Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008419.1 Hibiscus syriacus cultivar Beakdansim tig00111199_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: 1038719
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 5
Found at i:377535 original size:21 final size:22
Alignment explanation
Indices: 377497--377537 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
377487 TTAAATATTA
377497 TAAAGGTAATACCAATACTCAT
1 TAAAGGTAATACCAATACTCAT
* *
377519 TAAAGG-AGTACCGATACTC
1 TAAAGGTAATACCAATACTC
377538 CCTGTCCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (22 bp):
TAAAGGTAATACCAATACTCAT
Found at i:380245 original size:28 final size:28
Alignment explanation
Indices: 380190--380245 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
380180 TGTTCCTTAG
* * *
380190 AATTTTATAAGTTTAAGTTCGTCTCTAA
1 AATTTTATAAATTTAAGTTCATCCCTAA
380218 AATTTTATAAATTTAAGTTCATCCCTAA
1 AATTTTATAAATTTAAGTTCATCCCTAA
380246 CATAAAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (28 bp):
AATTTTATAAATTTAAGTTCATCCCTAA
Found at i:383944 original size:2 final size:2
Alignment explanation
Indices: 383937--384007 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
383927 CCAAACAAAT
383937 TA TA TA TA TA 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
383979 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
384008 TAATTTGAGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:384458 original size:28 final size:28
Alignment explanation
Indices: 384416--384474 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
384406 TCAACTTGTA
*
384416 TAAAATGTCACACTAAACCTCTCAAAAT
1 TAAAATGTCAAACTAAACCTCTCAAAAT
384444 TAAAATGTCAAACTAAACCTCTCAAAAT
1 TAAAATGTCAAACTAAACCTCTCAAAAT
384472 TAA
1 TAA
384475 CAATTTATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.25
Consensus pattern (28 bp):
TAAAATGTCAAACTAAACCTCTCAAAAT
Found at i:388807 original size:15 final size:14
Alignment explanation
Indices: 388770--388814 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
388760 ATATGTGTAA
388770 AATATTA-AA-TAT
1 AATATTATAATTAT
*
388782 AATA-AATAATTATT
1 AATATTATAATTA-T
388796 AATATTATAATTAT
1 AATATTATAATTAT
388810 AATAT
1 AATAT
388815 ATTTTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.04
12 6 0.22
13 2 0.07
14 11 0.41
15 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATTATAATTAT
Found at i:389150 original size:17 final size:15
Alignment explanation
Indices: 389122--389169 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 15
389112 TTAATTAATA
389122 TTATTT-TTTATTTT
1 TTATTTATTTATTTT
389136 TACTATTTATTTATTTGT
1 T--TATTTATTTATTT-T
389154 TTAGTTTATTTATTTT
1 TTA-TTTATTTATTTT
389170 GGTATTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 1 0.03
16 8 0.28
17 18 0.62
18 2 0.07
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (15 bp):
TTATTTATTTATTTT
Found at i:391063 original size:18 final size:18
Alignment explanation
Indices: 391040--391076 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
391030 TATTCAAGGT
391040 TTATGAATACAAGTTCAC
1 TTATGAATACAAGTTCAC
391058 TTATGAATACAAGTTCAC
1 TTATGAATACAAGTTCAC
391076 T
1 T
391077 CCCATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (18 bp):
TTATGAATACAAGTTCAC
Found at i:392009 original size:21 final size:22
Alignment explanation
Indices: 391971--392011 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
391961 TTAAATATTA
391971 TAAAGGTAATACCAATACTCAT
1 TAAAGGTAATACCAATACTCAT
* *
391993 TAAAGG-AGTACCGATACTC
1 TAAAGGTAATACCAATACTC
392012 CCTGTCCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (22 bp):
TAAAGGTAATACCAATACTCAT
Found at i:396307 original size:915 final size:915
Alignment explanation
Indices: 392597--397141 Score: 7178
Period size: 915 Copynumber: 5.0 Consensus size: 915
392587 GCTTCAATGT
* * * * * *
392597 TTAGAATGTCTAACAACCTTGAGACGATCCTTGAAGAATCTTTATCCATTTTTGACATAACTGAG
1 TTAGAATGTCTAACAACCCTGAGACGATCCTTGAAGAAGCTCTATCCATTTTCGACACAACTAAG
* * * * * *
392662 AAGATGGCGTCCACCTCCAGCTCGTTCCACATAGAAGACTCCCAATCGATCGACAAGCCTCCATA
66 AAAATGACGTCCACCTTCAGCTCATTCTACATAGAAGACTCACAATCGATCGACAAGCCTCCATA
* * * *
392727 CTTCAGTGGAGCCAACTACCGTCATTGGAAGAAATTAACGAATCTATTAATCCAATCCAATGATC
131 CTTCAATGGAGCCAACTACCGTCATTGGAAGAAATTAATGAAGCTATTCATCCAATCCAATGATC
* *
392792 TTGATGCATGGGAGATGATCGAGAACGACTACACTCCTCCAAAGAAGAAGATAAAGGAGTGGAGT
196 TTGATACATGGGAGATGATCGAGAACGACTACACTTCTCCAAAGAAGAAGATAAAGGAGTGGAGT
** * * * *
392857 GCCCAAGAATATAAGAAAACTCAAAAAAATGCTAAGGTCATGCACAC-TTATTTTGTGCATTTGG
261 GCCCAAGAATGGAAGAAAGCTCAACAAAATGCTAAGGTCATGCACACATTGTTTTATGCATTTGG
392921 TCTCAATGTCTATGAAGGAGTTTCTTCTTTTTCAAATGCCAATGAGCTTTGGAATAAGCTCGAAG
326 TCTCAATGTCTATGAAGGAGTTTCTTCTTTTTCAAATGCCAATGAGCTTTGGAATAAGCTCGAAG
* * *
392986 AGATCCATAGAAATAAGAAAGAACCAACAAAGGTGGTATTCTTAATGGCTCTTGAAGAGCCCGAA
391 AGATCCATAGAAATAAAAAAGAACCAACAAAGGTGGTATGCTTAATGGCTCTTGAAGATCCCGAA
* * * *
393051 GTATCTTTTAACTCAATTGAATCTGATTCATATTCTTTTGATAAGTTACAAGATACATATGATGA
456 GTATCTTCTAACTCAATTGAATCTGATTCATATTCTTTTGATGAGTTAGAAGATGCATATGATGA
* * * *
393116 ATTATTTTTAGAGTTTGAGAACATGAACTCCAAATACAAGGAAATGATTTCAAAACTTAAAGTTG
521 ATTATTTTTGGAGTTTTAGACCATGAATTCCAAATACAAGGAAATGATTTCAAAACTTAAAGTTG
*
393181 AAAATGATTTTCTTTTGAAAGAAAAAGTTCATTTTGAAAAACAAAATGAAATTTTGAAAAAGGAT
586 AAAACGATTTTCTTTTGAAAGAAAAAGTTCATTTTGAAAAACAAAATGAAATTTTGAAAAAGGAT
* * *
393246 TTAGAGCTTTCAAAAATGAAAATTGAAAATTTGAAAAAGAAATTTTTAATTTAAAGGTTAAGCTT
651 TTAGAGCTTTCAAAAATGAAAATTGAAAATTTGAAAAAAAAAGTTTTGATTTAAAGGTTAAGCTT
* *
393311 GAATGCTTAACAAAA-AAAAATAAATCATTTTAAATAATTCATCTAATTTCATAATGACAAAATA
716 GAATGCTTAACAAAAGAAAAATATATCATTTTAAATAATTCATCTAATTTCATAATGACAAAATG
393375 CTCACATTGTCATTATCATGGTCACAAGGAACATACTTGTCCTTTAAAGAAAGGAAAATGTTTTA
781 CTCACATTGTCATTATCATGGTCACAAGGAACATACTTGTCCTTTAAAGAAAGGAAAATGTTTTA
393440 AAATTAGAAAAGTATGGATTCCAAAGGGAACAAGGGGAATTGAAACTAACGTCCAAGGGAGCTTG
846 AAATTAGAAAAGTATGGATTCCAAAGGGAACAAGGGGAATTGAAACTAACGTCCAAGGGAGCTTG
*
393505 ACTCT
911 ACTCA
*
393510 TTAGAAGGTCTAACAACCCTGAGACGATCCTTGAAGAAGCTCTATCCATTTTCGACACAACTAAG
1 TTAGAATGTCTAACAACCCTGAGACGATCCTTGAAGAAGCTCTATCCATTTTCGACACAACTAAG
* * * * *
393575 AAAATGGCATTCACCTCCAGCTCATTCTACATGGAAGACTCACAATCGATCGACAAGCCTCCATA
66 AAAATGACGTCCACCTTCAGCTCATTCTACATAGAAGACTCACAATCGATCGACAAGCCTCCATA
* * *
393640 CTTCAATGGAGCCAACTACCATCATTGTAAGAAATTAATGAAGTTATTCATCCAATCCAATGATC
131 CTTCAATGGAGCCAACTACCGTCATTGGAAGAAATTAATGAAGCTATTCATCCAATCCAATGATC
* * * **
393705 TTGATACATGGGAGATGATTGAGAACAACTACTCTTCTCCAAAGAAGAAGACGAAGGAGTGGAGT
196 TTGATACATGGGAGATGATCGAGAACGACTACACTTCTCCAAAGAAGAAGATAAAGGAGTGGAGT
* ** *
393770 GCCCAAGAACGGAAGAAAGCTCAACAAAATGCTAAGGTCATGCACATGTTGTTTTATGCATTTGA
261 GCCCAAGAATGGAAGAAAGCTCAACAAAATGCTAAGGTCATGCACACATTGTTTTATGCATTTGG
* * * * * * * * *
393835 TCCCGATGTCTATGAAGGAATTTATT-TTTGTACAAATACCAAGGTGCTTTGGAATAAGCTCAAA
326 TCTCAATGTCTATGAAGGAGTTTCTTCTTT-TTCAAATGCCAATGAGCTTTGGAATAAGCTCGAA
* * * * * * *
393899 GATATCCATAGAAACAAGAAAGAAAAACCAACAAAAGTGGTATGGTTAATGACTTTTGAAGAGT-
390 GAGATCCATAGAAA-TA-AAA-AAGAACCAACAAAGGTGGTATGCTTAATGGCTCTTGAAGA-TC
* * * *
393963 CTGAGGTATCTTCTAACTCAAATGAATCTGAATCATATTCTTTTGATGAGTTAGAAGATGCATAT
451 CCGAAGTATCTTCTAACTCAATTGAATCTGATTCATATTCTTTTGATGAGTTAGAAGATGCATAT
*
394028 GATGAATTATTTTTGGAGTTTTAGACCATGAATTCCAAATACAAGGAAATGATTTCAAAACTTTA
516 GATGAATTATTTTTGGAGTTTTAGACCATGAATTCCAAATACAAGGAAATGATTTCAAAACTTAA
* *
394093 AGTTAAAAACGATTTTCTTTTGAAAGAAAAAGTTCATTTTGAAAAACAATATGAAATTTTGAAAA
581 AGTTGAAAACGATTTTCTTTTGAAAGAAAAAGTTCATTTTGAAAAACAAAATGAAATTTTGAAAA
394158 AGGATTTAGAGCTTTCAAAAATGAAAATTGAAAATTTGAAAAAAAAAAAGTTTTGATTTAAAGGT
646 AGGATTTAGAGCTTTCAAAAATGAAAATTGAAAATTTG--AAAAAAAAAGTTTTGATTTAAAGGT
*
394223 TAAGCTTGAATGCTTAACAAAAGAAAAAGATATCATTTTAAATAATTCATCTAATTTCATAATGA
709 TAAGCTTGAATGCTTAACAAAAGAAAAATATATCATTTTAAATAATTCATCTAATTTCATAATGA
*
394288 CAAAATGCTCACATTTTCATTATCATGGTCACAAGGAACATACTTGTCCTTTAAAGAAAGGAAAA
774 CAAAATGCTCACATTGTCATTATCATGGTCACAAGGAACATACTTGTCCTTTAAAGAAAGGAAAA
394353 TGTTTTAAAATTAGAAAAGTATGGATTCCAAAGGGAACAAGGGGAATTGAAACTAACGTCCAAGG
839 TGTTTTAAAATTAGAAAAGTATGGATTCCAAAGGGAACAAGGGGAATTGAAACTAACGTCCAAGG
* *
394418 GAGTTTTACTCA
904 GAGCTTGACTCA
* * *
394430 TTAGAATGTCTAAAAACCCTGAGACGATCCTTGAAGAAGATATATCCATTTTCGACACAACTAAG
1 TTAGAATGTCTAACAACCCTGAGACGATCCTTGAAGAAGCTCTATCCATTTTCGACACAACTAAG
* *
394495 AAAATGACGTCCACTTTCAGCTCATTCTATATAGAAGACTCACAATCGATCGACAAGCCTCCATA
66 AAAATGACGTCCACCTTCAGCTCATTCTACATAGAAGACTCACAATCGATCGACAAGCCTCCATA
394560 CTTCAATGGAGCCAACTACCGTCATTGGAAGAAATTAATGAAGCTATTCATCCAATCCAATGATC
131 CTTCAATGGAGCCAACTACCGTCATTGGAAGAAATTAATGAAGCTATTCATCCAATCCAATGATC
* *
394625 TGGATACATGGGAGATGATCGAGAATGACTACACTTCTCCAAAGAAGAAGATAAAGGAGTGGAGT
196 TTGATACATGGGAGATGATCGAGAACGACTACACTTCTCCAAAGAAGAAGATAAAGGAGTGGAGT
*
394690 GCCCAAGAATGGAAGAAAGCTCAACAAAATGCTAAGGTCATGTACACATTGTTTTATGCATTTGG
261 GCCCAAGAATGGAAGAAAGCTCAACAAAATGCTAAGGTCATGCACACATTGTTTTATGCATTTGG
* *
394755 TTTCAATGTCTATGAAGGAGTTTCTTCTTTTTCAAATGCCAATGAGATTTGGAATAAGCTCGAAG
326 TCTCAATGTCTATGAAGGAGTTTCTTCTTTTTCAAATGCCAATGAGCTTTGGAATAAGCTCGAAG
394820 AGATCCATAGAAATAAAAAAGAACCAACAAAGGTGGTATGCTTAATGGCTCTTGAAGATCCCGAA
391 AGATCCATAGAAATAAAAAAGAACCAACAAAGGTGGTATGCTTAATGGCTCTTGAAGATCCCGAA
* * * *
394885 GTATCTTCTAACTCAATTGAATCTGATTCATATTTTTTTTTATGAGTTACAAGATACATATGATG
456 GTATCTTCTAACTCAATTGAATCTGATTCATA-TTCTTTTGATGAGTTAGAAGATGCATATGATG
* * * * *
394950 AATTATTTTTAGAATTTGAGAACATGAACTCCAAATACAAGGAAATGATTTCAAAACTTAAAGTT
520 AATTATTTTTGGAGTTTTAGACCATGAATTCCAAATACAAGGAAATGATTTCAAAACTTAAAGTT
* * *
395015 GAAAATGATTTTCTTTTGAAAGAAAAAGTTCATTTTGAAAAACAAAATGAAAATTCGAAAAAGGA
585 GAAAACGATTTTCTTTTGAAAGAAAAAGTTCATTTTGAAAAACAAAATGAAATTTTGAAAAAGGA
*
395080 TTTAGAGCTTTCAAAAATGAAAATTGAAAATTTGAAAAAAAAAGTTTTGATTTAAAGGTTAAGCA
650 TTTAGAGCTTTCAAAAATGAAAATTGAAAATTTGAAAAAAAAAGTTTTGATTTAAAGGTTAAGCT
395145 TGAATGCTTAACAAAAGAAAAATATATCATTTTAAATAATTCATCTAATTTCATAATGACAAAAT
715 TGAATGCTTAACAAAAGAAAAATATATCATTTTAAATAATTCATCTAATTTCATAATGACAAAAT
395210 GCTCACATTGTCATTATCATGGTCACAAGGAACATACTTGTCCTTTAAAGAAAGGAAAATGTTTT
780 GCTCACATTGTCATTATCATGGTCACAAGGAACATACTTGTCCTTTAAAGAAAGGAAAATGTTTT
*
395275 AAAATTAGAAAAGTATGTATTCCAAAGGGAACAAGGGGAATTGAAACTAACGTCCAAGGGAGCTT
845 AAAATTAGAAAAGTATGGATTCCAAAGGGAACAAGGGGAATTGAAACTAACGTCCAAGGGAGCTT
*
395340 TACTCA
910 GACTCA
*
395346 TTAGAATGTCTAACAACCCTGAGACGATCCTTGAAGAAGCTCTATCCATTTTCGGCACAACTAAG
1 TTAGAATGTCTAACAACCCTGAGACGATCCTTGAAGAAGCTCTATCCATTTTCGACACAACTAAG
*
395411 AAAATGACGTCCAGCTTCAGCTCATTCTACATAGAAGACTCACAATCGATCGACAAGCCTCCATA
66 AAAATGACGTCCACCTTCAGCTCATTCTACATAGAAGACTCACAATCGATCGACAAGCCTCCATA
395476 CTTCAATGGAGCCAACTACCGTCATTGGAAGAAATTAATGAAGCTATTCATCCAATCCAATGATC
131 CTTCAATGGAGCCAACTACCGTCATTGGAAGAAATTAATGAAGCTATTCATCCAATCCAATGATC
* *
395541 TTGATACATGGGACATGATCGATAACGACTACACTTCTCCAAAGAAGAAGATAAAGGAGTGGAGT
