Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016478.1 Corchorus olitorius cultivar O-4 contig16511, 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: 63560
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1760 original size:36 final size:36
Alignment explanation
Indices: 1713--1781 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
1703 TCAATAACCA
*
1713 TACATTTTTTGTAATTTTGGTTATCATATTTCTTAT
1 TACATTTTTTGTAATTTTGATTATCATATTTCTTAT
1749 TACATTTTTTGTAATTTTGATTATCATATTTCT
1 TACATTTTTTGTAATTTTGATTATCATATTTCT
1782 CCAAAATCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (36 bp):
TACATTTTTTGTAATTTTGATTATCATATTTCTTAT
Found at i:2619 original size:45 final size:43
Alignment explanation
Indices: 2555--2638 Score: 114
Period size: 45 Copynumber: 1.9 Consensus size: 43
2545 GAACCTAAGA
*
2555 ATTTAATAAATGTAAGTATTTCAGTTATTATAGTATTATTATTAC
1 ATTTAATAAATGTAAGTATTTCAATTATTATA-TA-TATTATTAC
* * *
2600 ATTTAATTAATGTACGTATTTTAATTATTATATATATTA
1 ATTTAATAAATGTAAGTATTTCAATTATTATATATATTA
2639 CATAGGAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 5 0.14
44 2 0.06
45 28 0.80
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (43 bp):
ATTTAATAAATGTAAGTATTTCAATTATTATATATATTATTAC
Found at i:3386 original size:12 final size:12
Alignment explanation
Indices: 3369--3393 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3359 AGAGCTATGG
3369 ACTTGGTAGAGA
1 ACTTGGTAGAGA
3381 ACTTGGTAGAGA
1 ACTTGGTAGAGA
3393 A
1 A
3394 AGGGGGGAAA
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:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (12 bp):
ACTTGGTAGAGA
Found at i:20746 original size:19 final size:19
Alignment explanation
Indices: 20722--20761 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20712 ACAACTAAAG
20722 ATTAAAACTGATGTTTAAT
1 ATTAAAACTGATGTTTAAT
* * *
20741 ATTAAAATTGGTGTTTTAT
1 ATTAAAACTGATGTTTAAT
20760 AT
1 AT
20762 ATTTCAGATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (19 bp):
ATTAAAACTGATGTTTAAT
Found at i:21150 original size:26 final size:24
Alignment explanation
Indices: 21103--21154 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
21093 AATAAATATC
21103 AAATTAATTTTTAATATAATATGAA
1 AAATTAATTTTTAATATAATAT-AA
*
21128 AAATTAAGTTTTATAA-ATCATATAA
1 AAATTAA-TTTT-TAATATAATATAA
21153 AA
1 AA
21155 TAAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 11 0.46
26 10 0.42
27 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATTAATTTTTAATATAATATAA
Found at i:22248 original size:21 final size:21
Alignment explanation
Indices: 22222--22264 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
22212 TGCTCCCCTC
*
22222 GTTTTCTTCCTCTCCTGTCTG
1 GTTTTCTTCCTCTCCCGTCTG
*
22243 GTTTTCTTTCTCTCCCGTCTG
1 GTTTTCTTCCTCTCCCGTCTG
22264 G
1 G
22265 CCTTTTCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.33, G:0.16, T:0.51
Consensus pattern (21 bp):
GTTTTCTTCCTCTCCCGTCTG
Found at i:25278 original size:31 final size:31
Alignment explanation
Indices: 25240--25298 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
25230 TTTGTAAAAC
*
25240 TTTTGAAACGCCTATTGTACCCTTATTTAAT
1 TTTTGAAACGCCTATTATACCCTTATTTAAT
* *
25271 TTTTGAAACGTCTATTATATCCTTATTT
1 TTTTGAAACGCCTATTATACCCTTATTT
25299 GTCTAACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.49
Consensus pattern (31 bp):
TTTTGAAACGCCTATTATACCCTTATTTAAT
Found at i:26409 original size:12 final size:12
Alignment explanation
Indices: 26392--26429 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
26382 ATAATATTAG
26392 ATATATATAATT
1 ATATATATAATT
*
26404 ATATATATAATA
1 ATATATATAATT
26416 ATATATATAATT
1 ATATATATAATT
26428 AT
1 AT
26430 TAAACGGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATATAATT
Found at i:26409 original size:14 final size:15
Alignment explanation
Indices: 26377--26424 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 15
26367 TAATATAAAG
26377 ATATA-ATAAT-ATT
1 ATATATATAATAATT
*
26390 AGATATAT-ATAATT
1 ATATATATAATAATT
26404 ATATATATAATAA-T
1 ATATATATAATAATT
26418 ATATATA
1 ATATATA
26425 ATTATTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 6 0.20
14 20 0.67
15 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATATATAATAATT
Found at i:26424 original size:16 final size:16
Alignment explanation
Indices: 26366--26422 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
26356 AAGAACTAAT
*
26366 ATAATATAAAGATATA
1 ATAATATATAGATATA
26382 ATAATAT-TAGATATA
1 ATAATATATAGATATA
*
26397 TATAAT-TATATATATA
1 -ATAATATATAGATATA
26413 ATAATATATA
1 ATAATATATA
26423 TAATTATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 13 0.36
16 23 0.64
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (16 bp):
ATAATATATAGATATA
Found at i:27974 original size:15 final size:15
Alignment explanation
Indices: 27950--27986 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
