Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004093.1 Hibiscus syriacus cultivar Beakdansim tig00008953_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: 101477
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:9164 original size:22 final size:22
Alignment explanation
Indices: 9136--9192 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
9126 ATATCTACAT
9136 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
9158 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
9180 TTTTCAAAGATGA
1 TCTTCAAAGATGA
9193 AAGCTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAAATTCTC
Found at i:9914 original size:45 final size:45
Alignment explanation
Indices: 9850--10326 Score: 765
Period size: 45 Copynumber: 10.6 Consensus size: 45
9840 TTTCCCACAA
9850 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
1 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
* * *
9895 CTGTAAGCCCTTCAGTGCATGATGTTTGCAAAGCCTTTGGGTCAT
1 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
9940 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
1 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
* *
9985 CTGTAAGCCCTTCAGTGCATGTTGTTTTCAAAGCCTTCGGGTCAT
1 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
* *
10030 CTGTAATCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCAT
1 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
* *
10075 CTGTAAGCCCTTCAATGTATGATGTTTTCAAAACCTTCGGGTCAT
1 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
*
10120 CTGTAAGCCTTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
1 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
* * *
10165 CTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCAGGTTAT
1 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
10210 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
1 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
** * * *
10255 CCATAAGACCTGCAGTGCATGATGTTTTCAAAACCTTCGAGTCAT
1 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
* * *
10300 CTATAAGACCTTTAGTGCATGATGTTT
1 CTGTAAGCCCTTCAGTGCATGATGTTT
10327 CGGGTCATCT
Statistics
Matches: 400, Mismatches: 32, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 400 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (45 bp):
CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
Found at i:10517 original size:3 final size:3
Alignment explanation
Indices: 10509--10605 Score: 131
Period size: 3 Copynumber: 31.0 Consensus size: 3
10499 AAGTTTTCTT
**
10509 TTA TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
*
10558 TTA TATA TTA TTA TTA TTAA TAA TTA TATA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TT-A TTA TTA T-TA TTA TTA TTA TTA TTA TTA
10606 GATAAATAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
3 73 0.87
4 11 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:11978 original size:2 final size:2
Alignment explanation
Indices: 11971--11999 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11961 ATTATTATTT
11971 TA 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 TA T
12000 TTGTTTAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12017 original size:18 final size:18
Alignment explanation
Indices: 11996--12036 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
11986 ATATATATAT
*
11996 ATATTTGTTTAAATTTTA
1 ATATTTATTTAAATTTTA
**
12014 ATATTTATTTATTTTTTA
1 ATATTTATTTAAATTTTA
12032 ATATT
1 ATATT
12037 AAGAAATGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
ATATTTATTTAAATTTTA
Found at i:12925 original size:2 final size:2
Alignment explanation
Indices: 12920--12945 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12910 GGGGAAAAGA
12920 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
12946 GTTACTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21737 original size:14 final size:15
Alignment explanation
Indices: 21719--21760 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
