at i:51596697 original size:21 final size:21
Alignment explanation
Indices: 51596673--51596892 Score: 176
Period size: 21 Copynumber: 10.5 Consensus size: 21
51596663 TGTGTTTTAC
* * *
51596673 TTTCTGTTTAGCTCTTACGAG
1 TTTCTGTTCAACTCTTATGAG
* *
51596694 TTTCTATTTAACTCTTATGAG
1 TTTCTGTTCAACTCTTATGAG
* *
51596715 TTTCCGTTCAACTC-TATTGAC
1 TTTCTGTTCAACTCTTA-TGAG
* * * *
51596736 CTTCTATTCAACTTTTAAGAG
1 TTTCTGTTCAACTCTTATGAG
*
51596757 TTTCTGTTCAGCTCTTATGAG
1 TTTCTGTTCAACTCTTATGAG
* * * * *
51596778 CTTCTATTTAACTCATACGAG
1 TTTCTGTTCAACTCTTATGAG
* * *
51596799 TTTCTGTTTAGCTCTTACGAG
1 TTTCTGTTCAACTCTTATGAG
*
51596820 CTTT-TTTTCAACTCTTATGAG
1 -TTTCTGTTCAACTCTTATGAG
* *
51596841 TTTTTGTTCAGCTCTTATGAG
1 TTTCTGTTCAACTCTTATGAG
*
51596862 CTTT-TGTTCAACTCTTAAGAG
1 -TTTCTGTTCAACTCTTATGAG
51596883 TTTCTGTTCA
1 TTTCTGTTCA
51596893 GCTTACAAGC
Statistics
Matches: 157, Mismatches: 36, Indels: 12
0.77 0.18 0.06
Matches are distributed among these distances:
20 8 0.05
21 141 0.90
22 8 0.05
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (21 bp):
TTTCTGTTCAACTCTTATGAG
Found at i:51596893 original size:42 final size:42
Alignment explanation
Indices: 51596673--51596895 Score: 243
Period size: 42 Copynumber: 5.3 Consensus size: 42
51596663 TGTGTTTTAC
* * * *
51596673 TTTCTGTTTAGCTCTTACGAG-TTTCTATTTAACTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTT-TATTCAACTCTTAAGAG
* * * * *
51596715 TTTCCGTTCAACTC-TATTGACCTTCTATTCAACTTTTAAGAG
1 TTTCTGTTCAGCTCTTA-TGAGCTTTTATTCAACTCTTAAGAG
* * * *
51596757 TTTCTGTTCAGCTCTTATGAGCTTCTATTTAACTCATACGAG
1 TTTCTGTTCAGCTCTTATGAGCTTTTATTCAACTCTTAAGAG
* * * *
51596799 TTTCTGTTTAGCTCTTACGAGCTTTTTTTCAACTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTTTATTCAACTCTTAAGAG
* *
51596841 TTTTTGTTCAGCTCTTATGAGCTTTTGTTCAACTCTTAAGAG
1 TTTCTGTTCAGCTCTTATGAGCTTTTATTCAACTCTTAAGAG
51596883 TTTCTGTTCAGCT
1 TTTCTGTTCAGCT
51596896 TACAAGCTTC
Statistics
Matches: 149, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
41 2 0.01
42 143 0.96
43 4 0.03
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.47
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTTTATTCAACTCTTAAGAG
Found at i:51605366 original size:17 final size:16
Alignment explanation
Indices: 51605326--51605357 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
51605316 CACCAATATT
51605326 GACAAATTGTTGATTA
1 GACAAATTGTTGATTA
51605342 GACAAATTGTTGATTA
1 GACAAATTGTTGATTA
51605358 ACTCAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (16 bp):
GACAAATTGTTGATTA
Found at i:51610537 original size:30 final size:30
Alignment explanation
Indices: 51610501--51610560 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
51610491 ATTGCTTTAT
*
51610501 CACACACAAAAAAAAAGGGAACATAAACAA
1 CACACACAAAAAAAAAAGGAACATAAACAA
51610531 CACACACAAAAAAAAAAGGAACATAAACAA
1 CACACACAAAAAAAAAAGGAACATAAACAA
51610561 TCATAATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.68, C:0.20, G:0.08, T:0.03
Consensus pattern (30 bp):
CACACACAAAAAAAAAAGGAACATAAACAA
Found at i:51615968 original size:17 final size:17
Alignment explanation
Indices: 51615910--51615970 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
51615900 TCCGAATTTA
51615910 ATATATATATTTT-T--
1 ATATATATATTTTGTAC
*
51615924 ATA-ACTATATTATGTAC
1 ATATA-TATATTTTGTAC
51615941 ATATATATATTTTGTAC
1 ATATATATATTTTGTAC