196 TTGATACATGGGAGATGATCGAGAACGACTACACTTCTCCAAAGAAGAAGATAAAGGAGTGGAGT
395606 GCCCAAGAATGGAAGAAAGCTCAACAAAATGCTAAGGTCATGCACACATTGTTTTATGCATTTGG
261 GCCCAAGAATGGAAGAAAGCTCAACAAAATGCTAAGGTCATGCACACATTGTTTTATGCATTTGG
*
395671 TCTTAATGTCTATGAAGGAGTTTCTTCTTTTTCAAATGCCAATGAGCTTTGGAATAAGCTCGAAG
326 TCTCAATGTCTATGAAGGAGTTTCTTCTTTTTCAAATGCCAATGAGCTTTGGAATAAGCTCGAAG
*
395736 AGATCCATAGAAATAAAAAAAGAACCAACAAAGGTGGTATTCTTAATGGCTCTTGAAGATCCCGA
391 AGATCCATAGAAAT-AAAAAAGAACCAACAAAGGTGGTATGCTTAATGGCTCTTGAAGATCCCGA
*
395801 AGTATCTTCTAACTCAATTGAATCTGATTCATATTCTTTTGATGAGTTAGAAGATGTATATGATG
455 AGTATCTTCTAACTCAATTGAATCTGATTCATATTCTTTTGATGAGTTAGAAGATGCATATGATG
*
395866 AATTA-TTTTGGAGTTTTAGACCATGAATTCCAAATACAAGGAAATGATTTCAAAACTTTAAGTT
520 AATTATTTTTGGAGTTTTAGACCATGAATTCCAAATACAAGGAAATGATTTCAAAACTTAAAGTT
* *
395930 AAAAACGATTTTCTTTTGAAAGAAAAAGTTCATTTTGAAAAACAATATGAAATTTTGAAAAAGGA
585 GAAAACGATTTTCTTTTGAAAGAAAAAGTTCATTTTGAAAAACAAAATGAAATTTTGAAAAAGGA
* *
395995 TTTAGAGCTTTCAAAAATGAAAATTGAAAATTTGAAAAAAAAAGTTTTTATTTAAAGGTTAAGCA
650 TTTAGAGCTTTCAAAAATGAAAATTGAAAATTTGAAAAAAAAAGTTTTGATTTAAAGGTTAAGCT
396060 TGAATGCTTAACAAAAGAAAAATATATCATTTTAAATAATTCATCTAATTTCATAATGACAAAAT
715 TGAATGCTTAACAAAAGAAAAATATATCATTTTAAATAATTCATCTAATTTCATAATGACAAAAT
*
396125 GCTCACATTGTCATTATCATGGTCACAAGGAACATACTTGTCCTTTAAAAAAAGGAAAATGTTTT
780 GCTCACATTGTCATTATCATGGTCACAAGGAACATACTTGTCCTTTAAAGAAAGGAAAATGTTTT
396190 AAAATTAGAAAAGTATGGATTCCAAAGGGAACAAGGGGAATTGAAACTAACGTCCAAGGGAGCTT
845 AAAATTAGAAAAGTATGGATTCCAAAGGGAACAAGGGGAATTGAAACTAACGTCCAAGGGAGCTT
396255 GACTCA
910 GACTCA
* *
396261 TTAGAAGGTCTAACAACCCTGAGACGATCCTTGAAGAAGCTCTATCCAGTTTCGACACAACTAAG
1 TTAGAATGTCTAACAACCCTGAGACGATCCTTGAAGAAGCTCTATCCATTTTCGACACAACTAAG
* * *
396326 AAAATTACGTCCACCTTCAACTCATTCTACATTGAAGACTCACAATCGATCGACAAGCCTCCATA
66 AAAATGACGTCCACCTTCAGCTCATTCTACATAGAAGACTCACAATCGATCGACAAGCCTCCATA
*
396391 CTTCAATGGAGCCAACTATCGTCATTGGAAGAAATTAATGAAGCTATTCATCCAATCCAATGATC
131 CTTCAATGGAGCCAACTACCGTCATTGGAAGAAATTAATGAAGCTATTCATCCAATCCAATGATC
* * * **
396456 TTGATACATGGAAGGTGATCGAGAACGACTACTCTTCTCCAAAGAAGAAGACGAAGGAGTGGAGT
196 TTGATACATGGGAGATGATCGAGAACGACTACACTTCTCCAAAGAAGAAGATAAAGGAGTGGAGT
* * * ** * **
396521 GCCCAAGAACGGAAGAAAGATCAACAAAATGCTAAGGCCATGCACATGTTGTTTTGTGCATTTTA
261 GCCCAAGAATGGAAGAAAGCTCAACAAAATGCTAAGGTCATGCACACATTGTTTTATGCATTTGG
* * * * * *
396586 TCCCGATGTCTATAAAGGAATTTCTT-TTTGTACAAATGCCAATGAGCTTTGGAATAAGCTCAAA
326 TCTCAATGTCTATGAAGGAGTTTCTTCTTT-TTCAAATGCCAATGAGCTTTGGAATAAGCTCGAA
* * * * *
396650 GATATCCATA-TAATCAAGAAAGAA-AAAC-CA------A--C--AA---------AA-ATGCCC
390 GAGATCCATAGAAAT-AAAAAAGAACCAACAAAGGTGGTATGCTTAATGGCTCTTGAAGAT-CCC
* *
396692 GAGGTATCTTCTAACTCAAATGAAT-TCGATTCATATTCTTTTGATGAGTTAGAAGATGCATATG
453 GAAGTATCTTCTAACTCAATTGAATCT-GATTCATATTCTTTTGATGAGTTAGAAGATGCATATG
396756 ATGAATTATTTTTGGAGTTTTAGACCATGAATTCCAAATACAAGGAAATGATTTCAAAACTTAAA
517 ATGAATTATTTTTGGAGTTTTAGACCATGAATTCCAAATACAAGGAAATGATTTCAAAACTTAAA
*
396821 GTTGAAAACGATTTTCTTTTGAAATAAAAAGTTCATTTTGAAAAACAAAATGAAATTTTGAAAAA
582 GTTGAAAACGATTTTCTTTTGAAAGAAAAAGTTCATTTTGAAAAACAAAATGAAATTTTG-AAAA
* *
396886 ATGATTTAGAGCTTTCATAAATGAAAATTGAAAATTTTG-AAAAAAAAGTTTTGATTTAAAGGTT
646 AGGATTTAGAGCTTTCAAAAATGAAAATTGAAAA-TTTGAAAAAAAAAGTTTTGATTTAAAGGTT
* *
396950 AAGCTTGAATGCTTAACAAAAG-AAAATGAAATCATTTTAAATAATTCATGTAATTTCATAATGA
710 AAGCTTGAATGCTTAACAAAAGAAAAAT-ATATCATTTTAAATAATTCATCTAATTTCATAATGA
* * * * *
397014 CAAAATGCTCACATTGTCATT-TCATGTTCACACGTAACATACTTAT-TTTTAAAGAAAGGAAAA
774 CAAAATGCTCACATTGTCATTATCATGGTCACAAGGAACATACTTGTCCTTTAAAGAAAGGAAAA
* * *
397077 TGTTTTAAAATTAGACAAGTATGGATTCCAAAGGGAACAAGGGGCATAGAAACTAACGTCCAAGG
839 TGTTTTAAAATTAGAAAAGTATGGATTCCAAAGGGAACAAGGGGAATTGAAACTAACGTCCAAGG
397142 ATCCAAAGCA
Statistics
Matches: 3368, Mismatches: 244, Indels: 60
0.92 0.07 0.02
Matches are distributed among these distances:
892 3 0.00
893 149 0.04
894 138 0.04
895 136 0.04
896 4 0.00
902 2 0.00
904 1 0.00
906 1 0.00
912 1 0.00
913 279 0.08
914 92 0.03
915 740 0.22
916 651 0.19
917 401 0.12
918 184 0.05
919 45 0.01
920 538 0.16
921 3 0.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (915 bp):
TTAGAATGTCTAACAACCCTGAGACGATCCTTGAAGAAGCTCTATCCATTTTCGACACAACTAAG
AAAATGACGTCCACCTTCAGCTCATTCTACATAGAAGACTCACAATCGATCGACAAGCCTCCATA
CTTCAATGGAGCCAACTACCGTCATTGGAAGAAATTAATGAAGCTATTCATCCAATCCAATGATC
TTGATACATGGGAGATGATCGAGAACGACTACACTTCTCCAAAGAAGAAGATAAAGGAGTGGAGT
GCCCAAGAATGGAAGAAAGCTCAACAAAATGCTAAGGTCATGCACACATTGTTTTATGCATTTGG
TCTCAATGTCTATGAAGGAGTTTCTTCTTTTTCAAATGCCAATGAGCTTTGGAATAAGCTCGAAG
AGATCCATAGAAATAAAAAAGAACCAACAAAGGTGGTATGCTTAATGGCTCTTGAAGATCCCGAA
GTATCTTCTAACTCAATTGAATCTGATTCATATTCTTTTGATGAGTTAGAAGATGCATATGATGA
ATTATTTTTGGAGTTTTAGACCATGAATTCCAAATACAAGGAAATGATTTCAAAACTTAAAGTTG
AAAACGATTTTCTTTTGAAAGAAAAAGTTCATTTTGAAAAACAAAATGAAATTTTGAAAAAGGAT
TTAGAGCTTTCAAAAATGAAAATTGAAAATTTGAAAAAAAAAGTTTTGATTTAAAGGTTAAGCTT
GAATGCTTAACAAAAGAAAAATATATCATTTTAAATAATTCATCTAATTTCATAATGACAAAATG
CTCACATTGTCATTATCATGGTCACAAGGAACATACTTGTCCTTTAAAGAAAGGAAAATGTTTTA
AAATTAGAAAAGTATGGATTCCAAAGGGAACAAGGGGAATTGAAACTAACGTCCAAGGGAGCTTG
ACTCA
Found at i:402060 original size:65 final size:65
Alignment explanation
Indices: 401923--402132 Score: 234
Period size: 65 Copynumber: 3.2 Consensus size: 65
401913 GTGCACTAAG
* * * *
401923 AGTGCATCGGTGCATCAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGAT
* *
401987 TGTCCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGGA
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCGATGCATGGA
402051 T
65 T
* * **
402052 AGTGCATCGATGCAT-AAACTGCATTCGATG--TTCAATTTATTCATTG-GTGCATCGATGCATG
1 AGTGCATCGATGCATCAAA-TGCATTCGATGTTTTCAA--AATACCCTGAGTGCATCGATGCATG
402113 GATT
63 GA-T
*
402117 AGTGCATCGGTGCATC
1 AGTGCATCGATGCATC
402133 CCTTTGAAAA
Statistics
Matches: 125, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.38
65 70 0.56
66 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGAT
Found at i:407868 original size:20 final size:20
Alignment explanation
Indices: 407843--407885 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
407833 TCATATTCGT
407843 TAAATTTT-AAACCTAAACCC
1 TAAATTTTCAAACC-AAACCC
*
407863 TAAATTTTCAAACCATACCC
1 TAAATTTTCAAACCAAACCC
407883 TAA
1 TAA
407886 TTCCAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAATTTTCAAACCAAACCC
Found at i:408294 original size:3 final size:3
Alignment explanation
Indices: 408286--408314 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
408276 TTGAACACAA
408286 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
408315 CCCCATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:408846 original size:2 final size:2
Alignment explanation
Indices: 408839--408876 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
408829 GGTTGAATCA
408839 AT AT 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
408877 GATTATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:409495 original size:27 final size:27
Alignment explanation
Indices: 409434--409495 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
409424 TCTTTCAAAA
** *
409434 TTTAAAATTTATTTTATATATTTTATT
1 TTTAAAATTTAAATTATATATTATATT
*
409461 TTTTAAATTTAAATTATATA-TATATT
1 TTTAAAATTTAAATTATATATTATATT
409487 TATTAAAAT
1 T-TTAAAAT
409496 ATATTGGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTAAAATTTAAATTATATATTATATT
Found at i:414110 original size:15 final size:15
Alignment explanation
Indices: 414091--414120 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
414081 AAATTTCCTT
414091 AAAAATCAAAAAAATA
1 AAAAAT-AAAAAAATA
414107 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
414121 CATAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Found at i:414347 original size:13 final size:13
Alignment explanation
Indices: 414221--414348 Score: 53
Period size: 14 Copynumber: 9.2 Consensus size: 13
414211 TAAAAACGTA
414221 AAAAAAATAAATAT
1 AAAAAAATAAAT-T
* *
414235 AAAAAATTAAAAT
1 AAAAAAATAAATT
* *
414248 AATAAAATAACGAATC
1 AAAAAAAT-A--AATT
* **
414264 AAAGAAATAAAAG
1 AAAAAAATAAATT
414277 AAAGAAAATAAGA-T
1 AAA-AAAATAA-ATT
414291 AAAAATAGATCAAA-T
1 AAAAA-A-AT-AAATT
* *
414306 AAAAGAATAAATA
1 AAAAAAATAAATT
* *
414319 AAAAAAACATATTT
1 AAAAAAATA-AATT
414333 AAAAAAATAAATT
1 AAAAAAATAAATT
414346 AAA
1 AAA
414349 GTTATGGTAA
Statistics
Matches: 84, Mismatches: 20, Indels: 21
0.67 0.16 0.17
Matches are distributed among these distances:
12 3 0.04
13 29 0.35
14 32 0.38
15 10 0.12
16 10 0.12
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (13 bp):
AAAAAAATAAATT
Found at i:415078 original size:14 final size:14
Alignment explanation
Indices: 415059--415090 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
415049 TTGACACCTA
415059 GAAATCTTGATATT
1 GAAATCTTGATATT
415073 GAAATCTTGATATT
1 GAAATCTTGATATT
415087 GAAA
1 GAAA
415091 ATAAGGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (14 bp):
GAAATCTTGATATT
Found at i:423395 original size:15 final size:17
Alignment explanation
Indices: 423375--423406 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
423365 ATGAATTTTC
423375 TTAA-TTTGTAT-ATCA
1 TTAATTTTGTATCATCA
423390 TTAATTTTGTATCATCA
1 TTAATTTTGTATCATCA
423407 AACACAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 7 0.47
17 4 0.27
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (17 bp):
TTAATTTTGTATCATCA
Found at i:425470 original size:2 final size:2
Alignment explanation
Indices: 425463--425494 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
425453 ATTTGTTTCA
425463 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
425495 TCTAATAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:426714 original size:2 final size:2
Alignment explanation
Indices: 426707--426797 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
426697 AACGAAACAA
426707 AT AT AT AT 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
426749 AT AT AT AT 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
426791 AT AT AT A
1 AT AT AT A
426798 AAACGGTTGA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:427752 original size:32 final size:32
Alignment explanation
Indices: 427716--427783 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
427706 ATATTATTTT
427716 ATTAAAATTAAAATTTTAAAAAAATATAAAAG
1 ATTAAAATTAAAATTTTAAAAAAATATAAAAG
427748 ATTAAAATTAAAATTTTAAAAAAATATAAAAG
1 ATTAAAATTAAAATTTTAAAAAAATATAAAAG
427780 ATTA
1 ATTA
427784 CAAGTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (32 bp):
ATTAAAATTAAAATTTTAAAAAAATATAAAAG
Found at i:428441 original size:38 final size:38
Alignment explanation
Indices: 428390--428466 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
428380 AAAAGAAGTA
428390 AACAAGAAAACCTCTCAAAGTTAGGGTGTTTAAAAGAT
1 AACAAGAAAACCTCTCAAAGTTAGGGTGTTTAAAAGAT
428428 AACAAGAAAACCTCTCAAAGTTAGGGTGTTTAAAAGAT
