Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016701.1 Corchorus olitorius cultivar O-4 contig16734, 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: 4342
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Found at i:205 original size:17 final size:17
Alignment explanation
Indices: 164--207 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
154 TTTTGAGGAG
*
164 CTAATAAGGGAATGGGCT
1 CTAA-AAGGAAATGGGCT
*
182 TTAAAAGGAAATGGGCT
1 CTAAAAGGAAATGGGCT
*
199 CTGAAAGGA
1 CTAAAAGGA
208 TTAAACTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.39, C:0.09, G:0.32, T:0.20
Consensus pattern (17 bp):
CTAAAAGGAAATGGGCT
Found at i:465 original size:58 final size:58
Alignment explanation
Indices: 375--493 Score: 229
Period size: 58 Copynumber: 2.1 Consensus size: 58
365 TACCACTCCG
*
375 AGAGTTAGGAAGTGCGCAAAGATGTAGACACCCCTCTTTCTACGCTATTAAAAGATAA
1 AGAGTTAGGAAGTGCGCAAAGATGTAGACACCCCTCTTCCTACGCTATTAAAAGATAA
433 AGAGTTAGGAAGTGCGCAAAGATGTAGACACCCCTCTTCCTACGCTATTAAAAGATAA
1 AGAGTTAGGAAGTGCGCAAAGATGTAGACACCCCTCTTCCTACGCTATTAAAAGATAA
491 AGA
1 AGA
494 CCTGTCTGAG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (58 bp):
AGAGTTAGGAAGTGCGCAAAGATGTAGACACCCCTCTTCCTACGCTATTAAAAGATAA
Found at i:517 original size:25 final size:25
Alignment explanation
Indices: 483--535 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
473 TACGCTATTA
*
483 AAAGATAAAGACCTGTCTGAGGTCG
1 AAAGATAAAGACCCGTCTGAGGTCG
508 AAAGATAAAGACCCGTCTGAGGTCG
1 AAAGATAAAGACCCGTCTGAGGTCG
533 AAA
1 AAA
536 TTGAAACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (25 bp):
AAAGATAAAGACCCGTCTGAGGTCG
Found at i:648 original size:32 final size:32
Alignment explanation
Indices: 514--1464 Score: 1030
Period size: 32 Copynumber: 29.6 Consensus size: 32
504 GTCGAAAGAT
* * *
514 AAAGACCCGTCTGAGGTCGAAATTGAAACTTAG
1 AAAGACCTGTCTGAGGTCGAAA-TAAAACTGAG
* *
547 AAAGACCTGTCTGAGGTCGAAATTGAAA-T-AT
1 AAAGACCTGTCTGAGGTCGAAA-TAAAACTGAG
* * *
578 AAAGACCTGTCTTAGGTCGGAATTGAAAGCTGAG
1 AAAGACCTGTCTGAGGTC-GAAAT-AAAACTGAG
* *
612 AAAGACCTGTTTAAGGTCGAAATAAAACTGAG
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
* * *
644 AAAGACCTGTTTGAGGTCGGAATTGAAAGCTGAG
1 AAAGACCTGTCTGAGGTC-GAAAT-AAAACTGAG
* * *
678 AAAGACCTGTATGAGGTCGGAATTGAAAGCTGAG
1 AAAGACCTGTCTGAGGTC-GAAAT-AAAACTGAG
712 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
* * *
744 AAAGACCTGTCTGAGGTCGGAATTGAAA-T-AT
1 AAAGACCTGTCTGAGGTC-GAAATAAAACTGAG
* *
775 AAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
1 AAAGACCTGTCTGAGGTC-GAAAT-AAAACTGAG
* * ** *
809 AAAGACCTGTTTGAGGTCGGAATGGAACTGAT
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
* *
841 AAAGACCTGTCTAAGGTCGGAATTAAAAGCTGAG
1 AAAGACCTGTCTGAGGTC-GAAATAAAA-CTGAG
*
875 AAAGACCTGTCTGAGGTC-----AAAATTGAG
