Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006275.1 Hibiscus syriacus cultivar Beakdansim tig00014966_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: 48132
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1812 original size:49 final size:49
Alignment explanation
Indices: 1730--2013 Score: 468
Period size: 49 Copynumber: 5.9 Consensus size: 49
1720 TTGAGGCACC
*
1730 ATTATTATTAATA-TTAATGA-TTGATAG-AATGATTAGTAATAATAAA
1 ATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAA
*
1776 ATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAAGAATGAA
1 ATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAA
* * *
1825 ATTATTATTAATATTTAATGAATTGATGGTAATGATTAGTAATGATGAA
1 ATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAA
1874 ATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAA
1 ATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAA
*
1923 ATTATTATTAATATTTAATGATTTAATAGT-ATGATTAGTAATAATGAA
1 ATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAA
* *
1971 ATTATTATTAATATTTAATTATTTGATTGTAATGATTAGTAAT
1 ATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAAT
2014 TATTAATAAT
Statistics
Matches: 221, Mismatches: 13, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
46 13 0.06
47 7 0.03
48 52 0.24
49 149 0.67
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (49 bp):
ATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAA
Found at i:2037 original size:17 final size:18
Alignment explanation
Indices: 2011--2045 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2001 AATGATTAGT
2011 AATTATTAATAATAATGA
1 AATTATTAATAATAATGA
2029 AATTA-TAATAATAATGA
1 AATTATTAATAATAATGA
2046 TTTACTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTATTAATAATAATGA
Found at i:2564 original size:11 final size:12
Alignment explanation
Indices: 2540--2580 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
2530 AAACTATTTT
2540 TTTAA-TATAAC
1 TTTAACTATAAC
*
2551 TTTAACTAT-TC
1 TTTAACTATAAC
2562 TTT-ACTATAAC
1 TTTAACTATAAC
2573 TTTAACTA
1 TTTAACTA
2581 ATAAACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 5 0.20
11 13 0.52
12 7 0.28
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.49
Consensus pattern (12 bp):
TTTAACTATAAC
Found at i:2570 original size:22 final size:23
Alignment explanation
Indices: 2531--2580 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
2521 ACAACTAATA
*
2531 AACTATTTTTTTAATATAACTTT
1 AACTATTTCTTTAATATAACTTT
*
2554 AACTA-TTCTTTACTATAACTTT
1 AACTATTTCTTTAATATAACTTT
2576 AACTA
1 AACTA
2581 ATAAACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (23 bp):
AACTATTTCTTTAATATAACTTT
Found at i:2623 original size:29 final size:30
Alignment explanation
Indices: 2554--2648 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
2544 ATATAACTTT
* * *
2554 AACTATTCTTTACTATAACTTTAACTAATA
1 AACTATTTTTTAATATAACTTAAACTAATA
2584 AACTATTTTTTAATATAACTTAAACTAATA
1 AACTATTTTTTAATATAACTTAAACTAATA
* *
2614 AA-TGA-TTTTTAATTATAATTTATTACTAA-A
1 AACT-ATTTTTTAA-TATAACTTA-AACTAATA
2644 AACTA
1 AACTA
2649 ATTAACTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
29 8 0.14
30 42 0.75
31 6 0.11
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.44
Consensus pattern (30 bp):
AACTATTTTTTAATATAACTTAAACTAATA
Found at i:3474 original size:11 final size:11
Alignment explanation
Indices: 3458--3516 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
3448 CTGAAGGACT
3458 GCAATAATGCA
1 GCAATAATGCA
* *
3469 GCAATAAGGGCT
1 GCAATAA-TGCA
3481 GCAATAATGCA
1 GCAATAATGCA
* *
3492 TCAATAAGTGCT
1 GCAATAA-TGCA
3504 GCAATAATGCA
1 GCAATAATGCA
3515 GC
1 GC
3517 TGAATTCACG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 20 0.53
12 18 0.47
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (11 bp):
GCAATAATGCA
Found at i:3482 original size:23 final size:23
Alignment explanation
Indices: 3451--3516 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
3441 ACGTGAGCTG
*
3451 AAGGACTGCAATAATGCAGCAAT
1 AAGGGCTGCAATAATGCAGCAAT
*