21709 TTTTTCTCTA
*
21719 TTTTTATGTTTATCC
1 TTTTTATATTTATCC
*
21734 TTTTTTTATTTAT-C
1 TTTTTATATTTATCC
*
21748 TTTTTATCTTTAT
1 TTTTTATATTTAT
21761 GTTATTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTATATTTATCC
Found at i:21738 original size:26 final size:25
Alignment explanation
Indices: 21685--21746 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
21675 ATTGTTACCA
*
21685 TTTTCTTTATTTATTATTTATTCCT
1 TTTTCTCTATTTATTATTTATTCCT
21710 TTTTCTCTATTT-TTATGTT-TATCCT
1 TTTTCTCTATTTATTAT-TTAT-TCCT
21735 TTTT-T-TATTTAT
1 TTTTCTCTATTTAT
21747 CTTTTTATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 5 0.15
24 7 0.21
25 21 0.64
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTCTCTATTTATTATTTATTCCT
Found at i:21753 original size:23 final size:23
Alignment explanation
Indices: 21685--21781 Score: 67
Period size: 23 Copynumber: 4.1 Consensus size: 23
21675 ATTGTTACCA
*
21685 TTTTCTTTATTTAT-TATTTATTCC
1 TTTT-TTTATTTATCTTTTTA-TCC
* * *
21709 TTTTTCTCTATTTTTATGTTTATCC
1 TTTTT-T-TATTTATCTTTTTATCC
21734 TTTTTTTATTTATCTTTTTAT-C
1 TTTTTTTATTTATCTTTTTATCC
*
21756 TTTATGTTATTT-TCTTTATT-TCC
1 TTT-TTTTATTTATCTTT-TTATCC
21779 TTT
1 TTT
21782 GTCTTTCTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
22 10 0.16
23 26 0.43
24 6 0.10
25 14 0.23
26 5 0.08
ACGTcount: A:0.13, C:0.12, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTTTTATTTATCTTTTTATCC
Found at i:21773 original size:28 final size:26
Alignment explanation
Indices: 21684--21805 Score: 81
Period size: 28 Copynumber: 4.5 Consensus size: 26
21674 GATTGTTACC
*
21684 ATTTTCTTTATTTATTA--TTTATTCCT
1 ATTTTCTTTATTTTTTATCTTTATT--T
* *
21710 -TTTTCTCTA-TTTTTATGTTTATCCTT
1 ATTTTCTTTATTTTTTATCTTTAT--TT
* *
21736 TTTTTATTTATCTTTTTATCTTTATGTT
1 ATTTTCTTTAT-TTTTTATCTTTAT-TT
* *
21764 ATTTTCTTTATTTCCTTTGTCTTTCTTT
1 ATTTTCTTTATTT--TTTATCTTTATTT
21792 ATTTTCTTTATTTT
1 ATTTTCTTTATTTT
21806 CATTTTTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
24 5 0.06
25 8 0.10
26 7 0.09
27 9 0.12
28 27 0.35
29 21 0.27
ACGTcount: A:0.13, C:0.12, G:0.02, T:0.72
Consensus pattern (26 bp):
ATTTTCTTTATTTTTTATCTTTATTT
Found at i:21776 original size:9 final size:9
Alignment explanation
Indices: 21762--21819 Score: 73
Period size: 9 Copynumber: 6.3 Consensus size: 9
21752 TATCTTTATG
21762 TTATTTTCT
1 TTATTTTCT
*
21771 TTATTTCCT
1 TTATTTTCT
*
21780 TTGTCTTTCT
1 TTAT-TTTCT
21790 TTATTTTCT
1 TTATTTTCT
21799 TTATTTTCAT
1 TTATTTTC-T
21809 TT-TTTTCT
1 TTATTTTCT
21817 TTA
1 TTA
21820 ACACTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
8 3 0.07
9 29 0.69
10 10 0.24
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.74
Consensus pattern (9 bp):
TTATTTTCT
Found at i:25244 original size:21 final size:21
Alignment explanation
Indices: 25211--25250 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25201 GTGAAAAAGA
*
25211 TGGAAGAGAAGATTAAGATAC
1 TGGAAGAGAAGATGAAGATAC
**
25232 TGGAAGATCAGATGAAGAT
1 TGGAAGAGAAGATGAAGAT
25251 GGTCAAAGGG
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:0.45, C:0.05, G:0.30, T:0.20
Consensus pattern (21 bp):
TGGAAGAGAAGATGAAGATAC
Found at i:40052 original size:17 final size:16
Alignment explanation
Indices: 40030--40063 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
40020 TAAAAACAGT
40030 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
40047 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
40063 A
1 A
40064 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:40581 original size:23 final size:23
Alignment explanation
Indices: 40538--40583 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40528 ATAAAGAACC
*
40538 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
40561 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
40584 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:43280 original size:19 final size:20
Alignment explanation
Indices: 43258--43301 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
