Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold14
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: 2879421
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 64274 characters in sequence are not A, C, G, or T
File 4 of 17
Found at i:559481 original size:25 final size:25
Alignment explanation
Indices: 559452--559503 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
559442 TCTTACTCAT
559452 ATTATTTTTTTAT-T-TTTATATTTTA
1 ATTATTTTTTT-TGTGTTTAT-TTTTA
559477 ATTATTTTTTTTGTGTTTATTTTTA
1 ATTATTTTTTTTGTGTTTATTTTTA
559502 AT
1 AT
559504 AATCATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 1 0.04
25 19 0.76
26 5 0.20
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTATTTTTTTTGTGTTTATTTTTA
Found at i:560202 original size:6 final size:6
Alignment explanation
Indices: 560181--560224 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
560171 CAACAGACCT
* *
560181 TTTTTA TTATTA -TTTTA TTTTTA TTATTA TTTTTA TTTTGTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT-TA TT
560225 ACCTTCTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
5 4 0.12
6 24 0.75
7 4 0.12
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:560203 original size:17 final size:18
Alignment explanation
Indices: 560181--560225 Score: 74
Period size: 17 Copynumber: 2.5 Consensus size: 18
560171 CAACAGACCT
560181 TTTTTATTATTA-TTTTA
1 TTTTTATTATTATTTTTA
560198 TTTTTATTATTATTTTTA
1 TTTTTATTATTATTTTTA
560216 TTTTGTATTA
1 TTTT-TATTA
560226 CCTTCTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 12 0.46
18 9 0.35
19 5 0.19
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTATTATTATTTTTA
Found at i:560988 original size:41 final size:42
Alignment explanation
Indices: 560943--561028 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
560933 CGTCACTATT
*
560943 CATCACTGTTCATGTATCGAT-CATTGTGAATAGTATCGATA
1 CATCACTGTTCATGTATCGATACATTGTGAATAGTATCAATA
560984 CATCACTGTTCATGTATCGATACATTGTGAATAGTATCAATA
1 CATCACTGTTCATGTATCGATACATTGTGAATAGTATCAATA
561026 CAT
1 CAT
561029 TGAGTCCAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 21 0.49
42 22 0.51
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (42 bp):
CATCACTGTTCATGTATCGATACATTGTGAATAGTATCAATA
Found at i:561002 original size:22 final size:22
Alignment explanation
Indices: 560943--561008 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
560933 CGTCACTATT
560943 CATCACTGTTCATGTATCGAT-
1 CATCACTGTTCATGTATCGATA
**
560964 CAT---TGTGAATAGTATCGATA
1 CATCACTGTTCAT-GTATCGATA
560984 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
561006 CAT
1 CAT
561009 TGTGAATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
18 5 0.14
19 8 0.22
20 3 0.08
21 3 0.08
22 12 0.33
23 5 0.14
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:561026 original size:20 final size:20
Alignment explanation
Indices: 560956--561030 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
560946 CACTGTTCAT
560956 GTATCGAT-CATTGTGAATA
1 GTATCGATACATTGTGAATA
**
560975 GTATCGATACATCACTGTTCAT-
1 GTATCGATACAT---TGTGAATA
560997 GTATCGATACATTGTGAATA
1 GTATCGATACATTGTGAATA
*
561017 GTATCAATACATTG
1 GTATCGATACATTG
561031 AGTCCAACGA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 13 0.28
20 16 0.35
22 12 0.26
23 5 0.11
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (20 bp):
GTATCGATACATTGTGAATA
Found at i:561092 original size:20 final size:20
Alignment explanation
Indices: 561067--561120 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
561057 TTTCAAATGC
561067 ATGTATCGATACATTATGAA
1 ATGTATCGATACATTATGAA
561087 ATGTATCGATACATTATGAA
1 ATGTATCGATACATTATGAA
*
561107 TTGTATCGATACAT
1 ATGTATCGATACAT
561121 AGAAGCGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTATGAA
Found at i:563163 original size:16 final size:16
Alignment explanation
Indices: 563142--563183 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
563132 GAATTAGAGG
563142 AGAAAATGAATGAGTT
1 AGAAAATGAATGAGTT
563158 AGAAAA-GAAATGAGTT
1 AGAAAATG-AATGAGTT
563174 -GCAAAATGAA
1 AG-AAAATGAA
563184 AATGATGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.09
16 20 0.87
17 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (16 bp):
AGAAAATGAATGAGTT
Found at i:565386 original size:21 final size:21
Alignment explanation
Indices: 565345--565388 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
565335 CTCCCCTTTA
* *
565345 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
565366 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
565387 TC
1 TC
565389 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:567209 original size:13 final size:13
Alignment explanation
Indices: 567191--567216 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
567181 ATAATCACCC
567191 TGTATCGATACAA
1 TGTATCGATACAA
567204 TGTATCGATACAA
1 TGTATCGATACAA
567217 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:569306 original size:15 final size:15
Alignment explanation
Indices: 569286--569316 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
569276 ATTTCTTGTG
*
569286 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
569301 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
569316 G
1 G
569317 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:571147 original size:21 final size:21
Alignment explanation
Indices: 571118--571162 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
571108 AAGTTTTCAT
*
571118 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
571138 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
571160 TTT
1 TTT
571163 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:573387 original size:20 final size:20
Alignment explanation
Indices: 573362--573413 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
573352 TACAAGCCAA
** *
573362 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTGG
573382 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
573401 TGTATCGATACAA
1 TGTATCGATACAA
573414 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:573419 original size:19 final size:18
Alignment explanation
Indices: 573362--573419 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
573352 TACAAGCCAA
*
573362 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA--TTTGG
*
573382 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
573401 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
573420 CTACTGCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.58
20 12 0.36
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:576749 original size:20 final size:20
Alignment explanation
Indices: 576726--576778 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
576716 ATACTCAGAT
576726 GTATCGATACATTTTGCTTA
1 GTATCGATACATTTTGCTTA
576746 GTATCGATACATTTTGCTTA
1 GTATCGATACATTTTGCTTA
576766 GTATCGATACATT
1 GTATCGATACATT
576779 GTATCGATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
GTATCGATACATTTTGCTTA
Found at i:576784 original size:13 final size:13
Alignment explanation
Indices: 576766--576790 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
576756 ATTTTGCTTA
576766 GTATCGATACATT
1 GTATCGATACATT
576779 GTATCGATACAT
1 GTATCGATACAT
576791 AAAACTGGTA
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):
GTATCGATACATT
Found at i:576835 original size:10 final size:10
Alignment explanation
Indices: 576820--576858 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
576810 TCTTATTTTT
576820 ACTATTCATC
1 ACTATTCATC
576830 ACTATTCATC
1 ACTATTCATC
*
576840 ACTGTTCATC
1 ACTATTCATC
576850 ACTATTCAT
1 ACTATTCAT
576859 ATATCAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (10 bp):
ACTATTCATC
Found at i:580443 original size:28 final size:28
Alignment explanation
Indices: 580412--580466 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
580402 GAAATCAAGC
*
580412 CATTATCATTTTAAATTATTTTGAATTT
1 CATTATCATTTTAAATTATTTTAAATTT
580440 CATTATCATTTTAAATTATTTTAAATT
1 CATTATCATTTTAAATTATTTTAAATT
580467 CAAATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (28 bp):
CATTATCATTTTAAATTATTTTAAATTT
Found at i:581585 original size:69 final size:69
Alignment explanation
Indices: 581467--581675 Score: 330
Period size: 69 Copynumber: 3.0 Consensus size: 69
581457 GCCAAGAGAT
*
581467 GTTTCATTAATAACAGCAAGCTGCCCGTAACGTAACAGCCTCG-CTGTTTTCTCAATCATGCAGG
1 GTTTCATTAATAACAGCAAGCTGCCCGTAATGTAACAGCCTCGTC-GTTTTCTCAATCATGCAGG
581531 CAGGG
65 CAGGG
* * *
581536 GTTTCATTAATAACAGCAAGCTGCCCGTAATGTAATAGCCACGTCGTTTTCTCAATCATGCACGC
1 GTTTCATTAATAACAGCAAGCTGCCCGTAATGTAACAGCCTCGTCGTTTTCTCAATCATGCAGGC
581601 AGGG
66 AGGG
* * * *
581605 GTTTCATTAATTATAGCAAGCTGCCTGTAATGTAACAGCCTCATCGTTTTCTCAATCATGCAGGC
