Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015237.1 Corchorus capsularis cultivar CVL-1 contig15258, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 130663
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4818 original size:44 final size:44
Alignment explanation
Indices: 4681--4811 Score: 180
Period size: 43 Copynumber: 3.0 Consensus size: 44
4671 TTTATTAATC
4681 TCCAAAATCTTCTTTTGG-A-T-CTCTAAATAGAAAACTTTTATTT
1 TCCAAAATCTTCTTTTGGAATTACT-TAAATAGAAAAC-TTTATTT
* * *
4724 TCCAAAATCTTCTTTTGAAATTACTTTAA-AGAAAAATTTATTT
1 TCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACTTTATTT
*
4767 TCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACGTTATTT
1 TCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACTTTATTT
4811 T
1 T
4812 TGAAAATGCT
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
43 51 0.66
44 20 0.26
45 4 0.05
46 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.44
Consensus pattern (44 bp):
TCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACTTTATTT
Found at i:6169 original size:21 final size:21
Alignment explanation
Indices: 6143--6186 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6133 TTTCCCTGAT
* *
6143 TTTCTTATT-TTCTTGTTTTTC
1 TTTCTT-TTCTTCTTCTTCTTC
6164 TTTCTTTTCTTCTTCTTCTTC
1 TTTCTTTTCTTCTTCTTCTTC
6185 TT
1 TT
6187 CCCTTTAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTCTTTTCTTCTTCTTCTTC
Found at i:6899 original size:20 final size:20
Alignment explanation
Indices: 6874--6913 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6864 ATGAAATAAA
6874 TGAAAAATGAGTAACTTTTT
1 TGAAAAATGAGTAACTTTTT
*
6894 TGAAAAATGTGTAACTTTTT
1 TGAAAAATGAGTAACTTTTT
6914 GGTATTTCTG
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:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (20 bp):
TGAAAAATGAGTAACTTTTT
Found at i:10976 original size:14 final size:15
Alignment explanation
Indices: 10957--11051 Score: 78
Period size: 16 Copynumber: 6.7 Consensus size: 15
10947 TGTTTGATGG
10957 CTGTAGTTC-TATCT
1 CTGTAGTTCATATCT
*
10971 CTGTAGTTCAATTTCT
1 CTGTAGTTC-ATATCT
*
10987 CTGTAGTTCAATTTCT
1 CTGTAGTTC-ATATCT
* *
11003 CTGTTGTTCAAAT-T
1 CTGTAGTTCATATCT
*
11017 -TG--CTTC-TATCT
1 CTGTAGTTCATATCT
11028 CTGTAGTTC-TATCT
1 CTGTAGTTCATATCT
11042 CTGTAGTTCA
1 CTGTAGTTCA
11052 AATTTGCTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
10 2 0.03
11 4 0.06
12 2 0.03
13 2 0.03
14 27 0.40
15 2 0.03
16 28 0.42
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (15 bp):
CTGTAGTTCATATCT
Found at i:10989 original size:16 final size:16
Alignment explanation
Indices: 10968--11013 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
10958 TGTAGTTCTA
10968 TCTCTGTAGTTCAATT
1 TCTCTGTAGTTCAATT
10984 TCTCTGTAGTTCAATT
1 TCTCTGTAGTTCAATT
*
11000 TCTCTGTTGTTCAA
1 TCTCTGTAGTTCAA
11014 ATTTGCTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.17, C:0.20, G:0.13, T:0.50
Consensus pattern (16 bp):
TCTCTGTAGTTCAATT
Found at i:11051 original size:39 final size:40
Alignment explanation
Indices: 10984--11060 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
10974 TAGTTCAATT
* *
10984 TCTCTGTAGTTCAATTTCTCTGTTGTTCAAATTTGCTTCTA
1 TCTCTGTAGTTC-ATATCTCTGTAGTTCAAATTTGCTTCTA
11025 TCTCTGTAGTTC-TATCTCTGTAGTTCAAATTTGCTT
1 TCTCTGTAGTTCATATCTCTGTAGTTCAAATTTGCTT
11061 TTTAAATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 22 0.65
41 12 0.35
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.51
Consensus pattern (40 bp):
TCTCTGTAGTTCATATCTCTGTAGTTCAAATTTGCTTCTA
Found at i:12159 original size:9 final size:9
Alignment explanation
Indices: 12145--12175 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
12135 GCCAGCTAGC
12145 AAGTCTAAG
1 AAGTCTAAG
12154 AAGTCTAAG
1 AAGTCTAAG
12163 AAGTCTAAG
1 AAGTCTAAG
12172 AAGT
1 AAGT
12176 TTGAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.23
Consensus pattern (9 bp):
AAGTCTAAG
Found at i:14763 original size:10 final size:10
Alignment explanation
Indices: 14737--14784 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
14727 AAATATAAAT
14737 CAAAACCGA-
1 CAAAACCGAC
14746 CAAAACCGAC
1 CAAAACCGAC
*
14756 CGAAACCGAC
1 CAAAACCGAC
***
14766 CGCCACCGAC
1 CAAAACCGAC
14776 CAAAACCGA
1 CAAAACCGA
14785 TTAATCGGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 9 0.28
10 23 0.72
ACGTcount: A:0.44, C:0.42, G:0.15, T:0.00
Consensus pattern (10 bp):
CAAAACCGAC
Found at i:15240 original size:2 final size:2
Alignment explanation
Indices: 15233--15267 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
15223 TGTATCTACA
15233 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15268 CTAAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:17549 original size:2 final size:2
Alignment explanation
Indices: 17535--17571 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
17525 AACATAGTTT
*
17535 TA TA TA T- TG 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
17572 GTTAGTTAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40934 original size:30 final size:30
Alignment explanation
Indices: 40879--40937 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
40869 TGTCTTCAAG
**
40879 TCCATAATAAGTCCTTGGCGTATCATTCCT
