Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 25 of 27
Found at i:3940911 original size:22 final size:23
Alignment explanation
Indices: 3940886--3940931 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
3940876 TATGAACACA
3940886 ACATAAATAAAAAA-ATTA-AAAT
1 ACAT-AATAAAAAATATTATAAAT
*
3940908 ACATTATAAAAAATATTATAAAT
1 ACATAATAAAAAATATTATAAAT
3940931 A
1 A
3940932 TGATACGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
ACATAATAAAAAATATTATAAAT
Found at i:3941897 original size:56 final size:58
Alignment explanation
Indices: 3941836--3941946 Score: 165
Period size: 56 Copynumber: 1.9 Consensus size: 58
3941826 ATTTTTTTTA
*
3941836 AAATAAATCATTATAATAAATTATG-AAAA-ATGTCATGAATTGAA-ATATGATACTTT
1 AAATAAATCATTATAATAAATTATGTAAAATATGTCATGAA-TGAAGATACGATACTTT
* *
3941892 AAATAAATTATTATGATAAATTATGTAAAATATGTCATGAATGAAGATACGATAC
1 AAATAAATCATTATAATAAATTATGTAAAATATGTCATGAATGAAGATACGATAC
3941947 GACTATGACA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
56 23 0.47
57 8 0.16
58 18 0.37
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (58 bp):
AAATAAATCATTATAATAAATTATGTAAAATATGTCATGAATGAAGATACGATACTTT
Found at i:3942716 original size:15 final size:15
Alignment explanation
Indices: 3942688--3942727 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
3942678 ACATAAAATT
*
3942688 TTTTTCTTTGTCTTTC
1 TTTTT-TTTCTCTTTC
3942704 TTTTTTTTCTCTTTC
1 TTTTTTTTCTCTTTC
3942719 TTTTCTTTT
1 TTTT-TTTT
3942728 TTTCTCTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTTTTTCTCTTTC
Found at i:3942716 original size:21 final size:20
Alignment explanation
Indices: 3942686--3942745 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 20
3942676 AAACATAAAA
3942686 TTTTTTTCT-TTGTC-TTTCT
1 TTTTTTTCTCTT-TCTTTTCT
3942705 TTTTTTTCTCTTTCTTTTC-
1 TTTTTTTCTCTTTCTTTTCT
*
3942724 TTTTTTTCTCTCTCATTTTCT
1 TTTTTTTCTCTTTC-TTTTCT
3942745 T
1 T
3942746 CATTCTCTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 24 0.67
20 11 0.31
21 1 0.03
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTTTCTCTTTCTTTTCT
Found at i:3943243 original size:27 final size:26
Alignment explanation
Indices: 3943213--3943281 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
3943203 AAATATTTAA
*
3943213 AACATAAAATAAAAATAATATACAAAT
1 AACATAAAATAAAAAT-ATATAAAAAT
* * *
3943240 AACACAAACATAAATATGTATAAAAAT
1 AACATAAA-ATAAAAATATATAAAAAT
3943267 ATACATAAAATAAAA
1 A-ACATAAAATAAAA
3943282 TAAATTATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.68, C:0.09, G:0.01, T:0.22
Consensus pattern (26 bp):
AACATAAAATAAAAATATATAAAAAT
Found at i:3944778 original size:39 final size:39
Alignment explanation
Indices: 3944724--3944802 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
3944714 TTGCAAAATA
3944724 CCATCGTCATTTGCAAAATAAAGCAAGGAAGACTCTTTT
1 CCATCGTCATTTGCAAAATAAAGCAAGGAAGACTCTTTT
*
3944763 CCATCGTCATTTGCAAAATAAAGCAAGGAAGATTCTTTT
1 CCATCGTCATTTGCAAAATAAAGCAAGGAAGACTCTTTT
3944802 C
1 C
3944803 TTAGTACAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (39 bp):
CCATCGTCATTTGCAAAATAAAGCAAGGAAGACTCTTTT
Found at i:3945234 original size:2 final size:2
Alignment explanation
Indices: 3945227--3945256 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3945217 GATCAAAAGA
3945227 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
3945257 GCGCTAAACA
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:3945740 original size:16 final size:15
Alignment explanation
Indices: 3945721--3945787 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 15
3945711 TGTCATAATC
3945721 ATATTTAAAATATTTT
1 ATATTTAAAA-ATTTT
3945737 ATATTTATATAAATTTT
1 ATATTTA-A-AAATTTT
*
3945754 AATATATTAATAATTTT
1 -ATAT-TTAAAAATTTT
* *
3945771 ATAGTATATAAATTTT
1 ATA-TTTAAAAATTTT
3945787 A
1 A
3945788 CTGCATTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 19 0.45
17 13 0.31
18 7 0.17
19 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (15 bp):
ATATTTAAAAATTTT
Found at i:3945754 original size:17 final size:17
Alignment explanation
Indices: 3945732--3945787 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
3945722 TATTTAAAAT
3945732 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
3945749 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
3945766 ATTTTATA-GTATATAA
1 ATTTTATATTTATATAA
3945782 ATTTTA
1 ATTTTA
3945788 CTGCATTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
14 2 0.06
15 2 0.06
16 10 0.29
17 11 0.32
18 6 0.18
19 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:3962017 original size:5 final size:5
Alignment explanation
Indices: 3962002--3962059 Score: 50
Period size: 5 Copynumber: 11.4 Consensus size: 5
3961992 AATGAATTGA
*
3962002 TTAATT TTAAT TTAA- TTAAT TTAATT TTAAAT TATATT TTAA- TTAAT
1 TTAA-T TTAAT TTAAT TTAAT TTAA-T TT-AAT T-TAAT TTAAT TTAAT
3962049 TTAA- TTAAT TT
1 TTAAT TTAAT TT
3962060 TTTAAATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
4 12 0.27
5 17 0.39
6 12 0.27
7 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:3962021 original size:15 final size:15
Alignment explanation
Indices: 3962001--3962054 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
3961991 AAATGAATTG
3962001 ATTAATTTTAATTTA
1 ATTAATTTTAATTTA
3962016 ATTAA-TTTAATTTTAA
1 ATTAATTTTAA-TTT-A
3962032 ATTATATTTTAA-TTA
1 ATTA-ATTTTAATTTA
3962047 ATTTAATT
1 A-TTAATT
3962055 AATTTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 5 0.15
15 13 0.38
16 10 0.29
17 1 0.03
18 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTAATTTTAATTTA
Found at i:3962022 original size:9 final size:9
Alignment explanation
Indices: 3962008--3962059 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
3961998 TTGATTAATT
3962008 TTAATTTAA
1 TTAATTTAA
3962017 TTAATTTAA
1 TTAATTTAA
*
3962026 TT--TTAAA
1 TTAATTTAA
3962033 TTATATTTTAA
1 TTA-A-TTTAA
3962044 TTAATTTAA
1 TTAATTTAA
3962053 TTAATTT
1 TTAATTT
3962060 TTTAAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 6 0.16
9 23 0.62
10 1 0.03
11 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTAATTTAA
Found at i:3966718 original size:2 final size:2
Alignment explanation
Indices: 3966711--3966738 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3966701 GTAAAAGTTG
3966711 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
3966739 TTGTATCATT
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:3967150 original size:15 final size:17
Alignment explanation
Indices: 3967118--3967154 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
3967108 AAATTAAGTA
3967118 TTAATATGAAATTATAT
1 TTAATATGAAATTATAT
3967135 TTAATAT-AAA-TATAT
1 TTAATATGAAATTATAT
3967150 TTAAT
1 TTAAT
3967155 TTTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.50
16 3 0.15
17 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTAATATGAAATTATAT
