Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013594.1 Corchorus olitorius cultivar O-4 contig13627, 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: 63312
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:15828 original size:21 final size:21
Alignment explanation
Indices: 15804--15845 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
15794 TTAAGAGGAT
15804 CTCAACTTTGTTCTATTGGAA
1 CTCAACTTTGTTCTATTGGAA
15825 CTCAACTTTGTTCTATTGGAA
1 CTCAACTTTGTTCTATTGGAA
15846 GGGACTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (21 bp):
CTCAACTTTGTTCTATTGGAA
Found at i:28686 original size:31 final size:31
Alignment explanation
Indices: 28648--28729 Score: 105
Period size: 31 Copynumber: 2.6 Consensus size: 31
28638 ATTTTTAGCC
* *
28648 ACCAATTTGAGCATAAACTTTTTAAAAGTT-
1 ACCAATTTGAGCATAAACCTTTTAAAAATTG
28678 ACTCAATTTGAGTC-TAAACCTTTTAAAAATTG
1 AC-CAATTTGAG-CATAAACCTTTTAAAAATTG
28710 ACCAATTTGAGCATATAACC
1 ACCAATTTGAGCATA-AACC
28730 AGAAACAGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
30 3 0.07
31 35 0.78
32 7 0.16
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (31 bp):
ACCAATTTGAGCATAAACCTTTTAAAAATTG
Found at i:29066 original size:29 final size:29
Alignment explanation
Indices: 28996--29069 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
28986 CACCGGACGA
*
28996 TCTGATCGGTCCAACCTCGAACTGGCCAG
1 TCTGATCGGTCCAACCTCGAACAGGCCAG
* * *
29025 TCTGGTTGGTCCAACCTCGAAGCAGG-CGG
1 TCTGATCGGTCCAACCTCGAA-CAGGCCAG
*
29054 TCTGATCGATCCAACC
1 TCTGATCGGTCCAACC
29070 GTGAACCGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 34 0.92
30 3 0.08
ACGTcount: A:0.20, C:0.32, G:0.26, T:0.22
Consensus pattern (29 bp):
TCTGATCGGTCCAACCTCGAACAGGCCAG
Found at i:31206 original size:53 final size:53
Alignment explanation
Indices: 31143--31411 Score: 511
Period size: 53 Copynumber: 5.1 Consensus size: 53
31133 TGTTTATTCA
31143 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
31196 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
*
31249 ATTGAACATATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
*
31302 ATTGAACCTATTAAATAAGTACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
*
31355 ATTGAACCTATTAAATAAGCACACATACAAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
31408 ATTG
1 ATTG
31412 GATTTAAAGA
Statistics
Matches: 211, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 211 1.00
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.23
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Found at i:32171 original size:31 final size:31
Alignment explanation
Indices: 32130--32204 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 31
32120 ATGCTTACTT
32130 GCTTAGCCAGGTGTTTCTCTTTT-GGCCAAAG
1 GCTTAGCCAGGTGTTTCT-TTTTAGGCCAAAG
* *
32161 GTTTGGCCAGGTGTTTCTTTTTAGGCCAAAG
1 GCTTAGCCAGGTGTTTCTTTTTAGGCCAAAG
32192 GCTTAGCCAGGTG
1 GCTTAGCCAGGTG
32205 CTAATTGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 4 0.10
31 35 0.90
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.35
Consensus pattern (31 bp):
GCTTAGCCAGGTGTTTCTTTTTAGGCCAAAG
Found at i:36206 original size:19 final size:18
Alignment explanation
Indices: 36173--36208 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
36163 TTGAAATAAT
36173 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
36191 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
36209 TGAGTATTCA
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:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:37085 original size:17 final size:18
Alignment explanation
Indices: 37050--37085 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
