Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021799.1 Corchorus olitorius cultivar O-4 contig21832, 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: 63927
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:5750 original size:107 final size:105
Alignment explanation
Indices: 5526--5758 Score: 304
Period size: 107 Copynumber: 2.2 Consensus size: 105
5516 AAAGAAGATA
* * ** *
5526 AGTTTTAATCAATTAATGTTGAAACATGAAATTTGAGTATTCATCGATTAAAACTGTTTCCGGAG
1 AGTTTTAATCGATTAATGTTGAAACATGAAAATTGAGTATTCATCGATTAAAACTGCCTCCAGAG
**
5591 ATGTCGTCAACACTGCCACTTTGATACAATAAAGTTTTGG
66 ATGTCGTCAACACTGCCACTTTGATACAATAAAGACTTGG
* * *
5631 AGTTTTAATCGATTAATGTTGAAGCGTGAAAATTGAGTATTCATCGATTAATACTACGCCTCCAG
1 AGTTTTAATCGATTAATGTTGAAACATGAAAATTGAGTATTCATCGATTAAAACT--GCCTCCAG
* * * *
5696 AGATGTTGTCAACACTGCCACTTTGCTACAGTGAAGACTTGG
64 AGATGTCGTCAACACTGCCACTTTGATACAATAAAGACTTGG
* *
5738 AGTTTTAGTCGATTGATGTTG
1 AGTTTTAATCGATTAATGTTG
5759 GACTTCAAAC
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
105 50 0.45
107 60 0.55
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (105 bp):
AGTTTTAATCGATTAATGTTGAAACATGAAAATTGAGTATTCATCGATTAAAACTGCCTCCAGAG
ATGTCGTCAACACTGCCACTTTGATACAATAAAGACTTGG
Found at i:10574 original size:13 final size:13
Alignment explanation
Indices: 10556--10580 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10546 TATTTCAAAT
10556 TTTTTATTTATTA
1 TTTTTATTTATTA
10569 TTTTTATTTATT
1 TTTTTATTTATT
10581 TAATTAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTATTA
Found at i:12233 original size:31 final size:31
Alignment explanation
Indices: 12198--12298 Score: 107
Period size: 31 Copynumber: 3.3 Consensus size: 31
12188 CCATTTCACG
12198 GAGGGACTAAATTGATCTCTTTTCAATAGTA
1 GAGGGACTAAATTGATCTCTTTTCAATAGTA
*** * * *
12229 GAGGGACTAAATTGA-CAGATTT-GATAATG
1 GAGGGACTAAATTGATCTCTTTTCAATAGTA
* *
12258 GAGGGACTAAATTGATCTTTTTTCTATAGTA
1 GAGGGACTAAATTGATCTCTTTTCAATAGTA
*
12289 CAGGGACTAA
1 GAGGGACTAA
12299 TCAGGTACTT
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 19 0.35
30 8 0.15
31 28 0.51
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (31 bp):
GAGGGACTAAATTGATCTCTTTTCAATAGTA
Found at i:13167 original size:30 final size:30
Alignment explanation
Indices: 13133--13189 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
13123 AAGTGGTCAA
* * *
13133 TCTTCAATCATCGATCTCCAATTGATATTG
1 TCTTCAATCATCAATCTCAAATGGATATTG
13163 TCTTCAATCATCAATCTCAAATGGATA
1 TCTTCAATCATCAATCTCAAATGGATA
13190 CTGATAGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.37
Consensus pattern (30 bp):
TCTTCAATCATCAATCTCAAATGGATATTG
Found at i:20380 original size:18 final size:18
Alignment explanation
Indices: 20357--20392 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20347 CTTCGACTGA
20357 AAAAGAGTTAATTTAGTC
1 AAAAGAGTTAATTTAGTC
20375 AAAAGAGTTAATTTAGTC
1 AAAAGAGTTAATTTAGTC
