Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007026.1 Hibiscus syriacus cultivar Beakdansim tig00018185_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: 75003
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1655 original size:13 final size:13
Alignment explanation
Indices: 1637--1662 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1627 TTGAGTTCCC
1637 GTTATGAATAAGG
1 GTTATGAATAAGG
1650 GTTATGAATAAGG
1 GTTATGAATAAGG
1663 ATGAATCCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
GTTATGAATAAGG
Found at i:7189 original size:16 final size:16
Alignment explanation
Indices: 7168--7208 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
7158 TGAACAAATG
7168 AACGAACACGAACATA
1 AACGAACACGAACATA
7184 AACGAACACGAACATA
1 AACGAACACGAACATA
7200 AACGAACAC
1 AACGAACAC
7209 AAAAGTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.56, C:0.27, G:0.12, T:0.05
Consensus pattern (16 bp):
AACGAACACGAACATA
Found at i:7564 original size:34 final size:34
Alignment explanation
Indices: 7526--7617 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
7516 TGGGTTGAAT
* * * *
7526 ATAAACGAATGTAGATAAACGAACATACATGGAC
1 ATAAACGAACGAAGATAAACAAACATACACGGAC
* *
7560 ATAAATGAACGAATATAAACAAACATACACGGAC
1 ATAAACGAACGAAGATAAACAAACATACACGGAC
* *
7594 ATAAATGAACGAACATAAACAAAC
1 ATAAACGAACGAAGATAAACAAAC
7618 GGATTACCGA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.15
Consensus pattern (34 bp):
ATAAACGAACGAAGATAAACAAACATACACGGAC
Found at i:10645 original size:24 final size:23
Alignment explanation
Indices: 10590--10680 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 23
10580 TAGTGTTTTA
* *
10590 TTTATTTCATTTGTTTTTATAGAC-
1 TTTATTT-ATTTATTTTTAT-GTCT
10614 TTTATTTATTTATTTTTATGTCT
1 TTTATTTATTTATTTTTATGTCT
*
10637 TTTATTTTATTT-TATTTTATTTCAT
1 TTTA-TTTATTTAT-TTTTATGTC-T
* *
10662 TTCATTTCTTTATTTTTAT
1 TTTATTTATTTATTTTTAT
10681 TTAATTTACT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 2 0.04
23 16 0.28
24 34 0.60
25 5 0.09
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.71
Consensus pattern (23 bp):
TTTATTTATTTATTTTTATGTCT
Found at i:18461 original size:21 final size:23
Alignment explanation
Indices: 18435--18485 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
18425 AGGGAATTGA
18435 TCCCCCCTTG-AG-GGAACCGAT
1 TCCCCCCTTGAAGAGGAACCGAT
*
18456 TCCCCCTTTGAAGAGGAACCGAT
1 TCCCCCCTTGAAGAGGAACCGAT
18479 TCCCCCC
1 TCCCCCC
18486 ACAGGGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 2 0.08
23 15 0.58
ACGTcount: A:0.20, C:0.41, G:0.20, T:0.20
Consensus pattern (23 bp):
TCCCCCCTTGAAGAGGAACCGAT
Found at i:22430 original size:7 final size:7
Alignment explanation
Indices: 22363--22415 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
22353 CAATCAGAAC
22363 AAAAAGA
1 AAAAAGA
22370 AAAAAGA
1 AAAAAGA
22377 GAAAAA-A
1 -AAAAAGA
*
22384 ACAAAGA
1 AAAAAGA
* *
22391 GAAAATA
1 AAAAAGA
22398 AAAAAGA
1 AAAAAGA
22405 AAAAAGGA
1 AAAAA-GA
22413 AAA
1 AAA
22416 TTGCAGAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
6 4 0.11
7 23 0.62
8 10 0.27
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:23585 original size:32 final size:32
Alignment explanation
Indices: 23549--23669 Score: 120
Period size: 32 Copynumber: 3.8 Consensus size: 32
23539 GGAACAATGA
23549 GGGCA-TCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATTCTTTG-AGATTCAACATCAAATGTTG
* ** *
23581 GGGCATTTTTTTTTGATTTAACATCAAATGTTG
1 GGGCA-TTCTTTGAGATTCAACATCAAATGTTG
* * * *
23614 GGGCATTTTTTGAGATTTAACATCGAATATTG
1 GGGCATTCTTTGAGATTCAACATCAAATGTTG
*
23646 GGGCA-TCTTTGGGAATTCAACATC
1 GGGCATTCTTTGAG-ATTCAACATC
23670 CTCATACAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
31 6 0.08
32 42 0.56
33 23 0.31
34 4 0.05
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (32 bp):
GGGCATTCTTTGAGATTCAACATCAAATGTTG
Found at i:23605 original size:33 final size:33
Alignment explanation
Indices: 23556--23651 Score: 131
Period size: 32 Copynumber: 2.9 Consensus size: 33
23546 TGAGGGCATC
*
23556 TTTGAAGATTCAACATCAAATGTTGGGGCATTTT
1 TTTG-AGATTTAACATCAAATGTTGGGGCATTTT
**
23590 TTTTTGATTTAACATCAAATGTTGGGGCA-TTT
1 TTTGAGATTTAACATCAAATGTTGGGGCATTTT
* *
23622 TTTGAGATTTAACATCGAATATTGGGGCAT
1 TTTGAGATTTAACATCAAATGTTGGGGCAT
23652 CTTTGGGAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 28 0.52
33 23 0.43
34 3 0.06
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (33 bp):
TTTGAGATTTAACATCAAATGTTGGGGCATTTT
Found at i:24521 original size:106 final size:106
Alignment explanation
Indices: 24336--24582 Score: 361
Period size: 106 Copynumber: 2.3 Consensus size: 106
24326 AATTTCAGAG