43248 GAGAAAAGGT
43258 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
43277 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
43297 AAAAG
1 AAAAG
43302 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:49657 original size:17 final size:16
Alignment explanation
Indices: 49635--49668 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
49625 TAAAAACAGT
49635 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
49652 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
49668 A
1 A
49669 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:50187 original size:24 final size:24
Alignment explanation
Indices: 50143--50189 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
50133 ATAAAGAACC
*
50143 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
50167 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
50190 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:51951 original size:43 final size:43
Alignment explanation
Indices: 51903--51985 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
51893 AAGAGACCAT
* *
51903 CCACGATTTCAACTCCATGACGGAGGATATCGTACCCACAAAG
1 CCACGATTTCAACTCCACGACAGAGGATATCGTACCCACAAAG
*
51946 CCACGATTTCAACTCCACGACAGAGGATATCGTGCCCACA
1 CCACGATTTCAACTCCACGACAGAGGATATCGTACCCACA
51986 TCCACGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.31, C:0.33, G:0.18, T:0.18
Consensus pattern (43 bp):
CCACGATTTCAACTCCACGACAGAGGATATCGTACCCACAAAG
Found at i:54162 original size:14 final size:13
Alignment explanation
Indices: 54143--54192 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
54133 TCTTATTTAA
54143 ATATTTTATTATAT
1 ATATTTTATTAT-T
*
54157 ATATTTTTTTATT
1 ATATTTTATTATT
54170 AT-TTTTATTTGATT
1 ATATTTTA-TT-ATT
54184 AT-TTTTATT
1 ATATTTTATT
54193 TAAGCACTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 4 0.12
13 7 0.22
14 21 0.66
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
ATATTTTATTATT
Found at i:54193 original size:14 final size:14
Alignment explanation
Indices: 54167--54193 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54157 ATATTTTTTT
54167 ATTATTTTTATTTG
1 ATTATTTTTATTTG
54181 ATTATTTTTATTT
1 ATTATTTTTATTT
54194 AAGCACTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (14 bp):
ATTATTTTTATTTG
Found at i:54193 original size:31 final size:32
Alignment explanation
Indices: 54125--54185 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
54115 AGTCCCTTCG
* *
54125 TATTTTTTTCTTATTTAAATATTTTATTATATA
1 TATTTTTTTATTATTT-AATATTTGATTATATA
*
54158 TATTTTTTTATTATTT-TTATTTGATTAT
1 TATTTTTTTATTATTTAATATTTGATTAT
54186 TTTTATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 10 0.40
33 15 0.60
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (32 bp):
TATTTTTTTATTATTTAATATTTGATTATATA
Found at i:54268 original size:3 final size:3
Alignment explanation
Indices: 54260--54301 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
54250 ATTTATACGT
54260 TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT- TTA GTTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA -TTA TT
54302 TGATTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.78
4 6 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54407 original size:27 final size:26
Alignment explanation
Indices: 54377--54427 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
54367 ACTTTGTGTA
*
54377 TTTATTTTTAATTTTTTTATTATTCTC
1 TTTATTTTTAATTTATTT-TTATTCTC
*
54404 TTTATTTTTACTTTATTTTTATTC
1 TTTATTTTTAATTTATTTTTATTC
54428 CCTTGATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTATTTTTAATTTATTTTTATTCTC
Found at i:54531 original size:18 final size:18
Alignment explanation
Indices: 54508--54579 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 18
54498 ATTGTTGTTA
54508 TTTTCTTTATTTAT-TATT
1 TTTTCTTT-TTTATCTATT
*
54526 TTTTCTTTTTTTTCTATT
1 TTTTCTTTTTTATCTATT
* *
54544 TTTATCCCTTTTTTATTTTCTT
1 TTT-T--CTTTTTTA-TCTATT
54566 TTTTC-TTTTTATCT
