Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000213.1 Corchorus capsularis cultivar CVL-1 contig00213, 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, 952
Length: 1588
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:139 original size:16 final size:16
Alignment explanation
Indices: 118--148 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
108 GAATATATAT
*
118 ATATATATAACTAATA
1 ATATATATAAATAATA
134 ATATATATAAATAAT
1 ATATATATAAATAAT
149 TTTTATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATATATAAATAATA
Found at i:160 original size:13 final size:13
Alignment explanation
Indices: 144--168 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
134 ATATATATAA
144 ATAATTTTTATTT
1 ATAATTTTTATTT
157 ATAATTTTTATT
1 ATAATTTTTATT
169 CGGGTTCTCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATAATTTTTATTT
Found at i:511 original size:31 final size:31
Alignment explanation
Indices: 470--699 Score: 197
Period size: 31 Copynumber: 7.5 Consensus size: 31
460 AAAGGCTAAT
*
470 TGCTCAAATAAGGGCCTAACGTTTGTC-AAAA
1 TGCTCAAATAAGGGCCTAACG-TTATCGAAAA
* * * **
501 TGGTCAAATAAGGGCCTCATC-TT-T-TAATT
1 TGCTCAAATAAGGGCCT-AACGTTATCGAAAA
530 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
* * * **
561 TGCTCAAATAAGGACCTGATC-TT-T-TAATT
1 TGCTCAAATAAGGGCCT-AACGTTATCGAAAA
* * *
590 TGGTCAAATAAGGGCCAAACGTTACCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
* ** *
621 TGCTCAAATAAGGGCCAAACGTTGCCAAAAA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
652 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
*
683 TGCTCAAATATGGGCCT
1 TGCTCAAATAAGGGCCT
700 GGTGTCAGTT
Statistics
Matches: 158, Mismatches: 30, Indels: 22
0.75 0.14 0.10
Matches are distributed among these distances:
28 4 0.03
29 37 0.23
30 7 0.04
31 106 0.67
32 4 0.03
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTATCGAAAA
Found at i:568 original size:60 final size:60
Alignment explanation
Indices: 474--699 Score: 260
Period size: 60 Copynumber: 3.7 Consensus size: 60
464 GCTAATTGCT
* * *
474 CAAATAAGGGCCTAACGTTTGTC-AAAATGGTCAAATAAGGGCCTCATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGC
* * *
534 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGACCTGATCTTTTAATTTGGT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGC
* * * ** **
594 CAAATAAGGGCCAAACGTTACCGAAAATGCTCAAATAAGGGCC-AAACGTTGCCAAAAAT-GC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTAATC-TT--TTAATTTGGC
*
655 TCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATATGGGCCT
1 -CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCT
700 GGTGTCAGTT
Statistics
Matches: 142, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
59 6 0.04
60 92 0.65
61 1 0.01
62 43 0.30
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGC
Found at i:601 original size:29 final size:28
Alignment explanation
Indices: 473--605 Score: 104
Period size: 29 Copynumber: 4.5 Consensus size: 28
463 GGCTAATTGC
* **
473 TCAAATAAGGGCCTAACGTTTGTCAAAATGG
1 TCAAATAAGGGCCTATC-TTT-T-AATTTGG
504 TCAAATAAGGGCCTCATCTTTTAATTTGG
1 TCAAATAAGGGCCT-ATCTTTTAATTTGG
* * * ** *
533 CCAAATAAGGGCCTAACGTTATCGAAAATGC
1 TCAAATAAGGGCCTATC-TT-T-TAATTTGG
*
564 TCAAATAAGGACCTGATCTTTTAATTTGG
1 TCAAATAAGGGCCT-ATCTTTTAATTTGG
593 TCAAATAAGGGCC
1 TCAAATAAGGGCC
606 AAACGTTACC
Statistics
Matches: 80, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
28 2 0.03
29 36 0.45
30 3 0.04
31 35 0.44
32 4 0.05
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (28 bp):
TCAAATAAGGGCCTATCTTTTAATTTGG
Found at i:824 original size:60 final size:59
Alignment explanation
Indices: 731--891 Score: 180
Period size: 60 Copynumber: 2.7 Consensus size: 59
721 TGAGACAGGC
* * * * * * * *
731 CCTTATTTAAGTATTTTAGCAAACGTTAAGCCCTTTTTTGGCCTAATTCAAGGATGGGG
1 CCTTATTTGAGCATTTTAGCAAACGTTAGGCCCTTATTTGACCAAATTCAAAGATGAGG
* * *
790 ACCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTGAAAGATTAGG
1 -CCTTATTTGAGCATTTTAGCAAACGTTAGGCCCTTATTTGACCAAATTCAAAGATGAGG
*
850 CACTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTGA
1 C-CTTATTTGAGCATTTTAGCA-AACGTTAGGCCCTTATTTGA
892 ACAATTAGCC
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 2 0.02
60 85 0.98
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (59 bp):
CCTTATTTGAGCATTTTAGCAAACGTTAGGCCCTTATTTGACCAAATTCAAAGATGAGG
Found at i:826 original size:31 final size:29
Alignment explanation
Indices: 791--891 Score: 114
Period size: 31 Copynumber: 3.3 Consensus size: 29
781 AGGATGGGGA
791 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
1 CCTTATTTGAGCATTTT-G-AAACGTTAGGC
* **
822 CCTTATTTGACCAAATTGAAA-GATTAGGC
1 CCTTATTTGAGCATTTTGAAACG-TTAGGC
*
851 ACTTATTTGAGCATTTTCGATAACGTTAGGC
1 CCTTATTTGAGCATTTT-GA-AACGTTAGGC
882 CCTTATTTGA
1 CCTTATTTGA
892 ACAATTAGCC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.02
29 22 0.38
30 3 0.05
31 31 0.53
32 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (29 bp):
CCTTATTTGAGCATTTTGAAACGTTAGGC
Done.