Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003691.1 Hibiscus syriacus cultivar Beakdansim tig00007888_pilon, 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: 116979
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:766 original size:12 final size:12
Alignment explanation
Indices: 749--774 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
739 TATGTCTTTT
749 CTTGATTGTAAC
1 CTTGATTGTAAC
761 CTTGATTGTAAC
1 CTTGATTGTAAC
773 CT
1 CT
775 GAATTCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (12 bp):
CTTGATTGTAAC
Found at i:1595 original size:12 final size:12
Alignment explanation
Indices: 1565--1595 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1555 AATAAAATCT
1565 TATTTTTCTCTC
1 TATTTTTCTCTC
*
1577 TAGTTTTCTCTC
1 TATTTTTCTCTC
1589 TATTTTT
1 TATTTTT
1596 TCGCATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.19, G:0.03, T:0.68
Consensus pattern (12 bp):
TATTTTTCTCTC
Found at i:2082 original size:16 final size:18
Alignment explanation
Indices: 2061--2100 Score: 66
Period size: 16 Copynumber: 2.3 Consensus size: 18
2051 CTTTAAATTA
2061 TTTATTTAATT-TT-TCT
1 TTTATTTAATTGTTATCT
2077 TTTATTTAATTGTTATCT
1 TTTATTTAATTGTTATCT
2095 TTTATT
1 TTTATT
2101 GTAAAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.50
17 2 0.09
18 9 0.41
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTGTTATCT
Found at i:2199 original size:20 final size:20
Alignment explanation
Indices: 2127--2202 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
2117 AAAATCCCCT
* **
2127 TTTTTATCTTTACTATTATAA
1 TTTTTAT-TTTATTATTATCC
*
2148 TTTATTATTTTATTATTTTCC
1 TTT-TTATTTTATTATTATCC
2169 TTTTCTA-TTTATTATTAT-C
1 TTTT-TATTTTATTATTATCC
2188 TATTTTATTTTATTA
1 T-TTTTATTTTATTA
2203 AATCTTTCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 4 0.09
20 21 0.46
21 17 0.37
22 4 0.09
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTATTTTATTATTATCC
Found at i:2200 original size:14 final size:14
Alignment explanation
Indices: 2152--2200 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
2142 TTATAATTTA
2152 TTATTTTAT-TATT
1 TTATTTTATCTATT
**
2165 TTCCTTT-TCTA-T
1 TTATTTTATCTATT
2177 TTATTATTATCTATT
1 TTATT-TTATCTATT
2192 TTATTTTAT
1 TTATTTTAT
2201 TAAATCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
12 5 0.18
13 9 0.32
14 8 0.29
15 6 0.21
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTTTATCTATT
Found at i:4567 original size:26 final size:25
Alignment explanation
Indices: 4512--4573 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
4502 AAATGAAATT
4512 ATTTATAAATTTAAATTAAAAGAACAA
1 ATTTAT-AATTT-AATTAAAAGAACAA
*
4539 ATTTATAATTT-ATTACAAAGACACTA
1 ATTTATAATTTAATTA-AAAGA-ACAA
*
4565 ATTAATAAT
1 ATTTATAAT
4574 ATTGGTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 4 0.13
25 5 0.16
26 16 0.52
27 6 0.19
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.37
Consensus pattern (25 bp):
ATTTATAATTTAATTAAAAGAACAA
Found at i:15605 original size:40 final size:37
Alignment explanation
Indices: 15561--15686 Score: 139
Period size: 37 Copynumber: 3.3 Consensus size: 37
15551 ATCTCCACGG
15561 AAGAGTAGTGGAAACAA-GCAATGCAATCAAGCCTTCACAA
1 AAGAGTAGT-GAAACAATGCAA---AATCAAGCCTTCACAA
*
15601 AAGAGTAGTGAAGCAATGCAAAATCAAGCCTTCACAA
1 AAGAGTAGTGAAACAATGCAAAATCAAGCCTTCACAA
* * * * *
15638 AAGAGTGGTGAAGCAATACAAATTC-AGCTTTCACAAA
1 AAGAGTAGTGAAACAATGCAAAATCAAGCCTTCAC-AA
15675 AAGAGTAGTGAA
1 AAGAGTAGTGAA
15687 GCAAGATCAA
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
36 8 0.10
37 51 0.65
39 6 0.08
40 13 0.17
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (37 bp):
AAGAGTAGTGAAACAATGCAAAATCAAGCCTTCACAA
Found at i:15632 original size:37 final size:37
Alignment explanation
Indices: 15576--15690 Score: 164
Period size: 37 Copynumber: 3.2 Consensus size: 37
15566 TAGTGGAAAC
15576 AAGCAATGC--AATCAAGCCTTCACAAAAGAGTAGTG
1 AAGCAATGCAAAATCAAGCCTTCACAAAAGAGTAGTG
*
15611 AAGCAATGCAAAATCAAGCCTTCACAAAAGAGTGGTG
1 AAGCAATGCAAAATCAAGCCTTCACAAAAGAGTAGTG
* * *
15648 AAGCAATACAAATTC-AGCTTTCACAAAAAGAGTAGTG
1 AAGCAATGCAAAATCAAGCCTTCAC-AAAAGAGTAGTG
15685 AAGCAA
1 AAGCAA
15691 GATCAAATCA
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
35 9 0.12
36 8 0.11
37 55 0.76
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.17
Consensus pattern (37 bp):
AAGCAATGCAAAATCAAGCCTTCACAAAAGAGTAGTG
Found at i:18408 original size:19 final size:20
Alignment explanation
Indices: 18366--18408 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18356 CTAAATCCTT
* * *
18366 TTTCAAAATTTCATTTTGAT
1 TTTCAAAATCTCATTTTAAC
18386 TTTCAAAATCT-ATTTTAAC
1 TTTCAAAATCTCATTTTAAC
18405 TTTC
1 TTTC
18409 GGAGGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTCAAAATCTCATTTTAAC
Found at i:19795 original size:5 final size:5
Alignment explanation
Indices: 19785--20002 Score: 436
Period size: 5 Copynumber: 43.6 Consensus size: 5
19775 TAGGTTAAAT
19785 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
19835 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
19885 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
19935 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
19985 TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TAT
20003 CTATTCAGAA
Statistics
Matches: 213, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 213 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:20133 original size:3 final size:3
Alignment explanation
Indices: 20125--20180 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
20115 TGATGAGGAG
20125 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20173 ATT ATT AT
1 ATT ATT AT
20181 ATACATCATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21896 original size:18 final size:18
Alignment explanation
Indices: 21873--21907 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21863 ACAAAACCCA
21873 GGTTTTGTCGTTCATAAG
1 GGTTTTGTCGTTCATAAG
21891 GGTTTTGTCGTTCATAA
1 GGTTTTGTCGTTCATAA
21908 TACAGTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.11, G:0.26, T:0.46
Consensus pattern (18 bp):
GGTTTTGTCGTTCATAAG
Found at i:22564 original size:43 final size:43
Alignment explanation
Indices: 22459--22565 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 43
22449 TTACAATCAT
22459 ACAAGATGATGACCTTATCCTTCGAAGAGAAACTCAAAACAACAA
1 ACAAGATG-TGACCTTAT-CTTCGAAGAGAAACTCAAAACAACAA
* * * **
22504 ACAAAATGTGAATCTTATCTTCGAAGAG-AACTCAAAATAGTAA
1 ACAAGATGTG-ACCTTATCTTCGAAGAGAAACTCAAAACAACAA
*
22547 ACATGATGTTGACCTTATC
