Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004331.1 Hibiscus syriacus cultivar Beakdansim tig00009498_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: 66013
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1485 original size:21 final size:20
Alignment explanation
Indices: 1446--1517 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 20
1436 GGTGGGAGGG
*
1446 TGAACAATGAGAGGGCCTCT
1 TGAACGATGAGAGGGCCTCT
1466 TGAACGATGAGAGTGGCCTCT
1 TGAACGATGAGAG-GGCCTCT
*
1487 TAAACGAT-AGGAGGAGCCTCT
1 TGAACGATGA-GAGG-GCCTCT
1508 TGAACGATGA
1 TGAACGATGA
1518 CAGGTAATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.31
21 30 0.67
22 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.21
Consensus pattern (20 bp):
TGAACGATGAGAGGGCCTCT
Found at i:3613 original size:20 final size:20
Alignment explanation
Indices: 3590--3628 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3580 TTGAAACTTA
3590 AATTCGCAACACGAAAATGT
1 AATTCGCAACACGAAAATGT
*
3610 AATTCGCAACGCGAAAATG
1 AATTCGCAACACGAAAATG
3629 AAAATCGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
AATTCGCAACACGAAAATGT
Found at i:3636 original size:20 final size:20
Alignment explanation
Indices: 3593--3636 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3583 AAACTTAAAT
* *
3593 TCGCAACACGAAAATGTAAT
1 TCGCAACACGAAAATGAAAA
*
3613 TCGCAACGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
3633 TCGC
1 TCGC
3637 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:3693 original size:20 final size:20
Alignment explanation
Indices: 3643--3699 Score: 91
Period size: 18 Copynumber: 3.0 Consensus size: 20
3633 TCGCGTTGCG
*
3643 ATTTTCGTGTTGCGACTTTC
1 ATTTTCGTGTTGCGAATTTC
3663 ATTTT--TGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
3681 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
3700 AAGTTTCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
18 17 0.50
20 17 0.50
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.53
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:7881 original size:19 final size:19
Alignment explanation
Indices: 7857--7895 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
7847 TTAAACGGGA
7857 AACGGACGATTGAGCCGAT
1 AACGGACGATTGAGCCGAT
7876 AACGGACGATTGAGCCGAT
1 AACGGACGATTGAGCCGAT
7895 A
1 A
7896 GCGGGACGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.31, T:0.15
Consensus pattern (19 bp):
AACGGACGATTGAGCCGAT
Found at i:10057 original size:20 final size:21
Alignment explanation
Indices: 10032--10077 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
10022 CACTAATTTT
*
10032 AAAAAGTGCATTT-AAAATAA
1 AAAAAGTACATTTAAAAATAA
*
10052 AAAAAGTATATTTAAAAATAA
1 AAAAAGTACATTTAAAAATAA
10073 AAAAA
1 AAAAA
10078 TCAAAACACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (21 bp):
AAAAAGTACATTTAAAAATAA
Found at i:13800 original size:36 final size:37
Alignment explanation
Indices: 13738--13816 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 37
13728 ACTTAATGTT
13738 AAGTTTTGAACATGATACTAAAATGAAACAA-AATCTA
1 AAGTTTTGAACATGATACTAAAATGAAACAAGAAT-TA
*
13775 AAGTTTTTAACATG-TACTAAAATGAAACAAGAATTA
1 AAGTTTTGAACATGATACTAAAATGAAACAAGAATTA
13811 AA-TTTT
1 AAGTTTT
13817 AGGAATGGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 4 0.10
36 20 0.50
37 16 0.40
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.32
Consensus pattern (37 bp):
AAGTTTTGAACATGATACTAAAATGAAACAAGAATTA
Found at i:16740 original size:83 final size:80
Alignment explanation
Indices: 16535--16732 Score: 200
Period size: 83 Copynumber: 2.4 Consensus size: 80
16525 ATGTCATGAT
* * * * *
16535 AGAGTAGTACTATAACTGTGTTTTTTACAAACACTGTAATAGGGTTAATTTATAGTTTTTTTTTC
