Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 35 of 186
Found at i:10491084 original size:21 final size:21
Alignment explanation
Indices: 10491042--10491108 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
10491032 GAATACATTG
*
10491042 ACAGAAGCTTG-AA-AGCTAA
1 ACAGAAGCTCGTAAGAGCTAA
*
10491061 ACAGAAGCTCGTAAGAGCTTA
1 ACAGAAGCTCGTAAGAGCTAA
* * *
10491082 ACAGAAGCTCGTAGGAACTGA
1 ACAGAAGCTCGTAAGAGCTAA
10491103 ACAGAA
1 ACAGAA
10491109 AGTAAAACAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
19 10 0.24
20 2 0.05
21 29 0.71
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (21 bp):
ACAGAAGCTCGTAAGAGCTAA
Found at i:10491269 original size:17 final size:17
Alignment explanation
Indices: 10491249--10491285 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
10491239 ATTAAATTCG
*
10491249 ATAATATATTTCCAATA
1 ATAATATAATTCCAATA
*
10491266 ATAATTTAATTCCAATA
1 ATAATATAATTCCAATA
10491283 ATA
1 ATA
10491286 TAACATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATATAATTCCAATA
Found at i:10494413 original size:29 final size:30
Alignment explanation
Indices: 10494366--10494433 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
10494356 TGGCCCAAGA
* * *
10494366 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAACGACTAATAGT
*
10494396 GTAAATATGAAAAGTTGAACGACTAATAGT
1 GTAAATATCAAAAGTTGAACGACTAATAGT
*
10494426 GCAAATAT
1 GTAAATAT
10494434 TTTAAGGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAACGACTAATAGT
Found at i:10496631 original size:46 final size:45
Alignment explanation
Indices: 10496580--10496899 Score: 480
Period size: 46 Copynumber: 7.0 Consensus size: 45
10496570 AGTGTGCACT
*
10496580 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
*
10496625 TCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 -CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
*
10496671 TCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 -CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
*
10496717 CCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA
1 -CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
*
10496763 CGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA
1 C-TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
*
10496809 CGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA
1 C-TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
* * * *
10496855 CATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 C-TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
10496900 TCATGTCAAA
Statistics
Matches: 263, Mismatches: 9, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
45 2 0.01
46 261 0.99
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (45 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
Found at i:10497206 original size:16 final size:17
Alignment explanation
Indices: 10497185--10497217 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
10497175 ATGATGGAGC
10497185 ATGAAAT-ATTGATATA
1 ATGAAATAATTGATATA
10497201 ATGAAATAATTGATATA
1 ATGAAATAATTGATATA
10497218 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (17 bp):
ATGAAATAATTGATATA
Found at i:10503633 original size:47 final size:48
Alignment explanation
Indices: 10503516--10503640 Score: 162
Period size: 48 Copynumber: 2.6 Consensus size: 48
10503506 GTGCGAATGA
* ***
10503516 TACCTTGATTTGGCTAGGGGCCATGGTATAGGTATTTCAGAGAGAAGT
1 TACCTTGATTTGGCTAGGGGCCATGGTATAGATACAGCAGAGAGAAGT
* *
10503564 TACCTTTATTTGGCTAGGGGCCATGGTATAGATACAGCAG-GATAAGT
1 TACCTTGATTTGGCTAGGGGCCATGGTATAGATACAGCAGAGAGAAGT
* **
10503611 TACCTTGATTTGGTTACAGGCCATGGTATA
1 TACCTTGATTTGGCTAGGGGCCATGGTATA
10503641 AGTACTTATC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
47 32 0.48
48 35 0.52
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (48 bp):
TACCTTGATTTGGCTAGGGGCCATGGTATAGATACAGCAGAGAGAAGT
Found at i:10505262 original size:39 final size:39
Alignment explanation
Indices: 10505083--10505259 Score: 228
Period size: 39 Copynumber: 4.5 Consensus size: 39
10505073 CATTTTTGTT
10505083 AGTATTGTGATATATATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTG--ATATATGCTTGAATGTTATGTGATTATATG
* * *
10505124 AGTATTGTGAGATATGTTTGAATGTTATGTGATTATATA
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* * * *
10505163 AATATTGAGATATATGCTTGAACGTTATGTAATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* * *
10505202 AGTATTTTGATATATGCTTAAATATTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* *
10505241 TGTAATGTGATATATGCTT
1 AGTATTGTGATATATGCTT
10505260 AAAAGTTAAC
Statistics
Matches: 116, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
39 107 0.92
41 9 0.08
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.46
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
Found at i:10505569 original size:30 final size:30
Alignment explanation
Indices: 10505535--10505594 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
10505525 TCGTAGGTGT
*
10505535 TATTGTTGTTTGTTTTCATTTTGGGAATAA
1 TATTGTTGTTTATTTTCATTTTGGGAATAA
*
10505565 TATTGTTGTTTATTTTCGTTTTGGGAATAA
1 TATTGTTGTTTATTTTCATTTTGGGAATAA
10505595 GGCAATGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.20, C:0.03, G:0.20, T:0.57
Consensus pattern (30 bp):
TATTGTTGTTTATTTTCATTTTGGGAATAA
Found at i:10506693 original size:22 final size:22
Alignment explanation
Indices: 10506667--10506711 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
10506657 AGATCAACAC
10506667 AAATAT-AATCACATACATATCA
1 AAATATCAATCACAT-CATATCA
**
10506689 AAATATCAATTTCATCATATCA
1 AAATATCAATCACATCATATCA
10506711 A
1 A
10506712 TCATCATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATATCAATCACATCATATCA
Found at i:10506908 original size:22 final size:22
Alignment explanation
Indices: 10506883--10506925 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
10506873 AAACCACAAC
*
10506883 TGATCTGTAGATAAACTGCCAT
1 TGATCTGCAGATAAACTGCCAT
*
10506905 TGATTTGCAGATAAACTGCCA
1 TGATCTGCAGATAAACTGCCA
10506926 CTAATAACAC
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:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (22 bp):
TGATCTGCAGATAAACTGCCAT
Found at i:10507010 original size:73 final size:73
Alignment explanation
Indices: 10506871--10507049 Score: 286
Period size: 73 Copynumber: 2.5 Consensus size: 73
10506861 TCGTTTATGG
* * * *
10506871 ACAAACCACAACTGATCTGTAGATAAACTGCCATTGATTTGCAGATAAACTGCCACTAATAACAC
1 ACAAGCCACCACTGATTTGCAGATAAACTGCCATTGATTTGCAGATAAACTGCCACTAATAACAC
10506936 TGATGTGA
66 TGATGTGA
*
10506944 ACAAGCCACCACTGGTTTGCAGATAAACTGCCATTGATTTGCAGATAAACTGCCACTAATAACAC
1 ACAAGCCACCACTGATTTGCAGATAAACTGCCATTGATTTGCAGATAAACTGCCACTAATAACAC
*
10507009 TGATGTGG
66 TGATGTGA
* *
10507017 ACAAGCCACCATTGATTTGCAGATAAATTGCCA
1 ACAAGCCACCACTGATTTGCAGATAAACTGCCA
10507050 CTAATAACAC
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 97 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (73 bp):
ACAAGCCACCACTGATTTGCAGATAAACTGCCATTGATTTGCAGATAAACTGCCACTAATAACAC
TGATGTGA
Found at i:10507034 original size:51 final size:51
Alignment explanation
Indices: 10506974--10507078 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
10506964 AGATAAACTG
*
10506974 CCATTGATTTGCAGATAAACTGCCACTAATAACACTGATGTGGACAAGCCA
1 CCATTGATTTGCAGATAAACTGCCACTAATAACACTAATGTGGACAAGCCA
*
10507025 CCATTGATTTGCAGATAAATTGCCACTAATAACACTAATGTGGACAAGCCA
1 CCATTGATTTGCAGATAAACTGCCACTAATAACACTAATGTGGACAAGCCA
10507076 CCA
1 CCA
10507079 CTAAATTGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (51 bp):
CCATTGATTTGCAGATAAACTGCCACTAATAACACTAATGTGGACAAGCCA
Found at i:10512978 original size:145 final size:147
Alignment explanation
Indices: 10512699--10512982 Score: 473
Period size: 145 Copynumber: 1.9 Consensus size: 147
10512689 AACAGGAAAG
*
10512699 AGGATGCGAGAAATAAGATGCATATGCAAACTAGAAGATATCATAATAAAAAAGCATGGTAGGCA
1 AGGATGCGAGAAATAAGATGCATATGCAAACTAGAAGAAATCATAATAAAAAAGCATGGTAGGCA
* * *
10512764 AAGGAATGAGTGGTCGGGGTTTAAGGAAGAACTGAGAACAGAAGAAAGAAACAGACAAGAGAGCA
66 AAGGAATGAGTGGTCAGGGTTTAAGGAAGAACTGAGAACAGAAGAAAGAAACAGACAAAAGAACA
10512829 GGGGAGAGGCTGATGAA
131 GGGGAGAGGCTGATGAA
* * *
10512846 AGGATGGGAGAAATAAGATGCATATGC-AATTAGAAGAAATCATAATAGAAAAGCATGGTAGGCA
1 AGGATGCGAGAAATAAGATGCATATGCAAACTAGAAGAAATCATAATAAAAAAGCATGGTAGGCA
* *
10512910 AAGGAATGAGT-GTCAGGGTTTAAGGAAGAACTGAGAACAGAAGAAAGTAACAGGCAAAAGAACA
66 AAGGAATGAGTGGTCAGGGTTTAAGGAAGAACTGAGAACAGAAGAAAGAAACAGACAAAAGAACA
10512974 GGGGAGAGG
131 GGGGAGAGG
10512983 TTTTAGACTT
Statistics
Matches: 128, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
145 57 0.45
146 45 0.35
147 26 0.20
ACGTcount: A:0.45, C:0.09, G:0.31, T:0.14
Consensus pattern (147 bp):
AGGATGCGAGAAATAAGATGCATATGCAAACTAGAAGAAATCATAATAAAAAAGCATGGTAGGCA
AAGGAATGAGTGGTCAGGGTTTAAGGAAGAACTGAGAACAGAAGAAAGAAACAGACAAAAGAACA
GGGGAGAGGCTGATGAA
Found at i:10515915 original size:36 final size:37
Alignment explanation
Indices: 10515839--10515915 Score: 88
Period size: 36 Copynumber: 2.1 Consensus size: 37
10515829 ATTTTTCGAA
* *
10515839 AAATCTATTTTTACATATATTAATAAATTTATATTTT
1 AAATCTATTTTTACATATATCAATAAATTTATATTAT
*
10515876 AAAT-TATTTTTATATATACTACAAT-AATTTAT-TTAT
1 AAATCTATTTTTACATATA-T-CAATAAATTTATATTAT
10515912 AAAT
1 AAAT
10515916 AAATAAATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 20 0.57
37 12 0.34
38 3 0.09
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (37 bp):
AAATCTATTTTTACATATATCAATAAATTTATATTAT
Found at i:10521585 original size:21 final size:21
Alignment explanation
Indices: 10521548--10521633 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
10521538 CCTGATTAGA
* *
10521548 AAACGACACA-TAAGTGCCTG
1 AAACGACACACGAGGTGCCTG