37040 CTCCTCTATC
*
37050 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
37068 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
37085 A
1 A
37086 ATTAATTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:39233 original size:33 final size:33
Alignment explanation
Indices: 39173--39289 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
39163 CAGGGCAGCA
* **
39173 GCCCCGCGCTTGGCGCGTGGGCTGGCCTGGTGGT
1 GCCCCGTGC-TGGCGCGCAGGCTGGCCTGGTGGT
* *
39207 GCCCCGTGCTGGTGCGCAGGTTGGCCTGGTGGT
1 GCCCCGTGCTGGCGCGCAGGCTGGCCTGGTGGT
* *
39240 GCCCCGTGCTGGCGCGCGGGCTGGCCTGGTGAT
1 GCCCCGTGCTGGCGCGCAGGCTGGCCTGGTGGT
39273 GCCCCGTGCTGGCGCGC
1 GCCCCGTGCTGGCGCGC
39290 CGTTGCTGTG
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 66 0.89
34 8 0.11
ACGTcount: A:0.02, C:0.33, G:0.45, T:0.20
Consensus pattern (33 bp):
GCCCCGTGCTGGCGCGCAGGCTGGCCTGGTGGT
Found at i:41039 original size:10 final size:10
Alignment explanation
Indices: 41024--41062 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
41014 TTGAAATAAT
41024 TCTTCAATGA
1 TCTTCAATGA
*
41034 TCTTCAAATTA
1 TCTTC-AATGA
41045 TCTTCAATGA
1 TCTTCAATGA
41055 GTCTTCAA
1 -TCTTCAA
41063 ACACGAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:41042 original size:22 final size:22
Alignment explanation
Indices: 41012--41063 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
41002 AATTCTTGCT
*
41012 TCTTGAAATAATTCTTCAATGA-
1 TCTTCAAATAA-TCTTCAATGAG
*
41034 TCTTCAAATTATCTTCAATGAG
1 TCTTCAAATAATCTTCAATGAG
41056 TCTTCAAA
1 TCTTCAAA
41064 CACGAGCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAATGAG
Found at i:44282 original size:125 final size:125
Alignment explanation
Indices: 44141--44378 Score: 325
Period size: 125 Copynumber: 1.9 Consensus size: 125
44131 CCCTCAAAAC
* ** * * *
44141 GCGAACTTTTTTTTTGAATTTTCACTAGTTTTCTATGGAAGATAATAGTGTAAAAACCCTAAATC
1 GCGAACTTTTTTTTTGAATTTTCACTAGTTTTCGATAAAACATAATAGTATAAAAACCATAAATC
* *
44206 TAAAATTTCAAGTAAATCGCACCACTAATGAATGCAGAACAAAAATCAGAAATCCTCCCT
66 TAAAATTTCAAGTAAATCGAACCAATAATGAATGCAGAACAAAAATCAGAAATCCTCCCT
* * * *
44266 GCGAA-TTTGTTTTTTGAATTTTCACTATTTTTCGATAAAACCTAGTAGTATAAGAACCATAAAT
1 GCGAACTTT-TTTTTTGAATTTTCACTAGTTTTCGATAAAACATAATAGTATAAAAACCATAAAT
* * *
44330 CTCAAATTTCAAGTCAATCGAACCAATAATGAATGTAGAACAAAAATCA
65 CTAAAATTTCAAGTAAATCGAACCAATAATGAATGCAGAACAAAAATCA
44379 CAAAAATCTT
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
124 3 0.03
125 94 0.97
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (125 bp):
GCGAACTTTTTTTTTGAATTTTCACTAGTTTTCGATAAAACATAATAGTATAAAAACCATAAATC
TAAAATTTCAAGTAAATCGAACCAATAATGAATGCAGAACAAAAATCAGAAATCCTCCCT
Found at i:46228 original size:2 final size:2
Alignment explanation
Indices: 46215--46260 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
46205 TTGGGCTTTG
* *
46215 AT AT AT AC AT AT AT AC A- 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
46256 A- AT AT
1 AT AT AT
46261 CTTTGGTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:49150 original size:23 final size:23
Alignment explanation
Indices: 49124--49169 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
49114 AATTTAGCTG
* * *
49124 TATAGAGTTGATTGTTTAAACTT
1 TATAGAGATGACTATTTAAACTT
49147 TATAGAGATGACTATTTAAACTT
1 TATAGAGATGACTATTTAAACTT
49170 AGAAATTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (23 bp):
TATAGAGATGACTATTTAAACTT
Found at i:51931 original size:21 final size:21
Alignment explanation
Indices: 51905--51945 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
51895 ATTTTGCCCC
51905 GACATTATGTTTATGTTTAAT
1 GACATTATGTTTATGTTTAAT
*
51926 GACATTGTGTTTATGTTTAA
