Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 8 of 427
Found at i:2432260 original size:2 final size:2
Alignment explanation
Indices: 2432255--2432287 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2432245 AATATTGTAT
*
2432255 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2432288 GTTATGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2434351 original size:26 final size:26
Alignment explanation
Indices: 2434315--2434450 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
2434305 CATGATATTC
2434315 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
2434341 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
2434367 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
2434393 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
2434419 TTATCATGGAACATTTACCTAATCTA
1 TTATCATGAAACATTTACCTAACCCA
2434445 TTATCA
1 TTATCA
2434451 ATTTGTATCA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 105 1.00
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:2437072 original size:2 final size:2
Alignment explanation
Indices: 2437065--2437107 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2437055 ATAATACTTT
2437065 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2437106 TA
1 TA
2437108 GATGATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2438065 original size:2 final size:2
Alignment explanation
Indices: 2438058--2438099 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2438048 CAACAAGCTG
2438058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2438100 GATGATGTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2441665 original size:8 final size:8
Alignment explanation
Indices: 2441652--2441689 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
2441642 TTTTAGAAAA
2441652 ATTTTAAT
1 ATTTTAAT
2441660 ATTTTAAT
1 ATTTTAAT
*
2441668 TTTTTATAT
1 ATTTTA-AT
2441677 ATTTTAAT
1 ATTTTAAT
2441685 ATTTT
1 ATTTT
2441690 TTATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
ATTTTAAT
Found at i:2441669 original size:25 final size:25
Alignment explanation
Indices: 2441641--2441689 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2441631 CAAAATTATT
2441641 ATTTTAGAAAAATTTTAATATTTTA
1 ATTTTAGAAAAATTTTAATATTTTA
** * *
2441666 ATTTTTTATATATTTTAATATTTT
1 ATTTTAGAAAAATTTTAATATTTT
2441690 TTATATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
ATTTTAGAAAAATTTTAATATTTTA
Found at i:2441680 original size:17 final size:18
Alignment explanation
Indices: 2441653--2441698 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
2441643 TTTAGAAAAA
2441653 TTTTA-ATATTTTAAT-T
1 TTTTATATATTTTAATAT
2441669 TTTTATATATTTTAATAT
1 TTTTATATATTTTAATAT
2441687 TTTT-TATATTTT
1 TTTTATATATTTT
2441699 TAGAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.18
17 18 0.64
18 5 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTATATATTTTAATAT
Found at i:2441690 original size:9 final size:9
Alignment explanation
Indices: 2441653--2441700 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
2441643 TTTAGAAAAA
2441653 TTTTAATA-
1 TTTTAATAT
2441661 TTTTAAT-T
1 TTTTAATAT
2441669 TTTT-ATAT
1 TTTTAATAT
2441677 ATTTTAATAT
1 -TTTTAATAT
*
2441687 TTTTTATAT
1 TTTTAATAT
2441696 TTTTA
1 TTTTA
2441701 GAAATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
7 2 0.06
8 12 0.35
9 16 0.47
10 4 0.12
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTAATAT
Found at i:2441734 original size:19 final size:19
Alignment explanation
Indices: 2441710--2441761 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
2441700 AGAAATATAA
*
2441710 ATTTTGAATTTTTATAACT
1 ATTTTGAATTTTTAAAACT
* * *
2441729 ATTTTGAATTATAAAAATT
1 ATTTTGAATTTTTAAAACT
2441748 ATTTTGTAATTTTT
1 ATTTTG-AATTTTT
2441762 TTTGAGGGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAACT
Found at i:2444554 original size:17 final size:17
Alignment explanation
Indices: 2444532--2444566 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2444522 GATATGGATT
2444532 TTATTAAAAGTTTATAC
1 TTATTAAAAGTTTATAC
*
2444549 TTATTAAAAGTTTTTAC
1 TTATTAAAAGTTTATAC
2444566 T
1 T
2444567 CATCCTTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (17 bp):
TTATTAAAAGTTTATAC
Found at i:2452526 original size:66 final size:66
Alignment explanation
Indices: 2452441--2452565 Score: 214
Period size: 66 Copynumber: 1.9 Consensus size: 66
2452431 CATATATCAT
* *
2452441 TCATAGCACATCTAATTAGGAGCATTTGATTCATTTCGATCATAACATCCTAATTATTTTACACC
1 TCATAACACATCTAATTAGGAGCATTTGATTCATTTCGATCATAACATCCTAATCATTTTACACC
2452506 C
66 C
* *
2452507 TCATAACACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTT
1 TCATAACACATCTAATTAGGAGCATTTGATTCATTTCGATCATAACATCCTAATCATTT
2452566 GACATAAGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (66 bp):
TCATAACACATCTAATTAGGAGCATTTGATTCATTTCGATCATAACATCCTAATCATTTTACACC
C
Found at i:2452687 original size:43 final size:43
Alignment explanation
Indices: 2452640--2452790 Score: 155
Period size: 43 Copynumber: 3.5 Consensus size: 43
2452630 AGCATTAAAC
*
2452640 CCCTAAGCAGTAGGGTAACAGGATGAATTTACAGATCTCATCA
1 CCCTAAGCAGTAGGGAAACAGGATGAATTTACAGATCTCATCA
* * ** * *
2452683 CCCTAAGCAGTAGGGAAACA-GATCGAAGGTGA-AGGGC-CTTAAA
1 CCCTAAGCAGTAGGGAAACAGGAT-GAA-TTTACAGATCTCAT-CA
* *
2452726 CCCCTAAGCAGTAGGGTAACAGGATGAATTTACGGATCTCATCA
1 -CCCTAAGCAGTAGGGAAACAGGATGAATTTACAGATCTCATCA
*
2452770 CCCTAAGTAGTAGGGAAACAG
1 CCCTAAGCAGTAGGGAAACAG
2452791 ATCGAAGGTG
Statistics
Matches: 84, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
42 5 0.06
43 47 0.56
44 27 0.32
45 5 0.06
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGAAACAGGATGAATTTACAGATCTCATCA
Found at i:2452740 original size:44 final size:44
Alignment explanation
Indices: 2452683--2453051 Score: 290
Period size: 44 Copynumber: 8.5 Consensus size: 44
2452673 GATCTCATCA
2452683 CCCTAAGCAGTAGGGAAACAGATCGAAGGTGAAGGGCCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGGTGAAGGGCCTTAAAC
* * * * ** * *
2452727 CCCTAAGCAGTAGGGTAACAGGAT-GAA-TTTACGGATC-TCATC
1 CCCTAAGCAGTAGGGAAACA-GATCGAAGGTGAAGGGCCTTAAAC
*
2452769 ACCCTAAGTAGTAGGGAAACAGATCGAAGGTGAAGGGCCTTAAAC
1 -CCCTAAGCAGTAGGGAAACAGATCGAAGGTGAAGGGCCTTAAAC
* * * * *** *
2452814 CCCTAAGCAGTAGGGTAAC-GAGCTGAA-TTTACA-AATCTTAACC
1 CCCTAAGCAGTAGGGAAACAGATC-GAAGGTGA-AGGGCCTTAAAC
* *
2452857 CCCTAAGCAGTAGGGAAACAGATTGAAGGTGATGGGCCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGGTGAAGGGCCTTAAAC
* * * * ** *
2452901 CCCTAAGCAGTAGGGTAACAG-GCTGAA-TTTACA-GATCTTAACC
1 CCCTAAGCAGTAGGGAAACAGATC-GAAGGTGA-AGGGCCTTAAAC
* * ** *
2452944 CCCTAAACAGTAGGGAAACAAATCGAAGACGAAGGGCTTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGGTGAAGGGCCTTAAAC
* * *
2452988 CCCTAAGCGGTAGGGAAACAGATCAAAAGTGATA-GGCCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGGTGA-AGGGCCTTAAAC
*
2453032 CCCTAAGCAGTAGGGTAACA
1 CCCTAAGCAGTAGGGAAACA
2453052 AGCTAAAATT
Statistics
Matches: 243, Mismatches: 66, Indels: 32
0.71 0.19 0.09
Matches are distributed among these distances:
42 6 0.02
43 89 0.37
44 141 0.58
45 7 0.03
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (44 bp):
CCCTAAGCAGTAGGGAAACAGATCGAAGGTGAAGGGCCTTAAAC
Found at i:2452782 original size:87 final size:87
Alignment explanation
Indices: 2452634--2453008 Score: 554
Period size: 87 Copynumber: 4.3 Consensus size: 87
2452624 TTCACAAGCA
*
2452634 TTAAACCCCTAAGCAGTAGGGTAACAGGATGAATTTACAGATCTCATCACCCTAAGCAGTAGGGA
1 TTAAACCCCTAAGCAGTAGGGTAACAGGATGAATTTACAGATCTCAACACCCTAAGCAGTAGGGA
2452699 AACAGATCGAAGGTGAAGGGCC
66 AACAGATCGAAGGTGAAGGGCC
* * *
2452721 TTAAACCCCTAAGCAGTAGGGTAACAGGATGAATTTACGGATCTCATCACCCTAAGTAGTAGGGA
1 TTAAACCCCTAAGCAGTAGGGTAACAGGATGAATTTACAGATCTCAACACCCTAAGCAGTAGGGA
2452786 AACAGATCGAAGGTGAAGGGCC
66 AACAGATCGAAGGTGAAGGGCC
* * * *
2452808 TTAAACCCCTAAGCAGTAGGGTAAC-GAGCTGAATTTACAAATCTTAACCCCCTAAGCAGTAGGG
1 TTAAACCCCTAAGCAGTAGGGTAACAG-GATGAATTTACAGATCTCAACACCCTAAGCAGTAGGG
* *
2452872 AAACAGATTGAAGGTGATGGGCC
65 AAACAGATCGAAGGTGAAGGGCC
* * * *
2452895 TTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACCCCCTAAACAGTAGGGA
1 TTAAACCCCTAAGCAGTAGGGTAACAGGATGAATTTACAGATCTCAACACCCTAAGCAGTAGGGA
* ** *
2452960 AACAAATCGAAGACGAAGGGCT
66 AACAGATCGAAGGTGAAGGGCC
* *
2452982 TTAAACCCCTAAGCGGTAGGGAAACAG
1 TTAAACCCCTAAGCAGTAGGGTAACAG
2453009 ATCAAAAGTG
Statistics
Matches: 265, Mismatches: 21, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
86 1 0.00
87 263 0.99
88 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (87 bp):
TTAAACCCCTAAGCAGTAGGGTAACAGGATGAATTTACAGATCTCAACACCCTAAGCAGTAGGGA
AACAGATCGAAGGTGAAGGGCC
Found at i:2452864 original size:43 final size:42
Alignment explanation
Indices: 2452634--2453114 Score: 238
Period size: 44 Copynumber: 11.1 Consensus size: 42
2452624 TTCACAAGCA
*
2452634 TTAAACCCCTAAGCAGTAGGGTAACAGGATGAATTTACAGATC
1 TTAAACCCCTAAGCAGTAGGGTAACA-GCTGAATTTACAGATC
* * * * * * **
2452677 -TCATCACCCTAAGCAGTAGGGAAACAGATCGAAGGTGA-AGGGCC
1 TTAAAC-CCCTAAGCAGTAGGGTAACAGCT-GAA-TTTACA-GATC
* *
2452721 TTAAACCCCTAAGCAGTAGGGTAACAGGATGAATTTACGGATC
1 TTAAACCCCTAAGCAGTAGGGTAACA-GCTGAATTTACAGATC
* * * * * * * **
2452764 -TCATCACCCTAAGTAGTAGGGAAACAGATCGAAGGTGA-AGGGCC
1 TTAAAC-CCCTAAGCAGTAGGGTAACAGCT-GAA-TTTACA-GATC
*
2452808 TTAAACCCCTAAGCAGTAGGGTAACGAGCTGAATTTACAAATC
1 TTAAACCCCTAAGCAGTAGGGTAAC-AGCTGAATTTACAGATC
* * * * * ** **
2452851 TTAACCCCCTAAGCAGTAGGGAAACAGATTGAAGGTGATGGGCC
1 TTAAACCCCTAAGCAGTAGGGTAACAG-CTGAA-TTTACAGATC
2452895 TTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATC
1 TTAAACCCCTAAGCAGTAGGGTAACA-GCTGAATTTACAGATC
* * * ** * **
2452938 TTAACCCCCTAAACAGTAGGGAAACAAATCGAA--GACGAAGGGC
1 TTAAACCCCTAAGCAGTAGGGTAACAGCT-GAATTTAC--AGATC
* * ** * * * **
2452981 TTTAAACCCCTAAGCGGTAGGGAAACAGATCAAAAGTGATAGGCC
1 -TTAAACCCCTAAGCAGTAGGGTAACAG--CTGAATTTACAGATC
* *
2453026 TTAAACCCCTAAGCAGTAGGGTAACAAGCTAAAATTTACAGATA
1 TTAAACCCCTAAGCAGTAGGGTAAC-AGCT-GAATTTACAGATC
* * *
