Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009559.1 Kokia drynarioides strain JFW-HI SEQ_124271, whole genome shotgun sequence
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: 2902
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:861 original size:434 final size:430
Alignment explanation
Indices: 1--2635 Score: 2530
Period size: 434 Copynumber: 6.1 Consensus size: 430
* * * *
1 AATTAAAAA-TATATTTATGTGAGAATTATTTCTCTTTTCA-TTCTTAGACAAACTTCTGAACTT
1 AATTAAAAACT-TATTTACGTGAGAATTGTTTCTCTCTT-AGTTCTTAGACGAACTTCTGAACTT
* * * * * * * * **
64 GTCAAGCTTTTACTATTTCTCTATAATAACTTCGGTTGCTTAAACTATTCAAGATGATCCAATTC
64 GTCAAACTTTTACGAGTTCT-T-TTATAACTTAGGTTCCTTAAAGTATTTAAGGCGATCC-ATTC
* ** * * *
129 -TTCGAGCAATATTCTGAACATTCAATGCTCGGGAAATCGCATCATTTGGTCAAAATAGTTTGTC
126 TTTCAATAAAT-TTCTAAACATTCAATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTC
* * ** * * *
193 ATTTCT-TAAAAAAACTTGTGGTCACTGAATTAAATACTTATTTATGTGTA-AATTGTTTATCTC
190 ATTT-TGT-AAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTG-AGAATTGTTTCTCTC
* * ** * * ** *
256 TTGGTTCT--TGGACGAACTT-TCGAACTAGGAAAACTTTTACTATTTCAGTTATAACTTCAGTT
252 TTGGTTCTAATTGACG-ACTTCT-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT-GGTT
* * ** * ** *
318 CCGTAAAGTATTCAAGATGATCCGTTTGTTCGAGCAATGTTTCGAACATTCCATGCTCGAGAAAT
314 CCTTAAAGTATTCTAGGCGATCCATTCCTTCAAGCAAT-TTTCGAACATTCCATGCTCGAGAAAT
383 CGCATCACTT-GGTCTAAATAGTTTGTCATTTTGTAAAACAACTTTTGGTCTTTG
378 CGCATCA-TTCGGTCTAAATAGTTTGTCATTTTGT-AAACAACTTTTGGTCTTTG
* * * *
437 AATTAAAAACTTATTTACGCGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGACCTTTT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTAGACGAACTTCTGAACTTGT
*
502 CAAACTTTTACGAGTTCTTTTATGACATT-GGTTCCTTAAAGTATTTAAGGCGATCCATTCTTTC
66 CAAACTTTTACGAGTTCTTTTATAAC-TTAGGTTCCTTAAAGTATTTAAGGCGATCCATTCTTTC
* * * *
566 AATAAATATTCTAAACATTCCATGCTCGAGAAATCGCATCATTCGGCCTAAATATTTTGTCA-TT
130 AATAAAT-TTCTAAACATTCAATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTT
* * *
630 TGTAAACAACTTTTGGTTTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGATC
194 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT-GGTT
* * *
695 CTGAATTTACGACTTCTGAACTTGTCAAACTTTTACGAGTCCTTTTACAACTTAGGTTCCTTAAA
258 CT-AATTGACGACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT-GGTTCCTTAAA
* * * * ** * **
760 GCATTCTATGCGATCCATTCCCTCTA-CAAATTGTTCGAACATTGAATGTTCGTTAAATCGCATC
321 GTATTCTAGGCGATCCATTCCTTCAAGC-AATT-TTCGAACATTCCATGCTCGAGAAATCGCATC
* *
824 ATTTGATCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTG
384 ATTCGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTG
* * * * * * * *
871 AACTAAAAACTTATTGACTTGGGATTTGTTTCTCTCTTGGTTCTTAAACGAACTTCTGAACTTTT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTAGACGAACTTCTGAACTTGT
* * *
