Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 81 of 113
Found at i:17067797 original size:890 final size:878
Alignment explanation
Indices: 17065492--17067927 Score: 1992
Period size: 890 Copynumber: 2.7 Consensus size: 878
17065482 TAATAATAAC
* ** * * *
17065492 AAGATTTAAAAAATGAA-TCTATTTATTGAACAAGTTTAAATAATTATGA-CTATTTAAATAATT
1 AAGATTTAAAAAATAAATTC-ATTTATCAAATAAGTTCAAATAATTATGATC-ATTTAAACAATT
* * ** * * ** * *
17065555 ATCTATTTGAAATCGCTAT-AACTTTTTGTTTTGTCATAAAATAGTTTTTTCTATTCACACAA-C
64 ATCAATTTCAAATCATTATGAAC-TTTTGTTTTGTCATAAAACAATTGCTTCTATTCATACAAGT
*** * *
17065618 CTTATTTTGAATAAAATAATACAAATTTATTAATA--TTAAGACAATTAATAAGTAAAAGATTTA
128 C-TATTCAAAATAAAATAATACTAATTTATTAATATTTTAA-A-AATTAATAAGTACAAGATTTA
* * * * ** * * * *
17065681 AAAAATAAATCTGTTTACCGAACAAGTTCAAATCGTTTTGACTATT-TAAGCAATTATTTATTTC
190 AAAAATAAATATGCTTACCGAACAAATTCAAATAGTCATGTCCATTCGAA-CAATTATATATTTC
* * * * * * *
17065745 --ATCTTGTCTTGACTATTTGT-TTTTGTCATAAAACAATTATTTCTATTCATAC-AAGTT-CT-
254 AAATCAT-T-ATAAC-ATTT-TATTTTCTCATAAAACAATTATTTTTATTCATACAAAATTATTA
* * * * * * * *
17065804 AAATTAAAATAGTATTAATTTATTAATATTTTGACAATTAATAAGTAAAAGATTT-AAAAATAAA
315 AAAATAAAATAATACTAATCTAGTAATATTATAAAAATTAATAA-T---AGATTTAAAAAATAAA
* * * * * * * *
17065868 TATGTTTACTGAACAAGTTTAAATAGTCATGATTATTTGAATAATTATCTAT-TTCAAATCATTA
376 TTTG-TTATTGACCAA-TTTAAATAGTTAAGACTATATGAACAATTATCTATCTT-AAATCATTA
* * * * ** * * *
17065932 TGACCT-TTTCTTTTGTAATAAAA-TAATCATTTTAGTTCATACAAACTTATTTGAAGTAAAATA
438 T-A-ATATTTGTTTTGTCATAAAACAAATGTTTTTA-TTCATACAAGCTTATTCGAAATAAAAT-
* * *
17065995 AT-ACTAATTTATTAACA-TTCTAAAAATTAATGAGTAAGATAATTAAAAAA-AGAATTTGTTTA
499 ATCACTAA---ATTAATATTTC-AAAAATTAATAAG--AGAT--TTAAAAAATA-AATGTGTTTA
*** ** * * * * ** *
17066057 TTGAATAAGTTCAAATAGTTATGACTA-TATGAATAATTATCTATTTCAAAAT-ATTATGACCTT
555 CCAAACCAGTTCAAATAGTTATAACAATTA-GAACAATAATCTATTTC-AAATCATTACAACCAT
* * * *
17066120 TTGTTTTA-TCATAAAACAATTGGTTT-AGTTCATGCAAG-TATATTTTGAATAAAGTAATTTAA
618 TTG-TTTAGTCATAAAATAATT-GTTTCAATTCATACATGCT-TA-TTTG---AAA-T-A---AA
* * * * * * * *
17066182 ATTTATTAATATTCCAATAATTAAGAAGCAAAAATTTTAAAAATAAATCTATTTTCTAAACACGT
671 A--TAAT-ACATTCAAAAAATTAAGAAGCAAAAATTTAAAAAATAAATCTATTTACCAAACAAGT
* * * * * * *
17066247 TCAAATAATTATGACTATTTGAATAATTATCTATTTCAAATTATTATGATCTTTTGTTTTGTCAT
733 TCAAATAACTATGACTATATGAACAATTATCTATTTAAAATCATTATGACCTTTTGTTTTATCAT
* * * * *
17066312 AAACTAATTGTTTTTGTTCATAAAAGCTTATTAGGAATAAAATAATACTAATTTATGACAATTTA
798 AAACTAATTGTTTTAGTTCATAAAAACTTATCAGAAATAAAATAACACTAATTTATGACAATTTA
*
17066377 AAAAATTAATAAGTAA
863 AAAAATTAAGAAGTAA
* * * * * *
17066393 AAGATTTAAAACATAAATTTATTTATCGAGTAAGTTCAAATAGTTATGATTATTTAAACAATTAT
1 AAGATTTAAAAAATAAATTCATTTATCAAATAAGTTCAAATAATTATGATCATTTAAACAATTAT
** * *
17066458 TTATTTCAAATCATTATGATCTTTTGTTTTGTCATAAAACAATTGCTTCTATTCATACAAGTTTA
66 CAATTTCAAATCATTATGAACTTTTGTTTTGTCATAAAACAATTGCTTCTATTCATACAAGTCTA
* ***
17066523 TTCAAAATAAAATAATACTAATTTATTAATATTTTAAAAATTAATGAGTTGGAGATTTAAAAAAT
131 TTCAAAATAAAATAATACTAATTTATTAATATTTTAAAAATTAATAAGTACAAGATTTAAAAAAT
* * ** *
17066588 AAATCTGTTTACCGAACAAATTCAAATAGTCATGTCCATTCGAATTATTATTTATTTCAAATCAT
196 AAATATGCTTACCGAACAAATTCAAATAGTCATGTCCATTCGAACAATTATATATTTCAAATCAT
* * ** *
17066653 TATAACATTTTGTTTTGTTGTAAAACAATTGTTTTTATTCATACAAAATTATTAAAAATAAAATA
261 TATAACATTTTATTTTCTCATAAAACAATTATTTTTATTCATACAAAATTATTAAAAATAAAATA
* * * * *
17066718 ATACTAATTTATTAATATTTTAAAAATTAATAATAGATTTAAAAACTAAATTTGTTTATTGAACT
326 ATACTAATCTAGTAATATTATAAAAATTAATAATAGATTTAAAAAATAAATTTG-TTATTG-ACC
* * *
17066783 AATTTAAATAGTTATGACTATTTGAACAATTATCTATCTTAAATCATTATAATCTTTGTTTTGTC
389 AATTTAAATAGTTAAGACTATATGAACAATTATCTATCTTAAATCATTATAATATTTGTTTTGTC
* * *
17066848 ATAAAACAATTGTTTTTGTTCATACAAGCTTATTCGAAGTAAAATATCACTAAATTAATAATATT
454 ATAAAACAAATGTTTTTATTCATACAAGCTTATTCGAAATAAAATATCACTAAATTAAT-AT-TT
* *
17066913 CTAAAAATTAAAAAGTAAGAGATTTAAAAAATAAATGTGTTTGCTAAACCAGTTCAAATAGTTA-
517 C-AAAAATT---AA-TAAGAGATTTAAAAAATAAATGTGTTTACCAAACCAGTTCAAATAGTTAT
* * * * ** *
17066977 AGGCTATTAGAATAATAATCTATTTCAAATCATTCCAACTTTTTGTTTAGTTATAAAATAATTGT
577 A-ACAATTAGAACAATAATCTATTTCAAATCATTACAACCATTTGTTTAGTCATAAAATAATTGT
*
17067042 TTCAATTCATACATGCTTATTTGAAATAAAATAATACATTCAAAAAATTAATAAGCAAGAAATTT
641 TTCAATTCATACATGCTTATTTGAAATAAAATAATACATTCAAAAAATTAAGAAGCAA-AAATTT
* * **
17067107 AAAAAGAATAAATCTGTTTACCAAACAAGTTCATATAACTATGGTTATATGAACAATTATCTATT
705 -AAAA-AATAAATCTATTTACCAAACAAGTTCAAATAACTATGACTATATGAACAATTATCTATT
*
17067172 TAAAATCGTTATGACCTTTTGTTTTATCATAAAAC-AATTGTTTTAGTTCATAAAAACTTATCCA
768 TAAAATCATTATGACCTTTTGTTTTATCAT-AAACTAATTGTTTTAGTTCATAAAAACTTAT-CA
* * * * **
17067236 -AAATAAAATAACATTAATTTATTA-ATATTTCAAAAATTGAGAAGTTG
831 GAAATAAAATAACACTAATTTATGACA-ATTTAAAAAATTAAGAAGTAA
* * * * *
17067283 GAG-TTTAAAAAAT-AATTCAGTTTATCAAATCAA-TTCAAATAATTATGGTCGTTTGAATAATT
1 AAGATTTAAAAAATAAATTCA-TTTATCAAAT-AAGTTCAAATAATTATGATCATTTAAACAATT
**
17067345 ATCAATTTCCAAATTGTTATGAACTTTTGTTTTGTCATAAAACAATTG-TT-TATCATCATACAA
64 ATCAATTT-CAAATCATTATGAACTTTTGTTTTGTCATAAAACAATTGCTTCTAT--TCATACAA
**
17067408 GTCTATTTGAAATAAAATAATACTAATTTATTAATATTTT-AAAATTAA-AAGTACAAGATTTAA
126 GTCTATTCAAAATAAAATAATACTAATTTATTAATATTTTAAAAATTAATAAGTACAAGATTTAA
** * * * * *
17067471 AAAATAAATATGCTTATTGATTC-AATTCAAATAGTTATGAT-TATTTGAACAATTGTATATTTC
191 AAAATAAATATGCTTACCGA-ACAAATTCAAATAGTCATG-TCCATTCGAACAATTATATATTTC
* * ***
17067534 AAATCGTTATAACATTTTATTTTCTCATAAAACAATTATTTTTCTTCATAC-AAATTGATTTTGA
254 AAATCATTATAACATTTTATTTTCTCATAAAACAATTATTTTTATTCATACAAAATT-ATTAAAA
* * *
17067598 ATAAAATAATATTAATCTAGTAAT-TTATGAAATTTAATAACTGAGAGATTTAAAAAATAAATTT
318 ATAAAATAATACTAATCTAGTAATATTATAAAAATTAATAA-T---AGATTTAAAAAATAAATTT
** *
17067662 G-T-TTG-CCAATTTAAATAGTTAAGGTTATATGAATAATTATCTAT-TTCAAATCATTATAATA
379 GTTATTGACCAATTTAAATAGTTAAGACTATATGAACAATTATCTATCTT-AAATCATTATAATA
** ** * * **
17067723 TTCTGTTTTGTTGTAAAACAAATGTTTTTATTCATGTAAGTTTGTTCGAAATAAAATAAT-TTTA
443 TT-TGTTTTGTCATAAAACAAATGTTTTTATTCATACAAGCTTATTCGAAATAAAAT-ATCACTA
* *
17067787 ATTTATTAATATTTCAAAAATTAATAAGAGATTTAATAAATAAATTTGTTTACCAAACCAGTTCA
506 A---ATTAATATTTCAAAAATTAATAAGAGATTTAAAAAATAAATGTGTTTACCAAACCAGTTCA
* * * * ** *
17067852 ATTAGTTATAACAATTTGAACAATTATTTATTTCAAATCATTATGACCATTTGTTTTGTCATAAA
568 AATAGTTATAACAATTAGAACAATAATCTATTTCAAATCATTACAACCATTTGTTTAGTCATAAA
17067917 ATAATTGTTTC
633 ATAATTGTTTC
17067928 TATTAAATAC
Statistics
Matches: 1265, Mismatches: 212, Indels: 134
0.79 0.13 0.08
Matches are distributed among these distances:
883 97 0.08
884 3 0.00
885 2 0.00
886 48 0.04
887 92 0.07
888 153 0.12
889 65 0.05
890 228 0.18
891 24 0.02
893 1 0.00
894 1 0.00
895 3 0.00
896 5 0.00
897 1 0.00
898 19 0.02
899 148 0.12
900 101 0.08
901 213 0.17
902 11 0.01
903 50 0.04
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (878 bp):
AAGATTTAAAAAATAAATTCATTTATCAAATAAGTTCAAATAATTATGATCATTTAAACAATTAT
CAATTTCAAATCATTATGAACTTTTGTTTTGTCATAAAACAATTGCTTCTATTCATACAAGTCTA
TTCAAAATAAAATAATACTAATTTATTAATATTTTAAAAATTAATAAGTACAAGATTTAAAAAAT
AAATATGCTTACCGAACAAATTCAAATAGTCATGTCCATTCGAACAATTATATATTTCAAATCAT
TATAACATTTTATTTTCTCATAAAACAATTATTTTTATTCATACAAAATTATTAAAAATAAAATA
ATACTAATCTAGTAATATTATAAAAATTAATAATAGATTTAAAAAATAAATTTGTTATTGACCAA
TTTAAATAGTTAAGACTATATGAACAATTATCTATCTTAAATCATTATAATATTTGTTTTGTCAT
AAAACAAATGTTTTTATTCATACAAGCTTATTCGAAATAAAATATCACTAAATTAATATTTCAAA
AATTAATAAGAGATTTAAAAAATAAATGTGTTTACCAAACCAGTTCAAATAGTTATAACAATTAG
AACAATAATCTATTTCAAATCATTACAACCATTTGTTTAGTCATAAAATAATTGTTTCAATTCAT
ACATGCTTATTTGAAATAAAATAATACATTCAAAAAATTAAGAAGCAAAAATTTAAAAAATAAAT
CTATTTACCAAACAAGTTCAAATAACTATGACTATATGAACAATTATCTATTTAAAATCATTATG
ACCTTTTGTTTTATCATAAACTAATTGTTTTAGTTCATAAAAACTTATCAGAAATAAAATAACAC
TAATTTATGACAATTTAAAAAATTAAGAAGTAA
Found at i:17067983 original size:55 final size:55
Alignment explanation
Indices: 17067897--17068006 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
17067887 AATCATTATG
17067897 ACCATTTGTTTTGTCATAAAATAATTGTTTCTATTAAATACAATCTTATTCAAAA
1 ACCATTTGTTTTGTCATAAAATAATTGTTTCTATTAAATACAATCTTATTCAAAA
*
17067952 ACCATTTGTTTTGTCATAAAATAATTTTTTCTATTAAATACAATCTTATTCAAAA
1 ACCATTTGTTTTGTCATAAAATAATTGTTTCTATTAAATACAATCTTATTCAAAA
17068007 TAAAGTATTG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.45
Consensus pattern (55 bp):
ACCATTTGTTTTGTCATAAAATAATTGTTTCTATTAAATACAATCTTATTCAAAA
Found at i:17068303 original size:181 final size:178
Alignment explanation
Indices: 17067956--17068670 Score: 647
Period size: 181 Copynumber: 3.9 Consensus size: 178
17067946 TCAAAAACCA
* * * * *
17067956 TTTGTTTTGTCATAAAATAATT-TTTTCTATTAAATACAATCTTATTCAAAATAAAGT-ATTGCT
1 TTTGTTTTGTCATAAAATAATTGTTTT-TGTT-CATACAAGCTGATTCAGAATAAA-TAATT-CT
* * * * * * * ** *
17068019 AATTTATTAATATTCTAAAAAGC-AATAAAT-AACGAATTTAAAAAATGAATCTATTGACTTAAC
62 AATTTATTAATATTC-AAAAA-CTAATAAGTAAAAG-ATTTAAAAACTAAATTTGTTTACCAAAT
* * * *
17068082 CAGTACAGATAGTTATAACTATGTGAATAATTATCTATTTCAAATCGTTATAATCT
124 AAGTTCAAATAGTTATAACTATTTGAATAATTATCTATTTCAAATCGTTATAA-CT
* * * *
17068138 TTTGTTTTATCACAAAATAATTGTTTTTGTTTATACAAGCTGATTCGGAATAATATAATTCTAAT
1 TTTGTTTTGTCATAAAATAATTGTTTTTGTTCATACAAGCTGATTCAGAATAA-ATAATTCTAAT
* * * * * *
17068203 TTATTAATGTTCCAAAAAGTAGTAAGTAAAACATTTAAAAACTGAATTTGTTTATCAAATAAGTT
65 TTATTAATATT-CAAAAACTAATAAGTAAAAGATTTAAAAACTAAATTTGTTTACCAAATAAGTT
* * *
17068268 CAAATAG-TATTCACTATTTGAATAATTACCTATTTCAAATCGCTATAACCT
129 CAAATAGTTA-TAACTATTTGAATAATTATCTATTTCAAATCGTTATAA-CT
** * * * * * * * *
17068319 TTTGTTTTGTTGTAAAATAATT-TCTTCTATTCATACAAGTTTGTTTTA-ATTAAAATAATACAA
1 TTTGTTTTGTCATAAAATAATTGT-TTTTGTTCATACAAG-CTGATTCAGAAT-AAATAATTCTA
* *
17068382 ATCTATTAATATTCAAACAACTAAAAAGTAAAAGATTTAAAAACTAAATTTGTTTACCAAATAAG
63 ATTTATTAATATTCAAA-AACTAATAAGTAAAAGATTTAAAAACTAAATTTGTTTACCAAATAAG
* * *
17068447 TTCAAATAGTTATAACTATTTGAACAATTATTTATTTCAAATCATTATAACTT
127 TTCAAATAGTTATAACTATTTGAATAATTATCTATTTCAAATCGTTATAAC-T
* * *
17068500 TTTGTTTTGTCATAAAACAATTGTTTTTGTTCATACAAGCTTATTCAGATTTAAATAATAT-TAA
1 TTTGTTTTGTCATAAAATAATTGTTTTTGTTCATACAAGCTGATTCAGA-ATAAATAAT-TCTAA
** * * * * **
17068564 TTTATTAATATTTTGATAATTAATAAGTAAAAGATTTTGAAAA-TAAATATGTTTACCAAACGAG
64 TTTATTAATA-TTCAAAAACTAATAAGTAAAAGA-TTTAAAAACTAAATTTGTTTACCAAATAAG
*
17068628 TTCAAATAGTTATAACTATTTAAATAATTATCTATTTCAAATC
127 TTCAAATAGTTATAACTATTTGAATAATTATCTATTTCAAATC
17068671 TCATAATGAT
Statistics
Matches: 432, Mismatches: 82, Indels: 39
0.78 0.15 0.07
Matches are distributed among these distances:
180 12 0.03
181 365 0.84
182 51 0.12
183 4 0.01
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (178 bp):
TTTGTTTTGTCATAAAATAATTGTTTTTGTTCATACAAGCTGATTCAGAATAAATAATTCTAATT
TATTAATATTCAAAAACTAATAAGTAAAAGATTTAAAAACTAAATTTGTTTACCAAATAAGTTCA
AATAGTTATAACTATTTGAATAATTATCTATTTCAAATCGTTATAACT
Found at i:17070903 original size:58 final size:58
Alignment explanation
Indices: 17070827--17071109 Score: 230
Period size: 58 Copynumber: 4.7 Consensus size: 58
17070817 AAAAAAGACA
* *
17070827 TTTTAAGGAAAAGTTGAGAGCATCAATTTTTCTTGAAAATAAAAATTTTGAAAATATT
1 TTTTAAGGAAAAGTTGAGAGTATCAATTTTTCTTGAAAATAAAAATTTTAAAAATATT
* * * * *
17070885 TTTTGAGGAAAAGTTGAGAGTATCAATTTTTCCTT-AAAATTAAAATTTCAAAAAAAAAT
1 TTTTAAGGAAAAGTTGAGAGTATCAATTTTT-CTTGAAAATAAAAATTT-TAAAAATATT
* * * * * *
17070944 TTTTAAGAAAAAGTTGAAAGTATCAA-TTTTCTTTAAAAATGAAAATTTTAGAGAATGTTTTTTT
1 TTTTAAGGAAAAGTTGAGAGTATCAATTTTTC-TTGAAAATAAAAATTTTA-A-AA----ATATT
* * * *
17071008 TTTTTAGAAAAAGTTG-GAAGTATTAATTTTTCTTGAAAATAAAAAATTTCAAAAATATTT
1 TTTTAAGGAAAAGTTGAG-AGTATCAATTTTTCTTGAAAAT-AAAAATTTTAAAAATA-TT
* * * * * *
17071068 TTTTGAGGAAAAGTTAAAAGTATTAATTTTCCTTGAATATAA
1 TTTTAAGGAAAAGTTGAGAGTATCAATTTTTCTTGAAAATAA
17071110 GTAGTAATCT
Statistics
Matches: 180, Mismatches: 30, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
