Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 3 of 26
Found at i:463230 original size:47 final size:45
Alignment explanation
Indices: 463143--463250 Score: 114
Period size: 47 Copynumber: 2.4 Consensus size: 45
463133 TATAATTATT
463143 AAAATATAATATAAATAAAATAATTTAAATATATATTAAAATTTATA
1 AAAATATAATATAAATAAAATAATTTAAATATATATTAAAA--TATA
* **
463190 TAAATATAATATATTTTAAATATAA-TTATAATAT-TA-TAAAATATA
1 AAAATATAATATA-AATAAA-ATAATTTA-AATATATATTAAAATATA
*
463235 AAAATATAACATAAAT
1 AAAATATAATATAAAT
463251 TATTAAATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
44 1 0.02
45 15 0.29
47 17 0.33
48 9 0.18
49 9 0.18
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (45 bp):
AAAATATAATATAAATAAAATAATTTAAATATATATTAAAATATA
Found at i:464294 original size:18 final size:18
Alignment explanation
Indices: 464271--464310 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
464261 GGTCTTAGGT
*
464271 TTTCTTTGTTTTATATTG
1 TTTCTTTCTTTTATATTG
* *
464289 TTTCTTTCTTTTCTATTT
1 TTTCTTTCTTTTATATTG
464307 TTTC
1 TTTC
464311 CTATTTCGGG
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:0.07, C:0.12, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTCTTTCTTTTATATTG
Found at i:472699 original size:30 final size:32
Alignment explanation
Indices: 472643--472702 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
472633 ATTTAAATCA
**
472643 ATAATATTTGATTTAACTTAATTCAATTTTAT
1 ATAATATTCAATTTAACTTAATTCAATTTTAT
472675 ATAATATTCAATTTAA-TT-ATTCAATTTT
1 ATAATATTCAATTTAACTTAATTCAATTTT
472703 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 10 0.38
31 2 0.08
32 14 0.54
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (32 bp):
ATAATATTCAATTTAACTTAATTCAATTTTAT
Found at i:473022 original size:83 final size:83
Alignment explanation
Indices: 472883--473048 Score: 296
Period size: 83 Copynumber: 2.0 Consensus size: 83
472873 AATTTAATGA
* *
472883 TTACTGGTTTCAAATCAGTCTATTATTTTCATGTCTGAGTTTTTGTATACCTAAATGCCAACCGA
1 TTACTGGTTTCAAATCAGTCTATTATTTCCATGTCTGAGTTTATGTATACCTAAATGCCAACCGA
472948 TGAGCCATTTGTCAGCCT
66 TGAGCCATTTGTCAGCCT
* *
472966 TTACTGGTTTCAAATCATTCTATTATTTCCATGTCTGAGTTTATGTATACCTAAATGCCAACTGA
1 TTACTGGTTTCAAATCAGTCTATTATTTCCATGTCTGAGTTTATGTATACCTAAATGCCAACCGA
473031 TGAGCCATTTGTCAGCCT
66 TGAGCCATTTGTCAGCCT
473049 AATCTGTAAC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (83 bp):
TTACTGGTTTCAAATCAGTCTATTATTTCCATGTCTGAGTTTATGTATACCTAAATGCCAACCGA
TGAGCCATTTGTCAGCCT
Found at i:474962 original size:16 final size:16
Alignment explanation
Indices: 474936--474979 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
474926 ATTTTTTCAA
474936 TTAAA-TAAATTTAAT
1 TTAAATTAAATTTAAT
*
474951 TTAAATTAAATTGAAT
1 TTAAATTAAATTTAAT
*
474967 TTAAATTTAATTT
1 TTAAATTAAATTT
474980 TTTAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTAAATTAAATTTAAT
Found at i:477128 original size:16 final size:16
Alignment explanation
Indices: 477107--477140 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
477097 TTCTTTTTTT
* *
477107 GTTTTCTTTTGGTGAA
1 GTTTTCCTTTGGTCAA
477123 GTTTTCCTTTGGTCAA
1 GTTTTCCTTTGGTCAA
477139 GT
1 GT
477141 ATAACATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.53
Consensus pattern (16 bp):
GTTTTCCTTTGGTCAA
Found at i:477686 original size:2 final size:2
Alignment explanation
Indices: 477679--477711 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
477669 ACTTTTATTT
477679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
477712 GTAGATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:481805 original size:2 final size:2
Alignment explanation
Indices: 481798--481826 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
481788 GGAATTATGC
481798 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
481827 GTTATGGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:482877 original size:21 final size:20
Alignment explanation
Indices: 482831--482908 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 20
482821 TTTTAATTGC
*
482831 TTTTAATATGATTTTG-ATA
1 TTTTAATATAATTTTGAATA
482850 GTCTTTAATATAATTTTGACATA
1 -T-TTTAATATAATTTTGA-ATA
*
482873 TTTTAATAAAATTTT-AATAA
1 TTTTAATATAATTTTGAAT-A
*
482893 TTTTATATATGATTTT
1 TTTTA-ATATAATTTT
482909 TTAATCTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.04
20 8 0.16
21 35 0.71
22 1 0.02
23 3 0.06
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (20 bp):
TTTTAATATAATTTTGAATA
Found at i:483523 original size:30 final size:30
Alignment explanation
Indices: 483488--483544 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
483478 TTGGGAAAAT
*
483488 TTTTAATCTAATTCT-TTAAATTTTTTTGGA
1 TTTTAATCTAATT-TGATAAATTTTTTTGGA
*
483518 TTTTAATTTAATTTGATAAATTTTTTT
1 TTTTAATCTAATTTGATAAATTTTTTT
483545 TTTTTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (30 bp):
TTTTAATCTAATTTGATAAATTTTTTTGGA
Found at i:483888 original size:22 final size:22
Alignment explanation
Indices: 483863--483934 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
483853 TAATAAAATA
*
483863 TAAATTTAAACTTAAACCCATT
1 TAAATTTAAACTAAAACCCATT
* *
483885 TAAATTTAAACTAAAAATCCATC
1 TAAATTTAAACT-AAAACCCATT
*
483908 TAAATTTAAACTAAAAGCCCAAT
1 TAAATTTAAACTAAAA-CCCATT
483931 TAAA
1 TAAA
483935 ATAAAAAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
22 16 0.38
23 26 0.62
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (22 bp):
TAAATTTAAACTAAAACCCATT
Found at i:486758 original size:22 final size:22
Alignment explanation
Indices: 486730--486772 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
486720 CAATGAATTG
*
486730 ACTCAAGTACCCGAAGCTCCAA
1 ACTCAAGTACCCCAAGCTCCAA
*
486752 ACTCAAGTACCCCAAGGTCCA
1 ACTCAAGTACCCCAAGCTCCA
486773 GGCTTAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.37, G:0.14, T:0.14
Consensus pattern (22 bp):
ACTCAAGTACCCCAAGCTCCAA
Found at i:486916 original size:22 final size:22
Alignment explanation
Indices: 486891--486933 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
486881 AGCTTATATC
* *
486891 CTTTCATTTTTATAAAAATTAG
1 CTTTAATTTTTAAAAAAATTAG
486913 CTTTAATTTTTAAAAAAATTA
1 CTTTAATTTTTAAAAAAATTA
486934 ATTTATGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (22 bp):
CTTTAATTTTTAAAAAAATTAG
Found at i:486938 original size:21 final size:22
Alignment explanation
Indices: 486896--486938 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
486886 ATATCCTTTC
* *
486896 ATTTTTATAAAAATTAGCTTTA
1 ATTTTTAAAAAAATTAGATTTA
486918 ATTTTTAAAAAAATTA-ATTTA
1 ATTTTTAAAAAAATTAGATTTA
486939 TGTTAGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTTTTAAAAAAATTAGATTTA
Found at i:487022 original size:30 final size:29
Alignment explanation
Indices: 486960--487040 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 29
486950 TTTTTCAAGT
* **
486960 AAATTTAA-TTAAAATTTTATTTGGATAC
1 AAATTAAAGTTAAAATTTTATTTAAATAC
**
486988 AAATTAAAGTTTAAAATTTTATTTAAATGT
1 AAATTAAAG-TTAAAATTTTATTTAAATAC
* *
487018 AAATTAAAGGTAAAAATTTATTT
1 AAATTAAAGTTAAAATTTTATTT
487041 GAACATGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 7 0.16
29 12 0.27
30 25 0.57
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (29 bp):
AAATTAAAGTTAAAATTTTATTTAAATAC
Found at i:487707 original size:2 final size:2
Alignment explanation
Indices: 487700--487731 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
487690 TACATTATTA
487700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
487732 TTATGTAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:502842 original size:2 final size:2
Alignment explanation
Indices: 502837--502876 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
502827 ATGTGCTTAG
*
502837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
502877 CTGTATATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:505696 original size:234 final size:234
Alignment explanation