1 ACAAGATG-TGACCTTATC
22566 CTCCAAAGAG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
43 25 0.48
44 14 0.27
45 13 0.25
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (43 bp):
ACAAGATGTGACCTTATCTTCGAAGAGAAACTCAAAACAACAA
Found at i:23811 original size:30 final size:31
Alignment explanation
Indices: 23754--23816 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
23744 AAAATAAAAT
* *
23754 ATATGGTCATTTTTGTTTTTGTTTAATTAAG
1 ATATGGTCACTTTTATTTTTGTTTAATTAAG
*
23785 ATATGTTCACTTTTATTTTT-TTTAATTAAG
1 ATATGGTCACTTTTATTTTTGTTTAATTAAG
23815 AT
1 AT
23817 GTGATCACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (31 bp):
ATATGGTCACTTTTATTTTTGTTTAATTAAG
Found at i:24095 original size:32 final size:30
Alignment explanation
Indices: 24030--24103 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 30
24020 TTAACTTAAT
**
24030 AAATATAT-TTTATTATTATTTTAATTTTA
1 AAATATATATTTATTATTATTAAAATTTTA
*
24059 AAATATATATTTATTTTTATATAAAATTTTTA
1 AAATATATATTTATTATTAT-TAAAA-TTTTA
24091 AAATATATTATTT
1 AAATATA-TATTT
24104 TAACTTTGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 8 0.21
30 10 0.26
31 3 0.08
32 12 0.32
33 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
AAATATATATTTATTATTATTAAAATTTTA
Found at i:24097 original size:30 final size:29
Alignment explanation
Indices: 24025--24104 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 29
24015 TATTATTAAC
* **
24025 TTAATAAATATATTTTATTATTATTTTAATT
1 TTAA-AAATATA-TTTATTTTTATTAAAATT
24056 TTAAAATATATATTTATTTTTATATAAAATT
1 TTAAAA-ATATATTTATTTTTAT-TAAAATT
*
24087 TTTAAAATATA-TTATTTT
1 TTAAAAATATATTTATTTT
24105 AACTTTGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
29 7 0.16
30 17 0.40
31 19 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TTAAAAATATATTTATTTTTATTAAAATT
Found at i:25447 original size:55 final size:55
Alignment explanation
Indices: 25294--25853 Score: 691
Period size: 55 Copynumber: 10.2 Consensus size: 55
25284 ACTAAATAGA
* * * * *
25294 CACTAAGTGTGC-ATTCCACGGAATTCATCCT-ATGTGGATGAATAACCGTTTCA-G
1 CACTATGTGTGCAAATCCACGGAATTCATCATGA-GTTGATGAATAACCG-TACAGG
* * * * *
25348 CACTAAGAGTGC-ATTTCACGGAATTCATCATGAGTTGATGAATAACCGTATAGG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGG
* * *
25402 CACTATATGTGCAAACCCACGTAATTCATCATGAGTTGATGAATAACCGTACAGG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGG
25457 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGG
* * ** * *
25512 CACTATGTGTGCAAACCCGCATAATTCATCATTAGTTGATGAATAACCGTACAGA
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGG
* *
25567 CACTATGTGTACAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGG
* * * * *
25622 CATTATGTGTGCAAATCCATGGAATTCATCATGAGTTAATGAATAATCGTACATG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGG
* * *
25677 CACTATGTGTGCAAATCCAAGGAATTCATCATGAGTTGATGAATAATCGTACAAG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGG
* * * * *
25732 CACTAGGTGTGCAAATCCATGAAATTCATCTTGAGTTGATGAATAACCGTACATG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGG
* * * *
25787 CACGATGTGTGC-AACCCACGTAATTCATCATGAGTTGATGAACT-ACCGTATAGG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA-TAACCGTACAGG
* *
25841 TACTACGTGTGCA
1 CACTATGTGTGCA
25854 TCTTAATAAA
Statistics
Matches: 444, Mismatches: 57, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
53 2 0.00
54 95 0.21
55 347 0.78
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (55 bp):
CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGG
Found at i:26156 original size:23 final size:23
Alignment explanation
Indices: 26130--26202 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
26120 AAATGATGTC
26130 ATAAATGAAATGTATAACAGTGT
1 ATAAATGAAATGTATAACAGTGT
* ** *
26153 ATAAAAGGCATG-A-AA-GGATGT
1 ATAAATGAAATGTATAACAG-TGT
26174 CATAAATGAAATGTATAACAGTGT
1 -ATAAATGAAATGTATAACAGTGT
26198 ATAAA
1 ATAAA
26203 AGGCATGAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
20 1 0.03
21 5 0.14
22 10 0.27
23 15 0.41
24 5 0.14
25 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.26
Consensus pattern (23 bp):
ATAAATGAAATGTATAACAGTGT
Found at i:26173 original size:45 final size:45
Alignment explanation
Indices: 26104--26274 Score: 281
Period size: 45 Copynumber: 3.8 Consensus size: 45
26094 ATGCATAATG
* *
26104 GTGTAAAAAAGGCATGAAATGATGTCATAAATGAAATGTATAACA
1 GTGTATAAAAGGCATGAAAGGATGTCATAAATGAAATGTATAACA
26149 GTGTATAAAAGGCATGAAAGGATGTCATAAATGAAATGTATAACA
1 GTGTATAAAAGGCATGAAAGGATGTCATAAATGAAATGTATAACA
* * **
26194 GTGTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATCATG
1 GTGTATAAAAGGCATGAAAGGATGTCATAAATGAAATGTATAACA
26239 GTGTATAAAAGGCATGAAAGGATGT-ATAAATGAAAT
1 GTGTATAAAAGGCATGAAAGGATGTCATAAATGAAAT
26275 TAATAAATAA
Statistics
Matches: 119, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
44 11 0.09
45 108 0.91
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (45 bp):
GTGTATAAAAGGCATGAAAGGATGTCATAAATGAAATGTATAACA
Found at i:26644 original size:6 final size:6
Alignment explanation
Indices: 26592--26619 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
26582 CTTAATAGTG
26592 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
26620 ATCAAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:26804 original size:37 final size:36
Alignment explanation
Indices: 26742--26822 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 36
26732 GGGAAAAGGG
* * *
26742 AAAAATAAAATAGAATAAATTAAAAGGAAAAACAA-TA
1 AAAAATAAAACAAAATAAATCAAAA-GAAAAA-AATTA
*
26779 AAAAATAAAACAAAATATATCAAAAGAAAAAAATTA
1 AAAAATAAAACAAAATAAATCAAAAGAAAAAAATTA
26815 AACAAATA
1 AA-AAATA
26823 TGAGAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 2 0.05
36 10 0.26
37 26 0.68
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (36 bp):
AAAAATAAAACAAAATAAATCAAAAGAAAAAAATTA
Found at i:26913 original size:13 final size:13
Alignment explanation
Indices: 26895--26923 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
26885 AAAATTGAGT
26895 AAAAGAATATAAA
1 AAAAGAATATAAA
26908 AAAAGAATATAAA
1 AAAAGAATATAAA
26921 AAA
1 AAA
26924 TAAAAATTAA
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:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAGAATATAAA
Found at i:29013 original size:84 final size:84
Alignment explanation
Indices: 28462--30425 Score: 1954
Period size: 84 Copynumber: 23.4 Consensus size: 84
28452 CTTTAATGAT
* * * * ** *
28462 AGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGA
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCTTGGAGCTGAGCGTAGTCGA
