Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005526.1 Hibiscus syriacus cultivar Beakdansim tig00012770_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: 87226
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5589 original size:17 final size:17
Alignment explanation
Indices: 5567--5609 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
5557 TAGGAGTCTT
5567 TTTTCTTTTCTCTT-TTG
1 TTTTCTTTT-TCTTGTTG
5584 TTTTCTTCTTTCTTGTTG
1 TTTTCTT-TTTCTTGTTG
5602 TTTT-TTTT
1 TTTTCTTTT
5610 GTTGTAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (17 bp):
TTTTCTTTTTCTTGTTG
Found at i:5607 original size:20 final size:19
Alignment explanation
Indices: 5565--5607 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5555 TGTAGGAGTC
5565 TTTTTTCTTTTCTCTTTTG
1 TTTTTTCTTTTCTCTTTTG
*
5584 TTTTCTTC-TTTCT-TGTTG
1 TTTT-TTCTTTTCTCTTTTG
5602 TTTTTT
1 TTTTTT
5608 TTGTTGTAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 8 0.36
19 9 0.41
20 3 0.14
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTTTTCTTTTCTCTTTTG
Found at i:5839 original size:20 final size:20
Alignment explanation
Indices: 5816--5855 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5806 AATGAAAATG
* *
5816 AAATTGAAAAAGTAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
5836 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
5856 TGAAATGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (20 bp):
AAATGGAAAAAGGAAAGAAT
Found at i:6055 original size:35 final size:36
Alignment explanation
Indices: 6016--6117 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
6006 TGGAATTTGA
*
6016 TGATGATATAGGCGTGAT-ATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACGATGG
* *
6051 TGATGATATAGGCGTGATAATTGTGATGGAAGATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACGATGG
6087 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
6118 AGATTGTATC
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 18 0.30
36 43 0.70
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACGATGG
Found at i:6494 original size:19 final size:20
Alignment explanation
Indices: 6456--6498 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
6446 GAAACCCCTT
*
6456 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
6476 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
6495 TGAA
1 TGAA
6499 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:9863 original size:25 final size:20
Alignment explanation
Indices: 9807--9846 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9797 ATTGAAAATG
*
9807 AAATTGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
9827 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
9847 TGAAATGGAT
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:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (20 bp):
AAATGGAAAAAGGAAAGAAT
Found at i:10078 original size:36 final size:36
Alignment explanation
Indices: 10007--10112 Score: 178
Period size: 36 Copynumber: 2.9 Consensus size: 36
9997 TGGAATTTGA
**
10007 TGATGATATAGGCGTGAT-ATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAAGATGG
10042 TGATGATATAGGCGTGATAATGGTGATGGAAGATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAAGATGG
10078 TGATGATATAGGCGTGATAATGGTGATGGACAGAT
1 TGATGATATAGGCGTGATAATGGTGATGGA-AGAT
10113 TGTATCTTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 18 0.27
36 45 0.67
37 4 0.06
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.29
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAAGATGG
Found at i:38365 original size:22 final size:20
Alignment explanation
Indices: 38340--38379 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38330 ATGTTTGTTT
