Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008128.1 Corchorus capsularis cultivar CVL-1 contig08149, 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: 3179
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:855 original size:34 final size:34
Alignment explanation
Indices: 807--872 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
797 ACCTCAATTA
807 GGATTTTGACTTTTGAACATGAGATGCAGATTCT
1 GGATTTTGACTTTTGAACATGAGATGCAGATTCT
*
841 GGATTTTGAGTTTTGAACATGAGATGCAGATT
1 GGATTTTGACTTTTGAACATGAGATGCAGATT
873 TTGAACTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.26, T:0.38
Consensus pattern (34 bp):
GGATTTTGACTTTTGAACATGAGATGCAGATTCT
Found at i:883 original size:34 final size:33
Alignment explanation
Indices: 811--887 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 33
801 CAATTAGGAT
* *
811 TTTGACTTTTGAACATGAGATGCAGATTCTGGAT
1 TTTGA-TTTTGAACATGAGATGCAGATTCTGAAC
*
845 TTTGAGTTTTGAACATGAGATGCAGATTTTGAAC
1 TTTGA-TTTTGAACATGAGATGCAGATTCTGAAC
879 TTTGATTTT
1 TTTGATTTT
888 CAAATGGAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 4 0.10
34 35 0.90
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTGATTTTGAACATGAGATGCAGATTCTGAAC
Found at i:1047 original size:35 final size:35
Alignment explanation
Indices: 980--1048 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
970 TGAGATGTTG
* * * *
980 ATTTTGAACTTTGATTTTTGAATAATGAAATGCTA
1 ATTTCGAACTTTAATTTTCGAAGAATGAAATGCTA
1015 ATTTCGAACTTTAATTTTCGAAGAAT-AGAATGCT
1 ATTTCGAACTTTAATTTTCGAAGAATGA-AATGCT
1049 GAAATGCAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.03
35 28 0.97
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (35 bp):
ATTTCGAACTTTAATTTTCGAAGAATGAAATGCTA
Found at i:1140 original size:28 final size:28
Alignment explanation
Indices: 1073--1141 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
1063 GGATTTTGAC
** *
1073 TTTTGAAGAATGAACCATGAAATGCCGG
1 TTTTGAAGTTTGAACCATGAAATGCCGA
* * *
1101 TTTTGAATTTTGAACCATGAGATGCTGA
1 TTTTGAAGTTTGAACCATGAAATGCCGA
1129 TTTTGAAGTTTGA
1 TTTTGAAGTTTGA
1142 TTTTTGAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.36
Consensus pattern (28 bp):
TTTTGAAGTTTGAACCATGAAATGCCGA
Found at i:1141 original size:35 final size:35
Alignment explanation
Indices: 1102--1328 Score: 93
Period size: 35 Copynumber: 6.3 Consensus size: 35
1092 AAATGCCGGT
* * ** *
1102 TTTGAATTTTGAACCATGAGATGCTGATTTTGAAG
1 TTTGAATTTTGAACAATGAAATGCAAATTTTGAAC
* *
1137 TTTGATTTTTGAATAATGAAATGCAAATTTTGAAC
1 TTTGAATTTTGAACAATGAAATGCAAATTTTGAAC
* * * *
1172 TTTG-ATTTTCGAAGGATAGAATGCTGAAATGCAAGTTTTTAAT
1 TTTGAATTTT-----GA-ACAA---TGAAATGCAAATTTTGAAC
* * * *** **
1215 TTTGACTTTTGAAGAATGAACCGTG-AAATGCAG-GT
1 TTTGAATTTTGAACAATGAA--ATGCAAATTTTGAAC
* * **
1250 TTTGAATTTTGAACCATGAGATGCTGATTTTGAAC
1 TTTGAATTTTGAACAATGAAATGCAAATTTTGAAC
* *
1285 TTTGATTTTTGAATAATGAAATGCAAATTTTGAAC
1 TTTGAATTTTGAACAATGAAATGCAAATTTTGAAC
*
1320 ATTG-ATTTT
1 TTTGAATTTT
1329 CGAAGAATAG
Statistics
Matches: 138, Mismatches: 40, Indels: 29
0.67 0.19 0.14
Matches are distributed among these distances:
33 2 0.01
34 11 0.08
35 85 0.62
36 3 0.02
37 2 0.01
38 4 0.03
39 4 0.03
40 3 0.02
43 20 0.14
44 4 0.03
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (35 bp):
TTTGAATTTTGAACAATGAAATGCAAATTTTGAAC
