Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014327.1 Corchorus capsularis cultivar CVL-1 contig14348, 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: 43546
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1005 original size:2 final size:2
Alignment explanation
Indices: 994--1022 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
984 GTATCTCTAG
994 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1023 AACCTGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:9925 original size:35 final size:35
Alignment explanation
Indices: 9833--10004 Score: 265
Period size: 35 Copynumber: 4.9 Consensus size: 35
9823 GGTGAATCAG
* * *
9833 TAATAAGCAATTTAATTCAGGGCAATTAAGTGAGT
1 TAATAAGTAACTTAATTCAGGGTAATTAAGTGAGT
* * *
9868 CAGTAATTAACCTTAATTCAGGGTAATTAAGTGAGT
1 TAATAAGTAA-CTTAATTCAGGGTAATTAAGTGAGT
9904 TAATAAGTAACTTAATTCAGGGTAATTAAGTGAGT
1 TAATAAGTAACTTAATTCAGGGTAATTAAGTGAGT
9939 TAATAAGTAACTTAATTCAGGGTAATTAAGT-AGT
1 TAATAAGTAACTTAATTCAGGGTAATTAAGTGAGT
9973 TCAATAAGTAACTTAATTCAGGGTAATTAAGT
1 T-AATAAGTAACTTAATTCAGGGTAATTAAGT
10005 TTAGTAAGAA
Statistics
Matches: 126, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
34 4 0.03
35 92 0.73
36 30 0.24
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.34
Consensus pattern (35 bp):
TAATAAGTAACTTAATTCAGGGTAATTAAGTGAGT
Found at i:12885 original size:21 final size:21
Alignment explanation
Indices: 12859--12898 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12849 TAGAAAACCC
12859 TAAGCTACCTAAGCATTAGCT
1 TAAGCTACCTAAGCATTAGCT
*
12880 TAAGCTACCTAAGTATTAG
1 TAAGCTACCTAAGCATTAG
12899 TTTTTCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (21 bp):
TAAGCTACCTAAGCATTAGCT
Found at i:14805 original size:254 final size:259
Alignment explanation
Indices: 14515--15039 Score: 832
Period size: 259 Copynumber: 2.0 Consensus size: 259
14505 GCTTCTCAAA
*
14515 ATATATATATATATATATGTATTCTTGGCTCCCTTTGGGGAGTTAATGTGCCAAATTATGTGGAG
1 ATATATATATATATATATATATTCTTGGCTCCCTTTGGGGAGTTAATGTGCCAAATTATGTGGAG
* **
14580 GAACAAATGAGTTACAATTGGGTCT-T-T-A-A-TT-C-CTTTTTATATAATTCCTTTGTATCCT
66 GAACAAATGAGTT--AA-TGGGTCTATATAAGAGTTACAATTGATATATAATTCCTTTGTATCCT
*
14638 TTGTAATGTTTCTTTGTGATGATTGAACCAAATTAATTCTTATAATTATTGGTTTGTTTTTTATC
128 TTGTAACGTTTCTTTGTGATGATTGAACCAAATTAATTCTTATAATTATTGGTTTGTTTTTTATC
*
14703 TTAATATCAAATATCAATGATACTAAATGACAATAATTATTGTAATTTCCGTTATACTTTATATC
193 TTAATATCAAATATCAATGATACTAAATGACAATAATTATTGTAATTTCCGTTATACTTTATATA
14768 T-
258 TG
14769 ATATATATATATATATATATATTCTTGGCTCCCTTTGGGGAGTTAATGTGCCAAATTATGTGGAG
1 ATATATATATATATATATATATTCTTGGCTCCCTTTGGGGAGTTAATGTGCCAAATTATGTGGAG
* ** * *
14834 GAATAAATGAGTTAATGTTTTTATATAATGAGTTACAATTGATATATAATTTCTTTGTATCCTTT
66 GAACAAATGAGTTAATGGGTCTATATAA-GAGTTACAATTGATATATAATTCCTTTGTATCCTTT
*
14899 GTAACGTTTCTTTGTGATGATTGAATCAAATTAATTCTTATAATTATTGGTTTGTTTTTTATCTT
130 GTAACGTTTCTTTGTGATGATTGAACCAAATTAATTCTTATAATTATTGGTTTGTTTTTTATCTT
*
14964 AATATCAAATATCAATGATACTAAATGACAATAATTATTGTATTTTCCGTTATACTTTATATATG
195 AATATCAAATATCAATGATACTAAATGACAATAATTATTGTAATTTCCGTTATACTTTATATATG
15029 ACTATATATAT
1 A-TATATATAT
15040 GGATTCACCT
Statistics
Matches: 248, Mismatches: 13, Indels: 13
0.91 0.05 0.05
Matches are distributed among these distances:
251 4 0.02
252 3 0.01
253 1 0.00
254 77 0.31
256 1 0.00
257 2 0.01
258 1 0.00
259 149 0.60
260 1 0.00
261 9 0.04
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (259 bp):
ATATATATATATATATATATATTCTTGGCTCCCTTTGGGGAGTTAATGTGCCAAATTATGTGGAG
GAACAAATGAGTTAATGGGTCTATATAAGAGTTACAATTGATATATAATTCCTTTGTATCCTTTG
TAACGTTTCTTTGTGATGATTGAACCAAATTAATTCTTATAATTATTGGTTTGTTTTTTATCTTA