10521568 AAACGACACACGAGGTGCCTG
1 AAACGACACACGAGGTGCCTG
***
10521589 CTGCGACACACGAGGTGCCTG
1 AAACGACACACGAGGTGCCTG
*** *
10521610 CTGCGACACACAAGGTGCCTG
1 AAACGACACACGAGGTGCCTG
10521631 AAA
1 AAA
10521634 TATGACACAT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
20 10 0.18
21 46 0.82
ACGTcount: A:0.31, C:0.29, G:0.27, T:0.13
Consensus pattern (21 bp):
AAACGACACACGAGGTGCCTG
Found at i:10521890 original size:28 final size:29
Alignment explanation
Indices: 10521859--10521914 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
10521849 AACACACTAG
*
10521859 TATAATCC-TCCCAAACACACCAGAATAA
1 TATAATCCATCCAAAACACACCAGAATAA
10521887 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCCATCCAAAACACACCAGAATA
10521915 GCACAAAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.48, C:0.30, G:0.04, T:0.18
Consensus pattern (29 bp):
TATAATCCATCCAAAACACACCAGAATAA
Found at i:10526384 original size:20 final size:20
Alignment explanation
Indices: 10526359--10526397 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
10526349 TTATTTAAAT
10526359 TAATATAC-AGTTTTATATAC
1 TAATATACTA-TTTTATATAC
10526379 TAATATACTATTTTATATA
1 TAATATACTATTTTATATA
10526398 ATTTTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (20 bp):
TAATATACTATTTTATATAC
Found at i:10526442 original size:22 final size:22
Alignment explanation
Indices: 10526412--10526454 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
10526402 TTCAAATATG
10526412 TAAAATAATATACTGTTTTATT
1 TAAAATAATATACTGTTTTATT
*
10526434 TAAACTAATATACTGTTTTAT
1 TAAAATAATATACTGTTTTAT
10526455 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (22 bp):
TAAAATAATATACTGTTTTATT
Found at i:10528039 original size:39 final size:39
Alignment explanation
Indices: 10527994--10528070 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
10527984 AATGGATCAA
10527994 ACATGTTGATATCATCCAACTAAAATAGACAGCTTTCAT
1 ACATGTTGATATCATCCAACTAAAATAGACAGCTTTCAT
10528033 ACATGTTGATATCATCCAACTAAAATAGACAGCTTTCA
1 ACATGTTGATATCATCCAACTAAAATAGACAGCTTTCA
10528071 GAGATTAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (39 bp):
ACATGTTGATATCATCCAACTAAAATAGACAGCTTTCAT
Found at i:10528925 original size:23 final size:23
Alignment explanation
Indices: 10528875--10528925 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
10528865 CCTTAGAAAG
10528875 AGAGATTTGCCTTTGCCTGGTAA
1 AGAGATTTGCCTTTGCCTGGTAA
*
10528898 TGAGATTTGCCTTTGCCTGAG-AA
1 AGAGATTTGCCTTTGCCTG-GTAA
10528921 AGAGA
1 AGAGA
10528926 GAAAAAGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (23 bp):
AGAGATTTGCCTTTGCCTGGTAA
Found at i:10533116 original size:18 final size:18
Alignment explanation
Indices: 10533093--10533128 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10533083 GTCAATACAC
10533093 AATCTCAAATATCCATCT
1 AATCTCAAATATCCATCT
10533111 AATCTCAAATATCCATCT
1 AATCTCAAATATCCATCT
10533129 TTCTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (18 bp):
AATCTCAAATATCCATCT
Found at i:10538552 original size:22 final size:24
Alignment explanation
Indices: 10538510--10538553 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
10538500 TAACTAAGTT
10538510 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
10538534 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
10538554 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:10539620 original size:5 final size:5
Alignment explanation
Indices: 10539610--10539661 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
10539600 AATCTGTTTC
*
10539610 ATAAT ATAAT ATAAT ATAATT ATAAT ATAAT -CAAT -TAAT AGTAAT AT-AT
1 ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT
10539659 ATA
1 ATA
10539662 CCTAAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 10 0.24
5 21 0.51
6 10 0.24
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:10539635 original size:16 final size:15
Alignment explanation
Indices: 10539610--10539661 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
10539600 AATCTGTTTC
10539610 ATAATATAATATAAT
1 ATAATATAATATAAT
10539625 ATAATTATAATATAAT
1 ATAA-TATAATATAAT
*
10539641 -CAAT-TAATAGTAAT
1 ATAATATAATA-TAAT
10539655 AT-ATATA
1 ATAATATA
10539662 CCTAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 8 0.26
16 11 0.35
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
ATAATATAATATAAT
Found at i:10544993 original size:28 final size:27
Alignment explanation
Indices: 10544925--10545069 Score: 121
Period size: 28 Copynumber: 5.2 Consensus size: 27
10544915 TGGTGAATTA
** *
10544925 TGAAAAGAATATACTTTGTGGCGAACTC
1 TGAAAAGAATAGCCTGTGTGGCGAAC-C
* *
10544953 CGAAAAGAATAGCCTCTGTGGCGAACC
1 TGAAAAGAATAGCCTGTGTGGCGAACC
* **
10544980 ATGAAAAGAATAGCCTATGTACCGAA-C
1 -TGAAAAGAATAGCCTGTGTGGCGAACC
* * *
10545007 TGTAAAAATAATAGCCTGTGAGGCAAACTC
1 TG--AAAAGAATAGCCTGTGTGGCGAAC-C
*
10545037 TGAAAAGAATAGCTTGTGTGGCGAACTC
1 TGAAAAGAATAGCCTGTGTGGCGAAC-C
10545065 TGAAA
1 TGAAA
10545070 GGGATGCCTT
Statistics
Matches: 94, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 87 0.93
30 3 0.03
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (27 bp):
TGAAAAGAATAGCCTGTGTGGCGAACC
Found at i:10545006 original size:56 final size:56
Alignment explanation
Indices: 10544901--10545049 Score: 129
Period size: 56 Copynumber: 2.7 Consensus size: 56
10544891 AATGACAATT
* * * ** ** * ** *
10544901 AAGAATAGCCTTTATGGTGAATTATGAAAAGAATATACTTTGTGGCGAACTCCGAA
1 AAGAATAGCCTCTGTGGCGAACCATGAAAAGAATAGCCTATGTACCGAACTCCAAA
**
10544957 AAGAATAGCCTCTGTGGCGAACCATGAAAAGAATAGCCTATGTACCGAACTGTAAA
1 AAGAATAGCCTCTGTGGCGAACCATGAAAAGAATAGCCTATGTACCGAACTCCAAA
* * * *
10545013 AATAATAGCCTGTGAGGCAAACTC-TGAAAAGAATAGC
1 AAGAATAGCCTCTGTGGCGAAC-CATGAAAAGAATAGC
10545050 TTGTGTGGCG
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
56 74 0.99
57 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (56 bp):
AAGAATAGCCTCTGTGGCGAACCATGAAAAGAATAGCCTATGTACCGAACTCCAAA
Found at i:10545062 original size:56 final size:55
Alignment explanation
Indices: 10544924--10545064 Score: 140
Period size: 56 Copynumber: 2.5 Consensus size: 55
10544914 ATGGTGAATT
* * * *
10544924 ATGAAAAGAATATACTTTGTGGCGAACTCCGAAAAGAATAGCCTCTGTGGCGAACC
1 ATGAAAAGAATA-GCTTTGTGGCGAACTCCAAAAAGAATAGCCTCTGAGGCAAACC
* ** ** * *
10544980 ATGAAAAGAATAGCCTATGTACCGAACTGTAAAAATAATAGCCTGTGAGGCAAACTC
1 ATGAAAAGAATAG-CTTTGTGGCGAACTCCAAAAAGAATAGCCTCTGAGGCAAAC-C
10545037 -TGAAAAGAATAGCTTGTGTGGCGAACTC
1 ATGAAAAGAATAGCTT-TGTGGCGAACTC
10545065 TGAAAGGGAT
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
55 2 0.03
56 64 0.96
57 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.22
Consensus pattern (55 bp):
ATGAAAAGAATAGCTTTGTGGCGAACTCCAAAAAGAATAGCCTCTGAGGCAAACC
Found at i:10546873 original size:34 final size:34
Alignment explanation
Indices: 10546830--10546953 Score: 135
Period size: 34 Copynumber: 3.6 Consensus size: 34
10546820 ACATATACGA
*
10546830 ATATCATATCAGAATGTCATATTACCAGAAACAT
1 ATATCATATCAGAATGTCATATTTCCAGAAACAT
* *
10546864 ATATCATATCAAAATGTCGTATTTCCAGAAACAT
1 ATATCATATCAGAATGTCATATTTCCAGAAACAT
* * * * *
10546898 AT-GCTAGATTAGAATGTCATATTTTCATAAACAT
1 ATATC-ATATCAGAATGTCATATTTCCAGAAACAT
*
10546932 ATAT-TTGATCAGAATGTCATAT
1 ATATCAT-ATCAGAATGTCATAT
10546954 CAAATCAAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
33 1 0.01
34 72 0.99
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (34 bp):
ATATCATATCAGAATGTCATATTTCCAGAAACAT
Found at i:10547804 original size:30 final size:30
Alignment explanation
Indices: 10547768--10547830 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
10547758 ATTTATTTTA
10547768 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
10547798 TTGTTAATTTTGTTATTATTTTAGATACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
10547828 TTG
1 TTG
10547831 ATTGTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:10561103 original size:30 final size:30
Alignment explanation
Indices: 10561034--10561104 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
10561024 TTTTATAGTC
* * *
10561034 TATATTTTTATAATTTTTAAAAAATTAAAT
1 TATAATTTTATAATTTTTAAAAAATCAAAG
*
10561064 TA-AATTTTTATAA-TTTTAAAGAGATCAAAG
1 TATAA-TTTTATAATTTTTAAA-AAATCAAAG
10561094 TATAATTTTAT
1 TATAATTTTAT
10561105 TTTTATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 8 0.24
30 24 0.71
31 2 0.06
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (30 bp):
TATAATTTTATAATTTTTAAAAAATCAAAG
Found at i:10564987 original size:20 final size:21
Alignment explanation
Indices: 10564958--10565000 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
10564948 TTGTAAATTT
10564958 AAAAACTAAA-AAAAGACGAA
1 AAAAACTAAATAAAAGACGAA
* *
10564978 AAAAATTAAATAAAAGACTAA
1 AAAAACTAAATAAAAGACGAA
10564999 AA
1 AA
10565001 TACATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (21 bp):
AAAAACTAAATAAAAGACGAA
Found at i:10565721 original size:17 final size:17
Alignment explanation
Indices: 10565699--10565732 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
10565689 TACATACCAT
10565699 TTTTATTTTATAAAATA
1 TTTTATTTTATAAAATA
*
10565716 TTTTATTTTATGAAATA
1 TTTTATTTTATAAAATA
10565733 ATATCATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTATTTTATAAAATA
Found at i:10565956 original size:18 final size:17
Alignment explanation
Indices: 10565929--10565962 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
10565919 TCAATTAGTT
10565929 AATTTTAAAAAAATTAA
1 AATTTTAAAAAAATTAA
10565946 AATTATTAAAAAAATTA
1 AATT-TTAAAAAAATTA
10565963 TAAGAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTTTAAAAAAATTAA
Found at i:10566005 original size:18 final size:18
Alignment explanation
Indices: 10565921--10566007 Score: 54
Period size: 18 Copynumber: 4.7 Consensus size: 18
