Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 52 of 193
Found at i:16064799 original size:51 final size:48
Alignment explanation
Indices: 16064655--16064806 Score: 123
Period size: 51 Copynumber: 3.0 Consensus size: 48
16064645 CACTAAAACT
* * *
16064655 TTAGGGAGATAAAGATTTGCTTTTGTAGC-TCTATCCGACCCACTACAAC
1 TTAGGGAAATAAAGATTTGC-TTTGTAGCTTC-ATCTGACCCACTGCAAC
* * * *
16064704 TTCAAGGG-TAT-AAGATTTGGTATTGTAG-TCTCATCTTACTCCACTGTAAC
1 TT--AGGGAAATAAAGATTTGCT-TTGTAGCT-TCATCTGAC-CCACTGCAAC
16064754 TATAGGGAAATAAAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAAC
1 T-TAGGGAAATAAAGATTTGCTT-TGTAGCTTC-ATCTGACCCACTGCAAC
16064805 TT
1 TT
16064807 CAAGAGTATA
Statistics
Matches: 81, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
48 1 0.01
49 25 0.31
50 17 0.21
51 31 0.38
52 7 0.09
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (48 bp):
TTAGGGAAATAAAGATTTGCTTTGTAGCTTCATCTGACCCACTGCAAC
Found at i:16065035 original size:305 final size:303
Alignment explanation
Indices: 16064356--16065128 Score: 1020
Period size: 304 Copynumber: 2.5 Consensus size: 303
16064346 CATATTCAAA
* * *
16064356 GAGAT-AAGATTTGCTTTTGTAGCTTCAATCTGACCCACAGCAACTTC-AGAGGTATAAGATTTG
1 GAGATAAAGATTTGCTTTTGTAGC-TCTATCCGACCCACTGCAACTTCAAG-GGTATAAGATTTG
* *
16064419 GT-TCTGTAG-CTTTATCTTGCTCCATTGTAACTTTAAGGAAATAAAGATTTGCTTCTGTAGCTT
64 GTAT-TGTAGTC-TCATCTTGCTCCATTGTAAC-TTAGGGAAATAAAGATTTGCTTCTGTAGCTT
** * *
16064482 CAATCTGACCCACTGCAACTTCTGGAATATAGGATTTGACATTTTGTAGTCTTATCTTGCTTTAC
126 CAATCTGACCCACTGCAACTTCAAGAATATAGGATTTGACATTTTGTAGTCTCATATTGCTTTAC
* * * * *
16064547 TGCAACTTCAAAGAGATAAAGATTTGCCACCGTAATTTTAGTCCAATCCATTGCTACTTCAAGGA
191 TACAACTTCAAAGAGATAAAGATTTGACACCGTAATTTTAGTCCAATCCACTCCAACTTCAAGGA
**
16064612 TATTGGACTTGATGTCATAACTTCATCTTGCTCCACTAAAACTTTAGG
256 TATAAGACTTGATGTCATAACTTCATCTTGCTCCACTAAAACTTTAGG
*
16064660 GAGATAAAGATTTGCTTTTGTAGCTCTATCCGACCCACTACAACTTCAAGGGTATAAGATTTGGT
1 GAGATAAAGATTTGCTTTTGTAGCTCTATCCGACCCACTGCAACTTCAAGGGTATAAGATTTGGT
* *
16064725 ATTGTAGTCTCATCTTACTCCACTGTAACTATAGGGAAATAAAGATTTGCTTCTGTAGCTTCAAT
66 ATTGTAGTCTCATCTTGCTCCATTGTAACT-TAGGGAAATAAAGATTTGCTTCTGTAGCTTCAAT
* *
16064790 CTGACCCACTGCAACTTCAAGAGTATAGGATTTGACGTTTTGTAGTCTCATATTG-TTCTACTAC
130 CTGACCCACTGCAACTTCAAGAATATAGGATTTGACATTTTGTAGTCTCATATTGCTT-TACTAC
* * * *
16064854 AACTTCAGAGAGATAAAGATTTGACATCGTAATTTTCAGTCCAATCCACTCCAACTTTAGGGATA
194 AACTTCAAAGAGATAAAGATTTGACACCGTAATTTT-AGTCCAATCCACTCCAACTTCAAGGATA
* * * * *
16064919 TAAGATTTGATGTCATAACTTTATCTTGCTTCATTATAACTTTAGG
258 TAAGACTTGATGTCATAACTTCATCTTGCTCCACTAAAACTTTAGG
*
16064965 GAGATAAAGATTTGCTTTTGTAGCTCTATCCGACCCACTGCAACTTCAAGGGTATAAGATTTCGT
1 GAGATAAAGATTTGCTTTTGTAGCTCTATCCGACCCACTGCAACTTCAAGGGTATAAGATTTGGT
* * * * * * *
16065030 ATTGTAGTCTCATCTTGCTCTATTGCAACTTCAGAGAGATAAAGATTTGCTAAC-GTAGTTTTAA
66 ATTGTAGTCTCATCTTGCTCCATTGTAACTT-AGGGAAATAAAGATTTGCT-TCTGTAGCTTCAA
* * * * *
16065094 TCCGATCC-CTACAACTTCAAGGATATAGGACTTGA
129 TCTGACCCACTGCAACTTCAAGAATATAGGATTTGA
16065129 TGTCATACTG
Statistics
Matches: 413, Mismatches: 47, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
303 3 0.01
304 205 0.50
305 204 0.49
306 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (303 bp):
GAGATAAAGATTTGCTTTTGTAGCTCTATCCGACCCACTGCAACTTCAAGGGTATAAGATTTGGT
ATTGTAGTCTCATCTTGCTCCATTGTAACTTAGGGAAATAAAGATTTGCTTCTGTAGCTTCAATC
TGACCCACTGCAACTTCAAGAATATAGGATTTGACATTTTGTAGTCTCATATTGCTTTACTACAA
CTTCAAAGAGATAAAGATTTGACACCGTAATTTTAGTCCAATCCACTCCAACTTCAAGGATATAA
GACTTGATGTCATAACTTCATCTTGCTCCACTAAAACTTTAGG
Found at i:16065074 original size:202 final size:202
Alignment explanation
Indices: 16064750--16065135 Score: 526
Period size: 202 Copynumber: 1.9 Consensus size: 202
16064740 TACTCCACTG
*
16064750 TAACTATAGGGAAATAAAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACTTCAAGAGTA
1 TAACTATAGGGAAATAAAGATTTGCTTCTGTAGCTTCAATCCGACCCACTGCAACTTCAAGAGTA
* * *
16064815 TAGGATTTGACGTTTTGTAGTCTCATATTGTTCTACTACAACTTCAGAGAGATAAAGATTTGAC-
66 TAAGATTT-ACGTATTGTAGTCTCATATTGCTCTACTACAACTTCAGAGAGATAAAGATTTG-CT
* * * * * *
16064879 ATCGTAATTTTCAGTCCAATCCACTCCAACTTTAGGGATATAAGATTTGATGTCATAACTTTATC
129 AACGTAATTTT-AATCCAATCC-CTACAACTTCAAGGATATAAGACTTGATGTCATAACTTTATC
16064944 TTGCTTCATTA
192 TTGCTTCATTA
* * * * *
16064955 TAACTTTAGGGAGATAAAGATTTGCTTTTGTAGC-TCTATCCGACCCACTGCAACTTCAAGGGTA
1 TAACTATAGGGAAATAAAGATTTGCTTCTGTAGCTTCAATCCGACCCACTGCAACTTCAAGAGTA
* * *
16065019 TAAGATTT-CGTATTGTAGTCTCATCTTGCTCTATTGCAACTTCAGAGAGATAAAGATTTGCTAA
66 TAAGATTTACGTATTGTAGTCTCATATTGCTCTACTACAACTTCAGAGAGATAAAGATTTGCTAA
* * *
16065083 CGTAGTTTTAATCCGATCCCTACAACTTCAAGGATATAGGACTTGATGTCATA
131 CGTAATTTTAATCCAATCCCTACAACTTCAAGGATATAAGACTTGATGTCATA
16065136 CTGATCCCTT
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
200 29 0.18
201 9 0.06
202 56 0.35
204 34 0.21
205 31 0.19
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (202 bp):
TAACTATAGGGAAATAAAGATTTGCTTCTGTAGCTTCAATCCGACCCACTGCAACTTCAAGAGTA
TAAGATTTACGTATTGTAGTCTCATATTGCTCTACTACAACTTCAGAGAGATAAAGATTTGCTAA
CGTAATTTTAATCCAATCCCTACAACTTCAAGGATATAAGACTTGATGTCATAACTTTATCTTGC
TTCATTA
Found at i:16074249 original size:3 final size:3
Alignment explanation
Indices: 16074241--16074272 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
16074231 GCTACCTTGG
*
16074241 TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
16074273 CTTGGGCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:16081541 original size:24 final size:24
Alignment explanation
Indices: 16081514--16081568 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
16081504 ATAATCAATT
**
16081514 CATTTTATATTTCAGTTGCACTGA
1 CATTTTATATCACAGTTGCACTGA
* *
16081538 CATTTTGTATCACATTTGCACTGA
1 CATTTTATATCACAGTTGCACTGA
16081562 CGATTTT
1 C-ATTTT
16081569 TACTCTTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (24 bp):
CATTTTATATCACAGTTGCACTGA
Found at i:16084533 original size:3 final size:3
Alignment explanation
Indices: 16084525--16084553 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16084515 TGAAGATTCC
16084525 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
16084554 GGAAGAGATG
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:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:16089321 original size:16 final size:16
Alignment explanation
Indices: 16089252--16089323 Score: 64
Period size: 16 Copynumber: 4.7 Consensus size: 16
16089242 AGATTAGTAA
* *
16089252 TTTTATATACATA-AT
1 TTTTATACATATATAT
*
16089267 TTTTA-ACATTGTATAT
1 TTTTATACA-TATATAT
16089283 TTTT-TACATAT-T-T
1 TTTTATACATATATAT
16089296 TTTATATACATATATAT
1 TTT-TATACATATATAT
16089313 TTTTATACATA
1 TTTTATACATA
16089324 GATTAGTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
13 4 0.09
14 4 0.09
15 16 0.35
16 18 0.39
17 4 0.09
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (16 bp):
TTTTATACATATATAT
Found at i:16089386 original size:21 final size:22
Alignment explanation
Indices: 16089362--16089411 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 22
16089352 TTTATATATC
*
16089362 TATACATATACAC-TATTATTT
1 TATACATATACACATACTATTT
*
16089383 TAT--ATTTACACATACTATTT
1 TATACATATACACATACTATTT
16089403 T-TACATATA
1 TATACATATA
16089412 TACTGATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
19 8 0.35
20 8 0.35
21 7 0.30
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (22 bp):
TATACATATACACATACTATTT
Found at i:16094701 original size:24 final size:24
Alignment explanation
Indices: 16094667--16094721 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
16094657 ACAATCAATT
*
16094667 CATTTTATATTTCAGTTGCACTGA
1 CATTTTATATTACAGTTGCACTGA
* *
16094691 CATTTTGTATTACATTTGCACTGA
1 CATTTTATATTACAGTTGCACTGA
16094715 CAATTTT
1 C-ATTTT
16094722 TACTCTTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.47
Consensus pattern (24 bp):
CATTTTATATTACAGTTGCACTGA
Found at i:16098927 original size:23 final size:22
Alignment explanation
Indices: 16098891--16098934 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
16098881 AAAATATTTC
*
16098891 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
16098914 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
16098935 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:16119514 original size:36 final size:36
Alignment explanation
Indices: 16119465--16119568 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
16119455 TGGTAACAGG
16119465 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
* * * *
16119501 CATGACCTCTGGGTCAATAAGAAGTAAAACGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
* *
16119537 TATGACCTTTGGGTCAATGGGGAGTAAAATGA
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGA
16119569 ATAACGAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
Found at i:16119653 original size:18 final size:18
Alignment explanation
Indices: 16119630--16119669 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
16119620 TGTTCACCAC
16119630 ATGTTATTCGGTAAATTG
1 ATGTTATTCGGTAAATTG
*
16119648 ATGTTATTCGTTAAATTG
1 ATGTTATTCGGTAAATTG
16119666 ATGT
1 ATGT
16119670 ACCTTGCGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (18 bp):
ATGTTATTCGGTAAATTG
Found at i:16128331 original size:15 final size:15
Alignment explanation
Indices: 16128313--16128397 Score: 64
Period size: 15 Copynumber: 5.7 Consensus size: 15