57 1 0.01
58 48 0.27
59 48 0.27
60 37 0.21
63 2 0.01
64 31 0.17
65 13 0.07
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (58 bp):
TTTTAAGGAAAAGTTGAGAGTATCAATTTTTCTTGAAAATAAAAATTTTAAAAATATT
Found at i:17070960 original size:59 final size:59
Alignment explanation
Indices: 17070736--17070991 Score: 197
Period size: 58 Copynumber: 4.4 Consensus size: 59
17070726 TTTTCAATAA
* * * * * *
17070736 TTTT-CTT-AAAA-TAAAAATT-AAAAAAAATACTTTAGGGAAAAGTTAAAAGTATTAA-
1 TTTTCCTTAAAAATTAAAATTTAAAAAAAAAT-TTTTAAGGAAAAGTTGAGAGTATCAAT
* * * *
17070791 GTTTCCTT-AAAAGTAAAATTTAAAAAAAAAAAGACATTTTAAGGAAAAGTTGAGAGCATCAAT
1 TTTTCCTTAAAAATTAAAATTT---AAAAAAAA-A-TTTTTAAGGAAAAGTTGAGAGTATCAAT
* * ** * * *
17070854 TTTT-CTTGAAAATAAAAATTTTGAAAATATTTTTTGAGGAAAAGTTGAGAGTATCAAT
1 TTTTCCTTAAAAATTAAAATTTAAAAAAAAATTTTTAAGGAAAAGTTGAGAGTATCAAT
* *
17070912 TTTTCCTT-AAAATTAAAATTTCAAAAAAAAATTTTTAAGAAAAAGTTGAAAGTATCAA-
1 TTTTCCTTAAAAATTAAAATTT-AAAAAAAAATTTTTAAGGAAAAGTTGAGAGTATCAAT
* *
17070970 TTTTCTTTAAAAATGAAAATTT
1 TTTTCCTTAAAAATTAAAATTT
17070992 TAGAGAATGT
Statistics
Matches: 159, Mismatches: 29, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
55 3 0.02
56 7 0.04
57 7 0.04
58 48 0.30
59 44 0.28
60 5 0.03
61 7 0.04
62 24 0.15
63 14 0.09
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (59 bp):
TTTTCCTTAAAAATTAAAATTTAAAAAAAAATTTTTAAGGAAAAGTTGAGAGTATCAAT
Found at i:17071070 original size:65 final size:64
Alignment explanation
Indices: 17070943--17071071 Score: 154
Period size: 64 Copynumber: 2.0 Consensus size: 64
17070933 CAAAAAAAAA
* * * *
17070943 TTTTTAAGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATGAAAATTTTAGAGAATGTTTTTT
1 TTTTTAAGAAAAAGTTGAAAGTATCAATTTTCTTGAAAAATAAAAATTTCAGAAAATGTTTTTT
* * * *
17071007 TTTTTTAGAAAAAGTTGGAAGTATTAATTTTTCTTG-AAAATAAAAAATTTCA-AAAATATTTTT
1 TTTTTAAGAAAAAGTTGAAAGTATCAA-TTTTCTTGAAAAAT-AAAAATTTCAGAAAATGTTTTT
17071070 T
64 T
17071071 T
1 T
17071072 GAGGAAAAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
64 40 0.73
65 15 0.27
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (64 bp):
TTTTTAAGAAAAAGTTGAAAGTATCAATTTTCTTGAAAAATAAAAATTTCAGAAAATGTTTTTT
Found at i:17075100 original size:25 final size:25
Alignment explanation
Indices: 17075065--17075122 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
17075055 GATAAAGTGA
*
17075065 AAAAATGAAAAAAG-CAAAAAAATTG
1 AAAAATAAAAAAAGTCAAAAAAA-TG
* *
17075090 AAAAATAAAAAAGGTGAAAAAAATG
1 AAAAATAAAAAAAGTCAAAAAAATG
17075115 -AAAATAAA
1 AAAAATAAA
17075123 GACTCAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 8 0.28
25 14 0.48
26 7 0.24
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (25 bp):
AAAAATAAAAAAAGTCAAAAAAATG
Found at i:17076406 original size:17 final size:17
Alignment explanation
Indices: 17076386--17076462 Score: 50
Period size: 17 Copynumber: 4.5 Consensus size: 17
17076376 TTGTGAACCG
17076386 AAAAATCTTGCAAATCT
1 AAAAATCTTGCAAATCT
* * *
17076403 -AAAATTTCTGTAGA-CT
1 AAAAATCT-TGCAAATCT
*
17076419 AAAAATTCTTGCGAATCT
1 AAAAA-TCTTGCAAATCT
* * *
17076437 AAGAATCTTACGAATCT
1 AAAAATCTTGCAAATCT
*
17076454 AAGAATCTT
1 AAAAATCTT
17076463 ACGAATCTCC
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
16 8 0.17
17 31 0.66
18 8 0.17
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (17 bp):
AAAAATCTTGCAAATCT
Found at i:17076453 original size:9 final size:9
Alignment explanation
Indices: 17076425--17076470 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
17076415 GACTAAAAAT
*
17076425 TCTTGCGAA
1 TCTTACGAA
*
17076434 TC-TAAGAA
1 TCTTACGAA
17076442 TCTTACGAA
1 TCTTACGAA
*
17076451 TC-TAAGAA
1 TCTTACGAA
17076459 TCTTACGAA
1 TCTTACGAA
17076468 TCT
1 TCT
17076471 CCAGTTGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
8 13 0.43
9 17 0.57
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (9 bp):
TCTTACGAA
Found at i:17076463 original size:17 final size:17
Alignment explanation
Indices: 17076425--17076470 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
17076415 GACTAAAAAT
*
17076425 TCTTGCGAATCTAAGAA
1 TCTTACGAATCTAAGAA
17076442 TCTTACGAATCTAAGAA
1 TCTTACGAATCTAAGAA
17076459 TCTTACGAATCT
1 TCTTACGAATCT
17076471 CCAGTTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (17 bp):
TCTTACGAATCTAAGAA
Found at i:17076487 original size:51 final size:50
Alignment explanation
Indices: 17076422--17076555 Score: 119
Period size: 51 Copynumber: 2.6 Consensus size: 50
17076412 GTAGACTAAA
* *
17076422 AATTCTTGCGAATCTAAGAATCTTACGAATCTAAGAA-TCTTACGAATCTCC
1 AATTCTTACAAATCTAA-AATCTTACGAATCTAA-AAGTCTTACGAATCTCC
* * ** * *
17076473 AGTTGTTACAAATCTTCAAT-TCTAGCGAATCTAAAAGTCTTGCGAATCTTC
1 AATTCTTACAAATCTAAAATCT-TA-CGAATCTAAAAGTCTTACGAATCTCC
* *
17076524 AATTCTTGCAAATATGAAAATCTTACGAATCT
1 AATTCTTACAAATCT-AAAATCTTACGAATCT
17076556 CCAGTTGTTG
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
49 1 0.02
50 7 0.11
51 50 0.78
52 5 0.08
53 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (50 bp):
AATTCTTACAAATCTAAAATCTTACGAATCTAAAAGTCTTACGAATCTCC
Found at i:17076503 original size:17 final size:17
Alignment explanation
Indices: 17076483--17076750 Score: 135
Period size: 17 Copynumber: 15.8 Consensus size: 17
17076473 AGTTGTTACA
*
17076483 AATCTTCAATTCTAGCG
1 AATCTTCAATTCTTGCG
** *
17076500 AATCTAAAAGTCTTGCG
1 AATCTTCAATTCTTGCG
*
17076517 AATCTTCAATTCTTGCA
1 AATCTTCAATTCTTGCG
* ** * *
17076534 AATATGAAAATCTTACG
1 AATCTTCAATTCTTGCG
* * *
17076551 AATCTCCAGTTGTTGCG
1 AATCTTCAATTCTTGCG
*
17076568 AATCTTCAATGCTTGCG
1 AATCTTCAATTCTTGCG
* * *
17076585 AATTTTTAATTCTTGTG
1 AATCTTCAATTCTTGCG
* **
17076602 AATCTCCAATTCTTTTG
1 AATCTTCAATTCTTGCG
** * ***
17076619 AATCTGAAAATCTTATA
1 AATCTTCAATTCTTGCG
* * * *
17076636 AATCTCCAGTTGTTGCA
1 AATCTTCAATTCTTGCG
* *
17076653 AATCTTCAATTCTTACA
1 AATCTTCAATTCTTGCG
* *
17076670 AAT-TTGAAAGTCTTGCG
1 AATCTT-CAATTCTTGCG
*
17076687 AATCTCCAATTCTTGCG
1 AATCTTCAATTCTTGCG
** *
17076704 AATCTGAAAATCTTAG-G
1 AATCTTCAATTCTT-GCG
* * *
17076721 AATATTCAGTTATTGCG
1 AATCTTCAATTCTTGCG
17076738 AATCTTCAATTCT
1 AATCTTCAATTCT
17076751 ATTTTCTTAT
Statistics
Matches: 179, Mismatches: 68, Indels: 8
0.70 0.27 0.03
Matches are distributed among these distances:
16 3 0.02
17 174 0.97
18 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (17 bp):
AATCTTCAATTCTTGCG
Found at i:17076547 original size:85 final size:85
Alignment explanation
Indices: 17076420--17076751 Score: 373
Period size: 85 Copynumber: 3.9 Consensus size: 85
17076410 CTGTAGACTA
* * * * *
17076420 AAAATTCTTGCGAATCT-AAGAATCTTACGAATCT-AAGAATCTTACGAATCTCCAGTTGTTACA
1 AAAAGTCTTGCGAATCTCCA-ATTCTTGCGAATCTGAA-AATCTTACGAATCTCCAGTTGTTGCA
*
17076483 AATCTTCAATTCTAGCGAATCT
64 AATCTTCAATTCTAGCGAATTT
* * * *
17076505 AAAAGTCTTGCGAATCTTCAATTCTTGCAAATATGAAAATCTTACGAATCTCCAGTTGTTGCGAA
1 AAAAGTCTTGCGAATCTCCAATTCTTGCGAATCTGAAAATCTTACGAATCTCCAGTTGTTGCAAA
* *
17076570 TCTTCAATGCTTGCGAATTT
66 TCTTCAATTCTAGCGAATTT
** * * ** **
17076590 TTAATTCTTGTGAATCTCCAATTCTTTTGAATCTGAAAATCTTATAAATCTCCAGTTGTTGCAAA
1 AAAAGTCTTGCGAATCTCCAATTCTTGCGAATCTGAAAATCTTACGAATCTCCAGTTGTTGCAAA
*
17076655 TCTTCAATTCTTA-CAAATTT
66 TCTTCAATTC-TAGCGAATTT
* * * * * *
17076675 GAAAGTCTTGCGAATCTCCAATTCTTGCGAATCTGAAAATCTTAGGAATATTCAGTTATTGCGAA
1 AAAAGTCTTGCGAATCTCCAATTCTTGCGAATCTGAAAATCTTACGAATCTCCAGTTGTTGCAAA
17076740 TCTTCAATTCTA
66 TCTTCAATTCTA
17076752 TTTTCTTATG
Statistics
Matches: 206, Mismatches: 38, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
84 2 0.01
85 200 0.97
86 4 0.02
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (85 bp):
AAAAGTCTTGCGAATCTCCAATTCTTGCGAATCTGAAAATCTTACGAATCTCCAGTTGTTGCAAA
TCTTCAATTCTAGCGAATTT
Found at i:17077124 original size:85 final size:85
Alignment explanation
Indices: 17076966--17077164 Score: 258
Period size: 85 Copynumber: 2.3 Consensus size: 85
17076956 GTGAAGTCAA
* * * * * *
17076966 ACTTCGGTTCAATCCAAGTCATTTTGTTTTCGATTTTAACCTATGCTAGATCTTTTTTTGGTTTA
1 ACTTTGGTTCAATCCAAGTCATTTTGTTTTCGATTTCAACCTATGCCAGATCTTTTCTTGGATCA
*
17077031 GTCCAAGTTATTTATTTTAG
66 ATCCAAGTTATTTATTTTAG
* * *
17077051 ACTTTGGTT-AAGTCTAAGTCATTTTGTTTTTGATTTCGACCTATGCCAGATC-TTTCTTGAGAT
1 ACTTTGGTTCAA-TCCAAGTCATTTTGTTTTCGATTTCAACCTATGCCAGATCTTTTCTTG-GAT
*
17077114 CAATCCAAGTTATTTCTTTTAG
64 CAATCCAAGTTATTTATTTTAG
*
17077136 ACTTTGGTTCAATCCAAGTCATTATGTTT
1 ACTTTGGTTCAATCCAAGTCATTTTGTTT
17077165 CTAGCGCCAA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
84 8 0.08
85 88 0.90
86 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.15, T:0.47
Consensus pattern (85 bp):
ACTTTGGTTCAATCCAAGTCATTTTGTTTTCGATTTCAACCTATGCCAGATCTTTTCTTGGATCA
ATCCAAGTTATTTATTTTAG
Found at i:17078260 original size:13 final size:13
Alignment explanation
Indices: 17078229--17078268 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
17078219 TTTTTCTCTA
17078229 TTTATCTATTTATT
1 TTTAT-TATTTATT
* *
17078243 ATTATTATTTTTT
1 TTTATTATTTATT
17078256 TTTATTATTTATT
1 TTTATTATTTATT
17078269 AATTAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTATTATTTATT
Found at i:17078402 original size:58 final size:57
Alignment explanation
Indices: 17078326--17078692 Score: 369
Period size: 58 Copynumber: 6.2 Consensus size: 57
17078316 AATTTTCAAT
* **
17078326 AATTTT-CTTAAAATAAAAATTTTAAAAAAATACTTTAAGGAAAAGTTGAAAGTATC
1 AATTTTCCTTAAAATAAAAATTTCAAAAAAATTTTTTAAGGAAAAGTTGAAAGTATC
* ** * *
17078382 AATTTTTCTTAAAAGTAAAAATTAAAAAAAAAAATAGACATTTTAAGGAAAAGTTAAAAGTATC
1 AATTTTCCTTAAAA-TAAAAATT--TCAAAAAAAT----TTTTTAAGGAAAAGTTGAAAGTATC
* * **
17078446 AATTTTTCTTGAAAATAAAAATTTCAAAAATATTTTTTTGGGGAAAAGTT-AAAGTATC
1 AATTTTCCTT-AAAATAAAAATTTCAAAAA-AATTTTTTAAGGAAAAGTTGAAAGTATC
* *
17078504 AATTTTCCCTGAAAATAAAAATTTCAAAAAATATTTTTTTTAAGAAAAAGTTGAAAGTATC
1 AATTTT-CCTTAAAATAAAAATTTCAAAAAA-A--TTTTTTAAGGAAAAGTTGAAAGTATC
* ** * * *
17078565 AATTTTCCTTGAAAATAAAAACTTCAAAAGTATTTTTTGAGAAAAAGTTGACAGTATC
1 AATTTTCCTT-AAAATAAAAATTTCAAAAAAATTTTTTAAGGAAAAGTTGAAAGTATC
* *
17078623 AATTTTCCTTAAAAATAAAAATTTTCAAAAAATATTTTTTGAGGAAAAGTTGAAAGTATT
1 AATTTTCCTT-AAAATAAAAA-TTTCAAAAAA-ATTTTTTAAGGAAAAGTTGAAAGTATC
17078683 AATTTTCCTT
1 AATTTTCCTT
17078693 GAATAAAGGC
Statistics
Matches: 264, Mismatches: 29, Indels: 32
0.81 0.09 0.10
Matches are distributed among these distances:
56 6 0.02
57 8 0.03
58 85 0.32
59 22 0.08
60 60 0.23
61 31 0.12
62 5 0.02
63 2 0.01
64 41 0.16
65 4 0.02
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (57 bp):
AATTTTCCTTAAAATAAAAATTTCAAAAAAATTTTTTAAGGAAAAGTTGAAAGTATC
Found at i:17078581 original size:119 final size:118
Alignment explanation
Indices: 17078326--17078695 Score: 406
Period size: 119 Copynumber: 3.1 Consensus size: 118
17078316 AATTTTCAAT
* * * ** * * *
17078326 AATTTT-CTT-AAAATAAAAATTTTAAAAAAATACTTTAAGGAAAAGTTGAAAGTATCAATTTTT
1 AATTTTCCTTGAAAATAAAAACTTCAAAAATATTTTTTGAGAAAAAGTTGAAAGTATCAATTTTC
* * *** ** *
17078389 CTTAAAAGTAAAAATTAAAAAAAAAAATAGACATTTTAAGGAAAAGTTAAAAGTATC
66 CCTAAAAATAAAAATT--TTCAAAAAAT--ATTTTTTAAGGAAAAGTTGAAAGTATC
* * * *
17078446 AATTTTTCTTGAAAATAAAAATTTCAAAAATATTTTTTTGGGGAAAAGTT-AAAGTATCAATTTT
1 AATTTTCCTTGAAAATAAAAACTTCAAAAATA-TTTTTTGAGAAAAAGTTGAAAGTATCAATTTT
* *
17078510 CCCTGAAAATAAAAA-TTTCAAAAAATATTTTTTTTAAGAAAAAGTTGAAAGTATC
65 CCCTAAAAATAAAAATTTTCAAAAAATA--TTTTTTAAGGAAAAGTTGAAAGTATC
* *
17078565 AATTTTCCTTGAAAATAAAAACTTCAAAAGTATTTTTTGAGAAAAAGTTGACAGTATCAATTTTC
1 AATTTTCCTTGAAAATAAAAACTTCAAAAATATTTTTTGAGAAAAAGTTGAAAGTATCAATTTTC
* * *
17078630 CTTAAAAATAAAAATTTTCAAAAAATATTTTTTGAGGAAAAGTTGAAAGTATT
66 CCTAAAAATAAAAATTTTCAAAAAATATTTTTTAAGGAAAAGTTGAAAGTATC
17078683 AATTTTCCTTGAA
1 AATTTTCCTTGAA
17078696 TAAAGGCAGT
Statistics
Matches: 215, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
117 1 0.00
