Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021133.1 Corchorus olitorius cultivar O-4 contig21166, 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: 6421
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--48 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1 TCCC
*
5 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47 AT
1 AT
49 TCTAGTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:178 original size:22 final size:22
Alignment explanation
Indices: 112--184 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
102 TGTCTCTTTT
* * *
112 AAATTTTGATAATCACACAATC
1 AAATTTTGATAACCATACAATG
* *
134 AAATTTTGATAACCTTTA-TATG
1 AAATTTTGATAACC-ATACAATG
156 AAATTTTGATAACCATACAATG
1 AAATTTTGATAACCATACAATG
178 -AATTTTG
1 AAATTTTG
185 TCAACCTCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
21 9 0.21
22 32 0.76
23 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCATACAATG
Found at i:203 original size:43 final size:43
Alignment explanation
Indices: 105--214 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 43
95 AATTAAATGT
*
105 CTCTTT-TAAATTTTGATAATCACACAATCAAATTTTGATAAC
1 CTCTTTATAAATTTTGATAACCACACAATCAAATTTTGATAAC
* *
147 CT-TTATATGAAATTTTGATAACCATACAAT-GAATTTTG-TCAAC
1 CTCTT-TAT-AAATTTTGATAACCACACAATCAAATTTTGAT-AAC
* *
190 CTCTTTATAAAATTATAATAACCAC
1 CTCTTTAT-AAATTTTGATAACCAC
215 GTTATGAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
41 2 0.04
42 4 0.07
43 29 0.52
44 21 0.38
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (43 bp):
CTCTTTATAAATTTTGATAACCACACAATCAAATTTTGATAAC
Found at i:1229 original size:21 final size:22
Alignment explanation
Indices: 1192--1232 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1182 CCGTCCTTGA
*
1192 CACTATGAAATTTTGATAACCC
1 CACTATGAAAATTTGATAACCC
1214 CACTAT-AAAATTTGATAAC
1 CACTATGAAAATTTGATAAC
1233 ATATTTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (22 bp):
CACTATGAAAATTTGATAACCC
Found at i:1262 original size:22 final size:21
Alignment explanation
Indices: 1237--1488 Score: 87
Period size: 22 Copynumber: 11.9 Consensus size: 21
1227 GATAACATAT
*
1237 TTATGAATTTTTGATAATCTC
1 TTATGAAATTTTGATAATCTC
1258 ATTATGAAATTTT-ACTAA-CATCC
1 -TTATGAAATTTTGA-TAATC-T-C
*
1281 TTATGAAATTTTGTTAATCTC
1 TTATGAAATTTTGATAATCTC
* *
1302 -TATGAAGTTTTGATAATCACACC
1 TTATGAAATTTTGATAAT--C-TC
* * * * *
1325 ATAAATTAATTTTTGGTAACCTCC
1 -T-TATGAAATTTTGATAATCT-C
* * *
1349 TTATAAAATTTTGGT--T-AC
1 TTATGAAATTTTGATAATCTC
* *
1367 -AATGAAATTTTGACAATCTC
1 TTATGAAATTTTGATAATCTC
*
1387 ACTATGAAA-TTTGAATAA-C-C
1 -TTATGAAATTTTG-ATAATCTC
* *
1407 TTATGAAATTTCGATAATCGTA
1 TTATGAAATTTTGATAATC-TC
*
1429 TTATGAAATTTTGATAACTTTC
1 TTATGAAATTTTGATAA-TCTC
* * *
1451 CTATAAAATTTTG-TAACCTTC
1 TTATGAAATTTTGATAATC-TC
*
1472 TTATGAAAATTT-ATAAT
1 TTATGAAATTTTGATAAT
1489 TATACCATAT
Statistics
Matches: 168, Mismatches: 37, Indels: 51
0.66 0.14 0.20
Matches are distributed among these distances:
17 10 0.06
18 1 0.01
19 12 0.07
20 21 0.12
21 25 0.15
22 80 0.48
23 5 0.03
24 2 0.01
26 12 0.07
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (21 bp):
TTATGAAATTTTGATAATCTC
Found at i:1293 original size:44 final size:43
Alignment explanation
Indices: 1195--1301 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
1185 TCCTTGACAC
* * *
1195 TATGAAATTTTGATAACCCCACTATAAAATTTGATAACATATT
1 TATGAAATTTTGATAATCTCACTATAAAATTTGATAACATACT
* * * * *
1238 TATGAATTTTTGATAATCTCATTATGAAATTTTACTAACATCCT
1 TATGAAATTTTGATAATCTCACTATAAAATTTGA-TAACATACT
*
1282 TATGAAATTTTGTTAATCTC
1 TATGAAATTTTGATAATCTC
1302 TATGAAGTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
43 28 0.53
44 25 0.47
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.43
Consensus pattern (43 bp):
TATGAAATTTTGATAATCTCACTATAAAATTTGATAACATACT
Found at i:1423 original size:19 final size:19
Alignment explanation
Indices: 1389--1446 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 19
1379 ACAATCTCAC
*
1389 TATGAAATTTGAATAAC-CT
1 TATGAAATTTG-ATAACGAT
1408 TATGAAATTTCGATAATCGTAT
1 TATGAAATTT-GATAA-CG-AT
1430 TATGAAATTTTGATAAC
1 TATGAAA-TTTGATAAC
