Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003576.1 Hibiscus syriacus cultivar Beakdansim tig00007549_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: 121837
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1352 original size:20 final size:20
Alignment explanation
Indices: 1327--1371 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1317 GTTTATTTTA
1327 TAACTTTATTTCAATTATCG
1 TAACTTTATTTCAATTATCG
*
1347 TAACTTTGTTTCAATTATCG
1 TAACTTTATTTCAATTATCG
1367 -AACTT
1 TAACTT
1372 GAAGTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (20 bp):
TAACTTTATTTCAATTATCG
Found at i:1414 original size:33 final size:33
Alignment explanation
Indices: 1361--1459 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1351 TTTGTTTCAA
1361 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1393 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1426 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1459 T
1 T
1460 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1488 original size:13 final size:13
Alignment explanation
Indices: 1445--1499 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1435 TTGGAAGTAT
1445 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1458 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1472 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1485 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1498 TT
1 TT
1500 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1947 original size:17 final size:17
Alignment explanation
Indices: 1904--1947 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1894 TTAAAATCGG
*
1904 TTTTTTT-ATAACCGGT
1 TTTTTTTAAAAACCGGT
**
1920 TTTTTAAAAAAACCGGT
1 TTTTTTTAAAAACCGGT
1937 TTTTTTTAAAA
1 TTTTTTTAAAA
1948 CCGAAACCGG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (17 bp):
TTTTTTTAAAAACCGGT
Found at i:2068 original size:15 final size:17
Alignment explanation
Indices: 2042--2073 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2032 TCTATGGGAA
2042 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
2058 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
2074 CGATTGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:3922 original size:54 final size:54
Alignment explanation
Indices: 3840--3948 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
3830 ATTTTCCGCA
3840 ATCGCAGTTCTTGTTCAACAATAGATGGATAACAGACATCTAGAATGACATCAT
1 ATCGCAGTTCTTGTTCAACAATAGATGGATAACAGACATCTAGAATGACATCAT
3894 ATCGCAGTTCTTGTTCAACAATAGATGGATAACAGACATCTAGAATGACATCAT
1 ATCGCAGTTCTTGTTCAACAATAGATGGATAACAGACATCTAGAATGACATCAT
3948 A
1 A
3949 ATTGTTTATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (54 bp):
ATCGCAGTTCTTGTTCAACAATAGATGGATAACAGACATCTAGAATGACATCAT
Found at i:7551 original size:24 final size:23
Alignment explanation
Indices: 7511--7575 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
7501 TTCATAATAT
*
7511 TTTTATATATTACCTTAAAATATAA
1 TTTT-TATATTAACTTAAAATA-AA
*
7536 TTTTTATATTAACTT--ATTAAA
1 TTTTTATATTAACTTAAAATAAA
7557 TATTTTATTATTAACTTAA
1 T-TTTTA-TATTAACTTAA
7576 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
21 3 0.09
22 8 0.24
23 9 0.26
24 10 0.29
25 4 0.12
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTTATATTAACTTAAAATAAA
Found at i:7557 original size:26 final size:22
Alignment explanation
Indices: 7506--7575 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 22
7496 TTAAATTCAT
*
7506 AATATTTTTATATATTACCTTAA
1 AATATTTTT-TATATTAACTTAA
7529 AATATAATTTTTATATTAACTTATTA
1 AATAT--TTTTTATATTAACTTA--A
*
7555 AATATTTTAT-TATTAACTTAA
1 AATATTTTTTATATTAACTTAA
7576 TTTAAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 1 0.02
23 15 0.37
24 15 0.37
25 4 0.10
26 6 0.15
