Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014135.1 Corchorus olitorius cultivar O-4 contig14168, 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: 25225
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:99 original size:15 final size:17
Alignment explanation
Indices: 74--106 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
64 TAAAAAGTGA
74 TTTAAATAAAA-TATTT
1 TTTAAATAAAATTATTT
90 TTTAAA-AAAATTATTT
1 TTTAAATAAAATTATTT
106 T
1 T
107 CTTCTGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAATAAAATTATTT
Found at i:236 original size:31 final size:31
Alignment explanation
Indices: 137--277 Score: 135
Period size: 31 Copynumber: 4.6 Consensus size: 31
127 AGATGATAAG
* ***
137 CAAGCAATTTAGGATATAACGTTTTCTG-CCG
1 CAAGCAATTAAGGATATAACGTTTT-TGATTT
* ** ***
168 CAAGCAATTAAAGATATAACG--TTACAAAA
1 CAAGCAATTAAGGATATAACGTTTTTGATTT
*
197 CAAGCAATTAAGGATATAACGTTTTTTATTT
1 CAAGCAATTAAGGATATAACGTTTTTGATTT
* *
228 TAAGCAATTAAGGATATGACGTTTTTGATTT
1 CAAGCAATTAAGGATATAACGTTTTTGATTT
259 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
278 TCAGTAAGGG
Statistics
Matches: 89, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
29 22 0.25
31 67 0.75
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTTGATTT
Found at i:473 original size:29 final size:30
Alignment explanation
Indices: 407--486 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 30
397 CCTAACGGAC
407 TATATCCTTAATTGCTCATTTTTCGTAACGT
1 TATATCCTTAATTGCT-ATTTTTCGTAACGT
*
438 TATATCCTTAATTG-T-TTGTTTTGTAACGT
1 TATATCCTTAATTGCTATT-TTTCGTAACGT
**
467 TATATCCCAAATTGC-ATTTT
1 TATATCCTTAATTGCTATTTT
487 GCGGCAAACC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 3 0.07
31 14 0.33
ACGTcount: A:0.24, C:0.16, G:0.10, T:0.50
Consensus pattern (30 bp):
TATATCCTTAATTGCTATTTTTCGTAACGT
Found at i:1354 original size:41 final size:41
Alignment explanation
Indices: 1297--1376 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
1287 TAAATTTGAG
1297 GCGTTCGATATATAAGAGTTGAATAATAACAGTTAGATGAA
1 GCGTTCGATATATAAGAGTTGAATAATAACAGTTAGATGAA
*
1338 GCGTTCGATATATAAGAGTTGAATAATAACCGTTAGATG
1 GCGTTCGATATATAAGAGTTGAATAATAACAGTTAGATG
1377 TGTAACAGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (41 bp):
GCGTTCGATATATAAGAGTTGAATAATAACAGTTAGATGAA
Found at i:2090 original size:11 final size:11
Alignment explanation
Indices: 2070--2100 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2060 AAGATTTCAA
2070 CTGAAGATTAT
1 CTGAAGATTAT
*
2081 CTGGAGATTAT
1 CTGAAGATTAT
2092 CTGAAGATT
1 CTGAAGATT
2101 TAAGTAGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:15121 original size:44 final size:44
Alignment explanation
Indices: 15071--15160 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
15061 TCCTCCTTGG
*
15071 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
1 ATCTTCTTTGATAATAATCCTCAACATACGTGGATCTTCTTTCA
* * *
15115 ATCTTCTTTGATGATAATCCTCAACATCCGTGGGTCTTCTTTCA
1 ATCTTCTTTGATAATAATCCTCAACATACGTGGATCTTCTTTCA
15159 AT
1 AT
15161 AATCCAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.41
Consensus pattern (44 bp):
ATCTTCTTTGATAATAATCCTCAACATACGTGGATCTTCTTTCA
Found at i:15740 original size:26 final size:26
Alignment explanation
Indices: 15710--15761 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
15700 ATCTGGAGCT
*
15710 AAACATGGAAAGAGATCAACGTTAAC
1 AAACATGCAAAGAGATCAACGTTAAC
15736 AAACATGCAAAGAGATCAACGTTAAC
1 AAACATGCAAAGAGATCAACGTTAAC
