Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009694.1 Corchorus capsularis cultivar CVL-1 contig09715, 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: 21827
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1192 original size:33 final size:33
Alignment explanation
Indices: 1150--1225 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
1140 GGGGGTAATC
1150 TTTGATCACCTGTGGTGATCTTGGCAAGTTATT
1 TTTGATCACCTGTGGTGATCTTGGCAAGTTATT
1183 TTTGATCACCTGTGGTGATCTTGGCAAGTTATT
1 TTTGATCACCTGTGGTGATCTTGGCAAGTTATT
*
1216 TTAGATCACC
1 TTTGATCACC
1226 CCGTTTGGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (33 bp):
TTTGATCACCTGTGGTGATCTTGGCAAGTTATT
Found at i:1356 original size:17 final size:16
Alignment explanation
Indices: 1325--1375 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
1315 CATGTAATCT
* *
1325 TTGATCACCATTGATC
1 TTGATCACTAGTGATC
*
1341 TTGCATCACTGGTGATC
1 TTG-ATCACTAGTGATC
1358 TTTGATCACTAGTGATC
1 -TTGATCACTAGTGATC
1375 T
1 T
1376 GGGGGGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 4 0.14
17 22 0.76
18 3 0.10
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.39
Consensus pattern (16 bp):
TTGATCACTAGTGATC
Found at i:1839 original size:16 final size:16
Alignment explanation
Indices: 1820--1924 Score: 63
Period size: 16 Copynumber: 6.6 Consensus size: 16
1810 GTTTGAGTCA
1820 GGTCGGGTTAAATTTG
1 GGTCGGGTTAAATTTG
* *
1836 GGTCAGGTT-GATTTG
1 GGTCGGGTTAAATTTG
* *
1851 AGTTCGAGTTAAATTTG
1 -GGTCGGGTTAAATTTG
** * *
1868 GGTTAGGTT-GATTCG
1 GGTCGGGTTAAATTTG
* *
1883 TGTTCGGGTTAATTTTG
1 -GGTCGGGTTAAATTTG
*
1900 GGTCAGGTTAAA-TTG
1 GGTCGGGTTAAATTTG
1915 GGTTCGGGTT
1 GG-TCGGGTT
1925 CGGATTGGGT
Statistics
Matches: 62, Mismatches: 22, Indels: 10
0.66 0.23 0.11
Matches are distributed among these distances:
15 14 0.23
16 40 0.65
17 8 0.13
ACGTcount: A:0.17, C:0.07, G:0.35, T:0.41
Consensus pattern (16 bp):
GGTCGGGTTAAATTTG
Found at i:1864 original size:32 final size:32
Alignment explanation
Indices: 1826--1908 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
1816 GTCAGGTCGG
*
1826 GTTAAATTTGGGTCAGGTTGATTTGAGTTCGA
1 GTTAAATTTGGGTCAGGTTGATTCGAGTTCGA
* * *
1858 GTTAAATTTGGGTTAGGTTGATTCGTGTTCGG
1 GTTAAATTTGGGTCAGGTTGATTCGAGTTCGA
*
1890 GTTAATTTTGGGTCAGGTT
1 GTTAAATTTGGGTCAGGTT
1909 AAATTGGGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.18, C:0.06, G:0.33, T:0.43
Consensus pattern (32 bp):
GTTAAATTTGGGTCAGGTTGATTCGAGTTCGA
Found at i:1920 original size:32 final size:31
Alignment explanation
Indices: 1822--1924 Score: 116
Period size: 32 Copynumber: 3.2 Consensus size: 31
1812 TTGAGTCAGG
*
1822 TCGGGTTAAATTTGGGTCAGGTTGATTTGAGT
1 TCGGGTTAAATTTGGGTCAGGTT-AATTGAGT
* * * *
1854 TCGAGTTAAATTTGGGTTAGGTTGATTCGTGT
1 TCGGGTTAAATTTGGGTCAGGTTAATT-GAGT
* *
1886 TCGGGTTAATTTTGGGTCAGGTTAAATTGGGT
1 TCGGGTTAAATTTGGGTCAGGTT-AATTGAGT
1918 TCGGGTT
1 TCGGGTT
1925 CGGATTGGGT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
31 2 0.03
32 54 0.92
33 3 0.05
ACGTcount: A:0.17, C:0.07, G:0.34, T:0.42
Consensus pattern (31 bp):
TCGGGTTAAATTTGGGTCAGGTTAATTGAGT
Found at i:9650 original size:42 final size:42
Alignment explanation
Indices: 9572--9652 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
9562 CGAGCAACCC
