Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008033.1 Hibiscus syriacus cultivar Beakdansim tig00110515_pilon, 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: 3048429
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 14
Found at i:1371335 original size:77 final size:77
Alignment explanation
Indices: 1371237--1371399 Score: 256
Period size: 77 Copynumber: 2.1 Consensus size: 77
1371227 GCTTGTTTAA
*
1371237 TTGATTTGTAAAAGTTTATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGC-TGTTTAAT
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT-CTTGTTTAAT
1371301 TGATTTGTAAAAG
65 TGATTTGTAAAAG
* * ***
1371314 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTCTTGTTTAATT
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCTTGTTTAATT
1371379 GATTTGTAAAAG
66 GATTTGTAAAAG
1371391 TTGATTTGT
1 TTGATTTGT
1371400 TGTTTTAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
76 1 0.01
77 78 0.99
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (77 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCTTGTTTAATT
GATTTGTAAAAG
Found at i:1371522 original size:20 final size:20
Alignment explanation
Indices: 1371493--1371599 Score: 124
Period size: 20 Copynumber: 5.3 Consensus size: 20
1371483 CGTTGCGATG
* *
1371493 GTTGCAAAAGTCAAATTCAC
1 GTTGCGAAAGTCAAATTCGC
*
1371513 GTTGCGAAAGTCAAATTTGC
1 GTTGCGAAAGTCAAATTCGC
*
1371533 ATTGCGAAAGTCAAATTCGC
1 GTTGCGAAAGTCAAATTCGC
*
1371553 GTTGCGATAGTCAAATTCGC
1 GTTGCGAAAGTCAAATTCGC
**** *
1371573 AACACGAAAGTTAAATTCGC
1 GTTGCGAAAGTCAAATTCGC
1371593 GTTGCGA
1 GTTGCGA
1371600 TTTCACGTTT
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (20 bp):
GTTGCGAAAGTCAAATTCGC
Found at i:1371600 original size:40 final size:40
Alignment explanation
Indices: 1371499--1371600 Score: 141
Period size: 40 Copynumber: 2.5 Consensus size: 40
1371489 GATGGTTGCA
* * * ***
1371499 AAAGTCAAATTCACGTTGCGAAAGTCAAATTTGCATTGCG
1 AAAGTCAAATTCGCGTTGCGATAGTCAAATTCGCAACACG
1371539 AAAGTCAAATTCGCGTTGCGATAGTCAAATTCGCAACACG
1 AAAGTCAAATTCGCGTTGCGATAGTCAAATTCGCAACACG
*
1371579 AAAGTTAAATTCGCGTTGCGAT
1 AAAGTCAAATTCGCGTTGCGAT
1371601 TTCACGTTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (40 bp):
AAAGTCAAATTCGCGTTGCGATAGTCAAATTCGCAACACG
Found at i:1374235 original size:24 final size:24
Alignment explanation
Indices: 1374201--1374254 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1374191 CTGAAACATT
1374201 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1374225 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1374249 ATCAAA
1 ATCAAA
1374255 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1375018 original size:16 final size:15
Alignment explanation
Indices: 1374996--1375034 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1374986 GAAATCATTG
1374996 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
1375012 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
1375027 AAAAATTA
1 AAAAATTA
1375035 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:1375226 original size:21 final size:21
Alignment explanation
Indices: 1375192--1375304 Score: 126
Period size: 20 Copynumber: 5.5 Consensus size: 21
1375182 CTAAAACCTA
* *
1375192 TTGCGAAATTAAAATTC-GTG
1 TTGCGAATTTGAAATTCAGTG
* * * *
1375212 TTGTGAATTCGAAAATC-GAG
1 TTGCGAATTTGAAATTCAGTG
1375232 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAATTCAGTG
1375253 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAATTCAGTG
*
1375274 TTGCGAATTTGGAAA-TC-GCG
1 TTGCGAATTT-GAAATTCAGTG
1375294 TTGCGAATTTG
1 TTGCGAATTTG
1375305 GAAAATCGCA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 40 0.50
21 35 0.44
22 4 0.05
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (21 bp):
TTGCGAATTTGAAATTCAGTG
Found at i:1375237 original size:40 final size:42
Alignment explanation
Indices: 1375192--1375280 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 42
1375182 CTAAAACCTA
*
1375192 TTGCGAAATTAAAATTC-GTGTTGTGAATTCGAAAATC-GAG
1 TTGCGAAATTAAAATTCAGTGTTGCGAATTCGAAAATCAGAG
* * * * *
1375232 TTGCGAATTTGAAATTCAGTGTTGCGAATTTGAAATTCAGTG
1 TTGCGAAATTAAAATTCAGTGTTGCGAATTCGAAAATCAGAG
1375274 TTGCGAA
1 TTGCGAA
1375281 TTTGGAAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 15 0.37
41 17 0.41
42 9 0.22
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (42 bp):
TTGCGAAATTAAAATTCAGTGTTGCGAATTCGAAAATCAGAG
Found at i:1375239 original size:20 final size:20
Alignment explanation
Indices: 1375192--1375312 Score: 127
Period size: 21 Copynumber: 5.9 Consensus size: 20
1375182 CTAAAACCTA
*
1375192 TTGCGAAATT-AAAATTCGTG
1 TTGCGAATTTGAAAA-TCGTG
* * *
1375212 TTGTGAATTCGAAAATCGAG
1 TTGCGAATTTGAAAATCGTG
*
1375232 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAAATC-GTG
*
1375253 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAAATC-GTG
* *
1375274 TTGCGAATTTGGAAATCGCG
1 TTGCGAATTTGAAAATCGTG
1375294 TTGCGAATTTGGAAAATCG
1 TTGCGAATTT-GAAAATCG
1375313 CAATGCGATT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
20 37 0.43
21 49 0.57
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCGTG
Found at i:1375312 original size:21 final size:21
Alignment explanation
Indices: 1375222--1375345 Score: 103
Period size: 21 Copynumber: 6.0 Consensus size: 21
1375212 TTGTGAATTC
*
1375222 GAAAATCGAGTTGCGAATTT-
1 GAAAATCGCGTTGCGAATTTG
* *
1375242 GAAATTCAGTGTTGCGAATTT-
1 GAAAATC-GCGTTGCGAATTTG
* *
1375263 GAAATTCAGTGTTGCGAATTTG
1 GAAAATC-GCGTTGCGAATTTG
1375285 G-AAATCGCGTTGCGAATTTG
1 GAAAATCGCGTTGCGAATTTG
** *
1375305 GAAAATCGCAATGCG-ATTTA
1 GAAAATCGCGTTGCGAATTTG
* * *
1375325 CATATTCGCGTTGCGAATTTG
1 GAAAATCGCGTTGCGAATTTG
1375346 TTGGTCATTT
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
20 34 0.39
21 52 0.60
22 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (21 bp):
GAAAATCGCGTTGCGAATTTG
Found at i:1378062 original size:3 final size:3
Alignment explanation
Indices: 1378054--1378085 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1378044 TTTTTCGTCA
1378054 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1378086 TTATTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:1378090 original size:3 final size:3
Alignment explanation
Indices: 1378084--1378205 Score: 208
Period size: 3 Copynumber: 40.7 Consensus size: 3
1378074 CTACTACTAC
1378084 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1378132 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
1378180 TAT TAT TGT TGT TGT TGT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1378206 AATTTCATTT
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 117 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1380563 original size:131 final size:131
Alignment explanation
Indices: 1380307--1380664 Score: 361
Period size: 131 Copynumber: 2.8 Consensus size: 131
1380297 TGAGAATAAT
* * * * *
1380307 AATATCTTTTCATTTCGGTCGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTC----ATTCT
1 AATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGTTATGAAAGGTCATTTATTCT
* * * * * * *
1380368 -TGATTGGAAATGATTTGATATTATCGTTTTCTCTCGAATTAATATTGATTTTTAAGGTGGAATA
66 CT-ATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGCTGAAATA
*
1380432 GT
130 GC
* * * * *
1380434 GATATCTCTTCATTTCGATTGGATTAATAAATGAATGCTTTAAGTTATGATAGATCATTTATTCT
1 AATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGTTATGAAAGGTCATTTATTCT
* * *
1380499 CTATTGGAAATCATTAGATATTATCGTTTTCACTTGAATCGATATTGAATTTTAAGACT-AAATA
66 CTATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAG-CTGAAATA
1380563 GC
130 GC
* * * * * * *
1380565 AATATCTCTTTATTTCTATTGGGGTATTAAATGATTGTTTTAA-TGCACGAAAGGTCATTTATTC
1 AATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGT-TATGAAAGGTCATTTATTC
* * *
1380629 TCGATCGGAAGTAATTAGATATTATCGTTTTCACTC
65 TCTATTGGAAATAATTAGATATTATCGTTTTCACTC
1380665 TTAAAATAAT
Statistics
Matches: 188, Mismatches: 36, Indels: 10
0.80 0.15 0.04
Matches are distributed among these distances:
127 47 0.25
130 1 0.01
131 138 0.73
132 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (131 bp):
AATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGTTATGAAAGGTCATTTATTCT
CTATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGCTGAAATAG
C
Found at i:1381572 original size:17 final size:17
Alignment explanation
Indices: 1381550--1381587 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1381540 TCCATAGGGT
1381550 CCTCATGATGGTTTTCA
1 CCTCATGATGGTTTTCA
1381567 CCTCATGATGGTTTTCA
1 CCTCATGATGGTTTTCA
1381584 CCTC
1 CCTC
1381588 CGTATAGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.16, C:0.29, G:0.16, T:0.39
Consensus pattern (17 bp):
CCTCATGATGGTTTTCA
Found at i:1392803 original size:21 final size:18
Alignment explanation
Indices: 1392778--1392825 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1392768 TAAAGGTGAG
1392778 AATAAATAAATTATCAAAAT
1 AATAAATAAATT-T-AAAAT
*
1392798 ATATAAA-ACATTTAAAAT
1 A-ATAAATAAATTTAAAAT
1392816 AATAAATAAA
1 AATAAATAAA
1392826 AAACTTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 5 0.21
18 8 0.33
19 1 0.04
20 5 0.21
21 5 0.21
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAATAAATTTAAAAT
Found at i:1401357 original size:24 final size:24
Alignment explanation
Indices: 1401330--1401436 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
1401320 AAACGGAGAT
*
1401330 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
1401354 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
1401378 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
1401402 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1401426 ATCAGAAATCA
1 ATCAGAAATCA
1401437 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1401436 original size:48 final size:48
Alignment explanation
Indices: 1401330--1401438 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
1401320 AAACGGAGAT
* * * *
1401330 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1401378 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1401426 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1401439 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1403949 original size:29 final size:28
Alignment explanation
Indices: 1403908--1404034 Score: 112
Period size: 29 Copynumber: 4.4 Consensus size: 28
1403898 AATTTTACAC
*
1403908 AAATATCACCCAAACAGAATTTAATTCCCA
1 AAATAGCA-CCAAACAGAA-TTAATTCCCA
*
1403938 AAATAGCACCAAAACCGAATTAATTCCCA
1 AAATAGCACC-AAACAGAATTAATTCCCA
* * * *
1403967 AAATAGCACCAAAATAAAATTATTTACCA
1 AAATAGCACC-AAACAGAATTAATTCCCA
* *
1403996 AAATAGCACCAAA-ATCGAATTATTTACCA
1 AAATAGCACCAAACA--GAATTAATTCCCA
*
1404025 AAATATCACC
1 AAATAGCACC
1404035 TGTTTCGAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
27 1 0.01
28 3 0.04
29 67 0.79
30 14 0.16
ACGTcount: A:0.50, C:0.24, G:0.05, T:0.22
Consensus pattern (28 bp):
AAATAGCACCAAACAGAATTAATTCCCA
Found at i:1404049 original size:29 final size:29
Alignment explanation
Indices: 1403935--1404034 Score: 146
Period size: 29 Copynumber: 3.4 Consensus size: 29
1403925 AATTTAATTC
* * *
1403935 CCAAAATAGCACCAAAACCGAATTAATTC
1 CCAAAATAGCACCAAAATCGAATTATTTA
**
1403964 CCAAAATAGCACCAAAATAAAATTATTTA
1 CCAAAATAGCACCAAAATCGAATTATTTA
1403993 CCAAAATAGCACCAAAATCGAATTATTTA
1 CCAAAATAGCACCAAAATCGAATTATTTA
*
1404022 CCAAAATATCACC
1 CCAAAATAGCACC
1404035 TGTTTCGAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.50, C:0.24, G:0.05, T:0.21
Consensus pattern (29 bp):
CCAAAATAGCACCAAAATCGAATTATTTA
Found at i:1404953 original size:18 final size:17
Alignment explanation
Indices: 1404929--1404974 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1404919 TTTTACTTAA
*
1404929 ATTATTATTTTTAAAATT
1 ATTATTATTATTAAAA-T
*
1404947 ATTATTATTATTATAAT
1 ATTATTATTATTAAAAT
1404964 ATATATTATTA
1 AT-TATTATTA
1404975 ATATTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTATTATTATTAAAAT
Found at i:1404993 original size:24 final size:25
Alignment explanation
Indices: 1404925--1404995 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 25
1404915 TTCCTTTTAC
**
1404925 TTAA-ATTATTATTTTTAAA-ATTA
1 TTAATATTATTATAATTAAATATTA
* *
1404948 TTATTATTATTATAA-TATATATTA
1 TTAATATTATTATAATTAAATATTA
1404972 TTAATATTATTA-AATTAAATATTA
1 TTAATATTATTATAATTAAATATTA
1404996 CAAAACCCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 8 0.21
24 31 0.79
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAATATTATTATAATTAAATATTA
Found at i:1406251 original size:25 final size:23
Alignment explanation
Indices: 1406215--1406280 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 23
1406205 TGCAAATTAA
*
1406215 TATTATTGCTTTTTAATTATTATTT
1 TATTATTACTTTTT-A-TATTATTT
*
1406240 TGTTATTAC-TTTTATATTATTT
1 TATTATTACTTTTTATATTATTT
*
1406262 TATTATTA-TTTTCATATTA
1 TATTATTACTTTTTATATTA
1406281 GTCACATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 24 0.67
23 1 0.03
24 4 0.11
25 7 0.19
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (23 bp):
TATTATTACTTTTTATATTATTT
Found at i:1406279 original size:11 final size:10
Alignment explanation
Indices: 1406232--1406280 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
1406222 GCTTTTTAAT
*
1406232 TATTATTTTGT
1 TATTATTTT-A
1406243 TATTACTTTTA
1 TATTA-TTTTA
1406254 TATTATTTTA
1 TATTATTTTA
1406264 TTATTATTTTCA
1 -TATTATTTT-A
1406276 TATTA
1 TATTA
1406281 GTCACATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 5 0.15
11 24 0.71
12 5 0.15
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (10 bp):
TATTATTTTA
Found at i:1410589 original size:14 final size:15
Alignment explanation
Indices: 1410566--1410598 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1410556 AAGAAGAAGG
*
1410566 AAAAAGAAAAA-AAA
1 AAAAACAAAAATAAA
1410580 AAAAACAAAAATAAA
1 AAAAACAAAAATAAA
1410595 AAAA
1 AAAA
1410599 GGGAGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.91, C:0.03, G:0.03, T:0.03
Consensus pattern (15 bp):
AAAAACAAAAATAAA
Found at i:1416239 original size:153 final size:152
Alignment explanation
Indices: 1416035--1416323 Score: 542
Period size: 153 Copynumber: 1.9 Consensus size: 152
1416025 CTATTTCCCA
*
1416035 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1416100 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTT
1416165 TGATGTTTTCAAAGCCTTAGAGT
130 TGATGTTTTCAAAGCCTTAGAGT
*
1416188 CATCTATAAGTCCTACATTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1416253 AGCCTTAGTGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1416318 GATGTT
131 GATGTT
1416324 GTTATTTTGA
Statistics
Matches: 133, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
152 28 0.21
153 105 0.79
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (152 bp):
CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGAGT
Found at i:1416266 original size:76 final size:76
Alignment explanation
Indices: 1416035--1416323 Score: 533
Period size: 76 Copynumber: 3.8 Consensus size: 76
1416025 CTATTTCCCA
1416035 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1416100 AGCCTTAGGGT
66 AGCCTTAGAGT
1416111 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1416176 AAGCCTTAGAGT
65 AAGCCTTAGAGT
* *
1416188 CATCTATAAGTCCTACATTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1416253 AGCCTTAGTGT
66 AGCCTTAGAGT
1416264 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
1416324 GTTATTTTGA
Statistics
Matches: 206, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
76 133 0.65
77 73 0.35
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGAGT
Found at i:1416547 original size:76 final size:76
Alignment explanation
Indices: 1416448--1416634 Score: 347
Period size: 76 Copynumber: 2.5 Consensus size: 76
1416438 TTATTTTCCA
1416448 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1416513 AGCCTTAGGGT
66 AGCCTTAGGGT
1416524 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1416589 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
1416600 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
1416635 CATTTCCATC
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 108 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1416772 original size:18 final size:17
Alignment explanation
Indices: 1416751--1416796 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1416741 TTTCACTTAA
*
1416751 ATTATTATTTTTAAAATT
1 ATTATTATTATTAAAA-T
*
1416769 ATTATTATTATTATAAT
1 ATTATTATTATTAAAAT
1416786 ATATATTATTA
1 AT-TATTATTA
1416797 ATATTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTATTATTATTAAAAT
Found at i:1416815 original size:24 final size:25
Alignment explanation
Indices: 1416747--1416817 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 25
1416737 TTCCTTTCAC
**
1416747 TTAA-ATTATTATTTTTAAA-ATTA
1 TTAATATTATTATAATTAAATATTA
* *
1416770 TTATTATTATTATAA-TATATATTA
1 TTAATATTATTATAATTAAATATTA
1416794 TTAATATTATTA-AATTAAATATTA
1 TTAATATTATTATAATTAAATATTA
1416818 CAAAACCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 8 0.21
24 31 0.79
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAATATTATTATAATTAAATATTA
Found at i:1418085 original size:22 final size:22
Alignment explanation
Indices: 1418057--1418105 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1418047 TATTTTTAAT
*
1418057 TATTATTTTGTTATTACTTTT-A
1 TATTATTTTATTATTA-TTTTCA
1418079 TATTATTTTATTATTATTTTCA
1 TATTATTTTATTATTATTTTCA
1418101 TATTA
1 TATTA
1418106 GTCACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTTTATTATTATTTTCA
Found at i:1418104 original size:11 final size:10
Alignment explanation
Indices: 1418057--1418105 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
1418047 TATTTTTAAT
*
1418057 TATTATTTTGT
1 TATTATTTT-A
1418068 TATTACTTTTA
1 TATTA-TTTTA
1418079 TATTATTTTA
1 TATTATTTTA
1418089 TTATTATTTTCA
1 -TATTATTTT-A
1418101 TATTA
1 TATTA
1418106 GTCACATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 5 0.15
11 24 0.71
12 5 0.15
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (10 bp):
TATTATTTTA
Found at i:1418495 original size:2 final size:2
Alignment explanation
Indices: 1418488--1418519 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1418478 TGTTATTTAA
1418488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1418520 TCTTTAAATT
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):
AT
Found at i:1419202 original size:2 final size:2
Alignment explanation
Indices: 1419190--1419228 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1419180 TGCGATGGTC
*
1419190 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1419229 AGATTCTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1422513 original size:26 final size:27
Alignment explanation
Indices: 1422478--1422533 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
1422468 GCTAGTTTTG
**
1422478 TTTTTATAATTTTTAAAAGTTTTAATA
1 TTTTTATAATTTTTAAAAAATTTAATA
1422505 TTTTT-TAATTTTTAAAAAATTTAATA
1 TTTTTATAATTTTTAAAAAATTTAATA
1422531 TTT
1 TTT
1422534 AATATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTTATAATTTTTAAAAAATTTAATA
Found at i:1422540 original size:33 final size:34
Alignment explanation
Indices: 1422498--1422567 Score: 133
Period size: 33 Copynumber: 2.1 Consensus size: 34
1422488 TTTTAAAAGT
1422498 TTTAATATTTTTTAATTTTTAAAA-AATTTAATA
1 TTTAATATTTTTTAATTTTTAAAATAATTTAATA
1422531 TTTAATATTTTTTAATTTTTAAAATAATTTAATA
1 TTTAATATTTTTTAATTTTTAAAATAATTTAATA
1422565 TTT
1 TTT
1422568 TATTTATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 24 0.67
34 12 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TTTAATATTTTTTAATTTTTAAAATAATTTAATA
Found at i:1422542 original size:26 final size:26
Alignment explanation
Indices: 1422483--1422545 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
1422473 TTTTGTTTTT
** *
1422483 ATAATTTTTAAAAGTTTTAATATTTT
1 ATAATTTTTAAAAAATTTAATATTTA
*
1422509 TTAATTTTTAAAAAATTTAATATTTA
1 ATAATTTTTAAAAAATTTAATATTTA
*
1422535 ATATTTTTTAA
1 ATAATTTTTAA
1422546 TTTTTAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
ATAATTTTTAAAAAATTTAATATTTA
Found at i:1422561 original size:17 final size:17
Alignment explanation
Indices: 1422508--1422569 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
1422498 TTTAATATTT
1422508 TTTAATTTTTAAAA-AA
1 TTTAATTTTTAAAATAA
* * **
1422524 TTTAATATTTAATATTT
1 TTTAATTTTTAAAATAA
1422541 TTTAATTTTTAAAATAA
1 TTTAATTTTTAAAATAA
1422558 TTTAATATTTTA
1 TTTAAT-TTTTA
1422570 TTTATTTCAG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
16 12 0.33
17 19 0.53
18 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATTTTTAAAATAA
Found at i:1423231 original size:24 final size:22
Alignment explanation
Indices: 1423204--1423247 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
1423194 GACAAAAATT
1423204 AAATAATTAAAACAAAAATAAAAG
1 AAATAA-TAAAA-AAAAATAAAAG
*
1423228 AAATAATAAAAATAAATAAA
1 AAATAATAAAAAAAAATAAA
1423248 TAAATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (22 bp):
AAATAATAAAAAAAAATAAAAG
Found at i:1424565 original size:37 final size:38
Alignment explanation
Indices: 1424508--1424866 Score: 325
Period size: 37 Copynumber: 9.4 Consensus size: 38
1424498 ATTTTATATA
* *
1424508 ATATATATTTTCGAAAT-GTTT-AAAAATTATATATTAT
1 ATATATATTTTC-AAATATTTTCAAAAACTATATATTAT
*
1424545 ATATATATTTTCAAATTGTTTTCAAAAACTATATA-T-T
1 ATATATATTTTCAAA-TATTTTCAAAAACTATATATTAT
1424582 ATATATATTTTCAAAATATTTTCAAAAAC--TATATTAT
1 ATATATATTTTC-AAATATTTTCAAAAACTATATATTAT
1424619 ATATATATTTTTCAATATATTTTCAAAAACTATATATTAT
1 ATATATA-TTTTCAA-ATATTTTCAAAAACTATATATTAT
**
1424659 ATATATGCTTTCAAA-ACGTTTTCAAAAACTATATATTAT
1 ATATATATTTTCAAATA--TTTTCAAAAACTATATATTAT
* *
1424698 ATAT-TTTTTTCAAAATATTTTCGAAAACTATATATTAT
1 ATATATATTTTC-AAATATTTTCAAAAACTATATATTAT
**
1424736 ATATAT-TTTAAAAATATTTTCAAAAACTATATATATAT
1 ATATATATTTTCAAATATTTTCAAAAACTATATAT-TAT
* * * *
1424774 ATATATATATAT-ATATATTTTC-AAAA-TGT-T-TTCAA
1 ATATATAT-TTTCAAATATTTTCAAAAACTATATATT-AT
* * *
1424809 AAACTATATATTCAAAATGTTTTCAAAAACTATATATTTAT
1 ATA-TATATTTTC-AAATATTTTCAAAAACTATATA-TTAT
*
1424850 ATGTATATTATT-AAATA
1 ATATATATT-TTCAAATA
1424867 ACACCCCGGG
Statistics
Matches: 267, Mismatches: 27, Indels: 54
0.77 0.08 0.16
Matches are distributed among these distances:
34 1 0.00
35 9 0.03
36 10 0.04
37 81 0.30
38 76 0.28
39 62 0.23
40 22 0.08
41 4 0.01
42 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (38 bp):
ATATATATTTTCAAATATTTTCAAAAACTATATATTAT
Found at i:1424640 original size:38 final size:37
Alignment explanation
Indices: 1424502--1424777 Score: 330
Period size: 38 Copynumber: 7.4 Consensus size: 37
1424492 ATAAATATTT
* * *
1424502 TATATA-ATATATA-TTTTCGAAAT-GTTT-AAAAAT
1 TATATATATATATATTTTTCAAAATATTTTCAAAAAC
* *
1424535 TATATATTATATATATATTTTCAAATTGTTTTCAAAAAC
1 TATATA-TATATATAT-TTTTCAAAATATTTTCAAAAAC
1424574 TATATAT-TATATATATTTTCAAAATATTTTCAAAAAC
1 TATATATATATATAT-TTTTCAAAATATTTTCAAAAAC
*
1424611 TATATTATATATATATTTTTCAATATATTTTCAAAAAC
1 TATA-TATATATATATTTTTCAAAATATTTTCAAAAAC
* **
1424649 TATATATTATATATATGCTTTCAAAACGTTTTCAAAAAC
1 TATATA-TATATATAT-TTTTCAAAATATTTTCAAAAAC
* *
1424688 TATATATTATATATTTTTTTCAAAATATTTTCGAAAAC
1 TATATA-TATATATATTTTTCAAAATATTTTCAAAAAC
*
1424726 TATATAT-TATATATATTTTAAAAATATTTTCAAAAAC
1 TATATATATATATAT-TTTTCAAAATATTTTCAAAAAC
1424763 TATATATATATATAT
1 TATATATATATATAT
1424778 ATATATATAT
Statistics
Matches: 212, Mismatches: 19, Indels: 19
0.85 0.08 0.08
Matches are distributed among these distances:
33 6 0.03
35 7 0.03
36 6 0.03
37 70 0.33
38 72 0.34
39 51 0.24
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.47
Consensus pattern (37 bp):
TATATATATATATATTTTTCAAAATATTTTCAAAAAC
Found at i:1424766 original size:26 final size:26
Alignment explanation
Indices: 1424737--1424848 Score: 86