Indices: 505287--505757 Score: 762
Period size: 234 Copynumber: 2.0 Consensus size: 234
505277 ACAATGAAAT
* * * * *
505287 GCAAAATGCTTCTCACGTAGCTGGAACTTCACTATCTAATGCCACCTTTGATGCGAATTGCAATG
1 GCAAAATGCTTCTCACGGAGCTGAAACTTCACCATCTAATGCCACCATTGATGCGAATTGCAACG
* **
505352 TGTCCAATCCTGATGCCTCAGTTGTGGAGCTTAGAGATCAAATGCAGCAGTTGAGATCCATGGAA
66 TGTCCAATCCTGATGCCTCAGTTGTGGAGCTTAGAGACCAAATGCAGCAGTTGAGATCCACAGAA
* *
505417 TCAACTTCTAACCTCTCTTCTCCTGGTCTACCTTCAGTCAGTGCAATTGAACATCAATCAAGCAA
131 TCAACTTCTAACCTCCCTCCTCCTGGTCTACCTTCAGTCAGTGCAATTGAACATCAATCAAGCAA
* *
505482 TGAAGGCCAAACTGCCAACCAATGTGCTGAGGCTCCAAG
196 TGAAGGCCAAACTCCCAACCAAAGTGCTGAGGCTCCAAG
* * * *
505521 GCAAAATGCTTCTCAGGGAGCTGAAACTTCACCATTTAATGGCACCATTGATGTGAATTGCAACG
1 GCAAAATGCTTCTCACGGAGCTGAAACTTCACCATCTAATGCCACCATTGATGCGAATTGCAACG
505586 TGTCCAATCCTGATGCCTCAGTTGTGGAGCTTAGAGACCAAATGCAGCAGTTGAGATCCACAGAA
66 TGTCCAATCCTGATGCCTCAGTTGTGGAGCTTAGAGACCAAATGCAGCAGTTGAGATCCACAGAA
* * *
505651 TCAACTTTTAACCTCCCTCCTTCTGGTCTACCTTCAGTTAGTGCAATTGAACATCAATCAAGCAA
131 TCAACTTCTAACCTCCCTCCTCCTGGTCTACCTTCAGTCAGTGCAATTGAACATCAATCAAGCAA
*
505716 TGAAGGCCAAACTCCCAACCAAAGTGCTGAGGCTTCAAG
196 TGAAGGCCAAACTCCCAACCAAAGTGCTGAGGCTCCAAG
505755 GCA
1 GCA
505758 GCCAGAGGCA
Statistics
Matches: 217, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
234 217 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (234 bp):
GCAAAATGCTTCTCACGGAGCTGAAACTTCACCATCTAATGCCACCATTGATGCGAATTGCAACG
TGTCCAATCCTGATGCCTCAGTTGTGGAGCTTAGAGACCAAATGCAGCAGTTGAGATCCACAGAA
TCAACTTCTAACCTCCCTCCTCCTGGTCTACCTTCAGTCAGTGCAATTGAACATCAATCAAGCAA
TGAAGGCCAAACTCCCAACCAAAGTGCTGAGGCTCCAAG
Found at i:510266 original size:2 final size:2
Alignment explanation
Indices: 510259--510299 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
510249 CTCAAATTGA
510259 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
510300 ACAACTGGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:510504 original size:14 final size:14
Alignment explanation
Indices: 510482--510520 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
510472 TTAATACAAT
510482 ATATATTATTTATA
1 ATATATTATTTATA
*
510496 ATATTTTATTTATTA
1 ATATATTATTTA-TA
510511 ATCATATTAT
1 AT-ATATTAT
510521 ACTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 11 0.52
15 4 0.19
16 6 0.29
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATATTATTTATA
Found at i:512353 original size:2 final size:2
Alignment explanation
Indices: 512335--512370 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
512325 TGATAGATTG
*
512335 AT AT A- AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
512371 ATTCTCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:513398 original size:22 final size:23
Alignment explanation
Indices: 513357--513399 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
513347 AATTAAATTT
* *
513357 TAAATTTTTTATATATTTATACA
1 TAAATTTTTAATATAGTTATACA
513380 TAAATTTTTAAT-TAGTTATA
1 TAAATTTTTAATATAGTTATA
513400 GAAAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TAAATTTTTAATATAGTTATACA
Found at i:513406 original size:22 final size:23
Alignment explanation
Indices: 513358--513407 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
513348 ATTAAATTTT
* * *
513358 AAATTTTTTATATATTTATACAT
1 AAATTTTTAATATAGTTATACAA
*
513381 AAATTTTTAAT-TAGTTATAGAA
1 AAATTTTTAATATAGTTATACAA
513403 AAATT
1 AAATT
513408 ATACCGCACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (23 bp):
AAATTTTTAATATAGTTATACAA
Found at i:514167 original size:13 final size:13
Alignment explanation
Indices: 514149--514174 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
514139 ATTTTTTTTA
514149 TAAAAAATTTAAT
1 TAAAAAATTTAAT
514162 TAAAAAATTTAAT
1 TAAAAAATTTAAT
514175 CTCTTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAAAATTTAAT
Found at i:516228 original size:38 final size:36
Alignment explanation
Indices: 516152--516224 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
516142 TTAGTTAAAA
* *
516152 AAATATTTATAAAAATATAATTAATACATTAATTTT
1 AAATATTAATAAAAATATAATTAATACATAAATTTT
*
516188 AAATATTAATAAAAATAATATATTAA-AGATAAATTTT
1 AAATATTAATAAAAAT-ATA-ATTAATACATAAATTTT
516225 TAAAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 15 0.47
37 12 0.38
38 5 0.16
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (36 bp):
AAATATTAATAAAAATATAATTAATACATAAATTTT
Found at i:517378 original size:2 final size:2
Alignment explanation
Indices: 517371--517405 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
517361 AATCCTTACA
*
517371 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
517406 AAAGACAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:518023 original size:25 final size:27
Alignment explanation
Indices: 517995--518059 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 27
517985 ATGTAATACG
517995 TATTAAATAAAAAT-TATTTAAT-TAT
1 TATTAAATAAAAATATATTTAATATAT
* *
518020 TATT--TTAAATATATATTTAATATAT
1 TATTAAATAAAAATATATTTAATATAT
518045 TATTTTAAATAAAAA
1 TA--TTAAATAAAAA
518060 ATAAATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
23 6 0.20
24 8 0.27
25 9 0.30
27 2 0.07
29 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TATTAAATAAAAATATATTTAATATAT
Found at i:518051 original size:13 final size:13
Alignment explanation
Indices: 518007--518052 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
517997 TTAAATAAAA
518007 ATTA-TTTAAT-T
1 ATTATTTTAATAT
518018 ATTATTTTAA-AT
1 ATTATTTTAATAT
518030 A-TATATTTAATAT
1 ATTAT-TTTAATAT
518043 ATTATTTTAA
1 ATTATTTTAA
518053 ATAAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 7 0.23
12 12 0.40
13 8 0.27
14 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTATTTTAATAT
Found at i:535895 original size:48 final size:45
Alignment explanation
Indices: 535815--535907 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 45
535805 AATTAAGTAT
* * **
535815 ATCAAAATTATTTTTTTAATTATAAAATATTTTTATTTAAATTTA
1 ATCAAAATTATTTTTTAAATAATAAAATATTTTTAGATAAATTTA
535860 ATCATAAA-TATTATTTTAAATAATAAAATAAATTTTTAGATAAATTTA
1 ATCA-AAATTATT-TTTTAAATAATAAAAT--ATTTTTAGATAAATTTA
535908 GATGCATCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 8 0.20
46 17 0.43
48 15 0.38
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (45 bp):
ATCAAAATTATTTTTTAAATAATAAAATATTTTTAGATAAATTTA
Found at i:540328 original size:2 final size:2
Alignment explanation
Indices: 540321--540354 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
540311 GATTCTACAA
540321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
540355 TTGTATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:543778 original size:2 final size:2
Alignment explanation
Indices: 543771--543799 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
543761 TTATTAGGCC
543771 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
543800 AAATAAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:545308 original size:2 final size:2
Alignment explanation
Indices: 545301--545337 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
545291 ACCATCTCCA
545301 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
545338 CAAAATTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:547025 original size:3 final size:3
Alignment explanation
Indices: 547017--547042 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
547007 CAACGCAAAG
547017 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
547043 GGCCGGTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:547309 original size:4 final size:4
Alignment explanation
Indices: 547300--547330 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
547290 TCAAACACTA
547300 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
547331 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:547650 original size:2 final size:2
Alignment explanation
Indices: 547643--547674 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
