Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017546.1 Corchorus olitorius cultivar O-4 contig17579, 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: 90271
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:672 original size:332 final size:329
Alignment explanation
Indices: 1--1895 Score: 2509
Period size: 324 Copynumber: 5.8 Consensus size: 329
*
1 GTGAAAAGTCCTTCAATTCTTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCGGTTAAAA
1 GTGAAAAGCCCTTCAA-TCTTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCGGTTAAAA
* * * ** ** * * *
66 ATTCAGGAAAAATCTTTCTGTTCAATTTTTAAAAAAAGTTTCCCGAAATCATGTACGT-TATCAC
65 ATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTACCGAAATCGTGTAC-TCCATCAC
* * *
130 GGTTTTTAGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGACGCCAAGAC
129 GGTTTTTGGCTAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC
* * *
195 TCATTGAAATATCTATATTAATCAT-CCAAAATTTCAGCCACATTGGATTTAAAGATTTGTTTTT
194 TCATTGAAATATCTATATTAATCATACC-AAATATCAGCCACAATGGATTTAAGGATTTGTTTTT
*
259 ACGATCATCTGAATCTTGTTTCGATTTAATTAAGACATTAATTCGGGAAAGAATTGAAAAAATGA
258 ACGATCATCTGAATCTTGTTTCGATTTAA-TAA-AAATTAATTCGGGAAA-AATTGAAAAAATGA
324 TATTAGAAGC
320 TATTAGAAGC
*
334 GTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCGGTTAAAAA
1 GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCGGTTAAAAA
* * * *
399 TTCACGAAAAATCTTTCGGTTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCAC
66 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTACCGAAATCGTGTACT--CCATCAC
*
464 GGTTTTTGGCTAAAAACGCATTCCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC
129 GGTTTTTGGCTAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC
529 TCATTGAAATATCTATATTAATC-TAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTT
194 TCATTGAAATATCTATATTAATCAT-ACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTT
* *
593 ACGATCATTTGACTCTTGTTTCGATTTAGATAAAAATTAATTCGGGAAAAATTGAAAAAATGATA
258 ACGATCATCTGAATCTTGTTTCGATTTA-ATAAAAATTAATTCGGGAAAAATTGAAAAAATGATA
*
658 TTAGAAGT
322 TTAGAAGC
* *
666 GTGAAAAGCCCTTTAATCTTTTTCGCGTTGAATTATATATTTTTTACGAGTACTGCGGTTAAAAA
1 GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCGGTTAAAAA
* *
731 TTGAGGAAAAATCTTTCGGGTCAGTTTTTGCAAAATTTTTGCCGAAATCGTG------ATCACGG
66 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTACCGAAATCGTGTACTCCATCACGG
* * *
790 TTTTTGGCTAAAGACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
131 TTTTTGGCTAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
* * *
855 ATTGAAATATCTATATTAATCTTACCAAATATCAGCCACAATGGATTAAAGGATTTTTTTTTACG
196 ATTGAAATATCTATATTAATCATACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACG
* * * *
920 ATCATTTGAATCTTTTTTCGATTTAAATAGAAATTAATTCGGGAAAAATTGAAAAAATGATACTA
261 ATCATCTGAATCTTGTTTCGATTT-AATAAAAATTAATTCGGGAAAAATTGAAAAAATGATATTA
985 GAAGC
325 GAAGC
* * * *
990 GTGAAAAGCCCTTTAATCTTTTTGGCGTTGAATTATATATTTTTTAGGAGTATTGAGGTTAAAAA
1 GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCGGTTAAAAA
*
1055 TTGAGGAAAAATCTTTCGGGTCAGTTTTTGCAAAATTTTTACCGAAATCGTGTACTCCATCACGG
66 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTACCGAAATCGTGTACTCCATCACGG
* * * * * *
1120 TTTTTGGCTAAAAACGCATTCTGGTGCCACGTCTTA-TATTTGCTTGATTTTTGGCGCCAAGACT
131 TTTTTGGCTAAAAACGCATTCCGGGGCCCCGGCTCAGT-TTTGCATGATTTTTGGCGCCAAGACT
* * * * * * * * *
1184 CATTGAAATATGTTTATTCATCATCCCAAATCTCAGCTACATTGGATTGAAGGATTTGATTTTAC
195 CATTGAAATATCTATATTAATCATACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTAC
* * *
1249 GAGCATCTAAATCTTGTTTTGATTTAAATAGAAAA-TAATTCGGGAAAAA-TGAAAAAATGATAT
260 GATCATCTGAATCTTGTTTCGATTT-AATA-AAAATTAATTCGGGAAAAATTGAAAAAATGATAT
1312 TAGAAGC
323 TAGAAGC
* * * * * ** *
1319 ATGAGAAGCCCTTCAATCATTTTGGCGTTGAATTATAAATTTTTTGCGAACATTGCGGTTAAAAA
1 GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCGGTTAAAAA
* *
1384 ATGAGGAAAAATCTTTCGGGTCAATTTTTACAAAA----T-------T--T-T--TCC--CACGG