16128303 TCGTAACACG
16128313 AGTGTTCGCAACATC
1 AGTGTTCGCAACATC
* *** *
16128328 AGTGTTCTCATTGTG
1 AGTGTTCGCAACATC
* *
16128343 TGTGTTCGCAACATG
1 AGTGTTCGCAACATC
*
16128358 AGTGTTCG-AAGATCC
1 AGTGTTCGCAACAT-C
*
16128373 AGTGTTCGCAACATT
1 AGTGTTCGCAACATC
*
16128388 AGTGCTCGCA
1 AGTGTTCGCA
16128398 TTATTCATGT
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
14 4 0.08
15 44 0.85
16 4 0.08
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (15 bp):
AGTGTTCGCAACATC
Found at i:16138856 original size:17 final size:16
Alignment explanation
Indices: 16138834--16138875 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 16
16138824 TGTCAATATA
16138834 TTTCTTTTCTTTTCTCT
1 TTTCTTTTC-TTTCTCT
16138851 TTTCTTCTTCTTTCTCT
1 TTTCTT-TTCTTTCTCT
16138868 TTTCTTTT
1 TTTCTTTT
16138876 TTTGTGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.08
17 19 0.79
18 3 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTTTTCTTTCTCT
Found at i:16160834 original size:16 final size:16
Alignment explanation
Indices: 16160813--16160855 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
16160803 GTCATTACAT
16160813 TTTTATTGTCTCT-GCA
1 TTTTATTGT-TCTAGCA
16160829 TTTTATTTGTTCTAGCA
1 TTTTA-TTGTTCTAGCA
16160846 TTTGTATTGT
1 TTT-TATTGT
16160856 AGTTGAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.33
17 14 0.58
18 2 0.08
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.60
Consensus pattern (16 bp):
TTTTATTGTTCTAGCA
Found at i:16163080 original size:24 final size:23
Alignment explanation
Indices: 16163033--16163081 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
16163023 ACAATCAATC
* **
16163033 CATTTTCTATTAATTTACTTTGA
1 CATTTTATATTAATTTACACTGA
16163056 CATTTTATATTACATTTACACTGA
1 CATTTTATATTA-ATTTACACTGA
16163080 CA
1 CA
16163082 AGATTTAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (23 bp):
CATTTTATATTAATTTACACTGA
Found at i:16168509 original size:20 final size:21
Alignment explanation
Indices: 16168482--16168534 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
16168472 CAGTCGAAAC
16168482 CTTTTTTTTTTGAAGTCTAGA
1 CTTTTTTTTTTGAAGTCTAGA
16168503 CTTTTTTTTTTGAAGTCTAGA
1 CTTTTTTTTTTGAAGTCTAGA
16168524 CTTTTTTTTTT
1 CTTTTTTTTTT
16168535 AAAAAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.09, G:0.11, T:0.64
Consensus pattern (21 bp):
CTTTTTTTTTTGAAGTCTAGA
Found at i:16169446 original size:31 final size:31
Alignment explanation
Indices: 16169394--16169454 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
16169384 AATAATCACA
* *
16169394 ATAATAATATAATAGTGAAATAATATAAAAT
1 ATAATAATATAATAATGAAATAAAATAAAAT
*
16169425 ATAATAATACT-ATAATTAAATAAAATAAAA
1 ATAATAATA-TAATAATGAAATAAAATAAAA
16169455 AGAAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (31 bp):
ATAATAATATAATAATGAAATAAAATAAAAT
Found at i:16169537 original size:8 final size:8
Alignment explanation
Indices: 16169516--16169587 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 8
16169506 GAAAAATCAT
16169516 AAATGAAAA
1 AAAT-AAAA
16169525 AAATAAAA
1 AAATAAAA
*
16169533 CAATAAAA
1 AAATAAAA
* *
16169541 TGAATATAA
1 -AAATAAAA
16169550 AAATAATAGA
1 AAATAA-A-A
*
16169560 ATATAAAA
1 AAATAAAA
*
16169568 TAAATACAA
1 -AAATAAAA
16169577 AAATAAAA
1 AAATAAAA
16169585 AAA
1 AAA
16169588 GGTAGTCAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
8 26 0.52
9 18 0.36
10 6 0.12
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (8 bp):
AAATAAAA
Found at i:16169562 original size:25 final size:27
Alignment explanation
Indices: 16169514--16169584 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
16169504 GGGAAAAATC
*
16169514 ATAAATGAAAAAAATAAAAC-A-ATAAA
1 ATAAAT-ACAAAAATAAAACAATATAAA
* * * *
16169540 ATGAATATAAAAATAATAGAATATAAA
1 ATAAATACAAAAATAAAACAATATAAA
16169567 ATAAATACAAAAATAAAA
1 ATAAATACAAAAATAAAA
16169585 AAAGGTAGTC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 10 0.28
26 6 0.17
27 20 0.56
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (27 bp):
ATAAATACAAAAATAAAACAATATAAA
Found at i:16170116 original size:28 final size:25
Alignment explanation
Indices: 16170076--16170133 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
16170066 AAGTCAATTT
*
16170076 TTTTTGAAAAAAAATTCATTTCTTCTTC
1 TTTTT-AAAAAAAAATC-TTT-TTCTTC
*
16170104 TTTTTAAAAAAAAATCTTTTTTTTC
1 TTTTTAAAAAAAAATCTTTTTCTTC
16170129 TTTTT
1 TTTTT
16170134 TTTTTTGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 10 0.36
26 3 0.11
27 10 0.36
28 5 0.18
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTTTAAAAAAAAATCTTTTTCTTC
Found at i:16170135 original size:28 final size:28
Alignment explanation
Indices: 16170073--16170136 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
16170063 TAAAAGTCAA
*
16170073 TTTTTTTTGAAAAAAAATTCATTTCTTC
1 TTTTTTTTAAAAAAAAATTCATTTCTTC
* * *
16170101 TTCTTTTTAAAAAAAAA-TCTTTTTTTTC
1 TTTTTTTTAAAAAAAAATTC-ATTTCTTC
16170129 TTTTTTTT
1 TTTTTTTT
16170137 TTTGTCTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTTTTTAAAAAAAAATTCATTTCTTC
Found at i:16179396 original size:23 final size:20
Alignment explanation
Indices: 16179353--16179396 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 20
16179343 GGAAAAGATT
*
16179353 GGGAAGAGAGAAAAATAAAA
1 GGGAAGAGAAAAAAATAAAA
16179373 GGGAAGAAGAAAAGAAATATAAA
1 GGGAAG-AGAAAA-AAATA-AAA
16179396 G
1 G
16179397 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 5 0.25
23 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.07
Consensus pattern (20 bp):
GGGAAGAGAAAAAAATAAAA
Found at i:16179507 original size:21 final size:22
Alignment explanation
Indices: 16179474--16179517 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
16179464 AAATTACGTT
* *
16179474 AAAAGAAATGGAGAAGG-GAAG
1 AAAACAAAAGGAGAAGGAGAAG
16179495 AAAACAAAAGGAGAAGGAGAAG
1 AAAACAAAAGGAGAAGGAGAAG
16179517 A
1 A
16179518 GAATGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.02, G:0.34, T:0.02
Consensus pattern (22 bp):
AAAACAAAAGGAGAAGGAGAAG
Found at i:16180354 original size:15 final size:16
Alignment explanation
Indices: 16180326--16180355 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16180316 AAATTTTTTC
16180326 GAATTTTTATATATTA
1 GAATTTTTATATATTA
16180342 GAATTTTTA-ATATT
1 GAATTTTTATATATT
16180356 TTTAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
GAATTTTTATATATTA
Found at i:16184074 original size:45 final size:45
Alignment explanation
Indices: 16184010--16184100 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
16184000 AAATTATTAT
* * *
16184010 ACTGGCTCGAAAGTGCGATATATTATATTGGGAGCGATATACTGA
1 ACTGGCTCGAAAGAGCGATATACTATACTGGGAGCGATATACTGA
* * *
16184055 ACTGGCTCGTAAGAGCGATATACTGTACTGGGATCGATATACTGA
1 ACTGGCTCGAAAGAGCGATATACTATACTGGGAGCGATATACTGA
16184100 A
1 A
16184101 TGACTCATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (45 bp):
ACTGGCTCGAAAGAGCGATATACTATACTGGGAGCGATATACTGA
Found at i:16184139 original size:19 final size:19
Alignment explanation
Indices: 16184115--16184155 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
16184105 TCATAAAAAT
*
16184115 GATACTGGCTCGTAATAGC
1 GATACTGGCTCGTAAGAGC
16184134 GATACTGGCTCGTAAGAGC
1 GATACTGGCTCGTAAGAGC
16184153 GAT
1 GAT
16184156 TAACTGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (19 bp):
GATACTGGCTCGTAAGAGC
Found at i:16184234 original size:35 final size:36
Alignment explanation
Indices: 16184167--16184239 Score: 96
Period size: 35 Copynumber: 2.0 Consensus size: 36
16184157 AACTGATTGG
*
16184167 GCTCGTATGAGCAAAATTTTACTGAGAGACTTGAAGA
1 GCTCGTATGAGCAAAA-TTTACTGAGAAACTTGAAGA
*
16184204 GCTCGTATGAGCTAAA-TTACT-AGGAAACTTGAAGA
1 GCTCGTATGAGCAAAATTTACTGA-GAAACTTGAAGA
16184239 G
1 G
16184240 ATTGTTTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 1 0.03
35 17 0.52
37 15 0.45
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.26
Consensus pattern (36 bp):
GCTCGTATGAGCAAAATTTACTGAGAAACTTGAAGA
Found at i:16185695 original size:25 final size:25
Alignment explanation
Indices: 16185667--16185789 Score: 131
Period size: 25 Copynumber: 4.9 Consensus size: 25
16185657 AGATGGTTAA
*
16185667 CGCTC-TAGCGAGCCAAACAAAATAT
1 CGCTCTTA-CGAGCCAAACAGAATAT
*
16185692 CGCTCTTACGAGCCAAACAGAGTAT
1 CGCTCTTACGAGCCAAACAGAATAT
* *
16185717 CGCTCTTACGAGCTAGACAGAATAT
1 CGCTCTTACGAGCCAAACAGAATAT
* * * * *
16185742 CGCTCTTACAAACCATATAGAGTAT
1 CGCTCTTACGAGCCAAACAGAATAT
* *
16185767 CGCTCTTACGAGCTAGACAGAAT
1 CGCTCTTACGAGCCAAACAGAAT
16185790 TTCTTCATCG
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
25 78 0.98
26 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (25 bp):
CGCTCTTACGAGCCAAACAGAATAT
Found at i:16185780 original size:50 final size:50
Alignment explanation
Indices: 16185687--16185789 Score: 170
Period size: 50 Copynumber: 2.1 Consensus size: 50
16185677 AGCCAAACAA
* *
16185687 AATATCGCTCTTACGAGCCAAACAGAGTATCGCTCTTACGAGCTAGACAG
1 AATATCGCTCTTACAAACCAAACAGAGTATCGCTCTTACGAGCTAGACAG
* *
16185737 AATATCGCTCTTACAAACCATATAGAGTATCGCTCTTACGAGCTAGACAG
1 AATATCGCTCTTACAAACCAAACAGAGTATCGCTCTTACGAGCTAGACAG
16185787 AAT
1 AAT
16185790 TTCTTCATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (50 bp):
AATATCGCTCTTACAAACCAAACAGAGTATCGCTCTTACGAGCTAGACAG
Found at i:16211667 original size:275 final size:275
Alignment explanation
Indices: 16211176--16211729 Score: 930