547633 TGCTTAATAA
547643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
547675 TAATCAGCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:548269 original size:6 final size:7
Alignment explanation
Indices: 548254--548278 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
548244 GGAAGCTAGC
548254 TTTTATT
1 TTTTATT
548261 TTTTATT
1 TTTTATT
548268 TTTTATT
1 TTTTATT
548275 TTTT
1 TTTT
548279 TGGTATGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:548666 original size:17 final size:17
Alignment explanation
Indices: 548646--548679 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
548636 TTTAAATGTA
* *
548646 GATTAATTTCATTAATT
1 GATTAAATTAATTAATT
548663 GATTAAATTAATTAATT
1 GATTAAATTAATTAATT
548680 TTTTATGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
GATTAAATTAATTAATT
Found at i:551114 original size:21 final size:22
Alignment explanation
Indices: 551090--551139 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
551080 TCTTTGGTAC
*
551090 AAAAAATTCTA-AATTTTTTTT
1 AAAAAATTCAATAATTTTTTTT
*
551111 AAAAAATTGAATAATTTTTTTT
1 AAAAAATTCAATAATTTTTTTT
551133 AAGAAAA
1 AA-AAAA
551140 ATGGTTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.36
22 12 0.48
23 4 0.16
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
AAAAAATTCAATAATTTTTTTT
Found at i:552524 original size:20 final size:20
Alignment explanation
Indices: 552499--552536 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
552489 TATTATTAAA
552499 AATATTTAAAATTTTATATT
1 AATATTTAAAATTTTATATT
* *
552519 AATATTTATATTTTTATA
1 AATATTTAAAATTTTATA
552537 ATGAAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTTAAAATTTTATATT
Found at i:553057 original size:2 final size:2
Alignment explanation
Indices: 553052--553079 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
553042 TCTATATAAC
553052 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
553080 CACCACATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:554127 original size:32 final size:32
Alignment explanation
Indices: 554091--554153 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
554081 ATTACATATG
554091 TTTAAATAAATATAATATAAATAT-ATAATTTT
1 TTTAAATAAATAT-ATATAAATATAATAATTTT
** *
554123 TTTAAATTTATATATATATATATAATAATTT
1 TTTAAATAAATATATATAAATATAATAATTT
554154 AAATATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTAAATAAATATATATAAATATAATAATTTT
Found at i:561440 original size:20 final size:20
Alignment explanation
Indices: 561415--561457 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
561405 TTACATATTC
*
561415 ATAAAATATATATTAAA-AAA
1 ATAAAAAATA-ATTAAATAAA
561435 ATAAAAAATAATTAAATAAA
1 ATAAAAAATAATTAAATAAA
561455 ATA
1 ATA
561458 TTTGTCACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAAAAATAATTAAATAAA
Found at i:563668 original size:7 final size:6
Alignment explanation
Indices: 563640--563686 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
563630 TATTTTTATT
*
563640 TAAATA TATAT- TAAATA TAAATA TCAAATA TAAATA TTAAAATA TAA
1 TAAATA TAAATA TAAATA TAAATA T-AAATA TAAATA -T-AAATA TAA
563687 CGAAAAGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
5 4 0.11
6 18 0.51
7 8 0.23
8 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAATA
Found at i:563668 original size:13 final size:13
Alignment explanation
Indices: 563647--563686 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
563637 ATTTAAATAT
*
563647 ATATTAAATATAA
1 ATATAAAATATAA
*
563660 ATATCAAATATAA
1 ATATAAAATATAA
563673 ATATTAAAATATAA
1 ATA-TAAAATATAA
563687 CGAAAAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAAATATAA
Found at i:569274 original size:29 final size:29
Alignment explanation
Indices: 569241--569323 Score: 157
Period size: 29 Copynumber: 2.9 Consensus size: 29
569231 AAATCACTGA
569241 GATAGCTTGAAAATCAAGATTTTGGCGAG
1 GATAGCTTGAAAATCAAGATTTTGGCGAG
*
569270 GATAGCTTGAAAATCAAGATTTTGGCGGG
1 GATAGCTTGAAAATCAAGATTTTGGCGAG
569299 GATAGCTTGAAAATCAAGATTTTGG
1 GATAGCTTGAAAATCAAGATTTTGG
569324 GGTAGATTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.29
Consensus pattern (29 bp):
GATAGCTTGAAAATCAAGATTTTGGCGAG
Found at i:573696 original size:2 final size:2
Alignment explanation
Indices: 573689--573713 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
573679 AAGTAGGCTT
573689 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
573714 GTGCCATATG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:575669 original size:2 final size:2
Alignment explanation
Indices: 575662--575702 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
575652 TTGCTTTCTT
575662 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
575703 TTAAAATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:580802 original size:18 final size:18
Alignment explanation
Indices: 580768--580802 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
580758 TAAATAAACG
*
580768 CCCCCCCACCCCCCCCCC
1 CCCCCCCACCCCACCCCC
*
580786 CCCCCCCAGCCCACCCC
1 CCCCCCCACCCCACCCC
580803 AACTCATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.89, G:0.03, T:0.00
Consensus pattern (18 bp):
CCCCCCCACCCCACCCCC
Found at i:581205 original size:15 final size:15
Alignment explanation
Indices: 581187--581285 Score: 53
Period size: 15 Copynumber: 6.5 Consensus size: 15
581177 TTGTATAAAA
581187 ATATATATTATAATT
1 ATATATATTATAATT
* **
581202 ATATTTAAAAT-ATT
1 ATATATATTATAATT
*
581216 ATATATTTATATAAATT
1 ATATATAT-TAT-AATT
*
581233 TTAATATATTAATAATT
1 AT-ATATATT-ATAATT
* *
581250 -TATATTATAAAAATT
1 ATATA-TATTATAATT
581265 A-ATATATTCATAATT
1 ATATATATT-ATAATT
581280 AT-TATA
1 ATATATA
581286 ATATGAATTT
Statistics
Matches: 62, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
14 11 0.18
15 31 0.50
16 4 0.06
17 9 0.15
18 7 0.11
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATATTATAATT
Found at i:581211 original size:24 final size:22
Alignment explanation
Indices: 581184--581227 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
581174 ATTTTGTATA
581184 AAAATATATATTATAATTATATTT
1 AAAATAT-TA-TATAATTATATTT
*
581208 AAAATATTATATATTTATAT
1 AAAATATTATATAATTATAT
581228 AAATTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 2 0.11
24 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAAATATTATATAATTATATTT
Found at i:581230 original size:20 final size:20
Alignment explanation
Indices: 581191--581230 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
581181 ATAAAAATAT
*
581191 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
581211 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
581231 TTTTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:581500 original size:2 final size:2
Alignment explanation
Indices: 581493--581518 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
581483 TTCTAATAAA
581493 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
581519 TAGTAGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:581681 original size:16 final size:16
Alignment explanation
Indices: 581642--581683 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
581632 TTTATTTTTT
* *
581642 AATTTTAATTTTAAAA
1 AATTTAAATATTAAAA
*
581658 AA-TAAAATATTAAAA
1 AATTTAAATATTAAAA
581673 AATTTAAATAT
1 AATTTAAATAT
581684 ATAATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTAAATATTAAAA
Found at i:589014 original size:93 final size:93
Alignment explanation
Indices: 588861--589047 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
588851 GAAAATTGTG
588861 TTACACAATTTCTCTTCTGGAGCAAATAGAAAGTACAAAGCATGAGAATTTTTTTTTATATATAT
1 TTACACAATTTCTCTTCTGGAGCAAATAGAAAGTACAAAGCATGAGAATTTTTTTTTATATATAT
588926 GACATTGGTGTACTGAAACTTTGCAAAT
66 GACATTGGTGTACTGAAACTTTGCAAAT
588954 TTACACAATTTCTCTTCTGGAGCAAATAGAAAGTACAAAGCATGAGAATTTTTTTTTATATATAT
1 TTACACAATTTCTCTTCTGGAGCAAATAGAAAGTACAAAGCATGAGAATTTTTTTTTATATATAT