10565911 TCACATCATC
*
10565921 AATTAGTTAATTTTAAAAA
1 AATTAATTAA-TTTAAAAA
10565940 AATTAA--AATTATTAAAAA
1 AATTAATTAA-T-TTAAAAA
**
10565958 AATTATAAGAATTATAAAGAA
1 AATTA-ATTAATT-TAAA-AA
* *
10565979 TATT-TTTAATTTAAAAA
1 AATTAATTAATTTAAAAA
10565996 AATTAATTAATT
1 AATTAATTAATT
10566008 GCTAACGGGC
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
17 9 0.17
18 22 0.41
19 11 0.20
20 5 0.09
21 7 0.13
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AATTAATTAATTTAAAAA
Found at i:10569766 original size:31 final size:31
Alignment explanation
Indices: 10569717--10569829 Score: 120
Period size: 31 Copynumber: 3.6 Consensus size: 31
10569707 AAAAAAATAT
* *
10569717 TTTAAA-AATTAAATATAATAATAAATGAGA
1 TTTAAATAATTTAATATAATAATAAATGAAA
* * *
10569747 TTTAAATAATTTAATATAATGATAAATTATA
1 TTTAAATAATTTAATATAATAATAAATGAAA
* * * *
10569778 TTTAAATAATTTCATTTAATCATATATGAAAA
1 TTTAAATAATTTAATATAATAATAAATG-AAA
*
10569810 TTTAAATAATTCAATATAAT
1 TTTAAATAATTTAATATAAT
10569830 GGAATATAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
30 6 0.09
31 43 0.63
32 19 0.28
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (31 bp):
TTTAAATAATTTAATATAATAATAAATGAAA
Found at i:10570430 original size:15 final size:16
Alignment explanation
Indices: 10570409--10570462 Score: 74
Period size: 15 Copynumber: 3.3 Consensus size: 16
10570399 TTAGAATTGC
10570409 TATTTTTAGTGTTTGT
1 TATTTTTAGTGTTTGT
*
10570425 TATTTTTA-TGTTTGC
1 TATTTTTAGTGTTTGT
10570440 TATTTTTAAGTGTTTTGT
1 TATTTTT-AGTG-TTTGT
10570458 TATTT
1 TATTT
10570463 GAATTTATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 13 0.39
16 9 0.27
17 2 0.06
18 9 0.27
ACGTcount: A:0.15, C:0.02, G:0.15, T:0.69
Consensus pattern (16 bp):
TATTTTTAGTGTTTGT
Found at i:10570580 original size:30 final size:30
Alignment explanation
Indices: 10570544--10570600 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
10570534 TTGAATAATA
10570544 TTCATCAATTCAGTTTTCTTTTCTTTTATC
1 TTCATCAATTCAGTTTTCTTTTCTTTTATC
*
10570574 TTCATCAGTTCAGTTTTCTTTTCTTTT
1 TTCATCAATTCAGTTTTCTTTTCTTTT
10570601 CTGATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.14, C:0.19, G:0.05, T:0.61
Consensus pattern (30 bp):
TTCATCAATTCAGTTTTCTTTTCTTTTATC
Found at i:10574673 original size:93 final size:93
Alignment explanation
Indices: 10574561--10574731 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
10574551 GCCCATAAGT
* * * *
10574561 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
10574626 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
10574654 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
10574719 CGAGTTCGGATGC
66 CGAGCTCGGATGC
10574732 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:10574728 original size:46 final size:46
Alignment explanation
Indices: 10574553--10574728 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
10574543 TGTAACCCGC
* *
10574553 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
10574599 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** * *
10574645 ACATCTCTCGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
10574692 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
10574729 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 68 0.63
47 31 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:10576787 original size:197 final size:196
Alignment explanation
Indices: 10576452--10576846 Score: 745
Period size: 197 Copynumber: 2.0 Consensus size: 196
10576442 ACATCTTCGC
*
10576452 ACCAGTTGTTCATTTGGACACCATAAGACTTTTAAGTGTATCAGCTTGATGTAAAATTAGTTTTT
1 ACCAGTTGTTCATTTGGACACCATAAGACTTTTAAGTGTATCAGCTTGATGTAAAATTAGCTTTT
10576517 TTAAATGGCACTTTGTAGGAAGAAATTTATGTTGAATAGCCTAAAGGTTTTACGAAGAAAATGAG
66 TTAAATGGCACTTTGTAGGAAGAAATTTATGTTGAATAGCCTAAAGGTTTTACGAAGAAAATGAG
10576582 AAGAAGACAAGCTGTTTCTTCTTAATAAGGCTCTTTATGGGCTGAAACAAGCTCCAAGGAGCTTG
131 AAGAAGACAAGCTGTTTCTTCTTAATAAGGCTCTTTATGGGCTGAAACAAGCTCCAA-GAGCTTG
10576647 GT
195 GT
10576649 ACCAGTTGTTCATTTGGACACCATAAGACTTTTAAGTGTATCAGCTTGATGTAAAATTAGCTTTT
1 ACCAGTTGTTCATTTGGACACCATAAGACTTTTAAGTGTATCAGCTTGATGTAAAATTAGCTTTT
*
10576714 TTAAATGGCACTTTGTAGGAAGAAATTTATGTTGAGTAGCCTAAAGGTTTTACGAAGAAAATGAG
66 TTAAATGGCACTTTGTAGGAAGAAATTTATGTTGAATAGCCTAAAGGTTTTACGAAGAAAATGAG
* *
10576779 AGGAAGACAAGTTGTTTCTTCTTAATAAGGCTCTTTATGGGCTGAAACAAGCTCCAAGAGCTTGG
131 AAGAAGACAAGCTGTTTCTTCTTAATAAGGCTCTTTATGGGCTGAAACAAGCTCCAAGAGCTTGG
10576844 T
196 T
10576845 AC
1 AC
10576847 AGTAAGATAG
Statistics
Matches: 194, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
196 11 0.06
197 183 0.94
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (196 bp):
ACCAGTTGTTCATTTGGACACCATAAGACTTTTAAGTGTATCAGCTTGATGTAAAATTAGCTTTT
TTAAATGGCACTTTGTAGGAAGAAATTTATGTTGAATAGCCTAAAGGTTTTACGAAGAAAATGAG
AAGAAGACAAGCTGTTTCTTCTTAATAAGGCTCTTTATGGGCTGAAACAAGCTCCAAGAGCTTGG
T
Found at i:10577903 original size:16 final size:17
Alignment explanation
Indices: 10577882--10577913 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
10577872 TTTAGGACTC
10577882 CTATTTTTA-GTGTTTG
1 CTATTTTTAGGTGTTTG
10577898 CTATTTTTAGGTGTTT
1 CTATTTTTAGGTGTTT
10577914 TGTTATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.12, C:0.06, G:0.19, T:0.62
Consensus pattern (17 bp):
CTATTTTTAGGTGTTTG
Found at i:10584049 original size:46 final size:46
Alignment explanation
Indices: 10583982--10584072 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
10583972 TATATATATA
* *
10583982 TATATTTGTATTCTTGTTTTGGTCATCTAATTTTAAAAATTTTAAG
1 TATATTTGTATTCTTGTTTTGGTCATCCAATTTTAAAAAATTTAAG
* *
10584028 TATATTTGTGTTCTTGTTTTGGTCATCCCATTTTAAAAAATTTAA
1 TATATTTGTATTCTTGTTTTGGTCATCCAATTTTAAAAAATTTAA
10584073 TTTAGGTACT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (46 bp):
TATATTTGTATTCTTGTTTTGGTCATCCAATTTTAAAAAATTTAAG
Found at i:10584424 original size:20 final size:19
Alignment explanation
Indices: 10584391--10584428 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
10584381 TTTTAATTTA
10584391 ATAATAATTAAAATATTTTT
1 ATAATAATTAAAAT-TTTTT
10584411 ATAACTAATT-AAATTTTT
1 ATAA-TAATTAAAATTTTT
10584429 ATTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAATAATTAAAATTTTTT
Found at i:10595725 original size:12 final size:12
Alignment explanation
Indices: 10595708--10595732 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10595698 GGGAAGAAAG
10595708 TTGATGGCCAGA
1 TTGATGGCCAGA
10595720 TTGATGGCCAGA
1 TTGATGGCCAGA
10595732 T
1 T
10595733 AATTCTTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (12 bp):
TTGATGGCCAGA
Found at i:10599983 original size:52 final size:51
Alignment explanation
Indices: 10599903--10600107 Score: 245
Period size: 52 Copynumber: 3.9 Consensus size: 51
10599893 ATGGAATAGA
10599903 TGTGATATGTG-TGCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAT
1 TGTGATATGTGCT--CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAT
* *
10599955 TATGATATGTGCATCCATATAAGACCATAGCTGGGCTATGGCATCGGTGCAT
1 TGTGATATGTGC-TCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAT
* *
10600007 TGTGATATGTACTCTCGTATAAGACCATGGCTGGGCTATGGCATCGGT--AT
1 TGTGATATGTGCTC-CGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAT
** * *
10600057 GATGTGATAATGTGCCTCCGTATAAGACCATATATAGGATATGGCATCGGT
1 --TGTGAT-ATGTG-CTCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
10600108 ATGATATGTG
Statistics
Matches: 134, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
50 2 0.01
51 2 0.01
52 94 0.70
53 32 0.24
54 4 0.03
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (51 bp):
TGTGATATGTGCTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAT
Found at i:10605802 original size:31 final size:31
Alignment explanation
Indices: 10605767--10605831 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
10605757 CGTGAAAGAA
10605767 AGTTTTACAGTTTGGTAGAAAGGGAAAGCTT
1 AGTTTTACAGTTTGGTAGAAAGGGAAAGCTT
*
10605798 AGTTTTACGGTTTGGTAGAAAGGGAAAGCTT
1 AGTTTTACAGTTTGGTAGAAAGGGAAAGCTT
10605829 AGT
1 AGT
10605832 CCATGATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (31 bp):
AGTTTTACAGTTTGGTAGAAAGGGAAAGCTT
Found at i:10607624 original size:52 final size:52
Alignment explanation
Indices: 10607546--10607751 Score: 191
Period size: 52 Copynumber: 3.9 Consensus size: 52
10607536 ACGAAGTAGA
* * *
10607546 TGTGATATGTGCACCCTTATAAGACCATAGCTGAGCTTTGGCATTGGTACAT
1 TGTGATATGTGCACCCGTATAAGACCATAGCTGAGCTATGGCATCGGTACAT
* * *
10607598 TGTGATATGTGCGCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAT
1 TGTGATATGTGCACCCGTATAAGACCATAGCTGAGCTATGGCATCGGTACAT
* *** * * * * * * *
10607650 TGTGATATATATTCCTGTATAAGACCATGGTTGGGCTATGGCTTCAGTATGA-
1 TGTGATATGTGCACCCGTATAAGACCATAGCTGAGCTATGGCATCGGTA-CAT
* * *
10607702 TGTGATAATGTGC-CTCCGTATAAGACCATATCTGGGATATGGCATCGGTA
1 TGTGAT-ATGTGCAC-CCGTATAAGACCATAGCTGAGCTATGGCATCGGTA
10607752 TGATATGTGA
Statistics
Matches: 124, Mismatches: 27, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
52 92 0.74
53 32 0.26
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (52 bp):
TGTGATATGTGCACCCGTATAAGACCATAGCTGAGCTATGGCATCGGTACAT
Found at i:10611741 original size:16 final size:16
Alignment explanation
Indices: 10611722--10611754 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
10611712 TTTTATATAA
10611722 TTCTATGTAAATATTT
1 TTCTATGTAAATATTT
*
10611738 TTCTATGTATATATTT
1 TTCTATGTAAATATTT
10611754 T
1 T
10611755 CCTCTAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TTCTATGTAAATATTT
Found at i:10612469 original size:13 final size:13
Alignment explanation
Indices: 10612451--10612484 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
10612441 TGCCATGTTA
10612451 ATTATTGTTGTAT
1 ATTATTGTTGTAT
*
