Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008137.1 Hibiscus syriacus cultivar Beakdansim tig00110692_pilon, 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: 382795
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:251223 original size:20 final size:20
Alignment explanation
Indices: 251198--251252 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
251188 TAAGCATCAT
251198 GCTCGAAGGACTTATTGATG
1 GCTCGAAGGACTTATTGATG
251218 GCTCGAAGGACTTATTGATG
1 GCTCGAAGGACTTATTGATG
*
251238 GCCCGAAGGACTTAT
1 GCTCGAAGGACTTAT
251253 AAATTTTGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (20 bp):
GCTCGAAGGACTTATTGATG
Found at i:251946 original size:42 final size:41
Alignment explanation
Indices: 251828--251946 Score: 114
Period size: 42 Copynumber: 2.9 Consensus size: 41
251818 CATGTAGAAT
* * * *
251828 CATCATGCTCGAATGTCTTATGGATGGCCCGAAGGACTTAT
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTAG
* * * *
251869 CATCTTGCTCGAAAGACTTACAGACGACCCGAAGGA-TTAGAG
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTT--AG
* * *
251911 CATCATGCTCAAAAGACTTATTGATGGCCCAAAGGA
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGA
251947 ATTATAAATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
40 2 0.03
41 29 0.48
42 30 0.49
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (41 bp):
CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTAG
Found at i:252178 original size:465 final size:464
Alignment explanation
Indices: 251218--253669 Score: 3208
Period size: 465 Copynumber: 5.3 Consensus size: 464
251208 CTTATTGATG
* *
251218 GCTCGAAGGACTTATTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAA
1 GCTCGAAAGACTTATTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAA
* * *
251283 ACTTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATTTTTCGA
66 ACCTTTCTTACTTTTAAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGA
* * * * * *
251348 GAGACAAGTGAAAACATCCTGCCTGGAGGTCTTA-GAGATGGTCCGAATGACTTATCATCTTGCT
131 GAGACATGTGAAAACATCATGCCCGAAGGTCTTATG-GATGGCCCGAAGGACTTATCATCTTGCT
** * * *
251412 ATAATGACTTACTGATTACCCAAAGGATTTAAGCATCATGCAT-GAAAGACTTACTGAAT-GCCC
195 CGAAAGACTTACAGATGACCCAAAGGATTTAAGCATCATGC-TCGAAAGACTTACTG-ATGGCCC
*
251475 GAAGGACTTACCAATTTTGGAAATAGTTTACAAGGTAAGAAACCTTTCTTACTTTTCAAAAATTT
258 GAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTAC-TTTCAAAAATTT
* * *
251540 CAATATTCAGATTTAAATGAGAAA-CTTTCTCATTTTTCGAGAGACATGTGAAAATATCCAGCCC
322 CAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTCCGAGAGACATGTGAAAATATCCTGCCC
* * * * * *
251604 GAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGTTCGAAAGACTTACAAATGAACCAAAG
387 GAAGGTCTTATGGATGG-CCGAAGGACTTATCATCTTGCTCTAAAGACTTACTAGTGACCCAAAG
251669 GATTTAAGCATCAT
451 GATTTAAGCATCAT
* * * *
251683 GCTCGAAAGACTGATTGATGGCCCGAAGGACTTATAAATTTAGGAAATAATTTACTAGGTAAGAA
1 GCTCGAAAGACTTATTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAA
* *
251748 ACCTTTCTTACTTTTTAAAAAATTTCAATTTTCAGATTTAAATGAGAAATCTTTCTCATTTTTTG
66 ACCTTTCTTAC-TTTTAAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCG
* * * *
251813 AGATACATGT-AGAATCATCATGCTCGAATGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC
130 AGAGACATGTGA-AAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC
* * * *
251877 TCGAAAGACTTACAGACGACCCGAAGGA-TTAGAGCATCATGCTCAAAAGACTTATTGATGGCCC
194 TCGAAAGACTTACAGATGACCCAAAGGATTTA-AGCATCATGCTCGAAAGACTTACTGATGGCCC
* * **
251941 AAAGGAATTATAAATTTTGGAAATAGTTTACTAGGTAA-AAACCTTTCTTACATTTCAAAAATTT
258 GAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTAC-TTTCAAAAATTT
* * * * *
252005 CAATTTTCATATTTAAATGAGAAACCTTTCTCATTTTCCGAGAGATATGTGAAAACAACCTGCCT
322 CAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTCCGAGAGACATGTGAAAATATCCTGCCC
* * * **
252070 GAAGGTCTTCTGGATGGCCGAAGGACTTATCATCTTGCTATAATA-ACTTACTAGTTACCTTAAG
387 GAAGGTCTTATGGATGGCCGAAGGACTTATCATCTTGCTCTAA-AGACTTACTAGTGACCCAAAG
252134 GATTTAAGCATCAT
451 GATTTAAGCATCAT
* *** *
252148 GCTCGAAAGACTTACTGAAAACCAGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAA
1 GCTCGAAAGACTTATTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAA
* * * *
252213 ACCTTTCTTAATTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACATTTCTCATTTTTCGA
66 ACCTTTCTTACTTTTAAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGA
* * * * * * *
252278 GAGACATGTGAAAAAAATCTTGCCCGAAGGTCATATAGATTGCCCGAAGGACTTGTCATATTGCT
131 GAGACATGTG-AAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCT
* **
252343 CGAAAGACTTACAAATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTAA
195 CGAAAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGA
* * *
252408 AGGACTTGCCAATTTTGAAAATAGTTTACTAGGTATGAAACCTTTCTTACTTGTCAAAAATTTCA
260 AGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTT-TCAAAAATTTCA
* * * *
252473 ATTTTCAGATTTAAATGAGAAACATTTTTCA-TTTCTCAAAAGACATGTGAAAATATCCTGCCCG
324 ATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTC-CGAGAGACATGTGAAAATATCCTGCCCG
* * * * * * *
252537 AAGGTCTTATGGATGTCCCGAAGGATTTATCATCTTACTCGAAAGACTTACAAATGACCCAAAGT
388 AAGGTCTTATGGATG-GCCGAAGGACTTATCATCTTGCTCTAAAGACTTACTAGTGACCCAAAGG
* *
252602 ATTTAATCATAAT
452 ATTTAAGCATCAT
* * * * *
252615 GCTCGAAAGACTTATTGATGGCCTGAAGGACTTATAATTTTTTGAAATAATTTACTAGGTAAGAA
1 GCTCGAAAGACTTATTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAA
* * * ** *
252680 ACCTTTCTTACTTTTAAAAAAAATTCAATTTTCATAGTTAAACAAGAAAACTTTCTCATTTTTCG
66 ACCTTTCTTACTTTT-AAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCG
* * *
252745 AGAGACATGTGAAAACATCATGCCCAAAGGTCTTATGGATGGTCCGAAAGACTTATCATCTTGCT
130 AGAGACATGTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCT
* * * * * *
252810 AGAAATACTTACAGATGACCCGAAGG-TTAAAACATCATGCTCGAAAGACTTATTGATGGCCCGA
195 CGAAAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGA
*** *
252874 AGGACTTTTAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCATACTTTTCAAAAATTTCA
260 AGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTAC-TTTCAAAAATTTCA
* * * *
252939 ATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACATCATGCCCGA
324 ATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTCCGAGAGACATGTGAAAATATCCTGCCCGA
* * * * * *
253004 AGGTCTTATGGATGGCTGAAGGACTTAACATCTTGCTATAATGACTTACT-GATTACCCTAAGGA
389 AGGTCTTATGGATGGCCGAAGGACTTATCATCTTGCTCTAAAGACTTACTAG-TGACCCAAAGGA
253068 TTTAAGCATCAT
453 TTTAAGCATCAT
* * * * * *
253080 GCTCGAAAGACATACTGATGGCCTGAAGGACATACCAATTTTGGAAATAGCTTACTAGGTGAA-A
1 GCTCGAAAGACTTATTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGT-AAGA
* *
253144 AACCTTTCTTACTTTTAAAAATTTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTGTTCG
65 AACCTTTCTTACTTTTAAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCG
* * * *
253209 AGATACACGTGAAAAAAT-ATTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTA-CATCTTGC
130 AGAGACATGTGAAAACATCA-TGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC
* * * * *
253272 TCGAAAGACTTACAAATGACCCAAAGGATTTAAGCACCATGCTCAAAAAACTTACTGATGGCCTG
194 TCGAAAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCG
*
253337 AAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTGTCAAAAATTTA
259 AAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTT-TCAAAAATTTC
* * *
253402 AATTTTCAGATTTAAATGAGAAACATTTTTCA-TTTCTCGAGAGACATGTGAAAATATTCTGCCC
323 AATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTC-CGAGAGACATGTGAAAATATCCTGCCC
* * *
253466 GAAGGTCTTATGGATGGCCCGAAGGATTTATCATCTTGCTCTAAAGATTTA-TAGATGACCCGAA
387 GAAGGTCTTATGGATGG-CCGAAGGACTTATCATCTTGCTCTAAAGACTTACTAG-TGACCCAAA
*
253530 GGATTCAAGCATCAT
450 GGATTTAAGCATCAT
* *
253545 GCTCGAAAGACTTATTGATGGCCCGAAGGACTTACCAATTTTGAAAATAGTTTACTAGGTAAGAA
1 GCTCGAAAGACTTATTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAA
* * *
253610 ACCTTTCTTACTTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAATCTTTCTCATTT
66 ACCTTTCTTACTTTTAAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTT
253670 GTTAACTTAT
Statistics
Matches: 1711, Mismatches: 248, Indels: 56
0.85 0.12 0.03
Matches are distributed among these distances:
463 37 0.02
464 304 0.18
465 649 0.38
466 481 0.28
467 189 0.11
468 51 0.03
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (464 bp):
GCTCGAAAGACTTATTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAA
ACCTTTCTTACTTTTAAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGA
GAGACATGTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTC
GAAAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAA
GGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTCAAAAATTTCAAT
TTTCAGATTTAAATGAGAAACCTTTCTCATTTTCCGAGAGACATGTGAAAATATCCTGCCCGAAG
GTCTTATGGATGGCCGAAGGACTTATCATCTTGCTCTAAAGACTTACTAGTGACCCAAAGGATTT
AAGCATCAT
Found at i:252852 original size:233 final size:232
Alignment explanation
Indices: 250696--253669 Score: 3677
Period size: 232 Copynumber: 12.7 Consensus size: 232
250686 GTATCAAGTG
* * * *
250696 AGACTGACAGATGACCCGAA-GAGTTTAGGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGG
1 AGACTTACAGATGACCCGAAGGA-TTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGG
* *
250760 ACTTACCAATTTTTGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAATTTTCAATT
65 ACTTA-CAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
* * * *
250825 TTCATATTTAAATGAGAAACCTTTCACATTTTTCGAGAAACATGTGAAAATATCATGCCCGAAGG
129 TTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACATCATGCCCGAAGG
* *
250890 TCTTATGGATGGCCCGAAGAACTTATCATCTTACTCGAA
194 TCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
* * *
250929 AGACTTACAGATGA-TCGAAGGGTTTAATCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
1 AGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
* * * *
250993 CTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTACAAAAAAAATTCAAA
66 CTTA-CAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTC--AAAAATTTCAAT
* ** * * *
251058 TTTCAGATTTAAATGGGAAACCTTTCTCATTTTTCGAGAGATGTGTGAAAACATCCTGTCCTAAG
128 TTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACATCATGCCCGAAG
* * ** * *
251123 GTCATATAGATGGCCTTAAAGACTTATCATCTTGCTCAAA
193 GTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
* *
251163 AGGCTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAGGACTTATTGATGGCTCGAAGGA
1 AGACTTACAGATGACCCGAAGGATTTAAGCATCATGCT-------C-----GA-------AA-GA
* *
251228 CTTATTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTA
46 CTTATTGATGGCCCGAAGGACTTA-CAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTA
* *
251293 CTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACAAGTG
110 CTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTG
* * * * * **
251358 AAAACATCCTGCCTGGAGGTCTTA-GAGATGGTCCGAATGACTTATCATCTTGCTATAA
175 AAAACATCATGCCCGAAGGTCTTATG-GATGGCCCGAAGGACTTATCATCTTGCTCGAA
* * * * *
251416 TGACTTACTGATTACCCAAAGGATTTAAGCATCATGCAT-GAAAGACTTACTGAAT-GCCCGAAG
1 AGACTTACAGATGACCCGAAGGATTTAAGCATCATGC-TCGAAAGACTTATTG-ATGGCCCGAAG
*
251479 GACTTACCAATTTTGGAAATAGTTTACAAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAT
64 GACTTA-CAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAT
* *
251544 ATTCAGATTTAAATGAGAAA-CTTTCTCATTTTTCGAGAGACATGTGAAAATATCCA-GCCCGAA
128 TTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACAT-CATGCCCGAA
* *
251607 GGTCTTATGGATGGCCCGAAAGACTTATCATCTTGTTCGAA
192 GGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
* * * *
251648 AGACTTACAAATGAACCAAAGGATTTAAGCATCATGCTCGAAAGACTGATTGATGGCCCGAAGGA
1 AGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
* * * *
251713 CTTATAAATTTAGGAAATAATTTACTAGGTAAGAAACCTTTCTTACTTTTTAAAAAATTTCAATT
66 CTTA-CAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTAC-TTTTCAAAAATTTCAATT
* * * * * *
251778 TTCAGATTTAAATGAGAAATCTTTCTCATTTTTTGAGATACATGT-AGAATCATCATGCTCGAAT
129 TTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGA-AAACATCATGCCCGAAG
251842 GTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
193 GTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
* * *
251882 AGACTTACAGACGACCCGAAGGA-TTAGAGCATCATGCTCAAAAGACTTATTGATGGCCCAAAGG
1 AGACTTACAGATGACCCGAAGGATTTA-AGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGG
* * *
251946 AATTATAAATTTTGGAAATAGTTTACTAGGTAA-AAACCTTTCTTACATTTCAAAAATTTCAATT
65 ACTTA-CAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
* * * * * *
252010 TTCATATTTAAATGAGAAACCTTTCTCATTTTCCGAGAGATATGTGAAAACAACCTGCCTGAAGG
129 TTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACATCATGCCCGAAGG
* **
252075 TCTTCTGGATGG-CCGAAGGACTTATCATCTTGCTATAA
194 TCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
* ** * *** *
252113 TA-ACTTACTAG-TTACCTTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGAAAACCAGAAG
1 -AGACTTAC-AGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAG
*
252176 GACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTAATTTTCAAAAATTTCAAT
64 GACTTAC-AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAT
* * * *
252241 TTTTAGATTTAAATGAGAAACATTTCTCATTTTTCGAGAGACATGTGAAAAAAATCTTGCCCGAA
128 TTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTG-AAAACATCATGCCCGAA
* * * * *
252306 GGTCATATAGATTGCCCGAAGGACTTGTCATATTGCTCGAA
192 GGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
* * * **
252347 AGACTTACAAATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTAAAGGA
1 AGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
* * * *
252412 CTTGCCAATTTTGAAAATAGTTTACTAGGTATGAAACCTTTCTTACTTGTCAAAAATTTCAATTT
66 CTT-ACAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTT
* * * * * * *
252477 TCAGATTTAAATGAGAAACATTTTTCATTTCTCAAAAGACATGTGAAAATATCCTGCCCGAAGGT
130 TCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACATCATGCCCGAAGGT
* * *
252542 CTTATGGATGTCCCGAAGGATTTATCATCTTACTCGAA
195 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
* * * * * *
252580 AGACTTACAAATGACCCAAAGTATTTAATCATAATGCTCGAAAGACTTATTGATGGCCTGAAGGA
1 AGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
* * * * *
252645 CTTATAATTTTTTGAAATAATTTACTAGGTAAGAAACCTTTCTTACTTTTAAAAAAAATTCAATT
66 CTTACAA-TTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT-CAAAAATTTCAATT
* * ** * *
252710 TTCATAGTTAAACAAGAAAACTTTCTCATTTTTCGAGAGACATGTGAAAACATCATGCCCAAAGG
129 TTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACATCATGCCCGAAGG
* * *
252775 TCTTATGGATGGTCCGAAAGACTTATCATCTTGCTAGAA
194 TCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
* * *
252814 ATACTTACAGATGACCCGAAGG-TTAAAACATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
1 AGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
*
252878 CTTTTA-AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCATACTTTTCAAAAATTTCAATT
66 C--TTACAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
*
252942 TTCATATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACATCATGCCCGAAGG
129 TTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACATCATGCCCGAAGG
* * **
253007 TCTTATGGATGG-CTGAAGGACTTAACATCTTGCTATAA
194 TCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
* * * * * * *
253045 TGACTTACTGATTACCCTAAGGATTTAAGCATCATGCTCGAAAGACATACTGATGGCCTGAAGGA
1 AGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
* *
253110 CATACCAATTTTGGAAATAGCTTACTAGGTGAA-AAACCTTTCTTACTTTT-AAAAATTTTCAAT
66 CTTA-CAATTTTGGAAATAGTTTACTAGGT-AAGAAACCTTTCTTACTTTTCAAAAA-TTTCAAT
* * * * *
253173 TTTCAGATTTAAATGAGAAACCTTTCTCATTGTTCGAGATACACGTGAAAAAAT-ATTACCCGAA
128 TTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACATCA-TGCCCGAA
253237 GGTCTTATGGATGGCCCGAAGGACTTA-CATCTTGCTCGAA
192 GGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
* * * * * * *
253277 AGACTTACAAATGACCCAAAGGATTTAAGCACCATGCTCAAAAAACTTACTGATGGCCTGAAGGA
1 AGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
* *
253342 CTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTGTCAAAAATTTAAATTT
66 CTTA-CAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTT
* * * *
253407 TCAGATTTAAATGAGAAACATTTTTCATTTCTCGAGAGACATGTGAAAATATTC-TGCCCGAAGG
130 TCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACA-TCATGCCCGAAGG
* *
253471 TCTTATGGATGGCCCGAAGGATTTATCATCTTGCTCTAA
194 TCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
* * *
253510 AGATTTATAGATGACCCGAAGGATTCAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
1 AGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
*
253575 CTTACCAATTTTGAAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTT
66 CTTA-CAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTT
* *
253640 TTAGATTTAAATGAGAAATCTTTCTCATTT
130 TCAGATTTAAATGAGAAACCTTTCTCATTT
253670 GTTAACTTAT
Statistics
Matches: 2370, Mismatches: 308, Indels: 126
0.85 0.11 0.04
Matches are distributed among these distances:
230 2 0.00
231 148 0.06
232 843 0.36
233 591 0.25
234 556 0.23
235 23 0.01
241 2 0.00
242 1 0.00
247 2 0.00
253 128 0.05
254 3 0.00
255 71 0.03
