Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 9 of 117
Found at i:2419086 original size:31 final size:29
Alignment explanation
Indices: 2419024--2419091 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 29
2419014 TCATGCTATG
*
2419024 TAAAATATTATATTTATATTATATTTTATA
1 TAAAA-ATTATATTTATATTATATTTAATA
2419054 TAAAAATTATATATTATAATT-TATGTTAATA
1 TAAAAATTATAT-TTAT-ATTATAT-TTAATA
2419085 TAAAAAT
1 TAAAAAT
2419092 ATAAAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.21
30 12 0.35
31 15 0.44
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
TAAAAATTATATTTATATTATATTTAATA
Found at i:2419160 original size:23 final size:23
Alignment explanation
Indices: 2419134--2419178 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2419124 TTTTATTAAA
2419134 TTTTAAATTATATTACTTTTATT
1 TTTTAAATTATATTACTTTTATT
* * *
2419157 TTTTTATTTATATTATTTTTAT
1 TTTTAAATTATATTACTTTTAT
2419179 ATTATATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTAAATTATATTACTTTTATT
Found at i:2419164 original size:17 final size:16
Alignment explanation
Indices: 2419141--2419185 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
2419131 AAATTTTAAA
*
2419141 TTATATTACTTTTATTT
1 TTATATTA-TATTATTT
*
2419158 TTTTATTTATATTATTT
1 TTATA-TTATATTATTT
2419175 TTATATTATAT
1 TTATATTATAT
2419186 CATAATATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 6 0.25
17 15 0.62
18 3 0.12
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATATTATATTATTT
Found at i:2419179 original size:11 final size:11
Alignment explanation
Indices: 2419141--2419183 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2419131 AAATTTTAAA
*
2419141 TTATATTACTT
1 TTATATTATTT
* *
2419152 TTATTTTTTTAT
1 TTATATTATT-T
2419164 TTATATTATTT
1 TTATATTATTT
2419175 TTATATTAT
1 TTATATTAT
2419184 ATCATAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATATTATTT
Found at i:2419446 original size:18 final size:18
Alignment explanation
Indices: 2419412--2419446 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2419402 TAGATGTATG
*
2419412 ATTTTAATTTATAATAAT
1 ATTTTAATATATAATAAT
*
2419430 ATTTTAATATATTATAA
1 ATTTTAATATATAATAA
2419447 AATCAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAATATATAATAAT
Found at i:2419675 original size:21 final size:21
Alignment explanation
Indices: 2419659--2419697 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2419649 AATAAATTTA
2419659 TTAAT-TAAAAATTTAAAATT
1 TTAATATAAAAATTTAAAATT
*
2419679 TTAATATAAAAATTAAAAA
1 TTAATATAAAAATTTAAAA
2419698 GTTGATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAATATAAAAATTTAAAATT
Found at i:2430316 original size:24 final size:24
Alignment explanation
Indices: 2430265--2430319 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2430255 CATCTTCATG
* *
2430265 ATCATCATCTTCATCATCAGAAAT
1 ATCATCATCTTCATCACCAGAAAC
*
2430289 ATCATCATCTTCAATCACCA-AAGC
1 ATCATCATCTTC-ATCACCAGAAAC
2430313 ATCATCA
1 ATCATCA
2430320 ATCTCCACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (24 bp):
ATCATCATCTTCATCACCAGAAAC
Found at i:2435724 original size:2 final size:2
Alignment explanation
Indices: 2435719--2435753 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2435709 TTTTAGGAAA
*
2435719 AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2435754 ATATTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2437968 original size:3 final size:3
Alignment explanation
Indices: 2437960--2437988 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2437950 CTTAGCGTAT
2437960 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2437989 TGTTTGTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2439105 original size:54 final size:54
Alignment explanation
Indices: 2439027--2439137 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
2439017 CGTATGTTAG
*
2439027 TTTATGTTAGAATATACATCTATAAACTAAAACATGTTTTTATTTATTTATTTA
1 TTTATGTTAGAATATACATCTATAAACTAAAACATATTTTTATTTATTTATTTA
2439081 TTTATGTTAGAATATACATCTATAAACTAAAACATATTTTTATTTATTTATTTA
1 TTTATGTTAGAATATACATCTATAAACTAAAACATATTTTTATTTATTTATTTA
2439135 TTT
1 TTT
2439138 TGACTAAAGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (54 bp):
TTTATGTTAGAATATACATCTATAAACTAAAACATATTTTTATTTATTTATTTA
Found at i:2443868 original size:19 final size:19
Alignment explanation
Indices: 2443835--2443887 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2443825 ATTCAAGTAT
2443835 ATAATTATATTATTAAAAAA
1 ATAATTAT-TTATTAAAAAA
* * *
2443855 ATAATTATTTATTACATAT
1 ATAATTATTTATTAAAAAA
*
2443874 ATAAATATTTATTA
1 ATAATTATTTATTA
2443888 TTTAATTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATTATTTATTAAAAAA
Found at i:2445394 original size:5 final size:5
Alignment explanation
Indices: 2445384--2445413 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2445374 ACAACCACAT
2445384 TCATA TCATA TCAATA TCATA TCATA TCAT
1 TCATA TCATA TC-ATA TCATA TCATA TCAT
2445414 GTATATCTTT
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:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
TCATA
Found at i:2445402 original size:11 final size:10
Alignment explanation
Indices: 2445384--2445413 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
2445374 ACAACCACAT
2445384 TCATATCATA
1 TCATATCATA
2445394 TCAATATCATA
1 TC-ATATCATA
2445405 TCATATCAT
1 TCATATCAT
2445414 GTATATCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (10 bp):
TCATATCATA
Found at i:2446347 original size:2 final size:2
Alignment explanation
Indices: 2446340--2446400 Score: 79
Period size: 2 Copynumber: 31.0 Consensus size: 2
2446330 GGTCACTGCC
* * * *
2446340 CT CT CT CT CT CT TT CT CT TT CT TT TT CT CT -T CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2446381 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
2446401 GTGAGCGTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (2 bp):
CT
Found at i:2447712 original size:15 final size:15
Alignment explanation
Indices: 2447692--2447721 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2447682 TGCATTTATA
2447692 TGGGTTGTATACTTT
1 TGGGTTGTATACTTT
2447707 TGGGTTGTATACTTT
1 TGGGTTGTATACTTT
2447722 CTTTTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.27, T:0.53
Consensus pattern (15 bp):
TGGGTTGTATACTTT
Found at i:2452325 original size:19 final size:20
Alignment explanation
Indices: 2452287--2452336 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
2452277 GATATTTTTA
2452287 AATATTTATATTTAAAAAAT
1 AATATTTATATTTAAAAAAT
2452307 AATATTTATATTT-AAAAAT
1 AATATTTATATTTAAAAAAT
2452326 AATATTT-TATT
1 AATATTTATATT
2452337 AATTTCGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.13
19 13 0.43
20 13 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATATTTATATTTAAAAAAT
Found at i:2456050 original size:26 final size:26
Alignment explanation
Indices: 2455995--2456050 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
2455985 TTATTAAATT
**
2455995 TTTTTTTCAATTACAACTATCGTAAA
1 TTTTTTTCAATTACAACTATAATAAA
*
2456021 TTTTTTTCAATTACAACTATAATAAC
1 TTTTTTTCAATTACAACTATAATAAA
2456047 TTTT
1 TTTT
2456051 ATTATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTTTTCAATTACAACTATAATAAA
Found at i:2457353 original size:22 final size:22
Alignment explanation
Indices: 2457328--2457369 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2457318 ACAACCTAAA
2457328 ATACAAAACTGTGTTACTTAAT
1 ATACAAAACTGTGTTACTTAAT
2457350 ATACAAAACTGTGTTACTTA
1 ATACAAAACTGTGTTACTTA
2457370 GGCATGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (22 bp):
ATACAAAACTGTGTTACTTAAT
Found at i:2459287 original size:109 final size:109
Alignment explanation
Indices: 2459087--2459308 Score: 336
