Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_695 ID=scaffold_695-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: 6429
ACGTcount: A:0.20, C:0.21, G:0.11, T:0.18
Warning! 1896 characters in sequence are not A, C, G, or T
Found at i:1189 original size:46 final size:46
Alignment explanation
Indices: 92--1173 Score: 1431
Period size: 46 Copynumber: 23.6 Consensus size: 46
82 ATTTATAAGA
* * *
92 AAGACAAGATATGCAATCTTCGAT-TCCT-CGCT-CGC-AATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGC-CAAATACAGG
* * *
135 AAGACAAGATCTGCTATCCTCGATCTCCTCCGCTGCCAAATACATG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * **
181 AAGATAAGATCTACTATCTTCGATCCCCTGTGCTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* *
227 AAGACAAGATCTGCTATCTTCGATCCACTCCGTTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * * * * * * *
273 AAAACATGACCTCCTATCTTCGATCTCCTTCGTTGCCAAATATAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
319 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCT-CCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * *
364 AGGACAAGATCTACTATCTTTGATCCCCTCCGCTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * * * **
410 AAGACAAGATCTGATATCTTCAATCCCTTTCGCTGCCAAATTTAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* *
456 AAGACAAGATCTGATATCTTCGATCCCCTCTGCTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
*
502 AAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * * *
548 AAGACAAGATCTGGTATCTTCGATCCCCTCTGCTTCCAAATACAGC
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * *
594 AAGATAAGATCTGTTATCTTCGATCCCCTTCGCTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * * *
640 AAGACAAGATCTGATATCTTTGATCCCCTCTGCTGCCAATTACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * *
686 AAGACAATATCTGCTATCTTCGATCTCCTCTGCTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* *
732 AAGGCAAGATCTGCTATCTTCGATCCCCTTCGCTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* *
778 AAGACAAGATCTGGTATCTTCGATCCCCTCTGCTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * * *
824 AAGACAAGATCTGGTATCTTCGATCCCCTCTGCTTCCAAATACAGC
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * * * *
870 TAGACAAGATCTGTTGTCTTCAATCCCCTTCGCTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * *
916 AAGACAATATCTGCTATCTTCGATCTCCTCTGCTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * *
962 AAGGCAAGATCTGCTATCTTCGATCCCTTCCGCT-CCAAATATAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * *
1007 AACACAAGATCTGCTATCTTCGATCCCCTCTGCTACCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
* * * *
1053 AAGACAAGATCCGCTATCTCCGATCTCCTCCCCTGCCAAATACAGG
1 AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
*
1099 AAGA-ATAGATTTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
1 AAGACA-AGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
*
1145 AAGACAAGATCTGATATCTTCGATCCCCT
1 AAGACAAGATCTGCTATCTTCGATCCCCT
1174 TTACTACCAA
Statistics
Matches: 903, Mismatches: 128, Indels: 13
0.86 0.12 0.01
Matches are distributed among these distances:
43 21 0.02
44 4 0.00
45 87 0.10
46 790 0.87
47 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (46 bp):
AAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGG
Found at i:2024 original size:46 final size:46
Alignment explanation
Indices: 1957--2591 Score: 819
Period size: 46 Copynumber: 13.8 Consensus size: 46
1947 NNNNNNNNNN
*
1957 TGCCATATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
* * * *
2003 TGCCACATACAGGAAGACAAGATCTGCTACCTTCGATCTCCT-TCAC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCT-GC
* * *
2049 TGCCAAATACAGGAAGACAAGATCAGGTATCTTCGATCCCTTCTGC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
* * ** *
2095 TGCCAAATACAGGAAGACAAGATTTGCTCTCTTCTTTCCCCTCCGC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
* * * * *
2141 TGCCAAATACAGGAAGACAAGATTTGCTCTCTTTGATCCCCTTTAC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
* *
2187 TGCCAAATACAGGAAGACAACATCTGCTATCTTCGATCTCCTCTGC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
* * *
2233 TGCCAAATACAGGAAGGCAAGATCTGCTATCTTCGATCCCGTCCGC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
* *
2279 T-CCAAATATAGGAACACAAGATCTGCTATCTTCGATCCCCTCTGC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
