Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013468.1 Corchorus olitorius cultivar O-4 contig13501, 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: 14557
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:4040 original size:16 final size:16
Alignment explanation
Indices: 4019--4049 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4009 TCCTCCTCTC
*
4019 TACAATTATTAATAAT
1 TACAATTAATAATAAT
4035 TACAATTAATAATAA
1 TACAATTAATAATAA
4050 CAAGCAGGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
TACAATTAATAATAAT
Found at i:4163 original size:42 final size:43
Alignment explanation
Indices: 4112--4205 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 43
4102 AGTGCATTAC
4112 CTAA-ATTCTA-CTCCATCTCTA-AGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGA-TAATTCATCAAAATAAAG
4153 CTAATATTCTACCCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
*
4198 TTAATATT
1 CTAATATT
4206 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.77
46 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:6315 original size:211 final size:210
Alignment explanation
Indices: 5952--6332 Score: 552
Period size: 211 Copynumber: 1.8 Consensus size: 210
5942 GGAAATGGGT
* * * *
5952 AATTACAAAAAAGGGTAGCAGGAAAAAGAAGGGGGACACTCATAGAGGGGCTTTTTAGTCATCTG
1 AATTACAAAAAAGGGCAGCAGGAAAAAGAAGGGGGAAACTCATACAGGGCCTTTTTAGTCATCTG
* * * * * *
6017 AAAAGTGAGAAAATACCAAAAAAAGCCAAAAGGTCGCACCACATTAATCCTCAATTTGACCTTTT
66 AAAAATGAGAAAAGACCAAAAAAAGACAAAAGGACGCACCACATTAATCCGCAATTTGACCTTTA
* *
6082 AGTAATTTCCCTGGGTACTAAAAATAATATATAGTATATATGTAATTAAAATACACTTAATCATA
131 AGTAATTTCCATGAGTACTAAAAATAATATATAGTATATATGTAATTAAAATACACTTAATCATA
6147 AATATAAAAATAGTA
196 AATATAAAAATAGTA
* *
6162 AATTACAAAAAAGGGCAGCAGG-AAAAGTAAGGGAGGAAATTCATCCAGGGCCTTTTTAGTCA-C
1 AATTACAAAAAAGGGCAGCAGGAAAAAG-AAGGG-GGAAACTCATACAGGGCCTTTTTAGTCATC
* * *
6225 TCGAAAAATGCGAAAAGACCAAAAAAAGACAAAAGGAGGCACCACATTAATCCGCAATTTGGCCT
64 T-GAAAAATGAGAAAAGACCAAAAAAAGACAAAAGGACGCACCACATTAATCCGCAATTTGACCT
6290 TTAAGTAATTTCCAT-AGTCACTAAAAATAATATATAGTATATA
128 TTAAGTAATTTCCATGAGT-ACTAAAAATAATATATAGTATATA
6333 CAATAGGAAG
Statistics
Matches: 150, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
209 5 0.03
210 30 0.20
211 115 0.77
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (210 bp):
AATTACAAAAAAGGGCAGCAGGAAAAAGAAGGGGGAAACTCATACAGGGCCTTTTTAGTCATCTG
AAAAATGAGAAAAGACCAAAAAAAGACAAAAGGACGCACCACATTAATCCGCAATTTGACCTTTA
AGTAATTTCCATGAGTACTAAAAATAATATATAGTATATATGTAATTAAAATACACTTAATCATA
AATATAAAAATAGTA
Found at i:6808 original size:75 final size:75
Alignment explanation
Indices: 6629--6829 Score: 217
Period size: 75 Copynumber: 2.7 Consensus size: 75
6619 AAGGGCCCCA
* * * * *
6629 ATCAACTTTTAACGT-GGAAACACCTTTTCACCCCATTTTGGTCTTTTCACACTCTGGAAATTAC
1 ATCAACTTTTAACATAGGAGA-ACCTTTTCGCCCCGTTTTGGTCTTTTCTCACTCTGGAAATTAC
6693 CAATAGCTCCC
65 CAATAGCTCCC
* * * * *
6704 ATCAACTTTTAACGTAGGATAACCCTTTCGCCCCGTTTCGGTCTTTTCTCAC-CATGGAATTTAC
1 ATCAACTTTTAACATAGGAGAACCTTTTCGCCCCGTTTTGGTCTTTTCTCACTC-TGGAAATTAC
* *
6768 TAATAGGTCCC
65 CAATAGCTCCC
* * ** *
6779 ATCAACTTTTAATATGGGAGAATTTTTTCGCTCCGTTTTGGTCTTTTCTCA
1 ATCAACTTTTAACATAGGAGAACCTTTTCGCCCCGTTTTGGTCTTTTCTCA
6830 ATTTAGTTAA
Statistics
Matches: 106, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
74 1 0.01
75 101 0.95
76 4 0.04
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.37
Consensus pattern (75 bp):
ATCAACTTTTAACATAGGAGAACCTTTTCGCCCCGTTTTGGTCTTTTCTCACTCTGGAAATTACC