1 GTTTCATTAATAACAGCAAGCTGCCCGTAATGTAACAGCCTCGTCGTTTTCTCAATCATGCAGGC
581670 AGGG
66 AGGG
581674 GT
1 GT
581676 CCCTCCACAA
Statistics
Matches: 128, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
69 127 0.99
70 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (69 bp):
GTTTCATTAATAACAGCAAGCTGCCCGTAATGTAACAGCCTCGTCGTTTTCTCAATCATGCAGGC
AGGG
Found at i:582585 original size:2 final size:2
Alignment explanation
Indices: 582578--582617 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
582568 TTTGTGGCTT
582578 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
582618 CTAGTTTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:587810 original size:18 final size:18
Alignment explanation
Indices: 587788--587828 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
587778 ATATTTTATA
587788 ATAAAAATTAT-TAATAT
1 ATAAAAATTATATAATAT
*
587805 ATTAAAATTTATATAA-AT
1 A-TAAAAATTATATAATAT
587823 ATAAAA
1 ATAAAA
587829 TATTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 12 0.57
19 3 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAAATTATATAATAT
Found at i:587871 original size:45 final size:49
Alignment explanation
Indices: 587776--587871 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 49
587766 GGATATATTG
*
587776 AAATATTTTATAATAAAAATTATTAATATATTAAAATTTATATAAATATA
1 AAATATTTTATAATAAAAATTATTAATATAATAAAA-TTATATAAATATA
587826 AAATATTTTA-AAT-AAAATTA-TAATATAATAAAA-TATATAAATATA
1 AAATATTTTATAATAAAAATTATTAATATAATAAAATTATATAAATATA
587871 A
1 A
587872 TATAAATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
45 13 0.29
47 12 0.27
48 7 0.16
49 3 0.07
50 10 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (49 bp):
AAATATTTTATAATAAAAATTATTAATATAATAAAATTATATAAATATA
Found at i:588126 original size:17 final size:18
Alignment explanation
Indices: 588088--588154 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
588078 ATAAAATTTT
*
588088 TAAAAAAATTTAAAAAATAA
1 TAAAAAAA--TAATAAATAA
588108 TAAAAAAATAATAAA-AA
1 TAAAAAAATAATAAATAA
* * *
588125 TAAAATAATTATAAATAT
1 TAAAAAAATAATAAATAA
*
588143 TAATAAAATAAT
1 TAAAAAAATAAT
588155 TTTAATTGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 15 0.38
18 16 0.41
20 8 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAAAATAATAAATAA
Found at i:588129 original size:14 final size:15
Alignment explanation
Indices: 588098--588141 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
588088 TAAAAAAATT
588098 TAAAA-AATAATAAA
1 TAAAATAATAATAAA
588112 -AAAATAATAA-AAA
1 TAAAATAATAATAAA
*
588125 TAAAATAATTATAAA
1 TAAAATAATAATAAA
588140 TA
1 TA
588142 TTAATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 7 0.27
14 14 0.54
15 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAAATAATAATAAA
Found at i:588132 original size:11 final size:11
Alignment explanation
Indices: 588099--588124 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
588089 AAAAAAATTT
588099 AAAAAATAATA
1 AAAAAATAATA
588110 AAAAAATAATA
1 AAAAAATAATA
588121 AAAA
1 AAAA
588125 TAAAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:588976 original size:4 final size:4
Alignment explanation
Indices: 588967--588991 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
588957 TATTGATTAC
588967 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
588992 AATGTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:589808 original size:20 final size:20
Alignment explanation
Indices: 589783--589826 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
589773 TAAGAAAGTT
589783 ACCATTAATTCAAAGTATTG
1 ACCATTAATTCAAAGTATTG
* *
589803 ACCATTAATTCAAGGTTTTG
1 ACCATTAATTCAAAGTATTG
589823 ACCA
1 ACCA
589827 CTATCGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (20 bp):
ACCATTAATTCAAAGTATTG
Found at i:590086 original size:15 final size:16
Alignment explanation
Indices: 590066--590098 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
590056 CGTATAAGTA
590066 TAATTAATTA-ATTTT
1 TAATTAATTATATTTT
590081 TAATTAATTATATTTT
1 TAATTAATTATATTTT
590097 TA
1 TA
590099 TTTTTATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATTAATTATATTTT
Found at i:590884 original size:28 final size:28
Alignment explanation
Indices: 590845--590898 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
590835 TTTTTTAATG
* *
590845 TTTATACTATAATATTACATATTTATGT
1 TTTATACTATAAAATTACATAATTATGT
*
590873 TTTATA-TGATAAAATTATATAATTAT
1 TTTATACT-ATAAAATTACATAATTAT
590899 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 1 0.05
28 21 0.95
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (28 bp):
TTTATACTATAAAATTACATAATTATGT
Found at i:594483 original size:12 final size:12
Alignment explanation
Indices: 594466--594491 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
594456 CTGAGCAACC
594466 AAAAAAGAAAAA
1 AAAAAAGAAAAA
594478 AAAAAAGAAAAA
1 AAAAAAGAAAAA
594490 AA
1 AA
594492 GAGAGTTCTT
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):
AAAAAAGAAAAA
Found at i:595260 original size:58 final size:58
Alignment explanation
Indices: 595104--595291 Score: 193
Period size: 59 Copynumber: 3.2 Consensus size: 58
595094 ATAGGGACCA
* * * * * *
595104 TTTAGCAAATTTCATGCATTTTAGGGTCATTTAGATTATTTCATATAATCTAA-ATAAAT
1 TTTAGAAAATTTCATACATTTTAGGGCCATTTA-ATTATTTCACATAATCTAAGGT-CAT
* * *
595163 TTTA-AAAATTTGCATATATTTTAGGGCCATTTACGTTATTTCACATAATTTAAGGTCAT
1 TTTAGAAAATTT-CATACATTTTAGGGCCATTTA-ATTATTTCACATAATCTAAGGTCAT
* *
595222 TTTAGAAAACTTCAT-CATTTTAGGGCCATTTAATTTATTTTACATAATCTAAGGTCAT
1 TTTAGAAAATTTCATACATTTTAGGGCCATTTAA-TTATTTCACATAATCTAAGGTCAT
*
595280 TTTGGCAAAATT
1 TTTAG-AAAATT
595292 CATTATCTTA
Statistics
Matches: 107, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
58 48 0.45
59 52 0.49
60 7 0.07
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (58 bp):
TTTAGAAAATTTCATACATTTTAGGGCCATTTAATTATTTCACATAATCTAAGGTCAT
Found at i:595294 original size:58 final size:58
Alignment explanation
Indices: 595104--595309 Score: 186
Period size: 58 Copynumber: 3.5 Consensus size: 58
595094 ATAGGGACCA
* * * * * *
595104 TTTAGCAAATTTCATGCATTTTAGGGTCATTT-AGATTATTTCATATAATCTAA-ATAAAT
1 TTTAGAAAACTTCAT-CATTTTAGGGCCATTTAAG-TTATTTCACATAATCTAAGGT-CAT
* * * *
595163 TTTA-AAAATTTGCATATATTTTAGGGCCATTTACGTTATTTCACATAATTTAAGGTCAT
1 TTTAGAAAACTT-CAT-CATTTTAGGGCCATTTAAGTTATTTCACATAATCTAAGGTCAT
* *
595222 TTTAGAAAACTTCATCATTTTAGGGCCATTTAATTTATTTTACATAATCTAAGGTCAT
1 TTTAGAAAACTTCATCATTTTAGGGCCATTTAAGTTATTTCACATAATCTAAGGTCAT
* * * *
595280 TTTGGCAAAA-TTCATTATCTTAGGACCATT
1 TTTAG-AAAACTTCATCATTTTAGGGCCATT
595310 GAGTATTTTC
Statistics
Matches: 123, Mismatches: 19, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
58 65 0.53
59 50 0.41
60 8 0.07
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (58 bp):
TTTAGAAAACTTCATCATTTTAGGGCCATTTAAGTTATTTCACATAATCTAAGGTCAT
Found at i:597851 original size:16 final size:16
Alignment explanation
Indices: 597828--597919 Score: 78
Period size: 16 Copynumber: 5.8 Consensus size: 16
597818 TTAAGGTTCG
597828 TTCGGGTTCGAGCTTT
1 TTCGGGTTCGAGCTTT
* * *
597844 TTCAGGTTCGATCTTA
1 TTCGGGTTCGAGCTTT
* * *
597860 TTGGGGTTCGGGCTTA
1 TTCGGGTTCGAGCTTT
*
597876 TTCGGGTTCCGGGCTTT
1 TTCGGGTT-CGAGCTTT
* * *
597893 TT-AGGTTTGGGCTTT
1 TTCGGGTTCGAGCTTT
597908 TTCGGGTTCGAG
1 TTCGGGTTCGAG
597920 TTCGAGTTCA
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
15 9 0.15
16 42 0.70
17 9 0.15
ACGTcount: A:0.08, C:0.16, G:0.34, T:0.42
Consensus pattern (16 bp):
TTCGGGTTCGAGCTTT
Found at i:598157 original size:18 final size:18
Alignment explanation
Indices: 598118--598157 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
598108 ATATTTATAT
*
598118 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
598136 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTGTT-AA
598154 ATAA
1 ATAA
598158 TTTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:600950 original size:32 final size:32
Alignment explanation
Indices: 600914--600978 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
600904 TCAGGTTTGG
*
600914 GTTTTTGCGGGTTC-AGATTTTTCTAGGTTCAA
1 GTTTTTGCGGGTTCAAGATTTCTCT-GGTTCAA
** *
600946 GTTTTTTTGGGTTCAAGCTTTCTCTGGTTCAA
1 GTTTTTGCGGGTTCAAGATTTCTCTGGTTCAA
600978 G
1 G
600979 CTATCTCGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.14, C:0.14, G:0.25, T:0.48
Consensus pattern (32 bp):
GTTTTTGCGGGTTCAAGATTTCTCTGGTTCAA
Found at i:600951 original size:17 final size:16
Alignment explanation
Indices: 600931--600980 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
600921 CGGGTTCAGA
600931 TTTTTCTAGGTTCAAG-
1 TTTTTCT-GGTTCAAGC
*
600947 TTTTTTTGGGTTCAAGC
1 TTTTTCT-GGTTCAAGC