Found at i:3971513 original size:2 final size:2
Alignment explanation
Indices: 3971506--3971536 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3971496 AGATATTCTT
3971506 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 T
3971537 TGAATTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3976171 original size:3 final size:3
Alignment explanation
Indices: 3976163--3976189 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3976153 TAGTTACTTC
3976163 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
3976190 AGCTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3977892 original size:27 final size:26
Alignment explanation
Indices: 3977851--3977904 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
3977841 CTCAAGATAA
*
3977851 TATTTTAATATAAAATATTTTTATTTT
1 TATTTTAATATAAAATA-TGTTATTTT
3977878 TATTTTAAT-TCAAAATATGTTATTTT
1 TATTTTAATAT-AAAATATGTTATTTT
3977904 T
1 T
3977905 TAATATAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TATTTTAATATAAAATATGTTATTTT
Found at i:3986312 original size:40 final size:40
Alignment explanation
Indices: 3986255--3986338 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 40
3986245 TTTACGGTTA
* *
3986255 TAATTTTTAATGAATTAAATGAAGATATTATTATACATTG
1 TAATTTTTAATGAATTAAATGAAAATATTATTATACATCG
3986295 TAATTTTTAAT-ATATTAAATGAAAATATTATTATACATCG
1 TAATTTTTAATGA-ATTAAATGAAAATATTATTATACATCG
3986335 TAAT
1 TAAT
3986339 CTTAAAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 1 0.02
40 40 0.98
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (40 bp):
TAATTTTTAATGAATTAAATGAAAATATTATTATACATCG
Found at i:3986731 original size:2 final size:2
Alignment explanation
Indices: 3986724--3986767 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3986714 TTTGTTTGTT
3986724 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
3986766 TA
1 TA
3986768 AATTAATCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3987038 original size:18 final size:18
Alignment explanation
Indices: 3987003--3987051 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
3986993 TTACTTTTTG
* *
3987003 TTTATTTGTTTCTTA-TT
1 TTTATTTATTTTTTATTT
3987020 TTTAGTTTATTTTTTATTT
1 TTTA-TTTATTTTTTATTT
3987039 TTTATTTATTTTT
1 TTTATTTATTTTT
3987052 ACTTTCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 18 0.64
19 6 0.21
ACGTcount: A:0.14, C:0.02, G:0.04, T:0.80
Consensus pattern (18 bp):
TTTATTTATTTTTTATTT
Found at i:3989900 original size:2 final size:2
Alignment explanation
Indices: 3989893--3989918 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3989883 CAAAGCTGAA
3989893 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
3989919 TTATGTATTG
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:3991218 original size:2 final size:2
Alignment explanation
Indices: 3991211--3991240 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3991201 ATTAAGTACC
3991211 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
3991241 TATCTTAACC
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:3991252 original size:61 final size:60
Alignment explanation
Indices: 3991161--3991275 Score: 221
Period size: 61 Copynumber: 1.9 Consensus size: 60
3991151 TTAATTACAT
3991161 TATATATATATATATATATTATCTTAACCAGTTCTCATTGATTAAGTACCATATATATATA
1 TATATATATATATATATATTATCTTAACCAGTTCTCATTGATTAAGTACC-TATATATATA
3991222 TATATATATATATATATATTATCTTAACCAGTTCTCATTGATTAAGTACCTATA
1 TATATATATATATATATATTATCTTAACCAGTTCTCATTGATTAAGTACCTATA
3991276 AGTATTAAGT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 4 0.07
61 50 0.93
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.44
Consensus pattern (60 bp):
TATATATATATATATATATTATCTTAACCAGTTCTCATTGATTAAGTACCTATATATATA
Found at i:3991544 original size:2 final size:2
Alignment explanation
Indices: 3991537--3991569 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3991527 TCTCAAACTT
3991537 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
3991570 GTGTGTGTGT
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:3996416 original size:25 final size:27
Alignment explanation
Indices: 3996374--3996433 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
3996364 TAAATTTTTT
3996374 AATATATAATATACTTAT-ATATTAAA
1 AATATATAATATACTTATGATATTAAA
* * *
3996400 AATAT-TAATGTATTTATGATTTTAAA
1 AATATATAATATACTTATGATATTAAA
3996426 ATATATAT
1 A-ATATAT
3996434 TTAATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 10 0.36
26 13 0.46
27 4 0.14
28 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
AATATATAATATACTTATGATATTAAA
Found at i:3996618 original size:6 final size:6
Alignment explanation
Indices: 3996607--3996641 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3996597 ATTTATAACT
* *
3996607 TATATA TATATA TATATG TATATG TATATG TATAT
1 TATATG TATATG TATATG TATATG TATATG TATAT
3996642 TGAACGCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:3997723 original size:2 final size:2
Alignment explanation
Indices: 3997716--3997755 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3997706 TTTCTTACAC
3997716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3997756 CCTGAGGCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3997908 original size:22 final size:23
Alignment explanation
Indices: 3997865--3997909 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3997855 CAGTATTTTA
3997865 AAATATTAATAATTTTATTATAT
1 AAATATTAATAATTTTATTATAT
* *
3997888 AAATTTTAATATTTTTA-TATAT
1 AAATATTAATAATTTTATTATAT
3997910 TTTTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATATTAATAATTTTATTATAT
Found at i:3997911 original size:10 final size:10
Alignment explanation
Indices: 3997891--3997919 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3997881 ATTATATAAA
3997891 TTTTA-ATAT
1 TTTTATATAT
3997900 TTTTATATAT
1 TTTTATATAT
3997910 TTTTATATAT
1 TTTTATATAT
3997920 AATATTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATATAT
Found at i:3997972 original size:18 final size:17
Alignment explanation
Indices: 3997867--3997989 Score: 58
Period size: 18 Copynumber: 7.0 Consensus size: 17
3997857 GTATTTTAAA
*
3997867 ATATTAATAATTT-TATT
1 ATATT-ATATTTTATATT
*
3997884 ATA-TAAATTTTAATATT
1 ATATTATATTTT-ATATT
*
3997901 -TTTATATATTTTTATATAT
1 ATAT-TATA-TTTTATAT-T
*
3997920 AATATTTATGATTTTAT-TA
1 -ATA-TTAT-ATTTTATATT
***
3997939 ATATTATATCACATATT
1 ATATTATATTTTATATT
3997956 ATATTTATATTTTATATT
1 ATA-TTATATTTTATATT
*
3997974 ATATAATATTTT-TATT
1 ATATTATATTTTATATT
3997990 CAAAATTATT
Statistics
Matches: 80, Mismatches: 14, Indels: 25
0.67 0.12 0.21
Matches are distributed among these distances:
15 5 0.06
16 10 0.12
17 23 0.29
18 24 0.30
19 5 0.06
20 1 0.01
21 10 0.12
22 2 0.03
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:3998384 original size:5 final size:5