* * * * *
2324 TGCCCAATACAGGCAA-ACAAGATTTGCTATCTTCGTTCGCCTCCGC
1 TGCCAAATACAGG-AAGACAAGATCTGCTATCTTCGATCCCCTCTGC
* * * * **
2370 TGCCAAATACAGGAAGACAAGATCCGCTATCTCCAATCTCCTCCCC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
* *
2416 TGCCAAATACAGGAAGA-ATAGATTTGCTATCTTCGATCCCCTCCGC
1 TGCCAAATACAGGAAGACA-AGATCTGCTATCTTCGATCCCCTCTGC
* * *
2462 TGCCAAATACAGGAAGACAAGATGTGATATCTTCGATCCCTTCTGC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
*
2508 TGCCATATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
* *
2554 TGCCACATACAGGAAGACAAGATCTGCTACCTTCGATC
1 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATC
2592 TCCTTCACTG
Statistics
Matches: 510, Mismatches: 72, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
45 44 0.09
46 462 0.91
47 4 0.01
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (46 bp):
TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCTGC
Found at i:2922 original size:46 final size:46
Alignment explanation
Indices: 2855--3328 Score: 680
Period size: 46 Copynumber: 10.3 Consensus size: 46
2845 AATAGATTTC
* *
2855 CTATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGATCTG
1 CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTG
* * *
2901 CTATCTTCGATCCCCTCTGCTGCCAAATACAGGCAGACAAGATTTG
1 CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTG
* * *
2947 CTATCTTCGTTCCCCTCCACTGCCAAATACAGGAAGACAAGATCCG
1 CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTG
* * * * *
2993 TTATCTTCGATCTCCTCCCCTGCCAAATGCAGGAAGA-ATAGATTTG
1 CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACA-AGATCTG
*
3039 CTATCTTCGATCCCCTCCGCTACCAAATACAGGAAGACAAGATCTG
1 CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTG
* *
3085 CTATCTTCGATCCCCTCTGCTGCCACATACAGGAAGACAAGATCTG
1 CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTG
* *
3131 CTATCTTCGATCTCCTTCGCTGCCAAATACAGGAAGACAAGATCTG
1 CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTG
* * *
3177 GTATCTTCGATCCCCTCTGCTGCCAAATACAGGAAGACAAGATTTG
1 CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTG
* ** *
3223 CTCTCTTCTTTCCCCTCCGCTGCCAAATACAGGAAGACAAGATTTG
1 CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTG
*
3269 CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATTTG
1 CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTG
* *
3315 ATATCTTCAATCCC
1 CTATCTTCGATCCC
3329 TTNNNNNNNN
Statistics
Matches: 382, Mismatches: 44, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.00
46 380 0.99
47 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.26
Consensus pattern (46 bp):
CTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTG
Found at i:4230 original size:46 final size:46
Alignment explanation
Indices: 4128--6407 Score: 2060
Period size: 46 Copynumber: 49.0 Consensus size: 46
4118 NNNNNNNNNN
* * * *
4128 GAAGGCAAGATCTGCTATCTTCGATCCCTTCCGCT-CCAAATATAA
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
4173 GAACACAAGATCTGCTATCTTCGATCCCCTCTGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * *
4219 GAAGACAAGATCCGCTATCTCCGATCTCCTCCCCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
4265 GAAGA-ATAGATTTACTATCTTCGATCCCCTCCGCTGCCAAATACAG
1 GAAGACA-AGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *** *
4311 GAAGACAAGATCTGATATCTTCGATCCCCTTTACTACCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
4357 AAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATAC-AG
* *** *
4404 GAAGACCAAGGATCTGATATCCTTCGATCCCCTTTACTACCCAAATTACAAG
1 GAAGA-CAA-GATCTGCTAT-CTTCGATCCCCTCCGCT-GCCAAA-TAC-AG
*
4456 AAAGACAAGATCTTGCTATCCTTCGATCCCCCTCCGCTGCCCAATATACAAG
1 GAAGACAAGATC-TGCTAT-CTTCGAT-CCCCTCCGCTG-CCAA-ATAC-AG
4508 GAAGACCAAGGATCTGCTATCCTTCGATCCCCTTCCGCTGCCCAAATTACAAG
1 GAAGA-CAA-GATCTGCTAT-CTTCGATCCCC-TCCGCTG-CCAAA-TAC-AG
*
4561 GAAGACAAGATCTTGCTATCCTTCGATCCCCCTCCGCTACCCAAAATACAG
1 GAAGACAAGATC-TGCTAT-CTTCGAT-CCCCTCCGCT-GCC-AAATACAG
*
4612 GAAGACAAGATCTGCTATCTTCGATCCCTTCCGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
4658 GAACACAAGATCTGCTATCTTCGATCCCCTCCGCTACCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
4704 GAAGACAAGATCTGATATCTTCGATCCCCTCTGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
4750 GAAGACAAGATCTGGTATCTTCGATCCCCTCTGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
