Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007140.1 Corchorus capsularis cultivar CVL-1 contig07161, 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: 74211
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36 GTTAGACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17967 original size:28 final size:28
Alignment explanation
Indices: 17934--18000 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
17924 TTCTGTGTCT
* *
17934 TCTGCATTTTTATTTTCTTTGGGTTTGG
1 TCTGCATTTTTATTTTCGTTGCGTTTGG
**
17962 TCTGCATTTTCGTTTTCGTTGCGTTTGG
1 TCTGCATTTTTATTTTCGTTGCGTTTGG
*
17990 TTTGCATTTTT
1 TCTGCATTTTT
18001 GTTCTTCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.06, C:0.13, G:0.21, T:0.60
Consensus pattern (28 bp):
TCTGCATTTTTATTTTCGTTGCGTTTGG
Found at i:20062 original size:21 final size:21
Alignment explanation
Indices: 20038--20078 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
20028 TGAGCCCCTG
*
20038 CTTAAGTATCTAAACCTGGTT
1 CTTAAGTATCAAAACCTGGTT
20059 CTTAAGTATCAAAACCTGGT
1 CTTAAGTATCAAAACCTGGT
20079 ACTTGTGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (21 bp):
CTTAAGTATCAAAACCTGGTT
Found at i:20150 original size:41 final size:41
Alignment explanation
Indices: 20105--20187 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
20095 CCTAGTTTTG
*
20105 AGTATAATGGAGGATTGGCACAGTTGCTTGAAATGACACCT
1 AGTATAATGGAGGACTGGCACAGTTGCTTGAAATGACACCT
20146 AGTATAATGGAGGACTGGCACAGTTGCTTGAAATGACACCT
1 AGTATAATGGAGGACTGGCACAGTTGCTTGAAATGACACCT
20187 A
1 A
20188 ATTTAAGGAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.25
Consensus pattern (41 bp):
AGTATAATGGAGGACTGGCACAGTTGCTTGAAATGACACCT
Found at i:32121 original size:19 final size:19
Alignment explanation
Indices: 32083--32121 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
32073 AGGAAGAGAT
* *
32083 CGGCGTAGTTTAACGGATC
1 CGGCGTAGTTTAAAGAATC
*
32102 CGGCGTATTTTAAAGAATC
1 CGGCGTAGTTTAAAGAATC
32121 C
1 C
32122 TTTCTTCGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (19 bp):
CGGCGTAGTTTAAAGAATC
Found at i:40615 original size:49 final size:49
Alignment explanation
Indices: 40559--40657 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
40549 TCTATAGTAC
40559 TTTTCGTAAAATATTTTCACTTTGATTTTTATCTTTAACATTAGAAATT
1 TTTTCGTAAAATATTTTCACTTTGATTTTTATCTTTAACATTAGAAATT
40608 TTTTCGTAAAATATTTTCACTTTGATTTTTATCTTTAACATTAGAAATT
1 TTTTCGTAAAATATTTTCACTTTGATTTTTATCTTTAACATTAGAAATT
40657 T
1 T
40658 ATTAATTCTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (49 bp):
TTTTCGTAAAATATTTTCACTTTGATTTTTATCTTTAACATTAGAAATT
Found at i:47313 original size:60 final size:60
Alignment explanation
Indices: 47219--47381 Score: 229
Period size: 60 Copynumber: 2.7 Consensus size: 60
47209 GCTAATTGCT
* ** * *
47219 CAAATAAGGGCCTAACGTT-TGCTAAAATGTTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATACTCAAATAAGGGCCCGAGCTTTTAATTTGGC
47279 CAAATAAGGGCCTAACGTTATCGAAAATACTCAAATAAGGGCCCGAGCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATACTCAAATAAGGGCCCGAGCTTTTAATTTGGC
* * * *
47339 CAAATAAAGGTCTAACATTATCGAAAATTCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATACTCAAATAAGGGCC
47382 TAATGTTATA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 92 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATACTCAAATAAGGGCCCGAGCTTTTAATTTGGC
Found at i:47317 original size:31 final size:31
Alignment explanation
Indices: 47215--47411 Score: 106
Period size: 31 Copynumber: 6.5 Consensus size: 31
47205 CAAGGCTAAT
*
47215 TGCTCAAATAAGGGCCTAACGTT-TGCTAAAA
1 TGCTCAAATAAGGGCCTAACGTTAT-CGAAAA
* * * * **
47246 TGTTCAAATAAGGGTCCGATC-TT-T-TAATT
1 TGCTCAAATAAGGG-CCTAACGTTATCGAAAA
47275 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
* ** * **
47306 TACTCAAATAAGGGCCCGA-GCTT-T-TAATT
1 TGCTCAAATAAGGGCCTAACG-TTATCGAAAA
* * *
47335 TGGC-CAAATAAAGGTCTAACATTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
* * **
47366 TTCTCAAATAAGGGCCTAATGTTATAAAAAA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
47397 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
47412 ATGACGTCAG
Statistics