589019 GACATTGGTGTACTGAAACTTTGCAAAT
66 GACATTGGTGTACTGAAACTTTGCAAAT
589047 T
1 T
589048 GTGATTTAAG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (93 bp):
TTACACAATTTCTCTTCTGGAGCAAATAGAAAGTACAAAGCATGAGAATTTTTTTTTATATATAT
GACATTGGTGTACTGAAACTTTGCAAAT
Found at i:589879 original size:24 final size:24
Alignment explanation
Indices: 589852--589898 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
589842 ATAATATGAT
589852 ATTTAATATATAAATA-ATATTTAA
1 ATTTAA-ATATAAATATATATTTAA
*
589876 ATTTAAATTTAAATATATATTTA
1 ATTTAAATATAAATATATATTTA
589899 GTAATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTAAATATAAATATATATTTAA
Found at i:589918 original size:11 final size:12
Alignment explanation
Indices: 589868--589923 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
589858 TATATAAATA
*
589868 ATATTTAAATTT
1 ATATTTATATTT
* * *
589880 AAATTTAAATAT
1 ATATTTATATTT
589892 ATATTTAGTAATTT
1 ATATTTA-T-ATTT
589906 AT-TTTATATTT
1 ATATTTATATTT
589917 ATATTTA
1 ATATTTA
589924 AACCATCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
11 6 0.17
12 21 0.58
13 4 0.11
14 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
ATATTTATATTT
Found at i:594466 original size:3 final size:3
Alignment explanation
Indices: 594458--594488 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
594448 GTAATATTTA
594458 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
594489 GAACTTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:594812 original size:2 final size:2
Alignment explanation
Indices: 594805--594829 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
594795 TTTAATGTAC
594805 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
594830 AATGATGGTA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:596221 original size:2 final size:2
Alignment explanation
Indices: 596214--596248 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
596204 GTCACGCGTA
596214 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
596249 TTAGGCACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:601328 original size:21 final size:22
Alignment explanation
Indices: 601302--601346 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
601292 CATTTGAAAA
*
601302 TTTTTTAATGTAAAA-ATAGAT
1 TTTTTTAAAGTAAAATATAGAT
*
601323 TTTTTTAAAGTAAAATATATAT
1 TTTTTTAAAGTAAAATATAGAT
601345 TT
1 TT
601347 AATTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTTTTAAAGTAAAATATAGAT
Found at i:601501 original size:22 final size:21
Alignment explanation
Indices: 601457--601502 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
601447 AATTTTATTA
*
601457 ATAAATATATTATTATAATAT
1 ATAAATATATTATTATAAAAT
601478 ATAAATATTATTTATT-TAAAAT
1 ATAAATA-TA-TTATTATAAAAT
601500 ATA
1 ATA
601503 TTTTAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 10 0.45
23 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAAATATATTATTATAAAAT
Found at i:602767 original size:2 final size:2
Alignment explanation
Indices: 602760--602795 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
602750 AAATGAATGA
602760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
602796 TCACATTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:603094 original size:17 final size:18
Alignment explanation
Indices: 603062--603096 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
603052 AATTTAAAAT
*
603062 TAATTAATATATTATTTA
1 TAATTAATATAATATTTA
603080 TAATT-ATATAATATTTA
1 TAATTAATATAATATTTA
603097 ATGTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTAATATAATATTTA
Found at i:603615 original size:3 final size:3
Alignment explanation
Indices: 603607--603632 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
603597 AGTCAAAATA
603607 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
603633 AGAAGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:604945 original size:14 final size:14
Alignment explanation
Indices: 604926--604952 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
604916 TAAGTCTAAC
604926 ATTCAAAATTTAAA
1 ATTCAAAATTTAAA
604940 ATTCAAAATTTAA
1 ATTCAAAATTTAA
604953 GTCTAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTCAAAATTTAAA
Found at i:605094 original size:20 final size:20
Alignment explanation
Indices: 605069--605112 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
605059 AACTATGTTT
605069 TAAATTAAATAAAGAAA-AAA
1 TAAATT-AATAAAGAAATAAA
* *
605089 TAAATTTATTAAGAAATAAA
1 TAAATTAATAAAGAAATAAA
605109 TAAA
1 TAAA
605113 AGTAATATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAATTAATAAAGAAATAAA
Found at i:613185 original size:19 final size:20
Alignment explanation
Indices: 613163--613201 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
613153 TTTAGAATTA
* *
613163 AATTTATTTTTTAAA-AAAT
1 AATTTAATTTATAAATAAAT
613182 AATTTAATTTATAAATAAAT
1 AATTTAATTTATAAATAAAT
613202 TATAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTAATTTATAAATAAAT
Found at i:617975 original size:17 final size:18
Alignment explanation
Indices: 617939--617998 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
617929 TGATAAATAC
* *
617939 ATATTTAAT-ATATATTT
1 ATATTTAATAATTTATAT
*
617956 ATATTTAATATTTTA-AT
1 ATATTTAATAATTTATAT
*
617973 ATATTTTATAATTTATAT
1 ATATTTAATAATTTATAT
617991 CATATTTA
1 -ATATTTA
617999 TTTTTTTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 23 0.68
18 5 0.15
19 6 0.18
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATTTAATAATTTATAT
Found at i:620399 original size:2 final size:2
Alignment explanation
Indices: 620394--620445 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
620384 TGTGTGTGTG
*
620394 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
620436 TA TA TA TA TA
1 TA TA TA TA TA
620446 CACACACATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:624425 original size:2 final size:2
Alignment explanation
Indices: 624420--624467 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
624410 AAAAACAAAA
624420 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
624462 AA AG AG
1 AG AG AG
624468 TCCTTAAACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:625011 original size:14 final size:14
Alignment explanation
Indices: 624992--625021 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
624982 TGTAAGAAAC
624992 AAGAGAGAGAGAGA
1 AAGAGAGAGAGAGA
625006 AAGAGAGAGAGAGA
1 AAGAGAGAGAGAGA
625020 AA
1 AA
625022 TAAAGAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (14 bp):
AAGAGAGAGAGAGA
Found at i:626571 original size:3 final size:3
Alignment explanation
Indices: 626563--626598 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
626553 TTAATAAAAT
626563 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
626599 AATAGTGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:627748 original size:11 final size:11
Alignment explanation
Indices: 627734--627762 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
627724 ATTTTATGTT
627734 TTTTTTAAATA
1 TTTTTTAAATA
627745 TTTTTTAAATA
1 TTTTTTAAATA
627756 TTTTTTA
1 TTTTTTA
627763 TTAAAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:629911 original size:20 final size:20
Alignment explanation
Indices: 629874--629916 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
629864 AAAATTTTAT
* * *
629874 TTTGAAATTTTTATTTATGA
1 TTTGAAATTTTGAATTATAA
*
629894 TTTGGAATTTTGAATTATAA
1 TTTGAAATTTTGAATTATAA
629914 TTT
1 TTT
629917 AAAAATTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (20 bp):
TTTGAAATTTTGAATTATAA
Found at i:630405 original size:2 final size:2
Alignment explanation
Indices: 630398--630430 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
630388 TTCTGTAAAT
630398 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
630431 TGCTTTGCTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:635571 original size:18 final size:16
Alignment explanation
