Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_804 ID=scaffold_804-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: 4242
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.28
Warning! 652 characters in sequence are not A, C, G, or T
Found at i:556 original size:304 final size:303
Alignment explanation
Indices: 2--1454 Score: 2062
Period size: 303 Copynumber: 4.8 Consensus size: 303
1 G
*
2 CCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTAGGAAGTCCTCGTGTTGCACCCCTCCCA
1 CCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCA
*
67 TTTTATTTCATATAATGTTTTTTTTAGTTACATTTTCTCGACGTGGTGTAACTCATTCGTTATTT
66 TTTTATTTCATATAATGTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTT
** *
132 GCGTTTTGTGAAATAAATAATTTGAAACAATATTTGGTCGAATTTG-CCTCTAAATTGGAGGCGC
131 GCGTTTTGTGAAATAAATAATTTGAAACAATATTTGGTCGAATTTGTATTC-AAATTCGAGGCGC
* * *
196 AACTGCGATAAGGGGCAACCTTTATATGAATAGATTGCGCAAGAATTGACGGGTGCGATCATACC
195 AAGTGCGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACC
*
261 AGCAATAATGCACCGGATCCCATCAGAACTCCGCAGTGAAGCAT
260 AGCAATAATGCACCGGATCCCATCAGAACTCCGCAGTGAAGCGT
305 CCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCA
1 CCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCA
* *
370 TTTTATTTCATATAATGTTTTTATTTAGTTGCATTTTCTCGAGGTGGTGTAACTCATTCGTTACT
66 TTTTATTTCATATAATGTTTTT-TTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATT
* * * * *
435 TACATTTTGTGAAATAAATAATTTGAAATAATATTTGGTCAAATTTGTATTCAAAATCGAGGCTG
130 TGCGTTTTGTGAAATAAATAATTTGAAACAATATTTGGTCGAATTTGTATTCAAATTCGAGGC-G
* * *
500 -AAGTACGATAAGGGGCAGCCTTTTTATGAATATG-TTGCGCAAGAGTTGATGGGTGCGATCATA
194 CAAGTGCGATAAGGGGCAGCCTTTATATGAATA-GATTGCGCAAGAGTTGACGGGTGCGATCATA
* * * * *
563 CCAGCACTAATACACCGGATCCTATCAGAACTTCGAAGTGAAGCG-
258 CCAGCAATAATGCACCGGATCCCATCAGAACTCCGCAGTGAAGCGT
* *
608 CGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAATTCCACGTGTTGCACCCCTCCC
1 C-CTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCC
* * *
673 ATTTTATTTCATATAATGTTTTTTTTAGTTGCATTTTCTCGACTTGCTGTAGCTCATTCGTTATT
65 ATTTTATTTCATATAATGTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATT
* * *
738 TGCGTTTTGTGAAATAAATAATTTGAAACAATATTTTGTCGCATTTGTATTCAAATTCGAGGCTC
130 TGCGTTTTGTGAAATAAATAATTTGAAACAATATTTGGTCGAATTTGTATTCAAATTCGAGGCGC
* * ** ** * * **
803 AAATACGATAAGACGCAAACTTTTTATGAATAGGTTGCGCAAGAGTTGATTGGTGCGATCATACC
195 AAGTGCGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACC
* *
868 AGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGT
260 AGCAATAATGCACCGGATCCCATCAGAACTCCGCAGTGAAGCGT
* ** * * * *
912 GCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTAAGAAGTCCGCTTGTAGAACCCCTCCCA
1 CCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCA
* *
977 TTTTATTTCATATAATG--TTTTTTAGTTGCGTTTTCTCGACGTGGTGTAACTCATTCATTATTT
66 TTTTATTTCATATAATGTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTT
* * * * *
1040 GCGTTTCGTGAAGTAAATAATTTGAAACGATTTTTGGTCGAATTT-TCATTTAAATTCGAGGCGC
131 GCGTTTTGTGAAATAAATAATTTGAAACAATATTTGGTCGAATTTGT-ATTCAAATTCGAGGCGC
* * *
1104 AAGTGCGATAA-GGGCGAGCCTTTAT-TGAAAAGATTGCGTAAGAGTAGACGGGTGCGATCATAC
195 AAGTGCGATAAGGGGC-AGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATAC
*
1167 CAG-AACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGT
259 CAGCAA-TAATGCACCGGATCCCATCAGAACTCCGCAGTGAAGCGT
* * * * *
1212 GCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCTTGGGATGTTCTCGTGTTGCACCCCTCCCT
1 CCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCA
* * * *
1277 TTTTATTTCATATAATGGTTTCTTTAGTTGCGTTTTCTCGACGTGGTTTAACTCATTCGTTATTT
66 TTTTATTTCATATAATGTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTT
* * * * *
1342 GCGTTTTGTGAAATACATAATTTGGAACGATATTTGGTCGAATTTGTATTCAATTTTGAGGCGCA
131 GCGTTTTGTGAAATAAATAATTTGAAACAATATTTGGTCGAATTTGTATTCAAATTCGAGGCGCA
* *
1407 AGTGCGATAAGCGGCAGCCTTTATATGAATAGATTGTGCAAGAGTTGA
196 AGTGCGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGA
1455 NNNNNNNNNN
Statistics
Matches: 1023, Mismatches: 111, Indels: 32
0.88 0.10 0.03
Matches are distributed among these distances:
299 1 0.00
300 149 0.15
301 110 0.11
302 118 0.12
303 372 0.36
304 269 0.26
305 4 0.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (303 bp):
CCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCA
TTTTATTTCATATAATGTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTT
GCGTTTTGTGAAATAAATAATTTGAAACAATATTTGGTCGAATTTGTATTCAAATTCGAGGCGCA
AGTGCGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCA
GCAATAATGCACCGGATCCCATCAGAACTCCGCAGTGAAGCGT
Found at i:2978 original size:303 final size:303
Alignment explanation
Indices: 2307--4242 Score: 2981
Period size: 303 Copynumber: 6.4 Consensus size: 303
2297 ATTTAAATTC
2307 GAGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGC
1 GAGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGC
2372 ACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGAC
66 ACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGAC
* * * * *
2437 TTCCTGGGAAGTCCACGTGTTGCACTCCTCCCATTTTATTTCATATAAT-GTTTTTTTAGTTTCA
131 CTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATATTTTTTTTAGTTGCA
* *
2501 TTTTCCCGTACGTGGTGTAACTCTATTCGTTATTTGCATTTTGTGAAATAAATAATTTGAAACGA
196 TTTTCTCG-ACGTGGTGTAACTC-ATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGA
* *
2566 TATTTTGTCGAATTTGTATTCAAATTCGACGCACAAGTGCGATAA
259 TATTTTGTCGAATTTGTATTCAAATTCGAGGCGCAAGTGCGATAA
* * * *
2611 GAGGCAGCCCTTATATGAATAGATTGCACAACAGTTGACGGGTGCGATAATACCAGCACTAATGC
1 GAGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGC
** *
2676 ACCGGATCATATCAGAACTTCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGAC
66 ACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGAC
* *
2741 CTCCTAGGAAGTCCTCGTGCTGCACCCCTCCCATTTTATTTCATATAATATTTTTTTTAGTTGCA
131 CTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATATTTTTTTTAGTTGCA
*
2806 TTTTCTCGACATGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGATA
196 TTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGATA
* *
2871 TTTTGTCGAATTTGTAATCAAATTCGAGGTGCAAGTGCGATAA
261 TTTTGTCGAATTTGTATTCAAATTCGAGGCGCAAGTGCGATAA
* * *
2914 GAGGCAACCTTTATATGAATAGATTGTGCAAGAGTTGACGGCTGCGATCATACCAGCACTAATGC
1 GAGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGC
* * * *
2979 ACCGTATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGTGAGAGTAGTACTATGATCGGTGAC
66 ACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGAC
* *
3044 CTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCAGATAAT-GTTTTTTTAGGTTGC
131 CTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATATTTTTTTTA-GTTGC
* * * *
