Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016096.1 Corchorus olitorius cultivar O-4 contig16129, 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: 47473
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:366 original size:13 final size:13
Alignment explanation
Indices: 340--374 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
330 GGTTTAAATC
*
340 TATA-TATATCTA
1 TATATTATATATA
352 TATATTATATATA
1 TATATTATATATA
365 TATATTATAT
1 TATATTATAT
375 TAAAAAGTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATTATATATA
Found at i:634 original size:122 final size:128
Alignment explanation
Indices: 460--713 Score: 369
Period size: 130 Copynumber: 2.0 Consensus size: 128
450 CATTGTTTAA
*
460 ACTTTTATAGTTTTACTCAACTAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA-
1 ACTTTTACAGTTTTACTCAACTAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTAT
520 TGATTTTTACCATTTTACTATTTTAATTAAAAAAACT-TATATATATTAGAATTTTTTAAATAT
66 TGATTTTTACCATTTTACTATTTT-ATTAAAAAAACTATATATATATTAGAATTTTTTAAATAT
*
583 ACTTTTACAGTTTTACTCAACT-AAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCT
1 ACTTTTACAGTTTTACTCAACTAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTAT--CT
* ** *
647 ATTTTATTTTTACCATTTTACTATTTTATTTTAAAAATTATATATATATTAGAATTTTTTAAATA
64 A-TTGATTTTTACCATTTTACTATTTTATTAAAAAAACTATATATATATTAGAATTTTTTAAATA
712 T
128 T
713 A
1 A
714 TTTCTTAAAT
Statistics
Matches: 116, Mismatches: 6, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
122 31 0.27
123 22 0.19
124 1 0.01
125 1 0.01
128 2 0.02
129 9 0.08
130 50 0.43
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (128 bp):
ACTTTTACAGTTTTACTCAACTAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTAT
TGATTTTTACCATTTTACTATTTTATTAAAAAAACTATATATATATTAGAATTTTTTAAATAT
Found at i:3855 original size:6 final size:6
Alignment explanation
Indices: 3846--3877 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3836 GTTTTTAATT
3846 AACTAG AACTAG AACTAG AACTAG AACTAG AA
1 AACTAG AACTAG AACTAG AACTAG AACTAG AA
3878 TAATCAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACTAG
Found at i:9256 original size:10 final size:10
Alignment explanation
Indices: 9241--9276 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
9231 TATTCTCGAT
9241 ATATCCGTAA
1 ATATCCGTAA
9251 ATATCCGTAA
1 ATATCCGTAA
*
9261 GTATCCGTAA
1 ATATCCGTAA
9271 ATATCC
1 ATATCC
9277 ATATTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:10655 original size:26 final size:26
Alignment explanation
Indices: 10577--10648 Score: 117
Period size: 26 Copynumber: 2.8 Consensus size: 26
10567 CCACACATAC
*
10577 TATCTACACATACCTATAGTATATGT
1 TATCCACACATACCTATAGTATATGT
10603 TATCCACACATACCTATAGTATATGT
1 TATCCACACATACCTATAGTATATGT
* *
10629 TATCCACATATACTTATAGT
1 TATCCACACATACCTATAGT
10649 TTTTGTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.38
Consensus pattern (26 bp):
TATCCACACATACCTATAGTATATGT
Found at i:10847 original size:15 final size:15
Alignment explanation
Indices: 10827--10859 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10817 GTACTTTTTA
10827 ATATA-AAAT-ATAG
1 ATATATAAATAATAG
10840 ATATATAAATAATAG
1 ATATATAAATAATAG
10855 ATATA
1 ATATA
10860 GATAATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 4 0.22
15 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (15 bp):
ATATATAAATAATAG
Found at i:11636 original size:22 final size:23
Alignment explanation
Indices: 11611--11653 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11601 ATTTAAATAA
*
11611 AAATAAAT-ATAAATTAAGAAGT
1 AAATAAATAATAAAATAAGAAGT
11633 AAATAAATAATAAAATAAGAA
1 AAATAAATAATAAAATAAGAA
11654 TAATAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (23 bp):
AAATAAATAATAAAATAAGAAGT