10612464 ATTATTTTTGTAT
1 ATTATTGTTGTAT
10612477 -TTATTGTT
1 ATTATTGTT
10612485 CACCATCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (13 bp):
ATTATTGTTGTAT
Found at i:10614461 original size:40 final size:40
Alignment explanation
Indices: 10614417--10614498 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
10614407 TTTATAAAAA
10614417 AAAATAATGTCTTCATAAAGTGCTTTAAAAGGTGGAGTTT
1 AAAATAATGTCTTCATAAAGTGCTTTAAAAGGTGGAGTTT
10614457 AAAATAATGTCTTCATAAAGTGCTTTAAAAGGTGGAGTTT
1 AAAATAATGTCTTCATAAAGTGCTTTAAAAGGTGGAGTTT
10614497 AA
1 AA
10614499 CTTTGAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (40 bp):
AAAATAATGTCTTCATAAAGTGCTTTAAAAGGTGGAGTTT
Found at i:10622218 original size:15 final size:16
Alignment explanation
Indices: 10622198--10622227 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10622188 TCTCCTTGAA
10622198 TTTTGAAT-TTTTATT
1 TTTTGAATATTTTATT
10622213 TTTTGAATATTTTAT
1 TTTTGAATATTTTAT
10622228 GGTTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (16 bp):
TTTTGAATATTTTATT
Found at i:10623021 original size:26 final size:25
Alignment explanation
Indices: 10622978--10623033 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
10622968 TCATTATTTT
*
10622978 ATATTGTTTTTTTGTTTT-TTAATAAA
1 ATATTATTTTTTTGTTTTATT-A-AAA
10623004 ATATTATTTTTTAT-TTTTATTAAAA
1 ATATTATTTTTT-TGTTTTATTAAAA
10623029 ATATT
1 ATATT
10623034 TAAATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.30
26 16 0.59
27 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (25 bp):
ATATTATTTTTTTGTTTTATTAAAA
Found at i:10623574 original size:33 final size:32
Alignment explanation
Indices: 10623531--10623637 Score: 82
Period size: 33 Copynumber: 3.4 Consensus size: 32
10623521 GTTTTTTATA
*
10623531 ATTATTTTAAAAATAATTTGTTAGTAATTTAGG
1 ATTATGTTAAAAATAATTT-TTAGTAATTTAGG
* *
10623564 ATTATGTT-AAAAT--TTTTT-GT-GTTT-GTA
1 ATTATGTTAAAAATAATTTTTAGTAATTTAG-G
* *
10623591 ATTATATTAAAATTAATTTATTAGTAATTTAGG
1 ATTATGTTAAAAATAATTT-TTAGTAATTTAGG
* *
10623624 ATTAAGTTATAAAT
1 ATTATGTTAAAAAT
10623638 TGTTGTGTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
26 1 0.02
27 10 0.18
28 6 0.11
29 2 0.04
30 6 0.11
31 2 0.04
32 7 0.13
33 20 0.36
34 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.50
Consensus pattern (32 bp):
ATTATGTTAAAAATAATTTTTAGTAATTTAGG
Found at i:10623601 original size:60 final size:61
Alignment explanation
Indices: 10623515--10623648 Score: 182
Period size: 60 Copynumber: 2.2 Consensus size: 61
10623505 GAATGTAATT
* * * *
10623515 TTTTTTGTTTTTTATAATTATTTTAAAAATAATTTGTTAGTAATTTAGGATTATGTTA-AAA
1 TTTTTTG-TGTTTATAATTATATTAAAAATAATTTATTAGTAATTTAGGATTAAGTTATAAA
* *
10623576 TTTTTTGTGTTTGTAATTATATTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
1 TTTTTTGTGTTTATAATTATATTAAAAATAATTTATTAGTAATTTAGGATTAAGTTATAAA
*
10623637 -TTGTTGTGTTTA
1 TTTTTTGTGTTTA
10623649 GTTTAGTATT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
60 54 0.84
61 10 0.16
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (61 bp):
TTTTTTGTGTTTATAATTATATTAAAAATAATTTATTAGTAATTTAGGATTAAGTTATAAA
Found at i:10629093 original size:132 final size:132
Alignment explanation
Indices: 10628856--10629144 Score: 393
Period size: 132 Copynumber: 2.2 Consensus size: 132
10628846 TAAGTATCCA
10628856 TTTAAAAATTCTTTAAAACGAAGGCGAAATCTGATATTTGACAATTCGCGAAATAGTGCCCTAAC
1 TTTAAAAATTCTTTAAAACGAAGGCGAAATCTGATATTTGACAATTCGCGAAATAGTGCCCTAAC
* * * * *
10628921 GTGTTGGGTTGCAATTTCACGTTTGCTCAAAATAATCGAATGTCCTTTCAATATTTCATTCATGC
66 ATGTTGGGTTGCAATTTCACGTTCGCTCAAAATAATCGAATATCCCTTCAAAATTTCATTCATGC
10628986 CT
131 CT
** * *
10628988 TTTAAAAATTCTTTAAAACGAAGGCGATGTGC-GATATTT-AGCAATTCGCGGAATCGTGCCCTA
1 TTTAAAAATTCTTTAAAACGAAGGCGAAAT-CTGATATTTGA-CAATTCGCGAAATAGTGCCCTA
** * *
10629051 ACATGTTGGGTTGCAATTTCGTGTTCGCTTAAAATAATCGAATATCCCTTCAAAATTTCATTTAT
64 ACATGTTGGGTTGCAATTTCACGTTCGCTCAAAATAATCGAATATCCCTTCAAAATTTCATTCAT
*
10629116 GTCT
129 GCCT
* * *
10629120 TCTAAAAATTATTTAAAACAAAGGC
1 TTTAAAAATTCTTTAAAACGAAGGC
10629145 AATATTCGGC
Statistics
Matches: 138, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
131 1 0.01
132 136 0.99
133 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (132 bp):
TTTAAAAATTCTTTAAAACGAAGGCGAAATCTGATATTTGACAATTCGCGAAATAGTGCCCTAAC
ATGTTGGGTTGCAATTTCACGTTCGCTCAAAATAATCGAATATCCCTTCAAAATTTCATTCATGC
CT
Found at i:10638761 original size:53 final size:53
Alignment explanation
Indices: 10638681--10638788 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
10638671 CCTAAGTTGA
10638681 TTGATTATCGAAAACTGGTCCTTGAATTGGTCAAAGAGTTCAACGACATTACC
1 TTGATTATCGAAAACTGGTCCTTGAATTGGTCAAAGAGTTCAACGACATTACC
*
10638734 TTGATTATCGAAAACTGGTCCTTGAATTGGTCAAAGAGTTCGACGACATTACC
1 TTGATTATCGAAAACTGGTCCTTGAATTGGTCAAAGAGTTCAACGACATTACC
10638787 TT
1 TT
10638789 CCACTACCTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (53 bp):
TTGATTATCGAAAACTGGTCCTTGAATTGGTCAAAGAGTTCAACGACATTACC
Found at i:10641184 original size:44 final size:44
Alignment explanation
Indices: 10641123--10641525 Score: 574
Period size: 44 Copynumber: 9.2 Consensus size: 44
10641113 TGGCGAATCC
* * * *
10641123 AGCAAATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAATAT
1 AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGAT
*
10641167 AGCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGAT
1 AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * * *
10641211 AGCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGAT
1 AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * **
10641255 AGCAGATTTGGCGTCTCTATATTGGTAGAGAGCAGATCAAAGAT
1 AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGAT
10641299 AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGAT
1 AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * *
10641343 AGCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCAAAGAT
1 AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * * *
10641387 AGTAGATTTGGCGTCTCTGTATTGGCGAAGAGCAGATCAAATAT
1 AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGAT
*
10641431 AGCAGATTTGGCATATCTGTATTGGCGGAGAGCAGATCAAAGAT
1 AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * *
10641475 AGCAGATTTGACATCTCTG-ATGGGCGGAGAACAGATCAAAGAT
1 AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGAT
*
10641518 AACAGATT
1 AGCAGATT
10641526 GGTGTTCCCG
Statistics
Matches: 321, Mismatches: 38, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
43 29 0.09
44 292 0.91
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (44 bp):
AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGAT
Found at i:10644612 original size:132 final size:132
Alignment explanation
Indices: 10644375--10644665 Score: 399
Period size: 132 Copynumber: 2.2 Consensus size: 132
10644365 TAAGTATCCA
10644375 TTTAAAAATTCTTTAAAACGAAGGCAAAATCCGATATTTGACAATTCGCAGAATAGTGCCCTAAC
1 TTTAAAAATTCTTTAAAACGAAGGCAAAATCCGATATTTGACAATTCGCAGAATAGTGCCCTAAC
* * *
10644440 GTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATGTCCCTTCAAGA-TTTCATTCATG
66 GTGTTGGGTTGCAATTCCGCGTTCGCTCAAAATAATCGAATATCCCTTCAA-ATTTTCATTCATG
10644504 CCT
130 CCT
* ** * * *
10644507 TTTAAAAATTCTTTAAAACGAAGGCGATGTGCGATATTT-AGCAATTCGCGGAATCGTGCCCTAA
1 TTTAAAAATTCTTTAAAACGAAGGCAAAATCCGATATTTGA-CAATTCGCAGAATAGTGCCCTAA
* * *
10644571 CGTGTTGGGTTGCAATTCCGTGTTCGCTTAAAATAATCGAATATCCCTTCAAATTTTCATTTATG
65 CGTGTTGGGTTGCAATTCCGCGTTCGCTCAAAATAATCGAATATCCCTTCAAATTTTCATTCATG
*
10644636 TCT
130 CCT
* *
10644639 TCTAAAAATTATTTAAAA-GAAAGGCAA
1 TTTAAAAATTCTTTAAAACG-AAGGCAA
10644666 TATTCGGCGT
Statistics
Matches: 140, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
131 3 0.02
132 137 0.98
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (132 bp):
TTTAAAAATTCTTTAAAACGAAGGCAAAATCCGATATTTGACAATTCGCAGAATAGTGCCCTAAC
GTGTTGGGTTGCAATTCCGCGTTCGCTCAAAATAATCGAATATCCCTTCAAATTTTCATTCATGC
CT
Found at i:10645027 original size:130 final size:130
Alignment explanation
Indices: 10644789--10645027 Score: 318
Period size: 130 Copynumber: 1.8 Consensus size: 130
10644779 AAATACTTAA
* *
10644789 AAAACGAAGACAATGTTCAATGTTTGGCAATTTGAGAATCGTGCCCTACCATGCTGGGTCGCGCT
1 AAAACGAAGACAATATTCAATGTTTGGCAATTTGAGAATCGAGCCCTACCATGCTGGGTCGCGCT
* * *
10644854 TTTTCATTGGTCCGAAACAATTAAAGATCCCTTCAGAATTTCACTCACATTTTCTAAAATCTTTC
66 TTTTCATTGGTCCAAAACAATCAAAGATCCCTTCAGAAGTTCACTCACATTTTCTAAAATCTTTC
* * * * * *
10644919 AAAATGAAGACGATATTCAATGTTTGGCGATTTGAGAATCGAGCCCTATCGTGCTGGGTTGCGCT
1 AAAACGAAGACAATATTCAATGTTTGGCAATTTGAGAATCGAGCCCTACCATGCTGGGTCGCGCT
* * * * *
10644984 TTTTCATTTGTCCAAAATAATCGAATATCTCCTT-GGAAGTTCAC
66 TTTTCATTGGTCCAAAACAATCAAAGATC-CCTTCAGAAGTTCAC
10645028 ACGTATTTTA
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
130 88 0.96
131 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (130 bp):
AAAACGAAGACAATATTCAATGTTTGGCAATTTGAGAATCGAGCCCTACCATGCTGGGTCGCGCT
TTTTCATTGGTCCAAAACAATCAAAGATCCCTTCAGAAGTTCACTCACATTTTCTAAAATCTTTC
Found at i:10648129 original size:27 final size:27
Alignment explanation
Indices: 10648097--10648174 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
10648087 ACGTATGGGC
*
10648097 ACCATTTGCGCCTCTGGGATAGGCACA
1 ACCATTTGCGCCTCTGAGATAGGCACA
10648124 ACCATTTGCGCCTCTGAGATAGGCACA
1 ACCATTTGCGCCTCTGAGATAGGCACA
* *
10648151 ACCATTTGCGCCTCAGAGAAAGGC
1 ACCATTTGCGCCTCTGAGATAGGC
10648175 TCGATTAGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (27 bp):
ACCATTTGCGCCTCTGAGATAGGCACA
Found at i:10657790 original size:15 final size:14
Alignment explanation
Indices: 10657771--10657805 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
10657761 TCAAAAATAG
*
10657771 AAAATTCAAAGAAA
1 AAAATTAAAAGAAA
10657785 ATAAATTAAAAGAAA
1 A-AAATTAAAAGAAA
