Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007934.1 Corchorus capsularis cultivar CVL-1 contig07955, 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: 24764
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Found at i:1797 original size:13 final size:13
Alignment explanation
Indices: 1779--1805 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1769 TTCATGCACA
1779 TGGGTTGTATTTT
1 TGGGTTGTATTTT
1792 TGGGTTGTATTTT
1 TGGGTTGTATTTT
1805 T
1 T
1806 TAAAAGTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.30, T:0.63
Consensus pattern (13 bp):
TGGGTTGTATTTT
Found at i:2622 original size:6 final size:6
Alignment explanation
Indices: 2611--2639 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2601 CATGTAATAA
2611 CCCTAC CCCTAC CCCTAC CCCTAC CCCTA
1 CCCTAC CCCTAC CCCTAC CCCTAC CCCTA
2640 ACTGGTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.66, G:0.00, T:0.17
Consensus pattern (6 bp):
CCCTAC
Found at i:3428 original size:51 final size:51
Alignment explanation
Indices: 3359--3455 Score: 176
Period size: 51 Copynumber: 1.9 Consensus size: 51
3349 AAAATACAAT
3359 TCATGAATTTACAGTTTCTAACATTGACACCAGTGTCACTAACAATATAAA
1 TCATGAATTTACAGTTTCTAACATTGACACCAGTGTCACTAACAATATAAA
* *
3410 TCATTAATTTACATTTTCTAACATTGACACCAGTGTCACTAACAAT
1 TCATGAATTTACAGTTTCTAACATTGACACCAGTGTCACTAACAAT
3456 TGGAGTACCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (51 bp):
TCATGAATTTACAGTTTCTAACATTGACACCAGTGTCACTAACAATATAAA
Found at i:5271 original size:31 final size:30
Alignment explanation
Indices: 5233--5334 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 30
5223 AGTGGATGGA
*
5233 CTTATTTGAGACTTTCTGAC-AAGTTGGGGCC
1 CTTATTTGAGACTTT-T-ACAAAGTTCGGGCC
*
5264 CTTATTTGA-CCTTTTACAAAGTTCGGGCC
1 CTTATTTGAGACTTTTACAAAGTTCGGGCC
* *
5293 CTTATTTGAGA-TTTATGGCAAAGTTCGGGTAC
1 CTTATTTGAGACTTT-T-ACAAAGTTCGGG-CC
5325 C-TATTTGAGA
1 CTTATTTGAGA
5335 TTTCAGCGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
28 2 0.03
29 23 0.38
30 5 0.08
31 29 0.48
32 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (30 bp):
CTTATTTGAGACTTTTACAAAGTTCGGGCC
Found at i:9789 original size:16 final size:16
Alignment explanation
Indices: 9768--9802 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
9758 TGTAATTAGA
*
9768 TGGGGAAGGGGTTTGT
1 TGGGGAAGGGATTTGT
9784 TGGGGAAGGGATTTGT
1 TGGGGAAGGGATTTGT
9800 TGG
1 TGG
9803 CTCATAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.54, T:0.31
Consensus pattern (16 bp):
TGGGGAAGGGATTTGT
Found at i:10888 original size:70 final size:67
Alignment explanation
Indices: 10778--10909 Score: 219
Period size: 70 Copynumber: 1.9 Consensus size: 67
10768 GTTGGCAAAG
* *
10778 GGAAATTTTATTTGAGGTAAGGCTCACTTTATCGGGTTATAATATTTTGTGGGTGTTAGGGGGGA
1 GGAAATTTTATTTGAGGTAAGGCTCACTTTATCGGGTTATAATATCTCGTGGGTGTTAGGGGGGA
10843 TT
66 TT
10845 GGAAATTTTATTTAAGGAGGTAAGGCTCACTTTATCGGGTTATAATATCTCGTGGGTGTTAGGGG
1 GGAAATTTTATTT---GAGGTAAGGCTCACTTTATCGGGTTATAATATCTCGTGGGTGTTAGGGG
10910 ATTTCAATAT
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
67 13 0.22
70 47 0.78
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (67 bp):
GGAAATTTTATTTGAGGTAAGGCTCACTTTATCGGGTTATAATATCTCGTGGGTGTTAGGGGGGA
TT
Found at i:11803 original size:5 final size:5
Alignment explanation
