Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_573 ID=scaffold_573-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: 7909
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.26
Warning! 2333 characters in sequence are not A, C, G, or T
Found at i:4215 original size:518 final size:494
Alignment explanation
Indices: 3637--4902 Score: 1973
Period size: 495 Copynumber: 2.5 Consensus size: 494
3627 NNNNNNNNNN
* *
3637 CTATACATTTTAACTCT-CAACCATCATCATATACATGCTATCCAACAACATACCATTCTCACAT
1 CTATACATTTTAAATTTGCAA-CATCATCATATACATGCTATCCAACAACATACCATTCTCACAT
*
3701 CCATTCTAATGTCATCAATCTCTTCATATTTATCAAGTAGTTCTTATTTTCGATTTGATCCATTT
65 CCATTC-AATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTCGATTTGATCCATTT
* *
3766 TATAGAAAAAGCCATTAAATTTGCAATTATATATATTTAATATATATATACAAAAACACAATTAA
129 TATATAAAAAGCCATTAAATCTGCAATTATATATATTT-A-ATATATATACAAAAACACAATTAA
*
3831 AATATAATACGAAAATGCTGTAAGTTCTATATGAACTTACATAGAAAATGGCAACTAGAACGTTT
192 AATATAATACGAAAATGCTGTAAGTTCCATATGAACTTACATAGAAAATGGCAACTAGAACGTTT
*
3896 CAGGGACTAATCATCACAGATTGCTATATAATGATCCGATACG-GCTCAGTCGAGTTGTCGGGAA
257 CAGGGACTAATCATCACAGATTGCTATATAATGATCCGATACGTG-TCAGTCGAGCTGTCGGGAA
*
3960 TCCACAATTTATGCTGGATCTCAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTCCTTT
321 TCCACAATTTATGCTGG-TCTCAACCATCGAATAAATCTCTAATCACGATTCCCATTTCTCCTTT
* *
4025 TTATAACTATAATCACTTTCCATTCTTATCTA-AACCATTTGTTAAATTCATACAGGTTCTTTTA
385 TTATAACCATAATCACTTTCCATTCTTATCTATAA-CATTTG-----TT-AT--A--TTC--ATA
*
4089 CCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAATTC
437 -C-A----G--TCATTTCAAACACTTTAATTGTATACACACATTAGTTATTTTGAATAACAATTC
4154 T
494 T
4155 CTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACATACCATTCTCACATC
1 CTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACATACCATTCTCACATC
4220 CATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTTCGATTTGATCCATTTT
66 CATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTA-TTTTCGATTTGATCCATTTT
4285 ATATAAAAAGCCATTAAATCTGCAATTATATATATTTAATATATATACAAAAACACAATTAAAAT
130 ATATAAAAAGCCATTAAATCTGCAATTATATATATTTAATATATATACAAAAACACAATTAAAAT
* * * *
4350 ATAATACGAAAATTCAGTATGCTCCATATGAACTTACATAGAAAATGGCAACTAGAACGTTTCAG
195 ATAATACGAAAATGCTGTAAGTTCCATATGAACTTACATAGAAAATGGCAACTAGAACGTTTCAG
*
4415 GGACTAATCATCACATATTGCTATATAATGATCCGATACGTGTCAGTCGAGCTGTCGGGAATCCA
260 GGACTAATCATCACAGATTGCTATATAATGATCCGATACGTGTCAGTCGAGCTGTCGGGAATCCA
4480 CAATTTATGCTGGTCTCAACCATCGAATAAATCTCTAATCACGATTCCCATTTCTCCTTTTTATA
325 CAATTTATGCTGGTCTCAACCATCGAATAAATCTCTAATCACGATTCCCATTTCTCCTTTTTATA
* *
4545 ACCATAATCACTTTCCATTTTTATCTATAAGATTTGTTATATTCATACAGTCATTTCAAACACTT
390 ACCATAATCACTTTCCATTCTTATCTATAACATTTGTTATATTCATACAGTCATTTCAAACACTT
*
4610 TAATTGTATACACACATTAGTTATTTTGATTAACAATTCT
455 TAATTGTATACACACATTAGTTATTTTGAATAACAATTCT
* *
4650 CTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACTACATACCATTCCCACATC
1 CTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACATACCATTCTCACATC
* * * *
4715 CACTCAATGTCATGAATCTCTTTATATTTATCAAGTATTTCTTATTTTATGATTTGATCCATTTT
66 CATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTT-CGATTTGATCCATTTT
* *
4780 ATATAAAAAGCCATTAAGTCT-AAAGTTATATATATTTAATATATATACAAAAACACAATTAAAA
130 ATATAAAAAGCCATTAAATCTGCAA-TTATATATATTTAATATATATACAAAAACACAATTAAAA
* *
4844 TATAATACGAAAATGCTGTAAGTTCCATATGAACTTACCTAGAATATGGCAACTAGAAC
194 TATAATACGAAAATGCTGTAAGTTCCATATGAACTTACATAGAAAATGGCAACTAGAAC
4903 NNNNNNNNNN
Statistics
Matches: 709, Mismatches: 33, Indels: 35
0.91 0.04 0.05
Matches are distributed among these distances:
494 6 0.01
495 284 0.40
497 1 0.00
501 1 0.00
502 1 0.00
503 2 0.00
505 3 0.00
507 1 0.00
509 2 0.00
510 2 0.00
515 81 0.11
516 163 0.23
517 40 0.06
518 119 0.17
519 3 0.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (494 bp):
CTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACATACCATTCTCACATC
CATTCAATGTCATGAATCTCTTCATATTTATCAAGTAGTTCTTATTTTCGATTTGATCCATTTTA
