Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, whole genome shotgun sequence
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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 97 of 106
Found at i:20528696 original size:22 final size:22
Alignment explanation
Indices: 20528671--20528713 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20528661 TCAAGTAATA
*
20528671 TCTAACAAATCTCAAATAAATC
1 TCTAACAAATCTCAAACAAATC
20528693 TCTAACAAATCTCAAACAAAT
1 TCTAACAAATCTCAAACAAAT
20528714 TTTTTATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (22 bp):
TCTAACAAATCTCAAACAAATC
Found at i:20530108 original size:13 final size:13
Alignment explanation
Indices: 20530090--20530117 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20530080 TGTTCTTGTC
20530090 TTCTAATTTGAAT
1 TTCTAATTTGAAT
20530103 TTCTAATTTGAAT
1 TTCTAATTTGAAT
20530116 TT
1 TT
20530118 AATAAAGAAA
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:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TTCTAATTTGAAT
Found at i:20532911 original size:21 final size:21
Alignment explanation
Indices: 20532874--20532913 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20532864 AGTATTTTTG
*
20532874 TTATAGTATAGCTTGTTATTA
1 TTATAGTATAGATTGTTATTA
20532895 TTATAGTATA-ATATGTTAT
1 TTATAGTATAGAT-TGTTAT
20532914 AATATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (21 bp):
TTATAGTATAGATTGTTATTA
Found at i:20532932 original size:13 final size:13
Alignment explanation
Indices: 20532893--20532958 Score: 51
Period size: 15 Copynumber: 4.8 Consensus size: 13
20532883 AGCTTGTTAT
20532893 TATTATAGTATAA
1 TATTATAGTATAA
*
20532906 TATGTTATAATATAA
1 TA--TTATAGTATAA
* *
20532921 TATTATGGTATAG
1 TATTATAGTATAA
* *
20532934 TATTATTATTAGTAT
1 TATTA-TAGTA-TAA
20532949 TATTATAGTA
1 TATTATAGTA
20532959 ATTATATTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
13 15 0.37
14 7 0.17
15 19 0.46
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (13 bp):
TATTATAGTATAA
Found at i:20532942 original size:3 final size:3
Alignment explanation
Indices: 20532934--20533129 Score: 147
Period size: 3 Copynumber: 66.3 Consensus size: 3
20532924 TATGGTATAG
* * *
20532934 TAT TAT TAT TAG TAT TAT TA- TAGT AAT TA- TAT T-G TACGT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA--T TAT TAT
* * * *
20532978 TAT TAT TAT TGT TAT TAT TCT TAT TAT TAT CAT TA- TAT GA- TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * * *
20533022 TAT TA- TAC TAT AAT ATAT CAG TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
20533067 TAT TAT TAT TAT TAT TAT TAT CAT CAT CAT TAT CAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20533115 TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT T
20533130 TTTTCTTTCC
Statistics
Matches: 153, Mismatches: 27, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
2 14 0.09
3 132 0.86
4 5 0.03
5 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:20533039 original size:59 final size:60
Alignment explanation
Indices: 20532911--20533129 Score: 175
Period size: 59 Copynumber: 3.7 Consensus size: 60
20532901 TATAATATGT
* * * * *
20532911 TATAATATAATATTATGGTATAGTATTATTATTAGTATTATTATAGTAATTATATTGTACG
1 TATAATATATTATTATTGT-TATTATTATTATTATTATTATTATAGTAATTATATTATACG
* * *
20532972 T-TATTATATTATTATTGTTATTATTCTTATTATTATCATTATA-TGATATT-TATTATAC-
1 TATAATATATTATTATTGTTATTATTATTATTATTATTATTATAGT-A-ATTATATTATACG
* * * * *
20533030 TATAATATATCAGTATTATTATTATTATTATTATTATTATTATTA-TTATTATTATTAT-CA
1 TATAATATATTATTATTGTTATTATTATTATTATTATTATTA-TAGTAATTA-TATTATACG
* * **
20533090 TCATCAT-TATCATTATCATTATTATTATTATTATT-TTATT
1 T-ATAATATATTATTATTGTTATTATTATTATTATTATTATT
20533130 TTTTCTTTCC
Statistics
Matches: 132, Mismatches: 18, Indels: 18
0.79 0.11 0.11
Matches are distributed among these distances:
58 5 0.04
59 69 0.52
60 53 0.40
61 5 0.04
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (60 bp):
TATAATATATTATTATTGTTATTATTATTATTATTATTATTATAGTAATTATATTATACG
Found at i:20534159 original size:15 final size:15
Alignment explanation
Indices: 20534131--20534169 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
20534121 GAAAAAAAGA
20534131 CAAAAAAATGTTTT-
1 CAAAAAAATGTTTTC
*
20534145 CAAATAAAATTTTTTC
1 CAAA-AAAATGTTTTC
20534161 CAAAAAAAT
1 CAAAAAAAT
20534170 ACATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (15 bp):
CAAAAAAATGTTTTC
Found at i:20540064 original size:31 final size:31
Alignment explanation
Indices: 20540026--20540121 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 31
20540016 CCATTTATAG
* * *
20540026 GATATCTCATTAAAATTTTTTAGTGTTGTGA
1 GATATCTCATTTAGATTTTTTAGTGTTGTAA
20540057 GATATCTCATTTAGATTTTTTAGTGTTGTAA
1 GATATCTCATTTAGATTTTTTAGTGTTGTAA
* * * *
20540088 AATATCTTATTTAGATTTCTTAGTGATGTAA
1 GATATCTCATTTAGATTTTTTAGTGTTGTAA
20540119 GAT
1 GAT
20540122 TTTTTACTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (31 bp):
GATATCTCATTTAGATTTTTTAGTGTTGTAA
Found at i:20554131 original size:18 final size:19
Alignment explanation
Indices: 20554108--20554143 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20554098 ACTACAAAAA
20554108 ATTTTTATTTTCC-TTTTT
1 ATTTTTATTTTCCATTTTT
*
20554126 ATTTTTTTTTTCCATTTT
1 ATTTTTATTTTCCATTTT
20554144 CCCCTTCGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (19 bp):
ATTTTTATTTTCCATTTTT
Found at i:20554547 original size:14 final size:16
Alignment explanation
Indices: 20554530--20554562 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
20554520 ATTACTGTTT
20554530 TTAATA-TTAAAA-AA
1 TTAATATTTAAAATAA
20554544 TTAATATTTAAAATAA
1 TTAATATTTAAAATAA
20554560 TTA
1 TTA
20554563 TCTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 6 0.35
16 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAATATTTAAAATAA
Found at i:20554622 original size:14 final size:14
Alignment explanation
Indices: 20554603--20554632 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20554593 TAAATACTAT
20554603 TATTTATTATATTA
1 TATTTATTATATTA
*
20554617 TATTTATTTTATTA
1 TATTTATTATATTA
20554631 TA
1 TA
20554633 AATATTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTATTATATTA
Found at i:20556160 original size:10 final size:9
Alignment explanation
Indices: 20556123--20556161 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
20556113 TTTTTTAAGT
20556123 ATTAATTTA
1 ATTAATTTA
*
20556132 ACTAATTTA
1 ATTAATTTA
20556141 ATTAACTTTA
1 ATTAA-TTTA
20556151 ATTGAATTTA
1 ATT-AATTTA
20556161 A
1 A
20556162 GAGTCATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 12 0.46
10 12 0.46
11 2 0.08
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (9 bp):
ATTAATTTA
Found at i:20560138 original size:33 final size:33
Alignment explanation