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTTTTTATATTAACTTAA
Found at i:7611 original size:26 final size:26
Alignment explanation
Indices: 7554--7626 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
7544 TTAACTTATT
**
7554 AAATATTTTATTATTAACTTAATTTAA
1 AAATATTTTATT-TTATTTTAATTTAA
*
7581 AAATATTTTATTTTATTTTCATTTAA
1 AAATATTTTATTTTATTTTAATTTAA
*
7607 AAATA-TATATTTTATTTTAA
1 AAATATTTTATTTTATTTTAA
7627 AATTTATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
25 13 0.32
26 16 0.39
27 12 0.29
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (26 bp):
AAATATTTTATTTTATTTTAATTTAA
Found at i:7617 original size:25 final size:26
Alignment explanation
Indices: 7575--7624 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
7565 TATTAACTTA
*
7575 ATTTAAAAATATTTTATTTTATTTTC
1 ATTTAAAAATATTATATTTTATTTTC
7601 ATTTAAAAATA-TATATTTTATTTT
1 ATTTAAAAATATTATATTTTATTTT
7625 AAAATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTAAAAATATTATATTTTATTTTC
Found at i:7631 original size:27 final size:28
Alignment explanation
Indices: 7556--7632 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 28
7546 AACTTATTAA
7556 ATATTTTATTATTAACTTAATTTAAAAATATT
1 ATATTTTATT-TTAA---AATTTAAAAATATT
* *
7588 TTATTTTATTTT--CATTTAAAAATA-T
1 ATATTTTATTTTAAAATTTAAAAATATT
7613 ATATTTTATTTTAAAATTTA
1 ATATTTTATTTTAAAATTTA
7633 TTTAAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
25 12 0.31
26 11 0.28
27 5 0.13
31 2 0.05
32 9 0.23
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (28 bp):
ATATTTTATTTTAAAATTTAAAAATATT
Found at i:7639 original size:31 final size:30
Alignment explanation
Indices: 7583--7643 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
7573 TAATTTAAAA
*
7583 ATATTTTATTTTATTTTCATTTAAAAATAT
1 ATATTTTATTTTAATTTCATTTAAAAATAT
7613 ATATTTTATTTTAAAATTT-ATTTAAAAATAT
1 ATATTTTATTTT--AATTTCATTTAAAAATAT
7644 GATTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 12 0.43
31 12 0.43
32 4 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (30 bp):
ATATTTTATTTTAATTTCATTTAAAAATAT
Found at i:7643 original size:27 final size:26
Alignment explanation
Indices: 7554--7643 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 26
7544 TTAACTTATT
* *
7554 AAATATTTTATTATTAACTTAATTTAA
1 AAATATTTTATT-TTAAATTTATTTAA
*
7581 AAATATTTTATTTT-ATTTTCATTTAAAA
1 AAATATTTTATTTTAAATTT-ATTT--AA
7609 ATATATATTTTATTTTAAAATTTATTTAA
1 A-A-ATATTTTATTTT-AAATTTATTTAA
7638 AAATAT
1 AAATAT
7644 GATTAAATTG
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
25 3 0.06
26 6 0.11
27 16 0.30
28 4 0.08
29 4 0.08
30 12 0.23
31 4 0.08
32 4 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
AAATATTTTATTTTAAATTTATTTAA
Found at i:7791 original size:31 final size:31
Alignment explanation
Indices: 7753--7820 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
7743 TGATGACCAC
*
7753 ATCTTAATTAAATAAAAACGAAAGTGATCAT
1 ATCTTAATTAAATAAAAACGAAAGTAATCAT
*
7784 ATCTTAATTAAATAAAAACGAAAGTAATGAT
1 ATCTTAATTAAATAAAAACGAAAGTAATCAT
7815 ATCTTA
1 ATCTTA
7821 TATTTTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACGAAAGTAATCAT
Found at i:7918 original size:15 final size:16
Alignment explanation
Indices: 7889--7923 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
7879 TTGTTAACCC
*
7889 TTAATATAATTAAATT
1 TTAATATAATAAAATT
7905 TTAAT-TAATAAAATT
1 TTAATATAATAAAATT
7920 TTAA
1 TTAA
7924 AAATTACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAATATAATAAAATT
Found at i:8660 original size:10 final size:10
Alignment explanation
Indices: 8642--8671 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
8632 TTTCTGTACT
8642 TTTATTTATTA
1 TTTA-TTATTA
8653 TTTATTATTA
1 TTTATTATTA
8663 TTTATTATT
1 TTTATTATT
8672 TTTCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATTATTA
Found at i:17778 original size:20 final size:20
Alignment explanation
Indices: 17753--17790 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17743 TTTTGGTGCA
*
17753 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
17773 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
17791 CTTTGAAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:18166 original size:16 final size:16
Alignment explanation
Indices: 18134--18167 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18124 TATCCACAAC
* *
18134 AAAGTGTCGATTTAAA
1 AAAGTGTCGACTGAAA
18150 AAAGTGTCGACTGAAA
1 AAAGTGTCGACTGAAA
18166 AA
1 AA
18168 TGTAATAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (16 bp):
AAAGTGTCGACTGAAA
Found at i:18441 original size:22 final size:22
Alignment explanation
Indices: 18394--18441 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
18384 AAATTACATA
18394 ACTTTTTAAAAAAGTATCGATC
1 ACTTTTTAAAAAAGTATCGATC
*
18416 -CTTTTTATAAAAAGTATGGA-C
1 ACTTTTTA-AAAAAGTATCGATC
18437 ACTTT
1 ACTTT
18442 CAATATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
ACTTTTTAAAAAAGTATCGATC
Found at i:19730 original size:31 final size:31
Alignment explanation
Indices: 19676--19759 Score: 132
Period size: 32 Copynumber: 2.6 Consensus size: 31
19666 AAACATATGC
19676 AAAATTTATATTTTATGTATTTTTGATAATAT
1 AAAATTTATA-TTTATGTATTTTTGATAATAT
*
19708 AAAATTTATATTTACGTATTTTTTGATAATAT
1 AAAATTTATATTTATGTA-TTTTTGATAATAT
*
19740 AAAATTTACATTTATGTATT
1 AAAATTTATATTTATGTATT
19760 AAAGAGTAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
31 9 0.19
32 39 0.81
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (31 bp):
AAAATTTATATTTATGTATTTTTGATAATAT
Found at i:20758 original size:27 final size:27
Alignment explanation
Indices: 20720--20789 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
20710 CTATCACGTT
*
20720 TTGTCAGGGATTGCAACCATCCATGTA
1 TTGTTAGGGATTGCAACCATCCATGTA
*
20747 TTGTTAGGGATTGCAACCATCCATGTT
1 TTGTTAGGGATTGCAACCATCCATGTA
*
20774 TTGTTAGAGATTGCAA
1 TTGTTAGGGATTGCAA
20790 ATTACAATCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (27 bp):
TTGTTAGGGATTGCAACCATCCATGTA
Found at i:30972 original size:29 final size:29
Alignment explanation
Indices: 30937--30994 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
30927 TTGTTTAATC
30937 GGTTTCTAATTTGTATAATGTATTTATTT
1 GGTTTCTAATTTGTATAATGTATTTATTT
**
30966 GGTTTCTAATTTGTATGTTGTATTTATTT
1 GGTTTCTAATTTGTATAATGTATTTATTT
30995 CAGTCTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.03, G:0.16, T:0.60
Consensus pattern (29 bp):
GGTTTCTAATTTGTATAATGTATTTATTT
Found at i:37200 original size:34 final size:34
Alignment explanation
Indices: 37157--37221 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
37147 ACGGTCTATT
37157 TTACAGTTGATTCATGTCCATTCTATGGTTTATG
1 TTACAGTTGATTCATGTCCATTCTATGGTTTATG
* *
37191 TTACAGTTGATTCATGTCCGTTTTATGGTTT
1 TTACAGTTGATTCATGTCCATTCTATGGTTT
37222 CTATGGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.49
Consensus pattern (34 bp):
TTACAGTTGATTCATGTCCATTCTATGGTTTATG
Found at i:38886 original size:19 final size:19
Alignment explanation
Indices: 38862--38901 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
38852 GAAGTTTCAG
38862 GCACTCTTTTCCTCCTTCC
1 GCACTCTTTTCCTCCTTCC
38881 GCACTCTTTTCCTCCTTCC
1 GCACTCTTTTCCTCCTTCC
38900 GC
1 GC
38902 TGATTAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.05, C:0.47, G:0.07, T:0.40
Consensus pattern (19 bp):
GCACTCTTTTCCTCCTTCC
Found at i:55423 original size:20 final size:20
Alignment explanation
Indices: 55368--55426 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
55358 AGAACCCATG
*
55368 GGGGGTATCGGTTCCCTTAA
1 GGGGGTATCGGTTCCCTCAA
* *
55388 GGAGGGAATCGGTTCCCTCAT
