Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008538.1 Kokia drynarioides strain JFW-HI SEQ_123215, 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: 5859
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Found at i:386 original size:216 final size:215
Alignment explanation
Indices: 1--2400 Score: 2686
Period size: 216 Copynumber: 11.3 Consensus size: 215
1 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAA-TAAAAACTTATTTAC
1 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAC
* * * * *
65 GTGAGAATTATTTTTCTATTGGTCCTTGGCCAAACTTCCAAACTTGTCAAACTTTTACGAGTTCT
66 GTGAGAATTGTTTGTCTATTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCT
* * *
130 TTTATAACTTCGATTCCTTAAAGTATTCAAGATTATCCATTCCTTCGAGGAATTTCTCGAACATT
131 TTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTT-TCAAACATT
* *
195 CCATGCTCGCGAATTCGCATC
195 CCATGCTCGGGAAATCGCATC
* * *
216 ATTTGGTCTAAATAGTTTCTCATTTTGTAAACAACTTTTTGTCTTTGAGTTAAAAACTTATTTAC
1 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAC
* * * * *
281 GTGAGAATTGTTTGTCTCA-TGGTTCTTGGCCGAGCTACCAAACTTGTCAAAGTCTTACGAGTTC
66 GTGAGAATTGTTTGTCT-ATTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTC
** * * * *
345 TTGAAAAACTTAGGTTCCTTAAAGTATTGAAGACGATCCA----TTC---G-------AAA-ATT
130 TTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTTTCAAACATT
* *
395 CCATGCTCGAGAAATTGCATC
195 CCATGCTCGGGAAATCGCATC
* * * * *
416 ATTTGGT-CAAGTAGTTTGTCATTTTGTGAACAACCTTTTGTCTTTGAATTTAAAACTTATTTAG
1 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAC
* * * ** * * * *
480 GTGAGAATTGGTCGTCTCTTGGTTCTTGGATGAACATCCGAACTGGTAAAACTTGTACGAGTTCT
66 GTGAGAATTGTTTGTCTATTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCT
* * **
545 TTTATAACTTAGGTTCCTTAAAG-A--C-----GATCCTTTCCTTTTAGGAATTTTCTAAACATT
131 TTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTTTC-AAACATT
*
602 CCATGCTCGGGAAATCGCACC
195 CCATGCTCGGGAAATCGCATC
* *
623 ATTTGGTCCAAATAATTTGTCATTTTGTAAACAACTTTTTGGCTTTGAATTAAAAACTTATTTAC
1 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAC
* * ** * *
688 GTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAACAAT-CGAACTTGTCAAACTTTTTCGAGTTC
66 GTGAGAATTGTTTGTCTATTGGTTCTTGGCCGAAC-TTCCGAACTTGTCAAACTTTTACGAGTTC
* * * * *
752 TTTTATAACTTCGTTTACTTAAAGTATTCAAAATGATCCATTCCTTCGAGGAATTTTTCGAACAA
130 TTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAA-TTTTCAAACAT
** *
817 TCCATGCTTTGGAATTCGCATC
194 TCCATGCTCGGGAAATCGCATC
* * * * * * *
839 ATTAGG-CTCAAATAGTTTATCATTTTGTAAACAACTTTTGGACTTTAAATTTAAAACTTATTTT
1 ATTTGGTC-CAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTA
* * * ** *
903 CGTGAGAATTATTTTTCTATTGGTTCTTGGCCGACCTTTTGAACTTGT-ATAACCTTTACGAGTT
65 CGTGAGAATTGTTTGTCTATTGGTTCTTGGCCGAACTTCCGAACTTGTCA-AACTTTTACGAGTT
* * ** *
967 CTTTTATAACTTTGGTTACTTAAAGTATAAAAGATGATCCATTCCTTTGAGGAATTTTCCAAACA
129 CTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTTT-CAAACA
* *
1032 TTCCATTCT-TGGAAATCGCATC
193 TTCCATGCTCGGGAAATCGCATC
1054 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAA-TAAAAACTTATTTAC
1 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAC
* * **
1118 GTGAGAATTGTTTGTCTATTGGTCCTTAGCCGAACTTTTGAACTTGTCAAACTTTTACGAGTTCT
66 GTGAGAATTGTTTGTCTATTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCT
* * * ** ** *
1183 TTTATAACTCCAGTTCCTTAAAGTATTTGAA-AAAATCCATTCCTTCGAAAAATTTTCTGAACAT
131 TTTATAACTTCGGTTCCTTAAAGTA-TTCAAGATGATCCATTCCTTCGAGGAATTTTC-AAACAT
* * * *
1247 TTCATTCTTGGGAAATCGAATC
194 TCCATGCTCGGGAAATCGCATC
* * * *
1269 ATTTGGTCCAATTAGTTTGTCATTTTGTAAACAACTTTTTATCTTTGAATTTAAAACTTATTTAA
1 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAC
* * * ** * *
1334 GTGAGAATTATTTCTGTATTGGTTCTTGGTTGAACTTCTGAACTTGT-ACAACCTTTACGAGTTC
66 GTGAGAATTGTTTGTCTATTGGTTCTTGGCCGAACTTCCGAACTTGTCA-AACTTTTACGAGTTC
* * *
1398 TTTTATAACTTTGGCT-CTATAAAGTATTCAAGATGATCCATTCCTTCGAGGAGTTTTCCAAACA
130 TTTTATAACTTCGGTTCCT-TAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTTT-CAAACA
*
1462 TTCCATGCTCGGGAAATCGCATT
193 TTCCATGCTCGGGAAATCGCATC
* * *
1485 GTTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTCGAATTAAAAATTTATTTAC
1 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAC
* * * * * * *
1550 GAGAGAATTGTTTGTCTATTGGTCCTTGGACGAACTCCCGAACTTGTAAAAGTTTTACGAGTTCC
66 GTGAGAATTGTTTGTCTATTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCT
* ** * * * *
1615 TTTATAACTTCGATTCCTTAAAGTATTCAAGACAATCCATTCCTTAGAGCAATTTTTCGAACGTT
131 TTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAA-TTTTCAAACATT
* * *
1680 CCATTCTCGAGAAATTGCATC
195 CCATGCTCGGGAAATCGCATC