Alignment explanation
Indices: 3998375--3998433 Score: 54
Period size: 5 Copynumber: 12.4 Consensus size: 5
3998365 AATATTAAAT
* *
3998375 TAATA CAATA -AATA TAATA TAATA TAA-A TTAATA TAATA T-ATT TAAT-
1 TAATA TAATA TAATA TAATA TAATA TAATA -TAATA TAATA TAATA TAATA
*
3998422 TAATA TATTA TA
1 TAATA TAATA TA
3998434 TTTATATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 12 0.26
5 33 0.72
6 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:3998408 original size:29 final size:28
Alignment explanation
Indices: 3998365--3998428 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
3998355 TAACTTTAAA
3998365 AATATTAAATTAATACAATAAATATAATAT
1 AATA-TAAATTAATACAATAAATATAAT-T
* * *
3998395 AATATAAATTAATATAATATATTTAATT
1 AATATAAATTAATACAATAAATATAATT
3998423 AATATA
1 AATATA
3998429 TTATATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 7 0.23
29 20 0.65
30 4 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
AATATAAATTAATACAATAAATATAATT
Found at i:3998424 original size:18 final size:18
Alignment explanation
Indices: 3998385--3998437 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
3998375 TAATACAATA
*
3998385 AATATAATATAATATAAATT
1 AATATAATAT-AT-TTAATT
3998405 AATATAATATATTTAATT
1 AATATAATATATTTAATT
*
3998423 AATATATTATATTTA
1 AATATAATATATTTA
3998438 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 19 0.61
19 2 0.06
20 10 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATATAATATATTTAATT
Found at i:3998427 original size:13 final size:14
Alignment explanation
Indices: 3998374--3998430 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
3998364 AAATATTAAA
* *
3998374 TTAATACAATAAAT
1 TTAATATAATATAT
* *
3998388 ATAATATAATATAAA
1 TTAATATAATAT-AT
3998403 TTAATATAATATAT
1 TTAATATAATATAT
3998417 TTAAT-TAATATAT
1 TTAATATAATATAT
3998430 T
1 T
3998431 ATATTTATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
13 9 0.25
14 15 0.42
15 12 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATATAATATAT
Found at i:3998439 original size:24 final size:24
Alignment explanation
Indices: 3998412--3998488 Score: 66
Period size: 31 Copynumber: 3.0 Consensus size: 24
3998402 ATTAATATAA
3998412 TATATTTAATTAATATATTATATT
1 TATATTTAATTAATATATTATATT
3998436 TATATTTAAAATTTTAATATATTTAATAATT
1 TATATTT--AA--TTAATATA-TT-AT-ATT
* *
3998467 TATATTTTATTTATAT-TTATAT
1 TATATTTAATTAATATATTATAT
3998489 AATTAATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
23 2 0.05
24 9 0.20
25 2 0.05
26 2 0.05
27 6 0.14
28 8 0.18
29 3 0.07
30 2 0.05
31 10 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATATTTAATTAATATATTATATT
Found at i:3998440 original size:6 final size:6
Alignment explanation
Indices: 3998412--3998488 Score: 63
Period size: 6 Copynumber: 12.8 Consensus size: 6
3998402 ATTAATATAA
* * *
3998412 TATATT TA-ATT AATATAT TATATT TATATT TAAAATT T-TA-A TATATT
1 TATATT TATATT TATAT-T TATATT TATATT T-ATATT TATATT TATATT
3998459 TAATAATT TATATT T-TATT TATATT TATAT
1 T-AT-ATT TATATT TATATT TATATT TATAT
3998489 AATTAATAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
4 1 0.02
5 12 0.21
6 26 0.46
7 14 0.25
8 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
TATATT
Found at i:3998468 original size:17 final size:16
Alignment explanation
Indices: 3998436--3998497 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
3998426 ATATTATATT
3998436 TATATTTAA-AATTTTAA
1 TATATTTAATAA-TTT-A
3998453 TATATTTAATAATTTA
1 TATATTTAATAATTTA
*
3998469 TAT-TTTATTTATATTTA
1 TATATTTA-ATA-ATTTA
*
3998486 TATAATTAATAA
1 TATATTTAATAA
3998498 AAAATATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.11
16 7 0.18
17 22 0.58
18 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATTTAATAATTTA
Found at i:3998495 original size:42 final size:40
Alignment explanation
Indices: 3998404--3998496 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 40
3998394 TAATATAAAT
3998404 TAATATAATATATTTAATTAATATATTATATTTATATTTAA
1 TAAT-TAATATATTTAATTAATATATTATATTTATATTTAA
*
3998445 -AATTTTAATATATTTAA-TAATTTATATTTTATTTATATTTATA
1 TAA--TTAATATATTTAATTAA--TATATTATATTTATATTTA-A
3998488 TAATTAATA
1 TAATTAATA
3998497 AAAAATATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
40 5 0.11
41 12 0.27
42 25 0.56
43 1 0.02
44 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (40 bp):
TAATTAATATATTTAATTAATATATTATATTTATATTTAA
Found at i:4003448 original size:59 final size:59
Alignment explanation
Indices: 4003355--4003476 Score: 181
Period size: 59 Copynumber: 2.1 Consensus size: 59
4003345 ATCCCATTTC
* * * *
4003355 CTATCATTAGAACTTCATCTGTTTAATTGTATGTTTGCAGATGTAAACTGAAGGACATT
1 CTATCATTAGAACATCATATATTTAATTGAATGTTTGCAGATGTAAACTGAAGGACATT
* * *
4003414 CTATCATTAGTACATCATATATTTAATTGAATGTTTGCAGATGTAATCTGGAGGACATT
1 CTATCATTAGAACATCATATATTTAATTGAATGTTTGCAGATGTAAACTGAAGGACATT
4003473 CTAT
1 CTAT
4003477 TGGAGATGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.39
Consensus pattern (59 bp):
CTATCATTAGAACATCATATATTTAATTGAATGTTTGCAGATGTAAACTGAAGGACATT
Found at i:4012074 original size:12 final size:12
Alignment explanation
Indices: 4012057--4012083 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4012047 TTAATATGCA
4012057 AAAAGTAAAAAT
1 AAAAGTAAAAAT
4012069 AAAAGTAAAAAT
1 AAAAGTAAAAAT
4012081 AAA
1 AAA
4012084 TGCTTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAGTAAAAAT
Found at i:4016575 original size:11 final size:12
Alignment explanation
Indices: 4016558--4016586 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
4016548 AATCATTTGC
4016558 ATATTTAATTTT
1 ATATTTAATTTT
4016570 -TATTTAATTTT
1 ATATTTAATTTT
4016581 ATATTT
1 ATATTT
4016587 TTAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
ATATTTAATTTT
Found at i:4027177 original size:2 final size:2
Alignment explanation
Indices: 4027170--4027196 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4027160 AGATATTTTA
4027170 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4027197 AGTGATAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4029038 original size:3 final size:3
Alignment explanation
Indices: 4029030--4029058 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4029020 TGAAAGCCGA
4029030 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
4029059 TCAACACCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:4029380 original size:2 final size:2
Alignment explanation
Indices: 4029373--4029399 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4029363 ACACAATTAG
4029373 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 T
4029400 TAAAATTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4030316 original size:17 final size:17
Alignment explanation
Indices: 4030270--4030327 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
