Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001121.1 Corchorus capsularis cultivar CVL-1 contig01121, 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: 14493
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6439 original size:14 final size:13
Alignment explanation
Indices: 6416--6464 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 13
6406 CACCCCATTA
6416 ACCACACATAATT
1 ACCACACATAATT
*
6429 ACTACAGCATAATT
1 ACCACA-CATAATT
6443 ACCACACAT-A--
1 ACCACACATAATT
6453 ACCACACATAAT
1 ACCACACATAAT
6465 CCTCACCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
10 9 0.29
11 1 0.03
12 1 0.03
13 8 0.26
14 12 0.39
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (13 bp):
ACCACACATAATT
Found at i:11452 original size:13 final size:13
Alignment explanation
Indices: 11434--11473 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
11424 AATGCTGCAC
11434 ATGATATATATAT
1 ATGATATATATAT
*
11447 ATGATATAGATAT
1 ATGATATATATAT
11460 A-GATATGATATAT
1 ATGATAT-ATATAT
11473 A
1 A
11474 GACTAGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
ATGATATATATAT
Found at i:11460 original size:19 final size:19
Alignment explanation
Indices: 11436--11475 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
11426 TGCTGCACAT
*
11436 GATATATATAT-ATGATATA
1 GATATAGATATGAT-ATATA
11455 GATATAGATATGATATATA
1 GATATAGATATGATATATA
11474 GA
1 GA
11476 CTAGCTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (19 bp):
GATATAGATATGATATATA
Found at i:11465 original size:17 final size:17
Alignment explanation
Indices: 11439--11471 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11429 TGCACATGAT
*
11439 ATATATATATGATATAG
1 ATATAGATATGATATAG
11456 ATATAGATATGATATA
1 ATATAGATATGATATA
11472 TAGACTAGCT
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:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (17 bp):
ATATAGATATGATATAG
Found at i:13089 original size:26 final size:24
Alignment explanation
Indices: 13060--13120 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
13050 TTGTCCTTTA
*
13060 CCGTAAACTAATTCCATTAACTAATG
1 CCGTAAA-TAATTCCATTAA-AAATG
**
13086 CCGTTAAATGCTTCCATTAAAAATG
1 CCG-TAAATAATTCCATTAAAAATG
13111 CCGTTAAATA
1 CCG-TAAATA
13121 CTTACTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 13 0.43
26 13 0.43
27 4 0.13
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (24 bp):
CCGTAAATAATTCCATTAAAAATG
Found at i:13115 original size:25 final size:26
Alignment explanation
Indices: 13071--13119 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
13061 CGTAAACTAA
*
13071 TTCCATTAACTAATGCCGTTAAATGC
1 TTCCATTAACAAATGCCGTTAAATGC
13097 TTCCATTAA-AAATGCCGTTAAAT
1 TTCCATTAACAAATGCCGTTAAAT
13120 ACTTACTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (26 bp):
TTCCATTAACAAATGCCGTTAAATGC
Found at i:14430 original size:334 final size:333
Alignment explanation
Indices: 13761--14493 Score: 890
Period size: 334 Copynumber: 2.2 Consensus size: 333
13751 AAAAGAAATC
* * * **
13761 ATGTTTCGATTTAAT-AATAAATTAATTGGGAAAAATATAGGAAAA-TCATTATTAGAAGTGTGA
1 ATGTTTGGATTTAATCAA-AAATTAATTCGGAAAAATATAGGAAAATTGA-TATTAGAAACGTGA
* * * * *
13824 AAAGCTATTCAATCTTTTTGGCGTTGATTATATATATTTTTTATGAATATTTTGGCCAAAAATTG
64 AAAGCCATTCAATCTTTTTGGCATTGATTACACATATATTTTATGAATATTTTGGCCAAAAATTG
* * * * * * * *
13889 AGGTAAATTCTTTCGGGTCAATTTTTTCAGAATTTTTGCTGAAATCGTGAACTAACCATCATGGT
129 AGGAAAAATCTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGAACTAACCATCACGGT
* * * * * *
13954 TTTGCCTAAAAATGCGTTCCAGTGCTCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTTAT
194 TTTGCCTAAAAATGCGTTCCAGTGCTCCGACTAAGTTTTGCATGATATTTGACACCAAAACATAT
* * * * * *
14019 TGAAATATCAATATTCGTATAAGCAAATCTCAGTCATAATTAGTTTAAGGATTTAATTTGACGAG
259 TGAAATATAAATATTCATATAAGCAAATCTCAGCCACAATGAATTTAAGGATTTAATTTGACGAG
14084 AATCAAAGTA
324 AATCAAAGTA
* *
14094 ATGTTTGGACTTAATCAAAAATTAATTCGGAAAAATATAGGAAAATTGATATTATAAACGTGAAA
1 ATGTTTGGATTTAATCAAAAATTAATTCGGAAAAATATAGGAAAATTGATATTAGAAACGTGAAA
*
14159 AGCCCA-TCAATCTTTTTGGTATTGAATTACACA-A-ATTTTAT-AAGTATTTTGGCCAAAAATT
66 AG-CCATTCAATCTTTTTGGCATTG-ATTACACATATATTTTATGAA-TATTTTGGCCAAAAATT
*
14220 GAGGGGAAAAAT-TTTCGGGTAAATTTTTGCAAAATTTTAGCCCG-AATCGTGTACTAACCATCA
128 GA--GGAAAAATCTTTCGGGTAAATTTTTGCAAAATTTTAG-CCGAAATCGTGAACTAACCATCA
* *
14283 CGGTTTTTGCCTAAAAATGCGTTCTAGTGCTCTGACTAAGTTTTGCATGATATTTGACACCAAAA
190 CGG-TTTTGCCTAAAAATGCGTTCCAGTGCTCCGACTAAGTTTTGCATGATATTTGACACCAAAA
* * *
14348 CATATTGAAATA-AATATATTCATATAATCGAATCTCAGCCACAATGAATTTAAGGATTTGATTT
254 CATATTGAAATATAA-ATATTCATATAAGCAAATCTCAGCCACAATGAATTTAAGGATTTAATTT
* *
14412 TACGAGAATCAGAGTA
318 GACGAGAATCAAAGTA
* * * * **
14428 ATGTCTGGATTTAATCAGAAATTAATTCGAAAAAATATAGGAAAATCGATATTAGAAGTGTGAAA
1 ATGTTTGGATTTAATCAAAAATTAATTCGGAAAAATATAGGAAAATTGATATTAGAAACGTGAAA
14493 A
66 A
Statistics
Matches: 341, Mismatches: 49, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
331 2 0.01
332 25 0.07
333 116 0.34
334 198 0.58
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (333 bp):
ATGTTTGGATTTAATCAAAAATTAATTCGGAAAAATATAGGAAAATTGATATTAGAAACGTGAAA
AGCCATTCAATCTTTTTGGCATTGATTACACATATATTTTATGAATATTTTGGCCAAAAATTGAG
GAAAAATCTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGAACTAACCATCACGGTTT
TGCCTAAAAATGCGTTCCAGTGCTCCGACTAAGTTTTGCATGATATTTGACACCAAAACATATTG
AAATATAAATATTCATATAAGCAAATCTCAGCCACAATGAATTTAAGGATTTAATTTGACGAGAA
TCAAAGTA
Done.