Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006410.1 Corchorus capsularis cultivar CVL-1 contig06431, 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: 14506
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:1787 original size:10 final size:11
Alignment explanation
Indices: 1750--1788 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1740 AAGGTCCCGA
*
1750 AAAAAAAAGGG
1 AAAAAAAAGAG
*
1761 CAAAAAAAAGTG
1 -AAAAAAAAGAG
1773 AAAAAAAAGAG
1 AAAAAAAAGAG
1784 AAAAA
1 AAAAA
1789 GGTTTCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:2773 original size:35 final size:35
Alignment explanation
Indices: 2733--2889 Score: 219
Period size: 35 Copynumber: 4.5 Consensus size: 35
2723 AGTCTTCGGA
* *
2733 GATCAGAGTTGATCTCATTCTAAGAGGTTTCCAAC
1 GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
*
2768 GATCAGAGTTGATCTCATTTCCAAGAAGTTTTCGAA-
1 GATCAGAGTTGATCTCA-TTCCAAGAAG-TTTCCAAC
*
2804 GATCAGAGTTGATCTCATTCCAAGAAGTTTTCAAC
1 GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
* * *
2839 GATCAGAGTTGATCTCATTTCAA-AAGTTTTCAAT
1 GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
2873 GATCAGAGTTGATCTCA
1 GATCAGAGTTGATCTCA
2890 GATTGATCCG
Statistics
Matches: 112, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
34 32 0.29
35 49 0.44
36 25 0.22
37 6 0.05
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (35 bp):
GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
Found at i:2816 original size:71 final size:69
Alignment explanation
Indices: 2721--2889 Score: 259
Period size: 71 Copynumber: 2.4 Consensus size: 69
2711 GTGATCATTC
* * * *
2721 AAAGTCTTCGGAGATCAGAGTTGATCTCATTCTAAGAGGTTTCCAACGATCAGAGTTGATCTCAT
1 AAAGTTTTCGAAGATCAGAGTTGATCTCATTCCAAGAAGTTTCCAACGATCAGAGTTGATCTCAT
2786 TTCCA
66 TT-CA
*
2791 AGAAGTTTTCGAAGATCAGAGTTGATCTCATTCCAAGAAGTTTTCAACGATCAGAGTTGATCTCA
1 A-AAGTTTTCGAAGATCAGAGTTGATCTCATTCCAAGAAGTTTCCAACGATCAGAGTTGATCTCA
2856 TTTCA
65 TTTCA
2861 AAAGTTTTC-AATGATCAGAGTTGATCTCA
1 AAAGTTTTCGAA-GATCAGAGTTGATCTCA
2890 GATTGATCCG
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
68 2 0.02
69 25 0.27
70 4 0.04
71 61 0.66
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (69 bp):
AAAGTTTTCGAAGATCAGAGTTGATCTCATTCCAAGAAGTTTCCAACGATCAGAGTTGATCTCAT
TTCA
Found at i:2952 original size:35 final size:35
Alignment explanation
Indices: 2906--2978 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
2896 TCCGGTGCGG
2906 TCATTCCAAGAAGTTTTCAACAATCAGAGTTGAGC
1 TCATTCCAAGAAGTTTTCAACAATCAGAGTTGAGC
* ** *
2941 TCATTTCAAGAAGTTTTCAATGATCAGAGTTGATC
1 TCATTCCAAGAAGTTTTCAACAATCAGAGTTGAGC
2976 TCA
1 TCA
2979 AATTGATCCG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (35 bp):
TCATTCCAAGAAGTTTTCAACAATCAGAGTTGAGC
Found at i:3022 original size:89 final size:88
Alignment explanation
Indices: 2818--3027 Score: 348
Period size: 89 Copynumber: 2.4 Consensus size: 88
2808 AGAGTTGATC
*
2818 TCATTCCAAGAAGTTTTCAACGATCAGAGTTGATCTCATTTCAAAAGTTTTCAATGATCAGAGTT
1 TCATTCCAAGAAGTTTTCAACGATCAGAGTTGAGCTCATTTCAAAAGTTTTCAATGATCAGAGTT
*
2883 GATCTCAGATTGATCCGGTGCGG
66 GATCTCAAATTGATCCGGTGCGG
*
2906 TCATTCCAAGAAGTTTTCAACAATCAGAGTTGAGCTCATTTCAAGAAGTTTTCAATGATCAGAGT
1 TCATTCCAAGAAGTTTTCAACGATCAGAGTTGAGCTCATTTCAA-AAGTTTTCAATGATCAGAGT
*
2971 TGATCTCAAATTGATCCGGTGTGG
65 TGATCTCAAATTGATCCGGTGCGG
