Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021190.1 Corchorus olitorius cultivar O-4 contig21223, 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: 9270
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Found at i:3158 original size:21 final size:22
Alignment explanation
Indices: 3134--3175 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3124 TTTGCCTCAT
3134 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATGCCATG
*
3155 GCATTCATTCATGCATTCCAT
1 GCATTCATTCATGCATGCCAT
3176 TAAAGCCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (22 bp):
GCATTCATTCATGCATGCCATG
Found at i:5267 original size:22 final size:23
Alignment explanation
Indices: 5239--5281 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
5229 AAAAATAAAA
*
5239 AAAAAGAAAA-GAAGAAAAAATG
1 AAAAAGAAAATGAAAAAAAAATG
5261 AAAAAGAAAATGAAAAAAAAA
1 AAAAAGAAAATGAAAAAAAAA
5282 AGCACTTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (23 bp):
AAAAAGAAAATGAAAAAAAAATG
Found at i:5282 original size:12 final size:12
Alignment explanation
Indices: 5253--5282 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5243 AGAAAAGAAG
5253 AAAAAATGAAAA
1 AAAAAATGAAAA
*
5265 AGAAAATGAAAA
1 AAAAAATGAAAA
5277 AAAAAA
1 AAAAAA
5283 GCACTTGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (12 bp):
AAAAAATGAAAA
Found at i:5685 original size:5 final size:5
Alignment explanation
Indices: 5675--5773 Score: 55
Period size: 5 Copynumber: 19.6 Consensus size: 5
5665 AAATCATCAA
**
5675 AAATC AAATC AAAGTC -AAT- AAAAA AAATC AAAAATC AAATC AAAGTC
1 AAATC AAATC AAA-TC AAATC AAATC AAATC --AAATC AAATC AAA-TC
* ** *
5722 -AATA AAAAA AAATC AAATC AAAATT AAA-- AAATC AAATC AAATC AAAATC
1 AAATC AAATC AAATC AAATC -AAATC AAATC AAATC AAATC AAATC -AAATC
5771 AAA
1 AAA
5774 GGAGAATGGA
Statistics
Matches: 75, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
3 3 0.04
4 4 0.05
5 50 0.67
6 13 0.17
7 5 0.07
ACGTcount: A:0.68, C:0.13, G:0.02, T:0.17
Consensus pattern (5 bp):
AAATC
Found at i:5704 original size:19 final size:18
Alignment explanation
Indices: 5657--5761 Score: 68
Period size: 19 Copynumber: 6.1 Consensus size: 18
5647 AAGAAATTCA
5657 AATAAAAAAAATC--ATC
1 AATAAAAAAAATCAAATC
**
5673 AA-AAATCAAATCAAAGTC
1 AATAAAAAAAATCAAA-TC
5691 AATAAAAAAAATCAAA--
1 AATAAAAAAAATCAAATC
*
5707 AAT----CAAATCAAAGTC
1 AATAAAAAAAATCAAA-TC
5722 AATAAAAAAAAATCAAATC
1 AAT-AAAAAAAATCAAATC
5741 AA-AATTAAAAAATCAAATC
1 AATAA--AAAAAATCAAATC
5760 AA
1 AA
5762 ATCAAAATCA
Statistics
Matches: 69, Mismatches: 6, Indels: 25
0.69 0.06 0.25
Matches are distributed among these distances:
12 8 0.12
15 11 0.16
16 5 0.07
17 3 0.04
18 4 0.06
19 30 0.43
20 8 0.12
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.17
Consensus pattern (18 bp):
AATAAAAAAAATCAAATC
Found at i:5730 original size:32 final size:32
Alignment explanation
Indices: 5657--5738 Score: 139
Period size: 31 Copynumber: 2.5 Consensus size: 32
5647 AAGAAATTCA
5657 AATAAAAAAAATCATCAAAAATCAAATCAAAGTC
1 AATAAAAAAAA--ATCAAAAATCAAATCAAAGTC
5691 AAT-AAAAAAAATCAAAAATCAAATCAAAGTC
1 AATAAAAAAAAATCAAAAATCAAATCAAAGTC
5722 AATAAAAAAAAATCAAA
1 AATAAAAAAAAATCAAA
5739 TCAAAATTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
31 24 0.51
32 13 0.28
33 7 0.15
34 3 0.06
ACGTcount: A:0.70, C:0.12, G:0.02, T:0.16
Consensus pattern (32 bp):
AATAAAAAAAAATCAAAAATCAAATCAAAGTC
Found at i:6454 original size:50 final size:50