4030260 AATTTAATCA
*
4030270 TTTATATTTATATTATAT
1 TTTATATTTA-ATAATAT
*
4030288 TATAATTATTTAATAATAT
1 T-TTA-TATTTAATAATAT
* *
4030307 TTTATATTTATTAAAAT
1 TTTATATTTAATAATAT
4030324 TTTA
1 TTTA
4030328 AAATATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
17 15 0.45
18 3 0.09
19 9 0.27
20 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATATTTAATAATAT
Found at i:4030317 original size:21 final size:20
Alignment explanation
Indices: 4030274--4030318 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
4030264 TAATCATTTA
*
4030274 TATTTATATTATATTATAAT
1 TATTTATAATATATTATAAT
* *
4030294 TATTTAATAATATTTTATATT
1 TATTT-ATAATATATTATAAT
4030315 TATT
1 TATT
4030319 AAAATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTATAATATATTATAAT
Found at i:4032324 original size:23 final size:22
Alignment explanation
Indices: 4032272--4032317 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
4032262 TATTTGAAAA
4032272 AAATTTATAAATATTAAAATTT
1 AAATTTATAAATATTAAAATTT
* *
4032294 AAATTTTATACATATTAAATTTT
1 AAA-TTTATAAATATTAAAATTT
4032317 A
1 A
4032318 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATTTATAAATATTAAAATTT
Found at i:4034119 original size:2 final size:2
Alignment explanation
Indices: 4034112--4034139 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4034102 CAATAAAAGG
4034112 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
4034140 GTACACACTA
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:4034373 original size:2 final size:2
Alignment explanation
Indices: 4034366--4034393 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4034356 CCCTTATCCC
4034366 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4034394 TGGCAGAGAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4036451 original size:2 final size:2
Alignment explanation
Indices: 4036444--4036473 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4036434 AAGAAGCATG
4036444 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4036474 AGCCCACACG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4036882 original size:3 final size:3
Alignment explanation
Indices: 4036874--4036906 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4036864 ATTGCATTTG
4036874 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
4036907 AGATTTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:4037798 original size:2 final size:2
Alignment explanation
Indices: 4037791--4037820 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4037781 TTCAGTACTC
4037791 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
4037821 GATGCTGCTG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4060080 original size:2 final size:2
Alignment explanation
Indices: 4060073--4060103 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4060063 ATCAATGGAA
4060073 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 A
4060104 GCCACGAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4060922 original size:28 final size:27
Alignment explanation
Indices: 4060891--4060969 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
4060881 TATAATTTTG
* *
4060891 AATATAATATTATTATATAATAAAATAT
1 AATATAATATAAATATATAA-AAAATAT
*
4060919 AATATAATATAAATATATAAAAATTAT
1 AATATAATATAAATATATAAAAAATAT
* *
4060946 -ATA-AATATATAATATTTTAAAAAT
1 AATATAATATA-AATATATAAAAAAT
4060970 TTTGTAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
25 6 0.14
26 14 0.32
27 6 0.14
28 18 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AATATAATATAAATATATAAAAAATAT
Found at i:4060925 original size:15 final size:16
Alignment explanation
Indices: 4060891--4060935 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
4060881 TATAATTTTG
*
4060891 AATATAATATTATTATAT
1 AATATAA-A-TATAATAT
4060909 AATA-AAATATAATAT
1 AATATAAATATAATAT
4060924 AATATAAATATA
1 AATATAAATATA
4060936 TAAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 11 0.44
16 8 0.32
17 2 0.08
18 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATAAATATAATAT
Found at i:4060955 original size:27 final size:27
Alignment explanation
Indices: 4060915--4060994 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 27
4060905 ATATAATAAA
4060915 ATATAATATAATATAAATATATAAAAATT
1 ATATAA-AT-ATATAAATATATAAAAATT
*
4060944 ATATAAATATAT-AATATTTTAAAAATT
1 ATATAAATATATAAATA-TATAAAAATT
* *
4060971 TTGT-AATATATAAATATGATAAAA
1 ATATAAATATATAAATAT-ATAAAA
4060995 TATGAGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
26 12 0.27
27 24 0.55
28 2 0.05
29 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (27 bp):
ATATAAATATATAAATATATAAAAATT
Found at i:4061659 original size:19 final size:21
Alignment explanation
Indices: 4061637--4061676 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
4061627 TTTATATTTT
*
4061637 TATATATTA-TATAA-ATAAA
1 TATATAATATTATAATATAAA
4061656 TATATAATATTATAATATAAA
1 TATATAATATTATAATATAAA
4061677 CATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 5 0.28
21 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TATATAATATTATAATATAAA
Found at i:4062405 original size:19 final size:19
Alignment explanation
Indices: 4062374--4062416 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4062364 TACATTTATA
4062374 TTATAATTATATATTAATT
1 TTATAATTATATATTAATT
*
4062393 TTATGAATT-TATATTATTT
1 TTAT-AATTATATATTAATT
4062412 TTATA
1 TTATA
4062417 TTACGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 17 0.77
20 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATAATTATATATTAATT
Found at i:4063527 original size:15 final size:14
Alignment explanation
Indices: 4063496--4063532 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4063486 TCTTATCATA
4063496 TTTTTTAACTAAAT
1 TTTTTTAACTAAAT
* *
4063510 TTTTTTAATTCAAT
1 TTTTTTAACTAAAT
4063524 TTTTTTAAC
1 TTTTTTAAC
4063533 AATAATGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTTAACTAAAT
Found at i:4067036 original size:26 final size:24
Alignment explanation
Indices: 4067003--4067066 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
4066993 TATTCAAAAT
4067003 TAAA-TTAAATTTAAATTT-TAAAAA
1 TAAATTTAAATTTAAATTTGT--AAA
4067027 TAATATTTAAAATTT-AATTTGTAAA
1 TAA-ATTT-AAATTTAAATTTGTAAA
4067052 TAAATTT-AATTTAAA
1 TAAATTTAAATTTAAA
4067067 AATAACGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
22 5 0.14
23 2 0.06
24 7 0.20
25 7 0.20
26 7 0.20
27 7 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TAAATTTAAATTTAAATTTGTAAA
Found at i:4067069 original size:17 final size:17
Alignment explanation
Indices: 4067036--4067071 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4067026 ATAATATTTA
**
4067036 AAATTTAATTTGTAAAT
1 AAATTTAATTTAAAAAT
4067053 AAATTTAATTTAAAAAT
1 AAATTTAATTTAAAAAT
4067070 AA
1 AA