1 AGAGTAGTACTTTAGCAGCGTTTTTTACAAACGCTGTAATAGGGTTAATTTATAGTTTTTTTTTC
*
16600 AACAAACGCCACAAC
66 AACAAACACCACAAC
* ** * * * *
16615 AGAGTAGTACTTTAGTAGTATTTTTATATAAATGTTGTAATAGGGTTCATTTATA-TTAGTATTT
1 AGAGTAGTACTTTAGCAGCGTTTTT-TACAAACGCTGTAATAGGGTTAATTTATAGTT--T-TTT
*
16679 TTTCAACAAACATCACAAC
62 TTTCAACAAACACCACAAC
* *
16698 ATAGTAGTACTTTAGCGGCGTTTATTTACAAACGC
1 AGAGTAGTACTTTAGCAGCGTTT-TTTACAAACGC
16733 CGCAATAGTT
Statistics
Matches: 93, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
80 22 0.24
81 24 0.26
82 1 0.01
83 44 0.47
84 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (80 bp):
AGAGTAGTACTTTAGCAGCGTTTTTTACAAACGCTGTAATAGGGTTAATTTATAGTTTTTTTTTC
AACAAACACCACAAC
Found at i:20288 original size:21 final size:21
Alignment explanation
Indices: 20264--20305 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20254 TATGAGAAAT
*
20264 TGTTTTAAAATAT-AAAAATGA
1 TGTTTCAAAAT-TGAAAAATGA
20285 TGTTTCAAAATTGAAAAATGA
1 TGTTTCAAAATTGAAAAATGA
20306 AAATAAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (21 bp):
TGTTTCAAAATTGAAAAATGA
Found at i:24127 original size:20 final size:19
Alignment explanation
Indices: 24102--24161 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
24092 TTTTGGTGCA
*
24102 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCC-C
* *
24122 GAGGGAACCGATTCCCCCC
1 GAGGGAATCGATACCCCCC
24141 GCAGGGGAATCGATACCCCCC
1 G-A-GGGAATCGATACCCCCC
24162 TGGGGTTCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 1 0.03
20 17 0.52
21 15 0.45
ACGTcount: A:0.25, C:0.37, G:0.27, T:0.12
Consensus pattern (19 bp):
GAGGGAATCGATACCCCCC
Found at i:26421 original size:25 final size:25
Alignment explanation
Indices: 26387--26436 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
26377 TTAAAGAGTT
26387 TTAAAAGGGAGAAGTGTTAGAGTAA
1 TTAAAAGGGAGAAGTGTTAGAGTAA
*
26412 TTAAAGGGGAGAAGTGTTAGAGTAA
1 TTAAAAGGGAGAAGTGTTAGAGTAA
26437 GGGGGAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.34, T:0.24
Consensus pattern (25 bp):
TTAAAAGGGAGAAGTGTTAGAGTAA
Found at i:26443 original size:21 final size:22
Alignment explanation
Indices: 26388--26443 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 22
26378 TAAAGAGTTT
*
26388 TAAAAGGGAGAAGTGTTAGAGTAA
1 TAAAGGGGAGAAGTGTTAGAG--A
26412 TTAAAGGGGAGAAGTGTTAGAG-
1 -TAAAGGGGAGAAGTGTTAGAGA
*
26434 TAAGGGGGAG
1 TAAAGGGGAG
26444 TAATTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.31
25 20 0.69
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (22 bp):
TAAAGGGGAGAAGTGTTAGAGA
Found at i:29416 original size:33 final size:33
Alignment explanation
Indices: 29363--29444 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
29353 CACTTCCAAT
* * * *
29363 GTTTTAATCGTCTTCTATTGGTGCACCTTCAGG
1 GTTTCAATCATCTTCAATTGGTGCACCTCCAGG
*
29396 GTTTCAATCATCTTCAATTGGTGCATCTCCAGG
1 GTTTCAATCATCTTCAATTGGTGCACCTCCAGG
29429 GTTTCAATCATCTTCA
1 GTTTCAATCATCTTCA
29445 GCTAGCAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (33 bp):
GTTTCAATCATCTTCAATTGGTGCACCTCCAGG
Found at i:29870 original size:25 final size:24
Alignment explanation
Indices: 29799--29884 Score: 119
Period size: 25 Copynumber: 3.8 Consensus size: 24
29789 GCTTAGTGGT
29799 TTTTTTGTATATGGCTT-T-G-CA
1 TTTTTTGTATATGGCTTATGGTCA
29820 TTTTTTGTATATGGC-T-TGGTCA
1 TTTTTTGTATATGGCTTATGGTCA
*
29842 TTTTTTGTATATGCCTTAGTGGTCA
1 TTTTTTGTATATGGCTTA-TGGTCA
29867 TTTTTTGTATATGGCTTA
1 TTTTTTGTATATGGCTTA
29885 CTGGCTTAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.03
21 16 0.28
22 16 0.28
23 1 0.02
25 23 0.40
ACGTcount: A:0.15, C:0.09, G:0.20, T:0.56
Consensus pattern (24 bp):
TTTTTTGTATATGGCTTATGGTCA