10657800 AAAATT
1 AAAATT
10657806 TATTTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (14 bp):
AAAATTAAAAGAAA
Found at i:10659772 original size:147 final size:148
Alignment explanation
Indices: 10659504--10659876 Score: 562
Period size: 147 Copynumber: 2.6 Consensus size: 148
10659494 ACTTTTAGAG
* *
10659504 TTTGATTTTTATGCATCTAATTTTATCACTAGCTATAAATTTACATCAGCTGGTCAAACACCAAC
1 TTTGATTTTGATGCATCTAATTTTATCACTAGCTATAAATTTACATCAACTGGTCAAACACCAAC
*
10659569 TATTTGCCTTGTAAAACAATCATAAGAAATCATCACACTTTCAACTATTATTAAACTTATCTCCC
66 TATTTACCTTGTAAAACAATCATAAGAAATCATCACACTTTCAACTATTATTAAACTTATCTCCC
10659634 TCCAACGTGGAGGCAGAA
131 TCCAACGTGGAGGCAGAA
10659652 TTTGATTTTGATGCATCTAATTTTATCACTAGCTATAAATTTACATCAACT-GTCAAACACC-AC
1 TTTGATTTTGATGCATCTAATTTTATCACTAGCTATAAATTTACATCAACTGGTCAAACACCAAC
10659715 TTATTTACCTTGTAAAACAATCATAAGAAATCATCACACTTTCAACTATTATTAAACTTATCTCC
66 -TATTTACCTTGTAAAACAATCATAAGAAATCATCACACTTTCAACTATTATTAAACTTATCTCC
*
10659780 CTCCAATGTGGAGGCAGAA
130 CTCCAACGTGGAGGCAGAA
* *
10659799 TTTGA-TTT--TG------A---TA-CACTAGCTATAAATTTACATCAGCTGGTCAAACACCACC
1 TTTGATTTTGATGCATCTAATTTTATCACTAGCTATAAATTTACATCAACTGGTCAAACACCAAC
*
10659851 TATTTACCTCGTAAAA-AATCATAAGA
66 TATTTACCTTGTAAAACAATCATAAGA
10659877 CCACCTATTT
Statistics
Matches: 215, Mismatches: 7, Indels: 20
0.89 0.03 0.08
Matches are distributed among these distances:
134 34 0.16
135 27 0.13
136 1 0.00
138 1 0.00
144 2 0.01
146 5 0.02
147 96 0.45
148 49 0.23
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (148 bp):
TTTGATTTTGATGCATCTAATTTTATCACTAGCTATAAATTTACATCAACTGGTCAAACACCAAC
TATTTACCTTGTAAAACAATCATAAGAAATCATCACACTTTCAACTATTATTAAACTTATCTCCC
TCCAACGTGGAGGCAGAA
Found at i:10659881 original size:31 final size:32
Alignment explanation
Indices: 10659845--10659908 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
10659835 CTGGTCAAAC
10659845 ACCACCTATTTACCTCGTAAAA-AATCATAAG
1 ACCACCTATTTACCTCGTAAAACAATCATAAG
*
10659876 ACCACCTATTTACCTCGTAAAACAATTATAAG
1 ACCACCTATTTACCTCGTAAAACAATCATAAG
10659908 A
1 A
10659909 AATCATCACA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (32 bp):
ACCACCTATTTACCTCGTAAAACAATCATAAG
Found at i:10661378 original size:62 final size:62
Alignment explanation
Indices: 10661288--10661422 Score: 171
Period size: 62 Copynumber: 2.2 Consensus size: 62
10661278 AGTGTGTGTT
* * * * *
10661288 CGGGCTGTATAACTCACTGTTTATGGTATAAGACCACACGACCAGAGACACGGGCGTGTGCC
1 CGGGCCGTGTAACTCACTATTTATGGTATAAAACCACACGACCAGAGACACGGGCGTGTACC
** * ** *
10661350 TTGGCCGTGTAACTCACTATTTATGGTATAAAACCATACGGTCAGGGACACGGGCGTGTACC
1 CGGGCCGTGTAACTCACTATTTATGGTATAAAACCACACGACCAGAGACACGGGCGTGTACC
10661412 CGGGCCGTGTA
1 CGGGCCGTGTA
10661423 CCCGGGCTGT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (62 bp):
CGGGCCGTGTAACTCACTATTTATGGTATAAAACCACACGACCAGAGACACGGGCGTGTACC
Found at i:10661422 original size:13 final size:13
Alignment explanation
Indices: 10661400--10661434 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
10661390 GTCAGGGACA
10661400 CGGG-CGTGTACC
1 CGGGCCGTGTACC
10661412 CGGGCCGTGTACC
1 CGGGCCGTGTACC
*
10661425 CGGGCTGTGT
1 CGGGCCGTGT
10661435 GATTCATACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.06, C:0.31, G:0.43, T:0.20
Consensus pattern (13 bp):
CGGGCCGTGTACC
Found at i:10663667 original size:26 final size:24
Alignment explanation
Indices: 10663636--10663684 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
10663626 AATAAAAAAT
*
10663636 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAAT-AAATATA
10663662 TTTAAAAACATAAAAATAAATAT
1 TTTAAAAACATAAAAATAAATAT
10663685 TAAGACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 12 0.55
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
TTTAAAAACATAAAAATAAATATA
Found at i:10663704 original size:21 final size:22
Alignment explanation
Indices: 10663671--10663713 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
10663661 ATTTAAAAAC
* *
10663671 ATAAAAATAAATATTAAGACAA
1 ATAAAAATAAATACTAAAACAA
10663693 ATAAAAAT-AATACTAAAACAA
1 ATAAAAATAAATACTAAAACAA
10663714 TTCTTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (22 bp):
ATAAAAATAAATACTAAAACAA
Found at i:10666221 original size:40 final size:40
Alignment explanation
Indices: 10666166--10666289 Score: 187
Period size: 40 Copynumber: 3.1 Consensus size: 40
10666156 AGTTTTGTAC
* * *
10666166 ATAGCCGAAGCTATCTCAAATCGCACACTTAGTGCCATAT
1 ATAGCCGAAGTTATCTCGAATCGCACACTAAGTGCCATAT
* *
10666206 ATAGCTGAAGTTATCTCGAATCGCATACTAAGTGCCATAT
1 ATAGCCGAAGTTATCTCGAATCGCACACTAAGTGCCATAT
10666246 ATAGCCGAA-TCTATCTCGAATCGCACACTAAGTGCCATAT
1 ATAGCCGAAGT-TATCTCGAATCGCACACTAAGTGCCATAT
10666286 ATAG
1 ATAG
10666290 TCGATTTGTC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 75 0.99
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (40 bp):
ATAGCCGAAGTTATCTCGAATCGCACACTAAGTGCCATAT
Found at i:10666305 original size:40 final size:39
Alignment explanation
Indices: 10666177--10666306 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
10666167 TAGCCGAAGC
* * *
10666177 TATCTCAAATCGCACACTTAGTGCCATATATAGCTGAAGT
1 TATCTCGAATCGCACACTAAGTGCCATATATAGC-GAATT
* *
10666217 TATCTCGAATCGCATACTAAGTGCCATATATAGCCGAATC
1 TATCTCGAATCGCACACTAAGTGCCATATATAG-CGAATT
10666257 TATCTCGAATCGCACACTAAGTGCCATATATAGTCG-ATT
1 TATCTCGAATCGCACACTAAGTGCCATATATAG-CGAATT
*
10666296 TGTCTTCGAAT
1 TATC-TCGAAT
10666307 ATAACTGTAG
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 5 0.06
40 73 0.92
41 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (39 bp):
TATCTCGAATCGCACACTAAGTGCCATATATAGCGAATT
Found at i:10669534 original size:21 final size:21
Alignment explanation
Indices: 10669469--10669535 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
10669459 GAGGACAAGG
*
10669469 TCGTGTGACTAAAACACA-GC
1 TCGTGTGGCTAAAACACACGC
* * * * *
10669489 CCGTGTGGCTAAGATATACGG
1 TCGTGTGGCTAAAACACACGC
10669510 TCGTGTGGCTAAAACACACGC
1 TCGTGTGGCTAAAACACACGC
10669531 TCGTG
1 TCGTG
10669536 CGCGATTGAA
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (21 bp):
TCGTGTGGCTAAAACACACGC
Found at i:10671277 original size:555 final size:557
Alignment explanation
Indices: 10670564--10671656 Score: 1879
Period size: 557 Copynumber: 2.0 Consensus size: 557
10670554 ACCCACCTCC
* * *
10670564 AAGTAGGTTGATTCATATACTAACTAGCTATGCTTACACCTAATATTCATAATCTTCGTGGTTTT
1 AAGTAGGTTGATTCATATACTAACTAGCCATGCTCACACCTAATATTCATAATCTTCCTGGTTTT
10670629 TTTGTGCAAATAATCTTAGTGGTTGATTTGTAAGAATAGAGATTATGAATTGCATCCCAAATTGC
66 TTTGTGCAAATAATCTTAGTGGTTGATTTGTAAGAATAGAGATTATGAATTGCATCCCAAATTGC
**
10670694 TCAGGCAATATCACATATCACCAAATTAGGT-A-ATATGTCTGAACTAACAACAAATAACAACTA
131 AAAGGCAATATCACATATCACCAAATTAGGTAATATATGTCTGAACTAACAACAAATAACAACTA
* * *
10670757 GGATGTCGATGAATTATCTTCATTATCTTATGCAATTCTCTCAAGATTTTTGGTTCTTTGACAAG
196 GGATGTCGATGAACTATCTTCATTATCATATGCAATTCTCTCAAGATTTTTGGTTCTTTAACAAG
** * * *
10670822 ACTCATTGATTACAAACTTAGCAAGAATTGACTAAGTCCCTTCAAGATATATAACTTTAATCTAC
261 ACTCATCAACTACAAACTTAGCAAGAACTGAATAAGTCCCTTCAAGATATATAACTTTAATCTAC
* *
10670887 AACTTTTTACGATAAGATATACC-TTTT-TTTTTACAAAGGAAAGTTTGTCTGATCCAATTAAAT
326 AACTTTTTACGATAAGATATACCATTTTATTTTTACAAAGGAAAGTTTGCCTCATCCAATTAAAT
* *
10670950 ATTGATTTGTTTATTTGTAAAGTTATAACGTCATCTAATAACACTATTGTCCTGCAATTGTTATT
391 ATTGATTTATTTATTTGTAAAGTTATAACGTCATCTAATAACACTATTGTCCTACAATTGTTATT
* *
10671015 TGCAATTTCAAAAAACGTTTTGTTTACATAACACGATCATCTACATCATTTGATATGCAGGCTCT
456 TGCAATTTCAAAAAACGTTTTGTTTACATAACACAATCATCTACATCACTTGATATGCAGGCTCT
10671080 GATACCATATTAGAAAATNCCCCCCCCCCCCCCGCGCT
521 GATACCATATTAGAAAAT-CCCCCCCCCCCCCCGCGCT
10671118 AAGTAGGTTGATTCATATACTAACTAGCCATGCTCACACCTAATATTCATAATCTTCCTGGGTTT
1 AAGTAGGTTGATTCATATACTAACTAGCCATGCTCACACCTAATATTCATAATCTTCCT-GGTTT
10671183 TTTTGTGCAAATAATCTTAGTGGTTGATTTGTAAGAATAGAGATTATGAATTGCATCCCAAATTG
65 TTTTGTGCAAATAATCTTAGTGGTTGATTTGTAAGAATAGAGATTATGAATTGCATCCCAAATTG
10671248 CAAAGGCAATATCACATATCACCAAATTAGGTAATATATGTCTGAACTAACAACAAATAACAACT
130 CAAAGGCAATATCACATATCACCAAATTAGGTAATATATGTCTGAACTAACAACAAATAACAACT
* *
10671313 AGGATGTTGATGAACTATCTTTATTATCATATGCAATTCTCTCAAGATTTTTGGTTCTTTAACAA
195 AGGATGTCGATGAACTATCTTCATTATCATATGCAATTCTCTCAAGATTTTTGGTTCTTTAACAA
*
10671378 GACTCATCAACTACAAACTTAGCAAGAACTGAATAAGTTCCTTCAAGATATATAACTTTAATCTA
260 GACTCATCAACTACAAACTTAGCAAGAACTGAATAAGTCCCTTCAAGATATATAACTTTAATCTA
10671443 CAACTTTTTACGATAAGATATACCTATTTTATTTTTACAAAGGAAAGTTTGCCTCATCCAATTAA
325 CAACTTTTTACGATAAGATATACC-ATTTTATTTTTACAAAGGAAAGTTTGCCTCATCCAATTAA
*
10671508 ATATTGATTTATTTATTTGTAAAGTTATAACGTCATCTAATAACACTATTGTTCTACAATTGTTA
389 ATATTGATTTATTTATTTGTAAAGTTATAACGTCATCTAATAACACTATTGTCCTACAATTGTTA
* * * * *
10671573 TTTGTAATTTTAAAAAATGTTTTGTTTACATGACACAATCATCTACATCACTTGATATGTAGGCT
454 TTTGCAATTTCAAAAAACGTTTTGTTTACATAACACAATCATCTACATCACTTGATATGCAGGCT
10671638 CTGATACCATATTAGAAAA
519 CTGATACCATATTAGAAAA
10671657 CTTTATTTAA
Statistics
Matches: 505, Mismatches: 28, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
554 56 0.11
555 100 0.20
556 1 0.00
557 173 0.34
559 4 0.01
560 171 0.34
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (557 bp):
AAGTAGGTTGATTCATATACTAACTAGCCATGCTCACACCTAATATTCATAATCTTCCTGGTTTT
TTTGTGCAAATAATCTTAGTGGTTGATTTGTAAGAATAGAGATTATGAATTGCATCCCAAATTGC
AAAGGCAATATCACATATCACCAAATTAGGTAATATATGTCTGAACTAACAACAAATAACAACTA
GGATGTCGATGAACTATCTTCATTATCATATGCAATTCTCTCAAGATTTTTGGTTCTTTAACAAG
ACTCATCAACTACAAACTTAGCAAGAACTGAATAAGTCCCTTCAAGATATATAACTTTAATCTAC
AACTTTTTACGATAAGATATACCATTTTATTTTTACAAAGGAAAGTTTGCCTCATCCAATTAAAT
ATTGATTTATTTATTTGTAAAGTTATAACGTCATCTAATAACACTATTGTCCTACAATTGTTATT
TGCAATTTCAAAAAACGTTTTGTTTACATAACACAATCATCTACATCACTTGATATGCAGGCTCT
GATACCATATTAGAAAATCCCCCCCCCCCCCCGCGCT