2453070 TTAAACCCCTAAACAGTAAGGTAACAGGCTGAA-TTACAAATC
1 TTAAACCCCTAAGCAGTAGGGTAACA-GCTGAATTTACAGATC
2453112 TTA
1 TTA
2453115 CCTCCCTAAG
Statistics
Matches: 326, Mismatches: 84, Indels: 57
0.70 0.18 0.12
Matches are distributed among these distances:
41 2 0.01
42 25 0.08
43 115 0.35
44 161 0.49
45 21 0.06
47 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (42 bp):
TTAAACCCCTAAGCAGTAGGGTAACAGCTGAATTTACAGATC
Found at i:2453159 original size:261 final size:260
Alignment explanation
Indices: 2452629--2453188 Score: 586
Period size: 261 Copynumber: 2.1 Consensus size: 260
2452619 GTGAATTCAC
* * * *
2452629 AAGCATTAAACCCCTAAGCAGTAGGGTAACAGGATGAATTTACAGATCTCATCACCCTAAGCAGT
1 AAGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTCAACACCCTAAACAGT
* ** * * *
2452694 AGGGAAACAGATCGAAGGTGAAGGGCCTTAAACCCCTAAGCAGTAGGGTAACAGGATGAATTTAC
66 AGGGAAACAAATCGAAGACGAAGGGCCTTAAACCCCTAAGCAGTAGGGAAACAGGATAAATATAC
* * * * * * * *
2452759 GGATCTCATCACCCTAAGTAGTAGGGAAACAGATCGAAGGTGAAGGGCCTTAAACCCCTAAGCAG
131 GGATCTAAACACCCTAAGCAGTAGGGAAACAGATCAAAAGTGAAGGACATTAAACCCCTAAACAG
* * * *
2452824 TAGGGTAACGAGCTGAATTTACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGATTGAAGGTGA
196 TAAGGTAACGAGCTGAATTTACAAATCTTAACCCCCTAAGCAATAGGGAAACAGATAGAA-GCGA
2452889 T
260 T
** * *
2452890 GGGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACCCCCTAAACAGT
1 AAGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTCAACACCCTAAACAGT
* *
2452955 AGGGAAACAAATCGAAGACGAAGGGCTTTAAACCCCTAAGCGGTAGGGAAACA-GATCAAAAGTG
66 AGGGAAACAAATCGAAGACGAAGGGCCTTAAACCCCTAAGCAGTAGGGAAACAGGAT--AAA-T-
* * * * * *
2453019 ATA-GG-CCTTAAAC-CCCTAAGCAGTAGGGTAACA-AGCTAAAATTTACA-GATATTAAACCCC
127 ATACGGATC-TAAACACCCTAAGCAGTAGGGAAACAGATC-AAAAGTGA-AGGACATTAAACCCC
**
2453079 TAAACAGTAAGGTAAC-AGGCTGAA-TTACAAATCTT-ACCTCCCTAAGCAATAGTGG-AGTAGA
189 TAAACAGTAAGGTAACGA-GCTGAATTTACAAATCTTAACC-CCCTAAGCAATAG-GGAAACAGA
2453140 TCAGATA-CGAT
251 T-AGA-AGCGAT
2453151 AAGCCTT-AACCCCTTAAGCAGTAGGGTAACAGGCTGAA
1 AAGCCTTAAACCCC-TAAGCAGTAGGGTAACAGGCTGAA
2453189 AATTACAATT
Statistics
Matches: 248, Mismatches: 38, Indels: 26
0.79 0.12 0.08
Matches are distributed among these distances:
260 12 0.05
261 167 0.67
262 59 0.24
263 8 0.03
264 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.20
Consensus pattern (260 bp):
AAGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTCAACACCCTAAACAGT
AGGGAAACAAATCGAAGACGAAGGGCCTTAAACCCCTAAGCAGTAGGGAAACAGGATAAATATAC
GGATCTAAACACCCTAAGCAGTAGGGAAACAGATCAAAAGTGAAGGACATTAAACCCCTAAACAG
TAAGGTAACGAGCTGAATTTACAAATCTTAACCCCCTAAGCAATAGGGAAACAGATAGAAGCGAT
Found at i:2453320 original size:44 final size:43
Alignment explanation
Indices: 2453244--2453437 Score: 142
Period size: 44 Copynumber: 4.5 Consensus size: 43
2453234 GCCACAGCAG
* * * * * *
2453244 ATCTCCTTGAAGTTTCAGGGGAGTAGATTGAAGTCAATAGTCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATCAA-AGCCTT
* * *
2453288 GTCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AGCAAGTCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-ATCA--AAGCCTT
* * * * * *
2453333 ATATCCCTAAAGTTGCAATAGAGCAGA-TCAAAACAAA-CCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATCAAAGCCTT
* * * *
2453374 ATCTCTCTGAAGTTGAAGTGGAGCAGATTGAAATCACTAGCCCT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATCA-AAGCCTT
*
2453418 ATCTCCCTGAAGTTACAGTG
1 ATCTCCCTGAAGTTGCAGTG
2453438 AAGAGGATCG
Statistics
Matches: 115, Mismatches: 28, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
41 24 0.21
42 8 0.07
43 2 0.02
44 51 0.44
45 29 0.25
46 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATCAAAGCCTT
Found at i:2453651 original size:17 final size:17
Alignment explanation
Indices: 2453629--2453669 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2453619 AAAACTACCT
2453629 ACCCAAATA-ACCCCAAA
1 ACCCAAATAGA-CCCAAA
*
2453646 ACCCAATTAGACCCAAA
1 ACCCAAATAGACCCAAA
2453663 ACCCAAA
1 ACCCAAA
2453670 CCCTAGCCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.51, C:0.39, G:0.02, T:0.07
Consensus pattern (17 bp):
ACCCAAATAGACCCAAA
Found at i:2454812 original size:22 final size:22
Alignment explanation
Indices: 2454774--2454854 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 22
2454764 ATATTTTTGC
*
2454774 TATTATCTATTATTATCATATT
1 TATTATCTATTATTATCATATA
* *
2454796 TATTAT-TATTTTCTATCCTATA
1 TATTATCTATTAT-TATCATATA
* * *
2454818 TATTTTCTTTTTAGTATCA-ATCA
1 TATTATC-TATTATTATCATAT-A
2454841 TATTAT-TATTATTA
1 TATTATCTATTATTA
2454855 CTTTCCTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
21 11 0.25
22 20 0.45
23 10 0.23
24 3 0.07
ACGTcount: A:0.30, C:0.10, G:0.01, T:0.59
Consensus pattern (22 bp):
TATTATCTATTATTATCATATA
Found at i:2455063 original size:9 final size:9
Alignment explanation
Indices: 2455039--2455072 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2455029 TTTTGTATTT
*
2455039 TATTATTAT
1 TATTATTAC
*
2455048 TAGTATTAC
1 TATTATTAC
2455057 TATTATTAC
1 TATTATTAC
2455066 TATTATT
1 TATTATT
2455073 GTTAATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (9 bp):
TATTATTAC
Found at i:2455201 original size:76 final size:70
Alignment explanation
Indices: 2455121--2455263 Score: 169
Period size: 74 Copynumber: 2.0 Consensus size: 70
2455111 ACTATATATC
* * * *
2455121 TATTTATGTAACATTATTAATAATTATTTTTTTAACATTATTATTATTTTTAATACATGCATATA
1 TATTTATGTAACATTATTAAT-AGT-TGTTTTTAACATTATGATTATTTCT-A-ACATG--TATA
2455186 TATTATGTGTA
60 TATTATGTGTA
** *
2455197 TATTTATGTAGTATTATTAATAGTTGTTTTTAATATTATGATTATTTCTAACATGTATATATTAT
1 TATTTATGTAACATTATTAATAGTTGTTTTTAACATTATGATTATTTCTAACATGTATATATTAT
2455262 GT
66 GT
2455264 ACTTACTTCT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
70 12 0.20
72 5 0.08
73 1 0.02
74 21 0.35
75 2 0.03
76 19 0.32
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.55
Consensus pattern (70 bp):
TATTTATGTAACATTATTAATAGTTGTTTTTAACATTATGATTATTTCTAACATGTATATATTAT
GTGTA
Found at i:2455436 original size:3 final size:3
Alignment explanation
Indices: 2455428--2455577 Score: 58
Period size: 3 Copynumber: 49.7 Consensus size: 3
2455418 CCCTCATCAC
* * *
2455428 TAT TAT TAT T-T ATACT TTAT TAT TGT TACT TAT TAT T-T TAC TAT TGT
1 TAT TAT TAT TAT -TA-T T-AT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * * * * *
2455475 TAT CTAT TA- TAT CAT CAT TAT CAT TAT TTT TAT T-T TAC TAT TGT
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
2455519 AACT TAA TA- TAT TAG CAT TGT TAT TTT TAT TGT TAT TAT TAT TAT
1 TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2455564 TAT CAT TAT TAT TA
1 TAT TAT TAT TAT TA
2455578 CCATCTTATT
Statistics
Matches: 105, Mismatches: 31, Indels: 22
0.66 0.20 0.14
Matches are distributed among these distances:
2 9 0.09
3 83 0.79
4 11 0.10
5 2 0.02
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2455477 original size:14 final size:13
Alignment explanation
Indices: 2455430--2455469 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
2455420 CTCATCACTA
2455430 TTATTATTTATACT
1 TTATTATTT-TACT
2455444 TTATTATTGTTAC-
1 TTATTATT-TTACT
2455457 TTATTATTTTACT
1 TTATTATTTTACT
2455470 ATTGTTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.17
13 8 0.33
14 11 0.46
15 1 0.04
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (13 bp):
TTATTATTTTACT
Found at i:2455490 original size:65 final size:65
Alignment explanation
Indices: 2455421--2455542 Score: 156
Period size: 65 Copynumber: 1.9 Consensus size: 65
2455411 GTTATTACCC
* * * * *
2455421 TCATCACTATTATTATTTATACTTTATTATTGTTACTTATTATTTTA-CTATTGTTATCTATTAT
1 TCATCACTATCATTATTTATACTTTACTATTGTAACTTAATATATTAGC-ATTGTTATCTATTAT
2455485 A
65 A
* * *
2455486 TCATCATTATCATTATTTTTATTTTACTATTGTAACTTAATATATTAGCATTGTTAT
1 TCATCACTATCATTATTTATACTTTACTATTGTAACTTAATATATTAGCATTGTTAT
2455543 TTTTATTGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 47 0.98
66 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.04, T:0.57
Consensus pattern (65 bp):
TCATCACTATCATTATTTATACTTTACTATTGTAACTTAATATATTAGCATTGTTATCTATTATA
Found at i:2455597 original size:3 final size:3
Alignment explanation
Indices: 2455444--2455577 Score: 60
Period size: 3 Copynumber: 45.0 Consensus size: 3
2455434 TATTTATACT
* * * *
2455444 TTA TTA TTG TTA CTTA TTA TT- TTA CTA TTG TTA TCTA TTA -TA TCA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* * * * * * *
2455489 TCA TTA TCA TTA TTT TTA TT- TTA CTA TTG TAA CTTA ATA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
** * * * *
2455533 GCA TTG TTA TTT TTA TTG TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2455578 CCATCTTATT
Statistics
Matches: 93, Mismatches: 31, Indels: 14
0.67 0.22 0.10
Matches are distributed among these distances:
2 8 0.09
3 77 0.83
4 8 0.09
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2455701 original size:11 final size:11
Alignment explanation
Indices: 2455685--2455710 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2455675 TCATTGTTAT
2455685 TATTACTATTA
1 TATTACTATTA
2455696 TATTACTATTA
1 TATTACTATTA
2455707 TATT
1 TATT
2455711 TTTGCCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTACTATTA
Found at i:2462293 original size:20 final size:20
Alignment explanation
Indices: 2462268--2462305 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2462258 ATTGATTTCT
2462268 CCACAGGTGTGAAACGCAAA
1 CCACAGGTGTGAAACGCAAA
2462288 CCACAGGTGTGAAACGCA
1 CCACAGGTGTGAAACGCA
2462306 TGTTAAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.26, G:0.26, T:0.11
Consensus pattern (20 bp):
CCACAGGTGTGAAACGCAAA
Found at i:2466195 original size:24 final size:24
Alignment explanation
Indices: 2466163--2466230 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
2466153 TGAATTATAA
* *
2466163 ATATATTTTGTATTTTTTTTAAAT
1 ATATATTTTGAATTTTTTTAAAAT
2466187 ATATATTTTGAATTTTTTTAAAAT
1 ATATATTTTGAATTTTTTTAAAAT
*
2466211 ATAAATTTTGAATTTTTTTA
1 ATATATTTTGAATTTTTTTA