Found at i:11651 original size:23 final size:22
Alignment explanation
Indices: 11611--11670 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
11601 ATTTAAATAA
*
11611 AAATAAATATAAATTAAGAAGT
1 AAATAAATATAAAATAAGAAGT
11633 AAATAAATAATAAAATAAGAA-T
1 AAATAAAT-ATAAAATAAGAAGT
*
11655 -AATAATATTTAAAATA
1 AAATAA-ATATAAAATA
11671 CAGTAACTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 12 0.35
22 11 0.32
23 11 0.32
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (22 bp):
AAATAAATATAAAATAAGAAGT
Found at i:13452 original size:51 final size:50
Alignment explanation
Indices: 13351--13452 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
13341 GTTCTTCATA
* **
13351 TTTTCCTTGTTTAGATCTTGCCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGCCTCCGGACAAACAAACACTCGTACAGTGT
* *
13401 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGCCTCCGGACAAACAAACACTCGTACA-GTGT
13452 T
1 T
13453 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 7 0.16
51 36 0.82
52 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGCCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:18659 original size:29 final size:29
Alignment explanation
Indices: 18613--18690 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 29
18603 TTTTAAAAAC
* * * *
18613 CCAGGGGTATTTTGGTCATTTTTCACGTT
1 CCAGGGGCATTTTAGTCATTTTGCACATT
*
18642 CCAGGGGCATTTTAGTCA-TTTGCATATT
1 CCAGGGGCATTTTAGTCATTTTGCACATT
*
18670 -CAGGGGCATTTTAGTTATTTT
1 CCAGGGGCATTTTAGTCATTTT
18691 AAGTTCACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 16 0.38
28 10 0.24
29 16 0.38
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (29 bp):
CCAGGGGCATTTTAGTCATTTTGCACATT
Found at i:24365 original size:51 final size:50
Alignment explanation
Indices: 24264--24365 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
24254 GTTCTTCATA
* * **
24264 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTATCTCCGGACAAACAAACACTCGTACAGTGT
*
24314 TTTTCTCTTGTTTCA-ATCTTATCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTATCTCCGGACAAACAAACACTCGTACA-GTGT
24365 T
1 T
24366 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 7 0.16
51 36 0.82
52 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTATCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:25277 original size:23 final size:23
Alignment explanation
Indices: 25250--25294 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
25240 AGATGCTAAT
*
25250 ATATACTGT-GACTTGGCTAAAAA
1 ATATA-TGTAGACTTGGATAAAAA
*
25273 ATATATGTAGAGTTGGATAAAA
1 ATATATGTAGACTTGGATAAAA
25295 CATAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (23 bp):
ATATATGTAGACTTGGATAAAAA
Found at i:25880 original size:39 final size:38
Alignment explanation
Indices: 25802--25912 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 38
25792 TATACATATT
* **
25802 TATTATTTGGAATAAAATATACTCCTAT-TATA-TTTA
1 TATTATTTGGAATAAAATATAATTATATATATATTTTA
*
25838 TATTATTTGGAATAAAATATAATTATATACATATTTTAA
1 TATTATTTGGAATAAAATATAATTATATATATATTTT-A
* *
25877 TATTTATAT-AAATAAAAATATAATTATTATATATAT
1 TA-TTATTTGGAAT-AAAATATAATTA-TATATATAT
25913 AATATATAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
36 25 0.40
37 3 0.05
38 3 0.05
39 6 0.10
40 17 0.27
41 8 0.13
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (38 bp):
TATTATTTGGAATAAAATATAATTATATATATATTTTA
Found at i:25881 original size:36 final size:36
Alignment explanation
Indices: 25789--25881 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
25779 CAAAAAGTAT
*
25789 TTATATACATA-TTTATTATTTGGAATAAAATATAC
1 TTATATACATATTTTATTATTTGGAATAAAATATAA
** *
25824 TCCTAT-TATATTTATATTATTTGGAATAAAATATAA
1 TTATATACATATTT-TATTATTTGGAATAAAATATAA
*
25860 TTATATACATATTTTAATATTT
1 TTATATACATATTTTATTATTT