936 CAAGCTTTTACGAGTTCTTTTATGACATT-GGTTCCTTAAAGTATTCAAGGCGATCCATTCTTTC
66 CAAACTTTTACGAGTTCTTTTATAAC-TTAGGTTCCTTAAAGTATTTAAGGCGATCCATTCTTTC
* * * * *
1000 AATCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTTTGTCATTT
130 AATAAAT-TTCTAAACATTCAATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTT
* *
1065 TGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGCGAGAATTGTTTCTCTCTTGGTTC
194 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTC
* * *
1130 T--TAGACGAACTTCTGAACTTTTCAAACTTTTACGAGTTCTTTTATGACATTGGTTCCTTAAAG
259 TAATTGACG-ACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAAC-TTGGTTCCTTAAAG
* * *
1193 TATT-TAAGGCGATCCATTCTTTCAA-CAAATATTCTAAACATTCCATGCTCGAGAAATCGCATC
322 TATTCT-AGGCGATCCATTCCTTCAAGC-AATTTTC-GAACATTCCATGCTCGAGAAATCGCATC
* * *
1256 ATTCGGCCTAAATATTTTGTCAATTTGTAAACAACTTTTGGTCTTTG
384 ATTCGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTG
* * * * *
1303 AATTAAAAACTTATTTATGTGGGAATTGTTTCTCTCTTAGATCTTGGATTTGAACTTCTGAACTT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTAGA--CGAACTTCTGAACTT
* * * * * * *
1368 GTCAAACTTTTACGAGTCCATTTACAACTTAGGTTCCTTAAAGCATTCT-ATGTGATCCATTCCT
64 GTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATT-TAAGGCGATCCATTCTT
* * * * * * **
1432 TCTACAAATTTTTCGAACATTGAATGTTCG-GTAAATCGCATCATTTAATCTAAATAGTTTGTCA
128 TCAATAAATTTCT-AAACATTCAATGCTCGAG-AAATCGCATCATTTGGTCTAAATAGTTTGTCA
* * *
1496 TTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTGACGTGGGATTTGTTTCTCTCTTGG
191 TTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGG
* * * *
1561 TTCTTAAATGA--ACTTCTGAACTTTTCAAGCTTTTACGAGTTCTTTTATGACATTGGTTCCTTA
256 TTC-TAATTGACGACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAAC-TTGGTTCCTTA
* * * *
1624 AAGTATTCAAGGCGATCCATTCTTTCAAGCAATATTCCAAACATTCCATGCTCGAGAAATCGCAT
319 AAGTATTCTAGGCGATCCATTCCTTCAAGCAAT-TTTCGAACATTCCATGCTCGAGAAATCGCAT
*
1689 CATTCGGTCTAAATATTTTGTCATTTTGTAAACAACTTTTGGTCTTTG
383 CATTCGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTG
* * * *
1737 AATTAAAATCTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGATGAACTTCCGAACTTGT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTAGACGAACTTCTGAACTTGT
* * * * * *
1802 CAAACTTTTACGAGTCCTTTTACAACTTAGGTTCCTCAAAGCATTCT-ATGCGATCCATTCCTTC
66 CAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATT-TAAGGCGATCCATTCTTTC
* * * * * * * *
1866 TACAAATTTTTCGAACATTCAACGTTC-AGAAAATCGCATCATTTGATCTAAATAGTTTGTCATA
130 AATAAATTTCT-AAACATTCAATGCTCGAG-AAATCGCATCATTTGGTCTAAATAGTTTGTCATT
* * * * * * *
1930 TTGTGAACAACTTTCGGTCTTTGAATTAAAAAGTTATTGACGTGGGATTTGTTTCTTTCTTGGTT
193 TTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTT
* * * * ** *
1995 CT--TGGACGAACCTCCGGACTTGTCAAACTTTTATAAGTTCTTTTAAAACTTCGGTTCCTTGAA
258 CTAATTGACG-ACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT-GGTTCCTT-AA
