Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006296.1 Hibiscus syriacus cultivar Beakdansim tig00015049_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: 64976
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5550 original size:13 final size:13
Alignment explanation
Indices: 5532--5557 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5522 ATATATATAG
5532 TTTTTTAAAACAT
1 TTTTTTAAAACAT
5545 TTTTTTAAAACAT
1 TTTTTTAAAACAT
5558 ATAATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTTTAAAACAT
Found at i:5584 original size:14 final size:15
Alignment explanation
Indices: 5565--5593 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5555 CATATAATAT
5565 ATAGTTTTT-AAAAA
1 ATAGTTTTTGAAAAA
5579 ATAGTTTTTGAAAAA
1 ATAGTTTTTGAAAAA
5594 CGTATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
ATAGTTTTTGAAAAA
Found at i:5587 original size:37 final size:35
Alignment explanation
Indices: 5507--5611 Score: 122
Period size: 39 Copynumber: 2.9 Consensus size: 35
5497 TTTTTAAGTT
5507 AATATTTTTAAAA-ATATATATATAGTTTTTTAAAA
1 AATATTTTTAAAACATATATATATAG-TTTTTAAAA
* *
5542 CATTTTTTTAAAACATATAATATATAGTTTTTAAAA
1 AATATTTTTAAAACATAT-ATATATAGTTTTTAAAA
*
5578 AATAGTTTTTGAAAAACGTATATAATATAGTTTT
1 AATA-TTTTT--AAAACATATAT-ATATAGTTTT
5612 GAAATATATA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
35 11 0.19
36 15 0.25
37 13 0.22
38 2 0.03
39 18 0.31
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (35 bp):
AATATTTTTAAAACATATATATATAGTTTTTAAAA
Found at i:5615 original size:24 final size:25
Alignment explanation
Indices: 5579--5643 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
5569 TTTTTAAAAA
5579 ATAGTTTTTGAAAAACGTATATA-AT
1 ATAG-TTTTGAAAAACGTATATATAT
* **
5604 ATAGTTTTGAAATATATATATATAT
1 ATAGTTTTGAAAAACGTATATATAT
5629 ATAGTTTT-AAAAACG
1 ATAGTTTTGAAAAACG
5644 ACTTTTGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 19 0.58
25 14 0.42
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (25 bp):
ATAGTTTTGAAAAACGTATATATAT
Found at i:5691 original size:63 final size:63
Alignment explanation
Indices: 5543--5692 Score: 146
Period size: 63 Copynumber: 2.4 Consensus size: 63
5533 TTTTTAAAAC
* * * * *
5543 ATTTTTTTAAAACATATAATATATAGTTTTTAAAAAATAGTTTTTGAAAAACGTATATAATAT
1 ATTTTTTGAAAACATATTATATATAGTTTTTAAAAAAGAGCTTTTGAAAAACATATATAATAT
* * * *
5606 A-GTTTTGAAATATATATATATATATAG-TTTTAAAAACGA-CTTTTG-AAAGCATATATAATAT
1 ATTTTTTGAAA-ACATAT-TATATATAGTTTTTAAAAAAGAGCTTTTGAAAAACATATAT-A-AT
5667 AT
62 AT
5669 ATTTTGTTGAAAACATATTATATA
1 ATTTT-TTGAAAACATATTATATA
5693 GTTTTTGAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
61 9 0.13
62 13 0.19
63 27 0.39
64 15 0.21
65 6 0.09
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (63 bp):
ATTTTTTGAAAACATATTATATATAGTTTTTAAAAAAGAGCTTTTGAAAAACATATATAATAT
Found at i:5703 original size:22 final size:23
Alignment explanation
Indices: 5660--5713 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
5650 GAAAGCATAT
*
5660 ATAATATATATTTTGTTGAAAAC
1 ATAATATATAGTTTGTTGAAAAC
* *
5683 ATATTATATAGTTT-TTGAAAAT
1 ATAATATATAGTTTGTTGAAAAC
5705 ATAATATAT
1 ATAATATAT
5714 GTTATATAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (23 bp):
ATAATATATAGTTTGTTGAAAAC
Found at i:8377 original size:29 final size:29
Alignment explanation
Indices: 8345--8541 Score: 182
Period size: 29 Copynumber: 6.8 Consensus size: 29