TATAAAAAGCCATTAAATCTGCAATTATATATATTTAATATATATACAAAAACACAATTAAAATA
TAATACGAAAATGCTGTAAGTTCCATATGAACTTACATAGAAAATGGCAACTAGAACGTTTCAGG
GACTAATCATCACAGATTGCTATATAATGATCCGATACGTGTCAGTCGAGCTGTCGGGAATCCAC
AATTTATGCTGGTCTCAACCATCGAATAAATCTCTAATCACGATTCCCATTTCTCCTTTTTATAA
CCATAATCACTTTCCATTCTTATCTATAACATTTGTTATATTCATACAGTCATTTCAAACACTTT
AATTGTATACACACATTAGTTATTTTGAATAACAATTCT
Found at i:7783 original size:516 final size:518
Alignment explanation
Indices: 6809--7909 Score: 1956
Period size: 516 Copynumber: 2.1 Consensus size: 518
6799 NNNNNNNNNN
*
6809 ACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATCAATCTCTTCATATTTATC
1 ACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGAATCTCTTCATATTTATC
*
6874 AAGTAATTCTTATTTTTCGATTTGATCCATTTTATATAAAAAGCCATTAAATCTGCAATTATATA
66 AAGTAATTCTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAAATCTGCAATTATATA
* *
6939 TATTTAATATATATATACAAAAACACAATTAAAATATAATACGAAAATTCAGTATGTTCCATATG
131 TATTTAATATATATATACAAAAACACAATTAAAATATAATACGAAAATGCAGTAAGTTCCATATG
* * * * * *
7004 AACTTACTTAGAAAATGGCACCTAGAACGTTTCAGGGACTAATCATCACATATTGCTATATAATG
196 AACTTACATAGAAAATGGAAACTAGAACGATTCAGGGACTAATCATCACAGATTCCTATATAATG
*
7069 CTCCGATACGTGTCAATCGAGCTGTCGGGAATCCACAATTTATGCTGGATCTCAACCATCGAATA
261 ATCCGATACGTGTCAATCGAGCTGTCGGGAATCCACAATTTATGCTGGATCTCAACCATCGAATA
*
7134 AATCTCTACTCACAATTCCCATTTTTCCGTTTTATAACCATAATCACTTTCCATTCTTATCTAAA
326 AATCTCTAATCACAATTCCCATTTTTCCGTTTTATAACCATAATCACTTTCCATTCTTATCTAAA
*
7199 CCATTTGTTAAATTCATACAGGTTCTTTTACCAATTTCGTATCATTTCAAACTCTTTAATTGTAT
391 CCATTTGTTAAACTCATACAGGTTCTTTTACCAATTTCGTATCATTTCAAACTCTTTAATTGTAT
* *
7264 ACACACATTAGTTATTTTGAATAACAATTCTCTATACATTTTACATTTGCAACATCATCATAT
456 ACACACATTAGTTATTTTCAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATAT
7327 ACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGAATCTCTTCATATTTATC
1 ACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGAATCTCTTCATATTTATC
* *
7392 AAGTATTTCTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAAATCTGCAATTATATG
66 AAGTAATTCTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAAATCTGCAATTATATA
* *
7457 TATTT-A-ATATATATACAAAAACACAATTAAAATATAATGCGTAAATGCAGTAAGTTCCATATG
131 TATTTAATATATATATACAAAAACACAATTAAAATATAATACGAAAATGCAGTAAGTTCCATATG
*
7520 AACTTACATAGAAAATGGAAACTAGAACGATTCAGGGAGTAATCATCACAGATTCCTATATAATG
196 AACTTACATAGAAAATGGAAACTAGAACGATTCAGGGACTAATCATCACAGATTCCTATATAATG
* *
7585 ATCCGATAC-TGCTTAATCGAGCTGTCGGGAATCCACAATTTGTGCTGGATCTCAACCATCGAAT
261 ATCCGATACGTG-TCAATCGAGCTGTCGGGAATCCACAATTTATGCTGGATCTCAACCATCGAAT
* *
7649 AAATCTCTAATCACGATTCCCATTTTTCCTTTTTATAACCATAATCACTTTCCATTCTTATCTAA
325 AAATCTCTAATCACAATTCCCATTTTTCCGTTTTATAACCATAATCACTTTCCATTCTTATCTAA
7714 ACCATTTGTTAAACTCATACAGGTTCTTTTACCAATTTCGTATCATTTCAAACTCTTTAATTGTA
390 ACCATTTGTTAAACTCATACAGGTTCTTTTACCAATTTCGTATCATTTCAAACTCTTTAATTGTA
7779 TACACACATTAGTTATTTTCAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATAT
455 TACACACATTAGTTATTTTCAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATAT
7843 ACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGAATCTCTTCATATTTATC
1 ACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGAATCTCTTCATATTTATC
7908 AA
66 AA
Statistics
Matches: 558, Mismatches: 24, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
515 2 0.00
516 424 0.76
517 1 0.00
518 131 0.23
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (518 bp):
ACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGAATCTCTTCATATTTATC
AAGTAATTCTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAAATCTGCAATTATATA
TATTTAATATATATATACAAAAACACAATTAAAATATAATACGAAAATGCAGTAAGTTCCATATG
AACTTACATAGAAAATGGAAACTAGAACGATTCAGGGACTAATCATCACAGATTCCTATATAATG
ATCCGATACGTGTCAATCGAGCTGTCGGGAATCCACAATTTATGCTGGATCTCAACCATCGAATA
AATCTCTAATCACAATTCCCATTTTTCCGTTTTATAACCATAATCACTTTCCATTCTTATCTAAA
CCATTTGTTAAACTCATACAGGTTCTTTTACCAATTTCGTATCATTTCAAACTCTTTAATTGTAT
ACACACATTAGTTATTTTCAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATAT
Done.