Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006387.1 Hibiscus syriacus cultivar Beakdansim tig00015386_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: 82160
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1636 original size:12 final size:12
Alignment explanation
Indices: 1621--1655 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1611 TCTTATTCTT
1621 CTTCTTCTTTTC
1 CTTCTTCTTTTC
1633 CTTCTTC-TTTC
1 CTTCTTCTTTTC
1644 CTTCTTTCTTTT
1 CTTC-TTCTTTT
1656 TGATTATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.38
12 10 0.48
13 3 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
CTTCTTCTTTTC
Found at i:6048 original size:15 final size:15
Alignment explanation
Indices: 6023--6057 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
6013 AATATGTATT
6023 TGTCT-TGCCGCGTC
1 TGTCTATGCCGCGTC
6037 TGTCTATGCCGCGTC
1 TGTCTATGCCGCGTC
6052 TGTCTA
1 TGTCTA
6058 AGCTATGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.06, C:0.31, G:0.26, T:0.37
Consensus pattern (15 bp):
TGTCTATGCCGCGTC
Found at i:7438 original size:109 final size:111
Alignment explanation
Indices: 7244--7455 Score: 329
Period size: 109 Copynumber: 1.9 Consensus size: 111
7234 ATTAAAAAAA
* * * * *
7244 TTAATTCTTAATCTGATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
7309 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCTAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCTAGATAT
*
7355 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAA-TTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
* *
7418 AATTAAAATGTTAAAATGTTACCGTATCAGTAAAGTGT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
7456 AGAGATATAT
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
109 43 0.47
110 17 0.18
111 32 0.35
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCTAGATAT
Found at i:7622 original size:10 final size:10
Alignment explanation
Indices: 7586--7626 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
7576 ATCTTAAAAA
*
7586 GAGAGTATTT
1 GAGAGAATTT
7596 GAGAGAGATTT
1 GAGAGA-ATTT
7607 -AGAGAATTT
1 GAGAGAATTT
7616 GAGAGAATTT
1 GAGAGAATTT
7626 G
1 G
7627 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 4 0.14
10 20 0.71
11 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:7824 original size:51 final size:52
Alignment explanation
Indices: 7712--7843 Score: 173
Period size: 51 Copynumber: 2.6 Consensus size: 52
7702 GCGCGCTATG
* * * *
7712 TATCAGGGTATAGCGCGCTGCAGAGGCCGCGCTATACCCACGTGGCGCCAGC
1 TATCAGCGTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCGCCAGC
7764 TATC--CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCA-C
1 TATCAGCGTATAGCGCGGTGCAGGGGGCGCGCTATA-CCCACGTGGCGCCAGC
**
7814 -ATCAGCGTATAGCATGGTGCAGGGGGCGCG
1 TATCAGCGTATAGCGCGGTGCAGGGGGCGCG
7844 TTTTACTGCT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
49 3 0.04
50 27 0.38
51 37 0.52
52 4 0.06
ACGTcount: A:0.18, C:0.30, G:0.36, T:0.16
Consensus pattern (52 bp):
TATCAGCGTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCGCCAGC
Found at i:9828 original size:60 final size:59
Alignment explanation
Indices: 9760--9936 Score: 194
Period size: 61 Copynumber: 2.9 Consensus size: 59
9750 ATAGTTAGTT
* * *
9760 GATCATTTTATAACTTTTAATAGTCGATGGACTTAATAAAGTAATGTCCTACAGTCGGAG
1 GATCATTTTGTAACTTTTAATAGTCGA-GGACTTAACAAAGTAATGTCCTATAGTCGGAG
* * * *
9820 GATCATTTTTGTAACTTTTTATAGTCGAGAGA-TTCAACAAAGTAACGTTCTATAGTCAGAG
1 GATCA-TTTTGTAACTTTTAATAGTCGAG-GACTT-AACAAAGTAATGTCCTATAGTCGGAG
* * * * * *
9881 GAGCATTTTGTAACTTTTGATAGTTGGGGACTTAACAAAGTAGTATCCTATAGTCG
1 GATCATTTTGTAACTTTTAATAGTCGAGGACTTAACAAAGTAATGTCCTATAGTCG
9937 AAGTACTATA
Statistics
Matches: 97, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
59 20 0.21
60 30 0.31
61 47 0.48
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (59 bp):
