Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 8 of 120
Found at i:2350587 original size:31 final size:31
Alignment explanation
Indices: 2350545--2350619 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
2350535 AATTAAAATA
*
2350545 AAAATTTAAAAAAGTATTTTAAAAAAATTTT
1 AAAATTAAAAAAAGTATTTTAAAAAAATTTT
2350576 AAAATTAAAAAAAGTATTTTAAAAAAATTTT
1 AAAATTAAAAAAAGTATTTTAAAAAAATTTT
2350607 AAAATTAAAAAAA
1 AAAATTAAAAAAA
2350620 TTTAAAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (31 bp):
AAAATTAAAAAAAGTATTTTAAAAAAATTTT
Found at i:2350627 original size:17 final size:17
Alignment explanation
Indices: 2350563--2350626 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
2350553 AAAAAGTATT
2350563 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
*
2350580 TTAAAAAAAGTATT----
1 TTAAAAAAA-TTTTAAAA
2350594 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
2350611 TTAAAAAAA-TTTAAAA
1 TTAAAAAAATTTTAAAA
2350627 AAAGTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
13 3 0.08
14 9 0.22
16 7 0.17
17 18 0.45
18 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TTAAAAAAATTTTAAAA
Found at i:2350990 original size:12 final size:12
Alignment explanation
Indices: 2350969--2351007 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2350959 AATTGAATTG
*
2350969 AATTTTATTTCT
1 AATTTAATTTCT
2350981 AATTTAATTTCT
1 AATTTAATTTCT
2350993 AA-TTAATTT-T
1 AATTTAATTTCT
2351003 AATTT
1 AATTT
2351008 TATATGATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 3 0.12
11 9 0.36
12 13 0.52
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (12 bp):
AATTTAATTTCT
Found at i:2357650 original size:2 final size:2
Alignment explanation
Indices: 2357643--2357689 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2357633 NNNNTACTAC
2357643 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2357685 TA TA T
1 TA TA T
2357690 TCATATTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2359061 original size:13 final size:11
Alignment explanation
Indices: 2359029--2359071 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2359019 CCATTTTCTA
*
2359029 AATAAAATAAT
1 AATAAAATATT
2359040 AAT-AAATATTT
1 AATAAAATA-TT
2359051 AAGTAAAATATT
1 AA-TAAAATATT
2359063 AATAAAATA
1 AATAAAATA
2359072 ATTTTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:2361700 original size:13 final size:13
Alignment explanation
Indices: 2361684--2361711 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2361674 ACCCATATGC
2361684 GACACTTATATCA
1 GACACTTATATCA
2361697 GACACTTATATCA
1 GACACTTATATCA
2361710 GA
1 GA
2361712 GTCCGAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (13 bp):
GACACTTATATCA
Found at i:2370139 original size:167 final size:166
Alignment explanation
Indices: 2369864--2370203 Score: 653
Period size: 167 Copynumber: 2.0 Consensus size: 166
2369854 GACAAACTCG
*
2369864 ACCACCATCAGAAGCAATGTAAACACACCGCTGATCAATATTTTTGATCTCAAGGATCAGTAAAA
1 ACCACCATCAGAAGCAATGTAAACACACCGCTGATCAATATATTTGATCTCAAGGATCAGTAAAA
2369929 ATTTAAAATAAAAGAAAAAAAATACAGTACACAGGAGCAATGAAAACCACTAGTCCCATCTGCAC
66 ATTTAAAATAAAAGAAAAAAAATACAGTACACAGGAGCAATGAAAACCACTAGTCCCATCTGCAC
2369994 TCTAGTCTAATTTCAACATGATCATAGAAAACGAAT
131 TCTAGTCTAATTTCAACATGATCATAGAAAACGAAT
2370030 ACCACCATCAGAAGCAATGTAAACACACCGCTGATCAATATATTTGAATCTCAAGGATCAGTAAA
1 ACCACCATCAGAAGCAATGTAAACACACCGCTGATCAATATATTTG-ATCTCAAGGATCAGTAAA
2370095 AATTTAAAATAAAAGAAAAAAAATACAGTACACAGGAGCAATGAAAACCACTAGTCCCATCTGCA
65 AATTTAAAATAAAAGAAAAAAAATACAGTACACAGGAGCAATGAAAACCACTAGTCCCATCTGCA
2370160 CTCTAGTCTAATTTCAACATGATCATAGAAAACGAAT
130 CTCTAGTCTAATTTCAACATGATCATAGAAAACGAAT
*
2370197 ACAACCA
1 ACCACCA
2370204 AATATGGAGA
Statistics
Matches: 171, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
166 45 0.26
167 126 0.74
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (166 bp):
ACCACCATCAGAAGCAATGTAAACACACCGCTGATCAATATATTTGATCTCAAGGATCAGTAAAA
ATTTAAAATAAAAGAAAAAAAATACAGTACACAGGAGCAATGAAAACCACTAGTCCCATCTGCAC
TCTAGTCTAATTTCAACATGATCATAGAAAACGAAT
Found at i:2370359 original size:123 final size:123
Alignment explanation
Indices: 2370135--2370379 Score: 330
Period size: 123 Copynumber: 2.0 Consensus size: 123
2370125 CACAGGAGCA
* * *
2370135 ATGAAAACCACTAGTCCCATCTGCACTCTAGTCTAATTTCAACATGATCATAGAAAACGAATACA
1 ATGAAAACCACTAGTCACATCTGCACTCTAGTCCAATTTCAACATGATCATAGAAAACAAATACA
**** * * *
2370200 ACCAAATATGGAGACAGCAATGTGCTGGTTCAAAAGGGATTATATTAGGACATGCACG
66 ACCAAATATGGAGACAGCAAACAACTGGTTCAAAAGGGATTAGAATAGAACATGCACG
* *
2370258 ATGAAAACCACTAGTTACATCTGCACTCTAGTCCAATTTCAACATGATCATAGAAAACAAATAGA
1 ATGAAAACCACTAGTCACATCTGCACTCTAGTCCAATTTCAACATGATCATAGAAAACAAATACA
* * **
2370323 ACCAGATATGGATACAGCAACACAACT-GTTTGAAAGGGATTAGAATAGAACATGCAC
66 ACCAAATATGGAGACAGCAA-ACAACTGGTTCAAAAGGGATTAGAATAGAACATGCAC
2370380 TCAGTGGGAT
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
123 103 0.98
124 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (123 bp):
ATGAAAACCACTAGTCACATCTGCACTCTAGTCCAATTTCAACATGATCATAGAAAACAAATACA
ACCAAATATGGAGACAGCAAACAACTGGTTCAAAAGGGATTAGAATAGAACATGCACG
Found at i:2374220 original size:13 final size:13
Alignment explanation
Indices: 2374204--2374228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2374194 GAGAAAATTA
2374204 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
2374217 AAAAGAAAAAAA
1 AAAAGAAAAAAA
2374229 AAATAAGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:2378171 original size:5 final size:5
Alignment explanation
Indices: 2378161--2378192 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
2378151 AATGAGCATG
2378161 AATAT AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AA
2378193 AGGCCTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:2383865 original size:23 final size:23
Alignment explanation
Indices: 2383834--2383896 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
2383824 ACCTGTTTTT
2383834 TTTTA-ATTTATTAAATAATATA
1 TTTTATATTTATTAAATAATATA
*
2383856 TTTTATATTT-TTAAA-AATATG
1 TTTTATATTTATTAAATAATATA
* *
2383877 TATT-TATTAATTAAATAATA
1 TTTTATATTTATTAAATAATA
2383897 ATTAGTCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 4 0.11
21 13 0.37
22 14 0.40
23 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTATATTTATTAAATAATATA
Found at i:2384983 original size:15 final size:15
Alignment explanation
Indices: 2384933--2384984 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2384923 CCAAAACAGG
* *
2384933 ATAGAGCAGAACAGA
1 ATAGAGCAAAACTGA
*
2384948 GTAGAGCAAAACTGA
1 ATAGAGCAAAACTGA
*
2384963 ACAGAGCAAAA-TGGA
1 ATAGAGCAAAACT-GA
2384978 ATAGAGC
1 ATAGAGC
2384985 TACGCAAAGG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 1 0.03
15 29 0.97
ACGTcount: A:0.50, C:0.13, G:0.27, T:0.10
Consensus pattern (15 bp):
ATAGAGCAAAACTGA
Found at i:2385608 original size:121 final size:120
Alignment explanation
Indices: 2385380--2385620 Score: 369
Period size: 121 Copynumber: 2.0 Consensus size: 120
2385370 TTAACCCGAT
*
2385380 GTAGCCAAGGATCGTAAAAGTACCACAAAACTCTTTTTACTATATCTAAGATTGCATTTTAGCCA
1 GTAGCCAAGGATCGTAAAAGTACCACAAAACTCTTTTTACTATATCCAAGATTGCATTTTAGCCA
* * *
2385445 TTCTACTAAAAAATGAGCAAATTAGTCCTTGTACATTTGATGAGTGAGCAAAACA
66 TTATACTAAAAAATGAGCAAATTAGTCCATGTACATTAGATGAGTGAGCAAAACA
* *
2385500 GTAGCCAATGATCAGTAAAAGTACCACAAAACTCTTTTTACTATATCCCAGATTGCATTTTCA-C
1 GTAGCCAAGGATC-GTAAAAGTACCACAAAACTCTTTTTACTATATCCAAGATTGCATTTT-AGC
* *
2385564 CCTTATACTAAAAAAATGGGCAAATTAGT-CATGTACATTAGATGAGTGAGCAAAACA
64 CATTATACT-AAAAAATGAGCAAATTAGTCCATGTACATTAGATGAGTGAGCAAAACA
2385621 ATCGCTCCGT
Statistics
Matches: 110, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
120 12 0.11
121 79 0.72
122 19 0.17
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (120 bp):
GTAGCCAAGGATCGTAAAAGTACCACAAAACTCTTTTTACTATATCCAAGATTGCATTTTAGCCA
TTATACTAAAAAATGAGCAAATTAGTCCATGTACATTAGATGAGTGAGCAAAACA
Found at i:2385862 original size:21 final size:23
Alignment explanation
Indices: 2385836--2385884 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
2385826 TTTAAAATTT
*
2385836 AAAAATTATTAA-AAAA-TCATA
1 AAAAATTATAAACAAAATTCATA
*
2385857 AAAAATTATAAACAAAATTTATA
1 AAAAATTATAAACAAAATTCATA
2385880 AAAAA
1 AAAAA
2385885 AAGTTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.46
22 4 0.17
23 9 0.38
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAAATTATAAACAAAATTCATA
Found at i:2385867 original size:10 final size:10
Alignment explanation
Indices: 2385836--2385884 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
2385826 TTTAAAATTT
2385836 AAAAATTATTA
1 AAAAATTA-TA
*
2385847 AAAAATCATA
1 AAAAATTATA
2385857 AAAAATTATAA
1 AAAAATTAT-A
2385868 ACAAAATTTATA
1 A-AAAA-TTATA
2385880 AAAAA
1 AAAAA
2385885 AAGTTATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 10 0.30
11 13 0.39
12 6 0.18
13 4 0.12
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATTATA
Found at i:2393020 original size:20 final size:21
Alignment explanation
Indices: 2392963--2393020 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 21
2392953 AATGAGTTTC
*
2392963 TTTTTTTTATAAAT-TTTGAA
1 TTTTTTTCATAAATATTTGAA
* * * *
2392983 TATTATTCTTAAAAATTT-AA
1 TTTTTTTCATAAATATTTGAA
2393003 TTTTTTTCATAAATATTT
1 TTTTTTTCATAAATATTT
2393021 TCAAAAATAA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTTTTCATAAATATTTGAA
Found at i:2393669 original size:2 final size:2
Alignment explanation
Indices: 2393664--2393706 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2393654 AAAAAAAAAT
*
2393664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2393706 T
1 T
2393707 CATTTTGACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2397485 original size:23 final size:22
Alignment explanation
Indices: 2397459--2397537 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
2397449 TAAAACACTG
2397459 AATATAACACGCACAAGGTGCTA
1 AATATAACACGCACAAGG-GCTA
* *
2397482 AATATAACACGCATATAGCGCTA
1 AATATAACACGCACA-AGGGCTA
* *
2397505 AATGTAACATGCACAAAGGGCT-
1 AATATAACACGCAC-AAGGGCTA
*
2397527 GATATAACACG
1 AATATAACACG
2397538 TGTAAAGCAC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
22 8 0.18
23 34 0.76
24 3 0.07
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (22 bp):
AATATAACACGCACAAGGGCTA
Found at i:2397513 original size:46 final size:45
Alignment explanation
Indices: 2397436--2397537 Score: 107
Period size: 46 Copynumber: 2.2 Consensus size: 45
2397426 CAATCACACC
* *
2397436 AATATAACATGCATAAAACACTGAATATAACACGCAC-AAGGTGCT
1 AATATAACACGCATAAAACACTAAATATAACACGCACAAAGG-GCT
* * * * *
2397481 AAATATAACACGCATATAGCGCTAAATGTAACATGCACAAAGGGCT
1 -AATATAACACGCATAAAACACTAAATATAACACGCACAAAGGGCT
*
2397527 GATATAACACG
1 AATATAACACG
2397538 TGTAAAGCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
45 10 0.21
46 33 0.70
47 4 0.09
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (45 bp):