* *
28527 ACTCGAAGTTCTTTTGTTGGC
64 ACTCGAAGGTCTTTTGGTGGC
* * * * * *
28548 AGATAACCCTTCTTGCCTTGAGATATGCTGCAAACGATGTGCCTTTGAGCTGAGTGTAATCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* *
28613 TTGAAGGTC--TTGGTTGAC
66 TCGAAGGTCTTTTGG-TGGC
* * * * * * *
28631 AGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTGGATATGCCTTTGAGCTGAGTGTAATCGA
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA-T-GATGTGCCTTGGAGCTGAGCGTAGTCGA
**
28696 ACTCGAAGGTCTTTTATTGGC
64 ACTCGAAGGTCTTTTGGTGGC
* * * * * * * * * *
28717 ATATAGCCCTTCTTGCCTTGAGTTGTGTTTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
1 AGATAACCCTTCTAGCCTTGAGTTATG-CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
28782 CTCGAAGGTC--TT--CGAC
65 CTCGAAGGTCTTTTGGTGGC
* * * ** * *
28798 AGATAGCCCTTCTTGCCTTGAG-T-TGCTGCAAATGATGTGCCTTTGAGCTGAATGGAATCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
*
28861 TCGAAGGTCTTTAT--TGAC
66 TCGAAGGTCTTT-TGGTGGC
* * * * * *
28879 AGATAACCCTTCTATCCTTGAGTTATGTTGTAAATGATGTGCCTTTGAGCTGAGCGTAGTCAAAT
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* * *
28944 TCAAAGGTCTTTCGGTGGT
66 TCGAAGGTCTTTTGGTGGC
* * * **
28963 AGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCACAGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
29028 TCGAAGGTC-TTTGGTTGGC
66 TCGAAGGTCTTTTGG-TGGC
* * * *
29047 AGATAA--CTTCTAGCCTTGAGTTATGCTACAAATGATGTGTGATGTGTCTTAGAGATGAGCGTA
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGC-AA--A----TGATGTGCCTTGGAGCTGAGCGTA
*
29110 GTCGAACTC-ACAGGTCTTTTGGTGGA
59 GTCGAACTCGA-AGGTCTTTTGGTGGC
* ** * * *
29136 AGATAACCCTTCTAGCCTT-ATGCTATATTGTAAATTATGTGCCTTGGAGCTGAGCGTAATCGAA
1 AGATAACCCTTCTAGCCTTGA-GTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
29200 CTCGAAGGT-TATTGGTTGGC
65 CTCGAAGGTCTTTTGG-TGGC
* * * *
29220 AGATAACCCTTCTAGCCTTGAGTTATGCTCCAAATGATGTGTCTTGGAGCTGAGTGTAGTCAAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* * * *
29285 TCAAAGGTATTTTGGTTGT
66 TCGAAGGTCTTTTGGTGGC
* * * * * *
29304 AGATAGCCCTTCTAGCCTTAAGTTATACTACAAATGATGCGCCTAGGAGCTGAGCGTAGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
*
29369 TTGAAGGTCTTTTGGTGGC
66 TCGAAGGTCTTTTGGTGGC
* * * * * *
29388 AGATAACCCTTCTAGTCTTCAGCTATGCTGCAAATGATATGCCTTGTAGCTGAGCGTAGTCAAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* *
29453 TCGAATGTCTTTTGTTGGC
66 TCGAAGGTCTTTTGGTGGC
* * * * * * * *
29472 AAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATATTCCTTGGAGCTGAGCATGGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
*
29537 TCGAATGTCTTTTGGTGGC
66 TCGAAGGTCTTTTGGTGGC
* * * * * * *
29556 AGATAGCCCTTTTAGCCTTGAGTTATGTTGTAAATGATATGCCTTAGAGTTGAGCGTAGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* * * *
29621 TCGAAAGTATTTAT-TTGGT
66 TCGAAGGTCTTT-TGGTGGC
* * *
29640 AGATAACCCTTCTAGTCTTGAGTTATACT-CTAAATGATGTGTCTTGGAGCTGAGCGTAGTCGAA
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGC-AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
29704 CTCGCAGGTCTTTTGGTGGC
65 CTCGAAGGTCTTTTGGTGGC
* * * * * * *
29724 AGATAATCCTTCTAGACTTAAGCTATGCTGCAAATTATGTGCCTTGAAGCTGAGCGTAGTCGAAA
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
29789 TCGAAGGTC-TTTGGTTGGC
66 TCGAAGGTCTTTTGG-TGGC
* *
29808 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATCATATGCCTTGGAGCTGAGCGTAGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* *
29873 TCAAAGGTCTTTTTGTGGC
66 TCGAAGGTCTTTTGGTGGC
* * * *** *
29892 AGATAACCCTTCTAGCCTTAAGTTATGCTGTAATTGATGCATCTTGGAGCTGAGCGTAGTCGAAA
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* * * *
29957 TCGAACGTCTATTAGTGGT
66 TCGAAGGTCTTTTGGTGGC
* * * * * * *
29976 AGATAGCCCTTTTAGACTTGAGCTATGGTGCAAATGATATGCTTTGGAGCTGAGCGTAGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* * * *
30041 GCGAAGGTATTTTGTTAGC
66 TCGAAGGTCTTTTGGTGGC
* * * * * * *
30060 AAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATATGCCTTGGAGCTGAGCCTAGTCAAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
*
30125 TTGAAGGTCTTTTGGTGGC
66 TCGAAGGTCTTTTGGTGGC
* * * * * * * *
30144 ATATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATAATATGCCTTAGAGCTGACCGTAGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
*
30209 TTGAAGGTC-TTTGGTTGGC
66 TCGAAGGTCTTTTGG-TGGC
30228 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
*
30293 TCGAAGGTCTTTT-TTGGC
66 TCGAAGGTCTTTTGGTGGC
* * * * * *
30311 AAATAGCCCTTCTTGGCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* *
30376 TCAAAGGTCTTTTGTTGGC
66 TCGAAGGTCTTTTGGTGGC
* * *
30395 AAATATCCCTTCTTGCCTTGAGTTATGCTGC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGC
30426 CAATAATTTC
Statistics
Matches: 1569, Mismatches: 270, Indels: 80
0.82 0.14 0.04
Matches are distributed among these distances:
78 42 0.03
79 2 0.00
80 2 0.00
81 46 0.03
82 24 0.02
83 175 0.11
84 1052 0.67
85 91 0.06
86 58 0.04
87 9 0.01
88 2 0.00
89 42 0.03
90 8 0.01
91 16 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (84 bp):
AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
TCGAAGGTCTTTTGGTGGC
Found at i:31745 original size:99 final size:99
Alignment explanation
Indices: 31567--31835 Score: 314
Period size: 100 Copynumber: 2.7 Consensus size: 99
31557 GACTAGCTGG
* * * **
31567 ATCCATAAAGCCGGGGCGTTTAACCAA-TACTCTAGAGGAATAGCTCAA-TATCGTTGTATAGAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAGT-TTATTGTATAGAT
*
31630 ATTATAATCACCTTTATCAGGC-TAGCTGAATATT
65 ATTATAATCACCTTTATCAGGCTTAGCTAAATATT
*
31664 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATAGAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAG-TTTATTGTATAGAT
* *
31729 ATTATAATCACCTTTATCATGCTTAGCTAAATCTT
65 ATTATAATCACCTTTATCAGGCTTAGCTAAATATT
** * * * * * *
31764 ATCCATAAAGTTGGGGTGTTTAACTAATTG-TTTAAGAGGGACATCTCAAGTTTTATTGTATATA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCT-AGAGGGATAACTCAAG-TTTATTGTATAGA
31828 TA-TATAAT
64 TATTATAAT
31836 TATAATTTGG
Statistics
Matches: 148, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
97 26 0.18
98 18 0.12
99 40 0.27
100 64 0.43
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (99 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAGTTTATTGTATAGATA
TTATAATCACCTTTATCAGGCTTAGCTAAATATT
Found at i:35083 original size:20 final size:20
Alignment explanation
Indices: 35058--35101 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
35048 TATTTAGGTA
35058 GATCGGTCACCATCTTACCT
1 GATCGGTCACCATCTTACCT
35078 GATCGGTCACCATCTTACCT
1 GATCGGTCACCATCTTACCT
