Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020767.1 Corchorus olitorius cultivar O-4 contig20800, 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: 44493
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10110 original size:45 final size:45
Alignment explanation
Indices: 10042--10186 Score: 182
Period size: 45 Copynumber: 3.0 Consensus size: 45
10032 TAAATCTCAA
10042 GACTCAGCCTAACTATATGTATTTGTCATAAATAATTGCATAAAT
1 GACTCAGCCTAACTATATGTATTTGTCATAAATAATTGCATAAAT
*
10087 GACTCAGCCTAACTATATATATTTGTCATAAATAATTGTCATAAATAATT
1 GACTCAGCCTAACTATATGTATTTGTCATAAATAATTG-CAT--A-AA-T
** *
10137 GCATACTCAGCCTAACTATATGTATTCATCATGAATAATTGCATAAAT
1 G---ACTCAGCCTAACTATATGTATTTGTCATAAATAATTGCATAAAT
10185 GA
1 GA
10187 TCTGCAAGAC
Statistics
Matches: 87, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
45 38 0.44
46 3 0.03
48 3 0.03
49 4 0.05
50 3 0.03
52 3 0.03
53 33 0.38
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (45 bp):
GACTCAGCCTAACTATATGTATTTGTCATAAATAATTGCATAAAT
Found at i:10127 original size:13 final size:13
Alignment explanation
Indices: 10109--10141 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
10099 CTATATATAT
10109 TTGTCATAAATAA
1 TTGTCATAAATAA
10122 TTGTCATAAATAA
1 TTGTCATAAATAA
10135 TTG-CATA
1 TTGTCATA
10142 CTCAGCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (13 bp):
TTGTCATAAATAA
Found at i:10174 original size:53 final size:55
Alignment explanation
Indices: 10064--10193 Score: 158
Period size: 53 Copynumber: 2.3 Consensus size: 55
10054 CTATATGTAT
**
10064 TTGTCATAAATAATTGCATAAATGACTCAGCCTAACTATATATATTTGTCATAAATAA
1 TTGTCATAAATAATTGC---AATGACTCAGCCTAACTATATATATTCATCATAAATAA
* *
10122 TTGTCATAAATAATTGC-AT-ACTCAGCCTAACTATATGTATTCATCATGAATAA
1 TTGTCATAAATAATTGCAATGACTCAGCCTAACTATATATATTCATCATAAATAA
*
10175 TTG-CATAAATGATCTGCAA
1 TTGTCATAAATAAT-TGCAA
10194 GACCTATCAA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
52 9 0.14
53 36 0.55
54 3 0.05
58 17 0.26
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (55 bp):
TTGTCATAAATAATTGCAATGACTCAGCCTAACTATATATATTCATCATAAATAA
Found at i:14709 original size:12 final size:12
Alignment explanation
Indices: 14694--14730 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
14684 TTCGTACCCA
*
14694 TCTTTTTTCTTC
1 TCTTTCTTCTTC
14706 TCTTTCTTCTTC
1 TCTTTCTTCTTC
14718 TCTTTCTTCTTC
1 TCTTTCTTCTTC
14730 T
1 T
14731 TCTTCCTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTTTCTTCTTC
Found at i:29989 original size:13 final size:13
Alignment explanation
Indices: 29971--29996 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29961 TTTCCTCGTT
29971 ACCATTATATATA
1 ACCATTATATATA
29984 ACCATTATATATA
1 ACCATTATATATA
29997 CAAGACACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ACCATTATATATA
Found at i:30113 original size:33 final size:32
Alignment explanation
Indices: 30045--30111 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
30035 AGTTTATTTT
30045 AAATGGATAGTTTTTTTAAAATGATATAAATA
1 AAATGGATAGTTTTTTTAAAATGATATAAATA
*
30077 AAATGGGTAGTTTTTTTAAAATGATATAAATA
1 AAATGGATAGTTTTTTTAAAATGATATAAATA
30109 AAA
1 AAA
30112 ATTTTATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (32 bp):
AAATGGATAGTTTTTTTAAAATGATATAAATA
Found at i:34983 original size:7 final size:7
Alignment explanation
Indices: 34971--35008 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
34961 ATATATATAT
34971 ATACTAA
1 ATACTAA
34978 ATACTAA
1 ATACTAA
34985 ATACTAA
1 ATACTAA
34992 ATACTAA
1 ATACTAA
34999 ATACTAA
1 ATACTAA
35006 ATA
1 ATA
35009 AATAAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (7 bp):
ATACTAA
Found at i:34997 original size:21 final size:21
Alignment explanation
Indices: 34947--35008 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