66 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTACCGAAATCGTGTACTCCATCACGG
* * * * * *
1431 TTTTTGGCTAAAAACGCGTTCTGGGGCCACGGCTCAATTTTTCATGATTTTTGACGCCAAGACTC
131 TTTTTGGCTAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
* * * *
1496 ATTGAAATATATATATTAATCATTCCTAATTTCAGCCACAATGGATTTAAGGATTTGTTTTTACG
196 ATTGAAATATCTATATTAATCATACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACG
* * * *
1561 ATCATCTGAATCTTATTTCGGTTTAATTAGAAATTAATTTGGGAAAGAATTGAAAAAATGATATT
261 ATCATCTGAATCTTGTTTCGATTTAA-TAAAAATTAATTCGGGAAA-AATTGAAAAAATGATATT
1626 AGAAGC
324 AGAAGC
* *
1632 GTGAAAAGCCCTTCAATCTTTTTGGTGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAA
1 GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCGGTTAAAAA
* * * * * *
1697 TTGATGAAAAATCTTTCGGATCAATTTTTGCAAAATTTTTACCAAAATCTTGTATTAACCATCAT
66 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTACCGAAATCGTGTACT--CCATCAC
*
1762 GGTTTTTGGCTAAAAACGCATTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC
129 GGTTTTTGGCTAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC
* * * *
1827 TCATTGAAATTTCTTTATTAATCATCCCAAATATCAGCCACAATGGATTTAAGGATTTGCTTTTA
194 TCATTGAAATATCTATATTAATCATACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTA
1892 CGAT
259 CGAT
1896 AAAAACATAT
Statistics
Matches: 1387, Mismatches: 134, Indels: 82
0.87 0.08 0.05
Matches are distributed among these distances:
310 5 0.00
311 148 0.11
312 3 0.00
313 112 0.08
315 1 0.00
316 1 0.00
317 1 0.00
318 1 0.00
324 305 0.22
325 3 0.00
326 1 0.00
327 1 0.00
329 109 0.08
330 155 0.11
331 6 0.00
332 228 0.16
333 153 0.11
334 151 0.11
335 3 0.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Consensus pattern (329 bp):
GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCGGTTAAAAA
TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTACCGAAATCGTGTACTCCATCACGG
TTTTTGGCTAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
ATTGAAATATCTATATTAATCATACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACG
ATCATCTGAATCTTGTTTCGATTTAATAAAAATTAATTCGGGAAAAATTGAAAAAATGATATTAG
AAGC
Found at i:2131 original size:27 final size:26
Alignment explanation
Indices: 2096--2167 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
2086 AAAAATATAC
*
2096 AAAATTATATTTTAATAATGACATAGTT
1 AAAA-TATATTTTAAAAATGACA-AGTT
* *
2124 AAAATATATTTTAAAAATGTCAATTT
1 AAAATATATTTTAAAAATGACAAGTT
*
2150 AGAAATATATTTGAAAAA
1 A-AAATATATTTTAAAAA
2168 ATGGTACAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 4 0.10
27 31 0.79
28 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (26 bp):
AAAATATATTTTAAAAATGACAAGTT
Found at i:2264 original size:97 final size:97
Alignment explanation
Indices: 2083--2263 Score: 278
Period size: 97 Copynumber: 1.9 Consensus size: 97
2073 AAATATATTT
* *
2083 GAAAAAAATATACAAAATTATATTTTAATAATGACATAGTTAAAATATATTTTAAAAATGTCAAT
1 GAAAAAAATACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAAAAATGTCAAT
*
2148 TTAGAAATATATTTGAAAAAATGGTACAATGG
66 TTAAAAATATATTTGAAAAAATGGTACAATGG
* **
2180 GAAAAAAATACATAAAATTATATTTTAATAATGACATAATT-AAA-ATATTTTAATCATAG-CAA
1 GAAAAAAATACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAAAAAT-GTCAA
2242 TTTAAAAATATATTTGAAAAAA
65 TTTAAAAATATATTTGAAAAAA
2264 ATATATAATC
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
95 35 0.45
96 4 0.05
97 38 0.49
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (97 bp):
GAAAAAAATACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAAAAATGTCAAT
TTAAAAATATATTTGAAAAAATGGTACAATGG
Found at i:2278 original size:95 final size:97
Alignment explanation
Indices: 2083--2279 Score: 267
Period size: 95 Copynumber: 2.1 Consensus size: 97
2073 AAATATATTT
* *
2083 GAAAAAAATATACAAAATTATATTTTAATAATGACATAGTTAAAATATATTTTAAAAATGTCAAT
1 GAAAAAAATACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAAAAATGTCAAT
* * *
2148 TTAGAAATATATTTGAAAAAATGGTACAATGG