** * *
24336 CCAATTTCAACTTCACAGCGAAAAATATTGGACTCGAGAAAACACAAGTTCAACTTCACAGCGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACATCACAACGAA
* *
24401 GGGACGGCTGGTTGTCAATAAACAATTTACCAGTTTTAAAA
66 GGGACGGCTGGTTGTCAACAAACAATTTACCAGTTCTAAAA
*
24442 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACATCACAACGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACATCACAACGAA
* * * *
24507 GGGACGGCTGGTTGTCAACAAATAATTTCCCAGTTCTAGAG
66 GGGACGGCTGGTTGTCAACAAACAATTTACCAGTTCTAAAA
* *
24548 TCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 CCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
24583 AAAACAATAT
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
105 1 0.01
106 126 0.99
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (106 bp):
CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACATCACAACGAA
GGGACGGCTGGTTGTCAACAAACAATTTACCAGTTCTAAAA
Found at i:24907 original size:101 final size:101
Alignment explanation
Indices: 24730--24915 Score: 250
Period size: 101 Copynumber: 1.8 Consensus size: 101
24720 GACAATTTCC
* * * *
24730 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATATCTTTTCCTTGAAAC
1 AAGTTTTATCTCTCTTGAGACAATTTCCCTTGAAACAAAATCATTGAATAACTTTCCCTTGAAAC
24795 AAATTTCGTCTCCCTTGAGACATTTTTTTTGGAACT
66 AAATTTCGTCTCCCTTGAGACATTTTTTTTGGAACT
* *
24831 AAGTTTTATCTCTCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAA-AACATTTCCCTTGAA
1 AAGTTTTATCTCTCTTGAGACAATTTCCCTTGAAACA-AAATCATTGAATAAC-TTTCCCTTGAA
** * *
24894 ATGAATTTTGTCTCTCTTGAGA
64 ACAAATTTCGTCTCCCTTGAGA
24916 TAGTTTCCCT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
100 2 0.03
101 68 0.93
102 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (101 bp):
AAGTTTTATCTCTCTTGAGACAATTTCCCTTGAAACAAAATCATTGAATAACTTTCCCTTGAAAC
AAATTTCGTCTCCCTTGAGACATTTTTTTTGGAACT
Found at i:24929 original size:15 final size:15
Alignment explanation
Indices: 24909--24943 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
24899 TTTTGTCTCT
*
24909 CTTGAGATAGTTTCC
1 CTTGAGACAGTTTCC
*
24924 CTTGAGACAGTTTCT
1 CTTGAGACAGTTTCC
24939 CTTGA
1 CTTGA
24944 AGCATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
CTTGAGACAGTTTCC
Found at i:25153 original size:35 final size:37
Alignment explanation
Indices: 25088--25175 Score: 128
Period size: 35 Copynumber: 2.4 Consensus size: 37
25078 TTGAATACAA
25088 TTTCTCTTGAAACACAAAAAAAAAACCCTTTGAA-ATTG
1 TTTCTCTTGAAACAC-AAAAAAAAACCCTTTGAAGA-TG
*
25126 TTTCTCTTGAAACAC-AAAAAACA-CCTTTGAAGATG
1 TTTCTCTTGAAACACAAAAAAAAACCCTTTGAAGATG
25161 TTTCTCTTGAAACAC
1 TTTCTCTTGAAACAC
25176 CAAACCCTCA
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
35 25 0.52
36 8 0.17
38 15 0.31
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (37 bp):
TTTCTCTTGAAACACAAAAAAAAACCCTTTGAAGATG
Found at i:28429 original size:30 final size:31
Alignment explanation
Indices: 28370--28436 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
28360 GGGGACCATA
** *
28370 TTGTAAATGGACTAAATGTTGGGGGACTGTT
1 TTGTAAACAGACTAAATGTTGGAGGACTGTT
28401 TTGTAAACAGACTAAATGTT-GAGGACTGTT
1 TTGTAAACAGACTAAATGTTGGAGGACTGTT
28431 TTGTAA
1 TTGTAA
28437 GTTTTAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (31 bp):
TTGTAAACAGACTAAATGTTGGAGGACTGTT
Found at i:28707 original size:31 final size:31
Alignment explanation
Indices: 28663--28731 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
28653 GTAACGGCGT
*
28663 CAAACGACCAGTTACGTAGGGGACCATATTG
1 CAAACGGCCAGTTACGTAGGGGACCATATTG
* *
28694 CAAACGGCTAGTTACGTTGGGGACCATATTG
1 CAAACGGCCAGTTACGTAGGGGACCATATTG
28725 CAAACGG
1 CAAACGG
28732 ACTAAATGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (31 bp):
CAAACGGCCAGTTACGTAGGGGACCATATTG
Found at i:29677 original size:17 final size:18
Alignment explanation
Indices: 29655--29690 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29645 ATTATTAATG
*
29655 ATTAAATT-TTTTGAATT
1 ATTAAATTATTTTAAATT
29672 ATTAAATTATTTTAAATT
1 ATTAAATTATTTTAAATT
29690 A
1 A
29691 AAATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTAAATTATTTTAAATT
Found at i:30476 original size:4 final size:4
Alignment explanation
Indices: 30467--30494 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
30457 TTGACAATTC
30467 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
30495 GTATTCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:34826 original size:17 final size:18
Alignment explanation
Indices: 34804--34840 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
34794 TCTTATGCAC
34804 ATCAATA-GTTTTATCAG
1 ATCAATATGTTTTATCAG
*
34821 ATCAATATGTTTTTTCAG
1 ATCAATATGTTTTATCAG
34839 AT
1 AT
34841 TTATTAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
ATCAATATGTTTTATCAG
Found at i:37736 original size:21 final size:20