AATATAACACGCATAAAACACTAAATATAACACGCACAAAGGGCT
Found at i:2400512 original size:2 final size:2
Alignment explanation
Indices: 2400505--2400530 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2400495 ACTCTATTTT
2400505 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2400531 ACGTATACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2400959 original size:22 final size:20
Alignment explanation
Indices: 2400919--2400957 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2400909 TTAATACCAC
*
2400919 AATATATTAAATATATTTAA
1 AATATATAAAATATATTTAA
2400939 AATATATAATAATATATTT
1 AATATATAA-AATATATTT
2400958 TATCCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATAAAATATATTTAA
Found at i:2401568 original size:275 final size:277
Alignment explanation
Indices: 2401010--2401584 Score: 757
Period size: 275 Copynumber: 2.1 Consensus size: 277
2401000 ATATCTATAT
* * *
2401010 TATTATTTAAGTGTTTTACTGAGTTGGTATTACCTTCAATCGAGTCACCAACTCAATTGTTAAAT
1 TATTATTTAAGTGTTTTACTGAGTTGGTATCACCCTCAAACGAGTCACCAACTCAATTGTTAAAT
** * * * *
2401075 TACGGGAATACTCTCCTGTAATTAAGAAAGTTATATTATTCAAGGGTATTTTAATTTTTTTCATT
66 TACGAAAATACCCTCCTGTAATTAAAAAAGTTATATTATTCAAGGATATTTTAATATTTTTCATT
* * * *
2401140 TAAAAAAACCAATATGGTGACCCGTGTTGATTGCATCAATAAAACGTTTAATTTACCACTCAACT
131 TAAAAAAACCAAAATGATGA-CCATGTTAATTGCATCAATAAAACGTTTAATTTACCACTCAACT
* * * * * ** *
2401205 AAAGCTTTGTTTTGATATTTTTCTATGTTTTTATTTTATTATGCACATTTTATCACATTCATCAA
195 AAAACTTTATTTTAATATTCTTATACATTTTTATTTTATTATGCACACTTTATCACATTCATCAA
*
2401270 TTGTATATCTATACTTAC
260 TTGTACATCTATACTTAC
* *
2401288 TATTATTTAAGTGTTTTATTGAGTTGGTGTCACCCTCAAACGAGTCACCAACTCAATTGTTAAAT
1 TATTATTTAAGTGTTTTACTGAGTTGGTATCACCCTCAAACGAGTCACCAACTCAATTGTTAAAT
* ** *
2401353 TATGAAAATACCCTTTTGTAATTAAAAAAGTTATATTATTCGAGGATATTTTAATATTTTT-A-T
66 TACGAAAATACCCTCCTGTAATTAAAAAAGTTATATTATTCAAGGATATTTTAATATTTTTCATT
* * * * *
2401416 TACAAATCAA-TAAAATTATG-TCATGTTAATTGCATCAATAAAACTTTTAATTTACCACTCAAC
131 TA-AAA-AAACCAAAATGATGACCATGTTAATTGCATCAATAAAACGTTTAATTTACCACTCAAC
2401479 TAAAACTTTATTTTAATATTCTTATACATTTTTATTTTATTATGCACACTTTAT-A-ATTTCCAT
194 TAAAACTTTATTTTAATATTCTTATACATTTTTATTTTATTATGCACACTTTATCACA-TT-CAT
2401542 CAATTGTACATCTATACTTAC
257 CAATTGTACATCTATACTTAC
*
2401563 TATTATTTAAGTGTTTAACTGA
1 TATTATTTAAGTGTTTTACTGA
2401585 ATTGACGTCA
Statistics
Matches: 258, Mismatches: 35, Indels: 11
0.85 0.12 0.04
Matches are distributed among these distances:
273 1 0.00
274 3 0.01
275 128 0.50
276 3 0.01
277 10 0.04
278 113 0.44
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (277 bp):
TATTATTTAAGTGTTTTACTGAGTTGGTATCACCCTCAAACGAGTCACCAACTCAATTGTTAAAT
TACGAAAATACCCTCCTGTAATTAAAAAAGTTATATTATTCAAGGATATTTTAATATTTTTCATT
TAAAAAAACCAAAATGATGACCATGTTAATTGCATCAATAAAACGTTTAATTTACCACTCAACTA
AAACTTTATTTTAATATTCTTATACATTTTTATTTTATTATGCACACTTTATCACATTCATCAAT
TGTACATCTATACTTAC
Found at i:2411412 original size:3 final size:3
Alignment explanation
Indices: 2411404--2411455 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2411394 ATTCTTAAAT
2411404 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2411452 TAA T
1 TAA T
2411456 TGCTGCCATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2425812 original size:27 final size:27
Alignment explanation
Indices: 2425709--2425819 Score: 141
Period size: 27 Copynumber: 4.1 Consensus size: 27
2425699 AACATGTCAG
* * *
2425709 GAAAGAATAGCTTTTGTGGTGATCTTT
1 GAAAGAATAACCTTTGTGGTGAACTTT
*
2425736 GAAAGAATAACCTTTGTGGTGAATTTT
1 GAAAGAATAACCTTTGTGGTGAACTTT
*
2425763 GAAAGAATAACCTTTATGGTGAACTTT
1 GAAAGAATAACCTTTGTGGTGAACTTT
* * * *
2425790 AAAAGAATAACCCTTGTAGTGAACTCT
1 GAAAGAATAACCTTTGTGGTGAACTTT
2425817 GAA
1 GAA
2425820 TGGACATGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (27 bp):
GAAAGAATAACCTTTGTGGTGAACTTT
Found at i:2432568 original size:32 final size:34
Alignment explanation
Indices: 2432527--2432612 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 34
2432517 AACTTTTCCG
* *
2432527 GAAAATATTTT-CAGGAAATCTG-CCAAACAGCA
1 GAAAATATTTTACAGCAAATCTGACCAAACACCA
*
2432559 GAAAATATTTTACA-CAGAT-TGATCCAAACACCA
1 GAAAATATTTTACAGCAAATCTGA-CCAAACACCA
* *
2432592 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
2432613 ATTTTACAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
31 2 0.05
32 14 0.33
33 24 0.56
34 3 0.07
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.26
Consensus pattern (34 bp):
GAAAATATTTTACAGCAAATCTGACCAAACACCA
Found at i:2432611 original size:14 final size:15
Alignment explanation
Indices: 2432589--2432665 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
2432579 GATCCAAACA
2432589 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
2432603 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
2432618 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
2432638 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
2432652 AC-GAAAAACATTTT
1 CCAGAAAATCATTTT
2432666 ACTGGCAAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
13 1 0.02
14 24 0.48
15 11 0.22
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:2432630 original size:20 final size:20
Alignment explanation
Indices: 2432605--2432644 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2432595 AATATTTTCC
*
2432605 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
2432625 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
2432645 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:2432650 original size:34 final size:34
Alignment explanation
Indices: 2432593--2432658 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
2432583 CAAACACCAG
*
2432593 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
2432628 AAAACATTTTCCAG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
2432659 ACATTTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:2433189 original size:12 final size:11
Alignment explanation
Indices: 2433174--2433251 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 11
2433164 TAAAAATTAA
2433174 AAAAAGTATTTT
1 AAAAA-TATTTT
2433186 AAAAATATTTT
1 AAAAATATTTT
2433197 --AAA-A--TT
1 AAAAATATTTT
* **
2433203 AAAAAAATTAA
1 AAAAATATTTT
2433214 AAAAAGTATTTT
1 AAAAA-TATTTT
*
2433226 AAAAAAATTTT
1 AAAAATATTTT
*
2433237 AAAAAAATTTT
1 AAAAATATTTT
2433248 AAAA
1 AAAA
2433252 TTAAAAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
6 2 0.04
8 4 0.07
9 4 0.07
11 31 0.57
12 13 0.24
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:2433215 original size:8 final size:9
Alignment explanation
Indices: 2433197--2433268 Score: 56
Period size: 9 Copynumber: 7.3 Consensus size: 9
2433187 AAAATATTTT
2433197 AAAATTAAA
1 AAAATTAAA
2433206 AAAATTAAAA
1 AAAATT-AAA
2433216 AAAGTATTTTAAA
1 AAA--A--TTAAA
2433229 AAAATTTTAAA
1 AAAA--TTAAA
**
2433240 AAAATT-TT
1 AAAATTAAA
2433248 AAAATTAAA
1 AAAATTAAA
2433257 AAAATTAAA
1 AAAATTAAA
2433266 AAA
1 AAA
2433269 GTATTTTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
8 6 0.11
9 20 0.38
10 6 0.11
11 12 0.23
12 1 0.02
13 6 0.11
14 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (9 bp):
AAAATTAAA
Found at i:2433229 original size:11 final size:11
Alignment explanation
Indices: 2433201--2433251 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
2433191 TATTTTAAAA
2433201 TTAAAAAAA-T
1 TTAAAAAAATT
*
2433211 TAAAAAAAGTATT
1 TTAAAAAA--ATT
2433224 TTAAAAAAATT
1 TTAAAAAAATT
2433235 TTAAAAAAATT
1 TTAAAAAAATT
2433246 TTAAAA
1 TTAAAA
2433252 TTAAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
10 7 0.19
11 20 0.56
12 1 0.03
13 8 0.22
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
TTAAAAAAATT
Found at i:2433241 original size:51 final size:50
Alignment explanation
Indices: 2433181--2433289 Score: 182
Period size: 51 Copynumber: 2.2 Consensus size: 50
2433171 TAAAAAAAGT
*
2433181 ATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAA
1 ATTTTAAAAAAATTTTAAAATTAAAAAAATT-AAAAAAGTATTTTAAAAAA
**
2433232 ATTTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAGT
1 ATTTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAAA
2433282 ATTTTAAA
1 ATTTTAAA
2433290 GTTAAAAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 25 0.45
51 30 0.55
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (50 bp):
ATTTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAAA
Found at i:2433268 original size:17 final size:17
Alignment explanation
Indices: 2433235--2433268 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2433225 TAAAAAAATT
**
2433235 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTAAAAAA
2433252 TTAAAAAAATTAAAAAA
1 TTAAAAAAATTAAAAAA
2433269 GTATTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAAAAAATTAAAAAA
Found at i:2433279 original size:11 final size:11
Alignment explanation
Indices: 2433265--2433289 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2433255 AAAAAATTAA
2433265 AAAAGTATTTT
1 AAAAGTATTTT
2433276 AAAAGTATTTT
1 AAAAGTATTTT
2433287 AAA
1 AAA
2433290 GTTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:2433286 original size:39 final size:36
Alignment explanation
Indices: 2433224--2433305 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 36
2433214 AAAAAGTATT
2433224 TTAAAAAAATTTTAAAAAAATTTTAAAATTAAAAAAA
1 TTAAAAAAATTTTAAAAAAATTTTAAAATT-AAAAAA
** *
2433261 TTAAAAAAGTATTTTAAAAGTATTTTAAAGTTAAAAAA
1 TTAAAAAA--ATTTTAAAAAAATTTTAAAATTAAAAAA
2433299 -TAAAAAA
1 TTAAAAAA
2433306 TAAAAANNNN
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
37 15 0.38
38 6 0.15
39 19 0.47
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (36 bp):
TTAAAAAAATTTTAAAAAAATTTTAAAATTAAAAAA
Found at i:2439928 original size:171 final size:171
Alignment explanation
Indices: 2439643--2439978 Score: 566
Period size: 171 Copynumber: 2.0 Consensus size: 171
2439633 AGGGGGAACA
*
2439643 TATTTGCTTCTCCAAAGAATTACCCAAAACTCAATCCCATGATCCTGTCCCACCTTCACATGATG
1 TATTTGCTGCTCCAAAGAATTACCCAAAACTCAATCCCATGATCCTGTCCCACCTTCACATGATG
* *
2439708 AGATGGATCAGTTACAGGAACGTAATTGTAGTAGCTCCTTTCCTCCTGCTTCTCTAGATCCTCCA
66 AGATGGATCAGTTACAGGAACGTAATTGTAGCAGCTCCTTTCCTCCTGCTTCTCTAGATCCTACA
* *
2439773 TCCTCAGGTCAGAAGTTCGTATCTCCCATGGCAAAAGTTTG
131 TCCTCAGGTCAAAAGTTCGTATCTCCCATAGCAAAAGTTTG
* *
2439814 TATTTGCTGCTCCAAAGAATTACCCAAAACTCAATCCCATGATCCTGTGCCACCTTCACATGTTG
1 TATTTGCTGCTCCAAAGAATTACCCAAAACTCAATCCCATGATCCTGTCCCACCTTCACATGATG
* *
2439879 AGATGGATCAGTTACGGGATCGTAATTGTAGCAGCTCCCTTT-CTCCTGCTTCTCTAGATCCTAC
66 AGATGGATCAGTTACAGGAACGTAATTGTAGCAGCT-CCTTTCCTCCTGCTTCTCTAGATCCTAC
*
2439943 ATCCTCAGGTCAAAAGTTTGTATCTCCCATAGCAAA
130 ATCCTCAGGTCAAAAGTTCGTATCTCCCATAGCAAA
2439979 GGAAAATCAT
Statistics
Matches: 154, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
171 149 0.97
172 5 0.03
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (171 bp):
