Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_454 ID=scaffold_454-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: 8628
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.20
Warning! 1841 characters in sequence are not A, C, G, or T
Found at i:643 original size:307 final size:303
Alignment explanation
Indices: 1--646 Score: 827
Period size: 303 Copynumber: 2.1 Consensus size: 303
* **
1 CTTGCGCAATCTATTCATATTAAGGCTGCCCCTTATCGCACTTGCGCCTCGAAATTGAAGCCAAA
1 CTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAAATGCGCCTCGAAATTGAAGCCAAA
** * * * *
66 TTCGACCAAATATCGTTTCAAATTATTTATTTCGCACGACGCAAATCACGAATGTGTTACTCTAC
66 TTCGACCAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCAC
* * *
131 GTGGTGAAAATGCAACTAAAGGAAATATTATATGAAATAAAATGGGAGGGGTGCAACACGATGGC
131 GTGGAGAAAATGCAACTAAAAGAAACATTATATGAAATAAAATGGGAGGGGTGCAACACGATGGC
* * * * * *
196 TTCCCAGGAGGTCATCCATCCTCGTACTACTCTCGCCCAAAAACGCTTCAATGCGGAGTTCTGAT
196 TTCCCAGGAGGTCACCCATCCTAGTACTACACTCACCCAAAAACGCCTCAATACGGAGTTCTGAT
* *
261 GGGATACCATGTATTAGTGCTAGTATGATCGCACCCGTCAACT
261 GGGATACCATGCATTAGTGCTAGTATGAGCGCACCCGTCAACT
* * * * * *
304 CTTGTGCAATCTACTCATATAAAGGTTGCCCCTTATCGCAAATGCGCCTCGTATTTTAATG-CAA
1 CTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAAATGCGCCTCGAAATTGAA-GCCAA
368 ATTCGACCAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCA
65 ATTCGACCAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCA
* **
433 CGTGGAGAAAATGCAACTAACAA-AGAACATTGTATGAAATAATGTGGGAGGAGGGATGCAACAC
130 CGTGGAGAAAATGCAACTAA-AAGA-AACATTATATGAAATAAAATGGGA-G-GGG-TGCAACAC
* **
497 GA-GGACTTCCCAGGAGGTCACCCATCCTAGTACTACAGTCACCCAAGCACGCCT-AACTAC-GA
190 GATGG-CTTCCCAGGAGGTCACCCATCCTAGTACTACACTCACCCAAAAACGCCTCAA-TACGGA
* * * *
559 CGTTTTGATGGGAT-CCGGTGCATTAGTGCTGGTATGAGCGCACCCGTGAACT
253 -GTTCTGATGGGATACC-ATGCATTAGTGCTAGTATGAGCGCACCCGTCAACT
*
611 CTTGCGCAATCTATTCATATAAATGCTGCCCCTTAT
1 CTTGCGCAATCTATTCATATAAAGGCTGCCCCTTAT
647 AGCACTNNNN
Statistics
Matches: 293, Mismatches: 40, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
303 132 0.45
304 22 0.08
305 1 0.00
306 11 0.04
307 127 0.43
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (303 bp):
CTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAAATGCGCCTCGAAATTGAAGCCAAA
TTCGACCAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCAC
GTGGAGAAAATGCAACTAAAAGAAACATTATATGAAATAAAATGGGAGGGGTGCAACACGATGGC
TTCCCAGGAGGTCACCCATCCTAGTACTACACTCACCCAAAAACGCCTCAATACGGAGTTCTGAT
GGGATACCATGCATTAGTGCTAGTATGAGCGCACCCGTCAACT
Found at i:2389 original size:304 final size:304
Alignment explanation
Indices: 1840--5671 Score: 3759
Period size: 304 Copynumber: 12.4 Consensus size: 304
1830 NNNNNNTCTA
* * * * *
1840 TTCATATAAAGGCTGCCCCTTATAGCACTTCCGCCTCGAATTTGAAGGCAAATTCGACCAAATAG
1 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
* * * *
1905 CATTTCAAATTATTTATTTCGCAAAACGTAAATAACGAATGAGTTATACCACGTAGAGAAAATGC
66 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
* * * *
1970 AACTAACAAAAAACATTAAATGAAATAAAGTGCGAGCGGTGTAACACGAGGACTTCCCAGGAGGT
131 AACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGT
* *
2035 CACCCATCCTAGTACTACTCTCGCCCAAGCATGCTTAACTACGGCATTTTGATAGGATCCAGTGC
196 CACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTACGGCATTTTGATAGGATCCGGTGC
