Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold917
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: 4281
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.33
Warning! 339 characters in sequence are not A, C, G, or T
Found at i:983 original size:516 final size:515
Alignment explanation
Indices: 1--2251 Score: 3608
Period size: 516 Copynumber: 4.4 Consensus size: 515
*
1 GCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTACAACGTTTCAGGAACTAATCATCA
1 GCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAACGTTTCAGG-ACTAATCATCA
* * *
66 CGGATTGCTATATCATGATCCGATACTGCTCAGTCGAGCTGTCAGGAATCCACAATTTGTGCTGG
65 CAGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCAGGAATCCACAATTTGTGCTGG
* * * *
131 ATCTCAACCATGGAATAAATCTCTAATCACGATTCTCATTTTTCCTTTTTATAACCATAATAATT
130 ATCTCAACCATCGAATAAATCTCTTATCACGATTCCCATTTTTCCTTTTTATAACCATAATAACT
*
196 TTCCATTCTTATCTAAACCATTTGGTAAATTCATACAGGTTCTTTTACCAATTTCTTATCATTCG
195 TTCCATTCTTATCTAAACCATTTGGTAAATTCATACAGGTTCTTTTACCAATTTCGTATCATTCG
261 AAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAACTCTCTATACATTTTAAATTT
260 AAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAACTCTCTATACATTTTAAATTT
326 GCAACATCATCATATACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGAAT
325 GCAACATCATCATATACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGAAT
*
391 CTCTTCATATTTATCAAGTATTTCTTATTTTGCGATTTGATCCATTTTATATAAAAAGCCATTAA
390 CTCTTCATATTTATCAAGTATTTCTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAA
* * *
456 GTCTGCAATTATATCTATTTAATATATATACAAAAACCCAATTAAAATATAATACAAAAAT
455 ATCTACAATTATATCTATTTAATATATATACAAAAACACAATTAAAATATAATACAAAAAT
* *
517 GCGGTAACTTCCATATGAACTTACCTAGAAAATGGTAACTAGAACGTTTCATGGACTAATCATCA
1 GCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAACGTTTCA-GGACTAATCATCA
* * *
582 TAGATTGCTATATAATGATCCGATAGTGCTCACTCGACCTGTCAGGAATCCACAATTTGTGCTGG
65 CAGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCAGGAATCCACAATTTGTGCTGG
* * * * * **
647 ATCTCAACCATCGAATAAATCTCTTATCATGAGTCGCATTTATCCTTTTTATAACCATAGTCCCT
130 ATCTCAACCATCGAATAAATCTCTTATCACGATTCCCATTTTTCCTTTTTATAACCATAATAACT
* * *
712 TTCCATTCTTATCTAAACCATTTGTTAAATTCATACACGTTCTTTTACCAATTTCGTATCATTTG
195 TTCCATTCTTATCTAAACCATTTGGTAAATTCATACAGGTTCTTTTACCAATTTCGTATCATTCG
* * * *
777 AAACTCTTTAATTGTATACACACATTAGTTATTTTGAGTAACAATTTTGTATACATTTTAAATTT
260 AAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAACTCTCTATACATTTTAAATTT
*
842 GCAACATCATCATATACATGCTATCCAACAACATACCATTCCCACATCCATTCAATGTCATGAAT
325 GCAACATCATCATATACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGAAT
* * *
907 ATCTTCAAATTTATCAAGTATTTCTTATTTTATGATTTGATCCATTTTATATAAAAAGCCATTAA
390 CTCTTCATATTTATCAAGTATTTCTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAA
* * * *
972 ATCTACAATTATATGTATTTAATATATATACAAAAACACAATTTAAATAAAATTCAAAAAT
455 ATCTACAATTATATCTATTTAATATATATACAAAAACACAATTAAAATATAATACAAAAAT
* *
