Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_613 ID=scaffold_613-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: 5544
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.26
Warning! 300 characters in sequence are not A, C, G, or T
Found at i:4445 original size:44 final size:44
Alignment explanation
Indices: 4395--5059 Score: 600
Period size: 44 Copynumber: 14.9 Consensus size: 44
4385 TGAAAAGCAG
*
4395 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAA
*** * * *
4439 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAA
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAA
*
4484 CAGATCTTGTCTTCATGTACTGGCGTAAAGTAGATCAAA-AAAA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAA
* *** * *
4527 CAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCAAAGAAAA
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAA
*
4572 CAGATCTTGTTTTCATGTACTGGCGTGAAGTAGATCAAAG-AAA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAA
* *** *
4615 CAGATCTTGTCTCCCCATACTGGTGGTGGAA-TAGATCAAAGAAAA
1 CAGATCTTGTCTTCATGTACTGG-CGT-GAAGTAGATCAAAGAAAA
* *
4660 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGACAA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAA
*** * *
4704 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAAGAAGAAAA
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC---A-AAGAAAA
* * * *
4753 TAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAA
* * * * *
4797 CAGATTTTATCTTCATGTACTGGCATGAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAA
* *** * * * * *
4841 CATATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAG
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAA
* * * *
4886 CAGATCTTGTCTTCATATACTAGCATGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAA
* * * * * *
4930 CATATATTGTCTTCCTATACTGGTG-GCAAAGTAGATCGAAGAAAA
1 CAGATCTTGTCTTCATGTACTGGCGTG--AAGTAGATCAAAGAAAA
* * * *
4975 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAGGATAG
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAA
* * * * * * *
5019 TAGGTCTTGTCCTCATGTATTAGCATGAAGTAGATCGAAGA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA
5060 TACAAGTCTT
Statistics
Matches: 493, Mismatches: 112, Indels: 32
0.77 0.18 0.05
Matches are distributed among these distances:
43 48 0.10
44 245 0.50
45 163 0.33
46 1 0.00
48 12 0.02
49 24 0.05
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (44 bp):
CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAA
Found at i:4876 original size:226 final size:222
Alignment explanation
Indices: 4425--5061 Score: 731
Period size: 226 Copynumber: 2.9 Consensus size: 222
4415 TGGCGTGAAG
* ** * *** * * *
4425 TAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATC
1 TAGATCAAAGAAAACAGATCTTGTCTTCATATACTAG-CATGAAGTAGATCAAAGACAACAGATA
*** * * * * *** * *
4490 TTGTCTTCATGTACTGG-CGTAAAGTAGATC-AAAAAAACAGATCTTGTCTCCCCATACTGGTGG
65 TTGTCTTCCCATACTGGTGGCAAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGG-CG
* * * * * *
4553 TGGAGTAGATCAAAGAAAACAGATCTTGTTTTCATGTACTGGCGTGAAGTAGATCAAAGA-AACA
129 TGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCGAAGATAACA
* *
4617 GATCTTGTCTCCCCATACTGGTGGTGGAA
194 GATCTTGTCTCCCCATACTGGTGGCGAAA
* * * * *
4646 TAGATCAAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGACAACAGATCT
1 TAGATCAAAGAAAACAGATCTTGTCTTCATATACTAGCATGAAGTAGATCAAAGACAACAGATAT
* *
4711 TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAAGAAGAAAATAGATCTTGTCTTCATGTATTGG
66 TGTCTTCCCATACTGGTGGCAAAGTAGATC----GAAGAAAACAGATCTTGTCTTCATGTATTGG
* *
4776 CGTGAAGTAGATCAAAGATAGCAGATTTTATCTTCATGTACTGGCATGAAGTAGATCGAAGATAA
127 CGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCGAAGATAA
* *
4841 CATATCTTGTCTTCCCATACTGGTGGCGAAA
192 CAGATCTTGTCTCCCCATACTGGTGGCGAAA
* * * *
4872 TAGATCGAAGAAAGCAGATCTTGTCTTCATATACTAGCATGAAGTAGATCAAAGATAACATATAT
1 TAGATCAAAGAAAACAGATCTTGTCTTCATATACTAGCATGAAGTAGATCAAAGACAACAGATAT
*
4937 TGTCTTCCTATACTGGTGGCAAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTG
66 TGTCTTCCCATACTGGTGGCAAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTG
* * * * * *
5002 AAGTAGATCAAGGATAGTAGGTCTTGTCCTCATGTATTAGCATGAAGTAGATCGAAGATA
131 AAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCGAAGATA
5062 CAAGTCTTAT
Statistics
Matches: 354, Mismatches: 55, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
220 37 0.10
221 42 0.12
222 86 0.24
225 53 0.15
226 136 0.38
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (222 bp):
TAGATCAAAGAAAACAGATCTTGTCTTCATATACTAGCATGAAGTAGATCAAAGACAACAGATAT
TGTCTTCCCATACTGGTGGCAAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTG
AAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCGAAGATAACAGA
TCTTGTCTCCCCATACTGGTGGCGAAA
Found at i:4899 original size:89 final size:89
Alignment explanation
Indices: 4780--5017 Score: 343
Period size: 89 Copynumber: 2.7 Consensus size: 89
4770 TATTGGCGTG
* * * * *
4780 AAGTAGATCAAAGATAGCAGATTTTATCTTCATGTACTGGCATGAAGTAGATCGAAGATAACATA
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAACATA
*
4845 TCTTGTCTTCCCATACTGGTGGCGA
66 TATTGTCTTCCCATACTGGTGGC-A
* *
4870 AA-TAGATCGAAGAAAGCAGATCTTGTCTTCATATACTAGCATGAAGTAGATCAAAGATAACATA
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAACATA
*
4934 TATTGTCTTCCTATACTGGTGGCA
66 TATTGTCTTCCCATACTGGTGGCA
* * * *
4958 AAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAGGATA
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATA
5018 GTAGGTCTTG
Statistics
Matches: 132, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
88 3 0.02
89 127 0.96
90 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (89 bp):
AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAACATA
TATTGTCTTCCCATACTGGTGGCA
Done.