Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011888.1 Corchorus olitorius cultivar O-4 contig11921, 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: 6072
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Found at i:999 original size:54 final size:53
Alignment explanation
Indices: 898--1257 Score: 323
Period size: 54 Copynumber: 6.7 Consensus size: 53
888 GATCAAATTG
* * * *
898 GAGATCAACTCTGATCATCGGAAACTTCTT-GAACGACCACACTGGATCATCT
1 GAGATCAACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCT
* *
950 AGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCATACCGGATCATCT
1 -GAGATCAACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCT
* * * * *
1004 GAAGATCAACTCTGATCTTCGAAAATTTCTTGAAACGACAACACCGGATCATCGG
1 G-AGATCAACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATC-T
* * * * * * * *
1059 GAGATCAACTTTGATCTTTGAAAACTTCTAGGAA-GAACCGCACTGGACCTTTT
1 GAGATCAACTCTGATCTTCGAAAACTTCTTGGAATG-ACCACACCGGATCATCT
* * * * *
1112 GGAGATCAACTCTGATCATCAAAAACCTCTTGGAATGACCGCACGGGATCATCT
1 -GAGATCAACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCT
* * * * * *
1166 GAGGATCAACTCTGACCATT-GAAAACTTCTTGGAATGACCGCACTGGACCTTTT
1 GA-GATCAACTCTGATC-TTCGAAAACTTCTTGGAATGACCACACCGGATCATCT
* *
1220 GGGGATCAACTCTGACCATT-GAAAACTTCTTGGAATGA
1 -GAGATCAACTCTGATC-TTCGAAAACTTCTTGGAATGA
1258 GATCAACTCT
Statistics
Matches: 256, Mismatches: 42, Indels: 17
0.81 0.13 0.05
Matches are distributed among these distances:
53 32 0.12
54 220 0.86
55 4 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (53 bp):
GAGATCAACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCT
Found at i:1229 original size:162 final size:162
Alignment explanation
Indices: 897--1254 Score: 382
Period size: 162 Copynumber: 2.2 Consensus size: 162
887 GGATCAAATT
* * * * * * * * *
897 GGAGATCAACTCTGATCATCGGAAACTTCT-TGAACG-ACCACACTGGATCATCTAGAGATCAAC
1 GGAGATCAACTCTGACCATTGAAAACTTCTAGGAA-GAACCGCACTGGACCTTTTGGAGATCAAC
* * * * *
960 TCTGATCTTCGAAAACTTCTTGAAATGACCATACCGGATCATCTGAAGATCAACTCTGATCTTCG
65 TCTGATCATCAAAAACCTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTCTGACCTTCG
* *
1025 AAAATTTCTTGAAACGACAACACCGGATCATCG
130 AAAACTTCTTGAAACGACAACACCGGACCATCG
* * *
1058 GGAGATCAACTTTGATCTTTGAAAACTTCTAGGAAGAACCGCACTGGACCTTTTGGAGATCAACT
1 GGAGATCAACTCTGACCATTGAAAACTTCTAGGAAGAACCGCACTGGACCTTTTGGAGATCAACT
* * * *
1123 CTGATCATCAAAAACCTCTTGGAATGACCGCACGGGATCATCTGAGGATCAACTCTGACCATT-G
66 CTGATCATCAAAAACCTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTCTGACC-TTCG
* * ** * * *
1187 AAAACTTCTTGGAATGACCGCACTGGACCTTTTG
130 AAAACTTCTTGAAACGACAACACCGGACC-ATCG
*
1221 GG-GATCAACTCTGACCATTGAAAACTTCTTGGAA
1 GGAGATCAACTCTGACCATTGAAAACTTCTAGGAA
1255 TGAGATCAAC
Statistics
Matches: 161, Mismatches: 32, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
161 27 0.17
162 128 0.80
163 6 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (162 bp):
GGAGATCAACTCTGACCATTGAAAACTTCTAGGAAGAACCGCACTGGACCTTTTGGAGATCAACT
CTGATCATCAAAAACCTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTCTGACCTTCGA
AAACTTCTTGAAACGACAACACCGGACCATCG
Found at i:1257 original size:108 final size:108
Alignment explanation
Indices: 895--1254 Score: 415
Period size: 108 Copynumber: 3.3 Consensus size: 108
885 CTGGATCAAA
* *
895 TTGGAGATCAACTCTGATCATCGGAAACTTCTT-GAACGACCACACTGGATCATCT-AGAGATCA
1 TTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCA
* ** * * *
958 ACTCTGATCTTCGAAAACTTCTTGAAATGACCATACCGGATCAT
66 ACTCTGATCTT-GAAAACTTCTTGGAATGACCGCACTGGACCTT
* * * * * * *
1002 CTGAAGATCAACTCTGATCTTCGAAAATTTCTTGAAACGACAACACCGGATCATC-GGGAGATCA
1 TTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCA
* *
1066 ACTTTGATCTTTGAAAACTTCTAGGAA-GAACCGCACTGGACCTT
66 ACTCTGATC-TTGAAAACTTCTTGGAATG-ACCGCACTGGACCTT
* * * * *
1110 TTGGAGATCAACTCTGATCATCAAAAACCTCTTGGAATGACCGCACGGGATCATCTGAG-GATCA
1 TTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCA
*
1174 ACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGACCTT
66 ACTCTGATC-TTGAAAACTTCTTGGAATGACCGCACTGGACCTT
* * *
1218 TTGGGGATCAACTCTGACCATTGAAAACTTCTTGGAA
1 TTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAA
1255 TGAGATCAAC
Statistics
Matches: 209, Mismatches: 38, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
107 29 0.14
108 175 0.84
109 5 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (108 bp):
TTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCA
ACTCTGATCTTGAAAACTTCTTGGAATGACCGCACTGGACCTT
Found at i:1262 original size:35 final size:35
Alignment explanation
Indices: 1223--1488 Score: 334
Period size: 35 Copynumber: 7.4 Consensus size: 35
1213 ACCTTTTGGG
* ** *
1223 GATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
1258 GATCAACTCTGATCATAAAAAAAACTTCTTGGAATGA
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAATGA
1295 GATCAACTCTGATCATAAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT---AAAAAACTTCTTGAAATGA
*
1333 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* * *
1368 GATCAACTCTGATAATAAAAACCTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* *
1403 GATCAACTCTGATCATCAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* * *
1438 GATCAACTCTGATAAATAAAAAAACTTCTTGAGAGGA
1 GATCAACTCTGAT-CAT-AAAAAACTTCTTGAAATGA
*
1475 GATCAACTCAGATC
1 GATCAACTCTGATC
1489 TCAGAAAGCT
Statistics
Matches: 208, Mismatches: 18, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
35 108 0.52
36 2 0.01
37 62 0.30
38 36 0.17
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (35 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
Done.