Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017173.1 Corchorus olitorius cultivar O-4 contig17206, 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: 37207
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2051 original size:328 final size:333
Alignment explanation
Indices: 1332--2070 Score: 848
Period size: 328 Copynumber: 2.2 Consensus size: 333
1322 TTTTTCGGGT
* *
1332 CATCACGGTTTTTGGCTAAAAAAGTGTTTCGGGGCCTCGGCT-TAGTTTTGCATGATTTTTGGCG
1 CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCC-CGGCTCT-GTTTTGCATGATTTTTGGCG
* * * *
1396 CCGAGACTCCTTGATATATCTATACTCATCTAATCAAATCTCAGCCACATTAAATTTAAGGATTG
64 CCGAGACTCCCTGAAATATCTATACTCATCTAACCAAATCTCAGACACATTAAATTTAAGGATTG
*
1461 TTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAA
129 TTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAA
* * * *
1526 CAATATTAAAAGCGTCAAAAAGACTTTCAATTTTTTTGGCATTGAATTATATGTTTTTTTATGAG
194 CAATATTAAAAGCGTCAAAAAGACCTTCAATTTTTTTAGCATCGAATTATATGTTTTTTCATGAG
* ** *
1591 TATTTTTGTTAGAAATCGAGAAAAAAATCTTTCGGATCAATTTTTGCAAAAATTTTAGCGGAAAT
259 TATTTTAGCCAAAAATCGAGAAAAAAATCTTTCGGATCAATTTTTGCAAAAATTTTAGCGGAAAT
1656 CGTGTACGTTA
324 CGTGTAC-TTA
* ** * * * *
1667 CATCACGGTTCTCAGCTAAAAACGCGTTCCGGGGTCCGGCTCAGTTTTGC--GATTTTTGGTG-C
1 CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCGGCTCTGTTTTGCATGATTTTTGGCGCC
* *
1729 -A-AC-CCCTGAAATATCTATATTCATCTAACCAAATCTCAGACACATTAGATTTAAGGATTTGT
66 GAGACTCCCTGAAATATCTATACTCATCTAACCAAATCTCAGACACATTAAATTTAAGGA-TTGT
** *
1791 TTTTTTGAA-CATCTGAATC-TGTTTTCGATTTAATTAAAAATTAATTCTGAAAAA-ATTGGAAA
130 TTTTTACAAGCATCTGAATCTTG-TTTCGATTTAATTAAAAATTAATTCAGAAAAATA-T-GAAA
* * ** *
1853 AACAATATTAGAAGCGT-TAAAATCCCTTCAATCTTTTTTATC-TCGAA-T-TATGTATTTTTCA
192 AACAATATTAAAAGCGTCAAAAAGACCTTCAAT-TTTTTTAGCATCGAATTATATGT-TTTTTCA
* * * * *
1914 TGAGTATTTTAGCCAAAAATTGAG-GAAATATCTTTCGGGTCAATTTTTGC-AAAGTTTTAGAC-
255 TGAGTATTTTAGCCAAAAATCGAGAAAAAAATCTTTCGGATCAATTTTTGCAAAAATTTTAG-CG
1976 GAAATCGTGTA-TTAA
319 GAAATCGTGTACTT-A
* * * * *
1991 CCATCATGGTTTTTGGCTAAAAACGCGTTTCAGGACCACAGCTCTGTTTTGCATGATTTTTGGCA
1 -CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCC-CGGCTCTGTTTTGCATGATTTTTGGCG
*
2056 CCGAGACTCCTTGAA
64 CCGAGACTCCCTGAA
2071 TCGTGTACGT
Statistics
Matches: 337, Mismatches: 50, Indels: 37
0.79 0.12 0.09
Matches are distributed among these distances:
323 2 0.01
324 1 0.00
325 48 0.14
326 41 0.12
327 29 0.09
328 113 0.34
329 41 0.12
330 2 0.01
331 3 0.01
332 16 0.05
334 12 0.04
335 29 0.09
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (333 bp):
CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCGGCTCTGTTTTGCATGATTTTTGGCGCC
GAGACTCCCTGAAATATCTATACTCATCTAACCAAATCTCAGACACATTAAATTTAAGGATTGTT
TTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACA
ATATTAAAAGCGTCAAAAAGACCTTCAATTTTTTTAGCATCGAATTATATGTTTTTTCATGAGTA
TTTTAGCCAAAAATCGAGAAAAAAATCTTTCGGATCAATTTTTGCAAAAATTTTAGCGGAAATCG
TGTACTTA
Found at i:2106 original size:31 final size:31
Alignment explanation
Indices: 2068--2152 Score: 170
Period size: 31 Copynumber: 2.7 Consensus size: 31
2058 GAGACTCCTT
2068 GAATCGTGTACGTTAATCAAAATATTAGCTG
1 GAATCGTGTACGTTAATCAAAATATTAGCTG
2099 GAATCGTGTACGTTAATCAAAATATTAGCTG
1 GAATCGTGTACGTTAATCAAAATATTAGCTG
2130 GAATCGTGTACGTTAATCAAAAT
1 GAATCGTGTACGTTAATCAAAAT
2153 CACGGTTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (31 bp):
GAATCGTGTACGTTAATCAAAATATTAGCTG
Found at i:2831 original size:327 final size:332
Alignment explanation
Indices: 2289--3052 Score: 844
Period size: 327 Copynumber: 2.3 Consensus size: 332
2279 GTAAAACAAG
* * *
2289 CATCTGAATCTTGTTTCGCTTTAATTAGAAATTAATT--AAGAAAAATATGAAAAACGATATTAA
1 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATATGAAAAACAATATTAA
* * * * * **
2352 AAGCGTGAAAAAGACTTTGAATTTTTTTGGCATTGAATTATACGAATTTTATGAGTATTTTTGTT
66 AAGCGTGAAAAAGACCTTCAATCTTCTTGGCATTGAATTATACGAATTTTATGAGTATTTTAGCC
* *
2417 AGAAATCGAGAAAAATCTTTCGGATCAATTTTTGCAAAAATTTTAGCCGAAATCGTGTACTAACC
131 AAAAATCGAGAAAAATCTTTCGGATCAATTTTTACAAAAATTTTAGCCGAAATCGTGTACTAACC
* * * *
2482 ATCACGGTTCTCGGCTAAAAACGCGTTCCGGGGCC-CGGCTCAGTTTTACATGATTTTTGG-TGC
196 ATCACGGTTCTCGGCTAAAAACGAGTTCCAGGACCACAGCTCAGTTTTACATGATTTTTGGCTG-
2545 A-A-TCCTTGAAAAAT-TTATATTCATCTAACCAAATCTCA-GACACATTAGATTTAA-GAATTG
260 AGACTCCTTGAAAAATATT-TATTCATCTAACCAAATCTCAGGA-ACATTAGATTTAAGGAATTG
2605 TTTTTACGAA
323 TTTTTACGAA
*
2615 CATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCGAAAAAAAAT-TGGAAAAACAATATTA
1 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATAT-GAAAAACAATATTA
* ** ** * *
2679 GAAGC-TTTAAAATCCCTTCAATCTTCTT-G-ATCTCGAATTATA-TATTTTTCATGAGTATTTT
65 AAAGCGTGAAAAAGACCTTCAATCTTCTTGGCAT-T-GAATTATACGAATTTT-ATGAGTATTTT
* * * **
2740 AGCCAAAAATTGAGGAAATATCTTTCGGATCAATTTTTAC-AAAGTTTTAGTTGAAATCGTGTAC
127 AGCCAAAAATCGA-GAAAAATCTTTCGGATCAATTTTTACAAAAATTTTAGCCGAAATCGTGTAC
* * * * * *
2804 TAACCATCATGGTTTTTGGCTAAAAACGAGTTTCAGGACCACAGCTCTGTTTTGCATGATTTTTG
191 TAACCATCACGGTTCTCGGCTAAAAACGAGTTCCAGGACCACAGCTCAGTTTTACATGATTTTTG
* * ** *
2869 GCACTGAGACTCCTTGAAATATATTTATTCATGTAATTAAATCTCAGGAACATTGGATTTAAGGA
256 G--CTGAGACTCCTTGAAAAATATTTATTCATCTAACCAAATCTCAGGAACATTAGATTTAAGGA
* * **
2934 TTTGTTTTTATGTG
319 ATTGTTTTTACGAA
* * * *
2948 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AGAAAAACTATAAAAAACAAAATTAA
1 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATATGAAAAACAATATTAA
** *
3012 AAGCGTG-AAAAGTTCTTCAATCCTT-TTGGCATTGAGTTATA
66 AAGCGTGAAAAAGACCTTCAAT-CTTCTTGGCATTGAATTATA
3053 TATGTTTACG