* *
2100 ATTATTGCTGGTATGATCTCACCCGTCAACTCTTGCGCAATCTG
261 ATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTG
** * * *
2144 TTCATATAAAGGCAACCCCTTATTGGAGTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
1 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
* * * * * *
2209 CGTTTCAATTTATTTATTTTGCAAGACGCAAATAACAAAAGAGTTGCACCACGTGGAGAAAATGC
66 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
* * *
2274 AACTAACAAAAAACATTATATGAAATAATGTGGGAGGGGTGCAACACGAGGACTTCCCAAGACGT
131 AACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGT
** * *
2339 CACCCATCCTAGTACTACAGTCACCCAAGCACGCTTAACTACGGCATTTTGATACGATCCGGTGC
196 CACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTACGGCATTTTGATAGGATCCGGTGC
2404 ATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATC-G
261 ATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTG
* * * *
2447 ATTCATATAGAGGCTGCCCCTTATCGCACTTCCGCCTCGAATTTGAAGGCAAATTCGACCAAATA
1 -TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATA
* * * * * * * *
2512 TCATTTCAATTTATTTATTTTGCAAGACACAAATAACAAAAGAGTTGCACCACGTTGGAAGTAAA
65 TCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACG-TGG-AG-AAA
* * *
2577 ATTGCCAACTAA-AAAAATC-TTATATGAAATAAAATGGGAGGGGTGCAACACGAGGACTTCTCA
127 A-TG-CAACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACTTCCCA
* * * * *
2640 GGAGGTCACCCATCCTAGTATTACTCTCGCCCGAGCACGCTTAACTGCGG-AGTTCTGATGGGAT
190 GGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTACGGCA-TTTTGATAGGAT
* *
2704 CCGGTGCATTAGTGCTGGTATGATCTCACCCGTCAACTCTTACGCAATCTG
254 CCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTG
* *
2755 TTCATATAAAGGCTGCCCCTTATCGGAGTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
1 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
2820 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
66 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
* *
2885 AACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAAGACGAGGACTTCGCAGGAGGT
131 AACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGT
* * ** * *
2950 CACACATCCTAGGACTACTCTCGCCTTAGCACGCTTAACTACGGCGTTTTGATCGGATCCGGTGC
196 CACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTACGGCATTTTGATAGGATCCGGTGC
* * *
3015 ATTAGTGCTGATATGATCGCACCCGTCAACTCTTGCGCAATGTA
261 ATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTG
* * * *
3059 TTCATATAAAGGCTACCCCTTATCGAACTTTCGCCTCGAATTTTAATGCAAGTTCGACCAAATAT
1 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
*
3124 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGT
66 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
* * *
3189 AACTAACAAAAAACGTTAAATGAAATAAAGTGGGAGCGGTGCAACACGAGGACTTCCCAGGAGGT
131 AACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGT
* * *
3254 CACCCATCCTAGTACTACTCTCGCCCAAGCATGCTTAACTGCGGCGTTTTGATAGGATCCGGTGC
196 CACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTACGGCATTTTGATAGGATCCGGTGC
* *
3319 ATTAGTGCTGGTATGATCTCACCCGTCAACTCTTGCACAATCTG
261 ATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTG
* * *
3363 TTCATATAAAGGCAGCCCCTTATCGAAGTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
1 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
* * *
3428 CGTTTGAAATTATTTATTTCGCAAAACGAAAATAACGAATGAGTTACACCATGTGGAGAAAATGC