2466231 TAACTATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (24 bp):
ATATATTTTGAATTTTTTTAAAAT
Found at i:2469484 original size:17 final size:17
Alignment explanation
Indices: 2469462--2469498 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2469452 GATGGCCTGG
*
2469462 TGTTCAAGGGTATTAAC
1 TGTTCAAAGGTATTAAC
*
2469479 TGTTCAAAGGTATTCAC
1 TGTTCAAAGGTATTAAC
2469496 TGT
1 TGT
2469499 CCCAAGTGTG
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:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (17 bp):
TGTTCAAAGGTATTAAC
Found at i:2469534 original size:9 final size:9
Alignment explanation
Indices: 2469520--2469546 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2469510 CTTGGGTTTA
2469520 AATCGTGCT
1 AATCGTGCT
2469529 AATCGTGCT
1 AATCGTGCT
2469538 AATCGTGCT
1 AATCGTGCT
2469547 TGTTGTTCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (9 bp):
AATCGTGCT
Found at i:2470883 original size:21 final size:20
Alignment explanation
Indices: 2470834--2470883 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2470824 TATATGTATA
*
2470834 AAATGTAATTTATATAAAATT
1 AAATGTAA-ATATATAAAATT
*
2470855 AAAT-TAAATATATAATATT
1 AAATGTAAATATATAAAATT
2470874 ATAATGTAAA
1 A-AATGTAAA
2470884 CATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 11 0.44
20 6 0.24
21 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (20 bp):
AAATGTAAATATATAAAATT
Found at i:2477708 original size:43 final size:43
Alignment explanation
Indices: 2477661--2477826 Score: 206
Period size: 43 Copynumber: 3.9 Consensus size: 43
2477651 AAGCCTCTAT
* * *
2477661 AGAACATGACCTTTAGCAGCGCTTTTATCAAAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCACTAA
* * * * *
2477704 AGAACATAACTTTTAGCGGCACTTTTATCGCAAACGTCACTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCACTAA
* * *
2477747 AGAACATGATCTTTAGCGGCGCTTTTGTCGCAAACGCCACTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCACTAA
* * *
2477790 ATAACATGACCTTTAGCTGCGCTTTTACCACAAACGC
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGC
2477827 TGCTAACTTT
Statistics
Matches: 103, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 103 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (43 bp):
AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCACTAA
Found at i:2479330 original size:2 final size:2
Alignment explanation
Indices: 2479323--2479353 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2479313 CATTTTAACT
2479323 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 T
2479354 CACAAATCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2481510 original size:26 final size:28
Alignment explanation
Indices: 2481472--2481527 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 28
2481462 AATTATGATA
2481472 TTACATACAATTAAAAAATCGTAAA-ATC
1 TTACATACAATT-AAAAATCGTAAATATC
* *
2481500 TTAC-TAC-ATTATAATTCGTAAATATC
1 TTACATACAATTAAAAATCGTAAATATC
2481526 TT
1 TT
2481528 CATTAACATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 10 0.40
26 8 0.32
27 3 0.12
28 4 0.16
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.38
Consensus pattern (28 bp):
TTACATACAATTAAAAATCGTAAATATC
Found at i:2483536 original size:12 final size:13
Alignment explanation
Indices: 2483521--2483549 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2483511 CATCCTCTTT
2483521 ATCAGATTCAT-C
1 ATCAGATTCATCC
2483533 ATCAGATTCATCC
1 ATCAGATTCATCC
2483546 ATCA
1 ATCA
2483550 ATCTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (13 bp):
ATCAGATTCATCC
Found at i:2485253 original size:9 final size:9
Alignment explanation
Indices: 2485239--2485451 Score: 123
Period size: 9 Copynumber: 23.9 Consensus size: 9
2485229 TGATATTTAT
*
2485239 TTATGTCAG
1 TTATGTAAG
*
2485248 TTATGTAAA
1 TTATGTAAG
*
2485257 TAATGTAAG
1 TTATGTAAG
* *
2485266 TTATGAAAA
1 TTATGTAAG
2485275 TTATGTAAG
1 TTATGTAAG
*
2485284 TTATGTAAA
1 TTATGTAAG
*
2485293 TTATGTAAA
1 TTATGTAAG
*
2485302 TTACGTAAG
1 TTATGTAAG
2485311 TTATGTAAG
1 TTATGTAAG
*
2485320 TTATG-ACAT
1 TTATGTA-AG
*
2485329 TTATGATATG
1 TTATG-TAAG
* * *
2485339 ATATAT-AT
1 TTATGTAAG
2485347 TTATGT-A-
1 TTATGTAAG
2485354 TTATGTAAG
1 TTATGTAAG
2485363 TTATGTAAG
1 TTATGTAAG
* *
2485372 TTATAATATG
1 TTAT-GTAAG
* * *
2485382 ATATAT-AT
1 TTATGTAAG
*
2485390 TTATATAAG
1 TTATGTAAG
2485399 TTATGTAAG
1 TTATGTAAG
*
2485408 TTATGATATG
1 TTATG-TAAG
* * *
2485418 ATATAT-AT
1 TTATGTAAG
2485426 TTATGTAAG
1 TTATGTAAG
* *
2485435 CTATGTGAG
1 TTATGTAAG
2485444 TTATGTAA
1 TTATGTAA
2485452 TTTGCAAATT
Statistics
Matches: 153, Mismatches: 42, Indels: 18
0.72 0.20 0.08
Matches are distributed among these distances:
7 6 0.04
8 16 0.10
9 115 0.75
10 15 0.10
11 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:2485351 original size:36 final size:36
Alignment explanation
Indices: 2485226--2485448 Score: 164
Period size: 36 Copynumber: 6.0 Consensus size: 36
2485216 AAAGTTGACA
* * * *
2485226 ATATGATATTTATTTATGTCAGTTATGTAAATAATG
1 ATATGATATATATTTATGTAAGTTATGTAAGTTATG
* * * * *
2485262 -TAAGTTATGAAAATTATGTAAGTTATGTAAATTATG
1 ATATGATAT-ATATTTATGTAAGTTATGTAAGTTATG
* * ** * *
2485298 TAAATTACGTA-AGTTATGTAAGTTATG-ACATTTATG
1 -ATATGATATATATTTATGTAAGTTATGTA-AGTTATG
*
2485334 ATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATA
1 ATATG--ATATA--TA--T-TTATGTAAGTTATGTAAGTTATG
*
2485377 ATATGATATATATTTATATAAGTTATGTAAGTTATG
1 ATATGATATATATTTATGTAAGTTATGTAAGTTATG
* *
2485413 ATATGATATATATTTATGTAAGCTATGTGAGTTATG
1 ATATGATATATATTTATGTAAGTTATGTAAGTTATG
2485449 TAATTTGCAA
Statistics
Matches: 147, Mismatches: 27, Indels: 26
0.74 0.14 0.13
Matches are distributed among these distances:
35 10 0.07
36 97 0.66
37 5 0.03
38 2 0.01
39 2 0.01
40 1 0.01
41 5 0.03
43 24 0.16
44 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.45
Consensus pattern (36 bp):
ATATGATATATATTTATGTAAGTTATGTAAGTTATG
Found at i:2485363 original size:43 final size:44
Alignment explanation
Indices: 2485307--2485413 Score: 155
Period size: 43 Copynumber: 2.4 Consensus size: 44
2485297 GTAAATTACG
* * *
2485307 TAAGTTATGTAAGTTATGACATTTATGATATGATATATATTTATG
1 TAAGTTATGTAAGTTATGA-AGTTATAATATGATATATATTTATA
2485352 T-A-TTATGTAAGTTATGTAAGTTATAATATGATATATATTTATA
1 TAAGTTATGTAAGTTATG-AAGTTATAATATGATATATATTTATA
2485395 TAAGTTATGTAAGTTATGA
1 TAAGTTATGTAAGTTATGA
2485414 TATGATATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
43 37 0.66
44 4 0.07
45 15 0.27
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (44 bp):
TAAGTTATGTAAGTTATGAAGTTATAATATGATATATATTTATA
Found at i:2492690 original size:3 final size:3
Alignment explanation
Indices: 2492677--2492710 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2492667 GCAAGCTACC
2492677 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2492711 AAGCTGCAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2498195 original size:15 final size:15
Alignment explanation
Indices: 2498175--2498207 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2498165 CAATACTTCT
2498175 CAATAAGGGAACAAG
1 CAATAAGGGAACAAG
2498190 CAATAAGGGAACAAG
1 CAATAAGGGAACAAG
2498205 CAA
1 CAA
2498208 AAATGGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.24, T:0.06
Consensus pattern (15 bp):
CAATAAGGGAACAAG
Found at i:2500317 original size:12 final size:14
Alignment explanation
Indices: 2500281--2500311 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2500271 AATAATAAAT
*
2500281 AAATAAACATGTCA
1 AAATAAACATATCA
2500295 AAATAAACATATCA
1 AAATAAACATATCA
2500309 AAA
1 AAA
2500312 AACATACCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.13, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAAACATATCA
Found at i:2511719 original size:66 final size:66
Alignment explanation
Indices: 2511581--2511712 Score: 185
Period size: 66 Copynumber: 2.0 Consensus size: 66
2511571 CCTTCGGTTT
* * ** *
2511581 TCAA-TCTTCCTTGTTGGTTTTAGCAACCTCTTGAGAACCATCAGCTCCAGAAGGGTTCGCTTCA
1 TCAAGTCTTCCTTATTGGTTTTAGCAACCCCTACAGAACCATCAGCTCCAGAAGGGTTCACTTCA
2511645 C
66 C
* * *
2511646 TCAAGTCTTCCTTATTGGTTTTGGCAACCCCTACAGAATCATCAGCTTCAGAAGGGTTCACTTCA
1 TCAAGTCTTCCTTATTGGTTTTAGCAACCCCTACAGAACCATCAGCTCCAGAAGGGTTCACTTCA
2511711 C
66 C
2511712 T
1 T
2511713 TGAGTCTGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
65 4 0.07
66 54 0.93
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (66 bp):
TCAAGTCTTCCTTATTGGTTTTAGCAACCCCTACAGAACCATCAGCTCCAGAAGGGTTCACTTCA
C
Found at i:2512013 original size:9 final size:9
Alignment explanation
Indices: 2511999--2512023 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2511989 GGATTAAATG
2511999 AAGCTGCTA
1 AAGCTGCTA
2512008 AAGCTGCTA
1 AAGCTGCTA
2512017 AAGCTGC
1 AAGCTGC
2512024 AGCTCTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (9 bp):
AAGCTGCTA
Found at i:2514380 original size:34 final size:35
Alignment explanation
Indices: 2514330--2514396 Score: 127
Period size: 34 Copynumber: 1.9 Consensus size: 35
2514320 GAATAAGACG
2514330 CAAACCTTTTTTTATTAAGAGAGAATGTGAACATA
1 CAAACCTTTTTTTATTAAGAGAGAATGTGAACATA
2514365 CAAACC-TTTTTTATTAAGAGAGAATGTGAACA
1 CAAACCTTTTTTTATTAAGAGAGAATGTGAACA
2514397 AGTGGGGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 26 0.81
35 6 0.19
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (35 bp):
CAAACCTTTTTTTATTAAGAGAGAATGTGAACATA
Found at i:2527382 original size:38 final size:38
Alignment explanation
Indices: 2527331--2527404 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
2527321 TAAACTCAAT
2527331 TTAAATAAATCTATTTAGTCGAGACTATACAACAATAC
1 TTAAATAAATCTATTTAGTCGAGACTATACAACAATAC
* *
2527369 TTAAATAAGTCTATTTAGTCGAGTCTATACAACAAT
1 TTAAATAAATCTATTTAGTCGAGACTATACAACAAT
2527405 GTAAAAGTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (38 bp):
TTAAATAAATCTATTTAGTCGAGACTATACAACAATAC
Found at i:2527418 original size:34 final size:37
Alignment explanation
Indices: 2527332--2527419 Score: 119
Period size: 38 Copynumber: 2.4 Consensus size: 37