Alignment explanation
Indices: 37650--37807 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
37640 AAATGACCAA
**
37650 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
37669 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
37689 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
37709 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
37730 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
37751 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
37771 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
37792 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
37808 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:37800 original size:20 final size:20
Alignment explanation
Indices: 37775--37964 Score: 240
Period size: 20 Copynumber: 9.4 Consensus size: 20
37765 GATTTTCCAG
* ** *
37775 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
37795 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
37815 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37835 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37855 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37875 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37895 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
37915 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
37936 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37956 AATCGCAAC
1 AATCGCAAC
37965 TCGATTTTTA
Statistics
Matches: 148, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 128 0.86
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:38386 original size:33 final size:33
Alignment explanation
Indices: 38347--38417 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
38337 TTCACTTAGA
*
38347 TTTCATTTCGCGTTGCGT-TTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGC-TATTCTCTCATTGCGAT
38380 TTTCATTTCGCGTTGCTATTCTCTCATTGCGAT
1 TTTCATTTCGCGTTGCTATTCTCTCATTGCGAT
38413 TTTCA
1 TTTCA
38418 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 1 0.03
33 35 0.97
ACGTcount: A:0.10, C:0.24, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCTATTCTCTCATTGCGAT
Found at i:38523 original size:21 final size:21
Alignment explanation
Indices: 38497--38573 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
38487 TGCAGAAGAG
38497 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
38518 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
38538 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
38560 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
38574 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:38577 original size:14 final size:14
Alignment explanation
Indices: 38558--38614 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
38548 GAAAAATGAA
38558 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
38572 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
38591 AATCGCAACGAGAG
1 AATCGCAACGAGAG
38605 AATCGCAACG
1 AATCGCAACG
38615 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:38589 original size:33 final size:33
Alignment explanation
Indices: 38551--38630 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
38541 GCAACGAGAA
38551 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
38584 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
38617 AAACCAAAATCGCA
1 AAATGAAAATCGCA
38631 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:38648 original size:19 final size:19
Alignment explanation
Indices: 38626--38739 Score: 103
Period size: 19 Copynumber: 6.1 Consensus size: 19
38616 GAAACCAAAA
*
38626 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
38645 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
38664 TCGCGTTGCGA--TTC-TA
1 TCGCGTTGCGATTTTCATT
38680 T--CGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
38698 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
38718 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
38738 TC
1 TC
38740 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
14 8 0.10
16 5 0.06
17 3 0.04
18 1 0.01
19 32 0.41
20 19 0.24
21 11 0.14
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:38704 original size:21 final size:21
Alignment explanation
Indices: 38675--38739 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
38665 CGCGTTGCGA
*
38675 TTCTATCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
38696 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
38716 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
38737 TTC
1 TTC
38740 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.12, C:0.25, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:40688 original size:14 final size:14
Alignment explanation
