Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 123 of 222
Found at i:39985666 original size:882 final size:874
Alignment explanation
Indices: 39984215--39986286 Score: 2777
Period size: 882 Copynumber: 2.4 Consensus size: 874
39984205 AGAGAAGGAT
* * *
39984215 GAATGAAGAATGAAATTCT-ATGAAAAGTATT-TGCCAGAAACAAGTTAGAAGACCATATTATTA
1 GAATGAAGAATAAAAATCTGA-GAAAAGTATTCT-CCAGAAACAAGTTGGAAGACCATATTATTA
* * *
39984278 AATAAGTTCTAA-CGATCCTTTAGTAACAATGTGCAAGCACTGTGCAGGTAAAAGGGATGTTTTT
64 AAGAAGTTCTAATC-ATCCTTTAGTAACAATGTGCAAGCATTGTGCAGGTAAAAGGGATGCTTTT
* *
39984342 CTCACTAAGTTTTGATATGCTTACATGAGTTTATGTTTTTGTTTCAGGTTGATTGTGAATATGTG
128 CTCACTAAGTTCTGATA-GCTTACATGAGTTTATGTTTTTGTTTTAGGTTGATTGTGAATATGTG
* * * * *
39984407 ACTGCCTTCGGATGTACTAACGTCCAGAGATTGAATATTGTAATAAAATATAAATACAAGGCGAT
192 ACCGCCTACGGACGTACTAACGTCCAGAGATTGAAAATTGTAATAAAATATAAAAACAAGGCGAT
* * * * *
39984472 ATTCGCAAGTATACAGGTCGAGTTATAATATAGTTTTACAATGATGTAGGTGAGTACTCTGAGGA
257 ATCCCCAAGTAAACAGGTCAAGTTATAATATAGTTTTACAATGATATAGGTGAGTACTCTGAGGA
39984537 TCGTACCCAAGGAGACGACTACCAGATCAATTCTAACCTAAACACTAAAGGATCTAATTAGTACT
322 TCGTACCCAAGGAGACGACTACCAGATCAATTCTAACCTAAACACTAAAGGATCTAATTAGTACT
39984602 TTAAATTAGTTATAGTACGAAAGCATAAAATAAAGGATCTTTAGGGTTGTAATAATAAAACAAAA
387 TTAAATTAGTTATAGTACGAAAGCATAAAATAAAGGATCTTTAGGGTTGTAATAATAAAACAAAA
* * * * * *
39984667 TATTAAAAAGTAATAAACTTCAAGAGATAGAAATGGTGAATGAATCAAATCTTTATTATGGGTGA
452 TATTAAAAAGGAATAAACTTCAAGAGATAAAAAAGGAGAATAAATCAAATCTTAATTATGGGTGA
* * * *
39984732 TTAGCTCGCTTCGGTAATCCCTATTAACTTTCGTTTCAGGTTCCTCGTCAATCAACTAGTTGCTA
517 TTAGCTCGCTTCGGTAATCCCTAGTAACTGTCATTTCAGATTCCTCGTCAATCAACTAGTTGCTA
* *
39984797 CCTTAGTAGGATCTTTTGATCTTCCATTAACATAATGAGTCAGCAAGGATTGCTTATCTTCTGAC
582 CCCTAGTAGGATCTTTTGATCTTCCATTAACATAACGAGTCAGCAAGGATTGCTTATCTTCTGAC
* *
39984862 CTCACAGTCTAGACTGGCTTGGTGTGAAGGTGTTCATAGATGGATTATACCAAATTTGGGTTAAT
647 CTCACAGTCCAGACTGGCTTGGTGTGAAGGTGTTCATAGATGGATCATACCAAATTTGGGTTAAT
* * **
39984927 TCCCACCTTGATGACTTCCTAGGGTTGTCAGGCCTAGGTTTTGTTTCAT-GTTCGTCATTTCCCA
712 TCCCACCTTGATGACTTCATAGGGTTGTCAAGCCTAGGTTTTGTTTCATACCT-GTCATTTCCCA
* * **
39984991 AATAG-TGGATCTGTTGAGTAACCCTACAAAACAGTCAATAGATCATAACTTCACTCGTTAATCC
776 AATAGCT-AATCTGTTGAGTAACCCTACAAAACAGTCAATAGATCATAACTCCACTCACTAATCC
* * *
39985055 CCCAAAG-GAGGATTATTTCCTCATGGAAGAATGAG
840 ACCAAAGAG-GGATTAGTTCCTCATGGAAGAATGAA
*
39985090 GAATGAAGAATAAAAATCTGAGAAAAGTATTCTCCAGAAACAAGTTGGAAGACCAGATTATTAAA
1 GAATGAAGAATAAAAATCTGAGAAAAGTATTCTCCAGAAACAAGTTGGAAGACCATATTATTAAA
* * * * ** *
39985155 GAAGTTCTAATCATCCTTCAATAACAATGTGCAAGCATTCTGCAGGGAAAAAATGATGCTTTTAT
66 GAAGTTCTAATCATCCTTTAGTAACAATGTGCAAGCATTGTGCA-GGTAAAAGGGATGCTTTTCT
* * *
39985220 CACTAAATTCTGATGAGCTTACATGTGTTTCTGTTTTTGTTTTAGGTTGATTGTGAATATGTGAC
130 CACTAAGTTCTGAT-AGCTTACATGAGTTTATGTTTTTGTTTTAGGTTGATTGTGAATATGTGAC
* * * *
39985285 CGCCTACGGACGTACTAGCATTCCA-AG-TGTGAAAATTTTAATAAAATATAGAAAAATAAGGCG
194 CGCCTACGGACGTACTAAC-GTCCAGAGAT-TGAAAATTGTAATAAAATAT--AAAAACAAGGCG
* * *
39985348 TTATCCCCAAGTAAACATGTCAAGTTGTAATATAGTTTTACAATGATATAGGTGAGTACTCTGAG
255 ATATCCCCAAGTAAACAGGTCAAGTTATAATATAGTTTTACAATGATATAGGTGAGTACTCTGAG
* * * * * *
39985413 TATTGTACTCAAGGGAGGCGAGTGCCAGATCAATTCTAACCTAAACACTAAAGGATCTAATTAGT
320 GATCGTACCCAA-GGAGACGACTACCAGATCAATTCTAACCTAAACACTAAAGGATCTAATTAGT
** * *
39985478 ACTTTAAATTAGTTATAGTACGAAAGCATAAAATAACTGAT-TTCTGGGGTTTTTAGAATAATAA
384 ACTTTAAATTAGTTATAGTACGAAAGCATAAAATAAAGGATCTT-TAGGG-TTGT--AATAATAA
* *
39985542 AACAAAATATTAAAATGGAATAAACTTCAAGTGATAAAAAAGGAGAATAAATCAAATCTTAATTA
445 AACAAAATATTAAAAAGGAATAAACTTCAAGAGATAAAAAAGGAGAATAAATCAAATCTTAATTA
*
39985607 TGGGTGATTAGCTCGCTTCGGTAATCCCTAGTAACTGTCATTTCAGATTCCTTGTCAATCAACTA
510 TGGGTGATTAGCTCGCTTCGGTAATCCCTAGTAACTGTCATTTCAGATTCCTCGTCAATCAACTA
39985672 GTTGCTACCCTAGTAGGATCTTTTGATCTTCCATTAACATAACGAGTCAGCAAGGATTGCTTATC
575 GTTGCTACCCTAGTAGGATCTTTTGATCTTCCATTAACATAACGAGTCAGCAAGGATTGCTTATC
* *
39985737 TTCTGACCTTACAGTCCAGACTGGCTTGGTGTGAAGGTGTTCATAGATGGGTCATACCAAATTTG
640 TTCTGACCTCACAGTCCAGACTGGCTTGGTGTGAAGGTGTTCATAGATGGATCATACCAAATTTG
* *
39985802 GGTTAATTCCCACCTTGATGACTTCATGGGGTTGTCAAGCCTAGGTTTTGTTTCATACCTGTCCT
705 GGTTAATTCCCACCTTGATGACTTCATAGGGTTGTCAAGCCTAGGTTTTGTTTCATACCTGTCAT
* * *
39985867 TTCCTAAATAGCTAATCTGTTGAGTAACCCTACAAAATAGTCAATAGATCATACCTCCACTCACT
770 TTCCCAAATAGCTAATCTGTTGAGTAACCCTACAAAACAGTCAATAGATCATAACTCCACTCACT
*
39985932 AATCCACGAAAGAGGGATTAGTTCCTCATGGAAGAATGAA
835 AATCCACCAAAGAGGGATTAGTTCCTCATGGAAGAATGAA
* * * * * *
39985972 GAATGAAGACTAAATATCTGGGAAAAGCATTCGCCATAAACAAGTTGGAAGACCATATTATTAAA
1 GAATGAAGAATAAAAATCTGAGAAAAGTATTCTCCAGAAACAAGTTGGAAGACCATATTATTAAA
* * *
39986037 GAAGTTCAAATGATCCTTTAGTAACAATGTGCAAGCATTGTGCAGGTAAGAGGGATGCTTTTCTC
66 GAAGTTCTAATCATCCTTTAGTAACAATGTGCAAGCATTGTGCAGGTAAAAGGGATGCTTTTCTC
* * * * *
39986102 TA-TAAGTTCTGATTAGCTTACATGAGTTTATGATTTTG-CTTATGGATGGTTGTGAATATGTGG
131 -ACTAAGTTCTGA-TAGCTTACATGAGTTTATGTTTTTGTTTTA-GGTTGATTGTGAATATGTGA
* * * ** ** * * * *
39986165 CCACCT-CTGTATGTACGGATATCCAGAG--TGAGAATACTGTTACAAAATATTGAAATACAAGG
193 CCGCCTAC-GGACGTACTAACGTCCAGAGATTGA-AA-ATTGTAATAAAATA-T-AAAAACAAGG
** * * * * * *
39986227 CGATATCTGCAAGTATACAGGTCGAGTTGTAATATAATTTTACAACGATATAAGTGAGTA
253 CGATATCCCCAAGTAAACAGGTCAAGTTATAATATAGTTTTACAATGATATAGGTGAGTA
39986287 ATCTAATTAC
Statistics
Matches: 1042, Mismatches: 130, Indels: 44
0.86 0.11 0.04
Matches are distributed among these distances:
875 95 0.09
876 111 0.11
877 5 0.00
878 78 0.07
879 95 0.09
880 13 0.01
881 146 0.14
882 496 0.48
883 3 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (874 bp):
GAATGAAGAATAAAAATCTGAGAAAAGTATTCTCCAGAAACAAGTTGGAAGACCATATTATTAAA
GAAGTTCTAATCATCCTTTAGTAACAATGTGCAAGCATTGTGCAGGTAAAAGGGATGCTTTTCTC
ACTAAGTTCTGATAGCTTACATGAGTTTATGTTTTTGTTTTAGGTTGATTGTGAATATGTGACCG
CCTACGGACGTACTAACGTCCAGAGATTGAAAATTGTAATAAAATATAAAAACAAGGCGATATCC
CCAAGTAAACAGGTCAAGTTATAATATAGTTTTACAATGATATAGGTGAGTACTCTGAGGATCGT
ACCCAAGGAGACGACTACCAGATCAATTCTAACCTAAACACTAAAGGATCTAATTAGTACTTTAA
ATTAGTTATAGTACGAAAGCATAAAATAAAGGATCTTTAGGGTTGTAATAATAAAACAAAATATT
AAAAAGGAATAAACTTCAAGAGATAAAAAAGGAGAATAAATCAAATCTTAATTATGGGTGATTAG
CTCGCTTCGGTAATCCCTAGTAACTGTCATTTCAGATTCCTCGTCAATCAACTAGTTGCTACCCT
AGTAGGATCTTTTGATCTTCCATTAACATAACGAGTCAGCAAGGATTGCTTATCTTCTGACCTCA
CAGTCCAGACTGGCTTGGTGTGAAGGTGTTCATAGATGGATCATACCAAATTTGGGTTAATTCCC
ACCTTGATGACTTCATAGGGTTGTCAAGCCTAGGTTTTGTTTCATACCTGTCATTTCCCAAATAG
CTAATCTGTTGAGTAACCCTACAAAACAGTCAATAGATCATAACTCCACTCACTAATCCACCAAA
GAGGGATTAGTTCCTCATGGAAGAATGAA
Found at i:39995816 original size:50 final size:50
Alignment explanation
Indices: 39995705--39995951 Score: 191
Period size: 50 Copynumber: 4.8 Consensus size: 50
39995695 ATTTGGGTAA
* *
39995705 AGAGATCCAATGTAAGACCATGTCTGGGACATGGCATCGGCATCCTTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
39995761 AGAGGTCCCATGTAAGACCATGTCTAGGACATGG-AGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCA-TTGGCACCGAGATG
* * * * * *
39995811 AGAGGT-CCACTATAAGACCATGTCTGGGTCATGGCATGGGCACCAATATG
1 AGAGATCCCA-TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
39995861 AGA-ACTCTTATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACATG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
39995910 AAACATCCCATGTAAGACCATGTTTGGGACATGG-ATTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCA-TTGGCA
39995952 TGTTATTATC
Statistics
Matches: 157, Mismatches: 26, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
48 1 0.01
49 39 0.25
50 73 0.46
51 2 0.01
53 3 0.02
55 3 0.02
56 36 0.23
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:39998554 original size:49 final size:49
Alignment explanation
Indices: 39998434--39998560 Score: 159
Period size: 49 Copynumber: 2.6 Consensus size: 49
39998424 ACGAGAGGTA
*
39998434 CCATGTAAGACCATGTCTGGGACATGGCATGGACACCGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATGGACA-CGATATCAGAACTC
* * * *
39998484 CCTTGTAAGACCATATCTGGGATATGGCATTGACA-GTATATCA-AACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATGGACACG-ATATCAGAAC-TC
*
39998533 CCATGTAAGACCATGTTTGGGACATGGC
1 CCATGTAAGACCATGTCTGGGACATGGC
39998561 TTTGGCATGT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
48 4 0.06
49 31 0.47
50 31 0.47
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (49 bp):
CCATGTAAGACCATGTCTGGGACATGGCATGGACACGATATCAGAACTC
Found at i:40005546 original size:50 final size:50
Alignment explanation
Indices: 40005380--40005621 Score: 188
Period size: 50 Copynumber: 4.7 Consensus size: 50
40005370 GGTAAAGAGA
* * * **
40005380 TCCCATGTATGACCATGTCTGGGACATGGCATCGGCATCCTTGAGATCATGACAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GAT-ATGAGAAC
* * * * **
40005436 TCCCATGTAAGACCAAGTCTGGGACATGGCGTTGGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAAC
* *
40005486 ACCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAAC
* * * * *
40005536 TCCCATGTAAGACCATATTTGGGATATGACATTGGCA--GTACATGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-ATATGAGAAC
*
40005584 ATCCCATGTAAGACCATGTTTGGGACATGG-ATTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCA-TTGGCA
40005622 TGTTATTATC
Statistics
Matches: 156, Mismatches: 25, Indels: 17
0.79 0.13 0.09
Matches are distributed among these distances:
48 5 0.03
49 38 0.24
50 76 0.49
51 2 0.01
55 2 0.01
56 33 0.21
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAAC
Found at i:40023770 original size:28 final size:29
Alignment explanation
Indices: 40023711--40023772 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
40023701 ATATAAAGAT
*
40023711 ATTTTATAGAATATTATTTTATATATACA
1 ATTTTATAGAATATTATTCTATATATACA
* *
40023740 ATTTATATATAAT-TTATTCTATATGTA-A
1 ATTT-TATAGAATATTATTCTATATATACA
40023768 ATTTT
1 ATTTT
40023773 TGTATGTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 1 0.03
28 5 0.17
29 16 0.55
30 7 0.24
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTTATAGAATATTATTCTATATATACA
Found at i:40026798 original size:29 final size:29
Alignment explanation
Indices: 40026766--40026845 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
40026756 AAAAAAATTC
40026766 AAAA-AAAGTGAAAAAGAAA-TCGAGCAAAA
1 AAAAGAAAGTGAAAAA-AAAGT-GAGCAAAA
*
40026795 AAAAGAAA-AGAAAAAAAAGGTGAGCAAAA
1 AAAAGAAAGTGAAAAAAAA-GTGAGCAAAA
* *
40026824 AAAATAAAGT-TAAAAAAAGTGA
1 AAAAGAAAGTGAAAAAAAAGTGA
40026846 AAAGTCTTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 7 0.16
29 32 0.74
30 4 0.09
ACGTcount: A:0.70, C:0.04, G:0.17, T:0.09
Consensus pattern (29 bp):
AAAAGAAAGTGAAAAAAAAGTGAGCAAAA
Found at i:40034834 original size:42 final size:42
Alignment explanation
Indices: 40034760--40035232 Score: 557
Period size: 42 Copynumber: 11.3 Consensus size: 42
40034750 AAAGAAAACA
*
40034760 TTCATTGCATTTAG-GGTCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGG-ACCAGGTGTGGAGGTCCATTTACTT
* * *
40034802 TTCATTGCATTTAGAGGACCAGATGTGCAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGACCAGGTGTGGAGGTCCATTTACTT
*
40034844 TTCATTGCATTTAGAGG-CCTAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGGACC-AGGTGTGGAGGTCCATTTACTT
* * * * *
40034886 TTCAATACATTTAGAGG-CAAAGGTCTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGAC-CAGGTGTGGAGGTCCATTTACTT
* * * *
40034928 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTTCATTCACTT
1 TTCATTGCATTTAGAGGACCAGGTGTGGAGGTCCATTTACTT
* * *
40034970 TTCATTGCATTTA-AAGACCCAGGTGTGGAGCTCCATTGACTT
1 TTCATTGCATTTAGAGGA-CCAGGTGTGGAGGTCCATTTACTT
* * * *
40035012 TTCATTGCATTTAAAGGCCCAAGTATGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGACCAGGTGTGGAGGTCCATTTACTT
40035054 TTCATTGCATTTAGA-GACCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGA-CCAGGTGTGGAGGTCCATTTACTT
* *
40035096 TTCATTGCATTTAGA-GACCCAGGTGTTGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGGA-CCAGGTGTGGAGGTCCATTTACTT
* * *
40035138 TTCATTACATTTAGA-GACCCAAGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGGA-CCAGGTGTGGAGGTCCATTTACTT
* * *
40035180 TTCATTACATTTATA-GACCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGA-CCAGGTGTGGAGGTCCATTTACTT
40035222 TTCATTGCATT
1 TTCATTGCATT
40035233 CACTTTTCAT
Statistics
Matches: 378, Mismatches: 46, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
41 5 0.01
42 368 0.97
43 5 0.01
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGACCAGGTGTGGAGGTCCATTTACTT
Found at i:40034901 original size:84 final size:84
Alignment explanation
Indices: 40034760--40035232 Score: 635
Period size: 84 Copynumber: 5.6 Consensus size: 84
40034750 AAAGAAAACA
*
40034760 TTCATTGCATTTAG-GGTCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGA-CCA
1 TTCATTGCATTTAGAGG-CCCAGGTGTGGAGGTCCATTCACTTTTCATTGCATTTAGA-GACCCA
* * *
40034823 GATGTGCAGGTCCATTTATTT
64 GGTGTGGAGGTCCATTTACTT
* * * * **
40034844 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTCACTTTTCAATACATTTAGAGGCAAAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCAGG
* *
40034909 TCTGGAGGTTCATTTACTT
66 TGTGGAGGTCCATTTACTT
* * *
40034928 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTTCATTCACTTTTCATTGCATTTAAAGACCCAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCAGG
* *
40034993 TGTGGAGCTCCATTGACTT
66 TGTGGAGGTCCATTTACTT
* * * *
40035012 TTCATTGCATTTAAAGGCCCAAGTATGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCAGG
40035077 TGTGGAGGTCCATTTACTT
66 TGTGGAGGTCCATTTACTT
* * * *
40035096 TTCATTGCATTTAGAGACCCAGGTGTTGAGGTCCATTCACTTTTCATTACATTTAGAGACCCAAG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCAGG
*
40035161 TGTGGAGGTCCATTCACTT
66 TGTGGAGGTCCATTTACTT
* * * * *
40035180 TTCATTACATTTATAGACCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTCACTTTTCATTGCATT
40035233 CACTTTTCAT
Statistics
Matches: 338, Mismatches: 49, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
83 1 0.00
84 335 0.99
85 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (84 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCAGG
TGTGGAGGTCCATTTACTT
Found at i:40034972 original size:126 final size:125
Alignment explanation
Indices: 40034760--40035232 Score: 635
Period size: 126 Copynumber: 3.8 Consensus size: 125
40034750 AAAGAAAACA
* *
40034760 TTCATTGCATTTAG-GGTCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGA-CCA
1 TTCATTACATTTAGAGG--CCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGA-GACCCA
* * * * *
40034823 GATGTGCAGGTCCATTTATTTTTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTCACTT
63 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* * * * *
40034886 TTCAATACATTTAGAGGCAAAGGTCTGGAGGTTCATTTACTTTTCATTGCATTTAGAGGCCCAGG
1 TTCATTACATTTAGAGGCCAA-GTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGG
* * * * * *
40034951 TGTTGAGGTTCATTCACTTTTCATTGCATTTAAAGACCCAGGTGTGGAGCTCCATTGACTT
65 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* * *
40035012 TTCATTGCATTTAAAGGCCCAAGTATGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGG
1 TTCATTACATTTAGAGG-CCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGG
*
40035077 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTTGAGGTCCATTCACTT
65 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* * * *
40035138 TTCATTACATTTAGAGACCCAAGTGTGGAGGTCCATTCACTTTTCATTACATTTATAGACCCAGG
1 TTCATTACATTTAGAG-GCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGG
*
40035203 TGTGGAGGCCCATTTACTTTTCATTGCATT
65 TGTGGAGGTCCATTTACTTTTCATTGCATT
40035233 CACTTTTCAT
Statistics
Matches: 302, Mismatches: 40, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
125 3 0.01
126 294 0.97
127 5 0.02
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (125 bp):
TTCATTACATTTAGAGGCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGT
GTGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
Found at i:40035237 original size:16 final size:16
Alignment explanation
Indices: 40035213--40035248 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40035203 TGTGGAGGCC
* *
40035213 CATTTACTTTTCATTG
1 CATTCACTTTTCATTA
40035229 CATTCACTTTTCATTA
1 CATTCACTTTTCATTA
40035245 CATT
1 CATT
40035249 TAGAGGCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (16 bp):
CATTCACTTTTCATTA
Found at i:40036190 original size:157 final size:154
Alignment explanation
Indices: 40035956--40036400 Score: 587
Period size: 156 Copynumber: 2.9 Consensus size: 154
40035946 TGATATTTTT
* * *
40035956 AAAAAACAGAAAGTTTAGATTTT-AACAAATAAAAA-TGTTTTTTTT-TTTATTTTAAAGGAAAG
1 AAAAAAGAGAAAGTTTAGATTTTGAA-AAATAAAAATTGTTTTTTTTAGTCATTTTAAAGGAAAG
* *
40036018 TTTAAATTTTTAAAACAAAGTTTAGATTTTTTTCAACTATTTCAAAGTAAAATCTTTAATCTTTA
65 TTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAA-TAAAATCTTTAATCTTTA
40036083 AGAAAAATAGTGTTTT-TTTAAATAAA
129 AGAAAAATAGTGTTTTATTTAAA-AAA
*
40036109 AAAAAAGTAGAAAGTTTAG-TGTTTGAAAATTAAAAATCTGTTTTTTTTAGTCATTTTAAAGGAA
1 AAAAAAG-AGAAAGTTTAGAT-TTTGAAAAATAAAAAT-TGTTTTTTTTAGTCATTTTAAAGGAA
* * * *
40036173 AGTTTAAAATTTTAAAACAAAGTTTTGGTTTTTTTCAACTACTCCAAAATAAAAGCTTTAATCTT
63 AGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTC-AAATAAAATCTTTAATCTT
* * **
40036238 TAAGAGAGATAGTGTTTTATTTTTAAAA
127 TAAGAAAAATAGTGTTTTATTTAAAAAA
* *
40036266 AAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATATGTTTTTTTAAGTCATTTTAAAGAAAAG
1 AAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAAT-TGTTTTTTTTAGTCATTTTAAAGGAAAG
* * * *
40036331 TTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTAACTATTTTGAAAT-AAATTTTTAATTTTTA
65 TTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTA-TTTCAAATAAAATCTTTAATCTTTA
40036395 AGAAAA
129 AGAAAA
40036401 TTAAGGATTT
Statistics
Matches: 254, Mismatches: 28, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
153 7 0.03
154 22 0.09
155 19 0.07
156 103 0.41
157 96 0.38
158 7 0.03
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (154 bp):
AAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATTGTTTTTTTTAGTCATTTTAAAGGAAAGT
TTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAATAAAATCTTTAATCTTTAAG
AAAAATAGTGTTTTATTTAAAAAA
Found at i:40036331 original size:156 final size:155
Alignment explanation
Indices: 40035956--40036369 Score: 568
Period size: 157 Copynumber: 2.7 Consensus size: 155
40035946 TGATATTTTT
* ** *
40035956 AAAAAACAGAAAGTTTAGATTTT-AACAAAT-AAAA-ATGTTTTTTTTTTTATTTTAAAGGAAAG
1 AAAAAAGAGAAAGTTTAGATTTTGAA-AAATAAAAATATGTTTTTTTAGTCATTTTAAAGGAAAG
* * * * * *
40036018 TTTAAATTTTTAAAACAAAGTTTAGATTTTTTTCAACTATTTCAAAGTAAAATCTTTAATCTTTA
65 TTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTACTCCAAAATAAAAGCTTTAATCTTTA
40036083 AGAAAAATAGTGTTTTTTTAAATAAA
130 AGAAAAATAGTGTTTTTTTAAATAAA
* *
40036109 AAAAAAGTAGAAAGTTTAG-TGTTTGAAAATTAAAAATCTGTTTTTTTTAGTCATTTTAAAGGAA
1 AAAAAAG-AGAAAGTTTAGAT-TTTGAAAAATAAAAATATG-TTTTTTTAGTCATTTTAAAGGAA
*
40036173 AGTTTAAAATTTTAAAACAAAGTTTTGGTTTTTTTCAACTACTCCAAAATAAAAGCTTTAATCTT
63 AGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTACTCCAAAATAAAAGCTTTAATCTT
* * **
40036238 TAAGAGAGATAGTGTTTTATTTTTA-AAA
128 TAAGAAAAATAGTGTTTT-TTTAAATAAA
*
40036266 AAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATATGTTTTTTTAAGTCATTTTAAAGAAAAG
1 AAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATATGTTTTTTT-AGTCATTTTAAAGGAAAG
*
40036331 TTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTAACTA
65 TTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTA
40036370 TTTTGAAATA
Statistics
Matches: 230, Mismatches: 22, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
153 7 0.03
154 17 0.07
155 13 0.06
156 84 0.37
157 105 0.46
158 4 0.02
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (155 bp):
AAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATATGTTTTTTTAGTCATTTTAAAGGAAAGT
TTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTACTCCAAAATAAAAGCTTTAATCTTTAA
GAAAAATAGTGTTTTTTTAAATAAA
Found at i:40037471 original size:27 final size:27
Alignment explanation
Indices: 40037441--40037509 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
40037431 GACGGGTAAG
40037441 ATGACCCTAATGCCCCTGTAGGATAAA
1 ATGACCCTAATGCCCCTGTAGGATAAA
* *
40037468 ATGACCCTAATACCCCTGTAGGGTAAA
1 ATGACCCTAATGCCCCTGTAGGATAAA
*
40037495 ATGACCATAATGCCC
1 ATGACCCTAATGCCC
40037510 TAGTGGTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (27 bp):
ATGACCCTAATGCCCCTGTAGGATAAA
Found at i:40037534 original size:26 final size:25
Alignment explanation
Indices: 40037505--40037579 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 25
40037495 ATGACCATAA
40037505 TGCCCTAGTGGTTAAATGACTATTTT
1 TGCCCT-GTGGTTAAATGACTATTTT
* *
40037531 TGCCCTCGAGGTCAAATGA-T-TGTTT
1 TGCCCT-GTGGTTAAATGACTAT-TTT
*
40037556 TG-TCTGTGGTTAAATGACTGATTT
1 TGCCCTGTGGTTAAATGACT-ATTT
40037580 GTTTTTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
23 10 0.26
24 4 0.10
25 8 0.21
26 17 0.44
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (25 bp):
TGCCCTGTGGTTAAATGACTATTTT
Found at i:40037620 original size:24 final size:24
Alignment explanation
Indices: 40037568--40037627 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
40037558 TCTGTGGTTA
* *
40037568 AATGACTGATTTGTTTTTATTTGG
1 AATGACTGATTTGTTATGATTTGG
*
40037592 TATGACTGATTTGTCTATGATTT-G
1 AATGACTGATTTGT-TATGATTTGG
*
40037616 AATGACTAATTT
1 AATGACTGATTT
40037628 TGAGCATGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.50
Consensus pattern (24 bp):
AATGACTGATTTGTTATGATTTGG
Found at i:40037730 original size:27 final size:27
Alignment explanation
Indices: 40037690--40037752 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
40037680 ATGGAGGAAG
*
40037690 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTAGTGGCT-TGGCCACATA
40037715 TCACTGTTACTAGTGGCTTGGCCACATA
1 T-ACTGTTACTAGTGGCTTGGCCACATA
40037743 TACTGTTACT
1 TACTGTTACT
40037753 GGCAGCTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 1 0.03
26 5 0.15
27 25 0.76
28 2 0.06
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (27 bp):
TACTGTTACTAGTGGCTTGGCCACATA
Found at i:40037760 original size:27 final size:26
Alignment explanation
Indices: 40037708--40037786 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 26
40037698 TGGTGGCTCT
* **
40037708 GCCACAATCACTGTTACTAGTGGCTTG
1 GCCACAAT-ACTGTTACTGGCAGCTTG
*
40037735 GCCACATATACTGTTACTGGCAGCTTT
1 GCCACA-ATACTGTTACTGGCAGCTTG
** * *
40037762 GCTGCGATACTGTTGCTGGCAGCTT
1 GCCACAATACTGTTACTGGCAGCTT
40037787 TACTGCAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 18 0.42
27 23 0.53
28 2 0.05
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (26 bp):
GCCACAATACTGTTACTGGCAGCTTG
Found at i:40037780 original size:26 final size:26
Alignment explanation
Indices: 40037742--40037792 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
40037732 TTGGCCACAT
*
40037742 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTACTGCG
*
40037768 ATACTGTTGCTGGCAGCTTTACTGC
1 ATACTGTTACTGGCAGCTTTACTGC
40037793 AATGCTATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTACTGCG
Found at i:40037807 original size:26 final size:26
Alignment explanation
Indices: 40037752--40037807 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
40037742 ATACTGTTAC
* * * *
40037752 TGGCAGCTTTGCTGCGATACTGTTGC
1 TGGCAGCTTTACTGCAATACTATTGA
*
40037778 TGGCAGCTTTACTGCAATGCTATTGA
1 TGGCAGCTTTACTGCAATACTATTGA
40037804 TGGC
1 TGGC
40037808 TTTGTGACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (26 bp):
TGGCAGCTTTACTGCAATACTATTGA
Found at i:40037837 original size:32 final size:32
Alignment explanation
Indices: 40037801--40038000 Score: 231
Period size: 32 Copynumber: 6.3 Consensus size: 32
40037791 GCAATGCTAT
* * *
40037801 TGATGGCTTTGTGACAATCATATTACCATTGC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
* * *
40037833 TGATGGCTATGTGCCGATCATATTACCATTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
* *
40037865 TGATGGCTGTGTGCCAATCATATTACTACTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
* ** *
40037897 TGATGGCTTTCTGCTGATCATACTACTATTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
* * * *
40037929 TGATGGCTGTGTGCTAATCATATTACTACTAT
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
*
40037961 TGATGGCTTTGTGCCAATCATATTACT-GTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
*
40037992 TTATGGCTT
1 TGATGGCTT
40038001 GTAGTCATTC
Statistics
Matches: 143, Mismatches: 25, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
31 10 0.07
32 133 0.93
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (32 bp):
TGATGGCTTTGTGCCAATCATATTACTATTAC
Found at i:40037885 original size:64 final size:64
Alignment explanation
Indices: 40037801--40037986 Score: 255
Period size: 64 Copynumber: 2.9 Consensus size: 64
40037791 GCAATGCTAT
* * * * * *
40037801 TGATGGCTTTGTGACAATCATATTACCATTGCTGATGGCTATGTGCCGATCATATTACCATTAC
1 TGATGGCTGTGTGCCAATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTAC
* * * *
40037865 TGATGGCTGTGTGCCAATCATATTACTACTACTGATGGCTTTCTGCTGATCATACTACTATTAC
1 TGATGGCTGTGTGCCAATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTAC
* * *
40037929 TGATGGCTGTGTGCTAATCATATTACTACTATTGATGGCTTTGTGCCAATCATATTAC
1 TGATGGCTGTGTGCCAATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTAC
40037987 TGTACTTATG
Statistics
Matches: 106, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 106 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (64 bp):
TGATGGCTGTGTGCCAATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTAC
Found at i:40038808 original size:52 final size:52
Alignment explanation
Indices: 40038730--40038833 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
40038720 ATTGCATGTT
*
40038730 CACCATCCTGTTCACTGGACATTGAATCACTTGGGTCTCGTTCTATTAAACA
1 CACCATCCTATTCACTGGACATTGAATCACTTGGGTCTCGTTCTATTAAACA
*
40038782 CACCATCCTATTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
1 CACCATCCTATTCACTGGACATTGAATCACTTGGGTCTCGTTCTATTAAACA
40038834 ATTAAAAGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (52 bp):
CACCATCCTATTCACTGGACATTGAATCACTTGGGTCTCGTTCTATTAAACA
Found at i:40039035 original size:16 final size:16
Alignment explanation
Indices: 40039014--40039047 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
40039004 TTTATAGCAA
40039014 TAAACATACTTAATTT
1 TAAACATACTTAATTT
40039030 TAAACATACTTAATTT
1 TAAACATACTTAATTT
40039046 TA
