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 8 of 133
Found at i:1965310 original size:9 final size:9
Alignment explanation
Indices: 1965282--1965317 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
1965272 AAATATCATC
1965282 AATTAAATA
1 AATTAAATA
*
1965291 TAATTATATA
1 -AATTAAATA
1965301 AATTAAATA
1 AATTAAATA
1965310 AATTAAAT
1 AATTAAAT
1965318 TTTATGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AATTAAATA
Found at i:1965715 original size:17 final size:17
Alignment explanation
Indices: 1965693--1965727 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1965683 AAATTGTTTT
*
1965693 AAAAATTAATTTAATAA
1 AAAAATTAAATTAATAA
1965710 AAAAATTAAATTAATAA
1 AAAAATTAAATTAATAA
1965727 A
1 A
1965728 TTAATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATTAAATTAATAA
Found at i:1971351 original size:12 final size:12
Alignment explanation
Indices: 1971334--1971375 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1971324 TTTTATTATT
1971334 TATTTAATTTTA
1 TATTTAATTTTA
*
1971346 TATTTATATATT-
1 TATTTA-ATTTTA
*
1971358 TATTTAATTTAA
1 TATTTAATTTTA
1971370 TATTTA
1 TATTTA
1971376 CAAAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 3 0.12
12 18 0.72
13 4 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATTTAATTTTA
Found at i:1971357 original size:8 final size:8
Alignment explanation
Indices: 1971317--1971375 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
1971307 CCATTTGGTA
1971317 TATATATT
1 TATATATT
*
1971325 TTTATTATT
1 TATA-TATT
*
1971334 TATTTAATT
1 TATAT-ATT
1971343 T-TATATT
1 TATATATT
1971350 TATATATT
1 TATATATT
*
1971358 TATTTAATT
1 TATAT-ATT
1971367 TA-ATATT
1 TATATATT
1971374 TA
1 TA
1971376 CAAAATAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
7 9 0.22
8 17 0.41
9 15 0.37
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATATATT
Found at i:1971362 original size:24 final size:25
Alignment explanation
Indices: 1971319--1971375 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
1971309 ATTTGGTATA
*
1971319 TATATTTTTATTATTTATTTAATTT
1 TATATTTATATTATTTATTTAATTT
1971344 TATATTTATA-TATTTATTTAATTT
1 TATATTTATATTATTTATTTAATTT
*
1971368 AATATTTA
1 TATATTTA
1971376 CAAAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 21 0.70
25 9 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TATATTTATATTATTTATTTAATTT
Found at i:1971414 original size:29 final size:31
Alignment explanation
Indices: 1971378--1971437 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1971368 AATATTTACA
1971378 AAATAATATTTTAT-GTTAAAAA-TAATATT
1 AAATAATATTTTATAGTTAAAAATTAATATT
*
1971407 AAATAATATTTTATATTTAAAAATTAATATT
1 AAATAATATTTTATAGTTAAAAATTAATATT
1971438 TCATTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 14 0.50
30 7 0.25
31 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (31 bp):
AAATAATATTTTATAGTTAAAAATTAATATT
Found at i:1975056 original size:12 final size:12
Alignment explanation
Indices: 1975035--1975076 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1975025 TATTTTACGA
*
1975035 TAAAAATTTTAT
1 TAAAAATTTTAC
*
1975047 TAAAATTTTTAC
1 TAAAAATTTTAC
1975059 TAAAAATATTTA-
1 TAAAAAT-TTTAC
1975071 TAAAAA
1 TAAAAA
1975077 AAAATCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAAAATTTTAC
Found at i:1979268 original size:13 final size:13
Alignment explanation
Indices: 1979250--1979275 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1979240 GATGTTCCTT
1979250 TATTCTATATTTG
1 TATTCTATATTTG
1979263 TATTCTATATTTG
1 TATTCTATATTTG
1979276 GTCGTGTAGC
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:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTCTATATTTG
Found at i:1985001 original size:15 final size:15
Alignment explanation
Indices: 1984981--1985010 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1984971 GATTCTTTTC
*
1984981 ATCATCATTATCATT
1 ATCATCATCATCATT
1984996 ATCATCATCATCATT
1 ATCATCATCATCATT
1985011 CATGGTTTTA
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:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
ATCATCATCATCATT
Found at i:1985304 original size:17 final size:18
Alignment explanation
Indices: 1985273--1985310 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1985263 TTTAAAAATA
1985273 AATATATTAAATTTT-TT
1 AATATATTAAATTTTATT
* *
1985290 AATATATTTATTTTTATT
1 AATATATTAAATTTTATT
1985308 AAT
1 AAT
1985311 GTTTTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATATATTAAATTTTATT
Found at i:1986561 original size:62 final size:60
Alignment explanation
Indices: 1986490--1986607 Score: 175
Period size: 60 Copynumber: 1.9 Consensus size: 60
1986480 TGTATTATAT
*
1986490 TAATTAATCATAATTTAGATTTATTTGGGAT-TAATCAAAATTTTATATAGAACCCATACTTA
1 TAATTAATCATAATTTAGATTTA--TGGGATCT-ATCAAAATTTTATATACAACCCATACTTA
* *
1986552 TAATTAATCATAATTTAGATTTATGGGATCTATCGAAATTTTATATACAACTCATA
1 TAATTAATCATAATTTAGATTTATGGGATCTATCAAAATTTTATATACAACCCATA
1986608 AGTAATGGAC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
60 28 0.54
61 1 0.02
62 23 0.44
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (60 bp):
TAATTAATCATAATTTAGATTTATGGGATCTATCAAAATTTTATATACAACCCATACTTA
Found at i:1990689 original size:221 final size:222
Alignment explanation
Indices: 1990287--1990724 Score: 718
Period size: 221 Copynumber: 2.0 Consensus size: 222
1990277 TCACGCCCAC
*
1990287 CGTTTAAAAATAAGAGATAGGATGTATTAATTTTACATCAAATAAAAAAAATCATTAAAAATGAT
1 CGTTTAAAAATAAGAGATACGATGTATTAATTTTACATCAAATAAAAAAAATCATTAAAAATGAT
1990352 ATTATAAATCTTAATAAGTTGATTTTATAAAAAATAATTAATCATATAATAAGTGATATCAAAAT
66 ATTATAAATCTTAATAAGTTGATTTTATAAAAAATAATTAATCATATAATAAGTGATATCAAAAT
* *
1990417 TAATTTTTAATTCATCCAATTTTATATAGATCATCTTAGCAAAGATAGATAAGATAAGTTAATCT
131 TAAATTTTAATTCATCCAATTTTATATAGATCATCTTAGCAAAGATAGATAAAATAAGTTAATCT
1990482 ATCTACTTAATAAGATGTCACATCTAA
196 ATCTACTTAATAAGATGTCACATCTAA
* * *
1990509 CGTTTAAAAATAAGAGATTCGATGTATTAATTTTACATCAAA-GAAAAAAATCATTAGAAATGAT
1 CGTTTAAAAATAAGAGATACGATGTATTAATTTTACATCAAATAAAAAAAATCATTAAAAATGAT
* ** *
1990573 GTTATGCATTTTAATAAGTTGATTTTATAAAAAATAATTAATCATATAATAAGTGATATCAAAAT
66 ATTATAAATCTTAATAAGTTGATTTTATAAAAAATAATTAATCATATAATAAGTGATATCAAAAT
* * * * *
1990638 TAAATTTTAGTTCATCCGATTTTATATCA-ATCGTCTTAGTAAAGGTAGATAAAATAAGTTAATC
131 TAAATTTTAATTCATCCAATTTTATAT-AGATCATCTTAGCAAAGATAGATAAAATAAGTTAATC
1990702 TATCTACTTAATAAGATGTCACA
195 TATCTACTTAATAAGATGTCACA
1990725 ATAAGACATG
Statistics
Matches: 200, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
221 159 0.80
222 41 0.20
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (222 bp):
CGTTTAAAAATAAGAGATACGATGTATTAATTTTACATCAAATAAAAAAAATCATTAAAAATGAT
ATTATAAATCTTAATAAGTTGATTTTATAAAAAATAATTAATCATATAATAAGTGATATCAAAAT
TAAATTTTAATTCATCCAATTTTATATAGATCATCTTAGCAAAGATAGATAAAATAAGTTAATCT
ATCTACTTAATAAGATGTCACATCTAA
Found at i:1996445 original size:26 final size:26
Alignment explanation
Indices: 1996410--1996464 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
1996400 AAATAATAAT
* *
1996410 AAAAATTATTATAACTATAATTAAAA
1 AAAAATTATTACAACTACAATTAAAA
*
1996436 AAAAATTATTACAACTACGATTAAAA
1 AAAAATTATTACAACTACAATTAAAA
1996462 AAA
1 AAA
1996465 TGTTCATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (26 bp):
AAAAATTATTACAACTACAATTAAAA
Found at i:2000801 original size:29 final size:29
Alignment explanation
Indices: 2000740--2000828 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