15762 GGATAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.15
Consensus pattern (26 bp):
AAACATGCAAAGAGATCAACGTTAAC
Found at i:16460 original size:14 final size:14
Alignment explanation
Indices: 16441--16468 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16431 ATTAAATAAA
16441 TAATAATAATTATT
1 TAATAATAATTATT
16455 TAATAATAATTATT
1 TAATAATAATTATT
16469 ATTAAGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATAATAATTATT
Found at i:16461 original size:17 final size:17
Alignment explanation
Indices: 16439--16471 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16429 TTATTAAATA
16439 AATAATAATAATTATTT
1 AATAATAATAATTATTT
*
16456 AATAATAATTATTATT
1 AATAATAATAATTATT
16472 AAGATTATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAATAATAATTATTT
Found at i:17666 original size:27 final size:28
Alignment explanation
Indices: 17636--17689 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
17626 TTGCTCCGCG
*
17636 CAAA-ATCTCAAGCTCCGTGCTTTCTCT
1 CAAATATCTCAAGCTCCATGCTTTCTCT
*
17663 CAAATTATCTCAAGCTCTATGCTTTCT
1 CAAA-TATCTCAAGCTCCATGCTTTCT
17690 TTAAAACTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
29 19 0.83
ACGTcount: A:0.24, C:0.30, G:0.09, T:0.37
Consensus pattern (28 bp):
CAAATATCTCAAGCTCCATGCTTTCTCT
Found at i:19963 original size:108 final size:107
Alignment explanation
Indices: 19774--19987 Score: 392
Period size: 108 Copynumber: 2.0 Consensus size: 107
19764 AAGCACTAAT
19774 TTCTTTCAATTCACGACTCCTTGCCATTGTTAGATCACAATAAGCTACTAGGCATAAACTAGGTC
1 TTCTTTCAATTCACGACTCCTTGCCATTGTTAGATCACAATAAGCTACTAGGCATAAACTAGGTC
*
19839 CTTTATTCTTTTTTTTTTTCATGTGTGTACACACACACACACA
66 CTTTATTC-TTTTTTTTTTCATGTGTGCACACACACACACACA
*
19882 TTCTTTCAATTTACGACTCCTTGCCATTGTTAGATCACAATAAGCTACTAGGCATAAACTAGGTC
1 TTCTTTCAATTCACGACTCCTTGCCATTGTTAGATCACAATAAGCTACTAGGCATAAACTAGGTC
*
19947 CTTTATTCTTTTTTTTTTCATGTGTGCACACACACGCACAC
66 CTTTATTCTTTTTTTTTTCATGTGTGCACACACACACACAC
19988 TCATTTCGTG
Statistics
Matches: 103, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 31 0.30
108 72 0.70
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (107 bp):
TTCTTTCAATTCACGACTCCTTGCCATTGTTAGATCACAATAAGCTACTAGGCATAAACTAGGTC
CTTTATTCTTTTTTTTTTCATGTGTGCACACACACACACACA
Found at i:20176 original size:93 final size:94
Alignment explanation
Indices: 20016--20185 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 94
20006 TAATTGGCAC
20016 CATTAAATATGCACCCCCACACTTATTTCATTTCGTAGGGCTCGGTTTCCTTATGCCATAGTAAT
1 CATTAAATATGCACCCCCACACTTATTTCATTTCGTAGGGCTCGGTTTCCTTATGCCATAGTAAT
20081 TGGCACTTTTACACACACACACACACACA
66 TGGCACTTTTACACACACACACACACACA
* *
20110 CATTAAATATGCA-CCCCACACTTATTTCATTTCGTGGGGCTCGGTTTCCTTATGCCGTAGTAAT
1 CATTAAATATGCACCCCCACACTTATTTCATTTCGTAGGGCTCGGTTTCCTTATGCCATAGTAAT
20174 TGGCACTTTTAC
66 TGGCACTTTTAC
20186 GCGAAAGTTG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
93 61 0.82
94 13 0.18
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (94 bp):
CATTAAATATGCACCCCCACACTTATTTCATTTCGTAGGGCTCGGTTTCCTTATGCCATAGTAAT
TGGCACTTTTACACACACACACACACACA
Found at i:23162 original size:17 final size:17
Alignment explanation
Indices: 23140--23174 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
23130 GGGTTTGGGC
*
23140 TCGGGTTCAGGCTCAGG
1 TCGGGTTCAGACTCAGG
23157 TCGGGTTCAGACTCAGG
1 TCGGGTTCAGACTCAGG
23174 T
1 T
23175 TTGATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.23, G:0.37, T:0.26
Consensus pattern (17 bp):
TCGGGTTCAGACTCAGG
Done.