Period size: 26 Copynumber: 4.3 Consensus size: 26
1424727 ATATATTATA
1424737 TATATTTTAAAAATATTTTCAAAAAC
1 TATATTTTAAAAATATTTTCAAAAAC
* * * * * *
1424763 TATA-TATATATATATATAT-ATATA-
1 TATATTTTAAAAATAT-TTTCAAAAAC
* *
1424787 TATATTTTCAAAATGTTTTCAAAAAC
1 TATATTTTAAAAATATTTTCAAAAAC
* * *
1424813 TATATATTCAAAATGTTTTCAAAAAC
1 TATATTTTAAAAATATTTTCAAAAAC
1424839 TATATATTTA
1 TATAT-TTTA
1424849 TATGTATATT
Statistics
Matches: 64, Mismatches: 17, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
24 6 0.09
25 20 0.31
26 36 0.56
27 2 0.03
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (26 bp):
TATATTTTAAAAATATTTTCAAAAAC
Found at i:1424770 original size:2 final size:2
Alignment explanation
Indices: 1424763--1424791 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1424753 TTTCAAAAAC
1424763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1424792 TTTCAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1424795 original size:114 final size:111
Alignment explanation
Indices: 1424502--1424851 Score: 363
Period size: 114 Copynumber: 3.1 Consensus size: 111
1424492 ATAAATATTT
* * * * *
1424502 TATATAATATATATTTTCGAAAT-GTTT-AAAAATTATATATTATATATATATTTTCAAATTGTT
1 TATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATATATTAT-AAA-TGTT
1424565 TTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTA
64 TTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTA
* * *
1424613 TAT-TATATATATATTTTTCAATATATTTTCAAAAACTATATATTATATATATGCTT-TCAAAAC
1 TATAT-TATATATA-TTTTCAAAATATTTTCAAAAACTATATATTATATATAT-ATTAT--AAAT
* *
1424676 GTTTTCAAAAACTATATATTATATATTTTTTTCAAAATATTTTCGAAAACTA
61 GTTTTCAAAAACTATATATTATATA-TATTTTCAAAATATTTTCAAAAACTA
* * *
1424728 TATATTATATATATTTTAAAAATATTTTCAAAAACTATATATATATATATATATATATATATATT
1 TATATTATATATATTTTCAAAATATTTTCAAAAACTATATAT-TATATATATAT-TATAAATGTT
** * * * * *
1424793 TTCAAAATGT-TTTCA-AAAACTATATATTCAAAATGTTTTCAAAAACTA
64 TTCAAAAACTATAT-ATTATA-TATATTTTCAAAATATTTTCAAAAACTA
1424841 TATATT-TATAT
1 TATATTATATAT
1424852 GTATATTATT
Statistics
Matches: 201, Mismatches: 25, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
110 1 0.00
111 10 0.05
112 13 0.06
113 35 0.17
114 90 0.45
115 50 0.25
116 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (111 bp):
TATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATATATTATAAATGTTTT
CAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTA
Found at i:1424844 original size:28 final size:28
Alignment explanation
Indices: 1424785--1424845 Score: 99
Period size: 26 Copynumber: 2.2 Consensus size: 28
1424775 TATATATATA
*
1424785 TATATATTTTCAAAATGTTTTCAAAAAC
1 TATATATATTCAAAATGTTTTCAAAAAC
1424813 --TATATATTCAAAATGTTTTCAAAAAC
1 TATATATATTCAAAATGTTTTCAAAAAC
1424839 TATATAT
1 TATATAT
1424846 TTATATGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 25 0.83
28 5 0.17
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (28 bp):
TATATATATTCAAAATGTTTTCAAAAAC
Found at i:1429675 original size:15 final size:16
Alignment explanation
Indices: 1429648--1429677 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1429638 TAAAACAAAA
1429648 ATAATAGAAATTAAAG
1 ATAATAGAAATTAAAG
1429664 ATAATA-AAATTAAA
1 ATAATAGAAATTAAA
1429678 TAAATAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (16 bp):
ATAATAGAAATTAAAG
Found at i:1429790 original size:30 final size:30
Alignment explanation
Indices: 1429754--1429815 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
1429744 ACATGAATTG
1429754 AATAAAGAAAATGACCAAATTAAAAGAAGA
1 AATAAAGAAAATGACCAAATTAAAAGAAGA
*** * *
1429784 AATAAAGTGTATGACTAATTTAAAAGAAGA
1 AATAAAGAAAATGACCAAATTAAAAGAAGA
1429814 AA
1 AA
1429816 ACGAAATCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.61, C:0.05, G:0.15, T:0.19
Consensus pattern (30 bp):
AATAAAGAAAATGACCAAATTAAAAGAAGA
Found at i:1430943 original size:37 final size:37
Alignment explanation
Indices: 1430856--1430979 Score: 178
Period size: 37 Copynumber: 3.3 Consensus size: 37
1430846 ATTTTATTTA
** *
1430856 ATATATATTTTCGAAATG-TTTCAAAAATTATATAGTAT
1 ATATATATTTTTAAAATGTTTTCAAAAACTATATA-T-T
**
1430894 ATATATATTTTTAAAATGTTTTTGAAAACTATATATT
1 ATATATATTTTTAAAATGTTTTCAAAAACTATATATT
1430931 ATATATATTTTTAAAATGTTTTCAAAAACTATATATT
1 ATATATATTTTTAAAATGTTTTCAAAAACTATATATT
1430968 ATATATATTTTT
1 ATATATATTTTT
1430980 TTCAAAAACT
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
37 48 0.62
38 17 0.22
39 13 0.17
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (37 bp):
ATATATATTTTTAAAATGTTTTCAAAAACTATATATT
Found at i:1430964 original size:30 final size:28
Alignment explanation
Indices: 1430932--1431022 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
1430922 CTATATATTA
1430932 TATATATTTT-TAAAATGTTTTCAAAAAC
1 TATATATTTTATAAAAT-TTTTCAAAAAC
* **
1430960 TATATATTATATATATTTTTTTCAAAAAC
1 TATATATTTTATA-AAATTTTTCAAAAAC
1430989 TATATATTATTATATAAA-TTTTCAAAAAC
1 TATATATT-TTATA-AAATTTTTCAAAAAC
1431018 TATAT
1 TATAT
1431023 TATATATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
28 9 0.17
29 37 0.69
30 8 0.15
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (28 bp):
TATATATTTTATAAAATTTTTCAAAAAC
Found at i:1430991 original size:29 final size:29
Alignment explanation
Indices: 1430949--1431036 Score: 126
Period size: 29 Copynumber: 3.0 Consensus size: 29
1430939 TTTTAAAATG
1430949 TTTTCAAAAACTATATATTATATATATTT
1 TTTTCAAAAACTATATATTATATATATTT
**
1430978 TTTTCAAAAACTATATATTAT-TATATAAA
1 TTTTCAAAAACTATATATTATATATAT-TT
1431007 TTTTCAAAAACTATAT-TATATATATATTT
1 TTTTCAAAAACTATATAT-TATATATATTT
1431036 T
1 T
1431037 CGTCCGTGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
28 6 0.12
29 41 0.79
30 5 0.10
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (29 bp):
TTTTCAAAAACTATATATTATATATATTT
Found at i:1437997 original size:29 final size:29
Alignment explanation
Indices: 1437976--1438159 Score: 142
Period size: 29 Copynumber: 6.4 Consensus size: 29
1437966 TTAATTTAAA
1437976 TTATAAAAGTTTTGAGCCATTATTGTAAT
1 TTATAAAAGTTTTGAGCCATTATTGTAAT
** * *
1438005 TTGCAAAAGTTTT-ATGTCATTGTTGTAAT
1 TTATAAAAGTTTTGA-GCCATTATTGTAAT
* * * *
1438034 TTAGAAAACTTTT-ATGCCATTATTTTATT
1 TTATAAAAGTTTTGA-GCCATTATTGTAAT
* * *
1438063 TTGTAAAAGTCTTTG-GCAATTATTGAAAT
1 TTATAAAAGT-TTTGAGCCATTATTGTAAT
* * *
1438092 TTATAAAAGTTTTGGGCAATTATTATAAT
1 TTATAAAAGTTTTGAGCCATTATTGTAAT
* ** * *
1438121 TTATAAAATTTTTG-GTAATTACTATAAT
1 TTATAAAAGTTTTGAGCCATTATTGTAAT
1438149 TTATAAAAGTT
1 TTATAAAAGTT
1438160 ATGGGTAACT
Statistics
Matches: 126, Mismatches: 25, Indels: 9
0.79 0.16 0.06
Matches are distributed among these distances:
28 27 0.21
29 96 0.76
30 3 0.02
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (29 bp):
TTATAAAAGTTTTGAGCCATTATTGTAAT
Found at i:1438128 original size:58 final size:58
Alignment explanation
Indices: 1437943--1438164 Score: 184
Period size: 58 Copynumber: 3.8 Consensus size: 58
1437933 GTTTTTCTTG
* * * * *
1437943 TAATTTGTAAAA-TATTTGGGATATTAATTTAAA-TTATAAAAGTTTTGAGCCATTATTG
1 TAATTTGTAAAAGTTTTTGGCA-ATT-ATTGAAATTTATAAAAGTTTTGGGCCATTATTA
* * * * * * ** *
1438001 TAATTTGCAAAAGTTTTATGTC-ATTGTTGTAATTTAGAAAACTTTTATGCCATTATTT
1 TAATTTGTAAAAGTTTT-TGGCAATTATTGAAATTTATAAAAGTTTTGGGCCATTATTA
* * *
1438059 TATTTTGTAAAAGTCTTTGGCAATTATTGAAATTTATAAAAGTTTTGGGCAATTATTA
1 TAATTTGTAAAAGTTTTTGGCAATTATTGAAATTTATAAAAGTTTTGGGCCATTATTA
* * * *
1438117 TAATTTATAAAA-TTTTTGGTAATTACT-ATAATTTATAAAAGTTATGGG
1 TAATTTGTAAAAGTTTTTGGCAATTATTGA-AATTTATAAAAGTTTTGGG
1438165 TAACTACTGT
Statistics
Matches: 129, Mismatches: 30, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
56 1 0.01
57 37 0.29
58 86 0.67
59 3 0.02
60 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.46
Consensus pattern (58 bp):
TAATTTGTAAAAGTTTTTGGCAATTATTGAAATTTATAAAAGTTTTGGGCCATTATTA
Found at i:1438132 original size:28 final size:29
Alignment explanation
Indices: 1437943--1438164 Score: 134
Period size: 29 Copynumber: 7.7 Consensus size: 29
1437933 GTTTTTCTTG
*
1437943 TAATTTGTAAAA-TATTTGGG-ATATTAATT-
1 TAATTTATAAAAGT-TTTGGGCA-ATT-ATTA
* * * *
1437972 TAAATTATAAAAGTTTTGAGCCATTATTG
1 TAATTTATAAAAGTTTTGGGCAATTATTA
** * * * *
1438001 TAATTTGCAAAAGTTTTATGTC-ATTGTTG
1 TAATTTATAAAAGTTTT-GGGCAATTATTA
* * ** * *
1438030 TAATTTAGAAAACTTTTATGCCATTATTT
1 TAATTTATAAAAGTTTTGGGCAATTATTA
* *
1438059 TATTTTGTAAAAGTCTTT-GGCAATTATTGA
1 TAATTTATAAAAGT-TTTGGGCAATTATT-A
1438089 -AATTTATAAAAGTTTTGGGCAATTATTA
1 TAATTTATAAAAGTTTTGGGCAATTATTA
* * *
1438117 TAATTTATAAAA-TTTTTGGTAATTACTA
1 TAATTTATAAAAGTTTTGGGCAATTATTA
*
1438145 TAATTTATAAAAGTTATGGG
1 TAATTTATAAAAGTTTTGGG
1438165 TAACTACTGT
Statistics
Matches: 150, Mismatches: 33, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
28 33 0.22
29 112 0.75
30 5 0.03
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.46
Consensus pattern (29 bp):
TAATTTATAAAAGTTTTGGGCAATTATTA
Found at i:1438177 original size:29 final size:29
Alignment explanation
Indices: 1438089--1438187 Score: 119
Period size: 29 Copynumber: 3.4 Consensus size: 29
1438079 CAATTATTGA
* *
1438089 AATTTATAAAAGTTTTGGGCAATTATTAT
1 AATTTATAAAAGTTTTGGGTAATTACTAT
*
1438118 AATTTATAAAA-TTTTTGGTAATTACTAT
1 AATTTATAAAAGTTTTGGGTAATTACTAT
* * *
1438146 AATTTATAAAAGTTATGGGTAACTACTGT
1 AATTTATAAAAGTTTTGGGTAATTACTAT
1438175 AATTCATATAAAA
1 AATT--TATAAAA
1438188 TCTATCTCAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
28 25 0.42
29 28 0.47
31 7 0.12
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.42
Consensus pattern (29 bp):
AATTTATAAAAGTTTTGGGTAATTACTAT
Found at i:1438415 original size:20 final size:20
Alignment explanation
Indices: 1438392--1438444 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
1438382 GGTGACATTA
*
1438392 TATATTAATGTCACTAAATG
1 TATATAAATGTCACTAAATG
*
1438412 TATATAAATGTCGCTAAATG
1 TATATAAATGTCACTAAATG
1438432 TATGATAATATGT
1 TAT-ATAA-ATGT
1438445 GACAAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 21 0.72
21 4 0.14
22 4 0.14
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (20 bp):
TATATAAATGTCACTAAATG
Found at i:1442602 original size:16 final size:16
Alignment explanation
Indices: 1442581--1442641 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
1442571 AGTTTTGAGA
1442581 AACTGAAGACTATTCT
1 AACTGAAGACTATTCT
* *
1442597 AACTGAAGTCTAGTTTT
1 AACTGAAGACTA-TTCT
1442614 GAGAAACTGAAGACTATTCT
1 ----AACTGAAGACTATTCT
1442634 AACTGAAG
1 AACTGAAG
1442642 TCCCAATGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
16 19 0.53
17 3 0.08
20 3 0.08
21 11 0.31
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (16 bp):
AACTGAAGACTATTCT
Found at i:1442618 original size:37 final size:37
Alignment explanation
Indices: 1442568--1442643 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
1442558 AGCTAAACAA
1442568 TCTAGTTTTGAGAAACTGAAGACTATTCTAACTGAAG
1 TCTAGTTTTGAGAAACTGAAGACTATTCTAACTGAAG
1442605 TCTAGTTTTGAGAAACTGAAGACTATTCTAACTGAAG
1 TCTAGTTTTGAGAAACTGAAGACTATTCTAACTGAAG
1442642 TC
1 TC
1442644 CCAATGTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (37 bp):
TCTAGTTTTGAGAAACTGAAGACTATTCTAACTGAAG
Found at i:1442623 original size:21 final size:21
Alignment explanation
Indices: 1442568--1442625 Score: 63
Period size: 16 Copynumber: 3.0 Consensus size: 21
1442558 AGCTAAACAA
1442568 TCTAGTTTTGAGAAACTGAAG
1 TCTAGTTTTGAGAAACTGAAG
* *
1442589 ACTA-TTCT----AACTGAAG
1 TCTAGTTTTGAGAAACTGAAG
1442605 TCTAGTTTTGAGAAACTGAAG
1 TCTAGTTTTGAGAAACTGAAG
1442626 ACTATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
20 3 0.11
21 11 0.39
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (21 bp):
TCTAGTTTTGAGAAACTGAAG
Found at i:1445950 original size:29 final size:29
Alignment explanation
Indices: 1445887--1445949 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 29
1445877 AAATGATCTC
*
1445887 TATTTTCACCCAAACAAATGTATAATTAT