35098 GATC
1 GATC
35102 AGCGTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.34, G:0.16, T:0.30
Consensus pattern (20 bp):
GATCGGTCACCATCTTACCT
Found at i:35225 original size:6 final size:6
Alignment explanation
Indices: 35214--35248 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
35204 CTTAATAGCG
35214 AAAATT AAAATT AAAATT AAAATT AAAATTT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAA
35249 CAAAACCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:35253 original size:18 final size:18
Alignment explanation
Indices: 35214--35253 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
35204 CTTAATAGCG
*
35214 AAAATTAAAATTAAAATT
1 AAAATTAAAATTAAAATC
35232 AAAATTAAAATTTAAAA-C
1 AAAATTAAAA-TTAAAATC
35250 AAAA
1 AAAA
35254 CCTAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATTAAAATTAAAATC
Found at i:35474 original size:26 final size:24
Alignment explanation
Indices: 35433--35481 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
35423 ATATATCAAA
* *
35433 AGAAAAAAATATTAAATAAATATG
1 AGAAAAAAATAATAAAAAAATATG
35457 AGAATAAAAATAAATAAAAAAATAT
1 AGAA-AAAAAT-AATAAAAAAATAT
35482 TAATGTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 6 0.29
26 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.22
Consensus pattern (24 bp):
AGAAAAAAATAATAAAAAAATATG
Found at i:36968 original size:3 final size:3
Alignment explanation
Indices: 36906--36950 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
36896 AAAAGATTAG
* *
36906 ATA AAA ATA ATA ATAA ATAA ATA GTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
36951 AATTAACTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 30 0.81
4 7 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:37007 original size:16 final size:15
Alignment explanation
Indices: 36906--37023 Score: 60
Period size: 15 Copynumber: 7.5 Consensus size: 15
36896 AAAAGATTAG
36906 ATAAAAATAATAATAA
1 ATAAAAA-AATAATAA
*
36922 ATAAATAGTAATAAT-A
1 ATAAA-A-AAATAATAA
*
36938 ATAATAATAATAA-AA
1 ATAA-AAAAATAATAA
* **
36953 TTAACTGAAATAATAA
1 ATAA-AAAAATAATAA
* ***
36969 ATAAAAAGATGGGAA
1 ATAAAAAAATAATAA
36984 AGTAAAAAAAATGAATAA
1 A-T-AAAAAAAT-AATAA
*
37002 ATAAAAAAATATTAA
1 ATAAAAAAATAATAA
37017 ATAAAAA
1 ATAAAAA
37024 CGAAAACAAA
Statistics
Matches: 76, Mismatches: 18, Indels: 17
0.68 0.16 0.15
Matches are distributed among these distances:
15 32 0.42
16 25 0.33
17 16 0.21
18 3 0.04
ACGTcount: A:0.69, C:0.01, G:0.07, T:0.24
Consensus pattern (15 bp):
ATAAAAAAATAATAA
Found at i:37296 original size:20 final size:22
Alignment explanation
Indices: 37259--37304 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
37249 CTAAAATAAC
37259 AAAACAAGAACTTAAAAGG-CT
1 AAAACAAGAACTTAAAAGGACT
* *
37280 AAAAC-AGAATTTTAAAGGACT
1 AAAACAAGAACTTAAAAGGACT
37301 AAAA
1 AAAA
37305 TAACAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (22 bp):
AAAACAAGAACTTAAAAGGACT
Found at i:38747 original size:37 final size:36
Alignment explanation
Indices: 38697--38849 Score: 128
Period size: 37 Copynumber: 4.4 Consensus size: 36
38687 AAGATATCTG
*
38697 TTGTTTCATGAGAAACGGTCTCAAGGGAGAC-AAGATT
1 TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAA-A-T
*
38734 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAAT
1 TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAAAT
* * *
38770 TAGTTTCAA-AGAAACAGAT-TC-A---A-A-G-ATT
1 TTGTTTCAAGAGAAAC-GGTCTCAAGGGAGACGAAAT
* * * *
38798 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAAT
1 TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAAAT
38834 TTGTTTCAAGAGAAAC
1 TTGTTTCAAGAGAAAC
38850 TGCTTCAAAC
Statistics
Matches: 92, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
28 11 0.12
29 8 0.09
30 2 0.02
31 1 0.01
33 1 0.01
34 2 0.02
35 8 0.09
36 27 0.29
37 30 0.33
38 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAAAT
Found at i:38834 original size:64 final size:65
Alignment explanation
Indices: 38728--38880 Score: 218
Period size: 64 Copynumber: 2.3 Consensus size: 65
38718 CAAGGGAGAC
* *
38728 AAGATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTAGTTTCAA-AGAAACAGATTCA
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAGAAACAGATTCA
* * * *
38792 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGAGAAACTGCTTCA
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAGAAACAGATTCA
*
38857 AACATCTTGTGTTTCAAGGGAAAC
1 AAGAT-TT-TGTTTCAAGGGAAAC
38881 GTTTTCAAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 47 0.59
65 15 0.19
66 2 0.03
67 15 0.19
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (65 bp):
AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAGAAACAGATTCA
Found at i:38953 original size:36 final size:36
Alignment explanation
Indices: 38913--39064 Score: 124
Period size: 36 Copynumber: 4.4 Consensus size: 36
38903 AGAGAAATCG
* *
38913 TCTCAAGGGAGACAAAATTTATTCCAAGGGAAACTA
1 TCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTA
* *
38949 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAA-TGT
1 TCTCAAGAGAGACAAAATTTATTTCAAGGGAAACT-A
* * * ** *
38985 TTTC-A-A-TG-C----TTATGTTTCAAGAAAAACTG
1 TCTCAAGAGAGACAAAATT-TATTTCAAGGGAAACTA
*
39014 TCTCAAGGGAGACAAAATTTATTTCAAGGGAAACTA
1 TCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTA
39050 TCTCAAGAGAGACAA
1 TCTCAAGAGAGACAA
39065 TGGTGAGCAC
Statistics
Matches: 86, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
28 2 0.02
29 13 0.15
30 2 0.02
32 2 0.02
33 2 0.02
34 1 0.01
35 2 0.02
36 60 0.70
37 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTA
Found at i:39019 original size:101 final size:102
Alignment explanation
Indices: 38868--39064 Score: 326
Period size: 101 Copynumber: 1.9 Consensus size: 102
38858 ACATCTTGTG
* *
38868 TTTCAAGGGAAACGTTTTCAAAGTTTTATGTTTCAAGAGAAATCGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAACGTTTTCAAAGTCTTATGTTTCAAGAAAAATCGTCTCAAGGGAGACAAAATTT
38933 ATTCCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 ATTCCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* *
38970 TTTCAAGGGAAATGTTTTCAATG-CTTATGTTTCAAGAAAAA-CTGTCTCAAGGGAGACAAAATT
1 TTTCAAGGGAAACGTTTTCAAAGTCTTATGTTTCAAGAAAAATC-GTCTCAAGGGAGACAAAATT
*
39033 TATTTCAAGGGAAACTATCTCAAGAGAGACAA
65 TATTCCAAGGGAAACTATCTCAAGAGAGACAA
39065 TGGTGAGCAC
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
100 1 0.01
101 67 0.75
102 21 0.24
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (102 bp):
TTTCAAGGGAAACGTTTTCAAAGTCTTATGTTTCAAGAAAAATCGTCTCAAGGGAGACAAAATTT
ATTCCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:39374 original size:106 final size:106
Alignment explanation
Indices: 39189--40217 Score: 1592
Period size: 106 Copynumber: 9.6 Consensus size: 106
39179 GTATTGCTCC
*** * * * * * *
39189 GAGTCCAATATCCTTCACCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
39254 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
39295 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
39360 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
39401 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
39466 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
39507 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
39572 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
39613 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
39678 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
39719 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
39784 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
39825 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
39890 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
39931 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
39996 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
40037 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTGGAAAATTATTTA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---G----TTGTTTG
40102 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
59 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
40150 GAGTCCAATTTTCTTCGCTGCGAAGTTGAAATAGACTCTGAATGAAATTG-GAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC----TGAAATTGAG-AAGTTGTTTGTT
40214 GACA
61 GACA
40218 GACAACTTTT
Statistics
Matches: 851, Mismatches: 60, Indels: 20
0.91 0.06 0.02
Matches are distributed among these distances:
106 743 0.87
109 1 0.00
110 11 0.01
113 84 0.10
114 1 0.00
116 1 0.00
117 10 0.01
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:42707 original size:22 final size:22
Alignment explanation
Indices: 42682--42725 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
42672 CATTTTTGTC
*
42682 CATTTGATGCTCAATGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
*
42704 CATTTGATGTTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
42726 TGGGGTAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:43387 original size:16 final size:17
Alignment explanation
Indices: 43368--43422 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
43358 TCTTTTTGAA
*
43368 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
43384 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
* *
43401 TTTTTCT-TTGTTT-TT
1 TTTTGCTCTTGTTTCTC
43416 TTTTGCT
1 TTTTGCT
43423 TCTTTTCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 7 0.22
16 19 0.59
17 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:43404 original size:23 final size:25
Alignment explanation
Indices: 43369--43442 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 25
43359 CTTTTTGAAT
*
43369 TTTGCTCTTTTTTCCTTTTGTTCTTG
1 TTTGCT-TCTTTTCCTTTTGTTCTTG
* * *
43395 TTT-C-TCTTTTTC-TTTGTTTTTT
1 TTTGCTTCTTTTCCTTTTGTTCTTG
*
43417 TTTGCTTCTTTTCTTTTTTGTTCTTG
1 TTTGCTTCTTTTC-CTTTTGTTCTTG
43443 ATTGGATCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
22 11 0.31
23 7 0.19
24 6 0.17
25 1 0.03
26 11 0.31
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.74
Consensus pattern (25 bp):
TTTGCTTCTTTTCCTTTTGTTCTTG
Found at i:43441 original size:15 final size:16
Alignment explanation
Indices: 43384--43440 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
43374 TCTTTTTTCC
43384 TTTTGTTCTTGTTTCTCT
1 TTTTGTTC-TGTTTCT-T
*
43402 TTTTCTT-TGTTT-TT
1 TTTTGTTCTGTTTCTT
43416 TTTTGCTTCT-TTTCTT
1 TTTTG-TTCTGTTTCTT
43432 TTTTGTTCT
1 TTTTGTTCT
43441 TGATTGGATC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 5 0.15
15 10 0.29
16 13 0.38
18 6 0.18
ACGTcount: A:0.00, C:0.14, G:0.09, T:0.77
Consensus pattern (16 bp):
TTTTGTTCTGTTTCTT
Found at i:46485 original size:3 final size:3
Alignment explanation
Indices: 46419--46467 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
46409 AAAAGATTAG
* *
46419 ATA AAA ATA ATA ATAA ATAA ATAA ATA GTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA
46467 A
1 A
46468 AATTAACTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 30 0.73
4 11 0.27
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:46524 original size:16 final size:16
Alignment explanation
Indices: 46419--46541 Score: 79
Period size: 17 Copynumber: 7.4 Consensus size: 16
46409 AAAAGATTAG
*
46419 ATAAAAATAATAATAA
1 ATAAAAAAAATAATAA
*
46435 ATAAATAAATAGTAAT-A
1 ATAAA-AAA-AATAATAA
* *
46452 ATAATAATAATAATAAA
1 ATAAAAAAAATAAT-AA
***
46469 ATTAACTGAAATAATAA
1 A-TAAAAAAAATAATAA
* **
46486 AT-AAAAAGATAGGAA
1 ATAAAAAAAATAATAA
46501 AGTAAAAAAAATGAATAA
1 A-TAAAAAAAAT-AATAA
*
46519 ATAAAAAAAATATTAA
1 ATAAAAAAAATAATAA
46535 ATAAAAA
1 ATAAAAA
46542 CGAAAACAAA
Statistics
Matches: 80, Mismatches: 19, Indels: 16
0.70 0.17 0.14
Matches are distributed among these distances:
15 13 0.16
16 20 0.25
17 29 0.36
18 18 0.22
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.24
Consensus pattern (16 bp):
ATAAAAAAAATAATAA
Found at i:46611 original size:18 final size:18
Alignment explanation
Indices: 46423--46611 Score: 53
Period size: 18 Copynumber: 10.5 Consensus size: 18
46413 GATTAGATAA
*
46423 AAATAATAATAAATAAAT
1 AAATAATAAAAAATAAAT
*
46441 AAATAGTAATAATAAT-AAT
1 AAATAATAA-AA-AATAAAT
46460 -AATAATAAAATTAACTGAAAT
1 AAATAATAAAA--AA-T-AAAT
*
46481 -AATAAATAAAAAGATAGGA-
1 AAAT-AATAAAAA-ATA-AAT
* *
46500 AAGTAA-AAAAAATGAAT
1 AAATAATAAAAAATAAAT
*
46517 AAATAA-AAAAAAT-ATT
1 AAATAATAAAAAATAAAT
** *
46533 AAATAA-AAACGA-AAAC
1 AAATAATAAAAAATAAAT
*
46549 AAA-AGTGAAAATAATAAA-
1 AAATAAT-AAAA-AATAAAT
***
46567 ATAATAAT-AAAGGGAAAT
1 A-AATAATAAAAAATAAAT
46585 AAA-ATATAAAAAATAAAT
1 AAATA-ATAAAAAATAAAT
46603 AAATAATAA
1 AAATAATAA
46612 TAATGACGAT
Statistics
Matches: 126, Mismatches: 23, Indels: 44
0.65 0.12 0.23
Matches are distributed among these distances:
15 1 0.01
16 18 0.14
17 26 0.21
18 43 0.34
19 14 0.11
20 10 0.08
21 7 0.06
22 7 0.06
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.22
Consensus pattern (18 bp):
AAATAATAAAAAATAAAT
Found at i:46815 original size:20 final size:22
Alignment explanation
Indices: 46778--46823 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
46768 CTAAAATAAC
46778 AAAACAAGAACTTAAAAGG-CT
1 AAAACAAGAACTTAAAAGGACT
* *
46799 AAAAC-AGAATTTTAAAGGACT