*
600964 TTTCTCTGGTTCAAGC
1 TTTTTCTGGTTCAAGC
600980 T
1 T
600981 ATCTCGGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 24 0.83
17 5 0.17
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (16 bp):
TTTTTCTGGTTCAAGC
Found at i:600985 original size:16 final size:16
Alignment explanation
Indices: 600954--600998 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
600944 AAGTTTTTTT
*
600954 GGGTTCAAGCTTTCTC
1 GGGTTCAAGCTATCTC
*
600970 TGGTTCAAGCTATCTC
1 GGGTTCAAGCTATCTC
*
600986 GGGTTCAGGCTAT
1 GGGTTCAAGCTAT
600999 TTTGAGTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.36
Consensus pattern (16 bp):
GGGTTCAAGCTATCTC
Found at i:602017 original size:12 final size:12
Alignment explanation
Indices: 602000--602032 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
601990 GTGGTTAAGA
602000 CCTTACAATATT
1 CCTTACAATATT
602012 CCTTACAATATT
1 CCTTACAATATT
602024 CCTTACAAT
1 CCTTACAAT
602033 TATTTAGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39
Consensus pattern (12 bp):
CCTTACAATATT
Found at i:603398 original size:11 final size:11
Alignment explanation
Indices: 603377--603409 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
603367 TTACTTTCTA
603377 TAAAT-ATTAT
1 TAAATAATTAT
603387 TAAATAATTAT
1 TAAATAATTAT
*
603398 TAAATATTTAT
1 TAAATAATTAT
603409 T
1 T
603410 TAATTTACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAAATAATTAT
Found at i:606707 original size:16 final size:16
Alignment explanation
Indices: 606686--606734 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
606676 AGACATATTA
606686 AAAACACATGAAAGAC
1 AAAACACATGAAAGAC
*
606702 AAAACACATGAAAGAA
1 AAAACACATGAAAGAC
606718 AAAACACATGAAAGAC
1 AAAACACATGAAAGAC
606734 A
1 A
606735 CCCTTAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.65, C:0.16, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAACACATGAAAGAC
Found at i:608800 original size:20 final size:20
Alignment explanation
Indices: 608775--608826 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
608765 CATATAAAAC
608775 AAAAACATTAAGAAACATAG
1 AAAAACATTAAGAAACATAG
608795 AAAAACATTAAGAAACATAG
1 AAAAACATTAAGAAACATAG
*
608815 GAAAACA-TAAGA
1 AAAAACATTAAGA
608827 TGCAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.65, C:0.10, G:0.12, T:0.13
Consensus pattern (20 bp):
AAAAACATTAAGAAACATAG
Found at i:611252 original size:13 final size:13
Alignment explanation
Indices: 611234--611260 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
611224 ACAATTGTCC
611234 ATGTATCGATACA
1 ATGTATCGATACA
611247 ATGTATCGATACA
1 ATGTATCGATACA
611260 A
1 A
611261 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:613647 original size:22 final size:21
Alignment explanation
Indices: 613612--613661 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
613602 TTTGTTGATG
*
613612 ATTTTG-A-TGAAAAATGAAGC
1 ATTTTGAAGTGAAAAAT-AAGA
613632 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
613653 AATTTGAAG
1 ATTTTGAAG
613662 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.30
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:613658 original size:21 final size:22
Alignment explanation
Indices: 613619--613661 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
613609 ATGATTTTGA
* *
613619 TGAAAAATGAAGCATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
613641 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
613662 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.02, G:0.21, T:0.26
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:618240 original size:3 final size:3
Alignment explanation
Indices: 618232--618256 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
618222 TCCGAGTCAC
618232 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
618257 TTTGATGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:619896 original size:20 final size:19
Alignment explanation
Indices: 619849--619900 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
619839 GTTAGAAGCA
619849 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCA-C
619869 ATTGTATCGATACAATGTGC-C
1 A-TGTATCGATACAAT-T-CAC
619890 ATGTATCGATA
1 ATGTATCGATA
619901 AAAACAGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 11 0.38
21 16 0.55
22 1 0.03
23 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACAATTCAC
Found at i:619959 original size:20 final size:20
Alignment explanation
Indices: 619930--619986 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
619920 TACTGCCAGT
*
619930 TTCATATATCGATACAATTG
1 TTCATGTATCGATACAATTG
619950 TTCATGTATCGATACAA-TG
1 TTCATGTATCGATACAATTG
** *
619969 AACATGTATCAATACAAT
1 TTCATGTATCGATACAAT
619987 GTATCGATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35
Consensus pattern (20 bp):
TTCATGTATCGATACAATTG
Found at i:622618 original size:20 final size:19
Alignment explanation
Indices: 622566--622621 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
622556 TGTATTGATA
*
622566 CATTGTATCGATACATGCT
1 CATTGTATCGATACATACT
*
622585 CATTATATCGATACATACT
1 CATTGTATCGATACATACT
*
622604 CAATTGTAACGATACATA
1 C-ATTGTATCGATACATA
622622 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.34
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:623585 original size:17 final size:17
Alignment explanation
Indices: 623563--623597 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
623553 GGAAAATACA
623563 TTTGAGAATTATATGCT
1 TTTGAGAATTATATGCT
623580 TTTGAGAATTATATGCT
1 TTTGAGAATTATATGCT
623597 T
1 T
623598 AAGTATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.49
Consensus pattern (17 bp):
TTTGAGAATTATATGCT
Found at i:627455 original size:22 final size:20
Alignment explanation
Indices: 627441--627482 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
627431 CAAATGAAGA
627441 ACAAA-CCAACAAC-AATAG
1 ACAAATCCAACAACAAATAG
627459 ACAAATCCAACAACAAATCAG
1 ACAAATCCAACAACAAAT-AG
627480 ACA
1 ACA
627483 TGAAAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 3 0.14
21 5 0.24
ACGTcount: A:0.60, C:0.29, G:0.05, T:0.07
Consensus pattern (20 bp):
ACAAATCCAACAACAAATAG
Found at i:628428 original size:16 final size:16
Alignment explanation
Indices: 628404--628465 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
628394 TAAATTAAAA
*
628404 AAATTATTTTAAATTT
1 AAATAATTTTAAATTT
628420 AAATAATTTTAAATTT
1 AAATAATTTTAAATTT
* *
628436 AAATTAACTTT-AATTC
1 AAA-TAATTTTAAATTT
628452 AAAT-ATTTTAAATT
1 AAATAATTTTAAATT
628466 AATATTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
14 4 0.10
15 5 0.12
16 25 0.62
17 6 0.15
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATAATTTTAAATTT
Found at i:635685 original size:24 final size:24
Alignment explanation
Indices: 635653--635701 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
635643 TAAAATCTCT
635653 TTGAGTGTAAAATTATAGATTGAA
1 TTGAGTGTAAAATTATAGATTGAA
635677 TTGAGTGTAAAATTATAGATTGAA
1 TTGAGTGTAAAATTATAGATTGAA
635701 T
1 T
635702 ACAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (24 bp):
TTGAGTGTAAAATTATAGATTGAA
Found at i:635711 original size:24 final size:24
Alignment explanation
Indices: 635660--635711 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
635650 TCTTTGAGTG
** ***
635660 TAAAATTATAGATTGAATTGAGTG
1 TAAAATTATAGATTGAATACAAAA
635684 TAAAATTATAGATTGAATACAAAA
1 TAAAATTATAGATTGAATACAAAA
635708 TAAA
1 TAAA
635712 TTGGTACAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33
Consensus pattern (24 bp):
TAAAATTATAGATTGAATACAAAA
Found at i:647972 original size:2 final size:2
Alignment explanation
Indices: 647965--648029 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
647955 GTCAGTTGCT
647965 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
648007 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
648030 TATGGGGTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:657268 original size:13 final size:13
Alignment explanation
Indices: 657250--657274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
657240 TAAAGAACTA
657250 AAGCAAAATCACC
1 AAGCAAAATCACC
657263 AAGCAAAATCAC
1 AAGCAAAATCAC
657275 ATAATTTGAA
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:0.56, C:0.28, G:0.08, T:0.08
Consensus pattern (13 bp):
AAGCAAAATCACC
Found at i:659214 original size:33 final size:33
Alignment explanation
Indices: 659177--659243 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
659167 TTCAACGATT
659177 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
659210 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
659243 T
1 T
659244 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:659215 original size:13 final size:13
Alignment explanation
