Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010643.1 Corchorus capsularis cultivar CVL-1 contig10664, 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: 31231
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:2136 original size:30 final size:29
Alignment explanation
Indices: 2102--2201 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 29
2092 CCCATCCCCG
2102 TCCCCGACGGGGAATGGAAAATAATCTCCA
1 TCCCCGACGGGGAATGGAAAA-AATCTCCA
*** ** *** *
2132 TCCCCGACCCTGTTTCCCAAAAATACTCCTCG
1 TCCCCGACGGGGAATGGAAAAAAT-CT-C-CA
2164 TCCCCGACGGGGAATGGAAAACAATCTCCA
1 TCCCCGACGGGGAATGGAAAA-AATCTCCA
2194 TCCCCGAC
1 TCCCCGAC
2202 TCCGTTCCCC
Statistics
Matches: 48, Mismatches: 18, Indels: 8
0.65 0.24 0.11
Matches are distributed among these distances:
29 3 0.06
30 24 0.50
31 2 0.04
32 16 0.33
33 3 0.06
ACGTcount: A:0.28, C:0.36, G:0.18, T:0.18
Consensus pattern (29 bp):
TCCCCGACGGGGAATGGAAAAAATCTCCA
Found at i:2197 original size:62 final size:62
Alignment explanation
Indices: 2096--2231 Score: 229
Period size: 62 Copynumber: 2.2 Consensus size: 62
2086 CCATTCCCCA
* *
2096 TCCCCGTCCCCGACGGGGAATGGAAAATAATCTCCATCCCCGAC-CCTGTTTCCCAAAAATAC
1 TCCCCGTCCCCGACGGGGAATGGAAAACAATCTCCATCCCCGACTCC-GTTCCCCAAAAATAC
*
2158 TCCTCGTCCCCGACGGGGAATGGAAAACAATCTCCATCCCCGACTCCGTTCCCCAAAAATAC
1 TCCCCGTCCCCGACGGGGAATGGAAAACAATCTCCATCCCCGACTCCGTTCCCCAAAAATAC
2220 TCCCCGTCCCCG
1 TCCCCGTCCCCG
2232 CCCTAGCATC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 67 0.97
63 2 0.03
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.18
Consensus pattern (62 bp):
TCCCCGTCCCCGACGGGGAATGGAAAACAATCTCCATCCCCGACTCCGTTCCCCAAAAATAC
Found at i:15879 original size:14 final size:15
Alignment explanation
Indices: 15860--15888 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15850 AAATAAAATG
15860 CTTA-CCTTTTATTT
1 CTTACCCTTTTATTT
15874 CTTACCCTTTTATTT
1 CTTACCCTTTTATTT
15889 TCTCTTCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (15 bp):
CTTACCCTTTTATTT
Found at i:18054 original size:2 final size:2
Alignment explanation
Indices: 18009--18034 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17999 TTTGAGAGAT
18009 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
18035 AACCTAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20711 original size:6 final size:6
Alignment explanation
Indices: 20700--20730 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
20690 TGTTTCCTTT
20700 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC T
1 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC T
20731 CCTCGTTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.19
Consensus pattern (6 bp):
TGAGCC
Found at i:21048 original size:6 final size:6
Alignment explanation
Indices: 21037--21061 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21027 TATATAAGCA
21037 CTGTGT CTGTGT CTGTGT CTGTGT C
1 CTGTGT CTGTGT CTGTGT CTGTGT C
21062 CTTGTTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.32, T:0.48
Consensus pattern (6 bp):
CTGTGT
Found at i:25029 original size:2 final size:2
Alignment explanation
Indices: 25022--25052 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25012 AGGGTAATTT
25022 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 T
25053 TAATATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28492 original size:132 final size:132
Alignment explanation
Indices: 28348--28612 Score: 426
Period size: 132 Copynumber: 2.0 Consensus size: 132
28338 ATTTAAGAAA
* *