Indices: 20560101--20560168 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
20560091 GATATCAATA
20560101 TTAAAAGTGATCGTAAGATTGTTTCAAATGATT
1 TTAAAAGTGATCGTAAGATTGTTTCAAATGATT
20560134 TTAAAAGTGATCGTAAGATTGTTTCAAATGATT
1 TTAAAAGTGATCGTAAGATTGTTTCAAATGATT
20560167 TT
1 TT
20560169 TGTAGTATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (33 bp):
TTAAAAGTGATCGTAAGATTGTTTCAAATGATT
Found at i:20569645 original size:23 final size:24
Alignment explanation
Indices: 20569602--20569650 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
20569592 TTAAAAAATG
* *
20569602 ATATTTAATAATTTTTAAATTTTA
1 ATATTTAATAATTTTCAAATTATA
*
20569626 ATATTT-ATAATTTTCGAATTATA
1 ATATTTAATAATTTTCAAATTATA
20569649 AT
1 AT
20569651 CTTCTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
ATATTTAATAATTTTCAAATTATA
Found at i:20570916 original size:18 final size:18
Alignment explanation
Indices: 20570889--20570923 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20570879 AATGAAAGTT
20570889 AAGATCAAGTTTTATTTA
1 AAGATCAAGTTTTATTTA
*
20570907 AAGATTAAGTTTTATTT
1 AAGATCAAGTTTTATTT
20570924 GATAAAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (18 bp):
AAGATCAAGTTTTATTTA
Found at i:20572215 original size:53 final size:53
Alignment explanation
Indices: 20572150--20572255 Score: 126
Period size: 53 Copynumber: 2.0 Consensus size: 53
20572140 AGGTAAAAAT
* * *
20572150 GATATTTCTAAATTTAACCTAAAT-GATGAAAAATTTTA-AAATAAAACTTGTAA
1 GATATTTCTAAATTGAACCCAAATAG-TGAAAAA-TTTAGAAACAAAACTTGTAA
* * *
20572203 GATATTTTTAAATTGGACCCAAATAGTGAAAAATTTAGAAACGAAACTTGTAA
1 GATATTTCTAAATTGAACCCAAATAGTGAAAAATTTAGAAACAAAACTTGTAA
20572256 AATAAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
52 4 0.09
53 40 0.89
54 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.33
Consensus pattern (53 bp):
GATATTTCTAAATTGAACCCAAATAGTGAAAAATTTAGAAACAAAACTTGTAA
Found at i:20576242 original size:34 final size:34
Alignment explanation
Indices: 20576178--20576244 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
20576168 TTTTGACCAT
* **
20576178 AAAATTTATATAAAATTATTTAAATGAAATTTAG
1 AAAATTTATATAAAATAATTTAAAAAAAATTTAG
*
20576212 AAAATTTTTAT-AAATAATTTAATAAAAAATTTA
1 AAAATTTATATAAAATAATTTAA-AAAAAATTTA
20576245 CATTGATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (34 bp):
AAAATTTATATAAAATAATTTAAAAAAAATTTAG
Found at i:20594699 original size:12 final size:12
Alignment explanation
Indices: 20594684--20594709 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20594674 CTTTTCTTCT
20594684 TTTTCTACTTGG
1 TTTTCTACTTGG
20594696 TTTTCTACTTGG
1 TTTTCTACTTGG
20594708 TT
1 TT
20594710 GCTCTGTGTA
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:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (12 bp):
TTTTCTACTTGG
Found at i:20597782 original size:15 final size:15
Alignment explanation
Indices: 20597745--20597785 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
20597735 ATTGAATTGA
*
20597745 TATATAATTTT-TAT
1 TATATAATTTTAAAT
20597759 TA-A-AATTTTAAAT
1 TATATAATTTTAAAT
20597772 TATATAATTTTAAA
1 TATATAATTTTAAA
20597786 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 3 0.13
15 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATAATTTTAAAT
Found at i:20599800 original size:19 final size:19
Alignment explanation
Indices: 20599759--20599802 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
20599749 TTCAGTCATA
*
20599759 TAAATAATAAAATAAAAATT
1 TAAA-AATAAAATAAAAACT
* *
20599779 TAAAAATAAATTAAATACT
1 TAAAAATAAAATAAAAACT
20599798 TAAAA
1 TAAAA
20599803 CAATTGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAAATAAAATAAAAACT
Found at i:20604001 original size:3 final size:3
Alignment explanation
Indices: 20603993--20604022 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20603983 CTAGATGTCA
20603993 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20604023 TGTTAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20610958 original size:12 final size:12
Alignment explanation
Indices: 20610936--20610968 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20610926 TACGATATGA
20610936 AAATA-ATATAT
1 AAATATATATAT
20610947 AAATATATATAT
1 AAATATATATAT
20610959 AAATGATATA
1 AAAT-ATATA
20610969 ATTTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 10 0.50
13 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (12 bp):
AAATATATATAT
Found at i:20613191 original size:27 final size:27
Alignment explanation
Indices: 20613143--20613217 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 27
20613133 TTTTTAAATG
*
20613143 TAAT-ATAATATTAA-AATA-TTAAAA
1 TAATAATAATAATAATAATATTTAAAA
20613167 TAATAATAATAATAATAATATTTAAAA
1 TAATAATAATAATAATAATATTTAAAA
** *
20613194 TTTTAATAAAAATAATATATATTT
1 TAATAATAATAATAATA-ATATTT
20613218 GATAAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.09
25 9 0.21
26 4 0.09
27 20 0.47
28 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TAATAATAATAATAATAATATTTAAAA
Found at i:20613217 original size:21 final size:22
Alignment explanation
Indices: 20613193--20613236 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
20613183 AATATTTAAA
*
20613193 ATTTTAATAAAAA-TAATATAT
1 ATTTTAATAAAAATTAAAATAT
*
20613214 A-TTTGATAAAAATTAAAATAT
1 ATTTTAATAAAAATTAAAATAT
20613235 AT
1 AT
20613237 ATTATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
ATTTTAATAAAAATTAAAATAT
Found at i:20616592 original size:9 final size:8
Alignment explanation
Indices: 20616566--20616618 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 8
20616556 AGCCATTGCC
*
20616566 AAAGAAAG
1 AAAGAAAA
20616574 AAAGAAAA
1 AAAGAAAA
20616582 AAAGAAAA
1 AAAGAAAA
*
20616590 AAATAAATGA
1 AAAGAAA--A
20616600 AAAGGAAAGA
1 AAA-GAAA-A
20616610 AAAGAAAA
1 AAAGAAAA
20616618 A
1 A
20616619 TAAATAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
8 23 0.59
9 4 0.10
10 9 0.23
11 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (8 bp):
AAAGAAAA
Found at i:20616926 original size:2 final size:2
Alignment explanation
Indices: 20616914--20616943 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20616904 TTCAGACTAC
*
20616914 AT AT TT 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
20616944 TCATTTCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:20617192 original size:2 final size:2
Alignment explanation
Indices: 20617187--20617214 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20617177 TATATGTGTG
20617187 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
20617215 ACATAATTAT
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):
TA
Found at i:20618045 original size:25 final size:26
Alignment explanation
Indices: 20618017--20618067 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
20618007 ATTCGATTCA
* *
20618017 TTTATAAAAAT-TTATTTATATTTTT