1 AAAACAAGAACTTAAAAGGACT
46820 AAAA
1 AAAA
46824 TAACAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (22 bp):
AAAACAAGAACTTAAAAGGACT
Found at i:50229 original size:31 final size:30
Alignment explanation
Indices: 50191--50309 Score: 114
Period size: 31 Copynumber: 3.8 Consensus size: 30
50181 TAGGTCCATA
*
50191 AGGAATTACCAGTCGGTGCTGAACCTATCTG
1 AGGAATTACCA-TCAGTGCTGAACCTATCTG
* * * *
50222 AGGAATTACGAACAGTGACTGAACCT-GCATA
1 AGGAATTACCATCAGTG-CTGAACCTATC-TG
* *
50253 AGGAATTACCATTCAGTGCTTAACCTATCCG
1 AGGAATTACCA-TCAGTGCTGAACCTATCTG
*
50284 AGGAATTACCAACAGTGACTGAACCT
1 AGGAATTACCATCAGTG-CTGAACCT
50310 GCCAGAGTCT
Statistics
Matches: 70, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
30 10 0.14
31 54 0.77
32 6 0.09
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (30 bp):
AGGAATTACCATCAGTGCTGAACCTATCTG
Found at i:50287 original size:62 final size:62
Alignment explanation
Indices: 50187--50311 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
50177 CCCTTAGGTC
* * *
50187 CATAAGGAATTACCAGTCGGTGCTGAACCTATCTGAGGAATTACGAACAGTGACTGAACCTG
1 CATAAGGAATTACCAGTCAGTGCTGAACCTATCCGAGGAATTACCAACAGTGACTGAACCTG
* *
50249 CATAAGGAATTACCATTCAGTGCTTAACCTATCCGAGGAATTACCAACAGTGACTGAACCTG
1 CATAAGGAATTACCAGTCAGTGCTGAACCTATCCGAGGAATTACCAACAGTGACTGAACCTG
50311 C
1 C
50312 CAGAGTCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (62 bp):
CATAAGGAATTACCAGTCAGTGCTGAACCTATCCGAGGAATTACCAACAGTGACTGAACCTG
Found at i:51602 original size:16 final size:16
Alignment explanation
Indices: 51581--51611 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51571 TTAGAAATGC
*
51581 ATAACATGAAATATAA
1 ATAACAAGAAATATAA
51597 ATAACAAGAAATATA
1 ATAACAAGAAATATA
51612 TTTGTAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (16 bp):
ATAACAAGAAATATAA
Found at i:56530 original size:2 final size:2
Alignment explanation
Indices: 56525--56551 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56515 TCTCTCTCTC
56525 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
56552 GGGTTAGGAC
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:56840 original size:60 final size:59
Alignment explanation
Indices: 56757--56940 Score: 228
Period size: 60 Copynumber: 3.1 Consensus size: 59
56747 CATAAGTCCC
* *
56757 CAAACTATGATCCTTATTTTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCTTCCT
1 CAAACTATGAT-CTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCTTCCT
* *
56817 CAAACTATGACTCTCATTCTAAATCAGTCCTTAAACTTTTAAACATTCCAATTT-TATCCT
1 CAAACTATGA-TCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCT-TCCT
* * * * *
56877 CAAACAATGAATGTCATTCTAAATTGGTCCCTAAACTTTTAAATC-TTCTAATTTCATCCT
1 CAAACTATG-ATCTCATTCTAAATTAGTCCTTAAACTTTTAAA-CATTCTAATTTCTTCCT
56937 CAAA
1 CAAA
56941 TTCATCCAAA
Statistics
Matches: 108, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
59 1 0.01
60 104 0.96
61 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (59 bp):
CAAACTATGATCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCTTCCT
Found at i:62820 original size:22 final size:22
Alignment explanation
Indices: 62792--62835 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
62782 ATTCATGACA
62792 GAATTACGCATATGTAAGGAAT
1 GAATTACGCATATGTAAGGAAT
62814 GAATTACGCATATGTAAGGAAT
1 GAATTACGCATATGTAAGGAAT
62836 CAAGAGTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (22 bp):
GAATTACGCATATGTAAGGAAT
Found at i:69696 original size:3 final size:3
Alignment explanation
Indices: 69688--69712 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
69678 AATCACCATG
69688 ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC A
69713 TTACCCTCAT
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:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:69945 original size:27 final size:27
Alignment explanation
Indices: 69907--69960 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
69897 GTCAGAGGTG
69907 CCATATACTGAAATAATGACTGAGTCA
1 CCATATACTGAAATAATGACTGAGTCA
**
69934 CCATATACTGAAATGTTGACTGAGTCA
1 CCATATACTGAAATAATGACTGAGTCA
69961 AGTGAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (27 bp):
CCATATACTGAAATAATGACTGAGTCA
Found at i:71108 original size:13 final size:13
Alignment explanation
Indices: 71076--71113 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
71066 AAACAAATTT
71076 TAAAT-ATTATAAA
1 TAAATAATTA-AAA
71089 TAAATAATTAAAA
1 TAAATAATTAAAA
*
71102 TAAATAAATAAA
1 TAAATAATTAAA
71114 CATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATAATTAAAA
Found at i:71584 original size:22 final size:22
Alignment explanation
Indices: 71557--71598 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
71547 CCCTTCAAAT
*
71557 AAATAAATTAATAAATAATTCA
1 AAATAAATAAATAAATAATTCA
*
71579 AAATAAATAAATTAATAATT
1 AAATAAATAAATAAATAATT
71599 TATTTGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATAAATAAATAAATAATTCA
Found at i:73483 original size:21 final size:22
Alignment explanation
Indices: 73415--73467 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
73405 GGGTTTGTAT
*
73415 ATATTTTTAACCCAAATATGAA
1 ATATTTTTCACCCAAATATGAA
73437 ATATTTTTCACCCAAATATGAA
1 ATATTTTTCACCCAAATATGAA
73459 ATATTTTTC
1 ATATTTTTC
73468 CTCGAATAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.42
Consensus pattern (22 bp):
ATATTTTTCACCCAAATATGAA
Found at i:78916 original size:22 final size:23
Alignment explanation
Indices: 78874--78917 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
78864 ATGTGGTAGT
*
78874 TAGTCAGCAGCTTCTAGAAGGTC
1 TAGTCAGCAGCTTATAGAAGGTC
78897 TAGTCAGCAG-TTATAGAAGGT
1 TAGTCAGCAGCTTATAGAAGGT
78918 GGAAAAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (23 bp):
TAGTCAGCAGCTTATAGAAGGTC
Found at i:80472 original size:15 final size:15
Alignment explanation
Indices: 80432--80475 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
80422 TACCCATCCC
*
80432 AGCACTACCCCTTTT
1 AGCACTACCCATTTT
* * *
80447 ACCATTTCCCATTTT
1 AGCACTACCCATTTT
80462 AGCACTACCCATTT
1 AGCACTACCCATTT
80476 CAGCGTTGTC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.23, C:0.36, G:0.05, T:0.36
Consensus pattern (15 bp):
AGCACTACCCATTTT
Found at i:83270 original size:54 final size:54
Alignment explanation
Indices: 83201--83472 Score: 244
Period size: 54 Copynumber: 5.0 Consensus size: 54
83191 ACTATCGACT
* * * *
83201 CTATGTGTGAAACCCATGGAATTCATAATGAGTTTGTGAATTACTATATTGACA
1 CTATGTATGCAACCCATAGAATTCATAATGAGTTTGTGAATTACCATATTGACA
* * * * **
83255 CTATGCT-TGCAACCCACAGAATTCATAATGAGTTTGTGAATTATCGTATAGGTA
