Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_610 ID=scaffold_610-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: 10268
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.18
Warning! 5008 characters in sequence are not A, C, G, or T
Found at i:5084 original size:517 final size:515
Alignment explanation
Indices: 3949--5285 Score: 2237
Period size: 517 Copynumber: 2.6 Consensus size: 515
3939 NNNNNNATAC
* *
3949 ACACTTTAGTTATTTTGAATAACAATTGTCTATACATTTTAAATTTGGAACATCATCATAAACAT
1 ACACTTTAGTTATTTTGAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATAAACAT
4014 GCTATCCAACAACATACCATTCCCACATCAATAT-AATGTCATGAATCGCTTCATATTTATCAAG
66 GCTATCCAACAACATACCATTCCCACATCAAT-TCAATGTCATGAATCGCTTCATATTTATCAAG
* * *
4078 TAGTTTTTATTTTACGATTTGATCCATCTTATACAAAAAGCCATTAAATCTGCAATTATATATAT
130 TA-TTTTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAAATCTACAATTATATATAT
*
4143 TTAATATATATATACAAAAACACAATTCAAATATAATACGAAAATGGAGTAACTTCCATATGAAC
194 TT-A-ATATATATACAAAAACACAATTCAAATATAATACGAAAATGCAGTAACTTCCATATGAAC
* *
4208 TTACCTAGAAAATGGCAACTCGAAAGTTTCAGGGACTAATCATCACAGATTGCTATATAATGATC
257 TTACCTAGAAACTGGCAACTCGAAAGTTTCAGGGACTAATCATCACAGATTGCTAAATAATGATC
* *
4273 CGATACTGCTCACTCGAGCTGTCGAGAATCCACAATTTGTGCTGGATCTTAACCATCGAATAAAT
322 CGATACTGCTCACTCAAGCTGTCGAGAATCCACAATTTGTGCTGGATCTCAACCATCGAATAAAT
*
4338 CTGTAATCACGATTCCCATTTTTCCTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCA
387 CTCTAATCACGATTCCCATTTTTCCTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCA
* *
4403 TTTGTTAAATTCATACAGGTTATTTTACCATTTTCTTATCATTCCAAACTCTTTAATTGTATAC
452 TTTGTTAAATTCATACAGGTTATTTTACCATTTTCGTATCATTCCAAACTCTTTAATTGTATAA
* * * *
4467 ACACATCAGTTATTTTGAATAAAAATTCTCTATACATTTTAAATTTGCAACACCATCATAAACAT
1 ACACTTTAGTTATTTTGAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATAAACAT
*
4532 GCTATCCAACAACATACCATTCCCACATCAATTCAATGTCATGAATCTCTTCATATTTATCAAGT
66 GCTATCCAACAACATACCATTCCCACATCAATTCAATGTCATGAATCGCTTCATATTTATCAAGT
*
4597 ATTTATTATTTTAGGATTTGATCCATTTTATATAAAAAGCCATTAAATCTACAATTATATATATT
131 ATTT-TTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAAATCTACAATTATATATATT
* *
4662 TAATATATATACAAAAACACAATTCAAATATAATACGAAAATGCAGTAACCTCCATACGAACTTA
195 TAATATATATACAAAAACACAATTCAAATATAATACGAAAATGCAGTAACTTCCATATGAACTTA
4727 CCTAGAAACTGGCAACTCGAAAGTTTCAGGGACTAATCATCACAGATTGCTAAATAATGATCCGA
260 CCTAGAAACTGGCAACTCGAAAGTTTCAGGGACTAATCATCACAGATTGCTAAATAATGATCCGA
* * * *
4792 TACTGGTCACTCAAGCTTTCGAGAATCCATAATTTGTGCTGGATCTCAGCCATCGAATAAATCTC
325 TACTGCTCACTCAAGCTGTCGAGAATCCACAATTTGTGCTGGATCTCAACCATCGAATAAATCTC
* *
4857 TAATCACGATTCCCTTTTTTTCCTTTTTATAACCGTAATCACTTTCCATTCTTATCTAAACCATT
390 TAATCACGATTCCC-ATTTTTCCTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATT
* *
4922 TGTTAAATTCATACAGGTTTTTTTACCGA-TTTCGTATCATTTCAAACTCTTTAATTGTATAA
454 TGTTAAATTCATACAGGTTATTTTACC-ATTTTCGTATCATTCCAAACTCTTTAATTGTATAA
* *
4984 ACACTTTAGTTATTTTGAATAACAAGTCTCTCTACATTTTAAATTTGCAACATCATCATAAACAT
1 ACACTTTAGTTATTTTGAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATAAACAT
*
5049 GCTATCCAACAACATACCATTCCCACATGAATTCAATGTCATGAATCGCTTCATATTTATCAAGT
66 GCTATCCAACAACATACCATTCCCACATCAATTCAATGTCATGAATCGCTTCATATTTATCAAGT
* *
