Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019694.1 Corchorus olitorius cultivar O-4 contig19727, 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: 17163
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:2005 original size:9 final size:9
Alignment explanation
Indices: 1985--2038 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
1975 GTATATATTT
*
1985 TATTATAAA
1 TATTATATA
*
1994 TATTAAATA
1 TATTATATA
2003 TATT-TA-A
1 TATTATATA
*
2010 GATATATATA
1 TAT-TATATA
2020 TATTATATA
1 TATTATATA
2029 TATTATATA
1 TATTATATA
2038 T
1 T
2039 TAGTAATTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
7 3 0.08
8 2 0.05
9 29 0.78
10 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (9 bp):
TATTATATA
Found at i:4004 original size:24 final size:24
Alignment explanation
Indices: 3969--4014 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3959 CGTTGACATC
3969 CCTAACTAGAACAAAGATTAATGA
1 CCTAACTAGAACAAAGATTAATGA
*
3993 CCTAACTTGAACAAAGATTAAT
1 CCTAACTAGAACAAAGATTAAT
4015 TGTCTGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (24 bp):
CCTAACTAGAACAAAGATTAATGA
Found at i:6810 original size:18 final size:18
Alignment explanation
Indices: 6786--6827 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
6776 TATTTTCTAT
6786 CTGTTTGA-CCTCTTGGTC
1 CTGTTTGACCCT-TTGGTC
*
6804 TTGTTTGACCCTTTGGTC
1 CTGTTTGACCCTTTGGTC
6822 CTGTTT
1 CTGTTT
6828 TCTGCCTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.05, C:0.24, G:0.21, T:0.50
Consensus pattern (18 bp):
CTGTTTGACCCTTTGGTC
Found at i:6829 original size:47 final size:47
Alignment explanation
Indices: 6760--6951 Score: 230
Period size: 47 Copynumber: 4.1 Consensus size: 47
6750 AGTTTGCTCC
** * ** *
6760 GTTTGACCTTTC-GTTTTATTTTCTATCTGTTTGACCTCTTGGTCTT
1 GTTTGACCTTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTTGGTCCT
*
6806 GTTTGACCCTTT-GGTCCTGTTTTCTGCCTGTTCGACCTCTTGGTCCT
1 GTTTGA-CCTTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTTGGTCCT
* *
6853 GTTTGACCTTTCGGT-CTCGTTTTATGCCTGTTTTGACCCCTTGGTCCT
1 GTTTGACCTTTCGGTCCT-GTTTTCTGCCTG-TTTGACCTCTTGGTCCT
*
6901 GTTTGACCTTTCGGTCCTGTTTTCTGCTTGTTTGACCT-TTCGGTCCT
1 GTTTGACCTTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTT-GGTCCT
6948 GTTT
1 GTTT
6952 TTTTTTAGCC
Statistics
Matches: 126, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
46 15 0.12
47 69 0.55
48 40 0.32
49 2 0.02
ACGTcount: A:0.06, C:0.25, G:0.20, T:0.49
Consensus pattern (47 bp):
GTTTGACCTTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTTGGTCCT
Found at i:6903 original size:19 final size:19
Alignment explanation
Indices: 6879--6923 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
6869 TCGTTTTATG
6879 CCTGTTTTGACCCCTT-GGT
1 CCTGTTTTGA-CCCTTCGGT
*
6898 CCTG-TTTGACCTTTCGGT
1 CCTGTTTTGACCCTTCGGT
6916 CCTGTTTT
1 CCTGTTTT
6924 CTGCTTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 12 0.52
19 7 0.30
ACGTcount: A:0.04, C:0.29, G:0.20, T:0.47
Consensus pattern (19 bp):
CCTGTTTTGACCCTTCGGT
Found at i:11325 original size:13 final size:13
Alignment explanation
Indices: 11307--11333 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11297 AAACGGAAAA
11307 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
11320 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
11333 T
1 T
11334 TCAGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:13295 original size:16 final size:16
Alignment explanation
Indices: 13274--13304 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13264 ACACTTCCCT
13274 CACAATTGCTCGACTA
1 CACAATTGCTCGACTA
*
13290 CACAATTGCTTGACT
1 CACAATTGCTCGACT
13305 GCTCTCCACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (16 bp):
CACAATTGCTCGACTA
Found at i:14309 original size:23 final size:23
Alignment explanation
Indices: 14268--14312 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
14258 ATCAAGAGAG
*
14268 ATTACCTGAAGTTTGCCTTAGAA
1 ATTACCTGAAGCTTGCCTTAGAA
