Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017016.1 Corchorus olitorius cultivar O-4 contig17049, 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: 70542
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8722 original size:19 final size:18
Alignment explanation
Indices: 8689--8724 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8679 TGAAAATAAT
8689 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
8707 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
8725 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:20982 original size:30 final size:30
Alignment explanation
Indices: 20946--21007 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
20936 TTCAATATCT
*
20946 TTTTATAATTAATATATAAAAGTTTAATGA
1 TTTTATAATTAATAGATAAAAGTTTAATGA
20976 TTTTATAATTAATAGATAAAAGTTTAATGA
1 TTTTATAATTAATAGATAAAAGTTTAATGA
21006 TT
1 TT
21008 AAAAATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (30 bp):
TTTTATAATTAATAGATAAAAGTTTAATGA
Found at i:25155 original size:19 final size:19
Alignment explanation
Indices: 25131--25172 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
25121 AAATTAAATA
**
25131 TTTTTATTTTAATATATTT
1 TTTTTATTGAAATATATTT
*
25150 TTTTTATTGAAATTTATTT
1 TTTTTATTGAAATATATTT
25169 TTTT
1 TTTT
25173 AATAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTATTGAAATATATTT
Found at i:26930 original size:22 final size:22
Alignment explanation
Indices: 26889--26930 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
26879 CACAAACCTG
*
26889 TAACCCGAATGACCCGAGAAGT
1 TAACCCGAATGACCCAAGAAGT
* *
26911 TAACCCGGATGATCCAAGAA
1 TAACCCGAATGACCCAAGAA
26931 TACTATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.14
Consensus pattern (22 bp):
TAACCCGAATGACCCAAGAAGT
Found at i:27984 original size:105 final size:103
Alignment explanation
Indices: 27817--28013 Score: 306
Period size: 105 Copynumber: 1.9 Consensus size: 103
27807 GTTTTTAAAA
** *
27817 AAAATTAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 AAAATTAGTAAAATGATAAAAATAAAATAGGTATAAAAATATTAGATTTAATCAAATAAAAATAG
*
27882 AGTTTTTAGTTGAGTAAAACTATAAAAGTATTTTAATT
66 AGTTTTTAGTTAAGTAAAACTATAAAAGTATTTTAATT
* *
27920 AAAA-TAGTAAAATGGTAAAAATAAAATAGTACTTATAAAAATATTAGATTTAATCAAATAAAAA
1 AAAATTAGTAAAATGATAAAAATAAAATAG---GTATAAAAATATTAGATTTAATCAAATAAAAA
27984 TAGAGTTTTTAGTTAAGTAAAACTATAAAA
63 TAGAGTTTTTAGTTAAGTAAAACTATAAAA
28014 ATTTAAGCAA
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
102 24 0.28
103 4 0.05
105 57 0.67
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (103 bp):
AAAATTAGTAAAATGATAAAAATAAAATAGGTATAAAAATATTAGATTTAATCAAATAAAAATAG
AGTTTTTAGTTAAGTAAAACTATAAAAGTATTTTAATT
Found at i:28421 original size:23 final size:21
Alignment explanation
Indices: 28385--28427 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
28375 TTAACATAAT
*
28385 TCTTTTTTCCATTTCCTTTTA
1 TCTTTTTTCCATTTACTTTTA
28406 TCTTTTTGGTCCATTTACTTTT
1 TCTTTTT--TCCATTTACTTTT
28428 TGAGTCTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.09, C:0.21, G:0.05, T:0.65
Consensus pattern (21 bp):
TCTTTTTTCCATTTACTTTTA
Found at i:31009 original size:29 final size:29
Alignment explanation
Indices: 30931--30997 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
30921 GGCAAGGAAT
30931 GGCGGCGGCGTGGCTGAGGAAACCAGAGG
1 GGCGGCGGCGTGGCTGAGGAAACCAGAGG
30960 GGCGGCGGCGTGGCTGAGGAAACCAGAGG
1 GGCGGCGGCGTGGCTGAGGAAACCAGAGG
30989 GGCGGCGGC
1 GGCGGCGGC
30998 TATGTTGGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.18, C:0.22, G:0.54, T:0.06
Consensus pattern (29 bp):
GGCGGCGGCGTGGCTGAGGAAACCAGAGG
Found at i:32083 original size:38 final size:38
Alignment explanation
Indices: 32041--32230 Score: 240
Period size: 39 Copynumber: 4.9 Consensus size: 38
32031 AGGAATTTCC
32041 TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAGTT
1 TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAGTT
* * *
32079 TTCAAGGGTTTTCAATTTAGGGAAAGATCCGATCAAG-T
1 TTCAA-AGTTTTCAATTTAGGGAAAGATCCCATCCAGTT
*
32117 TTCAAAGGTTTTCAATTTAGGGAAAGATCCCATCTAGTT
1 TTCAAA-GTTTTCAATTTAGGGAAAGATCCCATCCAGTT
** *
32156 TTCAAAAGTTTTCGTTTTAGGAAAAGATCCCATCCAGTCTTT
1 TTC-AAAGTTTTCAATTTAGGGAAAGATCCCATCCAG---TT
32198 TTCAAAGTTTTCAA-TTAGGGGAAAGATCCCATC
1 TTCAAAGTTTTCAATTTA-GGGAAAGATCCCATC
32231 AAAGCTTTTA
Statistics
Matches: 131, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
38 39 0.30
39 58 0.44
40 6 0.05
41 23 0.18
42 5 0.04
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (38 bp):
TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAGTT
Found at i:32130 original size:77 final size:77
Alignment explanation
Indices: 32041--32230 Score: 249
Period size: 77 Copynumber: 2.4 Consensus size: 77
32031 AGGAATTTCC
** *
32041 TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAGTTTTCAAGGGTTTTCAATTTAGGGAAAGA
1 TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAGTTTTCAAAAGTTTTCAATTTAGGAAAAGA
*
32106 TCCGATCAAG-T
66 TCCCATCAAGTT
* **
32117 TTCAAAGGTTTTCAATTTAGGGAAAGATCCCATCTAGTTTTCAAAAGTTTTCGTTTTAGGAAAAG
1 TTCAAA-GTTTTCAATTTAGGGAAAGATCCCATCCAGTTTTCAAAAGTTTTCAATTTAGGAAAAG
*
32182 ATCCCATCCAGTCTTT
65 ATCCCATCAAG---TT
32198 TTCAAAGTTTTCAA-TTAGGGGAAAGATCCCATC
1 TTCAAAGTTTTCAATTTA-GGGAAAGATCCCATC
32231 AAAGCTTTTA
Statistics
Matches: 100, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
76 6 0.06
77 61 0.61
79 3 0.03
80 23 0.23
81 7 0.07
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (77 bp):
TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAGTTTTCAAAAGTTTTCAATTTAGGAAAAGA
TCCCATCAAGTT
Found at i:34334 original size:12 final size:12
Alignment explanation
Indices: 34303--34345 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
34293 GTTACTTTCC
*
34303 TTTAGTTTAGT-
1 TTTAGTTTTGTA
34314 TTT-GTTTTGTA
1 TTTAGTTTTGTA
34325 TTTAGTTTTGTA
1 TTTAGTTTTGTA
34337 TTTAGTTTT
1 TTTAGTTTT
34346 TTTTTTGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 6 0.21
11 6 0.21
12 17 0.59
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.70
Consensus pattern (12 bp):
TTTAGTTTTGTA
Found at i:36550 original size:12 final size:12
Alignment explanation
Indices: 36533--36557 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36523 GAGAAGTGTC
36533 AAAGAAAAAAAG
1 AAAGAAAAAAAG
36545 AAAGAAAAAAAG
1 AAAGAAAAAAAG
36557 A
1 A
36558 GTCAAGCTAA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:36744 original size:11 final size:10
Alignment explanation
Indices: 36726--36769 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
36716 TTTTTTTTAA
36726 AAAAAAAAAG
1 AAAAAAAAAG
*
36736 AAGAAAAAAATTA
1 AA-AAAAAAA--G
36749 AAAAAAAAAG
1 AAAAAAAAAG
36759 AAAAAAAAAG
1 AAAAAAAAAG
36769 A
1 A
36770 GAGACACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 13 0.45
11 7 0.24
12 7 0.24
13 2 0.07
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:36744 original size:12 final size:11
Alignment explanation
Indices: 36725--36767 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
36715 TTTTTTTTTA
36725 AAAAAAAAAAG
1 AAAAAAAAAAG
**
36736 AAGAAAAAAATT
1 AA-AAAAAAAAG
36748 AAAAAAAAAAG
1 AAAAAAAAAAG
36759 AAAAAAAAA
1 AAAAAAAAA
36768 GAGAGACACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.88, C:0.00, G:0.07, T:0.05
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:36751 original size:20 final size:20
Alignment explanation
Indices: 36727--36765 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
36717 TTTTTTTAAA
36727 AAAAAAAAGAAGAAAAAAATT
1 AAAAAAAA-AAGAAAAAAATT
36748 AAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAGAAAAAAA
36766 AAGAGAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.87, C:0.00, G:0.08, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAGAAAAAAATT
Found at i:36755 original size:23 final size:22
Alignment explanation
Indices: 36725--36767 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
36715 TTTTTTTTTA
36725 AAAAAAAAAAGAAGAAAAAAATT
1 AAAAAAAAAAGAA-AAAAAAATT
36748 AAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAGAAAAAAAAA
36768 GAGAGACACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.88, C:0.00, G:0.07, T:0.05
Consensus pattern (22 bp):
AAAAAAAAAAGAAAAAAAAATT
Found at i:40299 original size:16 final size:15
Alignment explanation
Indices: 40278--40313 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
40268 ACTTGTTTTG
40278 TTTCTAGTATAATTGC
1 TTTCTA-TATAATTGC
*
40294 TTTCTATTTAATTGC
1 TTTCTATATAATTGC
40309 TTTCT
1 TTTCT
40314 TTCAACCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.19, C:0.14, G:0.08, T:0.58
Consensus pattern (15 bp):
TTTCTATATAATTGC
Found at i:40703 original size:22 final size:22
Alignment explanation
Indices: 40678--40724 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
40668 TAACAACACA
**
40678 AAGGATCTAATTGAACTAAATT
1 AAGGATCTAATTGAAAAAAATT
*
40700 AAGGATTTAATTGAAAAAAATT
1 AAGGATCTAATTGAAAAAAATT
40722 AAG
1 AAG
40725 AAACTTACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (22 bp):
AAGGATCTAATTGAAAAAAATT
Found at i:49944 original size:42 final size:43
Alignment explanation
Indices: 49897--49979 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
49887 CGTGTTTGAC
*
49897 TTATCGTGTCTCGTGT-CTGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTGTCTCGTGTCCT-AATCGTGTCAAGACACGATTAAGA
*
49939 TTATCGTGTTTCGTGTCCTAATCGTGTCAAGACACGATTAA
1 TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAA
49980 CACGTTTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 24 0.65
43 13 0.35
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (43 bp):
TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAAGA
Found at i:49992 original size:20 final size:21
Alignment explanation
Indices: 49967--50009 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
49957 TAATCGTGTC
*
49967 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
49987 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
50008 AA
1 AA
50010 TTAACGGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:50486 original size:12 final size:12
Alignment explanation
Indices: 50469--50499 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
50459 TACCCTATGT
50469 AAACACGACACG
1 AAACACGACACG
50481 AAACACGACACG
1 AAACACGACACG
*
50493 GAACACG
1 AAACACG
50500 GATTGCCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.32, G:0.19, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:65599 original size:41 final size:42
Alignment explanation
Indices: 65556--65639 Score: 114
Period size: 44 Copynumber: 2.0 Consensus size: 42
65546 TTGGATATTC
*
65556 TTTGATAATAATTCTCCACATACATGGATCTTCTTTCAATCTTT
1 TTTGATAATAATCCTCCACATACATGGATCTTCTTTCAATC--T
* * *
65600 TTTTATAATAATCCTCCACATACGTGTATCTTCTTTCAAT
1 TTTGATAATAATCCTCCACATACATGGATCTTCTTTCAAT
65640 AGATCTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.45
Consensus pattern (42 bp):
TTTGATAATAATCCTCCACATACATGGATCTTCTTTCAATCT
Found at i:67219 original size:2 final size:2
Alignment explanation
Indices: 67212--67246 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
67202 GCGAGGCAGC
67212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
67247 CTAGCAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:70494 original size:25 final size:25
Alignment explanation
Indices: 70459--70515 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 25
70449 ACATCCCCCC
*
70459 TTTTTCTGTATTATGAACCCTCTCTG
1 TTTTT-TGTATTATGAACACTCTCTG
70485 TTTTTTGTATTATGAACACTCTCTG
1 TTTTTTGTATTATGAACACTCTCTG
70510 TTTTTT
1 TTTTTT
70516 TCAATTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.56
Consensus pattern (25 bp):
TTTTTTGTATTATGAACACTCTCTG
Done.