38340 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
38362 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
38380 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:42615 original size:22 final size:20
Alignment explanation
Indices: 42590--42629 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42580 ATGTTTGTTT
42590 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
42612 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
42630 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:52921 original size:92 final size:93
Alignment explanation
Indices: 52711--52931 Score: 241
Period size: 92 Copynumber: 2.4 Consensus size: 93
52701 AAACTACCAT
* * * *
52711 TCATTAATGGAACAACTTTGATAAGCTAACCTCCTTAGTCCATAAAACATCAAAATGTTTAGTTA
1 TCATTAATGTAACAACTTGGATAAGTTAACCTCCTTAGTCCATAAAACATCAAAATGCTTAGTTA
* ** *
52776 AGACATTTGAATGTTATTTAAAATTCCA
66 AAACATTCCAATGTTATTCAAAATTCCA
* **
52804 TCTATTAATGTAACAACTTGAATAAGTTAACCTTTTTAGTCCAT-AAACATC-AAATGCTTAGTT
1 TC-ATTAATGTAACAACTTGGATAAGTTAACCTCCTTAGTCCATAAAACATCAAAATGCTTAGTT
* * * * *
52867 AAAATATTCCAGTTTTATTCAAAGTTTCA
65 AAAACATTCCAATGTTATTCAAAATTCCA
* *
52896 TGCATTATTGTAACAACATGGATAAGTTAACC-CCTT
1 T-CATTAATGTAACAACTTGGATAAGTTAACCTCCTT
52932 TAATTGATAG
Statistics
Matches: 105, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
91 2 0.02
92 58 0.55
93 10 0.10
94 35 0.33
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (93 bp):
TCATTAATGTAACAACTTGGATAAGTTAACCTCCTTAGTCCATAAAACATCAAAATGCTTAGTTA
AAACATTCCAATGTTATTCAAAATTCCA
Found at i:53112 original size:93 final size:93
Alignment explanation
Indices: 52940--53433 Score: 515
Period size: 93 Copynumber: 5.3 Consensus size: 93
52930 TTTAATTGAT
* * * * * ** * *
52940 AGATGGAAGGTTGAATAGCTTTGAAAAGTGTTAACTAAACACTTTGATGTTTACAAACTGAGGAG
1 AGATTGAAGTTTGAATAGCATTGAAATGTCTTAACTAAACACTTTGATGTTTACGGACTAAAGAG
53005 GTTAACTTATCCAAGTTGTTACATTAAC
66 GTTAACTTATCCAAGTTGTTACATTAAC
* **
53033 AGATTGAGGTTTGAATAGCATTGAAATGTCTTAACTAATA-ACTTTGACATTTACGGACTAAAGA
1 AGATTGAAGTTTGAATAGCATTGAAATGTCTTAACTAA-ACACTTTGATGTTTACGGACTAAAGA
* * *
53097 GGTTAACCTAACCAAGTTGTTACATTAAT
65 GGTTAACTTATCCAAGTTGTTACATTAAC
* ** * * *** *
53126 GGAAGGAAATTTAAATATTGTTGAAATGTCTTAACTAAACACTTTGATGTTTACGGACTAAGGAG
1 AGATTGAAGTTTGAATAGCATTGAAATGTCTTAACTAAACACTTTGATGTTTACGGACTAAAGAG
* *
53191 GTTAACTTATCCAAGTTGTTACAAT-AG
66 GTTAACTTATCCAAGTTGTTACATTAAC
* * * * * * **
53218 TGAATGAAAGTTTGAATAACATTGAAATATCTTAACAAAACACTTTGATATTTAAAGACTAAAGA
1 AGATTG-AAGTTTGAATAGCATTGAAATGTCTTAACTAAACACTTTGATGTTTACGGACTAAAGA
**
53283 GGTTAACTTATCCAAGTTGTTACATTTGC
65 GGTTAACTTATCCAAGTTGTTACATTAAC
* * * * * *
53312 AGATTAAAGTTTGAATAGTATTGAAATCTATTAACTAAACACTTTGATGTTTACGAACTAAATAG
1 AGATTGAAGTTTGAATAGCATTGAAATGTCTTAACTAAACACTTTGATGTTTACGGACTAAAGAG
* * *
53377 GTTAACTTATGCAAGTTGTTACAATAAT
66 GTTAACTTATCCAAGTTGTTACATTAAC
* * * *
53405 GGGTGGAAGCTTGAATAGCATTGAAATGT
1 AGATTGAAGTTTGAATAGCATTGAAATGT
53434 TAAACTTCCA
Statistics
Matches: 325, Mismatches: 72, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
92 6 0.02
93 315 0.97
94 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (93 bp):
AGATTGAAGTTTGAATAGCATTGAAATGTCTTAACTAAACACTTTGATGTTTACGGACTAAAGAG
GTTAACTTATCCAAGTTGTTACATTAAC
Found at i:53284 original size:186 final size:185
Alignment explanation
Indices: 52960--53431 Score: 581
Period size: 186 Copynumber: 2.5 Consensus size: 185
52950 TTGAATAGCT
* * * *
52960 TTGAAAAGTGTTAACTAAACACTTTGATGTTTACAAACTGAGGAGGTTAACTTATCCAAGTTGTT
1 TTGAAATGTATTAACTAAACACTTTGATGTTTACGAACTAAGGAGGTTAACTTATCCAAGTTGTT
* * * * * * **
