Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003729.1 Hibiscus syriacus cultivar Beakdansim tig00007973_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: 95309
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:5830 original size:3 final size:3
Alignment explanation
Indices: 5822--5846 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5812 GAAGTTTTTC
5822 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
5847 GAAGAATACA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:8731 original size:30 final size:30
Alignment explanation
Indices: 8697--8755 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
8687 ATTAAATTTT
* *
8697 TTTATTTATA-AATATTTAAAATAATATTAG
1 TTTATTAATATAATAATT-AAATAATATTAG
*
8727 TTTATTAATATAATAATTAATTAATATTA
1 TTTATTAATATAATAATTAAATAATATTA
8756 TAAAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
TTTATTAATATAATAATTAAATAATATTAG
Found at i:8976 original size:15 final size:13
Alignment explanation
Indices: 8938--8980 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
8928 TTATGATTTC
8938 ATAAATTATTTTT
1 ATAAATTATTTTT
8951 ATAAATTATTTTT
1 ATAAATTATTTTT
*
8964 GTAAAATTTATTTTT
1 AT-AAA-TTATTTTT
8979 AT
1 AT
8981 GTAAATAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 3 0.12
15 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
ATAAATTATTTTT
Found at i:11657 original size:30 final size:30
Alignment explanation
Indices: 11621--11686 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
11611 AGAGAACCGA
*
11621 CGGTTCACACCGGTTTTACCGGTTTTCAGC
1 CGGTTCACACCGGTTTTACCGGTTCTCAGC
* *
11651 CGGTTCACACCGGTTTTGCCGGTTCTCAGT
1 CGGTTCACACCGGTTTTACCGGTTCTCAGC
11681 CGGTTC
1 CGGTTC
11687 TTCTGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.11, C:0.30, G:0.26, T:0.33
Consensus pattern (30 bp):
CGGTTCACACCGGTTTTACCGGTTCTCAGC
Found at i:13405 original size:17 final size:18
Alignment explanation
Indices: 13366--13405 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
13356 TGATAAACTC
13366 ATATAAGTGATTTAAGAT
1 ATATAAGTGATTTAAGAT
*
13384 A-ATAAGTGA-TTAATAT
1 ATATAAGTGATTTAAGAT
13400 ATATAA
1 ATATAA
13406 ATTCATAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 7 0.35
17 12 0.60
18 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (18 bp):
ATATAAGTGATTTAAGAT
Found at i:13983 original size:23 final size:23
Alignment explanation
Indices: 13934--13991 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
13924 TAAGCTACCA
*
13934 AAAGACAGAGAAAAACATGTCAC
1 AAAGACAGAGAAAAACATATCAC
** * *
13957 AAAGACAGAGAAAAATGTATTAT
1 AAAGACAGAGAAAAACATATCAC
13980 AAAGACAGAGAA
1 AAAGACAGAGAA
13992 CATTTCACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.59, C:0.10, G:0.19, T:0.12
Consensus pattern (23 bp):
AAAGACAGAGAAAAACATATCAC
Found at i:17613 original size:22 final size:23
Alignment explanation
Indices: 17582--17628 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
17572 TAATCGCGAG
17582 TTTAGAAGATACGA-TTCTGGGC
1 TTTAGAAGATACGATTTCTGGGC
* *
17604 TTTAGCAGATACGATTTTTGGGC
1 TTTAGAAGATACGATTTCTGGGC
17627 TT
1 TT
17629 ATTTAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (23 bp):
TTTAGAAGATACGATTTCTGGGC
Found at i:21282 original size:72 final size:73
Alignment explanation
Indices: 21117--21301 Score: 259