4067072 CGTATATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AAATTTAATTTAAAAAT
Found at i:4068462 original size:14 final size:15
Alignment explanation
Indices: 4068443--4068473 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4068433 TAGTGTAACT
4068443 AAAGAAAG-AAAAGA
1 AAAGAAAGAAAAAGA
4068457 AAAGAAAGAAAAAGA
1 AAAGAAAGAAAAAGA
4068472 AA
1 AA
4068474 GCTGTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAAGA
Found at i:4073358 original size:2 final size:2
Alignment explanation
Indices: 4073351--4073382 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4073341 TGATGGAGAC
4073351 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
4073383 TGGTGGATTA
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:4074305 original size:109 final size:109
Alignment explanation
Indices: 4074108--4074317 Score: 377
Period size: 109 Copynumber: 1.9 Consensus size: 109
4074098 GTCTGACCTG
*
4074108 TTTTTTACGGCATATCCATCCTATTCCCAACGTAAATAAGAGCACAGCTGAAAGTTACGGCATAA
1 TTTTTTACGGCATATCCATCCTATTCCCAACGTAAATAAGAGCACAGCTAAAAGTTACGGCATAA
4074173 CTTTAAATTTCAATTCAACTAATTTATATAATTATTCTCATCTA
66 CTTTAAATTTCAATTCAACTAATTTATATAATTATTCTCATCTA
4074217 TTTTTTACGGCATATCCATCCTATTCCCAACGTAAATAAGAAG-ACAGCTAAAAGTTACGGCATA
1 TTTTTTACGGCATATCCATCCTATTCCCAACGTAAATAAG-AGCACAGCTAAAAGTTACGGCATA
* *
4074281 ACTTTAAATTTCAATTTAATTAATTTATATAATTATT
65 ACTTTAAATTTCAATTCAACTAATTTATATAATTATT
4074318 TTTAATTTAA
Statistics
Matches: 97, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
109 95 0.98
110 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (109 bp):
TTTTTTACGGCATATCCATCCTATTCCCAACGTAAATAAGAGCACAGCTAAAAGTTACGGCATAA
CTTTAAATTTCAATTCAACTAATTTATATAATTATTCTCATCTA
Found at i:4074362 original size:14 final size:14
Alignment explanation
Indices: 4074341--4074392 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
4074331 TTAATTAATT
*
4074341 TATTTAAATAATAA
1 TATTTAAAAAATAA
*
4074355 TTTTTAAAAAATAA
1 TATTTAAAAAATAA
4074369 TATTTAATAAAATTAA
1 TATTTAA-AAAA-TAA
*
4074385 AATTTAAA
1 TATTTAAA
4074393 TAGTAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 18 0.56
15 5 0.16
16 9 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TATTTAAAAAATAA
Found at i:4080306 original size:102 final size:102
Alignment explanation
Indices: 4080172--4080378 Score: 333
Period size: 102 Copynumber: 2.0 Consensus size: 102
4080162 CTAAATCTGA
*
4080172 TGATGAATCCCCAGCATGTCGCCGGTGACCATCCTCCTCCTCAGGAGAATCAGAAAAGCTGTTAT
1 TGATGAATCCCCAGCATGCCGCCGGTGACCATCCTCCTCCTCAGGAGAATCAGAAAAGCTGTTAT
* * *
4080237 CATCATTGTCGCCATCAGCCTCAGACTGTTCCTCCAG
66 CATCATTGTCACCATAAGCCTCAGACCGTTCCTCCAG
* * * *
4080274 TGATGAATCCCCGGCATGCCTCCGGTGACCATCCTTCTCCTCAGGAGAATCTGAAAAGCTGTTAT
1 TGATGAATCCCCAGCATGCCGCCGGTGACCATCCTCCTCCTCAGGAGAATCAGAAAAGCTGTTAT
*
4080339 CATCATTGTCACCATAAGCCTCAGACCGTTCTTCCAG
66 CATCATTGTCACCATAAGCCTCAGACCGTTCCTCCAG
4080376 TGA
1 TGA
4080379 GTCCTCCACG
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 96 1.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (102 bp):
TGATGAATCCCCAGCATGCCGCCGGTGACCATCCTCCTCCTCAGGAGAATCAGAAAAGCTGTTAT
CATCATTGTCACCATAAGCCTCAGACCGTTCCTCCAG
Found at i:4082389 original size:16 final size:16
Alignment explanation
Indices: 4082368--4082409 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4082358 TTATTTATAT
* *
4082368 ATTTAATTTGAATTAA
1 ATTTAATTTAAAATAA
4082384 ATTTAATTTAAAATAA
1 ATTTAATTTAAAATAA
4082400 ATTTTAATTT
1 A-TTTAATTT
4082410 TTTATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATTTAATTTAAAATAA
Found at i:4082444 original size:25 final size:24
Alignment explanation
Indices: 4082380--4082452 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
4082370 TTAATTTGAA
*
4082380 TTAAATTTAATT-TAAAATAAATT
1 TTAAATTTAATTATAAAATATATT
* * *
4082403 TTAATTTTTTATTTATAAAATATTTAT
1 TTAA--ATTTAATTATAAAATATAT-T
4082430 TTAAATTTAATTATAAAATATAT
1 TTAAATTTAATTATAAAATATAT
4082453 AAATATTAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
23 4 0.10
25 22 0.56
26 8 0.21
27 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAAATTTAATTATAAAATATATT
Found at i:4082878 original size:25 final size:24
Alignment explanation
Indices: 4082846--4082895 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
4082836 AAAAAGTGTT
*
4082846 AATTAATATCTAATAATATTAATTA
1 AATTAATATCTAAAAATA-TAATTA
*
4082871 AATTAATATTTAAAAATATAATTA
1 AATTAATATCTAAAAATATAATTA
4082895 A
1 A
4082896 TAATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTAATATCTAAAAATATAATTA
Found at i:4083874 original size:16 final size:18
Alignment explanation
Indices: 4083847--4083903 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
4083837 ATCGTGTCAT
*
4083847 TATATTTAAATTATTTTA
1 TATATATAAATTATTTTA
4083865 TATA-AT-AATTATAATTTA
1 TATATATAAATTAT--TTTA
4083883 TATTATATAAATT-TTTTA
1 TA-TATATAAATTATTTTA
4083901 TAT
1 TAT
4083904 TTTTTTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
16 6 0.18
17 2 0.06
18 16 0.48
19 2 0.06
20 3 0.09
21 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATATAAATTATTTTA
Found at i:4087696 original size:15 final size:15
Alignment explanation
Indices: 4087676--4087706 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4087666 TAATTTTATT
4087676 TTTAAAATTATCAAA
1 TTTAAAATTATCAAA
*
4087691 TTTAAAATTATTAAA
1 TTTAAAATTATCAAA
4087706 T
1 T
4087707 AATTCAAATT
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAAAATTATCAAA
Found at i:4088150 original size:18 final size:18
Alignment explanation
Indices: 4088127--4088206 Score: 71
Period size: 18 Copynumber: 4.7 Consensus size: 18
4088117 AATTTTAAAC
* *
4088127 ATAAATAGATTATACAAT
1 ATAAATAAATTATAAAAT
4088145 ATAAATATAA-TATAAAAT
1 ATAAATA-AATTATAAAAT
*
4088163 ATAATTAAATTATAAAAT
1 ATAAATAAATTATAAAAT
**
4088181 A-ATTTAAA-TAT--AAT
1 ATAAATAAATTATAAAAT
4088195 ATAAATAAATTA
1 ATAAATAAATTA
4088207 AAATTTATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 4 0.08
15 5 0.10
16 5 0.10
17 8 0.15
18 29 0.56
19 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (18 bp):
ATAAATAAATTATAAAAT
Found at i:4088184 original size:16 final size:16
Alignment explanation
Indices: 4088163--4088206 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
4088153 AATATAAAAT
4088163 ATAATTAAATTATAAA
1 ATAATTAAATTATAAA
*
4088179 ATAATTTAAA-TATAAT
1 ATAA-TTAAATTATAAA
*
4088195 ATAAATAAATTA
1 ATAATTAAATTA
4088207 AAATTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 4 0.17
16 15 0.62
17 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATTAAATTATAAA
Found at i:4088189 original size:39 final size:39
Alignment explanation
Indices: 4088146--4088270 Score: 125
Period size: 39 Copynumber: 3.2 Consensus size: 39
4088136 TTATACAATA
4088146 TAAATATAATATAAAATATAATTAAATTATAAAATAATT