2000730 TGTGTAACTA
* *
2000740 TAATATTTTA--ATAATTAATTTAAGTTTT
1 TAATATTTTATTATAATTAA-TTAAATTCT
2000768 TAATATTTTATTATAATTAATTAAATTCT
1 TAATATTTTATTATAATTAATTAAATTCT
* * *
2000797 TAATA-TTTATTTTGATTTAATTAAACTCT
1 TAATATTTTATTAT-AATTAATTAAATTCT
2000826 TAA
1 TAA
2000829 ATGAACGAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 17 0.32
29 28 0.53
30 8 0.15
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.55
Consensus pattern (29 bp):
TAATATTTTATTATAATTAATTAAATTCT
Found at i:2001965 original size:33 final size:33
Alignment explanation
Indices: 2001904--2002002 Score: 81
Period size: 33 Copynumber: 2.8 Consensus size: 33
2001894 TGATAATTTG
*
2001904 TATATTTATATTATATAAAATATTAAAATTTTT
1 TATATTTATATTATATAAAATATAAAAATTTTT
* ***
2001937 TATATTTATATTTTATTTTATATAAAAATTATATAT
1 TATATTTATATTATATAAAATATAAAAATT-T-T-T
* *
2001973 TATAATTTGTATTGAAATAAAAATATAAAA
1 TAT-ATTTATATT-ATAT-AAAATATAAAA
2002003 TATATATTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
33 25 0.51
34 1 0.02
35 1 0.02
36 4 0.08
37 8 0.16
38 2 0.04
39 8 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (33 bp):
TATATTTATATTATATAAAATATAAAAATTTTT
Found at i:2002079 original size:15 final size:15
Alignment explanation
Indices: 2002061--2002092 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2002051 TTAAATTGTA
*
2002061 TTATTTTTATATTTT
1 TTATTTATATATTTT
2002076 TTATTTATATATTTT
1 TTATTTATATATTTT
2002091 TT
1 TT
2002093 TGATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTATTTATATATTTT
Found at i:2014634 original size:16 final size:16
Alignment explanation
Indices: 2014613--2014645 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2014603 GAAAATGCAC
*
2014613 TGATCTTAATTTATCA
1 TGATCTTAACTTATCA
2014629 TGATCTTAACTTATCA
1 TGATCTTAACTTATCA
2014645 T
1 T
2014646 ATGTACAAAA
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:0.30, C:0.15, G:0.06, T:0.48
Consensus pattern (16 bp):
TGATCTTAACTTATCA
Found at i:2015207 original size:16 final size:16
Alignment explanation
Indices: 2015183--2015214 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2015173 ATTATCTTTT
2015183 AAAACTATAAGTATAA
1 AAAACTATAAGTATAA
*
2015199 AAAATTATAAGTATAA
1 AAAACTATAAGTATAA
2015215 TCAAGTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (16 bp):
AAAACTATAAGTATAA
Found at i:2015353 original size:21 final size:21
Alignment explanation
Indices: 2015327--2015369 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2015317 AGAAAATCTA
2015327 TAACTATAATTAAGTATTATG
1 TAACTATAATTAAGTATTATG
2015348 TAACTATAATTAAGTATTATG
1 TAACTATAATTAAGTATTATG
2015369 T
1 T
2015370 TATTGAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (21 bp):
TAACTATAATTAAGTATTATG
Found at i:2017504 original size:11 final size:12
Alignment explanation
Indices: 2017479--2017537 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
2017469 ATATAACGAG
* *
2017479 AAATTTGATTTT
1 AAATTTAATTTA
2017491 AAATTTAATTTA
1 AAATTTAATTTA
*
2017503 AAACTTGTTATTTA
1 AAA-TT-TAATTTA
*
2017517 AAATTTAA-TTC
1 AAATTTAATTTA
2017528 AAATTTAATT
1 AAATTTAATT
2017538 GAGTTTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 10 0.26
12 16 0.41
13 4 0.10
14 9 0.23
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (12 bp):
AAATTTAATTTA
Found at i:2017729 original size:20 final size:20
Alignment explanation
Indices: 2017704--2017747 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2017694 TCATATATAT
2017704 ATATATAAATAAAATAATAAAA
1 ATATAT-AATAAAAT-ATAAAA
*
2017726 ATATATATTAAAATATAAAA
1 ATATATAATAAAATATAAAA
2017746 AT
1 AT
2017748 TTGATTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 7 0.33
22 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATATAATAAAATATAAAA
Found at i:2017791 original size:21 final size:20
Alignment explanation
Indices: 2017742--2017793 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
2017732 ATTAAAATAT
2017742 AAAAATTTGATTAAACTCAC
1 AAAAATTTGATTAAACTCAC
* *
2017762 AAATTATTTGAGTTAAACATTA-
1 AAA-AATTTGA-TTAAAC-TCAC
2017784 AAAAATTTGA
1 AAAAATTTGA
2017794 ATTTAGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.12
21 12 0.46
22 9 0.35
23 2 0.08
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (20 bp):
AAAAATTTGATTAAACTCAC
Found at i:2018593 original size:31 final size:32
Alignment explanation
Indices: 2018555--2018621 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
2018545 CCCATCAAAA
*
2018555 TATTACTTTAGCTTTCATT-CCCCGAAATTAT
1 TATTACTTCAGCTTTCATTCCCCCGAAATTAT
* *
2018586 TATTACTTCAGCTTTCCTTCCCCCGAATTTAT
1 TATTACTTCAGCTTTCATTCCCCCGAAATTAT
2018618 TATT
1 TATT
2018622 TGACTCTCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 17 0.53
32 15 0.47
ACGTcount: A:0.22, C:0.25, G:0.06, T:0.46
Consensus pattern (32 bp):
TATTACTTCAGCTTTCATTCCCCCGAAATTAT
Found at i:2019695 original size:3 final size:3
Alignment explanation
Indices: 2019687--2019716 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
2019677 TAAGATTACT
2019687 AAG AAG AAG AAG AAAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG -AAG AAG AAG AAG AAG AA
2019717 CGAATGATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2019705 original size:13 final size:13
Alignment explanation
Indices: 2019687--2019713 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2019677 TAAGATTACT
2019687 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
2019700 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
2019713 A
1 A
2019714 GAACGAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:2028268 original size:2 final size:2
Alignment explanation
Indices: 2028261--2028296 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2028251 TCTGTTTGAT
2028261 TA TA TA 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 TA TA TA
2028297 ATTAAAAGGC
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2035194 original size:20 final size:20
Alignment explanation
Indices: 2035166--2035232 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
2035156 TTATAATTGT
*
2035166 TAATATTAAAAATTAAAAAA
1 TAATTTTAAAAATTAAAAAA
2035186 TAATTTTAAAATATATAAAATAA
1 TAATTTTAAAA-AT-TAAAA-AA
* * *
2035209 GAGTTTTAAATATTAAAAAA
1 TAATTTTAAAAATTAAAAAA
2035229 -AATT
1 TAATT
2035233 ATAATTTTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.08
20 12 0.31
21 7 0.18
22 7 0.18
23 10 0.26
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TAATTTTAAAAATTAAAAAA
Found at i:2037326 original size:32 final size:32
Alignment explanation
Indices: 2037284--2037366 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 32
2037274 ATTAAAATAT
*
2037284 TAAATATTAAATTTAATTT-AATAATAAT-TTAA
1 TAAAT-TTAAATTTAATTTAAATAA-AATCTAAA
*
2037316 TCAAATTTAAATTTTATTTAAATAAAATCTAAA
1 T-AAATTTAAATTTAATTTAAATAAAATCTAAA
2037349 TAAATTATAAATATTAAT
1 TAAATT-TAAAT-TTAAT
2037367 ATATTTTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
32 21 0.49
33 18 0.42
34 4 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (32 bp):
TAAATTTAAATTTAATTTAAATAAAATCTAAA
Found at i:2043534 original size:2 final size:2
Alignment explanation
Indices: 2043527--2043552 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2043517 TTTCTACTTA
2043527 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
2043553 GGGGATCTAC
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):
AT
Found at i:2048598 original size:29 final size:30
Alignment explanation