1 TTTATAAAAATATTATTAAGATTTTT
*
20618042 TTTATAAATATATTATTAAGATTTTT
1 TTTATAAAAATATTATTAAGATTTTT
20618068 AAAATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTATAAAAATATTATTAAGATTTTT
Found at i:20618533 original size:2 final size:2
Alignment explanation
Indices: 20618526--20618564 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
20618516 GTATTATCAC
* * *
20618526 TA TA TA TA TT TT TG 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 TA TA TA T
20618565 TGTCTTTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (2 bp):
TA
Found at i:20618664 original size:29 final size:30
Alignment explanation
Indices: 20618626--20618692 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
20618616 GAATTTTATC
* *
20618626 ATTT-TATTTAGATAATTTTTTATATTTTT-
1 ATTTGTATTTAAATAAGTTTTTAT-TTTTTA
20618655 A-TTGTATTTAAATAAGTTTTTATTTTTTA
1 ATTTGTATTTAAATAAGTTTTTATTTTTTA
20618684 ATTTGTATT
1 ATTTGTATT
20618693 CAAGTATGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 7 0.21
29 19 0.58
30 7 0.21
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (30 bp):
ATTTGTATTTAAATAAGTTTTTATTTTTTA
Found at i:20618796 original size:30 final size:29
Alignment explanation
Indices: 20618761--20618833 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
20618751 CAATTAAAGG
*
20618761 ATAAAAACTTATTTGGATAGAAATTA-AAAT
1 ATAAAAATTTATTTGGAT-GAAA-TAGAAAT
* *
20618791 TTAAAAATTTATTTGGATGCAATAGAAAT
1 ATAAAAATTTATTTGGATGAAATAGAAAT
20618820 ATAAAAATTTATTT
1 ATAAAAATTTATTT
20618834 AAATAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 2 0.05
29 20 0.53
30 16 0.42
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (29 bp):
ATAAAAATTTATTTGGATGAAATAGAAAT
Found at i:20618824 original size:29 final size:30
Alignment explanation
Indices: 20618752--20618833 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
20618742 TTTAGATATC
** *
20618752 AATTAAAGGATAAAAACTTATTTGGATAGA
1 AATTAAAATATAAAAATTTATTTGGATAGA
* *
20618782 AATTAAAATTTAAAAATTTATTTGGAT-GC
1 AATTAAAATATAAAAATTTATTTGGATAGA
20618811 AA-TAGAAATATAAAAATTTATTT
1 AATTA-AAATATAAAAATTTATTT
20618834 AAATAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.04
29 20 0.44
30 23 0.51
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (30 bp):
AATTAAAATATAAAAATTTATTTGGATAGA
Found at i:20618843 original size:29 final size:28
Alignment explanation
Indices: 20618761--20618846 Score: 91
Period size: 29 Copynumber: 3.0 Consensus size: 28
20618751 CAATTAAAGG
*
20618761 ATAAAAACTTATTTGGATAGAAATTAAAAT
1 ATAAAAATTTATTTGGATA-AAA-TAAAAT
* **
20618791 TTAAAAATTTATTTGGATGCAATAGAAAT
1 ATAAAAATTTATTTGGATAAAATA-AAAT
**
20618820 ATAAAAATTTATTTAAATAAAATAAAA
1 ATAAAAATTTATTTGGATAAAATAAAA
20618847 AGTTTAAAGG
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 5 0.11
29 25 0.54
30 16 0.35
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (28 bp):
ATAAAAATTTATTTGGATAAAATAAAAT
Found at i:20619639 original size:73 final size:72
Alignment explanation
Indices: 20619526--20619670 Score: 204
Period size: 70 Copynumber: 2.0 Consensus size: 72
20619516 CAATCATTAA
*
20619526 AATTCATATCTTAACGTCTCAAATATATAAAAAAATAATAATAATAAAAAAAATAAAAATCCCAT
1 AATTCATATCTTAACATCTCAAATATATAAAAAAATAATAATAAT---AAAAATAAAAATCCCAT
*
20619591 AAATACAATT
63 AAAAACAATT
* * *
20619601 AATTCATATCTTAACATCTC-AA-GTATAAAATAATAATAATAATAAAAATGAAAATCCCATAAA
1 AATTCATATCTTAACATCTCAAATATATAAAAAAATAATAATAATAAAAATAAAAATCCCATAAA
20619664 AACAATT
66 AACAATT
20619671 GGTATACATC
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
70 25 0.38
73 19 0.29
74 2 0.03
75 19 0.29
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.28
Consensus pattern (72 bp):
AATTCATATCTTAACATCTCAAATATATAAAAAAATAATAATAATAAAAATAAAAATCCCATAAA
AACAATT
Found at i:20622590 original size:13 final size:14
Alignment explanation
Indices: 20622572--20622600 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20622562 TTATATTTAA
20622572 TAAATTT-AAAATT
1 TAAATTTCAAAATT
20622585 TAAATTTCAAAATT
1 TAAATTTCAAAATT
20622599 TA
1 TA
20622601 TATATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAATTTCAAAATT
Found at i:20627588 original size:16 final size:15
Alignment explanation
Indices: 20627567--20627597 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
20627557 CGTTAAAAGC
20627567 TTTTAATTTCGATTAA
1 TTTTAATTT-GATTAA
20627583 TTTTAATTTGATTAA
1 TTTTAATTTGATTAA
20627598 GTTAACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (15 bp):
TTTTAATTTGATTAA
Found at i:20633230 original size:2 final size:2
Alignment explanation
Indices: 20633218--20633247 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20633208 TCATTGTTGG
20633218 AT AT A- 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
20633248 ATAAGAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20636004 original size:2 final size:2
Alignment explanation
Indices: 20635993--20636022 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20635983 TTACAACAAT
20635993 AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
20636023 TCCTTGGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20637050 original size:2 final size:2
Alignment explanation
Indices: 20637043--20637079 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20637033 ACAAGCTGTG
20637043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20637080 AAGCCACAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20637288 original size:15 final size:17
Alignment explanation
Indices: 20637247--20637290 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
20637237 ATAAATAATT
20637247 ATTCAAATATTATATTA
1 ATTCAAATATTATATTA
20637264 ATT-AATATATT-TA-TA
1 ATTCAA-ATATTATATTA
20637279 ATTCAAATATTA
1 ATTCAAATATTA
20637291 AGCTAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 10 0.42
16 6 0.25
17 8 0.33
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTCAAATATTATATTA
Found at i:20637325 original size:28 final size:29
Alignment explanation
Indices: 20637247--20637340 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 29
20637237 ATAAATAATT
*
20637247 ATTCAAATATTATATTAATTAATATATTTATA
1 ATTCAAATATTATATTAA--AA-ATTTTTATA
*
20637279 ATTCAAATATTA-AGCTAAAAATTTTTA-A
1 ATTCAAATATTATA-TTAAAAATTTTTATA
* *
20637307 ATTTAAATATTATATTAAATATTTTATTATA
1 ATTCAAATATTATATTAAA-AATTT-TTATA
20637338 ATT
1 ATT
20637341 TAAAGGTCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
28 16 0.31
29 11 0.21
30 5 0.10
31 5 0.10
32 15 0.29
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (29 bp):
ATTCAAATATTATATTAAAAATTTTTATA
Found at i:20638499 original size:5 final size:5
Alignment explanation
Indices: 20638491--20638520 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
20638481 ATGATAACCC