Period size: 109 Copynumber: 2.0 Consensus size: 109
2459077 GAAAAACTTG
* *
2459087 GAGGACAAGCCAAACAGCCCAAGAAGACACTGTACTGCCAAAATCGCCGTACCGACGTCGTTTTA
1 GAGGACAAGCCAAACAGCCCAAGAAGACACTGTACTGCCAAAATCGCCGTACCGACGCCGTTGTA
* * * *
2459152 CTCTATTTACCTTTTTTATGATGAGTTAATTTTACTTTTTGAAC
66 CTCTATTGACCTTTTTCATGACGAGTTAATTTTACTTTTGGAAC
* ** *
2459196 GAGGACAAGCCAAATAGCCCAAGAAGACACTGTACTGTGAAAATCGCTGTACCGACGCCGTTGTA
1 GAGGACAAGCCAAACAGCCCAAGAAGACACTGTACTGCCAAAATCGCCGTACCGACGCCGTTGTA
* *
2459261 CTCTATTGGCCTTTTTCATTACGAGTTAATTTTACTTTTGGAAC
66 CTCTATTGACCTTTTTCATGACGAGTTAATTTTACTTTTGGAAC
2459305 GAGG
1 GAGG
2459309 CAGACGTACA
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
109 101 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (109 bp):
GAGGACAAGCCAAACAGCCCAAGAAGACACTGTACTGCCAAAATCGCCGTACCGACGCCGTTGTA
CTCTATTGACCTTTTTCATGACGAGTTAATTTTACTTTTGGAAC
Found at i:2459641 original size:22 final size:22
Alignment explanation
Indices: 2459616--2459658 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2459606 GTACATTATT
2459616 TATTAAATAAAAATAT-TTTTAA
1 TATTAAATAAAAA-ATGTTTTAA
**
2459638 TATTTTATAAAAAATGTTTTA
1 TATTAAATAAAAAATGTTTTA
2459659 TAAATGTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTAAATAAAAAATGTTTTAA
Found at i:2460571 original size:13 final size:12
Alignment explanation
Indices: 2460544--2460590 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 12
2460534 ATTAAATTTA
*
2460544 ATAATTTAAAAT
1 ATAATATAAAAT
2460556 ATAATATAATAAT
1 ATAATATAA-AAT
*
2460569 ATAATACAAAA-
1 ATAATATAAAAT
*
2460580 ATAAAATAAAA
1 ATAATATAAAA
2460591 AAATAACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 9 0.30
12 10 0.33
13 11 0.37
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:2460708 original size:12 final size:12
Alignment explanation
Indices: 2460674--2460718 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
2460664 ATCGACATTT
2460674 ATTATTATATATA
1 ATTATTATATA-A
*
2460687 ATTTTTATATAA
1 ATTATTATATAA
*
2460699 ATTATAATATAA
1 ATTATTATATAA
2460711 ATATATTA
1 AT-TATTA
2460719 ATTTTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 13 0.48
13 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTATTATATAA
Found at i:2481027 original size:3 final size:3
Alignment explanation
Indices: 2481019--2481047 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2481009 ATCTTTAGTT
2481019 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2481048 TTGATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2481359 original size:24 final size:24
Alignment explanation
Indices: 2481303--2481352 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2481293 CCCAACGTTT
*
2481303 CCCCTTTCAGCCTCTCTCGGACAC
1 CCCCTCTCAGCCTCTCTCGGACAC
* *
2481327 CCCCTCTCAGCCTCTCTTGGATAC
1 CCCCTCTCAGCCTCTCTCGGACAC
2481351 CC
1 CC
2481353 TTTCTCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.50, G:0.12, T:0.26
Consensus pattern (24 bp):
CCCCTCTCAGCCTCTCTCGGACAC
Found at i:2482617 original size:15 final size:15
Alignment explanation
Indices: 2482599--2482648 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2482589 TCTTAAATTC
*
2482599 AAACTCCTAAAATCT
1 AAACTCCTAAAATCA
* *
2482614 AAACCCCAAAAATTCA
1 AAACTCCTAAAA-TCA
*
2482630 AAACTCCTAAAATCC
1 AAACTCCTAAAATCA
2482645 AAAC
1 AAAC
2482649 CCCAAACCTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (15 bp):
AAACTCCTAAAATCA
Found at i:2482637 original size:31 final size:30
Alignment explanation
Indices: 2482593--2482654 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 30
2482583 ACTAATTCTT
*
2482593 AAATTCAAACTCCTAAAATCTAAACCCCAA
1 AAATTCAAACTCCTAAAATCCAAACCCCAA
2482623 AAATTCAAAACTCCTAAAATCCAAACCCCAA
1 AAATTC-AAACTCCTAAAATCCAAACCCCAA
2482654 A
1 A
2482655 CCTCAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.18
Consensus pattern (30 bp):
AAATTCAAACTCCTAAAATCCAAACCCCAA
Found at i:2482641 original size:16 final size:16
Alignment explanation
Indices: 2482593--2482647 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
2482583 ACTAATTCTT
2482593 AAATTC-AAACTCCTA
1 AAATTCAAAACTCCTA
* * *
2482608 AAA-TCTAAACCCCAA
1 AAATTCAAAACTCCTA
2482623 AAATTCAAAACTCCTA
1 AAATTCAAAACTCCTA
*
2482639 AAATCCAAA
1 AAATTCAAA
2482648 CCCCAAACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
14 2 0.06
15 13 0.41
16 17 0.53
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (16 bp):
AAATTCAAAACTCCTA
Found at i:2482917 original size:58 final size:57
Alignment explanation
Indices: 2482834--2483040 Score: 188
Period size: 58 Copynumber: 3.6 Consensus size: 57
2482824 CTTAAAAATG
* * * *
2482834 AAACCTCAAACCTTCCAAACCCTAAAATTAAAAACTTCACCTTTCAAACCCTACAATCA
1 AAACCCCAAACC-TCTAAACCCTAAAA-CAAAAACTTCACCTTTCAAACCCTAAAATCA
* * *
2482893 AAACCCCAAACCTCTAAGCTCTAAAATC-AAAACTTCAAACC-TTCAAACCCTAAAAT-T
1 AAACCCCAAACCTCTAAACCCTAAAA-CAAAAACTTC--ACCTTTCAAACCCTAAAATCA
** * ** *
2482950 AAACCGTAAATCCTCTAAACCCTAAAACCAAAACTTCAAATCTCAAACCCTAAAATCA
1 AAACCCCAAA-CCTCTAAACCCTAAAACAAAAACTTCACCTTTCAAACCCTAAAATCA
* *
2483008 AAATCCCAAATCTC-AAACCCTAAAATCAAAAAC
1 AAACCCCAAACCTCTAAACCCTAAAA-CAAAAAC
2483041 CTAAACCCCA
Statistics
Matches: 121, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
56 12 0.10
57 40 0.33
58 55 0.45
59 14 0.12
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.20
Consensus pattern (57 bp):
AAACCCCAAACCTCTAAACCCTAAAACAAAAACTTCACCTTTCAAACCCTAAAATCA
Found at i:2483004 original size:28 final size:28
Alignment explanation
Indices: 2482702--2483038 Score: 168
Period size: 29 Copynumber: 11.7 Consensus size: 28
2482692 TCTAAATTTT
* *
2482702 TCAAACCCTAAAAT-TAAACATT-AAAAC
1 TCAAACCCTAAAATCAAAAC-TTCAAATC
* *
2482729 TTCCAAACCCTCAAATCCAAAACCTTAAAAT-
1 -T-CAAACCCTAAAAT-CAAAA-CTTCAAATC
** * *
2482760 AAAAACCCTAAAAACGAAAC-TCTAAATTTC
1 TCAAACCCTAAAATCAAAACTTC-AAA--TC
* * *
2482790 TCAAACCCTAAAATTAAACCTT-AAACC
1 TCAAACCCTAAAATCAAAACTTCAAATC
* * * * *
2482817 TCTTAACCTTAAAAAT-GAAACCTCAAACC
1 TC-AAACCCT-AAAATCAAAACTTCAAATC
* ** *
2482846 TTCCAAACCCTAAAATTAAAAACTTCACCTT
1 -T-CAAACCCTAAAA-TCAAAACTTCAAATC
* ** *
2482877 TCAAACCCTACAATCAAAACCCCAAACC
1 TCAAACCCTAAAATCAAAACTTCAAATC
* * *
2482905 TCTAAGCTCTAAAATCAAAACTTCAAACC
1 TC-AAACCCTAAAATCAAAACTTCAAATC
* * *
2482934 TTCAAACCCTAAAATTAAACCGT-AAATCC
1 -TCAAACCCTAAAATCAAAACTTCAAAT-C
*
2482963 TCTAAACCCTAAAACCAAAACTTCAAATC
1 TC-AAACCCTAAAATCAAAACTTCAAATC
*
2482992 TCAAACCCTAAAATCAAAA-TCCCAAATC
1 TCAAACCCTAAAATCAAAACT-TCAAATC
2483020 TCAAACCCTAAAATCAAAA
1 TCAAACCCTAAAATCAAAA
2483039 ACCTAAACCC
Statistics
Matches: 232, Mismatches: 54, Indels: 46
0.70 0.16 0.14
Matches are distributed among these distances:
26 1 0.00
27 8 0.03
28 70 0.30
29 107 0.46
30 28 0.12
31 14 0.06
32 4 0.02
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.21
Consensus pattern (28 bp):
TCAAACCCTAAAATCAAAACTTCAAATC
Found at i:2483040 original size:15 final size:15
Alignment explanation
Indices: 2482994--2483045 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
2482984 TTCAAATCTC
2482994 AAACCCTAAAATCAA
1 AAACCCTAAAATCAA
* **
2483009 AATCCC--AAATCTC
1 AAACCCTAAAATCAA
2483022 AAACCCTAAAATCAA
1 AAACCCTAAAATCAA
2483037 AAA-CCTAAA
1 AAACCCTAAA
2483046 CCCCAAAATC
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 10 0.34
14 6 0.21
15 13 0.45
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (15 bp):
AAACCCTAAAATCAA
Found at i:2483048 original size:21 final size:22
Alignment explanation
Indices: 2483022--2483073 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
2483012 CCCAAATCTC
2483022 AAACCCTAAAATCAAAAACCT-
1 AAACCCTAAAATCAAAAACCTG
* ** *
2483043 AAACCCCAAAATCTGAAACTTG
