Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 18
Found at i:2409638 original size:44 final size:45
Alignment explanation
Indices: 2409570--2409673 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 45
2409560 TGCACTACCT
* *
2409570 GTGCATCGATACACAAATCACATTCGATGTTTGAATATT-AAGGG
1 GTGCATCGATACACTAATCACATTCGATGTTTGAATATTAAAGGA
* ** ** *
2409614 GTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAGGA
1 GTGCATCGATACACTAATCACATTCGATGTTTGAATATTAAAGGA
2409659 GTGCATCGATACACT
1 GTGCATCGATACACT
2409674 TCATATGCAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 32 0.63
45 19 0.37
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (45 bp):
GTGCATCGATACACTAATCACATTCGATGTTTGAATATTAAAGGA
Found at i:2429458 original size:19 final size:19
Alignment explanation
Indices: 2429434--2429487 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
2429424 AAAAACCGAA
2429434 CCGAACCGAACCGAAAAAC
1 CCGAACCGAACCGAAAAAC
* *
2429453 CCGAACCGTTA---AAAAAT
1 CCGAACCG-AACCGAAAAAC
2429470 CCGAACCGAACCGAAAAA
1 CCGAACCGAACCGAAAAA
2429488 ACCGGTTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
19 13 0.46
20 1 0.04
ACGTcount: A:0.48, C:0.31, G:0.15, T:0.06
Consensus pattern (19 bp):
CCGAACCGAACCGAAAAAC
Found at i:2432269 original size:64 final size:63
Alignment explanation
Indices: 2432201--2432396 Score: 220
Period size: 65 Copynumber: 3.0 Consensus size: 63
2432191 CTAAGAGTGT
*
2432201 ATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTGGTGC
1 ATCGATGCATAAAATGCATTCGATGTTTCAAAATA-CCTGAGTGCATCGATGCATGGATGGTGC
* * *
2432265 ATCGATGCATTAAATGCATTCGATGTTTTCATAAA-ACTCTGAGTGCATCGATGCAT-AATATGT
1 ATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAC-CTGAGTGCATCGATGCATGGAT-GGT
2432328 GC
62 GC
* * *
2432330 ATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGATTGGT
1 ATCGATGCATAAAATGCATTCGATGTTTCAA--AATACC-TGAGTGCATCGATGCATGGA-TGGT
2432393 GC
62 GC
2432395 AT
1 AT
2432397 TGGTGCATCA
Statistics
Matches: 113, Mismatches: 9, Indels: 19
0.80 0.06 0.13
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 42 0.37
65 62 0.55
66 4 0.04
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (63 bp):
ATCGATGCATAAAATGCATTCGATGTTTCAAAATACCTGAGTGCATCGATGCATGGATGGTGC
Found at i:2432330 original size:65 final size:64
Alignment explanation
Indices: 2432177--2432356 Score: 222
Period size: 65 Copynumber: 2.8 Consensus size: 64
2432167 TTGGACCCTT
* * *
2432177 AGTGCAACGATGCACTAAGAGTGTATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTG
1 AGTGCATCGATGCA-TAATAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTG
** * *
2432241 AGTGCATCGATGCATGGCTGGTGCATCGATGCATTAAATGCATTCGATGTTTTCATAAA-A-CTC
1 AGTGCATCGATGCAT-AATAGTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-C
2432304 TG
63 TG
*
2432306 AGTGCATCGATGCATAATATGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAATA-GTGCATCGATGCATAAAATGCATTCGATGTT
2432357 CAATTTATTC
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
63 1 0.01
64 42 0.42
65 54 0.54
66 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (64 bp):
AGTGCATCGATGCATAATAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTG
Found at i:2444857 original size:21 final size:21
Alignment explanation
Indices: 2444818--2444857 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2444808 CCCCCTTTGA
*
2444818 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
* *
2444839 AGGGGAATCGATACGCCCC
1 AGGGGAACCGATACCCCCC
2444858 TAGGGTTCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.38, G:0.28, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2449468 original size:23 final size:23
Alignment explanation
Indices: 2449426--2449487 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2449416 ATAGGGCAGA
* *
2449426 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
2449448 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
2449471 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
2449488 AGGGGAATCG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 13 0.37
23 22 0.63
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:2449493 original size:19 final size:19
Alignment explanation
Indices: 2449446--2449510 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
2449436 ACCCCCTTGA
*
2449446 AGGGGAACTGATTCCCCCTTT
1 AGGGGAACCGATTCCCCC--T
2449467 GAAGGGGAACCGATTCCCCCT
1 --AGGGGAACCGATTCCCCCT
* *
2449488 AGGGGAATCGATACCCCCT
1 AGGGGAACCGATTCCCCCT
2449507 -GGGG
1 AGGGG
2449511 TTCTGGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
18 4 0.10
19 17 0.44
21 1 0.03
23 17 0.44
ACGTcount: A:0.22, C:0.29, G:0.31, T:0.18
Consensus pattern (19 bp):
AGGGGAACCGATTCCCCCT
Found at i:2451816 original size:16 final size:16
Alignment explanation
Indices: 2451795--2451827 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2451785 AAGGGAGAGT
2451795 AGTATTTTTCAAAATC
1 AGTATTTTTCAAAATC
2451811 AGTATTTTTCAAAATC
1 AGTATTTTTCAAAATC
2451827 A
1 A
2451828 AAATTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (16 bp):
AGTATTTTTCAAAATC
Found at i:2452304 original size:20 final size:20
Alignment explanation
Indices: 2452279--2452333 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2452269 TTTACACTTA
2452279 GGGAACCGATTCCCCATGAG
1 GGGAACCGATTCCCCATGAG
* *
2452299 GGGAACTGATTCCCCATTAG
1 GGGAACCGATTCCCCATGAG
*
2452319 GGGTACCGATTCCCC
1 GGGAACCGATTCCCC
2452334 CTATGCTCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (20 bp):
GGGAACCGATTCCCCATGAG
Found at i:2453880 original size:23 final size:22
Alignment explanation
Indices: 2453843--2453919 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 22
2453833 CGACGGATGC
*
2453843 ATCGATGCATATTCAAGGCATG
1 ATCGATGCACATTCAAGGCATG
* * * *
2453865 AATCGGTGCACCTTCATGGTAT-
1 -ATCGATGCACATTCAAGGCATG
*
2453887 ATCGATGCACATTCAAGGGATG
1 ATCGATGCACATTCAAGGCATG
2453909 CATCGATGCAC
1 -ATCGATGCAC
2453920 TGTTAACTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 17 0.40
23 26 0.60
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (22 bp):
ATCGATGCACATTCAAGGCATG
Found at i:2459711 original size:45 final size:46
Alignment explanation
Indices: 2459645--2459752 Score: 159
Period size: 45 Copynumber: 2.4 Consensus size: 46
2459635 GGTGCACTAA
2459645 GAGTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGC-TT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-A-CTTT
*
2459690 GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTTT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACTTT
*
2459736 GAGTGCATCAATGCATA
1 GAGTGCATCGATGCATA
2459753 GTATGTGCAT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 31 0.54
46 23 0.40
47 3 0.05
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACTTT
Found at i:2469616 original size:14 final size:14
Alignment explanation
Indices: 2469599--2469625 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2469589 GAGAGAATGG
2469599 GAGAGAGAAAAGTA
1 GAGAGAGAAAAGTA
2469613 GAGAGAGAAAAGT
1 GAGAGAGAAAAGT
2469626 TAAAAGGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (14 bp):
GAGAGAGAAAAGTA
Found at i:2479183 original size:7 final size:7
Alignment explanation
Indices: 2479171--2479203 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
2479161 TTATATTAAA
2479171 TAATTTT
1 TAATTTT
2479178 TAATTTT
1 TAATTTT
2479185 TAATTTT
1 TAATTTT
2479192 TAATTTT
1 TAATTTT
2479199 TAATT
1 TAATT
2479204 AGACAAGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TAATTTT
Found at i:2481092 original size:24 final size:24
Alignment explanation
Indices: 2481053--2481159 Score: 115
Period size: 24 Copynumber: 4.5 Consensus size: 24
2481043 AAATAGAGAT
* * *
2481053 ATCAGAAATTAAAACAGAATTCAT
1 ATCAGAAATCATAACAGAATTCAG
* * * *
2481077 ATCATATATCATAACATAATCCAG
1 ATCAGAAATCATAACAGAATTCAG
*
2481101 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
* *
2481125 ATCAGAAATCATAACCGAATTCAA
1 ATCAGAAATCATAACAGAATTCAG
*
2481149 ATCGGAAATCA
1 ATCAGAAATCA
2481160 GATAAAACAT
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.50, C:0.18, G:0.10, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATTCAG
Found at i:2481113 original size:12 final size:12
Alignment explanation
Indices: 2481098--2481135 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2481088 TAACATAATC
2481098 CAGATCAGAAAT
1 CAGATCAGAAAT
* *
2481110 CAGAACAGAATT
1 CAGATCAGAAAT
2481122 CAGATCAGAAAT
1 CAGATCAGAAAT
2481134 CA
1 CA
2481136 TAACCGAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.16, T:0.16
Consensus pattern (12 bp):
CAGATCAGAAAT
Found at i:2481157 original size:48 final size:48
Alignment explanation
Indices: 2481053--2481161 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
2481043 AAATAGAGAT
* * * * * * *
2481053 ATCAGAAATTAAAACAGAATTCATATCATATATCATAACATAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGAAATCATAACAGAATCCAA
* *
2481101 ATCAGAAATCAGAACAGAATTCAGATCAGAAATCATAACCGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGAAATCATAACAGAATCCAA
*
2481149 ATCGGAAATCAGA
1 ATCAGAAATCAGA
2481162 TAAAACATTC
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGAAATCATAACAGAATCCAA
Found at i:2485245 original size:24 final size:24
Alignment explanation
Indices: 2485218--2485283 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
2485208 ATAAGCGAAG
* *
2485218 ATATCATAAATCAAAATAGAATTC
1 ATATCATAAATCAAAACAGAATCC
* *
2485242 ATATCATATATCAGAACAGAATCC
1 ATATCATAAATCAAAACAGAATCC
* *
2485266 ATATCAGAAATCAGAACA
1 ATATCATAAATCAAAACA
2485284 AAATTCAGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.52, C:0.17, G:0.08, T:0.24
Consensus pattern (24 bp):
ATATCATAAATCAAAACAGAATCC
Found at i:2485298 original size:24 final size:24
Alignment explanation
Indices: 2485237--2485328 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 24
2485227 ATCAAAATAG
* * * *
2485237 AATTCATATCATATATCAGAACAG
1 AATTCAGATCAGAAATCAGAACAA
* *
2485261 AATCCATATCAGAAATCAGAACAA
1 AATTCAGATCAGAAATCAGAACAA
* * *
2485285 AATTCAGATTAGAAATTAGAACAT
1 AATTCAGATCAGAAATCAGAACAA
*
2485309 AATTCAAATC-GAAAGTCAGA
1 AATTCAGATCAGAAA-TCAGA
2485329 TAAAACATTA
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 4 0.07
24 51 0.93
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (24 bp):
AATTCAGATCAGAAATCAGAACAA
Found at i:2489390 original size:236 final size:237
Alignment explanation
Indices: 2488970--2489419 Score: 812
Period size: 236 Copynumber: 1.9 Consensus size: 237
2488960 AGGACATTAT
* *
2488970 AAACATGTAATAAATAAATGGGTAAATTATTTAAATGATCACTTAATTATAGAATTAGTGTCGAT
1 AAACAAGTAATAAATAAATGGGTAAACTATTTAAATGATCACTTAATTATAGAATTAGTGTCGAT
*
2489035 ATGACTATTATTTTTAAAATTTCGTTAATATGACCACTTAACTATTTAATTAGTTTCAATATATT
66 ATGACTATTATTTTTAAAATTTCGTTAATATAACCACTTAACTATTTAATTAGTTTCAATATATT
*
2489100 CACATAACATTAAAATTTAATAGAAGTGCTTACATGATAATTAATAAAATTAATATAATTACATA
131 CACATAACATTAAAATTTAATAGAAGTACTTACATGATAATTAATAAAATTAATATAATTACATA
2489165 TGATAACCACCACCACCACCACCACCACTACTACGTCGGCGC
196 TGATAACCACCACCACCACCACCACCACTACTACGTCGGCGC
* * * *
2489207 AAACAAGTAATAAATGAATGGGTAAACTATTTGAATGATCACTTAATTATAGAGTTGGTGTCGAT
1 AAACAAGTAATAAATAAATGGGTAAACTATTTAAATGATCACTTAATTATAGAATTAGTGTCGAT
2489272 ATGACTATTATTTTTAAAATTTCGTTAATATAACCAC-TAACTATTTAATTAGTTTCAATATATT
66 ATGACTATTATTTTTAAAATTTCGTTAATATAACCACTTAACTATTTAATTAGTTTCAATATATT
*
2489336 CACATAACATTAAAATTTAATAGATGTACTTACATGATAATTAATAAAATTAATATAATTACATA
131 CACATAACATTAAAATTTAATAGAAGTACTTACATGATAATTAATAAAATTAATATAATTACATA
2489401 TGATAACCACCACCACCAC
196 TGATAACCACCACCACCAC
2489420 GACGTCGGCG
Statistics
Matches: 204, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
236 109 0.53
237 95 0.47
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (237 bp):
AAACAAGTAATAAATAAATGGGTAAACTATTTAAATGATCACTTAATTATAGAATTAGTGTCGAT
ATGACTATTATTTTTAAAATTTCGTTAATATAACCACTTAACTATTTAATTAGTTTCAATATATT
