Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012357.1 Corchorus olitorius cultivar O-4 contig12390, 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: 31257
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:9826 original size:21 final size:21
Alignment explanation
Indices: 9801--9843 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9791 ATGTGATGGG
*
9801 GAAGAAGTACCGCAGGAAGTA
1 GAAGAAGTACAGCAGGAAGTA
*
9822 GAAGAAGTATAGCAGGAAGTA
1 GAAGAAGTACAGCAGGAAGTA
9843 G
1 G
9844 TGGATTTCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.35, T:0.12
Consensus pattern (21 bp):
GAAGAAGTACAGCAGGAAGTA
Found at i:12987 original size:35 final size:37
Alignment explanation
Indices: 12918--12989 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 37
12908 TTAAATTATC
*
12918 TAAGAAAGCAATCAAGAAAATTAAAGAAAACAATTAA
1 TAAGAAAGCAATCAAGAAAACTAAAGAAAACAATTAA
* *
12955 TAAGAAAGCAATGAA-TAAACT-AAGAAAACAATTAA
1 TAAGAAAGCAATCAAGAAAACTAAAGAAAACAATTAA
12990 GAAAACCCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 14 0.44
36 4 0.12
37 14 0.44
ACGTcount: A:0.64, C:0.08, G:0.11, T:0.17
Consensus pattern (37 bp):
TAAGAAAGCAATCAAGAAAACTAAAGAAAACAATTAA
Found at i:14226 original size:30 final size:31
Alignment explanation
Indices: 14186--14246 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
14176 CAATTCCTGC
* * * *
14186 TTCTTGAAATAATTTTTCAATGA-TCTTCAA
1 TTCTTCAAATAAATCTTCAATAAGTCTTCAA
14216 TTCTTCAAATAAATCTTCAATAAGTCTTCAA
1 TTCTTCAAATAAATCTTCAATAAGTCTTCAA
14247 ACACGAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (31 bp):
TTCTTCAAATAAATCTTCAATAAGTCTTCAA
Found at i:18453 original size:18 final size:19
Alignment explanation
Indices: 18420--18455 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
18410 TCCTCTTTCA
18420 TGAAAACACTTCTTTTTAT
1 TGAAAACACTTCTTTTTAT
*
18439 TGAAAA-ACTTTTTTTTA
1 TGAAAACACTTCTTTTTA
18456 ACTACCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (19 bp):
TGAAAACACTTCTTTTTAT
Found at i:20819 original size:164 final size:164
Alignment explanation
Indices: 20548--20875 Score: 656
Period size: 164 Copynumber: 2.0 Consensus size: 164
20538 CCTTCTTTTC
20548 TTCCAAAGTATAGATAGTAGCAACTTGAGGTGTTCTTGGTCGATTAGATGAAGAAGCACGATTAG
1 TTCCAAAGTATAGATAGTAGCAACTTGAGGTGTTCTTGGTCGATTAGATGAAGAAGCACGATTAG
20613 GATTGAAACCAATGGGATAATGGTCATATCGCATAGGGGGTCTATAGGGTGGCCTATAGGGCTTA
66 GATTGAAACCAATGGGATAATGGTCATATCGCATAGGGGGTCTATAGGGTGGCCTATAGGGCTTA
20678 GCGCGATACCCATCAATCCTAGGCATGGGAAAAG
131 GCGCGATACCCATCAATCCTAGGCATGGGAAAAG
20712 TTCCAAAGTATAGATAGTAGCAACTTGAGGTGTTCTTGGTCGATTAGATGAAGAAGCACGATTAG
1 TTCCAAAGTATAGATAGTAGCAACTTGAGGTGTTCTTGGTCGATTAGATGAAGAAGCACGATTAG
20777 GATTGAAACCAATGGGATAATGGTCATATCGCATAGGGGGTCTATAGGGTGGCCTATAGGGCTTA
66 GATTGAAACCAATGGGATAATGGTCATATCGCATAGGGGGTCTATAGGGTGGCCTATAGGGCTTA
20842 GCGCGATACCCATCAATCCTAGGCATGGGAAAAG
131 GCGCGATACCCATCAATCCTAGGCATGGGAAAAG
20876 GCTTGCCCCA
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 164 1.00
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (164 bp):
TTCCAAAGTATAGATAGTAGCAACTTGAGGTGTTCTTGGTCGATTAGATGAAGAAGCACGATTAG
GATTGAAACCAATGGGATAATGGTCATATCGCATAGGGGGTCTATAGGGTGGCCTATAGGGCTTA
GCGCGATACCCATCAATCCTAGGCATGGGAAAAG
Found at i:21730 original size:21 final size:22
Alignment explanation
Indices: 21706--21754 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
21696 GCTTGGCCCG
*
21706 GCCTTGGT-GCG-GCATGGCCTT
1 GCCTTGGTCGCGCGC-TGGCCTA
21727 GCCTT-GTCGCGCGCTGGCCTA
1 GCCTTGGTCGCGCGCTGGCCTA
21748 GCCTTGG
1 GCCTTGG
21755 CCTGGCTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 19 0.79
22 3 0.12
ACGTcount: A:0.04, C:0.33, G:0.37, T:0.27
Consensus pattern (22 bp):
GCCTTGGTCGCGCGCTGGCCTA
Found at i:25770 original size:21 final size:21
Alignment explanation
Indices: 25736--25776 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25726 AAATACAAGA
* *
25736 CAACTTCGGTCCAGATGTTGT
1 CAACTTCGGCCCAGAAGTTGT
*
25757 CAACTTCTGCCCAGAAGTTG
1 CAACTTCGGCCCAGAAGTTG
25777 GCCTGTCGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
CAACTTCGGCCCAGAAGTTGT
Found at i:25860 original size:52 final size:52
Alignment explanation
Indices: 25790--25907 Score: 200
Period size: 52 Copynumber: 2.2 Consensus size: 52
25780 TGTCGAAAAG
* *
25790 AGAAGTTGTTGGCACAGGACAACTTTGGCCCAAAACTTGTTCAACTTCGGGAC
1 AGAAGTTGTT-GCGCAGGACAACTTCGGCCCAAAACTTGTTCAACTTCGGGAC
*
25843 AGAAGTTGTTGCGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGAC
1 AGAAGTTGTTGCGCAGGACAACTTCGGCCCAAAACTTGTTCAACTTCGGGAC
25895 AGAAGTTGTTGCG
1 AGAAGTTGTTGCG
25908 GAAAGAAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 52 0.84
53 10 0.16
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (52 bp):
AGAAGTTGTTGCGCAGGACAACTTCGGCCCAAAACTTGTTCAACTTCGGGAC
Found at i:25897 original size:22 final size:22
Alignment explanation
Indices: 25861--25904 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25851 TTGCGCAGGA
*
25861 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCACAGAACTTGTT
* *
25883 CAACTTCGGGACAGAAGTTGTT
1 CAACTTCGGCACAGAACTTGTT
25905 GCGGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTGTT
Done.