1 AACAAGAAAACCTCTCAAAGTTAGGGTGTTTAAAAGAT
428466 A
1 A
428467 TAATCTCACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.23
Consensus pattern (38 bp):
AACAAGAAAACCTCTCAAAGTTAGGGTGTTTAAAAGAT
Found at i:437053 original size:30 final size:30
Alignment explanation
Indices: 437017--437092 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
437007 AGTGAACCGG
* *
437017 CGGTTCAAACCGGTTTTGCCGGTTTTCAGC
1 CGGTTCAAACCGGTTTTACCGATTTTCAGC
**
437047 CGGTTCACCCCGGTTTTACCGATTTTCAGC
1 CGGTTCAAACCGGTTTTACCGATTTTCAGC
*
437077 CGGTTC-TACCGGTTTT
1 CGGTTCAAACCGGTTTT
437093 CAGCCGGCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 8 0.20
30 32 0.80
ACGTcount: A:0.12, C:0.29, G:0.24, T:0.36
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTACCGATTTTCAGC
Found at i:437081 original size:20 final size:20
Alignment explanation
Indices: 437056--437099 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
437046 CCGGTTCACC
*
437056 CCGGTTTTACCGATTTTCAG
1 CCGGTTCTACCGATTTTCAG
*
437076 CCGGTTCTACCGGTTTTCAG
1 CCGGTTCTACCGATTTTCAG
437096 CCGG
1 CCGG
437100 CTCATTGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.30, G:0.25, T:0.34
Consensus pattern (20 bp):
CCGGTTCTACCGATTTTCAG
Found at i:438218 original size:41 final size:41
Alignment explanation
Indices: 438173--438259 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
438163 TTCCATTTCG
*
438173 CGTTGCGGTAGTCTACAGTTGTCGTTGCAATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATT
*
438214 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATT
438255 CGTTG
1 CGTTG
438260 TAATAGTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATT
Found at i:438239 original size:22 final size:22
Alignment explanation
Indices: 438173--438244 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
438163 TTCCATTTCG
*
438173 CGTTGCGGTAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * * **
438195 CGTTGC-A-ATTTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
438214 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
438236 CGTTGCGAT
1 CGTTGCGAT
438245 TTTCCAAATT
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 7 0.19
20 7 0.19
21 6 0.17
22 16 0.44
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:438259 original size:19 final size:19
Alignment explanation
Indices: 438194--438259 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
438184 TCTACAGTTG
*
438194 TCGTTGCAATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
438213 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
438234 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
438254 TCGTTG
1 TCGTTG
438260 TAATAGTTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 15 0.43
20 5 0.14
21 5 0.14
22 10 0.29
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:438355 original size:6 final size:6
Alignment explanation
Indices: 438344--438433 Score: 166
Period size: 6 Copynumber: 15.3 Consensus size: 6
438334 GACACGTATT
438344 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
438392 ACCACG ACCACG ACCACG ACCACG ACCACG A-CACG A-CACG AC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG AC
438434 ACGGACGGCG
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.12
6 73 0.88
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:439087 original size:22 final size:22
Alignment explanation
Indices: 439061--439170 Score: 106
Period size: 22 Copynumber: 5.3 Consensus size: 22
439051 TTGGAAAATT
439061 GCAACGACAACTGTAGACTATC
1 GCAACGACAACTGTAGACTATC
439083 GCAACGACAACTGTAGACTATC
1 GCAACGACAACTGTAGACTATC
* * **
439105 GCAACG--AA-TTTGGAAAATC
1 GCAACGACAACTGTAGACTATC
* * **
439124 GCAAC-A-AA-TTTGGAAAATC
1 GCAACGACAACTGTAGACTATC
439143 GCAACGACAACTGTAGACTATC
1 GCAACGACAACTGTAGACTATC
439165 GCAACG
1 GCAACG
439171 CGAAATGAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
19 30 0.39
20 3 0.04
21 2 0.03
22 41 0.54
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (22 bp):
GCAACGACAACTGTAGACTATC
Found at i:439126 original size:19 final size:19
Alignment explanation
Indices: 439102--439149 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
439092 ACTGTAGACT
439102 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
*
439121 ATCGCAACAAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
439140 ATCGCAACGA
1 ATCGCAACGA
439150 CAACTGTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:439164 original size:60 final size:63
Alignment explanation
Indices: 439040--439170 Score: 196
Period size: 60 Copynumber: 2.1 Consensus size: 63
439030 CAACGAATTT
* **
439040 TCGCAACGAATTTGGAAAATTGCAACGACAACTGTAGACTATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGAAAATCGCAACGACAACTGTAGACTA
* *
439103 TCGCAACGAATTTGGAAAATCGCAAC-A-AA-TTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGAAAATCGCAACGACAACTGTAGACTA
439163 TCGCAACG
1 TCGCAACG
439171 CGAAATGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 35 0.56
61 2 0.03
62 1 0.02
63 25 0.40
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (63 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGAAAATCGCAACGACAACTGTAGACTA
Found at i:446327 original size:19 final size:19
Alignment explanation
Indices: 446304--446345 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
446294 TATTAAAAAA
446304 TAAAAAAT-A-TATTAATT
1 TAAAAAATAATTATTAATT
* *
446321 TAAAAAATAATTTTTTATT
1 TAAAAAATAATTATTAATT
446340 TAAAAA
1 TAAAAA
446346 TTTAAAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.38
18 1 0.05
19 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAAAAATAATTATTAATT
Found at i:446627 original size:16 final size:17
Alignment explanation
Indices: 446606--446647 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
446596 TTTTAAAATA
446606 TTAAAAAAAT-ATTGTT
1 TTAAAAAAATAATTGTT
* *
446622 TTAAAAAATTAATTTTT
1 TTAAAAAAATAATTGTT
446639 TTAAAAAAA
1 TTAAAAAAA
446648 ATTTAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAAAAAAATAATTGTT
Found at i:447492 original size:247 final size:252
Alignment explanation
Indices: 447031--447531 Score: 635
Period size: 262 Copynumber: 2.0 Consensus size: 252
447021 AAATTTTGAG
* * * * *
447031 TAAAGTATATAAATAGTTCCTAAACTATTAGGGTATTTTCATTTTGGTCACTCAATTTTTGAAAC
1 TAAAATATACAAATAGTCCCCAAACTATTAGGGTATTTTCATTTTGGTCACTCAATTTTTAAAAC
* * ** *
447096 TTACAATACAGTCATCGAACTTTTAATTCGTTCAGTAGGGTCTATGTCGTACCTCTGTTAGTTTT
66 TTACAATACAGTCATCAAACTTTTAATTCGTTCAGTAGGATCTATCCCATACCTCTGTTAGTTTT
447161 TGCTGTCACATGGTATTTCAAATAAAAAAATATTTTAAATATTAAAAATTTAAAAAAATTATTTT
131 TGCTGTCAC---GTATTTC-AATAAAAAAATATTTTAAATATTAAAAATTTAAAAAAA-TATTTT
*
447226 AAAAAATGGGTTTTATTTAAAATTTTAAAAGTTATTAAATATCTTTTTGAGTTTGAGAACTTATG
191 ---AAAT--GTTTTATTTAAAATTTTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAACTTATG
447291 GA
251 GA
* *
447293 TAAAATATACAAATAGTCCCCAAACTCTTAGGGTATTTTCATTTTGGTCGCTCAATTTTTAAAAC
1 TAAAATATACAAATAGTCCCCAAACTATTAGGGTATTTTCATTTTGGTCACTCAATTTTTAAAAC
* * *
447358 TTACAATATAGTTATCAAACTTTTAGTTCGTTTTCAGTAAGGATC-ATCCCATACCTCTGTTAGT
66 TTACAATACAGTCATCAAACTTTTAATTCG--TTCAGT-AGGATCTATCCCATACCTCTGTTAGT
* *
447422 TTTTGCTTTCAC-T-TTTC-A-AAAAAAATATTTTAAAATATTAAAAAATTT-ATAAAA-A-TTT
128 TTTTGCTGTCACGTATTTCAATAAAAAAATATTTT-AAATATT-AAAAATTTAAAAAAATATTTT
447480 -AAT-TTTTATTTAAAATTTTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAA
191 AAATGTTTTATTTAAAATTTTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAA
447532 TCTAAAGAAG
Statistics
Matches: 216, Mismatches: 18, Indels: 25
0.83 0.07 0.10
Matches are distributed among these distances:
247 48 0.22
250 3 0.01
254 3 0.01
255 1 0.00
256 13 0.06
257 13 0.06
258 8 0.04
259 4 0.02
260 1 0.00
262 84 0.39
264 33 0.15
265 5 0.02
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (252 bp):
TAAAATATACAAATAGTCCCCAAACTATTAGGGTATTTTCATTTTGGTCACTCAATTTTTAAAAC
TTACAATACAGTCATCAAACTTTTAATTCGTTCAGTAGGATCTATCCCATACCTCTGTTAGTTTT
TGCTGTCACGTATTTCAATAAAAAAATATTTTAAATATTAAAAATTTAAAAAAATATTTTAAATG
TTTTATTTAAAATTTTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAACTTATGGA
Found at i:448071 original size:16 final size:17
Alignment explanation
Indices: 448050--448083 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
448040 TTTAAAATAT
448050 TAAAAAAT-ATTTTTTA
1 TAAAAAATAATTTTTTA
*
448066 TAAAAATTAATTTTTTA
1 TAAAAAATAATTTTTTA
448083 T
1 T
448084 TTACAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAAAAATAATTTTTTA
Found at i:448513 original size:301 final size:302
Alignment explanation
Indices: 448092--448638 Score: 823
Period size: 302 Copynumber: 1.8 Consensus size: 302
448082 ATTTACAAAT
* *
448092 TTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAACTTAAAGAAGTGTTAAAAACATACGGGGCT
1 TTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAACTTAAAGAAATGTAAAAAACATACGGGGCT
* *
448157 TAACAAATTTTGGGTAAAGTATATAAATAGTCCCCCAAAGTATTAGGACATTTTCATTTTGATCA
66 TAACAAATTTTGGGTAAAGTATATAAATAGTCCCCCAAACTATTAGGACATTTTCATTTTGATAA
* * * *
448222 -TCAATTTTTGACACTTATAATATAGTCATCGAACTTTTAGTTCATATTCAATAAAGTCCATGCC
131 CTCAATTTTTGAAACTTACAATATAGTCATCAAACTTTTAGTTCATATTCAATAAAGTCCATGAC
* *
448286 ATACCTATGTTAGTTTTTGCTGTCACATGGTATTTCAAAAAAAAATATTTTTTTAAAAAATATTA
196 ATACCTATGTTAGATTTTGCTGTCACATGGCATTTCAAAAAAAAATATTTTTTTAAAAAATATTA
448351 AAAAATAAAAATATTATTTTAAAAGAATTAATTTTAAAGAAA
261 AAAAATAAAAATATTATTTTAAAAGAATTAATTTTAAAGAAA
* * *
448393 TTAAAATTTATTAAATACCTTTTTGAGTTTGAGAACTTAATGAAATGTAAAAAACATTATGGGGC
1 TTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAACTTAAAGAAATGTAAAAAACA-TACGGGGC
* * *
448458 TTAAC-AATATTTGGGTAAAGTATATAAATAGT-CCCCAAACTCTTAAGG-TATTTTCATTTTGG
65 TTAACAAAT-TTTGGGTAAAGTATATAAATAGTCCCCCAAACTATT-AGGACATTTTCATTTTGA
* ** * * * *
448520 TAACTCATTTTTTGAAACTTACAATATAGTCATCAAACTTTTAGTTTGTTTTTAGTAAGGTCCAT
128 TAACTCAATTTTTGAAACTTACAATATAGTCATCAAACTTTTAGTTCATATTCAATAAAGTCCAT
*
448585 GACATACCTATGTTAGATTTTGCTGTCACATGGCATTTCAAAAAAAATTATTTT
193 GACATACCTATGTTAGATTTTGCTGTCACATGGCATTTCAAAAAAAAATATTTT
448639 AAAATAAAAA
Statistics
Matches: 218, Mismatches: 24, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
301 79 0.36
302 139 0.64
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (302 bp):
TTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAACTTAAAGAAATGTAAAAAACATACGGGGCT
TAACAAATTTTGGGTAAAGTATATAAATAGTCCCCCAAACTATTAGGACATTTTCATTTTGATAA
CTCAATTTTTGAAACTTACAATATAGTCATCAAACTTTTAGTTCATATTCAATAAAGTCCATGAC
ATACCTATGTTAGATTTTGCTGTCACATGGCATTTCAAAAAAAAATATTTTTTTAAAAAATATTA
AAAAATAAAAATATTATTTTAAAAGAATTAATTTTAAAGAAA
Found at i:448652 original size:595 final size:586
Alignment explanation
Indices: 447293--448736 Score: 1853
Period size: 595 Copynumber: 2.5 Consensus size: 586
447283 AACTTATGGA
* * ** *
447293 TAAAATATACAAATAGTCCCCAAACTCTTAGGGTATTTTCATTTTGGTCGCTCAATTTTTAAAAC
1 TAAAGTATATAAATAGTCCCCAAACTCTTAGGGTATTTTCATTTTGGTAACTCAATTTTTGAAAC
* * * **