2527322 AAACTCAATT
* *
2527332 TAAATAAATCTATTTAGTCGAGACTATACAACAATACT
1 TAAATAAGTCTATTTAGTCGAGACTATACAACAATA-G
*
2527370 TAAATAAGTCTATTTAGTCGAGTCTATACAACAAT-G
1 TAAATAAGTCTATTTAGTCGAGACTATACAACAATAG
2527406 T-AA-AAGTCTATTTA
1 TAAATAAGTCTATTTA
2527420 AGCATAAAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
34 11 0.23
35 2 0.04
36 1 0.02
38 33 0.70
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (37 bp):
TAAATAAGTCTATTTAGTCGAGACTATACAACAATAG
Found at i:2528987 original size:31 final size:32
Alignment explanation
Indices: 2528951--2529010 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
2528941 ATATAGAAGG
*
2528951 GTTTAGATAAAAATATAAGCTCAA-AAAATTA
1 GTTTAGATAAAAAAATAAGCTCAACAAAATTA
*
2528982 GTTTAGTTAAAAAAATAAGCTCAACAAAA
1 GTTTAGATAAAAAAATAAGCTCAACAAAA
2529011 ATATAAGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (32 bp):
GTTTAGATAAAAAAATAAGCTCAACAAAATTA
Found at i:2530131 original size:29 final size:31
Alignment explanation
Indices: 2530077--2530141 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
2530067 AACAGTTTAT
*
2530077 ATTTTTATAATTTTTAAAGGATTAAATTA-A
1 ATTTTTATAATTTTTAAAGGATTAAAGTATA
2530107 ATTTTTATAATTTTTAAAGGA-TAAAGTATA
1 ATTTTTATAATTTTTAAAGGATTAAAGTATA
2530137 ATTTT
1 ATTTT
2530142 ATTATTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (31 bp):
ATTTTTATAATTTTTAAAGGATTAAAGTATA
Found at i:2530142 original size:29 final size:30
Alignment explanation
Indices: 2530074--2530152 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
2530064 TTTAACAGTT
* *
2530074 TATATTTTTATAATTTTTAAAGGATTAAAT
1 TATAATTTTATAATTTTTAAAGGATTAAAG
2530104 TA-AATTTTTATAATTTTTAAAGGA-TAAAG
1 TATAA-TTTTATAATTTTTAAAGGATTAAAG
* *
2530133 TATAATTTTATTATTATTAA
1 TATAATTTTATAATTTTTAA
2530153 TTTAAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 20 0.47
30 23 0.53
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (30 bp):
TATAATTTTATAATTTTTAAAGGATTAAAG
Found at i:2531208 original size:25 final size:25
Alignment explanation
Indices: 2531180--2531230 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2531170 GTTCCATATT
2531180 GATTTGATTTTAGTCGTTTTAGTTC
1 GATTTGATTTTAGTCGTTTTAGTTC
2531205 GATTTGATTTTAGTCGTTTTAGTTC
1 GATTTGATTTTAGTCGTTTTAGTTC
2531230 G
1 G
2531231 GTTGGTGCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.22, T:0.55
Consensus pattern (25 bp):
GATTTGATTTTAGTCGTTTTAGTTC
Found at i:2531507 original size:26 final size:26
Alignment explanation
Indices: 2531466--2531533 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
2531456 AATGGTATAA
*
2531466 ATTTAAAAT-TTATTTAATAT-CATTC
1 ATTTAAAATATT-TTTAATATACATAC
2531491 ATTTGAAAATATTTTT-ATATACATAC
1 ATTT-AAAATATTTTTAATATACATAC
2531517 A-TT-AAATATTTTTAATA
1 ATTTAAAATATTTTTAATA
2531534 AATTTAGAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
23 10 0.26
24 3 0.08
25 10 0.26
26 13 0.34
27 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (26 bp):
ATTTAAAATATTTTTAATATACATAC
Found at i:2559655 original size:52 final size:52
Alignment explanation
Indices: 2559576--2559695 Score: 186
Period size: 52 Copynumber: 2.3 Consensus size: 52
2559566 GCTCGGGGGA
* * ** *
2559576 GTTAAAATATTATTTTAGGGGAACTAAAAAGGAATAACAATTTTTTAGGAGG
1 GTTAAAGTATAATTTTTTGGGAACTAAAAAAGAATAACAATTTTTTAGGAGG
*
2559628 GTTAAAGTATACTTTTTTGGGAACTAAAAAAGAATAACAATTTTTTAGGAGG
1 GTTAAAGTATAATTTTTTGGGAACTAAAAAAGAATAACAATTTTTTAGGAGG
2559680 GTTAAAGTATAATTTT
1 GTTAAAGTATAATTTT
2559696 ATTGTTATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (52 bp):
GTTAAAGTATAATTTTTTGGGAACTAAAAAAGAATAACAATTTTTTAGGAGG
Found at i:2559686 original size:27 final size:27
Alignment explanation
Indices: 2559607--2559691 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
2559597 AACTAAAAAG
2559607 GAATAACAATTTTTTAGGAGGGTTAAA
1 GAATAACAATTTTTTAGGAGGGTTAAA
* * ** *
2559634 GTAT-AC--TTTTTTGGGA-ACTAAAAAA
1 GAATAACAATTTTTTAGGAGGGT--TAAA
2559659 GAATAACAATTTTTTAGGAGGGTTAAA
1 GAATAACAATTTTTTAGGAGGGTTAAA
*
2559686 GTATAA
1 GAATAA
2559692 TTTTATTGTT
Statistics
Matches: 41, Mismatches: 11, Indels: 12
0.64 0.17 0.19
Matches are distributed among these distances:
23 1 0.02
24 9 0.22
25 6 0.15
26 4 0.10
27 11 0.27
28 9 0.22
29 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (27 bp):
GAATAACAATTTTTTAGGAGGGTTAAA
Found at i:2560429 original size:26 final size:26
Alignment explanation
Indices: 2560400--2560453 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
2560390 ATAATAGTTG
*
2560400 ATAAATATATACCTTCTTTTTAATTT
1 ATAAATATATACCTTATTTTTAATTT
* * *
2560426 ATAAGTATATTCCTTATTTTTTATTT
1 ATAAATATATACCTTATTTTTAATTT
2560452 AT
1 AT
2560454 TGAAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.57
Consensus pattern (26 bp):
ATAAATATATACCTTATTTTTAATTT
Found at i:2563438 original size:20 final size:20
Alignment explanation
Indices: 2563413--2563456 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2563403 CGTATCGATA
* **
2563413 ATATAAATCTATATTAATTT
1 ATATAAATCAATACCAATTT
2563433 ATATAAATCAATACCAATTT
1 ATATAAATCAATACCAATTT
2563453 ATAT
1 ATAT
2563457 CGTTACGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAAATCAATACCAATTT
Found at i:2565166 original size:12 final size:11
Alignment explanation
Indices: 2565147--2565178 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
2565137 TGTATAACTC
2565147 TTATTTTATTA
1 TTATTTTATTA
2565158 TTAATTTTATTA
1 TT-ATTTTATTA
2565170 TTATTTTAT
1 TTATTTTAT
2565179 AGGTATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:2565335 original size:14 final size:14
Alignment explanation
Indices: 2565316--2565356 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
2565306 TTAATATTTT
2565316 AAAATAATAATATA
1 AAAATAATAATATA
2565330 AAAATAATAATATA
1 AAAATAATAATATA
*
2565344 AAAA-ATTAATATA
1 AAAATAATAATATA
2565357 GGCCAAGTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATAATAATATA
Found at i:2566816 original size:23 final size:23
Alignment explanation
Indices: 2566779--2566824 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2566769 TTAGAAGGAT
2566779 AAAAATTAAACTTAACCAAAAATA
1 AAAAATTAAACTTAA-CAAAAATA
* *
2566803 AAAAATTTAA-TTAATAAAAATA
1 AAAAATTAAACTTAACAAAAATA
2566825 TAAACGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAAATTAAACTTAACAAAAATA
Found at i:2568009 original size:27 final size:28
Alignment explanation
Indices: 2567970--2568026 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
2567960 TAAGCTTTCT
* *
2567970 ATTTTAATCAAAATTGATTTGTA-ATTAA
1 ATTTAAATCAAAAAT-ATTTGTATATTAA
*
2567998 ATTTAAAT-AAAAATATTTTTATATTAA
1 ATTTAAATCAAAAATATTTGTATATTAA
2568025 AT
1 AT
2568027 AATAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 6 0.24
27 12 0.48
28 7 0.28
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (28 bp):
ATTTAAATCAAAAATATTTGTATATTAA
Found at i:2569772 original size:13 final size:13
Alignment explanation
Indices: 2569754--2569799 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2569744 AAGATTAGCA
2569754 TAAATTTTAGTGT
1 TAAATTTTAGTGT
* *
2569767 TAAATTTTGGTAT
1 TAAATTTTAGTGT
2569780 ATAAATTTTAGTGT
1 -TAAATTTTAGTGT
*
2569794 TTAATT
1 TAAATT
2569800 ATATTTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (13 bp):
TAAATTTTAGTGT
Found at i:2575541 original size:26 final size:24
Alignment explanation
Indices: 2575511--2575560 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
2575501 TAAATAAAAA
*
2575511 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
2575537 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
2575561 TAAAACAAAT
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:2581604 original size:39 final size:39
Alignment explanation
Indices: 2581550--2581729 Score: 209
Period size: 39 Copynumber: 4.6 Consensus size: 39
2581540 TGATATTTGA
*
2581550 GAATTATATCTGGACTAAAAGTCCGCAGGCTATATGCGG
1 GAATTATATCTGGACTTAAAGTCCGCAGGCTATATGCGG
* * * * *
2581589 GAATTATATCCGGACTTAAAATCTGTAGGCTATATGCGA
1 GAATTATATCTGGACTTAAAGTCCGCAGGCTATATGCGG
* * *
2581628 GAATTATATCTAGACTTAAAGTTCGCAGGCTATATGCAG
1 GAATTATATCTGGACTTAAAGTCCGCAGGCTATATGCGG
* * **
2581667 GAATTATATCTGGACTTAAGGTCCGTAGGCTACGTGCTGG
1 GAATTATATCTGGACTTAAAGTCCGCAGGCTATATGC-GG
* *
2581707 GAA-TATATCCGGGCTTAAAGTCC
1 GAATTATATCTGGACTTAAAGTCC
2581730 CGAAGGCTTT
Statistics
Matches: 116, Mismatches: 24, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
39 112 0.97
40 4 0.03
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (39 bp):
GAATTATATCTGGACTTAAAGTCCGCAGGCTATATGCGG
Found at i:2581695 original size:78 final size:78
Alignment explanation
Indices: 2581548--2581698 Score: 230
Period size: 78 Copynumber: 1.9 Consensus size: 78
2581538 CATGATATTT
* * *
2581548 GAGAATTATATCTGGACTAAAAGTCCGCAGGCTATATGCGGGAATTATATCCGGACTTAAAATCT
1 GAGAATTATATCTAGACTAAAAGTCCGCAGGCTATATGCAGGAATTATATCCGGACTTAAAATCC
2581613 GTAGGCTATATGC
66 GTAGGCTATATGC
* * * **
2581626 GAGAATTATATCTAGACTTAAAGTTCGCAGGCTATATGCAGGAATTATATCTGGACTTAAGGTCC
1 GAGAATTATATCTAGACTAAAAGTCCGCAGGCTATATGCAGGAATTATATCCGGACTTAAAATCC
2581691 GTAGGCTA
66 GTAGGCTA
2581699 CGTGCTGGGA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (78 bp):
GAGAATTATATCTAGACTAAAAGTCCGCAGGCTATATGCAGGAATTATATCCGGACTTAAAATCC
GTAGGCTATATGC
Found at i:2582578 original size:5 final size:5
Alignment explanation
Indices: 2582568--2582592 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2582558 TATGGTATAT
2582568 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
2582593 TACAAGTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:2582998 original size:16 final size:16
Alignment explanation
Indices: 2582977--2583007 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2582967 GTAATCCAAT
*
2582977 TATCACATTTGCACAA
1 TATCACATTTACACAA
2582993 TATCACATTTACACA
1 TATCACATTTACACA
2583008 CACATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (16 bp):
TATCACATTTACACAA
Found at i:2584517 original size:13 final size:13