20638491 TCTTT TCTTT TCTTT TC-TT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
20638521 ATCCCACACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:20638513 original size:14 final size:14
Alignment explanation
Indices: 20638494--20638520 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20638484 ATAACCCTCT
20638494 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
20638508 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
20638521 ATCCCACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:20646605 original size:2 final size:2
Alignment explanation
Indices: 20646598--20646623 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20646588 CATATAGAAA
20646598 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
20646624 TAGTAACAGC
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:20649184 original size:3 final size:3
Alignment explanation
Indices: 20649176--20649224 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
20649166 AAGCAATCAA
*
20649176 AAT AAT AAT AAG 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 AAT AAT AAT
20649224 A
1 A
20649225 GTATATGGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20653230 original size:15 final size:15
Alignment explanation
Indices: 20653210--20653240 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20653200 GAGCAGTGCT
20653210 GAGGCTGAGTTTAGA
1 GAGGCTGAGTTTAGA
20653225 GAGGCTGAGTTTAGA
1 GAGGCTGAGTTTAGA
20653240 G
1 G
20653241 CAATGTCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.42, T:0.26
Consensus pattern (15 bp):
GAGGCTGAGTTTAGA
Found at i:20653608 original size:25 final size:25
Alignment explanation
Indices: 20653580--20653628 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
20653570 GAGTGTAGAA
20653580 ATCTAATTCTCCTACATTAGTGCAG
1 ATCTAATTCTCCTACATTAGTGCAG
* *
20653605 ATCTGATTCTCCTATATTAGTGCA
1 ATCTAATTCTCCTACATTAGTGCA
20653629 ATTTGATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (25 bp):
ATCTAATTCTCCTACATTAGTGCAG
Found at i:20657574 original size:21 final size:22
Alignment explanation
Indices: 20657548--20657588 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20657538 TCTTGTATAT
20657548 ATTT-AAAAATAAAAAAAATTA
1 ATTTAAAAAATAAAAAAAATTA
*
20657569 ATTTAAAAAATAAATAAAAT
1 ATTTAAAAAATAAAAAAAAT
20657589 ATAAGTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
ATTTAAAAAATAAAAAAAATTA
Found at i:20658879 original size:12 final size:12
Alignment explanation
Indices: 20658862--20658888 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20658852 TATTTTATGA
20658862 ATAAAAAATTTT
1 ATAAAAAATTTT
20658874 ATAAAAAATTTT
1 ATAAAAAATTTT
20658886 ATA
1 ATA
20658889 GATAAACTTA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAAAAAATTTT
Found at i:20660093 original size:23 final size:23
Alignment explanation
Indices: 20660050--20660093 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
20660040 ATATTTTATT
* *
20660050 CTTAGAAAAAATGAGTTAATAAA
1 CTTAGAAAAAATGACTAAATAAA
20660073 CTTAGCAAAAAAT-ACTAAATA
1 CTTAG-AAAAAATGACTAAATA
20660094 TTTTAGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (23 bp):
CTTAGAAAAAATGACTAAATAAA
Found at i:20661835 original size:14 final size:14
Alignment explanation
Indices: 20661818--20661851 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20661808 TACTTAATAT
*
20661818 AATATATGAATTAC
1 AATATACGAATTAC
*
20661832 AATATACGAATTAT
1 AATATACGAATTAC
20661846 AATATA
1 AATATA
20661852 ATTATTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (14 bp):
AATATACGAATTAC
Found at i:20662279 original size:2 final size:2
Alignment explanation
Indices: 20662272--20662297 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20662262 CATGTTGATG
20662272 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
20662298 TCTATTTAAG
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:20672216 original size:2 final size:2
Alignment explanation
Indices: 20672209--20672242 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20672199 CGCAAAGGAA
20672209 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20672243 GACTGGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20682606 original size:34 final size:34
Alignment explanation
Indices: 20682540--20682606 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
20682530 ATTGCTATCA
** * **
20682540 AAAATATATTTTTGGATAATTATGATGTTTTTTG
1 AAAATATATTTTTAAATAATTATAATACTTTTTG
20682574 AAAATATATTTTTAAATAATTATAATACTTTTT
1 AAAATATATTTTTAAATAATTATAATACTTTTT
20682607 TGTATGATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.52
Consensus pattern (34 bp):
AAAATATATTTTTAAATAATTATAATACTTTTTG
Found at i:20683030 original size:23 final size:22
Alignment explanation
Indices: 20682982--20683031 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
20682972 TTTTTAAATG
* *
20682982 AAATTATTTCATTATTTTTCTC
1 AAATTAATTCATTATTTTTCTA
20683004 AAATTAATTCATTCTATTTTT-TA
1 AAATTAATTCA-T-TATTTTTCTA
20683027 AAATT
1 AAATT
20683032 TGAATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.42
23 7 0.29
24 7 0.29
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATTAATTCATTATTTTTCTA
Found at i:20687021 original size:20 final size:20
Alignment explanation
Indices: 20686996--20687042 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
20686986 GGAAAAATGT
20686996 AAACCATATTACCCAAAAAC
1 AAACCATATTACCCAAAAAC
*
20687016 AAACCATATTCCCCAAAAAC
1 AAACCATATTACCCAAAAAC
20687036 AAACCAT
1 AAACCAT
20687043 TATCAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (20 bp):
AAACCATATTACCCAAAAAC
Found at i:20693213 original size:11 final size:12
Alignment explanation
Indices: 20693196--20693254 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 12
20693186 ATTGCTCATT
20693196 TTTTATTTATTA
1 TTTTATTTATTA
20693208 -TTTATTTATTA
1 TTTTATTTATTA
* *
20693219 TTTTATTTGTTT
1 TTTTATTTATTA
20693231 TTGTTGATTTATCTA
1 TT-TT-ATTTAT-TA
*
20693246 TTTTTTTTA
1 TTTTATTTA
20693255 GTTTTTAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 11 0.29
12 11 0.29
13 6 0.16
14 7 0.18
15 3 0.08
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.75
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:20694248 original size:8 final size:8
Alignment explanation
Indices: 20694233--20694281 Score: 75
Period size: 8 Copynumber: 6.4 Consensus size: 8
20694223 ATAAAAAAAG
20694233 AATA-AAA
1 AATATAAA
20694240 AATAT-AA
1 AATATAAA
20694247 AATATAAA
1 AATATAAA
*
20694255 AACATAAA
1 AATATAAA
20694263 AATATAAA
1 AATATAAA
20694271 AATATAAA
1 AATATAAA
20694279 AAT
1 AAT
20694282 TTGGGAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
7 11 0.29
8 27 0.71
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (8 bp):
AATATAAA
Found at i:20700454 original size:7 final size:8
Alignment explanation