118 51 0.24
119 84 0.39
120 18 0.08
121 4 0.02
122 44 0.20
123 13 0.06
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (118 bp):
AATTTTCCTTGAAAATAAAAACTTCAAAAATATTTTTTGAGAAAAAGTTGAAAGTATCAATTTTC
CCTAAAAATAAAAATTTTCAAAAAATATTTTTTAAGGAAAAGTTGAAAGTATC
Found at i:17078595 original size:34 final size:34
Alignment explanation
Indices: 17078496--17078597 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 34
17078486 GGGAAAAGTT
* *
17078496 AAAGTATCAATTTTCCCTGAAAATAAAAATTTCA
1 AAAGTATCAATTTTCCTTGAAAATAAAAACTTCA
* ** * * *
17078530 AAA-AAT--ATTTT--TT-TTAAGAAAAAGTT-G
1 AAAGTATCAATTTTCCTTGAAAATAAAAACTTCA
17078557 AAAGTATCAATTTTCCTTGAAAATAAAAACTTCA
1 AAAGTATCAATTTTCCTTGAAAATAAAAACTTCA
17078591 AAAGTAT
1 AAAGTAT
17078598 TTTTTGAGAA
Statistics
Matches: 48, Mismatches: 13, Indels: 14
0.64 0.17 0.19
Matches are distributed among these distances:
27 3 0.06
28 11 0.23
29 1 0.02
30 5 0.10
31 5 0.10
32 2 0.04
33 11 0.23
34 10 0.21
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (34 bp):
AAAGTATCAATTTTCCTTGAAAATAAAAACTTCA
Found at i:17079540 original size:24 final size:23
Alignment explanation
Indices: 17079501--17079597 Score: 90
Period size: 23 Copynumber: 4.2 Consensus size: 23
17079491 GAAGGAGAAA
* *
17079501 AGAACC-AAAAATAAAAGAAAAG
1 AGAACCAAAAAAAAAAAAAAAAG
17079523 AGAACCAAAAAAAGAAAAAAAAAAAG
1 AGAACC--AAAAA-AAAAAAAAAAAG
* **
17079549 AAAACCAAAATTAAAAAAAAAAG
1 AGAACCAAAAAAAAAAAAAAAAG
* *
17079572 TGAACTAAAAAAAAAAAAAAAA-
1 AGAACCAAAAAAAAAAAAAAAAG
17079594 AGAA
1 AGAA
17079598 AGAGAATGAA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
22 9 0.15
23 28 0.47
24 4 0.07
25 4 0.07
26 15 0.25
ACGTcount: A:0.78, C:0.07, G:0.09, T:0.05
Consensus pattern (23 bp):
AGAACCAAAAAAAAAAAAAAAAG
Found at i:17079557 original size:48 final size:47
Alignment explanation
Indices: 17079503--17079598 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 47
17079493 AGGAGAAAAG
*
17079503 AACCAAAAAT-AAAAGAAAAGAGAACCAAAAAAAGAAAAAAAAAAAGAA
1 AACCAAAAATAAAAAAAAAAGAGAA-CAAAAAAA-AAAAAAAAAAAGAA
* * *
17079551 AACCAAAATTAAAAAAAAAAGTGAACTAAAAAAAAAAAAAAAAAGAA
1 AACCAAAAATAAAAAAAAAAGAGAACAAAAAAAAAAAAAAAAAAGAA
17079598 A
1 A
17079599 GAGAATGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 15 0.35
48 16 0.37
49 12 0.28
ACGTcount: A:0.79, C:0.07, G:0.08, T:0.05
Consensus pattern (47 bp):
AACCAAAAATAAAAAAAAAAGAGAACAAAAAAAAAAAAAAAAAAGAA
Found at i:17089872 original size:45 final size:45
Alignment explanation
Indices: 17089820--17089909 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
17089810 ATATTCATGT
17089820 GCAAGTACTTCTAACATATATAAGTATAAGCTAAAATAATAAAGA
1 GCAAGTACTTCTAACATATATAAGTATAAGCTAAAATAATAAAGA
*
17089865 GCAAGTACTTCTAACATATATAAGTATAAGTTAAAATAATAAAGA
1 GCAAGTACTTCTAACATATATAAGTATAAGCTAAAATAATAAAGA
17089910 AGTCCATGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28
Consensus pattern (45 bp):
GCAAGTACTTCTAACATATATAAGTATAAGCTAAAATAATAAAGA
Found at i:17089895 original size:25 final size:25
Alignment explanation
Indices: 17089822--17089895 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
17089812 ATTCATGTGC
17089822 AAGTACTTCTAACATATATAAGTAT
1 AAGTACTTCTAACATATATAAGTAT
* *
17089847 AAG-----CTAAAATA-ATAAAG-AGC
1 AAGTACTTCTAACATATAT-AAGTA-T
17089867 AAGTACTTCTAACATATATAAGTAT
1 AAGTACTTCTAACATATATAAGTAT
17089892 AAGT
1 AAGT
17089896 TAAAATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 3 0.08
20 13 0.36
25 17 0.47
26 3 0.08
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (25 bp):
AAGTACTTCTAACATATATAAGTAT
Found at i:17090524 original size:30 final size:31
Alignment explanation
Indices: 17090490--17090563 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
17090480 CAAATATATA
17090490 AAATAAATTTTTAAAC-TTTAATTTATA-TCT
1 AAATAAATTTTTAAACTTTTAATTTATACT-T
* * *
17090520 AAATAAGTTCTT-ATCTTTTAATTTATACTT
1 AAATAAATTTTTAAACTTTTAATTTATACTT
17090550 AAATAAATTTTTAA
1 AAATAAATTTTTAA
17090564 TATAACTCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 2 0.06
30 32 0.89
31 2 0.06
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (31 bp):
AAATAAATTTTTAAACTTTTAATTTATACTT
Found at i:17090963 original size:6 final size:6
Alignment explanation
Indices: 17090954--17090984 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
17090944 CCCCCTACCG
*
17090954 CTAACC CTAACC CTAACC CTAACC CCAACC C
1 CTAACC CTAACC CTAACC CTAACC CTAACC C
17090985 CAAACCCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.55, G:0.00, T:0.13
Consensus pattern (6 bp):
CTAACC
Found at i:17093978 original size:2 final size:2
Alignment explanation
Indices: 17093973--17094009 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17093963 TCTCTCTCTC
17093973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17094010 TTAAGTAGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17094895 original size:261 final size:258
Alignment explanation
Indices: 17094411--17094896 Score: 819
Period size: 261 Copynumber: 1.9 Consensus size: 258
17094401 GTTTGACTTG
* *
17094411 AAATCCTTTAATATATATTTATATAATCATATAATTAGTTCGTTTATGTTTTTTGGTTAAAAAAA
1 AAATCCTTTAATATATATTTATATAATCATATAATTAGTTCGTTTATGTTATTTAGTTAAAAAAA
* *
17094476 TTAAATTAACTTTCACATTATAATTATTATTTGTTAATTTGTTAATTTAATTTTATGCATTGTAA
66 TTAAATTAACTTTCACATTATAATTATTATTAGTTAATTTGTTAATTTAATTTTATGCATTGCAA
* * * * * *
17094541 TTAGATATGTTCAAAGGTCGGGTTATCCATCCAAATTCAAAAGTTTGTTTAAGTTTTAAGAGGGT
131 TTAGACATATTCAAAGGTCGGGTTACCCATCCAAATCCAAAAGTCTGTTTAAGTTTTAAGAGAGT
* *
17094606 TTAGACAAAAAAATTAAGACTTGTTAAATGGGAGGGTCTACCCTCCCTTCCCCCCCGGAAAAA
196 TTAGACAAAAAAATTAAAACTCGTTAAATGGGAGGGTCTACCCTCCCTTCCCCCCCGGAAAAA
17094669 AAATCCTTTAATATATATGTTTATATAATCATATAATTAGTTCGTTTATGTTATTTAGTTAAAAA
1 AAATCCTTTAATATATA--TTTATATAATCATATAATTAGTTCGTTTATGTTATTTAGTT-AAAA
17094734 AAATTAAATTAACTTTCACATTATAATTATTATTAGTTAATTTGTTAATTTAATTTTATGCATTG
63 AAATTAAATTAACTTTCACATTATAATTATTATTAGTTAATTTGTTAATTTAATTTTATGCATTG
* *
17094799 CAATTAGACATATTCAAAGGTTGGGTTACCCATCCAAATCCAAAGGTCTGTTTAAGTTTTAAGAG
128 CAATTAGACATATTCAAAGGTCGGGTTACCCATCCAAATCCAAAAGTCTGTTTAAGTTTTAAGAG
17094864 AGTTTAGACAAAAAAATTAAAACTCGTTAAATG
193 AGTTTAGACAAAAAAATTAAAACTCGTTAAATG
17094897 AGTTTGAACA
Statistics
Matches: 211, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
258 17 0.08
260 39 0.18
261 155 0.73
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (258 bp):
AAATCCTTTAATATATATTTATATAATCATATAATTAGTTCGTTTATGTTATTTAGTTAAAAAAA
TTAAATTAACTTTCACATTATAATTATTATTAGTTAATTTGTTAATTTAATTTTATGCATTGCAA
TTAGACATATTCAAAGGTCGGGTTACCCATCCAAATCCAAAAGTCTGTTTAAGTTTTAAGAGAGT
TTAGACAAAAAAATTAAAACTCGTTAAATGGGAGGGTCTACCCTCCCTTCCCCCCCGGAAAAA
Found at i:17095013 original size:23 final size:23
Alignment explanation
Indices: 17094987--17095030 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17094977 TCCAGTCCGA
17094987 ATTTACATATATATAAATTATTT
1 ATTTACATATATATAAATTATTT
* * *
17095010 ATTTATATATATGTGAATTAT
1 ATTTACATATATATAAATTAT
17095031 ATAAAAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
ATTTACATATATATAAATTATTT
Found at i:17095133 original size:16 final size:17
Alignment explanation
Indices: 17095112--17095147 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
17095102 ATATATATAA
17095112 TTATAT-ATTTTTATTT
1 TTATATAATTTTTATTT
17095128 TTATATAATTTTTATTT
1 TTATATAATTTTTATTT
17095145 TTA
1 TTA
17095148 ATTTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATATAATTTTTATTT
Found at i:17095137 original size:24 final size:24
Alignment explanation
Indices: 17095105--17095158 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
17095095 AATTCACATA
17095105 TATATAATTATATATTTTT-ATTTT
1 TATATAATT-TATATTTTTAATTTT
*
17095129 TATATAATTTTTATTTTTAATTTT
1 TATATAATTTATATTTTTAATTTT
17095153 TATATA
1 TATATA
17095159 TATGTAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 8 0.29
24 20 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TATATAATTTATATTTTTAATTTT
Found at i:17101289 original size:43 final size:44
Alignment explanation
Indices: 17101196--17101324 Score: 224
Period size: 43 Copynumber: 2.9 Consensus size: 44
17101186 ACCTCTAATC
* *
17101196 TTTATACGTGTGTACATTTTGGTGACTAATTGTATTATGGTATAT
1 TTTATATGTGTGTATATTTTGGTGAC-AATTGTATTATGGTATAT
17101241 TTTATATGTGTGTATATTTTGGTGACAATTGTATTATGGTATA-
1 TTTATATGTGTGTATATTTTGGTGACAATTGTATTATGGTATAT
17101284 TTTATATGTGTGTATATTTTGGTGACAATTGTATTATGGTA
1 TTTATATGTGTGTATATTTTGGTGACAATTGTATTATGGTA
17101325 GGATTTTTTT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
43 41 0.50
44 17 0.21
45 24 0.29
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.50
Consensus pattern (44 bp):
TTTATATGTGTGTATATTTTGGTGACAATTGTATTATGGTATAT
Found at i:17103945 original size:137 final size:136
Alignment explanation
Indices: 17103762--17104037 Score: 444
Period size: 137 Copynumber: 2.0 Consensus size: 136
17103752 TAATGAGTGT
* * * *
17103762 TCTTCACCTAAAGACTTGTCATGGCACTAGCACCCAATATTTTCCTTAAGCTTTATATCAAATGA
1 TCTTCACCCAAAGACTCGTCATGGCACTAGCACCCAATATTTTCCTTAAACTTTATATCAAATAA
*
17103827 GCTTGAATGAAAAAAATTCTTTTTTAAATATTCTTAAGGAAATAAAAACTCTGGATGAATACTCT
66 GCTTGAATG-AAAAAATTCTTTTTTAAAGATTCTTAAGGAAATAAAAACTCTGGATGAATACTCT
17103892 TCCAATA
130 TCCAATA
* * * *
17103899 TCTTTACCCAAAGACTCGTCTTGGTACTAGTACCCAATATTTTCCTTAAACTTTATATCAAATAA
1 TCTTCACCCAAAGACTCGTCATGGCACTAGCACCCAATATTTTCCTTAAACTTTATATCAAATAA
*
17103964 GCTTGAATGAAAAAATTTTTTTTTAAAGATTCTTAAGGAAATAAAAACTCTGGATGAATACTCTT
66 GCTTGAATGAAAAAATTCTTTTTTAAAGATTCTTAAGGAAATAAAAACTCTGGATGAATACTCTT
*
17104029 CTAATA
131 CCAATA
17104035 TCT
1 TCT
17104038 CATGTTGTGT
Statistics
Matches: 128, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
136 62 0.48
137 66 0.52
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (136 bp):
TCTTCACCCAAAGACTCGTCATGGCACTAGCACCCAATATTTTCCTTAAACTTTATATCAAATAA
GCTTGAATGAAAAAATTCTTTTTTAAAGATTCTTAAGGAAATAAAAACTCTGGATGAATACTCTT
CCAATA
Found at i:17116689 original size:414 final size:416
Alignment explanation
Indices: 17115862--17116694 Score: 1391
Period size: 414 Copynumber: 2.0 Consensus size: 416
17115852 GTAGGTAAGC
17115862 TGAGGGGGTCAATAATAGGACAATTAGGACAAGTATGAATTGAAGTGGCACTGACTATGTTAGGC
1 TGAGGGGGTCAATAATAGGACAATTAGGACAAGTATGAATTGAAGTGGCACTGACTATGTTAGGC
** * * * *
17115927 CAACTTGACATGTTAGGTCAGACAAATGACAAAGATGCCTCTGGTTGTCTATTGAATGCTTCAAG
66 CAACTTGACATGTTAGGTCAGACAAATGACAAAGACACCCCCGATTGTCTACTGAATGCTTCAAG
* * *
17115992 AAGGGAAAAGACTACTATACCCTTTTGACCATCAAATGCCCCTAACACTTTATCCTCTTATCAGG
131 AAAGGAAAAGACCACTATACCCTTTTAACCATCAAATGCCCCTAACACTTTATCCTCTTATCAGG
*
17116057 CAGTCTAAGTATCAAATTGCCAAATTTGTTACCGACTTCCTCGATGTGGGACAGATTGGCTGCAT
196 CAGTCTAAGTATCAAATTGCCAAATTTGTTACCGACTTCCTCGATGTGGGACAAATTGGCTGCAT
*
17116122 GGTTCATCAAAGGCCGACGTTGCAAGAGGAGGTTGATTTTGGACGATAACTAACTTTGAACAACG
261 GGTTCATCAAAGGCCAACGTTGCAAGAGGAGGTTGATTTTGGACGATAACTAACTTTGAACAACG
* * *
17116187 ATTCAACCTGGTGGTTATCCGATCTCATGCATGTGTTCTAAACGAAGTGCATAATTAATTTAAAG
326 ATTCAACCTGGTGGTTATCCGATCTCATGCATATGTTCTAAACGAAGTGCATAATTAAATGAAAG
17116252 ATTGCTAAGGTGATAATTGTCTGGAG
391 ATTGCTAAGGTGATAATTGTCTGGAG
*
17116278 TGAGGGGG-CAATAATAGGACAATTAGGACAAGTATGAGTTGAAGTGGCACTGACT-TGTTAGGC
1 TGAGGGGGTCAATAATAGGACAATTAGGACAAGTATGAATTGAAGTGGCACTGACTATGTTAGGC
* *
17116341 CAGCTTGACATGTTAGGTTAGACAAATGACAAAGACACCCCCGATTGTCTACTGAATGCTTCAAG
66 CAACTTGACATGTTAGGTCAGACAAATGACAAAGACACCCCCGATTGTCTACTGAATGCTTCAAG
*
17116406 AAAGGAAAAGACCACTATACTCTTTTAACCATCAAATGCCCCTAACACTTTATCCTCTTATCAGG
131 AAAGGAAAAGACCACTATACCCTTTTAACCATCAAATGCCCCTAACACTTTATCCTCTTATCAGG
* * *
17116471 CAGTCTAAGTATCAGATTGTCAAATTTGTTACTGACTTCCTCGATGTGGGACAAATTGGCTGCAT
196 CAGTCTAAGTATCAAATTGCCAAATTTGTTACCGACTTCCTCGATGTGGGACAAATTGGCTGCAT
* * * * *