Found at i:31264 original size:13 final size:13
Alignment explanation
Indices: 31246--31270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31236 TATCATATCG
31246 AAATAAAAAAATT
1 AAATAAAAAAATT
31259 AAATAAAAAAAT
1 AAATAAAAAAAT
31271 ATTTTTATTA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAAAAATT
Found at i:34760 original size:2 final size:2
Alignment explanation
Indices: 34753--34781 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34743 CTCCCTACTT
34753 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34782 TGTTAAATCG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35924 original size:14 final size:14
Alignment explanation
Indices: 35905--35952 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
35895 AGATGTATGT
35905 CATGATGATGTTAA
1 CATGATGATGTTAA
* *
35919 CATGATTG-TTTTAT
1 CATGA-TGATGTTAA
35933 CATGATGATGTTAA
1 CATGATGATGTTAA
*
35947 CGTGAT
1 CATGAT
35953 TATTTTATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 2 0.07
14 23 0.85
15 2 0.07
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (14 bp):
CATGATGATGTTAA
Found at i:35936 original size:28 final size:28
Alignment explanation
Indices: 35904--35962 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
35894 TAGATGTATG
*
35904 TCATGATGATGTTAACATGATTGTTTTA
1 TCATGATGATGTTAACATGATTATTTTA
*
35932 TCATGATGATGTTAACGTGATTATTTTA
1 TCATGATGATGTTAACATGATTATTTTA
35960 TCA
1 TCA
35963 AAACGACGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (28 bp):
TCATGATGATGTTAACATGATTATTTTA
Found at i:40827 original size:6 final size:6
Alignment explanation
Indices: 40818--40842 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40808 GGGATGATAA
40818 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
40843 AAACCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:40922 original size:13 final size:13
Alignment explanation
Indices: 40906--40949 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
40896 GCCCCGATTA
*
40906 CCCGATTATCCGC
1 CCCGATTACCCGC
40919 CCCGATTACCCGC
1 CCCGATTACCCGC
*
40932 CCCGA-TACCCGA
1 CCCGATTACCCGC
40944 CCCGAT
1 CCCGAT
40950 AAATATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.18, C:0.50, G:0.16, T:0.16
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:40942 original size:12 final size:12
Alignment explanation
Indices: 40915--40950 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
40905 ACCCGATTAT
40915 CCGCCCCGATTAC
1 CCGCCCCGA-TAC
40928 CCGCCCCGATAC
1 CCGCCCCGATAC
*
40940 CCGACCCGATA
1 CCGCCCCGATA
40951 AATATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.19, C:0.53, G:0.17, T:0.11
Consensus pattern (12 bp):
CCGCCCCGATAC
Found at i:41082 original size:24 final size:24
Alignment explanation
Indices: 41055--41109 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
41045 ATATATATAT
* * *
41055 ATACCCGACCCGATTCTCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
*
41079 ATACCCGGCCCAATACCCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
41103 ATACCCG
1 ATACCCG
41110 TTTAAATAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.47, G:0.16, T:0.13
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:41089 original size:12 final size:12
Alignment explanation
Indices: 41072--41109 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
41062 ACCCGATTCT
41072 CGGCCCAATACC
1 CGGCCCAATACC
41084 CGGCCCAATACC
1 CGGCCCAATACC
41096 CGGCCCAATACC
1 CGGCCCAATACC
41108 CG
1 CG
41110 TTTAAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.24, C:0.50, G:0.18, T:0.08
Consensus pattern (12 bp):
CGGCCCAATACC
Found at i:43115 original size:25 final size:25
Alignment explanation
