Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005935.1 Hibiscus syriacus cultivar Beakdansim tig00013934_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: 62533
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8205 original size:15 final size:15
Alignment explanation
Indices: 8185--8243 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
8175 CGGGTCAGGT
8185 ATATATTTAAATTAA
1 ATATATTTAAATTAA
* *
8200 ATATA-TAAATATTAT
1 ATATATTTAA-ATTAA
8215 ATATAATTTAAATTAA
1 ATAT-ATTTAAATTAA
8231 AT-TATATTAAATT
1 ATATAT-TTAAATT
8244 TATTAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.14
15 21 0.58
16 7 0.19
17 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATTTAAATTAA
Found at i:10124 original size:20 final size:23
Alignment explanation
Indices: 10099--10146 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 23
10089 GATCCGATTC
10099 AAAATAATATA-TTTATT-AA-A
1 AAAATAATATATTTTATTCAATA
*
10119 AAAAT-ATTTATTTTATTCAATA
1 AAAATAATATATTTTATTCAATA
10141 AAAATA
1 AAAATA
10147 GGGATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 11 0.48
21 2 0.09
22 6 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAATAATATATTTTATTCAATA
Found at i:11780 original size:2 final size:2
Alignment explanation
Indices: 11768--11804 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
11758 TCGGATAACA
*
11768 AT AT TT 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 A
11805 AAAGATCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:15460 original size:2 final size:2
Alignment explanation
Indices: 15453--15485 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15443 ATATTTAAAA
15453 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
15486 CCTAATCGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:19537 original size:40 final size:40
Alignment explanation
Indices: 19492--19598 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 40
19482 TGGTGAATCT
19492 ATTAATATTTCAAATGAAATTCATCCAGAAGGA-CGAATAC
1 ATTAATATTTCAAATGAAATTCATCCAG-AGGAGCGAATAC
* * * * * * *
19532 GTTAATATTTTAAAGTAAAATTCATCCCGATGAGTGAATCC
1 ATTAATATTTCAAA-TGAAATTCATCCAGAGGAGCGAATAC
*
19573 ATTGATATTTCCAAATGAAATTCATC
1 ATTAATATTT-CAAATGAAATTCATC
19599 TCGAAAGATG
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
40 15 0.28
41 35 0.66
42 3 0.06
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (40 bp):
ATTAATATTTCAAATGAAATTCATCCAGAGGAGCGAATAC
Found at i:19581 original size:41 final size:38
Alignment explanation
Indices: 19445--19598 Score: 119
Period size: 40 Copynumber: 3.8 Consensus size: 38
19435 CCTTTAAGGA
* * * *
19445 TGAATCCACTGATATTCTGAAATAAATTCATCCTGAATGG
1 TGAATCCATTAATATT-TCAAATAAATTCATCCAG-ATGG
* *
19485 TGAATCTATTAATATTTCAAATGAAATTCATCCAGAAGG
1 TGAATCCATTAATATTTCAAAT-AAATTCATCCAGATGG
* * * * *
19524 ACGAATACGTTAATATTTTAAAGTAAAATTCATCCCGATGAG
1 -TGAATCCATTAATATTTCAAA-T-AAATTCATCCAGATG-G
*
19566 TGAATCCATTGATATTTCCAAATGAAATTCATC
1 TGAATCCATTAATATTT-CAAAT-AAATTCATC
19599 TCGAAAGATG
Statistics
Matches: 89, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
39 8 0.09
40 40 0.45
41 37 0.42
42 4 0.04
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (38 bp):
TGAATCCATTAATATTTCAAATAAATTCATCCAGATGG
Found at i:21315 original size:24 final size:24
Alignment explanation
Indices: 21281--21330 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
21271 TGAGAACCGG
* *
21281 ATAAATTAACTTAT-AAATGAGTTT
1 ATAAATGAACTT-TCAAATGAGATT
21305 ATAAATGAACTTTCAAATGAGATT
1 ATAAATGAACTTTCAAATGAGATT
21329 AT
1 AT
21331 TTGTGAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (24 bp):
ATAAATGAACTTTCAAATGAGATT
Found at i:21472 original size:2 final size:2
Alignment explanation
Indices: 21465--21491 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21455 GAACATCGTT