3474 AAGGGCTGCAATAATGCATCAAT
1 AAGGGCTGCAATAATGCAGCAAT
*
3497 AAGTGCTGCAATAATGCAGC
1 AAGGGCTGCAATAATGCAGC
3517 TGAATTCACG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (23 bp):
AAGGGCTGCAATAATGCAGCAAT
Found at i:3486 original size:12 final size:12
Alignment explanation
Indices: 3456--3510 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
3446 AGCTGAAGGA
3456 CTGCAATAA-TG
1 CTGCAATAAGTG
* *
3467 CAGCAATAAGGG
1 CTGCAATAAGTG
3479 CTGCAATAA-TG
1 CTGCAATAAGTG
3490 CAT-CAATAAGTG
1 C-TGCAATAAGTG
3502 CTGCAATAA
1 CTGCAATAA
3511 TGCAGCTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 17 0.47
12 19 0.53
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (12 bp):
CTGCAATAAGTG
Found at i:3713 original size:29 final size:29
Alignment explanation
Indices: 3671--3749 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
3661 CGTTGGATGC
3671 CGGGCGTGCATGGCGACCTATAAGGACGT
1 CGGGCGTGCATGGCGACCTATAAGGACGT
3700 CGGGCGTGCATGGCGACCTATAAGGACGT
1 CGGGCGTGCATGGCGACCTATAAGGACGT
*
3729 CGGGAGTGCATGGCGACCTAT
1 CGGGCGTGCATGGCGACCTAT
3750 GCTGGTTCGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.20, C:0.24, G:0.38, T:0.18
Consensus pattern (29 bp):
CGGGCGTGCATGGCGACCTATAAGGACGT
Found at i:4357 original size:17 final size:17
Alignment explanation
Indices: 4302--4362 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
4292 ACAATATAAA
*
4302 TTAAACAAAATATTTTTT
1 TTAAACACAATA-TTTTT
* *
4320 TTAAACAACACTAAATATTT
1 TTAAAC-ACA--ATATTTTT
4340 TTAAACACAATATTTTT
1 TTAAACACAATATTTTT
4357 TTAAAC
1 TTAAAC
4363 GGAAATTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 12 0.34
18 6 0.17
19 5 0.14
20 10 0.29
21 2 0.06
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAACACAATATTTTT
Found at i:4817 original size:42 final size:47
Alignment explanation
Indices: 4761--4918 Score: 139
Period size: 49 Copynumber: 3.4 Consensus size: 47
4751 TTTTAAAGAC
*
4761 ACTAACAAATTAATTAATATTTTTT-TAT-AT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAATATTTTTTATATAATATATATATAACTTAA
*
4803 ACTAATAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAA-T-ATTTTTTATATAATAT-ATATATAACTTAA
** * * * * *
4853 ACTAACAAACTAATATAATATAATTTAAACTAAAAAACTA-ATAATTTAT
1 ACTAACAAACTAAT-TAATATTTTTTATA-TAATATA-TATATAACTTAA
4902 ACTAACAAACTAATTAA
1 ACTAACAAACTAATTAA
4919 CTAGATTTTA
Statistics
Matches: 95, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
42 15 0.16
43 1 0.01
44 7 0.07
45 3 0.03
46 2 0.02
47 1 0.01
48 3 0.03
49 31 0.33
50 29 0.31
51 3 0.03
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (47 bp):
ACTAACAAACTAATTAATATTTTTTATATAATATATATATAACTTAA
Found at i:4873 original size:28 final size:30
Alignment explanation
Indices: 4833--4895 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
4823 ATTTTTTATA
*
4833 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAAAAAAC
*
4863 TAATAT-A-ATATAATTTAAACTAAAAAAC
1 TAATATAATATATAACTTAAACTAAAAAAC
4891 TAATA
1 TAATA
4896 ATTTATACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 24 0.77
29 1 0.03
30 6 0.19
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAAAAAAC
Found at i:4898 original size:21 final size:21
Alignment explanation
Indices: 4872--4915 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4862 CTAATATAAT
4872 ATAATTTAAACTAAAAAACTA
1 ATAATTTAAACTAAAAAACTA
* *
4893 ATAATTTATACTAACAAACTA
1 ATAATTTAAACTAAAAAACTA
4914 AT
1 AT
4916 TAACTAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAATTTAAACTAAAAAACTA
Found at i:4902 original size:28 final size:28
Alignment explanation
Indices: 4837--4902 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
4827 TTTATATAAT
*
4837 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAAAAAACTA
*
4865 AT-ATAATATAATTTAAACTAAAAAACTA
1 ATAAT-ATATAACTTAAACTAAAAAACTA
*
4893 ATAATTTATA
1 ATAATATATA
4903 CTAACAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAAAAAACTA
Found at i:5651 original size:13 final size:13
Alignment explanation