1 AAACCCTAAAATCAAAAACCTG
2483065 AAACCCTAA
1 AAACCCTAA
2483074 CCCTAAAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.52, C:0.29, G:0.04, T:0.15
Consensus pattern (22 bp):
AAACCCTAAAATCAAAAACCTG
Found at i:2487942 original size:16 final size:16
Alignment explanation
Indices: 2487921--2487961 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2487911 TTATACGATC
*
2487921 ATTTAAAAAAATTAAT
1 ATTTAAAAAAATTAAA
* *
2487937 ATTTAATAAATTTAAA
1 ATTTAAAAAAATTAAA
2487953 ATTTAAAAA
1 ATTTAAAAA
2487962 TCAAAATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTAAAAAAATTAAA
Found at i:2488510 original size:19 final size:21
Alignment explanation
Indices: 2488469--2488510 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
2488459 TAATATTGTA
* *
2488469 TTATATTCTTTAAATAATTAT
1 TTATATTCTTAAAATAATAAT
2488490 TTATATT-TTAAAATAA-AAT
1 TTATATTCTTAAAATAATAAT
2488509 TT
1 TT
2488511 TTAAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 8 0.42
21 7 0.37
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATATTCTTAAAATAATAAT
Found at i:2494967 original size:26 final size:26
Alignment explanation
Indices: 2494931--2495006 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
2494921 TAATATTTTT
2494931 TAAAA-AA-ATTATTTATTA-ATAAAA
1 TAAAATAATATTATTTATTATAT-AAA
* *
2494955 TAAAATAATATTATTTATTTTATTAA
1 TAAAATAATATTATTTATTATATAAA
* *
2494981 TAAAATAATATTATTCAGTATATAAA
1 TAAAATAATATTATTTATTATATAAA
2495007 ATTTATATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
24 5 0.12
25 2 0.05
26 34 0.79
27 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (26 bp):
TAAAATAATATTATTTATTATATAAA
Found at i:2504202 original size:21 final size:20
Alignment explanation
Indices: 2504174--2504213 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2504164 CTTCCCTCTC
2504174 TTTGCTCAAAACTAATTATA
1 TTTGCTCAAAACTAATTATA
**
2504194 TTTGACTCATCACTAATTAT
1 TTTG-CTCAAAACTAATTAT
2504214 GACTGGCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTGCTCAAAACTAATTATA
Found at i:2511400 original size:17 final size:17
Alignment explanation
Indices: 2511360--2511391 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2511350 TTATCTTAAA
2511360 ATTA-AAATTATTTTAC
1 ATTATAAATTATTTTAC
2511376 ATTATAAATTATTTTA
1 ATTATAAATTATTTTA
2511392 TATTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATAAATTATTTTAC
Found at i:2523457 original size:11 final size:11
Alignment explanation
Indices: 2523441--2523466 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2523431 AATCTAAAAT
2523441 ATATAAATATG
1 ATATAAATATG
2523452 ATATAAATATG
1 ATATAAATATG
2523463 ATAT
1 ATAT
2523467 GATTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
ATATAAATATG
Found at i:2524350 original size:22 final size:20
Alignment explanation
Indices: 2524294--2524350 Score: 53
Period size: 24 Copynumber: 2.6 Consensus size: 20
2524284 ATTTTATAAA
2524294 AAAAATCATTTTT-AATTTTC
1 AAAAAT-ATTTTTCAATTTTC
*
2524314 AAAAATATTGATTTCAATTTTTTT
1 AAAAATATT--TTTCAA--TTTTC
2524338 AAAAATATTTTTC
1 AAAAATATTTTTC
2524351 CTATGACACT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 3 0.10
20 6 0.19
21 3 0.10
22 6 0.19
24 13 0.42
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (20 bp):
AAAAATATTTTTCAATTTTC
Found at i:2536071 original size:1 final size:1
Alignment explanation
Indices: 2536065--2536090 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2536055 ACATCAACAG
2536065 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2536091 GGAATTCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2536587 original size:14 final size:14
Alignment explanation
Indices: 2536568--2536594 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2536558 TTATAAATGA
2536568 TAAAAAAAATAAAG
1 TAAAAAAAATAAAG
2536582 TAAAAAAAATAAA
1 TAAAAAAAATAAA
2536595 ATGATTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (14 bp):
TAAAAAAAATAAAG
Found at i:2546497 original size:12 final size:12
Alignment explanation
Indices: 2546471--2546530 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
2546461 TATATATAAA
*
2546471 AATTATT-TTTT
1 AATTATTATATT
2546482 AATTATTATATT
1 AATTATTATATT
2546494 AATTATATATATT
1 AATTAT-TATATT
*
2546507 TATATATT-TATTT
1 AAT-TATTATA-TT
2546520 AATT-TTATATT
1 AATTATTATATT
2546531 TATATTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
11 11 0.27
12 14 0.34
13 13 0.32
14 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
AATTATTATATT
Found at i:2546510 original size:8 final size:8
Alignment explanation
Indices: 2546499--2546539 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
2546489 ATATTAATTA
2546499 TATATATT
1 TATATATT
2546507 TATATATT
1 TATATATT
*
2546515 TATTTAATT
1 TATAT-ATT
2546524 T-TATATT
1 TATATATT
2546531 TATAT-TT
1 TATATATT
2546538 TA
1 TA
2546540 AAATAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
7 8 0.28
8 17 0.59
9 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATATATT
Found at i:2546531 original size:12 final size:12
Alignment explanation
Indices: 2546479--2546539 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 12
2546469 AAAATTATTT
2546479 TTTAATTATTATA
1 TTTAATT-TTATA
2546492 -TTAATTATATATA
1 TTTAATT-T-TATA
*
2546505 TTTATATATT-TA
1 TTTA-ATTTTATA
2546517 TTTAATTTTATA
1 TTTAATTTTATA
2546529 TTTATATTTTA
1 TTTA-ATTTTA
2546540 AAATAATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
11 4 0.10
12 20 0.49
13 11 0.27
14 4 0.10
15 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTAATTTTATA
Found at i:2546536 original size:18 final size:18
Alignment explanation
Indices: 2546479--2546537 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
2546469 AAAATTATTT
2546479 TTTAATTATTATA-TTA-A
1 TTTAATT-TTATATTTATA
2546496 TTATATATATTTATATATT-TA
1 TT-TA-AT-TTTATAT-TTATA
2546517 TTTAATTTTATATTTATA
1 TTTAATTTTATATTTATA
2546535 TTT
1 TTT
2546538 TAAAATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
17 4 0.11
18 14 0.40
19 9 0.26
20 3 0.09
21 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAATTTTATATTTATA
Found at i:2546546 original size:24 final size:26
Alignment explanation
Indices: 2546501--2546556 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 26
2546491 ATTAATTATA
* *
2546501 TATATTTATATATTT-ATTTA-ATTT
1 TATATTTATATATTTAAATAATATTT
2546525 TATATTTATAT-TTTAAAATAATATTT
1 TATATTTATATATTT-AAATAATATTT
2546551 TATATT
1 TATATT
2546557 AAAAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 3 0.11
24 11 0.41
25 3 0.11
26 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TATATTTATATATTTAAATAATATTT
Found at i:2546548 original size:19 final size:17
Alignment explanation
Indices: 2546526--2546568 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2546516 ATTTAATTTT
*
2546526 ATATTTATATTTTAAAATA
1 ATATTTATATATT-AAA-A
2546545 ATATTT-TATATTAAAA
1 ATATTTATATATTAAAA
2546561 ATATTTAT
1 ATATTTAT
2546569 TAATTTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.32
17 4 0.18
18 5 0.23
19 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTTATATATTAAAA
Found at i:2546569 original size:20 final size:21
Alignment explanation
Indices: 2546523--2546569 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
2546513 TTTATTTAAT
*
2546523 TTTATATTTATATTTTAAAATA
1 TTTAT-TTTATATTTAAAAATA
*
2546545 -ATATTTTATA-TTAAAAATA
1 TTTATTTTATATTTAAAAATA
2546564 TTTATT
1 TTTATT
2546570 AATTTTAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
19 8 0.38
20 10 0.48
21 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATTTTATATTTAAAAATA
Found at i:2547928 original size:21 final size:21
Alignment explanation