* * *** * * *
2058 GTGTATTATATATAAATGATCCACTT-CATCGAGCAATTTTCGAACATTCCATTCTCCGA-AAAT
320 ----AGTAT-TCTAGGCGATCCA-TTCCTTCAAGCAATTTTCGAACATTCCATGCT-CGAGAAAT
* * * * *
2121 CGAATCTTTTGGTTTAAATAGTTTATCATTTTGTAAACAACTTTTGGTCTTTG
378 CGCATCATTCGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTG
* * * * * * *
2174 AATTAAAAACTTATTTATGTGAAAATTGTCTCTCTCTTTGTTCTTCGACGAACTACCGAACTTGT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTAGACGAACTTCTGAACTTGT
* * * * * * * *
2239 AAAACTTTTACGAGTTATTTTATAACTTCGGTTCCTTAAAGTATTCAAGACCATCCGTT-TCTAC
66 CAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTTAAGGCGATCCATTCT-TTC
* * * * * *
2303 GAGTAATTTTCCAAACATTCGATGCTCGAGAAATTGCATCTTTTGGTCTAAATAGTTTGTCATTT
130 -AATAAATTTCTAAACATTCAATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTT
* * ** * *
2368 TGAAAACCAAGTTTTGGTCTTCAAACTAAAAACTTATTTATGTGAGAATTGTTTCTC-CTTTGGT
194 TGTAAA-CAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC-TTGGT
* *
2432 TCTTAGA-TGA--ACTT-TCGAACTGGTCAAGCTTTTTACGAGTTCTTTTATAACTTTGGTTCCT
257 TC-TA-ATTGACGACTTCT-GAACTTGTCAAAC-TTTTACGAGTTCTTTTATAAC-TTGGTTCCT
* * * * * * ** * *
2493 TAAAGTATTCAAGACGATCCATTCCTTCGATCAATATTCCGAACTTTCTGTGCTCGGGAAATAGC
317 TAAAGTATTCTAGGCGATCCATTCCTTCAAGCAAT-TTTCGAACATTCCATGCTCGAGAAATCGC
* *
2558 ATCATTCGGTCTAAATAGTTTGTCATTTTGGAAACAACTTTTTGGTCCTTG
381 ATCATTCGGTCTAAATAGTTTGTCATTTTGTAAACAAC-TTTTGGTCTTTG
*
2609 AATTAAAAA-TATATTTATGTGAGAATT
1 AATTAAAAACT-TATTTACGTGAGAATT
2636 ATTTNNNNNN
Statistics
Matches: 1855, Mismatches: 282, Indels: 125
0.82 0.12 0.06
Matches are distributed among these distances:
429 2 0.00
431 12 0.01
432 460 0.25
433 40 0.02
434 712 0.38
435 210 0.11
436 74 0.04
437 225 0.12
438 87 0.05
439 29 0.02
440 2 0.00
441 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (430 bp):
AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTAGACGAACTTCTGAACTTGT
CAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTTAAGGCGATCCATTCTTTCA
ATAAATTTCTAAACATTCAATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
TAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTA
ATTGACGACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTGGTTCCTTAAAGTATT
CTAGGCGATCCATTCCTTCAAGCAATTTTCGAACATTCCATGCTCGAGAAATCGCATCATTCGGT
CTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTG
Found at i:993 original size:216 final size:215
Alignment explanation
Indices: 1--2635 Score: 2629
Period size: 216 Copynumber: 12.1 Consensus size: 215
* * * ** *
1 AATTAAAAA-TATATTTATGTGAGAATTATTTCTCTTTTCATTCTTAGACAAACTTCTGAACTTG
1 AATTAAAAACT-TATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTG
* * * * * * * **
65 TCAAGCTTTTACTATTTCTCTATAATAACTTCGGTTGCTTAAACTATTCAAGATGATCCAATT-C
65 TCAAACTTTTACGAGTTCT-T-TTATAACTTAGGTTCCTTAAAGTATTCAAGGCGATCC-ATTCC
* * * * * *