5114 AGTTCTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAAGTCTACAATTATATATATT
131 A-TTTTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAAATCTACAATTATATATATT
* * *
5179 TAATGTATATACAAAAACACAATTCAAATATAATACGAGAATGCAGTAACTTCCTTATGAACTTA
195 TAATATATATACAAAAACACAATTCAAATATAATACGAAAATGCAGTAACTTCCATATGAACTTA
* *
5244 CCTAGAAACTGGCAACTAGAAAGTTTCAGGGATTAATCATCA
260 CCTAGAAACTGGCAACTCGAAAGTTTCAGGGACTAATCATCA
5286 NNNNNNNNNN
Statistics
Matches: 767, Mismatches: 47, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
516 195 0.25
517 390 0.51
518 182 0.24
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (515 bp):
ACACTTTAGTTATTTTGAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATAAACAT
GCTATCCAACAACATACCATTCCCACATCAATTCAATGTCATGAATCGCTTCATATTTATCAAGT
ATTTTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAAATCTACAATTATATATATTT
AATATATATACAAAAACACAATTCAAATATAATACGAAAATGCAGTAACTTCCATATGAACTTAC
CTAGAAACTGGCAACTCGAAAGTTTCAGGGACTAATCATCACAGATTGCTAAATAATGATCCGAT
ACTGCTCACTCAAGCTGTCGAGAATCCACAATTTGTGCTGGATCTCAACCATCGAATAAATCTCT
AATCACGATTCCCATTTTTCCTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTG
TTAAATTCATACAGGTTATTTTACCATTTTCGTATCATTCCAAACTCTTTAATTGTATAA
Found at i:7761 original size:515 final size:515
Alignment explanation
Indices: 7140--8895 Score: 2893
Period size: 516 Copynumber: 3.4 Consensus size: 515
7130 NNNCACATCC
* * *
7140 ATTCAATGTCATGAATCTCTTCATATTTATCAAGTATTTCTTATTTTATGATTTGCTCCATTTTA
1 ATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCATTTTA
* * * *
7205 TATAAAGAGCCATTAAATCTACATTTATATATATTTAATATATATACAAAAACACATTTAAAACA
66 TATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAATTAAAATA
*
7270 TAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAAAGTTTCAGG
131 TAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAATTGGCAACTAGAAAGTTTCAGG
* * * * *
7335 AACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCAGTTGAGTTGTCGAGAATCCAC
196 GACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCGAGAATCCAT
7400 AATTTGTGCTGGATCTCAACCATCGAATAAAACTCTAATCACGATTCCCATTTTCCTTTTTATAA
261 AATTTGTGCTGGATCTCAACCATCGAATAAAACTCTAATCACGATTCCCATTTTCCTTTTTATAA
* * * *
7465 CCTTAATCACTTTCCATTGTTATCGAAACCATTTGATAAATTCATGCAGGTTCTTTTACCAATTT
326 CCTTAATCACTTTCCATTCTTATCTAAACCATTTGATAAATTCATACAGGTTCTTTTACCGATTT
* * *
7530 CGTATAATTTCAAACTCTTTAATTGTGTACACACATTAGTTATTTTGAATAACAAGTCTCTATAC
391 CGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAATTCTCTATAC
* * *
7595 ATTTTAAATTTGCAACATCATCATAACCATGCTATCCAACAACTTAGAATTCCCACATGA
456 ATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATAGCATTCCCACATGA
*
7655 ATTCAATGTCATGATTCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCATTTTA
1 ATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCATTTTA
* * *
7720 TATAAAAAGCCATTACATCTACAATTATATATATTTAATATATATACAAAATCACAATTCAAATA
66 TATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAATTAAAATA
* * * *
7785 TAATACGAAAATGCAGTAACCTCCATACGAACTTACCTAGAAATTGGAAACTCGAAAGTTTCAGG
131 TAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAATTGGCAACTAGAAAGTTTCAGG
7850 GACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCGAGAATCCAT
196 GACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCGAGAATCCAT
* * * * *
7915 AATTTGTGCTAGATCTCAACCATCGAATAAATCTCTAATCAGGATTCTCATTTTTCTTTTTTATA
261 AATTTGTGCTGGATCTCAACCATCGAATAAAACTCTAATCACGATTCCCA-TTTTCCTTTTTATA
* *
7980 ACCATAATCACTTTCCATTCTTATCTAAACCATTTGCTAAATTCATACAGGTTCTTTTACCGATT
325 ACCTTAATCACTTTCCATTCTTATCTAAACCATTTGATAAATTCATACAGGTTCTTTTACCGATT
* * *
8045 TCGTATCAGTTCAAACTCTTTAACTGTATACACATATTAGTTATTTTGAATAACAATTCTCTATA
390 TCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAATTCTCTATA
**
8110 CATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATAGCATTCCCACATCC
455 CATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATAGCATTCCCACATGA
* *
8171 ATTCAATGTCATGAATCTCTTTATATTTATCAAGTAGTTCTTATTTTATGATTTGATCCATTTTA
1 ATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCATTTTA
* * *
8236 TATAAAAAGCCATTAAATCTACAGTTATATATATTTAATATATATAGAAAAACACAATTTAAATA
66 TATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAATTAAAATA
* *
8301 TAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAACTAGCAACTAGAAAGTTTCAGG
131 TAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAATTGGCAACTAGAAAGTTTCAGG
* *
8366 GACTAATCATCAAAGATTGCTATATAATGATCCGATACTGCTTACTCGAGCTGTCGAGAATCCAT
196 GACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCGAGAATCCAT
* * * *
8431 AATTTGTGCTGGATCTCAACCATCTAATAAACCTCTAATCACGAATCCCTTTTTTTCCTTTTTAT
261 AATTTGTGCTGGATCTCAACCATCGAATAAAACTCTAATCACGATTCCC--ATTTTCCTTTTTAT
* *
8496 AA-CTGTAATCACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGTTTTTTTACCGA
324 AACCT-TAATCACTTTCCATTCTTATCTAAACCATTTGATAAATTCATACAGGTTCTTTTACCGA
* *
8560 TTTCGTATCATTTCAAACTCTTTAATTGTATACACACTTTAGTTATTTTGAATAACAATTCTCTC
388 TTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAATTCTCTA
8625 TACATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATAGCATTCCCACATGA
453 TACATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATAGCATTCCCACATGA
* *
8688 ATTCAATGTCATGAATCGCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCATCTTA
1 ATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCATTTTA
*
8753 TATAAAAAGCCATTAAATCTACAATTATATATATTTCATATATATACAAAAACACAATTAAAATA
66 TATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAATTAAAATA
*
8818 TAACACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAATTGGCAACTAGAAAGTTTCAGG
131 TAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAATTGGCAACTAGAAAGTTTCAGG
8883 GACTAATCATCAC
196 GACTAATCATCAC
8896 NNNNNNNNNN
Statistics
Matches: 1148, Mismatches: 89, Indels: 6
0.92 0.07 0.00
Matches are distributed among these distances:
515 285 0.25
516 475 0.41
517 388 0.34
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (515 bp):
ATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTACGATTTGATCCATTTTA
TATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAATTAAAATA
TAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAATTGGCAACTAGAAAGTTTCAGG
GACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCGAGAATCCAT
AATTTGTGCTGGATCTCAACCATCGAATAAAACTCTAATCACGATTCCCATTTTCCTTTTTATAA
CCTTAATCACTTTCCATTCTTATCTAAACCATTTGATAAATTCATACAGGTTCTTTTACCGATTT
CGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAATTCTCTATAC
ATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATAGCATTCCCACATGA
Done.