Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, 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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 7 of 20
Found at i:2284999 original size:26 final size:26
Alignment explanation
Indices: 2284970--2285019 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
2284960 TAAGGCATCA
2284970 ATCCAC-TTTTGATGGTAAAATTATCC
1 ATCCACTTTTTG-TGGTAAAATTATCC
2284996 ATCCACTTTTTGTGGTAAAATTAT
1 ATCCACTTTTTGTGGTAAAATTAT
2285020 TTTGATAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (26 bp):
ATCCACTTTTTGTGGTAAAATTATCC
Found at i:2285143 original size:19 final size:19
Alignment explanation
Indices: 2285119--2285157 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2285109 TTAAATAATT
2285119 TTGCATTCACTTCAAGGGA
1 TTGCATTCACTTCAAGGGA
2285138 TTGCATTCACTTCAAGGGA
1 TTGCATTCACTTCAAGGGA
2285157 T
1 T
2285158 GGATGGATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (19 bp):
TTGCATTCACTTCAAGGGA
Found at i:2289332 original size:331 final size:332
Alignment explanation
Indices: 2288947--2289551 Score: 891
Period size: 331 Copynumber: 1.8 Consensus size: 332
2288937 AATCTTACAA
* *
2288947 GTATATATATCATAAATTTATCTAAATAAAGGTATATATATTATAATCAATAATTTTATAAGTTA
1 GTATATATATCATAAATTTATATAAACAAAGGTATATATATTATAATCAATAATTTTATAAGTTA
* *
2289012 TAATTTTTATAA-TATTAATACA-AAATAGAAAGTAATTATGTTTATATTTAAAGTGA-ATATAC
66 TAATTTTTATAACT-TT-A-ACATAAATAAAAAGTAAATATGTTTATATTTAAAGT-ATATATAC
* *
2289074 TAAAAGTATATATATAATAGTAATTATATTCTTTATAAATTAACACAATATATA-A-A-GTATA-
127 TAAAA--ATATATATAATAGTAATTATATTCCTTATAAATTAACACAATATATAGATATATATAT
* *
2289135 ATATTAAAAGACATTACAAGTTAGTTAATAATCACAATTTCATGAATTAATTCAATTAACAATAT
190 ATATTAAAAGACATTACAAGTTAATTAATAATCACAATTTCATGAATTAATTCAACTAACAATAT
2289200 GAGTTTGTCTTTAATTACAAATAATTAAAAAAACTATTTAGGTTTCAAAACTATTCTAATCTCAT
255 GAGTTTGTCTTTAATTACAAATAATTAAAAAAACTATTTAGGTTTCAAAACTATTCTAATCTCAT
2289265 AACTTCTCTTTAG
320 AACTTCTCTTTAG
* *
2289278 GTATATATATTATAAATTTATATAAACAAAGGTATATATATTATAATTAATAATTTTATAAGTTA
1 GTATATATATCATAAATTTATATAAACAAAGGTATATATATTATAATCAATAATTTTATAAGTTA
*
2289343 TAATTTTTGTAACTTTAACATAAATAAAAAGTAAATATGTTTATATTTAAAGTATATATACTAAA
66 TAATTTTTATAACTTTAACATAAATAAAAAGTAAATATGTTTATATTTAAAGTATATATACTAAA
* **
2289408 AATATATATAATGGTCCTTATATTCCTTATAAATTAACACAATATATAGATTATATATATATATT
131 AATATATATAATAGTAATTATATTCCTTATAAATTAACACAATATATAGA-TATATATATATATT
* * * * * * * *
2289473 AAAAGATATTATAAGTTAATTAATAATCATAGTTTTATGAATTAATTTAACTAGCAATATGGGTT
195 AAAAGACATTACAAGTTAATTAATAATCACAATTTCATGAATTAATTCAACTAACAATATGAGTT
*
2289538 TGTCTTTAGTTACA
260 TGTCTTTAATTACA
2289552 TGAAATTTTT
Statistics
Matches: 243, Mismatches: 23, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
328 43 0.18
329 5 0.02
330 42 0.17
331 75 0.31
332 5 0.02
333 73 0.30
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (332 bp):
GTATATATATCATAAATTTATATAAACAAAGGTATATATATTATAATCAATAATTTTATAAGTTA
TAATTTTTATAACTTTAACATAAATAAAAAGTAAATATGTTTATATTTAAAGTATATATACTAAA
AATATATATAATAGTAATTATATTCCTTATAAATTAACACAATATATAGATATATATATATATTA
AAAGACATTACAAGTTAATTAATAATCACAATTTCATGAATTAATTCAACTAACAATATGAGTTT
GTCTTTAATTACAAATAATTAAAAAAACTATTTAGGTTTCAAAACTATTCTAATCTCATAACTTC
TCTTTAG
Found at i:2291745 original size:36 final size:34
Alignment explanation
Indices: 2291705--2291771 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
2291695 TTATTTACAC
2291705 ATATAAGGGCCAGATATAAGGCATTGTACCACATGT
1 ATATAAGGG-CAGATATAAGGCA-TGTACCACATGT
* * *
2291741 ATATAAGGGCAGATGTGAGGTATGTACCACA
1 ATATAAGGGCAGATATAAGGCATGTACCACA
2291772 AAAATAGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 9 0.32
35 10 0.36
36 9 0.32
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (34 bp):
ATATAAGGGCAGATATAAGGCATGTACCACATGT
Found at i:2292422 original size:16 final size:16
Alignment explanation
Indices: 2292391--2292421 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2292381 ACCAAAATTA
2292391 AGATTTTGATTCTTTT
1 AGATTTTGATTCTTTT
2292407 AGATTTTGATT-TTTT
1 AGATTTTGATTCTTTT
2292422 TGATATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.19, C:0.03, G:0.13, T:0.65
Consensus pattern (16 bp):
AGATTTTGATTCTTTT
Found at i:2293716 original size:68 final size:68
Alignment explanation
Indices: 2293625--2293766 Score: 221
Period size: 68 Copynumber: 2.1 Consensus size: 68
2293615 ATACTATAAT
* *
2293625 ATGCATGATGAATACTGTAAGATTGTGTGTATGATGTAAATTCCATATACCATATGAAATGATTA
1 ATGCATAATGAATACTATAAGATTGTGTGTATGATGTAAATTCCATATACCATATGAAATGATTA
*
2293690 AGG
66 AGC
* * * *
2293693 ATGCATAATGAATACTATCAGATTGTGTGTATGATGTAAATTCTATATGCCATATGAAGTGATTA
1 ATGCATAATGAATACTATAAGATTGTGTGTATGATGTAAATTCCATATACCATATGAAATGATTA
2293758 AGC
66 AGC
2293761 ATGCAT
1 ATGCAT
2293767 TATCAATGCC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.35
Consensus pattern (68 bp):
ATGCATAATGAATACTATAAGATTGTGTGTATGATGTAAATTCCATATACCATATGAAATGATTA
AGC
Found at i:2299239 original size:25 final size:25
Alignment explanation
Indices: 2299192--2299239 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2299182 ACATGTCATG
*
2299192 TTGCTACCAGCCATGTTCTAAAATT
1 TTGCTACCAGCCATGTTCAAAAATT
*
2299217 TTGCTACACA-CCATGTTGAAAAA
1 TTGCTAC-CAGCCATGTTCAAAAA
2299240 ATGTCGTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (25 bp):
TTGCTACCAGCCATGTTCAAAAATT
Found at i:2299385 original size:26 final size:27
Alignment explanation
Indices: 2299314--2299387 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
2299304 AAGTTCAAAT
*
2299314 AAATTTTGTTACATGCCATTTTGAACA
1 AAATTTTGTTACATGCCATGTTGAACA
* * *
2299341 ACATCTTGTTACATACCATGTTGAA-A
1 AAATTTTGTTACATGCCATGTTGAACA
*
2299367 AAATTTTTTTACATGCCATGT
1 AAATTTTGTTACATGCCATGT
2299388 ACAAAAACAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 18 0.46
27 21 0.54
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (27 bp):
AAATTTTGTTACATGCCATGTTGAACA
Found at i:2299744 original size:15 final size:15
Alignment explanation
Indices: 2299720--2299777 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
2299710 TCTGTGAATG
*
2299720 TAAACCAATAAACCC
1 TAAACCAATAAACCA
*
2299735 TAAACTAATAAACCA
1 TAAACCAATAAACCA
* *
2299750 TAAACC-TTGAATCC-
1 TAAACCAAT-AAACCA
2299764 TAAACCAATAAACC
1 TAAACCAATAAACC
2299778 CAAGAACATA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
14 11 0.32
15 23 0.68
ACGTcount: A:0.52, C:0.28, G:0.02, T:0.19
Consensus pattern (15 bp):
TAAACCAATAAACCA
Found at i:2303992 original size:214 final size:218
Alignment explanation
Indices: 2303601--2304055 Score: 584
Period size: 214 Copynumber: 2.1 Consensus size: 218
2303591 AATATACAAA
*
2303601 TTATATATAAATTAAATATATGATATATAATATATATTACTTTATTATATAAAAGAAATTAATGA
1 TTATATATAAATTAAATATATGATAGATAATATATATTACTTTATTATATAAAAGAAATTAATGA
* * *
2303666 TACAAATTATATGTTATAATATTTTAATTTTTATATCAAAGTTTGTTATAAATAATAACTAGTTA
66 CACAAATTATATATTATAATA--TTAATTTTTATATCAAAGTTTGTTATAAATAATAACTAATTA
* * * * *
2303731 TAAGCAATATGTTATAAAAATTAAGGCGATAACTAATAACATTATTAAATGTAATTATGTAAATA
129 TAAACAATATGTTATAAAAACTAAAGCGATAACTAATAACATTATTAAATGTAATCATATAAATA
2303796 AAGTCTATCATAAGTTACAGTAATGC
194 AAGTCTATCATAAGTTACA-TAATGC
* * *
2303822 TTATATATAAATTAAATATATGTATAGAT-A-ATCTATTACTTTATTATTTACATATGAAATTAA
1 TTATATATAAATTAAATATATG-ATAGATAATATATATTACTTTATTATATA-A-AAGAAATTAA
*
2303885 TGACACAATTTATATATTAT-A-A-T-A-TTTTATATCAAAGTTTG-TATAAATAATAACTAATT
63 TGACACAAATTATATATTATAATATTAATTTTTATATCAAAGTTTGTTATAAATAATAACTAATT
* * * ** *
2303944 ATAAATAATATGTTATAAAAACTAAAGTGATAATTAATAAGTTTATTAAGTGTAATCATATAAAT
128 ATAAACAATATGTTATAAAAACTAAAGCGATAACTAATAACATTATTAAATGTAATCATATAAAT
* * *
2304009 AAAGTTTATTATAAGTTATATAATGC
193 AAAGTCTATCATAAGTTACATAATGC
* *
2304035 TTATTTACAAATTAAATATAT
1 TTATATATAAATTAAATATAT
2304056 ATAATGTTTA
Statistics
Matches: 207, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
213 25 0.12
214 88 0.43
215 17 0.08
216 1 0.00
217 1 0.00
220 19 0.09
221 25 0.12
222 31 0.15
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (218 bp):
TTATATATAAATTAAATATATGATAGATAATATATATTACTTTATTATATAAAAGAAATTAATGA
CACAAATTATATATTATAATATTAATTTTTATATCAAAGTTTGTTATAAATAATAACTAATTATA
AACAATATGTTATAAAAACTAAAGCGATAACTAATAACATTATTAAATGTAATCATATAAATAAA
GTCTATCATAAGTTACATAATGC
Found at i:2304069 original size:11 final size:10
Alignment explanation
Indices: 2304053--2304098 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
2304043 AAATTAAATA
2304053 TATATAATGTT
1 TATATAAT-TT
2304064 TATATAATTT
1 TATATAATTT
2304074 TATAT-ATATT
1 TATATAAT-TT
2304084 TATA-ACATTT
1 TATATA-ATTT
2304094 TATAT
1 TATAT
2304099 TACGAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.06
10 19 0.61
11 10 0.32
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (10 bp):
TATATAATTT
Found at i:2304288 original size:15 final size:14
Alignment explanation
Indices: 2304257--2304299 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2304247 ATATAAGTAA
2304257 AATTAAATTACTAT
1 AATTAAATTACTAT
*
2304271 AATTAAATTTCATAT
1 AATTAAATTAC-TAT
*
2304286 AA-TAAATTAATAT
1 AATTAAATTACTAT
2304299 A
1 A
2304300 CTTTAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 4 0.16
14 16 0.64
15 5 0.20
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTAAATTACTAT
Found at i:2304323 original size:16 final size:16
Alignment explanation
Indices: 2304302--2304335 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2304292 TTAATATACT
*
2304302 TTAAATATATTGTTAA
1 TTAAATATATTATTAA
*
2304318 TTAAATTTATTATTAA
1 TTAAATATATTATTAA
2304334 TT
1 TT
2304336 CTTTTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTAAATATATTATTAA
Found at i:2307201 original size:9 final size:9
Alignment explanation
Indices: 2307187--2307213 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2307177 AAGCAGAGTT
2307187 GGAAGAAGA
1 GGAAGAAGA
2307196 GGAAGAAGA
1 GGAAGAAGA
2307205 GGAAGAAGA
1 GGAAGAAGA
2307214 ACATGGGCAA
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:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
GGAAGAAGA
Found at i:2307582 original size:105 final size:105
Alignment explanation
Indices: 2307452--2307702 Score: 423
Period size: 105 Copynumber: 2.4 Consensus size: 105
2307442 AAATGGCAAG
* * * * *