129 TTCGAGC-AATATTCTGAACATTCAATGCTCGGGAAATCGCATCATTTGGTCAAAATAGTTTGTC
127 TTC-AACAAATTTTC-AAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTC
* * **
193 ATTTCT-TAAAAAAACTTGTGGTCACTG
190 ATTT-TGT-AAACAACTTTTGGTCTTTG
* * * * *
220 AATTAAATACTTATTTATGTGTA-AATTGTTTATCTCTTGGTTCTTGGACGAACTT-TCGAACTA
1 AATTAAAAACTTATTTACGTG-AGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCT-GAACTT
** * * ** * ** * **
283 GGAAAACTTTTACTATTTCAGTTATAACTTCA-GTTCCGTAAAGTATTCAAGATGATCCGTTTGT
64 GTCAAACTTTTACGAGTTCTTTTATAACTT-AGGTTCCTTAAAGTATTCAAGGCGATCCATTCCT
* * *
347 TCGAGC-AATGTTTCGAACATTCCATGCTCGAGAAATCGCATCACTTGGTCTAAATAGTTTGTCA
128 TC-AACAAAT-TTTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
411 TTTTGTAAAACAACTTTTGGTCTTTG
191 TTTTGT-AAACAACTTTTGGTCTTTG
* * *
437 AATTAAAAACTTATTTACGCGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGACCTTTT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTGT
* * *
502 CAAACTTTTACGAGTTCTTTTATGACATT-GGTTCCTTAAAGTATTTAAGGCGATCCATTCTTTC
66 CAAACTTTTACGAGTTCTTTTATAAC-TTAGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTC
* * * * *
566 AATAAATATTCTAAACATTCCATGCTCGAGAAATCGCATCATTCGGCCTAAATATTTTGTCA-TT
130 AACAAATTTTC-AAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTT
*
630 TGTAAACAACTTTTGGTTTTTG
194 TGTAAACAACTTTTGGTCTTTG
* * **
652 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGATCCTGAATTTACG-ACTTCTGAAC
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT-GGTTCT---TAGACGAACTTCTGAAC
* * * * *
716 TTGTCAAACTTTTACGAGTCCTTTTACAACTTAGGTTCCTTAAAGCATTCTATGCGATCCATTCC
62 TTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGGCGATCCATTCC
* * * ** * ** *
781 CTCTACAAATTGTTCGAACATTGAATGTTCGTTAAATCGCATCATTTGATCTAAATAGTTTGTCA
127 TTCAACAAATT-TTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
846 TTTTGTAAACAACTTTTGGTCTTTG
191 TTTTGTAAACAACTTTTGGTCTTTG
* * * * * * *
871 AACTAAAAACTTATTGACTTGGGATTTGTTTCTCTCTTGGTTCTTAAACGAACTTCTGAACTTTT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTGT
* * *
936 CAAGCTTTTACGAGTTCTTTTATGACATT-GGTTCCTTAAAGTATTCAAGGCGATCCATTCTTTC
66 CAAACTTTTACGAGTTCTTTTATAAC-TTAGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTC
* * *
1000 AATC-AATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTTTGTCATT
130 AA-CAAAT-TTTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATT
*
1064 TTGTAAACAAGTTTTGGTCTTTG
193 TTGTAAACAACTTTTGGTCTTTG
* *
1087 AATTAAAAACTTATTTACGCGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTTT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTGT
* * *
1152 CAAACTTTTACGAGTTCTTTTATGACATT-GGTTCCTTAAAGTATTTAAGGCGATCCATTCTTTC
66 CAAACTTTTACGAGTTCTTTTATAAC-TTAGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTC
* * * * *
1216 AACAAATATTCTAAACATTCCATGCTCGAGAAATCGCATCATTCGGCCTAAATATTTTGTCAATT
