Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015692.1 Corchorus olitorius cultivar O-4 contig15725, 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: 37753
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:273 original size:22 final size:22
Alignment explanation
Indices: 248--289 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
238 AAAGCTTCAA
* *
248 TGATTGTTCTAAAAAGTATAAG
1 TGATTATTCTAAAAACTATAAG
*
270 TGATTATTTTAAAAACTATA
1 TGATTATTCTAAAAACTATA
290 TTATTATCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (22 bp):
TGATTATTCTAAAAACTATAAG
Found at i:1704 original size:18 final size:17
Alignment explanation
Indices: 1675--1723 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
1665 GTAGTGATCA
1675 TATAACTAATAATAATTGT
1 TATAA-TAATAATAA-TGT
1694 TATAATAATAATAA-GT
1 TATAATAATAATAATGT
*
1710 T-TAATAATTATAAT
1 TATAATAATAATAAT
1724 AAGAAGATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
18 9 0.32
19 5 0.18
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (17 bp):
TATAATAATAATAATGT
Found at i:2024 original size:6 final size:6
Alignment explanation
Indices: 2006--2035 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1996 GTTTAGACTT
2006 ATATAG TATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATA
2036 TATAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:2030 original size:12 final size:13
Alignment explanation
Indices: 2006--2039 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1996 GTTTAGACTT
2006 ATATAGTATATAG
1 ATATAGTATATAG
2019 ATATAG-ATATAG
1 ATATAGTATATAG
2031 ATATA-TATA
1 ATATAGTATA
2040 ATTAATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (13 bp):
ATATAGTATATAG
Found at i:2183 original size:2 final size:2
Alignment explanation
Indices: 2176--2202 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2166 CATACTCTTT
2176 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2203 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10882 original size:3 final size:3
Alignment explanation
Indices: 10876--10901 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10866 TGAAACAACA
10876 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
10902 CGCGCGCCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:25876 original size:286 final size:274
Alignment explanation
Indices: 25376--25901 Score: 690
Period size: 286 Copynumber: 1.9 Consensus size: 274
25366 TGGAAAAAAA
*
25376 GGAATGATTCTTGATCATTGTCTTTCAATAACTTGAAAAAGAAAAAAGAATATTTGTTGTCACAG
1 GGAATGATTCTTCATCATTGTCTTTCAATAACTTGAAAAAGAAAAAAGAATATTTGTTGTCACAG
*
25441 TTGAAATATTATTGCTTGTCTTCGTAATTTATAACTTGACAAGTTTTCCTTGTCAAATCTTGATA
66 TTGAAATATTATTGCTTGTCTTCGTAATTTATAACTTGAAAAGTTTTCCTTGTCAAATCTTGATA
* * *
25506 AAAGCACATTTGGGGTTGTATTGTATATTCCTTGTTCAATGGGTCAAGAATATTTGGAAGAAAAG
131 AAAGCACATTTGGGG-TG-ATTGTATATTCCTTATGCAATAGGTCAAGAATATTTGGAAGAAAAG
