Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016812.1 Corchorus olitorius cultivar O-4 contig16845, 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: 8450
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1479 original size:9 final size:9
Alignment explanation
Indices: 1465--1491 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1455 AAATGGTTGC
1465 TTTGTTTTG
1 TTTGTTTTG
1474 TTTGTTTTG
1 TTTGTTTTG
1483 TTTGTTTTG
1 TTTGTTTTG
1492 ATGTTTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (9 bp):
TTTGTTTTG
Found at i:4996 original size:15 final size:15
Alignment explanation
Indices: 4976--5006 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4966 TTCCCATTCG
*
4976 AAAGAAGAAGAAAAA
1 AAAGAAAAAGAAAAA
4991 AAAGAAAAAGAAAAA
1 AAAGAAAAAGAAAAA
5006 A
1 A
5007 CTTGGCCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAAAA
Found at i:5151 original size:18 final size:18
Alignment explanation
Indices: 5106--5150 Score: 83
Period size: 17 Copynumber: 2.6 Consensus size: 18
5096 AGTCTCATGC
5106 TTTCAAAAAAGGATTTTT
1 TTTCAAAAAAGGATTTTT
5124 TTTCAAAAAAGGA-TTTT
1 TTTCAAAAAAGGATTTTT
5141 TTTCAAAAAA
1 TTTCAAAAAA
5151 ATGGTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (18 bp):
TTTCAAAAAAGGATTTTT
Found at i:5158 original size:16 final size:16
Alignment explanation
Indices: 5139--5176 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
5129 AAAAAGGATT
5139 TTTTTCAAAAAAATGG
1 TTTTTCAAAAAAATGG
5155 TTTTTC--AAAAATGG
1 TTTTTCAAAAAAATGG
5169 -TTTTCAAA
1 TTTTTCAAA
5177 TTTGTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 5 0.25
14 8 0.40
15 1 0.05
16 6 0.30
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (16 bp):
TTTTTCAAAAAAATGG
Found at i:5158 original size:17 final size:17
Alignment explanation
Indices: 5106--5165 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
5096 AGTCTCATGC
5106 TTTC-AAAAAAGGATTTTT
1 TTTCAAAAAAAGGA--TTT
5124 TTTC-AAAAAAGGATTTT
1 TTTCAAAAAAAGGA-TTT
5141 TTTCAAAAAAATGG--TT
1 TTTCAAAAAAA-GGATTT
5157 TTTCAAAAA
1 TTTCAAAAA
5166 TGGTTTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
16 11 0.28
17 8 0.20
18 19 0.47
19 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (17 bp):
TTTCAAAAAAAGGATTT
Found at i:5172 original size:13 final size:14
Alignment explanation
Indices: 5147--5176 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5137 TTTTTTTCAA
5147 AAAAATGGTTTTTC
1 AAAAATGGTTTTTC
5161 AAAAATGG-TTTTC
1 AAAAATGGTTTTTC
5174 AAA
1 AAA
5177 TTTGTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (14 bp):
AAAAATGGTTTTTC
Found at i:6959 original size:36 final size:35
Alignment explanation
Indices: 6736--7387 Score: 572
Period size: 35 Copynumber: 18.3 Consensus size: 35
6726 GGTATTTATT
* * *
6736 AGTTTATTTCAAGATGACCCAGGGCGGTCTTTCTTC
1 AGTTTATTTCAA-TTGATCCAGGGCGATCTTTCTTC
* * * * * * * *
6772 AATTCATTTCAGTTGACCCAGGGTGGTCCTTATTC
1 AGTTTATTTCAATTGATCCAGGGCGATCTTTCTTC
*
6807 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
1 AGTTTATTTCAATTGATCCAGGGCGATC-TTTCTTC
* ** * *
6843 AATTTATTTTGTTATTGACCCAGGGCGGTCTTTCTTC
1 AGTTTA-TTT-CAATTGATCCAGGGCGATCTTTCTTC
* * * * * * *
6880 AATTCATTTCAGTTGACCCAGGGTGGA-CCTTATTC
