Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007950.1 Corchorus capsularis cultivar CVL-1 contig07971, 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: 17220
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:921 original size:25 final size:25
Alignment explanation
Indices: 893--943 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
883 TAATCCTCCA
* *
893 CATATGTAAATCTTCTTTCAATCTT
1 CATACGTAAATCTTCCTTCAATCTT
**
918 CATACGTGGATCTTCCTTCAATCTT
1 CATACGTAAATCTTCCTTCAATCTT
943 C
1 C
944 TTTGATAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.25, G:0.08, T:0.43
Consensus pattern (25 bp):
CATACGTAAATCTTCCTTCAATCTT
Found at i:1534 original size:21 final size:22
Alignment explanation
Indices: 1497--1537 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1487 CGTGAAGAAC
1497 AAGAGAAAAAGGCACGGAGCCA
1 AAGAGAAAAAGGCACGGAGCCA
*
1519 AAGAGAATAA-GCACGGAGC
1 AAGAGAAAAAGGCACGGAGC
1538 TTGGTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.17, G:0.32, T:0.02
Consensus pattern (22 bp):
AAGAGAAAAAGGCACGGAGCCA
Found at i:8717 original size:20 final size:21
Alignment explanation
Indices: 8689--8743 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
8679 CTTGGTCTCG
*
8689 AGTCATTTG-CTCTTTAAGTA
1 AGTCATTTGACTCCTTAAGTA
* *
8709 AGTCGTTTGACTCCTTAAGTTG
1 AGTCATTTGACTCCTTAAG-TA
8731 AG-CATTTGACTCC
1 AGTCATTTGACTCC
8744 ATTATTAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.28
21 18 0.62
22 3 0.10
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (21 bp):
AGTCATTTGACTCCTTAAGTA
Found at i:12021 original size:119 final size:120
Alignment explanation
Indices: 11750--12032 Score: 390
Period size: 120 Copynumber: 2.4 Consensus size: 120
11740 CCCCGAGTCC
* *
11750 TTGCCCCCCAAGTCTTTCATCGATGAGACCAACCTAAGCCATGACCTGTTGATTGTTCACCTGAT
1 TTGCCCCCCAAGTCTTTCATCGATGAGACCAATCTAAGCCATGACCTGTGGATTGTTCACCTGAT
** * *
11815 GGTTAACTTGTTGAAGGGGAAGAGGACCGGGCTGGGCACCAAGCAGTTGTTGGTT
66 GGTTAACTTGTTGAAAAGGAAGAGGACCAGGCTGGACACCAAGCAGTTGTTGGTT
* * * *
11870 TTGCCCCCCAAGCCTTTCATCGATGAGACCAATCTCAGCCATGACTTGTGGGTTGTTCACCTGAT
1 TTGCCCCCCAAGTCTTTCATCGATGAGACCAATCTAAGCCATGACCTGTGGATTGTTCACCTGAT
* *
11935 GGTTGACTTGTTGAAAAGGCAGA-GACCAGGCTGGACACCAAGCAGTTGTTGGTT
66 GGTTAACTTGTTGAAAAGGAAGAGGACCAGGCTGGACACCAAGCAGTTGTTGGTT
* * * * *
11989 TT-CCCCTCCAAGTCTTTCTTCAATCAAACCAATCTTAGCCATGA
1 TTGCCCC-CCAAGTCTTTCATCGATGAGACCAATCTAAGCCATGA
12033 TGTTTTCTTT
Statistics
Matches: 144, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
118 4 0.03
119 62 0.43
120 78 0.54
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (120 bp):
TTGCCCCCCAAGTCTTTCATCGATGAGACCAATCTAAGCCATGACCTGTGGATTGTTCACCTGAT
GGTTAACTTGTTGAAAAGGAAGAGGACCAGGCTGGACACCAAGCAGTTGTTGGTT
Found at i:13008 original size:21 final size:21
Alignment explanation
Indices: 12984--13043 Score: 120
Period size: 21 Copynumber: 2.9 Consensus size: 21
12974 ACTGGTGGGC
12984 TTTACTTGCTGAGGAAGGTGT
1 TTTACTTGCTGAGGAAGGTGT
13005 TTTACTTGCTGAGGAAGGTGT
1 TTTACTTGCTGAGGAAGGTGT
13026 TTTACTTGCTGAGGAAGG
1 TTTACTTGCTGAGGAAGG
13044 CGAACTCTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.37
Consensus pattern (21 bp):
TTTACTTGCTGAGGAAGGTGT
Found at i:13231 original size:17 final size:17
Alignment explanation
Indices: 13193--13225 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13183 CTCATAGTAC