Indices: 2048551--2048632 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
2048541 TCATGCTAAA
2048551 AATTTATTTAAGTACAAATTAAAG-TTAAG
1 AATTTATTTAAGTACAAATTAAAGATTAAG
*
2048580 AATTTATTTGAA-TATAAATTAAAGATTAAG
1 AATTTATTT-AAGTACAAATTAAAGATTAAG
* * **
2048610 AACTTATTAAAGTGTAAATTAAA
1 AATTTATTTAAGTACAAATTAAA
2048633 AATTTATTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 22 0.48
30 24 0.52
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (30 bp):
AATTTATTTAAGTACAAATTAAAGATTAAG
Found at i:2057645 original size:2 final size:2
Alignment explanation
Indices: 2057638--2057670 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2057628 ACATTACAGG
2057638 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 A
2057671 AAGCAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2059035 original size:42 final size:42
Alignment explanation
Indices: 2058988--2059067 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
2058978 GATGAAATGG
2058988 AAGCCATGAACCTTTTTAACTTAAAGAAAGGTAGGAAGTGGA
1 AAGCCATGAACCTTTTTAACTTAAAGAAAGGTAGGAAGTGGA
*
2059030 AAGCCATTAACCTTTTTAACTTAAAGAAAGGTAGGAAG
1 AAGCCATGAACCTTTTTAACTTAAAGAAAGGTAGGAAG
2059068 CACTTAAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.25
Consensus pattern (42 bp):
AAGCCATGAACCTTTTTAACTTAAAGAAAGGTAGGAAGTGGA
Found at i:2061568 original size:2 final size:2
Alignment explanation
Indices: 2061563--2061592 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2061553 AAAAAAAAAC
2061563 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
2061593 TAAAAAACCC
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:2067821 original size:15 final size:14
Alignment explanation
Indices: 2067801--2067830 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2067791 TGAAACATAG
2067801 AAAATAAAAAATAAA
1 AAAATAAAAAA-AAA
2067816 AAAATAAAAAAAAA
1 AAAATAAAAAAAAA
2067830 A
1 A
2067831 TTACCTGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAATAAAAAAAAA
Found at i:2072640 original size:2 final size:2
Alignment explanation
Indices: 2072633--2072678 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
2072623 TCAACTGAAC
* * *
2072633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2072675 AT AT
1 AT AT
2072679 CAAGTATCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2075696 original size:22 final size:22
Alignment explanation
Indices: 2075671--2075715 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2075661 ATAACAGCAC
2075671 CCATCTGACCCAAAATAATTTT
1 CCATCTGACCCAAAATAATTTT
2075693 CCATCTGACCCAAAATAATTTT
1 CCATCTGACCCAAAATAATTTT
2075715 C
1 C
2075716 ACTTCAGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (22 bp):
CCATCTGACCCAAAATAATTTT
Found at i:2077534 original size:12 final size:12
Alignment explanation
Indices: 2077510--2077560 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
2077500 TATTAATAAT
2077510 TTATATATTTATA
1 TTATAT-TTTATA
2077523 TTATATTTTATA
1 TTATATTTTATA
* * *
2077535 TAAAATTATATA
1 TTATATTTTATA
*
2077547 TTATAATTTATA
1 TTATATTTTATA
2077559 TT
1 TT
2077561 TATACGAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 25 0.81
13 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:2078283 original size:7 final size:7
Alignment explanation
Indices: 2078271--2078297 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2078261 AATTAATTGA
2078271 ATTAAAT
1 ATTAAAT
2078278 ATTAAAT
1 ATTAAAT
2078285 ATTAAAT
1 ATTAAAT
2078292 ATTAAA
1 ATTAAA
2078298 ATTTATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATTAAAT
Found at i:2079940 original size:13 final size:13
Alignment explanation
Indices: 2079922--2079951 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2079912 TTGATAATTT
*
2079922 AAAATATTATAAA
1 AAAATAATATAAA
2079935 AAAATAATATAAA
1 AAAATAATATAAA
2079948 AAAA
1 AAAA
2079952 AAGTGATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATAATATAAA
Found at i:2082634 original size:2 final size:2
Alignment explanation
Indices: 2082627--2082664 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2082617 TCTATAATTC
2082627 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2082665 GTTCCTGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2092568 original size:18 final size:18
Alignment explanation
Indices: 2092545--2092587 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
2092535 TGGTTAAGAT
2092545 ATCTGTTTCATCTTATAG
1 ATCTGTTTCATCTTATAG
* *
2092563 ATCTGTTTTATCTTTTAG
1 ATCTGTTTCATCTTATAG
2092581 ACTCTGT
1 A-TCTGT
2092588 ACACTGTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (18 bp):
ATCTGTTTCATCTTATAG
Found at i:2102169 original size:17 final size:17
Alignment explanation
Indices: 2102147--2102186 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
2102137 GTAGGCATGA
2102147 AAACTTGCATGCAAACT
1 AAACTTGCATGCAAACT
2102164 AAACTTGCATGCAAACT
1 AAACTTGCATGCAAACT
2102181 AAACTT
1 AAACTT
2102187 CGTGAGGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (17 bp):
AAACTTGCATGCAAACT
Found at i:2103278 original size:2 final size:2
Alignment explanation
Indices: 2103271--2103303 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2103261 TGCGAAAGGC
2103271 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2103304 CAACCTGTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2107131 original size:231 final size:231
Alignment explanation
Indices: 2106773--2107193 Score: 565
Period size: 231 Copynumber: 1.8 Consensus size: 231
2106763 ATCTGATGAT
* * * *
2106773 TCAATCCTCTTCATTAAAGAAGCTGTCCTCTCACGTTCTTGAGCCAATTCAAATTTTGCAGTTTC
1 TCAATCCTCTTCATCAAAGAAACTGTCCTCTCACGTTCTTCAGCCAATTCAAATTTTACAGTTTC
* * * * *
2106838 TAAAGCATTACAAAGTTCTCGAAGTTTCTCTCCAAATTCATTTTTCATATGCACAGCTTGCTCTT
66 TAAAGCATCACAAACTTCTCGAAGTTTCTCTCCAAATTCACTTTCCATATGCAAAGCTTGCTCTT
* * *
2106903 CTAACTG-ACTTTGTCTCCCAGATGCTTCCTCTAGCATTTCTTTATACCTCTCAAGCTCTTCCTT
131 CCAACTGTA-TTTGACTCCCAGATGCTTCCTCAAGCATTTCTTTATACCTCTCAAGCTCTTCCTT
2106967 TGTCTGGAGCCACTGCTCTTCAATCTGATCCAAAGAC
195 TGTCTGGAGCCACTGCTCTTCAATCTGATCCAAAGAC
* * * * * *
2107004 TCAATCCTCTTCATCAAAGAAACTGTTCTCTCTCGTTCTTCAGTCAGTTCAGATTTTACTGTTTC
1 TCAATCCTCTTCATCAAAGAAACTGTCCTCTCACGTTCTTCAGCCAATTCAAATTTTACAGTTTC
* * *** * *
2107069 TAAATCATCACAAACTTCTCTAAGTTTCTCTCTGTATTTACTTTCCATCTGCAAAGCTTGCTCTT
66 TAAAGCATCACAAACTTCTCGAAGTTTCTCTCCAAATTCACTTTCCATATGCAAAGCTTGCTCTT
* * * *
2107134 CCGAGTGTATTTGACTCCTAGATGCTTCCTCAAGCCTTTCTTTATACCTCTCAAGCTCTT
131 CCAACTGTATTTGACTCCCAGATGCTTCCTCAAGCATTTCTTTATACCTCTCAAGCTCTT
2107194 TCTGCATCAG
Statistics
Matches: 160, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
231 159 0.99
232 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.38
Consensus pattern (231 bp):
TCAATCCTCTTCATCAAAGAAACTGTCCTCTCACGTTCTTCAGCCAATTCAAATTTTACAGTTTC
TAAAGCATCACAAACTTCTCGAAGTTTCTCTCCAAATTCACTTTCCATATGCAAAGCTTGCTCTT
CCAACTGTATTTGACTCCCAGATGCTTCCTCAAGCATTTCTTTATACCTCTCAAGCTCTTCCTTT
GTCTGGAGCCACTGCTCTTCAATCTGATCCAAAGAC
Found at i:2112711 original size:18 final size:19
Alignment explanation
Indices: 2112688--2112729 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2112678 TCGAATCGAA
* *
2112688 TTATAT-TTTTTTTAATTT
1 TTATATATTATTTAAATTT
2112706 TTATATATTATTTAAATTT
1 TTATATATTATTTAAATTT
2112725 TTATA
1 TTATA
2112730 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATATATTATTTAAATTT
Found at i:2112779 original size:21 final size:25
Alignment explanation