53025 ACATTAACAGATTGAGGTTTGAATAGCATTGAAATGTCTTAACTAATAACTTTGACATTTACGGA
66 ACAATAA-TGAATGAAGTTTGAATAGCATTGAAATATCTTAACTAAAAACTTTGACATTTAAAGA
* * *
53090 CTAAAGAGGTTAACCTAACCAAGTTGTTACATTAATGGA-AGGAAA-TTTAAATATTG
130 CTAAAGAGGTTAACCTAACCAAGTTGTTACATT--TGCAGAGGAAAGTTTAAATAGTA
* *
53146 TTGAAATGTCTTAACTAAACACTTTGATGTTTACGGACTAAGGAGGTTAACTTATCCAAGTTGTT
1 TTGAAATGTATTAACTAAACACTTTGATGTTTACGAACTAAGGAGGTTAACTTATCCAAGTTGTT
* * *
53211 ACAATAGTGAATGAAAGTTTGAATAACATTGAAATATCTTAAC-AAAACACTTTGATATTTAAAG
66 ACAATAATGAATG-AAGTTTGAATAGCATTGAAATATCTTAACTAAAA-ACTTTGACATTTAAAG
* * ** *
53275 ACTAAAGAGGTTAACTTATCCAAGTTGTTACATTTGCAGATTAAAGTTTGAATAGTA
129 ACTAAAGAGGTTAACCTAACCAAGTTGTTACATTTGCAGAGGAAAGTTTAAATAGTA
* ** *
53332 TTGAAATCTATTAACTAAACACTTTGATGTTTACGAACTAAATAGGTTAACTTATGCAAGTTGTT
1 TTGAAATGTATTAACTAAACACTTTGATGTTTACGAACTAAGGAGGTTAACTTATCCAAGTTGTT
** *
53397 ACAATAATGGGTGGAAGCTTGAATAGCATTGAAAT
66 ACAATAATGAAT-GAAGTTTGAATAGCATTGAAAT
53432 GTTAAACTTC
Statistics
Matches: 246, Mismatches: 35, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
184 3 0.01
185 11 0.04
186 231 0.94
187 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (185 bp):
TTGAAATGTATTAACTAAACACTTTGATGTTTACGAACTAAGGAGGTTAACTTATCCAAGTTGTT
ACAATAATGAATGAAGTTTGAATAGCATTGAAATATCTTAACTAAAAACTTTGACATTTAAAGAC
TAAAGAGGTTAACCTAACCAAGTTGTTACATTTGCAGAGGAAAGTTTAAATAGTA
Found at i:53598 original size:93 final size:90
Alignment explanation
Indices: 53433--53649 Score: 256
Period size: 93 Copynumber: 2.4 Consensus size: 90
53423 CATTGAAATG
* * *
53433 TTAAACTTCCATCCATTAATGTAACAACATAGATAAGTTTACCTCTTTAGTCCATAAACATCAAA
1 TTAAACTTCCAACCATTAATGTAACAAC-TTGATAAGTTAACCTCTTTAGTCCATAAACATCAAA
* * * *
53498 GTGTTTAGTTTAAACATTTGAATGTTTT
65 GTGTTTAG-TT-AACATTTCAAAGCTAT
**
53526 TTAAACTTCCAACCATTAATGTAACAACTTGCATAAGTTAACCTCTTTAGTCTGTAAACATCAAA
1 TTAAACTTCCAACCATTAATGTAACAACTTG-ATAAGTTAACCTCTTTAGTCCATAAACATCAAA
* * *
53591 TTTTTTAGTTGACATTTCAAAGCTAT
65 GTGTTTAGTTAACATTTCAAAGCTAT
* *
53617 TAAAACTTCCATA-TATTAATGTAACAACTTGAT
1 TTAAACTTCCA-ACCATTAATGTAACAACTTGAT
53650 GCGATCATAA
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
90 2 0.02
91 38 0.35
92 5 0.05
93 63 0.58
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (90 bp):
TTAAACTTCCAACCATTAATGTAACAACTTGATAAGTTAACCTCTTTAGTCCATAAACATCAAAG
TGTTTAGTTAACATTTCAAAGCTAT
Found at i:55287 original size:13 final size:13
Alignment explanation
Indices: 55269--55293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55259 AGTGCAAAAA
55269 CAAAAAGAAAGAT
1 CAAAAAGAAAGAT
55282 CAAAAAGAAAGA
1 CAAAAAGAAAGA
55294 AAAAGAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.16, T:0.04
Consensus pattern (13 bp):
CAAAAAGAAAGAT
Found at i:57698 original size:23 final size:23
Alignment explanation
Indices: 57668--57731 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
57658 TATTTTTTTT
57668 CAAAAAAACAAAAAAACAAA-AAA
1 CAAAAAAACAAAAAAA-AAAGAAA
*
57691 CAAAAAAAGGCAAAAAAAAAAGGCAA
1 CAAAAAAA--CAAAAAAAAAA-GAAA
57717 -AAAAAAACAAAAAAA
1 CAAAAAAACAAAAAAA
57732 GAGCCAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 16 0.44
24 3 0.08
25 15 0.42
26 2 0.06
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (23 bp):
CAAAAAAACAAAAAAAAAAGAAA
Found at i:57707 original size:12 final size:12
Alignment explanation
Indices: 57692--57743 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
57682 AACAAAAAAC
57692 AAAAAAAGGCAAA
1 AAAAAAAGGC-AA
57705 AAAAAAAGGCAA
1 AAAAAAAGGCAA
57717 AAAAAAA--CAA
1 AAAAAAAGGCAA
* *
57727 AAAAAGAGCCAA
1 AAAAAAAGGCAA
57739 AAAAA
1 AAAAA
57744 GACAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