Indices: 2547889--2547929 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2547879 TTGTGATATG
*
2547889 ATTAAATTTATTATATAATTA
1 ATTAAATTTAATATATAATTA
2547910 ATTAAATTTAA-ATATTAATT
1 ATTAAATTTAATATA-TAATT
2547930 TTAATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTAAATTTAATATATAATTA
Found at i:2547945 original size:27 final size:27
Alignment explanation
Indices: 2547915--2547989 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 27
2547905 AATTAATTAA
*
2547915 ATTTAAATATTAATTTTAATAAAATTT
1 ATTTAAATATTAATTTTAATAAAAATT
* *
2547942 ATTT-AATATAAAATATTTATTAAAAATT
1 ATTTAAATAT-TAAT-TTTAATAAAAATT
* *
2547970 -TTTAATTA-TAATTATAATAA
1 ATTTAAATATTAATTTTAATAA
2547990 TTTTATTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
25 6 0.16
26 8 0.21
27 10 0.26
28 14 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTAAATATTAATTTTAATAAAAATT
Found at i:2547977 original size:14 final size:13
Alignment explanation
Indices: 2547928--2547975 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2547918 TAAATATTAA
*
2547928 TTTTAATAAAATT
1 TTTTAATAAAAAT
2547941 TATTTAATATAAAAT
1 T-TTTAATA-AAAAT
* *
2547956 ATTTATTAAAAAT
1 TTTTAATAAAAAT
2547969 TTTTAAT
1 TTTTAAT
2547976 TATAATTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 11 0.39
14 13 0.46
15 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTAATAAAAAT
Found at i:2548146 original size:2 final size:2
Alignment explanation
Indices: 2548139--2548167 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2548129 CAATAAGATC
2548139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2548168 AGAGGTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2548300 original size:21 final size:20
Alignment explanation
Indices: 2548226--2548300 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
2548216 ATAATAAAAT
*
2548226 TAATTTTAATAAAATTA--A
1 TAATTATAATAAAATTATCA
* *
2548244 AAATTATAATACAAATTATTA
1 TAATTATAATA-AAATTATCA
*
2548265 TAATTA-AGACAAAAATTATCA
1 TAATTATA-A-TAAAATTATCA
2548286 TAATTATAATTAAAA
1 TAATTATAA-TAAAA
2548301 AAATTTATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
18 9 0.20
19 6 0.14
20 1 0.02
21 26 0.59
22 2 0.05
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (20 bp):
TAATTATAATAAAATTATCA
Found at i:2548315 original size:25 final size:25
Alignment explanation
Indices: 2548261--2548326 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
2548251 AATACAAATT
*
2548261 ATTATAATTAAGACAAAAATTATCATA
1 ATTATAATTAA-A-AAAAATTATCAAA
* *
2548288 ATTATAATTAAAAAAATTTATTAAA
1 ATTATAATTAAAAAAAATTATCAAA
*
2548313 ATTAATATTTAAAA
1 ATT-ATAATTAAAA
2548327 TTAATTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 13 0.38
26 10 0.29
27 11 0.32
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTATAATTAAAAAAAATTATCAAA
Found at i:2556818 original size:49 final size:49
Alignment explanation
Indices: 2556751--2556850 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
2556741 CATGCAAATA
* * *
2556751 AAACTAGGGTTAATTGTTACCATTCCTCTTAAATTATAATAAAATATTT
1 AAACCAGGGTTAAATGTTACCATTCCTCCTAAATTATAATAAAATATTT
2556800 AAACCAGGGTTAAATGTTACCATTCCTCCTAAATTATAATAAAATATTT
1 AAACCAGGGTTAAATGTTACCATTCCTCCTAAATTATAATAAAATATTT
2556849 AA
1 AA
2556851 TATTATATTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (49 bp):
AAACCAGGGTTAAATGTTACCATTCCTCCTAAATTATAATAAAATATTT
Found at i:2564381 original size:18 final size:17
Alignment explanation
Indices: 2564362--2564412 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
2564352 TTTATATTTA
*
2564362 AAAAATAAGATTTATAT
1 AAAAATAACATTTATAT
*
2564379 AAAAATAACATTTTATGTT
1 AAAAATAACA-TTTAT-AT
*
2564398 AAAAATAATATTTAT
1 AAAAATAACATTTAT
2564413 TAATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 9 0.31
18 10 0.34
19 10 0.34
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (17 bp):
AAAAATAACATTTATAT
Found at i:2570641 original size:24 final size:23
Alignment explanation
Indices: 2570625--2570675 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2570615 ATTCTAATTA
*
2570625 ATTTTATAAAAATAATTTATATT
1 ATTTAATAAAAATAATTTATATT
2570648 ATTTAATAAAAA-AA-TTAT-TT
1 ATTTAATAAAAATAATTTATATT
*
2570668 ATTAAATA
1 ATTTAATA
2570676 TATAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 9 0.35
21 4 0.15
22 2 0.08
23 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAATAAAAATAATTTATATT
Found at i:2570682 original size:20 final size:21
Alignment explanation
Indices: 2570634--2570688 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
2570624 AATTTTATAA
* *
2570634 AAATAATTTATATTATTTAAT
1 AAATAAATTATATTATTAAAT
*
2570655 AAAAAAATTAT-TTATTAAAT
1 AAATAAATTATATTATTAAAT
*
2570675 ATATAAATATATAT
1 AAATAAAT-TATAT
2570689 ATATATGTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 14 0.52
21 12 0.44
22 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATAAATTATATTATTAAAT
Found at i:2573847 original size:24 final size:24
Alignment explanation
Indices: 2573815--2573877 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
2573805 AACATCCTCC
2573815 ACCGCCGCTGCCACCTCCGCCATA
1 ACCGCCGCTGCCACCTCCGCCATA
*
2573839 ACCGCCGCTGCCACCTCCGCTATA
1 ACCGCCGCTGCCACCTCCGCCATA
* *
2573863 GCCGCCGCCGCCACC
1 ACCGCCGCTGCCACC
2573878 ACCATACCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.14, C:0.56, G:0.19, T:0.11
Consensus pattern (24 bp):
ACCGCCGCTGCCACCTCCGCCATA
Found at i:2581488 original size:16 final size:17
Alignment explanation
Indices: 2581458--2581492 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2581448 AATCATAATT
2581458 TAAATATTAAAAAATTTA
1 TAAATATT-AAAAATTTA
*
2581476 TAAATATTAAAATTTTA
1 TAAATATTAAAAATTTA
2581493 ATTTTAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATATTAAAAATTTA
Found at i:2585355 original size:35 final size:34
Alignment explanation
Indices: 2585305--2585371 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
2585295 TCGGAAATAG
*
2585305 ATTTTTGAGAAGTTTTAAAATTTTTTGAAAATTT
1 ATTTTTGAGAAGTTTTAAAACTTTTTGAAAATTT
**
2585339 ATTTCTTGAGAAGTTTTAAGCCTTTTTGAAAAT
1 ATTT-TTGAGAAGTTTTAAAACTTTTTGAAAAT
2585372 AGATTTTCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (34 bp):
ATTTTTGAGAAGTTTTAAAACTTTTTGAAAATTT
Found at i:2592469 original size:281 final size:281
Alignment explanation
Indices: 2591955--2592476 Score: 719
Period size: 281 Copynumber: 1.9 Consensus size: 281
2591945 AGGAGCTCGA
* * **
2591955 TTCAAAAAAAGAGTTTAAGTTCATGTTTTGAAGATCAATTTGTGCGAAGTGTAAAGACACATAAG
1 TTCAAAAAAAGAGTTTAAGTTCATATTTTGAAGATCAATTTATGCGAAGCATAAAGACACATAAG
* *
2592020 AAAAAATGATTGTAAGACTTTCATTATAGGTGAAACCAATCATGTTTAACATAAAAATTAATAAT
66 AAAAAATGATTGTAAGACTTTCATTATAGGTGAAACCAAACATGTCTAACATAAAAATTAATAAT
* * *
2592085 TGATGAAATTTGAGTCAAAATGAAGATTGTTGGTAATAGTAACTTAAATCCTATAATAGATTTGT
131 TAATGAAATTTGAGTCAAAATGAAGATTGTTGGTAATAGTAACTCAAATCCTATAATAGATTTAT
* *
2592150 TTATGATTGGTTAGATATTACTTGATGGATAATAAGACTTGCAAAAAAAATTCTAAAAAGGAAAA
196 TTATGATTGGTTAGATATTACTTGAAGGATAATAAGACTTACAAAAAAAATTCTAAAAAGGAAAA
2592215 GGCAAGCTCAGAGAAACGTTT
261 GGCAAGCTCAGAGAAACGTTT
* * * * *
2592236 TTCAAGAAAAA-AGTTTAAGTTTATATTTTGAGGATTAATTTATGTGAAGCATGAAGACACATAA
1 TTCAA-AAAAAGAGTTTAAGTTCATATTTTGAAGATCAATTTATGCGAAGCATAAAGACACATAA
* * ** * * *
2592300 GAAAATATGATTGTAAGACTTTCATTATAGGTGAAGCCAAACATGTCTAGTATGAAGATTGATAA
65 GAAAAAATGATTGTAAGACTTTCATTATAGGTGAAACCAAACATGTCTAACATAAAAATTAATAA
* * ** * *
2592365 TTAATTAAATTTGAGTTAAGGT-AGAGATTGTTAGG-AATAGTGACTCAAATTCTATAATAGATT
130 TTAATGAAATTTGAGTCAAAATGA-AGATTGTT-GGTAATAGTAACTCAAATCCTATAATAGATT
2592428 TATTTGA-GATTGGTTAGATATTACTTGAAGGATAATAAGACTTACAAAA
193 TATTT-ATGATTGGTTAGATATTACTTGAAGGATAATAAGACTTACAAAA
2592477 GAAGAATTAT
Statistics