** *
2995 TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGA
1 TCATTCCAAGAAGTTTTCAACGATCAGAGTTGA
3028 TCCCCAATTG
Statistics
Matches: 113, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
88 42 0.37
89 71 0.63
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (88 bp):
TCATTCCAAGAAGTTTTCAACGATCAGAGTTGAGCTCATTTCAAAAGTTTTCAATGATCAGAGTT
GATCTCAAATTGATCCGGTGCGG
Found at i:3023 original size:54 final size:54
Alignment explanation
Indices: 2941--3313 Score: 459
Period size: 54 Copynumber: 6.9 Consensus size: 54
2931 AGAGTTGAGC
* * *
2941 TCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCAAATTGATCCGGTGTGG
1 TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGTGG
* * * *
2995 TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCCCCAATTGATCTGGTATGG
1 TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGTGG
* * *
3049 TCA-TCTCAAGAAATTTTCAGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCGG
1 TCATTC-CAAGAAGTTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGTGG
* * * *
3103 TCATTCCAAGAAGTTTTCGGTGGTCAGAGTTGACCCCTAATTGATCCGGTGTGG
1 TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGTGG
* * * * *
3157 TC-GTCTAAAAAATTTTCAGTGGTCAGAGTTGATCTCAAATGGA-CCGGTGTGG
1 TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGTGG
* * *
3209 TCATTTCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCCAATTGATACGGTGTGG
1 TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGTGG
* * *
3263 T--TGTCTCACGAAGTTTTCGGTGGTCAGAGTTGATCTCGAATTGATCCGGTG
1 TCAT-TC-CAAGAAGTTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTG
3314 CAGTCATTTC
Statistics
Matches: 272, Mismatches: 41, Indels: 12
0.84 0.13 0.04
Matches are distributed among these distances:
52 12 0.04
53 69 0.25
54 189 0.69
55 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (54 bp):
TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGTGG
Found at i:3135 original size:108 final size:107
Alignment explanation
Indices: 2941--3321 Score: 516
Period size: 108 Copynumber: 3.6 Consensus size: 107
2931 AGAGTTGAGC
* * * * *
2941 TCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCAAATTGATCCGGTGTGGTCATTCCAAGA
1 TCATCTCAAGAAATTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGCGGTCATTCCAAGA
*
3006 AGTTTTCAGTGGTCAGAGTTGATCCCCAATTGATCTGGTATGG
66 AGTTTTCAGTGGTCAGAGTTGATCCCCAATTGATC-GGTGTGG
*
3049 TCATCTCAAGAAATTTTCAGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCGGTCATTCCAAGA
1 TCATCTCAAGAAATTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGCGGTCATTCCAAGA
*
3114 AGTTTTCGGTGGTCAGAGTTGA-CCCCTAATTGATCCGGTGTGG
66 AGTTTTCAGTGGTCAGAGTTGATCCCC-AATTGAT-CGGTGTGG
* * * * *
3157 TCGTCT-AAAAAATTTTCAGTGGTCAGAGTTGATCTCAAATGGA-CCGGTGTGGTCATTTCAAGA
1 TCATCTCAAGAAATTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGCGGTCATTCCAAGA
*
3220 AGTTTTCAGTGGTCAGAGTTGATCTCCAATTGATACGGTGTGG
66 AGTTTTCAGTGGTCAGAGTTGATCCCCAATTGAT-CGGTGTGG
** * * * * *
3263 TTGTCTCACGAAGTTTTCGGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCAGTCATT
1 TCATCTCAAGAAATTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGCGGTCATT
3322 TCAGAAAGAT
Statistics
Matches: 242, Mismatches: 26, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
106 59 0.24
107 72 0.30
108 110 0.45
109 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (107 bp):