1 TAAATATAATATAAAATATAATTAAATTATAAAATAATT
*
4088185 TAAATATAATAT-AAATA-AATTAAAATTTATATAAT-ATAT
1 TAAATATAATATAAAATATAATT-AAA-TTATAAAATAAT-T
* * * *
4088224 TAAATATGATTATAACATATAA--AAATATATAATATAATA
1 TAAATAT-AATATAAAATATAATTAAAT-TATAAAATAATT
4088263 TAAATATA
1 TAAATATA
4088271 TAAATTATTT
Statistics
Matches: 72, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
37 4 0.06
38 12 0.17
39 44 0.61
40 6 0.08
41 4 0.06
42 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (39 bp):
TAAATATAATATAAAATATAATTAAATTATAAAATAATT
Found at i:4088237 original size:20 final size:18
Alignment explanation
Indices: 4088154--4088272 Score: 82
Period size: 20 Copynumber: 6.3 Consensus size: 18
4088144 TATAAATATA
*
4088154 ATATAAAATATAATTAAAT
1 ATATATAATAT-ATTAAAT
*
4088173 -TATAAAATA-ATTTAAAT
1 ATATATAATATA-TTAAAT
*
4088190 ATAATATAAATAAATTAAAAT
1 AT-ATAT-AATATATT-AAAT
*
4088211 TTATATAATATATTAAAT
1 ATATATAATATATTAAAT
* *
4088229 ATGATTATAACATA-TAAAA
1 AT-A-TATAATATATTAAAT
4088248 ATATATAATATAATATAAAT
1 ATATATAATAT-AT-TAAAT
4088268 ATATA
1 ATATA
4088273 AATTATTTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.01
17 13 0.16
18 17 0.21
19 17 0.21
20 27 0.33
21 6 0.07
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (18 bp):
ATATATAATATATTAAAT
Found at i:4088358 original size:7 final size:7
Alignment explanation
Indices: 4088320--4088368 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
4088310 TATTTAGAAA
*
4088320 ATTTTTT
1 ATTTTTG
4088327 ATTTTTAG
1 ATTTTT-G
*
4088335 GTTTTT-
1 ATTTTTG
4088341 A-TTTTG
1 ATTTTTG
4088347 A-TTTTG
1 ATTTTTG
4088353 ATTTTTG
1 ATTTTTG
4088360 ATTTTTG
1 ATTTTTG
4088367 AT
1 AT
4088369 ATATACACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 4 0.11
6 7 0.19
7 20 0.56
8 5 0.14
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.71
Consensus pattern (7 bp):
ATTTTTG
Found at i:4088367 original size:14 final size:14
Alignment explanation
Indices: 4088320--4088368 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
4088310 TATTTAGAAA
*
4088320 ATTTTTTATTTTTAG
1 ATTTTTGATTTTT-G
*
4088335 GTTTTT-A-TTTTG
1 ATTTTTGATTTTTG
4088347 A-TTTTGATTTTTG
1 ATTTTTGATTTTTG
4088360 ATTTTTGAT
1 ATTTTTGAT
4088369 ATATACACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 4 0.14
12 2 0.07
13 10 0.34
14 8 0.28
15 5 0.17
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.71
Consensus pattern (14 bp):
ATTTTTGATTTTTG
Found at i:4088946 original size:15 final size:14
Alignment explanation
Indices: 4088920--4088974 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 14
4088910 ATTCATATCG
4088920 TATTTATATATTTT
1 TATTTATATATTTT
4088934 TATTTATTATATTTT
1 TATTTA-TATATTTT
* *
4088949 TATTTAAAATATTATA
1 TATTT-ATATATT-TT
4088965 TATTTATATA
1 TATTTATATA
4088975 AAATTTGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 6 0.17
15 22 0.63
16 7 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTTATATATTTT
Found at i:4088963 original size:20 final size:20
Alignment explanation
Indices: 4088938--4088978 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4088928 TATTTTTATT
* *
4088938 TATTATATTTTTATTTAAAA
1 TATTATATATTTATATAAAA
4088958 TATTATATATTTATATAAAA
1 TATTATATATTTATATAAAA
4088978 T
1 T
4088979 TTGATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATATATTTATATAAAA
Found at i:4089144 original size:3 final size:3
Alignment explanation
Indices: 4089126--4089168 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
4089116 TTGCTAAGGT
*
4089126 TTA TT- TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4089169 TTAAACTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4098962 original size:39 final size:39
Alignment explanation
Indices: 4098908--4098995 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 39
4098898 TATTTATTAC
* * *
4098908 ATTGATCATATACTTTCACTG-TTTTAAAATTTTAAATAAT
1 ATTGAT-ATACACTTTCAATGTTTTTAAAA-TTAAAATAAT
*
4098948 GATT-ATATACACTTTGAATGTTTTTAAAATTAAAATAAT
1 -ATTGATATACACTTTCAATGTTTTTAAAATTAAAATAAT
4098987 ATTGATATA
1 ATTGATATA
4098996 TATATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
38 3 0.07
39 25 0.61
40 10 0.24
41 3 0.07
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (39 bp):
ATTGATATACACTTTCAATGTTTTTAAAATTAAAATAAT
Found at i:4098998 original size:2 final size:2
Alignment explanation
Indices: 4098991--4099028 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4098981 AATAATATTG
4098991 AT 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 AT
4099029 GCGTGTGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4099527 original size:3 final size:3
Alignment explanation
Indices: 4099521--4099553 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4099511 TTTTTTTTGG
4099521 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4099554 CACCATGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4100021 original size:19 final size:17
Alignment explanation
Indices: 4099997--4100040 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
4099987 AAGTAGAATA
4099997 TAAATTTTGTTAAAAGATT
1 TAAATTTT-TT-AAAGATT
*
4100016 TAAATTTTTTTAAGATT
1 TAAATTTTTTAAAGATT
4100033 TAAATTTT
1 TAAATTTT
4100041 AAATATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 14 0.58
18 2 0.08
19 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (17 bp):
TAAATTTTTTAAAGATT
Found at i:4102655 original size:2 final size:2
Alignment explanation
Indices: 4102648--4102678 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4102638 TGCTTCAAGT
4102648 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 T
4102679 TTGCGCGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4107043 original size:2 final size:2
Alignment explanation
Indices: 4107036--4107060 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4107026 GAATAAACTC
4107036 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4107061 ATTTCTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4107979 original size:3 final size:3
Alignment explanation
Indices: 4107971--4108001 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
4107961 AACTTCAATT
4107971 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4108002 TTATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4108006 original size:3 final size:3
Alignment explanation
Indices: 4108000--4108029 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4107990 AATATAATAA
4108000 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4108030 TATATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4108076 original size:2 final size:2
Alignment explanation
Indices: 4108069--4108097 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4108059 TGAAAAATGC
4108069 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
4108098 AAATAAAATT