Period size: 275 Copynumber: 2.0 Consensus size: 275
16211166 TGTTCCAAAA
*
16211176 GGACATATGAACGTTGTCTTTGCTTGATCTTCCGGCATAATGACTATTTGGTTGTATCCAGAGTA
1 GGACATATGAACGTTGTCTTTGCTTGACCTTCCGGCATAATGACTATTTGGTTGTATCCAGAGTA
* * *
16211241 GCCATCCAGGAAGCAATAATAGGCTTTACCAGTTAGCCTATCTAGCATCTGATCGATGGAAGGTA
66 GCCATCCAAGAAGCAATAATAGGCTTTACCAGCTAGCCTATCTAGCATCTGATCGATGAAAGGTA
* *
16211306 GTGGAAAATGATCTTTCTTTGTAGCCACATTCAATCGCCTGTAATCCATGCATACTCGCCATCCA
131 GTGGAAAATGATCTTTCTTTGTAGCCACATTCAATCACCTATAATCCATGCATACTCGCCATCCA
* *
16211371 ATTGCGATGCGAGTAGGGATTAACTCATTCTTTTCATTGGTCAAGATTGTGAAACCACT-TTTTT
196 ATTGCGATACGAGTAGGGATTAACTCATTCTTTTCATTGGTC-AGACTGTGAAACCACTCTTTTT
16211435 AGGCACACATTGAACG
260 AGGCACACATTGAACG
** *
16211451 GGACATATGAACGTTGTCTTTGCTTGACCTTCCGGTGTAATGGCTATTTGGTTGTATCCAGAGTA
1 GGACATATGAACGTTGTCTTTGCTTGACCTTCCGGCATAATGACTATTTGGTTGTATCCAGAGTA
16211516 GCCATCCAAGAAGCAATAATAGGCTTTACCAGCTAGCCTATCTAGCATCTGATCGATGAAAGGTA
66 GCCATCCAAGAAGCAATAATAGGCTTTACCAGCTAGCCTATCTAGCATCTGATCGATGAAAGGTA
* * **
16211581 GTGGAAAATGGTCTTTCTTTGTGGCCGTATTCAATCACCTATAATCCATGCATACTCGCCATCCA
131 GTGGAAAATGATCTTTCTTTGTAGCCACATTCAATCACCTATAATCCATGCATACTCGCCATCCA
* * *
16211646 GTTGCGATACGAGTAGGGATTAACTCGTTCTTTTCATTGGTCCGACTGTGAAACCACTCTTTTTA
196 ATTGCGATACGAGTAGGGATTAACTCATTCTTTTCATTGGTCAGACTGTGAAACCACTCTTTTTA
16211711 GGCACACATTGAACG
261 GGCACACATTGAACG
16211726 GGAC
1 GGAC
16211730 TTACCCAATT
Statistics
Matches: 260, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
274 14 0.05
275 246 0.95
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (275 bp):
GGACATATGAACGTTGTCTTTGCTTGACCTTCCGGCATAATGACTATTTGGTTGTATCCAGAGTA
GCCATCCAAGAAGCAATAATAGGCTTTACCAGCTAGCCTATCTAGCATCTGATCGATGAAAGGTA
GTGGAAAATGATCTTTCTTTGTAGCCACATTCAATCACCTATAATCCATGCATACTCGCCATCCA
ATTGCGATACGAGTAGGGATTAACTCATTCTTTTCATTGGTCAGACTGTGAAACCACTCTTTTTA
GGCACACATTGAACG
Found at i:16222275 original size:23 final size:23
Alignment explanation
Indices: 16222230--16222275 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
16222220 AATATCACTC
* *
16222230 TTACGAGCCAAGCAGAGTCTCTT
1 TTACGAGCCAAGCAGAATATCTT
16222253 TTACGAGCC-AGACAGAATATCTT
1 TTACGAGCCAAG-CAGAATATCTT
16222276 CGTCGTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (23 bp):
TTACGAGCCAAGCAGAATATCTT
Found at i:16230042 original size:35 final size:36
Alignment explanation
Indices: 16229974--16230046 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 36
16229964 TACTGACTGG
* *
16229974 GCTCGTATGAGCTAAATTTTACTAGGAGACTTGAAGA
1 GCTCATATGAGCTAAA-TTTACTAGGAAACTTGAAGA
*
16230011 GCTCATATGAGCTAAA-TTATTAGGAAACTTGAAGA
1 GCTCATATGAGCTAAATTTACTAGGAAACTTGAAGA
16230046 G
1 G
16230047 ATCGTTTGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 18 0.55
37 15 0.45
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (36 bp):
GCTCATATGAGCTAAATTTACTAGGAAACTTGAAGA
Found at i:16239618 original size:21 final size:21
Alignment explanation
Indices: 16239594--16239637 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
16239584 ATTTGTGATA
*
16239594 CTTCTACCGATACAAGTCATG
1 CTTCTACCGATACAAGCCATG
*
16239615 CTTCTACTGATACAAGCCATG
1 CTTCTACCGATACAAGCCATG
16239636 CT
1 CT
16239638 ACTCTCGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.30
Consensus pattern (21 bp):
CTTCTACCGATACAAGCCATG
Found at i:16239647 original size:21 final size:22
Alignment explanation
Indices: 16239597--16239648 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
16239587 TGTGATACTT
* *
16239597 CTAC-CGATACAAGTCATGCTT
1 CTACTCGATACAAGCCATGCTA
16239618 CTACT-GATACAAGCCATGCTA
1 CTACTCGATACAAGCCATGCTA
16239639 CT-CTCGATAC
1 CTACTCGATAC
16239649 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (22 bp):
CTACTCGATACAAGCCATGCTA
Found at i:16240423 original size:41 final size:41
Alignment explanation
Indices: 16240352--16240534 Score: 240
Period size: 41 Copynumber: 4.4 Consensus size: 41
16240342 CTTTCTGAGT
* ** *
16240352 CATGAGTCTTCCTTTTTAACATAATCTCATGCTTATCCCGAGA
1 CATGAGTCTTCC--TTTAATATACCCTCATGCTCATCCCGAGA
* *
16240395 CATGAGTCTTCCTTTAATATCCCCTCATGCTCATCCCAAGA
1 CATGAGTCTTCCTTTAATATACCCTCATGCTCATCCCGAGA
*
16240436 CATGAGTATTCCTTTAATATACCCTCATGCTCATCCCGAGA
1 CATGAGTCTTCCTTTAATATACCCTCATGCTCATCCCGAGA
* * *
16240477 CATGAGTCTTCCTTTAATTTACCCTTATACTCATCCCGAGA
1 CATGAGTCTTCCTTTAATATACCCTCATGCTCATCCCGAGA
*
16240518 TATGAGTCTTCCATTTA
1 CATGAGTCTTCC-TTTA
16240535 TACATCAAGA
Statistics
Matches: 125, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
41 109 0.87
42 4 0.03
43 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.36
Consensus pattern (41 bp):
CATGAGTCTTCCTTTAATATACCCTCATGCTCATCCCGAGA
Found at i:16244582 original size:21 final size:21
Alignment explanation
Indices: 16244558--16244623 Score: 132
Period size: 21 Copynumber: 3.1 Consensus size: 21
16244548 TTGAATCAAG
16244558 CTGCATCGATCTACTCTTACT
1 CTGCATCGATCTACTCTTACT
16244579 CTGCATCGATCTACTCTTACT
1 CTGCATCGATCTACTCTTACT
16244600 CTGCATCGATCTACTCTTACT
1 CTGCATCGATCTACTCTTACT
16244621 CTG
1 CTG
16244624 AAATCCAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (21 bp):
CTGCATCGATCTACTCTTACT
Found at i:16245999 original size:21 final size:21
Alignment explanation
Indices: 16245975--16246029 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
16245965 ACTTGTGATA
16245975 CTTCTATCGATACAAGTCATG
1 CTTCTATCGATACAAGTCATG
*
16245996 CTTCTACCGATACAAGTCATG
1 CTTCTATCGATACAAGTCATG
*
16246017 CTACTATCGATAC
1 CTTCTATCGATAC
16246030 TAAAACCTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (21 bp):
CTTCTATCGATACAAGTCATG
Found at i:16246705 original size:42 final size:42
Alignment explanation
Indices: 16246649--16246888 Score: 135
Period size: 41 Copynumber: 5.7 Consensus size: 42
16246639 CACAAAACAA
** *
16246649 CCGAGTCATAAGTCTTCCTTTAAACGTAATCTCATGCTCATT
1 CCGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATT
* * ** *
16246691 CTGAGTCACGAGTCTTCCTTTAAAACATAACCTCACACTCTTT
1 CCGAGTCACGAGTCTTCCTTT-AAACATAATCTCATGCTCATT
* * * * *
16246734 CCGAGTCATGAGTTTTCCTTTTTAACATAATCTCATGCTTATC
1 CCGAGTCACGAGTCTTCC-TTTAAACATAATCTCATGCTCATT
* * * * * ***
16246777 CCGAGACATGAATCTT-CTTTTAATATCCCCTCATGCTCA-T
1 CCGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATT
* * * * *** *
16246817 CCTGAGACATGAGTCTT-CTTTTAATATCCCCTCATGCTCATC
1 CC-GAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATT
* * *
16246859 CCGAGACATGAGTCTTCCATTTATACATAA
1 CCGAGTCACGAGTCTTCC-TTTAAACATAA
16246889 AGAGATTCAA
Statistics
Matches: 158, Mismatches: 34, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
40 2 0.01
41 67 0.42
42 22 0.14
43 64 0.41
44 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (42 bp):
CCGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATT
Found at i:16246781 original size:43 final size:43
Alignment explanation
Indices: 16246649--16246888 Score: 152
Period size: 43 Copynumber: 5.7 Consensus size: 43
16246639 CACAAAACAA
* * *
16246649 CCGAGTCATAAGTCTTCC-TTTAAACGTAATCTCATGCTCATT
1 CCGAGTCATGAGTCTTCCTTTTAAACATAATCTCATGCTTATT
* * * * **
16246691 CTGAGTCACGAGTCTTCCTTTAAAACATAACCTCACACTCT-TT
1 CCGAGTCATGAGTCTTCCTTTTAAACATAATCTCATGCT-TATT
* * *
16246734 CCGAGTCATGAGTTTTCCTTTTTAACATAATCTCATGCTTATC
1 CCGAGTCATGAGTCTTCCTTTTAAACATAATCTCATGCTTATT
* * * *** *
16246777 CCGAGACATGAATCTT-CTTTT-AATATCCCCTCATGCTCA-T
1 CCGAGTCATGAGTCTTCCTTTTAAACATAATCTCATGCTTATT
* * *** * *
16246817 CCTGAGACATGAGTCTT-CTTTT-AATATCCCCTCATGCTCATC
1 CC-GAGTCATGAGTCTTCCTTTTAAACATAATCTCATGCTTATT
* * *
16246859 CCGAGACATGAGTCTTCCATTTATACATAA
1 CCGAGTCATGAGTCTTCCTTTTAAACATAA
16246889 AGAGATTCAA
Statistics
Matches: 157, Mismatches: 34, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
40 2 0.01
41 63 0.40
42 27 0.17
43 65 0.41
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (43 bp):
CCGAGTCATGAGTCTTCCTTTTAAACATAATCTCATGCTTATT
Found at i:16246810 original size:41 final size:41
Alignment explanation
Indices: 16246765--16246875 Score: 195
Period size: 41 Copynumber: 2.7 Consensus size: 41
16246755 TTAACATAAT
* *
16246765 CTCATGCTTATCCCGAGACATGAATCTTCTTTTAATATCCC
1 CTCATGCTCATCCCGAGACATGAGTCTTCTTTTAATATCCC
*
16246806 CTCATGCTCATCCTGAGACATGAGTCTTCTTTTAATATCCC
1 CTCATGCTCATCCCGAGACATGAGTCTTCTTTTAATATCCC
16246847 CTCATGCTCATCCCGAGACATGAGTCTTC
1 CTCATGCTCATCCCGAGACATGAGTCTTC
16246876 CATTTATACA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.34
Consensus pattern (41 bp):
CTCATGCTCATCCCGAGACATGAGTCTTCTTTTAATATCCC
Found at i:16253941 original size:23 final size:23
Alignment explanation
Indices: 16253915--16253991 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
16253905 ACAGTCATCA
16253915 ATTTAGCATGTAACATTTCATAC
1 ATTTAGCATGTAACATTTCATAC
* ** *
16253938 ATTTA-TAT-TGGCATATACAATAATC
1 ATTTAGCATGTAACAT-TTC-AT-A-C
16253963 AATTTAGCATGTAACATTTCATAC
1 -ATTTAGCATGTAACATTTCATAC
16253987 ATTTA
1 ATTTA
16253992 TATTGAGATA
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
21 4 0.10
22 4 0.10
23 12 0.31
24 2 0.05
25 2 0.05
26 7 0.18
27 4 0.10
28 4 0.10
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (23 bp):
ATTTAGCATGTAACATTTCATAC
Found at i:16253956 original size:49 final size:49
Alignment explanation
Indices: 16253903--16254010 Score: 182
Period size: 49 Copynumber: 2.2 Consensus size: 49
16253893 TAATCATGGC
*
