Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 83 of 198
Found at i:26452327 original size:100 final size:100
Alignment explanation
Indices: 26452149--26452630 Score: 617
Period size: 100 Copynumber: 4.8 Consensus size: 100
26452139 TAGATATTAT
* * * *
26452149 TTCCCCGGCGGTGCAGTGGAACAGATTAACGCCACAACAGTGAATCTTGCTTCCCCAACATTGCA
1 TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCA
* * *
26452214 GTTAGAAATATTAAAGCTACAACAGTGAATCTTAC
66 GTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC
*
26452249 TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGTTTCCCCGACATTGCA
1 TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCA
*
26452314 GTTAAAAAGATTAAAGCTACAACAGCGAATCTTAT
66 GTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC
*
26452349 TTCCCTA-GCAGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGC
1 TTCCC-AGGCGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGC
* *
26452413 AGTTAAAAAGATCAAAGCTACAACAGCGAATCTTAT
65 AGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC
* * *
26452449 TTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCA
1 TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCA
* * * *
26452514 GTTGAATAGATTAAAGCTGCAACAGCGGATCTTACC
66 GTTAAAAAGATTAAAGCTACAACAGCGAATCTTA-C
* ** * ** * * * * * * *
26452550 TTCCC-GACATTACAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTACTTCCCTGATAGTGCA
1 TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCA
** *
26452614 GTGGAACAGATTAAAGC
66 GTTAAAAAGATTAAAGC
26452631 CACATTGGTG
Statistics
Matches: 341, Mismatches: 38, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
100 335 0.98
101 6 0.02
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (100 bp):
TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCA
GTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC
Found at i:26452635 original size:150 final size:148
Alignment explanation
Indices: 26452145--26452666 Score: 551
Period size: 150 Copynumber: 3.5 Consensus size: 148
26452135 ATTATAGATA
* * * *
26452145 TTATTTCCCCGGCGGTGCAGTGGAACAGATTAACGCCACAACAGTGAATCTTGCTTCCCCAACAT
1 TTATTTCCCTGACAGTGCAGTGGAACAGATTAAAGCCACAACAGTGAATCTTGCTTCCCCAACAT
* * ** ** *
26452210 TGCAGTTAGAAATATTAAAGCTACAACAGTGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGAT
66 TGCAGTT-GAAAGATTAAAGCTACAACAGTGAATCTTACTTCCC-GACATTGCAGTTAAAAAGAT
* *
26452275 TAAAGCCACATCAGTGAATC
129 TAAAGCTACAACAGTGAATC
* * * ** * * * ** * * *
26452295 TTGTTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTATTTCCCTAGCAG
1 TTATTTCCCTGACAGTGCAGTGGAACAGATTAAAGCCACAACAGTGAATCTTGCTTCCCCAACAT
* * * *
26452360 TGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
66 TGCAGTTGAA-AGATTAAAGCTACAACAGTGAATCTTACTT-CCCGACATTGCAGTTAAAAAGAT
* *
26452425 CAAAGCTACAACAGCGAATC
129 TAAAGCTACAACAGTGAATC
* * * *
26452445 TTATTTCCCTGGC-GATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACA
1 TTATTTCCCTGACAG-TGCAGTGGAACAGATTAAAGCCACAACAGTGAATCTTGCTTCCCCAACA
* * * *
26452509 TTGCAGTTGAATAGATTAAAGCTGCAACAGCGGATCTTACCTTCCCGACATTACAGTTAAAAAGA
65 TTGCAGTTGAA-AGATTAAAGCTACAACAGTGAATCTTA-CTTCCCGACATTGCAGTTAAAAAGA
26452574 TTAAAGCTACAACAGTGAATC
128 TTAAAGCTACAACAGTGAATC
* * *** *
26452595 TTACTTCCCTGATAGTGCAGTGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCCCAAAAT
1 TTATTTCCCTGACAGTGCAGTGGAACAGATTAAAGCCACAACAGTGAATCTTGCTTCCCCAACAT
*
26452660 TACAGTT
66 TGCAGTT
26452667 AAAAAAAGGA
Statistics
Matches: 302, Mismatches: 65, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
149 3 0.01
150 292 0.97
151 7 0.02
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (148 bp):
TTATTTCCCTGACAGTGCAGTGGAACAGATTAAAGCCACAACAGTGAATCTTGCTTCCCCAACAT
TGCAGTTGAAAGATTAAAGCTACAACAGTGAATCTTACTTCCCGACATTGCAGTTAAAAAGATTA
AAGCTACAACAGTGAATC
Found at i:26454103 original size:23 final size:23
Alignment explanation
Indices: 26454059--26454104 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
26454049 TTTTTTTTAC
* *
26454059 ATTTTTTTATTAATTCATTTATT
1 ATTTTATTATTAATTAATTTATT
26454082 ATTTTATTATT-ATTAATGTTATT
1 ATTTTATTATTAATTAAT-TTATT
26454105 GGTATGTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
ATTTTATTATTAATTAATTTATT
Found at i:26458571 original size:16 final size:16
Alignment explanation
Indices: 26458550--26458581 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
26458540 GCATTGGAAC
*
26458550 TTTTACTTTTATTTTA
1 TTTTACTTATATTTTA
26458566 TTTTACTTATATTTTA
1 TTTTACTTATATTTTA
26458582 ATCATTTCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTACTTATATTTTA
Found at i:26461417 original size:385 final size:385
Alignment explanation
Indices: 26460702--26461477 Score: 1527
Period size: 385 Copynumber: 2.0 Consensus size: 385
26460692 GCTATTACAG
26460702 AAAGA-TGTTAAGTTTGAGTGGTCAGAAAAGTGCCAGAAAAGTTTCGATCAGTTGAAAGCTCTTT
1 AAAGATTGTTAAGTTTGAGTGGTCAGAAAAGTGCCAGAAAAGTTTCGATCAGTTGAAAGCTCTTT
26460766 TGACCAAGGCTCTAGTGTTAGTTCAGCTAGAATCGAGTAAATAATTTGTTATTTATAGTGATGCA
66 TGACCAAGGCTCTAGTGTTAGTTCAGCTAGAATCGAGTAAATAATTTGTTATTTATAGTGATGCA
26460831 TCTTTGAGTGGTTTGGGTTGTGTTTTGATGGAGGAAGGCAAAGTTATAGCTTATGCCTCGAGACA
131 TCTTTGAGTGGTTTGGGTTGTGTTTTGATGGAGGAAGGCAAAGTTATAGCTTATGCCTCGAGACA
26460896 GTTAAAGCCACATGAAAAGAACTATCCGACGCATGATCTCGAATTGGCCGCTATTGTGTTTGCTT
196 GTTAAAGCCACATGAAAAGAACTATCCGACGCATGATCTCGAATTGGCCGCTATTGTGTTTGCTT
* *
26460961 TGAAAATGTGGTGCCACTATTTGTTTGGTGAAAAATGTCATGTTTATTCTGATCATAAAAGTTTG
261 TGAAAATATGGTACCACTATTTGTTTGGTGAAAAATGTCATGTTTATTCTGATCATAAAAGTTTG
26461026 AAATATTTGATGACTTAGAAGGATCTGAATCTGAGAAAGCGACAGTGGTTAGAGTTGCTA
326 AAATATTTGATGACTTAGAAGGATCTGAATCTGAGAAAGCGACAGTGGTTAGAGTTGCTA
26461086 AAAGATTGTTAAGTTTGAGTGGTCAGAAAAGTGCCAGAAAAGTTTCGATCAGTTGAAAGCTCTTT
1 AAAGATTGTTAAGTTTGAGTGGTCAGAAAAGTGCCAGAAAAGTTTCGATCAGTTGAAAGCTCTTT
26461151 TGACCAAGGCTCTAGTGTTAGTTCAGCTAGAATCGAGTAAATAATTTGTTATTTATAGTGATGCA
66 TGACCAAGGCTCTAGTGTTAGTTCAGCTAGAATCGAGTAAATAATTTGTTATTTATAGTGATGCA
26461216 TCTTTGAGTGGTTTGGGTTGTGTTTTGATGGAGGAAGGCAAAGTTATAGCTTATGCCTCGAGACA
131 TCTTTGAGTGGTTTGGGTTGTGTTTTGATGGAGGAAGGCAAAGTTATAGCTTATGCCTCGAGACA
26461281 GTTAAAGCCACATGAAAAGAACTATCCGACGCATGATCTCGAATTGGCCGCTATTGTGTTTGCTT
196 GTTAAAGCCACATGAAAAGAACTATCCGACGCATGATCTCGAATTGGCCGCTATTGTGTTTGCTT
26461346 TGAAAATATGGTACCACTATTTGTTTGGTGAAAAATGTCATGTTTATTCTGATCATAAAAGTTTG
261 TGAAAATATGGTACCACTATTTGTTTGGTGAAAAATGTCATGTTTATTCTGATCATAAAAGTTTG
26461411 AAATATTTGATGACTTAGAAGGATCTGAATCTGAGAAAGCGACAGTGGTTAGAGTTGCTA
326 AAATATTTGATGACTTAGAAGGATCTGAATCTGAGAAAGCGACAGTGGTTAGAGTTGCTA
26461471 AAAGATT
1 AAAGATT
26461478 ACGAGCTTGT
Statistics
Matches: 389, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
384 5 0.01
385 384 0.99
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.33
Consensus pattern (385 bp):
AAAGATTGTTAAGTTTGAGTGGTCAGAAAAGTGCCAGAAAAGTTTCGATCAGTTGAAAGCTCTTT
TGACCAAGGCTCTAGTGTTAGTTCAGCTAGAATCGAGTAAATAATTTGTTATTTATAGTGATGCA
TCTTTGAGTGGTTTGGGTTGTGTTTTGATGGAGGAAGGCAAAGTTATAGCTTATGCCTCGAGACA
GTTAAAGCCACATGAAAAGAACTATCCGACGCATGATCTCGAATTGGCCGCTATTGTGTTTGCTT
TGAAAATATGGTACCACTATTTGTTTGGTGAAAAATGTCATGTTTATTCTGATCATAAAAGTTTG
AAATATTTGATGACTTAGAAGGATCTGAATCTGAGAAAGCGACAGTGGTTAGAGTTGCTA
Found at i:26464479 original size:42 final size:42
Alignment explanation
Indices: 26464367--26464519 Score: 186
Period size: 41 Copynumber: 3.7 Consensus size: 42
26464357 ACTATGTATT
* *
26464367 AGTTTTTATCAGGCTATAAGCCTAGCAGGCCTTGTGCCAGTG
1 AGTTTTTATCAGGCTATAAGCCTAGCAGGCCTAGTGCCGGTG
* * *
26464409 TG-ATATATCAGGCTATAAGCCTAGCAGGCCTAGTGCCGGTG
1 AGTTTTTATCAGGCTATAAGCCTAGCAGGCCTAGTGCCGGTG
* * * *
26464450 AGTTTTTATTAAGCTATAAGCCTAGCAGGCCTACTGTCGAG-G
1 AGTTTTTATCAGGCTATAAGCCTAGCAGGCCTAGTGCCG-GTG
*
26464492 AGTTTTTATCAGGCT-TGAGCCTAGCAGG
1 AGTTTTTATCAGGCTATAAGCCTAGCAGG
26464520 TTTTATGCCG
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
41 48 0.51
42 45 0.48
43 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (42 bp):
AGTTTTTATCAGGCTATAAGCCTAGCAGGCCTAGTGCCGGTG
Found at i:26469876 original size:16 final size:15
Alignment explanation
Indices: 26469849--26469882 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
26469839 ATAACTAGTA
*
26469849 TATAATTATATTTAT
1 TATAATTATATTAAT
26469864 TATAATATATATTAAT
1 TATAAT-TATATTAAT
26469880 TAT
1 TAT
26469883 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:26470438 original size:21 final size:20
Alignment explanation
Indices: 26470412--26470453 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
26470402 TCACGCCGTG
26470412 CCTTG-CTACTCGCACCAACAC
1 CCTTGCCTA-TCGCACC-ACAC
26470433 CCTTGCCTATCGCACCACAC
1 CCTTGCCTATCGCACCACAC
26470453 C
1 C
26470454 ATCAAGACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 12 0.60
22 3 0.15
ACGTcount: A:0.21, C:0.50, G:0.10, T:0.19
Consensus pattern (20 bp):
CCTTGCCTATCGCACCACAC
Found at i:26475812 original size:35 final size:36
Alignment explanation
Indices: 26475729--26475814 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
26475719 TTCTGTTGAT
* * * * *
26475729 ATTCTGATTCGCGTGTTAATCATGCCATTATTACTT
1 ATTCTGATTCGCATGCTAAGCATGCCACTATTACTG
26475765 ATTCTGATTCGCATGCTAAGCATGCCACTA-TACTG
1 ATTCTGATTCGCATGCTAAGCATGCCACTATTACTG
*
26475800 ATTCTGAATCGCATG
1 ATTCTGATTCGCATG
26475815 TAAAGGATGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 18 0.41
36 26 0.59
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (36 bp):
ATTCTGATTCGCATGCTAAGCATGCCACTATTACTG
Found at i:26475973 original size:43 final size:42
Alignment explanation
Indices: 26475923--26476014 Score: 130
Period size: 43 Copynumber: 2.2 Consensus size: 42
26475913 ATGGAGGAAT
** *
26475923 ACATTATCTGGAATTATATCAGCATTATCTGGTGGCTTGACC
1 ACATTATCTGGAATTATATCAGCATTATCTACTAGCTTGACC
* *
26475965 ACAATTATCTGGAATTATATCTGTATTATCTACTAGCTTGACC
1 AC-ATTATCTGGAATTATATCAGCATTATCTACTAGCTTGACC
26476008 ACATTAT
1 ACATTAT
26476015 TGGTGTGTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 7 0.16
43 37 0.84
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (42 bp):
ACATTATCTGGAATTATATCAGCATTATCTACTAGCTTGACC
Found at i:26479738 original size:20 final size:20
Alignment explanation
Indices: 26479707--26479808 Score: 87
Period size: 20 Copynumber: 5.1 Consensus size: 20
26479697 ATTTGTGAAA
*
26479707 AAGCCACCAGTAATGCAGAC
1 AAGCTACCAGTAATGCAGAC
* * ** *