CACATAACATTAAAATTTAATAGAAGTACTTACATGATAATTAATAAAATTAATATAATTACATA
TGATAACCACCACCACCACCACCACCACTACTACGTCGGCGC
Found at i:2495765 original size:4 final size:4
Alignment explanation
Indices: 2495756--2495784 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2495746 TAAGCAATCT
2495756 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
2495785 TGTTTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:2496145 original size:13 final size:13
Alignment explanation
Indices: 2496127--2496151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2496117 GTGGGAGTTA
2496127 AGGAGAGTAGCGG
1 AGGAGAGTAGCGG
2496140 AGGAGAGTAGCG
1 AGGAGAGTAGCG
2496152 AATTGGAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.52, T:0.08
Consensus pattern (13 bp):
AGGAGAGTAGCGG
Found at i:2499397 original size:2 final size:2
Alignment explanation
Indices: 2499390--2499414 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2499380 GAATGTTATT
2499390 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2499415 ATTTTGGCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2510403 original size:21 final size:21
Alignment explanation
Indices: 2510374--2510414 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2510364 AAGGGAGAAG
*
2510374 AAAATGATAGAAAGTAAAAGT
1 AAAAAGATAGAAAGTAAAAGT
*
2510395 AAAAAGATAGAAAGTGAAAG
1 AAAAAGATAGAAAGTAAAAG
2510415 GTGAAAACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (21 bp):
AAAAAGATAGAAAGTAAAAGT
Found at i:2516570 original size:19 final size:19
Alignment explanation
Indices: 2516538--2516586 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
2516528 TGGTATGTAC
2516538 AAATGAGAATGCTG-TG-GCA
1 AAATG-GAATGCTGATGTG-A
2516557 AAATGGAATAGCTGATGTGA
1 AAATGGAAT-GCTGATGTGA
2516577 AAATGGAATG
1 AAATGGAATG
2516587 ATGGTAGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 4 0.15
19 10 0.37
20 12 0.44
21 1 0.04
ACGTcount: A:0.41, C:0.06, G:0.31, T:0.22
Consensus pattern (19 bp):
AAATGGAATGCTGATGTGA
Found at i:2520036 original size:43 final size:43
Alignment explanation
Indices: 2519949--2520060 Score: 125
Period size: 43 Copynumber: 2.6 Consensus size: 43
2519939 TTTGTCTTAT
* * * ** *
2519949 AAACGCCGCAATATGTTTTGATATTTAGCGGTATTTTTGGCAC
1 AAACGCCGCAATAAGTGTTGAGATTTAGCAATATTTTTAGCAC
* * *
2519992 AAACACCGCAATAGGTGTTGAGATTTAGCAATATTTTTATCAC
1 AAACGCCGCAATAAGTGTTGAGATTTAGCAATATTTTTAGCAC
* *
2520035 AAATGCCGCTATAAGTGTTGAGATTT
1 AAACGCCGCAATAAGTGTTGAGATTT
2520061 TACGGAGTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (43 bp):
AAACGCCGCAATAAGTGTTGAGATTTAGCAATATTTTTAGCAC
Found at i:2520114 original size:42 final size:43
Alignment explanation
Indices: 2520000--2520116 Score: 123
Period size: 42 Copynumber: 2.7 Consensus size: 43
2519990 ACAAACACCG
* * *
2520000 CAATAGGTGTTGAGATTTAGCAATATTTTTATCACAAATGCCG
1 CAATAGGTGTTGAGATTTCGCAGTATTTTTATCACAAATGCCA
* * * **
2520043 CTATAAGTGTTGAGATTTTACGGAGT-TTTTT-GGA-AAATGCCA
1 CAATAGGTGTTGAGA-TTT-CGCAGTATTTTTATCACAAATGCCA
2520085 CAATAGGTGTTGAGATTTCGCAGTATTTTTAT
1 CAATAGGTGTTGAGATTTCGCAGTATTTTTAT
2520117 GATATAAACG
Statistics
Matches: 58, Mismatches: 12, Indels: 9
0.73 0.15 0.11
Matches are distributed among these distances:
40 5 0.09
41 8 0.14
42 20 0.34
43 14 0.24
44 8 0.14
45 3 0.05
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.38
Consensus pattern (43 bp):
CAATAGGTGTTGAGATTTCGCAGTATTTTTATCACAAATGCCA
Found at i:2520189 original size:43 final size:44
Alignment explanation
Indices: 2520110--2520289 Score: 200
Period size: 44 Copynumber: 4.1 Consensus size: 44
2520100 TTTCGCAGTA
* * * * *
2520110 TTTTTATGATATAAACGCTGCTAAAGGTATGTTATATAGTAGTG
1 TTTTTAGGATACAAACGCTGCTAAAGGTATGGTATATAGCAGCG
* * * *
2520154 TTTTTAGGATAAAAACGC-ACTAAAGGTATGATATATAGCGGCG
1 TTTTTAGGATACAAACGCTGCTAAAGGTATGGTATATAGCAGCG
* * * *
2520197 TTTTTAGGATACAAGCGCCGCTAAAGGTTTGGTATATAGCAGCA
1 TTTTTAGGATACAAACGCTGCTAAAGGTATGGTATATAGCAGCG
* * * *
2520241 TTTTTAGGATACAAACACTGCTAAAGGTCTGGTATATAGCGGCA
1 TTTTTAGGATACAAACGCTGCTAAAGGTATGGTATATAGCAGCG
2520285 TTTTT
1 TTTTT
2520290 TTACAAACGC
Statistics
Matches: 116, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
43 36 0.31
44 80 0.69
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (44 bp):
TTTTTAGGATACAAACGCTGCTAAAGGTATGGTATATAGCAGCG
Found at i:2520234 original size:44 final size:44
Alignment explanation
Indices: 2520104--2520306 Score: 198
Period size: 44 Copynumber: 4.7 Consensus size: 44
2520094 TTGAGATTTC
* * * * *
2520104 GCAGTATTTTTATGATATAAACGCTGCTAAAGGTATGTTATATA
1 GCAGCATTTTTAGGATACAAACGCCGCTAAAGGTATGGTATATA
* ** * * *
2520148 GTAGTGTTTTTAGGATAAAAACG-CACTAAAGGTATGATATATA
1 GCAGCATTTTTAGGATACAAACGCCGCTAAAGGTATGGTATATA
* * * *
2520191 GCGGCGTTTTTAGGATACAAGCGCCGCTAAAGGTTTGGTATATA
1 GCAGCATTTTTAGGATACAAACGCCGCTAAAGGTATGGTATATA
* * *
2520235 GCAGCATTTTTAGGATACAAACACTGCTAAAGGTCTGGTATATA
1 GCAGCATTTTTAGGATACAAACGCCGCTAAAGGTATGGTATATA
* *
2520279 GCGGCATTTTT---TTACAAACGCCGCTAAA
1 GCAGCATTTTTAGGATACAAACGCCGCTAAA
2520307 TAACACAGAA
Statistics
Matches: 133, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
41 14 0.11
43 35 0.26
44 84 0.63
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.32
Consensus pattern (44 bp):
GCAGCATTTTTAGGATACAAACGCCGCTAAAGGTATGGTATATA
Found at i:2527585 original size:76 final size:76
Alignment explanation
Indices: 2527459--2527600 Score: 266
Period size: 76 Copynumber: 1.9 Consensus size: 76
2527449 CTGCAAGGCG
* *
2527459 TCAATGGTGGCCACTGCAAGGCGGAGTTGCTGAAATGGATACTGAAAGGGGAATCAGAATGCTTG
1 TCAATGGTGGCCACTGCAAGGCGGAGTTGCTGAAATGGATACTGAAAGGGGAACCAGAACGCTTG
2527524 GACCGACGGCA
66 GACCGACGGCA
2527535 TCAATGGTGGCCACTGCAAGGCGGAGTTGCTGAAATGGATACTGAAAGGGGAACCAGAACGCTTG
1 TCAATGGTGGCCACTGCAAGGCGGAGTTGCTGAAATGGATACTGAAAGGGGAACCAGAACGCTTG
2527600 G
66 G
2527601 CTGAACGATG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.29, C:0.18, G:0.35, T:0.18
Consensus pattern (76 bp):
TCAATGGTGGCCACTGCAAGGCGGAGTTGCTGAAATGGATACTGAAAGGGGAACCAGAACGCTTG
GACCGACGGCA
Found at i:2527813 original size:42 final size:43
Alignment explanation
Indices: 2527767--2527930 Score: 117
Period size: 43 Copynumber: 3.9 Consensus size: 43
2527757 GCGTTTATAT
*
2527767 AAAAACGCCGCAAAATAGTA-A-CATATTGCGGCATTTGTTACA
1 AAAAACGCCACAAAATAGTATATC-TATTGCGGCATTTGTTACA
* *
2527809 AAAAATGCCACAAAATATTATATCTATTGCGGCATTTG-T--A
1 AAAAACGCCACAAAATAGTATATCTATTGCGGCATTTGTTACA
* * * * * * * *
2527849 TAAAACGCCA-ATACT-GGACAACTATATTGCGGCATTTGCTGCA
1 AAAAACGCCACAAAATAGTA-TA-TCTATTGCGGCATTTGTTACA
* * * *
2527892 AAAAACACCACAAAATATTATATCTATTGTGGCGTTTGT
1 AAAAACGCCACAAAATAGTATATCTATTGCGGCATTTGT
2527931 ATAAAACGCC
Statistics
Matches: 91, Mismatches: 22, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
38 1 0.01
39 4 0.04
40 24 0.26
41 1 0.01
42 18 0.20
43 37 0.41
44 5 0.05
45 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (43 bp):
AAAAACGCCACAAAATAGTATATCTATTGCGGCATTTGTTACA
Found at i:2527835 original size:83 final size:84
Alignment explanation
Indices: 2527748--2527940 Score: 241
Period size: 83 Copynumber: 2.3 Consensus size: 84
2527738 ATTGCCCTAC
* * * *
2527748 TCTATAGCGGCGTTTATATAAAAACGCCGCAA-AATAG-TAAC-ATATTGCGGCATTTGTTACAA
1 TCTATTGCGGCGTTTGTAT-AAAACGCC-CAATAATAGACAACTATATTGCGGCATTTGCTACAA
**
2527810 AAAATGCCACAAAATATTATA
64 AAAACACCACAAAATATTATA
* * * *
2527831 TCTATTGCGGCATTTGTATAAAACG-CCAATACTGGACAACTATATTGCGGCATTTGCTGCAAAA
1 TCTATTGCGGCGTTTGTATAAAACGCCCAATAATAGACAACTATATTGCGGCATTTGCTACAAAA
2527895 AACACCACAAAATATTATA
66 AACACCACAAAATATTATA
*
2527914 TCTATTGTGGCGTTTGTATAAAACGCC
1 TCTATTGCGGCGTTTGTATAAAACGCC
2527941 ACTACTGGAC
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
80 3 0.03
81 4 0.04
82 9 0.10
83 77 0.82
84 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (84 bp):
TCTATTGCGGCGTTTGTATAAAACGCCCAATAATAGACAACTATATTGCGGCATTTGCTACAAAA
AACACCACAAAATATTATA
Found at i:2527941 original size:83 final size:83
Alignment explanation
Indices: 2527789--2527956 Score: 273
Period size: 83 Copynumber: 2.0 Consensus size: 83
2527779 AAATAGTAAC
* **
2527789 ATATTGCGGCATTTGTTACAAAAAATGCCACAAAATATTATATCTATTGCGGCATTTGTATAAAA
1 ATATTGCGGCATTTGCTACAAAAAACACCACAAAATATTATATCTATTGCGGCATTTGTATAAAA
2527854 CGCCAATACTGGACAACT
66 CGCCAATACTGGACAACT
* * *
2527872 ATATTGCGGCATTTGCTGCAAAAAACACCACAAAATATTATATCTATTGTGGCGTTTGTATAAAA
1 ATATTGCGGCATTTGCTACAAAAAACACCACAAAATATTATATCTATTGCGGCATTTGTATAAAA
*
2527937 CGCCACTACTGGACAACT
66 CGCCAATACTGGACAACT
2527955 AT
1 AT
2527957 CTAGCGGCGT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (83 bp):
ATATTGCGGCATTTGCTACAAAAAACACCACAAAATATTATATCTATTGCGGCATTTGTATAAAA
CGCCAATACTGGACAACT
Found at i:2528165 original size:41 final size:41
Alignment explanation
Indices: 2528045--2528166 Score: 119
Period size: 41 Copynumber: 3.0 Consensus size: 41
2528035 ATTGTAGCTT
* ** *
2528045 TTGCGGCGTTTGTAT-ATAAACGCCACTACTGTAC-AA-ATA
1 TTGCGGCGTTTGTATGA-AAATGCCACTAAAGTACTAATCTA
* * *
2528084 TAGCGGCGTTTGT-TGAAAAATGCCACTATA-TATTATATCTA
1 TTGCGGCGTTTGTATG-AAAATGCCACTAAAGTACTA-ATCTA
2528125 TTGCGGCGTTTGTATGAAAATGCCACTAAAGTACTAATCTA
1 TTGCGGCGTTTGTATGAAAATGCCACTAAAGTACTAATCTA
2528166 T
1 T
2528167 ATCTACGTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
38 3 0.04
39 23 0.34
40 2 0.03
41 33 0.49
42 6 0.09
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (41 bp):
TTGCGGCGTTTGTATGAAAATGCCACTAAAGTACTAATCTA
Found at i:2529263 original size:22 final size:23
Alignment explanation
Indices: 2529232--2529279 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
2529222 TCAAGTTTTC
2529232 AAAAGCTATTA-TTTTCCTATTCG
1 AAAAGCTATTACTTTT-CTATTCG
2529255 AAAA-CTATTACTTTTCTATTCG
1 AAAAGCTATTACTTTTCTATTCG
2529277 AAA
1 AAA
2529280 GCAGAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (23 bp):
AAAAGCTATTACTTTTCTATTCG
Found at i:2530273 original size:15 final size:15
Alignment explanation
Indices: 2530253--2530286 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2530243 TTCAACCCCA
2530253 TTTTATTTTATTCAT
1 TTTTATTTTATTCAT
2530268 TTTTATTTTATTCAT
1 TTTTATTTTATTCAT
2530283 TTTT
1 TTTT
2530287 TTCCTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTTTATTCAT
Found at i:2542157 original size:20 final size:20
Alignment explanation
Indices: 2542132--2542170 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2542122 CGAATTTTAT
*
2542132 GAAATTTGGTGATCAAAGTA
1 GAAATTTGGTAATCAAAGTA
2542152 GAAATTTGGTAATCAAAGT
1 GAAATTTGGTAATCAAAGT
2542171 GGGGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (20 bp):
GAAATTTGGTAATCAAAGTA
Found at i:2546290 original size:20 final size:20
Alignment explanation
Indices: 2546265--2546314 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2546255 TTACCTCTAG
2546265 ATTGAGATGTAGAAAGTAAA
1 ATTGAGATGTAGAAAGTAAA
2546285 ATTGAGATGTAGAAAGTAAA
1 ATTGAGATGTAGAAAGTAAA
*
2546305 ATAGAGATGT
1 ATTGAGATGT
2546315 TTCCCGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (20 bp):
ATTGAGATGTAGAAAGTAAA
Found at i:2550955 original size:22 final size:22
Alignment explanation
Indices: 2550930--2550975 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2550920 ACTGATTATT
*
2550930 ATATATATGATTTTTATCATGA
1 ATATATATGATGTTTATCATGA
*
2550952 ATATATATGATGTTTATTATGA
1 ATATATATGATGTTTATCATGA
2550974 AT
1 AT
2550976 GTTACTTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (22 bp):
ATATATATGATGTTTATCATGA
Found at i:2554224 original size:19 final size:19
Alignment explanation
Indices: 2554202--2554238 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2554192 ATAAATCCTA
2554202 AATAA-AATTAAAATAACTT
1 AATAATAATT-AAATAACTT
2554221 AATAATAATTAAATAACT
1 AATAATAATTAAATAACT
2554239 AAACAGTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAATAATTAAATAACTT
Found at i:2558505 original size:2 final size:2
Alignment explanation
Indices: 2558498--2558551 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2558488 GAACCAAAAC