*
1701 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAG
1 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAC
* * * * * * *
1766 GTGAGAATTATTTGCCTATTGGTCCCTGGCCGAACTTCAGAACTTGTCAAACTTTTACAAGTACT
66 GTGAGAATTGTTTGTCTATTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCT
* * * *
1831 TTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGAAATTTTTCAAACGTT
131 TTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAA-TTTTCAAACATT
* ** *
1896 CCACGCTCAAGAAATTGCATC
195 CCATGCTCGGGAAATCGCATC
* * * * *
1917 ATTTGGTCCAAATAATTTTTCATTTTGTAAAAAAC---TTGTCTTTGAATTAAAAACTTATTCAG
1 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAC
* ** * *
1979 GTGAGAATTGTTTGTCTATTGG-TCATTGGTCGAACTTCCGAACTTGTTGAACTTTTTCAAGTTC
66 GTGAGAATTGTTTGTCTATTGGTTC-TTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTC
* * * * *
2043 TTTTATAACTTCGATTCCTTAAAGTATTCAAAATGATCCATTCCTTCGAGGAATTTTTCGACCAA
130 TTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAA-TTTTCAAACAT
* *
2108 TCCATGCTTGGGAAATCGTATC
194 TCCATGCTCGGGAAATCGCATC
* * * * **
2130 ATTAGGTCCAAATAGTATATCATTATAG-AAACAACTTTTTGTCTTTGAATTTGAAACTTATTTA
1 ATTTGGTCCAAATAGTTTGTCATT-TTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTA
* * * ** * *
2194 AGTGAGAATTATTTTTCTATTGGTTCTTGGTTGAACTTCTGAACTTGT-ACAACCTTTACGAGTT
65 CGTGAGAATTGTTTGTCTATTGGTTCTTGGCCGAACTTCCGAACTTGTCA-AACTTTTACGAGTT
* *
2258 CTTTTATAACTTTGGTT-CTATAAAGTATTCAAGATGATCCATTCCTTCGAGAAATTTTCCAAAC
129 CTTTTATAACTTCGGTTCCT-TAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTTT-CAAAC
2322 ATTCCATGCTCGGGAAATCGCATC
192 ATTCCATGCTCGGGAAATCGCATC
* *
2346 GTTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTCGAATTAAAA
1 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAA
2401 TTTCGAACTT
Statistics
Matches: 1842, Mismatches: 286, Indels: 113
0.82 0.13 0.05
Matches are distributed among these distances:
191 5 0.00
195 2 0.00
198 2 0.00
199 119 0.06
200 28 0.02
201 2 0.00
206 3 0.00
207 28 0.02
208 125 0.07
209 4 0.00
211 1 0.00
212 4 0.00
213 177 0.10
214 125 0.07
215 184 0.10
216 1017 0.55
217 16 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (215 bp):
ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAC
GTGAGAATTGTTTGTCTATTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCT
TTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTTTCAAACATTC
CATGCTCGGGAAATCGCATC
Found at i:2537 original size:179 final size:178
Alignment explanation
Indices: 2226--2578 Score: 462
Period size: 179 Copynumber: 2.0 Consensus size: 178
2216 GTTCTTGGTT
* *
2226 GAACTTCTGAACTTGTACAACCTTTACGAGTTCTTTTATAACTTTGGTTCTATAAAGTATTCAAG
1 GAACTTCCGAACTTGTACAACCTTTACGAGTTCGTTTATAACTTTGGTTCTATAAAGTATTCAAG
* * *
2291 ATGATCCATTCCTTCGAGAAATTTTCCAAACATTCCATGCTCGGGAAATCGCATCGTTTGGTCCA
66 ACGATCCATTCCTTCGAGAAATTTTCCAAACATTCCATGCTCGGGAAATCGCATCATTTGATCCA
* * * *
2356 AATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTCGAATTAAAATTTC
131 AATAGTATG-AATTTCGTAAACAACTTTTTGTCTTCGAATAAAAATTTC
* * *
2405 GAACTTCCGAGCTTGT-CAAACTTTTACGAGTTCGTTTATAACTTTGGTTCCT-TAAAGTGTTCA
1 GAACTTCCGAACTTGTAC-AACCTTTACGAGTTCGTTTATAACTTTGGTT-CTATAAAGTATTCA
* * * * * *
2468 A-AGCGATCCTTTCCTTTGAGGAA-TTTCTCGAACATTCCATGCTTGGGAAATCGGATCATTTGA
64 AGA-CGATCCATTCCTTCGAGAAATTTTC-CAAACATTCCATGCTCGGGAAATCGCATCATTTGA
*
2531 TCCAAATAGTATGAATTTCGTAAACAACTTTTTGTCTTTGAATAAAAA
127 TCCAAATAGTATGAATTTCGTAAACAACTTTTTGTCTTCGAATAAAAA
2579 CTTATTTAAG
Statistics
Matches: 151, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
178 37 0.25
179 112 0.74
180 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (178 bp):
GAACTTCCGAACTTGTACAACCTTTACGAGTTCGTTTATAACTTTGGTTCTATAAAGTATTCAAG
ACGATCCATTCCTTCGAGAAATTTTCCAAACATTCCATGCTCGGGAAATCGCATCATTTGATCCA
AATAGTATGAATTTCGTAAACAACTTTTTGTCTTCGAATAAAAATTTC
Found at i:3348 original size:216 final size:216
Alignment explanation
Indices: 2404--5859 Score: 3874
Period size: 216 Copynumber: 16.0 Consensus size: 216
2394 ATTAAAATTT
* * * * *
2404 CGAACTTCCGAGCTTGTCAAACTTTTACGAGTTCGTTTATAACTTTGGTTCCTTAAAGTGTTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * * * * * * *
2469 -AGCGATCCTTTCCTTTGAGGAATTTCTCGAACATTCCATGCTTGGGAAATCGGATCATTTGATC
66 GA-CGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTC
* * * *
2533 CAAATAGTATG-AATTTCGTAAACAACTTTTTGTCTTTGAA-TAAAAACTTATTTAAGTGAGAAT
130 CAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAAT
*
2596 TGTTTGTCTATTGGTCCTTGGC
195 TGTTTGTCTATTGGTTCTTGGC
* * * * * *
2618 TGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCATGAAGTATTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
