Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024226.1 Corchorus olitorius cultivar O-4 contig24259, 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: 67818
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2717 original size:55 final size:56
Alignment explanation
Indices: 2628--2740 Score: 201
Period size: 55 Copynumber: 2.0 Consensus size: 56
2618 TATCTGTTTC
*
2628 CTTTCACACAATAAATGTTATAATAAATCTTAT-CCCCTATATCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATATCTACTTAATTATT
*
2683 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATATCTACTTAATTATT
2739 CT
1 CT
2741 AAAAAATAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
55 32 0.58
56 23 0.42
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.41
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATATCTACTTAATTATT
Found at i:2843 original size:21 final size:21
Alignment explanation
Indices: 2819--2886 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
2809 TTGAGTTGAG
2819 TATTTCTTAATTTACAAAGAA
1 TATTTCTTAATTTACAAAGAA
*** *
2840 TATTT-TATAATTTGA-GTTGAG
1 TATTTCT-TAATTT-ACAAAGAA
*
2861 TATTTCTTAATTTACAGAGAA
1 TATTTCTTAATTTACAAAGAA
2882 T-TTTC
1 TATTTC
2887 AAGACTTAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 9
0.67 0.15 0.17
Matches are distributed among these distances:
20 6 0.17
21 27 0.77
22 2 0.06
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (21 bp):
TATTTCTTAATTTACAAAGAA
Found at i:9619 original size:47 final size:47
Alignment explanation
Indices: 9561--10122 Score: 833
Period size: 47 Copynumber: 12.0 Consensus size: 47
9551 TAAAATGAAC
* * *
9561 AGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAGTTAAACTAAAT
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
* *
9608 AGTAAAAGAAGAAGAAATTAGTTTAATTCTAGTTAATTAAACTAAGT
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
*
9655 AGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
*
9702 AGTAAAAGAA-AAGGAGATTAGTTTAATTCTAGGTAATTAAACTAAAT
1 AGTAAAAGAAGAA-GAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
* *
9749 AGTAAAAGAAGAAGAAATTAGTTTAATTCAAGGTAATTAAACTAAGT
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
* *
9796 AGTAGAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGT
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
*
9843 AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAGGT
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
* * *
9890 AGTAAAAGAGGAGGAGATTAGTTTAATTTTAGGTAATTAAACTAAGT
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
* *
9937 AGTAAAAGAGGAAGAGATTAGTTTAATTCTAGGTAATCAAACTAAGT
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
*
9984 AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTACTTAAACTAAGT
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
* * * * * *
10031 AGTAAAAGGAA-AAGAAATTGGTTTAAGTCCAGATAATTAAACTATGT
1 AGTAAAA-GAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
* * *
10078 AGCAGAAGAAGGAA-AGATTAGTTTAATTCTAGGTGATTAAACTAA
1 AGTAAAAGAA-GAAGAGATTAGTTTAATTCTAGGTAATTAAACTAA
10123 AGAAGAGGTT
Statistics
Matches: 468, Mismatches: 42, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
46 4 0.01
47 457 0.98
48 7 0.01
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.29
Consensus pattern (47 bp):
AGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGT
Found at i:14574 original size:10 final size:10
Alignment explanation
Indices: 14561--14591 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
14551 CCCCAATATA
14561 CATAAAAATC
1 CATAAAAATC
*
14571 CATAAAAATA
1 CATAAAAATC
14581 CATAAAAATC
1 CATAAAAATC
14591 C
1 C
14592 CAAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (10 bp):
CATAAAAATC
Found at i:28856 original size:18 final size:18
Alignment explanation
Indices: 28813--28859 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
28803 TATATATTAT
28813 TTACTTATT-TTTAACTAA
1 TTACTTATTATTTAAC-AA
*
28831 TTATTTATTATTTAA-AA
1 TTACTTATTATTTAACAA
28848 TATACTTATTAT
1 T-TACTTATTAT
28860 CTATTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 3 0.12
18 17 0.68
19 5 0.20
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TTACTTATTATTTAACAA
Found at i:29714 original size:21 final size:21
Alignment explanation
Indices: 29680--29728 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
29670 TAAAAATCAC