TCATCTCAAGAAATTTTCAGTGGTCAGAGTTGATCTCAAATTGATCCGGTGCGGTCATTCCAAGA
AGTTTTCAGTGGTCAGAGTTGATCCCCAATTGATCGGTGTGG
Found at i:3312 original size:29 final size:29
Alignment explanation
Indices: 3228--3313 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 29
3218 GAAGTTTTCA
*
3228 GTGGTCAGAGTTGATCTCCAATTGATACG
1 GTGGTCAGAGTTGATCTCGAATTGATACG
*
3257 GT-GT--G-GTTG-TCTCACGAAGTT--TTCG
1 GTGGTCAGAGTTGATCT--CGAA-TTGATACG
*
3282 GTGGTCAGAGTTGATCTCGAATTGATCCG
1 GTGGTCAGAGTTGATCTCGAATTGATACG
3311 GTG
1 GTG
3314 CAGTCATTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 20
0.66 0.04 0.30
Matches are distributed among these distances:
24 3 0.07
25 9 0.20
26 6 0.14
27 4 0.09
28 7 0.16
29 12 0.27
30 3 0.07
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (29 bp):
GTGGTCAGAGTTGATCTCGAATTGATACG
Found at i:3371 original size:214 final size:215
Alignment explanation
Indices: 2954--3342 Score: 568
Period size: 214 Copynumber: 1.8 Consensus size: 215
2944 TTTCAAGAAG
*
2954 TTTTCAATGATCAGAGTTGATCTCAAATTGATCCGGTGTGGTCATTCCAAGAAGTTTTCAGTGGT
1 TTTTCAATGATCAGAGTTGATCTCAAATGGATCCGGTGTGGTCATTCCAAGAAGTTTTCAGTGGT
3019 CAGAGTTGATCCCCAATTGATCTGGTATGGTCATCTCAAGAAATTTTCAGTGGTCAGAGTTGATC
66 CAGAGTTGATCCCCAATTGATCTGGTATGGTCATCTCAAGAAATTTTCAGTGGTCAGAGTTGATC
* * * ** *
3084 TCGAATTGATCCGGTGCGGTCATTCCAAGAAGTTTTCGGTGGTCAGAGTTGACCCCTAATTGATC
131 TCGAATTGATCCGGTGCAGTCATTCCAAGAAGATTTCAGTAATAAGAGTTGACCCCTAATTGATC
*
3149 CGGTGTGGTCGTCTAAAAAA
196 CAGTGTGGTCGTCTAAAAAA
* * *
3169 TTTTCAGTGGTCAGAGTTGATCTCAAATGGA-CCGGTGTGGTCATTTCAAGAAGTTTTCAGTGGT
1 TTTTCAATGATCAGAGTTGATCTCAAATGGATCCGGTGTGGTCATTCCAAGAAGTTTTCAGTGGT
* * ** * * *
3233 CAGAGTTGATCTCCAATTGATAC-GGTGTGGTTGTCTCACGAAGTTTTCGGTGGTCAGAGTTGAT
66 CAGAGTTGATCCCCAATTGAT-CTGGTATGGTCATCTCAAGAAATTTTCAGTGGTCAGAGTTGAT
*
3297 CTCGAATTGATCCGGTGCAGTCATTTC-AGAAAGATTTCAGTAATAA
130 CTCGAATTGATCCGGTGCAGTCATTCCAAG-AAGATTTCAGTAATAA
3343 AGGTTGGACC
Statistics
Matches: 154, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
213 2 0.01
214 123 0.80
215 29 0.19
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (215 bp):
TTTTCAATGATCAGAGTTGATCTCAAATGGATCCGGTGTGGTCATTCCAAGAAGTTTTCAGTGGT
CAGAGTTGATCCCCAATTGATCTGGTATGGTCATCTCAAGAAATTTTCAGTGGTCAGAGTTGATC
TCGAATTGATCCGGTGCAGTCATTCCAAGAAGATTTCAGTAATAAGAGTTGACCCCTAATTGATC
CAGTGTGGTCGTCTAAAAAA
Found at i:5061 original size:17 final size:17
Alignment explanation
Indices: 5041--5080 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5031 TATTATTTAT
*
5041 TATTATCTATTTAGTAC
1 TATTATCTATTTAATAC
5058 TATTATCTATTTAATAC
1 TATTATCTATTTAATAC
5075 TATTAT
1 TATTAT
5081 TTATCTACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (17 bp):
TATTATCTATTTAATAC
Found at i:5206 original size:24 final size:23
Alignment explanation
Indices: 5165--5241 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 23
5155 TTTACATACT
* *
5165 TATTTATCCATTTGTTTATATATC
1 TATTTAT-CTTTTTTTTATATATC
*
5189 TATTTATCTTTTTATTTATCTAT-
1 TATTTATCTTTTT-TTTATATATC
5212 TACTTT-TACTTTTTTTTATAGTTATC
1 TA-TTTAT-CTTTTTTTTATA--TATC
5238 TATT
1 TATT
5242 ACTTAATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
23 12 0.28
24 24 0.56
25 5 0.12
26 2 0.05
ACGTcount: A:0.22, C:0.10, G:0.03, T:0.65
Consensus pattern (23 bp):
TATTTATCTTTTTTTTATATATC
Done.