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (232 bp):
AGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
CTTACAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTT
CAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAACATCATGCCCGAAGGTC
TTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
Found at i:253570 original size:42 final size:41
Alignment explanation
Indices: 253472--253574 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 41
253462 GCCCGAAGGT
* * * * *
253472 CTTATGGATGGCCCGAAGGATTTATCATCTTGCTCTAAAGA
1 CTTATAGATGGCCCGAAGGATTAAGCATCATGCTCGAAAGA
* *
253513 TTTATAGATGACCCGAAGGATTCAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGATT-AAGCATCATGCTCGAAAGA
*
253555 CTTATTGATGGCCCGAAGGA
1 CTTATAGATGGCCCGAAGGA
253575 CTTACCAATT
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 19 0.37
42 32 0.63
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGATTAAGCATCATGCTCGAAAGA
Found at i:255374 original size:17 final size:16
Alignment explanation
Indices: 255353--255448 Score: 99
Period size: 17 Copynumber: 5.8 Consensus size: 16
255343 TTCTTCCTTT
255353 TTTTTTATTTTTTCTT-
1 TTTTTT-TTTTTTCTTC
255369 TATTTTTATTTTTTCTTC
1 T-TTTTT-TTTTTTCTTC
255387 TTTTTCTTTTTATTCTTC
1 TTTTT-TTTTT-TTCTTC
*
255405 TTTTTTTCTTTT-TT-
1 TTTTTTTTTTTTCTTC
*
255419 TTTTTTTTTTTTCTTG
1 TTTTTTTTTTTTCTTC
255435 TTTTTTCTTTTTTC
1 TTTTTT-TTTTTTC
255449 CCCTTTTTTC
Statistics
Matches: 71, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 11 0.15
15 4 0.06
16 9 0.13
17 34 0.48
18 13 0.18
ACGTcount: A:0.04, C:0.10, G:0.01, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTTTTCTTC
Found at i:255457 original size:1 final size:1
Alignment explanation
Indices: 255350--255447 Score: 70
Period size: 1 Copynumber: 98.0 Consensus size: 1
255340 TCTTTCTTCC
* * * * * * * * * * *
255350 TTTTTTTTTATTTTTTCTTTATTTTTATTTTTTCTTCTTTTTCTTTTTATTCTTCTTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
255415 TTTTTTTTTTTTTTTTCTTGTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
255448 CCCCTTTTTT
Statistics
Matches: 69, Mismatches: 28, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.04, C:0.09, G:0.01, T:0.86
Consensus pattern (1 bp):
T
Found at i:260057 original size:29 final size:29
Alignment explanation
Indices: 260008--260068 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
259998 AGTCCATTAT
*
260008 TCTTTTACTCAACAATGTTTAACTGTTCA
1 TCTTTTACTCAACAATGTTTAACCGTTCA
* * *
260037 TCTTTTACTCAATAGTTTTTAACCGTTCA
1 TCTTTTACTCAACAATGTTTAACCGTTCA
260066 TCT
1 TCT
260069 AACTGGCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.48
Consensus pattern (29 bp):
TCTTTTACTCAACAATGTTTAACCGTTCA
Found at i:260176 original size:81 final size:81
Alignment explanation
Indices: 260037--260193 Score: 255
Period size: 81 Copynumber: 1.9 Consensus size: 81
260027 TAACTGTTCA
* *
260037 TCTTTTACTCAATAGTTTTTAACCGTTCATCTAACTGGCATAATTGACACCATTCTGCCAATTGC
1 TCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCATTCTGCCAATTGC
260102 ACAGTTAGGCCATTTT
66 ACAGTTAGGCCATTTT
260118 TCTTTTACGT-AACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACC-TTCCTGCCAATT
1 TCTTTTAC-TCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCATT-CTGCCAATT
*
260181 GCATAGTTAGGCC
64 GCACAGTTAGGCC
260194 TCAAAGACAC
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
80 2 0.03
81 68 0.96
82 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCATTCTGCCAATTGC
ACAGTTAGGCCATTTT
Found at i:260580 original size:59 final size:59
Alignment explanation
Indices: 260456--260967 Score: 793
Period size: 59 Copynumber: 8.7 Consensus size: 59
260446 TAATTTTTTT
* * * * *
260456 AAATTCATACACTTAGTATGAGTTTCTTATC-TTTTTGCACATAAAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
260514 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
**
260573 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCTTATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
*
260632 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCCATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
* * * *
260691 AAATCCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTACCCCATACAA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
*
260750 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGAGCCTCAAATA-G-
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCC-C-AATACGA
*
260809 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCCATAC-A
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
* *
260867 GAAATTCATACACTTAATATGAATTTCTTAACATTTTAGCACACAAAGGGCCC-ATACGA
1 -AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
**
260926 AAATTCATACACTTAGTATGAA-TTAGTAACATTTTAGCACAC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
260968 TTATTGCCAT
Statistics
Matches: 423, Mismatches: 24, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
57 21 0.05
58 55 0.13
59 343 0.81
60 1 0.00
61 3 0.01
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.31
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
Found at i:265236 original size:2 final size:2
Alignment explanation
Indices: 265229--265281 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
265219 TATTGTACAT
*
265229 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
265271 TA TA TA TA TA T
1 TA TA TA TA TA T
265282 CATCCCTTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:265670 original size:68 final size:68
Alignment explanation
Indices: 265554--265766 Score: 318
Period size: 68 Copynumber: 3.1 Consensus size: 68
265544 TATTTAACCG
* * * * *
265554 TTCATCTAACTGGCATAATTGACACCTTCCTGCCAATTGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
265619 CCT
66 CCT
* * * * *
265622 TTTATCTAACTGGAATAAATGACACTTTTCTGTCAAATGCACAATTAGGCCTCAAAGGTACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
265687 CCT
66 CCT
*
265690 TTCATCTAACTGGCATAAATGACACATCTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
265755 CAT
66 CCT
265758 TTCATCTAA
1 TTCATCTAA
265767 TTTACAAGTT
Statistics
Matches: 129, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 129 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:269648 original size:54 final size:54
Alignment explanation
Indices: 269574--269684 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
269564 AAAGACATGT
269574 TTTAGCCGAGTTTTTGCATGTAAACCACTTGACCGCTAAAATAGAAACATGTCC
1 TTTAGCCGAGTTTTTGCATGTAAACCACTTGACCGCTAAAATAGAAACATGTCC
*
269628 TTTAGTCGAGTTTTTGCATGTAAACCACTTGACCGCTAAAATAGAAACATGTCC
1 TTTAGCCGAGTTTTTGCATGTAAACCACTTGACCGCTAAAATAGAAACATGTCC
269682 TTT
1 TTT
269685 CCAATGACCA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (54 bp):
TTTAGCCGAGTTTTTGCATGTAAACCACTTGACCGCTAAAATAGAAACATGTCC
Found at i:270372 original size:13 final size:13
Alignment explanation
Indices: 270346--270384 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
270336 TGAAAACACA
270346 AATAGAAATAATAAT
1 AATA-AAAT-ATAAT
270361 AATAAAATATAAT
1 AATAAAATATAAT
*
270374 AATAAATTATA
1 AATAAAATATA
270385 TTTTTCATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 15 0.65
14 4 0.17
15 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
AATAAAATATAAT
Found at i:272283 original size:15 final size:15
Alignment explanation
Indices: 272263--272291 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
272253 ATTTTTCACT
272263 TTATTTTTCTTCTTC
1 TTATTTTTCTTCTTC
272278 TTATTTTTCTTCTT
1 TTATTTTTCTTCTT
272292 TTTTTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTTCTTCTTC
Found at i:272942 original size:260 final size:260
Alignment explanation
Indices: 272483--273112 Score: 940
Period size: 260 Copynumber: 2.4 Consensus size: 260
272473 CCCGAAGGAC
* * *
272483 TTACTAAGTAAGAAACTTTGGAAATTGTTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACAT
1 TTACTAGGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAATAT
* * *
272548 TAAATGAGAAACTTTGAAAATTGCTTTCCTCATTTTTCACAAACATCATATGAAAGCATCTTGCC
66 TAAATGAGAAACTTTGGAAATCGCTTT-CTCATTTTTCACAAACATCATATGAAAACATCTTGCC
* *
272613 CAAATGTCTTATAGATGGCCCGGAGGACTTATCATCATACTCGAAAGAGTAACAGATAACCCAAA
130 CAAAGGTCTTATAGATGGCCCGAAGGACTTATCATCATACTCGAAAGAGTAACAGATAACCCAAA
* * *
272678 GGATTTAATTATCATGCTCGAAAGACTTATTGATGGCCCGAGGGACTTACCAATTTTGGAAATAG
195 GGATTTAATCACCATGCTCGAAAGACTTACTGATGGCCCGAGGGACTTACCAATTTTGGAAATAG
272743 T
260 T
* *
272744 TTACTTGGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTAAAAAATTTCATTTTCTAAAAATAT