Indices: 20700441--20700471 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
20700431 TGAAAGAAAG
20700441 AAAAAAAT
1 AAAAAAAT
20700449 AAAAAAAAT
1 -AAAAAAAT
20700458 AAAAAAAT
1 AAAAAAAT
20700466 AAAAAA
1 AAAAAA
20700472 GATGAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:20700455 original size:9 final size:9
Alignment explanation
Indices: 20700441--20700471 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
20700431 TGAAAGAAAG
20700441 AAAAAAATA
1 AAAAAAATA
20700450 AAAAAAAT-
1 AAAAAAATA
20700458 AAAAAAATA
1 AAAAAAATA
20700467 AAAAA
1 AAAAA
20700472 GATGAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:20700496 original size:17 final size:17
Alignment explanation
Indices: 20700425--20700498 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
20700415 ATAATGGGTG
20700425 AAAGAATGAAAGAAAGAAA
1 AAAGAA-GAAA-AAAGAAA
20700444 AAA-ATA-AAAAAA-ATAA
1 AAAGA-AGAAAAAAGA-AA
* **
20700460 AAA-AATAAAAAAGATG
1 AAAGAAGAAAAAAGAAA
20700476 AAAGAAGAAAAAAGAAA
1 AAAGAAGAAAAAAGAAA
20700493 AAAGAA
1 AAAGAA
20700499 ATACTCAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
15 2 0.04
16 18 0.40
17 20 0.44
18 1 0.02
19 4 0.09
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (17 bp):
AAAGAAGAAAAAAGAAA
Found at i:20701318 original size:23 final size:23
Alignment explanation
Indices: 20701287--20701330 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
20701277 GAAACCTCCG
*
20701287 AATGGTGATCAAATGATGAAAAT
1 AATGATGATCAAATGATGAAAAT
**
20701310 AATGATGATCAGTTGATGAAA
1 AATGATGATCAAATGATGAAA
20701331 CTTGTTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.27
Consensus pattern (23 bp):
AATGATGATCAAATGATGAAAAT
Found at i:20701580 original size:21 final size:20
Alignment explanation
Indices: 20701536--20701580 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20701526 TATATTGTTG
*
20701536 CATTTGCATTATTGAGAAAA
1 CATTTGCATTATTGACAAAA
*
20701556 CATTTGCATTATTGATCATAA
1 CATTTGCATTATTGA-CAAAA
20701577 CATT
1 CATT
20701581 CATTGTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (20 bp):
CATTTGCATTATTGACAAAA
Found at i:20701655 original size:22 final size:21
Alignment explanation
Indices: 20701630--20701725 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 21
20701620 AAATCTTTTG
* *
20701630 ATGAGAATTTTTGAGTTCTCAA
1 ATGAGAATCTTTGA-ATCTCAA
*
20701652 ATGAAAATCTTTGAATCTCAA
1 ATGAGAATCTTTGAATCTCAA
* *
20701673 ATGAGAATCTTTAAATTTCAA
1 ATGAGAATCTTTGAATCTCAA
* **
20701694 ATAAGAATCTTCAAAT-TCAA
1 ATGAGAATCTTTGAATCTCAA
20701714 ATGAGAATCTTT
1 ATGAGAATCTTT
20701726 TAGTTTTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 14 0.22
21 38 0.59
22 12 0.19
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (21 bp):
ATGAGAATCTTTGAATCTCAA
Found at i:20702332 original size:42 final size:42
Alignment explanation
Indices: 20702164--20702583 Score: 456
Period size: 42 Copynumber: 9.9 Consensus size: 42
20702154 ATTGTCAAGT
* *
20702164 AGCATTTTATATTTCAAAGTTGTGATTGCCTCTATTTAGA-G
1 AGCATTTTATTTTTCAAAGTTGTGGTTGCCTCTATTTAGATG
* *
20702205 AAACATTTTATTTTTCCTAAAGTTGTGGTTGCCTCTGTTTAGATG
1 -AGCATTTTATTTTT-C-AAAGTTGTGGTTGCCTCTATTTAGATG
* *
20702250 AGCATTTTATTTTTCTTAAAGTTGTGGTTACCTCTGTTTAGATG
1 AGCATTTTATTTTTC--AAAGTTGTGGTTGCCTCTATTTAGATG
* * * *
20702294 AGCATTTTATTTTTCAAAGTTGTAGTTACCTTTATTTAGAGG
1 AGCATTTTATTTTTCAAAGTTGTGGTTGCCTCTATTTAGATG
* *
20702336 AGCATTTTATTTTTCAAAGTTGTAGTTGCCTCTATTTAGAGG
1 AGCATTTTATTTTTCAAAGTTGTGGTTGCCTCTATTTAGATG
** * *
20702378 AATATTTTATTTTTCAAAATTATGGTTGCCTCTATTTAGA-G
1 AGCATTTTATTTTTCAAAGTTGTGGTTGCCTCTATTTAGATG
* * *
20702419 AAGCA-TTT-TGTTTCAAAGTTGTGATTACCTCTATTTAGATG
1 -AGCATTTTATTTTTCAAAGTTGTGGTTGCCTCTATTTAGATG
*
20702460 AGCATTTTATTTTTCAAAGTTGTGGTTGTCTCTATTTAGA-G
1 AGCATTTTATTTTTCAAAGTTGTGGTTGCCTCTATTTAGATG
* ** ** *
20702501 AAACATTTTATTTTTTTTTAAGTTGCAGTTGCTTCTATTTAGATG
1 -AGCATTTTA--TTTTTCAAAGTTGTGGTTGCCTCTATTTAGATG
* *
20702546 AGCAATTTATTTTTCTAAAGTTGTGG-TGCATCTATTTA
1 AGCATTTTATTTTTC-AAAGTTGTGGTTGCCTCTATTTA
20702584 AAGGAGCTTT
Statistics
Matches: 323, Mismatches: 42, Indels: 26
0.83 0.11 0.07
Matches are distributed among these distances:
40 30 0.09
41 9 0.03
42 163 0.50
43 9 0.03
44 110 0.34
45 2 0.01
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.48
Consensus pattern (42 bp):
AGCATTTTATTTTTCAAAGTTGTGGTTGCCTCTATTTAGATG
Found at i:20702467 original size:124 final size:126
Alignment explanation
Indices: 20702164--20702570 Score: 457
Period size: 124 Copynumber: 3.2 Consensus size: 126
20702154 ATTGTCAAGT
* * *
20702164 AGCATTTTATATTTCAAAGTTGTGATTGCCTCTATTTAGAGAAACATTTTATTTTTCCTAAAGTT
1 AGCATTTTATGTTTCAAAGTTGTGATTACCTCTATTTAGAG-AGCATTTTATTTTT-C-AAAGTT
* * * * * *
20702229 GTGGTTGCCTCTGTTTAGATGAGCATTTTATTTTTCTTAAAGTTGTGGTTACCTCTGTTTAGATG
63 GTGGTTGCCTCTATTTAGAGGAACATTTTATTTTTC-TAAAATTATGGTTACCTCTATTTAGATG
* *
20702294 AGCATTTTATTTTTCAAAGTTGT-AGTTACCTTTATTTAGAGGAGCATTTTATTTTTCAAAGTTG
1 AGCATTTTATGTTTCAAAGTTGTGA-TTACCTCTATTTAGA-GAGCATTTTATTTTTCAAAGTTG
* * *
20702358 TAGTTGCCTCTATTTAGAGGAATATTTTATTTTTC-AAAATTATGGTTGCCTCTATTTAGA-G
64 TGGTTGCCTCTATTTAGAGGAACATTTTATTTTTCTAAAATTATGGTTACCTCTATTTAGATG
20702419 AAGCA-TTT-TGTTTCAAAGTTGTGATTACCTCTATTTAGATGAGCATTTTATTTTTCAAAGTTG
1 -AGCATTTTATGTTTCAAAGTTGTGATTACCTCTATTTAGA-GAGCATTTTATTTTTCAAAGTTG
* * * ** * * *
20702482 TGGTTGTCTCTATTTAGAGAAACATTTTATTTTTTTTTAAGT-TGCAGTTGCTTCTATTTAGATG
64 TGGTTGCCTCTATTTAGAGGAACATTTTATTTTTCTAAAATTATG--GTTACCTCTATTTAGATG
* *
20702546 AGCAATTTATTTTTCTAAAGTTGTG
1 AGCATTTTATGTTTC-AAAGTTGTG
20702571 GTGCATCTAT
Statistics
Matches: 240, Mismatches: 26, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
124 82 0.34
125 8 0.03
126 44 0.18
127 4 0.02
128 42 0.17
129 11 0.05
130 48 0.20
131 1 0.00
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.48
Consensus pattern (126 bp):
AGCATTTTATGTTTCAAAGTTGTGATTACCTCTATTTAGAGAGCATTTTATTTTTCAAAGTTGTG
GTTGCCTCTATTTAGAGGAACATTTTATTTTTCTAAAATTATGGTTACCTCTATTTAGATG
Found at i:20702470 original size:82 final size:84
Alignment explanation
Indices: 20702164--20702583 Score: 449
Period size: 86 Copynumber: 5.0 Consensus size: 84
20702154 ATTGTCAAGT
* *
20702164 AGCATTTTATATTTCAAAGTTGTGATTGCCTCTATTTAGA-GAAACATTTTATTTTTCCTAAAGT
1 AGCATTTTATTTTTCAAAGTTGTGATTACCTCTATTTAGATG-AACATTTTATTTTT-C-AAAGT
*
20702228 TGTGGTTGCCTCTGTTTAGATG-
63 TGTGGTTGCCTCTATTTAGA-GA
* * *
20702250 AGCATTTTATTTTTCTTAAAGTTGTGGTTACCTCTGTTTAGATGAGCATTTTATTTTTCAAAGTT
1 AGCATTTTATTTTTC--AAAGTTGTGATTACCTCTATTTAGATGAACATTTTATTTTTCAAAGTT
* * * *
20702315 GTAGTTACCTTTATTTAGAGG
64 GTGGTTGCCTCTATTTAGAGA
* * * * *
20702336 AGCATTTTATTTTTCAAAGTTGT-AGTTGCCTCTATTTAGAGGAATATTTTATTTTTCAAAATTA
1 AGCATTTTATTTTTCAAAGTTGTGA-TTACCTCTATTTAGATGAACATTTTATTTTTCAAAGTTG