8335 TTATTAAGCT
* *
8345 TTTTGGTGTTTATTGTAGTTTTTAGAAAG
1 TTTTGGTATTTATTGTAATTTTTAGAAAG
* *
8374 TTTTGGTATTTATTATAATTTTTAAAAAG
1 TTTTGGTATTTATTGTAATTTTTAGAAAG
* * *
8403 TTTTGATTTTTATTGTAA-TTTTGGAAAG
1 TTTTGGTATTTATTGTAATTTTTAGAAAG
* * **
8431 TTTTGGTATTTATTTTAACTAATA-AAAG
1 TTTTGGTATTTATTGTAATTTTTAGAAAG
* * * *
8459 GTTTGGTATCTATTATAATTTATAGAAAG
1 TTTTGGTATTTATTGTAATTTTTAGAAAG
* * *
8488 TTTGGGTATTTATTGTAATTTATAAAAAAG
1 TTTTGGTATTTATTGTAATTT-TTAGAAAG
* * *
8518 TTTTAGTCTTTATTGTAATATTTA
1 TTTTGGTATTTATTGTAATTTTTA
8542 TAAAAATAGA
Statistics
Matches: 133, Mismatches: 32, Indels: 6
0.78 0.19 0.04
Matches are distributed among these distances:
28 46 0.35
29 65 0.49
30 22 0.17
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (29 bp):
TTTTGGTATTTATTGTAATTTTTAGAAAG
Found at i:8457 original size:57 final size:57
Alignment explanation
Indices: 8353--8541 Score: 193
Period size: 57 Copynumber: 3.3 Consensus size: 57
8343 CTTTTTGGTG
* * *
8353 TTTATTGTAGTTTTTAGAAAGTTTTGGTATTTATTATAATTTTTAAAAAGTTTTGATT
1 TTTATTGTA-ATTTTAGAAAGTTTTGGTATTTATTATAATTTATAAAAAGTTTTGATA
* * * * * *
8411 TTTATTGTAATTTTGGAAAGTTTTGGTATTTATTTTAACTAAT-AAAAGGTTTGGTA
1 TTTATTGTAATTTTAGAAAGTTTTGGTATTTATTATAATTTATAAAAAGTTTTGATA
* * * * *
8467 TCTATTATAATTTATAGAAAGTTTGGGTATTTATTGTAATTTATAAAAAAGTTTT-AGTC
1 TTTATTGTAATTT-TAGAAAGTTTTGGTATTTATTATAATTTAT-AAAAAGTTTTGA-TA
8526 TTTATTGTAATATTTA
1 TTTATTGTAAT-TTTA
8542 TAAAAATAGA
Statistics
Matches: 105, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
56 21 0.20
57 53 0.50
58 9 0.09
59 20 0.19
60 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (57 bp):
TTTATTGTAATTTTAGAAAGTTTTGGTATTTATTATAATTTATAAAAAGTTTTGATA
Found at i:10121 original size:42 final size:42
Alignment explanation
Indices: 10026--10187 Score: 218
Period size: 42 Copynumber: 3.8 Consensus size: 42
10016 GCAAAAATGA
* * * *
10026 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGCCTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAACAAAGGGA-CCT-GGGAAACTG
* * *
10070 TAAGACTTACCCTTGCACACAGCAAAGGGACCTAGGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGAAACTG
*
10112 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGAAACTG
10154 TAAGGCTTACCCTTGCACACAACAAAGGGACCTG
1 TAAGGCTTACCCTTGCACACAACAAAGGGACCTG
10188 CTGTAACGGT
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
42 79 0.74
43 22 0.21
44 6 0.06
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (42 bp):
TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGAAACTG
Found at i:10163 original size:84 final size:86
Alignment explanation
Indices: 10026--10186 Score: 245
Period size: 84 Copynumber: 1.9 Consensus size: 86
10016 GCAAAAATGA
* * * *
10026 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCTGGGGAAACTGTAAGACTTACCCTTGCACACA
1 TAAGGTCTTACCCTTGCACACAACAAAAGAACCTGGGGAAACTGTAAGACTTACCCTTGCACACA
*
10091 GCAAAGGGACCTAGGAAACTG
66 ACAAAGGGACCTAGGAAACTG
* *
10112 TAAGG-CTTACCCTTGCACACAACAAAGGAACCT-GGGAAACTGTAAGGCTTACCCTTGCACACA
1 TAAGGTCTTACCCTTGCACACAACAAAAGAACCTGGGGAAACTGTAAGACTTACCCTTGCACACA
10175 ACAAAGGGACCT
66 ACAAAGGGACCT
10187 GCTGTAACGG
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
84 40 0.59
85 23 0.34
86 5 0.07
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (86 bp):
TAAGGTCTTACCCTTGCACACAACAAAAGAACCTGGGGAAACTGTAAGACTTACCCTTGCACACA
ACAAAGGGACCTAGGAAACTG