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:4109499 original size:2 final size:2
Alignment explanation
Indices: 4109492--4109521 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4109482 CAATCAAAAC
4109492 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
4109522 TGTCTACACA
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:4117152 original size:2 final size:2
Alignment explanation
Indices: 4117147--4117190 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4117137 GCGCACACAC
4117147 AT AT AT 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 AT AT AT
4117189 AT
1 AT
4117191 GATAAAATCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4117268 original size:17 final size:15
Alignment explanation
Indices: 4117246--4117292 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
4117236 ACCATATAAA
*
4117246 TTTTTTTTTCTTGTT
1 TTTTTTTTTTTTGTT
4117261 TGTTTTTTTTTTTGGTT
1 T-TTTTTTTTTTT-GTT
*
4117278 TTTTTTGTTTTTGTT
1 TTTTTTTTTTTTGTT
4117293 AACTGGGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.14
16 20 0.71
17 4 0.14
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTTTTGTT
Found at i:4119799 original size:46 final size:46
Alignment explanation
Indices: 4119732--4119823 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
4119722 CTCAAGTTTG
*
4119732 CTCGTGTTCTGAATCAATTTGAGTTTGAACAAGTCACTCGAATCAT
1 CTCGTGTTCTGAATCAATTTGAGTCTGAACAAGTCACTCGAATCAT
*
4119778 CTCGTGTTTTGAATCAATTTGAGTCTGAACAAGTCACTCGAATCAT
1 CTCGTGTTCTGAATCAATTTGAGTCTGAACAAGTCACTCGAATCAT
4119824 TCAAAGTTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (46 bp):
CTCGTGTTCTGAATCAATTTGAGTCTGAACAAGTCACTCGAATCAT
Found at i:4121941 original size:2 final size:2
Alignment explanation
Indices: 4121934--4122032 Score: 117
Period size: 2 Copynumber: 49.5 Consensus size: 2
4121924 CGAGGCACGC
* *
4121934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
4121976 AT AT AC AT AT AT AT AC AC AC AC AT AT GT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4122018 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
4122033 AAAGAAAAAG
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:4123471 original size:23 final size:23
Alignment explanation
Indices: 4123445--4123491 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4123435 CACAATTTAA
*
4123445 AAATACTAAAATTTAAAATTATT
1 AAATACTAAAATTTAAAATAATT
* * *
4123468 AAATATTATATTTTAAAATAATT
1 AAATACTAAAATTTAAAATAATT
4123491 A
1 A
4123492 TATAAATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATACTAAAATTTAAAATAATT
Found at i:4124687 original size:99 final size:99
Alignment explanation
Indices: 4124521--4124714 Score: 361
Period size: 99 Copynumber: 2.0 Consensus size: 99
4124511 GGCAAGTAAG
*
4124521 ATATATATATATATTATTCATAACGAGGTTAGGGTATTTTTAAATGTGATTTAATATTTTTCTAG
1 ATATATATATATATTATTCATAACAAGGTTAGGGTATTTTTAAATGTGATTTAATATTTTTCTAG
*
4124586 TAATTTTATGGATGTATTCCTTCAAAATTTATAT
66 TAATTTTATGGATGTATTCATTCAAAATTTATAT
*
4124620 ATATATATATATATTATTCATAACAAGGTTAGGGTTTTTTTAAATGTGATTTAATATTTTTCTAG
1 ATATATATATATATTATTCATAACAAGGTTAGGGTATTTTTAAATGTGATTTAATATTTTTCTAG
4124685 TAATTTTATGGATGTATTCATTCAAAATTT
66 TAATTTTATGGATGTATTCATTCAAAATTT
4124715 TTATTTTCAA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.49
Consensus pattern (99 bp):
ATATATATATATATTATTCATAACAAGGTTAGGGTATTTTTAAATGTGATTTAATATTTTTCTAG
TAATTTTATGGATGTATTCATTCAAAATTTATAT
Found at i:4130029 original size:14 final size:14
Alignment explanation
Indices: 4130010--4130038 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4130000 TAAAAAGATT
4130010 GGGAGAGAGAGAGA
1 GGGAGAGAGAGAGA
4130024 GGGAGAGAGAGAGA
1 GGGAGAGAGAGAGA
4130038 G
1 G
4130039 AGCAAAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (14 bp):
GGGAGAGAGAGAGA
Found at i:4141258 original size:2 final size:2
Alignment explanation
Indices: 4141251--4141283 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4141241 CCCTCTTCTT
4141251 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
4141284 TTCAATTGTG
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:4143662 original size:2 final size:2
Alignment explanation
Indices: 4143655--4143690 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4143645 GGTTTTACTT
4143655 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
4143691 ATACCAAAGT
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):
TA
Found at i:4145659 original size:8 final size:9
Alignment explanation
Indices: 4145649--4145682 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
4145639 CAAAGACAAT
4145649 AAATAAAT-
1 AAATAAATA
4145657 AAATAAATA
1 AAATAAATA
4145666 AAATAAAATA
1 AAAT-AAATA
4145676 AAATAAA
1 AAATAAA
4145683 GAAGACCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:4155339 original size:21 final size:21
Alignment explanation
Indices: 4155295--4155336 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
4155285 CAACTTATTT
*
4155295 TTTAAATATGAACTAATCAAA
1 TTTAAATATGAAATAATCAAA
*
4155316 TTTAACATTTGAAATAATCAA
1 TTTAA-ATATGAAATAATCAA
4155337 TTTTTTGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
TTTAAATATGAAATAATCAAA
Found at i:4156001 original size:28 final size:30
Alignment explanation
Indices: 4155948--4156011 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
4155938 AATCATCATT
*
4155948 AAATAAAATTAATATTTATTAATTA-TATTA
1 AAAT-AAATTAATATTTATTAATTATTACTA
*
4155978 AAATAAA-TAATA-TTATTTATTTATTACTA
1 AAATAAATTAATATTTA-TTAATTATTACTA
4156007 AAATA
1 AAATA
4156012 TAAAATGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 3 0.10
28 11 0.37
29 12 0.40
30 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
AAATAAATTAATATTTATTAATTATTACTA
Found at i:4162149 original size:17 final size:18
Alignment explanation
Indices: 4162105--4162160 Score: 53
Period size: 20 Copynumber: 3.0 Consensus size: 18
4162095 AATTATTTTA
4162105 ATATTAAAAAT-ATTATCATT
1 ATATT-AAAATGATTAT--TT
4162125 ATTATTAAAATG-TTATTT
1 A-TATTAAAATGATTATTT
*
4162143 ATATTAATATGATTATTT
1 ATATTAAAATGATTATTT
4162161 TTTAAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 9 0.28
18 9 0.28
20 10 0.31
21 4 0.12
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (18 bp):
ATATTAAAATGATTATTT
Found at i:4162539 original size:26 final size:28
Alignment explanation
Indices: 4162509--4162579 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
4162499 AAATAATAAA
*
4162509 TAAAAT-TAATA-GTTATTAATTATTAT
1 TAAAATATAATATGATATTAATTATTAT
*
4162535 TAAAATAAATAATATGATATTATTTATTAT
1 TAAAAT--ATAATATGATATTAATTATTAT
4162565 TAAAATATAAATATG
1 TAAAATAT-AATATG
4162580 TATGTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 6 0.16
28 2 0.05
29 11 0.29
30 19 0.50
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (28 bp):
