Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004059.1 Corchorus capsularis cultivar CVL-1 contig04067, 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, 646
Length: 1078
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Found at i:586 original size:41 final size:40
Alignment explanation
Indices: 459--1068 Score: 496
Period size: 41 Copynumber: 15.7 Consensus size: 40
449 CCTAGGTTTC
*
459 TTTC-AAGTTGGAATCGGTTGGCCTTC--TAAAAT---GT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
* * * *
493 TTTCAGAGTTGGTATCTGTTGGCCTTCTCTAAAAATCAAGCT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCT-TTAAAATCAAG-T
* * *
535 TTTCAGAGTTGGCAACGGTTGGCCTTCTTTAAAGTCAAGTT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAG-T
*
576 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAAT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
* *
616 TTTCAAAAGATGGCATCGGTAGGCCTTC--T-AAA--AAGT
1 TTTC-AAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
*
652 TTTCAAAGGTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
** **
692 ATTTCAAAGTTGGCATCAATTGGCCTTCTTTAAAATCAAAC
1 -TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
*
733 TTTCAAAAGATGGCATCGGTTGGCCTTC--TAAAA--AAGT
1 TTTC-AAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
* * * *
770 TTTCAAAGTTGGCATTGGGTGGCCGTCTTTAAAATCGAGTT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAG-T
* *
811 TTTCAAAAGTTAGCATCGGTTGGCCCTT-TTTAAAA-AAAGT
1 TTTC-AAAGTTGGCATCGGTTGG-CCTTCTTTAAAATCAAGT
851 TTTCAAAGTTGGCATCGGTTGGCCTTC--T-AAA--AA-T
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
* * * **
885 TCTCAAAGTTGGAATCGGTTGGCCTTC-TTAAAGTTTTGAGT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAA--ATCAAGT
926 TTTCAAAGTTGGCATCGGTTGGCCTTC--T--AA--AAGT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
* * * **
960 TCTCAAAGTTGG-AGTCAGTT-GCCTTC-TTAAAGTTTTGAGT
1 TTTCAAAGTTGGCA-TCGGTTGGCCTTCTTTAAA--ATCAAGT
* * * **
1000 TCTCAAAGTTGGCATCGGTTGGCCTTC-ATAAAGTTTTGAGT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAA--ATCAAGT
1041 TTTCAAAGTTGGCATCGGTTGGCCTTCT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCT
1069 AAAAAGTTCT
Statistics
Matches: 478, Mismatches: 56, Indels: 76
0.78 0.09 0.12
Matches are distributed among these distances:
33 7 0.01
34 50 0.10
35 43 0.09
36 32 0.07
37 8 0.02
38 21 0.04
39 23 0.05
40 42 0.09
41 201 0.42
42 48 0.10
43 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (40 bp):
TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
Found at i:671 original size:117 final size:117
Alignment explanation
Indices: 534--953 Score: 557
Period size: 117 Copynumber: 3.6 Consensus size: 117
524 AAAATCAAGC
* * *
534 TTTTCAGAGTTGGCAACGGTTGGCCTTCTTTAAAGTCAAGTTTTTCAAAGTTGGCATCGGTTGGC
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTCAAAGTTGGCATCGGTTGGC
*
599 CTTCTTTAAAATCAAATTTTCAAAAGATGGCATCGGTAGGCCTTCTAAAAAG
66 CTTCTTTAAAATCAAATTTTCAAAAGATGGCATCGGTTGGCCTTCTAAAAAG
* * **
651 TTTTCAAAGGTGGCATCGGTTGGCCTTCTTTAAAATCAAGTATTTCAAAGTTGGCATCAATTGGC
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTCAAAGTTGGCATCGGTTGGC
*
716 CTTCTTTAAAATCAAACTTTCAAAAGATGGCATCGGTTGGCCTTCTAAAAAAG
66 CTTCTTTAAAATCAAATTTTCAAAAGATGGCATCGGTTGGCCTTCT-AAAAAG
* * * * *
769 TTTTCAAAGTTGGCATTGGGTGGCCGTCTTTAAAATCGAGTTTTTCAAAAGTTAGCATCGGTTGG
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTC-AAAGTTGGCATCGGTTGG
*
834 CCCTT-TTTAAAA--AAAGTTTTC-AAAGTTGGCATCGGTTGGCCTTCTAAAAA-
65 -CCTTCTTTAAAATCAAA-TTTTCAAAAGATGGCATCGGTTGGCCTTCTAAAAAG
* * * **
884 TTCTCAAAGTTGGAATCGGTTGGCCTTC-TTAAAGTTTTGAG-TTTTCAAAGTTGGCATCGGTTG
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAA--ATCAAGTTTTTCAAAGTTGGCATCGGTTG
