Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 77 of 135
Found at i:30214186 original size:17 final size:17
Alignment explanation
Indices: 30214156--30214188 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30214146 TTTTATTATT
30214156 TTTTAAAATATTTTAAA
1 TTTTAAAATATTTTAAA
30214173 TTTTATAAAT-TTTTAA
1 TTTTA-AAATATTTTAA
30214189 TAATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAAAATATTTTAAA
Found at i:30217203 original size:21 final size:20
Alignment explanation
Indices: 30217179--30217238 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
30217169 CATCATGTAA
*
30217179 AAAATAATAAAAATATATTTT
1 AAAATAATAAAAATA-ATTAT
30217200 AAAA-ATATAAAAATAATTAT
1 AAAATA-ATAAAAATAATTAT
* *
30217220 AAAATTGATAAAAAAAATT
1 AAAA-TAATAAAAATAATT
30217239 TATATAAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.27
21 24 0.73
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAATAATAAAAATAATTAT
Found at i:30217583 original size:30 final size:31
Alignment explanation
Indices: 30217549--30217612 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
30217539 CAGTTAGACT
* *
30217549 TGAATTTT-AAAATCTAAAAAGTAGAGGGAC
1 TGAATTTTAAAAATCCAAAAAGTACAGGGAC
*
30217579 TGAATTTTAAAAATCCAAAGAGTACAGGGAC
1 TGAATTTTAAAAATCCAAAAAGTACAGGGAC
30217610 TGA
1 TGA
30217613 TGGCAGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (31 bp):
TGAATTTTAAAAATCCAAAAAGTACAGGGAC
Found at i:30220664 original size:29 final size:29
Alignment explanation
Indices: 30220645--30220708 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
30220635 GTAAATGGAT
30220645 TAAATTCTTGAAAATAAAAGTACAAGAAC
1 TAAATTCTTGAAAATAAAAGTACAAGAAC
* *
30220674 TAAATTCTTGAAAATAAAAGTACAGGGAC
1 TAAATTCTTGAAAATAAAAGTACAAGAAC
30220703 TAAATT
1 TAAATT
30220709 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (29 bp):
TAAATTCTTGAAAATAAAAGTACAAGAAC
Found at i:30221049 original size:6 final size:6
Alignment explanation
Indices: 30221038--30221094 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
30221028 TTTTCCTCTA
* *
30221038 TTTTCC TTTTCC TTTTCCC TTTCACC TTCTTCTA TTTTCC TTTTCC TTTTCC
1 TTTTCC TTTTCC TTTT-CC TTT-TCC TT-TTC-C TTTTCC TTTTCC TTTTCC
*
30221090 CTTTC
1 TTTTC
30221095 ACGTTCTTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
6 26 0.62
7 13 0.31
8 3 0.07
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.61
Consensus pattern (6 bp):
TTTTCC
Found at i:30221074 original size:34 final size:34
Alignment explanation
Indices: 30221034--30221104 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
30221024 TTATTTTTCC
30221034 TCTATTTTCCTTTTCCTTTTCCCTTTCACCTTCT
1 TCTATTTTCCTTTTCCTTTTCCCTTTCACCTTCT
*
30221068 TCTATTTTCCTTTTCCTTTTCCCTTTCACGTTCT
1 TCTATTTTCCTTTTCCTTTTCCCTTTCACCTTCT
30221102 TCT
1 TCT
30221105 CTTATGTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.06, C:0.34, G:0.01, T:0.59
Consensus pattern (34 bp):
TCTATTTTCCTTTTCCTTTTCCCTTTCACCTTCT
Found at i:30223392 original size:28 final size:29
Alignment explanation
Indices: 30223359--30223423 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
30223349 CTTAGAGTTT
*
30223359 GAATTTAAAG-TTTAGAGTTTAAAATTCA
1 GAATTTAAAGATTTAGAATTTAAAATTCA
* * * *
30223387 GAATTT-TAGATTTATAATTTGATATTCA
1 GAATTTAAAGATTTAGAATTTAAAATTCA
30223415 GAATTTAAA
1 GAATTTAAA
30223424 TTAAAAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 2 0.07
28 26 0.90
29 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.43
Consensus pattern (29 bp):
GAATTTAAAGATTTAGAATTTAAAATTCA
Found at i:30223786 original size:23 final size:25
Alignment explanation
Indices: 30223756--30223807 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
30223746 ACTATGTCCA
30223756 ATTTAAAAG-AAAAA-AATTATACT
1 ATTTAAAAGAAAAAAGAATTATACT
30223779 ATTTAAAAGAAAAAAGAATTATACT
1 ATTTAAAAGAAAAAAGAATTATACT
30223804 ATTT
1 ATTT
30223808 TTTTCTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 9 0.33
24 5 0.19
25 13 0.48
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
ATTTAAAAGAAAAAAGAATTATACT
Found at i:30224369 original size:15 final size:16
Alignment explanation
Indices: 30224349--30224382 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
30224339 TTAAAATTTG
*
30224349 AAAAATACCAA-AACT
1 AAAAATAACAATAACT
30224364 AAAAATAACAATAACT
1 AAAAATAACAATAACT
30224380 AAA
1 AAA
30224383 TCTATAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAATAACAATAACT
Found at i:30226736 original size:6 final size:6
Alignment explanation
Indices: 30226725--30226751 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
30226715 CTATAACTAA
30226725 AAATAT AAATAT AAATAT AAATAT AAA
1 AAATAT AAATAT AAATAT AAATAT AAA
30226752 ATCTAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATAT
Found at i:30226737 original size:18 final size:18
Alignment explanation
Indices: 30226716--30226751 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30226706 TTTATATTTC
*
30226716 TATAACTAAAAATATAAA
1 TATAAATAAAAATATAAA
*
30226734 TATAAATATAAATATAAA
1 TATAAATAAAAATATAAA
30226752 ATCTAAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TATAAATAAAAATATAAA
Found at i:30228348 original size:15 final size:15
Alignment explanation
Indices: 30228325--30228360 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
30228315 GTTCCAAATG
*
30228325 TTGCAACAAGTTCTA
1 TTGCTACAAGTTCTA
30228340 TTGCTACAAGTTCTA
1 TTGCTACAAGTTCTA
30228355 TTGCTA
1 TTGCTA
30228361 AATTGTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (15 bp):
TTGCTACAAGTTCTA
Found at i:30229953 original size:20 final size:20
Alignment explanation
Indices: 30229923--30229960 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
30229913 ATAAATATAT
30229923 ATTTTTTATTTT-TAAAATA
1 ATTTTTTATTTTCTAAAATA
30229942 ATTTTTTAATTTTCTAAAA
1 ATTTTTT-ATTTTCTAAAA
30229961 ATTTTTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTTTATTTTCTAAAATA
Found at i:30236241 original size:92 final size:92
Alignment explanation
Indices: 30236137--30236526 Score: 568
Period size: 92 Copynumber: 4.2 Consensus size: 92
30236127 ATCCAATGCT
*
30236137 CAAATCAATTCAGCAATATATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
1 CAAATCAATTCAGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
*
30236202 TC-AATTCGGCAATGTATATCCATATA
66 TCAAATTCGGCAATGTATATCTATATA
**
30236228 CAAATCAAATTCAGCAATGTATAAACATATACAAATCAAATTCGGCAATGTATATCTATATACAA
1 CAAATC-AATTCAGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
**
30236293 ATCAAATTCAACAATGTATATCTATATA
65 ATCAAATTCGGCAATGTATATCTATATA
* * * *
30236321 CAAATCAATTC-GACAATGTATATCCATATACAAATCAAATTCGACAATGTATAACCATATAAAA
1 CAAATCAATTCAG-CAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
*
30236385 ATCAAATTAGGCAATGTATATCTATATA
65 ATCAAATTCGGCAATGTATATCTATATA
* * * * * * *
30236413 AAAATCAATTCGGCAATGTATATCTATAAACAATTCAAATTCGGCAATGTATACCTATAAACAAA
1 CAAATCAATTCAGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
*
30236478 TCAAATTCGGCAATGTATATCTTTATA
66 TCAAATTCGGCAATGTATATCTATATA
*
30236505 CAAATCAATTCGGCAATGTATA
1 CAAATCAATTCAGCAATGTATA
30236527 AAACATATAC
Statistics
Matches: 268, Mismatches: 27, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
91 7 0.03
92 233 0.87
93 28 0.10
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (92 bp):
CAAATCAATTCAGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
TCAAATTCGGCAATGTATATCTATATA
Found at i:30236535 original size:123 final size:122
Alignment explanation
Indices: 30236137--30236526 Score: 563
Period size: 123 Copynumber: 3.2 Consensus size: 122
30236127 ATCCAATGCT
* * *
30236137 CAAATC-AATTCAGCAATATATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
*
30236201 ATCAATTCGGCAATGTATATCCATATACAAATCAAATTCAGCAATGTATAAACATATA
66 ATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTAT-AACATATA
**
30236259 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCAACAATGTATATCTATATACAA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* *
30236324 ATCAATTCGACAATGTATATCCATATACAAATCAAATTCGACAATGTATAACCATATA
66 ATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAA-CATATA
* * * *
30236382 AAAATCAAATTAGGCAATGTATATCTATATAAAAATC-AATTCGGCAATGTATATCTATAAACAA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* * * *