1 TTTTCTTTTTTATCT
54580 TTATGTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
17 6 0.14
18 21 0.48
19 2 0.05
21 8 0.18
22 7 0.16
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTTATCTATT
Found at i:54548 original size:24 final size:24
Alignment explanation
Indices: 54515--54638 Score: 60
Period size: 23 Copynumber: 5.0 Consensus size: 24
54505 TTATTTTCTT
54515 TATTTATTATTTTTTCTTTTTTTTC
1 TATTT-TTATTTTTTCTTTTTTTTC
** *
54540 TATTTTTATCCCTTT-TTTATTTTC
1 TATTTTTAT-TTTTTCTTTTTTTTC
* * *
54564 T-TTTTTCTTTTTATC-TTTATGT-
1 TATTTTTATTTTT-TCTTTTTTTTC
*
54586 TATTTTT-TTATTTCTTTTGTCTTTC
1 TATTTTTATTTTTTCTTTT-T-TTTC
* *
54611 TTTATTTTATTTATTTTCATTTTTTTC
1 TAT-TTTTA-TT-TTTTCTTTTTTTTC
54638 T
1 T
54639 TTTACACATT
Statistics
Matches: 72, Mismatches: 15, Indels: 22
0.66 0.14 0.20
Matches are distributed among these distances:
21 2 0.03
22 10 0.14
23 16 0.22
24 15 0.21
25 10 0.14
26 4 0.06
27 5 0.07
28 3 0.04
29 7 0.10
ACGTcount: A:0.11, C:0.10, G:0.02, T:0.77
Consensus pattern (24 bp):
TATTTTTATTTTTTCTTTTTTTTC
Found at i:54567 original size:29 final size:28
Alignment explanation
Indices: 54524--54594 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
54514 TTATTTATTA
*
54524 TTTTTTCTTTTTTTTCTATTTTTATCCC
1 TTTTTTATTTTTTTTCTATTTTTATCCC
* *
54552 TTTTTTATTTTCTTTTTTCTTTTTAT--C
1 TTTTTTATTTT-TTTTCTATTTTTATCCC
54579 TTTATGTTATTTTTTT
1 TTT-T-TTATTTTTTT
54595 ATTTCTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 4 0.11
28 14 0.38
29 19 0.51
ACGTcount: A:0.08, C:0.11, G:0.01, T:0.79
Consensus pattern (28 bp):
TTTTTTATTTTTTTTCTATTTTTATCCC
Found at i:54600 original size:36 final size:36
Alignment explanation
Indices: 54552--54641 Score: 103
Period size: 36 Copynumber: 2.4 Consensus size: 36
54542 TTTTTATCCC
*
54552 TTTTTTATTTTCTTTTTTC-TT-TTTATCTTTATGTTAT
1 TTTTTTA-TTTCTTTTGTCTTTCTTTAT-TTTAT-TTAT
54589 TTTTTTATTTCTTTTGTCTTTCTTTATTTTATTTAT
1 TTTTTTATTTCTTTTGTCTTTCTTTATTTTATTTAT
*
54625 TTTCATTTTTTTCTTTT
1 TTT--TTTATTTCTTTT
54642 ACACATTTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
36 17 0.36
37 14 0.30
38 16 0.34
ACGTcount: A:0.10, C:0.09, G:0.02, T:0.79
Consensus pattern (36 bp):
TTTTTTATTTCTTTTGTCTTTCTTTATTTTATTTAT
Found at i:55212 original size:2 final size:2
Alignment explanation
Indices: 55205--55243 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55195 AAAACAATAA
55205 AT AT AT 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 AT AT AT A
55244 ATTAATAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60632 original size:7 final size:7
Alignment explanation
Indices: 60620--60686 Score: 134
Period size: 7 Copynumber: 9.6 Consensus size: 7
60610 CCTAATATAG
60620 AAAAGAA
1 AAAAGAA
60627 AAAAGAA
1 AAAAGAA
60634 AAAAGAA
1 AAAAGAA
60641 AAAAGAA
1 AAAAGAA
60648 AAAAGAA
1 AAAAGAA
60655 AAAAGAA
1 AAAAGAA
60662 AAAAGAA
1 AAAAGAA
60669 AAAAGAA
1 AAAAGAA
60676 AAAAGAA
1 AAAAGAA
60683 AAAA
1 AAAA
60687 AGAGACGGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:60636 original size:1 final size:1
Alignment explanation
Indices: 60620--60687 Score: 55
Period size: 1 Copynumber: 68.0 Consensus size: 1
60610 CCTAATATAG
* * * * * * * * *
60620 AAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
60685 AAA
1 AAA
60688 GAGACGGAAG
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:63030 original size:129 final size:129
Alignment explanation
Indices: 62800--63061 Score: 517
Period size: 129 Copynumber: 2.0 Consensus size: 129
62790 GAAAATAAAA
62800 ATGTTATTAATTTTTGTGGCTTAGGATAAAATTTGGGAGTTCTTGCATCATCCATTGGATAAAAA
1 ATGTTATTAATTTTTGTGGCTTAGGATAAAATTTGGGAGTTCTTGCATCATCCATTGGATAAAAA
62865 TATTATCTTTTGACTAAGAGATATCAGTTTAAAGAACTTAACAATCGTGTTCTTTTATCAGGTC
66 TATTATCTTTTGACTAAGAGATATCAGTTTAAAGAACTTAACAATCGTGTTCTTTTATCAGGTC
62929 ATGTTATTAATTTTTGTGGCTTAGGATAAAATTTGGGAGTTCTTGCATCATCCATTGGATAAAAA
1 ATGTTATTAATTTTTGTGGCTTAGGATAAAATTTGGGAGTTCTTGCATCATCCATTGGATAAAAA