16253903 ATACAGTCATCAATTTAGCATGTAACATTTCATACATTTATATTG-GCAT
1 ATACAATCATCAATTTAGCATGTAACATTTCATACATTTATATTGAG-AT
*
16253952 ATACAATAATCAATTTAGCATGTAACATTTCATACATTTATATTGAGAT
1 ATACAATCATCAATTTAGCATGTAACATTTCATACATTTATATTGAGAT
16254001 ATACAATCAT
1 ATACAATCAT
16254011 GGCTTAATCA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
49 54 0.98
50 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (49 bp):
ATACAATCATCAATTTAGCATGTAACATTTCATACATTTATATTGAGAT
Found at i:16259495 original size:26 final size:26
Alignment explanation
Indices: 16259450--16259549 Score: 164
Period size: 26 Copynumber: 3.8 Consensus size: 26
16259440 TCATTTCTGA
*
16259450 AGCAAATTCAATTATTCATTCAAAAAT
1 AGCAAACTC-ATTATTCATTCAAAAAT
16259477 AGCAAACTCATTATTCATTCAAAAAT
1 AGCAAACTCATTATTCATTCAAAAAT
*
16259503 AGCAAACTCATTACTCATTCAAAAAT
1 AGCAAACTCATTATTCATTCAAAAAT
*
16259529 AGCAAACTCATCATTCATTCA
1 AGCAAACTCATTATTCATTCA
16259550 TATTCATCCA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
26 61 0.88
27 8 0.12
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (26 bp):
AGCAAACTCATTATTCATTCAAAAAT
Found at i:16260284 original size:12 final size:12
Alignment explanation
Indices: 16260267--16260295 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
16260257 GACAGGTTCT
16260267 TCTTCTTCTTTC
1 TCTTCTTCTTTC
16260279 TCTTCTTCTTTC
1 TCTTCTTCTTTC
16260291 TCTTC
1 TCTTC
16260296 CTCGTCTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (12 bp):
TCTTCTTCTTTC
Found at i:16269077 original size:21 final size:21
Alignment explanation
Indices: 16269051--16269101 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
16269041 CAGTGTAGAC
**
16269051 TTCTACCGATACTTATGACAG-
1 TTCTACCGATACCAATGA-AGA
16269072 TTCTACCGATACCAATGAAGA
1 TTCTACCGATACCAATGAAGA
16269093 TTCTACCGA
1 TTCTACCGA
16269102 AACAAATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (21 bp):
TTCTACCGATACCAATGAAGA
Found at i:16269943 original size:52 final size:52
Alignment explanation
Indices: 16269861--16270041 Score: 299
Period size: 52 Copynumber: 3.5 Consensus size: 52
16269851 TTCTCATTTA
* * * *
16269861 ATACTCACGATGACACATTGTCATCGGACCTCATAATCTGAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCTGTAAAGGATTCAT
* *
16269913 ATACTCACGATGACACATAGTCATCAGACCTTATAATCCGTAAAGGATTAAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCTGTAAAGGATTCAT
*
16269965 ATACTCACGATGACACATAATCATCAGACCTTATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCTGTAAAGGATTCAT
16270017 ATACTCACGATGACACATAGTCATC
1 ATACTCACGATGACACATAGTCATC
16270042 GGATCTTTTG
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 119 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTTATAATCTGTAAAGGATTCAT
Found at i:16272458 original size:24 final size:24
Alignment explanation
Indices: 16272426--16272495 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
16272416 CGTTATTCTG
*
16272426 ATTCTGGGCTCGTAAGAGCTATCC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
16272450 ATTCTGGGCTCGTGAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
* * *
16272474 AATCTGGGCTCATATGAGCTAA
1 ATTCTGGGCTCGTAAGAGCTAA
16272496 TTTTGTTTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:16276621 original size:24 final size:24
Alignment explanation
Indices: 16276588--16276681 Score: 127
Period size: 24 Copynumber: 3.9 Consensus size: 24
16276578 CATTATTCTG
16276588 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
16276612 ATTCTAGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
* *
16276636 ATTCTGGGCTGGTGAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
* *
16276660 -TATCCGGGCTCGTATGAGCTAA
1 AT-TCTGGGCTCGTAAGAGCTAA
16276682 TTTTGTCTAG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 1 0.02
24 60 0.98
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:16282375 original size:26 final size:25
Alignment explanation
Indices: 16282346--16282403 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
16282336 TTTACCAAGG
16282346 TTATTAGTTATAGATAAATGAATATT
1 TTATTAGTTATAGATAAATGAATA-T
* * *
16282372 TTATTAATTTATCGATAAATTAATAT
1 TTATT-AGTTATAGATAAATGAATAT
16282398 TTATTA
1 TTATTA
16282404 ATTTAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 11 0.39
27 16 0.57
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (25 bp):
TTATTAGTTATAGATAAATGAATAT
Found at i:16282388 original size:27 final size:26
Alignment explanation
Indices: 16282353--16282408 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
16282343 AGGTTATTAG
16282353 TTATAGATAAATGAATATTTTATTAAT
1 TTATAGATAAATGAATA-TTTATTAAT
* *
16282380 TTATCGATAAATTAATATTTATTAAT
1 TTATAGATAAATGAATATTTATTAAT
16282406 TTA
1 TTA
16282409 GAGAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (26 bp):
TTATAGATAAATGAATATTTATTAAT
Found at i:16282590 original size:34 final size:33
Alignment explanation
Indices: 16282516--16282594 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 33
16282506 CATGTATCAA
** *
16282516 AGTTAATTGGTTCATGTATTAAAAAGAAAGAGTT
1 AGTTAATTGGTTCATGTACCAAAAAGAAAAAG-T
*
16282550 AATTAATTGGTTCATGTAACCAAAAAGGAAAAAG-
1 AGTTAATTGGTTCATGT-ACCAAAAA-GAAAAAGT
16282584 AGTTAA-TGGTT
1 AGTTAATTGGTT
16282595 TCAAAATCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
33 5 0.13
34 21 0.55
35 6 0.16
36 6 0.16
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (33 bp):
AGTTAATTGGTTCATGTACCAAAAAGAAAAAGT
Found at i:16283666 original size:19 final size:20
Alignment explanation
Indices: 16283620--16283668 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
16283610 ATTAGCATGA
16283620 GTTATATTAAGTATAAATAGG
1 GTTA-ATTAAGTATAAATAGG
*
16283641 TTTAATTAAG-ACTAAA-AGG
1 GTTAATTAAGTA-TAAATAGG
16283660 GTTAATTAA
1 GTTAATTAA
16283669 AGCTTAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.48
20 10 0.40
21 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (20 bp):
GTTAATTAAGTATAAATAGG
Found at i:16290465 original size:82 final size:82
Alignment explanation
Indices: 16290328--16290491 Score: 292
Period size: 82 Copynumber: 2.0 Consensus size: 82
16290318 GACACACAAG
* *
16290328 CTTTCAACGTCATCTTCAGTATCAGAAAGAATATTTTCACATAGTATACACCATTAGCATATGCA
1 CTTTCAACGTCATCTTCAGTATCAGAAAGAAAATTTTCACAAAGTATACACCATTAGCATATGCA
16290393 AGTTCACAGCATTGAAT
66 AGTTCACAGCATTGAAT
*
16290410 CTTTCAACGTCATCTTCAGTATCAGAATGAAAATTTTCACAAAGTATACACCATTAGCATATGCA
1 CTTTCAACGTCATCTTCAGTATCAGAAAGAAAATTTTCACAAAGTATACACCATTAGCATATGCA
*
16290475 AGTTCACTGCATTGAAT
66 AGTTCACAGCATTGAAT
16290492 TTCTTCATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (82 bp):
CTTTCAACGTCATCTTCAGTATCAGAAAGAAAATTTTCACAAAGTATACACCATTAGCATATGCA
AGTTCACAGCATTGAAT
Found at i:16306543 original size:12 final size:12
Alignment explanation
Indices: 16306526--16306555 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16306516 TATTTTGCGT
16306526 TTTTTTTCTATA
1 TTTTTTTCTATA
*
16306538 TTTTTTTCTTTA
1 TTTTTTTCTATA
16306550 TTTTTT
1 TTTTTT
16306556 GCTTTTTTTT
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:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTCTATA
Found at i:16306553 original size:21 final size:23
Alignment explanation
Indices: 16306509--16306553 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
16306499 TAAATGTATA
*
16306509 TCTATATTATTTTGCGTTTTTTT
1 TCTATATTATTTTGCGTTTATTT
*
16306532 TCTATATT-TTTTTC-TTTATTT
1 TCTATATTATTTTGCGTTTATTT
16306553 T
1 T
16306554 TTGCTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.73
Consensus pattern (23 bp):
TCTATATTATTTTGCGTTTATTT
Found at i:16313557 original size:21 final size:21
Alignment explanation
Indices: 16313528--16313583 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
16313518 TTGGAGTTTG
**
16313528 TTGTATCGGTAGAAGTGTTAC
1 TTGTATCGGTAGAAGTCATAC
* *
16313549 TTGTTTCGGTAGTAGTCATAC
1 TTGTATCGGTAGAAGTCATAC
16313570 TTGTATCGGTAGAA
1 TTGTATCGGTAGAA
16313584 CTATCACAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTCATAC
Found at i:16317296 original size:18 final size:18
Alignment explanation
Indices: 16317273--16317310 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
16317263 TAATATAGTT
*
16317273 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCAAA
16317291 TTATTCGAGTTATTCAAA
1 TTATTCGAGTTATTCAAA
16317309 TT
1 TT
16317311 CAAAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCAAA
Found at i:16317398 original size:23 final size:23
Alignment explanation
Indices: 16317355--16317399 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16317345 AAAAAAATTC
**
16317355 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
16317378 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
16317400 ATTGAATTTT
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:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:16318399 original size:26 final size:26
Alignment explanation
Indices: 16318360--16318507 Score: 145
Period size: 26 Copynumber: 5.7 Consensus size: 26
16318350 TAAGAGCGTT
* *
16318360 ACTCTATCTAGGCTTGAATGAGCTAA
1 ACTCTGTCTAGGCTCGAATGAGCTAA
* * * *
16318386 ACTTTGTTTGGGCTAGAATGAGCTAA
1 ACTCTGTCTAGGCTCGAATGAGCTAA
*
16318412 ACTCTGTCTAGGCTCGAATAAGCTAA
1 ACTCTGTCTAGGCTCGAATGAGCTAA
* * * *
16318438 ATTTTTTCTAGGCTCGTATGAGCTAA
1 ACTCTGTCTAGGCTCGAATGAGCTAA
* *
16318464 ACTCTGTCTGGGCT-TATATGAGCTAA
1 ACTCTGTCTAGGCTCGA-ATGAGCTAA
*
16318490 ACTCTATTCTAGGCTCGA
