Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008934.1 Corchorus capsularis cultivar CVL-1 contig08955, 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: 28012
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:1179 original size:23 final size:23
Alignment explanation
Indices: 1153--1225 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 23
1143 AAACTTGGAA
1153 TGAAATTCTTTTTTTTTTAATTT
1 TGAAATTCTTTTTTTTTTAATTT
***
1176 TG-AATT-TTGATTTTTTTGGGTTT
1 TGAAATTCTT--TTTTTTTTAATTT
* *
1199 TGAAAATC-TTTTTATTTAATTT
1 TGAAATTCTTTTTTTTTTAATTT
1221 TGAAA
1 TGAAA
1226 GACTCATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
21 2 0.05
22 18 0.47
23 14 0.37
24 4 0.11
ACGTcount: A:0.25, C:0.03, G:0.11, T:0.62
Consensus pattern (23 bp):
TGAAATTCTTTTTTTTTTAATTT
Found at i:4961 original size:29 final size:31
Alignment explanation
Indices: 4901--4963 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
4891 AACTTTATGT
* *
4901 TTTCCGATTGTACCCTTATTTTTAAAATATA
1 TTTCCAATTGTACCCTTATTTTAAAAATATA
4932 TTTCCAATTGTACCC-T-TTTTAAAAATATA
1 TTTCCAATTGTACCCTTATTTTAAAAATATA
4961 TTT
1 TTT
4964 TAAATTGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.50
30 1 0.03
31 14 0.47
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTAAAAATATA
Found at i:4969 original size:29 final size:31
Alignment explanation
Indices: 4907--4970 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
4897 ATGTTTTCCG
* *
4907 ATTGTACCCTTATTTTTAAAATATATTTCCA
1 ATTGTACCCTTATTTTAAAAATATATTTCAA
*
4938 ATTGTACCC-T-TTTTAAAAATATATTTTAA
1 ATTGTACCCTTATTTTAAAAATATATTTCAA
4967 ATTG
1 ATTG
4971 CCATTACCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 20 0.67
30 1 0.03
31 9 0.30
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTGTACCCTTATTTTAAAAATATATTTCAA
Found at i:5950 original size:19 final size:20
Alignment explanation
Indices: 5923--5960 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5913 TACTATTATT
5923 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
5943 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
5961 AATGTCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:6141 original size:21 final size:22
Alignment explanation
Indices: 6098--6144 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
6088 GTAGCTGATA
6098 TCATAAAGAGGTTATCAAAATT
1 TCATAAAGAGGTTATCAAAATT
*
6120 TCATAAAGAGGTTATCAAATTT
1 TCATAAAGAGGTTATCAAAATT
6142 TCA
1 TCA
6145 AAATGTGATT
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:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (22 bp):
TCATAAAGAGGTTATCAAAATT
Found at i:6318 original size:22 final size:22
Alignment explanation
Indices: 6293--6541 Score: 103
Period size: 22 Copynumber: 11.5 Consensus size: 22
6283 AGTTTAGTTT
6293 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* *
6315 TCAAAATTTCAT-AGTA-TGTAGA
1 TCAAAATTTCATAAG-AGGGT-TA
* *
6337 TCAAAATTTCATATG-GAGATTA
1 TCAAAATTTCATAAGAG-GGTTA
*
6359 ACAAAATTTCATAATGA-GGTTA