Indices: 2112748--2112803 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 25
2112738 ATAATAATTT
*
2112748 TATATCAAATTTTAT-TT-AAAT-A
1 TATATAAAATTTTATATTAAAATAA
2112770 TAT-TAAAATTTTATATTAAAATAA
1 TATATAAAATTTTATATTAAAATAA
2112794 TATATAAAAT
1 TATATAAAAT
2112804 CAAAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.34
22 5 0.17
23 4 0.14
24 4 0.14
25 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATATAAAATTTTATATTAAAATAA
Found at i:2112797 original size:13 final size:13
Alignment explanation
Indices: 2112766--2112803 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2112756 ATTTTATTTA
2112766 AATATATTAAAAT
1 AATATATTAAAAT
**
2112779 TTTATATTAAAAT
1 AATATATTAAAAT
2112792 AATATA-TAAAAT
1 AATATATTAAAAT
2112804 CAAAAAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATATATTAAAAT
Found at i:2113966 original size:11 final size:11
Alignment explanation
Indices: 2113950--2113974 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2113940 TCCCGCTTTG
2113950 AACCCCGAAGT
1 AACCCCGAAGT
2113961 AACCCCGAAGT
1 AACCCCGAAGT
2113972 AAC
1 AAC
2113975 GAAATTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.36, G:0.16, T:0.08
Consensus pattern (11 bp):
AACCCCGAAGT
Found at i:2115414 original size:25 final size:23
Alignment explanation
Indices: 2115354--2115420 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 23
2115344 TATTATTTTT
*
2115354 AATATAAATTATATTTT-AATTA
1 AATATAAATAATATTTTAAATTA
*
2115376 TATATAAATGTAATATTTTAAATTAA
1 AATATAAA--TAATATTTTAAATT-A
2115402 AATATTAAATAATATTTTA
1 AATA-TAAATAATATTTTA
2115421 TTAATATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 7 0.19
24 8 0.22
25 14 0.38
26 4 0.11
27 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (23 bp):
AATATAAATAATATTTTAAATTA
Found at i:2115438 original size:25 final size:25
Alignment explanation
Indices: 2115353--2115439 Score: 67
Period size: 25 Copynumber: 3.5 Consensus size: 25
2115343 ATATTATTTT
*
2115353 TAATATAAATTATATTTTAATT-ATA
1 TAATATAAATAATATTTT-ATTAATA
*
2115378 T-ATA-AATGTAATATTTTA--AATTA
1 TAATATAA-ATAATATTTTATTAA-TA
*
2115401 AAATATTAAATAATATTTTATTAATA
1 TAATA-TAAATAATATTTTATTAATA
*
2115427 TAATATATATAAT
1 TAATATAAATAAT
2115440 TAAATAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
22 1 0.02
23 5 0.10
24 14 0.29
25 18 0.38
26 8 0.17
27 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (25 bp):
TAATATAAATAATATTTTATTAATA
Found at i:2116055 original size:12 final size:12
Alignment explanation
Indices: 2116040--2116125 Score: 63
Period size: 11 Copynumber: 7.2 Consensus size: 12
2116030 AAATTTGTAT
2116040 AAAAATATAATA
1 AAAAATATAATA
2116052 AAAAATGATACA-A
1 AAAAAT-ATA-ATA
2116065 AAAAATATAA-A
1 AAAAATATAATA
* *
2116076 AATAATATAATTT
1 AAAAATATAA-TA
* *
2116089 AAAATTTTAATA
1 AAAAATATAATA
*
2116101 AAAATTATAA-A
1 AAAAATATAATA
*
2116112 TAAAAT-TAATA
1 AAAAATATAATA
2116123 AAA
1 AAA
2116126 TTAAAAAATA
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
10 3 0.05
11 19 0.32
12 19 0.32
13 17 0.29
14 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (12 bp):
AAAAATATAATA
Found at i:2116113 original size:13 final size:12
Alignment explanation
Indices: 2116038--2116116 Score: 56
Period size: 12 Copynumber: 6.5 Consensus size: 12
2116028 ATAAATTTGT
2116038 ATAAAAATAT-A
1 ATAAAAATATAA
2116049 ATAAAAAATGATACA
1 AT-AAAAAT-ATA-A
2116064 A-AAAAATATAA
1 ATAAAAATATAA
*
2116075 A-AATAATATAA
1 ATAAAAATATAA
* * * *
2116086 TTTAAAATTTTA
1 ATAAAAATATAA
2116098 ATAAAAATTATAA
1 ATAAAAA-TATAA
2116111 ATAAAA
1 ATAAAA
2116117 TTAATAAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
11 13 0.25
12 20 0.38
13 17 0.33
15 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (12 bp):
ATAAAAATATAA
Found at i:2134852 original size:6 final size:6
Alignment explanation
Indices: 2134831--2134915 Score: 68
Period size: 6 Copynumber: 14.2 Consensus size: 6
2134821 TGGGTTAAAC
* *
2134831 GGGAAT GTGAAT GGG-AT GGGGAAT AGGAAT GGGAAT GGGAAT GGGAAT
1 GGGAAT GGGAAT GGGAAT -GGGAAT GGGAAT GGGAAT GGGAAT GGGAAT
* * * *
2134879 GTGAAT GCGG--T GGAAAAT AGGAAT GAGAAT GGGAAT G
1 GGGAAT G-GGAAT GG-GAAT GGGAAT GGGAAT GGGAAT G
2134916 AAGTGCCAGG
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
4 1 0.02
5 4 0.07
6 51 0.84
7 5 0.08
ACGTcount: A:0.35, C:0.01, G:0.45, T:0.19
Consensus pattern (6 bp):
GGGAAT
Found at i:2134898 original size:42 final size:42
Alignment explanation
Indices: 2134831--2134915 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
2134821 TGGGTTAAAC
** *
2134831 GGGAATGTGAATGGGATGGGGAATAGGAATGGGAATGGGAAT
1 GGGAATGTGAATGGGATGGAAAATAGGAATGAGAATGGGAAT
2134873 GGGAATGTGAATGCGG-TGGAAAATAGGAATGAGAATGGGAAT
1 GGGAATGTGAATG-GGATGGAAAATAGGAATGAGAATGGGAAT
2134915 G
1 G
2134916 AAGTGCCAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
42 37 0.95
43 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.45, T:0.19
Consensus pattern (42 bp):
GGGAATGTGAATGGGATGGAAAATAGGAATGAGAATGGGAAT
Found at i:2135324 original size:2 final size:2
Alignment explanation
Indices: 2135317--2135357 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2135307 GCTGGAGTTG
2135317 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2135357 A
1 A
2135358 GATTATAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2144350 original size:15 final size:16
Alignment explanation
Indices: 2144332--2144364 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2144322 TGAAAAATCC
2144332 AAGGAAAGGAAA-TTG
1 AAGGAAAGGAAAGTTG
2144347 AAGGAAAGGAAAGTTG
1 AAGGAAAGGAAAGTTG
2144363 AA
1 AA
2144365 TTCCTTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (16 bp):
AAGGAAAGGAAAGTTG
Found at i:2150461 original size:15 final size:14
Alignment explanation
Indices: 2150431--2150464 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
2150421 ATTTAGACAT
*
2150431 ATATTTTTATATAA
1 ATATTTTTATAAAA
2150445 ATATTTTTAATAAAA
1 ATATTTTT-ATAAAA
2150460 ATATT
1 ATATT
2150465 AATAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATTTTTATAAAA
Found at i:2150560 original size:22 final size:21
Alignment explanation
Indices: 2150535--2150575 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2150525 TATATTATTA
2150535 ATTT-TTACATTTAACTTTATCC
1 ATTTATTA-ATTTAA-TTTATCC
2150557 ATTTATTAATTTAATTTAT
1 ATTTATTAATTTAATTTAT
2150576 TAATTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTATTAATTTAATTTATCC
Found at i:2151261 original size:25 final size:25
Alignment explanation
Indices: 2151217--2151284 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
2151207 ATGAGATTAA
*
2151217 AATTAATAATAAAATTTATTATAATTGT
1 AATTAA-AA-AAAA-TTATTATAACTGT
* * *
2151245 TATTGAAAAAAATTATTGTAACTGT
1 AATTAAAAAAAATTATTATAACTGT
2151270 AATTAAAAAAAATTA
1 AATTAAAAAAAATTA
2151285 ATAAAAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 24 0.71
26 4 0.12
27 2 0.06
28 4 0.12
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (25 bp):
AATTAAAAAAAATTATTATAACTGT
Found at i:2151604 original size:23 final size:24
Alignment explanation
Indices: 2151577--2151632 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
2151567 ATGTTCTATG
2151577 TTATTTTTTGA-ACATCTAAAATTA
1 TTATTTTTTGATA-ATCTAAAATTA
* *
2151601 -TATTTTTTTATAATTTAAAATTA
1 TTATTTTTTGATAATCTAAAATTA
2151624 TTATTTTTT
1 TTATTTTTT
2151633 ACTTTTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
TTATTTTTTGATAATCTAAAATTA