TATTTGCTGCTCCAAAGAATTACCCAAAACTCAATCCCATGATCCTGTCCCACCTTCACATGATG
AGATGGATCAGTTACAGGAACGTAATTGTAGCAGCTCCTTTCCTCCTGCTTCTCTAGATCCTACA
TCCTCAGGTCAAAAGTTCGTATCTCCCATAGCAAAAGTTTG
Found at i:2441707 original size:13 final size:12
Alignment explanation
Indices: 2441678--2441713 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
2441668 AAAAAATTAA
*
2441678 TTATAAATTTTT
1 TTATAATTTTTT
2441690 TTATAATTTTTGT
1 TTATAATTTTT-T
2441703 TTATAATTTTT
1 TTATAATTTTT
2441714 ATGCTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
TTATAATTTTTT
Found at i:2451031 original size:24 final size:24
Alignment explanation
Indices: 2450925--2451105 Score: 260
Period size: 25 Copynumber: 7.5 Consensus size: 24
2450915 ATACGGAACA
* *
2450925 AATA-CAGAGAGCACAAATGTGCT
1 AATATCAGAGAGCACCAACGTGCT
***
2450948 AA-A-CAGAGAGCACTGGCGTGCT
1 AATATCAGAGAGCACCAACGTGCT
2450970 AAATATCAGAGAGCACCAACGTGCT
1 -AATATCAGAGAGCACCAACGTGCT
2450995 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
2451020 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
2451044 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
2451069 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
*
2451093 AATATTAGAGAGC
1 AATATCAGAGAGC
2451106 GCGCTAAAGT
Statistics
Matches: 145, Mismatches: 8, Indels: 9
0.90 0.05 0.06
Matches are distributed among these distances:
22 16 0.11
23 4 0.03
24 61 0.42
25 64 0.44
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (24 bp):
AATATCAGAGAGCACCAACGTGCT
Found at i:2451037 original size:49 final size:49
Alignment explanation
Indices: 2450925--2451105 Score: 264
Period size: 49 Copynumber: 3.8 Consensus size: 49
2450915 ATACGGAACA
* * ***
2450925 AATA-CAGAGAGCACAAATGTGCT-A-AA-CAGAGAGCACTGGCGTGCT
1 AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
2450970 AAATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
1 -AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
2451020 AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
*
2451069 AATATCAGAGAGCACCAACGTGCTAAT-ATTAGAGAGC
1 AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGC
2451106 GCGCTAAAGT
Statistics
Matches: 125, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
46 4 0.03
47 17 0.14
48 10 0.08
49 78 0.62
50 16 0.13
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (49 bp):
AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
Found at i:2451959 original size:12 final size:13
Alignment explanation
Indices: 2451942--2451973 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2451932 GATTTCCATC
2451942 AATTCAAT-CACT
1 AATTCAATCCACT
2451954 AATTC-ATCCACT
1 AATTCAATCCACT
2451966 AATTCAAT
1 AATTCAAT
2451974 ATAAGCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 14 0.78
13 2 0.11
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (13 bp):
AATTCAATCCACT
Found at i:2452231 original size:5 final size:5
Alignment explanation
Indices: 2452221--2452255 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
2452211 TATATATATA
*
2452221 ATAAT ATAAT ATAAT ATTAT AATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAA
2452256 CAACTCACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:2452241 original size:21 final size:22
Alignment explanation
Indices: 2452212--2452255 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
2452202 CTTTTGATTT
2452212 ATATATATAATAATATAATATA
1 ATATATATAATAATATAATATA
2452234 ATAT-TATAATAATATAATATA
1 ATATATATAATAATATAATATA
2452255 A
1 A
2452256 CAACTCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATATAATAATATAATATA
Found at i:2457968 original size:24 final size:24
Alignment explanation
Indices: 2457862--2458042 Score: 260
Period size: 25 Copynumber: 7.5 Consensus size: 24
2457852 ATACGGAACA
* *
2457862 AATA-CAGAGAGCACAAATGTGCT
1 AATATCAGAGAGCACCAACGTGCT
***
2457885 AA-A-CAGAGAGCACTGGCGTGCT
1 AATATCAGAGAGCACCAACGTGCT
2457907 AAATATCAGAGAGCACCAACGTGCT
1 -AATATCAGAGAGCACCAACGTGCT
2457932 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
2457957 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
2457981 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
2458006 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
*
2458030 AATATTAGAGAGC
1 AATATCAGAGAGC
2458043 GCGCTAAAGT
Statistics
Matches: 145, Mismatches: 8, Indels: 9
0.90 0.05 0.06
Matches are distributed among these distances:
22 16 0.11
23 4 0.03
24 61 0.42
25 64 0.44
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (24 bp):
AATATCAGAGAGCACCAACGTGCT
Found at i:2457974 original size:49 final size:49
Alignment explanation
Indices: 2457862--2458042 Score: 264
Period size: 49 Copynumber: 3.8 Consensus size: 49
2457852 ATACGGAACA
* * ***
2457862 AATA-CAGAGAGCACAAATGTGCT-A-AA-CAGAGAGCACTGGCGTGCT
1 AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
2457907 AAATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
1 -AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
2457957 AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
*
2458006 AATATCAGAGAGCACCAACGTGCTAAT-ATTAGAGAGC
1 AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGC
2458043 GCGCTAAAGT
Statistics
Matches: 125, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
46 4 0.03
47 17 0.14
48 10 0.08
49 78 0.62
50 16 0.13
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (49 bp):
AATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
Found at i:2458893 original size:12 final size:13
Alignment explanation
Indices: 2458876--2458907 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2458866 GATTTCCATC
2458876 AATTCAAT-CACT
1 AATTCAATCCACT
2458888 AATTC-ATCCACT
1 AATTCAATCCACT
2458900 AATTCAAT
1 AATTCAAT
2458908 ATAAGCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 14 0.78
13 2 0.11
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (13 bp):
AATTCAATCCACT
Found at i:2459165 original size:5 final size:5
Alignment explanation
Indices: 2459155--2459189 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
2459145 TATATATATA
*
2459155 ATAAT ATAAT ATAAT ATTAT AATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAA
2459190 CAACTCACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:2459175 original size:21 final size:22
Alignment explanation
Indices: 2459146--2459189 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
2459136 CTTTTGATTT
2459146 ATATATATAATAATATAATATA
1 ATATATATAATAATATAATATA
2459168 ATAT-TATAATAATATAATATA
1 ATATATATAATAATATAATATA
2459189 A
1 A
2459190 CAACTCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATATAATAATATAATATA
Found at i:2462360 original size:41 final size:41
Alignment explanation
Indices: 2462299--2462509 Score: 343
Period size: 41 Copynumber: 5.1 Consensus size: 41
2462289 CTTTTGTGGC
*
2462299 GTTTTTGAAAAAGCGTCGCTAATGCTCGGGTCTTTAGCGGT
1 GTTTTTGAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGT
* *
2462340 GTTTTTGAAAAAGCACCGCTAATGCTCGGGTATTTAGCGGT
1 GTTTTTGAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGT
* * *
2462381 GTTTTTGAAAAAGCGTCGCTAATGCTCGTGTCTTTAGCGGC
1 GTTTTTGAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGT
*
2462422 GTTTTTGAAAAAGCACCGCTAATGCTCGGGTCTTTAGCGGT
1 GTTTTTGAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGT
2462463 GTTTTTGAAAAAGCGCCGCTAATGCTCGGGTCTTTAGC-GT
1 GTTTTTGAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGT
2462503 CGTTTTT
1 -GTTTTT
2462510 ATAAAAAAAA
Statistics
Matches: 156, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 2 0.01
41 154 0.99
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.34
Consensus pattern (41 bp):
GTTTTTGAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGT
Found at i:2465394 original size:16 final size:16
Alignment explanation
Indices: 2465372--2465436 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
2465362 CACTATATTG
2465372 GAATAGAGGCGTAATA
1 GAATAGAGGCGTAATA
* *
2465388 AAATAGAGGCGTAATG
1 GAATAGAGGCGTAATA
* *
2465404 GAATAGATGCGTAATG
1 GAATAGAGGCGTAATA
2465420 GAATAGAGGCGTAATA
1 GAATAGAGGCGTAATA
2465436 G
1 G
2465437 GTAATTCTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.42, C:0.06, G:0.32, T:0.20
Consensus pattern (16 bp):
GAATAGAGGCGTAATA
Found at i:2465498 original size:44 final size:46
Alignment explanation
Indices: 2465416--2465508 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
2465406 ATAGATGCGT
* *
2465416 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
2465462 AATGAAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
2465506 AAT
1 AAT
2465509 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 24 0.53
45 3 0.07
46 18 0.40
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (46 bp):
AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:2465504 original size:39 final size:44
Alignment explanation
Indices: 2465416--2465521 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 44
2465406 ATAGATGCGT
*
2465416 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
*
2465462 AATGAAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
*
2465501 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
2465522 CATAGGAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 18 0.33
40 2 0.04
43 1 0.02
44 13 0.24
45 3 0.05
46 18 0.33
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:2466026 original size:15 final size:16
Alignment explanation
Indices: 2465980--2466044 Score: 57
Period size: 18 Copynumber: 4.2 Consensus size: 16
2465970 ATAATACTAT
2465980 AAAATATAATTTAA-A
1 AAAATATAATTTAATA
* *
2465995 ATAAT-T-A-TTATTA
1 AAAATATAATTTAATA
*
2466008 AAAATATAATTTAGTAA
1 AAAATATAATTTAAT-A
2466025 AAATATATAATTTAATA
1 AAA-ATATAATTTAATA
2466042 AAA
1 AAA
2466045 TTCTTAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
12 3 0.08
13 6 0.15
14 2 0.05
15 5 0.13
16 4 0.10
17 8 0.21
18 11 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAATATAATTTAATA
Found at i:2466032 original size:18 final size:17
Alignment explanation
Indices: 2466007--2466044 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2465997 AATTATTATT
*
2466007 AAAAATATAATTTAGTA
1 AAAAATATAATTTAATA
2466024 AAAATATATAATTTAATA
1 AAAA-ATATAATTTAATA
2466042 AAA
1 AAA
2466045 TTCTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATATAATTTAATA
Found at i:2466063 original size:122 final size:121
Alignment explanation
Indices: 2465666--2466356 Score: 1196
Period size: 122 Copynumber: 5.7 Consensus size: 121
2465656 TTATTATTAA
* *
2465666 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATAT
*
2465731 AATACTATAAAATATAATTTAAAATAATTATTA-TCAAATATAATTTAATAAAAAT
66 AATACTATAAAATATAATTTAAAATAATTATTATTAAAATATAATTTAATAAAAAT
*
2465786 ATATAATTTAATAAAATTCGTAATATTTAAATATTCTTAAATGAATTTACTAAAATCATAATATA
1 ATATAATTTAATAAAATTCTTAATA-TTAAATATTCTTAAATGAATTTACTAAAATCATAATATA
2465851 TAATACTATAAAATATAATTTAAAATAATTATTATT-AAATATAATTTAATAAAAAT
