Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019661.1 Corchorus olitorius cultivar O-4 contig19694, 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: 17377
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Found at i:695 original size:341 final size:340
Alignment explanation
Indices: 21--1054 Score: 1396
Period size: 341 Copynumber: 3.1 Consensus size: 340
11 CCAATGTAGC
* * * * * * * * *
21 TGAGATTTGATTAAATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTA
1 TGAGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTCGGAGTCAAAAATCATGCAAAATTG
* ** * ** *
86 AGCCGGGGCCTCGGAACGCTTTTTTAGCCAAAAA----T-T-G-T-G---ATGGTTATTACACGA
66 AGGCGGTTCCTCGGAACGCATTTTTAGCCAAAAACCGTTATGGTTAGTTAATACTTAGTACACGA
* ** * * * * * ** *
140 TTTCGGCTAAAATTTTGTAAAAAAATGGGCCCGAAAGATATT-TCCTGAATTTTTTTCTAAAATA
131 TTTCGACT-AAATTTT-TGCAAAAATTGACACGAAAGAT-TTCTCATTAATTTTTGGCTAAAAAA
** * * * * *
204 CTCATAAAAATATATATTTCAACGCC-AAAAGGATTGAAGGGCTTTTGACG-TTTCTAATATCGT
193 CTCATCTAAATATATAATTCAACGCCAAAAAAGATTG--GGGCCTTTCACGCTTT-TAATATCGC
* * ** * * *
267 TTTTTTCTATTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAAC
255 ATTTCT-TATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTAGTAAAAAC
332 AAATCCTTAAATCCTATGTGGT
319 AAATCCTTAAATCCTATGTGGT
354 TGAGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTCGGAGTCAAAAATCATGCAAAATTG
1 TGAGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTCGGAGTCAAAAATCATGCAAAATTG
419 AGGCGGTTCCTCGGAACGCATTTTTAGCCAAAAACCGTTATGGTTAGTTAATACTTAGTACACGA
66 AGGCGGTTCCTCGGAACGCATTTTTAGCCAAAAACCGTTATGGTTAGTTAATACTTAGTACACGA
484 TTTCGACTAAATTTTTGCAAAAATTGACACGAAAGATTTCTCATTAATTTTTGGCTAAAAAACTC
131 TTTCGACTAAATTTTTGCAAAAATTGACACGAAAGATTTCTCATTAATTTTTGGCTAAAAAACTC
549 ATCTAAATATATAATTCAACGCCAAAAAAGATTGGGGCCTTTCACGCTTTTAATATCGCATTTCT
196 ATCTAAATATATAATTCAACGCCAAAAAAGATTGGGGCCTTTCACGCTTTTAATATCGCATTTCT
614 TATTTCTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTAGTAAAAACAAATCC
261 TATTT-TTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTAGTAAAAACAAATCC
679 TTAAATCCTATGTGGT
325 TTAAATCCTATGTGGT
* *
695 TGAGATTTGATTAGATGAATATAGATATTTCAAATAGTCTCGGAGTCAAAAATGATGCAAAATTG
1 TGAGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTCGGAGTCAAAAATCATGCAAAATTG
* *
760 AGGCGGTTCCTCGAAACGCATTTTTAGCCAAAAACCGTTATGGTTAGTTAGTACTTAGTACACGA
66 AGGCGGTTCCTCGGAACGCATTTTTAGCCAAAAACCGTTATGGTTAGTTAATACTTAGTACACGA
*
825 TTTCGACTAAATTTTTGCAAAAATTGATACGAAAGATTTCTCATTAATTTTTGGCT-AAAAACTC
131 TTTCGACTAAATTTTTGCAAAAATTGACACGAAAGATTTCTCATTAATTTTTGGCTAAAAAACTC
*
889 ATCTAAATATATAATTCAAAGCCAAAAAAGATTGGGGGCCTTTCACGCTTTTAATATCGCATTTC
196 ATCTAAATATATAATTCAACGCCAAAAAAGATT-GGGGCCTTTCACGCTTTTAATATCGCATTTC
954 TTATTTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTAGTAAAAACAAAT
260 TTA--TTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTAGTAAAAACAAAT
* * * *
1019 TCTTAAATGCAATGTGGC
323 CCTTAAATCCTATGTGGT
*
1037 TGAGATTTGGTTAGATGA
1 TGAGATTTGATTAGATGA
1055 TGTAAAGTAT
Statistics
Matches: 631, Mismatches: 52, Indels: 27
0.89 0.07 0.04
Matches are distributed among these distances:
333 86 0.14
337 1 0.00
338 1 0.00
339 1 0.00
340 46 0.07
341 310 0.49
342 148 0.23
