Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005719.1 Hibiscus syriacus cultivar Beakdansim tig00013371_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: 113209
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:10418 original size:32 final size:31
Alignment explanation
Indices: 10382--10451 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
10372 AAAGACTAGC
10382 TAGTGTGACATTCAGATAATGCACAACAGAGT
1 TAGTGTG-CATTCAGATAATGCACAACAGAGT
* * * *
10414 TAGTGTTGTATTTAGATAATGCACTACAGTGT
1 TAGTG-TGCATTCAGATAATGCACAACAGAGT
*
10446 CAGTGT
1 TAGTGT
10452 CATATTTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
31 1 0.03
32 29 0.91
33 2 0.06
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (31 bp):
TAGTGTGCATTCAGATAATGCACAACAGAGT
Found at i:10458 original size:32 final size:32
Alignment explanation
Indices: 10395--10459 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
10385 TGTGACATTC
* **
10395 AGATAATGCACAACAGAGTTAGTGTTGTATTT
1 AGATAATGCACAACAGAGTCAGTGTCATATTT
* *
10427 AGATAATGCACTACAGTGTCAGTGTCATATTT
1 AGATAATGCACAACAGAGTCAGTGTCATATTT
10459 A
1 A
10460 TAGAATATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (32 bp):
AGATAATGCACAACAGAGTCAGTGTCATATTT
Found at i:31191 original size:24 final size:24
Alignment explanation
Indices: 31159--31251 Score: 98
Period size: 24 Copynumber: 3.9 Consensus size: 24
31149 CGAAGTGCCA
* *
31159 CGTATAATTTGCCCCGATGGACCG
1 CGTAGAATTTGCCCCGAAGGACCG
*
31183 CGTAGAATTTGTCCCGAAGGACCG
1 CGTAGAATTTGCCCCGAAGGACCG
* * * *
31207 CGTAGAATTTGTCCCAAAGAACCA
1 CGTAGAATTTGCCCCGAAGGACCG
* *
31231 TGTAGAA-TTGTCCCGAAGGAC
1 CGTAGAATTTGCCCCGAAGGAC
31252 AACATTGATT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
23 12 0.20
24 48 0.80
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (24 bp):
CGTAGAATTTGCCCCGAAGGACCG
Found at i:31216 original size:48 final size:47
Alignment explanation
Indices: 31159--31251 Score: 114
Period size: 48 Copynumber: 2.0 Consensus size: 47
31149 CGAAGTGCCA
* * * * *
31159 CGTATAATTTGCCCCGATGGACCGCGTAGAATTTGTCCCGAAGGACCG
1 CGTAGAATTTGCCCCAAAGAACCACGTAGAA-TTGTCCCGAAGGACCG
* *
31207 CGTAGAATTTGTCCCAAAGAACCATGTAGAATTGTCCCGAAGGAC
1 CGTAGAATTTGCCCCAAAGAACCACGTAGAATTGTCCCGAAGGAC
31252 AACATTGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 14 0.37
48 24 0.63
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (47 bp):
CGTAGAATTTGCCCCAAAGAACCACGTAGAATTGTCCCGAAGGACCG
Found at i:34752 original size:23 final size:22
Alignment explanation
Indices: 34694--34767 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
34684 GAGCCTTTAT
*
34694 GGGGTATTGATATCC-TTACATA
1 GGGGTATTGATACCCATT-CATA
* *
34716 GGGGTGTTGGTACCCATTCATA
1 GGGGTATTGATACCCATTCATA
*
34738 GGGGGTATTGATACCTATTCATA
1 -GGGGTATTGATACCCATTCATA
*
34761 TGGGTAT
1 GGGGTAT
34768 CAGTATCTCT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 22 0.51
23 21 0.49
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (22 bp):
GGGGTATTGATACCCATTCATA
Found at i:36216 original size:43 final size:43
Alignment explanation
Indices: 36167--36258 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
36157 ATAAAAGAAA
* * *
36167 AATTAGGAAATAAGTTGTAAAGCTAGTAATAGCTCCAACATAG
1 AATTAGGAAATAAGTTGGAAAGATAGTAATAGCTCCAAAATAG
* * *
36210 TATTAGGAAATAAGTTGGAAAGATGGTAATTGCTCCAAAATAG
1 AATTAGGAAATAAGTTGGAAAGATAGTAATAGCTCCAAAATAG
36253 AATTAG
1 AATTAG