26479727 AAGCTGCTAGTAATGTGGTC
1 AAGCTACCAGTAATGCAGAC
* *
26479747 AAGCCACCAGTAATGCAGAT
1 AAGCTACCAGTAATGCAGAC
** * * *
26479767 AAATTGCCAGTAGTGCGGAC
1 AAGCTACCAGTAATGCAGAC
26479787 AAGCTACCAGTAATGCAGAC
1 AAGCTACCAGTAATGCAGAC
26479807 AA
1 AA
26479809 ATTGCTGGTA
Statistics
Matches: 57, Mismatches: 25, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (20 bp):
AAGCTACCAGTAATGCAGAC
Found at i:26479762 original size:40 final size:40
Alignment explanation
Indices: 26479707--26479845 Score: 188
Period size: 40 Copynumber: 3.5 Consensus size: 40
26479697 ATTTGTGAAA
** *
26479707 AAGCCACCAGTAATGCAGACAAGCTGCTAGTAATGTGGTC
1 AAGCCACCAGTAATGCAGACAAATTGCTAGTAATGTGGAC
* * * *
26479747 AAGCCACCAGTAATGCAGATAAATTGCCAGTAGTGCGGAC
1 AAGCCACCAGTAATGCAGACAAATTGCTAGTAATGTGGAC
* *
26479787 AAGCTACCAGTAATGCAGACAAATTGCTGGTAATGTGGAC
1 AAGCCACCAGTAATGCAGACAAATTGCTAGTAATGTGGAC
*
26479827 AAGCCACCAATAATGCAGA
1 AAGCCACCAGTAATGCAGA
26479846 TTAATTGTCA
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 84 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (40 bp):
AAGCCACCAGTAATGCAGACAAATTGCTAGTAATGTGGAC
Found at i:26486355 original size:13 final size:13
Alignment explanation
Indices: 26486328--26486394 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 13
26486318 AATATGTGTT
* *
26486328 AAATGTTTAGATG
1 AAATGGTTATATG
*
26486341 AAATGGTTATTTG
1 AAATGGTTATATG
**
26486354 AAAAAGTTATATG
1 AAATGGTTATATG
* *
26486367 AAATGATTGTATG
1 AAATGGTTATATG
*
26486380 AATTGGTTATATG
1 AAATGGTTATATG
26486393 AA
1 AA
26486395 TTTGTTACAC
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.39
Consensus pattern (13 bp):
AAATGGTTATATG
Found at i:26486395 original size:13 final size:13
Alignment explanation
Indices: 26486359--26486401 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
26486349 ATTTGAAAAA
*
26486359 GTTATATGAAATG
1 GTTATATGAATTG
* *
26486372 ATTGTATGAATTG
1 GTTATATGAATTG
*
26486385 GTTATATGAATTT
1 GTTATATGAATTG
26486398 GTTA
1 GTTA
26486402 CACGGAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.47
Consensus pattern (13 bp):
GTTATATGAATTG
Found at i:26489791 original size:49 final size:50
Alignment explanation
Indices: 26489676--26489803 Score: 154
Period size: 49 Copynumber: 2.6 Consensus size: 50
26489666 GAGGTTCCCC
* * *
26489676 GTAAGACCATGTCTGGGACATGGCATGGGTAACGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGTAACGATATGAAAAATCCCAT
** *
26489726 GTAAGACCATACCTGGGATATGGCATTGGTAGTAC-A-A-GAAAAATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGTA--ACGATATGAAAAATCCCAT
*
26489775 GTAAGACCATGTCTGGGACATGGCTTTGG
1 GTAAGACCATGTCTGGGACATGGCATTGG
26489804 CATGTTATTA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
49 35 0.53
50 28 0.42
51 1 0.02
52 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGTAACGATATGAAAAATCCCAT
Found at i:26496866 original size:50 final size:50
Alignment explanation
Indices: 26496738--26496979 Score: 197
Period size: 50 Copynumber: 4.8 Consensus size: 50
26496728 ACATTTGGGT
* * *
26496738 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATGGGCA-C--CGA
* ** *
26496789 GATTATGATAGGTCCCATGTAAGACCATGTCTGGGATATGGTGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACCGA
* *
26496842 GATGAGAGGTCCC-TCGTAAAACCATGTCTGGGACATGGCATGGGCACCGA
1 GATGAGAGGTCCCAT-GTAAGACCATGTCTGGGATATGGCATGGGCACCGA
* ** * *
26496892 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACCG-A
* * * ** *
26496941 CACGAAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGC
26496980 TTTCGCATGT
Statistics
Matches: 158, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
48 1 0.01
49 34 0.22
50 78 0.49
51 2 0.01
53 3 0.02
54 5 0.03
55 1 0.01
56 34 0.22
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACCGA
Found at i:26508808 original size:54 final size:53
Alignment explanation
Indices: 26508733--26508870 Score: 134
Period size: 54 Copynumber: 2.5 Consensus size: 53
26508723 GAATAGCCTC
* * * * *
26508733 TATGACAAACTCTTAATGAATAGTCTTTGTGGCGTACTCTAAAAGAATAGCA-TT
1 TATGGCAAACTCTGAAAGAATAG-CTTTGTGACGAACTCTAAAAGAATAG-AGTT
* * * *
26508787 TGTGGCAAACTTTGAAAGAATAGCGTTTATGACGAACTCTGAAAGAATAGAGTTT
1 TATGGCAAACTCTGAAAGAATAGC-TTTGTGACGAACTCTAAAAGAATAGAG-TT
*
26508842 TATGGCAAACTCTGAAAGAGTAGACTTTG
1 TATGGCAAACTCTGAAAGAATAG-CTTTG
26508871 CGGCAAACTT
Statistics
Matches: 67, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
53 2 0.03
54 39 0.58
55 25 0.37
56 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (53 bp):
TATGGCAAACTCTGAAAGAATAGCTTTGTGACGAACTCTAAAAGAATAGAGTT
Found at i:26508841 original size:27 final size:27
Alignment explanation
Indices: 26508768--26508890 Score: 122
Period size: 27 Copynumber: 4.5 Consensus size: 27
26508758 TTTGTGGCGT
* *
26508768 ACTCTAAAAGAATAGCA-TTTGTGGCAA
1 ACTCTGAAAGAATAG-AGTTTATGGCAA
* * * *
26508795 ACTTTGAAAGAATAGCGTTTATGACGA
1 ACTCTGAAAGAATAGAGTTTATGGCAA
26508822 ACTCTGAAAGAATAGAGTTTTATGGCAA
1 ACTCTGAAAGAATAGAG-TTTATGGCAA
* * **
26508850 ACTCTGAAAGAGTAGACTTTGCGGCAA
1 ACTCTGAAAGAATAGAGTTTATGGCAA
*
26508877 ACTTTGAAAGAATA
1 ACTCTGAAAGAATA
26508891 ACCTTTGTTG
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
27 55 0.71
28 23 0.29
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (27 bp):
ACTCTGAAAGAATAGAGTTTATGGCAA
Found at i:26508896 original size:27 final size:27
Alignment explanation
Indices: 26508738--26508913 Score: 111
Period size: 27 Copynumber: 6.5 Consensus size: 27
26508728 GCCTCTATGA
* * **
26508738 CAAACTCTTAATGAATAGTCTTTGTGG
1 CAAACTCTGAAAGAATAACCTTTGTGG
** * * *
26508765 CGTACTCTAAAAGAATAGCATTTGTGG
1 CAAACTCTGAAAGAATAACCTTTGTGG
* * * * *
26508792 CAAACTTTGAAAGAATAGCGTTTATGA
1 CAAACTCTGAAAGAATAACCTTTGTGG
* ** *
26508819 CGAACTCTGAAAGAATAGAGTTTTATGG
1 CAAACTCTGAAAGAATA-ACCTTTGTGG
* *
26508847 CAAACTCTGAAAGAGTAGA-CTTTGCGG
1 CAAACTCTGAAAGAATA-ACCTTTGTGG
* *
26508874 CAAACTTTGAAAGAATAACCTTTGTTG
1 CAAACTCTGAAAGAATAACCTTTGTGG
* *
26508901 CGAACTCTAAAAG
1 CAAACTCTGAAAG
26508914 GGATGCCTTT
Statistics
Matches: 116, Mismatches: 31, Indels: 4
0.77 0.21 0.03
Matches are distributed among these distances:
26 1 0.01
27 92 0.79
28 23 0.20
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (27 bp):
CAAACTCTGAAAGAATAACCTTTGTGG
Found at i:26511287 original size:29 final size:28
Alignment explanation
Indices: 26511194--26511287 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 28
26511184 CAGAGATCGT
*
26511194 CACAAAGGCATTTCCTTTC-AGAGATTTTC
1 CACAAAGGC-TTTCCTATCTAGAG-TTTTC
* * ** *
26511223 CACAAAGGCGTTCTTAAATAGAGGTTTC
1 CACAAAGGCTTTCCTATCTAGAGTTTTC
26511251 CACAAAGGCTTTCCTATCTAGAGTTTTGC
1 CACAAAGGCTTTCCTATCTAGAGTTTT-C
*
26511280 CATAAAGG
1 CACAAAGG
26511288 TTGTCCTTTA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
28 30 0.59
29 21 0.41
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (28 bp):
CACAAAGGCTTTCCTATCTAGAGTTTTC
Found at i:26511530 original size:53 final size:53
Alignment explanation
Indices: 26511443--26511595 Score: 204
Period size: 53 Copynumber: 2.9 Consensus size: 53
26511433 TTAAATTTCT
* *
26511443 CCATATGATGCTATAACCCACCAGTTA-TGATCTTACATGATATGTTCTTCTTC
1 CCATATGATGC-ATAACCCACCAGTTACAGATCTTACATGATATGGTCTTCTTC
*
26511496 CCATATGATGTCATAACCCACTAGTTACAG-TCTTACATGATATGGTCTTCTTC
1 CCATATGATG-CATAACCCACCAGTTACAGATCTTACATGATATGGTCTTCTTC
* * *
26511549 CCATATGATGCCATAACCAACCAGTTAC-GACCTTACAGGATATGGTC
1 CCATATGATG-CATAACCCACCAGTTACAGATCTTACATGATATGGTC
26511596 CTTTAGTGCC
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
52 1 0.01
53 86 0.97
54 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (53 bp):
CCATATGATGCATAACCCACCAGTTACAGATCTTACATGATATGGTCTTCTTC
Found at i:26517914 original size:18 final size:18
Alignment explanation
Indices: 26517893--26517932 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
26517883 GATTGAGAGT
* * *
26517893 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
26517911 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
26517929 GAAA
1 GAAA
26517933 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:26527766 original size:2 final size:2
Alignment explanation
Indices: 26527759--26527791 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
26527749 TTGGTAAAAC
26527759 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 A
26527792 ACTCGGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26530453 original size:16 final size:16
Alignment explanation
Indices: 26530415--26530445 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
26530405 CCCAATGCTG
26530415 TAGTCGAATAGATCCA
1 TAGTCGAATAGATCCA
26530431 TAGTCGAATAGATCC
1 TAGTCGAATAGATCC
26530446 TCGATCGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (16 bp):
TAGTCGAATAGATCCA
Found at i:26531227 original size:17 final size:18
Alignment explanation
Indices: 26531194--26531230 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
26531184 TATACACTTG
26531194 TAAAGTAAATTCAATAAT
1 TAAAGTAAATTCAATAAT
26531212 TAAA-TAAATATC-ATAAT
1 TAAAGTAAAT-TCAATAAT
26531229 TA
1 TA
26531231 TCCAGAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (18 bp):
TAAAGTAAATTCAATAAT
Found at i:26531378 original size:26 final size:23
Alignment explanation
Indices: 26531349--26531395 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
26531339 CTGGCATTTC
26531349 TTTTAATTAGCTTAATTAATTGATAG
1 TTTTAATTAG-TT--TTAATTGATAG
26531375 TTTTAATTAGTTTTAATTGAT
1 TTTTAATTAGTTTTAATTGAT
26531396 TCATTGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
25 2 0.10
26 10 0.48
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (23 bp):
TTTTAATTAGTTTTAATTGATAG
Found at i:26535616 original size:40 final size:40
Alignment explanation
Indices: 26535549--26535767 Score: 251
Period size: 40 Copynumber: 5.5 Consensus size: 40
26535539 GAGAATAAAA
* * * * *
26535549 AGGGGCACGTAAGTGCATTTAGAGGTACCAAAGTACAAAT
1 AGGGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAAC
* * * * *
26535589 AGGTGTATGTAAGTGGAATCAGGGGTACCGAATTACAAAC
1 AGGGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAAC
* * * * *
26535629 AGGGGCATGTAAGCGCAATCAGGGTTATCAAAGTACAAAC
1 AGGGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAAC
* * * *
26535669 AGAGGCACGTAAGTGCAATCAGGGGTATCGAAGTGCAAAT
1 AGGGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAAC
26535709 AGGGGCACGTAAGTGCAATCAGGGGTA-CGAAGTACAAAC
1 AGGGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAAC
*
26535748 AGTGGCACGTAAGTGCAATC
1 AGGGGCACGTAAGTGCAATC
26535768 CTACAATAAT
Statistics
Matches: 150, Mismatches: 29, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
39 29 0.19
40 121 0.81
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.18
Consensus pattern (40 bp):
AGGGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAAC
Found at i:26535651 original size:20 final size:20
Alignment explanation
Indices: 26535628--26535767 Score: 88
Period size: 20 Copynumber: 7.0 Consensus size: 20
26535618 GAATTACAAA
*
26535628 CAGGGGCATGTAAGCGCAAT
1 CAGGGGCATGTAAGTGCAAT
** ** * *
26535648 CAGGGTTATCAAAGTACAAA
1 CAGGGGCATGTAAGTGCAAT
* *
26535668 CAGAGGCACGTAAGTGCAAT
1 CAGGGGCATGTAAGTGCAAT
*
26535688 CAGGGGTATCG-AAGTGCAAAT
1 CAGGGGCAT-GTAAGTGC-AAT
*
26535709 -AGGGGCACGTAAGTGCAAT
1 CAGGGGCATGTAAGTGCAAT
* * * *
26535728 CAGGGGTACG-AAGTACAAA
1 CAGGGGCATGTAAGTGCAAT
* *
26535747 CAGTGGCACGTAAGTGCAAT
1 CAGGGGCATGTAAGTGCAAT
26535767 C
1 C
26535768 CTACAATAAT
Statistics
Matches: 88, Mismatches: 27, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
19 19 0.22
20 65 0.74
21 4 0.05
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (20 bp):
CAGGGGCATGTAAGTGCAAT
Found at i:26538231 original size:28 final size:30
Alignment explanation
Indices: 26538172--26538232 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
26538162 TTTTGAATGT
* *
26538172 TTAAATTGATGAACCTTGTGATGTTAGATG
1 TTAAATTGATGAACCTTGAGATATTAGATG
* *
26538202 TTAAA-TGATG-ACTTTGAGATATTAGTTG
1 TTAAATTGATGAACCTTGAGATATTAGATG
26538230 TTA
1 TTA
26538233 TAAAGAAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 17 0.63
29 5 0.19
30 5 0.19
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (30 bp):
TTAAATTGATGAACCTTGAGATATTAGATG
Found at i:26544119 original size:20 final size:20
Alignment explanation
Indices: 26544083--26544120 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
26544073 GACCCAAATA
*
26544083 CTAGCCCAACTAGCCTAAGC
1 CTAGCCCAACTACCCTAAGC
26544103 CTAGCCCAA-TAACCCTAA
1 CTAGCCCAACT-ACCCTAA
26544121 ATCATTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.34, C:0.39, G:0.11, T:0.16
Consensus pattern (20 bp):
CTAGCCCAACTACCCTAAGC
Found at i:26544256 original size:15 final size:17
Alignment explanation
Indices: 26544215--26544250 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
26544205 CCAGGCTTCC
26544215 CCCTCGCGCGTGTTGCG
1 CCCTCGCGCGTGTTGCG
*
26544232 CCCGCGCGCGTGTTGCG
1 CCCTCGCGCGTGTTGCG
26544249 CC
1 CC
26544251 TCCGCGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.44, G:0.36, T:0.19
Consensus pattern (17 bp):
CCCTCGCGCGTGTTGCG
Found at i:26544269 original size:19 final size:18
Alignment explanation
Indices: 26544247--26544287 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
26544237 GCGCGTGTTG
*
26544247 CGCCTCCGCGCCAAAGCCA
1 CGCCTCCGAGCCAAA-CCA
*
26544266 CGCCTCCGAGCCGAACCA
1 CGCCTCCGAGCCAAACCA
26544284 CGCC
1 CGCC
26544288 ACCACCAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (18 bp):
CGCCTCCGAGCCAAACCA
Found at i:26544822 original size:17 final size:15
Alignment explanation
Indices: 26544800--26544840 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
26544790 GAGCTCTCTG
26544800 TTTTCTTTTTATGTGTC
1 TTTTCTTTTTAT-T-TC
*
26544817 TTTTCTTTTTATTTT
1 TTTTCTTTTTATTTC
26544832 TTTTCTTTT
1 TTTTCTTTT
26544841 GTTTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.43
16 1 0.04
17 12 0.52
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTATTTC
Found at i:26548273 original size:32 final size:32
Alignment explanation
Indices: 26548228--26548293 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
26548218 TCGAACACTA
26548228 TCCCATTGACTACTAAAGTCATCTGTTATTTT
1 TCCCATTGACTACTAAAGTCATCTGTTATTTT
*
26548260 TCCCATTGGCTACTAAAGTCATCTGTTATTTT
1 TCCCATTGACTACTAAAGTCATCTGTTATTTT
26548292 TC
1 TC
26548294 AATCTCTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.44
Consensus pattern (32 bp):
TCCCATTGACTACTAAAGTCATCTGTTATTTT
Found at i:26553168 original size:19 final size:19
Alignment explanation
Indices: 26553144--26553183 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
26553134 ACTTAAGAGG
26553144 ATAGTTTTAAGTGTCCAAC
1 ATAGTTTTAAGTGTCCAAC
26553163 ATAGTTTTAAGTGTCCAAC
1 ATAGTTTTAAGTGTCCAAC
26553182 AT
1 AT
26553184 TAGAACTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (19 bp):
ATAGTTTTAAGTGTCCAAC
Found at i:26554819 original size:29 final size:30
Alignment explanation
Indices: 26554743--26554848 Score: 105
Period size: 29 Copynumber: 3.7 Consensus size: 30
26554733 ACTTAATTCA
* *
26554743 TTTGTGGCAATCTCAT-TTAATTGAATGCC
1 TTTGTGGCTATCTCATGTTAAATGAATGCC
* *
26554772 TTTCTGGCTATATCA-GTTAAATGAATGCC
1 TTTGTGGCTATCTCATGTTAAATGAATGCC
* * *
26554801 TTTGTGGCGATCT-ATGTTATGA-GAAAGCC
1 TTTGTGGCTATCTCATGTTA-AATGAATGCC
26554830 TTTGTGGCTATCTC-TGTTA
1 TTTGTGGCTATCTCATGTTA
26554849 TAAAAAAACA
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
28 1 0.02
29 61 0.97
30 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.41
Consensus pattern (30 bp):
TTTGTGGCTATCTCATGTTAAATGAATGCC
Found at i:26554849 original size:29 final size:29
Alignment explanation
Indices: 26554798--26554876 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
26554788 TTAAATGAAT
* * *
26554798 GCCTTTGTGGCGATCTATGTTATGAGAAA
1 GCCTTTGTGGCTATCTATGTTATAAAAAA
*
26554827 GCCTTTGTGGCTATCTCTGTTATAAAAAA
1 GCCTTTGTGGCTATCTATGTTATAAAAAA
* * *
26554856 ACATTTGCGGCTATCTATGTT
1 GCCTTTGTGGCTATCTATGTT
26554877 CAAAGGAATG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (29 bp):
GCCTTTGTGGCTATCTATGTTATAAAAAA
Found at i:26559402 original size:73 final size:73
Alignment explanation
Indices: 26559310--26559457 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 73
26559300 GAGAAGAGAA
*
26559310 AATTACCAAATAGCCCTTGTACTTAGTCTTTGTTCAATTTAGATAGGTAAGTTCGTATGAACTAT
1 AATTACCAAATAGCCCTTGTACTTAGTCTTTGTTCAATTTAGACAGGTAAGTTCGTATGAACTAT
26559375 AATCACTT
66 AATCACTT
26559383 AATTACCAAATAGCCCTTGTACTTAGTCTTTGTTCAATTTAGACAGGTAAGTTCGTATGAACTAT
1 AATTACCAAATAGCCCTTGTACTTAGTCTTTGTTCAATTTAGACAGGTAAGTTCGTATGAACTAT
26559448 AATCACTT
66 AATCACTT
26559456 AA
1 AA
26559458 ATGTTGATTA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (73 bp):
AATTACCAAATAGCCCTTGTACTTAGTCTTTGTTCAATTTAGACAGGTAAGTTCGTATGAACTAT
AATCACTT
Found at i:26564340 original size:28 final size:28
Alignment explanation
Indices: 26564300--26564355 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
26564290 AAGTAAGCTT
* *
26564300 CTCGAATTTGGAATCTTCGTTTTAATGA
1 CTCGAAGTTGGAATCTTCATTTTAATGA
*
26564328 CTCGAAGTTGGAATCTTTATTTTAATGA
1 CTCGAAGTTGGAATCTTCATTTTAATGA
26564356 TGTGATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (28 bp):
CTCGAAGTTGGAATCTTCATTTTAATGA
Found at i:26565969 original size:24 final size:24
Alignment explanation
Indices: 26565937--26565994 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
26565927 AAAGACTAAT
26565937 GTTGGATATGCCACAATCCACGTA
1 GTTGGATATGCCACAATCCACGTA
* *
26565961 GTTGGATATACCACAATCCATGTA
1 GTTGGATATGCCACAATCCACGTA
*
26565985 GTGGGATATG
1 GTTGGATATG
26565995 ATTGATCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (24 bp):
GTTGGATATGCCACAATCCACGTA
Found at i:26570627 original size:7 final size:7
Alignment explanation
Indices: 26570606--26570640 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
26570596 CTTTTAAGGG
*
26570606 TAATTAA
1 TAATCAA
26570613 TAAT-AA
1 TAATCAA
26570619 TAATCAA
1 TAATCAA
26570626 TAATCAA
1 TAATCAA
26570633 TAATCAA
1 TAATCAA
26570640 T
1 T
26570641 TTATTGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (7 bp):
TAATCAA
Found at i:26575048 original size:48 final size:49
Alignment explanation
Indices: 26574952--26575073 Score: 126
Period size: 48 Copynumber: 2.5 Consensus size: 49
26574942 GCAGTAGTAA
* * * *
26574952 TTTGCAAATTTGATGG-TTTATCCACAACCTACATGTTTCGGCACCTTG
1 TTTGCGAATTTGGTGGCTTTGTCCACAACCTACATGTCTCGGCACCTTG
* *
26575000 TTTGCGAATTTGGTGGCTTTGTCCACAA-CTATATGTACT-GGCAGCTTG
1 TTTGCGAATTTGGTGGCTTTGTCCACAACCTACATGT-CTCGGCACCTTG
* *
26575048 TCTT-TGAATTTGGTGGCTTCGTCCAC
1 T-TTGCGAATTTGGTGGCTTTGTCCAC
26575074 TGATATGTTG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
48 50 0.79
49 13 0.21
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (49 bp):
TTTGCGAATTTGGTGGCTTTGTCCACAACCTACATGTCTCGGCACCTTG
Found at i:26580464 original size:29 final size:28
Alignment explanation
Indices: 26580431--26580615 Score: 129
Period size: 29 Copynumber: 6.6 Consensus size: 28
26580421 TCTAAATGGT
*
26580431 AGCCTTTGTGGCTATCTTTGTTACAAAT-A
1 AGCCTTTGTGGCTATCTTAGTT--AAATGA
*
26580460 AGCCTTTATGGCTATCTTAGTTAAATGA
1 AGCCTTTGTGGCTATCTTAGTTAAATGA
26580488 ATGCCTTTGTGGCTAT-TTCAGTTAAATGGA
1 A-GCCTTTGTGGCTATCTT-AGTTAAAT-GA
* * *
26580518 TGCCTTTATGGCTATCTCAGTTAAATGGA
1 AGCCTTTGTGGCTATCTTAGTTAAAT-GA
* * *
26580547 TGCC-TT-T-G-T-TC-T-GCTAAAAGAA
1 AGCCTTTGTGGCTATCTTAGTTAAATG-A
*
26580569 AGCCTTTGTGGCTATCTCTA-TTGAAAGGA
1 AGCCTTTGTGGCTATCT-TAGTT-AAATGA
*
26580598 TGCCTTTGTGGCTATCTT
1 AGCCTTTGTGGCTATCTT
26580616 TGGAAAGGAA
Statistics
Matches: 128, Mismatches: 13, Indels: 31
0.74 0.08 0.18
Matches are distributed among these distances:
21 1 0.01
22 9 0.07
23 2 0.02
24 3 0.02
25 2 0.02
26 2 0.02
27 7 0.05
28 7 0.05
29 88 0.69
30 7 0.05
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (28 bp):
AGCCTTTGTGGCTATCTTAGTTAAATGA
Found at i:26580494 original size:58 final size:57
Alignment explanation
Indices: 26580432--26580555 Score: 162
Period size: 58 Copynumber: 2.1 Consensus size: 57
26580422 CTAAATGGTA
* *
26580432 GCCTTTGTGGCTATCTT-TGTTACAAAT-AAGCCTTTATGGCTATCTTAGTTAAATGAAT
1 GCCTTTGTGGCTAT-TTCAGTT--AAATGAAGCCTTTATGGCTATCTCAGTTAAATGAAT
* *
26580490 GCCTTTGTGGCTATTTCAGTTAAATGGATGCCTTTATGGCTATCTCAGTTAAATGGAT
1 GCCTTTGTGGCTATTTCAGTTAAAT-GAAGCCTTTATGGCTATCTCAGTTAAATGAAT
26580548 GCCTTTGT
1 GCCTTTGT
26580556 TCTGCTAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
56 4 0.07
57 2 0.03
58 53 0.90
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (57 bp):
GCCTTTGTGGCTATTTCAGTTAAATGAAGCCTTTATGGCTATCTCAGTTAAATGAAT