28348 TATATTTTAAAAATTCTAATATATCTAAGCTTTTTTAATTAAA-TGAGTAAAACGATAAAAATAA
1 TATATTTAAAAAATTCTAATATATATAAGCTTTTTTAATTAAAGT-AGTAAAACGATAAAAATAA
*
28412 AATAGGTATAAGGATATAAGATTTAATTAAATAAAAATAGAGATTTTTAGTTGAGT-AAACTATA
65 AATAGGTATAAGGATATAAGATTTAATTAAATAAAAATAGAG-TTTTTAGTTGAATAAAACTATA
28476 AAAG
129 AAAG
* * *
28480 TATATTTAAAAAATTCTAATATATATAAGCTTTTTTAATTAAAGTAGTAAAATGGTAAAAATTAA
1 TATATTTAAAAAATTCTAATATATATAAGCTTTTTTAATTAAAGTAGTAAAACGATAAAAATAAA
* *
28545 ATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAA
66 ATAGGTATAAGGATATAAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAA
28610 AG
131 AG
28612 T
1 T
28613 TTAAACAATG
Statistics
Matches: 123, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
131 12 0.10
132 110 0.89
133 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (132 bp):
TATATTTAAAAAATTCTAATATATATAAGCTTTTTTAATTAAAGTAGTAAAACGATAAAAATAAA
ATAGGTATAAGGATATAAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAA
AG
Found at i:28849 original size:227 final size:227
Alignment explanation
Indices: 28449--28903 Score: 813
Period size: 227 Copynumber: 2.0 Consensus size: 227
28439 TAAATAAAAA
28449 TAGAGATTTTTAGTTGAGTAAACTATAAAAGTATATTTAAAAAATTCTAATATATATAAGCTTTT
1 TAGAGATTTTTAGTTGAGTAAACTATAAAAGTATATTTAAAAAATTCTAATATATATAAGCTTTT
* * *
28514 TTAATTAAAGTAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATTTAATTAAATAAA
66 TTAATTAAAATAGGAAAATGGTAAAAATTAAATAGTTATAAGGATATAAGATTTAATTAAATAAA
28579 AATAGAGTTTTTAGTTGAATAAAACTATAAAAGTTTAAACAATGACATTTAAGAAATATATTCGA
131 AATAGAGTTTTTAGTTGAATAAAACTATAAAAGTTTAAACAATGACATTTAAGAAATATATTCGA
28644 AAAATAAGGGTATAATGGGCGATTCAAAAGTT
196 AAAATAAGGGTATAATGGGCGATTCAAAAGTT
*
28676 TAGAG-TTTTTAGTTGAGTAAACTATAAAAGTATATTTAAAAAATTCTAATATATATAAGTTTTT
1 TAGAGATTTTTAGTTGAGTAAACTATAAAAGTATATTTAAAAAATTCTAATATATATAAG-CTTT
28740 TTTAATTAAAATAGGAAAATGGTAAAAATTAAATAGTTATAAGGATATAAGATTTAATTAAATAA
65 TTTAATTAAAATAGGAAAATGGTAAAAATTAAATAGTTATAAGGATATAAGATTTAATTAAATAA
* * * *
28805 AAATAGAGTTTTTAGTTGAGTAAACCTATAAAAGTTTAAACAATGGCATTTAAGAAATATATTTG
130 AAATAGAGTTTTTAGTTGAATAAAACTATAAAAGTTTAAACAATGACATTTAAGAAATATATTCG
*
28870 AAAAATAAGGGTATAATGGGCGATTTAAAAGTT
195 AAAAATAAGGGTATAATGGGCGATTCAAAAGTT
28903 T
1 T
28904 TACAAGAGGT
Statistics
Matches: 218, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
226 54 0.25
227 164 0.75
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.36
Consensus pattern (227 bp):
TAGAGATTTTTAGTTGAGTAAACTATAAAAGTATATTTAAAAAATTCTAATATATATAAGCTTTT
TTAATTAAAATAGGAAAATGGTAAAAATTAAATAGTTATAAGGATATAAGATTTAATTAAATAAA
AATAGAGTTTTTAGTTGAATAAAACTATAAAAGTTTAAACAATGACATTTAAGAAATATATTCGA
AAAATAAGGGTATAATGGGCGATTCAAAAGTT
Found at i:28961 original size:27 final size:27
Alignment explanation
Indices: 28907--28961 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
28897 AAAGTTTTAC
** *
28907 AAGAGGTTGTACTTCTTTCTTTGCTAT
1 AAGAGGTTGTACTTCTTAATTAGCTAT
28934 AAGAGGTTGTACTTCTTAATATAG-TAT
1 AAGAGGTTGTACTTCTTAAT-TAGCTAT
28961 A
1 A
28962 TATTAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (27 bp):
AAGAGGTTGTACTTCTTAATTAGCTAT
Found at i:31080 original size:19 final size:19
Alignment explanation
Indices: 31052--31097 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
31042 TCGGTTTATG
* **
31052 AAGAAGAGGAAGGATGGAA
1 AAGAAAAGGAAGGAAAGAA
31071 AAGAAAAGGAAGGAAAGAA
1 AAGAAAAGGAAGGAAAGAA
31090 AAGAAAAG
1 AAGAAAAG
31098 AAGAAGAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (19 bp):
AAGAAAAGGAAGGAAAGAA
Done.