Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000995.1 Hibiscus syriacus cultivar Beakdansim tig00001992_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: 55952
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5679 original size:22 final size:23
Alignment explanation
Indices: 5653--5697 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
5643 CTCAAACTTT
*
5653 ATATTTATATAT-ATTTTTTAAA
1 ATATTTAAATATAATTTTTTAAA
5675 ATATTTAAATATAATTTTTTAAA
1 ATATTTAAATATAATTTTTTAAA
5698 CATAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATTTAAATATAATTTTTTAAA
Found at i:6118 original size:2 final size:2
Alignment explanation
Indices: 6111--6164 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
6101 TCTAGATTTT
* * *
6111 TA TA TA TA TA TA TA TA TA TA TA -A TT TGA -A TA TT TA -A AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
6151 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
6165 ATTTTTTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6190 original size:36 final size:36
Alignment explanation
Indices: 6112--6179 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
6102 CTAGATTTTT
*
6112 ATATATATATATATATATATAATTTGAATATTTAAA
1 ATATATATATATATATATATAATTTGAAAATTTAAA
**
6148 ATATATATATATATATA-ATTTTTTGAAAATTT
1 ATATATATATATATATATATAATTTGAAAATTT
6180 TGAAAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 12 0.41
36 17 0.59
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (36 bp):
ATATATATATATATATATATAATTTGAAAATTTAAA
Found at i:6195 original size:26 final size:28
Alignment explanation
Indices: 6160--6218 Score: 86
Period size: 26 Copynumber: 2.1 Consensus size: 28
6150 ATATATATAT
*
6160 ATATAATTTTTTGAAAA-TTTTGAAAA-
1 ATATAATTTTTAGAAAAGTTTTGAAAAC
6186 ATATAATTTTTAGAAAATGTTTTGAAAAC
1 ATATAATTTTTAGAAAA-GTTTTGAAAAC
6215 ATAT
1 ATAT
6219 TTTTTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 16 0.55
28 9 0.31
29 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (28 bp):
ATATAATTTTTAGAAAAGTTTTGAAAAC
Found at i:6278 original size:46 final size:44
Alignment explanation
Indices: 6227--6362 Score: 178
Period size: 39 Copynumber: 3.2 Consensus size: 44
6217 ATTTTTTTTT
6227 TATATATATATTATAGTTTTGAAAATGATTTTG-AAAA-A-ATA
1 TATATATATATTATAGTTTTGAAAATGATTTTGAAAAATATATA
*
6268 TATATA-ATA-TATAGTTTTGAAAA-CATTTTGAATATATATATATA
1 TATATATATATTATAGTTTTGAAAATGATTTTGAA-A-A-ATATATA
6312 TATATATATATTATAGTTTTGAAAATGATTTTTGAAAAATATATA
1 TATATATATATTATAGTTTTGAAAATGA-TTTTGAAAAATATATA
6357 T-TATAT
1 TATATAT
6363 GATTTTTGAA
Statistics
Matches: 83, Mismatches: 2, Indels: 17
0.81 0.02 0.17
Matches are distributed among these distances:
38 6 0.07
39 15 0.18
40 4 0.05
41 7 0.08
42 1 0.01
43 1 0.01
44 14 0.17
45 11 0.13
46 15 0.18
47 2 0.02
48 7 0.08
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (44 bp):
TATATATATATTATAGTTTTGAAAATGATTTTGAAAAATATATA
Found at i:6320 original size:48 final size:46
Alignment explanation
Indices: 6226--6362 Score: 166
Period size: 46 Copynumber: 3.1 Consensus size: 46
6216 TATTTTTTTT
*
6226 TTATATATATATTATAGTTTTGAAAATGA-TTTTG-AAAA-A-ATA
1 TTATATATATATTATAGTTTTGAAAATCATTTTTGAAAAATATATA
*
6268 -TATATA-ATA-TATAGTTTTGAAAA-CA-TTTTGAATATATATATA
1 TTATATATATATTATAGTTTTGAAAATCATTTTTGAA-AAATATATA
*
6310 TATATATATATATTATAGTTTTGAAAATGATTTTTGAAAAATATATA