130 AACAAATTTTC-AAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTT
1281 TGTAAACAACTTTTGGTCTTTG
194 TGTAAACAACTTTTGGTCTTTG
* * * * * *
1303 AATTAAAAACTTATTTATGTGGGAATTGTTTCTCTCTTAGATCTTGGATTTGAACTTCTGAACTT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGA--CGAACTTCTGAACTT
* * * * * * *
1368 GTCAAACTTTTACGAGTCCATTTACAACTTAGGTTCCTTAAAGCATTCTATGTGATCCATTCCTT
64 GTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTT
* * ** * **
1433 CTACAAATTTTTCGAACATTGAATGTTCG-GTAAATCGCATCATTTAATCTAAATAGTTTGTCAT
129 CAACAAA-TTTTCAAACATTCCATGCTCGAG-AAATCGCATCATTTGGTCTAAATAGTTTGTCAT
1497 TTTGTAAACAACTTTTGGTCTTTG
192 TTTGTAAACAACTTTTGGTCTTTG
* * * * * *
1521 AATTAAAAACTTATTGACGTGGGATTTGTTTCTCTCTTGGTTCTTAAATGAACTTCTGAACTTTT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTGT
* * *
1586 CAAGCTTTTACGAGTTCTTTTATGACATT-GGTTCCTTAAAGTATTCAAGGCGATCCATTCTTTC
66 CAAACTTTTACGAGTTCTTTTATAAC-TTAGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTC
* * *
1650 AAGC-AATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTTTGTCATT
130 AA-CAAAT-TTTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATT
1714 TTGTAAACAACTTTTGGTCTTTG
193 TTGTAAACAACTTTTGGTCTTTG
* * * * *
1737 AATTAAAATCTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGATGAACTTCCGAACTTGT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTGT
* * * * * * *
1802 CAAACTTTTACGAGTCCTTTTACAACTTAGGTTCCTCAAAGCATTCTATGCGATCCATTCCTTCT
66 CAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCA
* * * * * *
1867 ACAAATTTTTCGAACATTCAACGTTC-AGAAAATCGCATCATTTGATCTAAATAGTTTGTCATAT
131 ACAAA-TTTTCAAACATTCCATGCTCGAG-AAATCGCATCATTTGGTCTAAATAGTTTGTCATTT
* *
1931 TGTGAACAACTTTCGGTCTTTG
194 TGTAAACAACTTTTGGTCTTTG
* * * * * * * * *
1953 AATTAAAAAGTTATTGACGTGGGATTTGTTTCTTTCTTGGTTCTTGGACGAACCTCCGGACTTGT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTGT
** * * * * ***
2018 CAAACTTTTATAAGTTCTTTTAAAACTTCGGTTCCTTGAAGTGTATTATATATAAATGATCCACT
66 CAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTT-AA-AGTA-T-T-CA-AGGCGATCCA-T
* * * * * * *
2083 T-CATCGAGC-AATTTTCGAACATTCCATTCTCCGA-AAATCGAATCTTTTGGTTTAAATAGTTT
124 TCCTTC-AACAAATTTTCAAACATTCCATGCT-CGAGAAATCGCATCATTTGGTCTAAATAGTTT
*
2145 ATCATTTTGTAAACAACTTTTGGTCTTTG
187 GTCATTTTGTAAACAACTTTTGGTCTTTG
* * * * * * *
2174 AATTAAAAACTTATTTATGTGAAAATTGTCTCTCTCTTTGTTCTTCGACGAACTACCGAACTTGT
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTGT
* * * * * * * * *
2239 AAAACTTTTACGAGTTATTTTATAACTTCGGTTCCTTAAAGTATTCAAGACCATCCGTTTCTACG
66 CAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCA
** * * *
2304 AGTAATTTTCCAAACATTCGATGCTCGAGAAATTGCATCTTTTGGTCTAAATAGTTTGTCATTTT
131 ACAAATTTT-CAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT
* * **
2369 GAAAACCAAGTTTTGGTCTTCA
195 GTAAA-CAACTTTTGGTCTTTG
* * * *
2391 AACTAAAAACTTATTTATGTGAGAATTGTTTCTC-CTTTGGTTCTTAGATGAACTT-TCGAACTG