1 GG-GGGTATCGGTTCCCTCAA
*
55409 GGGGGTATCGATTCCCTC
1 GGGGGTATCGGTTCCCTC
55427 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.15, C:0.24, G:0.34, T:0.27
Consensus pattern (20 bp):
GGGGGTATCGGTTCCCTCAA
Found at i:61060 original size:13 final size:13
Alignment explanation
Indices: 61042--61066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61032 TCGAATATAC
61042 TTAGAAAATCTTT
1 TTAGAAAATCTTT
61055 TTAGAAAATCTT
1 TTAGAAAATCTT
61067 AAAATTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:61264 original size:25 final size:25
Alignment explanation
Indices: 61227--61275 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
61217 TTTTTTTCGT
** *
61227 TCCAATCTTTTCTCCGTTTGTTATC
1 TCCAATCAATTCTCCATTTGTTATC
*
61252 TCCAATCAATTCTTCATTTGTTAT
1 TCCAATCAATTCTCCATTTGTTAT
61276 GAGATCACTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.51
Consensus pattern (25 bp):
TCCAATCAATTCTCCATTTGTTATC
Found at i:66667 original size:22 final size:22
Alignment explanation
Indices: 66642--66684 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
66632 ATGACTTGGT
66642 TATATATGTCATA-TGAAATATA
1 TATATATG-CATATTGAAATATA
66664 TATATATGCATATTGAAATAT
1 TATATATGCATATTGAAATAT
66685 CATGATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (22 bp):
TATATATGCATATTGAAATATA
Found at i:73260 original size:15 final size:15
Alignment explanation
Indices: 73242--73276 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
73232 CTTGGGTATT
73242 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
*
73257 GTAGTCTTTCGGGAC
1 GTAGTCCTTCGGGAC
73272 GTAGT
1 GTAGT
73277 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.20, G:0.34, T:0.31
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:73520 original size:20 final size:20
Alignment explanation
Indices: 73495--73535 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
73485 ATGACTTGGT
73495 TATATATGTCATA-TGAAATA
1 TATATATG-CATATTGAAATA
73515 TATATATGCATATTGAAATA
1 TATATATGCATATTGAAATA
73535 T
1 T
73536 CATGATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
TATATATGCATATTGAAATA
Found at i:74588 original size:13 final size:13
Alignment explanation
Indices: 74570--74595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
74560 CTTTCGCTAA
74570 ATTTGTATCCCAC
1 ATTTGTATCCCAC
74583 ATTTGTATCCCAC
1 ATTTGTATCCCAC
74596 CAATATGGTA
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:0.31, G:0.08, T:0.38
Consensus pattern (13 bp):
ATTTGTATCCCAC
Found at i:76276 original size:14 final size:14
Alignment explanation
Indices: 76246--76294 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
76236 GACCCTACCA
**
76246 AGTCAACTCACCCG
1 AGTCAACTCGTCCG
* *
76260 AGTTAACTCGTCTG
1 AGTCAACTCGTCCG
76274 AGTCAACTCGTCCG
1 AGTCAACTCGTCCG
76288 AGTCAAC
1 AGTCAAC
76295 CCGTTGACTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (14 bp):
AGTCAACTCGTCCG
Found at i:83378 original size:55 final size:55
Alignment explanation
Indices: 83295--83671 Score: 264
Period size: 55 Copynumber: 6.9 Consensus size: 55
83285 TATGCAGTAA
* *
83295 GTGTATGTGTATTTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATTTATTCAT
1 GTGTGTGTGTA-TTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATATTCAT
* *
83351 GTGTGTGTTTATTTTTTTATTATGCAGTAAGTATGTGTATTTAATATATATTCA-
1 GTGTGTGTGTATTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATATTCAT
* * ** * *
83405 -TGTGTGTG--CTTTTTTATTATGCAGTAAGTGTGTGTGTTTTTTTTATTATGCA-
1 GTGTGTGTGTATTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATA-TATTCAT
** * * *
83457 GTAAGTGTGTGTA-TTTAATATATATTCA-T--GTGTGTGCT-TTT-TTAT-TATGCAGT
1 GT--GTGTGTGTATTTTTTTAT-TATGCAGTAAGTGTGTG-TATTTAATATATATTCA-T
* *
83510 AAGTGTGTGTGTATTTTTTTATTATACAGTAAGAGTGTGTGTATTTAATATATATTTAT
