Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015948.1 Corchorus capsularis cultivar CVL-1 contig15969, 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: 28853
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:232 original size:18 final size:18
Alignment explanation
Indices: 211--252 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
201 TGGCTTTTAG
211 CATTTTAC-TACTTTATTC
1 CATTTTACTTACTTT-TTC
*
229 CATTTTACTTACTTTTTG
1 CATTTTACTTACTTTTTC
247 CATTTT
1 CATTTT
253 CCATAGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.19, C:0.19, G:0.02, T:0.60
Consensus pattern (18 bp):
CATTTTACTTACTTTTTC
Found at i:5260 original size:2 final size:2
Alignment explanation
Indices: 5255--5291 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5245 TCTTATCACT
5255 TA TA TA TA 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 TA TA TA TA T
5292 GATAAGTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7768 original size:124 final size:124
Alignment explanation
Indices: 7548--7795 Score: 496
Period size: 124 Copynumber: 2.0 Consensus size: 124
7538 TTTCTCTATT
7548 CTAAAAATATGTTAATAGCTATAAGTAACATGAGATAAAAAAAAAGTGACAACTATGAGATTGTT
1 CTAAAAATATGTTAATAGCTATAAGTAACATGAGATAAAAAAAAAGTGACAACTATGAGATTGTT
7613 AGAGTGAAAACAGTGGCGTAGCCACGTGGTGAGGAGTGGGTCAATTGACCCTACTTAAA
66 AGAGTGAAAACAGTGGCGTAGCCACGTGGTGAGGAGTGGGTCAATTGACCCTACTTAAA
7672 CTAAAAATATGTTAATAGCTATAAGTAACATGAGATAAAAAAAAAGTGACAACTATGAGATTGTT
1 CTAAAAATATGTTAATAGCTATAAGTAACATGAGATAAAAAAAAAGTGACAACTATGAGATTGTT
7737 AGAGTGAAAACAGTGGCGTAGCCACGTGGTGAGGAGTGGGTCAATTGACCCTACTTAAA
66 AGAGTGAAAACAGTGGCGTAGCCACGTGGTGAGGAGTGGGTCAATTGACCCTACTTAAA
7796 ATTGTGCTCT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.24
Consensus pattern (124 bp):
CTAAAAATATGTTAATAGCTATAAGTAACATGAGATAAAAAAAAAGTGACAACTATGAGATTGTT
AGAGTGAAAACAGTGGCGTAGCCACGTGGTGAGGAGTGGGTCAATTGACCCTACTTAAA
Found at i:7900 original size:31 final size:32
Alignment explanation
Indices: 7853--7912 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
7843 ATTGACCCCA
*
7853 TTAAATTGAAATTTTTACAATATAGACCCTAT
1 TTAAATGGAAATTTTTACAATATAGACCCTAT
* *
7885 TTAAATGGAAA-TTTTATAATATTGACCC
1 TTAAATGGAAATTTTTACAATATAGACCC
7913 CACTAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (32 bp):
TTAAATGGAAATTTTTACAATATAGACCCTAT
Found at i:8604 original size:16 final size:16
Alignment explanation
Indices: 8583--8617 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
8573 GATCGGGCAG
8583 AGATTTGCAAGAATGT
1 AGATTTGCAAGAATGT
*
8599 AGATTTGGAAGAATGT
1 AGATTTGCAAGAATGT
8615 AGA
1 AGA
8618 CTTCGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.29, T:0.29
Consensus pattern (16 bp):
AGATTTGCAAGAATGT
Found at i:17180 original size:14 final size:14
Alignment explanation
Indices: 17161--17215 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
17151 TTGACTTTTG
*
17161 CCATATTTATATAA
1 CCATATATATATAA
17175 CCATATATATATACA
1 CCATATATATATA-A
*
17190 TACATATATATAT-A
1 -CCATATATATATAA
*
17204 -TATATATATATA
1 CCATATATATATA
17216 TCAATAATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
12 10 0.29
14 13 0.37
15 1 0.03
16 11 0.31
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (14 bp):
CCATATATATATAA
Found at i:17182 original size:2 final size:2
Alignment explanation
Indices: 17177--17216 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
17167 TTATATAACC
* *
17177 AT AT AT AT AT AC AT AC 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 AT AT AT AT AT
17217 CAATAATGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:17292 original size:24 final size:24
Alignment explanation
Indices: 17265--17314 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
17255 TTAATTAGCA
17265 TAGCTTCTAGTATATTTTTCTATT
1 TAGCTTCTAGTATATTTTTCTATT
17289 TAGCTTCTAGTATATTTTTCTATT
1 TAGCTTCTAGTATATTTTTCTATT
17313 TA
1 TA
17315 TTAATCGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (24 bp):
TAGCTTCTAGTATATTTTTCTATT
Found at i:25352 original size:66 final size:66
Alignment explanation
Indices: 25282--25406 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 66
25272 ATTCAATTAT
*
25282 AAAAATCATAATAAA-ATAAATAATTAAA-AGATAATTCT-AGATTTTGCCAATTTGTGGGAAGT
1 AAAAATCATAA-AAACATAAATAATTAAATA-ATAATT-TGAGATCTTGCCAATTTGTGGGAAGT
25344 CTAG
63 CTAG
* * *
25348 AAAAATCATAAAAACATAATTAATTAAATAATAATTTGGGGTCTTGCCAATTTGTGGGA
1 AAAAATCATAAAAACATAAATAATTAAATAATAATTTGAGATCTTGCCAATTTGTGGGA
25407 GACTAAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
65 4 0.08
66 47 0.90
67 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (66 bp):
AAAAATCATAAAAACATAAATAATTAAATAATAATTTGAGATCTTGCCAATTTGTGGGAAGTCTA
G
Found at i:25480 original size:26 final size:25
Alignment explanation
Indices: 25417--25472 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
25407 GACTAAATAA
25417 TAAAGATATGATTAAAATTCAAAAAC
1 TAAA-ATATGATTAAAATTCAAAAAC
*
25443 TAAAATATGATTAAAATTCGAAAAC
1 TAAAATATGATTAAAATTCAAAAAC
25468 TAAAA
1 TAAAA
25473 GTGAGATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (25 bp):
TAAAATATGATTAAAATTCAAAAAC
Found at i:28380 original size:17 final size:17
Alignment explanation
Indices: 28358--28392 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28348 AGTGAAAGGG
* *
28358 TTGTTTTTGGAATAAAA
1 TTGTTTTCGAAATAAAA
28375 TTGTTTTCGAAATAAAA
1 TTGTTTTCGAAATAAAA
28392 T
1 T
28393 GATGTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (17 bp):
TTGTTTTCGAAATAAAA
Done.