Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008516.1 Corchorus olitorius cultivar O-4 contig08543, 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, 823
Length: 1373
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Found at i:389 original size:25 final size:25
Alignment explanation
Indices: 360--407 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
350 ACTATTTAGT
*
360 ATATATATT-ATTAAATAAATAATAA
1 ATATATATTAAAT-AATAAATAATAA
*
385 ATATATTTTAAATAATAAATAAT
1 ATATATATTAAATAATAAATAAT
408 GAGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATATATTAAATAATAAATAATAA
Found at i:808 original size:6 final size:6
Alignment explanation
Indices: 787--835 Score: 80
Period size: 6 Copynumber: 7.8 Consensus size: 6
777 GCAAAACTTA
787 TATATC TATATAC TATATC TATATC TATATC TATATC TATATAC TATAT
1 TATATC TATAT-C TATATC TATATC TATATC TATATC TATAT-C TATAT
836 AAGTCTAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 29 0.71
7 12 0.29
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATC
Found at i:821 original size:25 final size:25
Alignment explanation
Indices: 787--835 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
777 GCAAAACTTA
787 TATATCTATATACTATATCTATATC
1 TATATCTATATACTATATCTATATC
812 TATATCTATAT-CTATATACTATAT
1 TATATCTATATACTATAT-CTATAT
836 AAGTCTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (25 bp):
TATATCTATATACTATATCTATATC
Found at i:1115 original size:112 final size:108
Alignment explanation
Indices: 942--1141 Score: 287
Period size: 112 Copynumber: 1.8 Consensus size: 108
932 TCCAACCAAA
942 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACGTTAAACAACTTATTAT
1 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACGTTAAACAACTTATTA-
1007 TATAATAATTATTAAAATTATTATTAGTTACTCCATATAATTACGT
65 T-T-ATAATTATTAAAATTATTATTAGTTACTCCATATAATTACGT
* * **
1053 TTTTCTTTCCATATTACAAAA-TCTAAAATAATAGTAACAATT-TTTTTACGTTAAACCTCTTAT
1 TTTTATTTCCATATTAAAAAAGTCTAAAAT-A-A-TAACAATTATTTTTACGTTAAACAACTTAT
*
1116 TATTATAATTATTAAACTTATTATTA
63 TATTATAATTATTAAAATTATTATTA
1142 TTATATTAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
109 21 0.26
110 9 0.11
111 21 0.26
112 22 0.27
113 8 0.10
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.46
Consensus pattern (108 bp):
TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACGTTAAACAACTTATTAT
TATAATTATTAAAATTATTATTAGTTACTCCATATAATTACGT
Found at i:1141 original size:15 final size:14
Alignment explanation
Indices: 1117--1159 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1107 ACCTCTTATT
*
1117 ATTATAATTATTAA
1 ATTATTATTATTAA
*
1131 ACTTATTATTATTAT
1 A-TTATTATTATTAA
1146 ATTAATTATTATTA
1 ATT-ATTATTATTA
1160 GTGGTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 22 0.88
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATTATTATTAA
Found at i:1144 original size:112 final size:110
Alignment explanation
Indices: 942--1141 Score: 291
Period size: 109 Copynumber: 1.8 Consensus size: 110
932 TCCAACCAAA
942 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACGTTAAACAACTTATTAT
1 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACGTTAAAC-ACTTATTAT
1007 TATAATAATTATTAAAATTATTATTAGTTACTCCATATAATTACGT
65 TATAATAATTATTAAAATTATTATTAGTTACTCCATATAATTACGT
* * *
1053 TTTTCTTTCCATATTACAAAA-TCTAAAATAATAGTAACAATT-TTTTTACGTTAAAC-C-TCTT
1 TTTTATTTCCATATTAAAAAAGTCTAAAAT-A-A-TAACAATTATTTTTACGTTAAACACTTATT
* *
1114 ATTATTATAATTATTAAACTTATTATTA
63 ATTATAATAATTATTAAAATTATTATTA
1142 TTATATTAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
109 29 0.36
110 9 0.11
111 20 0.25
112 15 0.19
113 8 0.10
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.46
Consensus pattern (110 bp):
TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACGTTAAACACTTATTATT
ATAATAATTATTAAAATTATTATTAGTTACTCCATATAATTACGT
Found at i:1154 original size:18 final size:21
Alignment explanation
Indices: 1111--1159 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1101 CGTTAAACCT
1111 CTTATTATTATAATTATTAAA
1 CTTATTATTATAATTATTAAA
*
1132 CTTATTATTATTA-TATT-AA
1 CTTATTATTATAATTATTAAA
1151 -TTATTATTA
1 CTTATTATTA
1160 GTGGTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
19 2 0.07
20 4 0.15
21 12 0.44
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
CTTATTATTATAATTATTAAA
Found at i:1211 original size:21 final size:20
Alignment explanation
Indices: 1179--1231 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
1169 TTATGTAAAT
1179 TATTATTATTATATATATATA
1 TATTA-TATTATATATATATA
* *
1200 TATCTATATTATCTATATCTA
1 TAT-TATATTATATATATATA
1221 TATTA-ATTATA
1 TATTATATTATA
1232 AAGCCAAGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 5 0.18
20 2 0.07
21 19 0.68
22 2 0.07
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTATATTATATATATATA
Found at i:1231 original size:15 final size:15
Alignment explanation
Indices: 1188--1225 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1178 TTATTATTAT
*
1188 TATATATATATATATC
1 TATAT-TATCTATATC
1204 TATATTATCTATATC
1 TATATTATCTATATC
1219 TATATTA
1 TATATTA
1226 ATTATAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTATCTATATC
Done.