36259 ACATATTACC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (43 bp):
AATTAGGAAATAAGTTGGAAAGATAGTAATAGCTCCAAAATAG
Found at i:38403 original size:214 final size:210
Alignment explanation
Indices: 38025--38429 Score: 697
Period size: 214 Copynumber: 1.9 Consensus size: 210
38015 AGGGGAACCC
*
38025 GGTGTCACACAACATCGATAAATTTTCGTCTAACTGAAACATTGGCTCATTCTCACATAGCCTTC
1 GGTGTCACACAACATCGATAAATTTTCGTCTAACTGAAACATTGACTCATTCTCACATAGCCTTC
*
38090 AAGCAAGCTTTAACATATATGATATTTTGCATGTACTCGTACTAACACCCCACCTACTATGAATA
66 AAGCAAGCCTTAACATATATGATATTTTGCATGTACTCGTACTAACACCCCACCTACTATGAATA
38155 CATAATAACCGAGTGGTAAAAACCATAATTTATGTGCATTGGAAGCTTACCCAAT-TGAACTGGT
131 CATAATAACCGAGTGGTAAAAACCATAATTTATGTGCATTGGAAGCTTACCC-ATCTGAACTGGT
38219 TTTCACATAGGCATCA
195 TTTCACATAGGCATCA
* *
38235 GGTGTCACAC-ACATCGATAAATTTTCGTCTAACTGAAGCATTGACTCGTTCTCACATAGCCTTC
1 GGTGTCACACAACATCGATAAATTTTCGTCTAACTGAAACATTGACTCATTCTCACATAGCCTTC
38299 AAGCCAAGCCTTAACATATATGATATATTTTGCATGTATCTCGTACTAACACCCCAGCCTACTAT
66 AAG-CAAGCCTTAACATATATG--ATATTTTGCATGTA-CTCGTACTAACACCCCA-CCTACTAT
*
38364 GAATACATAATAACCGAGTGGTAAAAACCGTAATTTATGTGCATTGGAAGCTTACCCATCTGAAC
126 GAATACATAATAACCGAGTGGTAAAAACCATAATTTATGTGCATTGGAAGCTTACCCATCTGAAC
38429 T
191 T
38430 AAATTGACAT
Statistics
Matches: 184, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
209 54 0.29
210 27 0.15
212 14 0.08
213 19 0.10
214 70 0.38
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (210 bp):
GGTGTCACACAACATCGATAAATTTTCGTCTAACTGAAACATTGACTCATTCTCACATAGCCTTC
AAGCAAGCCTTAACATATATGATATTTTGCATGTACTCGTACTAACACCCCACCTACTATGAATA
CATAATAACCGAGTGGTAAAAACCATAATTTATGTGCATTGGAAGCTTACCCATCTGAACTGGTT
TTCACATAGGCATCA
Found at i:42858 original size:24 final size:24
Alignment explanation
Indices: 42822--42872 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
42812 TAATTTCTTC
* *
42822 TATTTCTACTTTTATTCGTTTTTT
1 TATTTCTACTTTTATTCATTTTAT
* *
42846 TATTTTTATTTTTATTCATTTTAT
1 TATTTCTACTTTTATTCATTTTAT
42870 TAT
1 TAT
42873 ATCACATCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.73
Consensus pattern (24 bp):
TATTTCTACTTTTATTCATTTTAT
Found at i:43375 original size:20 final size:20
Alignment explanation
Indices: 43350--43423 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
43340 GATCCGACCC
43350 AAAATAATATATTTATTAAA
1 AAAATAATATATTTATTAAA
* *
43370 AAAATATTATTTTTATTCAATA
1 AAAATAATATATTTATT-AA-A
* * * *
43392 AAAGTAAGGAT-TTAATTGAA
1 AAAATAA-TATATTTATTAAA
43412 AAAATAATATAT
1 AAAATAATATAT
43424 AGAAGGTTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
19 2 0.05
20 23 0.56
21 3 0.07
22 11 0.27
23 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.39
Consensus pattern (20 bp):
AAAATAATATATTTATTAAA
Found at i:44951 original size:56 final size:56
Alignment explanation
Indices: 44879--44989 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
44869 AGAAAGTATT
*
44879 CGTGCATATATAATTATATTCTATTTGATATTTACCAATTATTTTTTGTTCCTATG
1 CGTGCATATATAATTATATTCTATGTGATATTTACCAATTATTTTTTGTTCCTATG
* *
44935 CGTGTATATATAATTATCTTCTATGTGATATTTACCAATTATTTTTTGTTCCTAT
1 CGTGCATATATAATTATATTCTATGTGATATTTACCAATTATTTTTTGTTCCTAT
44990 TCGTCTAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (56 bp):
CGTGCATATATAATTATATTCTATGTGATATTTACCAATTATTTTTTGTTCCTATG
Found at i:47441 original size:13 final size:13
Alignment explanation
Indices: 47423--47466 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
47413 ACCCCGATTA
