Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015732.1 Corchorus olitorius cultivar O-4 contig15765, 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: 44481
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:10674 original size:24 final size:24
Alignment explanation
Indices: 10646--10732 Score: 73
Period size: 24 Copynumber: 4.0 Consensus size: 24
10636 ATTAAAGTGC
*
10646 AACATATTTCATGTCCAACATAAA
1 AACATAATTCATGTCCAACATAAA
**
10670 AAC---A-TCAT-T-CAA-ATGCA
1 AACATAATTCATGTCCAACATAAA
10687 A-CATAATTCATGTCCAACATAAA
1 AACATAATTCATGTCCAACATAAA
* *
10710 AACATAATTCAAGTTCAACATAA
1 AACATAATTCATGTCCAACATAA
10733 TTTACACCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 16
0.68 0.10 0.23
Matches are distributed among these distances:
16 1 0.02
17 4 0.08
18 3 0.06
19 2 0.04
20 8 0.17
21 1 0.02
22 3 0.06
23 4 0.08
24 22 0.46
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (24 bp):
AACATAATTCATGTCCAACATAAA
Found at i:10697 original size:40 final size:40
Alignment explanation
Indices: 10606--10734 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 40
10596 TAATAAAGTT
* **
10606 CAACATAATTCATGTCCAACAT-GATTCATAATT-AAAGTG
1 CAACATAATTCATGTCCAACATAAAAACATAATTCAAA-TG
* *
10645 CAACATATTTCATGTCCAACATAAAAACATCATTCAAATG
1 CAACATAATTCATGTCCAACATAAAAACATAATTCAAATG
* *
10685 CAACATAATTCATGTCCAACATAAAAACATAATTCAAGTT
1 CAACATAATTCATGTCCAACATAAAAACATAATTCAAATG
10725 CAACATAATT
1 CAACATAATT
10735 TACACCAAAC
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 21 0.27
40 55 0.70
41 3 0.04
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (40 bp):
CAACATAATTCATGTCCAACATAAAAACATAATTCAAATG
Found at i:16286 original size:12 final size:12
Alignment explanation
Indices: 16265--16298 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16255 TTTAAATCCT
16265 AAAAAGAAAACG
1 AAAAAGAAAACG
* *
16277 AAAAATAAAACT
1 AAAAAGAAAACG
16289 AAAAAGAAAA
1 AAAAAGAAAA
16299 TTAACATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAACG
Found at i:18314 original size:26 final size:25
Alignment explanation
Indices: 18290--18389 Score: 105
Period size: 27 Copynumber: 3.9 Consensus size: 25
18280 AATAAAGAAA
*
18290 TTTTTTTTTTCAAAAACACAGAGAAAAC
1 TTTTTTTTTTCAAAAACGC--A-AAAAC
*
18318 TTTTTTTTTT--ATAACGCAAAAAC
1 TTTTTTTTTTCAAAAACGCAAAAAC
* *
18341 TTTTTTTTTTCGAAAACGCAAAACC
1 TTTTTTTTTTCAAAAACGCAAAAAC
18366 GATTTTTTTTTTCAAAAACGCAAA
1 --TTTTTTTTTTCAAAAACGCAAA
18390 CACAAAGCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
23 15 0.24
24 1 0.02
25 11 0.17
26 5 0.08
27 21 0.33
28 10 0.16
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (25 bp):
TTTTTTTTTTCAAAAACGCAAAAAC
Found at i:18645 original size:30 final size:31
Alignment explanation
Indices: 18601--18674 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
18591 CCGTACAGGT
18601 CCCTCTACTTACAAAAAAGGATCAATTTGGTC
1 CCCTCTACTTACAAAAAAGG-TCAATTTGGTC
**
18633 CCCT-TAC-TACAAAAACTGTCAATTTGGT-
1 CCCTCTACTTACAAAAAAGGTCAATTTGGTC
18661 CCCTCTACTTACAA
1 CCCTCTACTTACAA
18675 TTTGGTGTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 4 0.11
29 13 0.34
30 14 0.37
31 3 0.08
32 4 0.11
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.30
Consensus pattern (31 bp):
CCCTCTACTTACAAAAAAGGTCAATTTGGTC
Found at i:18669 original size:29 final size:31
Alignment explanation
Indices: 18598--18674 Score: 106
Period size: 29 Copynumber: 2.5 Consensus size: 31
18588 ATACCGTACA
18598 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTACTTACAAAAAAGGATCAATTT
**
18629 GGTCCC-CTTAC-TACAAAAACTG-TCAATTT
1 GGTCCCTC-TACTTACAAAAAAGGATCAATTT
18658 GGTCCCTCTACTTACAA
1 GGTCCCTCTACTTACAA
18675 TTTGGTGTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 16 0.39
30 16 0.39
31 9 0.22
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (31 bp):
GGTCCCTCTACTTACAAAAAAGGATCAATTT
Found at i:19040 original size:31 final size:30
Alignment explanation
Indices: 18972--19042 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
18962 ACCAAATTGC
*
18972 AAGTAGAGGGATCAAATTGACAGTTTTTAT
1 AAGTAGAGGGACCAAATTGACAGTTTTTAT
** *
19002 -AGTAGAGGGACCAAATTGATCCTTTTTTGT
1 AAGTAGAGGGACCAAATTGA-CAGTTTTTAT
19032 AAGTAGAGGGA
1 AAGTAGAGGGA
19043 TCTGTACGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.51
30 7 0.20
31 10 0.29
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.31
Consensus pattern (30 bp):
AAGTAGAGGGACCAAATTGACAGTTTTTAT
Found at i:22103 original size:2 final size:2
Alignment explanation
Indices: 22096--22164 Score: 63
Period size: 2 Copynumber: 35.5 Consensus size: 2
22086 CGTTTATGTA
*
22096 AT AT AT AT AT AT AT AT A- AT AT AT CAT AT AT AT TT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
* * * *