1 ACTCT-GTCTAGGCTCGA
16318508 GAAAGCTATA
Statistics
Matches: 95, Mismatches: 24, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
26 87 0.92
27 7 0.07
28 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (26 bp):
ACTCTGTCTAGGCTCGAATGAGCTAA
Found at i:16318459 original size:78 final size:79
Alignment explanation
Indices: 16318366--16318522 Score: 212
Period size: 78 Copynumber: 2.0 Consensus size: 79
16318356 CGTTACTCTA
* * *
16318366 TCTAGGCTTGAATGAGCTAAACTTTGTTTGGGC-TAGAATGAGCTAAACTCT-GTCTAGGCTCGA
1 TCTAGGCTCGAATGAGCTAAACTCTGTCTGGGCTTA-AATGAGCTAAACTCTAGTCTAGGCTCGA
16318429 -ATAAGCTAAATTTTT
65 GA-AAGCTAAATTTTT
* * *
16318444 TCTAGGCTCGTATGAGCTAAACTCTGTCTGGGCTTATATGAGCTAAACTCTATTCTAGGCTCGAG
1 TCTAGGCTCGAATGAGCTAAACTCTGTCTGGGCTTAAATGAGCTAAACTCTAGTCTAGGCTCGAG
*
16318509 AAAGCTATATTTTT
66 AAAGCTAAATTTTT
16318523 GTAATGACTC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
78 43 0.62
79 25 0.36
80 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (79 bp):
TCTAGGCTCGAATGAGCTAAACTCTGTCTGGGCTTAAATGAGCTAAACTCTAGTCTAGGCTCGAG
AAAGCTAAATTTTT
Found at i:16318488 original size:52 final size:52
Alignment explanation
Indices: 16318360--16318507 Score: 165
Period size: 52 Copynumber: 2.8 Consensus size: 52
16318350 TAAGAGCGTT
* * * *
16318360 ACTCTATCTAGGCTTGAATGAGCTAAACTTTGTT-TGGGCTAGAATGAGCTAA
1 ACTCTGTCTAGGCTT-AATGAGCTAAACTTTATTCTAGGCTCGAATGAGCTAA
* * * *
16318412 ACTCTGTCTAGGCTCGAATAAGCTAAA-TTTTTTCTAGGCTCGTATGAGCTAA
1 ACTCTGTCTAGGCT-TAATGAGCTAAACTTTATTCTAGGCTCGAATGAGCTAA
* *
16318464 ACTCTGTCTGGGCTTATATGAGCTAAACTCTATTCTAGGCTCGA
1 ACTCTGTCTAGGCTTA-ATGAGCTAAACTTTATTCTAGGCTCGA
16318508 GAAAGCTATA
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
51 6 0.08
52 60 0.76
53 13 0.16
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (52 bp):
ACTCTGTCTAGGCTTAATGAGCTAAACTTTATTCTAGGCTCGAATGAGCTAA
Found at i:16324735 original size:21 final size:21
Alignment explanation
Indices: 16324711--16324758 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
16324701 TTCATTAAGG
*
16324711 ATAAATTAGT-AAATTTAAAAA
1 ATAAATTAGTGAAA-CTAAAAA
*
16324732 ATAAATAAGTGAAACTAAAAA
1 ATAAATTAGTGAAACTAAAAA
16324753 A-AAATT
1 ATAAATT
16324759 TAATAGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 16 0.70
22 3 0.13
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (21 bp):
ATAAATTAGTGAAACTAAAAA
Found at i:16328920 original size:63 final size:63
Alignment explanation
Indices: 16328847--16328975 Score: 213
Period size: 63 Copynumber: 2.0 Consensus size: 63
16328837 AATAAAGAAA
*
16328847 CTATAAACAACCTAACCTACTACTATAAGCCTTACTTCTATTGCAGACCTTTTTTGTTAGATT
1 CTATAAACAACCTAACCTACTACTATAAGCCTTACTTCTATTGCAGACCTTCTTTGTTAGATT
* * * *
16328910 CTATAAACAACCTAACTTGCTACTATAAGCCTTACTTCTGTTGTAGACCTTCTTTGTTAGATT
1 CTATAAACAACCTAACCTACTACTATAAGCCTTACTTCTATTGCAGACCTTCTTTGTTAGATT
16328973 CTA
1 CTA
16328976 GGCATAATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (63 bp):
CTATAAACAACCTAACCTACTACTATAAGCCTTACTTCTATTGCAGACCTTCTTTGTTAGATT
Found at i:16333448 original size:23 final size:23
Alignment explanation
Indices: 16333385--16333451 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
16333375 ACATTCAATG
* *
16333385 GGTCGATCAAAGTCAACAGGTTA
1 GGTCGGTCAAAGTCAACGGGTTA
* *
16333408 AGTCGGTCAAAGTCAACGGGTTT
1 GGTCGGTCAAAGTCAACGGGTTA
16333431 GGTCGGTCAAAGTCAACGGGT
1 GGTCGGTCAAAGTCAACGGGT
16333452 CGAGCTCACG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.22
Consensus pattern (23 bp):
GGTCGGTCAAAGTCAACGGGTTA
Found at i:16337616 original size:30 final size:31
Alignment explanation
Indices: 16337549--16337619 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
16337539 CATAAAAATC
*
16337549 AGTGACTATTCTGTCACTTTTCGATAATGTT
1 AGTGACTGTTCTGTCACTTTTCGATAATGTT
*
16337580 AGTGACTGTTTTGTCACATTTTC-A-AA-GTT
1 AGTGACTGTTCTGTCAC-TTTTCGATAATGTT
16337609 GAGTGACTGTT
1 -AGTGACTGTT
16337620 GTGTTAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.33
31 16 0.44
32 5 0.14
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.44
Consensus pattern (31 bp):
AGTGACTGTTCTGTCACTTTTCGATAATGTT
Found at i:16339582 original size:28 final size:29
Alignment explanation
Indices: 16339550--16339613 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
16339540 AAGTCTAAAC
*
16339550 TAAAAAA-GTAATCTTAATTGCTTCAAAA
1 TAAAAAATATAATCTTAATTGCTTCAAAA
* * * *
16339578 TAAAAAATATAATTTTATTTGTTTTAAAA
1 TAAAAAATATAATCTTAATTGCTTCAAAA
16339607 TAAAAAA
1 TAAAAAA
16339614 ATTAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (29 bp):
TAAAAAATATAATCTTAATTGCTTCAAAA
Found at i:16341738 original size:16 final size:16
Alignment explanation
Indices: 16341712--16341754 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
16341702 CTTTCTCAAG
16341712 TTTGAACTTTTTTCTAA
1 TTTGAA-TTTTTTCTAA
*
16341729 TTTGAATTTTTTTTAA
1 TTTGAATTTTTTCTAA
*
16341745 ATTGAATTTT
1 TTTGAATTTT
16341755 CTCAGATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.63
Consensus pattern (16 bp):
TTTGAATTTTTTCTAA
Found at i:16342285 original size:2 final size:2
Alignment explanation
Indices: 16342278--16342304 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16342268 ATTATCTAGA
16342278 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 A
16342305 AGTCACAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16345059 original size:14 final size:14
Alignment explanation
Indices: 16345021--16345063 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
16345011 CAAAATGTAC
16345021 AATATAATTAAA-T
1 AATATAATTAAATT
16345034 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
16345049 AA-ATAATTTAATT
1 AATATAATTAAATT
16345062 AA
1 AA
16345064 GTATTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:16345425 original size:9 final size:9
Alignment explanation
Indices: 16345413--16345439 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
16345403 TGAATAAATT
16345413 GTGTAAAAA
1 GTGTAAAAA
16345422 GTGTAAAAA
1 GTGTAAAAA
16345431 GTGTAAAAA
1 GTGTAAAAA
16345440 TGTGCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (9 bp):
GTGTAAAAA
Found at i:16346497 original size:23 final size:25
Alignment explanation
Indices: 16346453--16346500 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
16346443 ATTATCGAAT
*
16346453 TTTCTTATCTATTTCATTTTCTTTA
1 TTTCTTATCTATTTCATGTTCTTTA
*
16346478 TTTCTT-T-TATTTTATGTTCTTTA
1 TTTCTTATCTATTTCATGTTCTTTA
16346501 ATTCAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 1 0.05
25 6 0.29
ACGTcount: A:0.15, C:0.12, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTCTTATCTATTTCATGTTCTTTA
Found at i:16349140 original size:15 final size:15
Alignment explanation
Indices: 16349122--16349157 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
16349112 TGAATGTAAT
16349122 ATAAAAAATTAACAA-
1 ATAAAAAATTAA-AAG
16349137 ATAAAAAATTAAAAG
1 ATAAAAAATTAAAAG
16349152 ATAAAA
1 ATAAAA
16349158 TTATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (15 bp):
ATAAAAAATTAAAAG
Found at i:16349342 original size:3 final size:3
Alignment explanation
Indices: 16349334--16349362 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16349324 TTATTTAAAA
16349334 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
16349363 TCCAGCATAA
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:16349829 original size:24 final size:24
Alignment explanation
Indices: 16349776--16349830 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
16349766 TCGATTCATA
* * *
16349776 TTTTTCTGTTGCTTTTAGATTGCT
1 TTTTTTTGTTGATTTTAGACTGCT
*
16349800 TTTTTTTGTTGATTTTGGACTGCT
1 TTTTTTTGTTGATTTTAGACTGCT
16349824 TTTTTTT
1 TTTTTTT
16349831 TATTATTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.07, C:0.09, G:0.16, T:0.67
Consensus pattern (24 bp):
TTTTTTTGTTGATTTTAGACTGCT
Found at i:16350418 original size:170 final size:170
Alignment explanation
Indices: 16350136--16350477 Score: 675
Period size: 170 Copynumber: 2.0 Consensus size: 170
16350126 CCCTGTTGAG
*
16350136 AACTCGATTATGTAAAAAATGAAGGAGGATATCAGCAACAACCATTTGGTTGATCTTAAACTAGA
1 AACTCGATTATGTAAAAAACGAAGGAGGATATCAGCAACAACCATTTGGTTGATCTTAAACTAGA
16350201 AATTAAAATAGTAACTTTAATTTTATAAATGGTTACGATGGTGTACATACAATCAAATACATGTT
66 AATTAAAATAGTAACTTTAATTTTATAAATGGTTACGATGGTGTACATACAATCAAATACATGTT
16350266 TTGGCAATAGTAGTTTAGGCAAGATTCATGTGCAAAACAC
131 TTGGCAATAGTAGTTTAGGCAAGATTCATGTGCAAAACAC
16350306 AACTCGATTATGTAAAAAACGAAGGAGGATATCAGCAACAACCATTTGGTTGATCTTAAACTAGA
1 AACTCGATTATGTAAAAAACGAAGGAGGATATCAGCAACAACCATTTGGTTGATCTTAAACTAGA
16350371 AATTAAAATAGTAACTTTAATTTTATAAATGGTTACGATGGTGTACATACAATCAAATACATGTT
66 AATTAAAATAGTAACTTTAATTTTATAAATGGTTACGATGGTGTACATACAATCAAATACATGTT
16350436 TTGGCAATAGTAGTTTAGGCAAGATTCATGTGCAAAACAC
131 TTGGCAATAGTAGTTTAGGCAAGATTCATGTGCAAAACAC
16350476 AA
1 AA
16350478 TTTTCTCCTA
Statistics
Matches: 171, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 171 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (170 bp):
AACTCGATTATGTAAAAAACGAAGGAGGATATCAGCAACAACCATTTGGTTGATCTTAAACTAGA
AATTAAAATAGTAACTTTAATTTTATAAATGGTTACGATGGTGTACATACAATCAAATACATGTT
TTGGCAATAGTAGTTTAGGCAAGATTCATGTGCAAAACAC
Found at i:16350910 original size:18 final size:20
Alignment explanation
Indices: 16350874--16350913 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
16350864 GGATTTCTTT