GATCATTTTGTAACTTTTAATAGTCGAGGACTTAACAAAGTAATGTCCTATAGTCGGAG
Found at i:15413 original size:117 final size:119
Alignment explanation
Indices: 15195--15429 Score: 386
Period size: 117 Copynumber: 2.0 Consensus size: 119
15185 AGAAGATTTT
*
15195 AATGTGTCAATCAGTTTTTCTTAATGACAATGATCATAATAAAAATAACTTAAAATTGAGAGATT
1 AATGTGTCAATCAGTTTTTCTTAATAACAATGATCATAATAAAAATAACTTAAAATTGAGAG--T
15260 ATTAGTGTAATTTACTCTAAAAAATTTAAAAGTTTAGTGACTAAAGTGAAAATCTTC
64 ATTA-TGTAATTTACTCTAAAAAATTTAAAAGTTTAGTGACTAAAGTGAAAATCTTC
*
15317 AATGTGTCAATCAGTTTTTCTTAATAAATAATGATCATAATAAAAATAACTTAAAATTGAGAG-A
1 AATGTGTCAATCAGTTTTTCTTAAT-AACAATGATCATAATAAAAATAACTTAAAATTGAGAGTA
*
15381 -T-TGTAATTTACTCTAAAAAATTTAAAAGTTTAGTGACTAAATTGAAAAT
65 TTATGTAATTTACTCTAAAAAATTTAAAAGTTTAGTGACTAAAGTGAAAAT
15430 TTTCTAAAAG
Statistics
Matches: 109, Mismatches: 3, Indels: 7
0.92 0.03 0.06
Matches are distributed among these distances:
117 47 0.43
119 1 0.01
120 1 0.01
122 25 0.23
123 35 0.32
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (119 bp):
AATGTGTCAATCAGTTTTTCTTAATAACAATGATCATAATAAAAATAACTTAAAATTGAGAGTAT
TATGTAATTTACTCTAAAAAATTTAAAAGTTTAGTGACTAAAGTGAAAATCTTC
Found at i:20112 original size:22 final size:20
Alignment explanation
Indices: 20087--20159 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 20
20077 TAATATATCT
20087 ATATATTATTTCTTTTAATTAA
1 ATATATTATTT-TTTTAA-TAA
20109 ATATA-TATTTTTATTTAATAA
1 ATATATTA-TTTT-TTTAATAA
* *
20130 A-A-ATAATTTTTTTAATAG
1 ATATATTATTTTTTTAATAA
20148 ATATATTATTTT
1 ATATATTATTTT
20160 AGATCGGGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
18 8 0.19
19 6 0.14
20 9 0.21
21 7 0.16
22 13 0.30
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (20 bp):
ATATATTATTTTTTTAATAA
Found at i:24601 original size:8 final size:8
Alignment explanation
Indices: 24588--24628 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
24578 CTCATTTTCA
24588 GAGAATTT
1 GAGAATTT
24596 GAGAATTT
1 GAGAATTT
*
24604 -AGAGTTT
1 GAGAATTT
*
24611 GGGAATTT
1 GAGAATTT
24619 GAGAATTT
1 GAGAATTT
24627 GA
1 GA
24629 AAGTTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:24620 original size:23 final size:24
Alignment explanation
Indices: 24590--24635 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
24580 CATTTTCAGA
*
24590 GAATTTGAGAATTT-AGAGTTTGG
1 GAATTTGAGAATTTGAAAGTTTGG
24613 GAATTTGAGAATTTGAAAGTTTG
1 GAATTTGAGAATTTGAAAGTTTG
24636 TGAACTGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (24 bp):
GAATTTGAGAATTTGAAAGTTTGG
Found at i:24916 original size:128 final size:128
Alignment explanation
Indices: 24698--25452 Score: 1196
Period size: 128 Copynumber: 5.9 Consensus size: 128
24688 ATAATCGGAG
24698 TACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTA--TT-TCAGAGAATATGTTA
1 TACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
* *
24760 CCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
* *
24823 TACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGTCTTCCATTATTTTATCAGAGAATATGTTA
1 TACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
24888 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
*
24951 CACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
1 TACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
* **
25016 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTATTTATATCAGTACCTATTATTT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
* *** * * *
25079 CT-CAAGGGACTTGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTT
1 -TACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTT
25143 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
65 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
* * * *
25207 CACTATTCATATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTA
1 TACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
* **