343 19 0.03
344 19 0.03
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (340 bp):
TGAGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTCGGAGTCAAAAATCATGCAAAATTG
AGGCGGTTCCTCGGAACGCATTTTTAGCCAAAAACCGTTATGGTTAGTTAATACTTAGTACACGA
TTTCGACTAAATTTTTGCAAAAATTGACACGAAAGATTTCTCATTAATTTTTGGCTAAAAAACTC
ATCTAAATATATAATTCAACGCCAAAAAAGATTGGGGCCTTTCACGCTTTTAATATCGCATTTCT
TATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTAGTAAAAACAAATCCT
TAAATCCTATGTGGT
Found at i:1579 original size:26 final size:28
Alignment explanation
Indices: 1534--1587 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
1524 CATAATTAAT
1534 AAAAAAGTTGAATGATCTAAAAA-AATA
1 AAAAAAGTTGAATGATCTAAAAAGAATA
1561 AAAAAAGTT-AATTGA-CTAAAAAGAATA
1 AAAAAAGTTGAA-TGATCTAAAAAGAATA
1588 CTTATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.63, C:0.04, G:0.11, T:0.22
Consensus pattern (28 bp):
AAAAAAGTTGAATGATCTAAAAAGAATA
Found at i:8864 original size:5 final size:5
Alignment explanation
Indices: 8821--8867 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
8811 TGCATCCCTT
* * *
8821 CTTT- CTTTT CTTT- CTTTC CTTTT CTTTC TTTTC CTTTC CTTTC CTTT
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTT
8868 AATTACTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
4 8 0.22
5 29 0.78
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (5 bp):
CTTTC
Found at i:15167 original size:87 final size:87
Alignment explanation
Indices: 15021--15195 Score: 305
Period size: 87 Copynumber: 2.0 Consensus size: 87
15011 GTGGTTCGGG
* *
15021 TTCGAGTTCGAGTCTTCTGAATACAAAAAATTCATTGTTAGAAGAGTTTTACATCATAATAGTGA
1 TTCGAGTTCGAGTCTTCTGAATACAAAAAATTCATTATCAGAAGAGTTTTACATCATAATAGTGA
15086 ATTAACCAGACTCGAATAAGGT
66 ATTAACCAGACTCGAATAAGGT
* **
15108 TTCGAGTTCGAGTCTTCTGAATACAAAAAATTCATTATCGGAAGAGTTTTATGTCATAATAGTGA
1 TTCGAGTTCGAGTCTTCTGAATACAAAAAATTCATTATCAGAAGAGTTTTACATCATAATAGTGA
15173 ATTAACCAGACTCGAATAAGGT
66 ATTAACCAGACTCGAATAAGGT
15195 T
1 T
15196 AGCTTAAAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (87 bp):
TTCGAGTTCGAGTCTTCTGAATACAAAAAATTCATTATCAGAAGAGTTTTACATCATAATAGTGA
ATTAACCAGACTCGAATAAGGT
Found at i:15223 original size:87 final size:86
Alignment explanation
Indices: 15040--15223 Score: 203
Period size: 87 Copynumber: 2.1 Consensus size: 86
15030 GAGTCTTCTG
* *
15040 AATACAAAAAATTCATTGTTAGAAGAGTTTTACATCATAATAGTGAATTAACCAGACTCGAATAA
1 AATACAAAAAATTCATTATCAGAAGAGTTTTACATCATAATAGTGAATTAACCAGACTCGAATAA
** * * * **
15105 GGTTTCGAGTTCGAGTCTTCTG
66 GGTTTC-AGTTAAAATATACAA
* **
15127 AATACAAAAAATTCATTATCGGAAGAGTTTTATGTCATAATAGTGAATTAACCAGACTCGAATAA
1 AATACAAAAAATTCATTATCAGAAGAGTTTTACATCATAATAGTGAATTAACCAGACTCGAATAA
15192 GG-TT-AGCTTAAAAATATACAAA
66 GGTTTCAG-TT-AAAATATAC-AA
15214 AATA-AAAAAA
1 AATACAAAAAA
15224 CTGACCAACT
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
84 2 0.02
85 2 0.02
86 12 0.15
87 66 0.80
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (86 bp):
AATACAAAAAATTCATTATCAGAAGAGTTTTACATCATAATAGTGAATTAACCAGACTCGAATAA
GGTTTCAGTTAAAATATACAA
Found at i:15994 original size:25 final size:24
Alignment explanation
Indices: 15957--16006 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
