Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016307.1 Corchorus capsularis cultivar CVL-1 contig16328, 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: 22346
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:734 original size:229 final size:229
Alignment explanation
Indices: 327--790 Score: 813
Period size: 229 Copynumber: 2.0 Consensus size: 229
317 ATTTTGCAAA
* *
327 AAAAAATTTTGTTCAAATTTTGGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAGG
1 AAAAATTTTTGTTCAAATTTTAGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAGG
* * *
392 TTGAAGGACTTTTCGTACTTTTCATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAAT
66 TTGAAGGACTTTTCATACTTTTCATATCGTTTTTAATATTTTTCTGAATTAATTTATAATTAAAT
*
457 CAAGACAAGATTCAGATGCTCGTACAAACAAATTCTTAACTTCAAATGCGGCTGACATTTGATTA
131 CAAGACAAGATTCAGATGCTCGTACAAACAAATCCTTAACTTCAAATGCGGCTGACATTTGATTA
* *
522 GATAAGTATAGATATTTCAAGGATTCTCGGTGCC
196 GATAAGTATAGATATTTCAAGGAGTCTCGGCGCC
556 AAAAATTTTTGTTCAAATTTTAGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAGG
1 AAAAATTTTTGTTCAAATTTTAGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAGG
621 TTGAAGGACTTTTCATACTTTTCATATCGTTTTTAATATTTTTCTGAATTAATTTATAATTAAAT
66 TTGAAGGACTTTTCATACTTTTCATATCGTTTTTAATATTTTTCTGAATTAATTTATAATTAAAT
*
686 CAAGACAATATTCAGATGCTCGTA-AAACCAAATCCTTAACTTCAAATGCGGCTGACATTTGATT
131 CAAGACAAGATTCAGATGCTCGTACAAA-CAAATCCTTAACTTCAAATGCGGCTGACATTTGATT
* *
750 AGATAAGTATAGGTATTTCGAGGAGTCTCGGCGCC
195 AGATAAGTATAGATATTTCAAGGAGTCTCGGCGCC
785 AAAAAT
1 AAAAAT
791 CATGCAAAAG
Statistics
Matches: 223, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
228 3 0.01
229 220 0.99
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (229 bp):
AAAAATTTTTGTTCAAATTTTAGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAGG
TTGAAGGACTTTTCATACTTTTCATATCGTTTTTAATATTTTTCTGAATTAATTTATAATTAAAT
CAAGACAAGATTCAGATGCTCGTACAAACAAATCCTTAACTTCAAATGCGGCTGACATTTGATTA
GATAAGTATAGATATTTCAAGGAGTCTCGGCGCC
Found at i:1176 original size:337 final size:335
Alignment explanation
Indices: 556--1636 Score: 1413
Period size: 338 Copynumber: 3.2 Consensus size: 335
546 TCTCGGTGCC
* * *
556 AAAAATTTTTGTTCAAATTTTAGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAGG
1 AAAAATTTTTCTTCAAATTTTGGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAGA
*
621 TTGAAGGACTTTTCATACTTTTCATATCGTTTTTAATATTTTTCTGAATTAATTTATAATTAAAT
66 TTGAAGGACTTTTC-TACTTTTCATATCGTTTTTAATATTTTTCTGAATTAATTTCTAATTAAAT
* *
686 CAAGACAATATTCAGATGCTCGTAAAACCAAATCCTTAACTTCAAATGCGGCTGACATTTGATTA
130 CAAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAACTTCAAATGCGGCTGACATTTGATTA
*
751 GATAAGTATAGGTATTTCGAGGAGTCTCGGCGCCAAAAATCATGCAAAAGTAAGACTAGGCCCCG
195 GATAAGTATAGGTATTTCGAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGACTAGGCCCCG
* *
816 AAACGTGCTTTTTTTGCAAAAAAAAAAACGTGATGGTTAGTATACGATTTCGGCTACAATTTTGC
260 AAACGCG-TTTTTTTGCAAAAAAAAAAACGTGATGGTTAGTACACGATTTCGGCTA-AATTTTGC
881 AAAAAATGACCCA
323 AAAAAATGACCCA
* *
894 AAAAATTTTTGTTCAAATTTTGGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAGG
1 AAAAATTTTTCTTCAAATTTTGGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAGA
959 TTGAAGGA-TTTTCGTACTTTTCATATCGTTTTTAATATTTTTCTGAATTAATTTCTAATTAAAT
66 TTGAAGGACTTTTC-TACTTTTCATATCGTTTTTAATATTTTTCTGAATTAATTTCTAATTAAAT
1023 CAAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAACTTCAAATGCGGCTGACATTTGATTA