2558498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2558540 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2558552 CATCATCATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2558738 original size:23 final size:23
Alignment explanation
Indices: 2558711--2558783 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
2558701 CACCAAAGTG
*
2558711 CCACATAGAAATGTCTCGAATGA
1 CCACATAGAAATGTCTCGAAAGA
* *
2558734 CCACATAGATATGTCCCGAAAGA
1 CCACATAGAAATGTCTCGAAAGA
* *
2558757 CCGCATAAAAATGTCTCGAAAGA
1 CCACATAGAAATGTCTCGAAAGA
2558780 CCAC
1 CCAC
2558784 GTAAAATTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (23 bp):
CCACATAGAAATGTCTCGAAAGA
Found at i:2558788 original size:23 final size:23
Alignment explanation
Indices: 2558711--2558794 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
2558701 CACCAAAGTG
* *
2558711 CCACATAGAAATGTCTCGAATGA
1 CCACATAAAAATGTCTCGAAAGA
* * *
2558734 CCACATAGATATGTCCCGAAAGA
1 CCACATAAAAATGTCTCGAAAGA
*
2558757 CCGCATAAAAATGTCTCGAAAGA
1 CCACATAAAAATGTCTCGAAAGA
* *
2558780 CCACGTAAAATTGTC
1 CCACATAAAAATGTC
2558795 CTTCAGGACC
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (23 bp):
CCACATAAAAATGTCTCGAAAGA
Found at i:2558908 original size:14 final size:15
Alignment explanation
Indices: 2558889--2558952 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 15
2558879 TTATATCATT
2558889 TCACATAG-CTTATA
1 TCACATAGACTTATA
* **
2558903 TCACATTGACAAATAA
1 TCACATAGACTTAT-A
*
2558919 TCACATAGAC-TATG
1 TCACATAGACTTATA
*
2558933 TCACAT-GGCTTATA
1 TCACATAGACTTATA
2558947 TCACAT
1 TCACAT
2558953 TTTCATATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
13 2 0.05
14 22 0.56
15 5 0.13
16 10 0.26
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (15 bp):
TCACATAGACTTATA
Found at i:2558963 original size:44 final size:44
Alignment explanation
Indices: 2558889--2559030 Score: 153
Period size: 44 Copynumber: 3.2 Consensus size: 44
2558879 TTATATCATT
**
2558889 TCACATAGCTTATATCACATTGACAAATAATCACATAGACTATG
1 TCACATAGCTTATATCACATTTTCAAATAATCACATAGACTATG
* * * * * *
2558933 TCACATGGCTTATATCACATTTTCATATAATCACGTAGTTCAATA
1 TCACATAGCTTATATCACATTTTCAAATAATCACATAG-ACTATG
* *
2558978 TCACATAG-TATATATCACATTTTCACATAATCCCATAGA-TCATG
1 TCACATAGCT-TATATCACATTTTCAAATAATCACATAGACT-ATG
2559022 TCACATAGC
1 TCACATAGC
2559031 ATGAAATATA
Statistics
Matches: 79, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
44 44 0.56
45 35 0.44
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (44 bp):
TCACATAGCTTATATCACATTTTCAAATAATCACATAGACTATG
Found at i:2562000 original size:15 final size:15
Alignment explanation
Indices: 2561980--2562008 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2561970 AAAAGCTGAG
2561980 AATATCTTCCGACTT
1 AATATCTTCCGACTT
2561995 AATATCTTCCGACT
1 AATATCTTCCGACT
2562009 CAGAGCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.38
Consensus pattern (15 bp):
AATATCTTCCGACTT
Found at i:2565684 original size:23 final size:23
Alignment explanation
Indices: 2565595--2565684 Score: 85
Period size: 23 Copynumber: 3.9 Consensus size: 23
2565585 TACCAGAGTG
2565595 CCACATAGAAATATCCCGAATG-A
1 CCACATAGAAATATCCCGAA-GAA
* *
2565618 CCATATAGATATATCCCGAAAGAA
1 CCACATAGAAATATCCCG-AAGAA
* * *
2565642 -CGCGTAAAAATATCCCGAAGAA
1 CCACATAGAAATATCCCGAAGAA
* *
2565664 CCACGTAGAATTATCCCGAAG
1 CCACATAGAAATATCCCGAAG
2565685 GATTGCGTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
22 5 0.09
23 46 0.85
24 3 0.06
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (23 bp):
CCACATAGAAATATCCCGAAGAA
Found at i:2569293 original size:23 final size:23
Alignment explanation
Indices: 2569259--2569314 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
2569249 ACGCAATCTA
* *
2569259 CGGGACAATTCTACGTGGTCCTT
1 CGGGACATTTCTACGCGGTCCTT
*
2569282 TGGGACATTTCTACGCGGTCCTT
1 CGGGACATTTCTACGCGGTCCTT
2569305 CGGGACATTT
1 CGGGACATTT
2569315 TTACAATGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (23 bp):
CGGGACATTTCTACGCGGTCCTT
Found at i:2569400 original size:24 final size:24
Alignment explanation
Indices: 2569349--2569394 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2569339 TATGTGGTCA
*
2569349 TTCGGTGCATATTCTACGCGGTAC
1 TTCGGTGCATATTCTACGCGGCAC
*
2569373 TTCGGTGCA-ATTCTATGCGGCA
1 TTCGGTGCATATTCTACGCGGCA
2569395 GTTTCGACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (24 bp):
TTCGGTGCATATTCTACGCGGCAC
Found at i:2569985 original size:17 final size:18
Alignment explanation
Indices: 2569963--2570004 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
2569953 TACAATATAT
*
2569963 AATATATTG-TTTTTTAA
1 AATATATTGATTTTTGAA
2569980 AATATA-TGATTTTTGAA
1 AATATATTGATTTTTGAA
2569997 AATATATT
1 AATATATT
2570005 ATATAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 19 0.86
18 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
AATATATTGATTTTTGAA
Found at i:2570110 original size:20 final size:22
Alignment explanation
Indices: 2570063--2570116 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
2570053 AAAAACATAT
2570063 ATAATA-TATATAATTTTTGAA
1 ATAATATTATATAATTTTTGAA
* *
2570084 ATCATATTATATAGTTTTT-AA
1 ATAATATTATATAATTTTTGAA
*
2570105 A-AATATAATATA
1 ATAATATTATATA
2570117 TGTTATATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 9 0.32
21 8 0.29
22 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
ATAATATTATATAATTTTTGAA
Found at i:2570122 original size:29 final size:27
Alignment explanation
Indices: 2570090--2570143 Score: 90
Period size: 29 Copynumber: 1.9 Consensus size: 27
2570080 TGAAATCATA
2570090 TTATATAGTTTTTAAAAATATAATATATG
1 TTATATAGTTTTT-AAAATA-AATATATG
2570119 TTATATAGTTTTTAAAATAAATATA
1 TTATATAGTTTTTAAAATAAATATA
2570144 GTGTACGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 6 0.24
28 6 0.24
29 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (27 bp):
TTATATAGTTTTTAAAATAAATATATG
Found at i:2570169 original size:10 final size:10
Alignment explanation
Indices: 2570154--2570430 Score: 228
Period size: 8 Copynumber: 32.1 Consensus size: 10
2570144 GTGTACGTAT
2570154 TATATATATA
1 TATATATATA
2570164 TATATATATA
1 TATATATATA
2570174 TATATATATA
1 TATATATATA
*
2570184 TATAT-TATT
1 TATATATATA
2570193 TATA-ATAT-
1 TATATATATA
2570201 TATAT-TATA
1 TATATATATA
2570210 T-TATAT-TA
1 TATATATATA
2570218 TAT-TATAT-
1 TATATATATA
2570226 TATAT-TATA
1 TATATATATA
2570235 T-TATAT-TA
1 TATATATATA
2570243 TAT-TATAT-
1 TATATATATA
2570251 TATAT-TATA
1 TATATATATA
2570260 T-TATAT-TA
1 TATATATATA
2570268 TAT-TATAT-
1 TATATATATA
2570276 TATAT-TATA
1 TATATATATA
2570285 T-TATAT-TA
1 TATATATATA
2570293 TAT-TATAT-
1 TATATATATA
2570301 TATAT-TATA
1 TATATATATA
2570310 T-TATAT-TA
1 TATATATATA
2570318 TAT-TATAT-
1 TATATATATA
2570326 TATAT-TATA
1 TATATATATA
2570335 T-TATATATA
1 TATATATATA
2570344 T-TATATATA
1 TATATATATA
2570353 T-TATAT-TA
1 TATATATATA
*
2570361 TAT-TATATT
1 TATATATATA
2570370 TATATATATA
1 TATATATATA
2570380 T-TATAT-TA
1 TATATATATA
2570388 TAT-TATAT-
1 TATATATATA
2570396 TATAT-TATA
1 TATATATATA
2570405 T-TATAT-TA
1 TATATATATA
2570413 TAT-TATAT-
1 TATATATATA
2570421 TATAT-TATA
1 TATATATATA
2570430 T
1 T
2570431 TATTATTATT
Statistics
Matches: 223, Mismatches: 3, Indels: 83
0.72 0.01 0.27
Matches are distributed among these distances:
8 118 0.53
9 74 0.33
10 31 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TATATATATA
Found at i:2570177 original size:20 final size:20
Alignment explanation
Indices: 2570154--2570430 Score: 228
Period size: 17 Copynumber: 16.1 Consensus size: 20
2570144 GTGTACGTAT
2570154 TATATATATATATATATATA
1 TATATATATATATATATATA
*
2570174 TATATATATATATAT-TATT
1 TATATATATATATATATATA
2570193 TATA-ATAT-TATAT-TATA
1 TATATATATATATATATATA
2570210 T-TATAT-TATAT-TATAT-
1 TATATATATATATATATATA
2570226 TATAT-TATAT-TATAT-TA
1 TATATATATATATATATATA
2570243 TAT-TATAT-TATAT-TATA
1 TATATATATATATATATATA
2570260 T-TATAT-TATAT-TATAT-
1 TATATATATATATATATATA
2570276 TATAT-TATAT-TATAT-TA
1 TATATATATATATATATATA
2570293 TAT-TATAT-TATAT-TATA
1 TATATATATATATATATATA
2570310 T-TATAT-TATAT-TATAT-
1 TATATATATATATATATATA
2570326 TATAT-TATAT-TATATATA
1 TATATATATATATATATATA
2570344 T-TATATATAT-TATAT-TA
1 TATATATATATATATATATA
*
2570361 TAT-TATATTTATATATATA
1 TATATATATATATATATATA
2570380 T-TATAT-TATAT-TATAT-
1 TATATATATATATATATATA
2570396 TATAT-TATAT-TATAT-TA
1 TATATATATATATATATATA
2570413 TAT-TATAT-TATAT-TATA
1 TATATATATATATATATATA
2570430 T
1 T
2570431 TATTATTATT
Statistics
Matches: 214, Mismatches: 4, Indels: 81
0.72 0.01 0.27
Matches are distributed among these distances:
16 34 0.16
17 126 0.59
18 26 0.12
19 13 0.06
20 15 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATATATATATATATATATA
Found at i:2570207 original size:5 final size:5
Alignment explanation
Indices: 2570151--2570454 Score: 476
Period size: 5 Copynumber: 60.2 Consensus size: 5
2570141 ATAGTGTACG
2570151 TATTA TATATA TATATA TATATA TATATA TATATA TATTA T-TTA TA--A
1 TATTA TAT-TA TAT-TA TAT-TA TAT-TA TAT-TA TATTA TATTA TATTA
2570198 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
2570248 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
2570298 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-TA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
2570347 TA-TA TATTA TATTA TATTA TATTTA TATATA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TA-TTA TAT-TA TATTA TATTA TATTA TATTA
*
2570398 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TTATTA T-TAA TATTAA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA -TATTA TATTA TATT-A
2570449 TATTA T
1 TATTA T
2570455 TTTTCGGTTT
Statistics
Matches: 286, Mismatches: 2, Indels: 22
0.92 0.01 0.07
Matches are distributed among these distances:
3 3 0.01
4 15 0.05
5 219 0.77
6 49 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:2574328 original size:36 final size:35
Alignment explanation
Indices: 2574279--2574420 Score: 158
Period size: 36 Copynumber: 4.0 Consensus size: 35
2574269 TGAATAAGAA
*
2574279 GAACGAAATGAAGCATCTACACTTTCGATTCAAGTC
1 GAACGAAAGGAAGCATC-ACACTTTCGATTCAAGTC
*
2574315 GAACGAAAGGAAGCATCAGCACTTTCGATTCAATTC
1 GAACGAAAGGAAGCATCA-CACTTTCGATTCAAGTC
* * ** * *
2574351 AAAAGGGAGGAAGTATCGTCACTTTCGATTCAAGTC
1 GAACGAAAGGAAGCATC-ACACTTTCGATTCAAGTC
* * *
2574387 GAATGGAAGGAGGCATCACACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCACACTTTCGATTCAAGT
2574421 GTTCATCTTT
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
35 17 0.19
36 72 0.81
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCACACTTTCGATTCAAGTC
Found at i:2575740 original size:25 final size:25
Alignment explanation
Indices: 2575712--2575873 Score: 249
Period size: 25 Copynumber: 6.6 Consensus size: 25
2575702 CAATGTTCCA
2575712 CGTAGAATATGCACACAAAGTGCCT
1 CGTAGAATATGCACACAAAGTGCCT
2575737 CGTAGAATATGCACACAAAGTGCCT
1 CGTAGAATATGCACACAAAGTGCCT
*
2575762 CATAGAATATGCACACAAAGTGCCT
1 CGTAGAATATGCACACAAAGTGCCT
* *
2575787 CGTAGAAT-TACACACAAAGTGTCT
1 CGTAGAATATGCACACAAAGTGCCT
* * *
2575811 CGTAGAAT-TTCTCACAAAATGCCT
1 CGTAGAATATGCACACAAAGTGCCT
2575835 CGTAGAATATGCACACAAAGTGCCT
1 CGTAGAATATGCACACAAAGTGCCT
2575860 CGTAGAAT-TGCACA
1 CGTAGAATATGCACA
2575874 AATAATACTC
Statistics
Matches: 125, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
24 48 0.38
25 77 0.62
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (25 bp):
CGTAGAATATGCACACAAAGTGCCT
Found at i:2575845 original size:73 final size:74
Alignment explanation
Indices: 2575712--2575873 Score: 254
Period size: 73 Copynumber: 2.2 Consensus size: 74
2575702 CAATGTTCCA
*
2575712 CGTAGAATATGCACACAAAGTGCCTCGTAGAATATGCACACAAAGTGCCTCATAGAATATGCACA
1 CGTAGAAT-TGCACACAAAGTGCCTCGTAGAATATGCACACAAAATGCCTCATAGAATATGCACA
2575777 CAAAGTGCCT
65 CAAAGTGCCT
* * * * *
2575787 CGTAGAATTACACACAAAGTGTCTCGTAGAAT-TTCTCACAAAATGCCTCGTAGAATATGCACAC