Alignment explanation
Indices: 6390--6539 Score: 237
Period size: 50 Copynumber: 3.0 Consensus size: 50
6380 AGTTTTACAA
* * *
6390 TAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGTTTTTTAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
*
6440 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* * *
6490 TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
6540 GACAGTGAAG
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 92 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
Found at i:7073 original size:79 final size:79
Alignment explanation
Indices: 6979--7134 Score: 258
Period size: 79 Copynumber: 2.0 Consensus size: 79
6969 CAAGTTATCA
* *
6979 AAGTTGACTGCACATTGGTCCTCTTCCATCATTAATCAAGAAATTTTCAGTTACAACATCAGACT
1 AAGTTGACCGCACATTGGTCCTCTTCCATCATCAATCAAGAAATTTTCAGTTACAACATCAGACT
7044 CAGAGTTATTTTTC
66 CAGAGTTATTTTTC
* * * *
7058 AAGTTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCAGATT
1 AAGTTGACCGCACATTGGTCCTCTTCCATCATCAATCAAGAAATTTTCAGTTACAACATCAGACT
7123 CAGAGTTATTTT
66 CAGAGTTATTTT
7135 CCAAAGGTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (79 bp):
AAGTTGACCGCACATTGGTCCTCTTCCATCATCAATCAAGAAATTTTCAGTTACAACATCAGACT
CAGAGTTATTTTTC
Found at i:7294 original size:50 final size:50
Alignment explanation
Indices: 7219--7601 Score: 615
Period size: 50 Copynumber: 7.7 Consensus size: 50
7209 CGAATGCTTT
* * * *
7219 GGCTTTCCCATAAGCCGAACTCGTTTCCATATGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
** * *
7269 GGCTTTTCCACAAGCCGGACTCGTTTCCATACGAGTCAATAATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
7319 GGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
7369 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
7419 GGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
7469 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
7519 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
7569 GGCTTTTCCACAAGCCACA-TCTGTTTCCATACG
1 GGCTTTTCCACAAGCCAAACTC-GTTTCCATACG
7602 GTGCATTACC
Statistics
Matches: 309, Mismatches: 23, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
49 2 0.01
50 307 0.99
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
Found at i:7690 original size:50 final size:50
Alignment explanation
Indices: 7613--7793 Score: 290
Period size: 50 Copynumber: 3.6 Consensus size: 50
7603 TGCATTACCT
*
7613 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGATGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
7663 TTTTAAGATTGAATTGGTAGACGGTTCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
7713 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* * * * *
7763 TTTTGATATTAAATTGGGAGACAATTCAAAG
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAG
7794 AAGTTGATCG
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 121 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:8120 original size:28 final size:28
Alignment explanation
Indices: 8063--8137 Score: 116
Period size: 28 Copynumber: 2.7 Consensus size: 28
8053 TTTCCATGTT
*
8063 CAGGGGTATTTTAGTCA-TTTGCACACC
1 CAGGGGCATTTTAGTCATTTTGCACACC
* *
8090 CAGGGGCATTTTGGTCATTTTGTACACC
1 CAGGGGCATTTTAGTCATTTTGCACACC
8118 CAGGGGCATTTTAGTCATTT
1 CAGGGGCATTTTAGTCATTT
8138 CATGAACCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 15 0.35
28 28 0.65
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (28 bp):
CAGGGGCATTTTAGTCATTTTGCACACC
Done.