Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015848.1 Corchorus olitorius cultivar O-4 contig15881, 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: 47623
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:10673 original size:47 final size:49
Alignment explanation
Indices: 10597--10696 Score: 150
Period size: 47 Copynumber: 2.1 Consensus size: 49
10587 ATTTTGGGAG
10597 AAACAGAAAACAAAGAGTGAGAAGAAGGAGAAGAGAGGGTTTTCGCGCTT
1 AAACAGAAAACAAAGAGT-AGAAGAAGGAGAAGAGAGGGTTTTCGCGCTT
* * *
10647 AAACAGAGAACAAAGAGT-G-AGAAGGAGAAGGGAGGGTTTTCGCTCTT
1 AAACAGAAAACAAAGAGTAGAAGAAGGAGAAGAGAGGGTTTTCGCGCTT
10694 AAA
1 AAA
10697 TGTCTTATGT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
47 29 0.62
48 1 0.02
50 17 0.36
ACGTcount: A:0.43, C:0.10, G:0.32, T:0.15
Consensus pattern (49 bp):
AAACAGAAAACAAAGAGTAGAAGAAGGAGAAGAGAGGGTTTTCGCGCTT
Found at i:18387 original size:29 final size:30
Alignment explanation
Indices: 18329--18389 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
18319 GTTCTAATTA
*
18329 ATGTATACATATAAATTATTTAAATTTATT
1 ATGTATAAATATAAATTATTTAAATTTATT
18359 ATGTATAAATAT-AATTATTT-AATTATATT
1 ATGTATAAATATAAATTATTTAAATT-TATT
18388 AT
1 AT
18390 ATTATTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 4 0.14
29 14 0.48
30 11 0.38
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTTAAATTTATT
Found at i:19535 original size:107 final size:105
Alignment explanation
Indices: 19305--19566 Score: 386
Period size: 107 Copynumber: 2.5 Consensus size: 105
19295 AATTTTTCTA
* **
19305 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
19368 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* * * *
19408 ACCATTTAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
19473 TTTCTAAAACCCTATAA-AGATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACA-AT--ATTATTAATTATGAAATTT
*
19515 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAATTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
19567 AGGCTAAACT
Statistics
Matches: 142, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
103 25 0.18
104 16 0.11
105 35 0.25
107 66 0.46
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:26725 original size:52 final size:52
Alignment explanation
Indices: 26663--26816 Score: 256
Period size: 51 Copynumber: 3.0 Consensus size: 52
26653 TTTCTGAAAT
* *
26663 TTTTGAAAACAGAAACAGCCTGCCAAACATGTTTTCACTGTTTTGTTTCCAA
1 TTTTGGAAACAGAAACAACCTGCCAAACATGTTTTCACTGTTTTGTTTCCAA
*
26715 TTTTGGAAACAGAAACAACCTGCCAAACATGTTTTCACTGTTTTG-TTCCAG
1 TTTTGGAAACAGAAACAACCTGCCAAACATGTTTTCACTGTTTTGTTTCCAA
* *
26766 TTTTGGAAACAGAAACAACATGTCAAACATGTTTTCACTGTTTTGTTTCCA
1 TTTTGGAAACAGAAACAACCTGCCAAACATGTTTTCACTGTTTTGTTTCCA
26817 TAAACAAAAA
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
51 48 0.50
52 48 0.50
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (52 bp):
TTTTGGAAACAGAAACAACCTGCCAAACATGTTTTCACTGTTTTGTTTCCAA
Found at i:27638 original size:18 final size:17
Alignment explanation
Indices: 27591--27639 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
27581 CAGCAGAAGA
* *
27591 AGGCGGAGCTGAGGCTG
1 AGGCAGAGCTGAGACTG
*
27608 AGGCTGAGACTGAGACTG
1 AGGCAGAG-CTGAGACTG
27626 AGGCAGAAGCTGAG
1 AGGCAG-AGCTGAG
27640 TCACCTGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.26
18 18 0.67
19 2 0.07
ACGTcount: A:0.27, C:0.16, G:0.45, T:0.12
Consensus pattern (17 bp):
AGGCAGAGCTGAGACTG
Found at i:30919 original size:21 final size:19
Alignment explanation
Indices: 30894--30949 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
30884 GCTGCTCTAA
30894 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
30915 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
30934 TAATCTCATCTGTACA
1 TAATCTCATCTGTACA