1 TCAAAATTTCATAA-GAGGGTTA
**
6381 TCAAAAAATCAT-AG-GGAGATTA
1 TCAAAATTTCATAAGAGG-G-TTA
*
6403 TCAAAATTT-GT---A--GTTA
1 TCAAAATTTCATAAGAGGGTTA
* **
6419 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCATAAGAGGGTTA
* * **
6441 TCAAAATTTTATAGGGAGATTTA
1 TCAAAATTTCATA-AGAGGGTTA
* * **
6464 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAAG-AGGGTTA
*
6487 TCAAAATTTCAT-AGCAAGGTTA
1 TCAAAATTTCATAAG-AGGGTTA
* * *
6509 TCACAATTTCAT-AGCATGATTA
1 TCAAAATTTCATAAG-AGGGTTA
6531 TCAAAATTTCA
1 TCAAAATTTCA
6542 GAGTGTAATT
Statistics
Matches: 176, Mismatches: 32, Indels: 38
0.72 0.13 0.15
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
20 3 0.02
21 7 0.04
22 113 0.64
23 40 0.23
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGGTTA
Found at i:6323 original size:44 final size:44
Alignment explanation
Indices: 6269--6541 Score: 135
Period size: 44 Copynumber: 6.3 Consensus size: 44
6259 TCAGGGAGGA
* *
6269 TATCAAAATTTCATAGT-T-TAGTTTTCAAAATTTCATAA-GAGGGT
1 TATCAAAATTTCATAGTATGTAG--ATCAAAATTTCATAAGGA-GAT
*
6313 TATCAAAATTTCATAGTATGTAGATCAAAATTTCATATGGAGAT
1 TATCAAAATTTCATAGTATGTAGATCAAAATTTCATAAGGAGAT
* * * * ** *
6357 TAACAAAATTTCATAATGAGGT-TATCAAAAAATCATAGGGAGAT
1 TATCAAAATTTCATAGT-ATGTAGATCAAAATTTCATAAGGAGAT
* * *
6401 TATCAAAA-TT--T-GTA-GT-TATCAAGATTTCATAA-GAAAGT
1 TATCAAAATTTCATAGTATGTAGATCAAAATTTCATAAGGAGA-T
* * ** *
6439 TATCAAAATTTTATAGGGA-GATTTATCAAAATTTTAT-AGGAAGATT
1 TATCAAAATTTCATA-GTATG-TAGATCAAAATTTCATAAGG-AGA-T
* * * * *
6485 TATCAAAATTTCATAGCAAGGT-TATCACAATTTCAT-AGCATGAT
1 TATCAAAATTTCATAG-TATGTAGATCAAAATTTCATAAGGA-GAT
6529 TATCAAAATTTCA
1 TATCAAAATTTCA
6542 GAGTGTAATT
Statistics
Matches: 185, Mismatches: 27, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
37 3 0.02
38 23 0.12
39 3 0.02
40 1 0.01
41 2 0.01
43 5 0.03
44 89 0.48
45 36 0.19
46 22 0.12
47 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (44 bp):
TATCAAAATTTCATAGTATGTAGATCAAAATTTCATAAGGAGAT
Found at i:6466 original size:23 final size:23
Alignment explanation
Indices: 6416--6539 Score: 119
Period size: 22 Copynumber: 5.5 Consensus size: 23
6406 AAATTTGTAG
* * * *
6416 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
*
6438 TTATCAAAATTTTATAGGGAGAT
1 TTATCAAAATTTTATAGGAAGAT
6461 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
* * *
6484 TTATCAAAATTTCATAGCAAG-G
1 TTATCAAAATTTTATAGGAAGAT
* * * *
6506 TTATCACAATTTCATAGCATGA-
1 TTATCAAAATTTTATAGGAAGAT
6528 TTATCAAAATTT
1 TTATCAAAATTT
6540 CAGAGTGTAA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
22 46 0.52
23 42 0.48
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:6620 original size:22 final size:22
Alignment explanation
Indices: 6592--6720 Score: 75
Period size: 22 Copynumber: 5.8 Consensus size: 22
6582 TCTATAACGT
*
6592 GGTTATCAATATATCATATGGA
1 GGTTATCAAAATATCATATGGA
* * **
6614 GGTTATCAACATCTCATAGTGTT
1 GGTTATCAAAATATCATA-TGGA
*
6637 GGTTATCAAAATTTCAT-TGGGA
1 GGTTATCAAAATATCATAT-GGA
* * * *