** * * * *
2683 GACGATCCATTCCTTCGAGGTATTTCTCTAACATTCCATGCTCGAGAAATCACATCAGTTGGTCC
66 GACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCC
* * * * *
2748 AAATAGTTTCTCATTTTGTAAAAAAAAAC-TTTTGTCTTTGAGTTAAAAACTGATTTACGTGAGA
131 AAATAGTTTGTCATTTTGT---AAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGA
*
2812 ATTGTTTGTCTCA-TGGTTCTGGGC
193 ATTGTTTGTCT-ATTGGTTCTTGGC
* * ** *
2836 CGAACTTCCGAACTTGTCAAAGTTTTACGAGTTCTTGAATTACTTAGGTTCCTTAAAGTATTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * * * *
2901 GACAATCCATTCCTTCGAGTAA-TTTCCTAAAAATTCCATGCTCGAGAAATCGCATCATTTGCG-
66 GACGATCCATTCCTTCGAGAAATTTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTG-GT
* * * * * *
2964 CCAATTAGTTTTGTCATTTTGTAAACAACTTTTTGTCTGTGGATTAAAAAACATATTTAAGTGAT
129 CCAAATAG-TTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATT-AAAAACTTATTTAGGTGAG
* * * **
3029 AATTGTTTATCTCTTGGGTCTTGTA
192 AATTGTTTGTCTATTGGTTCTTGGC
** * * * * *
3054 CGAAAATCCGAACTGGTAAAACTTTTACAAGTTCTTTTATAACATAGGTTCCTTAAAGTATTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * * * *
3119 AACGATGCATTCCTTCGAGAAATTTTTCGAACATTCTATTCTCGGGAAATCGCATCATTTGGTCC
66 GACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCC
* *
3184 AAATAGTTTGTCACTTTGTAAA-ACACTTTTTGTCTTTGAATTTAAAACTTATTTAGGTGAGAAT
131 AAATAGTTTGTCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAAT
* *
3248 TGTTTGTCTATTGGTCCTTGAC
195 TGTTTGTCTATTGGTTCTTGGC
* * * * * * *
3270 CGAACTTCTAAACTTCTCAAACCTTTACGAGTTCTTTTATAACTTCGATTCTTTAAAGTGTTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* *
3335 GACGATCCATTCCTTCGAGGAATTTCTT-GAACATTCCATGCTCGAGAAAAT-GCATCAATTGGT
66 GACGATCCATTCCTTCGAGAAATTT-TTCGAACATTCCATGCTCGAG-AAATCGCATCATTTGGT
* * * *
3398 CCAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCCTTGAGTTAAAAACTTATTTACGTGAGAA
129 CCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAA
* *
3463 TTGTTTGCCTCA-TGGTTCTTGGA
194 TTGTTTGTCT-ATTGGTTCTTGGC
* * * ** *
3486 CGAA-TATCCGAACTTGTCAAAGTTTTAAGAGTTCTTGAATAACATAGGTTCCTTAAAGTATTCA
1 CGAACT-TCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCA
* * *
3550 AGACGATCCATTCCTTCGAGCAA-TTTTCTGAACATTCCATGCTCGAGAAATCGTATCATTTGGA
65 AGACGATCCATTCCTTCGAGAAATTTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTGGT
* * *
3614 CCAATTAGTTTGTCATTTTGTAAAGAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAA
129 CCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAA
* *
3679 TTGTTTGTCTTTTGGTTCTTGGA
194 TTGTTTGTCTATTGGTTCTTGGC
* * ** * * * * *
3702 CGAACATCAGAACAAGTAAAACTTTTTCAAGTTCTTTTATAACTTATGTTCGTT-AAGTATT-AA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * * * * *
3765 TAACGATGCATTCCTTCAAGAAATTTTTCGAACATTCCATTCCCGGGAAATCGCATCATTTGGTC
66 -GACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTC
*
3830 CAAATAGTTTGTCATTTTGTAAA-ACACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAA
130 CAAATAGTTTGTCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAA
* * *
3894 CTGTTTGTCTATTGGTCCTTGGT
194 TTGTTTGTCTATTGGTTCTTGGC
* * * * * * * *
3917 CGAACTTTTGAAATAGTCAAACTTTTACGGGTTATTTTATAAGTTCGATTCCTTAAAGTATTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
** * * * * * * * *
3982 GATAATCCATTCCTTTGAGGAA-TTTCCTGAACATTTCATGCTAGGGAAATCGCATCATTCGGTT
66 GACGATCCATTCCTTCGAGAAATTTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTGGTC
* * * ** * * *
4046 TAAATAGTTTCTCATTTTGTAAACAACTTTTTGTCCTCAAATTAAAAACTTATTTACGTTAGATT
130 CAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAAT
*
4111 TGTTTGTC-ACATGGTTCTTGGC
195 TGTTTGTCTA-TTGGTTCTTGGC
* * * * ** *
4133 TGAAATTCTGAACTTGTCAAAGTTTTACAAGTTCTTGAATAACTTATGTTCCTTAAAGTATTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * *
4198 GACGATCCATTCCATT-GAGCAA-TTTTCTAAACATTCCACGCTCGAGAAATCGCATCATTTGGT
66 GACGATCCATTCC-TTCGAGAAATTTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTGGT
* * * *
4261 CCAATTAATTTGTCATTTTGTAAACAAC-TTTTGTCTTTGAATTAAAATCTTATTTTGGTGAGAA
129 CCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAA
* * * *
4325 TTGTCTGTCTCTTAGTTCTTGGA
194 TTGTTTGTCTATTGGTTCTTGGC
* * * * *
4348 CGAACATCCGAACTGGT-AAACCTTTTATGACTTCTTTTATAACTTA-GTATCCTTAAAGTATTC
1 CGAACTTCTGAACTTGTCAAA-CTTTTACGAGTTCTTTTATAACTTAGGT-TCCTTAAAGTATTC
* * * * *
4411 AAAACAATCCATTCCTTCGAGAAATTTTCCGAACATTCCATTCACGAGAAATCGCATCATTTGGT
64 AAGACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGT
* * *
4476 CCGAATAGTTTGTCATTTTGTAAA-ACACTTTTTGTCTTTAAATTAAAAACTTATTTTGGTGAGA
129 CCAAATAGTTTGTCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGA
*