30236446 TTCAAATTCGGCAATGTATA-CCTATAAACAAATCAAATTCGGCAATGTATATCTTTATA
66 ATC-AATTCGGCAATGTATATCC-ATATACAAATCAAATTCGGCAATGTATAAC-ATATA
30236505 CAAATC-AATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
30236527 AAACATATAC
Statistics
Matches: 241, Mismatches: 22, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
122 52 0.22
123 189 0.78
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (122 bp):
CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
ATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACATATA
Found at i:30236537 original size:31 final size:31
Alignment explanation
Indices: 30236137--30236526 Score: 540
Period size: 31 Copynumber: 12.7 Consensus size: 31
30236127 ATCCAATGCT
* * *
30236137 CAAATC-AATTCAGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
30236167 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
30236198 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
30236228 CAAATCAAATTCAGCAATGTATAAAC-ATATA
1 CAAATCAAATTCGGCAATGTAT-ATCTATATA
30236259 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
**
30236290 CAAATCAAATTCAACAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
30236321 CAAATC-AATTCGACAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
30236351 CAAATCAAATTCGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
30236382 AAAATCAAATTAGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
30236413 AAAATC-AATTCGGCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
30236443 CAATTCAAATTCGGCAATGTATACCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
30236474 CAAATCAAATTCGGCAATGTATATCTTTATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
30236505 CAAATC-AATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
30236527 AAACATATAC
Statistics
Matches: 327, Mismatches: 27, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
30 107 0.33
31 218 0.67
32 2 0.01
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCTATATA
Found at i:30242162 original size:29 final size:29
Alignment explanation
Indices: 30242120--30242184 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
30242110 AGATAAGCTT
30242120 ATTGGATCTCTATAGACTATCAAGGTCAA
1 ATTGGATCTCTATAGACTATCAAGGTCAA
*
30242149 ATTGGATCTCTATAGACTTTCAAGGTCAA
1 ATTGGATCTCTATAGACTATCAAGGTCAA
30242178 ATTGGAT
1 ATTGGAT
30242185 AAGTAAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (29 bp):
ATTGGATCTCTATAGACTATCAAGGTCAA
Found at i:30262347 original size:25 final size:25
Alignment explanation
Indices: 30262319--30262369 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
30262309 AGAATTCTTC
30262319 CAAGGCACCAATTGAAGAGCGGAAG
1 CAAGGCACCAATTGAAGAGCGGAAG
30262344 CAAGGCACCAATTGAAGAGCGGAAG
1 CAAGGCACCAATTGAAGAGCGGAAG
30262369 C
1 C
30262370 GATTTATGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.31, T:0.08
Consensus pattern (25 bp):
CAAGGCACCAATTGAAGAGCGGAAG
Found at i:30269478 original size:109 final size:110
Alignment explanation
Indices: 30269287--30269506 Score: 424
Period size: 109 Copynumber: 2.0 Consensus size: 110
30269277 CATTAGGAAA
30269287 ACTTAAGAATAAAACCAAATTAACAAAAATAAGAGGGAAATTCAGCCAGGTATTTAAATGGGTTG
1 ACTTAAGAATAAAACCAAATTAACAAAAATAAGAGGGAAATTCAGCCAGGTATTTAAATGGGTTG
30269352 CTTGGGCCGAATTTTAACATATAATATTCCTAAAG-CTAAAAATT
66 CTTGGGCCGAATTTTAACATATAATATTCCTAAAGCCTAAAAATT
*
30269396 ACTTAAGAATAAAACCTAATTAACAAAAATAAGAGGGAAATTCAGCCAGGTATTTAAATGGGTTG
1 ACTTAAGAATAAAACCAAATTAACAAAAATAAGAGGGAAATTCAGCCAGGTATTTAAATGGGTTG
30269461 CTTGGGCCGAATTTTAACATATAATATTCCTAAAGCCTAAAAATT
66 CTTGGGCCGAATTTTAACATATAATATTCCTAAAGCCTAAAAATT
30269506 A
1 A
30269507 AATTAACCAA
Statistics
Matches: 109, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
109 99 0.91
110 10 0.09
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (110 bp):
ACTTAAGAATAAAACCAAATTAACAAAAATAAGAGGGAAATTCAGCCAGGTATTTAAATGGGTTG
CTTGGGCCGAATTTTAACATATAATATTCCTAAAGCCTAAAAATT
Found at i:30297653 original size:22 final size:22
Alignment explanation
Indices: 30297628--30297676 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
30297618 TTGTTTTACT
*
30297628 TTTTGCTACTATTTTACTATCA
1 TTTTGCTACTATGTTACTATCA
* * * *
30297650 TTTTACTATTATGTTGCTATTA
1 TTTTGCTACTATGTTACTATCA
30297672 TTTTG
1 TTTTG
30297677 TTGTTAATGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.59
Consensus pattern (22 bp):
TTTTGCTACTATGTTACTATCA
Found at i:30299848 original size:21 final size:21
Alignment explanation
Indices: 30299818--30299858 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30299808 TGGGATAAAT
*
30299818 GTTGATCATCATGTAGCTCAA
1 GTTGAACATCATGTAGCTCAA
*
30299839 GTTGAACATCCTGTAGCTCA
1 GTTGAACATCATGTAGCTCA
30299859 TATTCACACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (21 bp):
GTTGAACATCATGTAGCTCAA
Found at i:30302784 original size:25 final size:25
Alignment explanation
Indices: 30302756--30302810 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
30302746 CTTTCCTGTC
*
30302756 TTTATTTTATAACAAT-TTTAATTTT
1 TTTATTGTATAA-AATATTTAATTTT
* * *
30302781 TTTAGTGTATTATATATTTAATTTT
1 TTTATTGTATAAAATATTTAATTTT
30302806 TTTAT
1 TTTAT
30302811 ATAAAAAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (25 bp):
TTTATTGTATAAAATATTTAATTTT
Found at i:30311527 original size:19 final size:21
Alignment explanation
Indices: 30311491--30311542 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
30311481 AAATATAAAA
30311491 TTTGAAATTTTTATAAA-TAT
1 TTTGAAATTTTTATAAATTAT
30311511 TTTG-AATTTTTGA-AAATTAT
1 TTTGAAATTTTT-ATAAATTAT
*
30311531 TTTAAAATTTTT
1 TTTGAAATTTTT
30311543 TGTAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 10 0.36
20 11 0.39
21 7 0.25
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (21 bp):
TTTGAAATTTTTATAAATTAT
Found at i:30323806 original size:30 final size:30
Alignment explanation
Indices: 30323770--30323844 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
30323760 AAAAATAAAA
30323770 ATTTACCAAAATATTACAAATTTTTCTTTT
1 ATTTACCAAAATATTACAAATTTTTCTTTT
30323800 ATTTACCAAAATATTACAAATTTTTCTTTT
1 ATTTACCAAAATATTACAAATTTTTCTTTT
30323830 ATTTACCAAAATATT
1 ATTTACCAAAATATT
30323845 GCTTTTTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (30 bp):
ATTTACCAAAATATTACAAATTTTTCTTTT
Found at i:30343888 original size:13 final size:13
Alignment explanation
Indices: 30343870--30343908 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
30343860 GGCTGTGTCA
30343870 GTTTTTGTTTTTT
1 GTTTTTGTTTTTT
*
30343883 GTTTTTGTCTTTT
1 GTTTTTGTTTTTT
30343896 GTTGTTT-TTTTTT
1 GTT-TTTGTTTTTT
30343909 TTATATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 20 0.87
14 3 0.13
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (13 bp):
GTTTTTGTTTTTT
Found at i:30343953 original size:27 final size:26
Alignment explanation
Indices: 30343913--30344010 Score: 124
Period size: 29 Copynumber: 3.5 Consensus size: 26
30343903 TTTTTTTTAT
30343913 ATATTTTGGTAAATAATAAAAAAAGTA
1 ATATTTTGGTAAATAA-AAAAAAAGTA
*
30343940 ATATTTTGGAAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAA---GTA
*
30343969 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAA--AGTA
30343997 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
30344011 TTTTATTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
26 7 0.11
27 15 0.24
28 17 0.27
29 24 0.38
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (26 bp):
ATATTTTGGTAAATAAAAAAAAAGTA
Found at i:30343969 original size:29 final size:29
Alignment explanation
Indices: 30343913--30344010 Score: 150
Period size: 28 Copynumber: 3.5 Consensus size: 29
30343903 TTTTTTTTAT
30343913 ATATTTTGGTAAATAATAAAAAAA---GTA
1 ATATTTTGGTAAATAA-AAAAAAAGTTGTA
*
30343940 ATATTTTGGAAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
30343969 ATATTTTGGTAAAT-AAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
30343997 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
30344011 TTTTATTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
26 7 0.11
27 15 0.23
28 28 0.42
29 16 0.24
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAAAAAAGTTGTA
Found at i:30345841 original size:26 final size:25
Alignment explanation
Indices: 30345799--30345855 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 25
