Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021199.1 Corchorus olitorius cultivar O-4 contig21232, 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: 7495
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:427 original size:28 final size:27
Alignment explanation
Indices: 374--500 Score: 112
Period size: 27 Copynumber: 4.7 Consensus size: 27
364 CTATGAAGTA
*
374 CAAATGACCAAAATG-CCTTGGAATGTG
1 CAAATGACCAAAATGCCCCTGG-ATGTG
*
401 TAAAATGACCAAAATGCCCCTGGATGTG
1 -CAAATGACCAAAATGCCCCTGGATGTG
* * * **
429 CAAATGACTAAAATACCCCTGAACATG
1 CAAATGACCAAAATGCCCCTGGATGTG
* * **
456 CAAATGACTAAAATGCCCCTGAACATG
1 CAAATGACCAAAATGCCCCTGGATGTG
* *
483 CAAAAGACTAAAATGCCC
1 CAAATGACCAAAATGCCC
501 ACCTAGGTGA
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
27 64 0.73
28 19 0.22
29 5 0.06
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.19
Consensus pattern (27 bp):
CAAATGACCAAAATGCCCCTGGATGTG
Found at i:441 original size:27 final size:27
Alignment explanation
Indices: 403--500 Score: 142
Period size: 27 Copynumber: 3.6 Consensus size: 27
393 GGAATGTGTA
* * **
403 AAATGACCAAAATGCCCCTGGATGTGC
1 AAATGACTAAAATGCCCCTGAACATGC
*
430 AAATGACTAAAATACCCCTGAACATGC
1 AAATGACTAAAATGCCCCTGAACATGC
457 AAATGACTAAAATGCCCCTGAACATGC
1 AAATGACTAAAATGCCCCTGAACATGC
*
484 AAAAGACTAAAATGCCC
1 AAATGACTAAAATGCCC
501 ACCTAGGTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAACATGC
Found at i:849 original size:30 final size:30
Alignment explanation
Indices: 806--1678 Score: 1214
Period size: 30 Copynumber: 29.0 Consensus size: 30
796 CAAATAAATT
* *
806 TAAAGTAATGATCCT-AAGCCAGGATTGAAA
1 TAAAGCAATGATCCTCAA-CCAGGATTAAAA
*
836 TAAAGCAACGATCCTCAACCAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
*
866 TAAAGCAACGATCCTCAACCAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
*
896 TAAAGCAACGATCCTCAACCAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
* *
926 TAAAGCAATGATCCTCAAACAAGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
* *
956 TATAGCAATGATCCTCAAACAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
*
986 TAAAGCAATGATCCTCAAACAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
*
1016 TAAAGCAAATGATCCTAAACCAGGATTAAAA
1 TAAAGC-AATGATCCTCAACCAGGATTAAAA
1047 TAAAGCAAAT-ATCCTCAACCAGGATTAAAAA
1 TAAAGC-AATGATCCTCAACCAGGATT-AAAA
* * * *
1078 TGAAGCAAAGATCCTCAAACAGGATTAAAG
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
*
1108 TGAAGCAATGATCCTCAACCAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
*
1138 TAAAGCAATGATCCTCAACTAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
**
1168 TAAAGCAACAATCCTCAACCAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
*
1198 TAAAGCAATAATCCTCAACCAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
**
1228 TAAAGCAATGATCCTCAAATAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
* * * *
1258 TGAAGCTATGATCCTCAAACAAGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
* * *
1288 TGAAGCTATGATCCTCAAACAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
*
1318 TAAAGCAATGATCCTCAAACAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
* *
1348 TAAAGCAAATGATTCTAAACCAGGATTAAAA
1 TAAAGC-AATGATCCTCAACCAGGATTAAAA
1379 TAAAGCAAAT-ATCCTCAACCAGGATTAAAAA
1 TAAAGC-AATGATCCTCAACCAGGATT-AAAA
* *
1410 TGAAGCAACGATCCTCAACCAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
*
1440 TAAAGCAATAATCCTCAACCAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
**
1470 TAAAGCAATGATCCTCAAATAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
* * *
1500 TGAAGCTATGATCCTCAAACAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
* * *
1530 TGAAGCTATGATCCTCAAACAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
* *
1560 TGAAGCTATGATCCTCAACCAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
*
1590 TAATGCAAAT-ATCCTCAACCAGGATTAAAA
1 TAAAGC-AATGATCCTCAACCAGGATTAAAA
*
1620 TAAAGCAATAATCCTCAACCAGGATTAAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAAA
*
1650 TAAAGCAATAATCCTCAACCAGGATTAAA
1 TAAAGCAATGATCCTCAACCAGGATTAAA
1679 TAACGATGAT
Statistics
Matches: 778, Mismatches: 56, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
29 3 0.00