66 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
* * * *
3493 AATTAATAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACATCGCAGGAGGT
131 AACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGT
* * * * * * *
3558 CATCCATCCTAGGACTACTCTCGCCCTAGCACGCTCAACTACGTCGTTTAGATAGGATCCGGTGC
196 CACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTACGGCATTTTGATAGGATCCGGTGC
* * * *
3623 ATTAGAGCAGGTATGATCTCACCCGTCAACTCTTGCGAAATCTG
261 ATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTG
3667 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
1 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
* * * * ****
3732 CGTGTCAAATTATTTATTTCGCAAAACGCAAATAACGATTCAGTTACACTACGTGGAGNNNNNNN
66 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAG---AAAA
*****************************************************************
3797 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
128 TGCAACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACTTCCCAGGA
**************************** * * * * *
3862 NNNNNNNNNNNNNNNNNNNNNNNNNNNNCACG-AGGACTTCCCAGGACGTCAC-CCATCCTAGTA
193 GGTCACCCATCCTAGTACTACTCTCGCCCAAGCACG-CTT---A--AC-T-ACGGCAT-TTTG-A
* * ** * * * * * * * * * * *
3925 CTACAGTCACCCAAGCACGCCTAACTACGAC-GTTTTGATGGGATCCGGTGCATTAGTGCTGGTG
248 -T--AG-GATCC--G-GTGCATTAGT--G-CTGGTATGATCGCA-CCCGT-CA--ACT-CTTGCG
** *
3989 TGAGC-G
298 CAATCTG
** *** * ** ** ** ** * ** *** * *
3995 CACCCGTGAACTCTTGCGCAATCTATTCATATCAAGGCTGCCCCTTATAGCACTTCCGCCTCGAA
1 TTCATATAAAGGC-TGC-CCCT-TA-TCGCA-C-TTGC-GCCTCGAATTTTA-AT--G---CAAA
* * * *
4060 TTTGAAGGCAAATTCGACCAAATAGCATTTCAAATTATTTATTTCGCAAAACGTAAATAACGAAT
53 TTCG-A--C---------CAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAAT
* * * * *
4125 GAGTTATACCACGTAGAGAAAATGCAACTAACAAAAAACATTAAATGAAATAAAGTGCGAGCGGT
106 GAGTTACACCACGTGGAGAAAATGCAACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGT
* *
4190 GTAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCATGCTTAACT
171 GCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACT
* * *
4255 ACGGCATTTTGATAGGATCCAGTGCATTATTGCTGGTATGATCTCACCCGTCAACTCTTGCGCAA
236 ACGGCATTTTGATAGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAA
4320 TCTG
301 TCTG
** * * *
4324 TTCATATAAAGGCAACCCCTTATTGGAGTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
1 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
* * * * * *
4389 CGTTTCAATTTATTTATTTTGCAAGACGCAAATAACAAAAGAGTTGCACCACGTGGAGAAAATGC
66 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
* * * *
4454 AACTAACAAAAAACAGTATATGAAATAAAATGGGAGGGGTGCAACACGAGGACTTCCTAAGAGGT
131 AACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGT
* * * * * * ***
4519 CACCCATCCTAGTACAACTTTCGTCCAAGCACGCTTAACTGCGG-AGTTTTGATGGGGTCAACTG
196 CACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTACGGCA-TTTTGATAGGATCCGGTG
* * * *
4583 CATTAGTGCTGGTGTGATCGCTCCCGTCAACTGTTGCGCAATCTA
260 CATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTG
* * * *
4628 TTCATATAGAGGCTGCCCCTTATCGCACTTGCGCCTCGAAATTGAATGTAAATTCGACCAAATAT
1 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
* ** * * * *
4693 CATTTCAAATTATTTATTTCGCACGACGCAAATCACGAATGTGTTACTCTACGTGGAGAAAATGC
66 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
