Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022491.1 Corchorus olitorius cultivar O-4 contig22524, 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: 125445
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:12690 original size:4 final size:4
Alignment explanation
Indices: 12681--12741 Score: 122
Period size: 4 Copynumber: 15.2 Consensus size: 4
12671 CTCATATATA
12681 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
12729 AAAT AAAT AAAT A
1 AAAT AAAT AAAT A
12742 GATAGAGAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:16103 original size:33 final size:33
Alignment explanation
Indices: 16066--16130 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
16056 ATATTCAAGC
16066 TTAAAATACAAGTATTCCTATTGTATTCCAATT
1 TTAAAATACAAGTATTCCTATTGTATTCCAATT
16099 TTAAAATACAAGTATTCCTATTGTATTCCAAT
1 TTAAAATACAAGTATTCCTATTGTATTCCAAT
16131 ACAAGTTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (33 bp):
TTAAAATACAAGTATTCCTATTGTATTCCAATT
Found at i:19025 original size:19 final size:19
Alignment explanation
Indices: 19001--19042 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
18991 ATAAACACAA
19001 ATTTAATAATATAATCAAG
1 ATTTAATAATATAATCAAG
* * *
19020 ATTTAATATTTTAATCTAG
1 ATTTAATAATATAATCAAG
19039 ATTT
1 ATTT
19043 TGTCTCACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (19 bp):
ATTTAATAATATAATCAAG
Found at i:21268 original size:126 final size:128
Alignment explanation
Indices: 21129--21386 Score: 364
Period size: 126 Copynumber: 2.0 Consensus size: 128
21119 CATTGTTTAA
*
21129 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
*
21190 -TGATTTTTACCATTTTACTATTTTAATTAAAAAAATTATATATATATTAGAATTTTTTTAAATA
66 TTGATTTTTACCATTTTACTATTTT-ATTAAAAAAACT-TATATATATTAGAA-TTTTTTAAATA
21254 T
128 T
*
21255 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTAT--C
* * **
21320 TATTTTATTTTTATCATTTTACTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATA
64 TA-TTGATTTTTACCATTTTACTATTTTATTAAAAAAACTTATATATATTAGAATTTTTTAAATA
21385 T
128 T
21386 A
1 A
21387 TTTCTTAAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
126 54 0.46
127 1 0.01
128 1 0.01
129 1 0.01
131 13 0.11
132 16 0.14
133 9 0.08
134 22 0.19
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (128 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
TTGATTTTTACCATTTTACTATTTTATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:21334 original size:23 final size:22
Alignment explanation
Indices: 21308--21352 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21298 TTAAATCTAA
*
21308 TATCCTTATACCTATTTTATTTT
1 TATCATTATA-CTATTTTATTTT
*
21331 TATCATTTTACTATTTTATTTT
1 TATCATTATACTATTTTATTTT
21353 AAAAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.64
Consensus pattern (22 bp):
TATCATTATACTATTTTATTTT
Found at i:22674 original size:2 final size:2
Alignment explanation
Indices: 22667--22695 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22657 GATAATTAAC
22667 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 A
22696 CCTGCATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31293 original size:6 final size:6
Alignment explanation
Indices: 31282--31307 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31272 CCCTTCGTAC
31282 TACTAT TACTAT TACTAT TACTAT TA
1 TACTAT TACTAT TACTAT TACTAT TA
31308 TTGCTACTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
TACTAT
Found at i:33598 original size:2 final size:2
Alignment explanation