1 TATTTTCACCCAAACAAATGCATAATTAT
*
1445916 TATTTTCA-CCAAACAAGTGCATAATTAT
1 TATTTTCACCCAAACAAATGCATAATTAT
1445944 TATTTT
1 TATTTT
1445950 TAGCTCAGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 24 0.75
29 8 0.25
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (29 bp):
TATTTTCACCCAAACAAATGCATAATTAT
Found at i:1459297 original size:64 final size:63
Alignment explanation
Indices: 1459090--1459299 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
1459080 TTTTTCAGAG
* * **
1459090 TGATGCACCGATGCACCAATTCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCACCAA--CATGCATCGATGCACTC-TGGA-TATTTTGAAACATCGAATGCA
1459153 TT
62 TT
* * * **
1459155 TCATGTATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-A-CATGCATCGATGCACTCTGGATATTT-TG-AAACATCGAATGCA
1459218 TT
62 TT
*
1459220 TGATGCATCGATGCACCAACAATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAAC-ATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
1459284 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1459300 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 50 0.41
65 62 0.51
66 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACCAACATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
Found at i:1459299 original size:17 final size:19
Alignment explanation
Indices: 1459271--1459319 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1459261 TATTTTGAAA
1459271 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1459289 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1459308 CACCGATGCACT
1 CATCGATGCACT
1459320 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1459315 original size:64 final size:63
Alignment explanation
Indices: 1459140--1459319 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 63
1459130 AATTAAATTG
* * *
1459140 AACATCGAATGCATTTCATGTATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCAC-T-CCATGCACCGATGCACTCAGGATTTTATGAA
* *
1459205 AACATCGAATGCATTTGATGCATCGATGCAC-CAACAATGCATCGATGCACTCTGGATATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACTC--C-ATGCACCGATGCACTCAGGAT-TTTATG
1459268 -A
62 AA
* *
1459269 AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTC-CA-TGCACCGATGCACT
1459320 AAGGGTCCAA
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 45 0.45
65 50 0.50
66 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCCATGCACCGATGCACTCAGGATTTTATGAA
Found at i:1466745 original size:21 final size:21
Alignment explanation
Indices: 1466703--1466746 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1466693 ACTCCGGGAG
* *
1466703 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
1466724 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
1466745 CT
1 CT
1466747 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:1467812 original size:20 final size:20
Alignment explanation
Indices: 1467787--1467842 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1467777 TTTCAGAGTG
1467787 ATGCACCGATGCACCAATTC
1 ATGCACCGATGCACCAATTC
1467807 ATGCACCGATGCACCAATTC
1 ATGCACCGATGCACCAATTC
*
1467827 ATGCATCGATGCACCA
1 ATGCACCGATGCACCA
1467843 TGAATTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.20
Consensus pattern (20 bp):
ATGCACCGATGCACCAATTC
Found at i:1467882 original size:65 final size:65
Alignment explanation
Indices: 1467804--1467952 Score: 155
Period size: 65 Copynumber: 2.3 Consensus size: 65
1467794 GATGCACCAA
* * * *
1467804 TTCATGCACCGATGCACCAAT-TCATGCATCGATGCACCATGA-ATTAAATTG-AACATCGAATG
1 TTCATGCATCGATGCACCAATACCATGCACCGATGCA-C-TGAGATTAAA-TGAAACATAGAATG
1467866 CAT
63 CAT
**
1467869 TTCATGCATCGATGCA-C-ATACCATGCACCGATGCACTGAGGATTTTATGAAAACATAGAATGC
1 TTCATGCATCGATGCACCAATACCATGCACCGATGCACTGA-GATTAAATG-AAACATAGAATGC
1467932 AT
64 AT
*
1467934 TTGATGCATCGATGCACCA
1 TTCATGCATCGATGCACCA
1467953 GCAATGCATA
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
62 3 0.04
63 5 0.07
64 18 0.26
65 43 0.61
66 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (65 bp):
TTCATGCATCGATGCACCAATACCATGCACCGATGCACTGAGATTAAATGAAACATAGAATGCAT
Found at i:1467960 original size:65 final size:65
Alignment explanation
Indices: 1467855--1468014 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
1467845 AATTAAATTG
* * * *
1467855 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACAATGCACAGATGCACTCAGGATATTT-TG
1467918 AA
65 -A
* * * * *
1467920 AACATAGAATGCATTTGATGCATCGATGCACCA-GCAATGCATAGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACAATGCACAGATGCACTCAGGATATTTTGA
*
1467984 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1468015 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 30 0.37
65 47 0.57
66 5 0.06
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACAATGCACAGATGCACTCAGGATATTTTGA
Found at i:1477554 original size:10 final size:10
Alignment explanation
Indices: 1477539--1477569 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1477529 TCACATATTT
1477539 GGCCCAAATG
1 GGCCCAAATG
1477549 GGCCCAAATG
1 GGCCCAAATG
*
1477559 GACCCAAATG
1 GGCCCAAATG
1477569 G
1 G
1477570 TTACAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.29, G:0.29, T:0.10
Consensus pattern (10 bp):
GGCCCAAATG
Found at i:1480516 original size:82 final size:82
Alignment explanation
Indices: 1480313--1481134 Score: 1045
Period size: 82 Copynumber: 10.1 Consensus size: 82
1480303 AATCATTTAG
* ** *
1480313 TCTTTTACCCAAAGGTATTTAGTCTTTCATCTAACTTG-CATAATTGACACCTTTCTGCCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAAC-TGACATAATTGACACCTTTCTGTCAAATG
*
1480377 CACAGCTAGG-CGTTAAA
65 CACAGCTAGGCCATTAAA
* * * * * * *
1480394 TCTTTAACTAAAAGGCATTTAGGCATTT-ATCTAACTGACATGATTGACACCTTTCTGTAAAATG
1 TCTTTTACTCAAAGGTATTTA-ACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATG
1480458 CACAGCTAGGCCATTAAA
65 CACAGCTAGGCCATTAAA
* * *
1480476 TCTTTTACTCAAAGGTATTTAACCTTTCACCTAACTGACATAATTGACACCTTTTTGTCAAATGT
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
* *
1480541 ATAACTAGGCCATT-AA
66 ACAGCTAGGCCATTAAA
* * *
1480557 TCTTTTACCCAAAGGCATTTAACCTTTCATCTGAA-TGGCATAATTGACACCTTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCT-AACTGACATAATTGACACCTTTCTGTCAAATG
* *
1480621 CACAACTAGGTCATTAAA
65 CACAGCTAGGCCATTAAA
* * * * * * * *
1480639 TATTTAACTCAAAGGCATTTAGCCTTTCATCTAATTGGCATAATTAACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
1480704 ACAGCTAGGCCATT-AA
66 ACAGCTAGGCCATTAAA
* * *
1480720 TCTTTTACTCAAAGGTATTTAACCTTTCGTCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
*
1480785 GCAGCTAGGCCATTAAA
66 ACAGCTAGGCCATTAAA
*
1480802 TCTTTTACTCAAAGGAATTTAACCTTTCATCTAACTGGA-ATAATTGACACCTTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GACATAATTGACACCTTTCTGTCAAATG
1480866 CACAGCTAGGCCATTAAA
65 CACAGCTAGGCCATTAAA
* * * * * * *
1480884 TCTTTTAGTCAAAGGTATATAACCTTTCATCTAACT-AGCGTAATTGACACTTTTTTATCAAATT
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGA-CATAATTGACACCTTTCTGTCAAATG
*
1480948 CACAGCTTGGCCATTAAA
65 CACAGCTAGGCCATTAAA
* * ** *
1480966 TCTTTTACTCAAAGGTATTTAGCATTTCATCTAACT-AGCATAATAAACA-CTTTCTGTCAAATA
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGA-CATAATTGACACCTTTCTGTCAAATG
*
1481029 CACAGCTAGGCCACT-AA
65 CACAGCTAGGCCATTAAA
* * *
1481046 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGATAACTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
1481111 ACAGCTAGGCCATTAAA
66 ACAGCTAGGCCATTAAA
1481128 TCTTTTA
1 TCTTTTA
1481135 TTTTAGAACA
Statistics
Matches: 646, Mismatches: 81, Indels: 27
0.86 0.11 0.04
Matches are distributed among these distances:
80 47 0.07
81 256 0.40
82 342 0.53
83 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (82 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCCATTAAA
Found at i:1480520 original size:163 final size:163
Alignment explanation
Indices: 1480313--1481134 Score: 1082
Period size: 163 Copynumber: 5.0 Consensus size: 163
1480303 AATCATTTAG
* * *
1480313 TCTTTTACCCAAAGGTATTTAGTCTTTCATCTAACTTG-CATAATTGACACCTTTCTGCCAAATG
1 TCTTTTACTCAAAGGTATTTAGCCTTTCATCTAAC-TGACATAATTGACACCTTTCTGTCAAATG
* * * * * * * *
1480377 CACAGCTAGG-CGTTAAATCTTTAACTAAAAGGCATTTAGGCATTT-ATCTAACTGACATGATTG
65 CACAGCTAGGCCATT-AATCTTTTACTCAAAGGTATTTA-ACCTTTCATCTAACTGGCATAATTG
*
1480440 ACACCTTTCTGTAAAATGCACAGCTAGGCCATTAAA
128 ACACCTTTCTGTCAAATGCACAGCTAGGCCATTAAA
* * * *
1480476 TCTTTTACTCAAAGGTATTTAACCTTTCACCTAACTGACATAATTGACACCTTTTTGTCAAATGT
1 TCTTTTACTCAAAGGTATTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
* * * *
1480541 ATAACTAGGCCATTAATCTTTTACCCAAAGGCATTTAACCTTTCATCTGAA-TGGCATAATTGAC
66 ACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCT-AACTGGCATAATTGAC
* *
1480605 ACCTTTCTGTCAAATGCACAACTAGGTCATTAAA
130 ACCTTTCTGTCAAATGCACAGCTAGGCCATTAAA
* * * * * * *
1480639 TATTTAACTCAAAGGCATTTAGCCTTTCATCTAATTGGCATAATTAACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
*
1480704 ACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCGTCTAACTGGCATAATTGACA
66 ACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA
* *
1480769 CATTTCTGTCAAATGCGCAGCTAGGCCATTAAA
131 CCTTTCTGTCAAATGCACAGCTAGGCCATTAAA
* *
1480802 TCTTTTACTCAAAGGAATTTAACCTTTCATCTAACTGGA-ATAATTGACACCTTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAGCCTTTCATCTAACT-GACATAATTGACACCTTTCTGTCAAATG
* * * *
1480866 CACAGCTAGGCCATTAAATCTTTTAGTCAAAGGTATATAACCTTTCATCTAACTAGCGTAATTGA
65 CACAGCTAGGCCATT-AATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGA
* * * * *
1480931 CACTTTTTTATCAAATTCACAGCTTGGCCATTAAA
129 CACCTTTCTGTCAAATGCACAGCTAGGCCATTAAA
* ** *
1480966 TCTTTTACTCAAAGGTATTTAGCATTTCATCTAACT-AGCATAATAAACA-CTTTCTGTCAAATA
1 TCTTTTACTCAAAGGTATTTAGCCTTTCATCTAACTGA-CATAATTGACACCTTTCTGTCAAATG
* *
1481029 CACAGCTAGGCCACTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAT
65 CACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAC
*
1481094 AACTTTCTGTCAAATGCACAGCTAGGCCATTAAA
130 ACCTTTCTGTCAAATGCACAGCTAGGCCATTAAA
1481128 TCTTTTA
1 TCTTTTA
1481135 TTTTAGAACA
Statistics
Matches: 573, Mismatches: 77, Indels: 19
0.86 0.12 0.03
Matches are distributed among these distances:
162 89 0.16
163 364 0.64
164 120 0.21
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (163 bp):
TCTTTTACTCAAAGGTATTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA
CCTTTCTGTCAAATGCACAGCTAGGCCATTAAA
Found at i:1481307 original size:55 final size:55
Alignment explanation
Indices: 1481241--1481605 Score: 536
Period size: 55 Copynumber: 6.7 Consensus size: 55
1481231 AGTAATCCAC
* * * * *
1481241 AACTTACTATGAATTTCTTAGTTTTGTACACACACTGCCTATATGGAAATTCATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATA
* * * * *
1481296 AACTTATTATGATTTTCTAACTTTTGCACACACAATGCCCATACAGAAATTCATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATA
* * * *
1481351 AACTTATTATGAATTTCATAATTTTGCACACATAGTGCCCATACTGAAATTCATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATA
1481406 AACTTATTATGAATTTCTTAGTTTT-CACACACAGTGCCCATACGGAAATTCATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATA
** *
1481460 AACTTATTATGAATTTCTTAGTTTCACACACATAGTGCCCATACGGAAATTCATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATA
*
1481515 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACTGAAATT-ATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATA
* *
1481569 AACTTATTATGAATTCCTTAGTGTTGCACACACAGTG
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTG
1481606 TCATTTGGTA
Statistics
Matches: 281, Mismatches: 28, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
54 89 0.32
55 192 0.68
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (55 bp):
AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATA
Found at i:1481490 original size:109 final size:110
Alignment explanation
Indices: 1481241--1481602 Score: 505
Period size: 109 Copynumber: 3.3 Consensus size: 110
1481231 AGTAATCCAC
* *** * * *