25272 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTATTTATATCAGTACCTATTATTT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
* *** * * *
25335 CT-CAAGGGACTTGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTT
1 -TACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTT
25399 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
25453 AATCAGGTAA
Statistics
Matches: 580, Mismatches: 44, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
125 44 0.08
127 2 0.00
128 534 0.92
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (128 bp):
TACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
Found at i:25151 original size:256 final size:256
Alignment explanation
Indices: 24699--25452 Score: 1318
Period size: 256 Copynumber: 3.0 Consensus size: 256
24689 TAATCGGAGT
*
24699 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTA--TT-TCAGAGAATATGTTAC
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* * **
24761 CATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT-TA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTATTTATATCAGTACCTATTATTTCT-
* *** * * * * *
24825 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGTCTTCCATTATTTTATCAGAGAATATGTTATC
130 CAAGGGACTTGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATC
24890 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
195 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
24952 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
25017 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTATTTATATCAGTACCTATTATTTCTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTATTTATATCAGTACCTATTATTTCTC
25082 AAGGGACTTGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
131 AAGGGACTTGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
25147 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
196 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* * *
25208 ACTATTCATATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
25273 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTATTTATATCAGTACCTATTATTTCTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTATTTATATCAGTACCTATTATTTCTC
25338 AAGGGACTTGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
131 AAGGGACTTGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
25403 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
196 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
25453 AATCAGGTAA
Statistics
Matches: 480, Mismatches: 17, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
253 44 0.09
255 2 0.00
256 433 0.90
257 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (256 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTATTTATATCAGTACCTATTATTTCTC
AAGGGACTTGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:25878 original size:34 final size:34
Alignment explanation
Indices: 25840--25940 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 34
25830 AAATTTAATG
*
25840 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * * *
25874 TTAAATTTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
25908 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
25941 AACATTTATC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:26513 original size:21 final size:21
Alignment explanation
Indices: 26460--26553 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
26450 TATGGTATAA
*
26460 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
26481 AA-CCTGGTGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
26502 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
26523 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
26544 AACCCTGCGG
1 AACCCTGCGG
26554 AGATGGCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 3 0.04
21 61 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:26577 original size:42 final size:42