3108 GTTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTCGTGAAGTAAATAATTTGGAACGAT
195 ATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGAT
* *
3173 ATTTGGTCGAATTTGTATTCAAATTCGACGCGCAAGTGCGATAA
260 ATTTTGTCGAATTTGTATTCAAATTCGAGGCGCAAGTGCGATAA
* * *
3217 GAGGCAGCCCTTATATGAATAGATTGCGCAACAGTTGACGGGTGCGATAATACCAGCACTAATGC
1 GAGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGC
**
3282 ACCGGATCATATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGAC
66 ACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGAC
3347 CTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATATTTTTTTTAGTTGCA
131 CTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATATTTTTTTTAGTTGCA
*
3412 TTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGAGAAATAAATAATTTGAAACGATA
196 TTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGATA
* *
3477 TTTTTTCGAATTTGTATTCAAATTCGAGGCACAAGTGCGATAA
261 TTTTGTCGAATTTGTATTCAAATTCGAGGCGCAAGTGCGATAA
* * *
3520 GGGGCAACCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCAATAATGC
1 GAGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGC
* * *
3585 ATCGGATCCCATCAGAAGTCCGCAGTTAAGCGTCCTTGGGCGAGAGTAGTACTAGGATGGGTGAC
66 ACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGAC
*
3650 CTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTATTTTAGTTT
131 CTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAAT-ATTTT-TTTTAG-TT
* * * *
3715 GCATTTTTCTCGAAGTGGTGTAACTCATTCGTTACTTACATTTTGTGAAAATAAATAATTTGAAA
193 GCA-TTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTG-AAATAAATAATTTGAAA
* * * * *
3780 CAATATTTGGTCGAATTTGTATTCAAATTCGAGGCTCAAATACGATAA
256 CGATATTTTGTCGAATTTGTATTCAAATTCGAGGCGCAAGTGCGATAA
* * *
3828 GACGCAGCCTTT-TATGAATAGGTTGCGCAAGAGTTGACGGGTGCGATCATACCTGCACTAATGC
1 GAGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGC
* *
3892 ACCGGATCCCATCAAAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGAATGGGTGAC
66 ACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGAC
* * * * *
3957 CTCCTGAGAAGTCCTCTTGTAGCACCCCTCCCATTTTATTTCATAT-A-ATGTTTTTTAGTTGCG
131 CTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATATTTTTTTTAGTTGCA
* * * *
4020 TTTTCTCGAGGTGGTGTAACTCATTCATTATTTGCGTTTTGTGAAGTAAATAATTTGAAACGATT
196 TTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGATA
* * *
4085 TTTTGTCGAATTT-TCATTTAAATTCGAGGCGCCAGTGCAATAA
261 TTTTGTCGAATTTGT-ATTCAAATTCGAGGCGCAAGTGCGATAA
* * *
4128 G-GGCGAGCCTTTAT-TGAAAAGATTGCGTC-AGAGTAGACGGGTGCGATCCTACCAGCACTAAT
1 GAGGC-AGCCTTTATATGAATAGATTGCG-CAAGAGTTGACGGGTGCGATCATACCAGCACTAAT
*
4190 GCACCGGATACCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTA
64 GCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTA
Statistics
Matches: 1486, Mismatches: 134, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
299 3 0.00
300 153 0.10
301 40 0.03
302 12 0.01
303 793 0.53
304 195 0.13
305 26 0.02
306 6 0.00
307 190 0.13
308 68 0.05
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (303 bp):
GAGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGC
ACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGAC
CTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATATTTTTTTTAGTTGCA
TTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGATA
TTTTGTCGAATTTGTATTCAAATTCGAGGCGCAAGTGCGATAA
Done.