447358 TTACAATATAGTTATCAAACTTTTAGTTCGTTTTCAGTAAGGAT-CATCCCATACCTCTGTTAGT
66 TTACAATATAGTCATCAAACTTTTAGTTTGTTTTTAGTAAGG-TCCATAACATACCTCTGTTAG-
* *
447422 TTTTGCTTTCAC-T---TTTCAAAAAAAA-TATTTTAAAATATTAAAAA-A---TTTATAAAAAT
129 TTTTGCTATCACATGGATTTCAAAAAAAATTATTTTAAAATATAAAAAATATTTTTTATAAAAA-
447478 TTAA-TTTTTATTTAAAATTTTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAA-TCTAAAGAA
193 TTAATTTTTTATTTAAAA-TTTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAACT-TAAAGAA
* * *
447541 GTGTAAAAAATATTATGGGGATTAACAATTTTGGGTAAAGTATATAAATAGTCCTCAAACTATTA
256 GTGTAAAAAACA-TACGGGGATTAACAATTTTGGGTAAAGTATATAAATAGTCCCCAAACTATTA
** * * **
447606 GGGTATCTTCATTTTGGTCACTTAATTTTTGAAACTTATAATATAATCATCGAACTTTTAGTTTG
320 GGACATCTTCATTTTGATCACTCAATTTTTGAAACTTATAATATAATCATCGAACTTTTAGTTCA
* *** * *
447671 TTTTTTGTAAGGTCCATGCCATACCTTTGTTAGTTTTTGCTGTCACATGGAATTTCAAAAAAATA
385 TATTCAATAAAGTCCATGCCATACCTATGTTAGTTTTTGCTGTCACATGGAATTTCAAAAAAATA
* * *
447736 TTTTAAAATATTAATAAATAAATGATATTGTTTTAAAAAAATAATTTTTATTTAAAAATTTAAAA
450 TTTTAAAATATTAAAAAATAAATAATATTATTTTAAAAAAATAATTTTTA--TAAAAATTTAAAA
* *
447801 GTTATTAAATACCTTTTTGAGTTTGAGAACTTAAAGAAGCGTTAAAAACATTATGGGGCTTAACA
513 GTTATTAAATACCTTTTTGAGTTTGAGAACTTAAAGAAACGTAAAAAACATTATGGGGCTTAACA
*
447866 ATTTTTGGG
578 ATATTTGGG
* * ** * *
447875 TAAAGTATATAAATAGTACCCAAACTATTAGGGTATTTTCATTTTAATTACTCAGTTTTTGAAAC
1 TAAAGTATATAAATAGTCCCCAAACTCTTAGGGTATTTTCATTTTGGTAACTCAATTTTTGAAAC
* * * *
447940 TTACAATATAGTCATCAAACATTTA-TTTCGTTTTTAGTAAGGTCCATAATAAACATCTGTTAGT
66 TTACAATATAGTCATCAAACTTTTAGTTT-GTTTTTAGTAAGGTCCATAACATACCTCTGTTAGT
*
448004 TTTGCTATCACATGGTATTTCAAAATAAAATTTTGATTTAAAATATTAAAAAATATTTTTTATAA
130 TTTGCTATCACATGG-ATTTCAAAA-AAAATTAT--TTTAAAATA-TAAAAAATATTTTTTATAA
448069 AAATTAATTTTTTATTTACAAATTTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAACTTAAAG
190 AAATTAATTTTTTATTTA-AAATTTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAACTTAAAG
* * *
448134 AAGTGTTAAAAACATACGGGGCTTAACAAATTTTGGGTAAAGTATATAAATAGTCCCCCAAAGTA
254 AAGTGTAAAAAACATACGGGGATTAAC-AATTTTGGGTAAAGTATATAAATAGT-CCCCAAACTA
* * *
448199 TTAGGACATTTTCATTTTGATCA-TCAATTTTTGACACTTATAATATAGTCATCGAACTTTTAGT
317 TTAGGACATCTTCATTTTGATCACTCAATTTTTGAAACTTATAATATAATCATCGAACTTTTAGT
*
448263 TCATATTCAATAAAGTCCATGCCATACCTATGTTAGTTTTTGCTGTCACATGGTATTTCAAAAAA
382 TCATATTCAATAAAGTCCATGCCATACCTATGTTAGTTTTTGCTGTCACATGGAATTTC--AAAA
*
448328 AAATATTTTTTTAAAAAATATTAAAAAATAAA-AATATTATTTTAAAAGAATTAA-TTTTA-AAG
445 AAATA---TTTT--AAAATATTAAAAAATAAATAATATTATTTTAAAA-AAATAATTTTTATAA-
* * *
448390 AAA-TTAAAATTTATTAAATACCTTTTTGAGTTTGAGAACTTAATGAAATGTAAAAAACATTATG
503 AAATTTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAACTTAAAGAAACGTAAAAAACATTATG
448454 GGGCTTAACAATATTTGGG
568 GGGCTTAACAATATTTGGG
* *
448473 TAAAGTATATAAATAGTCCCCAAACTCTTAAGGTATTTTCATTTTGGTAACTCATTTTTTGAAAC
1 TAAAGTATATAAATAGTCCCCAAACTCTTAGGGTATTTTCATTTTGGTAACTCAATTTTTGAAAC
* *
448538 TTACAATATAGTCATCAAACTTTTAGTTTGTTTTTAGTAAGGTCCATGACATACCTATGTTAGAT
66 TTACAATATAGTCATCAAACTTTTAGTTTGTTTTTAGTAAGGTCCATAACATACCTCTGTTAG-T
* *
448603 TTTGCTGTCACATGGCATTTCAAAAAAAATTATTTTAAAATAAAAAAAATATTATTTT-TAAAAA
130 TTTGCTATCACATGG-ATTTCAAAAAAAATTATTTTAAAATATAAAAAATATT-TTTTAT-AAAA
* *
448667 ATAAATTTTTTATTT---A---AAAA-TTATTAAATATCTTTTTGAGTTTGAG-ACTTTAAAGAA
192 ATTAATTTTTTATTTAAAATTTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAAC-TTAAAGAA
448724 GTGTAAAAAACAT
256 GTGTAAAAAACAT
448737 TAATCAATGT
Statistics
Matches: 753, Mismatches: 74, Indels: 64
0.85 0.08 0.07
Matches are distributed among these distances:
581 14 0.02
582 105 0.14
586 8 0.01
587 6 0.01
588 47 0.06
589 4 0.01
590 9 0.01
591 6 0.01
592 2 0.00
594 15 0.02
595 198 0.26
596 62 0.08
597 9 0.01
598 194 0.26
599 30 0.04
600 4 0.01
601 18 0.02
602 22 0.03
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.40
Consensus pattern (586 bp):
TAAAGTATATAAATAGTCCCCAAACTCTTAGGGTATTTTCATTTTGGTAACTCAATTTTTGAAAC
TTACAATATAGTCATCAAACTTTTAGTTTGTTTTTAGTAAGGTCCATAACATACCTCTGTTAGTT
TTGCTATCACATGGATTTCAAAAAAAATTATTTTAAAATATAAAAAATATTTTTTATAAAAATTA
ATTTTTTATTTAAAATTTAAAAGTTATTAAATACCTTTTTGAGTTTGAGAACTTAAAGAAGTGTA
AAAAACATACGGGGATTAACAATTTTGGGTAAAGTATATAAATAGTCCCCAAACTATTAGGACAT
CTTCATTTTGATCACTCAATTTTTGAAACTTATAATATAATCATCGAACTTTTAGTTCATATTCA
ATAAAGTCCATGCCATACCTATGTTAGTTTTTGCTGTCACATGGAATTTCAAAAAAATATTTTAA
AATATTAAAAAATAAATAATATTATTTTAAAAAAATAATTTTTATAAAAATTTAAAAGTTATTAA
ATACCTTTTTGAGTTTGAGAACTTAAAGAAACGTAAAAAACATTATGGGGCTTAACAATATTTGG
G
Found at i:448656 original size:22 final size:22
Alignment explanation
Indices: 448624--448665 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
448614 ATGGCATTTC
448624 AAAAAAAATTA-TTTTAAAATA
1 AAAAAAAATTATTTTTAAAATA
448645 AAAAAAATATTATTTTTAAAA
1 AAAAAAA-ATTATTTTTAAAA
448666 AATAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAAAAATTATTTTTAAAATA
Found at i:448667 original size:20 final size:20
Alignment explanation
Indices: 448624--448686 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
448614 ATGGCATTTC
*
448624 AAAAAAA-ATTATTTTAAAATA
1 AAAAAAATATTATTTT-TAA-A
448645 AAAAAAATATTATTTTTAAA
1 AAAAAAATATTATTTTTAAA
* *
448665 AAATAAAT-TTTTTATTTAAA
1 AAAAAAATATTATT-TTTAAA
448685 AA
1 AA
448687 TTATTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.11
20 16 0.43
21 9 0.24
22 8 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAAAATATTATTTTTAAA
Found at i:449567 original size:22 final size:21
Alignment explanation
Indices: 449541--449590 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
449531 TTTTTGATAA
449541 TTTTATCTAAATACCCTTATTT
1 TTTTATCTAAATACCCTT-TTT
* * *
449563 TTTTACCTAAGTACTCTTTTT
1 TTTTATCTAAATACCCTTTTT
449584 TTATTAT
1 TT-TTAT
449591 AAATAAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.24, C:0.16, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATCTAAATACCCTTTTT
Found at i:454108 original size:20 final size:20
Alignment explanation
Indices: 454083--454125 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
454073 ATTTAAAAGT
454083 TTTTGTCCAAACAATATCTC
1 TTTTGTCCAAACAATATCTC
454103 TTTTGTCCAAACAATATCTC
1 TTTTGTCCAAACAATATCTC
454123 TTT
1 TTT
454126 AGACTTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTTGTCCAAACAATATCTC
Found at i:454859 original size:12 final size:12
Alignment explanation
Indices: 454840--454877 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
454830 TGAAATGAAA
454840 TAAATATATTTT
1 TAAATATATTTT
* *
454852 TTAATATATATT
1 TAAATATATTTT
454864 TAAATA-ATTTT
1 TAAATATATTTT
454875 TAA
1 TAA
454878 TTTGAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAAATATATTTT
Found at i:466492 original size:141 final size:134
Alignment explanation
Indices: 466143--466591 Score: 464
Period size: 141 Copynumber: 3.3 Consensus size: 134
466133 CAGACTTCAG
* * *** *
466143 CTGACCAGATCTCCTCATCATGTAGGAGCAACGTCAACATTAGATAATCAGCCGTCCTCATTACG
1 CTGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCGTCCTCATTACG
* *
466208 TAGGAA-CTATGTTAT--CGC-T-ATAAA-ATGGCCAAGAACTCTTCATCACGTATG-AGCAGTG
66 TAGGAACCTA-GTTATCACCCTTCATAAAGATGGCC-AGAACTCTTCATCACGTATGAACCA-TG
466266 TCATCCC
128 TCATCCC
* * * * * * **
466273 CTGATTAGATCTCCTCATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGCTGTCCTCATCGCG
1 CTGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCGTCCTCATTACG
* * * *
466338 TAGGAACCAAGTTATCACCCTTCCTAAAGATGGCCAGAATTCTTCATCATGTATGAACCATGTCA
66 TAGGAACCTAGTTATCACCCTTCATAAAGATGGCCAGAACTCTTCATCACGTATGAACCATGTCA
466403 TCTACC
131 TC--CC
*
466409 CTTAGACGATCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCGTCCTCA
1 C-T----GATCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCGTCCTCA
* * * * *
466474 TTACGTAGGAACCTAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTATGAGCCG
61 TTACGTAGGAACCTAGTTATCACCCTTCATAAAGATGGCCAGAACTCTTCATCACGTATGAACCA
466539 TGTCAT-CC
126 TGTCATCCC
* * ** *
466547 CTCGACCAGATTTCCTCATCACGTAGGAATCGTGTCACCCTTAGA
1 CT-GATCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGA
466592 CGACCCAAAC
Statistics
Matches: 262, Mismatches: 43, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
130 62 0.24
131 2 0.01
132 2 0.01
133 1 0.00
134 66 0.25
135 9 0.03
136 3 0.01
137 2 0.01
138 3 0.01
141 112 0.43
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (134 bp):
CTGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCGTCCTCATTACG
TAGGAACCTAGTTATCACCCTTCATAAAGATGGCCAGAACTCTTCATCACGTATGAACCATGTCA
TCCC
Found at i:466792 original size:3 final size:3
Alignment explanation
Indices: 466786--466824 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
466776 TTTTTTAAAC
466786 TAT TAT TATT TAT TAT TAT TAT GT-T TAT TAT TAT TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
466825 ATCATTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 28 0.85
4 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:466812 original size:15 final size:14
Alignment explanation
Indices: 466786--466823 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
466776 TTTTTTAAAC
466786 TATTATTA-TTTAT
1 TATTATTATTTTAT
466799 TATTATTATGTTTAT
1 TATTATTAT-TTTAT
466814 TATTATTATT
1 TATTATTATT
466824 AATCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.35
14 1 0.04
15 14 0.61
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TATTATTATTTTAT
Found at i:467914 original size:2 final size:2
Alignment explanation
Indices: 467907--468002 Score: 192
Period size: 2 Copynumber: 48.0 Consensus size: 2
467897 TTGTATATTC
467907 AT AT AT AT 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
467949 AT AT AT AT 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
467991 AT AT AT AT AT AT
1 AT AT AT AT AT AT
468003 GTACACATAT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:473699 original size:99 final size:99
Alignment explanation
Indices: 473500--473755 Score: 332
Period size: 99 Copynumber: 2.5 Consensus size: 99
473490 TGTAAGTTGC
* *
473500 GTTGTTTCGAGGCCAATATCCTTCGTTGTGAAGTTGAAATTGACTTTGAAACTGGAAAGTTGTTT
1 GTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAC--T----CT-GAAAGTTGTTT
*
473565 GTTGACAGTCAGTCGCCCCTTCGCCGTGAAGTTGAGCTTGT
59 GTTGACAATCAGTCGCCCCTTCGCCGTGAAGTTGAGCTTGT
* *
473606 GTTGTCTCGAGTCTAATATCCTTCGTTGTGAAGTTGAGATTGACTCTGAAAGTTGTTTGTTGACA
1 GTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAAGTTGTTTGTTGACA
*
473671 ATCAGTCGCCCCTTCGTCGTGAAGTTGAGCTTGT
66 ATCAGTCGCCCCTTCGCCGTGAAGTTGAGCTTGT
* * * ** **
473705 GTTGTCTTGGGTCCAATATCCTTTGCCGTGAAGTTGAAATTGGTTCTGAAA
1 GTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAA
473756 TTGGGAAGCC
Statistics
Matches: 135, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
99 92 0.68
100 2 0.01
104 1 0.01
106 40 0.30
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (99 bp):
GTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAAGTTGTTTGTTGACA
ATCAGTCGCCCCTTCGCCGTGAAGTTGAGCTTGT
Found at i:474907 original size:9 final size:8
Alignment explanation
Indices: 474887--474934 Score: 60
Period size: 8 Copynumber: 5.6 Consensus size: 8
474877 ACCTACCTTA
474887 TTTTTCTT
1 TTTTTCTT
*
474895 TTTTTGTTCT
1 TTTTT-CT-T
474905 TTTTTCTTT
1 TTTTTC-TT
474914 TTTTTCTT
1 TTTTTCTT
474922 TTTTTCTT
1 TTTTTCTT
474930 TTTTT
1 TTTTT
474935 AAATTTAGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 20 0.57
9 8 0.23
10 7 0.20
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (8 bp):
TTTTTCTT
Found at i:474910 original size:18 final size:18
Alignment explanation
Indices: 474887--474934 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 18
474877 ACCTACCTTA
474887 TTTTTCTTTTTTTGTTC-T
1 TTTTTCTTTTTTT-TTCTT
474905 TTTTTC-TTTTTTTTCTT
1 TTTTTCTTTTTTTTTCTT
474922 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
474935 AAATTTAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.11
17 13 0.46
18 12 0.43
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTCTT
Found at i:485408 original size:24 final size:23
Alignment explanation
Indices: 485380--485425 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
485370 CAAGCAACAA
* *
485380 GAAAACGATAATAAGTAAACAAAG
1 GAAAACGAAAATAAAT-AACAAAG
*
485404 GAAAAGGAAAATAAATAACAAA
1 GAAAACGAAAATAAATAACAAA
485426 AAAAACGCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.67, C:0.07, G:0.15, T:0.11
Consensus pattern (23 bp):
GAAAACGAAAATAAATAACAAAG
Found at i:487124 original size:17 final size:17
Alignment explanation
Indices: 487102--487135 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
487092 ACGAAATTGA
487102 GTGTCTTCAATTTAGAT
1 GTGTCTTCAATTTAGAT
487119 GTGTCTTCAATTTAGAT
1 GTGTCTTCAATTTAGAT
487136 TAAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (17 bp):
GTGTCTTCAATTTAGAT
Found at i:488233 original size:20 final size:20
Alignment explanation
Indices: 488188--488233 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
488178 GACCAACAAA
* *
488188 ATCGCAATGCGATCTCTAAT
1 ATCGCAACGCGATCTCCAAT
*
488208 -TCGCAACGCGATCTCCATT
1 ATCGCAACGCGATCTCCAAT
488227 ATCGCAA
1 ATCGCAA
488234 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCTCCAAT
Found at i:488337 original size:20 final size:21
Alignment explanation
Indices: 488312--488404 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
488302 TTTTCCCAAT
*
488312 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
488332 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
488353 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
488373 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
488394 TCGCAATGCGA
1 TCGCAATGCGA
488405 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:488357 original size:41 final size:41
Alignment explanation
Indices: 488312--488404 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
488302 TTTTCCCAAT
488312 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
488353 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
488394 TCGCAATGCGA
1 TCGCAATGCGA
488405 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:488417 original size:41 final size:41
Alignment explanation
Indices: 488331--488465 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
488321 GAATAAGTAA
* *
488331 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
488372 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
488413 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
488454 TTCGCAACGCGA
1 ATCGCAACGCGA
488466 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:488418 original size:20 final size:20
Alignment explanation
Indices: 488393--488507 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
488383 AATTGGGAAA
*
488393 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
488413 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
488434 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
488454 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
488474 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
488494 TTCGCAACGCGATA
1 ATCGCAACGCGATA
488508 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:488466 original size:41 final size:41
Alignment explanation
Indices: 488390--488527 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
488380 GCGAATTGGG
* * *
488390 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
488431 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
488473 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
488512 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
488528 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:489018 original size:20 final size:20
Alignment explanation
Indices: 488959--489022 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
488949 GCGATTTTAG
*
488959 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
488979 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
488999 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
489019 TTTC
1 TTTC
489023 AGAAACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:490363 original size:18 final size:18
Alignment explanation
Indices: 490342--490386 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
490332 TCCACTTCGG
*
490342 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
490360 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
490378 GAGCCATCA
1 GAGCCATCA
490387 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:490922 original size:19 final size:20
Alignment explanation
Indices: 490868--490934 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
490858 TAGTTTACTT
* *
490868 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
490888 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
490908 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
490927 TCGCAACG
1 TCGCAACG
490935 ACAAAATCAC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:490930 original size:39 final size:34
Alignment explanation
Indices: 490887--490988 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 34
490877 GAAAATGACT
490887 ATCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAA
1 ATCGCAACGC-GAAAT-G--ATCGCAATGCGAAATG-AA
*
490926 ATCGCAACGAC-AAA--ATCACAATGCGAAATGAA
1 ATCGCAACG-CGAAATGATCGCAATGCGAAATGAA
490958 ATCGCAACGCGAAATGAAAATCGCAATGCGA
1 ATCGCAACGCGAAATG---ATCGCAATGCGA
490989 TTTGTGTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
31 1 0.02
32 14 0.26
33 15 0.28
37 11 0.20
38 3 0.06
39 9 0.17
40 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAAATGATCGCAATGCGAAATGAA
Found at i:490980 original size:19 final size:19
Alignment explanation
Indices: 490868--490988 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
490858 TAGTTTACTT
* **
490868 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
490888 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
490908 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
490927 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
* *
490941 TCACAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
490959 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
490978 TCGCAATGCGA
1 TCGCAACGCGA
490989 TTTGTGTTTC
Statistics
Matches: 82, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 17 0.21
19 26 0.32
20 24 0.29
21 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:491019 original size:14 final size:14
Alignment explanation
Indices: 491000--491057 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
490990 TTGTGTTTCG
491000 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
491014 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
491030 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
491046 CGTTGCGATTTT
1 CGTTGCGATTTT
491058 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:491024 original size:33 final size:32
Alignment explanation
Indices: 490984--491073 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
490974 AAAATCGCAA
*
490984 TGCGATTTGTGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTT-TATTTCGCGTTGCGATTTTGTCGT
*
491017 TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTATTTCGCGTTGCGATTTTGTCGT
*
491049 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTT-ATTTCGCGTTGCGAT
491074 AGCAATTTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.58
33 22 0.42
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.47
Consensus pattern (32 bp):
TGCGATTTTATTTCGCGTTGCGATTTTGTCGT
Found at i:491034 original size:32 final size:33
Alignment explanation
Indices: 490995--491073 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
490985 GCGATTTGTG
490995 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
491027 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
491060 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
491074 AGCAATTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:491072 original size:19 final size:17
Alignment explanation
Indices: 490995--491073 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 17
490985 GCGATTTGTG
490995 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
491011 TGTCG-TTGCGATTTCA
1 TTTCGCTTGCGATTTCA
491027 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
491043 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGA-TTTCA
491060 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
491074 AGCAATTTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
14 15 0.30
15 3 0.06
16 12 0.24
17 4 0.08
18 10 0.20
19 6 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTCGCTTGCGATTTCA
Found at i:491110 original size:20 final size:20
Alignment explanation
Indices: 491046--491114 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 20
491036 GCGATTTTGT
**
491046 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
*
491065 CATTGCGATAG-CAATTTTCCG
1 CGTTGCGATAGTC-ATTTT-CG
*
491086 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
491106 CGTTGCGAT
1 CGTTGCGAT
491115 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
18 1 0.02
19 9 0.22
20 13 0.32
21 17 0.41
22 1 0.02
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:493700 original size:24 final size:24
Alignment explanation
Indices: 493673--493719 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
493663 AGTCAGTATT
*
493673 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACC
*
493697 CGAACTTTGATATTGGTCAATAC
1 CGAAATTTGATATTGGTCAATAC
493720 ACGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACC
Found at i:493729 original size:24 final size:24
Alignment explanation
Indices: 493673--493731 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
493663 AGTCAGTATT
* * *
493673 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATATTGGTCAATACA
493697 CGAACTTTGATATTGGTCAATACA
1 CGAACTTTGATATTGGTCAATACA
* *
493721 CGGATTTTGAT