Indices: 33591--33620 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33581 TGAAAGACTC
33591 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33621 CACATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36494 original size:27 final size:27
Alignment explanation
Indices: 36430--36485 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
36420 TACAAAAGGT
* *
36430 TAAATAAACAACTCCTATAATTGAAAA
1 TAAAGAAACAACTACTATAATTGAAAA
36457 TAAAGAAACAACTACTATAATTGAAAA
1 TAAAGAAACAACTACTATAATTGAAAA
36484 TA
1 TA
36486 TAACCACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.25
Consensus pattern (27 bp):
TAAAGAAACAACTACTATAATTGAAAA
Found at i:40031 original size:48 final size:48
Alignment explanation
Indices: 39961--40056 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
39951 AATGTGTAGG
39961 GAAAGAAATTAGCCCCAATACCTAGGAAAGTGCCAATTTCCACAATCA
1 GAAAGAAATTAGCCCCAATACCTAGGAAAGTGCCAATTTCCACAATCA
40009 GAAAGAAATTAGCCCCAATACCTAGGAAAGTGCCAATTTCCACAATCA
1 GAAAGAAATTAGCCCCAATACCTAGGAAAGTGCCAATTTCCACAATCA
40057 AAACATCTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (48 bp):
GAAAGAAATTAGCCCCAATACCTAGGAAAGTGCCAATTTCCACAATCA
Found at i:40037 original size:25 final size:25
Alignment explanation
Indices: 39960--40038 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
39950 AAATGTGTAG
39960 GGAAAGAAATTAGCCCCAATACCTA
1 GGAAAGAAATTAGCCCCAATACCTA
* * *
39985 GGAAAGTGCCAATT-TCCACAAT--C-A
1 GGAAA--G-AAATTAGCCCCAATACCTA
40009 -GAAAGAAATTAGCCCCAATACCTA
1 GGAAAGAAATTAGCCCCAATACCTA
40033 GGAAAG
1 GGAAAG
40039 TGCCAATTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
20 4 0.10
21 7 0.17
23 5 0.12
24 2 0.05
25 11 0.28
27 7 0.17
28 4 0.10
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (25 bp):
GGAAAGAAATTAGCCCCAATACCTA
Found at i:43140 original size:52 final size:49
Alignment explanation
Indices: 43080--43178 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 49
43070 AGACTAGACA
*
43080 ATTGAATTTATTTTTTGACAGCCAGAAAAAAAAAAAACTAGACAATTGAAAT
1 ATTGAATTTATTTTTCGACAGCC---AAAAAAAAAAACTAGACAATTGAAAT
* ** *
43132 ATTGAATTTCTTTTTCGATGGCCAAAAAGAAAAACTAGACAATTGAA
1 ATTGAATTTATTTTTCGACAGCCAAAAAAAAAAACTAGACAATTGAA
43179 TTTGATTCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 23 0.55
52 19 0.45
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.29
Consensus pattern (49 bp):
ATTGAATTTATTTTTCGACAGCCAAAAAAAAAAACTAGACAATTGAAAT
Found at i:57268 original size:26 final size:26
Alignment explanation
Indices: 57232--57283 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
57222 CTCTTCTTGT
57232 TTTTAACATTATTTTGGATGATTTGA
1 TTTTAACATTATTTTGGATGATTTGA
57258 TTTTAACATTATTTTGGATGATTTGA
1 TTTTAACATTATTTTGGATGATTTGA
57284 GGGGAAACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.15, T:0.54
Consensus pattern (26 bp):
TTTTAACATTATTTTGGATGATTTGA
Found at i:65029 original size:15 final size:15
Alignment explanation
Indices: 65009--65038 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
64999 TCTATGGGGC
65009 ATTTTTAATAAATCA
1 ATTTTTAATAAATCA
*
65024 ATTTTTAATTAATCA
1 ATTTTTAATAAATCA
65039 GTAACCAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTAATAAATCA
Found at i:69080 original size:45 final size:44
Alignment explanation
Indices: 69031--69136 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 44
69021 TATGACTTTA
69031 TATATAGTTTTTTTAAAAAAATCATGTAATGAGTAAATAAAAGTT
1 TATATA-TTTTTTTAAAAAAATCATGTAATGAGTAAATAAAAGTT
* *
69076 TATATATAGTTTTAAAAAAAATCATGTAATGAGTAAATAAAAGTT