1033 GCAGTAACTTCCATATGAACTTATCTAGAAAATGGCAACTAGAAAGTTTCAGGGACTAATCATCA
1 GCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAACGTTTCA-GGACTAATCATCA
* * * *
1098 CCGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCGGGAATCCACAATTTGCGATGG
65 CAGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCAGGAATCCACAATTTGTGCTGG
* * * * * * *
1163 TTCTTAACCATCTAATAAATCTCTTATCATGGTTCCCATTTTTCCTTTTTATAACCATAGTCACT
130 ATCTCAACCATCGAATAAATCTCTTATCACGATTCCCATTTTTCCTTTTTATAACCATAATAACT
* *
1228 TTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGATCTTTTACCAATTTCGTATCATTTC
195 TTCCATTCTTATCTAAACCATTTGGTAAATTCATACAGGTTCTTTTACCAATTTCGTATCA-TTC
* *
1293 -AAACTCTTTAATTG-ATGACGCACATTAGTTATTTTGAATAACAATTCTCTATACATTTTAAAT
259 GAAACTCTTTAATTGTAT-ACACACATTAGTTATTTTGAATAACAACTCTCTATACATTTTAAAT
* *
1356 TTGCAACATCATCACATACATGCTGTCCAACAACATACCATTCTCACATCCATTCAATGTCATGA
323 TTGCAACATCATCATATACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGA
* *
1421 ATCTCTTCATATTTATCAAGTATTTCTTATTTTACGAATTGATCCATTGTATATAAAAAGCCATT
388 ATCTCTTCATATTTATCAAGTATTTCTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATT
* * * * * *
1486 AGATCTACAATTATATATATTTAGTATATATAAAAAAACACAATTAAAATGTAATACGAAAAT
453 AAATCTACAATTATATCTATTTAATATATATACAAAAACACAATTAAAATATAATACAAAAAT
1549 GCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAACGTTTCAGGAACTAATCATCA
1 GCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAACGTTTCAGG-ACTAATCATCA
* * * * *
1614 CAGAGTGCTATATAATAATCCGATACTGCTCACTAGAGCTGTC-GAGAATCCATAATTTGTGCTA
65 CAGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCAG-GAATCCACAATTTGTGCTG
* * * *
1678 GATCTCAACCATGGAATAAATCTCTAATCACGATTCTCATTTTTCCTTTTTATAACCATAATAAT
129 GATCTCAACCATCGAATAAATCTCTTATCACGATTCCCATTTTTCCTTTTTATAACCATAATAAC
*
1743 TTTCCATTCTTATCTAAACCATTTGGTAAATTCATACAGGTTCTTTTACCAATTTCTTATCATTC
194 TTTCCATTCTTATCTAAACCATTTGGTAAATTCATACAGGTTCTTTTACCAATTTCGTATCATTC
1808 GAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAACTCTCTATACATTTTAAATT
259 GAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAACTCTCTATACATTTTAAATT
* *
1873 TGCAACATCATCATATACATGCTATCCAACAACATACCATTCTCACGTCCATTCAATGTTATGAA
324 TGCAACATCATCATATACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGAA
* * * *
1938 TCTCTTCATACTTATCAAGTATTTCTTATTTTGCTATTTGATCCGTTTTATATAAAAAGCCATTA
389 TCTCTTCATATTTATCAAGTATTTCTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTA
* * *
2003 AATCTGCAATTATATCTATTTAATATATATACAAAAACCCAATTAAAATATAATACGAAAAT
454 AATCTACAATTATATCTATTTAATATATATACAAAAACACAATTAAAATATAATACAAAAAT
2065 GCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAACGTTTCAGGGACTAATCATCA
1 GCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAACGTTTCA-GGACTAATCATCA
* * *
2130 TAGATTGCTATATAATGATCCGATACTACTCACTCGACCTGTCAGGAATCCACAATTTGTGCTGG
65 CAGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCAGGAATCCACAATTTGTGCTGG
2195 ATCTCAACCATCGAATAAATCTCTTATCACGATTCCCATTTTTCCTTTTTATAACCA