1 T-TATATATATATTATAGTTTTGAAAATCATTTTTGAAAAATATATA
6357 TTATAT
1 TTATAT
6363 GATTTTTGAA
Statistics
Matches: 81, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
38 6 0.07
39 15 0.19
40 5 0.06
41 7 0.09
42 3 0.04
44 6 0.07
45 3 0.04
46 19 0.23
47 10 0.12
48 7 0.09
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.47
Consensus pattern (46 bp):
TTATATATATATTATAGTTTTGAAAATCATTTTTGAAAAATATATA
Found at i:6331 original size:85 final size:81
Alignment explanation
Indices: 6227--6406 Score: 249
Period size: 85 Copynumber: 2.2 Consensus size: 81
6217 ATTTTTTTTT
6227 TATATATATATTATAGTTTTGAAAATGA-TTTTGAAAAAATATATATAATATAT-AGTTTTGAAA
1 TATATATATATTATAGTTTTGAAAATGATTTTTG-AAAAATATATAT--TATATGAGTTTTG-AA
6290 ACATTTTGAATATATATATATA
62 ACATTTTGAA-ATATATATA-A
* *
6312 TATATATATATTATAGTTTTGAAAATGATTTTTGAAAAATATATATTATATGATTTTTGAAATAT
1 TATATATATATTATAGTTTTGAAAATGATTTTTGAAAAATATATATTATATGAGTTTTGAAACAT
*
6377 TTTTAAATATATATAA
66 TTTGAAATATATATAA
6393 TATAT-TATTATTAT
1 TATATATA-TATTAT
6407 TATATTTATT
Statistics
Matches: 89, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
80 2 0.02
81 12 0.13
82 9 0.10
83 15 0.17
84 6 0.07
85 40 0.45
86 5 0.06
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (81 bp):
TATATATATATTATAGTTTTGAAAATGATTTTTGAAAAATATATATTATATGAGTTTTGAAACAT
TTTGAAATATATATAA
Found at i:6354 original size:35 final size:34
Alignment explanation
Indices: 6315--6397 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 34
6305 ATATATATAT
6315 ATATATATTATA-G-TTTTGAAAATGATTTTTGAAAA
1 ATATATATTATATGATTTTG-AAAT-ATTTTT-AAAA
*
6350 ATATATATTATATGATTTTTGAAATATTTTTAAAT
1 ATATATATTATATGA-TTTTGAAATATTTTTAAAA
*
6385 ATATATAATATAT
1 ATATATATTATAT
6398 TATTATTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 27 0.63
36 7 0.16
37 4 0.09
38 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.49
Consensus pattern (34 bp):
ATATATATTATATGATTTTGAAATATTTTTAAAA
Found at i:6456 original size:17 final size:18
Alignment explanation
Indices: 6397--6456 Score: 79
Period size: 17 Copynumber: 3.4 Consensus size: 18
6387 ATATAATATA
*
6397 TTATTATTATTATATTTAT
1 TTATT-TTATTATATTTTT
*
6416 TTA-TTTATTATATGTTT
1 TTATTTTATTATATTTTT
6433 TTATTTTATTA-ATTTTT
1 TTATTTTATTATATTTTT
6450 TTATTTT
1 TTATTTT
6457 CTTTTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 26 0.70
18 8 0.22
19 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTATTTTATTATATTTTT
Found at i:7536 original size:10 final size:10
Alignment explanation
Indices: 7521--7550 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
7511 AATCCATCAA
7521 TTTCAATTTG
1 TTTCAATTTG
7531 TTTCAATTTG
1 TTTCAATTTG
7541 TTTCAATTTG
1 TTTCAATTTG
7551 ATCCTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (10 bp):
TTTCAATTTG
Found at i:7638 original size:48 final size:50
Alignment explanation
Indices: 7559--7664 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 50
7549 TGATCCTTTA
7559 TATTTTTAGCTATTCATTTTTTCTTTCTAA-TTAG-AT-TTTTTATATTAT
1 TATTTTTAGCTATTCATTTTTTCTTTCTAATTTAGTATGTTTTT-TATTAT
* *
7607 TATTTTTAGTTATTC-TTTTTTCCCTTT-TAATTTTAGTATGTTTTTTATTTT
1 TATTTTTAGCTATTCATTTTTT--CTTTCTAA-TTTAGTATGTTTTTTATTAT
7658 TATTTTT
1 TATTTTT
7665 TTCTAATTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
47 6 0.12
48 17 0.34
49 4 0.08
50 4 0.08
51 14 0.28
52 5 0.10