17116536 GGTTCATCAAAGGCCAATGTTGCAGGGGGAGGTTGATTTTGGATGATAACTAACTTTGAGCAACG
261 GGTTCATCAAAGGCCAACGTTGCAAGAGGAGGTTGATTTTGGACGATAACTAACTTTGAACAACG
* *
17116601 ATTCAACCTGGTGGTTATCCGATCTCATGCATATGTTCTAAATGGAGTGCATAATTAAATGAAAG
326 ATTCAACCTGGTGGTTATCCGATCTCATGCATATGTTCTAAACGAAGTGCATAATTAAATGAAAG
*
17116666 ATTGCTAAGGTGATAATTGTCTGGGG
391 ATTGCTAAGGTGATAATTGTCTGGAG
17116692 TGA
1 TGA
17116695 TTCGAGGTTA
Statistics
Matches: 388, Mismatches: 29, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
414 334 0.86
415 46 0.12
416 8 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (416 bp):
TGAGGGGGTCAATAATAGGACAATTAGGACAAGTATGAATTGAAGTGGCACTGACTATGTTAGGC
CAACTTGACATGTTAGGTCAGACAAATGACAAAGACACCCCCGATTGTCTACTGAATGCTTCAAG
AAAGGAAAAGACCACTATACCCTTTTAACCATCAAATGCCCCTAACACTTTATCCTCTTATCAGG
CAGTCTAAGTATCAAATTGCCAAATTTGTTACCGACTTCCTCGATGTGGGACAAATTGGCTGCAT
GGTTCATCAAAGGCCAACGTTGCAAGAGGAGGTTGATTTTGGACGATAACTAACTTTGAACAACG
ATTCAACCTGGTGGTTATCCGATCTCATGCATATGTTCTAAACGAAGTGCATAATTAAATGAAAG
ATTGCTAAGGTGATAATTGTCTGGAG
Found at i:17122525 original size:18 final size:19
Alignment explanation
Indices: 17122490--17122526 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17122480 TCGATTGAGC
*
17122490 ACATCTATTCTATCTTTTA
1 ACATCTATACTATCTTTTA
17122509 ACATCTATACT-TCTTTTA
1 ACATCTATACTATCTTTTA
17122527 CCAAGGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (19 bp):
ACATCTATACTATCTTTTA
Found at i:17128402 original size:3 final size:3
Alignment explanation
Indices: 17128396--17128446 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
17128386 TAATAATAAA
* *
17128396 GAT GAT GAT GAT GAT GAT GAT GAT GAT GCT GAT GCT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
17128444 GAT
1 GAT
17128447 AGTCAACAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:17143282 original size:17 final size:15
Alignment explanation
Indices: 17143249--17143279 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17143239 CTTGCTTTAT
*
17143249 TTTTTTCTCTACATA
1 TTTTTTCGCTACATA
17143264 TTTTTTCGCTACATA
1 TTTTTTCGCTACATA
17143279 T
1 T
17143280 ATTATTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTTTTCGCTACATA
Found at i:17147698 original size:13 final size:13
Alignment explanation
Indices: 17147682--17147721 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
17147672 AAGGTTTTAG
17147682 TTTAGGGTTTCAT
1 TTTAGGGTTTCAT
* *
17147695 TTTAGGATTTTAT
1 TTTAGGGTTTCAT
*
17147708 TTTGGGGTTTCAT
1 TTTAGGGTTTCAT
17147721 T
1 T
17147722 CTAAGGTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.15, C:0.05, G:0.23, T:0.57
Consensus pattern (13 bp):
TTTAGGGTTTCAT
Found at i:17147731 original size:26 final size:26
Alignment explanation
Indices: 17147670--17147732 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
17147660 TTGATTTTAC
17147670 CTAAGGTTTTAGTTTAGGGTTTCATT
1 CTAAGGTTTTAGTTTAGGGTTTCATT
* * *
17147696 -TTAGGATTTTATTTTGGGGTTTCATT
1 CTAAGG-TTTTAGTTTAGGGTTTCATT
17147722 CTAAGGTTTTA
1 CTAAGGTTTTA
17147733 CTGAGGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 4 0.13
26 23 0.74
27 4 0.13
ACGTcount: A:0.19, C:0.06, G:0.22, T:0.52
Consensus pattern (26 bp):
CTAAGGTTTTAGTTTAGGGTTTCATT
Found at i:17147887 original size:3 final size:3
Alignment explanation
Indices: 17147879--17147921 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
17147869 TTTTTATTTT
*
17147879 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17147922 ACTTTTTCCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17148524 original size:14 final size:14
Alignment explanation
Indices: 17148505--17148533 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17148495 ACTTGCAAAG
17148505 CTTTAAACTTTTCC
1 CTTTAAACTTTTCC
17148519 CTTTAAACTTTTCC
1 CTTTAAACTTTTCC
17148533 C
1 C
17148534 CATAAGCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (14 bp):
CTTTAAACTTTTCC
Found at i:17150335 original size:12 final size:12
Alignment explanation
Indices: 17150292--17150396 Score: 81
Period size: 12 Copynumber: 8.5 Consensus size: 12
17150282 TTAATCTTTA
*
17150292 TTATTATTTATTA
1 TTATT-TTTATTT
*
17150305 TTATATTTACTATT
1 TTATTTTTA-T-TT
*
17150319 ATATTTTTATTT
1 TTATTTTTATTT
17150331 TTATTTTTATTT
1 TTATTTTTATTT
*
17150343 TTGGTTTTTA-TT
1 TT-ATTTTTATTT
17150355 TTA-TTTTA-TT
1 TTATTTTTATTT
*
17150365 TTACTTTTTAATT
1 TTA-TTTTTATTT
*
17150378 TTATTATTATTTT
1 TTATTTTTA-TTT
17150391 TTATTT
1 TTATTT
17150397 AATGGCTAAC
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
10 10 0.13
12 33 0.44
13 24 0.32
14 8 0.11
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (12 bp):
TTATTTTTATTT
Found at i:17150341 original size:18 final size:19
Alignment explanation
Indices: 17150298--17150396 Score: 82
Period size: 18 Copynumber: 5.4 Consensus size: 19
17150288 TTTATTATTA
* *
17150298 TTTATTATTATATTTACTAT
1 TTTATTTTTATTTTTACT-T
*
17150318 TATATTTTTATTTTTA-TT
1 TTTATTTTTATTTTTACTT
*
17150336 TTTATTTTTGGTTTTTA--T
1 TTTATTTTT-ATTTTTACTT
17150354 TTTA-TTTTA-TTTTACTT
1 TTTATTTTTATTTTTACTT
* * *
17150371 TTTAATTTTATTATTATTT
1 TTTATTTTTATTTTTACTT
17150390 TTTATTT
1 TTTATTT
17150397 AATGGCTAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
15 5 0.08
17 9 0.14
18 19 0.29
19 19 0.29
20 13 0.20
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTATTTTTATTTTTACTT
Found at i:17150372 original size:29 final size:28
Alignment explanation
Indices: 17150272--17150390 Score: 89
Period size: 29 Copynumber: 4.0 Consensus size: 28
17150262 TTACTTATTG
17150272 TTTTTATTTATTAATCTTTATTATTA-TTTA
1 TTTTTATTT-TTAAT-TTTATT-TTATTTTA
* * *
17150302 TTATTATATTTACTATTATATTTTTATTTTTA
1 TTTTTATTTTTA--ATTTTA-TTTTA-TTTTA
**
17150334 TTTTTATTTTTGGTTTTTATTTTATTTTA
1 TTTTTATTTTT-AATTTTATTTTATTTTA
17150363 -TTTTACTTTTTAATTTTATTATTATTTT
1 TTTTTA-TTTTTAATTTTATT-TTATTTT
17150391 TTATTTAATG
Statistics
Matches: 71, Mismatches: 10, Indels: 17
0.72 0.10 0.17
Matches are distributed among these distances:
28 12 0.17
29 20 0.28
30 18 0.25
31 8 0.11
32 13 0.18
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.73
Consensus pattern (28 bp):
TTTTTATTTTTAATTTTATTTTATTTTA
Found at i:17150456 original size:12 final size:13
Alignment explanation
Indices: 17150438--17150467 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
17150428 AAGGATTAAT
17150438 ATTTTATTAGGCC
1 ATTTTATTAGGCC
17150451 -TTTTATTAGGCC
1 ATTTTATTAGGCC
17150463 ATTTT
1 ATTTT
17150468 GGGCTTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (13 bp):
ATTTTATTAGGCC
Found at i:17151126 original size:31 final size:32
Alignment explanation
Indices: 17151076--17151196 Score: 154
Period size: 32 Copynumber: 3.8 Consensus size: 32
17151066 GCTTAAAAAC
*
17151076 TTGGATGCCAGCTAAATTGGGCTTAAA-TTTCT
1 TTGG-TGCTAGCTAAATTGGGCTTAAATTTTCT
** *
17151108 TTGGTGCTAATTAAATTGGACTTAAATTTTCT
1 TTGGTGCTAGCTAAATTGGGCTTAAATTTTCT
* * * *
17151140 TTGGTGCCAGCTAGACTGAGCTTAAATTTTCT
1 TTGGTGCTAGCTAAATTGGGCTTAAATTTTCT
17151172 TTGGTGCTAGCTAAATTGGGCTTAA
1 TTGGTGCTAGCTAAATTGGGCTTAA
17151197 CTTTGGGTAC
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
31 18 0.25
32 55 0.75
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (32 bp):
TTGGTGCTAGCTAAATTGGGCTTAAATTTTCT
Found at i:17151187 original size:64 final size:64
Alignment explanation
Indices: 17151076--17151196 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
17151066 GCTTAAAAAC
* * *
17151076 TTGGATGCCAGCTAAATTGGGCTTAAATTTCTTTGGTGCTAATTAAATTGGACTTAAATTTTCT
1 TTGGATGCCAGCTAAACTGAGCTTAAATTTCTTTGGTGCTAACTAAATTGGACTTAAATTTTCT
* * *
17151140 TTGG-TGCCAGCTAGACTGAGCTTAAATTTTCTTTGGTGCTAGCTAAATTGGGCTTAA
1 TTGGATGCCAGCTAAACTGAGCTTAAA-TTTCTTTGGTGCTAACTAAATTGGACTTAA
17151197 CTTTGGGTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
63 19 0.38
64 31 0.62
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (64 bp):
TTGGATGCCAGCTAAACTGAGCTTAAATTTCTTTGGTGCTAACTAAATTGGACTTAAATTTTCT
Found at i:17151223 original size:28 final size:27
Alignment explanation
Indices: 17151170--17151224 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
17151160 CTTAAATTTT
* * * *
17151170 CTTTGGTGCTAGCTAAATTGGGCTTAA
1 CTTTGGTACTAGCTAAACTAGACTTAA
17151197 CTTTGGGTACTAGCTAAACTAGACTTAA
1 CTTT-GGTACTAGCTAAACTAGACTTAA
17151225 GACTTCATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (27 bp):
CTTTGGTACTAGCTAAACTAGACTTAA
Found at i:17151289 original size:34 final size:32
Alignment explanation
Indices: 17151208--17151291 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
17151198 TTTGGGTACT
* *
17151208 AGCTAAACTAGACTTAAGACTTCATGAGTGCC
1 AGCTAAACTAGGCTTAAAACTTCATGAGTGCC
** * * *
17151240 AATTAAACTAAGCTTAAAATTTCATTAGATGCC
1 AGCTAAACTAGGCTTAAAACTTCATGAG-TGCC
17151273 AGCTAATACTAGGCTTAAA
1 AGCTAA-ACTAGGCTTAAA
17151292 TTTTGGATAA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
32 21 0.52
33 8 0.20
34 11 0.28
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (32 bp):
AGCTAAACTAGGCTTAAAACTTCATGAGTGCC
Found at i:17151621 original size:61 final size:59
Alignment explanation
Indices: 17151496--17151622 Score: 137
Period size: 61 Copynumber: 2.1 Consensus size: 59
17151486 AATACTACGG
* * * * **
17151496 TTAAAACCTAGGTGACAGCTAATTGGACTTAAATTTGATTAATGCTAGTTAAATTGGGC
1 TTAAAATCTAGGTGACAGCTAACTAGACTTAAATTTGATTAATGCCAACTAAATTGGGC
* * * * *
17151555 CTAAAATCTAGGTGCCAGCTAAACTAGACTTAAATTTTTATTGATGCCAACTAAATTGGGT
1 TTAAAATCTAGGTGACAGCT-AACTAGACTTAAA-TTTGATTAATGCCAACTAAATTGGGC
17151616 TTAAAAT
1 TTAAAAT
17151623 TTCATTGGTT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
59 17 0.31
60 11 0.20
61 26 0.48
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (59 bp):
TTAAAATCTAGGTGACAGCTAACTAGACTTAAATTTGATTAATGCCAACTAAATTGGGC
Found at i:17151663 original size:22 final size:22
Alignment explanation
Indices: 17151638--17151680 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17151628 TGGTTACTAG
* *
17151638 CTAAACTGAGCTTATGTGCCAA
1 CTAAACTGAGCCTACGTGCCAA
17151660 CTAAACTGAGCCTACGTGCCA
1 CTAAACTGAGCCTACGTGCCA
17151681 TATATTTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (22 bp):
CTAAACTGAGCCTACGTGCCAA
Found at i:17159079 original size:16 final size:17
Alignment explanation
Indices: 17159060--17159097 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
17159050 TTTTAAATTA
*
17159060 TTAAATTTAAT-ATTTT
1 TTAAATATAATAATTTT
*
17159076 TTAAATATCATAATTTT
1 TTAAATATAATAATTTT
17159093 TTAAA
1 TTAAA
17159098 AAATTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAATATAATAATTTT
Found at i:17159108 original size:17 final size:16
Alignment explanation
Indices: 17159069--17159111 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
17159059 ATTAAATTTA
*
17159069 ATATTTTTTAAATATC
1 ATATTTTTTAAAAATC
*
17159085 ATAATTTTTTAAAAAATT
1 AT-ATTTTTT-AAAAATC
17159103 ATATTTTTT
1 ATATTTTTT
17159112 GAATTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 7 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTTTTAAAAATC
Found at i:17159263 original size:37 final size:38
Alignment explanation
Indices: 17159182--17159267 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 38
17159172 AATTTTCTAG
*
17159182 ATTTTTAAAAATATTAAATTTACTTTTTTCAAATATTTTA
1 ATTTTT-AAAATA-TAAATTCACTTTTTTCAAATATTTTA
* * *
17159222 ATTTTTAAAATA-AAATTCA-TTTTTTGAAATTTTTTCT
1 ATTTTTAAAATATAAATTCACTTTTTTCAAATATTTT-A
17159259 ATTTTTAAA
1 ATTTTTAAA
17159268 TTTTAGCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 14 0.34
37 15 0.37
39 6 0.15
40 6 0.15
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (38 bp):
ATTTTTAAAATATAAATTCACTTTTTTCAAATATTTTA
Found at i:17159623 original size:20 final size:20
Alignment explanation
Indices: 17159571--17159622 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
17159561 AACTCTGTCT
* * *
