Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018721.1 Corchorus olitorius cultivar O-4 contig18754, 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: 40867
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Found at i:3531 original size:22 final size:22
Alignment explanation
Indices: 3502--3567 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
3492 TTTCAAGAAC
3502 CATT-CTATGAAATTTTGTTAA
1 CATTCCTATGAAATTTTGTTAA
3523 CATTCCTATGAAATTTTGTTTAA
1 CATTCCTATGAAATTTTG-TTAA
*
3546 C--TCCTTATGAAATATTGTTAA
1 CATTCC-TATGAAATTTTGTTAA
3567 C
1 C
3568 CAGTCATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
21 12 0.29
22 24 0.59
23 5 0.12
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (22 bp):
CATTCCTATGAAATTTTGTTAA
Found at i:4617 original size:7 final size:7
Alignment explanation
Indices: 4601--4629 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4591 AGAGCCAATG
4601 AAAA-CC
1 AAAATCC
4607 AAAATCC
1 AAAATCC
4614 AAAATCC
1 AAAATCC
4621 AAAATCC
1 AAAATCC
4628 AA
1 AA
4630 TATATTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (7 bp):
AAAATCC
Found at i:6918 original size:39 final size:39
Alignment explanation
Indices: 6874--6952 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
6864 ATTCAGACAA
* *
6874 TATTGTATTTGAGAAGGCTTCTACAAATGAAAACATGTT
1 TATTGTATTTGAGAAAGCTTCTACAAATAAAAACATGTT
* *
6913 TATTGTATTTGAGAAAGCTTCTATAAATAAAAACGTGTT
1 TATTGTATTTGAGAAAGCTTCTACAAATAAAAACATGTT
6952 T
1 T
6953 TCCCCTGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (39 bp):
TATTGTATTTGAGAAAGCTTCTACAAATAAAAACATGTT
Found at i:15631 original size:47 final size:47
Alignment explanation
Indices: 15577--15731 Score: 116
Period size: 50 Copynumber: 3.2 Consensus size: 47
15567 ATGTCTTTAA
15577 TTTAATTTAATTTAATTCTAGCTTGTTAGTCGCTCAACATCCTCTAG
1 TTTAATTTAATTTAATTCTAGCTTGTTAGTCGCTCAACATCCTCTAG
* * * * * * * * ** * *
15624 TTTAATTT-TTCCGTTGATTAGTTAG-TTATCAGTTGATAAATCAATATTTTTAA
1 TTTAATTTAAT---TTAATT--CTAGCTTGTTAGTCGCTCAA-C-AT-CCTCTAG
15677 TTTAATTTAATTTAATTCTAGCTTGTTAGTCGCTCAACATCCTCTAG
1 TTTAATTTAATTTAATTCTAGCTTGTTAGTCGCTCAACATCCTCTAG
15724 TTTAATTT
1 TTTAATTT
15732 TTCCGTTGAT
Statistics
Matches: 74, Mismatches: 24, Indels: 20
0.63 0.20 0.17
Matches are distributed among these distances:
46 1 0.01
47 19 0.26
48 2 0.03
49 9 0.12
50 20 0.27
51 9 0.12
52 2 0.03
53 11 0.15
54 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.48
Consensus pattern (47 bp):
TTTAATTTAATTTAATTCTAGCTTGTTAGTCGCTCAACATCCTCTAG
Found at i:15733 original size:100 final size:100
Alignment explanation
Indices: 15560--15861 Score: 532
Period size: 100 Copynumber: 3.0 Consensus size: 100
15550 GCTCCACAGC
* *
15560 TAAATCAATGTCTTTAATTTAATTTAATTTAATTCTAGCTTGTTAGTCGCTCAACATCCTCTAGT
1 TAAATCAATATTTTTAATTTAATTTAATTTAATTCTAGCTTGTTAGTCGCTCAACATCCTCTAGT
15625 TTAATTTTTCCGTTGATTAGTTAGTTATCAGTTGA
66 TTAATTTTTCCGTTGATTAGTTAGTTATCAGTTGA
15660 TAAATCAATATTTTTAATTTAATTTAATTTAATTCTAGCTTGTTAGTCGCTCAACATCCTCTAGT
1 TAAATCAATATTTTTAATTTAATTTAATTTAATTCTAGCTTGTTAGTCGCTCAACATCCTCTAGT
15725 TTAATTTTTCCGTTGATTAGTTAGTTATCAGTTGA