1 TA
40039048 TCCTGTCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAACATACTTAATTT
Found at i:40041557 original size:45 final size:45
Alignment explanation
Indices: 40041493--40041588 Score: 151
Period size: 45 Copynumber: 2.1 Consensus size: 45
40041483 AGCAAGGCAA
40041493 TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAAT-AGGC
1 TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAATCA-GC
*
40041538 TAATGTGAAATTT-TGAGCTAATTTTCCATTATATAAACAATCAGC
1 TAATGTGAAATTTCT-AGCTAATGTTCCATTATATAAACAATCAGC
40041583 TAATGT
1 TAATGT
40041589 TCCATTTATA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
44 1 0.02
45 46 0.96
46 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (45 bp):
TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAATCAGC
Found at i:40043043 original size:10 final size:10
Alignment explanation
Indices: 40043028--40043059 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
40043018 GCCTAAAATT
40043028 ATATATAATG
1 ATATATAATG
40043038 ATATATAATG
1 ATATATAATG
40043048 ATATATAATG
1 ATATATAATG
40043058 AT
1 AT
40043060 GGGGATGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (10 bp):
ATATATAATG
Found at i:40050185 original size:18 final size:18
Alignment explanation
Indices: 40050158--40050206 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
40050148 GTCTTGTCGA
*
40050158 AAAATGATTAAATATTAT
1 AAAATAATTAAATATTAT
40050176 AAAATAATTAAATATTAT
1 AAAATAATTAAATATTAT
40050194 AAAATAATTAAAT
1 AAAATAATTAAAT
40050207 TATGTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AAAATAATTAAATATTAT
Found at i:40060216 original size:14 final size:14
Alignment explanation
Indices: 40060199--40060226 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40060189 AAATTTTTTA
40060199 CTTAGTTTTTAATC
1 CTTAGTTTTTAATC
40060213 CTTAGTTTTTAATC
1 CTTAGTTTTTAATC
40060227 ATCTTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
CTTAGTTTTTAATC
Found at i:40061420 original size:232 final size:232
Alignment explanation
Indices: 40060994--40061466 Score: 729
Period size: 232 Copynumber: 2.0 Consensus size: 232
40060984 CGTCATGGAT
* * * * *
40060994 TGAG-TATATTAAGGGTAAGTAGTTGGAGGATGAGTTGTTGGGTCTTCGATTCCGACAGATTGAA
1 TGAGTTATATGAAAGGTAAGCAGTTGGAGGATGAGTTGTTGGGTCTTCAATTCAGACAGATTGAA
* *
40061058 GGTGGTAGTACTACGGATTTTGGACTAAACAGTGATGGGGTACTCTGTTTTCGTGGGAGAATCTG
66 GGTGGTAGTACTACGAATTTTGGACTAAACAGTGATGGGGTACTCTATTTTCGTGGGAGAATCTG
* * *
40061123 TGTTCCGAATGATCCTAATTTGAGACAGGCCATACTGAGAGAGGCGCTTAGTAGCCCTTATGCTA
131 TGTTCCGAATGATACTAATTTGAGACAGGCCATACTGAGAGAGGCACATAGTAGCCCTTATGCTA
40061188 TACATCCTGGCAGAAATAAGATGTACCGAGACCTCCG
196 TACATCCTGGCAGAAATAAGATGTACCGAGACCTCCG
40061225 TGAGTTATATGAAAGGTAAGCAGTTGGAGGATGAGTCT-TTGGGTCTTCAATTCTAG-CAGATTG
1 TGAGTTATATGAAAGGTAAGCAGTTGGAGGATGAGT-TGTTGGGTCTTCAATTC-AGACAGATTG
* * * *
40061288 AGGGTGGTAGTACTATGAATTTTGGACTGAACAGTGATGGGGTGCTCTATTTTCGTGGGAGAATC
64 AAGGTGGTAGTACTACGAATTTTGGACTAAACAGTGATGGGGTACTCTATTTTCGTGGGAGAATC
*
40061353 TGTGTTTCGAATGATACTAATTTGAGACAGGCCATACTGAGAGA-GCAACATAGTAGCCCTTATG
129 TGTGTTCCGAATGATACTAATTTGAGACAGGCCATACTGAGAGAGGC-ACATAGTAGCCCTTATG
* * *
40061417 CTATGCATCCTGGCAGAAATAAGATGTACTGAGACCTCTG
193 CTATACATCCTGGCAGAAATAAGATGTACCGAGACCTCCG
40061457 TGAGTTATAT
1 TGAGTTATAT
40061467 TGGTGCCCAG
Statistics
Matches: 220, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
231 6 0.03
232 212 0.96
233 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (232 bp):
TGAGTTATATGAAAGGTAAGCAGTTGGAGGATGAGTTGTTGGGTCTTCAATTCAGACAGATTGAA
GGTGGTAGTACTACGAATTTTGGACTAAACAGTGATGGGGTACTCTATTTTCGTGGGAGAATCTG
TGTTCCGAATGATACTAATTTGAGACAGGCCATACTGAGAGAGGCACATAGTAGCCCTTATGCTA
TACATCCTGGCAGAAATAAGATGTACCGAGACCTCCG
Found at i:40075482 original size:12 final size:12
Alignment explanation
Indices: 40075465--40075499 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
40075455 TTGTTACAAG
40075465 GCCTAGCACATT
1 GCCTAGCACATT
40075477 GCCTAGCACATT
1 GCCTAGCACATT
40075489 GCCTAGCACAT
1 GCCTAGCACAT
40075500 GGCCGTGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (12 bp):
GCCTAGCACATT
Found at i:40081578 original size:19 final size:19
Alignment explanation
Indices: 40081523--40081579 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
40081513 GAGTTTGATA
*
40081523 TTGAGCCAGATGCTTTATT
1 TTGAACCAGATGCTTTATT
40081542 TT-AA-CA-AT--TTTGATT
1 TTGAACCAGATGCTTT-ATT
40081557 TTGAACCAGATGCTTTATT
1 TTGAACCAGATGCTTTATT
40081576 TTGA
1 TTGA
40081580 TCCAATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
14 3 0.10
15 5 0.16
16 4 0.13
17 4 0.13
18 3 0.10
19 9 0.29
20 3 0.10
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGAACCAGATGCTTTATT
Found at i:40082917 original size:20 final size:20
Alignment explanation
Indices: 40082889--40082930 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40082879 AATAGATGCT
40082889 AACAAAGGCACCAAAGTGCA
1 AACAAAGGCACCAAAGTGCA
* **
40082909 AACAGAGGCACTGAAGTGCA
1 AACAAAGGCACCAAAGTGCA
40082929 AA
1 AA
40082931 TCTCATACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.21, G:0.24, T:0.07
Consensus pattern (20 bp):
AACAAAGGCACCAAAGTGCA
Found at i:40084631 original size:23 final size:23
Alignment explanation
Indices: 40084559--40084797 Score: 185
Period size: 23 Copynumber: 10.4 Consensus size: 23
40084549 GTCGATTACA
* **
40084559 CCACAAAGGCCAAACAGAATATT
1 CCACAAAGGCCAAATAGAATACG
* * * * *
40084582 CCATAATGGCTAAACAAAATACG
1 CCACAAAGGCCAAATAGAATACG
*
40084605 CCACAAAGGCCAAATAGAGTACG
1 CCACAAAGGCCAAATAGAATACG
*
40084628 CCACAAAGGCCAAATAGAATAAG
1 CCACAAAGGCCAAATAGAATACG
* * *
40084651 CCACAAAGGCCAAATAGACTGCA
1 CCACAAAGGCCAAATAGAATACG
* * *
40084674 CCACAAA-GCAAAACAGAATAGG
1 CCACAAAGGCCAAATAGAATACG
* * ***
40084696 CCACAAAGGCCAAATATAGTGTT
1 CCACAAAGGCCAAATAGAATACG
* *
40084719 CCAAAAAGGCAAAATAGAATACG
1 CCACAAAGGCCAAATAGAATACG
* * *
40084742 CCACAGAGGTCAAACA-AAGTACG
1 CCACAAAGGCCAAATAGAA-TACG
* * * *
40084765 CCACAAAGGCAAAAAAAAATATG
1 CCACAAAGGCCAAATAGAATACG
40084788 CCACAAAGGC
1 CCACAAAGGC
40084798 TCTATTTGGA
Statistics
Matches: 165, Mismatches: 48, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
22 18 0.11
23 145 0.88
24 2 0.01
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (23 bp):
CCACAAAGGCCAAATAGAATACG
Found at i:40084703 original size:91 final size:92
Alignment explanation
Indices: 40084559--40084797 Score: 248
Period size: 91 Copynumber: 2.6 Consensus size: 92
40084549 GTCGATTACA
** * * *
40084559 CCACAAAGGCCAAACAGAA-TATTCCATAATGGCTAAACAAAATACGCCACAAAGGCCAAATAGA
1 CCACAAAGGCCAAACA-AACTACACCACAAAGGCAAAACAAAATACGCCACAAAGGCCAAATAGA
* *
40084623 GTACGCCACAAAGGCCAAATAGAATAAG
65 GTACGCCAAAAAGGCAAAATAGAATAAG
* * * * * *
40084651 CCACAAAGGCCAAATAGACTGCACCACAAA-GCAAAACAGAATAGGCCACAAAGGCCAAATATAG
1 CCACAAAGGCCAAACAAACTACACCACAAAGGCAAAACAAAATACGCCACAAAGGCCAAATAGAG
*** *
40084715 TGTTCCAAAAAGGCAAAATAGAATACG
66 TACGCCAAAAAGGCAAAATAGAATAAG
* * * * * *
40084742 CCACAGAGGTCAAACAAAGTACGCCACAAAGGCAAAAAAAAATATGCCACAAAGGC
1 CCACAAAGGCCAAACAAACTACACCACAAAGGCAAAACAAAATACGCCACAAAGGC
40084798 TCTATTTGGA
Statistics
Matches: 118, Mismatches: 27, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
91 75 0.64
92 43 0.36
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (92 bp):
CCACAAAGGCCAAACAAACTACACCACAAAGGCAAAACAAAATACGCCACAAAGGCCAAATAGAG
TACGCCAAAAAGGCAAAATAGAATAAG
Found at i:40090003 original size:51 final size:50
Alignment explanation
Indices: 40089921--40090206 Score: 342
Period size: 51 Copynumber: 5.6 Consensus size: 50
40089911 GATGAACACG
* *
40089921 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-TTGGTCACA
* * * * *
40089972 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATTTGGTCACA
* * * *
40090023 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-TTGGTCACA
* * *
40090074 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TTTGGTCACA
* * * *
40090125 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAT-AAATTTGGTCACA
40090175 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
40090207 TCGAATGATA
Statistics
Matches: 200, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
50 43 0.22
51 152 0.76
52 5 0.03
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATTTGGTCACA
Found at i:40090097 original size:102 final size:102
Alignment explanation
Indices: 40089921--40090198 Score: 434
Period size: 102 Copynumber: 2.7 Consensus size: 102
40089911 GATGAACACG
*
40089921 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTACTAAG
*
40089986 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACA
66 TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
* *
40090023 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTACTAAG
* *
40090088 TGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACG
66 TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
* * * * *
40090125 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTACTAT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTACTAA
40090188 GTGAAGGCTAC
65 GTGAAGGCTAC
40090199 TACGTGTATC
Statistics
Matches: 162, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
101 33 0.20
102 129 0.80
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (102 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTACTAAG
TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
Found at i:40093622 original size:50 final size:52
Alignment explanation
Indices: 40093497--40093627 Score: 151
Period size: 50 Copynumber: 2.6 Consensus size: 52
40093487 ATGACAAATG
* * * *
40093497 AGTTACTTAATGCA-AGACTTAATTTAATGATGCAAACTTAAACTATCATGGG
1 AGTTACATAATGCATA-ACTTTATTTAATGATGCAAACTTAAACTAGCATGGA
** * *
40093549 AGTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATGGA
1 AGTTACATAATGCATAACTTTATTTAATGATGCAAACTTAAACTAGCATGGA
*
40093599 AGTTACATAATGCATAACTTTATTAAATG
1 AGTTACATAATGCATAACTTTATTTAATG
40093628 CAAAACACAC
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
50 31 0.48
51 15 0.23
52 19 0.29
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (52 bp):
AGTTACATAATGCATAACTTTATTTAATGATGCAAACTTAAACTAGCATGGA
Found at i:40095313 original size:9 final size:11
Alignment explanation
Indices: 40095280--40095309 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
40095270 AATGTCATGA
*
40095280 TATATATAATT
1 TATATATAAGT
40095291 TATATATAAGT
1 TATATATAAGT
40095302 TATATATA
1 TATATATA
40095310 TTATGTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
TATATATAAGT
Found at i:40096847 original size:57 final size:57
Alignment explanation
Indices: 40096759--40096873 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
40096749 AATCTTGATG
*
40096759 TCCTTATAATTATGTAAGTATGTAAGGTATATTGGTAATGATCAAAGTGTTAATAGC
1 TCCTTATAATTATGTAAATATGTAAGGTATATTGGTAATGATCAAAGTGTTAATAGC
40096816 TCCTTATAATTATGTAAATATGTAAGGTATATTGGTAATGATCAAAGTGTTAATAGC
1 TCCTTATAATTATGTAAATATGTAAGGTATATTGGTAATGATCAAAGTGTTAATAGC
40096873 T
1 T
40096874 TGAAAGTTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (57 bp):
TCCTTATAATTATGTAAATATGTAAGGTATATTGGTAATGATCAAAGTGTTAATAGC
Found at i:40100435 original size:40 final size:40
Alignment explanation
Indices: 40100352--40100654 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
40100342 TTGAATGCTG
* * * * * *
40100352 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
40100392 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
40100432 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
40100472 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40100512 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40100552 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40100592 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40100631 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40100655 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:40115521 original size:40 final size:40
Alignment explanation
Indices: 40115438--40115740 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
40115428 TTGAATGCTG
* * * * * *
40115438 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
40115478 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
40115518 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
40115558 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40115598 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40115638 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40115678 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40115717 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40115741 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:40121244 original size:84 final size:85
Alignment explanation
Indices: 40120963--40121246 Score: 464
Period size: 85 Copynumber: 3.4 Consensus size: 85
40120953 ATCCGTTACT
* * *
40120963 CGGTGGATTCAGCACTTAGCAACCACC-TTAAATTTAGTGATACGGGGAATCATCACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTTAGTGATACGGGGAATCAGCACATAGCAAC
*
40121027 CCCTTTCACAATCAAAGATA
66 CCCTTTCACAATCAAATATA
* *
40121047 CGGTGGAATCAGCACTTAGAAACCACCTTTATATTTAGTGATACGGGGAATCAGCACATATCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTTAGTGATACGGGGAATCAGCACATAGCAAC
