Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003282.1 Hibiscus syriacus cultivar Beakdansim tig00006909_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: 82712
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:5896 original size:33 final size:33
Alignment explanation
Indices: 5855--5944 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 33
5845 TTAGGAAGCC
5855 GTTA-AATGGTTGTTAGTTGTTAGCTGTTAACT
1 GTTAGAATGGTTGTTAGTTGTTAGCTGTTAACT
5887 GTTAGAATGGTTGTTA---GTT---T-TTAACT
1 GTTAGAATGGTTGTTAGTTGTTAGCTGTTAACT
5913 GTTAGAAATGGTTGTTAGTTGTTAGCTGTTAA
1 GTTAG-AATGGTTGTTAGTTGTTAGCTGTTAA
5945 GCAGTTATAG
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
26 11 0.22
27 12 0.24
30 6 0.12
32 4 0.08
33 12 0.24
34 4 0.08
ACGTcount: A:0.23, C:0.04, G:0.26, T:0.47
Consensus pattern (33 bp):
GTTAGAATGGTTGTTAGTTGTTAGCTGTTAACT
Found at i:6113 original size:10 final size:10
Alignment explanation
Indices: 6098--6130 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
6088 GGATGTTAAA
6098 TTTCAGAAAC
1 TTTCAGAAAC
6108 TTTCAGAAAC
1 TTTCAGAAAC
*
6118 TTTCATAAAC
1 TTTCAGAAAC
6128 TTT
1 TTT
6131 ATAAACCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (10 bp):
TTTCAGAAAC
Found at i:6136 original size:9 final size:10
Alignment explanation
Indices: 6094--6136 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
6084 TAGAGGATGT
6094 TAAA-TTTCA
1 TAAACTTTCA
*
6103 GAAACTTTCA
1 TAAACTTTCA
*
6113 GAAACTTTCA
1 TAAACTTTCA
6123 TAAACTTT-A
1 TAAACTTTCA
6132 TAAAC
1 TAAAC
6137 CTATCATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 9 0.29
10 22 0.71
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (10 bp):
TAAACTTTCA
Found at i:11161 original size:35 final size:35
Alignment explanation
Indices: 11114--11188 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
11104 TTTATGTCCG
* *
11114 TAATTAGCATTCAATATTATTTGAGA-TCTTTGAAT
1 TAATTAGAATTCAATATTATTTGA-ATTCTCTGAAT
* *
11149 TAATTAGAATTCATTATTCTTTGAATTCTCTGAAT
1 TAATTAGAATTCAATATTATTTGAATTCTCTGAAT
11184 TAATT
1 TAATT
11189 TAACTATACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (35 bp):
TAATTAGAATTCAATATTATTTGAATTCTCTGAAT
Found at i:16359 original size:46 final size:46
Alignment explanation
Indices: 16306--16401 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
16296 AATGCCTTTG
* * *
16306 ACTACGCTGTAGAGGTTGCCCGTAGATAACTCACATATGAGATCTT
1 ACTACGCTATAGAGATTGCCCGTAGATAACTCACATATGAAATCTT
*
16352 ACTACGCTATAGAGATTGCCCGTAGATAACTCATATATGAAATCTT
1 ACTACGCTATAGAGATTGCCCGTAGATAACTCACATATGAAATCTT
16398 ACTA
1 ACTA
16402 AAATGATAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (46 bp):
ACTACGCTATAGAGATTGCCCGTAGATAACTCACATATGAAATCTT
Found at i:17247 original size:24 final size:24
Alignment explanation
Indices: 17220--17269 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
17210 TGGTGGTTGA
17220 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTCTTGAACTTTATT
* *
17244 TTTAATGGTGTCTTTAAGTTTATT
1 TTTAATGGTGTCTTGAACTTTATT
17268 TT
1 TT
17270 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.20, C:0.04, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTCTTGAACTTTATT
Found at i:23811 original size:13 final size:13
Alignment explanation
Indices: 23793--23818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23783 TAAGTTTTTC
23793 TTTATTTTTATTT
1 TTTATTTTTATTT
23806 TTTATTTTTATTT
1 TTTATTTTTATTT
23819 CATTTTGTAA
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTATTTTTATTT
Found at i:24163 original size:19 final size:21