1 CGTAGAATTGCACACAAAGTGCCTCGTAGAATATGCACACAAAATGCCTCATAGAATATGCACAC
2575851 AAAGTGCCT
66 AAAGTGCCT
2575860 CGTAGAATTGCACA
1 CGTAGAATTGCACA
2575874 AATAATACTC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
73 50 0.62
74 22 0.28
75 8 0.10
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (74 bp):
CGTAGAATTGCACACAAAGTGCCTCGTAGAATATGCACACAAAATGCCTCATAGAATATGCACAC
AAAGTGCCT
Found at i:2578443 original size:29 final size:30
Alignment explanation
Indices: 2578372--2578443 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
2578362 ATATTTATAT
* *
2578372 TTTTAGTCCCTAAACTTTTACAAATTTACA
1 TTTTAGTCACTAAACTTTCACAAATTTACA
* * *
2578402 CTTTGGTCTCTAAACTTTCA-AAATTTA-A
1 TTTTAGTCACTAAACTTTCACAAATTTACA
2578430 TTTTCAGTCACTAA
1 TTTT-AGTCACTAA
2578444 TCCTAAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
28 4 0.12
29 14 0.41
30 16 0.47
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (30 bp):
TTTTAGTCACTAAACTTTCACAAATTTACA
Found at i:2582520 original size:65 final size:64
Alignment explanation
Indices: 2582411--2582566 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 64
2582401 TACACTTGGG
* * * *
2582411 GTGCATCGGTACACT-AATTACATTCGATGCTTCAAAAGAGCCAGGAGTGTATCAATGCATGGTC
1 GTGCATCGGTACA-TAAAATGCATTCGATGCTTCAAAAGAACCAGGAGTGCATCAATGCATGGT-
2582475 T
64 T
* *
2582476 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCATGGTT
1 GTGCATCGGTACATAAAATGCATTCGATGCTTCAA-AAGAACCAGGAGTGCATCAATGCATGGTT
* *
2582540 GTGCATCGGTACACAAAAAGCATTCGA
1 GTGCATCGGTACATAAAATGCATTCGA
2582567 AATAGGGTGT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 27 0.33
65 52 0.64
66 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATGCATTCGATGCTTCAAAAGAACCAGGAGTGCATCAATGCATGGTT
Found at i:2585508 original size:20 final size:20
Alignment explanation
Indices: 2585469--2585505 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
2585459 TTTGTGTATT
*
2585469 TTTTTAAAATATAATTTTAA
1 TTTTTAAAATAGAATTTTAA
2585489 TTTTT-AAATAGAATTTT
1 TTTTTAAAATAGAATTTT
2585506 TAAAATTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTTAAAATAGAATTTTAA
Found at i:2588148 original size:3 final size:3
Alignment explanation
Indices: 2588140--2588194 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
2588130 TTTTTAAAGG
*
2588140 TAA TAA TAA TAA TAA TAA TAA TAA T-A TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2588187 TAA TAA TA
1 TAA TAA TA
2588195 TTGTCAGCCA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2590450 original size:8 final size:8
Alignment explanation
Indices: 2590424--2590467 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
2590414 ATTTTCGTCC
*
2590424 ATATTTTT
1 ATATATTT
* *
2590432 ATACATAT
1 ATATATTT
2590440 ATATATTT
1 ATATATTT
2590448 ATATATTT
1 ATATATTT
2590456 ATATA-TT
1 ATATATTT
2590463 ATATA
1 ATATA
2590468 GTTTGCAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
7 7 0.23
8 24 0.77
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
ATATATTT
Found at i:2590551 original size:37 final size:37
Alignment explanation
Indices: 2590480--2590747 Score: 253
Period size: 37 Copynumber: 7.1 Consensus size: 37
2590470 TTGCAAATGG
* * *
2590480 TTTTTGAAAATGCGTATACAATATATAGTTTTTAAATCA
1 TTTTTGAAAAT--ATATATAATATATAGTTTTTAAAACA
* * * *
2590519 TTTTTGAAAATATGTATATTATATAATTTTTAAAACG
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
2590556 TTTTTGAAAAT-TATATAATATATAGTTTTTAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* * *
2590592 TTTTAGAAAATATATATAATATATATATAGGTTTTGAAAAAA
1 TTTTTG-AAA-ATATAT-ATA-ATATATA-GTTTTTAAAACA
2590634 TCATTTT-AAAA-ATATATAATATATAGTTTTTTAAAACA
1 T--TTTTGAAAATATATATAATATATAG-TTTTTAAAACA
* *
2590672 -TTTTGAAAACTATATATAATATATAGTTTTGAAAATA
1 TTTTTGAAAA-TATATATAATATATAGTTTTTAAAACA
* *
2590709 -TTTT-AAAATATATATAATATAT-GATTTTGAAAATA
1 TTTTTGAAAATATATATAATATATAG-TTTTTAAAACA
2590744 TTTT
1 TTTT
2590748 AATATATATT
Statistics
Matches: 196, Mismatches: 19, Indels: 31
0.80 0.08 0.13
Matches are distributed among these distances:
34 1 0.01
35 29 0.15
36 37 0.19
37 47 0.24
38 33 0.17
39 17 0.09
40 7 0.04
41 8 0.04
42 14 0.07
44 3 0.02
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:2590648 original size:35 final size:38
Alignment explanation
Indices: 2590603--2590800 Score: 158
Period size: 35 Copynumber: 5.4 Consensus size: 38
2590593 TTTAGAAAAT
2590603 ATATATAATATATATATAGGTTTTGAAAAAATCATTTTAAA
1 ATATAT-ATA-ATATATA-GTTTTGAAAAAATCATTTTAAA
**
2590644 A-ATATATAATATATAGTTTT-TTAAAA-CATTTTGAAA
1 ATATATATAATATATAGTTTTGAAAAAATCATTTT-AAA
2590680 ACTATATATAATATATAGTTTTG--AAAAT-ATTTTAAA
1 A-TATATATAATATATAGTTTTGAAAAAATCATTTTAAA
2590716 ATATATATAATATAT-GATTTTG--AAAAT-ATTTT--A
1 ATATATATAATATATAG-TTTTGAAAAAATCATTTTAAA
* * *
2590749 ATATATAT--TATGTAGTTTT-AAAATAAT-TTTTTATA
1 ATATATATAATATATAGTTTTGAAAA-AATCATTTTAAA
*
2590784 CTATATATATATATATA
1 ATATATATA-ATATATA
2590801 TTATTATATT
Statistics
Matches: 136, Mismatches: 6, Indels: 33
0.78 0.03 0.19
Matches are distributed among these distances:
31 8 0.06
32 3 0.02
33 16 0.12
34 1 0.01
35 43 0.32
36 12 0.09
37 14 0.10
38 31 0.23
39 3 0.02
40 4 0.03
41 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (38 bp):
ATATATATAATATATAGTTTTGAAAAAATCATTTTAAA
Found at i:2590669 original size:80 final size:73
Alignment explanation
Indices: 2590494--2590748 Score: 245
Period size: 73 Copynumber: 3.4 Consensus size: 73
2590484 TGAAAATGCG
* * * * * * *
2590494 TATACAATATAT-AGTTTTTAAATCATTTTTG-AAAATATGTATATTATATAATTTTTAAAACGT
1 TATATAATATATGA-TTTTTAAAACATTTTAGAAAAATATATATAATATATAGTTTTGAAAA--T
2590557 -TTTTGAAAAT-
63 ATTTT-AAAATA
2590567 TATATAATATAT-AGTTTTTAAAACATTTTAGAAAATATATATAATATATATATAGGTTTTGAAA
1 TATATAATATATGA-TTTTTAAAACATTTTAGAAAA-ATATAT-ATA-ATATATA-GTTTTG--A
2590631 AAATCATTTTAAAA-A
59 AAAT-ATTTTAAAATA
* *
2590646 TATATAATATATAGTTTTTTAAAACATTTT-GAAAACTATATATAATATATAGTTTTGAAAATAT
1 TATATAATATAT-GATTTTTAAAACATTTTAGAAAAATATATATAATATATAGTTTTGAAAATAT
2590710 TTTAAAATA
65 TTTAAAATA
* *
2590719 TATATAATATATGATTTTGAAAATATTTTA
1 TATATAATATATGATTTTTAAAACATTTTA
2590749 ATATATATTA
Statistics
Matches: 156, Mismatches: 12, Indels: 28
0.80 0.06 0.14
Matches are distributed among these distances:
72 23 0.15
73 46 0.29
74 3 0.02
75 11 0.07
76 10 0.06
77 9 0.06
78 10 0.06
79 21 0.13
80 23 0.15
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (73 bp):
TATATAATATATGATTTTTAAAACATTTTAGAAAAATATATATAATATATAGTTTTGAAAATATT
TTAAAATA
Found at i:2590686 original size:115 final size:117
Alignment explanation
Indices: 2590513--2590730 Score: 302
Period size: 115 Copynumber: 1.9 Consensus size: 117
2590503 TATAGTTTTT
* * * *
2590513 AAATCATTTTTGAAAATATGTATATTATATAATTTTTAAAACGTTTTTGAAAA-TTATATAATAT
1 AAATCATTTTTGAAAATATATATAATATATAATTTTTAAAACGATTTTGAAAACATATATAATAT
*
2590577 ATAGTTTTTAAAACATTTTAGAAAATATATATAATATATATATAGGTTTTGAAA
66 ATAGTTTTGAAAACATTTT--AAAATATATATAATATATATATAGGTTTTGAAA
*
2590631 AAATCA-TTTT-AAAA-ATATATAATATATAGTTTTTTAAAAC-ATTTTGAAAACTATATATAAT
1 AAATCATTTTTGAAAATATATATAATATATA-ATTTTTAAAACGATTTTGAAAAC-ATATATAAT
*
2590692 ATATAGTTTTGAAAATATTTTAAAATATATATAATATAT
64 ATATAGTTTTGAAAACATTTTAAAATATATATAATATAT
2590731 GATTTTGAAA
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
115 39 0.43
116 14 0.16
117 31 0.34
118 6 0.07
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (117 bp):
AAATCATTTTTGAAAATATATATAATATATAATTTTTAAAACGATTTTGAAAACATATATAATAT
ATAGTTTTGAAAACATTTTAAAATATATATAATATATATATAGGTTTTGAAA
Found at i:2590718 original size:26 final size:26
Alignment explanation
Indices: 2590672--2590722 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2590662 TTTTAAAACA
*
2590672 TTTTGAAAACTATATATAATATATAG
1 TTTTGAAAACTATATAAAATATATAG
*
2590698 TTTTGAAAA-TATTTTAAAATATATA
1 TTTTGAAAACTA-TATAAAATATATA
2590723 TAATATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (26 bp):
TTTTGAAAACTATATAAAATATATAG
Found at i:2590735 original size:24 final size:24
Alignment explanation
Indices: 2590708--2590754 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2590698 TTTTGAAAAT
2590708 ATTTT-AAAATATATATAATATATG
1 ATTTTGAAAATAT-TATAATATATG
*
2590732 ATTTTGAAAATATTTTAATATAT
1 ATTTTGAAAATATTATAATATAT
2590755 ATTATGTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTTTGAAAATATTATAATATATG
Found at i:2590781 original size:33 final size:33
Alignment explanation
Indices: 2590683--2590798 Score: 112
Period size: 33 Copynumber: 3.4 Consensus size: 33
2590673 TTTGAAAACT
* **
2590683 ATATATAATATATAGTTTTGAAAATATTTTAAA
1 ATATATATTATATAGTTTTGAAAATATTTTTTA
*
2590716 ATATATATAATATATGATTTTGAAAATA--TTTTA
1 ATATATATTATATA-G-TTTTGAAAATATTTTTTA
*
2590749 ATATATATTATGTAGTTTT-AAAATAATTTTTTA
1 ATATATATTATATAGTTTTGAAAAT-ATTTTTTA
2590782 TACTATATATATATATA
1 -A-TATATAT-TATATA
2590799 TATTATTATA
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
30 5 0.07
31 5 0.07
32 1 0.01
33 32 0.47
34 2 0.03
35 18 0.26
36 5 0.07
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (33 bp):
ATATATATTATATAGTTTTGAAAATATTTTTTA
Found at i:2590942 original size:136 final size:135
Alignment explanation
Indices: 2590789--2591060 Score: 463
Period size: 136 Copynumber: 2.0 Consensus size: 135
2590779 TTATACTATA
** *
2590789 TATATATATATATTATTATATTCATTTTTATTTTTATTATTATTTTGTTTTGTTTTATTATTTAC
1 TATATATATATATTATTATATTCATTTTTATTAATATTATTATTTTGTTTTATTTTATTATTTAC
*
2590854 TTGTCGTTTTTCTTCTTTTTTTTAGGTACAAAGTTGAGGTAATGTATGCGGGTCCAGATACCCAA
66 TTGTCATTTTTCTTC-TTTTTTTAGGTACAAAGTTGAGGTAATGTATGCGGGTCCAGATACCCAA
2590919 TTAGGG
130 TTAGGG
* *
2590925 TATATATATATGTTATTATATTCATTTTTATTAATATTATTGTTTTGTTTTATTTTATTATTTAC
1 TATATATATATATTATTATATTCATTTTTATTAATATTATTATTTTGTTTTATTTTATTATTTAC
* *
2590990 TTGTCATTTTTCTTCTTTTTTTAGGTCCAAAGTTGAGGTAATGTATGTGGGTCCAGATACCCAAT
66 TTGTCATTTTTCTTCTTTTTTTAGGTACAAAGTTGAGGTAATGTATGCGGGTCCAGATACCCAAT
2591055 TAGGG
131 TAGGG
2591060 T
1 T
2591061 TGGGCCTGAC
Statistics
Matches: 128, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
135 54 0.42
136 74 0.58
ACGTcount: A:0.24, C:0.09, G:0.14, T:0.53
Consensus pattern (135 bp):
TATATATATATATTATTATATTCATTTTTATTAATATTATTATTTTGTTTTATTTTATTATTTAC
TTGTCATTTTTCTTCTTTTTTTAGGTACAAAGTTGAGGTAATGTATGCGGGTCCAGATACCCAAT
TAGGG
Found at i:2592133 original size:13 final size:14
Alignment explanation
Indices: 2592115--2592145 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
2592105 AACGTTTTTG
2592115 TTTTATTCATTCT-
1 TTTTATTCATTCTA
2592128 TTTTATTCATTCTA
1 TTTTATTCATTCTA
2592142 TTTT
1 TTTT
2592146 CATTTTCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATTCATTCTA
Found at i:2597342 original size:84 final size:83
Alignment explanation
Indices: 2597241--2598923 Score: 1136
Period size: 84 Copynumber: 20.3 Consensus size: 83
2597231 GGGCTATCTG
* * * * * *
2597241 CCAAAGACCCTCGAGTTCGATTACACTCAATTTCAAGGGCATATCATTTACAACATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTCAA-GGCACATCATTTACAGCATAACTCAAGG
*
2597306 CTATAA-GGTTATCTGTCA
65 CTAGAAGGGTTATCTGTCA
* * * *
2597324 CCAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCATATCATTTGCAGCATAACTTAAG
1 CC-AAAGACCTTCGAGTTCGACTACGCTCAACTTC-AAGGCACATCATTTACAGCATAACTCAAG
* * *
2597388 TCGAGGAGGGTTATCT-TCCA
64 GCTAGAAGGGTTATCTGT-CA
* * ** * ** *** * *
2597408 ACAAAGACTTTTTAGTTCGATTACGCTCAAC-TCAACAACACATCATTTGTGGTATAGCTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTCAA-GGCACATCATTTACAGCATAACTCAAGG
* * *
2597472 CTAGAAAGGCTATATG---
65 CTAGAAGGGTTATCTGTCA
* * * * * * *
2597488 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTTTAAGGCATATCATTTGCAACATAACTTAA-GT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTCAAGGCACATCATTTACAGCATAACTCAAGGC
* *
2597552 TGAGGAGGGTTATCTGCCA
66 T-AGAAGGGTTATCTGTCA
* * * * *
2597571 ACAAAGACCTTTGAGTTCGATTACGCTCAGC-TCAACGGCACATCATTTA-TG-ATATAGCTCAA
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTCAA-GGCACATCATTTACAGCATA-A-CTCAA