17159571 AAAACAAAAAAAATATATAA
1 AAAACATAAAAATTTTATAA
*
17159591 AAAATATAAAAATTTTATAGA
1 AAAACATAAAAATTTTATA-A
17159612 AAAACATAAAA
1 AAAACATAAAA
17159623 TAAAAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAACATAAAAATTTTATAA
Found at i:17159825 original size:18 final size:18
Alignment explanation
Indices: 17159776--17159826 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
17159766 AATATTTAAT
*
17159776 ATTTTTAAAAAATCTATGA
1 ATTTTT-AAAAATATATGA
*
17159795 ATTTTCTTAAAATAT-TGA
1 ATTTT-TAAAAATATATGA
17159813 ATTTTTAAGAAATA
1 ATTTTTAA-AAATA
17159827 AAACCAGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 2 0.07
18 13 0.48
19 11 0.41
20 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (18 bp):
ATTTTTAAAAATATATGA
Found at i:17161611 original size:99 final size:99
Alignment explanation
Indices: 17161490--17161680 Score: 319
Period size: 99 Copynumber: 1.9 Consensus size: 99
17161480 AGATTTACTT
*
17161490 TATTCTCTTTAATCCAAGTTCTTTATTTATATTGATACTTTATTTACATTTTGTTTTAATCATGT
1 TATTCTCTTTAATCCAAGTTCTTTATTTATATTCATACTTTATTTACATTTTGTTTTAATCATGT
*
17161555 TAAATTCACATTTTATTTATATTTTTATCTAAAG
66 TAAATTCACATTTTATTCATATTTTTATCTAAAG
* * * *
17161589 TATTCTCTTTATTCCAAGTTCTTTATTTATATTCATCCTTTTTTTACATTTTGTTTTAATTATGT
1 TATTCTCTTTAATCCAAGTTCTTTATTTATATTCATACTTTATTTACATTTTGTTTTAATCATGT
*
17161654 TAAATTCACGTTTTATTCATATTTTTA
66 TAAATTCACATTTTATTCATATTTTTA
17161681 AAGAATTTAT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 85 1.00
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.58
Consensus pattern (99 bp):
TATTCTCTTTAATCCAAGTTCTTTATTTATATTCATACTTTATTTACATTTTGTTTTAATCATGT
TAAATTCACATTTTATTCATATTTTTATCTAAAG
Found at i:17166695 original size:22 final size:23
Alignment explanation
Indices: 17166652--17166706 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
17166642 TTAATTTTTT
*
17166652 ATTTTTATATATTATTTTAATAA
1 ATTTTTATATATTATTTAAATAA
17166675 GATTTTTA-ATA-TATTTAAATAA
1 -ATTTTTATATATTATTTAAATAA
17166697 ATTTATTATA
1 ATTT-TTATA
17166707 AAATAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.14
22 13 0.46
23 4 0.14
24 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTTTATATATTATTTAAATAA
Found at i:17169620 original size:63 final size:61
Alignment explanation
Indices: 17169455--17169636 Score: 186
Period size: 63 Copynumber: 2.9 Consensus size: 61
17169445 AAAAAGGTAT
* * * * * * *
17169455 AGGAATATTTAAGGCGTTTTCCAACTAGAAATATCTTAAATAATCTTGTTCTATTTTTTTATT
1 AGGATTATTTAAGGCATTTTTCGACTAAAAATATCTTAAATAATCCT-TT-TATTTTTTTATG
* * *
17169518 AGAGATTATTTAAGGCATTTCTAG-CTAGAAAACATCTTAAATAATACCTTTTATTTTTTATATG
1 AG-GATTATTTAAGGCATTTTTCGACTA-AAAATATCTTAAATAAT-CCTTTTATTTTTT-TATG
* *
17169582 AGGATTATTTAAGGCATTTTTCGACCAAAAATACCTTAAATAATCCATTTTATTT
1 AGGATTATTTAAGGCATTTTTCGACTAAAAATATCTTAAATAATCC-TTTTATTT
17169637 AAAGGGGATT
Statistics
Matches: 98, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
62 2 0.02
63 55 0.56
64 39 0.40
65 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (61 bp):
AGGATTATTTAAGGCATTTTTCGACTAAAAATATCTTAAATAATCCTTTTATTTTTTTATG
Found at i:17172501 original size:19 final size:17
Alignment explanation
Indices: 17172465--17172498 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17172455 AGCTTCCTAT
17172465 ATAGAGAGATCAAGGGG
1 ATAGAGAGATCAAGGGG
17172482 ATAGAGAGATCAAGGGG
1 ATAGAGAGATCAAGGGG
17172499 GGACAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.41, T:0.12
Consensus pattern (17 bp):
ATAGAGAGATCAAGGGG
Found at i:17180925 original size:34 final size:33
Alignment explanation
Indices: 17180885--17180980 Score: 106
Period size: 34 Copynumber: 2.9 Consensus size: 33
17180875 AAATTTTTGG
17180885 AAATAAATTTTCAAAAAGTTATAAAATTTTCCAC
1 AAATAAATTTTCAAAAA-TTATAAAATTTTCCAC
* ** *
17180919 AAATAAATTTTCAGAATATTATAAACCTTTCCAG
1 AAATAAATTTTCA-AAAATTATAAAATTTTCCAC
* *
17180953 AAATGAATTTTTAAAAA--ATAAAATTTTC
1 AAATAAATTTTCAAAAATTATAAAATTTTC
17180981 GAAAAAGTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
31 9 0.17
33 3 0.06
34 37 0.71
35 3 0.06
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.36
Consensus pattern (33 bp):
AAATAAATTTTCAAAAATTATAAAATTTTCCAC
Found at i:17190520 original size:2 final size:2
Alignment explanation
Indices: 17190513--17190543 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17190503 GGGTATCAGA
17190513 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17190544 ATACTGTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17195239 original size:5 final size:5
Alignment explanation
Indices: 17195230--17195274 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
17195220 TCATTTGAGG
*
17195230 GAAAA AAAAA GAAAA GAAAA G--AA GAAAA G-AAA GAGAAA GAAAA GA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GA-AAA GAAAA GA
17195275 GTGCCGCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
3 3 0.09
4 4 0.12
5 22 0.65
6 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:17195268 original size:23 final size:22
Alignment explanation
Indices: 17195232--17195274 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
17195222 ATTTGAGGGA
17195232 AAAAAAAAGAAAAGAAAAGAAG
1 AAAAAAAAGAAAAGAAAAGAAG
*
17195254 AAAAGAAAGAGAAAGAAAAGA
1 AAAAAAAAGA-AAAGAAAAGA
17195275 GTGCCGCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAAAAAAGAAAAGAAAAGAAG
Found at i:17211994 original size:3 final size:3
Alignment explanation
Indices: 17211979--17212032 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
17211969 ATTAAAAAAT
*
17211979 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17212027 TTA TTA
1 TTA TTA
17212033 AGCTCTCCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17213074 original size:1 final size:1
Alignment explanation
Indices: 17213040--17213066 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
17213030 GGTGAATTGG
17213040 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
17213067 GCTTTTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17213932 original size:6 final size:6
Alignment explanation
Indices: 17213923--17213988 Score: 71
Period size: 6 Copynumber: 11.0 Consensus size: 6
17213913 ACTTCTAATA
* * * *
17213923 AAAATC AAAATT AAAATAA AAAATC AATATT AAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAAT-T AAAATT AAAATT AAAATT AAAATT AAAATT
*
17213972 AAAA-T CAAATT AAAATT
1 AAAATT AAAATT AAAATT
17213989 CTTGGGTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
5 4 0.08
6 41 0.82
7 5 0.10
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:17213946 original size:19 final size:18
Alignment explanation
Indices: 17213919--17213976 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
17213909 TTTAACTTCT
17213919 AATAAAAATCAAAATTAA
1 AATAAAAATCAAAATTAA
*
17213937 AATAAAAAATCAATATTAA
1 AAT-AAAAATCAAAATTAA
* *
17213956 AATTAAAATTAAAATTAA
1 AATAAAAATCAAAATTAA
17213974 AAT
1 AAT
17213977 CAAATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAAAAATCAAAATTAA
Found at i:17213958 original size:31 final size:29
Alignment explanation
Indices: 17213923--17213987 Score: 94
Period size: 31 Copynumber: 2.2 Consensus size: 29
17213913 ACTTCTAATA
17213923 AAAATCAAAATTAAAATAAAAAATCAATATT
1 AAAATCAAAATTAAAAT-AAAAATCAA-ATT
* *
17213954 AAAATTAAAATTAAAATTAAAATCAAATT
1 AAAATCAAAATTAAAATAAAAATCAAATT
17213983 AAAAT
1 AAAAT
17213988 TCTTGGGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 8 0.25
30 8 0.25
31 16 0.50
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (29 bp):
AAAATCAAAATTAAAATAAAAATCAAATT
Found at i:17215471 original size:20 final size:20
Alignment explanation
Indices: 17215448--17215490 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
17215438 AAGAATACAA
17215448 AAATCAAT-AGATAAATAAAT
1 AAATCAATGA-ATAAATAAAT
* *
17215468 AAATGAATGAATAAGTAAAT
1 AAATCAATGAATAAATAAAT
17215488 AAA
1 AAA
17215491 ATAACATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (20 bp):
AAATCAATGAATAAATAAAT
Found at i:17216640 original size:66 final size:67
Alignment explanation
Indices: 17216536--17216753 Score: 162
Period size: 67 Copynumber: 3.3 Consensus size: 67
17216526 ATTTAACCGT
* * * * * * * * **
17216536 AAGTCA-AAAAAATAAAATAA-CTTGTATCGAGTCGAGGTCGAAAATGAGTTACTGATATTGAAC
1 AAGTCAGAAAAACTAAAATAACCTAG-AACGAGCCAAGGTCGAAAATGAATGACTGACATAAAAC
17216599 CAT-
65 C-TC
* * *
17216602 AAGTC-GAAAAACTAAAATAACCTA-AATTGAGCCAAGGTCGAAGATGAATGACTGGCATAAAAC
1 AAGTCAGAAAAACTAAAATAACCTAGAA-CGAGCCAAGGTCGAAAATGAATGACTGACATAAAAC
17216665 CTC
65 CTC
* ** * **
17216668 AGGTCAGAAAAACTAAAATAACCTAGAACGAGCCAAGGTCGATTATGAATGA-TCGAGATTGAA-
1 AAGTCAGAAAAACTAAAATAACCTAGAACGAGCCAAGGTCGAAAATGAATGACT-GACATAAAAC
17216731 CTGC
65 CT-C
*
17216735 AGGTCAGAAAAACTAAAAT
1 AAGTCAGAAAAACTAAAAT
17216754 GGCATTGATT
Statistics
Matches: 123, Mismatches: 21, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
65 2 0.02
66 52 0.42
67 67 0.54
68 2 0.02
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (67 bp):
AAGTCAGAAAAACTAAAATAACCTAGAACGAGCCAAGGTCGAAAATGAATGACTGACATAAAACC
TC
Found at i:17216850 original size:66 final size:66
Alignment explanation
Indices: 17216607--17216852 Score: 237
Period size: 67 Copynumber: 3.7 Consensus size: 66
17216597 ACCATAAGTC
* * * * *
17216607 GAAAAACTAAAATAACCTAAATTGAGCCAAGGTCGAAGATGAATGA-CTGGCATAAAACC-TCAG
1 GAAAAACTAAAATGA-CTAGACTGAGCCAAGGTCGAAGATGAATGATC-GGGATTAAACCGT-AG
17216670 GTCA
63 GTCA
* ** * * * *
17216674 GAAAAACTAAAATAACCTAGAAC-GAGCCAAGGTCGATTATGAATGATCGAGATTGAACTGCAGG
1 GAAAAACTAAAATGA-CTAG-ACTGAGCCAAGGTCGAAGATGAATGATCGGGATTAAACCGTAGG
17216738 TCA
64 TCA
* * * *
17216741 GAAAAACTAAAATGGCATTGATTGAGCCGAGGTCGAAGATGAATGATCGGGATTAAACCGTAGGT
1 GAAAAACTAAAATGAC-TAGACTGAGCCAAGGTCGAAGATGAATGATCGGGATTAAACCGTAGGT
17216806 CA
65 CA
* * * *
17216808 AAAAAATTAAAATGACTAGACTGAGCTAAGATCGAAGATGAATGA
1 GAAAAACTAAAATGACTAGACTGAGCCAAGGTCGAAGATGAATGA
17216853 CCAAAATTGA
Statistics
Matches: 145, Mismatches: 29, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
66 26 0.18
67 117 0.81
68 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.20
Consensus pattern (66 bp):
GAAAAACTAAAATGACTAGACTGAGCCAAGGTCGAAGATGAATGATCGGGATTAAACCGTAGGTC
A
Found at i:17217548 original size:22 final size:23
Alignment explanation
Indices: 17217523--17217611 Score: 82
Period size: 22 Copynumber: 4.0 Consensus size: 23
17217513 TTATTTTAAA
17217523 AAAATATTTAGA-GATTCACA-TC
1 AAAATATTTA-ATGATTCACATTC
**
17217545 AAAAGT-TTTAATGATTTGCATTC
1 AAAA-TATTTAATGATTCACATTC
17217568 GAAAA-A-TTAGAT-ATTCACATTC
1 -AAAATATTTA-ATGATTCACATTC
17217590 AAAATATTTAATGATTCACATT
1 AAAATATTTAATGATTCACATT
17217612 TGAAAAATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
21 5 0.09
22 28 0.52
23 17 0.31
24 4 0.07
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (23 bp):
AAAATATTTAATGATTCACATTC
Found at i:17217638 original size:45 final size:43
Alignment explanation
Indices: 17217530--17217651 Score: 136
Period size: 45 Copynumber: 2.7 Consensus size: 43
17217520 AAAAAAATAT
**
17217530 TTAGAGATTCACATCAAAAGTTTTAATGATTTGCATTCGAAAAA
1 TTAGAGATTCACATCAAAA-TTTTAATGATTCACATTCGAAAAA
* *
17217574 TTAGATATTCACATTCAAAATATTTAATGATTCACATTTGAAAAA
1 TTAGAGATTCACA-TCAAAAT-TTTAATGATTCACATTCGAAAAA
* * * *
17217619 TTAGAGATTTATATCCAAAATTTCAAAGATTCA
1 TTAGAGATTCACAT-CAAAATTTTAATGATTCA
17217652 AAATTTTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
44 24 0.36
45 42 0.64
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (43 bp):
TTAGAGATTCACATCAAAATTTTAATGATTCACATTCGAAAAA
Found at i:17218718 original size:10 final size:10
Alignment explanation
Indices: 17218705--17218746 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
17218695 AGTCTTTCTC
17218705 TTTCTTTTTT
1 TTTCTTTTTT
17218715 TTTCTTTGTTT