Indices: 43087--43140 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
43077 TGTGAAGAAG
* *
43087 CTTTTGCTTGTTTCTGGTATTTGTT
1 CTTTTACTTGTTTCTGGTACTTGTT
43112 CTTTTACTTGTTTCTGGTACTTGTT
1 CTTTTACTTGTTTCTGGTACTTGTT
43137 CTTT
1 CTTT
43141 GCACTCGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.06, C:0.15, G:0.17, T:0.63
Consensus pattern (25 bp):
CTTTTACTTGTTTCTGGTACTTGTT
Found at i:46893 original size:21 final size:20
Alignment explanation
Indices: 46851--46911 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
46841 AAACTTGGTA
*
46851 TTTCTTAATGATTTTT-TAAT
1 TTTCTTTATG-TTTTTATAAT
46871 TTTCTTTATGTTCTTTATAAT
1 TTTCTTTATGTT-TTTATAAT
**
46892 TTTAATTAT-TTTTTATAAT
1 TTTCTTTATGTTTTTATAAT
46911 T
1 T
46912 AAAAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 11 0.31
20 14 0.39
21 11 0.31
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTCTTTATGTTTTTATAAT
Found at i:46906 original size:19 final size:20
Alignment explanation
Indices: 46862--46911 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
46852 TTCTTAATGA
**
46862 TTTTT-TAATTTTCTTTATG
1 TTTTTATAATTTTAATTATG
46881 TTCTTTATAATTTTAATTAT-
1 TT-TTTATAATTTTAATTATG
46901 TTTTTATAATT
1 TTTTTATAATT
46912 AAAAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 11 0.41
20 5 0.19
21 11 0.41
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTATAATTTTAATTATG
Found at i:47637 original size:16 final size:16
Alignment explanation
Indices: 47616--47652 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
47606 ATATAAATTA
*
47616 AATAAAGATATTTAAT
1 AATAAAGATATTAAAT
47632 AATAAAGATATTAAAT
1 AATAAAGATATTAAAT
47648 AATAA
1 AATAA
47653 GGAGATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
AATAAAGATATTAAAT
Found at i:52274 original size:35 final size:35
Alignment explanation
Indices: 52229--52299 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
52219 GTGAACAATA
52229 AATATAGTTAACCAATAATTTTATTAATCACTCTC
1 AATATAGTTAACCAATAATTTTATTAATCACTCTC
52264 AATATAGTTAACCAATAATTTTATTAATCACTCTC
1 AATATAGTTAACCAATAATTTTATTAATCACTCTC
52299 A
1 A
52300 TTTGTTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (35 bp):
AATATAGTTAACCAATAATTTTATTAATCACTCTC
Found at i:52501 original size:15 final size:16
Alignment explanation
Indices: 52457--52503 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
52447 AAAATTAAAT
*
52457 TTGAAAGTTAGAGTGA
1 TTGAAAGTTAGAGTAA
52473 TT-AAA-TTAGGAGTAA
1 TTGAAAGTTA-GAGTAA
52488 TTGAAAGTTA-AGTAA
1 TTGAAAGTTAGAGTAA
52503 T
1 T
52504 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.11
15 16 0.59
16 5 0.19
17 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (16 bp):
TTGAAAGTTAGAGTAA
Found at i:52867 original size:55 final size:55
Alignment explanation
Indices: 52764--52874 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
52754 AGAGTGGGAC
* *
52764 AATTCTGTTGTTTGTGTAGGTCCCTGTGGTGGATCGGTAACCTTAAAAAAGGCAA
1 AATTATGTTGTTTGTGTAGGTCCCTGTGGTGGATCAGTAACCTTAAAAAAGGCAA
* *
52819 AATTATGTTGTTTGTGTGGGTCCCTGTGGTGG-TCAGTGACCTTAAAAAAGGCAA
1 AATTATGTTGTTTGTGTAGGTCCCTGTGGTGGATCAGTAACCTTAAAAAAGGCAA
52873 AA
1 AA
52875 CTGAATGGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 22 0.42
55 30 0.58
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (55 bp):
AATTATGTTGTTTGTGTAGGTCCCTGTGGTGGATCAGTAACCTTAAAAAAGGCAA
Found at i:64704 original size:3 final size:3
Alignment explanation
Indices: 64696--64775 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
64686 TACAACATTT
64696 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
64744 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
64776 ATATTCAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Done.