Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012316.1 Corchorus olitorius cultivar O-4 contig12349, 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: 9465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:696 original size:18 final size:18
Alignment explanation
Indices: 646--699 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
636 ATTCCTATTT
* *
646 TCTTCTCTTTTTCTTTTCC
1 TCTTC-CTTTCTCTTTTTC
665 TCTTCCTTTCTCTTTTTC
1 TCTTCCTTTCTCTTTTTC
*
683 T-TTCCTTATGTCTTTTT
1 TCTTCCTT-TCTCTTTTT
700 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.19
18 20 0.65
19 5 0.16
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.69
Consensus pattern (18 bp):
TCTTCCTTTCTCTTTTTC
Found at i:4689 original size:88 final size:88
Alignment explanation
Indices: 4540--4720 Score: 353
Period size: 88 Copynumber: 2.1 Consensus size: 88
4530 AGGAATTAGG
4540 CCATTTACTCGAGTTCTTATGTCAGATTTGGCATCAACATTGCTTTTGTGCAGCCAATGTTTTTG
1 CCATTTACTCGAGTTCTTATGTCAGATTTGGCATCAACATTGCTTTTGTGCAGCCAATGTTTTTG
4605 GTTGTCAATGAAATTGTTGTTGA
66 GTTGTCAATGAAATTGTTGTTGA
*
4628 CCATTTACTTGAGTTCTTATGTCAGATTTGGCATCAACATTGCTTTTGTGCAGCCAATGTTTTTG
1 CCATTTACTCGAGTTCTTATGTCAGATTTGGCATCAACATTGCTTTTGTGCAGCCAATGTTTTTG
4693 GTTGTCAATGAAATTGTTGTTGA
66 GTTGTCAATGAAATTGTTGTTGA
4716 CCATT
1 CCATT
4721 GAATTCAAGT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 92 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (88 bp):
CCATTTACTCGAGTTCTTATGTCAGATTTGGCATCAACATTGCTTTTGTGCAGCCAATGTTTTTG
GTTGTCAATGAAATTGTTGTTGA
Found at i:7786 original size:22 final size:22
Alignment explanation
Indices: 7761--7802 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
7751 GTCAAATGGA
7761 CGGGTTGGGCAGGTTCGGGTCT
1 CGGGTTGGGCAGGTTCGGGTCT
*
7783 CGGGTTGGGCGGGTTCGGGT
1 CGGGTTGGGCAGGTTCGGGT
7803 TTTGGCTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.02, C:0.17, G:0.55, T:0.26
Consensus pattern (22 bp):
CGGGTTGGGCAGGTTCGGGTCT
Found at i:8066 original size:42 final size:42
Alignment explanation
Indices: 8019--8100 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
8009 TTGATATTAA
*
8019 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTGAG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTGAG
8061 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTG
8101 TGTCTCAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTGAG
Found at i:8904 original size:69 final size:65
Alignment explanation
Indices: 8697--9336 Score: 368
Period size: 67 Copynumber: 9.6 Consensus size: 65
8687 ACAAACCTTG
* * * * * * *
8697 CCCTTTGACCGAAAGGGCATTTTTGGAAGGTAGAA-TAAA-CTGAAGTGCGAAAATGATGAAACT
1 CCCTTCGACCGAAAGGGTATTTTTGGAAAGAAAAACTAAACCT-AAATGC-AAAAAGATGAAACT
8760 GA
64 GA
* ** * ** * * *
8762 CCTTTTAACTGAAAGGGTATTTTTGGAAATCAAAAGTAAA-CTCAAACT-CAAGAATGA-CAGAA
1 CCCTTCGACCGAAAGGGTATTTTTGGAAAGAAAAACTAAACCT-AAA-TGCAA-AAAGATGA-AA
*
8824 TTGA
62 CTGA
* * * * **
8828 CCCTTCGACCGAAAGGGTATTCTTTGGAAAGAGAGACTAGACTTAAATGCAATATCCTGATGAAA
1 CCCTTCGACCGAAAGGGTATT-TTTGGAAAGAAAAACTAAACCTAAATGCAA-A--AAGATGAAA
8893 CTGA
62 CTGA
* * *
8897 CCCTTCGACCGGAAGGGTATTTTTTGGAAAGAAAAACTAAACCTGAATGCAAAAAGATGAAACCG
1 CCCTTCGACCGAAAGGGTA-TTTTTGGAAAGAAAAACTAAACCTAAATGCAAAAAGATGAAACTG
