Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009428.1 Corchorus capsularis cultivar CVL-1 contig09449, 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: 28780
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Found at i:6786 original size:12 final size:13
Alignment explanation
Indices: 6766--6798 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
6756 TTTTAGTGCC
6766 TCTCTTTTTCCTT
1 TCTCTTTTTCCTT
*
6779 TC-CTTTTTCTTT
1 TCTCTTTTTCCTT
6791 TCTCTTTT
1 TCTCTTTT
6799 AATTTTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TCTCTTTTTCCTT
Found at i:10266 original size:4 final size:4
Alignment explanation
Indices: 10259--10308 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
10249 TATTTGTGTG
* * * *
10259 TATA TATA TATA TATA TATA TATA TATA TGTA TGTA TGTA TGTA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
10307 TA
1 TA
10309 ACAAATTGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:11241 original size:426 final size:429
Alignment explanation
Indices: 10428--11512 Score: 1293
Period size: 426 Copynumber: 2.5 Consensus size: 429
10418 CCCGTTCTCA
* * * * * * *
10428 ATAAACAAATACTTTTTTGT--TGGATTATTTATCAAATAATCCGTATACTTTTACGCTTTTTGC
1 ATAAACAAATA-TTTTTTTTACTGGATTATTTATTAAATGATCCTTATACTTTTATGATTTATGC
* * * * * *
10491 TATTTAGTCCC-CACAAGTTTTGGGTTAGACAATTGAACGTTTTGGCTTTAATTCTTTTACTTTT
65 TATTTAATCCCTCACAAATTATGGGTTGGACGATTTAACG-TTTGGCTTTAATTCTTTTA-TTTT
* * * * *
10555 TGTTTTGCTTATCCGATCAAGGTGATTCAAATGTCTATTAAAAGGTAATTCCATGATCTACAACT
128 TGTTATGTTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACT
* * * * * * * ** *
10620 TTCATGAAGGAA-TCAGAAGTCAATTTTAATGTTTTGATTTTAAAAAATGCTTCTGAAATTTTGT
193 TTCATTAA-GAACTCAAAAGCCAATTTTAAGGTTTCGATTCTAAAAAATACTTCCAAAATTTGGT
* * * *
10684 GGTCTCGATTGTCAGTCTCTCTAAAATTGTATAATTTTCGGTCCACTTGTCCAATTGAGATTGTT
257 GGTCTCGATTGCCAGTCTATCTAAAAATGTATAATTTTCGGTCCACGTGTCCAATTGAGATTGTT
*
10749 CAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCGTTAAGGACCTGAAAACTGAATTT
322 CAAGTGTCGGTTAAAAAGTTATTGTGTGATCTACGACTTTCGTTAAGGACCTGAAAACTGAATTT
10814 GATTAATGAGTTTC-G-AG-GG-AATTTTTATGTTT-GATATCC
387 GATTAATGAGTTTCAGTAGAGGTAATTTTTATGTTTAG-TATCC
* *
10853 ATAAACAAATATTTTTTTTACTGGATTATTTATTAAATGATCCTTATACTTTTGTGATTTACGCT
1 ATAAACAAATATTTTTTTTACTGGATTATTTATTAAATGATCCTTATACTTTTATGATTTATGCT
*
10918 ATTTAATCCCTCACAAATTCTGGGTTGGACGATTTAACGTTTCGGCTTTAATTCTTTTATGTTTT
66 ATTTAATCCCTCACAAATTATGGGTTGGACGATTTAACGTTT-GGCTTTAATTCTTTTAT-TTTT
* * *
10983 GTTATGTTTGTCCGATTAAGGTGATTCAAGTGCCTATTAAAAGGTAATTTAATGATCTACAACTT
129 GTTATGTTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTT
* *
11048 TCATTAAGAACTCAAAAGCCAATTTTGAGGTTTCGGTTCTAAAAAATACTTCCAAAATTTGGTGG
194 TCATTAAGAACTCAAAAGCCAATTTTAAGGTTTCGATTCTAAAAAATACTTCCAAAATTTGGTGG
* * * *
11113 TCTCG-TTGCCGGTTTATCTAAAAATGTATAATTTTCGGTTCACGTGTCCGATTGA-AGTTGTTC
259 TCTCGATTGCCAGTCTATCTAAAAATGTATAATTTTCGGTCCACGTGTCCAATTGAGA-TTGTTC
* *
11176 AAGTGTTGGTTAAAAAGTTATTGTGTGATCTACGACTTTCGTTAAGGACCTGAAAGCTGAATTTG
323 AAGTGTCGGTTAAAAAGTTATTGTGTGATCTACGACTTTCGTTAAGGACCTGAAAACTGAATTTG
*
11241 ATTAATGAGTTTCATGGAAGGTTCAAGAGGTAATTTTTATGTTTAGTCTCC
388 ATTAATGAGTTTC-----A-G-T--AGAGGTAATTTTTATGTTTAGTATCC
* ** * *
11292 ATAAACTAATA-TTTTTTTACTGGATTATTTATCT-AATGGCCCTCATACTTTTATGTTTTATGC
1 ATAAACAAATATTTTTTTTACTGGATTATTTAT-TAAATGATCCTTATACTTTTATGATTTATGC
* * * * * *
11355 TATTGAATCCTTTAC-AATTATGGGTTGGATGATTTAACGCGTTGAC-TTATATT-TTTGTATTT
65 TATTTAATCCCTCACAAATTATGGGTTGGACGATTTAACG-TTTGGCTTTA-ATTCTTT-TA-TT
* * *
11417 TTTGTTCTGTTTGTCCGATCAAGGTGATTCAAGTGTCTATTATAAGGTGATTTCATGATCTACAA