66 TTAAAAATATATTTGAAAAAATGATACAATCG
* **
2180 GAAAAAAATACATAAAATTATATTTTAATAATGACATAATT-AAA-ATATTTTAATCATAG-CAA
1 GAAAAAAATACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAAAAAT-GTCAA
*
2242 TTTAAAAATATATTTGAAAAAAAT-ATATAATCG
65 TTTAAAAATATATTTG-AAAAAATGATACAATCG
2275 GAAAA
1 GAAAA
2280 CATAAAGTTC
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
95 40 0.45
96 11 0.12
97 38 0.43
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.34
Consensus pattern (97 bp):
GAAAAAAATACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAAAAATGTCAAT
TTAAAAATATATTTGAAAAAATGATACAATCG
Found at i:5729 original size:2 final size:2
Alignment explanation
Indices: 5722--5773 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
5712 AGTTTTTGTC
*
5722 TA TA TA TA TA TA TG TA 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 TA TA TA TA TA TA TA TA
5764 TA TA TA TA TA
1 TA TA TA TA TA
5774 AAAATCAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7791 original size:29 final size:28
Alignment explanation
Indices: 7730--7799 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
7720 GTGTAATGCG
* *
7730 TATAAGTGC-ATTTTTTTTTTTTTAGGG
1 TATAAGTGCAACTTTTTTTTTTTTAGGA
7757 TATAAGTGCAACTTTTTTTTTTTTA-GA
1 TATAAGTGCAACTTTTTTTTTTTTAGGA
7784 TAAGTAAGTGCAACTT
1 T-A-TAAGTGCAACTT
7800 ATTAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 11 0.29
28 15 0.39
29 12 0.32
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (28 bp):
TATAAGTGCAACTTTTTTTTTTTTAGGA
Found at i:19965 original size:77 final size:77
Alignment explanation
Indices: 19838--19989 Score: 241
Period size: 77 Copynumber: 2.0 Consensus size: 77
19828 TTTATAAGTG
*
19838 TTCGATATTCTCACCCTTATTAGAGTGGAGACTAATTACTACTTCAATCAATCACTAGTTGTGGT
1 TTCGATATTCTCACCCTTATTAGAGTGGAGACTAATTACTACTCCAATCAATCACTAGTTGTGGT
*
19903 ACATTTCAAATA
66 ACATTACAAATA
* * ** *
19915 TTCGATGTTCTCACCCTTATTAGAGTGGAGGCTGCTTACTACTCCAATCAATCACTATTTGTGGT
1 TTCGATATTCTCACCCTTATTAGAGTGGAGACTAATTACTACTCCAATCAATCACTAGTTGTGGT
19980 ACATTACAAA
66 ACATTACAAA
19990 GTTTAGAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (77 bp):
TTCGATATTCTCACCCTTATTAGAGTGGAGACTAATTACTACTCCAATCAATCACTAGTTGTGGT
ACATTACAAATA
Found at i:24496 original size:20 final size:20
Alignment explanation
Indices: 24471--24536 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 20
24461 ACATGGCACA
24471 ATGATTAAGATTCTACATAT
1 ATGATTAAGATTCTACATAT
*
24491 ATGATTGAAATAATTCTACATAT
1 ATGATT--AA-GATTCTACATAT
* *
24514 ATGTCTTTAAGATTCCACATAT
1 ATG--ATTAAGATTCTACATAT
24536 A
1 A
24537 AGCTTAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 6 0.16
22 13 0.35
23 16 0.43
25 2 0.05
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (20 bp):
ATGATTAAGATTCTACATAT
Found at i:30114 original size:28 final size:28
Alignment explanation
Indices: 30074--30131 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
30064 CAAAGGGCTC
30074 ACATGTTCGGATTAGCCGTTAGATTATG
1 ACATGTTCGGATTAGCCGTTAGATTATG
30102 ACATGTTCGGATTAGCCGTTAGATTATG
1 ACATGTTCGGATTAGCCGTTAGATTATG
30130 AC
1 AC
30132 GTAGTACACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (28 bp):
ACATGTTCGGATTAGCCGTTAGATTATG
Found at i:42144 original size:26 final size:26
Alignment explanation
Indices: 42114--42166 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
42104 TTTCTATCTG
42114 GGCTTTGAAATCAGACCGTTTTAAAT
1 GGCTTTGAAATCAGACCGTTTTAAAT
42140 GGCTTTGAAATCAGACCGTTTTAAAT
1 GGCTTTGAAATCAGACCGTTTTAAAT
42166 G
1 G
42167 TCTTGGGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (26 bp):
GGCTTTGAAATCAGACCGTTTTAAAT
Found at i:86985 original size:16 final size:13
Alignment explanation
Indices: 86949--86974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
86939 TTATTACTAT
86949 TTTCTTTTTATTA
1 TTTCTTTTTATTA
86962 TTTCTTTTTATTA
1 TTTCTTTTTATTA
86975 GTATATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTTTTTATTA
Done.