51615958 ATATCAT-TATTTT
1 ATAT-ATATATTTT
51615971 ATATTATTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 1 0.03
14 10 0.26
15 1 0.03
17 24 0.62
18 3 0.08
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATATATATTTTGTAC
Found at i:51625325 original size:15 final size:15
Alignment explanation
Indices: 51625300--51625357 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
51625290 TCATATATAT
51625300 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
51625316 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
51625331 AATAATTTCAATCAA
1 TATAAATTCAATCAA
51625346 TATAAATTCAAT
1 TATAAATTCAAT
51625358 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:51626640 original size:5 final size:5
Alignment explanation
Indices: 51626627--51626719 Score: 177
Period size: 5 Copynumber: 18.4 Consensus size: 5
51626617 TTCTTTAGTT
51626627 TATATA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
51626678 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA
51626720 ATATACTAAA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 83 0.95
6 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:51629168 original size:14 final size:14
Alignment explanation
Indices: 51629149--51629178 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
51629139 GCTGAGGTAA
*
51629149 TTTCAATTTATGTT
1 TTTCAATTTATATT
51629163 TTTCAATTTATATT
1 TTTCAATTTATATT
51629177 TT
1 TT
51629179 GCAAAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTCAATTTATATT
Found at i:51629386 original size:89 final size:87
Alignment explanation
Indices: 51629106--51629659 Score: 541
Period size: 87 Copynumber: 6.6 Consensus size: 87
51629096 AAGTCGACTT
* * * *
51629106 ATATTGCAAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTATGTTTTTCAATT
1 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATT
* *
51629171 TATATTTTGCAAAAATCAATTC
66 TATATTTTTCAAAAATCAACTC
** * *
51629193 ATATTATGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTCTGTTCTT-AA-T
1 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATT
* *
51629256 GACTGTTTTT---AAATCAACTC
66 TA-TATTTTTCAAAAATCAACTC
*
51629276 ATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTTCCAA
1 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTG-TTTTT-CAA
*
51629341 TCTATATTTTTCAAAAATCAACTC
64 TTTATATTTTTCAAAAATCAACTC
* * *
51629365 ATATTGCGAGAGGTGAATTGAGCCTCAGGACACGTTGAGGTATTTTCGATTT-TCGTTTTTCAAT
1 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT-GTTTTTCAAT
* *
51629429 TTATGTTTTTCAAAAATCAATTC
65 TTATATTTTTCAAAAATCAACTC
* * * * * *
51629452 ATATTACGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTAATTTCAATTCCT-TTTTTTAA--
1 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATT
**
51629514 -A-A----AAAAAAAGTCAACTC
66 TATATTTTTCAAAAA-TCAACTC
** * ** *
51629531 ATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCTGTCTTTC----
1 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATT
51629592 -A-A------AAAAATCAACTC
66 TATATTTTTCAAAAATCAACTC
* *
51629606 ATATTGCGAGAGGTGAGTTAAGCCCCAGGTCACACGCTGAGGTATTTTCAATTT
1 ATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTT
51629660 TTTGCTTTTT
Statistics
Matches: 396, Mismatches: 57, Indels: 38
0.81 0.12 0.08
Matches are distributed among these distances:
75 31 0.08
76 5 0.01
77 21 0.05
78 7 0.02
79 52 0.13
80 4 0.01
83 61 0.15
84 4 0.01
85 2 0.01