30345789 AGCTCCGGAA
30345799 AGCCATTAACGGGAAGCTCACAAAG
1 AGCCATTAACGGGAAGCTCACAAAG
* *
30345824 AGCCTTTAATCGGGAAGCTCACGAAG
1 AGCCATTAA-CGGGAAGCTCACAAAG
30345850 AGCCAT
1 AGCCAT
30345856 ATATCGGGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.16
Consensus pattern (25 bp):
AGCCATTAACGGGAAGCTCACAAAG
Found at i:30345870 original size:26 final size:26
Alignment explanation
Indices: 30345731--30345863 Score: 93
Period size: 24 Copynumber: 5.3 Consensus size: 26
30345721 ATTCGAGTTG
* *
30345731 TATAACGGGAAGCTCA-TAAGAGCCA
1 TATATCGGGAAGCTCACGAAGAGCCA
* * * * *
30345756 -AAATCGGGAAGTTTAAG-CGAGCCA
1 TATATCGGGAAGCTCACGAAGAGCCA
*
30345780 -ATATCGGGGAGCTC-CGGAA-AGCCA
1 TATATCGGGAAGCTCAC-GAAGAGCCA
* *
30345804 T-TAACGGGAAGCTCACAAAGAGCC-
1 TATATCGGGAAGCTCACGAAGAGCCA
*
30345828 TTTAATCGGGAAGCTCACGAAGAGCCA
1 TAT-ATCGGGAAGCTCACGAAGAGCCA
30345855 TATATCGGG
1 TATATCGGG
30345864 GCGCTCATAA
Statistics
Matches: 81, Mismatches: 18, Indels: 17
0.70 0.16 0.15
Matches are distributed among these distances:
24 47 0.58
25 6 0.07
26 26 0.32
27 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.28, T:0.17
Consensus pattern (26 bp):
TATATCGGGAAGCTCACGAAGAGCCA
Found at i:30349407 original size:46 final size:46
Alignment explanation
Indices: 30349354--30349447 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
30349344 CCATGGCAAA
*
30349354 TTGTGAAAAGTAGGTATGGTGTTTCAGTG-AAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAAG-AAACCATACTGAG
30349400 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAAGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAAGAAACCATACTGAG
30349446 TT
1 TT
30349448 ATAGCATTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 43 0.93
47 3 0.07
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.30
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTATTTCAGTGAAAGAAACCATACTGAG
Found at i:30352546 original size:17 final size:17
Alignment explanation
Indices: 30352526--30352560 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30352516 GAATTATTTG
30352526 TTAAAAATTA-ATAATAT
1 TTAAAAA-TACATAATAT
30352543 TTAAAAATACATAATAT
1 TTAAAAATACATAATAT
30352560 T
1 T
30352561 ACTTAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATACATAATAT
Found at i:30354791 original size:1 final size:1
Alignment explanation
Indices: 30354781--30354814 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
30354771 ACTTACACTC
*
30354781 TTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
30354815 GAGTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:30375822 original size:21 final size:22
Alignment explanation
Indices: 30375790--30375832 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
30375780 TCGGAAACCC
*
30375790 AACTCAGTTTCAACGA-GTTCA
1 AACTCAGTTTCAAAGATGTTCA
30375811 AACTCAAG-TTCAAAGATGTTCA
1 AACTC-AGTTTCAAAGATGTTCA
30375833 TCAAATGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (22 bp):
AACTCAGTTTCAAAGATGTTCA
Found at i:30404411 original size:17 final size:17
Alignment explanation
Indices: 30404389--30404424 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30404379 TTTGTTAACT
*
30404389 TTTTAAAGAGAAATATA
1 TTTTAAAGAAAAATATA
*
30404406 TTTTAAGGAAAAATATA
1 TTTTAAAGAAAAATATA
30404423 TT
1 TT
30404425 GGTATTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (17 bp):
TTTTAAAGAAAAATATA
Found at i:30405050 original size:38 final size:37
Alignment explanation
Indices: 30404977--30405051 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
30404967 TGCAATTGTA
**
30404977 ATATATGAAATTTAATTTGATTTAATTTTGATAAATTG
1 ATATATGAAATCAAATTTGATTTAATTTT-ATAAATTG
*
30405015 ATATATGAAATCAAAGTTTGGTTTAATGTTT-TAAATT
1 ATATATGAAATCAAA-TTTGATTTAAT-TTTATAAATT
30405052 TTGATAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 19 0.59
39 10 0.31
40 3 0.09
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (37 bp):
ATATATGAAATCAAATTTGATTTAATTTTATAAATTG
Found at i:30410214 original size:114 final size:114
Alignment explanation
Indices: 30410014--30410243 Score: 460
Period size: 114 Copynumber: 2.0 Consensus size: 114
30410004 CCTTGTTTGA
30410014 GTGATTGGTGAATATATATAAGTTATTAAGTCTACCAAAATGTTCATTATATATGGAATAGCTTG
1 GTGATTGGTGAATATATATAAGTTATTAAGTCTACCAAAATGTTCATTATATATGGAATAGCTTG
30410079 TATAGTTTTGTGGTTGGTTAAAAGGATGAATCAACATGTGTTTAGATTG
66 TATAGTTTTGTGGTTGGTTAAAAGGATGAATCAACATGTGTTTAGATTG
30410128 GTGATTGGTGAATATATATAAGTTATTAAGTCTACCAAAATGTTCATTATATATGGAATAGCTTG
1 GTGATTGGTGAATATATATAAGTTATTAAGTCTACCAAAATGTTCATTATATATGGAATAGCTTG
30410193 TATAGTTTTGTGGTTGGTTAAAAGGATGAATCAACATGTGTTTAGATTG
66 TATAGTTTTGTGGTTGGTTAAAAGGATGAATCAACATGTGTTTAGATTG
30410242 GT
1 GT
30410244 TTTATGCAGG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 116 1.00
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (114 bp):
GTGATTGGTGAATATATATAAGTTATTAAGTCTACCAAAATGTTCATTATATATGGAATAGCTTG
TATAGTTTTGTGGTTGGTTAAAAGGATGAATCAACATGTGTTTAGATTG
Found at i:30411882 original size:148 final size:149
Alignment explanation
Indices: 30411710--30412007 Score: 589
Period size: 148 Copynumber: 2.0 Consensus size: 149
30411700 TTAAAATAAG
30411710 TTAATTATATTTATATTTATAATGTATATTAAATAGTAATAAAAATAACTAATCAAAACCCATTA
1 TTAATTATATTTATATTTATAATGTATATTAAATAGTAATAAAAATAACTAATCAAAACCCATTA
30411775 AGTAATAACAAAAGACTTATGTTGAAATAAAATCCAAATTGACATCAAATTTCGAGTTCAATTCT
66 AGTAATAACAAAAGACTTATGTTGAAATAAAATCCAAATTGACATCAAATTTCGAGTTCAATTCT
30411840 TGCATATGAGATGATATTC
131 TGCATATGAGATGATATTC
30411859 TTAATTATA-TTATATTTATAATGTATATTAAATAGTAATAAAAATAACTAATCAAAACCCATTA
1 TTAATTATATTTATATTTATAATGTATATTAAATAGTAATAAAAATAACTAATCAAAACCCATTA
30411923 AGTAATAACAAAAGACTTATGTTGAAATAAAATCCAAATTGACATCAAATTTCGAGTTCAATTCT
66 AGTAATAACAAAAGACTTATGTTGAAATAAAATCCAAATTGACATCAAATTTCGAGTTCAATTCT
30411988 TGCATATGAGATGATATTC
131 TGCATATGAGATGATATTC
30412007 T
1 T
30412008 AGAAACCCTT
Statistics
Matches: 149, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 140 0.94
149 9 0.06
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (149 bp):
TTAATTATATTTATATTTATAATGTATATTAAATAGTAATAAAAATAACTAATCAAAACCCATTA
AGTAATAACAAAAGACTTATGTTGAAATAAAATCCAAATTGACATCAAATTTCGAGTTCAATTCT
TGCATATGAGATGATATTC
Found at i:30438610 original size:21 final size:22
Alignment explanation
Indices: 30438569--30438611 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
30438559 TAAATAAATG
30438569 TGTAATAAATATATGTATACATT
1 TGTAATAAATATATG-ATACATT
*
30438592 TGTAATTAATATATG-TACAT
1 TGTAATAAATATATGATACAT
30438612 ACTTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (22 bp):
TGTAATAAATATATGATACATT
Found at i:30438752 original size:27 final size:26
Alignment explanation
Indices: 30438705--30438761 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
30438695 GCAGAATAGC
* * *
30438705 AAAACGAAAACAGGGGAGAAAGGAAAG
1 AAAAAGAAAACAGGGAAGAAA-CAAAG
30438732 AAAAAGAAAA-AGGGAAGGAAACAAAG
1 AAAAAGAAAACAGGGAA-GAAACAAAG
30438758 AAAA
1 AAAA
30438762 TTTAGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAACAGGGAAGAAACAAAG
Found at i:30440237 original size:37 final size:37
Alignment explanation
Indices: 30440136--30440237 Score: 91
Period size: 37 Copynumber: 2.6 Consensus size: 37
30440126 CGACCTTGAG
30440136 TCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCA-AC--TTACTTCGGATA-AT
** ** *
30440177 TCGATGAGGTACTGGGTACCAACTTACTTCGG-T-TT
1 TCGATGAGACACTGGGTGTCAACTTACTTCGGATAAT
30440212 TGCCGATGAGACACTGGGTGTCAACT
1 T--CGATGAGACACTGGGTGTCAACT
30440238 ATTGCTTCGA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
35 2 0.04
37 20 0.40
38 9 0.18
40 2 0.04
41 17 0.34
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (37 bp):
TCGATGAGACACTGGGTGTCAACTTACTTCGGATAAT
Found at i:30440726 original size:17 final size:18
Alignment explanation
Indices: 30440695--30440728 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30440685 ATAAATAGAA
30440695 ATGATAATGAATGAGTTG
1 ATGATAATGAATGAGTTG
*
30440713 ATGA-AATGATTGAGTT
1 ATGATAATGAATGAGTT
30440729 TGTATGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (18 bp):
ATGATAATGAATGAGTTG
Found at i:30450895 original size:3 final size:3
Alignment explanation
Indices: 30450887--30450913 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
