Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_966 ID=scaffold_966-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: 4382
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.16
Warning! 2526 characters in sequence are not A, C, G, or T
Found at i:1193 original size:624 final size:623
Alignment explanation
Indices: 1--1199 Score: 2121
Period size: 624 Copynumber: 1.9 Consensus size: 623
1 CCATGACCGGAACCTTCTTCCTCTCTGTTATTCGATTTGCAAAATAGCAAATTAGAGGAGATGAT
1 CCATGACCGGAACCTTCTTCCTCTCTGTTATTCGATTTGCAAAATAGCAAATTAGAGGAGATGAT
* * * * *
66 AACATTTTTTTCTTTTAGTTTGTGTTAATTTCCATTTCATTACAAATTTAGAATTTTTCCCTTAA
66 AACATTTTTGTCTTTTACTTTGTGTTAATTTCCATTTCATTACAAATTTACAAATGTTCCCTTAA
* **
131 AAATCAAATTTCATGCATTTAATCACCGAAAACCATCCACTTTAAGTTCATTTGGTGCATTTACC
131 AAATCAAATTTCATGCATTTAATCACCCAAAACCATCCACCCTAAGTTCATTTGGTGCATTTACC
* * *
196 ATTTAAGTCCATTAGTTTGATAATCCATAATAAATTGACCCGTTTACCTGATAGAAATCTACTTT
196 AATTAAGTCCATTAGTTTGATAATCCATAATAAATTGACCCCTTTACCTAATAGAAATCTACTTT
* *
261 TGCACCTTTTTCAATTTAGTGATTTTTACTTAATTAATTATTTGTACACATAATATAAATCTGTT
261 TGCACCTCTTTCAATTTAGTGATTTTTACTTAATTAATTATCTGTACACATAATATAAATCTGTT
* * *
326 ACATTCATTTCAAAATCGTGAAACCACAAGATTTGCCACGACGAAATATTCATTTTCCATTAGTA
326 ACATCCATTTCAAAATCGTGAAACCACAAGATTTGCCACGACCAAATATTCACTTTCCATTAGTA
391 CTTAATTCCAACATTTAATAATTTACAAGCAAACAATGAAATTTTCACATTAATTATAACTGAAC
391 CTTAATTCCAACATTTAATAATTTACAAGCAAACAATGAAATTTTCACATTAATTATAACTGAAC
* *
456 TAACAATTGATATACATAATCATAAGGAAACACACATATATATTATATACTACATACTTACCTCG
456 TAACAATTGATATACATAATCATAAGGAAACAAACATATATATTATATACTACAAACTTACCTCG
521 ACAAATATAGTTGTAAAAATGAAGCAGCCGACAAATCTGACACATTAGCTTTTCCTCGGTTTAGA
521 ACAAATATAGTTGTAAAAATGAAGCAGCCGACAAATCTGACACATTAGCTTTTCCTCGGTTTAGA
586 CTTGTTTGGTTAATTTCTTGATCATGCATGTAAAAACT
586 CTTGTTTGGTTAATTTCTTGATCATGCATGTAAAAACT
624 CCATGACCGGAACCTTCTTCCTCTCTGTTATTCGATTTGCAAAATAGCAAATTAGAGGAGATGAT
1 CCATGACCGGAACCTTCTTCCTCTCTGTTATTCGATTTGCAAAATAGCAAATTAGAGGAGATGAT
*
689 AACATTTTTGTCTTTTACTTTGTTTTAATTTCCA-TTCAATTACAAATTTACAAATGTTCCCTTA
66 AACATTTTTGTCTTTTACTTTGTGTTAATTTCCATTTC-ATTACAAATTTACAAATGTTCCCTT-
*
753 AAAAATCAAATTTCATGCATTTAATCACCCAAAACCGTCCACCCTAAGTTCATTTGGTGCATTTA
129 AAAAATCAAATTTCATGCATTTAATCACCCAAAACCATCCACCCTAAGTTCATTTGGTGCATTTA
* *
818 CCAATTAAGTCCATTAGTTTGATAATCCATTATAAATTGACCCCTTTACCTAATAGAAATCTATT
194 CCAATTAAGTCCATTAGTTTGATAATCCATAATAAATTGACCCCTTTACCTAATAGAAATCTACT
883 TTTGCACCTCTTTCAATTTAGTGATTTTTACTTAATTAATTATCTGTACACATAATATAAATCTG
259 TTTGCACCTCTTTCAATTTAGTGATTTTTACTTAATTAATTATCTGTACACATAATATAAATCTG
* * *
948 TTACATCCATTTCAAAATTGTGAAACCACAAGATTTGCCACGGCCAAATATTCACTTTCCATTTG
324 TTACATCCATTTCAAAATCGTGAAACCACAAGATTTGCCACGACCAAATATTCACTTTCCATTAG
* *
1013 TACTTAATTCCAACATTTAATAATTTACAAGCAAACAATGAAATTTTCACATTAATTATAATTTA
389 TACTTAATTCCAACATTTAATAATTTACAAGCAAACAATGAAATTTTCACATTAATTATAACTGA
1078 ACTAACAATTGATATACATAATCATAAGGAAACAAACATATATATTATATACTACAAACTTACCT
454 ACTAACAATTGATATACATAATCATAAGGAAACAAACATATATATTATATACTACAAACTTACCT
*
1143 CGACAAATATAGTTGTAAAAATGAAGCAGCCGACAAATCTGACTCATTAGCTTTTCC
519 CGACAAATATAGTTGTAAAAATGAAGCAGCCGACAAATCTGACACATTAGCTTTTCC
1200 CTTGTTCAGA
Statistics
Matches: 546, Mismatches: 28, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
622 3 0.01
623 118 0.22
624 425 0.78
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (623 bp):
CCATGACCGGAACCTTCTTCCTCTCTGTTATTCGATTTGCAAAATAGCAAATTAGAGGAGATGAT
AACATTTTTGTCTTTTACTTTGTGTTAATTTCCATTTCATTACAAATTTACAAATGTTCCCTTAA
AAATCAAATTTCATGCATTTAATCACCCAAAACCATCCACCCTAAGTTCATTTGGTGCATTTACC
AATTAAGTCCATTAGTTTGATAATCCATAATAAATTGACCCCTTTACCTAATAGAAATCTACTTT
TGCACCTCTTTCAATTTAGTGATTTTTACTTAATTAATTATCTGTACACATAATATAAATCTGTT
ACATCCATTTCAAAATCGTGAAACCACAAGATTTGCCACGACCAAATATTCACTTTCCATTAGTA
CTTAATTCCAACATTTAATAATTTACAAGCAAACAATGAAATTTTCACATTAATTATAACTGAAC
TAACAATTGATATACATAATCATAAGGAAACAAACATATATATTATATACTACAAACTTACCTCG
ACAAATATAGTTGTAAAAATGAAGCAGCCGACAAATCTGACACATTAGCTTTTCCTCGGTTTAGA
CTTGTTTGGTTAATTTCTTGATCATGCATGTAAAAACT
Done.