30 659 0.85
31 116 0.15
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (30 bp):
TAAAGCAATGATCCTCAACCAGGATTAAAA
Found at i:1425 original size:332 final size:330
Alignment explanation
Indices: 806--1678 Score: 1363
Period size: 332 Copynumber: 2.6 Consensus size: 330
796 CAAATAAATT
* * *
806 TAAAGTAATGATCCT-AAGCCAGGATTGAAATAAAGCAACGATCCTCAACCAGGATTAAAATAAA
1 TAAAGCAATGATCCTCAA-CTAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAAAATAAA
* *
870 GCAACGATCCTCAACCAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAAAATAAAGCAAT
65 GCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAAT-AAGCAAT
935 GATCCTCAAACAAGATTAAAATATAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
129 GATCCTCAAACAAGATTAAAATA-AGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
1000 TCAAACAGGATTAAAATAAAGCAAATGATCCTAAACCAGGATTAAAATAAAGCAAATATCCTCAA
193 TCAAACAGGATTAAAATAAAGCAAATGATCCTAAACCAGGATTAAAATAAAGCAAATATCCTCAA
* * *
1065 CCAGGATTAAAAATGAAGCAAAGATCCTCAAACAGGATTAAAGTGAAGCAATGATCCTCAACCAG
258 CCAGGATTAAAAATGAAGCAAAGATCCTCAAACAGGATTAAAATAAAGCAATAATCCTCAACCAG
1130 GATTAAAA
323 GATTAAAA
*
1138 TAAAGCAATGATCCTCAACTAGGATTAAAATAAAGCAACAATCCTCAACCAGGATTAAAATAAAG
1 TAAAGCAATGATCCTCAACTAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAAAATAAAG
* ** *
1203 CAATAATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAAATAGGATTAAAATGAAGCTATG
66 CAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAAT-AAGCAATG
*
1268 ATCCTCAAACAAGATTAAAATGAAGCTATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCT
130 ATCCTCAAACAAGATTAAAAT-AAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCT
*
1333 CAAACAGGATTAAAATAAAGCAAATGATTCTAAACCAGGATTAAAATAAAGCAAATATCCTCAAC
194 CAAACAGGATTAAAATAAAGCAAATGATCCTAAACCAGGATTAAAATAAAGCAAATATCCTCAAC
* *
1398 CAGGATTAAAAATGAAGCAACGATCCTCAACCAGGATTAAAATAAAGCAATAATCCTCAACCAGG
259 CAGGATTAAAAATGAAGCAAAGATCCTCAAACAGGATTAAAATAAAGCAATAATCCTCAACCAGG
1463 ATTAAAA
324 ATTAAAA
* * * * * *
1470 TAAAGCAATGATCCTCAAATAGGATTAAAATGAAGCTATGATCCTCAAACAGGATTAAAATGAAG
1 TAAAGCAATGATCCTCAACTAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAAAATAAAG
* * * *
1535 CTATGATCCTCAAACAGGATTAAAATGAAGCTATGATCCTCAACCAGGATTAAAATAATGCAAAT
66 CAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAA-GC-AAT
* * * * *
1600 -ATCCTCAACCAGGATTAAAATAAAGCAATAATCCTCAACCAGGATTAAAATAAAGCAATAATCC
129 GATCCTCAAACAAGATTAAAAT-AAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
*
1664 TCAACCAGGATTAAA
193 TCAAACAGGATTAAA
1679 TAACGATGAT
Statistics
Matches: 496, Mismatches: 41, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
331 2 0.00
332 489 0.99
333 5 0.01
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (330 bp):
TAAAGCAATGATCCTCAACTAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAAAATAAAG
CAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAGCAATGA
TCCTCAAACAAGATTAAAATAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCA
AACAGGATTAAAATAAAGCAAATGATCCTAAACCAGGATTAAAATAAAGCAAATATCCTCAACCA
GGATTAAAAATGAAGCAAAGATCCTCAAACAGGATTAAAATAAAGCAATAATCCTCAACCAGGAT
TAAAA
Found at i:1691 original size:38 final size:39
Alignment explanation
Indices: 1649--1776 Score: 156
Period size: 38 Copynumber: 3.3 Consensus size: 39
1639 CAGGATTAAA
*
1649 ATAAAGCAATAATCCTCAACCAGGATT-AAATAACGA-TG
1 ATAAAGCAATAATCCTCAAACAGGATTGAAATAA-GACTG
**
1687 ATAAAGCAATAATCCT-AAACAGGATTGGGATAAGACTG
1 ATAAAGCAATAATCCTCAAACAGGATTGAAATAAGACTG
* *
1725 ATAAAGCAATAATCC-CATATCAGGATTGAAATAAAACTG
1 ATAAAGCAATAATCCTCA-AACAGGATTGAAATAAGACTG
*
1764 ACAAAGCAATAAT
1 ATAAAGCAATAAT
1777 AAGAAATCAT
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
37 11 0.14
38 38 0.49
39 29 0.37
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (39 bp):
ATAAAGCAATAATCCTCAAACAGGATTGAAATAAGACTG
Found at i:4077 original size:5 final size:6
Alignment explanation
Indices: 4059--4092 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
4049 AGGCCAAGTA
4059 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTCT TTC
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTT-T TTC
4093 GAATGGGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTCTTT
Done.