Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022913.1 Corchorus olitorius cultivar O-4 contig22946, 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: 6702
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Found at i:216 original size:17 final size:17
Alignment explanation
Indices: 189--229 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
179 TTTTTATTTT
189 ATTATTTGACTATAATTA
1 ATTA-TTGACTATAATTA
207 ATTATTGACTATAATTA
1 ATTATTGACTATAATTA
*
224 TTTATT
1 ATTATT
230 ATTGTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (17 bp):
ATTATTGACTATAATTA
Found at i:4234 original size:91 final size:91
Alignment explanation
Indices: 4124--4436 Score: 515
Period size: 91 Copynumber: 3.4 Consensus size: 91
4114 GCATGCTTAC
* *
4124 ACAT-TTTTATCA-TTTTTTGATGGAAGTATATGCCAATATGCATAATTTGAGCTATTATGATCA
1 ACATGTTTTATCATTTTTTTGATGGAAGTATATGCCTATATGCATAAATTGAGCTATTATGATCA
4187 TGCAAGAGCATCGTTTAAGCATGATA
66 TGCAAGAGCATCGTTTAAGCATGATA
4213 ACATGTTTTATCATTTTTTTGATGGAAGTATATGCCTATATGCATAAATTGAGCTATTATGATCA
1 ACATGTTTTATCATTTTTTTGATGGAAGTATATGCCTATATGCATAAATTGAGCTATTATGATCA
4278 TGCAAGAGCATCGTTTAAGCATGATA
66 TGCAAGAGCATCGTTTAAGCATGATA
* **
4304 ACATGTTTTATCATTTTTTCGATAAAAGTATATGCCTGCCTATATGCATAAATTGAGCTATTATG
1 ACATGTTTTATCATTTTTTTGATGGAAGTATA----TGCCTATATGCATAAATTGAGCTATTATG
4369 ATCATGCAAGAGCATCGTTTAAGCATGATA
62 ATCATGCAAGAGCATCGTTTAAGCATGATA
4399 ACATGTTTTATCATTTTTTTGAT-GATAGTATATGCCTA
1 ACATGTTTTATCATTTTTTTGATGGA-AGTATATGCCTA
4437 GTACTTATAC
Statistics
Matches: 210, Mismatches: 7, Indels: 12
0.92 0.03 0.05
Matches are distributed among these distances:
89 4 0.02
90 8 0.04
91 110 0.52
94 1 0.00
95 87 0.41
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (91 bp):
ACATGTTTTATCATTTTTTTGATGGAAGTATATGCCTATATGCATAAATTGAGCTATTATGATCA
TGCAAGAGCATCGTTTAAGCATGATA
Found at i:4809 original size:50 final size:50
Alignment explanation
Indices: 4755--4904 Score: 183
Period size: 50 Copynumber: 3.0 Consensus size: 50
4745 TTCTCAGCAG
4755 TAAGTCCCCATGTTGGGCAATAAGACCGGATCAAGACTTATTATCGGCAA
1 TAAGTCCCCATGTTGGGCAATAAGACCGGATCAAGACTTATTATCGGCAA
* *** * *
4805 TAAGTCCCCGTGTTGGGCAATAAGACTATATCAAGACTTATTATCGACAG
1 TAAGTCCCCATGTTGGGCAATAAGACCGGATCAAGACTTATTATCGGCAA
** * * * *
4855 TAACACCCCCTTGATGGGTAGTAAGACCGGATCAAGACTTATTATCGGCA
1 TAA-GTCCCCATGTTGGGCAATAAGACCGGATCAAGACTTATTATCGGCA
4905 GTAACACCCC
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 47 0.57
51 36 0.43
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (50 bp):
TAAGTCCCCATGTTGGGCAATAAGACCGGATCAAGACTTATTATCGGCAA
Found at i:4895 original size:51 final size:51
Alignment explanation
Indices: 4775--4942 Score: 194
Period size: 51 Copynumber: 3.3 Consensus size: 51
4765 TGTTGGGCAA
* * ** * * * *
4775 TAAGACCGGATCAAGACTTATTATCGGCAATAA-GTCCCCGTGTTGGGCAA
1 TAAGACCAGATCAAGACTTATTATCGGCAGTAACACCCCCTTGATGGGTAG
* * *
4825 TAAGACTATATCAAGACTTATTATCGACAGTAACACCCCCTTGATGGGTAG
1 TAAGACCAGATCAAGACTTATTATCGGCAGTAACACCCCCTTGATGGGTAG
* **
4876 TAAGACCGGATCAAGACTTATTATCGGCAGTAACACCCCCTTGACAGGTAG
1 TAAGACCAGATCAAGACTTATTATCGGCAGTAACACCCCCTTGATGGGTAG
*
4927 TAAGACCAGATGAAGA
1 TAAGACCAGATCAAGA
4943 GCCCTCTTAA
Statistics
Matches: 98, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 28 0.29
51 70 0.71
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.23
Consensus pattern (51 bp):
TAAGACCAGATCAAGACTTATTATCGGCAGTAACACCCCCTTGATGGGTAG
Found at i:5187 original size:123 final size:123
Alignment explanation
Indices: 4967--5222 Score: 408
Period size: 123 Copynumber: 2.1 Consensus size: 123
4957 CCAGAGATAT
*
4967 CGGCAGGCGATCGACATGAACCATCCTTAACCGAATATGGTAAATGATGAAGCCCCTAAGGGGCC
1 CGGCAGGCGATCGACATGAACCATCCTTAACCGAATATGGTAAATGATGAAGCCCCCAAGGGGCC
* *
5032 CAACGCCAACAAGAGAGCTATCAAGCAAGGCCGAGCTCGACTTAGTATGGCCCCCGAC
66 CAACGCCAACAAGAGAGCGATCAAGCAAGGCCGAGCTCGACCTAGTATGGCCCCCGAC
* *
5090 TGGCAGGCGATCGACATGAACCATTCC-TGACC-AAGTATGGTAAATGATGAAGCCCCCAAGGGG
1 CGGCAGGCGATCGACATGAACCA-TCCTTAACCGAA-TATGGTAAATGATGAAGCCCCCAAGGGG
* * *
5153 CCCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTATGGCCCCCGAC
64 CCCAACGCCAACAAGAGAGCGATCAAGCAAGGCCGAGCTCGACCTAGTATGGCCCCCGAC
5213 CGGCAGGCGA
1 CGGCAGGCGA
5223 CTAATTTAAG
Statistics
Matches: 122, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
122 2 0.02
123 117 0.96
124 3 0.02
ACGTcount: A:0.29, C:0.30, G:0.28, T:0.13
Consensus pattern (123 bp):
CGGCAGGCGATCGACATGAACCATCCTTAACCGAATATGGTAAATGATGAAGCCCCCAAGGGGCC
CAACGCCAACAAGAGAGCGATCAAGCAAGGCCGAGCTCGACCTAGTATGGCCCCCGAC
Found at i:6683 original size:2 final size:2
Alignment explanation
Indices: 6676--6702 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6666 CTATAACACT
6676 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.