30450877 TCTATAACAA
30450887 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
30450914 TATATACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:30451847 original size:20 final size:20
Alignment explanation
Indices: 30451822--30451863 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
30451812 TAGAGTTTTA
* *
30451822 AGTTCAGAGTTCAGGGTTTG
1 AGTTCAAAGTTCACGGTTTG
*
30451842 AGTTCAAAGTTTACGGTTTG
1 AGTTCAAAGTTCACGGTTTG
30451862 AG
1 AG
30451864 GTACATGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.36
Consensus pattern (20 bp):
AGTTCAAAGTTCACGGTTTG
Found at i:30452310 original size:16 final size:15
Alignment explanation
Indices: 30452282--30452312 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30452272 TATAATCCTT
30452282 TAAAAATTATAAAAA
1 TAAAAATTATAAAAA
*
30452297 TAAAAATTATTAAAA
1 TAAAAATTATAAAAA
30452312 T
1 T
30452313 CATATTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAAATTATAAAAA
Found at i:30455024 original size:22 final size:21
Alignment explanation
Indices: 30454999--30455043 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
30454989 AAAAATTCAA
*
30454999 AAAAATGAATATATAAAAAATG
1 AAAAATGAAAATA-AAAAAATG
30455021 AAAAATGAAAATAAAAAAATG
1 AAAAATGAAAATAAAAAAATG
30455042 AA
1 AA
30455044 GTTAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (21 bp):
AAAAATGAAAATAAAAAAATG
Found at i:30455024 original size:24 final size:24
Alignment explanation
Indices: 30454986--30455043 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
30454976 TATTATAAAC
* * *
30454986 TATAAAAATTCAAAAAAATGAATA
1 TATAAAAAATGAAAAAAATGAAAA
30455010 TATAAAAAATG--AAAAATGAAAA
1 TATAAAAAATGAAAAAAATGAAAA
30455032 TA-AAAAAATGAA
1 TATAAAAAATGAA
30455044 GTTAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 8 0.28
22 12 0.41
24 9 0.31
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.21
Consensus pattern (24 bp):
TATAAAAAATGAAAAAAATGAAAA
Found at i:30455404 original size:23 final size:23
Alignment explanation
Indices: 30455378--30455435 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
30455368 CTAAATTTGT
30455378 TATTTTTATTTTCAA-TTTATATA
1 TATTTTTATTTTCAAGTTTATA-A
*
30455401 TATTCTTT-TTTTGAAGTTTATAA
1 TATT-TTTATTTTCAAGTTTATAA
30455424 T-TTTTATATTTT
1 TATTTT-TATTTT
30455436 TTAACAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
21 2 0.07
22 3 0.10
23 16 0.53
24 9 0.30
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (23 bp):
TATTTTTATTTTCAAGTTTATAA
Found at i:30462446 original size:18 final size:19
Alignment explanation
Indices: 30462419--30462468 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
30462409 GATAGCATAA
*
30462419 AAGAATGAAGGTAAAA-AG
1 AAGAAGGAAGGTAAAAGAG
*
30462437 AAGAAGGAAGAATAAAAGAG
1 AAGAAGGAAG-GTAAAAGAG
30462457 ACAG-AGGAAGGT
1 A-AGAAGGAAGGT
30462469 TGAAAAAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 9 0.35
19 6 0.23
20 9 0.35
21 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.32, T:0.08
Consensus pattern (19 bp):
AAGAAGGAAGGTAAAAGAG
Found at i:30468185 original size:14 final size:14
Alignment explanation
Indices: 30468166--30468193 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30468156 ACTAAATTCT
30468166 TGAAAATTAAATTA
1 TGAAAATTAAATTA
30468180 TGAAAATTAAATTA
1 TGAAAATTAAATTA
30468194 CAAATATACA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
TGAAAATTAAATTA
Found at i:30476027 original size:20 final size:21
Alignment explanation
Indices: 30475986--30476028 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
30475976 TAAAAATGAT
*
30475986 ATTAAATGTTTAATTGATTTA
1 ATTAAATGTTTAAATGATTTA
30476007 ATTAAA-GTTTAAAT-ATATTA
1 ATTAAATGTTTAAATGAT-TTA
30476027 AT
1 AT
30476029 ATCCATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.60
21 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
ATTAAATGTTTAAATGATTTA
Found at i:30478050 original size:79 final size:79
Alignment explanation
Indices: 30477957--30478114 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
30477947 TATTCTATCA
30477957 ATTTGATCTTAGTTCTAAATAATTCAATAAATTTAACCTTTCACATTTATAAATTCTATCAATTT
1 ATTTGATCTTAGTTCTAAATAATTCAATAAATTTAACCTTTCACATTTATAAATTCTATCAATTT
30478022 GATCATCAAACTTT
66 GATCATCAAACTTT
*
30478036 ATTTGATCTTAGTTCTAAATAATTTAATAAATTTAACCTTTCACATTTATAAATTCTATCAATTT
1 ATTTGATCTTAGTTCTAAATAATTCAATAAATTTAACCTTTCACATTTATAAATTCTATCAATTT
30478101 GATCATCAAACTTT
66 GATCATCAAACTTT
30478115 CTAACCAAAA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.45
Consensus pattern (79 bp):
ATTTGATCTTAGTTCTAAATAATTCAATAAATTTAACCTTTCACATTTATAAATTCTATCAATTT
GATCATCAAACTTT
Found at i:30485378 original size:19 final size:19
Alignment explanation
Indices: 30485340--30485378 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30485330 AAATAGTGAG
*
30485340 AATTTATTTTCTAAGTATA
1 AATTTATTTTCTAAGAATA
30485359 AATTCTATTTTCT-AGAATA
1 AATT-TATTTTCTAAGAATA
30485378 A
1 A
30485379 CAATTCTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:30486234 original size:9 final size:9
Alignment explanation
Indices: 30486220--30486268 Score: 82
Period size: 9 Copynumber: 5.4 Consensus size: 9
30486210 TGTAGGATTC
30486220 AATTCGGTT
1 AATTCGGTT
30486229 AATTCGGTT
1 AATTCGGTT
30486238 AATTCGAG-T
1 AATTCG-GTT
30486247 AATTCGGTT
1 AATTCGGTT
30486256 AATTCGGTT
1 AATTCGGTT
30486265 AATT
1 AATT
30486269 TTTAACCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 1 0.03
9 36 0.95
10 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:30494716 original size:29 final size:30
Alignment explanation
Indices: 30494683--30494741 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
30494673 TTTAGTCTAA
*
30494683 TGTGCAATGTTATATATGGATT-TTGATTT
1 TGTGCAATGTTATATATGAATTGTTGATTT
*
30494712 TGTGCAATTTTATATATGAATTGTTGATTT
1 TGTGCAATGTTATATATGAATTGTTGATTT
30494742 GATTTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (30 bp):
TGTGCAATGTTATATATGAATTGTTGATTT
Found at i:30494971 original size:2 final size:2
Alignment explanation
Indices: 30494964--30494991 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30494954 TGTAATAGAG
30494964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30494992 TTGTTGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30497769 original size:166 final size:166
Alignment explanation
Indices: 30497571--30497907 Score: 647
Period size: 166 Copynumber: 2.0 Consensus size: 166
30497561 GCCATGTGGT
30497571 TATGTTTGAAGTCGAAGATGATGCTTATTTGTTTAGTAGGTAGGTAATTAACTAGATGAAAGCCT
1 TATGTTTGAAGTCGAAGATGATGCTTATTTGTTTAGTAGGTAGGTAATTAACTAGATGAAAGCCT
*
30497636 TCGCTCTTTAAAGATATGAATAATCTAAGGGTTCTCATAGGTACTTATTGAAACCATGATGGGGC
66 TCGCTCTTTAAAGATATGAATAATCTAAGGGTTCTCATAGGTACTTACTGAAACCATGATGGGGC
*
30497701 TTTGATTAGTGAAGTTATAATGTCTCTTAAGGAATA
131 TTTGATTAGTGAAGTTATAATGTCTCTGAAGGAATA
*
30497737 TATGTTTTAAGTCGAAGATGATGCTTATTTGTTTAGTAGGTAGGTAATTAACTAGATGAAAGCCT
1 TATGTTTGAAGTCGAAGATGATGCTTATTTGTTTAGTAGGTAGGTAATTAACTAGATGAAAGCCT
30497802 TCGCTCTTTAAAGATATGAATAATCTAAGGGTTCTCATAGGTACTTACTGAAACCATGATGGGGC
66 TCGCTCTTTAAAGATATGAATAATCTAAGGGTTCTCATAGGTACTTACTGAAACCATGATGGGGC
30497867 TTTGATTAGTGAAGTTATAATGTCTCTGAAGGAATA
131 TTTGATTAGTGAAGTTATAATGTCTCTGAAGGAATA
30497903 TATGT
1 TATGT
30497908 CTAACATCTT
Statistics
Matches: 168, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
166 168 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.36
Consensus pattern (166 bp):
TATGTTTGAAGTCGAAGATGATGCTTATTTGTTTAGTAGGTAGGTAATTAACTAGATGAAAGCCT
TCGCTCTTTAAAGATATGAATAATCTAAGGGTTCTCATAGGTACTTACTGAAACCATGATGGGGC
TTTGATTAGTGAAGTTATAATGTCTCTGAAGGAATA
Found at i:30505943 original size:2 final size:2
Alignment explanation
Indices: 30505936--30505965 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30505926 CCCTCCCCCT
30505936 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
30505966 AATGCAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:30508617 original size:21 final size:21
Alignment explanation
Indices: 30508591--30508631 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
30508581 TGCTGAATAG
30508591 TACTTAGCCTGTGATTTTATT
1 TACTTAGCCTGTGATTTTATT
30508612 TACTTAGCCTGTGATTTTAT
1 TACTTAGCCTGTGATTTTAT
30508632 AGGCATGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.51