130 ATCTCAACCATCGAATAAATCTCTTATCACGATTCCCATTTTTCCTTTTTATAACCA
2252 NNNNNNNNNN
Statistics
Matches: 1589, Mismatches: 137, Indels: 18
0.91 0.08 0.01
Matches are distributed among these distances:
515 8 0.01
516 1572 0.99
517 9 0.01
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (515 bp):
GCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAACGTTTCAGGACTAATCATCAC
AGATTGCTATATAATGATCCGATACTGCTCACTCGAGCTGTCAGGAATCCACAATTTGTGCTGGA
TCTCAACCATCGAATAAATCTCTTATCACGATTCCCATTTTTCCTTTTTATAACCATAATAACTT
TCCATTCTTATCTAAACCATTTGGTAAATTCATACAGGTTCTTTTACCAATTTCGTATCATTCGA
AACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAACTCTCTATACATTTTAAATTTG
CAACATCATCATATACATGCTATCCAACAACATACCATTCTCACATCCATTCAATGTCATGAATC
TCTTCATATTTATCAAGTATTTCTTATTTTACGATTTGATCCATTTTATATAAAAAGCCATTAAA
TCTACAATTATATCTATTTAATATATATACAAAAACACAATTAAAATATAATACAAAAAT
Found at i:4224 original size:514 final size:514
Alignment explanation
Indices: 2591--4281 Score: 2554
Period size: 516 Copynumber: 3.3 Consensus size: 514
2581 NNNNNNNNNN
*
2591 CTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGATCTT
1 CTTTTTATAACCATAATAACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGATCTT
*
2656 TTACCAATTTCGTATCATTTCAAACTCTTTAACTGTATACACACATTAGTTATTTTGAATAACAA
66 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
*
2721 TTCTCTATACATTTTAAATTTGCCACATCATCACATACATGCTATCCAACAACATACCATTCTCA
131 TTCTCTATACATTTTAAATTTGCAACATCATCACATACAT-C--TCC--CAACATACCATTCTCA
** *
2786 CATCCATTCAATGTCATGAATCTCTTCATATTTATCAAGTATTTCACATTTTACTATTTGATCCA
191 CATCCATTCAATGTCATGAATCTCTTCATATTTATCAAGTATTTCTTATTTTACGATTTGATCCA
* * *
2851 TTTTATATAAAAAGTCATTAAATCTACTATTATATATATTTA-ATATATATACAT--AAACACAA
256 TTTTATATAAAAAGCCATTAAATCTACAATTATATATATTTATATATATATATATAAAAACACAA
*
2913 TTAAAATATAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAAAAC
321 TTAAAATATAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAAC
*
2978 GTTTCAGGGACTAATCATCACAGATTGCTATATAATGATCTGATACTGCTCACTAGAGCTGTCGA
386 GTTTCAGGGACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCACTAGAGCTGTCGA
*
3043 GAATCCATAATTTGTGCTAGATCTCAACCATGGAATAAATCTCTAATCACGATTCTCATTTTTC
451 GAATCCATAATTTGTGCTAGATCTCAACCATCGAATAAATCTCTAATCACGATTCTCATTTTTC
* * * *
3107 CTTTTTATAAACATAATAATTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACTGGTTCTT
1 CTTTTTATAACCATAATAACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGATCTT
* ** * * *
3172 TTACCATTTTATTATCATTTGAAACTCTTTAATTGTATGCACACCTTAGTTATTTTGAATAACAA
66 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
* * * *
3237 TTCTCTACACATTTTCAATTTGCAACATCATCATATACATCCTATCCAACAACTTACCATTCTCA
131 TTCTCTATACATTTTAAATTTGCAACATCATCACATACAT-C--TCC--CAACATACCATTCTCA
* *
3302 CATCCATTCAAAGTCATGAATCTCTTCATATTTAACAAGTATTTCTTATTTTACGATTTGATCCA
191 CATCCATTCAATGTCATGAATCTCTTCATATTTATCAAGTATTTCTTATTTTACGATTTGATCCA
* *
3367 TTTTATATAAAAAGCCATTAAATCTGCAATTATATATA-TT-TA-ATATATATACAAAAACACAA