1 CTATG-TATGCAACCCATAGAATTCATAATGAGTTTGTGAATTACCATATTGACA
* * * * *
83309 ATATGTATGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCGACA
1 CTATGTATGCAACCCATAGAATTCATAATGAGTTTGTGAATTACCATATTGACA
* * * * * * * *
83363 TTATATATGCAATCTACT-GAATTCGTAACGAGTTTCTGAATTACCGTATT-AGCA
1 CTATGTATGCAACCCA-TAGAATTCATAATGAGTTTGTGAATTACCATATTGA-CA
* * ** *
83417 CTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTTTCATATCGACA
1 CTATGTATGCAACCCATAGAATTCATAATGAGTTTGTGAATTACCATATTGACA
83471 CT
1 CT
83473 TAGGTGCAAT
Statistics
Matches: 175, Mismatches: 37, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
53 3 0.02
54 170 0.97
55 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (54 bp):
CTATGTATGCAACCCATAGAATTCATAATGAGTTTGTGAATTACCATATTGACA
Found at i:83396 original size:108 final size:108
Alignment explanation
Indices: 83219--83472 Score: 296
Period size: 108 Copynumber: 2.4 Consensus size: 108
83209 GAAACCCATG
* * * *
83219 GAATTCATAATGAGTTTGTGAATTACTATATTGACACTATGCTTGCAACCCACAGAATTCATAAT
1 GAATTCATAATGAGTTTGTGAATTACCATATCGACACTATGATTGCAACCCACAGAATTCATAAC
* * *
83284 GAGTTTGTGAATTATCGTA-TAGGTAATATGTATGCAACCCACA
66 GAGTTTCTGAATTACCGTATTA-GCAATATGTATGCAACCCACA
* * * * * * *
83327 TAATTCATAATGAGTTTGTGAATTACCGTATCGACATTAT-ATATGCAATCTACTGAATTCGTAA
1 GAATTCATAATGAGTTTGTGAATTACCATATCGACACTATGAT-TGCAACCCACAGAATTCATAA
* * **
83391 CGAGTTTCTGAATTACCGTATTAGCACTATGTGTGCAACCCATG
65 CGAGTTTCTGAATTACCGTATTAGCAATATGTATGCAACCCACA
**
83435 GAATTCATAATGAGTTTGTGAATTTTCATATCGACACT
1 GAATTCATAATGAGTTTGTGAATTACCATATCGACACT
83473 TAGGTGCAAT
Statistics
Matches: 121, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
107 1 0.01
108 118 0.98
109 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (108 bp):
GAATTCATAATGAGTTTGTGAATTACCATATCGACACTATGATTGCAACCCACAGAATTCATAAC
GAGTTTCTGAATTACCGTATTAGCAATATGTATGCAACCCACA
Found at i:89138 original size:54 final size:54
Alignment explanation
Indices: 89053--89326 Score: 295
Period size: 54 Copynumber: 5.1 Consensus size: 54
89043 CTATATGTAC
* * *
89053 TATCGAAACTATATGTTCAACCCACAGAATTCATAATGAGTTTGTGAATTACCG
1 TATCGGAACTATGTGTACAACCCACAGAATTCATAATGAGTTTGTGAATTACCG
* **
89107 TATCGGAACTATGTGTACAACCCA-TGAAATTCATAATGAGTTTGTGAATTACTA
1 TATCGGAACTATGTGTACAACCCACAG-AATTCATAATGAGTTTGTGAATTACCG
* * *
89161 TATCGGCACTATGTGTGCAACCCACGGAATTCATAATGAGTTTGTGAATTACCG
1 TATCGGAACTATGTGTACAACCCACAGAATTCATAATGAGTTTGTGAATTACCG
* * * * * **
89215 TATCGGCATTATGTGTGCAACCCACAGAATTAATAATAAG--TGTGAATTAGTG
1 TATCGGAACTATGTGTACAACCCACAGAATTCATAATGAGTTTGTGAATTACCG
* * * * * * *
89267 TATC-GACATTATGTGTACAACCCATACAATTCATAACGAGTTTATGAATTTCCA
1 TATCGGA-ACTATGTGTACAACCCACAGAATTCATAATGAGTTTGTGAATTACCG
89321 TATCGG
1 TATCGG
89327 CACTTAGGTG
Statistics
Matches: 185, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
51 1 0.01
52 41 0.22
53 1 0.01
54 140 0.76
55 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (54 bp):
TATCGGAACTATGTGTACAACCCACAGAATTCATAATGAGTTTGTGAATTACCG
Found at i:89251 original size:108 final size:106
Alignment explanation
Indices: 89053--89330 Score: 333
Period size: 108 Copynumber: 2.6 Consensus size: 106
89043 CTATATGTAC
* * * *
89053 TATCGAAACTATATGTTCAACCCACAGAATTCATAATGAGTTTGTGAATTACCGTATCGGAACTA
1 TATCGACACTATGTGTACAACCCACAGAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTA
* * *
89118 TGTGTACAACCCATGAAATTCATAATGAGTTTGTGAATTACTA
66 TGTGTACAACCCAAGAAATTAATAATAAG--TGTGAATTACTA
* * * *
89161 TATCGGCACTATGTGTGCAACCCACGGAATTCATAATGAGTTTGTGAATTACCGTATCGGCATTA
1 TATCGACACTATGTGTACAACCCACAGAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTA
* * *
89226 TGTGTGCAACCCACAG-AATTAATAATAAGTGTGAATTAGTG
66 TGTGTACAACCCA-AGAAATTAATAATAAGTGTGAATTACTA
* * * * * * *
89267 TATCGACATTATGTGTACAACCCATACAATTCATAACGAGTTTATGAATTTCCATATCGGCACT
1 TATCGACACTATGTGTACAACCCACAGAATTCATAATGAGTTTGTGAATTACCGTATCGGCACT
89331 TAGGTGCGAT
Statistics
Matches: 145, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
106 63 0.43
108 81 0.56
109 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (106 bp):
TATCGACACTATGTGTACAACCCACAGAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTA
TGTGTACAACCCAAGAAATTAATAATAAGTGTGAATTACTA
Found at i:94891 original size:13 final size:13
Alignment explanation
Indices: 94853--94897 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
94843 TGTGGACATG
* *
94853 ATATTTTAAACAG
1 ATATTTCAAACAA
94866 ATATTTCAAACAA
1 ATATTTCAAACAA
94879 ATATTTCAAACAA
1 ATATTTCAAACAA
*
94892 TTATTT
1 ATATTT
94898 AAAAAAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTCAAACAA
Found at i:103488 original size:45 final size:44
Alignment explanation
Indices: 103363--103525 Score: 195
Period size: 45 Copynumber: 3.6 Consensus size: 44
103353 CAATACTTTA
* *
103363 ATTATTATGTTGCCGAAAGTATAAT-AAAAGGATTAGTTCCCTTTG
1 ATTATTATGTTGCC-AAAGTAAAATCAAAA-GATTAGTTCCTTTTG
* *
103408 ATTATT-TGGTTGTCAAAGTAAAATCAAACGATTAGTTCCTTTTG
1 ATTATTAT-GTTGCCAAAGTAAAATCAAAAGATTAGTTCCTTTTG
*
103452 ATTATTATGCTGCCAACAGTAAAATCAAAAGATTAGTTCCTTTTG
1 ATTATTATGTTGCCAA-AGTAAAATCAAAAGATTAGTTCCTTTTG
* * *
103497 AATATTATATTGTCAAAAGTAAAATCAAA
1 ATTATTATGTTG-CCAAAGTAAAATCAAA
103526 TGGTTAGCTC
Statistics
Matches: 102, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
44 36 0.35
45 63 0.62
46 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (44 bp):
ATTATTATGTTGCCAAAGTAAAATCAAAAGATTAGTTCCTTTTG
Found at i:103541 original size:45 final size:45
Alignment explanation
Indices: 103378--103547 Score: 175
Period size: 45 Copynumber: 3.8 Consensus size: 45
103368 TATGTTGCCG
* * * *
103378 AAAGTATAAT-AAAAGGATTAGTTCCCTTTGATTATT-TGGTTGTC-
1 AAAGTAAAATCAAAA-GATTAGTTCCTTTTGAATATTAT-ATTGTCA
* * ** *
103422 AAAGTAAAATCAAACGATTAGTTCCTTTTGATTATTATGCTGCCA
1 AAAGTAAAATCAAAAGATTAGTTCCTTTTGAATATTATATTGTCA
*
103467 ACAGTAAAATCAAAAGATTAGTTCCTTTTGAATATTATATTGTCA
1 AAAGTAAAATCAAAAGATTAGTTCCTTTTGAATATTATATTGTCA
* * * *
103512 AAAGTAAAATCAAATGGTTAGCTCATTTTGAATATT
1 AAAGTAAAATCAAAAGATTAGTTCCTTTTGAATATT
103548 GAGTTGTGAA
Statistics
Matches: 107, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
44 33 0.31
45 74 0.69
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (45 bp):
AAAGTAAAATCAAAAGATTAGTTCCTTTTGAATATTATATTGTCA
Found at i:103856 original size:58 final size:58
Alignment explanation
Indices: 103787--104272 Score: 506
Period size: 58 Copynumber: 8.4 Consensus size: 58
103777 GATTCTAATA
* *
103787 GAAAATAAATTGTTGAATTTATTTCCTTGGGAATCTAGAATGATTCTAACTTTGTTAG