ATATCAAATATCAATGATACTAAATGACAATAATTATTGTAATTTCCGTTATACTTTATATATG
Found at i:15086 original size:127 final size:127
Alignment explanation
Indices: 14927--15181 Score: 458
Period size: 127 Copynumber: 2.0 Consensus size: 127
14917 GATTGAATCA
*
14927 AATTAATTCTTATAATTATTGGTTTGTTTTTTATCTTAATATCAAATATCAATGATACTAAATGA
1 AATTAATTCCTATAATTATTGGTTTGTTTTTTATCTTAATATCAAATATCAATGATACTAAATGA
*
14992 CAATAATTATTGT-ATTTTCCGTTATACTTTATATATGACTATATATATGGATTCACCTCTAT
66 CAAAAATTATTGTCA-TTTCCGTTATACTTTATATATGACTATATATATGGATTCACCTCTAT
15054 AATTAATTCCTATAATTATTGGTTTGTTTTTTATCTTAATATCAAATATCAATGATACTAAATGA
1 AATTAATTCCTATAATTATTGGTTTGTTTTTTATCTTAATATCAAATATCAATGATACTAAATGA
* *
15119 CAAAAATTATTGTCATTTCCGTTATACTTTGTATATGACTATATATATGGATTCACCTTTAT
66 CAAAAATTATTGTCATTTCCGTTATACTTTATATATGACTATATATATGGATTCACCTCTAT
15181 A
1 A
15182 GCTCACTCTG
Statistics
Matches: 123, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
127 122 0.99
128 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.46
Consensus pattern (127 bp):
AATTAATTCCTATAATTATTGGTTTGTTTTTTATCTTAATATCAAATATCAATGATACTAAATGA
CAAAAATTATTGTCATTTCCGTTATACTTTATATATGACTATATATATGGATTCACCTCTAT
Found at i:17557 original size:2 final size:2
Alignment explanation
Indices: 17552--17596 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
17542 TGTGTGTGTG
* *
17552 TA TA TA TA TA TA TA TG CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17594 TA T
1 TA T
17597 TTACTTGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22645 original size:35 final size:35
Alignment explanation
Indices: 22596--22662 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
22586 GTACGAACTC
22596 AAAAATCTTAATTAATCAATTACTAAAATACCCTT
1 AAAAATCTTAATTAATCAATTACTAAAATACCCTT
*
22631 AAAAATCTTTATTAATCAATTACTAAAATACC
1 AAAAATCTTAATTAATCAATTACTAAAATACC
22663 TTTATTATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.34
Consensus pattern (35 bp):
AAAAATCTTAATTAATCAATTACTAAAATACCCTT
Found at i:22851 original size:30 final size:30
Alignment explanation
Indices: 22816--22877 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
22806 TATAATTTTT
22816 AATCATTAAAAGTTTATTTATTAATTATAA
1 AATCATTAAAAGTTTATTTATTAATTATAA
**
22846 AATCATTAAACTTTTATTTATTAATTATAA
1 AATCATTAAAAGTTTATTTATTAATTATAA
22876 AA
1 AA
22878 AGATATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (30 bp):
AATCATTAAAAGTTTATTTATTAATTATAA
Found at i:26975 original size:90 final size:90
Alignment explanation
Indices: 26868--27031 Score: 247
Period size: 90 Copynumber: 1.8 Consensus size: 90
26858 ACAAATATTA
* ** * * *
26868 AAAAATTGGAGATTTGACTTAGTATGTAATTGTTATATGAATTCATGACTTGAGTAAGACATTAT
1 AAAAATTGAAGATTTGACTTAGTACATAATTGTTATATGAATTCATGACATGAGTAAAACATAAT
*
26933 TTTTTTTAAGCGATAACTTTTTCTT
66 TTATTTTAAGCGATAACTTTTTCTT
* *
26958 AAAAATTGAAGATTTGACTTGGTACATAATTGTTATATGAATTCATGAGATGAGTAAAACATAAT
1 AAAAATTGAAGATTTGACTTAGTACATAATTGTTATATGAATTCATGACATGAGTAAAACATAAT
27023 TTATTTTAA
66 TTATTTTAA
27032 CCCCGCAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 65 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (90 bp):
AAAAATTGAAGATTTGACTTAGTACATAATTGTTATATGAATTCATGACATGAGTAAAACATAAT
TTATTTTAAGCGATAACTTTTTCTT
Found at i:32124 original size:18 final size:18
Alignment explanation
Indices: 32097--32132 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32087 TGACTCAATG
*
32097 GTAAGGTGTATAATCACT
1 GTAAGATGTATAATCACT
*
32115 GTAAGATGTATACTCACT
1 GTAAGATGTATAATCACT
32133 CAATCACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (18 bp):
GTAAGATGTATAATCACT
Done.