Indices: 40669--40725 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
40659 CGAAACTTAA
40669 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
40683 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
40702 AATCGCAACGACAG
1 AATCGCAACGAGAG
40716 AATCGCAACG
1 AATCGCAACG
40726 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:40707 original size:19 final size:18
Alignment explanation
Indices: 40683--40774 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
40673 GCAACGAGAG
40683 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
40702 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
40716 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
40735 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
40749 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
40768 AATCGCA
1 AATCGCA
40775 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:40709 original size:33 final size:33
Alignment explanation
Indices: 40651--40774 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
40641 TAGTTTACTT
* * *
40651 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
40685 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
40718 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
40751 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
40775 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:40751 original size:14 final size:14
Alignment explanation
Indices: 40700--40758 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
40690 ACGCGAAATG
40700 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
40714 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
40733 AAAATCGCAACGAC
1 AAAATCGCAACGAC
40747 AAAATCGCAACG
1 AAAATCGCAACG
40759 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:40792 original size:19 final size:19
Alignment explanation
Indices: 40770--40961 Score: 179
Period size: 19 Copynumber: 10.6 Consensus size: 19
40760 GAAACCAAAA
*
40770 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
40789 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
40803 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
* *
40822 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
40838 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
40855 TCGCGTTGCGACTTTCATT
1 TCGCGTTGCGATTTTCATT
**
40874 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
40893 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
40912 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
40931 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
40951 TCGTGTTGCGA
1 TCGCGTTGCGA
40962 AAGTAAACTA
Statistics
Matches: 141, Mismatches: 21, Indels: 21
0.77 0.11 0.11
Matches are distributed among these distances:
14 17 0.12
16 7 0.05
17 7 0.05
19 98 0.70
20 12 0.09
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:40817 original size:33 final size:33
Alignment explanation
Indices: 40775--40943 Score: 176
Period size: 33 Copynumber: 4.8 Consensus size: 33
40765 CAAAATCGCA
40775 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* * *
40808 TTGCGATTTTAATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
40841 TTGCGATTTTCATTTCGCGTTGCGACTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
** *
40879 TTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA---T--TCTCTCG
*
40917 TTGCGATTCTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
40944 TTAAGTTTCG
Statistics
Matches: 113, Mismatches: 15, Indels: 16
0.78 0.10 0.11
Matches are distributed among these distances:
33 54 0.48
35 4 0.04
38 52 0.46
39 2 0.02
41 1 0.01
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:42908 original size:14 final size:14
Alignment explanation
Indices: 42889--42924 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
42879 ATTGTTTAAT
42889 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
42903 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
42917 TGATTTGT
1 TGATTTGT
42925 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:43048 original size:20 final size:19
Alignment explanation
Indices: 43031--43148 Score: 139
Period size: 19 Copynumber: 6.6 Consensus size: 19
43021 AAAAATGACT
43031 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
43051 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
43070 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
43084 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
43103 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
43123 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
43137 ATCGCAATGCGA
1 ATCGCAATGCGA
43149 TTTTCATTTC
Statistics
Matches: 87, Mismatches: 2, Indels: 21
0.79 0.02 0.19
Matches are distributed among these distances:
14 21 0.24
15 2 0.02
16 4 0.05
17 3 0.03
18 2 0.02
19 29 0.33
20 26 0.30
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:43118 original size:53 final size:52
Alignment explanation
Indices: 43031--43148 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 52
43021 AAAAATGACT
*
43031 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAA
43084 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAA
43137 ATCGCAATGCGA
1 ATCGCAATGCGA
43149 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 19 0.30
53 44 0.70
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:43181 original size:53 final size:53
Alignment explanation
Indices: 43144--43361 Score: 297
Period size: 53 Copynumber: 4.1 Consensus size: 53
43134 AAAATCGCAA
*
43144 TGCGATTTTCATTTCGTATTGCGATTTTCATTTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCTCTCGT
*
43197 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCTCTCGT
*
43250 TGCGATTTTCATTTCGCATTGCGATTTTCA-TTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTTCGCATTGCGA--TTC-TCT-CG--T
*
43308 TGCGATTTTCA--T-G--TTGGGATTTTCA-TTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCTCTCGT
43355 TGCGATT
1 TGCGATT
43362 GTAATTTCCG
Statistics
Matches: 153, Mismatches: 6, Indels: 18
0.86 0.03 0.10
Matches are distributed among these distances:
47 8 0.05
49 2 0.01
50 2 0.01
51 3 0.02
52 12 0.08
53 105 0.69
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCTCTCGT
Found at i:43225 original size:72 final size:73
Alignment explanation
Indices: 43138--43347 Score: 270
Period size: 72 Copynumber: 2.9 Consensus size: 73
43128 AACGAGAAAA
* * * * *
43138 TCGCAATGCGATTTTCATTT-CGTATTGCGATTTTCAT--TTTCGCA-TTGCGATTCTCTCGTTG
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATCGTTGCG-ATTTGC-ATT-TCGCATTG
43199 CGATTTTCATT
63 CGATTTTCATT
* *
43210 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGA
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATCGTTGCGATTTGCATTTCGCATTGCGA
43274 TTTTCATT
66 TTTTCATT
* *
43282 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGA
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATCGTTGCGATTTGCATTTCGCATTGCGA
43346 TT
66 TT
43348 CTCTCGTTGC
Statistics
Matches: 124, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
72 99 0.80
73 18 0.15
74 7 0.06
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (73 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATCGTTGCGATTTGCATTTCGCATTGCGA
TTTTCATT
Found at i:43369 original size:33 final size:33
Alignment explanation
Indices: 43215--43361 Score: 188
Period size: 33 Copynumber: 4.2 Consensus size: 33
43205 TCATTTCGCA
43215 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
43249 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
43285 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
43321 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
43354 TTGCGATT
1 TTGCGATT
43362 GTAATTTCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 32 0.32
34 29 0.29
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 10 0.10
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:43589 original size:20 final size:20
Alignment explanation
Indices: 43564--43644 Score: 117
Period size: 20 Copynumber: 4.0 Consensus size: 20
43554 AGCCAGTTGT
43564 GATTTACGGATACGCATTGC
1 GATTTACGGATACGCATTGC
43584 GATTTACGGATACGCATTGC
1 GATTTACGGATACGCATTGC
* * *
43604 GATTTACGGATACACGTTGT
1 GATTTACGGATACGCATTGC
* *
43624 GGTTTACGGATACGCGTTGC
1 GATTTACGGATACGCATTGC
43644 G
1 G
43645 TACTACTTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (20 bp):
GATTTACGGATACGCATTGC
Found at i:44185 original size:20 final size:20
Alignment explanation
Indices: 44160--44345 Score: 232
Period size: 20 Copynumber: 9.3 Consensus size: 20
44150 AAATTTCAGT
* * *
44160 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
44180 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
** * *
44200 GTTGCGATTTACAAATTCTC
1 GTTGCGATTTACGGATACGC
*
44220 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
44240 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
44260 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
44280 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
44300 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
44320 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
44340 GTTGCG
1 GTTGCG
44346 TACTACTTCT
Statistics
Matches: 148, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
19 3 0.02
20 143 0.97
21 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:44889 original size:20 final size:20
Alignment explanation
Indices: 44861--45089 Score: 208
Period size: 20 Copynumber: 11.4 Consensus size: 20