1481241 AACTTACTATGAATTTCTTAGTTTTGTACACACACTGCCTATA-TGGAAATTCATAAACTTATTA
1 AACTTATTATGAATTTCTTAGTTTCACACACATAGTGCCCATACT-GAAATTCATAAACTTATTA
* * * *
1481305 TGATTTTCTAACTTTTGCACACACAATGCCCATACAGAAATTCATA
65 TGAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAATTCATA
* * **
1481351 AACTTATTATGAATTTCATAATTTTGCACACATAGTGCCCATACTGAAATTCATAAACTTATTAT
1 AACTTATTATGAATTTCTTAGTTTCACACACATAGTGCCCATACTGAAATTCATAAACTTATTAT
*
1481416 GAATTTCTTAGTTTT-CACACACAGTGCCCATACGGAAATTCATA
66 GAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAATTCATA
*
1481460 AACTTATTATGAATTTCTTAGTTTCACACACATAGTGCCCATACGGAAATTCATAAACTTATTAT
1 AACTTATTATGAATTTCTTAGTTTCACACACATAGTGCCCATACTGAAATTCATAAACTTATTAT
*
1481525 GAATTTCTTAGTTTTGCACACACAGTGCCCATACTGAAATT-ATA
66 GAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAATTCATA
*
1481569 AACTTATTATGAATTCCTTAGTGTTGCACACACA
1 AACTTATTATGAATTTCTTAGT-TT-CACACACA
1481603 GTGTCATTTG
Statistics
Matches: 229, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
109 126 0.55
110 94 0.41
111 9 0.04
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (110 bp):
AACTTATTATGAATTTCTTAGTTTCACACACATAGTGCCCATACTGAAATTCATAAACTTATTAT
GAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAATTCATA
Found at i:1481501 original size:164 final size:163
Alignment explanation
Indices: 1481241--1481605 Score: 545
Period size: 164 Copynumber: 2.2 Consensus size: 163
1481231 AGTAATCCAC
* * * * *
1481241 AACTTACTATGAATTTCTTAGTTTTGTACACACACTGCCTATATGGAAATTCATAAACTTATTAT
1 AACTTATTATGAATTTCTTAGTTTT-CACACACAGTGCCCATACGGAAATTCATAAACTTATTAT
* *
1481306 GATTTTCTAACTTTTGCACACACAATGCCCATACAGAAATTCATAAACTTATTATGAATTTCATA
65 GAATTTCTAACGTTTGCACACACAATGCCCATACAGAAATTCATAAACTTATTATGAATTTCATA
*
1481371 ATTTTGCACACATAGTGCCCATACTGAAATTCATA
130 ATTTTGCACACACAGTGCCCATACTGAAATT-ATA
1481406 AACTTATTATGAATTTCTTAGTTTTCACACACAGTGCCCATACGGAAATTCATAAACTTATTATG
1 AACTTATTATGAATTTCTTAGTTTTCACACACAGTGCCCATACGGAAATTCATAAACTTATTATG
* * *
1481471 AATTTCTTA-GTTT-CACACACATAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTT
66 AATTTCTAACGTTTGCACACACA-A-TGCCCATACAGAAATTCATAAACTTATTATGAATTTCAT
*
1481534 AGTTTTGCACACACAGTGCCCATACTGAAATTATA
129 AATTTTGCACACACAGTGCCCATACTGAAATTATA
* *
1481569 AACTTATTATGAATTCCTTAGTGTTGCACACACAGTG
1 AACTTATTATGAATTTCTTAGT-TTTCACACACAGTG
1481606 TCATTTGGTA
Statistics
Matches: 183, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
162 8 0.04
163 28 0.15
164 123 0.67
165 24 0.13
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (163 bp):
AACTTATTATGAATTTCTTAGTTTTCACACACAGTGCCCATACGGAAATTCATAAACTTATTATG
AATTTCTAACGTTTGCACACACAATGCCCATACAGAAATTCATAAACTTATTATGAATTTCATAA
TTTTGCACACACAGTGCCCATACTGAAATTATA
Found at i:1484771 original size:82 final size:82
Alignment explanation
Indices: 1484576--1485438 Score: 1101
Period size: 82 Copynumber: 10.7 Consensus size: 82
1484566 AATCATTTAG
* * ** * * *
1484576 TCTTTTAC-CCAAGGCATTTAGTCTTTCATCTAACTTGCATAATTGACACGTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
1484640 ACATCTAGG-CATTAAA
66 ACAGCTAGGCCATTAAA
* * * * * *
1484656 TCTTTAACTCAAAGGCATTTAGCCTTTTATCTAACTGGCATGATTGACACCTTTCTTTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1484721 ACAGCTAGGCCATTAAA
66 ACAGCTAGGCCATTAAA
* * * *
1484738 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGTA-AATTGACACTTTTTTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1484802 ACAGCTAGGCCATT-AA
66 ACAGCTAGGCCATTAAA
* * *
1484818 TCTTTTACTCAAAGGTATTTAACCTTTTATTTAACTGGCATAATTGGCACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
1484883 ACAACTAGGCCATTAAA
66 ACAGCTAGGCCATTAAA
* * * *
1484900 TCTTTTACTCAAAAGTATTTAACCTTTCATCTAAGTGGCATAATTGACACATTTCTCTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
1484965 ATAGCTAGGCCATT-AA
66 ACAGCTAGGCCATTAAA
* * * *
1484981 TCTTTTACTCAAAGG--TTTAACCTTTCATCTAACTGGAATAATTGACACTTTTTTGTCACATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1485044 ACAAG-TAGGCCATTAAA
66 AC-AGCTAGGCCATTAAA
* * * *
1485061 TCTTTTACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAATTGAAACTTTTTTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* *
1485126 ATAGCTAGGCCTTTAAA
66 ACAGCTAGGCCATTAAA
* * * *
1485143 TCTTTCACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAATTTACACCTTTATGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
1485208 ACACCTAGGCCATTAAA
66 ACAGCTAGGCCATTAAA
* * * * * * *
1485225 TCTTTTACTTAAAGGTATTTAACATTTCATCTAACTAGCATAATTGCCAACTTTATGTCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1485290 ACAGCTAGGCCATTAAA
66 ACAGCTAGGCCATTAAA
* * * *
1485307 TCTTTTACTCACAGGTATTTAACCTTTCATTTAACTAGCATAATTGACACCTTTCTGTCCAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
1485372 ACAACT-GGCCATTAAA
66 ACAGCTAGGCCATTAAA
* *
1485388 TC-TTTACTTAAAGGTA---AACCTTTCA---AACTGGCATAATTAACACCTTTCTGT
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGT
1485439 TTATTTTACA
Statistics
Matches: 691, Mismatches: 83, Indels: 24
0.87 0.10 0.03
Matches are distributed among these distances:
74 24 0.03
77 9 0.01
79 52 0.08
80 77 0.11
81 152 0.22
82 377 0.55
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (82 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCCATTAAA
Found at i:1485071 original size:243 final size:245
Alignment explanation
Indices: 1484576--1485436 Score: 1124
Period size: 243 Copynumber: 3.6 Consensus size: 245
1484566 AATCATTTAG
* * ** * * * *
1484576 TCTTTTAC-CCAAGGCATTTAGTCTTTCATCTAACTTGCATAATTGACACGTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATTTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* * * * *
1484640 ACATCTAGG-CATTAAATCTTTAACTCAAAGGCATTTAGCCTTTTATCTAACTGGCATGATTGAC
66 ACAACTAGGCCATTAAATCTTTAACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAC
*
1484704 ACCTTTCTTTCAAATGCACAGCTAGGCCATTAAATCTTTTACTCAAAGGTATTTAACCTTTCATC
131 ACCTTTCTCTCAAATGCACAGCTAGGCCATTAAATCTTTTACTCAAAGG-ATTTAACCTTTCATC
* *
1484769 TAACTGGTA-AATTGACACTTTTTTGCCAAATGCACAGCTAGGCCATT-AA
195 TAACTGGAATAATTGACACTTTTTTGTCAAATGCACAGCTAGGCCATTAAA
* *
1484818 TCTTTTACTCAAAGGTATTTAACCTTTTATTTAACTGGCATAATTGGCACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATTTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* * *
1484883 ACAACTAGGCCATTAAATCTTTTACTCAAAAGTATTTAACCTTTCATCTAAGTGGCATAATTGAC
66 ACAACTAGGCCATTAAATCTTTAACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAC
* *
1484948 ACATTTCTCTCAAATGCATAGCTAGGCCATT-AATCTTTTACTCAAAGG-TTTAACCTTTCATCT
131 ACCTTTCTCTCAAATGCACAGCTAGGCCATTAAATCTTTTACTCAAAGGATTTAACCTTTCATCT
*
1485011 AACTGGAATAATTGACACTTTTTTGTCACATGCACAAG-TAGGCCATTAAA
196 AACTGGAATAATTGACACTTTTTTGTCAAATGCAC-AGCTAGGCCATTAAA
** * * *
1485061 TCTTTTACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAATTGAAACTTTTTTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATTTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* * * * * *
1485126 ATAGCTAGGCCTTTAAATCTTTCACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAATTTAC
66 ACAACTAGGCCATTAAATCTTTAACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAC
* * * * *
1485191 ACCTTTATGTCAAATGCACACCTAGGCCATTAAATCTTTTACTTAAAGGTATTTAACATTTCATC
131 ACCTTTCTCTCAAATGCACAGCTAGGCCATTAAATCTTTTACTCAAAGG-ATTTAACCTTTCATC
* * * * *
1485256 TAACTAGCATAATTGCCAAC-TTTATGTCAAATACACAGCTAGGCCATTAAA
195 TAACTGGAATAATTGAC-ACTTTTTTGTCAAATGCACAGCTAGGCCATTAAA
* * *
1485307 TCTTTTACTCACAGGTATTTAACCTTTCATTTAACTAGCATAATTGACACCTTTCTGTCCAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATTTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* *
1485372 ACAACT-GGCCATTAAATCTTT-ACTTAAAGGTA---AACCTTTCA---AACTGGCATAATTAAC
66 ACAACTAGGCCATTAAATCTTTAACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAC
1485429 ACCTTTCT
131 ACCTTTCT
1485437 GTTTATTTTA
Statistics
Matches: 543, Mismatches: 66, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
238 22 0.04
241 31 0.06
242 41 0.08
243 216 0.40
244 102 0.19
245 16 0.03
246 113 0.21
247 2 0.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (245 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATTTAACTGGCATAATTGACACCTTTCTGTCAAATGC
ACAACTAGGCCATTAAATCTTTAACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAC
ACCTTTCTCTCAAATGCACAGCTAGGCCATTAAATCTTTTACTCAAAGGATTTAACCTTTCATCT
AACTGGAATAATTGACACTTTTTTGTCAAATGCACAGCTAGGCCATTAAA
Found at i:1485161 original size:325 final size:326
Alignment explanation
Indices: 1484598--1485425 Score: 1096
Period size: 325 Copynumber: 2.6 Consensus size: 326
1484588 GGCATTTAGT
* * *
1484598 CTTTCATCTAACTTGCATAATTGACACGTTTCTGC-CAAATGCACATCTAGG-CATTAAATCTTT
1 CTTTCATCTAACTAGCATAATTGACACATTTCT-CTCAAATGCACAGCTAGGCCATTAAATCTTT
* * * * * *
1484661 AACTCAAAGGCATTTAGCCTTTTATCTAACTGGCATGATTGACACCTTTCTT-TCAAATGCAC-A
65 TACTCAAAGG-ATTTAACCTTTCATCTAACTGGCATAATTGACA-CTTTTTTGTCACATGCACAA
* * *
1484724 GCTAGGCCATTAAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGTA-AATTGACACT
128 G-TAGGCCATTAAATCTTTTACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAATTGAAACT
* * **
1484788 TTTTTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTTATTTAAC
192 TTTTTGCCAAATGCACAGCTAGGCCATTAATCTTTCACTCAAAGGTATTTAACCTTTCATCAAAC
* *
1484853 TGGCATAATTGGCACCTTTCTGTCAAATGCACAACTAGGCCATTAAATCTTTTACTCAAAAGTAT
257 TGGCATAATTGACACCTTTATGTCAAATGCACAACTAGGCCATTAAATCTTTTACTCAAAAGTAT
1484918 TTAAC
322 TTAAC
* * *
1484923 CTTTCATCTAAGTGGCATAATTGACACATTTCTCTCAAATGCATAGCTAGGCCATT-AATCTTTT
1 CTTTCATCTAACTAGCATAATTGACACATTTCTCTCAAATGCACAGCTAGGCCATTAAATCTTTT
*
1484987 ACTCAAAGG-TTTAACCTTTCATCTAACTGGAATAATTGACACTTTTTTGTCACATGCACAAGTA
66 ACTCAAAGGATTTAACCTTTCATCTAACTGGCATAATTGACACTTTTTTGTCACATGCACAAGTA
1485051 GGCCATTAAATCTTTTACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAATTGAAACTTTTT
131 GGCCATTAAATCTTTTACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAATTGAAACTTTTT
* * *
1485116 TGTCAAATGCATAGCTAGGCCTTTAAATCTTTCACTCAAAGGTATTTAACCTTTCATCAAACTGG
196 TGCCAAATGCACAGCTAGGCCATT-AATCTTTCACTCAAAGGTATTTAACCTTTCATCAAACTGG
* * * *
1485181 CATAATTTACACCTTTATGTCAAATGCACACCTAGGCCATTAAATCTTTTACTTAAAGGTATTTA
260 CATAATTGACACCTTTATGTCAAATGCACAACTAGGCCATTAAATCTTTTACTCAAAAGTATTTA
1485246 AC
325 AC
* * * * *
1485248 ATTTCATCTAACTAGCATAATTGCCA-ACTTTATGTCAAATACACAGCTAGGCCATTAAATCTTT
1 CTTTCATCTAACTAGCATAATTGACACA-TTTCTCTCAAATGCACAGCTAGGCCATTAAATCTTT
* * * * *
1485312 TACTCACAGGTATTTAACCTTTCATTTAACTAGCATAATTGACACCTTTCTGTC-CAATGCACAA
65 TACTCAAAGG-ATTTAACCTTTCATCTAACTGGCATAATTGACACTTTTTTGTCAC-ATGCACAA
* *
1485376 CT-GGCCATTAAATC-TTTACTTAAAGGTA---AACC-TT--TCAAACTGGCATAATT
128 GTAGGCCATTAAATCTTTTACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAATT
1485426 AACACCTTTC
Statistics
Matches: 448, Mismatches: 44, Indels: 27
0.86 0.08 0.05
Matches are distributed among these distances:
320 16 0.04
322 8 0.02
323 91 0.20
324 38 0.08
325 203 0.45
326 33 0.07
327 13 0.03
328 46 0.10
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (326 bp):
CTTTCATCTAACTAGCATAATTGACACATTTCTCTCAAATGCACAGCTAGGCCATTAAATCTTTT
ACTCAAAGGATTTAACCTTTCATCTAACTGGCATAATTGACACTTTTTTGTCACATGCACAAGTA
GGCCATTAAATCTTTTACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAATTGAAACTTTTT
TGCCAAATGCACAGCTAGGCCATTAATCTTTCACTCAAAGGTATTTAACCTTTCATCAAACTGGC
ATAATTGACACCTTTATGTCAAATGCACAACTAGGCCATTAAATCTTTTACTCAAAAGTATTTAA
C
Found at i:1485618 original size:55 final size:55
Alignment explanation
Indices: 1485548--1485914 Score: 574
Period size: 55 Copynumber: 6.7 Consensus size: 55
1485538 GGTAATCCAC
* *
1485548 AACTTACTATAAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAATTCATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAATTCATA
* *
1485603 AACTTTTTATGAATTTCTTAGTTTTACACACACAGTGCCCATAC-GAAAATTCATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAG-AAATTCATA
* * * *