6659 AGTTATCAAAATTTTATATTGA
1 GGTTATCAAAATATCATATGGA
* *
6681 GGTCT-TCAAAAT-TCCTTAGGGA
1 GGT-TATCAAAATAT-CATATGGA
* *
6703 GGTTAACAAAATTTCATA
1 GGTTATCAAAATATCATA
6721 AGGTTAAAGA
Statistics
Matches: 82, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
21 3 0.04
22 59 0.72
23 20 0.24
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (22 bp):
GGTTATCAAAATATCATATGGA
Found at i:6726 original size:19 final size:19
Alignment explanation
Indices: 6702--6740 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6692 TTCCTTAGGG
6702 AGGTT-AACAAAATTTCATA
1 AGGTTAAACAAAATTT-ATA
*
6721 AGGTTAAAGAAAATTTATA
1 AGGTTAAACAAAATTTATA
6740 A
1 A
6741 AATGTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (19 bp):
AGGTTAAACAAAATTTATA
Found at i:12327 original size:30 final size:30
Alignment explanation
Indices: 12273--12336 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
12263 CTTCATTATC
* * *
12273 TTCTACCATCTCTTCCTCATCCTCTCAAAT
1 TTCTACCAACTCTTCCTCACCCTCTAAAAT
**
12303 TTCTACCAACTCTTCCTTGCCCTCTAAAAT
1 TTCTACCAACTCTTCCTCACCCTCTAAAAT
12333 TTCT
1 TTCT
12337 GGACATTCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.38, G:0.02, T:0.41
Consensus pattern (30 bp):
TTCTACCAACTCTTCCTCACCCTCTAAAAT
Found at i:13141 original size:15 final size:15
Alignment explanation
Indices: 13121--13150 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13111 GGAAGGTCTA
13121 ACATGGGTAACGGTT
1 ACATGGGTAACGGTT
*
13136 ACATGGGTAATGGTT
1 ACATGGGTAACGGTT
13151 TGCTTCCAAT
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:0.27, C:0.10, G:0.33, T:0.30
Consensus pattern (15 bp):
ACATGGGTAACGGTT
Found at i:17417 original size:54 final size:54
Alignment explanation
Indices: 17307--18276 Score: 765
Period size: 53 Copynumber: 17.4 Consensus size: 54
17297 TTTACTCTTG
* * *
17307 TTAGTTTAATTACTCTGAATTAAACTAATCTACTGCTTACTCTTTCTTTTCTTCT
1 TTAGCTTAATTACTCTGAATTAAACT-ATCTACTGATTACTCTTTCTTTACTTCT
* * *
17362 TTAGCTTAATTACTCTGAATTAAACTGAT-TATTGCTTACTCTTTCTATACTTCT
1 TTAGCTTAATTACTCTGAATTAAACT-ATCTACTGATTACTCTTTCTTTACTTCT
17416 TTAGCTTAATTACTCTGAATTAAACTATCTACT-ATTACTCTTTCTTTACTTCT
1 TTAGCTTAATTACTCTGAATTAAACTATCTACTGATTACTCTTTCTTTACTTCT
* * * *
17469 TTATCTTAATTACTCCGAATTAAACTATCCACTG-TTACTCTTTCTTTACCTCT
1 TTAGCTTAATTACTCTGAATTAAACTATCTACTGATTACTCTTTCTTTACTTCT
17522 TTAGCTTAATTACTCTGAATTAAACTATCTACTGATTACTCTTTCTTTTACTTCT
1 TTAGCTTAATTACTCTGAATTAAACTATCTACTGATTACTCTTTC-TTTACTTCT
** *
17577 TTAGCTTAATTGTTCTGAATTAAACTATCTACT-ATTACTCTTTCTTTACCTCT
1 TTAGCTTAATTACTCTGAATTAAACTATCTACTGATTACTCTTTCTTTACTTCT
* *
17630 TTAGCTTAATTACTCTGAATTAAACTAACTACTGATTACTTTTTCTTCTAC-TCT
1 TTAGCTTAATTACTCTGAATTAAACTATCTACTGATTACTCTTTCTT-TACTTCT
* * * *
17684 GTAGTTTAATTACTCTGAATTAAACTAATCTACTAATT--TCTCTCTTTAC-TCT
1 TTAGCTTAATTACTCTGAATTAAACT-ATCTACTGATTACTCTTTCTTTACTTCT
* *** * * * *
17736 GAATTAAAC-TAA-T-CTACTG-ATTTCTCTTTTTACTATGAATTAAACTAATCTACTGATTACT
1 ---TT-AGCTTAATTACT-CTGAATTAAACTATCTAC--TG-ATT--ACT-CT-TTCT--TTA--
