Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006445.1 Hibiscus syriacus cultivar Beakdansim tig00015582_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: 62000
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:4433 original size:2 final size:2
Alignment explanation
Indices: 4428--4484 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
4418 AATTTTTTTA
4428 AT AT AT -T AT AT AT AT AT AT AT AT A- 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
4468 AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT
4485 CAACTGTTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 49 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6231 original size:32 final size:31
Alignment explanation
Indices: 6171--6233 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
6161 AGTAATTTTG
*
6171 TGATTATATGTTATTACATACGTCGAAATAA
1 TGATTATATGTTATTACATAAGTCGAAATAA
* * *
6202 TGATGTATATGTTGTTACATAATTTGAAATAA
1 TGAT-TATATGTTATTACATAAGTCGAAATAA
6234 GCTTTGGATC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.41
Consensus pattern (31 bp):
TGATTATATGTTATTACATAAGTCGAAATAA
Found at i:7316 original size:14 final size:14
Alignment explanation
Indices: 7306--7947 Score: 359
Period size: 14 Copynumber: 46.8 Consensus size: 14
7296 GTAATTATTA
7306 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
7320 TTAAATCATTAAAA
1 TTAAATCATTAAAG
* *
7334 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
7348 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
7362 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
* **
7376 TTATATTGTTAAAG
1 TTAAATCATTAAAG
* * * *
7390 CTAAGTAATTATTA-
1 TTAAATCATTA-AAG
7404 TTAAATCATTAAAG
1 TTAAATCATTAAAG
7418 TTAAATCATT-AAG
1 TTAAATCATTAAAG
*
7431 -T-AATTATT--A-
1 TTAAATCATTAAAG
* *
7440 TTATATCATTAAAT
1 TTAAATCATTAAAG
*
7454 TTAAATCATTAAAC
1 TTAAATCATTAAAG
* *
7468 TTAAATAATTAGTA-
1 TTAAATCATTA-AAG
* *
7482 TTAAATTATTAAAT
1 TTAAATCATTAAAG
*
7496 TTAAATCATTAAAA
1 TTAAATCATTAAAG
* * *
7510 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
7524 TTAAATCATTAAAG
1 TTAAATCATTAAAG
7538 TTAAATCATTAAA-
1 TTAAATCATTAAAG
*
7551 -T-AATTATT--A-
1 TTAAATCATTAAAG
* *
7560 TTAAATCGTTAAAT
1 TTAAATCATTAAAG
*
7574 TTAAATCATTAAAC
1 TTAAATCATTAAAG
* *
7588 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
* *
7602 TTAAATTATTAAAT
1 TTAAATCATTAAAG
*
7616 TTAAATCATTAAAC
1 TTAAATCATTAAAG
* *
7630 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
*
7644 TTAAA-CATTAAAA
1 TTAAATCATTAAAG
* * *
7657 TTAAATAAATATTA-
1 TTAAATCATTA-AAG
* *
7671 TTAAATTATTAAAT
1 TTAAATCATTAAAG
7685 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
7699 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
*
7713 TTAAATTATTAAAG
1 TTAAATCATTAAAG
7727 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
7741 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
7755 TTAAATCATTAAAG
1 TTAAATCATTAAAG
7769 TTAAAT-ATTTAAAG
1 TTAAATCA-TTAAAG
* * *
7783 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
* *
7797 TTAAATCATTAGAT
1 TTAAATCATTAAAG
7811 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
7825 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
*
7839 TCAAATCATTAAAG
1 TTAAATCATTAAAG
7853 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