1485658 AACTTATTATGAATTTCTTAGTATTGCACGCACTGTGCCCATACGGAAATTCATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAATTCATA
*
1485713 AACTTATTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACAGAAATTCATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAATTCATA
* * *
1485768 TACTTATTATGATTTTCTTAGTTTTGCACACACAGTGCCCTTACAGAAATTCATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAATTCATA
* * *
1485823 AAGTTATTATGAATTTCTTAGTTTTGCACACACAATGCCCATACGGAAATTCATA
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAATTCATA
*
1485878 AACTTATTATGAATTTCTTAGTTTTACACACACAGTG
1 AACTTATTATGAATTTCTTAGTTTTGCACACACAGTG
1485915 TCATTTGGTA
Statistics
Matches: 283, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
54 1 0.00
55 281 0.99
56 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (55 bp):
AACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAATTCATA
Found at i:1489099 original size:82 final size:82
Alignment explanation
Indices: 1488927--1489676 Score: 949
Period size: 82 Copynumber: 9.2 Consensus size: 82
1488917 GCATTTAGTT
* * * * *
1488927 TTTCATCTAACTTGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGG-TATTAAATCTTTAA
1 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
* *
1488991 CTCAAAGGCATTTAGCC
66 CTCAAAGGTATTTAACC
* * * * *
1489008 TTTTATCTAACTAGAATGATTGACATC-TTTCTGTCAAATGCACAACTAGGCCATTAAATCTTTT
1 TTTCATCTAACTGGCATAATTGACA-CATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTT
*
1489072 ACTCAAAGGCATTTAACC
65 ACTCAAAGGTATTTAACC
* * * *
1489090 TTTCATCTAACTAGTATAATTGACACATTTCTGTCAAATTCACAGTTAGGCCATT-AATCTTTTA
1 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
1489154 CTCAAAGGTATTTAACC
66 CTCAAAGGTATTTAACC
* * ** * *
1489171 TTTCATCTAACTGGTATAATTGACACTTTTCTGTCAAATAAATAGTTAGGCCATTAAATCTTTTA
1 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
* *
1489236 CTCAAAGTTATTTAACT
66 CTCAAAGGTATTTAACC
* * *
1489253 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATACATAGCTTGGCCATT-AATCTTTTA
1 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
**
1489317 CTCAAATCTATTTAACC
66 CTCAAAGGTATTTAACC
* * ** *
1489334 TTTCATCTAACTGGCATAATTGACACTTTTCTATCAAATGCGTAGCTAGGCCATTAAATATTTTA
1 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
1489399 CTCAAAGGTATTTAACC
66 CTCAAAGGTATTTAACC
* * * * * *
1489416 TTTCATCTAACTGGCAAAATTAACACATTTCTTTTAAATGCATAGCTAGGCCATTAAAT-ATTTA
1 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
1489480 CTCAAA-GTATTTAACC
66 CTCAAAGGTATTTAACC
* ** *
1489496 ATTCATCTAACTACCATAA-TGACACATTTCTGTCAAATGCACAACTAGGCCATTAAATCTTTTA
1 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
*
1489560 CTCAAATGTATTTAACC
66 CTCAAAGGTATTTAACC
* * *
1489577 TTCCATCTAACTGGCATAATTGACATC-TTTCTATCAAATGCAGAGCTAGGCCATTAAATCTTTT
1 TTTCATCTAACTGGCATAATTGACA-CATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTT
* **
1489641 ACTCAAAAGTATTTAATA
65 ACTCAAAGGTATTTAACC
*
1489659 TTTCATCTAACTGACATA
1 TTTCATCTAACTGGCATA
1489677 CACTACAAGA
Statistics
Matches: 592, Mismatches: 68, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
79 34 0.06
80 35 0.06
81 226 0.38
82 296 0.50
83 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (82 bp):
TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
CTCAAAGGTATTTAACC
Found at i:1489113 original size:163 final size:163
Alignment explanation
Indices: 1488927--1489670 Score: 926
Period size: 163 Copynumber: 4.6 Consensus size: 163
1488917 GCATTTAGTT
* * * * *
1488927 TTTCATCTAACTTGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGG-TATTAAATCTTTAA
1 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
* * * *
1488991 CTCAAAGGCATTTAGCCTTTTATCTAACTAGAATGATTGACA-TCTTTCTGTCAAATGCACAACT
66 CTCAAA-GCATTTAACCTTTCATCTAACTAGCATAATTGACACT-TTTCTGTCAAATGCACAACT
*
1489055 AGGCCATTAAATCTTTTACTCAAAGGCATTTAACC
129 AGGCCATTAAATCTTTTACTCAAAGGTATTTAACC
* * * *
1489090 TTTCATCTAACTAGTATAATTGACACATTTCTGTCAAATTCACAGTTAGGCCATT-AATCTTTTA
1 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
* * * ** * **
1489154 CTCAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGACACTTTTCTGTCAAATAAATAGTTA
66 CTCAAA-GCATTTAACCTTTCATCTAACTAGCATAATTGACACTTTTCTGTCAAATGCACAACTA
* *
1489219 GGCCATTAAATCTTTTACTCAAAGTTATTTAACT
130 GGCCATTAAATCTTTTACTCAAAGGTATTTAACC
* * *
1489253 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATACATAGCTTGGCCATT-AATCTTTTA
1 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
* * * ** *
1489317 CTCAAATCTATTTAACCTTTCATCTAACTGGCATAATTGACACTTTTCTATCAAATGCGTAGCTA
66 CTCAAAGC-ATTTAACCTTTCATCTAACTAGCATAATTGACACTTTTCTGTCAAATGCACAACTA
*
1489382 GGCCATTAAATATTTTACTCAAAGGTATTTAACC
130 GGCCATTAAATCTTTTACTCAAAGGTATTTAACC
* * * * * *
1489416 TTTCATCTAACTGGCAAAATTAACACATTTCTTTTAAATGCATAGCTAGGCCATTAAAT-ATTTA
1 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
* * * *
1489480 CTCAAAGTATTTAACCATTCATCTAACTACCATAA-TGACACATTTCTGTCAAATGCACAACTAG
66 CTCAAAGCATTTAACCTTTCATCTAACTAGCATAATTGACACTTTTCTGTCAAATGCACAACTAG
*
1489544 GCCATTAAATCTTTTACTCAAATGTATTTAACC
131 GCCATTAAATCTTTTACTCAAAGGTATTTAACC
* * *
1489577 TTCCATCTAACTGGCATAATTGACATC-TTTCTATCAAATGCAGAGCTAGGCCATTAAATCTTTT
1 TTTCATCTAACTGGCATAATTGACA-CATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTT
* **
1489641 ACTCAAAAGTATTTAATATTTCATCTAACT
65 ACTC-AAAGCATTTAACCTTTCATCTAACT
1489671 GACATACACT
Statistics
Matches: 506, Mismatches: 68, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
161 106 0.21
162 32 0.06
163 361 0.71
164 7 0.01
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (163 bp):
TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCTTTTA
CTCAAAGCATTTAACCTTTCATCTAACTAGCATAATTGACACTTTTCTGTCAAATGCACAACTAG
GCCATTAAATCTTTTACTCAAAGGTATTTAACC
Found at i:1490045 original size:19 final size:20
Alignment explanation
Indices: 1490009--1490047 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1489999 TTGTAGACCA
* *
1490009 AACACTTTCTCCTTCTCATC
1 AACACTTTCTACTCCTCATC
1490029 AACA-TTTCTACTCCTCATC
1 AACACTTTCTACTCCTCATC
1490048 GGCGGCGCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
AACACTTTCTACTCCTCATC
Found at i:1494089 original size:2 final size:2
Alignment explanation
Indices: 1494082--1494115 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1494072 TTAATCTACA
1494082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1494116 CAATAATTTA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1494292 original size:13 final size:13
Alignment explanation
Indices: 1494274--1494322 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
1494264 CACTCAATGA
*
1494274 CGTCATAAATGCG
1 CGTCATAAATGTG
*
1494287 CGTCATAAATGTA
1 CGTCATAAATGTG
*
1494300 TGTCATAAATGTG
1 CGTCATAAATGTG
1494313 CGTCATAAAT
1 CGTCATAAAT
1494323 TTATGACGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (13 bp):
CGTCATAAATGTG
Found at i:1494304 original size:26 final size:26
Alignment explanation
Indices: 1494275--1494327 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1494265 ACTCAATGAC
1494275 GTCATAAATGCGCGTCATAAATGTAT
1 GTCATAAATGCGCGTCATAAATGTAT
* *
1494301 GTCATAAATGTGCGTCATAAATTTAT
1 GTCATAAATGCGCGTCATAAATGTAT
1494327 G
1 G
1494328 ACGCACAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (26 bp):
GTCATAAATGCGCGTCATAAATGTAT
Found at i:1494680 original size:81 final size:81
Alignment explanation
Indices: 1494450--1494729 Score: 421
Period size: 81 Copynumber: 3.5 Consensus size: 81
1494440 CTATTGATAG
* *
1494450 TTGACACCTTTCTGTCAAATGCATAGCTAGGCCATTAAATCTTTTACTTAAAGGTATTTAACCTT
1 TTGACACATTTCTGTCAAATGCATAGCTAGGCCATTAAATCTTTTACTCAAAGGTATTTAACCTT
*
1494515 TATCTAACTGGCATAA
66 AATCTAACTGGCATAA
*
1494531 -TGACACCTTTCTGTCAAATG----GCTAGGCCATTAAATCTTTTACTCAAAGGTA-TTAACCTT
1 TTGACACATTTCTGTCAAATGCATAGCTAGGCCATTAAATCTTTTACTCAAAGGTATTTAACC-T
*
1494590 TAATTTAACTGGCATAA
65 TAATCTAACTGGCATAA
*
1494607 TTGACACATTTCTGTCAAATGCATAGCTAGGTCATT-AATCTTTTACTCAAAGGTATTTAACCAT
1 TTGACACATTTCTGTCAAATGCATAGCTAGGCCATTAAATCTTTTACTCAAAGGTATTTAACC-T
*
1494671 TCATCTAACTGGCATAA
65 TAATCTAACTGGCATAA
*
1494688 TTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAAATCT
1 TTGACACATTTCTGTCAAATGCATAGCTAGGCCATTAAATCT
1494730 ATTATTTTAG
Statistics
Matches: 181, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
75 6 0.03
76 46 0.25
77 19 0.10
80 39 0.22
81 66 0.36
82 5 0.03
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (81 bp):
TTGACACATTTCTGTCAAATGCATAGCTAGGCCATTAAATCTTTTACTCAAAGGTATTTAACCTT
AATCTAACTGGCATAA
Found at i:1494875 original size:55 final size:52
Alignment explanation
Indices: 1494755--1494954 Score: 202
Period size: 50 Copynumber: 3.9 Consensus size: 52
1494745 TGCCTACTCT
* * * *
1494755 AATTCATAAAATTATTATGAATTTTTTA--ATTACACACACAGTGCCCTACGG
1 AATTCATAAACTTATTATGAATTTCTTAGTTTTACAC-CACAGTGCCCTACGA
* *
1494806 AA-TCATAAACTTATTATGAATTTCTTAGTTTTACACGCACAATGCCCATAAGAA
1 AATTCATAAACTTATTATGAATTTCTTAGTTTTACAC-CACAGTGCCC-TACG-A
*
1494860 AATTCATAAACTTATTTTGAATTTCTTAGTTTTGA-A-CACAGTGCCCTTACGGA
1 AATTCATAAACTTATTATGAATTTCTTAGTTTT-ACACCACAGTGCCC-TAC-GA
*
1494913 AATTCATAAACTTA-TATGAA-TT-TTAGTTTTGCA-CACAGTGCC
1 AATTCATAAACTTATTATGAATTTCTTAGTTTTACACCACAGTGCC
1494955 ATTTGGTAAT
Statistics
Matches: 128, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
50 41 0.32
51 4 0.03
52 20 0.16
53 29 0.23
54 3 0.02
55 30 0.23
56 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (52 bp):
AATTCATAAACTTATTATGAATTTCTTAGTTTTACACCACAGTGCCCTACGA
Found at i:1495795 original size:25 final size:24
Alignment explanation
Indices: 1495747--1495795 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1495737 TATGCTAGTA
*
1495747 AACATCAATAAAAACTCATATTCT
1 AACATCAATAAAAACCCATATTCT
* *
1495771 AACATCATTCAAAAACCCATTTTCT
1 AACATCAAT-AAAAACCCATATTCT
1495796 TAAATCTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (24 bp):
AACATCAATAAAAACCCATATTCT
Found at i:1497292 original size:383 final size:380
Alignment explanation
Indices: 1496587--1497351 Score: 1394
Period size: 383 Copynumber: 2.0 Consensus size: 380
1496577 CATTGTACTA
*
1496587 ATAACTCTCAATGCACATACAATGGTTTTATATCAAAAATCATATCATTCATCTATAAATTATCC
1 ATAACTCTCAATGCACATACAAGGGTTTTATATCAAAAATCATATCATTCATCTATAAATTATCC
1496652 ATAGATACTCGTATATAAAAATAGCATAAATCAGTGCATTGAGCAATTCATACAAGAAAACATTC
66 ATAGATACTCG-ATATAAAAATAGCATAAATCAGTGCATTGAGCAATTCATACAAGAAAACATTC
1496717 AAATACCATTTGGTAAAACAATATCAAAATATCAAAATACGATTCAAAACCTTTTCTTTTCAAAT
130 AAATACCATTTGGTAAAACAATATCAAAATATCAAAATACGATTCAAAACCTTTTCTTTTCAAAT
*
1496782 CATGCAAGGTTGACTCATCGCAAGTCTCTCATATCATATATAATAGTATAAGTAAAAATGCACTC
195 CATGCAAGGTTGACTCATCACAAGTCTCTCATATCATATATAATAGTATAAGTAAAAATGCACTC
1496847 AATTGGTATACTTAGTTTGCACACTTTAATTAACGATATAAGCCTTATTTTTTGACTTCTCCTTA
260 AATTGGTATACTTAGTTTGCACACTTTAATTAACGATATAAGCCTTATTTTTTGACTTCTCCTTA
1496912 GCTTTTAGTTTGCTTTATTCTCGATTTTGGTCATGATCTATACGAATATCATTTAC
325 GCTTTTAGTTTGCTTTATTCTCGATTTTGGTCATGATCTATACGAATATCATTTAC
1496968 ATAACTCTCAATGCA-ATACAAGGGTTTTATATCAAAAATCATATATCATTCATCTATAAAATTA
1 ATAACTCTCAATGCACATACAAGGGTTTTATATCAAAAATC--ATATCATTCATCTAT-AAATTA
1497032 TCCATAGATACTCG-TATAAAAATAGCATAAATCAGTGCATTGAGCAATTCATACAAGAAAACAT
63 TCCATAGATACTCGATATAAAAATAGCATAAATCAGTGCATTGAGCAATTCATACAAGAAAACAT
1497096 TCAAATACCATTTGGTAAAACAATATCAAAATATATCAAAATACGATTCAAAACCTTTTC-TTTC
128 TCAAATACCATTTGGTAAAACAATATC-AAA-ATATCAAAATACGATTCAAAACCTTTTCTTTTC
* *
1497160 AAATCATTCAAGGTTGACTCATCACAAGTCTTCCTCATATCATATAT-ATAGTATAAGTAAGAAT
191 AAATCATGCAAGGTTGACTCATCACAAGTC-T-CTCATATCATATATAATAGTATAAGTAAAAAT
1497224 GCACTCAATTGGTATACTTAGTTTGCACACTTTAATTAACGATATAAGCCTTATTTTTTGACTTC
254 GCACTCAATTGGTATACTTAGTTTGCACACTTTAATTAACGATATAAGCCTTATTTTTTGACTTC
1497289 TCCTTAGCTTTTAGTTTGCTTTATTCTCGATTTTGGTCATGATCTATACGAATATCATTTAC
319 TCCTTAGCTTTTAGTTTGCTTTATTCTCGATTTTGGTCATGATCTATACGAATATCATTTAC
1497351 A
1 A
1497352 AAACATATAC
Statistics
Matches: 373, Mismatches: 4, Indels: 12