2597633 GGCTAGAAGGGTTATCTG---
63 GGCTAGAAGGGTTATCTGTCA
** * * * **
2597651 CCAAAGACCCCCAAGTTCGATTACACTCAGTTTCAAGGGCACATCATTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTCAA-GGCACATCATTTACAGCATAACTCAAGG
2597716 CTAGAAGGGTTATCTGTCA
65 CTAGAAGGGTTATCTGTCA
* * * * ** * *
2597735 CCAAAATACCTTCGAGTTCGACTACCCT-AAGCTCCAAGGCATATCATTTGTAGCACAACTTAAG
1 CC-AAAGACCTTCGAGTTCGACTACGCTCAA-CTTCAAGGCACATCATTTACAGCATAACTCAAG
* * * *
2597799 TCTAGAAGGGTTGTATGCCAA
64 GCTAGAAGGGTTATCTGTC-A
* * * * * * * * *
2597820 CAAAAGACCTTCGGGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTCAAGGCACATCATTTACAGCATAACTCAAGGC
* * * *
2597885 GAGTAGGGCTATCTGCCAA
66 TAGAAGGGTTATCTGTC-A
* * ** * * * *
2597904 CCGAAGACCTTCGAGTTCGATTATACTCAGCTTCGAGGGTACATCATTTACAACATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTC-AAGGCACATCATTTACAGCATAACTCAAGG
2597969 CTAGAAGGGTTATCTGTCA
65 CTAGAAGGGTTATCTGTCA
* * * * * * *
2597988 TCAAAAGACCTTCGAGTTTGACTACGCTCAGC-TCTAAGGCATATCATTTGCATCATAACTTAAG
1 -CCAAAGACCTTCGAGTTCGACTACGCTCAACTTC-AAGGCACATCATTTACAGCATAACTCAAG
*
2598052 TCGT-GAAGGGTTATCTG-CAA
64 GC-TAGAAGGGTTATCTGTC-A
* * * * *
2598072 CCCAAAGACCTTCGAGTTTGACTACACTCAGC-TCTAAGGCACATCATTT--AGCATAACTTAAT
1 -CCAAAGACCTTCGAGTTCGACTACGCTCAACTTC-AAGGCACATCATTTACAGCATAACTCAAG
* * *
2598134 TCGAGAAGGGCTATCTG---
64 GCTAGAAGGGTTATCTGTCA
* * ** * * *
2598151 CCAAAGACCCTCGAGTTCGATTATACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTC-AAGGCACATCATTTACAGCATAACTCAAGG
2598216 CTAGAAGGGTTATCTGTCA
65 CTAGAAGGGTTATCTGTCA
* * * *
2598235 CCAAAAGACCTTTGAGTTCGACTATGCTCAAC-TCTAAGGCATATCATTTACAGCATAACTTAAG
1 CC-AAAGACCTTCGAGTTCGACTACGCTCAACTTC-AAGGCACATCATTTACAGCATAACTCAAG
* * **
2598299 TCGAGAAGGGTTATCTACCAA
64 GCTAGAAGGGTTATCTGTC-A
* * * * * * * *
2598320 CCAAAGACCTTTGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTCAAGGCACATCATTTACAGCATAACTCAAGGC
* * * *
2598385 GAGGAGGGCTCTCTG---
66 TAGAAGGGTTATCTGTCA
* * * *
2598400 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTCAA-GGCACATCATTTACAGCATAACTCAAGG
* *
2598465 CTAGAAGGGTTATATGTGA
65 CTAGAAGGGTTATCTGTCA
* * * * * * *
2598484 CCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGT
1 CC-AAAGACCTTCGAGTTCGACTACGCTCAACTTCAAGGCACATCATTTACAGCATAACTCAAGG
* * *
2598549 CGAGAAGGATTATCTGCCAA
65 CTAGAAGGGTTATCTGTC-A
* * * * * * * * *
2598569 CCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAAGCACATTATTTGCATCATAGC-CTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTCAAGGCACATCATTTACAGCATAACTC-AAGG
* * * *
2598633 CGAAAAGAGCTATCTGT--
65 CTAGAAGGGTTATCTGTCA
* * * * * * ** *
2598650 -CAAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCATATCATTTACAATATAACTCAATG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTC-AAGGCACATCATTTACAGCATAACTCAAGG
*
2598714 CTAAAAGGGTTATCTGTCA
65 CTAGAAGGGTTATCTGTCA
* * * * * *
2598733 CCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTTCAGCATAGC-CTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTCAAGGCACATCATTTACAGCATAACTC-AAGG
* * *
2598797 CGAGAA-GTTCTATATG---
65 CTAGAAGGGT-TATCTGTCA
* * * * * * *
2598813 CCTAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAACATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAACTTC-AAGGCACATCATTTACAGCATAACTCAAGG
*
2598878 CTAAAAGGGTTATCTGTCA
65 CTAGAAGGGTTATCTGTCA
* * **
2598897 CCAAAGACTTTTGAGTTTTACTACGCT
1 CCAAAGACCTTCGAGTTCGACTACGCT
2598924 AAGATCCAAC
Statistics
Matches: 1252, Mismatches: 289, Indels: 117
0.76 0.17 0.07
Matches are distributed among these distances:
78 27 0.02
79 17 0.01
80 158 0.13
81 169 0.13
82 40 0.03
83 176 0.14
84 516 0.41
85 149 0.12
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (83 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAACTTCAAGGCACATCATTTACAGCATAACTCAAGGC
TAGAAGGGTTATCTGTCA
Found at i:2597507 original size:163 final size:163
Alignment explanation
Indices: 2597204--2598601 Score: 1140
Period size: 163 Copynumber: 8.4 Consensus size: 163
2597194 TTTAAGACAA
* * * * * * *
2597204 CATTTGTAGCATAGCTTAAGTAGCGAAGGGCTATC-TGC--CAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAGACCTTCGAGTTCGATTACA
** * * * * * *
2597266 CTCAATTTCAAGGGCATATCATTTACAACATAACTCAAGGCTATAA-GGTTATCTGTCACCAAAA
66 CTC-AGCTCAACGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATATG---CC-AAA
*
2597330 GACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATAT
126 GACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACAT
* * ** *
2597368 CATTTGCAGCATAACTTAAGTCGAGGAGGGTTATCTTCCAACAAAGACTTTTTAGTTCGATTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAGACCTTCGAGTTCGATTACA
* ** * * * * * *
2597433 CTCAACTCAACAACACATCATTTGTGGTATAGCTCAAGGCTAGAAAGGCTATATGCCAAAGACCT
66 CTCAGCTCAACGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATATGCCAAAGACCT
* *
2597498 TCGAGTTCGACTACGCTCAGCTTTAAGGCATAT
131 TCGAGTTCGACTACGCTCAGCTCTAAGGCACAT
* * * * * *
2597531 CATTTGCAACATAACTTAAGTTGAGGAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGATTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAGACCTTCGAGTTCGATTACA
*
2597596 CTCAGCTCAACGGCACATCATTTAT-G-ATATAGCTCAAGGCTAGAAGGGTTATCTGCCAAAGAC
66 CTCAGCTCAACGGCACATCATTTATAGCATA-A-CTCAAGGCTAGAAGGGTTATATGCCAAAGAC
** * * * *
2597659 CCCCAAGTTCGATTACACTCAG-TTTCAAGGGCACAT
129 CTTCGAGTTCGACTACGCTCAGCTCT-AA-GGCACAT
* * * * * * *
2597695 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-CACCAAAATACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAAC-AAAGACCTTCGAGTTCGATTA
* * * * * * * *
2597759 CCCTAAGCTCCAA-GGCATATCATTTGTAGCACAACTTAAGTCTAGAAGGGTTGTATGCCAACAA
64 CACTCAGCT-CAACGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATATG-C--C-A
* * *
2597823 AAGACCTTCGGGTTTGACTACGCTCAGCTCCAAGGCACAT
124 AAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACAT
* * * * * *
2597863 CATTTGCAGCATAGCTTAAGTCGAGTAGGGCTATCTGCCAACCGAAGACCTTCGAGTTCGATTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAA-CAAAGACCTTCGAGTTCGATTAC
* * * * * *
2597928 ACTCAGCTTCGAGGGTACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCATCAAA
65 ACTCAGC-TCAACGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATATG-C--C-AA
* *
2597993 AGACCTTCGAGTTTGACTACGCTCAGCTCTAAGGCATAT
125 AGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACAT
* * * * *
2598032 CATTTGCATCATAACTTAAGTCGTGAAGGGTTATC-TGCAACCCAAAGACCTTCGAGTTTGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAA--CAAAGACCTTCGAGTTCGATTA
* ** * * *
2598096 CACTCAGCTCTAA-GGCACATCA-TT-TAGCATAACTTAATTCGAGAAGGGCTATCTGCCAAAGA
64 CACTCAGCTC-AACGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATATGCCAAAGA
* * ** * *
2598158 CCCTCGAGTTCGATTATACTCAGCTTCGAGGGCACAT
128 CCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCACAT
* * * * * * * *
2598195 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGT-CACCAAAAGACCTTTGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAAC-AAAGACCTTCGAGTTCGATTA
** * * * * * * **
2598259 TGCTCAACTCTAA-GGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCA
64 CACTCAGCTC-AACGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTA--TA--TGCCA
* * *
2598323 AAGACCTTTGAGTTTGACTACGCTCAGCTCCAAGGCACAT
124 AAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACAT
* * * * * *
2598363 CATTTGCAGCATAGCTTAAGTCGAGGAGGGCTCTC-TGC--CAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAGACCTTCGAGTTCGATTACA
* *
2598425 CTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTGACCAAAA
66 CTCAGC-TCAACGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATA--TG-CC-AAA
* * *
2598490 GACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATAT
126 GACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACAT
* * * *
2598528 CATTTGCAGCATAACTTAAGTCGAGAAGGATTATCTGCCAACCAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAA-CAAAGACCTTCGAGTTCGATTAC
*
2598593 GCTCAGCTC
65 ACTCAGCTC
2598602 CAAAGCACAT
Statistics
Matches: 992, Mismatches: 199, Indels: 82
0.78 0.16 0.06
Matches are distributed among these distances:
161 3 0.00
162 29 0.03
163 246 0.25
164 100 0.10
165 192 0.19
166 61 0.06
167 35 0.04
168 115 0.12
169 210 0.21
170 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (163 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAGACCTTCGAGTTCGATTACA
CTCAGCTCAACGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATATGCCAAAGACCT
TCGAGTTCGACTACGCTCAGCTCTAAGGCACAT
Found at i:2598493 original size:249 final size:249
Alignment explanation
Indices: 2597243--2598803 Score: 1874
Period size: 249 Copynumber: 6.3 Consensus size: 249
2597233 GCTATCTGCC
* * * ** * * * * * *
2597243 AAAGACCCTCGAGTTCGATTACACTCAATTTCAAGGGCATATCATTTACAACATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGCATAACTTAAGTCG
* * * * *
2597308 ATAA-GGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATATCAT
65 AGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCAT
* * * * ** ** *
2597371 TTGCAGCATAACTTAAGTCGAGGAGGGTTATCTTCCAACAAAGACTTTTTAGTTCGATTACGCTC
129 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATC-TGC--CAAAGACCCTCGAGTTCGATTACACTC
* *** ***** * * * *
2597436 AAC-TCAACAACACATCATTTGTGGTATAGCTCAAGGCTAGAAAGGCTATATG---CC-
191 AGCTTCAAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCA
** * *
2597490 AAAGACCTTCGAGTTCGACTACGCTCAGCTTTAAGGCATATCATTTGCAACATAACTTAAGTTGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGA
* * * *
2597555 GGAGGGTTATCTGCCAA-CAAAGACCTTTGAGTTCGATTACGCTCAGCT-CAACGGCACATCATT
66 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAA-GGCACATCATT
* * * * * * *
2597618 T--ATGATATAGCTCAAGGCTAGAAGGGTTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAG
130 TGCA-G-CATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAG
* *
2597681 TTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCA
193 CTTCAAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCA
* * * * * *
2597738 AAATACCTTCGAGTTCGACTACCCTAAGCTCCAAGGCATATCATTTGTAGCACAACTTAAGTCTA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGA
* * * *
2597803 GAAGGGTTGTATGCCAACAAAAGACCTTCGGGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
66 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
* * *
2597868 GCAGCATAGCTTAAGTCGAGTAGGGCTATCTGCCAACCGAAGACCTTCGAGTTCGATTATACTCA
131 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-A---AAGACCCTCGAGTTCGATTACACTCA
* * *
2597933 GCTTCGAGGGTACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCATCA
192 GCTTCAAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCA
* * * *
2597991 AAAGACCTTCGAGTTTGACTACGCTCAGCTCTAAGGCATATCATTTGCATCATAACTTAAGTCGT
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGA
* *
2598056 GAAGGGTTATCTG-CAACCCAAAGACCTTCGAGTTTGACTACACTCAGCTCTAAGGCACATCATT
66 GAAGGGTTATCTGCCAA-CCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
* * *
2598120 T--AGCATAACTTAATTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTATACTCAGCT
130 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCT
*
2598183 TCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCA
195 TCAAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCA
* * * * *
2598238 AAAGACCTTTGAGTTCGACTATGCTCAACTCTAAGGCATATCATTTACAGCATAACTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGA
* *
2598303 GAAGGGTTATCTACCAACCAAAGACCTTTGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
66 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
* *
2598368 GCAGCATAGCTTAAGTCGAGGAGGGCTCTCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTT
131 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTT
* * *
2598433 CAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTGACCA
196 CAAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCA
*
2598487 AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGA
* * *
2598552 GAAGGATTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAAGCACATTATTT
66 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
* * * * * * *
2598617 GCATCATAGCCTAAGTCGAAAAGAGCTATCTGTCAAAGACCCTCAAGTTCGATTACACTCAACTT
131 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTT
* * * * *
2598682 CGAGGGCATATCATTTACAATATAACTCAATGCTAAAAGGGTTATCTGTCACC-
196 CAAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCA
* * * * *
2598735 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTTCAGCATAGCCTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGA
2598800 GAAG
66 GAAG
2598804 TTCTATATGC
Statistics
Matches: 1139, Mismatches: 153, Indels: 43
0.85 0.11 0.03
Matches are distributed among these distances:
243 22 0.02
244 39 0.03
245 5 0.00
246 86 0.08
247 237 0.21
248 136 0.12
249 390 0.34
250 6 0.01
251 30 0.03
252 3 0.00
253 185 0.16
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (249 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGA
GAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTT
CAAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCA
Found at i:2598768 original size:164 final size:163
Alignment explanation
Indices: 2597327--2599012 Score: 1087
Period size: 164 Copynumber: 10.2 Consensus size: 163
2597317 TCTGTCACCA
* * * * * * * * * *
2597327 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCATATCATTTGCAGCATAACTTAAGTCG
1 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAG-CT
* * * ** * *
2597391 AGGAGGGTTATCT-TCCAACAAAGACTTTTTAGTTCGATTACGCTCAACTCAACAA--CACATCA
65 AGAAGGGTTATCTGT-CACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC--CAAGGCACATCA
** * * * * *
2597453 TTTGTGGTATAG-CTCAAGGCTAGAAAGGCTATATGCC
127 TTTGCAGCATAGCCT-AAGTCGAGAAGGGCTATCTGCC
* * * * * * * * *
2597490 AAAGACCTTCGAGTTCGACTACGCTCAGCTT-TAAGGCATATCATTTGCAACATAACTTAAGTTG
1 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGCT-
* * * * *
2597554 AGGAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGATTACGCTCAGCT-CAACGGCACATCATT
65 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATT
* * * *
2597618 T--ATGATATAG-CTCAAGGCTAGAAGGGTTATCTGCC
129 TGCA-G-CATAGCCT-AAGTCGAGAAGGGCTATCTGCC
* * * * *
2597653 AAAGACCCCCAAGTTCGATTACACTCAGTTTCAAGGGCACATCATTTACAGCATAACTCAAGGCT
1 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAA-GCT
* * * *
2597718 AGAAGGGTTATCTGTCACCAAAATACCTTCGAGTTCGACTACCCTAAGCTCCAAGGCATATCATT
65 AGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * * * * * *
2597783 TGTAGCACAACTTAAGTCTAGAAGGGTTGTATGCCAAC
129 TGCAGCATAGCCTAAGTCGAGAAGGGCTATCTG-C--C
* * * * * * * * * * *
2597821 AAAAGACCTTCGGGTTTGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 -AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAG-C
* * * * * * ** * * *
2597885 GAGTAGGGCTATCTGCCAACCGAAGACCTTCGAGTTCGATTATACTCAGCTTCGAGGGTACATCA
64 TAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCA
* * * * * *
2597950 TTTACAACATA-ACTCAAGGCTAGAAGGGTTATCTGTCATC
127 TTTGCAGCATAGCCT-AAGTCGAGAAGGGCTATCTG-C--C
* * * * * * * * * *
2597990 AAAAGACCTTCGAGTTTGACTACGCTCAGC-TCTAAGGCATATCATTTGCATCATAACTTAAGTC
1 -AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAG-C
* * *
2598054 GT-GAAGGGTTATCTG-CAACCCAAAGACCTTCGAGTTTGACTACACTCAGCTCTAAGGCACATC
64 -TAGAAGGGTTATCTGTC-A-CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * *
2598117 ATTT--AGCATAACTTAATTCGAGAAGGGCTATCTGCC
126 ATTTGCAGCATAGCCTAAGTCGAGAAGGGCTATCTGCC
*
2598153 AAAGACCCTCGAGTTCGATTATACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
1 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAA-GCT
* * * * *
2598218 AGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTATGCTCAACTCTAAGGCATATCATT
65 AGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * * *
2598283 TACAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACC
129 TGCAGCATAGCCTAAGTCGAGAAGGGCTATCT----GCC
* * * * * * * * * * * *
2598322 AAAGACCTTTGAGTTTGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
1 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAG-CT
* * * * * * *
2598386 AGGAGGGCTCTCTG---CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATT
65 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATT
* * * * * *
2598448 TACAGCATA-ACTCAAGGCTAGAAGGGTTATATGTGACC
129 TGCAGCATAGCCT-AAGTCGAGAAGGG--CTATCTG-CC
* * * * * * * * * *
2598486 AAAAGACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTC
1 -AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAG-C
* * * * * *
2598550 GAGAAGGATTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAAGCACATTAT
64 TAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * * *
2598615 TTGCATCATAGCCTAAGTCGAAAAGAGCTATCTGTC
128 TTGCAGCATAGCCTAAGTCGAGAAGGGCTATCTGCC
* * * *
2598651 AAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCATATCATTTACAATATAACTCAATGCT
1 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAA-GCT
* *
2598716 AAAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
65 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* ** *
2598781 TCAGCATAGCCTAAGTCGAGAAGTTCTATATGCC
130 GCAGCATAGCCTAAGTCGAGAAGGGCTATCTGCC
* * *
2598815 TAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
1 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAA-GCT
* * * ** * * *
2598880 AAAAGGGTTATCTGTCACCAAAGACTTTTGAGTTTTACTACGCTAAGATCCAACGCACATCATTT
65 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * * *
2598945 GCATCATAGCTTAAGTCGAAAAGAGCTATATGCC
130 GCAGCATAGCCTAAGTCGAGAAGGGCTATCTGCC
* *
2598979 AACCGAAGACCTTTGAGTTCGATTACACTCAGCT
1 -A---AAGACCCTCGAGTTCGATTACACTCAGCT
2599013 CAGAGGCAAA
Statistics
Matches: 1244, Mismatches: 224, Indels: 105
0.79 0.14 0.07
Matches are distributed among these distances:
160 3 0.00
162 28 0.02
163 245 0.20
164 314 0.25
165 228 0.18
166 33 0.03
167 8 0.01
168 169 0.14
169 216 0.17
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (163 bp):
AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGCTA
GAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
CAGCATAGCCTAAGTCGAGAAGGGCTATCTGCC
Found at i:2599753 original size:40 final size:39
Alignment explanation
Indices: 2599667--2599818 Score: 165
Period size: 37 Copynumber: 3.9 Consensus size: 39
2599657 CAATATATGG
2599667 TTTTT-AAAACATTTTAGAAAATAATATATATATATATATAGTT
1 TTTTTAAAAACATTTT-G--AA-AATATATATA-ATATATAGTT
**
2599710 TTTAAAAAAATCATTTTG-AAA-ATATATAATATATAGTT
1 TTTTTAAAAA-CATTTTGAAAATATATATAATATATAGTT
2599748 TTTTTAAAAACATTTTGAAAATTATATATAATATATAG--
1 TTTTTAAAAACATTTTGAAAA-TATATATAATATATAGTT
*
2599786 -TTTTGAAAACATTTT-AAAATATATATAATATAT
1 TTTTTAAAAACATTTTGAAAATATATATAATATAT
2599819 GATTTTGTAA
Statistics
Matches: 99, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
35 14 0.14
36 4 0.04
37 21 0.21
38 21 0.21
39 7 0.07
40 17 0.17
41 1 0.01
43 3 0.03
44 5 0.05
45 6 0.06
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (39 bp):
TTTTTAAAAACATTTTGAAAATATATATAATATATAGTT
Found at i:2599809 original size:35 final size:36
Alignment explanation
Indices: 2599689--2599818 Score: 156
Period size: 40 Copynumber: 3.4 Consensus size: 36
2599679 TTTAGAAAAT
*
2599689 AATATATATATATATATAGTTTTTAAAAAAATCATTTTGA
1 AATATATATA-ATATATAGTTTTT--AAAAA-CATTTTAA
2599729 AA-ATATATAATATATAGTTTTTTTAAAAACATTTTGAA
1 AATATATATAATATATAG--TTTTTAAAAACATTTT-AA
*
2599767 AATTATATATAATATATAG-TTTTGAAAACATTTTAA
1 AA-TATATATAATATATAGTTTTTAAAAACATTTTAA
2599803 AATATATATAATATAT
1 AATATATATAATATAT
2599819 GATTTTGTAA
Statistics
Matches: 83, Mismatches: 2, Indels: 15
0.83 0.02 0.15
Matches are distributed among these distances:
35 14 0.17
36 4 0.05
37 20 0.24
38 16 0.19
39 7 0.08
40 22 0.27
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (36 bp):
AATATATATAATATATAGTTTTTAAAAACATTTTAA
Found at i:2599835 original size:35 final size:35
Alignment explanation
Indices: 2599721--2599844 Score: 117
Period size: 35 Copynumber: 3.4 Consensus size: 35
2599711 TTAAAAAAAT
* * *
2599721 CATTTTGAAA-ATATATAATATATAGTTTTTTTAAAAA
1 CATTTTAAAATATATATAATATAT-GATTTTGT--AAA
*
2599758 CATTTTGAAAATTATATATAATATAT-AGTTTTGAAAA
1 CATTTT-AAAA-TATATATAATATATGA-TTTTGTAAA
2599795 CATTTTAAAATATATATAATATATGATTTTGTAAA
1 CATTTTAAAATATATATAATATATGATTTTGTAAA
* * *
2599830 TATTTTTATATATAT
1 CATTTTAAAATATAT
2599845 TATGTAGTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
35 34 0.46
36 5 0.07
37 15 0.20
38 3 0.04
39 4 0.05
40 13 0.18
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (35 bp):
CATTTTAAAATATATATAATATATGATTTTGTAAA
Found at i:2599899 original size:3 final size:3
Alignment explanation
Indices: 2599887--2599927 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
2599877 TATATATATG
2599887 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2599928 TACTTGTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:2601185 original size:16 final size:17
Alignment explanation
Indices: 2601166--2601207 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2601156 TTTTGACTTT
2601166 TTTATTCATTTATTT-A
1 TTTATTCATTTATTTGA
*
2601182 TTTATTC-TTTCTTTGA
1 TTTATTCATTTATTTGA
2601198 TTTATT-ATTT
1 TTTATTCATTT
2601208 TGGTGTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTATTCATTTATTTGA
Found at i:2602894 original size:3 final size:3
Alignment explanation
Indices: 2602886--2603009 Score: 97
Period size: 3 Copynumber: 41.0 Consensus size: 3
2602876 TATTTATTTG
* * *
2602886 TTA TTA TTA TTA TTTA TTTA TTA TTA TTA TCA TTA TTA -TA ATA ATA
1 TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * * *
2602932 ATA TTA TTA TTA CTA ATG TTA TTA TTA TTA ATA ATA ATG TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2602980 TTA ATA TTA ATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2603010 CAGGCCCAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.02
3 92 0.91
4 7 0.07
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:2605065 original size:34 final size:36
Alignment explanation
Indices: 2605018--2605084 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 36
2605008 ATGAAAGATT
*
2605018 AATAAGTATTATTTAATTAATTTTAAA-ATTAATTA
1 AATAAGTAATATTTAATTAATTTTAAATATTAATTA
* *
2605053 AATAA-TAATATTTATTTATTTTTAAATATTAA
1 AATAAGTAATATTTAATTAATTTTAAATATTAA
2605085 GAAATGGCGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 18 0.64
35 10 0.36
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (36 bp):
AATAAGTAATATTTAATTAATTTTAAATATTAATTA
Found at i:2605160 original size:4 final size:4
Alignment explanation
Indices: 2605153--2605183 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2605143 TATCATGCTT
2605153 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
2605184 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:2606501 original size:8 final size:8
Alignment explanation
Indices: 2606488--2606525 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
2606478 GTACTAACCA
2606488 TTTTATTT
1 TTTTATTT
2606496 TTTTATTT
1 TTTTATTT
2606504 TTTTATTT
1 TTTTATTT
2606512 TTTTATTT
1 TTTTATTT
2606520 TTTTAT
1 TTTTAT
2606526 GCATTGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTATTT
Found at i:2607435 original size:12 final size:12
Alignment explanation
Indices: 2607374--2607445 Score: 65
Period size: 12 Copynumber: 5.8 Consensus size: 12
2607364 ACCTTCGTTG
2607374 CATTTGCATTTT
1 CATTTGCATTTT
*
2607386 CACTTTGCATTCGTA
1 CA-TTTGCATT--TT
* * *
2607401 CTTTTACGTTTT
1 CATTTGCATTTT
2607413 CA-TTGCATTTT
1 CATTTGCATTTT
*
2607424 CATTTTCATTTT
1 CATTTGCATTTT
2607436 CATTTGCATT
1 CATTTGCATT
2607446 CGCATTTTTG
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
11 9 0.20
12 21 0.46
13 8 0.17
14 6 0.13
15 2 0.04
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (12 bp):
CATTTGCATTTT
Found at i:2610609 original size:10 final size:10
Alignment explanation
Indices: 2610590--2610633 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
2610580 ATTCATCAGG
2610590 AAAA-AAAGA
1 AAAATAAAGA
2610599 AAAATAAAGA
1 AAAATAAAGA
2610609 AAAATAAAGA
1 AAAATAAAGA