1 TTACTAGGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAATAT
* * * * *
272809 TAAGTGGGAAACTTTGGAAATCGCTTTCTCATTTTTCATAAACATCATTTGAAAACATCTTGCCT
66 TAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCACAAACATCATATGAAAACATCTTGCCC
* * * * * * * *
272874 AAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAATATTAACAGATGACCCGAAG
131 AAAGGTCTTATAGATGGCCCGAAGGACTTATCATCATACTCGAAAGAGTAACAGATAACCCAAAG
* *
272939 GATTTAATCGCCATGCTCGAAAGACTTACTGATGGCCCGATGGACTTACCAATTTTGGAAATAGT
196 GATTTAATCACCATGCTCGAAAGACTTACTGATGGCCCGAGGGACTTACCAATTTTGGAAATAGT
*
273004 TTACTAGGTAAGAAACTTTGGAAATCGCTTTT-TTACTTTTCAAAAATTAT-ATTTTCTGAAAAT
1 TTACTAGGTAAGAAACTTTGGAAATCG-TTTTCTTACTTTTCAAAAATT-TCATTTTCTAAAAAT
* *
273067 ATTAAATGAGAAAATTTGGAAATCACTTTCTCATTTTTCACAAACA
64 ATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCACAAACA
273113 ACTTAATAGT
Statistics
Matches: 331, Mismatches: 36, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
260 243 0.73
261 88 0.27
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (260 bp):
TTACTAGGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAATAT
TAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCACAAACATCATATGAAAACATCTTGCCC
AAAGGTCTTATAGATGGCCCGAAGGACTTATCATCATACTCGAAAGAGTAACAGATAACCCAAAG
GATTTAATCACCATGCTCGAAAGACTTACTGATGGCCCGAGGGACTTACCAATTTTGGAAATAGT
Found at i:272978 original size:42 final size:41
Alignment explanation
Indices: 272886--272986 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 41
272876 AGGTTTTATG
* * *
272886 GATGGCCCGAAGGACTTATCATCTTGCTCGAAATATTAACA
1 GATGGCCCGAAGGACTTATCACCATGCTCGAAAGATTAACA
* * * *
272927 GATGACCCGAAGGATTTAATCGCCATGCTCGAAAGACTT-ACT
1 GATGGCCCGAAGGACTT-ATCACCATGCTCGAAAGA-TTAACA
*
272969 GATGGCCCGATGGACTTA
1 GATGGCCCGAAGGACTTA
272987 CCAATTTTGG
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
41 16 0.33
42 30 0.62
43 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTATCACCATGCTCGAAAGATTAACA
Found at i:274804 original size:6 final size:6
Alignment explanation
Indices: 274787--274870 Score: 76
Period size: 6 Copynumber: 14.8 Consensus size: 6
274777 TTTTAATCTA
*
274787 TCTTTT TC--TT TCTTTT TC-TTT TCTTTT T-TCTTT TATTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCT-TTT TCTTTT TCTTTT
274832 T-TTCTT T-TTTCT T-TTTT TCTTTT TCTTTT TC-TTT TCTTT
1 TCTT-TT TCTTT-T TCTTTT TCTTTT TCTTTT TCTTTT TCTTT
274871 CTGTTAGGTA
Statistics
Matches: 68, Mismatches: 1, Indels: 18
0.78 0.01 0.21
Matches are distributed among these distances:
4 4 0.06
5 16 0.24
6 47 0.69
7 1 0.01
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (6 bp):
TCTTTT
Found at i:274809 original size:11 final size:11
Alignment explanation
Indices: 274787--274870 Score: 93
Period size: 11 Copynumber: 7.5 Consensus size: 11
274777 TTTTAATCTA
274787 TCTTTTTC-TT
1 TCTTTTTCTTT
274797 TCTTTTTCTTT
1 TCTTTTTCTTT
274808 TCTTTTTTCTTT
1 TC-TTTTTCTTT
*
274820 TATTTTTCTTT
1 TCTTTTTCTTT
274831 T-TTTCTT-TTT
1 TCTTT-TTCTTT
274841 TCTTTTTTTCTTTT
1 TC--TTTTTC-TTT
274855 TCTTTTTCTTT
1 TCTTTTTCTTT
274866 TCTTT
1 TCTTT
274871 CTGTTAGGTA
Statistics
Matches: 65, Mismatches: 1, Indels: 15
0.80 0.01 0.19
Matches are distributed among these distances:
10 15 0.23
11 24 0.37
12 18 0.28
13 3 0.05
14 5 0.08
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:274810 original size:15 final size:15
Alignment explanation
Indices: 274792--274872 Score: 82
Period size: 15 Copynumber: 5.5 Consensus size: 15
274782 ATCTATCTTT
274792 TTCTTTCTTTTTCTT-
1 TTCTTTCTTTTT-TTC
*
274807 TTCTTT-TTTCTTTTA
1 TTCTTTCTTT-TTTTC
274822 TT-TTTCTTTTTTTC
1 TTCTTTCTTTTTTTC
*
274836 TTTTTTCTTTTTTTC
1 TTCTTTCTTTTTTTC
274851 TT-TTTCTTTTTCTT-
1 TTCTTTCTTTTT-TTC
274865 TTCTTTCT
1 TTCTTTCT
274873 GTTAGGTATG
Statistics
Matches: 59, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
14 25 0.42
15 34 0.58
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (15 bp):
TTCTTTCTTTTTTTC
Found at i:274841 original size:26 final size:27
Alignment explanation
Indices: 274790--274866 Score: 97
Period size: 26 Copynumber: 2.9 Consensus size: 27
274780 TAATCTATCT
*
274790 TTTTCTTTCTTTTTC-TTTTCTTTTTTC
1 TTTT-TTTCTTCTTCTTTTTCTTTTTTC
274817 TTTTATTT-TTCTT-TTTTTCTTTTTTC
1 TTTT-TTTCTTCTTCTTTTTCTTTTTTC
*
274843 TTTTTTTCTTTTTCTTTTTCTTTT
1 TTTTTTTCTTCTTCTTTTTCTTTT
274867 CTTTCTGTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
25 3 0.07
26 24 0.55
27 17 0.39
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.84
Consensus pattern (27 bp):
TTTTTTTCTTCTTCTTTTTCTTTTTTC
Found at i:275768 original size:17 final size:17
Alignment explanation
Indices: 275746--275799 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
275736 TATTAAGAAA
275746 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
275763 AAAATAA-AGTAAAATAT
1 AAAATAATAG-AAAAAAT
*
275780 AATATATATA-AAAAAAT
1 AAAATA-ATAGAAAAAAT
275797 AAA
1 AAA
275800 TAGAATATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 2 0.07
17 26 0.87
18 1 0.03
19 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:275834 original size:35 final size:34
Alignment explanation
Indices: 275735--275855 Score: 99
Period size: 33 Copynumber: 3.5 Consensus size: 34
275725 GATATACATG
*
275735 ATATTAAGAAAA-AAATAATAGAAAAAATAAAATAA
1 ATATTAAGAAAATATAT-ATA-AAAAAATAAAATAA
* * *
275770 AGTA-AAATATAATATATATAAAAAAAT-AAATAGA
1 A-TATTAAGAAAATATATATAAAAAAATAAAATA-A
* *
275804 ATATT-AGAAAATATATATAAAAACGTATAAAATAT
1 ATATTAAGAAAATATATATAAAAA--AATAAAATAA
275839 ATATTAAGAAAA-ATATA
1 ATATTAAGAAAATATATA
275856 ACATAGTAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
33 23 0.33
34 9 0.13
35 21 0.30
36 16 0.23
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.26
Consensus pattern (34 bp):
ATATTAAGAAAATATATATAAAAAAATAAAATAA
Found at i:275855 original size:23 final size:21
Alignment explanation
Indices: 275811--275856 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
275801 AGAATATTAG
**
275811 AAAATATATATAAAAACGTAT
1 AAAATATATATAAAAAAATAT
275832 AAAATATATATTAAGAAAAATAT
1 AAAATATATA-TAA-AAAAATAT
275855 AA
1 AA
275857 CATAGTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 3 0.14
23 8 0.38
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAATATATATAAAAAAATAT
Found at i:275973 original size:2 final size:2
Alignment explanation
Indices: 275968--276013 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
275958 AAATAAAAAA
275968 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
276009 AT AT A
1 AT AT A
276014 GGATGAAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:277248 original size:34 final size:35
Alignment explanation
Indices: 277210--277296 Score: 115
Period size: 34 Copynumber: 2.5 Consensus size: 35
277200 TGAGGGTTTG
*
277210 GTGTTTCAAGAGAAA-CATCTTCAAAGG-TTTTTTT
1 GTGTTTCAAGAGAAATAAT-TTCAAAGGTTTTTTTT
277244 GTGTTTCAAGAGAAATAATTTCAAAGGTTTTTTTTTT
1 GTGTTTCAAGAGAAATAATTTCAAAGG--TTTTTTTT
*
277281 ATGTTTCAAGAGAAAT
1 GTGTTTCAAGAGAAAT
277297 TGTATTCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
34 23 0.49
35 2 0.04
37 22 0.47
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (35 bp):
GTGTTTCAAGAGAAATAATTTCAAAGGTTTTTTTT
Found at i:277422 original size:29 final size:29
Alignment explanation
Indices: 277367--277422 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
277357 ATTCAAATAT
* * *
277367 TTTATGTTTCAAGGGAAACGTTTTCAAAG
1 TTTATGCTTCAAGAGAAACGTTCTCAAAG
277396 TTTATGCTTCAAGAGAAAC-TGTCTCAA
1 TTTATGCTTCAAGAGAAACGT-TCTCAA
277423 GGGAGACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (29 bp):
TTTATGCTTCAAGAGAAACGTTCTCAAAG
Found at i:277464 original size:15 final size:15
Alignment explanation
Indices: 277440--277477 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
277430 AAAATATGCT
*
277440 TCAAGAGAAACTGTC
1 TCAAGAGAAACTATC
*
277455 TCAAGGGAAACTATC
1 TCAAGAGAAACTATC
277470 TCAAGAGA
1 TCAAGAGA
277478 GACAAAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.18
Consensus pattern (15 bp):
TCAAGAGAAACTATC
Found at i:277575 original size:102 final size:102
Alignment explanation
Indices: 277468--277654 Score: 261
Period size: 102 Copynumber: 1.8 Consensus size: 102
277458 AGGGAAACTA
* * *
277468 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATG-TTTTCAATG-TTTATGTTTCAAGAGAAAC
1 TCTCAAGAGAGACAAAATTCATTTCAA-GGAAAAGATATTCAAAGATTT-TGTTTCAAGAGAAAC
