Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_866 ID=scaffold_866-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: 5151
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.14
Warning! 2218 characters in sequence are not A, C, G, or T
Found at i:68 original size:46 final size:46
Alignment explanation
Indices: 1--949 Score: 1353
Period size: 46 Copynumber: 20.6 Consensus size: 46
1 CTTCGATCCCCTCCGCTGCCAAATTA-AGGAAGACAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAA-TACAGGAAGACAAGATCTGCTAT
* * *
47 CTTCGATCTCCTCCGCTGCCAAATACAAGAAAACAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* *
93 CTT-GTATCCCTTCCGCTGCCAAATACAGGAAGACAAGATCTGATAT
1 CTTCG-ATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* *
139 CTTCGATCCCTTCCGCTGCCAAATACAGGAAAACAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* *
185 CTTCGATCCCCTCCGCTGCCAAATACAGGAAAACATGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* * * *
231 CTTCGATCTCCTTCGTTGCCAAATATAGGAAGACAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* * * *
277 CTTCAATCCCATCCGCTACCAAATATAGGAAGACAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
*
323 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGGCAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* * * *
369 CTTCGATCTCCTCCGCTGCCAAGTAAAGGAAGACAAGATTTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* * *
415 CTTCGATCTCCTCCGCAGCCATATACAGGAAGACAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
*
461 CTTCGATCCCCTCCACTGCCAAATACAGGAAGACAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* * *
507 CTTCGATCTCCTCCGTTGCCAAATAAAGGAAGACAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* * * *
553 CTTCGATCTCCTCCGCAGCCAAACACAGGAAGACAAGATCTGATAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* **
599 CTTCAATCCCCTCCGCTATCAAATACAGGAAGACAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* * * *
645 CTTCGATCCCCTCCACTGCCAGATACAGAAAGACAAGATCTGATAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
**
691 CTTCGATCCCCTCCGCTATCAAATACAGGAAGACAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* * *
737 CTTCGATCTCCTCCGCTGCCAAATAAAGGAAGACAAGATTTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* * * *
783 CTTCGATCTCCTCCGCAGCCATATACAGGAATACAAGATCTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* * * *
829 CTTCGATCCCCTCCACTGCCAAATTCAGGAAGACAGGATTTGCTAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
* * *
875 CTTCGATCCCTTCCGCTGCCAAATACAGGAAGAAAAGATCTGATAT
1 CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
*
921 CTTCGATCCCCTCCGCGGCCAAATACAGG
1 CTTCGATCCCCTCCGCTGCCAAATACAGG
950 NNNNNNNNNN
Statistics
Matches: 801, Mismatches: 99, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
45 3 0.00
46 797 1.00
47 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (46 bp):
CTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTAT
Found at i:2671 original size:137 final size:138
Alignment explanation
Indices: 2421--2798 Score: 492
Period size: 137 Copynumber: 2.8 Consensus size: 138
2411 NNNATACAGG
* * * * *
2421 AAGACAAGATCAGCTATCTTCAATC-CCCCCACTACCAAATACAGGAAGACAAGATCTGCTATCT
1 AAGACAAGATCTGCTATCTTCGATCACCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCT
* * * * * * *
2485 TCGATCCCCTCCGCTGCCAAATACAAGAAAACATGATTTGCTATCTTCGATCTCCTTCGTTGCCA
66 TCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCA
*
2550 AATATAGA
131 AATAAAGA
* *
2558 AAGACAAGATCTGCTATCTTCGATCACTTTCGCT-CCAAATACAGGAAGACAAGATCTGCTATCT
1 AAGACAAGATCTGCTATCTTCGATCACCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCT
* * * * *
2622 TCTATCTCCTCCGCTGCTAAATACAGGAAGACAAGATCTGTTATTTTCGATCCCCTCCGCTGCCA
66 TCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCA
*
2687 AATAAAGG
131 AATAAAGA
* * * *
2695 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAAGAAAACAAGATCTGATATCT
1 AAGACAAGATCTGCTATCTTCGATCACCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCT
*
2760 TCGATCCCCTCCGCTGCCAAAAAC-GGAAAGACAAGATCT
66 TCGATCCCCTCCGCTGCCAAATACAGG-AAGACAAGATCT
2799 ACAATCTTTG
Statistics
Matches: 208, Mismatches: 30, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
137 145 0.70
138 63 0.30
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (138 bp):
AAGACAAGATCTGCTATCTTCGATCACCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCT
TCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCA
AATAAAGA
Found at i:2806 original size:46 final size:46
Alignment explanation
Indices: 2414--2798 Score: 506
Period size: 46 Copynumber: 8.4 Consensus size: 46
2404 NNNNNNNNNN
* * * *
2414 ATACAGGAAGACAAGATCAGCTATCTTCAATCCCC-CCACTACCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAA
2459 ATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAA
* * * * * * *
2505 ATACAAGAAAACATGATTTGCTATCTTCGATCTCCTTCGTTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAA
* * * * *
2551 ATATAGAAAGACAAGATCTGCTATCTTCGATCACTTTCGCT-CCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAA
* * *
2596 ATACAGGAAGACAAGATCTGCTATCTTCTATCTCCTCCGCTGCTAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAA
* *
2642 ATACAGGAAGACAAGATCTGTTATTTTCGATCCCCTCCGCTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAA
*
2688 ATAAAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAA
* * *
2734 ATACAAGAAAACAAGATCTGATATCTTCGATCCCCTCCGCTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAA
*
2780 AAAC-GGAAAGACAAGATCT
1 ATACAGG-AAGACAAGATCT
2799 ACAATCTTTG
Statistics
Matches: 295, Mismatches: 42, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
45 73 0.25
46 222 0.75
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.24
Consensus pattern (46 bp):
ATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAA
Found at i:3633 original size:46 final size:45
Alignment explanation
Indices: 3564--5129 Score: 1907
Period size: 46 Copynumber: 34.0 Consensus size: 45
3554 NNNNNNNNNN
* * *
3564 TCTGATATCTTCGATCTCCTCCGCAGCCAAATACAGGAAAACAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
* * * *
3610 TCTGATATCTTCGATCCCTTCCGCTGCCAAAAACAAGAAAACAAGA
1 TCTGCTATCTTCGATCCC-TCCGCTGCCAAATACAGGAAGACAAGA
* *
3656 TCTGCTATCTTCGATCTCCTCAGCTGCCAAATTCAGGAAGACAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
*
3702 TCTGCTATCTTCGATCTCCTCCGCTGCCAAATAAAGGAAGACAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
* *
3748 TCTTCTATCTTCGATCTCCTCCGCAGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
* * **
3794 TCTGATATCTTCGATCCCCTGCGCTATCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
*
3840 TCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGGCAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
* * *
3886 TATGCTATCTTCGATCCCCTCCGCCGCCAAATATAGGAAGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
*
3932 TCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGCAGACAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
*
3978 TCTGCTATCTTCGATCCCTTCCACTGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGATCCC-TCCGCTGCCAAATACAGGAAGACAAGA
* * * *
4024 TCTGATATCTTCGATCCCCTCTGCTACCAAATTCAGGAAGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
*
4070 TCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGATAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
* *
4116 TCTGCTATCTTCGATCTCCTCCGCTGCCAAATAAAGGAAAACAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
* * *
4162 TCTGCTATCTTCGATCCCCTCCGCTGCCAAATAGAAGAAAACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
* *
4208 TCTGATATCTTCGATCCCCTCCGCTGCCAAATACAGAAAGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
*** ** *
4254 TCTTAAATCTTCGATCCCCTGTGCTGCCAAATACA-AAATGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAA-GACAAGA
* *
4300 TCTGATATCTTCGATCTCCTCCGTTGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
*
4346 TCTGCTATCTTCGATCCCCTCCACTGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
* * *
4392 TTTGATATCTTCGATCCCCTCCGCTGCCAGATACAGGAAGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
**
4438 TCTGCTATCTTCGATCCCCTTTGCTGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
*
4484 TCTGCTATCTTCGATCTCCTCCGCTTCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
*
4530 TCTGCTATCTTCGATCCCCTCCGCTGCCAAATAGAGGAAGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
* *
4576 TCTGCTATCTTCGATCTCCTCCGCAGCCAAATACAGGAAAACAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
* * * * *
4622 TCTGATATCTTCGATCCCTTCCGCTGGCAAAAACAAGAAAACAAGA
1 TCTGCTATCTTCGATCCC-TCCGCTGCCAAATACAGGAAGACAAGA
4668 TCTGCTATCTT-GTATCCCTTCCGCTGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCG-ATCCC-TCCGCTGCCAAATACAGGAAGACAAGA
* * * * * * * **
4714 TCCGATGTTTTCGTTCCCCTTCGCCGCCAAATACAGGAACTCAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
* **
4760 TATGCTATCTTCGATCCCCTTTGCTGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
* * * * * ** * * * *
4806 TTTGCTTTTTTTGCTTCCCTGGGATGCCAAATACCGGAAGCCAGGA
1 TCTGCTATCTTCG-ATCCCTCCGCTGCCAAATACAGGAAGACAAGA
* *
4852 TAC-CCTATCTTCGA-CCCCCTCGCGTGCCAAATACAGGAAGACAAGA
1 T-CTGCTATCTTCGATCCCTC-CGC-TGCCAAATACAGGAAGACAAGA
* **
4898 TGTGGAATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
* * * *
4944 TTTGATATCTTTGATCCCTTCTGCTGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGATCCC-TCCGCTGCCAAATACAGGAAGACAAGA
*
4990 TCTGCTATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
*
5036 TCTGCTATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGATC-CCTCCGCTGCCAAATACAGGAAGACAAGA
* ** *
5082 TTTGCTATCTTCCTTCCCCTCCGCAGCCAAATACAGGAAGACAAGA
1 TCTGCTATCTTCGAT-CCCTCCGCTGCCAAATACAGGAAGACAAGA
5128 TC
1 TC
5130 CGCTCAATCT
Statistics
Matches: 1333, Mismatches: 158, Indels: 58
0.86 0.10 0.04
Matches are distributed among these distances:
44 3 0.00
45 19 0.01
46 1285 0.96
47 22 0.02
48 4 0.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (45 bp):
TCTGCTATCTTCGATCCCTCCGCTGCCAAATACAGGAAGACAAGA
Done.