Found at i:10671837 original size:14 final size:14
Alignment explanation
Indices: 10671805--10671847 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
10671795 ATAGTTGTGG
10671805 ATAACTAATTACAA
1 ATAACTAATTACAA
*
10671819 ATAAC-AATTATAA
1 ATAACTAATTACAA
10671832 AGTAACTAATTA-AA
1 A-TAACTAATTACAA
10671846 AT
1 AT
10671848 TGATAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 9 0.35
14 12 0.46
15 5 0.19
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (14 bp):
ATAACTAATTACAA
Found at i:10680702 original size:33 final size:32
Alignment explanation
Indices: 10680663--10680726 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
10680653 TAGCAAAATT
* *
10680663 AACAACAGAATAATAATTATACAATATCCAAAC
1 AACAACAAAATAATAATAATACAATA-CCAAAC
* *
10680696 AACAACAAAATAGTAATAATATAATACCAAA
1 AACAACAAAATAATAATAATACAATACCAAA
10680727 ATGATAGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.61, C:0.16, G:0.03, T:0.20
Consensus pattern (32 bp):
AACAACAAAATAATAATAATACAATACCAAAC
Found at i:10684162 original size:51 final size:51
Alignment explanation
Indices: 10684082--10684184 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
10684072 ACAAATCAGA
*
10684082 ATGAATATACTCCAATATTCTCTTTGTGTTATGGATTTCTCTGGTGAATCT
1 ATGAATATACTCCAATATTCTCTTCGTGTTATGGATTTCTCTGGTGAATCT
10684133 ATGAATATACTCCAATATTCTCTTCGTGTTATGGATTTCTCTGGTGAATCT
1 ATGAATATACTCCAATATTCTCTTCGTGTTATGGATTTCTCTGGTGAATCT
10684184 A
1 A
10684185 ACTCTCTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.44
Consensus pattern (51 bp):
ATGAATATACTCCAATATTCTCTTCGTGTTATGGATTTCTCTGGTGAATCT
Found at i:10691838 original size:16 final size:17
Alignment explanation
Indices: 10691802--10691838 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
10691792 TTGTATTTAA
10691802 ATAA-TAATATAAAATC
1 ATAATTAATATAAAATC
10691818 A-AATTAATATAAAAT-
1 ATAATTAATATAAAATC
10691833 ATAATT
1 ATAATT
10691839 GTTGAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATTAATATAAAATC
Found at i:10703084 original size:18 final size:18
Alignment explanation
Indices: 10703053--10703113 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
10703043 AAAAATTATT
*
10703053 AAAATTATTAAAAAATAGAA
1 AAAATTA-T-AAAAATACAA
*
10703073 AAAATTATAAAATTACAA
1 AAAATTATAAAAATACAA
*
10703091 AACAA-TAT-AAAATATAA
1 AA-AATTATAAAAATACAA
10703108 AAAATT
1 AAAATT
10703114 TCTAATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.06
17 10 0.29
18 13 0.37
19 3 0.09
20 7 0.20
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAATTATAAAAATACAA
Found at i:10703097 original size:28 final size:29
Alignment explanation
Indices: 10703042--10703102 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
10703032 AAAAATTACA
*
10703042 AAAAAATTATTAAAATTATTAAAAAATAG
1 AAAAAATTATTAAAATTATCAAAAAATAG
*
10703071 AAAAAATTA-TAAAATTA-CAAAACAATAT
1 AAAAAATTATTAAAATTATCAAAA-AATAG
10703099 AAAA
1 AAAA
10703103 TATAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 4 0.14
28 16 0.55
29 9 0.31
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (29 bp):
AAAAAATTATTAAAATTATCAAAAAATAG
Found at i:10703458 original size:19 final size:19
Alignment explanation
Indices: 10703436--10703474 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
10703426 ATATTTAGCA
*
10703436 TTTTTATACTTTTATAATT
1 TTTTTATAATTTTATAATT
*
10703455 TTTTTGTAATTTTATAATT
1 TTTTTATAATTTTATAATT
10703474 T
1 T
10703475 ATCCATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTATAATTTTATAATT
Found at i:10703580 original size:12 final size:11
Alignment explanation
Indices: 10703553--10703582 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
10703543 TTTTTTTTGT
10703553 AATTTTTAAAG
1 AATTTTTAAAG
10703564 AATTTTTAAAG
1 AATTTTTAAAG
10703575 ATATTTTT
1 A-ATTTTT
10703583 GAATGATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (11 bp):
AATTTTTAAAG
Found at i:10703760 original size:27 final size:27
Alignment explanation
Indices: 10703722--10703783 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
10703712 GGATTGGAAT
*
10703722 GGGTAAAAGAACTTTAAGGACTAAAGC
1 GGGTAAAAGAACTTTAAGGACCAAAGC
*
10703749 GGGTAAAAGAACTTTAAGGACCAAAGT
1 GGGTAAAAGAACTTTAAGGACCAAAGC
*
10703776 GGGAAAAA
1 GGGTAAAA
10703784 CAGTATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.47, C:0.10, G:0.27, T:0.16
Consensus pattern (27 bp):
GGGTAAAAGAACTTTAAGGACCAAAGC
Found at i:10714404 original size:13 final size:13
Alignment explanation
Indices: 10714383--10714440 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
10714373 AAATTTTTCC
10714383 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
10714396 AAAGTACTTCTCA
1 AAAGCACTTCTCA
* *
10714409 AAAGCACTTTTCC
1 AAAGCACTTCTCA
* *
10714422 ACAGCACTTTTCA
1 AAAGCACTTCTCA
10714435 AAAGCA
1 AAAGCA
10714441 ATGAAGAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.38, C:0.28, G:0.09, T:0.26
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:10726037 original size:43 final size:42
Alignment explanation
Indices: 10725959--10726040 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 42
10725949 TATGGGACAT
* * *
10725959 TGGCATCGTATATGATTTCGTGTAAGACCCTGTCTGGGATAG
1 TGGCATCGTATATGATTACATATAAGACCCTGTCTGGGATAG
*
10726001 TGGCATCGATATTTGATTACATATAAGACCAC-GTCTGGGA
1 TGGCATCG-TATATGATTACATATAAGACC-CTGTCTGGGA
10726041 CGTTGGAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 8 0.24
43 25 0.74
44 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (42 bp):
TGGCATCGTATATGATTACATATAAGACCCTGTCTGGGATAG
Found at i:10735388 original size:13 final size:13
Alignment explanation
Indices: 10735370--10735394 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10735360 GGTTTGTTTA
10735370 TTAAACTAATTAT
1 TTAAACTAATTAT
10735383 TTAAACTAATTA
1 TTAAACTAATTA
10735395 ACTAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:10738449 original size:44 final size:45
Alignment explanation
Indices: 10738383--10738475 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 45
10738373 GATGTTGAAG
10738383 AGGCCGAAGTTAGTCACGTGTGCATTCGACATGCACATAAATAGT
1 AGGCCGAAGTTAGTCACGTGTGCATTCGACATGCACATAAATAGT
*
10738428 AGGCC-AAGTTAGTCACTTGTGCATTCGACATGCACATAAATAGT
1 AGGCCGAAGTTAGTCACGTGTGCATTCGACATGCACATAAATAGT
10738472 AGGC
1 AGGC
10738476 GTCGTGGGTG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 42 0.89
45 5 0.11
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (45 bp):
AGGCCGAAGTTAGTCACGTGTGCATTCGACATGCACATAAATAGT
Found at i:10740975 original size:31 final size:31
Alignment explanation
Indices: 10740934--10740997 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
10740924 CCTTTTCATA
*
10740934 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
10740965 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
10740996 TT
1 TT
10740998 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:10741242 original size:24 final size:24
Alignment explanation
Indices: 10741191--10741309 Score: 181
Period size: 23 Copynumber: 5.0 Consensus size: 24
10741181 GCTTTATCAT
*
10741191 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
10741216 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
10741240 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
10741263 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
10741286 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
10741310 CACTTCCTCC
Statistics
Matches: 88, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
23 46 0.52
24 30 0.34
25 12 0.14
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:10741266 original size:47 final size:46
Alignment explanation
Indices: 10741190--10741307 Score: 175
Period size: 47 Copynumber: 2.5 Consensus size: 46
10741180 TGCTTTATCA
*
10741190 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTT
1 TATAACTGG-GGCATAAGCC-C-TTTAATAACTGGGGCAAAAGCCCTTT
*
10741238 TAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTT
1 T-ATAACTGGGGCATAAGCCCTTTAATAACTGGGGCAAAAGCCCTTT
10741285 TATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
10741308 TACACTTCCT
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
46 22 0.33
47 26 0.39
48 6 0.09
49 12 0.18
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (46 bp):
TATAACTGGGGCATAAGCCCTTTAATAACTGGGGCAAAAGCCCTTT
Found at i:10741383 original size:20 final size:20
Alignment explanation
Indices: 10741358--10741424 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
10741348 TTATGAATAC
10741358 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
10741378 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
10741398 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
10741418 ACCATGT
1 ATCATGT
10741425 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:10741389 original size:11 final size:11
Alignment explanation
Indices: 10741358--10741413 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
10741348 TTATGAATAC
10741358 ATCATGTGCAT
1 ATCATGTGCAT
*
10741369 ATCA--TACAT
1 ATCATGTGCAT
10741378 ATCATGTGCAT
1 ATCATGTGCAT
*
10741389 ATCA--TACAT
1 ATCATGTGCAT
*
10741398 GTCATGTGCAT
1 ATCATGTGCAT
10741409 ATCAT
1 ATCAT
10741414 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:10741493 original size:25 final size:25
Alignment explanation
Indices: 10741461--10741508 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
10741451 ATACATAAAC
* * *
10741461 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
10741486 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
10741509 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:10749649 original size:24 final size:24
Alignment explanation
Indices: 10749597--10749762 Score: 239