TAAAATATAATATGATATTAATTATTAT
Found at i:4162562 original size:30 final size:29
Alignment explanation
Indices: 4162522--4162579 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
4162512 AATTAATAGT
4162522 TATTAATTATTATTAAAATAAATAATATGA
1 TATTAATTATTATTAAAATAAA-AATATGA
* *
4162552 TATTATTTATTATTAAAATATAAATATG
1 TATTAATTATTATTAAAATAAAAATATG
4162580 TATGTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (29 bp):
TATTAATTATTATTAAAATAAAAATATGA
Found at i:4163703 original size:2 final size:2
Alignment explanation
Indices: 4163696--4163724 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4163686 TATGTTTATG
4163696 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 T
4163725 CATCATTAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4164246 original size:12 final size:12
Alignment explanation
Indices: 4164210--4164248 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
4164200 TATTAACAAT
4164210 ATTTTTATATTAA
1 ATTTTT-TATTAA
*
4164223 ATTTTGTAATTAA
1 ATTTT-TTATTAA
4164236 ATTTTTTATTAA
1 ATTTTTTATTAA
4164248 A
1 A
4164249 CAGTAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 15 0.65
14 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
ATTTTTTATTAA
Found at i:4166753 original size:18 final size:17
Alignment explanation
Indices: 4166707--4166753 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
4166697 ATAATTTTCA
4166707 TAAA-AAAATTAAAAAT
1 TAAACAAAATTAAAAAT
4166723 TAAACAAATATTAGAAAAT
1 TAAACAAA-ATTA-AAAAT
**
4166742 TTTACAAAATTA
1 TAAACAAAATTA
4166754 TTATTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 4 0.15
17 3 0.12
18 8 0.31
19 11 0.42
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAACAAAATTAAAAAT
Found at i:4168383 original size:24 final size:23
Alignment explanation
Indices: 4168356--4168403 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4168346 AGTTTCTTGG
*
4168356 TATATTTATGTACAAAAGGTTCAC
1 TATA-TTATATACAAAAGGTTCAC
* *
4168380 TATATTATATAGACAAGGTTCAC
1 TATATTATATACAAAAGGTTCAC
4168403 T
1 T
4168404 TAAGCTTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (23 bp):
TATATTATATACAAAAGGTTCAC
Found at i:4173222 original size:13 final size:13
Alignment explanation
Indices: 4173204--4173231 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4173194 ATAAAGGATG
4173204 CACTATCTTTAGA
1 CACTATCTTTAGA
4173217 CACTATCTTTAGA
1 CACTATCTTTAGA
4173230 CA
1 CA
4173232 ATACAGGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (13 bp):
CACTATCTTTAGA
Found at i:4180753 original size:28 final size:31
Alignment explanation
Indices: 4180705--4180763 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
4180695 ATAATATTTA
4180705 ATATATTATATTTATTAAATTTTA-AAATAT
1 ATATATTATATTTATTAAATTTTATAAATAT
4180735 ATATATTA-ATTCTA-T-AATTTTATAAATAT
1 ATATATTATATT-TATTAAATTTTATAAATAT
4180764 CATTTTAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 7 0.26
29 10 0.37
30 10 0.37
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (31 bp):
ATATATTATATTTATTAAATTTTATAAATAT
Found at i:4185976 original size:27 final size:27
Alignment explanation
Indices: 4185915--4185976 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
4185905 AGAATATCAG
4185915 TTATTTTTATATAAGTAAAATAATAAA
1 TTATTTTTATATAAGTAAAATAATAAA
* * * *
4185942 ATAATTTTATATAA-TAATATAACTAAT
1 TTATTTTTATATAAGTAAAATAA-TAAA
4185969 TTATTTTT
1 TTATTTTT
4185977 TAATCGTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (27 bp):
TTATTTTTATATAAGTAAAATAATAAA
Found at i:4196056 original size:3 final size:3
Alignment explanation
Indices: 4196048--4196086 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4196038 CTTGAAAAAC
4196048 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4196087 TCAAACTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4197485 original size:2 final size:2
Alignment explanation
Indices: 4197478--4197505 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4197468 TAGCCTGATC
4197478 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
4197506 TTGTTGGAAA
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:4202404 original size:21 final size:21
Alignment explanation
Indices: 4202379--4202420 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4202369 AATTTTTATT
*
4202379 TAAATTTAATAATA-AAAAATA
1 TAAA-TTAAAAATATAAAAATA
4202400 TAAATTAAAAATATAAAAATA
1 TAAATTAAAAATATAAAAATA
4202421 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAATTAAAAATATAAAAATA
Found at i:4202429 original size:22 final size:20
Alignment explanation
Indices: 4202381--4202420 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4202371 TTTTTATTTA
*
4202381 AATTTAATAATAAAAAATAT
1 AATTTAAAAATAAAAAATAT
*
4202401 AAATTAAAAATATAAAAATA
1 AATTTAAAAATA-AAAAATA
4202421 ATATTTTAAT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AATTTAAAAATAAAAAATAT
Found at i:4202464 original size:20 final size:19
Alignment explanation
Indices: 4202395--4202464 Score: 50
Period size: 20 Copynumber: 3.4 Consensus size: 19
4202385 TAATAATAAA
* *
4202395 AAATATAAATTAAAAATAT
1 AAATATAAATTAAAATTTT
* **
4202414 AAAAATAATATTTTAATTTTTT
1 AAATATAA-A--TTAAAATTTT
4202436 AAATAATAAATTAAAATTTT
1 AAAT-ATAAATTAAAATTTT
4202456 CAAATATAA
1 -AAATATAA
4202465 TGAATCAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
19 7 0.18
20 13 0.34
21 4 0.11
22 10 0.26
23 4 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATAAATTAAAATTTT
Found at i:4208932 original size:2 final size:2
Alignment explanation
Indices: 4208927--4208971 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4208917 AAAAGAAGGA
*
4208927 AG AG AG AG AG AG AG AG AG TG 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
4208969 AG A
1 AG A
4208972 TTCAATCCCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:4209628 original size:29 final size:29
Alignment explanation
Indices: 4209585--4209643 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
4209575 TTATGGCATC
*
4209585 ATAAAGTAAATAATATTCTTAATTCCTGG
1 ATAAAGTAAACAATATTCTTAATTCCTGG
4209614 ATAAAGTAAACAATATTCTTAATTCCTGG
1 ATAAAGTAAACAATATTCTTAATTCCTGG
4209643 A
1 A
4209644 AAGGATTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (29 bp):
ATAAAGTAAACAATATTCTTAATTCCTGG
Found at i:4225669 original size:30 final size:28
Alignment explanation
Indices: 4225631--4225706 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
4225621 ATATTAAAAA
*
4225631 TAATAAATAAAATTATTAATAATTATATT
1 TAATAAATAAAATTATAAATAA-TATATT
**
4225660 TAATAAAATATTATTATAAATAATATATT
1 TAAT-AAATAAAATTATAAATAATATATT
* **
4225689 TTATATTTAAAATTATAA
1 TAATAAATAAAATTATAA
4225707 TGAATAAGTC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
28 10 0.26
29 13 0.34
30 15 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATAAATAAAATTATAAATAATATATT
Done.