44851 AAATTTCAGT
* * *
44861 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
44881 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
44901 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
44921 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* * *
44941 GTTGTGATTTACGGGTACGC
1 GTTGCGATTTACGGATTCGC
* *
44961 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
44981 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
45001 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* * *
45021 GTTGCGGTTTACAGATACGC
1 GTTGCGATTTACGGATTCGC
*
45041 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
45061 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
45081 GTTGCGATT
1 GTTGCGATT
45090 CTGAAAAATC
Statistics
Matches: 175, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
20 174 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:44907 original size:701 final size:701
Alignment explanation
Indices: 43559--45046 Score: 2841
Period size: 701 Copynumber: 2.1 Consensus size: 701
43549 GGTGAAGCCA
* * *
43559 GTTGTGATTTACGGATACGCATTGCGATTTACGGATACGCATTGCGATTTACGGATACACGTTGT
1 GTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTACGGATACACGTTGC
43624 GGTTTACGGATACGCGTTGCGTACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTTGT
66 GGTTTACGGATACGCGTTGCGTACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTTGT
43689 GAAACACTAATGTAAGCAATGAATCGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTACC
131 GAAACACTAATGTAAGCAATGAATCGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTACC
43754 ATTTCTCTGATAAGATAGCCTAAATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTA
196 ATTTCTCTGATAAGATAGCCTAAATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTA
*
43819 GCATTAGAGTTTCATAAGTTAACTTTTGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAATGC
261 GCATTAGAGTTTCATAAGTTAACTTTTGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAGGC
43884 ATATATTGTAAAACACCATGAACATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATG
326 ATATATTGTAAAACACCATGAACATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATG
43949 ATCAACATTAGATGATTTCATGGTTGCAAATTAATTTACTAAACAGACGAGCTGCGAAACTAAAA
391 ATCAACATTAGATGATTTCATGGTTGCAAATTAATTTACTAAACAGACGAGCTGCGAAACTAAAA
*
44014 CTTGTTGCCGGATTGGGAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGATAG
456 CCTGTTGCCGGATTGGGAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGATAG
44079 ATGGAGATGGAATGAGTTGCGATTTAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATA
521 ATGGAGATGGAATGAGTTGCGATTTAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATA
44144 TACCCAAAATTTCAGTGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATT
586 TACCCAAAATTTCAGTGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATT
44209 TACAAATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGC
651 TACAAATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGC
44260 GTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTACGGATACACGTTGC
1 GTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTACGGATACACGTTGC
44325 GGTTTACGGATACGCGTTGCGTACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTTGT
66 GGTTTACGGATACGCGTTGCGTACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTTGT
44390 GAAACACTAATGTAAGCAATGAATCGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTACC
131 GAAACACTAATGTAAGCAATGAATCGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTACC
*
44455 ATTTCTCTGATAAGATAGCCTAAATTCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTA
196 ATTTCTCTGATAAGATAGCCTAAATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTA
44520 GCATTAGAGTTTCATAAGTTAACTTTTGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAGGC
261 GCATTAGAGTTTCATAAGTTAACTTTTGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAGGC
*
44585 ATATATTGTAAAACACCATGAACATTATCCCATGACCCTCCAAAACACAAATTTATCCAAACATG
326 ATATATTGTAAAACACCATGAACATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATG
*
44650 ATCAACATTAGATGATTTCATGGTTGTAAATTAATTTACTAAACAGACGAGCTGCGAAACTAAAA
391 ATCAACATTAGATGATTTCATGGTTGCAAATTAATTTACTAAACAGACGAGCTGCGAAACTAAAA
44715 CCTGTTGCCGGATTGGGAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGATAG
456 CCTGTTGCCGGATTGGGAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGATAG
44780 ATGGAGATGGAATGAGTTGCGATTTAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATA
521 ATGGAGATGGAATGAGTTGCGATTTAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATA
*
44845 TACCCAAAATTTCAGTGTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATT
586 TACCCAAAATTTCAGTGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATT
* * *
44910 TACAGATTCTCGTTGCGATTTACGGATTATCGTTGTGATTTACGGGTACGC
