Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011887.1 Corchorus olitorius cultivar O-4 contig11920, 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: 9726
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:958 original size:27 final size:28
Alignment explanation
Indices: 892--967 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
882 AGGATCACCT
* *
892 AGGGGCATTTTGGTAATTTTCAAAAATCC
1 AGGGGCATTTTGGTCATTTGC-AAAATCC
* *
921 AGGGGCATTTTGGTCATTTGC-ACATTC
1 AGGGGCATTTTGGTCATTTGCAAAATCC
*
948 AGGGGCATTTTTGTCATTTG
1 AGGGGCATTTTGGTCATTTG
968 AAGTTAACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 23 0.55
29 19 0.45
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.38
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTGCAAAATCC
Found at i:3489 original size:11 final size:11
Alignment explanation
Indices: 3473--3507 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
3463 TTTTTCTGTT
3473 TTTTGTTTTTG
1 TTTTGTTTTTG
*
3484 TTTTGTTTTCG
1 TTTTGTTTTTG
3495 TTTTGTTTTTG
1 TTTTGTTTTTG
3506 TT
1 TT
3508 GCACTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:8350 original size:33 final size:33
Alignment explanation
Indices: 8308--8374 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
8298 TTTGTGAGTT
*
8308 CAAGATCAAAATTCGCTTTTCAAAACAAGTTTG
1 CAAGATCAAAATTCGCTTTTCAAAACAAGATTG
8341 CAAGATCAAAATTCGCTTTTCAAAACAAGATTG
1 CAAGATCAAAATTCGCTTTTCAAAACAAGATTG
8374 C
1 C
8375 TTTCCATTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (33 bp):
CAAGATCAAAATTCGCTTTTCAAAACAAGATTG
Found at i:8402 original size:49 final size:49
Alignment explanation
Indices: 8343--8456 Score: 149
Period size: 49 Copynumber: 2.3 Consensus size: 49
8333 CAAGTTTGCA
8343 AGATCAAAATTCGCTTTTCAAAACAAGATTGC-TTTCCATTTGTGAGCCC
1 AGATCAAAATTCGCTTTTCAAAACAAGATTGCATTT-CATTTGTGAGCCC
* ** **
8392 AGATTAAAATTCGCTTTTCAAAGTAAGATTGCATTTCATTTGTGAGTCTA
1 AGATCAAAATTCGCTTTTCAAAACAAGATTGCATTTCATTTGTGAG-CCC
*
8442 AGATCAAAACTCGCT
1 AGATCAAAATTCGCT
8457 CTTCGAGGGG
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
49 39 0.70
50 17 0.30
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (49 bp):
AGATCAAAATTCGCTTTTCAAAACAAGATTGCATTTCATTTGTGAGCCC
Found at i:9312 original size:105 final size:105
Alignment explanation
Indices: 9187--9481 Score: 455
Period size: 105 Copynumber: 2.8 Consensus size: 105
9177 TCCATAAGCC
* * *
9187 AAACTCGTTTCCATATGAGTCAGTTGAAGCCTTGGTTCCACCCAAGCAACAGGGGCTTTTCCATA
1 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAACAGGGGCTTTTCCATA
*
9252 AGCCAAGCTCATTTCCATATGAATTCAGTCTTCCAAGACT
66 AGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
* *
9292 AAACTTGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAACAGGGGCTTTCCCATA
1 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAACAGGGGCTTTTCCATA
9357 AGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
66 AGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
* ** * ** *
9397 AAACTCGTTTCCATGCGAGTCAGTTCAAACCTTGGTTCCGTCCAAGCCACATAGGCTTTTCCACA
1 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAACAGGGGCTTTTCCATA
*
9462 AGCCATAGTTCGTTTCCATA
66 AGCCA-AGTTCATTTCCATA
9482 CGGTGCATTA
Statistics
Matches: 173, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
105 160 0.92
106 13 0.08
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (105 bp):
AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAACAGGGGCTTTTCCATA
AGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
Found at i:9545 original size:35 final size:35
Alignment explanation
Indices: 9499--9719 Score: 320
Period size: 35 Copynumber: 6.3 Consensus size: 35
9489 TTACCATCTT
9499 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC
1 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC
* *
9534 CAGATGACTCGGTGAAGCATCTTCAAAGTTGATTC
1 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC
* * *
9569 TAGATGACTCGGTGTAGCATCTTTAAAGTCGAATC
1 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC
* *
9604 CAGATGACTCGGTGCAGCATCTTCAAAGATGAA-C
1 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC
* *
9638 TCAGATGACTCGGTGCAGCATCTTCAAAATTGAATC
1 -CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC
*
9674 CAGATGACTCGGTGTAGCATCTTCAAAATTGAA-C
1 CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC
9708 TCAGATGACTCG
1 -CAGATGACTCG
9720 ATGCAGC
Statistics
Matches: 168, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
34 2 0.01
35 165 0.98
36 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (35 bp):
CAGATGACTCGGTGTAGCATCTTCAAAGTTGAATC
Done.