8962 A
65 A
* * * * ** * * *
8963 CCCTTTGACCGAAAGGGTATTTCTGGAAATAAAAATACTAAACTTGGACGCAAAAAGA-CAAAAT
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA-GAAAA-ACTAAACCTAAATGCAAAAAGATGAAACT
9027 CGA
64 -GA
* * * ** ** *
9030 CCCTTTGACCGAAAGGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAAAAGACAAAACC
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA-GAAAA-ACTAAACCTAAATGCAAAAAGATGAAACT
9095 GA
64 GA
* * * * ** * *
9097 CCCTTTGACCGAAATGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAAAAGA-CAAAAT
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA-GAAAA-ACTAAACCTAAATGCAAAAAGATGAAACT
9161 CGA
64 -GA
* * * * *
9164 CCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTAGATG-AAAAAGA-CAAAAT
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA-GAAAA-ACTAAACCTAAATGCAAAAAGATGAAACT
9227 CGA
64 -GA
* * ** * *
9230 CCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGCAAAAAGA-CAAAAT
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA-GAAAA-ACTAAACCTAAATGCAAAAAGATGAAACT
9294 CGA
64 -GA
* * *
9297 CCCTTTGACCGAGAA-GGTATTTCTAGAAAGAGAAAA-TAAA
1 CCCTTCGACCGA-AAGGGTATTTTTGGAAAGA-AAAACTAAA
9337 ACTTTACTTT
Statistics
Matches: 495, Mismatches: 61, Indels: 38
0.83 0.10 0.06
Matches are distributed among these distances:
65 43 0.09
66 142 0.29
67 249 0.50
68 7 0.01
69 51 0.10
70 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (65 bp):
CCCTTCGACCGAAAGGGTATTTTTGGAAAGAAAAACTAAACCTAAATGCAAAAAGATGAAACTGA
Found at i:9032 original size:67 final size:67
Alignment explanation
Indices: 8895--9334 Score: 672
Period size: 67 Copynumber: 6.6 Consensus size: 67
8885 TGATGAAACT
* * * * * **
8895 GACCCTTCGACCGGAAGGGTATTTTTTGGAAA-GAAAA-ACTAAACCTGAATGCAAAAAGATGAA
1 GACCCTTTGACCGAAAGGGTA-TTTCTGGAAATGAAAATACTAAACTTGGATGCAAAAAGACAAA
*
8958 ACC
65 ATC
* *
8961 GACCCTTTGACCGAAAGGGTATTTCTGGAAATAAAAATACTAAACTTGGACGCAAAAAGACAAAA
1 GACCCTTTGACCGAAAGGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAAAAGACAAAA
9026 TC
66 TC
9028 GACCCTTTGACCGAAAGGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAAAAGACAAAA
1 GACCCTTTGACCGAAAGGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAAAAGACAAAA
*
9093 CC
66 TC
*
9095 GACCCTTTGACCGAAATGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAAAAGACAAAA
1 GACCCTTTGACCGAAAGGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAAAAGACAAAA
9160 TC
66 TC
* *
9162 GACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTAGATG-AAAAAGACAAAA
1 GACCCTTTGACCGAAAGGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAAAAGACAAAA
9226 TC
66 TC
*
9228 GACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGCAAAAAGACAAAA
1 GACCCTTTGACCGAAAGGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAAAAGACAAAA
9293 TC
66 TC
* *
9295 GACCCTTTGACCGAGAA-GGTATTTCTAGAAAGAGAAAATA
1 GACCCTTTGACCGA-AAGGGTATTTCTGGAAA-TGAAAATA
9335 AAACTTTACT
Statistics
Matches: 347, Mismatches: 22, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
65 9 0.03
66 88 0.25
67 241 0.69
68 9 0.03
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.22
Consensus pattern (67 bp):
GACCCTTTGACCGAAAGGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAAAAGACAAAA
TC
Done.