Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009742.1 Corchorus capsularis cultivar CVL-1 contig09763, 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: 45914
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1751 original size:32 final size:32
Alignment explanation
Indices: 1696--1756 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1686 AATGGGCCTT
*
1696 GACCAAAGCAAAAGATCCAAAAGCTAAAGAAA
1 GACCAAAACAAAAGATCCAAAAGCTAAAGAAA
* * *
1728 GACCAAAACAAGATATCCCAAAGCTAAAG
1 GACCAAAACAAAAGATCCAAAAGCTAAAG
1757 CCCAAAGCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.56, C:0.21, G:0.15, T:0.08
Consensus pattern (32 bp):
GACCAAAACAAAAGATCCAAAAGCTAAAGAAA
Found at i:1762 original size:13 final size:13
Alignment explanation
Indices: 1744--1768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1734 AACAAGATAT
1744 CCCAAAGCTAAAG
1 CCCAAAGCTAAAG
1757 CCCAAAGCTAAA
1 CCCAAAGCTAAA
1769 TGTACACAAT
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:0.48, C:0.32, G:0.12, T:0.08
Consensus pattern (13 bp):
CCCAAAGCTAAAG
Found at i:2643 original size:2 final size:2
Alignment explanation
Indices: 2638--2665 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2628 TATATATATA
2638 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2666 ATATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:8013 original size:31 final size:31
Alignment explanation
Indices: 7950--8013 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
7940 CCTCTCTAAC
* *
7950 TATATATAAAAATATTCTATTTAAATTAGGA
1 TATATATAAAAATATTATATTCAAATTAGGA
* *
7981 TATATATATATATATATATATTCAAATT-GGA
1 TATATATAAAAATAT-TATATTCAAATTAGGA
8012 TA
1 TA
8014 ATTGTCACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (31 bp):
TATATATAAAAATATTATATTCAAATTAGGA
Found at i:8358 original size:2 final size:2
Alignment explanation
Indices: 8351--8381 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8341 TTTGCGGCTG
8351 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 T
8382 TCTTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9964 original size:13 final size:13
Alignment explanation
Indices: 9946--9970 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9936 TTTAATGTTC
9946 TAAATATTATATA
1 TAAATATTATATA
9959 TAAATATTATAT
1 TAAATATTATAT
9971 TTGGAATTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATATTATATA
Found at i:13803 original size:28 final size:29
Alignment explanation
Indices: 13769--13843 Score: 107
Period size: 30 Copynumber: 2.6 Consensus size: 29
13759 ACTTGTAGCG
13769 TTTGGACATTTTGCCCCTGAACT-TCAAT
1 TTTGGACATTTTGCCCCTGAACTCTCAAT
* *
13797 TTTGGACATTTTCCCCTCTGAACTCTTAAT
1 TTTGGACATTTTGCCC-CTGAACTCTCAAT
*
13827 TTTGGACGTTTTGCCCC
1 TTTGGACATTTTGCCCC
13844 CTCTGAAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 15 0.37
29 8 0.20
30 18 0.44
ACGTcount: A:0.17, C:0.27, G:0.15, T:0.41
Consensus pattern (29 bp):
TTTGGACATTTTGCCCCTGAACTCTCAAT
Found at i:13830 original size:30 final size:29
Alignment explanation
Indices: 13769--13850 Score: 103
Period size: 28 Copynumber: 2.8 Consensus size: 29
13759 ACTTGTAGCG
*
13769 TTTGGACATTTTGCCC-CTGAACTTCAAT
1 TTTGGACATTTTCCCCTCTGAACTTCAAT
*
13797 TTTGGACATTTTCCCCTCTGAACTCTTAAT
1 TTTGGACATTTTCCCCTCTGAACT-TCAAT
*
13827 TTTGGACGTTTTGCCCCCTCTGAA
1 TTTGGACATTTT--CCCCTCTGAA
13851 ATGATTAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
28 15 0.32
29 7 0.15
30 15 0.32
32 10 0.21
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (29 bp):
TTTGGACATTTTCCCCTCTGAACTTCAAT
Found at i:13982 original size:29 final size:30
Alignment explanation
Indices: 13916--13990 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 30
13906 GTTTGAGAGG
*
13916 GGGCAAAACGTCTAAAATTGAAAGTTCAGA
1 GGGCAAAACGTCCAAAATTGAAAGTTCAGA
* *
13946 GGGGAAAATGTCCAAAATTG-AAGTTCATGA
1 GGGCAAAACGTCCAAAATTGAAAGTTCA-GA
13976 -GGCAAAACGTCCAAA
1 GGGCAAAACGTCCAAA
13991 CGCTACAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.51
30 19 0.49
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.19
Consensus pattern (30 bp):
GGGCAAAACGTCCAAAATTGAAAGTTCAGA
Found at i:27152 original size:80 final size:77
Alignment explanation
Indices: 27019--27169 Score: 248
Period size: 80 Copynumber: 1.9 Consensus size: 77
27009 CCATAAAAAA
*
27019 TACGTAAGTTTTGTCCTCATCAAGGCTTGTTTGTTATATTAAATATTAAAAAAAAAATTGCATCT
1 TACGTAAGTTTTATCCTCATCAAGGCTTGTTTGTTATATTAAATATT--AAAAAAAA-TGCATCT
27084 GAAAATATAGTCAAT
63 GAAAATATAGTCAAT
* *
27099 TACGTAAGTTTTATCCTCATCCAGGCTTGTTTGTTATATTAAATATTAAAAAAAATGCATCTGGA
1 TACGTAAGTTTTATCCTCATCAAGGCTTGTTTGTTATATTAAATATTAAAAAAAATGCATCTGAA
27164 AATATA
66 AATATA
27170 ATTATGGGAA
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
77 15 0.22
78 8 0.12
80 45 0.66
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (77 bp):
TACGTAAGTTTTATCCTCATCAAGGCTTGTTTGTTATATTAAATATTAAAAAAAATGCATCTGAA
AATATAGTCAAT
Found at i:32590 original size:13 final size:13
Alignment explanation
Indices: 32572--32597 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32562 GTCTTAATAT
32572 AGATGCTAACTCC
1 AGATGCTAACTCC
32585 AGATGCTAACTCC
1 AGATGCTAACTCC
32598 TCCGTAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (13 bp):
AGATGCTAACTCC
Found at i:38206 original size:22 final size:23
Alignment explanation
Indices: 38178--38235 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 23
38168 AGGAGGTGGC
38178 ATAACAAAT-TACAAA-AAAGGAA
1 ATAACAAATATA-AAATAAAGGAA
38200 ATAACAAAGTGAATAAAATAAAGGAA
1 ATAACAAA-T--ATAAAATAAAGGAA
38226 ATAACAAATA
1 ATAACAAATA
38236 CTACTGCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
22 8 0.26
23 2 0.06
25 4 0.13
26 17 0.55
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.16
Consensus pattern (23 bp):
ATAACAAATATAAAATAAAGGAA
Found at i:43419 original size:33 final size:32
Alignment explanation
Indices: 43372--43478 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 32
43362 CCAATAGCGA
*
43372 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGCCGGACATCTCCA-GTCGCG
* *
43405 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
* * *
43438 TGGCCAGTGTTGGCCGGACTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
43471 TGGCCGGT
1 TGGCCGGT
43479 CACTAGTGCT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
33 60 0.97
34 2 0.03
ACGTcount: A:0.10, C:0.29, G:0.37, T:0.23
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGACATCTCCAGTCGCG
Done.