2307452 GATTCCCAAGGGTGGCAGGCGATCCCTAAACACGAGGGACAGTTAGATGAGAAGAATGTGCCTCA
1 GATTCCAAAGGATGGCAGGCAATCCCTAAACACAAGGGACAGTTAGATGACAAGAATGTGCCTCA
2307517 AAGAACTGAAGCTGCTGCTCCTCTAGAACAGGGCGTCAAA
66 AAGAACTGAAGCTGCTGCTCCTCTAGAACAGGGCGTCAAA
*
2307557 GATTCCAAAGGATGGCAGGCAATCCCTAAACCCAAGGGACAGTTAGATGACAAGAATGTGCCTCA
1 GATTCCAAAGGATGGCAGGCAATCCCTAAACACAAGGGACAGTTAGATGACAAGAATGTGCCTCA
2307622 AAGAACTGAAGCTGCTGCTCCTCTAGAACAGGGCGTCAAA
66 AAGAACTGAAGCTGCTGCTCCTCTAGAACAGGGCGTCAAA
*
2307662 GATTCCAAGGGATGGCAGGCAATCCCTAAAC-CAAAGGGACA
1 GATTCCAAAGGATGGCAGGCAATCCCTAAACAC-AAGGGACA
2307703 CTCAGCTCTG
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
104 1 0.01
105 137 0.99
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.16
Consensus pattern (105 bp):
GATTCCAAAGGATGGCAGGCAATCCCTAAACACAAGGGACAGTTAGATGACAAGAATGTGCCTCA
AAGAACTGAAGCTGCTGCTCCTCTAGAACAGGGCGTCAAA
Found at i:2317855 original size:17 final size:17
Alignment explanation
Indices: 2317817--2317854 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2317807 ATTGTCAAGC
*
2317817 CTTTTCTATCAGAAAGT
1 CTTTTCTATCAGAAAAT
*
2317834 CTTTTCTGTCAGAAAAT
1 CTTTTCTATCAGAAAAT
2317851 -TTTT
1 CTTTT
2317855 TTTACCACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (17 bp):
CTTTTCTATCAGAAAAT
Found at i:2317932 original size:28 final size:27
Alignment explanation
Indices: 2317901--2317987 Score: 102
Period size: 28 Copynumber: 3.1 Consensus size: 27
2317891 ATGTAACAAC
* *
2317901 TTTTTATCATGACATGTAATAACTAAAT
1 TTTTTAT-ATGGCATGTAATAATTAAAT
*
2317929 TTTTTAATATGGTATGTAATAATTAAAT
1 TTTTT-ATATGGCATGTAATAATTAAAT
* **
2317957 CTTCAATATGGCATGTAATAATTAAAT
1 TTTTTATATGGCATGTAATAATTAAAT
2317984 TTTT
1 TTTT
2317988 CAAAATGGGT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
27 23 0.47
28 24 0.49
29 2 0.04
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (27 bp):
TTTTTATATGGCATGTAATAATTAAAT
Found at i:2318029 original size:27 final size:27
Alignment explanation
Indices: 2317914--2318037 Score: 117
Period size: 27 Copynumber: 4.6 Consensus size: 27
2317904 TTATCATGAC
2317914 ATGTAATAACTAAATTTTTTAATATGGT
1 ATGTAATAACTAAA-TTTTTAATATGGT
* * * *
2317942 ATGTAATAATTAAATCTTCAATATGGC
1 ATGTAATAACTAAATTTTTAATATGGT
* *
2317969 ATGTAATAATTAAATTTTTCAAAATGGGT
1 ATGTAATAACTAAATTTTT-AATAT-GGT
* *
2317998 A--TAACAACTAAATTTTTAATATGAT
1 ATGTAATAACTAAATTTTTAATATGGT
* *
2318023 ATGTAACAAATAAAT
1 ATGTAATAACTAAAT
2318038 CTTCAACTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
25 3 0.04
26 4 0.05
27 52 0.66
28 17 0.22
29 3 0.04
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (27 bp):
ATGTAATAACTAAATTTTTAATATGGT
Found at i:2318081 original size:81 final size:81
Alignment explanation
Indices: 2317889--2318083 Score: 204
Period size: 81 Copynumber: 2.4 Consensus size: 81
2317879 TTATGTCATG
* * * * * *
2317889 GCATGTAACAACT--TTTT-ATCATGACATGTAATAACTAAATTTTTTAATATGGTATGTAATAA
1 GCATGTAACAACTAATTTTCAACATGACGTATAACAACTAAATTTTTTAATATGATATGTAACAA
* *
2317951 TTAAATCTTCAATATG
66 ATAAATCTTCAATATA
* * * *
2317967 GCATGTAATAATTAAATTTTTCAAAATG-GGTATAACAACTAAA-TTTTTAATATGATATGTAAC
1 GCATGTAACAACT-AA-TTTTCAACATGACGTATAACAACTAAATTTTTTAATATGATATGTAAC
2318030 AAATAAATCTTCAACT-TA
64 AAATAAATCTTCAA-TATA
2318048 GCATGTAACAACTACATTTTCAACATGACGTATAAC
1 GCATGTAACAACTA-ATTTTCAACATGACGTATAAC
2318084 TAAAAGAGAA
Statistics
Matches: 93, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
78 11 0.12
80 11 0.12
81 51 0.55
82 16 0.17
83 4 0.04
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (81 bp):
GCATGTAACAACTAATTTTCAACATGACGTATAACAACTAAATTTTTTAATATGATATGTAACAA
ATAAATCTTCAATATA
Found at i:2319250 original size:92 final size:91
Alignment explanation
Indices: 2318938--2319350 Score: 586
Period size: 92 Copynumber: 4.5 Consensus size: 91
2318928 AAAGAGAAAA
* *
2318938 AAAAAACATAGAATAAACCTTC-ATTCTAATAACTAAAGGTATAAATTAATACACTTTCAGGTTT
1 AAAAAGCATAGAATAAACCTTCAATTCTAATAACTAAAGGTATAAATTAATAAACTTTCAGGTTT
* *
2319002 CTACAAAAAGGT-T-CAAAAAA-AA-
66 CTACAAAAAGATATGAAAAAAATAAT
** * *
2319024 AAAGGGCATAGAATAAGCCTTCAAATTCTAATAACTAAAGGTATAAATTAATGAACTTTCAGGTT
1 AAAAAGCATAGAATAAACCTTC-AATTCTAATAACTAAAGGTATAAATTAATAAACTTTCAGGTT
*
2319089 TCTACAAAACGATATGAAGAAAAAAATAAT
65 TCTACAAAAAGATAT---GAAAAAAATAAT
* *
2319119 AAAAAGCATAGAATAAACCTTCAATTCTAATAATTAAAGGTATAAATTAATAAACTTTGAGGTTT
1 AAAAAGCATAGAATAAACCTTCAATTCTAATAACTAAAGGTATAAATTAATAAACTTTCAGGTTT
2319184 CTACAAAAAGATATGAAAAGAAATAAT
66 CTACAAAAAGATATGAAAA-AAATAAT
* *
2319211 AAAAAGCATAGAATAAACCTTCAGTTCTAATAACTAAAGGTATACATTAATAAACTTTCAGGTTT
1 AAAAAGCATAGAATAAACCTTCAATTCTAATAACTAAAGGTATAAATTAATAAACTTTCAGGTTT
*
2319276 CTACAAAAAGATATTAAACAAAGA-AAT
66 CTACAAAAAGATATGAAA-AAA-ATAAT
*
2319303 AAAAAGGATAGAATAAACCTTCAATTCTAATAACTAAAGGTATAAATT
1 AAAAAGCATAGAATAAACCTTCAATTCTAATAACTAAAGGTATAAATT
2319351 CTAATAACTA
Statistics
Matches: 291, Mismatches: 24, Indels: 18
0.87 0.07 0.05
Matches are distributed among these distances:
86 18 0.06
88 50 0.17
89 1 0.00
91 5 0.02
92 135 0.46
93 8 0.03
94 55 0.19
95 19 0.07
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.27
Consensus pattern (91 bp):
AAAAAGCATAGAATAAACCTTCAATTCTAATAACTAAAGGTATAAATTAATAAACTTTCAGGTTT
CTACAAAAAGATATGAAAAAAATAAT
Found at i:2319350 original size:22 final size:22
Alignment explanation
Indices: 2319325--2319372 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
2319315 ATAAACCTTC
2319325 AATTCTAATAACTAAAGGTATA
1 AATTCTAATAACTAAAGGTATA
*
2319347 AATTCTAATAACTAAAGGTCTA
1 AATTCTAATAACTAAAGGTATA
2319369 AATT
1 AATT
2319373 AATAAACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.33
Consensus pattern (22 bp):
AATTCTAATAACTAAAGGTATA
Found at i:2319382 original size:114 final size:114
Alignment explanation
Indices: 2319235--2319464 Score: 338
Period size: 114 Copynumber: 2.0 Consensus size: 114
2319225 AAACCTTCAG
* *
2319235 TTCTAATAACTAAAGGTATACATTAATAAACTTTCAGGTTTCTACAAAAAGATATTAA-ACAAAG
1 TTCTAATAACTAAAGGTATAAATTAATAAACTTTCAGGTTTCTACAAAAAGATATGAAGA-AAA-
* * *
2319299 A-AATAAAAAGGATAGAATAAACCTTCAATTCTAATAACTAAAGGTATAAA
64 ATAACAAAAAGCATAGAATAAACCTTCAATTCTAATAACTAAAGGTAAAAA
* *
2319349 TTCTAATAACTAAAGGTCTAAATTAATAAACTTTGAGGTTTCTACAAAAAGATATGAAGAAAAAT
1 TTCTAATAACTAAAGGTATAAATTAATAAACTTTCAGGTTTCTACAAAAAGATATGAAGAAAAAT
* **
2319414 AACAAAAAGCATAGAATAAACCTTCAATTCTTATGGCTAAAGGTAAAAA
66 AACAAAAAGCATAGAATAAACCTTCAATTCTAATAACTAAAGGTAAAAA
2319463 TT
1 TT
2319465 AATAACCTTT
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
113 1 0.01
114 102 0.98
115 1 0.01
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (114 bp):
TTCTAATAACTAAAGGTATAAATTAATAAACTTTCAGGTTTCTACAAAAAGATATGAAGAAAAAT
AACAAAAAGCATAGAATAAACCTTCAATTCTAATAACTAAAGGTAAAAA
Found at i:2319504 original size:92 final size:94
Alignment explanation
Indices: 2319347--2319602 Score: 333
Period size: 94 Copynumber: 2.8 Consensus size: 94
2319337 TAAAGGTATA
* * *
2319347 AATTCTAATAACTAAAGGTCTAAATTAATAAACTTTGAGGTTTCTAC-AAAAAGATATG--AAGA
1 AATTCTAACAACTAAAGGTATAAATTAATAAACTTTGAGGTTTCTACAAAAAAGATATGAAAAAA
*
2319409 AAAATAACAAAAAGCATAGAATAAACCTTC
66 AAAATAA-TAAAAGCATAGAATAAACCTTC
* *** * * *
2319439 AATTCTTATGGCTAAAGGTAAAAATTAATAACCTTTGAGGTTTCTACAAAAAAGATAAGAAAAAA
1 AATTCTAACAACTAAAGGTATAAATTAATAAACTTTGAGGTTTCTACAAAAAAGATATGAAAAAA
*
2319504 AAAATAATAAAAGCATAGAATAAACTTTC
66 AAAATAATAAAAGCATAGAATAAACCTTC
* *
2319533 AATTCTAACAACTAAAGGTATAAATTAATAAACTTTCAGGTTTC--CATAAAAAGGTATGAAAAA
1 AATTCTAACAACTAAAGGTATAAATTAATAAACTTTGAGGTTTCTACA-AAAAAGATATGAAAAA
2319596 AAAAATA
65 AAAAATA
2319603 GTATCTTTGT
Statistics
Matches: 141, Mismatches: 19, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
92 43 0.30
93 31 0.22
94 57 0.40
95 10 0.07
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27
Consensus pattern (94 bp):
AATTCTAACAACTAAAGGTATAAATTAATAAACTTTGAGGTTTCTACAAAAAAGATATGAAAAAA
AAAATAATAAAAGCATAGAATAAACCTTC
Found at i:2319954 original size:26 final size:26
Alignment explanation
Indices: 2319921--2319974 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
2319911 AACAAATGAC
2319921 AATGTGAGGAGAAAAAAAATAAAAAT
1 AATGTGAGGAGAAAAAAAATAAAAAT
*
2319947 AATGTGAGGAGCAAAAAAATAAAAAT
1 AATGTGAGGAGAAAAAAAATAAAAAT
2319973 AA
1 AA
2319975 CAGGAACACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.65, C:0.02, G:0.19, T:0.15
Consensus pattern (26 bp):
AATGTGAGGAGAAAAAAAATAAAAAT
Found at i:2326098 original size:2 final size:2
Alignment explanation
Indices: 2326091--2326142 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
2326081 AATTTTAACG
* * * * *
2326091 TA TA TA TA TA CA TA TG TG TA TA TA TA TA TA TA TA CA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2326133 TA TA TG TA TA
1 TA TA TA TA TA
2326143 GAGAGAGAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2326147 original size:2 final size:2
Alignment explanation
Indices: 2326142--2326175 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2326132 ATATATGTAT
2326142 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
2326176 GTATGAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2332006 original size:39 final size:40
Alignment explanation
Indices: 2331931--2332010 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
2331921 TGGACATTAC
**
2331931 TCACCTTAGTGGGGTTTCCTAACCTCACCATGATTGGTGT
1 TCACCTTAGTGGGGTTTCCTAACCTCACCACAATTGGTGT
2331971 TCACCTTAGTGGGGTTT-CTAACCTCACCACAATTGGTGT
1 TCACCTTAGTGGGGTTTCCTAACCTCACCACAATTGGTGT
2332010 T
1 T
2332011 TTCACAACGC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 21 0.55
40 17 0.45
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (40 bp):
TCACCTTAGTGGGGTTTCCTAACCTCACCACAATTGGTGT
Found at i:2333208 original size:15 final size:15
Alignment explanation
Indices: 2333190--2333228 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
2333180 AGAAGAAGTT
2333190 ATGGAAGAATTTATC
1 ATGGAAGAATTTATC
2333205 ATGGAAGAATTTATC
1 ATGGAAGAATTTATC
2333220 ATGGAAGAA
1 ATGGAAGAA
2333229 ATAGAAGACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (15 bp):
ATGGAAGAATTTATC
Found at i:2343330 original size:75 final size:74
Alignment explanation
Indices: 2343248--2343387 Score: 226
Period size: 75 Copynumber: 1.9 Consensus size: 74
2343238 AAACCTATAC
* * *