7867 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
7881 TTAAATCATTAAAG
1 TTAAATCATTAAAG
7895 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
7909 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
*
7923 TTAAATCATTAAAC
1 TTAAATCATTAAAG
*
7937 TTAAATAATTA
1 TTAAATCATTA
7948 TTATTAAATA
Statistics
Matches: 483, Mismatches: 104, Indels: 82
0.72 0.16 0.12
Matches are distributed among these distances:
9 1 0.00
10 3 0.01
11 22 0.05
12 3 0.01
13 28 0.06
14 411 0.85
15 15 0.03
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:7822 original size:126 final size:126
Alignment explanation
Indices: 7644--7947 Score: 504
Period size: 126 Copynumber: 2.4 Consensus size: 126
7634 ATAATTATTA
* * * *
7644 TTAAA-CATTAAAATTAAATAAATATTATTAAATTATTAAATTTAAATCATTAAAGTTAAGTAAT
1 TTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAATTTAAATCATTAAAGTTAAGTAAT
* *
7708 TATTATTAAATTATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAG
66 TATTATCAAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAG
*
7769 TTAAAT-ATTTAAAGTTAAGTAATTATTATTAAATCATTAGATTTAAATCATTAAAGTTAAGTAA
1 TTAAATCA-TTAAAGTTAAGTAATTATTATTAAATCATTAAATTTAAATCATTAAAGTTAAGTAA
7833 TTATTATCAAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAG
65 TTATTATCAAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAG
* *
7895 TTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAACTTAAATAATTA
1 TTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAATTTAAATCATTA
7948 TTATTAAATA
Statistics
Matches: 166, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
125 6 0.04
126 159 0.96
127 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (126 bp):
TTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAATTTAAATCATTAAAGTTAAGTAAT
TATTATCAAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAG
Found at i:7923 original size:84 final size:84
Alignment explanation
Indices: 7259--7662 Score: 350
Period size: 78 Copynumber: 4.8 Consensus size: 84
7249 GCATATTTAC
* * * *
7259 TATTATTATATCAATAAA-TATAAATAATTAAAGTCAAGTAATTATTATTAAATCATTAAAGTTA
1 TATTATTAAATCATTAAAGT-TAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTA
* *
7323 AATCATTAAAATTAAATAAT
65 AATCATTAAAGTTAAGTAAT
* *
7343 TATTATTAAATCATTAAAGTTAAGTAATTATTATTATATTGTTAAAGCTAAGTAATTATTATTAA
1 TATTATTAAATCATTAAAGTT-A--AATCATTA--A-A--GTT-AAG-TAA-TTATTA---TTAA
7408 ATCATTAAAGTTAAATC-----A-TTAAGTAAT
52 ATCATTAAAGTTAAATCATTAAAGTTAAGTAAT
* * * * * * *
7435 TATTATTATATCATTAAATTTAAATCATTAAACTTAAATAATTAGTATTAAATTATTAAATTTAA
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTAA
*
7500 ATCATTAAAATTAAGTAAT
66 ATCATTAAAGTTAAGTAAT
* *
7519 TATTATTAAATCATTAAAGTTAAATCATT--A---AA-TAATTATTATTAAATCGTTAAATTTAA
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTAA
* *
7578 ATCATTAAACTTAAATAAT
66 ATCATTAAAGTTAAGTAAT
* * * * *
7597 TATTATTAAATTATTAAATTTAAATCATTAAACTTAAATAATTATTATTAAA-CATTAAAATTAA
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTAA
7661 AT
66 AT
7663 AAATATTATT
Statistics
Matches: 267, Mismatches: 26, Indels: 55
0.77 0.07 0.16
Matches are distributed among these distances:
78 87 0.33
79 2 0.01
80 1 0.00
81 4 0.01
82 4 0.01
83 17 0.06
84 69 0.26
85 2 0.01
86 1 0.00
87 8 0.03
89 8 0.03
90 1 0.00
91 1 0.00
92 29 0.11
93 4 0.01
94 3 0.01
