Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006756.1 Corchorus capsularis cultivar CVL-1 contig06777, 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: 8680
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Found at i:96 original size:19 final size:18
Alignment explanation
Indices: 72--107 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
62 TGAAGATTTC
72 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
91 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
108 ATCATTTCAA
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
Found at i:5868 original size:17 final size:17
Alignment explanation
Indices: 5846--5879 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5836 GAATCGGCTA
5846 TGAATTTTTGAAGTTTC
1 TGAATTTTTGAAGTTTC
*
5863 TGAATTTTTGAATTTTC
1 TGAATTTTTGAAGTTTC
5880 AAGAAGGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (17 bp):
TGAATTTTTGAAGTTTC
Found at i:6737 original size:33 final size:32
Alignment explanation
Indices: 6700--6806 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
6690 CGCCAAGCGA
* *
6700 TGGCCGGTTG-TGGCCGGACATGTCCATGTCGCG
1 TGGCCGG-TGATGGCCGGGCATCTCCA-GTCGCG
6733 TGGCCGGTGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG
* * *
6766 TGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG
6799 TGGCCGGT
1 TGGCCGGT
6807 CACTCGCGCC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 2 0.03
33 63 0.95
34 1 0.02
ACGTcount: A:0.08, C:0.29, G:0.40, T:0.22
Consensus pattern (32 bp):
TGGCCGGTGATGGCCGGGCATCTCCAGTCGCG
Found at i:6973 original size:27 final size:27
Alignment explanation
Indices: 6943--7010 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
6933 GTCAGACTCT
* *
6943 CATTCCAAGTTAGTCAAGACAG-TTCTC
1 CATTCAAAGTTAGTCAAAACAGTTTC-C
*
6970 CATTCAAAGCTAGTCAAAACAGTTTCC
1 CATTCAAAGTTAGTCAAAACAGTTTCC
6997 CATTCAAAGTTAGT
1 CATTCAAAGTTAGT
7011 TCCCTAGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 33 0.92
28 3 0.08
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (27 bp):
CATTCAAAGTTAGTCAAAACAGTTTCC
Found at i:7899 original size:50 final size:49
Alignment explanation
Indices: 7814--8321 Score: 346
Period size: 49 Copynumber: 10.3 Consensus size: 49
7804 ATTTTAAGAA
* * * *
7814 AAAAAGCAAGTGAAACTAA-TGCCTTTCATCCGGGAAGGGCGTTTTAGG
1 AAAAAGCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGG
* * * * ** *
7862 AAAAAGCAAGTAAAAATTAGTGTCTTTCTGTCGGGGAAGGGCACTTTGGG
1 AAAAAGCAAGTAAAAATAAGTG-CCTTCCGTCCGGGAAGGGCGTTTTAGG
* *** * * * ** * *
7912 GAAAAGTGGGTAAAAGTGAGCGTTTTCCATCCGGGAAGGGCGTTTTCGG
1 AAAAAGCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGG
* * *
7961 AAAATAGCAAGT-AAAATAAGTGCCTTCCGTCCGGGGAGAGCATTTT-GAG
1 AAAA-AGCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTAG-G
* * * * * * * *
8010 AAAAA-CAGGTAGAGATTAGTGTCTTCCATCCGGGAATGGCGCTTTAGG
1 AAAAAGCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGG
* * * ** *
8058 ACAAAGCAAGTAAAAATCAGTGCCTTCCATCCGGGAAGGGCACTTTGGG
1 AAAAAGCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGG
* * *
8107 AAAAATGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGG
1 AAAAA-GCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGG
* * * * * * *
8157 AAAAA-CAGGTAAAAATAAATGCCTGCAGTCCGGGACGGGCATTTTGAGAAA
1 AAAAAGCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTT-AG--G
* * * * *
8208 AAAAAGCAAGT-AAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGG
1 AAAAAGCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGG
* * * *
8256 AAATAGCAAGTAAAAATGAA-TGGCTTCCGTCTGGGAAGGGCGTTTTGGGG
1 AAAAAGCAAGTAAAAAT-AAGTGCCTTCCGTCCGGGAAGGGCGTTTT-AGG
* *
8306 GAAAAGCAAGTGAAAA
1 AAAAAGCAAGTAAAAA
8322 CCGAAAATTG
Statistics
Matches: 356, Mismatches: 89, Indels: 28
0.75 0.19 0.06
Matches are distributed among these distances:
47 4 0.01
48 88 0.25
49 127 0.36
50 101 0.28
51 32 0.09
52 4 0.01
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.22
Consensus pattern (49 bp):
AAAAAGCAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGG
Found at i:8074 original size:97 final size:97
Alignment explanation
Indices: 7814--8316 Score: 392
Period size: 99 Copynumber: 5.1 Consensus size: 97
7804 ATTTTAAGAA
* * * *
7814 AAAAAGCAAGTGAA-ACTAATGCCTTTCATCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAA
1 AAAAAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGG-AAAAGCAAGTAAAAA
* * * * *
7878 TTAGTGTCTTTCTGT-CGGGGAAGGGCACTTTGGG
65 TAAGTG-CCTTCCGTCCGGGG-AGGGCATTTTGAG
* *** * * ** *
7912 GAAAAGTGGGTAAA-AGTGAGCGTTTTCCATCCGGGAAGGGCGTTTTCGGAAAATAGCAAGT-AA
1 AAAAAGCAAGTAAAGA-TTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGG-AAA-AGCAAGTAAA
*
7975 AATAAGTGCCTTCCGTCCGGGGAGAGCATTTTGAG
63 AATAAGTGCCTTCCGTCCGGGGAGGGCATTTTGAG
* * * * *
8010 AAAAA-CAGGTAGAGATTAGTGTCTTCCATCCGGGAATGGCGCTTTAGGACAAAGCAAGTAAAAA
1 AAAAAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGGA-AAAGCAAGTAAAAA
* * * * *
8074 TCAGTGCCTTCCATCCGGGAAGGGCACTTTGGG
65 TAAGTGCCTTCCGTCCGGGGAGGGCATTTTGAG
* *
8107 AAAAATGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGGAAAAACAGGTAAAAA
1 AAAAA-GCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGGAAAAGCAAGTAAAAA
* * *
8172 TAAATGCCTGCAGTCC-GGGACGGGCATTTTGAG
65 TAAGTGCCTTCCGTCCGGGGA-GGGCATTTTGAG
* * * * * * *
8205 AAAAAAAAGCAAGTAAA-ATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAA
1 ---AAAAAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGGAAA-AGCAAGTAA
* * * * *
8269 AAATGAA-TGGCTTCCGTCTGGGAAGGGCGTTTTGGGG
62 AAAT-AAGTGCCTTCCGTCCGGGGAGGGCATTTT-GAG
*
8306 GAAAAGCAAGT
1 AAAAAGCAAGT
8317 GAAAACCGAA
Statistics
Matches: 322, Mismatches: 67, Indels: 32
0.76 0.16 0.08
Matches are distributed among these distances:
96 8 0.02
97 73 0.23
98 74 0.23
99 112 0.35
100 43 0.13
101 12 0.04
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (97 bp):
AAAAAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGGAAAAGCAAGTAAAAAT
AAGTGCCTTCCGTCCGGGGAGGGCATTTTGAG
Done.