20393 GCCAGGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (18 bp):
AAAAGAGTTAATTTAGTC
Found at i:26100 original size:27 final size:27
Alignment explanation
Indices: 26017--26113 Score: 97
Period size: 27 Copynumber: 3.6 Consensus size: 27
26007 GTCACCCAGT
* *
26017 GGCATTTTGGTCATTCGCATGTTCAGG
1 GGCATTTTGGTCATTTGCATATTCAGG
** ** *
26044 GGCATTTTGGTCATTT-TTTACACTAAG
1 GGCATTTTGGTCATTTGCATATTC-AGG
26071 GGCATTTTGGTCATTTGCATATTCAGG
1 GGCATTTTGGTCATTTGCATATTCAGG
**
26098 GGCACGTTGGTCATTT
1 GGCATTTTGGTCATTT
26114 TAAGTCCACT
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
26 2 0.04
27 49 0.91
28 3 0.06
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.40
Consensus pattern (27 bp):
GGCATTTTGGTCATTTGCATATTCAGG
Found at i:32829 original size:49 final size:49
Alignment explanation
Indices: 32772--32871 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
32762 TAATTTCTTT
32772 AAAGTTCCATTTTTCCTTGAGTGAATTGTAATTCACAAGGAACTTGCCA
1 AAAGTTCCATTTTTCCTTGAGTGAATTGTAATTCACAAGGAACTTGCCA
32821 AAAGTTCCATTTTTCCTTGAGTGAATTGTAATTCACAAGGAACTTGCCA
1 AAAGTTCCATTTTTCCTTGAGTGAATTGTAATTCACAAGGAACTTGCCA
32870 AA
1 AA
32872 CTACAGAGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (49 bp):
AAAGTTCCATTTTTCCTTGAGTGAATTGTAATTCACAAGGAACTTGCCA
Found at i:35775 original size:21 final size:22
Alignment explanation
Indices: 35735--35775 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
35725 GACAAACTCG
*
35735 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
35757 TAACCC-AATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
35776 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.46, C:0.29, G:0.15, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:37105 original size:20 final size:21
Alignment explanation
Indices: 37080--37124 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
37070 ATGGAATTAA
*
37080 ATATCCGTCGATATCTC-GAT
1 ATATCCGTCGATATATCTGAT
*
37100 ATATCCGTTGATATATCTGAT
1 ATATCCGTCGATATATCTGAT
37121 ATAT
1 ATAT
37125 GTACCCCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (21 bp):
ATATCCGTCGATATATCTGAT
Found at i:38239 original size:19 final size:19
Alignment explanation
Indices: 38193--38239 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
38183 TTAATGTGGA
38193 TATACTTGTTTATACATGT
1 TATACTTGTTTATACATGT
*
38212 TAT--TTGTTT-TGCATGT
1 TATACTTGTTTATACATGT
38228 GTATACTTGTTT
1 -TATACTTGTTT
38240 CCACACGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
19 9 0.38
ACGTcount: A:0.19, C:0.09, G:0.15, T:0.57
Consensus pattern (19 bp):
TATACTTGTTTATACATGT
Found at i:38416 original size:16 final size:16
Alignment explanation
Indices: 38395--38429 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38385 ACTTCATTGG
* *
38395 TTTTTGTCGCTTCGGT
1 TTTTTGTCACTTCGAT
38411 TTTTTGTCACTTCGAT
1 TTTTTGTCACTTCGAT
38427 TTT
1 TTT
38430 CTCGCTTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.17, G:0.17, T:0.60