40121112 CCCTTTCACAATCAAATATA
66 CCCTTTCACAATCAAATATA
* * * *
40121132 CGGTGGAATCAGCACTTACCAACAACCTTTATATTTAGTGATACGAGGATTCAGCACATAGCAA-
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTTAGTGATACGGGGAATCAGCACATAGCAAC
40121196 CCCTTTCACAATCAAATATA
66 CCCTTTCACAATCAAATATA
40121216 CGGTGGAATCAGCACTTAGCAACCACCTTTA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA
40121247 GAATCAATAA
Statistics
Matches: 185, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
84 74 0.40
85 111 0.60
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTATATTTAGTGATACGGGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAATATA
Found at i:40121267 original size:169 final size:169
Alignment explanation
Indices: 40120963--40121284 Score: 448
Period size: 169 Copynumber: 1.9 Consensus size: 169
40120953 ATCCGTTACT
* * * * *
40120963 CGGTGGATTCAGCACTTAGCAACCACCTTAAATTTAGTGATACGGGGAATCATCACATAGCAACC
1 CGGTGGAATCAGCACTTACCAACAACCTTAAATTTAGTGATACGAGGAATCAGCACATAGCAACC
* * * * * *
40121028 CCTTTCACAATCAAAGATACGGTGGAATCAGCACTTAGAAACCACCTTTATATTTAGTGATACGG
66 CCTTTCACAATCAAAGATACGGTGGAATCAGCACTTAGAAACCACCTTTAGAATCAATAATACAG
* *
40121093 GGAATCAGCACATATCAACCCCTTTCACAATCAAATATA
131 GGAATCAACACATAGCAACCCCTTTCACAATCAAATATA
* *
40121132 CGGTGGAATCAGCACTTACCAACAACCTTTATATTTAGTGATACGAGGATTCAGCACATAGCAA-
1 CGGTGGAATCAGCACTTACCAACAACC-TTAAATTTAGTGATACGAGGAATCAGCACATAGCAAC
* * **
40121196 CCCTTTCACAATCAAATATACGGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTTA
65 CCCTTTCACAATCAAAGATACGGTGGAATCAGCACTTAGAAACCACCTTTAGAATCAATAATACA
*
40121261 GGGAATCAACACTTAGCAACCCCT
130 GGGAATCAACACATAGCAACCCCT
40121285 CGGGGAATCT
Statistics
Matches: 132, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
169 100 0.76
170 32 0.24
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (169 bp):
CGGTGGAATCAGCACTTACCAACAACCTTAAATTTAGTGATACGAGGAATCAGCACATAGCAACC
CCTTTCACAATCAAAGATACGGTGGAATCAGCACTTAGAAACCACCTTTAGAATCAATAATACAG
GGAATCAACACATAGCAACCCCTTTCACAATCAAATATA
Found at i:40121278 original size:84 final size:85
Alignment explanation
Indices: 40120963--40121284 Score: 418
Period size: 85 Copynumber: 3.8 Consensus size: 85
40120953 ATCCGTTACT
* * *
40120963 CGGTGGATTCAGCACTTAGCAACCACC-TTA-AATTTAGTGATACGGGGAATCATCACATAGCAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATAA-TTAGTGATACAGGGAATCAGCACATAGCAA
*
40121026 CCCCTTTCACAATCAAAGATA
65 CCCCTTTCACAATCAAATATA
* * * *
40121047 CGGTGGAATCAGCACTTAGAAACCACCTTTATATTTAGTGATACGGGGAATCAGCACATATCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATAATTAGTGATACAGGGAATCAGCACATAGCAAC
40121112 CCCTTTCACAATCAAATATA
66 CCCTTTCACAATCAAATATA
* * * *
40121132 CGGTGGAATCAGCACTTACCAACAACCTTTATATTTAGTGATAC-GAGGATTCAGCACATAGCAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATAATTAGTGATACAG-GGAATCAGCACATAGCAA
40121196 -CCCTTTCACAATCAAATATA
65 CCCCTTTCACAATCAAATATA
* * * * ** * *
40121216 CGGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTTAGGGAATCAACACTTAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATAATTAGTGATACAGGGAATCAGCACATAGCAAC
40121281 CCCT
66 CCCT
40121285 CGGGGAATCT
Statistics
Matches: 210, Mismatches: 23, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
84 96 0.46
85 113 0.54
86 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTATAATTAGTGATACAGGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAATATA
Found at i:40121290 original size:26 final size:26
Alignment explanation
Indices: 40121261--40121310 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
40121251 CAATAATTTA
40121261 GGGAATCAACACTTAGCAACCCCTCG
1 GGGAATCAACACTTAGCAACCCCTCG
** *
40121287 GGGAATCTGCACTTAGCGACCCCT
1 GGGAATCAACACTTAGCAACCCCT
40121311 TTTTATCCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.22, T:0.18
Consensus pattern (26 bp):
GGGAATCAACACTTAGCAACCCCTCG
Found at i:40121681 original size:30 final size:30
Alignment explanation
Indices: 40121647--40121704 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40121637 TCCTTAACTC
40121647 AAACTTTTGCAAAATTACAATTTTGCCCTT
1 AAACTTTTGCAAAATTACAATTTTGCCCTT
* * *
40121677 AAACTTTTGCATATTTACACTTTTGCCC
1 AAACTTTTGCAAAATTACAATTTTGCCC
40121705 CAAAGCTCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCTT
Found at i:40141005 original size:37 final size:37
Alignment explanation
Indices: 40140955--40141029 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
40140945 CACTAATAAC
*
40140955 TACCACTACTACCACCTCGACTCGAGTTTTAGCTTTT
1 TACCACCACTACCACCTCGACTCGAGTTTTAGCTTTT
40140992 TACCACCACTACCACCTCGACTCGAGTTTTAGCTTTT
1 TACCACCACTACCACCTCGACTCGAGTTTTAGCTTTT
40141029 T
1 T
40141030 CTCTACCACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.35
Consensus pattern (37 bp):
TACCACCACTACCACCTCGACTCGAGTTTTAGCTTTT
Found at i:40141036 original size:32 final size:33
Alignment explanation
Indices: 40140962--40141039 Score: 104
Period size: 37 Copynumber: 2.3 Consensus size: 33
40140952 AACTACCACT
40140962 ACTACCACCTCGACTCGAGTTTTAGCTTTTTACCACC
1 ACTACCACCTCGACTCGAGTTTTAGCTTTTT----CC
40140999 ACTACCACCTCGACTCGAGTTTTAGCTTTTT-C
1 ACTACCACCTCGACTCGAGTTTTAGCTTTTTCC
*
40141031 TCTACCACC
1 ACTACCACC
40141040 ACAGCCACTC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
32 9 0.22
37 31 0.77
ACGTcount: A:0.21, C:0.36, G:0.10, T:0.33
Consensus pattern (33 bp):
ACTACCACCTCGACTCGAGTTTTAGCTTTTTCC
Found at i:40141787 original size:21 final size:19
Alignment explanation
Indices: 40141762--40141808 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
40141752 TTGGATCCGA
*
40141762 TTTCAATTCAAGCTTTATTT
1 TTTCAATT-AAGCTTTAGTT
*
40141782 TCTTCAATTAATCTTTAGTT
1 T-TTCAATTAAGCTTTAGTT
40141802 TTTCAAT
1 TTTCAAT
40141809 CATTTGTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 11 0.46
21 7 0.29
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTCAATTAAGCTTTAGTT
Found at i:40142728 original size:7 final size:6
Alignment explanation
Indices: 40142708--40142739 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
40142698 ACGATTTTTA
*
40142708 TTTATT TTTATT TTTATT TTTAAT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TT
40142740 GGTTTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:40145574 original size:47 final size:47
Alignment explanation
Indices: 40145522--40146070 Score: 882
Period size: 47 Copynumber: 11.6 Consensus size: 47
40145512 GATAATTGTG
* *
40145522 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40145569 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40145616 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40145663 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40145712 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40145759 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40145806 ATGTGAAAGTGTATATTTTTGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATA--TATGTGATAAGGCCTAATGGCCGATGTGATGA
40145855 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40145904 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40145951 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
40145998 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40146045 ATGTGAAAGCGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
40146071 TCCCGAAGGG
Statistics
Matches: 469, Mismatches: 27, Indels: 12
0.92 0.05 0.02
Matches are distributed among these distances:
47 338 0.72
49 127 0.27
51 4 0.01
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:40145685 original size:143 final size:143
Alignment explanation
Indices: 40145522--40146070 Score: 917
Period size: 143 Copynumber: 3.9 Consensus size: 143
40145512 GATAATTGTG
40145522 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
40145585 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATG
66 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATG
40145650 GCCAATGTGATGA
131 GCCAATGTGATGA
40145663 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
40145728 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATG
66 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATG
40145793 GCCAATGTGATGA
131 GCCAATGTGATGA
* *
40145806 ATGTGAAAGTGTATATTTTTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
*
40145871 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
64 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
* *
40145936 TAGCCGATGTGATGA
129 TGGCCAATGTGATGA
*
40145951 ATGTGAAAGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * * * * * * * *
40146014 ATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGCGTATAAATGTGATAAG
66 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
40146071 TCCCGAAGGG
Statistics
Matches: 387, Mismatches: 17, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
141 58 0.15
142 2 0.01
143 236 0.61
145 91 0.24
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (143 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATG
GCCAATGTGATGA
Found at i:40148987 original size:18 final size:18
Alignment explanation
Indices: 40148950--40148987 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40148940 AATCTCTTGA
*
40148950 ATTTTATTTCTTTATGTT
1 ATTTTATTTCTTTATATT
40148968 ATTTTATTT-TTTATTATT
1 ATTTTATTTCTTTA-TATT
40148986 AT
1 AT
40148988 AAAAACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTTATTTCTTTATATT
Found at i:40150042 original size:94 final size:94
Alignment explanation
Indices: 40149881--40150068 Score: 279
Period size: 94 Copynumber: 2.0 Consensus size: 94
40149871 TAGTTCAGAT
*
40149881 ACAAAATTTCTATTATGGGTTAGACAATCAAAATAGACGAAAATTTGACATTATGACTAGGGAAG
1 ACAAAATTTCTATTATGGGTTAGACAATCAAAATAGACGAAAATTCGACATTATGACTAGGGAAG
**
40149946 TATTTGGACTAAAACCCAGGAGAAAGTTA
66 TATTTGGAAGAAAACCCAGGAGAAAGTTA
* * * * *
40149975 ACAAATTTTCTTTTATGGGTTGGACAATCAAAATAGATG-GAATTCGACATTATGACTAAGGGAA
1 ACAAAATTTCTATTATGGGTTAGACAATCAAAATAGACGAAAATTCGACATTATGACT-AGGGAA
*
40150039 GTATTTGGAAGAAAACCCAGGAGGAAGTTA
65 GTATTTGGAAGAAAACCCAGGAGAAAGTTA
40150069 TGGAAATATT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
93 16 0.19
94 68 0.81
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.27
Consensus pattern (94 bp):
ACAAAATTTCTATTATGGGTTAGACAATCAAAATAGACGAAAATTCGACATTATGACTAGGGAAG
TATTTGGAAGAAAACCCAGGAGAAAGTTA
Found at i:40153278 original size:21 final size:21
Alignment explanation
Indices: 40153238--40153278 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40153228 ACCTGCTCTC
* **
40153238 GATGTCGCGACATCGCTGAGG
1 GATGACGCGACATCAATGAGG
40153259 GATGACGCGACATCAATGAG
1 GATGACGCGACATCAATGAG
40153279 TAACTCTGTT
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:0.27, C:0.22, G:0.34, T:0.17
Consensus pattern (21 bp):
GATGACGCGACATCAATGAGG
Found at i:40154834 original size:50 final size:50
Alignment explanation
Indices: 40154724--40154972 Score: 182
Period size: 50 Copynumber: 4.9 Consensus size: 50
40154714 ACATTTGGGT
* * * *
40154724 GATGAGA--TCCCATGTAAGACCATGTTTGGAACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGA
* *
40154775 GATTATGAGAGGTCCCATGTAAGAACGTGTCTGGGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
** * * * *
40154828 GATGAGAGGTCCCCCGTAAGACCATGTCTAGGACAAGGCATGGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* ** * **
40154878 TATGAGAACTCCCATGTAAGACCATATCTGGGATGTGGCGTTGGCA--GTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-A
* * * ** * *
40154927 CAAGAAACATCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
40154973 TGTTATTATC
Statistics
Matches: 156, Mismatches: 36, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
48 1 0.01
49 37 0.24
50 75 0.48
51 1 0.01
53 3 0.02
54 6 0.04
55 1 0.01
56 32 0.21
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
Found at i:40159107 original size:50 final size:50
Alignment explanation
Indices: 40159032--40159200 Score: 257
Period size: 50 Copynumber: 3.4 Consensus size: 50
40159022 TACACGGAAT
* * *
40159032 CACTTATCATTTATCTCTTGTCACTGATCAGATAAGTGTTGCTAAGCTAC
1 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTAC
* *
40159082 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAGGTTAC
1 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTAC
* *
40159132 CACTTAATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCGAAGCTAC
1 CACTT-ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTAC
*
40159183 CACTTATCACTTGTCACT
1 CACTTATCACTTATCACT
40159201 GATCAGAAGT
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
50 63 0.58
51 46 0.42
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (50 bp):
CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTAC
Found at i:40159136 original size:43 final size:43
Alignment explanation
Indices: 40159089--40159207 Score: 139
Period size: 51 Copynumber: 2.6 Consensus size: 43
40159079 TACCACTTAT
* * *
40159089 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAGGTTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCGAAGCTAC
40159132 CACTTAATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCGAAGCTAC
1 CAC-T--T-A----TCACTTGTCACTGATCAGATAAGTGTAGCGAAGCTAC