1 TTTCTTT-TTT
*
17218726 TAT-TTTTTT
1 TTTCTTTTTT
17218735 TTTCATTTTTT
1 TTTC-TTTTTT
17218746 T
1 T
17218747 ACACACCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 5 0.19
10 10 0.37
11 12 0.44
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.86
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:17218732 original size:20 final size:20
Alignment explanation
Indices: 17218709--17218747 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
17218699 TTTCTCTTTC
17218709 TTTTTTTTTC-TTTGTTTTAT
1 TTTTTTTTTCATTT-TTTTAT
17218729 TTTTTTTTTCATTTTTTTA
1 TTTTTTTTTCATTTTTTTA
17218748 CACACCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.08, C:0.05, G:0.03, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTCATTTTTTTAT
Found at i:17219052 original size:9 final size:9
Alignment explanation
Indices: 17219038--17219087 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
17219028 TACCCAATCA
17219038 ATTTTTTTC
1 ATTTTTTTC
17219047 ATTTTTTTC
1 ATTTTTTTC
*
17219056 TCTTTTTTTC
1 -ATTTTTTTC
17219066 ATTTTTCTTC
1 ATTTTT-TTC
*
17219076 TTTTTCTTTC
1 ATTTT-TTTC
17219086 AT
1 AT
17219088 CATTTTTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 14 0.41
10 19 0.56
11 1 0.03
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTTTTTC
Found at i:17219064 original size:20 final size:19
Alignment explanation
Indices: 17219039--17219087 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
17219029 ACCCAATCAA
17219039 TTTTTTTCATTTTT-TTCT
1 TTTTTTTCATTTTTCTTCT
17219057 CTTTTTTTCATTTTTCTTCT
1 -TTTTTTTCATTTTTCTTCT
17219077 TTTTCTTTCAT
1 TTTT-TTTCAT
17219088 CATTTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTTCATTTTTCTTCT
Found at i:17219898 original size:12 final size:12
Alignment explanation
Indices: 17219883--17219922 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
17219873 TCTTAACAAA
17219883 GTTCTTTGTTAT
1 GTTCTTTGTTAT
* *
17219895 GTTCCTTATTAT
1 GTTCTTTGTTAT
17219907 GTTCTTTGTTAT
1 GTTCTTTGTTAT
17219919 GTTC
1 GTTC
17219923 CTTATCATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.15, T:0.62
Consensus pattern (12 bp):
GTTCTTTGTTAT
Found at i:17219935 original size:24 final size:24
Alignment explanation
Indices: 17219884--17219935 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
17219874 CTTAACAAAG
* *
17219884 TTCTTTGTTATGTTCCTTATTATG
1 TTCTTTGTTATGTTCCTTATCATC
17219908 TTCTTTGTTATGTTCCTTATCATC
1 TTCTTTGTTATGTTCCTTATCATC
17219932 TTCT
1 TTCT
17219936 CATAATAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.62
Consensus pattern (24 bp):
TTCTTTGTTATGTTCCTTATCATC
Found at i:17224840 original size:31 final size:30
Alignment explanation
Indices: 17224777--17224842 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
17224767 GAAGAGACTT
* *
17224777 AAAAAAAAAGAATAAGGAAAAAAAAGCCAA
1 AAAAAAAAAGAAAAAGGAAAAAAAAGACAA
* * *
17224807 AAAAAAAAAGAACAAAGGAACAAAAGGAGAA
1 AAAAAAAAAGAA-AAAGGAAAAAAAAGACAA
17224838 AAAAA
1 AAAAA
17224843 TGGATGGAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (30 bp):
AAAAAAAAAGAAAAAGGAAAAAAAAGACAA
Found at i:17226598 original size:3 final size:3
Alignment explanation
Indices: 17226590--17226616 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17226580 CATGTCATAA
17226590 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
17226617 GAGGCAATTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17226668 original size:3 final size:3
Alignment explanation
Indices: 17226662--17226698 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
17226652 TAAAAAAAGA
17226662 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17226699 GTAAAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17226983 original size:15 final size:17
Alignment explanation
Indices: 17226960--17226994 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
17226950 CTTTCAAAAA
17226960 AATTAAATTAAAAAT-T
1 AATTAAATTAAAAATGT
17226976 AATT-AATTAAAAATGT
1 AATTAAATTAAAAATGT
17226992 AAT
1 AAT
17226995 AATAATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTAAATTAAAAATGT
Found at i:17227980 original size:3 final size:3
Alignment explanation
Indices: 17227974--17228005 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17227964 AAACAAACAA
17227974 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17228006 AAACATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17228633 original size:3 final size:3
Alignment explanation
Indices: 17228627--17228685 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
17228617 AAACAAACAA
17228627 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17228675 AAT AAT AAT AA
1 AAT AAT AAT AA
17228686 CATGTTTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17229172 original size:3 final size:3
Alignment explanation
Indices: 17229157--17229217 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
17229147 TAAGTTTTTT
* * * * *
17229157 ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ACA ACA ATA ACA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
17229205 ACA ATA ATA ATA A
1 ATA ATA ATA ATA A
17229218 AAAGAAAGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.08, G:0.02, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:17234474 original size:23 final size:23
Alignment explanation
Indices: 17234448--17234507 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
17234438 ACCTAAGCCC
* * *
17234448 AGATCAGCTGGCATTTTAAACCT
1 AGATTAGCTGACACTTTAAACCT
* *
17234471 AGATTGGCTGACACTTTAACCCT
1 AGATTAGCTGACACTTTAAACCT
17234494 AGATTAGCTGACAC
1 AGATTAGCTGACAC
17234508 CCAGATCATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (23 bp):
AGATTAGCTGACACTTTAAACCT
Found at i:17234630 original size:67 final size:67
Alignment explanation
Indices: 17234518--17234658 Score: 248
Period size: 67 Copynumber: 2.1 Consensus size: 67
17234508 CCAGATCATG
*
17234518 CTAAGCCCAGATCAATTGGCACCTAAACTTAGATTAGTTAGCACTTTAAACCCAGATTAATTTAC
1 CTAAGCCCAGATCAATTGGCACCTAAACTCAGATTAGTTAGCACTTTAAACCCAGATTAATTTAC
17234583 AC
66 AC
*
17234585 CTAAGCCCAGATCAATTGGCACCTAAACTCAGATTAGTT-GACACTTTAAGCCCAGATTAATTTA
1 CTAAGCCCAGATCAATTGGCACCTAAACTCAGATTAGTTAG-CACTTTAAACCCAGATTAATTTA
17234649 CAC
65 CAC
17234652 CTAAGCC
1 CTAAGCC
17234659 TATATTATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 1 0.01
67 70 0.99
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.27
Consensus pattern (67 bp):
CTAAGCCCAGATCAATTGGCACCTAAACTCAGATTAGTTAGCACTTTAAACCCAGATTAATTTAC
AC
Found at i:17234653 original size:45 final size:44
Alignment explanation
Indices: 17234564--17234655 Score: 112
Period size: 45 Copynumber: 2.1 Consensus size: 44
17234554 GTTAGCACTT
* *
17234564 TAAACCCAGATTAATTTACACCTAAGCCCAGATCAATTGGCACC
1 TAAACCCAGATTAATTGACACCTAAGCCCAGATCAATTGACACC
* * * * *
17234608 TAAACTCAGATTAGTTGACACTTTAAGCCCAGATTAATTTACACC
1 TAAACCCAGATTAATTGACAC-CTAAGCCCAGATCAATTGACACC
17234653 TAA
1 TAA
17234656 GCCTATATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (44 bp):
TAAACCCAGATTAATTGACACCTAAGCCCAGATCAATTGACACC
Found at i:17234665 original size:22 final size:22
Alignment explanation
Indices: 17234518--17234658 Score: 104
Period size: 22 Copynumber: 6.3 Consensus size: 22
17234508 CCAGATCATG
* *
17234518 CTAAGCCCAGATCAATTGGCAC
1 CTAAGCCCAGATTAATTGACAC
* ** *
17234540 CTAAACTTAGATTAGTT-AGCAC
1 CTAAGCCCAGATTAATTGA-CAC
* * *
17234562 TTTAAACCCAGATTAATTTACAC
1 -CTAAGCCCAGATTAATTGACAC
* *
17234585 CTAAGCCCAGATCAATTGGCAC
1 CTAAGCCCAGATTAATTGACAC
* * *
17234607 CTAAACTCAGATTAGTTGACAC
1 CTAAGCCCAGATTAATTGACAC
* *
17234629 TTTAAGCCCAGATTAATTTACAC
1 -CTAAGCCCAGATTAATTGACAC
17234652 CTAAGCC
1 CTAAGCC
17234659 TATATTATAT
Statistics
Matches: 89, Mismatches: 26, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
22 55 0.62
23 33 0.37
24 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.27
Consensus pattern (22 bp):
CTAAGCCCAGATTAATTGACAC
Found at i:17234798 original size:45 final size:46
Alignment explanation
Indices: 17234734--17234824 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 46
17234724 CTATATGATA
* * *
17234734 TTTAAGCCTAGTTTAACTGGTACC-TAAACCAAGATTAGTTGGCAC
1 TTTAAGCCTAGATTAACTGGCACCTTAAACCAAGATTAGTTAGCAC
* *
17234779 TTTAAGCCTAGATTAACTGGCACCTTAAGCCAAGTTTAGTTAGCAC
1 TTTAAGCCTAGATTAACTGGCACCTTAAACCAAGATTAGTTAGCAC
17234825 AGTTGAGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 22 0.55
46 18 0.45
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (46 bp):
TTTAAGCCTAGATTAACTGGCACCTTAAACCAAGATTAGTTAGCAC
Found at i:17234799 original size:23 final size:23
Alignment explanation
Indices: 17234734--17234809 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
17234724 CTATATGATA
* *
17234734 TTTAAGCCTAGTTTAACTGGTAC
1 TTTAAGCCTAGATTAACTGGCAC
* * * **
17234757 -CTAAACCAAGATTAGTTGGCAC
1 TTTAAGCCTAGATTAACTGGCAC
17234779 TTTAAGCCTAGATTAACTGGCAC
1 TTTAAGCCTAGATTAACTGGCAC
*
17234802 CTTAAGCC
1 TTTAAGCC
17234810 AAGTTTAGTT
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
22 15 0.38
23 24 0.62
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (23 bp):
TTTAAGCCTAGATTAACTGGCAC
Found at i:17234824 original size:23 final size:23
Alignment explanation
Indices: 17234762--17234824 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
17234752 GGTACCTAAA
*
17234762 CCAAGATTAGTTGGCACTTTAAG
1 CCAAGATTAGTTGGCACCTTAAG
* **
17234785 CCTAGATTAACTGGCACCTTAAG
1 CCAAGATTAGTTGGCACCTTAAG
* *
17234808 CCAAGTTTAGTTAGCAC
1 CCAAGATTAGTTGGCAC
17234825 AGTTGAGATT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (23 bp):
CCAAGATTAGTTGGCACCTTAAG
Found at i:17234893 original size:23 final size:23
Alignment explanation
Indices: 17234867--17234949 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
17234857 TTAAGTTTAG
* *
17234867 ATTAGTTGGCACTTTAAGCTCAA
1 ATTAGCTGGCACTTTAAGCACAA
* *
17234890 ATTAGCTGACACTTTAACCACAA
1 ATTAGCTGGCACTTTAAGCACAA
* * *
17234913 ATTAACTAGCACTTTAAGCCCAA
1 ATTAGCTGGCACTTTAAGCACAA
*
17234936 ATTAGCTGGTACTT
1 ATTAGCTGGCACTT
17234950 AAATCCAATT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (23 bp):
ATTAGCTGGCACTTTAAGCACAA
Found at i:17234923 original size:100 final size:100
Alignment explanation
Indices: 17234741--17234924 Score: 219
Period size: 100 Copynumber: 1.8 Consensus size: 100
17234731 ATATTTAAGC
* *
17234741 CTAGTTTAACTGGTACCTAAACCAAGATTAGTTGGCACTTTAAGCCTAGATTAACTGGCACCTTA
1 CTAGTTTAACTGGTACCTAAACCAAGATTAGTTGGCACTTTAAGCCTAAATTAACTGACACCTTA
** **
17234806 AGCCAAGTTTAGTTAGCACAGTTGAGATTTTAAAT
66 AGCCAAAATTAACTAGCACAGTTGAGATTTTAAAT
* **** * *
17234841 CTAGTTTAACTGGTACTTAAGTTTAGATTAGTTGGCACTTTAAG-CTCAAATTAGCTGACACTTT
1 CTAGTTTAACTGGTACCTAAACCAAGATTAGTTGGCACTTTAAGCCT-AAATTAACTGACACCTT
17234905 AA-CCACAAATTAACTAGCAC
65 AAGCCA-AAATTAACTAGCAC
17234925 TTTAAGCCCA
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
99 5 0.07
100 64 0.93
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (100 bp):
CTAGTTTAACTGGTACCTAAACCAAGATTAGTTGGCACTTTAAGCCTAAATTAACTGACACCTTA
AGCCAAAATTAACTAGCACAGTTGAGATTTTAAAT
Found at i:17235407 original size:23 final size:23
Alignment explanation
Indices: 17235377--17235421 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
17235367 TCTTTGAGTC
17235377 AAATTAACTCCCACCTTAAGCCT
1 AAATTAACTCCCACCTTAAGCCT
*
17235400 AAATTAACTCGCACCTTAAGCC
1 AAATTAACTCCCACCTTAAGCC
17235422 CATATTTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.33, G:0.07, T:0.24
Consensus pattern (23 bp):
AAATTAACTCCCACCTTAAGCCT
Found at i:17236069 original size:329 final size:330
Alignment explanation
Indices: 17234950--17236277 Score: 1678
Period size: 352 Copynumber: 3.9 Consensus size: 330
17234940 GCTGGTACTT
* * * * * * * * *
17234950 AAATCCAATTTAACTGGCACCCAAATGACATTTAAGTTCAGTTTAGTTGGCATAGTTATCTGGCA
