Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009391.1 Corchorus capsularis cultivar CVL-1 contig09412, 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: 40410
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:4004 original size:8 final size:8
Alignment explanation
Indices: 3976--4009 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3966 CGATGCAAGA
3976 TGAATTTT
1 TGAATTTT
*
3984 TGAAGTTTC
1 TGAA-TTTT
3993 TGAATTTT
1 TGAATTTT
4001 TGAATTTT
1 TGAATTTT
4009 T
1 T
4010 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:5014 original size:33 final size:33
Alignment explanation
Indices: 4977--5083 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 33
4967 CGCTAAGTGA
* *
4977 TGGCCGGTTGTGGCCGGACATGTCC-ATGTCGCG
1 TGGCCGGTGGTGGCCGGACATCTCCGA-GTCGCG
*
5010 TGGCCGGTGGTGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTGGTGGCCGGACATCTCCGAGTCGCG
* * * * * *
5043 TGGCCGGTGTTGGCCAGTCTTCTCCAAGTCGCA
1 TGGCCGGTGGTGGCCGGACATCTCCGAGTCGCG
5076 TGGCCGGT
1 TGGCCGGT
5084 CACTCGCACC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 63 0.98
34 1 0.02
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.23
Consensus pattern (33 bp):
TGGCCGGTGGTGGCCGGACATCTCCGAGTCGCG
Found at i:10138 original size:22 final size:22
Alignment explanation
Indices: 10106--10151 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
10096 CTAAAATTCA
* *
10106 GGACAAGTTCTGCCCAGAACTT
1 GGACAACTTCTACCCAGAACTT
*
10128 GGACAACTTCTACCCAGGACTT
1 GGACAACTTCTACCCAGAACTT
10150 GG
1 GG
10152 CCTGTTGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (22 bp):
GGACAACTTCTACCCAGAACTT
Found at i:10519 original size:10 final size:10
Alignment explanation
Indices: 10497--10535 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
10487 AAATCTCGAT
*
10497 ATATCCGTAA
1 ATATCCATAA
10507 ATATCCATAA
1 ATATCCATAA
*
10517 ATATCCGTAA
1 ATATCCATAA
10527 ATATCCATA
1 ATATCCATA
10536 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (10 bp):
ATATCCATAA
Found at i:10520 original size:20 final size:20
Alignment explanation
Indices: 10497--10535 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
10487 AAATCTCGAT
10497 ATATCCGTAAATATCCATAA
1 ATATCCGTAAATATCCATAA
10517 ATATCCGTAAATATCCATA
1 ATATCCGTAAATATCCATA
10536 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
ATATCCGTAAATATCCATAA
Found at i:11556 original size:13 final size:12
Alignment explanation
Indices: 11538--11568 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
11528 CATCGATACC
11538 TCGATATATCCG
1 TCGATATATCCG
11550 TTCGATATATCCG
1 -TCGATATATCCG
11563 TCGATA
1 TCGATA
11569 CCTGTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:12504 original size:220 final size:212
Alignment explanation
Indices: 12130--12524 Score: 646
Period size: 220 Copynumber: 1.8 Consensus size: 212
12120 ATAGTGGATT
* * *
12130 CATCTTAACTCCAATTGCTTTGAAATTTCAGATTTGGAGTCCTTATAACAAGTAGTTATATTGCA
1 CATCTTAACTCCAATTGCTTTGAAATTTCAGATTTGAAGTCCTTATAACAAGTAGTTATATCGAA
* *
12195 AAATATCAAAAAAAAAAATTCGACCAGAAACTTGTGATTTTTGTTCTGGGTTCGTTTGAAGTCGG
66 AAATATCAAAAAAAAAAATTAGACCAGAAACTTGTGATTTCTGTTCTGGGTTCGTTTGAAGTCGG
12260 AAAGCTTTGAAATTTGAGATTTAGACTTCTTTTAGTGTGATCTTTGATCTTTCTAGGAAAAATAT
131 AAAGCTTTGAAATTTGAGATTTAGACTTCTTTTAGTGTGATCTTTGATCTTTCTAGGAAAAATAT
12325 TGGAAAAATTTCATATC
196 TGGAAAAATTTCATATC
* *
12342 CATCTTAACTCCAATTGCTTTGAAATTTCAGATTTGAAGTCCTTATATCTAGTAGTTATATCGAA
1 CATCTTAACTCCAATTGCTTTGAAATTTCAGATTTGAAGTCCTTATAACAAGTAGTTATATCGAA
*
12407 AAATATCAAAAAATAAATAAAAAAAATTAGGCCAGAAACTTGTGATTTCTGTTCTGGGTTCGTTT
66 AAATATC-------AAA-AAAAAAAATTAGACCAGAAACTTGTGATTTCTGTTCTGGGTTCGTTT
12472 GAAGTCGGAAAGCTTTGAAATTTGAGATTTAGACTTCTTTTAGTGTGATCTTT
123 GAAGTCGGAAAGCTTTGAAATTTGAGATTTAGACTTCTTTTAGTGTGATCTTT
12525 CTGGGAAAAA
Statistics
Matches: 167, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
212 67 0.40
219 3 0.02
220 97 0.58
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (212 bp):
CATCTTAACTCCAATTGCTTTGAAATTTCAGATTTGAAGTCCTTATAACAAGTAGTTATATCGAA
AAATATCAAAAAAAAAAATTAGACCAGAAACTTGTGATTTCTGTTCTGGGTTCGTTTGAAGTCGG
AAAGCTTTGAAATTTGAGATTTAGACTTCTTTTAGTGTGATCTTTGATCTTTCTAGGAAAAATAT
TGGAAAAATTTCATATC
Found at i:24696 original size:12 final size:12
Alignment explanation
Indices: 24679--24707 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
24669 AAACATTTTT
24679 AATTTTCTTCAA
1 AATTTTCTTCAA
24691 AATTTTCTTCAA
1 AATTTTCTTCAA
24703 AATTT
1 AATTT
24708 GTCTCTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (12 bp):
AATTTTCTTCAA
Found at i:34855 original size:12 final size:12
Alignment explanation
Indices: 34815--34857 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
34805 GGCCATGACC
*
34815 GGCCAACGCATG
1 GGCCATCGCATG
* * *
34827 GGGCATTGCACG
1 GGCCATCGCATG
34839 GGCCATCGCATG
1 GGCCATCGCATG
34851 GGCCATC
1 GGCCATC
34858 CGGCCATAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.19, C:0.33, G:0.35, T:0.14
Consensus pattern (12 bp):
GGCCATCGCATG
Found at i:34883 original size:42 final size:42
Alignment explanation
Indices: 34835--34915 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
34825 TGGGGCATTG
* * * *
34835 CACGGGCCATCGCATGGGCCATCCGGCCATAATCGGCCATCA
1 CACGGGCCAACGCACGGGCCATCCGGCCACAACCGGCCATCA
34877 CACGGGCCAACGCACGGGCCATCCGGCCACAACCGGCCA
1 CACGGGCCAACGCACGGGCCATCCGGCCACAACCGGCCA
34916 CTTGATCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.42, G:0.27, T:0.09
Consensus pattern (42 bp):
CACGGGCCAACGCACGGGCCATCCGGCCACAACCGGCCATCA
Found at i:35943 original size:8 final size:8
Alignment explanation
Indices: 35924--35953 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
35914 AGTTATATCG
35924 AAAAATATA
1 AAAAATA-A
35933 AAAAATAA
1 AAAAATAA
35941 AAAAATAA
1 AAAAATAA
35949 AAAAA
1 AAAAA
35954 CATTTCGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Done.