Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023350.1 Corchorus olitorius cultivar O-4 contig23383, 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: 72083
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5888 original size:25 final size:26
Alignment explanation
Indices: 5843--5894 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
5833 AGACTAATGT
5843 ATTTTTTTGTGATTTTCAATT-TTCA
1 ATTTTTTTGTGATTTTCAATTATTCA
*
5868 ATTTTTTTGTG-TTTTGTAATTATTCA
1 ATTTTTTTGTGATTTT-CAATTATTCA
5894 A
1 A
5895 GTGTATTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 15 0.62
26 5 0.21
ACGTcount: A:0.21, C:0.06, G:0.10, T:0.63
Consensus pattern (26 bp):
ATTTTTTTGTGATTTTCAATTATTCA
Found at i:6307 original size:27 final size:27
Alignment explanation
Indices: 6258--6335 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
6248 TAAAACGACC
* * * *
6258 AAAATGCCCCTGGACATGCAAATGACT
1 AAAATGCCCCTAGACGTGTAAATGACA
6285 AAAATGCCCCTAGACGTGTAAATGACA
1 AAAATGCCCCTAGACGTGTAAATGACA
*
6312 AAAATGCCCCTAGATGTGTAAATG
1 AAAATGCCCCTAGACGTGTAAATG
6336 CCAATTAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (27 bp):
AAAATGCCCCTAGACGTGTAAATGACA
Found at i:11279 original size:19 final size:18
Alignment explanation
Indices: 11255--11293 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
11245 AAATATCTCC
*
11255 AATTAGGGCTAATTGCACA
1 AATTAGAGC-AATTGCACA
*
11274 AATTAGATCAATTGCACA
1 AATTAGAGCAATTGCACA
11292 AA
1 AA
11294 CACAAGAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (18 bp):
AATTAGAGCAATTGCACA
Found at i:12436 original size:29 final size:28
Alignment explanation
Indices: 12372--12436 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 28
12362 AGTGTTCATG
12372 ATTTAG-GGTTACTAACCATTTTATTTT
1 ATTTAGAGGTTACTAACCATTTTATTTT
*
12399 ATTTTGAGGTTACTAA-CACTCTTTATTTT
1 ATTTAGAGGTTACTAACCA-T-TTTATTTT
12428 -TTTCAGAGG
1 ATTT-AGAGG
12437 GACAATACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 7 0.22
28 13 0.41
29 12 0.38
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (28 bp):
ATTTAGAGGTTACTAACCATTTTATTTT
Found at i:17319 original size:7 final size:7
Alignment explanation
Indices: 17307--17334 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
17297 TACAGAGAAA
17307 AAAAAAC
1 AAAAAAC
17314 AAAAAAC
1 AAAAAAC
17321 AAAAAAC
1 AAAAAAC
17328 AAAAAAC
1 AAAAAAC
17335 TAAACTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:17738 original size:15 final size:15
Alignment explanation
Indices: 17718--17769 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
17708 GTAAGCAAAG
17718 CAGTAAGTTCAAAAA
1 CAGTAAGTTCAAAAA
*
17733 CAGTAAAG--CAGCAAAG
1 CAGT-AAGTTCA--AAAA
17749 CAGTAAGTTCAAAAA
1 CAGTAAGTTCAAAAA
17764 CAGTAA
1 CAGTAA
17770 AGCACATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 2 0.07
15 16 0.53
16 10 0.33
17 2 0.07
ACGTcount: A:0.52, C:0.15, G:0.17, T:0.15
Consensus pattern (15 bp):
CAGTAAGTTCAAAAA
Found at i:17748 original size:31 final size:31
Alignment explanation
Indices: 17711--17773 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
17701 AACAAGGGTA
17711 AGCAAAGCAGTAAGTTCAAAAACAGTAAAGC
1 AGCAAAGCAGTAAGTTCAAAAACAGTAAAGC
17742 AGCAAAGCAGTAAGTTCAAAAACAGTAAAGC