277531 TATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATG
64 TATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATG
* * ** * *
277570 TCTCAAGGGAGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGATTTTGTTTCAAGGGAAACTG
1 TCTCAAGAGAGACAAAATTCATTTCAAGGAAAAGATATTCAAAGATTTTGTTTCAAGAGAAACTA
277635 TCTCAAGAGAGACAAAACTT
66 TCTCAAGAGAGACAAAACTT
277655 GGAAACTGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
101 6 0.08
102 65 0.88
103 3 0.04
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (102 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGAAAAGATATTCAAAGATTTTGTTTCAAGAGAAACTA
TCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATG
Found at i:278716 original size:31 final size:31
Alignment explanation
Indices: 278653--278766 Score: 120
Period size: 31 Copynumber: 3.6 Consensus size: 31
278643 CATCAGGATA
* * * *
278653 TTGAATTCCCAAAGATGCCCCAATATTCGATG
1 TTGAA-TCTCAAAAATGCCCCAACATTTGATG
*
278685 TTGAATCTCAAAAATGCCTCAACATTTGATG
1 TTGAATCTCAAAAATGCCCCAACATTTGATG
* * * *
278716 TTAAATATAAAAAATACCCCAACATTTGATG
1 TTGAATCTCAAAAATGCCCCAACATTTGATG
*
278747 TTGAATCTTCAAAGATGCCC
1 TTGAATC-TCAAAAATGCCC
278767 TCATTGTTCC
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
31 52 0.79
32 14 0.21
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (31 bp):
TTGAATCTCAAAAATGCCCCAACATTTGATG
Found at i:283028 original size:11 final size:11
Alignment explanation
Indices: 283014--283039 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
283004 CAAAACACGT
283014 AAAAAATAATA
1 AAAAAATAATA
283025 AAAAAATAATA
1 AAAAAATAATA
283036 AAAA
1 AAAA
283040 TAAACGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:283122 original size:17 final size:16
Alignment explanation
Indices: 283102--283143 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
283092 TTAATGGAGT
*
283102 AAAAAATAAAAAAGTA
1 AAAAAATAAAAAAGGA
*
283118 AAAAAATTAAAAAGGA
1 AAAAAATAAAAAAGGA
283134 ATAAAAATAA
1 A-AAAAATAA
283144 TGTGTACCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (16 bp):
AAAAAATAAAAAAGGA
Found at i:283215 original size:37 final size:35
Alignment explanation
Indices: 283174--283262 Score: 92
Period size: 37 Copynumber: 2.5 Consensus size: 35
283164 TTACTAAAAC
283174 AAATAAAAATAAATATAATACTAAGTAAAACAAATAA-
1 AAATAAAAATAAA-ATAATACTAAG-AAAA-AAATAAT
* * *
283211 AAATAAAAATATACATGATATTAAGAAAAAAATAAT
1 AAATAAAAATA-AAATAATACTAAGAAAAAAATAAT
*
283247 AGA-AAAAATAAAATAA
1 AAATAAAAATAAAATAA
283263 AGTAAAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
34 4 0.09
35 13 0.30
36 6 0.14
37 20 0.45
38 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.21
Consensus pattern (35 bp):
AAATAAAAATAAAATAATACTAAGAAAAAAATAAT
Found at i:283271 original size:16 final size:16
Alignment explanation
Indices: 283239--283284 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
283229 TATTAAGAAA
*
283239 AAAATAATAGAAAAAAT
1 AAAATAA-AGTAAAAAT
283256 AAAATAAAGTAAAAAT
1 AAAATAAAGTAAAAAT
* *
283272 ATAATAAAATAAA
1 AAAATAAAGTAAA
283285 TAAATAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (16 bp):
AAAATAAAGTAAAAAT
Found at i:283279 original size:21 final size:21
Alignment explanation
Indices: 283253--283298 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
283243 TAATAGAAAA
*
283253 AATAAAATAAAGTAAA-AATAT
1 AATAAAATAAA-TAAATAATAG
283274 AATAAAATAAATAAATAATAG
1 AATAAAATAAATAAATAATAG
283295 AATA
1 AATA
283299 TTAAGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (21 bp):
AATAAAATAAATAAATAATAG
Found at i:283291 original size:8 final size:9
Alignment explanation
Indices: 283239--283288 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
283229 TATTAAGAAA
283239 AAAAT-AAT
1 AAAATAAAT
283247 AGAAA-AAAT
1 A-AAATAAAT
283256 AAAATAAAGT
1 AAAATAAA-T
283266 AAAAATATAAT
1 -AAAATA-AAT
283277 AAAATAAAT
1 AAAATAAAT
283286 AAA
1 AAA
283289 TAATAGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
8 4 0.11
9 16 0.44
10 7 0.19
11 7 0.19
12 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:283291 original size:16 final size:16
Alignment explanation
Indices: 283168--283298 Score: 55
Period size: 16 Copynumber: 8.4 Consensus size: 16
283158 TAGTATTTAC
*
283168 TAAAACAAATAAA-AA
1 TAAAATAAATAAATAA
*
283183 T-AAATATAAT-ACTAA
1 TAAAATA-AATAAATAA
*
283198 GTAAAACAAATAAA-AA
1 -TAAAATAAATAAATAA
* * *
283214 TAAAA-ATATACATGA
1 TAAAATAAATAAATAA
* * *
283229 TATTAAGAAAAAAATAA
1 TA-AAATAAATAAATAA
283246 TAGAAA-AAAT-AA-AA
1 TA-AAATAAATAAATAA
*
283260 TAAAGTAAA-AATATAA
1 TAAAATAAATAA-ATAA
283276 TAAAATAAATAAATAA
1 TAAAATAAATAAATAA
*
283292 TAGAATA
1 TAAAATA
283299 TTAAGAAAAT
Statistics
Matches: 85, Mismatches: 18, Indels: 25
0.66 0.14 0.20
Matches are distributed among these distances:
13 2 0.02
14 18 0.21
15 17 0.20
16 31 0.36
17 17 0.20
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (16 bp):
TAAAATAAATAAATAA
Found at i:283317 original size:38 final size:37
Alignment explanation
Indices: 283267--283351 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 37
283257 AAATAAAGTA
283267 AAAATATA-ATAAAATAAATA-AATAATAGAATATTAAG
1 AAAATATATATAAAA-AAATATAA-AATAGAATATTAAG
** **
283304 AAAATATATATAAAAACGTATAAAATCTAATATTAAG
1 AAAATATATATAAAAAAATATAAAATAGAATATTAAG
283341 AAAA-ATATATA
1 AAAATATATATA
283352 GTAAATAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 7 0.17
37 27 0.64
38 8 0.19
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (37 bp):
AAAATATATATAAAAAAATATAAAATAGAATATTAAG
Found at i:283382 original size:2 final size:2
Alignment explanation
Indices: 283375--283418 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
283365 TTAATACATC
283375 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA -A TGA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
283415 TA TA
1 TA TA
283419 ATAAAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.87
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:283399 original size:19 final size:19
Alignment explanation
Indices: 283375--283422 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
283365 TTAATACATC
*
283375 TATATATATTAT-ATATATA
1 TATATATATAATGATATA-A
283394 TATATATATAATGATATAA
1 TATATATATAATGATATAA
283413 TATATA-ATAA
1 TATATATATAA
283423 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 18 0.67
20 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TATATATATAATGATATAA
Found at i:289501 original size:18 final size:19
Alignment explanation
Indices: 289478--289514 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
289468 TGAACGAAAT
*
289478 AAATAAT-AATAATGTAAA
1 AAATAATAAAGAATGTAAA
289496 AAATAATAAAGAATGTAAA
1 AAATAATAAAGAATGTAAA
289515 GAACGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (19 bp):
AAATAATAAAGAATGTAAA
Found at i:292915 original size:25 final size:25
Alignment explanation
Indices: 292886--292944 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
292876 CAACTATATC
292886 AATTCAATATTTTACCTTTGGGAAT
1 AATTCAATATTTTACCTTTGGGAAT
292911 AATTCAATATTTTACCTTTGGGAAT
1 AATTCAATATTTTACCTTTGGGAAT
292936 AATTCAATA
1 AATTCAATA
292945 CGATGTATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (25 bp):
AATTCAATATTTTACCTTTGGGAAT
Found at i:294639 original size:2 final size:2
Alignment explanation
Indices: 294632--294681 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
294622 GCTAAAAAGG
294632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
294673 TA TA TA TA T
1 TA TA TA TA T
294682 CATTGATCCC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:298284 original size:504 final size:505
Alignment explanation
Indices: 297294--298304 Score: 1942
Period size: 504 Copynumber: 2.0 Consensus size: 505
297284 AATTTGGGAT
297294 TCCAATCTGGTTTATATAAGGAATTTCCTTATAGATCCACTTCTCATTCGGAGGCTACTGTGGCT
1 TCCAATCTGGTTTATATAAGGAATTTCCTTATAGATCCACTTCTCATTCGGAGGCTACTGTGGCT
297359 GGACATACAATGGTGTAACCAATCCGGCTTTGAGCATTTCTGAATGCAGTTTTTCCCACGAAAAA
66 GGACATACAATGGTGTAACCAATCCGGCTTTGAGCATTTCTGAATGCAGTTTTTCCCACGAAAAA
297424 TGGAAGGGAGGGAACTGACAACCCTGCTATTTCCTTTTATTCTCAAACTTATTACAATTACCATT
131 TGGAAGGGAGGGAACTGACAACCCTGCTATTTCCTTTTATTCTCAAACTTATTACAATTACCATT
297489 CAAGCAACATATAACCATTTCAACCACACCATTTACGCGCTTTTAGAACGTAAGCACTTAGCATT
196 CAAGCAACATATAACCATTTCAACCACACCATTTACGCGCTTTTAGAACGTAAGCACTTAGCATT
297554 ATTATCTATGATATAAGTTTCACATAAATATCATCAAAGCATTTACACACCAAGAAAATATTACA
261 ATTATCTATGATATAAGTTTCACATAAATATCATCAAAGCATTTACACACCAAGAAAATATTACA