Alignment explanation
Indices: 2584499--2584525 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2584489 TAAATCCTTT
2584499 TCCCAATTCTAAC
1 TCCCAATTCTAAC
2584512 TCCCAATTCTAAC
1 TCCCAATTCTAAC
2584525 T
1 T
2584526 TGAAATTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (13 bp):
TCCCAATTCTAAC
Found at i:2584823 original size:5 final size:5
Alignment explanation
Indices: 2584813--2584906 Score: 181
Period size: 5 Copynumber: 19.0 Consensus size: 5
2584803 TGTTTATATA
2584813 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
2584862 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
2584907 TACTTATTTA
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.05
5 84 0.95
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:2587625 original size:14 final size:14
Alignment explanation
Indices: 2587606--2587633 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2587596 AATTTTATGA
2587606 ATTTCATATGTATT
1 ATTTCATATGTATT
2587620 ATTTCATATGTATT
1 ATTTCATATGTATT
2587634 GATGATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
ATTTCATATGTATT
Found at i:2587791 original size:35 final size:35
Alignment explanation
Indices: 2587752--2588053 Score: 424
Period size: 35 Copynumber: 8.6 Consensus size: 35
2587742 CATGGCAAAG
2587752 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
*
2587787 TGTGAAACGTAAGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
* * * * *
2587822 TATGAAATGTAGGTACGGTATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
* * *
2587857 TGTGAAACGTAGGTACGGTATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
* * * *
2587892 TGTGAAACGTAGGTACGGTATCATCCATTCTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
*
2587927 TGTGAAACGTAGGTATGGTATTAACCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
*
2587962 TGTGAAACCTAGGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
* ** *
2587997 TGTGAAACGTAGGTATGGCATTTCCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
*
2588032 TGTGAAATGTAGGTATGGTATT
1 TGTGAAACGTAGGTATGGTATT
2588054 TCAATAAGGA
Statistics
Matches: 243, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 243 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
Found at i:2590281 original size:35 final size:35
Alignment explanation
Indices: 2590235--2590301 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
2590225 TTGAGAGGAG
* *
2590235 TAAATGTAGATATGTATGCTCTGAGTAGTGAAGTT
1 TAAATGCAGATATGTATGCTCTGAGTAATGAAGTT
2590270 TAAATGCAGATATGTATGCTCTGAGTAATGAA
1 TAAATGCAGATATGTATGCTCTGAGTAATGAA
2590302 TGTAACACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (35 bp):
TAAATGCAGATATGTATGCTCTGAGTAATGAAGTT
Found at i:2590967 original size:46 final size:45
Alignment explanation
Indices: 2590907--2591172 Score: 339
Period size: 46 Copynumber: 6.0 Consensus size: 45
2590897 TTTGACATGA
* * * * * *
2590907 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
*** *
2590953 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
2590999 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
*
2591045 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
2591091 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
2591129 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAG
2591173 AGAGCACACT
Statistics
Matches: 197, Mismatches: 13, Indels: 20
0.86 0.06 0.09
Matches are distributed among these distances:
38 34 0.17
40 3 0.02
43 1 0.01
44 3 0.02
45 4 0.02
46 149 0.76
47 3 0.02
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:2591136 original size:38 final size:38
Alignment explanation
Indices: 2591085--2591160 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2591075 ACATTTTATA
2591085 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
2591123 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
2591161 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:2593324 original size:11 final size:11
Alignment explanation
Indices: 2593308--2593359 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
2593298 TATACTAAAT
2593308 AAATAATAATA
1 AAATAATAATA
*
2593319 AAATAAT-ATT
1 AAATAATAATA
* *
2593329 AAATATCTCATA
1 AAATA-ATAATA
*
2593341 AAATATTAATA
1 AAATAATAATA
2593352 AAATAATA
1 AAATAATA
2593360 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:2594740 original size:33 final size:32
Alignment explanation
Indices: 2594679--2594740 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
2594669 TTTGTGTATT
*
2594679 TATGTTGTGATGGTTTCGATCATACTTTTTTG
1 TATGTTGTGATGGTTTCGATAATACTTTTTTG
*
2594711 TATGTTGTGATGGGTTTTGATTAAT-CTTTT
1 TATGTTGTGAT-GGTTTCGA-TAATACTTTT
2594741 GCAAATATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 11 0.42
33 12 0.46
34 3 0.12
ACGTcount: A:0.16, C:0.06, G:0.23, T:0.55
Consensus pattern (32 bp):
TATGTTGTGATGGTTTCGATAATACTTTTTTG
Found at i:2599997 original size:37 final size:40
Alignment explanation
Indices: 2599912--2600001 Score: 164
Period size: 40 Copynumber: 2.3 Consensus size: 40
2599902 TATATATATA
*
2599912 ATATAAT-ATAATATAATTAGAACATAAAGTATCTTTATT
1 ATATAATAATAATATAATTAAAACATAAAGTATCTTTATT
2599951 ATATAATAATAATATAATTAAAACATAAAGTATCTTTATT
1 ATATAATAATAATATAATTAAAACATAAAGTATCTTTATT
2599991 ATATAATAATA
1 ATATAATAATA
2600002 TAATAATAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 7 0.14
40 42 0.86
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (40 bp):
ATATAATAATAATATAATTAAAACATAAAGTATCTTTATT
Found at i:2600008 original size:40 final size:41
Alignment explanation
Indices: 2599900--2600012 Score: 160
Period size: 40 Copynumber: 2.7 Consensus size: 41
2599890 GCTTCTTTAG
*
2599900 TTTATATATATAATATAATATAATATAATTAGAACATAAAGTATC
1 TTTAT-TATAT-A-ATAATAT-ATATAATTAAAACATAAAGTATC
2599945 TTTATTATATAATAATA-ATATAATTAAAACATAAAGTATC
1 TTTATTATATAATAATATATATAATTAAAACATAAAGTATC
2599985 TTTATTATATAATAATATA-ATAA-TAAAA
1 TTTATTATATAATAATATATATAATTAAAA
2600013 TAATATACTA
Statistics
Matches: 66, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
39 5 0.08
40 43 0.65
41 1 0.02
42 6 0.09
43 1 0.02
44 5 0.08
45 5 0.08
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (41 bp):
TTTATTATATAATAATATATATAATTAAAACATAAAGTATC
Found at i:2610937 original size:5 final size:5
Alignment explanation
Indices: 2610924--2610960 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
2610914 TTCTTTAGTT
*
2610924 TATATA TATAA TATAA TATAA AATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA T
2610961 TAAAACATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:2617398 original size:24 final size:25
Alignment explanation
Indices: 2617354--2617407 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 25
2617344 GTATTAGGAA
2617354 TGTGTCAGGAATATTTACTATTCCT
1 TGTGTCAGGAATATTTACTATTCCT
2617379 TGTGTCAGGAA-ATTTACTATTCCT
1 TGTGTCAGGAATATTTACTATTCCT
2617403 TGTGT
1 TGTGT
2617408 ACCATATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 18 0.62
25 11 0.38
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (25 bp):
TGTGTCAGGAATATTTACTATTCCT
Found at i:2621377 original size:29 final size:29
Alignment explanation
Indices: 2621335--2621392 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2621325 AAAAAAAAAG
2621335 AAAGGAAAAGGGTTTCGGCTTAGGGCGTC
1 AAAGGAAAAGGGTTTCGGCTTAGGGCGTC
2621364 AAAGGAAAAGGGTTTCGGCTTAGGGCGTC
1 AAAGGAAAAGGGTTTCGGCTTAGGGCGTC
2621393 CCTTTTGCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.38, T:0.21
Consensus pattern (29 bp):
AAAGGAAAAGGGTTTCGGCTTAGGGCGTC
Found at i:2625577 original size:6 final size:7
Alignment explanation
Indices: 2625560--2625585 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2625550 TTTGCTTCTT
2625560 TTTTTTC
1 TTTTTTC
2625567 TTTTTTC
1 TTTTTTC
2625574 TTTTTTC
1 TTTTTTC
2625581 TTTTT
1 TTTTT
2625586 ATTTCTCGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:2629258 original size:12 final size:13
Alignment explanation
Indices: 2629223--2629260 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
2629213 ATGCAAAATC
2629223 ATTAATTTTATAAT
1 ATTAATTTT-TAAT
*
2629237 ATTTATTTTTAA-
1 ATTAATTTTTAAT
2629249 ATTAATTTTTAA
1 ATTAATTTTTAA
2629261 CATATGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 3 0.14
14 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTAATTTTTAAT
Found at i:2629357 original size:30 final size:31
Alignment explanation
Indices: 2629307--2629366 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
2629297 AAAAATTTAA
2629307 TATATTAAAATAACGATAAT-AATTAATAAT
1 TATATTAAAATAACGATAATAAATTAATAAT
2629337 TATATTAAAA-ATAC-ATTAATAAATTAATAA
1 TATATTAAAATA-ACGA-TAATAAATTAATAA
2629367 AATTTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 2 0.07
30 16 0.59
31 9 0.33
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (31 bp):
TATATTAAAATAACGATAATAAATTAATAAT
Found at i:2630211 original size:4 final size:4
Alignment explanation
Indices: 2630202--2630227 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2630192 AGCAACTTTG
2630202 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
2630228 ACTTTAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:2631410 original size:19 final size:19
Alignment explanation
Indices: 2631351--2631410 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
2631341 TATTTGTTCG
**
2631351 ATTAAAAAGTATTTAAAATT
1 ATTAAAAA-TATAAAAAATT
*
2631371 -TTAAAAA-ATAAATAATAT
1 ATTAAAAATATAAAAAAT-T
2631389 ATTAAAAATATAAAAAATT
1 ATTAAAAATATAAAAAATT
2631408 ATT
1 ATT
2631411 TAATTGGCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 6 0.18
18 1 0.03
19 18 0.55
20 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
ATTAAAAATATAAAAAATT
Found at i:2631413 original size:20 final size:18
Alignment explanation
Indices: 2631365--2631413 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
2631355 AAAAGTATTT
2631365 AAAAT-TTTAAAAAATAA
1 AAAATATTTAAAAAATAA
*
2631382 ATAATATATTAAAAATATAA
1 AAAATAT-TTAAAAA-ATAA
2631402 AAAATTATTTAA