95 5 0.02
98 21 0.08
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (84 bp):
TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTAA
ATCATTAAAGTTAAGTAAT
Found at i:7929 original size:42 final size:42
Alignment explanation
Indices: 7259--7662 Score: 369
Period size: 42 Copynumber: 9.6 Consensus size: 42
7249 GCATATTTAC
* * * * * * *
7259 TATTATTATATCAATAAATATAAATAATTAAAGTCAAGTAAT
1 TATTATTAAATCATTAAATTTAAATCATTAAACTTAAATAAT
* *
7301 TATTATTAAATCATTAAAGTTAAATCATTAAAATTAAATAAT
1 TATTATTAAATCATTAAATTTAAATCATTAAACTTAAATAAT
* * * * * **
7343 TATTATTAAATCATTAAAGTTAAGTAATTATTA-TTATATTGT
1 TATTATTAAATCATTAAATTTAAATCATTA-AACTTAAATAAT
* * * * *
7385 TAAAGCTAAGTAATTATTATTAAATCATTAAA--GTTAAATCATTAAGTAAT
1 T--A--TTATTAA--ATCATTAAAT--TTAAATCATTAAA-C-TTAAATAAT
*
7435 TATTATTATATCATTAAATTTAAATCATTAAACTTAAATAAT
1 TATTATTAAATCATTAAATTTAAATCATTAAACTTAAATAAT
* * * *
7477 TAGTATTAAATTATTAAATTTAAATCATTAAAATTAAGTAAT
1 TATTATTAAATCATTAAATTTAAATCATTAAACTTAAATAAT
*
7519 TATTATTAAATCATTAAAGTTAAATC-----A-TTAAATAAT
1 TATTATTAAATCATTAAATTTAAATCATTAAACTTAAATAAT
*
7555 TATTATTAAATCGTTAAATTTAAATCATTAAACTTAAATAAT
1 TATTATTAAATCATTAAATTTAAATCATTAAACTTAAATAAT
*
7597 TATTATTAAATTATTAAATTTAAATCATTAAACTTAAATAAT
1 TATTATTAAATCATTAAATTTAAATCATTAAACTTAAATAAT
*
7639 TATTATTAAA-CATTAAAATTAAAT
1 TATTATTAAATCATTAAATTTAAAT
7663 AAATATTATT
Statistics
Matches: 296, Mismatches: 46, Indels: 41
0.77 0.12 0.11
Matches are distributed among these distances:
36 32 0.11
37 1 0.00
41 13 0.04
42 201 0.68
43 2 0.01
44 15 0.05
46 9 0.03
47 1 0.00
48 12 0.04
50 10 0.03
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (42 bp):
TATTATTAAATCATTAAATTTAAATCATTAAACTTAAATAAT
Found at i:10744 original size:77 final size:77
Alignment explanation
Indices: 10617--10772 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 77
10607 ATTATCTCGA
*
10617 CAGTTTTGCCAAATTTCAATACTAAAAATCATATGGCAAATAGTGATAAAGGTAAAATTGATGTT
1 CAGTTTTGCCAAATTTCAATACTAAAAATCATATGGCAAATAGTGATAAAGGTAAAATCGATGTT
10682 AAGAAAGGTAAG
66 AAGAAAGGTAAG
10694 CAGTTTTGCCAAATTTCAATACTAAAAATCATATGGCAAATAGTGATAAAGGTAAAATCGATGTT
1 CAGTTTTGCCAAATTTCAATACTAAAAATCATATGGCAAATAGTGATAAAGGTAAAATCGATGTT
10759 AAGAAAGGTAAG
66 AAGAAAGGTAAG
10771 CA
1 CA
10773 TCAAAGCATG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (77 bp):
CAGTTTTGCCAAATTTCAATACTAAAAATCATATGGCAAATAGTGATAAAGGTAAAATCGATGTT
AAGAAAGGTAAG
Found at i:15700 original size:21 final size:21
Alignment explanation
Indices: 15648--15702 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
15638 TTTGCTATTT
*
15648 TTTCAAAAAAAAAAGGCAAAA
1 TTTCAAAAAAAAAAGCCAAAA
***
15669 -AAAAAACAAAAAAAGCCAAAA
1 TTTCAAA-AAAAAAAGCCAAAA
15690 TTTCAAAAAAAAA
1 TTTCAAAAAAAAA
15703 TGCAAACGAA
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.73, C:0.11, G:0.05, T:0.11
Consensus pattern (21 bp):
TTTCAAAAAAAAAAGCCAAAA
Found at i:23491 original size:228 final size:228
Alignment explanation
Indices: 23225--23673 Score: 627
Period size: 228 Copynumber: 2.0 Consensus size: 228
23215 TTAATCAAAT
23225 AATTAAATTTAAAATGACAATAAAATAATAAAAATTAATTTTACCTTCTAAAAACTATAA-AAAA
1 AATTAAATTTAAAATGACAATAAAATAATAAAAATTAATTTTACCTTCTAAAAACTATAACAAAA
* * ** *
23289 TCTACTTAAATTGATAAAGAAAAATTATAGAATGAAT-AATATGGAATTAAATTTTAGTGTTATT