1 AAATCCAATTTAACTAGCACCCAGATAACATTTAAGCTCAGTTTAATTGGCACAATTAGCTAGCA
* * * * *
17235015 ATTTAAGCCCAGATGAGCTGACTCTTTGAGTCCAAATTGACTCGCACTTTAAGCCCATATTAGCT
66 GTTTAAGCCCAGATGAGCTGGCTCTTTGAGT-CAAATTAACTCGCACCTTAAGCCCAAATTAGCT
* * *
17235080 AGTACCAATAAGATTTAAGTCTAGTTTAACTAGCACCTAGATTTTAAGCCCAATGAAATTGGCAC
130 AATACCAATAAGATTTAAGTCTAGTTTAACTAGAACCTAGATTTTAAGCCCAACGAAATTGGCAC
* * *
17235145 CAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACCAAATTACTTGGTGGTAATATCTAAAGTTCA
195 CAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTACTTGGTGGTAATATC-GAAGTTAA
** * *
17235210 AAAAATCTTAAAAATTGAAT-TT-TTTTTTTTACAAGCAAATTTTCAGAAAATGATTTGCAAGCT
259 AAAAATCTTAAAAATTGAATGTTCCCTTTTTTACAAGCAAAATTTCAGAAAATAATTTGCAAGCT
17235273 AGCACCC
324 AGCACCC
* * * * *
17235280 AAATCCAATTTAACTGGCACCCAGATGACATTTAAGCCCAGTTTAATTGGCATAGTTAGCTAGCA
1 AAATCCAATTTAACTAGCACCCAGATAACATTTAAGCTCAGTTTAATTGGCACAATTAGCTAGCA
*
17235345 GTTTAAGCCCAGATGAGCTAGCTCTTTGAGTCAAATTAACTCCCACCTTAAGCCTAAATTAACTC
66 GTTTAAGCCCAGATGAGCTGGCTCTTTGAG------------------T----C-AAATTAACTC
* *
17235410 GCACCTTAAGCCCATATTTGCTAATACCAATAAGATTTAAGTCTAGTTTAACTAGAACCTAGATT
108 GCACCTTAAGCCCAAATTAGCTAATACCAATAAGATTTAAGTCTAGTTTAACTAGAACCTAGATT
17235475 TTAAGCCCAACGAAATTGGCACCAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTACT
173 TTAAGCCCAACGAAATTGGCACCAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTACT
17235540 TGGTGGTAATATCCGAAGTTCAAAAAAA-CTTAAAAATTGAATGTTCCCTTTTTTACAAGCAAAA
238 TGGTGGTAATAT-CGAAGTT-AAAAAAATCTTAAAAATTGAATGTTCCCTTTTTTACAAGCAAAA
17235604 TTTCAGAAAATAATTTGCAAGCTAGCACCC
301 TTTCAGAAAATAATTTGCAAGCTAGCACCC
*
17235634 AAATCCAATTTAACTAGCACCCAGATAACATTTAAGCTCAGTTTAATTGGCACAGTTAGCTAGCA
1 AAATCCAATTTAACTAGCACCCAGATAACATTTAAGCTCAGTTTAATTGGCACAATTAGCTAGCA
* *
17235699 GTTTAAGCCCAGATGAGTTGGCTCTTTGAGTCAAATTAACTCGCACCTTAAGCCCAAATTAACTA
66 GTTTAAGCCCAGATGAGCTGGCTCTTTGAGTCAAATTAACTCGCACCTTAAGCCCAAATTAGCTA
* * * *
17235764 TTACCAATAAGATTTAAGTCTAGTTTAACTAGCACCTAGATTTTAAACCTAACGAAATTGGCACC
131 ATACCAATAAGATTTAAGTCTAGTTTAACTAGAACCTAGATTTTAAGCCCAACGAAATTGGCACC
*
17235829 AGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTACTTAGTGGTAATATCGAAGTTAAAA
196 AGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTACTTGGTGGTAATATCGAAGTTAAAA
*
17235894 AAATCTTAAAAATTGAATGTTCCCTTTTTTACAAGC-AAATTTCAGAAAATGATTTGCAAGCTAG
261 AAATCTTAAAAATTGAATGTTCCCTTTTTTACAAGCAAAATTTCAGAAAATAATTTGCAAGCTAG
17235958 CACCC
326 CACCC
*
17235963 AAATCCAATTTAACT-GACACCCAGATGACATTTAAGC-CTAGTTTAATTGGCACAATTAGCTAG
1 AAATCCAATTTAACTAG-CACCCAGATAACATTTAAGCTC-AGTTTAATTGGCACAATTAGCTAG
* *
17236026 TAGTTTAAGTCCAGATGAGCTGGCTCTTTGAGTCAAATTAACTCGCACCTTAAGCTTAAATTAAC
64 CAGTTTAAGCCCAGATGAGCTGGCTCTTTGAGTCAAATTAACTCGCACCTTAAG-----------
* *
17236091 TCGTACCTTAAGCCCATATTAGCTAGTACCAATAAGATTTAAGTCTAGTTTAACTAGTACCTAGA
118 -C---CC---A----A-ATTAGCTAATACCAATAAGATTTAAGTCTAGTTTAACTAGAACCTAGA
* *
17236156 TTTTAAGCCCAATGAAATTGGCACTAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTA
171 TTTTAAGCCCAACGAAATTGGCACCAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTA
* * *
17236221 CTTGGTGGTAATATCTAAAGTTCAAAAAATCTTAAAAATTGAATGTTCCATTTTTTA
236 CTTGGTGGTAATATC-GAAGTTAAAAAAATCTTAAAAATTGAATGTTCCCTTTTTTA
17236278 ATTGGCATAG
Statistics
Matches: 892, Mismatches: 53, Indels: 83
0.87 0.05 0.08
Matches are distributed among these distances:
328 2 0.00
329 147 0.16
330 125 0.14
331 144 0.16
332 1 0.00
336 1 0.00
341 1 0.00
344 2 0.00
347 1 0.00
348 1 0.00
351 3 0.00
352 284 0.32
353 47 0.05
354 133 0.15
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (330 bp):
AAATCCAATTTAACTAGCACCCAGATAACATTTAAGCTCAGTTTAATTGGCACAATTAGCTAGCA
GTTTAAGCCCAGATGAGCTGGCTCTTTGAGTCAAATTAACTCGCACCTTAAGCCCAAATTAGCTA
ATACCAATAAGATTTAAGTCTAGTTTAACTAGAACCTAGATTTTAAGCCCAACGAAATTGGCACC
AGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTACTTGGTGGTAATATCGAAGTTAAAA
AAATCTTAAAAATTGAATGTTCCCTTTTTTACAAGCAAAATTTCAGAAAATAATTTGCAAGCTAG
CACCC
Found at i:17236090 original size:23 final size:23
Alignment explanation
Indices: 17236060--17236103 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
17236050 TCTTTGAGTC
17236060 AAATTAACTCGCACCTTAAGCTT
1 AAATTAACTCGCACCTTAAGCTT
*
17236083 AAATTAACTCGTACCTTAAGC
1 AAATTAACTCGCACCTTAAGC
17236104 CCATATTAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (23 bp):
AAATTAACTCGCACCTTAAGCTT
Found at i:17236111 original size:23 final size:23
Alignment explanation
Indices: 17236059--17236120 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
17236049 CTCTTTGAGT
* *
17236059 CAAATTAACTCGCACCTTAAGCT
1 CAAATTAACTCGTACCTTAAGCC
*
17236082 TAAATTAACTCGTACCTTAAGCC
1 CAAATTAACTCGTACCTTAAGCC
* * *
17236105 CATATTAGCTAGTACC
1 CAAATTAACTCGTACC
17236121 AATAAGATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (23 bp):
CAAATTAACTCGTACCTTAAGCC
Found at i:17236257 original size:683 final size:684
Alignment explanation
Indices: 17234950--17236277 Score: 2221
Period size: 683 Copynumber: 1.9 Consensus size: 684
17234940 GCTGGTACTT
* * * * * * *
17234950 AAATCCAATTTAACTGGCACCCAAATGACATTTAAGTTCAGTTTAGTTGGCATAGTTATCTGGCA
1 AAATCCAATTTAACTAGCACCCAAATAACATTTAAGCTCAGTTTAATTGGCACAGTTAGCTAGCA
* * * *
17235015 ATTTAAGCCCAGATGAGCTGACTCTTTGAGTCCAAATTGACTCGCACTTTAAGCCCATATTAGCT
66 ATTTAAGCCCAGATGAGCTGACTCTTTGAGTCCAAATTAACTCGCACCTTAAGCCCAAATTAACT
* *
17235080 AGTACCAATAAGATTTAAGTCTAGTTTAACTAGCACCTAGATTTTAAGCCCAATGAAATTGGCAC
131 AGTACCAATAAGATTTAAGTCTAGTTTAACTAGCACCTAGATTTTAAACCCAACGAAATTGGCAC
* * *
17235145 CAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACCAAATTACTTGGTGGTAATATCTAAAGTTCA
196 CAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTACTTAGTGGTAATATCTAAAGTTAA
**
17235210 AAAAATCTTAAAAATTGAATTTTTTTTTTTACAAGCAAATTTTCAGAAAATGATTTGCAAGCTAG
261 AAAAATCTTAAAAATTGAATTTCCTTTTTTACAAGCAAATTTTCAGAAAATGATTTGCAAGCTAG
* * *
17235275 CACCCAAATCCAATTTAACTGGCACCCAGATGACATTTAAGCCCAGTTTAATTGGCATAGTTAGC
326 CACCCAAATCCAATTTAACTGACACCCAGATGACATTTAAGCCCAGTTTAATTGGCACAATTAGC
17235340 TAGCAGTTTAAGCCCAGATGAGCTAGCTCTTTGAGTCAAATTAACTCCCACCTTAAGCCTAAATT
391 TAGCAGTTTAAGCCCAGATGAGCTAGCTCTTTGAGTCAAATTAACTCCCACCTTAAGCCTAAATT
*
17235405 AACTCGCACCTTAAGCCCATATTTGCTAATACCAATAAGATTTAAGTCTAGTTTAACTAGAACCT
456 AACTCGCACCTTAAGCCCATATTAGCTAATACCAATAAGATTTAAGTCTAGTTTAACTAGAACCT
17235470 AGATTTTAAGCCCAACGAAATTGGCACCAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAA
521 AGATTTTAAGCCCAACGAAATTGGCACCAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAA
* *
17235535 TTACTTGGTGGTAATATCCGAAGTTCAAAAAAACTTAAAAATTGAATGTTCCCTTTTTTACAAGC
586 TTACTTGGTGGTAATATCCAAAGTTCAAAAAAACTTAAAAATTGAATGTTCCATTTTTTACAAGC
17235600 AAAATTTCAGAAAATAATTTGCAAGCTAGCACCC
651 AAAATTTCAGAAAATAATTTGCAAGCTAGCACCC
*
17235634 AAATCCAATTTAACTAGCACCCAGATAACATTTAAGCTCAGTTTAATTGGCACAGTTAGCTAGCA
1 AAATCCAATTTAACTAGCACCCAAATAACATTTAAGCTCAGTTTAATTGGCACAGTTAGCTAGCA
* * *
17235699 GTTTAAGCCCAGATGAGTTGGCTCTTTGAGT-CAAATTAACTCGCACCTTAAGCCCAAATTAACT
66 ATTTAAGCCCAGATGAGCTGACTCTTTGAGTCCAAATTAACTCGCACCTTAAGCCCAAATTAACT
* *
17235763 ATTACCAATAAGATTTAAGTCTAGTTTAACTAGCACCTAGATTTTAAACCTAACGAAATTGGCAC
131 AGTACCAATAAGATTTAAGTCTAGTTTAACTAGCACCTAGATTTTAAACCCAACGAAATTGGCAC
*
17235828 CAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTACTTAGTGGTAATATC-GAAGTTAA
196 CAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTACTTAGTGGTAATATCTAAAGTTAA
17235892 AAAAATCTTAAAAATTGAATGTTCCCTTTTTTACAAGCAAA-TTTCAGAAAATGATTTGCAAGCT
261 AAAAATCTTAAAAATTGAAT-TT-CCTTTTTTACAAGCAAATTTTCAGAAAATGATTTGCAAGCT
*
17235956 AGCACCCAAATCCAATTTAACTGACACCCAGATGACATTTAAGCCTAGTTTAATTGGCACAATTA
324 AGCACCCAAATCCAATTTAACTGACACCCAGATGACATTTAAGCCCAGTTTAATTGGCACAATTA
* * * * *
17236021 GCTAGTAGTTTAAGTCCAGATGAGCTGGCTCTTTGAGTCAAATTAACTCGCACCTTAAGCTTAAA
389 GCTAGCAGTTTAAGCCCAGATGAGCTAGCTCTTTGAGTCAAATTAACTCCCACCTTAAGCCTAAA
* * *
17236086 TTAACTCGTACCTTAAGCCCATATTAGCTAGTACCAATAAGATTTAAGTCTAGTTTAACTAGTAC
454 TTAACTCGCACCTTAAGCCCATATTAGCTAATACCAATAAGATTTAAGTCTAGTTTAACTAGAAC
* *
17236151 CTAGATTTTAAGCCCAATGAAATTGGCACTAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAA
519 CTAGATTTTAAGCCCAACGAAATTGGCACCAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAA
* *
17236216 AATTACTTGGTGGTAATATCTAAAGTTCAAAAAATCTTAAAAATTGAATGTTCCATTTTTTA
584 AATTACTTGGTGGTAATATCCAAAGTTCAAAAAAACTTAAAAATTGAATGTTCCATTTTTTA
17236278 ATTGGCATAG
Statistics
Matches: 598, Mismatches: 44, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
682 26 0.04
683 472 0.79
684 100 0.17
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (684 bp):
AAATCCAATTTAACTAGCACCCAAATAACATTTAAGCTCAGTTTAATTGGCACAGTTAGCTAGCA
ATTTAAGCCCAGATGAGCTGACTCTTTGAGTCCAAATTAACTCGCACCTTAAGCCCAAATTAACT
AGTACCAATAAGATTTAAGTCTAGTTTAACTAGCACCTAGATTTTAAACCCAACGAAATTGGCAC
CAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAATTACTTAGTGGTAATATCTAAAGTTAA
AAAAATCTTAAAAATTGAATTTCCTTTTTTACAAGCAAATTTTCAGAAAATGATTTGCAAGCTAG
CACCCAAATCCAATTTAACTGACACCCAGATGACATTTAAGCCCAGTTTAATTGGCACAATTAGC
TAGCAGTTTAAGCCCAGATGAGCTAGCTCTTTGAGTCAAATTAACTCCCACCTTAAGCCTAAATT
AACTCGCACCTTAAGCCCATATTAGCTAATACCAATAAGATTTAAGTCTAGTTTAACTAGAACCT
AGATTTTAAGCCCAACGAAATTGGCACCAGTTAAAAAAAATGTTGTAATCAAGTTTTCTACAAAA
TTACTTGGTGGTAATATCCAAAGTTCAAAAAAACTTAAAAATTGAATGTTCCATTTTTTACAAGC
AAAATTTCAGAAAATAATTTGCAAGCTAGCACCC
Found at i:17236367 original size:23 final size:23
Alignment explanation
Indices: 17236329--17236384 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
17236319 CTCTTTTAGT
* *
17236329 CAAATTAACTCGCACCTTAAGCC
1 CAAATTAGCTCACACCTTAAGCC
*
17236352 TAAATTAGCTCACACCTTAAGCC
1 CAAATTAGCTCACACCTTAAGCC
*
17236375 CAGATTAGCT
1 CAAATTAGCT
17236385 AGTACCAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.25
Consensus pattern (23 bp):
CAAATTAGCTCACACCTTAAGCC
Found at i:17236964 original size:49 final size:49
Alignment explanation
Indices: 17236776--17236969 Score: 175
Period size: 50 Copynumber: 3.9 Consensus size: 49
17236766 CAATTTAAAT
* * *
17236776 TTTTAAAGTTTCAAAG-TCTCTGTTTAATA-AGAGCCATTTTCAAATAAAA
1 TTTTAAAATTTCAAAGCT-TCTGTTTAA-AGGGAGCCATTTTCAAATAAGA
17236825 TTTTTAAAATTTCAAAGCCTT-TGTTT--AGGGAGAACCATTTTCAAATAAGGA
1 -TTTTAAAATTTCAAAG-CTTCTGTTTAAAGGGAG--CCATTTTCAAATAA-GA
* * * * * *
17236876 TTTTAAAATTCCAAAGCCTCTATTTAGAGTGAGCAATTTTCAAACT-AGA
1 TTTTAAAATTTCAAAGCTTCTGTTTAAAGGGAGCCATTTTCAAA-TAAGA
*
17236925 TTTTAAAGTTTCAAAGCTTCTGTTTAAAGGGAGCCATTTTTCAAA
1 TTTTAAAATTTCAAAGCTTCTGTTTAAAGGGAGCCA-TTTTCAAA
17236970 ATCTTTAAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
47 1 0.01
48 3 0.03
49 33 0.28
50 72 0.61
51 3 0.03
52 6 0.05
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (49 bp):
TTTTAAAATTTCAAAGCTTCTGTTTAAAGGGAGCCATTTTCAAATAAGA
Found at i:17237104 original size:16 final size:15
Alignment explanation
Indices: 17237057--17237166 Score: 78
Period size: 17 Copynumber: 6.7 Consensus size: 15
17237047 TATTTTTGTG
*
17237057 AAAAAATAAAAAAATT
1 AAAAAAT-AAAAAATC
* *
17237073 AATAATAATAATAAATG
1 AA-AA-AATAAAAAATC
17237090 ACAAAAATAAAAAAT-
1 A-AAAAATAAAAAATC
*
17237105 AAACAATCAAAAAAATC
1 AAAAAAT--AAAAAATC
17237122 AAAAAAATTAAAAAATC
1 -AAAAAA-TAAAAAATC
17237139 AAAAAAATTAAAAAATC
1 -AAAAAA-TAAAAAATC
*
17237156 AAAAAACAAAA
1 AAAAAATAAAA
17237167 CAAAACAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 17
0.78 0.06 0.17
Matches are distributed among these distances:
14 5 0.06
15 5 0.06
16 24 0.30
17 36 0.45
18 9 0.11
19 1 0.01
ACGTcount: A:0.76, C:0.06, G:0.01, T:0.16
Consensus pattern (15 bp):
AAAAAATAAAAAATC
Found at i:17237118 original size:17 final size:17
Alignment explanation
Indices: 17237092--17237161 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
17237082 AATAAATGAC
17237092 AAAAATAAAAAAT-AAA