Period size: 72 Copynumber: 2.5 Consensus size: 73
21107 ACAGAAAGCT
** *
21117 GAAAGCCTATCATGCATGTGTATAAGTAAAGAAATGAATGAGAAAATACCAACACACTCTAATGC
1 GAAAGCCTATCATGCATGCATATAAGTAAACAAATGAATGAGAAAATACCAACACAC-CTAATGC
*
21182 CTACAAACA
65 CCACAAACA
* * *
21191 GAAAGCCTATCATGCATGCATAAAAGTACAA-AAATGAATGAGAGAAA-ACCGATACA-CTAATG
1 GAAAGCCTATCATGCATGCATATAAGTA-AACAAATGAATGAGA-AAATACCAACACACCTAATG
21253 CCCACAAACA
64 CCCACAAACA
21263 GAAAGCCTATCATGCATGCATATAAGTAAACAAATGAAT
1 GAAAGCCTATCATGCATGCATATAAGTAAACAAATGAAT
21302 TGAGTGAATA
Statistics
Matches: 101, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
71 2 0.02
72 50 0.50
74 44 0.44
75 5 0.05
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (73 bp):
GAAAGCCTATCATGCATGCATATAAGTAAACAAATGAATGAGAAAATACCAACACACCTAATGCC
CACAAACA
Found at i:22375 original size:105 final size:104
Alignment explanation
Indices: 22194--22402 Score: 400
Period size: 105 Copynumber: 2.0 Consensus size: 104
22184 AACATAAGAA
22194 ACTAATATATTAAAACGATTGGCAAAGAGGACTAGTTATAAATGAAAGAAAGAATTTTCAAGCAA
1 ACTAATATATTAAAACGATTGGCAAAGAGGACTAGTTATAAATGAAAGAAAGAATTTTCAAGCAA
22259 CATCATACAAAACCAAAGAAAAAGAGAATGAATCAAAAG
66 CATCATACAAAACCAAAGAAAAAGAGAATGAATCAAAAG
22298 ACTAATATATTAAAACAGATTGGCAAAGAGGACTAGTTATAAATGAAAGAAAGAATTTTCAAGCA
1 ACTAATATATTAAAAC-GATTGGCAAAGAGGACTAGTTATAAATGAAAGAAAGAATTTTCAAGCA
*
22363 ACATCATACAAAACCAAAGAAAAAGGGAATGAATCAAAAG
65 ACATCATACAAAACCAAAGAAAAAGAGAATGAATCAAAAG
22403 TCAAAGTTCA
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 16 0.16
105 87 0.84
ACGTcount: A:0.54, C:0.11, G:0.16, T:0.19
Consensus pattern (104 bp):
ACTAATATATTAAAACGATTGGCAAAGAGGACTAGTTATAAATGAAAGAAAGAATTTTCAAGCAA
CATCATACAAAACCAAAGAAAAAGAGAATGAATCAAAAG
Found at i:25475 original size:12 final size:12
Alignment explanation
Indices: 25460--25504 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
25450 TATTTAAACG
25460 GGTATTGGGCCA
1 GGTATTGGGCCA
*
25472 GGTATTGGGTCA
1 GGTATTGGGCCA
* *
25484 AGTATTGGGTC-
1 GGTATTGGGCCA
25495 GGTATTGGGC
1 GGTATTGGGC
25505 TGGGAATCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.16, C:0.11, G:0.42, T:0.31
Consensus pattern (12 bp):
GGTATTGGGCCA
Found at i:26642 original size:21 final size:21
Alignment explanation
Indices: 26617--26664 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
26607 TACATATATC
*
26617 ATCATCTACTTTC-TTAGCATT
1 ATCATCTA-TATCATTAGCATT
* *
26638 ATCATATATATCATTATCATT
1 ATCATCTATATCATTAGCATT
26659 ATCATC
1 ATCATC
26665 GAATTATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.31, C:0.21, G:0.02, T:0.46
Consensus pattern (21 bp):
ATCATCTATATCATTAGCATT
Found at i:27147 original size:149 final size:149
Alignment explanation
Indices: 26875--27180 Score: 585
Period size: 149 Copynumber: 2.1 Consensus size: 149
26865 CACCGAAGTG
26875 CACGTAGAATTGCACCGTAGTACCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGA
1 CACGTAGAATTGCACCGTAGTACCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGA
26940 ATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATA
66 ATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATA
27005 TATATATATCCCGAAGGAC
131 TATATATATCCCGAAGGAC
* * *
27024 CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCATATATCATTCCTTAAGA
1 CACGTAGAATTGCACCGTAGTACCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGA
27089 ATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATA
66 ATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATA
27154 TATATATATCCCGAAGGAC
131 TATATATATCCCGAAGGAC
27173 CACGTAGA
1 CACGTAGA
27181 CCCTCGACTC
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (149 bp):
CACGTAGAATTGCACCGTAGTACCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGA
ATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATA
TATATATATCCCGAAGGAC
Found at i:29466 original size:35 final size:36
Alignment explanation
Indices: 29421--29501 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 36
29411 TTCAGGTATT
* * *
29421 TTTTTATTATTTAATGTTTCATAAAAAAATT-GGTA
1 TTTTTCTTATTAAAGGTTTCATAAAAAAATTGGGTA
* *
29456 TTTTTCTTATTAAAGGTTTCATAATAAATTTGGGTA
1 TTTTTCTTATTAAAGGTTTCATAAAAAAATTGGGTA
29492 -TTTTCTTATT
1 TTTTTCTTATT
29502 GAAGATTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 36 0.90
36 4 0.10
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (36 bp):
TTTTTCTTATTAAAGGTTTCATAAAAAAATTGGGTA
Found at i:39986 original size:23 final size:21
Alignment explanation
Indices: 39934--39995 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
39924 TTTTGGTGCA
*
39934 GAGGGAATCGA-TCCCCCATT
1 GAGGGAACCGATTCCCCCATT
*
39954 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCATT
39975 GAAGGGGAACCGATTTCCCCC
1 G-A-GGGAACCGA-TTCCCCC
39996 CCACAGGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 9 0.25
24 7 0.19
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCATT
Found at i:43590 original size:37 final size:37
Alignment explanation
Indices: 43519--43591 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
43509 TGGAAAATAT
* * *
43519 TTATATATTTTCTTTTAAAAATTTAAATTCATAAAAC
1 TTATATATTTTCTTATAAAAATTGAAAATCATAAAAC
43556 TTATATAATTTT-TTATACAAAATTGAAAAT-ATAAAA
1 TTATAT-ATTTTCTTATA-AAAATTGAAAATCATAAAA
43592 AGGTTTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (37 bp):
TTATATATTTTCTTATAAAAATTGAAAATCATAAAAC
Found at i:44762 original size:31 final size:30
Alignment explanation
Indices: 44727--44794 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
44717 TTTAGATATT
* *
44727 AAATTAATAT-TTTTATTGAAATTTAATAATC
1 AAATTAATATATTAT-TTAAAATTTAA-AATC
*
44758 AAATTGATATATTATTTAAAATTTAAAATC
1 AAATTAATATATTATTTAAAATTTAAAATC
*
44788 AGATTAA
1 AAATTAA
44795 CATTATGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 9 0.29
31 19 0.61
32 3 0.10
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATTAATATATTATTTAAAATTTAAAATC
Found at i:45416 original size:29 final size:29
Alignment explanation
Indices: 45372--45429 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
45362 TCTCCATCCA
45372 TTAACATATTGAATTATATTTAATAACTT
1 TTAACATATTGAATTATATTTAATAACTT
45401 TTAACATATT-ATATTATATTTAATAACTT
1 TTAACATATTGA-ATTATATTTAATAACTT
45430 ATCCAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (29 bp):
TTAACATATTGAATTATATTTAATAACTT
Found at i:48658 original size:2 final size:2
Alignment explanation
Indices: 48651--48679 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48641 GATGTGATTA
48651 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 A
48680 ATTTGGGATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49288 original size:18 final size:18
