Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 22 of 133
Found at i:5402473 original size:21 final size:22
Alignment explanation
Indices: 5402396--5402471 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
5402386 ACAATTAAGT
*
5402396 TATCATTGATTTACTACTATGC
1 TATCAATGATTTACTACTATGC
*
5402418 TATCAATGATTTACTATTATGC
1 TATCAATGATTTACTACTATGC
* *
5402440 TATAAATGATTTACTA-TAAGC
1 TATCAATGATTTACTACTATGC
5402461 TATCAAT-ATTT
1 TATCAATGATTT
5402472 TATTACTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 4 0.08
21 10 0.20
22 35 0.71
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (22 bp):
TATCAATGATTTACTACTATGC
Found at i:5402507 original size:22 final size:22
Alignment explanation
Indices: 5402482--5402533 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
5402472 TATTACTAAA
* *
5402482 TTATTAATAATTTCTGAATGAT
1 TTATTAATAAATTATGAATGAT
*
5402504 TTATTACTAAATTATGAATGAT
1 TTATTAATAAATTATGAATGAT
5402526 TTATTAAT
1 TTATTAAT
5402534 TTATGATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (22 bp):
TTATTAATAAATTATGAATGAT
Found at i:5402539 original size:19 final size:21
Alignment explanation
Indices: 5402482--5402548 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
5402472 TATTACTAAA
*
5402482 TTATTAATAATTTCTGAATGAT
1 TTATT-ATAATTTATGAATGAT
*
5402504 TTATTACTAAATTATGAATGAT
1 TTATTA-TAATTTATGAATGAT
* *
5402526 TTA-T-TAATTTATGATTAAT
1 TTATTATAATTTATGAATGAT
5402545 TTAT
1 TTAT
5402549 CAACAATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 15 0.39
21 2 0.05
22 21 0.55
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.52
Consensus pattern (21 bp):
TTATTATAATTTATGAATGAT
Found at i:5404887 original size:15 final size:16
Alignment explanation
Indices: 5404863--5404900 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5404853 CACCGTCATC
* *
5404863 AAATATAAAAA-ATAA
1 AAATAAAAAAAGACAA
5404878 AAATAAAAAAAGACAA
1 AAATAAAAAAAGACAA
5404894 AAATAAA
1 AAATAAA
5404901 CCCATAGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (16 bp):
AAATAAAAAAAGACAA
Found at i:5405276 original size:20 final size:20
Alignment explanation
Indices: 5405228--5405277 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5405218 ACTAGAAAAG
5405228 AAAAGAGAAAAAAAAAGTAA
1 AAAAGAGAAAAAAAAAGTAA
* *
5405248 AAAAG-GAAATGAAAGAG-AA
1 AAAAGAGAAA-AAAAAAGTAA
5405267 AAAAGAGAAAA
1 AAAAGAGAAAA
5405278 TAGTGATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (20 bp):
AAAAGAGAAAAAAAAAGTAA
Found at i:5406381 original size:11 final size:11
Alignment explanation
Indices: 5406365--5406390 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5406355 TTAAAAAAAG
5406365 ATAAAATATTT
1 ATAAAATATTT
5406376 ATAAAATATTT
1 ATAAAATATTT
5406387 ATAA
1 ATAA
5406391 GAGTTTTTTT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAAAATATTT
Found at i:5408326 original size:38 final size:38
Alignment explanation
Indices: 5408277--5408371 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
5408267 AAATGATGGA
* * *
5408277 AATAATAAGATAATATATGTACCCCATCTT-ATGCACAT
1 AATAATAAGATAATACATATACCCCAT-TTCATACACAT
5408315 AATAATAAGATAATACATATACCCCATTTCATACACAT
1 AATAATAAGATAATACATATACCCCATTTCATACACAT
*
5408353 CATAATAAGATAATACATA
1 AATAATAAGATAATACATA
5408372 CATTCCATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
37 2 0.04
38 50 0.96
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (38 bp):
AATAATAAGATAATACATATACCCCATTTCATACACAT
Found at i:5408385 original size:32 final size:35
Alignment explanation
Indices: 5408310--5408385 Score: 86
Period size: 38 Copynumber: 2.2 Consensus size: 35
5408300 CCATCTTATG
* *
5408310 CACATAATAATAAGATAATACATATACCCCATTTCATA
1 CACATCATAATAAGATAATACA-ATA--CCATTCCATA
5408348 CACATCATAATAAGATAATAC-ATA-CATTCCAT-
1 CACATCATAATAAGATAATACAATACCATTCCATA
5408380 CACATC
1 CACATC
5408386 CATATTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 6 0.17
33 7 0.19
36 3 0.08
38 20 0.56
ACGTcount: A:0.46, C:0.24, G:0.03, T:0.28
Consensus pattern (35 bp):
CACATCATAATAAGATAATACAATACCATTCCATA
Found at i:5414943 original size:78 final size:78
Alignment explanation
Indices: 5414819--5414965 Score: 197
Period size: 78 Copynumber: 1.9 Consensus size: 78
5414809 AAAAAATCAC
* * * *
5414819 ATTTGCATCAATGACATGAGCATCATCAGAAAAACATTTAATCTACATGTTGTAAAAATAA-AAA
1 ATTTGCATCAATGACATGAGCATCATAAGAAAAACATTTAACCTACATGCTATAAAAA-AATAAA
5414883 AAATAGACATTTGT
65 AAATAGACATTTGT
* ** * *
5414897 ATTTGCATCAATGACATGTGCATCATAAGAATGATATTTGACCTACATGCTATAAAAAAATAAAA
1 ATTTGCATCAATGACATGAGCATCATAAGAAAAACATTTAACCTACATGCTATAAAAAAATAAAA
5414962 AATA
66 AATA
5414966 AAAAAAACAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 2 0.03
78 57 0.97
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (78 bp):
ATTTGCATCAATGACATGAGCATCATAAGAAAAACATTTAACCTACATGCTATAAAAAAATAAAA
AATAGACATTTGT
Found at i:5415257 original size:41 final size:41
Alignment explanation
Indices: 5415206--5415290 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 41
5415196 TCGCATTTGT
* *
5415206 ATCTACATCATAAAAAAGACATTCACAGTTGCATCATTTAC
1 ATCTACATCATAAAAAAGACATTCACAGTTACATCATCTAC
* * * * *
5415247 ATCTATATCATGAAAAATACATTCGCATTTACATCATCTAC
1 ATCTACATCATAAAAAAGACATTCACAGTTACATCATCTAC
5415288 ATC
1 ATC
5415291 ATAACCAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (41 bp):
ATCTACATCATAAAAAAGACATTCACAGTTACATCATCTAC
Found at i:5415316 original size:26 final size:27
Alignment explanation
Indices: 5415287--5415347 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
5415277 ACATCATCTA
5415287 CATCATAACCAAA-ACATTCATATTTG
1 CATCATAACCAAATACATTCATATTTG
* **
5415313 CATCATAA-GAAATACATTTGTATTTG
1 CATCATAACCAAATACATTCATATTTG
*
5415339 CATTATAAC
1 CATCATAAC
5415348 ATCCTCATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 3 0.10
26 26 0.90
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (27 bp):
CATCATAACCAAATACATTCATATTTG
Found at i:5415867 original size:103 final size:103
Alignment explanation
Indices: 5415732--5416241 Score: 462
Period size: 104 Copynumber: 4.9 Consensus size: 103
5415722 GGCATCCAAG
*
5415732 ATAATCTTTAAGA-CTTCT-AGACAAAATATTTTAAATTTTTAAAGTTTTAATGCCTCTAATACG
1 ATAATCTTTAA-ACCTT-TAAG-CAAAATATTTTAAATTTTTAAAGTTTTAATGCCTCTGATACG
* * * *
5415795 ATGAGCA-TCTAAAGATGTCGAG-TTTGTAA-AACTTTCAAGT
63 AAGAGCATTC-AAAGATGTCGAGATTTGTAAGATC-TTCAGGC
* * * * * *
5415835 ATAATCTTTAAGGCCTTTAAACAAAACATTTTAAATTTTTTAAGTTTTAATGCCTTTGATACAAA
1 ATAATCTTTAA-ACCTTTAAGCAAAATATTTTAAATTTTTAAAGTTTTAATGCCTCTGATACGAA
* * ** * *
5415900 GAACATTAAAAGATGTTAAAATTTGTAAGA-CCTCTAGGC
65 GAGCATTCAAAGATGTCGAGATTTGTAAGATCTTC-AGGC
* * * *
5415939 ATAATCTCTAAAACTTTCGAGCAAAATATTTTAAATTTTTAAAGTTTCAATGCCTCTGATACG-A
1 ATAATCTTTAAACCTTT-AAGCAAAATATTTTAAATTTTTAAAGTTTTAATGCCTCTGATACGAA
** *
5416003 GAAGCATTCAAAGATGTTTAGATTTGTAAGATCGTCAGGC
65 G-AGCATTCAAAGATGTCGAGATTTGTAAGATCTTCAGGC
* * * * * *
5416043 ATAAT-TTGTAAGACATCTGAGTAAAATATTTTAAATTTTTAAAGTTTTAATACCTCTGATATGA
1 ATAATCTT-TAA-ACCTTTAAGCAAAATATTTTAAATTTTTAAAGTTTTAATGCCTCTGATACGA
* * *
5416107 AGAGCATTTAAAGATATCGAGATTTGTGAGATCTTCAGGC
64 AGAGCATTCAAAGATGTCGAGATTTGTAAGATCTTCAGGC
* * * * * * * *
5416147 ATAATCTCTAAAACC-TCAAGGTAAAACATTTTAAATTTTCAAAGTTTCAATACCTCTGATACAA
1 ATAATCT-TTAAACCTTTAA-GCAAAATATTTTAAATTTTTAAAGTTTTAATGCCTCTGATACGA
*
5416211 AGAGCATTCAAAGATGTTGAGATTTGTAAGA
64 AGAGCATTCAAAGATGTCGAGATTTGTAAGA
5416242 CCTCCGCGCA
Statistics
Matches: 333, Mismatches: 59, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
103 74 0.22
104 246 0.74
105 12 0.04
106 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (103 bp):
ATAATCTTTAAACCTTTAAGCAAAATATTTTAAATTTTTAAAGTTTTAATGCCTCTGATACGAAG
AGCATTCAAAGATGTCGAGATTTGTAAGATCTTCAGGC
Found at i:5416180 original size:208 final size:209
Alignment explanation
Indices: 5415753--5416241 Score: 546
Period size: 208 Copynumber: 2.4 Consensus size: 209
5415743 GACTTCTAGA
* * *
5415753 CAAAATATTTTAAATTTTTAAAGTTTTAATGCCTCTAATACGATG-AGCA-TCTAAAGATGTCGA
1 CAAAATATTTTAAATTTTTAAAGTTTCAATGCCTCTGATACGA-GAAGCATTC-AAAGATGTTGA
* * * * * *
5415816 G-TTTGTAA-AACTTTCAAGTATAATCTTTAAGGCCTTTAAACAAAACATTTTAAATTTTTTAAG
64 GATTTGTAAGAACTGTCAAGCATAATCTTTAAGACATCTAAACAAAACATTTTAAATTTTTAAAG
* * * *
5415879 TTTTAATGCCTTTGATACAAAGAACATTAAAAGATGTTAAAATTTGTAAGACCTCTAGGCATAAT
129 TTTTAATACCTCTGATACAAAGAACATTAAAAGATATCAAAATTTGTAAGACCTCTAGGCATAAT
* *
5415944 CTCTAAAACTTTCGAG
194 CTCTAAAACTCTCAAG
*
5415960 CAAAATATTTTAAATTTTTAAAGTTTCAATGCCTCTGATACGAGAAGCATTCAAAGATGTTTAGA
1 CAAAATATTTTAAATTTTTAAAGTTTCAATGCCTCTGATACGAGAAGCATTCAAAGATGTTGAGA
* * * ** *
5416025 TTTGTAAGATC-GTCAGGCATAAT-TTGTAAGACATCTGAGTAAAATATTTTAAATTTTTAAAGT
66 TTTGTAAGAACTGTCAAGCATAATCTT-TAAGACATCTAAACAAAACATTTTAAATTTTTAAAGT
** * * * * * *
5416088 TTTAATACCTCTGATATGAAGAGCATTTAAAGATATCGAGATTTGTGAGATCT-TCAGGCATAAT
130 TTTAATACCTCTGATACAAAGAACATTAAAAGATATCAAAATTTGTAAGACCTCT-AGGCATAAT
5416152 CTCTAAAAC-CTCAAGG
194 CTCTAAAACTCTCAA-G
* * * * *
5416168 TAAAACATTTTAAATTTTCAAAGTTTCAATACCTCTGATAC-AAAGAGCATTCAAAGATGTTGAG
1 CAAAATATTTTAAATTTTTAAAGTTTCAATGCCTCTGATACGAGA-AGCATTCAAAGATGTTGAG
5416232 ATTTGTAAGA
65 ATTTGTAAGA
5416242 CCTCCGCGCA
Statistics
Matches: 238, Mismatches: 36, Indels: 15
0.82 0.12 0.05
Matches are distributed among these distances:
206 1 0.00
207 63 0.26
208 172 0.72
209 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (209 bp):
CAAAATATTTTAAATTTTTAAAGTTTCAATGCCTCTGATACGAGAAGCATTCAAAGATGTTGAGA
TTTGTAAGAACTGTCAAGCATAATCTTTAAGACATCTAAACAAAACATTTTAAATTTTTAAAGTT
TTAATACCTCTGATACAAAGAACATTAAAAGATATCAAAATTTGTAAGACCTCTAGGCATAATCT
CTAAAACTCTCAAG
Found at i:5418729 original size:15 final size:14