Alignment explanation
Indices: 26460--26577 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
26450 TATGGTATAA
26460 AACCCTGCGGGCTAGGCATGTAACCTGGTGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGCATGTAACCTGGTGGGCTAGGAATGT
* * * *
26502 AACCCTGCGGGCTCGGAATGTAACCCT-GCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGCATGTAA-CCTGGTGGGCTAGGAATGT
* * *
26544 AACCCTGCGGAGAT-GGCATATAAACTGGTGGGCT
1 AACCCTGCGG-GCTAGGCATGTAACCTGGTGGGCT
26578 TGGCATATGA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 2 0.03
42 57 0.89
43 5 0.08
ACGTcount: A:0.22, C:0.24, G:0.34, T:0.20
Consensus pattern (42 bp):
AACCCTGCGGGCTAGGCATGTAACCTGGTGGGCTAGGAATGT
Found at i:26583 original size:21 final size:21
Alignment explanation
Indices: 26557--26604 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
26547 CCTGCGGAGA
*
26557 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
26578 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
26599 GGGCAT
1 TGGCAT
26605 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:28372 original size:34 final size:31
Alignment explanation
Indices: 28327--28403 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 31
28317 TTAATAATTC
* *
28327 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATA-TA--TTAA
*
28361 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTACATAAATATATTAA
28392 TATAAAAAATAA
1 TA-AAAAAATAA
28404 CTATTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 6 0.15
32 9 0.23
33 2 0.05
34 22 0.56
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTACATAAATATATTAA
Found at i:33745 original size:229 final size:229
Alignment explanation
Indices: 33334--34023 Score: 1166
Period size: 229 Copynumber: 3.0 Consensus size: 229
33324 TCAAGATCTT
*
33334 AAGCAGTGAATGTAATTGGAGAAGCACCAAGCTATTTGTAGGTAAAGATTAAAGTCGGCATTCAT
1 AAGCAGTGAATGTAATTGGAGAAGCACCAAGCTATTTGTAGGTAAAGATTAAAGTCAGCATTCAT
33399 TGGATTTTACCACTGGCGGAGCCCAATGTTAAACCTCCAAAATTAAATCTTAAACCCTGTCTCCA
66 TGGATTTTACCACTGGCGGAGCCCAATGTTAAACCTCCAAAATTAAATCTTAAACCCTGTCTCCA
*
33464 CATGCATAACTACAAACCCTAAAACTAAACATGATATACGTAGACACCAAACTTCAACCATAATA
131 CATGCATAACTACAAACCCTAAAACTAAACATGATATACGTAGACACCAAACTTCAACCATAAAA
*
33529 TATTACTTTCACCGTTGATGCAGAAGACAATAAA
196 TATTTCTTTCACCGTTGATGCAGAAGACAATAAA
* * *
33563 AAGCAATGAATGTAATTGGAGAAGCACCAAGCTATTTGTAGGCAAAGATTAAAGTCAGCATTCAA
1 AAGCAGTGAATGTAATTGGAGAAGCACCAAGCTATTTGTAGGTAAAGATTAAAGTCAGCATTCAT
* *
33628 TGGATTTTATCACTGGCGGAGCCCAATGTTAAACCTCAAAAATTAAATCTTAAACCCTGTCTCCA
66 TGGATTTTACCACTGGCGGAGCCCAATGTTAAACCTCCAAAATTAAATCTTAAACCCTGTCTCCA
* * *
33693 CATGCATAAC-CCTAAACCCTAAAACTAAACATGATATACGTAGACTCCAAACTTCAGCCATAAA
131 CATGCATAACTAC-AAACCCTAAAACTAAACATGATATACGTAGACACCAAACTTCAACCATAAA
33757 ATATTTCTTTCACCGTTGATGCAGAAGACAATAAA
195 ATATTTCTTTCACCGTTGATGCAGAAGACAATAAA
*
33792 AAGCAGTGAATGTAATTGGAGAAGCACCAAGCTATTTGTACGTAAAGATTAAAGTCAGCATTCAT
1 AAGCAGTGAATGTAATTGGAGAAGCACCAAGCTATTTGTAGGTAAAGATTAAAGTCAGCATTCAT
* * * *
33857 TGGATTTTACCACTGGCGGGGCCCAATGTTGAACCTCCGAAATTAAATCTTAAACCCTGTCCCGA
66 TGGATTTTACCACTGGCGGAGCCCAATGTTAAACCTCCAAAATTAAATCTTAAACCCTGT--C-T
* * *
33922 CCACATGCATAGCTACAAACCCTAAAACTAAACATGATAGACGTAAACACCAAACTTCAACCATA
128 CCACATGCATAACTACAAACCCTAAAACTAAACATGATATACGTAGACACCAAACTTCAACCATA
33987 AAATATTTCTTTCACCGTTGATGCAGAAGACAATAAA
193 AAATATTTCTTTCACCGTTGATGCAGAAGACAATAAA
34024 TTCGTAACTA
Statistics
Matches: 429, Mismatches: 27, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
228 1 0.00
229 332 0.77
231 1 0.00
232 94 0.22
233 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (229 bp):
AAGCAGTGAATGTAATTGGAGAAGCACCAAGCTATTTGTAGGTAAAGATTAAAGTCAGCATTCAT
TGGATTTTACCACTGGCGGAGCCCAATGTTAAACCTCCAAAATTAAATCTTAAACCCTGTCTCCA
CATGCATAACTACAAACCCTAAAACTAAACATGATATACGTAGACACCAAACTTCAACCATAAAA
TATTTCTTTCACCGTTGATGCAGAAGACAATAAA
