Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009269.1 Corchorus capsularis cultivar CVL-1 contig09290, 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: 17646
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:814 original size:33 final size:33
Alignment explanation
Indices: 724--814 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 33
714 CCGGTTGTGA
* * * *
724 CCGGCCATGTCCATGTCGCGTGGCCGGTGTTGG
1 CCGGACATCTCCAAGTCGCGTGGCCGATGTTGG
* * *
757 CCGGGCATCTCCGAGTCACGTGGCCGATGTTGG
1 CCGGACATCTCCAAGTCGCGTGGCCGATGTTGG
* *
790 CCGGACTTCTCCAAGTCGCATGGCC
1 CCGGACATCTCCAAGTCGCGTGGCC
815 AGTCACTAGT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.11, C:0.33, G:0.34, T:0.22
Consensus pattern (33 bp):
CCGGACATCTCCAAGTCGCGTGGCCGATGTTGG
Found at i:2346 original size:80 final size:77
Alignment explanation
Indices: 2212--2362 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 77
2202 CATCTTTTAC
* * *
2212 CTCTTTAAATCTTTTGAGAAGATCATCATTGATTTATTGAAACTTGTTGAGAAGATCATCCTTGA
1 CTCTTGAAATCTTTTGAAAAGATCATCATTGATCTATTGAAACTTGTTGAGAAGATCATCCTTGA
2277 CCCCTTTTAAAG
66 CCCCTTTTAAAG
* * *
2289 CTCTTGAAATCTTTTGAAAAGATTATCATCCTTGATCTCTTGAAATCTT-TTGAGAAGATTATCC
1 CTCTTGAAATCTTTTGAAAAG---ATCATCATTGATCTATTGAAA-CTTGTTGAGAAGATCATCC
*
2353 TTGATCCCTT
62 TTGACCCCTT
2363 GAAATCTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
77 19 0.30
80 41 0.65
81 3 0.05
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (77 bp):
CTCTTGAAATCTTTTGAAAAGATCATCATTGATCTATTGAAACTTGTTGAGAAGATCATCCTTGA
CCCCTTTTAAAG
Found at i:2358 original size:33 final size:33
Alignment explanation
Indices: 2289--2407 Score: 141
Period size: 33 Copynumber: 3.5 Consensus size: 33
2279 CCTTTTAAAG
*
2289 CTCTTGAAATCTTTTGAAAAGATTATCATCCTTGAT
1 CTCTTGAAATCTTTTGAGAAGA-T-T-ATCCTTGAT
2325 CTCTTGAAATCTTTTGAGAAGATTATCCTTGAT
1 CTCTTGAAATCTTTTGAGAAGATTATCCTTGAT
* * * *
2358 CCCTTGAAATCTTTTGAGAAGATCATCTTTTAT
1 CTCTTGAAATCTTTTGAGAAGATTATCCTTGAT
*
2391 -TCCTTGAAAACTTTTGA
1 CT-CTTGAAATCTTTTGA
2408 TTCCCTTGAA
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
33 52 0.69
34 1 0.01
35 1 0.01
36 21 0.28
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (33 bp):
CTCTTGAAATCTTTTGAGAAGATTATCCTTGAT
Found at i:2416 original size:19 final size:17
Alignment explanation
Indices: 2384--2418 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
2374 AGAAGATCAT
2384 CTTTTATTCCTTGAAAA
1 CTTTTATTCCTTGAAAA
2401 CTTTTGATTCCCTTGAAA
1 CTTTT-ATT-CCTTGAAA
2419 TCATTGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.46
Consensus pattern (17 bp):
CTTTTATTCCTTGAAAA
Found at i:3139 original size:104 final size:104
Alignment explanation
Indices: 3016--3374 Score: 523
Period size: 104 Copynumber: 3.5 Consensus size: 104
3006 ATTTTTTAGA
*
3016 AATAAAATATGAAAATAATTTCACTAAATTTAGCCCCGAATTAAAATTTTATTTTTATTTTAAGA
1 AATAAAATATGAAAATAATTTCACTAAATTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGA
3081 GTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTT
66 GTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTT
*
3120 AATAAAATATGAAAATAATTTCACTAAATTTAGCCCCGAATTAAAATTTTATTTTTATTTTAAGA
1 AATAAAATATGAAAATAATTTCACTAAATTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGA
3185 GTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTT
66 GTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTT
* * *
3224 AATAAAATA-CAAAACTAATTTCACTAAGTTTAGCCCTAAATTAAAATTTTATTTTTATTTTAAG
1 AATAAAATATGAAAA-TAATTTCACTAAATTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAG
* * * *
3288 TGTAAATTCCATAATTAATAA--TATTGTTATAGTGTTTT