1 TCCATAATAAGTCCTTGGCACATCATTCCT
40909 TCCATAATAAG-CCTTGGGCACATCATTCC
1 TCCATAATAAGTCCTT-GGCACATCATTCC
40938 CTCCCCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (30 bp):
TCCATAATAAGTCCTTGGCACATCATTCCT
Found at i:41318 original size:30 final size:30
Alignment explanation
Indices: 41282--41395 Score: 120
Period size: 33 Copynumber: 3.6 Consensus size: 30
41272 CTCGTCACCT
*
41282 AAAACAGATTTATTTTCAATGCTATCAACC
1 AAAACAGAATTATTTTCAATGCTATCAACC
* *
41312 AAAACAGGATTATTTGCAATGCTATAATCAACC
1 AAAACAGAATTATTTTCAATGC--T-ATCAACC
* *
41345 AAAACAGAATTGTTTTTAATGCTATGTTCAACC
1 AAAACAGAATTATTTTCAATGCTA---TCAACC
*
41378 AAAACAGAATTGTTTTCA
1 AAAACAGAATTATTTTCA
41396 TCACAATTAG
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
30 20 0.29
31 1 0.01
32 1 0.01
33 48 0.69
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (30 bp):
AAAACAGAATTATTTTCAATGCTATCAACC
Found at i:41456 original size:33 final size:33
Alignment explanation
Indices: 41416--41539 Score: 160
Period size: 33 Copynumber: 3.8 Consensus size: 33
41406 CATCCAAAAC
* * *
41416 AGATTTAGTTTTATTGCAAACAACACTCAAATT
1 AGATTTAGTATCATCGCAAACAACACTCAAATT
* **
41449 AGGTTTAGTATCATCGCAAACAACA-TCTAAAAC
1 AGATTTAGTATCATCGCAAACAACACTC-AAATT
* *
41482 AGATTTAGTGTCATTGCAAACAACACTCAAATT
1 AGATTTAGTATCATCGCAAACAACACTCAAATT
41515 AGATTTAGTATCATCGCAAACAACA
1 AGATTTAGTATCATCGCAAACAACA
41540 TCTAAAAGAC
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
32 2 0.03
33 72 0.95
34 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (33 bp):
AGATTTAGTATCATCGCAAACAACACTCAAATT
Found at i:41463 original size:66 final size:66
Alignment explanation
Indices: 41406--41546 Score: 219
Period size: 66 Copynumber: 2.1 Consensus size: 66
41396 TCACAATTAG
* * * *
41406 CATCCAAAACAGATTTAGTTTTATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAACA
1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGATTTAGTATCATCACAAACA
41471 A
66 A
* *
41472 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGATTTAGTATCATCGCAAACA
1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGATTTAGTATCATCACAAACA
41537 A
66 A
*
41538 CATCTAAAA
1 CATCCAAAA
41547 GACTCTTTTC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.28
Consensus pattern (66 bp):
CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGATTTAGTATCATCACAAACA
A
Found at i:49652 original size:34 final size:33
Alignment explanation
Indices: 49586--49653 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
49576 TCGCAAAATT
* * **
49586 TTTTTTTTTTAGAAAAATCAGAAAAAGGAAAAC
1 TTTTTTTTATAGAAAAAACAGAAAAACAAAAAC
49619 TTTTTTTTATAGAAAAAACAGAAAAAACAAAAAC
1 TTTTTTTTATAGAAAAAACAG-AAAAACAAAAAC
49653 T
1 T
49654 AATTCTTGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 19 0.63
34 11 0.37
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (33 bp):
TTTTTTTTATAGAAAAAACAGAAAAACAAAAAC
Found at i:49807 original size:20 final size:22
Alignment explanation
Indices: 49784--49827 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
49774 GTAAAAACAC
*
49784 ATATAAAAGTAGC-A-AAAAAT
1 ATATAAAAATAGCTATAAAAAT
49804 ATATAAAAATAGCTATAAAAAT
1 ATATAAAAATAGCTATAAAAAT
49826 AT
1 AT
49828 GTTTAAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (22 bp):
ATATAAAAATAGCTATAAAAAT
Found at i:52794 original size:973 final size:975
Alignment explanation
Indices: 50899--52849 Score: 3444
Period size: 973 Copynumber: 2.0 Consensus size: 975
50889 AAACGTTCGG
*
50899 GTCCGGGGAACCCTGCCGAAACGACTTTTGAAAAGAGGAAGGAGTTGCCACTAATCTTTTTTCTA
1 GTCCGGGGAACCCTGCCGAAACGACTTTTGAAAAGAGGAAGGAGTCGCCACTAATCTTTTTTCTA
*
50964 GGTGTGATTAGCCACTTATCCATGTTATCAAGTCTAATATTAACCTAAACTTGGCGAAGGAAATA
66 GGTGTGATTAGCCACCTATCCATGTTATCAAGTCTAATATTAACCTAAACTTGGCGAAGGAAATA
*
51029 CTAACCTAACACGGTCTGCTTAACCAGAGTCTATGAGTTCGGGAGTCGGTTATGCTCGGGGAAGG
131 CTAACCTAACACGGTCTGCTTAACCAGAGTCTATGAGTTCGGGAGTCGGTTACGCTCGGGGAAGG
51094 ATTAGCACCCCCGAAACGCCCGTCAAACGACGGTACCTCTAGTCTAAAAAAAATCTAATGGGTCT
196 ATTAGCACCCCCGAAACGCCCGTCAAACGACGGTACCTCTAGTCTAAAAAAAATCTAATGGGTCT
* * *
51159 AATACTAAGGTTGCTTTTATCTCAGTCCTGTTTGTTAATAGAAAATGTTATAAAAGAAAAATAAA
261 AAAACTAAGGTTGCTTTTATCTCAATCCTGTTTGTTAATAGAAAATATTATAAAAG----A-AAA
*
51224 AAGAAAAGTTTTTTAAAACAAGTTTAGATGTCGAGAATTTTGAAGAATATAATCGAACGATCGTC
321 AAGAAAAGTTTTTTAAAACAAGTTTAGATATCGAGAATTTTGAAGAATATAATCGAACGATCGTC
* *
51289 GATTAATTCCTCTTTCAATTGTCTTTCACTATTTGTTCTCTTGTTGAATCTTCCGCACCAGGAAG
386 GATTAATTCCTCTTTCAACTCTCTTTCACTATTTGTTCTCTTGTTGAATCTTCCGCACCAGGAAG
51354 AAATTTTGAAAATGATGTGACAAAACTTTTTTTTTCATTTTGGATTTTTTTCAAAATTTGATTGA
451 AAATTTTGAAAATGATGTGACAAAACTTTTTTTTTCATTTTGGATTTTTTTCAAAATTTGATTGA
51419 TTTTATTACTTTCCAAAAACCCTCTTTCGGAATTGCTTGAATTGAAAAAAAAAGTTCTTTTCTGA
516 TTTTATTACTTTCCAAAAACCCTCTTTCGGAATTGCTTGAATT--AAAAAAAAGTTCTTTTCTGA
*
51484 AGATGCTTATCTTGAAAACTCTTGAATTACCAATTTTTAAATTTTTTGAAAACTTAATAAGAGAA
579 AGATGCTTACCTTGAAAACTCTTGAATTACCAATTTTTAAATTTTTTGAAAACTTAATAAGAGAA
*
51549 CAGATTTGATAAAAACATTTTGGAAACACTTTTTATTGCATCTTTTAAGTTTCTGATTTTTCCCT
644 CAAATTTGATAAAAACATTTTGGAAACACTTTTTATTGCATCTTTTAAGTTTCTGATTTTTCCCT
51614 TTTTTTTGGATTTTCTTTGATTTCTTAACCTAAATCTTAATTAATGCATGTATGAAATGATGAAT
709 TTTTTTTGGATTTTCTTTGATTTCTTAACCTAAATCTTAATTAATGCATGTATGAAATGATGAAT
