Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012845.1 Corchorus capsularis cultivar CVL-1 contig12866, 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: 39114
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5074 original size:3 final size:3
Alignment explanation
Indices: 5066--5098 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5056 ATTAATTAGG
5066 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5099 TAGGAGATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:7765 original size:5 final size:5
Alignment explanation
Indices: 7745--7779 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
7735 TAAAGTTCAC
*
7745 TCTTT T-TTT CCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
7780 TTCCTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 3 0.11
5 24 0.89
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:7775 original size:15 final size:14
Alignment explanation
Indices: 7745--7791 Score: 62
Period size: 13 Copynumber: 3.4 Consensus size: 14
7735 TAAAGTTCAC
7745 TCTTTTTTTCCTTT
1 TCTTTTTTTCCTTT
*
7759 TCTTTTCTTTTCTTT
1 TCTTTT-TTTCCTTT
7774 TC-TTTTTTCCTTT
1 TCTTTTTTTCCTTT
7787 T-TTTT
1 TCTTTT
7792 AATTCGTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 11 0.38
14 9 0.31
15 9 0.31
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TCTTTTTTTCCTTT
Found at i:7789 original size:10 final size:9
Alignment explanation
Indices: 7745--7791 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
7735 TAAAGTTCAC
7745 TCTTTTTTT
1 TCTTTTTTT
*
7754 CCTTTTCTTT
1 TCTTTT-TTT
7764 TCTTTTCTTT
1 TCTTTT-TTT
7774 TC-TTTTTT
1 TCTTTTTTT
*
7782 CCTTTTTTT
1 TCTTTTTTT
7791 T
1 T
7792 AATTCGTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 4 0.12
9 14 0.44
10 14 0.44
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:19110 original size:12 final size:12
Alignment explanation
Indices: 19095--19237 Score: 67
Period size: 12 Copynumber: 11.9 Consensus size: 12
19085 TAAGATTAAA
19095 ATAAATAAATAT
1 ATAAATAAATAT
* *
19107 ATAATTAAGTA-
1 ATAAATAAATAT
* *
19118 ATAGATAACTAT
1 ATAAATAAATAT
* * *
19130 AAAAAAGAAAAAGT
1 -ATAAATAAATA-T
* *
19144 AAAAAT-AATAG
1 ATAAATAAATAT
* *
19155 ATAAATAAAAAG
1 ATAAATAAATAT
*
19167 ATAAATAGATAT
1 ATAAATAAATAT
* *
19179 ATAAACAAATAG
1 ATAAATAAATAT
*
19191 ATAAATAAGTAT
1 ATAAATAAATAT
* *
19203 GTAAATATATAT
1 ATAAATAAATAT
* *
19215 ATATATATATA-
1 ATAAATAAATAT
19226 ATTAAATAAATA
1 A-TAAATAAATA
19238 ATAGCTTAAA
Statistics
Matches: 95, Mismatches: 31, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
11 14 0.15
12 69 0.73
13 11 0.12
14 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (12 bp):
ATAAATAAATAT
Found at i:19309 original size:17 final size:17
Alignment explanation
Indices: 19287--19326 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
19277 AGATAGATAA
*
19287 ATAATAGTATTAAATAG
1 ATAATAGTACTAAATAG
19304 ATAATAGTACTAAATAG
1 ATAATAGTACTAAATAG
19321 ATAATA
1 ATAATA
19327 ATAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (17 bp):
ATAATAGTACTAAATAG
Found at i:19329 original size:27 final size:26
Alignment explanation
Indices: 19299--19377 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
19289 AATAGTATTA
*
19299 AATAGATAATAGTACTAAATAGATAAT
1 AATA-ATAATAGTACTAAATAGATAAG
19326 AATAAATAATAGTTAC-AAATAGATAAG
1 AAT-AATAATAG-TACTAAATAGATAAG
* *
19353 AA-AATGAATACTAGTAAATAGATAA
1 AATAAT-AATAGTACTAAATAGATAA
19378 AACAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 5 0.11
26 14 0.31
27 22 0.49
28 4 0.09
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.27
Consensus pattern (26 bp):
AATAATAATAGTACTAAATAGATAAG
Found at i:20490 original size:22 final size:21
Alignment explanation