Found at i:26582980 original size:19 final size:20
Alignment explanation
Indices: 26582936--26582980 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
26582926 ATCATGTTTA
26582936 TATTTTTAACATAATTTAGT
1 TATTTTTAACATAATTTAGT
26582956 TA-TTTTATA-AT-ATTTAGT
1 TATTTTTA-ACATAATTTAGT
26582974 TATTTTT
1 TATTTTT
26582981 CGACAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.39
19 11 0.48
20 3 0.13
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (20 bp):
TATTTTTAACATAATTTAGT
Found at i:26584687 original size:42 final size:41
Alignment explanation
Indices: 26584594--26584857 Score: 230
Period size: 42 Copynumber: 6.3 Consensus size: 41
26584584 CGAGGGTTTT
* * *
26584594 CTAAGTGCTGATTCCACCGTAT-ATTTGATTGTGAAAGGGGTTG
1 CTAAGTGCTGATTCC-CCGTATCA-CTGAATAT-AAAGGGGTTG
* *
26584637 CTATGTGCTGATTCCCTGTATCACTGAATATAAAGGTGGTTG
1 CTAAGTGCTGATTCCCCGTATCACTGAATATAAAGG-GGTTG
* * *
26584679 CTAAGTGCT-ATTCCACCGTAT-ATTTGATTGTGAAAGGGGTTG
1 CTAAGTGCTGATTCC-CCGTATCA-CTGAATAT-AAAGGGGTTG
* *
26584721 TTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTG
1 CTAAGTGCTGATTCCCCGTATCACTGAATATAAAGG-GGTTG
* ** * *
26584763 CTAAGTGTTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTG
1 CTAAGTGCTGATTCC-CCGTATCACTGAATAT-AAAGGGGTTG
* * * *
26584806 CTATGTGCTGATTCCCCTTATCACTAAAT-TTAAGGTGGTTG
1 CTAAGTGCTGATTCCCCGTATCACTGAATATAAAGG-GGTTG
26584847 CTAAGTGCTGA
1 CTAAGTGCTGA
26584858 ATCCACTGAG
Statistics
Matches: 179, Mismatches: 31, Indels: 24
0.76 0.13 0.10
Matches are distributed among these distances:
40 4 0.02
41 32 0.18
42 82 0.46
43 56 0.31
44 5 0.03
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
CTAAGTGCTGATTCCCCGTATCACTGAATATAAAGGGGTTG
Found at i:26584820 original size:85 final size:85
Alignment explanation
Indices: 26584594--26584863 Score: 454
Period size: 84 Copynumber: 3.2 Consensus size: 85
26584584 CGAGGGTTTT
*
26584594 CTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCTGTATC
1 CTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATC
26584659 ACTGAATATAAAGGTGGTTG
66 ACTGAATATAAAGGTGGTTG
*
26584679 CTAAGTGCT-ATTCCACCGTATATTTGATTGTGAAAGGGGTTGTTATGTGCTGATTCCCCGTATC
1 CTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATC
26584743 ACTGAATATAAAGGTGGTTG
66 ACTGAATATAAAGGTGGTTG
* * *
26584763 CTAAGTGTTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCTTATC
1 CTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATC
* *
26584828 ACTAAAT-TTAAGGTGGTTG
66 ACTGAATATAAAGGTGGTTG
*
26584847 CTAAGTGCTGAATCCAC
1 CTAAGTGCTGATTCCAC
26584864 TGAGTAACGG
Statistics
Matches: 174, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
84 107 0.61
85 67 0.39
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (85 bp):
CTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATC
ACTGAATATAAAGGTGGTTG
Found at i:26600352 original size:12 final size:12
Alignment explanation
Indices: 26600309--26600353 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
26600299 CCACCCTTAA
26600309 GAACATTACATT
1 GAACATTACATT
* *
26600321 GAATATCACATT
1 GAACATTACATT
*
26600333 GAATATTACATT
1 GAACATTACATT
26600345 GAACATTAC
1 GAACATTAC
26600354 CCTTAAGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (12 bp):
GAACATTACATT
Found at i:26606932 original size:26 final size:26
Alignment explanation
Indices: 26606896--26606949 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
26606886 TTAGATAGGT
*
26606896 TGACAATGCACAATGCTATGGTTGAC
1 TGACAAGGCACAATGCTATGGTTGAC
26606922 TGACAAGGCACAATGCTATGGTTGAC
1 TGACAAGGCACAATGCTATGGTTGAC
26606948 TG
1 TG
26606950 TCGAACTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (26 bp):
TGACAAGGCACAATGCTATGGTTGAC
Found at i:26612800 original size:15 final size:15
Alignment explanation
Indices: 26612780--26612812 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
26612770 TAAATGTGTG
*
26612780 CTTATTGTTATTTAA
1 CTTATTGTTATATAA
26612795 CTTATTGTTATATAA
1 CTTATTGTTATATAA
26612810 CTT
1 CTT
26612813 GTTATAGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (15 bp):
CTTATTGTTATATAA
Found at i:26614048 original size:53 final size:53
Alignment explanation
Indices: 26613991--26614098 Score: 155
Period size: 53 Copynumber: 2.0 Consensus size: 53
26613981 CCTTAAATTC
* *
26613991 TTCCATATGATGTCATAACTCACCAGTTACGG-CATTACACGATATGGTCTTCT
1 TTCCATATGATGCCATAACCCACCAGTTACGGTC-TTACACGATATGGTCTTCT
* * *
26614044 TTCCATATGATGCCATAACCCACTAGTTATGGTCTTACACGATATGTTCTTCT
1 TTCCATATGATGCCATAACCCACCAGTTACGGTCTTACACGATATGGTCTTCT
26614097 TT
1 TT
26614099 AGTGCCATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
53 48 0.98
54 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (53 bp):
TTCCATATGATGCCATAACCCACCAGTTACGGTCTTACACGATATGGTCTTCT
Found at i:26616743 original size:13 final size:12
Alignment explanation
Indices: 26616720--26616762 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
26616710 TAATTTATTA
26616720 TTTATTATTTGGTT
1 TTTA-TATTT-GTT
26616734 TTTATATTTGTT
1 TTTATATTTGTT
*
26616746 TATTTTATTTGTT
1 T-TTATATTTGTT
26616759 TTTA
1 TTTA
26616763 GGCCAGGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 6 0.23
13 16 0.62
14 4 0.15
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTATATTTGTT
Found at i:26624114 original size:15 final size:15
Alignment explanation
Indices: 26624090--26624165 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 15
26624080 GAGAAAGAAA
*
26624090 AGAAATTTGAAAAAG
1 AGAAAATTGAAAAAG
26624105 AGAAAATTGAAAAAG
1 AGAAAATTGAAAAAG
26624120 A-AATTGAGATTGAAAAAG
1 AGAA---A-ATTGAAAAAG
*
26624138 -G--AAGTGAAAAAG
1 AGAAAATTGAAAAAG
*
26624150 AGAAAATCGAAAAAG
1 AGAAAATTGAAAAAG
26624165 A
1 A
26624166 AATTGAAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
12 9 0.18
13 2 0.04
14 2 0.04
15 25 0.51
17 1 0.02
18 10 0.20
ACGTcount: A:0.62, C:0.01, G:0.22, T:0.14
Consensus pattern (15 bp):
AGAAAATTGAAAAAG
Found at i:26638598 original size:12 final size:12
Alignment explanation
Indices: 26638583--26638608 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
26638573 AATAAAATAG
26638583 AAAAAAAAAGAA
1 AAAAAAAAAGAA
26638595 AAAAAAAAAGAA
1 AAAAAAAAAGAA
26638607 AA
1 AA
26638609 GGGAACGCAC
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:26646025 original size:45 final size:45
Alignment explanation
Indices: 26645815--26646016 Score: 305
Period size: 45 Copynumber: 4.5 Consensus size: 45
26645805 ACTAGAAACG
*
26645815 AGTAAGACCATTATTGAAAGACGTTATGGCATCACTATTCTATCA
1 AGTAAGACCATGATTGAAAGACGTTATGGCATCACTATTCTATCA
* * * *
26645860 AGTAAGACCACGACTAAAAGACGTTATGGCATCACTATTCTGTCA
1 AGTAAGACCATGATTGAAAGACGTTATGGCATCACTATTCTATCA
* * * *
26645905 AGTAAGACCATAACTGAAAGACGTTATGGCATTACTATTCTATCG
1 AGTAAGACCATGATTGAAAGACGTTATGGCATCACTATTCTATCA
*
26645950 AGTAAGACCATGATTGAAAGACGTTATGGCATCACTATTTTATCA
1 AGTAAGACCATGATTGAAAGACGTTATGGCATCACTATTCTATCA
*
26645995 AGTAAGACCATGGTTGAAAGAC
1 AGTAAGACCATGATTGAAAGAC
26646017 ACCATGGCAC
Statistics
Matches: 140, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 140 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (45 bp):
AGTAAGACCATGATTGAAAGACGTTATGGCATCACTATTCTATCA
Found at i:26646918 original size:20 final size:20
Alignment explanation
Indices: 26646893--26646934 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
26646883 AAGATAAAGT
26646893 TGCAATGAAAAGTAAGTAAA
1 TGCAATGAAAAGTAAGTAAA
*
26646913 TGCAATGGAAAGTAAGTAAA
1 TGCAATGAAAAGTAAGTAAA
26646933 TG
1 TG
26646935 GAAGGGTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.21
Consensus pattern (20 bp):
TGCAATGAAAAGTAAGTAAA
Found at i:26648857 original size:42 final size:42
Alignment explanation
Indices: 26648806--26648973 Score: 192
Period size: 42 Copynumber: 4.0 Consensus size: 42
26648796 AGAGCACAAC
* * * *
26648806 CACTCAAGCTCACATGGGGAGCTTTACTGATACACAACTTGT
1 CACTTAAGCTCATATGGGGAGCTTCACTGATACACAACTTAT
* * *
26648848 CACTTAAGCTCATTTGGGGAGCATCGCTGATACACAACTTAT
1 CACTTAAGCTCATATGGGGAGCTTCACTGATACACAACTTAT
* * * *
26648890 CATTTAAGCTCATATGAGGAGTTTCACTAATACACAACTTAT
1 CACTTAAGCTCATATGGGGAGCTTCACTGATACACAACTTAT
* * * **
26648932 CACTTCAGCTTATGTGGGGAGCTTCGTTGATACACAACTTAT
1 CACTTAAGCTCATATGGGGAGCTTCACTGATACACAACTTAT
26648974 AAAACTGTTT
Statistics
Matches: 103, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 103 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (42 bp):
CACTTAAGCTCATATGGGGAGCTTCACTGATACACAACTTAT
Found at i:26648935 original size:84 final size:84
Alignment explanation
Indices: 26648811--26648973 Score: 229
Period size: 84 Copynumber: 1.9 Consensus size: 84
26648801 ACAACCACTC
* * * *
26648811 AAGCTCACATGGGGAGCTTTACTGATACACAACTTGTCACTTAAGCTCATTTGGGGAGCATCGCT
1 AAGCTCACATGAGGAGCTTTACTAATACACAACTTATCACTTAAGCTCATGTGGGGAGCATCGCT
26648876 GATACACAACTTATCATTT
66 GATACACAACTTATCATTT
* * * * *
26648895 AAGCTCATATGAGGAG-TTTCACTAATACACAACTTATCACTTCAGCTTATGTGGGGAGCTTCGT
1 AAGCTCACATGAGGAGCTTT-ACTAATACACAACTTATCACTTAAGCTCATGTGGGGAGCATCGC
26648959 TGATACACAACTTAT
65 TGATACACAACTTAT
26648974 AAAACTGTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 3 0.04
84 66 0.96
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (84 bp):
AAGCTCACATGAGGAGCTTTACTAATACACAACTTATCACTTAAGCTCATGTGGGGAGCATCGCT
GATACACAACTTATCATTT
Found at i:26660913 original size:19 final size:19
Alignment explanation
Indices: 26660889--26660966 Score: 86
Period size: 20 Copynumber: 4.0 Consensus size: 19
26660879 TCTAACTTTT
26660889 TTAAAATCATTTTGA-TGTG
1 TTAAAATCATTTTGACT-TG
* *
26660908 TTAAAATGATTTTAACTTG
1 TTAAAATCATTTTGACTTG
*
26660927 ATTGAAATCATTTTGACTTGG
1 -TTAAAATCATTTTGACTT-G
*
26660948 TTAAAATCATTTTCACTTG
1 TTAAAATCATTTTGACTTG
26660967 AATTTAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 16 0.33
20 32 0.65
21 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (19 bp):
TTAAAATCATTTTGACTTG
Found at i:26660924 original size:39 final size:40
Alignment explanation
Indices: 26660889--26660976 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
26660879 TCTAACTTTT
*
26660889 TTAAAATCATTTTGA--TGTGTTAAAATGATTTTAACTTGA
1 TTAAAATCATTTTGACTTG-GTTAAAATCATTTTAACTTGA
* *
26660928 TTGAAATCATTTTGACTTGGTTAAAATCATTTTCACTTGAA
1 TTAAAATCATTTTGACTTGGTTAAAATCATTTTAACTTG-A
26660969 TTTAAAAT
1 -TTAAAAT
26660977 TGTTCCAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 14 0.34