1 AGCAAAGCAGTAAGTTCAAAAACAGTAAAGC
17773 A
1 A
17774 CATACAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (31 bp):
AGCAAAGCAGTAAGTTCAAAAACAGTAAAGC
Found at i:20915 original size:13 final size:14
Alignment explanation
Indices: 20887--20920 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
20877 TAGTATCTAG
20887 TTTAATTGATTTATT
1 TTTAATTGA-TTATT
20902 TTTAATTG-TTATT
1 TTTAATTGATTATT
20915 TTTAAT
1 TTTAAT
20921 CCCCTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
15 8 0.42
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTAATTGATTATT
Found at i:36634 original size:32 final size:32
Alignment explanation
Indices: 36598--36683 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
36588 GAACCCGTCC
*
36598 GACCCGAGACCCGAATCG-CCCGCAACCC-AGAT
1 GACCCGAAACCCGAAT-GACCCGCAACCCGAG-T
* *
36630 GACCCGAAACCCAAATGACCCGTAACCCGAGT
1 GACCCGAAACCCGAATGACCCGCAACCCGAGT
*
36662 GACCCGAAACCCGAATAACCCG
1 GACCCGAAACCCGAATGACCCG
36684 ACAAGTTAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 1 0.02
32 44 0.94
33 2 0.04
ACGTcount: A:0.33, C:0.41, G:0.20, T:0.07
Consensus pattern (32 bp):
GACCCGAAACCCGAATGACCCGCAACCCGAGT
Found at i:36674 original size:16 final size:16
Alignment explanation
Indices: 36598--36684 Score: 88
Period size: 16 Copynumber: 5.4 Consensus size: 16
36588 GAACCCGTCC
*
36598 GACCCGAGACCCGAAT
1 GACCCGAAACCCGAAT
*
36614 CG-CCCGCAACCC-AGAT
1 -GACCCGAAACCCGA-AT
*
36630 GACCCGAAACCCAAAT
1 GACCCGAAACCCGAAT
* *
36646 GACCCGTAACCCGAGT
1 GACCCGAAACCCGAAT
36662 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
*
36678 AACCCGA
1 GACCCGA
36685 CAAGTTAACC
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
15 2 0.03
16 54 0.93
17 2 0.03
ACGTcount: A:0.33, C:0.40, G:0.20, T:0.07
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:37492 original size:16 final size:16
Alignment explanation
Indices: 37473--37572 Score: 105
Period size: 16 Copynumber: 6.2 Consensus size: 16
37463 AGATCCGGTG
37473 GACCCGAAATCCGAAT
1 GACCCGAAATCCGAAT
37489 GACCC-AGAATCCGAAT
1 GACCCGA-AATCCGAAT
* *
37505 GACCCGAAA-CTAGTAT
1 GACCCGAAATC-CGAAT
*
37521 GACCCGATATCCGAAT
1 GACCCGAAATCCGAAT
* *
37537 GACCCGAGACCCGAAT
1 GACCCGAAATCCGAAT
* *
37553 AACCCGAAACCCGAAT
1 GACCCGAAATCCGAAT
37569 GACC
1 GACC
37573 TAAGAAAACT
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
15 2 0.03
16 66 0.94
17 2 0.03
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.12
Consensus pattern (16 bp):
GACCCGAAATCCGAAT
Found at i:37571 original size:48 final size:48
Alignment explanation
Indices: 37473--37572 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 48
37463 AGATCCGGTG
* * * *
37473 GACCCGAAATCCGAATGACCCAGAATCCGAATGACCCGAAACTAGTAT
1 GACCCGAAATCCGAATGACCCAGAACCCGAATAACCCGAAACCAGAAT
* *
37521 GACCCGATATCCGAATGACCC-GAGACCCGAATAACCCGAAACCCGAAT
1 GACCCGAAATCCGAATGACCCAGA-ACCCGAATAACCCGAAACCAGAAT
37569 GACC
1 GACC
37573 TAAGAAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 2 0.04
48 43 0.96
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.12
Consensus pattern (48 bp):
GACCCGAAATCCGAATGACCCAGAACCCGAATAACCCGAAACCAGAAT
Found at i:41192 original size:54 final size:54
Alignment explanation