2343248 TTATAAATATATATTTATTAAATGATGATTATTGAAATATTTTTTTATTATAATTATTAGTAAGA
1 TTATAAATATATATTCATCAAATGATGATCATTGAAATA-TTTTTTATTATAATTATTAGTAAGA
2343313 TTTAAACCTA
65 TTTAAACCTA
* *
2343323 TTATAAATGTGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATATATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
2343388 ATATTCCACT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
74 26 0.43
75 34 0.57
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.48
Consensus pattern (74 bp):
TTATAAATATATATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
TTAAACCTA
Found at i:2343403 original size:74 final size:76
Alignment explanation
Indices: 2343245--2343405 Score: 229
Period size: 74 Copynumber: 2.2 Consensus size: 76
2343235 CCAAAACCTA
* * *
2343245 TACTTATAAATATATATTTATTAAATGATGATTATTGAAATATTTTTTTATTATAATTATTAGTA
1 TACTTATAAATATATATTCATCAAATGATGATCATTGAAATATTTTTTTATTATAATTATTAGTA
*
2343310 AGATTTAAACC
66 AGATATAAACC
* *
2343321 TA-TTATAAATGTGTATTCATCAAATGATGATCATTGAAATA-TTTTTTATTATAATTATTAGTA
1 TACTTATAAATATATATTCATCAAATGATGATCATTGAAATATTTTTTTATTATAATTATTAGTA
**
2343384 AGATATATTCC
66 AGATATAAACC
2343395 -ACTTATAAATA
1 TACTTATAAATA
2343406 AAAAATTCAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
73 1 0.01
74 38 0.51
75 34 0.45
76 2 0.03
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (76 bp):
TACTTATAAATATATATTCATCAAATGATGATCATTGAAATATTTTTTTATTATAATTATTAGTA
AGATATAAACC
Found at i:2343414 original size:75 final size:75
Alignment explanation
Indices: 2343248--2343414 Score: 194
Period size: 75 Copynumber: 2.2 Consensus size: 75
2343238 AAACCTATAC
* * * * *
2343248 TTATAAATATATATTTATTAAATGATGATTATTGAAATATTTTTTTATTATAATTATTAGTAAGA
1 TTATAAATAAAAATTCATCAAATGATGATCATTGAAATATTTTTTTATTATAATTATTAGTAAGA
*
2343313 TTTAAACCTA
66 TATAAACCTA
****
2343323 TTATAAATGTGTATTCATCAAATGATGATCATTGAAATA-TTTTTTATTATAATTATTAGTAAGA
1 TTATAAATAAAAATTCATCAAATGATGATCATTGAAATATTTTTTTATTATAATTATTAGTAAGA
**
2343387 TATATTCC-A
66 TATAAACCTA
2343396 CTTATAAATAAAAAATTCA
1 -TTATAAAT-AAAAATTCA
2343415 ATTGCATTGA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
73 1 0.01
74 38 0.49
75 39 0.50
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (75 bp):
TTATAAATAAAAATTCATCAAATGATGATCATTGAAATATTTTTTTATTATAATTATTAGTAAGA
TATAAACCTA
Found at i:2343544 original size:31 final size:31
Alignment explanation
Indices: 2343453--2343552 Score: 103
Period size: 31 Copynumber: 3.1 Consensus size: 31
2343443 TATTTTTTTA
* * *
2343453 ATTTTAATTGTATTGTATAATTTAAATATTACT
1 ATTTTAATT-AATT-TATAAATTAAATATTAAT
* *
2343486 ATTTTAAATTAATTTTTAAGTTAAATATTAAT
1 ATTTT-AATTAATTTATAAATTAAATATTAAT
*
2343518 ATTTT-TTTAATATTATAAATTAAATATTAAT
1 ATTTTAATTAAT-TTATAAATTAAATATTAAT
2343549 ATTT
1 ATTT
2343553 ATCAAACTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
30 5 0.09
31 21 0.36
32 20 0.34
33 8 0.14
34 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (31 bp):
ATTTTAATTAATTTATAAATTAAATATTAAT
Found at i:2347106 original size:13 final size:13
Alignment explanation
Indices: 2347075--2347100 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2347065 CTAGTTACTT
2347075 AATATATCCAAAA
1 AATATATCCAAAA
2347088 AATATATCCAAAA
1 AATATATCCAAAA
2347101 GTTATAACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
AATATATCCAAAA
Found at i:2348032 original size:18 final size:18
Alignment explanation
Indices: 2348009--2348044 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2347999 GAATATCATC
2348009 ATAGAGATACCCAAATTT
1 ATAGAGATACCCAAATTT
*
2348027 ATAGAGATATCCAAATTT
1 ATAGAGATACCCAAATTT
2348045 TTGAGTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (18 bp):
ATAGAGATACCCAAATTT
Found at i:2358894 original size:13 final size:13
Alignment explanation
Indices: 2358876--2358903 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2358866 TAAATTAAAA
2358876 TAGGAAAGTATGC
1 TAGGAAAGTATGC
2358889 TAGGAAAGTATGC
1 TAGGAAAGTATGC
2358902 TA
1 TA
2358904 CCCCAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.29, T:0.25
Consensus pattern (13 bp):
TAGGAAAGTATGC
Found at i:2363727 original size:66 final size:66
Alignment explanation
Indices: 2363629--2363788 Score: 187
Period size: 66 Copynumber: 2.4 Consensus size: 66
2363619 GTCTAGTATA
* * *
2363629 CATATGCAATCAGCATGCGAAACCAAAAACATGAATCCTATCCAAG-AATTTGACACCCATGACC
1 CATATGCAATC--CATGCAAAACCAAAAACATGAATCCTAT-CAAGTAATTCGACACCCACGACC
2363693 AAAT
63 AAAT
* * * * ** *
2363697 CATATGCAATCCATGCAAAACTAACAACATGAATCCTATCTAGTAATTCGAGACCCACGATTAGA
1 CATATGCAATCCATGCAAAACCAAAAACATGAATCCTATCAAGTAATTCGACACCCACGACCAAA
2363762 T
66 T
*
2363763 TATATGCAATCCATGCAAAACCAAAA
1 CATATGCAATCCATGCAAAACCAAAA
2363789 CTAGATATAT
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
65 3 0.04
66 64 0.82
68 11 0.14
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.21
Consensus pattern (66 bp):
CATATGCAATCCATGCAAAACCAAAAACATGAATCCTATCAAGTAATTCGACACCCACGACCAAA
T
Found at i:2365660 original size:21 final size:21
Alignment explanation
Indices: 2365636--2365684 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2365626 GCTTCCTATT
** *
2365636 TCTAACAGTTAAAATATTGTG
1 TCTAACAGCCAAAATATTGCG
*
2365657 TCTAATAGCCAAAATATTGCG
1 TCTAACAGCCAAAATATTGCG
2365678 TCTAACA
1 TCTAACA
2365685 ATTAGTTGGG
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:0.16, G:0.12, T:0.33
Consensus pattern (21 bp):
TCTAACAGCCAAAATATTGCG
Found at i:2376224 original size:2 final size:2
Alignment explanation
Indices: 2376219--2376248 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2376209 TGTGTGTGTG
2376219 TA TA 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 TA TA
2376249 GATTCGGTGA
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):
TA
Found at i:2396532 original size:17 final size:17
Alignment explanation
Indices: 2396506--2396540 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2396496 AAAAGTAACA
2396506 AACTAACTTAAA-TAAT
1 AACTAACTTAAATTAAT
2396522 AACTAAACTTAAATTAAT
1 AACT-AACTTAAATTAAT
2396540 A
1 A
2396541 CATTATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (17 bp):
AACTAACTTAAATTAAT
Found at i:2399026 original size:24 final size:24
Alignment explanation
Indices: 2398982--2399028 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2398972 CTCTCGAATC
*
2398982 TCTTCTTCCCATCCACGTAGCTAA
1 TCTTCTTCCCATCCACATAGCTAA
* *
2399006 TCTTCTTCCTATCCATATAGCTA
1 TCTTCTTCCCATCCACATAGCTA
2399029 GCCATAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTTCTTCCCATCCACATAGCTAA
Found at i:2400140 original size:12 final size:12
Alignment explanation
Indices: 2400123--2400148 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2400113 TGACAAGGAG
2400123 AAATCTAATAAA
1 AAATCTAATAAA
2400135 AAATCTAATAAA
1 AAATCTAATAAA
2400147 AA
1 AA
2400149 GTATTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATCTAATAAA
Found at i:2414301 original size:13 final size:13
Alignment explanation
Indices: 2414285--2414328 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
2414275 ATTTAAATAT
2414285 TTTTAAATAATTA
1 TTTTAAATAATTA
2414298 TTTTAAAT-A-T-
1 TTTTAAATAATTA
2414308 TTTTAAATAATTA
1 TTTTAAATAATTA
2414321 TTTTAAAT
1 TTTTAAAT
2414329 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.29
11 2 0.07
12 2 0.07
13 16 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTAAATAATTA
Found at i:2414304 original size:23 final size:23
Alignment explanation
Indices: 2414276--2414334 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
2414266 TTTAATTTTA
2414276 TTTAAATATTTTTAAATAATTAT
1 TTTAAATATTTTTAAATAATTAT
2414299 TTTAAATATTTTTAAATAATTAT
1 TTTAAATATTTTTAAATAATTAT
*
2414322 TTTAAATTTTTTT
1 TTTAAATATTTTT
2414335 TTAAATTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTAAATATTTTTAAATAATTAT
Found at i:2414334 original size:10 final size:10
Alignment explanation
Indices: 2414259--2414334 Score: 55
Period size: 10 Copynumber: 7.0 Consensus size: 10
2414249 TAATAGGAAA
*
2414259 AAATTATTTT
1 AAATTTTTTT
2414269 -AATTTTATTT
1 AAATTTT-TTT
*
2414279 AAATATTTTT
1 AAATTTTTTT
2414289 AAATAATTATTTT
1 AAAT--TT-TTTT
*
2414302 AAATATTTTT
1 AAATTTTTTT
2414312 AAATAATTATTTT
1 AAAT--TT-TTTT
2414325 AAATTTTTTT
1 AAATTTTTTT
2414335 TTAAATTTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
9 5 0.09
10 22 0.42
11 8 0.15
12 2 0.04
13 16 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
AAATTTTTTT
Found at i:2417110 original size:18 final size:18
Alignment explanation
Indices: 2417087--2417131 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
2417077 GTGGGGGAGA
2417087 AGAAGAAAAGAAGAATTC
1 AGAAGAAAAGAAGAATTC
2417105 AGAAGAAAAGAAGAATTC
1 AGAAGAAAAGAAGAATTC
2417123 AGAAGAAAA
1 AGAAGAAAA
2417132 AAAATGAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.64, C:0.04, G:0.22, T:0.09
Consensus pattern (18 bp):
AGAAGAAAAGAAGAATTC
Found at i:2417110 original size:21 final size:21
Alignment explanation
Indices: 2417084--2417134 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 21
2417074 TAAGTGGGGG
2417084 AGAAGAAGAAAAGAAGAATTC
1 AGAAGAAGAAAAGAAGAATTC
2417105 ---AGAAGAAAAGAAGAATTC
1 AGAAGAAGAAAAGAAGAATTC
*
2417123 AGAAGAAAAAAA
1 AGAAGAAGAAAA
2417135 ATGAGGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 18 0.69
21 8 0.31
ACGTcount: A:0.67, C:0.04, G:0.22, T:0.08
Consensus pattern (21 bp):
AGAAGAAGAAAAGAAGAATTC
Found at i:2418376 original size:2 final size:2
Alignment explanation
Indices: 2418369--2418399 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2418359 TATGATTATG
*
2418369 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2418400 GTATTGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2427879 original size:15 final size:15
Alignment explanation
Indices: 2427859--2427926 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
2427849 GATATTATGT
2427859 TTAAATTTAAACAAA
1 TTAAATTTAAACAAA
*
2427874 TTAAATTTAAATATAA
1 TTAAATTTAAACA-AA
* *
2427890 TT-AATCTT----TAT
1 TTAAAT-TTAAACAAA
2427901 TTAAATTTAAACAAA
1 TTAAATTTAAACAAA
2427916 TTAAATTTAAA
1 TTAAATTTAAA
2427927 TTTATATCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
11 5 0.12
12 3 0.07
15 27 0.66
16 6 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAATTTAAACAAA
Found at i:2427882 original size:21 final size:21