66 TCTACTTAAATTAATAAAG-AAAATTATAGAA-CAATAAATATAAAATTAAATTTTAGTGTGATT
* * *
23353 TTATGTTTATTGACGATGCTATTTATATAGGAGGGGTGACTGAT-TCACAAGGTTCGA-GTAATG
129 TTATATTTATTGACGATGCTATTTATATAGGAGAGGTGACTGATAT-ACAAGATT-GAGGTAATG
* * * *
23416 ATGGAGTACCTAATAATTTAAATAAATAATTTAAGGA
192 ATAGAATACCCAATAATTTAAAAAAATAATTTAAGGA
*
23453 AATTAAATTTAAAATGACAATAAAATAATAAAAATTAATTTTACTTTCTAAAAACTATAACAAAA
1 AATTAAATTTAAAATGACAATAAAATAATAAAAATTAATTTTACCTTCTAAAAACTATAACAAAA
** * *
23518 TCTACTTAGCTTAATAGAGAAAATTATAGAACAATAAATATAAAATTAAATTTTGGTGTGATTTT
66 TCTACTTAAATTAATAAAGAAAATTATAGAACAATAAATATAAAATTAAATTTTAGTGTGATTTT
* * * * * *
23583 ATATTTATTGACGGTGTTATTTATATGGGAGAGGTGAGTGATATGCAAGATTTAGGTAATGATAG
131 ATATTTATTGACGATGCTATTTATATAGGAGAGGTGACTGATATACAAGATTGAGGTAATGATAG
23648 AATACCCAATAATTTAAAAAAATAAT
196 AATACCCAATAATTTAAAAAAATAAT
23674 AGAATGCGTG
Statistics
Matches: 194, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
227 4 0.02
228 170 0.88
229 20 0.10
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (228 bp):
AATTAAATTTAAAATGACAATAAAATAATAAAAATTAATTTTACCTTCTAAAAACTATAACAAAA
TCTACTTAAATTAATAAAGAAAATTATAGAACAATAAATATAAAATTAAATTTTAGTGTGATTTT
ATATTTATTGACGATGCTATTTATATAGGAGAGGTGACTGATATACAAGATTGAGGTAATGATAG
AATACCCAATAATTTAAAAAAATAATTTAAGGA
Found at i:24044 original size:32 final size:32
Alignment explanation
Indices: 23995--24060 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
23985 ACCACAGACC
23995 ATGAATGCGACTCTCAAACGTTAAATCAACAA
1 ATGAATGCGACTCTCAAACGTTAAATCAACAA
* *
24027 ATGAATGTGACTTTCAAACGTTAAATCAACAA
1 ATGAATGCGACTCTCAAACGTTAAATCAACAA
24059 AT
1 AT
24061 ACCACCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (32 bp):
ATGAATGCGACTCTCAAACGTTAAATCAACAA
Found at i:24664 original size:23 final size:23
Alignment explanation
Indices: 24620--24664 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
24610 AGTGTTATAT
*
24620 TATATTTTAAAAATGTTAATTAG
1 TATATTTTAAAAATCTTAATTAG
* *
24643 TATATTTTAAATATCTTTATTA
1 TATATTTTAAAAATCTTAATTA
24665 AAATATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATCTTAATTAG
Found at i:24670 original size:23 final size:23
Alignment explanation
Indices: 24621--24671 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
24611 GTGTTATATT
* **
24621 ATATTTTAAAAATGTTAATTAGT
1 ATATTTTAAAAATCTTAATTAAA
* *
24644 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATCTTAATTAAA
24667 ATATT
1 ATATT
24672 ATTAGATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATCTTAATTAAA
Found at i:24751 original size:27 final size:26
Alignment explanation
Indices: 24702--24764 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 26
24692 TTAAATATAC
24702 AAATAATATTATTCATTATTAA-TAATT
1 AAATAATATTATTCA-TATTAATTAA-T
*
24729 TAATAATATTATTTCA-ATGTAATTAAT
1 AAATAATATTA-TTCATAT-TAATTAAT
24756 AAATAATAT
1 AAATAATAT
24765 AAATTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 22 0.71
28 7 0.23
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (26 bp):
AAATAATATTATTCATATTAATTAAT
Found at i:24882 original size:34 final size:33
Alignment explanation
Indices: 24780--24884 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 33
24770 TTATTAAAAA
* *
24780 TTTATTAT-ATATTATTAAAATAAAAATATAATATCT
1 TTTATTATAATATTA--AAAAT-ATAATA-AATATAT
* * * **