Found at i:15107 original size:43 final size:43
Alignment explanation
Indices: 14974--15136 Score: 186
Period size: 43 Copynumber: 3.8 Consensus size: 43
14964 GCAAAAATGA
* * *
14974 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGCCTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGAAACTG
* * ** * * *
15018 TAAGGCTGACCTTTGCACACAAAAAATGAACC-GGGGAAACTA
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
*
15060 TAAGGCTTACCCTTGCAAACAGCAAAGGGACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
*
15103 TAAGGCTTACCCTTGCTCACAGCAAAGGGACCTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
15137 CTGTAACGGT
Statistics
Matches: 98, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
42 34 0.35
43 58 0.59
44 6 0.06
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
Found at i:17945 original size:49 final size:49
Alignment explanation
Indices: 17888--17982 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
17878 TGAATGCCCA
* * *
17888 GTCAAAGCCGGTCAAAGTTTTGGTCAACATTAGTTAACGCCGATCACCG
1 GTCAAAGCCGGTAAAAGTTTTGGTCAACATTAGTCAACACCGATCACCG
17937 GTCAAAGCCGGTAAAAGTTTTGGTCAACATTAGTCAACACCGATCA
1 GTCAAAGCCGGTAAAAGTTTTGGTCAACATTAGTCAACACCGATCA
17983 ACTATCAACG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (49 bp):
GTCAAAGCCGGTAAAAGTTTTGGTCAACATTAGTCAACACCGATCACCG
Found at i:18007 original size:13 final size:13
Alignment explanation
Indices: 17989--18013 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17979 ATCAACTATC
17989 AACGGGTCGGGTA
1 AACGGGTCGGGTA
18002 AACGGGTCGGGT
1 AACGGGTCGGGT
18014 CGGGTTGTAA
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:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:20886 original size:112 final size:110
Alignment explanation
Indices: 20700--20914 Score: 313
Period size: 112 Copynumber: 1.9 Consensus size: 110
20690 TCGACAAACT
* * * * * *
20700 TTGTGTATGATAGTATCGATCGATTTTGTTTAATGCATAATGGTGCATTTTCGGCATAAAAGATG
1 TTGTGTATGAAAGTATCGATCAATTTTGCTAAATGCATAACGGTGCATTTTCGGAATAAAAGATG
20765 CCACACATGGTATTCATAATGAGGTGAATTACTATTTCGATATACA
66 CCACACATGGTATTCATAATGAGGTGAATTAC-ATTTCGATATACA
* * * *
20811 TTGTGTATGAAAGTTATCGATCAATTTTGCTAAATGTATAACGGTGCATTTTCTGAATAAATGGT
1 TTGTGTATGAAAG-TATCGATCAATTTTGCTAAATGCATAACGGTGCATTTTCGGAATAAAAGAT
*
20876 GCCACCCATGGTATTCATAATGAGGTGAATTACATTTCG
65 GCCACACATGGTATTCATAATGAGGTGAATTACATTTCG
20915 GCACTTCAGT
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
111 18 0.20
112 74 0.80
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (110 bp):
TTGTGTATGAAAGTATCGATCAATTTTGCTAAATGCATAACGGTGCATTTTCGGAATAAAAGATG
CCACACATGGTATTCATAATGAGGTGAATTACATTTCGATATACA
Found at i:26647 original size:19 final size:19
Alignment explanation
Indices: 26623--26686 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
26613 TGCATTGGGA
* *
26623 TATGAATTTGAAATTAAGC
1 TATGAATCTGAAAATAAGC
26642 TATGAATCT-AAAAGTAAGC
1 TATGAATCTGAAAA-TAAGC
*
26661 TATGAATCTGAAAATAAGT
1 TATGAATCTGAAAATAAGC
26680 TATGAAT
1 TATGAAT
26687 TTGGATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.08
19 33 0.82
20 4 0.10
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (19 bp):
TATGAATCTGAAAATAAGC
Found at i:26788 original size:13 final size:13
Alignment explanation
Indices: 26754--26796 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
26744 ATAAGAGATG
*
26754 TGAAAATGAATG-
1 TGAAAATGAAAGA
*