21465 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 T
21492 GAAAACGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23016 original size:21 final size:21
Alignment explanation
Indices: 22973--23017 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22963 ATTCTCGTTA
* *
22973 TTATTTTTAAAGATCATAAAT
1 TTATTTATAAAGATCACAAAT
* *
22994 TTATTTATAGAGATCACAGAT
1 TTATTTATAAAGATCACAAAT
23015 TTA
1 TTA
23018 AGCATTAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (21 bp):
TTATTTATAAAGATCACAAAT
Found at i:23652 original size:21 final size:17
Alignment explanation
Indices: 23614--23647 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
23604 ACTAATCCTG
23614 AATTTTTAATTTATTTC
1 AATTTTTAATTTATTTC
23631 AATTTTTAATTTATTTC
1 AATTTTTAATTTATTTC
23648 GTTCATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTTTTAATTTATTTC
Found at i:23667 original size:21 final size:21
Alignment explanation
Indices: 23628--23667 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
23618 TTTAATTTAT
* *
23628 TTCAATTTTTAATTTATTTCG
1 TTCAATTTTTAAATAATTTCG
*
23649 TTCATTTTTTAAATAATTT
1 TTCAATTTTTAAATAATTT
23668 ATATTTTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (21 bp):
TTCAATTTTTAAATAATTTCG
Found at i:24725 original size:13 final size:13
Alignment explanation
Indices: 24707--24733 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24697 TTTAATGGTT
24707 TTATGAGTTATTA
1 TTATGAGTTATTA
24720 TTATGAGTTATTA
1 TTATGAGTTATTA
24733 T
1 T
24734 ATTAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (13 bp):
TTATGAGTTATTA
Found at i:27108 original size:19 final size:19
Alignment explanation
Indices: 27084--27122 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
27074 ACAAAGAATG
*
27084 TTTTAA-AATATAATTAAAA
1 TTTTAATAA-ATAAATAAAA
27103 TTTTAATAAATAAATAAAA
1 TTTTAATAAATAAATAAAA
27122 T
1 T
27123 GTTTGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTTAATAAATAAATAAAA
Found at i:30396 original size:60 final size:63
Alignment explanation
Indices: 30323--30446 Score: 173
Period size: 60 Copynumber: 2.0 Consensus size: 63
30313 ATTATCTTTG
* * *
30323 AACATATCATATTTTATACTAATCTCGTATTAA-CAAAGAAA-TTA-AGTCAAAATTATTATC
1 AACATATCATATTTTATACTAACCTCGTATTAATAAAAAAAAGTTACAGTCAAAATTATTATC
* * *
30383 AACATATCCTATTTTGTACTAACCTCGTATTAATAAAAAAAAGTTACATTCAAAATTATTATC
1 AACATATCATATTTTATACTAACCTCGTATTAATAAAAAAAAGTTACAGTCAAAATTATTATC
30446 A
1 A
30447 CATTAATAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 30 0.55
61 6 0.11
62 3 0.05
63 16 0.29
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (63 bp):
AACATATCATATTTTATACTAACCTCGTATTAATAAAAAAAAGTTACAGTCAAAATTATTATC
Found at i:32161 original size:14 final size:14
Alignment explanation
Indices: 32142--32180 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
32132 TAATGGGGAG
32142 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
32156 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
32170 GAATCTCTGCA
1 TAATCCCTGCA
32181 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:34547 original size:21 final size:21
Alignment explanation
Indices: 34478--34551 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
34468 TATCGCAAAT
34478 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
* * ** **
34499 TCACGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAATTGAAAA
* *
34519 TGGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
34540 TCGCGTTGCGAT
1 TCGCGTTGCGAT
34552 TTTCCAGTTC
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:34573 original size:41 final size:41
Alignment explanation
Indices: 34477--34574 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 41
34467 CTATCGCAAA
* *
34477 TTCGCGTTGCGATAATTGAAAATCACGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCAG
* *
34518 TTGGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCAG
*
34559 TTCGCATTGCGATAGT
1 TTCGCGTTGCGATAGT
34575 CTACAGTTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.36
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCAG
Found at i:35288 original size:22 final size:22
Alignment explanation
Indices: 35259--35312 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
35249 AATTTGGAAA
35259 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * *
35281 TTCGCAACAATAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
35303 ATCGCAACGA
1 ATCGCAACGA
35313 ATTTGGAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:35346 original size:40 final size:40
Alignment explanation
Indices: 35297--35392 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 40
35287 ACAATAACTG
*
35297 TAGACTATCGCAACGAATTTGGAAAATCACAACGAC-A-TTA
1 TAGACTATCGCAACGAA-ATGGAAAATCACAAC-ACGATTTA
* *
35337 TAGACTATCGCAACACGAAATGGAAAATCGCAACACGATTTT
1 TAGACTATCGC-A-ACGAAATGGAAAATCACAACACGATTTA
35379 TA-ACTATCGCAACG
1 TAGACTATCGCAACG
35393 CGAAATGCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
39 3 0.06
40 14 0.29
41 23 0.47
42 9 0.18
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (40 bp):
TAGACTATCGCAACGAAATGGAAAATCACAACACGATTTA
Found at i:36763 original size:16 final size:16
Alignment explanation
Indices: 36744--36791 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
36734 AATTTATAAT
36744 AAATTATATATTATTA
1 AAATTATATATTATTA
36760 AAATTATATATTATTA
1 AAATTATATATTATTA
**
36776 AAAGCATATATTATTA
1 AAATTATATATTATTA
36792 TAATATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATTATATATTATTA
Found at i:37607 original size:23 final size:23
Alignment explanation
Indices: 37546--37614 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
37536 TAATTATGTA
*
37546 TTTGTGACACG--TTT-TATGTC
1 TTTGTGACACGTTTTTCTCTGTC
* * * *
37566 TTTATGATACATTTATCTCTGTC
1 TTTGTGACACGTTTTTCTCTGTC
*
37589 TTTGTGACACGTTTTTCTCTGCC
1 TTTGTGACACGTTTTTCTCTGTC
37612 TTT
1 TTT
37615 TGGTAGCTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
20 8 0.22
22 2 0.06
23 26 0.72
ACGTcount: A:0.14, C:0.19, G:0.14, T:0.52
Consensus pattern (23 bp):
TTTGTGACACGTTTTTCTCTGTC
Found at i:42555 original size:81 final size:81
Alignment explanation
Indices: 42420--42577 Score: 253
Period size: 81 Copynumber: 2.0 Consensus size: 81
42410 TCAAACTGGG
* * *
42420 AGAAGCCGAATCACTGTTGTCTCTCTTCTTTCTTTTCAAAGTCTGTACTGATTCTTTCGAGCTTC
1 AGAAGCAGAATCACCGTTGTCTCTCTTCTTTCTTTTCAAAGTCTGTACTGATTCTTTCGAACTTC
42485 CCAAAGGAACATTGGA
66 CCAAAGGAACATTGGA
* * * *
42501 AGAAGCAGAATCGCCGTTGTCTCTCTTCTTTCTTTTCAGAGTTTGTGCTGATTCTTTCGAACTTC
1 AGAAGCAGAATCACCGTTGTCTCTCTTCTTTCTTTTCAAAGTCTGTACTGATTCTTTCGAACTTC
42566 CCAAAGGAACAT
66 CCAAAGGAACAT
42578 CAGGAGAAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (81 bp):
AGAAGCAGAATCACCGTTGTCTCTCTTCTTTCTTTTCAAAGTCTGTACTGATTCTTTCGAACTTC
CCAAAGGAACATTGGA
Found at i:52530 original size:155 final size:154
Alignment explanation
Indices: 52229--52540 Score: 534
Period size: 155 Copynumber: 2.0 Consensus size: 154
52219 TTAGATCCTG
* * * * *
52229 CATATTAAAGAATGGAAATAAAAAAACAAATCCTATAATAGATCTCATTCCGCAGCAAGCACCGA
1 CATAATAAAGAATAGAAATAAAAAAACAAATCCTATAATAGATCCCATTCAGCACCAAGCACCGA
* * *
52294 AGACCTGTCCCGAGTACACCCCTTTAATCTCAGCGTAACATTACTCTTTATCAGTGAAACTATAC
66 AGACCTGCCCCGAGTACACACCTTTAATCTCAACGTAACATTACTCTTTATCAGTGAAACTATAC
52359 CCTAAATTCCACTATGACTAACTC
131 CCTAAATTCCACTATGACTAACTC
52383 CATAATAAAGAATAGAAATAAAAAAAACAAATCCTATAATAGATCCCATTCAGCACCAAGCACCG
1 CATAATAAAGAATAGAAAT-AAAAAAACAAATCCTATAATAGATCCCATTCAGCACCAAGCACCG
52448 AAGACCTGCCCCGAGTACACACCTTTAATCTCAACGTAACATTACTCTTTATCAGTGAAACTATA
65 AAGACCTGCCCCGAGTACACACCTTTAATCTCAACGTAACATTACTCTTTATCAGTGAAACTATA
*
52513 CCCTAAATTCCTCTATGACTAACTC
130 CCCTAAATTCCACTATGACTAACTC
52538 CAT