17797 CTTTCTT
50 C-TTC-T
** * * ** * * *
17804 TTA-CATTTTTTAGT-TTAATTACCCTGCAT-TAAACTAATCTACTGATTACTCTTTCCTTATTC
1 TTAGC-TTAATTACTCTGAATTAAACT--ATCT--ACTGAT-TACT-CTT--TCTTTAC---TTC
17866 T
54 T
* * * * *
17867 TTAGCTTAATTTCTCTAAATTAAACCATCTACTAATTACTCTTTCTTTTACTCTTT
1 TTAGCTTAATTACTCTGAATTAAACTATCTACTGATTACTCTTTC-TTTACT-TCT
* * * *
17923 TTAGTTTAATTACTCTAAATTAAACTAATCTACTGCTTACTCTTTTCTTTTACTCTTT
1 TTAGCTTAATTACTCTGAATTAAACT-ATCTACTGATTACTC-TTTC-TTTACT-TCT
* * * *
17981 TTAGTTTAATTACCCTGAATTAAACTAATCTACTGATTACTTTTTCCTTAC-TCT
1 TTAGCTTAATTACTCTGAATTAAACT-ATCTACTGATTACTCTTTCTTTACTTCT
* * * *
18035 TTAGCTTAATTTCTCTGAATTAAACCATCTACTAATTACTCTTTCTTTTACTCTTT
1 TTAGCTTAATTACTCTGAATTAAACTATCTACTGATTACTCTTTC-TTTACT-TCT
* * *
18091 TTAGTTTAATTACTCTGAATTAAACTAATCTACTGCTTACTCTTTCTTTTACTCTTT
1 TTAGCTTAATTACTCTGAATTAAACT-ATCTACTGATTACTCTTTC-TTTACT-TCT
* * *
18148 TTAGTTTAATTACTCTGAATTAAACTAATCT-CTTCATTACTCTTTGTTTTACTT-T
1 TTAGCTTAATTACTCTGAATTAAACT-ATCTAC-TGATTACTCTTT-CTTTACTTCT
** *
18203 TTATTTTAATTACTCTGAACTAAACTATTCTACTGATTAC-CATTTCTTTACCTT-T
1 TTAGCTTAATTACTCTGAATTAAACTA-TCTACTGATTACTC-TTTCTTTA-CTTCT
18258 TTAGCTTAATTACTCTGAA
1 TTAGCTTAATTACTCTGAA
18277 CTAGGTTCTT
Statistics
Matches: 759, Mismatches: 97, Indels: 118
0.78 0.10 0.12
Matches are distributed among these distances:
52 10 0.01
53 167 0.22
54 150 0.20
55 144 0.19
56 58 0.08
57 94 0.12
58 57 0.08
59 3 0.00
60 5 0.01
61 8 0.01
62 3 0.00
63 14 0.02
64 15 0.02
65 10 0.01
66 11 0.01
67 6 0.01
68 2 0.00
69 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.05, T:0.49
Consensus pattern (54 bp):
TTAGCTTAATTACTCTGAATTAAACTATCTACTGATTACTCTTTCTTTACTTCT
Found at i:17799 original size:36 final size:36
Alignment explanation
Indices: 17693--17800 Score: 180
Period size: 36 Copynumber: 3.0 Consensus size: 36
17683 TGTAGTTTAA
* *
17693 TTACTCTGAATTAAACTAATCTACTAATTTCTCTCT
1 TTACTCTGAATTAAACTAATCTACTGATTTCTCTTT
17729 TTACTCTGAATTAAACTAATCTACTGATTTCTCTTT
1 TTACTCTGAATTAAACTAATCTACTGATTTCTCTTT
* *
17765 TTACTATGAATTAAACTAATCTACTGATTACTCTTT
1 TTACTCTGAATTAAACTAATCTACTGATTTCTCTTT
17801 CTTTTACATT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (36 bp):
TTACTCTGAATTAAACTAATCTACTGATTTCTCTTT
Found at i:18050 original size:168 final size:167
Alignment explanation
Indices: 17773--18273 Score: 744
Period size: 168 Copynumber: 3.0 Consensus size: 167
17763 TTTTACTATG
* *
17773 AATTAAACTAATCTACTGATTACTCTTTCTTTTACAT-TTTTTAGTTTAATTACCCTGCATTAAA
1 AATTAAACTAATCTACTGCTTACTCTTTCTTTTAC-TCTTTTTAGTTTAATTACCCTGAATTAAA
* * *
17837 CTAATCTACTGATTACTCTTTCCTTATTCTTTAGCTTAATTTCTCTAAATTAAACCATCTACTAA
65 CTAATCTACTGATTACTTTTTCCTTACTCTTTAGCTTAATTTCTCTGAATTAAACCATCTACTAA
17902 TTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTA
130 TTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTA
17940 AATTAAACTAATCTACTGCTTACTCTTTTCTTTTACTCTTTTTAGTTTAATTACCCTGAATTAAA
1 AATTAAACTAATCTACTGCTTACTC-TTTCTTTTACTCTTTTTAGTTTAATTACCCTGAATTAAA
