Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016872.1 Corchorus olitorius cultivar O-4 contig16905, 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: 30163
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:6556 original size:15 final size:16
Alignment explanation
Indices: 6532--6571 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
6522 AGAGGTTGAA
*
6532 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
6547 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
6563 AGAAAACAA
1 AGAAAACAA
6572 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:12256 original size:32 final size:32
Alignment explanation
Indices: 12215--12275 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
12205 TCCGACAGCA
*
12215 TACTCGAAAGGGACATTGATCGATCCAAAGCG
1 TACTCGAAAGGGACATTGATCGAGCCAAAGCG
12247 TACTCGAAAGGGACATTGATCGAGCCAAA
1 TACTCGAAAGGGACATTGATCGAGCCAAA
12276 AAAAAATCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (32 bp):
TACTCGAAAGGGACATTGATCGAGCCAAAGCG
Found at i:16024 original size:65 final size:65
Alignment explanation
Indices: 15910--16039 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 65
15900 GGAAAAACTG
* ** * * * *
15910 GTCCTACCCATGCATGGGGTAACCTTGGCCTACCCATGCCTGGGTTAGTGTAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTAACCTTGGCCTACCCATGCAAGGGCTAGTGCAGAAAATTGGAATC
*
15975 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCATGCAAGGGCTAGTGCAGAAAATTGGAATC
1 GTCCAACCCATGCATGGGGTAACCTTGGCCTACCCATGCAAGGGCTAGTGCAGAAAATTGGAATC
16040 AATAGCTAGC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTAACCTTGGCCTACCCATGCAAGGGCTAGTGCAGAAAATTGGAATC
Found at i:20020 original size:89 final size:89
Alignment explanation
Indices: 19815--20102 Score: 479
Period size: 89 Copynumber: 3.2 Consensus size: 89
19805 CAAACGGCCT
*
19815 GTGGCGTTGGTATAGTCATAAACCAAAAAATGGTATGATTGGAGATATACCTACGACTTACGTTG
1 GTGGCGTTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCTACGACTTACGTTG
*
19880 CTATAG-ATGTATACCAACAACGG
66 CTATAGAATGTATACCAACAGCGG
* * *
19903 GTGGCGTTGGTATAGCCACAAACAAAAAAATGGTATGATTGGAGATATACCTACGGCTTACGTTG
1 GTGGCGTTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCTACGACTTACGTTG
* *
19968 CTATAGAATGTATACCAATAGCGA
66 CTATAGAATGTATACCAACAGCGG
* *
19992 GTGACATTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCTACGACTTACGTTG
1 GTGGCGTTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCTACGACTTACGTTG
20057 CTATAGAATGTATACCAACAGCGG
66 CTATAGAATGTATACCAACAGCGG
*
20081 GGGGCGTTGGTATAGCCATAAA
1 GTGGCGTTGGTATAGCCATAAA
20103 TAGCCAACAG
Statistics
Matches: 182, Mismatches: 17, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
88 67 0.37
89 115 0.63
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (89 bp):
GTGGCGTTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCTACGACTTACGTTG
CTATAGAATGTATACCAACAGCGG
Found at i:20128 original size:89 final size:88
Alignment explanation
Indices: 19815--20137 Score: 420
Period size: 89 Copynumber: 3.6 Consensus size: 88
19805 CAAACGGCCT
*
19815 GTGGCGTTGGTATAGTCAT-AAACCAAAAAATGGTATGATTGGAGATATACCTACGACTTACGTT
1 GTGGCGTTGGTATAGCCATAAAACC--AAAATGGTATGATTGGAGATATACCTACGACTTACGTT
*
19879 GCTATAG-ATGTATACCAACAACGG
64 GCTATAGAATGTATACCAACAGCGG
* ** *
19903 GTGGCGTTGGTATAGCCACAAACAAAAAAATGGTATGATTGGAGATATACCTACGGCTTACGTTG
1 GTGGCGTTGGTATAGCCATAAA-ACCAAAATGGTATGATTGGAGATATACCTACGACTTACGTTG
* *
19968 CTATAGAATGTATACCAATAGCGA
65 CTATAGAATGTATACCAACAGCGG
* *
19992 GTGACATTGGTATAGCCAT-AAACCAAAAAATGGTATGATTGGAGATATACCTACGACTTACGTT
1 GTGGCGTTGGTATAGCCATAAAACC--AAAATGGTATGATTGGAGATATACCTACGACTTACGTT
20056 GCTATAGAATGTATACCAACAGCGG
64 GCTATAGAATGTATACCAACAGCGG
* * * * *
20081 GGGGCGTTGGTATAGCCATAAATAGCCAACA-GGTTTGATGGGGGATATACCTACGAC
1 GTGGCGTTGGTATAGCCATAAA-A-CCAAAATGGTATGATTGGAGATATACCTACGAC
20138 GAAGAAACTA
Statistics
Matches: 204, Mismatches: 23, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
87 1 0.00
88 63 0.31
89 131 0.64
90 6 0.03
91 1 0.00
92 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (88 bp):
GTGGCGTTGGTATAGCCATAAAACCAAAATGGTATGATTGGAGATATACCTACGACTTACGTTGC
TATAGAATGTATACCAACAGCGG
Found at i:28960 original size:21 final size:21
Alignment explanation
Indices: 28921--28969 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
28911 ACAATGCTTT
**
28921 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
28943 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
28964 A-GAAGC
1 AGGAAGC
28970 TACAATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Done.