40 18 0.44
41 3 0.07
42 6 0.15
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (40 bp):
TTAAAATCATTTTGACTTGGTTAAAATCATTTTAACTTGA
Found at i:26660966 original size:40 final size:39
Alignment explanation
Indices: 26660892--26660967 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
26660882 AACTTTTTTA
*
26660892 AAATCATTTTGATGTGTTAAAATGATTTTAACTTGATTG
1 AAATCATTTTGATGTGTTAAAATCATTTTAACTTGATTG
*
26660931 AAATCATTTTGACT-TGGTTAAAATCATTTTCACTTGA
1 AAATCATTTTGA-TGT-GTTAAAATCATTTTAACTTGA
26660968 ATTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 13 0.39
40 20 0.61
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (39 bp):
AAATCATTTTGATGTGTTAAAATCATTTTAACTTGATTG
Found at i:26663065 original size:20 final size:19
Alignment explanation
Indices: 26663017--26663084 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 19
26663007 AATAGCCCAT
26663017 GGTATCGAT-TTATTTACAAA
1 GGTATCGATATT-TTTA-AAA
*
26663037 --TATCAATATTGTTATAAAA
1 GGTATCGATATT-TT-TAAAA
26663056 -GTATCGATATTTTTAAAA
1 GGTATCGATATTTTTAAAA
26663074 TGGTATCGATA
1 -GGTATCGATA
26663085 CCAATTTACA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 11 0.28
19 9 0.22
20 20 0.50
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.41
Consensus pattern (19 bp):
GGTATCGATATTTTTAAAA
Found at i:26708674 original size:24 final size:24
Alignment explanation
Indices: 26708647--26708740 Score: 118
Period size: 24 Copynumber: 3.9 Consensus size: 24
26708637 TTTACTGCAA
* *
26708647 TATTGAGTGGTTTGTCCACAACGT
1 TATTGAGTGGCTTGACCACAACGT
* *
26708671 TATT-AGGTGGCTTGGCCACAAAGT
1 TATTGA-GTGGCTTGACCACAACGT
*
26708695 TATTGAGTGGCTTGACCACAACAT
1 TATTGAGTGGCTTGACCACAACGT
*
26708719 TATTGAGTGACTTGACCACAAC
1 TATTGAGTGGCTTGACCACAAC
26708741 ATGCAACTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
23 1 0.02
24 59 0.97
25 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (24 bp):
TATTGAGTGGCTTGACCACAACGT
Found at i:26708832 original size:48 final size:48
Alignment explanation
Indices: 26708759--26708851 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
26708749 TGTCTGCATT
*
26708759 TTGAGTGGCTTGGACACAACATTATTGAATGGCTTCACCACAATGATA
1 TTGAGTGCCTTGGACACAACATTATTGAATGGCTTCACCACAATGATA
* * * * *
26708807 TTGAGTGCCTTGGCCACAGCGTTATTGACTGGCTTGACCACAATG
1 TTGAGTGCCTTGGACACAACATTATTGAATGGCTTCACCACAATG
26708852 TACAGCTTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (48 bp):
TTGAGTGCCTTGGACACAACATTATTGAATGGCTTCACCACAATGATA
Found at i:26708847 original size:24 final size:24
Alignment explanation
Indices: 26708759--26708849 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
26708749 TGTCTGCATT
* *
26708759 TTGAGTGGCTTGGA-CACAACATTA
1 TTGAATGGCTT-GACCACAACGTTA
* * *
26708783 TTGAATGGCTTCACCACAATGATA
1 TTGAATGGCTTGACCACAACGTTA
* * * *
26708807 TTGAGTGCCTTGGCCACAGCGTTA
1 TTGAATGGCTTGACCACAACGTTA
*
26708831 TTGACTGGCTTGACCACAA
1 TTGAATGGCTTGACCACAA
26708850 TGTACAGCTT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
23 1 0.02
24 49 0.98
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
TTGAATGGCTTGACCACAACGTTA
Found at i:26722112 original size:16 final size:16
Alignment explanation
Indices: 26722091--26722123 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
26722081 CGACAATAAT
26722091 GGTTTCGGGGCCCCAA
1 GGTTTCGGGGCCCCAA
26722107 GGTTTCGGGGCCCCAA
1 GGTTTCGGGGCCCCAA
26722123 G
1 G
26722124 TTAGGTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.30, G:0.39, T:0.18
Consensus pattern (16 bp):
GGTTTCGGGGCCCCAA
Found at i:26723423 original size:45 final size:45
Alignment explanation
Indices: 26723371--26723567 Score: 132
Period size: 45 Copynumber: 4.4 Consensus size: 45
26723361 AGACCATAGT
*
26723371 TGAAAGACACTATGGCACCATACCA-AAAACT-AGTAAGACCATGAC
1 TGAAAGACATTATGGCACC--ACCATAAAACTGAGTAAGACCATGAC
* * * * * *
26723416 TGAAAGACGTTATGGCATCACGATTATATTGAGTAAGACCATGAC
1 TGAAAGACATTATGGCACCACCATAAAACTGAGTAAGACCATGAC
* * *** * *
26723461 TGAAAGACATTATGGCATCACGATTGTA-TCGAGTAATACCATTAC
1 TGAAAGACATTATGGCACCACCATAAAACT-GAGTAAGACCATGAC
* * *** *
26723506 TGAAAGACATTATGGCATCACGATTCTA-TCAAGTAAGACCATGAC
1 TGAAAGACATTATGGCACCACCATAAAACT-GAGTAAGACCATGAC
* *
26723551 TAAAAGACGTTATGGCA
1 TGAAAGACATTATGGCA
26723568 TCACGATTCT
Statistics
Matches: 132, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
43 3 0.02
44 4 0.03
45 125 0.95
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (45 bp):
TGAAAGACATTATGGCACCACCATAAAACTGAGTAAGACCATGAC
Found at i:26723568 original size:45 final size:45
Alignment explanation
Indices: 26723402--26723616 Score: 324
Period size: 45 Copynumber: 4.8 Consensus size: 45
26723392 ACCAAAAACT
* *
26723402 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTATATTG
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCG
* *
26723447 AGTAAGACCATGACTGAAAGACATTATGGCATCACGATTGTATCG
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCG
* * * *
26723492 AGTAATACCATTACTGAAAGACATTATGGCATCACGATTCTATCA
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCG
*
26723537 AGTAAGACCATGACTAAAAGACGTTATGGCATCACGATTCTATCG
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCG
*
26723582 AGTAAGACCAT-AGCTAAAAGACGTTATGGCATCAC
1 AGTAAGACCATGA-CTGAAAGACGTTATGGCATCAC
26723617 AAATCAAATT
Statistics
Matches: 157, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
44 1 0.01
45 156 0.99
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (45 bp):
AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCG
Found at i:26727029 original size:19 final size:18
Alignment explanation
Indices: 26726993--26727031 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
26726983 GGTGACCAAT
* *
26726993 TTTTTCCTTTTTGCTTCC
1 TTTTTCCTTTTCGATTCC
26727011 TTTTTCTCTTTTCGATTCC
1 TTTTTC-CTTTTCGATTCC
26727030 TT
1 TT
26727032 AGTGATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.03, C:0.26, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTTCCTTTTCGATTCC
Found at i:26727077 original size:21 final size:20
Alignment explanation
Indices: 26727042--26727082 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
26727032 AGTGATTAAA
* *
26727042 ACTTATTTTTTATTTCTTTC
1 ACTTATTTATTATTTATTTC
26727062 ACTTATTTGATTATTTATTTC
1 ACTTATTT-ATTATTTATTTC
26727083 TAGATCACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (20 bp):
ACTTATTTATTATTTATTTC
Found at i:26729695 original size:50 final size:50
Alignment explanation
Indices: 26729588--26729924 Score: 347
Period size: 50 Copynumber: 6.6 Consensus size: 50
26729578 TTCCAAAGCT
* ** * * * * *
26729588 ATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-CTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCC
* * * ** * * *
26729637 ATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCC
** * *
26729687 ATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCGACGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCC
* *
26729737 ATGTCCCAGACATGGTCTTAC-TCGGGACCTCTTATCTAGATGCCAACGCC
1 ATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATCTAGGTGCCAACGCC
26729787 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCA-GTGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-AGGTGCCAACGCC
* *
26729837 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAAAGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCT---AGGTGCCAACGCC
* *
26729893 ATGTCCCAAACATGGTCTTACATGGGATCTCT
1 ATGTCCCAGACATGGTCTTACATGGGACCTCT
26729925 TTACCCAAAT
Statistics
Matches: 244, Mismatches: 34, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
49 29 0.12
50 169 0.69
51 2 0.01
53 4 0.02
55 1 0.00
56 39 0.16
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCC
Found at i:26734669 original size:51 final size:51
Alignment explanation
Indices: 26734601--26734801 Score: 230
Period size: 51 Copynumber: 4.0 Consensus size: 51
26734591 ATTACTGATA
* * * *
26734601 CCGGTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATCACTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
* *
26734652 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTAT
* * * * * *
26734703 CCGGTACGCATAGTAGCCCGCACATGGTACTACACATGCGACCTATCA-T-T
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTAT
*
26734753 CTGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
26734802 TTCACTTTCA
Statistics
Matches: 123, Mismatches: 21, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
49 4 0.03
50 40 0.33
51 76 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (51 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
Found at i:26734788 original size:101 final size:102
Alignment explanation
Indices: 26734609--26734793 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
26734599 TACCGGTTCA
* *
26734609 CATAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCCACACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
26734674 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * * *
26734711 CATAGTAGCCCGCACATGGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCCACACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTGC
26734774 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
26734794 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 40 0.53
102 32 0.42
103 4 0.05
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (102 bp):
CATAGTAGCCCACACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:26738649 original size:61 final size:60
Alignment explanation
Indices: 26738584--26738788 Score: 248
Period size: 61 Copynumber: 3.4 Consensus size: 60
26738574 TAAACAGAAG
* * * *
26738584 TTGCCACAAAGGTTGTCATTTTCATTTAGTACTCCCCACAAAGGCTTTACTGTCCAGAGTT
1 TTGCCACAAAGGTTGTCCTTTACATCTAGTACTCGCCACAAAGG-TTTACTGTCCAGAGTT
* * *
26738645 TTGCCACAAAGGTTGTCCTTTAAATCTAGTACTCGCCACAAAGGGTTTCCTATCCAGAGTT
1 TTGCCACAAAGGTTGTCCTTTACATCTAGTACTCGCCACAAA-GGTTTACTGTCCAGAGTT
* * * ** *
26738706 TTGCAACAAAGGTTGTCCTTTACATCCAGTTCTCGTAACAAAGGTTTTCATGTCCAGAGTT
1 TTGCCACAAAGGTTGTCCTTTACATCTAGTACTCGCCACAAAGGTTTAC-TGTCCAGAGTT
* *
26738767 TTTCCATAAAGGTTGTCCTTTA
1 TTGCCACAAAGGTTGTCCTTTA
26738789 ACTGGTCTTT
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
60 6 0.05
61 116 0.94
62 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (60 bp):
TTGCCACAAAGGTTGTCCTTTACATCTAGTACTCGCCACAAAGGTTTACTGTCCAGAGTT