Alignment explanation
Indices: 2427858--2427930 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
2427848 GGATATTATG
2427858 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAAATTAAA
* ** **
2427879 TTTAAATAT-AATTAATCTTTA
1 TTTAAATTTAAACAAAT-TAAA
2427900 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAAATTAAA
2427921 TTTAAATTTA
1 TTTAAATTTA
2427931 TATCCTATCT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 5 0.12
21 30 0.75
22 5 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAAATTTAAACAAATTAAA
Found at i:2449437 original size:13 final size:13
Alignment explanation
Indices: 2449395--2449437 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
2449385 CTCTAAATCG
2449395 AAAAGAAAGAA-A
1 AAAAGAAAGAAGA
2449407 GAAAAGAAA-AAGAA
1 -AAAAGAAAGAAG-A
2449421 AAAAGAAAGAAGA
1 AAAAGAAAGAAGA
2449434 AAAA
1 AAAA
2449438 AAAACCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.07
13 21 0.78
14 4 0.15
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAGA
Found at i:2450096 original size:22 final size:22
Alignment explanation
Indices: 2450051--2450098 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2450041 TGGGGCAAAT
*
2450051 ATAATCAAATTAAAATAAATAA
1 ATAATAAAATTAAAATAAATAA
*
2450073 ATAATAAAAGTTAAAATTAA-AA
1 ATAATAAAA-TTAAAATAAATAA
2450095 ATAA
1 ATAA
2450099 AAATAGTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
ATAATAAAATTAAAATAAATAA
Found at i:2460606 original size:27 final size:27
Alignment explanation
Indices: 2460564--2461065 Score: 162
Period size: 27 Copynumber: 18.4 Consensus size: 27
2460554 NNNNNNTAGA
*
2460564 GGCGCTCCAAGTACAGAAGCACCTAAG
1 GGCGTTCCAAGTACAGAAGCACCTAAG
*
2460591 GGCGTTCCAAGCACAGAAATGC-CC-AA-
1 GGCGTTCCAAGTACAG-AA-GCACCTAAG
* * *
2460617 GGTGTTCTAAGTACAGAAGCACCCAAG
1 GGCGTTCCAAGTACAGAAGCACCTAAG
* *
2460644 GGCGTTCTAAGTACAGAAGCGCTTAAACACCCAA-
1 GGCGTTCCAAGTACAGAA--G------CACCTAAG
* * * *
2460678 GGTGTTCTAAGTACAGAAGCGCCTAGG
1 GGCGTTCCAAGTACAGAAGCACCTAAG
** *
2460705 GGCGTTCCAAGCGCAGAAGCACCAAAG
1 GGCGTTCCAAGTACAGAAGCACCTAAG
** * ** *
2460732 GATGTTCCAAGAACAGAAGTGCCCAAG
1 GGCGTTCCAAGTACAGAAGCACCTAAG
* *
2460759 GGCGTTCCAAGTGCAG-AG-ACGCTCAG
1 GGCGTTCCAAGTACAGAAGCAC-CTAAG
* ** *
2460785 GGCGTTCTAAG-AGCAGAAG-TGCTCAGG
1 GGCGTTCCAAGTA-CAGAAGCACCT-AAG
*** * *
2460812 GGCGTTCCAAGCGTAGAAACACCCAA-
1 GGCGTTCCAAGTACAGAAGCACCTAAG
* * * *
2460838 GGTGTTCTAAATACAGAAGCACCCAAAG
1 GGCGTTCCAAGTACAGAAGCA-CCTAAG
* * *
2460866 GGTGTTCCAAGTACAGAAGCACCCAGG
1 GGCGTTCCAAGTACAGAAGCACCTAAG
* * * *
2460893 GGAGTTTCAAGTACAGAAACGCCT-AG
1 GGCGTTCCAAGTACAGAAGCACCTAAG
* * * * * *
2460919 GGTGTTCTAAGTATAGAAACGCCTAGG
1 GGCGTTCCAAGTACAGAAGCACCTAAG
** * *
2460946 GGCGTTCCAAGCGCAAAAGCACCCAAAG
1 GGCGTTCCAAGTACAGAAGCA-CCTAAG
* * * ** * *
2460974 GGTGTTCCAAGCACAAAAGTGCCCAGG
1 GGCGTTCCAAGTACAGAAGCACCTAAG
* ** * * *
2461001 GGTGTTCCAAGTGTAGAAACGCC-CAG
1 GGCGTTCCAAGTACAGAAGCACCTAAG
* ** * *
2461027 GGTGTTATAAGTACAGAAGCGCCTAGG
1 GGCGTTCCAAGTACAGAAGCACCTAAG
2461054 GGCGTTCCAAGT
1 GGCGTTCCAAGT
2461066 GCAAAAGTGC
Statistics
Matches: 348, Mismatches: 102, Indels: 50
0.70 0.20 0.10
Matches are distributed among these distances:
24 2 0.01
25 5 0.01
26 93 0.27
27 175 0.50
28 45 0.13
29 3 0.01
32 1 0.00
34 17 0.05
35 7 0.02
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.16
Consensus pattern (27 bp):
GGCGTTCCAAGTACAGAAGCACCTAAG
Found at i:2460660 original size:53 final size:53
Alignment explanation
Indices: 2460572--2460883 Score: 230
Period size: 53 Copynumber: 5.7 Consensus size: 53
2460562 GAGGCGCTCC
* *
2460572 AAGTACAGAAGCACCTAAGGGCGTTCCAAGCACAGAAATGCCCAAGGTGTTCT
1 AAGTACAGAAGCACCCAAGGGCGTTCCAAGCACAGAAACGCCCAAGGTGTTCT
* * *
2460625 AAGTACAGAAGCACCCAAGGGCGTTCTAAGTACAGAAGCGCTTAAACACCCAAGGTGTTCT
1 AAGTACAGAAGCACCCAAGGGCGTTCCAAG--CA-CA--G---AAACGCCCAAGGTGTTCT
* * * * * * * *
2460686 AAGTACAGAAGCGCCTAGGGGCGTTCCAAGCGCAGAAGCACCAAAGGATGTTCC
1 AAGTACAGAAGCACCCAAGGGCGTTCCAAGCACAGAAACGCCCAAGG-TGTTCT
* ** ** * * * *
2460740 AAGAACAGAAGTGCCCAAGGGCGTTCCAAGTGCAGAGACGCTCAGGGCGTTCT
1 AAGTACAGAAGCACCCAAGGGCGTTCCAAGCACAGAAACGCCCAAGGTGTTCT
** * * ** *
2460793 AAG-AGCAGAAGTGCTCAGGGGCGTTCCAAGCGTAGAAACACCCAAGGTGTTCT
1 AAGTA-CAGAAGCACCCAAGGGCGTTCCAAGCACAGAAACGCCCAAGGTGTTCT
* * *
2460846 AAATACAGAAGCACCCAAAGGGTGTTCCAAGTACAGAA
1 AAGTACAGAAGCACCC-AAGGGCGTTCCAAGCACAGAA
2460884 GCACCCAGGG
Statistics
Matches: 202, Mismatches: 45, Indels: 23
0.75 0.17 0.09
Matches are distributed among these distances:
52 1 0.00
53 94 0.47
54 58 0.29
55 2 0.01
56 2 0.01
58 2 0.01
59 1 0.00
61 42 0.21
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.16
Consensus pattern (53 bp):
AAGTACAGAAGCACCCAAGGGCGTTCCAAGCACAGAAACGCCCAAGGTGTTCT
Found at i:2460818 original size:107 final size:107
Alignment explanation
Indices: 2460681--2460920 Score: 260
Period size: 107 Copynumber: 2.2 Consensus size: 107
2460671 CACCCAAGGT
*
2460681 GTTCTAAGTACAGAAGCGCCTAGGGGCGTTCCAAGCGCAGAAGCACCAAAGGATGTTCCAAGA-A
1 GTTCTAAGTACAGAAGCGCCTAGGGGCGTTCCAAGCGCAGAAACACCAAAGG-TGTTCCAA-ATA
** *
2460745 CAGAAGTGCCC-AAGGGCGTTCCAAGTGCAGAGACGCTCAGGGC
64 CAGAAGCACCCAAAGGGCGTTCCAAGTACAGAGACGCTCAGGGC
* * * *
2460788 GTTCTAAG-AGCAGAAGTG-CTCAGGGGCGTTCCAAGCGTAGAAACACCCAAGGTGTTCTAAATA
1 GTTCTAAGTA-CAGAAGCGCCT-AGGGGCGTTCCAAGCGCAGAAACACCAAAGGTGTTCCAAATA
* *
2460851 CAGAAGCACCCAAAGGGTGTTCCAAGTACAGAAGCAC-C-CAGGGGA
64 CAGAAGCACCCAAAGGGCGTTCCAAGTACAG-AG-ACGCTCA-GGGC
*
2460896 GTT-TCAAGTACAGAAACGCCTAGGG
1 GTTCT-AAGTACAGAAGCGCCTAGGG
2460921 TGTTCTAAGT
Statistics
Matches: 111, Mismatches: 12, Indels: 19
0.78 0.08 0.13
Matches are distributed among these distances:
105 1 0.01
106 20 0.18
107 63 0.57
108 22 0.20
109 5 0.05
ACGTcount: A:0.32, C:0.24, G:0.29, T:0.15
Consensus pattern (107 bp):
GTTCTAAGTACAGAAGCGCCTAGGGGCGTTCCAAGCGCAGAAACACCAAAGGTGTTCCAAATACA
GAAGCACCCAAAGGGCGTTCCAAGTACAGAGACGCTCAGGGC
Found at i:2460904 original size:134 final size:135
Alignment explanation
Indices: 2460718--2460980 Score: 313
Period size: 134 Copynumber: 2.0 Consensus size: 135
2460708 GTTCCAAGCG
** * * *
2460718 CAGAAGCACCAAAGGATGTTCCAAGAACAGAAGTGCCCAAGGGCGTTCCAAGTGCAGAGACG-CT
1 CAGAAGCACCAAAGGATGTTCCAAGAACAGAAGCACCCAAGGGAGTTCCAAGTACAGAAACGCCT
** *
2460782 CAGGGCGTTCTAAG-AGCAGAAGTG-CTCAGGGGCGTTCCAAGCGTAGAAA-CACCC-AA-GGTG
66 -AGGGCGTTCTAAGTA-CAGAAACGCCT-AGGGGCGTTCCAAGCGCA-AAAGCACCCAAAGGGTG
2460842 TTCTAAATA
127 TTCTAAATA
* * * *
2460851 CAGAAGCACCCAAAGGGTGTTCCAAGTACAGAAGCACCCAGGGGAGTTTCAAGTACAGAAACGCC
1 CAGAAGCA-CCAAAGGATGTTCCAAGAACAGAAGCACCCAAGGGAGTTCCAAGTACAGAAACGCC
* *
2460916 TAGGGTGTTCTAAGTATAGAAACGCCTAGGGGCGTTCCAAGCGCAAAAGCACCCAAAGGGTGTTC
65 TAGGGCGTTCTAAGTACAGAAACGCCTAGGGGCGTTCCAAGCGCAAAAGCACCCAAAGGGTGTTC
2460981 CAAGCACAAA
Statistics
Matches: 109, Mismatches: 14, Indels: 11
0.81 0.10 0.08
Matches are distributed among these distances:
133 11 0.10
134 84 0.77
135 7 0.06
136 7 0.06
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (135 bp):
CAGAAGCACCAAAGGATGTTCCAAGAACAGAAGCACCCAAGGGAGTTCCAAGTACAGAAACGCCT
AGGGCGTTCTAAGTACAGAAACGCCTAGGGGCGTTCCAAGCGCAAAAGCACCCAAAGGGTGTTCT
AAATA
Found at i:2460931 original size:53 final size:53
Alignment explanation
Indices: 2460863--2461118 Score: 228
Period size: 53 Copynumber: 4.8 Consensus size: 53
2460853 GAAGCACCCA
* * * *
2460863 AAGGGTGTTCCAAGTACAGAAGCACCCAGGGGAGTTTCAAGTACAGAAACGCC
1 AAGGGTGTTCCAAGTACAGAAGCGCCCAGGGGCGTTCCAAGTGCAGAAACGCC
* * * * * * *
2460916 TAGGGTGTTCTAAGTATAGAAACGCCTAGGGGCGTTCCAAGCGCA-AAAGCACCC
1 AAGGGTGTTCCAAGTACAGAAGCGCCCAGGGGCGTTCCAAGTGCAGAAA-C-GCC
* * * * *
2460970 AAAGGGTGTTCCAAGCACAAAAGTGCCCAGGGGTGTTCCAAGTGTAGAAACGCC
1 -AAGGGTGTTCCAAGTACAGAAGCGCCCAGGGGCGTTCCAAGTGCAGAAACGCC
* ** * *
2461024 CAGGGTGTTATAAGTACAGAAGCGCCTAGGGGCGTTCCAAGTGCA-AAAGTGCCC
1 AAGGGTGTTCCAAGTACAGAAGCGCCCAGGGGCGTTCCAAGTGCAGAAA-CG-CC
* ** *
2461078 AAGGGTGTTACAAGTATTGAAGCGCCCAGGGGTGTTCCAAG
1 AAGGGTGTTCCAAGTACAGAAGCGCCCAGGGGCGTTCCAAG
2461119 CGTAGAAGTT
Statistics
Matches: 158, Mismatches: 39, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
52 6 0.04
53 73 0.46
54 41 0.26
55 35 0.22
56 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.30, T:0.18
Consensus pattern (53 bp):
AAGGGTGTTCCAAGTACAGAAGCGCCCAGGGGCGTTCCAAGTGCAGAAACGCC
Found at i:2460978 original size:108 final size:108
Alignment explanation
Indices: 2460854--2461118 Score: 361
Period size: 108 Copynumber: 2.5 Consensus size: 108
2460844 CTAAATACAG
* * * *
2460854 AAGCACCCAAAGGGTGTTCCAAGTACAGAAGCACCCAGGGGAGTTTCAAGTACAGAAACGCCTAG
1 AAGCACCCAAAGGGTGTTCCAAGTACAGAAGCGCCCAGGGGTGTTCCAAGTACAGAAACGCCCAG
* *
2460919 GGTGTTCTAAGTATAGAAACGCCTAGGGGCGTTCCAAGCGCAA
66 GGTGTTATAAGTACAGAAACGCCTAGGGGCGTTCCAAGCGCAA
* * * **
2460962 AAGCACCCAAAGGGTGTTCCAAGCACAAAAGTGCCCAGGGGTGTTCCAAGTGTAGAAACGCCCAG
1 AAGCACCCAAAGGGTGTTCCAAGTACAGAAGCGCCCAGGGGTGTTCCAAGTACAGAAACGCCCAG
* *
2461027 GGTGTTATAAGTACAGAAGCGCCTAGGGGCGTTCCAAGTGCAA
66 GGTGTTATAAGTACAGAAACGCCTAGGGGCGTTCCAAGCGCAA
** * **
2461070 AAGTGCCC-AAGGGTGTTACAAGTATTGAAGCGCCCAGGGGTGTTCCAAG
1 AAGCACCCAAAGGGTGTTCCAAGTACAGAAGCGCCCAGGGGTGTTCCAAG
2461119 CGTAGAAGTT
Statistics
Matches: 136, Mismatches: 21, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
107 35 0.26
108 101 0.74
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (108 bp):
AAGCACCCAAAGGGTGTTCCAAGTACAGAAGCGCCCAGGGGTGTTCCAAGTACAGAAACGCCCAG
GGTGTTATAAGTACAGAAACGCCTAGGGGCGTTCCAAGCGCAA
Found at i:2461126 original size:27 final size:27
Alignment explanation
Indices: 2460678--2461158 Score: 236
Period size: 27 Copynumber: 17.9 Consensus size: 27
2460668 AAACACCCAA
* * *
2460678 GGTGTTCTAAGTACAGAAGCGCCTAGG
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* * * * *
2460705 GGCGTTCCAAGCGCAGAAGCACCAAAG
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* ** * *
2460732 GATGTTCCAAGAACAGAAGTGCCCAAG
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* *
2460759 GGCGTTCCAAGTGCAG-AGACGCTCA-G
1 GGTGTTCCAAGTGCAGAAG-CGCCCAGG
* * * * *
2460785 GGCGTTCTAAGAGCAGAAGTGCTCAGG
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* * * * * *
2460812 GGCGTTCCAAGCGTAGAAACACCCA-A
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* * * * *
2460838 GGTGTTCTAAATACAGAAGCACCCAAAG
