Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012868.1 Corchorus olitorius cultivar O-4 contig12901, 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: 10042
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Found at i:3774 original size:43 final size:43
Alignment explanation
Indices: 3660--4004 Score: 469
Period size: 43 Copynumber: 8.0 Consensus size: 43
3650 TTCTTTTATA
*
3660 CCAAAAATGCCCCTTCTTGGTTGGAAGGTCCCTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
* * * * * *
3703 CAAAAAAATGCTCCTT-CTCGATTAGAAGGTCCTTGTTTTCAGTT
1 C-CAAAAATGCCCCTTCCT-GGTTGGAAGGTCCCTGTTTTCATTT
* *
3747 CCGAAAATGCCTCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
* * * *
3790 CCAAAAATGCCCCTTCCTGGTCGGAAGGTTCTTGTTTTCATTA
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
*
3833 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTATTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
* * * *
3876 CAAAAAAATGCTCCTTCCTGGTCGGAAGGTCCTTGTTTTCATTT
1 C-CAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
*
3920 -CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
*
3962 CCAAGAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
1 CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
4005 TGATTTTCAT
Statistics
Matches: 261, Mismatches: 36, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
42 39 0.15
43 149 0.57
44 73 0.28
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (43 bp):
CCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTT
Found at i:4132 original size:40 final size:40
Alignment explanation
Indices: 4070--4301 Score: 229
Period size: 40 Copynumber: 5.8 Consensus size: 40
4060 AATATTCCAA
* * *
4070 AGTTTGTCATTCCTCA-CTGGAAGGTGTTGTTTAAATTCTC
1 AGTTTGCCCTTCCTCATC-GGAAGGTGTTGTTTAAATTCCC
* * * *
4110 AGTTTGCCCTTCCTCGTCGGAAGGTGTTG-TCAGCATCCCC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-AATTCCC
4150 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
** **
4190 AGTTTGCCCTTCCTCATCGGAAGGTGCAGTTTAAATTCTT
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
* * * * *
4230 AATTTGCCCTTCCCCACCGGAAGGTTTTGATTT-CATT-CC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTTAAATTCCC
* **
4269 TGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTT
1 AG-TTTGCCCTTCCTCATCGGAAGGTGTTGTTT
4302 TCAATGTTTT
Statistics
Matches: 156, Mismatches: 31, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
39 5 0.03
40 145 0.93
41 6 0.04
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.38
Consensus pattern (40 bp):
AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
Found at i:4304 original size:40 final size:40
Alignment explanation
Indices: 4079--4480 Score: 204
Period size: 40 Copynumber: 9.7 Consensus size: 40
4069 AAGTTTGTCA
** *
4079 TTCCTCA-CTGGAAGGTGTTGTTTAAATTCTCAG-TTTGCCC
1 TTCCTCATC-GGAAGGTGTTGTTTTCATTC-CTGTTTTGCCC
* *** * *
4119 TTCCTCGTCGGAAGGTGTTGTCAGCATCCCCAG-TTTGCCC
1 TTCCTCATCGGAAGGTGTTGTTTTCAT-TCCTGTTTTGCCC
** *
4159 TTCCTCATCGGAAGGTGTTGTTTAAATTCCCAG-TTTGCCC
1 TTCCTCATCGGAAGGTGTTGTTTTCATT-CCTGTTTTGCCC
** ** * **
4199 TTCCTCATCGGAAGGTGCAGTTTAAATTCTTAATTTGCCC
1 TTCCTCATCGGAAGGTGTTGTTTTCATTCCTGTTTTGCCC
* * * *
4239 TTCCCCACCGGAAGGTTTTGATTTCATTCCTGTTTTGCCC
1 TTCCTCATCGGAAGGTGTTGTTTTCATTCCTGTTTTGCCC
** *
4279 TTCCTGGTCGGAAGGTGTTGTTTTCAATGTTTTATTTCC-ATTTTGCCC
1 TTCCTCATCGGAAGGTGTTGTTTTC--------A-TTCCTGTTTTGCCC
* * * * *
4327 TTCCCCACCGGAAGGTTTTGATTTCATTCCTGATTTGCCC