86 22 0.06
87 121 0.31
88 7 0.02
89 59 0.15
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (87 bp):
ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATT
TATATTTTTCAAAAATCAACTC
Found at i:51629549 original size:79 final size:75
Alignment explanation
Indices: 51629440--51629704 Score: 246
Period size: 79 Copynumber: 3.4 Consensus size: 75
51629430 TATGTTTTTC
* * *
51629440 AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTAATTTCAATTCC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTTCAATTCC
* *
51629505 TTTTTTTAAAAAA
66 TGTCTTT---AAA
** ** * *
51629518 AAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTTCAATTC
*
51629583 CTGTCTTTCAA
65 CTGTCTTTAAA
* * * *
51629594 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCCCAGGTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-GACACACTGAGGTATTTTCAATT
* * **
51629659 -TTTTGCTTTTTCA
64 CCTGT-C-TTTAAA
*
51629672 AAAGATCAACTCATAATT-CGAGAGGTGAGTTGA
1 AAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGA
51629705 ACTTCGGGTT
Statistics
Matches: 154, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
75 29 0.19
76 9 0.06
77 21 0.14
78 36 0.23
79 59 0.38
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTTCAATTCC
TGTCTTTAAA
Found at i:51629974 original size:30 final size:29
Alignment explanation
Indices: 51629940--51630028 Score: 115
Period size: 30 Copynumber: 3.0 Consensus size: 29
51629930 ATAAAAAATG
51629940 CATTTTGACCCCTAAACTTTTCCTAAATTT
1 CATTTTGACCCCTAAAC-TTTCCTAAATTT
* *
51629970 CATTTTGACCCTTAAACTTTCTTTAAATTT
1 CATTTTGACCCCTAAACTTTC-CTAAATTT
* *
51630000 CACTTAGACCCCTAAACTTTCCTTAAATT
1 CATTTTGACCCCTAAACTTTCC-TAAATT
51630029 GTATTTTAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
29 4 0.08
30 47 0.92
ACGTcount: A:0.28, C:0.26, G:0.03, T:0.43
Consensus pattern (29 bp):
CATTTTGACCCCTAAACTTTCCTAAATTT
Found at i:51630293 original size:16 final size:17
Alignment explanation
Indices: 51630272--51630315 Score: 65
Period size: 15 Copynumber: 2.7 Consensus size: 17
51630262 GAGAAAAAAG
51630272 AGCAAAAAAAAATTTC-
1 AGCAAAAAAAAATTTCT
*
51630288 AGC-AAAAAAATTTTCT
1 AGCAAAAAAAAATTTCT
51630304 AGCAAAAAAAAA
1 AGCAAAAAAAAA
51630316 CAACAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 11 0.46
16 6 0.25
17 7 0.29
ACGTcount: A:0.64, C:0.11, G:0.07, T:0.18
Consensus pattern (17 bp):
AGCAAAAAAAAATTTCT
Found at i:51631124 original size:17 final size:17
Alignment explanation
Indices: 51631066--51631126 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
51631056 TCCGAATTTA
51631066 ATATATATATTTT-T--
1 ATATATATATTTTGTAC
*
51631080 ATA-ACTATATTATGTAC
1 ATATA-TATATTTTGTAC
51631097 ATATATATATTTTGTAC
1 ATATATATATTTTGTAC
51631114 ATATCAT-TATTTT
1 ATAT-ATATATTTT
51631127 ATATTATTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 1 0.03
14 10 0.26
15 1 0.03
17 24 0.62
18 3 0.08
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATATATATTTTGTAC
Found at i:51631288 original size:51 final size:58
Alignment explanation
Indices: 51631187--51631291 Score: 134
Period size: 57 Copynumber: 1.9 Consensus size: 58
51631177 TAATATTTTC
* *
51631187 TTTTATTGTAGATATTATTATTATTACATATATTTATTATATGCATATATATATGTAT
1 TTTTATTGTACATATTATTATTATTACATATATTTATTATATGCAAATATATATGTAT
*
51631245 TTTTA-TGTACATATTATTATT-TTATAT-TA-TTA-T-TAT-CAAATATATAT
1 TTTTATTGTACATATTATTATTATTACATATATTTATTATATGCAAATATATAT