Consensus pattern (16 bp):
TTTTTGTCACTTCGAT
Found at i:39380 original size:223 final size:224
Alignment explanation
Indices: 38991--39439 Score: 787
Period size: 223 Copynumber: 2.0 Consensus size: 224
38981 ATTATTATAT
* *
38991 GAGTCAATTTTTATAGATTGTTTTTTTGCTCTATAAATGTGAACGTGTTTTCTGTGGGTTTAAAT
1 GAGTCAATTTTTATACATTGTTTTTTTGCTCTATAAATGTGAACGCGTTTTCTGTGGGTTTAAAT
*
39056 ATAATAAATATGATTTATGAGGCTATAGAGTGATGGAATACAAATCGATTCAGTGTAACCGCATG
66 ATAATAAATATAATTTATGAGGCTATAGAGTGATGGAATACAAATCGATTCAGTGTAACCGCATG
39121 TGAAAAATGACTAAAACGGGGCGATAAGGTCGTCCCAGGTTAAAAGTT-GAAAGGAGCATTTAGT
131 TGAAAAATGACTAAAACGGGGCGATAAGGTCGTCCCAGGTTAAAAGTTAG-AAGGAGCATTTAGT
39185 AATTTT-ACCTGGTTACAAAAATAATATGTA
195 -ATTTTCACCTGGTTACAAAAATAATATGTA
*
39215 GAGTCAATTTTTATACATTG-TTTTTTGCTCTGTAAATGTGAACGCGTTTTCTGTGGGTTTAAAT
1 GAGTCAATTTTTATACATTGTTTTTTTGCTCTATAAATGTGAACGCGTTTTCTGTGGGTTTAAAT
* * *
39279 ATAATAAATATAATTTATGAGGTTATAGAGTGATGGAATACGAATCGATTCGGTGTAACCGCATG
66 ATAATAAATATAATTTATGAGGCTATAGAGTGATGGAATACAAATCGATTCAGTGTAACCGCATG
*
39344 TGAGAAATGACTAAAACGGGGCGATAAGGTCGTCCCAGGTTAAAAGTTAGAAGGAGCATTTAGTA
131 TGAAAAATGACTAAAACGGGGCGATAAGGTCGTCCCAGGTTAAAAGTTAGAAGGAGCATTTAGTA
39409 TTTTCACCTGGTTACAAAAATAATATGTA
196 TTTTCACCTGGTTACAAAAATAATATGTA
39438 GA
1 GA
39440 ATATATATTT
Statistics
Matches: 215, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
222 5 0.02
223 190 0.88
224 20 0.09
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.34
Consensus pattern (224 bp):
GAGTCAATTTTTATACATTGTTTTTTTGCTCTATAAATGTGAACGCGTTTTCTGTGGGTTTAAAT
ATAATAAATATAATTTATGAGGCTATAGAGTGATGGAATACAAATCGATTCAGTGTAACCGCATG
TGAAAAATGACTAAAACGGGGCGATAAGGTCGTCCCAGGTTAAAAGTTAGAAGGAGCATTTAGTA
TTTTCACCTGGTTACAAAAATAATATGTA
Found at i:39854 original size:14 final size:14
Alignment explanation
Indices: 39823--39853 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
39813 AAAAGCTTGG
39823 TTTTGAATAAGTGC
1 TTTTGAATAAGTGC
39837 TTTTGAAT-AGTGC
1 TTTTGAATAAGTGC
39850 TTTT
1 TTTT
39854 TAAAATTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (14 bp):
TTTTGAATAAGTGC
Found at i:40311 original size:31 final size:29
Alignment explanation
Indices: 40270--40338 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
40260 CAAATTTAGG
*
40270 CTCAAATTGGTGCATTTTGATAAGGTTTAAA
1 CTCAAATTGGTGCAGTTT-AT-AGGTTTAAA
* * *
40301 CTCAATTTGGTTCAGTTTATAGGTTTAGA
1 CTCAAATTGGTGCAGTTTATAGGTTTAAA
40330 CTCAAATTG
1 CTCAAATTG
40339 AGTAAGCTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 16 0.48
30 2 0.06
31 15 0.45
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (29 bp):
CTCAAATTGGTGCAGTTTATAGGTTTAAA
Found at i:40332 original size:29 final size:31
Alignment explanation
Indices: 40264--40338 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
40254 CCCCATCAAA
* *
40264 TTTAGGCTCAAATTGGTGCATTTTGATAAGG
1 TTTAGACTCAAATTGGTGCAGTTTGATAAGG
* * *
