Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_376 ID=scaffold_376-JGI_221_v2.0
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: 7707
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Found at i:6116 original size:45 final size:45
Alignment explanation
Indices: 6062--6380 Score: 125
Period size: 44 Copynumber: 7.2 Consensus size: 45
6052 CCTAGGTTGT
* * *
6062 AGCGGAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTGCACCGAT
1 AGCGAAGCAGGATAAAAATAGCAGATCTTGCCTTCCTGCACCGAC
* * * * * * ****
6107 AGCGAAGCA-GATCGAAGACACCAG-CCTTGCCTCCCTGGGTTG-C
1 AGCGAAGCAGGAT-AAAAATAGCAGATCTTGCCTTCCTGCACCGAC
* * *
6150 AGCGAAGCAGGTTAAAAATAGCAGATCTTTCCTTCCTGCACCAAC
1 AGCGAAGCAGGATAAAAATAGCAGATCTTGCCTTCCTGCACCGAC
* * * * * * ****
6195 AGCGAAGCA-GATCGAAGACACCAG-CCTTGCCTCCCTGGGTTG-C
1 AGCGAAGCAGGAT-AAAAATAGCAGATCTTGCCTTCCTGCACCGAC
* * * * * *
6238 AGCGGAGTAGGTTAAAAATAGCAGATATTACCTTCCTACACCGAC
1 AGCGAAGCAGGATAAAAATAGCAGATCTTGCCTTCCTGCACCGAC
* * * * * * **** *
6283 AGCGAAGCA-GATCGAAGACACCAG-CCTTGCCTCCCTGGGTTG-T
1 AGCGAAGCAGGAT-AAAAATAGCAGATCTTGCCTTCCTGCACCGAC
* * * *
6326 AGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTTCTGTACCGAC
1 AGCGAAGCAGGATAAAAATAGCAGATCTTGCCTTCCTGCACCGAC
6371 AGCGAAGCAG
1 AGCGAAGCAG
6381 ATCGATGACC
Statistics
Matches: 175, Mismatches: 87, Indels: 24
0.61 0.30 0.08
Matches are distributed among these distances:
43 46 0.26
44 73 0.42
45 56 0.32
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (45 bp):
AGCGAAGCAGGATAAAAATAGCAGATCTTGCCTTCCTGCACCGAC
Found at i:6136 original size:44 final size:44
Alignment explanation
Indices: 6088--6319 Score: 135
Period size: 44 Copynumber: 5.3 Consensus size: 44
6078 AATAGCAGAT
* *
6088 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
**** * ** * * * *
6132 CTTGCCTCCCTGGGTTG-CAGCGAAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAG-C
* * *
6176 CTTTCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
**** * * * ** * * * *
6220 CTTGCCTCCCTGGGTTG-CAGCGGAGTAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAG-C
* * * *
6264 ATTACCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
6308 CTTGCCTCCCTG
1 CTTGCCTCCCTG
6320 GGTTGTAGCG
Statistics
Matches: 120, Mismatches: 64, Indels: 8
0.62 0.33 0.04
Matches are distributed among these distances:
43 35 0.29
44 49 0.41
45 36 0.30
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (44 bp):
CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
Found at i:6429 original size:88 final size:88
Alignment explanation
Indices: 5731--6385 Score: 1022
Period size: 88 Copynumber: 7.4 Consensus size: 88
5721 GTGAAGATAA
* ** *
5731 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGATTCTCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
5796 GTAGCGGAGTAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
5819 CAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
5884 GCAGCGGAGCAGGTTAAAAAAAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * *
5907 CAGATCTTGCTTTTCTGCACCGACAGCGAAACAGATTGAAGACACCAGCCTTGCATCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
5972 GCAGCGGAGCAGGTTAAAAATTG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
5995 TAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
6060 GTAGCGGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
*
6083 CAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
6148 GCAGCGAAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
6171 CAGATCTTTCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
6236 GCAGCGGAGTAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
6259 CAGATATTACCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
6324 GTAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
6347 CAGATCTTGCCTTTCTGTACCGACAGCGAAGCAGATCGA
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
6386 TGACCCCAAC
Statistics
Matches: 513, Mismatches: 54, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 513 1.00
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:6561 original size:44 final size:45
Alignment explanation
Indices: 6396--6561 Score: 248
Period size: 44 Copynumber: 3.8 Consensus size: 45
6386 TGACCCCAAC
* *
6396 CCTATCCCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGT-GAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAGAAT
*
6440 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTG-AGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAGAAT
* * * *
6484 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTAG-GT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAGAAT
6528 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAA
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAA
6562 TCCTATCTCC
Statistics
Matches: 109, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
44 107 0.98
45 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (45 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAGAAT
Found at i:7039 original size:44 final size:44
Alignment explanation
Indices: 6943--7050 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
6933 GTAGATGGCA
* *
6943 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTAC
* * *
6987 AATCTTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATC-AC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTAC
* *
7030 AGATTTTATCTCTCTGAAGTT
1 A-ATCTTATCTCCCTGAAGTT
7051 ACAGAAAACA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 2 0.04
44 53 0.96
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTAC
Found at i:7114 original size:37 final size:37
Alignment explanation
Indices: 7070--7142 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
7060 AGATCGTATA
* * *
7070 TAGTCTTATTTTCCTGAAGTTGCAGTGGAGCAGACTC
1 TAGTCTTATCTCCCTGAAGTTGCAGAGGAGCAGACTC
7107 TAGTCTTATCTCCCTGAAGTTGCAGAGGAGCAGACT
1 TAGTCTTATCTCCCTGAAGTTGCAGAGGAGCAGACT
7143 GAGAAAGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (37 bp):
TAGTCTTATCTCCCTGAAGTTGCAGAGGAGCAGACTC
Found at i:7197 original size:44 final size:44
Alignment explanation
Indices: 7110--7218 Score: 114
Period size: 44 Copynumber: 2.5 Consensus size: 44
7100 CAGACTCTAG
*
7110 TCTTATCTCCCTGAAGTTGCAGAGGAGCAGACTGAGAAAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGAGGAGCAGACTAAGAAAGCAAA
* * **
7154 TCTTATCCCCCTGAAGTTGCACG-GG-GCAGATTAAAGATGGCAAA
1 TCTTATCTCCCTGAAGTTGCA-GAGGAGCAGACT-AAGAAAGCAAA
* * *
7198 TCCTATCTCCATAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCA
7219 ATGGAGCGGA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
43 6 0.11
44 47 0.87
45 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGAGGAGCAGACTAAGAAAGCAAA
Done.