1 TTCCTCATCGGAAGGTGTTGTTTTCATTCCTGTTTTGCCC
** *
4367 TTGCC-GGTCGGAAGGTGTTGTTTTCAATGTTTTATTCCCGTTTTGCCC
1 TT-CCTCATCGGAAGGTGTTGTTTTC--------ATTCCTGTTTTGCCC
* * * *
4415 TTCCCCACCGGAAGGTTTTGATTTCATTCCTGTTTTGCCC
1 TTCCTCATCGGAAGGTGTTGTTTTCATTCCTGTTTTGCCC
**
4455 TTCCTGGTCGGAAGGTGTTGTTTTCA
1 TTCCTCATCGGAAGGTGTTGTTTTCA
4481 ATATTTTATT
Statistics
Matches: 276, Mismatches: 62, Indels: 48
0.72 0.16 0.12
Matches are distributed among these distances:
39 5 0.02
40 203 0.74
41 4 0.01
47 2 0.01
48 58 0.21
49 4 0.01
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.40
Consensus pattern (40 bp):
TTCCTCATCGGAAGGTGTTGTTTTCATTCCTGTTTTGCCC
Found at i:4327 original size:48 final size:47
Alignment explanation
Indices: 4265--4507 Score: 167
Period size: 48 Copynumber: 5.4 Consensus size: 47
4255 TTTGATTTCA
*
4265 TTCCTGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
1 TTCC-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-TTTTAT
* *** * *
4314 TTCCATTTTGCCCTTCCCCACCGGAA---G--GTTTT-GA-TTTCA-
1 TTCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATTTTTAT
* *
4353 TTCCTGATTTGCCCTTGCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
1 TTCC-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-TTTTAT
* *** * *
4402 TCCCGTTTTGCCCTTCCCCACCGGAA---G--GTTTT-GA-TTTCA-
1 TTCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATTTTTAT
*
4441 TTCCTGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATATTTTAT
1 TTCC-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-TTTTAT
*
4490 TCCCGTTTTGCCCTTCCC
1 TTCCGTTTTGCCCTTCCC
4508 ATTGGAAGGA
Statistics
Matches: 142, Mismatches: 32, Indels: 41
0.66 0.15 0.19
Matches are distributed among these distances:
39 7 0.05
40 42 0.30
42 2 0.01
43 12 0.08
45 12 0.08
46 2 0.01
48 55 0.39
49 10 0.07
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.44
Consensus pattern (47 bp):
TTCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATTTTTAT
Found at i:4381 original size:88 final size:88
Alignment explanation
Indices: 4232--4507 Score: 500
Period size: 88 Copynumber: 3.1 Consensus size: 88
4222 AAATTCTTAA
4232 TTTGCCCTTCCCCACCGGAAGGTTTTGATTTCATTCCTGTTTTGCCCTTCCTGGTCGGAAGGTGT
1 TTTGCCCTTCCCCACCGGAAGGTTTTGATTTCATTCCTGTTTTGCCCTTCCTGGTCGGAAGGTGT
* *
4297 TGTTTTCAATGTTTTATTTCCAT
66 TGTTTTCAATGTTTTATTCCCGT
*
4320 TTTGCCCTTCCCCACCGGAAGGTTTTGATTTCATTCCTGATTTGCCCTTGCC-GGTCGGAAGGTG
1 TTTGCCCTTCCCCACCGGAAGGTTTTGATTTCATTCCTGTTTTGCCCTT-CCTGGTCGGAAGGTG
4384 TTGTTTTCAATGTTTTATTCCCGT
65 TTGTTTTCAATGTTTTATTCCCGT
4408 TTTGCCCTTCCCCACCGGAAGGTTTTGATTTCATTCCTGTTTTGCCCTTCCTGGTCGGAAGGTGT
1 TTTGCCCTTCCCCACCGGAAGGTTTTGATTTCATTCCTGTTTTGCCCTTCCTGGTCGGAAGGTGT
*
4473 TGTTTTCAATATTTTATTCCCGT
66 TGTTTTCAATGTTTTATTCCCGT
4496 TTTGCCCTTCCC
1 TTTGCCCTTCCC
4508 ATTGGAAGGA
Statistics
Matches: 181, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
87 2 0.01
88 177 0.98
89 2 0.01
ACGTcount: A:0.12, C:0.26, G:0.20, T:0.43
Consensus pattern (88 bp):
TTTGCCCTTCCCCACCGGAAGGTTTTGATTTCATTCCTGTTTTGCCCTTCCTGGTCGGAAGGTGT
TGTTTTCAATGTTTTATTCCCGT
Found at i:6460 original size:16 final size:17
Alignment explanation
Indices: 6439--6474 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
6429 TGACTATATT
6439 TATATCTAT-ATCCATC
1 TATATCTATAATCCATC
*
6455 TATATCTATAATCTATC
1 TATATCTATAATCCATC
6472 TAT
1 TAT
6475 CTATGTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATCTATAATCCATC
Done.