1 AAAAATAAAAAATCAAA
**
17237108 CAATCA-AAAAAATCAAA
1 -AAAAATAAAAAATCAAA
*
17237125 AAAATTAAAAAATCAAA
1 AAAAATAAAAAATCAAA
*
17237142 AAAATTAAAAAATCAAA
1 AAAAATAAAAAATCAAA
17237159 AAA
1 AAA
17237162 CAAAACAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
16 9 0.20
17 37 0.80
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAATAAAAAATCAAA
Found at i:17237123 original size:9 final size:9
Alignment explanation
Indices: 17237109--17237222 Score: 78
Period size: 9 Copynumber: 12.9 Consensus size: 9
17237099 AAAAATAAAC
17237109 AATCAAAAA
1 AATCAAAAA
17237118 AATCAAAAA
1 AATCAAAAA
*
17237127 AAT-TAAAA
1 AATCAAAAA
17237135 AATCAAAAA
1 AATCAAAAA
*
17237144 AAT-TAAAA
1 AATCAAAAA
17237152 AATC-AAAA
1 AATCAAAAA
17237160 AA-CAAAACA
1 AATCAAAA-A
*
17237169 AAACAAAAA
1 AATCAAAAA
* * *
17237178 TAAACATTAAT
1 -AATCA-AAAA
*
17237189 AAT-AACAAT
1 AATCAA-AAA
*
17237198 AACCAAAAA
1 AATCAAAAA
17237207 AATC-AAAA
1 AATCAAAAA
17237215 AATCAAAA
1 AATCAAAA
17237223 CAAAACAATA
Statistics
Matches: 85, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
7 1 0.01
8 31 0.36
9 37 0.44
10 14 0.16
11 2 0.02
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.14
Consensus pattern (9 bp):
AATCAAAAA
Found at i:17237127 original size:26 final size:26
Alignment explanation
Indices: 17237057--17237177 Score: 85
Period size: 26 Copynumber: 4.8 Consensus size: 26
17237047 TATTTTTGTG
* * *
17237057 AAAAAAT-AAAAAAATTAATAATAAT
1 AAAAAATCAAAAAAATCAAAAAAAAT
* * *
17237082 AATAAATGACAAAAAT---AAAAAAT
1 AAAAAATCAAAAAAATCAAAAAAAAT
* *
17237105 AAACAATCAAAAAAATCAAAAAAATT
1 AAAAAATCAAAAAAATCAAAAAAAAT
*
17237131 AAAAAATCAAAAAAAT--TAAAAAAT
1 AAAAAATCAAAAAAATCAAAAAAAAT
*
17237155 CAAAAAA-CAAAACAAAACAAAAA
1 -AAAAAATCAAAA-AAATCAAAAA
17237178 TAAACATTAA
Statistics
Matches: 74, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
23 17 0.23
24 11 0.15
25 15 0.20
26 28 0.38
27 3 0.04
ACGTcount: A:0.77, C:0.07, G:0.01, T:0.15
Consensus pattern (26 bp):
AAAAAATCAAAAAAATCAAAAAAAAT
Found at i:17237171 original size:11 final size:11
Alignment explanation
Indices: 17237158--17237287 Score: 63
Period size: 11 Copynumber: 11.9 Consensus size: 11
17237148 AAAAAATCAA
17237158 AAAAC-AAAAC
1 AAAACAAAAAC
17237168 AAAACAAAAA-
1 AAAACAAAAAC
* ** *
17237178 TAAACATTAAT
1 AAAACAAAAAC
*
17237189 AATAACAATAAC
1 AA-AACAAAAAC
* *
17237201 CAAA-AAAATC
1 AAAACAAAAAC
*
17237211 AAAAAATCAAAAC
1 AAAACA--AAAAC
*
17237224 AAAACAATAAC
1 AAAACAAAAAC
*
17237235 AAAACAATAAC
1 AAAACAAAAAC
*
17237246 AAAAAAAATAAC
1 AAAACAAA-AAC
*
17237258 -AAA-AATAAC
1 AAAACAAAAAC
**
17237267 AAAACAAAATG
1 AAAACAAAAAC
17237278 AAAACAAAAA
1 AAAACAAAAA
17237288 AATAAATAAA
Statistics
Matches: 91, Mismatches: 20, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
9 3 0.03
10 24 0.26
11 44 0.48
12 11 0.12
13 9 0.10
ACGTcount: A:0.75, C:0.14, G:0.01, T:0.10
Consensus pattern (11 bp):
AAAACAAAAAC
Found at i:17237205 original size:46 final size:43
Alignment explanation
Indices: 17237157--17237273 Score: 114
Period size: 46 Copynumber: 2.7 Consensus size: 43
17237147 TAAAAAATCA
* * *
17237157 AAAAACAAAACAAAACAAAA-ATAAACATTAATAATAACAATAACC
1 AAAAAAAAAACAAAACAAAACA-AAACAATAACAA-AACAATAA-C
*
17237202 AAAAAAATCAAA-AAATCAAAACAAAACAATAACAAAACAATAAC
1 AAAAAAA--AAACAAAACAAAACAAAACAATAACAAAACAATAAC
*
17237246 AAAAAAAATAACAAAA-ATAACAAAACAA
1 AAAAAAAA-AACAAAACAAAACAAAACAA
17237274 AATGAAAACA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
42 1 0.02
43 13 0.21
44 11 0.18
45 14 0.23
46 18 0.30
47 4 0.07
ACGTcount: A:0.75, C:0.15, G:0.00, T:0.10
Consensus pattern (43 bp):
AAAAAAAAAACAAAACAAAACAAAACAATAACAAAACAATAAC
Found at i:17237214 original size:6 final size:5
Alignment explanation
Indices: 17237213--17237286 Score: 60
Period size: 5 Copynumber: 13.8 Consensus size: 5
17237203 AAAAAATCAA
*
17237213 AAAATC AAAAC AAAAC AATAAC AAAAC AATAAC AAAAAA AATAAC AAAA-
1 AAAA-C AAAAC AAAAC AA-AAC AAAAC AA-AAC -AAAAC AA-AAC AAAAC
* *
17237262 ATAAC AAAAC AAAATG AAAAC AAAA
1 AAAAC AAAAC AAAA-C AAAAC AAAA
17237287 AAATAAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
4 3 0.05
5 29 0.52
6 22 0.39
7 2 0.04
ACGTcount: A:0.77, C:0.14, G:0.01, T:0.08
Consensus pattern (5 bp):
AAAAC
Found at i:17237243 original size:45 final size:47
Alignment explanation
Indices: 17237192--17237302 Score: 131
Period size: 48 Copynumber: 2.4 Consensus size: 47
17237182 CATTAATAAT
* *
17237192 AACAATAACCAAAAAAAT-CAAAAA-ATCAAAACAAAA-CAATAACAA
1 AACAATAACAAAAAAAATACAAAAATAACAAAACAAAATCAA-AACAA
*
17237237 AACAATAACAAAAAAAATAACAAAAATAACAAAACAAAATGAAAACAA
1 AACAATAACAAAAAAAAT-ACAAAAATAACAAAACAAAATCAAAACAA
* *
17237285 AAAAATAA-ATAAAAAATA
1 AACAATAACAAAAAAAATA
17237303 AGAAAAAGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
45 17 0.30
46 1 0.02
47 14 0.25
48 23 0.40
49 2 0.04
ACGTcount: A:0.77, C:0.13, G:0.01, T:0.10
Consensus pattern (47 bp):
AACAATAACAAAAAAAATACAAAAATAACAAAACAAAATCAAAACAA
Found at i:17237256 original size:63 final size:61
Alignment explanation
Indices: 17237092--17237261 Score: 165
Period size: 63 Copynumber: 2.8 Consensus size: 61
17237082 AATAAATGAC
* * * * *
17237092 AAAAAT-AAAAA-ATAAAC-AATCAAAAA-AATCAAAAAAATTAA-AAAATCAAAAAAATTA
1 AAAAATCAAAAACA-AAACAAAACAAAAATAAACAAAAAAAATAACAAAACCAAAAAAATCA
** *
17237149 AAAAATCAAAAAACAAAACAAAACAAAAATAAACATTAATAATAACAATAACCAAAAAAATCA
1 AAAAATC-AAAAACAAAACAAAACAAAAATAAACAAAAAAAATAACAA-AACCAAAAAAATCA
17237212 AAAAATC-AAAACAAAACAATAACAAAACA-ATAACAAAAAAAATAACAAAA
1 AAAAATCAAAAACAAAACAA-AACAAAA-ATA-AACAAAAAAAATAACAAAA
17237262 ATAACAAAAC
Statistics
Matches: 92, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
57 6 0.07
59 9 0.10
60 9 0.10
61 22 0.24
62 12 0.13
63 34 0.37
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (61 bp):
AAAAATCAAAAACAAAACAAAACAAAAATAAACAAAAAAAATAACAAAACCAAAAAAATCA
Found at i:17237261 original size:56 final size:55
Alignment explanation
Indices: 17237148--17237287 Score: 155
Period size: 57 Copynumber: 2.5 Consensus size: 55
17237138 CAAAAAAATT
* * * *
17237148 AAAAAATCAAAAAACAAAACAAAACAAAAATAAACATTAATAATAACAATAACCA
1 AAAAAATCAAAAAACAAAACAAAACAAAAATAAACAATAACAAAAAAAATAACCA
17237203 AAAAAATCAAAAAATCAAAACAAAACAATAACA-AAACAATAACAAAAAAAATAA-C-
1 AAAAAATCAAAAAA-CAAAACAAAACAA-AA-ATAAACAATAACAAAAAAAATAACCA
*
17237258 -AAAAAT-AACAAAACAAAATGAAAACAAAAA
1 AAAAAATCAA-AAAACAAAA-CAAAACAAAAA
17237288 AATAAATAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
52 1 0.01
53 9 0.12
54 17 0.23
55 14 0.19
56 14 0.19
57 19 0.25
58 1 0.01
ACGTcount: A:0.76, C:0.14, G:0.01, T:0.10
Consensus pattern (55 bp):
AAAAAATCAAAAAACAAAACAAAACAAAAATAAACAATAACAAAAAAAATAACCA
Found at i:17237265 original size:72 final size:69
Alignment explanation
Indices: 17237099--17237290 Score: 167
Period size: 72 Copynumber: 2.6 Consensus size: 69
17237089 GACAAAAATA
* *
17237099 AAAAATAAACAATCAAAAA-AATCAAAAAAATTAAAAAATCAAAAAAATTAAAAAATCAAAAAAC
1 AAAAATAAACAA-CAAAAATAA-C-AAAACA--AAAAAATCAAAAAAATCAAAAAA-CAAAAAAC
17237163 AAAACAAAAC
60 AAAACAAAAC
** *
17237173 AAAAATAAACATTAATAATAACAATAACCAAAAAAATC-AAAAAATCAAAACAA-AACAATAACA
1 AAAAATAAACAACAAAAATAACAA-AA-CAAAAAAATCAAAAAAATCAAAA-AACAA-AA-AACA
17237236 AAACAATAAC
61 AAACAA-AAC
* *
17237246 AAAAA-AAATAACAAAAATAACAAAACAAAATGAAAACAAAAAAAT
1 AAAAATAAACAACAAAAATAACAAAACAAAA--AAATCAAAAAAAT
17237291 AAATAAAAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
70 7 0.07
71 15 0.15
72 40 0.41
73 22 0.22
74 14 0.14
ACGTcount: A:0.76, C:0.12, G:0.01, T:0.12
Consensus pattern (69 bp):
AAAAATAAACAACAAAAATAACAAAACAAAAAAATCAAAAAAATCAAAAAACAAAAAACAAAACA
AAAC
Found at i:17237292 original size:48 final size:47
Alignment explanation
Indices: 17237138--17237309 Score: 133
Period size: 47 Copynumber: 3.6 Consensus size: 47
17237128 ATTAAAAAAT
*
17237138 CAAAAAAATTAA-AAAATCAAAA-AACAAAACAAAACAAAA-ATAAACATTAA
1 CAAAAAAA-TAACAAAA--AAAATAAC-AAA-AAAACAAAACA-AAACAATAA
* * * *
17237188 TAATAACAATAACCAAAAAAAT--CAAAAAATCAAAACAAAACAATAA
1 CAA-AAAAATAACAAAAAAAATAACAAAAAAACAAAACAAAACAATAA
* *
17237234 CAAAACAATAACAAAAAAAATAACAAAAATAACAAAACAAAATGAA-AA
1 CAAAAAAATAACAAAAAAAATAACAAAAA-AACAAAACAAAA-CAATAA
* *
17237282 CAAAAAAATAA-ATAAAAAATAAGAAAAA
1 CAAAAAAATAACAAAAAAAATAACAAAAA
17237310 GAAGAAAGAG
Statistics
Matches: 102, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
45 17 0.17
46 18 0.18
47 25 0.25
48 24 0.24
49 6 0.06
50 5 0.05
51 7 0.07
ACGTcount: A:0.76, C:0.12, G:0.01, T:0.11
Consensus pattern (47 bp):
CAAAAAAATAACAAAAAAAATAACAAAAAAACAAAACAAAACAATAA
Found at i:17238189 original size:20 final size:19
Alignment explanation
Indices: 17238166--17238219 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 19
17238156 AAAAAAGTAC
17238166 AAAAAGGAAAGCAAAAAAA-A
1 AAAAAGG-AA-CAAAAAAACA
17238186 AAAAAGGAACAAAAAAACA
1 AAAAAGGAACAAAAAAACA
17238205 AAAGAA-GAA-AAAAAA
1 AAA-AAGGAACAAAAAA
17238220 TAAGGAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 14 0.44
19 9 0.28
20 9 0.28
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAGGAACAAAAAAACA
Found at i:17238199 original size:16 final size:16
Alignment explanation
Indices: 17238180--17238226 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
17238170 AGGAAAGCAA
17238180 AAAAAAAAAAAGGAAC
1 AAAAAAAAAAAGGAAC
*
17238196 AAAAAAACAAAA-GAAG
1 AAAAAAA-AAAAGGAAC
*
17238212 AAAAAAAATAAGGAA
1 AAAAAAAAAAAGGAA
17238227 GTTGAGAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 3 0.11
16 20 0.74
17 4 0.15
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAAGGAAC
Found at i:17238199 original size:17 final size:16
Alignment explanation
Indices: 17238179--17238219 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
17238169 AAGGAAAGCA
17238179 AAAAAAAAAAAAGGAAC
1 AAAAAAAAAAAA-GAAC
* *
17238196 AAAAAAACAAAAGAAG
1 AAAAAAAAAAAAGAAC
17238212 AAAAAAAA
1 AAAAAAAA
17238220 TAAGGAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAGAAC
Found at i:17240011 original size:3 final size:3
Alignment explanation
Indices: 17240005--17240052 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
17239995 AAAAAAAAGA
17240005 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17240052 A
1 A
17240053 GTAGAAATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17240336 original size:16 final size:16
Alignment explanation
Indices: 17240315--17240349 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
17240305 CTTTCAAAAA
17240315 AATTAAATTAAAAAT-T
1 AATT-AATTAAAAATAT
17240331 AATTAATTAAAAATAT
1 AATTAATTAAAAATAT
17240347 AAT
1 AAT
17240350 AATAGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTAATTAAAAATAT
Found at i:17240338 original size:15 final size:15
Alignment explanation
Indices: 17240315--17240361 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
17240305 CTTTCAAAAA
17240315 AATTAAATTAAAAATT
1 AATT-AATTAAAAATT
17240331 AATTAATTAAAAATAT
1 AATTAATTAAAAAT-T
*
17240347 AA-TAA-TAGAAATT
1 AATTAATTAAAAATT
17240360 AA
1 AA
17240362 AAATTAGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.10
14 6 0.21
15 13 0.45
16 7 0.24
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
AATTAATTAAAAATT
Found at i:17240393 original size:36 final size:36
Alignment explanation
Indices: 17240319--17240389 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
17240309 CAAAAAAATT
*
17240319 AAATTAAAAATTAATTAATTAAAAATATAATAATAG
1 AAATTAAAAATTAATTAAATAAAAATATAATAATAG
*
17240355 AAATTAAAAATTAGGATTAGAATAAAATTA-AATAA
1 AAATTAAAAATTA--ATTA-AATAAAAATATAATAA
17240390 GAAAGGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 13 0.43
38 9 0.30
39 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (36 bp):
AAATTAAAAATTAATTAAATAAAAATATAATAATAG
Done.