1 GAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTAGAATGATTCTAACTTTGTAAG
* * * * *
103845 GAAAATGAATTGTTGCA-TT-TTTCTTTGAGAATCTAGAATTATTCTAACTTTATAAG
1 GAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTAGAATGATTCTAACTTTGTAAG
** * * *
103901 GGGAA-AAATCGTTGAATTTTTTTCCTTGAGAATCTAGAATGACTT-TAACTTTATTAA-
1 GAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTAGAATGA-TTCTAACTTT-GTAAG
* * * **
103958 GAAAATGAATTGTTGAATTTATTTTCTTG-GAATC-ATGAACGAATTCTAA-TTTCACAAG
1 GAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTA-GAATG-ATTCTAACTTT-GTAAG
* * * * *
104016 GAAAATTAATTGTTTAATTTATTTCCTTGAAAAT-TAAGAGTGATTCTAACTTTGTTAG
1 GAAAATAAATTGTTGAATTTATTTCCTTGAGAATCT-AGAATGATTCTAACTTTGTAAG
* * *
104074 GAAAATGAATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAA
1 GAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTAGAATGATTCTAACTTTGTAAG
* * * * *
104132 AATAAATAAATTGTTGAATTTATATCATTGAGAATCTTGAATGATTTTAACTTTGTAAG
1 GA-AAATAAATTGTTGAATTTATTTCCTTGAGAATCTAGAATGATTCTAACTTTGTAAG
* * * * *
104191 GAAAATAAATAGTTGAATTTATTTCCTTTAGAATCTTGAATGATTCT-ATTTTGTAAAA
1 GAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTAGAATGATTCTAACTTTGT-AAG
*
104249 GTAAATAAATTGTTGAATTTATTT
1 GAAAATAAATTGTTGAATTTATTT
104273 TCTTAGGAAT
Statistics
Matches: 355, Mismatches: 57, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
55 8 0.02
56 38 0.11
57 54 0.15
58 192 0.54
59 62 0.17
60 1 0.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (58 bp):
GAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTAGAATGATTCTAACTTTGTAAG
Found at i:104066 original size:116 final size:114
Alignment explanation
Indices: 103787--104272 Score: 454
Period size: 117 Copynumber: 4.2 Consensus size: 114
103777 GATTCTAATA
*
103787 GAAAATAAATTGTTGAATTTATTTCCTTGGGAATCTAGAATGATTCTAACTTTGTTAGGAAAATG
1 GAAAAT-AATTGTTGAATTTATTTCCTTGAGAATCTAGAATGATTCTAACTTTGTTAGGAAAATG
* * * *
103852 AATTGTTGCATTT-TTCT-TTGAGAATCTAGAATTATTCTAACTTTATAAGG
65 AATTGTTGAATTTATTTTCTTGAGAATCT-GAA-GATTCTAACTTTACAAGG
* * * * *
103902 GGAAA-AATCGTTGAATTTTTTTCCTTGAGAATCTAGAATGACTT-TAACTTTATTAAGAAAATG
1 GAAAATAATTGTTGAATTTATTTCCTTGAGAATCTAGAATGA-TTCTAACTTTGTTAGGAAAATG
103965 AATTGTTGAATTTATTTTCTTG-GAATCATGAACGAATTCTAA-TTTCACAA-G
65 AATTGTTGAATTTATTTTCTTGAGAATC-TGAA-G-ATTCTAACTTT-ACAAGG
* * *
104016 GAAAATTAATTGTTTAATTTATTTCCTTGAAAAT-TAAGAGTGATTCTAACTTTGTTAGGAAAAT
1 GAAAA-TAATTGTTGAATTTATTTCCTTGAGAATCT-AGAATGATTCTAACTTTGTTAGGAAAAT
* ** *
104080 GAATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAA-A
64 GAATTGTTGAATTTATTTTCTTGAGAATC-TGAA-GATTCTAACTTTACAAGG
* * * * * *
104132 AATAAATAAATTGTTGAATTTATATCATTGAGAATCTTGAATGATTTTAACTTTGTAAGGAAAAT
1 GA-AAAT-AATTGTTGAATTTATTTCCTTGAGAATCTAGAATGATTCTAACTTTGTTAGGAAAAT
* * * * ** *
104197 AAATAGTTGAATTTATTTCCTTTAGAATCTTGAATGATTCTATTTTGTA-AA-A
64 GAATTGTTGAATTTATTTTCTTGAGAATC-TGAA-GATTCTAACTT-TACAAGG
*
104249 GTAAATAAATTGTTGAATTTATTT
1 GAAAAT-AATTGTTGAATTTATTT
104273 TCTTAGGAAT
Statistics
Matches: 312, Mismatches: 43, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
113 62 0.20
114 21 0.07
115 21 0.07
116 99 0.32
117 107 0.34
118 2 0.01
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (114 bp):
GAAAATAATTGTTGAATTTATTTCCTTGAGAATCTAGAATGATTCTAACTTTGTTAGGAAAATGA
ATTGTTGAATTTATTTTCTTGAGAATCTGAAGATTCTAACTTTACAAGG
Found at i:104333 original size:116 final size:117
Alignment explanation
Indices: 103789--104329 Score: 344
Period size: 116 Copynumber: 4.7 Consensus size: 117
103779 TTCTAATAGA
* * * * * * * *
103789 AAATAAATTGTTGAATTTATTTCCTTGGGAATCTAGAATGATTCTAACTTTGTTAGGAAAATGAA
1 AAATAAATTGTTGAATTTATATCATTGAGAATCTTGAAGGATCCTAACTTTGTAAGGAAAATAAA
* * * * * * * ***
103854 TTGTTGCA-TT-TTTCTTTGAGAATCTAGAATTATTCTAACTTTAT-AAGGG
66 TAGTAGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAAAAT
* * * * * * * * * *
103903 GAA-AAATCGTTGAATTTTTTTCCTTGAGAATCTAGAATGA-CTTTAACTTTATTAA-GAAAATG
1 AAATAAATTGTTGAATTTATATCATTGAGAATCTTGAAGGATC-CTAACTTT-GTAAGGAAAATA
* * * * * * *
103965 AATTGTTGAATTTATTTTCTTG-GAATCATGAACGAATTCTAA-TTT-CACAAGGA-
64 AATAGTAGAATTTATTTCCTTGAGAATCTTGAATG-ATTCTAACTTTGTA-AA-AAT
* * * * * * * * *
104018 AAATTAATTGTTTAATTTATTTCCTTGA-AA-ATTAAGAGTGATTCTAACTTTGTTAGGAAAATG
1 AAATAAATTGTTGAATTTATATCATTGAGAATCTTGA-AG-GATCCTAACTTTGTAAGGAAAATA
* *
104081 AATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAAAAT
64 AATAGTAGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAAAAT
* **
104135 AAATAAATTGTTGAATTTATATCATTGAGAATCTTGAATGATTTTAACTTTGTAAGGAAAATAAA
1 AAATAAATTGTTGAATTTATATCATTGAGAATCTTGAAGGATCCTAACTTTGTAAGGAAAATAAA
* * * *
104200 TAGTTGAATTTATTTCCTTTAGAATCTTGAATGATTCT-ATTTTGTAAAAGT
66 TAGTAGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAAAAT
*
104251 AAATAAATTGTTGAATTTATTTTC-TT-AGGAATCTTGAAGGATCCT-A-TTATGTAAAGG-AAA
1 AAATAAATTGTTGAATTTA-TATCATTGA-GAATCTTGAAGGATCCTAACTT-TGT-AAGGAAAA
* **
104311 TAAATCGTAGCTTTTATTT
62 TAAATAGTAGAATTTATTT
104330 TCCTGTTTTG
Statistics
Matches: 347, Mismatches: 57, Indels: 45
0.77 0.13 0.10
Matches are distributed among these distances:
113 57 0.16
114 21 0.06
115 45 0.13
116 116 0.33
117 101 0.29
118 4 0.01
119 3 0.01
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (117 bp):
AAATAAATTGTTGAATTTATATCATTGAGAATCTTGAAGGATCCTAACTTTGTAAGGAAAATAAA
TAGTAGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAAAAT
Found at i:104481 original size:39 final size:39
Alignment explanation
Indices: 104393--104504 Score: 120
Period size: 39 Copynumber: 2.9 Consensus size: 39
104383 ATGATTCTGG
*
104393 TTTGTAAAAGGAAATAAATCGTAGAATTTATTTTCATGT
1 TTTGTAAAAGGAAATAAATCATAGAATTTATTTTCATGT
* * * * *
104432 TATGTTAAAGGAAATAAATCATTGGATTTATTTT-TTGTT
1 TTTGTAAAAGGAAATAAATCATAGAATTTATTTTCATG-T
* *
104471 TTTGTAAAAGGAGATAAATCACT-GAATTTGTTTT
1 TTTGTAAAAGGAAATAAATCA-TAGAATTTATTTT
104505 AATCTTATAT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 2 0.03
39 57 0.95
40 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (39 bp):
TTTGTAAAAGGAAATAAATCATAGAATTTATTTTCATGT
Found at i:113669 original size:15 final size:15
Alignment explanation
Indices: 113628--113670 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
113618 TACCCATCCC
*
113628 AGCACTACCCCTTTT
1 AGCACTACCCATTTT
* *
113643 A-CATTTCCCATTTT
1 AGCACTACCCATTTT
113657 AGCACTACCCATTT
1 AGCACTACCCATTT
113671 CAGCGTTGTC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.23, C:0.35, G:0.05, T:0.37
Consensus pattern (15 bp):
AGCACTACCCATTTT
Done.