26766 TGAAAGTGAAAGA
1 TGAAAATGAAAGA
*
26779 TGAAAATGAAATA
1 TGAAAATGAAAGA
26792 TGAAA
1 TGAAA
26797 GTTCTGAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (13 bp):
TGAAAATGAAAGA
Found at i:27012 original size:2 final size:2
Alignment explanation
Indices: 27007--27038 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26997 TTATATAAGG
27007 AT AT 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
27039 TTTTTAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28394 original size:23 final size:23
Alignment explanation
Indices: 28364--28412 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
28354 TGGTAGTTGG
*
28364 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
28387 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
28410 TTT
1 TTT
28413 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:28933 original size:9 final size:11
Alignment explanation
Indices: 28904--28928 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28894 TTCTTTTCAT
28904 TTTATTTACTG
1 TTTATTTACTG
28915 TTTATTTACTG
1 TTTATTTACTG
28926 TTT
1 TTT
28929 TTACTATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTATTTACTG
Found at i:31890 original size:45 final size:45
Alignment explanation
Indices: 31791--31891 Score: 143
Period size: 45 Copynumber: 2.2 Consensus size: 45
31781 TTGCCAGAAT
*
31791 AATCTAGCTTAATGGAGTCCGACCACTTTCCAATTTTGGTGGATG
1 AATCTAGCTTAATGGAGTCCGACCACTTTCCAATTTTGGAGGATG
**
31836 -ATAAAAGCTTAATGGAGTCCGACCACTTTCCAATTTTGGAGGA-G
1 AAT-CTAGCTTAATGGAGTCCGACCACTTTCCAATTTTGGAGGATG
31880 CAATCTAGCTTA
1 -AATCTAGCTTA
31892 CTACAAGCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
44 3 0.06
45 43 0.90
46 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (45 bp):
AATCTAGCTTAATGGAGTCCGACCACTTTCCAATTTTGGAGGATG
Found at i:34272 original size:23 final size:23
Alignment explanation
Indices: 34242--34290 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
34232 TGGTGGTTAG
*
34242 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
34265 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
34288 TTT
1 TTT
34291 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:40969 original size:55 final size:55
Alignment explanation
Indices: 40887--41282 Score: 614
Period size: 55 Copynumber: 7.2 Consensus size: 55
40877 CACAAACTTA
* * * * *
40887 TTAGTTTGAATTTCATACTTCTT-CACACATAGTGCCCACACGGAAATTCACACAC
1 TTAGTATGAATTTCTTAATT-TTGCACACATAGTGCCCATACGGAAATTCATACAC
* * * *
40942 ATAGTATGAATTTCCTAATTTTGCACACATAGTGTCCATACGAAAATTCATACAC
1 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACAC
* **
40997 TTAGTATGAATTTCTTAATTTTTCACACATAGTGCTTATACGGAAATTCATACAC
1 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACAC
41052 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACAC
1 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACAC
* * *
41107 TTAGAATTAATTTCTTAATTTTGCACACATAGTGGCCATACGGAAATTCATACAC
1 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACAC
41162 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACAC
1 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACAC
* * *
41217 TTAGAATTAATTTCTTAATTTTGCACACATAGTGGCCATACGGAAATTCATACAC
1 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACAC
41272 TTAGTATGAAT
1 TTAGTATGAAT
41283 ATTTTAACTT
Statistics
Matches: 311, Mismatches: 29, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