51679 GCACAATCCGATTATTAAAAGTTGACTCACGTAACCCGGGTTATTGAAAGCCCTTCCCGGAATAT
774 GCACAATCCGATTATTAAAAGTTGACTCACGTAACCCGGGTTATTGAAAGCCCTTCCCGGAATAT
* * *
51744 ATGGTCGGAACCCCAACGCATTCCGAAAAGAACTGTCTCATCCTCGGAGACATTCAGTGGCCCCG
839 ATGCTCGAAACCCCAACGCATTCCGAAAAGAACCGTCTCATCCTCGGAGACATTCAGTGGCCCCG
51809 AATAATCGACCACACACTGAAAGCCTCTTCTTCGGAAGGCTACGGTTATCAACTATCATTTAGTG
904 AATAATCGACCACACACTGAAAGCCTCTTCTTCGGAAGGCTACGGTTATCAACTATCATTTAGTG
51874 GCAACCA
969 GCAACCA
*
51881 GTCCGGGGAACCCTGCCGAAACGACTTTTGGAAAGAGGAAGGAGTCGCCACTAATCTTTTTTCTA
1 GTCCGGGGAACCCTGCCGAAACGACTTTTGAAAAGAGGAAGGAGTCGCCACTAATCTTTTTTCTA
* * *
51946 GGTGTGATTAGCCACCTATCCATGTTATTAAGTCTAATATTAACCTAAGCTTGGCGAAGGTAATA
66 GGTGTGATTAGCCACCTATCCATGTTATCAAGTCTAATATTAACCTAAACTTGGCGAAGGAAATA
*
52011 CTAAACCTAACACGGTCTGCTTAACCAGAGTCTATGGGTTCGGGAGTCGGTTACGCTCGGGGAAG
131 CT-AACCTAACACGGTCTGCTTAACCAGAGTCTATGAGTTCGGGAGTCGGTTACGCTCGGGGAAG
* *
52076 GATTAGCACCCCCGAGACGCCCGTCAAACGACGGTACCTCTAGTCTAAACAAAATCTAATGGGTC
195 GATTAGCACCCCCGAAACGCCCGTCAAACGACGGTACCTCTAGTCTAAAAAAAATCTAATGGGTC
52141 TAAAACTAAGGTTGCTTTTATCTCAATCCTGTTTGTTAATAGAAAATATTATAAAAG-AAAAAGA
260 TAAAACTAAGGTTGCTTTTATCTCAATCCTGTTTGTTAATAGAAAATATTATAAAAGAAAAAAGA
52205 AAAGTTTTTTAAAACAAGTTTAGATATCGAGAATTTTGAAGAATATAATCGAACGATCGTCGATT
325 AAAGTTTTTTAAAACAAGTTTAGATATCGAGAATTTTGAAGAATATAATCGAACGATCGTCGATT
*
52270 AATTCCTCTTTCAACTCTTTTTCACTATTTGTTCTCTTGTTGAATCTTCCGCACCAGGAAGAAAT
390 AATTCCTCTTTCAACTCTCTTTCACTATTTGTTCTCTTGTTGAATCTTCCGCACCAGGAAGAAAT
*
52335 TTTGAAAATGCTGTGACAAAACTTTTTTTTTCATTTTGGA-TTTTTTCAAAATTTGATTGATTTT
455 TTTGAAAATGATGTGACAAAACTTTTTTTTTCATTTTGGATTTTTTTCAAAATTTGATTGATTTT
* * *
52399 ATTACTTTTCAAGAACCCTCTTTCGGAATTGCTTGAATT-AAAAAAAGTTCTTTTTTGAAGATGC
520 ATTACTTTCCAAAAACCCTCTTTCGGAATTGCTTGAATTAAAAAAAAGTTCTTTTCTGAAGATGC
*
52463 TTACCTTGAAAACTCTTGAATTAGCAATTTTTAAA-TTTTTGAAAACTTAATAAGAGAACAAATT
585 TTACCTTGAAAACTCTTGAATTACCAATTTTTAAATTTTTTGAAAACTTAATAAGAGAACAAATT
* * *
52527 TGATAAAAACATTTTGGAGACACTTTTTATTGTATCTTTTAATTTTCTGATTTTTCCCTTTCTTT
650 TGATAAAAACATTTTGGAAACACTTTTTATTGCATCTTTTAAGTTTCTGATTTTTCCCTTT-TTT
52592 TTGGATTTTCTTTGATTTCTTAACCTAAATCTTAATTAATGCATGTATGAAATGATGAATGCA-A
714 TTGGATTTTCTTTGATTTCTTAACCTAAATCTTAATTAATGCATGTATGAAATGATGAATGCACA
52656 ATTCCGATTATTAAAAGTTGACTCACGTAACCCGGGTTATTGAAAGCCCTTCCCGGAATATATGC
779 A-TCCGATTATTAAAAGTTGACTCACGTAACCCGGGTTATTGAAAGCCCTTCCCGGAATATATGC
* * * *
52721 TCGAAACCCCGACGCATTCCGAGAAGAACCGTCTCATCCTCGGAGACATTTAGTGGTCCCGAATA
843 TCGAAACCCCAACGCATTCCGAAAAGAACCGTCTCATCCTCGGAGACATTCAGTGGCCCCGAATA
* * *
52786 CTCGACCACACACTGAAAGCCTTTTCTTCGGAAGGCTACGGTTATCAACTGTCATTTAGTGGCA
908 ATCGACCACACACTGAAAGCCTCTTCTTCGGAAGGCTACGGTTATCAACTATCATTTAGTGGCA
52850 TGCCATGTAT
Statistics
Matches: 929, Mismatches: 37, Indels: 15
0.95 0.04 0.02
Matches are distributed among these distances:
972 88 0.09
973 305 0.33
976 61 0.07
977 172 0.19
982 126 0.14
983 177 0.19
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (975 bp):
GTCCGGGGAACCCTGCCGAAACGACTTTTGAAAAGAGGAAGGAGTCGCCACTAATCTTTTTTCTA
GGTGTGATTAGCCACCTATCCATGTTATCAAGTCTAATATTAACCTAAACTTGGCGAAGGAAATA
CTAACCTAACACGGTCTGCTTAACCAGAGTCTATGAGTTCGGGAGTCGGTTACGCTCGGGGAAGG
ATTAGCACCCCCGAAACGCCCGTCAAACGACGGTACCTCTAGTCTAAAAAAAATCTAATGGGTCT
AAAACTAAGGTTGCTTTTATCTCAATCCTGTTTGTTAATAGAAAATATTATAAAAGAAAAAAGAA
AAGTTTTTTAAAACAAGTTTAGATATCGAGAATTTTGAAGAATATAATCGAACGATCGTCGATTA
ATTCCTCTTTCAACTCTCTTTCACTATTTGTTCTCTTGTTGAATCTTCCGCACCAGGAAGAAATT
TTGAAAATGATGTGACAAAACTTTTTTTTTCATTTTGGATTTTTTTCAAAATTTGATTGATTTTA
TTACTTTCCAAAAACCCTCTTTCGGAATTGCTTGAATTAAAAAAAAGTTCTTTTCTGAAGATGCT
TACCTTGAAAACTCTTGAATTACCAATTTTTAAATTTTTTGAAAACTTAATAAGAGAACAAATTT
GATAAAAACATTTTGGAAACACTTTTTATTGCATCTTTTAAGTTTCTGATTTTTCCCTTTTTTTT
GGATTTTCTTTGATTTCTTAACCTAAATCTTAATTAATGCATGTATGAAATGATGAATGCACAAT
CCGATTATTAAAAGTTGACTCACGTAACCCGGGTTATTGAAAGCCCTTCCCGGAATATATGCTCG
AAACCCCAACGCATTCCGAAAAGAACCGTCTCATCCTCGGAGACATTCAGTGGCCCCGAATAATC
GACCACACACTGAAAGCCTCTTCTTCGGAAGGCTACGGTTATCAACTATCATTTAGTGGCAACCA
Found at i:53379 original size:3 final size:3
Alignment explanation
Indices: 53371--53397 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53361 AATACCAACA
53371 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
53398 TTTTTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:57002 original size:21 final size:22
Alignment explanation
Indices: 56978--57024 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
56968 CTGTCCGTAA
56978 TTAGCTC-GGGCAATCTACATT
1 TTAGCTCTGGGCAATCTACATT
* **
56999 TTAGTTCTTTGCAATCTACATT
1 TTAGCTCTGGGCAATCTACATT
57021 TTAG
1 TTAG
57025 TTCTTTGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (22 bp):
TTAGCTCTGGGCAATCTACATT
Found at i:57012 original size:22 final size:22
Alignment explanation
Indices: 56987--57032 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
56977 ATTAGCTCGG
56987 GCAATCTACATTTTAGTTCTTT
1 GCAATCTACATTTTAGTTCTTT
57009 GCAATCTACATTTTAGTTCTTT
1 GCAATCTACATTTTAGTTCTTT
57031 GC
1 GC
57033 TTAACTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (22 bp):
GCAATCTACATTTTAGTTCTTT
Found at i:57628 original size:27 final size:28
Alignment explanation
Indices: 57555--57628 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 28