20702400 TGGTTGCCTCTATTTAGAGA
65 TGGTTGCCTCTATTTAGAGA
* *
20702420 AGCA-TTT-TGTTTCAAAGTTGTGATTACCTCTATTTAGATGAGCATTTTATTTTTCAAAGTTGT
1 AGCATTTTATTTTTCAAAGTTGTGATTACCTCTATTTAGATGAACATTTTATTTTTCAAAGTTGT
*
20702483 GGTTGTCTCTATTTAGAGA
66 GGTTGCCTCTATTTAGAGA
* ** * * * * *
20702502 AACATTTTATTTTTTTTTAAGTTG-CAGTTGCTTCTATTTAGATGAGCAATTTATTTTTCTAAAG
1 AGCATTTTA--TTTTTCAAAGTTGTGA-TTACCTCTATTTAGATGAACATTTTATTTTTC-AAAG
*
20702566 TTGTGG-TGCATCTATTTA
62 TTGTGGTTGCCTCTATTTA
20702584 AAGGAGCTTT
Statistics
Matches: 283, Mismatches: 39, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
82 68 0.24
83 7 0.02
84 60 0.21
85 2 0.01
86 99 0.35
87 11 0.04
88 35 0.12
89 1 0.00
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.48
Consensus pattern (84 bp):
AGCATTTTATTTTTCAAAGTTGTGATTACCTCTATTTAGATGAACATTTTATTTTTCAAAGTTGT
GGTTGCCTCTATTTAGAGA
Found at i:20702597 original size:166 final size:165
Alignment explanation
Indices: 20702166--20702597 Score: 440
Period size: 166 Copynumber: 2.6 Consensus size: 165
20702156 TGTCAAGTAG
* * * * * *
20702166 CATTTTATATTTCAAAGTTG-TGATTGCCTCTATTTAGAGAAACATTTTATTTTTCCTAAAGTTG
1 CATTTTATTTTTCAAAGTTGCAG-TTGCCTCTATTTAGAGGAACAATTTATTTTT-C-AAAATTA
* * * * * *
20702230 TGGTTGCCTCTGTTTAGATG-AGCATTTTATTTTTCTTAAAGTTGTGGTTACCTCTGTTTAGATG
63 TGGTTGCATCTATTTA-AAGAAGCA--TT-TGTTTC--AAAGTTGTGATTACCTCTATTTAGATG
* * *
20702294 AGCATTTTATTTTTCAAAGTTGTAGTTACCTTTATTTAGAGGAG
122 AGCATTTTATTTTTCAAAGTTGTAGTTACCTCTATTTAGAGAAA
* * *
20702338 CATTTTATTTTTCAAAGTTGTAGTTGCCTCTATTTAGAGGAATATTTTATTTTTCAAAATTATGG
1 CATTTTATTTTTCAAAGTTGCAGTTGCCTCTATTTAGAGGAACAATTTATTTTTCAAAATTATGG
* *
20702403 TTGCCTCTATTTAGAGAAGCATTTTGTTTCAAAGTTGTGATTACCTCTATTTAGATGAGCATTTT
66 TTGCATCTATTTAAAGAAGCA-TTTGTTTCAAAGTTGTGATTACCTCTATTTAGATGAGCATTTT
* **
20702468 ATTTTTCAAAGTTGTGGTTGTCTCTATTTAGAGAAA
130 ATTTTTCAAAGTTGTAGTTACCTCTATTTAGAGAAA
** * * * * *
20702504 CATTTTATTTTTTTTTAAGTTGCAGTTGCTTCTATTTAGATGAGCAATTTATTTTTCTAAAGTTG
1 CATTTTA--TTTTTCAAAGTTGCAGTTGCCTCTATTTAGAGGAACAATTTATTTTTC-AAAATTA
*
20702569 TGG-TGCATCTATTTAAAGGAGC-TTTGTTT
63 TGGTTGCATCTATTTAAAGAAGCATTTGTTT
20702598 AAAAAAAAAA
Statistics
Matches: 224, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
166 77 0.34
168 61 0.27
169 12 0.05
170 24 0.11
171 1 0.00
172 48 0.21
173 1 0.00
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.48
Consensus pattern (165 bp):
CATTTTATTTTTCAAAGTTGCAGTTGCCTCTATTTAGAGGAACAATTTATTTTTCAAAATTATGG
TTGCATCTATTTAAAGAAGCATTTGTTTCAAAGTTGTGATTACCTCTATTTAGATGAGCATTTTA
TTTTTCAAAGTTGTAGTTACCTCTATTTAGAGAAA
Found at i:20704006 original size:17 final size:16
Alignment explanation
Indices: 20703984--20704028 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
20703974 ATTTATTTTC
20703984 AAAATAAAAAAAGAATA
1 AAAATAAAAAAA-AATA
* *
20704001 AAAATATAAAAATATA
1 AAAATAAAAAAAAATA
20704017 AAAATATAAAAA
1 AAAATA-AAAAA
20704029 TTTTGCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (16 bp):
AAAATAAAAAAAAATA
Found at i:20704009 original size:8 final size:8
Alignment explanation
Indices: 20703984--20704029 Score: 65
Period size: 8 Copynumber: 5.6 Consensus size: 8
20703974 ATTTATTTTC
*
20703984 AAAATAAA
1 AAAATATA
*
20703992 AAAAGAATA
1 AAAA-TATA
20704001 AAAATATA
1 AAAATATA
20704009 AAAATATA
1 AAAATATA
20704017 AAAATATA
1 AAAATATA
20704025 AAAAT
1 AAAAT
20704030 TTTGCAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 28 0.82
9 6 0.18
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (8 bp):
AAAATATA
Found at i:20705106 original size:15 final size:18
Alignment explanation
Indices: 20705071--20705105 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20705061 GTGAGAAATC
20705071 TTCCCATTTCTTTCTTTT
1 TTCCCATTTCTTTCTTTT
20705089 TTCCCATTT-TTT-TTTT
1 TTCCCATTTCTTTCTTTT
20705105 T
1 T
20705106 CAAAATTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 3 0.18
18 9 0.53
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (18 bp):
TTCCCATTTCTTTCTTTT
Found at i:20705304 original size:13 final size:12
Alignment explanation
Indices: 20705286--20705315 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
20705276 TTTTCTTCAT
20705286 ATTTTTAATAATG
1 ATTTTTAAT-ATG
20705299 ATTTTTAATATG
1 ATTTTTAATATG
20705311 ATTTT
1 ATTTT
20705316 AGCTTATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (12 bp):
ATTTTTAATATG
Found at i:20705447 original size:158 final size:158
Alignment explanation
Indices: 20705245--20705940 Score: 828
Period size: 158 Copynumber: 4.5 Consensus size: 158
20705235 TTTGTTGTTA
* * * * ** *
20705245 TTGATAATT-TTTTATTTTATCTTCATAATTCTTTTCTTCA-TATTTTTAATAATGATTTTTAAT
1 TTGATAATTGTTTGATTTTGTCTTTATAATTCTTTTCTT-ATTATTTTTATTGGTGATTTTTAAG
* * * * *
20705308 ATGATTTTAGCTTATTCTT-TATTTTTTTATGATT-TAGGATTTGAATGTTAATCTAA-TAAAGA
65 ATGACTTTAGCTGATT-TTCCATTTTTTTATGATTCAAAG-TTTGAATGTTAATCTAACT-AAGA
* * * *
20705370 CTGATTATTGCATGAAATGATTAAATTAGTTC
127 CTGATTATTGCATGAAATGATTGAGTTGGTTT
* *
20705402 TTGATAATTGTTTGATTTTGTCTTTATAATTCTTTTCTTATTATTTCTATTGGTGATTTTTAAGC
1 TTGATAATTGTTTGATTTTGTCTTTATAATTCTTTTCTTATTATTTTTATTGGTGATTTTTAAGA
* * * * *
20705467 TGACTTTAGTTGATTCTCCA-TTTTTTGTGATTCAAAGTTTAAATGTTAATCTAACTAAAACTGA
66 TGACTTTAGCTGATTTTCCATTTTTTTATGATTCAAAGTTTGAATGTTAATCTAACTAAGACTGA
* * * *
20705531 TTGTTACATGAAATGATTGGGTTGGTTA
131 TTATTGCATGAAATGATTGAGTTGGTTT
* * *
20705559 TTGATAGTAGTTTGATTTTGTCTTTATAATTCTTTTCTTTTTATTTTTATTGGTGATTTTTAAGA
1 TTGATAATTGTTTGATTTTGTCTTTATAATTCTTTTCTTATTATTTTTATTGGTGATTTTTAAGA
* * * *
20705624 TGACTTTAGCTGATTTTCCATTTTTTTGTGATTCAAAGTTTGAAGGTTAATCTAACTAAGATTGG
66 TGACTTTAGCTGATTTTCCATTTTTTTATGATTCAAAGTTTGAATGTTAATCTAACTAAGACTGA
* * *
20705689 TTATTGCATGGAATAATTGGGTTGGTTT
131 TTATTGCATGAAATGATTGAGTTGGTTT
* *
20705717 TTGATAATTGTTTAATTTTGTCTTTATAATTCTTTTCTTCTTATTTTTATTGGTGATTTTTAAGA
1 TTGATAATTGTTTGATTTTGTCTTTATAATTCTTTTCTTATTATTTTTATTGGTGATTTTTAAGA
* * *
20705782 TGACTTTAGCTGATTTTCTATTTTTTTTATGATTCAGAGTTTGAA-GATTAATCTAACTAAGAAT
66 TGACTTTAGCTGATTTTCCA-TTTTTTTATGATTCAAAGTTTGAATG-TTAATCTAACTAAGACT
* *
20705846 AATTATTGCATGATATG-TTGAGTTGGTTT
129 GATTATTGCATGAAATGATTGAGTTGGTTT
*
20705875 TTGATAATTTTTTGATTTTGTCTTTATAATTCTTTTC----T-TTTTT-TT-GTGATTTTTAAGA
1 TTGATAATTGTTTGATTTTGTCTTTATAATTCTTTTCTTATTATTTTTATTGGTGATTTTTAAGA
20705933 TGACTTTA
66 TGACTTTA
20705941 ATTAATTCTC
Statistics
Matches: 472, Mismatches: 59, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
151 21 0.04
152 2 0.00
153 5 0.01
154 1 0.00
157 144 0.31
158 249 0.53
159 50 0.11
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.53
Consensus pattern (158 bp):
TTGATAATTGTTTGATTTTGTCTTTATAATTCTTTTCTTATTATTTTTATTGGTGATTTTTAAGA
TGACTTTAGCTGATTTTCCATTTTTTTATGATTCAAAGTTTGAATGTTAATCTAACTAAGACTGA
TTATTGCATGAAATGATTGAGTTGGTTT