Found at i:34323 original size:16 final size:16
Alignment explanation
Indices: 34300--34342 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
34290 TTAAACCTCA
*
34300 TCTTTCTTCTTCTTCT
1 TCTTTCTTCTTCTCCT
* *
34316 TTTTTCTTTTTCTCCT
1 TCTTTCTTCTTCTCCT
34332 TCTTTCTTCTT
1 TCTTTCTTCTT
34343 GATTATGTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
TCTTTCTTCTTCTCCT
Found at i:35451 original size:2 final size:2
Alignment explanation
Indices: 35444--35482 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35434 TATAAGCATA
35444 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
35483 AAACTTGAAT
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:42598 original size:20 final size:20
Alignment explanation
Indices: 42552--42604 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
42542 TATATTAACT
42552 TTTAAATTTTGAATATCATATA
1 TTTAAA-TTT-AATATCATATA
*
42574 TTTAAATTTAATAT-ATATC
1 TTTAAATTTAATATCATATA
42593 TATTAAATTTAA
1 T-TTAAATTTAA
42605 CATGTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.17
20 15 0.52
21 3 0.10
22 6 0.21
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTAAATTTAATATCATATA
Found at i:43226 original size:3 final size:3
Alignment explanation
Indices: 43178--43211 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
43168 CATTCGAGTT
43178 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43212 ATGTATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:44550 original size:2 final size:2
Alignment explanation
Indices: 44543--44576 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
44533 ATGTGCTTTG
44543 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
44577 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:44581 original size:2 final size:2
Alignment explanation
Indices: 44576--44608 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44566 TCTCTCTCTC
44576 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 T
44609 TTGTTGAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52169 original size:2 final size:2
Alignment explanation
Indices: 52162--52186 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52152 TAAAAATTGA
52162 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 A
52187 ATTTTATAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54276 original size:16 final size:16
Alignment explanation
Indices: 54255--54288 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
54245 TACTCTGGAC
54255 AAAAATAATAAGAGAA
1 AAAAATAATAAGAGAA
54271 AAAAATAATAAGAGAA
1 AAAAATAATAAGAGAA
54287 AA
1 AA
54289 TAACCTCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAAATAATAAGAGAA
Found at i:54471 original size:21 final size:21
Alignment explanation
Indices: 54447--54499 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
54437 ATTCTGACTA
*
54447 TCGCATTGTGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
54468 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
54489 TCGCAATGCGA
1 TCGCATTGCGA
54500 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:54531 original size:20 final size:20
Alignment explanation
Indices: 54489--54581 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
54479 TTTTCCGAAT
* *
54489 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACTA
54509 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTATGACTA
* *
54529 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* **
54549 TCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTATGACTA
54569 TCGCAATGCGATT
1 TCGCAATGCGATT
54582 TTCAAAGCGT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
19 1 0.02
20 64 0.98
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.26
Consensus pattern (20 bp):
TCGCAATGCGATTATGACTA
Found at i:54786 original size:22 final size:22
Alignment explanation