65 TAATACTATAAAATATAATTTAAAATAATTATTATTAAAATATAATTTAATAAAAAT
2465907 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATAT
*
2465972 AATACTATAAAATATAATTTAAAATAATTATTATTAAAAATATAATTTAGTAAAAAT
66 AATACTATAAAATATAATTTAAAATAATTATTATT-AAAATATAATTTAATAAAAAT
*
2466029 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTTCTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATAT
* *
2466094 AATACTATAAAATATAATTTAAATTAATTATTATTAAAAATATAATTTAGTAAAAAT
66 AATACTATAAAATATAATTTAAAATAATTATTATT-AAAATATAATTTAATAAAAAT
2466151 ATATAATTTAATAAAATTCTTAATATTAAATATTCTT--A-GAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATAT
* * *
2466213 AATACTATAAAATATAATTTAAATTAATTATT-TTTAAATATAATCTAATAAAAAT
66 AATACTATAAAATATAATTTAAAATAATTATTATTAAAATATAATTTAATAAAAAT
* *
2466268 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATAT
2466333 AATACTATAAAATATAATTTAAAA
66 AATACTATAAAATATAATTTAAAA
2466357 GAATAAAATT
Statistics
Matches: 551, Mismatches: 13, Indels: 14
0.95 0.02 0.02
Matches are distributed among these distances:
117 55 0.10
118 2 0.00
119 56 0.10
120 146 0.26
121 115 0.21
122 177 0.32
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (121 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATAT
AATACTATAAAATATAATTTAAAATAATTATTATTAAAATATAATTTAATAAAAAT
Found at i:2466154 original size:18 final size:17
Alignment explanation
Indices: 2466129--2466166 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2466119 AATTATTATT
*
2466129 AAAAATATAATTTAGTA
1 AAAAATATAATTTAATA
2466146 AAAATATATAATTTAATA
1 AAAA-ATATAATTTAATA
2466164 AAA
1 AAA
2466167 TTCTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATATAATTTAATA
Found at i:2466194 original size:53 final size:53
Alignment explanation
Indices: 2466137--2466305 Score: 144
Period size: 60 Copynumber: 3.0 Consensus size: 53
2466127 TTAAAAATAT
* *
2466137 AATTTAGTAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAG
1 AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAA
* * * * *
2466190 AATTTACT-AAAATCATAATATATAATACTATAAAATATAATTTAA-ATTAATTATTTTTAA
1 AATTTAATAAAAAT-AT-ATA-AT-TTA--ATAAAAT-T--CTTAATATTAAATATTCTTAA
2466250 ATATAATCTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTA
1 A-AT--T-TAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTA
2466306 TATAAATTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
52 5 0.06
53 9 0.10
54 3 0.03
55 2 0.02
56 6 0.07
57 12 0.13
58 8 0.09
59 8 0.09
60 13 0.14
61 8 0.09
62 2 0.02
63 4 0.04
64 5 0.06
65 5 0.06
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (53 bp):
AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAA
Found at i:2466211 original size:241 final size:239
Alignment explanation
Indices: 2465666--2466356 Score: 1181
Period size: 241 Copynumber: 2.9 Consensus size: 239
2465656 TTATTATTAA
*
2465666 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTC-T-TATGAATTTACTAAAATCATAATATAT
*
2465731 AATACTATAAAATATAATTTAAAATAATTATTA-TCAAATATAATTTAATAAAAATATATAATTT
64 AATACTATAAAATATAATTTAAAATAATTATTATTAAAATATAATTTAATAAAAATATATAATTT
*
2465795 AATAAAATTCGTAATATTTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTAT
129 AATAAAATTCTTAATA-TTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTAT
2465860 AAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
193 AAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
2465907 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTT--ATGAATTTACTAAAATCATAATATAT
*
2465972 AATACTATAAAATATAATTTAAAATAATTATTATTAAAAATATAATTTAGTAAAAATATATAATT
64 AATACTATAAAATATAATTTAAAATAATTATTATT-AAAATATAATTTAATAAAAATATATAATT
*
2466037 TAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTTCTAAAATCATAATATATAATACTAT
128 TAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTAT
* *
2466102 AAAATATAATTTAAATTAATTATTATTAAAAATATAATTTAGTAAAAAT
193 AAAATATAATTTAAAATAATTATTATT--AAATATAATTTAATAAAAAT
2466151 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTA-GAATTTACTAAAATCATAATATATAA
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATGAATTTACTAAAATCATAATATATAA
* * *
2466215 TACTATAAAATATAATTTAAATTAATTATT-TTTAAATATAATCTAATAAAAATATATAATTTAA
66 TACTATAAAATATAATTTAAAATAATTATTATTAAAATATAATTTAATAAAAATATATAATTTAA
* *
2466279 TAAAATTCTTAATATTAAATATTCTTATATAAATTTACTAAAATCATAATATATAATACTATAAA
131 TAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAA
2466344 ATATAATTTAAAA
196 ATATAATTTAAAA
2466357 GAATAAAATT
Statistics
Matches: 429, Mismatches: 15, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
239 104 0.24
240 3 0.01
241 148 0.34
242 75 0.17
243 43 0.10
244 56 0.13
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (239 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATGAATTTACTAAAATCATAATATATAA
TACTATAAAATATAATTTAAAATAATTATTATTAAAATATAATTTAATAAAAATATATAATTTAA
TAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAA
ATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
Found at i:2466285 original size:361 final size:362
Alignment explanation
Indices: 2465666--2466356 Score: 1226
Period size: 361 Copynumber: 1.9 Consensus size: 362
2465656 TTATTATTAA
*
2465666 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTAATAAAATCATAATATAT
*
2465731 AATACTATAAAATATAATTTAAAATAATTATTATCAAATATAATTTAATAAAAATATATAATTTA
66 AATACTATAAAATATAATTTAAAATAATTATTATAAAATATAATTTAATAAAAATATATAATTTA
2465796 ATAAAATTCGTAATATTTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATA
131 ATAAAATTCGTAATATTTAAATATTCTT-AATGAATTTACTAAAATCATAATATATAATACTATA
*
2465861 AAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC
195 AAATATAATTTAAAATAATTATTATTAAATATAATCTAATAAAAATATATAATTTAATAAAATTC
*
2465926 TTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATT
260 TTAATATTAAATATTCTTAAATAAATTTACTAAAATCATAATATATAATACTATAAAATATAATT
2465991 TAAAATAATTATTATTAAAAATATAATTTAGTAAAAAT
325 TAAAATAATTATTATTAAAAATATAATTTAGTAAAAAT
**
2466029 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTTCTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTAATAAAATCATAATATAT
* *
2466094 AATACTATAAAATATAATTTAAATTAATTATTATTAAAAATATAATTTAGTAAAAATATATAATT
66 AATACTATAAAATATAATTTAAAATAATTATTA-T-AAAATATAATTTAATAAAAATATATAATT
*
2466159 TAATAAAATTCTTAATA-TTAAATATTCTT-A-GAATTTACTAAAATCATAATATATAATACTAT
129 TAATAAAATTCGTAATATTTAAATATTCTTAATGAATTTACTAAAATCATAATATATAATACTAT
* *
2466221 AAAATATAATTTAAATTAATTATTTTTAAATATAATCTAATAAAAATATATAATTTAATAAAATT
194 AAAATATAATTTAAAATAATTATTATTAAATATAATCTAATAAAAATATATAATTTAATAAAATT
*
2466286 CTTAATATTAAATATTCTTATATAAATTTACTAAAATCATAATATATAATACTATAAAATATAAT
259 CTTAATATTAAATATTCTTAAATAAATTTACTAAAATCATAATATATAATACTATAAAATATAAT
2466351 TTAAAA
324 TTAAAA
2466357 GAATAAAATT
Statistics
Matches: 314, Mismatches: 12, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
361 163 0.52
362 1 0.00
363 94 0.30
364 13 0.04
365 43 0.14
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (362 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTAATAAAATCATAATATAT
AATACTATAAAATATAATTTAAAATAATTATTATAAAATATAATTTAATAAAAATATATAATTTA
ATAAAATTCGTAATATTTAAATATTCTTAATGAATTTACTAAAATCATAATATATAATACTATAA
AATATAATTTAAAATAATTATTATTAAATATAATCTAATAAAAATATATAATTTAATAAAATTCT
TAATATTAAATATTCTTAAATAAATTTACTAAAATCATAATATATAATACTATAAAATATAATTT
AAAATAATTATTATTAAAAATATAATTTAGTAAAAAT
Found at i:2466405 original size:20 final size:20
Alignment explanation
Indices: 2466358--2466396 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2466348 AATTTAAAAG
*
2466358 AATAAAATTTGAATCGATTA
1 AATAATATTTGAATCGATTA
* *
2466378 AATGATATTTGAATTGATT
1 AATAATATTTGAATCGATT
2466397 TGATAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (20 bp):
AATAATATTTGAATCGATTA
Found at i:2469691 original size:14 final size:14
Alignment explanation
Indices: 2469672--2469699 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2469662 AGCAGAAATC
2469672 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
2469686 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
2469700 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:2469980 original size:58 final size:58
Alignment explanation
Indices: 2469890--2470017 Score: 247
Period size: 58 Copynumber: 2.2 Consensus size: 58
2469880 TAGACACGGA
2469890 AGGGAATAGGGGTGTAATAGGATTACACCCAACCAAATGTCTGTTTGGTGGTGGGCCC
1 AGGGAATAGGGGTGTAATAGGATTACACCCAACCAAATGTCTGTTTGGTGGTGGGCCC
*
2469948 AGGGAATAGGGGTGTAATAGGATTACACCCAACCAAATGTCTGTTTGGTGGTGGGCCT
1 AGGGAATAGGGGTGTAATAGGATTACACCCAACCAAATGTCTGTTTGGTGGTGGGCCC
2470006 AGGGAATAGGGG
1 AGGGAATAGGGG
2470018 GAATGCATTC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 69 1.00
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.23
Consensus pattern (58 bp):
AGGGAATAGGGGTGTAATAGGATTACACCCAACCAAATGTCTGTTTGGTGGTGGGCCC
Found at i:2470096 original size:23 final size:23
Alignment explanation
Indices: 2470070--2470775 Score: 544
Period size: 23 Copynumber: 30.9 Consensus size: 23
2470060 TAAATATTGT
2470070 AAATTGAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
* * *
2470093 AAATTAAAGTATTT-AGTTGCTGG
1 AAATTGAAGTGTTTAAG-TGCTGC
*
2470116 AAATTG-AGATGTTTTA-T-C-GC
1 AAATTGAAG-TGTTTAAGTGCTGC
* * * *
2470136 AGTAATT-AAGGTGTATAAATGTTGT
1 A--AATTGAA-GTGTTTAAGTGCTGC
*
2470161 TAATTGATA-TGTTTAAGTGCTGC
1 AAATTGA-AGTGTTTAAGTGCTGC
*
2470184 AAATTTAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
*
2470207 AAATTG-AGATGTTTTA-TCGCTG-
1 AAATTGAAG-TGTTTAAGT-GCTGC
* * * * *
2470229 TAATTGAAGTGTATAAATGTTGT
1 AAATTGAAGTGTTTAAGTGCTGC
*
2470252 TAATTGATA-TGTTTAAGTGCTGC
1 AAATTGA-AGTGTTTAAGTGCTGC
* *
2470275 AAATTTAAGTTTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
*
2470298 AAATTGAAGTGTTTAAGTGCTGT
1 AAATTGAAGTGTTTAAGTGCTGC
* *
2470321 AAATTG-AGATATTTTA-TCGCTG-
1 AAATTGAAG-TGTTTAAGT-GCTGC
* * * * * *
2470343 TAATTGAGGTGTATAAATGTTGT
1 AAATTGAAGTGTTTAAGTGCTGC
*
2470366 TAATTGATA-TGTTTAAGTGCTGC
1 AAATTGA-AGTGTTTAAGTGCTGC
* * *
2470389 AAATTTAAGTGTTTAAATGCTGT
1 AAATTGAAGTGTTTAAGTGCTGC
2470412 AAATTGAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
2470435 AAATTGAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
2470458 AAATTG-AGATGTATT-A-TCGCTG-
1 AAATTGAAG-TGT-TTAAGT-GCTGC
* * * * * *
2470480 TAATTGATGTGTATAAATGTTGT
1 AAATTGAAGTGTTTAAGTGCTGC
* *
2470503 TAATTGATA-TGTTAAAGTGCTGC
1 AAATTGA-AGTGTTTAAGTGCTGC
* **
2470526 AAATTGAAGTGTTTAAATGCTAT
1 AAATTGAAGTGTTTAAGTGCTGC
2470549 AAATTGAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
2470572 AAATTGAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
* **
2470595 AAATTGAAGTGTTTAAATGCTAT
1 AAATTGAAGTGTTTAAGTGCTGC
2470618 AAATTGAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
2470641 AAATTGAAGTGTTTAAGTGCTGC
1 AAATTGAAGTGTTTAAGTGCTGC
2470664 AAATTG-AGATGTCTT-A-TCGCTG-
1 AAATTGAAG-TGT-TTAAGT-GCTGC
* * * * * *