1 TATATAT-TTTTTTAAAAAAATCATGTAATGAGTAAATAAAAGTT
69121 TGATATGAATTTTTTT
1 T-ATAT--ATTTTTTT
69137 CCTTCCTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
44 1 0.02
45 42 0.79
46 4 0.08
47 4 0.08
48 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (44 bp):
TATATATTTTTTTAAAAAAATCATGTAATGAGTAAATAAAAGTT
Found at i:71301 original size:24 final size:24
Alignment explanation
Indices: 71274--71321 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
71264 TGAATTTACT
71274 GAATTAATTTGATTTTAGTTTTAA
1 GAATTAATTTGATTTTAGTTTTAA
71298 GAATTAATTTGATTTTAGTTTTAA
1 GAATTAATTTGATTTTAGTTTTAA
71322 TGTAACTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (24 bp):
GAATTAATTTGATTTTAGTTTTAA
Found at i:73661 original size:24 final size:24
Alignment explanation
Indices: 73630--73688 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
73620 GCTTAATGTA
73630 AATAATAATCTCAATCGCTGCTCT
1 AATAATAATCTCAATCGCTGCTCT
*
73654 AATAATAATCTCAATTGCTGCTCT
1 AATAATAATCTCAATCGCTGCTCT
73678 AATAATAATCT
1 AATAATAATCT
73689 TATCTGTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (24 bp):
AATAATAATCTCAATCGCTGCTCT
Found at i:73755 original size:22 final size:22
Alignment explanation
Indices: 73730--73771 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
73720 AATCTCATTT
*
73730 ACAAAGTAAGGTGACAAAGTAA
1 ACAAAGTAAGATGACAAAGTAA
73752 ACAAAGTAAGATGACAAAGT
1 ACAAAGTAAGATGACAAAGT
73772 GAGTGTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.10, G:0.21, T:0.14
Consensus pattern (22 bp):
ACAAAGTAAGATGACAAAGTAA
Found at i:73800 original size:33 final size:33
Alignment explanation
Indices: 73761--73827 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
73751 AACAAAGTAA
* *
73761 GATGACAAAGTGAGTGTCAATAACATCACTACC
1 GATGACAAAATAAGTGTCAATAACATCACTACC
*
73794 GATGACAAAATAAGTGTCAATAGCATCACTACC
1 GATGACAAAATAAGTGTCAATAACATCACTACC
73827 G
1 G
73828 CACCATTCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (33 bp):
GATGACAAAATAAGTGTCAATAACATCACTACC
Found at i:75848 original size:2 final size:2
Alignment explanation
Indices: 75841--75874 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
75831 GTGACAATGT
75841 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75875 CTAGAATTTG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:78064 original size:15 final size:16
Alignment explanation
Indices: 78044--78073 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
78034 TTGCATAGTT
78044 TGTTAATT-ATTAGAA
1 TGTTAATTAATTAGAA
78059 TGTTAATTAATTAGA
1 TGTTAATTAATTAGA
78074 TTTTTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (16 bp):
TGTTAATTAATTAGAA
Found at i:78358 original size:21 final size:19
Alignment explanation
Indices: 78334--78391 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
78324 GCTGCTCTAA
*
78334 TAATTTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
78355 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
78374 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
78392 TGCTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:80299 original size:2 final size:2
Alignment explanation
Indices: 80292--80320 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
80282 GGTTTTATCC
80292 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
80321 TGTAATACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:87639 original size:22 final size:22
Alignment explanation
Indices: 87611--87682 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