24816 TATATTATATTATT-ATAATATAATTGAT-TAT
1 TTTATTATAATATTAAAAATATAATAAATATAT
24847 TTTATTATAATATTAAAAATATTAATAAATATAT
1 TTTATTATAATATTAAAAATA-TAATAAATATAT
24881 TTTA
1 TTTA
24885 AATATTTTAA
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
31 14 0.26
32 7 0.13
33 10 0.19
34 11 0.21
36 7 0.13
37 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (33 bp):
TTTATTATAATATTAAAAATATAATAAATATAT
Found at i:24886 original size:23 final size:24
Alignment explanation
Indices: 24859--24907 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
24849 TATTATAATA
24859 TTAAAAATATTAATAAAT-ATATT
1 TTAAAAATATTAATAAATAATATT
* * *
24882 TTAAATATTTTAATAATTAATATT
1 TTAAAAATATTAATAAATAATATT
24906 TT
1 TT
24908 GATTAAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAAAAATATTAATAAATAATATT
Found at i:25157 original size:42 final size:42
Alignment explanation
Indices: 25110--25189 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
25100 ACCAAACACT
**
25110 AAAAAATATTTTTCAGTAAATAAATTACATAAAACAAATGCG
1 AAAAAATATTTTTCAAAAAATAAATTACATAAAACAAATGCG
* *
25152 AAAAAATATTTTTCAAAAAATAAATTACGTGAAACAAA
1 AAAAAATATTTTTCAAAAAATAAATTACATAAAACAAA
25190 AAAATAAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (42 bp):
AAAAAATATTTTTCAAAAAATAAATTACATAAAACAAATGCG
Found at i:29031 original size:12 final size:13
Alignment explanation
Indices: 28995--29036 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
28985 CAATTTATTA
28995 TTTTA-ATTAAATT
1 TTTTATATT-AATT
29008 TTATTATATTAATT
1 TT-TTATATTAATT
29022 TTTT-TATTAATT
1 TTTTATATTAATT
29034 TTT
1 TTT
29037 GCAGTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 11 0.41
13 4 0.15
14 9 0.33
15 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTATATTAATT
Found at i:29155 original size:18 final size:16
Alignment explanation
Indices: 29125--29168 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
29115 TTTTAAATTC
29125 TATTTTAATTTTTAAT
1 TATTTTAATTTTTAAT
*
29141 TATTGTTAATATTTTATT
1 TATT-TTAAT-TTTTAAT
29159 TA-TTTAATTT
1 TATTTTAATTT
29169 GTTTAGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 9 0.36
17 6 0.24
18 8 0.32
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTTTAATTTTTAAT
Found at i:30160 original size:2 final size:2
Alignment explanation
Indices: 30153--30221 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
30143 TGATAAGAAT
30153 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30195 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
30222 TAGTTTGAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32056 original size:18 final size:19
Alignment explanation
Indices: 32000--32058 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 19
31990 AACAATATTC
32000 ATAAAATTATTATAAATAACCATT
1 ATAAAATTATTATAAAT----A-T
*
32024 ATAATATTATTATAAATAT
1 ATAAAATTATTATAAATAT
32043 ATAAAATT-TTATAAAT
1 ATAAAATTATTATAAAT
32059 TAATAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 8 0.24
19 8 0.24
20 1 0.03
24 16 0.48
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAAATTATTATAAATAT
Found at i:32294 original size:26 final size:24
Alignment explanation
Indices: 32247--32294 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
32237 TTTTTTTTAA
*
32247 ATTTTATTTTTAAAAAATTTAAAT
1 ATTTTATTTTTAAAAAACTTAAAT
*