1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC-TTGGTTCTTAGACGAACTTCT-GAACTT
* * *
2454 GTCAAGCTTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCT
64 GTCAAAC-TTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGGCGATCCATTCCT
* * * * ** * * *
2519 TCGATC-AATATTCCGAACTTTCTGTGCTCGGGAAATAGCATCATTCGGTCTAAATAGTTTGTCA
128 TC-AACAAAT-TTTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCA
* *
2583 TTTTGGAAACAACTTTTTGGTCCTTG
191 TTTTGTAAACAAC-TTTTGGTCTTTG
*
2609 AATTAAAAA-TATATTTATGTGAGAATT
1 AATTAAAAACT-TATTTACGTGAGAATT
2636 ATTTNNNNNN
Statistics
Matches: 2018, Mismatches: 337, Indels: 123
0.81 0.14 0.05
Matches are distributed among these distances:
214 2 0.00
215 85 0.04
216 842 0.42
217 344 0.17
218 438 0.22
219 137 0.07
220 5 0.00
221 148 0.07
222 13 0.01
223 4 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (215 bp):
AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTGT
CAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCA
ACAAATTTTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
TAAACAACTTTTGGTCTTTG
Found at i:1243 original size:650 final size:648
Alignment explanation
Indices: 144--2635 Score: 2923
Period size: 650 Copynumber: 3.8 Consensus size: 648
134 GCAATATTCT
* * * * * *
144 GAACATTCAATGCTCGGGAAATCGCATCATTTGGTCAAAATAGTTTGTCATTTCT-TAAAAAAAC
1 GAACATTGAATGTTC-GTAAATCGCATCATTTGATCTAAATAGTTTGTCATTT-TGT-AAACAAC
* ** * * ** * * **
208 TTGTGGTCACTGAATTAAATACTTATTTA-TGTGTAAATTGTTTATCTCTTGGTTCTTGGACGAA
63 TTTTGGTCTTTGAATTAAAAACTTATTGACT-TGGGATTTGTTTCTCTCTTGGTTCTTAAACGAA
**** * * * ** * * * *
272 CTT-TCGAACTAGGAAAACTTTTACTATTTCAGTTATAAC-TTCAGTTCCGTAAAGTATTCAAGA
127 CTTCT-GAACTTTTCAAGCTTTTACGAGTTCTTTTATGACATT-GGTTCCTTAAAGTATTCAAGG
* * * * * * *
335 TGATCCGTT-TGTTCGAGCAATGTTTCGAACATTCCATGCTCGAGAAATCGCATCACTT-GGTCT
190 CGATCCATTCT-TTCAATCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCA-TTCGGTCT
398 AAATAGTTTGTCATTTTGTAAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGCGAGAAT
253 AAATAGTTTGTCATTTTGT-AAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGCGAGAAT
* * *
463 TGTTTCTCTCTTGGTTCTTAGACGAACTTCTGACCTTTTCAAACTTTTACGAGTTCTTTTATGAC
317 TGTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAAC
* *
528 ATTGGTTCCTTAAAGTATTTAAGGCGATCCATTCTTTCAATAAATATTCTAAACATTCCATGCTC
382 ATTGGTTCCTTAAAGTATTTAAGGCGATCCATTCCTTCAACAAATATTCTAAACATTCCATGCTC
* *
593 GAGAAATCGCATCATTCGGCCTAAATATTTTGTCATTTGTAAACAACTTTTGGTTTTTGAATTAA
447 GAGAAATCGCATCATTCGGCCTAAATAGTTTGTCATTTGTAAACAACTTTTGGTCTTTGAATTAA
658 AAACTTATTTACGTGAGAATTGTTTCTCTCTTAGATCCTGAATTTACG-ACTTCTGAACTTGTCA
512 AAACTTATTTACGTGAGAATTGTTTCTCTCTTAGATCCTG-ATTTACGAACTTCTGAACTTGTCA
* *
722 AACTTTTACGAGTCCTTTTACAACTTAGGTTCCTTAAAGCATTCTATGCGATCCATTCCCTCTAC
576 AACTTTTACGAGTCCTTTTACAACTTAGGTTCCTTAAAGCATTCTATGTGATCCATTCCATCTAC