Indices: 659197--659221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
659187 CATAAAATGT
659197 TGTATCGATACAA
1 TGTATCGATACAA
659210 TGTATCGATACA
1 TGTATCGATACA
659222 TATTTTTTTG
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:659303 original size:13 final size:13
Alignment explanation
Indices: 659285--659309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
659275 ATTACTCACA
659285 TGTATCGATACAT
1 TGTATCGATACAT
659298 TGTATCGATACA
1 TGTATCGATACA
659310 CTGATCTTTG
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:659374 original size:52 final size:52
Alignment explanation
Indices: 659318--659438 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
659308 CACTGATCTT
* *
659318 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAAGTTGCCCAGATGTATCGATACACTATAAAA
*
659370 TGTATCGATACATGCAGGCAAAGTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAAGTTGCCCAGATGTATCGATACACTATAAAA
659422 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
659439 ATAAATTTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAAGTTGCCCAGATGTATCGATACACTATAAAA
Found at i:666668 original size:15 final size:15
Alignment explanation
Indices: 666636--666693 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
666626 TTCCAAACAC
*
666636 AAAAAAAAGCAACAAA
1 AAAAAAAAG-AAAAAA
*
666652 AAAAAAAA-AAAAGA
1 AAAAAAAAGAAAAAA
*
666666 AAAAAGAAGAAAAAA
1 AAAAAAAAGAAAAAA
* *
666681 ACAAAACAGAAAA
1 AAAAAAAAGAAAA
666694 TCTCGATAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
14 11 0.32
15 15 0.44
16 8 0.24
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAA
Found at i:666670 original size:18 final size:18
Alignment explanation
Indices: 666636--666686 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
666626 TTCCAAACAC
666636 AAAAAAAAGCAACAAAAAAA
1 AAAAAAAAG-AA-AAAAAAA
*
666656 AAAAAAAAGAAAAAAGAA
1 AAAAAAAAGAAAAAAAAA
* *
666674 GAAAAAAACAAAA
1 AAAAAAAAGAAAA
666687 CAGAAAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 17 0.61
19 2 0.07
20 9 0.32
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAAAA
Found at i:666691 original size:18 final size:18
Alignment explanation
Indices: 666646--666691 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
666636 AAAAAAAAGC
666646 AACAAAAAA-AA-AAAAA
1 AACAAAAAAGAAGAAAAA
*
666662 AAGAAAAAAGAAGAAAAA
1 AACAAAAAAGAAGAAAAA
*
666680 AACAAAACAGAA
1 AACAAAAAAGAA
666692 AATCTCGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 8 0.32
17 2 0.08
18 15 0.60
ACGTcount: A:0.85, C:0.07, G:0.09, T:0.00
Consensus pattern (18 bp):
AACAAAAAAGAAGAAAAA
Found at i:667732 original size:31 final size:31
Alignment explanation
Indices: 667694--667804 Score: 176
Period size: 31 Copynumber: 3.7 Consensus size: 31
667684 ATACCTTTTT
667694 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
667725 AAAGTCCACGACTCAGTGGCAATCTCTT-T-
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
667754 AAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
667784 AAAGTCCACGACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGCA
667805 TTTTTTCTTT
Statistics
Matches: 75, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
27 2 0.03
28 3 0.04
29 21 0.28
30 21 0.28
31 28 0.37
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTC
Found at i:667803 original size:59 final size:60
Alignment explanation
Indices: 667691--667804 Score: 196
Period size: 59 Copynumber: 1.9 Consensus size: 60
667681 CAAATACCTT
667691 TTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTC
1 TTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTC
*
667751 TTTAAAGTCCACGACTCAGTGGC-AT-TTTGTCTCAAAGTCCACGACTCAGTGGCA
1 TTTAAAGTCCACGACTCAGTGGCAATCTCT-TCTCAAAGTCCACGACTCAGTGGCA
667805 TTTTTTCTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
58 2 0.04
59 27 0.52
60 23 0.44
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (60 bp):
TTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTC
Found at i:667858 original size:33 final size:34
Alignment explanation
Indices: 667812--668511 Score: 715
Period size: 34 Copynumber: 20.9 Consensus size: 34
667802 GCATTTTTTC
*
667812 TTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT
*
667846 TTT-AAGTCCACAACTCCGTGGCA-C-----CCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT
* * *
667873 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCAT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT
*
667907 CTTT-AAGTCCACAACTCCGTGGCA-C-----CCT
1 -TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT
* * * *
667935 TTTAAAGCCCACAATTCTGTGGCACTTTTTTCAT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT
* *
667969 CTTT-AAGTCCACAACTCCGTGGCA-C-----CCG
1 -TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT
*
667997 TTT-AAGCCCACAACTCCGTGGCACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT
*
668030 TTTAAAGCCCACAACTCCGTGGCA-CTTTTTTCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT
*
668063 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCCT
* * *
668098 TTT-AAGTCCACAACTCCGTGGCATCTTTCTCCCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTT-TTCCT
* * * *
668132 TCCTAAAGCCCACACAAGTCGGTGGCAACCTTCTT-CT
1 T-TTAAAG-CC-CACAACTCCGTGGC-ACCTTTTTCCT
*
668169 TTTCAAAGCCCACAACTCCGTGGCACCTTCTT-CT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCT
*
668203 TTTAAAGCCCACAACTCCGTGGCACCTTCTT-CT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT
**
668236 TTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-C-TTTTTCCT
668272 TTTCAAAGCCCACAACTCCGTGGCACCTTTTT-CT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCT
668306 GTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 -TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCT
*
668343 TTTCAAAGCCCACAATTCCGTGGCACCTTTTT-CT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCT
668377 GTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 -TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCT
*
668414 TTTCAAAGCCCACAACTCCGTGGCA-CTTTTTTCT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCT
668448 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCT
* *
668484 TTT-AAGTCCACAACTCCGTGGCATCTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTT
668512 CTCCCTTCCC
Statistics
Matches: 565, Mismatches: 52, Indels: 98
0.79 0.07 0.14
Matches are distributed among these distances:
27 31 0.05
28 39 0.07
32 1 0.00
33 132 0.23
34 155 0.27
35 87 0.15
36 29 0.05
37 74 0.13
38 13 0.02
39 4 0.01
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.33
Consensus pattern (34 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT
Found at i:668008 original size:27 final size:27
Alignment explanation
Indices: 667970--668021 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
667960 TTTTTTCATC
*
667970 TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAGCCCACAACTCCGTGGCACCCG
667997 TTTAAGCCCACAACTCCGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
668022 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCG
Found at i:668333 original size:71 final size:70
Alignment explanation
Indices: 668000--668511 Score: 672
Period size: 71 Copynumber: 7.4 Consensus size: 70
667990 GCACCCGTTT
668000 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCA--CTTTTTT-C
1 AAGCCCACAACTCCGTGGCACCTTTTTC-TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTTCC
668062 TTTT-A
65 TTTTCA
* * *
668067 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT-AAGTCCACAACTCCGTGGCA-TC-TTTCTC
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTTC
* *
668129 CCTTCCTA
64 CTTTTC-A
* * * *
668137 AAGCCCACACAAGTCGGTGGCAACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCAC-C-TTCT
1 AAG-CC-CACAACTCCGTGGC-ACCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTT
668200 T-CTTTT-A
62 TCCTTTTCA
* **
668207 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTTCCT
668272 TTTCA
66 TTTCA
*
668277 AAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 AAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTTCC
668342 TTTTCA
65 TTTTCA
* *
668348 AAGCCCACAATTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 AAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTTCC
668413 TTTTCA
65 TTTTCA
* *
668419 AAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTTCCT
668484 TTT--
66 TTTCA
* *
668487 AAGTCCACAACTCCGTGGCATCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
668512 CTCCCTTCCC
Statistics
Matches: 399, Mismatches: 29, Indels: 33
0.87 0.06 0.07
Matches are distributed among these distances:
66 20 0.05
67 58 0.15
68 51 0.13
69 8 0.02
70 76 0.19
71 141 0.35
72 20 0.05
73 25 0.06