Indices: 11788--11824 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
11778 TGTATGTGTT
*
11788 TTTTG -TTTG TTTTG TTTTG TCTTG TTTTG TTTT- TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
11825 CGAATGGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:11812 original size:15 final size:14
Alignment explanation
Indices: 11788--11820 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
11778 TGTATGTGTT
11788 TTTTGTTTGTTTTG
1 TTTTGTTTGTTTTG
11802 TTTTGTCTTGTTTTG
1 TTTTGT-TTGTTTTG
11817 TTTT
1 TTTT
11821 TTTTCGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.00, C:0.03, G:0.18, T:0.79
Consensus pattern (14 bp):
TTTTGTTTGTTTTG
Found at i:20234 original size:21 final size:21
Alignment explanation
Indices: 20208--20249 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20198 TGGTGCTACT
*
20208 TTATTTCACTTGCTCATTTTA
1 TTATTTCACCTGCTCATTTTA
20229 TTATTTCACCTGCTCATTTTA
1 TTATTTCACCTGCTCATTTTA
20250 ACCCCTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.55
Consensus pattern (21 bp):
TTATTTCACCTGCTCATTTTA
Found at i:22105 original size:30 final size:30
Alignment explanation
Indices: 22069--22128 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
22059 GAGGGAGTAC
*
22069 TTTTTTTTCTT-A-CCCAACTCTTTATTAG
1 TTTTTTTTTTTGAGCCCAACTCTTTATTAG
**
22097 TTTTTTTTTTTGAGTTCAACTCTTTATTAG
1 TTTTTTTTTTTGAGCCCAACTCTTTATTAG
22127 TT
1 TT
22129 CTAATCTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 10 0.37
29 1 0.04
30 16 0.59
ACGTcount: A:0.17, C:0.15, G:0.07, T:0.62
Consensus pattern (30 bp):
TTTTTTTTTTTGAGCCCAACTCTTTATTAG
Found at i:22940 original size:32 final size:33
Alignment explanation
Indices: 22899--22973 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 33
22889 AAATTTGGTC
**
22899 TAGCCGCCCCACCG-GGGCGGCCTGCCGTGGC-A
1 TAGCCGCCCCA-CGAGGGCAACCTGCCGTGGCGA
*
22931 TAGCCGCCCCATGAGGGCAACCTGCCGTGGCGA
1 TAGCCGCCCCACGAGGGCAACCTGCCGTGGCGA
22964 -AGCCGCCCCA
1 TAGCCGCCCCA
22974 GTGGGGAGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 1 0.03
32 36 0.95
33 1 0.03
ACGTcount: A:0.15, C:0.43, G:0.33, T:0.09
Consensus pattern (33 bp):
TAGCCGCCCCACGAGGGCAACCTGCCGTGGCGA
Found at i:23010 original size:33 final size:33
Alignment explanation
Indices: 22954--23047 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
22944 AGGGCAACCT
* *
22954 GCCGTGGC-GAAGCCGCCCCAGTGGGGAGGCTCC
1 GCCGTGGCTG-AGCCTCCCTAGTGGGGAGGCTCC
* *
22987 GCCGTGGTTGAGCCTCCCTAGTGGGGAGGTTCC
1 GCCGTGGCTGAGCCTCCCTAGTGGGGAGGCTCC
*
23020 GCCGTGGCTGAGCCGT-CCTAGTGAGGAG
1 GCCGTGGCTGAGCC-TCCCTAGTGGGGAG
23048 CCTCAGTGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
33 51 0.96
34 2 0.04
ACGTcount: A:0.12, C:0.30, G:0.41, T:0.17
Consensus pattern (33 bp):
GCCGTGGCTGAGCCTCCCTAGTGGGGAGGCTCC
Found at i:23257 original size:30 final size:31
Alignment explanation
Indices: 23221--23298 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 31
23211 ACGTAAAGTT
23221 AACTATAGTTAATAT-TT-TACACCAAAAAAA
1 AACTATAGTTAATATATTCT-CACCAAAAAAA
**
23251 AACTATAGTTAATATAGTTCTGGCCAAAAAAA
1 AACTATAGTTAATATA-TTCTCACCAAAAAAA
23283 AACTATAGTTAATATA
1 AACTATAGTTAATATA
23299 GACAAATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 15 0.35
32 27 0.63
33 1 0.02
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.31
Consensus pattern (31 bp):
AACTATAGTTAATATATTCTCACCAAAAAAA
Done.