** * *
4758 AACTAA-AGGAAATATTATATGAAATAAAATGGGAGGGGTGCAACACGATGG-CTTCCCAGGAGG
131 AACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGA-GGACTTCCCAGGAGG
* * * * * * * * *
4821 TCATCCATCCTCGTACTACTCTCGCCCAAACACGCTTCAGTGCGG-AGTTCTGATGGGATACC-A
195 TCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTACGGCA-TTTTGATAGGAT-CCGG
* * * *
4884 TGTATTAGTGCTAGTATGATCGCACCCGTCAACTCTTGTGCAATCTA
258 TGCATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTG
* * ** *
4931 CTCATATAAAGGTTGCCCCTTATCGCAAATGCGCCTCGTATTTTAATGCAAATTCGACCAAATAT
1 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
*
4996 CGTTTCAAATTATTTATTTCGCAAAATGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
66 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
* *
5061 AACTAACAAAAAACATTGTATGAAATAATGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGT
131 AACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGT
** * * * * * *
5126 CACCCATCCTAGTACTACAGTCACCCAAGCACGCCTAACTACGACGTTTTGATGGGACCCGGTGC
196 CACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTACGGCATTTTGATAGGATCCGGTGC
* * * *
5191 ATTAGTGCTGGTATGAGCGAACCCGTGAACTCTTGCGCAATCTA
261 ATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTG
* * * * *
5235 TTCATATAAAGGCTGCCCCTTATAGCACTTCCGCCTCGAATTTGAAGGCAAATTCGACCAAATAG
1 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
*
5300 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACTTGGAGAAAATGC
66 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
* * * *
5365 AACTAACAAAAAACATTAAATGAAATAAAGTGGGAGCGGTGTAACACGAGGACTTCTCAGGAGGT
131 AACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGT
* * *
5430 CACCCATCCTAGTACTACTCTCGCCCAAGCATGCTTAAC-ATTGGCGTTTTGATAGGATCCGGTG
196 CACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTA-CGGCATTTTGATAGGATCCGGTG
* *
5494 CATTAGTGCTGGTATGATCTCACCCGTCAACTCTTGCGCAATCTA
260 CATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTG
* *
5539 TTCATATAAAGGCTGCCCCTTATCGGAGTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
1 TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
*
5604 CGTTTCAAATTACTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
66 CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
5669 AAC
131 AAC
5672 ACGAGGACTT
Statistics
Matches: 2830, Mismatches: 622, Indels: 152
0.79 0.17 0.04
Matches are distributed among these distances:
302 7 0.00
303 272 0.10
304 2047 0.72
305 5 0.00
306 8 0.00
307 251 0.09
308 9 0.00
309 7 0.00
310 1 0.00
312 2 0.00
313 4 0.00
314 5 0.00
315 2 0.00
316 7 0.00
318 2 0.00
319 4 0.00
321 2 0.00
322 11 0.00
323 2 0.00
324 8 0.00
325 7 0.00
326 4 0.00
327 2 0.00
328 15 0.01
329 17 0.01
330 2 0.00
331 4 0.00
332 8 0.00
333 9 0.00
334 2 0.00
335 12 0.00
336 1 0.00
338 4 0.00
339 2 0.00
341 7 0.00
342 2 0.00
343 4 0.00
344 5 0.00
345 2 0.00
347 1 0.00
350 6 0.00
351 2 0.00
353 56 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.25
Consensus pattern (304 bp):
TTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATAT
CGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAATGC
AACTAACAAAAAACATTATATGAAATAAAGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGT
CACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTACGGCATTTTGATAGGATCCGGTGC
ATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTG
Found at i:5897 original size:261 final size:262
Alignment explanation
Indices: 5407--5932 Score: 851
Period size: 261 Copynumber: 2.0 Consensus size: 262
5397 GGAGCGGTGT
* * * *
5407 AACACGAGGACTTCTCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCATGCTTAACATT
1 AACACGAGGACTTCGCAGGAGGTCACCCATCCTAGGACTACTCTCGCCCAAGCACGCTTAACATC
* *
5472 GGCGTTTTGATAGGATCCGGTGCATTAGTGCTGGTATGATCTCACCCGTCAACTCTTGCGCAATC
66 GGCGTTTTGATAGGATCCGGTGCATTAGTGCTGATATGATCGCACCCGTCAACTCTTGCGCAATC
* *
5537 TATTCATATAAAGGCTGCCCCTTATCGGAGTTGCGCCTCGAATTTTAATGCAAATTCGACCAAAT
131 TATTCATATAAAGGCTACCCCTTATCGGACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAAT
*
5602 ATCGTTTCAAATTACTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAAT
196 ATCGTGTCAAATTACTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAAT
5667 GC
261 GC
* *
5669 AACACGAGGACTTCGCAGGA-GTCATCCATCCTAGGACTACTCTCGCCCTAGCACGCTTAAC-TA
1 AACACGAGGACTTCGCAGGAGGTCACCCATCCTAGGACTACTCTCGCCCAAGCACGCTTAACAT-
* * *
5732 CGGCGTTTTGATCGGATCCGGTGCATTAGTGCTGATATGATCGCACCCGTCAAGTCTTGCGTAAT
65 CGGCGTTTTGATAGGATCCGGTGCATTAGTGCTGATATGATCGCACCCGTCAACTCTTGCGCAAT
* * *
5797 GTATTCATATAAAGGCTACCCCTTATC-GATCTTTCGCCTCGAATTTTAATGCAAATTCGGCCAA
130 CTATTCATATAAAGGCTACCCCTTATCGGA-CTTGCGCCTCGAATTTTAATGCAAATTCGACCAA
*
5861 ATATCGTGTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAA
194 ATATCGTGTCAAATTACTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAA
5926 ATGC
259 ATGC
5930 AAC
1 AAC
5933 TAACAAAAAA
Statistics
Matches: 244, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
260 3 0.01
261 222 0.91
262 19 0.08
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (262 bp):
AACACGAGGACTTCGCAGGAGGTCACCCATCCTAGGACTACTCTCGCCCAAGCACGCTTAACATC
GGCGTTTTGATAGGATCCGGTGCATTAGTGCTGATATGATCGCACCCGTCAACTCTTGCGCAATC
TATTCATATAAAGGCTACCCCTTATCGGACTTGCGCCTCGAATTTTAATGCAAATTCGACCAAAT
ATCGTGTCAAATTACTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAAT
GC
Found at i:6198 original size:565 final size:566
Alignment explanation
Indices: 5100--6236 Score: 1733
Period size: 565 Copynumber: 2.0 Consensus size: 566
5090 GTGGGAGGGG
* *
5100 TGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACAGTCACCCAAGCACGCCTAAC
1 TGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGGACTACACTCACCCAAGCACGCCTAAC
* * *
5165 TACGACGTTTTGATGGGACCCGGTGCATTAGTGCTGGTATGAGCGAACCCGTGAACTCTTGCGCA
66 TACGACGTTTTGATCGGACCCGGTGCATTAGTGCTGATATGAGCGAACCCGTCAACTCTTGCGCA
*
5230 ATCTATTCATATAAAGGCTGCCCCTTATAGCACTTCCGCCTCGAATTTGAAGGCAAATTCGACCA
131 ATCTATTCATATAAAGGCTACCCCTTATAGCACTTCCGCCTCGAATTTGAAGGCAAATTCGACCA
* *
5295 AATAGCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACTTGGAGAA
196 AATAGCGTGTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAA
*
5360 AATGCAACTAACAAAAAACATTAAATGAAATAAAGTGGGAGCGGTGTAACACGAGGACTTCTCAG
261 AATGCAACTAACAAAAAACATTAAATGAAATAAAGTGGGAGCGGTGCAACACGAGGACTTCTCAG
* * * * * *
5425 GAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCATGCTTAACATTGGCGTTTTGATAGGATCC
326 GAGGTCACCCATCCTAGTACTACACTCACCCAAGCACGCCTAACATCGACGTTTTGATAGGATCC
* *
5490 GGTGCATTAGTGCTGGTATGATCTCACCCGTCAACTCTTGCGCAATCTATTCATATAAAGGCTGC
391 GGTGCATTAGTGCTGGTATGAGCGCACCCGTCAACTCTTGCGCAATCTATTCATATAAAGGCTGC