Indices: 20462--20504 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
20452 GCCTAAGTAG
*
20462 ATAGATAGATAGATAATAATAA
1 ATAGATAGATAAATAA-AATAA
20484 ATAGATAGATAAATAAAATAA
1 ATAGATAGATAAATAAAATAA
20505 TTTAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.26
Consensus pattern (21 bp):
ATAGATAGATAAATAAAATAA
Found at i:27102 original size:172 final size:171
Alignment explanation
Indices: 26816--27159 Score: 519
Period size: 172 Copynumber: 2.0 Consensus size: 171
26806 AGCACAAGTC
* * *
26816 GAGAAATTATTAGGTGGGACGGACCCACCGCGTCATCCATGGGACTAATCAATAGAATCTTGCCA
1 GAGAAATTATTAGGTGGGACGGACCCACCACGTCATCCATGGGACTAACCAATAGAATCTTACCA
* * ** * *
26881 TGTCAAATGATCTCCTTAAATTTAGGCATGATTTTAGTCCAAGGTTTAGCCCCCTTTTAAAATAA
66 TGTCAAATAAGCTCCTTAAATTTAGGCACAATTTTAGCCCAAGGTTTAGCCCCCTTTTAAAACAA
* * *
26946 ACCATGTATTCAA-GGTAAGTTCCCAAATTTAAGATATTATTG
131 ACCATATA-TAAAGGGT-AGTCCCCAAATTTAAGATATTATTG
*
26988 GAGAAATTATTAGGTGGGACGGACCCACCACGTCATCCATGGGACTAACCAATAGAATTTTACCA
1 GAGAAATTATTAGGTGGGACGGACCCACCACGTCATCCATGGGACTAACCAATAGAATCTTACCA
27053 TGTCAAATAAGCTCCTTAAATTTAGGCACAATTTTAGCCCAAGGTTTAGCCCCCTTTTAAAACAA
66 TGTCAAATAAGCTCCTTAAATTTAGGCACAATTTTAGCCCAAGGTTTAGCCCCCTTTTAAAACAA
* * *
27118 ACCCTATATAAAGGGTAGTCCCCAAATTTGAGATTTTATTG
131 ACCATATATAAAGGGTAGTCCCCAAATTTAAGATATTATTG
27159 G
1 G
27160 GATAGGGTTT
Statistics
Matches: 155, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
171 26 0.17
172 129 0.83
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (171 bp):
GAGAAATTATTAGGTGGGACGGACCCACCACGTCATCCATGGGACTAACCAATAGAATCTTACCA
TGTCAAATAAGCTCCTTAAATTTAGGCACAATTTTAGCCCAAGGTTTAGCCCCCTTTTAAAACAA
ACCATATATAAAGGGTAGTCCCCAAATTTAAGATATTATTG
Found at i:27316 original size:101 final size:101
Alignment explanation
Indices: 27153--27351 Score: 346
Period size: 101 Copynumber: 2.0 Consensus size: 101
27143 ATTTGAGATT
*
27153 TTATTGGGATAGGGTTTAGAAAATTGATGAGTTGTCTTCATATTATTGGTTGGTCCCATAGATGA
1 TTATTGGGATAGGGTTTAGAAAATTGATGAATTGTCTTCATATTATTGGTTGGTCCCATAGATGA
*
27218 CGTGGTGGGTACGTCC-CACCTAATAATTTCTCATA
66 CGTGGTGGGTACATCCGCACCTAATAATTTCTCATA
*
27253 TTATTGGGATAGGGTTTTAGAAAATTGATGAATTGTCTTCATATTATTGGTTGGTCTCATAGATG
1 TTATTGGGATAGGG-TTTAGAAAATTGATGAATTGTCTTCATATTATTGGTTGGTCCCATAGATG
*
27318 ACGTGGTGGGTCCATCCGCACCTAATAATTTCTC
65 ACGTGGTGGGTACATCCGCACCTAATAATTTCTC
27352 CAGCTCAAAA
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
100 14 0.15
101 63 0.68
102 16 0.17
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (101 bp):
TTATTGGGATAGGGTTTAGAAAATTGATGAATTGTCTTCATATTATTGGTTGGTCCCATAGATGA
CGTGGTGGGTACATCCGCACCTAATAATTTCTCATA
Found at i:30143 original size:17 final size:17
Alignment explanation
Indices: 30123--30157 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
30113 CAACCAGAAT
30123 AAAAGAAAAATAAGAAAAA
1 AAAAG-AAAA-AAGAAAAA
30142 AAAAGAAAAAAGAAAA
1 AAAAGAAAAAAGAAAA
30158 TGAATATGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAA
Found at i:31587 original size:13 final size:13
Alignment explanation
Indices: 31569--31594 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31559 AGAATCCTAC
31569 TTAGTGAGGTAGG
1 TTAGTGAGGTAGG
31582 TTAGTGAGGTAGG
1 TTAGTGAGGTAGG
31595 CTAATAGGCT
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:0.23, C:0.00, G:0.46, T:0.31
Consensus pattern (13 bp):
TTAGTGAGGTAGG
Found at i:35920 original size:13 final size:13
Alignment explanation
Indices: 35894--35936 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
35884 CGGCACAAAT
*
35894 TATATATGGTGTA
1 TATATATAGTGTA
*
35907 TATTTATAGTGTA
1 TATATATAGTGTA
*
35920 TATATATA-TATA
1 TATATATAGTGTA
35932 TATAT
1 TATAT
35937 GTATATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (13 bp):
TATATATAGTGTA
Done.