Found at i:20707292 original size:17 final size:17
Alignment explanation
Indices: 20707270--20707302 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20707260 ATCTATCTTG
20707270 GTTCTTACTATTGCTTA
1 GTTCTTACTATTGCTTA
*
20707287 GTTCTTGCTATTGCTT
1 GTTCTTACTATTGCTT
20707303 TTGCTACCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.18, G:0.15, T:0.55
Consensus pattern (17 bp):
GTTCTTACTATTGCTTA
Found at i:20708003 original size:121 final size:122
Alignment explanation
Indices: 20707785--20708009 Score: 274
Period size: 121 Copynumber: 1.9 Consensus size: 122
20707775 AAGATAGTTA
** * ** *
20707785 AGTTATTAATTTATACACTATATATTCCTTTGAAAGTATATATATTACATCTTAGATTAATTAGT
1 AGTTATTAATTTATACACTATATATTCAATTGAAAGTATATATATTACATCCTAGATTAACCAAT
* * * *
20707850 GTATGTAGTGTACTTTTAATACATTATATATATTTCATATGCAATCAAGATGGTGGG
66 GTATATAATGTACTTTTAATACACTATATATATTCCATATGCAATCAAGATGGTGGG
* * *
20707907 AGTTATTACTTTATACATTTTATATTCAATTGAAAGTATATAT-TT-CATACCTAGATTAACCAA
1 AGTTATTAATTTATACACTATATATTCAATTGAAAGTATATATATTACAT-CCTAGATTAACCAA
* ***
20707970 TGTATATAATGTATTTTTAATGTGCTATATATATTCCATA
65 TGTATATAATGTACTTTTAATACACTATATATATTCCATA
20708010 GATGATTAAG
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
120 3 0.04
121 44 0.52
122 38 0.45
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (122 bp):
AGTTATTAATTTATACACTATATATTCAATTGAAAGTATATATATTACATCCTAGATTAACCAAT
GTATATAATGTACTTTTAATACACTATATATATTCCATATGCAATCAAGATGGTGGG
Found at i:20710985 original size:19 final size:18
Alignment explanation
Indices: 20710955--20711001 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
20710945 AAAGGCATAC
20710955 AAAACAAAAAAAAATGAA
1 AAAACAAAAAAAAATGAA
20710973 AAAACAAACAAAAAATGAA
1 AAAACAAA-AAAAAATGAA
20710992 AAAA-AAAAAA
1 AAAACAAAAAA
20711002 GAGAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.11
18 11 0.39
19 14 0.50
ACGTcount: A:0.85, C:0.06, G:0.04, T:0.04
Consensus pattern (18 bp):
AAAACAAAAAAAAATGAA
Found at i:20711135 original size:24 final size:25
Alignment explanation
Indices: 20711104--20711155 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
20711094 TAACTTTATT
* * *
20711104 AATAAAAAAT-TATAAAAAATAAAA
1 AATAAAAAATAAAAAAAAAAGAAAA
20711128 AATAAAAAATAAAAAAAAAAGAAAA
1 AATAAAAAATAAAAAAAAAAGAAAA
20711153 AAT
1 AAT
20711156 TATGATAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (25 bp):
AATAAAAAATAAAAAAAAAAGAAAA
Found at i:20711145 original size:18 final size:19
Alignment explanation
Indices: 20711119--20711155 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20711109 AAAATTATAA
*
20711119 AAAATAAAAAATAAAAAAT
1 AAAATAAAAAAGAAAAAAT
20711138 AAAA-AAAAAAGAAAAAAT
1 AAAATAAAAAAGAAAAAAT
20711156 TATGATAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (19 bp):
AAAATAAAAAAGAAAAAAT
Found at i:20711154 original size:7 final size:7
Alignment explanation
Indices: 20711115--20711147 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
20711105 ATAAAAAATT
20711115 ATAAAAA
1 ATAAAAA
20711122 ATAAAAA
1 ATAAAAA
20711129 ATAAAAA
1 ATAAAAA
20711136 ATAAAAA
1 ATAAAAA
20711143 A-AAAA
1 ATAAAA
20711148 GAAAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.15
7 22 0.85
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
ATAAAAA
Found at i:20711629 original size:7 final size:7
Alignment explanation
Indices: 20711630--20711744 Score: 230
Period size: 7 Copynumber: 16.4 Consensus size: 7
20711620 AATAAAAAAT
20711630 AATTAAA
1 AATTAAA
20711637 AATTAAA
1 AATTAAA
20711644 AATTAAA
1 AATTAAA
20711651 AATTAAA
1 AATTAAA
20711658 AATTAAA
1 AATTAAA
20711665 AATTAAA
1 AATTAAA
20711672 AATTAAA
1 AATTAAA
20711679 AATTAAA
1 AATTAAA
20711686 AATTAAA
1 AATTAAA
20711693 AATTAAA
1 AATTAAA
20711700 AATTAAA
1 AATTAAA
20711707 AATTAAA
1 AATTAAA
20711714 AATTAAA
1 AATTAAA
20711721 AATTAAA
1 AATTAAA
20711728 AATTAAA
1 AATTAAA
20711735 AATTAAA
1 AATTAAA
20711742 AAT
1 AAT
20711745 GTGCTAATGA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 108 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATTAAA
Found at i:20713522 original size:25 final size:25
Alignment explanation
Indices: 20713476--20713524 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
20713466 ATCAAGTGAG
**
20713476 TTATTAAAAAATAAAATTTAAAAAA
1 TTATTAAAAAATAAAAAATAAAAAA
*
20713501 TTATTAAAATATAAAAAATAAAAA
1 TTATTAAAAAATAAAAAATAAAAA
20713525 TAAAAAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
TTATTAAAAAATAAAAAATAAAAAA
Found at i:20713529 original size:13 final size:14
Alignment explanation
Indices: 20713480--20713531 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 14
20713470 AGTGAGTTAT
*
20713480 TAAAAAATAAAATT
1 TAAAAAATAAAATA
20713494 TAAAAAATTATTAAAATA
1 T-AAAAA--A-TAAAATA
20713512 TAAAAAATAAAA-A
1 TAAAAAATAAAATA
20713525 TAAAAAA
1 TAAAAAA
20713532 AAGAGAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
13 8 0.24
14 6 0.18
15 6 0.18
17 6 0.18
18 7 0.21
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAAAAATAAAATA
Found at i:20713859 original size:16 final size:17
Alignment explanation
Indices: 20713823--20713858 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
20713813 AAAAATTATT
*
20713823 AAATTATAAAAAAAGAA
1 AAATTAGAAAAAAAGAA
20713840 AAATTAGAAAAAAAGAA
1 AAATTAGAAAAAAAGAA
20713857 AA
1 AA
20713859 TGTTACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (17 bp):
AAATTAGAAAAAAAGAA
Found at i:20714553 original size:27 final size:28
Alignment explanation
Indices: 20714493--20714556 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 28
20714483 AATTTTAAAC
* *
20714493 TAAA-TTTTATTTTGATATCTATTTTTT
1 TAAAGTTTTAATTTGATATCTATTTTTA
*
20714520 TTAAGTTTTAATTTGATATCTA-TTTTA
1 TAAAGTTTTAATTTGATATCTATTTTTA
20714547 TAAAGTTTTA
1 TAAAGTTTTA
20714557 TTATTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 16 0.50
28 16 0.50
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (28 bp):
TAAAGTTTTAATTTGATATCTATTTTTA
Found at i:20714845 original size:13 final size:13
Alignment explanation
Indices: 20714824--20714853 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20714814 TCCATCTTGT
*
20714824 AAAATAAAAAATA
1 AAAACAAAAAATA
20714837 AAAACAAAAAATA
1 AAAACAAAAAATA
20714850 AAAA
1 AAAA
20714854 AATTGGTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAACAAAAAATA
Found at i:20715109 original size:31 final size:30
Alignment explanation
Indices: 20715014--20715110 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 30
20715004 TCATTCTAAC
* * *
20715014 AAATTTCACATCATTTTAAAAATTAAGGAGA
1 AAATTTCATATCACTTTAAAAATTAAGTA-A
* * *
20715045 AAATTTTATATCATTTTAGAAAAATTAAATAA
1 AAATTTCATATCACTTT--AAAAATTAAGTAA
**
20715077 AAATTTCATATTGCTTTAAAATATTAAGTAA
1 AAATTTCATATCACTTTAAAA-ATTAAGTAA
20715108 AAA
1 AAA