Alignment explanation
Indices: 5418705--5418735 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
5418695 AATCTTAATT
5418705 ATAAAAAAATAAAA
1 ATAAAAAAATAAAA
5418719 ATAATAAAAATAAAA
1 ATAA-AAAAATAAAA
5418734 AT
1 AT
5418736 TTCAATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
ATAAAAAAATAAAA
Found at i:5420598 original size:19 final size:20
Alignment explanation
Indices: 5420574--5420613 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
5420564 AAAAAAAAAG
5420574 TATTAAAAAAA-TTATCTAA
1 TATTAAAAAAATTTATCTAA
5420593 TATTAAAAAAATTTATCTAA
1 TATTAAAAAAATTTATCTAA
5420613 T
1 T
5420614 CTTGTAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
TATTAAAAAAATTTATCTAA
Found at i:5420716 original size:13 final size:13
Alignment explanation
Indices: 5420698--5420722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5420688 ATTTTTTTTA
5420698 AAAAAATAAAAAT
1 AAAAAATAAAAAT
5420711 AAAAAATAAAAA
1 AAAAAATAAAAA
5420723 GTTACATGTG
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:5421150 original size:16 final size:17
Alignment explanation
Indices: 5421126--5421181 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 17
5421116 ATAATATTTG
5421126 TAATA-AATAAAAATAT
1 TAATATAATAAAAATAT
**
5421142 TAA-ATAATAAATTTAT
1 TAATATAATAAAAATAT
*
5421158 TAATATAAT-AATATAT
1 TAATATAATAAAAATAT
*
5421174 AAATATAA
1 TAATATAA
5421182 AATGAAATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 28 0.82
17 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATATAATAAAAATAT
Found at i:5422131 original size:3 final size:3
Alignment explanation
Indices: 5422123--5422155 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5422113 GCTTAAACAA
5422123 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5422156 TTTTAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5422381 original size:61 final size:61
Alignment explanation
Indices: 5422286--5422402 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
5422276 ATAAAAATCA
5422286 ACAAAGACCAATTCTACCTACTATAAAAGGTTTTTGTCAATAAAAGCAGCTGTGTGCATAT
1 ACAAAGACCAATTCTACCTACTATAAAAGGTTTTTGTCAATAAAAGCAGCTGTGTGCATAT
* * * * *
5422347 ACAAAGACCAATTCTATCTACTGTTATAGGTTTTTGTCAATAAAAGCAGGTGTGTG
1 ACAAAGACCAATTCTACCTACTATAAAAGGTTTTTGTCAATAAAAGCAGCTGTGTG
5422403 TATACATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (61 bp):
ACAAAGACCAATTCTACCTACTATAAAAGGTTTTTGTCAATAAAAGCAGCTGTGTGCATAT
Found at i:5424741 original size:2 final size:2
Alignment explanation
Indices: 5424734--5424769 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5424724 CGATAAATAC
5424734 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5424770 GTGATAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5428309 original size:39 final size:35
Alignment explanation
Indices: 5428236--5428314 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 35
5428226 AAAAATAAAG
*
5428236 ATTAAAAATAAAAAAATTATTAATTTAATAATTAA
1 ATTAAAAATAAAAAAATTATAAATTTAATAATTAA
*
5428271 ATTATAAAATAAAAAACAATTATAAATTTTAATCATTAA
1 ATTA-AAAAT-AAAAA-AATTATAAA-TTTAATAATTAA
5428310 ATTAA
1 ATTAA
5428315 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
35 4 0.11
36 5 0.13
37 5 0.13
38 9 0.24
39 15 0.39
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (35 bp):
ATTAAAAATAAAAAAATTATAAATTTAATAATTAA
Found at i:5428812 original size:28 final size:27
Alignment explanation
Indices: 5428758--5428823 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
5428748 ATTTTTATCT
*
5428758 TATATATTTAA-ATAATTTTTTAATAAA
1 TATATA-TTAATATAATTTTTCAATAAA
*
5428785 TATATATTAATATATATTTTTCCATAAA
1 TATATATTAATATA-ATTTTTCAATAAA
5428813 -AGTATATTAAT
1 TA-TATATTAAT
5428824 TTTAATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 4 0.12
27 10 0.29
28 20 0.59
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (27 bp):
TATATATTAATATAATTTTTCAATAAA
Found at i:5429416 original size:21 final size:22
Alignment explanation
Indices: 5429374--5429418 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
5429364 ATTGATAGGT
*
5429374 TTTAATAAAAATATCAATAATA
1 TTTAATAAAAATATCAAAAATA
* *
5429396 TTTAA-AAAATTATTAAAAATA
1 TTTAATAAAAATATCAAAAATA
5429417 TT
1 TT
5429419 ATTTATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAATAAAAATATCAAAAATA
Found at i:5429490 original size:26 final size:27
Alignment explanation
Indices: 5429448--5429500 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
5429438 TAAATAGTTA
*
5429448 TTTAACAATAAACATTT-TATTAAAAT
1 TTTAACAATAAACATTTATATAAAAAT
*
5429474 TTTAACTAA-AAATATTTATATAAAAAT
1 TTTAAC-AATAAACATTTATATAAAAAT
5429501 ATATCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (27 bp):
TTTAACAATAAACATTTATATAAAAAT
Found at i:5436524 original size:27 final size:27
Alignment explanation
Indices: 5436494--5436549 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
5436484 ATCTAATACT
5436494 AAAAA-ATTAACAAAAATACAAATACAA
1 AAAAACATT-ACAAAAATACAAATACAA
* * *
5436521 AAAAACCTTACTAAAATTCAAATACAA
1 AAAAACATTACAAAAATACAAATACAA
5436548 AA
1 AA
5436550 TCATAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (27 bp):
AAAAACATTACAAAAATACAAATACAA
Found at i:5452809 original size:256 final size:257
Alignment explanation
Indices: 5452306--5452820 Score: 757
Period size: 256 Copynumber: 2.0 Consensus size: 257
5452296 GGGTGTTCCC
* *
5452306 TACATTTGCACTCCGACACATAAGTCAGTAGAGATTAGGTCGAAAAAAAAAAAGAGGAAGGAGAA
1 TACATTTGCACTCCGACACACAAGTCAATAGAGATTAGGTCG-AAAAAAAAAAGAGGAAGGAGAA
* *
5452371 AGAAAAAAAAGTAGGTGGGATGAATCTAGCTTTATGGTACTTGAGTCTTCATATTTATAGGTAAG
65 AGAAAAAAAAGTAGGTGGGATAAATCTAGCTTTATGGTACTTGAGTCTTCATATTTATAAGTAAG
5452436 CTGAAGGGGACCATAAGGGGACAATTAGGATAGGGCTGAGCTGAAGTAACACTGATCATGTCAGG
130 CTGAAGGGGACCATAAGGGGACAATTAGGATAGGGCTGAGCTGAAGTAACACTGATCATGTCAGG
* * **
5452501 CCAACCCAACATATCAAATTGGCACAAATGATAAAGATACCCCTGGTTATCTGCTGAAGGCTT
195 CCAACCCAACATATCAAATTGGCACAAATGACAAAAATACCCCTAATTATCTGCTGAAGGCTT
* * * * *
5452564 TACATTTGCACTTCGACACGCAAGTCAATAGAGATTAGGTTG-AAAAAAAAAGTATGAAGGAGAG
1 TACATTTGCACTCCGACACACAAGTCAATAGAGATTAGGTCGAAAAAAAAAAG-AGGAAGGAGAA
5452628 AGAAAAAAAAGTAGGTGGGATAAATCTAGCTTTATGGTACTTGAGTCTTCATATTTATAAGTAAG
65 AGAAAAAAAAGTAGGTGGGATAAATCTAGCTTTATGGTACTTGAGTCTTCATATTTATAAGTAAG
* * * * * *
5452693 TTG-GGGGGACCATAATGGGACAATTAGGATAGGGCTGAGCTGAGGTAGCACTGA-CTATGTTAG
130 CTGAAGGGGACCATAAGGGGACAATTAGGATAGGGCTGAGCTGAAGTAACACTGATC-ATGTCAG
* * * * * *
5452756 GCCAACCTAACATGTCAAGTTGGTACAAATGACAAAAATACCCTTAATTATCTGTTGAAGGCTT
194 GCCAACCCAACATATCAAATTGGCACAAATGACAAAAATACCCCTAATTATCTGCTGAAGGCTT
5452820 T
1 T
5452821 GAAAGAGGAA
Statistics
Matches: 230, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
255 1 0.00
256 118 0.51
257 74 0.32
258 37 0.16
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (257 bp):
TACATTTGCACTCCGACACACAAGTCAATAGAGATTAGGTCGAAAAAAAAAAGAGGAAGGAGAAA
GAAAAAAAAGTAGGTGGGATAAATCTAGCTTTATGGTACTTGAGTCTTCATATTTATAAGTAAGC
TGAAGGGGACCATAAGGGGACAATTAGGATAGGGCTGAGCTGAAGTAACACTGATCATGTCAGGC
CAACCCAACATATCAAATTGGCACAAATGACAAAAATACCCCTAATTATCTGCTGAAGGCTT
Found at i:5458209 original size:22 final size:22
Alignment explanation
Indices: 5458184--5458229 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
5458174 AACTTAATTT
*
5458184 TAATTTTTATTTTTTATATATA
1 TAATTTTTATTTTTAATATATA
*
5458206 TAATTTTTATTTTTAATTTATA
1 TAATTTTTATTTTTAATATATA
5458228 TA
1 TA
5458230 TATATGTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TAATTTTTATTTTTAATATATA
Found at i:5458209 original size:28 final size:28
Alignment explanation
Indices: 5458178--5458234 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
5458168 TTATTAAACT
* *
5458178 TAATTTTAATTTTTATTTTTTATATATA
1 TAATTTTAATTTTTAATTTATATATATA
*
5458206 TAATTTTTATTTTTAATTTATATATATA
1 TAATTTTAATTTTTAATTTATATATATA
5458234 T
1 T
5458235 GTGAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TAATTTTAATTTTTAATTTATATATATA
Found at i:5458851 original size:34 final size:34
Alignment explanation
Indices: 5458807--5458889 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
5458797 ATATATATAT
* * * *
5458807 ATATCCAAAAAGTTTGACA-ATCTTTTGAAAATGC
1 ATATCCAAAAAATTT-AAAGATATTTTGAAAATAC
*
5458841 ATATCTAAAAAATTTAAAGATATTTTGAAAATAC
1 ATATCCAAAAAATTTAAAGATATTTTGAAAATAC
*
5458875 ATATCCAGAAAATTT
1 ATATCCAAAAAATTT
5458890 TTAAATTATC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 2 0.05
34 39 0.95
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (34 bp):
ATATCCAAAAAATTTAAAGATATTTTGAAAATAC
Found at i:5459000 original size:34 final size:34
Alignment explanation
Indices: 5458921--5458991 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
5458911 TTTCAAAAGC
* * *
5458921 TTTTCGAAA-ATGCATTTTTGGAAGGCCTTTAAA
1 TTTTCCAAATATGTATTTTCGGAAGGCCTTTAAA
**
5458954 TTTTCCAAATATGTATTTTCGGAAGGTTTTTAAA
1 TTTTCCAAATATGTATTTTCGGAAGGCCTTTAAA
5458988 TTTT
1 TTTT
5458992 TTGAATATGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 8 0.25
34 24 0.75
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (34 bp):
TTTTCCAAATATGTATTTTCGGAAGGCCTTTAAA
Found at i:5461557 original size:2 final size:2
Alignment explanation
Indices: 5461550--5461574 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5461540 AATTATGATG
5461550 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 T
5461575 TAAAGGGCTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5462747 original size:21 final size:21
Alignment explanation
Indices: 5462700--5462748 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5462690 ATCATTAATT
* * *
5462700 TTAATTTTATTATTACAATAC
1 TTAATCTTATGATTACAATAA
*
5462721 TCAATCTTATGATTACAATAA
1 TTAATCTTATGATTACAATAA
5462742 TTAATCT
1 TTAATCT