40159183 CACTTATCACTTGTCACTGATCAGA
1 CACTTATCACTTGTCACTGATCAGA
40159208 AGTACTCAAC
Statistics
Matches: 65, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
43 22 0.34
44 1 0.02
46 1 0.02
47 2 0.03
48 1 0.02
50 1 0.02
51 37 0.57
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (43 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGTAGCGAAGCTAC
Found at i:40171668 original size:50 final size:50
Alignment explanation
Indices: 40171588--40171800 Score: 336
Period size: 50 Copynumber: 4.2 Consensus size: 50
40171578 TACACGGAAT
* * * * *
40171588 CACTTGTCACTTATCTCTTATCGCTAATCAGATAAGTGTAGCTAAGCTAC
1 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTAC
*
40171638 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTAC
*
40171688 CACTTAATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTAC
1 CACTT-ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTAC
* *
40171739 CACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCGAAGCTAC
1 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTAC
40171789 CACTTATCACTT
1 CACTTATCACTT
40171801 GTCATAGATC
Statistics
Matches: 153, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
50 105 0.69
51 48 0.31
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (50 bp):
CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTAC
Found at i:40171738 original size:101 final size:100
Alignment explanation
Indices: 40171614--40171804 Score: 346
Period size: 101 Copynumber: 1.9 Consensus size: 100
40171604 CTTATCGCTA
40171614 ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAG
1 ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAG
* *
40171679 CTAGGCTACCACTTAATCACTTGTCACTTGTCACTG
66 CGAAGCTACCACTT-ATCACTTGTCACTTGTCACTG
*
40171715 ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAG
1 ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAG
40171780 CGAAGCTACCACTTATCACTTGTCA
66 CGAAGCTACCACTTATCACTTGTCA
40171805 TAGATCAGAA
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
100 11 0.13
101 76 0.87
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (100 bp):
ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAG
CGAAGCTACCACTTATCACTTGTCACTTGTCACTG
Found at i:40171801 original size:50 final size:50
Alignment explanation
Indices: 40171614--40171804 Score: 346
Period size: 50 Copynumber: 3.8 Consensus size: 50
40171604 CTTATCGCTA
*
40171614 ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTATCACTTGTCACTG
1 ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTCACTTGTCACTG
*
40171664 ATCAGATAAGTGTAGCTAGGCTACCACTTAATCACTTGTCACTTGTCACTG
1 ATCAGATAAGTGTAGCTAAGCTACCACTT-ATCACTTGTCACTTGTCACTG
40171715 ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTCACTTGTCACTG
1 ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTCACTTGTCACTG
*
40171765 ATCAGATAAGTGTAGCGAAGCTACCACTTATCACTTGTCA
1 ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTCA
40171805 TAGATCAGAA
Statistics
Matches: 136, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
50 88 0.65
51 48 0.35
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (50 bp):
ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTCACTTGTCACTG
Found at i:40178439 original size:3 final size:3
Alignment explanation
Indices: 40178431--40178457 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40178421 AAACAAACCT
40178431 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
40178458 ACCAAATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:40180214 original size:131 final size:131
Alignment explanation
Indices: 40180072--40180364 Score: 462
Period size: 131 Copynumber: 2.2 Consensus size: 131
40180062 ATAATTTTTT
*
40180072 CAACCTACTCCACTGCTG-CTCAGGGAAATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTA
1 CAACCTACTCCACTGCTGAC-CAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTA
* * * *
40180136 GGGAAGATAAGATTCACCATCTTCGATCTGCTCTACTATTGCTTAAGAAGATGAGATCTGTAATT
65 GGGAAGACAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAAGAAGATGAGATCAGTAATT
40180201 TC
130 TC
* *
40180203 CAACCTACTCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCTTGG
1 CAACCTACTCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTAG
* * * *
40180268 GGAAGACAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATGAGATCAGTAATTT
66 GGAAGACAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAAGAAGATGAGATCAGTAATTT
40180333 C
131 C
*
40180334 CAACCTATTCCACTGCTGACCAGGGAGATAG
1 CAACCTACTCCACTGCTGACCAGGGAGATAG
40180365 AATTACTGGC
Statistics
Matches: 149, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
131 148 0.99
132 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (131 bp):
CAACCTACTCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTAG
GGAAGACAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAAGAAGATGAGATCAGTAATTT
C
Found at i:40180375 original size:131 final size:132
Alignment explanation
Indices: 40180070--40180946 Score: 807
Period size: 132 Copynumber: 6.7 Consensus size: 132
40180060 CTATAATTTT
* * * * * *
40180070 TTCAACCTACTCCACTGCTG-CTCAGGGAAATAGGACTT-GTGGCTTAAATCTGCTTCCC-T-AC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATA-GAATTACTGGCTTAAATGTACTTCCCGTAAC
* * * * * * * * *
40180131 TC-CTAGGGAAGATAAGATTCACCATCTTCGATCTGCTCTACTATTGCTTAAGAAGATGAGATCT
64 TCAC-AGGG-AGGTAAAATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCA
40180195 GTAAT-
127 GTAATC
* * * * *
40180200 TTCCAACCTACTCCACTGCTGACCAGGGAGATAGGACTT-GTGGCTTAAATCTGCTTCCC-T-AC
1 TT-CAACCTATTCCACTGCTGACCAGGGAGATA-GAATTACTGGCTTAAATGTACTTCCCGTAAC
*** * * *
40180262 TCTTGGGGAAG-ACAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATGAGATCA
64 TCACAGGGAGGTA-AA-ATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCA
40180326 GTAAT-
127 GTAATC
* *
40180331 TTCCAACCTATTCCACTGCTGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACCGTAAC
1 TT-CAACCTATTCCACTGCTGACCAGGGAGATAGAATTACTGGCTTAAATGTACTTC-CCGTAAC
* * *
40180396 T-TCAGGGAGGTAAAA-TCTGCCATCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTA
64 TCACAGGGAGGTAAAATTC-GCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC-A
40180459 -TAATC
127 GTAATC
* * * * *
40180464 TTCAATCTATTCCGCTGCTG-CCTAGGAAGATAGAA-TATTGGCTTTAATGTAC-TCCACTGTAA
1 TTCAACCTATTCCACTGCTGACC-AGGGAGATAGAATTACTGGCTTAAATGTACTTCC-C-GTAA
*
40180526 C-CACAGGGAGGTAAAA-TCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
63 CTCACAGGGAGGTAAAATTC-GCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC-
40180589 A-TAATC
126 AGTAATC
* ** *
40180595 TTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACTGGCTTTAATGTAC-TCCACTGTAAC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGAATTACTGGCTTAAATGTACTTCC-C-GTAAC
* *
40180659 -CACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
64 TCACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCAGT
40180723 AATC
129 AATC
* * ** * * *
40180727 TTCAATCTATTCCACTACCAACTAGGGAGATAGAATTACTAGCTTCAATGTAC-TCCACTGTAAC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGAATTACTGGCTTAAATGTACTTCC-C-GTAAC
* * * * *
40180791 -CACAGGTAGGTAAAATCCGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
64 TCACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCAGT
40180855 AATC
129 AATC
* * ** * * *
40180859 TTTAATCTATTCCACTGCCAACCAGAGAGATAGAATTACTAGCTTCAATGTAC-TCCACTGTAAC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGAATTACTGGCTTAAATGTACTTCC-C-GTAAC
40180923 -CACAGGGAGGTAAAATTCGCCATC
64 TCACAGGGAGGTAAAATTCGCCATC
40180947 AACCTGTTCC
Statistics
Matches: 669, Mismatches: 57, Indels: 40
0.87 0.07 0.05
Matches are distributed among these distances:
129 2 0.00
130 10 0.01
131 269 0.40
132 371 0.55
133 13 0.02
134 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGAATTACTGGCTTAAATGTACTTCCCGTAACTC
ACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCAGTAA
TC
Found at i:40180447 original size:44 final size:44
Alignment explanation
Indices: 40180399--40180874 Score: 134
Period size: 44 Copynumber: 10.8 Consensus size: 44
40180389 CCGTAACTTC
* *
40180399 AGGGAGGTAAAATCTGCCATCTTTGATCTACTCCACTACTGCTT
1 AGGGAGATAAAATCTGCCATCTTTAATCTACTCCACTACTGCTT
* *** * * * * *
40180443 AGGGAGATAAGATCTATAATCTTCAATCTATTCCGCTGCTGCCT
1 AGGGAGATAAAATCTGCCATCTTTAATCTACTCCACTACTGCTT
* * * **
40180487 AGGAAGATAGAATAT-TG---GCTTTAATGTACTCCACTGTAAC--CAC
1 AGGGAGATA-AA-ATCTGCCATCTTTAATCTACTCCAC--T-ACTGCTT
* * *
40180530 AGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTT
1 AGGGAGATAAAATCTGCCATCTTTAATCTACTCCACTACTGCTT
* *** * * * ** *
40180574 AGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCAAC-C
1 AGGGAGATAAAATCTGCCATCTTTAATCTACTCCACT-ACTGCTT
* * *** * **
40180618 AGGGAGATAGAAT-TACTGGCTTTAATGTACTCCACTGTAAC--CAC
1 AGGGAGATAAAATCTGCCATCTTTAATCTACTCCAC--T-ACTGCTT
* * ** *
40180662 AGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAAATCTGCCATCTTTAATCTACTCCACTACTGCTT
* ** * * **
40180706 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACCAAC-T
1 AGGGAGATAAAATCTGCCATCTTTAATCTACTCCACTA-CTGCTT
* * * * * * **
40180750 AGGGAGATAGAAT-TACTAGCTTCAATGTACTCCACTGTAAC--CAC
1 AGGGAGATAAAATCTGCCATCTTTAATCTACTCCAC--T-ACTGCTT
* * * * * *
40180794 AGGTAGGTAAAATCCGTCATCTTTGATCTGCTCCACTACTGCTT
1 AGGGAGATAAAATCTGCCATCTTTAATCTACTCCACTACTGCTT
* ** *
40180838 AGGGAGATAAGATCTGTAATCTTTAATCTATTCCACT
1 AGGGAGATAAAATCTGCCATCTTTAATCTACTCCACT
40180875 GCCAACCAGA
Statistics
Matches: 298, Mismatches: 108, Indels: 52
0.65 0.24 0.11
Matches are distributed among these distances:
41 2 0.01
42 22 0.07
43 44 0.15
44 177 0.59
45 50 0.17
46 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
AGGGAGATAAAATCTGCCATCTTTAATCTACTCCACTACTGCTT
Found at i:40180474 original size:132 final size:132
Alignment explanation
Indices: 40180286--40180946 Score: 990
Period size: 132 Copynumber: 5.0 Consensus size: 132
40180276 AGATTCGCCG
* * *
40180286 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATGAGATC-AGTAAT-TTCCAACCTATTCCACTG
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTA-TAATCTT-CAATCTATTCCACTG
** * **
40180349 CTGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACCGTAACTTCAGGGAGGTAAAATCT
64 CCAACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT
40180414 GCCA
129 GCCA
* *
40180418 TCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCGCTG-C
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCC
** * * *
40180482 TGCCTAGGAAGATAGAA-TATTGGCTTTAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTG
66 AACC-AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTG
40180546 CCA
130 CCA
40180549 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCC
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCC
* *
40180614 AACCAGGGAGATAGAATTACTGGCTTTAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGC
66 AACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGC
40180679 CA
131 CA
* * *
40180681 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACC
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCC
* * * * *
40180746 AACTAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGTAGGTAAAATCCGT
66 AACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGC
40180811 CA
131 CA
* *
40180813 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCC
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCC
* *
40180878 AACCAGAGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT-TCG
66 AACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-G
40180942 CCA
130 CCA
40180945 TC
1 TC
40180947 AACCTGTTCC
Statistics
Matches: 486, Mismatches: 37, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
131 119 0.24
132 364 0.75
133 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCC
AACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGC
CA
Found at i:40180650 original size:263 final size:264
Alignment explanation
Indices: 40180281--40180946 Score: 1007
Period size: 263 Copynumber: 2.5 Consensus size: 264
40180271 AGACAAGATT
* * * *
40180281 CGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATGAGATC-AGTAAT-TTCCAACCTATTC
1 CGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTA-TAATCTT-CAATCTATTC
** * **
40180344 CACTGCTGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACCGTAACTTCAGGGAGGTAA
64 CACTGCCAACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAA
*
40180409 AATCTGCCATCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTAT
129 AATCTGCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTAT
* * *** * * *
40180474 TCCGCTGCTGCCTAGGAAGATAGAA-TATTGGCTTTAATGTACTCCACTGTAACCACAGGGAGGT
194 TCCACTACCAACTAGGAAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGT
40180538 AAAATC
259 AAAATC
*
40180544 TGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCA
1 CGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCA
*
40180609 CTGCCAACCAGGGAGATAGAATTACTGGCTTTAATGTACTCCACTGTAACCACAGGGAGGTAAAA
66 CTGCCAACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAA
* * *
40180674 TCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTC
131 TCTGCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTC
* *
40180739 CACTACCAACTAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGTAGGTAA
196 CACTACCAACTAGGAAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAA
40180804 AATC
261 AATC
* * *
40180808 CGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCA
1 CGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCA
* *
40180873 CTGCCAACCAGAGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAA
66 CTGCCAACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAA
40180938 T-TCGCCATC
131 TCT-GCCATC
40180947 AACCTGTTCC
Statistics
Matches: 366, Mismatches: 33, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
263 192 0.52
264 174 0.48
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (264 bp):
CGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCA
CTGCCAACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAA
TCTGCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTC
CACTACCAACTAGGAAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAA
AATC
Found at i:40181119 original size:87 final size:88
Alignment explanation
Indices: 40180947--40181120 Score: 244
Period size: 87 Copynumber: 2.0 Consensus size: 88
40180937 ATTCGCCATC
* *
40180947 AACCTGTTCCACTACAACCGAGGGAGGCAAGGTTGGTATCTTCGATCTGCTTTGCTACCAATGTA
1 AACCTGTTCCACTACAACCGAGGGAGGCAAGGTTGGTATCTTCGATCTGCTTCGCTACCAATGCA
40181012 GGAAGGCAAAATCTGCTATCTTT
66 GGAAGGCAAAATCTGCTATCTTT
* * ** *
40181035 AACCTGTTCCACTGCAACCGAGGGAGGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTCGATGC
1 AACCTGTTCCACTACAACCGAGGGAGGCAAGG-TTGGTATCTTCGATCTGCTTCGCTACCAATGC
* *
40181098 AGGAAGGCAAGATCTGTTATCTT
65 AGGAAGGCAAAATCTGCTATCTT
40181121 CACTGATCTA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
87 40 0.53
88 32 0.42
89 4 0.05
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.29
Consensus pattern (88 bp):
AACCTGTTCCACTACAACCGAGGGAGGCAAGGTTGGTATCTTCGATCTGCTTCGCTACCAATGCA
GGAAGGCAAAATCTGCTATCTTT
Found at i:40183271 original size:16 final size:16
Alignment explanation
Indices: 40183250--40183282 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40183240 CGCATTGGTC
*
40183250 TCTCCTTTTTTCTTTT
1 TCTCCTTTTTTATTTT
40183266 TCTCCTTTTTTATTTT
1 TCTCCTTTTTTATTTT
40183282 T
1 T
40183283 ATTTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TCTCCTTTTTTATTTT
Found at i:40183281 original size:6 final size:6
Alignment explanation
Indices: 40183272--40183378 Score: 67
Period size: 6 Copynumber: 17.8 Consensus size: 6
40183262 TTTTTCTCCT
* * * * * *
40183272 TTTTTA TTTTTA TTTTTA TTTTGA TTTTTCC TTTTTGC TTTTGA CTTTGA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT-A TTTTT-A TTTTTA TTTTTA
* * * *
40183322 TTTTTC TTTTT- TTTTT- CTTCT- TTTTTA TTTTTTA TTTTTA TTTTGA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA
*
40183368 TTTTGA TTTTT
1 TTTTTA TTTTT
40183379 TTATTGAATC
Statistics
Matches: 82, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
5 11 0.13
6 55 0.67
7 16 0.20
ACGTcount: A:0.10, C:0.07, G:0.06, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:40183344 original size:14 final size:13
Alignment explanation
Indices: 40183322--40183365 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
40183312 TTGACTTTGA
40183322 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
40183335 TTTCTTCTTTTTTAT
1 TTT-TTCTTTTTT-T
*
40183350 TTTTTATTTTTATT
1 TTTTTCTTTTT-TT
40183364 TT
1 TT
40183366 GATTTTGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 3 0.11
14 19 0.70
15 5 0.19
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:40184202 original size:25 final size:25
Alignment explanation
Indices: 40184149--40184208 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
40184139 AAGAAAGTCT
* *
40184149 AAAAGAATGAAAGAATAATTATTCC
1 AAAAGAATGAAAGAATAATTACTCA
*
40184174 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
40184199 AAAATGAATG
1 AAAA-GAATG
40184209 CAAATATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.10
25 22 0.73
26 5 0.17
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.22
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:40194240 original size:16 final size:16
Alignment explanation
Indices: 40194219--40194274 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
40194209 AATCGGATGT
40194219 GGAATTAATTAACTAA
1 GGAATTAATTAACTAA
* **
40194235 GGAATTAAGGTTTA-TGT
1 GGAATTAA--TTAACTAA
40194252 GGAATTAATTAACTAA
1 GGAATTAATTAACTAA
40194268 GGAATTA
1 GGAATTA
40194275 GGGTTTACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 3 0.10
16 16 0.52
17 9 0.29
18 3 0.10
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.34
Consensus pattern (16 bp):
GGAATTAATTAACTAA
Found at i:40194257 original size:33 final size:33
Alignment explanation
Indices: 40194215--40194281 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
40194205 TAACAATCGG
40194215 ATGTGGAATTAATTAACTAAGGAATTAAGGTTT
1 ATGTGGAATTAATTAACTAAGGAATTAAGGTTT
*
40194248 ATGTGGAATTAATTAACTAAGGAATTAGGGTTT
1 ATGTGGAATTAATTAACTAAGGAATTAAGGTTT
40194281 A
1 A
40194282 CTTTAGAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (33 bp):
ATGTGGAATTAATTAACTAAGGAATTAAGGTTT
Found at i:40205796 original size:6 final size:6
Alignment explanation
Indices: 40205785--40205829 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
40205775 CAATACACTA
*
40205785 ATACAT ATACAT ATACAT ATATAT ATACAT ATACAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATA
40205830 TGTGATTGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (6 bp):
ATACAT
Found at i:40205817 original size:24 final size:24
Alignment explanation
Indices: 40205785--40205830 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
40205775 CAATACACTA
40205785 ATACATATACATATACATATATAT
1 ATACATATACATATACATATATAT
40205809 ATACATATACATATACATATAT
1 ATACATATACATATACATATAT
40205831 GTGATTGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (24 bp):
ATACATATACATATACATATATAT
Found at i:40211258 original size:10 final size:10
Alignment explanation
Indices: 40211240--40211312 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
40211230 ATATAAGAAT
*
40211240 AATTATATTG
1 AATTATATTA
*
40211250 AATTTTATTA
1 AATTATATTA
40211260 AATTATA-T-
1 AATTATATTA
* *
40211268 ATTTTTATTA
1 AATTATATTA
*
40211278 AATTATATTT
1 AATTATATTA
40211288 AA-TA-A-T-
1 AATTATATTA
*
40211294 AATTATTTTA
1 AATTATATTA
40211304 AATTATATT
1 AATTATATT
40211313 TTATAGTATT
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
6 2 0.04
7 3 0.06
8 6 0.13
9 5 0.11
10 31 0.66
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (10 bp):
AATTATATTA
Found at i:40211286 original size:28 final size:27
Alignment explanation
Indices: 40211237--40211312 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 27
40211227 TTCATATAAG
* *
40211237 AATAATTA-TATTGAATTTTATTAAAT
1 AATAATTATTATTAAATTATATTAAAT
* * *
40211263 TATATATTTTTATTAAATTATATTTAAT
1 AATA-ATTATTATTAAATTATATTAAAT
40211291 AATAATTATT-TTAAATTATATT
1 AATAATTATTATTAAATTATATT
40211313 TTATAGTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
26 15 0.37
27 8 0.20
28 18 0.44
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
AATAATTATTATTAAATTATATTAAAT
Found at i:40211360 original size:59 final size:58
Alignment explanation
Indices: 40211190--40211360 Score: 161
Period size: 59 Copynumber: 2.9 Consensus size: 58
40211180 TAGATTATAT
* * * *
40211190 ATTAT-TTTTATAGATTATATAATATGATTTTAGTAAATTCATATAAGAATA-ATTAT
1 ATTATATTTTATAGATTATATATTATGATTTTAGTAAATTCATATAAAAATATTTTAA
* * * ** * * * *
40211246 ATTGA-ATTTTATTAAATTATATATTTTTATTAAATTATATTTA-ATAATAATTATTTTAA
1 ATT-ATATTTTA-TAGATTATATATTATGATTTTAGTAAATTCATATAA-AAATATTTTAA
40211305 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAAAATATTT
1 ATTATATTTTATAG-ATTATATATTATGATTTTAGTAAATTCATATAAAAATATTT
40211361 AATACTAGGA
Statistics
Matches: 85, Mismatches: 22, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
56 3 0.04
57 10 0.12
58 28 0.33
59 40 0.47
60 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (58 bp):
ATTATATTTTATAGATTATATATTATGATTTTAGTAAATTCATATAAAAATATTTTAA
Found at i:40211433 original size:117 final size:117
Alignment explanation
Indices: 40211189--40211434 Score: 292
Period size: 117 Copynumber: 2.1 Consensus size: 117
40211179 GTAGATTATA
* *
40211189 TATTATTTTTATAGATTATATAATATGATTTTAGTAAATTCATATAAGAATAATTATATTGAATT
1 TATTATTTTTATAGATTATATAATATGATTTTAGTAAATTCATATAAAAATAATTATATGGAATT
** * * *
40211254 TTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
66 TTATTAAATTATATATTAATAATAAATTATAGTTAATAATAATGA-TTTAAAT
* *
40211307 TA-TA-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAAAATATTTAATACTAGG
1 TATTATTTTTATAG-ATTATATAATATGATTTTAGTAAATTCATATAAAAATAATT-ATA-T-GG
40211370 AATTTTATTAAATTATAT-TTAATAAT-AATTAT-GTTAA-AAT-ATGA-TTAAAT
62 AATTTTATTAAATTATATATTAATAATAAATTATAGTTAATAATAATGATTTAAAT
40211420 TATTTATTATTTATA
1 TA-TTATT-TTTATA
40211435 TTAATAAACT
Statistics
Matches: 111, Mismatches: 9, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
113 8 0.07
115 5 0.05
116 12 0.11
117 50 0.45
118 11 0.10
119 6 0.05
120 19 0.17
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (117 bp):
TATTATTTTTATAGATTATATAATATGATTTTAGTAAATTCATATAAAAATAATTATATGGAATT
TTATTAAATTATATATTAATAATAAATTATAGTTAATAATAATGATTTAAAT
Found at i:40211579 original size:39 final size:41
Alignment explanation
Indices: 40211534--40211639 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
40211524 GTTACTTATG
* *
40211534 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
40211574 C-ATTACGCCTCTAATCCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTC---T--ATTCCATTCAACCAAACAAAAGAATTAC
*
40211619 CTATTACGCCACTATTCCATT
1 CTATTACGCCTCTATTCCATT
40211640 ACGCATCTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 9 0.16
40 1 0.02
41 8 0.14
42 1 0.02
43 1 0.02
44 23 0.41
45 4 0.07
46 9 0.16
ACGTcount: A:0.37, C:0.32, G:0.04, T:0.27
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:40211614 original size:44 final size:46
Alignment explanation
Indices: 40211547--40211639 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
40211537 TTACACCTCT
* *
40211547 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTAATCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCACTAATCC
*
40211591 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCACTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCACTAATCC
40211637 ATT
1 ATT
40211640 ACGCATCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.52
45 4 0.09
46 17 0.39
ACGTcount: A:0.39, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCACTAATCC
Found at i:40211642 original size:16 final size:16
Alignment explanation
Indices: 40211621--40211673 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
40211611 AGAATTACCT
40211621 ATTACGCCACTATTCC
1 ATTACGCCACTATTCC
40211637 ATTACG-CATCTATTCC
1 ATTACGCCA-CTATTCC
*
40211653 ATTACGCCTCTATTCC
1 ATTACGCCACTATTCC
40211669 ATTAC
1 ATTAC
40211674 AGCGAACCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
15 2 0.06
16 31 0.91
17 1 0.03
ACGTcount: A:0.25, C:0.34, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCACTATTCC
Found at i:40212134 original size:41 final size:40
Alignment explanation
Indices: 40212080--40212216 Score: 131
Period size: 41 Copynumber: 3.5 Consensus size: 40
40212070 CGACTTCAAG
*
40212080 TCGAAGAGACACTGGGTGTCAATTTACTACTTCGGATTAAT
1 TCGATGAGACACTGGGTGTCAATTTACTACTTCGGATT-AT
* *
40212121 TCGATGAGGCACTGGGTGCCAATTTACT--TT--GATT-T
1 TCGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAT
* * *
40212156 AGCTGATGAGACACTGGGTGTCAATTTATTTACTTCGAATTAT
1 -TC-GATGAGACACTGGGTGTCAATTTA-CTACTTCGGATTAT
* *
40212199 CCGATGAGGCACTGGGTG
1 TCGATGAGACACTGGGTG
40212217 CCAAATTGGT
Statistics
Matches: 78, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
35 1 0.01
36 1 0.01
37 26 0.33
38 1 0.01
39 2 0.03
40 2 0.03
41 40 0.51
42 4 0.05
43 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAT
Found at i:40218903 original size:85 final size:85
Alignment explanation
Indices: 40218805--40218979 Score: 269
Period size: 85 Copynumber: 2.1 Consensus size: 85
40218795 GACTAAATTC
* * *
40218805 GAATTTAGGCAAATAATGAGTAAATTTTTTTTAAAATATTAAATATAAGATTGAATTGTGTTGTA
1 GAATTTAGGCAAATAATGAGTAAAATTTTTTTAAAATATTAAATATAAGATTGAATTGAGTTATA
*
40218870 TTGATGAATTTTAATTGTTT
66 TTGATGAATTTTAATTATTT
* ** *
40218890 GAATTTGGGCAAATGTTGAGTAAAATTTTTTTGAAATATTAAATATAAGATTGAATTGAGTTATA
1 GAATTTAGGCAAATAATGAGTAAAATTTTTTTAAAATATTAAATATAAGATTGAATTGAGTTATA
40218955 TTGATGAATTTTAATTATTT
66 TTGATGAATTTTAATTATTT
*
40218975 TAATT
1 GAATT
40218980 CCATAGCTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.46
Consensus pattern (85 bp):
GAATTTAGGCAAATAATGAGTAAAATTTTTTTAAAATATTAAATATAAGATTGAATTGAGTTATA
TTGATGAATTTTAATTATTT
Found at i:40224348 original size:37 final size:36
Alignment explanation
Indices: 40224288--40224381 Score: 116
Period size: 37 Copynumber: 2.6 Consensus size: 36
40224278 AGTACATAAG
* * *
40224288 TAATCCAACCAAAACACGCCAAATTCTCATGAGAGC
1 TAATCCAACCATAACACGCCAAATGCTCATAAGAGC
* *