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
902 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
* *
934 AAAGACTTGTCTGAGGTCGGAATAAAACTGAG
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
* * *
966 AAAGACCTGTCTAAGGTCGGAATTAAAA-T-AT
1 AAAGACCTGTCTGAGGTC-GAAATAAAACTGAG
997 AAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAG
1 AAAGACCTGTCTGAGGTCGAAA-TAAAA-CTGAG
*
1031 AAAGACCTGTTTGAGGTCGAAATAAAACTGAG
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
* * *
1063 AAAGACCTGTCTGATGTCGGAATTGAAAGCTGAG
1 AAAGACCTGTCTGAGGTC-GAAAT-AAAACTGAG
1097 AAAGACCTGTCTGAGGTCG-----AAACTGAG
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
**
1124 AAAGACCTGTCTGAGGTCGAAATTAGAAGTTGAG
1 AAAGACCTGTCTGAGGTCGAAA-TA-AAACTGAG
*
1158 AAAGACCTGTCTAAGGTCGAAATAAAACTGAG
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
* * *
1190 AAAGACCTGTCTGAGGTCGGAATTGAAA-T-AT
1 AAAGACCTGTCTGAGGTC-GAAATAAAACTGAG
1221 AAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAG
1 AAAGACCTGTCTGAGGTCGAAA-TAAAA-CTGAG
* * *
1255 AAAGACCTGTCTGAGGTCGGAA-AGAACTGAT
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
* * *
1286 AAAGACCTGTCTGAGGTCGGAATTGAAA-T-AT
1 AAAGACCTGTCTGAGGTC-GAAATAAAACTGAG
1317 AAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAG
1 AAAGACCTGTCTGAGGTCGAAA-TAAAA-CTGAG
1351 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
1383 AAAGACCTGTCTGAGGTCTG-AATAAAACTGAG
1 AAAGACCTGTCTGAGGTC-GAAATAAAACTGAG
*
1415 AAAGACCTGTCTGAGGTC-ACAATAAAACTGAT
1 AAAGACCTGTCTGAGGTCGA-AATAAAACTGAG
1447 AAAGACCTGTCTGAGGTC
1 AAAGACCTGTCTGAGGTC
1465 TGGAACTTCG
Statistics
Matches: 792, Mismatches: 81, Indels: 91
0.82 0.08 0.09
Matches are distributed among these distances:
27 48 0.06
28 4 0.01
30 9 0.01
31 136 0.17
32 269 0.34
33 93 0.12
34 233 0.29
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (32 bp):
AAAGACCTGTCTGAGGTCGAAATAAAACTGAG
Found at i:653 original size:97 final size:99
Alignment explanation
Indices: 514--1469 Score: 1136
Period size: 97 Copynumber: 9.9 Consensus size: 99
504 GTCGAAAGAT
* * * *
514 AAAGACCCGTCTGAGGTCGAAATTGAAACTTAGAAAGACCTGTCTGAGGTCGAAATTGAAA-T-A
1 AAAGACCTGTCTGAGGTCGAAA-TAAAACTGAGAAAGACCTGTCTGAGGTCGAAATTAAAACTGA
* *
577 TAAAGACCTGTCTTAGGTCGGAATTGAAAGCTGAG
65 GAAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
* * * * *
612 AAAGACCTGTTTAAGGTCGAAATAAAACTGAGAAAGACCTGTTTGAGGTCGGAATTGAAAGCTGA
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAGAAAGACCTGTCTGAGGTCGAAATT-AAAACTGA
*
677 GAAAGACCTGTATGAGGTCGGAATTGAAAGCTGAG
65 GAAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
* * *
712 AAAGACCTGTCTGAGGTCGAAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATTGAAA-T-AT