ACGTcount: A:0.19, C:0.08, G:0.05, T:0.69
Consensus pattern (50 bp):
TATTTTTAGCTATTCATTTTTTCTTTCTAATTTAGTATGTTTTTTATTAT
Found at i:7666 original size:14 final size:14
Alignment explanation
Indices: 7647--7720 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 14
7637 TTTTAGTATG
7647 TTTTTTATTTTTATT
1 TTTTTTATTTTTA-T
*
7662 TTTTTCTAATTATTAT
1 TTTTT-T-ATTTTTAT
* *
7678 TTGTTTATTTGTTTT
1 TTTTTTATTT-TTAT
7693 TTTTATTATTTTTAT
1 TTTT-TTATTTTTAT
*
7708 TTTATTACTTTTT
1 TTTTTTA-TTTTT
7721 TTAAATTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.13
15 23 0.49
16 12 0.26
17 6 0.13
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTTTTATTTTTAT
Found at i:7708 original size:30 final size:31
Alignment explanation
Indices: 7650--7709 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
7640 TAGTATGTTT
* *
7650 TTTATTTTTATTTTTTTCTAATTATTATTTG
1 TTTATTTGTATTTTTTTATAATTATTATTTG
* *
7681 TTTATTTGT-TTTTTTTATTATTTTTATTT
1 TTTATTTGTATTTTTTTATAATTATTATTT
7710 TATTACTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (31 bp):
TTTATTTGTATTTTTTTATAATTATTATTTG
Found at i:7711 original size:27 final size:26
Alignment explanation
Indices: 7648--7724 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 26
7638 TTTAGTATGT
*
7648 TTTTTATTTT-TATTTTTTTCTAATTA
1 TTTTTATTTTAT-TTTTTTTTTAATTA
* *
7674 TTATTT-GTTTATTTGTTTTTTTTATTA
1 TT-TTTATTTTATTT-TTTTTTTAATTA
*
7701 TTTTTATTTTATTACTTTTTTTAA
1 TTTTTATTTTATT-TTTTTTTTAA
7725 ATTTAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
26 10 0.25
27 30 0.75
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (26 bp):
TTTTTATTTTATTTTTTTTTTAATTA
Found at i:13348 original size:23 final size:21
Alignment explanation
Indices: 13295--13373 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 21
13285 TCGAAATAGA
* *
13295 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTGCAGGG
* *
13315 GTGCATCGATGCACTAG-TGGTAG
1 GTGCATGGATGCACT-GCAGG--G
13338 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
13359 GTGCATGGATGCACT
1 GTGCATGGATGCACT
13374 TTGACACCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
20 14 0.29
21 16 0.33
22 1 0.02
23 17 0.35
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:13618 original size:21 final size:21
Alignment explanation
Indices: 13594--13633 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13584 ATGTTTAATG
13594 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
13615 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
13634 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:14768 original size:19 final size:20
Alignment explanation
Indices: 14738--14775 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
14728 CAAAATTTCA
14738 TTTTGATTTTCAAAATCAAC
1 TTTTGATTTTCAAAATCAAC
14758 TTTTG-TTTTCAAAATCAA
1 TTTTGATTTTCAAAATCAA
14776 ATTATCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTGATTTTCAAAATCAAC
Found at i:16787 original size:21 final size:21
Alignment explanation
Indices: 16757--16814 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
16747 ACTAGTGGCA
16757 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
**
16778 GGTGTGTGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
16799 GGTGCATGGATGCACT
1 GGTGCATGGATGCACT
16815 TTGACACCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:19239 original size:85 final size:86