Consensus pattern (21 bp):
TACTTAGCCTGTGATTTTATT
Found at i:30518415 original size:30 final size:30
Alignment explanation
Indices: 30518379--30518467 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 30
30518369 AGAATAAGTT
* *
30518379 GCTCACACAAGCTGACAGTATACCAAGGTC
1 GCTCACACAAGCTGACATTATAACAAGGTC
* ** *
30518409 GCTCACACAAGTTGACATTATAACAAAATT
1 GCTCACACAAGCTGACATTATAACAAGGTC
* *
30518439 GCTCACACAAGCTGATATTATATCAAGGT
1 GCTCACACAAGCTGACATTATAACAAGGT
30518468 TGACCGTCCT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.24
Consensus pattern (30 bp):
GCTCACACAAGCTGACATTATAACAAGGTC
Found at i:30524372 original size:178 final size:180
Alignment explanation
Indices: 30523992--30524400 Score: 383
Period size: 178 Copynumber: 2.3 Consensus size: 180
30523982 AGTTCAACTT
* * * * * * * ** *
30523992 CAACATAACAACAATAATCATAATCAGTCAAAGAAATTCTGAACAAAGAAGCTAAACTGAAAGAC
1 CAACACAACAACAATCATCATAATTAATCAAAGTAATTCAGAAGAAAGAAGCTAAACCAAAAAAC
* * * *
30524057 TAGTGGAAAGCAAGATTTAACCTATTACAACAC------GATCACAAGATTGTTTCCGGGACAAA
66 TAATGGAAAGCAAGATTCAACCTATTTCAACACATAGATGATCACAAGATTGTTT-CAGGACAAA
* * * * ** *
30524116 GTTCTGGAGTTTGAATTGTGTATAAATGAAGACCTATTTTTGTAAGTAGTC
130 GTTCAGCAGTTCGAATTGTGTATAAATCAAGACCTATTTACGTAAGCAGTC
* * * *
30524167 CAACACAACAACTA-CTATCACAATTAATCCATAGTAATTCAGATGAAAGAAGCTAAACCAAAAA
1 CAACACAACAACAATC-ATCATAATTAAT-CAAAGTAATTCAGAAGAAAGAAGCTAAACCAAAAA
* *
30524231 ACTAATTGAAAGCAAGATTCAAGCTATTTCAACACATAGATGATCACAA-ATTGTTTCAGGCACA
64 ACTAATGGAAAGCAAGATTCAACCTATTTCAACACATAGATGATCACAAGATTGTTTCAGG-ACA
* * * *
30524295 AAGTTCAGGAGTTCGAATTG-G-GT-AATCAAGACCTATATACGTAACCAGTC
128 AAGTTCAGCAGTTCGAATTGTGTATAAATCAAGACCTATTTACGTAAGCAGTC
* *
30524345 AAACACAACAACAATCATCATAATTAATAACAAA-TAATTAAGAAGAAAGAAGCTAA
1 CAACACAACAACAATCATCATAATTAAT--CAAAGTAATTCAGAAGAAAGAAGCTAA
30524401 GCAACAACTC
Statistics
Matches: 187, Mismatches: 36, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
175 21 0.11
176 57 0.30
178 64 0.34
179 5 0.03
180 4 0.02
181 28 0.15
182 8 0.04
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.24
Consensus pattern (180 bp):
CAACACAACAACAATCATCATAATTAATCAAAGTAATTCAGAAGAAAGAAGCTAAACCAAAAAAC
TAATGGAAAGCAAGATTCAACCTATTTCAACACATAGATGATCACAAGATTGTTTCAGGACAAAG
TTCAGCAGTTCGAATTGTGTATAAATCAAGACCTATTTACGTAAGCAGTC
Found at i:30528266 original size:27 final size:27
Alignment explanation
Indices: 30528213--30528276 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
30528203 TAAAAAAATA
**** *
30528213 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAAAAAATTCATTT
30528240 ACCAAAATATTATAAAAAAATTCATTT
1 ACCAAAATATTATAAAAAAATTCATTT
*
30528267 ATCAAAATAT
1 ACCAAAATAT
30528277 ACCAAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (27 bp):
ACCAAAATATTATAAAAAAATTCATTT
Found at i:30528283 original size:27 final size:27
Alignment explanation
Indices: 30528236--30528287 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
30528226 AAATTTTTTT
*
30528236 ATTTACCAAAATATTATAAAAAAATTC
1 ATTTACCAAAATATTACAAAAAAATTC
*
30528263 ATTTATCAAAATA-TACCAAAAAAAT
1 ATTTACCAAAATATTA-CAAAAAAAT
30528288 AAAAAATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (27 bp):
ATTTACCAAAATATTACAAAAAAATTC
Found at i:30528357 original size:27 final size:27
Alignment explanation
Indices: 30528326--30528385 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
30528316 GCCTGATCAG
* *
30528326 GCCAATCACATTGACGGCACTAAAGGT
1 GCCAAACACATTGACGGCACCAAAGGT
* * * *
30528353 GCCAAAGAGATTGGCGGCACCAATGGT
1 GCCAAACACATTGACGGCACCAAAGGT
30528380 GCCAAA
1 GCCAAA
30528386 AGACTAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (27 bp):
GCCAAACACATTGACGGCACCAAAGGT
Found at i:30528914 original size:90 final size:88
Alignment explanation
Indices: 30528811--30528994 Score: 323
Period size: 90 Copynumber: 2.1 Consensus size: 88
30528801 ATTTGGGTTA
*
30528811 CATTTATGGGTGATCAGTTTTATTATTACTTCTGATTTTTCAATAAGGCATGTCTGGTATTTCTA
1 CATTTATGGGTGATCAGTTTTATTATTACTTCTGATTTTTCAATAAGGCATGCCTGGTATTTCTA
30528876 TTATTATTTTTAATTAGAATTCTCT
66 TTA-T-TTTTTAATTAGAATTCTCT
* *
30528901 CATTTATGGGTGATCAGTTTTATTATTACTTCTGGTTTTTCAATAAGGCATGCCTGGTATTTCTC
1 CATTTATGGGTGATCAGTTTTATTATTACTTCTGATTTTTCAATAAGGCATGCCTGGTATTTCTA
30528966 TTATTTTTTAATTAGAATTCTCT
66 TTATTTTTTAATTAGAATTCTCT
30528989 CATTTA
1 CATTTA
30528995 ATAACTCTAT
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
88 25 0.27
89 1 0.01
90 65 0.71
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (88 bp):
CATTTATGGGTGATCAGTTTTATTATTACTTCTGATTTTTCAATAAGGCATGCCTGGTATTTCTA
TTATTTTTTAATTAGAATTCTCT
Found at i:30529111 original size:18 final size:19
Alignment explanation
Indices: 30529048--30529106 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
30529038 ACTTGATTTT
30529048 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
30529067 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
30529085 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
30529104 TTA
1 TTA
30529107 CTTAATTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:30530189 original size:14 final size:13
Alignment explanation
Indices: 30530156--30530215 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
30530146 GATAAATTGA
* *
30530156 AAAATTAAATATG
1 AAAATTAAGTATT
*
30530169 AATAATTAAGTGTT
1 AA-AATTAAGTATT
30530183 AGAAATTAAGTATT
1 A-AAATTAAGTATT
*
30530197 AAATTTAAGT-TAT
1 AAAATTAAGTAT-T
30530210 AAAATT
1 AAAATT
30530216 TGTTTGGTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.03
13 16 0.42
14 20 0.53
15 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (13 bp):
AAAATTAAGTATT
Found at i:30538281 original size:13 final size:13
Alignment explanation
Indices: 30538263--30538288 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30538253 TCAAGATGAG
30538263 TTAGTCCAAAAAA
1 TTAGTCCAAAAAA
30538276 TTAGTCCAAAAAA
1 TTAGTCCAAAAAA
30538289 CTCGTGTAAT
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:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
TTAGTCCAAAAAA
Found at i:30539076 original size:57 final size:57
Alignment explanation
Indices: 30538985--30539092 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 57
30538975 ATTTGAGCAT
* * ** * *
30538985 TTAAAAAAAAGAATAAATATACACATTTATATATATAAATGTA-AAAAAAACATTCG
1 TTAAAAAAAAAAATAAATACACACATACATATATACAAATATATAAAAAAACATTCG
*
30539041 TTAAAAAATAAAAATATATACACACATACATATATACAAATATATAAAAAAA
1 TTAAAAAA-AAAAATAAATACACACATACATATATACAAATATATAAAAAAA
30539093 TCGAAATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
56 8 0.19
57 28 0.65
58 7 0.16
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (57 bp):
TTAAAAAAAAAAATAAATACACACATACATATATACAAATATATAAAAAAACATTCG
Found at i:30541226 original size:40 final size:40
Alignment explanation
Indices: 30541182--30541264 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
30541172 CCCATCGGAA
30541182 GACACCTTAAGAGAGCAGAGGCTCGAAGACACCCCAAACC
1 GACACCTTAAGAGAGCAGAGGCTCGAAGACACCCCAAACC
*
30541222 GACACCTTAAGAGAGCAGAGGCTCGAATACACCCCAAACC
1 GACACCTTAAGAGAGCAGAGGCTCGAAGACACCCCAAACC
30541262 GAC
1 GAC
30541265 TGAAATCAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.37, C:0.33, G:0.22, T:0.08
Consensus pattern (40 bp):
GACACCTTAAGAGAGCAGAGGCTCGAAGACACCCCAAACC
Found at i:30542635 original size:21 final size:21
Alignment explanation
Indices: 30542609--30542657 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
30542599 TTCAATAATT
30542609 GGCTTGGAGTTGTGA-TCTCGG
1 GGCTTGGAGTTGTGACT-TCGG
*
30542630 GGCTTGGAGTTGTGACTTTGG
1 GGCTTGGAGTTGTGACTTCGG
30542651 GGCTTGG
1 GGCTTGG
30542658 TGTCGCGACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.08, C:0.12, G:0.45, T:0.35
Consensus pattern (21 bp):
GGCTTGGAGTTGTGACTTCGG
Found at i:30542667 original size:21 final size:21
Alignment explanation
Indices: 30542628--30542669 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30542618 TTGTGATCTC
* *
30542628 GGGGCTTGGAGTTGTGACTTT
1 GGGGCTTGGAGTCGCGACTTT
*
30542649 GGGGCTTGGTGTCGCGACTTT
1 GGGGCTTGGAGTCGCGACTTT
30542670 AACGACAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.14, G:0.43, T:0.36
Consensus pattern (21 bp):
GGGGCTTGGAGTCGCGACTTT
Found at i:30544507 original size:3 final size:3