0.96 0.01 0.03
Matches are distributed among these distances:
380 24 0.06
381 92 0.25
382 50 0.13
383 193 0.52
384 14 0.04
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (380 bp):
ATAACTCTCAATGCACATACAAGGGTTTTATATCAAAAATCATATCATTCATCTATAAATTATCC
ATAGATACTCGATATAAAAATAGCATAAATCAGTGCATTGAGCAATTCATACAAGAAAACATTCA
AATACCATTTGGTAAAACAATATCAAAATATCAAAATACGATTCAAAACCTTTTCTTTTCAAATC
ATGCAAGGTTGACTCATCACAAGTCTCTCATATCATATATAATAGTATAAGTAAAAATGCACTCA
ATTGGTATACTTAGTTTGCACACTTTAATTAACGATATAAGCCTTATTTTTTGACTTCTCCTTAG
CTTTTAGTTTGCTTTATTCTCGATTTTGGTCATGATCTATACGAATATCATTTAC
Found at i:1498561 original size:31 final size:31
Alignment explanation
Indices: 1498524--1498629 Score: 123
Period size: 31 Copynumber: 3.5 Consensus size: 31
1498514 TTAAAATTAC
1498524 AATTTAGTCC-CTAAACCTTTCCTAAGTTTAT
1 AATTTAG-CCACTAAACCTTTCCTAAGTTTAT
* ** *
1498555 ACTTTAGCCACTAAA-CTTT--TAAAATTAC
1 AATTTAGCCACTAAACCTTTCCTAAGTTTAT
1498583 AATTTAGTCC-CTAAACCTTTCCTAAGTTTAT
1 AATTTAG-CCACTAAACCTTTCCTAAGTTTAT
1498614 AATTTAGCCACTAAAC
1 AATTTAGCCACTAAAC
1498630 TTTTAATTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
28 17 0.28
29 6 0.10
30 8 0.13
31 30 0.49
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.38
Consensus pattern (31 bp):
AATTTAGCCACTAAACCTTTCCTAAGTTTAT
Found at i:1498577 original size:59 final size:59
Alignment explanation
Indices: 1498512--1498635 Score: 239
Period size: 59 Copynumber: 2.1 Consensus size: 59
1498502 CCACATAACT
*
1498512 TTTTAAAATTACAATTTAGTCCCTAAACCTTTCCTAAGTTTATACTTTAGCCACTAAAC
1 TTTTAAAATTACAATTTAGTCCCTAAACCTTTCCTAAGTTTATAATTTAGCCACTAAAC
1498571 TTTTAAAATTACAATTTAGTCCCTAAACCTTTCCTAAGTTTATAATTTAGCCACTAAAC
1 TTTTAAAATTACAATTTAGTCCCTAAACCTTTCCTAAGTTTATAATTTAGCCACTAAAC
1498630 TTTTAA
1 TTTTAA
1498636 TTTATTCATT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (59 bp):
TTTTAAAATTACAATTTAGTCCCTAAACCTTTCCTAAGTTTATAATTTAGCCACTAAAC
Found at i:1508672 original size:2 final size:2
Alignment explanation
Indices: 1508667--1508698 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1508657 ATTTTTTCAA
1508667 AT AT AT AT AT AT -T 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
1508699 AGAGAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1508681 original size:107 final size:109
Alignment explanation
Indices: 1508507--1508725 Score: 381
Period size: 107 Copynumber: 2.0 Consensus size: 109
1508497 TAAAACCAAT
*
1508507 AATGAAAATATTAAACATGTAATTTACCCTAATATTTATGTATATTTTTTCAAATATCTATATAT
1 AATGAAAATATTAAACATGTAATTTACCCTAATATTTATG--TATTTTTTCAAATATATATATAT
1508572 TATATATATATATATATATAAGAGAAAATAACTTCAGTGACCAAAA
64 TATATATATATATATATATAAGAGAAAATAACTTCAGTGACCAAAA
1508618 AATGAAAATATTAAACATGTAA-TTACCCTAA-ATTTTATG-ATTTTTTCAAATATATATATATT
1 AATGAAAATATTAAACATGTAATTTACCCTAATA-TTTATGTATTTTTTCAAATATATATATATT
1508680 ATATATATATATATATATAAGAGAAAATAACTTCAGTGACCAAAA
65 ATATATATATATATATATAAGAGAAAATAACTTCAGTGACCAAAA
1508725 A
1 A
1508726 TGCCTTATAA
Statistics
Matches: 106, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
107 68 0.64
109 1 0.01
110 15 0.14
111 22 0.21
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (109 bp):
AATGAAAATATTAAACATGTAATTTACCCTAATATTTATGTATTTTTTCAAATATATATATATTA
TATATATATATATATATAAGAGAAAATAACTTCAGTGACCAAAA
Found at i:1508853 original size:20 final size:20
Alignment explanation
Indices: 1508808--1508853 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1508798 CTCTAATTTT
* *
1508808 GCAACACAGTTTTCAAATTC
1 GCAACTCAGTTTTAAAATTC
1508828 GCAACTCAGTTTTAAAATTC
1 GCAACTCAGTTTTAAAATTC
1508848 GCAACT
1 GCAACT
1508854 AGAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (20 bp):
GCAACTCAGTTTTAAAATTC
Found at i:1509047 original size:20 final size:20
Alignment explanation
Indices: 1508976--1509050 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 20
1508966 TGCAACTCGA
**
1508976 TTTCTGAATTCGCAACGTGAT
1 TTTCT-AATTCGCAACAAGAT
* *
1508997 TTT-TAAATCGCAACACA-AG
1 TTTCTAATTCGCAACA-AGAT
*
1509016 TTTCT-TTTCGCAACAAGAT
1 TTTCTAATTCGCAACAAGAT
1509035 TTTCTAATTCGCAACA
1 TTTCTAATTCGCAACA
1509051 CGAATTTGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
18 1 0.02
19 27 0.64
20 11 0.26
21 3 0.07
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (20 bp):
TTTCTAATTCGCAACAAGAT
Found at i:1509076 original size:40 final size:39
Alignment explanation
Indices: 1508994--1509097 Score: 113
Period size: 40 Copynumber: 2.7 Consensus size: 39
1508984 TTCGCAACGT
* *
1508994 GATTTT-TAAATCGCAACAC-AAGTTTCTTTTCGCAACAA
1 GATTTTCTAATTCGCAACACGAA-TTTCTTTTCACAACAA
* **
1509032 GATTTTCTAATTCGCAACACGAATTTGTTTTTCACAACTC
1 GATTTTCTAATTCGCAACACGAATTT-CTTTTCACAACAA
* *
1509072 GATTTTCGAATTTGCAACACGAATTT
1 GATTTTCTAATTCGCAACACGAATTT
1509098 TAATTTCGCA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 6 0.11
39 15 0.27
40 35 0.62
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (39 bp):
GATTTTCTAATTCGCAACACGAATTTCTTTTCACAACAA
Found at i:1509108 original size:20 final size:21
Alignment explanation
Indices: 1508943--1509110 Score: 99
Period size: 20 Copynumber: 8.4 Consensus size: 21
1508933 AAATTTGGTA
*
1508943 TTCGCAACACGAAATTTCAAAT
1 TTCGCAACACG-AATTTCTAAT
*
1508965 TT-GCAACTCG-ATTTCTGAA-
1 TTCGCAACACGAATTTCT-AAT
** *
1508984 TTCGCAACGTG-ATTTTTAA-
1 TTCGCAACACGAATTTCTAAT
*
1509003 ATCGCAACAC-AAGTTTCT--T
1 TTCGCAACACGAA-TTTCTAAT
* *
1509022 TTCGCAACAAGATTTTCTAA-
1 TTCGCAACACGAATTTCTAAT
* *
1509042 TTCGCAACACGAATTTGT-TT
1 TTCGCAACACGAATTTCTAAT
* * * *
1509062 TTCACAACTCGATTTTCGAAT
1 TTCGCAACACGAATTTCTAAT
1509083 TT-GCAACACGAATTT-TAAT
1 TTCGCAACACGAATTTCTAAT
1509102 TTCGCAACA
1 TTCGCAACA
1509111 ACTTTTATTT
Statistics
Matches: 109, Mismatches: 26, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
19 35 0.32
20 62 0.57
21 10 0.09
22 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (21 bp):
TTCGCAACACGAATTTCTAAT
Found at i:1512673 original size:20 final size:21
Alignment explanation
Indices: 1512645--1512687 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
1512635 AATTAGATAT
* *
1512645 ACTACTAATAATATACAA-AA
1 ACTAATAATAATACACAATAA
*
1512665 ACTAATAATTATACACAATAA
1 ACTAATAATAATACACAATAA
1512686 AC
1 AC
1512688 AGACATGGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (21 bp):
ACTAATAATAATACACAATAA
Found at i:1513435 original size:26 final size:26
Alignment explanation
Indices: 1513396--1513445 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1513386 ATTTGTGTTA
* * * *
1513396 CGAAATTAATATTCGTGTTTCAAATT
1 CGAAAATAAAATTCGCGTTGCAAATT
1513422 CGAAAATAAAATTCGCGTTGCAAA
1 CGAAAATAAAATTCGCGTTGCAAA
1513446 AATAAACGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (26 bp):
CGAAAATAAAATTCGCGTTGCAAATT
Found at i:1513483 original size:20 final size:20
Alignment explanation
Indices: 1513458--1513506 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1513448 TAAACGTACT
1513458 TTGCGAATTTAACTTATGTG
1 TTGCGAATTTAACTTATGTG
* *
1513478 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTAACTTATGTG
1513498 TTGCGAATT
1 TTGCGAATT
1513507 CTAAATTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTAACTTATGTG
Found at i:1514396 original size:26 final size:27
Alignment explanation
Indices: 1514365--1514426 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 27
1514355 AGTGTAATAT
1514365 TAAAAACATTAGATATCTAGA-TGATC
1 TAAAAACATTAGATATCTAGATTGATC
1514391 TAAAAACATTAGATATCTAGATTGATC
1 TAAAAACATTAGATATCTAGATTGATC
1514418 T-AAAACATT
1 TAAAAACATT
1514427 TTAAGCACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 29 0.83
27 6 0.17
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (27 bp):
TAAAAACATTAGATATCTAGATTGATC
Found at i:1515382 original size:32 final size:32
Alignment explanation
Indices: 1515341--1515404 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1515331 CATAATATAA
1515341 ATCTTGATGTCTTTCTTAGAATTCATGAATTT
1 ATCTTGATGTCTTTCTTAGAATTCATGAATTT
1515373 ATCTTGATGTCTTTCTTAGAATTCATGAATTT
1 ATCTTGATGTCTTTCTTAGAATTCATGAATTT
1515405 GAAACAACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (32 bp):
ATCTTGATGTCTTTCTTAGAATTCATGAATTT
Found at i:1515512 original size:16 final size:16
Alignment explanation
Indices: 1515491--1515523 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1515481 GTCTCTAAAA
1515491 TAAATTATTACTTATT
1 TAAATTATTACTTATT
*
1515507 TAAATTGTTACTTATT
1 TAAATTATTACTTATT
1515523 T
1 T
1515524 TTTCTTTGTT
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:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
TAAATTATTACTTATT
Found at i:1516501 original size:20 final size:20
Alignment explanation
Indices: 1516476--1516564 Score: 83
Period size: 21 Copynumber: 4.3 Consensus size: 20
1516466 CACCACAGCT
1516476 CACATAATTTACCGAAGTG-C
1 CACATAATTTACCGAAG-GAC
*
1516496 CACATAATTGTCCCGAAGGAC
1 CACATAATT-TACCGAAGGAC
* *
1516517 CACATAATTTGTCCCAAAGGA-
1 CACATAA-TT-TACCGAAGGAC
*
1516538 CACATAATTTGTCCGAAGGAC
1 CACATAATTT-ACCGAAGGAC
1516559 CACATA
1 CACATA
1516565 GAACCCTCGA
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
19 1 0.02
20 19 0.32
21 28 0.47
22 12 0.20
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (20 bp):
CACATAATTTACCGAAGGAC
Found at i:1516513 original size:21 final size:22
Alignment explanation
Indices: 1516487--1516564 Score: 110
Period size: 21 Copynumber: 3.7 Consensus size: 22
1516477 ACATAATTTA
1516487 CCGAAGTG-CCACATAA-TTGTC
1 CCGAAG-GACCACATAATTTGTC
1516508 CCGAAGGACCACATAATTTGTC
1 CCGAAGGACCACATAATTTGTC
*
1516530 CCAAAGGA-CACATAATTTGT-
1 CCGAAGGACCACATAATTTGTC
1516550 CCGAAGGACCACATA
1 CCGAAGGACCACATA
1516565 GAACCCTCGA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
20 8 0.15
21 32 0.62
22 12 0.23
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.21
Consensus pattern (22 bp):
CCGAAGGACCACATAATTTGTC
Found at i:1517147 original size:17 final size:17
Alignment explanation
Indices: 1517108--1517147 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1517098 CGATATTTCC
*
1517108 TTTCTGGTATCGATACCC
1 TTTC-GGTATCGATACCA
*
1517126 CTTCGGTATCGATACCA
1 TTTCGGTATCGATACCA
1517143 TTTCG
1 TTTCG
1517148 AATATTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (17 bp):
TTTCGGTATCGATACCA
Found at i:1521811 original size:28 final size:28
Alignment explanation
Indices: 1521756--1521813 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
1521746 TTTGGATAAG
* **
1521756 AAATTACCAAAATAGCCTTATGGGGTAA
1 AAATTACCAAAATAACCTTATACGGTAA
* *
1521784 AAATTACGAAAATAACCTTATACTGTAA
1 AAATTACCAAAATAACCTTATACGGTAA
1521812 AA
1 AA
1521814 GACCAAGACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (28 bp):
AAATTACCAAAATAACCTTATACGGTAA
Found at i:1525325 original size:23 final size:23
Alignment explanation
Indices: 1525297--1525383 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
1525287 AGAATATGCA
*
1525297 CCGAAGTG-CCACATAGATATGTC
1 CCGAAG-GACCACATAGAAATGTC
* *
1525320 CTGAAGGACCACGTAGAAATGTC
1 CCGAAGGACCACATAGAAATGTC
* * *
1525343 CCGAAGGACCACGTAGAATTATC
1 CCGAAGGACCACATAGAAATGTC
*
1525366 CCAAAGGACCACATAGAA
1 CCGAAGGACCACATAGAA
1525384 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 1 0.02
23 54 0.98
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:1525524 original size:22 final size:22
Alignment explanation
Indices: 1525463--1525529 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
1525453 CATATTTCAC
* *
1525463 ATAGCTTGTATCACATAGACAT
1 ATAGCTTGTATCACATTGTCAT
* * * *
1525485 ATAATCATGTAGCTCATTGTCAT
1 AT-AGCTTGTATCACATTGTCAT
*
1525508 ATAGCTTGTATCACATTTTCAT
1 ATAGCTTGTATCACATTGTCAT
1525530 GTAATCATAT
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
22 17 0.52
23 16 0.48
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (22 bp):
ATAGCTTGTATCACATTGTCAT
Found at i:1525535 original size:45 final size:45
Alignment explanation