1 --GTGTGTGTGTATTTTTTTATTATGCAGT-A-AGTGTGTGTATTTAATATATATTCAT
* * ** * * *
83569 GTGTTTATGCCTTTTTTTATTATGCAGTACGTGTGTGTGTTTAATAAATATGT-AT
1 GTGTGTGTGTATTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATAT-TCAT
* * * * * *
83624 GTGTGTGTG---CTTTTTATTTTGCAATACGTGTGTGTGTTTAATGTATAT
1 GTGTGTGTGTATTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATAT
83672 ATGAAATGTG
Statistics
Matches: 262, Mismatches: 37, Indels: 48
0.76 0.11 0.14
Matches are distributed among these distances:
51 37 0.14
52 39 0.15
53 25 0.10
54 17 0.06
55 79 0.30
56 18 0.07
57 29 0.11
58 10 0.04
59 4 0.02
60 4 0.02
ACGTcount: A:0.22, C:0.05, G:0.20, T:0.53
Consensus pattern (55 bp):
GTGTGTGTGTATTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATATTCAT
Found at i:83439 original size:30 final size:28
Alignment explanation
Indices: 83277--83551 Score: 150
Period size: 27 Copynumber: 10.0 Consensus size: 28
83267 ATATAAAAGA
* *
83277 TTTTTTATTATGCAGTAAGTGTATGTGTATT
1 TTTTTTATTATGCAGTAAG-G--TGTGTGTC
*
83308 TTTTTTATTATGCAGTAA-GTGTGTGTA
1 TTTTTTATTATGCAGTAAGGTGTGTGTC
** * * *
83335 TTTAATATTTATTCA-T--GTGTGTGTTTAT
1 TTTTTTA-TTATGCAGTAAG-GTGTGTGT-C
* *
83363 TTTTTTATTATGCAGTAA-GTATGTGTA
1 TTTTTTATTATGCAGTAAGGTGTGTGTC
** *
83390 TTTAATATATATTCA-T---GTGTGTG-C
1 TTTTTTAT-TATGCAGTAAGGTGTGTGTC
*
83414 TTTTTTATTATGCAGTAAGTGTGTGTGTT
1 TTTTTTATTATGCAGTAAG-GTGTGTGTC
*
83443 TTTTTTATTATGCAGTAA-GTGTGTGTA
1 TTTTTTATTATGCAGTAAGGTGTGTGTC
** *
83470 TTTAATATATATTCA-T---GTGTGTG-C
1 TTTTTTAT-TATGCAGTAAGGTGTGTGTC
*
83494 TTTTTTATTATGCAGTAAGTGTGTGTGTAT
1 TTTTTTATTATGCAGTAAG-GTGTGTGT-C
*
83524 TTTTTTATTATACAGTAAGAGTGTGTGT
1 TTTTTTATTATGCAGTAAG-GTGTGTGT
83552 ATTTAATATA
Statistics
Matches: 189, Mismatches: 33, Indels: 45
0.71 0.12 0.17
Matches are distributed among these distances:
23 10 0.05
24 14 0.07
25 13 0.07
27 47 0.25
28 42 0.22
29 19 0.10
30 26 0.14
31 18 0.10
ACGTcount: A:0.23, C:0.04, G:0.20, T:0.53
Consensus pattern (28 bp):
TTTTTTATTATGCAGTAAGGTGTGTGTC
Found at i:83454 original size:80 final size:81
Alignment explanation
Indices: 83351--83608 Score: 401
Period size: 80 Copynumber: 3.1 Consensus size: 81
83341 ATTTATTCAT
* *
83351 GTGTGTGTTTATTTTTTTATTATGCAGTAAGTATGTGTATTTAATATATATTCATGTGTGTGCTT
1 GTGTGTGTGTATTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATATTCATGTGTGTGCTT
83416 TTTTATTATGCAGTAA
66 TTTTATTATGCAGTAA
83432 GTGTGTGTGT-TTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATATTCATGTGTGTGCTT
1 GTGTGTGTGTATTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATATTCATGTGTGTGCTT
83496 TTTTATTATGCAGTAA
66 TTTTATTATGCAGTAA
* * *
83512 GTGTGTGTGTATTTTTTTATTATACAGTAAGAGTGTGTGTATTTAATATATATTTATGTGTTTAT
1 GTGTGTGTGTATTTTTTTATTATGCAGT-A-AGTGTGTGTATTTAATATATATTCATGTG--TGT
*
83577 GCCTTTTTTTATTATGCAGTAC
62 G-C-TTTTTTATTATGCAGTAA
83599 GTGTGTGTGT
1 GTGTGTGTGT
83609 TTAATAAATA
Statistics
Matches: 164, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
80 79 0.48
81 25 0.15
82 1 0.01
83 28 0.17
85 3 0.02
86 1 0.01
87 27 0.16
ACGTcount: A:0.22, C:0.05, G:0.21, T:0.53
Consensus pattern (81 bp):
GTGTGTGTGTATTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATATTCATGTGTGTGCTT
TTTTATTATGCAGTAA
Found at i:83489 original size:135 final size:132
Alignment explanation
Indices: 83277--83519 Score: 398
Period size: 135 Copynumber: 1.8 Consensus size: 132
83267 ATATAAAAGA
83277 TTTTTTATTATGCAGTAAGTGTATGTGTATTTTTTTTATTATGCAGTAAGTGTGTGTATTTAATA
1 TTTTTTATTATGCAGTAAGTG-ATGTGTATTTTTTTTATTATGCAGTAAGTGTGTGTATTTAATA
* *
83342 TTTATTCATGTGTGTGTTTATTTTTTTATTATGCAGTAAGTATGTGTATTTAATATATATTCATG
65 TATATTCATGTGTGTG----CTTTTTTATTATGCAGTAAGTATGTGTATTTAATATATATTCATG
83407 TGTGTGC
126 TGTGTGC
*
