Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019406.1 Corchorus olitorius cultivar O-4 contig19439, 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: 21221
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:7317 original size:332 final size:329
Alignment explanation
Indices: 6324--7555 Score: 1054
Period size: 330 Copynumber: 3.7 Consensus size: 329
6314 CCATGATGGT
* * * *
6324 AAAAA-TGATCCGAAAGATTTTTGCTCAATTTT-TTGTAAAAAATACTCATAAAATATATATAAT
1 AAAAATTGACCCGAAAGATTTTTTCTCAATTTTATGGT--AAAATACTCATAAAAAATATATAAT
* ** * * **
6387 TCAACGCCAAAAAAATTGTAGAACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTCTGAA
64 TCAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCAAA
* * * * * * * *
6451 TTAATTTCT-ATTAATTCGAAACAAAATTAATTCAAATACACGTAAAAATAAATCTTTAAATCCA
129 TTAATTTATAATTAAATCGAAACAAGATT-A---AGATGCTCGTAAAAACAAATCCTTAAATCCA
* * * * * * **
6515 ATGTGGCTGAGATTTGATTAGATGAATAAAGATAT--TTCAAAGAGT-TTCGGCGTCAAAAACCA
190 ATGT-GCTGAAATTTGGTTAAATGAAT-AAGATATACTTCAAGGAGTCTT-AGC-ACAAAAAATA
** * ** * ** *
6577 TGTAAATC-AGAGCCATAGCCTCGGAACGCGTTTTTACTTTTTAGCCAAAAAAAAAACCGTGATG
251 TACAAAACTA-AG-CGGAGCCTCGAAACGC------A--TTTT-G---AACCAAAAACCATGATG
*
6641 GTTAGTACACGATTTCGGCTAAAATTTTAC
302 G-T-GTACACGATTTCGGCTAAAATTTTGC
* * *
6671 AAAAAATGACCCGAAAGA-TATCTCATCAATTTT-TGGTTAAAATACTCATAAAAAATATATAAT
1 AAAAATTGACCCGAAAGATTTTTTC-TCAATTTTATGG-TAAAATACTCATAAAAAATATATAAT
* ** * * * * * *
6734 TCGACATCAGAAAGATTGAAGGGCTTTTAATGCTTCTAATATTGTTTTTCCT-TTTTTTTCCGAA
64 TCAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCAAA
*
6798 TTAATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
129 TTAATTTATAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * *
6863 AGTTGAGATTTGGTTAAATGAAT-ATATATACTTCAAGGAGTCTTGGCACAAAAAATATACAAAA
194 -GCTGAAATTTGGTTAAATGAATAAGATATACTTCAAGGAGTCTTAGCACAAAAAATATACAAAA
* * * * *
6927 CTAAGCTGAGCCTCGAAACGCATTTTGAGCCGAAAACCGTGATGGTTAGTATACGATTTCGGCT-
258 CTAAGCGGAGCCTCGAAACGCATTTTGAACCAAAAACCATGATGG-T-GTACACGATTTCGGCTA
6991 AAATTTTGC
321 AAATTTTGC
* * *
7000 AAAAATTGACCCGAAAGATTTTTTCTCAATTTCTATCG-AAAATACTCAT-TAAAATATATAGTT
1 AAAAATTGACCCGAAAGATTTTTTCTCAATTT-TATGGTAAAATACTCATAAAAAATATATAATT
* *
7063 CAACGCCAAAAAAATTGAAAGTCTTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTATTTCCA
65 CAACGCCAAAAAAATTGAAGGGC--TTTTCACGCTTCTAATATCGTTTTTCCTATTTT-TTTCCA
* * * * *
7128 AATTAATTTTTGATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAATCCTTAAATACAAT
127 AATTAATTTATAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * *
7193 GTGCCTGAAATTTGGTTAGATGAATAAAGATATATTTTAAGGAGTCTTAGCGCAAAAAATCATGC
192 GTG-CTGAAATTTGGTTAAATGAAT-AAGATATACTTCAAGGAGTCTTAGCACAAAAAAT-ATAC
* ** *
7258 AAAACTGACA-CGG-GACC-CGGAACGTGTTTTTAACCAAAAACCCATGAT-G-GTACACGATTT
254 AAAACT-A-AGCGGAG-CCTCGAAACGCATTTTGAACCAAAAA-CCATGATGGTGTACACGATTT
*
7318 CGGCTAAAATTTTGT
315 CGGCTAAAATTTTGC
* * * *
7333 AAAAATTGACCCAAAATATTTTTT-TCAATTTT-TAGGCACAATACTCATAAAAAATATATAATT
1 AAAAATTGACCCGAAAGATTTTTTCTCAATTTTAT-GGTAAAATACTCATAAAAAATATATAATT
*
7396 CAACGCCAAAAAAATTGAAGGGCTTCTCACGCTTCTAATATCGTTTTTCCTATTTTTTT-CAAAT
65 CAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCAAAT
* * * * *
7460 TAATTTCTAATTAAATCGAAACATGATTCAAAATGCTCGCAAGAACAAATCCTTAAATCCAATGT
130 TAATTTATAATTAAATCGAAACAAGATT-AAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* *
7525 GACT-AAGATTTGTTTATATGAATATAGATAT
194 G-CTGAA-ATTTGGTTAAATGAATA-AGATAT
7556 TACAAGGATT
Statistics
Matches: 742, Mismatches: 112, Indels: 79
0.80 0.12 0.08
Matches are distributed among these distances:
328 28 0.04
329 76 0.10
330 119 0.16
331 41 0.06
332 117 0.16
333 64 0.09
334 32 0.04
335 28 0.04
336 12 0.02
337 1 0.00
342 18 0.02
343 14 0.02
344 62 0.08
345 2 0.00
347 89 0.12
348 38 0.05
349 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (329 bp):
AAAAATTGACCCGAAAGATTTTTTCTCAATTTTATGGTAAAATACTCATAAAAAATATATAATTC
AACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCAAATT
AATTTATAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGC
TGAAATTTGGTTAAATGAATAAGATATACTTCAAGGAGTCTTAGCACAAAAAATATACAAAACTA
AGCGGAGCCTCGAAACGCATTTTGAACCAAAAACCATGATGGTGTACACGATTTCGGCTAAAATT
TTGC
Found at i:10546 original size:17 final size:18
Alignment explanation
Indices: 10524--10558 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10514 CAGAGTGATA
10524 TATATA-TTTGAAAAAAT
1 TATATAGTTTGAAAAAAT
10541 TATATAGTTTGAAAAAAT
1 TATATAGTTTGAAAAAAT
10559 AGGGTTCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
TATATAGTTTGAAAAAAT
Found at i:11161 original size:31 final size:29
Alignment explanation
Indices: 11115--11193 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
11105 AAAGAGTACA
* *
11115 ATTTTCCCCCTTGAACTTGTAGCGGTTGGAC
1 ATTTTGCCCCTTGAACTT-TA-AGGTTGGAC
* **
11146 ATTTTGCCCCATGAACTTTAATTTTGGAC
1 ATTTTGCCCCTTGAACTTTAAGGTTGGAC
11175 ATTTTGCCCCTTTGAACTT
1 ATTTTGCCCC-TTGAACTT
11194 CAATTTTGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.39
30 9 0.22
31 16 0.39
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (29 bp):
ATTTTGCCCCTTGAACTTTAAGGTTGGAC
Found at i:11180 original size:29 final size:30
Alignment explanation
Indices: 11140--11215 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
11130 CTTGTAGCGG
*
11140 TTGGACATTTTGCCCC-ATGAACTTTAATT
1 TTGGACATTTTGCCCCTATGAACTTCAATT
*
11169 TTGGACATTTTGCCCCTTTGAACTTCAATT
1 TTGGACATTTTGCCCCTATGAACTTCAATT
*
11199 TTGGGACGTTTTGCCCC
1 TT-GGACATTTTGCCCC
11216 CTCAGGTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
29 16 0.38
30 13 0.31
31 13 0.31
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (30 bp):
TTGGACATTTTGCCCCTATGAACTTCAATT
Found at i:11361 original size:29 final size:30
Alignment explanation
Indices: 11315--11383 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
11305 CGTTAGTCTG
*
11315 AGGGGGCAAAACGTTCCAAAATTAAAGTTC
1 AGGGGGTAAAACGTTCCAAAATTAAAGTTC
* *
11345 AGGGGGTAAAATG-TCCAAAATTGAAGTTC
1 AGGGGGTAAAACGTTCCAAAATTAAAGTTC
* *
11374 AAGGGATAAA
1 AGGGGGTAAA
11384 CATCCAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (30 bp):
AGGGGGTAAAACGTTCCAAAATTAAAGTTC
Found at i:14817 original size:23 final size:23
Alignment explanation
Indices: 14788--14831 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
14778 ACAGATGTGT
14788 GCAGATACTGCATCATTAGTCAA
1 GCAGATACTGCATCATTAGTCAA
14811 GCAGATACTGCATCATTAGTC
1 GCAGATACTGCATCATTAGTC
14832 TGCATTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (23 bp):
GCAGATACTGCATCATTAGTCAA
Found at i:19434 original size:43 final size:43
Alignment explanation
Indices: 19373--19479 Score: 169
Period size: 43 Copynumber: 2.5 Consensus size: 43
19363 TGGCTTTAAG
*
19373 ATATTGCGTCTCTTCTCACTCCCGCATCAAGACTGTTTTGGTT
1 ATATTGCATCTCTTCTCACTCCCGCATCAAGACTGTTTTGGTT
*
19416 ATATTGCATCTCTTCTCACTCGCGCATCAAGACTGTTTTGGTT
1 ATATTGCATCTCTTCTCACTCCCGCATCAAGACTGTTTTGGTT
* * *
19459 ATGTCGCATCTCTTTTCACTC
1 ATATTGCATCTCTTCTCACTC
19480 ATGCAGCTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.17, C:0.28, G:0.15, T:0.40
Consensus pattern (43 bp):
ATATTGCATCTCTTCTCACTCCCGCATCAAGACTGTTTTGGTT