Indices: 1525460--1525589 Score: 140
Period size: 45 Copynumber: 3.0 Consensus size: 45
1525450 TTACATATTT
*** * * * *
1525460 CACATAGCTTGTATCACATAGACATATAATCATGTAGCTCATTGT
1 CACATAGCTTGTATCACATTTTCATGTAATCATATAGCTCAATGC
* *
1525505 CATATAGCTTGTATCACATTTTCATGTAATCATATAGGTCAATGC
1 CACATAGCTTGTATCACATTTTCATGTAATCATATAGCTCAATGC
* *
1525550 CACATA-C-T-TATCACATTTTCATGTAATCACATAGATCAAT
1 CACATAGCTTGTATCACATTTTCATGTAATCATATAGCTCAAT
1525590 ATCATATAAC
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 30 0.41
43 1 0.01
44 1 0.01
45 41 0.56
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (45 bp):
CACATAGCTTGTATCACATTTTCATGTAATCATATAGCTCAATGC
Found at i:1529057 original size:2 final size:2
Alignment explanation
Indices: 1529050--1529078 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1529040 TTTGGCGGTA
1529050 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 A
1529079 CAATACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 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):
AT
Found at i:1533937 original size:22 final size:22
Alignment explanation
Indices: 1533909--1533962 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1533899 TGCAATACTC
1533909 AAATGAAATTGAAGTCCAAAGT
1 AAATGAAATTGAAGTCCAAAGT
1533931 AAATGAAATTGAAGTCCAAAGT
1 AAATGAAATTGAAGTCCAAAGT
*
1533953 AAATAAAATT
1 AAATGAAATT
1533963 CACTACAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (22 bp):
AAATGAAATTGAAGTCCAAAGT
Found at i:1538076 original size:30 final size:31
Alignment explanation
Indices: 1538040--1538099 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1538030 CTTAGCTTTA
**
1538040 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
1538070 TATTATGTTTTCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
1538100 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:1538996 original size:19 final size:20
Alignment explanation
Indices: 1538972--1539021 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1538962 GGCGAAGAGG
*
1538972 ATGTATCTTCA-TTAAAATC
1 ATGTATTTTCATTTAAAATC
1538991 ATGTATTTTCATTTAAAATC
1 ATGTATTTTCATTTAAAATC
1539011 ATGTATTTTCA
1 ATGTATTTTCA
1539022 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (20 bp):
ATGTATTTTCATTTAAAATC
Found at i:1539765 original size:22 final size:22
Alignment explanation
Indices: 1539706--1539765 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 22
1539696 TTAGAGTGCA
* *
1539706 AAAAGAAAGAAAAAG-ACAAAAG
1 AAAAGGAA-AAAAAGAAAAAAAG
* *
1539728 AAGA-GAAAAATCAGAAAAAAAG
1 AAAAGGAAAAA-AAGAAAAAAAG
1539750 AAAAGGAAAAAAAGAA
1 AAAAGGAAAAAAAGAA
1539766 TTTCAAAAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
20 3 0.10
21 4 0.14
22 16 0.55
23 6 0.21
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (22 bp):
AAAAGGAAAAAAAGAAAAAAAG
Found at i:1542179 original size:29 final size:30
Alignment explanation
Indices: 1542135--1542193 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1542125 ACTTAGCTTA
**
1542135 TATTATGTTTACATATGTTTTAGAT-TCAT
1 TATTATGTTTACATATCATTTAGATATCAT
**
1542164 TATTATGTTTGTATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
1542194 GGCAACATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (30 bp):
TATTATGTTTACATATCATTTAGATATCAT
Found at i:1543080 original size:19 final size:21
Alignment explanation
Indices: 1543056--1543107 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1543046 CGGCGAAGAG
*
1543056 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
1543075 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
1543096 CATGTATTTTCA
1 CATGTATTTTCA
1543108 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:1543470 original size:155 final size:152
Alignment explanation
Indices: 1543132--1543439 Score: 487
Period size: 155 Copynumber: 2.0 Consensus size: 152
1543122 ATGGCCGAAC
*
1543132 CATGTATCTATTCGGCCTAAACCCTTTGAAAACTATAAATAGGTTTTGGCATTTCATTTGTAAAC
1 CATGTAGCTATT--GCCT-AACCCTTTGAAAACTATAAATAGGTTTTGGCATTTCATTTGTAAAC
1543197 TCATCTCATCTCTTATATAAATACTCTTGTGAGTTATTTCTCTTCAAAGTTTCTTTGTGAACTTA
63 TCATCTCATCTCTTATATAAATACTCTTGTGAGTTATTTCTCTTCAAAGTTTCTTTGTGAACTTA
1543262 TCGATTAAACAAGTATAGTTCCCAT
128 TCGATTAAACAAGTATAGTTCCCAT
*
1543287 CATGTATCTATTCGGCCTAAACCCTTTGAAAACTATAAATAGGTTTTGGCATTTCATTTGT-AAC
1 CATGTAGCTATT--GCCT-AACCCTTTGAAAACTATAAATAGGTTTTGGCATTTCATTTGTAAAC
1543351 TCATCTCATCTCTTATATAAAATATACTCTTGTGAGTTATTTCTCTTCAAAG-TTCTTTGTGAAC
63 TCATCTCATCTCTTATAT--AA-ATACTCTTGTGAGTTATTTCTCTTCAAAGTTTCTTTGTGAAC
1543415 TTTATCGATTAAAC-AGTATAGTTCC
125 -TTATCGATTAAACAAGTATAGTTCC
1543440 TATACTTGTG
Statistics
Matches: 149, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
154 21 0.14
155 61 0.41
156 25 0.17
157 42 0.28
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.41
Consensus pattern (152 bp):
CATGTAGCTATTGCCTAACCCTTTGAAAACTATAAATAGGTTTTGGCATTTCATTTGTAAACTCA
TCTCATCTCTTATATAAATACTCTTGTGAGTTATTTCTCTTCAAAGTTTCTTTGTGAACTTATCG
ATTAAACAAGTATAGTTCCCAT
Found at i:1543670 original size:22 final size:22
Alignment explanation
Indices: 1543644--1543692 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
1543634 TATCCTTTCT
1543644 TTATTT-TATATCA-TTCTTATTA
1 TTATTTCT-TATCATTTCTTA-TA
*
1543666 TTATTTCTTTTCATTTCTTATA
1 TTATTTCTTATCATTTCTTATA
1543688 TTATT
1 TTATT
1543693 ATCCCCTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTTCTTATCATTTCTTATA
Found at i:1544228 original size:74 final size:71
Alignment explanation
Indices: 1544140--1544483 Score: 227
Period size: 73 Copynumber: 4.7 Consensus size: 71
1544130 ATTTTTTTTG
* * *
1544140 TCTCACTTAAGATAGTTTTTCTTAAAACAAGTTTCGTCTCACTCGAGACAGTTTCTCTCAAAACA
1 TCTCACTTAAGATA-TTTTTCTTAAAAAAAATTTC-TCTCACTCGAGACAGTTTCTCTCGAAACA
1544205 ATAATTCTA
64 A-AATTCTA
* * * * *
1544214 TCTCACTTGAGATAGTTTTCCTCAAAAAAAAATTTCATATCACTCGAGATAGTTTCTCTCGAAAC
1 TCTCACTTAAGATA-TTTTTCT-TAAAAAAAATTTC-TCTCACTCGAGACAGTTTCTCTCGAAAC
*
1544279 AAAATTTTA
63 AAAATTCTA
* * * * * * *
1544288 TCTCACTAAAGATATTTTCTCTTGAAATAAATTTCTCCTCACTTGAGACAATCTC-CTTGAAACA
1 TCTCACTTAAGATATTTT-TCTTAAAAAAAATTTCT-CTCACTCGAGACAGTTTCTCTCGAAAC-
1544352 AAAATTGC-A
63 AAAATT-CTA
* * * ** * * * *
1544361 TCTCACTTGAGATATTTTCCCTT--GAAATTTTTATCTCACTCGAGACGGATTC-CCCTGAAACA
1 TCTCACTTAAGATATTTT-TCTTAAAAAAAATTTCTCTCACTCGAGACAGTTTCTCTC-GAAACA
1544423 AAATT-TCA
64 AAATTCT-A
* * * * *
1544431 TCTAACTTGAGATATTTTCTCTT--GAAAAATTTAGTCTCACTCGAGACATTTTC
1 TCTCACTTAAGATATTTT-TCTTAAAAAAAATTT-CTCTCACTCGAGACAGTTTC
1544484 CTACATGACT
Statistics
Matches: 215, Mismatches: 46, Indels: 21
0.76 0.16 0.07
Matches are distributed among these distances:
70 49 0.23
71 27 0.13
72 8 0.04
73 54 0.25
74 40 0.19
75 37 0.17
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (71 bp):
TCTCACTTAAGATATTTTTCTTAAAAAAAATTTCTCTCACTCGAGACAGTTTCTCTCGAAACAAA
ATTCTA
Found at i:1544265 original size:37 final size:37
Alignment explanation
Indices: 1544140--1544309 Score: 139
Period size: 37 Copynumber: 4.6 Consensus size: 37
1544130 ATTTTTTTTG
** * * * * *
1544140 TCTCACTTAAGATAGTTTTTCT-TAAAACAAGTTTCG
1 TCTCACTCGAGATAGTTTCTCTCAAAAAAAAATTTCA
* *
1544176 TCTCACTCGAGACAGTTTCTCTCAAAACAATAA-TTCTA
1 TCTCACTCGAGATAGTTTCTCTCAAAA-AAAAATTTC-A
*
1544214 TCTCACTTGAGATAGTTT-TCCTCAAAAAAAAATTTCA
1 TCTCACTCGAGATAGTTTCT-CTCAAAAAAAAATTTCA
* * * *
1544251 TATCACTCGAGATAGTTTCTCTCGAAACAAAATTTTA
1 TCTCACTCGAGATAGTTTCTCTCAAAAAAAAATTTCA
** *
1544288 TCTCACTAAAGATATTTTCTCT
1 TCTCACTCGAGATAGTTTCTCT
1544310 TGAAATAAAT
Statistics
Matches: 107, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
36 18 0.17
37 60 0.56
38 29 0.27
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.37
Consensus pattern (37 bp):
TCTCACTCGAGATAGTTTCTCTCAAAAAAAAATTTCA
Found at i:1544271 original size:75 final size:73
Alignment explanation
Indices: 1544140--1544306 Score: 210
Period size: 74 Copynumber: 2.3 Consensus size: 73
1544130 ATTTTTTTTG
* * * * * *
1544140 TCTCACTTAAGATAGTTTTTCTTAAAACAAGTTTCGTCTCACTCGAGACAGTTTCTCTCAAAACA
1 TCTCACTTAAGATAGTTTTCCTAAAAAAAAATTTCATATCACTCGAGACAGTTTCTCTCAAAACA
1544205 ATAATTCTA
66 A-AATTCTA
* * *
1544214 TCTCACTTGAGATAGTTTTCCTCAAAAAAAAATTTCATATCACTCGAGATAGTTTCTCTCGAAAC
1 TCTCACTTAAGATAGTTTTCCT-AAAAAAAAATTTCATATCACTCGAGACAGTTTCTCTCAAAAC
*
1544279 AAAATTTTA
65 AAAATTCTA
*
1544288 TCTCACTAAAGATA-TTTTC
1 TCTCACTTAAGATAGTTTTC
1544307 TCTTGAAATA
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
73 5 0.06
74 38 0.47
75 37 0.46
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (73 bp):
TCTCACTTAAGATAGTTTTCCTAAAAAAAAATTTCATATCACTCGAGACAGTTTCTCTCAAAACA
AAATTCTA
Found at i:1544439 original size:70 final size:69
Alignment explanation
Indices: 1544176--1544478 Score: 232
Period size: 73 Copynumber: 4.2 Consensus size: 69
1544166 ACAAGTTTCG
* * * * **
1544176 TCTCACTCGAGACAGTTTCTCTCAAAACAATAA-TTCTATCTCACTTGAGATAGTTTTCCTCAAA
1 TCTCACTCGAGACAATCTCCCT-GAAACAA-AATTTC-ATCTCACTTGAGATA-TTTT-CTC-TT
* *
1544240 AAAAAATTTCA
60 GAAATATTT-A
* * * * * * **
1544251 TATCACTCGAGATAGTTTCTCTCGAAACAAAATTTTATCTCACTAAAGATATTTTCTCTTGAAAT
1 TCTCACTCGAGACAATCTCCCT-GAAACAAAATTTCATCTCACTTGAGATATTTTCTCTTGAAAT
*
1544316 AAATTTC
65 --ATTTA
* * * *
1544323 TCCTCACTTGAGACAATCTCCTTGAAACAAAAATTGCATCTCACTTGAGATATTTTCCCTTGAAA
1 T-CTCACTCGAGACAATCTCCCTGAAAC-AAAATTTCATCTCACTTGAGATATTTTCTCTTGAAA
*
1544388 TTTTTA
64 TATTTA
* *
1544394 TCTCACTCGAGACGGAT-TCCCCTGAAACAAAATTTCATCTAACTTGAGATATTTTCTCTTGAAA
1 TCTCACTCGAGAC-AATCT-CCCTGAAACAAAATTTCATCTCACTTGAGATATTTTCTCTTGAAA
*
1544458 AATTTA
64 TATTTA
1544464 GTCTCACTCGAGACA
1 -TCTCACTCGAGACA
1544479 TTTTCCTACA
Statistics
Matches: 186, Mismatches: 34, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
70 49 0.26
71 30 0.16
72 9 0.05
73 54 0.29
74 15 0.08
75 29 0.16
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (69 bp):
TCTCACTCGAGACAATCTCCCTGAAACAAAATTTCATCTCACTTGAGATATTTTCTCTTGAAATA
TTTA
Found at i:1550365 original size:81 final size:81
Alignment explanation
Indices: 1550280--1550443 Score: 231
Period size: 81 Copynumber: 2.0 Consensus size: 81
1550270 CACAACTAGT
* * * *
1550280 CCATTATTCTTTTACTCAACAGTGTTTAACCATTCATCTAACTGGCATCATTGACACCTTTCTT-
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGACATAATTAACACC-TTCTTG
1550344 CCAATTGCACAGTTAGG
65 CCAATTGCACAGTTAGG
* * * **
1550361 CCATTATTGTTTTACTTAACGGTATTTAACTGTTCATCTAACTGACATAATTAACACCTTCTTGC
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGACATAATTAACACCTTCTTGC
1550426 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
1550442 CC
1 CC
1550444 TCAAAGGCAC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 5 0.07
81 68 0.93
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (81 bp):
CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGACATAATTAACACCTTCTTGC
CAATTGCACAGTTAGG
Found at i:1550505 original size:68 final size:68
Alignment explanation
Indices: 1550393--1550741 Score: 556
Period size: 68 Copynumber: 5.1 Consensus size: 68
1550383 TATTTAACTG
* * * *
1550393 TTCATCTAACTGACATAATTAACACC-TTCTTGCCAATTGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGACATAAATGACACCTTTC-TGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
1550457 GCCT
65 GCCT
* * * *
1550461 TTCATCTAACTGACATATATGACACCTTTCTGTCAAATGTACAGTTAGGCCTCAAATGCACTTAA
1 TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1550526 CCT
66 CCT
*
1550529 TTCATCTAACTGACATAAATGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1550594 CCT
66 CCT
* * *
1550597 TTCATCTAACTGGCATAAATGACACATTTCTGTTAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1550662 CCT
66 CCT
* *
1550665 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1550730 CCT
66 CCT
1550733 TTCATCTAA
1 TTCATCTAA
1550742 TTGGCATTTC
Statistics
Matches: 262, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
68 259 0.99
69 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Done.