54 2 0.01
55 309 0.99
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (55 bp):
TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACAC
Found at i:41100 original size:165 final size:165
Alignment explanation
Indices: 40811--41282 Score: 626
Period size: 165 Copynumber: 2.8 Consensus size: 165
40801 CCCACTACAA
* * * * ** * *
40811 ATACGAAAATTCA-CCTACTTATTATGAATTTCTT-ATGCTTGTACATGTAGTTCCCATACGAAA
1 ATACGAAAATTCATAC-ACTTAGTATGAATTTCTTAAT-TTTGCACACATAGTGCCCATACGGAA
* * * * * * *
40874 ATTCACAAACTTATTAGTTTGAATTTCATACTTCTT-CACACATAGTGCCCACACGGAAATTCAC
64 ATTCATACAC---TTAGTATGAATTTCTTAATT-TTGCACACATAGTGCCCATACGGAAATTCAT
* *
40938 ACACATAGTATGAATTTCCTAATTTTGCACACATAGTGTCC
125 ACACTTAGTATGAATTTCCTAATTTTGCACACATAGTGGCC
* **
40979 ATACGAAAATTCATACACTTAGTATGAATTTCTTAATTTTTCACACATAGTGCTTATACGGAAAT
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAAT
41044 TCATACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACACTT
66 TCATACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACACTT
* * *
41109 AGAATTAATTTCTTAATTTTGCACACATAGTGGCC
131 AGTATGAATTTCCTAATTTTGCACACATAGTGGCC
*
41144 ATACGGAAATTCATACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAAT
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAAT
* * *
41209 TCATACACTTAGAATTAATTTCTTAATTTTGCACACATAGTGGCCATACGGAAATTCATACACTT
66 TCATACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACACTT
41274 AGTATGAAT
131 AGTATGAAT
41283 ATTTTAACTT
Statistics
Matches: 269, Mismatches: 32, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
164 2 0.01
165 209 0.78
168 55 0.20
169 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (165 bp):
ATACGAAAATTCATACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAAT
TCATACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACACTT
AGTATGAATTTCCTAATTTTGCACACATAGTGGCC
Found at i:50768 original size:13 final size:13
Alignment explanation
Indices: 50752--50786 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
50742 CGCAATGAGC
* *
50752 GTCATTAATGTGT
1 GTCATAAATGTGA
50765 GTCATAAATGTGA
1 GTCATAAATGTGA
50778 GTCATAAAT
1 GTCATAAAT
50787 TTATGACGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (13 bp):
GTCATAAATGTGA
Found at i:54490 original size:16 final size:17
Alignment explanation
Indices: 54467--54500 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54457 CGGCAAAAAA
*
54467 CAAAAAATATGACTTTT
1 CAAAAATTATGACTTTT
*
54484 CAAAAATTTTGACTTTT
1 CAAAAATTATGACTTTT
54501 TGGTCAAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
CAAAAATTATGACTTTT
Found at i:59524 original size:39 final size:38
Alignment explanation
Indices: 59471--59625 Score: 145
Period size: 39 Copynumber: 4.0 Consensus size: 38
59461 GTACACCCAA
*
59471 TAAGGAC-TACCCTGTGCACAAAGCAGAGGAGCCTGCAC
1 TAAGGACTTA-CCTGTGCACAAAGCAGAGGAGCCTGCAG
* * * *
59509 TAAGGTCTTATCCTGTGCACAAAGCATATGAGCCTGTAG
1 TAAGGACTTA-CCTGTGCACAAAGCAGAGGAGCCTGCAG
**
59548 TAAGGACTTACACTAAGCACAAAGTC-GAGGAGCCTGCAG
1 TAAGGACTTAC-CTGTGCACAAAG-CAGAGGAGCCTGCAG
** *
59587 TAAGGACTTACACTGAACACAAAGCCA-AGGAGCTTGCAG
1 TAAGGACTTAC-CTGTGCACAAAG-CAGAGGAGCCTGCAG
59626 AAAGCGGTAA
Statistics
Matches: 97, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
38 7 0.07
39 89 0.92
40 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.18
Consensus pattern (38 bp):
TAAGGACTTACCTGTGCACAAAGCAGAGGAGCCTGCAG
Done.