14291 ATTACCTGAAAGCTT-CCTTAGA
1 ATTACCTG-AAGCTTGCCTTAGA
14313 GATTTACTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (23 bp):
ATTACCTGAAGCTTGCCTTAGAA
Found at i:16878 original size:322 final size:318
Alignment explanation
Indices: 15952--17058 Score: 1033
Period size: 322 Copynumber: 3.4 Consensus size: 318
15942 ATGTTAGAAA
* * * * * * *
15952 TGACCC-AAAAATTTTTCCTCAA-TTTTTGGCAAAAATACTCATAAAATATTTATAATTCAACGT
1 TGACCCGAAAAGTTTTTACACAATTTTTTTGCAAAAATACTCATAAAAAATATATAATTCAACGC
* * * * * *
16015 CAAAAATATTGTAGGACTTTTCACGATTTTAATATTGTTTTTCATATTTTTTCTTGAATTAATTT
66 CAAAAATATTG-AGGGCTTTTCACGCTTCTAATATCGTTTTCCCT-TTTTTTC-TGAATTAATTT
* * *
16080 CTAATTAAATCGAAACAGATTTAGATGCAT-GTAAAAACAAATCCTTAAATTCAATGTGGCTGAG
128 CTAATTAAATCGAAAAAGATTTAGATGC-TCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAG
* * *
16144 ATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTTTATGCA--AAAAACCATGCAAAACTAAG
192 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTC-TT-TGCACCAAAAATCATGCAAAACTAAG
* ** * * *
16207 ACGAGCCCCCGAAACGCGTTTTTGCTTTTTAGCCAAAA-ATTG-TGATAACGTACATGATTTCGG
255 CCG-GGACCCGAAACGC------G-TTTTTAGCCAAAACCTTGATGATTA-GTACACGATTTCGG
*
16270 CTAAAAAT
311 CTAAAAAC
* * * * *
16278 TGACCCGAAAAGTTTTTCCTCAATTTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGC
1 TGACCCGAAAAGTTTTTACACAATTTTTTTGCAAAAATACTCATAAAAAATATATAATTCAACGC
* * * *
16343 CAAAAAAATTGAAGGG-TTTTACACGCTTCTAATATCGTTTTCCCATTTTTTC-CAATTTATTTC
66 CAAAAATATTG-AGGGCTTTT-CACGCTTCTAATATCGTTTTCCCTTTTTTTCTGAATTAATTTC
* * *
16406 TAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAGAAATCCTTAAATCCATTATGGCTGAGA
129 TAATTAAATCGAAA-AAGATTTAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGA
* *
16471 TTTGGTTAGATGAATATAGATATTTTAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTAAGCC
193 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGC-ACCAAAAATCATGCAAAACTAAGCC
* * * * * *
16535 TGGACCCCCACACGTGTTTTTAATCCAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAAC
257 GGGA-CCCGAAACGCGTTTTT-AGCCAAAACCTTGATGATTAGTACACGATTTCGGCTAAAAAC
* * * *
16599 TGACCCGAAAAGTTTTTACACAATTTTTTTTG-AAAAATATTCATAAAAAATGTAAAATTCAATG
1 TGACCCGAAAAGTTTTTACACAA-TTTTTTTGCAAAAATACTCATAAAAAATATATAATTCAACG
*
16663 CCAAAAATGATTGACGGGCTTTTTACGCTTCTAATATCGTTTTCCCTTTTTTTCTGAATTAATTT
65 CCAAAAAT-ATTGA-GGGCTTTTCACGCTTCTAATATCGTTTTCCCTTTTTTTCTGAATTAATTT
* *
16728 CTAATTAAATCGAAATAAGATTCAGATGCTCG-AAAAAAAAATCCTTATATCCAATGTGGCTGAG
128 CTAATTAAATCGAAA-AAGATTTAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAG
** * * * *
16792 ATTTGGTTCTATTAATATAGATATTTCAAGAAGTCTTTGCACCAAAAATCATGCAAAATTGAGCC
192 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGCAAAACTAAGCC
* * * *
16857 GGGTCTCCGGAACGCGTTTTTAGCCAAAAACCTTGATGGTTAGTACGCGATTTCGACTAAAATTT
257 GGGAC-CCGAAACGCGTTTTTAGCC-AAAACCTTGATGATTAGTACACGATTTCG----------
*
16922 TGCAAAAAAC
310 -GCTAAAAAC
** * * * * * * *
16932 TGACATGAAAATTTTTTCCTCAA-TTTTTTACCATAATACTCA-AAAAAATATATAATCCAACGC
1 TGACCCGAAAAGTTTTTACACAATTTTTTTGCAAAAATACTCATAAAAAATATATAATTCAACGC
* * *
16995 CAAAAA-ATTTGAAGGGTTTTTCACGCTTC-AAGTATCGTTTTTCCC-TTTTTTCCGAATTTATT
66 CAAAAATA-TTG-AGGGCTTTTCACGCTTCTAA-TATCG-TTTTCCCTTTTTTTCTGAATTAATT
17057 TC
127 TC
17059 AGATGCTCGT
Statistics
Matches: 647, Mismatches: 98, Indels: 68
0.80 0.12 0.08
Matches are distributed among these distances:
319 5 0.01
320 8 0.01
321 80 0.12
322 171 0.26
323 44 0.07
324 1 0.00
325 27 0.04
326 107 0.17
327 26 0.04
328 65 0.10
329 3 0.00
330 39 0.06
331 37 0.06
332 8 0.01
333 26 0.04
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (318 bp):
TGACCCGAAAAGTTTTTACACAATTTTTTTGCAAAAATACTCATAAAAAATATATAATTCAACGC
CAAAAATATTGAGGGCTTTTCACGCTTCTAATATCGTTTTCCCTTTTTTTCTGAATTAATTTCTA
ATTAAATCGAAAAAGATTTAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTT
GGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGCAAAACTAAGCCGGGA
CCCGAAACGCGTTTTTAGCCAAAACCTTGATGATTAGTACACGATTTCGGCTAAAAAC
Done.