Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_819 ID=scaffold_819-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: 6181
ACGTcount: A:0.19, C:0.11, G:0.05, T:0.20
Warning! 2765 characters in sequence are not A, C, G, or T
Found at i:1032 original size:516 final size:516
Alignment explanation
Indices: 1--2052 Score: 3315
Period size: 516 Copynumber: 4.0 Consensus size: 516
* *
1 AGAATCCACAATTTGTGCTGGATCTCAACCATCGAATAAATCGCTAATCACGATTCCCA-TTTTC
1 AGAATCCATAATTTGTGCTGGATCTCAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTC
* * * * *
65 CTTTTTATAACCTTAGTCACTTTCCATTGTTATCTAAACAATTTGATAAATTCATGCAGGTTCTT
66 CTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGATAAATTCATACAGGTTCTT
* *
130 TTACCAATTTCGTATCATTTCAAACACTTTAATTGTATACACACATTAGTTATTTTGACTAACAA
131 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
*
195 GTCTCTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACATACCATTCCCA
196 GTCTCTATACATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATACCATTCCCA
* *
260 CATCCATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATTCA
261 CATCAATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCA
* *
325 TTTTATATAAAAAGCCATTAAATGTACAATTATATATATTTAATATATATACAAAAACACAAGTC
326 TTTTATATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAATTC
* *
390 AAATATAATACGAAAAT-TCAGTAACTTCCATATGAACTTACCTAGAAACTGGCAACTAGAGAGT
391 AAATATAATACGAAAATGT-AGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAAAGT
*
454 TTCAGGGACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCG
455 TTCAGGGACTAATCATCACATATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCG
*
516 AGAATCCATAATTTGTGCTGGATCTCAACCATCGAATAAATCTCTAATCACGATTCCCTTTTTTC
1 AGAATCCATAATTTGTGCTGGATCTCAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTC
* *
581 CTTTTTATAACCGTAATCACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGTTCTT
66 CTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGATAAATTCATACAGGTTCTT
* * *
646 TTACCGATTTCGTATCATTTCAAACTCTTTAATTGTATACAAACTTTAGTTATTTTGAATAACAA
131 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
* *
711 GTCTCTATACAATTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATAGCATTCCCA
196 GTCTCTATACATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATACCATTCCCA
* * *
776 CATCCATTCAATGCCATGAATCTCTTTATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCA
261 CATCAATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCA
* *
841 TTTTATTTAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAATTA
326 TTTTATATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAATTC
* * * *
906 AAATAT-ATCACGAAAATGTTGTAACTTCCATATGGACATACCTTGAAAATGGCAACTAGAAAGT
391 AAATATAAT-ACGAAAATGTAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAAAGT
* * * *
970 TTCAGGGACTAATCATTATATATTGCTATATAATGATCCGATACTACTCAGTCGAGCTGTCG
455 TTCAGGGACTAATCATCACATATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCG
**
1032 AGAATCCATTCTTTGTGCTGGATCTCAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTC
1 AGAATCCATAATTTGTGCTGGATCTCAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTC
* *
1097 CTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGATAAATTCATGCTGGTTCTT
66 CTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGATAAATTCATACAGGTTCTT
1162 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
131 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
* *
1227 GTCTCTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACATACCACTCCCA
196 GTCTCTATACATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATACCATTCCCA
* * * *
1292 CATCAATTCAATGTCATGAATCTCTTCATATTTACCAAGTATTTATTATTTTATGATTTGATCCA
261 CATCAATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCA
*
1357 TTTTATATAAAAAGCCATTAAATCTACAATTATATATATTTAATATCTATACAAAAACACAATTC
326 TTTTATATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAATTC
* * *
1422 AAATATAATACGAAAATGCAGTAACTTCCATATGAACTTTCCTAGAAAATGGCAACTAGAACGTT
391 AAATATAATACGAAAATGTAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAAAGTT
* * * *
1487 TTAGGGACTAATCGTCACATATTGCTATATAATGATCCGATACTGCTCACTGGAGCCGTCG
456 TCAGGGACTAATCATCACATATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCG
* * *
1548 AGAATCCATAAGTTCTGCTGGATCTCAACCATCGAATAAATCTCTAATCACGATTCTCATTTTTC
1 AGAATCCATAATTTGTGCTGGATCTCAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTC
* *
1613 TTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGTTCTT
66 CTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGATAAATTCATACAGGTTCTT
** *
1678 TTACTGATTTCGTATCAGTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
131 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
* * * ** *
1743 TTCTCTATACATTTTAAATTTGCAACATCATCATAACCATGCTATCCAACAACTTAGAATTCCGA
196 GTCTCTATACATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATACCATTCCCA
* *
1808 CATGAATTCAATGTCATGATTCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCA
261 CATCAATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCA
* *
1873 TCTTATATAAAAAGCCATTAAATCTACAATTATCTAT-TTTAATATATATATACAAAAACACAAT
326 TTTTATATAAAAAGCCATTAAATCTACAATTATATATATTT-A-ATATATATACAAAAACACAAT
* * *
1937 TCAAATATAATACGAAAATGGAGTAACTTCCATATGAACTTTCCTAGAAAATGGCAACTAGATA-
389 TCAAATATAATACGAAAATGTAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAAAG
* *
2001 TTTTA-GGACTAATCATCACATATTGCTATATAATGATCCGCTACTGCTCACT
454 TTTCAGGGACTAATCATCACATATTGCTATATAATGATCCGATACTGCTCACT
2053 GNNNNNNNNN
Statistics
Matches: 1423, Mismatches: 108, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
515 106 0.07
516 1233 0.87
517 84 0.06
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (516 bp):
AGAATCCATAATTTGTGCTGGATCTCAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTC
CTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGATAAATTCATACAGGTTCTT
TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
GTCTCTATACATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATACCATTCCCA
CATCAATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCA
TTTTATATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAATTC
AAATATAATACGAAAATGTAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAAAGTT
TCAGGGACTAATCATCACATATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCG
Done.