*
16350874 TATTTTTTGTGGTTATATTC
1 TATTTTTGGTGGTTATATTC
16350894 TATTTTTGGT-GTT-TATTC
1 TATTTTTGGTGGTTATATTC
16350912 TA
1 TA
16350914 GCAATTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.15, C:0.05, G:0.15, T:0.65
Consensus pattern (20 bp):
TATTTTTGGTGGTTATATTC
Found at i:16353114 original size:18 final size:18
Alignment explanation
Indices: 16353078--16353133 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
16353068 GAAATAACTT
*
16353078 TTACGATCTAGTAATGCTC
1 TTACGAGCTAGT-ATGCTC
16353097 TTACGAGCTAGTATGCTC
1 TTACGAGCTAGTATGCTC
** *
16353115 AAATGAGCTAGTATGCTC
1 TTACGAGCTAGTATGCTC
16353133 T
1 T
16353134 AACTTACGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 21 0.66
19 11 0.34
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (18 bp):
TTACGAGCTAGTATGCTC
Found at i:16360048 original size:18 final size:18
Alignment explanation
Indices: 16360008--16360067 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
16359998 AATGCTCTTG
*
16360008 CGAGCCAGTATACTCAAA
1 CGAGCCAGTATGCTCAAA
* ** *
16360026 TGAGCTTGTATGCTCTAA
1 CGAGCCAGTATGCTCAAA
16360044 CGAGCCAGTATGCTCAAA
1 CGAGCCAGTATGCTCAAA
16360062 CGAGCC
1 CGAGCC
16360068 GATAAGCTTT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (18 bp):
CGAGCCAGTATGCTCAAA
Found at i:16365317 original size:40 final size:40
Alignment explanation
Indices: 16365262--16365355 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
16365252 CCATAGCTTG
* * *
16365262 GCTTGAATTTTAACACTGGCACATAGCCTGCTAAGTCGTA
1 GCTTGAATTTTAACACCGACACATAGCCTGCTAAGCCGTA
* *
16365302 GCTTGAATTTTAACACCGACTCATAGCTTGCTAAGCCGTA
1 GCTTGAATTTTAACACCGACACATAGCCTGCTAAGCCGTA
16365342 GCTTGAA-TTTAACA
1 GCTTGAATTTTAACA
16365356 TTTCATGGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 7 0.14
40 42 0.86
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (40 bp):
GCTTGAATTTTAACACCGACACATAGCCTGCTAAGCCGTA
Found at i:16366887 original size:13 final size:13
Alignment explanation
Indices: 16366871--16366942 Score: 74
Period size: 13 Copynumber: 5.5 Consensus size: 13
16366861 ATATAACTTA
16366871 TTCATATAACCAT
1 TTCATATAACCAT
**
16366884 TTCATATATTCAT
1 TTCATATAACCAT
*
16366897 TTTATATAACCATT
1 TTCATATAACCA-T
*
16366911 TTGA-ATAACCAT
1 TTCATATAACCAT
* *
16366923 ATCATATAAACAT
1 TTCATATAACCAT
16366936 TTCATAT
1 TTCATAT
16366943 TACAGTTAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
12 3 0.06
13 40 0.85
14 4 0.09
ACGTcount: A:0.39, C:0.17, G:0.01, T:0.43
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:16367232 original size:45 final size:45
Alignment explanation
Indices: 16367168--16367468 Score: 306
Period size: 45 Copynumber: 6.7 Consensus size: 45
16367158 TTTTACAAAA
* * * * ** *
16367168 GATGCCACAGCGTCTTTCAACCAAGGTCTTACACACTTCCGATAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGATAT
* * *
16367213 GATGCCATAGTGTCTTTCAATTATGGTCTTATTTATTTCCGACAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGATAT
* * *
16367258 GATGCCATAGTTTCTTTCAACTACGGTCTTATTCATTTCCGACAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGATAT
* * *
16367303 GATGTCATAGTGTCTTTCAACTATGGCCTTATACATTTCC-ATCAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGAT-AT
*
16367348 G-TAGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTG-TCAT
1 GAT-GCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGAT-AT
* * * * *
16367393 GTTGCCATACTGTCTTTCAACTATGGTCTTACTC--GTCTGAATCAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCG-AT-AT
**
16367438 GATGCCATAGCATCTTTCAACTATGGTCTTA
1 GATGCCATAGTGTCTTTCAACTATGGTCTTA
16367469 CTCTTACTCG
Statistics
Matches: 219, Mismatches: 31, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
43 4 0.02
44 2 0.01
45 212 0.97
46 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (45 bp):
GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGATAT
Found at i:16367439 original size:135 final size:134
Alignment explanation
Indices: 16367168--16367468 Score: 338
Period size: 135 Copynumber: 2.2 Consensus size: 134
16367158 TTTTACAAAA
* * * * * * *
16367168 GATGCCACAGCGTCTTTCAACCAAGGTCTTACACACTTCCGAT-ATG-ATGCCATAGTGTCTTTC
1 GATGCCATAGCATCTTTCAACTATGGCCTTATACATTTCC-ATCATGTA-GCCATAGTGTCTTTC
* * * * * *
16367231 AATTATGGTCTTATTTATTTCCGACATGATGCCATAGTTTCTTTCAACTACGGTCTTATTCATTT
64 AACTATGGTCTTATTCATTTCCGACATGATGCCATACTGTCTTTCAACTACGGTCTTACTCA-GT
16367296 CCGACAT
128 CCGACAT
* **
16367303 GATGTCATAGTGTCTTTCAACTATGGCCTTATACATTTCCATCATGTAGCCATAGTGTCTTTCAA
1 GATGCCATAGCATCTTTCAACTATGGCCTTATACATTTCCATCATGTAGCCATAGTGTCTTTCAA
* * * * *
16367368 CTATGGTCTTATTCATTTCTGTCATGTTGCCATACTGTCTTTCAACTATGGTCTTACTC-GTCTG
66 CTATGGTCTTATTCATTTCCGACATGATGCCATACTGTCTTTCAACTACGGTCTTACTCAGTCCG
16367432 AATCAT
131 -A-CAT
*
16367438 GATGCCATAGCATCTTTCAACTATGGTCTTA
1 GATGCCATAGCATCTTTCAACTATGGCCTTA
16367469 CTCTTACTCG
Statistics
Matches: 139, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
133 3 0.02
134 3 0.02
135 132 0.95
136 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (134 bp):
GATGCCATAGCATCTTTCAACTATGGCCTTATACATTTCCATCATGTAGCCATAGTGTCTTTCAA
CTATGGTCTTATTCATTTCCGACATGATGCCATACTGTCTTTCAACTACGGTCTTACTCAGTCCG
ACAT
Found at i:16379008 original size:27 final size:25
Alignment explanation
Indices: 16378978--16379039 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
16378968 AAAATTTTAA
16378978 TGCAGAAAAAGTAAAAGTGTGATCAAG
1 TGCA-AAAAA-TAAAAGTGTGATCAAG
* **
16379005 TGCAAAGAATGGAAGTGTGATCAAG
1 TGCAAAAAATAAAAGTGTGATCAAG
16379030 TGCAAAAAAT
1 TGCAAAAAAT
16379040 GGAGTGGATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 23 0.74
26 4 0.13
27 4 0.13
ACGTcount: A:0.47, C:0.08, G:0.26, T:0.19
Consensus pattern (25 bp):
TGCAAAAAATAAAAGTGTGATCAAG
Found at i:16379020 original size:25 final size:25
Alignment explanation
Indices: 16378992--16379050 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
16378982 GAAAAAGTAA
*
16378992 AAGTGTGATCAAGTGCAAAGAATGG
1 AAGTGTGATCAAGTGCAAAAAATGG
16379017 AAGTGTGATCAAGTGCAAAAAATGG
1 AAGTGTGATCAAGTGCAAAAAATGG
16379042 -AGTG-GATCA
1 AAGTGTGATCA
16379051 CTAACTTCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 5 0.15
24 4 0.12
25 24 0.73
ACGTcount: A:0.41, C:0.08, G:0.31, T:0.20
Consensus pattern (25 bp):
AAGTGTGATCAAGTGCAAAAAATGG
Found at i:16381649 original size:15 final size:15
Alignment explanation
Indices: 16381629--16381659 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16381619 CTATTTCTCA
16381629 TTTCCTTCTTCTTTC
1 TTTCCTTCTTCTTTC
16381644 TTTCCTTCTTCTTTC
1 TTTCCTTCTTCTTTC
16381659 T
1 T
16381660 CAGGCTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTCCTTCTTCTTTC
Found at i:16387260 original size:18 final size:18
Alignment explanation
Indices: 16387237--16387298 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
16387227 TCCTTGCATA
16387237 TGTGGCTGCATTCTAGCT
1 TGTGGCTGCATTCTAGCT
*
16387255 TGTGGCTGCA-TCTGGCT
1 TGTGGCTGCATTCTAGCT
*
16387272 ATGT-AC--CATTCTAGCT
1 -TGTGGCTGCATTCTAGCT
*
16387288 TGTGGTTGCAT
1 TGTGGCTGCAT
16387299 CTAATATGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 7 0.21
18 16 0.47
ACGTcount: A:0.13, C:0.21, G:0.27, T:0.39
Consensus pattern (18 bp):
TGTGGCTGCATTCTAGCT
Found at i:16390101 original size:25 final size:25
Alignment explanation
Indices: 16390047--16390204 Score: 203
Period size: 25 Copynumber: 6.4 Consensus size: 25
16390037 TTACATATTA
*
16390047 ATCACATTAACAC--ATAAGCATTT
1 ATCACATTAACACATATAAGCATAT
* * *
16390070 ATAACATTAACACCTATAAGCATGT
1 ATCACATTAACACATATAAGCATAT
* *
16390095 ATCACATTAACACCTATAAGCATGT
1 ATCACATTAACACATATAAGCATAT
16390120 ATCACATTAACACATATAAGCATAT
1 ATCACATTAACACATATAAGCATAT
* *
16390145 ATCACGTTGACACATATAAGCATAT
1 ATCACATTAACACATATAAGCATAT
* * *
16390170 ACCACATTAACACATATGAGTATAT
1 ATCACATTAACACATATAAGCATAT
16390195 ATCACATTAA
1 ATCACATTAA
16390205 TCAATAGCCA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
23 12 0.10
25 108 0.90
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (25 bp):
ATCACATTAACACATATAAGCATAT
Found at i:16393133 original size:21 final size:21
Alignment explanation
Indices: 16393104--16393143 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16393094 GGATAGCAAA
16393104 TCAGATTTTCCCTCTTGAATT
1 TCAGATTTTCCCTCTTGAATT
* **
16393125 TCAGCTTTTTTCTCTTGAA
1 TCAGATTTTCCCTCTTGAA
16393144 AAAATTCAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.10, T:0.50
Consensus pattern (21 bp):
TCAGATTTTCCCTCTTGAATT
Found at i:16403175 original size:20 final size:21
Alignment explanation
Indices: 16403152--16403208 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
16403142 CCCTAATCAC
*
16403152 TAAACCCTAACCTTAAAA-CT
1 TAAACCCTAACCATAAAACCT
*
16403172 TAAACCCTAAGCATAAAACCT
1 TAAACCCTAACCATAAAACCT
16403193 TAAACCCTAAACCATA
1 TAAACCCT-AACCATA
16403209 TGTAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 16 0.50
21 10 0.31
22 6 0.19
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (21 bp):
TAAACCCTAACCATAAAACCT
Found at i:16403204 original size:14 final size:14
Alignment explanation
Indices: 16403132--16403205 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
16403122 TTTAAACATA
16403132 AAACCTTAAACCCT
1 AAACCTTAAACCCT
*
16403146 AATCAC-TAAACCCT
1 AAAC-CTTAAACCCT
* *
16403160 -AACCTTAAAACTT
1 AAACCTTAAACCCT
* * *
16403173 AAACCCT-AAGCAT
