Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016410.1 Corchorus capsularis cultivar CVL-1 contig16431, 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: 13375
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:6554 original size:31 final size:31
Alignment explanation
Indices: 6519--6584 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
6509 CATTTTATGT
* * *
6519 TTTCCGATTGTACCCTTATT-TTTAAAATATA
1 TTTCCAATTATACCCTT-TTCTTTAAAACATA
6550 TTTCCAATTATACCCTTTTCTTTAAAACATA
1 TTTCCAATTATACCCTTTTCTTTAAAACATA
6581 TTTC
1 TTTC
6585 TAAATTACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTCCAATTATACCCTTTTCTTTAAAACATA
Found at i:6749 original size:38 final size:35
Alignment explanation
Indices: 6685--6761 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 35
6675 AATTTGGCAT
6685 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTG-C-TTTGTC
**
6722 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCTTTGTC
6758 TTTG
1 TTTG
6762 GTCTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 10 0.27
37 12 0.32
38 15 0.41
ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57
Consensus pattern (35 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCTTTGTC
Found at i:6925 original size:19 final size:21
Alignment explanation
Indices: 6893--6935 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
6883 TTCTTTACTA
6893 TTACTTTTTAAATTT-AATATT
1 TTACTTTTTAAATTTCAAT-TT
6914 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTAAATTTCAATTT
6933 TTA
1 TTA
6936 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (21 bp):
TTACTTTTTAAATTTCAATTT
Found at i:7186 original size:44 final size:43
Alignment explanation
Indices: 7107--7193 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 43
7097 GTCTCTATGT
* ** *
7107 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTGCATAAGATGGTTACCAAAATTTCAT-AGGA
*
7151 GGTTATCAAAATTGCAT-AGTGTGGTTACCAAAATTTCATAGGA
1 GGTTATCAAAATTGCATAAG-ATGGTTACCAAAATTTCATAGGA
7194 TCACGTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 6 0.16
44 31 0.84
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTGCATAAGATGGTTACCAAAATTTCATAGGA
Found at i:7191 original size:22 final size:22
Alignment explanation
Indices: 7105--7190 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
7095 TGGTCTCTAT
7105 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATCAAAATTTCATAAG
* * * *
7127 ATGGTTATTATAATTTCATGAG
1 GTGGTTATCAAAATTTCATAAG
* *
7149 GAGGTTATCAAAATTGCAT-AG
1 GTGGTTATCAAAATTTCATAAG
*
7170 TGTGGTTACCAAAATTTCATA
1 -GTGGTTATCAAAATTTCATA
7191 GGATCACGTT
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
21 2 0.04
22 48 0.96
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (22 bp):
GTGGTTATCAAAATTTCATAAG
Found at i:7230 original size:22 final size:22
Alignment explanation
Indices: 7105--7245 Score: 70
Period size: 22 Copynumber: 6.3 Consensus size: 22
7095 TGGTCTCTAT
* * *
7105 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATTAAAATCTCATAGG
* * *
7127 ATGGTTATTATAATTTCAT-GAG
1 GTGGTTATTAAAATCTCATAG-G
* * *
7149 GAGGTTATCAAAAT-TGCATAGT
1 GTGGTTATTAAAATCT-CATAGG
** *
7171 GTGGTTACCAAAATTTCATAGG
1 GTGGTTATTAAAATCTCATAGG
* * *
7193 ATCACGTTATTAAAATCTCTTAGG
1 GT--GGTTATTAAAATCTCATAGG
* * *
7217 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATCTCATAGG
7239 GTGGTTA
1 GTGGTTA
7246 ATTATTTCAA
Statistics
Matches: 89, Mismatches: 24, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
21 1 0.01
22 70 0.79
23 2 0.02
24 16 0.18
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (22 bp):
GTGGTTATTAAAATCTCATAGG
Found at i:7412 original size:22 final size:22
Alignment explanation
Indices: 7365--7669 Score: 76
Period size: 22 Copynumber: 13.7 Consensus size: 22
7355 TCATGGGGAG
* **
7365 GTTATCAAAATTTTATAGTGTG
1 GTTATCAAAATTTCATAGTGAA
7387 GTTATCAAAATTTCATA-TGAAA
1 GTTATCAAAATTTCATAGTG-AA
* *
7409 GTTATAAAAGTCTCAATTTCATA-AGAA
