Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015042.1 Corchorus capsularis cultivar CVL-1 contig15063, 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: 49838
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:8019 original size:13 final size:14
Alignment explanation
Indices: 7986--8021 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
7976 ATTGAACGTT
7986 GATTAATTAGTCAA
1 GATTAATTAGTCAA
*
8000 GAATAATTAGT-AA
1 GATTAATTAGTCAA
8013 GATTAATTA
1 GATTAATTA
8022 ATTTTACAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (14 bp):
GATTAATTAGTCAA
Found at i:8169 original size:2 final size:2
Alignment explanation
Indices: 8162--8190 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8152 TGTAGGTAAG
8162 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8191 AAAAGCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8682 original size:226 final size:226
Alignment explanation
Indices: 8288--8743 Score: 876
Period size: 226 Copynumber: 2.0 Consensus size: 226
8278 AAAATTACTC
8288 GCATCCTAATTAAACTAGGACATAGATATTTCCTTCCGATATCACGATAGTCTGAAGGCATTAAT
1 GCATCCTAATTAAACTAGGACATAGATATTTCCTTCCGATATCACGATAGTCTGAAGGCATTAAT
*
8353 ACTTGCAAGTCGCAAACGGAGCTACTTGAAAATGGAGCTACTGATCAATCAAAGAAGTGATCCAA
66 ACTTGCAAGTCGCAAAAGGAGCTACTTGAAAATGGAGCTACTGATCAATCAAAGAAGTGATCCAA
8418 TCAGGACACCAAGAACACATTATTAACTCGTCTGCAACGATTGACCCTTCCAAATATAGCATGTA
131 TCAGGACACCAAGAACACATTATTAACTCGTCTGCAACGATTGACCCTTCCAAATATAGCATGTA
*
8483 ATATATCATAATACTATGCTACCCTAACATA
196 ATATATCATAATACTATGCTACCATAACATA
8514 GCATCCTAATTAAACTAGGACATAGATATTTCCTTCCGATATCACGATAGTCTGAAGGCATTAAT
1 GCATCCTAATTAAACTAGGACATAGATATTTCCTTCCGATATCACGATAGTCTGAAGGCATTAAT
*
8579 ACTTGCAAGTTGCAAAAGGAGCTACTTGAAAATGGAGCTACTGATCAATCAAAGAAGTGATCCAA
66 ACTTGCAAGTCGCAAAAGGAGCTACTTGAAAATGGAGCTACTGATCAATCAAAGAAGTGATCCAA
8644 TCAGGACACCAAGAACACATTATTAACTCGTCTGCAACGATTGACCCTTCCAAATATAGCATGTA
131 TCAGGACACCAAGAACACATTATTAACTCGTCTGCAACGATTGACCCTTCCAAATATAGCATGTA
*
8709 ATATATCATAATACTATGCTACTATAACATA
196 ATATATCATAATACTATGCTACCATAACATA
8740 GCAT
1 GCAT
8744 ACCATTACAA
Statistics
Matches: 226, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
226 226 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (226 bp):
GCATCCTAATTAAACTAGGACATAGATATTTCCTTCCGATATCACGATAGTCTGAAGGCATTAAT
ACTTGCAAGTCGCAAAAGGAGCTACTTGAAAATGGAGCTACTGATCAATCAAAGAAGTGATCCAA
TCAGGACACCAAGAACACATTATTAACTCGTCTGCAACGATTGACCCTTCCAAATATAGCATGTA
ATATATCATAATACTATGCTACCATAACATA
Found at i:8853 original size:31 final size:32
Alignment explanation
Indices: 8817--8880 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
8807 TTTCCGATTA
*
8817 TACCCTTATTTTTAAAA-CATATTTCT-AATTG
1 TACCCTT-TTTTAAAAATCATATTTCTAAATTG
*
8848 TACCCTTTTTTAAAAATTATATTTCTAAATTG
1 TACCCTTTTTTAAAAATCATATTTCTAAATTG
8880 T
1 T
8881 CATTACTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 8 0.28
31 15 0.52
32 6 0.21
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.50
Consensus pattern (32 bp):
TACCCTTTTTTAAAAATCATATTTCTAAATTG
Found at i:8942 original size:15 final size:15
Alignment explanation
Indices: 8898--8948 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
8888 AAATAATATT
8898 TTAATTATTCCATTA
1 TTAATTATTCCATTA
** *
8913 TT--TT-TTTAATCA
1 TTAATTATTCCATTA
8925 TTAATTATTCCATTA
1 TTAATTATTCCATTA
8940 TTAATTATT
1 TTAATTATT
