Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023079.1 Corchorus olitorius cultivar O-4 contig23112, 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: 18753
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:2471 original size:60 final size:61
Alignment explanation
Indices: 2384--2545 Score: 238
Period size: 60 Copynumber: 2.7 Consensus size: 61
2374 GCTAATTGTT
* * *
2384 CAAATAAGGGCTTAATGTTTGTC-AAAATGCTCAAATAAGGGTCCGATATTTTAATTTGAC
1 CAAATAAGGGCCTAATGTTTATCGAAAATGCTCAAATAAGGGTCCGATATATTAATTTGAC
* * * *
2444 CAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATATGGGTCCGATCTATTAATTTGGC
1 CAAATAAGGGCCTAATGTTTATCGAAAATGCTCAAATAAGGGTCCGATATATTAATTTGAC
*
2504 CAAATAAAGGCCTAATGTTTATCGAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAATGTTTATCGAAAATGCTCAAATAAGGG
2546 CATGGCGTCA
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
59 4 0.04
60 63 0.70
61 23 0.26
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (61 bp):
CAAATAAGGGCCTAATGTTTATCGAAAATGCTCAAATAAGGGTCCGATATATTAATTTGAC
Found at i:2739 original size:60 final size:60
Alignment explanation
Indices: 2590--2748 Score: 185
Period size: 60 Copynumber: 2.6 Consensus size: 60
2580 CGACGCCAGA
* * * * **
2590 CCCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCTAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTCGATAACATTAGGCACTTATTTGACCAAATTAAAAGATCAAG
* * *
2650 CCCTTATTTGAACATTTTCGATAATATTAGACACTTATTTGACCAAATTAAAAGATCAAG
1 CCCTTATTTGAGCATTTTCGATAACATTAGGCACTTATTTGACCAAATTAAAAGATCAAG
** * *
2710 TTCTTATTTGAGCATTTTGGCA-AACATTAGGCCCTTATT
1 CCCTTATTTGAGCATTTTCG-ATAACATTAGGCACTTATT
2749 AGTAAGCTTT
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 81 0.99
61 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACATTAGGCACTTATTTGACCAAATTAAAAGATCAAG
Found at i:6658 original size:3 final size:3
Alignment explanation
Indices: 6652--6677 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6642 TTTTTTTTAA
6652 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
6678 AGAATTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:7711 original size:28 final size:28
Alignment explanation
Indices: 7671--7726 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
7661 AATCGGATGC
7671 GATTCAATTCTGGATTAGTCATATCCCA
1 GATTCAATTCTGGATTAGTCATATCCCA
7699 GATTCAATTCTGGATTAGTCATATCCCA
1 GATTCAATTCTGGATTAGTCATATCCCA
7727 TGTGGCTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (28 bp):
GATTCAATTCTGGATTAGTCATATCCCA
Found at i:14069 original size:37 final size:37
Alignment explanation
Indices: 14023--14103 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
14013 GATACGGGCA
14023 GAATT-ATGATCCGACTCGAAATATTAAGAGCAACCC
1 GAATTGATGATCCGACTCGAAATATTAAGAGCAACCC
*
14059 GAATTGATGATCCGACTCGAAATATTGAGAGCAACCC
1 GAATTGATGATCCGACTCGAAATATTAAGAGCAACCC
14096 GAATTGAT
1 GAATTGAT
14104 AGATTATTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 5 0.12
37 38 0.88
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (37 bp):
GAATTGATGATCCGACTCGAAATATTAAGAGCAACCC
Found at i:16246 original size:27 final size:28
Alignment explanation
Indices: 16209--16273 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
16199 TACACAAAGT
16209 TATATTTTAA-TAATGACATAATTA-AAA
1 TATATTTTAATTAATGACA-AATTAGAAA
* *
16236 TATTTTTTAATTAATGACAATTTAGAAA
1 TATATTTTAATTAATGACAAATTAGAAA
16264 TATATTTTAA
1 TATATTTTAA
16274 AAAAGGATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 13 0.39
28 20 0.61
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (28 bp):
TATATTTTAATTAATGACAAATTAGAAA
Found at i:16345 original size:10 final size:10
Alignment explanation
Indices: 16321--16357 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
16311 TTCGTACTTT
*
16321 TATATATAG-
1 TATAGATAGA
16330 TATAGATAGA
1 TATAGATAGA
16340 TATAGATAGA
1 TATAGATAGA
16350 TATAGATA
1 TATAGATA
16358 TATTTCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (10 bp):
TATAGATAGA
Found at i:17537 original size:2 final size:2
Alignment explanation
Indices: 17530--17562 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17520 CCCCTTATTT
*
17530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17563 GAATTACGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Done.