Indices: 54761--54804 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
54751 ACATCCGTCC
54761 CCATCTCCGACGAAATCAGTCT
1 CCATCTCCGACGAAATCAGTCT
*
54783 CCATCTCCGACGAAATCCGTCT
1 CCATCTCCGACGAAATCAGTCT
54805 ATCTCCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCT
Found at i:54879 original size:19 final size:20
Alignment explanation
Indices: 54855--54902 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
54845 CAGTCTCTAA
54855 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
*
54874 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
54894 TGCGATTTT
1 TGCGATTTT
54903 AAGTTTCAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.10, C:0.17, G:0.21, T:0.52
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:58151 original size:20 final size:20
Alignment explanation
Indices: 58128--58183 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
58118 TCTGAAACTT
*
58128 AAAATCGTAACACGAAAATG
1 AAAATCGCAACACGAAAATG
58148 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
58168 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
58184 TTTAACTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:58625 original size:22 final size:22
Alignment explanation
Indices: 58596--58652 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
58586 GATAGAGATA
58596 GACAGATTTCGCCGAAGATGGG
1 GACAGATTTCGCCGAAGATGGG
* *
58618 GACTGATTTCGTCGAAGATGGG
1 GACAGATTTCGCCGAAGATGGG
*
58640 GACAGATGTCGCC
1 GACAGATTTCGCC
58653 TTAGAGAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (22 bp):
GACAGATTTCGCCGAAGATGGG
Found at i:58852 original size:20 final size:20
Alignment explanation
Indices: 58819--58912 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
58809 GCGCTTTGAA
* * *
58819 AATCGCATTACGATAATCAG
1 AATCGCGTTGCGATAGTCAG
*
58839 CATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
58859 AATCTCGTTGCGATGGTCAG
1 AATCGCGTTGCGATAGTCAG
*
58879 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
58899 AATCGCGTTGCGAT
1 AATCGCGTTGCGAT
58913 TTACATATTT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:58951 original size:20 final size:20
Alignment explanation
Indices: 58908--58951 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
58898 TAATCGCGTT
* **
58908 GCGATTTACATATTTGCATT
1 GCGATTTACATATTCGCAAC
58928 GCGATTTACATATTCGCAAC
1 GCGATTTACATATTCGCAAC
58948 GCGA
1 GCGA
58952 ATTCGGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (20 bp):
GCGATTTACATATTCGCAAC
Found at i:58969 original size:21 final size:21
Alignment explanation
Indices: 58945--58985 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
58935 ACATATTCGC
*
58945 AACGCGAATTCGGAAAATCGA
1 AACGCGAATTCGAAAAATCGA
*
58966 AACGCGAATTTGAAAAATCG
1 AACGCGAATTCGAAAAATCG
58986 CGTTGCGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
AACGCGAATTCGAAAAATCGA
Found at i:63691 original size:179 final size:185
Alignment explanation
Indices: 63349--63710 Score: 520
Period size: 179 Copynumber: 2.0 Consensus size: 185
63339 ATCCAGCACG
* * * *
63349 TGCAAAAACAAAACAAAAAAATTCTAATACGACCAGGAAAAAATTAAAATTTTGATATATATATT
1 TGCAAAAACAAAACAAAAAAATTCTAATACGACCAGGAAAAAAATAAAAATTTAACATATATATT
* * *
63414 GGATCAACGTTTAAAATTCAAAAAATCAAAGCAAAGCAAAATCAACCTTCTTCGTACCGAATCCA
66 GGATCAACGTATAAAATTCAAAAAATC--AG-AAAGCAAAATCAAACTTCTTCGCACCGAATCCA
* *
63479 AAGAAACGGCCGATTAATCGTCAAAGGAAAACAATATTTAAGATAAAATTAAAGCGCA
128 AAGAAACGGCCGATTAATCGTCAAACGAAAACAAGATTTAAGATAAAATTAAAGCGCA
* *
63537 TGCAAAAACAAAACAAAAAAA-TCTAATACGATC-GTAAAAAAATAAAAATTTAACATATATATT
1 TGCAAAAACAAAACAAAAAAATTCTAATACGACCAGGAAAAAAATAAAAATTTAACATATATATT
* * *
63600 GGATCAACG-ATCAAATTCAGAAAATC-G-AAGCAAAATCAAACTTCTTCGCACCGATTCCAAA-
66 GGATCAACGTATAAAATTCAAAAAATCAGAAAGCAAAATCAAACTTCTTCGCACCGAATCCAAAG
*
63661 AAACGGCCGATTAATCGTCAAACGAAAACAAGATTTAAGATACAATTAAA
131 AAACGGCCGATTAATCGTCAAACGAAAACAAGATTTAAGATAAAATTAAA