Found at i:2162062 original size:12 final size:13
Alignment explanation
Indices: 2162042--2162070 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2162032 TACGGGATTG
2162042 ATTAGATTAATTA
1 ATTAGATTAATTA
2162055 ATTA-ATTAATTA
1 ATTAGATTAATTA
2162067 ATTA
1 ATTA
2162071 CAATTAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
ATTAGATTAATTA
Found at i:2163398 original size:51 final size:49
Alignment explanation
Indices: 2163337--2163487 Score: 160
Period size: 51 Copynumber: 3.0 Consensus size: 49
2163327 AATTTAACTG
*
2163337 GTAATATTTTATTTGGATCATCTTAAATATATAATTTATAATCATTATTAA
1 GTAATTTTTTATTTGGATCAT-TTAAATATATAATTTATAATCATTATT-A
** * * * *
2163388 GTAATTTTTTATTTGGATCAATTTAAATGCATAATTCACAATCATAATTT
1 GTAATTTTTTATTTGGATC-ATTTAAATATATAATTTATAATCATTATTA
* *
2163438 GATAATTTTTTGTTTGGATCATTTGAAATATAAAATTTATAAAT-ATTATT
1 G-TAATTTTTTATTTGGATCATTT-AAATATATAATTTAT-AATCATTATT
2163488 TTTTAAATTA
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
50 5 0.06
51 72 0.88
52 5 0.06
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (49 bp):
GTAATTTTTTATTTGGATCATTTAAATATATAATTTATAATCATTATTA
Found at i:2166545 original size:17 final size:17
Alignment explanation
Indices: 2166523--2166557 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2166513 ATTGCAGTTC
2166523 AAGTGACCCTGACATTG
1 AAGTGACCCTGACATTG
* *
2166540 AAGTGACCTTGACCTTG
1 AAGTGACCCTGACATTG
2166557 A
1 A
2166558 CCTTGAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (17 bp):
AAGTGACCCTGACATTG
Found at i:2167821 original size:10 final size:10
Alignment explanation
Indices: 2167804--2167834 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2167794 AAAATCAAGG
2167804 TCTTTTTTTT
1 TCTTTTTTTT
*
2167814 TTTTTTTTTT
1 TCTTTTTTTT
2167824 TCTTTTTTTT
1 TCTTTTTTTT
2167834 T
1 T
2167835 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:2182100 original size:23 final size:23
Alignment explanation
Indices: 2182055--2182100 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2182045 GTAAAATTTG
* *
2182055 TAAAATTTTAAAAAAAGATTTAA
1 TAAAAATTTAAAAAAAGACTTAA
2182078 TAAAAATTTAAATAAAA-ACTTAA
1 TAAAAATTTAAA-AAAAGACTTAA
2182101 ATCGATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAAATTTAAAAAAAGACTTAA
Found at i:2182148 original size:16 final size:16
Alignment explanation
Indices: 2182127--2182157 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2182117 AATTTAATGT
*
2182127 AAAAATTAATAATATA
1 AAAAATTAAAAATATA
2182143 AAAAATTAAAAATAT
1 AAAAATTAAAAATAT
2182158 TATTTATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATTAAAAATATA
Found at i:2182223 original size:13 final size:12
Alignment explanation
Indices: 2182196--2182220 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2182186 TATTCAATGA
2182196 TAATATTTTTAT
1 TAATATTTTTAT
2182208 TAATATTTTTAT
1 TAATATTTTTAT
2182220 T
1 T
2182221 TAAAATATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATATTTTTAT
Found at i:2182480 original size:3 final size:3
Alignment explanation
Indices: 2182472--2182517 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2182462 AAAACGGAAC
2182472 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2182518 ATTCAACATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2183493 original size:15 final size:16
Alignment explanation
Indices: 2183473--2183507 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
2183463 CAAAGTACTA
2183473 AAAATTTTAAGATTT-
1 AAAATTTTAAGATTTC
2183488 AAAA-TTTAAGATTTC
1 AAAATTTTAAGATTTC
2183503 AAAAT
1 AAAAT
2183508 ATTTTCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (16 bp):
AAAATTTTAAGATTTC
Found at i:2183746 original size:14 final size:16
Alignment explanation
Indices: 2183722--2183755 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
2183712 CAAAGTATTA
2183722 AAAATTTTAAGATTT-
1 AAAATTTTAAGATTTC
2183737 AAAA-TTTAAGATTTC
1 AAAATTTTAAGATTTC
2183752 AAAA
1 AAAA
2183756 ATATCTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (16 bp):
AAAATTTTAAGATTTC
Found at i:2186052 original size:3 final size:3
Alignment explanation
Indices: 2186044--2186076 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2186034 ATTGGAGGTT
2186044 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2186077 AAATGAATTC
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):
TAA
Found at i:2190621 original size:14 final size:15
Alignment explanation
Indices: 2190602--2190630 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2190592 NNNNNNAAAT
2190602 TTTAAGATTT-AAAA
1 TTTAAGATTTCAAAA
2190616 TTTAAGATTTCAAAA
1 TTTAAGATTTCAAAA
2190631 ATATTTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.41
Consensus pattern (15 bp):
TTTAAGATTTCAAAA
Found at i:2190920 original size:14 final size:16
Alignment explanation
Indices: 2190896--2190929 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
2190886 CAAAGTATTA
2190896 AAAATTTTAAGATTT-
1 AAAATTTTAAGATTTC
2190911 AAAA-TTTAAGATTTC
1 AAAATTTTAAGATTTC
2190926 AAAA
1 AAAA
2190930 ATATCTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (16 bp):
AAAATTTTAAGATTTC
Found at i:2191968 original size:3 final size:3
Alignment explanation
Indices: 2191944--2191985 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
2191934 AAAACCAAAC
*
2191944 ATT ATT -TT ATTT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2191986 TTAAAGTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:2192428 original size:2 final size:2
Alignment explanation
Indices: 2192421--2192454 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2192411 ACACAATAAA
*
2192421 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2192455 GTATGCACGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2193266 original size:3 final size:3
Alignment explanation
Indices: 2193258--2193290 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2193248 ATTAGAGGTT
2193258 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2193291 ATTGAATTCT
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):
TAA
Found at i:2204908 original size:2 final size:2
Alignment explanation
Indices: 2204903--2204927 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2204893 ATACATATAT
2204903 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2204928 GAAAAACCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2215254 original size:100 final size:100
Alignment explanation
Indices: 2215067--2215256 Score: 258
Period size: 100 Copynumber: 1.9 Consensus size: 100
2215057 AAGATTTAGA
**
2215067 TATTCACTCTTCCAGCGTCTCAGATCAGTTTGACCGTCACGATTCACACCCTTATAAGATATTAT
1 TATTCACTCTTCCAGCGTCTCAGATCAGTTTGACCACCACGATTCACACCCTTATAAGATATTAT
* *
2215132 CCGCTCTGACTTCCTGATCTCACGGCGATCTTGGG
66 CCGCTCTGACTCCCTGACCTCACGGCGATCTTGGG
* * * * *
2215167 TATTCACTCTTTC-GACGTCTCAGATCAGTTTGACCACCATGATTCACACCCTTATGAGGTATTG
1 TATTCACTCTTCCAG-CGTCTCAGATCAGTTTGACCACCACGATTCACACCCTTATAAGATATTA
*
2215231 TCCGCTCT-AGCTCCCTGGCCTCACGG
65 TCCGCTCTGA-CTCCCTGACCTCACGG
2215257 TTTTGTCCTA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
99 2 0.03
100 76 0.97
ACGTcount: A:0.20, C:0.31, G:0.17, T:0.32
Consensus pattern (100 bp):
TATTCACTCTTCCAGCGTCTCAGATCAGTTTGACCACCACGATTCACACCCTTATAAGATATTAT
CCGCTCTGACTCCCTGACCTCACGGCGATCTTGGG
Found at i:2217410 original size:330 final size:330
Alignment explanation
Indices: 2216789--2217447 Score: 1124
Period size: 330 Copynumber: 2.0 Consensus size: 330
2216779 AAAGAGGTAG