83414 TTTTTTATTATGCAGTAAGTG-TGTGTGTTTTTTTTATTATGCAGTAAGTGTGTGTATTTAATAT
1 TTTTTTATTATGCAGTAAGTGATGTGTATTTTTTTTATTATGCAGTAAGTGTGTGTATTTAATAT
*
83478 ATATTCATGTGTGTGCTTTTTTATTATGCAGTAAGTGTGTGT
66 ATATTCATGTGTGTGCTTTTTTATTATGCAGTAAGTATGTGT
83520 GTATTTTTTT
Statistics
Matches: 102, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
131 25 0.25
135 56 0.55
137 21 0.21
ACGTcount: A:0.22, C:0.05, G:0.20, T:0.53
Consensus pattern (132 bp):
TTTTTTATTATGCAGTAAGTGATGTGTATTTTTTTTATTATGCAGTAAGTGTGTGTATTTAATAT
ATATTCATGTGTGTGCTTTTTTATTATGCAGTAAGTATGTGTATTTAATATATATTCATGTGTGT
GC
Found at i:83547 original size:32 final size:30
Alignment explanation
Indices: 83405--83552 Score: 127
Period size: 30 Copynumber: 5.3 Consensus size: 30
83395 TATATATTCA
* *
83405 TGTGTGTGCTTTTTTATTATGCAGTAAGTG
1 TGTGTGTACTTTTTTATTATACAGTAAGTG
* *
83435 TGTGTGT-TTTTTTTATTATGCAGTAA--G
1 TGTGTGTACTTTTTTATTATACAGTAAGTG
* * * *
83462 TGTGTGTA----TTTAATATATATTCA-TG
1 TGTGTGTACTTTTTTATTATACAGTAAGTG
*
83487 TGTGTG--CTTTTTTATTATGCAGTAAGTG
1 TGTGTGTACTTTTTTATTATACAGTAAGTG
* *
83515 TGTGTGTATTTTTTTATTATACAGTAAGAG
1 TGTGTGTACTTTTTTATTATACAGTAAGTG
83545 TGTGTGTA
1 TGTGTGTA
83553 TTTAATATAT
Statistics
Matches: 95, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
24 10 0.11
25 7 0.07
27 18 0.19
28 8 0.08
29 18 0.19
30 34 0.36
ACGTcount: A:0.21, C:0.05, G:0.23, T:0.51
Consensus pattern (30 bp):
TGTGTGTACTTTTTTATTATACAGTAAGTG
Found at i:83629 original size:57 final size:52
Alignment explanation
Indices: 83523--83665 Score: 144
Period size: 52 Copynumber: 2.7 Consensus size: 52
83513 TGTGTGTGTA
* * * *
83523 TTTTTTTATTATACAGTAAGAGTGTGTGTATTTAATATATATTTATGTGTTTATGCC
1 TTTTTTTATTATGCAGT-A-CGTGTGTGTGTTTAATAAATATTTATGTG--TATG-C
* *
83580 TTTTTTTATTATGCAGTACGTGTGTGTGTTTAATAAATATGTATGTGTGTG-
1 TTTTTTTATTATGCAGTACGTGTGTGTGTTTAATAAATATTTATGTGTATGC
* * *
83631 TGCTTTTTATTTTGCAATACGTGTGTGTGTTTAAT
1 T-TTTTTTATTATGCAGTACGTGTGTGTGTTTAAT
83666 GTATATATGA
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
51 1 0.01
52 30 0.39
53 3 0.04
55 25 0.33
56 1 0.01
57 16 0.21
ACGTcount: A:0.22, C:0.06, G:0.20, T:0.52
Consensus pattern (52 bp):
TTTTTTTATTATGCAGTACGTGTGTGTGTTTAATAAATATTTATGTGTATGC
Found at i:83785 original size:51 final size:52
Alignment explanation
Indices: 83670--83785 Score: 166
Period size: 53 Copynumber: 2.2 Consensus size: 52
83660 TTTAATGTAT
* *
83670 ATATGAAATGTGTGTGTGACTTATTATAATATAAAGGGTATGTGCTCTTTTA
1 ATATGAAATGTGTGTGTGAATTATTATAATATAAAGGGTATGTGCTCTGTTA
*
83722 ATATGAAATGTGTGTGAGTGAATT-TTATAATATAAAGGGTGTGTG-T-TGTTA
1 ATATGAAATGTGTGT--GTGAATTATTATAATATAAAGGGTATGTGCTCTGTTA
83773 ATATGAAATGTGT
1 ATATGAAATGTGT
83786 TAGCTTTTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
51 17 0.29
52 16 0.27
53 20 0.34
54 6 0.10
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.41
Consensus pattern (52 bp):
ATATGAAATGTGTGTGTGAATTATTATAATATAAAGGGTATGTGCTCTGTTA
Found at i:85852 original size:14 final size:14
Alignment explanation
Indices: 85811--85860 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
85801 TTCATGGGGT
* *
85811 AAGAAGACAACATCT
1 AAGAAGA-AACGTCA
85826 AAGAAGAAAACGTCA
1 AAGAAG-AAACGTCA
85841 AAGAAGAAACGTCA
1 AAGAAGAAACGTCA
85855 AAGAAG
1 AAGAAG
85861 GAAAAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 14 0.44
15 17 0.53
16 1 0.03
ACGTcount: A:0.58, C:0.14, G:0.20, T:0.08
Consensus pattern (14 bp):
AAGAAGAAACGTCA
Found at i:85864 original size:15 final size:15
Alignment explanation
Indices: 85826--85864 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
85816 GACAACATCT
*
85826 AAGAAGAAAACGTCA
1 AAGAAGGAAACGTCA
85841 AAGAA-GAAACGTCA
1 AAGAAGGAAACGTCA
85855 AAGAAGGAAA
1 AAGAAGGAAA