57545 AAGTGAACTT
57555 AAAATGACCAAAATGCCCCTGAATGTGC
1 AAAATGACCAAAATGCCCCTGAATGTGC
* *
57583 -AAATGACCCAAAAT-ACCCT-TA-GTGC
1 AAAATGA-CCAAAATGCCCCTGAATGTGC
*
57608 AAAAAAGACCAAAATGCCCCT
1 -AAAATGACCAAAATGCCCCT
57629 AGGTGACCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
25 4 0.11
26 8 0.21
27 19 0.50
28 7 0.18
ACGTcount: A:0.43, C:0.27, G:0.14, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAATGTGC
Found at i:77338 original size:2 final size:2
Alignment explanation
Indices: 77331--77356 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
77321 TTTGTTAATA
77331 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
77357 TAATTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78593 original size:26 final size:26
Alignment explanation
Indices: 78564--78614 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
78554 TTAATAATTT
*
78564 CTTTTTTCCCCTTAAAATTCCATCCG
1 CTTTTTTCCCCATAAAATTCCATCCG
*
78590 CTTTTTTCCCCATCAAATTCCATCC
1 CTTTTTTCCCCATAAAATTCCATCC
78615 TTGGTTGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.20, C:0.37, G:0.02, T:0.41
Consensus pattern (26 bp):
CTTTTTTCCCCATAAAATTCCATCCG
Found at i:78852 original size:22 final size:22
Alignment explanation
Indices: 78809--78859 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
78799 AAAGTTACAT
**
78809 ATTGAATTTGGATTAATTTGAA
1 ATTGAATTTGGATTAAACTGAA
78831 ATTGAATTTGGATTAAACTGAA
1 ATTGAATTTGGATTAAACTGAA
*
78853 ATCGAAT
1 ATTGAAT
78860 CGTATCAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (22 bp):
ATTGAATTTGGATTAAACTGAA
Found at i:79609 original size:13 final size:14
Alignment explanation
Indices: 79591--79621 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
79581 CAGTGTTACT
79591 TTATAGTATAT-AA
1 TTATAGTATATAAA
79604 TTATAGTATATAAA
1 TTATAGTATATAAA
79618 TTAT
1 TTAT
79622 CTAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
TTATAGTATATAAA
Found at i:79910 original size:2 final size:2
Alignment explanation
Indices: 79903--79940 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
79893 GTAGTGGAGC
79903 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
79941 CTATTACTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:81719 original size:20 final size:20
Alignment explanation
Indices: 81682--81720 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
81672 TACTCTTATT
81682 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
81702 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
81721 AATGTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:81956 original size:22 final size:21
Alignment explanation
Indices: 81889--82025 Score: 94
Period size: 22 Copynumber: 6.1 Consensus size: 21
81879 CTCTATATGA
**
81889 TTATCAAAATTTCATAAGAAGG
1 TTATCAAAATTTCAT-AGGTGG
* * *
81911 TTATTATAATTTCATGAGGAGG
1 TTATCAAAATTTCAT-AGGTGG
81933 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GTGG
* *
81955 TTACCAAAATTTCATTGGATCAGG
1 TTATCAAAATTTCATAGG-T--GG
* * *
81979 TTATTAAAATTTCTTAGATTGG
1 TTATCAAAATTTCATAG-GTGG
**
82001 TTATTGAAATTTCATAGGGTGG
1 TTATCAAAATTTCATA-GGTGG
82023 TTA
1 TTA
82026 ATTATCACAA
Statistics
Matches: 92, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
21 3 0.03
22 72 0.78
23 1 0.01
24 16 0.17
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTGG
Found at i:82107 original size:22 final size:21
Alignment explanation
Indices: 82082--82209 Score: 96
Period size: 22 Copynumber: 5.9 Consensus size: 21
82072 TTATAGTGTT
82082 GTTATCAAAATTTCAAAACGAG
1 GTTATCAAAATTTCAAAA-GAG
* * *
82104 GTTATCAAAATTACATAATGTG
1 GTTATCAAAATTTCA-AAAGAG
* * *
82126 ATCATCAAAATTTC-ATAGATGG
1 GTTATCAAAATTTCAAAAGA--G
* * **
82148 GTCAACAAAATTTTGTAAAGAG
1 GTTATCAAAA-TTTCAAAAGAG
82170 GTTATCAAAATTTCACAAAGAG
1 GTTATCAAAATTTCA-AAAGAG
*
82192 GTTATCAAATTTTCAAAA
1 GTTATCAAAATTTCAAAA
82210 TGTGATTACA
Statistics
Matches: 82, Mismatches: 18, Indels: 13
0.73 0.16 0.12
Matches are distributed among these distances:
20 2 0.02
21 6 0.07
22 65 0.79
23 5 0.06
24 4 0.05
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (21 bp):
GTTATCAAAATTTCAAAAGAG
Found at i:82115 original size:44 final size:43
Alignment explanation
Indices: 82061--82227 Score: 117
Period size: 44 Copynumber: 3.8 Consensus size: 43
82051 ATCAAAAAGA
* *
82061 TTATTAAAATTTTATAGTGTTGTTATCAAAATTTCA-AAACGAGG
1 TTATCAAAATTTTATAATG-TGTTATCAAAATTTCACAAA-GAGG
** * * *
82105 TTATCAAAATTACATAATGTGATCATCAAAATTTCATAGATG-GG
1 TTATCAAAATTTTATAATGTG-TTATCAAAATTTCACA-AAGAGG
* * * * *
82149 TCAACAAAATTTTGTAAAGAGGTTATCAAAATTTCACAAAGAGG
1 TTATCAAAATTTTATAATG-TGTTATCAAAATTTCACAAAGAGG
*
82193 TTATC-AAATTTTCAAAATGTGATTA-CAAAAATTTC
1 TTATCAAAATTTT-ATAATGTG-TTATC-AAAATTTC
82228 GTAGTGATAA
Statistics
Matches: 93, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
43 13 0.14
44 76 0.82
45 3 0.03
46 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (43 bp):
TTATCAAAATTTTATAATGTGTTATCAAAATTTCACAAAGAGG
Found at i:82271 original size:22 final size:22
Alignment explanation
Indices: 82246--82894 Score: 253
Period size: 22 Copynumber: 29.9 Consensus size: 22
82236 AATTCTGGGG
82246 AGGTTATCAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
* *