1 GTTAT-CAA-----AATTTCATAGTGAA
* *
7436 G-TACCAAAATTTGATA--GAA
1 GTTATCAAAATTTCATAGTGAA
*
7455 GGTTATC-AAATCTCATAGAGTG-A
1 -GTTATCAAAATTTCAT--AGTGAA
* **
7478 -CTATCAAAATTTCATAGACATCA
1 GTTATCAAAATTTCATAGTGA--A
*
7501 GATTATCAAAATTT-ATAG-AAA
1 G-TTATCAAAATTTCATAGTGAA
* * **
7522 TATTATCAAATTTTCATAGTGTT
1 -GTTATCAAAATTTCATAGTGAA
* * *
7545 GTTATCAAAATTTCAAAGCGAG
1 GTTATCAAAATTTCATAGTGAA
*
7567 GTTATCAAAATTACATAATGTG-A
1 GTTATCAAAATTTCAT-A-GTGAA
* * **
7590 -TTATCAGAATTTCATAGAGGG
1 GTTATCAAAATTTCATAGTGAA
* * * ** *
7611 GTCAGCAAAATTTTATAAAGAG
1 GTTATCAAAATTTCATAGTGAA
** *
7633 GTTATCAAAATTTCATAAAGAG
1 GTTATCAAAATTTCATAGTGAA
*
7655 GTTATCAAATTTTCA
1 GTTATCAAAATTTCA
7670 AAATGTTATT
Statistics
Matches: 211, Mismatches: 46, Indels: 52
0.68 0.15 0.17
Matches are distributed among these distances:
19 3 0.01
20 20 0.09
21 22 0.10
22 125 0.59
23 6 0.03
24 7 0.03
25 13 0.06
26 2 0.01
27 3 0.01
28 10 0.05
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAA
Found at i:7510 original size:25 final size:22
Alignment explanation
Indices: 7440--7669 Score: 96
Period size: 22 Copynumber: 10.5 Consensus size: 22
7430 TAAGAAGTAC
* *
7440 CAAAATTTGATAG-AAGGTTAT
1 CAAAATTTCATAGAAAGATTAT
* ** *
7461 C-AAATCTCATAGAGTGACTAT
1 CAAAATTTCATAGAAAGATTAT
7482 CAAAATTTCATAGACATCAGATTAT
1 CAAAATTTCATAGA-A--AGATTAT
*
7507 CAAAATTT-ATAGAAATATTAT
1 CAAAATTTCATAGAAAGATTAT
* ***
7528 CAAATTTTCATAGTGTTG-TTAT
1 CAAAATTTCATAG-AAAGATTAT
* ** *
7550 CAAAATTTCAAAGCGAGGTTAT
1 CAAAATTTCATAGAAAGATTAT
* **
7572 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-AAGATTAT
* ** * * *
7594 CAGAATTTCATAGAGGGGTCAG
1 CAAAATTTCATAGAAAGATTAT
* *
7616 CAAAATTTTATA-AAGAGGTTAT
1 CAAAATTTCATAGAA-AGATTAT
*
7638 CAAAATTTCATA-AAGAGGTTAT
1 CAAAATTTCATAGAA-AGATTAT
*
7660 CAAATTTTCA
1 CAAAATTTCA
7670 AAATGTTATT
Statistics
Matches: 158, Mismatches: 40, Indels: 21
0.72 0.18 0.10
Matches are distributed among these distances:
20 9 0.06
21 21 0.13
22 108 0.68
23 2 0.01
24 5 0.03
25 13 0.08
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGAAAGATTAT
Found at i:7594 original size:44 final size:44
Alignment explanation
Indices: 7501--7691 Score: 147
Period size: 44 Copynumber: 4.4 Consensus size: 44
7491 ATAGACATCA
* * ** * *
7501 GATTATCAAAATTT-ATAGAAATATTATCAAATTTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
7545 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * * *
7588 GATTATCAGAATTTCATAGAGGGGTCAGCAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * *
7632 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
*
7676 TATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
7692 TAGTGGTATT
Statistics
Matches: 112, Mismatches: 31, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
43 15 0.13
44 96 0.86
45 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:7669 original size:66 final size:66
Alignment explanation
Indices: 7503--7669 Score: 171
Period size: 66 Copynumber: 2.5 Consensus size: 66
7493 AGACATCAGA
* * ** * * *
7503 TTATCAAAATTT-ATAGAA-ATATTATCAAATTTTCATAGTGTTGTTATCAAAATTTCAAAGCGA
1 TTATCAAAATTTCATA-AAGAGATTATCAAATTTTCATAGAGGGGTCAGCAAAATTTCAAAGAGA
7566 GG
65 GG
* * * *
7568 TTATCAAAATTACATAATGTGATTATCAGAA-TTTCATAGAGGGGTCAGCAAAATTTTATAA-AG
1 TTATCAAAATTTCATAAAGAGATTATCA-AATTTTCATAGAGGGGTCAGCAAAATTTCA-AAGAG
7631 AGG
64 AGG
*
7634 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 TTATCAAAATTTCATAAAGAGATTATCAAATTTTCA
7670 AAATGTTATT
Statistics
Matches: 82, Mismatches: 15, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
65 14 0.17
66 64 0.78
67 4 0.05
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (66 bp):
TTATCAAAATTTCATAAAGAGATTATCAAATTTTCATAGAGGGGTCAGCAAAATTTCAAAGAGAG
G
Found at i:7800 original size:20 final size:20
Alignment explanation
Indices: 7775--7825 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
7765 TTATGGAGTA
7775 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