Alignment explanation
Indices: 49233--49288 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
49223 TTAATTAATT
49233 AATATTAATTTAGG-TTTA
1 AATATTAATTT-GGATTTA
49251 AA-AGTT-A-TTGGATCTTA
1 AATA-TTAATTTGGAT-TTA
49268 AATATTAATTTGGATTTA
1 AATATTAATTTGGATTTA
49286 AAT
1 AAT
49289 GATTTGGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
15 2 0.06
16 3 0.09
17 9 0.28
18 12 0.38
19 6 0.19
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.46
Consensus pattern (18 bp):
AATATTAATTTGGATTTA
Found at i:55123 original size:59 final size:59
Alignment explanation
Indices: 55025--55152 Score: 150
Period size: 59 Copynumber: 2.2 Consensus size: 59
55015 AGCAGGCTGT
** * *
55025 ATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTAGG-CACAACCTTGTGTGTC
1 ATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGT-GGACACAACCTTATGTGTC
* ** * *
55084 ATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTC
1 ATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGTC
*
55143 ATACTCGGGA
1 ATATTCGGGA
55153 TTGCATTACG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 2 0.03
59 56 0.97
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (59 bp):
ATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGTC
Found at i:56067 original size:37 final size:37
Alignment explanation
Indices: 56014--56094 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
56004 GAGTAAGGTA
56014 GGGTCGGGTCAAGCGCTCAGGTCGGACACATGTCAAC
1 GGGTCGGGTCAAGCGCTCAGGTCGGACACATGTCAAC
**
56051 GGGTCGGGTCGGGCGCTCAGGTCGGACACATGTCAAC
1 GGGTCGGGTCAAGCGCTCAGGTCGGACACATGTCAAC
56088 GGGTCGG
1 GGGTCGG
56095 ATTAACTTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.17, C:0.26, G:0.41, T:0.16
Consensus pattern (37 bp):
GGGTCGGGTCAAGCGCTCAGGTCGGACACATGTCAAC
Found at i:62645 original size:121 final size:121
Alignment explanation
Indices: 62508--62756 Score: 489
Period size: 121 Copynumber: 2.1 Consensus size: 121
62498 TATTTGTAAA
*
62508 CCAATTTTTTTTTTATCAAATCTTGTAGTTAGGCAAGATTCAAATTAATCCTAAAAACACAAATT
1 CCAATTTTTTTTTTATCAAATCTTGTAGTTAGACAAGATTCAAATTAATCCTAAAAACACAAATT
62573 TTGCAAAATTTACCGAAACTTATAGCCAAGGTTTTGGTTCGTGGCATAAAAGATAC
66 TTGCAAAATTTACCGAAACTTATAGCCAAGGTTTTGGTTCGTGGCATAAAAGATAC
62629 CCAATTTTTTTTTTATCAAATCTTGTAGTTAGACAAGATTCAAATTAATCCTAAAAACACAAATT
1 CCAATTTTTTTTTTATCAAATCTTGTAGTTAGACAAGATTCAAATTAATCCTAAAAACACAAATT
62694 TTGCAAAATTTACCGAAACTTATAGCCAAGGTTTTGGTTCGTGGCATAAAAGATAC
66 TTGCAAAATTTACCGAAACTTATAGCCAAGGTTTTGGTTCGTGGCATAAAAGATAC
62750 CCAATTT
1 CCAATTT
62757 GCATCACATC
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 127 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (121 bp):
CCAATTTTTTTTTTATCAAATCTTGTAGTTAGACAAGATTCAAATTAATCCTAAAAACACAAATT
TTGCAAAATTTACCGAAACTTATAGCCAAGGTTTTGGTTCGTGGCATAAAAGATAC
Found at i:64529 original size:22 final size:22
Alignment explanation
Indices: 64501--64545 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
64491 CCCAACACAT
64501 AGGTCGCCATACCCTCCGGGCG
1 AGGTCGCCATACCCTCCGGGCG
* *
64523 AGGTCGCCATGCTCTCCGGGCG
1 AGGTCGCCATACCCTCCGGGCG
64545 A
1 A
64546 CCTTGTAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.13, C:0.38, G:0.33, T:0.16
Consensus pattern (22 bp):
AGGTCGCCATACCCTCCGGGCG