Alignment explanation
Indices: 24126--24168 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
24116 TAACTTTTTC
*
24126 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
24146 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
24166 TTT
1 TTT
24169 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:27490 original size:24 final size:24
Alignment explanation
Indices: 27463--27512 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
27453 TGGTGGTTGA
27463 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
27487 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
27511 TT
1 TT
27513 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:29441 original size:14 final size:14
Alignment explanation
Indices: 29397--29441 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
29387 TCTTTGCATT
* *
29397 TTTGCACCTTGTTC
1 TTTGCACCATATTC
**
29411 TTTGCACCATAGCC
1 TTTGCACCATATTC
29425 TTTGCACCATATTC
1 TTTGCACCATATTC
29439 TTT
1 TTT
29442 ATTCTTACAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.16, C:0.29, G:0.11, T:0.44
Consensus pattern (14 bp):
TTTGCACCATATTC
Found at i:32380 original size:13 final size:12
Alignment explanation
Indices: 32359--32405 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
32349 TGCTTAGTAT
*
32359 AAAATGAAAGAAA
1 AAAAAGAAA-AAA
32372 AAAAAG-AAAAA
1 AAAAAGAAAAAA
32383 AAAAAGAAAAAA
1 AAAAAGAAAAAA
32395 AAAAATGAAAA
1 AAAAA-GAAAA
32406 TGAGGGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 9 0.29
12 12 0.39
13 10 0.32
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:32386 original size:24 final size:24
Alignment explanation
Indices: 32359--32405 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
32349 TGCTTAGTAT
*
32359 AAAATGAAAGAAAAAAAA-GAAAAA
1 AAAAAGAAA-AAAAAAAATGAAAAA
32383 AAAAAGAAAAAAAAAAATGAAAA
1 AAAAAGAAAAAAAAAAATGAAAA
32406 TGAGGGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (24 bp):
AAAAAGAAAAAAAAAAATGAAAAA
Found at i:32405 original size:11 final size:11
Alignment explanation
Indices: 32369--32398 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
32359 AAAATGAAAG
32369 AAAAAAAAGAA
1 AAAAAAAAGAA
32380 AAAAAAAAGAA
1 AAAAAAAAGAA
32391 AAAAAAAA
1 AAAAAAAA
32399 ATGAAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:34481 original size:20 final size:20
Alignment explanation
Indices: 34445--34482 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34435 ATCCTATTAT
**
34445 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
34465 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
34483 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:35698 original size:35 final size:32
Alignment explanation
Indices: 35620--35693 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
35610 ACAACCGTGA
*
35620 ACGGTGGTCGGGAAAGAGGACCATCACGATGT
1 ACGGTGGTCGGGAAAGAAGACCATCACGATGT
*
35652 ACGGTGGTCGGGAAAGAAGAGCATCACGATGT
1 ACGGTGGTCGGGAAAGAAGACCATCACGATGT
35684 ACGGTGGTCG
1 ACGGTGGTCG
35694 TCGGGTTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.27, C:0.18, G:0.39, T:0.16
Consensus pattern (32 bp):
ACGGTGGTCGGGAAAGAAGACCATCACGATGT
Found at i:37608 original size:57 final size:57
Alignment explanation
Indices: 37401--37741 Score: 512
Period size: 57 Copynumber: 6.0 Consensus size: 57
37391 ACATATAGTT
*
37401 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAA--TTTTGCACACATAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* * *
37456 CCCATACGAAAATTCATACACTTGGTATGAACTTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