47423 CCCGATTACCCGG
1 CCCGATTACCCGG
*
47436 CCCGATTACCCAG
1 CCCGATTACCCGG
*
47449 CCCGA-TACCCGA
1 CCCGATTACCCGG
47461 CCCGAT
1 CCCGAT
47467 AAATATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.20, C:0.48, G:0.18, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGG
Found at i:53363 original size:20 final size:20
Alignment explanation
Indices: 53334--53372 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53324 AGAGCACATA
*
53334 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
53354 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
53373 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:53723 original size:23 final size:23
Alignment explanation
Indices: 53697--53750 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
53687 CTCCCAGGAT
*
53697 GGACCACTACTAGCTACCCAAGG
1 GGACCACTACTAGATACCCAAGG
* * * *
53720 GGACCACTGCTAGATGCCTAGGG
1 GGACCACTACTAGATACCCAAGG
53743 GGACCACT
1 GGACCACT
53751 GCCACTTATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.31, G:0.28, T:0.15
Consensus pattern (23 bp):
GGACCACTACTAGATACCCAAGG
Found at i:54531 original size:27 final size:26
Alignment explanation
Indices: 54500--54554 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 26
54490 ACTAAACACA
54500 ATTTTATTTGTCACGACATTTCCATCC
1 ATTTT-TTTGTCACGACATTTCCATCC
54527 A---TTTTGTCACGACATTTCCATCC
1 ATTTTTTTGTCACGACATTTCCATCC
54550 ATTTT
1 ATTTT
54555 GCCACGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
23 22 0.88
24 1 0.04
26 1 0.04
27 1 0.04
ACGTcount: A:0.22, C:0.25, G:0.07, T:0.45
Consensus pattern (26 bp):
ATTTTTTTGTCACGACATTTCCATCC
Found at i:54533 original size:23 final size:23
Alignment explanation
Indices: 54506--54571 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
54496 CACAATTTTA
54506 TTTGTCACGACATTTCCATCCAT
1 TTTGTCACGACATTTCCATCCAT
54529 TTTGTCACGACATTTCCATCCAT
1 TTTGTCACGACATTTCCATCCAT
* *
54552 TTTGCCACGACATCTCCATC
1 TTTGTCACGACATTTCCATC
54572 TGCTTCTACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.36
Consensus pattern (23 bp):
TTTGTCACGACATTTCCATCCAT
Found at i:70062 original size:21 final size:21
Alignment explanation
Indices: 70036--70075 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
70026 AGAACCCCAG
*
70036 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
70057 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
70076 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:70107 original size:21 final size:23
Alignment explanation
Indices: 70056--70107 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
70046 GATTCCCCTG
*
70056 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCAGTTCCCCTTCA
**
70079 AAGGGGGAATCAGTT-CCC-TCA
1 TGGGGGGAATCAGTTCCCCTTCA
70100 TGGGGGGA
1 TGGGGGGA
70108 TCGATTCCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.21
Consensus pattern (23 bp):
TGGGGGGAATCAGTTCCCCTTCA
Found at i:73965 original size:22 final size:21
Alignment explanation
Indices: 73923--73962 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
73913 GAGTTTGTTT
*
73923 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
73944 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
73963 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:86731 original size:15 final size:15
Alignment explanation
Indices: 86711--86752 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
86701 CTTCATGGGG
*
86711 TAAGAAGACAACGTC