Indices: 5633--5662 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5623 CCCATTTGAA
5633 CACTTAATCTGAG
1 CACTTAATCTGAG
5646 CACTTAATCTGAG
1 CACTTAATCTGAG
5659 CACT
1 CACT
5663 GCATTATCTC
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:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (13 bp):
CACTTAATCTGAG
Found at i:7643 original size:14 final size:14
Alignment explanation
Indices: 7624--7653 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7614 TCCCATAATC
7624 TGCTGCTGCAACGA
1 TGCTGCTGCAACGA
*
7638 TGCTGCTGCCACGA
1 TGCTGCTGCAACGA
7652 TG
1 TG
7654 ACATGTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (14 bp):
TGCTGCTGCAACGA
Found at i:22997 original size:37 final size:37
Alignment explanation
Indices: 22942--23016 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 37
22932 AACATAACGT
22942 TAGAGTTTTACTAGGATTCAAAC-TCTTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTTC-TAAAAATAGGA
* *
22979 TAGAGTTTTCCTATGATTCAAACTTCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTTCTAAAAATAGGA
23016 T
1 T
23017 CCACAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 33 0.94
38 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTTCTAAAAATAGGA
Found at i:23641 original size:3 final size:3
Alignment explanation
Indices: 23633--23670 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
23623 TTTGCTGTTT
*
23633 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23671 CTATTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:24631 original size:19 final size:19
Alignment explanation
Indices: 24607--24646 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
24597 TATCTTATGT
24607 CTTCGTGTGAATTTATTCA
1 CTTCGTGTGAATTTATTCA
24626 CTTCGTGTGAATTTATTCA
1 CTTCGTGTGAATTTATTCA
24645 CT
1 CT
24647 GCACAAACAT
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:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (19 bp):
CTTCGTGTGAATTTATTCA
Found at i:26984 original size:11 final size:11
Alignment explanation
Indices: 26962--27024 Score: 56
Period size: 12 Copynumber: 5.4 Consensus size: 11
26952 CAATCAGAAC
26962 AAAAAGAAAAA
1 AAAAAGAAAAA
26973 AGAGAAA-AAAAA
1 A-A-AAAGAAAAA
*
26985 ACAAAGAAAAA
1 AAAAAGAAAAA
26996 ACAAAGAGAAAATA
1 A-AAA-AGAAAA-A
*
27010 AAAAAGAAACA
1 AAAAAGAAAAA
27021 AAAA
1 AAAA
27025 TAAAGGCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
10 3 0.07
11 12 0.28
12 14 0.33
13 12 0.28
14 2 0.05
ACGTcount: A:0.83, C:0.05, G:0.11, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:26985 original size:12 final size:12
Alignment explanation
Indices: 26968--27024 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 12
26958 GAACAAAAAG
26968 AAAAAAGAGAAAA
1 AAAAAAGAG-AAA
*
26981 AAAAACAAAGAAA
1 AAAAA-AGAGAAA
26994 AAACAAAGAGAAA
1 AAA-AAAGAGAAA
27007 ATAAAAA-AGAAA
1 A-AAAAAGAGAAA
27019 CAAAAA
1 -AAAAA
27025 TAAAGGCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 9 0.24
13 22 0.58
14 7 0.18
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (12 bp):
AAAAAAGAGAAA
Found at i:26985 original size:14 final size:14
Alignment explanation
Indices: 26962--27029 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
26952 CAATCAGAAC
26962 AAAAAGAAAAAAGAG
1 AAAAA-AAAAAAGAG
26977 AAAAAAAAACAA-AG
1 AAAAAAAAA-AAGAG
*
26991 -AAAAAACAAAGAG
1 AAAAAAAAAAAGAG
*
27004 AAAATAAAAAAGA-
1 AAAAAAAAAAAGAG
*
27017 AACAAAAATAAAG
1 AA-AAAAAAAAAG
27030 GCAAAAGTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
12 2 0.05
13 11 0.25
14 24 0.55
15 7 0.16
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAAAGAG
Found at i:27023 original size:27 final size:27
Alignment explanation
Indices: 26959--27013 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
26949 TTTCAATCAG
*
26959 AACAAA-AAGAAA-AAAGAGAAAAAAA
1 AACAAAGAAAAAACAAAGAGAAAAAAA
26984 AACAAAGAAAAAACAAAGAGAAAATAAA
1 AACAAAGAAAAAACAAAGAGAAAA-AAA
27012 AA
1 AA
27014 AGAAACAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.23
26 5 0.19
27 10 0.38
28 5 0.19
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (27 bp):