* *
29680 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAGCAAAGTA
29700 AATTAGAAAACAAAGCAAAGTA
1 AATTA-AAAACAAAGCAAAGTA
29722 AATTAAA
1 AATTAAA
29729 TCTAAGTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 11 0.44
22 9 0.36
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.18
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGTA
Found at i:30509 original size:17 final size:18
Alignment explanation
Indices: 30472--30509 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
30462 ACCCTTGCCT
*
30472 AAAACTAGAAGAAAACTA
1 AAAACTAGAAGAAAACGA
30490 AAAACTAGAAGAAAA-GA
1 AAAACTAGAAGAAAACGA
30507 AAA
1 AAA
30510 TATCTATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.71, C:0.08, G:0.13, T:0.08
Consensus pattern (18 bp):
AAAACTAGAAGAAAACGA
Found at i:32284 original size:44 final size:44
Alignment explanation
Indices: 32219--32366 Score: 197
Period size: 44 Copynumber: 3.3 Consensus size: 44
32209 ATCTTTCATA
* * * * *
32219 ATCTTCCTTGAATCTTCTTTGATAATGATCCTCCACATACGTGG
1 ATCTTCTTTCAATCTTTTTTGATGATAATCCTCCACATACGTGG
**
32263 ATCTTCTTTCAATCTTTTTTGATGATAATCCTATACATACGTGG
1 ATCTTCTTTCAATCTTTTTTGATGATAATCCTCCACATACGTGG
*
32307 ATCTTCTTTCAATCTTCTCTGATGATGATAATCCTCCACATACGTGG
1 ATCTTCTTTCAATCTT-T-T-TTGATGATAATCCTCCACATACGTGG
32354 ATCTTCTTTCAAT
1 ATCTTCTTTCAAT
32367 AATCTTCCTT
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
44 53 0.58
45 1 0.01
46 1 0.01
47 36 0.40
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (44 bp):
ATCTTCTTTCAATCTTTTTTGATGATAATCCTCCACATACGTGG
Found at i:32673 original size:42 final size:42
Alignment explanation
Indices: 32610--32697 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
32600 ATTTTGATTG
* *
32610 GTCAAACCATTAGATATTGAAATCTGATTGGTTAGACCATGT
1 GTCAAAACATTAGATAATGAAATCTGATTGGTTAGACCATGT
32652 GTCAAAACATTAGATAATGAAATCTGATTGGTTAGACCATGT
1 GTCAAAACATTAGATAATGAAATCTGATTGGTTAGACCATGT
32694 GTCA
1 GTCA
32698 TATTTATCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (42 bp):
GTCAAAACATTAGATAATGAAATCTGATTGGTTAGACCATGT
Found at i:33235 original size:65 final size:64
Alignment explanation
Indices: 33146--33272 Score: 173
Period size: 65 Copynumber: 2.0 Consensus size: 64
33136 AGTTCATTTA
* * **
33146 TTTTTGTGCTCTAAGTTTTGCCTAAACCGTCCTTTGTAGGATTTTCAACTTAGCGAGGCTTTTTG
1 TTTTTCTGCTCTAACTTTTGCCTAAACCGTCCTTTACAGGATTTTCAACTTAGCGA-GCTTTTTG
* * * *
33211 TTTTTCTGCTCTATCTTTTTCCTAAGCTGTCCTTTACAGGATTTTCAACTTAGCGAGCTTTT
1 TTTTTCTGCTCTAACTTTTGCCTAAACCGTCCTTTACAGGATTTTCAACTTAGCGAGCTTTT
33273 CTTTCTTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
64 6 0.11
65 48 0.89
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (64 bp):
TTTTTCTGCTCTAACTTTTGCCTAAACCGTCCTTTACAGGATTTTCAACTTAGCGAGCTTTTTG
Found at i:35332 original size:47 final size:44
Alignment explanation
Indices: 35227--35362 Score: 202
Period size: 47 Copynumber: 3.0 Consensus size: 44
35217 TCCTCCTTGG
*
35227 ATCTTCTTTG-TAATGATCCTCCACATACGTGGATCTTCTTTCA
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
*
35270 ATCTTCTTTGATAATAATGCTCCACATACGTGGATCTTCTTTCA
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
* *
35314 ATCTTTTTTTATGATAATAATCCTCCACATACATGGATCTTCTTTCA
1 ATC--TTCTT-TGATAATAATCCTCCACATACGTGGATCTTCTTTCA
35361 AT
1 AT
35363 AATCTTCCTT
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
43 10 0.12
44 34 0.40
46 4 0.05
47 36 0.43
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.43
Consensus pattern (44 bp):
ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
Found at i:38430 original size:11 final size:11
Alignment explanation
Indices: 38414--38438 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38404 GGGGAATAAT
38414 CAATCCAAAAA
1 CAATCCAAAAA
38425 CAATCCAAAAA
1 CAATCCAAAAA
38436 CAA
1 CAA
38439 ACAATTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (11 bp):
CAATCCAAAAA
Found at i:40241 original size:34 final size:37
Alignment explanation
Indices: 40173--40242 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
40163 GCTGCCTTGT
40173 GCGCGGACTGAGGCAGCAGCAGCGGCCTGATGCTGCGC
1 GCGCGGACTGAGGCAGCAGCAGCGGCCT-ATGCTGCGC
*
40211 GCGCGGGCT-AGGCAGCAGCAGCGG-CT-TGCTGC
1 GCGCGGACTGAGGCAGCAGCAGCGGCCTATGCTGC
40243 TTGGCGCGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 6 0.19
36 2 0.06
37 15 0.48
38 8 0.26