*
2610619 AAAGAAAAAGA
1 AAA-ATAAAGA
2610630 AAAA
1 AAAA
2610634 AAGAAAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
9 4 0.12
10 19 0.59
11 9 0.28
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (10 bp):
AAAATAAAGA
Found at i:2610622 original size:15 final size:14
Alignment explanation
Indices: 2610592--2610644 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
2610582 TCATCAGGAA
2610592 AAAAAGAAAAATAAAG
1 AAAAAG-AAAA-AAAG
*
2610608 AAAAATAAAGAAAAG
1 AAAAAGAAA-AAAAG
2610623 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
2610637 -AAAAGAAA
1 AAAAAGAAA
2610645 TTGAATCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 8 0.24
14 5 0.15
15 15 0.44
16 6 0.18
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:2610641 original size:19 final size:19
Alignment explanation
Indices: 2610589--2610644 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
2610579 CATTCATCAG
*
2610589 GAAAAAAAGAAAA-ATAAA
1 GAAAAAAAGAAAAGAAAAA
2610607 GAAAAATAAAGAAAAGAAAAA
1 G-AAAA-AAAGAAAAGAAAAA
2610628 GAAAAAAAGAAAAGAAA
1 GAAAAAAAGAAAAGAAA
2610645 TTGAATCAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 12 0.35
21 5 0.15
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (19 bp):
GAAAAAAAGAAAAGAAAAA
Found at i:2612538 original size:75 final size:75
Alignment explanation
Indices: 2612415--2612669 Score: 393
Period size: 75 Copynumber: 3.4 Consensus size: 75
2612405 TCAACAAAAA
* * * * * *
2612415 AGCAAATGCTGGGGTATGCTGAAAACCCATTTCAATCATAATAAGGAATATTGATGCATTTTGAA
1 AGCAAATGCTGGGGCATGTTGAAAGCCCATTTCAATCAGAATGAGGAATATTGACGCATTTTGAA
*
2612480 TGTTTGTATC
66 CGTTTGTATC
2612490 AGCAAATGCTGGGGCATGTTGAAAGCCCATTTCAATCAGAATGAGGAATATTGACGCATTTTGAA
1 AGCAAATGCTGGGGCATGTTGAAAGCCCATTTCAATCAGAATGAGGAATATTGACGCATTTTGAA
2612555 CGTTTGTATC
66 CGTTTGTATC
* *
2612565 AGCAAATGCTGGGGCATGTTGAAAGCCCATTTCAATCAGAATGAGGAATGTTGGCGCATTTTGAA
1 AGCAAATGCTGGGGCATGTTGAAAGCCCATTTCAATCAGAATGAGGAATATTGACGCATTTTGAA
*
2612630 CGTTTGTATT
66 CGTTTGTATC
** *
2612640 AGCAAATATTGGGGCATGTTGAAGGCCCAT
1 AGCAAATGCTGGGGCATGTTGAAAGCCCAT
2612670 ATCTTCTTAT
Statistics
Matches: 167, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 167 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (75 bp):
AGCAAATGCTGGGGCATGTTGAAAGCCCATTTCAATCAGAATGAGGAATATTGACGCATTTTGAA
CGTTTGTATC
Found at i:2613960 original size:22 final size:22
Alignment explanation
Indices: 2613935--2614029 Score: 138
Period size: 22 Copynumber: 4.3 Consensus size: 22
2613925 ACATCTATAT
*
2613935 TCTTTAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
2613957 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
2613979 TCTTCAAAGATGATAGATACAT-
1 TCTTCAAAGATGATAGATTC-TC
*
2614001 TCTTCAAAGATGATAGGTTCTC
1 TCTTCAAAGATGATAGATTCTC
*
2614023 TTTTCAA
1 TCTTCAA
2614030 TGTGAAAACT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
21 1 0.02
22 64 0.97
23 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:2614634 original size:123 final size:123
Alignment explanation
Indices: 2614411--2614991 Score: 957
Period size: 123 Copynumber: 4.7 Consensus size: 123
2614401 CTCACTCGAG
** *
2614411 GCATCAACATTTTCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCA
1 GCATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
*
2614476 TAATGAGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCA
66 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCA
*
2614534 GCATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTTA
1 GCATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
*
2614599 TAATGAGAAGAACTTGTTCAACATTTTGCTCGACTCTATCACAGAAGGAGATAGATCA
66 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCA
*
2614657 GCATCAACATTGCAAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
1 GCATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
* *
2614722 TAATGAGAAG-ACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGATATATATCA
66 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCA
*
2614779 GTATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
1 GCATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
* * * * *
2614844 TAATGAGAAGAATTTGCTCAACCTTTTCCTCGACTCTATCATAGAAGAAGATAGATCA
66 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCA
* ** * * *
2614902 ACATCAACATTGCCATTTAGAGTTTATAATGAGAAAAACTCATCTGAAGAGGAAGAACAAGTTCA
1 GCATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
*
2614967 TAATGAGAAGAACTTGTTCGACCTT
66 TAATGAGAAGAACTTGTTCAACCTT
2614992 AGCTTGATTC
Statistics
Matches: 427, Mismatches: 30, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
122 117 0.27
123 310 0.73
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (123 bp):
GCATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCA
Found at i:2614849 original size:245 final size:245
Alignment explanation
Indices: 2614411--2614991 Score: 948
Period size: 245 Copynumber: 2.4 Consensus size: 245
2614401 CTCACTCGAG
* *
2614411 GCATCAACATTTTCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCA
1 GCATCAACA-TTGCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
*
2614476 TAATGAGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAGCATCAA
65 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCATCAA
*
2614541 CATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTTATAATGAG
130 CATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAG
* * *
2614606 AAGAACTTGTTCAACATTTTGCTCGACTCTATCACAGAAGGAGATAGATCA
195 AAGAACTTGCTCAACATTTTCCTCGACTCTATCACAGAAGAAGATAGATCA
2614657 GCATCAACATTGCAAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
1 GCATCAACATTGC-AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
* * *
2614722 TAATGAGAAG-ACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGATATATATCAGTATCAA
65 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCATCAA
2614786 CATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAG
130 CATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAG
* * *
2614851 AAGAATTTGCTCAACCTTTTCCTCGACTCTATCATAGAAGAAGATAGATCA
195 AAGAACTTGCTCAACATTTTCCTCGACTCTATCACAGAAGAAGATAGATCA
* ** * * *
2614902 ACATCAACATTGCCATTTAGAGTTTATAATGAGAAAAACTCATCTGAAGAGGAAGAACAAGTTCA
1 GCATCAACATTG-CAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
*
2614967 TAATGAGAAGAACTTGTTCGACCTT
65 TAATGAGAAGAACTTGTTCAACCTT
2614992 AGCTTGATTC
Statistics
Matches: 312, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
245 229 0.73
246 83 0.27
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (245 bp):
GCATCAACATTGCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCATCAAC
ATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGCTCAACATTTTCCTCGACTCTATCACAGAAGAAGATAGATCA
Found at i:2615074 original size:139 final size:137
Alignment explanation
Indices: 2614921--2615266 Score: 464
Period size: 139 Copynumber: 2.5 Consensus size: 137
2614911 TTGCCATTTA
* * *
2614921 GAGTTTATAATGAGAAAAACTCATCTGAAGAGGAAGAACAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* * * * *
2614986 GACCTTAG-CTTGATTCATCACCTATGGAGTTGAATGAAAGAAGAACCTCACTTGAGGATCAATA
66 AACCTT-GCCTTAATTCATCACATATGAAGTT-AATGAAACAA-AACCTCACTTGAGGATCAATA
2615050 TTTACAG-AG
128 TTTACAGAAG
* *
2615059 GAAGTTCATAATGAGAAGAACTCATCTGAAAATGAAGAAAAAGTTCATAATGAGAAGAACTTGTT
1 G-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTT
* ** * **
2615124 CAACCTTGCCTTAATTCATCACATATGAAGTTTATTCAACAATACCTCTTTTGAGGATCAATATT
65 CAACCTTGCCTTAATTCATCACATATGAAGTTAATGAAACAAAACCTCACTTGAGGATCAATATT
*
2615189 TCCAGAAG
130 TACAGAAG
* *
2615197 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAA-AAAAAGTTCATAAGGATAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
2615261 AACCTT
66 AACCTT
2615267 TTGCTAGATT
Statistics
Matches: 184, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
136 33 0.18
137 56 0.30
138 11 0.06
139 84 0.46
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (137 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
AACCTTGCCTTAATTCATCACATATGAAGTTAATGAAACAAAACCTCACTTGAGGATCAATATTT
ACAGAAG
Found at i:2615477 original size:4 final size:4
Alignment explanation
Indices: 2615468--2615510 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
2615458 TTTTTTGCCC
* *
2615468 ATTT ATTT ATTT ATTT ATTT GTTT TTATT A-TT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATT
2615511 ATTATTATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.85
5 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:2615500 original size:3 final size:3
Alignment explanation
Indices: 2615492--2615616 Score: 126
Period size: 3 Copynumber: 41.3 Consensus size: 3
2615482 TTATTTGTTT
* * * *
2615492 TTA TTA TTA TTTA TTTA TTA TTA TTA TCA TTA TAA TGA -TA ATA TTA
1 TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** * * *
2615538 TTA TTA TTA ATG TTA TTA TTA TTA AAA ATA ATG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2615586 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2615617 ATTGTTGTTG
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
2 1 0.01
3 96 0.92
4 7 0.07
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2615503 original size:20 final size:20
Alignment explanation
Indices: 2615478--2615616 Score: 115
Period size: 21 Copynumber: 6.9 Consensus size: 20
2615468 ATTTATTTAT
* *
2615478 TTATTTATTTGTTTTTATTA
1 TTATTTATTTATTATTATTA
2615498 TTATTTATTTATTATTATTA
1 TTATTTATTTATTATTATTA
* * *
2615518 TCATTATAATGATAATATTATTA
1 TTATT-T-AT-TTATTATTATTA
*
2615541 TTATTAATGTTATTATTATTA
1 TTATTTAT-TTATTATTATTA
** * *
2615562 AAAATAATGTTATTATTATTA
1 TTATTTAT-TTATTATTATTA
2615583 TTA-TTA-TTATTATTATTA
1 TTATTTATTTATTATTATTA
2615601 TTA-TTA-TTATTATTAT
1 TTATTTATTTATTATTAT
2615617 ATTGTTGTTG
Statistics
Matches: 101, Mismatches: 15, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
18 28 0.28
20 24 0.24
21 33 0.33
22 2 0.02
23 14 0.14
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.62
Consensus pattern (20 bp):
TTATTTATTTATTATTATTA
Found at i:2615624 original size:3 final size:3
Alignment explanation
Indices: 2615618--2615646 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2615608 TATTATTATA
2615618 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
2615647 ATTATTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2617530 original size:19 final size:18
Alignment explanation
Indices: 2617483--2617531 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
2617473 CAAATAAATA
*
2617483 TATAGTTATTTTTCAATT
1 TATATTTATTTTTCAATT
* *
2617501 TATTATATATTTCTTCATTT
1 TA-TATTTATTT-TTCAATT
2617521 TATATTTATTT
1 TATATTTATTT
2617532 AATTTTAGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 15 0.60
20 8 0.32
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (18 bp):
TATATTTATTTTTCAATT
Found at i:2617564 original size:2 final size:2
Alignment explanation
Indices: 2617559--2617583 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2617549 TATGTGTGTG
2617559 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2617584 GAAAGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2621314 original size:14 final size:14
Alignment explanation
Indices: 2621295--2621324 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2621285 GTTAATCATT
2621295 ATGAACGTATTCAA
1 ATGAACGTATTCAA
2621309 ATGAACGTATTCAA
1 ATGAACGTATTCAA
2621323 AT
1 AT
2621325 ATATATGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (14 bp):
ATGAACGTATTCAA
Found at i:2629092 original size:21 final size:20
Alignment explanation
Indices: 2629058--2629097 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2629048 TCATTAAAAT
*
2629058 TTAAATATTTTTAAAAATTA
1 TTAAATAATTTTAAAAATTA
2629078 TTAATATAATTTTAAAAATT
1 TTAA-ATAATTTTAAAAATT
2629098 CAGTTGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAATAATTTTAAAAATTA
Found at i:2631088 original size:181 final size:182
Alignment explanation
Indices: 2630784--2631146 Score: 719