1 AAACCTTAAACCCT
16403186 AAAACCTTAAACCCT
1 -AAACCTTAAACCCT
16403201 AAACC
1 AAACC
16403206 ATATGTAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
12 1 0.02
13 12 0.27
14 27 0.60
15 5 0.11
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.20
Consensus pattern (14 bp):
AAACCTTAAACCCT
Found at i:16403286 original size:64 final size:63
Alignment explanation
Indices: 16403206--16403349 Score: 252
Period size: 64 Copynumber: 2.3 Consensus size: 63
16403196 ACCCTAAACC
*
16403206 ATATGTAAAATTTAAGTCGGTATATAAATATGAAATTTAAATAAATAGTCAAATGAGTTAAAAT
1 ATATGTAAAATTTAAGTCGGTATATAAATATGAAATTTAAATAAATAGTCAAATAAGTT-AAAT
*
16403270 ATATGTGAAATTTAAGTCGGTATATAAATATGAAATTTAAATAAATAGTCAAATAAGTTAAAT
1 ATATGTAAAATTTAAGTCGGTATATAAATATGAAATTTAAATAAATAGTCAAATAAGTTAAAT
*
16403333 ATATGTTAAATTTAAGT
1 ATATGTAAAATTTAAGT
16403350 AAAAAGTCAT
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
63 20 0.26
64 57 0.74
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.36
Consensus pattern (63 bp):
ATATGTAAAATTTAAGTCGGTATATAAATATGAAATTTAAATAAATAGTCAAATAAGTTAAAT
Found at i:16403395 original size:17 final size:18
Alignment explanation
Indices: 16403370--16403412 Score: 79
Period size: 17 Copynumber: 2.4 Consensus size: 18
16403360 CAATAAAACT
16403370 CATCAATAGTCAAATATA
1 CATCAATAGTCAAATATA
16403388 CA-CAATAGTCAAATATA
1 CATCAATAGTCAAATATA
16403405 CATCAATA
1 CATCAATA
16403413 AAACCCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.26
Consensus pattern (18 bp):
CATCAATAGTCAAATATA
Found at i:16404224 original size:43 final size:43
Alignment explanation
Indices: 16404163--16404259 Score: 158
Period size: 43 Copynumber: 2.3 Consensus size: 43
16404153 AACTGCACAA
*
16404163 TTAATAACATGTCACGATATTAACAAGAGTCAAGAAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGTCAAGAAATATAAT
* * *
16404206 TTAATAACATGCCACGATATTAACACGGGTCAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGTCAAGAAATATAAT
16404249 TTAATAACATG
1 TTAATAACATG
16404260 TCAAGGAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.29
Consensus pattern (43 bp):
TTAATAACATGCCACGATATTAACAAGAGTCAAGAAATATAAT
Found at i:16405224 original size:19 final size:19
Alignment explanation
Indices: 16405185--16405224 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16405175 TAGTTAATAT
**
16405185 AACCTAATTTAAATTTGTA
1 AACCTAATTTAAATTCATA
*
16405204 AACCTAATTTAACTTCATA
1 AACCTAATTTAAATTCATA
16405223 AA
1 AA
16405225 TTACATAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.38
Consensus pattern (19 bp):
AACCTAATTTAAATTCATA
Found at i:16405868 original size:11 final size:12
Alignment explanation
Indices: 16405840--16405865 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16405830 CTAACAAACT
16405840 AAATAAATTTAA
1 AAATAAATTTAA
16405852 AAATAAATTTAA
1 AAATAAATTTAA
16405864 AA
1 AA
16405866 TAACCATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATAAATTTAA
Found at i:16405920 original size:12 final size:12
Alignment explanation
Indices: 16405892--16405934 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
16405882 AATAAATTAA
16405892 CTTTCTTTTCCTT
1 CTTTC-TTTCCTT
*
16405905 -TTTCTTTCTTT
1 CTTTCTTTCCTT
16405916 CTTTCTTTCCTT
1 CTTTCTTTCCTT
*
16405928 CCTTCTT
1 CTTTCTT
16405935 CTCTCTTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
CTTTCTTTCCTT
Found at i:16406895 original size:14 final size:15
Alignment explanation
Indices: 16406873--16406914 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
16406863 TAAAAACATA
16406873 AAAATTTTAAAAATT
1 AAAATTTTAAAAATT
* *
16406888 ATAA-TTTAAAATTT
1 AAAATTTTAAAAATT
16406902 AAAATTTTAAAAA
1 AAAATTTTAAAAA
16406915 AATATATGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTTTAAAAATT
Found at i:16406932 original size:29 final size:29
Alignment explanation
Indices: 16406873--16406934 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
16406863 TAAAAACATA
* *
16406873 AAAATTTTAAAAATTATAATTTAAAATTT
1 AAAATTTTAAAAAATATAATTGAAAATTT
16406902 AAAATTTTAAAAAA-AT-ATATGAAAATGTT
1 AAAATTTTAAAAAATATAAT-TGAAAAT-TT
16406931 AAAA
1 AAAA
16406935 ACTATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 2 0.07
28 8 0.28
29 19 0.66
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTTTAAAAAATATAATTGAAAATTT
Found at i:16407496 original size:18 final size:19
Alignment explanation
Indices: 16407461--16407498 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
16407451 TTAAACATCT
16407461 TCAAGGTTAAATTGTTCAC
1 TCAAGGTTAAATTGTTCAC
*
16407480 TCAAGTTTAAA-TGTTCAC
1 TCAAGGTTAAATTGTTCAC
16407498 T
1 T
16407499 TGAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (19 bp):
TCAAGGTTAAATTGTTCAC
Found at i:16407507 original size:19 final size:19
Alignment explanation
Indices: 16407467--16407508 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
16407457 ATCTTCAAGG
*
16407467 TTAAATTGTTCACTCAAGT
1 TTAAATTGTTCACTCAAAT
*
16407486 TTAAA-TGTTCACTTGAAAT
1 TTAAATTGTTCAC-TCAAAT
16407505 TTAA
1 TTAA
16407509 GTGGATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (19 bp):
TTAAATTGTTCACTCAAAT
Found at i:16411818 original size:24 final size:24
Alignment explanation
Indices: 16411757--16411819 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
16411747 TAGAGTAATA
* * *
16411757 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
16411781 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
16411805 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
16411820 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:16419639 original size:28 final size:26
Alignment explanation
Indices: 16419587--16419672 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 26
16419577 AATGATTAAA
*
16419587 AAATAT-AAAAAAACATTAAAAATTAT
1 AAATATCAGAAAAA-ATTAAAAATTAT
*
16419613 AAATATCATGAAAAATATTAAAGATTAT
1 AAATATCA-GAAAAA-ATTAAAAATTAT
* * * *
16419641 AAAAATTAGAAAAAATTAAATATTAA
1 AAATATCAGAAAAAATTAAAAATTAT
16419667 AAATAT
1 AAATAT
16419673 TAAATTGATA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 21 0.42
27 7 0.14
28 22 0.44
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.29
Consensus pattern (26 bp):
AAATATCAGAAAAAATTAAAAATTAT
Found at i:16419674 original size:16 final size:16
Alignment explanation
Indices: 16419625--16419677 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
16419615 ATATCATGAA
*
16419625 AAATATTAAAGAT-TAT
1 AAATATTAAAAATAT-T
* *
16419641 AAAAATTAGAAAAAATT
1 AAATATTA-AAAATATT
16419658 AAATATTAAAAATATT
1 AAATATTAAAAATATT
16419674 AAAT
1 AAAT
16419678 TGATATAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 18 0.60
17 11 0.37
18 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (16 bp):
AAATATTAAAAATATT
Found at i:16419708 original size:19 final size:18
Alignment explanation
Indices: 16419684--16419733 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
16419674 AAATTGATAT
16419684 AAACTTATAATACTTATAA
1 AAACTTATAATA-TTATAA
16419703 AAACTTATAAATATTATAA
1 AAACTTAT-AATATTATAA
*
16419722 AAACATATAATA
1 AAACTTATAATA
16419734 AATCTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 4 0.14
19 21 0.72
20 4 0.14
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
AAACTTATAATATTATAA
Found at i:16419710 original size:10 final size:9
Alignment explanation
Indices: 16419674--16419996 Score: 93
Period size: 10 Copynumber: 33.3 Consensus size: 9
16419664 TAAAAATATT
16419674 AAATTGATATA
1 AAATT-ATA-A
*
16419685 AACTTATAA
1 AAATTATAA
* *
16419694 TACTTATAA
1 AAATTATAA
16419703 AAACTTATAA
1 AAA-TTATAA
*
16419713 ATATTATAA
1 AAATTATAA
*
16419722 AAACATATAA
1 AAA-TTATAA
16419732 TAAATCTA-ATA
1 -AAAT-TATA-A
*
16419743 AAATTCTAAA
1 AAATTAT-AA
*
16419753 AAAATATAA
1 AAATTATAA
16419762 AAATTAATAA
1 AAATT-ATAA
16419772 ACATATT-TAA
1 A-A-ATTATAA
*
16419782 AATTTTATAA
1 AA-ATTATAA
*
16419792 AAACCTATAA
1 AAA-TTATAA
*
16419802 AAATCATAA
1 AAATTATAA
16419811 AAATTATTAA
1 AAATTA-TAA
**
16419821 ATGTTATTAA
1 AAATTA-TAA
*
16419831 ATATTA-AA
1 AAATTATAA
* *
16419839 AAAATATTA
1 AAATTATAA
* **
16419848 AAATCGATGT
1 AAAT-TATAA
16419858 AAATTATAA
1 AAATTATAA
*
16419867 AAAATATAA
1 AAATTATAA
*
16419876 TAA-TATAA
1 AAATTATAA
16419884 TAAATTATAAA
1 -AAATTAT-AA
16419895 CAAATT-TATA
1 -AAATTATA-A
16419905 AAATTAATAA
1 AAATT-ATAA
*
16419915 AATATATTTAA
1 AA-AT-TATAA
16419926 AATATT-TAA
1 AA-ATTATAA
**
16419935 TATTTTATAA
1 -AAATTATAA
*
16419945 GAAGTTATAA
1 -AAATTATAA
16419955 AAATTCATAA
1 AAATT-ATAA
*
16419965 AAACTTTTAA
1 AAA-TTATAA
*
16419975 ATAA-TATTAT
1 A-AATTA-TAA
16419985 AAATTATAA
1 AAATTATAA
16419994 AAA
1 AAA
16419997 AATATCATTT
Statistics
Matches: 236, Mismatches: 46, Indels: 62
0.69 0.13 0.18
Matches are distributed among these distances:
8 11 0.05
9 79 0.33
10 107 0.45
11 35 0.15
12 4 0.02
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (9 bp):
AAATTATAA
Found at i:16419887 original size:27 final size:27
Alignment explanation
Indices: 16419857--16419920 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
16419847 AAAATCGATG
16419857 TAAATTATAAA-AAA-TATAATAATATAA
1 TAAATTATAAACAAATTATAA-AAT-TAA
16419884 TAAATTATAAACAAATTTATAAAATTAA
1 TAAATTATAAACAAA-TTATAAAATTAA
*
16419912 TAAAATATA
1 TAAATTATA
16419921 TTTAAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 11 0.33
28 14 0.42
29 3 0.09
30 5 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