1 GGTGTTCCAAGTGCAGAAGCGCCC-AGG
* *
2460866 GGTGTTCCAAGTACAGAAGCACCCAGG
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* * * * *
2460893 GGAGTTTCAAGTACAGAAACGCCTA-G
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* ** * *
2460919 GGTGTTCTAAGTATAGAAACGCCTAGG
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* * * * *
2460946 GGCGTTCCAAGCGCAAAAGCACCCAAAG
1 GGTGTTCCAAGTGCAGAAGCGCCC-AGG
** * *
2460974 GGTGTTCCAAGCACAAAAGTGCCCAGG
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* *
2461001 GGTGTTCCAAGTGTAGAAACGCCCA-G
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
** * *
2461027 GGTGTTATAAGTACAGAAGCGCCTAGG
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* * * *
2461054 GGCGTTCCAAGTGCAAAAGTGCCCAAG
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* ***
2461081 GGTGTTACAAGTATTGAAGCGCCCAGG
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
* * ** * *
2461108 GGTGTTCCAAGCGTAGAAGTTCCTAGA
1 GGTGTTCCAAGTGCAGAAGCGCCCAGG
*
2461135 GG-GTTCCAAGCGCAGAAGCGCCCA
1 GGTGTTCCAAGTGCAGAAGCGCCCA
2461159 AAGCACTGCA
Statistics
Matches: 340, Mismatches: 106, Indels: 17
0.73 0.23 0.04
Matches are distributed among these distances:
26 99 0.29
27 197 0.58
28 44 0.13
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.17
Consensus pattern (27 bp):
GGTGTTCCAAGTGCAGAAGCGCCCAGG
Found at i:2461141 original size:80 final size:80
Alignment explanation
Indices: 2460917--2461159 Score: 202
Period size: 80 Copynumber: 3.0 Consensus size: 80
2460907 AGAAACGCCT
* * * * * * * * *
2460917 AGGGTGTT-CTAAGTATAGAAACGCCTAGGGGCGTTCCAAGCGCAAAAGCACCCAAAGGGTGTTC
1 AGGGTGTTAC-AAGTATAGAAACGCCCA-GGGTGTTACAAGCACAGAAGCGCCTAGA-GGCGTTC
*
2460981 CAAGCACAAAAGTGCCCA
63 CAAGCGCAAAAGTGCCCA
* * * * * *
2460999 GGGGTGTTCCAAGTGTAGAAACGCCCAGGGTGTTATAAGTACAGAAGCGCCTAGGGGCGTTCCAA
1 AGGGTGTTACAAGTATAGAAACGCCCAGGGTGTTACAAGCACAGAAGCGCCTAGAGGCGTTCCAA
*
2461064 GTGCAAAAGTGCCCA
66 GCGCAAAAGTGCCCA
* * * ** **
2461079 AGGGTGTTACAAGTATTGAAGCGCCCAGGGGTGTTCCAAGCGTAGAAGTTCCTAGAGG-GTTCCA
1 AGGGTGTTACAAGTATAGAAACGCCCA-GGGTGTTACAAGCACAGAAGCGCCTAGAGGCGTTCCA
* *
2461143 AGCGCAGAAGCGCCCA
65 AGCGCAAAAGTGCCCA
2461159 A
1 A
2461160 AGCACTGCAA
Statistics
Matches: 127, Mismatches: 32, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
80 64 0.50
81 40 0.31
82 22 0.17
83 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.30, T:0.18
Consensus pattern (80 bp):
AGGGTGTTACAAGTATAGAAACGCCCAGGGTGTTACAAGCACAGAAGCGCCTAGAGGCGTTCCAA
GCGCAAAAGTGCCCA
Found at i:2465185 original size:135 final size:134
Alignment explanation
Indices: 2464915--2465321 Score: 517
Period size: 135 Copynumber: 3.0 Consensus size: 134
2464905 CCCTTGGACA
* * * * * * * * *
2464915 CTTTTGCACTTAGAACGTCCCTGGGTGCTTCTGTACTTAAAACACCCTAGGCGCTTCTGCACTTG
1 CTTTTGCACTTGGAACGCCCCTAGGCGTTTCTATACTTAGAACACCCTGGGCGTTTCTGCACTTG
*
2464980 GAACACCCCTGAGCGTTTTGTGCTTGAAACGCCCCTGGGCACTTTTGTACTTGGAACTCCTTTTG
66 GAACACCCCTGAGCTTTTTGTGCTTGAAACGCCCCTGGGCACTTTTGTACTTGGAACTCCTTTTG
2465045 GGTG
131 GGTG
*
2465049 CTTTTGCACTTGGAACGCCCCTAAGCGTTTCTATACTTAGAACACCCTGGGCGTTTCTGCACTTG
1 CTTTTGCACTTGGAACGCCCCTAGGCGTTTCTATACTTAGAACACCCTGGGCGTTTCTGCACTTG
*
2465114 GAACACCCCTGAGCATTTTTGTGCTTGAAACGCCCCTGGGCACTTTTGTATTTGGAACTCCTTTT
66 GAACACCCCTGAGC-TTTTTGTGCTTGAAACGCCCCTGGGCACTTTTGTACTTGGAACTCCTTTT
2465179 GGGTG
130 GGGTG
* * * ***
2465184 CTTTTGCACTTGGAATGCCCCTAGGCGTTTCTATACTTAGAACAACCTGGGCATTTCTGTGTTTG
1 CTTTTGCACTTGGAACGCCCCTAGGCGTTTCTATACTTAGAACACCCTGGGCGTTTCTGCACTTG
* * * * * * * ** * * * *
2465249 GAACGCCCCTAAGCGTTTTTGTACTTGGAACTCCCTTAGGTGCTTTCGCACTTGGAACACCCTTT
66 GAACACCCCTGAGC-TTTTTGTGCTTGAAACGCCCCTGGGCACTTTTGTACTTGGAACTCCTTTT
2465314 GGGTG
130 GGGTG
2465319 CTT
1 CTT
2465322 CTGTACTTAG
Statistics
Matches: 238, Mismatches: 34, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
134 69 0.29
135 169 0.71
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (134 bp):
CTTTTGCACTTGGAACGCCCCTAGGCGTTTCTATACTTAGAACACCCTGGGCGTTTCTGCACTTG
GAACACCCCTGAGCTTTTTGTGCTTGAAACGCCCCTGGGCACTTTTGTACTTGGAACTCCTTTTG
GGTG
Found at i:2465271 original size:108 final size:107
Alignment explanation
Indices: 2465083--2465393 Score: 329
Period size: 108 Copynumber: 2.9 Consensus size: 107
2465073 GCGTTTCTAT
* * * * * * *
2465083 ACTTAGAACA-CCCTGGGCGTTTCTGCACTTGGAACACCCCTGAGCATTTTTGTGCTTGAAACGC
1 ACTTGGAACACCCCTAGGCGTTTCTGTACTTAGAACA-CCCTGGGCATTTCTGTGCTTGGAACGC
** ** * * * *
2465147 CCCTGGGCACTTTTGTATTTGGAACTCCTTTTGGGTGCTTTTGC
65 CCCTAAGCGTTTTTGTACTTGGAACTCC-CTTAGGTGCTTTCGC
** * * *
2465191 ACTTGGAATGCCCCTAGGCGTTTCTATACTTAGAACAACCTGGGCATTTCTGTGTTTGGAACGCC
1 ACTTGGAACACCCCTAGGCGTTTCTGTACTTAGAACACCCTGGGCATTTCTGTGCTTGGAACGCC
2465256 CCTAAGCGTTTTTGTACTTGGAACTCCCTTAGGTGCTTTCGC
66 CCTAAGCGTTTTTGTACTTGGAACTCCCTTAGGTGCTTTCGC
* * * * *
2465298 ACTTGGAACACCCTTTGG-GTGCTTCTGTACTTAGAATACCCTGGGCGTTTCTGCGCTTGGAACG
1 ACTTGGAACACCCCTAGGCGT--TTCTGTACTTAGAACACCCTGGGCATTTCTGTGCTTGGAACG
* *
2465362 CCCCTAAGCGTTTTTGTGCTTGGAACGCCCTT
64 CCCCTAAGCGTTTTTGTACTTGGAACTCCCTT
2465394 GAGCACTTTT
Statistics
Matches: 168, Mismatches: 32, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
106 2 0.01
107 26 0.15
108 118 0.70
109 22 0.13
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.33
Consensus pattern (107 bp):
ACTTGGAACACCCCTAGGCGTTTCTGTACTTAGAACACCCTGGGCATTTCTGTGCTTGGAACGCC
CCTAAGCGTTTTTGTACTTGGAACTCCCTTAGGTGCTTTCGC
Found at i:2465276 original size:27 final size:27
Alignment explanation
Indices: 2464869--2465391 Score: 174
Period size: 27 Copynumber: 19.4 Consensus size: 27
2464859 AACTTCTACG
* * *
2464869 CTTGGAATGCCCCCGGGCGTTTCTGTA
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* * * * ** *
2464896 CTTGTAACACCCTTGGACACTTTTGCA
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* * * * *
2464923 CTTAGAACGTCCCTGGGTGCTTCTGTA
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
** * * * * *
2464950 CTTAAAAC-ACCCTAGGCGCTTCTGCA
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* * *
2464976 CTTGGAACACCCCTGAGCG-TTTTGTG
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* **
2465002 CTTGAAACGCCCCTGGGCACTTTTGTA
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* ** * * *
2465029 CTTGGAACTCCTTTTGGGTGCTTTTGCA
1 CTTGGAACGCC-CCTGGGCGTTTTTGTA
** * *
2465057 CTTGGAACGCCCCTAAGCGTTTCTATA
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* * * *
2465084 CTTAGAAC-ACCCTGGGCGTTTCTGCA
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* * * *
2465110 CTTGGAACACCCCTGAGCATTTTTGTG
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* **
2465137 CTTGAAACGCCCCTGGGCACTTTTGTA
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* * ** * * *
2465164 TTTGGAACTCCTTTTGGGTGCTTTTGCA
1 CTTGGAACGCC-CCTGGGCGTTTTTGTA
* * * *
2465192 CTTGGAATGCCCCTAGGCGTTTCTATA
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* ** * * *
2465219 CTTAGAAC-AACCTGGGCATTTCTGTG
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* **
2465245 TTTGGAACGCCCCTAAGCGTTTTTGTA
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* * * * * * *
2465272 CTTGGAACTCCCTTAGGTGCTTTCGCA
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
* * * * *
2465299 CTTGGAACACCCTTTGGGTGCTTCTGTA
1 CTTGGAACGCCC-CTGGGCGTTTTTGTA
* ** * **
2465327 CTTAGAA-TACCCTGGGCGTTTCTGCG
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
** *
2465353 CTTGGAACGCCCCTAAGCGTTTTTGTG
1 CTTGGAACGCCCCTGGGCGTTTTTGTA
2465380 CTTGGAACGCCC
1 CTTGGAACGCCC
2465392 TTGAGCACTT
Statistics
Matches: 351, Mismatches: 137, Indels: 16
0.70 0.27 0.03
Matches are distributed among these distances:
26 93 0.26
27 201 0.57
28 57 0.16
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (27 bp):
CTTGGAACGCCCCTGGGCGTTTTTGTA
Found at i:2465329 original size:28 final size:27
Alignment explanation
Indices: 2465266--2465339 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
2465256 CCTAAGCGTT
*
2465266 TTTGTACTTGGAACTCCC-TTAGGTGC
1 TTTGTACTTGGAACACCCTTTAGGTGC
* *
2465292 TTTCGCACTTGGAACACCCTTTGGGTGC
1 TTT-GTACTTGGAACACCCTTTAGGTGC
* *
2465320 TTCTGTACTTAGAATACCCT
1 TT-TGTACTTGGAACACCCT
2465340 GGGCGTTTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 3 0.08
27 13 0.33
28 22 0.56
29 1 0.03
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (27 bp):
TTTGTACTTGGAACACCCTTTAGGTGC
Found at i:2465403 original size:27 final size:27
Alignment explanation
Indices: 2465352--2465410 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
2465342 GCGTTTCTGC
**
2465352 GCTTGGAACGCCCCTAAGCGTTTTTGT
1 GCTTGGAACGCCCCTAAGCACTTTTGT
* *
2465379 GCTTGGAACGCCCTTGAGCACTTTTGT
1 GCTTGGAACGCCCCTAAGCACTTTTGT
*
2465406 TCTTG
1 GCTTG
2465411 AAACATGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (27 bp):
GCTTGGAACGCCCCTAAGCACTTTTGT
Found at i:2465457 original size:108 final size:108
Alignment explanation
Indices: 2465218--2465458 Score: 243
Period size: 108 Copynumber: 2.2 Consensus size: 108
2465208 GCGTTTCTAT
* * * * * *
2465218 ACTTAGAACAACCTGGGCATTTCTGTGTTTGGAACGCCCCTAAGCGTTTTTGTACTTGGAACTCC
1 ACTTAGAAGACCCTAGGCATTTCTGCGCTTGGAACGCCCCTAAGCGTTTTTGTACTTGGAACGCC
** * * *
2465283 CTTAGGTGCTTTCGCACTTGGAACACCCTTTGGGTGCTTCTGT
66 CTTAGGCACTTTCGCACTTGAAACACCCTTTGAGTGCTTCTGC
* * * *
2465326 ACTTAGAATACCCTGGGCGTTTCTGCGCTTGGAACGCCCCTAAGCGTTTTTGTGCTTGGAACGCC
1 ACTTAGAAGACCCTAGGCATTTCTGCGCTTGGAACGCCCCTAAGCGTTTTTGTACTTGGAACGCC
* ** **
2465391 CTT-GAGCACTTTTGTTCTTGAAACATGCTTT-AGTGCTTCTGC
66 CTTAG-GCACTTTCGCACTTGAAACACCCTTTGAGTGCTTCTGC
* * *
2465433 GCTTGGAACGCCCCTAGGCATTTCTG
1 ACTTAGAA-GACCCTAGGCATTTCTG
2465459 TACTTAGAAC
Statistics
Matches: 108, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
107 16 0.15
108 92 0.85
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.34
Consensus pattern (108 bp):
ACTTAGAAGACCCTAGGCATTTCTGCGCTTGGAACGCCCCTAAGCGTTTTTGTACTTGGAACGCC
CTTAGGCACTTTCGCACTTGAAACACCCTTTGAGTGCTTCTGC
Found at i:2465578 original size:27 final size:27
Alignment explanation
Indices: 2465486--2465599 Score: 95
Period size: 27 Copynumber: 4.3 Consensus size: 27
2465476 GTGTTTAAGC
* ** *
2465486 GCTTCTGTACTTGAAACACCCCTGGGT
1 GCTTCTGTACTTGGAACACCTTTAGGT
* * *
2465513 GCTTCTGTACTTAGAACACC-TTGGGC
1 GCTTCTGTACTTGGAACACCTTTAGGT
* * * *
2465539 GTTTCTGTGCTTGGAACGCCTTTAAGT