Matches: 208, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
280 1 0.00
281 199 0.96
282 8 0.04
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (281 bp):
TTCAAAAAAAGAGTTTAAGTTCATATTTTGAAGATCAATTTATGCGAAGCATAAAGACACATAAG
AAAAAATGATTGTAAGACTTTCATTATAGGTGAAACCAAACATGTCTAACATAAAAATTAATAAT
TAATGAAATTTGAGTCAAAATGAAGATTGTTGGTAATAGTAACTCAAATCCTATAATAGATTTAT
TTATGATTGGTTAGATATTACTTGAAGGATAATAAGACTTACAAAAAAAATTCTAAAAAGGAAAA
GGCAAGCTCAGAGAAACGTTT
Found at i:2596274 original size:17 final size:17
Alignment explanation
Indices: 2596242--2596275 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2596232 ATTAATTTTA
*
2596242 AAAAATAATTGAAAAAT
1 AAAAATAATTCAAAAAT
2596259 AAAAATAATTCTAAAAA
1 AAAAATAATTC-AAAAA
2596276 AGATTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAATAATTCAAAAAT
Found at i:2597434 original size:15 final size:15
Alignment explanation
Indices: 2597414--2597449 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
2597404 AACTATATTA
2597414 TTGGAGAACATGAAC
1 TTGGAGAACATGAAC
*
2597429 TTGGAGAACCTGAAC
1 TTGGAGAACATGAAC
2597444 TCTGGA
1 T-TGGA
2597450 ACCCAATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (15 bp):
TTGGAGAACATGAAC
Found at i:2614143 original size:36 final size:38
Alignment explanation
Indices: 2614096--2614166 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 38
2614086 TTTATGACAT
*
2614096 TTTATATAGTCATATTTT-TTATTTAAATA-ATTTTTA
1 TTTAAATAGTCATATTTTCTTATTTAAATATATTTTTA
* *
2614132 TTTAAATAGTCATGTTTTCTTGTTTAAATATATTT
1 TTTAAATAGTCATATTTTCTTATTTAAATATATTT
2614167 ATTCGGACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 16 0.53
37 10 0.33
38 4 0.13
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (38 bp):
TTTAAATAGTCATATTTTCTTATTTAAATATATTTTTA
Found at i:2614149 original size:19 final size:15
Alignment explanation
Indices: 2614111--2614139 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2614101 ATAGTCATAT
2614111 TTTTTATTTAAATAA
1 TTTTTATTTAAATAA
2614126 TTTTTATTTAAATA
1 TTTTTATTTAAATA
2614140 GTCATGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTATTTAAATAA
Found at i:2614399 original size:11 final size:11
Alignment explanation
Indices: 2614383--2614417 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
2614373 ACTTACCTAC
2614383 TTTAAATAATA
1 TTTAAATAATA
2614394 TTTAAATAATTA
1 TTTAAATAA-TA
2614406 TTTAAATAATA
1 TTTAAATAATA
2614417 T
1 T
2614418 AAATAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TTTAAATAATA
Found at i:2614409 original size:12 final size:12
Alignment explanation
Indices: 2614383--2614415 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2614373 ACTTACCTAC
2614383 TTTAAATAA-TA
1 TTTAAATAATTA
2614394 TTTAAATAATTA
1 TTTAAATAATTA
2614406 TTTAAATAAT
1 TTTAAATAAT
2614416 ATAAATAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTTAAATAATTA
Found at i:2614432 original size:23 final size:23
Alignment explanation
Indices: 2614383--2614469 Score: 69
Period size: 23 Copynumber: 3.9 Consensus size: 23
2614373 ACTTACCTAC
*
2614383 TTTAAATAATATTTAAATAA--TTA
1 TTTAAATAATA--TAAATAATCTTT
2614406 TTTAAATAATATAAATAATCTTT
1 TTTAAATAATATAAATAATCTTT
* *
2614429 TTT--A-AA-CTAAATAATCTCT
1 TTTAAATAATATAAATAATCTTT
2614448 TTTAAATTATATATAAATAATC
1 TTTAAA-TA-ATATAAATAATC
2614470 AACTTAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
19 14 0.27
20 2 0.04
21 9 0.17
23 17 0.33
24 1 0.02
25 9 0.17
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAAATAATATAAATAATCTTT
Found at i:2614441 original size:19 final size:19
Alignment explanation
Indices: 2614417--2614453 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2614407 TTAAATAATA
*
2614417 TAAATAATCTTTTTTAAAC
1 TAAATAATCTCTTTTAAAC
2614436 TAAATAATCTCTTTTAAA
1 TAAATAATCTCTTTTAAA
2614454 TTATATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATAATCTCTTTTAAAC
Found at i:2614463 original size:21 final size:20
Alignment explanation
Indices: 2614419--2614463 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
2614409 AAATAATATA
* *
2614419 AATAATCTTTTTTAAACTA-
1 AATAATCTCTTTTAAATTAT
2614438 AATAATCTCTTTTAAATTAT
1 AATAATCTCTTTTAAATTAT
2614458 ATATAA
1 A-ATAA
2614464 ATAATCAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 1 0.05
21 4 0.18
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATCTCTTTTAAATTAT
Found at i:2614744 original size:5 final size:5
Alignment explanation
Indices: 2614728--2614776 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
2614718 AATAATTATA
* *
2614728 TAAAT T-AAT TAAAT TAAAT TGTAAT TATA- TAAAT T-AAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT T-AAAT TAAAT TAAAT TAAAT TAAAT TAAAT
2614776 T
1 T
2614777 TTAATTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
4 11 0.31
5 21 0.58
6 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (5 bp):
TAAAT
Found at i:2614752 original size:29 final size:29
Alignment explanation
Indices: 2614720--2614787 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
2614710 TTTTTAAAAA
2614720 TAATTATATAAATTAATTAAATTAAATTG
1 TAATTATATAAATTAATTAAATTAAATTG
*
2614749 TAATTATATAAATTAATTAAATTAAATTT
1 TAATTATATAAATTAATTAAATTAAATTG
*
2614778 TAATTTTATA
1 TAATTATATA
2614788 TTTTTTAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TAATTATATAAATTAATTAAATTAAATTG
Found at i:2614961 original size:25 final size:25
Alignment explanation
Indices: 2614907--2614956 Score: 86
Period size: 23 Copynumber: 2.1 Consensus size: 25
2614897 CTCTTAATCA
2614907 TTTTAACCATTAAAATTTTTTTTCT
1 TTTTAACCATTAAAATTTTTTTTCT
2614932 TTTTAACCATT-AAA-TTTTTTTCT
1 TTTTAACCATTAAAATTTTTTTTCT
2614955 TT
1 TT
2614957 ATTTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 11 0.44
24 3 0.12
25 11 0.44
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTAACCATTAAAATTTTTTTTCT
Found at i:2618092 original size:174 final size:173
Alignment explanation
Indices: 2617796--2618316 Score: 801
Period size: 174 Copynumber: 3.0 Consensus size: 173
2617786 TATAAAAGCT
* * * ** * *
2617796 GAAGAGTCTGGAAAGAAACCAGATACAGATCAGGAGCCGAAGCCAAATACCCCCGTGATCAGAGA
1 GAAGAGTCTGGAAAGAAAGCAGATACATATCAGGAGCTGAAGCCAAGCACCCCTGTGATTAGAGA
* * *
2617861 ACGTGAAATTCAACCTGCTTC-AGTGTCTTCATCATATGTTAAATCTATAAATTCTGCTACCCCT
66 ACGTGAAATTCCACCTGC-TCAAGTGTCTTCATCATCTGTTAAATCTA-AAATTCTGCTACTCCT
* * * * * **
2617925 CCTCATCCTGCTGTCCATGGGCATGCTGCTCTACTATTGGATCCG
129 TCTCGTCCTGCTGGCCTTGGGCGTGCTGCTCCGCTATTGGATCCG
2617970 GAAGAGTCTGGAAAGAAAGCAGATACATATCAGGAGCTGAAGCCAAGCACCCCTGTGATTAGAGA
1 GAAGAGTCTGGAAAGAAAGCAGATACATATCAGGAGCTGAAGCCAAGCACCCCTGTGATTAGAGA
2618035 ACGTGAAATTCCACCTGCTCAAGTGTCTTCATCATCTGTTAAATCTAAAAGTTCTGCTACTCCTT
66 ACGTGAAATTCCACCTGCTCAAGTGTCTTCATCATCTGTTAAATCTAAAA-TTCTGCTACTCCTT
* *
2618100 CTCGTCCTGCTGGCCTTGGGCGTGCTTCTCCGCTGTTGGATCCG
130 CTCGTCCTGCTGGCCTTGGGCGTGCTGCTCCGCTATTGGATCCG
*
2618144 GAAGAGTCTGGAAAGAAAGCAGATACATATCAGGAGGTGAAGCCAAGCACCCCTGTGATTAGAGA
1 GAAGAGTCTGGAAAGAAAGCAGATACATATCAGGAGCTGAAGCCAAGCACCCCTGTGATTAGAGA
* *
2618209 ACGTGAAATTCCACCTGCTCAAGTGTCTTCATCATCTGTCAAATCTAAAAACTCTGCTACTCCTT
66 ACGTGAAATTCCACCTGCTCAAGTGTCTTCATCATCTGTTAAATCT-AAAATTCTGCTACTCCTT
2618274 CTCGTCCTGCTGGCCTTGGGCGTGCTGCTCCGCTATTGGATCC
130 CTCGTCCTGCTGGCCTTGGGCGTGCTGCTCCGCTATTGGATCC
2618317 TGCTCCTAGG
Statistics
Matches: 320, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
173 5 0.02
174 311 0.97
175 4 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (173 bp):
GAAGAGTCTGGAAAGAAAGCAGATACATATCAGGAGCTGAAGCCAAGCACCCCTGTGATTAGAGA
ACGTGAAATTCCACCTGCTCAAGTGTCTTCATCATCTGTTAAATCTAAAATTCTGCTACTCCTTC
TCGTCCTGCTGGCCTTGGGCGTGCTGCTCCGCTATTGGATCCG
Found at i:2626483 original size:2 final size:2