40224324 TAATCCAACCGATAACACGTCAAATGCTCATAAGAGT
1 TAATCCAACC-ATAACACGCCAAATGCTCATAAGAGC
*
40224361 TAATCCAACTAATAACACGCC
1 TAATCCAAC-CATAACACGCC
40224382 TCGACACTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 10 0.20
37 39 0.80
ACGTcount: A:0.41, C:0.29, G:0.11, T:0.19
Consensus pattern (36 bp):
TAATCCAACCATAACACGCCAAATGCTCATAAGAGC
Found at i:40225581 original size:39 final size:41
Alignment explanation
Indices: 40225508--40225628 Score: 124
Period size: 39 Copynumber: 3.0 Consensus size: 41
40225498 TTTTGAGTTT
* *
40225508 TCGGGGCTTTAGT-GGCGTTTTTCAAAAAGCGTCGCTAATGCA
1 TCGGGGCTTTA-TCGGCATTTTT-GAAAAGCGTCGCTAATGCA
* *
40225550 T-GGGGCTTTATCGGC-TTTTTGAAAAGTGTCGCTAATG-T
1 TCGGGGCTTTATCGGCATTTTTGAAAAGCGTCGCTAATGCA
* * *
40225588 TCGAGGCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGC
1 TCGGGGCTTTATCGGCATTTTTGAA-AAGCGTCGCTAATGC
40225629 TCAGTGCTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
38 1 0.01
39 27 0.40
40 14 0.21
41 24 0.36
42 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (41 bp):
TCGGGGCTTTATCGGCATTTTTGAAAAGCGTCGCTAATGCA
Found at i:40225627 original size:41 final size:41
Alignment explanation
Indices: 40225512--40225731 Score: 193
Period size: 41 Copynumber: 5.4 Consensus size: 41
40225502 GAGTTTTCGG
* * * *
40225512 GGCTTTAGTGGCGTTTTTCAAAAAGCGTCGCTAATGCAT-GG
1 GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC-TCGA
* * * *
40225553 GGCTTTATCGGC-TTTTTG-AAAAGTGTCGCTAATGTTCGA
1 GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGA
* *
40225592 GGCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGCTC-A
1 GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGA
* * **
40225632 GTGCTTTAGCAGTGTTTTTGAAGAAA-CGCCGCTAATGCTATA
1 G-GCTTTAGCGGCGTTTTTGAA-AAAGCGCCGCTAATGCTCGA
** * *
40225674 -TTTTTAACGGCGTTTTTGAAAAAGTGCCGCTAATGCTCG-
1 GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGA
40225713 GGTCTTTAGCGGCGTTTTT
1 GG-CTTTAGCGGCGTTTTT
40225732 TAATGCTCAG
Statistics
Matches: 143, Mismatches: 27, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
38 1 0.01
39 30 0.21
40 40 0.28
41 69 0.48
42 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (41 bp):
GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGA
Found at i:40226183 original size:15 final size:14
Alignment explanation
Indices: 40226163--40226200 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
40226153 CCTATCTTAA
40226163 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
40226177 GGGTTTAGGGATTAT
1 -GGTTTATGGATTAT
40226192 GGTTTATGG
1 GGTTTATGG
40226201 TTTAAGGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:40226216 original size:21 final size:22
Alignment explanation
Indices: 40226192--40226258 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
40226182 TAGGGATTAT
*
40226192 GGTTTATGGTTTAAGGG-TCGG
1 GGTTTATGGTTTAAGGGTTAGG
* *
40226213 GGTTTAAGGTTTAGGGGTTAGG
1 GGTTTATGGTTTAAGGGTTAGG
* * *
40226235 GGTTTATGATTTATGGTTTAGG
1 GGTTTATGGTTTAAGGGTTAGG
40226257 GG
1 GG
40226259 ATAGGGGTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 15 0.39
22 23 0.61
ACGTcount: A:0.16, C:0.01, G:0.42, T:0.40
Consensus pattern (22 bp):
GGTTTATGGTTTAAGGGTTAGG
Found at i:40226253 original size:36 final size:36
Alignment explanation
Indices: 40226213--40226283 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
40226203 TAAGGGTCGG
** *
40226213 GGTTTAAGGTTTAGGGGTTAGGGGTTTATGATTTAT
1 GGTTTAAGGGATAGGGGTTAGGGGTTTACGATTTAT
*
40226249 GGTTTAGGGGATAGGGGTTAGGGGTTTACGATTTA
1 GGTTTAAGGGATAGGGGTTAGGGGTTTACGATTTA
40226284 GATTAATTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.20, C:0.01, G:0.39, T:0.39
Consensus pattern (36 bp):
GGTTTAAGGGATAGGGGTTAGGGGTTTACGATTTAT
Found at i:40226284 original size:29 final size:30
Alignment explanation
Indices: 40226211--40226276 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
40226201 TTTAAGGGTC
*
40226211 GGGGTTTAAGGTTTAGGGGTTAGGGGTTTA
1 GGGGTTTAAGGTTTAGGGGATAGGGGTTTA
* * *
40226241 -TGATTTATGGTTTAGGGGATAGGGG-TTA
1 GGGGTTTAAGGTTTAGGGGATAGGGGTTTA
40226269 GGGGTTTA
1 GGGGTTTA
40226277 CGATTTAGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.18, C:0.00, G:0.44, T:0.38
Consensus pattern (30 bp):
GGGGTTTAAGGTTTAGGGGATAGGGGTTTA
Found at i:40226452 original size:14 final size:15
Alignment explanation
Indices: 40226418--40226452 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
40226408 CCTATCTTAA
40226418 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
40226433 GGTTTAGGGATTAT-
1 GGTTTAGGGATTATG
40226447 GGTTTA
1 GGTTTA
40226453 TGGTTTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:40226509 original size:7 final size:7
Alignment explanation
Indices: 40226418--40226539 Score: 77
Period size: 7 Copynumber: 17.0 Consensus size: 7
40226408 CCTATCTTAA
40226418 GGTTTAG
1 GGTTTAG
*
40226425 GGATTATG
1 GGTTTA-G
40226433 GGTTTAG
1 GGTTTAG
* *
40226440 GGATTAT
1 GGTTTAG
*
40226447 GGTTTAT
1 GGTTTAG
40226454 GGTTTAAG
1 GGTTT-AG
*
40226462 GG-TTGG
1 GGTTTAG
*
40226468 GGTTTAA
1 GGTTTAG
*
40226475 GATTTAAG
1 GGTTT-AG
40226483 GG-TTAG
1 GGTTTAG
*
40226489 GAGTTTAT
1 G-GTTTAG
*
40226497 GATTTAG
1 GGTTTAG
40226504 GGTTTAG
1 GGTTTAG
*
40226511 GGATTAGG
1 GGTTTA-G
* *
40226519 GGTTAAA
1 GGTTTAG
40226526 GGTTTAG
1 GGTTTAG
40226533 GGTTTAG
1 GGTTTAG
40226540 ATTAATTAGT
Statistics
Matches: 86, Mismatches: 22, Indels: 14
0.70 0.18 0.11
Matches are distributed among these distances:
6 6 0.07
7 60 0.70
8 20 0.23
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:40226509 original size:29 final size:30
Alignment explanation
Indices: 40226477--40226538 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
40226467 GGGTTTAAGA
* *
40226477 TTTAAGGG-TTAGGAGTTTATGATTTAGGG
1 TTTAAGGGATTAGGAGTTAAAGATTTAGGG
* *
40226506 TTT-AGGGATTAGGGGTTAAAGGTTTAGGG
1 TTTAAGGGATTAGGAGTTAAAGATTTAGGG
40226535 TTTA
1 TTTA
40226539 GATTAATTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.40
Consensus pattern (30 bp):
TTTAAGGGATTAGGAGTTAAAGATTTAGGG
Found at i:40226548 original size:255 final size:257
Alignment explanation
Indices: 40226032--40226626 Score: 953
Period size: 255 Copynumber: 2.3 Consensus size: 257
40226022 CATTACTGAT
*
40226032 TGTTTTTTAATTTATATATTAAATAGTTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAA
1 TGTTTTTTAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAA
40226097 AATATTAAATTAATTATCATTATAGTTTAGGGTTTAAGGTTTAAGGTTTAGGAGTACCTATCTTA
66 AATATTAAATTAATTATCATTATAGTTTA-GG--T--GGTTTAAGGTTTAGGAGTACCTATCTTA
* * *
40226162 AGGTTTATGGATTATGGGTTTAGGGATTATGGTTTATGGTTTAAGGGTCGGGGTTTAAGGTTTAG
126 AGGTTTAGGGATTATGGGTTTAGGGATTATGGTTTATGGTTTAAGGGTCGGGGTTTAAGATTTAA
* * **
40226227 GGGTTAGGGGTTTATGATTTATGGTTTAGGGGATAGGGGTTAGGGGTTTACGATTTAGATTAATT
191 GGGTTAGGAGTTTATGATTTAGGGTTTAGGGGATAGGGGTTAAAGGTTTACGATTTAGATTAATT
40226292 AG
256 AG
40226294 TGTTTTTTAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAA
1 TGTTTTTTAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAA
*
40226359 AATATTGAATTAATTATCATTATAGTTTA-G-GGTTTAAGGTTTAGGAGTACCTATCTTAAGGTT
66 AATATTAAATTAATTATCATTATAGTTTAGGTGGTTTAAGGTTTAGGAGTACCTATCTTAAGGTT
*
40226422 TAGGGATTATGGGTTTAGGGATTATGGTTTATGGTTTAAGGGTTGGGGTTTAAGATTTAAGGGTT
131 TAGGGATTATGGGTTTAGGGATTATGGTTTATGGTTTAAGGGTCGGGGTTTAAGATTTAAGGGTT
* *
40226487 AGGAGTTTATGATTTAGGGTTTA-GGGATTAGGGGTTAAAGGTTTAGGGTTTAGATTAATTAG
196 AGGAGTTTATGATTTAGGGTTTAGGGGA-TAGGGGTTAAAGGTTTACGATTTAGATTAATTAG
* * * *
40226549 TGTTTTTTAATTTATATATTAAATAATTTCTTATATAATTGTAGAAGAGATAATATTAATTTTAT
1 TGTTTTTTAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAA
*
40226614 TATATTAACATTA
66 AATATTAA-ATTA
40226627 TGACTATAGT
Statistics
Matches: 313, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
254 4 0.01
255 212 0.68
256 4 0.01
260 1 0.00
262 92 0.29
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (257 bp):
TGTTTTTTAATTTATATATTAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAA
AATATTAAATTAATTATCATTATAGTTTAGGTGGTTTAAGGTTTAGGAGTACCTATCTTAAGGTT
TAGGGATTATGGGTTTAGGGATTATGGTTTATGGTTTAAGGGTCGGGGTTTAAGATTTAAGGGTT
AGGAGTTTATGATTTAGGGTTTAGGGGATAGGGGTTAAAGGTTTACGATTTAGATTAATTAG
Found at i:40228237 original size:48 final size:48
Alignment explanation
Indices: 40228177--40228274 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
40228167 ACTAATAAAC
40228177 ACCAGTTACTTTAAATTTTCATGAACCCATGGTATCATAATAGAGCGT
1 ACCAGTTACTTTAAATTTTCATGAACCCATGGTATCATAATAGAGCGT
40228225 ACCAGTTACTTTAAATTTTCATGAACCCATGGTATCATAATAGAGCGT
1 ACCAGTTACTTTAAATTTTCATGAACCCATGGTATCATAATAGAGCGT
40228273 AC
1 AC
40228275 ATTCTGTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (48 bp):
ACCAGTTACTTTAAATTTTCATGAACCCATGGTATCATAATAGAGCGT
Found at i:40230836 original size:43 final size:43
Alignment explanation
Indices: 40230789--40230917 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 43
40230779 GTTTGCGATA
* *
40230789 AAAAGTGCTGCTAAAAGTCATGTTTTTTAGCGGTATTTGTGAT
1 AAAAGTGCTGCTAAAAGTCATGTTTTTTAGCGGCATTTGTGAC
* *
40230832 AAAAGTGCCGCT-AAAG----GTTTTTTAGTGGCATTTGTGAC
1 AAAAGTGCTGCTAAAAGTCATGTTTTTTAGCGGCATTTGTGAC
* * ***
40230870 AAAAGCG-TCGCTAAAGGTCATGACATTTAGCGGCATTTGTGAC
1 AAAAGTGCT-GCTAAAAGTCATGTTTTTTAGCGGCATTTGTGAC
40230913 AAAAG
1 AAAAG
40230918 CGCCATTAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
38 28 0.41
39 3 0.04
42 4 0.06
43 34 0.49
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (43 bp):
AAAAGTGCTGCTAAAAGTCATGTTTTTTAGCGGCATTTGTGAC
Found at i:40230865 original size:38 final size:38
Alignment explanation
Indices: 40230810--40230930 Score: 125
Period size: 38 Copynumber: 3.1 Consensus size: 38
40230800 TAAAAGTCAT
* * *
40230810 GTTTTTTAGCGGTATTTGTGATAAAAGTGCCGCTAAAG
1 GTTTTTTAGCGGCATTTGTGACAAAAGCGCCGCTAAAG
* *
40230848 GTTTTTTAGTGGCATTTGTGACAAAAGCGTCGCTAAAG
1 GTTTTTTAGCGGCATTTGTGACAAAAGCGCCGCTAAAG
* **
40230886 GTCATGACATTTAGCGGCATTTGTGACAAAAGCGCCATTAAAG
1 GT--T---TTTTAGCGGCATTTGTGACAAAAGCGCCGCTAAAG
40230929 GT
1 GT
40230931 CATGATCTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
38 35 0.51
40 1 0.01
43 32 0.47
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (38 bp):
GTTTTTTAGCGGCATTTGTGACAAAAGCGCCGCTAAAG
Found at i:40230918 original size:43 final size:42
Alignment explanation
Indices: 40230814--40231065 Score: 172
Period size: 43 Copynumber: 6.2 Consensus size: 42
40230804 AGTCATGTTT
* * * *
40230814 TTTAGCGGTATTTGTGATAAAAGTGCCGCTAAAGGT--T--T
1 TTTAGCGGCATTTGTGACAAAAGCGCCGCTAAAGGTCATGAC
* *
40230852 TTTAGTGGCATTTGTGACAAAAGCGTCGCTAAAGGTCATGAC
1 TTTAGCGGCATTTGTGACAAAAGCGCCGCTAAAGGTCATGAC
**
40230894 ATTTAGCGGCATTTGTGACAAAAGCGCCATTAAAGGTCATGATC
1 -TTTAGCGGCATTTGTGACAAAAGCGCCGCTAAAGGTCATGA-C
* *
40230938 TTTAGCGGC----GT-----TA-CGCTGCTAAAGGTCATGATC
1 TTTAGCGGCATTTGTGACAAAAGCGCCGCTAAAGGTCATGA-C
* * * * * *
40230971 TTTAGCGGCGTTTGTGATAGAAGCGCCACTAAAGGCCATGATT
1 TTTAGCGGCATTTGTGACAAAAGCGCCGCTAAAGGTCATGA-C
* * * **
40231014 TTTAGCAGCATTTGTGATAAAAGCGCAGCTAAAGACCATGGAC
1 TTTAGCGGCATTTGTGACAAAAGCGCCGCTAAAGGTCAT-GAC
40231057 TTTAGCGGC
1 TTTAGCGGC
40231066 GTTGTCTATA
Statistics
Matches: 170, Mismatches: 27, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
33 26 0.15
34 1 0.01
37 2 0.01
38 31 0.18
39 2 0.01
40 1 0.01
42 1 0.01
43 103 0.61
44 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (42 bp):
TTTAGCGGCATTTGTGACAAAAGCGCCGCTAAAGGTCATGAC
Found at i:40230985 original size:76 final size:76
Alignment explanation
Indices: 40230879--40231019 Score: 212
Period size: 76 Copynumber: 1.9 Consensus size: 76
40230869 CAAAAGCGTC
* *
40230879 GCTAAAGGTCATGACATTTAGCGGCATTTGTGACAAAAGCGCCATTAAAGGTCATGATCTTTAGC
1 GCTAAAGGTCATGACATTTAGCGGCATTTGTGACAAAAGCGCCACTAAAGGCCATGATCTTTAGC
40230944 GGCGTTACGCT
66 GGCGTTACGCT
* * * *
40230955 GCTAAAGGTCATGATC-TTTAGCGGCGTTTGTGATAGAAGCGCCACTAAAGGCCATGATTTTTAG
1 GCTAAAGGTCATGA-CATTTAGCGGCATTTGTGACAAAAGCGCCACTAAAGGCCATGATCTTTAG
40231019 C
65 C
40231020 AGCATTTGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
76 57 0.98
77 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (76 bp):
GCTAAAGGTCATGACATTTAGCGGCATTTGTGACAAAAGCGCCACTAAAGGCCATGATCTTTAGC
GGCGTTACGCT
Found at i:40231063 original size:119 final size:119
Alignment explanation
Indices: 40230852--40231068 Score: 276
Period size: 119 Copynumber: 1.8 Consensus size: 119
40230842 CTAAAGGTTT
* * * * *
40230852 TTTAGTGGCATTTGTGACAAAAGCGTCGCTAAAGGTCATGACATTTAGCGGCATTTGTGACAAAA
1 TTTAGCGGCATTTGTGACAAAAGCGCCACTAAAGGCCATGACATTTAGCAGCATTTGTGACAAAA
* **
40230917 GCGCCATTAAAGGTCATGATCTTTAGCGGCGTTACGCTGCTAAAGGTCATGATC
66 GCGCCACTAAAGACCATGATCTTTAGCGGCGTTACGCTGCTAAAGGTCATGATC
* * * ** *
40230971 TTTAGCGGCGTTTGTGATAGAAGCGCCACTAAAGGCCATGATTTTTAGCAGCATTTGTGATAAAA
1 TTTAGCGGCATTTGTGACAAAAGCGCCACTAAAGGCCATGACATTTAGCAGCATTTGTGACAAAA
40231036 GCG-CAGCTAAAGACCATGGA-CTTTAGCGGCGTT
66 GCGCCA-CTAAAGACCAT-GATCTTTAGCGGCGTT
40231069 GTCTATAGCG
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
118 2 0.02
119 78 0.95
120 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (119 bp):