22137 -T CT TT AT AT AT AT AA AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22165 ATAATTTATA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
1 3 0.05
2 50 0.91
3 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:22145 original size:22 final size:22
Alignment explanation
Indices: 22097--22164 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 22
22087 GTTTATGTAA
22097 TATATATATATATATAATATAT
1 TATATATATATATATAATATAT
* * *
22119 CATATATATTTATATAAT-TCT
1 TATATATATATATATAATATAT
*
22140 T-TATATATATAAAT-ATATAT
1 TATATATATATATATAATATAT
22160 T-TATA
1 TATATA
22165 ATAATTTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.05
20 18 0.47
21 2 0.05
22 16 0.42
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATATATATATATAATATAT
Found at i:22174 original size:18 final size:18
Alignment explanation
Indices: 22094--22185 Score: 68
Period size: 16 Copynumber: 5.3 Consensus size: 18
22084 ACCGTTTATG
*
22094 TAAT-ATATATATATATA
1 TAATAATATATATATTTA
22111 TAATATATCATATATATTTA
1 TAATA-AT-ATATATATTTA
* * *
22131 T-ATAAT-TCTTTATATA
1 TAATAATATATATATTTA
22147 T-ATAA-ATATATATTTA
1 TAATAATATATATATTTA
* *
22163 TAATAATTTATAAATTTA
1 TAATAATATATATATTTA
*
22181 AAATA
1 TAATA
22186 CTGAAAATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
16 20 0.34
17 8 0.14
18 15 0.25
19 5 0.08
20 11 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATAATATATATATTTA
Found at i:26276 original size:19 final size:19
Alignment explanation
Indices: 26228--26277 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
26218 CCTTTTGTTT
*
26228 ACATTTCTGTAATTCTGTT
1 ACATTTCTGTAATTCTGTA
* *
26247 GCAATTCTGTAATTCTGTA
1 ACATTTCTGTAATTCTGTA
*
26266 ACATTTATGTAA
1 ACATTTCTGTAA
26278 GTGATTATGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (19 bp):
ACATTTCTGTAATTCTGTA
Found at i:26583 original size:14 final size:14
Alignment explanation
Indices: 26566--26593 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
26556 GCTTTGGACT
26566 TTGGTAGTTGGTAC
1 TTGGTAGTTGGTAC
26580 TTGGTAGTTGGTAC
1 TTGGTAGTTGGTAC
26594 AAATCTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.36, T:0.43
Consensus pattern (14 bp):
TTGGTAGTTGGTAC
Found at i:37118 original size:16 final size:16
Alignment explanation
Indices: 37097--37129 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
37087 CATGCATCAT
37097 AATCTTAATATATGCC
1 AATCTTAATATATGCC
37113 AATCTTAATATATGCC
1 AATCTTAATATATGCC
37129 A
1 A
37130 TAATTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (16 bp):
AATCTTAATATATGCC
Found at i:42438 original size:2 final size:2
Alignment explanation
Indices: 42425--42491 Score: 74
Period size: 2 Copynumber: 36.5 Consensus size: 2
42415 GGATTTTCTT
* *
42425 TA TA TA TG TA TA TA -A TA TA -A TA TA TA TA TA CA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42464 -A TA TA -A TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42492 GTAGATCTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
1 6 0.11
2 49 0.89
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:42465 original size:25 final size:24
Alignment explanation
Indices: 42433--42491 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 24
42423 TTTATATATG
42433 TATATAATATAATATATATATACA
1 TATATAATATAATATATATATACA
*
42457 TAATATAATATAATATATATATATA
1 T-ATATAATATAATATATATATACA
42482 TATATAATAT
1 TATATAATAT
42492 GTAGATCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 10 0.30
25 23 0.70
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TATATAATATAATATATATATACA
Found at i:43189 original size:20 final size:20
Alignment explanation
Indices: 43147--43190 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
43137 AACGAATATT
* * * *
43147 AAAGGATTTTTTTTAAGTTA
1 AAAGGATTTTATTAAAATGA
43167 AAAGGATTTTATTAAAATGA
1 AAAGGATTTTATTAAAATGA
43187 AAAG
1 AAAG
43191 CAAGTTGCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (20 bp):
AAAGGATTTTATTAAAATGA
Found at i:43383 original size:30 final size:31
Alignment explanation
Indices: 43321--43399 Score: 151
Period size: 31 Copynumber: 2.6 Consensus size: 31
43311 AACTTTGATT
43321 AATTTTAAATGGGCACCATTACTTCAAAAAA
1 AATTTTAAATGGGCACCATTACTTCAAAAAA
43352 AATTTTAAATGGGCACCATTACTTC-AAAAA
1 AATTTTAAATGGGCACCATTACTTCAAAAAA
43382 AATTTTAAATGGGCACCA
1 AATTTTAAATGGGCACCA
43400 CCAAAAAAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 23 0.48
31 25 0.52
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.29
Consensus pattern (31 bp):
AATTTTAAATGGGCACCATTACTTCAAAAAA
Found at i:44450 original size:2 final size:2
Alignment explanation
Indices: 44443--44480 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
44433 CAAACTATTT
44443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44481 C
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.