297619 TAACTTCCTATTTACAAAATATATATACAATCAACAAGTCAAACCCATATGCCACCATGTAAGAG
326 TAACTTCCTATTTACAAAATATATATACAATCAACAAGTCAAACCCATATGCCACCATGTAAGAG
297684 TTAAACAAAAGAACATTTCACTAATGATCCCGAGAGTGACTTGTAATCCTTAGAATGCAATCTCG
391 TTAAACAAAAGAACATTTCACTAATGATCCCGAGAGTGACTTGTAATCCTTAGAATGCAATCTCG
297749 ATATGTATACGAATATTGAATACCTACAAAGATGTTAAACAATTACAATAA
456 ATATGTATACGAATATTGAATACCTACAAAGA-GTTAAACAATTACAATAA
297800 TCCAATCTGGTTTATATAAGGAATTTCCTTATAGATCCAC-T-TCATTCGGAGGCTACTGTGGCT
1 TCCAATCTGGTTTATATAAGGAATTTCCTTATAGATCCACTTCTCATTCGGAGGCTACTGTGGCT
297863 GGACATACAATGGTGTAACCAATCCGGCTTTGAGCATTTCTGAATGCAGTTTTTCCCACGAAAAA
66 GGACATACAATGGTGTAACCAATCCGGCTTTGAGCATTTCTGAATGCAGTTTTTCCCACGAAAAA
297928 TGGAAGGGAGGGAACTGACAACCCTGCTATTTCCTTTTATTCTCAAACTTATTACAATTACCATT
131 TGGAAGGGAGGGAACTGACAACCCTGCTATTTCCTTTTATTCTCAAACTTATTACAATTACCATT
297993 CAAGCAACATATAACCATTTCAA-C-CA-CATTTACGCGCTTTTAGAACGTAAGCACTTTAGCAT
196 CAAGCAACATATAACCATTTCAACCACACCATTTACGCGCTTTTAGAACGTAAGCAC-TTAGCAT
298055 TATTTATCTATGATATAAGTTTCACATAAATATCATCAAAGCATTTACACACCAAGAAAATATTA
260 TA-TTATCTATGATATAAGTTTCACATAAATATCATCAAAGCATTTACACACCAAGAAAATATTA
298120 CATAACTTCCTATTTACAAAATATATATACAATCAACAAGTCAAACCCATATGCCACCATGTAAG
324 CATAACTTCCTATTTACAAAATATATATACAATCAACAAGTCAAACCCATATGCCACCATGTAAG
298185 AGTTTAAACAAAAGAACATTTCACTAATGATCCCGAGAGTGACTTGTAATCCTTAGAATGCAATC
389 AG-TTAAACAAAAGAACATTTCACTAATGATCCCGAGAGTGACTTGTAATCCTTAGAATGCAATC
*
298250 TCGATATGTCTACGAATATTGAATACCTACAAAGAGTTAAACAATTACAATAA
453 TCGATATGTATACGAATATTGAATACCTACAAAGAGTTAAACAATTACAATAA
298303 TC
1 TC
298305 TTGCATATCT
Statistics
Matches: 501, Mismatches: 1, Indels: 9
0.98 0.00 0.02
Matches are distributed among these distances:
501 28 0.06
502 11 0.02
503 150 0.30
504 271 0.54
505 1 0.00
506 40 0.08
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (505 bp):
TCCAATCTGGTTTATATAAGGAATTTCCTTATAGATCCACTTCTCATTCGGAGGCTACTGTGGCT
GGACATACAATGGTGTAACCAATCCGGCTTTGAGCATTTCTGAATGCAGTTTTTCCCACGAAAAA
TGGAAGGGAGGGAACTGACAACCCTGCTATTTCCTTTTATTCTCAAACTTATTACAATTACCATT
CAAGCAACATATAACCATTTCAACCACACCATTTACGCGCTTTTAGAACGTAAGCACTTAGCATT
ATTATCTATGATATAAGTTTCACATAAATATCATCAAAGCATTTACACACCAAGAAAATATTACA
TAACTTCCTATTTACAAAATATATATACAATCAACAAGTCAAACCCATATGCCACCATGTAAGAG
TTAAACAAAAGAACATTTCACTAATGATCCCGAGAGTGACTTGTAATCCTTAGAATGCAATCTCG
ATATGTATACGAATATTGAATACCTACAAAGAGTTAAACAATTACAATAA
Found at i:298506 original size:228 final size:234
Alignment explanation
Indices: 298105--298567 Score: 875
Period size: 228 Copynumber: 2.0 Consensus size: 234
298095 GCATTTACAC
298105 ACCAAGAAAATATTACATAACTTCCTATTTACAAAATATATATACAATCAACAAGTCAAACCCAT
1 ACCAAGAAAATATTACATAACTTCCTATTTACAAAATATATATACAATCAACAAGTCAAACCCAT
298170 ATGCCACCATGTAAGAGTTTAAACAAAAGAACATTTCACTAATGATCCCGAGAGTGACTTGTAAT
66 ATGCCACCATGTAAGAGTTTAAACAAAAGAACATTTCACTAATGATCCCGAGAGTGACTTGTAAT
298235 CCTTAGAATGCAATCTCGATATGTCTACGAATATTGAATACCTACAAAGA-GTTAAACAATTACA
131 CCTTAGAATGCAATCTCGATATGTCTACGAATATTGAATACCTACAAAGATGTTAAACAATTACA
298299 ATAATCTTGCATATC-TAGTGAGGTAACCCTAAACAACA
196 ATAATCTTGCATATCTTAGTGAGGTAACCCTAAACAACA
*
298337 ACCAAGAAAATATTACATAACTTCCTTTTTAC-AAA-ATATATACAATCAACAAGTCAAACCCAT
1 ACCAAGAAAATATTACATAACTTCCTATTTACAAAATATATATACAATCAACAAGTCAAACCCAT
298400 ATGCCACCATGT-A-AGTTTAAACAAAAGAACATTTCACTAATGATCCCGAGAGTGACTTGTAAT
66 ATGCCACCATGTAAGAGTTTAAACAAAAGAACATTTCACTAATGATCCCGAGAGTGACTTGTAAT
298463 CCTTAGAATGCAATCTCGATATGTCTACGAATATTGAATACCTACAAAGATGTTAAACAATTACA
131 CCTTAGAATGCAATCTCGATATGTCTACGAATATTGAATACCTACAAAGATGTTAAACAATTACA
298528 ATAATCTTGCATATCTTAGTGAGGTAACCCTAAACAACA
196 ATAATCTTGCATATCTTAGTGAGGTAACCCTAAACAACA
298567 A
1 A
298568 TTAAACACTA
Statistics
Matches: 228, Mismatches: 1, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
228 100 0.44
229 30 0.13
230 64 0.28
231 3 0.01
232 31 0.14
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (234 bp):
ACCAAGAAAATATTACATAACTTCCTATTTACAAAATATATATACAATCAACAAGTCAAACCCAT
ATGCCACCATGTAAGAGTTTAAACAAAAGAACATTTCACTAATGATCCCGAGAGTGACTTGTAAT
CCTTAGAATGCAATCTCGATATGTCTACGAATATTGAATACCTACAAAGATGTTAAACAATTACA
ATAATCTTGCATATCTTAGTGAGGTAACCCTAAACAACA
Found at i:302433 original size:31 final size:34
Alignment explanation
Indices: 302385--302463 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
302375 TTAAAATAGT
* *
302385 TATTATATTTTATATTAATAT-A-ATT-ATATAAA
1 TATTAT-TTTTTTATTAAAATAATATTGATATAAA
*
302417 TATTATTTTTTTATTAAAATAATATTGATATAAT
1 TATTATTTTTTTATTAAAATAATATTGATATAAA
*
302451 TATTATTTATTTA
1 TATTATTTTTTTA
302464 AATTTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 12 0.30
32 7 0.17
33 3 0.08
34 18 0.45
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTGATATAAA
Found at i:304236 original size:21 final size:21
Alignment explanation
Indices: 304210--304281 Score: 110
Period size: 21 Copynumber: 3.4 Consensus size: 21
304200 ATGTCATCTT
304210 CGCAGGGTTACATTCCTAGCC
1 CGCAGGGTTACATTCCTAGCC
304231 CGCAGGGTTACATTCCTAGCC
1 CGCAGGGTTACATTCCTAGCC
* *
304252 CGCCA-GGTTATATGCCTAGCC
1 CG-CAGGGTTACATTCCTAGCC
304273 CGCAGGGTT
1 CGCAGGGTT
304282 TTATACCATA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
20 2 0.04
21 43 0.91
22 2 0.04
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (21 bp):
CGCAGGGTTACATTCCTAGCC
Found at i:304847 original size:34 final size:34
Alignment explanation
Indices: 304804--304910 Score: 169
Period size: 34 Copynumber: 3.1 Consensus size: 34
304794 ATAAATGTTT
304804 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
304838 TTAAAATACAAATAATATTATTCGAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* *
304872 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
304906 TTAAA
1 TTAAA
304911 TTCAACTTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:305547 original size:127 final size:127
Alignment explanation
Indices: 305333--305872 Score: 866
Period size: 127 Copynumber: 4.3 Consensus size: 127
305323 GCGCTTTAAA
* * * **
305333 GTCCCCTAAGAAAATAGTAGGTATTGACATGAATAG-TCCCGAGGGACATAAGTGACATAATAGG
1 GTCCCCTAAG-GAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATTCGTGACATAATAGG
* * *
305397 GCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGTGCCCCCGAGAACGCGTCTTCACG
65 GCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* * *
305460 GTCCCCTAAGGAATAATAGGCATTGACATGAATAGTTCCTGGGGGATATTCGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATTCGTGACATAATAGGG
* * *
305525 CAATGATAATATATTCTTTGACAAAATAATCGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
**
305587 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCTAGGGGACATTCGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATTCGTGACATAATAGGG
* * *
305652 CAATGATAACATATTCTCTAACAAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
*
305714 ATCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATTCGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATTCGTGACATAATAGGG
* *
305779 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGTGCCCCCGGGAACGTGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
305841 GTCCCCTAAGGAATAATAGGTATTGACATGAA
1 GTCCCCTAAGGAATAATAGGTATTGACATGAA
305873 CAATACATAT
Statistics
Matches: 381, Mismatches: 31, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
126 22 0.06
127 359 0.94
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.23
Consensus pattern (127 bp):
GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATTCGTGACATAATAGGG
CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
Found at i:306624 original size:13 final size:13
Alignment explanation
Indices: 306606--306632 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
306596 CTCGTTTAAG
306606 GAGAAGACACTGA
1 GAGAAGACACTGA
306619 GAGAAGACACTGA
1 GAGAAGACACTGA
306632 G
1 G
306633 TCCTGGGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.33, T:0.07
Consensus pattern (13 bp):
GAGAAGACACTGA
Found at i:316786 original size:18 final size:18
Alignment explanation
Indices: 316747--316788 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
316737 ATCACGAAAT
* *
316747 AAGTAGATTAATTCCTGC
1 AAGTAGATTAATTCCAGA
*
316765 AAGTAGATTAATTTCAGA
1 AAGTAGATTAATTCCAGA
316783 AAGTAG
1 AAGTAG
316789 GAGACAAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (18 bp):
AAGTAGATTAATTCCAGA
Found at i:317026 original size:13 final size:13
Alignment explanation
Indices: 316996--317027 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
316986 TATATTTGGC