27940 GATTAGATAT
* *
27950 TCGAGTTACCCGGGC
1 TCGAGCTACCCGAGC
27965 TCGAGCTACCCGAGC
1 TCGAGCTACCCGAGC
27980 TCGAGCT
1 TCGAGCT
27987 CAGCTTGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.35, G:0.30, T:0.19
Consensus pattern (15 bp):
TCGAGCTACCCGAGC
Found at i:29831 original size:36 final size:36
Alignment explanation
Indices: 29790--29869 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
29780 AGGTATAAAA
* *
29790 AAGAAGGCTGAGAAAGATAGTG-GACAGAAGAACGAG
1 AAGAAGGCTGAGAAAGAT-GGGAGAAAGAAGAACGAG
*
29826 GAGAAGGCTGAGAAAGATGGGAGAAAGAAGAACGAG
1 AAGAAGGCTGAGAAAGATGGGAGAAAGAAGAACGAG
29862 AAGAAGGC
1 AAGAAGGC
29870 AGAGTAGATC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 2 0.05
36 37 0.95
ACGTcount: A:0.47, C:0.07, G:0.39, T:0.06
Consensus pattern (36 bp):
AAGAAGGCTGAGAAAGATGGGAGAAAGAAGAACGAG
Found at i:32320 original size:60 final size:58
Alignment explanation
Indices: 32254--32416 Score: 175
Period size: 60 Copynumber: 2.7 Consensus size: 58
32244 GCTAATTACT
*
32254 CAAATAAGGGCGTAACGTTTGTCAAAATGATCAAATAAGGGTCCAAT-TTTTAAATTTGGC
1 CAAATAAGGGC-TAACGTTT-TCAAAATGCTCAAATAAGGGTCCAATCTTTT-AATTTGGC
* * * ** *
32314 CAAATAAGGATCTTACGTTATTGAAAATGCTCAAATAAGGACCCGATCTTTTAATTTGGC
1 CAAATAAGG-GCTAACGTT-TTCAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGC
* *
32374 CAAATAGGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTC
1 CAAATAAGGG-CTAACGTTTTC-AAAATGCTCAAATAAGGGTC
32417 TTGCGTCAGT
Statistics
Matches: 84, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
59 1 0.01
60 77 0.92
61 6 0.07
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (58 bp):
CAAATAAGGGCTAACGTTTTCAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGC
Found at i:32556 original size:60 final size:60
Alignment explanation
Indices: 32462--32620 Score: 212
Period size: 60 Copynumber: 2.6 Consensus size: 60
32452 TGCCAGAACT
* * * * ** *
32462 CTTATTTGAGCATTTTCG-ATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATTGGATT
1 CTTATTTGAGCATTTTGGCA-AACATTAGGCCCTTATTTGGCCAAATTAAAAAATCAGATC
* *
32522 TTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGTCAAATTAAAAAATCAGATC
1 CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAAATCAGATC
*
32582 CTTATTTGAGCATTTTGGCAAACATTAAGCCCTTATTTG
1 CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTG
32621 AGCAGTTAGT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 86 0.99
61 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (60 bp):
CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAAATCAGATC
Found at i:32619 original size:31 final size:31
Alignment explanation
Indices: 32523--32624 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
32513 GATTGGATTT
*
32523 TTATTTGAGCATTTTGGCAAACATTAGGCCC
1 TTATTTGAGCATTTTGGCAAACATTAAGCCC
** * * * *
32554 TTATTTG-GTCAAATT---AAAAAATCAGATCC
1 TTATTTGAG-CATTTTGGCAAACATTAAG-CCC
32583 TTATTTGAGCATTTTGGCAAACATTAAGCCC
1 TTATTTGAGCATTTTGGCAAACATTAAGCCC
32614 TTATTTGAGCA
1 TTATTTGAGCA
32625 GTTAGTTATC
Statistics
Matches: 52, Mismatches: 13, Indels: 12
0.68 0.17 0.16
Matches are distributed among these distances:
28 6 0.12
29 13 0.25
30 2 0.04
31 24 0.46
32 7 0.13
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (31 bp):
TTATTTGAGCATTTTGGCAAACATTAAGCCC
Found at i:44743 original size:2 final size:2
Alignment explanation
Indices: 44738--44767 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44728 GAGAAGGGTT
44738 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
44768 CGTGCGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:45643 original size:41 final size:41
Alignment explanation
Indices: 45586--45667 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
45576 GAAGACACGA
45586 TAATTTTATTATATTGGACCAGCAATTTCACGGGTGAGTGG
1 TAATTTTATTATATTGGACCAGCAATTTCACGGGTGAGTGG
45627 TAATTTTATTATATTGGACCAGCAATTTCACGGGTGAGTGG
1 TAATTTTATTATATTGGACCAGCAATTTCACGGGTGAGTGG
45668 AGTTAAGAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (41 bp):
TAATTTTATTATATTGGACCAGCAATTTCACGGGTGAGTGG
Found at i:49591 original size:13 final size:13
Alignment explanation
Indices: 49573--49600 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49563 TTTCGTAGAA
49573 CATTTCTTAATGG
1 CATTTCTTAATGG
49586 CATTTCTTAATGG
1 CATTTCTTAATGG
49599 CA
1 CA
49601 ATTTTAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (13 bp):
CATTTCTTAATGG
Found at i:52675 original size:24 final size:24
Alignment explanation
Indices: 52647--52696 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
52637 TCCTGTTCGA
*
52647 CGTCGTAGATC-CCCATCACCTTTG
1 CGTCGTAGATCACCC-TCACCTGTG
52671 CGTCGTAGATCACCCTCACCTGTG
1 CGTCGTAGATCACCCTCACCTGTG
52695 CG
1 CG
52697 CCGCAGGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.16, C:0.38, G:0.20, T:0.26
Consensus pattern (24 bp):
CGTCGTAGATCACCCTCACCTGTG
Done.