87601 ACGGAATAAT
87611 AACCGCACGGGCGCGAACGGTA
1 AACCGCACGGGCGCGAACGGTA
*** *
87633 AACCGCACTTTCGC---CGTTTA
1 AACCGCACGGGCGCGAACG-GTA
*
87653 TACCGCACGGGCGCGAACGGTA
1 AACCGCACGGGCGCGAACGGTA
*
87675 CACCGCAC
1 AACCGCAC
87683 TTCGCCGTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
19 2 0.06
20 12 0.33
22 20 0.56
23 2 0.06
ACGTcount: A:0.24, C:0.36, G:0.28, T:0.12
Consensus pattern (22 bp):
AACCGCACGGGCGCGAACGGTA
Found at i:87671 original size:42 final size:41
Alignment explanation
Indices: 87612--87691 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 41
87602 CGGAATAATA
87612 ACCGCACGGGCGCGAACGGTAAACCGCACTTTCGCCGTTTAT
1 ACCGCACGGGCGCGAACGGTAAACCGCAC-TTCGCCGTTTAT
*
87654 ACCGCACGGGCGCGAACGGTACACCGCACTTCGCCGTT
1 ACCGCACGGGCGCGAACGGTAAACCGCACTTCGCCGTT
87692 ACTGTTTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 9 0.24
42 28 0.76
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.16
Consensus pattern (41 bp):
ACCGCACGGGCGCGAACGGTAAACCGCACTTCGCCGTTTAT
Found at i:98919 original size:2 final size:2
Alignment explanation
Indices: 98912--98941 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
98902 AATGGGATGT
98912 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
98942 AACTAGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:103430 original size:95 final size:95
Alignment explanation
Indices: 103267--103456 Score: 362
Period size: 95 Copynumber: 2.0 Consensus size: 95
103257 ATCTTATTTA
*
103267 AGACCATATTCATCCCAAAAAGAGTCAGATAATTTGGGATAAAAGGAGTATATAATTATATAAGC
1 AGACCATATTCATCCCAAAAAGAGTCAGATAATTTGAGATAAAAGGAGTATATAATTATATAAGC
*
103332 TTTGACTTTCACTTTTTAGTCATGGTGGTC
66 TTTGACTTTCACTTTTTAGCCATGGTGGTC
103362 AGACCATATTCATCCCAAAAAGAGTCAGATAATTTGAGATAAAAGGAGTATATAATTATATAAGC
1 AGACCATATTCATCCCAAAAAGAGTCAGATAATTTGAGATAAAAGGAGTATATAATTATATAAGC
103427 TTTGACTTTCACTTTTTAGCCATGGTGGTC
66 TTTGACTTTCACTTTTTAGCCATGGTGGTC
103457 GAGGAGAAGT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (95 bp):
AGACCATATTCATCCCAAAAAGAGTCAGATAATTTGAGATAAAAGGAGTATATAATTATATAAGC
TTTGACTTTCACTTTTTAGCCATGGTGGTC
Found at i:105810 original size:7 final size:7
Alignment explanation
Indices: 105798--105830 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
105788 CTTTCTTTCT
105798 TTCTCAA
1 TTCTCAA
105805 TTCTCAA
1 TTCTCAA
105812 TTCTCAA
1 TTCTCAA
105819 TTCTCAA
1 TTCTCAA
*
105826 ATCTC
1 TTCTC
105831 CACCCCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.42
Consensus pattern (7 bp):
TTCTCAA
Found at i:106639 original size:26 final size:23
Alignment explanation
Indices: 106587--106639 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 23
106577 GCTCCCTCCT
*
106587 TCCCTCTCTCTCCTCCTCTTCGC
1 TCCCTCTCTCTCCTCCTCTTCCC
*
106610 -CCCTCTTTCTCTCTCCTCTTTCCCC
1 TCCCTCTCTCTC-CTCCTC-TT-CCC
106635 TCCCT
1 TCCCT
106640 GCTAAACCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 10 0.42
23 6 0.25
24 2 0.08
25 2 0.08
26 4 0.17
ACGTcount: A:0.00, C:0.57, G:0.02, T:0.42
Consensus pattern (23 bp):
TCCCTCTCTCTCCTCCTCTTCCC
Found at i:118913 original size:21 final size:19
Alignment explanation
Indices: 118888--118945 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
118878 GCTGCTCTAA
118888 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
118909 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
118928 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
118946 TGTTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Done.