787 AAATTGTTC
641 AAATT-TTC
796 GAACATTGAATGTTCGTTAAATCGCATCATTTGATCTAAATAGTTTGTCATTTTGTAAACAACTT
1 GAACATTGAATGTTCG-TAAATCGCATCATTTGATCTAAATAGTTTGTCATTTTGTAAACAACTT
*
861 TTGGTCTTTGAACTAAAAACTTATTGACTTGGGATTTGTTTCTCTCTTGGTTCTTAAACGAACTT
65 TTGGTCTTTGAATTAAAAACTTATTGACTTGGGATTTGTTTCTCTCTTGGTTCTTAAACGAACTT
926 CTGAACTTTTCAAGCTTTTACGAGTTCTTTTATGACATTGGTTCCTTAAAGTATTCAAGGCGATC
130 CTGAACTTTTCAAGCTTTTACGAGTTCTTTTATGACATTGGTTCCTTAAAGTATTCAAGGCGATC
*
991 CATTCTTTCAATCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATATT
195 CATTCTTTCAATCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATAGT
*
1056 TTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGCGAGAATTGTTTCTC
260 TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGCGAGAATTGTTTCTC
* *
1121 TCTTGGTTCTTAGACGAACTTCTGAACTTTTCAAACTTTTACGAGTTCTTTTATGACATTGGTTC
325 TCTTGGTTCTTAGACGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACATTGGTTC
*
1186 CTTAAAGTATTTAAGGCGATCCATTCTTTCAACAAATATTCTAAACATTCCATGCTCGAGAAATC
390 CTTAAAGTATTTAAGGCGATCCATTCCTTCAACAAATATTCTAAACATTCCATGCTCGAGAAATC
*
1251 GCATCATTCGGCCTAAATATTTTGTCAATTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTA
455 GCATCATTCGGCCTAAATAGTTTGTC-ATTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTA
* * *
1316 TTTATGTGGGAATTGTTTCTCTCTTAGATCTTGGATTT--GAACTTCTGAACTTGTCAAACTTTT
519 TTTACGTGAGAATTGTTTCTCTCTTAGATCCT-GATTTACGAACTTCTGAACTTGTCAAACTTTT
* *
1379 ACGAGTCCATTTACAACTTAGGTTCCTTAAAGCATTCTATGTGATCCATTCCTTCTACAAATTTT
583 ACGAGTCCTTTTACAACTTAGGTTCCTTAAAGCATTCTATGTGATCCATTCCATCTACAAA-TTT
1444 TC
647 TC
*
1446 GAACATTGAATGTTCGGTAAATCGCATCATTTAATCTAAATAGTTTGTCATTTTGTAAACAACTT
1 GAACATTGAATGTTC-GTAAATCGCATCATTTGATCTAAATAGTTTGTCATTTTGTAAACAACTT
* *
1511 TTGGTCTTTGAATTAAAAACTTATTGACGTGGGATTTGTTTCTCTCTTGGTTCTTAAATGAACTT
65 TTGGTCTTTGAATTAAAAACTTATTGACTTGGGATTTGTTTCTCTCTTGGTTCTTAAACGAACTT
1576 CTGAACTTTTCAAGCTTTTACGAGTTCTTTTATGACATTGGTTCCTTAAAGTATTCAAGGCGATC
130 CTGAACTTTTCAAGCTTTTACGAGTTCTTTTATGACATTGGTTCCTTAAAGTATTCAAGGCGATC
* *
1641 CATTCTTTCAAGCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATATT
195 CATTCTTTCAATCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATAGT
* *
1706 TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTGTTTCTC
260 TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGCGAGAATTGTTTCTC
* * * * * *
1771 TCTTAGTTCTTGGATGAACTTCCGAACTTGTCAAACTTTTACGAGTCCTTTTACAAC-TTAGGTT
325 TCTTGGTTCTTAGACGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACATT-GGTT
* * * * * * * * *
1835 CCTCAAAGCATTCT-ATGCGATCCATTCCTTCTACAAAT-TTTTCGAACATTCAACGTTC-AGAA
389 CCTTAAAGTATT-TAAGGCGATCCATTCCTTCAACAAATATTCT-AAACATTCCATGCTCGAG-A
* ** * *
1897 AATCGCATCATTTGATCTAAATAGTTTGTCATATTGTGAACAACTTTCGGTCTTTGAATTAAAAA