TTTAGCGGCATTTGTGACAAAAGCGCCACTAAAGGCCATGACATTTAGCAGCATTTGTGACAAAA
GCGCCACTAAAGACCATGATCTTTAGCGGCGTTACGCTGCTAAAGGTCATGATC
Found at i:40234103 original size:50 final size:50
Alignment explanation
Indices: 40234014--40234198 Score: 239
Period size: 50 Copynumber: 3.7 Consensus size: 50
40234004 TTATGAGAAC
*
40234014 CCCCATGTAAGACCAT-TCTGGGACATGACGTTGGCACCGAGATGAGAGGT
1 CCCC-TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
* *
40234064 CCCCTGTAAGACCATGTTTGGAACATGGCGTTGGCACCGAGATGAGAGGT
1 CCCCTGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
* * * **
40234114 CCCC-GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACT
1 CCCCTGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
* * * *
40234163 CCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 CCCCTGTAAGACCATGTCTGGGACATGGCGTTGGCA
40234199 GTACAGAAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 52 0.44
50 67 0.56
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (50 bp):
CCCCTGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
Found at i:40234191 original size:99 final size:98
Alignment explanation
Indices: 40234020--40234198 Score: 241
Period size: 99 Copynumber: 1.8 Consensus size: 98
40234010 GAACCCCCAT
* * ** * * *
40234020 GTAAGACCATTCTGGGACATGACGTTGGCACCGAGATGAGAGGTCCCCTGTAAGACCATGTTTGG
1 GTAAGACCATTCTGGGACATGACATGGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTGG
*
40234085 AACATGGCGTTGGCACCGAGATGAGAGGTCCCC
66 AACATGGCATTGGCACCGAGATGAGAGGTCCCC
* *
40234118 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTG
1 GTAAGACCAT-TCTGGGACATGACATGGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
* *
40234183 GGATATGGCATTGGCA
65 GAACATGGCATTGGCA
40234199 GTACAGAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
98 10 0.15
99 58 0.85
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.21
Consensus pattern (98 bp):
GTAAGACCATTCTGGGACATGACATGGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTGG
AACATGGCATTGGCACCGAGATGAGAGGTCCCC
Found at i:40234232 original size:49 final size:49
Alignment explanation
Indices: 40234015--40234237 Score: 148
Period size: 49 Copynumber: 4.5 Consensus size: 49
40234005 TATGAGAACC
* * * * * * **
40234015 CCCATGTAAGACCAT-TCTGGGACATGACGTTGGCACCGAGATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CGATAAGAAAACT
* * * * * * * * **
40234064 CCCCTGTAAGACCATGTTTGGAACATGGCGTTGGCACCGAGATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CGATAAGAAAACT
* * *
40234114 CCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CGATAAGAAAACT
* * *
40234163 CCCATGTAAGACCATATCTGGGATATGGCATTGGCA-G-TACAGAAAACAT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACGATA-AGAAAAC-T
*
40234212 CCCATGTAAGACTATGTCTGGGACAT
1 CCCATGTAAGACCATGTCTGGGACAT
40234238 AGCTTTGGCA
Statistics
Matches: 149, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
47 2 0.01
48 6 0.04
49 79 0.53
50 62 0.42
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (49 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACGATAAGAAAACT
Found at i:40234464 original size:12 final size:12
Alignment explanation
Indices: 40234447--40234485 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40234437 ATGAGTTATT
40234447 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
40234459 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
40234471 TAAGTGAGTAAG
1 TAAGTAAGCAAG
40234483 TAA
1 TAA
40234486 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:40237922 original size:23 final size:26
Alignment explanation
Indices: 40237891--40237938 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 26
40237881 GTGAAAACAG
*
40237891 GCCTCAACTACTAGT-CA-AATTTCT
1 GCCTCAACTACGAGTACACAATTTCT
40237915 GCCT-AACTACGAGTACACAATTTC
1 GCCTCAACTACGAGTACACAATTTC
40237939 GATCCAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 6 0.29
25 6 0.29
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.29
Consensus pattern (26 bp):
GCCTCAACTACGAGTACACAATTTCT
Found at i:40239759 original size:20 final size:20
Alignment explanation
Indices: 40239734--40239774 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40239724 CCTTAAATTG
40239734 TTTTATTTATAAGGTTATTA
1 TTTTATTTATAAGGTTATTA
40239754 TTTTATTTATAAGGTTATTA
1 TTTTATTTATAAGGTTATTA
40239774 T
1 T
40239775 GTTAATAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (20 bp):
TTTTATTTATAAGGTTATTA
Found at i:40239782 original size:17 final size:18
Alignment explanation
Indices: 40239741--40239782 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
40239731 TTGTTTTATT
*
40239741 TATAAGGTTATTATTTTA
1 TATAAGGTTATTATGTTA
40239759 TTTATAAGGTTATTATGTTA
1 --TATAAGGTTATTATGTTA
40239779 -ATAA
1 TATAA
40239783 ACAAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
20 17 0.81
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (18 bp):
TATAAGGTTATTATGTTA
Found at i:40239833 original size:21 final size:21
Alignment explanation
Indices: 40239809--40239849 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40239799 AAATTGCTAA
*
40239809 AAATATATTAATTTATTTTTT
1 AAATATATTAATGTATTTTTT
* *
40239830 AAATATTTTTATGTATTTTT
1 AAATATATTAATGTATTTTT
40239850 ATTGAAAAAT
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:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
AAATATATTAATGTATTTTTT
Found at i:40243301 original size:78 final size:78
Alignment explanation
Indices: 40243207--40243395 Score: 222
Period size: 80 Copynumber: 2.4 Consensus size: 78
40243197 AGTTTCGCTA
*
40243207 CTTCAGTGAAGGAAATAATGGTATTTGAGTTAAAGA-AAAAA-AAA-AAAGCAAAAGAAACTTAA
1 CTTCAGTGAAGTAAATAATGGTATTTGAGTTAAA-ATAAAAATAAATAAA-CAAAAGAAACTTAA
40243269 AAAGTTAGCTGCACCG
64 AAAGTT-GCTGCACCG
* * * * *
40243285 CTTCAGTGAAGTAAATAACGATGTTTGAGTTTTAAAATAAAAATAAATAAATAAAGGAAACTTAA
1 CTTCAGTGAAGTAAATAATGGTATTTGAG--TTAAAATAAAAATAAATAAACAAAAGAAACTTAA
* *
40243350 ATAGTTGCTTCACCG
64 AAAGTTGCTGCACCG
* *
40243365 CGTCAGTGAAATAAATAATGGTATTTGAGTT
1 CTTCAGTGAAGTAAATAATGGTATTTGAGTT
40243396 TTAGACAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
78 27 0.29
79 1 0.01
80 42 0.45
81 20 0.22
82 3 0.03
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.27
Consensus pattern (78 bp):
CTTCAGTGAAGTAAATAATGGTATTTGAGTTAAAATAAAAATAAATAAACAAAAGAAACTTAAAA
AGTTGCTGCACCG
Found at i:40250512 original size:18 final size:17
Alignment explanation
Indices: 40250485--40250518 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
40250475 TTCAATTGAT
40250485 AATGAAACCATTAAGTC
1 AATGAAACCATTAAGTC
40250502 AATGTAAACCATTAAGT
1 AATG-AAACCATTAAGT
40250519 TAATCTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (17 bp):
AATGAAACCATTAAGTC
Found at i:40254793 original size:88 final size:87
Alignment explanation
Indices: 40254638--40254899 Score: 331
Period size: 88 Copynumber: 3.0 Consensus size: 87
40254628 TTAAGTGTGT
* * *
40254638 AAAAA-ACCCTCAAAATTTTTC-AAAAAAGCAATTAAGCCCTTGCTTTTTTTTTTCACTCAATTA
1 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCC-TGC--CTTTTTTTCACTCAATTG
40254701 GGTACTTGAACTTTCAAAATGCATC
63 GGTACTTGAACTTTCAAAATGCATC
*
40254726 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGTCCCTGCCTTTTTTGCACTCAATTGGG
1 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAG-CCCTGCCTTTTTTTCACTCAATTGGG
*
40254791 TACTTGAACTATCAAAATGCATC
65 TACTTGAACTTTCAAAATGCATC
** * *
40254814 AAAAAG-CCCTCAAAC-TTTAAAAAAAAAACAATTAAGCCCCT-ACTTTTTTCTCACTCAATTGG
1 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAG-CCCTGCCTTTTTT-TCACTCAATTGG
40254876 GTACTTGAA-TTGTC-AAATGCATC
64 GTACTTGAACTT-TCAAAATGCATC
40254899 A
1 A
40254900 TCAAAAAGGC
Statistics
Matches: 157, Mismatches: 12, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
85 18 0.11
86 44 0.28
87 9 0.06
88 50 0.32
89 15 0.10
90 18 0.11
91 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (87 bp):
AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCTGCCTTTTTTTCACTCAATTGGGT
ACTTGAACTTTCAAAATGCATC
Found at i:40255107 original size:28 final size:28
Alignment explanation
Indices: 40255036--40255107 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
40255026 ATAAAAATAT
* *
40255036 ATAAAAGTTATAAAATTTATTAAATTTTA
1 ATAAAAATTA-AAAATATATTAAATTTTA
40255065 ATAAAAATGTAAAAATAT-TTAAATTTTA
1 ATAAAAAT-TAAAAATATATTAAATTTTA
*
40255093 CTAAAAATTAGAAAA
1 ATAAAAATTA-AAAA
40255108 AAATATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 2 0.05
28 21 0.55
29 13 0.34
30 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (28 bp):
ATAAAAATTAAAAATATATTAAATTTTA
Found at i:40255136 original size:11 final size:10
Alignment explanation
Indices: 40255095--40255176 Score: 62
Period size: 10 Copynumber: 8.3 Consensus size: 10
40255085 AAATTTTACT
*
40255095 AAAAATTAGA
1 AAAAATTATA
*
40255105 AAAAAATAT-
1 AAAAATTATA
40255114 AAAAA-TAGTA
1 AAAAATTA-TA
40255124 AAAATATTATA
1 AAAA-ATTATA
* *
40255135 AATAATTGT-
1 AAAAATTATA
* *
40255144 AAAATTTTTA
1 AAAAATTATA
*
40255154 AAAAATAATA
1 AAAAATTATA
40255164 AAAAATTATA
1 AAAAATTATA
40255174 AAA
1 AAA
40255177 TGCATAAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
8 2 0.04
9 12 0.21
10 34 0.61
11 6 0.11
12 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:40255149 original size:48 final size:48
Alignment explanation
Indices: 40255007--40255138 Score: 119
Period size: 47 Copynumber: 2.8 Consensus size: 48
40254997 ACGTGACATG
* * * *
40255007 TAGAAAAAAATTATAAAAA-ATAAAAATATATAAA-AGTTA-TAAAATT
1 TAGAAAAAAATAATAAAAATGTAAAAATATTTAAATA-TTACTAAAAAT
** *** *
40255053 TATTAAATTTTAATAAAAATGTAAAAATATTTAAATTTTACTAAAAAT
1 TAGAAAAAAATAATAAAAATGTAAAAATATTTAAATATTACTAAAAAT
40255101 TAGAAAAAAAT-ATAAAAATAGTAAAAATATTATAAATA
1 TAGAAAAAAATAATAAAAAT-GTAAAAATATT-TAAATA
40255139 ATTGTAAAAT
Statistics
Matches: 65, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
46 13 0.20
47 24 0.37
48 23 0.35
49 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.33
Consensus pattern (48 bp):
TAGAAAAAAATAATAAAAATGTAAAAATATTTAAATATTACTAAAAAT
Found at i:40255176 original size:19 final size:19
Alignment explanation
Indices: 40255094--40255176 Score: 60
Period size: 19 Copynumber: 4.3 Consensus size: 19
40255084 TAAATTTTAC
* * *
40255094 TAAAAATTAGAAAAAAATA
1 TAAAAATAATAAAAAATTA
*
40255113 TAAAAATAGTAAAAATATTA
1 TAAAAATAATAAAAA-ATTA
** * *
40255133 TAAATAATTGT-AAAATTTT
1 TAAA-AATAATAAAAAATTA
40255152 TAAAAAATAATAAAAAATTA
1 T-AAAAATAATAAAAAATTA
40255172 TAAAA
1 TAAAA
40255177 TGCATAAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
19 23 0.47
20 21 0.43
21 5 0.10
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
TAAAAATAATAAAAAATTA
Found at i:40255369 original size:21 final size:20
Alignment explanation
Indices: 40255345--40255403 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
40255335 TTTTGGTACA
40255345 ATAATTTTTATAGTTTTTTTT
1 ATAATTTTTATA-TTTTTTTT
* *
40255366 ATAAATTTTATA-TTTCTTT
1 ATAATTTTTATATTTTTTTT
* *
40255385 ACATTTTTTATAATTTTTT
1 ATAATTTTTAT-ATTTTTT
40255404 CTCCTATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 14 0.47
20 1 0.03
21 15 0.50
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (20 bp):
ATAATTTTTATATTTTTTTT
Found at i:40255435 original size:10 final size:10
Alignment explanation
Indices: 40255361--40255506 Score: 61
Period size: 10 Copynumber: 14.7 Consensus size: 10
40255351 TTTATAGTTT
40255361 TTTTTATA-A
1 TTTTTATATA
*
40255370 ATTTTATAT-
1 TTTTTATATA
*
40255379 TTCTTTACAT-
1 TT-TTTATATA
*
40255389 TTTTTATAATT
1 TTTTTAT-ATA
*
40255400 TTTTCTCCTATA
1 TTTT-T-ATATA
* *
40255412 TTTCTATATG
1 TTTTTATATA
40255422 TTTTTATATA
1 TTTTTATATA
*
40255432 TTTTTACA-A
1 TTTTTATATA
*
40255441 TTTTTATAAA
1 TTTTTATATA
* * *
40255451 ATTTTAAAAA
1 TTTTTATATA
*
40255461 TTTTAATAT-
1 TTTTTATATA
*
40255470 TTTTTATTAAA
1 TTTTTA-TATA
* *
40255481 ATTTAATA-A
1 TTTTTATATA
*
40255490 TTTTTATTTA
1 TTTTTATATA
40255500 TTTTTAT
1 TTTTTAT
40255507 TTTTATTTTA
Statistics
Matches: 101, Mismatches: 26, Indels: 19
0.69 0.18 0.13
Matches are distributed among these distances:
9 31 0.31
10 54 0.53
11 9 0.09
12 6 0.06
13 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTTATATA
Found at i:40255446 original size:19 final size:19
Alignment explanation
Indices: 40255422--40255473 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
40255412 TTTCTATATG
*
40255422 TTTTTATATATTTTTACAA
1 TTTTTATATATTTTTAAAA
* *
40255441 TTTTTATAAAATTTTAAAA
1 TTTTTATATATTTTTAAAA
*
40255460 ATTTTA-ATATTTTT
1 TTTTTATATATTTTT
40255474 TATTAAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTATATATTTTTAAAA
Found at i:40255455 original size:29 final size:29
Alignment explanation
Indices: 40255423--40255495 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
40255413 TTCTATATGT
40255423 TTTTATATATTTTTACAATTTTTA-TAAAA
1 TTTTATA-ATTTTTACAATTTTTATTAAAA
* *
40255452 TTTTAAAAATTTTA-ATATTTTTTATTAAAA
1 TTTTATAATTTTTACA-A-TTTTTATTAAAA
*
40255482 TTTAATAATTTTTA
1 TTTTATAATTTTTA
40255496 TTTATTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 7 0.19
29 12 0.33
30 16 0.44
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTATAATTTTTACAATTTTTATTAAAA
Done.