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAGAAAGACCTGTCTGAGGTCGAAATTAAAACTGAG
775 AAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
66 AAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
* * ** * * *
809 AAAGACCTGTTTGAGGTCGGAATGGAACTGATAAAGACCTGTCTAAGGTCGGAATTAAAAGCTGA
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAGAAAGACCTGTCTGAGGTCGAAATTAAAA-CTGA
*
874 GAAAGACCTGTCTGAGGTC---A---AAA-TTGAG
65 GAAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
* *
902 AAAGACCTGTCTGAGGTCGAAATAAAACTGAGAAAGACTTGTCTGAGGTCGGAA-TAAAACTGAG
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAGAAAGACCTGTCTGAGGTCGAAATTAAAACTGAG
* * *
966 AAAGACCTGTCTAAGGTCGGAATT-AAA-AT-AT
66 AAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
*
997 AAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTTTGAGGTCGAAA-TAAAACTG
1 AAAGACCTGTCTGAGGTCGAAA-TAAAA-CTGAGAAAGACCTGTCTGAGGTCGAAATTAAAACTG
*
1061 AGAAAGACCTGTCTGATGTCGGAATTGAAAGCTGAG
64 AGAAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
**
1097 AAAGACCTGTCTGAGGTCG-----AAACTGAGAAAGACCTGTCTGAGGTCGAAATTAGAAGTTGA
1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAGAAAGACCTGTCTGAGGTCGAAATTA-AAACTGA
* * *
1157 GAAAGACCTGTCTAAGGTC-GAAAT-AAAACTGAG
65 GAAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
* * *
1190 AAAGACCTGTCTGAGGTCGGAATTGAAA-T-ATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTG
1 AAAGACCTGTCTGAGGTC-GAAATAAAACTGAGAAAGACCTGTCTGAGGTCGAAATTAAAA-CTG
* *
1253 AGAAAGACCTGTCTGAGGTCGGAA-AG-AA-CTGAT
64 AGAAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
* * *
1286 AAAGACCTGTCTGAGGTCGGAATTGAAA-T-ATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTG
1 AAAGACCTGTCTGAGGTC-GAAATAAAACTGAGAAAGACCTGTCTGAGGTCGAAATTAAAA-CTG
* *
1349 AGAAAGACCTGTCTGAGGTC-GAAAT-AAAACTGAG
64 AGAAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
1383 AAAGACCTGTCTGAGGTCTG-AATAAAACTGAGAAAGACCTGTCTGAGGTC-ACAA-TAAAACTG
1 AAAGACCTGTCTGAGGTC-GAAATAAAACTGAGAAAGACCTGTCTGAGGTCGA-AATTAAAACTG
*
1445 ATAAAGACCTGTCTGAGGTCTGGAA
64 AGAAAGACCTGTCTGAGGTC-GGAA
1470 CTTCGAAATC
Statistics
Matches: 758, Mismatches: 65, Indels: 70
0.85 0.07 0.08
Matches are distributed among these distances:
91 22 0.03
92 5 0.01
93 103 0.14
94 14 0.02
95 48 0.06
96 127 0.17
97 253 0.33
98 53 0.07
99 8 0.01
100 125 0.16
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (99 bp):
AAAGACCTGTCTGAGGTCGAAATAAAACTGAGAAAGACCTGTCTGAGGTCGAAATTAAAACTGAG
AAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAG
Found at i:668 original size:66 final size:65
Alignment explanation
Indices: 514--1464 Score: 1042
Period size: 66 Copynumber: 14.8 Consensus size: 65
504 GTCGAAAGAT
* * * * *
514 AAAGACCCGTCTGAGGTCGAAATTGAAACTTAGAAAGACCTGTCTGAGGTCGAAATTGAAA-T-A