Alignment explanation
Indices: 19085--19242 Score: 205
Period size: 85 Copynumber: 1.8 Consensus size: 86
19075 TACAGTATAG
* * *
19085 CTCAAGGCGAGAAAGGGCTATCTGTCAACCAAAACCTTTGAGTTCGATTATATTCAGCTCAAGGG
1 CTCAAGGCGAGAAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTATATTCAACTCAAGGA
19150 CATATCAAATTTACAACATAA
66 CATATCAAATTTACAACATAA
* * ** *
19171 CTCAAGGCGAG-AAGGGTTATCTGTCAA-CACAAA-CTATCGAGTTCGATTCTATTCAACTTGAT
1 CTCAAGGCGAGAAAGGGCTATCTGTCAACCA-AAACCT-TCGAGTTCGATTATATTCAACTCAAG
19233 GACATATCAA
64 GACATATCAA
19243 CCGCATGGTA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
84 4 0.06
85 47 0.76
86 11 0.18
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (86 bp):
CTCAAGGCGAGAAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTATATTCAACTCAAGGA
CATATCAAATTTACAACATAA
Found at i:21706 original size:44 final size:43
Alignment explanation
Indices: 21650--21793 Score: 150
Period size: 44 Copynumber: 3.3 Consensus size: 43
21640 TTACTTTTAA
* *
21650 TATTTAACATTTTTTATTTTTTTATTTTGTTTTTCCCTTTAATT
1 TATTTAATATTTTTTATTTTTTT-TTTTATTTTTCCCTTTAATT
* **
21694 TATTTAATATTTTTTATTTTTATTTTTATTTTT---TTTCTTT
1 TATTTAATATTTTTTATTTTTTTTTTTATTTTTCCCTTTAATT
* *
21734 TCCTTTAATATTTTTTATTTTTATTTTTTAAAATTTTTCCCTTTGATT
1 T-ATTTAATATTTTTTATTTTT-TTTTTT---ATTTTTCCCTTTAATT
21782 TATTTAATATTT
1 TATTTAATATTT
21794 ATTTCTTATT
Statistics
Matches: 82, Mismatches: 10, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
40 6 0.07
41 19 0.23
42 5 0.06
43 9 0.11
44 21 0.26
45 6 0.07
47 10 0.12
48 6 0.07
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.72
Consensus pattern (43 bp):
TATTTAATATTTTTTATTTTTTTTTTTATTTTTCCCTTTAATT
Found at i:21717 original size:20 final size:20
Alignment explanation
Indices: 21692--21759 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
21682 TTCCCTTTAA
21692 TTTATTTAATATTTTTTATT
1 TTTATTTAATATTTTTTATT
* *
21712 TTTATTT-TTATTTTTTTTCT
1 TTTATTTAATATTTTTTAT-T
*
21732 TTTCCTTTAATATTTTTTATT
1 TTT-ATTTAATATTTTTTATT
21753 TTTATTT
1 TTTATTT
21760 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 9 0.23
20 14 0.36
21 7 0.18
22 9 0.23
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTATTTAATATTTTTTATT
Found at i:21891 original size:13 final size:13
Alignment explanation
Indices: 21873--21902 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
21863 TGAATCGAGT
21873 TTTTAAATTTTAA
1 TTTTAAATTTTAA
21886 TTTTAAATTTTAA
1 TTTTAAATTTTAA
21899 TTTT
1 TTTT
21903 CTCAATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:23235 original size:19 final size:18
Alignment explanation
Indices: 23200--23245 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
23190 GTGTTTGTTA
*
23200 TGATTATATGTGCTATAT
1 TGATTATATGTACTATAT
*
23218 GTGATTATATGTATTATAT
1 -TGATTATATGTACTATAT
*
23237 TAATTATAT
1 TGATTATAT
23246 ATGTATGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (18 bp):
TGATTATATGTACTATAT
Found at i:23786 original size:23 final size:23
Alignment explanation
Indices: 23718--23786 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
23708 ACATTTTATT
*
23718 TGGCACTTCGGTGCATTTCTACA
1 TGGCACTTCGGTGCATTTCTACG
* * *
23741 CGGCACTTAGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
23764 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