Indices: 41110--41219 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
41100 TAAGAATACA
41110 ATTAATCTTAATCTGAGCACATTACTAAGGCTAATAGGCCGATAATCTTTTACT
1 ATTAATCTTAATCTGAGCACATTACTAAGGCTAATAGGCCGATAATCTTTTACT
41164 ATTAATCTTAATCTGAGCACATTACTAAGGCTAATAGGCCGATAATCTTTTACT
1 ATTAATCTTAATCTGAGCACATTACTAAGGCTAATAGGCCGATAATCTTTTACT
41218 AT
1 AT
41220 GCTTGGATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (54 bp):
ATTAATCTTAATCTGAGCACATTACTAAGGCTAATAGGCCGATAATCTTTTACT
Found at i:45435 original size:19 final size:18
Alignment explanation
Indices: 45411--45453 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
45401 AAATAATAAA
*
45411 TATATAATTATATATTAT-T
1 TATATAAATAT-TATT-TCT
45430 TATATAAATATTATTTCT
1 TATATAAATATTATTTCT
45448 TATATA
1 TATATA
45454 TATAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 11 0.50
19 10 0.45
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATAAATATTATTTCT
Found at i:67358 original size:29 final size:29
Alignment explanation
Indices: 67304--67359 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
67294 GATCAATTGA
* * **
67304 AAATAACTTGAGAAAGACCATTCTAGAAT
1 AAATAACTTAAGAAAGAACACCCTAGAAT
67333 AAATAACTTAAGAAAGAACACCCTAGA
1 AAATAACTTAAGAAAGAACACCCTAGA
67360 TTGACCAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (29 bp):
AAATAACTTAAGAAAGAACACCCTAGAAT
Found at i:67438 original size:16 final size:16
Alignment explanation
Indices: 67417--67448 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
67407 GATCATTCTG
67417 AAATAAACTGAAGAAA
1 AAATAAACTGAAGAAA
*
67433 AAATAAATTGAAGAAA
1 AAATAAACTGAAGAAA
67449 GACCACCCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.12, T:0.16
Consensus pattern (16 bp):
AAATAAACTGAAGAAA
Found at i:67493 original size:8 final size:8
Alignment explanation
Indices: 67477--67506 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
67467 GAAATAAATC
*
67477 GAAGCATT
1 GAAGAATT
67485 GAAGAATT
1 GAAGAATT
67493 GAAGAATT
1 GAAGAATT
67501 GAAGAA
1 GAAGAA
67507 AGAGATCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.27, T:0.20
Consensus pattern (8 bp):
GAAGAATT
Found at i:67587 original size:47 final size:47
Alignment explanation
Indices: 67503--67603 Score: 139
Period size: 47 Copynumber: 2.1 Consensus size: 47
67493 GAAGAATTGA
* * *
67503 AGAAAGAGATCAACTGTGGTCACCAAACTGTAGACTCGCATGGAAGCG
1 AGAAA-AGACCAACTGTGGTCACCAAACTGCAAACTCGCATGGAAGCG
* * *
67551 AGAAAAGACCAACTTTGGTCACTAAATTGCAAACTCGCATGGAAGCG
1 AGAAAAGACCAACTGTGGTCACCAAACTGCAAACTCGCATGGAAGCG
67598 AGAAAA
1 AGAAAA
67604 AATTACTTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 42 0.89
48 5 0.11
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.17
Consensus pattern (47 bp):
AGAAAAGACCAACTGTGGTCACCAAACTGCAAACTCGCATGGAAGCG
Found at i:69705 original size:26 final size:26
Alignment explanation
Indices: 69648--69705 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
69638 TTCATCCTTT
**
69648 TCTTTTCACTTTCTTTTTCAATTTTC
1 TCTTTTCACTTTCACTTTCAATTTTC
** * *
69674 AATTTTGACTTTCACTTTCACTTTTC
1 TCTTTTCACTTTCACTTTCAATTTTC
69700 TCTTTT
1 TCTTTT
69706 TTCATTTTTT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.14, C:0.22, G:0.02, T:0.62
Consensus pattern (26 bp):
TCTTTTCACTTTCACTTTCAATTTTC
Done.