*
37513 CCCATAC-GAAATTCATAAACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* * *
37569 TCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTACACCCAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* *
37626 CCCATACAGAAATTCATACACTTAGTATGAATTTCTTAAC-TTTT-CATAAGCAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCA-CA-CAAAGTG
* * *
37683 TCCATACGGAAATTCATACACTTAGTATCAACTTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
37740 CC
1 CC
37742 ATTTGGTAAT
Statistics
Matches: 257, Mismatches: 22, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
55 38 0.15
56 55 0.21
57 157 0.61
58 5 0.02
59 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.33
Consensus pattern (57 bp):
CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
Found at i:43378 original size:57 final size:57
Alignment explanation
Indices: 43290--43427 Score: 222
Period size: 57 Copynumber: 2.4 Consensus size: 57
43280 AGTGCACATA
* * * *
43290 TTCTTAACTTTTTGAACACAAAGTGCCCATACGGAAATTCATACACTTAGTATGAAT
1 TTCTTAACTTTTTGCACACAAAGTGCACATACGAAAATTCATACACTTAGTATGAAC
* *
43347 TTCTTAACTTTTTTCCCACAAAGTGCACATACGAAAATTCATACACTTAGTATGAAC
1 TTCTTAACTTTTTGCACACAAAGTGCACATACGAAAATTCATACACTTAGTATGAAC
43404 TTCTTAACTTTTTGCACACAAAGT
1 TTCTTAACTTTTTGCACACAAAGT
43428 TCCATTTGGT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 73 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (57 bp):
TTCTTAACTTTTTGCACACAAAGTGCACATACGAAAATTCATACACTTAGTATGAAC
Found at i:47548 original size:12 final size:12
Alignment explanation
Indices: 47531--47555 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47521 TATAAAATAC
47531 TATACTCTTAAT
1 TATACTCTTAAT
47543 TATACTCTTAAT
1 TATACTCTTAAT
47555 T
1 T
47556 TAAAAGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TATACTCTTAAT
Found at i:48764 original size:13 final size:12
Alignment explanation
Indices: 48745--48774 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
48735 ATTCCCTATA
48745 AAGAAGAAAAAG
1 AAGAAGAAAAAG
48757 AGAGAAGAAAAAG
1 A-AGAAGAAAAAG
48770 AAGAA
1 AAGAA
48775 AATTTTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:51034 original size:31 final size:31
Alignment explanation
Indices: 50987--51063 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
50977 TTGGTCAAAA
* *
50987 TCGGATCGGGTTAATATCGAATCT-GTTGGCT
1 TCGGATCGGGTCAATATCAAAT-TGGTTGGCT
* *
51018 TCGGGTCGGGTCAATATTAAATTGGTTGGCT
1 TCGGATCGGGTCAATATCAAATTGGTTGGCT
* *
51049 TCGGTTTGGGTCAAT
1 TCGGATCGGGTCAAT
51064 CATTAGATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 1 0.03
31 38 0.97
ACGTcount: A:0.18, C:0.14, G:0.31, T:0.36
Consensus pattern (31 bp):
TCGGATCGGGTCAATATCAAATTGGTTGGCT
Found at i:59477 original size:48 final size:48
Alignment explanation
Indices: 59421--59531 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 48
59411 AAATATTTTA
* *
59421 TCTGATTTCCGACT-TAAATTCTGTTATGATA-CATTACCTGAATTCTGT
1 TCTGATTTCCGA-TATAAATTCTGTTATGATATC-TGACATGAATTCTGT
* ** *
59469 TCTGATTTCTGATATGGATTCTGTTATGATATCTGATATGAATTCTGT
1 TCTGATTTCCGATATAAATTCTGTTATGATATCTGACATGAATTCTGT
* *
59517 TTTGATTTCTGATAT
1 TCTGATTTCCGATAT
59532 CTCCGTTTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (48 bp):
TCTGATTTCCGATATAAATTCTGTTATGATATCTGACATGAATTCTGT
Found at i:59478 original size:12 final size:12
Alignment explanation
Indices: 59463--59527 Score: 60
Period size: 12 Copynumber: 5.4 Consensus size: 12
59453 ATTACCTGAA
*
59463 TTCTGTTCTGAT
1 TTCTGTTATGAT