Found at i:1166 original size:148 final size:148
Alignment explanation
Indices: 810--1372 Score: 857
Period size: 148 Copynumber: 3.8 Consensus size: 148
800 TCAATTAGGA
* * * * * * * * *
810 TTTTGACTTTTGAA-CATGAGATGCAGATTCTGGATTTTGAGTTTTGAA-CATGAGATGCAGATT
1 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCAAATT
* ** *
873 TTGAACTTTGATTTTC--A-AATGGAATGCTGAAATGCAAGTTTTGAATTAAGACTTTTGAATAA
66 TTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAA
935 TGAACCGTGAAATGCAGG
131 TGAACCGTGAAATGCAGG
* * *
953 TTTTGAATTTTGAGCCATGAGATGTTGATTTTGAACTTTGATTTTTGAATAATGAAATGCTAATT
1 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCAAATT
* * *
1018 TCGAACTTTAATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGGATTTTGACTTTTGAAGAA
66 TTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAA
* *
1083 TGAACCATGAAATGCCGG
131 TGAACCGTGAAATGCAGG
*
1101 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAAGTTTGATTTTTGAATAATGAAATGCAAATT
1 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCAAATT
* *
1166 TTGAACTTTGATTTTCGAAGGATAGAATGCTGAAATGCAAGTTTTTAATTTTGACTTTTGAAGAA
66 TTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAA
1231 TGAACCGTGAAATGCAGG
131 TGAACCGTGAAATGCAGG
1249 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCAAATT
1 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCAAATT
* *
1314 TTGAACATTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGATTTTT
66 TTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTT
1373 TTTTAAGAAT
Statistics
Matches: 378, Mismatches: 37, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
143 12 0.03
144 28 0.07
145 25 0.07
147 1 0.00
148 312 0.83
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (148 bp):
TTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCAAATT
TTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAA
TGAACCGTGAAATGCAGG
Found at i:1262 original size:28 final size:28
Alignment explanation
Indices: 1231--1289 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1221 TTTTGAAGAA
* * *
1231 TGAACCGTGAAATGCAGGTTTTGAATTT
1 TGAACCATGAAATGCAGATTTTGAACTT
* *
1259 TGAACCATGAGATGCTGATTTTGAACTT
1 TGAACCATGAAATGCAGATTTTGAACTT
1287 TGA
1 TGA
1290 TTTTTGAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (28 bp):
TGAACCATGAAATGCAGATTTTGAACTT
Found at i:1614 original size:37 final size:36
Alignment explanation
Indices: 1572--1870 Score: 276
Period size: 37 Copynumber: 8.1 Consensus size: 36
1562 TGGTTTTTGA
*
1572 ACACCTAAACAGGCATCTTGAACAAGGTTTTGATGAG
1 ACACCTAAACAGG-ATCTTAAACAAGGTTTTGATGAG
* * *
1609 ACACCTAAACAGGTACCTTAAACAATGATTTTGATAAG
1 ACACCTAAACAGG-ATCTTAAACAA-GGTTTTGATGAG
* * *
1647 AAACCTAAATAGGAATAC-TAAACAAGATTTTGATGAG
1 ACACCTAAACAGG-AT-CTTAAACAAGGTTTTGATGAG
* * * * *
1684 ACACCTAAACAAGGACCTTAACCAAGGATTTAATAAG
1 ACACCTAAAC-AGGATCTTAAACAAGGTTTTGATGAG
* * *
1721 AAACCTAAACATGAATCTTAAACAAGATTTTGATGAG
1 ACACCTAAACA-GGATCTTAAACAAGGTTTTGATGAG
* * * *
1758 ACACCTAAACAGGGATTTTAAATAAGGATTTGATAAG
1 ACACCTAAACA-GGATCTTAAACAAGGTTTTGATGAG
* * *
1795 AAACCTAAACAGGCATCTTGAACAAGGTTTTGATGAC
1 ACACCTAAACAGG-ATCTTAAACAAGGTTTTGATGAG
* * *
1832 ACACCTAAACAAGGACCTTAAACAAGGATTTGACGAG
1 ACACCTAAAC-AGGATCTTAAACAAGGTTTTGATGAG
1869 AC
1 AC
1871 TGAATTTTTT
Statistics
Matches: 208, Mismatches: 47, Indels: 14
0.77 0.17 0.05