2216789 GAAAACTAGTTGAAAAACCAGTTCAAGAGATATATGGTCTACCATGGACGGTAAGGTGGCCAAGG
1 GAAAACTAGTTGAAAAACCAGTTCAAGAGATATATGGTCTACCATGGACGGTAAGGTGGCCAAGG
2216854 TGGAGGTGACCATAGGTGACATGAGGGAGAAGCTTGAGGAGGTCGAGACTCACATTACATCGCTA
66 TGGAGGTGACCATAGGTGACATGAGGGAGAAGCTTGAGGAGGTCGAGACTCACATTACATCGCTA
* *
2216919 GACTCCATAAGGGAGGAGATCTAAGGTGAGCTACAAGTTACTTTCAACAAAGGCATGGATGTGAT
131 GACTCCATAAGGGAAGAGATCTAAGGTGAGCTACAAGCTACTTTCAACAAAGGCATGGATGTGAT
* * *
2216984 AACCCAAAAAAATGGAGCCTTTGAGGCTTATGGTCTACCATGGACGGTAGGTTGGCCAAGGTGGA
196 AACCCAAAAAAATGGAGCCTTTGAGGCTTATGGTCTACCATGGACGGTAGGCTGACCAAGGTGAA
*
2217049 GGTGACCATGGACGACAAGGGGGAAAAGCTTGAGGAGGTCGAGACTCACATTGCATCACTAGACT
261 GGTGACCATGGACGACAAGGAGGAAAAGCTTGAGGAGGTCGAGACTCACATTGCATCACTAGACT
2217114 CCATA
326 CCATA
*
2217119 GAAAACTAGTTGGAAAACCAGTTCAAGAGATATATGGTCTACCATGGACGGT-AGGCTGGCCAAG
1 GAAAACTAGTTGAAAAACCAGTTCAAGAGATATATGGTCTACCATGGACGGTAAGG-TGGCCAAG
* *
2217183 GTGGAGGTGACCATAGGTGACATGAGGGAGAAGTTTGAGGAGGTCGAGACTCACATTACATCGTT
65 GTGGAGGTGACCATAGGTGACATGAGGGAGAAGCTTGAGGAGGTCGAGACTCACATTACATCGCT
** *
2217248 AGACTCCATAAGGGAAGAGATCTAAGGTGAGCTGTAAGCTACTTTCAACGAAGGCATGGATGTGA
130 AGACTCCATAAGGGAAGAGATCTAAGGTGAGCTACAAGCTACTTTCAACAAAGGCATGGATGTGA
* *
2217313 TAACCCAAAAGAATGGGGCCTTTGAGGCTTATGGTCTACCATGGACGGTAGGCTGACCAAGGTGA
195 TAACCCAAAAAAATGGAGCCTTTGAGGCTTATGGTCTACCATGGACGGTAGGCTGACCAAGGTGA
* * * *
2217378 AGGTGACCAT-GAGCGACAATGAGGAGAAGCTTGATGAGGTCGAGACTCACATTGCATCATTAGA
260 AGGTGACCATGGA-CGACAAGGAGGAAAAGCTTGAGGAGGTCGAGACTCACATTGCATCACTAGA
2217442 CTCCAT
324 CTCCAT
2217448 GGGGGAGGAG
Statistics
Matches: 309, Mismatches: 18, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
329 5 0.02
330 304 0.98
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (330 bp):
GAAAACTAGTTGAAAAACCAGTTCAAGAGATATATGGTCTACCATGGACGGTAAGGTGGCCAAGG
TGGAGGTGACCATAGGTGACATGAGGGAGAAGCTTGAGGAGGTCGAGACTCACATTACATCGCTA
GACTCCATAAGGGAAGAGATCTAAGGTGAGCTACAAGCTACTTTCAACAAAGGCATGGATGTGAT
AACCCAAAAAAATGGAGCCTTTGAGGCTTATGGTCTACCATGGACGGTAGGCTGACCAAGGTGAA
GGTGACCATGGACGACAAGGAGGAAAAGCTTGAGGAGGTCGAGACTCACATTGCATCACTAGACT
CCATA
Found at i:2217495 original size:191 final size:191
Alignment explanation
Indices: 2217151--2217530 Score: 550
Period size: 191 Copynumber: 2.0 Consensus size: 191
2217141 TCAAGAGATA
* * *
2217151 TATGGTCTACCATGGACGGTAGGCTGGCCAAGGTGGAGGTGACCATAGGTGACATGAGGGAGAAG
1 TATGGTCTACCATGGACGGTAGGCTGACCAAGGTGAAGGTGACCATAGGCGACATGAGGGAGAAG
* * *
2217216 TTTGAGGAGGTCGAGACTCACATTACATCGTTAGACTCCATAAGGGAAGAGATCTAAGGTGAGCT
66 CTTGAGGAGGTCGAGACTCACATTACATCATTAGACTCCATAAGGGAAGAGATCCAAGGTGAGCT
* * * * *
2217281 GTAAGCTACTTTCAACGAAGGCATGGATGTGATAACCCAAAAGAATGGGGCCTTTGAGGCT
131 GTAAGCTACTCTCAACAAAGGCATAGATGTGATAACCCAAAAGAATGAGGCATTTGAGGCT
2217342 TATGGTCTACCATGGACGGTAGGCTGACCAAGGTGAAGGTGACCAT-GAGCGACAATGA-GGAGA
1 TATGGTCTACCATGGACGGTAGGCTGACCAAGGTGAAGGTGACCATAG-GCGAC-ATGAGGGAGA
* * ** *
2217405 AGCTTGATGAGGTCGAGACTCACATTGCATCATTAGACTCCATGGGGGAGGAGATCCAAGGTGAG
64 AGCTTGAGGAGGTCGAGACTCACATTACATCATTAGACTCCATAAGGGAAGAGATCCAAGGTGAG
* *
2217470 CT-TCAAGCTGCTCTCAACAAAGGCATAGATGTGATCACCCAAAAGAATGAGGCATTTGAGG
129 CTGT-AAGCTACTCTCAACAAAGGCATAGATGTGATAACCCAAAAGAATGAGGCATTTGAGG
2217531 TTGAAGTGCT
Statistics
Matches: 168, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
190 2 0.01
191 162 0.96
192 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.31, T:0.21
Consensus pattern (191 bp):
TATGGTCTACCATGGACGGTAGGCTGACCAAGGTGAAGGTGACCATAGGCGACATGAGGGAGAAG
CTTGAGGAGGTCGAGACTCACATTACATCATTAGACTCCATAAGGGAAGAGATCCAAGGTGAGCT
GTAAGCTACTCTCAACAAAGGCATAGATGTGATAACCCAAAAGAATGAGGCATTTGAGGCT
Found at i:2237304 original size:2 final size:2
Alignment explanation
Indices: 2237297--2237322 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2237287 TAAAGGAAAC
2237297 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
2237323 GTCTAGCCCC
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):
AT
Found at i:2240771 original size:5 final size:5
Alignment explanation
Indices: 2240761--2240791 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
2240751 GAAGTGGTAT
2240761 TAGAG TAGAG TAGAG TAGAG TAGAG TAGAG T
1 TAGAG TAGAG TAGAG TAGAG TAGAG TAGAG T
2240792 GATAGGGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.23
Consensus pattern (5 bp):
TAGAG
Found at i:2244566 original size:18 final size:19
Alignment explanation
Indices: 2244539--2244575 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2244529 AATCAAGCCA
2244539 ATTAAATTATATAT-TTTT
1 ATTAAATTATATATATTTT
*
2244557 ATTAATTTATATATATTTT
1 ATTAAATTATATATATTTT
2244576 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTAAATTATATATATTTT
Found at i:2244625 original size:20 final size:21
Alignment explanation
Indices: 2244596--2244636 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2244586 ATAATTATTT
2244596 TATATAAAATTTTAT-TTAAA
1 TATATAAAATTTTATATTAAA
*
2244616 TATATTAAATTTTATATTAAA
1 TATATAAAATTTTATATTAAA
2244637 ATAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATAAAATTTTATATTAAA
Found at i:2245706 original size:15 final size:16
Alignment explanation
Indices: 2245686--2245715 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2245676 TTTTATACAG
2245686 TATTCAAAT-TTAAAT
1 TATTCAAATATTAAAT
2245701 TATTCAAATATTAAA
1 TATTCAAATATTAAA
2245716 ATTTTCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTCAAATATTAAAT
Found at i:2250143 original size:21 final size:20
Alignment explanation
Indices: 2250108--2250146 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2250098 AATAATTAAA
2250108 TAAAATAAAAAATTAAAAAT
1 TAAAATAAAAAATTAAAAAT
*
2250128 TAAAATCAATAAATTAAAA
1 TAAAAT-AAAAAATTAAAA
2250147 TATCTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAATAAAAAATTAAAAAT
Found at i:2250396 original size:23 final size:24
Alignment explanation
Indices: 2250352--2250396 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2250342 ATTTAAATTT
* * *
2250352 TTTATTAAAATTTTTATTAAATCA
1 TTTAATAAAATTTTCATCAAATCA
2250376 TTTAATAAAATTTTCA-CAAAT
1 TTTAATAAAATTTTCATCAAAT
2250397 TTCACTTAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTAATAAAATTTTCATCAAATCA
Found at i:2252558 original size:12 final size:13
Alignment explanation
Indices: 2252534--2252562 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2252524 CTTATTTTGG
2252534 TTAATTAAATTAA
1 TTAATTAAATTAA
2252547 TTAATT-AATTAA
1 TTAATTAAATTAA
2252559 TTAA
1 TTAA
2252563 AATATTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAATTAAATTAA
Found at i:2256532 original size:3 final size:3
Alignment explanation
Indices: 2256524--2256557 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2256514 ATTTTTCTAG
2256524 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2256558 TATTTATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2256562 original size:4 final size:4
Alignment explanation
Indices: 2256553--2256632 Score: 58
Period size: 4 Copynumber: 19.8 Consensus size: 4
2256543 ATTATTATTA
* * * *
2256553 TTAT TTAT TTAT CTAT TTAT TTGT TTTT TTAT TTAT GTT-T TCA- TTATT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTA-T
*
2256601 TTAT TTAT TTGT TATAT ATTAT TTA- TTAT TTA
1 TTAT TTAT TTAT T-TAT -TTAT TTAT TTAT TTA
2256633 ATTGTAAATA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
3 6 0.10
4 43 0.72
5 10 0.17
6 1 0.02
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:2256569 original size:12 final size:11