34937 TACTATTTAG
* *
34947 TACTAAATA-TATATA-TATA
1 TACTAAATACTAAATACTAAA
*
34966 TA-TATATACTAAATACTAAA
1 TACTAAATACTAAATACTAAA
34986 TACTAAATACTAAATACTAAA
1 TACTAAATACTAAATACTAAA
35007 TA
1 TA
35009 AATAAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.14
19 7 0.19
20 5 0.14
21 19 0.53
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (21 bp):
TACTAAATACTAAATACTAAA
Found at i:39152 original size:59 final size:59
Alignment explanation
Indices: 39060--39177 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
39050 AAAATAAACA
* *
39060 AACTAACTAAAACCCACATTCCGTGGGACTTGAAACCAAGATCTCACGGTTTAGACACG
1 AACTAACTAAAACCCACATTCCGTGAGACTTGAAACCAAGATCTCACGGTTTAAACACG
*
39119 AACTAACTAAAACCCGCATTCCGTGAGACTTGAAACCAAGATCTCACGGTTTAAACACG
1 AACTAACTAAAACCCACATTCCGTGAGACTTGAAACCAAGATCTCACGGTTTAAACACG
39178 GTATACCGAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (59 bp):
AACTAACTAAAACCCACATTCCGTGAGACTTGAAACCAAGATCTCACGGTTTAAACACG
Found at i:39842 original size:49 final size:47
Alignment explanation
Indices: 39733--39828 Score: 129
Period size: 52 Copynumber: 1.9 Consensus size: 47
39723 CTTCCTGACA
*
39733 ATTACTAATAATTAAGGTCAATTTGCATATATTAGTTCTTCCCAGATT
1 ATTACTAATTATTAAGGTCAATTTGCATATATTAGTTCTTCCCAGA-T
*
39781 ATTACTCCATTATTAAGGTCAATTTCTTGCATATATTAGTTCTTCCCA
1 ATTACT-AATTATTAAGGTCAA--T-TTGCATATATTAGTTCTTCCCA
39829 AATCTGGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
48 6 0.14
49 13 0.31
51 1 0.02
52 22 0.52
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (47 bp):
ATTACTAATTATTAAGGTCAATTTGCATATATTAGTTCTTCCCAGAT
Found at i:42448 original size:23 final size:22
Alignment explanation
Indices: 42422--42500 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
42412 TATTTTTATG
42422 AAATTTTGATAACTATACTATTA
1 AAATTTTGATAACTATACTA-TA
* * *
42445 AAATTTTGATAACCATGCTATG
1 AAATTTTGATAACTATACTATA
* *
42467 AAATTTTAATAA-TTTACCTATA
1 AAATTTTGATAACTATA-CTATA
*
42489 AAATTGTGATAA
1 AAATTTTGATAA
42501 ATTCCATATG
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 1 0.02
22 26 0.58
23 18 0.40
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACTATACTATA
Found at i:42473 original size:22 final size:22
Alignment explanation
Indices: 42418--42568 Score: 78
Period size: 22 Copynumber: 6.8 Consensus size: 22
42408 TGAATATTTT
*
42418 TATGAAATTTTGATAACTATAC
1 TATGAAATTTTGATAACCATAC
* *
42440 TATTAAAATTTTGATAACCATGC
1 TA-TGAAATTTTGATAACCATAC
* **
42463 TATGAAATTTTAATAA-TTTACC
1 TATGAAATTTTGATAACCATA-C
* * *
42485 TATAAAATTGTGATAA--ATTCC
1 TATGAAATTTTGATAACCA-TAC
* * *
42506 ATATGAAACTTTAATAACC-TAAT
1 -TATGAAATTTTGATAACCAT-AC
* * *
42529 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCATAC
42552 TATGAAATTTTG-TAACC
1 TATGAAATTTTGATAACC
42569 TTCCTATATA
Statistics
Matches: 97, Mismatches: 23, Indels: 19
0.70 0.17 0.14
Matches are distributed among these distances:
21 6 0.06
22 56 0.58
23 34 0.35
24 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATAC
Found at i:42570 original size:21 final size:23
Alignment explanation
Indices: 42445--42575 Score: 80
Period size: 22 Copynumber: 6.0 Consensus size: 23
42435 TATACTATTA
* * *
42445 AAATTTTGAT-AACCATGCTATG
1 AAATTTTAATAAACCTTCCTATG
* *
42467 AAATTTTAAT-AA-TTTACCTATA
1 AAATTTTAATAAACCTT-CCTATG
* *
42489 AAATTGTGATAAA--TTCCATATG
1 AAATTTTAATAAACCTTCC-TATG
* ***
42511 AAACTTTAAT-AACCTAATTATG
1 AAATTTTAATAAACCTTCCTATG
42533 AAATTTTAATAAACCTTCCTATG
1 AAATTTTAATAAACCTTCCTATG
*
42556 AAATTTT-GT-AACCTTCCTAT
1 AAATTTTAATAAACCTTCCTAT
42576 ATATGATTTT
Statistics
Matches: 84, Mismatches: 19, Indels: 13
0.72 0.16 0.11
Matches are distributed among these distances:
21 16 0.19
22 49 0.58
23 19 0.23
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (23 bp):
AAATTTTAATAAACCTTCCTATG
Done.