1 AAAA-TATTTAA
2631414 TTGGCCCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 4 0.15
18 1 0.04
19 7 0.27
20 11 0.42
21 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATATTTAAAAAATAA
Found at i:2633067 original size:8 final size:8
Alignment explanation
Indices: 2633057--2633489 Score: 252
Period size: 8 Copynumber: 55.8 Consensus size: 8
2633047 GACTCTCATT
*
2633057 CTCTCTCT
1 CTCTCTCC
*
2633065 CTCCCTCC
1 CTCTCTCC
*
2633073 CTCCCTCC
1 CTCTCTCC
2633081 C-CTCTCC
1 CTCTCTCC
*
2633088 CTCTCTCG
1 CTCTCTCC
*
2633096 CTCCCTCC
1 CTCTCTCC
2633104 CTCTCCCTCC
1 CTCT--CTCC
*
2633114 CCCTCTCC
1 CTCTCTCC
*
2633122 CTCCCCTCC
1 CT-CTCTCC
2633131 C-C-CT-C
1 CTCTCTCC
2633136 C-CTCTCC
1 CTCTCTCC
*
2633143 CTCAC-CC
1 CTCTCTCC
* *
2633150 TTCCCCTCC
1 CT-CTCTCC
*
2633159 CTCTCACTC
1 CTCTCTC-C
*
2633168 C-CTGTCC
1 CTCTCTCC
2633175 CTCT-T-C
1 CTCTCTCC
2633181 CTCTCTCC
1 CTCTCTCC
2633189 CTCTCTCC
1 CTCTCTCC
2633197 CTCTC-CC
1 CTCTCTCC
2633204 TCTCTCTCC
1 -CTCTCTCC
2633213 C-CTC-CC
1 CTCTCTCC
*
2633219 TTTCTCTCC
1 -CTCTCTCC
*
2633228 CTCTCTCT
1 CTCTCTCC
*
2633236 CTCCCTCC
1 CTCTCTCC
2633244 CTCTCT-C
1 CTCTCTCC
*
2633251 C-CTCACC
1 CTCTCTCC
2633258 CTCCTCTCC
1 CT-CTCTCC
2633267 CTCTC-CC
1 CTCTCTCC
*
2633274 TCTCCCTCC
1 -CTCTCTCC
*
2633283 CTCCCTCC
1 CTCTCTCC
2633291 CTCTCTCC
1 CTCTCTCC
2633299 CTCTCTCC
1 CTCTCTCC
*
2633307 CTC-CT-T
1 CTCTCTCC
2633313 CTCT-TCC
1 CTCTCTCC
2633320 TCTCTCTCTC
1 -CTCTCTC-C
*
2633330 CTCACCCTCC
1 CT--CTCTCC
2633340 CTCTCTCC
1 CTCTCTCC
*
2633348 CTCT-T-T
1 CTCTCTCC
* *
2633354 CTTTTTCC
1 CTCTCTCC
* *
2633362 CTCCCTCT
1 CTCTCTCC
*
2633370 CTCTCTCT
1 CTCTCTCC
2633378 CTCTCTCC
1 CTCTCTCC
* *
2633386 CTTTCTCT
1 CTCTCTCC
2633394 CTCTCT-C
1 CTCTCTCC
2633401 C-CTCTCC
1 CTCTCTCC
2633408 CTCTCT-C
1 CTCTCTCC
2633415 C-CTCT-C
1 CTCTCTCC
2633421 C-CTCTCC
1 CTCTCTCC
*
2633428 CTCTCTCT
1 CTCTCTCC
*
2633436 CTCTCTCT
1 CTCTCTCC
*
2633444 CTCTCTCT
1 CTCTCTCC
*
2633452 CTCTCTCT
1 CTCTCTCC
*
2633460 CTCTCTCT
1 CTCTCTCC
*
2633468 CTCTCTCT
1 CTCTCTCC
*
2633476 CTCTCTCT
1 CTCTCTCC
2633484 CTCTCT
1 CTCTCT
2633490 TAATTTGGCA
Statistics
Matches: 343, Mismatches: 46, Indels: 72
0.74 0.10 0.16
Matches are distributed among these distances:
5 3 0.01
6 35 0.10
7 38 0.11
8 224 0.65
9 28 0.08
10 11 0.03
11 4 0.01
ACGTcount: A:0.01, C:0.61, G:0.00, T:0.38
Consensus pattern (8 bp):
CTCTCTCC
Found at i:2633109 original size:6 final size:6
Alignment explanation
Indices: 2633057--2633486 Score: 246
Period size: 6 Copynumber: 72.8 Consensus size: 6
2633047 GACTCTCATT
* * *
2633057 CTCTCT CTCTCC CTCCCTCC CTC-CC CTCTCC CTCTCT CGCT-C C-CTCC
1 CTCTCC CTCTCC CT--CTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
* *
2633104 CTCTCC CTCCCC CTCTCC CTC-CC CTC-CC C-CTCC CTCTCC CTCACC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
* *
2633149 CT-TCC C-CTCC CTCT-- CACTCC CTGTCC CTCTTCC TCTCTCCC TCTCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTC-TCC -CTCT-CC -CTCTCC
* *
2633197 CTCTCC CTCT-- CTCTCC C-CTCC CT-T-T CTCTCC CTCTCT CTCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
*
2633240 CTC-CC TCTCTCC CTC-AC C-CT-C CTCTCC CTCTCC CTCTCC CTCCCTCC
1 CTCTCC -CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CT--CTCC
* * *
2633287 CTC-CC TCTCTCC CTCTCTC C-CTCC TTCTCTTC CTCTCT CTCT-C CTCACC
1 CTCTCC -CTCTCC CTCTC-C CTCTCC --CTCTCC CTCTCC CTCTCC CTCTCC
* * * * *
2633336 CTC-CC TCTCTCC CTCTTTCT TTTTCC CTC-CC TCTCTCT CTCTCT CTCTCC
1 CTCTCC -CTCTCC CTC--TCC CTCTCC CTCTCC -CTCTCC CTCTCC CTCTCC
* * *
2633386 CT-T-T CTCTCT CTCTCC CTCTCCC TCTCTCC CTCTCC CTCTCC CTCTCT
1 CTCTCC CTCTCC CTCTCC CTCT-CC -CTCTCC CTCTCC CTCTCC CTCTCC
* * * * * * * *
2633434 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
2633482 CTCTC
1 CTCTC
2633487 TCTTAATTTG
Statistics
Matches: 348, Mismatches: 33, Indels: 86
0.75 0.07 0.18
Matches are distributed among these distances:
4 17 0.05
5 51 0.15
6 228 0.66
7 20 0.06
8 32 0.09
ACGTcount: A:0.01, C:0.61, G:0.00, T:0.38
Consensus pattern (6 bp):
CTCTCC
Found at i:2633368 original size:4 final size:4
Alignment explanation
Indices: 2633065--2633350 Score: 130
Period size: 4 Copynumber: 70.8 Consensus size: 4
2633055 TTCTCTCTCT
* * *
2633065 CTCC CTCC CTCC CTCC C-CT CTCC CTCT CTCG CTCC CTCC CT-- CTCC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC
* *
2633110 CTCC C-CC TCTCC CTCC C-CTC C-CC CTCC CT-- CTCC CTCA C-CC TTCCC
1 CTCC CTCC -CTCC CTCC CTC-C CTCC CTCC CTCC CTCC CTCC CTCC CT-CC
* *
2633155 CTCC CTCTC ACTCC CTGTCC CTCTTC CTCT CTCC CTCT CTCC CT-- CTCC
1 CTCC CTC-C -CTCC C--TCC CTC--C CTCC CTCC CTCC CTCC CTCC CTCC
* * * * * *
2633203 CTCT CTCT C-CC CTCC CTTTCT CTCC CTCT CTCT CTCC CTCC CTCT CTCC
1 CTCC CTCC CTCC CTCC C--TCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC
* *
2633252 CTCACC CTCC TCTCC CTCTC C-CT CTCC CTCC CTCC CTCC CTCT CTCC
1 CT--CC CTCC -CTCC CTC-C CTCC CTCC CTCC CTCC CTCC CTCC CTCC
* * * * * * * *
2633299 CTCT CTCC CTCC TTCT CTTC CTCT CTCT CTCC TCACC CTCC CTCT CTCC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC -CTCC CTCC CTCC CTCC
2633348 CTC
1 CTC
2633351 TTTCTTTTTC
Statistics
Matches: 215, Mismatches: 39, Indels: 56
0.69 0.13 0.18
Matches are distributed among these distances:
2 6 0.03
3 11 0.05
4 164 0.76
5 16 0.07
6 18 0.08
ACGTcount: A:0.01, C:0.65, G:0.01, T:0.33
Consensus pattern (4 bp):
CTCC
Found at i:2633955 original size:32 final size:30
Alignment explanation
Indices: 2633898--2633956 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
2633888 ACCAAATCTC
2633898 AAAAAAAAAAAGATTAGGTACCAAATTAGG
1 AAAAAAAAAAAGATTAGGTACCAAATTAGG
*
2633928 AAAAAATAATAAA-ATTCAGGTATCAAATT
1 AAAAAA-AA-AAAGATT-AGGTACCAAATT
2633957 TGACCCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 6 0.24
31 5 0.20
32 14 0.56
ACGTcount: A:0.59, C:0.07, G:0.12, T:0.22
Consensus pattern (30 bp):
AAAAAAAAAAAGATTAGGTACCAAATTAGG
Found at i:2635460 original size:14 final size:14
Alignment explanation
Indices: 2635441--2635490 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
2635431 ATAAATAATA
2635441 TAAATTTTAATATT
1 TAAATTTTAATATT
*
2635455 TAAATTTTATTATT
1 TAAATTTTAATATT
** *
2635469 TAGTTTTTAATTATG
1 TAAATTTTAA-TATT
2635484 TAAATTT
1 TAAATTT
2635491 CAAATAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 20 0.71
15 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (14 bp):
TAAATTTTAATATT
Found at i:2640355 original size:22 final size:23
Alignment explanation
Indices: 2640323--2640367 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
2640313 ACCCATATAT
2640323 ATATATATATATATTAAAATTTTC
1 ATATATATAT-TATTAAAATTTTC
*
2640347 ATATTTATATTATTAAAATTT
1 ATATATATATTATTAAAATTT
2640368 AAAAAAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATATATATTATTAAAATTTTC
Found at i:2641749 original size:2 final size:2
Alignment explanation
Indices: 2641742--2641766 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2641732 ACATTAAAGA
2641742 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 A
2641767 AGAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2642337 original size:37 final size:38
Alignment explanation
Indices: 2642245--2642338 Score: 95
Period size: 38 Copynumber: 2.5 Consensus size: 38
2642235 AAAAAAAAAG
*
2642245 TTTAAAAAAATCATAAAAAATTACAAAAACCATTTCAAA
1 TTTAAAAAAAT-ATAAAAAATTACAAAAACAATTTCAAA
* * * *
2642284 -TTACAAAATTATTAAAAATATA-AAAAATAATATT-AAA
1 TTTAAAAAAATATAAAAAAT-TACAAAAACAAT-TTCAAA
2642321 TTTAAAAAAATATAAAAA
1 TTTAAAAAAATATAAAAA
2642339 CAAATTTACT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
37 18 0.41
38 26 0.59
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (38 bp):
TTTAAAAAAATATAAAAAATTACAAAAACAATTTCAAA
Found at i:2644112 original size:13 final size:13
Alignment explanation
Indices: 2644094--2644118 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2644084 ATCCCTTTAA
2644094 AATTTAATTTTTC
1 AATTTAATTTTTC
2644107 AATTTAATTTTT
1 AATTTAATTTTT
2644119 TTACCGTAAA
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTAATTTTTC
Found at i:2663013 original size:5 final size:5
Alignment explanation
Indices: 2663003--2663027 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2662993 TTCATTAAAT
2663003 ATTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA
2663028 TAATTAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTAA
Found at i:2673034 original size:30 final size:30
Alignment explanation
Indices: 2673000--2673062 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2672990 ACTTATTTTA
*
2673000 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
2673030 TTGTTAATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
2673060 TTG
1 TTG
2673063 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:2673135 original size:18 final size:19
Alignment explanation
Indices: 2673113--2673160 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
2673103 TTGTTGGGAA
2673113 ATATTTATTTTGATGT-TT
1 ATATTTATTTTGATGTATT
*
2673131 TTA-TTATTTTTGATGTATT
1 ATATTTA-TTTTGATGTATT
*
2673150 ATATATATTTT
1 ATATTTATTTT
2673161 TAAAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 3 0.12
18 11 0.46
19 8 0.33
20 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
ATATTTATTTTGATGTATT
Found at i:2678715 original size:2 final size:2
Alignment explanation
Indices: 2678708--2678748 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2678698 TTAAATTATG
2678708 AT AT AT AT AT 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 AT AT AT AT AT A
2678749 GGTTTTCGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2695527 original size:60 final size:60
Alignment explanation
Indices: 2695418--2695542 Score: 142
Period size: 60 Copynumber: 2.1 Consensus size: 60
2695408 TCTAAATATA
* * * * * *
2695418 AAAAAATGAACAAATTTAGCCCTCAATGTTTACAAAATTTGCCATTTTAGTTATAATTCT
1 AAAAAATGAACAAATTTAACCCTCAATATTTACAAAATCTACCAATTTAGTCATAATTCT
