Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013220.1 Corchorus olitorius cultivar O-4 contig13253, 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: 27100
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Found at i:5326 original size:20 final size:20
Alignment explanation
Indices: 5303--5357 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
5293 AAAAGCTTAC
5303 AAGATTACTAAAATT-TAATA
1 AAGATTACTAAAATTGTAA-A
*
5323 AAGACTACTAAAAATTGTAAA
1 AAGATTACT-AAAATTGTAAA
*
5344 AACGGTTACTAAAA
1 AA-GATTACTAAAA
5358 CGTTTAGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 8 0.28
21 13 0.45
22 8 0.28
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (20 bp):
AAGATTACTAAAATTGTAAA
Found at i:5736 original size:21 final size:21
Alignment explanation
Indices: 5712--5766 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
5702 GGTCACTAAA
* *
5712 TAAAAAT-TTAAGTAAGGTCTC
1 TAAAAATCTTAA-TAAGATCAC
*
5733 TAAAACATGTTAATAAGATCAC
1 TAAAA-ATCTTAATAAGATCAC
5755 TAAAAATCTTAA
1 TAAAAATCTTAA
5767 ACGAGGTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 11 0.38
22 14 0.48
23 4 0.14
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (21 bp):
TAAAAATCTTAATAAGATCAC
Found at i:5853 original size:86 final size:87
Alignment explanation
Indices: 5756--5927 Score: 294
Period size: 86 Copynumber: 2.0 Consensus size: 87
5746 TAAGATCACT
*
5756 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAA-AAAGCTTTTAAGTTTAA
1 AAAAATCTTAAACAAGGTGATTGAATAAATTTAAGAAAACTATTTAAGAAA-CTTTTAAGTTTAA
* *
5820 TGAAAAGTTTA-TAAGCTTACCA
65 TGAAAAATTGATTAAGCTTACCA
5842 AAAAATCTTAAACAAGGTGATTGAATAAATTTAAGAAAACTATTTAAGAAACTTTTAAGTTTAAT
1 AAAAATCTTAAACAAGGTGATTGAATAAATTTAAGAAAACTATTTAAGAAACTTTTAAGTTTAAT
5907 GAAAAATTGATTAAGCTTACC
66 GAAAAATTGATTAAGCTTACC
5928 TAGAAAATTT
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
86 68 0.84
87 13 0.16
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (87 bp):
AAAAATCTTAAACAAGGTGATTGAATAAATTTAAGAAAACTATTTAAGAAACTTTTAAGTTTAAT
GAAAAATTGATTAAGCTTACCA
Found at i:6500 original size:20 final size:20
Alignment explanation
Indices: 6464--6516 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
6454 ATACTTGCTT
* *
6464 ACTAAAAAGGTTT-TAAGGTT
1 ACTAAAAA-ATTTATAAGGTG
*
6484 ATTAAAAAATTTATAAGGTG
1 ACTAAAAAATTTATAAGGTG
*
6504 ACTAATAAATTTA
1 ACTAAAAAATTTA
6517 AAATATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (20 bp):
ACTAAAAAATTTATAAGGTG
Found at i:7436 original size:2 final size:2
Alignment explanation
Indices: 7429--7489 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
7419 AAATTCACAT
7429 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
7471 TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
7490 AAAACCTATC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:8769 original size:16 final size:16
Alignment explanation
Indices: 8748--8783 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
8738 TACGTGTCAT
8748 CACTCATCACATGCCA
1 CACTCATCACATGCCA
* *
8764 CACTCATCACGTGCTA
1 CACTCATCACATGCCA
8780 CACT
1 CACT
8784 TTCAGATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.42, G:0.08, T:0.22
Consensus pattern (16 bp):
CACTCATCACATGCCA
Found at i:10618 original size:13 final size:13
Alignment explanation
Indices: 10585--10619 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
10575 AGGGTTTGGT
10585 GAAG-AGAAAAGG
1 GAAGAAGAAAAGG
10597 GAA-AAGAAAAGG
1 GAAGAAGAAAAGG
10609 GAAGAAGAAAA
1 GAAGAAGAAAA
10620 TAGGGTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAAAGG
Found at i:11518 original size:37 final size:37
Alignment explanation
Indices: 11477--11693 Score: 207
Period size: 37 Copynumber: 5.9 Consensus size: 37