Alignment explanation
Indices: 30544499--30544528 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
30544489 AACGATACGG
*
30544499 TGA TGA TGA TGA TGA TGA TGA CGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
30544529 GAAAAGTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:30548460 original size:22 final size:22
Alignment explanation
Indices: 30548421--30548462 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30548411 AGGATTGTAT
*
30548421 TTTTAAATAAATATTTTAAAGA
1 TTTTAAATAAATAGTTTAAAGA
30548443 TTTTAAATAAACT-GTTTAAA
1 TTTTAAATAAA-TAGTTTAAA
30548463 ACATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
TTTTAAATAAATAGTTTAAAGA
Found at i:30548655 original size:14 final size:16
Alignment explanation
Indices: 30548636--30548668 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
30548626 AATATAATTT
30548636 TAAAAT-TTTAAA-GA
1 TAAAATATTTAAAGGA
30548650 TAAAATATTTAAAGGA
1 TAAAATATTTAAAGGA
30548666 TAA
1 TAA
30548669 TATTAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 6 0.35
16 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (16 bp):
TAAAATATTTAAAGGA
Found at i:30551279 original size:2 final size:2
Alignment explanation
Indices: 30551272--30551300 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30551262 CCATTCACCC
30551272 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
30551301 CTATTGCCTA
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:30559527 original size:28 final size:27
Alignment explanation
Indices: 30559495--30559549 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
30559485 CTAACATCTT
30559495 CCATTCTACAATTCTTTATCTTTTAAAC
1 CCATTCTA-AATTCTTTATCTTTTAAAC
* **
30559523 CCATTTTAGTTTCTTTATCTTTTAAAC
1 CCATTCTAAATTCTTTATCTTTTAAAC
30559550 TTGGTTGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.25, C:0.22, G:0.02, T:0.51
Consensus pattern (27 bp):
CCATTCTAAATTCTTTATCTTTTAAAC
Found at i:30561964 original size:31 final size:32
Alignment explanation
Indices: 30561929--30562003 Score: 93
Period size: 30 Copynumber: 2.4 Consensus size: 32
30561919 TTTTTGGGGT
*
30561929 TTAATTTAAATTTTCT-AAAATTCTTAGGAG-C
1 TTAATTAAAATTTTCTAAAAATT-TTAGGAGCC
*
30561960 TTAA-TAAAATTTTTTAAAAATTTTAGGAGCC
1 TTAATTAAAATTTTCTAAAAATTTTAGGAGCC
*
30561991 TTACTTAAAATTT
1 TTAATTAAAATTT
30562004 CCAAAGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 16 0.42
31 14 0.37
32 8 0.21
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (32 bp):
TTAATTAAAATTTTCTAAAAATTTTAGGAGCC
Found at i:30578133 original size:41 final size:41
Alignment explanation
Indices: 30578083--30578166 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
30578073 AATCAGTATA
30578083 AAATTATAATTAACCTATATAATTTAAATACTAATTAATAC
1 AAATTATAATTAACCTATATAATTTAAATACTAATTAATAC
*
30578124 AAATTATAATTAACTTATATAATTTAAATACTAATTAATAC
1 AAATTATAATTAACCTATATAATTTAAATACTAATTAATAC
30578165 AA
1 AA
30578167 GCTTACTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.39
Consensus pattern (41 bp):
AAATTATAATTAACCTATATAATTTAAATACTAATTAATAC
Found at i:30593255 original size:2 final size:2
Alignment explanation
Indices: 30593248--30593288 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30593238 ATAAAACATA
30593248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30593289 CATAAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30600209 original size:23 final size:22
Alignment explanation
Indices: 30600165--30600209 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
30600155 TAATCAATTC
**
30600165 TAATCCCTATAAATATGTTATA
1 TAATCCCTATAAATATACTATA
*
30600187 TAATCTCCTATAAATCTACTATA
1 TAATC-CCTATAAATATACTATA
30600210 CAAATATTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (22 bp):
TAATCCCTATAAATATACTATA
Found at i:30601468 original size:14 final size:14
Alignment explanation
Indices: 30601449--30601478 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
30601439 AAAAGTTTTG
30601449 AAAACATCAAAATC
1 AAAACATCAAAATC
30601463 AAAACATCAAAATC
1 AAAACATCAAAATC
30601477 AA
1 AA
30601479 TCTTTTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.20, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAACATCAAAATC
Found at i:30602316 original size:16 final size:16
Alignment explanation
Indices: 30602295--30602343 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
30602285 CGCTGTATTG
30602295 GAATAGAGGCGTAATA
1 GAATAGAGGCGTAATA
* *
30602311 GAATAGATGCGTAATG
1 GAATAGAGGCGTAATA
30602327 GAATAGAGGCGTAATA
1 GAATAGAGGCGTAATA
30602343 G
1 G
30602344 GTAATTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.41, C:0.06, G:0.33, T:0.20
Consensus pattern (16 bp):
GAATAGAGGCGTAATA
Found at i:30602409 original size:44 final size:46
Alignment explanation
Indices: 30602323--30602418 Score: 142
Period size: 44 Copynumber: 2.1 Consensus size: 46
30602313 ATAGATGCGT
* *
30602323 AATGGAATAGAGGCGTAATAGGTAATTCTTTTATTTGGTTGAATGG
1 AATGGAATACAGGCGTAATAGGTAATTCTTGTATTTGGTTGAATGG
* *
30602369 AATGGCATACAGGCGTAATA-GT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATACAGGCGTAATAGGTAATTCTTGTATTTGGTTGAATGG
30602413 AATGGA
1 AATGGA
30602419 GGTGTAATAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
44 25 0.56
45 2 0.04
46 18 0.40
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (46 bp):
AATGGAATACAGGCGTAATAGGTAATTCTTGTATTTGGTTGAATGG
Found at i:30605321 original size:15 final size:14
Alignment explanation
Indices: 30605295--30605330 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
30605285 ACCGGTGGGA
30605295 ATAAACAATAAAATG
1 ATAAA-AATAAAATG
30605310 ATGAAAAATAAAATG
1 AT-AAAAATAAAATG
30605325 ATAAAA
1 ATAAAA
30605331 TTAATCATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 13 0.65
16 3 0.15
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.19
Consensus pattern (14 bp):
ATAAAAATAAAATG
Found at i:30605863 original size:10 final size:10
Alignment explanation
Indices: 30605848--30605874 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
30605838 GTAGCATCTA
30605848 TAACAATGCT
1 TAACAATGCT
30605858 TAACAATGCT
1 TAACAATGCT
30605868 TAACAAT
1 TAACAAT
30605875 TAATAAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (10 bp):
TAACAATGCT
Found at i:30618796 original size:37 final size:37
Alignment explanation
Indices: 30618719--30618807 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
30618709 GCCACTCCGA
** *
30618719 CCACCCTGCACACCACTTATAGGTTATGATAAGCCTAT
1 CCACCCTGCACACCAC-TATAGGCCATGATAAGCCCAT
*
30618757 CCACCCTGCACACCAC-ATAGGACCATGATAGGCCCAT
1 CCACCCTGCACACCACTATAGG-CCATGATAAGCCCAT
* *
30618794 CCACTCTACACACC
1 CCACCCTGCACACC
30618808 GCGTAGTGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
36 5 0.11
37 23 0.52
38 16 0.36
ACGTcount: A:0.29, C:0.39, G:0.12, T:0.19
Consensus pattern (37 bp):
CCACCCTGCACACCACTATAGGCCATGATAAGCCCAT
Found at i:30621452 original size:21 final size:21
Alignment explanation
Indices: 30621412--30621452 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30621402 TGGAAATCTC
* * *
30621412 ACACGCCCGTGTGGCTAAGGG
1 ACACGACCGTGTGACCAAGGG
30621433 ACACGACCGTGTGACCAAGG
1 ACACGACCGTGTGACCAAGG
30621453 TATATGCCCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.34, T:0.12
Consensus pattern (21 bp):
ACACGACCGTGTGACCAAGGG
Found at i:30629144 original size:21 final size:22
Alignment explanation
Indices: 30629102--30629144 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30629092 ATTCTCTCAA
30629102 TAAAAGATAATAGACGAATGGT
1 TAAAAGATAATAGACGAATGGT
* *
30629124 TAAAATATAATA-ACTAATGGT
1 TAAAAGATAATAGACGAATGGT
30629145 AACTATTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (22 bp):
TAAAAGATAATAGACGAATGGT
Found at i:30632538 original size:31 final size:31
Alignment explanation
Indices: 30632503--30632565 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
30632493 GTTAACCAAG
30632503 AGTAAAGAATATGCTATATCCTTAAGAATCT
1 AGTAAAGAATATGCTATATCCTTAAGAATCT
30632534 AGTAAAGAATATGCTATATCCTTAAGAATCT
1 AGTAAAGAATATGCTATATCCTTAAGAATCT
30632565 A
1 A
30632566 TCATTAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.32
Consensus pattern (31 bp):
AGTAAAGAATATGCTATATCCTTAAGAATCT
Found at i:30636153 original size:13 final size:14
Alignment explanation