Found at i:64565 original size:29 final size:29
Alignment explanation
Indices: 64523--64606 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
64513 CCTCCGGGCG
*
64523 AGGTCGCCATGCTCTCCGGGCGACCTTGT
1 AGGTCGCCATGCTCTCCGGGCAACCTTGT
*
64552 AGGTCGCTATGCTCTCCGGGCAACCTTGT
1 AGGTCGCCATGCTCTCCGGGCAACCTTGT
* *
64581 AGGTTGCCATGCACTCCGGGCAACCT
1 AGGTCGCCATGCTCTCCGGGCAACCT
64607 ACCCTTGCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.14, C:0.33, G:0.29, T:0.24
Consensus pattern (29 bp):
AGGTCGCCATGCTCTCCGGGCAACCTTGT
Found at i:64661 original size:33 final size:33
Alignment explanation
Indices: 64624--64687 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
64614 CTCGGCTGCC
*
64624 CTCGCATAGCTCGCTCGGATGGCCTCGGATGTT
1 CTCGCATAGCTCGCTCGGATGACCTCGGATGTT
* *
64657 CTCGCATAGCTCGGTTGGATGACCTCGGATG
1 CTCGCATAGCTCGCTCGGATGACCTCGGATG
64688 CCCAGCGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.27
Consensus pattern (33 bp):
CTCGCATAGCTCGCTCGGATGACCTCGGATGTT
Found at i:67869 original size:20 final size:20
Alignment explanation
Indices: 67844--67883 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
67834 TCCAAATTCT
67844 CAACGCGAATATGTAAATCG
1 CAACGCGAATATGTAAATCG
*
67864 CAACGCGAATTTGTAAATCG
1 CAACGCGAATATGTAAATCG
67884 TAACACAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
CAACGCGAATATGTAAATCG
Found at i:67918 original size:20 final size:20
Alignment explanation
Indices: 67893--68066 Score: 142
Period size: 20 Copynumber: 8.8 Consensus size: 20
67883 GTAACACAGA
*
67893 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCAAT
* *
67913 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCAAT
* *
67933 AGTCAATTTCTCAACGCAAT
1 AGTCAAATTCGCAACGCAAT
67953 AGTCAAATTCGCAACGCGAATT
1 AGTCAAATTCGCAACGC-AA-T
* * *
67975 TGT-TAA-TCGCAACAC-AT
1 AGTCAAATTCGCAACGCAAT
* * *
67992 AAGTCAAATTCGTAATGCGAT
1 -AGTCAAATTCGCAACGCAAT
* *
68013 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCAAT
*
68033 AGTTAAATTCGCAACTG-AAT
1 AGTCAAATTCGCAAC-GCAAT
*
68053 -TTCAAATTCGCAAC
1 AGTCAAATTCGCAAC
68067 ACGAATTTAC
Statistics
Matches: 120, Mismatches: 27, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
17 1 0.01
18 3 0.03
19 14 0.12
20 93 0.77
21 6 0.05
22 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCAAT
Found at i:67957 original size:60 final size:59
Alignment explanation
Indices: 67893--68047 Score: 170
Period size: 60 Copynumber: 2.6 Consensus size: 59
67883 GTAACACAGA
*
67893 AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAATTTC-TCAACGCAAT
1 AGTCAAATTCGCAACGCGATAGT-AAATTCGCAACACAAAAGTCAAATTCGT-AACGCAAT
* * * * *
67953 AGTCAAATTCGCAACGCGAATTTGTTAA-TCGCAACACATAAGTCAAATTCGTAATGCGAT
1 AGTCAAATTCGCAACGCG-A-TAGTAAATTCGCAACACAAAAGTCAAATTCGTAACGCAAT
* * *
68013 AGTCAAATTCGCAACACAAAAGTTAAATTCGCAAC
1 AGTCAAATTCGCAACGCGATAG-TAAATTCGCAAC
68048 TGAATTTCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
58 1 0.01
59 4 0.05
60 67 0.85
61 4 0.05
62 3 0.04
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (59 bp):
AGTCAAATTCGCAACGCGATAGTAAATTCGCAACACAAAAGTCAAATTCGTAACGCAAT
Found at i:67973 original size:100 final size:100
Alignment explanation
Indices: 67836--68074 Score: 333
Period size: 100 Copynumber: 2.4 Consensus size: 100
67826 TTAGATTTTC
*