Indices: 635546--635588 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
635536 ATAAAATAAT
*
635546 TAAAAATATTATT--A
1 TAAAAATAATATTACA
635560 TAAAATATAATATTACA
1 TAAAA-ATAATATTACA
635577 TAAAAATAATAT
1 TAAAAATAATAT
635589 GAATAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 5 0.20
15 7 0.28
16 7 0.28
17 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAATAATATTACA
Found at i:635596 original size:15 final size:14
Alignment explanation
Indices: 635535--635596 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
635525 TATATTACAT
*
635535 AATAAAATAATTAAA
1 AATAATATAA-TAAA
* *
635550 AATATTATTATAAA
1 AATAATATAATAAA
635564 ATATAATATTACATAAA
1 A-ATAATA-TA-ATAAA
635581 AATAATATGAATAAA
1 AATAATAT-AATAAA
635596 A
1 A
635597 TAAAAATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
14 5 0.13
15 19 0.50
16 8 0.21
17 6 0.16
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (14 bp):
AATAATATAATAAA
Found at i:636630 original size:2 final size:2
Alignment explanation
Indices: 636619--636649 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
636609 TTAAATAAAA
636619 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
636650 GATAACTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:640305 original size:107 final size:105
Alignment explanation
Indices: 640116--640308 Score: 260
Period size: 107 Copynumber: 1.8 Consensus size: 105
640106 GTGCAAAGGC
* * * * * * *
640116 AGAGGAGAAATCCAACATCATTAGACATGCGAGAGAATCCAATGAAATGCACCAAATGAAGGAGT
1 AGAGGAGAAATCCAACATCATTAGACAAGCGAAAAAACCCAACGAAACGCACCAAATGAAAGAGT
*
640181 GGATGAGGGAAGGGAAAACAAGGGGTAGGGTGGGATGAGG
66 GGATGAGGGAAGAGAAAACAAGGGGTAGGGTGGGATGAGG
* * * *
640221 AGAGGAGAAATCCAAGATTATTAGACAAGCAAGAAAAAACCCAGCGAAACGCACCAACTGAAAGA
1 AGAGGAGAAATCCAACATCATTAGACAAGC--GAAAAAACCCAACGAAACGCACCAAATGAAAGA
640286 GTGGATGAGGGAAGAGAAAACAA
64 GTGGATGAGGGAAGAGAAAACAA
640309 CATCTGTTCC
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
105 27 0.36
107 47 0.64
ACGTcount: A:0.45, C:0.13, G:0.31, T:0.11
Consensus pattern (105 bp):
AGAGGAGAAATCCAACATCATTAGACAAGCGAAAAAACCCAACGAAACGCACCAAATGAAAGAGT
GGATGAGGGAAGAGAAAACAAGGGGTAGGGTGGGATGAGG
Found at i:642410 original size:3 final size:3
Alignment explanation
Indices: 642402--642429 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
642392 ATTTCACTTA
642402 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
642430 CGACTATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:642769 original size:19 final size:19
Alignment explanation
Indices: 642726--642769 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
642716 AAAAAGAAAT
642726 TTTTTTAATATTTATATAA
1 TTTTTTAATATTTATATAA
* *
642745 TATTTTAATTATTTA-ATTA
1 TTTTTTAA-TATTTATATAA
642764 TTTTTT
1 TTTTTT
642770 TTAATAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTAATATTTATATAA
Found at i:644874 original size:20 final size:21
Alignment explanation
Indices: 644849--644900 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
644839 AACATAATAA
*
644849 AATATTAAAATTTTTAT-ATT
1 AATATTAAAATATTTATAATT
*
644869 AATATTTAAATATTTATAATT
1 AATATTAAAATATTTATAATT
*
644890 AA-ATTTAAATA
1 AATATTAAAATA
644901 AAAATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATTAAAATATTTATAATT
Found at i:644990 original size:25 final size:23
Alignment explanation
Indices: 644936--644983 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
644926 ATATTATTTT
644936 AAATTAAATTAATTCAAATAAAA
1 AAATTAAATTAATTCAAATAAAA
*
644959 AATATTAAATTTAATTCCAATAAAA
1 AA-ATTAAA-TTAATTCAAATAAAA
644984 TGAATTATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 6 0.27
25 14 0.64
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATTAAATTAATTCAAATAAAA
Found at i:646994 original size:2 final size:2
Alignment explanation
Indices: 646987--647013 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
646977 TGCCTATCCT
646987 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
647014 TTTTTCTTTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:654530 original size:20 final size:20
Alignment explanation
Indices: 654507--654547 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
654497 ATTAAATTAA
*
654507 ATTTAAATAATAATAATTTT
1 ATTTAAATAATAATAAATTT
**
654527 ATTTATTTAATAATAAATTT
1 ATTTAAATAATAATAAATTT
654547 A
1 A
654548 AAAAAGTATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAAATAATAATAAATTT
Found at i:654544 original size:36 final size:34
Alignment explanation
Indices: 654504--654573 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 34
654494 TAAATTAAAT
*
654504 TAAATTTAAATAA-TAATAATTTTATTTATTTAATAA
1 TAAATTTAAAAAAGT-ATAA-TTTA-TTATTTAATAA
*
654540 TAAATTTAAAAAAGTATGATTTATTATTTAATAA
1 TAAATTTAAAAAAGTATAATTTATTATTTAATAA
654574 ATTATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 11 0.35
35 4 0.13
36 15 0.48
37 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (34 bp):
TAAATTTAAAAAAGTATAATTTATTATTTAATAA
Found at i:654606 original size:17 final size:18
Alignment explanation
Indices: 654558--654606 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
654548 AAAAAGTATG
654558 ATTTATTATTTAATAAATT
1 ATTTATTATTT-ATAAATT
* *
654577 ATATTAATATTTATATATT
1 AT-TTATTATTTATAAATT
654596 -TTTATTATTTA
1 ATTTATTATTTA
654607 AATAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 9 0.35
18 1 0.04
19 8 0.31
20 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTATTATTTATAAATT
Found at i:655866 original size:19 final size:18
Alignment explanation
Indices: 655844--655910 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 18
655834 TATATAATCT
655844 TGATGAAAATAAATAAATA
1 TGAT-AAAATAAATAAATA
*
655863 TGATATTAAAAAAAATTAAATA
1 TG--A-TAAAATAAA-TAAATA
* *
655885 TAATATAAATATATAAATA
1 TGATA-AAATAAATAAATA
655904 TGATAAA
1 TGATAAA
655911 TTTAATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
18 2 0.05
19 14 0.37
20 6 0.16
21 8 0.21
22 8 0.21
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
TGATAAAATAAATAAATA
Found at i:655882 original size:22 final size:21
Alignment explanation
Indices: 655849--655890 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
655839 AATCTTGATG
* *
655849 AAAATAAATAAATATGATATT
1 AAAAAAAATAAATATAATATT
655870 AAAAAAAATTAAATATAATAT
1 AAAAAAAA-TAAATATAATAT
655891 AAATATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAAAAAATAAATATAATATT
Found at i:655909 original size:22 final size:21
Alignment explanation
Indices: 655849--655909 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
655839 AATCTTGATG
*
655849 AAAATAAATAAATATGATATT
1 AAAATAAATAAATATGATAAT
* *
655870 AAAAAAAATTAA-AT-ATAAT
1 AAAATAAATAAATATGATAAT
*
655889 ATAAATATATAAATATGATAA
1 A-AAATAAATAAATATGATAA
655910 ATTTAATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.16
20 10 0.32
21 12 0.39
22 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (21 bp):
AAAATAAATAAATATGATAAT
Found at i:655912 original size:33 final size:33
Alignment explanation
Indices: 655875--655970 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
655865 ATATTAAAAA
*
655875 AAATTAAATATAATATAAATATATAAATATGA-T
1 AAATTTAATATAATATAAATATATAAATAT-ATT
* *
655908 AAATTTAATAAAATATAAAT-TATTAATATATT
1 AAATTTAATATAATATAAATATATAAATATATT
* *
655940 AAATTTTATAT-ATATAAATATTTTAAATATA
1 AAATTTAATATAATATAAATA-TATAAATATA
655971 ATTACGATAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
31 9 0.17
32 18 0.34
33 26 0.49
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (33 bp):
AAATTTAATATAATATAAATATATAAATATATT
Found at i:655957 original size:15 final size:15
Alignment explanation
Indices: 655882--655971 Score: 58
Period size: 16 Copynumber: 5.7 Consensus size: 15
655872 AAAAAATTAA
*
655882 ATATAATATAAATATAT
1 ATAT-ATATAAAT-TTT
* *
655899 AAATATGATAAATTTA
1 ATATAT-ATAAATTTT
*
655915 ATAAAATATAAATTATT
1 AT-ATATATAAATT-TT
655932 A-ATATATTAAATTTT