5462749 CAATATTATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAATCTTATGATTACAATAA
Found at i:5463072 original size:16 final size:17
Alignment explanation
Indices: 5463051--5463082 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5463041 TAAAAATTAT
5463051 AAAATA-TATATTTTTA
1 AAAATATTATATTTTTA
5463067 AAAATATTATATTTTT
1 AAAATATTATATTTTT
5463083 TATATGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAATATTATATTTTTA
Found at i:5463808 original size:15 final size:15
Alignment explanation
Indices: 5463784--5463813 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5463774 CTCATATACA
*
5463784 AAATTTTTTCATAAG
1 AAATTCTTTCATAAG
5463799 AAATTCTTTCATAAG
1 AAATTCTTTCATAAG
5463814 TTGTTGTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (15 bp):
AAATTCTTTCATAAG
Found at i:5465260 original size:32 final size:32
Alignment explanation
Indices: 5465199--5465279 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
5465189 TACCAATGAA
5465199 ATCAAATGAAATCTAAA--TGCATTAATATTTT
1 ATCAAATGAAATC-AAATGTGCATTAATATTTT
*
5465230 ATCAAATGAAATCAAATGTGCATTAGTATTTT
1 ATCAAATGAAATCAAATGTGCATTAATATTTT
*
5465262 -GCTAAATGAAATCAAATG
1 ATC-AAATGAAATCAAATG
5465280 AAGTCATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
30 3 0.07
31 14 0.31
32 28 0.62
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (32 bp):
ATCAAATGAAATCAAATGTGCATTAATATTTT
Found at i:5465938 original size:20 final size:21
Alignment explanation
Indices: 5465913--5465976 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 21
5465903 ACATGGATTA
*
5465913 ATATTTTATCAAATG-AAATC
1 ATATTTAATCAAATGTAAATC
*
5465933 ATATTTAATGAAATGTAAAT-
1 ATATTTAATCAAATGTAAATC
* *
5465953 GTA-TTAATCAAATATAAATTC
1 ATATTTAATCAAATGTAAA-TC
5465974 ATA
1 ATA
5465977 AAATATTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 13 0.37
20 16 0.46
21 6 0.17
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (21 bp):
ATATTTAATCAAATGTAAATC
Found at i:5466398 original size:262 final size:269
Alignment explanation
Indices: 5466020--5466536 Score: 798
Period size: 262 Copynumber: 1.9 Consensus size: 269
5466010 ATTAATTTGA
*
5466020 TATATTTGCTTTATATATTTACATACATTATGAAATACATCAATTATTCAAATGGATACTATATT
1 TATATTTGCTTTATATATTTACA-ACATTA-GAAATACATCAATTA-TC--ATGAATACTATATT
* *
5466085 TAATCAAATATAAAATGTATTAAATAATTAATTAGAAAATCAATTATTTTATAATTATAATTATA
61 TAATCAAATATAAAATGTATCAAATAATTAATTAGAAAATCAACTATTTTATAATTATAATTATA
*
5466150 GTATTTATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAATTTAAGAAAATTTTAAAA
126 GTATTTATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAGAAAATTTTAAAA
*
5466215 TTTTAATAC-TTTTAATATGAATTGAATTGAGAGTGATTTAAAATCAAT-ATAAAATATAATCAA
191 ATTTAATACTTTTTAATATGAATTGAATTGAGAGTGATTTAAAATCAATAATAAAA-ATAATCAA
5466278 TCTAGTTTTTTAAAT
255 TCTAGTTTTTTAAAT
5466293 TATATTTGCTTTATATATTTAC-ACA-TA-AAATACATCAATTA-C-TGAATACTATATTTAATC
1 TATATTTGCTTTATATATTTACAACATTAGAAATACATCAATTATCATGAATACTATATTTAATC
* * * *
5466353 AAATAT-AAATGTATCAAATAATTGATTAGAGAATCAACTATTTTATAATTGTAATTGTAGTATT
66 AAATATAAAATGTATCAAATAATTAATTAGAAAATCAACTATTTTATAATTATAATTATAGTATT
* *
5466417 TATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAATTATGAAATTTTTAAAAATTTA
131 TATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAGAAAATTTTAAAAATTTA
* * *
5466482 GTACTTTTTAATATGAATTGAATTGAGAGTGATTTAAGATTAATAATAAAAATAA
196 ATACTTTTTAATATGAATTGAATTGAGAGTGATTTAAAATCAATAATAAAAATAA
5466537 AAATAAAAAA
Statistics
Matches: 228, Mismatches: 14, Indels: 14
0.89 0.05 0.05
Matches are distributed among these distances:
262 116 0.51
263 64 0.28
264 6 0.03
266 1 0.00
268 14 0.06
270 2 0.01
271 3 0.01
273 22 0.10
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (269 bp):
TATATTTGCTTTATATATTTACAACATTAGAAATACATCAATTATCATGAATACTATATTTAATC
AAATATAAAATGTATCAAATAATTAATTAGAAAATCAACTATTTTATAATTATAATTATAGTATT
TATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAGAAAATTTTAAAAATTTA
ATACTTTTTAATATGAATTGAATTGAGAGTGATTTAAAATCAATAATAAAAATAATCAATCTAGT
TTTTTAAAT
Found at i:5467390 original size:807 final size:799
Alignment explanation
Indices: 5465920--5468199 Score: 3308
Period size: 807 Copynumber: 2.9 Consensus size: 799
5465910 TTAATATTTT
* * *
5465920 ATCAAATGAAATCATATTTAATGAAATGTAAATGTATTAATCAAATATAAATTCATAAAATATTT
1 ATCAAATGAAATCATATTTAATGAAATATAAATGTATCAATCAAATATAAATTAATAAAATATTT
* * *
5465985 TATTCCATTAATTTAATTATGAATAATTAATTTGATATATTTGCTTTATATAT-TTACATACATT
66 TATTCCATTAATTTAATTATGAAGAATTAATTTGATATATTTACTTTATATATATTA-ATACATC
* * *
5466049 ATGAAATACATCAATTATTCAAATGGATACTATATTTAATCAAATATAAAATGTATTAAATAATT
130 ATGAAATACATCAATTACTCAAATGGATATTATATTTAATCAAATAT-AAATGTATCAAATAATT
*
5466114 AATTAGAAAATCAATTATTTTATAATTATAATTATAGTATTTATTAATTTATTAATTATATATTG
194 AATTAGAGAATCAATTATTTTATAATTATAATTATAGTATTTATTAATTTATTAATTATATATTG
*
5466179 ATTGATTTAATTTGTCAATTTAAGAAAATTTTAAAATTTTAATACTTTTAATATGAATTGAATTG
259 ATTGATTTAATTTGTCAAATTAAGAAAATTTTAAAATTTTAATACTTTTAATATGAATTGAATTG
* * *
5466244 AGAGTGATTTAAAAT--C-AA-T---ATA-AAATATAATCAATCTAGTTTTTTAAATTATATTTG
324 AGAGTGATTTAAAATCACTAATTAAAACATAAATATAATCAATTTAGTTTTTTGAATTATATTTG
* * *
5466301 CTTTATATATTTACACATAAAATACATCAATTACTGAATACTATATTTAATCAAATATAAATGTA
389 CTTTATATATTTACACATGAAATACATTAATTACTGGATACTATATTTAATCAAATATAAATGTA
5466366 TCAAATAATTGATTAGAGAATCAACTATTTTATAATTGTAATTGTAGTATTTATTAATTTATTAA
454 TCAAATAATTGATTAGAGAATCAACTATTTTATAATTGTAATTGTAG-------T-ATTTATTAA
*
5466431 TTATATATTGATTGATTTAATTTGTCAAATTATGAAATTTTTAAAAATTTAGTACTTTTTAATAT
511 TTATATATTGATTGATTTAATTTGTCAAATTA-GAAATTTTTAAAATTTTAGTAC-TTTTAATAT
* ** *
5466496 GAATTGAATTGAGAGTGATTTAAGATTAATAATAAAAATA-AAA-ATAA--AAAATAATTAATTT
574 GAATTGAATTGAGAGTGATTTAAGGTTAATAATAAAAATATAAATATAATCAATTTAA-TATTTT
* * * * ** *
5466557 -AGT-TTTTTGAGTT----ATTTTTAAATAAAATAAAATATATTTATCATGTGT-AGCGTGATGA
638 AATTATTTTTAAATTAAAAATTATTAAATAAAATAAAATATATTTATCAAATGTCA-CATGATGA
* *
5466615 TTTTTAAAACAATTCACATATCAACATTTTAAGCCATCCACATAGGATTTTTT-TCATTTTTGCC
702 TTTTTAAAACAATTAACATATCAACATTTTAAGCCATCCACATAGGATTTTTTCT-ATTTTTGAC
5466679 AAAAGCTTTGGCTTTTATATATTTATATAAGAAA
766 AAAAGCTTTGGCTTTTATATATTTATATAAGAAA
*
5466713 ATCAAATGAAATCATATTTAATGAAATATAAATGTATCAATCAAATATAAATTAATAAGATATTT
1 ATCAAATGAAATCATATTTAATGAAATATAAATGTATCAATCAAATATAAATTAATAAAATATTT
5466778 TATTCCATTAATTTAATTATGAAGAATTAATTTGATATATTTACTTTATATATTAACACTTGAAA
66 TATTCCATTAATTTAATTATGAAGAATTAATTTGATATATTTACTTTATATA-T---A-TT--AA
* *
5466843 TACATCATGAAATACATTAATTACTCAAATGGATATTATACTTAATCAAATATAAATGTATCAAA
124 TACATCATGAAATACATCAATTACTCAAATGGATATTATATTTAATCAAATATAAATGTATCAAA
*
5466908 TAATTAATTAGAGAATCAATTA-TTTATAATTATAATTGTAGTATTTATTAATTTATTAATTATA
189 TAATTAATTAGAGAATCAATTATTTTATAATTATAATTATAGTATTTATTAATTTATTAATTATA
* * *
5466972 TATTGATTGATTTAATTTATCAAATTAAGAAATTTTTAAAATTTTAATACTTTTAATAGGAATTG
254 TATTGATTGATTTAATTTGTCAAATTAAGAAAATTTTAAAATTTTAATACTTTTAATATGAATTG
*
5467037 AATTGAGAGTGATTTAAAATCACTAATTAAAACATAAATATAATCAATTTAGTTTTTTTGAATGA
319 AATTGAGAGTGATTTAAAATCACTAATTAAAACATAAATATAATCAATTTAG-TTTTTTGAATTA
* * *
5467102 TATTTGCTTTATATATTTACATATGAAATACATTAATTATTGGATATTATATTTAATCAAATATA
383 TATTTGCTTTATATATTTACACATGAAATACATTAATTACTGGATACTATATTTAATCAAATATA
5467167 AATGTATCAAATAATTGATTAGAGAATCAACTATTTTATAATTGTAATTGTAGTATTTATTAATT
448 AATGTATCAAATAATTGATTAGAGAATCAACTATTTTATAATTGTAATTGTAGTATTTATTAATT
* * * * *
5467232 ATATATTGATTGATTTAATTTTTCAAATTA-AAATTTTTAAAATTTTAATACTTTCAGTATAAAT
513 ATATATTGATTGATTTAATTTGTCAAATTAGAAATTTTTAAAATTTTAGTACTTTTAATATGAAT
* * *
5467296 TGAATTGAGAGTTATTTAAGGTTGATAATAAAAATATAAATATAATCAATTTAGTATTTTGAATT
578 TGAATTGAGAGTGATTTAAGGTTAATAATAAAAATATAAATATAATCAATTTAATATTTT-AATT
* * * *
5467361 ATTTTTAAATTAAAAATGTATTGAATAAAATAAAATACATTTATTAAATGTCACATGATGCTTTT
642 ATTTTTAAATTAAAAAT-TATTAAATAAAATAAAATATATTTATCAAATGTCACATGATGATTTT
* * * ** * *
5467426 TAAAACCATTAACATGTCAACATTTTAAGCCGTTTACATATGATTTTTTCTATTTTTGACAAAAT
706 TAAAACAATTAACATATCAACATTTTAAGCCATCCACATAGGATTTTTTCTATTTTTGACAAAAG
5467491 CTTTGGCTTTTATATATTTATATAAGAAA
771 CTTTGGCTTTTATATATTTATATAAGAAA
*
5467520 ATCAAATGAAATAATATTTAATGAAATATAAATGTATCAATCAAATATAAATTAATAAAATATTT
1 ATCAAATGAAATCATATTTAATGAAATATAAATGTATCAATCAAATATAAATTAATAAAATATTT
** *
5467585 TATTTTATTAATTTATTTATGAAGAATTAATTTGATATATTTAC-TT-TATATATT--TACA-CA
66 TATTCCATTAATTTAATTATGAAGAATTAATTTGATATATTTACTTTATATATATTAATACATCA
*
5467645 TGAAATACATCAATTACTCAAATGAATATTATATTTAATCAAATATAAATGTATCAAATAATTAA
131 TGAAATACATCAATTACTCAAATGGATATTATATTTAATCAAATATAAATGTATCAAATAATTAA
* * *
5467710 TTAGAGAAACAACTATTTTATAATTGTAATTATAGTATTTATTAATTTATTAATTATATATTGAT
196 TTAGAGAATCAATTATTTTATAATTATAATTATAGTATTTATTAATTTATTAATTATATATTGAT
5467775 TGATTTAATTTGTCAAATTAAGAAAATTTTAAAATTTTAATACTTTTAATATGAATTGAATTGAG
261 TGATTTAATTTGTCAAATTAAGAAAATTTTAAAATTTTAATACTTTTAATATGAATTGAATTGAG
* *
5467840 AGTGATTTAAAATCAATAATAAAAACATAAATATAATCAATTTAG-TTTTTGAATTTATATTTG-
326 AGTGATTTAAAATCACTAATTAAAACATAAATATAATCAATTTAGTTTTTTGAA-TTATATTTGC
* *
5467903 TTTATATATTTACACATGAAATACATTAATTACT-GATACTATATTTAATTAAATATAAATATAT
390 TTTATATATTTACACATGAAATACATTAATTACTGGATACTATATTTAATCAAATATAAATGTAT
* ** * * *
5467967 CAAATAATTTATTATTGAATTAATTATTTTATAATTGTAATTATAGTATTTATTAATTATATATT
455 CAAATAATTGATTAGAGAATCAACTATTTTATAATTGTAATTGTAGTATTTATTAATTATATATT
*
5468032 GATTGATTTAATTTGTCAAATTAAGAAATTTTTAAAATTTTAGTAATTTTAATATGAATTGAATT
520 GATTGATTTAATTTGTCAAATT-AGAAATTTTTAAAATTTTAGTACTTTTAATATGAATTGAATT
* * * * *
5468097 TAGAATGATATAAGGTTAATAATAAAAACATAAATATAATCAATTTAATTTTTTAAATTATTTTT
584 GAGAGTGATTTAAGGTTAATAATAAAAATATAAATATAATCAATTTAATATTTT-AATTATTTTT
*
5468162 AAATTAAAAATATATAAAATAAAATAAAATATATTTAT
648 AAATTAAAAAT-TATTAAATAAAATAAAATATATTTAT