1 GCTTCTGTACTTGGAACACCTTTAGGT
* * *
2465566 GCTTCTGTACTTGGAGCGCCTCTAGGT
1 GCTTCTGTACTTGGAACACCTTTAGGT
2465593 GCTTCTG
1 GCTTCTG
2465600 CGCTTAGAAT
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
26 20 0.29
27 50 0.71
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.34
Consensus pattern (27 bp):
GCTTCTGTACTTGGAACACCTTTAGGT
Found at i:2465716 original size:107 final size:107
Alignment explanation
Indices: 2465514--2465716 Score: 230
Period size: 107 Copynumber: 1.9 Consensus size: 107
2465504 CCCCTGGGTG
* * * * ** *
2465514 CTTCTGTACTTAGAACACCTTGGGCGTTTCTGTGCTTGGAACGCCTTTAAGTGCTTCTGTACTTG
1 CTTCTGTACTTAAAACACCTTAGGCGTTTCTGCGCTTGGAACACCCCTAAGCGCTTCTGTACTTG
* * *
2465579 GAGCGCCTCTAGGTGCTTCTGCGCTTAGAATGCCCCTGGACA
66 GAACGCCTCTAGGTGCTTCTACGCTCAGAATGCCCCTGGACA
* * *
2465621 CTTCTGTACTTAAAACACTTTAGGCGCTTT-TGCGCTTGGAACACCCCTAAGCGCTTTTGTAGTT
1 CTTCTGTACTTAAAACACCTTAGGCG-TTTCTGCGCTTGGAACACCCCTAAGCGCTTCTGTACTT
* * *
2465685 GGAATGCC-CTTGGATGCTTCTATGCTCAGAAT
65 GGAACGCCTCTAGG-TGCTTCTACGCTCAGAAT
2465717 ACTCCTGGGC
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
106 4 0.05
107 71 0.91
108 3 0.04
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.33
Consensus pattern (107 bp):
CTTCTGTACTTAAAACACCTTAGGCGTTTCTGCGCTTGGAACACCCCTAAGCGCTTCTGTACTTG
GAACGCCTCTAGGTGCTTCTACGCTCAGAATGCCCCTGGACA
Found at i:2465756 original size:16 final size:16
Alignment explanation
Indices: 2465735--2465767 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2465725 GCGCTTCCAC
*
2465735 GCTTGGAATACCTTTG
1 GCTTGGAACACCTTTG
2465751 GCTTGGAACACCTTTG
1 GCTTGGAACACCTTTG
2465767 G
1 G
2465768 GAAAATGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.33
Consensus pattern (16 bp):
GCTTGGAACACCTTTG
Found at i:2469190 original size:60 final size:60
Alignment explanation
Indices: 2469120--2469238 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
2469110 ACCTTTGTGC
* * *
2469120 ATTTTGAGCATTTTGGAGTGATTTTTGATACACGAAGAAAAACCTTTGAGCATTTTGAGA
1 ATTTTAAGCATTTTGGAGTGATTTTTGATACACAAAGAAAAACCTTTAAGCATTTTGAGA
* * * *
2469180 ATTTTAAGCATTTTGGAGTGGTTTTTGATAGATAAAGAAAAACTTTTAAGCATTTTGAG
1 ATTTTAAGCATTTTGGAGTGATTTTTGATACACAAAGAAAAACCTTTAAGCATTTTGAG
2469239 CATTCTTCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.39
Consensus pattern (60 bp):
ATTTTAAGCATTTTGGAGTGATTTTTGATACACAAAGAAAAACCTTTAAGCATTTTGAGA
Found at i:2469436 original size:44 final size:44
Alignment explanation
Indices: 2469345--2469442 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
2469335 GTTTTGGTAG
* * * * *
2469345 TTTTTAAGTATTGTGTAACCAGTTTTTGGGCATTGCATGACTAA
1 TTTTTAAGTATTGCGTAACCAGTTTTTAGACATTACATAACTAA
* * * *
2469389 TTTTTAAGTATTGCGTGACTAGTTTTTAGACATTACGTAACTGA
1 TTTTTAAGTATTGCGTAACCAGTTTTTAGACATTACATAACTAA
*
2469433 TTTTAAAGTA
1 TTTTTAAGTA
2469443 CTACTTGACT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (44 bp):
TTTTTAAGTATTGCGTAACCAGTTTTTAGACATTACATAACTAA
Found at i:2469573 original size:22 final size:22
Alignment explanation
Indices: 2469517--2469574 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2469507 NNNNNNNAAT
*
2469517 TAGTTACGCAATGCCTACAACC
1 TAGTCACGCAATGCCTACAACC
*
2469539 TAGTCACACAATGCCTACAACC
1 TAGTCACGCAATGCCTACAACC
*
2469561 TAGTCACGTAATGC
1 TAGTCACGCAATGC
2469575 TTAAAAACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (22 bp):
TAGTCACGCAATGCCTACAACC
Found at i:2469651 original size:22 final size:22
Alignment explanation
Indices: 2469626--2469667 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2469616 AATCAATCTT
*
2469626 ACAATACCTAAAACCTAGTAAC
1 ACAATACCTAAAAACTAGTAAC
**
2469648 ACAATGTCTAAAAACTAGTA
1 ACAATACCTAAAAACTAGTA
2469668 CTGCCATATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (22 bp):
ACAATACCTAAAAACTAGTAAC
Found at i:2471256 original size:22 final size:22
Alignment explanation
Indices: 2471223--2471275 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
2471213 NACATAATGT
*
2471223 CTAAAAACTAATCACGCAATAC
1 CTAAAAATTAATCACGCAATAC
* *
2471245 TTAAAAATTAATCATGCAATAC
1 CTAAAAATTAATCACGCAATAC
2471267 CTAAAAATT
1 CTAAAAATT
2471276 GGTTACACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.26
Consensus pattern (22 bp):
CTAAAAATTAATCACGCAATAC
Found at i:2505599 original size:20 final size:21
Alignment explanation
Indices: 2505574--2505613 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2505564 AACTTCTTAA
* *
2505574 AAATTACATTTAT-TGAATTT
1 AAATTAAATTAATGTGAATTT
2505594 AAATTAAATTAATGTGAATT
1 AAATTAAATTAATGTGAATT
2505614 AAGGCAACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATTAAATTAATGTGAATTT
Found at i:2524837 original size:17 final size:18
Alignment explanation
Indices: 2524798--2524837 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2524788 AGTTTTAGGC
*
2524798 TTATCTAATTTATTTTGT
1 TTATGTAATTTATTTTGT
*
2524816 TTATGTAATTTCTTTT-T
1 TTATGTAATTTATTTTGT
2524833 TTATG
1 TTATG
2524838 CATGAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (18 bp):
TTATGTAATTTATTTTGT
Found at i:2529375 original size:72 final size:72
Alignment explanation
Indices: 2529299--2529515 Score: 242
Period size: 72 Copynumber: 3.0 Consensus size: 72
2529289 NNNNNNNNNN
* *
2529299 CCAATGGAATTAGGCAATGCTCCAGAGAGATTTGTAAAACTTAGATCCAAAACTTTAAATGAAAC
1 CCAATGGAATTAGGCAATGCTCCAGAGAGATTTGTAAAACTTAGATCCAAAAGTTTCAATGAAAC
2529364 TAAATTG
66 TAAATTG
* * * ** * * *
2529371 CCAATAGATTTAGGCAATGCTCCAAAGAGATTCATAAATCTTAGAGCC-AAAGTTTCCAATAAAA
1 CCAATGGAATTAGGCAATGCTCCAGAGAGATTTGTAAAACTTAGATCCAAAAGTTT-CAATGAAA
*
2529435 CTAAGTTG
65 CTAAATTG
* * * * *
2529443 CCAATGGAATTAGGTAATTCTCCAGAGAGGGATGTGT--CACTTAGATCCAAATGTTTCAATGAA
1 CCAATGGAATTAGGCAATGCTCCAGAGA--GATTTGTAAAACTTAGATCCAAAAGTTTCAATGAA
2529506 ACTAAATTG
64 ACTAAATTG
2529515 C
1 C
2529516 NNNNNNNNNN
Statistics
Matches: 116, Mismatches: 25, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
71 6 0.05
72 100 0.86
73 6 0.05
74 4 0.03
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.27
Consensus pattern (72 bp):
CCAATGGAATTAGGCAATGCTCCAGAGAGATTTGTAAAACTTAGATCCAAAAGTTTCAATGAAAC
TAAATTG
Found at i:2530860 original size:17 final size:18
Alignment explanation
Indices: 2530840--2530873 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2530830 TTAATTTATG
2530840 CATAAA-AAAAGAAATTA
1 CATAAACAAAAGAAATTA
*
2530857 CATAAACAAAATAAATT
1 CATAAACAAAAGAAATT
2530874 GGGTAAGCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.68, C:0.09, G:0.03, T:0.21
Consensus pattern (18 bp):
CATAAACAAAAGAAATTA
Found at i:2544166 original size:14 final size:15
Alignment explanation
Indices: 2544144--2544189 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
2544134 CAATTTATAT
2544144 TATTATTTTTATTTA
1 TATTATTTTTATTTA
2544159 TATT-TTTTTATTT-
1 TATTATTTTTATTTA
* *
2544172 TTTTATTTCTATTT-
1 TATTATTTTTATTTA
2544186 TATT
1 TATT
2544190 TGTTCATATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 3 0.11
14 20 0.74
15 4 0.15
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (15 bp):
TATTATTTTTATTTA
Found at i:2544177 original size:22 final size:23
Alignment explanation
Indices: 2544143--2544186 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
2544133 TCAATTTATA
2544143 TTATTATTTTTATTTATATTTTT
1 TTATTATTTTTATTTATATTTTT
*
2544166 TTATT-TTTTTATTTCTATTTT
1 TTATTATTTTTATTTATATTTT
2544187 ATTTGTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (23 bp):
TTATTATTTTTATTTATATTTTT
Found at i:2544177 original size:28 final size:27
Alignment explanation
Indices: 2544137--2544190 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
2544127 CTTCTCTCAA
*
2544137 TTTATATTATTATTTTTATTTATATTTT
1 TTTATATTATTATTTCTATTT-TATTTT
* *
2544165 TTTATTTTTTTATTTCTATTTTATTT
1 TTTATATTATTATTTCTATTTTATTT
2544191 GTTCATATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTATATTATTATTTCTATTTTATTTT
Found at i:2550190 original size:19 final size:19
Alignment explanation
Indices: 2550153--2550191 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2550143 CTTATGAGAT
*
2550153 AATTACAATTATAAGTAAA
1 AATTACAATTACAAGTAAA
* *
2550172 AATTTCAATTACAATTAAA
1 AATTACAATTACAAGTAAA
2550191 A
1 A
2550192 TTATTTTCNN
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (19 bp):
AATTACAATTACAAGTAAA
Found at i:2558734 original size:27 final size:27
Alignment explanation
Indices: 2558668--2558930 Score: 164
Period size: 29 Copynumber: 9.5 Consensus size: 27
2558658 TATGCAAGAG
* *
2558668 CATG-TGAAAAAAAATGTTGTGACATGT
1 CATGTTGAAAAAAAA-GTTGTTACAAGT
* * *
2558695 CATATTGAAAAAAAAAAGTTGTCACAAGC
1 CATGTTG--AAAAAAAAGTTGTTACAAGT
* *
2558724 CATGTTGAAAACAAAA-TTATTACACA-C
1 CATGTTGAAAA-AAAAGTTGTTACA-AGT
*
2558751 CATGTTGAAAAAAAA-TTATTACATA-T
1 CATGTTGAAAAAAAAGTTGTTACA-AGT
2558777 CATGTTGAAAAAAAAGTTGTTACAAGT
1 CATGTTGAAAAAAAAGTTGTTACAAGT
** *
2558804 CATGTTGAAAAGATATTGTTGTTACACGT
1 CATGTTGAAAA-A-AAAGTTGTTACAAGT
* * * *
2558833 CATATT--CAAAAAAGTTATTACATGT
1 CATGTTGAAAAAAAAGTTGTTACAAGT
* * *
2558858 CATGTTGAAAAAATATCGTTGTTACATGC
1 CATGTTGAAAAAA-A-AGTTGTTACAAGT
* *
2558887 CATATTGGAAAAAAAAGATTGTTACATA-C
1 CATGTT-GAAAAAAAAG-TTGTTACA-AGT
2558916 CATGTTAGAAAAAAA
1 CATGTT-GAAAAAAA
2558931 NNNNNNNNNN
Statistics
Matches: 191, Mismatches: 29, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
25 16 0.08
26 30 0.16
27 50 0.26
28 10 0.05
29 70 0.37
30 15 0.08
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.30
Consensus pattern (27 bp):
CATGTTGAAAAAAAAGTTGTTACAAGT
Found at i:2558772 original size:26 final size:25
Alignment explanation
Indices: 2558704--2558814 Score: 114
Period size: 27 Copynumber: 4.2 Consensus size: 25
2558694 TCATATTGAA
* *
2558704 AAAAAAAAGTTGTCACAAGCCATGTTG
1 AAAAAAAA-TTATTACAA-CCATGTTG
2558731 AAAACAAAATTATTACACACCATGTTG
1 AAAA-AAAATTATTACA-ACCATGTTG
*
2558758 AAAAAAAATTATTACATATCATGTTG
1 AAAAAAAATTATTACA-ACCATGTTG
* *
2558784 AAAAAAAAGTTGTTACAAGTCATGTTG
1 AAAAAAAA-TTATTACAA-CCATGTTG
2558811 AAAA
1 AAAA
2558815 GATATTGTTG
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
26 29 0.39
27 41 0.55
28 5 0.07
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.27
Consensus pattern (25 bp):
AAAAAAAATTATTACAACCATGTTG
Found at i:2558834 original size:29 final size:26
Alignment explanation