** *
9572 AATATACATGTCGGACACCAATTTGTACCAAGAAATCTACCT
1 AATATACATGTCGGACACCAACCTGAACCAAGAAATCTACCT
9614 AATATACATGTCGGACACCAACCTGAACCCAA-AAATCTA
1 AATATACATGTCGGACACCAACCTGAA-CCAAGAAATCTA
9653 GATTAATGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 31 0.89
43 4 0.11
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (42 bp):
AATATACATGTCGGACACCAACCTGAACCAAGAAATCTACCT
Found at i:16790 original size:4 final size:4
Alignment explanation
Indices: 16781--16812 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
16771 TAATCCCAAG
16781 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
16813 TCCAAGAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:17892 original size:438 final size:433
Alignment explanation
Indices: 16950--18015 Score: 1111
Period size: 438 Copynumber: 2.4 Consensus size: 433
16940 GGACATCTAG
* * * * ** *
16950 ATCAAAAATAATATGATATTAACTAGATTGTCAATTA-AAATCACAAAATTTCA--AAAGCATTT
1 ATCAAAAATTATACGATATTAAATAGA-CGTCAACAACAAACCACAAAATTT-AGGAAA-CATTT
* * *
17012 TTTAGAATTGAAACATAAAAA-TTAACTTTTGAGTCTTTCATGAAAGTTGTAGATCATAAAATTA
63 TTTAGAATTGAAACATAAAAATTTGA-TTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTA
* * * * * * *
17076 CTTTTTAATTGACACCTAAATTACCTTAATTGGACAAATAGAATAAAGAAAATTAAAAAAAATGA
127 CCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAA-AAAG--AA-T-AAAAAAATAA
*
17141 AGCGTTAAATTGAGTAAAATAGAATTTGTAAAGAACTAAGTAGCATAAAATTGAAAAGTATGAGG
187 AGCGTTAAATTGAGTAAAATAGAATTTGTAAAGAACTAAGTAGCATAAAATAGAAAAGTATGAGG
* * * **
17206 GTGATTTGATAACTAATTTAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAAAATTC
252 GTCATTGGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAAAATTC
* * * *
17271 CCTTTTGAATCCTTCATGAAACTCGTAGATCAAATTGACTTTCATTCTTCATGAAAAGTCGTAAA
317 CCTTTTGAACCCTTCACGAAACTCGTAGATCAAATTGACTTTCATCCTTCATGAAAAGTCGGAAA
* * * * *
17336 TCATATAATAACCTTTTAAACGACACTTGAACAACTTTAATTGGACATGTGA
382 TCATACAATAACATTTTAAACGACACTTCAACAACTTCAATCGGACATGTGA
* * * *
17388 ATCAAAAATTATATGGTATTAAATAGACGTCCAACAATCGAAACGACCAAATTTAGGAAACATTT
1 ATCAAAAATTATACGATATTAAATAGACGT-CAACAA-C-AAACCACAAAATTTAGGAAACATTT
* * * *
17453 TTTTGAATTGAAATATAAAAATTTGATTTTGAGTCCCTCATGAAAGTTGTATATCATGAAATTAC
63 TTTAGAATTGAAACATAAAAATTTGATTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTAC
* * * *
17518 CATTTAATAGATACATGAATCA-ATTAATCGGACAAATAAAACAAAGAATAAAAAAATAAAGC-T
128 CTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAA-AAAGAATAAAAAAATAAAGCGT
* * * * * * * *
17581 TAAATGTTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAGGTATTAGTGT
192 TAAA--TT-GAGTAAAATAGAATTTGTAAAGAACTAAGTAGCATAAAATAGAAAAGTATGAGGGT
*
17646 CATTGGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACATAAAAATTCCC
254 CATTGGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAAAATTCCC
*
17711 TTTTTGAACCCTTCACGAAACTCGTAGATCAAATTTAGA-TTTCGGGTCCTTCATG-AAAGTCGG
319 -TTTTGAACCCTTCACGAAACTCGTAGATCAAA-TT-GACTTTC--ATCCTTCATGAAAAGTCGG
* *
17774 AAATCA-AGCAATAACATTTTAACCGACACTTCAATAACTTCAATCGGACATGT-A
379 AAATCATA-CAATAACATTTTAAACGACACTTCAACAACTTCAATCGGACATGTGA
* * * *
17828 CA-CAAAATATTATACGATATTAAGTTA-ACGGT-AATCAA-AATCTCA-AAAATTTTGGAATCA
1 -ATCAAAA-ATTATACGATATTAA-ATAGAC-GTCAA-CAACAAAC-CACAAAATTTAGGAAACA