5468200 TAGATGTTAT
Statistics
Matches: 1343, Mismatches: 109, Indels: 68
0.88 0.07 0.04
Matches are distributed among these distances:
793 218 0.16
794 42 0.03
795 210 0.16
796 199 0.15
797 22 0.02
798 126 0.09
799 79 0.06
800 57 0.04
801 6 0.00
802 9 0.01
804 1 0.00
805 6 0.00
806 20 0.01
807 346 0.26
808 2 0.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (799 bp):
ATCAAATGAAATCATATTTAATGAAATATAAATGTATCAATCAAATATAAATTAATAAAATATTT
TATTCCATTAATTTAATTATGAAGAATTAATTTGATATATTTACTTTATATATATTAATACATCA
TGAAATACATCAATTACTCAAATGGATATTATATTTAATCAAATATAAATGTATCAAATAATTAA
TTAGAGAATCAATTATTTTATAATTATAATTATAGTATTTATTAATTTATTAATTATATATTGAT
TGATTTAATTTGTCAAATTAAGAAAATTTTAAAATTTTAATACTTTTAATATGAATTGAATTGAG
AGTGATTTAAAATCACTAATTAAAACATAAATATAATCAATTTAGTTTTTTGAATTATATTTGCT
TTATATATTTACACATGAAATACATTAATTACTGGATACTATATTTAATCAAATATAAATGTATC
AAATAATTGATTAGAGAATCAACTATTTTATAATTGTAATTGTAGTATTTATTAATTATATATTG
ATTGATTTAATTTGTCAAATTAGAAATTTTTAAAATTTTAGTACTTTTAATATGAATTGAATTGA
GAGTGATTTAAGGTTAATAATAAAAATATAAATATAATCAATTTAATATTTTAATTATTTTTAAA
TTAAAAATTATTAAATAAAATAAAATATATTTATCAAATGTCACATGATGATTTTTAAAACAATT
AACATATCAACATTTTAAGCCATCCACATAGGATTTTTTCTATTTTTGACAAAAGCTTTGGCTTT
TATATATTTATATAAGAAA
Found at i:5479226 original size:64 final size:64
Alignment explanation
Indices: 5479099--5479226 Score: 193
Period size: 64 Copynumber: 2.0 Consensus size: 64
5479089 CATTGCTCTT
* * * ** *
5479099 GGTTTGTCTTTAGATAGGTAGACAATGGCATGAGTTCATTAAACTTGTCATATATGTCCTTGAA
1 GGTTTGTCTTCAGATAGGTAGACAATGGCATAAGTTCATTAAACTCGTCATATACCTCATTGAA
*
5479163 GGTTTGTCTTCAGATAGGTAGATAATGGCATAAGTTCATTAAACTCGTCATATACCTCATTGAA
1 GGTTTGTCTTCAGATAGGTAGACAATGGCATAAGTTCATTAAACTCGTCATATACCTCATTGAA
5479227 CACAACAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (64 bp):
GGTTTGTCTTCAGATAGGTAGACAATGGCATAAGTTCATTAAACTCGTCATATACCTCATTGAA
Found at i:5481218 original size:27 final size:27
Alignment explanation
Indices: 5481175--5481238 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 27
5481165 TAAGTCTATA
*
5481175 TTTTTTATTTCTTCA-TTTTATTTTTAT
1 TTTTTTATTTCTACATTTTTA-TTTTAT
5481202 TTTTTGTATTT-TACATTTTTATTTTAT
1 TTTTT-TATTTCTACATTTTTATTTTAT
5481229 TTTTATTATT
1 TTTT-TTATT
5481239 ATTATTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 22 0.67
28 11 0.33
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (27 bp):
TTTTTTATTTCTACATTTTTATTTTAT
Found at i:5481290 original size:20 final size:20
Alignment explanation
Indices: 5481189--5481287 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
5481179 TTATTTCTTC
* *
5481189 ATTTTATTTTTATTTTTTGT
1 ATTTTATTATTATTTTTTAT
* *
5481209 ATTTTA-CATTTTTATTTTAT
1 ATTTTATTATTATT-TTTTAT
5481229 -TTTTATTATTATTATTTTAT
1 ATTTTATTATTATT-TTTTAT
*
5481249 ATATGTA-TA-TATATTTTT-T
1 AT-TTTATTATTAT-TTTTTAT
*
5481268 CTTTTATTATTATTTTTTAT
1 ATTTTATTATTATTTTTTAT
5481288 CTTAGGTATT
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
18 3 0.05
19 18 0.29
20 34 0.55
21 4 0.06
22 3 0.05
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (20 bp):
ATTTTATTATTATTTTTTAT
Found at i:5481741 original size:9 final size:10
Alignment explanation
Indices: 5481718--5481742 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5481708 TAGCAAAAAT
5481718 TTTTTGGAGA
1 TTTTTGGAGA
5481728 TTTTTGGAGA
1 TTTTTGGAGA
5481738 TTTTT
1 TTTTT
5481743 TTTTGGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (10 bp):
TTTTTGGAGA
Found at i:5482317 original size:5 final size:5
Alignment explanation
Indices: 5482295--5482446 Score: 79
Period size: 5 Copynumber: 30.2 Consensus size: 5
5482285 TTTGAATTTG
** **
5482295 TTTA- TTTA- TTTA- TTTAT TTTA- TTTAT TTTA- TTTAT TAGA- TTTGG
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
* *
5482339 TTTAT TTAATAT TCT-T TTTAT CTTTAT TTTATT TTTATT TTTGT TTTACT
1 TTTAT TT--TAT TTTAT TTTAT -TTTAT TTTA-T TTTA-T TTTAT TTTA-T
*
5482389 TTT-C TTTAT TTTAT TTTATT TTTAT TTT-T ATTTAT TTTCACT TTTAT
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT -TTTAT TTT-A-T TTTAT
*
5482436 TTTGT TTTAT T
1 TTTAT TTTAT T
5482447 ATTCTATTTT
Statistics
Matches: 117, Mismatches: 15, Indels: 31
0.72 0.09 0.19
Matches are distributed among these distances:
4 28 0.24
5 54 0.46
6 27 0.23
7 8 0.07
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:5482346 original size:4 final size:4
Alignment explanation
Indices: 5482290--5482330 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
5482280 TTTTTTTTGA
*
5482290 ATTT GTTT ATTT ATTT ATTT ATTTT ATTT ATTTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT A-TTT ATTT A-TTT ATTT ATT
5482331 AGATTTGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 25 0.76
5 8 0.24
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:5482370 original size:11 final size:11
Alignment explanation
Indices: 5482354--5482456 Score: 81
Period size: 11 Copynumber: 9.4 Consensus size: 11
5482344 TTAATATTCT
*
5482354 TTTTATCTTTA
1 TTTTATTTTTA
5482365 TTTTATTTTTA
1 TTTTATTTTTA
5482376 TTTT-TGTTTTA
1 TTTTAT-TTTTA
* *
5482387 CTTT-TCTTTA
1 TTTTATTTTTA
5482397 TTTTA-TTTTA
1 TTTTATTTTTA
5482407 TTTTTATTTTTA
1 -TTTTATTTTTA
*
5482419 -TTTATTTTCA
1 TTTTATTTTTA
*
5482429 CTTTTA-TTTTG
1 -TTTTATTTTTA
5482440 TTTTATTATTCTA
1 TTTTATT-TT-TA
5482453 TTTT
1 TTTT
5482457 CTTTAAATAA
Statistics
Matches: 74, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
10 26 0.35
11 32 0.43
12 11 0.15
13 5 0.07
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:5482374 original size:6 final size:6
Alignment explanation
Indices: 5482353--5482438 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
5482343 TTTAATATTC
* * *
5482353 TTTTTA TCTTTA -TTTTA TTTTTA TTTTT- GTTTTA CTTTTCTT TATTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTT-TA T-TTTTA
* *
5482402 -TTTTA TTTTTA TTTTTA --TTTA TTTTCA CTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
5482439 GTTTTATTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
4 4 0.06
5 13 0.21
6 36 0.58
7 5 0.08
8 4 0.06
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:5482418 original size:32 final size:31
Alignment explanation
Indices: 5482359--5482461 Score: 104
Period size: 32 Copynumber: 3.2 Consensus size: 31
5482349 ATTCTTTTTA
*
5482359 TCTTTATTTTATTTTTATTTTT-GTTTTACTTT
1 TCTTTATTTTA-TTTTATTTTTATTTTTA-TTT
5482391 TCTTTATTTTATTTTATTTTTATTTTTATTT
1 TCTTTATTTTATTTTATTTTTATTTTTATTT
*
5482422 AT-TTTCACTTTTATTTT-GTTTTATTATTCTATTT
1 -TCTTT-A-TTTTATTTTATTTTTATT-TT-TATTT
5482456 TCTTTA
1 TCTTTA
5482462 AATAAAAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
31 16 0.26
32 25 0.40
33 13 0.21
34 8 0.13
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.76
Consensus pattern (31 bp):
TCTTTATTTTATTTTATTTTTATTTTTATTT
Found at i:5482434 original size:12 final size:10
Alignment explanation
Indices: 5482295--5482446 Score: 79
Period size: 9 Copynumber: 15.1 Consensus size: 10
5482285 TTTGAATTTG
5482295 TTTA-TTTA-
1 TTTATTTTAT
5482303 TTTA-TTTAT
1 TTTATTTTAT
5482312 TTTA-TTTAT
1 TTTATTTTAT
5482321 TTTA-TTTAT
1 TTTATTTTAT
** **
5482330 TAGA-TTTGG
1 TTTATTTTAT
5482339 TTTATTTAATAT
1 TTTATTT--TAT
*
5482351 TCT-TTTTAT
1 TTTATTTTAT
5482360 CTTTATTTTATT
1 -TTTATTTTA-T
*
5482372 TTTATTTTTGT
1 TTTA-TTTTAT
*
5482383 TTTACTTTT-C
1 TTTA-TTTTAT
5482393 TTTATTTTAT
1 TTTATTTTAT
5482403 TTTATTTTTAT
1 TTTA-TTTTAT
5482414 TTT-TATTTAT
1 TTTAT-TTTAT
5482424 TTTCACTTTTAT
1 TTT-A-TTTTAT
*
5482436 TTTGTTTTAT
1 TTTATTTTAT
5482446 T
1 T
5482447 ATTCTATTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 26
0.74 0.10 0.17
Matches are distributed among these distances:
8 8 0.07
9 33 0.29
10 27 0.23
11 30 0.26
12 16 0.14
13 1 0.01
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:5482536 original size:58 final size:58
Alignment explanation
Indices: 5482472--5482868 Score: 442
Period size: 59 Copynumber: 6.7 Consensus size: 58
5482462 AATAAAAATA
5482472 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
* * * *
5482530 AAAAAAAAAGTTTTTGAGAAAAAGTTGAAAGTATTAATTTTTCTTGAAAATCAAAGTTTTC
1 AAAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAA-TTTTC
* *
5482591 -AAAGAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
*** * * * * *
5482648 AAAAAAGGGTTTTGGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATCAAGGTTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AA-ATTTTC
* * * *
5482708 -AAAAAATATTTTAGAGGAAAAGTTGAACGCATCAATTTTTCTTAAAAATAAATTTTAAA
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTT--C
* * ** * *
5482767 AAAAAAATCAATTTTTGAGGAAAAGTTGAAAGTATTAATTTTCCTCGAAATTAAAGTTTC
1 AAAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
* *
5482827 AAAAGAATATTTTTGA-GAAAAGTTGAAAGTATTAATTTTTCT
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
5482869 CGCACAAAAA
Statistics
Matches: 285, Mismatches: 41, Indels: 27
0.81 0.12 0.08
Matches are distributed among these distances:
57 34 0.12
58 61 0.21
59 117 0.41
60 28 0.10
61 5 0.02
62 40 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (58 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
Found at i:5482694 original size:117 final size:117
Alignment explanation
Indices: 5482477--5482868 Score: 531
Period size: 117 Copynumber: 3.3 Consensus size: 117
5482467 AAATAAAAAA
5482477 AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAAAGTT
1 AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC-AAAAAAAAGTT
* *
5482542 TTTGAGAAAAAGTTGAAAGTATTAATTTTTCTTGAAAATCAAAGTTTTCAAAG
65 TTTGAGGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATCAAAGTTTTCAAAG
* **
5482595 AATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGGTT
1 AATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAAGTT
* * * * *
5482659 TTGGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATCAAGGTTTTCAAAA
65 TTTGAGGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATCAAAGTTTTCAAAG
* * * *
5482712 AATATTTTAGAGGAAAAGTTGAACGCATCAATTTTTCTTAAAAATAAATTTTAAAAAAAAAATCA
1 AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTT--CAAAAAAA--A
* * *
5482777 ATTTTTGAGGAAAAGTTGAAAGTATTAATTTTCCTCG-AAATTAAAG-TTTCAAAAG
62 GTTTTTGAGGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATCAAAGTTTTC-AAAG
*
5482832 AATATTTTTGA-GAAAAGTTGAAAGTATTAATTTTTCT
1 AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
5482869 CGCACAAAAA
Statistics
Matches: 238, Mismatches: 29, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
117 102 0.43
118 51 0.21
119 33 0.14
120 20 0.08
121 32 0.13
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (117 bp):
AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAAGTTT
TTGAGGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATCAAAGTTTTCAAAG
Found at i:5486419 original size:11 final size:10
Alignment explanation
Indices: 5486405--5486437 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
5486395 AAAAGGTCTC
5486405 AAAAATAAAA
1 AAAAATAAAA
5486415 AAAAATAAAA
1 AAAAATAAAA
*
5486425 AAAAAGAAAA
1 AAAAATAAAA
5486435 AAA
1 AAA
5486438 TGCCACACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:5486779 original size:11 final size:11
Alignment explanation
Indices: 5486765--5486822 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
5486755 ATAATGGATG
5486765 AAAAATGAGAAA
1 AAAAATGAG-AA
*
5486777 AAAAATGATAA
1 AAAAATGAGAA
**
5486788 AAAAAAAAGAA
1 AAAAATGAGAA
*
5486799 AAAAA-GAAGGA
1 AAAAATG-AGAA
5486810 AAAAATGAGAA
1 AAAAATGAGAA
5486821 AA
1 AA
5486823 TGAAAAAAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (11 bp):
AAAAATGAGAA
Found at i:5486782 original size:12 final size:12
Alignment explanation
Indices: 5486765--5486803 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5486755 ATAATGGATG
5486765 AAAAATGAGAAA
1 AAAAATGAGAAA
*
5486777 AAAAATGATAAA
1 AAAAATGAGAAA
*
5486789 AAAAA-AAGAAA
1 AAAAATGAGAAA
5486800 AAAA
1 AAAA
5486804 GAAGGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (12 bp):
AAAAATGAGAAA
Found at i:5488125 original size:41 final size:41
Alignment explanation
Indices: 5488080--5488220 Score: 219
Period size: 41 Copynumber: 3.4 Consensus size: 41
5488070 CATGATTGTC
*
5488080 AAGGAGTAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTA
1 AAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTA
*
5488121 AAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTTTGTTTA
1 AAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTA
* * * *
5488162 GATGAGCAATTTACTTTTCAAAGTCGCGGTGCCTCTGTTTA
1 AAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTA
*
5488203 GAGGAGCAATTTATTTTT
1 AAGGAGCAATTTATTTTT
5488221 TTCAAAGTTG
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 91 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.40
Consensus pattern (41 bp):
AAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTA
Found at i:5488531 original size:17 final size:19
Alignment explanation
Indices: 5488489--5488532 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
5488479 TTTCTTCATT
*
5488489 TTATTTTTTGTATTTTGCA
1 TTATTATTTGTATTTTGCA
*
5488508 TTTTTATTT-TATTTT-CA
1 TTATTATTTGTATTTTGCA
5488525 TTATTATT
1 TTATTATT
5488533 ATTTTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 9 0.41
18 6 0.27
19 7 0.32
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (19 bp):
TTATTATTTGTATTTTGCA
Found at i:5488534 original size:20 final size:19
Alignment explanation
Indices: 5488483--5488539 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
5488473 TTTTTTTTTC
*
5488483 TTCATTTTATTTTTTGTATT
1 TTCATTTTATTATTT-TATT
5488503 TTGCA-TTT-TTATTTTATT
1 TT-CATTTTATTATTTTATT
5488521 TTCATTATTATTATTTTAT
1 TTCATT-TTATTATTTTAT
5488540 ATATGTATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 2 0.06
18 7 0.22
19 7 0.22
20 14 0.44
21 2 0.06
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.72
Consensus pattern (19 bp):
TTCATTTTATTATTTTATT
Found at i:5489038 original size:16 final size:17
Alignment explanation
Indices: 5489017--5489049 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5489007 TTAGCAAAAA
5489017 TTTTTTGGAG-ATTTTT
1 TTTTTTGGAGAATTTTT
*
5489033 TTTTTTTGAGAATTTTT
1 TTTTTTGGAGAATTTTT
5489050 GAAAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (17 bp):
TTTTTTGGAGAATTTTT
Found at i:5489039 original size:17 final size:17
Alignment explanation
Indices: 5489017--5489049 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5489007 TTAGCAAAAA
5489017 TTTTTTG-GAGATTTTTT
1 TTTTTTGAGA-ATTTTTT
5489034 TTTTTTGAGAATTTTT
1 TTTTTTGAGAATTTTT
5489050 GAAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (17 bp):
TTTTTTGAGAATTTTTT
Found at i:5489596 original size:11 final size:11
Alignment explanation
Indices: 5489564--5489692 Score: 54
Period size: 11 Copynumber: 11.6 Consensus size: 11
5489554 TTTTTTTTAA
5489564 TTTATTTATTT
1 TTTATTTATTT
*
5489575 CTTTGTTTATTT
1 -TTTATTTATTT
*
5489587 TTTATTTATTAC
1 TTTATTTATT-T
*
5489599 ATTAGGTTTATTT
1 TTTA--TTTATTT
**
5489612 AATATTCT-TTT
1 TTTATT-TATTT
* *
5489623 TATCTTTATTT
1 TTTATTTATTT
5489634 TATT-TTTATTT
1 T-TTATTTATTT
*
5489645 TTGT-TTTA-CT
1 TT-TATTTATTT
*
5489655 TTTCTTTATTT
1 TTTATTTATTT
*
5489666 TAT-TTTATTT
1 TTTATTTATTT
*
5489676 TTTATTT-TTA
1 TTTATTTATTT
5489686 TTTATTT
1 TTTATTT
5489693 TCACTTTTAT
Statistics
Matches: 93, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
9 1 0.01
10 27 0.29
11 41 0.44
12 15 0.16
13 3 0.03
14 6 0.06
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:5489637 original size:5 final size:5
Alignment explanation
Indices: 5489620--5489723 Score: 76
Period size: 5 Copynumber: 20.8 Consensus size: 5
5489610 TTAATATTCT
* *
5489620 TTTTA TCTTTA TTTTA TTTTTA TTTTTG TTTTA CTTTT- CTTTA TTTTA
1 TTTTA T-TTTA TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTTTA TTTTA
* *
5489668 TTTTA TTTT- TTAT- TTTTA -TTTA TTTTCA CTTTTA TTTTG TTTTA --TTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A -TTTTA TTTTA TTTTA TTTTA
5489715 TTTTA TTTT
1 TTTTA TTTT
5489724 CTTTAAATAA
Statistics
Matches: 81, Mismatches: 8, Indels: 20
0.74 0.07 0.18
Matches are distributed among these distances:
3 3 0.04
4 13 0.16
5 40 0.49
6 21 0.26
7 4 0.05
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:5489641 original size:17 final size:17
Alignment explanation
Indices: 5489619--5489723 Score: 88
Period size: 17 Copynumber: 5.9 Consensus size: 17
5489609 TTTAATATTC
*
5489619 TTTTTATCTTTATTTTA
1 TTTTTATTTTTATTTTA
*
5489636 TTTTTATTTTTGTTTTA
1 TTTTTATTTTTATTTTA
*
5489653 CTTTTCTTTATTTTATTTTA
1 -TTTT-TAT-TTTTATTTTA
5489673 TTTTTTATTTTTA-TTTA
1 -TTTTTATTTTTATTTTA
* *
5489690 TTTTCACTTTTATTTT-
1 TTTTTATTTTTATTTTA
*
5489706 GTTTTATTATTTTATTTT
1 TTTTTA-T-TTTTATTTT
5489724 CTTTAAATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
16 14 0.20
17 22 0.31
18 18 0.25
19 4 0.06
20 13 0.18
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTTATTTTA
Found at i:5489872 original size:117 final size:116
Alignment explanation
Indices: 5489740--5490096 Score: 513
Period size: 117 Copynumber: 3.1 Consensus size: 116
5489730 ATAAAAATAA
5489740 AAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
1 AAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT-AAAAAAA
* *
5489805 AGTTTTTGAGAAAAAGTTGAAAGTATTAATTTTTCTTGAAAATCAAAGTTTCC
64 AGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTCC
* * * *
5489858 AAAGAATATTTTTGGAGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTAAAAAAAAG
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTAAAAAAAA-
*
5489922 GGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAATGTTTCC
65 -GTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTCC
* *
5489975 AAAAAATATTTTTGAGGAAAAGTTGAAAGCATCAATTTTCCTTAAAAATAAATTTTTAAAAAAAT
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTTAAAAAAA-
* * * * *
5490040 A-TTTTTGAGGAAAAGTTGAAAGCATCAATTTTCCTTAAAAAT-AAATTTTCA
64 AGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTCC
5490091 AAAAAA
1 AAAAAA
5490097 AATCAACTTT
Statistics
Matches: 215, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
115 8 0.04
116 15 0.07
117 177 0.82
118 4 0.02
119 10 0.05
120 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (116 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTAAAAAAAAG
TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTCC
Found at i:5490096 original size:58 final size:58
Alignment explanation
Indices: 5489739--5490096 Score: 461
Period size: 58 Copynumber: 6.1 Consensus size: 58
5489729 AATAAAAATA
*
5489739 AAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * * *
5489798 AAAAAAA-AGTTTTTGAGAAAAAGTTGAAAGTATTAATTTTTCTTGAAAATCAAAGTTTC
1 AAAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
* * * * *
5489857 CAAAGAATATTTTTG-GAGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTA
1 AAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
** * * *
5489914 AAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAATGTTTC
1 AAAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAT-TTTC
* * *
5489974 CAAAAAATATTTTTGAGGAAAAGTTGAAAGCATCAATTTTCCTTAAAAATAAATTTTT
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
5490032 AAAAAAATATTTTTGAGGAAAAGTTGAAAGCATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
5490090 AAAAAAA
1 AAAAAAA
5490097 AATCAACTTT
Statistics
Matches: 260, Mismatches: 31, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