Found at i:26738985 original size:94 final size:94
Alignment explanation
Indices: 26738867--26739045 Score: 277
Period size: 94 Copynumber: 1.9 Consensus size: 94
26738857 GGACACCAGA
* * * *
26738867 GAACCCCATTAGGTAATAAGCTTCCTTAAACTTTCTCATATGATGTCATAACCGACCAATTACGG
1 GAACCACATTAGGTAATAACCTTCCTTAAACTTTCTCATATGATGTCATAACCCACCAATTACGA
* * *
26738932 TTTTACACGATATGGTCTTCTTTCCATAT
66 TATTACACAATATGATCTTCTTTCCATAT
* *
26738961 GAACCACATTAGGTAATAACCTTCCTTAAATTTTCTCATATGATGTCATAACCCACCAATTGCGA
1 GAACCACATTAGGTAATAACCTTCCTTAAACTTTCTCATATGATGTCATAACCCACCAATTACGA
26739026 TATTACACAATATGATCTTC
66 TATTACACAATATGATCTTC
26739046 AGCGCCATGG
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 76 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (94 bp):
GAACCACATTAGGTAATAACCTTCCTTAAACTTTCTCATATGATGTCATAACCCACCAATTACGA
TATTACACAATATGATCTTCTTTCCATAT
Found at i:26750621 original size:50 final size:50
Alignment explanation
Indices: 26750512--26750711 Score: 215
Period size: 50 Copynumber: 3.9 Consensus size: 50
26750502 ACATTTGGGT
* * * *
26750512 GATGAGA--TCCCATGTAAGACCATGTTTGGAACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA-C--CGA
*
26750563 GATTATGAGAGGTCCCATGTAAGACCATGTCTAGGATATGGCATTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGA
** * *
26750616 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGA
* ** *
26750666 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA
26750712 GTACAAGAAA
Statistics
Matches: 126, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
50 82 0.65
51 1 0.01
53 3 0.02
54 6 0.05
55 1 0.01
56 33 0.26
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGA
Found at i:26762783 original size:24 final size:26
Alignment explanation
Indices: 26762735--26762790 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 26
26762725 CACTGCTCAA
*
26762735 TTTTTCTTCTCTCGATCTTTCTTTTC
1 TTTTTCTTCTCTCGATCTTTATTTTC
26762761 TTCTTTCTT-TCTC-AT-TTTATTTTC
1 TT-TTTCTTCTCTCGATCTTTATTTTC
26762785 TTTTTC
1 TTTTTC
26762791 ATTTTCTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.14
24 10 0.36
25 2 0.07
26 6 0.21
27 6 0.21
ACGTcount: A:0.05, C:0.23, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTTCTTCTCTCGATCTTTATTTTC
Found at i:26764901 original size:18 final size:18
Alignment explanation
Indices: 26764861--26764903 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
26764851 AACACTTCAC
***
26764861 TTTTTTTTTACTTTGTAT
1 TTTTTTTTTACTTCAAAT
*
26764879 ATTTTTTTTACTTCAAAT
1 TTTTTTTTTACTTCAAAT
26764897 TTTTTTT
1 TTTTTTT
26764904 CAATTACAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTTTTTTACTTCAAAT
Found at i:26767057 original size:19 final size:20
Alignment explanation
Indices: 26767019--26767057 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
26767009 CGGTTTTTTT
*
26767019 GAAAAATCAGAATGAAATAG
1 GAAAAATCAGAATCAAATAG
*
26767039 GAAAAA-CAGAATCATATAG
1 GAAAAATCAGAATCAAATAG
26767058 TAATTATAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (20 bp):
GAAAAATCAGAATCAAATAG
Found at i:26771659 original size:61 final size:60
Alignment explanation
Indices: 26771561--26771763 Score: 237
Period size: 61 Copynumber: 3.3 Consensus size: 60
26771551 TTCTTAAACA
* * *
26771561 GCCACAAAGGTTGTCATTTATATCTAGTACTCCCCACAAAGGCTTTACTATCCAGATTTTT
1 GCCACAAAGGTTGTCCTTTACATCTAGTACTCGCCACAAAGG-TTTACTATCCAGATTTTT
* * * * * *
26771622 GCCACAAAAGTTGTCCTTTACATCCAATACTCGCCACAAAGGGATTCCTATCCAGAGTTTT
1 GCCACAAAGGTTGTCCTTTACATCTAGTACTCGCCACAAA-GGTTTACTATCCAGATTTTT
* * * *
26771683 GCCACAAAGGTTGTCCTTTACATCTAGTACTCGCAACAAAGGTTTTCATGTCCAAAGTTTTT
1 GCCACAAAGGTTGTCCTTTACATCTAGTACTCGCCACAAAGGTTTAC-TATCCAGA-TTTTT
*
26771745 -CCATAAAGGTTGTCCTTTA
1 GCCACAAAGGTTGTCCTTTA
26771764 ACTGGTGTTT
Statistics
Matches: 120, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
60 5 0.04
61 109 0.91
62 6 0.05
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (60 bp):
GCCACAAAGGTTGTCCTTTACATCTAGTACTCGCCACAAAGGTTTACTATCCAGATTTTT
Found at i:26771699 original size:29 final size:27
Alignment explanation
Indices: 26771594--26771699 Score: 61
Period size: 29 Copynumber: 3.6 Consensus size: 27
26771584 CTAGTACTCC
*
26771594 CCACAAAGGCTTTACTATCCAGATTTTTG
1 CCACAAAGG-TTTCCTATCCAGA-TTTTG
* * *
26771623 CCACAAAAGTTGTCCTTTACATCCA-ATACTCG
1 CCACAAAGGTT-TCC--T--ATCCAGAT-TTTG
*
26771655 CCACAAAGGGATTCCTATCCAGAGTTTTG
1 CCACAAA-GGTTTCCTATCCAGA-TTTTG
26771684 CCACAAAGGTTGTCCT
1 CCACAAAGGTT-TCCT
26771700 TTACATCTAG
Statistics
Matches: 58, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
28 10 0.17
29 24 0.41
30 2 0.03
31 2 0.03
32 13 0.22
33 7 0.12
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (27 bp):
CCACAAAGGTTTCCTATCCAGATTTTG
Found at i:26771961 original size:16 final size:16
Alignment explanation
Indices: 26771937--26771968 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
26771927 TTTTTATATG
26771937 AACCACATTAGGTAAT
1 AACCACATTAGGTAAT
*
26771953 AACCCCATTAGGTAAT
1 AACCACATTAGGTAAT
26771969 GACCTTCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (16 bp):
AACCACATTAGGTAAT
Found at i:26774573 original size:27 final size:27
Alignment explanation
Indices: 26774543--26775044 Score: 654
Period size: 27 Copynumber: 18.6 Consensus size: 27
26774533 AGTTGTGGGC
*
26774543 AAATGACCAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
26774570 AAATGACCGAAATACCC-CTAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
26774596 AAATGATCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
26774623 AAATTACTGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
26774650 AAATAACCGAAATACCC-CTAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
26774676 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* ** *
26774703 AAATAACTAAAATACCC-CTAAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
* *
26774730 AAATAACCGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
26774757 AAATAACTGAAATACCTTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
26774784 AAATGATCGAAATACCCTCGAAGGGTAA
1 AAATGACCGAAATACCCTCGAAGGGT-A
**
26774812 AAATGACTAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
26774839 AAATGATCGAAATACGCC-CGAAGGGTA
1 AAATGACCGAAATAC-CCTCGAAGGGTA
*
26774866 AAATGATCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
26774893 AAATGACTGAAATACCGC-CGAAGGGTA
1 AAATGACCGAAATACC-CTCGAAGGGTA
** *
26774920 AAATGACTAAAATTCCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
26774947 AAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
26774974 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** *
26775001 AAATGATTGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
26775028 AAATGACTGAAATACCC
1 AAATGACCGAAATACCC
26775045 CTGACCCTCG
Statistics
Matches: 422, Mismatches: 44, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
26 52 0.12
27 342 0.81
28 28 0.07
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:26775062 original size:34 final size:34
Alignment explanation
Indices: 26775014--26775079 Score: 116
Period size: 34 Copynumber: 1.9 Consensus size: 34
26775004 TGATTGAAAT
26775014 ACCCTCAAAGGGTAAAATGACTGAAATACCCCTG
1 ACCCTCAAAGGGTAAAATGACTGAAATACCCCTG
26775048 ACCCTCGAAA-GGTAAAATGACTGAAATACCCC
1 ACCCTC-AAAGGGTAAAATGACTGAAATACCCC
26775080 CATAGGGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 28 0.90
35 3 0.10
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (34 bp):
ACCCTCAAAGGGTAAAATGACTGAAATACCCCTG
Found at i:26775399 original size:28 final size:28
Alignment explanation
Indices: 26775356--26775460 Score: 131
Period size: 28 Copynumber: 3.8 Consensus size: 28
26775346 ACTGTAATGT
* *
26775356 TACTGTATTGGGCTAAGGCCAACACTGA
1 TACTATATTGGGCTAAGGCCCACACTGA
*
26775384 TACTATATTGGACTAAGGCCCACACTGA
1 TACTATATTGGGCTAAGGCCCACACTGA
* * * *
26775412 TATTGTATTTGGCTAAGGCCCACACTGC
1 TACTATATTGGGCTAAGGCCCACACTGA
26775440 TACTGA-ATTGGGCTAAGGCCC
1 TACT-ATATTGGGCTAAGGCCC
26775461 TCATTGTACA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.27
Consensus pattern (28 bp):
TACTATATTGGGCTAAGGCCCACACTGA
Found at i:26782349 original size:27 final size:26
Alignment explanation
Indices: 26782318--26782371 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 26
26782308 AAAATTTGAT
* *
26782318 TTTTTTAAATTTATTATTACATAAATTA
1 TTTTATAAATATATT-TTA-ATAAATTA
26782346 TTTTAATAAATATATTTTAATAAATT
1 TTTT-ATAAATATATTTTAATAAATT
26782372 GAGAATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 7 0.30
29 9 0.39
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTATAAATATATTTTAATAAATTA
Found at i:26782363 original size:14 final size:13
Alignment explanation
Indices: 26782323--26782371 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
26782313 TTGATTTTTT
26782323 TAAATTTATTATTACA
1 TAAA-TTATT-TTA-A
26782339 TAAATTATTTTAA
1 TAAATTATTTTAA
26782352 TAAATATATTTTAA
1 TAAAT-TATTTTAA
26782366 TAAATT
1 TAAATT
26782372 GAGAATTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.22
14 16 0.50
15 5 0.16
16 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
TAAATTATTTTAA
Found at i:26785648 original size:14 final size:16
Alignment explanation
Indices: 26785624--26785655 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
26785614 TGTTGACATC
26785624 TTTCAAGATTTTC-TT
1 TTTCAAGATTTTCATT
26785639 TTTC-AGATTTTCATT
1 TTTCAAGATTTTCATT
26785654 TT
1 TT
26785656 AAGGCAGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.19, C:0.12, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTCAAGATTTTCATT
Found at i:26789040 original size:15 final size:16
Alignment explanation
Indices: 26789020--26789049 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26789010 AAAAATGTAG
26789020 AAAAAA-TATATTTAT
1 AAAAAATTATATTTAT
26789035 AAAAAATTATATTTA
1 AAAAAATTATATTTA
26789050 AACCAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAAATTATATTTAT
Found at i:26793175 original size:35 final size:35
Alignment explanation
Indices: 26793136--26793207 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
26793126 CTTAATTCCA
*
26793136 CTTCAATGACTATTC-AGGAACTTCAATTGTCAAAG
1 CTTCAATGACTATTCGA-GAACTCCAATTGTCAAAG
*
26793171 CTTCAATGACTGTTCGAGAACTCCAATTGTCAAAG
1 CTTCAATGACTATTCGAGAACTCCAATTGTCAAAG
26793206 CT
1 CT