130 CAAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAACTTCAAATGCGGCTGACATTTGATTA
1088 GATAAGTATAGGTATTTCGAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGACTAGGCCCCG
195 GATAAGTATAGGTATTTCGAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGACTAGGCCCCG
*
1153 AAACGCGTTTTTTTGCAAAAAAAAAAAACCGTGATGGTTAGTACACGA-TTCTAGCTTAAATTTT
260 AAACGCGTTTTTTTGC-AAAAAAAAAAA-CGTGATGGTTAGTACACGATTTC-GGC-TAAATTTT
* *
1217 GCAGAAAAT-AACCA
321 GCAAAAAATGACCCA
* * * * *
1231 AAAAAGTTTCTCCTCAATTTTTGGCTAAAATACCCATAAAATATATATAATTTAACGCCAAAAAG
1 AAAAA-TTTTTCTTCAAATTTTGGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAG
* ** * *
1296 ATTCG-AGGACTTTTC-ACGATTTTAATATCGTTTTTCGTATCTTTCTGAATTAGTTTCTAATTA
65 ATT-GAAGGACTTTTCTAC--TTTTCATATCGTTTTTAATATTTTTCTGAATTAATTTCTAATTA
** * * * * * * * *
1359 AATCGAA-ACAAGATTCAGATGCTTATATAGACTAATACTTAAATGC-AATGTGGCTGAAATTTG
127 AATC-AAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAACTTCAAATGCGGCTGACATTTG
** * * * * **
1422 ATTAGATAAGTATATATAGTTCAAGGAGTCTCGACGCCAACAATCATGCAAAACGGAG-CTAGAG
191 ATTAGATAAGTATAGGTATTTCGAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGACTAG-G
* * * * * * *
1486 TCCCGAAACACG-TTTTTAGC---AGAAAAACCGTGATGGTTAGTACACGATGTCGGCAAAAATT
255 CCCCGAAACGCGTTTTTTTGCAAAAAAAAAAACGTGATGGTTAGTACACGATTTCGGC-TAAATT
* *
1547 TTGCAAAATATGACCCG
319 TTGCAAAAAATGACCCA
* *
1564 AAAAATTTTTCTTCAATTTTTGGCTTAAAT----A-TAAATATATATAATTTAACGCCAAAAAGA
1 AAAAATTTTTCTTCAAATTTTGGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAGA
* *
1624 TTGGAGGAGTTTT
66 TTGAAGGACTTTT
1637 AACGCTTTTA
Statistics
Matches: 670, Mismatches: 59, Indels: 39
0.87 0.08 0.05
Matches are distributed among these distances:
326 1 0.00
327 38 0.06
328 1 0.00
332 57 0.09
333 16 0.02
336 9 0.01
337 223 0.33
338 241 0.36
339 82 0.12
340 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (335 bp):
AAAAATTTTTCTTCAAATTTTGGCTAAAATACACATTAAATATATATAATTTAACGCCAAAAAGA
TTGAAGGACTTTTCTACTTTTCATATCGTTTTTAATATTTTTCTGAATTAATTTCTAATTAAATC
AAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAACTTCAAATGCGGCTGACATTTGATTAG
ATAAGTATAGGTATTTCGAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGACTAGGCCCCGA
AACGCGTTTTTTTGCAAAAAAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAATTTTGCAAA
AAATGACCCA
Found at i:2957 original size:15 final size:16
Alignment explanation
Indices: 2936--2972 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2926 ATTAAATAAT
2936 AATATTATAAT-TAAA
1 AATATTATAATCTAAA
*
2951 TATATTATAATCTAAA
1 AATATTATAATCTAAA
2967 AATATT
1 AATATT
2973 TATTAGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATTATAATCTAAA
Found at i:3067 original size:11 final size:11
Alignment explanation
Indices: 3051--3085 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
3041 AAATATTGGA
3051 TTTACAATATC
1 TTTACAATATC
*
3062 TTTACAATA-A
1 TTTACAATATC
3072 TTTACAATATC
1 TTTACAATATC
3083 TTT
1 TTT
3086 CCATAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (11 bp):
TTTACAATATC
Found at i:3076 original size:21 final size:20
Alignment explanation
Indices: 3050--3093 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
3040 TAAATATTGG
3050 ATTTACAATATCTTTACAATA
1 ATTTACAATATCTTT-CAATA
*
3071 ATTTACAATATCTTTCCATA
1 ATTTACAATATCTTTCAATA
3091 ATT
1 ATT
3094 ATTAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTACAATATCTTTCAATA
Found at i:5198 original size:45 final size:45
Alignment explanation
Indices: 5108--5198 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