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.33
Consensus pattern (70 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTTCCT
TTTCA
Found at i:668543 original size:38 final size:33
Alignment explanation
Indices: 668515--668584 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 33
668505 CATCTTTCTC
668515 CCTTCCCAAAGCCCACACAAGTCGGTGGCAACCT
1 CCTT-CCAAAGCCCACACAAGTCGGTGGCAACCT
*
668549 TCTTCCAAAGCCCACACAAGTCGGTGGCAACC-
1 CCTTCCAAAGCCCACACAAGTCGGTGGCAACCT
668581 CCTT
1 CCTT
668585 TAAGCCCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 3 0.09
33 28 0.82
34 3 0.09
ACGTcount: A:0.26, C:0.40, G:0.17, T:0.17
Consensus pattern (33 bp):
CCTTCCAAAGCCCACACAAGTCGGTGGCAACCT
Found at i:668703 original size:49 final size:49
Alignment explanation
Indices: 668582--669141 Score: 709
Period size: 49 Copynumber: 11.9 Consensus size: 49
668572 GTGGCAACCC
* * * *
668582 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCGCCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-G-GCATCTT-CAT
* * *
668634 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
* *
668683 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
* *
668732 CTTTAAGTCCAATGTAGCTGGCCTTGATTCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
* *
668775 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
*
668824 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
* *
668867 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
*
668916 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
* *
668959 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
*
669008 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
* * *
669051 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
*
669100 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
669142 CCTTTAAGCC
Statistics
Matches: 441, Mismatches: 43, Indels: 51
0.82 0.08 0.10
Matches are distributed among these distances:
43 154 0.35
45 4 0.01
47 4 0.01
49 240 0.54
50 4 0.01
51 1 0.00
52 34 0.08
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (49 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
Found at i:668803 original size:92 final size:92
Alignment explanation
Indices: 668683--669188 Score: 958
Period size: 92 Copynumber: 5.5 Consensus size: 92
668673 GCACCTTCAT
668683 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
668748 GCTGGCCTTGATTCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
668775 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
668840 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
668867 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
668932 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
668959 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
669024 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
669051 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
669116 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * *
669143 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
669189 TATCACTTTT
Statistics
Matches: 409, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 409 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:668914 original size:184 final size:184
Alignment explanation
Indices: 668581--669188 Score: 1036
Period size: 184 Copynumber: 3.3 Consensus size: 184
668571 GGTGGCAACC
* * *
668581 CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCGCCTTTTCCATCTTTAAGTCCAA
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATT-G-GCATCTT-CATCTTTAAGTCCAA
*
668646 TGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCTTGAA
*
668711 TCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGATTCAGCACATTGGCA
122 TCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
*
668774 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
668839 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
668904 TGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
131 TGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
*
668958 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
669023 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATAT
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
669088 TGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
131 TGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* * *
669142 CCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
669189 TATCACTTTT
Statistics
Matches: 404, Mismatches: 11, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
184 316 0.78
186 1 0.00
190 44 0.11
191 5 0.01
192 1 0.00
193 37 0.09
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (184 bp):
CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
TGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
Found at i:669289 original size:52 final size:53
Alignment explanation
Indices: 669206--669363 Score: 185
Period size: 52 Copynumber: 3.0 Consensus size: 53
669196 TTTCTCATCA
*
669206 TCATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTC
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTC
* * * * *
669259 -CATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTC
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC
* * * *
669313 TCATCTTTAAG-CCTAATATCGTTGGCCATGAATCAACATATTGGCATCTTT
1 TCATCTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
669364 ATCACTTTTC
Statistics
Matches: 86, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
52 39 0.45
53 5 0.06
54 7 0.08
55 35 0.41
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (53 bp):
TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTC
Found at i:669433 original size:174 final size:174
Alignment explanation
Indices: 669143--669541 Score: 753
Period size: 174 Copynumber: 2.3 Consensus size: 174
669133 ACATTGGCAC
*
669143 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGCCTAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
669208 ATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCA
66 ATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCA
669273 ATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
131 ATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
669317 CTTTAAGCCTAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGCCTAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
669382 ATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCA
66 ATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCA
669447 ATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
131 ATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * * *
669491 CTTTATGCCTAATATCGTTGGCCGTGAATCAACATATTGGCACCTTCATCA
1 CTTTAAGCCTAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCA
669542 TCTCTAAAAC
Statistics
Matches: 220, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 220 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (174 bp):
CTTTAAGCCTAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
ATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCA
ATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:669463 original size:52 final size:53
Alignment explanation
Indices: 669380--669536 Score: 183
Period size: 52 Copynumber: 2.9 Consensus size: 53
669370 TTTCTCATCA
*
669380 TCATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTC
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTC
* * * * *
669433 -CATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTC
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC
* * * *
669487 TCATCTTTATG-CCTAATATCGTTGGCCGTGAATCAACATATTGGCACCTT
1 TCATCTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
669537 CATCATCTCT
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
52 39 0.46
53 4 0.05
54 8 0.09
55 34 0.40
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (53 bp):
TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTC
Found at i:670374 original size:33 final size:33
Alignment explanation
Indices: 670337--670403 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
670327 TTCAACGATT
670337 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
670370 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
670403 T
1 T
670404 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:670375 original size:13 final size:13
Alignment explanation
Indices: 670357--670381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
670347 CATAAAATGT
670357 TGTATCGATACAA
1 TGTATCGATACAA
670370 TGTATCGATACA
1 TGTATCGATACA
670382 TATTTTTTTG
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:670463 original size:13 final size:13
Alignment explanation
Indices: 670445--670469 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