51631292 TTTTTCCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
51 10 0.23
52 3 0.07
53 1 0.02
54 3 0.07
55 2 0.05
56 5 0.11
57 15 0.34
58 5 0.11
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (58 bp):
TTTTATTGTACATATTATTATTATTACATATATTTATTATATGCAAATATATATGTAT
Found at i:51641537 original size:58 final size:56
Alignment explanation
Indices: 51641467--51641674 Score: 174
Period size: 58 Copynumber: 3.6 Consensus size: 56
51641457 ATTTTTGTAC
*
51641467 TGGTGCCGGCCATTAAAAGACCAGCACTCAAAAAATTTTGAATTTTTTTTTACTACAG
1 TGGTGCCGGCCATTAGAAGACCAGCAC-CAAAAAATTTTGAATTTTTTTTTACTA-AG
* * * * * *
51641525 TGGTGTCGGCCATTAGAAGGCCAGCAGCAAAAAAAAAAAATTCCTG-ATATTTTTGTACT-A-
1 TGGTGCCGGCCATTAGAAGACCAGCA-C-----CAAAAAATT-TTGAATTTTTTTTTACTAAG
* *
51641585 --GTGCTGGCCATTAGAAGACTAGCACCCAAAAAATTTTGAAAATTTTTTTTTACTAGAG
1 TGGTGCCGGCCATTAGAAGACCAGCA-CCAAAAAATTTTG--AATTTTTTTTTACTA-AG
*
51641643 TGGTGCCGGCCATTAGAAGGCCAGCACCAAAA
1 TGGTGCCGGCCATTAGAAGACCAGCACCAAAA
51641675 TTATTTTTTT
Statistics
Matches: 116, Mismatches: 20, Indels: 27
0.71 0.12 0.17
Matches are distributed among these distances:
52 2 0.02
53 8 0.07
55 11 0.09
57 1 0.01
58 44 0.38
59 7 0.06
60 21 0.18
61 1 0.01
63 19 0.16
64 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (56 bp):
TGGTGCCGGCCATTAGAAGACCAGCACCAAAAAATTTTGAATTTTTTTTTACTAAG
Found at i:51641623 original size:116 final size:118
Alignment explanation
Indices: 51641418--51641674 Score: 419
Period size: 116 Copynumber: 2.2 Consensus size: 118
51641408 TTTGCCTGTT
*
51641418 CATTAGAAGGCCAGCACCAAAAAAAAAAAATTCCTTGATATTTTTGTACTGGTGCCGGCCATTAA
1 CATTAGAAGGCCAGCACCAAAAAAAAAAAATTCCTTGATATTTTTGTACTAGTGCCGGCCATTAA
* *
51641483 AAGACCAGCACTCAAAAAATTTTG-AATTTTTTTTTACTACAGTGGTGTCGGC
66 AAGACCAGCACCCAAAAAATTTTGAAATTTTTTTTTACTACAGTGGTGCCGGC
* * *
51641535 CATTAGAAGGCCAGCAGCAAAAAAAAAAAATTCC-TGATATTTTTGTACTAGTGCTGGCCATTAG
1 CATTAGAAGGCCAGCACCAAAAAAAAAAAATTCCTTGATATTTTTGTACTAGTGCCGGCCATTAA
* *
51641599 AAGACTAGCACCCAAAAAATTTTGAAAATTTTTTTTTACTAGAGTGGTGCCGGC
66 AAGACCAGCACCCAAAAAATTTTG-AAATTTTTTTTTACTACAGTGGTGCCGGC
51641653 CATTAGAAGGCCAGCACCAAAA
1 CATTAGAAGGCCAGCACCAAAA
51641675 TTATTTTTTT
Statistics
Matches: 129, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
116 49 0.38
117 33 0.26
118 47 0.36
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (118 bp):
CATTAGAAGGCCAGCACCAAAAAAAAAAAATTCCTTGATATTTTTGTACTAGTGCCGGCCATTAA
AAGACCAGCACCCAAAAAATTTTGAAATTTTTTTTTACTACAGTGGTGCCGGC
Found at i:51645148 original size:26 final size:24
Alignment explanation
Indices: 51645113--51645436 Score: 145
Period size: 26 Copynumber: 12.4 Consensus size: 24
51645103 CTTGCTTATC
51645113 TTATTTATTTAAAATCTTTTCATATA
1 TTATTTATTTAAAAT-TTTT-ATATA
* *
51645139 TTGTTTATTTTAAAATTTTTATTTA
1 TTATTTA-TTTAAAATTTTTATATA
*
51645164 TTAGTTATTTTAAACATTATTTATAATA
1 TTATTTA-TTTAAA-ATT-TTTAT-ATA
*
51645192 TTATTTATTTTAAACTATTTTATATA
1 TTATTTA-TTTAAAAT-TTTTATATA
*
51645218 TTATCTATTTAAAATTTTTACGTATA
1 TTATTTATTTAAAATTTTTA--TATA
* * * *
51645244 ATATTCAATTTAAATTGTTTTATCTA
1 TTATT-TATTTAAAAT-TTTTATATA
* * *
51645270 TTATTCATTTTAAAA-ATTT-CATA
1 TTATTTA-TTTAAAATTTTTATATA
**
51645293 TTATTTATTTTAAGCTGTTTTATTATTA
1 TTATTTA-TTTAAAAT-TTTTA-TA-TA
** *
51645321 TTATTTATTTTAAGTTTTTTTCATACA
1 TTATTTA-TTTAA-AATTTTT-ATATA
*
51645348 TTATTTATTTGAAACTTTTTTTTAATATA