67836 CAAATTCTCAACGCGAATATGT-AAA-TCGCAACGCGAATTTGTAAATCGTAACACAGAAGTCAA
1 CAAATTCTCAACGC-AATA-GTCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAA
67899 ATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
64 ATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
* * *
67936 CAATTTCTCAACGCAATAGTCAAATTCGCAACGCGAATTTGTTAATCGCAACACATAAGTCAAAT
1 CAAATTCTCAACGCAATAGTCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
* *
68001 TCGTAATGCGATAGTCAAATTCGCAACACAAAAGT
66 TCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
* * * *
68036 TAAATTCGCAACTG-AAT-TTCAAATTCGCAACACGAATTT
1 CAAATTCTCAAC-GCAATAGTCAAATTCGCAACGCGAATTT
68075 ACTTTCGCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
98 2 0.02
99 27 0.22
100 95 0.76
101 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (100 bp):
CAAATTCTCAACGCAATAGTCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
TCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
Found at i:68074 original size:20 final size:20
Alignment explanation
Indices: 68015--68074 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
68005 AATGCGATAG
* *
68015 TCAAATTCGCAACACAAAAGT
1 TCAAATTCGCAACAC-GAATT
*
68036 T-AAATTCGCAAC-TGAATT
1 TCAAATTCGCAACACGAATT
68054 TCAAATTCGCAACACGAATT
1 TCAAATTCGCAACACGAATT
68074 T
1 T
68075 ACTTTCGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 4 0.12
19 11 0.33
20 17 0.52
21 1 0.03
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.27
Consensus pattern (20 bp):
TCAAATTCGCAACACGAATT
Found at i:68834 original size:12 final size:12
Alignment explanation
Indices: 68813--68846 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
68803 ACCACATTTC
*
68813 CAATACCAAACA
1 CAATATCAAACA
68825 CAATATCAAACA
1 CAATATCAAACA
*
68837 CAATCTCAAA
1 CAATATCAAA
68847 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:71292 original size:18 final size:18
Alignment explanation
Indices: 71269--71304 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
71259 AAGCAAAAGG
*
71269 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
71287 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
71305 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:71646 original size:20 final size:20
Alignment explanation
Indices: 71621--71664 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
71611 AAACCGAAAA
71621 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
*
71641 TCGCGTTGTGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
71661 TCGC
1 TCGC
71665 AACGCTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTT
Found at i:73536 original size:4 final size:4
Alignment explanation
Indices: 73504--73553 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
73494 GAACCGCTGA
* * * *
73504 AAAT AAAT TAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
73552 AA
1 AA
73554 TGCCGAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:73804 original size:21 final size:21
Alignment explanation
Indices: 73776--73825 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
73766 ACCATTATCT
*
73776 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
*
73797 TGACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
73818 TCACGTAA
1 TCACGTAA
73826 TTCCCCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:75549 original size:19 final size:19