85865 AAGAAAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.62, C:0.10, G:0.23, T:0.05
Consensus pattern (15 bp):
AAGAAGGAAACGTCA
Found at i:86907 original size:18 final size:18
Alignment explanation
Indices: 86884--86921 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
86874 ATTAAACTTT
86884 TTCTAACTTCTAATATGA
1 TTCTAACTTCTAATATGA
86902 TTCTAACTTCTAATATGA
1 TTCTAACTTCTAATATGA
86920 TT
1 TT
86922 TAGGCAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (18 bp):
TTCTAACTTCTAATATGA
Found at i:96201 original size:2 final size:2
Alignment explanation
Indices: 96196--96236 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
96186 TATTGTATGC
96196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
96237 ATTTACGACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:96429 original size:15 final size:15
Alignment explanation
Indices: 96409--96500 Score: 175
Period size: 15 Copynumber: 6.1 Consensus size: 15
96399 GACGCGTAAT
96409 GCGCGTCATAAATGC
1 GCGCGTCATAAATGC
96424 GCGCGTCATAAATGC
1 GCGCGTCATAAATGC
96439 GCGCGTCATAAATGC
1 GCGCGTCATAAATGC
96454 GCGCGTCATAAATGC
1 GCGCGTCATAAATGC
*
96469 GCGCTTCATAAATGC
1 GCGCGTCATAAATGC
96484 GCGCGTCATAAATGC
1 GCGCGTCATAAATGC
96499 GC
1 GC
96501 ATCTTAGATT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 75 1.00
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.21
Consensus pattern (15 bp):
GCGCGTCATAAATGC
Found at i:101670 original size:26 final size:26
Alignment explanation
Indices: 101634--101686 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
101624 TCAGGTTCGA
101634 GCACCAGGAATGTCAGGGGTGTGAGT
1 GCACCAGGAATGTCAGGGGTGTGAGT
*
101660 GCACTAGGAATGTCAGGGGTGTGAGT
1 GCACCAGGAATGTCAGGGGTGTGAGT
101686 G
1 G
101687 TTCAATGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.13, G:0.43, T:0.21
Consensus pattern (26 bp):
GCACCAGGAATGTCAGGGGTGTGAGT
Found at i:103922 original size:15 final size:15
Alignment explanation
Indices: 103898--103929 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
103888 TGGCAGATCC
*
103898 AAATCTAGAACGGGA
1 AAATCCAGAACGGGA
103913 AAATCCAGAACGGGA
1 AAATCCAGAACGGGA
103928 AA
1 AA
103930 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.16, G:0.25, T:0.09
Consensus pattern (15 bp):
AAATCCAGAACGGGA
Found at i:112797 original size:2 final size:2
Alignment explanation
Indices: 112790--112819 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
112780 ATTAAGACAT
112790 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
112820 ACGTACGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:113624 original size:127 final size:131
Alignment explanation
Indices: 113385--113655 Score: 331
Period size: 131 Copynumber: 2.1 Consensus size: 131
113375 ATAAAAACTA
*
113385 ATATATATATATATATGATTTTTAAATAGGGTATTTATTTATTTAAAAATATCAAAAAAGAACAT
1 ATATATATATATATATGATTTTTAAATAAGGTATTTATTTATTTAAAAATATCAAAAAAGAACAT
* * *
113450 CAAGTTACTTTAAGACAGTTCCTTTCTTCAATATTAAAAAATGAATAAATATTAATATATATATA
66 CAAGTTAATTTAAGACAGATCCTTTCTTCAATATTAAAAAATAAATAAATATTAATATATATATA
113515 T
131 T
* * * * * * *
113516 ATATATATATATTTTTGTTTTTTAAGTAAGGTATTTATTTATTTTAAAATATCGGAATAAG-AC-
1 ATATATATATATATATGATTTTTAAATAAGGTATTTATTTATTTAAAAATATC-AAAAAAGAACA
* * *
113579 TCTAGTTAATTTAAGACAGAT-CTTT-TT-AATATTTAAAAATAAATAAATATT-ATTTA-ATCA
65 TCAAGTTAATTTAAGACAGATCCTTTCTTCAATATTAAAAAATAAATAAATATTAATATATAT-A
*
113639 AAT
129 TAT
*
113642 ATATATATTTATAT
1 ATATATATATATAT
113656 GACTAAAATG
Statistics
Matches: 121, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
125 2 0.02
126 19 0.16
127 22 0.18
128 2 0.02
129 4 0.03
130 18 0.15
131 49 0.40
132 5 0.04
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (131 bp):
ATATATATATATATATGATTTTTAAATAAGGTATTTATTTATTTAAAAATATCAAAAAAGAACAT