1 TTATTTATTT-AAA---ATTTTT-ATATA
* *
51645377 TTATTTACTTT-AAGTTGTTTCATTTA
1 TTATTTA-TTTAAAATT-TTT-ATATA
*
51645403 TTATTTATTTTAAATCTTTT-TAT-
1 TTATTTATTTAAAAT-TTTTATATA
51645426 TTACTTTATTT
1 TTA-TTTATTT
51645437 TTTTATATAT
Statistics
Matches: 236, Mismatches: 36, Indels: 54
0.72 0.11 0.17
Matches are distributed among these distances:
23 17 0.07
24 17 0.07
25 32 0.14
26 65 0.28
27 39 0.17
28 44 0.19
29 19 0.08
30 3 0.01
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (24 bp):
TTATTTATTTAAAATTTTTATATA
Found at i:51645399 original size:55 final size:55
Alignment explanation
Indices: 51645292--51645428 Score: 161
Period size: 55 Copynumber: 2.5 Consensus size: 55
51645282 AAAATTTCAT
* * * *
51645292 ATTATTTATTTTAAGCTGTTTTATT-ATTATTATTTATTTTAAGTTTTTTTCATAC
1 ATTATTTATTTTAAACT-TTTTTTTAATTATTATTTACTTTAAGTTTGTTTCATAC
* **
51645347 ATTATTTATTTGAAACTTTTTTTTAATATATTATTTACTTTAAG-TTGTTTCATTT
1 ATTATTTATTTTAAACTTTTTTTTAAT-TATTATTTACTTTAAGTTTGTTTCATAC
51645402 ATTATTTATTTTAAATCTTTTTATTTA
1 ATTATTTATTTTAAA-CTTTTT-TTTA
51645429 CTTTATTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
54 6 0.09
55 39 0.56
56 21 0.30
57 4 0.06
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (55 bp):
ATTATTTATTTTAAACTTTTTTTTAATTATTATTTACTTTAAGTTTGTTTCATAC
Found at i:51645436 original size:28 final size:28
Alignment explanation
Indices: 51645293--51645441 Score: 75
Period size: 27 Copynumber: 5.4 Consensus size: 28
51645283 AAATTTCATA
* *
51645293 TTATTTATTTT-AAGCTGTTTTA-TTATT
1 TTATTTATTTTAAATCT-TTTTATTTACT
* * *
51645320 ATTATTTATTTTAAGT-TTTTT-TCATACA
1 -TTATTTATTTTAAATCTTTTTAT-TTACT
* *
51645348 TTATTTATTTGAAA-CTTTTT-TTTAATAT
1 TTATTTATTTTAAATCTTTTTATTT-A-CT
* * *
51645376 ATTATTTACTTTAAGT-TGTTTCATTTA--
1 -TTATTTATTTTAAATCT-TTTTATTTACT
51645403 TTATTTATTTTAAATCTTTTTATTTACT
1 TTATTTATTTTAAATCTTTTTATTTACT
51645431 TTATTT-TTTTA
1 TTATTTATTTTA
51645442 TATATTATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 27
0.67 0.13 0.20
Matches are distributed among these distances:
26 22 0.24
27 29 0.32
28 20 0.22
29 13 0.14
30 4 0.04
31 3 0.03
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (28 bp):
TTATTTATTTTAAATCTTTTTATTTACT
Found at i:51652168 original size:14 final size:14
Alignment explanation
Indices: 51652146--51652181 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
51652136 GCACTCTCAA
51652146 ATCACTTAAAATGG
1 ATCACTTAAAATGG
*
51652160 ATCATTTAAAATGG
1 ATCACTTAAAATGG
*
51652174 ATTACTTA
1 ATCACTTA
51652182 CATTAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (14 bp):
ATCACTTAAAATGG
Found at i:51658468 original size:19 final size:20
Alignment explanation
Indices: 51658412--51658468 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
51658402 AAAATAAAAG
51658412 TTTAGAATTTTTTATAAA-TAT
1 TTTA-AATTTTTTA-AAATTAT
**
51658433 TTTAAATTTTTGGAAATTAT
1 TTTAAATTTTTTAAAATTAT
*
51658453 TTT-GATTTTTTAAAAT
1 TTTAAATTTTTTAAAAT
51658469 CTTTGTTGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 13 0.43
20 13 0.43
21 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (20 bp):
TTTAAATTTTTTAAAATTAT
Found at i:51659386 original size:17 final size:17
Alignment explanation
Indices: 51659364--51659412 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
51659354 ATAGAATCAA
* *
51659364 ATCTTCTAAGATTGCAT
1 ATCTTCGAAGATTACAT