25571 ATTAATGATTATGCACAGA-C-AATGCCTCTATGAATATCATACCAACAAGGTAAAACTTTGAAG
194 ATTAATGATTATGCACAGACCAAATGCCTCTATGAATATCATACCAACAAGGTAAAACTTTGAAG
25634 TTCTTTAATGAGTTGG
259 TTCTTTAATGAGTTGG
* * *
25650 GGAATGATTCTTCATCATTTTCTTTCAATAACTTGAAAAAG-GATAAGAATATGTGTTGTCAGTG
1 GGAATGATTCTTCATCATTGTCTTTCAATAACTTGAAAAAGAAAAAAGAATA--T-TTGT---TG
25714 TCACATAGTTTGAAATATTATATATTGCTTGTCTTCGTAAATATTTATAACTTGAAAAGTTTT-C
60 TCAC--AG-TTG-AA-A-TAT-TATTGCTTGTCTTCGT--A-ATTTATAACTTGAAAAGTTTTCC
25778 TATGTC-AATCTTGATGAAAAGCACATATAT-GGG-G-TTGTATATTCCTTATGCAATAGGTCAA
115 T-TGTCAAATCTTGAT-AAAAGCACAT-T-TGGGGTGATTGTATATTCCTTATGCAATAGGTCAA
* *
25839 GAATATTTGGAGGAAAAGATTAATGATTATGCACAGACCAATAATGTCTCTATGAATATCATA
176 GAATATTTGGAAGAAAAGATTAATGATTATGCACAGACC-A-AATGCCTCTATGAATATCATA
25902 TATATCAAGG
Statistics
Matches: 218, Mismatches: 10, Indels: 32
0.84 0.04 0.12
Matches are distributed among these distances:
273 8 0.04
274 39 0.18
275 1 0.00
276 4 0.02
279 6 0.03
281 2 0.01
282 3 0.01
283 2 0.01
284 1 0.00
285 3 0.01
286 76 0.35
287 1 0.00
288 13 0.06
289 34 0.16
290 24 0.11
291 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (274 bp):
GGAATGATTCTTCATCATTGTCTTTCAATAACTTGAAAAAGAAAAAAGAATATTTGTTGTCACAG
TTGAAATATTATTGCTTGTCTTCGTAATTTATAACTTGAAAAGTTTTCCTTGTCAAATCTTGATA
AAAGCACATTTGGGGTGATTGTATATTCCTTATGCAATAGGTCAAGAATATTTGGAAGAAAAGAT
TAATGATTATGCACAGACCAAATGCCTCTATGAATATCATACCAACAAGGTAAAACTTTGAAGTT
CTTTAATGAGTTGG
Found at i:31694 original size:18 final size:18
Alignment explanation
Indices: 31673--31731 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
31663 TTCACCCAAT
31673 TCCTCTTTGTCAATATCC
1 TCCTCTTTGTCAATATCC
* *
31691 TCCTCTTCT-TCACTCAT-T
1 TCCTCTT-TGTCAAT-ATCC
*
31709 TCCTCTATGTCAATATCC
1 TCCTCTTTGTCAATATCC
31727 TCCTC
1 TCCTC
31732 CTCTTCACTC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
17 3 0.09
18 26 0.81
19 3 0.09
ACGTcount: A:0.15, C:0.37, G:0.03, T:0.44
Consensus pattern (18 bp):
TCCTCTTTGTCAATATCC
Found at i:31749 original size:36 final size:36
Alignment explanation
Indices: 31617--31739 Score: 201
Period size: 36 Copynumber: 3.4 Consensus size: 36
31607 GACCTCCTTA
*
31617 CCTCCTCTTCTTCACCCAATTCCTTTTTGTCAATAT
1 CCTCCTCTTCTTCACCCAATTCCTCTTTGTCAATAT
31653 CCTCCTCTTCTTCACCCAATTCCTCTTTGTCAATAT
1 CCTCCTCTTCTTCACCCAATTCCTCTTTGTCAATAT
* * *
31689 CCTCCTCTTCTTCACTCATTTCCTCTATGTCAATAT
1 CCTCCTCTTCTTCACCCAATTCCTCTTTGTCAATAT
*
31725 CCTCCTCCTCTTCAC
1 CCTCCTCTTCTTCAC
31740 TCTCTTCCTC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.15, C:0.40, G:0.02, T:0.42
Consensus pattern (36 bp):
CCTCCTCTTCTTCACCCAATTCCTCTTTGTCAATAT
Found at i:31760 original size:15 final size:15
Alignment explanation
Indices: 31727--31791 Score: 57
Period size: 15 Copynumber: 4.3 Consensus size: 15
31717 GTCAATATCC
31727 TCCTCCTCTTCACTCTCT
1 TCCTCCTCTT--CT-TCT
31745 TCCTCCTCTTCTTCT