62994 TATTATCTTTTGACTAAGAGATATCAGTTTAAAGAACTTAACAATCGTGTTCTTTTATCAGGTC
66 TATTATCTTTTGACTAAGAGATATCAGTTTAAAGAACTTAACAATCGTGTTCTTTTATCAGGTC
63058 -TGTT
1 ATGTT
63062 TACATTGTTT
Statistics
Matches: 133, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 4 0.03
129 129 0.97
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (129 bp):
ATGTTATTAATTTTTGTGGCTTAGGATAAAATTTGGGAGTTCTTGCATCATCCATTGGATAAAAA
TATTATCTTTTGACTAAGAGATATCAGTTTAAAGAACTTAACAATCGTGTTCTTTTATCAGGTC
Found at i:65157 original size:2 final size:2
Alignment explanation
Indices: 65150--65211 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
65140 TTGTATTTGC
65150 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
65192 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
65212 GGATAGGATC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65916 original size:65 final size:65
Alignment explanation
Indices: 65840--65996 Score: 224
Period size: 65 Copynumber: 2.4 Consensus size: 65
65830 CACACCCATT
* *
65840 TCGAATGCATTTTGTGTATCGATGCACAAACCATGCATTGATGCACTCTTGAATATTTTGAAACA
1 TCGAATGCATTTTGTGTATCGATGCACAAACCATGCATCGATGCACTCCTGAATATTTTGAAACA
* * * * *
65905 TCGAATACATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGACTCTTTTGAAACA
1 TCGAATGCATTTTGTGTATCGATGCACAAACCATGCATCGATGCACTCCTGAATATTTTGAAACA
* * *
65970 TCGAATGTAATTAGTGTATCGATGCAC
1 TCGAATGCATTTTGTGTATCGATGCAC
65997 CCCTAGTGTA
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 80 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTATCGATGCACAAACCATGCATCGATGCACTCCTGAATATTTTGAAACA
Found at i:71814 original size:23 final size:23
Alignment explanation
Indices: 71786--71866 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
71776 CACTAGACAA
71786 TGCATCGATGCATC-CCTTGAATG
1 TGCATCGATGCA-CACCTTGAATG
* *
71809 TTCATCGA-G-ACACCATGAATG
1 TGCATCGATGCACACCTTGAATG
* * *
71830 TGCACCGATACACTCCTTGAATG
1 TGCATCGATGCACACCTTGAATG
71853 TGCATCGATGCACA
1 TGCATCGATGCACA
71867 ATGATATGCA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.02
21 15 0.33
22 1 0.02
23 28 0.62
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCACACCTTGAATG
Found at i:71842 original size:21 final size:21
Alignment explanation
Indices: 71803--71886 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
71793 ATGCATCCCT
* *
71803 TGAATGTTCATCGAGACACCA
1 TGAATGTGCATCGATACACCA
* *
71824 TGAATGTGCACCGATACACTCCT
1 TGAATGTGCATCGATACA--CCA
* *
71847 TGAATGTGCATCGATGCACAA
1 TGAATGTGCATCGATACACCA
*
71868 TG-ATATGCATCGATACACC
1 TGAATGTGCATCGATACACC
71887 CATCAGATTT
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
20 14 0.28
21 18 0.36
23 18 0.36
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
TGAATGTGCATCGATACACCA
Found at i:72287 original size:16 final size:16
Alignment explanation
Indices: 72266--72302 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
72256 TTTCAAAATG
72266 TTTAAAAAATTATTAT
1 TTTAAAAAATTATTAT
*
72282 TTTAAAAAATTATTGT
1 TTTAAAAAATTATTAT
72298 TTTAA
1 TTTAA
72303 TTGATGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTAAAAAATTATTAT
Found at i:73205 original size:19 final size:20
Alignment explanation
Indices: 73163--73204 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
73153 AACCAGATTG
*
73163 CCCATATGGTACCCGTACCC
1 CCCAGATGGTACCCGTACCC
73183 CCCAGATGGTA-CCGATACCC
1 CCCAGATGGTACCCG-TACCC
73203 CC
1 CC
73205 ATGCCAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.21, C:0.45, G:0.17, T:0.17
Consensus pattern (20 bp):
CCCAGATGGTACCCGTACCC
Found at i:79046 original size:23 final size:22
Alignment explanation
Indices: 79020--79080 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
79010 TTGTGAGCTA
79020 GGTATCGATACCCCCTTTGAATG
1 GGTATCGATACCCCC-TTGAATG
*
79043 GGTATCGATACCATCCTTGAATG
1 GGTATCGATACC-CCCTTGAATG
*
79066 GGTACCGATACCCCC
1 GGTATCGATACCCCC
79081 CATGAGGGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.06
23 30 0.88
24 2 0.06