Indices: 30636119--30636150 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
30636109 AAGACATGTT
*
30636119 ATTTTAGTTAATGG
1 ATTTTAATTAATGG
30636133 ATTTTAATTAATGG
1 ATTTTAATTAATGG
30636147 ATTT
1 ATTT
30636151 AATGGCTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (14 bp):
ATTTTAATTAATGG
Found at i:30644031 original size:2 final size:2
Alignment explanation
Indices: 30644000--30644042 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
30643990 CGATGAATAG
* * * *
30644000 AT AT AG AT AT AG AT AT AG AT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30644042 A
1 A
30644043 AATCCATGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (2 bp):
AT
Found at i:30644042 original size:6 final size:6
Alignment explanation
Indices: 30643996--30644040 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
30643986 TCACCGATGA
* * *
30643996 ATAGAT ATAGAT ATAGAT ATAGAT ATAAAT ATATAT ATATAT ATA
1 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATA
30644041 TAAATCCATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (6 bp):
ATAGAT
Found at i:30645392 original size:75 final size:77
Alignment explanation
Indices: 30645264--30645410 Score: 253
Period size: 75 Copynumber: 1.9 Consensus size: 77
30645254 ATTGTACCAA
*
30645264 AAATATATTATACAAAATTTTAAGTTTAATTCAATCATTTGTATTTTAAAAAATAAATATATCA-
1 AAATATATTATACAAAATTTTAAGTTTAACTCAATCATTTGTATTTTAAAAAATAAATATATCAT
30645328 TTTATTATCATC
66 TTTATTATCATC
* *
30645340 AAATATA-TATACAAAATTTTAAGTTTGACTCAATTATTTGTATTTTAAAAAATAAATATATCAT
1 AAATATATTATACAAAATTTTAAGTTTAACTCAATCATTTGTATTTTAAAAAATAAATATATCAT
30645404 TTTATTA
66 TTTATTA
30645411 AGAAGTTAGA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
75 53 0.79
76 14 0.21
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (77 bp):
AAATATATTATACAAAATTTTAAGTTTAACTCAATCATTTGTATTTTAAAAAATAAATATATCAT
TTTATTATCATC
Found at i:30647765 original size:47 final size:47
Alignment explanation
Indices: 30647714--30647808 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
30647704 ACCAGGAGTA
30647714 CTTCTTCCAACACGTTTCATGCATATATCAAGGAAGCCGCTTACATG
1 CTTCTTCCAACACGTTTCATGCATATATCAAGGAAGCCGCTTACATG
30647761 CTTCTTCCAACACGTTTCATGCATATATCAAGGAAGCCGCTTACATG
1 CTTCTTCCAACACGTTTCATGCATATATCAAGGAAGCCGCTTACATG
30647808 C
1 C
30647809 AGGCTCACTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (47 bp):
CTTCTTCCAACACGTTTCATGCATATATCAAGGAAGCCGCTTACATG
Found at i:30650782 original size:42 final size:42
Alignment explanation
Indices: 30650724--30650807 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
30650714 CTTTAGTAGG
* *
30650724 CGGTTCCTGGCTACCATCAGCCCCAAAATTCTCAACTTTACC
1 CGGTTCCTGACCACCATCAGCCCCAAAATTCTCAACTTTACC
* * * *
30650766 CGGTTCCTGACCACCATCTGCCTCAAATTTCTCATCTTTACC
1 CGGTTCCTGACCACCATCAGCCCCAAAATTCTCAACTTTACC
30650808 TAACTCAGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.21, C:0.38, G:0.11, T:0.30
Consensus pattern (42 bp):
CGGTTCCTGACCACCATCAGCCCCAAAATTCTCAACTTTACC
Found at i:30659208 original size:33 final size:33
Alignment explanation
Indices: 30659159--30659256 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 33
30659149 TGGAATGTTG
* *
30659159 TTTGCATCTGTATGGTATACTTTTTAAGTTACC
1 TTTGGATCTGTATGGTATGCTTTTTAAGTTACC
* * *
30659192 TTTGGATCTGTCTGGTATGCTTTTTATGTTA-T
1 TTTGGATCTGTATGGTATGCTTTTTAAGTTACC
* *
30659224 TTTTGATTCTGTATGATATGCTTTTTAAGTTAC
1 TTTGGA-TCTGTATGGTATGCTTTTTAAGTTAC
30659257 ATTGTCACAT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
32 5 0.09
33 49 0.91
ACGTcount: A:0.18, C:0.11, G:0.17, T:0.53
Consensus pattern (33 bp):
TTTGGATCTGTATGGTATGCTTTTTAAGTTACC
Found at i:30660787 original size:19 final size:18
Alignment explanation
Indices: 30660750--30660788 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30660740 TTTTCTTATT
* *
30660750 TTGAAAAAATAATAGAGA
1 TTGAAAAAAAAATAAAGA
30660768 TTGAAAAAAAAAGTAAAGA
1 TTGAAAAAAAAA-TAAAGA
30660787 TT
1 TT
30660789 AGGGTTGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
TTGAAAAAAAAATAAAGA
Found at i:30666609 original size:16 final size:15
Alignment explanation
Indices: 30666584--30666613 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30666574 CTTGGAACAG
30666584 TTTTTTTTTAATATT
1 TTTTTTTTTAATATT
30666599 TTTTATTTTTAATAT
1 TTTT-TTTTTAATAT
30666614 GGATGGATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTTTAATATT
Found at i:30674896 original size:16 final size:17
Alignment explanation
Indices: 30674870--30674905 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
30674860 TCTTAAACCT
30674870 TTTATATTTTTTTATAA
1 TTTATATTTTTTTATAA
30674887 TTTA-ATTTTTTTATAA
1 TTTATATTTTTTTATAA
30674903 TTT
1 TTT
30674906 TAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATATTTTTTTATAA
Found at i:30678626 original size:24 final size:24
Alignment explanation
Indices: 30678530--30678627 Score: 92
Period size: 24 Copynumber: 4.0 Consensus size: 24
30678520 AGTTACCCGT
30678530 TAAGCTCGCATGAGCTTTCTGATT-
1 TAAGCTCGCATGAGCTTTCTG-TTA
** *
30678554 TAAGCTCTTATGAGCTTCCTGTTA
1 TAAGCTCGCATGAGCTTTCTGTTA
* * *
30678578 TTAAGC-CTGGATAAGCTTTCCGTTA
1 -TAAGCTC-GCATGAGCTTTCTGTTA
*
30678603 TAAGCTCACATGAGCTTTCTGTTA
1 TAAGCTCGCATGAGCTTTCTGTTA
30678627 T
1 T
30678628 TTGGCTTGGA
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
23 2 0.03
24 38 0.66
25 18 0.31
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (24 bp):
TAAGCTCGCATGAGCTTTCTGTTA
Found at i:30687681 original size:18 final size:18
Alignment explanation
Indices: 30687658--30687701 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
30687648 AAGTATTTCT
30687658 GAAAGTTTCACCTTGGAA
1 GAAAGTTTCACCTTGGAA
30687676 GAAAGTTTCACCTTGGAA
1 GAAAGTTTCACCTTGGAA
30687694 GAAAGTTT
1 GAAAGTTT
30687702 TTCGATTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (18 bp):
GAAAGTTTCACCTTGGAA
Found at i:30689614 original size:24 final size:24
Alignment explanation
Indices: 30689585--30689640 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
30689575 GAGTTATCTG
30689585 TTAAGCTCGCACGAGCTTTCTGAT
1 TTAAGCTCGCACGAGCTTTCTGAT
* *
30689609 TTAAGCTCGCATGTGCTTTCTGAT
1 TTAAGCTCGCACGAGCTTTCTGAT
30689633 TTAAGCTC
1 TTAAGCTC
30689641 TTATGAGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (24 bp):
TTAAGCTCGCACGAGCTTTCTGAT
Found at i:30689650 original size:24 final size:24
Alignment explanation
Indices: 30689585--30689703 Score: 89
Period size: 24 Copynumber: 4.9 Consensus size: 24
30689575 GAGTTATCTG
* *
30689585 TTAAGCTCGCACGAGCTTTCTGAT
1 TTAAGCTCTCATGAGCTTTCTGAT
* *
30689609 TTAAGCTCGCATGTGCTTTCTGAT
1 TTAAGCTCTCATGAGCTTTCTGAT
* * *
30689633 TTAAGCTCTTATGAGCTTCCTGTT
1 TTAAGCTCTCATGAGCTTTCTGAT
* * **
30689657 ATTAAGC-CTGTATAAGC-TTCCCAT
1 -TTAAGCTCT-CATGAGCTTTCTGAT
*
30689681 TATAAGCTCACATGAGCTTTCTG
1 T-TAAGCTCTCATGAGCTTTCTG
30689704 TTATTTGGCT
Statistics
Matches: 73, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
23 1 0.01
24 56 0.77
25 16 0.22
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.38
Consensus pattern (24 bp):
TTAAGCTCTCATGAGCTTTCTGAT
Found at i:30689683 original size:25 final size:25
Alignment explanation
Indices: 30689633--30689689 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
30689623 GCTTTCTGAT
* **
30689633 TTAAGCTCTTATGAGCTTCCTGTTA
1 TTAAGCTCTTATAAGCTTCCCATTA
30689658 TTAAGC-CTGTATAAGCTTCCCATTA
1 TTAAGCTCT-TATAAGCTTCCCATTA
30689683 -TAAGCTC
1 TTAAGCTC
30689690 ACATGAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (25 bp):
TTAAGCTCTTATAAGCTTCCCATTA
Found at i:30691287 original size:33 final size:33
Alignment explanation
Indices: 30691221--30691289 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
30691211 GAAGACAAAA
*
30691221 ACACTAGTAAAGGGTTTAGATTTTACGACGAAG
1 ACACTAGTAAAGGGTTTAGATTTGACGACGAAG
* * *
30691254 ACACTAGTAAATGGTTTAGATTTGATGATGAAG
1 ACACTAGTAAAGGGTTTAGATTTGACGACGAAG
30691287 ACA
1 ACA
30691290 TGTATCATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (33 bp):
ACACTAGTAAAGGGTTTAGATTTGACGACGAAG
Found at i:30692810 original size:13 final size:14
Alignment explanation
Indices: 30692792--30692825 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
30692782 AACAACCAAA
30692792 AACAATACTT-GTG
1 AACAATACTTCGTG