670435 ATTACTCACA
670445 TGTATCGATACAT
1 TGTATCGATACAT
670458 TGTATCGATACA
1 TGTATCGATACA
670470 CTGATCTTTG
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:670534 original size:52 final size:52
Alignment explanation
Indices: 670478--670598 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
670468 CACTGATCTT
* *
670478 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAAGTTGCCCAGATGTATCGATACACTATAAAA
*
670530 TGTATCGATACATGCAGGCAAAGTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAAGTTGCCCAGATGTATCGATACACTATAAAA
670582 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
670599 ATAAATTTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAAGTTGCCCAGATGTATCGATACACTATAAAA
Found at i:677795 original size:17 final size:17
Alignment explanation
Indices: 677770--677807 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
677760 TCAAATATAT
*
677770 AATTGTATATTTAATAA
1 AATTATATATTTAATAA
*
677787 AATTATATATTTACTAA
1 AATTATATATTTAATAA
677804 AATT
1 AATT
677808 TTCATTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
AATTATATATTTAATAA
Found at i:679347 original size:33 final size:32
Alignment explanation
Indices: 679305--679368 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
679295 TACAAGCCAA
* *
679305 TGTATCGATACATTTTGGGATGTATTGATACAG
1 TGTATCGATACATATTGGG-TGTATCGATACAG
*
679338 TGTATCGATACATATTGTGTGTATCGATACA
1 TGTATCGATACATATTGGGTGTATCGATACA
679369 AACAGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATATTGGGTGTATCGATACAG
Found at i:679450 original size:20 final size:21
Alignment explanation
Indices: 679399--679451 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
679389 GCCAATGACC
*
679399 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
* *
679420 AGTATCAATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
679440 TGTATCGATACA
1 TGTATCGATACA
679452 ATGTATCGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:679457 original size:13 final size:13
Alignment explanation
Indices: 679439--679463 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
679429 ACATTTGGTC
679439 ATGTATCGATACA
1 ATGTATCGATACA
679452 ATGTATCGATAC
1 ATGTATCGATAC
679464 TATGCAATCT
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):
ATGTATCGATACA
Found at i:680044 original size:20 final size:22
Alignment explanation
Indices: 680019--680061 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
680009 TTTTCTTTTC
680019 TCTCCCCCTTAA-AAAA-AATT
1 TCTCCCCCTTAATAAAATAATT
680039 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
680061 T
1 T
680062 AACAAATTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.57
21 4 0.19
22 5 0.24
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:681465 original size:21 final size:21
Alignment explanation
Indices: 681434--681485 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
681424 GCTGCTAGTG
*
681434 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGG-TGCCCGGTCGCGACC
681456 TGGGGGTG-CCGGTCGCGACC
1 TGGGGGTGCCCGGTCGCGACC
681476 TGGTGGGTGC
1 TGG-GGGTGC
681486 TGCCTAGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 14 0.52
21 7 0.26
22 6 0.22
ACGTcount: A:0.04, C:0.27, G:0.50, T:0.19
Consensus pattern (21 bp):
TGGGGGTGCCCGGTCGCGACC
Found at i:682146 original size:8 final size:8
Alignment explanation
Indices: 682133--682158 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
682123 AACATCATTC
682133 ATCACAAA
1 ATCACAAA
682141 ATCACAAA
1 ATCACAAA
682149 ATCACAAA
1 ATCACAAA
682157 AT
1 AT
682159 TTTAGTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:688092 original size:13 final size:13
Alignment explanation
Indices: 688074--688100 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
688064 ATATTTTGGG
688074 ATGTATCGATACA
1 ATGTATCGATACA
688087 ATGTATCGATACA
1 ATGTATCGATACA
688100 A
1 A
688101 ACAGTTAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:688192 original size:20 final size:21
Alignment explanation
Indices: 688141--688193 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
688131 GCCAATGACC
*
688141 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
* *
688162 AGTATCAATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
688182 TGTATCGATACA
1 TGTATCGATACA
688194 ATGTATCGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:688199 original size:13 final size:13
Alignment explanation
Indices: 688181--688205 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
688171 ACATTTGGTC
688181 ATGTATCGATACA
1 ATGTATCGATACA
688194 ATGTATCGATAC
1 ATGTATCGATAC
688206 TGTGCAATCT
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):
ATGTATCGATACA
Found at i:690350 original size:3 final size:3
Alignment explanation
Indices: 690344--690381 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
690334 GTTGTTCTTT
690344 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
690382 TGTAAATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:690484 original size:12 final size:12
Alignment explanation
Indices: 690467--690518 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
690457 TTATTAAGTA
690467 AATATTATATTT
1 AATATTATATTT
* *
690479 AATATTATAATC
1 AATATTATATTT
690491 ACATATTTAATATTT
1 A-ATA-TT-ATATTT
690506 AAT-TTATATTT
1 AATATTATATTT
690517 AA
1 AA
690519 ATTGAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
11 8 0.24
12 13 0.39
13 3 0.09
14 4 0.12
15 5 0.15
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (12 bp):
AATATTATATTT
Found at i:692778 original size:21 final size:20
Alignment explanation
Indices: 692754--692805 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
692744 TTTAGTTATT
*
692754 AAAAGTTGCATTTTTCATCC
1 AAAAATTGCATTTTTCATCC
*
692774 AAAAAATGCATTTTTTCATCC
1 AAAAATTGCA-TTTTTCATCC
*
692795 AAACATTGCAT
1 AAAAATTGCAT
692806 CATTTCATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (20 bp):
AAAAATTGCATTTTTCATCC
Found at i:692811 original size:21 final size:21
Alignment explanation
Indices: 692766--692814 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
692756 AAGTTGCATT
**
692766 TTTCATCCAAAAAATGCATTT
1 TTTCATCCAAAAAATGCATCA
* *
692787 TTTCATCCAAACATTGCATCA
1 TTTCATCCAAAAAATGCATCA
692808 TTTCATC
1 TTTCATC
692815 TAAATGCACC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (21 bp):
TTTCATCCAAAAAATGCATCA
Found at i:693925 original size:18 final size:18
Alignment explanation
Indices: 693898--693933 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
693888 AGTGGTTTGA
693898 TTGTTACAATATTTATAT
1 TTGTTACAATATTTATAT
*
693916 TTGTTGCAATATTTATAT
1 TTGTTACAATATTTATAT
693934 GTACGGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (18 bp):
TTGTTACAATATTTATAT
Found at i:695880 original size:13 final size:13
Alignment explanation
Indices: 695862--695887 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
695852 CAATTTTTTG
695862 TGTATCGATACAT
1 TGTATCGATACAT
695875 TGTATCGATACAT
1 TGTATCGATACAT
695888 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:695902 original size:32 final size:33
Alignment explanation
Indices: 695842--695905 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
695832 TACAAGCCAA
** *
695842 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
695875 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
695906 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:700564 original size:15 final size:15
Alignment explanation
Indices: 700544--700574 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
700534 ATTTCGTTTG
*
700544 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
700559 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
700574 G
1 G
700575 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:702401 original size:21 final size:22
Alignment explanation
Indices: 702376--702428 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
702366 GCAAGTTTTC
*
702376 ATTTTTCTTAGCTAAC-TCATT
1 ATTTTTCTTAGCCAACTTCATT
* *
702397 ATTTTTATTAGCCAACTTCTTT
1 ATTTTTCTTAGCCAACTTCATT
702419 ATTTTATCTT
1 ATTTT-TCTT
702429 GCAAATCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 14 0.54
22 9 0.35
23 3 0.12
ACGTcount: A:0.23, C:0.17, G:0.04, T:0.57
Consensus pattern (22 bp):
ATTTTTCTTAGCCAACTTCATT
Found at i:704636 original size:13 final size:13
Alignment explanation
Indices: 704618--704643 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
704608 TATAAGCCAA
704618 TGTATCGATACAT
1 TGTATCGATACAT
704631 TGTATCGATACAT
1 TGTATCGATACAT
704644 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:716442 original size:31 final size:32
Alignment explanation
Indices: 716404--716475 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 32