7795 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
7814 ATCAAAATTTCA
1 ATCAAAATTTCA
7826 TATTTTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:7947 original size:22 final size:22
Alignment explanation
Indices: 7880--8085 Score: 102
Period size: 22 Copynumber: 9.5 Consensus size: 22
7870 TAGTATGTAG
* *
7880 ATCAAAATTTCATAGGGAGAAT
1 ATCAAAAATTCATAGGGAGATT
* **
7902 AACAAAAATTCATAATGAGATT
1 ATCAAAAATTCATAGGGAGATT
* *
7924 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAAATTCATAGGGAGATT
*
7946 ATC-AAAATT--T--GTAG-TT
1 ATCAAAAATTCATAGGGAGATT
* * * *
7962 ATCAAGATTTCATA-AGAAAGTT
1 ATCAAAAATTCATAGGGAGA-TT
* * *
7984 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAAATTCATAGGGA-GATT
* * *
8007 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAAATTCATAGGGAGA-TT
* * *
8030 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAAATTCATAGGGAGATT
* * * *
8052 ATCACAATTTCATAGTGTGATT
1 ATCAAAAATTCATAGGGAGATT
*
8074 ATCAAAATTTCA
1 ATCAAAAATTCA
8086 AAGTGTGATT
Statistics
Matches: 142, Mismatches: 33, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
16 5 0.04
17 7 0.05
19 2 0.01
20 1 0.01
21 5 0.04
22 83 0.58
23 39 0.27
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (22 bp):
ATCAAAAATTCATAGGGAGATT
Found at i:8010 original size:23 final size:23
Alignment explanation
Indices: 7960--8264 Score: 132
Period size: 22 Copynumber: 13.7 Consensus size: 23
7950 AAATTTGTAG
* * * *
7960 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTCATAGGGAGGT
*
7982 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
8005 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGGAGGT
*
8028 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* * * *
8050 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGT
* * * *
8072 TTATCAAAATTTCAAAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGT
*
8094 TTA-CTAACAA-TTCATATGGAGGT
1 TTATC-AA-AATTTCATAGGGAGGT
* * ** *
8117 TT-TTAAATTTTCATAACGTGG-
1 TTATCAAAATTTCATAGGGAGGT
* * *
8138 TTATCAATATATCATATGGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* * **
8160 TTATCAACATCTCATAGTGTTGG-
1 TTATCAAAATTTCATAG-GGAGGT
* *
8183 TTATCAAAATTTCATTGGGAAG-
1 TTATCAAAATTTCATAGGGAGGT
* **
8205 TTATCAAAATTTTATATTGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
8228 CT-TCAAAATTCCTTAGGGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* *
8249 TTAACTAAATTTCATA
1 TTATCAAAATTTCATA
8265 AGAAGGTTGA
Statistics
Matches: 212, Mismatches: 60, Indels: 22
0.72 0.20 0.07
Matches are distributed among these distances:
21 6 0.03
22 144 0.68
23 62 0.29
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:8011 original size:45 final size:44
Alignment explanation
Indices: 7959--8065 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 44
7949 AAAATTTGTA
* *
7959 GTTATCAAGATTTCATAAGAA-AGTTATCAAAATTTTATAGGGAG
1 GTTATCAA-ATTTCATAAGAAGAGTTATCAAAATTTCATAGCGAG
* * *
8003 GTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
1 G-TTATC-AAATTTCATAAGAAGAGTTATCAAAATTTCATAGCGAG
8049 GTTATCACAATTTCATA
1 GTTATCA-AATTTCATA
8066 GTGTGATTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 2 0.04
45 28 0.53
46 23 0.43
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (44 bp):
GTTATCAAATTTCATAAGAAGAGTTATCAAAATTTCATAGCGAG
Found at i:8175 original size:44 final size:45
Alignment explanation
Indices: 8105--8212 Score: 105
Period size: 45 Copynumber: 2.4 Consensus size: 45
8095 TACTAACAAT
* * * *
8105 TCATATGGAGGTTTTTAAATTTTCATAACG-TGGTTATCAATATA
1 TCATATGGAGGTTATCAAATTCTCATAACGTTGGTTATCAAAATA
** *
8149 TCATATGGAGGTTATCAACA-TCTCATAGTGTTGGTTATCAAAATT
1 TCATATGGAGGTTATCAA-ATTCTCATAACGTTGGTTATCAAAATA
*
8194 TCAT-TGGGAAGTTATCAAA
1 TCATAT-GGAGGTTATCAAA
8213 ATTTTATATT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
44 25 0.47
45 28 0.53
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (45 bp):
TCATATGGAGGTTATCAAATTCTCATAACGTTGGTTATCAAAATA
Done.