Alignment explanation
Indices: 2626478--2626513 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2626468 CTTGTGTGTC
*
2626478 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2626514 GTATGTATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2626498 original size:15 final size:15
Alignment explanation
Indices: 2626478--2626506 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2626468 CTTGTGTGTC
2626478 TATATATATATATAA
1 TATATATATATATAA
2626493 TATATATATATATA
1 TATATATATATATA
2626507 TGTATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:2626518 original size:10 final size:10
Alignment explanation
Indices: 2626478--2626521 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
2626468 CTTGTGTGTC
*
2626478 TATATATATA
1 TATATATATG
*
2626488 TATAATATATA
1 TAT-ATATATG
2626499 TATATATATG
1 TATATATATG
*
2626509 TATATGTATG
1 TATATATATG
2626519 TAT
1 TAT
2626522 GTAAAACCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 21 0.68
11 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:2627760 original size:13 final size:13
Alignment explanation
Indices: 2627742--2627767 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2627732 TTTTTAATGG
2627742 TAATTACAAATAA
1 TAATTACAAATAA
2627755 TAATTACAAATAA
1 TAATTACAAATAA
2627768 GCAATATGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATTACAAATAA
Found at i:2629315 original size:21 final size:22
Alignment explanation
Indices: 2629294--2629350 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
2629284 TTGGTTGAAT
* *
2629294 ATTAAACTTTTAATTTTTAATA
1 ATTAAAATTTAAATTTTTAATA
*
2629316 ATTAAAATTTAAA-TTTTAACA
1 ATTAAAATTTAAATTTTTAATA
*
2629337 ATTTAAAATATAAA
1 A-TTAAAATTTAAA
2629351 AAATAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 8 0.27
22 22 0.73
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTAAAATTTAAATTTTTAATA
Found at i:2629342 original size:22 final size:21
Alignment explanation
Indices: 2629302--2629350 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2629292 ATATTAAACT
* *
2629302 TTTAATTTTTAATAATTAAAA
1 TTTAAATTTTAACAATTAAAA
2629323 TTTAAATTTTAACAATTTAAAA
1 TTTAAATTTTAACAA-TTAAAA
*
2629345 TATAAA
1 TTTAAA
2629351 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAAATTTTAACAATTAAAA
Found at i:2631083 original size:27 final size:28
Alignment explanation
Indices: 2631048--2631102 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
2631038 ATTCATTCAA
2631048 TTTAATAAAAATAT-TAATATATATATT
1 TTTAATAAAAATATCTAATATATATATT
2631075 TTTAATAAAAATATCTAATATATATATT
1 TTTAATAAAAATATCTAATATATATATT
2631103 AGATAGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTAATAAAAATATCTAATATATATATT
Found at i:2631472 original size:116 final size:116
Alignment explanation
Indices: 2631286--2631517 Score: 410
Period size: 116 Copynumber: 2.0 Consensus size: 116
2631276 AACTTTACCT
* *
2631286 TAAAACTTTCTGACTAATTATATCATTCTTAAATCTAAAACAAATCATCAATTTGTCACCAACTG
1 TAAAACTTCCTGACTAATTATATCATTCTTAAATCCAAAACAAATCATCAATTTGTCACCAACTG
*
2631351 TGAGGCTAATAATTGTGAAAGTCAACGATTTATAATTCAACTATAACCATA
66 TGAGGCCAATAATTGTGAAAGTCAACGATTTATAATTCAACTATAACCATA
*
2631402 TAAAACTTCCTGACTAATTATATCATTCTTAAATCCAAAACAAATCATCAATTTGTTACCAACTG
1 TAAAACTTCCTGACTAATTATATCATTCTTAAATCCAAAACAAATCATCAATTTGTCACCAACTG
* *
2631467 TGAGGCCAATAATTGTGAGAGTCAACTATTTATAATTCAACTATAACCATA
66 TGAGGCCAATAATTGTGAAAGTCAACGATTTATAATTCAACTATAACCATA
2631518 AATACATTAT
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 110 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (116 bp):
TAAAACTTCCTGACTAATTATATCATTCTTAAATCCAAAACAAATCATCAATTTGTCACCAACTG
TGAGGCCAATAATTGTGAAAGTCAACGATTTATAATTCAACTATAACCATA
Found at i:2638669 original size:30 final size:30
Alignment explanation
Indices: 2638616--2638694 Score: 115
Period size: 29 Copynumber: 2.6 Consensus size: 30
2638606 TTATATTGTC
*
2638616 TTTAATTTTTAATTTA-GTTTAAATAAATT
1 TTTAATTTTTAATTTATATTTAAATAAATT
*
2638645 TTTAACTTTTAATTTATATTTAAATAAATT
1 TTTAATTTTTAATTTATATTTAAATAAATT
*
2638675 TTAAAATTTTTAATTTATAT
1 TT-TAATTTTTAATTTATAT
2638695 CAAAATAAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 15 0.34
30 14 0.32
31 15 0.34
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTAATTTTTAATTTATATTTAAATAAATT
Found at i:2638689 original size:31 final size:30
Alignment explanation
Indices: 2638619--2638694 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 30
2638609 TATTGTCTTT
* *
2638619 AATTTTTAATTTA-GTTTAAATAAATTTTT
1 AATTTTTAATTTATATTTAAATAAATTTTA
*
2638648 AACTTTTAATTTATATTTAAATAAATTTTAA
1 AATTTTTAATTTATATTTAAATAAATTTT-A
2638679 AATTTTTAATTTATAT
1 AATTTTTAATTTATAT
2638695 CAAAATAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 12 0.29
30 14 0.34
31 15 0.37
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (30 bp):
AATTTTTAATTTATATTTAAATAAATTTTA
Found at i:2638702 original size:31 final size:29
Alignment explanation
Indices: 2638619--2638694 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
2638609 TATTGTCTTT
*
2638619 AATTTTTAATTTAGT-TTAAATAAATTTTT
1 AATTTTTAATTTA-TATTAAATAAATTTTA
*
2638648 AACTTTTAATTTATATTTAAATAAATTTTAA
1 AATTTTTAATTTATA-TTAAATAAATTTT-A
2638679 AATTTTTAATTTATAT
1 AATTTTTAATTTATAT
2638695 CAAAATAAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.02
29 12 0.29
30 14 0.34
31 14 0.34
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (29 bp):
AATTTTTAATTTATATTAAATAAATTTTA
Found at i:2638710 original size:31 final size:31
Alignment explanation
Indices: 2638651--2638712 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2638641 AATTTTTAAC
** **
2638651 TTTTAATTTATATTTAAATAAATTTTAAAAT
1 TTTTAATTTATATCAAAATAAAGCTTAAAAT
*
2638682 TTTTAATTTATATCAAAATAAGGCTTAAAAT
1 TTTTAATTTATATCAAAATAAAGCTTAAAAT
2638713 AAATCAGTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTTAATTTATATCAAAATAAAGCTTAAAAT
Found at i:2639172 original size:85 final size:85
Alignment explanation
Indices: 2639029--2639198 Score: 304
Period size: 85 Copynumber: 2.0 Consensus size: 85
2639019 GTCACAGCAG
2639029 TTCCATACAAAAACATCAAATCTGTTAGACGGTTCCAAAGAGAAAGTCCCTCGTTATATCAAAGG
1 TTCCATACAAAAACATCAAATCTGTTAGACGGTTCCAAAGAGAAAGTCCCTCGTTATATCAAAGG
*
2639094 ATTCAGAAAATGGAGGTTTT
66 ATTCAGAAAAAGGAGGTTTT
* * *
2639114 TTCCATAGAAAAACATCAAATCTGTTAGGCGGTTCCAAAGAGAAAGTCCCTGGTTATATCAAAGG
1 TTCCATACAAAAACATCAAATCTGTTAGACGGTTCCAAAGAGAAAGTCCCTCGTTATATCAAAGG
2639179 ATTCAGAAAAAGGAGGTTTT
66 ATTCAGAAAAAGGAGGTTTT
2639199 CTTAGCCTAG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (85 bp):
TTCCATACAAAAACATCAAATCTGTTAGACGGTTCCAAAGAGAAAGTCCCTCGTTATATCAAAGG
ATTCAGAAAAAGGAGGTTTT
Found at i:2643895 original size:9 final size:9
Alignment explanation
Indices: 2643880--2643951 Score: 90
Period size: 9 Copynumber: 8.0 Consensus size: 9
2643870 AAGAAGGGCG
2643880 ATGGTGGCA
1 ATGGTGGCA
*
2643889 TTGGTGGCA
1 ATGGTGGCA
2643898 ATGGTGGCA
1 ATGGTGGCA
2643907 ATGGTGGCA
1 ATGGTGGCA
2643916 ATGGTGGCA
1 ATGGTGGCA
** *
2643925 GCGGAGGCA
1 ATGGTGGCA
*
2643934 ATCGTGGCA
1 ATGGTGGCA
*
2643943 ATGGGGGCA
1 ATGGTGGCA
2643952 GCCTGAATGT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 52 1.00
ACGTcount: A:0.21, C:0.14, G:0.46, T:0.19
Consensus pattern (9 bp):
ATGGTGGCA
Found at i:2649638 original size:7 final size:7
Alignment explanation
Indices: 2649626--2649659 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
2649616 ATTTTAAAAT
2649626 ATTTTAA
1 ATTTTAA
2649633 ATTTTAA
1 ATTTTAA
2649640 ATTTTAA
1 ATTTTAA
*
2649647 ATTTCAA
1 ATTTTAA
2649654 ATTTTA
1 ATTTTA
2649660 CAAATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTTTAA
Found at i:2654097 original size:14 final size:15