57 9 0.03
58 146 0.56
59 95 0.37
60 10 0.04
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (58 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:5490223 original size:57 final size:58
Alignment explanation
Indices: 5490126--5490248 Score: 187
Period size: 57 Copynumber: 2.1 Consensus size: 58
5490116 GTTTCCTTGA
*
5490126 AAATAAAAGTTTTCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTCG
1 AAATAAAAGTTTTCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTCG
* *
5490184 AAATTAAAG-TTTCAAAAGAATATTTTT-GGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAATAAAAGTTTTCAAAA-AATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTCG
*
5490241 AAAAAAAA
1 AAATAAAA
5490249 ATAATAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
57 42 0.71
58 17 0.29
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.35
Consensus pattern (58 bp):
AAATAAAAGTTTTCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTCG
Found at i:5496483 original size:25 final size:25
Alignment explanation
Indices: 5496452--5496502 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
5496442 CTTATTTAAA
*
5496452 ATTATACTATATGTTCAAGTATATT
1 ATTATACTACATGTTCAAGTATATT
**
5496477 ATTATACTACATGTTTGAGTATATT
1 ATTATACTACATGTTCAAGTATATT
5496502 A
1 A
5496503 CAATATGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (25 bp):
ATTATACTACATGTTCAAGTATATT
Found at i:5503709 original size:20 final size:22
Alignment explanation
Indices: 5503665--5503714 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
5503655 AGTATCATTA
5503665 TAATT-ATTTATAATTTAATAT
1 TAATTGATTTATAATTTAATAT
*
5503686 TAATTGATTTA-AATTTGA-AT
1 TAATTGATTTATAATTTAATAT
5503706 TAATTGATT
1 TAATTGATT
5503715 GTGATAGCCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.41
21 11 0.41
22 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (22 bp):
TAATTGATTTATAATTTAATAT
Found at i:5506347 original size:21 final size:20
Alignment explanation
Indices: 5506300--5506347 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
5506290 TAAAATTATT
*
5506300 ACAAATATAATAAATCATAA
1 ACAAATATAATAAAACATAA
* *
5506320 TCTAAATATATTACAAACATAA
1 AC-AAATATAATA-AAACATAA
5506342 ACAAAT
1 ACAAAT
5506348 TTAACATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 13 0.59
22 8 0.36
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.27
Consensus pattern (20 bp):
ACAAATATAATAAAACATAA
Found at i:5506490 original size:61 final size:61
Alignment explanation
Indices: 5506414--5506530 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
5506404 AAAATCTCAT
* * * *
5506414 AAATTCTTACCATAAATAATAGAATTATAAAATACATAAAACATATTAAATTAAAACTAAC
1 AAATTCTCACAATAAATAATAGAATTATAAAATACATAAAACATAGTAAACTAAAACTAAC
* * * * *
5506475 AAATTCTCACAATAAATGATGGAATTATGAAATATATAAAACTTAGTAAACTAAAA
1 AAATTCTCACAATAAATAATAGAATTATAAAATACATAAAACATAGTAAACTAAAA
5506531 TTTAAATATC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (61 bp):
AAATTCTCACAATAAATAATAGAATTATAAAATACATAAAACATAGTAAACTAAAACTAAC
Found at i:5506810 original size:14 final size:15
Alignment explanation
Indices: 5506767--5506812 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
5506757 TAAGATGAAT
5506767 AAATAA-ATATCAT-A
1 AAATAATATAT-ATAA
*
5506781 AAATAATATATTTAA
1 AAATAATATATATAA
5506796 AAATAATA-ATATAA
1 AAATAATATATATAA
5506810 AAA
1 AAA
5506813 ATGAATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAATATATATAA
Found at i:5506813 original size:15 final size:15
Alignment explanation
Indices: 5506767--5506829 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
5506757 TAAGATGAAT
* *
5506767 AAATAA-ATATCATA
1 AAATAATATATTAAA
*
5506781 AAATAATATATTTAA
1 AAATAATATATTAAA
5506796 AAATAATA-ATATAAA
1 AAATAATATAT-TAAA
5506811 AAATGAAT-TAGTTAAA
1 AAAT-AATATA-TTAAA
5506827 AAA
1 AAA
5506830 GATAATATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 8 0.20
15 20 0.50
16 11 0.28
17 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (15 bp):
AAATAATATATTAAA
Found at i:5516538 original size:20 final size:20
Alignment explanation
Indices: 5516513--5516557 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
5516503 ATCCAATAGT
5516513 ATTAATAGTATTTAACTTAA
1 ATTAATAGTATTTAACTTAA
5516533 ATTAATAGTATTTAACTTAA
1 ATTAATAGTATTTAACTTAA
5516553 ATTAA
1 ATTAA
5516558 AAATACTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (20 bp):
ATTAATAGTATTTAACTTAA
Found at i:5516571 original size:10 final size:10
Alignment explanation
Indices: 5516558--5516598 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
5516548 CTTAAATTAA
5516558 AAATACTATT
1 AAATACTATT
5516568 AAATACTATT
1 AAATACTATT
* *
5516578 AAA-AATTTT
1 AAATACTATT
5516587 AAATACTATT
1 AAATACTATT
5516597 AA
1 AA
5516599 TAATCCTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (10 bp):
AAATACTATT
Found at i:5516578 original size:22 final size:21
Alignment explanation
Indices: 5516553--5516610 Score: 75
Period size: 19 Copynumber: 2.8 Consensus size: 21
5516543 TTTAACTTAA
5516553 ATTAAAAATACTATTAAATACT
1 ATTAAAAAT-CTATTAAATACT
5516575 ATTAAAAAT-T-TTAAATACT
1 ATTAAAAATCTATTAAATACT
*
5516594 ATTAATAATCCTATTAA
1 ATTAAAAAT-CTATTAA
5516611 TAGTATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 17 0.53
20 1 0.03
21 1 0.03
22 13 0.41
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTAAAAATCTATTAAATACT
Found at i:5516703 original size:16 final size:16
Alignment explanation
Indices: 5516682--5516716 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5516672 CAAGATTGCA
5516682 TATATATTGTCGTTAT
1 TATATATTGTCGTTAT
5516698 TATATATTGTCGTTAT
1 TATATATTGTCGTTAT
5516714 TAT
1 TAT
5516717 GAGCTTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (16 bp):
TATATATTGTCGTTAT
Found at i:5517019 original size:20 final size:22
Alignment explanation
Indices: 5516975--5517024 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
5516965 AGTATCATTA
5516975 TAATT-ATTTATAATTTAATAT
1 TAATTGATTTATAATTTAATAT
*
5516996 TAATTGATTTA-AATTTGA-AT
1 TAATTGATTTATAATTTAATAT
5517016 TAATTGATT
1 TAATTGATT
5517025 GTGATAGCCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.41
21 11 0.41
22 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (22 bp):
TAATTGATTTATAATTTAATAT
Found at i:5533798 original size:56 final size:56
Alignment explanation
Indices: 5533738--5534016 Score: 328
Period size: 56 Copynumber: 5.0 Consensus size: 56
5533728 ACAAGAAACA
* * *
5533738 TTTTAAGGAAAAATTAAAAATATCAATTTTTCTTGAAAACGAAAATTTCAAAAATG
1 TTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAAATGAAAATTTCAAAAATG
* * * *
5533794 TTTTAAGGAAAAGTTAAAATTATTAATTTTT-TTTAAAATGAAAATTTCAATAAAATA
1 TTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAAATGAAAATTTC-A-AAAATG
* * * *
5533851 TTTTACA-GAAAAGTCAAAAGTATAAATTTTCCTTGAAAACGAAAATTTCAAAAATG
1 TTTTA-AGGAAAAGTTAAAAGTATCAATTTTTCTTGAAAATGAAAATTTCAAAAATG
* * * *
5533907 TTTTAAGGAAAAGTTGAAAGTATTAATTTTTCTTGACAATAAAAATTTCAAAAATG
1 TTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAAATGAAAATTTCAAAAATG
* ** * * *
5533963 TTTTAAGAAAAAGTCGAAAGTATCGATTTTTCTTGAAAATAAAAACTTCAAAAA
1 TTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAAATGAAAATTTCAAAAA
5534017 AATGTTAAAA
Statistics
Matches: 192, Mismatches: 26, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
55 16 0.08
56 129 0.67
57 31 0.16
58 16 0.08
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (56 bp):
TTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAAATGAAAATTTCAAAAATG
Found at i:5533854 original size:113 final size:111
Alignment explanation
Indices: 5533737--5534016 Score: 364
Period size: 113 Copynumber: 2.5 Consensus size: 111
5533727 CACAAGAAAC
* *
5533737 ATTTTAAGGAAAAATTAAAAATATCAATTTTTCTTGAAAACGAAAATTTCAAAAATGTTTTAAGG
1 ATTTTAA-GAAAAATCAAAAGTATCAATTTTTCTTGAAAACGAAAATTTCAAAAATGTTTTAAGG
* * *
5533802 AAAAGTTAAAATTATTAATTTTT-TTTAAAATGAAAATTTCAATAAAAT
65 AAAAGTTAAAAGTATTAATTTTTCTTGAAAATAAAAATTTC-A-AAAAT
* * *
5533850 ATTTTACAGAAAAGTCAAAAGTATAAATTTTCCTTGAAAACGAAAATTTCAAAAATGTTTTAAGG
1 ATTTTA-AGAAAAATCAAAAGTATCAATTTTTCTTGAAAACGAAAATTTCAAAAATGTTTTAAGG
* *
5533915 AAAAGTTGAAAGTATTAATTTTTCTTGACAATAAAAATTTCAAAAAT
65 AAAAGTTAAAAGTATTAATTTTTCTTGAAAATAAAAATTTCAAAAAT
* * * ** *
5533962 GTTTTAAGAAAAAGTCGAAAGTATCGATTTTTCTTGAAAATAAAAACTTCAAAAA
1 ATTTTAAGAAAAA-TCAAAAGTATCAATTTTTCTTGAAAACGAAAATTTCAAAAA
5534017 AATGTTAAAA
Statistics
Matches: 145, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
111 6 0.04
112 44 0.30
113 80 0.55
114 15 0.10
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (111 bp):
ATTTTAAGAAAAATCAAAAGTATCAATTTTTCTTGAAAACGAAAATTTCAAAAATGTTTTAAGGA
AAAGTTAAAAGTATTAATTTTTCTTGAAAATAAAAATTTCAAAAAT
Found at i:5534088 original size:11 final size:11
Alignment explanation
Indices: 5534072--5534115 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
5534062 TTCTTAAAAA
5534072 TAAAAAAATTT
1 TAAAAAAATTT
*
5534083 TAAAAAAATAT
1 TAAAAAAATTT
*
5534094 TAAAAAATGCTTT
1 TAAAAAA--ATTT
5534107 TAAAAAAAT
1 TAAAAAAAT
5534116 GAAAGTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 18 0.67
13 9 0.33
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
TAAAAAAATTT
Found at i:5534104 original size:72 final size:68
Alignment explanation
Indices: 5533947--5534143 Score: 206
Period size: 68 Copynumber: 2.8 Consensus size: 68
5533937 TCTTGACAAT
* * * *
5533947 AAAAAT-TTCAAAAATGTTT-TAAGAAAAAGTCGAAAGTATCGATTTTTCTTGAAAAT--AAAAA
1 AAAAATATTAAAAAATGCTTTTAA-AAAAA-T-GAAAGTATCAATTTTTCTTAAAAATAAAAAAA
5534008 CTTCAA
63 CTTCAA
*
5534014 AAAAATGTTAAAAAATGCTTTTAAAGAAAAAAAT-AGAAGTATCAATTTTTCTTAAAAATAAAAA
1 AAAAATATTAAAAAATGCTTTT----AAAAAAATGA-AAGTATCAATTTTTCTTAAAAATAAAAA