AATAGCTCCC
Found at i:7507 original size:16 final size:17
Alignment explanation
Indices: 7486--7518 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
7476 GAACTATTCG
7486 TCTTCCC-TCCTTTTTT
1 TCTTCCCATCCTTTTTT
*
7502 TCTTCCCATCGTTTTTT
1 TCTTCCCATCCTTTTTT
7519 GGTTTTTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.03, C:0.33, G:0.03, T:0.61
Consensus pattern (17 bp):
TCTTCCCATCCTTTTTT
Found at i:7881 original size:140 final size:140
Alignment explanation
Indices: 7629--7911 Score: 451
Period size: 140 Copynumber: 2.0 Consensus size: 140
7619 TCGTCCCTCT
*
7629 CTTCGAAACGCAACATTAGTTTTGGGATTGGCCAATTTATTTTATTGACCTTAGGAGTGTATGTT
1 CTTCGAAACACAACATTAGTTTTGGGATTGGCCAATTTATTTTATTGACCTTAGGAGTGTATGTT
*
7694 CCTAGGATTTTGATTGCTTAGAATAATGGTTTAGAGTAAATGTCGTCCAGGGGGTGCGCTCCCTT
66 CCTAGGATTTTGATTGCTTAGAATAATGGTTTAGAGTAAATGTCGTCCAAGGGGTGCGCTCCCTT
7759 TCATCACCCA
131 TCATCACCCA
* * * *
7769 CTTCGAAACACCACATTAGTTTTGGGTTTTGTCAATTTATTTTATTGACCTTAGGAGTAG-ATGT
1 CTTCGAAACACAACATTAGTTTTGGGATTGGCCAATTTATTTTATTGACCTTAGGAGT-GTATGT
* * *
7833 TCTTAGGATTTTGATTGCTTAGAATAATGGTTTAGGGTAATTGTCGTCCAAGGGGTGCGCTCCCT
65 TCCTAGGATTTTGATTGCTTAGAATAATGGTTTAGAGTAAATGTCGTCCAAGGGGTGCGCTCCCT
* *
7898 TTGATCACGCA
130 TTCATCACCCA
7909 CTT
1 CTT
7912 TCTCTTTTCT
Statistics
Matches: 131, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
140 130 0.99
141 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (140 bp):
CTTCGAAACACAACATTAGTTTTGGGATTGGCCAATTTATTTTATTGACCTTAGGAGTGTATGTT
CCTAGGATTTTGATTGCTTAGAATAATGGTTTAGAGTAAATGTCGTCCAAGGGGTGCGCTCCCTT
TCATCACCCA
Found at i:12244 original size:28 final size:28
Alignment explanation
Indices: 12207--12266 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
12197 AAAAATGCAA
* * *
12207 TTTAGTCAACCATGGGTAAAA-TGGTAAT
1 TTTAGCCAACCAAGGG-AAAATTCGTAAT
12235 TTTAGCCAACCAAGGGAAAATTCGTAAT
1 TTTAGCCAACCAAGGGAAAATTCGTAAT
12263 TTTA
1 TTTA
12267 ACATCTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (28 bp):
TTTAGCCAACCAAGGGAAAATTCGTAAT
Found at i:13054 original size:11 final size:11
Alignment explanation
Indices: 13033--13066 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
13023 ATTAAAAAAA
13033 TTCTCTTTTTTT
1 TTCT-TTTTTTT
13045 TTCTTTTTTTT
1 TTCTTTTTTTT
*
13056 TCCTTTTTTTT
1 TTCTTTTTTTT
13067 CCTTTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:13063 original size:21 final size:21
Alignment explanation
Indices: 13037--13080 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
13027 AAAAAATTCT
* *
13037 CTTTTTTTTTCTTTTTTTTTC
1 CTTTTTTTTCCTTTTCTTTTC
13058 CTTTTTTTTCCTTTTCTTTTC
1 CTTTTTTTTCCTTTTCTTTTC
13079 CT
1 CT
13081 ATCCTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
CTTTTTTTTCCTTTTCTTTTC
Found at i:13077 original size:11 final size:10
Alignment explanation
Indices: 13039--13080 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
13029 AAAATTCTCT
*
13039 TTTTTTTTCT
1 TTTTTTTTCC
13049 TTTTTTTTCC
1 TTTTTTTTCC
13059 TTTTTTTTCC
1 TTTTTTTTCC
13069 TTTTCTTTTCC
1 TTTT-TTTTCC
13080 T
1 T
13081 ATCCTTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTTTCC
Found at i:14100 original size:23 final size:23
Alignment explanation
Indices: 14074--14117 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
14064 CTACCACACC
14074 AATTTAATCTCAA-ATAAAATTCT
1 AATTTAAT-TCAATATAAAATTCT
*
14097 AATTTAATTCAATTTAAAATT
1 AATTTAATTCAATATAAAATT
14118 TAGGCTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAATTCAATATAAAATTCT
Done.