Alignment explanation
Indices: 2654071--2654099 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2654061 GAAAGAGGAG
2654071 TAAATTGAAAATAAT
1 TAAATTGAAAATAAT
2654086 TAAATT-AAAATAAT
1 TAAATTGAAAATAAT
2654100 AGCAGACCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
TAAATTGAAAATAAT
Found at i:2656413 original size:17 final size:17
Alignment explanation
Indices: 2656391--2656427 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2656381 TTTAGTTCAT
*
2656391 ATTAAGAATGTAATCGA
1 ATTAAGAATATAATCGA
2656408 ATTAAGAATATAATCGA
1 ATTAAGAATATAATCGA
2656425 ATT
1 ATT
2656428 GAGTCGAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (17 bp):
ATTAAGAATATAATCGA
Found at i:2665192 original size:2 final size:2
Alignment explanation
Indices: 2665185--2665217 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2665175 TATGTATGTG
2665185 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2665218 GTAGGGCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2667121 original size:25 final size:27
Alignment explanation
Indices: 2667093--2667156 Score: 96
Period size: 25 Copynumber: 2.4 Consensus size: 27
2667083 TGCGTTTGGT
2667093 ATATAAAATTATG-ATAAAATAAAA-A
1 ATATAAAATTATGAATAAAATAAAATA
*
2667118 ATATAATATTATGAATAAAATAAAATA
1 ATATAAAATTATGAATAAAATAAAATA
*
2667145 AAATAAAATTAT
1 ATATAAAATTAT
2667157 TTTATCTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 12 0.35
26 11 0.32
27 11 0.32
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (27 bp):
ATATAAAATTATGAATAAAATAAAATA
Found at i:2667873 original size:33 final size:33
Alignment explanation
Indices: 2667836--2667921 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
2667826 GGGGTTTTGG
* **
2667836 CTTGTAGATAGGAACAGGTGGTGGAAGTGGTTT
1 CTTGTAGATAGGAACAGGAGAAGGAAGTGGTTT
* * *
2667869 CTTGTAGATTGGAACTGGAGAAGGGAGTGGTTT
1 CTTGTAGATAGGAACAGGAGAAGGAAGTGGTTT
* * *
2667902 CTTGTATATCGGAACTGGAG
1 CTTGTAGATAGGAACAGGAG
2667922 GAAGCTTATG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.24, C:0.08, G:0.37, T:0.30
Consensus pattern (33 bp):
CTTGTAGATAGGAACAGGAGAAGGAAGTGGTTT
Found at i:2668001 original size:15 final size:15
Alignment explanation
Indices: 2667981--2668016 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2667971 TTTCTTGTAT
*
2667981 ACTGGAGGTTTATAA
1 ACTGGAGGCTTATAA
2667996 ACTGGAGGCTTATAA
1 ACTGGAGGCTTATAA
*
2668011 ATTGGA
1 ACTGGA
2668017 ACTGGAGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (15 bp):
ACTGGAGGCTTATAA
Found at i:2669862 original size:16 final size:17
Alignment explanation
Indices: 2669833--2669865 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2669823 GTTGGAATGT
2669833 TAAAAACTAATTATAAA
1 TAAAAACTAATTATAAA
*
2669850 TAAAAAC-ATTTATAAA
1 TAAAAACTAATTATAAA
2669866 GAAGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAAACTAATTATAAA
Found at i:2671346 original size:19 final size:18
Alignment explanation
Indices: 2671322--2671377 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
2671312 TTTTTGTAAA
*
2671322 AAATATCATATATATAATC
1 AAATATAATAT-TATAATC
*
2671341 AAATATAATATTATAATAA
1 AAATATAATATTATAAT-C
*
2671360 AAATATGAATATAATAAT
1 AAATAT-AATATTATAAT
2671378 TTTTTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.19
19 16 0.50
20 10 0.31
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.36
Consensus pattern (18 bp):
AAATATAATATTATAATC
Found at i:2675353 original size:6 final size:6
Alignment explanation
Indices: 2675344--2675373 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2675334 ATGAAAATTA
2675344 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
2675374 GAAATGATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:2676003 original size:2 final size:2
Alignment explanation
Indices: 2675996--2676020 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2675986 GCAAGCACAT
2675996 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2676021 AAGTACCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2679397 original size:17 final size:16
Alignment explanation
Indices: 2679377--2679408 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2679367 AATTTATTTG
2679377 ATTAAAAAATATAAAAA
1 ATTAAAAAA-ATAAAAA
2679394 ATTAAAAAAATAAAA
1 ATTAAAAAAATAAAA
2679409 CAGAAGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
ATTAAAAAAATAAAAA
Found at i:2691246 original size:26 final size:26
Alignment explanation
Indices: 2691217--2691268 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2691207 TTCTTCAAAA
2691217 TATAGTACTATATATAGCATCATACC
1 TATAGTACTATATATAGCATCATACC
2691243 TATAGTACTATATATAGCATCATACC
1 TATAGTACTATATATAGCATCATACC
2691269 AGCCAGCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (26 bp):
TATAGTACTATATATAGCATCATACC
Found at i:2692668 original size:21 final size:20
Alignment explanation
Indices: 2692644--2692684 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2692634 GAATTTTGAA
2692644 TTAAATTTAATTAATTATTTT
1 TTAAATTTAATTAATT-TTTT
* *
2692665 TTAAGTTTGATTAATTTTTT
1 TTAAATTTAATTAATTTTTT
2692685 AATACAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TTAAATTTAATTAATTTTTT
Found at i:2693691 original size:21 final size:23
Alignment explanation
Indices: 2693658--2693708 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
2693648 ATATATTTTT
* *
2693658 TAAAATAATATTATAATTT-AATA
1 TAAAA-AATATTACAATTTAAAAA
2693681 TAAAAAA-ATTACAATTTAAAAA
1 TAAAAAATATTACAATTTAAAAA
2693703 TAAAAA
1 TAAAAA
2693709 GATTGTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.36
22 11 0.44
23 5 0.20
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAAAAATATTACAATTTAAAAA
Found at i:2694082 original size:12 final size:12
Alignment explanation
Indices: 2694065--2694094 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2694055 CTTGACTACT
2694065 TGATTCCCACAA
1 TGATTCCCACAA
2694077 TGATTCCCACAA
1 TGATTCCCACAA
*
2694089 TAATTC
1 TGATTC
2694095 AACACAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (12 bp):
TGATTCCCACAA
Found at i:2695461 original size:44 final size:45
Alignment explanation
Indices: 2695411--2695521 Score: 143
Period size: 44 Copynumber: 2.5 Consensus size: 45
2695401 GTGAAAATGG
* * *
2695411 AGAGCACTTAATTGGTATATATCTATTGTATTTTTCCAAAA-GGA
1 AGAGCACTTACTTGGTATATATCCATTGTATTTTTCCAAAATGAA
* * * **
2695455 AGAGCACTCACTAGGCATATATCCATTGTATTTTTTGAAAATGAA
1 AGAGCACTTACTTGGTATATATCCATTGTATTTTTCCAAAATGAA
2695500 AGAGCACTTACTTGGTATATAT
1 AGAGCACTTACTTGGTATATAT
2695522 GGGAAAATAA
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
44 34 0.62
45 21 0.38
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (45 bp):
AGAGCACTTACTTGGTATATATCCATTGTATTTTTCCAAAATGAA
Found at i:2698022 original size:172 final size:171
Alignment explanation
Indices: 2697702--2698038 Score: 525
Period size: 172 Copynumber: 2.0 Consensus size: 171
2697692 TAAATTCACA
*
2697702 CAATTTAGTTCATCAAAGACATTGTAACTCACAAATAGAACAAATAACATGTAGTACTTGACAAA
1 CAATTCAGTTCATCAAAGACATTGTAACTCACAAATAGAACAAATAACATGTAGTACTTGACAAA
*
2697767 CAAAGGTAGATTTAGTTCCATGTCGAACACCTTCCACAGCCACAATAGTAAGGTCACTGACAACA
66 CAAAGGTAGATTTAGTTCCATGTCGAACACCTTCCACAACCACAATAGTAAGGTCACTGACAACA
* *
2697832 ATCCTTAGAGAGGCAACAAACAAGGACTCGTAATATGCACG
131 ATCCTTAGAGAAGCAACAAACAAGGACTAGTAATATGCACG
*
2697873 CAATTCAGTTCATCAAAGACATTGTAACTCATAAATAGAACAAATAAC-TAGTAGTACTTGACAA
1 CAATTCAGTTCATCAAAGACATTGTAACTCACAAATAGAACAAATAACAT-GTAGTACTTGACAA
* * * * *
2697937 ACTAAAGGTAGATTTAGTTCCATGTCGAACATCTTCCACAACCACAATGGTGAGGTCGGC-GGCA
65 AC-AAAGGTAGATTTAGTTCCATGTCGAACACCTTCCACAACCACAATAGTAAGGTC-ACTGACA
* *
2698001 AGAATCCTTAGAGAAGCAACAAACAATGACTAGTAATA