Alignment explanation
Indices: 2256524--2256632 Score: 61
Period size: 12 Copynumber: 9.8 Consensus size: 11
2256514 ATTTTTCTAG
2256524 TATTA-TTA-T
1 TATTATTTATT
2256533 TATTA-TTA-T
1 TATTATTTATT
2256542 TATTA-TTA-T
1 TATTATTTATT
2256551 TATTATTTATT
1 TATTATTTATT
2256562 TATCTATTTATT
1 TAT-TATTTATT
* *
2256574 TGTTTTTTTATT
1 T-ATTATTTATT
2256586 TATGT-TTTCATT
1 TAT-TATTT-ATT
*
2256598 ATTTTATTTATT
1 -TATTATTTATT
*
2256610 TGTTATATATTATT
1 T-AT-TAT-TTATT
2256624 TATTATTTA
1 TATTATTTA
2256633 ATTGTAAATA
Statistics
Matches: 84, Mismatches: 5, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
9 23 0.27
10 3 0.04
11 12 0.14
12 30 0.36
13 10 0.12
14 6 0.07
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.70
Consensus pattern (11 bp):
TATTATTTATT
Found at i:2256664 original size:16 final size:16
Alignment explanation
Indices: 2256638--2256672 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2256628 ATTTAATTGT
2256638 AAATATTTTTTAAA-A
1 AAATATTTTTTAAATA
2256653 AAATATTTTTTTAAATA
1 AAATA-TTTTTTAAATA
2256670 AAA
1 AAA
2256673 ATGAATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 9 0.50
17 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATATTTTTTAAATA
Found at i:2256762 original size:59 final size:60
Alignment explanation
Indices: 2256662--2256777 Score: 137
Period size: 59 Copynumber: 1.9 Consensus size: 60
2256652 AAAATATTTT
* *
2256662 TTTAAATAAAAATGAATCTTACAAACATATTAGAGGGTTCAAATCTTCTAA-AAATTAAATG
1 TTTAAATAAAAA-GAATCTTACAAACATATTAGAAGATTCAAAT-TTCTAATAAATTAAATG
** * * *
2256723 TTTAAATAAAAA-AATCTTATTAATATATTAGAATATTCAAATTTTTAATAAATTA
1 TTTAAATAAAAAGAATCTTACAAACATATTAGAAGATTCAAATTTCTAATAAATTA
2256778 TTTAATAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
58 5 0.11
59 30 0.64
61 12 0.26
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.38
Consensus pattern (60 bp):
TTTAAATAAAAAGAATCTTACAAACATATTAGAAGATTCAAATTTCTAATAAATTAAATG
Found at i:2256833 original size:21 final size:21
Alignment explanation
Indices: 2256781--2256826 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2256771 TAAATTATTT
2256781 AATAAAATAAAAAATCTTATC
1 AATAAAATAAAAAATCTTATC
*
2256802 AATAAAATAAACAATCTTATC
1 AATAAAATAAAAAATCTTATC
2256823 AATA
1 AATA
2256827 TATTAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (21 bp):
AATAAAATAAAAAATCTTATC
Found at i:2256990 original size:120 final size:121
Alignment explanation
Indices: 2256826--2257062 Score: 350
Period size: 120 Copynumber: 2.0 Consensus size: 121
2256816 TCTTATCAAT
* * * *
2256826 ATATTAAAAGGTAATTTGATTTTCAAAATAAAATTATATTAATATATTGGAGAACCTTATTAATT
1 ATATTAAAAGATAATTTAATTTTCAAAATAAAATTATATCAATATATTAGAGAACCTTATTAATT
* * *
2256891 TTTTAT-AAAAAACAAATTTTAAGAGAAAAATAGTTTTTAATGAAGCTTTACTAAC
66 TTTTATAAAAAAACAAATTTTAAAAGAAAAATAGTTTTCAATGAAGCCTTACTAAC
* * * * * *
2256946 ATATTAACAGATAATTTAATTTTTAAGATAAGATTTTATCAATATATTAGAGAATCTTATTAATT
1 ATATTAAAAGATAATTTAATTTTCAAAATAAAATTATATCAATATATTAGAGAACCTTATTAATT
2257011 TTTTATAAAAAAACAAATTTTAAAAGAAAAATAGTTTTCAATGAAGCCTTAC
66 TTTTATAAAAAAACAAATTTTAAAAGAAAAATAGTTTTCAATGAAGCCTTAC
2257063 AAGACAATTT
Statistics
Matches: 103, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
120 61 0.59
121 42 0.41
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.39
Consensus pattern (121 bp):
ATATTAAAAGATAATTTAATTTTCAAAATAAAATTATATCAATATATTAGAGAACCTTATTAATT
TTTTATAAAAAAACAAATTTTAAAAGAAAAATAGTTTTCAATGAAGCCTTACTAAC
Found at i:2263767 original size:61 final size:61
Alignment explanation
Indices: 2263673--2263790 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 61
2263663 TTATAAAGGA
*
2263673 TTATTCAAGGCATTTTCTAACCAAAAATACCTTGAATAATCCCTTAAAAAAATTAAATGGGG
1 TTATTCAAGGCATTTTCTAACCAAAAACACCTTGAATAATCCC-TAAAAAAATTAAATGGGG
* * * * * *
2263735 TTATTTAAGGTATTTT-TAGCCAAAAACGCCTTGAATAATCCCTAAAATATTTAAAT
1 TTATTCAAGGCATTTTCTAACCAAAAACACCTTGAATAATCCCTAAAAAAATTAAAT
2263791 CATTTTCCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
60 12 0.24
61 23 0.47
62 14 0.29
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (61 bp):
TTATTCAAGGCATTTTCTAACCAAAAACACCTTGAATAATCCCTAAAAAAATTAAATGGGG
Found at i:2263911 original size:20 final size:20
Alignment explanation
Indices: 2263883--2263920 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2263873 TAGCCTAATC
*
2263883 TCCATCTCTCATAAACTCTT
1 TCCACCTCTCATAAACTCTT
*
2263903 TCCACCTCTCATTAACTC
1 TCCACCTCTCATAAACTC
2263921 AACAAACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.39, G:0.00, T:0.37
Consensus pattern (20 bp):
TCCACCTCTCATAAACTCTT
Found at i:2268583 original size:21 final size:21
Alignment explanation
Indices: 2268557--2268597 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2268547 GAAGATATGA
*
2268557 ATGAGCCAGTTATAATTAGTG
1 ATGAGCCAGATATAATTAGTG
* *
2268578 ATGAGCTAGATGTAATTAGT
1 ATGAGCCAGATATAATTAGT
2268598 TTTGAGTAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (21 bp):
ATGAGCCAGATATAATTAGTG
Found at i:2268603 original size:21 final size:20
Alignment explanation
Indices: 2268569--2268609 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2268559 GAGCCAGTTA
2268569 TAATTAGTGATGAGCTAGATG
1 TAATTAGTGATGAG-TAGATG
**
2268590 TAATTAGTTTTGAGTAGATG
1 TAATTAGTGATGAGTAGATG
2268610 GAGCAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.32, C:0.02, G:0.27, T:0.39
Consensus pattern (20 bp):
TAATTAGTGATGAGTAGATG
Found at i:2273225 original size:2 final size:2
Alignment explanation
Indices: 2273218--2273253 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2273208 AACAAGAAGA
*
2273218 AG AG AG AG AG AG AC 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
2273254 TTCATGGTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2276395 original size:2 final size:2
Alignment explanation
Indices: 2276388--2276413 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2276378 GGAATCTTAC
2276388 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
2276414 GTTTGTGTTG
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):
AT
Found at i:2278752 original size:2 final size:2
Alignment explanation
Indices: 2278745--2278784 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2278735 TATCTCCTCC
*
2278745 CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2278785 GTGTTTAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:2278756 original size:10 final size:10
Alignment explanation
Indices: 2278737--2278783 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
2278727 CAATGCAATA
2278737 TCTC-CTCCC
1 TCTCTCTCCC
2278746 TCTCTCTCCC
1 TCTCTCTCCC
*
2278756 TCTCTCTCTC
1 TCTCTCTCCC
*
2278766 TCTCTCTCTC
1 TCTCTCTCCC
2278776 TCTCTCTC
1 TCTCTCTC
2278784 TGTGTTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
9 4 0.11
10 32 0.89
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (10 bp):
TCTCTCTCCC
Found at i:2280240 original size:13 final size:13
Alignment explanation
Indices: 2280224--2280253 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2280214 AAAAGCAGAA
2280224 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
2280237 AAAAAAAGAAAAG
1 AAAAAAAAAAAAG
2280250 AAAA
1 AAAA
2280254 GTCATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:2282277 original size:2 final size:2
Alignment explanation
Indices: 2282272--2282296 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2282262 TCTCCTTATG