1 TCCTCCTCTTCTTCT
*
31760 TCACT-ATCTTC--C-
1 TC-CTCCTCTTCTTCT
31772 TCCTCCTCTTCTTCT
1 TCCTCCTCTTCTTCT
31787 TCCTC
1 TCCTC
31792 TTCACTATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
11 2 0.05
12 7 0.17
13 1 0.03
14 1 0.03
15 15 0.38
16 4 0.10
18 10 0.25
ACGTcount: A:0.05, C:0.48, G:0.00, T:0.48
Consensus pattern (15 bp):
TCCTCCTCTTCTTCT
Found at i:31760 original size:24 final size:24
Alignment explanation
Indices: 31724--31785 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
31714 TATGTCAATA
* *
31724 TCCTCCTCCTCTTCACTCTCTTCC
1 TCCTCCTCTTCTTCACTATCTTCC
*
31748 TCCTCTTCTTCTTCACTATCTTCC
1 TCCTCCTCTTCTTCACTATCTTCC
31772 TCCTCCTCTTCTTC
1 TCCTCCTCTTCTTC
31786 TTCCTCTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.05, C:0.48, G:0.00, T:0.47
Consensus pattern (24 bp):
TCCTCCTCTTCTTCACTATCTTCC
Found at i:31794 original size:24 final size:26
Alignment explanation
Indices: 31724--31788 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
31714 TATGTCAATA
* * *
31724 TCCTCCTCCTCTTCAC-TC-TCTTCC
1 TCCTCTTCTTCTTCACATCTTCCTCC
31748 TCCTCTTCTTCTTCACTATCTTCCTCC
1 TCCTCTTCTTCTTCAC-ATCTTCCTCC
31775 TCCTCTTCTTCTTC
1 TCCTCTTCTTCTTC
31789 CTCTTCACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.40
26 2 0.06
27 19 0.54
ACGTcount: A:0.05, C:0.48, G:0.00, T:0.48
Consensus pattern (26 bp):
TCCTCTTCTTCTTCACATCTTCCTCC
Found at i:34950 original size:36 final size:36
Alignment explanation
Indices: 34904--34987 Score: 168
Period size: 36 Copynumber: 2.3 Consensus size: 36
34894 TTAACTATGC
34904 AAAAACAGAGTACCCTGCTTCTGATAAAAACAGAGA
1 AAAAACAGAGTACCCTGCTTCTGATAAAAACAGAGA
34940 AAAAACAGAGTACCCTGCTTCTGATAAAAACAGAGA
1 AAAAACAGAGTACCCTGCTTCTGATAAAAACAGAGA
34976 AAAAACAGAGTA
1 AAAAACAGAGTA
34988 GGATGTTAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.50, C:0.18, G:0.17, T:0.15
Consensus pattern (36 bp):
AAAAACAGAGTACCCTGCTTCTGATAAAAACAGAGA
Found at i:37314 original size:31 final size:31
Alignment explanation
Indices: 37279--37339 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
37269 AAATCGGTAC
37279 AATAATGGAAATTGTTATAACATGTGACGGT
1 AATAATGGAAATTGTTATAACATGTGACGGT
37310 AATAATGGAAATTGTTATAACATGTGACGG
1 AATAATGGAAATTGTTATAACATGTGACGG
37340 CAAATTAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (31 bp):
AATAATGGAAATTGTTATAACATGTGACGGT
Found at i:37392 original size:20 final size:21
Alignment explanation
Indices: 37367--37428 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 21
37357 TTAATGGGTA
37367 TTACTAAAT-ACCGCCCCCTT
1 TTACTAAATCACCGCCCCCTT
*
37387 TTACT-AGTCACCGCCCCCTT
1 TTACTAAATCACCGCCCCCTT
* *
37407 TTACT-AGTCACCGCTCCCTT
1 TTACTAAATCACCGCCCCCTT
37427 TT
1 TT
37429 GGACTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 2 0.05
20 37 0.95
ACGTcount: A:0.18, C:0.40, G:0.08, T:0.34
Consensus pattern (21 bp):
TTACTAAATCACCGCCCCCTT
Done.