Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_480 ID=scaffold_480-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: 7011
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.27
Warning! 458 characters in sequence are not A, C, G, or T
Found at i:4285 original size:47 final size:48
Alignment explanation
Indices: 4222--4377 Score: 208
Period size: 48 Copynumber: 3.2 Consensus size: 48
4212 AAAGGTGGGA
*
4222 CCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAAG-GG
1 CCAAGGTGAAACCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAAGAGG
* *
4269 CCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTCAAAAAAAAAAGAGA
1 CCAAGGTGAAACCCTACAAA-GGGCGCTTTGAGTCAAAAAAAAAAGAGG
* * *
4318 CCAGGGTGAAACCCTACAAAGGGAGCCTTGAGT-AAAAAAAATAGAGAGG
1 CCAAGGTGAAACCCTACAAAGGGCGCTTTGAGTCAAAAAAAA-A-AGAGG
*
4367 CTAAGGTGAAA
1 CCAAGGTGAAA
4378 ATTCGCAAAG
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
47 27 0.28
48 35 0.37
49 33 0.35
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.13
Consensus pattern (48 bp):
CCAAGGTGAAACCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAAGAGG
Found at i:4328 original size:49 final size:48
Alignment explanation
Indices: 4220--4364 Score: 199
Period size: 47 Copynumber: 3.0 Consensus size: 48
4210 TAAAAGGTGG
*
4220 GACCAAGGTGAAAGCCTACAAA-GGGCGCTTTGAGTCAAAAAAAAAAG-
1 GACCAAGGTGAAACCCTACAAAGGGGC-CTTTGAGTCAAAAAAAAAAGA
*
4267 GGCCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTCAAAAAAAAAAGA
1 GACCAAGGTGAAACCCTACAAAGGGGC-CTTTGAGTCAAAAAAAAAAGA
* *
4316 GACCAGGGTGAAACCCTACAAAGGGAGCC-TTGAGT-AAAAAAAATAGA
1 GACCAAGGTGAAACCCTACAAAGGG-GCCTTTGAGTCAAAAAAAAAAGA
4363 GA
1 GA
4365 GGCTAAGGTG
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
47 33 0.37
48 30 0.34
49 24 0.27
50 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.13
Consensus pattern (48 bp):
GACCAAGGTGAAACCCTACAAAGGGGCCTTTGAGTCAAAAAAAAAAGA
Found at i:4375 original size:49 final size:47
Alignment explanation
Indices: 4222--4377 Score: 199
Period size: 49 Copynumber: 3.2 Consensus size: 47
4212 AAAGGTGGGA
* *
4222 CCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAAG-GG
1 CCAAGGTGAAACCCTACAAAGGG-GCCTTGAGTCAAAAAAAAAAGAGG
*
4269 CCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTCAAAAAAAAAAGAGA
1 CCAAGGTGAAACCCTACAAAGGGGC-C-TTGAGTCAAAAAAAAAAGAGG
*
4318 CCAGGGTGAAACCCTACAAAGGGAGCCTTGAGT-AAAAAAAATAGAGAGG
1 CCAAGGTGAAACCCTACAAAGGG-GCCTTGAGTCAAAAAAAA-A-AGAGG
*
4367 CTAAGGTGAAA
1 CCAAGGTGAAA
4378 ATTCGCAAAG
Statistics
Matches: 96, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
46 2 0.02
47 30 0.31
48 25 0.26
49 37 0.39
50 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.13
Consensus pattern (47 bp):
CCAAGGTGAAACCCTACAAAGGGGCCTTGAGTCAAAAAAAAAAGAGG
Found at i:5715 original size:44 final size:44
Alignment explanation
Indices: 5651--5902 Score: 234
Period size: 44 Copynumber: 5.7 Consensus size: 44
5641 CCGGTGGCAG
* * *
5651 AGTAGATCCAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGA
1 AGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGA
* * * * *** * *
5695 AGTAGATCGAAGATACCAGATCTTGTCTCCCCATACTGGTGGTGG
1 AGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGA
* *
5740 AGTAGATTAAATAAAACAGATCTTGTCTTCATGTACTGGCGTGA
1 AGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGA
* * *** * *
5784 AGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGA
* * *
5829 AGTAGATCGAAGAAAATAGATCTTGTCTTCATGTACTGGTGTGA
1 AGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGA
* * * *
5873 AGTAGATCAAATATAGCAGATCTTGCCTTC
1 AGTAGATCAAAGAAAACAGATCTTGTCTTC
5903 CTACATAGAC
Statistics
Matches: 161, Mismatches: 45, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
44 93 0.58
45 68 0.42
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (44 bp):
AGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGA
Found at i:5715 original size:89 final size:88
Alignment explanation
Indices: 5605--5903 Score: 384
Period size: 89 Copynumber: 3.4 Consensus size: 88
5595 TGTCGGTAGC
* * * * * * *
5605 GAAGTGGATCGAATATA-CAGATTTTATCTTCCCATACCGGTGGCAGAGTAGATCCAAGAAAGCA
1 GAAGTAGATCGAAGATACCAGATCTTGTCTTCCCATACTGGTGGC-GAGTAGATCAAAGAAAACA
*
5669 GATCTTGTCTTCATGTATTGGCGT
65 GATCTTGTCTTCATGTACTGGCGT
* * * *
5693 GAAGTAGATCGAAGATACCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATTAAATAAAACA
1 GAAGTAGATCGAAGATACCAGATCTTGTCTTCCCATACTGGTGG-CGAGTAGATCAAAGAAAACA
5758 GATCTTGTCTTCATGTACTGGCGT
65 GATCTTGTCTTCATGTACTGGCGT
* * *
5782 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAATA
1 GAAGTAGATCGAAGATACCAGATCTTGTCTTCCCATACTGGTGGCG-AGTAGATCAAAGAAAACA
*
5847 GATCTTGTCTTCATGTACTGGTGT
65 GATCTTGTCTTCATGTACTGGCGT
* * * *
5871 GAAGTAGATCAAATATAGCAGATCTTGCCTTCC
1 GAAGTAGATCGAAGATACCAGATCTTGTCTTCC
5904 TACATAGACA
Statistics
Matches: 185, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
88 16 0.09
89 169 0.91
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (88 bp):
GAAGTAGATCGAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAGTAGATCAAAGAAAACAG
ATCTTGTCTTCATGTACTGGCGT
Done.