* *
5534078 AATTTTAA
61 AACTTCAA
*
5534086 AAAAATATTAAAAAATGCTTTTAAAAAAATGAAAGTATTAATTTTTCTTAGAAAATAA
1 AAAAATATTAAAAAATGCTTTTAAAAAAATGAAAGTATCAATTTTTCTTA-AAAATAA
5534144 GTTTTTTCCA
Statistics
Matches: 111, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
67 6 0.05
68 36 0.32
69 10 0.09
70 21 0.19
71 1 0.01
72 35 0.32
73 2 0.02
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (68 bp):
AAAAATATTAAAAAATGCTTTTAAAAAAATGAAAGTATCAATTTTTCTTAAAAATAAAAAAACTT
CAA
Found at i:5534157 original size:68 final size:66
Alignment explanation
Indices: 5533947--5534236 Score: 198
Period size: 72 Copynumber: 4.1 Consensus size: 66
5533937 TCTTGACAAT
* * **
5533947 AAAAATTTCAAAAATG-TTTTAAGAAAAAGTCGAAAGTATCGATTTTTCTT-GAAAATAAAAACT
1 AAAAATTTAAAAAATGCTTTTAA-AAAAA-T-GAAAGTATCAATTTTTCTTAGAAAATAAAATTT
5534010 TCAA
63 TCAA
5534014 AAAAATGTTAAAAAATGCTTTTAAAGAAAAAAAT-AGAAGTATCAATTTTTCTTA-AAAATAAAA
1 AAAAAT-TTAAAAAATGCTTTT----AAAAAAATGA-AAGTATCAATTTTTCTTAGAAAAT---A
5534077 AAATTTT-AA
57 AAATTTTCAA
* **
5534086 AAAAATATTAAAAAATGCTTTTAAAAAAATGAAAGTATTAATTTTTCTTAGAAAATAAGTTTTTT
1 AAAAAT-TTAAAAAATGCTTTTAAAAAAATGAAAGTATCAATTTTTCTTAGAAAATAA-AATTTT
5534151 CCAA
64 -CAA
* * * *
5534155 AAATGTATTTCAAAAGAAATGTTTTTAAGGAAAAGATAAAAATATCAATTTTTCTTA-AAAATGA
1 AAA--AATTT--AAA-AAATGCTTTTAA--AAAA-ATGAAAGTATCAATTTTTCTTAGAAAAT-A
*
5534219 AAA-CTTCAA
57 AAATTTTCAA
5534228 AAAATATTT
1 AAAA-ATTT
5534237 TTTTGAAGAA
Statistics
Matches: 180, Mismatches: 17, Indels: 47
0.74 0.07 0.19
Matches are distributed among these distances:
66 2 0.01
67 10 0.06
68 34 0.19
69 16 0.09
70 23 0.13
71 3 0.02
72 35 0.19
73 25 0.14
74 2 0.01
75 9 0.05
76 21 0.12
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (66 bp):
AAAAATTTAAAAAATGCTTTTAAAAAAATGAAAGTATCAATTTTTCTTAGAAAATAAAATTTTCA
A
Found at i:5534320 original size:59 final size:59
Alignment explanation
Indices: 5534161--5534325 Score: 190
Period size: 60 Copynumber: 2.8 Consensus size: 59
5534151 CCAAAAATGT
* *
5534161 ATTTCAAAAGAA-ATGTTTTTAAGGAAAAGA-TAAAAATATCAATTTTTCTTAAAAATGAAA
1 ATTTCAAAA-AATAT-TTTTTGAGGAAAA-ATTAAAAATATCAATTTTTCTTAAAAATAAAA
* * * * * * *
5534221 ACTTCAAAAAATATTTTTTTGAAGAAAAGTTGAGATTATCAATTTTTCTTAAAAGTAAAA
1 ATTTCAAAAAATA-TTTTTTGAGGAAAAATTAAAAATATCAATTTTTCTTAAAAATAAAA
*
5534281 ATTTCAAAAAATATTTTTTGAGGAAAAATTAAAAGTATCAATTTT
1 ATTTCAAAAAATATTTTTTGAGGAAAAATTAAAAATATCAATTTT
5534326 ATTTGAATAA
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
59 29 0.33
60 57 0.66
61 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (59 bp):
ATTTCAAAAAATATTTTTTGAGGAAAAATTAAAAATATCAATTTTTCTTAAAAATAAAA
Found at i:5535097 original size:2 final size:2
Alignment explanation
Indices: 5535090--5535135 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
5535080 AAAAGCAAAC
*
5535090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5535132 AT AT
1 AT AT
5535136 CGTTGTAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5539295 original size:3 final size:3
Alignment explanation
Indices: 5539289--5539323 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5539279 AAAAAAGTAC
5539289 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5539324 CCAGCATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5545030 original size:21 final size:21
Alignment explanation
Indices: 5545001--5545040 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5544991 CTAACAGCAC
*
5545001 TTTCAATCTCCTTTTCCGCTG
1 TTTCAATCTCCTTCTCCGCTG
*
5545022 TTTCGATCTCCTTCTCCGC
1 TTTCAATCTCCTTCTCCGC
5545041 CATCTTCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.38, G:0.10, T:0.45
Consensus pattern (21 bp):
TTTCAATCTCCTTCTCCGCTG
Found at i:5545071 original size:42 final size:42
Alignment explanation
Indices: 5545025--5545106 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 42
5545015 TCCGCTGTTT
*
5545025 CGATCTCCT-TCTCCGCCATCTTCAACCCTTTCTCCACCGTAA
1 CGATC-CCTCTCTCCGCCATCTCCAACCCTTTCTCCACCGTAA
* ** * *
5545067 CGATCCCTCTTTCCGCTGTCTCCAGCCCTTTCTCCGCCGT
1 CGATCCCTCTCTCCGCCATCTCCAACCCTTTCTCCACCGT
5545107 CTCGAACCCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
41 3 0.09
42 30 0.91
ACGTcount: A:0.11, C:0.46, G:0.11, T:0.32
Consensus pattern (42 bp):
CGATCCCTCTCTCCGCCATCTCCAACCCTTTCTCCACCGTAA
Found at i:5545116 original size:21 final size:21
Alignment explanation
Indices: 5545033--5545117 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
5545023 TTCGATCTCC
*
5545033 TTCTCCGCCATCTTC-AACCCT
1 TTCTCCGCCGTC-TCGAACCCT
* ** *
5545054 TTCTCCACCGTAACGATCCCT
1 TTCTCCGCCGTCTCGAACCCT
* * *
5545075 CTT-TCCGCTGTCTCCAGCCCT
1 -TTCTCCGCCGTCTCGAACCCT
5545096 TTCTCCGCCGTCTCGAACCCT
1 TTCTCCGCCGTCTCGAACCCT
5545117 T
1 T
5545118 CCTTCACGAT
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
20 3 0.06
21 42 0.89
22 2 0.04
ACGTcount: A:0.12, C:0.46, G:0.11, T:0.32
Consensus pattern (21 bp):
TTCTCCGCCGTCTCGAACCCT
Found at i:5545808 original size:29 final size:30
Alignment explanation
Indices: 5545753--5545810 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
5545743 AAAATATATA
5545753 TTTTATATTTTATATTTTAAATAATTATTG
1 TTTTATATTTTATATTTTAAATAATTATTG
*
5545783 TTTTA-ATTTTA-ATTTTAATATGATTATT
1 TTTTATATTTTATATTTTAA-ATAATTATT
5545811 TTAATTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.27
29 14 0.54
30 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (30 bp):
TTTTATATTTTATATTTTAAATAATTATTG
Found at i:5545813 original size:20 final size:19
Alignment explanation
Indices: 5545788--5545837 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
5545778 TATTGTTTTA
5545788 ATTTTAATTTTAATATGATT
1 ATTTTAATTTTAATATGA-T
*
5545808 ATTTTAATTCATTTATATGAT
1 ATTTTAATT--TTAATATGAT
5545829 A-TTTAATTT
1 ATTTTAATTT
5545838 ATATAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.04
20 16 0.59
21 2 0.07
22 8 0.30
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (19 bp):
ATTTTAATTTTAATATGAT
Found at i:5545856 original size:26 final size:25
Alignment explanation
Indices: 5545819--5545868 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
5545809 TTTTAATTCA
5545819 TTTATATGATAT-TTAATTTATATAAT
1 TTTATATGATATATT-ATTTA-ATAAT
5545845 TTTATTAT-ATATATTATTTAATAA
1 TTTA-TATGATATATTATTTAATAA
5545869 ATAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
25 4 0.18
26 13 0.59
27 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTATATGATATATTATTTAATAAT
Found at i:5561807 original size:20 final size:19
Alignment explanation
Indices: 5561771--5561810 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5561761 TTTTTTTTTG
**
5561771 TTAAAAAAAATGGAAGAAA
1 TTAAAAAAAATAAAAGAAA
5561790 TTAAAGAAAAATAAAAGAAA
1 TTAAA-AAAAATAAAAGAAA
5561810 T
1 T
5561811 AACTAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (19 bp):
TTAAAAAAAATAAAAGAAA
Found at i:5565436 original size:2 final size:2
Alignment explanation
Indices: 5565429--5565458 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5565419 ATATTCAATC
5565429 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
5565459 CTCTTTTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5566549 original size:3 final size:3
Alignment explanation
Indices: 5566541--5566578 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5566531 ATTTTCAGAT
5566541 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
5566579 GTGAAAACGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:5568638 original size:2 final size:2
Alignment explanation
Indices: 5568631--5568657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5568621 CTAGTTGGAA
5568631 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 A
5568658 GTGCCACCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5570238 original size:2 final size:2
Alignment explanation
Indices: 5570231--5570255 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5570221 TTAAGAAAAC
5570231 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 T
5570256 TCAAGGAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5570378 original size:14 final size:14
Alignment explanation
Indices: 5570361--5570387 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5570351 TAAATATACG
5570361 ATTTTAAATTATTT
1 ATTTTAAATTATTT
5570375 ATTTTAAATTATT
1 ATTTTAAATTATT
5570388 AAATAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTAAATTATTT
Found at i:5572376 original size:15 final size:15
Alignment explanation
Indices: 5572353--5572388 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5572343 AGTTCTAGTT
*
5572353 TAATATTAATAGTAA
1 TAATATTAATAATAA
*
5572368 TAATTTTAATAATAA
1 TAATATTAATAATAA
5572383 TAATAT
1 TAATAT
5572389 CAGTTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
TAATATTAATAATAA
Found at i:5573659 original size:18 final size:18
Alignment explanation
Indices: 5573602--5573666 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 18
5573592 AATAAGTAAG
5573602 ATAATAAT-TAAAAAATA
1 ATAATAATCTAAAAAATA
* *
5573619 TATATTAAAATGCTTAAATAATA
1 -ATA--ATAAT-C-TAAAAAATA
5573642 ATAATAATCTAAAAAATA
1 ATAATAATCTAAAAAATA
*
5573660 GTAATAA
1 ATAATAA
5573667 AAATTAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
18 17 0.46
19 1 0.03
20 8 0.22
22 3 0.08
23 8 0.22
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
ATAATAATCTAAAAAATA
Found at i:5573783 original size:24 final size:26
Alignment explanation
Indices: 5573756--5573807 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
5573746 CTACATGTTG
*
5573756 AAAAATTAT-AAAAA-GAAAATTAAT
1 AAAAAGTATAAAAAATGAAAATTAAT
* *
5573780 AAAAGGTATAAAAAATTAAAATTAAT
1 AAAAAGTATAAAAAATGAAAATTAAT
5573806 AA
1 AA
5573808 TAATAATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 5 0.22
