Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017122.1 Corchorus olitorius cultivar O-4 contig17155, 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, 898
Length: 1497
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Found at i:1104 original size:35 final size:35
Alignment explanation
Indices: 1058--1497 Score: 549
Period size: 35 Copynumber: 12.3 Consensus size: 35
1048 ATCAATGTGA
*
1058 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
1093 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCAT--CAAAAACTTCTTGAAATG
* *
1130 AGATCAACTCTGACCATATAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATC--ATCAAAAACTTCTTGAAATG
* *
1167 AGATCAACTCTGACCATATAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATC--ATCAAAAACTTCTTGAAATG
* *
1204 AGATCAACTCTGATCAACAAAAAC-TCTTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTC-TTGAAATG
*
1239 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
1274 AGATCAACTCTGATCATCGAAAACTTCTTGAAATA
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
1309 AGATCAACTCTGATCATAAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAATG
*
1345 AGATCAACTCTGATCATATAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAATG
* * * *
1381 AGATCAACTCTGATCAACGAAAACTCCTTGAAATA
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
1416 AGATCAACTCTGATCATAAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAATG
* * * **
1452 AGATCAACTCTGATCAACGAAAACTCCTTGAAACA
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
1487 AGATCAACTCT
1 AGATCAACTCT
Statistics
Matches: 361, Mismatches: 36, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
34 2 0.01
35 165 0.46
36 95 0.26
37 97 0.27
39 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (35 bp):
AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
Found at i:1359 original size:71 final size:71
Alignment explanation
Indices: 1058--1497 Score: 573
Period size: 71 Copynumber: 6.2 Consensus size: 71
1048 ATCAATGTGA
*
1058 AGATCAACTCTGATCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAAAACTTCT
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAACTCTGATCAT-AAAAAAACTTCT
*
1123 TGAAAGG
65 TGAAATG
* * *
1130 AGATCAACTCTGACCATATAAAAAACTTCTTGAAATGAGATCAACTCTGACCATATAAAAAACTT
1 AGATCAACTCTGATC--ATCAAAAACTTCTTGAAATGAGATCAACTCTGATCATA-AAAAAACTT
1195 CTTGAAATG
63 CTTGAAATG
* * **
1204 AGATCAACTCTGATCAACAAAAAC-TCTTTGAAACGAGATCAACTCTGATCAT-CGAAAACTTCT
1 AGATCAACTCTGATCATCAAAAACTTC-TTGAAATGAGATCAACTCTGATCATAAAAAAACTTCT
1267 TGAAATG
65 TGAAATG
* *
1274 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAACTTCTT
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAAACTTCTT
*
1339 GAAAGG
66 GAAATG
* ** *
1345 AGATCAACTCTGATCATATAAAAACTTCTTGAAATGAGATCAACTCTGATCA-ACGAAAACTCCT
1 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAAACTTCT
*
1409 TGAAATA
65 TGAAATG
* * ** *
1416 AGATCAACTCTGATCATAAAAAAACTTCTTGAAAGGAGATCAACTCTGATCA-ACGAAAACTCCT
1 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAAACTTCT
**
1480 TGAAACA
65 TGAAATG
1487 AGATCAACTCT
1 AGATCAACTCT
Statistics
Matches: 331, Mismatches: 30, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
70 61 0.18
71 129 0.39
72 75 0.23
73 1 0.00
74 65 0.20
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (71 bp):
AGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAAACTTCTT
GAAATG
Found at i:1371 original size:107 final size:107
Alignment explanation
Indices: 1058--1497 Score: 654
Period size: 107 Copynumber: 4.1 Consensus size: 107
1048 ATCAATGTGA
*
1058 AGATCAACTCTGATCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAAAACTTCT
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCAT-AAAAAAACTTCT
* *
1123 TGAAAGGAGATCAACTCTGACCATATAAAAAACTTCTTGAAATG
65 TGAAAGGAGATCAACTCTGATCATA-CAAAAACTTCTTGAAATG
* ** * *
1167 AGATCAACTCTGACCATATAAAAAACTTCTTGAAATGAGATCAACTCTGATCA-ACAAAAAC-TC
1 AGATCAACTCTGATC--ATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAACTTC
* *
1230 TTTGAAACGAGATCAACTCTGATCAT-CGAAAACTTCTTGAAATG
64 -TTGAAAGGAGATCAACTCTGATCATACAAAAACTTCTTGAAATG
1274 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAACTTCTT
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAACTTCTT
*
1339 GAAAGGAGATCAACTCTGATCATATAAAAACTTCTTGAAATG
66 GAAAGGAGATCAACTCTGATCATACAAAAACTTCTTGAAATG
* *
1381 AGATCAACTCTGATCAACGAAAACTCCTTGAAATAAGATCAACTCTGATCATAAAAAAACTTCTT
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAACTTCTT
* * **
1446 GAAAGGAGATCAACTCTGATCA-ACGAAAACTCCTTGAAACA
66 GAAAGGAGATCAACTCTGATCATACAAAAACTTCTTGAAATG
1487 AGATCAACTCT
1 AGATCAACTCT
Statistics
Matches: 302, Mismatches: 23, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
105 33 0.11
106 56 0.19
107 133 0.44
108 2 0.01
109 44 0.15
111 34 0.11
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (107 bp):
AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAACTTCTT
GAAAGGAGATCAACTCTGATCATACAAAAACTTCTTGAAATG
Done.