1 TAAGAAGAAAACGTC
86726 TAAGAAGAAAACGTC
1 TAAGAAGAAAACGTC
*
86741 AAAGAAGAAAAC
1 TAAGAAGAAAAC
86753 ATTAAAGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.57, C:0.14, G:0.19, T:0.10
Consensus pattern (15 bp):
TAAGAAGAAAACGTC
Found at i:86759 original size:15 final size:15
Alignment explanation
Indices: 86712--86767 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
86702 TTCATGGGGT
* * *
86712 AAGAAGACAACGTCT
1 AAGAAGAAAACATCA
*
86727 AAGAAGAAAACGTCA
1 AAGAAGAAAACATCA
*
86742 AAGAAGAAAACATTA
1 AAGAAGAAAACATCA
86757 AAGAAGGAAAA
1 AAGAA-GAAAA
86768 AGAAAACATC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 31 0.86
16 5 0.14
ACGTcount: A:0.61, C:0.11, G:0.20, T:0.09
Consensus pattern (15 bp):
AAGAAGAAAACATCA
Found at i:90713 original size:51 final size:51
Alignment explanation
Indices: 90603--90713 Score: 122
Period size: 51 Copynumber: 2.2 Consensus size: 51
90593 AACTTGTTGA
* * *
90603 AAAAGAAGAGGAGAAAGGAGAAGGGACACTGAAGACGGAAAAAGAGAAAGT
1 AAAAGAAGAGGAGAAAGGAGAAGGGACACTCAAGAAGGAAAAAGAGAAAGG
*
90654 AAAGGAAGAGG-GTAAAGGAGAAGGGACAC-CACA-AAGGAAAAAG-GAAGAGG
1 AAAAGAAGAGGAG-AAAGGAGAAGGGACACTCA-AGAAGGAAAAAGAGAA-AGG
90704 AGAAAGAAGA
1 A-AAAGAAGA
90714 AGGGACACCG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
49 3 0.06
50 14 0.27
51 34 0.67
ACGTcount: A:0.55, C:0.06, G:0.36, T:0.03
Consensus pattern (51 bp):
AAAAGAAGAGGAGAAAGGAGAAGGGACACTCAAGAAGGAAAAAGAGAAAGG
Found at i:90760 original size:90 final size:89
Alignment explanation
Indices: 90601--90763 Score: 213
Period size: 90 Copynumber: 1.8 Consensus size: 89
90591 AGAACTTGTT
* * * **
90601 GAAAAAGAAGAGGAGAAAGGAGAAGGGACACTGAAGACGGAAAAAGAGAAAGTAAAGGAAGAGGG
1 GAAAAAGAAGAGGAGAAAGAAGAAGGGACACCGAAGACGGAAAAAGAGAAAGTAAAGGAACACCG
90666 TAAAGGAGAAGGGACACCACAAAG
66 TAAAGGAGAAGGGACACCACAAAG
* * *
90690 GAAAAAGGAAGAGGAGAAAGAAGAAGGGACACCGAAGAGGGAAAGAA-AGAAGAG-GAATGAACA
1 GAAAAA-GAAGAGGAGAAAGAAGAAGGGACACCGAAGACGGAAA-AAGAGAA-AGTAAAGGAACA
90753 CCGTAAAGGAG
63 CCGTAAAGGAG
90764 GAGGACGAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
89 6 0.10
90 53 0.84
91 4 0.06
ACGTcount: A:0.53, C:0.08, G:0.36, T:0.03
Consensus pattern (89 bp):
GAAAAAGAAGAGGAGAAAGAAGAAGGGACACCGAAGACGGAAAAAGAGAAAGTAAAGGAACACCG
TAAAGGAGAAGGGACACCACAAAG
Found at i:91275 original size:12 final size:12
Alignment explanation
Indices: 91255--91285 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
91245 TAATCCCGGG
*
91255 TTTGTTTTTTCA
1 TTTGATTTTTCA
91267 TTTGATTTTTCA
1 TTTGATTTTTCA
91279 TTTGATT
1 TTTGATT
91286 ATCAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.06, G:0.10, T:0.71
Consensus pattern (12 bp):
TTTGATTTTTCA
Found at i:92694 original size:4 final size:4
Alignment explanation
Indices: 92685--92741 Score: 60
Period size: 4 Copynumber: 14.2 Consensus size: 4
92675 TCAATCTACA
* * * * * *
92685 ATAT ATAT ATAT ATAT TTAT TTAT TTAT TTAT TTAT ATTT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
92733 ATAT ATAT A
1 ATAT ATAT A
92742 ATTTCTGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (4 bp):
ATAT
Found at i:92696 original size:6 final size:6
Alignment explanation
Indices: 92685--92741 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
92675 TCAATCTACA
* * * * * *
92685 ATATAT ATATAT ATATTT ATTTAT TTATTT ATTTAT ATTTAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
92733 ATATAT ATA
1 ATATAT ATA
92742 ATTTCTGAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