Indices: 2558676--2558871 Score: 110
Period size: 27 Copynumber: 7.3 Consensus size: 26
2558666 AGCATGTGAA
* * *
2558676 AAAAAATGTTGTGACATGTCATATTG
1 AAAAAATGTTGTTACAAGTCATGTTG
* * *
2558702 AAAAAAAAAAGTTGTCACAAGCCATGTTG
1 ---AAAAAATGTTGTTACAAGTCATGTTG
** * *
2558731 AAAACAAAATTATTACACA-CCATGTTG
1 AAAA-AATGTTGTTACA-AGTCATGTTG
** *
2558758 AAAAAAAATTATTACATA-TCATGTTG
1 AAAAAATGTTGTTACA-AGTCATGTTG
*
2558784 AAAAAAAAGTTGTTACAAGTCATGTTG
1 -AAAAAATGTTGTTACAAGTCATGTTG
* * *
2558811 AAAAGATATTGTTGTTACACGTCATATTC
1 AAAA-A-A-TGTTGTTACAAGTCATGTTG
* *
2558840 AAAAAA-GTTATTACATGTCATGTTG
1 AAAAAATGTTGTTACAAGTCATGTTG
2558865 AAAAAAT
1 AAAAAAT
2558872 ATCGTTGTTA
Statistics
Matches: 139, Mismatches: 20, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
25 21 0.15
26 29 0.21
27 45 0.32
28 3 0.02
29 41 0.29
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.31
Consensus pattern (26 bp):
AAAAAATGTTGTTACAAGTCATGTTG
Found at i:2558899 original size:54 final size:54
Alignment explanation
Indices: 2558786--2558892 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 54
2558776 TCATGTTGAA
* * * *
2558786 AAAAAAGTTGTTACAAGTCATGTTGAAAAGATATTGTTGTTACACGTCATATTC
1 AAAAAAGTTATTACAAGTCATGTTGAAAAAATATCGTTGTTACACGCCATATTC
* *
2558840 AAAAAAGTTATTACATGTCATGTTGAAAAAATATCGTTGTTACATGCCATATT
1 AAAAAAGTTATTACAAGTCATGTTGAAAAAATATCGTTGTTACACGCCATATT
2558893 GGAAAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (54 bp):
AAAAAAGTTATTACAAGTCATGTTGAAAAAATATCGTTGTTACACGCCATATTC
Found at i:2560735 original size:33 final size:33
Alignment explanation
Indices: 2560693--2560761 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
2560683 TCACTGTTAC
2560693 TTTGATATGACAGATCTAAAAGTTTTTTTAAAT
1 TTTGATATGACAGATCTAAAAGTTTTTTTAAAT
2560726 TTTGATATGACAGATCTAAAAGTTTTTTTAAAT
1 TTTGATATGACAGATCTAAAAGTTTTTTTAAAT
2560759 TTT
1 TTT
2560762 TTTTTGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.48
Consensus pattern (33 bp):
TTTGATATGACAGATCTAAAAGTTTTTTTAAAT
Found at i:2561812 original size:29 final size:28
Alignment explanation
Indices: 2561705--2561965 Score: 121
Period size: 29 Copynumber: 9.5 Consensus size: 28
2561695 TGATTGTAAA
* * *
2561705 ATTTTTTCAACATGATATGTAATAA-TT
1 ATTTTTTCAACATGACATGTAACAACAT
* * * *
2561732 TTTTTTTCTAGCATGGCATGTACCAATC-T
1 ATTTTTTC-AACATGACATGTAACAA-CAT
* * * *
2561761 TTTTTTTCCAATATGGCACGTAACAACGAT
1 ATTTTTT-CAACATGACATGTAACAAC-AT
*
2561791 ATTTTTTCAGCATGACATGTAAC-A-A-
1 ATTTTTTCAACATGACATGTAACAACAT
* * *
2561816 A-TTTTTGAATATGACGTGTAACAACAAT
1 ATTTTTTCAACATGACATGTAACAAC-AT
2561844 ATTTTGTT-AACATGACATGTAACAAC-T
1 ATTTT-TTCAACATGACATGTAACAACAT
** *
2561871 -TTTTTTCAACATGATGTGTAATAAC-T
1 ATTTTTTCAACATGACATGTAACAACAT
* * * * * **
2561897 TTTTTTTCAACATGGCGTGTGATAATTT
1 ATTTTTTCAACATGACATGTAACAACAT
* * * *
2561925 TTTTTTTCAATATGATATGTCACAACAT
1 ATTTTTTCAACATGACATGTAACAACAT
*
2561953 TTTTTTTC-ACATG
1 ATTTTTTCAACATG
2561966 CTCTTGTATA
Statistics
Matches: 182, Mismatches: 37, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
24 17 0.09
25 4 0.02
26 21 0.12
27 34 0.19
28 44 0.24
29 52 0.29
30 10 0.05
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (28 bp):
ATTTTTTCAACATGACATGTAACAACAT
Found at i:2561829 original size:24 final size:25
Alignment explanation
Indices: 2561801--2561884 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 25
2561791 ATTTTTTCAG
2561801 CATGACATGTAACAAATTTTTG-AA
1 CATGACATGTAACAAATTTTTGTAA
* *
2561825 TATGACGTGTAACAACAATATTTTGTTAA
1 CATGACATGTAAC-A-AAT-TTTTG-TAA
* *
2561854 CATGACATGTAACAACTTTTTTTCAA
1 CATGACATGTAACAAATTTTTGT-AA
2561880 CATGA
1 CATGA
2561885 TGTGTAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
24 11 0.23
25 2 0.04
26 14 0.29
27 7 0.15
28 1 0.02
29 13 0.27
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (25 bp):
CATGACATGTAACAAATTTTTGTAA
Found at i:2561909 original size:53 final size:54
Alignment explanation
Indices: 2561706--2561965 Score: 154
Period size: 53 Copynumber: 4.8 Consensus size: 54
2561696 GATTGTAAAA
* * * * * *
2561706 TTTTTTCAACATGATATGTAATAA-TTTTTTTTTCTAGCATGGCATGTACCAATCTT
1 TTTTTTCAACATGACATGTAACAACATTTTTTTTC-AACATGACATGTAACAA-C-T
* * * * *
2561762 TTTTTTCCAATATGGCACGTAACAACGATATTTTTTCAGCATGACATGTAACAA--
1 TTTTTT-CAACATGACATGTAACAAC-ATTTTTTTTCAACATGACATGTAACAACT
* * * * *
2561816 ATTTTTGAATATGACGTGTAACAACAATATTTTGTT-AACATGACATGTAACAACT
1 TTTTTTCAACATGACATGTAACAAC-AT-TTTTTTTCAACATGACATGTAACAACT
** * * * * * *
2561871 TTTTTTCAACATGATGTGTAATAAC-TTTTTTTTCAACATGGCGTGTGATAATTTT
1 TTTTTTCAACATGACATGTAACAACATTTTTTTTCAACATGACATGTAACAA--CT
* * *
2561926 TTTTTTCAATATGATATGTCACAACATTTTTTTTC-ACATG
1 TTTTTTCAACATGACATGTAACAACATTTTTTTTCAACATG
2561966 CTCTTGTATA
Statistics
Matches: 161, Mismatches: 33, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
52 6 0.04
53 47 0.29
54 10 0.06
55 47 0.29
56 15 0.09
57 13 0.08
58 15 0.09
59 8 0.05
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (54 bp):
TTTTTTCAACATGACATGTAACAACATTTTTTTTCAACATGACATGTAACAACT
Found at i:2561916 original size:27 final size:27
Alignment explanation
Indices: 2561817--2561965 Score: 97
Period size: 28 Copynumber: 5.4 Consensus size: 27
2561807 ATGTAACAAA
* * *
2561817 TTTTTGAATATGACGTGTAACAACAATATT
1 TTTTTCAACATGACGTGTAATAAC--T-TT
* * *
2561847 TTGTT-AACATGACATGTAACAAC-TT
1 TTTTTCAACATGACGTGTAATAACTTT
*
2561872 TTTTTCAACATGATGTGTAATAACTTT
1 TTTTTCAACATGACGTGTAATAACTTT
* * *
2561899 TTTTTCAACATGGCGTGTGATAATTTTT
1 TTTTTCAACATGACGTGTAATAA-CTTT
* ** * *
2561927 TTTTTCAATATGATATGTCACAACATTT
1 TTTTTCAACATGACGTGTAATAAC-TTT
2561955 TTTTTC-ACATG
1 TTTTTCAACATG
2561966 CTCTTGTATA
Statistics
Matches: 96, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
25 6 0.06
26 15 0.16
27 26 0.27
28 29 0.30
29 16 0.17
30 4 0.04
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (27 bp):
TTTTTCAACATGACGTGTAATAACTTT
Found at i:2565134 original size:5 final size:5
Alignment explanation
Indices: 2565124--2565152 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2565114 AATATGTGCA
2565124 CTTTT CTTTT CTTTT CTTTT CTTTT -TTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
2565153 ACAAAGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
CTTTT
Found at i:2569727 original size:20 final size:20
Alignment explanation
Indices: 2569702--2569762 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
2569692 AACATTTAAA
2569702 TTATAAATAATATTAATATT
1 TTATAAATAATATTAATATT
2569722 TTATAATATTAATAATTAA-A--
1 TTATAA-A-TAAT-ATTAATATT
* *
2569742 TTATAAAAAATATTATTATT
1 TTATAAATAATATTAATATT
2569762 T
1 T
2569763 AAAAAATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 1 0.03
20 13 0.39
21 1 0.03
22 5 0.15
23 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATAAATAATATTAATATT
Found at i:2569776 original size:40 final size:40
Alignment explanation
Indices: 2569697--2569777 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
2569687 ATAATAACAT
* * * *
2569697 TTAAATTATAAATAATATTAATATTTTATAATATTAATAA
1 TTAAATTATAAAAAATATTAATATTTAAAAATATCAATAA
*
2569737 TTAAATTATAAAAAATATTATTATTTAAAAA-ATACAATAA
1 TTAAATTATAAAAAATATTAATATTTAAAAATAT-CAATAA
2569777 T
1 T
2569778 AATAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 33 0.94
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (40 bp):
TTAAATTATAAAAAATATTAATATTTAAAAATATCAATAA
Found at i:2569796 original size:12 final size:13
Alignment explanation
Indices: 2569772--2569801 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2569762 TAAAAAATAC
2569772 AATAATAATAAAT
1 AATAATAATAAAT
2569785 AATAAT-ATAAAT
1 AATAATAATAAAT
2569797 AATAA
1 AATAA
2569802 AGGGTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:2571802 original size:27 final size:29
Alignment explanation
Indices: 2571756--2571813 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 29
2571746 NNNNNNNTTT
* *
2571756 ATTTATTTTTAAATATTAATATTTTG-TA
1 ATTTATTTTAAAATAATAATATTTTGATA
2571784 ATTTA-TTTAAAATAATAATATTTTGATA
1 ATTTATTTTAAAATAATAATATTTTGATA
2571812 AT
1 AT
2571814 ATACATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTATTTTAAAATAATAATATTTTGATA
Found at i:2575407 original size:35 final size:35
Alignment explanation
Indices: 2575359--2575467 Score: 146
Period size: 35 Copynumber: 3.1 Consensus size: 35
2575349 GAATAATGAG
* *
2575359 AACAATTAGAACAAGTGAAACATTATTTTACGCAA
1 AACAATTAGAACAAGTGAAACACTACTTTACGCAA
* *
2575394 AACAATTAAAACAAGTGAAACACTACTTTGCGCAA
1 AACAATTAGAACAAGTGAAACACTACTTTACGCAA
* * * *
2575429 AACAACTAGAATAAGTGAAACACTACTTCACTCAA
1 AACAATTAGAACAAGTGAAACACTACTTTACGCAA
2575464 AACA
1 AACA
2575468 NNNNNNNNNN
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.21
Consensus pattern (35 bp):
AACAATTAGAACAAGTGAAACACTACTTTACGCAA
Found at i:2578000 original size:35 final size:35
Alignment explanation
Indices: 2577961--2578063 Score: 125
Period size: 35 Copynumber: 2.9 Consensus size: 35
2577951 TTGTTACACA
* * *
2577961 TGAAGTAATGTTCCATTTATTTTAGTTATTTTGAG
1 TGAAGTAGTGTTTCATTTATTTTAGTTGTTTTGAG
* * *
2577996 TGAAGTAGTGTTTCACTTATTCTAGTTGTTTTGCG
1 TGAAGTAGTGTTTCATTTATTTTAGTTGTTTTGAG
* * *
2578031 TAAAGTAGTGTTTCATTTGTTTTAATTGTTTTG
1 TGAAGTAGTGTTTCATTTATTTTAGTTGTTTTG
2578064 CGCAAAATAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 57 1.00
ACGTcount: A:0.21, C:0.07, G:0.19, T:0.52
Consensus pattern (35 bp):
TGAAGTAGTGTTTCATTTATTTTAGTTGTTTTGAG
Found at i:2578037 original size:70 final size:70
Alignment explanation
Indices: 2577963--2578095 Score: 158
Period size: 70 Copynumber: 1.9 Consensus size: 70
2577953 GTTACACATG
* ** * * *
2577963 AAGTAATGTTCCATTTATTTTAGTTATTTTGAGTGAAGTAGTGTTTCACTTATTCTAGTTGTTTT
1 AAGTAATGTTCCATTTATTTTAATTATTTTGAGCAAAATAATGTTTCACTTATTCTAATTGTTTT
2578028 GCGTA
66 GCGTA
* * * * * *
2578033 AAGTAGTGTTTCATTTGTTTTAATTGTTTTGCGCAAAATAATGTTTCACTTGTTCTAATTGTT
1 AAGTAATGTTCCATTTATTTTAATTATTTTGAGCAAAATAATGTTTCACTTATTCTAATTGTT
2578096 CCTATTATTC
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
70 51 1.00
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.50
Consensus pattern (70 bp):
AAGTAATGTTCCATTTATTTTAATTATTTTGAGCAAAATAATGTTTCACTTATTCTAATTGTTTT
GCGTA
Found at i:2578064 original size:35 final size:35
Alignment explanation