5098 CTTTGGATCT
* * **
5108 TGCTTTTATGTACTCTGGTTCGGATCTTGTCGTTAAGTCTGTGGC
1 TGCTTTTATGTACTCTGCTTCGGATCTTGTCCTTAAGTCCATGGC
*
5153 TGCTTTTATGTACTCTGCTTCGGATCTTGTCCTTATGTCCATGGC
1 TGCTTTTATGTACTCTGCTTCGGATCTTGTCCTTAAGTCCATGGC
5198 T
1 T
5199 TTGGGTTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (45 bp):
TGCTTTTATGTACTCTGCTTCGGATCTTGTCCTTAAGTCCATGGC
Found at i:9037 original size:12 final size:12
Alignment explanation
Indices: 9013--9047 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
9003 CTCAGCTTTT
*
9013 TCTCTCTCACAA
1 TCTCTCACACAA
*
9025 TCTGTCACACAA
1 TCTCTCACACAA
9037 TCTCTCACACA
1 TCTCTCACACA
9048 CTATTCTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.40, G:0.03, T:0.29
Consensus pattern (12 bp):
TCTCTCACACAA
Found at i:9079 original size:27 final size:27
Alignment explanation
Indices: 9049--9103 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
9039 TCTCACACAC
9049 TATTCTTTGACACACACCAAATTCTGT
1 TATTCTTTGACACACACCAAATTCTGT
9076 TATTCTTTGACACACACCAAATTCTGT
1 TATTCTTTGACACACACCAAATTCTGT
9103 T
1 T
9104 TATTTATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.38
Consensus pattern (27 bp):
TATTCTTTGACACACACCAAATTCTGT
Found at i:9840 original size:21 final size:21
Alignment explanation
Indices: 9816--9856 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9806 GGGACAAGGA
* *
9816 AGAGGTGGTAGAGGATAGTGT
1 AGAGGTAGTAGAAGATAGTGT
*
9837 AGAGGTAGTGGAAGATAGTG
1 AGAGGTAGTAGAAGATAGTG
9857 AAGAAGAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.22
Consensus pattern (21 bp):
AGAGGTAGTAGAAGATAGTGT
Found at i:16225 original size:11 final size:11
Alignment explanation
Indices: 16209--16239 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
16199 GAAACGAAAC
16209 AAAAAGAAAAG
1 AAAAAGAAAAG
16220 AAAAAGAAAAG
1 AAAAAGAAAAG
*
16231 AAAAGGAAA
1 AAAAAGAAA
16240 GGAATATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:17197 original size:24 final size:24
Alignment explanation
Indices: 17170--17216 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
17160 GGCATGAGGT
17170 TCGTATCGACATGGGAGATGAGCA
1 TCGTATCGACATGGGAGATGAGCA
17194 TCGTATCGACATGGGAGATGAGC
1 TCGTATCGACATGGGAGATGAGC
17217 TTAGTACTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.21
Consensus pattern (24 bp):
TCGTATCGACATGGGAGATGAGCA
Found at i:17415 original size:51 final size:50
Alignment explanation
Indices: 17353--17597 Score: 319
Period size: 51 Copynumber: 5.0 Consensus size: 50
17343 CTGATCTTAT
17353 GTCTACTTTGGCTGCGTCTACTAGGTCTGATGCTCAGGATACTACTTCAGG
1 GTCTACTTTGGCTGCGTCTACT-GGTCTGATGCTCAGGATACTACTTCAGG
* *
17404 GTCTACTTTGGCT--G------GGTCTGATGCTCAGGATATTATTTCAGG
1 GTCTACTTTGGCTGCGTCTACTGGTCTGATGCTCAGGATACTACTTCAGG
* * *
17446 GTCTACTTTGACTGCGTCTACTAGTCCTGATGCTCAGGATACTATTTCAGG
1 GTCTACTTTGGCTGCGTCTACTGGT-CTGATGCTCAGGATACTACTTCAGG
17497 GTCTACTTTGGCTGCGTCTACTGGTGCTGATGCTCAGGATACTACTTCAGG
1 GTCTACTTTGGCTGCGTCTACTGGT-CTGATGCTCAGGATACTACTTCAGG
* *
17548 GACTACTGTGGCTGCG-CATACTGGGTCTGATGCTCAGGATACTACTTCAG
1 GTCTACTTTGGCTGCGTC-TACT-GGTCTGATGCTCAGGATACTACTTCAG
17598 TCTCTAGCAT
Statistics
Matches: 172, Mismatches: 11, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
42 38 0.22
44 1 0.01
49 1 0.01
50 3 0.02
51 126 0.73
52 3 0.02
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.33
Consensus pattern (50 bp):
GTCTACTTTGGCTGCGTCTACTGGTCTGATGCTCAGGATACTACTTCAGG
Done.