66 TTAATTTTTCCGTTGATTAGTTAGTTATCAGTTGA
* *
15760 TAAATCAATATTTTTAATTTAATTTAATTTAATTCTAGCTTGTTAGTCACTCAACATCCCCTAAG
1 TAAATCAATATTTTTAATTTAATTTAATTTAATTCTAGCTTGTTAGTCGCTCAACATCCTCT-AG
** *
15825 TTTAATTTTTCTATTGATTAGTTAGTTATCAATTGA
65 TTTAATTTTTCCGTTGATTAGTTAGTTATCAGTTGA
15861 T
1 T
15862 TGGTTAGTTA
Statistics
Matches: 194, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
100 158 0.81
101 36 0.19
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (100 bp):
TAAATCAATATTTTTAATTTAATTTAATTTAATTCTAGCTTGTTAGTCGCTCAACATCCTCTAGT
TTAATTTTTCCGTTGATTAGTTAGTTATCAGTTGA
Found at i:15861 original size:19 final size:19
Alignment explanation
Indices: 15837--15874 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
15827 TAATTTTTCT
15837 ATTGATTAGTTAGTTATCA
1 ATTGATTAGTTAGTTATCA
*
15856 ATTGATTGGTTAGTTATCA
1 ATTGATTAGTTAGTTATCA
15875 GTTAATGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.47
Consensus pattern (19 bp):
ATTGATTAGTTAGTTATCA
Found at i:27922 original size:14 final size:15
Alignment explanation
Indices: 27903--27931 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27893 ATTTGTGGAA
27903 TCCAAT-TCCAAATT
1 TCCAATGTCCAAATT
27917 TCCAATGTCCAAATT
1 TCCAATGTCCAAATT
27932 CTAAATCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (15 bp):
TCCAATGTCCAAATT
Found at i:28011 original size:12 final size:12
Alignment explanation
Indices: 27996--28020 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27986 AATAAATAAA
27996 TTTAAATTTATT
1 TTTAAATTTATT
28008 TTTAAATTTATT
1 TTTAAATTTATT
28020 T
1 T
28021 AAATAACATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAAATTTATT
Found at i:31017 original size:21 final size:20
Alignment explanation
Indices: 30993--31035 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
30983 TCCTTCCACC
30993 TTTGCC-GTGTGTGAATTTCTT
1 TTTGCCGGTG-GTGAATTT-TT
*
31014 TTTGGCGGTGGTGAATTTTT
1 TTTGCCGGTGGTGAATTTTT
31034 TT
1 TT
31036 GTGCTGGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 13 0.65
22 3 0.15
ACGTcount: A:0.09, C:0.09, G:0.28, T:0.53
Consensus pattern (20 bp):
TTTGCCGGTGGTGAATTTTT
Found at i:35358 original size:19 final size:19
Alignment explanation
Indices: 35334--35380 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
35324 ATACTTTATT
**
35334 TGTGGAATACTCATGTGTG
1 TGTGGAATACTCACATGTG
* *
35353 TGTGGATTATTCACATGTG
1 TGTGGAATACTCACATGTG
35372 TGTGGAATA
1 TGTGGAATA
35381 TGAATATTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.38
Consensus pattern (19 bp):
TGTGGAATACTCACATGTG
Found at i:35446 original size:19 final size:19
Alignment explanation
Indices: 35422--35461 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
35412 AGAATATTCA
*
35422 TGTGTGAAATATTCGTATG
1 TGTGTGAAATATTCATATG
*
35441 TGTGTGGAATATTCATATG
1 TGTGTGAAATATTCATATG
35460 TG
1 TG
35462 AATGTGTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.05, G:0.28, T:0.42
Consensus pattern (19 bp):
TGTGTGAAATATTCATATG
Found at i:35498 original size:47 final size:46
Alignment explanation
Indices: 35422--35538 Score: 171