15947 ATATATATAT
*
15957 ATATATATATATGTGAATT-CTTA
1 ATATATATATATGGGAATTACTTA
15980 ATATATATGACTATGGGAATTACTTA
1 ATATATAT-A-TATGGGAATTACTTA
16006 A
1 A
16007 AGGCCAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 8 0.35
24 1 0.04
25 9 0.39
26 5 0.22
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (24 bp):
ATATATATATATGGGAATTACTTA
Found at i:16173 original size:31 final size:30
Alignment explanation
Indices: 16135--16239 Score: 97
Period size: 31 Copynumber: 3.5 Consensus size: 30
16125 TTAGACTAGT
*
16135 TGCTCAAATAAGGACCTAACGCTTGTCAAAA
1 TGCTCAAATAAGGGCCTAA-GCTTGTCAAAA
* * * **
16166 TGCTCAAATAAGGGCCTGATCTT-TTAATT
1 TGCTCAAATAAGGGCCTAAGCTTGTCAAAA
* *
16195 TGGC-CAAATAAGGGCCTAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAA-GCTTGTCAAAA
16226 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
16240 TCTGGCGTCG
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
29 18 0.32
30 9 0.16
31 30 0.53
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAAGCTTGTCAAAA
Found at i:16350 original size:29 final size:28
Alignment explanation
Indices: 16317--16413 Score: 88
Period size: 28 Copynumber: 3.3 Consensus size: 28
16307 AACGTTAGAT
16317 CCTTATTTGGCCAAATTAAAAGATCGGAC
1 CCTTATTTGGCCAAATTAAAAGATCGG-C
** * * *
16346 CCTTATTTGAG-CATTTTCGATAACGTTAGGC
1 CCTTATTTG-GCCAAATT--A-AAAGATCGGC
*
16377 CCTTATTTGGCCAAATTAAAAGATCGGG
1 CCTTATTTGGCCAAATTAAAAGATCGGC
16405 CCTTATTTG
1 CCTTATTTG
16414 AGCATTTTGG
Statistics
Matches: 52, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
28 15 0.29
29 14 0.27
30 2 0.04
31 15 0.29
32 6 0.12
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (28 bp):
CCTTATTTGGCCAAATTAAAAGATCGGC
Found at i:16383 original size:31 final size:29
Alignment explanation
Indices: 16345--16448 Score: 86
Period size: 31 Copynumber: 3.5 Consensus size: 29
16335 AAAGATCGGA
*
16345 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTT-GA-AAAGTTAGG
** * *
16376 CCCTTATTTG-GCCAAATT-AAAAGATCGG
1 CCCTTATTTGAG-CATTTTGAAAAGTTAGG
* *
16404 GCCTTATTTGAGCATTTTGGCAAATGTTAGG
1 CCCTTATTTGAGCATTTT-G-AAAAGTTAGG
16435 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
16449 ATTAGCCTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
28 19 0.34
29 2 0.04
30 1 0.02
31 34 0.61
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTGAAAAGTTAGG
Found at i:16438 original size:59 final size:60
Alignment explanation
Indices: 16282--16444 Score: 231
Period size: 60 Copynumber: 2.7 Consensus size: 60
16272 ACTGACGCCA
* **
16282 GACCCTTATTTGAGCATTTTATTATAACGTTAGATCCTTATTTGGCCAAATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTA-GATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
*
16343 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTAGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* * *
16403 G-GCCTTATTTGAGCATTTTGGCA-AATGTTAGGCCCTTATTTG
1 GACCCTTATTTGAGCATTTTAG-ATAACGTTAGGCCCTTATTTG
16445 AGCAATTAGC
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
59 36 0.38
60 38 0.40
61 20 0.21
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (60 bp):
GACCCTTATTTGAGCATTTTAGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Done.