1 ATATATA-TAAATTTT
655947 ATATATATAAATATTT
1 ATATATATAAAT-TTT
*
655963 -TAAATATAA
1 ATATATATAA
655972 TTACGATAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
15 20 0.34
16 25 0.42
17 14 0.24
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (15 bp):
ATATATATAAATTTT
Found at i:669842 original size:16 final size:17
Alignment explanation
Indices: 669821--669853 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
669811 CCATAATTTA
669821 TATTATATAA-TTATTG
1 TATTATATAATTTATTG
*
669837 TATTATGTAATTTATTG
1 TATTATATAATTTATTG
669854 AGTTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (17 bp):
TATTATATAATTTATTG
Found at i:670012 original size:16 final size:16
Alignment explanation
Indices: 669989--670028 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
669979 ACATATTTAA
669989 AATTAAATAAA-AATT
1 AATTAAATAAATAATT
670004 AATTTAAATAAATAATT
1 AA-TTAAATAAATAATT
670021 AATTAAAT
1 AATTAAAT
670029 TTATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 15 0.65
17 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTAAATAAATAATT
Found at i:670036 original size:21 final size:21
Alignment explanation
Indices: 669989--670042 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
669979 ACATATTTAA
*
669989 AATTAAATAA-AAATTAATTT
1 AATTAAATAATTAATTAATTT
*
670009 AAATAAATAATTAATTAAATTT
1 AATTAAATAATTAATT-AATTT
*
670031 -ATTAAATTATTA
1 AATTAAATAATTA
670043 TATTTTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 9 0.32
21 14 0.50
22 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAAATAATTAATTAATTT
Found at i:670063 original size:19 final size:18
Alignment explanation
Indices: 670017--670068 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
670007 TTAAATAAAT
670017 AATTAATTA-AATTTATTA
1 AATT-ATTATAATTTATTA
*
670035 AATTATTATATTTTATTA
1 AATTATTATAATTTATTA
670053 TAATTGA-TATAATTTA
1 -AATT-ATTATAATTTA
670069 ATTTTACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 12 0.41
19 12 0.41
20 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTATTATAATTTATTA
Found at i:670177 original size:25 final size:26
Alignment explanation
Indices: 670122--670173 Score: 74
Period size: 23 Copynumber: 2.1 Consensus size: 26
670112 ATAAAATTTT
670122 TAATAATTTTTAAGTTATTTTATAAA
1 TAATAATTTTTAAGTTATTTTATAAA
*
670148 T-ATAATTTTT-TG-TATTTTATAAA
1 TAATAATTTTTAAGTTATTTTATAAA
670171 TAA
1 TAA
670174 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 12 0.50
24 2 0.08
25 9 0.38
26 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
TAATAATTTTTAAGTTATTTTATAAA
Found at i:670189 original size:23 final size:23
Alignment explanation
Indices: 670163--670232 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 23
670153 TTTTTTGTAT
670163 TTTATAAATAAATAAATAAATAA
1 TTTATAAATAAATAAATAAATAA
* *
670186 TTTA-AATATAAATAATTAAATTTA
1 TTTATAA-ATAAATAAATAAA-TAA
*
670210 TTATATATATAAATAAAATAAAT
1 TT-TATAAATAAAT-AAATAAAT
670233 TTATTATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.05
23 16 0.42
24 4 0.11
25 9 0.24
26 7 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTATAAATAAATAAATAAATAA
Found at i:670198 original size:15 final size:14
Alignment explanation
Indices: 670165--670206 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
670155 TTTTGTATTT
*
670165 TATAAATAAAT-AA
1 TATAAATAATTAAA
670178 -ATAAATAATTTAAA
1 TATAAATAA-TTAAA
670192 TATAAATAATTAAA
1 TATAAATAATTAAA
670206 T
1 T
670207 TTATTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 8 0.32
13 1 0.04
14 8 0.32
15 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TATAAATAATTAAA
Found at i:670198 original size:19 final size:20
Alignment explanation
Indices: 670170--670225 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
670160 TATTTTATAA
670170 ATAA-ATAAATAAATAATTT
1 ATAATATAAATAAATAATTT
*
670189 A-AATATAAATAATTAAATTT
1 ATAATATAAATAAAT-AATTT
* *
670209 ATTATATATATAAATAA
1 ATAATATAAATAAATAA
670226 AATAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.07
19 10 0.33
20 8 0.27
21 10 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAATATAAATAAATAATTT
Found at i:670242 original size:53 final size:52
Alignment explanation
Indices: 670165--670274 Score: 125
Period size: 53 Copynumber: 2.1 Consensus size: 52
670155 TTTTGTATTT
* *
670165 TATAAATAAATAAATAAATAATTTAAATATAAATAAT-TAAATTT-ATTATATA
1 TATAAATAAATAAATAAATAATTT--ATACAAATAATATAAATTTAAATATATA
** * *
670217 TATAAATAAAATAAATTTATTATTTATACGAATAATATAAATTTAAATATATA
1 TATAAAT-AAATAAATAAATAATTTATACAAATAATATAAATTTAAATATATA
670270 TATAA
1 TATAA
670275 TTTTATATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
51 9 0.18
52 14 0.29
53 26 0.53
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (52 bp):
TATAAATAAATAAATAAATAATTTATACAAATAATATAAATTTAAATATATA
Found at i:670781 original size:15 final size:15
Alignment explanation
Indices: 670753--670800 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
670743 ACTCTCATTT
* *
670753 CGACGAAGAAGATGA
1 CGACCAAGACGATGA
*
670768 CGACCAATACGATGA
1 CGACCAAGACGATGA
* *
670783 CGACGACGACGATGA
1 CGACCAAGACGATGA
670798 CGA
1 CGA
670801 TTTCGGGAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.29, T:0.08
Consensus pattern (15 bp):
CGACCAAGACGATGA
Found at i:673959 original size:24 final size:24
Alignment explanation
Indices: 673927--673973 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
673917 ACTCCAAAAA
* *
673927 CCAGTTTCAGCTCCCAAAGATGAT
1 CCAGCTTCAACTCCCAAAGATGAT
*
673951 CCAGCTTCAACTCCCAAGGATGA
1 CCAGCTTCAACTCCCAAAGATGA
673974 ACTGGGTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (24 bp):
CCAGCTTCAACTCCCAAAGATGAT
Found at i:676232 original size:2 final size:2
Alignment explanation
Indices: 676225--676254 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
676215 AAAGTTCTTA
676225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
676255 GAACAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:676646 original size:14 final size:15
Alignment explanation
Indices: 676621--676649 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
676611 TAAATTTATA
676621 TTATATTAATATTTT
1 TTATATTAATATTTT
676636 TTATA-TAATATTTT
1 TTATATTAATATTTT
676650 AATTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATTAATATTTT
Found at i:676852 original size:18 final size:19
Alignment explanation
Indices: 676809--676855 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
676799 TCCGAATATG
676809 ATATATTTAATAAATATAAA
1 ATATATTTAAT-AATATAAA
*
676829 AAATATTTAAT-ATATAAA
1 ATATATTTAATAATATAAA
*
676847 TTATATTTA
1 ATATATTTA
676856 CATTTATACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 14 0.58
20 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATATTTAATAATATAAA
Found at i:677057 original size:86 final size:87
Alignment explanation
Indices: 676930--677094 Score: 251
Period size: 86 Copynumber: 1.9 Consensus size: 87
676920 TGAATTGTAC
* * *
676930 GTTCAATTTGATCTTTACCAATTTGGTGTTTCGACTGCTGTGATTTACTATATGGAAAGATGGGA
1 GTTCAATTTGATCTTTACCAATTCGGTATTTCGACTGCTGTGATTTACTATATAGAAAGATGGGA
676995 AAGGAGATCCCCCCCACTATAA
66 AAGGAGATCCCCCCCACTATAA
* * *
677017 GTTCAATTTGATC-TTGCCAATTCGGTATTTCTACTGCTGTGATTTACTATATAGAAAGATGGGG
1 GTTCAATTTGATCTTTACCAATTCGGTATTTCGACTGCTGTGATTTACTATATAGAAAGATGGGA
* *
677081 AAGGTGATTCCCCC
66 AAGGAGATCCCCCC
677095 TTGACCGATG
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 57 0.81
87 13 0.19
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (87 bp):
GTTCAATTTGATCTTTACCAATTCGGTATTTCGACTGCTGTGATTTACTATATAGAAAGATGGGA
AAGGAGATCCCCCCCACTATAA
Found at i:683355 original size:52 final size:52
Alignment explanation
Indices: 683285--683405 Score: 217
Period size: 52 Copynumber: 2.3 Consensus size: 52
683275 GAAAATTTAT
683285 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATGA-TGTATCGATACATCTGGGCAAATTTGC
*