Matches are distributed among these distances:
36 4 0.02
37 168 0.81
38 35 0.17
39 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (36 bp):
ACACCTAAACAGGATCTTAAACAAGGTTTTGATGAG
Found at i:1757 original size:74 final size:74
Alignment explanation
Indices: 1574--1864 Score: 397
Period size: 74 Copynumber: 3.9 Consensus size: 74
1564 GTTTTTGAAC
* * * *
1574 ACCTAAACAGGCATCTTGAACAAGGTTTTGATGAGACACCTAAAC-AGGTACCTTAAACAATGAT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAAGG-ACCTTAAACAAGGA-
1638 TTTGATAAGAA
64 TTTGATAAGAA
* *
1649 ACCTAAATAGGAATAC-TAAACAAGATTTTGATGAGACACCTAAACAAGGACCTTAACCAAGGAT
1 ACCTAAACAGGAAT-CTTAAACAAGATTTTGATGAGACACCTAAACAAGGACCTTAAACAAGGAT
*
1713 TTAATAAGAA
65 TTGATAAGAA
* * ** *
1723 ACCTAAACATGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGATTTTAAATAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAAGGACCTTAAACAAGGATT
1788 TGATAAGAA
66 TGATAAGAA
* * * *
1797 ACCTAAACAGGCATCTTGAACAAGGTTTTGATGACACACCTAAACAAGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAAGGACCTTAAACAAGGATT
1862 TGA
66 TGA
1865 CGAGACTGAA
Statistics
Matches: 189, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
73 1 0.01
74 133 0.70
75 51 0.27
76 4 0.02
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (74 bp):
ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAAGGACCTTAAACAAGGATT
TGATAAGAA
Found at i:1821 original size:111 final size:112
Alignment explanation
Indices: 1574--1870 Score: 334
Period size: 111 Copynumber: 2.7 Consensus size: 112
1564 GTTTTTGAAC
* * *
1574 ACCTAAACAGGCATCTTGAACAAGGTTTTGATGAGACACCTAAACAGGTACCTTAAACAATGATT
1 ACCTAAACAGGCATCTTGAACAAGGTTTTGATGAGACACCTAAACAAGAACCTTAAACAAGGATT
* * * * *
1639 TTGATAAGAAACCTAAATAGGAATACTAAACAAGATTTTGATGAGAC
66 TTGATGAGACACCTAAACAGGAATACTAAACAAGATTTTGATAAGAA
* * * * * * *
1686 ACCTAAACAAGG-ACCTT-AACCAAGGATTTAATAAGAAACCTAAACATGAATCTTAAACAA-GA
1 ACCTAAAC-AGGCATCTTGAA-CAAGGTTTTGATGAGACACCTAAACAAGAACCTTAAACAAGGA
* ** *
1748 TTTTGATGAGACACCTAAACAGGGATTTTAAATAAGGA-TTTGATAAGAA
64 TTTTGATGAGACACCTAAACAGGAATACTAAACAA-GATTTTGATAAGAA
* *
1797 ACCTAAACAGGCATCTTGAACAAGGTTTTGATGACACACCTAAACAAGGACCTTAAACAAGGA-T
1 ACCTAAACAGGCATCTTGAACAAGGTTTTGATGAGACACCTAAACAAGAACCTTAAACAAGGATT
*
1861 TTGACGAGAC
66 TTGATGAGAC
1871 TGAATTTTTT
Statistics
Matches: 152, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
110 3 0.02
111 95 0.62
112 51 0.34
113 3 0.02
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (112 bp):
ACCTAAACAGGCATCTTGAACAAGGTTTTGATGAGACACCTAAACAAGAACCTTAAACAAGGATT
TTGATGAGACACCTAAACAGGAATACTAAACAAGATTTTGATAAGAA
Found at i:2631 original size:87 final size:87
Alignment explanation
Indices: 2485--2652 Score: 255
Period size: 87 Copynumber: 1.9 Consensus size: 87
2475 TGATTGATGC
* * * *
2485 CCCAAACCTTCTTCCAATTTGGTCATGTATTGATATTCCCAACTCAATTGATGTTTCTGGATCAG
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG
2550 CTTCTCACCTCAAGAATTATTT
66 CTTCTCACCTCAAGAATTATTT
* *
2572 CCCAAATCTTCCTCCAATTTGATCATGCATTGATATTCCCAGCTCAATTGATATTTCTGGATCAG
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG
* * *
2637 TTTCTCATCTTAAGAA
66 CTTCTCACCTCAAGAA
2653 ATTTTCAAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (87 bp):
CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG
CTTCTCACCTCAAGAATTATTT
Done.