Matches: 120, Mismatches: 34, Indels: 24
0.67 0.19 0.13
Matches are distributed among these distances:
28 4 0.03
29 32 0.27
30 8 0.07
31 72 0.60
32 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTATCGAAAA
Found at i:47491 original size:31 final size:31
Alignment explanation
Indices: 47456--47555 Score: 107
Period size: 31 Copynumber: 3.3 Consensus size: 31
47446 GATGGCAGGT
47456 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
** * * *
47487 CCTTATTTG-GCCAAATT--AAAAGGTTGGGC
1 CCTTATTTGAG-CATTTTGGCAAACGTTAGGC
*
47516 CCTTATTTGAGCATTTTGGCAAATGTTAGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
*
47547 CTTTATTTG
1 CCTTATTTG
47556 GCCAAATTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
29 22 0.41
30 2 0.04
31 30 0.56
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (31 bp):
CCTTATTTGAGCATTTTGGCAAACGTTAGGC
Found at i:47521 original size:29 final size:29
Alignment explanation
Indices: 47480--47568 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
47470 TTTGGCAAAC
47480 GTTAGGCCCTTATTTGGCCAAATTAAAAG
1 GTTAGGCCCTTATTTGGCCAAATTAAAAG
* ** * *
47509 GTTGGGCCCTTATTTGAG-CATTTTGGCAAAT
1 GTTAGGCCCTTATTTG-GCCAAATT--AAAAG
*
47540 GTTAGGCCTTTATTTGGCCAAATTAAAAG
1 GTTAGGCCCTTATTTGGCCAAATTAAAAG
47569 ATGTCCTTAT
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
29 22 0.49
30 2 0.04
31 21 0.47
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (29 bp):
GTTAGGCCCTTATTTGGCCAAATTAAAAG
Found at i:47553 original size:60 final size:57
Alignment explanation
Indices: 47456--47612 Score: 224
Period size: 60 Copynumber: 2.7 Consensus size: 57
47446 GATGGCAGGT
*
47456 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGGTTGGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAA-GAT--GC
* * *
47516 CCTTATTTGAGCATTTTGGCAAATGTTAGGCCTTTATTTGGCCAAATTAAAAGATGT
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATGC
* * *
47573 CCTTATTTGAGCATTTTGGAAAACATTAGACCCTTATTTG
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
47613 AGCAATTAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
57 36 0.41
59 2 0.02
60 50 0.57
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (57 bp):
CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATGC
Found at i:48943 original size:17 final size:16
Alignment explanation
Indices: 48920--48957 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
48910 CTTCTTTTAA
*
48920 TTCTTTTT-TTCTCTTT
1 TTCTTTTTCTTC-CATT
48936 TTCTTTTTCTTCCATT
1 TTCTTTTTCTTCCATT
48952 TTCTTT
1 TTCTTT
48958 CTTCACTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTTTCTTCCATT
Found at i:63892 original size:16 final size:16
Alignment explanation
Indices: 63871--63901 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63861 TTGAAAAATA
63871 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
63887 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
63902 AATATATAGA
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:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:64464 original size:18 final size:18
Alignment explanation
Indices: 64441--64477 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
64431 AGTCTACACC
64441 TATATTGATTCATGTAAA
1 TATATTGATTCATGTAAA
64459 TATATTGATTCATGTAAA
1 TATATTGATTCATGTAAA
64477 T
1 T
64478 GTAAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (18 bp):
TATATTGATTCATGTAAA
Found at i:71223 original size:22 final size:23
Alignment explanation
Indices: 71198--71244 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
71188 ACATTCTCAT
*
71198 TATTATAACTCATAGAACA-TCA
1 TATTATAACTCATAAAACATTCA
* *
71220 TATTTTCACTCATAAAACATTCA
1 TATTATAACTCATAAAACATTCA
71243 TA
1 TA
71245 CAGCTACTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (23 bp):
TATTATAACTCATAAAACATTCA
Found at i:72739 original size:19 final size:18
Alignment explanation
Indices: 72715--72750 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
72705 TGAAGATTTC
72715 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
72734 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
72751 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.