82268 AGGTATAT-AAACTTTTATTATGG-
1 AGGT-TATCAAAATTTCA-TA-GGA
*
82291 A-GTAATCAAAATTTCAT-GG-
1 AGGTTATCAAAATTTCATAGGA
* *
82310 AGGATATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATAGGA
* **
82332 AGGTTATTAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG-GA
* *
82355 A-GTTTTCAAAATTTCATAAGA
1 AGGTTATCAAAATTTCATAGGA
* * *
82376 GGGTCATCAAAATTTCATA-GT
1 AGGTTATCAAAATTTCATAGGA
* * *
82397 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATAGGA
* * *
82420 AGATTAACAAAATTTCATATTG-
1 AGGTTATCAAAATTTCATA-GGA
** *
82442 AGGTTATCAAAAAATCATAGGG
1 AGGTTATCAAAATTTCATAGGA
* *
82464 AGTTTATCAAAA-TT--T--GT
1 AGGTTATCAAAATTTCATAGGA
* *
82481 A-GTTATCAAGATTTCATAAGA
1 AGGTTATCAAAATTTCATAGGA
* *
82502 AAGTTATCAAAATTTTATAGGAA
1 AGGTTATCAAAATTTCATAGG-A
* *
82525 AGTTTATCAAAATTTTATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
82547 AGATTTATCAAAATTTCATAGCG-
1 AG-GTTATCAAAATTTCATAG-GA
*
82570 AGGTTATCATAATTTCATAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* *
82592 TGAG-TATCAAAATTTCAGAGTG-
1 AG-GTTATCAAAATTTCATAG-GA
* *
82614 TGATTA-CTAACAA-TTCATATGG-
1 AGGTTATC-AA-AATTTCATA-GGA
* * * *
82636 AGTTTTTTAAATTTTCATA--A
1 AGGTTATCAAAATTTCATAGGA
* * *
82656 CGTGATTATCAATATATCATATGG-
1 AG-G-TTATCAAAATTTCATA-GGA
* ** * *
82680 CGGTTATCAACGTCTCATAGTGT
1 AGGTTATCAAAATTTCATAG-GA
* *
82703 TGGTTATCAAAATTTCATTGGGA
1 AGGTTATCAAAATTTCA-TAGGA
*
82726 A-GTTATCAAAATTTCATA-TA
1 AGGTTATCAAAATTTCATAGGA
* **
82746 GAGGTCT-TCAAAA-TTCCTTTGA
1 -AGGT-TATCAAAATTTCATAGGA
* *
82768 GAGGTTAACAAAATTTCATAAGA
1 -AGGTTATCAAAATTTCATAGGA
* * **
82791 AGGTTA-AAAAAATT-ATAAAA
1 AGGTTATCAAAATTTCATAGGA
* * * *
82811 AGATT-TCGAAATTCCATAGTA
1 AGGTTATCAAAATTTCATAGGA
** *
82832 TCGTTATTAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
82854 AGCTTATCAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
82876 AGCTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
82895 ATGGGATCAT
Statistics
Matches: 472, Mismatches: 108, Indels: 94
0.70 0.16 0.14
Matches are distributed among these distances:
16 8 0.02
17 4 0.01
19 5 0.01
20 29 0.06
21 33 0.07
22 310 0.66
23 76 0.16
24 7 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:84484 original size:120 final size:120
Alignment explanation
Indices: 84303--84620 Score: 344
Period size: 127 Copynumber: 2.6 Consensus size: 120
84293 ATGTAGCCAG
* *
84303 TGCCTCGTTAAAAACCTTAAG-CTGGAAAACCCAATGGGACAAAACC-AGTCATAAGGAAAAAAG
1 TGCCTCATTAAAAACCTTAAGTC-GGAAAACCC-ATGGGACAAAACCGA-TCATAAGGGAAAAAG
* *
84366 AGTGCAACATATCAAGTCCAT-T-TGTCTTCTA-GACAA-ATAT-TATATGTGCTCTTTAT
63 AGTGCAACA-ATCAAGTCCATGTATGTCTTC-AGGACAATACATCTATATGTGCT-ATTAT
** * *
84422 TGCCTCATTAAAAAACCTTGTGTCGGAAAACCCAGTGGGACAAAACCGAACAGAAGGGAAAAAGA
1 TGCCTCATT-AAAAACCTTAAGTCGGAAAACCCA-TGGGACAAAACCGATCATAAGGGAAAAAGA
* * *
84487 GTGCTAGAGCAATTAAGTGCATGTAAATGTCTTCAGGACAATTACATCTATATGTGCTATTGT
64 GTGC-A-A-CAATCAAGTCCATGT--ATGTCTTCAGGACAA-TACATCTATATGTGCTATTAT
*
84550 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCTATGGGACAAAACCGATCATAAGGGAAAAAGTG
1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCC-ATGGGACAAAACCGATCATAAGGGAAAAAGAG
84615 TGCAAC
65 TGCAAC
84621 GCACTTTAAA
Statistics
Matches: 167, Mismatches: 16, Indels: 27
0.80 0.08 0.13
Matches are distributed among these distances:
119 9 0.05
120 48 0.29
121 3 0.02
122 10 0.06
123 3 0.02
124 1 0.01
125 2 0.01
126 13 0.08
127 52 0.31
128 16 0.10
129 10 0.06
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (120 bp):
TGCCTCATTAAAAACCTTAAGTCGGAAAACCCATGGGACAAAACCGATCATAAGGGAAAAAGAGT
GCAACAATCAAGTCCATGTATGTCTTCAGGACAATACATCTATATGTGCTATTAT
Found at i:88452 original size:30 final size:30
Alignment explanation
Indices: 88416--88472 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
88406 TCAATTGAAT
* *
88416 AAAATCATGACATCTTCAAGTGTCAATTGC
1 AAAATCATAACAACTTCAAGTGTCAATTGC
* *
88446 AAAATCATAATAACTTCTAGTGTCAAT
1 AAAATCATAACAACTTCAAGTGTCAAT
88473 AACGATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (30 bp):
AAAATCATAACAACTTCAAGTGTCAATTGC
Found at i:88554 original size:30 final size:30
Alignment explanation
Indices: 88497--89319 Score: 819
Period size: 30 Copynumber: 26.7 Consensus size: 30
88487 CATTGTGTAT
88497 ATGACAACTTCTGGTGTCAA-T--AAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
88524 ATGACATCTT-TAAGTGTCAATTGCAAAATC
1 ATGACAACTTCT-GGTGTCAATTGCAAAATC
*
88554 ATAACAACTTCTGGTGTCAATTGCAAAAATC
1 ATGACAACTTCTGGTGTCAATTGC-AAAATC
88585 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * *
88615 ATGACAATTTCTAGTGTCAATTGTAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
88645 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
88675 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
88705 ATGACAACTTTTGGTGTCAATTGTAAAAATC
1 ATGACAACTTCTGGTGTCAATTG-CAAAATC
* *
88736 ATGACACCTTCTAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
88766 ATGACAACTTCTAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
**
88796 ATGACAACTTCTGGTGTCAATAACGATTTAAAATTC
1 ATGACAACTTCTGGTGTCAAT-----TGCAAAA-TC
* *
88832 ATTGTGTATATGACAACTTCTGGAGTCAATTGAATAAAATC
1 ---------ATGACAACTTCTGGTGTCAATTG--CAAAATC
* **
88873 ATGACATCTTCAAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