Indices: 2577963--2578095 Score: 122
Period size: 35 Copynumber: 3.8 Consensus size: 35
2577953 GTTACACATG
* * * * * * *
2577963 AAGTAATGTTCCATTTATTTTAGTTATTTTGAGTG
1 AAGTAATGTTTCACTTATTCTAATTGTTTTGCGTA
* *
2577998 AAGTAGTGTTTCACTTATTCTAGTTGTTTTGCGTA
1 AAGTAATGTTTCACTTATTCTAATTGTTTTGCGTA
* * * * *
2578033 AAGTAGTGTTTCATTTGTTTTAATTGTTTTGCGCA
1 AAGTAATGTTTCACTTATTCTAATTGTTTTGCGTA
* *
2578068 AAATAATGTTTCACTTGTTCTAATTGTT
1 AAGTAATGTTTCACTTATTCTAATTGTT
2578096 CCTATTATTC
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 82 1.00
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.50
Consensus pattern (35 bp):
AAGTAATGTTTCACTTATTCTAATTGTTTTGCGTA
Found at i:2580818 original size:25 final size:27
Alignment explanation
Indices: 2580790--2580844 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
2580780 TTTTGTAATA
*
2580790 TTTTTTG-T-ACAATTAAAAATTATAT
1 TTTTTTGATGACAATTAAAAATTACAT
*
2580815 TTTTTTGAATGGCAATTAAAAATTACAT
1 TTTTTTG-ATGACAATTAAAAATTACAT
2580843 TT
1 TT
2580845 AATTAACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.28
27 1 0.04
28 17 0.68
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (27 bp):
TTTTTTGATGACAATTAAAAATTACAT
Found at i:2589334 original size:3 final size:3
Alignment explanation
Indices: 2589326--2589362 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2589316 AAGATAGCTG
*
2589326 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AAC AGC A
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC A
2589363 ACAAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.38, C:0.32, G:0.30, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:2596447 original size:6 final size:6
Alignment explanation
Indices: 2596436--2596461 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2596426 GAATGATGGT
2596436 GTGAGA GTGAGA GTGAGA GTGAGA GT
1 GTGAGA GTGAGA GTGAGA GTGAGA GT
2596462 CATTGGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.50, T:0.19
Consensus pattern (6 bp):
GTGAGA
Found at i:2599288 original size:42 final size:42
Alignment explanation
Indices: 2599229--2599312 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
2599219 TACTGTGTAT
*
2599229 AAGTATGCAACACAAAATCTGTA-AATCTAGCGATAGAAAATG
1 AAGTATGCAACACAAAATCTGTACAAT-TAGCAATAGAAAATG
* *
2599271 AAGTATGCAATACAAAATCTGTACAGTTAGCAATAGAAAATG
1 AAGTATGCAACACAAAATCTGTACAATTAGCAATAGAAAATG
2599313 CATCACTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 36 0.95
43 2 0.05
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.23
Consensus pattern (42 bp):
AAGTATGCAACACAAAATCTGTACAATTAGCAATAGAAAATG
Found at i:2612370 original size:21 final size:18
Alignment explanation
Indices: 2612344--2612393 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 18
2612334 TATTTTCATT
2612344 TTTTTAAAATTTTAATTAAAA
1 TTTTTAAAATTTT-ATT--AA
*
2612365 TTTTTAATAAATTTATTAA
1 TTTTTAA-AATTTTATTAA
2612384 TTTTTAAAAT
1 TTTTTAAAAT
2612394 AAATACTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.08
19 9 0.35
21 10 0.38
22 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTTAAAATTTTATTAA
Found at i:2612671 original size:22 final size:22
Alignment explanation
Indices: 2612622--2612672 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
2612612 TTATTTTTTT
*
2612622 TATTTTTTAAAAAATATAATAA
1 TATTTTTTAAAAAATATAAAAA
*
2612644 TAATTTTTTAAATTAATA-AAAAA
1 T-ATTTTTTAAA-AAATATAAAAA
2612667 TATTTT
1 TATTTT
2612673 ACTTTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 6 0.24
23 15 0.60
24 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTTTTAAAAAATATAAAAA
Found at i:2613942 original size:21 final size:18
Alignment explanation
Indices: 2613906--2613943 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2613896 GCTGTTGTTA
2613906 AAGTAATAATAAATTATT
1 AAGTAATAATAAATTATT
*
2613924 AAGTAATAATAATTTATT
1 AAGTAATAATAAATTATT
2613942 AA
1 AA
2613944 ATTATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
AAGTAATAATAAATTATT
Found at i:2614266 original size:18 final size:20
Alignment explanation
Indices: 2614226--2614266 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 20
2614216 TAGAGAACAT
2614226 AATACATTACTTTAATTTTG
1 AATACATTACTTTAATTTTG
2614246 AATA-ATTA-TTT-ATTTTAG
1 AATACATTACTTTAATTTT-G
2614264 AAT
1 AAT
2614267 TTTTATTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.25
18 7 0.35
19 4 0.20
20 4 0.20
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
AATACATTACTTTAATTTTG
Found at i:2628907 original size:6 final size:6
Alignment explanation
Indices: 2628898--2628924 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2628888 AATATTTATT
2628898 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
2628925 TTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:2628934 original size:17 final size:18
Alignment explanation
Indices: 2628912--2628947 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2628902 AATTTAAATT
2628912 TAAATTTA-AATTTTTAA
1 TAAATTTATAATTTTTAA
2628929 TAAATTTATTAATTTTTAA
1 TAAATTTA-TAATTTTTAA
2628948 AATAAATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
19 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATTTATAATTTTTAA
Found at i:2629271 original size:20 final size:20
Alignment explanation
Indices: 2629246--2629302 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
2629236 AGATGATATG
2629246 AAAATATTTTATATTTTTTA
1 AAAATATTTTATATTTTTTA
*
2629266 AAAATA-TATA-AGTTTTTTA
1 AAAATATTTTATA-TTTTTTA
* *
2629285 AGAAATTTTTTTTATTTT
1 A-AAATATTTTATATTTT
2629303 AAAATTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 10 0.34
21 6 0.21
22 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
AAAATATTTTATATTTTTTA
Found at i:2630192 original size:26 final size:26
Alignment explanation
Indices: 2630155--2630207 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
2630145 ATTTAAATTT
*
2630155 TTTTTATTTTTTTATGTTT-AATTAAA
1 TTTTTATATTTTTAT-TTTAAATTAAA
2630181 TTTTTATATTTTTATTTTAAATTAAA
1 TTTTTATATTTTTATTTTAAATTAAA
2630207 T
1 T
2630208 AAATTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTTATATTTTTATTTTAAATTAAA
Found at i:2631982 original size:63 final size:63
Alignment explanation
Indices: 2631912--2632033 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 63
2631902 CCACAGCACG
* * *
2631912 ATGATGATGGTACTCAATAGAGAGTTGACAGAACTGATACAGCTCAGAGAGTTGAGAGAACTA
1 ATGATGATGATACTCAACAGAGAGTTGACAGAACTGATACAACTCAGAGAGTTGAGAGAACTA
* ** * *
2631975 ATGATGATGATGCTCAACAGAGAGTTGACAGAGTTGATACAATTTAGAGAGTTGAGAGA
1 ATGATGATGATACTCAACAGAGAGTTGACAGAACTGATACAACTCAGAGAGTTGAGAGA
2632034 GATGAGCGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.24
Consensus pattern (63 bp):
ATGATGATGATACTCAACAGAGAGTTGACAGAACTGATACAACTCAGAGAGTTGAGAGAACTA
Found at i:2635678 original size:7 final size:8
Alignment explanation
Indices: 2635657--2635693 Score: 56
Period size: 8 Copynumber: 4.4 Consensus size: 8
2635647 TCAAAAAATA
2635657 AATTTTTT
1 AATTTTTT
2635665 AATTTTTT
1 AATTTTTT
2635673 AATTTTTT
1 AATTTTTT
2635681 AAAATTTTTT
1 --AATTTTTT
2635691 AAT
1 AAT
2635694 CTCTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 19 0.70
10 8 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
AATTTTTT
Found at i:2635686 original size:18 final size:16
Alignment explanation
Indices: 2635657--2635693 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
2635647 TCAAAAAATA
2635657 AATTTTTTAATTTTTT
1 AATTTTTTAATTTTTT
2635673 AATTTTTTAAAATTTTTT
1 AATTTTTT--AATTTTTT
2635691 AAT
1 AAT
2635694 CTCTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTTTTAATTTTTT
Found at i:2635700 original size:18 final size:17
Alignment explanation
Indices: 2635665--2635705 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
2635655 TAAATTTTTT
* *
2635665 AATTTTTTAATTTTTTAA
1 AATTTTTTAATCTCTT-A
2635683 AATTTTTTAATCTCTTA
1 AATTTTTTAATCTCTTA
2635700 AATTTT
1 AATTTT
2635706 AGTTAACATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
AATTTTTTAATCTCTTA
Found at i:2635700 original size:26 final size:26
Alignment explanation
Indices: 2635656--2635705 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2635646 TTCAAAAAAT
* * *
2635656 AAATTTTTTAATTTTTTAATTTTTTA
1 AAATTTTTTAATCTCTTAAATTTTTA
2635682 AAATTTTTTAATCTCTTAAATTTT
1 AAATTTTTTAATCTCTTAAATTTT
2635706 AGTTAACATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (26 bp):
AAATTTTTTAATCTCTTAAATTTTTA
Found at i:2636665 original size:18 final size:18
Alignment explanation
Indices: 2636642--2636695 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
2636632 ACAAGTGTAC
*
2636642 TAATCGTTTAGGTAATAA
1 TAATCGTTTAAGTAATAA
2636660 TAATCGTTTAAGTAATAA
1 TAATCGTTTAAGTAATAA
2636678 TAATCGTTTAAGTAATAA
1 TAATCGTTTAAGTAATAA
2636696 AGAGATAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.39
Consensus pattern (18 bp):
TAATCGTTTAAGTAATAA
Found at i:2637209 original size:35 final size:35
Alignment explanation
Indices: 2637163--2637231 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
2637153 GATCATGCTC
2637163 TTAATATACTAGCCCAAGGATCAAGTTTTCAAAAT
1 TTAATATACTAGCCCAAGGATCAAGTTTTCAAAAT
2637198 TTAATATACTAGCCCAAGGATCAAGTTTTCAAAA
1 TTAATATACTAGCCCAAGGATCAAGTTTTCAAAA
2637232 GAAATGACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (35 bp):
TTAATATACTAGCCCAAGGATCAAGTTTTCAAAAT
Found at i:2638633 original size:14 final size:14
Alignment explanation
Indices: 2638616--2638642 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2638606 TTAGTATTAT
2638616 TTAATTATTTTAAA
1 TTAATTATTTTAAA
2638630 TTAATTATTTTAA
1 TTAATTATTTTAA
2638643 GTGAGTCAAT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAATTATTTTAAA
Found at i:2639014 original size:23 final size:22
Alignment explanation
Indices: 2638983--2639060 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
2638973 AGTAATTATG
*
2638983 ATTTGTATTTTTTAATTATTTAA
1 ATTTTTATTTTTTAATTATTT-A
*
2639006 ATTTTTATTTGTGT--TT-TTTA
1 ATTTTTATTT-TTTAATTATTTA
* *
2639026 ATATTTATTTTTTAATATTTTTA
1 ATTTTTATTTTTTAAT-TATTTA
*
2639049 ATTTCTATTTTT
1 ATTTTTATTTTT
2639061 ATTAAATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.05
20 10 0.23
21 4 0.09
22 3 0.07
23 23 0.52
24 2 0.05
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (22 bp):
ATTTTTATTTTTTAATTATTTA
Done.