30950 ATTACTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:41156 original size:18 final size:18
Alignment explanation
Indices: 41129--41172 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
41119 TAATGGTTCC
* * *
41129 GTTAAAGGCGGTTCCATG
1 GTTAACGGCGGATCAATG
41147 GTTAACGGCGGATCAATG
1 GTTAACGGCGGATCAATG
*
41165 GTGAACGG
1 GTTAACGG
41173 ATCGGATATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.16, G:0.36, T:0.23
Consensus pattern (18 bp):
GTTAACGGCGGATCAATG
Found at i:42080 original size:20 final size:19
Alignment explanation
Indices: 42043--42084 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42033 TTCATTTTTC
*
42043 TTTTTCATTTTTTGTGTAT
1 TTTTTAATTTTTTGTGTAT
*
42062 TTTTTAATTTTATTTTGTAT
1 TTTTTAATTTT-TTGTGTAT
42082 TTT
1 TTT
42085 ATGAATGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (19 bp):
TTTTTAATTTTTTGTGTAT
Found at i:42880 original size:56 final size:56
Alignment explanation
Indices: 42813--42925 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
42803 CCCGCACCAC
42813 ACGATTATCCAGCTCTTTTTTTTAGAGAGAGAATGTGCTAATACATTGGCTTCCCT
1 ACGATTATCCAGCTCTTTTTTTTAGAGAGAGAATGTGCTAATACATTGGCTTCCCT
42869 ACGATTATCCAGCTCTTTTTTTTAGAGAGAGAATGTGCTAATACATTGGCTTCCCT
1 ACGATTATCCAGCTCTTTTTTTTAGAGAGAGAATGTGCTAATACATTGGCTTCCCT
42925 A
1 A
42926 TTTACAAAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (56 bp):
ACGATTATCCAGCTCTTTTTTTTAGAGAGAGAATGTGCTAATACATTGGCTTCCCT
Found at i:42974 original size:36 final size:36
Alignment explanation
Indices: 42927--42996 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
42917 GCTTCCCTAT
*
42927 TTACAAAGAAAACTTACATTCCATGAGAGTAGAAAA
1 TTACAAAGAAAACTCACATTCCATGAGAGTAGAAAA
* * *
42963 TTACAAAGAAAACTCATATTTCGTGAGAGTAGAA
1 TTACAAAGAAAACTCACATTCCATGAGAGTAGAA
42997 CCCAAGACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (36 bp):
TTACAAAGAAAACTCACATTCCATGAGAGTAGAAAA
Found at i:45473 original size:41 final size:41
Alignment explanation
Indices: 45416--45498 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
45406 GCTGTCGATC
45416 CAATTTGGGATTTACGAATCCATTGGACTTTCACCTACGGA
1 CAATTTGGGATTTACGAATCCATTGGACTTTCACCTACGGA
*
45457 CAATTTGGGATTTACGAATCCATTGGACTTTCACCTGCGGA
1 CAATTTGGGATTTACGAATCCATTGGACTTTCACCTACGGA
45498 C
1 C
45499 TTTTCGGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Consensus pattern (41 bp):
CAATTTGGGATTTACGAATCCATTGGACTTTCACCTACGGA
Found at i:45511 original size:41 final size:41
Alignment explanation
Indices: 45416--45517 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 41
45406 GCTGTCGATC
*
45416 CAATTTGGGATTTACGAATCCATTGGACTTTCACCTACGGA
1 CAATTTGGAATTTACGAATCCATTGGACTTTCACCTACGGA
* *
45457 CAATTTGGGATTTACGAATCCATTGGACTTTCACCTGCGGA
1 CAATTTGGAATTTACGAATCCATTGGACTTTCACCTACGGA
* *
45498 C-TTTTCGGAATTTACAAATC
1 CAATTT-GGAATTTACGAATC
45518 ACCTACCAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
40 3 0.05
41 53 0.95
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (41 bp):
CAATTTGGAATTTACGAATCCATTGGACTTTCACCTACGGA
Found at i:47548 original size:17 final size:16
Alignment explanation
Indices: 47526--47565 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 16
47516 TCTTTCTTTC
47526 TTTTTTATTTTTTTATT
1 TTTTTTA-TTTTTTATT
47543 TTTTTTATTTTTTATT
1 TTTTTTATTTTTTATT
47559 TTTTTTA
1 TTTTTTA
47566 CCTCACCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTATTTTTTATT
Found at i:47565 original size:9 final size:8
Alignment explanation
Indices: 47526--47563 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
47516 TCTTTCTTTC
47526 TTTTTTAT
1 TTTTTTAT
47534 TTTTTTAT
1 TTTTTTAT
47542 TTTTTT-T
1 TTTTTTAT
47549 ATTTTTTAT
1 -TTTTTTAT
47558 TTTTTT
1 TTTTTT
47564 TACCTCACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.04
8 26 0.93
9 1 0.04
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTAT
Done.