32271 ATTTTTTTATTTAAAAAACCTTAA
1 ATTTTATT-TTTAAAAAA-CTTAA
32295 TTCTACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 9 0.45
26 4 0.20
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTTATTTTTAAAAAACTTAAAT
Found at i:33693 original size:14 final size:14
Alignment explanation
Indices: 33674--33701 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33664 AAAAATATAA
33674 AAATTGACGAGGAT
1 AAATTGACGAGGAT
33688 AAATTGACGAGGAT
1 AAATTGACGAGGAT
33702 GAGTCGGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.29, T:0.21
Consensus pattern (14 bp):
AAATTGACGAGGAT
Found at i:42945 original size:23 final size:23
Alignment explanation
Indices: 42919--42963 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
42909 AGGTAAAGAA
42919 AAACATACCACAAAGACAGAGAT
1 AAACATACCACAAAGACAGAGAT
* ** *
42942 AAACGTGTCATAAAGACAGAGA
1 AAACATACCACAAAGACAGAGA
42964 ACATGTGACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.53, C:0.18, G:0.18, T:0.11
Consensus pattern (23 bp):
AAACATACCACAAAGACAGAGAT
Found at i:43194 original size:2 final size:2
Alignment explanation
Indices: 43187--43214 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43177 ATTAAATTTA
43187 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
43215 TATGTTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44222 original size:4 final size:4
Alignment explanation
Indices: 44203--44247 Score: 72
Period size: 4 Copynumber: 11.2 Consensus size: 4
44193 AGGAGAGGAG
* *
44203 AAGA AATA AGGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
44248 GAACTCAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:44441 original size:18 final size:18
Alignment explanation
Indices: 44403--44444 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
44393 ATAGAGTTTT
*
44403 TTTTATTTGTTTCGATTA
1 TTTTATTTGTTTAGATTA
44421 TTTT-TTTGTTTAGATTA
1 TTTTATTTGTTTAGATTA
*
44438 ATTTATT
1 TTTTATT
44445 GTTAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.19, C:0.02, G:0.10, T:0.69
Consensus pattern (18 bp):
TTTTATTTGTTTAGATTA
Found at i:46585 original size:64 final size:65
Alignment explanation
Indices: 46472--46609 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 65
46462 TTCAGTGTGT
* *
46472 ATCGATGCA-CCCATTAAAAATGGAAACATCGAATGCAATTAGTGCATCGATGCATAAGG-AGTG
1 ATCGATGCACCCCATTAAAAATGAAAACATCGAAGGCAATTAGTGCATCGATGCAT-AGGTAGTG
46535 C
65 C
* ** * * *
46536 ATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTGATTTGTGTATCGATGCATGGGTAGTGC
1 ATCGATGCACCCCATTAAAAATGAAAACATCGAAGGCAATTAGTGCATCGATGCATAGGTAGTGC
46600 ATCGATGCAC
1 ATCGATGCAC
46610 TTCAAGAGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.03
64 57 0.89
65 5 0.08
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (65 bp):
ATCGATGCACCCCATTAAAAATGAAAACATCGAAGGCAATTAGTGCATCGATGCATAGGTAGTGC
Found at i:46902 original size:6 final size:6
Alignment explanation
Indices: 46884--46918 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
46874 TAGTATTGTG
46884 CATGAA GCATGAA CATGAA CATGAA CATGAA CATG
1 CATGAA -CATGAA CATGAA CATGAA CATGAA CATG
46919 TGTTTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (6 bp):
CATGAA
Found at i:46965 original size:20 final size:18
Alignment explanation
Indices: 46923--46971 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