*
59475 TTCTGATATGGA-
1 TTCTGTTAT-GAT
59487 TTCTGTTATGAT
1 TTCTGTTATGAT
* * *
59499 ATCTGATATGAA
1 TTCTGTTATGAT
*
59511 TTCTGTTTTGAT
1 TTCTGTTATGAT
59523 TTCTG
1 TTCTG
59528 ATATCTCCGT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.05
12 37 0.90
13 2 0.05
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.52
Consensus pattern (12 bp):
TTCTGTTATGAT
Found at i:59489 original size:24 final size:24
Alignment explanation
Indices: 59459--59531 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
59449 ATACATTACC
*
59459 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
* *
59483 TGGATTCTGTTATGATATCTGATA
1 TGAATTCTGTTATGATTTCTGATA
*
59507 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
59531 T
1 T
59532 CTCCGTTTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:60142 original size:26 final size:27
Alignment explanation
Indices: 60096--60148 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
60086 AATTGTATTT
*
60096 TGTTTTAATATTTGATTCTGA-AAATC
1 TGTTTTAATATTTGATACTGATAAATC
*
60122 TGTTTT-ATTTTTGTATACTGATAAATC
1 TGTTTTAATATTTG-ATACTGATAAATC
60149 ATTTTATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 6 0.26
26 12 0.52
27 5 0.22
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (27 bp):
TGTTTTAATATTTGATACTGATAAATC
Found at i:64176 original size:48 final size:48
Alignment explanation
Indices: 64120--64230 Score: 138
Period size: 48 Copynumber: 2.3 Consensus size: 48
64110 AAATATTTTA
*
64120 TCTGATTTCTGACT-T-GAATTTTGTTATGATA-CATTACCTGAATTCTGT
1 TCTGATTTCTGA-TATAG-ATTTTGTTATAATATC-TTACCTGAATTCTGT
* *
64168 TCTGATTTCTGATATAGATTTTGTTCTAATATCTTATCTGAATTCTGT
1 TCTGATTTCTGATATAGATTTTGTTATAATATCTTACCTGAATTCTGT
*
64216 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
64231 CTCCGTTTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
47 1 0.02
48 53 0.95
49 2 0.04
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.51
Consensus pattern (48 bp):
TCTGATTTCTGATATAGATTTTGTTATAATATCTTACCTGAATTCTGT
Found at i:64192 original size:24 final size:24
Alignment explanation
Indices: 64158--64230 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
64148 ATACATTACC
64158 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* * * * *
64182 T-AGATTTTGTTCTAATATCTTATC
1 TGA-ATTCTGTTCTGATTTCTGATA
*
64206 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
64230 T
1 T
64231 CTCCGTTTAC
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:65352 original size:18 final size:18
Alignment explanation
Indices: 65329--65385 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
65319 ACCGGTCACA
65329 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
65347 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* * *
65365 AACCAACCCGACCCATTG
1 ACCCGACCCGACCCGTTG
65383 ACC
1 ACC
65386 GTTGACCCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.23, C:0.49, G:0.18, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:65398 original size:15 final size:15
Alignment explanation
Indices: 65374--65407 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
65364 GAACCAACCC
65374 GACCCATTGACCGTT
1 GACCCATTGACCGTT
*
65389 GACCCGTTGACCGTT
1 GACCCATTGACCGTT
65404 GACC
1 GACC
65408 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
GACCCATTGACCGTT
Found at i:66744 original size:18 final size:18
Alignment explanation
Indices: 66718--66753 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
66708 TCGAAAGGAC
*
66718 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