*
13193 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGATA
13210 CTAGGTAGTATGAGAT
1 CTAGGTAGTATGAGAT
13226 GATAGGCTGC
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:0.30, C:0.06, G:0.33, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGATA
Found at i:16073 original size:30 final size:31
Alignment explanation
Indices: 16015--16073 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
16005 ATGTTTCCCG
* *
16015 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCCTATTTTAAAAACATATTTCCA
*
16046 ATTGTACCCCT-TTTTAAAAATATATTTC
1 ATTGTACCCCTATTTTAAAAACATATTTC
16074 TAAATTGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.32, C:0.19, G:0.03, T:0.46
Consensus pattern (31 bp):
ATTGTACCCCTATTTTAAAAACATATTTCCA
Found at i:16080 original size:31 final size:31
Alignment explanation
Indices: 16015--16081 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
16005 ATGTTTCCCG
* * *
16015 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCCTATTTTAAAAACATATTTCAA
*
16046 ATTGTACCCCT-TTTTAAAAATATATTTCTAA
1 ATTGTACCCCTATTTTAAAAACATATTTC-AA
16077 ATTGT
1 ATTGT
16082 CATTACTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.46
Consensus pattern (31 bp):
ATTGTACCCCTATTTTAAAAACATATTTCAA
Found at i:16266 original size:36 final size:36
Alignment explanation
Indices: 16192--16282 Score: 112
Period size: 38 Copynumber: 2.5 Consensus size: 36
16182 TTGACTTTTA
16192 GTTTCCATCGTCCTATTTAATTTTGCCTTTTGTCTTT
1 GTTTCCATCGTCCTATTTAATTTTG-CTTTTGTCTTT
**
16229 GTTTCCAATCGTTGTATTTAATTTTG-TTTTGTCTTT
1 GTTTCC-ATCGTCCTATTTAATTTTGCTTTTGTCTTT
* * *
16265 GTCTCAAACGTCCTATTT
1 GTTTCCATCGTCCTATTT
16283 GGCCTTAGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
35 9 0.20
36 14 0.30
37 6 0.13
38 17 0.37
ACGTcount: A:0.14, C:0.19, G:0.12, T:0.55
Consensus pattern (36 bp):
GTTTCCATCGTCCTATTTAATTTTGCTTTTGTCTTT
Found at i:16444 original size:22 final size:22
Alignment explanation
Indices: 16416--16555 Score: 122
Period size: 22 Copynumber: 6.3 Consensus size: 22
16406 TGTCTCTATG
*
16416 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
16438 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
16461 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
16482 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
16504 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
16528 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
16550 TGGTTA
1 TGGTTA
16556 ATTATCACAA
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
21 3 0.03
22 72 0.76
23 3 0.03
24 17 0.18
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:16689 original size:22 final size:22
Alignment explanation
Indices: 16632--16714 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
16622 TTTCATATGT
* *
16632 GGTTAACAAAATTTCATTAGGA
1 GGTTATCAAAATTTCATTGGGA
*
16654 GGTTA-CTAATATTTCATTGGGA
1 GGTTATC-AAAATTTCATTGGGA
* * * *
16676 GGTTATCAAAATTTTATAGTGT
1 GGTTATCAAAATTTCATTGGGA
16698 GGTTATCAAAATTTCAT
1 GGTTATCAAAATTTCAT
16715 ATGAAAGTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 1 0.02
22 49 0.96
23 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (22 bp):
GGTTATCAAAATTTCATTGGGA
Found at i:16724 original size:22 final size:22
Alignment explanation
Indices: 16592--16729 Score: 67