AACAAAGAAAAAACAAAGAGAAAAAAA
Found at i:27023 original size:29 final size:27
Alignment explanation
Indices: 26959--27024 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
26949 TTTCAATCAG
*
26959 AACAAA-AAGAAA-AAAGAGAAAAAAA
1 AACAAACAAAAAACAAAGAGAAAAAAA
*
26984 AACAAAGAAAAAACAAAGAGAAAATAAAA
1 AACAAACAAAAAACAAAGAG-AAA-AAAA
*
27013 AAGAAACAAAAA
1 AACAAACAAAAA
27025 TAAAGGCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.18
26 5 0.15
27 6 0.18
28 3 0.09
29 14 0.41
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.02
Consensus pattern (27 bp):
AACAAACAAAAAACAAAGAGAAAAAAA
Found at i:28149 original size:32 final size:32
Alignment explanation
Indices: 28098--28186 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
28088 AGGAACACTG
* * * *
28098 GGGGCATCTTTGAATATTCAACATTAAATGTT
1 GGGGCATCTTTGGAGATTCAACATCAAATATT
* *
28130 GGGGCATTTTTGGAGATTCAACATCGAATATT
1 GGGGCATCTTTGGAGATTCAACATCAAATATT
* *
28162 GGGGTATCTTTGGGGATTCAACATC
1 GGGGCATCTTTGGAGATTCAACATC
28187 CTGGTGCTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (32 bp):
GGGGCATCTTTGGAGATTCAACATCAAATATT
Found at i:28932 original size:21 final size:21
Alignment explanation
Indices: 28907--29007 Score: 64
Period size: 21 Copynumber: 5.4 Consensus size: 21
28897 TGAGACAGTT
28907 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
28928 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
*
28945 -C-CTTGAAATAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* * *
28964 TCTCTTG--AGATA-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
28981 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
29000 TCTCTTGA
1 TCTCTTGA
29008 GACAGTTTCC
Statistics
Matches: 57, Mismatches: 11, Indels: 24
0.62 0.12 0.26
Matches are distributed among these distances:
15 10 0.18
16 2 0.04
17 8 0.14
18 8 0.14
19 8 0.14
20 2 0.04
21 19 0.33
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.43
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:28932 original size:36 final size:36
Alignment explanation
Indices: 28877--29027 Score: 266
Period size: 36 Copynumber: 4.2 Consensus size: 36
28867 AATTTACTCA
*
28877 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
28914 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
28950 AAATAAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
28986 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
29022 AAACAA
1 AAACAA
29028 GATCTTTAAA
Statistics
Matches: 109, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 102 0.94
37 7 0.06
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:29103 original size:37 final size:36
Alignment explanation
Indices: 29043--29201 Score: 203
Period size: 37 Copynumber: 4.4 Consensus size: 36
29033 TTAAATGTGT
* * * *
29043 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAT
1 TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
* *
29078 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAG
* *
29115 TTTCTCTTGAAACAAATTTTGTCTCTCTTGATACAG
1 TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
* *
29151 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAA
1 TTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAG
29188 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
29202 CAAAAAAAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
35 4 0.04
36 40 0.38
37 62 0.58
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
Found at i:29124 original size:138 final size:138
Alignment explanation
Indices: 28905--29165 Score: 416
Period size: 138 Copynumber: 1.9 Consensus size: 138
28895 CTTGAGACAG
* *
28905 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
*
28970 GAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAGATCTTT
66 GAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAGATCTTT
29035 AAATGTGT
131 AAATGTGT
* ** * *
29043 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
* *
29107 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGATACAGTTTCCCTTGAAACAA
65 TGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
29166 AGTTTTGTCT
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
137 34 0.30
138 78 0.70
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (138 bp):
TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAGATCTTT
AAATGTGT
Found at i:29393 original size:83 final size:85
Alignment explanation
Indices: 29239--29414 Score: 250
Period size: 83 Copynumber: 2.1 Consensus size: 85
29229 CTTGAAACAG
* *
29239 AAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGAGCATATCATTTGCAACATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACACTCAGCTTCAAGAGCATATCATTTGCAACATAACTCAAGGCG
* *
29304 AGAAGGGTTATCTGTCAA-C
66 AGAAGGGCTATATGTCAACC
* * *
29323 AAAGACCTTCGAGTTCGATTACACTCAGC-TCAA-AGGCATATCATTTGCAACATAACTTAAGTC
1 AAAGACCTTCGAGTTCGACTACACTCAGCTTCAAGA-GCATATCATTTGCAACATAACTCAAGGC
*
29386 GAGAAGGGCTATATGTTAACC
65 GAGAAGGGCTATATGTCAACC
29407 AAAGACCT
1 AAAGACCT
29415 AGAGTCAAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
82 1 0.01
83 44 0.54
84 37 0.45
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (85 bp):
AAAGACCTTCGAGTTCGACTACACTCAGCTTCAAGAGCATATCATTTGCAACATAACTCAAGGCG
AGAAGGGCTATATGTCAACC
Found at i:37669 original size:12 final size:12
Alignment explanation
Indices: 37652--37681 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
37642 AAGCTGAACC
37652 GGAGCAGCCCGA
1 GGAGCAGCCCGA
37664 GGAGCAGCCCGA
1 GGAGCAGCCCGA
*
37676 AGAGCA
1 GGAGCA
37682 AGCACAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.40, T:0.00
Consensus pattern (12 bp):
GGAGCAGCCCGA
Found at i:39587 original size:37 final size:37
Alignment explanation
Indices: 39542--39612 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
39532 AACATAACGT
39542 TAGAGTTTTACTAGGATTCAAACTACTAAAAATATGA
1 TAGAGTTTTACTAGGATTCAAACTACTAAAAATATGA
* *
39579 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTAGGATTCAAACTACTAAAAATA
39613 GGATCCACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTACTAAAAATATGA
Found at i:40192 original size:29 final size:29
Alignment explanation
Indices: 40128--40196 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
40118 TTTATTGCAA
* *
40128 ATATTATATTTATTATTACATATATACAT
1 ATATTTTATTTATTATTACATATACACAT
* *
40157 ATATTTTATTTATTATT-CTTATACACTT
1 ATATTTTATTTATTATTACATATACACAT
*
40185 CTATTTTTATTT
1 ATA-TTTTATTT
40197 TCTTTTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (29 bp):
ATATTTTATTTATTATTACATATACACAT
Found at i:47149 original size:26 final size:27
Alignment explanation
Indices: 47120--47172 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
47110 AAGTCAATTG
47120 GTGTCTGA-TCGAAAAATAATGATTAA
1 GTGTCTGATTCGAAAAATAATGATTAA
*
47146 GTGTCTGATTTGGAAAAATAATGATTA
1 GTGTCTGA-TTCGAAAAATAATGATTA
47173 TAAGGATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.33
28 16 0.67
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.34
Consensus pattern (27 bp):
GTGTCTGATTCGAAAAATAATGATTAA
Found at i:47328 original size:27 final size:28
Alignment explanation
Indices: 47247--47329 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 28
47237 GTACTTACAA
47247 TATTTTTTTGTCAAAGT-ATATATAAAG
1 TATTTTTTTGTCAAAGTAATATATAAAG
* **
47274 TTATTTTTTT-TC-AA--AATATGT-ACC
1 -TATTTTTTTGTCAAAGTAATATATAAAG
47298 TATTTTTTTGTCAAAGTAATAT-TAAAG
1 TATTTTTTTGTCAAAGTAATATATAAAG
47325 TATTT
1 TATTT
47330 AAGCTTATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
23 9 0.20
24 3 0.07
25 7 0.16
26 3 0.07
27 13 0.30
28 9 0.20
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (28 bp):
TATTTTTTTGTCAAAGTAATATATAAAG
Found at i:47498 original size:25 final size:26
Alignment explanation
Indices: 47455--47507 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
47445 TAGGTACATG
*
47455 TTTTAAAAAAAAATAACTTCACATAC
1 TTTTAAAAAAAAATAACTTAACATAC
* *
47481 TTTTAAAAAAATAT-ACTTAAGATAC
1 TTTTAAAAAAAAATAACTTAACATAC
47506 TT
1 TT
47508 AGGTAAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (26 bp):
TTTTAAAAAAAAATAACTTAACATAC
Done.