26793208 GATCAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 33 0.97
36 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (35 bp):
CTTCAATGACTATTCGAGAACTCCAATTGTCAAAG
Found at i:26803047 original size:37 final size:37
Alignment explanation
Indices: 26802944--26803126 Score: 309
Period size: 37 Copynumber: 5.0 Consensus size: 37
26802934 TACGTATGAT
* *
26802944 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
26802979 CACCTATCACTTTGTTTC-TGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
26803015 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
26803052 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
26803089 CACTTATCACTTTGTTTCTTGATCAGATAAGTATAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
26803126 C
1 C
26803127 GAAGCTATCA
Statistics
Matches: 141, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
35 9 0.06
36 38 0.27
37 94 0.67
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:26803168 original size:52 final size:52
Alignment explanation
Indices: 26803106--26803410 Score: 373
Period size: 46 Copynumber: 5.9 Consensus size: 52
26803096 CACTTTGTTT
26803106 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
*
26803158 CTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTTCCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCAC--T----TTT-CACTTGTCA
* *
26803217 CTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCAC---T---TTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
26803263 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCAC---T---TTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
* *
26803309 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
* ** *
26803361 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTT-TCACTTG
26803411 ATCAGAAGTA
Statistics
Matches: 227, Mismatches: 12, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
46 88 0.39
50 1 0.00
52 81 0.36
53 6 0.03
54 1 0.00
58 3 0.01
59 47 0.21
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (52 bp):
CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
Found at i:26803205 original size:59 final size:58
Alignment explanation
Indices: 26803132--26803258 Score: 218
Period size: 59 Copynumber: 2.2 Consensus size: 58
26803122 TAGCCGAAGC
*
26803132 TATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTT-TCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
*
26803191 TATCACTTTCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTT-CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
26803250 TATCACTTT
1 TATCACTTT
26803259 GTCACTTGAT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
58 1 0.02
59 64 0.98
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (58 bp):
TATCACTTTCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:26816566 original size:19 final size:17
Alignment explanation
Indices: 26816543--26816584 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 17
26816533 ATTTAGTCAT
26816543 TTTTTATTTTAATTTTAA
1 TTTTTATTTTAA-TTTAA
26816561 TATTTTATTTTAATTTAA
1 T-TTTTATTTTAATTTAA
26816579 TTTTTA
1 TTTTTA
26816585 CATCCTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 7 0.30
19 11 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTATTTTAATTTAA
Found at i:26825689 original size:20 final size:20
Alignment explanation
Indices: 26825659--26825756 Score: 65
Period size: 20 Copynumber: 4.9 Consensus size: 20
26825649 GTGGATGCAT
*
26825659 AACAAGGGCACCGAAGTGTA
1 AACAGGGGCACCGAAGTGTA
* * *
26825679 GACAGGGGCA-CAAATGTGCA
1 AACAGGGGCACCGAA-GTGTA
* *
26825699 AACAGGGCCACTGTAA-TGTA
1 AACAGGGGCACCG-AAGTGTA
* * *
26825719 AATAGAGACACCGAAGTGTA
1 AACAGGGGCACCGAAGTGTA
* *
26825739 TACAGGGGCACAGAAGTG
1 AACAGGGGCACCGAAGTG
26825757 CAAATCTCAT
Statistics
Matches: 56, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
19 5 0.09
20 49 0.88
22 2 0.04
ACGTcount: A:0.38, C:0.18, G:0.31, T:0.13
Consensus pattern (20 bp):
AACAGGGGCACCGAAGTGTA
Found at i:26829903 original size:28 final size:28
Alignment explanation
Indices: 26829861--26829948 Score: 135
Period size: 28 Copynumber: 3.2 Consensus size: 28
26829851 TGCTCTCCCC
26829861 AAATCCC-CCTCCAAAATCCTCTTGTAA
1 AAATCCCTCCTCCAAAATCCTCTTGTAA
26829888 AAATCCCTCCTCCAAAATCCT-TGTGTAA
1 AAATCCCTCCTCCAAAATCCTCT-TGTAA
* *
26829916 CAATCCCTCCTCCAAAATCCTCGTGTAA
1 AAATCCCTCCTCCAAAATCCTCTTGTAA
26829944 AAATC
1 AAATC
26829949 TCTCACCTCT
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
27 8 0.15
28 47 0.85
ACGTcount: A:0.33, C:0.35, G:0.06, T:0.26
Consensus pattern (28 bp):
AAATCCCTCCTCCAAAATCCTCTTGTAA
Found at i:26832483 original size:40 final size:40
Alignment explanation
Indices: 26832439--26832746 Score: 334
Period size: 40 Copynumber: 7.7 Consensus size: 40
26832429 GATACCAGAG
* *
26832439 TACAAACAGGGGCATGTATGTGCAATCAGGGGTATTGAAA
1 TACAAACAGGGGCACGTATGTGCAATCAGGGGTACTGAAA
* * * *
26832479 TACAAACAAGGGCAGGTATGTGCATTCAGGGGTACTGAAG
1 TACAAACAGGGGCACGTATGTGCAATCAGGGGTACTGAAA
** * * * *
26832519 TACAAACAGGGGCATATATGTACAATCAAGGG-AATCAAA
1 TACAAACAGGGGCACGTATGTGCAATCAGGGGTACTGAAA
* * *
26832558 GTACAAACAGGGGCACATATGTGCAATCAGGGTTA-TCAAA
1 -TACAAACAGGGGCACGTATGTGCAATCAGGGGTACTGAAA
* * * * *
26832598 GTACAAAAAAGGGCACGTATGTGCAATCAAGGGTACCGGAA
1 -TACAAACAGGGGCACGTATGTGCAATCAGGGGTACTGAAA
* * *
26832639 TACAAACAGGGGCACATATGTGCAATCAAGGGTAC-CAAA
1 TACAAACAGGGGCACGTATGTGCAATCAGGGGTACTGAAA
* * *
26832678 GTACAAATAGGGGCACGTATGTGCAATCAGGGGTACCGAAG
1 -TACAAACAGGGGCACGTATGTGCAATCAGGGGTACTGAAA
26832719 TACAAACAGGGGCACGTATGTGCAATCA
1 TACAAACAGGGGCACGTATGTGCAATCA
26832747 TACAATAGTT
Statistics
Matches: 226, Mismatches: 37, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
39 6 0.03
40 215 0.95
41 5 0.02
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (40 bp):
TACAAACAGGGGCACGTATGTGCAATCAGGGGTACTGAAA
Found at i:26832541 original size:20 final size:20
Alignment explanation
Indices: 26832518--26832589 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
26832508 GGGTACTGAA
26832518 GTACAAACAGGGGCATATAT
1 GTACAAACAGGGGCATATAT
* * * *
26832538 GTACAATCAAGGGAATCA-AA
1 GTACAAACAGGGGCAT-ATAT
*
26832558 GTACAAACAGGGGCACATAT
1 GTACAAACAGGGGCATATAT
* *
26832578 GTGCAATCAGGG
1 GTACAAACAGGG
26832590 TTATCAAAGT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (20 bp):
GTACAAACAGGGGCATATAT
Found at i:26832650 original size:120 final size:120
Alignment explanation
Indices: 26832426--26832746 Score: 439
Period size: 120 Copynumber: 2.7 Consensus size: 120
26832416 TATTTGATTC
* * *
26832426 AGGGATACCAGAGTACAAACAGGGGCATGTATGTGCAATCAGGGGTATTGAAA-TACAAACAAGG
1 AGGGA-ACCAAAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTA-TCAAAGTACAAACAAGG
* * * * *
26832490 GCAGGTATGTGCATTCAGGGGTACTGAAGTACAAACAGGGGCATATATGTACAATCA
64 GCACGTATGTGCAATCAAGGGTACGGAAGTACAAACAGGGGCACATATGTACAATCA
* * * *
26832547 AGGGAATCAAAGTACAAACAGGGGCACATATGTGCAATCAGGGTTATCAAAGTACAAAAAAGGGC
1 AGGGAACCAAAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTATCAAAGTACAAACAAGGGC
*
26832612 ACGTATGTGCAATCAAGGGTACCGGAA-TACAAACAGGGGCACATATGTGCAATCA
66 ACGTATGTGCAATCAAGGGTA-CGGAAGTACAAACAGGGGCACATATGTACAATCA
* * * * *
26832667 AGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGC
1 AGGGAACCAAAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTATCAAAGTACAAACAAGGGC
26832732 ACGTATGTGCAATCA
66 ACGTATGTGCAATCA
26832747 TACAATAGTT
Statistics
Matches: 176, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
119 4 0.02
120 163 0.93
121 9 0.05
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (120 bp):
AGGGAACCAAAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTATCAAAGTACAAACAAGGGC
ACGTATGTGCAATCAAGGGTACGGAAGTACAAACAGGGGCACATATGTACAATCA
Found at i:26832728 original size:20 final size:20
Alignment explanation
Indices: 26832628--26832730 Score: 57
Period size: 20 Copynumber: 5.2 Consensus size: 20
26832618 GTGCAATCAA
26832628 GGGTACCGGAA-TACAAACAG
1 GGGTACC-GAAGTACAAACAG
* ** * * * *
26832648 GGGCACATATGTGCAATCAA
1 GGGTACCGAAGTACAAACAG
* *
26832668 GGGTACCAAAGTACAAATAG
1 GGGTACCGAAGTACAAACAG
* * * *
26832688 GGGCA-CGTATGTGCAATCAG
1 GGGTACCG-AAGTACAAACAG
26832708 GGGTACCGAAGTACAAACAG
1 GGGTACCGAAGTACAAACAG
26832728 GGG
1 GGG
26832731 CACGTATGTG
Statistics
Matches: 55, Mismatches: 25, Indels: 6
0.64 0.29 0.07
Matches are distributed among these distances:
19 2 0.04
20 51 0.93
21 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.31, T:0.15
Consensus pattern (20 bp):
GGGTACCGAAGTACAAACAG
Found at i:26841885 original size:26 final size:26
Alignment explanation
Indices: 26841831--26841915 Score: 120
Period size: 26 Copynumber: 3.3 Consensus size: 26
26841821 TATAACAGTC
*
26841831 ATTTTACCCTATGGAGGTATTTC-AGTA
1 ATTTTACCCTTTGGA-GTATTTCGA-TA
*
26841858 ATTTTATCCTTTGGAGTATTTCGATA
1 ATTTTACCCTTTGGAGTATTTCGATA
26841884 ATTTTACCCTTTGG-GTATTTCGATA
1 ATTTTACCCTTTGGAGTATTTCGATA
26841909 ATTTTAC
1 ATTTTAC
26841916 GGCCCATGGA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
25 18 0.33
26 22 0.41
27 14 0.26
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (26 bp):
ATTTTACCCTTTGGAGTATTTCGATA
Found at i:26844435 original size:28 final size:28
Alignment explanation
Indices: 26844403--26844460 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
26844393 TTGCATCATG
* * * *
26844403 TCATCGTAGAATGTACGGTTGCCCGCTA
1 TCATCGTAAAATGCACCGTTGCCCACTA
26844431 TCATCGTAAAATGCACCGTTGCCCACTA
1 TCATCGTAAAATGCACCGTTGCCCACTA
26844459 TC
1 TC
26844461 TTCCAACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (28 bp):
TCATCGTAAAATGCACCGTTGCCCACTA
Found at i:26848584 original size:41 final size:41
Alignment explanation
Indices: 26848527--26848611 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
26848517 TAAGGGTGAC
26848527 ACAAACTTAGTAGAAAACTTAATAAATAGTATAGATATACA
1 ACAAACTTAGTAGAAAACTTAATAAATAGTATAGATATACA
26848568 ACAAACTTAGTAGAAAACTTAATAAATAGTATAGATATACA
1 ACAAACTTAGTAGAAAACTTAATAAATAGTATAGATATACA
26848609 ACA
1 ACA
26848612 GATGGAGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.26
Consensus pattern (41 bp):
ACAAACTTAGTAGAAAACTTAATAAATAGTATAGATATACA
Found at i:26850258 original size:30 final size:27
Alignment explanation
Indices: 26850200--26850258 Score: 73
Period size: 30 Copynumber: 2.1 Consensus size: 27