Alignment explanation
Indices: 75498--75551 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
75488 AGAAGTTTCT
*
75498 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
75518 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
75538 GAAACTAAAATCGC
1 GAAACTAAAATCGC
75552 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:76073 original size:20 final size:20
Alignment explanation
Indices: 76048--76232 Score: 121
Period size: 20 Copynumber: 9.2 Consensus size: 20
76038 GCGTAAAAAC
* *
76048 ATTTGACTTTCGCGTTGCAA
1 ATTTGACTATCGCGTTGCGA
*
76068 ATTTGACTATCGCGTTACGA
1 ATTTGACTATCGCGTTGCGA
*
76088 ATGTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
**
76108 ATTTGACT-TCTATGTTGCG-
1 ATTTGACTATC-GCGTTGCGA
* * *
76127 ATTT-ACAAATTTGAGTTGCGA
1 ATTTGAC-TA-TCGCGTTGCGA
* * * * * *
76148 ATTTTATTTTTGTGTTACGA
1 ATTTGACTATCGCGTTGCGA
76168 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
76188 ATTTGACTTAT-GTGTTGCG-
1 ATTTGAC-TATCGCGTTGCGA
*
76207 ATTT-ACATATTCGCGTTGTGA
1 ATTTGAC-TA-TCGCGTTGCGA
76228 ATTTG
1 ATTTG
76233 GAAAATCACA
Statistics
Matches: 127, Mismatches: 27, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
18 6 0.05
19 11 0.09
20 97 0.76
21 12 0.09
22 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.42
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:76145 original size:40 final size:40
Alignment explanation
Indices: 76097--76232 Score: 150
Period size: 40 Copynumber: 3.4 Consensus size: 40
76087 AATGTGACTA
* * *
76097 TCGCGTTGCGAATTTGACTTCTATGTTGCGATTTACAAAT
1 TCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACATAT
* * * * * *
76137 TTGAGTTGCGAATTTTATTTTTGTGTTACGAATTTGAC-TA-
1 TCGCGTTGCGAATTTGACTTATGTGTTGCG-ATTT-ACATAT
76177 TCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACATAT
1 TCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACATAT
*
76217 TCGCGTTGTGAATTTG
1 TCGCGTTGCGAATTTG
76233 GAAAATCACA
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 2 0.03
39 6 0.08
40 62 0.81
41 5 0.06
42 2 0.03
ACGTcount: A:0.21, C:0.13, G:0.22, T:0.44
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACATAT
Found at i:76194 original size:80 final size:80
Alignment explanation
Indices: 76081--76231 Score: 239
Period size: 80 Copynumber: 1.9 Consensus size: 80
76071 TGACTATCGC
* *
76081 GTTACGAATGTGACTATCGCGTTGCGAATTTGACTTCTATGTTGCGATTTACAAATTTGAGTTGC
1 GTTACGAATGTGACTATCGCGTTGCGAATTTGACTTATATGTTGCGATTTACAAATTCGAGTTGC
76146 GAATTTTATTTTTGT
66 GAATTTTATTTTTGT
* * * * *
76161 GTTACGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACATATTCGCGTTGT
1 GTTACGAATGTGACTATCGCGTTGCGAATTTGACTTATATGTTGCGATTTACAAATTCGAGTTGC
76226 GAATTT
66 GAATTT
76232 GGAAAATCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 64 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (80 bp):
GTTACGAATGTGACTATCGCGTTGCGAATTTGACTTATATGTTGCGATTTACAAATTCGAGTTGC
GAATTTTATTTTTGT
Found at i:76267 original size:20 final size:20
Alignment explanation
Indices: 76201--76268 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
76191 TGACTTATGT
76201 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
* ** * * *
76221 GTTGTGAATTTGGAAAATCAC
1 GTTGCG-ATTTACATATTCGC
**
76242 AATGCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
