Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014464.1 Corchorus olitorius cultivar O-4 contig14497, 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: 11317
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5115 original size:2 final size:2
Alignment explanation
Indices: 5101--5221 Score: 50
Period size: 2 Copynumber: 66.0 Consensus size: 2
5091 CCCGTATTAC
*
5101 TA TA TA T- TA -A TA TA TA TA TA TA TA TA T- TA TA -A TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
5139 TA TT TA T- TA TT TC GA AA TA TA TA TA -A TA TA TA TA -A CA TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* * * *
5179 CA -A TA TA TA -A TA TA TA T- TA TA T- TA AA TA -A AA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5216 TA TA TA
1 TA TA TA
5222 AAAATATGGC
Statistics
Matches: 89, Mismatches: 17, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
1 12 0.13
2 76 0.85
3 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:5115 original size:8 final size:10
Alignment explanation
Indices: 5101--5221 Score: 50
Period size: 9 Copynumber: 13.2 Consensus size: 10
5091 CCCGTATTAC
5101 TATATAT-TA
1 TATATATATA
5110 -ATATATATA
1 TATATATATA
5119 TATATATAT-
1 TATATATATA
*
5128 TATA-ATACA
1 TATATATATA
*
5137 TATATTTAT-
1 TATATATATA
* ** *
5146 TATTTCGAAA
1 TATATATATA
5156 TATATATA-A
1 TATATATATA
5165 TATATATA-A
1 TATATATATA
* *
5174 CATCACA-ATA
1 TAT-ATATATA
5184 TATA-ATATA
1 TATATATATA
5193 TAT-TATAT-
1 TATATATATA
* *
5201 TAAATA-AAA
1 TATATATATA
*
5210 TATATTTATA
1 TATATATATA
5220 TA
1 TA
5222 AAAATATGGC
Statistics
Matches: 82, Mismatches: 18, Indels: 23
0.67 0.15 0.19
Matches are distributed among these distances:
8 13 0.16
9 45 0.55
10 24 0.29
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (10 bp):
TATATATATA
Found at i:5126 original size:20 final size:19
Alignment explanation
Indices: 5101--5147 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
5091 CCCGTATTAC
*
5101 TATATATTAATATATATATA
1 TATATATTAATA-ATACATA
5121 TATATATT-ATAATACATA
1 TATATATTAATAATACATA
*
5139 TATTTATTA
1 TATATATTA
5148 TTTCGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 13 0.54
19 3 0.12
20 8 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATATTAATAATACATA
Found at i:5133 original size:22 final size:22
Alignment explanation
Indices: 5101--5199 Score: 66
Period size: 22 Copynumber: 4.5 Consensus size: 22
5091 CCCGTATTAC
5101 TATATA-T-TAATATATATATA
1 TATATATTATAATATATATATA
* *
5121 TATATATTATAATACATATATT
1 TATATATTATAATATATATATA
5143 TAT-TATT-TCGAAATATATATAATA
1 TATATATTAT---AATATATAT-ATA
**
5167 TATATAACATCACA-ATATATA-A
1 TATATATTAT-A-ATATATATATA
5189 TATATATTATA
1 TATATATTATA
5200 TTAAATAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.11
21 6 0.10
22 23 0.38
23 9 0.15
24 12 0.20
25 3 0.05
26 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (22 bp):
TATATATTATAATATATATATA
Found at i:5139 original size:26 final size:25
Alignment explanation
Indices: 5110--5221 Score: 78
Period size: 23 Copynumber: 4.6 Consensus size: 25
5100 CTATATATTA
*
5110 ATATATATATATATATATTATAATAC
1 ATATATATATATATATATTA-AATAT
5136 ATATAT-T-TAT-TAT-TTCGAAATAT
1 ATATATATATATATATATT--AAATAT
* *
5159 ATATA-ATATATATAACATCACAATAT
1 ATATATATATATAT-ATATTA-AATAT
5185 ATA-ATATATAT-TATATTAAATA-
1 ATATATATATATATATATTAAATAT
* *
5207 AAATATATTTATATA
1 ATATATATATATATA
5222 AAAATATGGC
Statistics
Matches: 68, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
22 4 0.06
23 24 0.35
24 13 0.19
25 5 0.07
26 21 0.31
27 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (25 bp):
ATATATATATATATATATTAAATAT
Found at i:7643 original size:17 final size:17
Alignment explanation
Indices: 7621--7653 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
7611 ATTAATGATA
7621 TTTATTT-TGATTTTTGT
1 TTTATTTAT-ATTTTTGT
7638 TTTATTTATATTTTTG
1 TTTATTTATATTTTTG
7654 ACAATTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTATTTATATTTTTGT
Found at i:8031 original size:28 final size:28
Alignment explanation
Indices: 7995--8082 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
7985 ATAAATGTTA
7995 TAATAAATCCTATCCCCCTATCTCTACT
1 TAATAAATCCTATCCCCCTATCTCTACT
* * * * * *** **
8023 TAATTAAT-CTTTCACACAATAAATGTT
1 TAATAAATCCTATCCCCCTATCTCTACT
8050 ATAATAAATCCTATCCCCCTATCTCTACT
1 -TAATAAATCCTATCCCCCTATCTCTACT
8079 TAAT
1 TAAT
8083 TATTCTACAA
Statistics
Matches: 38, Mismatches: 20, Indels: 4
0.61 0.32 0.06
Matches are distributed among these distances:
27 10 0.26
28 18 0.47
29 10 0.26
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.38
Consensus pattern (28 bp):
TAATAAATCCTATCCCCCTATCTCTACT
Found at i:8061 original size:56 final size:56
Alignment explanation
Indices: 7975--8084 Score: 220
Period size: 56 Copynumber: 2.0 Consensus size: 56
7965 TATCCGTTTC
7975 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTAAT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTAAT
8031 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTA
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTA
8085 TTCTACAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.37
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTAAT
Found at i:9028 original size:56 final size:56
Alignment explanation
Indices: 8961--9074 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
8951 TATCCGTTTC
8961 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTATACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTATACTTAATTATT
*
9017 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTATACTTAATTATT
9073 CT
1 CT
9075 ACAAAATAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTATACTTAATTATT
Found at i:9200 original size:42 final size:42
Alignment explanation
Indices: 9141--9220 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
9131 AAGGATCAGA
9141 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATG
1 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATG
*
9183 ATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
9221 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (42 bp):
ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATG
Done.