1 CGAACTTTGAT
493732 GATGTTTTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAACTTTGATATTGGTCAATACA
Found at i:496244 original size:19 final size:19
Alignment explanation
Indices: 496222--496280 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
496212 GAAAATTACT
496222 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
496241 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
496255 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
496274 ATCGCAA
1 ATCGCAA
496281 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:496423 original size:13 final size:14
Alignment explanation
Indices: 496407--496442 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
496397 CATCAATTAA
496407 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
496420 ACAAATCACCTTTT
1 ACAAATCAACTTTT
496434 ACAAATCAA
1 ACAAATCAA
496443 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:499967 original size:20 final size:21
Alignment explanation
Indices: 499922--499978 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
499912 TCTTTTGGTT
499922 GAAATGAAAATCGC-A-ACGA
1 GAAATGAAAATCGCAACACGA
*
499941 GATAATGAGAATCGCAACACG-
1 GA-AATGAAAATCGCAACACGA
**
499962 GAAATGATTATCGCAAC
1 GAAATGAAAATCGCAAC
499979 GAGAGAATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 2 0.06
20 24 0.75
21 3 0.09
22 3 0.09
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.16
Consensus pattern (21 bp):
GAAATGAAAATCGCAACACGA
Found at i:500007 original size:33 final size:33
Alignment explanation
Indices: 499947--500083 Score: 148
Period size: 33 Copynumber: 4.0 Consensus size: 33
499937 ACGAGATAAT
* *
499947 GAGAATCGCAACACGGAAATGATTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAATATCGCAACGA
* *
499981 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGAATATCGCAACGA
*
500014 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAA
1 GAGAATCGCAACGCGAAATGAATATCGCAA--CG--A
* * *
500051 TAAAAATCGCAACGCGAAATGAAAATCGCAACG
1 -GAGAATCGCAACGCGAAATGAATATCGCAACG
500084 CGAAATGAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
33 44 0.49
34 13 0.14
35 2 0.02
36 2 0.02
37 1 0.01
38 28 0.31
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAATATCGCAACGA
Found at i:500059 original size:38 final size:38
Alignment explanation
Indices: 500017--500105 Score: 151
Period size: 38 Copynumber: 2.3 Consensus size: 38
500007 GCGACGAGAG
500017 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
500055 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
* *
500093 AATCACAATGCGA
1 AATCGCAACGCGA
500106 TTTTTGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:500105 original size:19 final size:19
Alignment explanation
Indices: 499922--500096 Score: 163
Period size: 19 Copynumber: 9.6 Consensus size: 19
499912 TCTTTTGGTT
*
499922 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
499941 GATAATGAGAATCGCAACAC
1 GA-AATGAAAATCGCAACGC
**
499961 GGAAATGATTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
499979 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
499995 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
500012 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
500028 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
500047 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
500066 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
500085 GAAATGAAAATC
1 GAAATGAAAATC
500097 ACAATGCGAT
Statistics
Matches: 128, Mismatches: 16, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
14 17 0.13
15 2 0.02
16 4 0.03
17 3 0.02
18 3 0.02
19 71 0.55
20 26 0.20
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:500123 original size:19 final size:19
Alignment explanation
Indices: 500101--500145 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
500091 AAAATCACAA
*
500101 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
500120 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
500139 TGCGATT
1 TGCGATT
500146 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:500720 original size:20 final size:20
Alignment explanation
Indices: 500695--500747 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
500685 GCGCTATGTA
500695 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
500715 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
500735 TATCTCGTTGCGA
1 AATCGCGTTGCGA
500748 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:500900 original size:21 final size:21
Alignment explanation
Indices: 500860--500900 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
500850 ACTGTAGACC
**
500860 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
500881 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
500901 ACGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:501208 original size:92 final size:93
Alignment explanation
Indices: 501105--501291 Score: 358
Period size: 93 Copynumber: 2.0 Consensus size: 93
501095 TGATTATCTG
*
501105 GCGATTT-AAAAAAAAATCCAAATATATATTATTTACTTATCAGACATCGTTTCTTCAACTATTA
1 GCGATTTAAAAAAAAAATCCAAATATATATTATTTACCTATCAGACATCGTTTCTTCAACTATTA
501169 TTGATTTAACACTCTTTTATAGTAAAGC
66 TTGATTTAACACTCTTTTATAGTAAAGC
501197 GCGATTTAAAAAAAAAATCCAAATATATATTATTTACCTATCAGACATCGTTTCTTCAACTATTA
1 GCGATTTAAAAAAAAAATCCAAATATATATTATTTACCTATCAGACATCGTTTCTTCAACTATTA
501262 TTGATTTAACACTCTTTTATAGTAAAGC
66 TTGATTTAACACTCTTTTATAGTAAAGC
501290 GC
1 GC
501292 AATTGACCAA
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 7 0.08
93 86 0.92
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (93 bp):
GCGATTTAAAAAAAAAATCCAAATATATATTATTTACCTATCAGACATCGTTTCTTCAACTATTA
TTGATTTAACACTCTTTTATAGTAAAGC
Found at i:506252 original size:14 final size:15
Alignment explanation
Indices: 506233--506265 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
506223 TTCCTAGCCT
*
506233 CGATGATCT-AACTC
1 CGATGACCTCAACTC
506247 CGATGACCTCAACTC
1 CGATGACCTCAACTC
506262 CGAT
1 CGAT
506266 AAGACAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.24
Consensus pattern (15 bp):
CGATGACCTCAACTC
Found at i:514519 original size:152 final size:155
Alignment explanation
Indices: 514331--514617 Score: 393
Period size: 155 Copynumber: 1.9 Consensus size: 155
514321 GAAATGTGTT
* *** * *
514331 ATTGTATATTAAATGGTATAAGAAAAGGATTTTTTTCATTAAAGGG-A-AATTCAAAAACATCAT
1 ATTGTATATTAAATGGTATAAGAAAAGAACGGTTTTCATTAAAGGGAACAAGTCAAAAACAACAT
* * * * *
514394 TCAATGGTCTC-ATATATCATTGAATTGAAGTGATGTATTATTGAA-TTTTTTTTGAAATGAGGT
66 TCAATGGTC-CGATATATCACTGAATTGAAGTGATATATCACTGAATTTTTTTTTGAAATGAAGT
514457 GATTGAAAACTGAAAAGTTTTTTGTC
130 GATTGAAAACTGAAAAGTTTTTTGTC
* * *
514483 ATTGTGTATTAAATGGTTTGAGAAAAGAACGGTTTTCATTAAAGGGAAACAAGTCAAAAACAACA
1 ATTGTATATTAAATGGTATAAGAAAAGAACGGTTTTCATTAAAGGG-AACAAGTCAAAAACAACA
*
514548 TTCAATGGTCCGATGTATCACTGAATTGAAGTGATATATCACTGAATTTTTTTTTGAAATGAAGT
65 TTCAATGGTCCGATATATCACTGAATTGAAGTGATATATCACTGAATTTTTTTTTGAAATGAAGT
514613 GATTG
130 GATTG
514618 GATGGTCATT
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
152 39 0.34
154 2 0.02
155 52 0.45
156 22 0.19
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (155 bp):
ATTGTATATTAAATGGTATAAGAAAAGAACGGTTTTCATTAAAGGGAACAAGTCAAAAACAACAT
TCAATGGTCCGATATATCACTGAATTGAAGTGATATATCACTGAATTTTTTTTTGAAATGAAGTG
ATTGAAAACTGAAAAGTTTTTTGTC
Found at i:518922 original size:41 final size:39
Alignment explanation
Indices: 518850--518927 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 39
518840 ATCATCCTAA
*
518850 AACCTAAATTCTAAACCCCAAACCTAACTTAAAACCATT
1 AACCTAAACTCTAAACCCCAAACCTAACTTAAAACCATT
* *
518889 AACCATAAACTCTAAACCCTAATCACTAACTTAAAACCA
1 AACC-TAAACTCTAAACCCCAAAC-CTAACTTAAAACCA
518928 CAAACAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 4 0.12
40 16 0.47
41 14 0.41
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (39 bp):
AACCTAAACTCTAAACCCCAAACCTAACTTAAAACCATT
Found at i:522515 original size:21 final size:21
Alignment explanation
Indices: 522400--522515 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
522390 GCGAAATAAA
**
522400 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
522420 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
522440 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
522461 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
522481 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
522503 AATCGCAACGCGA
1 AATCGCAACGCGA
522516 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:522528 original size:20 final size:20
Alignment explanation
Indices: 522503--522655 Score: 75
Period size: 20 Copynumber: 7.7 Consensus size: 20
522493 GATTTTCCAG
* *
522503 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
522523 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
522543 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
522563 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
522583 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
522603 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
522623 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
522643 AATCGCAACGCGA
1 AATCGCAACGCGA
522656 TTTTTAAAGC
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
19 2 0.02
20 117 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:522550 original size:40 final size:40
Alignment explanation
Indices: 522503--522654 Score: 135
Period size: 40 Copynumber: 3.8 Consensus size: 40
522493 GATTTTCCAG
*
522503 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAAC-CATA
* * * * * *
522543 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * * * *
522583 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * *
522623 TATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AATCGCAACGCGAATACGAAAATCGCAACGCG
522655 ATTTTTAAAG
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 98 0.98
41 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
Found at i:522586 original size:60 final size:59
Alignment explanation
Indices: 522503--522655 Score: 207
Period size: 60 Copynumber: 2.6 Consensus size: 59
522493 GATTTTCCAG
* ** *
522503 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATAAATCGCAACGCGTATCCGTA
* * * *
522563 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATAAATCGCAACGCGTATCCGTA
*
522623 TATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
522656 TTTTTAAAGC
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
59 1 0.01
60 79 0.96
61 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (59 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGTA
Found at i:523076 original size:33 final size:33
Alignment explanation
Indices: 523032--523104 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
523022 ATTTCACTTA
523032 GATTTT-ATTTCGCGTTACGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
523064 GATTTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