2282272 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
2282297 TTTCACTTTC
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:2285049 original size:86 final size:87
Alignment explanation
Indices: 2284952--2285121 Score: 288
Period size: 87 Copynumber: 2.0 Consensus size: 87
2284942 TTTAAATACT
* *
2284952 ACATTAATTAATATATTAATAATTTAAATATTACATTA-AAAATTTTAAAATTTAGATATTATAT
1 ACATTAATTAATAGATTAATAATTCAAATATTACATTATAAAATTTTAAAATTTAGATATTATAT
*
2285016 TAAATATTTTATTATAATTATC
66 TAAATATTTTACTATAATTATC
* *
2285038 ACATTAATTAATAGATTCATAATTCAAATATTACATTATAAATTTTTAAAATTTAGATATTATAT
1 ACATTAATTAATAGATTAATAATTCAAATATTACATTATAAAATTTTAAAATTTAGATATTATAT
2285103 TAAATATTTTACTATAATT
66 TAAATATTTTACTATAATT
2285122 TAAAAGTTAT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
86 35 0.45
87 43 0.55
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (87 bp):
ACATTAATTAATAGATTAATAATTCAAATATTACATTATAAAATTTTAAAATTTAGATATTATAT
TAAATATTTTACTATAATTATC
Found at i:2290997 original size:33 final size:33
Alignment explanation
Indices: 2290960--2291037 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
2290950 ATATGATACG
* *
2290960 AATATACGAATTATCAATATTTTACAAAATATA
1 AATATACGAATTATCAATATTTTACAAAACACA
*
2290993 AATATATGAATTATCAATATTTTACAAAACACA
1 AATATACGAATTATCAATATTTTACAAAACACA
2291026 AATATACGAATT
1 AATATACGAATT
2291038 GCTAAATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (33 bp):
AATATACGAATTATCAATATTTTACAAAACACA
Found at i:2291276 original size:2 final size:2
Alignment explanation
Indices: 2291269--2291315 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2291259 TTCCTTTCAT
*
2291269 AG AG AG AG AG AG AG AG AG AG AG AG AG TG 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
2291311 AG AG A
1 AG AG A
2291316 ATGACAAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:2295114 original size:2 final size:2
Alignment explanation
Indices: 2295101--2295135 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2295091 ACATACATAC
* *
2295101 AT AT AT AA AT AT AT AT AT GT 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
2295136 GTTAGAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2299074 original size:8 final size:8
Alignment explanation
Indices: 2299061--2299086 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2299051 TTCAGATATA
2299061 AGACAAAT
1 AGACAAAT
2299069 AGACAAAT
1 AGACAAAT
2299077 AGACAAAT
1 AGACAAAT
2299085 AG
1 AG
2299087 TATAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.15, T:0.12
Consensus pattern (8 bp):
AGACAAAT
Found at i:2301744 original size:39 final size:40
Alignment explanation
Indices: 2301678--2301755 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 40
2301668 AAAACATTGT
* *
2301678 TTGCACAAAGGTATCCCGTTCATCAAAAAGATTTTAACCA
1 TTGCACAAAAGTATCCCGTTCAACAAAAAGATTTTAACCA
2301718 TTGC-CAAAAGTATCTCC-TTCAACAAAAAGATTTTAACC
1 TTGCACAAAAGTATC-CCGTTCAACAAAAAGATTTTAACC
2301756 GTTGTCAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
39 29 0.83
40 6 0.17
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.28
Consensus pattern (40 bp):
TTGCACAAAAGTATCCCGTTCAACAAAAAGATTTTAACCA
Found at i:2303911 original size:31 final size:31
Alignment explanation
Indices: 2303875--2303934 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2303865 AAAAAAATAA
* *
2303875 TTATTAATGAAATAATATTATTTGATTTATT
1 TTATTAATAAAATAATATTATTTAATTTATT
2303906 TTATTAATAAAATAATATTATTTAATTTA
1 TTATTAATAAAATAATATTATTTAATTTA
2303935 CTGTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TTATTAATAAAATAATATTATTTAATTTATT
Found at i:2308470 original size:84 final size:84
Alignment explanation
Indices: 2308378--2308542 Score: 276
Period size: 84 Copynumber: 2.0 Consensus size: 84
2308368 AAAATAAATA
* *
2308378 TTTTTCCTACAACTACAACCCAGCTTAAGCTCCAATGTCTGGGTTATTGTCCATTTCGAAGGCAA
1 TTTTTCCTACAACTACAACCCAGCTTAAGCTCCAATGTCTGGGTAATTGTCCATTTCAAAGGCAA
*
2308443 ATGTTTAGGTTAGTGTATT
66 ATGTTTAGGCTAGTGTATT
* *
2308462 TTTTTCCTACGACTACAACCCAGCTTAAGCTCCAATGTCTTGGTAATTGTCCATTTCAAAGGCAA
1 TTTTTCCTACAACTACAACCCAGCTTAAGCTCCAATGTCTGGGTAATTGTCCATTTCAAAGGCAA
*
2308527 ATGTTTGGGCTAGTGT
66 ATGTTTAGGCTAGTGT
2308543 TTTGTGGCCA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (84 bp):
TTTTTCCTACAACTACAACCCAGCTTAAGCTCCAATGTCTGGGTAATTGTCCATTTCAAAGGCAA
ATGTTTAGGCTAGTGTATT
Found at i:2311260 original size:48 final size:48
Alignment explanation
Indices: 2311206--2311301 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
2311196 CTAGTTGTGC
*
2311206 TGCTTTTGTAGTTTTGATTTTATCAGATTCCCCTCAATCATGGTAGGA
1 TGCTTTTGTAGTTTTGATTTTATCAGATTCCCCTCAATCATAGTAGGA
*
2311254 TGCTTTTGTAGTTTTGGTTTTATCAGATTCCCCTCAATCATAGTAGGA
1 TGCTTTTGTAGTTTTGATTTTATCAGATTCCCCTCAATCATAGTAGGA
2311302 GATTTTCTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.44
Consensus pattern (48 bp):
TGCTTTTGTAGTTTTGATTTTATCAGATTCCCCTCAATCATAGTAGGA
Found at i:2312687 original size:20 final size:20
Alignment explanation
Indices: 2312662--2312701 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2312652 ACTGTACCTG
2312662 GAGATGTGTCTGCTATGGTT
1 GAGATGTGTCTGCTATGGTT
2312682 GAGATGTGTCTGCTATGGTT
1 GAGATGTGTCTGCTATGGTT
2312702 CCTGGTGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.35, T:0.40
Consensus pattern (20 bp):
GAGATGTGTCTGCTATGGTT
Found at i:2322368 original size:32 final size:32
Alignment explanation
Indices: 2322295--2322377 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 32
2322285 GTTTGAAAGC
*
2322295 TTTTAAAAATTTATTTTTGAAAAGTTACATGATT
1 TTTTGAAAATTTATTTTTGAAAAGTTA-AT-ATT
2322329 TTTTGAAAATTTATTTTTGAAGAAGTGT-AT-TT
1 TTTTGAAAATTTATTTTTGAA-AAGT-TAATATT
2322361 TTTTGAAAATTTATTTT
1 TTTTGAAAATTTATTTT
2322378 CAAAAATTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
32 19 0.41
34 22 0.48
35 4 0.09
36 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.11, T:0.54
Consensus pattern (32 bp):
TTTTGAAAATTTATTTTTGAAAAGTTAATATT
Found at i:2335035 original size:2 final size:2
Alignment explanation
Indices: 2335028--2335060 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2335018 TTGCTAAGTA
2335028 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2335061 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2335065 original size:2 final size:2
Alignment explanation
Indices: 2335060--2335091 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2335050 TCTCTCTCTC
2335060 TA 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 TA
2335092 AAATGCAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2347763 original size:13 final size:13
Alignment explanation
Indices: 2347745--2347771 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2347735 GGCATATTTT
2347745 GGAATACTATCAA
1 GGAATACTATCAA
2347758 GGAATACTATCAA
1 GGAATACTATCAA
2347771 G
1 G
2347772 TATCATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (13 bp):
GGAATACTATCAA
Found at i:2352490 original size:26 final size:26
Alignment explanation
Indices: 2352461--2352518 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
2352451 TTTTAACTTG
*
2352461 TATATTTAGATAAATTTTT-ATAAATA
1 TATATTTA-ATAAATTTTTAATAAAAA
*
2352487 TATA-TTAATATATTTTTCAATAAAAA
1 TATATTTAATAAATTTTT-AATAAAAA
2352513 TATATT
1 TATATT
2352519 AATTTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 9 0.33
25 3 0.11
26 14 0.52
27 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (26 bp):
TATATTTAATAAATTTTTAATAAAAA
Done.