Statistics
Matches: 362, Mismatches: 55, Indels: 36
0.80 0.12 0.08
Matches are distributed among these distances:
325 2 0.01
326 42 0.12
327 97 0.27
328 71 0.20
330 1 0.00
331 3 0.01
332 84 0.23
333 60 0.17
334 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (332 bp):
CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATATGAAAAACAATATTAA
AAGCGTGAAAAAGACCTTCAATCTTCTTGGCATTGAATTATACGAATTTTATGAGTATTTTAGCC
AAAAATCGAGAAAAATCTTTCGGATCAATTTTTACAAAAATTTTAGCCGAAATCGTGTACTAACC
ATCACGGTTCTCGGCTAAAAACGAGTTCCAGGACCACAGCTCAGTTTTACATGATTTTTGGCTGA
GACTCCTTGAAAAATATTTATTCATCTAACCAAATCTCAGGAACATTAGATTTAAGGAATTGTTT
TTACGAA
Found at i:15263 original size:19 final size:20
Alignment explanation
Indices: 15241--15278 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
15231 TTCTTTTTTA
15241 ATATTATTATTTTT-TGTAC
1 ATATTATTATTTTTATGTAC
15260 ATATTATTATTTTTATGTA
1 ATATTATTATTTTTATGTA
15279 TATGTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
ATATTATTATTTTTATGTAC
Found at i:16820 original size:105 final size:104
Alignment explanation
Indices: 16600--16860 Score: 346
Period size: 105 Copynumber: 2.5 Consensus size: 104
16590 AAGTTTAGCC
* *
16600 TTAATTTCACTAAATTTAACCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAAT
1 TTAATTTCACTAAGTTTAA-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAA-
* * *
16665 TTTAATTTATTGTTAAAGGGTTTTAGAAATTAAATACAAAA
64 TTTAATATATTATTAAAGGGTTTTAGAAATAAAATACAAAA
* *
16706 CTAATTTCACTAAGTTTAACCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAA-T
1 TTAATTTCACTAAGTTTAACCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* *
16770 TAATAATATTATTATAGGGTTTTAGAAATAAAATATATATAA
66 TAAT-ATATTATTAAAGGGTTTTAGAAATAAAATACA-A-AA
* ** *
16812 TTAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGG
1 TTAATTTCACTAAGTTTAACCCAAATTAAAATTTTATTTTTATTTTAAGG
16861 ATTAGAAAAA
Statistics
Matches: 138, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
103 5 0.04
104 27 0.20
105 84 0.61
106 22 0.16
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.43
Consensus pattern (104 bp):
TTAATTTCACTAAGTTTAACCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
TAATATATTATTAAAGGGTTTTAGAAATAAAATACAAAA
Found at i:23058 original size:24 final size:24
Alignment explanation
Indices: 23031--23079 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
23021 AATCCCAAAC
*
23031 TGGGTTAGCGGTTTATCCTGACCT
1 TGGGTTAACGGTTTATCCTGACCT
23055 TGGGTTAACGGTTTATCCTGACCT
1 TGGGTTAACGGTTTATCCTGACCT
23079 T
1 T
23080 AGAGATGGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (24 bp):
TGGGTTAACGGTTTATCCTGACCT
Found at i:23869 original size:2 final size:2
Alignment explanation
Indices: 23850--23922 Score: 55
Period size: 2 Copynumber: 37.0 Consensus size: 2
