Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014643.1 Corchorus olitorius cultivar O-4 contig14676, 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: 22401
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:765 original size:259 final size:258
Alignment explanation
Indices: 301--808 Score: 935
Period size: 259 Copynumber: 2.0 Consensus size: 258
291 GTGGGACTTA
301 ACCTTAGACCATAAGGCTTCAAAGAGTATGCACCTATCATTGAGTCAAAGGTTCAAGATCTTGCG
1 ACCTTAGACCATAAGGCTTCAAAGAGTATGCACCTATCATTGAGTCAAAGGTTCAAGATCTTGCG
* *
366 TACGCAGTTGTTCATGTTGGTTTGTACCTCACCCATTAAAACCAGGTGTGCGATGCGGGTCGGAT
66 TACGCAGTTGTTCACGTTGGTTGGTACCTCACCCATTAAAACCAGGTGTGCGATGCGGGTCGGAT
* *
431 TCAGATTAGTCAGAATAAAACTCTAGATACCAGATATGGTATAAAAAAATAAAAAATAAAACCAT
131 TCAGATTAGTCAGAATAAAACTCTAGATACCAAATATGATATAAAAAAATAAAAAATAAAACCAT
496 CTATTGTAGTAGCAAAATCATCCCATGCTCGCCGAGGGATCAATATTTTAAATTTTAAAATAT
196 CTATTGTAGTAGCAAAATCATCCCATGCTCGCCGAGGGATCAATATTTTAAATTTTAAAATAT
559 ACCTTAAGACCATAAGGCTTCAAAGAGTATGCACCTATCATTGAGTCAAAGGTTCAAGATCTTGC
1 ACCTT-AGACCATAAGGCTTCAAAGAGTATGCACCTATCATTGAGTCAAAGGTTCAAGATCTTGC
* *
624 GTACGCAGTTGTTCACGTTGGTTGGTACCTCACCCATTAAAACTAGGTGTGCGATGTGGGTCGGA
65 GTACGCAGTTGTTCACGTTGGTTGGTACCTCACCCATTAAAACCAGGTGTGCGATGCGGGTCGGA
*
689 TTCAGATTAGTCAGAATAAAACTCTAGATACCAAATGTGATATAAAAAAATAAAAAATAAAACCA
130 TTCAGATTAGTCAGAATAAAACTCTAGATACCAAATATGATATAAAAAAATAAAAAATAAAACCA
*
754 TCTATTGTAGTAGCAAAATCATCCCATGCTCGTCGAGGGATCAATATTTTAAATT
195 TCTATTGTAGTAGCAAAATCATCCCATGCTCGCCGAGGGATCAATATTTTAAATT
809 ATATAAATTG
Statistics
Matches: 241, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
258 5 0.02
259 236 0.98
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (258 bp):
ACCTTAGACCATAAGGCTTCAAAGAGTATGCACCTATCATTGAGTCAAAGGTTCAAGATCTTGCG
TACGCAGTTGTTCACGTTGGTTGGTACCTCACCCATTAAAACCAGGTGTGCGATGCGGGTCGGAT
TCAGATTAGTCAGAATAAAACTCTAGATACCAAATATGATATAAAAAAATAAAAAATAAAACCAT
CTATTGTAGTAGCAAAATCATCCCATGCTCGCCGAGGGATCAATATTTTAAATTTTAAAATAT
Found at i:956 original size:17 final size:17
Alignment explanation
Indices: 936--968 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
926 AAGAATAAAT
936 TAAA-TGATTATAATATA
1 TAAATTGATTA-AATATA
953 TAAATTGATTAAATAT
1 TAAATTGATTAAATAT
969 TTATAATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
TAAATTGATTAAATATA
Found at i:7806 original size:29 final size:30
Alignment explanation
Indices: 7735--7806 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
7725 ATACCGTACA
* *
7735 GGTCCCTCTACTTACAAAAAGGGATCGATTT
1 GGTCCCTCTAC-TACAAAAACGGATCAATTT
*
7766 GGTCCC-CTTACTACAAAAACTG-TCAATTT
1 GGTCCCTC-TACTACAAAAACGGATCAATTT
7795 GGTCCCTCTACT
1 GGTCCCTCTACT
7807 TATAATTTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 16 0.44
30 11 0.31
31 9 0.25
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (30 bp):
GGTCCCTCTACTACAAAAACGGATCAATTT
Found at i:8169 original size:29 final size:30
Alignment explanation
Indices: 8110--8170 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
8100 TGATACCAAA
*
8110 TTATAAGTAGAGGGACCAAATTGACAGTTT
1 TTATAAGTAGAGGGACCAAATTGACACTTT
* *
8140 TTAT-AGTATAGGGATCAAATTGATC-CTTT
1 TTATAAGTAGAGGGACCAAATTGA-CACTTT
8169 TT
1 TT
8171 TGAAACTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (30 bp):
TTATAAGTAGAGGGACCAAATTGACACTTT
Found at i:9964 original size:32 final size:32
Alignment explanation
Indices: 9919--9986 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
9909 TTTTATCTTC
*
9919 TAAT-AAGTTGATCATGTGACTCGAACAGGAT
1 TAATCAAGTTGATCATGTGACTCGAACAGAAT
9950 TAATCAAGTTGATCATGTGACTCGAACAGAAT
1 TAATCAAGTTGATCATGTGACTCGAACAGAAT
9982 TAATC
1 TAATC
9987 GTATACTCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 31 0.89
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (32 bp):
TAATCAAGTTGATCATGTGACTCGAACAGAAT
Found at i:12667 original size:2 final size:2
Alignment explanation
Indices: 12660--12685 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12650 GAAATTAGGT
12660 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
12686 CAATCAGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.