TAAATTATAAACAAATTATAAAATTAA
Found at i:16421388 original size:59 final size:57
Alignment explanation
Indices: 16421313--16421683 Score: 324
Period size: 59 Copynumber: 6.4 Consensus size: 57
16421303 AATAAGGATC
* * * *
16421313 AAAATGGAATTTTTGGACGTTTGAGGGT-AAAATGGTAATTTTTGGAAGTTTGGGGGGGT
1 AAAATGTAATTTTTGGAAGTTCGAGGGTAAAAAT-GTAATTTTTGGAAG-TT-GGGGGCT
* * * *
16421372 AAAATGTAACTTTTGGAAGTTTCG-GGGTAAAAATGGAA-TTTTGGAAGTTCGGGAGCA
1 AAAATGTAATTTTTGGAAG-TTCGAGGGTAAAAATGTAATTTTTGGAAGTT-GGGGGCT
*
16421429 AAAATGTAATTTTTAGAAGTCTCGA-GGTCAAAAATGTAATTTTTGGAAGTTCGGGGG-T
1 AAAATGTAATTTTTGGAAGT-TCGAGGGT-AAAAATGTAATTTTTGGAAGTT-GGGGGCT
* * * * * * **
16421487 AAAAATGTAATTTTGGAGAAGTTTGGGGGTCAAAATGGAATTTTTGGAAGTTCGAGGGAA
1 -AAAATGTAATTTTTG-GAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTT-GGGGGCT
* * ** *
16421547 AAAATATAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTAGAAGTTTCGAGCT
1 AAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTGGGGGCT
* * *
16421604 CAAACATGTAATTTTTGGAAGTTCGGGGGT-AAAATGTAATTTTTAGAAGTTTTGGGG-T
1 -AAA-ATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAG-TTGGGGGCT
*
16421662 CAAAATGGAATTTTTGGAAGTT
1 -AAAATGTAATTTTTGGAAGTT
16421684 TTATAAGCTT
Statistics
Matches: 260, Mismatches: 39, Indels: 28
0.80 0.12 0.09
Matches are distributed among these distances:
56 1 0.00
57 48 0.18
58 75 0.29
59 120 0.46
60 16 0.06
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTGGGGGCT
Found at i:16421684 original size:87 final size:86
Alignment explanation
Indices: 16421313--16421684 Score: 382
Period size: 87 Copynumber: 4.3 Consensus size: 86
16421303 AATAAGGATC
* *
16421313 AAAATGGAATTTTTGGACGTTT-GAGGGT-AAAATGGTAATTTTTGGAAGTTTGGGGGGGTAAAA
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTCAAAAT-GTAATTTTTGGAAG-TT-CGGGGGTAAAA
*
16421376 TGTAACTTTTGGAAGTTTCGGGGTA
62 TGTAATTTTTGGAAGTTTCGGGGTA
* * *
16421401 AAAATGGAA-TTTTGGAAG-TTCG-GGAGCAAAAATGTAATTTTTAGAAGTCTC-GAGGTCAAAA
1 AAAATGGAATTTTTGGAAGTTTCGAGG-TC-AAAATGTAATTTTTGGAAGT-TCGGGGGT--AAA
16421462 ATGTAATTTTTGGAAG-TTCGGGGGTA
61 ATGTAATTTTTGGAAGTTTC-GGGGTA
* * * * * ** *
16421488 AAAATGTAATTTTGGAGAAGTTTGGGGGTCAAAATGGAATTTTTGGAAGTTCGAGGGAAAAAATA
1 AAAATGGAATTTTTG-GAAGTTTCGAGGTCAAAATGTAATTTTTGGAAGTTCG-GGGGTAAAATG
16421553 TAATTTTTGGAAG-TTCGAGGGTA
64 TAATTTTTGGAAGTTTCG-GGGTA
* * *
16421576 AAAATGTAATTTTTAGAAGTTTCGAGCTCAAACATGTAATTTTTGGAAGTTCGGGGGTAAAATGT
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAA-ATGTAATTTTTGGAAGTTCGGGGGTAAAATGT
* * *
16421641 AATTTTTAGAAGTTTTGGGGTC
65 AATTTTTGGAAGTTTCGGGGTA
16421663 AAAATGGAATTTTTGGAAGTTT
1 AAAATGGAATTTTTGGAAGTTT
16421685 TATAAGCTTG
Statistics
Matches: 237, Mismatches: 30, Indels: 35
0.78 0.10 0.12
Matches are distributed among these distances:
85 6 0.03
86 6 0.03
87 114 0.48
88 81 0.34
89 22 0.09
90 6 0.03
91 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (86 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAATGTAATTTTTGGAAGTTCGGGGGTAAAATGTA
ATTTTTGGAAGTTTCGGGGTA
Found at i:16421685 original size:29 final size:29
Alignment explanation
Indices: 16421311--16421684 Score: 347
Period size: 29 Copynumber: 12.8 Consensus size: 29
16421301 AAAATAAGGA
* *
16421311 TCAAAATGGAATTTTTGGACGTTT-GAGGG
1 TCAAAATGTAATTTTTGGAAGTTTCG-GGG
*
16421340 T-AAAATGGTAATTTTTGGAAGTTTGGGGGGG
1 TCAAAAT-GTAATTTTTGGAAGTTT--CGGGG
*
16421371 T-AAAATGTAACTTTTGGAAGTTTCGGGG
1 TCAAAATGTAATTTTTGGAAGTTTCGGGG
* *
16421399 TAAAAATGGAA-TTTTGGAAG-TTCGGGAG
1 TCAAAATGTAATTTTTGGAAGTTTCGGG-G
* * *
16421427 -CAAAAATGTAATTTTTAGAAGTCTCGAGG
1 TC-AAAATGTAATTTTTGGAAGTTTCGGGG
16421456 TCAAAAATGTAATTTTTGGAAG-TTCGGGGG
1 TC-AAAATGTAATTTTTGGAAGTTTC-GGGG
* * *
16421486 TAAAAATGTAATTTTGGAGAAGTTTGGGGG
1 TCAAAATGTAATTTTTG-GAAGTTTCGGGG
*
16421516 TCAAAATGGAATTTTTGGAAG-TTCGAGGG
1 TCAAAATGTAATTTTTGGAAGTTTCG-GGG
** *
16421545 AAAAAATATAATTTTTGGAAG-TTCGAGGG
1 TCAAAATGTAATTTTTGGAAGTTTCG-GGG
* * * *
16421574 TAAAAATGTAATTTTTAGAAGTTTCGAGC
1 TCAAAATGTAATTTTTGGAAGTTTCGGGG
16421603 TCAAACATGTAATTTTTGGAAG-TTCGGGGG
1 TCAAA-ATGTAATTTTTGGAAGTTTC-GGGG
* *
16421633 T-AAAATGTAATTTTTAGAAGTTTTGGGG
1 TCAAAATGTAATTTTTGGAAGTTTCGGGG
*
16421661 TCAAAATGGAATTTTTGGAAGTTT
1 TCAAAATGTAATTTTTGGAAGTTT
16421685 TATAAGCTTG
Statistics
Matches: 289, Mismatches: 37, Indels: 38
0.79 0.10 0.10
Matches are distributed among these distances:
27 6 0.02
28 51 0.18
29 132 0.46
30 88 0.30
31 11 0.04
32 1 0.00
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.34
Consensus pattern (29 bp):
TCAAAATGTAATTTTTGGAAGTTTCGGGG
Found at i:16425665 original size:63 final size:63
Alignment explanation
Indices: 16425592--16425720 Score: 197
Period size: 63 Copynumber: 2.0 Consensus size: 63
16425582 ACTAAAGAAA
* *
16425592 CTATAAACAACCTAACCTGCTACTATAAG-TCTTACTTCTATTGCAGACCTTTTTTGTCAGATT
1 CTATAAACAACCTAACCTGCTACTATAAGCT-TTACTTCTACTGCAGACCTTCTTTGTCAGATT
* * *
16425655 CTATAAACAACCTAACCTGCTACTATAAGCTTTACTTCTGCTGTAGACCTTCTTTGTTAGATT
1 CTATAAACAACCTAACCTGCTACTATAAGCTTTACTTCTACTGCAGACCTTCTTTGTCAGATT
16425718 CTA
1 CTA
16425721 GGCATAATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 59 0.98
64 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (63 bp):
CTATAAACAACCTAACCTGCTACTATAAGCTTTACTTCTACTGCAGACCTTCTTTGTCAGATT
Found at i:16429674 original size:26 final size:27
Alignment explanation
Indices: 16429622--16429675 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
16429612 ATACCAGAAT
* * * *
16429622 ATCATCATACTGACATCATAACTCAAA
1 ATCATCACACTGACAACACAACACAAA
16429649 ATCATCACA-TGACAACACAACACAAA
1 ATCATCACACTGACAACACAACACAAA
16429675 A
1 A
16429676 CATTACCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.50, C:0.28, G:0.04, T:0.19
Consensus pattern (27 bp):
ATCATCACACTGACAACACAACACAAA
Found at i:16430183 original size:23 final size:23
Alignment explanation
Indices: 16430154--16430215 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
16430144 AATGGGTCAA
16430154 TCAAAGTCAACAGGT-TAAGTCGG
1 TCAAAGTCAACAGGTCT-AGTCGG
* *
16430177 TCAAAGTCAACGGGTCTGGTCGG
1 TCAAAGTCAACAGGTCTAGTCGG
*
16430200 TCAAAGTCAACGGGTC
1 TCAAAGTCAACAGGTC
16430216 GAGCTCATGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (23 bp):
TCAAAGTCAACAGGTCTAGTCGG
Found at i:16434346 original size:31 final size:30
Alignment explanation
Indices: 16434311--16434381 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 30
16434301 CATAAAAATC
16434311 AGTGACTGTTCTGTCAC-TTTTCGATAATGTT-
1 AGTGACTGTTCTGTCACATTTTC-A-AA-GTTG
*
16434342 AGTGACTGTTTTGTCACATTTTCAAAGTTG
1 AGTGACTGTTCTGTCACATTTTCAAAGTTG
16434372 AGTGACTGTT
1 AGTGACTGTT
16434382 GTGTTAAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.32
31 17 0.46
32 5 0.14
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (30 bp):
AGTGACTGTTCTGTCACATTTTCAAAGTTG
Found at i:16436355 original size:28 final size:29
Alignment explanation
Indices: 16436323--16436386 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
16436313 AAGTCTAAAC
*
16436323 TAAAAAA-GTAATCTTAATTGCTTCAAAA
1 TAAAAAATATAATCTTAATTGCTTCAAAA
* * * *
16436351 TAAAAAATATAATTTTATTTGTTTTAAAA
1 TAAAAAATATAATCTTAATTGCTTCAAAA
16436380 TAAAAAA
1 TAAAAAA
16436387 ATTAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (29 bp):
TAAAAAATATAATCTTAATTGCTTCAAAA
Found at i:16438503 original size:18 final size:17
Alignment explanation
Indices: 16438466--16438520 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
16438456 CGGCTCAAAC
16438466 TTTTTCAAGTTTGAATT
1 TTTTTCAAGTTTGAATT
16438483 TTTTTCTAA-TTTGAATAT
1 TTTTTC-AAGTTTGAAT-T
* *
16438501 TTTTT-TAGATTGAATT
1 TTTTTCAAGTTTGAATT
16438517 TTTT
1 TTTT
16438521 CAGATTCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 6 0.18
17 19 0.58
18 8 0.24
ACGTcount: A:0.24, C:0.04, G:0.09, T:0.64
Consensus pattern (17 bp):
TTTTTCAAGTTTGAATT
Found at i:16438814 original size:2 final size:2
Alignment explanation
Indices: 16438807--16438831 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16438797 ATTATCTAGA
16438807 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 A
16438832 AAAGTCACAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16441574 original size:14 final size:14
Alignment explanation
Indices: 16441536--16441579 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
16441526 CAAAATGTAC
16441536 AATATAATTAAA-T
1 AATATAATTAAATT
16441549 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
16441564 AA-ATAATTTAATT
1 AATATAATTAAATT
16441577 AAT
1 AAT
16441580 TATTTACCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:16442988 original size:18 final size:17
Alignment explanation
Indices: 16442956--16442995 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
16442946 AGATTTTCGA
16442956 ATTTTCTTATCTATTTC
1 ATTTTCTTATCTATTTC
* *
16442973 ATTTTCTTTATTTATTTT
1 ATTTTC-TTATCTATTTC
16442991 ATTTT
1 ATTTT
16442996 ATGTTCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTCTTATCTATTTC
Found at i:16445612 original size:15 final size:15
Alignment explanation
Indices: 16445594--16445629 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
16445584 TGAATGTAAT
16445594 ATAAAAAATTAACAA-
1 ATAAAAAATTAA-AAG
16445609 ATAAAAAATTAAAAG
1 ATAAAAAATTAAAAG
16445624 ATAAAA
1 ATAAAA
16445630 TTATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (15 bp):
ATAAAAAATTAAAAG
Done.