23840 TCGTTTTGAT
*
23850 TA TA -A TA TA -A TCA TA TA TA T- TA TA TC TGA TA TA -A TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
* * *
23890 TT TT TA GTT 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
23923 ACTAAACTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
1 4 0.07
2 50 0.86
3 4 0.07
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27232 original size:13 final size:13
Alignment explanation
Indices: 27193--27253 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
27183 GTTTCAGGTA
27193 CAATTCTGTTTTT
1 CAATTCTGTTTTT
* *
27206 CAATACTATTTTT
1 CAATTCTGTTTTT
*
27219 CAATTCTGTATTT
1 CAATTCTGTTTTT
*
27232 CAATTCTGTTTTG
1 CAATTCTGTTTTT
*
27245 CATTTCTGT
1 CAATTCTGT
27254 GTTGAAGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
CAATTCTGTTTTT
Found at i:27285 original size:38 final size:38
Alignment explanation
Indices: 27242--27357 Score: 169
Period size: 38 Copynumber: 3.1 Consensus size: 38
27232 CAATTCTGTT
27242 TTGCATTTCTGTGTTGAAGTTTCTGTTTTACTTTTCAA
1 TTGCATTTCTGTGTTGAAGTTTCTGTTTTACTTTTCAA
* * ***
27280 TTGCATTTTTGTGTTGAAGTTTCTGTTTTACTTCTGTT
1 TTGCATTTCTGTGTTGAAGTTTCTGTTTTACTTTTCAA
* *
27318 TTGCATTTCTGTGTTGAAGTTTCTGTTTTGCATTTCAA
1 TTGCATTTCTGTGTTGAAGTTTCTGTTTTACTTTTCAA
27356 TT
1 TT
27358 TTGTTTAGTG
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.14, C:0.12, G:0.17, T:0.57
Consensus pattern (38 bp):
TTGCATTTCTGTGTTGAAGTTTCTGTTTTACTTTTCAA
Found at i:27329 original size:13 final size:13
Alignment explanation
Indices: 27222--27353 Score: 76
Period size: 13 Copynumber: 10.2 Consensus size: 13
27212 TATTTTTCAA
*
27222 TTCTGTATTT-CAA
1 TTCTGT-TTTGCAT
27235 TTCTGTTTTGCAT
1 TTCTGTTTTGCAT
* *
27248 TTCTGTGTTGAAGT
1 TTCTGTTTTGCA-T
*
27262 TTCTGTTTTAC-T
1 TTCTGTTTTGCAT
***
27274 TT-TCAATTGCAT
1 TTCTGTTTTGCAT
* * *
27286 TTTTGTGTTGAAGT
1 TTCTGTTTTGCA-T
*
27300 TTCTGTTTT--AC
1 TTCTGTTTTGCAT
27311 TTCTGTTTTGCAT
1 TTCTGTTTTGCAT
* *
27324 TTCTGTGTTGAAGT
1 TTCTGTTTTGCA-T
27338 TTCTGTTTTGCAT
1 TTCTGTTTTGCAT
27351 TTC
1 TTC
27354 AATTTTGTTT
Statistics
Matches: 89, Mismatches: 22, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
11 13 0.15
12 10 0.11
13 38 0.43
14 28 0.31
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.58
Consensus pattern (13 bp):
TTCTGTTTTGCAT
Found at i:27411 original size:20 final size:21
Alignment explanation
Indices: 27362--27412 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
27352 TCAATTTTGT
*
27362 TTAGTGTTTTGCATTTTTCAA
1 TTAGTATTTTGCATTTTTCAA
*
27383 TT-CTATTTTGCATTTTTCAA
1 TTAGTATTTTGCATTTTTCAA
27403 TTAGT-TTTTG
1 TTAGTATTTTG
27413 AATTCTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.18, C:0.10, G:0.12, T:0.61
Consensus pattern (21 bp):
TTAGTATTTTGCATTTTTCAA
Done.