716394 CGACAACCCC
*
716404 CAATGGCATCCCTTTTTTCAAAGTCCAC-ATT
1 CAATGGCATCCCTTTTTTCAAAGTCCACGACT
716435 CAATGGCAT--CTTTTTTCAAAGTCCACGACT
1 CAATGGCATCCCTTTTTTCAAAGTCCACGACT
*
716465 CAGTGGCATCC
1 CAATGGCATCC
716476 ATTCTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 17 0.47
30 10 0.28
31 9 0.25
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (32 bp):
CAATGGCATCCCTTTTTTCAAAGTCCACGACT
Found at i:716741 original size:41 final size:41
Alignment explanation
Indices: 716584--717017 Score: 329
Period size: 41 Copynumber: 10.4 Consensus size: 41
716574 TACATTTTAA
* *
716584 TCCTCAAAGAGCAGGACGCACATTTTTTTCCTTTTCTCCTTTG
1 TCCTCAAGGAGCAGGACGCA-TTTTTTTTCCTTTTC-CCTTTG
* * * * * *
716627 TCCTCAAGGAGTAGGACCCATTTCATTCTCTTTTTTCCTTTG
1 TCCTCAAGGAGCAGGACGCATTT-TTTTTCCTTTTCCCTTTG
* * * ** **
716669 TCCTCAAAGAGCAGCACGC-CTTCATCCCCTTTTCCCTTTG
1 TCCTCAAGGAGCAGGACGCATTTTTTTTCCTTTTCCCTTTG
* *
716709 TCCTCAAGGAGCAGGATGCATTTTTTTTCCTTTTTCCTTTG
1 TCCTCAAGGAGCAGGACGCATTTTTTTTCCTTTTCCCTTTG
* * *
716750 TCCTCAAGGAGCATGATGCATTTTTTTTCCTATTT-ACTTTG
1 TCCTCAAGGAGCAGGACGCATTTTTTTTCCT-TTTCCCTTTG
* * * ** **
716791 TCCTCAAAGAGCATGATGCATTTAATCCCCTTTTCCCTTTG
1 TCCTCAAGGAGCAGGACGCATTTTTTTTCCTTTTCCCTTTG
* * * * * *
716832 T-CTTAAAGAGTAGGATGCATTCTTTTTTCCTTTTTCTTTTG
1 TCCTCAAGGAGCAGGACGCATT-TTTTTTCCTTTTCCCTTTG
* * * * *
716873 TCTTCAAGGAACAGAATGCATTTTTATCTCCTTTTCCCTTTG
1 TCCTCAAGGAGCAGGACGCATTTTT-TTTCCTTTTCCCTTTG
* * *
716915 TCCTCAAGGAGCATGACGCATTCTTTTTTTCC-TTTCTCTTTTT
1 TCCTCAAGGAGCAGGACGCA-T-TTTTTTTCCTTTTC-CCTTTG
* * *
716958 TCCTTAAGGAGCAGGACCCATTTCATTCTT-CTTTTCCCTTTG
1 TCCTCAAGGAGCAGGACGCATTT--TTTTTCCTTTTCCCTTTG
*
717000 TCCTCAAAGAGCAGGACG
1 TCCTCAAGGAGCAGGACG
717018 TACTCCTTTC
Statistics
Matches: 308, Mismatches: 70, Indels: 27
0.76 0.17 0.07
Matches are distributed among these distances:
40 49 0.16
41 103 0.33
42 93 0.30
43 59 0.19
44 4 0.01
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.41
Consensus pattern (41 bp):
TCCTCAAGGAGCAGGACGCATTTTTTTTCCTTTTCCCTTTG
Found at i:716759 original size:123 final size:123
Alignment explanation
Indices: 716584--716934 Score: 377
Period size: 123 Copynumber: 2.8 Consensus size: 123
716574 TACATTTTAA
* * *
716584 TCCTCAAAGAGCAGGACGCACATTTTTTTCCTTTTCTCCTTTGTCCTCAAGGAGTAGGACCCATT
1 TCCTCAAAGAGCAGGATGCA-TTTTTTTTCCTTTT-TCCTTTGTCCTCAAGGAGCAGGACCCATT
* * * *
716649 TCATTCTCTTTTTTCCTTTGTCCTCAAAGAGCA-GCACGC-CTTCATCCCCTTTTCCCTTTG
64 T-ATTCTCCTATTTACTTTGTCCTCAAAGAGCATG-ACGCACTTAATCCCCTTTTCCCTTTG
* * ** *
716709 TCCTCAAGGAGCAGGATGCATTTTTTTTCCTTTTTCCTTTGTCCTCAAGGAGCATGATGCATTTT
1 TCCTCAAAGAGCAGGATGCATTTTTTTTCCTTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTA
* * *
716774 TTTTCCTATTTACTTTGTCCTCAAAGAGCATGATGCATTTAATCCCCTTTTCCCTTTG
66 TTCTCCTATTTACTTTGTCCTCAAAGAGCATGACGCACTTAATCCCCTTTTCCCTTTG
* * * * * * **
716832 T-CTTAAAGAGTAGGATGCATTCTTTTTTCCTTTTTCTTTTGTCTTCAAGGAACAGAATGCATTT
1 TCCTCAAAGAGCAGGATGCATT-TTTTTTCCTTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTT
* * *
716896 TTATCTCCT-TTTCCCTTTGTCCTCAAGGAGCATGACGCA
65 AT-TCTCCTATTT-ACTTTGTCCTCAAAGAGCATGACGCA
716935 TTCTTTTTTT
Statistics
Matches: 194, Mismatches: 27, Indels: 11
0.84 0.12 0.05
Matches are distributed among these distances:
122 46 0.24
123 89 0.46
124 41 0.21
125 18 0.09
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.41
Consensus pattern (123 bp):
TCCTCAAAGAGCAGGATGCATTTTTTTTCCTTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTA
TTCTCCTATTTACTTTGTCCTCAAAGAGCATGACGCACTTAATCCCCTTTTCCCTTTG
Found at i:717199 original size:31 final size:31
Alignment explanation
Indices: 717161--717679 Score: 476
Period size: 31 Copynumber: 16.8 Consensus size: 31
717151 CCATTAGAAT
717161 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
** ** ** * *
717192 GTCAAAGCCTGCATAAGTTGGCAGCACTCGA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
* * *
717223 GTCTAAGCCCACATGAGTTAGTGGCACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
* * *
717254 GTCAAAGCCCACATGAGTTGG-GGCATCCGA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
* *
717284 GTCTAAGCCCACACGAGTTGG-GGGACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
*
717314 GTTC-AAGCCCACACGAGTTGGTGGCAGCCTA
1 G-TCAAAGCCCACACGAGTTGGTGGCACCCTA
* * * * *
717345 GTCAAAGTCGCA-A-AAGTTGGCGGTACCCAA
1 GTCAAAG-CCCACACGAGTTGGTGGCACCCTA
** * *
717375 CCCTAAGCCCACACGAGTTAGTGGCACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
*** * *
717406 GTCAAAGCTTGCACAAGTTGGTGACA-CCTGA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCT-A
*
717437 GTCTAAGCCCACACGAGTTGGTGGCACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
*
717468 GTCAAAGCTCACACCG-GTTGGTGGCACCCTA
1 GTCAAAGCCCACA-CGAGTTGGTGGCACCCTA
*
717499 GTCAAAGCCCACATGAGTTGGTGGCACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
*
717530 ATCAAAGCCCACACGAGTTGGTGGCACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
* * * * * *
717561 GTCAAAGCTCGCACAAGTTGGCGGTACCCAA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
* * * *
717592 GTCTAAGCCTACACGAGTTGGTAGCACCCAA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
* * *** *
717623 GTCAAAGCCCGCACAAGTTGACAGCACCCGA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
* *
717654 GTCAAAGCCCACAAGAGTTAGTGGCA
1 GTCAAAGCCCACACGAGTTGGTGGCA
717680 TTTAAGTCCG
Statistics
Matches: 385, Mismatches: 93, Indels: 20
0.77 0.19 0.04
Matches are distributed among these distances:
29 3 0.01
30 73 0.19
31 301 0.78
32 8 0.02
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.18
Consensus pattern (31 bp):
GTCAAAGCCCACACGAGTTGGTGGCACCCTA
Found at i:718275 original size:20 final size:20
Alignment explanation
Indices: 718231--718284 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
718221 TGCTACAATT
** *
718231 TGTATCGATACAATTGGTGAA
1 TGTATCGATAC-ATAAGTAAA
718252 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAAGTAAA
718272 TGTATCGATACAT
1 TGTATCGATACAT
718285 GTCTTAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAAGTAAA
Found at i:718389 original size:21 final size:20
Alignment explanation
Indices: 718350--718389 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
718340 TACATAAGTA
* *
718350 AATGTATCGATACATTTTCG
1 AATGGATCGATAAATTTTCG
718370 AATGGATCGATAAAATTTTC
1 AATGGATCGAT-AAATTTTC
718390 TTTGTATCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (20 bp):
AATGGATCGATAAATTTTCG
Found at i:721972 original size:20 final size:20
Alignment explanation
Indices: 721948--722003 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
721938 TTTTAATTAC
*
721948 AAATTTTATATTTTATAGTA
1 AAATTTTATATTTTATAATA
* *
721968 TAATTATATATTTTATAATA
1 AAATTTTATATTTTATAATA
721988 AAAGTTTTA-ATTTTAT
1 AAA-TTTTATATTTTAT
722004 TTTACTAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
AAATTTTATATTTTATAATA
Found at i:725255 original size:78 final size:77
Alignment explanation
Indices: 725123--725322 Score: 206
Period size: 78 Copynumber: 2.6 Consensus size: 77
725113 GATAATAACG
* * * * * * * *
725123 GGGTTGGAGTGTTCCCTTGAAAATAACGAGGCTCGAGTATCCCCGGTTGTGAGAAATCGATGA-T
1 GGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAGTTATGAGAAATCAAT-ATT
725187 TAGAAAAAAAATC
65 TAGAAAAAAAATC
725200 GGGATTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAAG-TATGAGAAATCAATAT
1 GGG-TTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCC-AGTTATGAGAAATCAATA-
* * * *
725264 TTTGGGAATAAAGTC
63 TTTAGAAAAAAAATC
* * *
725279 AGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCC
1 -GGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCC
725323 TGATGAAATA
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
77 4 0.04
78 48 0.47
79 48 0.47
80 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (77 bp):
GGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAGTTATGAGAAATCAATATTT
AGAAAAAAAATC
Found at i:725312 original size:28 final size:28
Alignment explanation
Indices: 725280--725349 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
725270 AATAAAGTCA
*
725280 GGGTTGGAGTATCCCCTCG-GAAGTAACG
1 GGGTTGGAGTATCCCCT-GAGAAATAACG
725308 GGGTTGGAGTAT-CCCTGATGAAATAACG
1 GGGTTGGAGTATCCCCTGA-GAAATAACG
*
725336 AGGTTGGAGTATCC
1 GGGTTGGAGTATCC
725350 TCGATTGTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.03
27 4 0.11
28 31 0.84
29 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCTGAGAAATAACG
Found at i:725545 original size:51 final size:51
Alignment explanation
Indices: 725337--725558 Score: 219
Period size: 52 Copynumber: 4.3 Consensus size: 51
725327 GAAATAACGA
* * * * *
725337 GGTTGGAGTATCCTCGATTGTGAAAATTTGGTATTTTTGGAAATAAAATCGA