26 11 0.48
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (26 bp):
AAAAAGTATAAAAAATGAAAATTAAT
Found at i:5574030 original size:14 final size:14
Alignment explanation
Indices: 5574013--5574058 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
5574003 CCCTAAAACC
5574013 AAAACTGAAACCTT
1 AAAACTGAAACCTT
*
5574027 AAAACTGAAACCCT
1 AAAACTGAAACCTT
5574041 AAAACTGAAACCTT
1 AAAACTGAAACCTT
5574055 AAAA
1 AAAA
5574059 TCCAAAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.54, C:0.22, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAACTGAAACCTT
Found at i:5587044 original size:35 final size:35
Alignment explanation
Indices: 5587005--5587077 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
5586995 TTTTGCTTTC
*
5587005 TGACTTGCGGTTTAGTCCCAATTGTCTTTAATCTT
1 TGACTCGCGGTTTAGTCCCAATTGTCTTTAATCTT
* * *
5587040 TGACTCGCGGTTTAGTCTCAGTTGTTTTTAATCTT
1 TGACTCGCGGTTTAGTCCCAATTGTCTTTAATCTT
5587075 TGA
1 TGA
5587078 ATTACAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.16, C:0.18, G:0.19, T:0.47
Consensus pattern (35 bp):
TGACTCGCGGTTTAGTCCCAATTGTCTTTAATCTT
Found at i:5587700 original size:21 final size:21
Alignment explanation
Indices: 5587674--5587715 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5587664 TCAGTTCTAG
* *
5587674 TTTAATAGTAATAGTAATAAT
1 TTTAATAATAATACTAATAAT
5587695 TTTAATAATAATACTAATAAT
1 TTTAATAATAATACTAATAAT
5587716 AATATCGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (21 bp):
TTTAATAATAATACTAATAAT
Found at i:5589081 original size:27 final size:26
Alignment explanation
Indices: 5589029--5589081 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
5589019 GGAGAATTAT
**
5589029 AAAAATAAAATTAATAAAAGGTATAA
1 AAAAATAAAATTAATAAAAGCAATAA
5589055 AAAAATTAAAATTAATAATAA-CAATAA
1 AAAAA-TAAAATTAATAA-AAGCAATAA
5589082 TAATACTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 16 0.70
28 2 0.09
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAAATAAAATTAATAAAAGCAATAA
Found at i:5590886 original size:21 final size:21
Alignment explanation
Indices: 5590862--5590903 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5590852 ATTTAAATCA
*
5590862 ATAAATTA-ATTTAATAAAAGG
1 ATAAATTATATATAA-AAAAGG
5590883 ATAAATTATATATAAAAAAGG
1 ATAAATTATATATAAAAAAGG
5590904 TTATAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
ATAAATTATATATAAAAAAGG
Found at i:5591004 original size:22 final size:21
Alignment explanation
Indices: 5590979--5591025 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5590969 TACACACTTT
5590979 ATTTATATAATAAGAATTTTTA
1 ATTTATATAATAA-AATTTTTA
* * *
5591001 ATTTATCTATTTAAATTTTTA
1 ATTTATATAATAAAATTTTTA
5591022 ATTT
1 ATTT
5591026 TCACTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTATATAATAAAATTTTTA
Found at i:5591075 original size:14 final size:14
Alignment explanation
Indices: 5591058--5591084 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5591048 AATAAAAAAT
5591058 TTTAAAAATTTCAC
1 TTTAAAAATTTCAC
5591072 TTTAAAAATTTCA
1 TTTAAAAATTTCA
5591085 TCGATAAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAAAAATTTCAC
Found at i:5599201 original size:3 final size:3
Alignment explanation
Indices: 5599193--5599228 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5599183 GATTGATTGA
5599193 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5599229 TTGTTAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5599872 original size:16 final size:16
Alignment explanation
Indices: 5599843--5599901 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
5599833 CTTGAATTCA
* *
5599843 AAAATTATTTAAATTT
1 AAAATGATTCAAATTT
*
5599859 GAAATGATTCAAATTTT
1 AAAATGATTCAAA-TTT
* *
5599876 AAAATAATTCAAATCT
1 AAAATGATTCAAATTT
5599892 AAAATGATTC
1 AAAATGATTC
5599902 GATACGACTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
16 21 0.60
17 14 0.40
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (16 bp):
AAAATGATTCAAATTT
Found at i:5606797 original size:2 final size:2
Alignment explanation
Indices: 5606792--5606826 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5606782 TTTTAGTTTG
5606792 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 A
5606827 GTGTCAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5610196 original size:2 final size:2
Alignment explanation
Indices: 5610189--5610213 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5610179 ACTCCACCTC
5610189 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
5610214 AATTTCATAT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5622982 original size:21 final size:22
Alignment explanation
Indices: 5622941--5622982 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5622931 TAATTCTTGT
*
5622941 TCTGTCAACCATTACTATTTTC
1 TCTGTCAACCATCACTATTTTC
5622963 TCTGTCAACCATCA-TATTTT
1 TCTGTCAACCATCACTATTTT
5622983 GCTTGCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.24, C:0.26, G:0.05, T:0.45
Consensus pattern (22 bp):
TCTGTCAACCATCACTATTTTC
Found at i:5630408 original size:3 final size:3
Alignment explanation
Indices: 5630400--5630446 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
5630390 TTCCCTTTCT
* * *
5630400 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTA TTA TTG TTA TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
5630447 TTTTGTATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.06, C:0.00, G:0.26, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:5635375 original size:2 final size:2
Alignment explanation
Indices: 5635368--5635393 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5635358 CCTTTTAGCT
5635368 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5635394 GTCATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5635513 original size:13 final size:13
Alignment explanation
Indices: 5635495--5635524 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
5635485 TTTAATTAAA
5635495 TTTTAAATTTTTT
1 TTTTAAATTTTTT
5635508 TTTT-AATTTTTT
1 TTTTAAATTTTTT
5635520 TTTTA
1 TTTTA
5635525 GTGAACAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTAAATTTTTT
Found at i:5638321 original size:88 final size:88
Alignment explanation
Indices: 5638172--5638341 Score: 313
Period size: 88 Copynumber: 1.9 Consensus size: 88
5638162 TGGAATACAG
*
5638172 TACTCTTCTATAATTCAATTACATGCTGAGACACAAACATATACATTTTGCGCACATTTGGTAAT
1 TACTCTTCTATAATTCAATTACATGCTGAGACACAAACATATACATTTTGCACACATTTGGTAAT
5638237 AGTTTGGCTAGGGACTAATGCAA
66 AGTTTGGCTAGGGACTAATGCAA
* *
5638260 TACTCTTCTATAATTCAATTATATGCTGAGACACAAACATATACATTTTGCACACATTTGGTACT
1 TACTCTTCTATAATTCAATTACATGCTGAGACACAAACATATACATTTTGCACACATTTGGTAAT
5638325 AGTTTGGCTAGGGACTA
66 AGTTTGGCTAGGGACTA
5638342 GGGGCTAATT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (88 bp):
TACTCTTCTATAATTCAATTACATGCTGAGACACAAACATATACATTTTGCACACATTTGGTAAT
AGTTTGGCTAGGGACTAATGCAA
Found at i:5641179 original size:64 final size:63
Alignment explanation
Indices: 5641078--5641205 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 63
5641068 TTATGACCTC
*
5641078 GAATCACTGTCTTTTTGTTACTGATCAGCTATAAATTATAAAAGACATAAGACTAGAATTAGGT
1 GAATCACTGTCTTTTTATTACTGATCAGCTATAAATTATAAAAGACAT-AGACTAGAATTAGGT
5641142 GAATCACTGTCTTTTTATTACTGCA-CAGCTATAAATTATAAAAGACATAGACTAGAATTAGGT
1 GAATCACTGTCTTTTTATTACTG-ATCAGCTATAAATTATAAAAGACATAGACTAGAATTAGGT
5641205 G
1 G
5641206 TTTGTCTTTC
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
63 16 0.26
64 45 0.73
65 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (63 bp):
GAATCACTGTCTTTTTATTACTGATCAGCTATAAATTATAAAAGACATAGACTAGAATTAGGT
Found at i:5649997 original size:2 final size:2
Alignment explanation
Indices: 5649990--5650036 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
5649980 ACTGATATGA
5649990 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5650032 AG AG A
1 AG AG A
5650037 AGGTGGAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5650349 original size:18 final size:20
Alignment explanation
Indices: 5650313--5650350 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
5650303 ATATACCAAC
*
5650313 TAATAAAAATATTATATTCA
1 TAATAAAAATATTAAATTCA
5650333 TAAT-AAAA-ATTAAATTCA
1 TAATAAAAATATTAAATTCA
5650351 GGATGAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATAAAAATATTAAATTCA
Found at i:5650748 original size:6 final size:6
Alignment explanation
Indices: 5650737--5650769 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5650727 TTTGAAAGCC
5650737 TTTTGT TTTTGT TTTTGT TTTT-T TTTT-T TTTTG
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTG
5650770 GAGTAATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTGT
Found at i:5651211 original size:28 final size:28
Alignment explanation
Indices: 5651171--5651239 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
5651161 TAACTTATTA
*
5651171 ATTAATAAA-TTTAAAATTTAAGTATCAT
1 ATTAA-AAATTTTAAAATTTAAGTATAAT
5651199 ATTAAAAATTTTAAAATTTAAGTATAAT
1 ATTAAAAATTTTAAAATTTAAGTATAAT
*
5651227 ATTAAATATTTTA
1 ATTAAAAATTTTA
5651240 TTATAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 3 0.08
28 35 0.92
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (28 bp):
ATTAAAAATTTTAAAATTTAAGTATAAT
Found at i:5652739 original size:19 final size:18
Alignment explanation
Indices: 5652715--5652758 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
5652705 TAAAATATTA
*
5652715 AAATTTTATTTTAATGATT
1 AAATTTTAATTT-ATGATT
5652734 AAATTTTAATTTATGA-T
1 AAATTTTAATTTATGATT
5652751 -AATTTTAA
1 AAATTTTAA
5652759 ATATATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
17 1 0.04
18 4 0.17
19 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
AAATTTTAATTTATGATT
Done.