* * * * * * * *
5555 CCCTTATCGGAGTTGCGCCTCGAATTTTAATGCAAATTCGACCAAATATCGTTTCAAATTACTTA
456 CCCTTATAGCACTTCCGCCTCGAATTTGAAGGCAAATTCGACCAAATAGCATTTCAAATTACTTA
* *
5620 TTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAA
521 TTTCACAAAACGCAAATAACGAATGAGTTACACCACGAGGAGAAAA
* * * * * *
5666 TGCAACACGAGGACTTCGCAGGA-GTCATCCATCCTAGGACTACTCTCGCCCTAGCACGCTTAAC
1 TGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGGACTACACTCACCCAAGCACGCCTAAC
* * * * * *
5730 TACGGCGTTTTGATCGGATCCGGTGCATTAGTGCTGATATGATCGCACCCGTCAAGTCTTGCGTA
66 TACGACGTTTTGATCGGACCCGGTGCATTAGTGCTGATATGAGCGAACCCGTCAACTCTTGCGCA
* * * * * *
5795 ATGTATTCATATAAAGGCTACCCCTTATCG-ATCTTTCGCCTCGAATTTTAATGCAAATTCGGCC
131 ATCTATTCATATAAAGGCTACCCCTTATAGCA-CTTCCGCCTCGAATTTGAAGGCAAATTCGACC
*
5859 AAATATCGTGTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGA
195 AAATAGCGTGTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGA
** * *
5924 AAATGCAACTAACAAAAAACATTGTATGAAATAATGTGGGAGGGGTGCAACACGAGGACTTC-CT
260 AAATGCAACTAACAAAAAACATTAAATGAAATAAAGTGGGAGCGGTGCAACACGAGGACTTCTC-
* *
5988 AGGAGGTCACCCATCCTAGTACTACAGTCACCCAAGCACGCCTAAC-TACGACGTTTTGATGGGA
324 AGGAGGTCACCCATCCTAGTACTACACTCACCCAAGCACGCCTAACAT-CGACGTTTTGATAGGA
*
6052 TCCGGTGCATTAGTGCTGGTATGAGCGCACCCGTGAACTCTTGCGCAATCTATTCATATAAAGGC
388 TCCGGTGCATTAGTGCTGGTATGAGCGCACCCGTCAACTCTTGCGCAATCTATTCATATAAAGGC
*
6117 TGCCCCTTATAGCACTTCCGCCTCGAATTTGAAGGCAAATTCGACCAAATAGCATTTCAAATTAT
453 TGCCCCTTATAGCACTTCCGCCTCGAATTTGAAGGCAAATTCGACCAAATAGCATTTCAAATTAC
6182 TTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGAGGAGAAAA
518 TTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGAGGAGAAAA
6231 TGCAAC
1 TGCAAC
6237 TAACAAAAAA
Statistics
Matches: 514, Mismatches: 54, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
564 3 0.01
565 489 0.95
566 22 0.04
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (566 bp):
TGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGGACTACACTCACCCAAGCACGCCTAAC
TACGACGTTTTGATCGGACCCGGTGCATTAGTGCTGATATGAGCGAACCCGTCAACTCTTGCGCA
ATCTATTCATATAAAGGCTACCCCTTATAGCACTTCCGCCTCGAATTTGAAGGCAAATTCGACCA
AATAGCGTGTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAA
AATGCAACTAACAAAAAACATTAAATGAAATAAAGTGGGAGCGGTGCAACACGAGGACTTCTCAG
GAGGTCACCCATCCTAGTACTACACTCACCCAAGCACGCCTAACATCGACGTTTTGATAGGATCC
GGTGCATTAGTGCTGGTATGAGCGCACCCGTCAACTCTTGCGCAATCTATTCATATAAAGGCTGC
CCCTTATAGCACTTCCGCCTCGAATTTGAAGGCAAATTCGACCAAATAGCATTTCAAATTACTTA
TTTCACAAAACGCAAATAACGAATGAGTTACACCACGAGGAGAAAA
Found at i:6243 original size:304 final size:303
Alignment explanation
Indices: 5666--6310 Score: 961
Period size: 304 Copynumber: 2.1 Consensus size: 303
5656 GTGGAGAAAA
* * * * *
5666 TGCAACACGAGGACTTCGCAGGA-GTCATCCATCCTAGGACTACTCTCGCCCTAGCACGCTTAAC
1 TGCAACACGAGGACTTC-CAGGAGGTCACCCATCCTAGGACTACACTCACCCAAGCACGCCTAAC
* * * *
5730 TACGGCGTTTTGATCGGATCCGGTGCATTAGTGCTGATATGATCGCACCCGTCAAGTCTTGCGTA
65 TACGACGTTTTGATCGGATCCGGTGCATTAGTGCTGATATGAGCGCACCCGTCAACTCTTGCGCA
* * * * * *
5795 ATGTATTCATATAAAGGCTACCCCTTATCGATCTTTCGCCTCGAATTTTAATGCAAATTCGGCCA
130 ATCTATTCATATAAAGGCTACCCCTTATAGATCTTCCGCCTCGAATTTGAAGGCAAATTCGACCA
* * * *
5860 AATATCGTGTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAA
195 AATAGCATGTCAAATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGAGGAGAA
** * * *
5925 AATGCAACTAACAAAAAACATTGTATGAAATAATGTGGGAGGGG
260 AATGCAACTAACAAAAAACATTAAAAGAAATAAAGTGGGAGCGG
* *
5969 TGCAACACGAGGACTTCCTAGGAGGTCACCCATCCTAGTACTACAGTCACCCAAGCACGCCTAAC
1 TGCAACACGAGGACTTCC-AGGAGGTCACCCATCCTAGGACTACACTCACCCAAGCACGCCTAAC
* * *
6034 TACGACGTTTTGATGGGATCCGGTGCATTAGTGCTGGTATGAGCGCACCCGTGAACTCTTGCGCA
65 TACGACGTTTTGATCGGATCCGGTGCATTAGTGCTGATATGAGCGCACCCGTCAACTCTTGCGCA
*
6099 ATCTATTCATATAAAGGCTGCCCCTTATAGCA-CTTCCGCCTCGAATTTGAAGGCAAATTCGACC
130 ATCTATTCATATAAAGGCTACCCCTTATAG-ATCTTCCGCCTCGAATTTGAAGGCAAATTCGACC
*
6163 AAATAGCATTTCAAATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGAGGAGA
194 AAATAGCATGTCAAATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGAGGAGA
6228 AAATGCAACTAACAAAAAACATTAAAAGAAATAAAGTGGGAGCGG
259 AAATGCAACTAACAAAAAACATTAAAAGAAATAAAGTGGGAGCGG
6273 TGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAG
1 TGCAACACGAGGACTT-CCAGGAGGTCACCCATCCTAG
6311 ANNNNNNNNN
Statistics
Matches: 307, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
302 1 0.00
303 21 0.07
304 282 0.92
305 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (303 bp):
TGCAACACGAGGACTTCCAGGAGGTCACCCATCCTAGGACTACACTCACCCAAGCACGCCTAACT
ACGACGTTTTGATCGGATCCGGTGCATTAGTGCTGATATGAGCGCACCCGTCAACTCTTGCGCAA
TCTATTCATATAAAGGCTACCCCTTATAGATCTTCCGCCTCGAATTTGAAGGCAAATTCGACCAA
ATAGCATGTCAAATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGAGGAGAAA
ATGCAACTAACAAAAAACATTAAAAGAAATAAAGTGGGAGCGG
Found at i:7430 original size:304 final size:304
Alignment explanation
Indices: 6870--8627 Score: 2497
Period size: 304 Copynumber: 5.8 Consensus size: 304
6860 NNNNNNNNNN
* * * * *
6870 AGTGGGAGGGGTGCAACACGAGGACATCGCAGGAGGTCATCCATCCTAGGACTACTCTCGCCCTA
1 AGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
* * * * *
6935 GCACGCTCAACTACGGCGTTTTGATAGGATCCGGTGCATTAGAGCAGGTATGATCTCACCCGTCA
66 GCACGCTTAACTACGGCGTTTTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCA
* * *
7000 ACTCTTGCGCAATCTGTTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTTAATGC
131 ACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTGAAGGC
* * * * *
7065 AAATTCGACAAAATATCGTGTCAAATTTTTTATTTCGCAAAACGCAAATAAGGATTGAGTTACAC
196 AAATTCGACCAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACAC
*
7130 CACGTGGAGAAAATGCAACTAACAAAAAACATTGTATGAAATAA
261 CACGTGGAGAAAATGCAACTAACAAAAAACATTATATGAAATAA
* ** *
7174 TGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACAGTCACCCAA
1 AGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
* * * * *
7239 GCACGCCTAACTACGACGTTTTGATGGGATCCGGTGCATTAGTGCTGGTATAAGCGCACCCGTGA
66 GCACGCTTAACTACGGCGTTTTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCA
* * *
7304 ACTCTTGCGCAATCTATTCATATAAATGCTGCCCCTTATAGCACTTCCGCCTCGAATTTGAAGGC
131 ACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTGAAGGC
*
7369 AAATTCGACCAAATAGCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACAC
196 AAATTCGACCAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACAC
* *
7434 CACGTAGAGAAAATGCAACTAACAAAAAACATTAAATGAAATAA
261 CACGTGGAGAAAATGCAACTAACAAAAAACATTATATGAAATAA
* * * *
7478 AGTGGGAGGGGTGCAACACGAGGACTTCGCAGGAGGTCATCCATCCTAGGACTACTCTCGCCCTA
1 AGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