** * * * * * * * *
17888 TTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAATTCTTAATGAAAATTGTAGATCATGGAAT
60 TTTTTTAGAATTGAAACATAAAAATTTGATTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAAT
* *
17953 TACCTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGGAAAAA-AATACAAAAATAAA
125 TACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATA-GAAAAAGAATAAAAAAATAAA
18016 AGCCAACGCG
Statistics
Matches: 521, Mismatches: 83, Indels: 48
0.80 0.13 0.07
Matches are distributed among these distances:
435 5 0.01
436 12 0.02
437 5 0.01
438 237 0.45
439 49 0.09
440 38 0.07
441 157 0.30
442 18 0.03
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (433 bp):
ATCAAAAATTATACGATATTAAATAGACGTCAACAACAAACCACAAAATTTAGGAAACATTTTTT
AGAATTGAAACATAAAAATTTGATTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTT
TTAATAGACACATGAATCACCTTAATCGGACAAATAGAAAAAGAATAAAAAAATAAAGCGTTAAA
TTGAGTAAAATAGAATTTGTAAAGAACTAAGTAGCATAAAATAGAAAAGTATGAGGGTCATTGGA
TAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAA
CCCTTCACGAAACTCGTAGATCAAATTGACTTTCATCCTTCATGAAAAGTCGGAAATCATACAAT
AACATTTTAAACGACACTTCAACAACTTCAATCGGACATGTGA
Found at i:20967 original size:96 final size:96
Alignment explanation
Indices: 20851--21086 Score: 222
Period size: 88 Copynumber: 2.4 Consensus size: 96
20841 ATGAGTTAAT
*
20851 TTTTTTTAATTT-GGAGCTAAACTTAGTAAAATTCATTTTTTTCTTTTTCTAAAATCCTATAATA
1 TTTTTTTAATTTGGGA-CTAAA-TTAGT-AAATTCATTTTTTT-TTTTTCTAAAACCCTATAATA
*
20915 AT-AAAATTTTAATTTCACAACTTA-CC-TTGAAA
62 ATAAAAAATTTAATTTCACAACTTACCCTTTGAAA
* *
20947 TTTTTTTAATTTGGGACTAAATTCAGT-GA-T-A---ATTTTTTTTCTAAAACCCTATAATAATA
1 TTTTTTTAATTTGGGACTAAATT-AGTAAATTCATTTTTTTTTTTTCTAAAACCCTATAATAATA
*
21006 CAAAAATTTAATTTCACAACTTACCCTTTTAAA
65 -AAAAATTTAATTTCACAACTTACCCTTTGAAA
*
21039 TGAACTTCTTTTAAATTTGGGACTAAATTTAATGAAATTCATTTTTTT
1 T----TT-TTTT-AATTTGGGACTAAA-TTAGT-AAATTCATTTTTTT
21087 AATTTATTTT
Statistics
Matches: 112, Mismatches: 8, Indels: 31
0.74 0.05 0.21
Matches are distributed among these distances:
88 22 0.20
89 3 0.03
90 21 0.19
91 2 0.02
92 7 0.06
93 1 0.01
94 1 0.01
95 2 0.02
96 22 0.20
97 7 0.06
98 16 0.14
99 2 0.02
100 1 0.01
101 1 0.01
102 1 0.01
105 3 0.03
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (96 bp):
TTTTTTTAATTTGGGACTAAATTAGTAAATTCATTTTTTTTTTTTCTAAAACCCTATAATAATAA
AAAATTTAATTTCACAACTTACCCTTTGAAA
Found at i:21084 original size:98 final size:88
Alignment explanation
Indices: 20894--21084 Score: 222
Period size: 98 Copynumber: 2.1 Consensus size: 88
20884 CATTTTTTTC
* *
20894 TTTTTCTAAAATCCTATAATAATAAAATTTTAATTTCACAACTTACCTTGAAATTTTTTTAATTT
1 TTTTTCTAAAACCCTATAATAATAAAAATTTAATTTCACAACTTACCTTGAAATTTTTTTAATTT
* *
20959 GGGACTAAATTCAGTGATAATTT
66 GGGACTAAATTCAATGATAATTA
*
20982 TTTTTCTAAAACCCTATAATAATACAAAAATTTAATTTCACAACTTACCCTTTTAAATGAACTTC
1 TTTTTCTAAAACCCTATAATAAT--AAAAATTTAATTTCACAACTTA-CC-TTGAAAT----TT-
*
21047 TTTTAAATTTGGGACTAAATTTAATGA-AATTCA
57 TTTT-AATTTGGGACTAAATTCAATGATAATT-A
21080 TTTTT
1 TTTTT
21085 TTAATTTATT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
88 22 0.26
90 21 0.24
91 2 0.02
92 6 0.07
96 2 0.02
97 8 0.09
98 25 0.29
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (88 bp):
TTTTTCTAAAACCCTATAATAATAAAAATTTAATTTCACAACTTACCTTGAAATTTTTTTAATTT
GGGACTAAATTCAATGATAATTA
Done.