1 GACATTATGTTTATGTTTAA
51946 GAAAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.17, T:0.51
Consensus pattern (21 bp):
GACATTATGTTTATGTTTAAT
Found at i:52168 original size:17 final size:17
Alignment explanation
Indices: 52133--52171 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
52123 TAAGTTTTTG
**
52133 TTATTAATTTTTAACTT
1 TTATTAATTTAGAACTT
*
52150 TTATTAATTTAGAATTT
1 TTATTAATTTAGAACTT
52167 TTATT
1 TTATT
52172 TCAATTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (17 bp):
TTATTAATTTAGAACTT
Found at i:57883 original size:22 final size:23
Alignment explanation
Indices: 57841--57886 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
57831 AGATCCCATC
57841 AAGTTTTCAAAGAAATTCAATTT
1 AAGTTTTCAAAGAAATTCAATTT
*
57864 AAGTTTTCAAAG-TATTCAATTT
1 AAGTTTTCAAAGAAATTCAATTT
57886 A
1 A
57887 GCTCTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
AAGTTTTCAAAGAAATTCAATTT
Found at i:57921 original size:52 final size:52
Alignment explanation
Indices: 57865--58078 Score: 342
Period size: 52 Copynumber: 4.1 Consensus size: 52
57855 ATTCAATTTA
57865 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATC
57917 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATC
* * * * *
57969 AATTTTCAAAGTATTCAATTGAGCTCATCTTCAACTTGGGAAAGTTCCCATC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATC
*
58021 AGTTTTCAAAGTATTCAATTTAGGTC-TTTTCAAATTGGGAAAG-TCCTCATC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATTGGGAAAGTTCC-CATC
58072 AAGTTTT
1 -AGTTTT
58079 AGTTTTCAAA
Statistics
Matches: 150, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
50 3 0.02
51 19 0.13
52 128 0.85
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (52 bp):
AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATC
Found at i:57951 original size:25 final size:25
Alignment explanation
Indices: 57867--57951 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
57857 TCAATTTAAG
57867 TTTTCAAAGTATTCAATTTAGCTCT
1 TTTTCAAAGTATTCAATTTAGCTCT
* **** * ** *
57892 TTTTCAAATTGGGAAAGTTCCCATCAG
1 TTTTCAAAGTATTCAATTTAGC-TC-T
57919 TTTTCAAAGTATTCAATTTAGCTCT
1 TTTTCAAAGTATTCAATTTAGCTCT
57944 TTTTCAAA
1 TTTTCAAA
57952 TTGGGAAAGT
Statistics
Matches: 40, Mismatches: 18, Indels: 4
0.65 0.29 0.06
Matches are distributed among these distances:
25 22 0.55
26 4 0.10
27 14 0.35
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (25 bp):
TTTTCAAAGTATTCAATTTAGCTCT
Found at i:58085 original size:34 final size:35
Alignment explanation
Indices: 58047--58181 Score: 143
Period size: 34 Copynumber: 3.8 Consensus size: 35
58037 AATTTAGGTC
58047 TTTTCAAATTGGGAAAG-TCCTCATCAAGTTTTAG
1 TTTTCAAATTGGGAAAGTTCCTCATCAAGTTTTAG
*
58081 TTTTCAAATTGGGAAAGTTCC-CATCAGGTTTTAG
1 TTTTCAAATTGGGAAAGTTCCTCATCAAGTTTTAG
* * *
58115 TTCTCAATTTAGGGAAAGTTCCT-ATCATTTTCGGTTTTAG
1 TTTTCAAATT-GGGAAAGTTCCTCATCA-----AGTTTTAG
*
58155 TTTTCAAAGTGGGAAAGTT-CTCATCAA
1 TTTTCAAATTGGGAAAGTTCCTCATCAA
58182 AAGCATTTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 18
0.77 0.06 0.16
Matches are distributed among these distances:
34 37 0.44
35 18 0.21
38 2 0.02
39 13 0.15
40 15 0.18
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (35 bp):
TTTTCAAATTGGGAAAGTTCCTCATCAAGTTTTAG
Found at i:60891 original size:16 final size:15
Alignment explanation
Indices: 60853--60894 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
60843 ACAGAGGTTG
*
60853 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
60868 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
60883 ACTAGAAAACAA
1 AC-AGAAAACAA
60895 AGCAGTGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.