51659381 ATCTTCGAAGATTACAT
1 ATCTTCGAAGATTACAT
*
51659398 ATCTTTGAAGATTAC
1 ATCTTCGAAGATTAC
51659413 TTCCCATACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (17 bp):
ATCTTCGAAGATTACAT
Found at i:51661131 original size:31 final size:31
Alignment explanation
Indices: 51661088--51661149 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
51661078 TTACAAAATG
* **
51661088 GTCATTAAACTATTTGAAAGTTTTTATTTAA
1 GTCACTAAACTATCCGAAAGTTTTTATTTAA
51661119 GTCACTAAACTATCCGAAAGTTTTTATTTAA
1 GTCACTAAACTATCCGAAAGTTTTTATTTAA
51661150 ATCATTAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (31 bp):
GTCACTAAACTATCCGAAAGTTTTTATTTAA
Found at i:51664431 original size:7 final size:7
Alignment explanation
Indices: 51664419--51664445 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
51664409 ACAAACAGCC
51664419 TTTTCAG
1 TTTTCAG
51664426 TTTTCAG
1 TTTTCAG
51664433 TTTTCAG
1 TTTTCAG
51664440 TTTTCA
1 TTTTCA
51664446 CTTTCCTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.59
Consensus pattern (7 bp):
TTTTCAG
Found at i:51674153 original size:2 final size:2
Alignment explanation
Indices: 51674148--51674174 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51674138 TCTCTCTTTT
51674148 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
51674175 TTATTCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51678273 original size:17 final size:18
Alignment explanation
Indices: 51678240--51678287 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 18
51678230 TGTTCATGAT
51678240 ATTTAAATTTAATTAATA
1 ATTTAAATTTAATTAATA
51678258 ATTTAAATTCATTAATTAATA
1 ATTTAAA-T--TTAATTAATA
*
51678279 ATTAAAATT
1 ATTTAAATT
51678288 AAGTATGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.31
19 1 0.04
20 1 0.04
21 16 0.62
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTAAATTTAATTAATA
Found at i:51678274 original size:21 final size:21
Alignment explanation
Indices: 51678248--51678287 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
51678238 ATATTTAAAT
*
51678248 TTAATTAATAATTTAAATTCA
1 TTAATTAATAATTAAAATTCA
51678269 TTAATTAATAATTAAAATT
1 TTAATTAATAATTAAAATT
51678288 AAGTATGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATTAATAATTAAAATTCA
Found at i:51681518 original size:25 final size:25
Alignment explanation
Indices: 51681466--51681556 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 25
51681456 TGTACATATG
*
51681466 TATTAAAATAAATACATAATAATA-T
1 TATTAAAATATATACATAA-AATAGT
* *
51681491 TA--AAAGTGTATACATAAAATAGT
1 TATTAAAATATATACATAAAATAGT
* * *
51681514 GT-TAAAAATACATACATAATATAGT
1 -TATTAAAATATATACATAAAATAGT
51681539 TATTAAAATATATACATA
1 TATTAAAATATATACATA
51681557 TATATACATA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
22 4 0.08
23 13 0.25
24 2 0.04
25 33 0.63
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (25 bp):
TATTAAAATATATACATAAAATAGT
Found at i:51681561 original size:10 final size:10
Alignment explanation
Indices: 51681546--51681570 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
51681536 AGTTATTAAA
51681546 ATATATACAT
1 ATATATACAT
51681556 ATATATACAT
1 ATATATACAT
51681566 ATATA
1 ATATA
51681571 ATAAACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATACAT
Found at i:51681581 original size:23 final size:23
Alignment explanation
Indices: 51681552--51681597 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