523097 GATTTTCA
1 GATTTTCA
523105 AGTTAGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 6 0.16
33 32 0.84
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.48
Consensus pattern (33 bp):
GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:523210 original size:21 final size:20
Alignment explanation
Indices: 523184--523290 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
523174 TGCAGAAGAG
523184 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
523205 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
523225 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
523247 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
523261 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
523280 TCGCAACGAGA
1 TCGCAACGAGA
523291 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:523264 original size:14 final size:14
Alignment explanation
Indices: 523245--523301 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
523235 GAAAAATGAA
523245 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
523259 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
523278 AATCGCAACGAGAG
1 AATCGCAACGAGAG
523292 AATCGCAACG
1 AATCGCAACG
523302 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:523276 original size:33 final size:33
Alignment explanation
Indices: 523238--523317 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
523228 GCAACGAGAA
523238 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
523271 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
523304 AAACCAAAATCGCA
1 AAATGAAAATCGCA
523318 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:523335 original size:19 final size:19
Alignment explanation
Indices: 523313--523440 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
523303 GAAACCAAAA
*
523313 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
523332 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
523346 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
523365 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
523379 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
523399 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
523419 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
523439 TC
1 TC
523441 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:523354 original size:14 final size:14
Alignment explanation
Indices: 523335--523391 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
523325 TTTCATTTCG
523335 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
523349 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
523368 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
523382 CGTTGCGATT
1 CGTTGCGATT
523392 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:523360 original size:33 final size:33
Alignment explanation
Indices: 523318--523440 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
523308 CAAAATCGCA
523318 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
523351 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
523384 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
523425 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
523441 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:523402 original size:21 final size:21
Alignment explanation
Indices: 523376--523440 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
523366 CGCGTTGCGA
523376 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
523397 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
523417 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
523438 TTC
1 TTC
523441 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:525264 original size:93 final size:93
Alignment explanation
Indices: 525105--525480 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
525095 TAGATTGCTT
*
525105 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
525170 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
525198 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
525263 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
525291 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
525356 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
525384 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
525449 TTTGTCTTTGTTTTGTCTATTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
525476 AGTAA
1 AGTAA
525481 TGCAATCCAT
Statistics
Matches: 281, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 275 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:525565 original size:14 final size:14
Alignment explanation
Indices: 525546--525602 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
525536 CGAAACTTAA
525546 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
525560 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
525579 AATCGCAACGACAG
1 AATCGCAACGAGAG
525593 AATCGCAACG
1 AATCGCAACG
525603 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:525584 original size:19 final size:18
Alignment explanation
Indices: 525560--525651 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
525550 GCAACGAGAG
525560 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
525579 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
525593 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
525612 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
525626 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
525645 AATCGCA
1 AATCGCA
525652 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:525586 original size:33 final size:33
Alignment explanation
Indices: 525528--525651 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
525518 TAGTTTACTT
* * *
525528 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
525562 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
525595 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
525628 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
525652 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:525628 original size:14 final size:14
Alignment explanation
Indices: 525577--525635 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
525567 ACGCGAAATG
525577 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
525591 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
525610 AAAATCGCAACGAC
1 AAAATCGCAACGAC
525624 AAAATCGCAACG
1 AAAATCGCAACG
525636 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:525669 original size:19 final size:19
Alignment explanation
Indices: 525647--525786 Score: 146
Period size: 19 Copynumber: 7.6 Consensus size: 19
525637 GAAACCAAAA
*
525647 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
525666 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
525682 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
525699 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
525718 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
525737 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
525756 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
525776 TCGTGTTGCGA
1 TCGCGTTGCGA
525787 AAGTAAACTA
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
14 8 0.08
16 5 0.05
17 5 0.05
19 72 0.71
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:527726 original size:14 final size:14
Alignment explanation
Indices: 527707--527742 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
527697 ATTGTTTAAT
527707 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
527721 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
527735 TGATTTGT
1 TGATTTGT
527743 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:527857 original size:19 final size:19
Alignment explanation
Indices: 527833--527920 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
527823 GCATTATGTT
527833 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
527852 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
527869 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
*
527885 GAAATAAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
527904 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
527921 CGAGAGAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 28 0.47
20 15 0.25
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:527952 original size:53 final size:53
Alignment explanation
Indices: 527833--527939 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
527823 GCATTATGTT
*
527833 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATAAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
527885 GAAATAAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATAAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
527938 GA
1 GA
527940 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 18 0.34
53 35 0.66
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (53 bp):
GAAATAAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:528016 original size:72 final size:69
Alignment explanation
Indices: 527930--528223 Score: 280
Period size: 72 Copynumber: 4.2 Consensus size: 69
527920 ACGAGAGAAT
*
527930 CGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1 CGCATTGCGATTTTC-TTTCG--TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
527995 TTCATTT-
62 TTCATTTC
* * * * *
528002 CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGA
1 CGCATTGCGATTTTC-TTTCG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGA
528064 TTTTCATTTC
60 TTTTCATTTC
* *
528074 CGCATTGCGA--TTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
1 CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGAT
528137 TTTCATTTC
61 TTTCATTTC
* * *
528146 CGCATTGCGATTTTC-TT-GTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAA
1 CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
528209 TTTC
66 TTTC
**
528213 CGTGTTGCGAT
1 CGCATTGCGAT
528224 AGTCAAATGC
Statistics
Matches: 188, Mismatches: 20, Indels: 33
0.78 0.08 0.14
Matches are distributed among these distances:
65 9 0.05
66 3 0.02
67 31 0.16
68 2 0.01
69 8 0.04
70 8 0.04
71 18 0.10
72 95 0.51
73 7 0.04
74 7 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.45
Consensus pattern (69 bp):
CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
TTTC
Found at i:528055 original size:105 final size:109
Alignment explanation
Indices: 527935--528204 Score: 434
Period size: 105 Copynumber: 2.6 Consensus size: 109
527925 AGAATCGCAA
527935 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
528000 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-T
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
528040 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
528105 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-AT
*
528151 TGCGATTTTC--TT-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
528205 GTAATTTCCG
Statistics