683337 CTGCATGTATCGATACATTTTATGATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATGATGTATCGATACATCTGGGCAAATTTGC
683389 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
683406 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
52 66 0.99
53 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATGATGTATCGATACATCTGGGCAAATTTGC
Found at i:683418 original size:52 final size:51
Alignment explanation
Indices: 683285--683425 Score: 205
Period size: 52 Copynumber: 2.7 Consensus size: 51
683275 GAAAATTTAT
683285 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
683337 CTGCATGTATCGATACATT-TTATGATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTAATA-G-TGTATCGATACATCTGGGCAAATTTGC
*
683389 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
683426 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
50 2 0.02
51 3 0.04
52 73 0.90
53 2 0.02
54 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:683432 original size:13 final size:13
Alignment explanation
Indices: 683414--683438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
683404 CAAAGATCAG
683414 TGTATCGATACAA
1 TGTATCGATACAA
683427 TGTATCGATACA
1 TGTATCGATACA
683439 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:683522 original size:13 final size:13
Alignment explanation
Indices: 683504--683528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
683494 CAAAAAAATA
683504 TGTATCGATACAT
1 TGTATCGATACAT
683517 TGTATCGATACA
1 TGTATCGATACA
683529 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:683524 original size:33 final size:33
Alignment explanation
Indices: 683482--683548 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
683472 AGTAGCTTAA
683482 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
683515 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
683548 A
1 A
683549 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:684637 original size:173 final size:171
Alignment explanation
Indices: 684346--684742 Score: 656
Period size: 173 Copynumber: 2.3 Consensus size: 171
684336 TTTTAGAGAT
*
684346 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAATATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAATATGAGAAAA
*
684411 GTGATAAAGATGCCAATATGTTGATTCATGGCCAATGATATTGGGTCTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGTCTAAAGATGAGAAAAAGGA
684476 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
*
684517 GATGAAGATGCCAATATGCTGCTGATTCAAGGCCAGCGATATTGGACTTAAA-ATG-ATGATGAG
1 GATGAAGATGCCAATA---TGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAT-ATGAG
684580 AAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGG-CTTAAAGATGAGAAA
62 AAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGTC-TAAAGATGAGAAA
684644 AAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
126 AAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
684690 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
684743 GTGCCAATGT
Statistics
Matches: 212, Mismatches: 5, Indels: 15
0.91 0.02 0.06
Matches are distributed among these distances:
171 15 0.07
172 3 0.01
173 150 0.71
174 36 0.17
176 8 0.04
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (171 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAATATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGTCTAAAGATGAGAAAAAGGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:684799 original size:49 final size:49
Alignment explanation
Indices: 684657--685111 Score: 583
Period size: 49 Copynumber: 9.4 Consensus size: 49
684647 GATGTCAACG
* *
684657 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
684709 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
684752 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
684801 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
684844 TGCTGAGTCAAGGCCAGCTACATTGGACTTCAAGATGATGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
684893 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
684942 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
684991 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* *
685040 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG---AAGATGCCAATA
685092 TGCTGATTCAAGGCCAGCTA
1 TGCTGATTCAAGGCCAGCTA
685112 TATGAAGGTG
Statistics
Matches: 353, Mismatches: 35, Indels: 30
0.84 0.08 0.07
Matches are distributed among these distances:
43 70 0.20
44 5 0.01
45 2 0.01
46 3 0.01
47 1 0.00
48 5 0.01
49 206 0.58
50 1 0.00
51 2 0.01
52 58 0.16
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:684830 original size:92 final size:93
Alignment explanation
Indices: 684656--685215 Score: 780
Period size: 98 Copynumber: 5.9 Consensus size: 93
684646 GGATGTCAAC
* * *
684656 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATATGCTGATTCAAG
*
684721 GCCAGCTATATTGGACTTA-AAGGTGCCAAT
63 GCCAGCGATATTGGACTTAGAAGGTGCCAAT
*
684751 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
684816 AGCGATATTGGACTTA-AAGGTGCCAAT
66 AGCGATATTGGACTTAGAAGGTGCCAAT
* *
684843 GTGCTGAGTCAAGGCCAGCTACATTGGACTTCAAGATGATGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
684908 AGCGATATTGGACTTAAAGATGAAGGTGCCAAT
66 AGCGATATTGGACTT----A-GAAGGTGCCAAT
684941 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
685006 AGCGATATTGGACTTAAAGATGAAGGTGCCAAT
66 AGCGATATTGGACTT----A-GAAGGTGCCAAT
*
685039 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG---AAGATGCCAATATGCTGATTCAAG
685104 GCCAGC--TA-T--A--T-GAAGGTGCCAAT
63 GCCAGCGATATTGGACTTAGAAGGTGCCAAT
*
685127 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAG
* *
685192 GCCAGCTATATTGGGCTTAGAAGG
63 GCCAGCGATATTGGACTTAGAAGG
685216 GTTGCCACCG
Statistics
Matches: 437, Mismatches: 10, Indels: 35
0.91 0.02 0.07
Matches are distributed among these distances:
88 81 0.19
89 1 0.00
90 2 0.00
91 1 0.00
92 126 0.29
94 5 0.01
95 37 0.08
96 7 0.02
98 146 0.33
99 2 0.00
101 29 0.07
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (93 bp):
GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAGAAGGTGCCAAT
Found at i:685174 original size:88 final size:88
Alignment explanation
Indices: 685025--685202 Score: 347
Period size: 88 Copynumber: 2.0 Consensus size: 88
685015 GGACTTAAAG
685025 ATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAAGGTGCCAA
1 ATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAAGGTGCCAA
685090 TATGCTGATTCAAGGCCAGCTAT
66 TATGCTGATTCAAGGCCAGCTAT
*
685113 ATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAA
1 ATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAAGGTGCCAA
685178 TATGCTGATTCAAGGCCAGCTAT
66 TATGCTGATTCAAGGCCAGCTAT
685201 AT
1 AT
685203 TGGGCTTAGA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (88 bp):
ATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAAGGTGCCAA
TATGCTGATTCAAGGCCAGCTAT
Found at i:685279 original size:34 final size:34
Alignment explanation
Indices: 685210--685275 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
685200 TATTGGGCTT
685210 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGA
685244 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTGG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGG
685276 GAAGGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 28 0.88
34 4 0.12
ACGTcount: A:0.17, C:0.18, G:0.38, T:0.27
Consensus pattern (34 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGA
Found at i:685353 original size:34 final size:34
Alignment explanation
Indices: 685282--686237 Score: 834
Period size: 34 Copynumber: 29.0 Consensus size: 34
685272 TTGGGAAGGA
*
685282 AAAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--G
685316 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
685350 AAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA--G
*
685386 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AG
685421 AAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-G