63711 ACAATTATTA
Statistics
Matches: 159, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
179 47 0.30
180 31 0.19
182 1 0.01
185 14 0.09
186 34 0.21
187 11 0.07
188 21 0.13
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.22
Consensus pattern (185 bp):
TGCAAAAACAAAACAAAAAAATTCTAATACGACCAGGAAAAAAATAAAAATTTAACATATATATT
GGATCAACGTATAAAATTCAAAAAATCAGAAAGCAAAATCAAACTTCTTCGCACCGAATCCAAAG
AAACGGCCGATTAATCGTCAAACGAAAACAAGATTTAAGATAAAATTAAAGCGCA
Found at i:72025 original size:11 final size:11
Alignment explanation
Indices: 72004--72050 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
71994 CAGCAGTCAA
*
72004 TGATGAGATTT
1 TGATCAGATTT
*
72015 TTATCAGATTT
1 TGATCAGATTT
*
72026 TGATGAGATTT
1 TGATCAGATTT
72037 TGATCAGATTT
1 TGATCAGATTT
72048 TGA
1 TGA
72051 GATTAAAGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (11 bp):
TGATCAGATTT
Found at i:72032 original size:22 final size:22
Alignment explanation
Indices: 72004--72050 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
71994 CAGCAGTCAA
*
72004 TGATGAGATTTTTATCAGATTT
1 TGATGAGATTTTGATCAGATTT
72026 TGATGAGATTTTGATCAGATTT
1 TGATGAGATTTTGATCAGATTT
72048 TGA
1 TGA
72051 GATTAAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (22 bp):
TGATGAGATTTTGATCAGATTT
Found at i:72651 original size:5 final size:5
Alignment explanation
Indices: 72641--72667 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
72631 TTAATAACTC
72641 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
72668 TCCAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:73901 original size:43 final size:43
Alignment explanation
Indices: 73782--73985 Score: 186
Period size: 42 Copynumber: 4.8 Consensus size: 43
73772 GTAATCCTAC
* * **
73782 TTTTTATCTTTATAATTGAGGCCTTTAATTTTTTTTCAATCACAA
1 TTTTTACCTTTATAATTAAGGCCCCTAA-TTTTTTTCAATCAC-A
* * * * * *
73827 TATGTACCTTTATAATTAA-GCTCATGA-TTTTTTCAATCTCA
1 TTTTTACCTTTATAATTAAGGCCCCTAATTTTTTTCAATCACA
* *
73868 TATTTTACCTTTATAAGTAAGGCCCCT-ATTTTTTTCAATCCCA
1 T-TTTTACCTTTATAATTAAGGCCCCTAATTTTTTTCAATCACA
*
73911 TTTTTA-CTTATATAATTTAGGCCCCTAATTTTTTT-AATCAC-
1 TTTTTACCTT-TATAATTAAGGCCCCTAATTTTTTTCAATCACA
* * *
73952 TTTTTACCTTTATAATCAAAGTCCCTAATTTTTT
1 TTTTTACCTTTATAATTAAGGCCCCTAATTTTTT
73986 ACATCAAACC
Statistics
Matches: 131, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
41 31 0.24
42 55 0.42
43 26 0.20
44 4 0.03
45 15 0.11
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.50
Consensus pattern (43 bp):
TTTTTACCTTTATAATTAAGGCCCCTAATTTTTTTCAATCACA
Found at i:76511 original size:20 final size:20
Alignment explanation
Indices: 76474--76512 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
76464 TCCAAACCAC
*
76474 TAATATAAAATTATTATTTG
1 TAATATAAAATTACTATTTG
76494 TAATA-AAAATTAACTATTT
1 TAATATAAAATT-ACTATTT
76513 CAAATACCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
TAATATAAAATTACTATTTG
Found at i:78849 original size:46 final size:44
Alignment explanation
Indices: 78785--78875 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 44
78775 TAAGCTTCGT
*
78785 AGCTCATTGTTTCTTTCTTTTTCAGATTATCCAAATATGGGACC
1 AGCTCATTGTTTCTTTCTTTTTCAGATTATCCAAATATGAGACC
*
78829 AGCTCACTCTGTTTCTTTCTTTTTCAGATTATCCAGATATGAGACC
1 AGCTCA-T-TGTTTCTTTCTTTTTCAGATTATCCAAATATGAGACC
78875 A
1 A
78876 ATTTAGCTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 6 0.14
45 1 0.02
46 36 0.84
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (44 bp):
AGCTCATTGTTTCTTTCTTTTTCAGATTATCCAAATATGAGACC
Found at i:81189 original size:13 final size:13
Alignment explanation
Indices: 81171--81196 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
81161 ATGGCCTAAA
81171 CATGTTTGAACAT
1 CATGTTTGAACAT
81184 CATGTTTGAACAT
1 CATGTTTGAACAT
81197 TATTGTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
CATGTTTGAACAT
Done.