4540 ATTGTTTGTCTATTGGTCCTTGGC
193 ATTGTTTGTCTATTGGTTCTTGGC
* * * * * *
4564 CAAACTTCTGAACTTCTCAAACTTTAACGAGTTCTTTTATAACTTCGATTCCTTAATGTATTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * *
4629 GACGATCCATTCCTTCGAGGAATTTCTCGAACATTCCATGCTCGAGAAATCGCATCAATTGGTCC
66 GACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCC
* * * * *
4694 AAATAGTTTCTAACTTTGTAAACAACTTTTTGTCTTTGAGTTAAAAAATTATTT--GTGAGAATT
131 AAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAATT
*
4757 GTTTGTCTCA-TGGTTTTTGGC
196 GTTTGTCT-ATTGGTTCTTGGC
** * ** *
4778 CGAACTTCCAAACTTGTCAAAGTTTTACGAGTTCTTGAATAACTTAGGTTCCTTAAAATATTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * * * * *
4843 GACGATCCATTACTTCGAGCAAA-TTTTCGAAAATTCAAAGCTCGAGAAATTGCATCATTTGGAC
66 GACGATCCATTCCTTCGAG-AAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTC
* *
4907 CAATTAGTTTGTCATTTTGTAAACAACTTTTTATCTTTGAA-TAAAAACTTATTTAGGTGAGAAT
130 CAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAAT
* *
4971 TGTTTGTCTCTTGGTTCTT-GA
195 TGTTTGTCTATTGGTTCTTGGC
* * * *
4992 CGAACATT-TGTACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGGATCCTTAAAGTATTCA
1 CGAAC-TTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCA
* * * *
5056 AAACGA-CACATTCCTTCGAGAAA-TTTTCTGAACATTCCATTCTCGGGAAATCGTATCATTTGG
65 AGACGATC-CATTCCTTCGAGAAATTTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTGG
* * * * *
5119 TCAAAATAGTTTGTCATTTTGTAAA-ACACTTTTTATCTTTGAGTTAAAAACTTATTTTGGTAAG
128 TCCAAATAGTTTGTCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAG
* *
5183 AATTGTTTGTCTATTGGTCCTTGGT
192 AATTGTTTGTCTATTGGTTCTTGGC
* * *
5208 CGAACTTCTTAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * ** * *
5273 GACGATCCATTCCTTTGAGGAATTTCCCGAACATTTCATGCTCGAGAAATTGCATCATTTGGTCC
66 GACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCC
* * **
5338 AATTAGTTTGTCATTTTGTAAACAACTTTTTATCTTTGAATTAAAATA-TTATTTTTGTGAGAAT
131 AAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAA-ACTTATTTAGGTGAGAAT
* *
5402 TGTTTGTCTCTTGGTTCTTGGA
195 TGTTTGTCTATTGGTTCTTGGC
* * * * * *
5424 TGTACGTCTGAAC-TATAAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAATGTATTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * * * *
5488 AACGATTCATTCCTTCGAGAAATTTTTTGAACATTTCATTCTCGAGAAATCGCATCATTTGGTCC
66 GACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCC
* * *
5553 AAATAGTTTTTCATTTTGTAAA-ACACTTTTTATCTTTGAATTAAAAACTTATTTTGGTGAGAAT
131 AAATAGTTTGTCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAAT
*
5617 AT-TTTGTCTATTGGTCCTTGGC
195 -TGTTTGTCTATTGGTTCTTGGC
* * *
5639 CGAACATCTGAACTTGTCAAACTATTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA
1 CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * * * **
5704 GACGATCCATTCTTTTGAGCAATTTTTTTGAATGTTCCATGCTCGAGAAATCGCATCATTTGGTC
66 GACGATCCATTCCTTCGAG-AAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTC
* * * * * *
5769 CATATAGTTTGTCATTTTGTAAACAACTTTCTATCTTTAAATTAAAAACATATTTAGGTTAGAAT
130 CAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAAT
* * *
5834 TGGTTGTCTCTTGGTTCTTGGA
195 TGTTTGTCTATTGGTTCTTGGC
5856 CGAA
1 CGAA
Statistics
Matches: 2715, Mismatches: 459, Indels: 133
0.82 0.14 0.04
Matches are distributed among these distances:
213 22 0.01
214 431 0.16
215 611 0.23
216 1136 0.42
217 199 0.07
218 298 0.11
219 18 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (216 bp):
CGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
GACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCC
AAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAATT
GTTTGTCTATTGGTTCTTGGC
Found at i:3966 original size:647 final size:647
Alignment explanation
Indices: 2404--5859 Score: 4534
Period size: 647 Copynumber: 5.3 Consensus size: 647
2394 ATTAAAATTT
* * * * * * *
2404 CGAACTTCCGAGCTTGTCAAACTTTTACGAGTTCGTTTATAACTTTGGTTCCTTAAAGTGTTCAA
1 CGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * * * * * * * *
2469 AGCGATCCTTTCCTTTGAGGAATTTCTCGAACATTCCATGCTTGGGAAATCGGATCATTTGATCC
66 AACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCC
* * * *
2534 AAATAGTATG-AATTTCGT-AAACAACTTTTTGTCTTTGAA-TAAAAACTTATTTAAGTGAGAAT
131 AAATAGTTTGTCATTTTGTAAAAC-ACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAAT
* *
2596 TGTTTGTCTATTGGTCCTTGGCTGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAC
195 TGTTTGTCTATTGGTCCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAAC
* * *
2661 TTCGATTCCATGAAGTATTCAAGACGATCCATTCCTTCGAGGTATTTCTCT-AACATTCCATGCT
260 TTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGGAATTTCT-TGAACATTCCATGCT