46913 AACATGTGTT
*
46923 TGTTATGTATGAGTTATA
1 TGTTATGTATGAGTTACA
*
46941 TGTTATAGTATGTGTTGACA
1 TGTTAT-GTATGAGTT-ACA
46961 TGTTATTGTAT
1 TGTTA-TGTAT
46972 ATGTATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 6 0.23
19 8 0.31
20 11 0.42
21 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.22, T:0.51
Consensus pattern (18 bp):
TGTTATGTATGAGTTACA
Found at i:47825 original size:2 final size:2
Alignment explanation
Indices: 47818--47849 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47808 GAACATGTAA
47818 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
47850 GATAAGACAT
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:48275 original size:23 final size:23
Alignment explanation
Indices: 48241--48308 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
48231 AACCTTATAT
*
48241 GGCACTTCGGTGCATTTTTACGC
1 GGCACTTCGGTGCATTTATACGC
* * * *
48264 GGCACTAT-GGTGCAATTCTAAGT
1 GGCACT-TCGGTGCATTTATACGC
48287 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTATACG
48309 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.94
24 1 0.03
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTATACGC
Found at i:50715 original size:23 final size:22
Alignment explanation
Indices: 50670--50728 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
50660 GAAGTTGAAC
*
50670 TAAATAAATAA-ATTAACTTAG
1 TAAATAAATAATATTAACTAAG
50691 TATAATAAATAATATTAGA-TAAG
1 TA-AATAAATAATATTA-ACTAAG
*
50714 TAATATAAATTATAT
1 TAA-ATAAATAATAT
50729 GTTATAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 2 0.06
22 10 0.31
23 19 0.59
24 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (22 bp):
TAAATAAATAATATTAACTAAG
Found at i:51438 original size:23 final size:23
Alignment explanation
Indices: 51412--51478 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
51402 ATTTTATATA
*
51412 GCACTTCGGTGCATTTTTACGTG
1 GCACTTCGGTGCATTTATACGTG
* *
51435 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCATTTATACGTG
*
51458 GCACTTCGATGCATTTATACG
1 GCACTTCGGTGCATTTATACG
51479 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (23 bp):
GCACTTCGGTGCATTTATACGTG
Found at i:51529 original size:16 final size:17
Alignment explanation
Indices: 51508--51541 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
51498 GTGCACAACC
51508 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
51524 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
51541 T
1 T
51542 GTACATTAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:51682 original size:20 final size:21
Alignment explanation
Indices: 51646--51689 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
51636 TATGATGATG
*
51646 TGTGTTCTTCATTTGTGAATA
1 TGTGTGCTTCATTTGTGAATA
51667 TGTGTGCTTC-TTTGTGAATA
1 TGTGTGCTTCATTTGTGAATA
51687 TGT
1 TGT
51690 ATGTATATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.16, C:0.09, G:0.23, T:0.52
Consensus pattern (21 bp):
TGTGTGCTTCATTTGTGAATA
Found at i:51772 original size:2 final size:2
Alignment explanation
Indices: 51765--51840 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
51755 TAATGAAACG
51765 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
51807 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
51841 GCTTGGATTC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.