2470686 TAATTGATGTGTATAAATGTTGT
1 AAATTGAAGTGTTTAAGTGCTGC
* *
2470709 TAATTGATA-TGTTAAAGTGCTGC
1 AAATTGA-AGTGTTTAAGTGCTGC
* *
2470732 AAATTGAAGTGTTTAAATGCTGT
1 AAATTGAAGTGTTTAAGTGCTGC
*
2470755 AAATTGAAGTGTTAAAGTGCT
1 AAATTGAAGTGTTTAAGTGCT
2470776 ATGCATCGAT
Statistics
Matches: 545, Mismatches: 93, Indels: 90
0.75 0.13 0.12
Matches are distributed among these distances:
20 2 0.00
21 3 0.01
22 81 0.15
23 450 0.83
24 7 0.01
25 2 0.00
ACGTcount: A:0.31, C:0.07, G:0.23, T:0.40
Consensus pattern (23 bp):
AAATTGAAGTGTTTAAGTGCTGC
Found at i:2470167 original size:45 final size:44
Alignment explanation
Indices: 2470117--2470265 Score: 149
Period size: 45 Copynumber: 3.3 Consensus size: 44
2470107 AGTTGCTGGA
2470117 AATTGAGATGTTTTATCGCAGTAATTAAGGTGTATAAATGTTGTT
1 AATTGAGATGTTTTATCGCAGTAATTAA-GTGTATAAATGTTGTT
* * * * * **
2470162 AATTGATATGTTTAAGTGCTGCA--AATTTAAGTGTTTAAGTGCTGCA
1 AATTGAGATGTTTTA-T-C-GCAGTAA-TTAAGTGTATAAATGTTGTT
*
2470208 AATTGAGATGTTTTATCGCTGTAATTGAAGTGTATAAATGTTGTT
1 AATTGAGATGTTTTATCGCAGTAATT-AAGTGTATAAATGTTGTT
*
2470253 AATTGATATGTTT
1 AATTGAGATGTTT
2470266 AAGTGCTGCA
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
43 2 0.02
44 3 0.04
45 41 0.51
46 27 0.33
47 5 0.06
48 3 0.04
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.43
Consensus pattern (44 bp):
AATTGAGATGTTTTATCGCAGTAATTAAGTGTATAAATGTTGTT
Found at i:2470293 original size:114 final size:114
Alignment explanation
Indices: 2470162--2470775 Score: 708
Period size: 114 Copynumber: 5.4 Consensus size: 114
2470152 AAATGTTGTT
*
2470162 AATTGATA-TGTTTAAGTGCTGCAAATTTAAGTGTTTAAGTGCTGCAAATTGAGATGTTTTATCG
1 AATTGA-AGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGATGTTTTATCG
2470226 CTGTAATTGAAGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCA
65 CTGTAATTGAAGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCA
* * * *
2470276 AATTTAAGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGC
1 AATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGATGTTTTATCGC
*
2470341 TGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCA
66 TGTAATTGAAGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCA
* * * *
2470390 AATTTAAGTGTTTAAATGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGA-AGTGTTTAAGT-
1 AATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGA-TGTTTTA-TC
* * * * * * * **
2470453 GCTGCAAATTG-AGATGTAT-TATCGCTG-TAATTGATGTGTATAAATGTTGTT
64 GCTG-TAATTGAAG-TGTATAAAT-GTTGTTAATTGATATGTTTAAGTGCTGCA
* * ** *
2470504 AATTGATA-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTATAAATTGA-AGTGTTTAAGT
1 AATTGA-AGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGA-TGTTTTA-T
* * * * ** * **
2470567 -GCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGA-AGTGTTTAAATGCTATA
63 CGCTG-TAATTGAAGTGTATAAATGTTGTTAATTGATA-TGTTTAAGTGCTGCA
*
2470619 AATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGATGTCTTATCGC
1 AATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGATGTTTTATCGC
* *
2470684 TGTAATTGATGTGTATAAATGTTGTTAATTGATATGTTAAAGTGCTGCA
66 TGTAATTGAAGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCA
* * *
2470733 AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGCT
1 AATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCT
2470776 ATGCATCGAT
Statistics
Matches: 427, Mismatches: 58, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
113 2 0.00
114 333 0.78
115 91 0.21
116 1 0.00
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (114 bp):
AATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGATGTTTTATCGC
TGTAATTGAAGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCA
Found at i:2470609 original size:206 final size:206
Alignment explanation
Indices: 2470367--2470775 Score: 757
Period size: 206 Copynumber: 2.0 Consensus size: 206
2470357 AAATGTTGTT
* *
2470367 AATTGATATGTTTAAGTGCTGCAAATTTAAGTGTTTAAATGCTGTAAATTGAAGTGTTTAAGTGC
1 AATTGATATGTTTAAGTGCTGCAAATTGAAGTGTTTAAATGCTATAAATTGAAGTGTTTAAGTGC
2470432 TGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGATGTATTATCGCTGTAATTGATGTGTATAAA
66 TGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGATGTATTATCGCTGTAATTGATGTGTATAAA
2470497 TGTTGTTAATTGATATGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTATAAATTGAAGTGTT
131 TGTTGTTAATTGATATGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTATAAATTGAAGTGTT
*
2470562 TAAGTGCTGCA
196 AAAGTGCTGCA
2470573 AATTGA-AGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAATGCTATAAATTGAAGTGTTTAAGTG
1 AATTGATA-TGTTTAAGTGCTGCAAATTGAAGTGTTTAAATGCTATAAATTGAAGTGTTTAAGTG
*
2470637 CTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGATGTCTTATCGCTGTAATTGATGTGTATAA
65 CTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGATGTATTATCGCTGTAATTGATGTGTATAA
*
2470702 ATGTTGTTAATTGATATGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGAAGTGT
130 ATGTTGTTAATTGATATGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTATAAATTGAAGTGT
2470767 TAAAGTGCT
195 TAAAGTGCT
2470776 ATGCATCGAT
Statistics
Matches: 197, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
205 1 0.01
206 196 0.99
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (206 bp):
AATTGATATGTTTAAGTGCTGCAAATTGAAGTGTTTAAATGCTATAAATTGAAGTGTTTAAGTGC
TGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAGATGTATTATCGCTGTAATTGATGTGTATAAA
TGTTGTTAATTGATATGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTATAAATTGAAGTGTT
AAAGTGCTGCA
Found at i:2470773 original size:137 final size:134
Alignment explanation
Indices: 2470053--2470775 Score: 605
Period size: 137 Copynumber: 5.3 Consensus size: 134
2470043 AACATGCTCT
** * * * * *
2470053 AAGTGTTTAAATATTGTAAATTGAAGTGTTTAAGTGCTGCAAATTAAAGTATTT-AGTTGCTGGA
1 AAGTGTTTAAATGCTGTAAATTGAAGTG-TTAAATGCTGCTAATTGAAGTGTTTAAG-TGCTGCA
* * * * * **
2470117 AATTGAGATGTTTTATCGCAGTAATT-AAGGTGTATAAATGTTGTTAATTGATA-TGTTTAAGTG
64 AATTGA-ATGTTTAAT-GCTGTAATTGAA-GTGTTTAAGTGCTGCAAATTGA-AGTGTTTAAGTG
*
2470180 CTGCAAATTT
125 CTGCAAATTG
* * ** * * * **
2470190 AAGTGTTTAAGTGCTGCAAATTG-AGATGTTTTATCGCTG-TAATTGAAGTGTATAAATGTTGTT
1 AAGTGTTTAAATGCTGTAAATTGAAG-TGTTAAAT-GCTGCTAATTGAAGTGTTTAAGTGCTGCA
* * *
2470253 AATTGATATGTTTAAGTGCTGCAAATTTAAGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGC
64 AATTGA-ATGTTTAA-TGCTG-TAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGC
*
2470318 TGTAAATTG
126 TGCAAATTG
* * * * *
2470327 -AGATATTT-TATCGCTGT-AATTGAGGTGTATAAATGTTGTTAATTGATA-TGTTTAAGTGCTG
1 AAG-TGTTTAAAT-GCTGTAAATTGAAGTGT-TAAATGCTGCTAATTGA-AGTGTTTAAGTGCTG
*
2470388 CAAATTTAAGTGTTTAAATGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGT
62 CAAATTGAA-TGTTT-AATGCTGT-AATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGT
2470453 GCTGCAAATTG
124 GCTGCAAATTG
* * * *
2470464 -AGATGTATT--ATCGCTGT-AATTGATGTGTATAAATGTTGTTAATTGATA-TGTTAAAGTGCT
1 AAG-TGT-TTAAAT-GCTGTAAATTGAAGTGT-TAAATGCTGCTAATTGA-AGTGTTTAAGTGCT
*
2470524 GCAAATTGAAGTGTTTAAATGCTATAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAG
61 GCAAATTGAA-TGTTT-AATGCTGT-AATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAG
2470589 TGCTGCAAATTG
123 TGCTGCAAATTG
* * *
2470601 AAGTGTTTAAATGCTATAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAA
1 AAGTGTTTAAATGCTGTAAATTGAAGTG-TTAAATGCTGCTAATTGAAGTGTTTAAGTGCTGCAA
* * * * ** *
2470666 ATTGAGATGTCTT-ATCGCTGTAATTGATGTGTATAAATGTTGTTAATTGATA-TGTTAAAGTGC
65 ATTGA-ATGT-TTAAT-GCTGTAATTGAAGTGTTTAAGTGCTGCAAATTGA-AGTGTTTAAGTGC
2470729 TGCAAATTG
126 TGCAAATTG
2470738 AAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGCT
1 AAGTGTTTAAATGCTGTAAATTGAAGTGTTAAA-TGCT
2470776 ATGCATCGAT
Statistics
Matches: 491, Mismatches: 67, Indels: 56
0.80 0.11 0.09
Matches are distributed among these distances:
136 57 0.12
137 369 0.75
138 61 0.12
139 4 0.01
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (134 bp):
AAGTGTTTAAATGCTGTAAATTGAAGTGTTAAATGCTGCTAATTGAAGTGTTTAAGTGCTGCAAA
TTGAATGTTTAATGCTGTAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAA
ATTG
Found at i:2471657 original size:43 final size:43
Alignment explanation
Indices: 2471606--2471791 Score: 284
Period size: 43 Copynumber: 4.3 Consensus size: 43
2471596 TTTTTGTGAC
* *
2471606 CTTTAGCGGCGTTT-TTGGAGAAAGCGCCGCTAAAGGTCTTGTT
1 CTTTAGCGGCGTTTGTGGGA-AAAGCGCCGCTAAAGGTCTTGGT
* *
2471649 CTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
* *
2471692 CTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
*
2471735 CTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
*
2471778 CTTTAGCGGAGTTT
1 CTTTAGCGGCGTTT
2471792 TTTTCGGCGC
Statistics
Matches: 131, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
43 128 0.98
44 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.30
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
Found at i:2480509 original size:57 final size:56
Alignment explanation
Indices: 2480421--2480693 Score: 255
Period size: 57 Copynumber: 4.9 Consensus size: 56
2480411 CTAAACCATA
* * *
2480421 TAAACCTTCAACACCTTCACTACCTTGACTGCCACCAACCTCAACACCCTTCCCACC
1 TAAACCTTCAACACCCTCACCACCTTGACTGCCAACAACCTCAACACCC-TCCCACC
* * * *
2480478 TAAACCTTCACCACTCTCACCACCTTGACTGCCAACAACCTCAGCACCCTTCCCACA
1 TAAACCTTCAACACCCTCACCACCTTGACTGCCAACAACCTCAACACCC-TCCCACC
* * * * ** * *
2480535 TAAATCTTCAACACCCTCACCACATTTACTGCTAACAAAATCAACA--C-CCGATC
1 TAAACCTTCAACACCCTCACCACCTTGACTGCCAACAACCTCAACACCCTCCCACC
* * * * * * **
2480588 TAAACCTTCACCACCCTCACCACCTTCACTACCAGCAACCTGAAACACCCTCTCTATT
1 TAAACCTTCAACACCCTCACCACCTTGACTGCCAACAACCT-CAACACCCTC-CCACC
* * *
2480646 TAAACCTTCAACACCCTCACCACCTTTACTGCTAATAACCTCAACACC
1 TAAACCTTCAACACCCTCACCACCTTGACTGCCAACAACCTCAACACC
2480694 TTATTTACCA
Statistics
Matches: 173, Mismatches: 38, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
53 35 0.20
54 4 0.02
55 1 0.01
56 1 0.01
57 94 0.54
58 38 0.22
ACGTcount: A:0.31, C:0.44, G:0.04, T:0.22
Consensus pattern (56 bp):
TAAACCTTCAACACCCTCACCACCTTGACTGCCAACAACCTCAACACCCTCCCACC
Found at i:2480627 original size:110 final size:111
Alignment explanation
Indices: 2480477--2480680 Score: 286
Period size: 111 Copynumber: 1.8 Consensus size: 111
2480467 CCCTTCCCAC
* * * * * *
2480477 CTAAACCTTCACCACTCTCACCACCTTGACTGCCAACAACCT-CAGCACCCT-TCCCACATAAAT
1 CTAAACCTTCACCACCCTCACCACCTTCACTACCAACAACCTGAAACACCCTCT-CCACATAAAC
2480540 CTTCAACACCCTCACCACATTTACTGCTAACAAAATCAACACCCGAT
65 CTTCAACACCCTCACCACATTTACTGCTAACAAAATCAACACCCGAT
* * **
2480587 CTAAACCTTCACCACCCTCACCACCTTCACTACCAGCAACCTGAAACACCCTCTCTATTTAAACC
1 CTAAACCTTCACCACCCTCACCACCTTCACTACCAACAACCTGAAACACCCTCTCCACATAAACC
*
2480652 TTCAACACCCTCACCACCTTTACTGCTAA
66 TTCAACACCCTCACCACATTTACTGCTAA
2480681 TAACCTCAAC
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
110 38 0.47
111 42 0.52
112 1 0.01
ACGTcount: A:0.31, C:0.43, G:0.04, T:0.22
Consensus pattern (111 bp):