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (22 bp):
GGTATCGATACCCCCTTGAATG
Found at i:83080 original size:65 final size:65
Alignment explanation
Indices: 83005--83158 Score: 195
Period size: 65 Copynumber: 2.4 Consensus size: 65
82995 ACCCATTTCG
* *
83005 AATGCATTTTGTGTATCGATGCACA-AGTCATGCATCGATGCAC-TCTTGAATATTTTGAAACAT
1 AATGCATTTTGTGTACCGATGCACAGA-CCATGCATCGATGCACTTC-TGAATATTTTGAAACAT
83068 CA
64 CA
** *
83070 AATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTTCTGGCTCTTTTGAAACATCA
1 AATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTTCTGAATATTTTGAAACATCA
** * *
83135 AATATAATTAGTGTACCGATGCAC
1 AATGCATTTTGTGTACCGATGCAC
83159 CCCTAGTGTA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 75 0.96
66 3 0.04
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (65 bp):
AATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTTCTGAATATTTTGAAACATCA
Found at i:83182 original size:17 final size:18
Alignment explanation
Indices: 83143--83182 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
83133 CAAATATAAT
83143 TAGTGTACCGATGCACCCC
1 TAGTGTACCGATGCA-CCC
83162 TAGTGTACCGATGCA-CC
1 TAGTGTACCGATGCACCC
83179 TAGT
1 TAGT
83183 CTTATAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.29
19 15 0.71
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (18 bp):
TAGTGTACCGATGCACCC
Found at i:90592 original size:2 final size:2
Alignment explanation
Indices: 90587--90623 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
90577 CTCTGTACTT
90587 TA TA TA TA TA 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 TA TA TA TA TA T
90624 TAATAGAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:90715 original size:2 final size:2
Alignment explanation
Indices: 90708--90732 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
90698 CGATATAAAG
90708 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 T
90733 TAATAGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90732 original size:109 final size:109
Alignment explanation
Indices: 90599--90816 Score: 436
Period size: 109 Copynumber: 2.0 Consensus size: 109
90589 TATATATATA
90599 TATATATATATATATATATATATATTAATAGAACTGATTAGTCATTTTTGTTTAATAACTTTTGT
1 TATATATATATATATATATATATATTAATAGAACTGATTAGTCATTTTTGTTTAATAACTTTTGT
90664 TAATTTGGTTTCAGGTTTAGGAAAGGTTTGAGGTCGATATAAAG
66 TAATTTGGTTTCAGGTTTAGGAAAGGTTTGAGGTCGATATAAAG
90708 TATATATATATATATATATATATATTAATAGAACTGATTAGTCATTTTTGTTTAATAACTTTTGT
1 TATATATATATATATATATATATATTAATAGAACTGATTAGTCATTTTTGTTTAATAACTTTTGT
90773 TAATTTGGTTTCAGGTTTAGGAAAGGTTTGAGGTCGATATAAAG
66 TAATTTGGTTTCAGGTTTAGGAAAGGTTTGAGGTCGATATAAAG
90817 GAGCTTCCTG
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.45
Consensus pattern (109 bp):
TATATATATATATATATATATATATTAATAGAACTGATTAGTCATTTTTGTTTAATAACTTTTGT
TAATTTGGTTTCAGGTTTAGGAAAGGTTTGAGGTCGATATAAAG
Found at i:94545 original size:31 final size:31
Alignment explanation
Indices: 94476--94545 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
94466 ACAAGCTTTA
* * *
94476 GAAAAA-TTTAGGGACCATTTTGTAATTTTC
1 GAAAAAGTTGAGGGACCAATTCGTAATTTTC
*
94506 G-AAAAGTTGAGGGACCAATTCGTAATTTTG
1 GAAAAAGTTGAGGGACCAATTCGTAATTTTC
94536 GAAAAAGTTG
1 GAAAAAGTTG
94546 GGAATGTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.12
30 22 0.65
31 8 0.24
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.33
Consensus pattern (31 bp):
GAAAAAGTTGAGGGACCAATTCGTAATTTTC
Found at i:95507 original size:38 final size:38
Alignment explanation
Indices: 95450--95545 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
95440 TACGAGACAT
* * *
95450 ATGATAGGTCCTTCAGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCATTCGGGACACAGATGACATCCTTCGGG
*
95488 ATGATAGGTCATTCGGGACACATATGACATCCTTCGGG
1 ATGATAGGTCATTCGGGACACAGATGACATCCTTCGGG
*
95526 ATGATAGGTCATTCGAGACA
1 ATGATAGGTCATTCGGGACA
95546 TAGTTTATAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (38 bp):
ATGATAGGTCATTCGGGACACAGATGACATCCTTCGGG
Done.