256 TTTTATATAAAAAGCCATTAAATCTACAATTATATATATTTATATATATATATATAAAAACACAA
*
3429 TTAAAATATAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAAA
321 TTAAAATATAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAAC
* *
3494 GTTTCAGGAACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCACT-GAGCTGTCGG
386 GTTTCAGGGACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCACTAGAGCTGTCGA
* * * * * * * * * *
3558 GAGTCCACAATTTGTGCTGGATCTTAACCATCTAATACATCTCTTATCATGGTTCCCATTTTTC
451 GAATCCATAATTTGTGCTAGATCTCAACCATCGAATAAATCTCTAATCACGATTCTCATTTTTC
* * * *
3622 CTTTTTATAGCCATAGTCACTTTCCATTCTTATCTAAACCATTTGTTCAATTCATACAGGATCTT
1 CTTTTTATAACCATAATAACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGATCTT
* * *
3687 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTGGTTATTTTGGATAATAA
66 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
* * * * * *
3752 TTCTTTATACATTTTAAATTTGCAACAACATCACATACA-C-GCCAACATAGCATTCCCACATCA
131 TTCTCTATACATTTTAAATTTGCAACATCATCACATACATCTCCCAACATACCATTCTCACATCC
* **
3815 ATTCAATGTCATGAATCGCTTCATATTTATCAAGTAGATCTTATTTTACGATTTGATCCATTTTA
196 ATTCAATGTCATGAATCTCTTCATATTTATCAAGTATTTCTTATTTTACGATTTGATCCATTTTA
* *
3880 TATAAAAAGCCATTAAATCCACAATTATATATATTTAATATATATATATATACAAAACACAATTC
261 TATAAAAAGCCATTAAATCTACAATTATATATATTT-ATATATATATATATA-AAAACACAATTA
*
3945 AAATATAATACGAAAATGCAGAAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAACGTT
324 AAATATAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAACGTT
* *
4010 TCAGGGACTAACCATCACAGATTGCCATATAATGATCCGATACTGCTCACTAGAGCTGTCGAGAA
389 TCAGGGACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCACTAGAGCTGTCGAGAA
*
4075 TCCATAATTTGTGCTAGATCTGAACCATCGAATAAATCTCTAATCACGATTCTCATTTTTC
454 TCCATAATTTGTGCTAGATCTCAACCATCGAATAAATCTCTAATCACGATTCTCATTTTTC
* * * * *
4136 CTTTTTATAACCACAATAATTTTACATTCTTATCTAAACCATTTGTTAAATTCATACAGGTTCAT
1 CTTTTTATAACCATAATAACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGATCTT
* * *
4201 TTACCAATTTCGTATCATTTCAAACTCTTTACTTGTATATACACATTAGTTATTTTCAATAACAA
66 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
4266 TTCTCTATACATTTTA
131 TTCTCTATACATTTTA
Statistics
Matches: 1054, Mismatches: 112, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
508 108 0.10
509 2 0.00
510 1 0.00
511 2 0.00
512 10 0.01
513 123 0.12
514 201 0.19
515 212 0.20
516 395 0.37
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (514 bp):
CTTTTTATAACCATAATAACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGATCTT
TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
TTCTCTATACATTTTAAATTTGCAACATCATCACATACATCTCCCAACATACCATTCTCACATCC
ATTCAATGTCATGAATCTCTTCATATTTATCAAGTATTTCTTATTTTACGATTTGATCCATTTTA
TATAAAAAGCCATTAAATCTACAATTATATATATTTATATATATATATATAAAAACACAATTAAA
ATATAATACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAACGTTTC
AGGGACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCACTAGAGCTGTCGAGAATC
CATAATTTGTGCTAGATCTCAACCATCGAATAAATCTCTAATCACGATTCTCATTTTTC
Done.