Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016227.1 Corchorus capsularis cultivar CVL-1 contig16248, 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: 29971
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Found at i:1249 original size:29 final size:29
Alignment explanation
Indices: 1207--1265 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1197 TTTTAGTCCA
*
1207 AGATTTAGCTCCCTTTTAAAACAAACCCT
1 AGATTTAGCCCCCTTTTAAAACAAACCCT
1236 AGATTTAGCCCCCTTTTAAAACAAACCCT
1 AGATTTAGCCCCCTTTTAAAACAAACCCT
1265 A
1 A
1266 TATAAAGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (29 bp):
AGATTTAGCCCCCTTTTAAAACAAACCCT
Found at i:6909 original size:94 final size:94
Alignment explanation
Indices: 6809--6998 Score: 371
Period size: 94 Copynumber: 2.0 Consensus size: 94
6799 AACAAGAAAA
6809 AAAAATGTATAGATAGCTTTTACTAGAATACCTTGAAGCACGGTCCTGCTGCATGCAGGGAATGC
1 AAAAATGTATAGATAGCTTTTACTAGAATACCTTGAAGCACGGTCCTGCTGCATGCAGGGAATGC
6874 AAGGGCAGAAATCGGAACAACATTATTAC
66 AAGGGCAGAAATCGGAACAACATTATTAC
*
6903 AAAAATGTATAGATTGCTTTTACTAGAATACCTTGAAGCACGGTCCTGCTGCATGCAGGGAATGC
1 AAAAATGTATAGATAGCTTTTACTAGAATACCTTGAAGCACGGTCCTGCTGCATGCAGGGAATGC
6968 AAGGGCAGAAATCGGAACAACATTATTAC
66 AAGGGCAGAAATCGGAACAACATTATTAC
6997 AA
1 AA
6999 TGTTTTAATC
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (94 bp):
AAAAATGTATAGATAGCTTTTACTAGAATACCTTGAAGCACGGTCCTGCTGCATGCAGGGAATGC
AAGGGCAGAAATCGGAACAACATTATTAC
Found at i:12806 original size:32 final size:32
Alignment explanation
Indices: 12764--12845 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
12754 CCATTGTGTT
*
12764 CTTCATGTCCATGATAAGCCCTTGACGCATCA
1 CTTCACGTCCATGATAAGCCCTTGACGCATCA
* ** *
12796 CTTCAGGTCCATGATAAGTTCTTGGCGCATCA
1 CTTCACGTCCATGATAAGCCCTTGACGCATCA
*
12828 -TTC-CCTCCATGATAAGCC
1 CTTCACGTCCATGATAAGCC
12846 ATGGGCGCAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 11 0.26
31 3 0.07
32 28 0.67
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.29
Consensus pattern (32 bp):
CTTCACGTCCATGATAAGCCCTTGACGCATCA
Found at i:15207 original size:35 final size:35
Alignment explanation
Indices: 15166--15253 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 35
15156 ATTTCATCAA
* *
15166 ATTCAACACTTGGGGGCTCCTGCAACCCCTTCATC
1 ATTCAACACTTGGGGGCTCCAGCAACCCATTCATC
* * * *
15201 ATTCAACGCTTGGGGACTGCAGCAACTCATTCATC
1 ATTCAACACTTGGGGGCTCCAGCAACCCATTCATC
*
15236 ATTCAATACTTGGGGGCT
1 ATTCAACACTTGGGGGCT
15254 TCAACAACGA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (35 bp):
ATTCAACACTTGGGGGCTCCAGCAACCCATTCATC
Found at i:16050 original size:41 final size:41
Alignment explanation
Indices: 15995--16158 Score: 193
Period size: 41 Copynumber: 4.0 Consensus size: 41
15985 AGGCAATTTT
* * *
15995 CTCTTTCAATGTCCTCAAACACAATTATAACATAGGGGCAA
1 CTCTCTCAAAGTCCTCAAACACAATTATAACACAGGGGCAA
* * * *
16036 CTCTCTCAAAGTCCTCAAACACATTTATAACACAGAGCCAT
1 CTCTCTCAAAGTCCTCAAACACAATTATAACACAGGGGCAA
* * * *
16077 CTATATCAAAGTCCCCAAACACAATTATAACACAAGGGCAA
1 CTCTCTCAAAGTCCTCAAACACAATTATAACACAGGGGCAA
* * *
16118 CTCTCTCTAAAGTCCTCAAGCACATTTATAACACAGAGGCA
1 CTCTCTC-AAAGTCCTCAAACACAATTATAACACAGGGGCA
16159 TATATGTCAA
Statistics
Matches: 100, Mismatches: 22, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
41 72 0.72
42 28 0.28
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.23
Consensus pattern (41 bp):
CTCTCTCAAAGTCCTCAAACACAATTATAACACAGGGGCAA
Found at i:16169 original size:83 final size:82
Alignment explanation
Indices: 16000--16208 Score: 271
Period size: 83 Copynumber: 2.6 Consensus size: 82
15990 ATTTTCTCTT
* * * *
16000 TCAATGTCCTCAAACACAATTATAACATAGGGGCAACTCTCTCAAAGTCCTCAAACACATTTATA
1 TCAAAGTCCCCAAACACAATTATAACACAAGGGCAACTCTCTCAAAGTCCTCAAACACATTTATA
*
16065 ACACAGAGCCATCTATA
66 ACACAGAGCCATATATA
*
16082 TCAAAGTCCCCAAACACAATTATAACACAAGGGCAACTCTCTCTAAAGTCCTCAAGCACATTTAT
1 TCAAAGTCCCCAAACACAATTATAACACAAGGGCAACTCTCTC-AAAGTCCTCAAACACATTTAT
* *
16147 AACACAGAGGCATATATG
65 AACACAGAGCCATATATA
* * * * *
16165 TCAAAGTCTCTAAGCAC-A-TGTAACACAAAGGCAA-TCTCTCAAAG
1 TCAAAGTCCCCAAACACAATTATAACACAAGGGCAACTCTCTCAAAG
16209 GTGATAAAAC
Statistics
Matches: 113, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
79 4 0.04
80 6 0.05
81 14 0.12
82 40 0.35
83 49 0.43
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22
Consensus pattern (82 bp):
TCAAAGTCCCCAAACACAATTATAACACAAGGGCAACTCTCTCAAAGTCCTCAAACACATTTATA
ACACAGAGCCATATATA
Found at i:23700 original size:26 final size:26
Alignment explanation
Indices: 23664--23740 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
23654 GCTATTGTAG
23664 AAATTGAATTTTTCTAAATAAAATAA
1 AAATTGAATTTTTCTAAATAAAATAA
* *
23690 AAATTCAATTTTTCTAACTAAAATAA
1 AAATTGAATTTTTCTAAATAAAATAA
* *
23716 AATTTGAAATTTTCTAAATAAAATA
1 AAATTGAATTTTTCTAAATAAAATA
23741 TTTTAATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (26 bp):
AAATTGAATTTTTCTAAATAAAATAA
Found at i:27239 original size:12 final size:13
Alignment explanation
Indices: 27224--27268 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
27214 AATCTAAATC
27224 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
27236 TAAAGCAAATTAA
1 TAAAGCAGATTAA
27249 TAAAGCAGATTAA
1 TAAAGCAGATTAA
27262 TAAAGCA
1 TAAAGCA
27269 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:27275 original size:25 final size:25
Alignment explanation
Indices: 27224--27276 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
27214 AATCTAAATC
*
27224 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
27249 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
27274 TAA
1 TAA
27277 TTAAAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Done.