1447 TTTCCTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 14 0.42
20 2 0.06
21 1 0.03
22 13 0.39
23 3 0.09
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (19 bp):
TATGAAATTTGATAACGAT
Found at i:2276 original size:42 final size:42
Alignment explanation
Indices: 2228--2307 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
2218 ATGTTGGCAG
2228 TTCAAGGGGGCTATATAGTAAGACGACCATATGCAAAATTTA
1 TTCAAGGGGGCTATATAGTAAGACGACCATATGCAAAATTTA
*
2270 TTCAAGGGGGCTATATAGTAAGACGACGATATGCAAAA
1 TTCAAGGGGGCTATATAGTAAGACGACCATATGCAAAA
2308 GTTACAATAG
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:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (42 bp):
TTCAAGGGGGCTATATAGTAAGACGACCATATGCAAAATTTA
Found at i:2499 original size:6 final size:6
Alignment explanation
Indices: 2488--2517 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
2478 AAAAAAAGGA
2488 TATATC TATATC TATATC TATATAC TATAT
1 TATATC TATATC TATATC TATAT-C TATAT
2518 AAGTCTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:2790 original size:39 final size:40
Alignment explanation
Indices: 2734--2814 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
2724 TTTAATTCCT
2734 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
2774 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
2813 AT
1 AT
2815 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:2841 original size:25 final size:24
Alignment explanation
Indices: 2805--2851 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
2795 AATACTTACA
2805 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
2829 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
2852 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:3326 original size:201 final size:204
Alignment explanation
Indices: 2923--3333 Score: 695
Period size: 201 Copynumber: 2.0 Consensus size: 204
2913 TTCCTTAATA
2923 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
* *
2988 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTTGGTATAGTTCTATATATATAATA
66 ATTTAATAAATCAACCACTAATGTTCAACTAA-TCTTTTTTTGGTATAATTCTATATATATAATA
* *
3053 GTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGCAATCTTAGACTTAAAAAATTAATAACA
130 ATAATGTGATGTATCTTATTCACTACAACTTTGTTAGCAATCTTAGACTTAAAAAATTAATAACA
3118 TTCACCATTG
195 TTCACCATTG
*
3128 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGGCATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
3193 AATTTAATAAATTAACCACTAATGTTCAACT-A-CTTTTTTTGGTATAATT-T-TATATATAATA
65 AATTTAATAAATCAACCACTAATGTTCAACTAATCTTTTTTTGGTATAATTCTATATATATAATA
* * *
3254 ATAATGTGATGTATCTTATTCACTATAACTTTGTTAGTAATTTTAGACTTAAAAAATTAATAACA
130 ATAATGTGATGTATCTTATTCACTACAACTTTGTTAGCAATCTTAGACTTAAAAAATTAATAACA
3319 TTCACCATTG
195 TTCACCATTG
3329 ATAAA
1 ATAAA
3334 GTTATTAAGC
Statistics
Matches: 196, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
201 86 0.44
202 1 0.01
203 15 0.08
205 17 0.09
206 77 0.39
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (204 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTAATCTTTTTTTGGTATAATTCTATATATATAATAA
TAATGTGATGTATCTTATTCACTACAACTTTGTTAGCAATCTTAGACTTAAAAAATTAATAACAT
TCACCATTG
Found at i:3892 original size:36 final size:36
Alignment explanation
Indices: 3845--3914 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
3835 GATATTTTGG
* *
3845 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
3881 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
3915 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:5009 original size:45 final size:45
Alignment explanation
Indices: 4955--5051 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
4945 CATTAATTAC
* * ** *
4955 CTAA-ATTCTACTATTCCGTCTCTAGGTAATTCATTAAAATAAAG
1 CTAATATTCTACTACTCCATCTCTAAATAATTCATCAAAATAAAG
*
4999 CTAATATTCTACTCCTCCATCTCTAAATAATTCATCAAAATAAAG
1 CTAATATTCTACTACTCCATCTCTAAATAATTCATCAAAATAAAG
*
5044 TTAATATT
1 CTAATATT
5052 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 4 0.09
45 41 0.91
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (45 bp):
CTAATATTCTACTACTCCATCTCTAAATAATTCATCAAAATAAAG
Done.