Period size: 22 Copynumber: 6.4 Consensus size: 22
16582 TCAAAGAGAA
* *
16592 TATCAAAATGTCATAG-CAAGGT
1 TATCAAAATTTCATAGTGAA-GT
16614 TAT-AAGAATTTCATATGTG--GT
1 TATCAA-AATTTCATA-GTGAAGT
* *
16635 TAACAAAATTTCATTAG-GAGGT
1 TATCAAAATTTCA-TAGTGAAGT
* * * *
16657 TA-CTAATATTTCATTGGGAGGT
1 TATC-AAAATTTCATAGTGAAGT
* **
16679 TATCAAAATTTTATAGTGTGGT
1 TATCAAAATTTCATAGTGAAGT
16701 TATCAAAATTTCATA-TGAAAGT
1 TATCAAAATTTCATAGTG-AAGT
16723 TAT-AAAA
1 TATCAAAA
16730 GTCTCAATTT
Statistics
Matches: 92, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
20 1 0.01
21 23 0.25
22 66 0.72
23 2 0.02
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGAAGT
Found at i:16804 original size:22 final size:23
Alignment explanation
Indices: 16752--17006 Score: 135
Period size: 22 Copynumber: 11.6 Consensus size: 23
16742 TAAGGAGTGC
* *
16752 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
16773 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
16794 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
*
16819 CAAAATTT-ATAGA-AAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
16840 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* ** *
16862 CAAAATTTCAAACCGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
16884 CAAAATTACATA-ATG-TAATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * * * * *
16906 CAGAATTTCATGGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* * *
16928 CAAAATTTTATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
16950 CAAAATTTCATAAAGA-GATTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
16972 CAAATTTTCA-AAATATGATTA-
1 CAAAATTTCATAGAGATGATTAT
16993 CAAAAATTTCATAG
1 C-AAAATTTCATAG
17007 TGGTATTTCT
Statistics
Matches: 180, Mismatches: 38, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
20 10 0.06
21 27 0.15
22 120 0.67
23 5 0.03
24 5 0.03
25 13 0.07
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:16981 original size:66 final size:65
Alignment explanation
Indices: 16815--16978 Score: 165
Period size: 66 Copynumber: 2.5 Consensus size: 65
16805 AGAGATCGGA
* ** * * *
16815 TTATCAAAATTT-ATAGAA-AGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAACCGA
1 TTATCAAAATTTCATA-AAGAGATTATC-AAATTTCATAGAGGGGTCAACAAAATTTCAAACAGA
16878 GG
64 GG
* * * *
16880 TTATCAAAATTACATAATGTA-ATTATCAGAATTTCATGGAGGGGTCAACAAAATTTTATAA-AG
1 TTATCAAAATTTCATAAAG-AGATTATCA-AATTTCATAGAGGGGTCAACAAAATTTCA-AACAG
16943 AGG
63 AGG
16946 TTATCAAAATTTCATAAAGAGATTATCAAATTT
1 TTATCAAAATTTCATAAAGAGATTATCAAATTT
16979 TCAAAATATG
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
65 19 0.23
66 59 0.73
67 3 0.04
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (65 bp):
TTATCAAAATTTCATAAAGAGATTATCAAATTTCATAGAGGGGTCAACAAAATTTCAAACAGAGG
Found at i:17134 original size:22 final size:23
Alignment explanation
Indices: 17106--17185 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 23
17096 TCAGGGAGGA
17106 TATCAAAATTTCATA-TGAAGGT
1 TATCAAAATTTCATAGTGAAGGT
**
17128 TATCAAAATTTCATAGTTCA-GT
1 TATCAAAATTTCATAGTGAAGGT
* * *
17150 TTTCAAAATTTCA-ATTAAGAGGAT
1 TATCAAAATTTCATAGTGA-AGG-T
17174 TATCAAAATTTC
1 TATCAAAATTTC
17186 GTTGAAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.04
22 30 0.64
23 3 0.06
24 12 0.26
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (23 bp):
TATCAAAATTTCATAGTGAAGGT
Done.