Period size: 181 Copynumber: 2.0 Consensus size: 182
2630774 AGAGGAGGAA
2630784 GTATATGGTACTCGGGGAAATTTCCCTAAAATACAGCATAACCGATTAGAATCTCTTGAAAGAGC
1 GTATATGGTACTCGGGGAAATTTCCCTAAAATACAGCATAACCGATTAGAATCTCTTGAAAGAGC
2630849 AGTCGAGGATAATGAAATTAAGGAGGCTCTATTTGATATGAGCCCCTTAAAGGCCTCATGGGCTG
66 AGTCGAGGATAATGAAATTAAGGAGGCTCTATTTGATATGAGCCCCTTAAAGGCCTCATGGGCTG
2630914 ATGGTATACATTTGATATTTTATCACAGAAATTGGGGCAC-GTTGGAAAGAG
131 ATGGTATACATTTGATATTTTATCACAGAAATTGGGGCACAGTTGGAAAGAG
2630965 GTATATGGTACTCGGGGAAATTTCCCTAAAATACAGCATAACCGATTAGAATCTCTTGAAAGAGC
1 GTATATGGTACTCGGGGAAATTTCCCTAAAATACAGCATAACCGATTAGAATCTCTTGAAAGAGC
2631030 AGTCGAGGATAATGAAATTAAGGAGGCTCTATTTGATATGAGCCCCTTAAAGGCCTCATGGGCTG
66 AGTCGAGGATAATGAAATTAAGGAGGCTCTATTTGATATGAGCCCCTTAAAGGCCTCATGGGCTG
2631095 ATGGTATACATTTGATATTTTATCACAGAAATTGGGGCACAGTTGGAAAGAG
131 ATGGTATACATTTGATATTTTATCACAGAAATTGGGGCACAGTTGGAAAGAG
2631147 TGTGCCAAAT
Statistics
Matches: 181, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
181 170 0.94
182 11 0.06
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (182 bp):
GTATATGGTACTCGGGGAAATTTCCCTAAAATACAGCATAACCGATTAGAATCTCTTGAAAGAGC
AGTCGAGGATAATGAAATTAAGGAGGCTCTATTTGATATGAGCCCCTTAAAGGCCTCATGGGCTG
ATGGTATACATTTGATATTTTATCACAGAAATTGGGGCACAGTTGGAAAGAG
Found at i:2632064 original size:22 final size:22
Alignment explanation
Indices: 2632039--2632080 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2632029 ATTAGAACAA
2632039 AAATAAAAGAAAT-AATAAAAGT
1 AAAT-AAAGAAATAAATAAAAGT
*
2632061 AAATAAATAAATAAATAAAA
1 AAATAAAGAAATAAATAAAA
2632081 TGTCGGATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (22 bp):
AAATAAAGAAATAAATAAAAGT
Found at i:2632066 original size:13 final size:13
Alignment explanation
Indices: 2632039--2632071 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
2632029 ATTAGAACAA
2632039 AAATAAAAGAAAT
1 AAATAAAAGAAAT
2632052 -AATAAAAGTAAAT
1 AAATAAAAG-AAAT
2632065 AAATAAA
1 AAATAAA
2632072 TAAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 4 0.22
14 6 0.33
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (13 bp):
AAATAAAAGAAAT
Found at i:2634651 original size:65 final size:65
Alignment explanation
Indices: 2634516--2634673 Score: 180
Period size: 65 Copynumber: 2.4 Consensus size: 65
2634506 GACCCTTAGG
* *
2634516 GCATCGATGCATGAAATGGATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGT
1 GCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTGGT
* * * *
2634580 GTATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGTATAG-TA
1 GCATCGATGCATGAAATGCATTCGATGTTTTCA-AAATAGC-CAGAGTGCATCGATGCATAGCT-
*
2634642 TGT
63 GGT
* *
2634645 GCATCGATGTATGAAATGTATTCGATGTT
1 GCATCGATGCATGAAATGCATTCGATGTT
2634674 CAATTTATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
64 26 0.33
65 50 0.63
66 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (65 bp):
GCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTGGT
Found at i:2636941 original size:13 final size:13
Alignment explanation
Indices: 2636923--2636947 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2636913 AATCAAAAAC
2636923 ATCAAATTTAGAA
1 ATCAAATTTAGAA
2636936 ATCAAATTTAGA
1 ATCAAATTTAGA
2636948 TTTTCGATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
ATCAAATTTAGAA
Found at i:2638716 original size:80 final size:79
Alignment explanation
Indices: 2638583--2638741 Score: 309
Period size: 80 Copynumber: 2.0 Consensus size: 79
2638573 TAGCTCCCCC
2638583 ATCATGCTCATCTTGAATTCACTTTGCATTCGCTTAGAAAATTCTTGGCAAAGAACATCATTAGT
1 ATCATGCTCATCTTGAATTCACTTTGCATTCGCTTAGAAAATTCTTGGCAAAGAACATCATTAGT
2638648 AGAACCAAATATTAT
66 A-AACCAAATATTAT
2638663 ATCATGCTCATCTTGAATTCACTTTGCATTCGCTTAGAAAATTCTTGGCAAAGAACATCATTAGT
1 ATCATGCTCATCTTGAATTCACTTTGCATTCGCTTAGAAAATTCTTGGCAAAGAACATCATTAGT
2638728 AAACCAAATATTAT
66 AAACCAAATATTAT
2638742 CTCAACATAA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 13 0.16
80 66 0.84
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (79 bp):
ATCATGCTCATCTTGAATTCACTTTGCATTCGCTTAGAAAATTCTTGGCAAAGAACATCATTAGT
AAACCAAATATTAT
Found at i:2643417 original size:63 final size:65
Alignment explanation
Indices: 2643335--2643476 Score: 193
Period size: 65 Copynumber: 2.2 Consensus size: 65
2643325 TGCACTAAGA
*
2643335 GTGCATCGATGCATGAAATGCATTCGATG-TTTCA-AAATA-GCAGAGAGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACGCAGAGAGCATCGATGCATGG-T
2643397 -G
64 AG
* * * *
2643398 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACGCAGAGAGCATCGATGCATGGTAG
2643463 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2643477 GGTATGTGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
63 28 0.40
64 7 0.10
65 35 0.50
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACGCAGAGAGCATCGATGCATGGTAG
Found at i:2643468 original size:19 final size:19
Alignment explanation
Indices: 2643444--2643496 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
2643434 AAAACTCTGA
2643444 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
2643463 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
*
2643482 GTGCATTGATGCATG
1 GTGCATCGATGCATG
2643497 AAATATATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.15, G:0.32, T:0.32
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:2644429 original size:23 final size:25
Alignment explanation
Indices: 2644383--2644432 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
2644373 TTAGTAGTAT
2644383 TTTATTTATATACTAATTTAATATA
1 TTTATTTATATACTAATTTAATATA
* *
2644408 TTTATTTA-ATTC-AATTTCATATA
1 TTTATTTATATACTAATTTAATATA
2644431 TT
1 TT
2644433 CCTTATAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 3 0.13
25 8 0.35
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTATTTATATACTAATTTAATATA
Found at i:2645347 original size:21 final size:22
Alignment explanation
Indices: 2645321--2645372 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
2645311 ATGTTCCCTT
2645321 GTATCGATACC-CTCCACATA-G
1 GTATCGATACCTCTCC-CATATG
*
2645342 GTATCGATACCTCTTCCATATG
1 GTATCGATACCTCTCCCATATG
2645364 GTATCGATA
1 GTATCGATA
2645373 TTGTTCATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (22 bp):
GTATCGATACCTCTCCCATATG
Found at i:2646571 original size:20 final size:20
Alignment explanation
Indices: 2646516--2646622 Score: 151
Period size: 20 Copynumber: 5.3 Consensus size: 20
2646506 AATCTGTAAA
*
2646516 TCGCAACACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* ** * *
2646536 TCACAATGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
2646556 CCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
2646576 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
2646596 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
2646616 TCGCAAC
1 TCGCAAC
2646623 GCGGAATTTC
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.17
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:2646673 original size:20 final size:19
Alignment explanation
Indices: 2646610--2646682 Score: 92
Period size: 19 Copynumber: 3.7 Consensus size: 19
2646600 AACACAAAAG
*
2646610 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
2646631 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
2646650 TCAAATTTGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
2646670 TCAAATTCGCAAC
1 TCAAATTCGCAAC
2646683 GCTTTGAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
19 19 0.40
20 16 0.34
21 12 0.26
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:2648113 original size:18 final size:18
Alignment explanation
Indices: 2648090--2648125 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2648080 AAGCAAAAGG
2648090 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
2648108 AAATCAAAATCCCAATCA
1 AAATCAAAATCACAATCA
2648126 GAACCGGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:2649928 original size:20 final size:20
Alignment explanation
Indices: 2649905--2649968 Score: 119
Period size: 20 Copynumber: 3.2 Consensus size: 20
2649895 AAACTTAAAT
2649905 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
2649925 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
2649945 TCGCAACGAGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
2649965 TCGC
1 TCGC
2649969 GAAACTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:2649978 original size:20 final size:19
Alignment explanation
Indices: 2649913--2649979 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
2649903 ATTCGCAACG
*
2649913 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAA-A
2649933 CGAAAATGAAAATCGC-AA
1 CGAAAATGAAAATCGCAAA
2649951 CGAGAAAATGAAAATCGCGAAA
1 C--GAAAATGAAAATCGC-AAA
*
2649973 CTAAAAT
1 CGAAAAT
2649980 CGTGTTGCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 36 0.88
22 3 0.07
ACGTcount: A:0.54, C:0.16, G:0.18, T:0.12
Consensus pattern (19 bp):
CGAAAATGAAAATCGCAAA
Found at i:2650018 original size:14 final size:14
Alignment explanation
Indices: 2650001--2650027 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2649991 TTTCATTTCC
2650001 GTGTTGCGATTTTG
1 GTGTTGCGATTTTG
2650015 GTGTTGCGATTTT
1 GTGTTGCGATTTT
2650028 CATTTTCGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.33, T:0.52
Consensus pattern (14 bp):
GTGTTGCGATTTTG
Found at i:2650407 original size:20 final size:22
Alignment explanation
Indices: 2650382--2650446 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
2650372 TCTGAGAGAT
2650382 GGAGAT-A-GACGAATTTCGCC
1 GGAGATGAGGACGAATTTCGCC
* *
2650402 GGAGATGAGGATGAATTTCGTC
1 GGAGATGAGGACGAATTTCGCC
* * *
2650424 GGAGATGGGGACGGATGTCGCC
1 GGAGATGAGGACGAATTTCGCC
2650446 G
1 G
2650447 TAGAGAGTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 29 0.81
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.20
Consensus pattern (22 bp):
GGAGATGAGGACGAATTTCGCC
Found at i:2650579 original size:20 final size:20
Alignment explanation
Indices: 2650548--2650769 Score: 282
Period size: 20 Copynumber: 11.1 Consensus size: 20
2650538 TAATATTGTG
*
2650548 TTTCACGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
2650568 TTCCGTGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
2650588 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
2650608 TTTTGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
2650628 TTTCGCGTTACAAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
2650648 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
2650668 TTTTGTGTTGCGAATTTGGC
1 TTTCGCGTTGCGAATTTGAC
*
2650688 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
2650708 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
2650728 TTTTGTGTTGCGGATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
2650748 TATCGCGTTGCAAAATTGAC
1 TTTCGCGTTGCGAATTTGAC
2650768 TT
1 TT
2650770 CTGTGTTGCG
Statistics
Matches: 171, Mismatches: 31, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 171 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:2650780 original size:60 final size:60
Alignment explanation
Indices: 2650554--2650768 Score: 324
Period size: 60 Copynumber: 3.6 Consensus size: 60
2650544 TGTGTTTCAC
* * * *
2650554 GTTGCGAATTTGACT-TCCGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTTTGC
1 GTTGCGAATTTGACTAT-CGCGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* *
2650614 GTTGCGAATTTGACTTTCGCGTTACAAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGCGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* *
2650674 GTTGCGAATTTGGCTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGCGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* *
2650734 GTTGCGGATTTGACTATCGCGTTGCAAAATTGACT
1 GTTGCGAATTTGACTATCGCGTTGCAAATTTGACT
2650769 TCTGTGTTGC
Statistics
Matches: 141, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
60 140 0.99
61 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (60 bp):
GTTGCGAATTTGACTATCGCGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
Done.