1 AAAGACCTGTCTGAGGTCGGAATTAAAACTGAGAAAGACCTGTCTGAGGTCGAAA-TAAAACTGA
*
577 T
65 G
* * * *
578 AAAGACCTGTCTTAGGTCGGAATTGAAAGCTGAGAAAGACCTGTTTAAGGTCGAAATAAAACTGA
1 AAAGACCTGTCTGAGGTCGGAATT-AAAACTGAGAAAGACCTGTCTGAGGTCGAAATAAAACTGA
643 G
65 G
* * * * *
644 AAAGACCTGTTTGAGGTCGGAATTGAAAGCTGAGAAAGACCTGTATGAGGTCGGAATTGAAAGCT
1 AAAGACCTGTCTGAGGTCGGAATT-AAAACTGAGAAAGACCTGTCTGAGGTC-GAAAT-AAAACT
709 GAG
63 GAG
* * *
712 AAAGACCTGTCTGAGGTC-GAAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATTGAAA-T-A
1 AAAGACCTGTCTGAGGTCGGAATTAAAACTGAGAAAGACCTGTCTGAGGTC-GAAATAAAACTGA
*
774 T
65 G
* * * **
775 AAAGACCTGTCTGAGGTCGGAATTGAAAGCTGAGAAAGACCTGTTTGAGGTCGGAATGGAACTGA
1 AAAGACCTGTCTGAGGTCGGAATT-AAAACTGAGAAAGACCTGTCTGAGGTCGAAATAAAACTGA
*
840 T
65 G
* *
841 AAAGACCTGTCTAAGGTCGGAATTAAAAGCTGAGAAAGACCTGTCTGAGGTC-----AAAATTGA
1 AAAGACCTGTCTGAGGTCGGAATTAAAA-CTGAGAAAGACCTGTCTGAGGTCGAAATAAAACTGA
901 G
65 G
* * *
902 AAAGACCTGTCTGAGGTC-GAAATAAAACTGAGAAAGACTTGTCTGAGGTCGGAATAAAACTGAG
1 AAAGACCTGTCTGAGGTCGGAATTAAAACTGAGAAAGACCTGTCTGAGGTCGAAATAAAACTGAG
* *
966 AAAGACCTGTCTAAGGTCGGAATTAAAA-T-ATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTG
1 AAAGACCTGTCTGAGGTCGGAATTAAAACTGAGAAAGACCTGTCTGAGGTCGAAA-TAAAA-CTG
1029 AG
64 AG
* * * * *
1031 AAAGACCTGTTTGAGGTC-GAAATAAAACTGAGAAAGACCTGTCTGATGTCGGAATTGAAAGCTG
1 AAAGACCTGTCTGAGGTCGGAATTAAAACTGAGAAAGACCTGTCTGAGGTC-GAAAT-AAAACTG
1095 AG
64 AG
**
1097 AAAGACCTGTCTGAGGTC-G-----AAACTGAGAAAGACCTGTCTGAGGTCGAAATTAGAAGTTG
1 AAAGACCTGTCTGAGGTCGGAATTAAAACTGAGAAAGACCTGTCTGAGGTCGAAA-TA-AAACTG
1156 AG
64 AG
* * * *
1158 AAAGACCTGTCTAAGGTC-GAAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATTGAAA-T-A
1 AAAGACCTGTCTGAGGTCGGAATTAAAACTGAGAAAGACCTGTCTGAGGTC-GAAATAAAACTGA
*
1220 T
65 G
* * *
1221 AAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGTCGGAA-AGAACTGA
1 AAAGACCTGTCTGAGGTCGGAATTAAAA-CTGAGAAAGACCTGTCTGAGGTCGAAATAAAACTGA
*
1285 T
65 G
* *
1286 AAAGACCTGTCTGAGGTCGGAATTGAAA-T-ATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTG
1 AAAGACCTGTCTGAGGTCGGAATTAAAACTGAGAAAGACCTGTCTGAGGTCGAAA-TAAAA-CTG
1349 AG
64 AG
*
1351 AAAGACCTGTCTGAGGTC-GAAATAAAACTGAGAAAGACCTGTCTGAGGTCTG-AATAAAACTGA
1 AAAGACCTGTCTGAGGTCGGAATTAAAACTGAGAAAGACCTGTCTGAGGTC-GAAATAAAACTGA
1414 G
65 G
** *
1415 AAAGACCTGTCTGAGGTCACAA-TAAAACTGATAAAGACCTGTCTGAGGTC
1 AAAGACCTGTCTGAGGTCGGAATTAAAACTGAGAAAGACCTGTCTGAGGTC
1465 TGGAACTTCG
Statistics
Matches: 767, Mismatches: 79, Indels: 82
0.83 0.09 0.09
Matches are distributed among these distances:
59 22 0.03
60 12 0.02
61 73 0.10
62 22 0.03
63 61 0.08
64 146 0.19
65 171 0.22
66 217 0.28
67 18 0.02
68 25 0.03
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (65 bp):
AAAGACCTGTCTGAGGTCGGAATTAAAACTGAGAAAGACCTGTCTGAGGTCGAAATAAAACTGAG
Done.