11467 AAAGCATTTC
11477 CTTCATAGTTTTCAAATTGGGAAAGTTCCCATCAAGT
1 CTTCATAGTTTTCAAATTGGGAAAGTTCCCATCAAGT
*
11514 CTTCATGGTTTTCAAATTGGGAAAGTTCCCATCAAGTT
1 CTTCATAGTTTTCAAATTGGGAAAGTTCCCATCAAG-T
* * * * *
11552 TTTCA-AGTTTTCAGATTGGGAAAATTCCGATCAGGT
1 CTTCATAGTTTTCAAATTGGGAAAGTTCCCATCAAGT
*
11588 -TT--TAGTTTTCAAATTGGGAAAGTTCCCATC-AGA
1 CTTCATAGTTTTCAAATTGGGAAAGTTCCCATCAAGT
* * * **
11621 ATT--TAGTTTTCAATTTAGGGAAAGTTCCCGTCATTTT
1 CTTCATAGTTTTCAAATT-GGGAAAGTTCCCATCA-AGT
* *
11658 CGGTTTA-AGTTTTCAAAGTGGGAAAGTTCCCATCAA
1 C--TTCATAGTTTTCAAATTGGGAAAGTTCCCATCAA
11694 AAGCATTTTT
Statistics
Matches: 148, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
33 1 0.01
34 38 0.26
35 16 0.11
36 1 0.01
37 60 0.41
38 5 0.03
39 17 0.11
40 10 0.07
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (37 bp):
CTTCATAGTTTTCAAATTGGGAAAGTTCCCATCAAGT
Found at i:11608 original size:71 final size:74
Alignment explanation
Indices: 11478--11618 Score: 207
Period size: 71 Copynumber: 1.9 Consensus size: 74
11468 AAGCATTTCC
* *
11478 TTCATAGTTTTCAAATTGGGAAAGTTCCCATCAAGTCTTCATGGTTTTCAAATTGGGAAAGTTCC
1 TTCATAGTTTTCAAATTGGGAAAATTCCCATCAAGTCTT-ATAGTTTTCAAATTGGGAAAGTTCC
11543 CATCAAGTTT
65 CATCAAGTTT
* * *
11553 TTCA-AGTTTTCAGATTGGGAAAATTCCGATCAGGT-TT-TAGTTTTCAAATTGGGAAAGTTCCC
1 TTCATAGTTTTCAAATTGGGAAAATTCCCATCAAGTCTTATAGTTTTCAAATTGGGAAAGTTCCC
11615 ATCA
66 ATCA
11619 GAATTTAGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
71 28 0.46
73 2 0.03
74 27 0.44
75 4 0.07
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (74 bp):
TTCATAGTTTTCAAATTGGGAAAATTCCCATCAAGTCTTATAGTTTTCAAATTGGGAAAGTTCCC
ATCAAGTTT
Found at i:11671 original size:108 final size:107
Alignment explanation
Indices: 11482--11692 Score: 259
Period size: 108 Copynumber: 2.0 Consensus size: 107
11472 ATTTCCTTCA
*
11482 TAGTTTTCAAATTGGGAAAGTTCCCATCAAGTCTTCATGGTTTTCAAATTGGGAAAGTTCCCATC
1 TAGTTTTCAAATTGGGAAAGTTCCCATCAAATCTTCA-GGTTTTCAAATTGGGAAAGTTCCCATC
* * *
11547 AAGTTTTTCAAGTTTTCAGATTGGGAAAATTCCGATCAGGTTT
65 AAGTTTTTCAAGTTTTCAAAGTGGGAAAATTCCCATCAGGTTT
* *
11590 TAGTTTTCAAATTGGGAAAGTTCCCATCAGAAT-TT-A-GTTTTCAATTTAGGGAAAGTTCCCGT
1 TAGTTTTCAAATTGGGAAAGTTCCCATCA-AATCTTCAGGTTTTCAAATT-GGGAAAGTTCCCAT
* * *
11652 C-ATTTTCGGTTTAAGTTTTCAAAGTGGGAAAGTTCCCATCA
64 CAAGTTT---TTCAAGTTTTCAAAGTGGGAAAATTCCCATCA
11693 AAAGCATTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
105 14 0.16
106 14 0.16
107 1 0.01
108 58 0.65
109 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (107 bp):
TAGTTTTCAAATTGGGAAAGTTCCCATCAAATCTTCAGGTTTTCAAATTGGGAAAGTTCCCATCA
AGTTTTTCAAGTTTTCAAAGTGGGAAAATTCCCATCAGGTTT
Found at i:14445 original size:50 final size:51
Alignment explanation
Indices: 14386--14497 Score: 124
Period size: 51 Copynumber: 2.2 Consensus size: 51
14376 ATTTTTTTTT
*
14386 TCAAAAACGCAAAACACAAAAAATT-AAA-AACG-C-AAATTTTTTTTTTTAGA
1 TCAAAAACGCAAAA-A-AAAAAATTAAAAGAAAGACGAAA-TTTTTTTTTTAGA
** *
14436 TCAAAAACGCCGAAAAGAAAATTAAAAGAAAGACGAAATTTTTTTTTTAGA
1 TCAAAAACGCAAAAAAAAAAATTAAAAGAAAGACGAAATTTTTTTTTTAGA
*
14487 TTAAAAACGCA
1 TCAAAAACGCA
14498 TAGATCAAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
48 7 0.13
49 4 0.08
50 15 0.29
51 23 0.44
52 3 0.06
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.26
Consensus pattern (51 bp):
TCAAAAACGCAAAAAAAAAAATTAAAAGAAAGACGAAATTTTTTTTTTAGA
Found at i:17394 original size:19 final size:18
Alignment explanation
Indices: 17356--17394 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
17346 TATATGCATG
*
17356 AAATTCAAAATTTTCGAA
1 AAATTCAAAATTTTCCAA
17374 AAATTCAAAATTTTTCCAA
1 AAATTCAAAA-TTTTCCAA
17393 AA
1 AA
17395 TTCCATGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (18 bp):
AAATTCAAAATTTTCCAA
Done.