651 TACAAATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGC
* *
44961 GTTGCGATATACGGATACGCATTGCGATTTACGGATACGCGTTGCTATTTACGGATACACGTTGC
1 GTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTACGGATACACGTTGC
*
45026 GGTTTACAGATACGCGTTGCG
66 GGTTTACGGATACGCGTTGCG
45047 ATTTATGTGT
Statistics
Matches: 772, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
701 772 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (701 bp):
GTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTACGGATACACGTTGC
GGTTTACGGATACGCGTTGCGTACTACTTCTAGGTTCAACAACATACAATGTAACATCATCTTGT
GAAACACTAATGTAAGCAATGAATCGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTACC
ATTTCTCTGATAAGATAGCCTAAATCCACTTAGGGGCTCTAAATTCAATTTCTTTGAAACACGTA
GCATTAGAGTTTCATAAGTTAACTTTTGTAAAGACAATTTTAGTTGAAGATTCATGGGTAAAGGC
ATATATTGTAAAACACCATGAACATTATCCCATGACCCTCCAAAACACAAATCTATCCAAACATG
ATCAACATTAGATGATTTCATGGTTGCAAATTAATTTACTAAACAGACGAGCTGCGAAACTAAAA
CCTGTTGCCGGATTGGGAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGATAG
ATGGAGATGGAATGAGTTGCGATTTAGGGATTTAGTTTATGATTTGCTGCTGTTGCGTAGTTATA
TACCCAAAATTTCAGTGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATT
TACAAATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGC
Found at i:45150 original size:42 final size:43
Alignment explanation
Indices: 45057--45155 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 43
45047 ATTTATGTGT
* *
45057 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTGAAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTCAAAAA
** * *
45098 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTCAAAAA
*
45140 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
45156 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 8 0.17
42 35 0.76
43 3 0.07
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTCAAAAA
Found at i:54954 original size:13 final size:13
Alignment explanation
Indices: 54936--54961 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54926 CTACCTGAAA
54936 GGCAAATTTGGTC
1 GGCAAATTTGGTC
54949 GGCAAATTTGGTC
1 GGCAAATTTGGTC
54962 AAGTCAATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
GGCAAATTTGGTC
Found at i:59278 original size:18 final size:16
Alignment explanation
Indices: 59243--59273 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59233 AATCACAAAC
59243 TTTTTTTTTATATTTG
1 TTTTTTTTTATATTTG
*
59259 TTTTATTTTATATTT
1 TTTTTTTTTATATTT
59274 TTGTTAATTT
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:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTATATTTG
Found at i:60654 original size:21 final size:21
Alignment explanation
Indices: 60628--60672 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
60618 GATTTCTGGG
* *
60628 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
60649 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
60670 CAA
1 CAA
60673 ACGAACAAAA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:62543 original size:103 final size:103
Alignment explanation
Indices: 62359--62571 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
62349 GGGTCTACGC
*
62359 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
62424 CCTTGGAATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGAATATATATATGATTCTTAAGGAATGATATGT
62462 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
62527 CCCTAGTATATATATATGATTCTTAAGGAATGATATGT
66 CCCTAGAATATATATATGATTCTTAAGGAATGATATGT
*
62565 AGTCCTT
1 GGTCCTT
62572 ATGGACATTA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGAATATATATATGATTCTTAAGGAATGATATGT
Found at i:62621 original size:23 final size:23
Alignment explanation
Indices: 62588--62655 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
62578 ATTATTATAT
62588 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
62611 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
62634 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
62656 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:68003 original size:24 final size:24
Alignment explanation
Indices: 67958--68007 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
67948 TGGTGGTTGG
*
67958 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
67982 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
68006 TT
1 TT
68008 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:74836 original size:19 final size:20
Alignment explanation
Indices: 74800--74841 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
74790 TTAACTTTTC
74800 TTTTCTCTTTCTTATTAA-T
1 TTTTCTCTTTCTTATTAACT
74819 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTC-TTATTAACT
74839 TTT
1 TTT
74842 ACTTTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTCTCTTTCTTATTAACT
Done.