947 GCCTTCT
64 GCCTTCT
954 AAAAGTTCTC
Statistics
Matches: 268, Mismatches: 28, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
113 4 0.01
114 23 0.09
115 28 0.10
116 9 0.03
117 128 0.48
118 50 0.19
119 22 0.08
120 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (117 bp):
TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTCAAAGTTGGCATCGGTTGGC
CTTCTTTAAAATCAAATTTTCAAAAGATGGCATCGGTTGGCCTTCTAAAAAG
Found at i:760 original size:158 final size:151
Alignment explanation
Indices: 471--1073 Score: 464
Period size: 158 Copynumber: 3.9 Consensus size: 151
461 TCAAGTTGGA
* * * * *
471 ATCGGTTGGCCTTCTAAAATGTTTTCAGAGTTGGTATCTGTTGGCCTTCTCTAAAAATCAAGCTT
1 ATCGG-TGGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCT-TTAAAATCAAG-TT
* * * ** *
536 TTCAGAGTTGGCAACGGTTGGCCTTCTTTAAAGTCAAGTTTTTCAAAGTTGGCATCGGTTGGCCT
63 TTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGACTTTCAAAGATGGCATCGGTTGGCCT
601 TCTTTAAAATCAAATTTTCAAAAGATGGC
128 TC--TAAAA--AAATTTTC-AAAGATGGC
*
630 ATCGGTAGGCCTTCTAAAAAGTTTTCAAAGGTGGCATCGGTTGGCCTTCTTTAAAATCAAGTATT
1 ATCGGT-GGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT-TT
**
695 TCAAAGTTGGCATCAATTGGCCTTCTTTAAAATCAA-ACTTTCAAAAGATGGCATCGGTTGGCCT
64 TCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGACTTTC-AAAGATGGCATCGGTTGGCCT
* *
759 TCTAAAAAAGTTTTCAAAGTTGGC
128 TCTAAAAAAATTTTCAAAGATGGC
* * *
783 ATTGGGTGGCCGTCTTTAAAATCGAGTTTTTCAAAAGTTAGCATCGGTTGGCCCTT-TTTAAAA-
1 A-TCGGTGGCC-T-TCTAAAA---AG-TTTTC-AAAGTTGGCATCGGTTGG-CCTTCTTTAAAAT
* * *
846 AAAGTTTTCAAAGTTGGCATCGGTTGGCCTTC--T--AA--AA-A-TTCTCAAAGTTGGAATCGG
57 CAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGACTT-TCAAAGATGGCATCGG
** * *
903 TTGGCCTTCTTAAAGTTTTGAGTTTTCAAAGTTGGC
121 TTGGCCTTC-TAAA----AAAATTTTCAAAGATGGC
* * * **
939 ATCGGTTGGCCTTCT-AAAAGTTCTCAAAGTTGG-AGTCAGTT-GCCTTC-TTAAAGTTTTGAGT
1 ATCGG-TGGCCTTCTAAAAAGTTTTCAAAGTTGGCA-TCGGTTGGCCTTCTTTAAA--ATCAAGT
* * * *** * *
1000 TCTCAAAGTTGGCATCGGTTGGCCTTC-ATAAAGTTTTGAGTTTTCAAAGTTGGCATCGGTTGGC
62 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGA-CTTTCAAAGATGGCATCGGTTGGC
1064 CTTCTAAAAA
126 CTTCTAAAAA
1074 GTTCT
Statistics
Matches: 370, Mismatches: 42, Indels: 72
0.76 0.09 0.15
Matches are distributed among these distances:
146 9 0.02
147 2 0.01
148 12 0.03
149 33 0.09
150 3 0.01
151 23 0.06
152 10 0.03
153 16 0.04
154 16 0.04
155 15 0.04
156 52 0.14
157 7 0.02
158 93 0.25
159 52 0.14
160 23 0.06
161 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (151 bp):
ATCGGTGGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTC
AAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGACTTTCAAAGATGGCATCGGTTGGCCTTCT
AAAAAAATTTTCAAAGATGGC
Found at i:1034 original size:74 final size:75
Alignment explanation
Indices: 848--1031 Score: 316
Period size: 75 Copynumber: 2.5 Consensus size: 75
838 TTTTAAAAAA
* *
848 AGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATTCTCAAAGTTGGAATCGGTTGGCCTTCT
1 AGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAGTTCTCAAAGTTGGAATCAGTTGGCCTTCT
913 TAAAGTTTTG
66 TAAAGTTTTG
*
923 AGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAGTTCTCAAAGTTGGAGTCAGTT-GCCTTCT
1 AGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAGTTCTCAAAGTTGGAATCAGTTGGCCTTCT
987 TAAAGTTTTG
66 TAAAGTTTTG
*
997 AGTTCTCAAAGTTGGCATCGGTTGGCCTTCATAAA
1 AGTTTTCAAAGTTGGCATCGGTTGGCCTTC-TAAA
1032 GTTTTGAGTT
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
74 46 0.44
75 58 0.56
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (75 bp):
AGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAGTTCTCAAAGTTGGAATCAGTTGGCCTTCT
TAAAGTTTTG
Done.