* * * * * *
2695478 AAAAAATTAATAAATTTAACTCTCAATATTTACAAAATCTATCAATTTAGTCCTAATTGT
1 AAAAAATGAACAAATTTAACCCTCAATATTTACAAAATCTACCAATTTAGTCATAATTCT
2695538 AAAAA
1 AAAAA
2695543 TTTTAAAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.36
Consensus pattern (60 bp):
AAAAAATGAACAAATTTAACCCTCAATATTTACAAAATCTACCAATTTAGTCATAATTCT
Found at i:2700314 original size:17 final size:17
Alignment explanation
Indices: 2700292--2700324 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2700282 TGGTTCATCG
2700292 ATCAAAATAGAAAATTC
1 ATCAAAATAGAAAATTC
2700309 ATCAAAATAGAAAATT
1 ATCAAAATAGAAAATT
2700325 TAGGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.24
Consensus pattern (17 bp):
ATCAAAATAGAAAATTC
Found at i:2700886 original size:18 final size:17
Alignment explanation
Indices: 2700841--2700890 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 17
2700831 TTCATCTGTC
2700841 TGTAAATTTTAATTAA-
1 TGTAAATTTTAATTAAT
*
2700857 -CTAAA-TTTAATTAAT
1 TGTAAATTTTAATTAAT
2700872 TGTAAATTTTAAATTAAT
1 TGTAAATTTT-AATTAAT
2700890 T
1 T
2700891 ACATGTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 9 0.32
15 4 0.14
16 4 0.14
17 3 0.11
18 8 0.29
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (17 bp):
TGTAAATTTTAATTAAT
Found at i:2702317 original size:8 final size:8
Alignment explanation
Indices: 2702304--2702359 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
2702294 CCTTTCTCCT
2702304 TCTCTTTC
1 TCTCTTTC
2702312 TCTCTTTC
1 TCTCTTTC
2702320 TCTCTTTC
1 TCTCTTTC
**
2702328 TCATGCAATC
1 TC-T-CTTTC
2702338 TCTC--TC
1 TCTCTTTC
*
2702344 TCTCTCTC
1 TCTCTTTC
2702352 TCTCTTTC
1 TCTCTTTC
2702360 GCAGGCATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
6 6 0.15
8 28 0.68
9 2 0.05
10 5 0.12
ACGTcount: A:0.05, C:0.39, G:0.02, T:0.54
Consensus pattern (8 bp):
TCTCTTTC
Found at i:2703295 original size:14 final size:14
Alignment explanation
Indices: 2703276--2703304 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2703266 AACTCGAAAG
2703276 ATTGAACATTGGAT
1 ATTGAACATTGGAT
2703290 ATTGAACATTGGAT
1 ATTGAACATTGGAT
2703304 A
1 A
2703305 ATCTTTTTAT
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:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (14 bp):
ATTGAACATTGGAT
Found at i:2708710 original size:20 final size:20
Alignment explanation
Indices: 2708661--2708710 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2708651 ACAATTTAAA
*
2708661 ATATAAAAAATTATTAATAT
1 ATATAAAAATTTATTAATAT
* *
2708681 GTATATAAATTTATTAATAT
1 ATATAAAAATTTATTAATAT
*
2708701 ATGTAAAAAT
1 ATATAAAAAT
2708711 AACTTTTATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
ATATAAAAATTTATTAATAT
Found at i:2708840 original size:14 final size:15
Alignment explanation
Indices: 2708821--2708857 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2708811 CAAAAAAATT
*
2708821 AATTATTTTTC-AAA
1 AATTATTTTCCGAAA
2708835 AATTATTTTCCGAAA
1 AATTATTTTCCGAAA
2708850 AA-TATTTT
1 AATTATTTT
2708858 ACTGGCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (15 bp):
AATTATTTTCCGAAA
Found at i:2725232 original size:81 final size:81
Alignment explanation
Indices: 2725097--2725262 Score: 314
Period size: 81 Copynumber: 2.0 Consensus size: 81
2725087 CAAAGATGTT
2725097 AATTGGAACAACCTATTTGGTATGCTATGCTATTTTTTATGGAAACAAAGGAATTCTTTTGTTTT
1 AATTGGAACAACCTATTTGGTATGCTATGCTATTTTTTATGGAAACAAAGGAATTCTTTTGTTTT
2725162 TGGAAATGTTCCTCAG
66 TGGAAATGTTCCTCAG
*
2725178 AATTGGAACACCCTATTTGGTATGCTATGCTATTTTTTATGGAAACAAAGGAATTCTTTTGTTTT
1 AATTGGAACAACCTATTTGGTATGCTATGCTATTTTTTATGGAAACAAAGGAATTCTTTTGTTTT
*
2725243 TGGAAATGTTCCTCAT
66 TGGAAATGTTCCTCAG
2725259 AATT
1 AATT
2725263 CTGGTATGGT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (81 bp):
AATTGGAACAACCTATTTGGTATGCTATGCTATTTTTTATGGAAACAAAGGAATTCTTTTGTTTT
TGGAAATGTTCCTCAG
Found at i:2726747 original size:22 final size:23
Alignment explanation
Indices: 2726719--2726762 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2726709 CACAAAATAT
2726719 TGTTAA-TTCACTATTTTACTAG
1 TGTTAATTTCACTATTTTACTAG
*
2726741 TGTTAATTTTACTATTTTACTA
1 TGTTAATTTCACTATTTTACTA
2726763 TTTTACTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.55
Consensus pattern (23 bp):
TGTTAATTTCACTATTTTACTAG
Found at i:2726757 original size:8 final size:8
Alignment explanation
Indices: 2726728--2726770 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
2726718 TTGTTAATTC
2726728 ACTATTTT
1 ACTATTTT
*
2726736 ACTAGTGTT
1 ACTA-TTTT
2726745 A--ATTTT
1 ACTATTTT
2726751 ACTATTTT
1 ACTATTTT
2726759 ACTATTTT
1 ACTATTTT
2726767 ACTA
1 ACTA
2726771 GTGTCCTACC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 4 0.13
7 1 0.03
8 21 0.70
9 4 0.13
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (8 bp):
ACTATTTT
Found at i:2727109 original size:23 final size:24
Alignment explanation
Indices: 2727068--2727125 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
2727058 ACATGTATCA
* *
2727068 TAATATTTTATAAATATTT-TAAT
1 TAATTTTTTATAAACATTTATAAT
*
2727091 TAATTTTTTATAACCATTTATAAT
1 TAATTTTTTATAAACATTTATAAT
*
2727115 T-ATTTATTATA
1 TAATTTTTTATA
2727126 TTAAATGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 25 0.83
24 5 0.17
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATTTTTTATAAACATTTATAAT
Found at i:2733976 original size:76 final size:75
Alignment explanation
Indices: 2733880--2734640 Score: 899
Period size: 76 Copynumber: 10.1 Consensus size: 75
2733870 TATGTGGATG
* * *
2733880 TTTC-ATTTCTGTTT-TAAAAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGGGGCA
1 TTTCAATTTTTGTTTGTCAAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCGGGACA
* *
2733943 CGCTAATGTAT
65 CGCTGAGGTAT
** *
2733954 TTTCAATTACTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
1 TTTCAATTTTTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
2734019 GCTGAGGTAT
66 GCTGAGGTAT
* * * * * * *
2734029 TTTCAATTATTGTTTATAAAAAAAAATCAACTCATTTTGCGGGAGTTGAGTTGAGCCTCGGGGCA
1 TTTCAATTTTTGTTTGT-CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
*
2734094 TGCTGAGGTAT
65 CGCTGAGGTAT
* * * *
2734105 TTTCAATTATTGTTTGTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGAGACAT
1 TTTCAATTTTTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
2734170 GCTGAGGTAT
66 GCTGAGGTAT
* *** *
2734180 TGTT-AATTTTTTGTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 T-TTCAA-TTTTTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
*
2734244 ACGCTGAGGTAA
64 ACGCTGAGGTAT
* *
2734256 TTTCAATTTCTGTTTGTC---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCATCGGGACAC
1 TTTCAATTTTTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
2734318 GCTGAGGTAT
66 GCTGAGGTAT
* * *** *
2734328 TGTCAATTTTTTGTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCATCGGGACA
1 TTTCAA-TTTTTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
2734393 CGCTGAGGTAT
65 CGCTGAGGTAT
* * *** * *
2734404 TGTCAATTTTTTGTATGTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCATCGGGACA
1 TTTCAA-TTTTTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
2734469 CGCTGAGGTAT
65 CGCTGAGGTAT
* * *** *
2734480 TGTCAATTTTTTGTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTCAA-TTTTTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
*
2734545 TGCTGAGGTAT
65 CGCTGAGGTAT
* * * *
2734556 TTTCAATTTCTGTCCT-TCAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGA
1 TTTCAATTTTTGT-TTGTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGA
2734620 CACGCT-AGGGTAT
63 CACGCTGA-GGTAT
2734633 TTTCAATT
1 TTTCAATT
2734641 GATGTTTTTT
Statistics
Matches: 621, Mismatches: 52, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
72 56 0.09
73 9 0.01
74 4 0.01
75 135 0.22
76 358 0.58
77 59 0.10
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (75 bp):
TTTCAATTTTTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
GCTGAGGTAT
Found at i:2734105 original size:151 final size:151
Alignment explanation
Indices: 2733898--2734728 Score: 1043
Period size: 151 Copynumber: 5.4 Consensus size: 151
2733888 CTGTTTTAAA
* * * *
2733898 AAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTAATGTATTTTCAATTA
1 AAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTT
*
2733963 CTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTA
65 CTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA
****
2734028 TTTTCAATTATTGTT-TAT-AAAA
130 TTTTCAATT-TT-TTGTATGTTTC
* * * * *
2734050 AAAAATCAACTCATTTTGCGGGAGTTGAGTTGAGCCTCGGGGCATGCTGAGGTATTTTCAATTAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATT-T
* * *
2734115 -TGTTTGTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGAGACATGCTGAGGTA
65 CTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA
2734179 TTGTT-AATTTTTTGTATGTTTC
130 TT-TTCAATTTTTTGTATGTTTC
* *
2734201 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTC
*
2734266 TGTTTGTC---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCATCGGGACACGCTGAGGTAT
66 TGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAT
*
2734328 TGTCAATTTTTTGTATGTTTC
131 TTTCAATTTTTTGTATGTTTC
* *
2734349 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCATCGGGACACGCTGAGGTATTGTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA-TTT
* * *** * *
2734414 TTGTATGTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCATCGGGACACGCTGAGGTA
65 CTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA
*
2734479 TTGTCAATTTTTTGTATGTTTC
130 TTTTCAATTTTTTGTATGTTTC
* *
2734501 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTC
* * *
2734566 TGTCCT-TCAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCT-AGG
66 TGT-TTGTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGA-G
*
2734629 GTATTTTCAATTGATGTTTTTTCAATTTACGCTTTTC
127 GTATTTTCAA-T--T-TTTTGT--A--T--G--TTTC
*
2734666 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGA-ACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTATTTTCAATT
2734729 AATGTTTTTT
Statistics
Matches: 599, Mismatches: 53, Indels: 41
0.86 0.08 0.06
Matches are distributed among these distances:
147 1 0.00
148 125 0.21
149 11 0.02
150 6 0.01
151 180 0.30
152 149 0.25
153 54 0.09
154 1 0.00
156 1 0.00
157 5 0.01
159 1 0.00
161 1 0.00
163 1 0.00
165 60 0.10
166 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (151 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTC
TGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAT
TTTCAATTTTTTGTATGTTTC
Found at i:2734526 original size:300 final size:301
Alignment explanation
Indices: 2733898--2734728 Score: 1073
Period size: 300 Copynumber: 2.7 Consensus size: 301
2733888 CTGTTTTAAA
* * * * *
2733898 AAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTAATGTATTTTCAATTA
1 AAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
*
2733963 CTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTA
65 CTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA
**** * * * *
2734028 TTTTCAATTATTGTTTAT-AAAAAAAAATCAACTCATTTTGCGGGAGTTGAGTTGAGCCTCGGGG
128 TTTTCAATTATT-TTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGA
* * *
2734092 CATGCTGAGGTATTTTCAA-TTATTGTTTGTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTT
192 CACGCTGAGGTATTTTCAATTTATTGTATGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
* * *
2734156 GAGCCTCGAGACATGCTGAGGTATTGTTAATTTTTTGTATGTTTC
257 GAGCATCGAGACACGCTGAGGTATTGTCAATTTTTTGTATGTTTC
*
2734201 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* *
2734266 TGTTTGTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCATCGGGACACGCTGAGGTATTG
66 TGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTT
*
2734330 TCAATT-TTTTGTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCATCGGGACAC
131 TCAATTATTTT-TATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
* * *** *
2734394 GCTGAGGTATTGTCAATTTTTTGTATGTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAG
195 GCTGAGGTATTTTCAATTTATTGTATGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
*
2734459 CATCGGGACACGCTGAGGTATTGTCAATTTTTTGTATGTTTC
260 CATCGAGACACGCTGAGGTATTGTCAATTTTTTGTATGTTTC
*
2734501 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* * *
2734566 TGTCCT-TCAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCT-AGG
66 TGT-TTGTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGA-G
*
2734629 GTATTTTCAATTGATGTTTTTTCAATTTACGCTTTTCAAAAATCAACTCATATTACGAGAGGTGA
125 GTATTTTCAATT-A---TTTTT--A--T--G--TTTCAAAAATCAACTCATATTGCGAGAGGTGA
2734694 GTTGAGCCTCGGGGA-ACGCTGAGGTATTTTCAATT
178 GTTGAGCCTC-GGGACACGCTGAGGTATTTTCAATT
2734729 AATGTTTTTT
Statistics
Matches: 463, Mismatches: 41, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
297 2 0.00
298 5 0.01
299 113 0.24
300 147 0.32
301 1 0.00
302 53 0.11
303 14 0.03
304 1 0.00
305 56 0.12
309 1 0.00
310 4 0.01
311 1 0.00
313 1 0.00
315 1 0.00
317 59 0.13
318 4 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (301 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTT
TCAATTATTTTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
CTGAGGTATTTTCAATTTATTGTATGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
ATCGAGACACGCTGAGGTATTGTCAATTTTTTGTATGTTTC
Found at i:2734713 original size:88 final size:89
Alignment explanation
Indices: 2734578--2734876 Score: 369
Period size: 88 Copynumber: 3.4 Consensus size: 89
2734568 TCCTTCAAAA
** *
2734578 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTC-AGGACACGCT-AGGGTATTTTCAATT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGACACGCTGA-GGTATTTTCAATT
*
2734641 GATGTTTTTTCAATTTACGCTTTTC
65 AATGTTTTTTCAATTTACGCTTTTC
2734666 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGA-ACGCTGAGGTATTTTCAATTA
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGACACGCTGAGGTATTTTCAATTA
*
2734730 ATGTTTTTTCAATTTATGCTTTTC
66 ATGTTTTTTCAATTTACGCTTTTC
* * **
2734754 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCCAAGGTATTTTCAA--
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG-GACACGCTGAGGTATTTTCAATT
* * *
2734817 AATCTGTTTTGCAAATT-CTG-TTTTC
65 AATGT-TTTTTCAATTTAC-GCTTTTC
* *
2734842 AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
1 --AAAAATCAACTCATATTACGAGAGGTGAGTTGA
2734877 ACCTTTGCTC
Statistics
Matches: 188, Mismatches: 15, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
88 127 0.68
89 15 0.08
90 46 0.24
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (89 bp):
AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGACACGCTGAGGTATTTTCAATTA
ATGTTTTTTCAATTTACGCTTTTC
Found at i:2734836 original size:14 final size:13
Alignment explanation
Indices: 2734810--2734845 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
2734800 TGCCAAGGTA
2734810 TTTTCAAAATCTG
1 TTTTCAAAATCTG
*
2734823 TTTTGCAAATTCTG
1 TTTT-CAAAATCTG
2734837 TTTTCAAAA
1 TTTTCAAAA
2734846 AAATCAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (13 bp):
TTTTCAAAATCTG
Found at i:2734902 original size:90 final size:88
Alignment explanation
Indices: 2734754--2734964 Score: 219
Period size: 90 Copynumber: 2.4 Consensus size: 88
2734744 TATGCTTTTC
* * * * *
2734754 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCCAAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGCTCACATGCCAAGCTATTTTCAAAA
2734819 TCTGTTTTGCAAAT-TCT-GTTTTCAA
66 TCTGTTTT---AATGTCTAGTTTT-AA
** * ** **
2734844 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTTTGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGCTCACATGCCAAGCTATTTTCAAAA
*
2734909 TCTGTTTTAATGTCTAGTTTTTA
66 TCTGTTTTAATGTCTAGTTTTAA
* * * *
2734932 AAGAGTCAATTCATATTGCGAGAAATGAGTTGA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGA
2734965 GCTCAAGATC
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
87 3 0.03
88 33 0.32
89 5 0.05
90 61 0.60
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (88 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGCTCACATGCCAAGCTATTTTCAAAA
TCTGTTTTAATGTCTAGTTTTAA
Found at i:2735272 original size:132 final size:132
Alignment explanation
Indices: 2735038--2735280 Score: 312
Period size: 132 Copynumber: 1.8 Consensus size: 132
2735028 CTCCTTGAAA
* * *
2735038 TTACAGTGAAGGAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAATAAGTTGAAAA
1 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCACTGTGCTTATAGGGAACAAGTTGAAAA
** *
2735103 CAGTAGATTTGGCATCCCTGTGCTTATATGGAACAGATCGAAGATAGCAGATCTGACATTCCTGT
66 CAACAGATTTGGCATCCCTGTGCTTACATGGAACAGATCGAAGATAGCAGATCTGACATTCCTGT
2735168 GC
131 GC
* * *
2735170 TTACAGTGAAGCAGATTGAAGATTTCAGCATGGTATCACTGTGTTTATAGGGAACAAGTT-AAAG
1 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCACTGTGCTTATAGGGAACAAGTTGAAA-
* * * * *
2735234 ATAACCGATTTGGCGTCTCTGTG-TTGACA-GAGAGCAGATCGAAGATA
65 ACAACAGATTTGGCATCCCTGTGCTT-ACATG-GAACAGATCGAAGATA
2735281 ACAGTTTTGG
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
131 6 0.06
132 88 0.94
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (132 bp):
TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCACTGTGCTTATAGGGAACAAGTTGAAAA
CAACAGATTTGGCATCCCTGTGCTTACATGGAACAGATCGAAGATAGCAGATCTGACATTCCTGT
GC
Found at i:2735401 original size:44 final size:43
Alignment explanation
Indices: 2735230--2735411 Score: 193
Period size: 44 Copynumber: 4.1 Consensus size: 43
2735220 GGAACAAGTT
* * * *
2735230 AAAGATAACCGATTTGGCGTCTCTGTGTTGACAGAGAGCAGATC
1 AAAGATGACAGATTTGGCGTCTCTG-ATTGACGGAGAGCAGATC
* * * *
2735274 GAAGATAACAGTTTTGGCGTCTCTGTGTTGACGGAGAGCAGATC
1 AAAGATGACAGATTTGGCGTCTCTG-ATTGACGGAGAGCAGATC
* * * *
2735318 AAAGATGATAGATTTGGCGTCTTTGTATTGTCAGAGAGCAGATC
1 AAAGATGACAGATTTGGCGTCTCTG-ATTGACGGAGAGCAGATC
* * *
2735362 AAAGATGACAGATTTGGCATCTCTGATTAGGCGGGGAGCAGATC
1 AAAGATGACAGATTTGGCGTCTCTGATT-GACGGAGAGCAGATC
2735406 AAAGAT
1 AAAGAT
2735412 AGTAGATATC
Statistics
Matches: 119, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
43 3 0.03
44 116 0.97
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (43 bp):
AAAGATGACAGATTTGGCGTCTCTGATTGACGGAGAGCAGATC
Found at i:2735418 original size:88 final size:88
Alignment explanation
Indices: 2735240--2735411 Score: 238
Period size: 88 Copynumber: 2.0 Consensus size: 88
2735230 AAAGATAACC
* * * * *
2735240 GATTTGGCGTCTCTGTGTTGACAGAGAGCAGATCGAAGATAACAGTTTTGGCGTCTCTGTGTTGA
1 GATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATAACAGATTTGGCATCTCTGTGTAGA
2735305 CGGAGAGCAGATCAAAGATGATA
66 CGGAGAGCAGATCAAAGATGATA
* * *
2735328 GATTTGGCGTCTTTGTATTGTCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGAT-TAG
1 GATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATAACAGATTTGGCATCTCTG-TGTAG
* *
2735392 GCGGGGAGCAGATCAAAGAT
65 ACGGAGAGCAGATCAAAGAT
2735412 AGTAGATATC
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 72 0.99
89 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (88 bp):
GATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATAACAGATTTGGCATCTCTGTGTAGA
CGGAGAGCAGATCAAAGATGATA
Found at i:2736917 original size:25 final size:23
Alignment explanation
Indices: 2736875--2736927 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
2736865 AAATTTATTT
*
2736875 TTATTATTAATTCTATTATTACTA
1 TTATTATTAATTCCATTATT-CTA
2736899 CTTATTATT-ATTGCCATTATTCTA
1 -TTATTATTAATT-CCATTATTCTA
2736923 TTATT
1 TTATT
2736928 TCTTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 6 0.23
25 15 0.58
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATTATTAATTCCATTATTCTA
Found at i:2737033 original size:23 final size:23
Alignment explanation
Indices: 2736996--2737044 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2736986 ATAATCATTA
* *
2736996 TTATTCTTTATTTGTTATTGTTG
1 TTATTCTTTATTTGTCATTATTG
2737019 TTATTCTATTA-TTGTCATTATTG
1 TTATTCT-TTATTTGTCATTATTG
2737042 TTA
1 TTA
2737045 ATATTGAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.18, C:0.06, G:0.10, T:0.65
Consensus pattern (23 bp):
TTATTCTTTATTTGTCATTATTG
Done.