**
685456 AAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAG
1 -AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
685491 AAGAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
* * * *
685525 AAGAAG-GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGG
1 AAAAAGAG-TGCCACGGA-GT-TGTGGGCTTTA--AA-AG
* *
685564 AGAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--G
685598 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
685632 AAAAA-AGGTGCCACGGAGTTATGGAC-TTAAAGATG
1 AAAAAGA-GTGCCACGGAGTTGTGGGCTTTAAA-A-G
*
685667 AAAAA-AGTGCCACGGAGTTTTGGGC-TTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
685699 -----G-GTGCCACGGAGTTGTGGGC-TTAGAAGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTA-AAAG
* * *
685727 AAAAAGAGTGCCACAGAGTTGTGGGC-TTAGGAGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTA-AAAG
685761 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-----
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
685790 AAAAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
* *
685825 AAGAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
* *
685859 AAGAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
*
685893 AAGAAG-GTGCCACGGAGTTGTGGGCTTT-----
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
685921 --AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT--AAA-AG
685956 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AG
685991 AAAAAG-GTGCCACGGAGTTGTGGGCTTT----G
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
686020 ---AAGAGTGCCACGAAGTTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
686051 AAGAAG-GTGCCACGGAGTTGTGGGC-TT-----
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
686078 -AAAAGAGTGCCACGGAGTCGTGGAC-TTAAAGATG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-A-G
* *
686112 AAAAA-AGTGCCACGGAATTGTGGGCTTCAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
686145 -----G-GTGCCACGGAGTTGTGGAC-TTAAAAGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-G
*
686173 AACAAG-GTGCCACGGAGTTGTGGGCTTT-AAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* * *
686205 AAAAA-A-TGCCACTGAGTCGTGGACTTTGAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
686238 GTATTTGAAG
Statistics
Matches: 787, Mismatches: 54, Indels: 163
0.78 0.05 0.16
Matches are distributed among these distances:
26 10 0.01
27 87 0.11
28 21 0.03
29 29 0.04
31 19 0.02
32 8 0.01
33 98 0.12
34 291 0.37
35 90 0.11
36 39 0.05
37 80 0.10
38 10 0.01
39 5 0.01
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.20
Consensus pattern (34 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
Found at i:685366 original size:68 final size:67
Alignment explanation
Indices: 685280--686226 Score: 822
Period size: 61 Copynumber: 14.4 Consensus size: 67
685270 CTTTGGGAAG
*
685280 GAAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAAG-TGCCACGGAGTTGTGGGCTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
685345 AAAA
64 AAAA
685349 GAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 GAAAAAAGTGCCACGGAGTTGTGGGC-TT-AAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
685414 TAAACG
63 TAAA-A
* **
685420 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTT
1 GAAAAAAGTGCCACGGAGTTGTGGGC-TT-AAAAGG-AAAAAGAGTGCCACGGAGTTGTGGGCTT
685485 TAAAA
63 TAAAA
* * * * *
685490 GAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAG-GTTGCCACCGACTTGTGTGGGC
1 GAAAAAAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAAAAAGAG-TGCCACGGA-GT-TGTGGGC
*
685553 TTTAGGAAG
61 TTTA--AAA
* * *
685562 GGAGAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAAG-TGCCACGGAGTTGTGGGCTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
685627 AAAA
64 AAAA
* * * *
685631 GAAAAAAGGTGCCACGGAGTTATGGACTTAAAGATGAAAAA-AGTGCCACGGAGTTTTGGGC-TT
1 GAAAAAA-GTGCCACGGAGTTGTGGGCTTAAA-AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
685694 AAAA
64 AAAA
* * *
685698 G-----GGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGC-TTAG
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA-
* *
685757 GAG
65 AAA
* *
685760 GAAAAAGAGTGCCACGGAGTTGTGGGCTT-----TAAAAAGAGTGCCACGGAGTCGTGGGCTTTG
1 GAAAAA-AGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-
685820 AAAA
64 AAAA
* * * * *
685824 GAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAA-GAAGAAG-GTGCCACAGAGTTGTGGGCTTT
1 GAAAAAAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
685887 GAAAA
64 -AAAA
* * * *
685892 GAAGAAGGTGCCACGGAGTTGTGGGCTT-------TAAAGAGTGCCACGGAGTCGTGGGCTTTGA
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT--
685950 AAAGA
64 AAA-A
685955 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACA-GAAAAAG-GTGCCACGGAGTTGTGGGCTT
1 GAAAAA-AGTGCCACGGAGTTGTGGGC-TTAAA-AGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
686018 T----
63 TAAAA
* * *
686019 G--AAGAGTGCCACGAAGTTGTGGGCTTTAAAA-GAAGAAG-GTGCCACGGAGTTGTGGGC-TTA
1 GAAAAAAGTGCCACGGAGTTGTGGGC-TTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
686079 AAA
65 AAA
* * * * *
686082 G-----AGTGCCACGGAGTCGTGGACTTAAAGATGAAAAA-AGTGCCACGGAATTGTGGGCTTCA
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTAAA-AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
686141 AAA
65 AAA
* * *
686144 G-----GGTGCCACGGAGTTGTGGACTTAAAAGGAACAAG-GTGCCACGGAGTTGTGGGCTTT-A
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
686202 AA
66 AA
* *
686204 GAAAAAA-TGCCACTGAGTCGTGG
1 GAAAAAAGTGCCACGGAGTTGTGG
686227 ACTTTGAAAA
Statistics
Matches: 747, Mismatches: 74, Indels: 119
0.79 0.08 0.13
Matches are distributed among these distances:
59 7 0.01
60 58 0.08
61 136 0.18
62 36 0.05
63 49 0.07
64 44 0.06
65 3 0.00
67 10 0.01
68 119 0.16
69 52 0.07
70 87 0.12
71 99 0.13
72 15 0.02
73 31 0.04
74 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.20
Consensus pattern (67 bp):
GAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
AA
Found at i:685998 original size:98 final size:93
Alignment explanation
Indices: 685729--686205 Score: 432
Period size: 98 Copynumber: 5.1 Consensus size: 93
685719 TTAGAAGGAA
* *
685729 AAAGAGTGCCACAGAGTTGTGGGC-TTAGGAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT--A
1 AAAGAGTGCCACAGAGTTGTGGGCTTTA-AAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
* *
685791 A-AAAGA-GTGCCACGGAGTCGTGGGCTTT
64 AGAAAAAGGTGCCACGGAGTTGTGGGCTTT
* *
685819 GAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGC
1 ----A-AAG-A-GTGCCACAGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGC
*
685884 TTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT
58 TTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
* *
685921 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAGAGTGCCACAGAGTTGTGGGCTTT--AAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTA
685986 AACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
62 AA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTT
* *
686019 GAAGAGTGCCAC-GAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGC-TTAAAA
1 AAAGAGTGCCACAG-AGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
* *
686082 G----A-GTGCCACGGAGTCGTGGACTTAAAGAT
65 GAAAAAGGTGCCACGGAGTTGTGGGCTT-----T
* * * * *
686111 GAAAAAAGTGCCACGGAATTGTGGGCTTCAAAAG-----GGTGCCACGGAGTTGTGGAC-TTAAA
1 --AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
*
686170 AGGAACAAGGTGCCACGGAGTTGTGGGCTTT
64 A-GAAAAAGGTGCCACGGAGTTGTGGGCTTT
686201 AAAGA
1 AAAGA
686206 AAAAATGCCA
Statistics
Matches: 328, Mismatches: 26, Indels: 64
0.78 0.06 0.15
Matches are distributed among these distances:
87 19 0.06
88 5 0.02
89 25 0.08
90 2 0.01
92 3 0.01
93 5 0.02
94 47 0.14
95 50 0.15
96 8 0.02
97 54 0.16
98 83 0.25
99 1 0.00
100 2 0.01
101 3 0.01
102 21 0.06
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (93 bp):
AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAG
AAAAAGGTGCCACGGAGTTGTGGGCTTT
Done.