ATATAT
Found at i:92725 original size:18 final size:18
Alignment explanation
Indices: 92688--92740 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
92678 ATCTACAATA
*
92688 TATATATATATATTTATT
1 TATATATATATATATATT
* * *
92706 TATTTATTTATTTATATT
1 TATATATATATATATATT
92724 TATATATATATATATAT
1 TATATATATATATATAT
92741 AATTTCTGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATATATATATATATT
Found at i:92890 original size:85 final size:84
Alignment explanation
Indices: 92801--93061 Score: 362
Period size: 85 Copynumber: 3.1 Consensus size: 84
92791 GACGTGTGCA
* * *
92801 TCAATGACACGCAATGTAAGTCATATATGCGTGTCATAAATTTACGACACACAAATGTATGTTAA
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATG-TAA
*
92866 GC-AGATTTATGATGGGGGCT
65 GCTA-ATTTATGACGGGGGCT
* * * *
92886 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACATACAAATGTGTGTCAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGTAAG
92951 CTTAATTTATGACGGGGGCT
66 C-TAATTTATGACGGGGGCT
* * * *
92971 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGTAAG
*
93036 CTTAATTTATGGCGGGGGCT
66 C-TAATTTATGACGGGGGCT
93056 TCAATG
1 TCAATG
93062 GCACTCAAAG
Statistics
Matches: 163, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
84 3 0.02
85 159 0.98
86 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (84 bp):
TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGTAAG
CTAATTTATGACGGGGGCT
Found at i:93086 original size:85 final size:85
Alignment explanation
Indices: 92801--93096 Score: 348
Period size: 85 Copynumber: 3.5 Consensus size: 85
92791 GACGTGTGCA
* * * * * *
92801 TCAATGACACGCAATGTAAGTCATATATGCGTGTCATAAATTTACGACACACAAATGTATGTTAA
1 TCAATGACACGCAAAGTAAGCCATACATGCGTGTCATAAATTTATGACACACAAATGTGTG-TCA
* *
92866 GC--AGATTTATGATGGGGGCT
65 TCTTA-ATTTATGACGGGGGCT
* * * *
92886 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACATACAAATGTGTGTCAT
1 TCAATGACACGCAAAGTAAGCCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCAT
92951 CTTAATTTATGACGGGGGCT
66 CTTAATTTATGACGGGGGCT
* * * *
92971 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
1 TCAATGACACGCAAAGTAAGCCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCAT
*
93036 CTTAATTTATGGCGGGGGCT
66 CTTAATTTATGACGGGGGCT
* * *
93056 TCAATGGCACTCAAAG-AACGCCATTA-ATGCGCGTCATAAAT
1 TCAATGACACGCAAAGTAA-GCCA-TACATGCGTGTCATAAAT
93097 GTGCGTCATA
Statistics
Matches: 190, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
84 5 0.03
85 182 0.96
86 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (85 bp):
TCAATGACACGCAAAGTAAGCCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCAT
CTTAATTTATGACGGGGGCT
Found at i:99618 original size:13 final size:13
Alignment explanation
Indices: 99600--99642 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
99590 CTTAATATGC
*
99600 GTCATAAATGTGT
1 GTCATAAATGCGT
99613 GTCATAAATGCGT
1 GTCATAAATGCGT
99626 GTCATAAATGCGT
1 GTCATAAATGCGT
99639 GTCA
1 GTCA
99643 CAGATTTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:106866 original size:18 final size:18
Alignment explanation
Indices: 106843--106879 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
106833 GTGAGTTACG
106843 AGGCTCGAGGTATAGAGA
1 AGGCTCGAGGTATAGAGA
106861 AGGCTCGAGGTATAGAGA
1 AGGCTCGAGGTATAGAGA
106879 A
1 A
106880 CCCTCCGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.38, T:0.16
Consensus pattern (18 bp):
AGGCTCGAGGTATAGAGA
Done.