4796 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCAGCCAAATATAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
*
4842 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATATAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * *
4888 GAAAACATGATCTGCTATCTTCGATCTCCTTCGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * *
4934 GAAGGCAAGATCTGATATCATCGATCCCCTCAGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
*
4980 GAAGACGAGATCTGCTATCTTCGA-CCCCTTCCGCT-CCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCC-TCCGCTGCCAAATACAG
* *
5025 GAACACAAGATCTACTATCTTCGATCCCCTCCGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
*
5071 GAAGACGAGATCTGCTATCTTCGA-CCCCTTCCGCT-CCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCC-TCCGCTGCCAAATACAG
* *
5116 GAACACAAGATCTACTATCTTCGATCCCCTCCGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * ** * *
5162 GCAGACAAGATTTGCTCTCTTCTTTCCCCTCCACTGTCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
5208 GAAGACAAGATTTGCTATCTTCGATCTCCTCCGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * * * * * *
5254 GAAGACAAGATTTGATATCTTCAATCACTTTCGCTGCGAAATTCAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
5300 GAAGACAAGATCTGATATCTTCGATCCCCTCTGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
5346 GAAGACAAGATCTGCTATCTTCGATCTCCTCTGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* ** *
5392 GAAGACAAGATCTGCTATCTTCCATCCTTTCCGCT-CCAAATATAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * * *
5437 GAACACAAGATCTGCTATCTTTGATCCCTTCTGCTGCTAAATACA-
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * *
5482 GACAGACAAGATTTGCTATCTTCGTTCCCCTCCACTGCCAAATACACGG
1 GA-AGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACA--G
* * *
5531 GAAGACAAGATCCGCTATCTTCGATCTCCTCCCCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
************************************
5577 GAAGACAAGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 GAAGACAAGA----TCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
**********************************************
5627 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
************** * *
5673 NNNNNNNNNNNNNNCTATCTTCGATCTCCTCCCCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
*
5719 GAAGA-ATAGATTTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
1 GAAGACA-AGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * * *
5765 GAAGACAAGATGTGATATCTTCGATCCCTTCTGCTGCCATATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
5811 GAAGACAAGATCTGCTATCTTCGATCCCCTCTGCTGCCACATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * *
5857 GAAGACAAGATCTGCTACCTTCGATCTCCTTCACTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * *
5903 GAAGACAAGATCAGGTATCTTCGATCCCTTCTGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * **
5949 GAAGACAAGATTTGCTCTCTTCTTTCCCCTCCGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
*
5995 GAAGACAAGATTTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * * * * *
6041 GAAGACAAGATTTGATATCTTCAATCCCTTTCGCTGCGAAATTCAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * *
6087 GAAGACAAGATCTGATATCTTCGATCCCCTCTGCTACCAAATAGAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
6133 GAAGACAAGATCTGCTATCTTCGATCTCCTCTGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * *
6179 GAAGGCAAGATCTGCTATCTTCGATCCCTTCCGCT-CCAAATATAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* *
6224 GAACACAAGATCTGCTATCTTCGATCCCCTCTGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * *
6270 GCAGACAAGATTTGCTATCTTCGTTTCCCTCCGCTGCCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * * *
6316 GAAGACAAGATCTGGTATCTTCGATCCCCTCTGCTGCCAAATATAA
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
* * *
6362 GAACACAAGATCTGCTATCTTCGATCCCCTCTGCTACCAAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
6408 CTTCTTTCCC
Statistics
Matches: 1873, Mismatches: 323, Indels: 77
0.82 0.14 0.03
Matches are distributed among these distances:
45 195 0.10
46 1422 0.76
47 10 0.01
48 50 0.03
49 18 0.01
50 23 0.01
51 39 0.02
52 64 0.03
53 48 0.03
54 4 0.00
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.24
Consensus pattern (46 bp):
GAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAG
Done.