*
316996 ATTTCGCATTCCA
1 ATTTTGCATTCCA
317009 ATTTTGCATTCCA
1 ATTTTGCATTCCA
317022 ATTTTG
1 ATTTTG
317028 TATATTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (13 bp):
ATTTTGCATTCCA
Found at i:318434 original size:21 final size:21
Alignment explanation
Indices: 318410--318470 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
318400 ATAGCTAAAG
318410 AAGAAAAATAAAAATAGAGAA
1 AAGAAAAATAAAAATAGAGAA
*
318431 AAGAAAGAA-AGAATATAGA-AA
1 AAGAAA-AATA-AAAATAGAGAA
* *
318452 AAG-AAAGTAAAAAAAGAGA
1 AAGAAAAATAAAAATAGAGA
318471 TAGAAAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
19 7 0.22
20 4 0.12
21 12 0.38
22 9 0.28
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (21 bp):
AAGAAAAATAAAAATAGAGAA
Found at i:318458 original size:25 final size:23
Alignment explanation
Indices: 318430--318491 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
318420 AAAATAGAGA
*
318430 AAAGAAAGAAAGAATATAGAAAAAG
1 AAAGAAA-AAAGAAGATAG-AAAAG
318455 AAAGTAAAAAA-AGAGATAGAAAAG
1 AAAG-AAAAAAGA-AGATAGAAAAG
*
318479 AAAGCAAAAAGAA
1 AAAGAAAAAAGAA
318492 AAACCAGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
23 6 0.19
24 11 0.34
25 12 0.38
26 3 0.09
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (23 bp):
AAAGAAAAAAGAAGATAGAAAAG
Found at i:319208 original size:28 final size:28
Alignment explanation
Indices: 319168--319230 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
319158 GAAGCCAACA
*
319168 TGAAACATATTACC-CCCTCAAATTAACC
1 TGAAACATATTACCTCCC-CAAATTAAAC
*
319196 TGAAACATATTACCTCCCCAAATTAAAT
1 TGAAACATATTACCTCCCCAAATTAAAC
319224 TGAAACA
1 TGAAACA
319231 CTCTACTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (28 bp):
TGAAACATATTACCTCCCCAAATTAAAC
Found at i:320641 original size:53 final size:54
Alignment explanation
Indices: 320583--320694 Score: 165
Period size: 53 Copynumber: 2.1 Consensus size: 54
320573 TTTGAACTTG
*
320583 ATTTTCAGGGTTTCTTAATGTTTTCTAA-TGAATTTTT-AAATAAGCTAAGCCTA
1 ATTTTCAAGGTTTCTTAATGTTTTC-AATTGAATTTTTAAAATAAGCTAAGCCTA
* **
320636 ATTTTCAAGGTTTCTTGATGTTTTCAATTGTTTTTTTAAAATAAGCTAAGCCTA
1 ATTTTCAAGGTTTCTTAATGTTTTCAATTGAATTTTTAAAATAAGCTAAGCCTA
320690 ATTTT
1 ATTTT
320695 TTAGGGGTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
52 2 0.04
53 30 0.57
54 21 0.40
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (54 bp):
ATTTTCAAGGTTTCTTAATGTTTTCAATTGAATTTTTAAAATAAGCTAAGCCTA
Found at i:322615 original size:204 final size:203
Alignment explanation
Indices: 322078--322595 Score: 808
Period size: 204 Copynumber: 2.5 Consensus size: 203
322068 AACCTTAGCA
* *
322078 CGATTCCATCATAGAAGGAGGTAGATCAACATTTTCAGTGG-AGAGTTCATAATGAGAAGAACTC
1 CGATTCCATCACAGAAGGAGGTAGATCAACATTTCCAGTGGAAG-GTTCATAATGAGAAGAACTC
* * * *
322142 ATTCGATGAGGGAGAATAAGTTCATAATAAGAAGAACTTGTTCAACCTTAGCTTGTTTCCCTCAC
65 ATCCGATGAGGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCAC
* *
322207 ATAAGGAGTTGGAACAACACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATCAT
130 ATAAGAAGTTGGAACAACACCAATACTTGGCTCATCCATAGCATATGGAGTTGGATCAGCATCAT
322272 CACTTTGTT
195 CACTTTGTT
*
322281 CGATTCCATCACAGAAGGAGGTAGATCAACATTTCTAGTGGTGAA-GTTCATAATGAGAAGAACT
1 CGATTCCATCACAGAAGGAGGTAGATCAACATTTCCAGT-G-GAAGGTTCATAATGAGAAGAACT
* * *
322345 CATCCGATGA-GGATGAAGAAATTCATAATGAGAAGAACTTTTTCAACCTTAGCTTGTTTCCATC
64 CATCCGATGAGGGA-GAACAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATC
*
322409 ACATAAGAAGTTGGAACAACACTAATACTTGGCTCATCCATAGCATATGGAGTTGGATCAGCATC
128 ACATAAGAAGTTGGAACAACACCAATACTTGGCTCATCCATAGCATATGGAGTTGGATCAGCATC
322474 ATCACTTTGTT
193 ATCACTTTGTT
* * * *
322485 CGATTCCACCACAGAATGAGGTGGATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTC
1 CGATTCCATCACAGAAGGAGGTAGATCAACATTTCCAGTGGAA-GGTTCATAATGAGAAGAACTC
*
322550 ATCCAATGAGGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAAC
65 ATCCGATGAGGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAAC
322596 TTCACCTCAA
Statistics
Matches: 287, Mismatches: 21, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
202 3 0.01
203 40 0.14
204 239 0.83
205 4 0.01
206 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (203 bp):
CGATTCCATCACAGAAGGAGGTAGATCAACATTTCCAGTGGAAGGTTCATAATGAGAAGAACTCA
TCCGATGAGGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCACA
TAAGAAGTTGGAACAACACCAATACTTGGCTCATCCATAGCATATGGAGTTGGATCAGCATCATC
ACTTTGTT
Found at i:322701 original size:117 final size:118
Alignment explanation
Indices: 322494--322712 Score: 352
Period size: 117 Copynumber: 1.9 Consensus size: 118
322484 TCGATTCCAC
** * *
322494 CACAGAATGAGGTGGATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATCCAATGA
1 CACAGAAAAAGGTGGATCAACATCTCCAATGGAAGAGTTCATAATGAGAAGAACTCATCCAATGA
322559 GGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAACTTCACCTCAATTTCAT
66 GGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAACTTCACCTCAATTTCAT
*
322612 CACAGAAAAAGGTGGATCAACATCT-CAAGTGG-AGAGTTCATAATGAGAAGAACTCATCCGATG
1 CACAGAAAAAGGTGGATCAACATCTCCAA-TGGAAGAGTTCATAATGAGAAGAACTCATCCAATG
* *
322675 AGGGATAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
65 AGGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAAC
322713 CTTAGCTCGT
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
117 68 0.73
118 25 0.27
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (118 bp):
CACAGAAAAAGGTGGATCAACATCTCCAATGGAAGAGTTCATAATGAGAAGAACTCATCCAATGA
GGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAACTTCACCTCAATTTCAT
Found at i:322713 original size:321 final size:320
Alignment explanation
Indices: 322283--323042 Score: 1051
Period size: 321 Copynumber: 2.4 Consensus size: 320
322273 ACTTTGTTCG
* * *
322283 ATTCCATCACAGAAGGAGGTAGATCAACATTTCTAGTGGTGAAGTTCATAATGAGAAGAACTCAT
1 ATTCCATCACAGAAAGAGGTGGATCAACATTTCTAGTGGAG-AGTTCATAATGAGAAGAACTCAT
*
322348 CCGATGA-GGATGAAGAAATTCATAATGAGAAGAACTTTTTCAACCTTAGCTTGTTTCCATCACA
65 CCGATGAGGGAT-AAGAAGTTCATAATGAGAAGAAC-TTTTCAACCTTAGCTTGTTTCCATCACA
* ** *
322412 TAAGAAGTTGGAACAACACTAATACTTGGCTCATCCATAGCATATGGAGTTGGATCAGCATCATC
128 TAAGAAGTTGGAACAACACCAATACTTGGCTCATCCATAGCATATGGAGTTAAATCAACATCATC
*
322477 ACTTTGTTCGATTCCACCACAGAATG-AGGTGGATCAACATTTCCAATGGAAGGGTTCATAATGA
193 ACTTTGTTCGATTCCACCACAGAA-GAAGGTGGATCAACATTTCCAATGAAAGGGTTCATAATGA
* **
322541 GAAGAACTCATCCAATGAGGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAA-CTT-CACCTC
257 GAAGAACTCAACCAATGAAAGAGAACAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCA--TC
322604 A
320 A
* * * *
322605 ATTTCATCACAGAAAAAGGTGGATCAACATCTCAAGTGGAGAGTTCATAATGAGAAGAACTCATC
1 ATTCCATCACAGAAAGAGGTGGATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATC
* *
322670 CGATGAGGGATAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCATATA
66 CGATGAGGGATAAGAAGTTCATAATGAGAAGAACTT-TTCAACCTTAGCTTGTTTCCATCACATA
* *
322735 AGGAGTTGGAACAACACCAATACTTGGCTCATCCATCGCATATGGAGTTAAATCAACATCATCAC
130 AGAAGTTGGAACAACACCAATACTTGGCTCATCCATAGCATATGGAGTTAAATCAACATCATCAC
* * * * * *
322800 TTTGTTTGATTCCATCACATAAGAATGTGGATCAATATTTCCAATGAAATGGTTCATAATGAGAA
195 TTTGTTCGATTCCACCACAGAAGAAGGTGGATCAACATTTCCAATGAAAGGGTTCATAATGAGAA
** * * * *
322865 GAACTCAACTGATGAAAGAGAAGAAGTTCATAATGGGAAGAACTTGTTCAACCTTGGATCG
260 GAACTCAACCAATGAAAGAGAACAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCA
* ** * *
322926 ATTCCATCACAGAATGAGGTGGATTGACATTTCTAGTGGAGTGTTCGTAATGAGAAGAACTCATC
1 ATTCCATCACAGAAAGAGGTGGATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATC
* * * *
322991 CGATGAGGGAGAAAAAGTTCATAATGAGAAGATCTTTCTCAACCTTATCTTG
66 CGATGAGGGATAAGAAGTTCATAATGAGAAGAACTTT-TCAACCTTAGCTTG
323043 GTACTACACC
Statistics
Matches: 386, Mismatches: 46, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
320 4 0.01
321 340 0.88
322 41 0.11
323 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (320 bp):
ATTCCATCACAGAAAGAGGTGGATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATC
CGATGAGGGATAAGAAGTTCATAATGAGAAGAACTTTTCAACCTTAGCTTGTTTCCATCACATAA
GAAGTTGGAACAACACCAATACTTGGCTCATCCATAGCATATGGAGTTAAATCAACATCATCACT
TTGTTCGATTCCACCACAGAAGAAGGTGGATCAACATTTCCAATGAAAGGGTTCATAATGAGAAG
AACTCAACCAATGAAAGAGAACAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCA
Found at i:324243 original size:59 final size:59
Alignment explanation
Indices: 324163--324555 Score: 633
Period size: 59 Copynumber: 6.7 Consensus size: 59
324153 TCATACAAAC
* * *
324163 AGTATGATTTCCTTATCATTTTAGCACATAGAGTGCCCTATCTGGAAATTCATACACTT