65 AGTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTT
* * *
3326 AGAAATAAAATAT-ATAACTAA-TTCACTAAGTTTA-ACCCAAATTAAAATT
1 ---AATAAAATATGA-AAATAATTTCACTAAATTTAGCCCCAAATTAAAATT
3375 AAAATTTTAT
Statistics
Matches: 238, Mismatches: 11, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
102 16 0.07
103 17 0.07
104 190 0.80
105 13 0.05
106 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (104 bp):
AATAAAATATGAAAATAATTTCACTAAATTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGA
GTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTT
Found at i:9934 original size:269 final size:267
Alignment explanation
Indices: 9455--9985 Score: 855
Period size: 269 Copynumber: 2.0 Consensus size: 267
9445 GGACCAAATT
*
9455 GTACATTAACTCTGAGTAAAGCGACCAATTGGGTACTTTAACCTGCAAAACAGTAAGGGTTGAAG
1 GTACATTAACTCTGAGTAAAGCGACCAATTGGGTACTTTAACCTGCAAAACAGCAAGGGTTGAAG
* * *
9520 TCTCTGATCCTTGTCGCGCGTAGAAAGGCACCCATGTCGTGCGTGGTGAACACCTGGACAAAAAC
66 TCTCTGATCCTTGTCACGCGTAGAAAGGCACCCATGCCGTGCGTGGCGAACACCTGGACAAAAAC
* * * * *
9585 GGACTCTCTGATGCTTGCCATGCACGGGGAGCCCCACTTGCCGCGTATGGGGAGGGTCCTGAGAA
131 GGACTCTCTGATGCTTGCCATGCACAGGGAGCCCCACTTGCCACATATGGGGAAGGTCATGAGAA
*
9650 GTTGCAATTTTTAGCTGATTTTCCTAATTTTGGCAAGCTTTCTCCAAGATTCCAACTCCTAGTTA
196 ATTGCAATTTTTAGCTGATTTT-CTAATTTTGGCAAGCTTTCTCCAAGATTCC-ACTCCTAGTTA
9715 AATCTTGGA
259 AATCTTGGA
* *
9724 GTACATTACCTCTGAGTATAGCGACCAATTGGGTACTTTAACCTGCAAAACAGCAAGGGTTGAAG
1 GTACATTAACTCTGAGTAAAGCGACCAATTGGGTACTTTAACCTGCAAAACAGCAAGGGTTGAAG
* * *
9789 TCTTTGATCCTTGTCACGCGTAGAAAGGCACCCATGCCGTGCGTGGCGAGCACCTGGACAAAAAT
66 TCTCTGATCCTTGTCACGCGTAGAAAGGCACCCATGCCGTGCGTGGCGAACACCTGGACAAAAAC
9854 GGACTCTCTGATGCTTGCCATGCACAGGGAGCCCCACTTGCCACATATGGGGAAGGTCATGAGAA
131 GGACTCTCTGATGCTTGCCATGCACAGGGAGCCCCACTTGCCACATATGGGGAAGGTCATGAGAA
* *** * *
9919 ATTGCGATTTTTAGCTGATTTTCTAATTTTGGTGGGCTTTCTCCTAGATTTCACTCCTAGTTAAA
196 ATTGCAATTTTTAGCTGATTTTCTAATTTTGGCAAGCTTTCTCCAAGATTCCACTCCTAGTTAAA
9984 TC
261 TC
9986 CCATAACTTA
Statistics
Matches: 241, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
267 15 0.06
268 25 0.10
269 201 0.83
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (267 bp):
GTACATTAACTCTGAGTAAAGCGACCAATTGGGTACTTTAACCTGCAAAACAGCAAGGGTTGAAG
TCTCTGATCCTTGTCACGCGTAGAAAGGCACCCATGCCGTGCGTGGCGAACACCTGGACAAAAAC
GGACTCTCTGATGCTTGCCATGCACAGGGAGCCCCACTTGCCACATATGGGGAAGGTCATGAGAA
ATTGCAATTTTTAGCTGATTTTCTAATTTTGGCAAGCTTTCTCCAAGATTCCACTCCTAGTTAAA
TCTTGGA
Found at i:12406 original size:25 final size:25
Alignment explanation
Indices: 12376--12449 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
12366 GTTGGCAAAT
12376 TCATCAATGACAAGAAGTCAAATTA
1 TCATCAATGACAAGAAGTCAAATTA
** * *
12401 TCATC-ATG----GTTGGCATA-T-
1 TCATCAATGACAAGAAGTCAAATTA
12419 TCATCAATGACAAGAAGTCAAATTA
1 TCATCAATGACAAGAAGTCAAATTA
12444 TCATCA
1 TCATCA
12450 TAGTTGGCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
18 5 0.15
19 4 0.12
20 5 0.15
23 5 0.15
24 4 0.12
25 11 0.32
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.28
Consensus pattern (25 bp):
TCATCAATGACAAGAAGTCAAATTA
Found at i:12426 original size:43 final size:43
Alignment explanation
Indices: 12365--12457 Score: 168
Period size: 43 Copynumber: 2.2 Consensus size: 43
12355 ATGAAGATGG
12365 GGTTGGCAAATTCATCAATGACAAGAAGTCAAATTATCATCAT
1 GGTTGGCAAATTCATCAATGACAAGAAGTCAAATTATCATCAT
*
12408 GGTTGGCATATTCATCAATGACAAGAAGTCAAATTATCATCAT
1 GGTTGGCAAATTCATCAATGACAAGAAGTCAAATTATCATCAT
*
12451 AGTTGGC
1 GGTTGGC
12458 TAGATTTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (43 bp):
GGTTGGCAAATTCATCAATGACAAGAAGTCAAATTATCATCAT
Done.