51681542 TAAAATATAT
51681552 ACATATA-T-ATACATATATAATAA
1 ACATATACTAATA-ATA-ATAATAA
51681575 ACATATACTAATAATAATAATAA
1 ACATATACTAATAATAATAATAA
51681598 TATGCATACG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 14 0.67
24 4 0.19
25 3 0.14
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (23 bp):
ACATATACTAATAATAATAATAA
Found at i:51681829 original size:23 final size:24
Alignment explanation
Indices: 51681797--51681850 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
51681787 ATATAATAAT
* * *
51681797 ATATACATAAGATGGTATT-AAAA
1 ATATATATAACATAGTATTCAAAA
51681820 ATATATATAACATAGTATTCAAAA
1 ATATATATAACATAGTATTCAAAA
*
51681844 ATTTATA
1 ATATATA
51681851 CATGAGATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.35
Consensus pattern (24 bp):
ATATATATAACATAGTATTCAAAA
Found at i:51681929 original size:22 final size:21
Alignment explanation
Indices: 51681817--51681960 Score: 96
Period size: 22 Copynumber: 6.4 Consensus size: 21
51681807 GATGGTATTA
*
51681817 AAAATATATATAACATAGTAT-T
1 AAAA-ATATAT-ACATAATATAT
* *
51681839 CAAAAATTTATACATGAGATGAAAT
1 -AAAAATATATACAT-A-AT-ATAT
51681864 AAAAATATATACATGAA-ATAGT
1 AAAAATATATACAT-AATATA-T
*
51681886 AAAAGAAATATACATAATATAT
1 AAAA-ATATATACATAATATAT
51681908 AAAAATATATA-ACTAATGATAT
1 AAAAATATATACA-TAAT-ATAT
* *
51681930 CAAAATATGTACATAATAATAT
1 AAAAATATATACATAAT-ATAT
51681952 ATAAAATAT
1 A-AAAATAT
51681961 TAAAAGAAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.01
21 16 0.16
22 39 0.39
23 26 0.26
24 16 0.16
25 1 0.01
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (21 bp):
AAAAATATATACATAATATAT
Found at i:51682155 original size:14 final size:14
Alignment explanation
Indices: 51682115--51682215 Score: 78
Period size: 15 Copynumber: 6.7 Consensus size: 14
51682105 AAGTAATTAA
51682115 AATAATACTATATAT
1 AATAATAC-ATATAT
51682130 ATATACATACATATAT
1 A-ATA-ATACATATAT
*
51682146 AATAAAACATATACT
1 AATAATACATATA-T
* *
51682161 AATATTATATATAT
1 AATAATACATATAT
* *
51682175 AATAATACTAGAAAT
1 AATAATAC-ATATAT
51682190 AATAATA-ACTAGTAAT
1 AATAATACA-TA-T-AT
51682206 AATAATACAT
1 AATAATACAT
51682216 TAGTAATACA
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
13 1 0.01
14 16 0.24
15 26 0.38
16 20 0.29
17 5 0.07
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (14 bp):
AATAATACATATAT
Found at i:51682364 original size:3 final size:3
Alignment explanation
Indices: 51682316--51682351 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
51682306 ATAGTAAAAT
51682316 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
51682352 GAAGTGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51685236 original size:17 final size:17
Alignment explanation
Indices: 51685188--51685238 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
51685178 AAAATATATC
* *
51685188 AAAATATAAAAAATACTA
1 AAAATATATAAAAT-TTA
*
51685206 AAAATA-ATTTAAATTTA
1 AAAATATA-TAAAATTTA
51685223 AAAATATATAAAATTT
1 AAAATATATAAAATTT
51685239 TAGGTAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATATAAAATTTA
Found at i:51706933 original size:42 final size:42
Alignment explanation
Indices: 51706883--51706965 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
51706873 GAAATATGAA
*
51706883 AATTTGGAAAGTTGAGCATAAACTAGTAAAGTTTGAAACTAT
1 AATTTGGAAAGTTGAGCATAAAATAGTAAAGTTTGAAACTAT
