Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017282.1 Corchorus olitorius cultivar O-4 contig17315, 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: 3145
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Found at i:1033 original size:30 final size:30
Alignment explanation
Indices: 997--1453 Score: 512
Period size: 30 Copynumber: 15.0 Consensus size: 30
987 ACTGATGAAA
997 CAATGATCCTAAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
*
1027 CAATGATCCTCAAA-CATGATTAAAATAAAG
1 CAATGATCCT-AAACCAGGATTAAAATAAAG
* *
1057 CAACGATCCTAAACCAGGATTAACTCATAAAG
1 CAATGATCCTAAACCAGGATTAA--AATAAAG
*
1089 CAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
1119 CAATGATCCTCAAA-CAGGATTAAAATAAAG
1 CAATGATCCT-AAACCAGGATTAAAATAAAG
* * * *
1149 CAACGATCATCAACCAGGATTAACTCATAAAG
1 CAATGATCCTAAACCAGGATTAA--AATAAAG
* *
1181 CAATGATCCTCAACCAGGATTAACTCATAAAG
1 CAATGATCCTAAACCAGGATTAA--AATAAAG
*
1213 CAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
* * *
1243 CAAGGATCGTCAAA-CACGATTAAAATAAAG
1 CAATGATCCT-AAACCAGGATTAAAATAAAG
* * * **
1273 CAACGATCCTCAACCATGATTATCATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
* *
1303 CAATGATCCTCAAA-CAAGATTAACTCATAAAG
1 CAATGATCCT-AAACCAGGATTAA--AATAAAG
*
1335 CAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
1365 CAATGATCCTCAAA-CAGGATTAAAATAAAG
1 CAATGATCCT-AAACCAGGATTAAAATAAAG
* * * *
1395 CAACGATCCTCAACCAGGATTGACATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
1425 CAATGATCCTCAAA-CAGGATTAAAATAAA
1 CAATGATCCT-AAACCAGGATTAAAATAAA
1454 ACTGATAAAG
Statistics
Matches: 369, Mismatches: 41, Indels: 34
0.83 0.09 0.08
Matches are distributed among these distances:
29 9 0.02
30 234 0.63
31 15 0.04
32 111 0.30
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.20
Consensus pattern (30 bp):
CAATGATCCTAAACCAGGATTAAAATAAAG
Found at i:1127 original size:92 final size:92
Alignment explanation
Indices: 981--1447 Score: 588
Period size: 92 Copynumber: 5.1 Consensus size: 92
971 TCCTACATCG
* * *
981 GGATTAACTGATGAAA-CAATGATCCTAAACCAGGATTAAAATAAAGCAATGATCCTCAAACATG
1 GGATTAACTAAT-AAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAAACAGG
1045 ATTAAAATAAAGCAACGATCCTAAACCA
65 ATTAAAATAAAGCAACGATCCTAAACCA
*
1073 GGATTAACTCATAAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAAACAGGA
1 GGATTAACTAATAAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAAACAGGA
* *
1138 TTAAAATAAAGCAACGATCATCAACCA
66 TTAAAATAAAGCAACGATCCTAAACCA
* * *
1165 GGATTAACTCATAAAGCAATGATCCTCAACCAGGATTAACTCATAAAGCAATGATCCTCAACCAG
1 GGATTAACTAATAAAGCAATGATCCTCAACCAGGATTAA--AATAAAGCAATGATCCTCAAACAG
* *
1230 GATTAAAATAAAGCAAGGATCGTCAAA-CA
64 GATTAAAATAAAGCAACGATCCT-AAACCA
* * * ** *
1259 CGATTAA--AATAAAGCAACGATCCTCAACCATGATTATCATAAAGCAATGATCCTCAAACAAGA
1 GGATTAACTAATAAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAAACAGGA
* * *
1322 TTAACTCATAAAGCAATGATCCTCAACCA
66 TTAA--AATAAAGCAACGATCCTAAACCA
* * *
1351 GGATTAA--AATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAACGATCCTCAACCAGGA
1 GGATTAACTAATAAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAAACAGGA
* * *
1414 TTGACATAAAGCAATGATCCTCAAA-CA
66 TTAAAATAAAGCAACGATCCT-AAACCA
1441 GGATTAA
1 GGATTAA
1448 AATAAAACTG
Statistics
Matches: 335, Mismatches: 32, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
90 54 0.16
91 7 0.02
92 221 0.66
94 51 0.15
95 2 0.01
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.20
Consensus pattern (92 bp):
GGATTAACTAATAAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAAACAGGA
TTAAAATAAAGCAACGATCCTAAACCA
Found at i:1170 original size:122 final size:122
Alignment explanation
Indices: 997--1447 Score: 726
Period size: 122 Copynumber: 3.7 Consensus size: 122
987 ACTGATGAAA
* * * * *
997 CAATGATCCT-AAACCAGGATTAAAATAAAGCAATGATCCTCAAACATGATTAAAATAAAGCAAC
1 CAATGATCCTCAAA-CAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAACATAAAGCAAT
1061 GATCCT-AAACCAGGATTAACTCATAAAGCAATGATCCTCAACCAGGATTAAAATAAAG
65 GATCCTCAAA-CAGGATTAACTCATAAAGCAATGATCCTCAACCAGGATTAAAATAAAG
*
1119 CAATGATCCTCAAACAGGATTAAAATAAAGCAACGATCATCAACCAGGATTAACTCATAAAGCAA
1 CAATGATCCTCAAACAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAA--CATAAAGCAA
*
1184 TGATCCTCAACCAGGATTAACTCATAAAGCAATGATCCTCAACCAGGATTAAAATAAAG
64 TGATCCTCAAACAGGATTAACTCATAAAGCAATGATCCTCAACCAGGATTAAAATAAAG
* * * * *
1243 CAAGGATCGTCAAACACGATTAAAATAAAGCAACGATCCTCAACCATGATTATCATAAAGCAATG
1 CAATGATCCTCAAACAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAACATAAAGCAATG
*
1308 ATCCTCAAACAAGATTAACTCATAAAGCAATGATCCTCAACCAGGATTAAAATAAAG
66 ATCCTCAAACAGGATTAACTCATAAAGCAATGATCCTCAACCAGGATTAAAATAAAG
*
1365 CAATGATCCTCAAACAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTGACATAAAGCAATG
1 CAATGATCCTCAAACAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAACATAAAGCAATG
1430 ATCCTCAAACAGGATTAA
66 ATCCTCAAACAGGATTAA
1448 AATAAAACTG
Statistics
Matches: 303, Mismatches: 22, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
122 188 0.62
123 3 0.01
124 110 0.36
125 2 0.01
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.20
Consensus pattern (122 bp):
CAATGATCCTCAAACAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAACATAAAGCAATG
ATCCTCAAACAGGATTAACTCATAAAGCAATGATCCTCAACCAGGATTAAAATAAAG
Found at i:1825 original size:36 final size:36
Alignment explanation
Indices: 1724--2235 Score: 559
Period size: 36 Copynumber: 14.4 Consensus size: 36
1714 CAGTCAATTA
* * * * *
1724 AAATAAACTGCAGAGAAGATCGCCCAGGAGCTACTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
* * * *
1760 AAGTAAATTG-AGGAAAGATCGCCCTGGATCAATTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
* * *
1795 AAATAAACTAAAGAAAAGGTCGCCCTGGATCAAGTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
* *
1831 AAATAGACTGAAGAAAAGATCGCCCTGGATCAATTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
*
1867 AAATAAATTGAAGAAAAGATCGCCCTGGATCAACTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
* *
1903 AAATAAATTGAAGAAAAGATCACCCTGGATCAACTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
* * *
1939 AAATAAACTGAAGAAATGATCGCCCTGGATCAATTA
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
* *
1975 AAATAAACTGAAG-AAAGACCACCCTGGATCAACTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
*
2010 AAATAAACTGAAGAAAAGATCACCCTGGATCAACTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
* * * * *
2046 AAATAAACTGAA-CAAGGACCACCCTAGG-TCAGCTG
1 AAATAAACTGAAGAAAAGATCGCCCT-GGATCAACTG
* * **
2081 AAATAAATTGAAGGAAAGATCGCCCTGGATTGACTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
* * * **
2117 AAATAAATTGGATAAAA-ATCATCCTGGATCAACTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
* * * * *
2152 AAATAGACTGAAG-AAAGACCACCCTGGGTCAATTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
* * * *
2187 AAATAAATTGAAGAAAGGATCGCCCCGGATCAATTG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
2223 AAATAAACTGAAG
1 AAATAAACTGAAG
2236 CATCTGTAAT
Statistics
Matches: 401, Mismatches: 68, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
34 3 0.01
35 133 0.33
36 265 0.66
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (36 bp):
AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTG
Found at i:1864 original size:72 final size:72
Alignment explanation
Indices: 1724--2235 Score: 568
Period size: 71 Copynumber: 7.2 Consensus size: 72
1714 CAGTCAATTA
* * * * * * * * *
1724 AAATAAACTGCAGAGAAGATCGCCCAGGAGCTACTGAAGTAAATTG-AGGAAAGATCGCCCTGGA
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
*
1788 TCAATTG
66 TCAACTG
* * * * *
1795 AAATAAACTAAAGAAAAGGTCGCCCTGGATCAAGTGAAATAGACTGAAGAAAAGATCGCCCTGGA
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
*
1860 TCAATTG
66 TCAACTG
* *
1867 AAATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAAAGATCACCCTGGA
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
1932 TCAACTG
66 TCAACTG
* * * *
1939 AAATAAACTGAAGAAATGATCGCCCTGGATCAATTAAAATAAACTGAAG-AAAGACCACCCTGGA
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
2003 TCAACTG
66 TCAACTG
* * * *
2010 AAATAAACTGAAGAAAAGATCACCCTGGATCAACTGAAATAAACTGAA-CAAGGACCACCCTAGG
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCACCCT-GG
*
2074 -TCAGCTG
65 ATCAACTG
* * ** * * * *
2081 AAATAAATTGAAGGAAAGATCGCCCTGGATTGACTGAAATAAATTGGATAAAA-ATCATCCTGGA
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
2145 TCAACTG
66 TCAACTG
* * * * * * * * *
2152 AAATAGACTGAAG-AAAGACCACCCTGGGTCAATTGAAATAAATTGAAGAAAGGATCGCCCCGGA
1 AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
*
2216 TCAATTG
66 TCAACTG
2223 AAATAAACTGAAG
1 AAATAAACTGAAG
2236 CATCTGTAAT
Statistics
Matches: 375, Mismatches: 60, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
70 32 0.09
71 207 0.55
72 136 0.36
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (72 bp):
AAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
TCAACTG
Done.