76262 GTTGCGA
1 GTTGCGA
76269 AATTGGAAAC
Statistics
Matches: 31, Mismatches: 16, Indels: 2
0.63 0.33 0.04
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:81048 original size:14 final size:14
Alignment explanation
Indices: 81029--81057 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
81019 TTACTCGTGG
81029 AATATACACTAATC
1 AATATACACTAATC
81043 AATATACACTAATC
1 AATATACACTAATC
81057 A
1 A
81058 CACCCTTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (14 bp):
AATATACACTAATC
Found at i:82596 original size:11 final size:11
Alignment explanation
Indices: 82582--82608 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
82572 CTATATAGAG
82582 TTATGTCGTAC
1 TTATGTCGTAC
82593 TTATGTCGTAC
1 TTATGTCGTAC
82604 TTATG
1 TTATG
82609 CATATGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.48
Consensus pattern (11 bp):
TTATGTCGTAC
Found at i:85726 original size:157 final size:156
Alignment explanation
Indices: 85388--85751 Score: 372
Period size: 157 Copynumber: 2.3 Consensus size: 156
85378 CATCCGATTC
* * *
85388 ATCTTTCATTTTAAGT-TTATTTTTTTACCAAATTTGAATCACATGCTCTTAAACCATTTTAAGA
1 ATCTTTCATTTTAAGTCCT-TTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATTTTAAGA
* * * ** * *
85452 TACCTTTGTGTCTTCAATTTCTATTTTTGATAACAAATGTTCTATTTTTTCAATTTAGTCCACAA
65 TAACTATGTATCTTCAATTTCTATTTTTGAT---AAATGTTCTATACTGTCAATTTAATCCACAA
* * *
85517 CTTTAAATGATTTTCTTATCCCTTCAATTC
127 CTTCAAATGATTTCCTTATCCCTTCAATTA
*
85547 AT-TGTTCATTTTAATTCC--TTTTTTACCAAATTTGAACCACATGCTCCTAAACCATTTT-AGA
1 ATCT-TTCATTTTAAGTCCTTTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATTTTAAG-
*
85608 ATAACTATGTATCTTCAA-TTCT-TCATTTTGAT-AAT-TTTTATACTGTCAATTTAATCC-CTT
64 ATAACTATGTATCTTCAATTTCTAT--TTTTGATAAATGTTCTATACTGTCAATTTAATCCAC--
**
85668 AAC-TCAACATGATTTCCTTATTTCTTCAATTA
125 AACTTCAA-ATGATTTCCTTATCCCTTCAATTA
* *
85700 ATCTTTCATTTTAAGTCCATTTTTTTTATCAAATTTGAACCACACGCTCCTA
1 ATCTTTCATTTTAAGTCC-TTTTTTTTACCAAATTTGAACCACATGCTCCTA
85752 TACAACTATA
Statistics
Matches: 173, Mismatches: 20, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
151 1 0.01
152 20 0.12
153 41 0.24
154 1 0.01
155 1 0.01
156 35 0.20
157 60 0.35
158 1 0.01
159 13 0.08
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (156 bp):
ATCTTTCATTTTAAGTCCTTTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATTTTAAGAT
AACTATGTATCTTCAATTTCTATTTTTGATAAATGTTCTATACTGTCAATTTAATCCACAACTTC
AAATGATTTCCTTATCCCTTCAATTA
Found at i:87911 original size:2 final size:2
Alignment explanation
Indices: 87904--87978 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
87894 TTTGAGGTTA
87904 AT AT AT AT AT 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 AT AT AT AT AT
87946 AT 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 A
87979 AAGTAAAATG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:88784 original size:24 final size:25
Alignment explanation
Indices: 88756--88802 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
88746 AGAAACGTGC
*
88756 CACAAGAGCAGAGAAAAA-GTGTGA
1 CACAAGAGCAAAGAAAAACGTGTGA
88780 CACAAGAGCAAAGAAAAACGTGT
1 CACAAGAGCAAAGAAAAACGTGT
88803 TACAAGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.26, T:0.09
Consensus pattern (25 bp):
CACAAGAGCAAAGAAAAACGTGTGA
Done.