128 ACAATCCTTAGAGAAGCAACAAACAAGGACTAGTAATA
2698039 CCGATCCTGC
Statistics
Matches: 151, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
170 1 0.01
171 62 0.41
172 87 0.58
173 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.23
Consensus pattern (171 bp):
CAATTCAGTTCATCAAAGACATTGTAACTCACAAATAGAACAAATAACATGTAGTACTTGACAAA
CAAAGGTAGATTTAGTTCCATGTCGAACACCTTCCACAACCACAATAGTAAGGTCACTGACAACA
ATCCTTAGAGAAGCAACAAACAAGGACTAGTAATATGCACG
Found at i:2704005 original size:18 final size:16
Alignment explanation
Indices: 2703982--2704028 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
2703972 GATTGGTTTT
2703982 TAAAATTTTAAAATAATA
1 TAAAATTTTAAAAT-A-A
* *
2704000 TAAAATATAAAAATAA
1 TAAAATTTTAAAATAA
2704016 TAAAA-TTTAAAAT
1 TAAAATTTTAAAAT
2704029 TTTGATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 6 0.24
16 6 0.24
17 1 0.04
18 12 0.48
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATTTTAAAATAA
Found at i:2704165 original size:15 final size:16
Alignment explanation
Indices: 2704138--2704168 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2704128 TATATGTATT
2704138 TAATATGAAATAAATA
1 TAATATGAAATAAATA
2704154 TAATAT-AAATAAATA
1 TAATATGAAATAAATA
2704169 AATTGACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
TAATATGAAATAAATA
Found at i:2705227 original size:2 final size:2
Alignment explanation
Indices: 2705220--2705246 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2705210 ATTTACAAGC
2705220 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2705247 CCTTGTCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2710025 original size:15 final size:14
Alignment explanation
Indices: 2709998--2710029 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
2709988 GAAATAATTT
2709998 TAATAATTAATAAA
1 TAATAATTAATAAA
2710012 TAATAATATAATAAA
1 TAATAAT-TAATAAA
2710027 TAA
1 TAA
2710030 ATATGACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATTAATAAA
Found at i:2716008 original size:21 final size:20
Alignment explanation
Indices: 2715975--2716014 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2715965 TCATAAAAAG
*
2715975 AAAAAATATATAAAGAAATA
1 AAAAAATAAATAAAGAAATA
*
2715995 AAAAAATCAAATAAATAAAT
1 AAAAAAT-AAATAAAGAAAT
2716015 TTTCCTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (20 bp):
AAAAAATAAATAAAGAAATA
Found at i:2717720 original size:26 final size:25
Alignment explanation
Indices: 2717678--2717731 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
2717668 AAATAATGAT
*
2717678 AAAAATTATTATAATTATGATTAAA
1 AAAAATTATTATAATTATAATTAAA
*
2717703 AAAATATTATTATTATTATAATTAAA
1 AAAA-ATTATTATAATTATAATTAAA
2717729 AAA
1 AAA
2717732 TTTATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
AAAAATTATTATAATTATAATTAAA
Found at i:2727891 original size:2 final size:2
Alignment explanation
Indices: 2727884--2727914 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2727874 AAACACTCAA
2727884 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2727915 ATGAACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2728778 original size:19 final size:18
Alignment explanation
Indices: 2728751--2728789 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2728741 TGAGTCATCA
2728751 TTTTTTTTTCAAATTTAT
1 TTTTTTTTTCAAATTTAT
**
2728769 TTTTTCTTTTTTAATTTAT
1 TTTTT-TTTTCAAATTTAT
2728788 TT
1 TT
2728790 ATGAGTGTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTTTTCAAATTTAT
Found at i:2735434 original size:16 final size:15
Alignment explanation
Indices: 2735403--2735436 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2735393 ATTGATTTGA
*
2735403 TTTGATTTATTTAAT
1 TTTGATTTAATTAAT
2735418 TTTGATTATAATTAAT
1 TTTGATT-TAATTAAT
2735434 TTT
1 TTT
2735437 TTGAATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTGATTTAATTAAT
Found at i:2737470 original size:113 final size:112
Alignment explanation
Indices: 2737288--2737542 Score: 318
Period size: 113 Copynumber: 2.3 Consensus size: 112
2737278 CGTTTGACAT
* * *
2737288 TAAAAAACACCTTAAATGATCATCAAATATTCATTTTTTATAACAATTTATTATTTAAGACATTT
1 TAAAAAACGCCTTAAATGATCATCAAATATTCATTTTTTATAACAATATATAATTTAAGACATTT
* * *
2737353 TTGTTTAA-AAA-ATGCTACAAATGATGATCATTTAAGACGTTTTT-CC
66 TTGTTGAAGAAACAT-C-ACAAATAATGATCATTTAAGACATTTTTCCC
* * * * * * *
2737399 TTAGAAATGCCTTAAATGACCATCAAATATCTTATTTTTTTATTACAATATATAATTTAAGGCAT
1 TAAAAAACGCCTTAAATGATCATCAAATAT-TCA-TTTTTTATAACAATATATAATTTAAGACAT
*
2737464 TTTTGTTGAAGAAACATCATAAATAATGATCATTTAAGACATTTTTCCC
64 TTTTGTTGAAGAAACATCACAAATAATGATCATTTAAGACATTTTTCCC
*
2737513 TAAAAAACGCCTTAAATGATTATCAAATAT
1 TAAAAAACGCCTTAAATGATCATCAAATAT
2737543 GGTGTTTTCT
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
111 25 0.21
112 2 0.02
113 60 0.50
114 31 0.26
115 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (112 bp):
TAAAAAACGCCTTAAATGATCATCAAATATTCATTTTTTATAACAATATATAATTTAAGACATTT
TTGTTGAAGAAACATCACAAATAATGATCATTTAAGACATTTTTCCC
Found at i:2744964 original size:63 final size:64
Alignment explanation
Indices: 2744827--2744970 Score: 197
Period size: 63 Copynumber: 2.3 Consensus size: 64
2744817 GTTTGCTTAA
* *
2744827 AGAAA-CGCCTTAAATGATCCATTTATATTTTAATAAAAAGATTATTTAAGGTGTTTGTGAATG
1 AGAAATCGCCTTAAATAATCCATTTATATTTTAATAAAAAGATTATTTAAGGTGTTTATGAATG
* * * *
2744890 AAAAAT-ACCTTAAATAAT-CATTTTATATTTTTATAAATAGATTATTTAAGGTGTTTATGAAT-
1 AGAAATCGCCTTAAATAATCCA-TTTATATTTTAATAAAAAGATTATTTAAGGTGTTTATGAATG
2744952 AGAAATCGCCTTAAATAAT
1 AGAAATCGCCTTAAATAAT
2744971 ATATTTTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
62 7 0.10
63 63 0.90
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.40
Consensus pattern (64 bp):
AGAAATCGCCTTAAATAATCCATTTATATTTTAATAAAAAGATTATTTAAGGTGTTTATGAATG
Found at i:2745072 original size:18 final size:18
Alignment explanation
Indices: 2745049--2745084 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2745039 TTTTTAACGG
2745049 GGATTATTTAAGGCGTTT
1 GGATTATTTAAGGCGTTT
*
2745067 GGATTATTTAAGGTGTTT
1 GGATTATTTAAGGCGTTT
2745085 TTGATCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (18 bp):
GGATTATTTAAGGCGTTT
Found at i:2745147 original size:81 final size:81
Alignment explanation
Indices: 2744990--2745147 Score: 228
Period size: 81 Copynumber: 2.0 Consensus size: 81
2744980 TAAATGATAG
* **
2744990 TATTTAAGGTATTTTTTATCAAAAAATACCTTAAATAATCCCTTAATATTTTTTAACGGGGATTA
1 TATTTAAGGTATTTTTGATCAAAAAATACCTTAAATAATCCCTTAATATTTTTTAACGAAGATTA
2745055 TTTAAGGCGTTTGGAT
66 TTTAAGGCGTTTGGAT
* * * *
2745071 TATTTAAGGTGTTTTTGATCTAAAAATACCTTAAATAATCTCTTAATATTTTTTTACGAAGATT-
1 TATTTAAGGTATTTTTGATCAAAAAATACCTTAAATAATCCCTTAATATTTTTTAACGAAGATTA
*
2745135 TTTTAGGACGTTT
66 TTTAAGG-CGTTT
2745148 TTAGACAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 6 0.09
81 62 0.91
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (81 bp):
TATTTAAGGTATTTTTGATCAAAAAATACCTTAAATAATCCCTTAATATTTTTTAACGAAGATTA
TTTAAGGCGTTTGGAT
Found at i:2745401 original size:63 final size:60
Alignment explanation
Indices: 2745273--2745401 Score: 154
Period size: 63 Copynumber: 2.1 Consensus size: 60
2745263 TTAAAGCATT
*
2745273 TTAAATAATCTCTTTATTTTTTAAAGGACATTATTTAAGGCGTTTTTAATCCTAAAATGTT
1 TTAAATAATCTCTTTATTTTTTAAAGGA-ATTATTTAAGGCGTTTTTAATCCTAAAATGTC
* **
2745334 TTAAATAATCTCCTGTTATTTTTTAATAAGG-ATTATTTAAGGTGTTTTTGGT-CTAGAAATGTC
1 TTAAATAATCT-CT-TTATTTTTT-A-AAGGAATTATTTAAGGCGTTTTTAATCCTA-AAATGTC
2745397 TTAAA
1 TTAAA
2745402 CAATAAGGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
61 11 0.19
62 5 0.08
63 38 0.64
64 1 0.02
65 4 0.07
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (60 bp):
TTAAATAATCTCTTTATTTTTTAAAGGAATTATTTAAGGCGTTTTTAATCCTAAAATGTC
Done.