451 AATCGCATCATTCGGCCTAAATAGTTTGTCAT-TTGTAAACAACTTTTGGTCTTTGAATTAAAAA
* * * * * * * ** * * *
1962 GTTATTGACGTGGGATTTGTTTCTTTCTT-GGTTCT--TGGACGAACCTCCGGACTTGTCAAACT
515 CTTATTTACGTGAGAATTGTTTCTCTCTTAGATCCTGATTTACGAACTTCTGAACTTGTCAAACT
** * * * * * * *
2024 TTTATAAGTTCTTTTAAAACTTCGGTTCCTTGAAGTGTATTATATATAAATGATCCACTT-CATC
580 TTTACGAGTCCTTTTACAACTTAGGTTCCTT-AA-AGCA-T-TCTAT--GTGATCCA-TTCCATC
*
2088 GAGC-AATTTTC
638 TA-CAAATTTTC
** * * * * * *
2099 GAACATTCCAT-TCTCCGAAAATCGAATCTTTTGGTTTAAATAGTTTATCATTTTGTAAACAACT
1 GAACATTGAATGT-T-CGTAAATCGCATCATTTGATCTAAATAGTTTGTCATTTTGTAAACAACT
* ** * * * **
2163 TTTGGTCTTTGAATTAAAAACTTATTTA-TGTGAAAATTGTCTCTCTCTTTGTTCTTCGACGAAC
64 TTTGGTCTTTGAATTAAAAACTTATTGACT-TGGGATTTGTTTCTCTCTTGGTTCTTAAACGAAC
* * * * * * * * *
2227 TACCGAACTTGTAAAACTTTTACGAGTTATTTTATAAC-TTCGGTTCCTTAAAGTATTCAAGACC
128 TTCTGAACTTTTCAAGCTTTTACGAGTTCTTTTATGACATT-GGTTCCTTAAAGTATTCAAGGCG
* * * * * * * *
2291 ATCCGTT-TCTACGAGT-AATTTTCCAAACATTCGATGCTCGAGAAATTGCATCTTTTGGTCTAA
192 ATCCATTCT-TTC-AATCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAA
* * ** * * *
2354 ATAGTTTGTCATTTTGAAAACCAAGTTTTGGTCTTCAAACTAAAAACTTATTTATGTGAGAATTG
255 ATAGTTTGTCATTTTGTAAA-CAACTTTTGGTCTTTGAATTAAAAACTTATTTACGCGAGAATTG
* * *
2419 TTTCTC-CTTTGGTTCTTAGATGAACTT-TCGAACTGGTCAAGCTTTTTACGAGTTCTTTTATAA
319 TTTCTCTC-TTGGTTCTTAGACGAACTTCT-GAACTTGTCAAAC-TTTTACGAGTTCTTTTATAA
* * * * ** * **
2482 CTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGATC-AATATTCCGAACTTTCTGTGC
381 CATTGGTTCCTTAAAGTATTTAAGGCGATCCATTCCTTC-AACAAATATTCTAAACATTCCATGC
* * * * *
2546 TCGGGAAATAGCATCATTCGGTCTAAATAGTTTGTCATTTTGGAAACAACTTTTTGGTCCTTGAA
445 TCGAGAAATCGCATCATTCGGCCTAAATAGTTTGTCA-TTTGTAAACAAC-TTTTGGTCTTTGAA
*
2611 TTAAAAA-TATATTTATGTGAGAATT
508 TTAAAAACT-TATTTACGTGAGAATT
2636 ATTTNNNNNN
Statistics
Matches: 1611, Mismatches: 184, Indels: 86
0.86 0.10 0.05
Matches are distributed among these distances:
646 1 0.00
648 44 0.03
649 15 0.01
650 785 0.49
651 247 0.15
652 61 0.04
653 230 0.14
654 87 0.05
655 103 0.06
656 38 0.02
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (648 bp):
GAACATTGAATGTTCGTAAATCGCATCATTTGATCTAAATAGTTTGTCATTTTGTAAACAACTTT
TGGTCTTTGAATTAAAAACTTATTGACTTGGGATTTGTTTCTCTCTTGGTTCTTAAACGAACTTC
TGAACTTTTCAAGCTTTTACGAGTTCTTTTATGACATTGGTTCCTTAAAGTATTCAAGGCGATCC
ATTCTTTCAATCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATAGTT
TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGCGAGAATTGTTTCTCT
CTTGGTTCTTAGACGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACATTGGTTCC
TTAAAGTATTTAAGGCGATCCATTCCTTCAACAAATATTCTAAACATTCCATGCTCGAGAAATCG
CATCATTCGGCCTAAATAGTTTGTCATTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATT
TACGTGAGAATTGTTTCTCTCTTAGATCCTGATTTACGAACTTCTGAACTTGTCAAACTTTTACG
AGTCCTTTTACAACTTAGGTTCCTTAAAGCATTCTATGTGATCCATTCCATCTACAAATTTTC
Done.