51706925 AATTTGGAAAGTTGAGCATAAAATAGTAAAGTTTGAAACTA
1 AATTTGGAAAGTTGAGCATAAAATAGTAAAGTTTGAAACTA
51706966 CAGGGTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (42 bp):
AATTTGGAAAGTTGAGCATAAAATAGTAAAGTTTGAAACTAT
Found at i:51706960 original size:21 final size:20
Alignment explanation
Indices: 51706890--51706957 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
51706880 GAAAATTTGG
*
51706890 AAAGTTGAGCATAAACTAGT
1 AAAGTTGAGCATAAAATAGT
* * * *
51706910 AAAGTTTGA-AACTATAATTTGG
1 AAAG-TTGAGCA-TA-AAATAGT
51706932 AAAGTTGAGCATAAAATAGT
1 AAAGTTGAGCATAAAATAGT
51706952 AAAGTT
1 AAAGTT
51706958 TGAAACTACA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
20 15 0.42
21 12 0.33
22 9 0.25
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (20 bp):
AAAGTTGAGCATAAAATAGT
Found at i:51711426 original size:21 final size:21
Alignment explanation
Indices: 51711402--51711442 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
51711392 TGGTATTTTT
* *
51711402 CCTAAGGAGGATGAAATTGTG
1 CCTAACGAGAATGAAATTGTG
51711423 CCTAACGAGAATGAAATTGT
1 CCTAACGAGAATGAAATTGT
51711443 AGACATACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (21 bp):
CCTAACGAGAATGAAATTGTG
Found at i:51716417 original size:4 final size:4
Alignment explanation
Indices: 51716408--51716434 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
51716398 CGTTCTTCTA
51716408 TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TAT
51716435 ATTCAAACGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:51734875 original size:2 final size:2
Alignment explanation
Indices: 51734868--51734898 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51734858 GAAAATAAAA
51734868 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
51734899 ATAGGAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:51739714 original size:15 final size:16
Alignment explanation
Indices: 51739694--51739727 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
51739684 TGATATGACA
51739694 AATAAAA-TGTTTTTG
1 AATAAAATTGTTTTTG
51739709 AATAAAATTTGTTTTTG
1 AATAAAA-TTGTTTTTG
51739726 AA
1 AA
51739728 CAAAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (16 bp):
AATAAAATTGTTTTTG
Found at i:51741744 original size:11 final size:11
Alignment explanation
Indices: 51741723--51741756 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
51741713 AAGATAATGG
51741723 AAGAGGGATTTT
1 AAGA-GGATTTT
*
51741735 AGGAGGATTTT
1 AAGAGGATTTT
51741746 AAGAGGATTTT
1 AAGAGGATTTT
51741757 GTGGAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (11 bp):
AAGAGGATTTT
Found at i:51751038 original size:16 final size:16
Alignment explanation
Indices: 51751017--51751051 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
51751007 GATGAAGGCA
51751017 AGTGTACCTATCGAAC
1 AGTGTACCTATCGAAC
51751033 AGTGTACCTATCGAAC
1 AGTGTACCTATCGAAC
51751049 AGT
1 AGT
51751052 AGTATAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (16 bp):
AGTGTACCTATCGAAC
Found at i:51757372 original size:25 final size:25
Alignment explanation
Indices: 51757323--51757372 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
51757313 TTTTGTATAC
* *
51757323 ATAATATATAAATTTTTTTACGAAA
1 ATAATATATAAATTTTATTAAGAAA
51757348 ATAATATATATAA-TTTATTAAGAAA
1 ATAATATATA-AATTTTATTAAGAAA
51757373 CTACAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
ATAATATATAAATTTTATTAAGAAA
Done.