18005 CTAATCTACTGATTACTTTTTCCTTACTCTTTAGCTTAATTTCTCTGAATTAAACCATCTACTAA
65 CTAATCTACTGATTACTTTTTCCTTACTCTTTAGCTTAATTTCTCTGAATTAAACCATCTACTAA
*
18070 TTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTG
130 TTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTA
*
18108 AATTAAACTAATCTACTGCTTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTGAATTAAAC
1 AATTAAACTAATCTACTGCTTACTCTTTCTTTTACTCTTTTTAGTTTAATTACCCTGAATTAAAC
* * * ** * * *
18173 TAATCT-CTTCATTACTCTTTGT-TTTACTTTTTATTTTAATTACTCTGAACTAAACTATTCTAC
66 TAATCTAC-TGATTACT-TTT-TCCTTACTCTTTAGCTTAATTTCTCTGAATTAAACCA-TCTAC
* *
18236 TGATTAC-CATTTC-TTTAC-CTTTTTAGCTTAATTACTCT
127 TAATTACTC-TTTCTTTTACTCTTTTTAGTTTAATTACTCT
18274 GAACTAGGTT
Statistics
Matches: 310, Mismatches: 17, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
166 1 0.00
167 96 0.31
168 197 0.64
169 16 0.05
ACGTcount: A:0.26, C:0.20, G:0.04, T:0.50
Consensus pattern (167 bp):
AATTAAACTAATCTACTGCTTACTCTTTCTTTTACTCTTTTTAGTTTAATTACCCTGAATTAAAC
TAATCTACTGATTACTTTTTCCTTACTCTTTAGCTTAATTTCTCTGAATTAAACCATCTACTAAT
TACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTA
Found at i:18098 original size:110 final size:111
Alignment explanation
Indices: 17765--18276 Score: 601
Period size: 110 Copynumber: 4.6 Consensus size: 111
17755 ATTTCTCTTT
* * *
17765 TTACTATGAATTAAACTAATCTACTGATTACTCTTTCTTTTACATTTTTTAGTTTAATTACCCTG
1 TTACTCTGAATTAAACTAATCTACTGATTACTCTTTCTTTTAC--TCTTTAGTTTAATTACTCTG
* * * *
17830 CATTAAACTAATCTACTGATTACTCTTTC-CTTAT-TCTTTAGCTTAA
64 AATTAAACTAATCTACTGATTACTCTTTCTTTTATCTTTTTAGTTTAA
* * * * *
17876 TTTCTCTAAATTAAAC-CATCTACTAATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTA
1 TTACTCTGAATTAAACTAATCTACTGATTACTCTTTCTTTTACTC--TTTAGTTTAATTACTCTG
*
17940 AATTAAACTAATCTACTGCTTACTCTTTTCTTTTACTCTTTTTAGTTTAA
64 AATTAAACTAATCTACTGATTACTC-TTTCTTTTA-TCTTTTTAGTTTAA
* * * * *
17990 TTACCCTGAATTAAACTAATCTACTGATTACTTTTTC-CTTACTCTTTAGCTTAATTTCTCTGAA
1 TTACTCTGAATTAAACTAATCTACTGATTACTCTTTCTTTTACTCTTTAGTTTAATTACTCTGAA
* *
18054 TTAAAC-CATCTACTAATTACTCTTTCTTTTACTCTTTTTAGTTTAA
66 TTAAACTAATCTACTGATTACTCTTTCTTTTA-TCTTTTTAGTTTAA
*
18100 TTACTCTGAATTAAACTAATCTACTGCTTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTG
1 TTACTCTGAATTAAACTAATCTACTGATTACTCTTTCTTTTACTC--TTTAGTTTAATTACTCTG
* * *
18165 AATTAAACTAATCT-CTTCATTACTCTTTGTTTTA-CTTTTTATTTTAA
64 AATTAAACTAATCTAC-TGATTACTCTTTCTTTTATCTTTTTAGTTTAA
* * * *
18212 TTACTCTGAACTAAACTATTCTACTGATTAC-CATTTC-TTTACCTTTTTAGCTTAATTACTCTG
1 TTACTCTGAATTAAACTAATCTACTGATTACTC-TTTCTTTTA-CTCTTTAGTTTAATTACTCTG
18275 AA
64 AA
18277 CTAGGTTCTT
Statistics
Matches: 346, Mismatches: 41, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
108 1 0.00
110 140 0.40
111 41 0.12
112 72 0.21
113 26 0.08
114 49 0.14
115 17 0.05
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (111 bp):
TTACTCTGAATTAAACTAATCTACTGATTACTCTTTCTTTTACTCTTTAGTTTAATTACTCTGAA
TTAAACTAATCTACTGATTACTCTTTCTTTTATCTTTTTAGTTTAA