26850190 TATAACTTAC
26850200 TTTTAATATTTTAATAAATAATAATAA
1 TTTTAATATTTTAATAAATAATAATAA
* *
26850227 TTTTAAATATTTCTAAGTAATTAATATTAA
1 TTTT-AATATTT-TAA-TAAATAATAATAA
26850257 TT
1 TT
26850259 ATTTATTAAA
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 3 0.11
30 13 0.48
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTTTAATATTTTAATAAATAATAATAA
Found at i:26850320 original size:21 final size:21
Alignment explanation
Indices: 26850268--26850324 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
26850258 TATTTATTAA
*
26850268 ATATAATTAGAATATATAAACT
1 ATATAATTA-AATATTTAAACT
26850290 ATAT--TTAAATATTTAAA-T
1 ATATAATTAAATATTTAAACT
26850308 ATAATAATTAAATATTT
1 AT-ATAATTAAATATTT
26850325 GTAATTAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.10
19 11 0.35
20 3 0.10
21 10 0.32
22 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATAATTAAATATTTAAACT
Found at i:26852214 original size:75 final size:73
Alignment explanation
Indices: 26852088--26852262 Score: 235
Period size: 75 Copynumber: 2.4 Consensus size: 73
26852078 AAAATCACAT
* * * * *
26852088 ATAAACAACCATTAATAAAAC-TAATTTAATAAAAAATAAGTGGAACATAAATTCAATATCTAAA
1 ATAAACAACTATTAATAAAACATAATTGAACAAAAAATAAGTAGAACATAAATTCAATATCCAAA
*
26852152 GACCAAAC
66 AACCAAAC
26852160 ATAAACAACTATTAATAAAACATAATTGATACACAAAAATAAGTAGAACATAAATTCAATATCCA
1 ATAAACAACTATTAATAAAACATAATTGA-ACA-AAAAATAAGTAGAACATAAATTCAATATCCA
*
26852225 AAAACTAAAC
64 AAAACCAAAC
* *
26852235 ATAAATAACTATTGATAAAAACATAATT
1 ATAAACAACTATTAAT-AAAACATAATT
26852263 CGCTTAAGCC
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
72 20 0.22
73 6 0.07
74 2 0.02
75 51 0.57
76 11 0.12
ACGTcount: A:0.58, C:0.13, G:0.05, T:0.25
Consensus pattern (73 bp):
ATAAACAACTATTAATAAAACATAATTGAACAAAAAATAAGTAGAACATAAATTCAATATCCAAA
AACCAAAC
Found at i:26852722 original size:18 final size:18
Alignment explanation
Indices: 26852701--26852748 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
26852691 TCCATCAATT
26852701 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
26852719 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
26852737 AGAACATCATTT
1 TGAACATCATTT
26852749 CTCATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:26853528 original size:23 final size:22
Alignment explanation
Indices: 26853496--26853551 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
26853486 AAACAATATC
*
26853496 AAAAATTTAACTATATACATGA
1 AAAAAATTAACTATATACATGA
26853518 TAAAAAATTAAACTATATACATGA
1 -AAAAAATT-AACTATATACATGA
*
26853542 ACAAAATTAA
1 AAAAAATTAA
26853552 GTCAATATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 14 0.47
24 14 0.47
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.29
Consensus pattern (22 bp):
AAAAAATTAACTATATACATGA
Found at i:26853531 original size:24 final size:23
Alignment explanation
Indices: 26853496--26853551 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 23
26853486 AAACAATATC
*
26853496 AAAAATTTAACTATATACATGATA
1 AAAAATTAAACTATATACATGA-A
26853520 AAAAATTAAACTATATACATGAA
1 AAAAATTAAACTATATACATGAA
*
26853543 CAAAATTAA
1 AAAAATTAA
26853552 GTCAATATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.29
Consensus pattern (23 bp):
AAAAATTAAACTATATACATGAA
Found at i:26869307 original size:19 final size:19
Alignment explanation
Indices: 26869266--26869380 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 19
26869256 ATTACAAAAC
*
26869266 AAATTCAAAACAATTTTTAA
1 AAATTCAAAATAA-TTTTAA
26869286 AAATTCAAAATAATTTTCAA
1 AAATTCAAAATAATTTT-AA
26869306 AAATTCAAAAT-ATTTATAA
1 AAATTCAAAATAATTT-TAA
26869325 AAATTCAAAAAAATATATTTTAAA
1 AAATTC---AAAATA-ATTTT-AA
* *
26869349 AAATT-ATAATAATTTAAA
1 AAATTCAAAATAATTTTAA
* *
26869367 AAAATCTAAATAAT
1 AAATTCAAAATAAT
26869381 ATATAAATAA
Statistics
Matches: 80, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.08
19 26 0.32
20 31 0.39
22 5 0.06
23 1 0.01
24 11 0.14
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATTCAAAATAATTTTAA
Found at i:26869369 original size:42 final size:43
Alignment explanation
Indices: 26869292--26869384 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 43
26869282 TTAAAAATTC
* *
26869292 AAAATA-ATTTTCAAAAATTCAAAATATTTATAAAAATTCAAA
1 AAAATATATTTTAAAAAATTCAAAATATTTATAAAAAATCAAA
* *
26869334 AAAATATATTTTAAAAAATT-ATAATAATTTA-AAAAAATCTAA
1 AAAATATATTTTAAAAAATTCAAAAT-ATTTATAAAAAATCAAA
*
26869376 ATAATATAT
1 AAAATATAT
26869385 AAATAAAGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
42 27 0.61
43 17 0.39
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (43 bp):
AAAATATATTTTAAAAAATTCAAAATATTTATAAAAAATCAAA
Found at i:26869387 original size:21 final size:19
Alignment explanation
Indices: 26869335--26869380 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
26869325 AAATTCAAAA
*
26869335 AAATATATTTTAAAAAAT-T
1 AAATA-ATTTAAAAAAATCT
26869354 ATAATAATTTAAAAAAATCT
1 A-AATAATTTAAAAAAATCT
26869374 AAATAAT
1 AAATAAT
26869381 ATATAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATAATTTAAAAAAATCT
Found at i:26869396 original size:21 final size:22
Alignment explanation
Indices: 26869354--26869397 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
26869344 TTAAAAAATT
* *
26869354 ATAATAATTTAAAAAAATCTAA
1 ATAATAATATAAAAAAAGCTAA
*
26869376 ATAAT-ATATAAATAAAGCTAA
1 ATAATAATATAAAAAAAGCTAA
26869397 A
1 A
26869398 ATTTTAAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAATAATATAAAAAAAGCTAA
Found at i:26881235 original size:30 final size:30
Alignment explanation
Indices: 26881200--26881440 Score: 302
Period size: 30 Copynumber: 7.9 Consensus size: 30
26881190 GTACATGTTT
* * *
26881200 TATATATTGCTGAATTAATTTGTATATGGATA
1 TATACATTGCCGAATTGATTTGTATATGG--A
* * * * *
26881232 TATATATTGCCAAATTTATTTATATATAGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
26881262 TATATATATAGCCGAATTGATTTGTATATGGA
1 TATACAT-T-GCCGAATTGATTTGTATATGGA
*
26881294 TATACATTGCCGAATTGATTTGTATATAGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
26881324 TATACATTGCTGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
26881354 TATACATTGCCGAATTGATTTGTATATGAA
1 TATACATTGCCGAATTGATTTGTATATGGA
* * *
26881384 TATACATTACCGAAGTGATTTGTATATAGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
26881414 TATACATTACCGAATTGATTTGTATAT
1 TATACATTGCCGAATTGATTTGTATAT
26881441 TTATGAGGTC
Statistics
Matches: 187, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
30 137 0.73
31 2 0.01
32 48 0.26
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.42
Consensus pattern (30 bp):
TATACATTGCCGAATTGATTTGTATATGGA
Found at i:26882644 original size:37 final size:37
Alignment explanation
Indices: 26882583--26882697 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 37
26882573 CTAAGTGTTA
* * *
26882583 CTCAACTGAGC-ATTACCTATTGATATACCGACTAAAG
1 CTCAACTGAGCGA-TATCTACTGATATACCGAATAAAG
**
26882620 CTCAACTGAGCGATATCTACTGATATACTAAATAAAG
1 CTCAACTGAGCGATATCTACTGATATACCGAATAAAG
* * * * * * *
26882657 CTCAATTGAGAGTTGTTTACTGATATGCCGAGT-AAG
1 CTCAACTGAGCGATATCTACTGATATACCGAATAAAG
26882693 CTCAA
1 CTCAA
26882698 TCAAGTATTA
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
36 8 0.13
37 54 0.86
38 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (37 bp):
CTCAACTGAGCGATATCTACTGATATACCGAATAAAG
Found at i:26883787 original size:21 final size:21
Alignment explanation
Indices: 26883748--26883787 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
26883738 TTAATATAAA
*
26883748 TTACAAATTACAATTATTTTT
1 TTACAAATTACAATGATTTTT
* *
26883769 TTACAATTTATAATGATTT
1 TTACAAATTACAATGATTT
26883788 ATCAAAATTA
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:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
TTACAAATTACAATGATTTTT
Found at i:26885118 original size:22 final size:23
Alignment explanation
Indices: 26885093--26885213 Score: 94
Period size: 22 Copynumber: 5.5 Consensus size: 23
26885083 GTATAAATCT
26885093 CTATG-TTGATCTAAATCAATTA
1 CTATGATTGATCTAAATCAATTA
** *
26885115 CTATGATTGAT-TGTATAAATCT-
1 CTATGATTGATCTAAATCAAT-TA
* *
26885137 CTATG-TTGGTCTAAATCGATTA
1 CTATGATTGATCTAAATCAATTA
** *
26885159 CTATGATTGAT-TGTATAAATCT-
1 CTATGATTGATCTAAATCAAT-TA
*
26885181 CTATG-TTGATCTAAATCGATTA
1 CTATGATTGATCTAAATCAATTA
26885203 CTATGATTGAT
1 CTATGATTGAT
26885214 TGGAAAGGTT
Statistics
Matches: 73, Mismatches: 17, Indels: 17
0.68 0.16 0.16
Matches are distributed among these distances:
21 11 0.15
22 46 0.63
23 16 0.22
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (23 bp):
CTATGATTGATCTAAATCAATTA
Found at i:26885130 original size:44 final size:44
Alignment explanation
Indices: 26885080--26885215 Score: 254
Period size: 44 Copynumber: 3.1 Consensus size: 44
26885070 AAGGTTGCAT
*
26885080 ATTGTATAAATCTCTATGTTGATCTAAATCAATTACTATGATTG
1 ATTGTATAAATCTCTATGTTGATCTAAATCGATTACTATGATTG
*
26885124 ATTGTATAAATCTCTATGTTGGTCTAAATCGATTACTATGATTG
1 ATTGTATAAATCTCTATGTTGATCTAAATCGATTACTATGATTG
26885168 ATTGTATAAATCTCTATGTTGATCTAAATCGATTACTATGATTG
1 ATTGTATAAATCTCTATGTTGATCTAAATCGATTACTATGATTG
26885212 ATTG
1 ATTG
26885216 GAAAGGTTTC
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 89 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (44 bp):
ATTGTATAAATCTCTATGTTGATCTAAATCGATTACTATGATTG
Found at i:26886587 original size:29 final size:29
Alignment explanation
Indices: 26886545--26886600 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
26886535 GCCTTGGTCA
*
26886545 CAAATCTAAACGCACGATTAACCCATTCG
1 CAAATCTAAACGCACAATTAACCCATTCG
26886574 CAAATCTAAACGCACAATTAACCCATT
1 CAAATCTAAACGCACAATTAACCCATT
26886601 TTAGTCATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.30, G:0.07, T:0.21
Consensus pattern (29 bp):
CAAATCTAAACGCACAATTAACCCATTCG
Found at i:26886713 original size:28 final size:28
Alignment explanation
Indices: 26886630--26886714 Score: 143
Period size: 28 Copynumber: 3.0 Consensus size: 28
26886620 ATAACTTAGA
* *
26886630 TTTTAATGCGTGATCTAATGTGAAAATA
1 TTTTAATACGTGATCTAATGTGAAAATC
26886658 TTTTAATACGTGATCTAATGTGAAAATC
1 TTTTAATACGTGATCTAATGTGAAAATC
*
26886686 TTTTAATACGTTATCTAATGTGAAAATC
1 TTTTAATACGTGATCTAATGTGAAAATC
26886714 T
1 T
26886715 CAGCAAACAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.41
Consensus pattern (28 bp):
TTTTAATACGTGATCTAATGTGAAAATC
Done.