8949 ATTAGATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 2 0.07
15 16 0.59
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAATTATTCCATTA
Found at i:13779 original size:17 final size:17
Alignment explanation
Indices: 13757--13790 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13747 CAATTGGTTT
13757 TATATAATATGGTGTTC
1 TATATAATATGGTGTTC
13774 TATATAATATGGTGTTC
1 TATATAATATGGTGTTC
13791 GTCGCAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (17 bp):
TATATAATATGGTGTTC
Found at i:24679 original size:2 final size:2
Alignment explanation
Indices: 24672--24696 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24662 GGACGAATTG
24672 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
24697 ACTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:25575 original size:2 final size:2
Alignment explanation
Indices: 25568--25600 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25558 ATTAGTATCT
25568 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 T
25601 GTATTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30943 original size:25 final size:25
Alignment explanation
Indices: 30891--30948 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
30881 CATCATTTTT
* *
30891 ATTAATCTCATTTTTTTTTGTCTCA
1 ATTAATCTCATTTTTTTATGACTCA
*
30916 ATTAATCTCATTTTTGTTAT-ACTTA
1 ATTAATCTCATTTTT-TTATGACTCA
30941 ATTTAATC
1 A-TTAATC
30949 GTATGTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 19 0.68
26 9 0.32
ACGTcount: A:0.26, C:0.14, G:0.03, T:0.57
Consensus pattern (25 bp):
ATTAATCTCATTTTTTTATGACTCA
Found at i:31699 original size:19 final size:18
Alignment explanation
Indices: 31677--31770 Score: 51
Period size: 19 Copynumber: 5.5 Consensus size: 18
31667 CCTTAATTGA
*
31677 TTAATTCATCATTGTGCGC
1 TTAAGTCATCATTGTGC-C
*
31696 TTAAGT-A--ATAGT-CC
1 TTAAGTCATCATTGTGCC
*
31710 TTAATTCATCATTGTGCCC
1 TTAAGTCATCATTGTG-CC
*
31729 TTAAGTCAT-A--G-ACC
1 TTAAGTCATCATTGTGCC
* *
31743 TTAATTTATCATTGTGCCC
1 TTAAGTCATCATTGTG-CC
31762 TTAAGTCAT
1 TTAAGTCAT
31771 AGTCCGTAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 20
0.64 0.13 0.24
Matches are distributed among these distances:
14 15 0.28
15 3 0.06
16 5 0.09
17 5 0.09
18 2 0.04
19 24 0.44
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (18 bp):
TTAAGTCATCATTGTGCC
Found at i:31714 original size:33 final size:33
Alignment explanation
Indices: 31677--31775 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
31667 CCTTAATTGA
* *
31677 TTAATTCATCATTGTGCGCTTAAGTAATAGTCC
1 TTAATTCATCATTGTGCCCTTAAGTCATAGTCC
*
31710 TTAATTCATCATTGTGCCCTTAAGTCATAGACC
1 TTAATTCATCATTGTGCCCTTAAGTCATAGTCC
*
31743 TTAATTTATCATTGTGCCCTTAAGTCATAGTCC
1 TTAATTCATCATTGTGCCCTTAAGTCATAGTCC
31776 GTAAACCATT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (33 bp):
TTAATTCATCATTGTGCCCTTAAGTCATAGTCC
Found at i:39715 original size:25 final size:24
Alignment explanation
Indices: 39687--39733 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
39677 TTAAATCTTA
39687 GTGGGT-TTCGTCTAATATTATATAT
1 GTGGGTGTTCGT-TAAT-TTATATAT
*
39712 GTGGGTGTTTGTTAATTTATAT
1 GTGGGTGTTCGTTAATTTATAT
39734 GTTACTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 10 0.50
26 4 0.20
ACGTcount: A:0.21, C:0.04, G:0.23, T:0.51
Consensus pattern (24 bp):
GTGGGTGTTCGTTAATTTATATAT
Found at i:39835 original size:25 final size:24
Alignment explanation