* * *
2725 CGAGAAATCACATCAGTTGGTCCAAATAGTTTCTCATTTTGTAAAAAAAAAC-TTTTGTCTTTGA
324 CGAGAAATCGCATCAATTGGTCCAAATAGTTTCTCATTTTGT---AAACAACTTTTTGTCTTTGA
* * *
2789 GTTAAAAACTGATTTACGTGAGAATTGTTTGTCTCATGGTTCTGGGCCGAACTTCCGAACTTGTC
386 GTTAAAAACTTATTTACGTGAGAATTGTTTGTCTCATGGTTCTTGGACGAA-TTCCGAACTTGTC
* *
2854 AAAGTTTTACGAGTTCTTGAATTACTTAGGTTCCTTAAAGTATTCAAGACAATCCATTCCTTCGA
450 AAAGTTTTACGAGTTCTTGAATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGA
* * * *
2919 GTAATTTCCTAAAAATTCCATGCTCGAGAAATCGCATCATTTGCG-CCAATTAGTTTTGTCATTT
515 GCAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTG-GACCAATTAG-TTTGTCATTT
* * * ** * * *
2983 TGTAAACAACTTTTTGTCTGTGGATTAAAAAACATATTTAAGTGATAATTGTTTATCTCTTGGGT
578 TGTAAACAACTTTTTGTCTTTGAATT-AAAAACTTATTTTGGTGAGAATTGTTTGTCTCTTGGTT
*
3048 CTTGTA
642 CTTGGA
* * *
3054 CGAAAATCCGAACTGGTAAAACTTTTACAAGTTCTTTTATAACATAGGTTCCTTAAAGTATTCAA
1 CGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* *
3119 AACGATGCATTCCTTCGAGAAATTTTTCGAACATTCTATTCTCGGGAAATCGCATCATTTGGTCC
66 AACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCC
* *
3184 AAATAGTTTGTCACTTTGTAAAACACTTTTTGTCTTTGAATTTAAAACTTATTTAGGTGAGAATT
131 AAATAGTTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAATT
* * * *
3249 GTTTGTCTATTGGTCCTTGACCGAACTTCTAAACTTCTCAAACCTTTACGAGTTCTTTTATAACT
196 GTTTGTCTATTGGTCCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACT
* *
3314 TCGATTCTTTAAAGTGTTCAAGACGATCCATTCCTTCGAGGAATTTCTTGAACATTCCATGCTCG
261 TCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGGAATTTCTTGAACATTCCATGCTCG
* * *
3379 AGAAAAT-GCATCAATTGGTCCAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCCTTGAGTTA
326 AG-AAATCGCATCAATTGGTCCAAATAGTTTCTCATTTTGTAAACAACTTTTTGTCTTTGAGTTA
*
3443 AAAACTTATTTACGTGAGAATTGTTTGCCTCATGGTTCTTGGACGAATATCCGAACTTGTCAAAG
390 AAAACTTATTTACGTGAGAATTGTTTGTCTCATGGTTCTTGGACGAAT-TCCGAACTTGTCAAAG
* *
3508 TTTTAAGAGTTCTTGAATAACATAGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
454 TTTTACGAGTTCTTGAATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
*
3573 TTTTCTGAACATTCCATGCTCGAGAAATCGTATCATTTGGACCAATTAGTTTGTCATTTTGTAAA
519 TTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGACCAATTAGTTTGTCATTTTGTAAA
* *
3638 GAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTTTTGGTTCTTGGA
584 CAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTCTTGGTTCTTGGA
* ** * * * *
3702 CGAACATCAGAACAAGTAAAACTTTTTCAAGTTCTTTTATAACTTATGTTCGTT-AAGTATT-AA
1 CGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * *
3765 TAACGATGCATTCCTTCAAGAAATTTTTCGAACATTCCATTCCCGGGAAATCGCATCATTTGGTC
66 -AACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTC
* *
3830 CAAATAGTTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAAC
130 CAAATAGTTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAAT
* * * * * * *
3895 TGTTTGTCTATTGGTCCTTGGTCGAACTTTTGAAATAGTCAAACTTTTACGGGTTATTTTATAAG
195 TGTTTGTCTATTGGTCCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAAC
** * * * *
3960 TTCGATTCCTTAAAGTATTCAAGATAATCCATTCCTTTGAGGAATTTCCTGAACATTTCATGCTA
260 TTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGGAATTTCTTGAACATTCCATGCTC
* ** * ** *
4025 GGGAAATCGCATC-ATTCGGTTTAAATAGTTTCTCATTTTGTAAACAACTTTTTGTCCTCAAATT
325 GAGAAATCGCATCAATT-GGTCCAAATAGTTTCTCATTTTGTAAACAACTTTTTGTCTTTGAGTT
* * * *
4089 AAAAACTTATTTACGTTAGATTTGTTTGTCACATGGTTCTTGG-CTGAAATTCTGAACTTGTCAA
389 AAAAACTTATTTACGTGAGAATTGTTTGTCTCATGGTTCTTGGAC-G-AATTCCGAACTTGTCAA
* *
4153 AGTTTTACAAGTTCTTGAATAACTTATGTTCCTTAAAGTATTCAAGACGATCCATTCCATT-GAG
452 AGTTTTACGAGTTCTTGAATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTCC-TTCGAG
* * * *
4217 CAATTTTCTAAACATTCCACGCTCGAGAAATCGCATCATTTGGTCCAATTAATTTGTCATTTTGT
516 CAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGACCAATTAGTTTGTCATTTTGT
* * *
4282 AAACAAC-TTTTGTCTTTGAATTAAAATCTTATTTTGGTGAGAATTGTCTGTCTCTTAGTTCTTG
581 AAACAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTCTTGGTTCTTG
4346 GA
646 GA
* * *
4348 CGAACATCCGAACTGGTAAACCTTTTATGACTTCTTTTATAACTTA-GTATCCTTAAAGTATTCA
1 CGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGGT-TCCTTAAAGTATTCA
* * * *
4412 AAACAATCCATTCCTTCGAGAAATTTTCCGAACATTCCATTCACGAGAAATCGCATCATTTGGTC
65 AAACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTC
* * *
4477 CGAATAGTTTGTCATTTTGTAAAACACTTTTTGTCTTTAAATTAAAAACTTATTTTGGTGAGAAT
130 CAAATAGTTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAAT
* * *
4542 TGTTTGTCTATTGGTCCTTGGCCAAACTTCTGAACTTCTCAAACTTTAACGAGTTCTTTTATAAC
195 TGTTTGTCTATTGGTCCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAAC
* *
4607 TTCGATTCCTTAATGTATTCAAGACGATCCATTCCTTCGAGGAATTTCTCGAACATTCCATGCTC
260 TTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGGAATTTCTTGAACATTCCATGCTC
* *
4672 GAGAAATCGCATCAATTGGTCCAAATAGTTTCTAACTTTGTAAACAACTTTTTGTCTTTGAGTTA
325 GAGAAATCGCATCAATTGGTCCAAATAGTTTCTCATTTTGTAAACAACTTTTTGTCTTTGAGTTA
* * * *
4737 AAAAATTATTT--GTGAGAATTGTTTGTCTCATGGTTTTTGGCCGAACTTCCAAACTTGTCAAAG
390 AAAACTTATTTACGTGAGAATTGTTTGTCTCATGGTTCTTGGACGAA-TTCCGAACTTGTCAAAG
* *
4800 TTTTACGAGTTCTTGAATAACTTAGGTTCCTTAAAATATTCAAGACGATCCATTACTTCGAGCAA
454 TTTTACGAGTTCTTGAATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGC-A
* * * *
4865 ATTTTC-GAAAATTCAAAGCTCGAGAAATTGCATCATTTGGACCAATTAGTTTGTCATTTTGTAA
518 ATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGACCAATTAGTTTGTCATTTTGTAA
* *
4929 ACAACTTTTTATCTTTGAA-TAAAAACTTATTTAGGTGAGAATTGTTTGTCTCTTGGTTCTT-GA
583 ACAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTCTTGGTTCTTGGA
** * *
4992 CGAACATTTGTACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGGATCCTTAAAGTATTCAA
1 CGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
*
5057 AACGA-CACATTCCTTCGAGAAA-TTTTCTGAACATTCCATTCTCGGGAAATCGTATCATTTGGT
66 AACGATC-CATTCCTTCGAGAAATTTTTC-GAACATTCCATTCTCGGGAAATCGCATCATTTGGT
* * * * *
5120 CAAAATAGTTTGTCATTTTGTAAAACACTTTTTATCTTTGAGTTAAAAACTTATTTTGGTAAGAA
129 CCAAATAGTTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAA
* * *
5185 TTGTTTGTCTATTGGTCCTTGGTCGAACTTCTTAACTTGTCAAACTTTTACAAGTTCTTTTATAA
194 TTGTTTGTCTATTGGTCCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAA
* * * ** *
5250 CTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTCCCGAACATTTCATGCT
259 CTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGGAATTTCTTGAACATTCCATGCT
* * * * * *
5315 CGAGAAATTGCATCATTTGGTCCAATTAGTTTGTCATTTTGTAAACAACTTTTTATCTTTGAATT
324 CGAGAAATCGCATCAATTGGTCCAAATAGTTTCTCATTTTGTAAACAACTTTTTGTCTTTGAGTT
** * * ** * * *
5380 AAAATA-TTATTTTTGTGAGAATTGTTTGTCTCTTGGTTCTTGGATGTACGTCTGAAC-TATAAA
389 AAAA-ACTTATTTACGTGAGAATTGTTTGTCTCATGGTTCTTGGACG-AATTCCGAACTTGTCAA
* ** * * * *
5443 ACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAATGTATTCAAAACGATTCATTCCTTCGAGA
452 AGTTTTACGAGTTCTTGAATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGC
* * * * * *
5508 AATTTTTTGAACATTTCATTCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTTTCATTTTGTA
517 AATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGACCAATTAGTTTGTCATTTTGTA
* * *
5573 AA-ACACTTTTTATCTTTGAATTAAAAACTTATTTTGGTGAGAATAT-TTTGTCTATTGGTCCTT
582 AACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAAT-TGTTTGTCTCTTGGTTCTT
*
5636 GGC
645 GGA
* * * * *
5639 CGAACATCTGAACTTGTCAAACTATTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA
1 CGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
* * * * * ** * *
5704 GACGATCCATTCTTTTGAGCAATTTTTTTGAATGTTCCATGCTCGAGAAATCGCATCATTTGGTC
66 AACGATCCATTCCTTCGAG-AAATTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTC
* * * * * *
5769 CATATAGTTTGTCATTTTGT-AAACAACTTTCTATCTTTAAATTAAAAACATATTTAGGTTAGAA
130 CAAATAGTTTGTCATTTTGTAAAAC-ACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAA
* * * *
5833 TTGGTTGTCTCTTGGTTCTTGGACGAA
194 TTGTTTGTCTATTGGTCCTTGGCCGAA
Statistics
Matches: 2470, Mismatches: 297, Indels: 80
0.87 0.10 0.03
Matches are distributed among these distances:
643 5 0.00
644 364 0.15
645 321 0.13
646 197 0.08
647 843 0.34
648 200 0.08
649 44 0.02
650 295 0.12
651 22 0.01
652 175 0.07
653 4 0.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (647 bp):
CGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA
AACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCC
AAATAGTTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAATT
GTTTGTCTATTGGTCCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACT
TCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGGAATTTCTTGAACATTCCATGCTCG
AGAAATCGCATCAATTGGTCCAAATAGTTTCTCATTTTGTAAACAACTTTTTGTCTTTGAGTTAA
AAACTTATTTACGTGAGAATTGTTTGTCTCATGGTTCTTGGACGAATTCCGAACTTGTCAAAGTT
TTACGAGTTCTTGAATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATT
TTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGACCAATTAGTTTGTCATTTTGTAAACA
ACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTCTTGGTTCTTGGA
Found at i:4014 original size:431 final size:432
Alignment explanation
Indices: 2416--5859 Score: 3880
Period size: 431 Copynumber: 8.0 Consensus size: 432
2406 AACTTCCGAG
* * * *
2416 CTTGTCAAACTTTTACGAGTTCGTTTATAACTTTGGTTCCTTAAAGTGTTCAA-AGCGATCCTTT
1 CTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGA-CGATCCATT