66736 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
66754 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:67935 original size:24 final size:24
Alignment explanation
Indices: 67908--68002 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 24
67898 ATTTCCGACT
** *
67908 TGAATTCTGTTCTGATAAATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
67932 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
67956 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
67980 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
68003 ATCTTCGTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:67946 original size:12 final size:12
Alignment explanation
Indices: 67931--68000 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
67921 GATAAATGAC
67931 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
67943 CTGATTTCTGAT
1 CTGAATTCTGTT
*
67955 CTGGATTCTGTT
1 CTGAATTCTGTT
67967 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
67979 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
67991 TTGATTTCTG
1 CTGAATTCTG
68001 ATATCTTCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
11 2 0.04
12 45 0.92
13 2 0.04
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:67999 original size:48 final size:48
Alignment explanation
Indices: 67894--68002 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
67884 AAATATTTTA
* *
67894 TCTGATTTCCGA-CTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTCTGATAAATGACCTGAATTCTGT
** **
67942 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATAAATGACCTGAATTCTGT
*
67990 TTTGATTTCTGAT
1 TCTGATTTCTGAT
68003 ATCTTCGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:69123 original size:425 final size:423
Alignment explanation
Indices: 68353--69170 Score: 1219
Period size: 425 Copynumber: 1.9 Consensus size: 423
68343 TGTTCGGAAA
* * *
68353 CAATAAGGAAATATATGTTTATTTGTATCTGCACGTTCTTCAGCATCATCTGGTAGTTCTGTATT
1 CAATAAGGAAAAATACGTTTATCTGTATCTGCACGTTCTTCAGCATCATCTGGTAGTTCTGTATT
* * *
68418 ACTGAGCTTTTCGAAGCTCATTCTATTACTCACATTTTCAGGTTAAAAGAATTGTACCAGTGCAT
66 ACTGAGCTTTCCGAAGCTCACTCTATTACTCACATTTTCAGGTTAAAAGAATCGTACCAGTGCAT
* * * * *
68483 CTATCGACTTCAGTAAGGGAGTTCTTTCGGCGTTGTTGCAGAGTATGGTACATGTGATTAGGGGG
131 CTATCGACTTCAGTAAAGGAATCCCTCCGGCGTTGTTGCAGAGTATGGTACATGTGATTAGGGGG
68548 CATGTAATTGTATTTTGATTTATATATGAGTCTGAAAATCTGTTTTATTTTTAAATAGCGACAAA
196 CATGTAATTGTATTTTGATTTATATATGAGTCTGAAAATCTGTTTTATTTTTAAATAGCGACAAA
* * *
68613 TGATTTTATAAGTTTGCATGTTCTGATAAAAAGTTTTAAATTTTCCGCTATTTTTACAGTGGGTC
261 TCATTTTATAAG-TTGCAAGTTCTAATAAAAAGTTTTAAATTTTCCGCTATTTTTACAGTGGGTC
* * ** *
68678 GCTCCGGTGGCCCTAATGTGACACCCCGGATCGGATAGGGCTACCCTTATCGGTCTGTGGGGGTT
325 GCTCCAGTGGCCCTAATGTGACACCCC-AATCGGATAGGGCTACCCGCATCGGTCTGAGGGGGTT
68743 ACACTTAACATAAAGAAATCTGTAAATATCTGAAC
389 ACACTTAACATAAAGAAATCTGTAAATATCTGAAC
68778 CAATAAGGAAAAATACGTTTATCTGTATCTGCACGTTCTTCAGCATCATCTGGTAGTTCTGTATT
1 CAATAAGGAAAAATACGTTTATCTGTATCTGCACGTTCTTCAGCATCATCTGGTAGTTCTGTATT
* *
68843 ACTGAGCTTTCCGAAGCTCACTCTGTTACTCACCTTTTCAGGTTAAAAGAATCGTACCAGTGCAG
66 ACTGAGCTTTCCGAAGCTCACTCTATTACTCACATTTTCAGGTTAAAAGAATCGTACCAGTGCA-
* * *
68908 T-TATTGACTTCAGTAAATGAATCCCTCCGGCGTTGGTTGCAGAGTATGGTACTTGTGATTAGGG
130 TCTATCGACTTCAGTAAAGGAATCCCTCCGGCGTT-GTTGCAGAGTATGGTACATGTGATTAGGG
* * * ** ** *
68972 GGCATGTAATTGTATTTTGTTTTAATATTTGATTCTGAAAATCTGTTTTATTTTTGTATATTGAT
194 GGCATGTAATTGTATTTTGATTT-ATATATGAGTCTGAAAATCTGTTTTATTTTTAAATAGCGAC
*
69037 AAATCATTTTATAAG-TGACAAGTTTTAAT-AAAAGTTTTAAATTTTCCGCTATTTTTACAGTGG
