Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_886 ID=scaffold_886-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: 5629
ACGTcount: A:0.15, C:0.14, G:0.08, T:0.12
Warning! 2874 characters in sequence are not A, C, G, or T
Found at i:68 original size:46 final size:46
Alignment explanation
Indices: 1--1867 Score: 1722
Period size: 46 Copynumber: 40.8 Consensus size: 46
*
1 CAAATACAGGAAGACAAGATCTGGTATCTTCGATCCCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
*
47 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCTTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* *
93 CAAATACAGGAAGACAAGATCTGTTATCTTCGATCCCCTCTGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* *
139 CAAATACAGGAAGACAAGATCTGATATCTTCGATCCCTTCC-CTTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGC-TGC
* * *
185 CAAATTCAGGAAGACAAGATCTGCTATCTTTGATCTCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * *
231 CAAATACAGGGAGACAAGATCTGATATCTTCGATCCCCTCTGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* *
277 CAAATATAGGAAGACAAGATCTGCTGTCTTCGATCCCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * * * *
323 CAAATACAGGAAGATAAGATCTGATATTTTCGATCCCTTTCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
*
369 CAAATACAGGAAGACAAGATCTACTATCTTCGATCCCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * *
415 CAAATATAGGAAGACAAGATCTGATATCTTCGATCCCTTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* *
461 CAAAGACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
*
507 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCATCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * * *
553 GAAATTCAGGAAGACAAGATCTGATATCTTCGATCTCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * * *
599 CAAATAAAGGAAGACAAGATCTACTATCTTCGATCTCCTCCGCAGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
*
645 CAAATACAGGAAGACAAGATCTGATATCTTCGATCCCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* *
691 AAAATACAGGAAGACAAGATCTGCTATCTTTGATCCCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * * *
737 CAAATATAGAAATACAAGATCTGCTATCTTCGATCCCCTCCACTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* ** * *
783 CAAATACAGGAAGACAAGATCTGATATCTTTAATCCCTTTCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * * **
829 CAAATGCAGGAAGGCAAGATCTGATATCTTCGATCCCCTCTACAT-C
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGC-TGC
* * *
875 CAAATACCGAAAGACAAGATCTGCTATCGTCGATCCCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * *
921 CAAATACAGGAAGAAAAGATCTGATATCTTCGATCCACTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
** * *
967 CAAATACAGGAAGACAAGATCTGAGATCTTCGATCCGCTTCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* *
1013 CAAATACAGGAAGACAAGATCTGCTATCCTCGATCTCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * * * *
1059 CAAATACATGAAGATAAGATCTACTATCTTTGATCCCCTCTGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * *
1105 CAAATACAGGAAGACAAGATCTGCTATCTTCAATCCCC-CTCACTAC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTC-CGCTGC
*
1151 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTTCGCT--
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
**************************************
1195 C-----CANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
**********************************************
1236 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
**************** *
1282 NNNNNNNNNNNNNNNNAGATCTGCTATCTTCGATCCCCTCCACTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* ** * *
1328 CAAATACAGGAAGACAAGATCTGATATCTTTAATCCCTTTCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * * *
1374 AAAATTCAGGAAGACAAGATCTGATATCTTCGATCCCCT-CGCTGG
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* *
1419 CAAGTACAGGAAGACAAGATCTGCTATCTTCGTTCCCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * * *
1465 CAAATACAAGAAGACAAGATCTGATATCTTCGATCCCTTCTGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * * * *
1511 CAAATACAGGAAGACACGATCTGTTATCTTCGATCTCTTCCGATGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * *
1557 CAGATACAGGAAAACAAGATCTGCTATCGTCGATCCCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * *
1603 CAAATATAGGAAGAAAAGATCTGCTATCGTCGATCCCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * *
1649 CAAATACAGGAAGAAAAGATCTGATATCTTCGATCCACTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * *
1695 CAAATACAGGAAGACAAGATCTGATATCTTCGATCCCTTTCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * * *
1741 CAAATTCAGGAAAACAAGATCTGATATCTTCGATCCCCTCTGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
* * *
1787 CAAATACCGGAAGACAAGATCTGCTATCGTCGATCTCCTCCGCTGC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
1833 CAAATACAGGAAGACAAGATCTGCTATCTTCGATC
1 CAAATACAGGAAGACAAGATCTGCTATCTTCGATC
1868 TNNNNNNNNN
Statistics
Matches: 1525, Mismatches: 282, Indels: 28
0.83 0.15 0.02
Matches are distributed among these distances:
39 2 0.00
44 1 0.00
45 42 0.03
46 1478 0.97
47 2 0.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.23
Consensus pattern (46 bp):
CAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC
Found at i:4690 original size:46 final size:46
Alignment explanation
Indices: 4543--5132 Score: 754
Period size: 46 Copynumber: 12.9 Consensus size: 46
4533 NNNNNNNNNN
* *
4543 TCTGATATCTTCGATCCCCT-CGCTGGCAAGTACAGGAAGACAAGA
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
* * * *
4588 TCTGCTATCTTCGATCTCTTCTGCTGCCAAAT-CAGGAAGACAAGA
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
* * * *
4633 TCTGCTATCTTCGTTCCCCTCCGCTGCCAAATACAAGAAGACAATA
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
* *
4679 TCTGATATCTTCGATCCCTTCTGCTGCCAAATACAGGAAGACAAGA
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
* * * * *
4725 TCTGTTATCTTCGATCTCTTCCGCTGCCAGATACAGGAAAACAAGA
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
* * * *
4771 TCTGCTATCGTCGATCCCCTCTGCTGCCAAATACAGGAAGAAAAGA
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
* *
4817 TTTGATATCTTCGATCCCCTCCGCTGCCAGATACAGGAAGACAAGA
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
* **
4863 TCT-ACTATCTTCGATTCCCTCCGCTGTAAAATACAGGAAGACAAGA
1 TCTGA-TATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
* * * *
4909 TCTGATATCTTCAATCCCTTTCGCTGCCAAATTCAGGAAGACAAGA
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
* ** * *
4955 TCTGGTATCTTCGATCCCCTCTACTGCCAAATACGGGAAGGCAAGA
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
* * * *
5001 TCTGCTATCATCGATCCCCTCCACTGCCAAATACAGGAAGAAAAGA
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
5047 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
* * * * *
5093 TTTGCTATCTTCGATCCCATTCGCTGCCACATACAGGAAG
1 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
5133 GNNNNNNNNN
Statistics
Matches: 468, Mismatches: 73, Indels: 7
0.85 0.13 0.01
Matches are distributed among these distances:
45 59 0.13
46 408 0.87
47 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (46 bp):
TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
Found at i:5302 original size:46 final size:46
Alignment explanation
Indices: 5235--5629 Score: 526
Period size: 46 Copynumber: 8.6 Consensus size: 46
5225 NNNNNNNNNT
* *
5235 AAGATCT-ACTATCTTTGATCCCCTCTGCTGCCAAATACAGGAAGAC
1 AAGATCTGA-TATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGAC
* *
5281 AAGATCTGATATCCTCGATCCCCTCCGCTGCCAAATACAGCAAGAC
1 AAGATCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGAC
* *
5327 AAGATCT-ACTATCTTCGATCTCCTCCGCTGCCAAATACAGGAAAAC
1 AAGATCTGA-TATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGAC
* * *
5373 AAGATCTGCTATCTTCGATCCCTTCCGCTGCCAAATACAGGCAGAC
1 AAGATCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGAC
**
5419 AAGATCTGATATCTTCGATCCCCTCTACTGCCAAATACAGGAAGAC
1 AAGATCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGAC
* * *
5465 AAGATCTGCTATCTT-GTATCCCTTCCGCTCCCAAATACAGGAAGAC
1 AAGATCTGATATCTTCG-ATCCCCTCCGCTGCCAAATACAGGAAGAC
** *
5511 AAGATCTGATATCTTCGATCCCCTCCGCTGCCAAATACAAAAAAAC
1 AAGATCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGAC
* * *
5557 AAGATCTGCTATATTCGATCCCCTCCGCTGCCAAATACAAGAAGAC
1 AAGATCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGAC
* * * *
5603 CAGATTTGCTATCTTCGTTCCCCTCCG
1 AAGATCTGATATCTTCGATCCCCTCCG
Statistics
Matches: 307, Mismatches: 37, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
45 2 0.01
46 303 0.99
47 2 0.01
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (46 bp):
AAGATCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGAC
Done.