CAAGTTAATTTAAGACAGATCCTTTCTTCAATATTAAAAAATAAATAAATATTAATATATATATA
T
Found at i:113807 original size:21 final size:20
Alignment explanation
Indices: 113775--113819 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
113765 CTGAAACAAA
113775 TAAAATTAAAATA-ATAAGAT
1 TAAAATTAAAATATATAA-AT
113795 TAAAATGTAAAATATATAAAT
1 TAAAAT-TAAAATATATAAAT
113816 TAAA
1 TAAA
113820 GGCCTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
TAAAATTAAAATATATAAAT
Found at i:115317 original size:137 final size:137
Alignment explanation
Indices: 115064--115366 Score: 412
Period size: 137 Copynumber: 2.2 Consensus size: 137
115054 CAACTGGTGT
* **
115064 ATGACATTGTTCCTTCGTGATGAGGACATCTAACCATCTTTGAAGATATTTGAGATAACATGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTAACCATCTTTAAAGATATTTGAGATAACACAGTT
* * *
115129 CTTTCGTGATGAGGACGTCTGGTTATCTGAGGATTACTCGACTCCTACGTGATGAGGAGTTCT-A
66 CTTTCGTGATGAGGACATCTGGTTATCTAAGGATGACTCGACTCCTACGTGATGAGGAGTTCTGA
*
115193 GTCAGTGG
131 -TCAGTAG
* **
115201 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGTCATCTTTAAAGATATTTGAGATAACACAGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTAACCATCTTTAAAGATATTTGAGATAACACAGTT
* * * * * *
115266 TTTTTGTGATGAGGACATCTGGTTATCTAAGGATGATGTTGA-TTCTTCGTGATGAGGAGTTCTG
66 CTTTCGTGATGAGGACATCTGGTTATCTAAGGATGA-CTCGACTCCTACGTGATGAGGAGTTCTG
*
115330 ATCGGTAG
130 ATCAGTAG
*
115338 ATGACATTGTTCCTTCGTGATAAGGACAT
1 ATGACATTGTTCCTTCGTGATGAGGACAT
115367 GGCTATCTAA
Statistics
Matches: 145, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
137 141 0.97
138 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (137 bp):
ATGACATTGTTCCTTCGTGATGAGGACATCTAACCATCTTTAAAGATATTTGAGATAACACAGTT
CTTTCGTGATGAGGACATCTGGTTATCTAAGGATGACTCGACTCCTACGTGATGAGGAGTTCTGA
TCAGTAG
Found at i:118464 original size:27 final size:27
Alignment explanation
Indices: 118433--118495 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
118423 AAAATCATCT
*
118433 TTTAAAAGAGTTTTTAAGAAAATACTA
1 TTTAAAAGAGTTTTTAAGAAAACACTA
*
118460 TTTAAAAGTGTTTTTAAGAAAACACTA
1 TTTAAAAGAGTTTTTAAGAAAACACTA
118487 TTTAAAAGA
1 TTTAAAAGA
118496 TAAATCGGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.37
Consensus pattern (27 bp):
TTTAAAAGAGTTTTTAAGAAAACACTA
Found at i:118748 original size:2 final size:2
Alignment explanation
Indices: 118743--118773 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
118733 TATAAAACTA
118743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
118774 GGATTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:118950 original size:2 final size:2
Alignment explanation
Indices: 118909--118937 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
118899 TAAAACACTA
118909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
118938 ATTTTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:119208 original size:21 final size:20
Alignment explanation
Indices: 119176--119220 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
119166 CTGAAACAAA
119176 TAAAATTAAAATA-ATAAGAT
1 TAAAATTAAAATATATAA-AT
119196 TAAAATGTAAAATATATAAAT
1 TAAAAT-TAAAATATATAAAT
119217 TAAA
1 TAAA
119221 GGCCTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
TAAAATTAAAATATATAAAT
Found at i:120142 original size:31 final size:32
Alignment explanation
Indices: 120104--120170 Score: 127
Period size: 31 Copynumber: 2.1 Consensus size: 32
120094 AAGAGGTGTA
120104 CGGCTCTCCTGCGGCTTCTGGAGTCTT-TGTG
1 CGGCTCTCCTGCGGCTTCTGGAGTCTTCTGTG
120135 CGGCTCTCCTGCGGCTTCTGGAGTCTTCTGTG
1 CGGCTCTCCTGCGGCTTCTGGAGTCTTCTGTG
120167 CGGC
1 CGGC
120171 GGTGACGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 27 0.77
32 8 0.23
ACGTcount: A:0.03, C:0.31, G:0.33, T:0.33
Consensus pattern (32 bp):
CGGCTCTCCTGCGGCTTCTGGAGTCTTCTGTG
Done.