* * *
7543 GCACGCTTAACTACGGCGTTTTGATCGGATCCGGTGCATTACTGCTGATATGATCGCACCCGTCA
66 GCACGCTTAACTACGGCGTTTTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCA
* * * * * * *
7608 ACTCTTGCGCAATCTGTTCATATAAAGGCAGCCCCTTATCGGAGTTGTGCCTCGAATTTTAATGC
131 ACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTGAAGGC
* * * * * *
7673 AAATTCGACCAAATATCGTTTCAATTTATTTATTTTGCAAGACGCAAATAACAAAAGAGTTGCAC
196 AAATTCGACCAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACAC
7738 CACGTGGAGAAAATGCAACTAACAAAAAACATTATATGAAATAA
261 CACGTGGAGAAAATGCAACTAACAAAAAACATTATATGAAATAA
* * ** *
7782 TGTGGGAGGGGTGCAACACGAGGACTTCCCAGGACGTCACCCATCCTAGTACTACAGTCACCCAA
1 AGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
* *
7847 GCACGCTTAACTACGGCATTTTGAT-AGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCA
66 GCACGCTTAACTACGGCGTTTTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCA
* * *
7911 ACTCTTGCGCAATCGATTCATATAGAGGCTGCCCCTTATCGCACTTCCGCCTCGAATTTGAAGGC
131 ACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTGAAGGC
* * * * * *
7976 AAATTCGACCAAATATCATTTCAATTTATTTATTTTGCAAGACGCAAATAACGAAAGAGTTGCAC
196 AAATTCGACCAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACAC
* * *
8041 AACGTGGAAAAAATGCAACTAA-AAAAAATATTATATGAAATAA
261 CACGTGGAGAAAATGCAACTAACAAAAAACATTATATGAAATAA
* * * **
8084 AATGGGAGGAGTGCAACTCGAGGACTTCCCAGGAGGTCACCCATCCTAGTGTTACTCTCGCCCAA
1 AGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
* * * * *
8149 GCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGAGCGCACCCGTGA
66 GCACGCTTAACTACGGCGTTTTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCA
* * * *
8214 ACTCTTGCGTAATCTATTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTTGAATTTTAATGC
131 ACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTGAAGGC
* * * *
8279 AAATTCGGCCAAATGTCGTTTCAAATTATTTATTTCGCATAACGCATATAACGAATGAGTTACAC
196 AAATTCGACCAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACAC
8344 CACGTGGAGAAAATGCAGA-TAACAAAAAACATTATATGAAATAA
261 CACGTGGAGAAAATGCA-ACTAACAAAAAACATTATATGAAATAA
* * * * * * *
8388 AATAGGA-GGGTG---CAGGAGGACTTCCCAGGAGGTCGCCCACCCTAGTAATCCTCTCGCCCAA
1 AGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
*
8449 GCACGCTTAACTGCGGCG-TTTGAATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTC
66 GCACGCTTAACTACGGCGTTTTG-ATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTC
* * * *
8513 AACTCTTGCGCAATCTATTCATATTAAGGCTGCCCCTTATCGCACTTGCGCCTTGAAATTGAAGC
130 AACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTGAAGG
**
8578 CAAATTCGACCAAATATCGTTTCAAATTATTTATTTCGCACGACGCAAAT
195 CAAATTCGACCAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAAT
8628 C
Statistics
Matches: 1292, Mismatches: 158, Indels: 12
0.88 0.11 0.01
Matches are distributed among these distances:
299 3 0.00
300 202 0.16
302 96 0.07
303 345 0.27
304 646 0.50
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (304 bp):
AGTGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
GCACGCTTAACTACGGCGTTTTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCA
ACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATTTGAAGGC
AAATTCGACCAAATATCGTTTCAAATTATTTATTTCGCAAAACGCAAATAACGAATGAGTTACAC
CACGTGGAGAAAATGCAACTAACAAAAAACATTATATGAAATAA
Done.