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTA-TTTTGGAAATAAAATCGG
* * * ** * * *
725389 AGTTGGAGTATCCTCGATTAAAGGTAAATTGGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTATTTTGGAAATAAAATCGG
* * * * * *
725441 GGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTTGGAAATAAAATCGG
* * *
725493 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGG
725544 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
725559 TTGGAAATAA
Statistics
Matches: 138, Mismatches: 30, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
51 38 0.28
52 92 0.67
53 8 0.06
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGG
Found at i:725581 original size:28 final size:31
Alignment explanation
Indices: 725528--725586 Score: 88
Period size: 28 Copynumber: 2.0 Consensus size: 31
725518 AATCAATATT
*
725528 TTGGAAATAAAGTCGGGGTTGGAGTATCCCC
1 TTGGAAATAAAGTCGGGGTTGAAGTATCCCC
725559 TTGGAAAT-AA-T-GGGGTTGAAGTATCCCC
1 TTGGAAATAAAGTCGGGGTTGAAGTATCCCC
725587 GATTGTGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 16 0.59
29 1 0.04
30 2 0.07
31 8 0.30
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (31 bp):
TTGGAAATAAAGTCGGGGTTGAAGTATCCCC
Found at i:725582 original size:79 final size:82
Alignment explanation
Indices: 725491--725640 Score: 207
Period size: 82 Copynumber: 1.9 Consensus size: 82
725481 CAATAAAACC
* * *
725491 GGGGTTGGAGTATCCCCGATTATGAA-AAA-T-CAATATTTTGGAAATAAAGTCGGGGTTGGAGT
1 GGGGTTGAAGTATCCCCGATTATGAAGAAATTGCAATATTTTGGAAATAAAATCGGAGTTGGAGT
725553 ATCCCCTTGGAAATAAT
66 ATCCCCTTGGAAATAAT
* *** *
725570 GGGGTTGAAGTATCCCCGATTGTGAAGAAATTGGGGTTTTTTGGAAATAAAATCGGAGTTGGAGT
1 GGGGTTGAAGTATCCCCGATTATGAAGAAATTGCAATATTTTGGAAATAAAATCGGAGTTGGAGT
725635 ATCCCC
66 ATCCCC
725641 GATTAAAGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
79 24 0.40
80 3 0.05
81 1 0.02
82 32 0.53
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (82 bp):
GGGGTTGAAGTATCCCCGATTATGAAGAAATTGCAATATTTTGGAAATAAAATCGGAGTTGGAGT
ATCCCCTTGGAAATAAT
Found at i:725682 original size:133 final size:131
Alignment explanation
Indices: 725439--725691 Score: 312
Period size: 133 Copynumber: 1.9 Consensus size: 131
725429 AAATAAAATC
* * *
725439 GGGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTAT
1 GGGGTTGAAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAGTAT
* * * * *
725504 CCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTTGGAAATAA
66 CCCCGATTAAGAAAAATCAATATTTTGAAAATAAAATCGGAGTTGGAATATCCCCTTGGAAATAA
725569 T
131 T
* * * * *
725570 GGGGTTGAAGTATCCCCGATTGT-GAAGAAATTGGGGTTTTTTGGAAATAAAATCGGAGTTGGAG
1 GGGGTTGAAGTATCCCCAATTGTGGAA-AAATT--AGTGTTTTAGAAATAAAACCGGAGTTGGAG
* * *
725634 TATCCCCGATTAA-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCC
63 TATCCCCGATTAAGA-AAAATCAATATTTTGAAAATAAAATCGGAGTTGGAATATCCCC
725692 GATTGTGGAG
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
130 3 0.03
131 26 0.25
132 1 0.01
133 72 0.71
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (131 bp):
GGGGTTGAAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAGTAT
CCCCGATTAAGAAAAATCAATATTTTGAAAATAAAATCGGAGTTGGAATATCCCCTTGGAAATAA
T
Found at i:725706 original size:51 final size:51
Alignment explanation
Indices: 725580--725706 Score: 146
Period size: 51 Copynumber: 2.4 Consensus size: 51
725570 GGGGTTGAAG
* * * * *
725580 TATCCCCGATTGTGAAGAAATTGGGGTTTTTTGGAAATAAAATCGGAGTTGGAG
1 TATCCCCGATTGTGGAG-AATT--AGTGTTTTGAAAATAAAATCGGAGTTGGAA
*** *
725634 TATCCCCGATTAAAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAA
1 TATCCCCGATTGTGGAGAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAA
725685 TATCCCCGATTGTGGAGAATTA
1 TATCCCCGATTGTGGAGAATTA
725707 AGAAACTCAA
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
51 44 0.73
53 4 0.07
54 12 0.20
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (51 bp):
TATCCCCGATTGTGGAGAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAA
Found at i:728461 original size:80 final size:80
Alignment explanation
Indices: 728336--728488 Score: 261
Period size: 80 Copynumber: 1.9 Consensus size: 80
728326 GCGAAAATAC
* * * *
728336 TTTTTTAGATTTTTATGACTTTTTGTTAAGTCGAATCCATTTCCCATTGTCCTTAGTTGAGTTAG
1 TTTTTTAGATTTTCATGACTTTTTGTTAAGTCGAATCCATTTCCCATCGTCCTTAGTCGAGATAG
728401 AGTGTTTGAAAATGG
66 AGTGTTTGAAAATGG
*
728416 TTTTTTAGATTTTCATGACTTTTTGTTAAGTCGAATCTATTTCCCATCGTCCTTAGTCGAGATAG
1 TTTTTTAGATTTTCATGACTTTTTGTTAAGTCGAATCCATTTCCCATCGTCCTTAGTCGAGATAG
728481 AGTGTTTG
66 AGTGTTTG
728489 GAAGGCAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (80 bp):
TTTTTTAGATTTTCATGACTTTTTGTTAAGTCGAATCCATTTCCCATCGTCCTTAGTCGAGATAG
AGTGTTTGAAAATGG
Found at i:728610 original size:19 final size:19
Alignment explanation
Indices: 728585--728635 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
728575 TTTCAGCGAT
728585 ATGTATCGATACATAAGTG
1 ATGTATCGATACATAAGTG
*
728604 TTGTATCGATACATAAGTG
1 ATGTATCGATACATAAGTG
728623 ATGTATCGATACA
1 ATGTATCGATACA
728636 ATGTATCGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACATAAGTG
Found at i:728705 original size:13 final size:13
Alignment explanation
Indices: 728687--728712 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
728677 CATTATTCCA
728687 TGTATCGATACAT
1 TGTATCGATACAT
728700 TGTATCGATACAT
1 TGTATCGATACAT
728713 GGATCTCTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:731135 original size:51 final size:52
Alignment explanation
Indices: 731074--731196 Score: 151
Period size: 51 Copynumber: 2.4 Consensus size: 52
731064 CAATTCTCTG
* * * * * *
731074 CAATTGGGGATATTCCCACTCTGATTTTATTTTC-AAAACACTAA-TTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
*
731125 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTTTTCA
731178 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
731197 CCCGTTAATC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 28 0.46
53 28 0.46
54 5 0.08
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCA
Found at i:731210 original size:27 final size:28
Alignment explanation
Indices: 731180--731254 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 28
731170 ATTTTTCACA
731180 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
731207 ATCGAGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
731235 -TAAGGGGATACTCCAACCCC
1 AT-CGGGGATACTCCAACCCC
731255 TGCTTTATTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:731302 original size:79 final size:79
Alignment explanation
Indices: 731207--731372 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
731197 CCCGTTAATC
* * * *
731207 ATCGAGGATACTCCAACCCCGTTATTTC-TAAGGGGATACTCCAACCCCTGCTTTA-TTCTTAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCGGAA-GGGATACTCCAACCCCGGCTTTATTTC-CAAA
*
731270 ATATTAATTTCTCATT
64 ATATTAATTTCTCATA
* * *
731286 ATCGGGGATACTCCAACCCCGTTTTTTCGGAAGGGATATTCCGACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCGGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
* *
731351 GTTGATTTCTCATA
66 ATTAATTTCTCATA
731365 ATCGGGGA
1 ATCGGGGA
731373 GGGATACTCC
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
79 70 0.93
80 5 0.07
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCGGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
ATTAATTTCTCATA
Found at i:731526 original size:52 final size:48
Alignment explanation
Indices: 731374--731540 Score: 192
Period size: 51 Copynumber: 3.3 Consensus size: 48
731364 AATCGGGGAG
**
731374 GGATACTCCAACCCCGGTTTTATTTGTAAAACATTAATTTTCCACAATCGA
1 GGATACTCCAA-CCCGGTTTTATTT-TAAAACACCAATTTT-CACAATCGA
*
731425 GGATACTCCAACCCGGTTTTATTTTCAAAACACCAATTTTC-CTTTAATCGG
1 GGATACTCCAACCCGGTTTTATTTT-AAAACACCAATTTTCAC---AATCGA
*
731476 GGATACTCCAACTCCGATTTTATTTCTAAAAACACCAAATTTTCACAATCGA
1 GGATACTCCAAC-CCGGTTTTATTT-T-AAAACACC-AATTTTCACAATCGA
731528 GGATACTCCAACC
1 GGATACTCCAACC
731541 TCATTATTTC
Statistics
Matches: 102, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
48 1 0.01
49 2 0.02
50 25 0.25
51 29 0.28
52 28 0.27
53 9 0.09
54 7 0.07
55 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (48 bp):
GGATACTCCAACCCGGTTTTATTTTAAAACACCAATTTTCACAATCGA
Found at i:731575 original size:28 final size:27
Alignment explanation
Indices: 731528--731604 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 27
731518 TCACAATCGA
* *
731528 GGATACTCCAACCTCATTATTTC-ATCAG
1 GGATACTCCAACCCCGTTATTTCGA--AG
*
731556 GGATACTCCAACCCCGTTATCTTCGAGG
1 GGATACTCCAACCCCGTTAT-TTCGAAG
731584 GGATACTCCAACCCCGTTATT
1 GGATACTCCAACCCCGTTATT
731605 ATCTCCAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
27 1 0.02
28 39 0.89
29 3 0.07
30 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.29
Consensus pattern (27 bp):
GGATACTCCAACCCCGTTATTTCGAAG
Done.