Period size: 24 Copynumber: 7.0 Consensus size: 24
10749587 GCTTTATCAT
*
10749597 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
10749622 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
10749646 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
10749669 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
10749693 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
10749717 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
10749740 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
10749763 TCACTTCCTC
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
23 43 0.33
24 74 0.57
25 12 0.09
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:10749673 original size:47 final size:48
Alignment explanation
Indices: 10749596--10749762 Score: 241
Period size: 47 Copynumber: 3.5 Consensus size: 48
10749586 TGCTTTATCA
* *
10749596 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTT
*
10749645 TATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCGTAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
* *
10749692 GATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
*
10749739 AATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTT
10749763 TCACTTCCTC
Statistics
Matches: 109, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
47 70 0.64
48 26 0.24
49 13 0.12
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (48 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
Found at i:10749697 original size:71 final size:71
Alignment explanation
Indices: 10749597--10749762 Score: 262
Period size: 71 Copynumber: 2.3 Consensus size: 71
10749587 GCTTTATCAT
* *
10749597 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAA
10749661 GCCCTTTA
64 GCCCTTTA
* * *
10749669 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
10749734 CCTTTA
66 CCTTTA
10749740 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
10749763 TCACTTCCTC
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
71 76 0.86
72 12 0.14
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (71 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
CCTTTA
Found at i:10749837 original size:20 final size:20
Alignment explanation
Indices: 10749812--10749878 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
10749802 TTATGATTAC
10749812 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
10749832 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
10749852 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
10749872 ACCATGT
1 ATCATGT
10749879 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:10749843 original size:11 final size:11
Alignment explanation
Indices: 10749812--10749867 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
10749802 TTATGATTAC
10749812 ATCATGTGCAT
1 ATCATGTGCAT
*
10749823 ATCA--TACAT
1 ATCATGTGCAT
10749832 ATCATGTGCAT
1 ATCATGTGCAT
*
10749843 ATCA--TACAT
1 ATCATGTGCAT
*
10749852 GTCATGTGCAT
1 ATCATGTGCAT
10749863 ATCAT
1 ATCAT
10749868 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:10760906 original size:34 final size:34
Alignment explanation
Indices: 10760867--10760935 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
10760857 ATTGTCCAAA
10760867 TCATTCAGTTTTCCAAAAAGTTATTTCCCCAATT
1 TCATTCAGTTTTCCAAAAAGTTATTTCCCCAATT
10760901 TCATTCAGTTTTCCAAAAAGTTATTTCCCCAATT
1 TCATTCAGTTTTCCAAAAAGTTATTTCCCCAATT
10760935 T
1 T
10760936 ACTTTTTGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (34 bp):
TCATTCAGTTTTCCAAAAAGTTATTTCCCCAATT
Found at i:10766651 original size:17 final size:17
Alignment explanation
Indices: 10766602--10766693 Score: 66
Period size: 17 Copynumber: 5.5 Consensus size: 17
10766592 AGTAAATGAA
*
10766602 AGAAAAAGGAATGAAAT
1 AGAAAAAGGAAAGAAAT
*
10766619 A-AAAGAAAGAAAGAAAT
1 AGAAA-AAGGAAAGAAAT
* * *
10766636 AGAATAAGGAACGAAAC
1 AGAAAAAGGAAAGAAAT
* * *
10766653 AG-AGAAGGAAGGAAAG
1 AGAAAAAGGAAAGAAAT
10766669 A-AAGAAAGGAAAGAAA-
1 AGAA-AAAGGAAAGAAAT
10766685 AGAAAAAGG
1 AGAAAAAGG
10766694 GAAAATTAAG
Statistics
Matches: 59, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
16 22 0.37
17 35 0.59
18 2 0.03
ACGTcount: A:0.66, C:0.02, G:0.27, T:0.04
Consensus pattern (17 bp):
AGAAAAAGGAAAGAAAT
Found at i:10767399 original size:26 final size:24
Alignment explanation
Indices: 10767369--10767418 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
10767359 AAATAAAAAA
*
10767369 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
10767395 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
10767419 TAAAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:10767438 original size:21 final size:20
Alignment explanation
Indices: 10767358--10767447 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 20
10767348 CTTATTTCAT
10767358 TAAATAAAAAAAT-TTAAAAA
1 TAAATAAAAAAATATT-AAAA
10767378 TATAATAAATCAAATATATTTAAAA
1 TA-AATAAA--AAA-ATA-TTAAAA
*
10767403 -ACATAAAAACAAATATTAAAA
1 TAAAT-AAAA-AAATATTAAAA
*
10767424 TAAATAAAAATAATACTAAAA
1 TAAATAAAAA-AATATTAAAA
10767445 TAA
1 TAA
10767448 TTCTTAAAAC
Statistics
Matches: 57, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
20 3 0.05
21 28 0.49
22 7 0.12
23 7 0.12
24 6 0.11
25 4 0.07
26 2 0.04
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAATAAAAAAATATTAAAA
Found at i:10768296 original size:6 final size:6
Alignment explanation
Indices: 10768282--10768311 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
10768272 TATGTACCGC
*
10768282 TACTGT TACTAT TACTGT TACTGT TACTGT
1 TACTGT TACTGT TACTGT TACTGT TACTGT
10768312 GTATCCTGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (6 bp):
TACTGT
Found at i:10768440 original size:18 final size:18
Alignment explanation
Indices: 10768417--10768464 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
10768407 CAAAAAAAGG
10768417 TACTGAAAAATTGACTAC
1 TACTGAAAAATTGACTAC
* * **
10768435 TACTGAATATTTGACTGT
1 TACTGAAAAATTGACTAC
10768453 TACTGAATAAAT
1 TACTGAA-AAAT
10768465 GATTGACTGA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (18 bp):
TACTGAAAAATTGACTAC
Found at i:10768499 original size:24 final size:22
Alignment explanation
Indices: 10768453--10768499 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
10768443 ATTTGACTGT
* *
10768453 TACTGAATAAATGATTGACTGA
1 TACTGAATAAATGATTAAATGA
10768475 TACTGAATAATAATGATTAAATGA
1 TACTGAAT-A-AATGATTAAATGA
10768499 T
1 T
10768500 TGTTATTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 1 0.05
24 12 0.57
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (22 bp):
TACTGAATAAATGATTAAATGA
Found at i:10776523 original size:47 final size:48
Alignment explanation
Indices: 10776346--10776521 Score: 207
Period size: 49 Copynumber: 3.6 Consensus size: 48
10776336 GGATAAGTTA
* *
10776346 CCGATGCCATGTCCCAAACATGGTCTTACACTAGTTATCATCATCGAGG
1 CCGATG-CATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGG
* * * *
10776395 CCGATGCCATGTCCCTGACATGGTCTTGCACTAGCTGTCTTAT-ATACG-TG
1 CCGATG-CATGTCCCAGACATGGTCTTACACTAGCTATC--ATCAT-CGAGG
*
10776445 CCGATGCATGTCCCAGACAT-GTCTTACACTGGCTATCATCATCGAGG
1 CCGATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGG
*
10776492 CCAATGCATGTCCCAGACAT-GTCTTACACT
1 CCGATGCATGTCCCAGACATGGTCTTACACT
10776522 GGTACACAAT
Statistics
Matches: 110, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
46 4 0.04
47 32 0.29
48 14 0.13
49 47 0.43
50 9 0.08
51 4 0.04
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (48 bp):
CCGATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGG
Found at i:10779181 original size:47 final size:48
Alignment explanation
Indices: 10779004--10779179 Score: 207
Period size: 49 Copynumber: 3.6 Consensus size: 48
10778994 GGATAAGTTA
* *
10779004 CCGATGCCATGTCCCAAACATGGTCTTACACTAGTTATCATCATCGAGG
1 CCGATG-CATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGG
* * * *
10779053 CCGATGCCATGTCCCTGACATGGTCTTGCACTAGCTGTCTTAT-ATACG-TG
1 CCGATG-CATGTCCCAGACATGGTCTTACACTAGCTATC--ATCAT-CGAGG
*
10779103 CCGATGCATGTCCCAGACAT-GTCTTACACTGGCTATCATCATCGAGG
1 CCGATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGG
*
10779150 CCAATGCATGTCCCAGACAT-GTCTTACACT
1 CCGATGCATGTCCCAGACATGGTCTTACACT
10779180 GGTACACAAT
Statistics
Matches: 110, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
46 4 0.04
47 32 0.29
48 14 0.13
49 47 0.43
50 9 0.08
51 4 0.04
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (48 bp):
CCGATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGG
Found at i:10790694 original size:35 final size:35
Alignment explanation
Indices: 10790655--10790816 Score: 200
Period size: 35 Copynumber: 4.6 Consensus size: 35
10790645 CATGGAAAAG
* * *
10790655 TGTGAAACTTAGGTATGGTATCATCCATGCCGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* *
10790690 TGTGAAACGTAGATATGGTATTAACCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* *
10790725 TGTGAAAAGTAGGTATGGTATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
** * *
10790760 TAAGAAACATAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTAT-CCATACCGAGT
*
10790795 TGTGAAATGTAGGTATGGTATT
1 TGTGAAACGTAGGTATGGTATT
10790817 TCAATGAGGA
Statistics
Matches: 106, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
34 1 0.01
35 105 0.99
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
Found at i:10790950 original size:31 final size:30
Alignment explanation
Indices: 10790912--10791003 Score: 139
Period size: 31 Copynumber: 3.0 Consensus size: 30
10790902 ATAAGTAATT
10790912 TGATCAGTGAGAAGTGGTAGCTCCGGCTACC
1 TGATCAGTGA-AAGTGGTAGCTCCGGCTACC
*
10790943 TGATCAGTGAAAAGTGGTAGGTCCGGCTACC
1 TGATCAGTG-AAAGTGGTAGCTCCGGCTACC
*
10790974 TGATCAGTGAATAGTGGTAGCTTCGGCTAC
1 TGATCAGTGAA-AGTGGTAGCTCCGGCTAC
