Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_963 ID=scaffold_963-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: 2774
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.18
Warning! 867 characters in sequence are not A, C, G, or T
Found at i:244 original size:132 final size:132
Alignment explanation
Indices: 1--897 Score: 1348
Period size: 132 Copynumber: 6.8 Consensus size: 132
* *
1 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCATAAAGCCTTGTCTCTCTAAGTAG
1 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAG
* *
66 CAGCGGAGAAGGATGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATG
66 CAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
131 GC
131 GC
* * *
133 AAAT-TATATCTTTCCAAGATAGTGGGAAGCATATTTAAGCCATAAAGCCTTGTCTCTCTGAGCA
1 AAATCT-TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGTA
* *
197 GCAGCGGAAAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGAT
65 GCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
*
262 GGT
130 GGC
* * * *
265 AAATCTTATATTTCCAAGATAGTGGAAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTGAGCAG
1 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAG
*
330 CAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATG
66 CAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
*
395 TC
131 GC
*
397 AAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAG
1 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAG
* * ** * * *
462 TAGTGGAGAAGGTTGAAGATTGTCTACCTTATATCCCTAAGCAGTAGTGGAGCAGATCAAAGACG
66 CAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
*
527 AC
131 GC
* * * *
529 AAATCTTATGTTTCCAAGATAGTGGGAAGCAGACTTAAGCCACCAAGCCTTGTCTCCCTGAGTAG
1 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAG
* ** * * *
594 TAGCAAAGTAGGTTGAAGATTGTAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGTTCAAAGATG
66 CAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
*
659 GG
131 GC
* *
661 AAAT-TGTAGATCTTTCGAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTAGTCTCTCTGAG
1 AAATCT-T--ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAG
* * *
725 CAGCAGCGGAGAAGGTTGAAGATTGGAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAG
63 TAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAG
790 ATGGC
128 ATGGC
* *
795 AAATCTTATCTTTCGAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTGGTCTCTCTGAGTAG
1 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAG
*
860 CTGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT
66 CAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT
898 NNNNNNNNNN
Statistics
Matches: 690, Mismatches: 69, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
131 2 0.00
132 572 0.83
133 1 0.00
134 114 0.17
135 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (132 bp):
AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAG
CAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
GC
Found at i:2154 original size:132 final size:132
Alignment explanation
Indices: 1765--2774 Score: 1535
Period size: 132 Copynumber: 7.7 Consensus size: 132
1755 NNNNNNNNNN
* *
1765 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTG-AGATTGTAGATCTTAT
1 ATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTAT
* * * *
1829 CTCCCTAAACAGTAGTGGAGCATATCAAAGTTGGTAAATCTTATCTTTCCAAGATAGTGGGAAGC
66 CTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGC
*
1894 GG
131 AG
* * * *
1896 ATTTAAGCCACAAATCCTTGTCTCTCTGAGCAGCAGTGGAGAAGGTTGAAGATTTTAGATCTTAT
1 ATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTAT
* *
1961 CT-CCTAAGCAGTAGTGGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGT
66 CTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGC
*
2025 AA
131 AG
* * ** * * *
2027 ATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAGCAGCACAGAATGTTGAATATTGTAGATCTGAT
1 ATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTAT
* * *
2092 CTCCCTAAGCAGAAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGC
66 CTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGC
2157 AG
131 AG
* * *
2159 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGATGATTGTAGATCTTAT
1 ATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTAT
* * *
2224 CTCCCTAAGCAGTAGTGGAGCAGATAAAAGATGGTAAATCTTATCTTTGCAAGATAGTGGGAAGC
66 CTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGC
2289 AG
131 AG
* * * *
2291 ATTTAAGCCACAAAGCCTTGTCTCTCTAAGCAGCAGCGGAGAAGGTTCAAAATTGTAGATCTTAT
1 ATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTAT
*
2356 CTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGC
66 CTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGC
2421 AG
131 AG
* * *
2423 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAGATCTTAT
1 ATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTAT
*
2488 CTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGCAAAT-TATATCTTTCCAAGATAGTGGGAAG
66 CTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCT-TATCTTTCCAAGATAGTGGGAAG
*
2552 CAT
130 CAG
* * *
2555 ATTTAAGCCATAAAGCCTTGTCTCTCTGAGCAGCAGCGGAAAAGGTTGAAGATTGTAGATCTTAT
1 ATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTAT
* * * *
2620 CTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGTAAATCTTATATTTCCAAGATAGTGGAAAGC
66 CTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGC
2685 AG
131 AG
*
2687 ATTTAAGCCAAAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTG-AGA-TGTAGATCTTAT
1 ATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTAT
*
2750 CTCCCTAAGCAGTAGTGGAGTAGAT
66 CTCCCTAAGCAGTAGTGGAGCAGAT
Statistics
Matches: 794, Mismatches: 81, Indels: 9
0.90 0.09 0.01
Matches are distributed among these distances:
130 35 0.04
131 161 0.20
132 597 0.75
133 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (132 bp):
ATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTAT
CTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGC
AG
Found at i:2397 original size:44 final size:44
Alignment explanation
Indices: 2349--2526 Score: 110
Period size: 44 Copynumber: 4.0 Consensus size: 44
2339 AAAATTGTAG
2349 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAA
* ** ****
2393 ATCTTATCTTTCC-AAG--ATAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAATAGT-GG-AGCAGATCAAAGATGGCAA
** * * * * * * ** * * *
2437 GCCTTGTCTCCCTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAA
* *
2481 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAA
2525 AT
1 AT
2527 TATATCTTTC
Statistics
Matches: 94, Mismatches: 34, Indels: 12
0.67 0.24 0.09
Matches are distributed among these distances:
42 5 0.05
43 5 0.05
44 76 0.81
45 5 0.05
46 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAA
Done.