Found at i:20157 original size:121 final size:122
Alignment explanation
Indices: 19932--20172 Score: 324
Period size: 121 Copynumber: 2.0 Consensus size: 122
19922 CATTGCATTG
* * * * *
19932 ATTTGCTTGCTGTGATTTTCCTTTTTCTGCGATGATGGTTTCTTGATAGTGTTTCTTCTCATCTG
1 ATTTGCTTGCTGTGAGTTTCCCTTTTCTGCGATAATGGTTTCTGGATAATGTTTCTTCTCATCTG
* ** *
19997 CAGTTGTCTTCCCATTGGAGCTGAGTTTATCCCTGTGGCAGCTAGGATTGCCTTCAA
66 CAGTTGTCTTCACATTGGAGCTGAGCATATCCCTGTGGCAGCAAGGATTGCCTTCAA
*** *
20054 ATTTGCTTGCTGTGAGTTTCCCTTTTCTGTTTTAATGGTTTCTGGATAATGTTT-TTCTCCTCTG
1 ATTTGCTTGCTGTGAGTTTCCCTTTTCTGCGATAATGGTTTCTGGATAATGTTTCTTCTCATCTG
* *
20118 CAGTTGTC-TCTACGTTGGAGCTGAGCATATCCTTGTGGCAGCAAGGATTGCCTTC
66 CAGTTGTCTTC-ACATTGGAGCTGAGCATATCCCTGTGGCAGCAAGGATTGCCTTC
20173 CTGTTTTGAC
Statistics
Matches: 103, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
120 2 0.02
121 55 0.53
122 46 0.45
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (122 bp):
ATTTGCTTGCTGTGAGTTTCCCTTTTCTGCGATAATGGTTTCTGGATAATGTTTCTTCTCATCTG
CAGTTGTCTTCACATTGGAGCTGAGCATATCCCTGTGGCAGCAAGGATTGCCTTCAA
Found at i:20544 original size:81 final size:81
Alignment explanation
Indices: 20237--20610 Score: 597
Period size: 81 Copynumber: 4.6 Consensus size: 81
20227 ATTGAGGGCC
20237 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATTAAGGCAAGTTCAAT
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAA-TAAGGCAAGTTCAAT
*
20302 GTGAATTGGGAAAGTTG
65 GTCAATTGGGAAAGTTG
20319 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
*
20384 TGAATTGGGAAAGTTG
66 TCAATTGGGAAAGTTG
*
20400 AATGTGAA-TAAGGCAAGTTCAATGTGAATTAGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
* *
20464 TCATTTGGGAAATTTG
66 TCAATTGGGAAAGTTG
* * * *
20480 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGTGATTAAGGCAAGTTCAATG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
* *
20545 TCAATTGGAAAATTTG
66 TCAATTGGGAAAGTTG
* * **
20561 AATGTGAATGAAGGCAAGTTCAATGTCAATTGGGAAAGTTTTATGTGAAT
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAAT
20611 GCGCTGCGTA
Statistics
Matches: 275, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
80 76 0.28
81 150 0.55
82 49 0.18
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.30
Consensus pattern (81 bp):
AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
TCAATTGGGAAAGTTG
Found at i:20611 original size:41 final size:41
Alignment explanation
Indices: 20237--20610 Score: 594
Period size: 41 Copynumber: 9.2 Consensus size: 41
20227 ATTGAGGGCC
20237 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
20278 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
20319 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
20360 AATGTGAA-TAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
*
20400 AATGTGAA-TAAGGCAAGTTCAATGTGAATTAGGAAAGTTG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
* * *
20440 AATGTGAA-TAAGGCAAGTTCAATGTCATTTGGGAAATTTG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
* * *
20480 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
* * *
20521 AATGTG-ATTAAGGCAAGTTCAATGTCAATTGGAAAATTTG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
* * *
20561 AATGTGAATGAAGGCAAGTTCAATGTCAATTGGGAAAGTTT
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
*
20602 TATGTGAAT
1 AATGTGAAT
20611 GCGCTGCGTA
Statistics
Matches: 313, Mismatches: 18, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
40 151 0.48
41 162 0.52
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.30
Consensus pattern (41 bp):
AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
Done.