10791004 AAGTGACAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
30 2 0.04
31 53 0.95
32 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.25
Consensus pattern (30 bp):
TGATCAGTGAAAGTGGTAGCTCCGGCTACC
Found at i:10795333 original size:5 final size:5
Alignment explanation
Indices: 10795323--10795350 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
10795313 ATCTTGTAAA
10795323 GATTT GATTT GATTT GATTT GATTT GAT
1 GATTT GATTT GATTT GATTT GATTT GAT
10795351 GTAATCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (5 bp):
GATTT
Found at i:10802700 original size:13 final size:13
Alignment explanation
Indices: 10802684--10802716 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
10802674 TTTAATTAAA
*
10802684 TTAGTTAATTAGT
1 TTAGATAATTAGT
10802697 TTAGATAATTAGT
1 TTAGATAATTAGT
10802710 TTA-ATAA
1 TTAGATAA
10802717 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:10804091 original size:86 final size:86
Alignment explanation
Indices: 10803883--10804126 Score: 289
Period size: 85 Copynumber: 2.8 Consensus size: 86
10803873 AACCAAATGG
* * * *
10803883 TGGCGCCATTTAGAATGGCTACACCAAATAAAATATTATTTTTCAAAAATTTTAAATAAAA-AAA
1 TGGCGCCATTTAGAATGGCTCCACCAAAAAAAATA-TATATTT--AAAATATT--ATAAAACAAA
10803947 TAAATTTAAAAAACATTTAAATGAACTAA
61 T-AA--TAAAAAACATTTAAATGAACTAA
* *
10803976 TGGCGCCATTTAGAATGGCTCTACCAAAAAAAATATACATTTAAAATATTATAAAACAAATAATA
1 TGGCGCCATTTAGAATGGCTCCACCAAAAAAAATATATATTTAAAATATTATAAAACAAATAATA
* *
10804041 AAAAA-AGTTTAAATTAACTGGA
66 AAAAACA-TTTAAATGAACT-AA
*
10804063 -GGCGCCATTTAGAATGGCTCCA-CAAAAAATATATATATTTAAAATATTATAAAACAAATAATA
1 TGGCGCCATTTAGAATGGCTCCACCAAAAAAAATATATATTTAAAATATTATAAAACAAATAATA
10804126 A
66 A
10804127 TAATAAAAAA
Statistics
Matches: 137, Mismatches: 11, Indels: 14
0.85 0.07 0.09
Matches are distributed among these distances:
85 41 0.30
86 39 0.28
87 1 0.01
88 8 0.06
89 4 0.03
90 7 0.05
92 5 0.04
93 32 0.23
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.29
Consensus pattern (86 bp):
TGGCGCCATTTAGAATGGCTCCACCAAAAAAAATATATATTTAAAATATTATAAAACAAATAATA
AAAAACATTTAAATGAACTAA
Found at i:10804112 original size:85 final size:85
Alignment explanation
Indices: 10803883--10804126 Score: 280
Period size: 86 Copynumber: 2.8 Consensus size: 85
10803873 AACCAAATGG
* * *
10803883 TGGCGCCATTTAGAATGGCTACACCAAATAAAATATTATTTTTCAAAAATTTTAAATAAAA-AAA
1 TGGCGCCATTTAGAATGGCTCCACCAAA-AAAATA-TATATTT--AAAATATT--ATAAAACAAA
10803947 TAAATTTAAAAAACATTTAAATGAACTAA
60 T-AA--TAAAAAACATTTAAATGAACTAA
* *
10803976 TGGCGCCATTTAGAATGGCTCTACCAAAAAAAATATACATTTAAAATATTATAAAACAAATAATA
1 TGGCGCCATTTAGAATGGCTCCACC-AAAAAAATATATATTTAAAATATTATAAAACAAATAATA
* *
10804041 AAAAA-AGTTTAAATTAACTGGA
65 AAAAACA-TTTAAATGAACT-AA
10804063 -GGCGCCATTTAGAATGGCTCCA-CAAAAAATATATATATTTAAAATATTATAAAACAAATAATA
1 TGGCGCCATTTAGAATGGCTCCACCAAAAAA-ATATATATTTAAAATATTATAAAACAAATAATA
10804126 A
65 A
10804127 TAATAAAAAA
Statistics
Matches: 137, Mismatches: 9, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
84 6 0.04
85 35 0.26
86 39 0.28
87 1 0.01
88 8 0.06
89 4 0.03
90 7 0.05
92 5 0.04
93 29 0.21
94 3 0.02
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.29
Consensus pattern (85 bp):
TGGCGCCATTTAGAATGGCTCCACCAAAAAAATATATATTTAAAATATTATAAAACAAATAATAA
AAAACATTTAAATGAACTAA
Found at i:10805531 original size:14 final size:13
Alignment explanation
Indices: 10805508--10805539 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
10805498 GGGATATCAA
10805508 AACAATAATTAAG
1 AACAATAATTAAG
10805521 AACACATAATTAAG
1 AACA-ATAATTAAG
10805535 AACAA
1 AACAA
10805540 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:10807225 original size:13 final size:13
Alignment explanation
Indices: 10807209--10807241 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
10807199 TTTAATTAAA
*
10807209 TTAGTTAATTAGT
1 TTAGATAATTAGT
10807222 TTAGATAATTAGT
1 TTAGATAATTAGT
10807235 TTA-ATAA
1 TTAGATAA
10807242 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:10808616 original size:86 final size:86
Alignment explanation
Indices: 10808408--10808651 Score: 289
Period size: 85 Copynumber: 2.8 Consensus size: 86
10808398 AACCAAATGG
* * * *
10808408 TGGCGCCATTTAGAATGGCTACACCAAATAAAATATTATTTTTCAAAAATTTTAAATAAAA-AAA
1 TGGCGCCATTTAGAATGGCTCCACCAAAAAAAATA-TATATTT--AAAATATT--ATAAAACAAA
10808472 TAAATTTAAAAAACATTTAAATGAACTAA
61 T-AA--TAAAAAACATTTAAATGAACTAA
* *
10808501 TGGCGCCATTTAGAATGGCTCTACCAAAAAAAATATACATTTAAAATATTATAAAACAAATAATA
1 TGGCGCCATTTAGAATGGCTCCACCAAAAAAAATATATATTTAAAATATTATAAAACAAATAATA
* *
10808566 AAAAA-AGTTTAAATTAACTGGA
66 AAAAACA-TTTAAATGAACT-AA
*
10808588 -GGCGCCATTTAGAATGGCTCCA-CAAAAAATATATATATTTAAAATATTATAAAACAAATAATA
1 TGGCGCCATTTAGAATGGCTCCACCAAAAAAAATATATATTTAAAATATTATAAAACAAATAATA
10808651 A
66 A
10808652 TAATAAAAAA
Statistics
Matches: 137, Mismatches: 11, Indels: 14
0.85 0.07 0.09
Matches are distributed among these distances:
85 41 0.30
86 39 0.28
87 1 0.01
88 8 0.06
89 4 0.03
90 7 0.05
92 5 0.04
93 32 0.23
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.29
Consensus pattern (86 bp):
TGGCGCCATTTAGAATGGCTCCACCAAAAAAAATATATATTTAAAATATTATAAAACAAATAATA
AAAAACATTTAAATGAACTAA
Found at i:10808637 original size:85 final size:85
Alignment explanation
Indices: 10808408--10808651 Score: 280
Period size: 86 Copynumber: 2.8 Consensus size: 85
10808398 AACCAAATGG
* * *
10808408 TGGCGCCATTTAGAATGGCTACACCAAATAAAATATTATTTTTCAAAAATTTTAAATAAAA-AAA
1 TGGCGCCATTTAGAATGGCTCCACCAAA-AAAATA-TATATTT--AAAATATT--ATAAAACAAA
10808472 TAAATTTAAAAAACATTTAAATGAACTAA
60 T-AA--TAAAAAACATTTAAATGAACTAA
* *
10808501 TGGCGCCATTTAGAATGGCTCTACCAAAAAAAATATACATTTAAAATATTATAAAACAAATAATA
1 TGGCGCCATTTAGAATGGCTCCACC-AAAAAAATATATATTTAAAATATTATAAAACAAATAATA
* *
10808566 AAAAA-AGTTTAAATTAACTGGA
65 AAAAACA-TTTAAATGAACT-AA
10808588 -GGCGCCATTTAGAATGGCTCCA-CAAAAAATATATATATTTAAAATATTATAAAACAAATAATA
1 TGGCGCCATTTAGAATGGCTCCACCAAAAAA-ATATATATTTAAAATATTATAAAACAAATAATA
10808651 A
65 A
10808652 TAATAAAAAA
Statistics
Matches: 137, Mismatches: 9, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
84 6 0.04
85 35 0.26
86 39 0.28
87 1 0.01
88 8 0.06
89 4 0.03
90 7 0.05
92 5 0.04
93 29 0.21
94 3 0.02
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.29
Consensus pattern (85 bp):
TGGCGCCATTTAGAATGGCTCCACCAAAAAAATATATATTTAAAATATTATAAAACAAATAATAA
AAAACATTTAAATGAACTAA
Found at i:10810252 original size:43 final size:43
Alignment explanation
Indices: 10810204--10810290 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
10810194 ATATAAAGAA
* *
10810204 AACCCAAAACTTCTGAAGGGAAATTGAGGAGCGATCTTCAGTC
1 AACCCAAAACTTCTGAAAGGAAATTGAGGAGAGATCTTCAGTC
10810247 AACCCAAAACTTCTGAAAGGAAATTGAGGAGAGATCTTCAGTC
1 AACCCAAAACTTCTGAAAGGAAATTGAGGAGAGATCTTCAGTC
10810290 A
1 A
10810291 TGATGATGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.21
Consensus pattern (43 bp):
AACCCAAAACTTCTGAAAGGAAATTGAGGAGAGATCTTCAGTC
Found at i:10810616 original size:74 final size:74
Alignment explanation
Indices: 10810493--10810637 Score: 202
Period size: 74 Copynumber: 2.0 Consensus size: 74
10810483 CGCCTGTGTA
* * * * *
10810493 CGATTACTTCAGGCCGTGTTTGAGGCTATCAAATTGACATGGCCGTGTGGTCTACCCGTGCGAAT
1 CGATTACTTCAGGCCATGTTTGAGGCTACCAAATTGACACGACCATGTGGTCTACCCGTGCGAAT
*
10810558 TGTGCTGTG
66 CGTGCTGTG
* *
10810567 CGATTACTTTAGGCCATGTTTGA-GCTTACCAAATTGACACGACCATGTGGTCTACCCGTGTGAA
1 CGATTACTTCAGGCCATGTTTGAGGC-TACCAAATTGACACGACCATGTGGTCTACCCGTGCGAA
10810631 TCGTGCT
65 TCGTGCT
10810638 TTGATTTTTC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 2 0.03
74 60 0.97
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (74 bp):
CGATTACTTCAGGCCATGTTTGAGGCTACCAAATTGACACGACCATGTGGTCTACCCGTGCGAAT
CGTGCTGTG
Found at i:10810742 original size:19 final size:19
Alignment explanation
Indices: 10810709--10810747 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
10810699 TGAGTTCGTA
*
10810709 TTTTGGCCCATTTTCTCTGT
1 TTTTGGCCCAGTTTCT-TGT
10810729 TTTTGGCCC-GTTTCTTGT
1 TTTTGGCCCAGTTTCTTGT
10810747 T
1 T
10810748 CCTTTCGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.03, C:0.23, G:0.18, T:0.56
Consensus pattern (19 bp):
TTTTGGCCCAGTTTCTTGT
Found at i:10811259 original size:12 final size:12
Alignment explanation
Indices: 10811242--10811272 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
10811232 CATTTATAGT
*
10811242 CAAATACATCGC
1 CAAATACATCAC
10811254 CAAATACATCAC
1 CAAATACATCAC
10811266 CAAATAC
1 CAAATAC
10811273 TACCTACTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.32, G:0.03, T:0.16
Consensus pattern (12 bp):
CAAATACATCAC
Found at i:10812158 original size:26 final size:26
Alignment explanation
Indices: 10812103--10812172 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
10812093 TTTCTCACTA
* * *
10812103 AGCTCACAGCTTTCACA-TCTTGCTG
1 AGCTTACAGCTTGCACATTCTTGCTC
* *
10812128 AGCTTGCAGCTTGCACATTTTTGCTC
1 AGCTTACAGCTTGCACATTCTTGCTC
*
10812154 AGCTTACAACTTGCACATT
1 AGCTTACAGCTTGCACATT
10812173 GGAAAGCTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 14 0.38
26 23 0.62
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (26 bp):
AGCTTACAGCTTGCACATTCTTGCTC
Found at i:10827555 original size:7 final size:7
Alignment explanation
Indices: 10827543--10827580 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
10827533 GGAGCTCACA
10827543 TGAAGGC
1 TGAAGGC
10827550 TGAAGGC
1 TGAAGGC
*
10827557 TGGAGGC
1 TGAAGGC
10827564 TGAAGGC
1 TGAAGGC
10827571 TGAAGG-
1 TGAAGGC
10827577 TGAA
1 TGAA
10827581 AGGGTTTGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 4 0.14
7 25 0.86
ACGTcount: A:0.29, C:0.11, G:0.45, T:0.16
Consensus pattern (7 bp):
TGAAGGC
Done.