1 AGTTTATTTCAATTGATCCAGGG-CGATCTTTCTTC
*
6915 AGTTTATTTCAATTGATCCAAGGCGATCTTTTCTTC
1 AGTTTATTTCAATTGATCCAGGGCGATC-TTTCTTC
* * *
6951 AGTTTATTTCGATTTGACCCAGGGCGGTCTTTCTTC
1 AGTTTATTTC-AATTGATCCAGGGCGATCTTTCTTC
* * * *
6987 AATTCATTTCAATTGATCCAGGGCGATCTTACCTC
1 AGTTTATTTCAATTGATCCAGGGCGATCTTTCTTC
* *
7022 AAG-TTATTTTAATTGATCCAGGGCGATCTTCCTTC
1 -AGTTTATTTCAATTGATCCAGGGCGATCTTTCTTC
* * * *
7057 AGTTCATTTCAATTGACCCAGGGCGATCTTACCTC
1 AGTTTATTTCAATTGATCCAGGGCGATCTTTCTTC
*
7092 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
1 AGTTTATTTCAATTGATCCAGGGCGATC-TTTCTTC
** *
7128 AACTTATCT-AAGTTGATCCAGGGCGATCTTTTCTTC
1 AGTTTATTTCAA-TTGATCCAGGGCGATC-TTTCTTC
* * *
7164 AGTTCATATCAGTTGATCCAGGGCGATCTTTTCTTC
1 AGTTTATTTCAATTGATCCAGGGCGATC-TTTCTTC
* * *
7200 TGTTTATTTCAGTTGATCCAGGGCGGTCTTTCTTC
1 AGTTTATTTCAATTGATCCAGGGCGATCTTTCTTC
* * * * * * *
7235 AATTCATTTCAGTTGACCCAGAGTGGTCTTTCTTC
1 AGTTTATTTCAATTGATCCAGGGCGATCTTTCTTC
* * * * * *
7270 AATTTACTTCAGTTGATCCAAGGCAATCTTTTCTTA
1 AGTTTATTTCAATTGATCCAGGGCGATC-TTTCTTC
* *
7306 AATTTATTTCAATGGATCCAGGGCGATCTTTTCTTC
1 AGTTTATTTCAATTGATCCAGGGCGATC-TTTCTTC
*
7342 AGTTTATTTCAATTGATCCAGGGCGATCTTTTCTGC
1 AGTTTATTTCAATTGATCCAGGGCGATC-TTTCTTC
7378 AGTTTATTTC
1 AGTTTATTTC
7388 CGTTGACCGC
Statistics
Matches: 504, Mismatches: 99, Indels: 26
0.80 0.16 0.04
Matches are distributed among these distances:
34 4 0.01
35 235 0.47
36 221 0.44
37 30 0.06
38 14 0.03
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.40
Consensus pattern (35 bp):
AGTTTATTTCAATTGATCCAGGGCGATCTTTCTTC
Found at i:7066 original size:142 final size:143
Alignment explanation
Indices: 6736--7395 Score: 656
Period size: 142 Copynumber: 4.6 Consensus size: 143
6726 GGTATTTATT
* * * * * * * * * * *
6736 AGTTTATTTCAAGATGACCCAGGGCGGTCTTTCTTCAATTCATTTCAGTTGACCCAGGGTGGTCC
1 AGTTCATTTCAA-TTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCT
* * ** *
6801 TTATTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAATTTATTTTGTTATTGACCCAG
65 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTTCTTCAATTTA-TTT-CAATTGATCCAG
*
6866 GGCGGTC-TTTCTTCA
128 GGCGATCTTTTCTTCA
* * * * * *
6881 A-TTCATTTCAGTTGACCCAGGGTGGA-CCTTATTCAGTTTATTTCAATTGATCCAAGGCGATCT
1 AGTTCATTTCAATTGATCCAGGG-CGATCTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATC-
* * *
6944 TTTCTTCAGTTTATTTCGATTTGACCCAGGGCGGTC-TTTCTTCAATTCATTTCAATTGATCCAG
64 TTTCTTCAGTTTATTTC-AGTTGACCCAGGGCGATCTTTTCTTCAATTTATTTCAATTGATCCAG
* *
7008 GGCGATC-TTACCTCA
128 GGCGATCTTTTCTTCA
* * * *
7023 AGTT-ATTTTAATTGATCCAGGGCGATCTTCCTTCAGTTCATTTCAATTGACCCAGGGCGATCTT
1 AGTTCATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTT
* * * * *
7087 ACCTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAACTTATCT-AAGTTGATCCAGGG
66 TCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTTCTTCAATTTATTTCAA-TTGATCCAGGG
7151 CGATCTTTTCTTC-
130 CGATCTTTTCTTCA
* * * * *
7164 AGTTCATATCAGTTGATCCAGGGCGATCTTTTCTTCTGTTTATTTCAGTTGATCCAGGGCGGTCT
1 AGTTCATTTCAATTGATCCAGGGCGATC-TTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCT
* * * * * * * *
7229 TTCTTCAATTCATTTCAGTTGACCCAGAGTGGTC-TTTCTTCAATTTACTTCAGTTGATCCAAGG