1 AGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTT
** *
324222 AGTATGATTTCCTTAATATTTTAGCACACAAAGTGCCCTATCTAGAAATTCATACACTT
1 AGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTT
*
324281 AGTATGATCTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTT
1 AGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTT
* * * *
324340 AGTATGATTTGCTTACCATTTTAGAACACAATGTGCCCTATCTGTAAATTCATACACTT
1 AGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTT
* *
324399 AGTATGATTTCTTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACAT
1 AGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTT
* *
324458 AGTATGATTTCCTTACCATTTTAGCACACAATGTGCCCTATCTAGAAATTCATACACTT
1 AGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTT
* *
324517 AGTATGATTTCCTTACCATTCTAGCGCACAAAGTGCCCT
1 AGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
324556 TTGGTAATTC
Statistics
Matches: 307, Mismatches: 27, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 307 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (59 bp):
AGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTT
Found at i:324836 original size:22 final size:23
Alignment explanation
Indices: 324780--324837 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
324770 ATTTTCAGCC
324780 CTTA-GGTATCGATAC--CCCTA
1 CTTAGGGTATCGATACTACCCTA
*
324800 CTTATGGTATCGATACTACCCTA
1 CTTAGGGTATCGATACTACCCTA
*
324823 -TTAGGGTATTGATAC
1 CTTAGGGTATCGATAC
324838 CCTCTTCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.12
21 11 0.33
22 13 0.39
23 5 0.15
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (23 bp):
CTTAGGGTATCGATACTACCCTA
Found at i:327989 original size:36 final size:36
Alignment explanation
Indices: 327942--328016 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
327932 AAACTTCCGT
327942 AATATTATTGGGAGATTGCCAATCTATTATGGCTTG
1 AATATTATTGGGAGATTGCCAATCTATTATGGCTTG
*
327978 AATATTCTTGGGAGATTGCCAATCTATTATGGCTTG
1 AATATTATTGGGAGATTGCCAATCTATTATGGCTTG
328014 AAT
1 AAT
328017 TTTCCCCTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (36 bp):
AATATTATTGGGAGATTGCCAATCTATTATGGCTTG
Found at i:339654 original size:5 final size:5
Alignment explanation
Indices: 339646--339681 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
339636 ACAAGACAAT
339646 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
339682 AGACTCAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:342128 original size:12 final size:12
Alignment explanation
Indices: 342113--342142 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
342103 TTAAATATCA
342113 TATAATAATATT
1 TATAATAATATT
*
342125 TATAATAATTTT
1 TATAATAATATT
342137 TATAAT
1 TATAAT
342143 GTATATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATAATAATATT
Found at i:343523 original size:15 final size:15
Alignment explanation
Indices: 343499--343533 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
343489 GACCACCAGA
*
343499 GCTTCTTCTCCCTCT
1 GCTTCCTCTCCCTCT
343514 GCTTCCTCTCCCTCT
1 GCTTCCTCTCCCTCT
343529 GCTTC
1 GCTTC
343534 TATTAGGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.49, G:0.09, T:0.43
Consensus pattern (15 bp):
GCTTCCTCTCCCTCT
Found at i:345432 original size:59 final size:59
Alignment explanation
Indices: 345369--345878 Score: 842
Period size: 59 Copynumber: 8.6 Consensus size: 59
345359 CATAAAAACG
* * *
345369 GTATGATTTCTTTATCATTTTAGCACACAGAGTGCCCTATCTGGAAATTCATACACTTA
1 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTA
* **
345428 GTATGATTTCCTTACTC-TTTTAGCACACAAAGTGCCATATCTATAAATTCATACACTTA
1 GTATGATTTCCTTAC-CATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTA
*
345487 GTATGATTTCCTTACCATTTGAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTA
1 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTA
* *
345546 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAGTTCATGCACTTA
1 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTA
* * *
345605 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGAAAATTCATACCCTTT
1 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTA
* * *
345664 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCTTATCTTGAAATTCATACACATA
1 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTA
* *
345723 GTATGATTTCCTTACCATTTTAGCACACAAAATGCCCTATCTGGAAATTCATACACATA
1 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTA
*
345782 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATATGGAAATTCATACACTTA
1 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTA
345841 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
1 GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
345879 TTGGTAATTC
Statistics
Matches: 419, Mismatches: 30, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
58 1 0.00
59 417 1.00
60 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (59 bp):
GTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTA
Found at i:350817 original size:29 final size:29
Alignment explanation
Indices: 350771--350857 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
350761 AACTCTCACC
350771 TAATTAAATTGATGTAAGCAATGACATCAT
1 TAATTAAA-TGATGTAAGCAATGACATCAT
*
350801 TAATTAAATGATGTAAGCAATGACATCTT
1 TAATTAAATGATGTAAGCAATGACATCAT
*
350830 TAATTAAATGATGTAAGTAATGACATCA
1 TAATTAAATGATGTAAGCAATGACATCA
350858 ATTTAGTTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 46 0.85
30 8 0.15
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (29 bp):
TAATTAAATGATGTAAGCAATGACATCAT
Found at i:355583 original size:29 final size:29
Alignment explanation
Indices: 355537--355623 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
355527 AACTCTCACC
355537 TAATTAAATTGATGTAAGCAATGACATCAT
1 TAATTAAA-TGATGTAAGCAATGACATCAT
*
355567 TAATTAAATGATGTAAGCAATGACATCTT
1 TAATTAAATGATGTAAGCAATGACATCAT
*
355596 TAATTAAATGATGTAAGTAATGACATCA
1 TAATTAAATGATGTAAGCAATGACATCA
355624 ATTTAGTTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 46 0.85
30 8 0.15
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (29 bp):
TAATTAAATGATGTAAGCAATGACATCAT
Found at i:370753 original size:3 final size:3
Alignment explanation
Indices: 370745--370807 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
370735 CATATGATAT
370745 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
370793 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
370808 ATCGTTAGTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:377584 original size:24 final size:24
Alignment explanation
Indices: 377529--377584 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
377519 TTTTTGTAAT
*
377529 TCTAGCCTCGTCCACGACCTCGACT
1 TCTA-CCTCGTCCACGACCTCGACA
* * *
377554 TCCACCTCGTCCATGACCTCTACA
1 TCTACCTCGTCCACGACCTCGACA
377578 TCTACCT
1 TCTACCT
377585 TGGCCACGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.18, C:0.45, G:0.11, T:0.27
Consensus pattern (24 bp):
TCTACCTCGTCCACGACCTCGACA
Found at i:378627 original size:3 final size:3
Alignment explanation
Indices: 378581--378610 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
378571 AATATTTATG
*
378581 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
378611 ATAATAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:380601 original size:22 final size:22
Alignment explanation
Indices: 380576--380627 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
380566 TAATTCATTA
380576 TCTTATTTTATTT-ATTTATTTT
1 TCTT-TTTTATTTGATTTATTTT
*
380598 TCTTTTTTCTTTGATTTATTTAT
1 TCTTTTTTATTTGATTTATTT-T
*
380621 TCATTTT
1 TCTTTTT
380628 ATATAACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 7 0.27
22 12 0.46
23 7 0.27
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (22 bp):
TCTTTTTTATTTGATTTATTTT
Found at i:381043 original size:6 final size:6
Alignment explanation
Indices: 381032--381057 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
381022 GCGAAAATGG
381032 TAAATT TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
381058 TTATTCGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:382322 original size:18 final size:19
Alignment explanation
Indices: 382301--382345 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
382291 ATTTAGACAT
382301 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTGTTATTTTC
382319 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
382338 TTTGCATT
1 TTTGCATT
382346 CACATTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Done.