88903 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * *
88933 ATGACAACTTCTAGTGTCAATTTGAAAAATG
1 ATGACAACTTCTGGTGTCAA-TTGCAAAATC
*
88964 ATGACAACTTATGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
88994 ATGACAACTTCTAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * * * *
89024 ATGACAACTTCTAGTGTCATTTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * * * * *
89054 ATAACAACTTCTAGTGTCATTTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * * *
89084 ATGACAACTTCTGGTGTCATTTGTAAGATT
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * *
89114 ATTGATAACTTCTTGTGTCAATTGTAAAATC
1 A-TGACAACTTCTGGTGTCAATTGCAAAATC
* ** * *
89145 ATGACAACTTCTGGTGTCATTTATAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * * *
89175 ATGACAACTTCTGGTGTCATTTGTAAGATT
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
89205 ATTGACAACTTCTGGTGTCAA-TGAAGATTAATC
1 A-TGACAACTTCTGGTGTCAATTGCA-A--AATC
* * * **
89238 ATGACAACATCTGGTGTCATTTGTAAGGTC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
** * *
89268 ATTGACAACTTCTGGTGTCAATTATAACACC
1 A-TGACAACTTCTGGTGTCAATTGCAAAATC
89299 ATTGACAACTTCTGGTGTCAA
1 A-TGACAACTTCTGGTGTCAA
89320 ACTGTCAATG
Statistics
Matches: 685, Mismatches: 79, Indels: 60
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.00
27 16 0.02
28 1 0.00
30 419 0.61
31 170 0.25
32 37 0.05
33 6 0.01
35 5 0.01
36 2 0.00
40 1 0.00
41 2 0.00
42 5 0.01
45 20 0.03
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAAATC
Found at i:88571 original size:102 final size:103
Alignment explanation
Indices: 88345--88574 Score: 381
Period size: 107 Copynumber: 2.2 Consensus size: 103
88335 GGAATTAGTT
88345 ATAACAACTTCTGGTGTCAATAACGATTTAAAATTCATTGTGTATATGACAACTTCTGGAGTCAA
1 ATAACAACTTCTGGTGTCAATAACGATTTAAAATTCATTGTGTATATGACAACTTCTGGAGTC-A
88410 TTGAATAAAATCATGACATCTTCAAGTGTCAATTGCAAAATC
65 ---AATAAAATCATGACATCTTCAAGTGTCAATTGCAAAATC
* * *
88452 ATAATAACTTCTAGTGTCAATAACGATTTAAAATTCATTGTGTATATGACAACTTCTGGTGTC-A
1 ATAACAACTTCTGGTGTCAATAACGATTTAAAATTCATTGTGTATATGACAACTTCTGGAGTCAA
*
88516 ATAAAATCATGACATCTTTAAGTGTCAATTGCAAAATC
66 ATAAAATCATGACATCTTCAAGTGTCAATTGCAAAATC
88554 ATAACAACTTCTGGTGTCAAT
1 ATAACAACTTCTGGTGTCAAT
88575 TGCAAAAATC
Statistics
Matches: 117, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
102 57 0.49
107 60 0.51
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (103 bp):
ATAACAACTTCTGGTGTCAATAACGATTTAAAATTCATTGTGTATATGACAACTTCTGGAGTCAA
ATAAAATCATGACATCTTCAAGTGTCAATTGCAAAATC
Found at i:88652 original size:91 final size:90
Alignment explanation
Indices: 88497--89319 Score: 855
Period size: 91 Copynumber: 8.9 Consensus size: 90
88487 CATTGTGTAT
* * * *
88497 ATGACAACTTCTGGTGTCAA-T--AAAATCATGACATCTT-TAAGTGTCAATTGCAAAATCATAA
1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCT-GGTGTCAATTGTAAAATCATGA
88558 CAACTTCTGGTGTCAATTGCAAAAATC
65 CAACTTCTGGTGTCAATTG-AAAAATC
* *
88585 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAATTTCTAGTGTCAATTGTAAAATCATGAC
1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGTAAAATCATGAC
*
88650 AACTTCTGGTGTCAATTGCAAAATC
66 AACTTCTGGTGTCAATTGAAAAATC
*
88675 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTTTGGTGTCAATTGTAAAAATCATGA
1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGT-AAAATCATGA
* * *
88740 CACCTTCTAGTGTCAATTGCAAAATC
65 CAACTTCTGGTGTCAATTGAAAAATC
* *
88766 ATGACAACTTCTAGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATAACGATTTAAAATT
1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAAT-----TGTAAAA-T
*
88831 CATTGTGTATATGACAACTTCTGGAGTCAATTGAATAAAATC
60 C---------ATGACAACTTCTGGTGTCAATTG-A-AAAATC
* ** *
88873 ATGACATCTTCAAGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGTAAAATCATGAC
* *
88938 AACTTCTAGTGTCAATTTGAAAAATG
66 AACTTCTGGTGTCAA-TTGAAAAATC
* * *
88964 ATGACAACTTATGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGAC
1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGTAAAATCATGAC
* * * * *
89029 AACTTCTAGTGTCATTTGTAAGACC
66 AACTTCTGGTGTCAATTGAAAAATC
* * * * * * * * *
89054 ATAACAACTTCTAGTGTCATTTGTAAGACCATGACAACTTCTGGTGTCATTTGTAAGATTATTGA
1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGTAAAATCA-TGA
* * *
89119 TAACTTCTTGTGTCAATTGTAAAATC
65 CAACTTCTGGTGTCAATTGAAAAATC
* ** * * * * *
89145 ATGACAACTTCTGGTGTCATTTATAAGACCATGACAACTTCTGGTGTCATTTGTAAGATTATTGA
1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGTAAAATCA-TGA
89210 CAACTTCTGGTGTCAA-TGAAGATTAATC
65 CAACTTCTGGTGTCAATTGAA-A--AATC
* * * ** * * *
89238 ATGACAACATCTGGTGTCATTTGTAAGGTCATTGACAACTTCTGGTGTCAATTATAACACCATTG
1 ATGACAACTTCTGGTGTCAATTGCAAAATCA-TGACAACTTCTGGTGTCAATTGTAAAATCA-TG
89303 ACAACTTCTGGTGTCAA
64 ACAACTTCTGGTGTCAA
89320 ACTGTCAATG
Statistics
Matches: 641, Mismatches: 66, Indels: 50
0.85 0.09 0.07
Matches are distributed among these distances:
88 20 0.03
89 1 0.00
90 115 0.18
91 316 0.49
92 20 0.03
93 34 0.05
94 45 0.07
95 4 0.01
96 4 0.01
101 2 0.00
102 5 0.01
105 20 0.03
107 55 0.09
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (90 bp):
ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGTAAAATCATGAC
AACTTCTGGTGTCAATTGAAAAATC
Found at i:88734 original size:121 final size:120