* * * * * * * *
2480 CCTTTGAGGAATTTCTCGAACATTCCATGCTTGGGAAATCGGATCATTTGATCCAAATAGTATG-
65 CCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGT
* * **
2544 AATTTCGTAAACAACTTTTTGTCTTTGAA-TAAAAACTTATTTAAGTGAGAATTGTTTGTCTATT
130 CATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTATT
* * *
2608 GGTCCTTGG-CTGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCAT
195 GGTCCTTGGTC-GAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTT
* ** *
2672 GAAGTATTCAAGACGATCCATTCCTTCGAGGTATTTCTCT-AACATTCCATGCTCGAGAAATCAC
259 AAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTC-CTGAACATTCCATGCTCGAGAAATCGC
* * * * * *
2736 ATCAGTTGGTCCAAATAGTTTCTCATTTTGTAAAAAAAAAC-TTTTGTCTTTGAGTTAAAAACTG
323 ATCATTTGGTCCAATTAGTTTGTCATTTTGT---AAACAACTTTTTGTCTTTGAATTAAAAACTT
* * * * * *
2800 ATTTACGTGAGAATTGTTTGTCTCATGGTTCTGGGCCGAACTTCCGAA
385 ATTTAGGTGAGAATTGTTTGTCTCTTGGTTCTTGGACGAACATCTGAA
* ** * *
2848 CTTGTCAAAGTTTTACGAGTTCTTGAATTACTTAGGTTCCTTAAAGTATTCAAGACAATCCATTC
1 CTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTC
* * * * *
2913 CTTCGAGTAA-TTTCCTAAAAATTCCATGCTCGAGAAATCGCATCATTTGCG-CCAATTAGTTTT
66 CTTCGAGAAATTTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTG-GTCCAAATAG-TTT
* * * ** * *
2976 GTCATTTTGTAAACAACTTTTTGTCTGTGGATTAAAAAACATATTTAAGTGATAATTGTTTATCT
128 GTCATTTTGTAAACAACTTTTTGTCTTTGAATT-AAAAACTTATTTTGGTGAGAATTGTTTGTCT
* ** * * * *
3041 CTTGGGT-CTT-GTACGAAAATCCGAACTGGTAAAACTTTTACAAGTTCTTTTATAACATAGGTT
192 ATT-GGTCCTTGGT-CGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTT
* * * * * *
3104 CCTTAAAGTATTCAAAACGATGCATTCCTTCGAGAAATTT-TTCGAACATTCTATTCTCGGGAAA
255 CCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTCCT-GAACATTCCATGCTCGAGAAA
* * *
3168 TCGCATCATTTGGTCCAAATAGTTTGTCACTTTGTAAA-ACACTTTTTGTCTTTGAATTTAAAAC
319 TCGCATCATTTGGTCCAATTAGTTTGTCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAAC
* * * *
3232 TTATTTAGGTGAGAATTGTTTGTCTATTGGTCCTT-GACCGAACTTCTAAA
383 TTATTTAGGTGAGAATTGTTTGTCTCTTGGTTCTTGGA-CGAACATCTGAA
* * * * * *
3282 CTTCTCAAACCTTTACGAGTTCTTTTATAACTTCGATTCTTTAAAGTGTTCAAGACGATCCATTC
1 CTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTC
* *
3347 CTTCGAGGAATTTCTT-GAACATTCCATGCTCGAGAAAAT-GCATCAATTGGTCCAAATAGTTTG
66 CTTCGAGAAATTT-TTCGAACATTCCATGCTCGAG-AAATCGCATCATTTGGTCCAAATAGTTTG
* * * ** *
3410 TCATTTTGTAAACAAGTTTTTGTCCTTGAGTTAAAAACTTATTTACGTGAGAATTGTTTGCCTCA
129 TCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCT-A
* * * * ** *
3475 -TGGTTCTTGGACGAA-TATCCGAACTTGTCAAAGTTTTAAGAGTTCTTGAATAACATAGGTTCC
193 TTGGTCCTTGGTCGAACT-TCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCC
* *
3538 TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAATCG
257 TTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTCCTGAACATTCCATGCTCGAGAAATCG
* * *
3603 TATCATTTGGACCAATTAGTTTGTCATTTTGTAAAGAACTTTTTGTCTTTGAATTAAAAACTTAT
322 CATCATTTGGTCCAATTAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTAT
* * *
3668 TTTGGTGAGAATTGTTTGTCTTTTGGTTCTTGGACGAACATCAGAA
387 TTAGGTGAGAATTGTTTGTCTCTTGGTTCTTGGACGAACATCTGAA
** * * * * * * *
3714 CAAGTAAAACTTTTTCAAGTTCTTTTATAACTTATGTTCGTT-AAGTATT-AATAACGATGCATT
1 CTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAA-GACGATCCATT
* * * *
3777 CCTTCAAGAAATTTTTCGAACATTCCATTCCCGGGAAATCGCATCATTTGGTCCAAATAGTTTGT
65 CCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGT
*
3842 CATTTTGTAAA-ACACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAACTGTTTGTCTAT
130 CATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTAT
** * * * * * * *
3906 TGGTCCTTGGTCGAACTTTTGAAATAGTCAAACTTTTACGGGTTATTTTATAAGTTCGATTCCTT
194 TGGTCCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTT
** * * * * *
3971 AAAGTATTCAAGATAATCCATTCCTTTGAGGAATTTCCTGAACATTTCATGCTAGGGAAATCGCA
259 AAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTCCTGAACATTCCATGCTCGAGAAATCGCA
* ** * * * **
4036 TCATTCGGTTTAAATAGTTTCTCATTTTGTAAACAACTTTTTGTCCTCAAATTAAAAACTTATTT
324 TCATTTGGTCCAATTAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTT
* * * * *
4101 ACGTTAGATTTGTTTGTCACATGGTTCTTGG-CTGAA-ATTCTGAA
389 AGGTGAGAATTGTTTGTCTCTTGGTTCTTGGAC-GAACA-TCTGAA
* * ** *
4145 CTTGTCAAAGTTTTACAAGTTCTTGAATAACTTATGTTCCTTAAAGTATTCAAGACGATCCATTC
1 CTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTC
* * * * *
4210 CATT-GAGCAA-TTTTCTAAACATTCCACGCTCGAGAAATCGCATCATTTGGTCCAATTAATTTG
66 C-TTCGAGAAATTTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTG
* * *
4273 TCATTTTGTAAACAAC-TTTTGTCTTTGAATTAAAATCTTATTTTGGTGAGAATTGTCTGTCTCT