CTAAACCTTCACCACCCTCACCACCTTCACTACCAACAACCTGAAACACCCTCTCCACATAAACC
TTCAACACCCTCACCACATTTACTGCTAACAAAATCAACACCCGAT
Found at i:2481656 original size:15 final size:15
Alignment explanation
Indices: 2481610--2481659 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
2481600 AATTGGAATA
*
2481610 CCCC-AAACAAAAAT
1 CCCCAAAACCAAAAT
*
2481624 CCCCAAAATCAAAA-
1 CCCCAAAACCAAAAT
* *
2481638 CCCCTAACCCAAAAT
1 CCCCAAAACCAAAAT
2481653 CCCCAAA
1 CCCCAAA
2481660 TTCGACCACC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.50, C:0.42, G:0.00, T:0.08
Consensus pattern (15 bp):
CCCCAAAACCAAAAT
Found at i:2481660 original size:28 final size:30
Alignment explanation
Indices: 2481614--2481694 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 30
2481604 GGAATACCCC
* *
2481614 AAACAAAAATCCCCAAAATCAAAACC-CCT
1 AAACCAAAATCCCCAAACTCAAAACCACCT
* * *
2481643 AACCCAAAATCCCCAAATTC--GACCACCT
1 AAACCAAAATCCCCAAACTCAAAACCACCT
*
2481671 AAACCAAAATCTCCAAACTCAAAA
1 AAACCAAAATCCCCAAACTCAAAA
2481695 ACCTTAAACA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 3 0.07
28 20 0.49
29 17 0.41
30 1 0.02
ACGTcount: A:0.51, C:0.36, G:0.01, T:0.12
Consensus pattern (30 bp):
AAACCAAAATCCCCAAACTCAAAACCACCT
Found at i:2481866 original size:2 final size:2
Alignment explanation
Indices: 2481859--2481894 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2481849 TCACTATATG
* *
2481859 CT CT CT CT CT CT CT CT CC CC CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2481895 TATTAACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:2482260 original size:19 final size:19
Alignment explanation
Indices: 2482238--2482358 Score: 56
Period size: 19 Copynumber: 6.3 Consensus size: 19
2482228 TAGGTTACAT
2482238 TTTTCATAATTTTATATAA
1 TTTTCATAATTTTATATAA
* *
2482257 TTTTTAT-ATTTCTCTATTAA
1 TTTTCATAATTT-TATA-TAA
* * * *
2482277 GTTTTAATAAATTTCTTTTTTA
1 -TTTTCAT-AATTT-TATATAA
2482299 TTTTGC--AATTTT-TATAA
1 TTTT-CATAATTTTATATAA
**
2482316 TTTTTGTAATTTTATATAGA
1 TTTTCATAATTTTATATA-A
2482336 -TTTCATATATTTTA-ATAA
1 TTTTCATA-ATTTTATATAA
2482354 TTTTC
1 TTTTC
2482359 TATTATTGTT
Statistics
Matches: 78, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
17 7 0.09
18 12 0.15
19 30 0.38
20 10 0.13
21 10 0.13
22 2 0.03
23 7 0.09
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTCATAATTTTATATAA
Found at i:2482326 original size:18 final size:20
Alignment explanation
Indices: 2482299--2482338 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
2482289 TTCTTTTTTA
2482299 TTTTGCAATTTT-TATA-AT
1 TTTTGCAATTTTATATAGAT
*
2482317 TTTTGTAATTTTATATAGAT
1 TTTTGCAATTTTATATAGAT
2482337 TT
1 TT
2482339 CATATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 4 0.21
20 4 0.21
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (20 bp):
TTTTGCAATTTTATATAGAT
Found at i:2483419 original size:19 final size:20
Alignment explanation
Indices: 2483365--2483424 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 20
2483355 CTTGAACCCT
*
2483365 AAATCTCGAACCC-AAATCC
1 AAATCTTGAACCCTAAATCC
* * *
2483384 AAATTTTGAATCTTAAATCC
1 AAATCTTGAACCCTAAATCC
*
2483404 AAA-CTTGAACCCTAAACCC
1 AAATCTTGAACCCTAAATCC
2483423 AA
1 AA
2483425 GTTAATGGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 23 0.72
20 9 0.28
ACGTcount: A:0.43, C:0.28, G:0.05, T:0.23
Consensus pattern (20 bp):
AAATCTTGAACCCTAAATCC
Found at i:2484311 original size:29 final size:29
Alignment explanation
Indices: 2484269--2484326 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2484259 TTCTTAGATA
2484269 CATTTCTTATATTAGCTTAAAACCCAATC
1 CATTTCTTATATTAGCTTAAAACCCAATC
2484298 CATTTCTTATATTAGCTTAAAACCCAATC
1 CATTTCTTATATTAGCTTAAAACCCAATC
2484327 TTTTTTTCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
CATTTCTTATATTAGCTTAAAACCCAATC
Found at i:2490364 original size:22 final size:22
Alignment explanation
Indices: 2490336--2490394 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
2490326 TTTATTGTTC
2490336 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
2490358 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
2490380 AGCCATGAGAGCTTA
1 AAACATGAGAGCTTA
2490395 TTTAGGTGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:2493180 original size:127 final size:128
Alignment explanation
Indices: 2492953--2493207 Score: 422
Period size: 127 Copynumber: 2.0 Consensus size: 128
2492943 ATGGGAACTT
* *
2492953 GAATTTAACTTAATAATTTGGAATTCTAACACATGGGTAAGACATGCTAGTTTGAGATGATTATG
1 GAATTTAACTTAATAATTTGGAATTCTAACACATGAGTAAGACATGCTAGTTTGAGAGGATTATG
* *
2493018 AATTAAAAAAAATCCAAGGAAAATACACATATTTACCTTATCAATTTGTTGGCCGAATGTGAA
66 AATTAAAAAAAATCCAAGGAAAATACACATATTTACCTTATCAAATTGTTAGCCGAATGTGAA
2493081 GAATTTAACTTAATAATTTGGAATTCTAACACAT-AGTAAGACATGCTAGTTTGAGAGGATTATG
1 GAATTTAACTTAATAATTTGGAATTCTAACACATGAGTAAGACATGCTAGTTTGAGAGGATTATG
* * * * *
2493145 AATTCACAAAACTCCAAGGAAGATACACATATTTACTTTATCAAATTGTTAGCCGAATGTGAA
66 AATTAAAAAAAATCCAAGGAAAATACACATATTTACCTTATCAAATTGTTAGCCGAATGTGAA
2493208 TAAGAAAGCT
Statistics
Matches: 118, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
127 84 0.71
128 34 0.29
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (128 bp):
GAATTTAACTTAATAATTTGGAATTCTAACACATGAGTAAGACATGCTAGTTTGAGAGGATTATG
AATTAAAAAAAATCCAAGGAAAATACACATATTTACCTTATCAAATTGTTAGCCGAATGTGAA
Found at i:2494799 original size:68 final size:66
Alignment explanation
Indices: 2494722--2495048 Score: 245
Period size: 68 Copynumber: 4.8 Consensus size: 66
2494712 AAACCCTAAT
* * *
2494722 AAGGCGAAGTACTTTAAGAAGT-TCACAACTTGATAAGGTTGAGAA-CTTTGAAAAGTTAAGTGT
1 AAGGTGAAGTACTTTAAGAAGTAT-GCAACTTGA-AAGGTTGA-AAGCTTTGAAAAGATAAGTG-
2494785 CTGAG
62 CTGAG
* * * * *
2494790 AAGGTGAAGTACTTTAAGAAATATGCAACCTGAAATAGATGAAAGCTTTGAAAA-ACTAAATGCC
1 AAGGTGAAGTACTTTAAGAAGTATGCAACTTGAAA-GGTTGAAAGCTTTGAAAAGA-TAAGTG-C
2494854 TGAG
63 TGAG
* **
2494858 AAGGTAAAGTACTTTAAGAAGTATGCAACTCAAGAAGGTTGAAAGCTTTGAAAAGATAAGTGCTT
1 AAGGTGAAGTACTTTAAGAAGTATGCAACTTGA-AAGGTTGAAAGCTTTGAAAAGATAAGTGC-T
*
2494923 AAG
64 GAG
* * *
2494926 AAGAT-AATGTACTTTAAGAAGTACCTAAGCAA--AG-AAGGTTGAAAGCTTTGAAAAGCTAAGT
1 AAGGTGAA-GTACTTTAAGAAGTA--T--GCAACTTGAAAGGTTGAAAGCTTTGAAAAGATAAGT
*
2494987 GCATAAG
61 GC-TGAG
** * ** * **
2494994 AAGGCAAAGTACTTTAATAAGTATGTGACTTGAAAAGGTGGAAAATTTTGAAAAG
1 AAGGTGAAGTACTTTAAGAAGTATGCAACTTG-AAAGGTTGAAAGCTTTGAAAAG
2495049 CTAATTTCCT
Statistics
Matches: 210, Mismatches: 32, Indels: 34
0.76 0.12 0.12
Matches are distributed among these distances:
64 2 0.01
66 2 0.01
67 7 0.03
68 188 0.90
69 6 0.03
70 1 0.00
72 4 0.02
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (66 bp):
AAGGTGAAGTACTTTAAGAAGTATGCAACTTGAAAGGTTGAAAGCTTTGAAAAGATAAGTGCTGA
G
Found at i:2494849 original size:136 final size:136
Alignment explanation
Indices: 2494693--2494945 Score: 307
Period size: 136 Copynumber: 1.9 Consensus size: 136
2494683 CTAAGAAGGT
* * * * ** *
2494693 TGAAAGTTTTGAAAAGCTAAAACCCTAATAAGGCGAAGTACTTTAAGAAGT-TCACAACTTGATA
1 TGAAAGCTTTGAAAAACTAAAACCCTAAGAAGGCAAAGTACTTTAAGAAGTAT-ACAACTCAAGA
* * *
2494757 AGGTTGAGAA-CTTTGAAAAGTTAAGTG-TCTGAGAAGGTGAA-GTACTTTAAGAAATATGCAAC
65 AGGTTGA-AAGCTTTGAAAAGATAAGTGCT-TAAGAAGAT-AATGTACTTTAAGAAATATGCAAC
2494819 CTGAAATAGA
127 CTGAAATAGA
** * * *
2494829 TGAAAGCTTTGAAAAACTAAATGCCTGAGAAGGTAAAGTACTTTAAGAAGTATGCAACTCAAGAA
1 TGAAAGCTTTGAAAAACTAAAACCCTAAGAAGGCAAAGTACTTTAAGAAGTATACAACTCAAGAA
2494894 GGTTGAAAGCTTTGAAAAGATAAGTGCTTAAGAAGATAATGTACTTTAAGAA
66 GGTTGAAAGCTTTGAAAAGATAAGTGCTTAAGAAGATAATGTACTTTAAGAA
2494946 GTACCTAAGC
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
135 4 0.04
136 92 0.94
137 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.26
Consensus pattern (136 bp):
TGAAAGCTTTGAAAAACTAAAACCCTAAGAAGGCAAAGTACTTTAAGAAGTATACAACTCAAGAA
GGTTGAAAGCTTTGAAAAGATAAGTGCTTAAGAAGATAATGTACTTTAAGAAATATGCAACCTGA
AATAGA
Found at i:2494995 original size:34 final size:34
Alignment explanation
Indices: 2494889--2494997 Score: 86
Period size: 34 Copynumber: 3.2 Consensus size: 34
2494879 TATGCAACTC
* *
2494889 AAGAAGGTTGAAAGCTTTGAAAAGATAAGTGCTT
1 AAGAAGGTTGAAAGCTTTGAAAAGCTAAGTGCAT
* *
2494923 AAGAA-GAT-AATGTACTTT-AAGAAGTACCTAA--GCA-
1 AAGAAGGTTGAAAG--CTTTGAA-AAG---CTAAGTGCAT
2494957 AAGAAGGTTGAAAGCTTTGAAAAGCTAAGTGCAT
1 AAGAAGGTTGAAAGCTTTGAAAAGCTAAGTGCAT
2494991 AAGAAGG
1 AAGAAGG
2494998 CAAAGTACTT
Statistics
Matches: 57, Mismatches: 6, Indels: 24
0.66 0.07 0.28
Matches are distributed among these distances:
31 4 0.07
32 3 0.05
33 7 0.12
34 31 0.54
35 6 0.11
36 3 0.05
37 3 0.05
ACGTcount: A:0.44, C:0.08, G:0.25, T:0.23
Consensus pattern (34 bp):
AAGAAGGTTGAAAGCTTTGAAAAGCTAAGTGCAT
Found at i:2497094 original size:21 final size:21
Alignment explanation
Indices: 2497069--2497190 Score: 136
Period size: 21 Copynumber: 5.8 Consensus size: 21
2497059 AGCTTTGGCT
2497069 GAAACCGAGGCGAAGCCAGCC
1 GAAACCGAGGCGAAGCCAGCC
* *
2497090 GAAACCGAGGTGCAGCCAGCC
1 GAAACCGAGGCGAAGCCAGCC
* *
2497111 GAAACCGAGGCGAATCCAGCT
1 GAAACCGAGGCGAAGCCAGCC
* *
2497132 GAAACCAAGGTGAAGCCAGCC
1 GAAACCGAGGCGAAGCCAGCC
* * * *
2497153 GAAACTGAGGCGAAACCAACA
1 GAAACCGAGGCGAAGCCAGCC
* *
2497174 GAACCCGAGGCCAAGCC
1 GAAACCGAGGCGAAGCC
2497191 CACGGAAGCT
Statistics
Matches: 81, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 81 1.00
ACGTcount: A:0.35, C:0.31, G:0.30, T:0.04
Consensus pattern (21 bp):
GAAACCGAGGCGAAGCCAGCC
Found at i:2497130 original size:42 final size:42
Alignment explanation
Indices: 2497069--2497166 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
2497059 AGCTTTGGCT
* *
2497069 GAAACCGAGGCGAAGCCAGCCGAAACCGAGGTGCAGCCAGCC
1 GAAACCGAGGCGAAGCCAGCCGAAACCAAGGTGAAGCCAGCC
* *
2497111 GAAACCGAGGCGAATCCAGCTGAAACCAAGGTGAAGCCAGCC
1 GAAACCGAGGCGAAGCCAGCCGAAACCAAGGTGAAGCCAGCC
*
2497153 GAAACTGAGGCGAA
1 GAAACCGAGGCGAA
2497167 ACCAACAGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.05
Consensus pattern (42 bp):
GAAACCGAGGCGAAGCCAGCCGAAACCAAGGTGAAGCCAGCC
Found at i:2497182 original size:63 final size:63
Alignment explanation
Indices: 2497066--2497184 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 63
2497056 AGAAGCTTTG
* * * * * *
2497066 GCTGAAACCGAGGCGAAGCCAGCCGAAACCGAGGTGCAGCCAGCCGAAACCGAGGCGAATCCA
1 GCTGAAACCAAGGCGAAGCCAGCCGAAACCGAGGCGAAACCAACAGAAACCGAGGCGAATCCA
* * *
2497129 GCTGAAACCAAGGTGAAGCCAGCCGAAACTGAGGCGAAACCAACAGAACCCGAGGC
1 GCTGAAACCAAGGCGAAGCCAGCCGAAACCGAGGCGAAACCAACAGAAACCGAGGC
2497185 CAAGCCCACG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 47 1.00
ACGTcount: A:0.34, C:0.30, G:0.30, T:0.05
Consensus pattern (63 bp):
GCTGAAACCAAGGCGAAGCCAGCCGAAACCGAGGCGAAACCAACAGAAACCGAGGCGAATCCA
Found at i:2502513 original size:26 final size:27
Alignment explanation
Indices: 2502467--2502533 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
2502457 TCTCCCAAAT
* * **
2502467 CCCCAAAACTTTTTTCCTCTTGCT-TTC