Indices: 39807--39853 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
39797 TTAAATCTTA
39807 GTGGGT-TTCGTCTAATATTATATAT
1 GTGGGTGTTCGT-TAAT-TTATATAT
*
39832 GTGGGTGTTTGTTAATTTATAT
1 GTGGGTGTTCGTTAATTTATAT
39854 GTTACTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 10 0.50
26 4 0.20
ACGTcount: A:0.21, C:0.04, G:0.23, T:0.51
Consensus pattern (24 bp):
GTGGGTGTTCGTTAATTTATATAT
Found at i:39878 original size:120 final size:120
Alignment explanation
Indices: 39552--39867 Score: 580
Period size: 120 Copynumber: 2.6 Consensus size: 120
39542 TTGAGGTCTT
* **
39552 GTGTTTAAATCCTAGTGGGTTTTC-TCTGAATATTATATATGTGGGTGTTTGTCGATTTATATGT
1 GTGTTTAAATCTTAGTGGG-TTTCGTCT-AATATTATATATGTGGGTGTTTGTTAATTTATATGT
39616 TACTATTGTTTCATCAGTTTGTTTAATGATTTCTTACTAATTAAATAATAAGTTATC
64 TACTATTGTTTCATCAGTTTGTTTAATGATTTCTTACTAATTAAATAATAAGTTATC
39673 GTGTTTAAATCTTAGTGGGTTTCGTCTAATATTATATATGTGGGTGTTTGTTAATTTATATGTTA
1 GTGTTTAAATCTTAGTGGGTTTCGTCTAATATTATATATGTGGGTGTTTGTTAATTTATATGTTA
39738 CTATTGTTTCATCAGTTTGTTTAATGATTTCTTACTAATTAAATAATAAGTTATC
66 CTATTGTTTCATCAGTTTGTTTAATGATTTCTTACTAATTAAATAATAAGTTATC
39793 GTGTTTAAATCTTAGTGGGTTTCGTCTAATATTATATATGTGGGTGTTTGTTAATTTATATGTTA
1 GTGTTTAAATCTTAGTGGGTTTCGTCTAATATTATATATGTGGGTGTTTGTTAATTTATATGTTA
39858 CTATTGTTTC
66 CTATTGTTTC
39868 GTTAGCTTGT
Statistics
Matches: 191, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
120 170 0.89
121 21 0.11
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (120 bp):
GTGTTTAAATCTTAGTGGGTTTCGTCTAATATTATATATGTGGGTGTTTGTTAATTTATATGTTA
CTATTGTTTCATCAGTTTGTTTAATGATTTCTTACTAATTAAATAATAAGTTATC
Found at i:41310 original size:18 final size:18
Alignment explanation
Indices: 41287--41324 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
41277 TAAAAGTTTA
41287 TTTCTATTGAAAGTGATG
1 TTTCTATTGAAAGTGATG
41305 TTTCTATTGAAAGTGATG
1 TTTCTATTGAAAGTGATG
41323 TT
1 TT
41325 AATTAAGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.47
Consensus pattern (18 bp):
TTTCTATTGAAAGTGATG
Found at i:43483 original size:2 final size:2
Alignment explanation
Indices: 43478--43510 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
43468 GGGTTGGAGC
43478 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 T
43511 TTCTTCACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46124 original size:16 final size:15
Alignment explanation
Indices: 46099--46128 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
46089 ATAGTTAATT
46099 TTTCTGGCTTTTCCA
1 TTTCTGGCTTTTCCA
46114 TTTCTTGGCTTTTCC
1 TTTC-TGGCTTTTCC
46129 TGTGATTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.03, C:0.27, G:0.13, T:0.57
Consensus pattern (15 bp):
TTTCTGGCTTTTCCA
Found at i:48353 original size:3 final size:3
Alignment explanation
Indices: 48345--48376 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
48335 CTTGTTTGGG
48345 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
48377 ATTGTTTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:48751 original size:20 final size:20
Alignment explanation
Indices: 48726--48770 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
48716 TATAAATAAC
48726 CCTAAATCATGTAAG-AGAAG
1 CCTAAATC-TGTAAGAAGAAG
*
48746 CCTAAATCTTTAAGAAGAAG
1 CCTAAATCTGTAAGAAGAAG
48766 CCTAA
1 CCTAA
48771 TGAAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (20 bp):
CCTAAATCTGTAAGAAGAAG
Done.