65 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTTCTTCAATTTATTTCAATTGATCCAGGG
*
7293 CAATCTTTTCTT-A
130 CGATCTTTTCTTCA
* * *
7306 AATTTATTTCAATGGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCT
1 AGTTCATTTCAATTGATCCAGGGCGATC-TTTCTTCAGTTTATTTCAATTGATCCAGGGCGATC-
* *
7371 TTTCTGCAGTTTATTTCCGTTGACC
64 TTTCTTCAGTTTATTTCAGTTGACC
7396 GCAAATTGGT
Statistics
Matches: 421, Mismatches: 81, Indels: 28
0.79 0.15 0.05
Matches are distributed among these distances:
140 17 0.04
141 50 0.12
142 182 0.43
143 120 0.29
144 36 0.09
145 16 0.04
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (143 bp):
AGTTCATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTT
TCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTTCTTCAATTTATTTCAATTGATCCAGGGC
GATCTTTTCTTCA
Found at i:7353 original size:355 final size:353
Alignment explanation
Indices: 6698--7371 Score: 892
Period size: 355 Copynumber: 1.9 Consensus size: 353
6688 ATTTCAGATG
* * * *
6698 CTTCAGTTCAATTCATTTGACCTAGGGCGGTATTTATTAGTTTATTTCAAGATGACCCAGGGCGG
1 CTTCAGTTCAATTCAATTGACCCAGGGCGGTATTTATCAGTTTATTTCAAGATGACCCAGGGCGA
* * * * * *
6763 TCTTTCTTCAATTCATTTCAGTTGACCCAGGGTGGTCCTTATTCAGTTTATTTCAGTTGATCCAG
66 TCTTTCTTCAATTCATCTAAGTTGACCCAGGGCGATCCTTATTCAGTTCATATCAGTTGATCCAG
*
6828 GGCGATCTTTTCTTCAATTTATTTTGTTATTGACCCAGGGCGGTCTTTCTTCAATTCATTTCAGT
131 GGCGATCTTTTCTTCAATTTATTTAG-T-TTGACCCAGGGCGGTCTTTCTTCAATTCATTTCAGT
* * * * * *
6893 TGACCCAGGGTGGACCTTATTCAGTTTATTTCAATTGATCCAAGGCGATCTTTTCTTCAGTTTAT
194 TGACCCAGAGTGGACCTTATTCAATTTACTTCAATTGATCCAAGGCAATCTTTTCTTAAATTTAT
* * *
6958 TTCGATTTGACCCAGGGCGGTCTTTCTTCAATTCATTTCAATTGATCCAGGGCGATCTTACCTCA
259 TTCGAATGGACCCAGGGCGATCTTTCTTCAATTCATTTCAATTGATCCAGGGCGATCTTACCTCA
7023 AGTTATTTTAATTGATCCAGGGCGATCTTC
324 AGTTATTTTAATTGATCCAGGGCGATCTTC
* * *
7053 CTTCAGTTCATTTCAATTGACCCAGGGC-G-ATCTTACCTCAGTTTATTTC-AGTTGATCCAGGG
1 CTTCAGTTCAATTCAATTGACCCAGGGCGGTAT-TTA--TCAGTTTATTTCAAGATGACCCAGGG
* * *
7115 CGATCTTTTCTTCAACTT-ATCTAAGTTGATCCAGGGCGATCTTTTCTTCAGTTCATATCAGTTG
63 CGATC-TTTCTTCAA-TTCATCTAAGTTGACCCAGGGCGATC-CTTATTCAGTTCATATCAGTTG
** *
7179 ATCCAGGGCGATCTTTTCTTCTGTTTATTTCAG-TTGATCCAGGGCGGTCTTTCTTCAATTCATT
125 ATCCAGGGCGATCTTTTCTTCAATTTATTT-AGTTTGACCCAGGGCGGTCTTTCTTCAATTCATT
* * * *
7243 TCAGTTGACCCAGAGTGGTCTTTCTTCAATTTACTTCAGTTGATCCAAGGCAATCTTTTCTTAAA
189 TCAGTTGACCCAGAGTGGACCTTATTCAATTTACTTCAATTGATCCAAGGCAATCTTTTCTTAAA
* * *
7308 TTTATTTC-AATGGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTT
254 TTTATTTCGAATGGACCCAGGGCGATC-TTTCTTCAATTCATTTCAATTGATCCAGGGCGATCTT
7372 TTCTGCAGTT
Statistics
Matches: 275, Mismatches: 36, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
353 2 0.01
354 18 0.07
355 168 0.61
356 38 0.14
357 48 0.17
358 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.40
Consensus pattern (353 bp):
CTTCAGTTCAATTCAATTGACCCAGGGCGGTATTTATCAGTTTATTTCAAGATGACCCAGGGCGA
TCTTTCTTCAATTCATCTAAGTTGACCCAGGGCGATCCTTATTCAGTTCATATCAGTTGATCCAG
GGCGATCTTTTCTTCAATTTATTTAGTTTGACCCAGGGCGGTCTTTCTTCAATTCATTTCAGTTG
ACCCAGAGTGGACCTTATTCAATTTACTTCAATTGATCCAAGGCAATCTTTTCTTAAATTTATTT
CGAATGGACCCAGGGCGATCTTTCTTCAATTCATTTCAATTGATCCAGGGCGATCTTACCTCAAG
TTATTTTAATTGATCCAGGGCGATCTTC
Done.