1 CCCCAAAAC-TTTTACCTCTTCCTAAAC
*
2502494 CCCCAAAACTTTTACTTCTTCCTAAAC
1 CCCCAAAACTTTTACCTCTTCCTAAAC
2502521 CCCCAAAACTTTT
1 CCCCAAAACTTTT
2502534 TTTTTTCGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.24, C:0.37, G:0.01, T:0.37
Consensus pattern (27 bp):
CCCCAAAACTTTTACCTCTTCCTAAAC
Found at i:2519299 original size:18 final size:18
Alignment explanation
Indices: 2519276--2519311 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2519266 TACAGTGCAT
2519276 TAGAACGTCCTTGTTGAC
1 TAGAACGTCCTTGTTGAC
2519294 TAGAACGTCCTTGTTGAC
1 TAGAACGTCCTTGTTGAC
2519312 GATCCATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (18 bp):
TAGAACGTCCTTGTTGAC
Found at i:2531431 original size:78 final size:78
Alignment explanation
Indices: 2531337--2531491 Score: 301
Period size: 78 Copynumber: 2.0 Consensus size: 78
2531327 CAAGGATGCG
2531337 GTAATTCTGAAGTAGCCTTCAATGAAGTGTCAGTAATAATTCACTAACCCAAGGAAAGATCGCAA
1 GTAATTCTGAAGTAGCCTTCAATGAAGTGTCAGTAATAATTCACTAACCCAAGGAAAGATCGCAA
2531402 CTCTGTTACCTTA
66 CTCTGTTACCTTA
*
2531415 GTAATTCTGAAGTAGCCTTCAATGAAGTGTCAGTAATAATTCACTAACCCAAGGAAAGATCGCGA
1 GTAATTCTGAAGTAGCCTTCAATGAAGTGTCAGTAATAATTCACTAACCCAAGGAAAGATCGCAA
2531480 CTCTGTTACCTT
66 CTCTGTTACCTT
2531492 GGTTGGTGGC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (78 bp):
GTAATTCTGAAGTAGCCTTCAATGAAGTGTCAGTAATAATTCACTAACCCAAGGAAAGATCGCAA
CTCTGTTACCTTA
Found at i:2533619 original size:12 final size:12
Alignment explanation
Indices: 2533602--2533631 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2533592 CCTCACACGC
2533602 CCGTGTGCTAGG
1 CCGTGTGCTAGG
2533614 CCGTGTGCTAGG
1 CCGTGTGCTAGG
2533626 CCGTGT
1 CCGTGT
2533632 AACTGTCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.27, G:0.40, T:0.27
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:2534525 original size:36 final size:36
Alignment explanation
Indices: 2534485--2534673 Score: 270
Period size: 36 Copynumber: 5.2 Consensus size: 36
2534475 CAAATCAAGA
* *
2534485 AAAACACACTAAATGCTCACACGAGTCAATCCCTCC
1 AAAACACACCAAATGCTCACATGAGTCAATCCCTCC
* *
2534521 AAAACACACCAGATGCTCACATGAGCCAATCCCTCC
1 AAAACACACCAAATGCTCACATGAGTCAATCCCTCC
* * *
2534557 AAAACACGCCAGATGCTCACATGAGTCAATCTCTCC
1 AAAACACACCAAATGCTCACATGAGTCAATCCCTCC
* *
2534593 AAAACACACCAAATGCTCACATGTGCCAATCCCTCC
1 AAAACACACCAAATGCTCACATGAGTCAATCCCTCC
* * *
2534629 AAAACACACCAGATGTTCACACGAGTCAATCCCTCC
1 AAAACACACCAAATGCTCACATGAGTCAATCCCTCC
2534665 AAAACACAC
1 AAAACACAC
2534674 TAAACAGAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 136 1.00
ACGTcount: A:0.38, C:0.37, G:0.10, T:0.16
Consensus pattern (36 bp):
AAAACACACCAAATGCTCACATGAGTCAATCCCTCC
Found at i:2534602 original size:72 final size:72
Alignment explanation
Indices: 2534485--2534673 Score: 306
Period size: 72 Copynumber: 2.6 Consensus size: 72
2534475 CAAATCAAGA
* * *
2534485 AAAACACACTAAATGCTCACACGAGTCAATCCCTCCAAAACACACCAGATGCTCACATGAGCCAA
1 AAAACACACCAGATGCTCACACGAGTCAATCCCTCCAAAACACACCAAATGCTCACATGAGCCAA
2534550 TCCCTCC
66 TCCCTCC
* * * *
2534557 AAAACACGCCAGATGCTCACATGAGTCAATCTCTCCAAAACACACCAAATGCTCACATGTGCCAA
1 AAAACACACCAGATGCTCACACGAGTCAATCCCTCCAAAACACACCAAATGCTCACATGAGCCAA
2534622 TCCCTCC
66 TCCCTCC
*
2534629 AAAACACACCAGATGTTCACACGAGTCAATCCCTCCAAAACACAC
1 AAAACACACCAGATGCTCACACGAGTCAATCCCTCCAAAACACAC
2534674 TAAACAGAGA
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 106 1.00
ACGTcount: A:0.38, C:0.37, G:0.10, T:0.16
Consensus pattern (72 bp):
AAAACACACCAGATGCTCACACGAGTCAATCCCTCCAAAACACACCAAATGCTCACATGAGCCAA
TCCCTCC
Found at i:2538405 original size:65 final size:61
Alignment explanation
Indices: 2538324--2538458 Score: 155
Period size: 61 Copynumber: 2.1 Consensus size: 61
2538314 ATAATACTTA
* * *
2538324 AATAACGAAATTAAAATAAAATCATCACATATTTTATATTAG-CCAAAGAAAGTAGTTAACAATA
1 AATAACAAAACTAAAATAAAATCAT---ATATTTTATACTAGTCC--AGAAAGTAGTTAACAATA
2538388 C
61 C
* * *
2538389 AATAACAAAACTAAAATCAAATCATGTGTTTTATACTAGTCCAGAAAGTAGTTAACAATAC
1 AATAACAAAACTAAAATAAAATCATATATTTTATACTAGTCCAGAAAGTAGTTAACAATAC
*
2538450 AATTACAAA
1 AATAACAAA
2538459 TAAAAATAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
61 27 0.44
62 11 0.18
63 2 0.03
65 22 0.35
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.27
Consensus pattern (61 bp):
AATAACAAAACTAAAATAAAATCATATATTTTATACTAGTCCAGAAAGTAGTTAACAATAC
Found at i:2550738 original size:103 final size:104
Alignment explanation
Indices: 2550553--2550759 Score: 362
Period size: 103 Copynumber: 2.0 Consensus size: 104
2550543 TAAAGTACAA
*
2550553 TGACTAAATCACAACTTTCATAAGTAATGGGACTAATGGTAGAATTTAACATTTTCTTTCCACTT
1 TGACTAAATCACAACTTTCATAAGTAATAGGACTAATGGTAGAATTTAACATTTTCTTTCCACTT
2550618 TTCTATTCAACCAAGCACACCCTGAACACCATGTAGGTG
66 TTCTATTCAACCAAGCACACCCTGAACACCATGTAGGTG
*
2550657 TGACTAAATCACAACTTTCATAAGTAATAGGACT-ATGGTAGAATTTAACATTTTCTTTCGACTT
1 TGACTAAATCACAACTTTCATAAGTAATAGGACTAATGGTAGAATTTAACATTTTCTTTCCACTT
* * *
2550721 TTCTATTCAACCGAGCACACTCTGAAGACCATGTAGGTG
66 TTCTATTCAACCAAGCACACCCTGAACACCATGTAGGTG
2550760 CCACTTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
103 65 0.66
104 33 0.34
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (104 bp):
TGACTAAATCACAACTTTCATAAGTAATAGGACTAATGGTAGAATTTAACATTTTCTTTCCACTT
TTCTATTCAACCAAGCACACCCTGAACACCATGTAGGTG
Found at i:2555679 original size:67 final size:66
Alignment explanation
Indices: 2555513--2555958 Score: 425
Period size: 67 Copynumber: 6.7 Consensus size: 66
2555503 GGGCTATAAA
* * * * *
2555513 GGGGTATAATGTATAAGACCATAGCTCGACTATGGCAACTTAGAGAG-TC-CACAGAACATTAAA
1 GGGGTATGATGTGTAAGACCATAGCTCGGCTATGACAACATAGAGAGTTCGC-CAG-ACATTAAA
2555576 CAT
64 CAT
* * * ** * * *
2555579 GGGGTATGATGTCTAAGACCACAACTCAACTATGACAACATTGAGAGTTCACCATGATATTAAAC
1 GGGGTATGATGTGTAAGACCATAGCTCGGCTATGACAACATAGAGAGTTCGCCA-GACATTAAAC
2555644 AT
65 AT
* * * * * * *
2555646 CGAGTATAATGTGTAAGAACC-TAGCTCGGCTATGGCAACGTAGCGAGTTTGCCAGTACATTAAA
1 GGGGTATGATGTGTAAG-ACCATAGCTCGGCTATGACAACATAGAGAGTTCGCCAG-ACATTAAA
*
2555710 AAT
64 CAT
* * * * * *
2555713 GGGGTATGATATGTAAGACCATAGCTCGACTATGGCAACAAAGAAAGTAT-GCTAGATCATTAAA
1 GGGGTATGATGTGTAAGACCATAGCTCGGCTATGACAACATAGAGAGT-TCGCCAGA-CATTAAA
2555777 CAT
64 CAT
* *
2555780 GGGGTATGATGTGTAAGACCTTAGCTCGGCTATGACAACATAGAGAGTCCGCCAGGACATTAAAC
1 GGGGTATGATGTGTAAGACCATAGCTCGGCTATGACAACATAGAGAGTTCGCCA-GACATTAAAC
*
2555845 -G
65 AT
* * * *
2555846 GGGGTTTGATGTGTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCCACCAGGACATTAAAC
1 GGGGTATGATGTGTAAGACCATAGCTCGGCTATGACAACATAGAGAGTTCGCCA-GACATTAAAC
2555911 AT
65 AT
* * * **
2555913 GAGGTATAATGTGTAAGACCCTAGCTCGATTATGACAACATAGAGA
1 GGGGTATGATGTGTAAGACCATAGCTCGGCTATGACAACATAGAGA
2555959 TTCTATTGGG
Statistics
Matches: 312, Mismatches: 57, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
66 105 0.34
67 199 0.64
68 8 0.03
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (66 bp):
GGGGTATGATGTGTAAGACCATAGCTCGGCTATGACAACATAGAGAGTTCGCCAGACATTAAACA
T
Found at i:2555913 original size:133 final size:131
Alignment explanation
Indices: 2555513--2555958 Score: 471
Period size: 133 Copynumber: 3.3 Consensus size: 131
2555503 GGGCTATAAA
* * * *
2555513 GGGGTATAATGTATAAGACCATAGCTCGACTATGGCAACTTAGAGAGTCC-ACAGAACATTAAAC
1 GGGGTATAATGTGTAAGACC-TAGCTCGACTATGACAACATAGAGAGTCCGCCAGAACATTAAAC
* * * * * * * *
2555577 ATGGGGTATGATGTCTAAGACCACAACTCAACTATGACAACATTGAGAGTTCACCATGATATTAA
65 -TGGGGTATGATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTACACCA-GACATTAA
2555642 ACAT
128 ACAT
* * * * * * ** *
2555646 CGAGTATAATGTGTAAGAACCTAGCTCGGCTATGGCAACGTAGCGAGTTTGCCAGTACATTAAAA
1 GGGGTATAATGTGTAAG-ACCTAGCTCGACTATGACAACATAGAGAGTCCGCCAGAACATT-AAA
* * * * ** *
2555711 ATGGGGTATGATATGTAAGACCATAGCTCGACTATGGCAACAAAGAAAGTATGCTAGATCATTAA
64 CTGGGGTATGATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTACACCAGA-CATTAA
2555776 ACAT
128 ACAT
* * *
2555780 GGGGTATGATGTGTAAGACCTTAGCTCGGCTATGACAACATAGAGAGTCCGCCAGGACATTAAAC
1 GGGGTATAATGTGTAAGACC-TAGCTCGACTATGACAACATAGAGAGTCCGCCAGAACATTAAAC
* * * *
2555845 GGGGGTTTGATGTGTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCCACCAGGACATTAAA
65 TGGGGTATGATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTACACCA-GACATTAAA
2555910 CAT
129 CAT
* *
2555913 GAGGTATAATGTGTAAGACCCTAGCTCGATTATGACAACATAGAGA
1 GGGGTATAATGTGTAAGA-CCTAGCTCGACTATGACAACATAGAGA
2555959 TTCTATTGGG
Statistics
Matches: 257, Mismatches: 49, Indels: 14
0.80 0.15 0.04
Matches are distributed among these distances:
133 140 0.54
134 114 0.44
135 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (131 bp):
GGGGTATAATGTGTAAGACCTAGCTCGACTATGACAACATAGAGAGTCCGCCAGAACATTAAACT
GGGGTATGATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTACACCAGACATTAAACA
T
Found at i:2565973 original size:31 final size:30
Alignment explanation
Indices: 2565930--2565991 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
2565920 ATAAGCCCCA
2565930 AGTATTTAATTTATA-TCCAAAAAAACCTTTT
1 AGTATTTAATTTATACT-CAAAAAAA-CTTTT
* *
2565961 AGTATTTTATTTATACTCAAATAAACTTTT
1 AGTATTTAATTTATACTCAAAAAAACTTTT
2565991 A
1 A
2565992 ACATAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 6 0.21
31 21 0.75
32 1 0.04
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.45
Consensus pattern (30 bp):
AGTATTTAATTTATACTCAAAAAAACTTTT
Found at i:2576854 original size:14 final size:14
Alignment explanation
Indices: 2576803--2576847 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
2576793 TTTATTTTTA
2576803 TTATAATATTTTATT
1 TTATAATA-TTTATT
*
2576818 ATATCAAT-TTTATT
1 TTAT-AATATTTATT
2576832 TTATAATATTTATT
1 TTATAATATTTATT
2576846 TT
1 TT
2576848 TAGATATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 3 0.12
14 17 0.65
15 3 0.12
16 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATAATATTTATT
Found at i:2580515 original size:25 final size:24
Alignment explanation
Indices: 2580487--2580533 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2580477 TATGTAATCA
2580487 TTACCTTCCATTAATCTTCCTTTTT
1 TTACCTTCCATTAAT-TTCCTTTTT
* * *
2580512 TTACTTTCCGTTTATTTCCTTT
1 TTACCTTCCATTAATTTCCTTT
2580534 CCTTTCCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.60
Consensus pattern (24 bp):
TTACCTTCCATTAATTTCCTTTTT
Found at i:2581403 original size:38 final size:39
Alignment explanation
Indices: 2581351--2581424 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 39
2581341 AATAAAATTC
2581351 TCTCTTAATTAGTTTGTTGATTAAGTTTAGATGAAGTCA
1 TCTCTTAATTAGTTTGTTGATTAAGTTTAGATGAAGTCA
* *
2581390 TCTC-TAATTAGTTTGTTGTTTATGTTTAGATGAAG
1 TCTCTTAATTAGTTTGTTGATTAAGTTTAGATGAAG
2581425 CTAAAACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 29 0.88
39 4 0.12
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.49
Consensus pattern (39 bp):
TCTCTTAATTAGTTTGTTGATTAAGTTTAGATGAAGTCA
Found at i:2591612 original size:43 final size:43