Period size: 47 Copynumber: 2.5 Consensus size: 46
35412 AGAATATTCA
* *
35422 TGTGTGAAATATTCGTATGTGTGTGGAATATTCATATGTGAATGTG
1 TGTGTGAAATATTCGTATGTGTGTAGAATATTCACATGTGAATGTG
* *
35468 TGTGTGAGATATTTTGTATGTGTGTAGAATATTCACATGTGAATGTG
1 TGTGTGAAATA-TTCGTATGTGTGTAGAATATTCACATGTGAATGTG
* *
35515 TGTGTGGAATATTCATATGTGTGT
1 TGTGTGAAATATTCGTATGTGTGT
35539 GTGGTGCAGC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 21 0.34
47 41 0.66
ACGTcount: A:0.25, C:0.04, G:0.28, T:0.43
Consensus pattern (46 bp):
TGTGTGAAATATTCGTATGTGTGTAGAATATTCACATGTGAATGTG
Found at i:35541 original size:27 final size:27
Alignment explanation
Indices: 35439--35535 Score: 111
Period size: 27 Copynumber: 3.9 Consensus size: 27
35429 AATATTCGTA
35439 TGTGTGTGGAATATTCATATGTGAATG
1 TGTGTGTGGAATATTCATATGTGAATG
35466 TGTGTGT-GAGATATT--T-TGT--A--
1 TGTGTGTGGA-ATATTCATATGTGAATG
* *
35486 TGTGTGTAGAATATTCACATGTGAATG
1 TGTGTGTGGAATATTCATATGTGAATG
35513 TGTGTGTGGAATATTCATATGTG
1 TGTGTGTGGAATATTCATATGTG
35536 TGTGTGGTGC
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
20 12 0.21
21 2 0.03
22 1 0.02
23 3 0.05
24 3 0.05
25 2 0.03
26 2 0.03
27 33 0.57
ACGTcount: A:0.25, C:0.04, G:0.29, T:0.42
Consensus pattern (27 bp):
TGTGTGTGGAATATTCATATGTGAATG
Found at i:40716 original size:22 final size:22
Alignment explanation
Indices: 40688--40752 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
40678 TTTTCCGCAA
*
40688 CAAGTCCTAGG-CAGGAGTTGTC
1 CAAGTCCT-GGACAGGACTTGTC
40710 CAAGTCCTGGACAGGACTTGTC
1 CAAGTCCTGGACAGGACTTGTC
40732 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCTGGACAGGACTTGT
40753 TCTGAATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 2 0.05
22 39 0.95
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAGGACTTGTC
Found at i:40808 original size:21 final size:21
Alignment explanation
Indices: 40782--40823 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
40772 TTCAACAGAC
*
40782 CAAGTCGTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
40803 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
40824 TCTGATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.40, T:0.24
Consensus pattern (21 bp):
CAAGTCCTGGGCAGGAGTTGT
Found at i:40826 original size:71 final size:72
Alignment explanation
Indices: 40709--40867 Score: 239
Period size: 71 Copynumber: 2.2 Consensus size: 72
40699 CAGGAGTTGT
* *
40709 CCAAGTCCTGGACAGGACTTGTCCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTCCGTTTTT
1 CCAAGTCCTGGGCAGGACTTGTCCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTCCGTCTTT
40774 CAACAGA
66 CAACAGA
* * * * *
40781 CCAAGTCGTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTCCGTCTTT
1 CCAAGTCCTGGGCAGGACTTGTCCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTCCGTCTTT
40845 CAACAGA
66 CAACAGA
*
40852 CCAGGTCCTGGGCAGG
1 CCAAGTCCTGGGCAGG
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 59 0.76
72 19 0.24
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.30
Consensus pattern (72 bp):
CCAAGTCCTGGGCAGGACTTGTCCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTCCGTCTTT
CAACAGA
Done.