129 TCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTAT
* * * * * * *
4337 TAGTTCTTGGACGAACATCCGAACTGGT-AAACCTTTTATGACTTCTTTTATAACTTA-GTATCC
194 TGGTCCTTGGTCGAACTTCCGAACTTGTCAAA-CTTTTACGAGTTCTTTTATAACTTAGGT-TCC
* * * *
4400 TTAAAGTATTCAAAACAATCCATTCCTTCGAGAAATTTTCC-GAACATTCCATTCACGAGAAATC
257 TTAAAGTATTCAAGACGATCCATTCCTTCGAGAAA-TTTCCTGAACATTCCATGCTCGAGAAATC
*
4464 GCATCATTTGGTCCGAA-TAGTTTGTCATTTTGTAAA-ACACTTTTTGTCTTTAAATTAAAAACT
321 GCATCATTTGGTCC-AATTAGTTTGTCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACT
* * * * * *
4527 TATTTTGGTGAGAATTGTTTGTCTATTGGTCCTTGGCCAAACTTCTGAA
384 TATTTAGGTGAGAATTGTTTGTCTCTTGGTTCTTGGACGAACATCTGAA
* * * * *
4576 CTTCTCAAACTTTAACGAGTTCTTTTATAACTTCGATTCCTTAATGTATTCAAGACGATCCATTC
1 CTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTC
* * * * *
4641 CTTCGAGGAATTTCTCGAACATTCCATGCTCGAGAAATCGCATCAATTGGTCCAAATAGTTTCTA
66 CTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTC
* * *
4706 ACTTTGTAAACAACTTTTTGTCTTTGAGTTAAAAAATTA-TTT-GTGAGAATTGTTTGTCTCA-T
131 ATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCT-ATT
** * * * **
4768 GGTTTTTGGCCGAACTTCCAAACTTGTCAAAGTTTTACGAGTTCTTGAATAACTTAGGTTCCTTA
195 GGTCCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTA
* * * * * * *
4833 AAATATTCAAGACGATCCATTACTTCGAGCAAATTTTC-GAAAATTCAAAGCTCGAGAAATTGCA
260 AAGTATTCAAGACGATCCATTCCTTCGAG-AAATTTCCTGAACATTCCATGCTCGAGAAATCGCA
* *
4897 TCATTTGGACCAATTAGTTTGTCATTTTGTAAACAACTTTTTATCTTTGAA-TAAAAACTTATTT
324 TCATTTGGTCCAATTAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTT
* *
4961 AGGTGAGAATTGTTTGTCTCTTGGTTCTT-GACGAACATTTGTA
389 AGGTGAGAATTGTTTGTCTCTTGGTTCTTGGACGAACATCTGAA
* * * *
5004 CTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGGATCCTTAAAGTATTCAAAACGA-CACATT
1 CTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGACGATC-CATT
* * * *
5068 CCTTCGAGAAA-TTTTCTGAACATTCCATTCTCGGGAAATCGTATCATTTGGTCAAAATAGTTTG
65 CCTTCGAGAAATTTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTG
* * *
5132 TCATTTTGTAAA-ACACTTTTTATCTTTGAGTTAAAAACTTATTTTGGTAAGAATTGTTTGTCTA
129 TCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTA
** * *
5196 TTGGTCCTTGGTCGAACTTCTTAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCT
193 TTGGTCCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCT
* * * * *
5261 TAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTCCCGAACATTTCATGCTCGAGAAATTGC
258 TAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTCCTGAACATTCCATGCTCGAGAAATCGC
*
5326 ATCATTTGGTCCAATTAGTTTGTCATTTTGTAAACAACTTTTTATCTTTGAATTAAAATA-TTAT
323 ATCATTTGGTCCAATTAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAA-ACTTAT
** * * *
5390 TTTTGTGAGAATTGTTTGTCTCTTGGTTCTTGGATGTACGTCTGAA
387 TTAGGTGAGAATTGTTTGTCTCTTGGTTCTTGGACGAACATCTGAA
* * * * *
5436 C-TATAAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAATGTATTCAAAACGATTCATTC
1 CTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTC
* * * *
5500 CTTCGAGAAATTTTTTGAACATTTCATTCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTTTC
66 CTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTC
*
5565 ATTTTGTAAA-ACACTTTTTATCTTTGAATTAAAAACTTATTTTGGTGAGAATAT-TTTGTCTAT
131 ATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAAT-TGTTTGTCTAT
* * * * *
5628 TGGTCCTTGGCCGAACATCTGAACTTGTCAAACTATTACGAGTTCTTTTATAACTTTGGTTCCTT
194 TGGTCCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTT
* * * ** **
5693 AAAGTATTCAAGACGATCCATTCTTTTGAGCAATTTTTTTGAATGTTCCATGCTCGAGAAATCGC
259 AAAGTATTCAAGACGATCCATTCCTTCGAG-AAATTTCCTGAACATTCCATGCTCGAGAAATCGC
* * * *
5758 ATCATTTGGTCC-ATATAGTTTGTCATTTTGTAAACAACTTTCTATCTTTAAATTAAAAACATAT
323 ATCATTTGGTCCAAT-TAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTAT
* *
5822 TTAGGTTAGAATTGGTTGTCTCTTGGTTCTTGGACGAA
387 TTAGGTGAGAATTGTTTGTCTCTTGGTTCTTGGACGAA
Statistics
Matches: 2547, Mismatches: 394, Indels: 142
0.83 0.13 0.05
Matches are distributed among these distances:
427 6 0.00
428 148 0.06
429 51 0.02
430 345 0.14
431 1005 0.39
432 592 0.23
433 52 0.02
434 179 0.07
435 8 0.00
436 157 0.06
437 4 0.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (432 bp):
CTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGACGATCCATTC
CTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTC
ATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTATTG
GTCCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAA
AGTATTCAAGACGATCCATTCCTTCGAGAAATTTCCTGAACATTCCATGCTCGAGAAATCGCATC
ATTTGGTCCAATTAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTAG
GTGAGAATTGTTTGTCTCTTGGTTCTTGGACGAACATCTGAA
Done.