ACGTcount: A:0.14, C:0.31, G:0.43, T:0.11
Consensus pattern (37 bp):
GCGCGGACTGAGGCAGCAGCAGCGGCCTATGCTGCGC
Found at i:49889 original size:76 final size:76
Alignment explanation
Indices: 49739--49890 Score: 166
Period size: 76 Copynumber: 2.0 Consensus size: 76
49729 ACAAGGGCCC
* * * **
49739 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGGACTCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAC
49804 GGGCGGTGTCA
66 GGGCGGTGTCA
* * * *
49815 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGCACCCA
*
49877 GACGGGCTGTGTCA
63 GACGGGCGGTGTCA
49891 TAGCTCATCA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
75 4 0.06
76 53 0.84
77 6 0.10
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAC
GGGCGGTGTCA
Found at i:59426 original size:20 final size:21
Alignment explanation
Indices: 59395--59433 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
59385 AATTTGTAAG
59395 AAATTATTATTAATAATAATA
1 AAATTATTATTAATAATAATA
59416 AAATT-TTATTAATAATAA
1 AAATTATTATTAATAATAA
59434 AAATAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTATTATTAATAATAATA
Found at i:59702 original size:42 final size:44
Alignment explanation
Indices: 59651--59744 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 44
59641 AATGCATTAC
59651 CTAA-ATTCTACT-CT-ATCTCTAGG-TAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCT-GGATAATTCATCAAAATAAAG
*
59692 CTAATATTCTACTCCTCCATCTCTGGATAATTCATCAAAATAGAG
1 CTAATATTCTACTCCT-CATCTCTGGATAATTCATCAAAATAAAG
59737 CTAATATT
1 CTAATATT
59745 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
43 2 0.04
44 2 0.04
45 31 0.66
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTGGATAATTCATCAAAATAAAG
Found at i:61519 original size:22 final size:23
Alignment explanation
Indices: 61494--61539 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
61484 TAATATCCAC
61494 ACACAATTAAT-ATATAAT-TAAA
1 ACACAATTAATCATA-AATATAAA
*
61516 ACACACTTAATCATAAATATAAA
1 ACACAATTAATCATAAATATAAA
61539 A
1 A
61540 ATAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (23 bp):
ACACAATTAATCATAAATATAAA
Found at i:61721 original size:3 final size:3
Alignment explanation
Indices: 61715--61910 Score: 292
Period size: 3 Copynumber: 65.3 Consensus size: 3
61705 TATAGTATAT
61715 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
61763 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GAGT- ATA A-G
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA ATA ATA
* * *
61808 ATA GTA CTTA CTA TATA AT- ATA AT- ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
61853 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
61901 ATA ATA ATA A
1 ATA ATA ATA A
61911 GCTTTAATCA
Statistics
Matches: 179, Mismatches: 6, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
2 6 0.03
3 167 0.93
4 5 0.03
5 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:63576 original size:28 final size:29
Alignment explanation
Indices: 63544--63599 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
63534 TTTTTCTTTA
63544 TTTTTGG-CCATGAGCCAAAATAGTTTCT
1 TTTTTGGACCATGAGCCAAAATAGTTTCT
63572 TTTTTGGCACCATGAGCCAAAATAGTTT
1 TTTTTGG-ACCATGAGCCAAAATAGTTT
63600 AAAGAGCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 7 0.27
30 19 0.73
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (29 bp):
TTTTTGGACCATGAGCCAAAATAGTTTCT
Found at i:64062 original size:9 final size:9
Alignment explanation
Indices: 64042--64070 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
64032 ATCTATTTTT
64042 TATTAT-TA
1 TATTATATA
64050 TATTATATA
1 TATTATATA
64059 TATTATATA
1 TATTATATA
64068 TAT
1 TAT
64071 ATACATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATATA
Found at i:67720 original size:3 final size:3
Alignment explanation
Indices: 67714--67779 Score: 125
Period size: 3 Copynumber: 22.3 Consensus size: 3
67704 GTTGATTTCC
67714 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
67762 TCT TCT TCT TCT T-T TCT T
1 TCT TCT TCT TCT TCT TCT T
67780 TCTTTCTTTC
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:67783 original size:4 final size:4
Alignment explanation
Indices: 67774--67804 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
67764 TTCTTCTTCT
67774 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
67805 TTATTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Done.