Found at i:24793 original size:50 final size:51
Alignment explanation
Indices: 24727--24842 Score: 166
Period size: 50 Copynumber: 2.3 Consensus size: 51
24717 ATCTTTAGCT
*
24727 AAAAGATGGGATTTTTGATTAAGTTGTAAATAAGAATGGAATTTTTAAATG
1 AAAAGATGAGATTTTTGATTAAGTTGTAAATAAGAATGGAATTTTTAAATG
* * *
24778 AAAA-ATGAGATTTTTGATTAAGTTGTAATTAAGAATGGATTTTTTAAGTG
1 AAAAGATGAGATTTTTGATTAAGTTGTAAATAAGAATGGAATTTTTAAATG
24828 -AAAGATTGA-ATTTTT
1 AAAAGA-TGAGATTTTT
24843 TTAAGTAAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
49 3 0.05
50 49 0.83
51 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.41
Consensus pattern (51 bp):
AAAAGATGAGATTTTTGATTAAGTTGTAAATAAGAATGGAATTTTTAAATG
Found at i:24832 original size:21 final size:22
Alignment explanation
Indices: 24808--24848 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
24798 AGTTGTAATT
*
24808 AAGAATGGA-TTTTTTAAGTGA
1 AAGAATGAATTTTTTTAAGTGA
*
24829 AAGATTGAATTTTTTTAAGT
1 AAGAATGAATTTTTTTAAGT
24849 AAGTTGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.44
Consensus pattern (22 bp):
AAGAATGAATTTTTTTAAGTGA
Found at i:25577 original size:35 final size:35
Alignment explanation
Indices: 25538--26038 Score: 646
Period size: 35 Copynumber: 14.3 Consensus size: 35
25528 TTTAAAAGAA
*
25538 GGTAATTAAGTAAGTCGGTAATTAACTTAATTCAG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* *
25573 GGTAATTAAGTGAGTCAGTAATCAACTTAATTCAG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* *
25608 GGTAATTAAGTATGTCAGTAATAAACTTAATTCAG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* *
25643 GGTAATTAAGTAACTCAGTAATCAACTTAATTCAG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* * *
25678 GGTAATTAAGTAATTCGGTAATTAATTTAATTCAG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
*
25713 GGTAATTAAGTAAGTCGGTAATTAACTTAATTCAG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* *
25748 GGTAATTAAGTGAGTCAGTAATCAACTTAATTCAG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* *
25783 GGTAATTAAGTATGTCAGTAATAAACTTAATTCAG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* * *
25818 GGTAATTAATTAAGTCAGTAAGTAGCTTAATTCAG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* *
25853 GGTAATTAAGTAATTCAGTAATAAACTTAATTCAG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* * **
25888 GGTAATTAAGTGAGTCAGTAATCAACTTAATTTTG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* * *
25923 GGTAATTAAGTAATTCGGTAATTAACTTAATTCAA
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* * * * * *
25958 GATAATTAAGTGAGTTAATAATCAACTTAATTTAG
1 GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
* *
25993 GG-AAGTTAAGT-AGTTCAATAAGTAACTTAATTCAG
1 GGTAA-TTAAGTAAG-TCAGTAATTAACTTAATTCAG
*
26028 GGAAATTAAGT
1 GGTAATTAAGT
26039 TTAGTAAGAA
Statistics
Matches: 406, Mismatches: 57, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
34 4 0.01
35 400 0.99
36 2 0.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (35 bp):
GGTAATTAAGTAAGTCAGTAATTAACTTAATTCAG
Done.