Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011974.1 Corchorus olitorius cultivar O-4 contig12007, 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: 48980
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:6177 original size:16 final size:17
Alignment explanation
Indices: 6153--6185 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6143 ACGGTGTACG
6153 TATAAATTATAT-TTAA
1 TATAAATTATATATTAA
*
6169 TATATATTATATATTAA
1 TATAAATTATATATTAA
6186 CAAATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAAATTATATATTAA
Found at i:13099 original size:21 final size:20
Alignment explanation
Indices: 13042--13102 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
13032 CTATTTGGCA
*
13042 ACTGTGCAGATGAGATTA-T
1 ACTGTACAGATGAGATTATT
* *
13061 ACTGTACAGATTAAATTATGT
1 ACTGTACAGATGAGATTAT-T
13082 ACTGTACAGATGAGATTATT
1 ACTGTACAGATGAGATTATT
13102 A
1 A
13103 GAGCAGCGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 15 0.43
20 2 0.06
21 18 0.51
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
ACTGTACAGATGAGATTATT
Found at i:13174 original size:19 final size:19
Alignment explanation
Indices: 13150--13186 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
13140 TTTGGTCCCA
13150 AAACGGTGGTGAAACGGTC
1 AAACGGTGGTGAAACGGTC
13169 AAACGGTGGTGAAACGGT
1 AAACGGTGGTGAAACGGT
13187 TACAGATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.14, G:0.38, T:0.16
Consensus pattern (19 bp):
AAACGGTGGTGAAACGGTC
Found at i:15238 original size:79 final size:79
Alignment explanation
Indices: 15144--15302 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
15134 TAGTAAGAAG
* *
15144 ATATTGCATTGGCTGTAGGTTAATCAGTTAGGAGAAACTCATATATCCAAACAAATAATTCGCAT
1 ATATTGCATTGGCTGTAAGTTAATCAGTTAGGAGAAACTCATACATCCAAACAAATAATTCGCAT
15209 ATATAAAGCAAAAC
66 ATATAAAGCAAAAC
15223 ATATTGCATTGGCTGTAAGTTAATCAGTTAGGAGAAACTCATACATCCAAACAAATAATTCGCAT
1 ATATTGCATTGGCTGTAAGTTAATCAGTTAGGAGAAACTCATACATCCAAACAAATAATTCGCAT
15288 ATATAAAGCAAAAC
66 ATATAAAGCAAAAC
15302 A
1 A
15303 CATGACCTCT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (79 bp):
ATATTGCATTGGCTGTAAGTTAATCAGTTAGGAGAAACTCATACATCCAAACAAATAATTCGCAT
ATATAAAGCAAAAC
Found at i:16941 original size:105 final size:107
Alignment explanation
Indices: 16764--17021 Score: 393
Period size: 105 Copynumber: 2.5 Consensus size: 107
16754 TTTTTCTAAT
* * **
16764 CCTTAAAATAAAATTTAAATTTTAATTT-GAACTAAACTTAGTG-AATTAGTTATATATTTAATT
1 CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTAATT
*
16827 TCTAAAACCCTATAACAAT-AA-TATTAATTATGGAATTTAC
66 TCTAAAACCCTATAACAATAAATTATTAATTATGAAATTTAC
* * *
16867 CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATT
1 CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTAATT
*
16932 TCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTAC
66 TCTAAAACCCTATAACAATAAATTATTAATTATGAAATTTAC
16974 CCTTAAAATAAAAA-AAAA-TTTAATTTGGGGCTAAACTTAGTGAAATTA
1 CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
17022 AGGCTAAACT
Statistics
Matches: 142, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
103 26 0.18
104 13 0.09
105 66 0.46
106 6 0.04
107 31 0.22
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.39
Consensus pattern (107 bp):
CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTAATT
TCTAAAACCCTATAACAATAAATTATTAATTATGAAATTTAC
Found at i:17785 original size:30 final size:30
Alignment explanation
Indices: 17749--17810 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
17739 GTTAATAAAC
17749 CATTAAAATTTGAGGGTATAAG-AGAAAAGT
1 CATTAAAATTTGAGGGTATAAGAAG-AAAGT
17779 CATTAAAATTTGAGGGTATAAGAAGAAAGT
1 CATTAAAATTTGAGGGTATAAGAAGAAAGT
17809 CA
1 CA
17811 AGATAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.26
Consensus pattern (30 bp):
CATTAAAATTTGAGGGTATAAGAAGAAAGT
Found at i:18587 original size:17 final size:17
Alignment explanation
Indices: 18565--18600 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
18555 GTTACGGAGA
*
18565 TATGAATAAAAGAAAAC
1 TATGAATAAAACAAAAC
18582 TATGAATAAAACAAAAC
1 TATGAATAAAACAAAAC
18599 TA
1 TA
18601 AAGATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.19
Consensus pattern (17 bp):
TATGAATAAAACAAAAC
Found at i:22477 original size:2 final size:2
Alignment explanation
Indices: 22472--22521 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
22462 TTTTTTAGTA
22472 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
22514 TG TT TG TG
1 TG TG TG TG
22522 CGCTTATTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:26617 original size:22 final size:22
Alignment explanation
Indices: 26589--26633 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
26579 GTGATCTTTG
26589 TAATACTGAATTAGGCAAACCA
1 TAATACTGAATTAGGCAAACCA
26611 TAATACTGAATTAGGCAAACCA
1 TAATACTGAATTAGGCAAACCA
26633 T
1 T
26634 CGATTCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (22 bp):
TAATACTGAATTAGGCAAACCA
Found at i:29989 original size:29 final size:30
Alignment explanation
Indices: 29949--30024 Score: 102
Period size: 29 Copynumber: 2.5 Consensus size: 30
29939 TTTGAGGAAA
*
29949 TGCTCAATTTAGTCCTAAACCTTT-AAACC
1 TGCTCAATTTAGTCCTAAACATTTCAAACC
29978 TGCTCAATTTAGTACC-AAACATTTCGAAACC
1 TGCTCAATTTAGT-CCTAAACATTTC-AAACC
*
30009 TGCTCAATTCAGTCCT
1 TGCTCAATTTAGTCCT
30025 TTTTTAGACC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 20 0.49
30 4 0.10
31 17 0.41
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (30 bp):
TGCTCAATTTAGTCCTAAACATTTCAAACC
Found at i:45570 original size:56 final size:57
Alignment explanation
Indices: 45494--45605 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 57
45484 TGATAGCCAC
*
45494 CCTAAAGTTTGATAGTCAAACCACAAAAAACATTT-ATTGTAAATACATGATCAAAT
1 CCTAAAGTTTGATAATCAAACCACAAAAAACATTTCATTGTAAATACATGATCAAAT
* * * * *
45550 CCTAAATTTTGGTAATCAAACCACAAAAAACATTTCATTGTACATGCATGGTCAAA
1 CCTAAAGTTTGATAATCAAACCACAAAAAACATTTCATTGTAAATACATGATCAAA
45606 CCCCAAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
56 32 0.65
57 17 0.35
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.29
Consensus pattern (57 bp):
CCTAAAGTTTGATAATCAAACCACAAAAAACATTTCATTGTAAATACATGATCAAAT
Done.