Alignment explanation
Indices: 88497--89319 Score: 855
Period size: 121 Copynumber: 6.7 Consensus size: 120
88487 CATTGTGTAT
* * * *
88497 ATGACAACTTCTGGTGTCAA---TAAAATCATGACATCTT-TAAGTGTCAATTGCAAAATCATAA
1 ATGACAACTTCTAGTGTCAATTGTAAAATCATGACAACTTCT-GGTGTCAATTGCAAAATCATGA
* *
88558 CAACTTCTGGTGTCAATTGCAAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
65 CAACTTCTGGTGTCAATTG-TAAAATCATGACAACTTCTGGTGTCAATTGAAAAATC
*
88615 ATGACAATTTCTAGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
1 ATGACAACTTCTAGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
* *
88680 AACTTCTGGTGTCAATTGCAAAATCATGACAACTTTTGGTGTCAATTGTAAAAATC
66 AACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTG-AAAAATC
* * *
88736 ATGACACCTTCTAGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGAC
1 ATGACAACTTCTAGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
* *
88801 AACTTCTGGTGTCAATAACGATTTAAAATTCATTGTGTATATGACAACTTCTGGAGTCAATTGAA
66 AACTTCTGGTGTCAAT-----TGTAAAA-TC---------ATGACAACTTCTGGTGTCAATTG-A
88866 TAAAATC
115 -AAAATC
* * *
88873 ATGACATCTTCAAGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
1 ATGACAACTTCTAGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
* * * * *
88938 AACTTCTAGTGTCAATTTGAAAAATGATGACAACTTATGGTGTCAATTGCAAAATC
66 AACTTCTGGTGTCAA-TTGTAAAATCATGACAACTTCTGGTGTCAATTGAAAAATC
* * * * * * *
88994 ATGACAACTTCTAGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCATTTGTAAGACCATAAC
1 ATGACAACTTCTAGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
* * * * * * * *
89059 AACTTCTAGTGTCATTTGTAAGACCATGACAACTTCTGGTGTCATTTGTAAGATT
66 AACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGAAAAATC
* * * ** * *
89114 ATTGATAACTTCTTGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCATTTATAAGACCATGA
1 A-TGACAACTTCTAGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGA
* * *
89179 CAACTTCTGGTGTCATTTGTAAGATTATTGACAACTTCTGGTGTCAA-TGAAGATTAATC
65 CAACTTCTGGTGTCAATTGTAAAATCA-TGACAACTTCTGGTGTCAATTGAA-A--AATC
* * * ** ** * *
89238 ATGACAACATCTGGTGTCATTTGTAAGGTCATTGACAACTTCTGGTGTCAATTATAACACCATTG
1 ATGACAACTTCTAGTGTCAATTGTAAAATCA-TGACAACTTCTGGTGTCAATTGCAAAATCA-TG
89303 ACAACTTCTGGTGTCAA
64 ACAACTTCTGGTGTCAA
89320 ACTGTCAATG
Statistics
Matches: 609, Mismatches: 67, Indels: 51
0.84 0.09 0.07
Matches are distributed among these distances:
118 18 0.03
120 60 0.10
121 299 0.49
122 20 0.03
123 45 0.07
124 31 0.05
125 18 0.03
126 5 0.01
127 2 0.00
132 1 0.00
133 5 0.01
136 22 0.04
137 82 0.13
138 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (120 bp):
ATGACAACTTCTAGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
AACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGAAAAATC
Found at i:89035 original size:228 final size:226
Alignment explanation
Indices: 88615--89042 Score: 705
Period size: 228 Copynumber: 1.9 Consensus size: 226
88605 TTGCAAAATC
* * **
88615 ATGACAATTTCTAGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
1 ATGACAACTTCTAGAGTCAATTGTAAAATCATGACAACTTCAAGTGTCAATTGCAAAATCATGAC
* * *
88680 AACTTCTGGTGTCAATTGCAAAATCATGACAACTTTTGGTGTCAATTGTAAAAATCATGACACCT
66 AACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGTAAAAATCATGACAACT
* *
88745 TCTAGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGACAACTTCTGG
131 TATAGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGACAACTTCTAG
88810 TGTCAATAACGATTTAAAATTCATTGTGTAT
196 TGTCAATAACGATTTAAAATTCATTGTGTAT
* *
88841 ATGACAACTTCTGGAGTCAATTGAATAAAATCATGACATCTTCAAGTGTCAATTGCAAAATCATG
1 ATGACAACTTCTAGAGTCAATTG--TAAAATCATGACAACTTCAAGTGTCAATTGCAAAATCATG
*
88906 ACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATT-TGAAAAATGATGACA
64 ACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGT-AAAAATCATGACA
*
88970 ACTTATGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGACAACTTC
128 ACTTATAGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGACAACTTC
89035 TAGTGTCA
193 TAGTGTCA
89043 TTTGTAAGAC
Statistics
Matches: 186, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
226 20 0.11
227 1 0.01
228 165 0.89
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (226 bp):
ATGACAACTTCTAGAGTCAATTGTAAAATCATGACAACTTCAAGTGTCAATTGCAAAATCATGAC
AACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGTAAAAATCATGACAACT
TATAGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGACAACTTCTAG
TGTCAATAACGATTTAAAATTCATTGTGTAT
Found at i:92770 original size:16 final size:15
Alignment explanation
Indices: 92747--92789 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
92737 AGAAAATAGC
*
92747 AAAAGAAGAGAAGAA
1 AAAAGAAGAAAAGAA
92762 AAAAGGAAGAAAAGAA
1 AAAA-GAAGAAAAGAA
92778 AAGAA-AAGAAAA
1 AA-AAGAAGAAAA
92790 AAGCTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 11 0.44
16 12 0.48
17 2 0.08
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAAAGAA
Found at i:92949 original size:30 final size:29
Alignment explanation
Indices: 92913--92973 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
92903 ACGAAGGCAC
*
92913 AAATTGATAATTCAGGGGGTAAAATGTCCA
1 AAATTGA-AATTCAGGGGGTAAAACGTCCA
* *
92943 AAATTGAAGTTGAGGGGGTAAAACGTCCA
1 AAATTGAAATTCAGGGGGTAAAACGTCCA
92972 AA
1 AA
92974 CGCTACAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.41, C:0.10, G:0.26, T:0.23