Alignment explanation
Indices: 2591564--2591688 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 43
2591554 TGTAATCTCG
2591564 TATCGATGCCAATAG-CCCA-ACCAAGGTCTTACACGAAATCACA
1 TATCGATGCCAAT-GTCCCAGA-CAAGGTCTTACACGAAATCACA
* * * *
2591607 TATCGATGCTAATGTCCCAGACATGGTCTTACACGAATTCTCA
1 TATCGATGCCAATGTCCCAGACAAGGTCTTACACGAAATCACA
* * * * * *
2591650 TATCGATGTC-ATATCTCAGATATGGTCTTACACGTAATC
1 TATCGATGCCAATGTCCCAGACAAGGTCTTACACGAAATC
2591689 TCGGTAACCC
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 25 0.36
43 43 0.62
44 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
TATCGATGCCAATGTCCCAGACAAGGTCTTACACGAAATCACA
Found at i:2601901 original size:5 final size:5
Alignment explanation
Indices: 2601891--2601920 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2601881 TGCCAAAGAT
2601891 TTGAA TTGAA TTGAA TTGAA TATGAA TTGA
1 TTGAA TTGAA TTGAA TTGAA T-TGAA TTGA
2601921 TTTTAAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
TTGAA
Found at i:2602573 original size:24 final size:24
Alignment explanation
Indices: 2602546--2602622 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
2602536 CCCGATATTA
2602546 GCTCGTATGAGCTTCCTGTTA-ATG
1 GCTC-TATGAGCTTCCTGTTACATG
*
2602570 GCTCTCTAGAGCTTCCTGTTACATG
1 GCTCTAT-GAGCTTCCTGTTACATG
* * * *
2602595 ACTCACATGAGCTTCCTGCTATATG
1 GCTC-TATGAGCTTCCTGTTACATG
2602620 GCT
1 GCT
2602623 TGAAAGAGCT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
23 2 0.05
24 17 0.40
25 23 0.53
26 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (24 bp):
GCTCTATGAGCTTCCTGTTACATG
Found at i:2602612 original size:25 final size:24
Alignment explanation
Indices: 2602552--2602612 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
2602542 ATTAGCTCGT
* *
2602552 ATGAGCTTCCTGTTAATGGCTCTC
1 ATGAGCTTCCTGTTAATGACTCAC
2602576 -TAGAGCTTCCTGTTACATGACTCAC
1 AT-GAGCTTCCTGTTA-ATGACTCAC
2602601 ATGAGCTTCCTG
1 ATGAGCTTCCTG
2602613 CTATATGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 1 0.03
24 13 0.41
25 17 0.53
26 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (24 bp):
ATGAGCTTCCTGTTAATGACTCAC
Found at i:2603407 original size:12 final size:12
Alignment explanation
Indices: 2603392--2603422 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2603382 TTGATTTTAG
*
2603392 GCTTGTTTGATT
1 GCTTGTTTAATT
2603404 GCTTGTTTAATT
1 GCTTGTTTAATT
2603416 GCTTGTT
1 GCTTGTT
2603423 GTGGCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.10, G:0.23, T:0.58
Consensus pattern (12 bp):
GCTTGTTTAATT
Found at i:2611798 original size:17 final size:16
Alignment explanation
Indices: 2611771--2611806 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2611761 ACTTTTAATT
*
2611771 TTTAAATAAATCAATA
1 TTTAAATAAATCAACA
2611787 TTTAACATAAATCAACA
1 TTTAA-ATAAATCAACA
2611804 TTT
1 TTT
2611807 TTATTTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTAAATAAATCAACA
Found at i:2612270 original size:25 final size:25
Alignment explanation
Indices: 2612242--2612295 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
2612232 AATTGGAAAA
2612242 CTTTGTTGAATTATAATTCAATTAT
1 CTTTGTTGAATTATAATTCAATTAT
2612267 CTTTGTTGAATTATAATTCAATTAT
1 CTTTGTTGAATTATAATTCAATTAT
2612292 CTTT
1 CTTT
2612296 TCATTCAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (25 bp):
CTTTGTTGAATTATAATTCAATTAT
Found at i:2613801 original size:24 final size:25
Alignment explanation
Indices: 2613766--2613813 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
2613756 TTATGAAATT
2613766 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
2613790 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
2613814 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:2613994 original size:120 final size:120
Alignment explanation
Indices: 2613854--2614146 Score: 486
Period size: 120 Copynumber: 2.4 Consensus size: 120
2613844 AATTATTTTA
* * * *
2613854 AATTTTATGT-AATCATATATTTTAATTAAAAAATATTTAATATTAATTAT-TTCAAATTT-TCA
1 AATTTTAT-TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-A
2613916 -TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
62 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
2613974 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
2614039 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
2614094 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
2614147 TAAATATGAT
Statistics
Matches: 165, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
119 7 0.04
120 156 0.95
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:2614014 original size:15 final size:15
Alignment explanation
Indices: 2613979--2614030 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2613969 TTAAGAATTT
*
2613979 TATTAAATTAT-ATA
1 TATTTAATTATAATA
2613993 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2614007 TATTTAATAATAAT-
1 TATTTAATTATAATA
2614021 TATGTTAATT
1 TAT-TTAATT
2614031 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2614112 original size:61 final size:61
Alignment explanation
Indices: 2613927--2614114 Score: 201
Period size: 61 Copynumber: 3.1 Consensus size: 61
2613917 TTATAGTATC
2613927 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
2613988 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
2614046 C
61 T
2614047 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
2614108 ATATATT
1 ATATATT
2614115 TTAATTATAA
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.16
61 25 0.26
62 8 0.08
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:2614129 original size:16 final size:16
Alignment explanation
Indices: 2614108--2614149 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2614098 TTATTAAATT
*
2614108 ATATATTTTAATTATA
1 ATATATTTTAATAATA
2614124 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
2614139 AT-TATGTTTAA
1 ATATAT-TTTAA
2614150 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:2614134 original size:15 final size:15
Alignment explanation
Indices: 2614099--2614140 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2614089 TTAAGAATTT
*
2614099 TATTAAATTAT-ATA
1 TATTTAATTATAATA
2614113 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2614127 TATTTAATAATAAT
1 TATTTAATTATAAT
2614141 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2614305 original size:16 final size:16
Alignment explanation
Indices: 2614284--2614318 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2614274 ATATATTAAA
2614284 TAACAATAACAATATT
1 TAACAATAACAATATT
2614300 TAACAATAACAATATT
1 TAACAATAACAATATT
2614316 TAA
1 TAA
2614319 TAATTTACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (16 bp):
TAACAATAACAATATT
Found at i:2614383 original size:18 final size:17
Alignment explanation
Indices: 2614355--2614389 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2614345 ATTATTAAGA
*
2614355 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2614372 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2614390 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2623858 original size:7 final size:8
Alignment explanation
Indices: 2623830--2623857 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2623820 TTGTAAAAAG
2623830 AAAAATGA
1 AAAAATGA
2623838 AAAAATGA
1 AAAAATGA
2623846 AAAAATGA
1 AAAAATGA
2623854 AAAA
1 AAAA
2623858 TAAGATAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAATGA
Found at i:2626330 original size:5 final size:5
Alignment explanation
Indices: 2626322--2626347 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2626312 ATTTATTTTA
2626322 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
2626348 TAAGAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2626355 original size:15 final size:15
Alignment explanation
Indices: 2626322--2626355 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2626312 ATTTATTTTA
*
2626322 AAAATAAAATAAAAT
1 AAAATAAAATAAAAG
*
2626337 AAAATAAAATATAAG
1 AAAATAAAATAAAAG
2626352 AAAA
1 AAAA
2626356 ATTAAGTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAATAAAATAAAAG
Found at i:2632616 original size:31 final size:30
Alignment explanation
Indices: 2632572--2632629 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2632562 TTTTTAATTT
2632572 TTTAAAATATTTATATTATTTTAATTTAATA
1 TTTAAAATATTTATA-TATTTTAATTTAATA
*
2632603 TTTAATAAT-TTTATATATTTTTATTTA
1 TTTAA-AATATTTATATATTTTAATTTA
2632630 TTGAACTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 11 0.44
31 11 0.44
32 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTAAAATATTTATATATTTTAATTTAATA
Found at i:2632629 original size:30 final size:31
Alignment explanation
Indices: 2632551--2632629 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
2632541 TAGGCTCACC
* *
2632551 TATATACTTTTTTTTTAATTTTTTAAAATATT
1 TATATA-TTTTTATTTAATTATTTAAAATATT
*
2632583 TATATTATTTTAATTTAA-TATTTAATAAT-TT
1 TATA-TATTTTTATTTAATTATTTAA-AATATT
2632614 TATATATTTTTATTTA
1 TATATATTTTTATTTA
2632630 TTGAACTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 11 0.27
31 12 0.29
32 16 0.39
33 2 0.05
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (31 bp):
TATATATTTTTATTTAATTATTTAAAATATT
Found at i:2641479 original size:131 final size:131
Alignment explanation
Indices: 2641247--2641537 Score: 443
Period size: 131 Copynumber: 2.3 Consensus size: 131
2641237 TAGTGTACCG
*
2641247 ACTTAAACTCTTTCTAAGAACATGAT----G-ACAACTGTTCTGATTGTGACTTGTGAAGAAGAA
1 ACTTAAACTCTTTCTAAGAACATGATGGCAGTACAACTGTTCTGATTGTGACTCGTGAAGAAGAA
* * *
2641307 GAGTAAGGCTAAACGCTATACCTATATATAGTGTCCCGACTGGTGACTGAGTATATGTCCTAAGC
66 GAGGAAGGCTAAACGCTATACCTATAAATAGTGTCCCGACTGGTGACTGAGTATATGTCCTAAAC
2641372 A
131 A
* *
2641373 ACTTAAACTCTTTCTAAGAACATGATGGCAGTATAACTGTTCTGATTGTGACTCGTGGAGAAGAA
1 ACTTAAACTCTTTCTAAGAACATGATGGCAGTACAACTGTTCTGATTGTGACTCGTGAAGAAGAA
*
2641438 GAGGAAGGCTAAACGCTCA-ATCTATAAATAGTG-CCCAGACTGGTGACTGAGTATATGTCCTAA
66 GAGGAAGGCTAAACGCT-ATACCTATAAATAGTGTCCC-GACTGGTGACTGAGTATATGTCCTAA
2641501 ACA
129 ACA
*
2641504 ACTCAAACTCTTTCTAAGAACATGATGGCAGTAC
1 ACTTAAACTCTTTCTAAGAACATGATGGCAGTAC
2641538 TGTTTGTATA
Statistics
Matches: 149, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
126 26 0.17
130 4 0.03
131 118 0.79
132 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (131 bp):
ACTTAAACTCTTTCTAAGAACATGATGGCAGTACAACTGTTCTGATTGTGACTCGTGAAGAAGAA
GAGGAAGGCTAAACGCTATACCTATAAATAGTGTCCCGACTGGTGACTGAGTATATGTCCTAAAC
A
Found at i:2646026 original size:21 final size:20
Alignment explanation
Indices: 2646004--2646042 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2645994 TTATTATATA
2646004 ATAAT-ATAAATAC-TTTTT
1 ATAATGATAAATACATTTTT
2646022 ATAATGATAAATACATTTTT
1 ATAATGATAAATACATTTTT
2646042 A
1 A
2646043 ATTATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 8 0.42
20 6 0.32
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
ATAATGATAAATACATTTTT
Done.