1 CAT
52541 GCCATCTATC
Statistics
Matches: 148, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
154 17 0.11
155 131 0.89
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.25
Consensus pattern (154 bp):
CATAATAAAGAATAGAAATAAAAAAACAAATCCTATAATAGATCCCATTCAGCACCAAGCACCGA
AGACCTGCCCCGAGTACACACCTTTAATCTCAACGTAACATTACTCTTTATCAGTGAAACTATAC
CCTAAATTCCACTATGACTAACTC
Found at i:53500 original size:64 final size:65
Alignment explanation
Indices: 53387--53533 Score: 192
Period size: 64 Copynumber: 2.3 Consensus size: 65
53377 CATTCATAAG
* * *
53387 TGCATCGATGCATTCC-TTTAAAAGAAAGAACATCGAATGCCTTTGATGCATCGATGCA-TAGCT
1 TGCATCGATGCA-TCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAG-T
53450 AA
64 AA
* * *
53452 TGCATCGATGCATCCTTTTAAAATAAA-AACATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
53516 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
53534 CATTGAAAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
64 45 0.62
65 28 0.38
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (65 bp):
TGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
Found at i:54044 original size:17 final size:19
Alignment explanation
Indices: 54022--54057 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
54012 GATTTACATG
54022 AATACATGT-ATAT-ATAT
1 AATACATGTGATATGATAT
54039 AATACATGTGATATGATAT
1 AATACATGTGATATGATAT
54058 GAGATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (19 bp):
AATACATGTGATATGATAT
Found at i:54285 original size:31 final size:31
Alignment explanation
Indices: 54191--54298 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
54181 AGTCGAGGGT
* *
54191 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
54222 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
54253 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
54284 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
54299 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:54305 original size:30 final size:30
Alignment explanation
Indices: 54213--54319 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
54203 TTTCGAGACA
* * * *
54213 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
* *
54244 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
54275 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
54305 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
54320 GGGTCTGTGT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 29 0.46
31 30 0.48
32 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:54598 original size:31 final size:31
Alignment explanation
Indices: 54504--54611 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
54494 GCATGAGGGT
* *
54504 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
54535 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
54566 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
54597 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
54612 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:54618 original size:30 final size:30
Alignment explanation
Indices: 54526--54632 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
54516 TTTCGAGACA
* * * *
54526 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
* *
54557 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
54588 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
54618 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
54633 GGGTCTGTGT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 29 0.46
31 30 0.48
32 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:54753 original size:313 final size:313
Alignment explanation
Indices: 54185--54812 Score: 1256
Period size: 313 Copynumber: 2.0 Consensus size: 313
54175 GCCAAGAGTC
54185 GAGGGTTTTACCTATGTCTTTCGAGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGA
1 GAGGGTTTTACCTATGTCTTTCGAGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGA
54250 CAGTTTACCTAGGTTCTTTGGGACCTATGGACAGTTGCCGAGGTTCTTTATGACCTCTGGATAGT
66 CAGTTTACCTAGGTTCTTTGGGACCTATGGACAGTTGCCGAGGTTCTTTATGACCTCTGGATAGT
54315 TACCGGGGTCTGTGTGACCTCTGGATAGGTCCTTCGGGACATTTATACGAGCTGTTGTGACAGCA
131 TACCGGGGTCTGTGTGACCTCTGGATAGGTCCTTCGGGACATTTATACGAGCTGTTGTGACAGCA
54380 TTAGTGCACAACCTCAATGTACTCACATACCTCTATTCTCAATAATATACATGGGCAATGAAATT
196 TTAGTGCACAACCTCAATGTACTCACATACCTCTATTCTCAATAATATACATGGGCAATGAAATT
54445 GAAAGACAAATGAAAGTGAAAGTGATAAAAGAAGGTAAGTTGCATGTGTGCAT
261 GAAAGACAAATGAAAGTGAAAGTGATAAAAGAAGGTAAGTTGCATGTGTGCAT
54498 GAGGGTTTTACCTATGTCTTTCGAGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGA
1 GAGGGTTTTACCTATGTCTTTCGAGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGA
54563 CAGTTTACCTAGGTTCTTTGGGACCTATGGACAGTTGCCGAGGTTCTTTATGACCTCTGGATAGT
66 CAGTTTACCTAGGTTCTTTGGGACCTATGGACAGTTGCCGAGGTTCTTTATGACCTCTGGATAGT
54628 TACCGGGGTCTGTGTGACCTCTGGATAGGTCCTTCGGGACATTTATACGAGCTGTTGTGACAGCA
131 TACCGGGGTCTGTGTGACCTCTGGATAGGTCCTTCGGGACATTTATACGAGCTGTTGTGACAGCA
54693 TTAGTGCACAACCTCAATGTACTCACATACCTCTATTCTCAATAATATACATGGGCAATGAAATT
196 TTAGTGCACAACCTCAATGTACTCACATACCTCTATTCTCAATAATATACATGGGCAATGAAATT
54758 GAAAGACAAATGAAAGTGAAAGTGATAAAAGAAGGTAAGTTGCATGTGTGCAT
261 GAAAGACAAATGAAAGTGAAAGTGATAAAAGAAGGTAAGTTGCATGTGTGCAT
54811 GA
1 GA
54813 CCTGATTGTA
Statistics
Matches: 315, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
313 315 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (313 bp):
GAGGGTTTTACCTATGTCTTTCGAGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGA
CAGTTTACCTAGGTTCTTTGGGACCTATGGACAGTTGCCGAGGTTCTTTATGACCTCTGGATAGT
TACCGGGGTCTGTGTGACCTCTGGATAGGTCCTTCGGGACATTTATACGAGCTGTTGTGACAGCA
TTAGTGCACAACCTCAATGTACTCACATACCTCTATTCTCAATAATATACATGGGCAATGAAATT
GAAAGACAAATGAAAGTGAAAGTGATAAAAGAAGGTAAGTTGCATGTGTGCAT
Found at i:58016 original size:64 final size:64
Alignment explanation
Indices: 57877--58024 Score: 176
Period size: 64 Copynumber: 2.3 Consensus size: 64
57867 CACATTCATA
* * *
57877 AGTGCATCGATGCATTCC-TTTAAAAGAAAGAACATCGAATGCCTTTGATGATCGATGCATAGCT
1 AGTGCATCGATGCA-TCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGACCGATGCAAAGCT
* * *
57941 AATGCATCGATGCATCCTTTTAAAATAAA-AACATCGAATGCATTTTATGCACCGATGCACAAG-
1 AGTGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGATG-ACCGATGCA-AAGC
58004 T
64 T
*
58005 AGTGCACCGATGCATACCTT
1 AGTGCATCGATGCAT-CCTT
58025 CATTGAAAGA
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
63 21 0.29
64 45 0.62
65 6 0.08
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (64 bp):
AGTGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGACCGATGCAAAGCT
Found at i:58720 original size:31 final size:29
Alignment explanation
Indices: 58682--58771 Score: 76
Period size: 30 Copynumber: 3.0 Consensus size: 29
58672 TCGAGGGTTT
58682 TACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTCTTT-G-GACATATGGACAGTA
* *
58713 TACCTATGT-TTAAGGAACATATGGACAGTT
1 TACCTATGTCTT-TGG-ACATATGGACAGTA
* *
58743 TA-CTAGGTTCTTTGGGACCTATGGACAGT
1 TACCTATG-TCTTT-GGACATATGGACAGT
58772 TGCCGAGGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
29 5 0.10
30 31 0.63
31 13 0.27
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (29 bp):
TACCTATGTCTTTGGACATATGGACAGTA
Found at i:58792 original size:30 final size:30
Alignment explanation
Indices: 58732--58802 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
58722 TTAAGGAACA
* * *
58732 TATGGACAGTTTACTAGGTTCTTTGGGACC
1 TATGGACAGTTGACGAGGTTCTTTAGGACC
* *
58762 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTGACGAGGTTCTTTAGGACC
* *
58792 TCTGGATAGTT
1 TATGGACAGTT
58803 ACCGGGGTCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (30 bp):
TATGGACAGTTGACGAGGTTCTTTAGGACC
Done.