Consensus pattern (29 bp):
AAATTGAAATTCAGGGGGTAAAACGTCCA
Found at i:93933 original size:2 final size:2
Alignment explanation
Indices: 93926--93955 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
93916 AATAAAATTA
93926 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
93956 TTGTGGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94316 original size:3 final size:3
Alignment explanation
Indices: 94308--94341 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
94298 ATTTAGTGGG
94308 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
94342 GATGATGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:94328 original size:14 final size:14
Alignment explanation
Indices: 94309--94337 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
94299 TTTAGTGGGT
94309 TATTATTATTATTA
1 TATTATTATTATTA
94323 TATTATTATTATTA
1 TATTATTATTATTA
94337 T
1 T
94338 TATTGATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:94330 original size:17 final size:17
Alignment explanation
Indices: 94308--94340 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
94298 ATTTAGTGGG
94308 TTATTATTATTATTATA
1 TTATTATTATTATTATA
94325 TTATTATTATTATTAT
1 TTATTATTATTATTAT
94341 TGATGATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTATTATTATA
Found at i:94571 original size:2 final size:2
Alignment explanation
Indices: 94564--94600 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
94554 ACGATTACCA
94564 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
94601 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:97318 original size:37 final size:37
Alignment explanation
Indices: 97249--97379 Score: 147
Period size: 37 Copynumber: 3.5 Consensus size: 37
97239 TGTTTTTTGA
* * *
97249 CGGGATCTTTCCCTTCCTAA-AGTGAAAGTAAAACTAG
1 CGGGATCTTTCCCTTCTTAAGA-CGAAAATAAAACTAG
* * *
97286 TGGGATCTTTCCCTTCTTAAGACAAAAATAAAACTAA
1 CGGGATCTTTCCCTTCTTAAGACGAAAATAAAACTAG
* * * *
97323 CGGGATCTTTCCCCTCTTAGGACGAAATTAAAACAAG
1 CGGGATCTTTCCCTTCTTAAGACGAAAATAAAACTAG
*
97360 CGGAATCTTTCCCTTCTTAA
1 CGGGATCTTTCCCTTCTTAA
97380 AAAGAAAAAA
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
37 76 0.99
38 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (37 bp):
CGGGATCTTTCCCTTCTTAAGACGAAAATAAAACTAG
Found at i:100373 original size:2 final size:2
Alignment explanation
Indices: 100368--100406 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
100358 TATATATATA
100368 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
100407 TGAACAGAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:101419 original size:7 final size:7
Alignment explanation
Indices: 101409--101433 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
101399 AAAAATCCAA
101409 AAAATTC
1 AAAATTC
101416 AAAATTC
1 AAAATTC
101423 AAAATTC
1 AAAATTC
101430 AAAA
1 AAAA
101434 CAAAATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTC
Found at i:120127 original size:21 final size:21
Alignment explanation
Indices: 120101--120145 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
120091 ATCTCACAAT
*
120101 CTTCGGGCTCGTCTAGCCAAG
1 CTTCGGGCTCGGCTAGCCAAG
* *
120122 CTTCGGGTTCGGCTAGTCAAG
1 CTTCGGGCTCGGCTAGCCAAG
120143 CTT
1 CTT
120146 GGCCCAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.29
Consensus pattern (21 bp):
CTTCGGGCTCGGCTAGCCAAG
Found at i:120948 original size:50 final size:50
Alignment explanation
Indices: 120854--120999 Score: 215
Period size: 50 Copynumber: 2.9 Consensus size: 50
120844 GACAACACCG
* * *
120854 AGCTTTCCTCAAGCTCA-AACAAGTGCTCCCCACACTAATCACAAACCTA
1 AGCTTTCCTCAAGCTCAGAACAAGTGCTCCCCGCACTGATTACAAACCTA
*
120903 AGCTTTCCTCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAAACCTA
1 AGCTTTCCTCAAGCTCAGAACAAGTGCTCCCCGCACTGATTACAAACCTA
* *
120953 AGCTTTCC-CTAATCTCAGAACAAGTGCTCCCTGCACTGATTACAAAC
1 AGCTTTCCTC-AAGCTCAGAACAAGTGCTCCCCGCACTGATTACAAAC
121000 AAAAAGATAG
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
49 17 0.19
50 71 0.81
ACGTcount: A:0.32, C:0.34, G:0.12, T:0.23
Consensus pattern (50 bp):
AGCTTTCCTCAAGCTCAGAACAAGTGCTCCCCGCACTGATTACAAACCTA
Found at i:127766 original size:13 final size:12
Alignment explanation
Indices: 127743--127782 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
127733 TTAATACATG
127743 TATCGACGGATA
1 TATCGACGGATA
127755 TATCGAACGGATA
1 TATCG-ACGGATA
127768 TATCGACGGATA
1 TATCGACGGATA
127780 TAT
1 TAT
127783 TGAGGTATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:129081 original size:10 final size:10
Alignment explanation
Indices: 129065--129100 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
129055 AATTTAATAT
129065 GGATATTTAC
1 GGATATTTAC
*
129075 AGATATTTAC
1 GGATATTTAC
129085 GGATATTTAC
1 GGATATTTAC
129095 GGATAT
1 GGATAT
129101 ATCGAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (10 bp):
GGATATTTAC
Found at i:130135 original size:16 final size:15
Alignment explanation
Indices: 130114--130143 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
130104 TTTTACATAT
130114 ATTATATATAAAATAA
1 ATTATATA-AAAATAA
130130 ATTATATAAAAATA
1 ATTATATAAAAATA
130144 CTATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTATATAAAAATAA
Done.