Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021842.1 Corchorus olitorius cultivar O-4 contig21875, 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: 4710
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Found at i:851 original size:35 final size:35
Alignment explanation
Indices: 808--1111 Score: 409
Period size: 35 Copynumber: 8.8 Consensus size: 35
798 GAAGATCAAC
* * *
808 TCAT-AAAAACTTCTTAAAATGCGATCAATTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* * *
842 TCATCAAAAACTTCTTAAAATGTGATCAACTCTTA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
*
877 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* * * *
912 TCACCGAAAACTTCTTGAAACGAGATCAACTCTAA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* * *
947 TCATCGAAAGCTTCTTGAAAGGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
*
982 TCAT-AAAAACTTCTTGAAAGGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
*
1016 TCAT-AAAATCTTCTTGAAATGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* *
1050 TTATAAAAAACTTCTTGAAATGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
*
1085 TCATC-GAAACTTCTTGAAATGAGATCA
1 TCATCAAAAACTTCTTGAAATGAGATCA
1112 CTAGATCATC
Statistics
Matches: 244, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
34 88 0.36
35 156 0.64
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.29
Consensus pattern (35 bp):
TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
Found at i:1151 original size:87 final size:88
Alignment explanation
Indices: 1038--1199 Score: 254
Period size: 87 Copynumber: 1.9 Consensus size: 88
1028 CTTGAAATGA
* *
1038 GATCAACTCTGATTATAAAAAACTTCTTGAAATGAGATCAACTCTGATCATCG-AAACTTCTTGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGACCATCGAAAACTTCTTGA
*
1102 AATGAGATCACTAGATCATCTGG
66 AACGAGATCACTAGATCATCTGG
* ** *
1125 GATCAACTCTGATCCTCGAAAACTTCTTGAAATGAGATCAACTCTGACCATTGAAAACTTCTTGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGACCATCGAAAACTTCTTGA
1190 AACGAGATCA
66 AACGAGATCA
1200 ACTCTGATCA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
87 47 0.70
88 20 0.30
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (88 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGACCATCGAAAACTTCTTGA
AACGAGATCACTAGATCATCTGG
Found at i:1171 original size:35 final size:35
Alignment explanation
Indices: 1125--1338 Score: 306
Period size: 35 Copynumber: 6.1 Consensus size: 35
1115 GATCATCTGG
*
1125 GATCAACTCTGATCCTCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* * *
1160 GATCAACTCTGACCATTGAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
1195 GATCAACTCTGATCATCGAAAACTTCTTAAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
1230 GATCAACTCTGATCAT--AAAGACTTCTTGGAATGA
1 GATCAACTCTGATCATCGAAA-ACTTCTTGAAATGA
*
1264 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* * *
1299 GATTAACTCTGATAATCGAAAACTTCCTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
1334 GATCA
1 GATCA
1339 CTAGATCATT
Statistics
Matches: 158, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
33 3 0.02
34 27 0.17
35 125 0.79
36 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
Found at i:1267 original size:104 final size:104
Alignment explanation
Indices: 1125--1338 Score: 313
Period size: 104 Copynumber: 2.0 Consensus size: 104
1115 GATCATCTGG
* *
1125 GATCAACTCTGATCCTCGAAAACTTCTTGAAATGAGATCAACTCTGACCATTGAAAACTTCTTGA
1 GATCAACTCTGATCATC-AAAACTTCTTGAAATGAGATCAACTCTGACCATCGAAAACTTCTTGA
* *
1190 AACGAGATCAACTCTGATCATCGAAAACTTCTTAAAAGGA
65 AACGAGATCAACTCTGATAATCGAAAACTTCCTAAAAGGA
* *
1230 GATCAACTCTGATCAT-AAAGACTTCTTGGAATGAGATCAACTCTGATCATCGAAAACTTCTTGA
1 GATCAACTCTGATCATCAAA-ACTTCTTGAAATGAGATCAACTCTGACCATCGAAAACTTCTTGA
* * * *
1294 AAGGAGATTAACTCTGATAATCGAAAACTTCCTGAAATGA
65 AACGAGATCAACTCTGATAATCGAAAACTTCCTAAAAGGA
1334 GATCA
1 GATCA
1339 CTAGATCATT
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
103 3 0.03
104 80 0.82
105 15 0.15
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (104 bp):
GATCAACTCTGATCATCAAAACTTCTTGAAATGAGATCAACTCTGACCATCGAAAACTTCTTGAA
ACGAGATCAACTCTGATAATCGAAAACTTCCTAAAAGGA
Found at i:1409 original size:34 final size:35
Alignment explanation
Indices: 1370--1455 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 35
1360 CTGATCCTCG
*
1370 AAAACTTCTTGAAATGAGATCAACTCT-GCCATCA
1 AAAACTTCTTGAAATGAGATCAACTCTAACCATCA
* * * *
1404 AAAACTTCTTGAAACGAGATTAACTCTAATCATTA
1 AAAACTTCTTGAAATGAGATCAACTCTAACCATCA
*
1439 AAAACTTCTTGGAATGA
1 AAAACTTCTTGAAATGA
1456 CCGCACTGGA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
34 25 0.57
35 19 0.43
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.29
Consensus pattern (35 bp):
AAAACTTCTTGAAATGAGATCAACTCTAACCATCA
Found at i:1468 original size:122 final size:124
Alignment explanation
Indices: 1250--1480 Score: 313
Period size: 122 Copynumber: 1.9 Consensus size: 124
1240 GATCATAAAG
* * * * *
1250 ACTTCTTGGAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATTAACTCTGATAAT
1 ACTTCTTGAAATGAGATCAACTCTGACCATCAAAAACTTCTTGAAACGAGATTAACTCTAATAAT
* * * *
1315 CGAAAACTTCCTGAAATGAGATCACTAGATCATTTG-GGATCAATTCTGATCCTCGAAA
66 CAAAAACTTCCTGAAATGACAGCACTAGATCATCTGAGGATCAATTCTGATCCTCGAAA
*
1373 ACTTCTTGAAATGAGATCAACTCTG-CCATCAAAAACTTCTTGAAACGAGATTAACTCTAATCAT
1 ACTTCTTGAAATGAGATCAACTCTGACCATCAAAAACTTCTTGAAACGAGATTAACTCTAATAAT
* * * * *
1437 TAAAAACTTCTTGGAATGACCGCACTGGATCATCTGAGGATCAA
66 CAAAAACTTCCTGAAATGACAGCACTAGATCATCTGAGGATCAA
1481 AAAACCGCAC
Statistics
Matches: 92, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
122 61 0.66
123 31 0.34
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (124 bp):
ACTTCTTGAAATGAGATCAACTCTGACCATCAAAAACTTCTTGAAACGAGATTAACTCTAATAAT
CAAAAACTTCCTGAAATGACAGCACTAGATCATCTGAGGATCAATTCTGATCCTCGAAA
Done.