25882 ATATAAATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
34 3 0.06
35 6 0.13
36 32 0.68
37 6 0.13
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.49
Consensus pattern (36 bp):
TTATATACATATTTTATTATTTGGAATAAAATATAA
Found at i:25923 original size:27 final size:24
Alignment explanation
Indices: 25877--25926 Score: 64
Period size: 27 Copynumber: 2.0 Consensus size: 24
25867 CATATTTTAA
25877 TATTTATATAAATAAAAATATAAT
1 TATTTATATAAATAAAAATATAAT
*
25901 TATTATATATATAATATATAATATAA
1 TATT-TATATA-AATA-AAAATATAA
25927 ACGAACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 6 0.27
26 4 0.18
27 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TATTTATATAAATAAAAATATAAT
Found at i:33595 original size:12 final size:12
Alignment explanation
Indices: 33578--33604 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33568 CTAAAATTAC
33578 AAAAAAGTTATA
1 AAAAAAGTTATA
33590 AAAAAAGTTATA
1 AAAAAAGTTATA
33602 AAA
1 AAA
33605 GTTATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (12 bp):
AAAAAAGTTATA
Found at i:33622 original size:21 final size:21
Alignment explanation
Indices: 33580--33623 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
33570 AAAATTACAA
*
33580 AAAAGTTATAAAAAAAGTTAT
1 AAAAGTTATAAAAAAAGCTAT
** *
33601 AAAAGTTATTTAAATAGCTAT
1 AAAAGTTATAAAAAAAGCTAT
33622 AA
1 AA
33624 TGCTTTCTAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (21 bp):
AAAAGTTATAAAAAAAGCTAT
Found at i:34008 original size:68 final size:68
Alignment explanation
Indices: 33899--34034 Score: 206
Period size: 68 Copynumber: 2.0 Consensus size: 68
33889 TTTGCTTGAA
* *
33899 ATGCATTGTCTTTAAATGTAATTTTAGCATTTGGATGTAATTAATGGTG-TCTCTACCATTTTTT
1 ATGCATTGTCTTTAAATGTAATTTTAGCAATTGGATGTAATTAATGGTGCTC-CCACCATTTTTT
33963 TCCT
65 TCCT
33967 ATGCATTGTC-TTAATATGTAATTTTAG-AATTGAGATGTAATTAATGGTGCTCCCACCATTTTT
1 ATGCATTGTCTTTAA-ATGTAATTTTAGCAATTG-GATGTAATTAATGGTGCTCCCACCATTTTT
34030 TTCCT
64 TTCCT
34035 TATTTGTTTA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
67 8 0.13
68 53 0.84
69 2 0.03
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (68 bp):
ATGCATTGTCTTTAAATGTAATTTTAGCAATTGGATGTAATTAATGGTGCTCCCACCATTTTTTT
CCT
Found at i:37252 original size:149 final size:148
Alignment explanation
Indices: 36983--37282 Score: 537
Period size: 149 Copynumber: 2.0 Consensus size: 148
36973 TCTGACAAAC
36983 TGATGAGATTTGTGCGGTAAAGAAATTATAATTTTTAATATATATTATTTAATTTAGTTGATAAA
1 TGATGAGATTTGTGCGGTAAAGAAATTATAATTTTTAATATATATTATTTAATTTAGTTGATAAA
*
37048 TGAAATTACATATTAAATCTTAAAAGTTAAATATAATATTTAAAATTAAGAAGGATATTTTAGAT
66 TGAAATTACATATTAAACCTTAAAAGTTAAATATAATATTTAAAATTAAGAAGGATATTTTAGAT
* * *
37113 ATTTTAGGTCAAGTTTTT
131 ATTTCAAGTCAAGATTTT
*
37131 TGATGAGATTTGTGCGGTAAAGAAATTATAATTTTTTGATATATATTATTTAATTTAGTTGATAA
1 TGATGAGATTTGTGCGGTAAAGAAATTATAA-TTTTTAATATATATTATTTAATTTAGTTGATAA
*
37196 ATGAAATTACATATTAAACCTTAAAAGTTAAATCTAATATTTAAAATTAAGAAGGATATTTTAGA
65 ATGAAATTACATATTAAACCTTAAAAGTTAAATATAATATTTAAAATTAAGAAGGATATTTTAGA
37261 TATTTCAAGTCAAGATTTT
130 TATTTCAAGTCAAGATTTT
37280 TGA
1 TGA
37283 AGTTTAGACT
Statistics
Matches: 145, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
148 31 0.21
149 114 0.79
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.42
Consensus pattern (148 bp):
TGATGAGATTTGTGCGGTAAAGAAATTATAATTTTTAATATATATTATTTAATTTAGTTGATAAA
TGAAATTACATATTAAACCTTAAAAGTTAAATATAATATTTAAAATTAAGAAGGATATTTTAGAT
ATTTCAAGTCAAGATTTT
Found at i:37316 original size:2 final size:2
Alignment explanation
Indices: 37309--37334 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37299 ATATAAAGAG
37309 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
37335 TCAAGTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.