10 9 0.25
12 17 0.47
13 10 0.28
ACGTcount: A:0.79, C:0.10, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAGGCAA
Found at i:57708 original size:13 final size:13
Alignment explanation
Indices: 57692--57723 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
57682 AACAAAAAAC
57692 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
57705 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
57718 AAAAAA
1 AAAAAA
57724 CAAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGCAAA
Found at i:57709 original size:14 final size:14
Alignment explanation
Indices: 57687--57723 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
57677 AAAAAAACAA
57687 AAAACAAAAAAAGGC
1 AAAA-AAAAAAAGGC
57702 -AAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
57715 AAAAAAAAA
1 AAAAAAAAA
57724 CAAAAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:57741 original size:13 final size:12
Alignment explanation
Indices: 57692--57750 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 12
57682 AACAAAAAAC
57692 AAAAAAAG-GCA
1 AAAAAAAGAGCA
*
57703 AAAAAAAAAGGCA
1 AAAAAAAGA-GCA
57716 AAAAAAA-A-C-
1 AAAAAAAGAGCA
*
57725 AAAAAAAGAGCC
1 AAAAAAAGAGCA
57737 AAAAAAAGA-CA
1 AAAAAAAGAGCA
57748 AAA
1 AAA
57751 TTTCAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 7 0.17
10 2 0.05
11 12 0.29
12 10 0.24
13 10 0.24
ACGTcount: A:0.78, C:0.10, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAGCA
Found at i:73185 original size:19 final size:21
Alignment explanation
Indices: 73142--73193 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
73132 AAAACCCCTT
73142 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
73163 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
73182 TGAAGATACATG
1 TGAAAATACATG
73194 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:75205 original size:24 final size:24
Alignment explanation
Indices: 75160--75214 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
75150 AACTCTCGGC
* * *
75160 ACTTCAAATGACGTTTCTTTTGGA
1 ACTTCAAATGACATATCTTTTGAA
75184 ACTTCAAATGACATCATC-TTTGAA
1 ACTTCAAATGACAT-ATCTTTTGAA
*
75208 ACATCAA
1 ACTTCAA
75215 GAGACATGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (24 bp):
ACTTCAAATGACATATCTTTTGAA
Found at i:77347 original size:19 final size:21
Alignment explanation
Indices: 77304--77355 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
77294 GAAACCCCTT
77304 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
77325 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
77344 TGAAGATACATG
1 TGAAAATACATG
77356 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:80492 original size:37 final size:37
Alignment explanation
Indices: 80450--80521 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
80440 GAAGTGATCG
*
80450 AATTACCAAATGATTCATCCATTAGGATGATAATTGC
1 AATTACCAAATGATTCATCCATTAAGATGATAATTGC
* * *
80487 AATTACTAACTGGTTCATCCATTAAGATGATAATT
1 AATTACCAAATGATTCATCCATTAAGATGATAATT
80522 CCAACTATCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (37 bp):
AATTACCAAATGATTCATCCATTAAGATGATAATTGC
Found at i:80536 original size:37 final size:37
Alignment explanation
Indices: 80463--80542 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
80453 TACCAAATGA
* * *
80463 TTCATCCATTAGGATGATAATTGCAATTACTAACTGG
1 TTCATCCATTAAGATGATAATTCCAACTACTAACTGG
*
80500 TTCATCCATTAAGATGATAATTCCAACTA-TCGACTGG
1 TTCATCCATTAAGATGATAATTCCAACTACT-AACTGG
80537 TTCATC
1 TTCATC
80543 TCATCGATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 1 0.03
37 37 0.97
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (37 bp):
TTCATCCATTAAGATGATAATTCCAACTACTAACTGG
Done.