23787 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:24154 original size:3 final size:3
Alignment explanation
Indices: 24146--24170 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
24136 GATATACATG
24146 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
24171 GAATTAGGAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:35003 original size:25 final size:24
Alignment explanation
Indices: 34975--35022 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
34965 TCCTTTTAAT
*
34975 TTATCCAATATTTGTTTACTATTTG
1 TTATCCAACATTTGTTTAC-ATTTG
* *
35000 TTATCTAACATTTTTTTACATTT
1 TTATCCAACATTTGTTTACATTT
35023 TTTAGAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.58
Consensus pattern (24 bp):
TTATCCAACATTTGTTTACATTTG
Found at i:37867 original size:22 final size:22
Alignment explanation
Indices: 37825--37907 Score: 97
Period size: 22 Copynumber: 3.9 Consensus size: 22
37815 TTTTACTTAA
37825 ATTATTATTAAAATTATTATTATT
1 ATTATTATT-AAA-TATTATTATT
37849 ATTATTATTAAATATTATTATT
1 ATTATTATTAAATATTATTATT
37871 A-TATTA-T--ATA-TATTA-T
1 ATTATTATTAAATATTATTATT
37887 ATTATTATTAAATAATTATTA
1 ATTATTATTAAAT-ATTATTA
37908 CAAGCCCAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.04
17 10 0.19
18 4 0.08
20 3 0.06
21 6 0.11
22 16 0.30
23 3 0.06
24 9 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTATTATTAAATATTATTATT
Found at i:37907 original size:3 final size:3
Alignment explanation
Indices: 37825--37896 Score: 78
Period size: 3 Copynumber: 24.3 Consensus size: 3
37815 TTTTACTTAA
** *
37825 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
37871 A-T ATT A-T ATAT ATT A-T ATT ATT ATT A
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT A
37897 AATAATTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 6 0.10
3 47 0.81
4 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:39209 original size:2 final size:2
Alignment explanation
Indices: 39190--39223 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
39180 TATATCAGTC
* *
39190 AT AT AA AT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39224 CTTTTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:39355 original size:31 final size:33
Alignment explanation
Indices: 39320--39382 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
39310 ATAATTAAAC
39320 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
39351 ATTATTAAAATTTTAATATTTATTTTTATTTA
1 ATTATAAAAATTATAATATTTAGTTTTATTTA
39383 TTAATATCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 12 0.44
32 1 0.04
33 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:39432 original size:132 final size:131
Alignment explanation
Indices: 39296--39583 Score: 296
Period size: 134 Copynumber: 2.2 Consensus size: 131
39286 GGATGTCCTA
* * * * **
39296 TTCTGGTATTTTAAATAATTAAACAT-TATAAAAATTATAATTTAGTTTT-ATTTAAATTATTAA
1 TTCTGGTATTTTAAATAAATAAACATCT-TAAAAATTA-AAATAAATTTTCA-TTAAATTAAGAA
*
39359 AA-TTTTAAT-ATTTATTTTTATTTATTAATATCGAAGAAAAGAGCTGTCTTAAGGTACCTAGAA
63 AAGTTTTAATCATTTA--TTTATTTATTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAA
*
39422 GCCCTT
126 GCCATT
* * ** * **
39428 TTCTGGTATTTTTTGAATAAATAAATATCTTCTATATTAAAATAAATTTTCATTATCTTAAGAAA
1 TTCTGGTA--TTTTAAATAAATAAACATCTTAAAAATTAAAATAAATTTTCATTAAATTAAGAAA
* * *
39493 ATGTTTTAGTCATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGT
64 A-GTTTTAATCATTTATTTATTTATTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGC
39558 CATT
128 CATT
* *
39562 TTCTGATATTCTAAATAAATAA
1 TTCTGGTATTTTAAATAAATAA
39584 TTTTTTTATA
Statistics
Matches: 128, Mismatches: 21, Indels: 14
0.79 0.13 0.09
Matches are distributed among these distances:
132 20 0.16
133 18 0.14
134 78 0.61
135 7 0.05
136 5 0.04
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.44
Consensus pattern (131 bp):
TTCTGGTATTTTAAATAAATAAACATCTTAAAAATTAAAATAAATTTTCATTAAATTAAGAAAAG
TTTTAATCATTTATTTATTTATTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCCAT
T
Found at i:39603 original size:27 final size:28
Alignment explanation
Indices: 39567--39623 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
39557 TCATTTTCTG
*
39567 ATATTCTAAATAAATA-ATTTTTTTATAA
1 ATATTCTAAATAAATATATTTTCTTA-AA
*
39595 ATATT-TAAATTAATATATTTTCTTAAA
1 ATATTCTAAATAAATATATTTTCTTAAA
39622 AT
1 AT
39624 TATAGTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (28 bp):
ATATTCTAAATAAATATATTTTCTTAAA
Found at i:44742 original size:2 final size:2
Alignment explanation
Indices: 44735--44773 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
44725 TATCCTTTAA
44735 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44774 CATTTGTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:45111 original size:23 final size:23
Alignment explanation
Indices: 45067--45118 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
45057 CTCATCCAGC
* * *
45067 AAAGAAAGAAGAAGAAGAAAAAA
1 AAAGAAAAAACAAAAAGAAAAAA
*
45090 AAAGAAAAAACAAAAAGGAAAAA
1 AAAGAAAAAACAAAAAGAAAAAA
45113 AAAGAA
1 AAAGAA
45119 GGAAAATTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAACAAAAAGAAAAAA
Found at i:45120 original size:13 final size:13
Alignment explanation
Indices: 45078--45124 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
45068 AAGAAAGAAG
*
45078 AAGAAGAAAAAAA
1 AAGAAGGAAAAAA
*
45091 AAGAA--AAAACA
1 AAGAAGGAAAAAA
45102 AA-AAGGAAAAAA
1 AAGAAGGAAAAAA
45114 AAGAAGGAAAA
1 AAGAAGGAAAA
45125 TTGAATCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 2 0.07
11 7 0.24
12 7 0.24
13 13 0.45
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (13 bp):
AAGAAGGAAAAAA
Found at i:45782 original size:30 final size:32
Alignment explanation
Indices: 45729--45788 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
45719 GTCATACACA
*
45729 AGAAGTATCTCTACCAGATGAGCATAACAACG
1 AGAAGTATCTCTACCAGATGAGCAAAACAACG
45761 AGAAGTATCTCTA-CA-ATGAGCAAAACAA
1 AGAAGTATCTCTACCAGATGAGCAAAACAA
45789 TCATTTCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 12 0.44
31 2 0.07
32 13 0.48
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (32 bp):
AGAAGTATCTCTACCAGATGAGCAAAACAACG
Found at i:47634 original size:114 final size:112
Alignment explanation
Indices: 47417--47634 Score: 346
Period size: 114 Copynumber: 1.9 Consensus size: 112
47407 CACGTTCTCG
*
47417 TAGTAGAAAAAAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGG
1 TAGTAGAAAAAAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGG
* * *
47482 TATGAATCCCAAAACCAATCATTGGATTTGAAAAATGAATTTGCTCA
66 TAGGAACCCCAAAACCAATCATTGGATTAGAAAAATGAATTTGCTCA
*
47529 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAA-AA-AAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * *
47594 GGTAGGAACCCCAGAACCAATCATTGGATTAGGAAGATGAA
64 GGTAGGAACCCCAAAACCAATCATTGGATTAGAAAAATGAA
47635 CTGCATGATC
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
112 9 0.09
113 2 0.02
114 85 0.89
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (112 bp):
TAGTAGAAAAAAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGG
TAGGAACCCCAAAACCAATCATTGGATTAGAAAAATGAATTTGCTCA
Found at i:51038 original size:76 final size:76
Alignment explanation
Indices: 50939--51870 Score: 1679
Period size: 76 Copynumber: 12.4 Consensus size: 76
50929 CTATTTCCCA
*
50939 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
51004 AACCTTAGGGT
66 AACCTTAGGGT
*
51015 CATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
51080 AACCTTAGGGT
66 AACCTTAGGGT
* *
51091 CATTTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTGTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
51156 AACCTTAGGGT
66 AACCTTAGGGT
51167 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
51232 AACCTTAGGGT
66 AACCTTAGGGT
* * *
51243 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGC-TTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
51307 AACCCTAGGGT
66 AACCTTAGGGT
51318 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
51383 AACCTTAGGGT
66 AACCTTAGGGT
51394 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
51459 AAACCTTAGGGT
65 AAACCTTAGGGT
51471 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
51536 AACCTTAGGGT
66 AACCTTAGGGT
51547 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
51612 AACCTTAGGGT
66 AACCTTAGGGT
51623 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
51688 AACCTTAGGGT
66 AACCTTAGGGT
* *
51699 CATTTGTAAGTTCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
51764 AACCTTAGGGT
66 AACCTTAGGGT
51775 CATCTGTAAGT-C--C--TGCATGATG-TTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
51833 AGCCTTAGGGT
66 AACCTTAGGGT
51844 --TCTGTAAGTCCTGCAG-GCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
51871 TTAAGACCTC
Statistics
Matches: 829, Mismatches: 19, Indels: 20
0.96 0.02 0.02
Matches are distributed among these distances:
67 9 0.01
68 1 0.00
69 16 0.02
70 31 0.04
71 17 0.02
72 2 0.00
73 1 0.00
75 72 0.09
76 604 0.73
77 76 0.09
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGGGT
Found at i:52049 original size:22 final size:21
Alignment explanation
Indices: 52021--52088 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 21
52011 TTTTACTTAA
52021 ATTATTATTATTACTATTAAAT
1 ATTATTATTATTACTA-TAAAT
* *
52043 ATTATTATTA-TATTATATAT
1 ATTATTATTATTACTATAAAT
52063 ATTA-TATTATTA-T-TAAAT
1 ATTATTATTATTACTATAAAT
52081 AATTATTA
1 -ATTATTA
52089 CAAACCCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 4 0.10
19 10 0.25
20 12 0.30
21 4 0.10
22 10 0.25
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATTATTATTACTATAAAT
Found at i:52088 original size:3 final size:3
Alignment explanation
Indices: 52021--52077 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
52011 TTTTACTTAA
* *
52021 ATT ATT ATT ATT ACT ATT AAAT ATT ATT ATT A-T ATT A-T ATAT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT AT-T ATT
52066 A-T ATT ATT ATT A
1 ATT ATT ATT ATT A
52078 AATAATTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
2 6 0.13
3 34 0.76
4 5 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Done.