Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018933.1 Corchorus olitorius cultivar O-4 contig18966, 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: 31144
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Found at i:114 original size:16 final size:17
Alignment explanation
Indices: 87--162 Score: 79
Period size: 16 Copynumber: 4.7 Consensus size: 17
77 GTCGGGTTGA
87 TCGGGTTCGGGTCATTT
1 TCGGGTTCGGGTCATTT
*
104 T-GGGTTTGGGTCATTT
1 TCGGGTTCGGGTCATTT
*
120 TCGGGTTCGGGTC-GTT
1 TCGGGTTCGGGTCATTT
* * *
136 T-GGATTAGGGT-AATT
1 TCGGGTTCGGGTCATTT
151 TCGGGTTCGGGT
1 TCGGGTTCGGGT
163 ACCCAAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
15 11 0.23
16 26 0.54
17 11 0.23
ACGTcount: A:0.08, C:0.12, G:0.39, T:0.41
Consensus pattern (17 bp):
TCGGGTTCGGGTCATTT
Found at i:211 original size:17 final size:17
Alignment explanation
Indices: 171--211 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
161 GTACCCAAAA
171 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
188 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
204 TTTCGGGT
1 TTTCGGGT
212 TGGGTGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:707 original size:53 final size:53
Alignment explanation
Indices: 644--749 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
634 TCTTTAAATC
644 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
*
697 CAATAGTTCATTGCATTTTGTATTTTTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
750 TAATTGAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.52
Consensus pattern (53 bp):
CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
Found at i:1030 original size:1 final size:1
Alignment explanation
Indices: 1024--1048 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1014 AAGAAAATTT
1024 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1049 CTAACTCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3824 original size:1 final size:1
Alignment explanation
Indices: 3818--3842 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3808 CCAAGAGGGC
3818 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
3843 GGAACTCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5907 original size:21 final size:22
Alignment explanation
Indices: 5881--5924 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5871 ATGAATATGC
*
5881 TAATAAAAAAAATT-GTCAAAT
1 TAATAAAAAAAATTCATCAAAT
*
5902 TAATAACAAAAATTCATCAAAT
1 TAATAAAAAAAATTCATCAAAT
5924 T
1 T
5925 CATTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (22 bp):
TAATAAAAAAAATTCATCAAAT
Found at i:11591 original size:16 final size:16
Alignment explanation
Indices: 11570--11604 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
11560 TTCATATAAG
11570 AAAAAGATCAGAATAC
1 AAAAAGATCAGAATAC
*
11586 AAAAAGATCAGGATAC
1 AAAAAGATCAGAATAC
11602 AAA
1 AAA
11605 GACATCGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.11, G:0.14, T:0.11
Consensus pattern (16 bp):
AAAAAGATCAGAATAC
Found at i:13310 original size:21 final size:24
Alignment explanation
Indices: 13281--13331 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
13271 TTTTGAACTC
13281 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
13304 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
13327 ATTAT
1 ATTAT
13332 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:13326 original size:25 final size:25
Alignment explanation
Indices: 13281--13329 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
13271 TTTTGAACTC
*
13281 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
13306 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
13330 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:18847 original size:25 final size:25
Alignment explanation
Indices: 18814--18868 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
18804 AAGTTAAATT
* *
18814 TTCTC-CAAACAAATAATACTTGTA
1 TTCTCACAAAAAAAAAATACTTGTA
18838 TTCTCACAAAAAAAAAATACTTGTA
1 TTCTCACAAAAAAAAAATACTTGTA
18863 TTCTCA
1 TTCTCA
18869 TATTTACCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.33
Consensus pattern (25 bp):
TTCTCACAAAAAAAAAATACTTGTA
Found at i:20267 original size:2 final size:2
Alignment explanation
Indices: 20260--20293 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20250 CCCAATCGTG
20260 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
20294 AGACAAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20551 original size:2 final size:2
Alignment explanation
Indices: 20546--20584 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
20536 TTTTCAAAAA
20546 AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20584 A
1 A
20585 CACTATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.12
2 29 0.88
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:20567 original size:15 final size:15
Alignment explanation
Indices: 20549--20597 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
20539 TCAAAAAATA
20549 TATATATATATATAT
1 TATATATATATATAT
20564 TATAT-TATATTATAT
1 TATATATATA-TATAT
*
20579 TATATACACTATA-AT
1 TATATATA-TATATAT
20594 TATA
1 TATA
20598 GACAAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.13
15 21 0.70
16 3 0.10
17 2 0.07
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:20569 original size:5 final size:5
Alignment explanation
Indices: 20547--20583 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
20537 TTTCAAAAAA
20547 TATAT ATATAT ATATAT TATAT TATAT TATAT TATAT
1 TATAT -TATAT -TATAT TATAT TATAT TATAT TATAT
20584 ACACTATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 20 0.65
6 11 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:27458 original size:24 final size:22
Alignment explanation
Indices: 27426--27471 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
27416 CCGCCCATAT
*
27426 TTATTTTTTAAAATAAAATAATAA
1 TTATATTTT-AAATAAAA-AATAA
*
27450 TTATATTTTTAATAAAAAATAA
1 TTATATTTTAAATAAAAAATAA
27472 AATTTAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 7 0.35
24 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTATATTTTAAATAAAAAATAA
Found at i:27475 original size:24 final size:24
Alignment explanation
Indices: 27426--27475 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
27416 CCGCCCATAT
27426 TTATTTTTTAAAATAAAATAATAA
1 TTATTTTTTAAAATAAAATAATAA
27450 TTATATTTTTAATAA-AAAATAA-AA
1 TTAT-TTTTTAA-AATAAAATAATAA
27474 TT
1 TT
27476 TAAACATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 8 0.33
25 14 0.58
26 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTATTTTTTAAAATAAAATAATAA
Found at i:27637 original size:29 final size:30
Alignment explanation
Indices: 27579--27639 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
27569 GTTCTAATTA
* *
27579 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
27609 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
27638 AT
1 AT
27640 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:29399 original size:14 final size:14
Alignment explanation
Indices: 29382--29423 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
29372 TCATGCACCC
29382 AAAATCATTTAATA
1 AAAATCATTTAATA
29396 AAAATCATTTAA-A
1 AAAATCATTTAATA
*
29409 AACA--ATTTAATA
1 AAAATCATTTAATA
29421 AAA
1 AAA
29424 CAGTAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 6 0.24
12 3 0.12
13 4 0.16
14 12 0.48
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATCATTTAATA
Done.