126 TTTGTTATGTTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAA
*
11482 CTTTTATTAAGAACTCAAAAGCCAATTTTAA
191 CTTTCATTAAGAACTCAAAAGCCAATTTTAA
11513 TATGTTTTGA
Statistics
Matches: 565, Mismatches: 69, Indels: 40
0.84 0.10 0.06
Matches are distributed among these distances:
424 7 0.01
425 12 0.02
426 175 0.31
427 154 0.27
433 1 0.00
436 6 0.01
437 120 0.21
438 61 0.11
439 28 0.05
440 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (429 bp):
ATAAACAAATATTTTTTTTACTGGATTATTTATTAAATGATCCTTATACTTTTATGATTTATGCT
ATTTAATCCCTCACAAATTATGGGTTGGACGATTTAACGTTTGGCTTTAATTCTTTTATTTTTGT
TATGTTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTC
ATTAAGAACTCAAAAGCCAATTTTAAGGTTTCGATTCTAAAAAATACTTCCAAAATTTGGTGGTC
TCGATTGCCAGTCTATCTAAAAATGTATAATTTTCGGTCCACGTGTCCAATTGAGATTGTTCAAG
TGTCGGTTAAAAAGTTATTGTGTGATCTACGACTTTCGTTAAGGACCTGAAAACTGAATTTGATT
AATGAGTTTCAGTAGAGGTAATTTTTATGTTTAGTATCC
Found at i:12083 original size:24 final size:26
Alignment explanation
Indices: 12055--12116 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 26
12045 TCTTTCTTCC
*
12055 ATTCTTTTCT-TTTACTC-CATCTCA
1 ATTCTTCTCTCTTTACTCTCATCTCA
12079 ATTCTTCTCTCTTTACTCTTCATCTCA
1 ATTCTTCTCTCTTTACTC-TCATCTCA
12106 ATT-TTCTCTCT
1 ATTCTTCTCTCT
12117 CAAGTACCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
24 9 0.26
25 7 0.21
26 8 0.24
27 10 0.29
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTCTTCTCTCTTTACTCTCATCTCA
Found at i:13958 original size:31 final size:31
Alignment explanation
Indices: 13923--13985 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
13913 ATTTCTGTCC
13923 TTATTTT-TAGATTTAGGTTAGT-ATAAGGCTT
1 TTATTTTCT-GATTTAGGTTAGTAAT-AGGCTT
*
13954 TTATTTTCTTATTTAGGTTAGTAATAGGCTT
1 TTATTTTCTGATTTAGGTTAGTAATAGGCTT
13985 T
1 T
13986 ATGGGCTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (31 bp):
TTATTTTCTGATTTAGGTTAGTAATAGGCTT
Found at i:15068 original size:16 final size:16
Alignment explanation
Indices: 15047--15079 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
15037 GGAAGAAGAC
15047 GACAAGTGAGCTACTG
1 GACAAGTGAGCTACTG
*
15063 GACAAGTGAGCTGCTG
1 GACAAGTGAGCTACTG
15079 G
1 G
15080 TTTGGATGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.18
Consensus pattern (16 bp):
GACAAGTGAGCTACTG
Found at i:15961 original size:23 final size:23
Alignment explanation
Indices: 15935--15981 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
15925 TGAGGCCATA
15935 CCCATCTGTCCCATAACTTGCTT
1 CCCATCTGTCCCATAACTTGCTT
15958 CCCATCTGTCCCATAACTTGCTT
1 CCCATCTGTCCCATAACTTGCTT
15981 C
1 C
15982 AGAGTAGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.40, G:0.09, T:0.34
Consensus pattern (23 bp):
CCCATCTGTCCCATAACTTGCTT
Found at i:18374 original size:36 final size:36
Alignment explanation
Indices: 18295--18363 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
18285 ATAATCCCAA
* *
18295 TTCTTTTATTTATTTGTCAACAATGTAATATGTAAT
1 TTCTTTTATGTATTTGTCAACAATGTAACATGTAAT
*
18331 TTCTTTTATGTATTTTTCAACAATGTAACATGT
1 TTCTTTTATGTATTTGTCAACAATGTAACATGT
18364 GAGTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (36 bp):
TTCTTTTATGTATTTGTCAACAATGTAACATGTAAT
Found at i:27259 original size:11 final size:11
Alignment explanation
Indices: 27243--27277 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
27233 TTGAAAGCGT
27243 AACAAAAACAA
1 AACAAAAACAA
* *
27254 AACAAAATCGA
1 AACAAAAACAA
27265 AACAAAAACAA
1 AACAAAAACAA
27276 AA
1 AA
27278 AACAAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.03, T:0.03
Consensus pattern (11 bp):
AACAAAAACAA
Done.