258 AAATCATTTTATAAGTTG-CAAGTTCTAATAAAAAGTTTTAAATTTTCCGCTATTTTTACAGTGG
* * * * *
69100 GTCGCTCCAGTGGCTCTAATGTGACACTCCAATCGGATCGGGTTACCCGCATTGGTCTGAGGGGG
322 GTCGCTCCAGTGGCCCTAATGTGACACCCCAATCGGATAGGGCTACCCGCATCGGTCTGAGGGGG
69165 TTACAC
387 TTACAC
69171 CATGTCATAG
Statistics
Matches: 351, Mismatches: 38, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
424 34 0.10
425 210 0.60
426 59 0.17
427 48 0.14
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (423 bp):
CAATAAGGAAAAATACGTTTATCTGTATCTGCACGTTCTTCAGCATCATCTGGTAGTTCTGTATT
ACTGAGCTTTCCGAAGCTCACTCTATTACTCACATTTTCAGGTTAAAAGAATCGTACCAGTGCAT
CTATCGACTTCAGTAAAGGAATCCCTCCGGCGTTGTTGCAGAGTATGGTACATGTGATTAGGGGG
CATGTAATTGTATTTTGATTTATATATGAGTCTGAAAATCTGTTTTATTTTTAAATAGCGACAAA
TCATTTTATAAGTTGCAAGTTCTAATAAAAAGTTTTAAATTTTCCGCTATTTTTACAGTGGGTCG
CTCCAGTGGCCCTAATGTGACACCCCAATCGGATAGGGCTACCCGCATCGGTCTGAGGGGGTTAC
ACTTAACATAAAGAAATCTGTAAATATCTGAAC
Found at i:72969 original size:15 final size:15
Alignment explanation
Indices: 72949--72991 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
72939 AATATCCTTT
72949 AAAATAATTTTAAGA
1 AAAATAATTTTAAGA
72964 AAAATAATTTTAAGA
1 AAAATAATTTTAAGA
72979 AAAATAATTTTAA
1 AAAATAATTTTAA
72992 AAGATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (15 bp):
AAAATAATTTTAAGA
Found at i:75733 original size:13 final size:13
Alignment explanation
Indices: 75715--75739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75705 ATAACAACAT
75715 AAATAATAATAAC
1 AAATAATAATAAC
75728 AAATAATAATAA
1 AAATAATAATAA
75740 TAATAACCCA
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:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAATAATAAC
Found at i:75746 original size:19 final size:18
Alignment explanation
Indices: 75704--75742 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
75694 AATTAATATA
75704 AATAACAACATAAATAAT
1 AATAACAACATAAATAAT
75722 AATAACAA-AT-AATAAT
1 AATAACAACATAAATAAT
75738 AATAA
1 AATAA
75743 TAACCCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.52
17 2 0.10
18 8 0.38
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (18 bp):
AATAACAACATAAATAAT
Found at i:78231 original size:19 final size:19
Alignment explanation
Indices: 78207--78246 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
78197 TGAGAAATGT
78207 TTCTCTATT-TTTCTATTTA
1 TTCTCT-TTGTTTCTATTTA
*
78226 TTCTCTTTGTTTTTATTTA
1 TTCTCTTTGTTTCTATTTA
78245 TT
1 TT
78247 TGACGCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (19 bp):
TTCTCTTTGTTTCTATTTA
Found at i:78886 original size:14 final size:14
Alignment explanation
Indices: 78867--78893 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
78857 CTAAAGTTCA
78867 ATGTCCATTATAAG
1 ATGTCCATTATAAG
78881 ATGTCCATTATAA
1 ATGTCCATTATAA
78894 AAGGTTTTAA
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:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (14 bp):
ATGTCCATTATAAG
Found at i:80397 original size:38 final size:39
Alignment explanation
Indices: 80346--80427 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 39
80336 CTATCTTGCC
*
80346 TGTTTTTTAAAGTTAT-ATATT-TACAAAA-ATTGATGTCA
1 TGTTTTTTAAAGTTATGAAATTCT-CAAAATA-TGATGTCA
*
80384 TGTTTTTTAAAGTTGTGAAATTCTCAAAATATGATGTCA
1 TGTTTTTTAAAGTTATGAAATTCTCAAAATATGATGTCA
80423 TGTTT
1 TGTTT
80428 ATTTTGATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
38 15 0.38
39 22 0.56
40 2 0.05
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (39 bp):
TGTTTTTTAAAGTTATGAAATTCTCAAAATATGATGTCA
Done.