Matches: 157, Mismatches: 2, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
105 122 0.78
106 14 0.09
107 3 0.02
108 3 0.02
109 4 0.03
111 11 0.07
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (109 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
Found at i:528219 original size:53 final size:52
Alignment explanation
Indices: 527935--528204 Score: 415
Period size: 53 Copynumber: 5.1 Consensus size: 52
527925 AGAATCGCAA
527935 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
527988 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
528040 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
528093 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
528151 TGCGATTTTC--TT-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
528198 TGCGATT
1 TGCGATT
528205 GTAATTTCCG
Statistics
Matches: 207, Mismatches: 3, Indels: 20
0.90 0.01 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 62 0.30
53 109 0.53
54 3 0.01
55 3 0.01
56 4 0.02
58 11 0.05
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:530505 original size:12 final size:12
Alignment explanation
Indices: 530488--530512 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
530478 TCTTCGGGGA
530488 CTTTTTCTTCTT
1 CTTTTTCTTCTT
530500 CTTTTTCTTCTT
1 CTTTTTCTTCTT
530512 C
1 C
530513 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:530721 original size:24 final size:24
Alignment explanation
Indices: 530687--530733 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
530677 CTGAAACATC
530687 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
530711 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
530734 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:531454 original size:20 final size:20
Alignment explanation
Indices: 531426--531654 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
531416 AAATTTCAGT
* * *
531426 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
531446 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATTCGC
* *
531466 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
531486 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
531506 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
531526 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
531546 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
531566 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
531586 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
531606 GTTGCGATATATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
531626 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
531646 GTTGCGATT
1 GTTGCGATT
531655 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:531707 original size:21 final size:20
Alignment explanation
Indices: 531622--531719 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
531612 ATATATGTGT
* *
531622 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
531642 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
531663 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
531684 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
531705 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
531720 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:531715 original size:42 final size:43
Alignment explanation
Indices: 531622--531720 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
531612 ATATATGTGT
* *
531622 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
531663 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
531705 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
531721 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:534679 original size:24 final size:24
Alignment explanation
Indices: 534647--534695 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
534637 TCGTGATCTA
534647 TCCCTTAACATTTCATAATATGAC
1 TCCCTTAACATTTCATAATATGAC
534671 TCCCTTAACATTTCATAATATGAC
1 TCCCTTAACATTTCATAATATGAC
534695 T
1 T
534696 TTGATAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (24 bp):
TCCCTTAACATTTCATAATATGAC
Found at i:546218 original size:457 final size:457
Alignment explanation
Indices: 545364--546277 Score: 1801
Period size: 457 Copynumber: 2.0 Consensus size: 457
545354 TTTTATATAA
545364 AATACTATGCATTATTTAAGAAAGTAGAAAACCTACAACAAATACCAAGGAGACTCCTCATAACA
1 AATACTATGCATTATTTAAGAAAGTAGAAAACCTACAACAAATACCAAGGAGACTCCTCATAACA
545429 AAACTAGGAAATACTCCAAGCATCACAAAGTCGCCTATTCACAATGTTTGTAAAATCTATACAAC
66 AAACTAGGAAATACTCCAAGCATCACAAAGTCGCCTATTCACAATGTTTGTAAAATCTATACAAC
545494 GCTTTCTAGTTTTAATTCTAACTATATCTCTTATTATAGTGTCAAAAATCTCATCACCCATACAA
131 GCTTTCTAGTTTTAATTCTAACTATATCTCTTATTATAGTGTCAAAAATCTCATCACCCATACAA
*
545559 ATTTCCCCCCTAAAAATTCGGCAATTCCTTTTATTCCAAACACAGTATATATGAGCACCTCAAGC
196 ATTTCCCCCCTAAAAATTCGGCAATTCCTTTTATTCCAAACACAGTAGATATGAGCACCTCAAGC
545624 AATCCGGGAAACATAAGGTAGCAACGACTTCCCCCTTATTTTCGATGCAAGCCCAAGCTAGCTCG
261 AATCCGGGAAACATAAGGTAGCAACGACTTCCCCCTTATTTTCGATGCAAGCCCAAGCTAGCTCG
*
545689 TGCTCCCAGTCCACAACTGGTCGACCAATATTACAAAGTCGAAGAATTTTCTCTCAAATGCATCG
326 TGCTCCCAGTCCACAACAGGTCGACCAATATTACAAAGTCGAAGAATTTTCTCTCAAATGCATCG
545754 AGAGAAGGAGCAAGCAAAAAAGAGATGCTCTCTCGACTCCATATCAAAACAAAAACATAAAGAGG
391 AGAGAAGGAGCAAGCAAAAAAGAGATGCTCTCTCGACTCCATATCAAAACAAAAACATAAAGAGG
545819 GT
456 GT
545821 AATACTATGCATTATTTAAGAAAGTAGAAAACCTACAACAAATACCAAGGAGACTCCTCATAACA
1 AATACTATGCATTATTTAAGAAAGTAGAAAACCTACAACAAATACCAAGGAGACTCCTCATAACA
545886 AAACTAGGAAATACTCCAAGCATCACAAAGTCGCCTATTCACAATGTTTGTAAAATCTATACAAC
66 AAACTAGGAAATACTCCAAGCATCACAAAGTCGCCTATTCACAATGTTTGTAAAATCTATACAAC
545951 GCTTTCTAGTTTTAATTCTAACTATATCTCTTATTATAGTGTCAAAAATCTCATCACCCATACAA
131 GCTTTCTAGTTTTAATTCTAACTATATCTCTTATTATAGTGTCAAAAATCTCATCACCCATACAA
*
546016 ATTTCCCCCCTAAAAATTTGGCAATTCCTTTTATTCCAAACACAGTAGATATGAGCACCTCAAGC
196 ATTTCCCCCCTAAAAATTCGGCAATTCCTTTTATTCCAAACACAGTAGATATGAGCACCTCAAGC
546081 AATCCGGGAAACATAAGGTAGCAACGACTTCCCCCTTATTTTCGATGCAAGCCCAAGCTAGCTCG
261 AATCCGGGAAACATAAGGTAGCAACGACTTCCCCCTTATTTTCGATGCAAGCCCAAGCTAGCTCG
546146 TGCTCCCAGTCCACAACAGGTCGACCAATATTACAAAGTCGAAGAATTTTCTCTCAAATGCATCG
326 TGCTCCCAGTCCACAACAGGTCGACCAATATTACAAAGTCGAAGAATTTTCTCTCAAATGCATCG
546211 AGAGAAGGAGCAAGCAAAAAAGAGATGCTCTCTCGACTCCATATCAAAACAAAAACATAAAGAGG
391 AGAGAAGGAGCAAGCAAAAAAGAGATGCTCTCTCGACTCCATATCAAAACAAAAACATAAAGAGG
546276 GT
456 GT
546278 CAACAACAAT
Statistics
Matches: 454, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
457 454 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (457 bp):
AATACTATGCATTATTTAAGAAAGTAGAAAACCTACAACAAATACCAAGGAGACTCCTCATAACA
AAACTAGGAAATACTCCAAGCATCACAAAGTCGCCTATTCACAATGTTTGTAAAATCTATACAAC
GCTTTCTAGTTTTAATTCTAACTATATCTCTTATTATAGTGTCAAAAATCTCATCACCCATACAA
ATTTCCCCCCTAAAAATTCGGCAATTCCTTTTATTCCAAACACAGTAGATATGAGCACCTCAAGC
AATCCGGGAAACATAAGGTAGCAACGACTTCCCCCTTATTTTCGATGCAAGCCCAAGCTAGCTCG
TGCTCCCAGTCCACAACAGGTCGACCAATATTACAAAGTCGAAGAATTTTCTCTCAAATGCATCG
AGAGAAGGAGCAAGCAAAAAAGAGATGCTCTCTCGACTCCATATCAAAACAAAAACATAAAGAGG
GT
Found at i:566801 original size:25 final size:24
Alignment explanation
Indices: 566752--566828 Score: 100
Period size: 25 Copynumber: 3.1 Consensus size: 24
566742 GCACCAAGGG
*
566752 TGCGTTCAGTTTTGCAGTTACGAC
1 TGCGTTCAGTTTTACAGTTACGAC
*
566776 TGCGTTCAGTTTTACTAGTTATGAC
1 TGCGTTCAGTTTTAC-AGTTACGAC
* *
566801 TGCATTCAGTTTAAGCAGTTACGAC
1 TGCGTTCAGTTTTA-CAGTTACGAC
566826 TGC
1 TGC
566829 ATATTGTGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 14 0.30
25 31 0.67
26 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (24 bp):
TGCGTTCAGTTTTACAGTTACGAC
Found at i:570121 original size:12 final size:12
Alignment explanation
Indices: 570104--570132 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
570094 TTGTTGTGCT
570104 TGCTCCTCGGGC
1 TGCTCCTCGGGC
570116 TGCTCCTCGGGC
1 TGCTCCTCGGGC
570128 TGCTC
1 TGCTC
570133 AGGCTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:575693 original size:22 final size:21
Alignment explanation
Indices: 575651--575690 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
575641 GAGTTTATTT
*
575651 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
575672 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
575691 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:587850 original size:22 final size:22
Alignment explanation
Indices: 587825--587869 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
587815 TAATATTTCC
587825 TTGTATAGTCCTTATGTGATCT
1 TTGTATAGTCCTTATGTGATCT
*
587847 TTGTATGGTCCTTATGTGATCT
1 TTGTATAGTCCTTATGTGATCT
587869 T
1 T
587870 AAGTTGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.16, C:0.13, G:0.20, T:0.51
Consensus pattern (22 bp):
TTGTATAGTCCTTATGTGATCT
Found at i:592932 original size:14 final size:16
Alignment explanation
Indices: 592901--592937 Score: 60
Period size: 14 Copynumber: 2.4 Consensus size: 16
592891 AATAAATAAT
592901 TTTATGATTTATATTA
1 TTTATGATTTATATTA
592917 TTTAT-ATTTA-ATTA
1 TTTATGATTTATATTA
592931 TTTATGA
1 TTTATGA
592938 CCAATCAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 6 0.30
16 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTATGATTTATATTA
Found at i:593643 original size:61 final size:62
Alignment explanation
Indices: 593567--593759 Score: 185
Period size: 65 Copynumber: 3.0 Consensus size: 62
593557 AACATGTGTG
* *** * * *
593567 TTGATTATTGGAACTAAAAAGGGGGGGAA-AAGGGGAGAA-AGGAGGAGGTCACACGTTTAAT
1 TTGATTATT-GAACTAAAAAAGGGAAAAAGAAAGGGAGAAGAGGAGAAGGTCACACGATTAAT
*
593628 TTGATTATTGCAACTAAAAAAGGGAAAAAGAAAGGGAGAATGGAGGAGAAGGTCACGCGATTAAT
1 TTGATTATTG-AACTAAAAAAGGGAAAAAGAAAGGGAGAA--GAGGAGAAGGTCACACGATTAAT
* * * *
593693 TTGATTATTAGAACTAAAAAATGGG-AAAAGAAATGGAGAAATGAGGAGAATGTCACGCGTTTAA
1 TTGATTATT-GAACTAAAAAA-GGGAAAAAGAAAGGGAG-AA-GAGGAGAAGGTCACACGATTAA
593757 T
62 T
593758 TT
1 TT
593760 TTTCATTAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
60 1 0.01
61 23 0.21
62 9 0.08
65 73 0.65
66 6 0.05
ACGTcount: A:0.42, C:0.07, G:0.30, T:0.22
Consensus pattern (62 bp):
TTGATTATTGAACTAAAAAAGGGAAAAAGAAAGGGAGAAGAGGAGAAGGTCACACGATTAAT
Found at i:593697 original size:65 final size:65
Alignment explanation
Indices: 593606--593759 Score: 215
Period size: 65 Copynumber: 2.4 Consensus size: 65
593596 AAGGGGAGAA
* *
593606 AGGAGGAGGTCACACGTTTAATTTGATTATT-GCAACTAAAAAA-GGGAAAAAGAAAGGGAG-AA
1 AGGAGAAGGTCACGCGTTTAATTTGATTATTAG-AACTAAAAAATGGG-AAAAGAAAGGGAGAAA
593668 TGG
64 T-G
* *
593671 AGGAGAAGGTCACGCGATTAATTTGATTATTAGAACTAAAAAATGGGAAAAGAAATGGAGAAATG
1 AGGAGAAGGTCACGCGTTTAATTTGATTATTAGAACTAAAAAATGGGAAAAGAAAGGGAGAAATG
*
593736 AGGAGAATGTCACGCGTTTAATTT
1 AGGAGAAGGTCACGCGTTTAATTT
593760 TTTCATTAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
65 73 0.91
66 7 0.09
ACGTcount: A:0.42, C:0.08, G:0.27, T:0.23
Consensus pattern (65 bp):
AGGAGAAGGTCACGCGTTTAATTTGATTATTAGAACTAAAAAATGGGAAAAGAAAGGGAGAAATG
Done.