40295 TTTAAACTCAATTTGGTTCAGTTT-AT-AGG
1 TTTAGACTCAAATTGGTGCAGTTTGATAAGG
40324 TTTAGACTCAAATTG
1 TTTAGACTCAAATTG
40339 AGTAAGCTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 16 0.43
30 2 0.05
31 19 0.51
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (31 bp):
TTTAGACTCAAATTGGTGCAGTTTGATAAGG
Found at i:40613 original size:12 final size:12
Alignment explanation
Indices: 40596--40620 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40586 CATCGATACC
40596 TCGATATATCCG
1 TCGATATATCCG
40608 TCGATATATCCG
1 TCGATATATCCG
40620 T
1 T
40621 TGATCTCCGA
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:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:40730 original size:41 final size:41
Alignment explanation
Indices: 40669--40750 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
40659 CCCCCGCAGG
*
40669 GCAGTTAGAGGCAGGCTTTTAAGGAGAGTATTATTTTGTTT
1 GCAGTTAGAGGCAGGCTTTTAAGAAGAGTATTATTTTGTTT
* *
40710 GCAGTTGGAGGCAGGGTTTTAAGAAGAGTATTATTTTGTTT
1 GCAGTTAGAGGCAGGCTTTTAAGAAGAGTATTATTTTGTTT
40751 TTGAGAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.24, C:0.06, G:0.30, T:0.39
Consensus pattern (41 bp):
GCAGTTAGAGGCAGGCTTTTAAGAAGAGTATTATTTTGTTT
Found at i:51913 original size:114 final size:117
Alignment explanation
Indices: 51706--51939 Score: 393
Period size: 114 Copynumber: 2.0 Consensus size: 117
51696 ATTTCTTCCG
* *
51706 AAGGATACTCTCAAAATGCATGGCTTCAAGCTTATAATAAGTAAACTACAAGTTTATTTAGTCCC
1 AAGGATACTCTCAAAATGCATGGCTTCAAGCTTATAATAACTAAACTACAAGTTTATTTAGTCAC
* * *
51771 TACATCTACAGAAAGAGACTCGTCCTTACATTTGAAGACCATCTAAACAGTT
66 TACATCTAAAGAAAGAGACTCATCCTTACATTTGAAGACCATCAAAACAGTT
*
51823 AAGGATGCTCTCAAAATGCATGGCTTCAAGCTTATAAT-ACT-AACTACAAG-TTATTTAGTCAC
1 AAGGATACTCTCAAAATGCATGGCTTCAAGCTTATAATAACTAAACTACAAGTTTATTTAGTCAC
51885 TACATCTAAAGAAAGAGACTCATCCTTACATTTGAAGACCATCAAAACAGTT
66 TACATCTAAAGAAAGAGACTCATCCTTACATTTGAAGACCATCAAAACAGTT
51937 AAG
1 AAG
51940 CGCTACCCGA
Statistics
Matches: 111, Mismatches: 6, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
114 63 0.57
115 9 0.08
116 2 0.02
117 37 0.33
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (117 bp):
AAGGATACTCTCAAAATGCATGGCTTCAAGCTTATAATAACTAAACTACAAGTTTATTTAGTCAC
TACATCTAAAGAAAGAGACTCATCCTTACATTTGAAGACCATCAAAACAGTT
Found at i:54693 original size:12 final size:12
Alignment explanation
Indices: 54676--54700 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54666 GAACCCCAAT
54676 TCCTGTTTCACG
1 TCCTGTTTCACG
54688 TCCTGTTTCACG
1 TCCTGTTTCACG
54700 T
1 T
54701 GAAGCCAATT
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:0.08, C:0.32, G:0.16, T:0.44
Consensus pattern (12 bp):
TCCTGTTTCACG
Found at i:63893 original size:2 final size:2
Alignment explanation
Indices: 63886--63927 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
63876 CAGTCAATGC
63886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.