30692805 AACAATA-TTCGTG
1 AACAATACTTCGTG
30692818 AACAATAC
1 AACAATAC
30692826 CCATGAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 17 0.89
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (14 bp):
AACAATACTTCGTG
Found at i:30697155 original size:87 final size:87
Alignment explanation
Indices: 30697009--30697190 Score: 346
Period size: 87 Copynumber: 2.1 Consensus size: 87
30696999 CTTCATTACA
30697009 ACTTCATCGACAGTGGAACCATTCTCCCCAAGGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
1 ACTTCATCGACAGTGGAACCATTCTCCCCAAGGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
*
30697074 GTCATGGCTTGGCGTCTCTTCG
66 GCCATGGCTTGGCGTCTCTTCG
30697096 ACTTCATCGACAGTGGAACCATTCTCCCCAAGGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
1 ACTTCATCGACAGTGGAACCATTCTCCCCAAGGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
*
30697161 GCCGTGGCTTGGCGTCTCTTCG
66 GCCATGGCTTGGCGTCTCTTCG
30697183 ACTTCATC
1 ACTTCATC
30697191 TTCCGAACTG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 93 1.00
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.30
Consensus pattern (87 bp):
ACTTCATCGACAGTGGAACCATTCTCCCCAAGGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
GCCATGGCTTGGCGTCTCTTCG
Found at i:30701671 original size:27 final size:27
Alignment explanation
Indices: 30701641--30701694 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
30701631 GTTATTTTTC
30701641 AACGCATAGGTGAAAGATCGGATTGAA
1 AACGCATAGGTGAAAGATCGGATTGAA
* *
30701668 AACGCGTAGGTGAAAGATCTGATTGAA
1 AACGCATAGGTGAAAGATCGGATTGAA
30701695 GTTATCGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.20
Consensus pattern (27 bp):
AACGCATAGGTGAAAGATCGGATTGAA
Found at i:30704614 original size:19 final size:21
Alignment explanation
Indices: 30704575--30704617 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
30704565 TTGATTGGCC
*
30704575 AAAATTATTAAGAATTATTTA
1 AAAATTATTAAGAACTATTTA
30704596 AAAATTA-TAA-AACTATTTA
1 AAAATTATTAAGAACTATTTA
30704615 AAA
1 AAA
30704618 TGAATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 3 0.14
21 7 0.33
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAATTATTAAGAACTATTTA
Found at i:30704688 original size:29 final size:28
Alignment explanation
Indices: 30704639--30704697 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
30704629 GCAAAATGTT
*
30704639 ATATAGAAAAATTAAAAATTATTTAAAA
1 ATATAGAAAAATTAAAAATTATTAAAAA
*
30704667 ATATA-AAAACATATAATAATTATTAAAAA
1 ATATAGAAAA-AT-TAAAAATTATTAAAAA
30704696 AT
1 AT
30704698 TTATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 4 0.15
28 7 0.26
29 16 0.59
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
ATATAGAAAAATTAAAAATTATTAAAAA
Found at i:30705509 original size:38 final size:39
Alignment explanation
Indices: 30705449--30705526 Score: 124
Period size: 38 Copynumber: 2.0 Consensus size: 39
30705439 ATCCAACCCA
*
30705449 ACCCAATTACCCAACCTAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCTAATAAAAATAAAACTAAAGTCT
30705488 ACCCAATTA-CCAA-CTCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCCAACCT-AATAAAAATAAAACTAAAGTCT
30705526 A
1 A
30705527 ACTCTAAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
37 2 0.05
38 26 0.70
39 9 0.24
ACGTcount: A:0.51, C:0.26, G:0.03, T:0.21
Consensus pattern (39 bp):
ACCCAATTACCCAACCTAATAAAAATAAAACTAAAGTCT
Found at i:30705677 original size:17 final size:17
Alignment explanation
Indices: 30705657--30705722 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
30705647 TAATTTCAAG
30705657 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
30705674 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
30705692 AGACTTATGTAATGTTTTT
1 A-A-TTATGTAATGTTTTT
*
30705711 AATTAAGTAATG
1 AATTATGTAATG
30705723 ATTTAACCAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 20 0.54
18 4 0.11
19 4 0.11
20 9 0.24
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:30705700 original size:37 final size:37
Alignment explanation
Indices: 30705654--30705725 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
30705644 TGTTAATTTC
* *
30705654 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATGTTTTTAATTAAGTAATGATTCA
*
30705691 AAGACTTATGTAATGTTTTTAATTAAGTAATGATT
1 AAGAATTATGTAATGTTTTTAATTAAGTAATGATT
30705726 TAACCAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (37 bp):
AAGAATTATGTAATGTTTTTAATTAAGTAATGATTCA
Found at i:30705900 original size:12 final size:12
Alignment explanation
Indices: 30705883--30705907 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30705873 AGTAATTTCG
30705883 GGTCGGTTAACC
1 GGTCGGTTAACC
30705895 GGTCGGTTAACC
1 GGTCGGTTAACC
30705907 G
1 G
30705908 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:30711367 original size:32 final size:31
Alignment explanation
Indices: 30711330--30711411 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
30711320 TAAACATTTC
* *
30711330 AAAATGGTCAAATAAGGGCCAAATCTTTTTTT
1 AAAATGCTCAAATAAGGGCCAAAT-TTTTTTA
*
30711362 AAAATGCTCAAATAAGGACCAAATTTTTTTA
1 AAAATGCTCAAATAAGGGCCAAATTTTTTTA
*
30711393 AAAATACTCAAATAAGGGC
1 AAAATGCTCAAATAAGGGC
30711412 TTTTCAAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 23 0.51
32 22 0.49
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (31 bp):
AAAATGCTCAAATAAGGGCCAAATTTTTTTA
Found at i:30719949 original size:23 final size:23
Alignment explanation
Indices: 30719883--30719955 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 23
30719873 ACAGCGTCCT
30719883 GTTATTAGCTC-TCATGAGCTTCCC
1 GTTA-TAGCTCTTCA-GAGCTTCCC
*
30719907 GTTATATGGTTCTTGC-GAGCTTCCC
1 GTTATA--GCTCTT-CAGAGCTTCCC
*
30719932 GTTATAGCTCTTCAGAGCATCCC
1 GTTATAGCTCTTCAGAGCTTCCC
30719955 G
1 G
30719956 ATAGGTTGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
22 1 0.02
23 16 0.39
24 4 0.10
25 18 0.44
26 1 0.02
27 1 0.02
ACGTcount: A:0.16, C:0.27, G:0.21, T:0.36
Consensus pattern (23 bp):
GTTATAGCTCTTCAGAGCTTCCC
Found at i:30725843 original size:25 final size:25
Alignment explanation
Indices: 30725812--30725909 Score: 99
Period size: 25 Copynumber: 3.9 Consensus size: 25
30725802 AATCTCTTTC
* *
30725812 GAGCCATGTAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGA
* *
30725837 GAGCCATATAACGGGAAGCTCTTGC
1 GAGCCATATAACGGGAAGCTCATGA
* **
30725862 GAGCCA-ATTATCGGGAAGCTCCGGA
1 GAGCCATA-TAACGGGAAGCTCATGA
* *
30725887 GAGCCAAATAACGAGAAGCTCAT
1 GAGCCATATAACGGGAAGCTCAT
30725910 AAAAGCCAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
24 1 0.02
25 58 0.97
26 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.29, T:0.17
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGA
Found at i:30725880 original size:50 final size:50
Alignment explanation
Indices: 30725805--30725927 Score: 131
Period size: 50 Copynumber: 2.5 Consensus size: 50
30725795 AATCGAAAAT
* * * * * *
30725805 CTCTTTCGAGCC-ATGTAACGGGAAGCTCATGTGAGCCATATAACGGGAAG
1 CTCTTACGAGCCAAT-TATCGGGAAGCTCAGGAGAGCCAAATAACGAGAAG
* *
30725855 CTCTTGCGAGCCAATTATCGGGAAGCTCCGGAGAGCCAAATAACGAGAAG
1 CTCTTACGAGCCAATTATCGGGAAGCTCAGGAGAGCCAAATAACGAGAAG
* **
30725905 CTCATAAAAGCCAATTATCGGGA
1 CTCTTACGAGCCAATTATCGGGA
30725928 CACTCATAAG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 59 0.97
51 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.20
Consensus pattern (50 bp):
CTCTTACGAGCCAATTATCGGGAAGCTCAGGAGAGCCAAATAACGAGAAG
Found at i:30727400 original size:7 final size:7
Alignment explanation
Indices: 30727390--30727414 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30727380 TAAATTATAA
30727390 AAAAGTG
1 AAAAGTG
30727397 AAAAGTG
1 AAAAGTG
30727404 AAAAGTG
1 AAAAGTG
30727411 AAAA
1 AAAA
30727415 TATGGAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (7 bp):
AAAAGTG
Found at i:30727964 original size:23 final size:23
Alignment explanation
Indices: 30727938--30728000 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
30727928 CGTTATAATT
30727938 TGCACTTCGGTGCCCCTGACATA
1 TGCACTTCGGTGCCCCTGACATA
*
30727961 TGCAC-TCTGGTGCCCCTAACATA
1 TGCACTTC-GGTGCCCCTGACATA
**
30727984 -GCACTTATGTGCCCCTG
1 TGCACTTCGGTGCCCCTG
30728001 TTTATTCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.17, C:0.35, G:0.21, T:0.27
Consensus pattern (23 bp):
TGCACTTCGGTGCCCCTGACATA
Done.