20715111 ATTGCATTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
30 4 0.07
31 26 0.48
32 14 0.26
33 10 0.19
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (30 bp):
AAATTTCATATCACTTTAAAAATTAAGTAA
Found at i:20717309 original size:33 final size:33
Alignment explanation
Indices: 20717271--20717360 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
20717261 TACTACTTTA
20717271 TTATTTTTTCATTATTTGAATATAA-TT--TTAT
1 TTATTTTTT-ATTATTTGAATATAATTTAATTAT
* * *
20717302 TT-TTATTTATTATTTTAATATAATATAATTAT
1 TTATTTTTTATTATTTGAATATAATTTAATTAT
* *
20717334 TTATTTTTTATTGTTTGGATATAATTT
1 TTATTTTTTATTATTTGAATATAATTT
20717361 GATCACTTGC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
29 14 0.30
30 6 0.13
31 2 0.04
32 6 0.13
33 19 0.40
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (33 bp):
TTATTTTTTATTATTTGAATATAATTTAATTAT
Found at i:20717321 original size:29 final size:30
Alignment explanation
Indices: 20717267--20717345 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
20717257 TGACTACTAC
20717267 TTTATTATTT-TTTCATTATTTGAATATAAT
1 TTTATTATTTATTT-ATTATTTGAATATAAT
*
20717297 TTTATT-TTTATTTATTATTTTAATATAAT
1 TTTATTATTTATTTATTATTTGAATATAAT
* * *
20717326 ATAATTATTTATTTTTTATT
1 TTTATTATTTATTTATTATT
20717346 GTTTGGATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (30 bp):
TTTATTATTTATTTATTATTTGAATATAAT
Found at i:20720690 original size:32 final size:31
Alignment explanation
Indices: 20720651--20720773 Score: 104
Period size: 32 Copynumber: 3.9 Consensus size: 31
20720641 TTAATAAATC
*
20720651 AATTTTTAAAATGATATAAAAAATTTTACTT
1 AATTTTTAAAATAATATAAAAAATTTTACTT
* * **
20720682 AATATTTTAAAACAATAT-ATAGTTTCTTACTT
1 AAT-TTTTAAAATAATATAAAAAATT-TTACTT
* * * * * *
20720714 AATTTTCAAACTATTTTAGAAAATTTTATTT
1 AATTTTTAAAATAATATAAAAAATTTTACTT
*
20720745 AATTTTTTAAAATAATATGAAAAATTTTA
1 AA-TTTTTAAAATAATATAAAAAATTTTA
20720774 AAAAGAGTAT
Statistics
Matches: 67, Mismatches: 21, Indels: 7
0.71 0.22 0.07
Matches are distributed among these distances:
31 23 0.34
32 44 0.66
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (31 bp):
AATTTTTAAAATAATATAAAAAATTTTACTT
Found at i:20720777 original size:21 final size:20
Alignment explanation
Indices: 20720748--20720794 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
20720738 TTTATTTAAT
* *
20720748 TTTTTAAAATAATATGAAAAA
1 TTTTAAAAAGAATATG-AAAA
*
20720769 TTTTAAAAAGAGTATGAAAA
1 TTTTAAAAAGAATATGAAAA
20720789 TTTTAA
1 TTTTAA
20720795 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (20 bp):
TTTTAAAAAGAATATGAAAA
Found at i:20721684 original size:20 final size:22
Alignment explanation
Indices: 20721661--20721717 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 22
20721651 ATAATAATTT
20721661 TATATTAAAATTTAT-TT-AAA
1 TATATTAAAATTTATATTAAAA
20721681 TATATTAAAATTTTATATTAAAA
1 TATATTAAAA-TTTATATTAAAA
20721704 TAATATATAAAATT
1 T-ATAT-TAAAATT
20721718 GAATTAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.31
21 5 0.16
22 2 0.06
23 4 0.12
24 6 0.19
25 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATATTAAAATTTATATTAAAA
Found at i:20721699 original size:13 final size:13
Alignment explanation
Indices: 20721656--20721717 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 13
20721646 TAAAAATAAT
20721656 AATTTTATATTAA
1 AATTTTATATTAA
20721669 AA-TTTAT-TT-A
1 AATTTTATATTAA
20721679 AA---TATATTAA
1 AATTTTATATTAA
20721689 AATTTTATATTAA
1 AATTTTATATTAA
**
20721702 AATAATATA-TAA
1 AATTTTATATTAA
20721714 AATT
1 AATT
20721718 GAATTAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
8 3 0.07
9 2 0.05
10 6 0.15
11 2 0.05
12 11 0.27
13 17 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTTTATATTAA
Found at i:20731590 original size:22 final size:22
Alignment explanation
Indices: 20731562--20731605 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20731552 CTAAATCTTC
*
20731562 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20731584 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20731606 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:20735482 original size:22 final size:22
Alignment explanation
Indices: 20735454--20735497 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20735444 CTAAATCTTC
*
20735454 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20735476 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20735498 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:20737022 original size:116 final size:116
Alignment explanation
Indices: 20736818--20737048 Score: 399
Period size: 116 Copynumber: 2.0 Consensus size: 116
20736808 ACTGAGCCCC
* *
20736818 AGGTTCAGTAGGTCCTGTTAGTCATTTTGCTTCTGTCTAACTTATTTCTTATGTTTATGGGAGCT
1 AGGTTCAGTAGGTCCTGTTAGTCATTTTGCTTCAGTCTAACTTATTTCTTACGTTTATGGGAGCT
* *
20736883 GCCATTAGAGGATTTAGCCCTAATCATCCCCCTAAGGCAGCTGGGTGAACT
66 ACCATTAGAGGATTTAGACCTAATCATCCCCCTAAGGCAGCTGGGTGAACT
* *
20736934 AGGTTCATTAGGTCCTGTTAGTCATTTTGCTTCAGTCTAACTTATTTTTTACGTTTATGGGAGCT
1 AGGTTCAGTAGGTCCTGTTAGTCATTTTGCTTCAGTCTAACTTATTTCTTACGTTTATGGGAGCT
*
20736999 ACCATTGGAGGATTTAGACCTAATCATCCCCCTAAGGCAGCTGGGTGAAC
66 ACCATTAGAGGATTTAGACCTAATCATCCCCCTAAGGCAGCTGGGTGAAC
20737049 CATTGAGATT
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 108 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (116 bp):
AGGTTCAGTAGGTCCTGTTAGTCATTTTGCTTCAGTCTAACTTATTTCTTACGTTTATGGGAGCT
ACCATTAGAGGATTTAGACCTAATCATCCCCCTAAGGCAGCTGGGTGAACT
Found at i:20737790 original size:103 final size:102
Alignment explanation
Indices: 20737560--20737790 Score: 214
Period size: 103 Copynumber: 2.2 Consensus size: 102
20737550 TTTTTTTGTG
* * * * * *
20737560 TAAAAAAAACTTTTATTTATGAAAACAATTTATTTTCAAAAATATCTTCCAATATGTTAATAAAA
1 TAAAAAATATTTTTTTTTA-GAAAAAAAATTATTTTCAAAAATATCTTCCAATATATTAATAAAA
* **
20737625 TTTTTTGTCAAAAATTATCCTCCAATATGTTAGTAGGATT
65 TTTTTCGTC--AAATTATCCTCCAATATGTTAGTAAAATT
* ** * * * ** ** *
20737665 GAAAATTTATTTGTTTGT-GAAAAAAAATTATTTTCAGAAATATCTTTTAATATATTGGTAAGAT
1 TAAAAAATATTTTTTTTTAGAAAAAAAATTATTTTCAAAAATATCTTCCAATATATTAATAAAAT
*
20737729 TTTTCGTC-AATTATCCTCCAATATGTTTGTAAAATTT
66 TTTTCGTCAAATTATCCTCCAATATGTTAGTAAAA-TT
20737766 TAAAAAATATTTTTTTTTAAGAAAA
1 TAAAAAATATTTTTTTTT-AGAAAA
20737791 TTCATCAAGT
Statistics
Matches: 97, Mismatches: 26, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
100 23 0.24
101 15 0.15
103 49 0.51
105 10 0.10
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.43
Consensus pattern (102 bp):
TAAAAAATATTTTTTTTTAGAAAAAAAATTATTTTCAAAAATATCTTCCAATATATTAATAAAAT
TTTTCGTCAAATTATCCTCCAATATGTTAGTAAAATT
Found at i:20737959 original size:22 final size:21
Alignment explanation
Indices: 20737934--20737986 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
20737924 ATCATGCAAA
20737934 ATAATATTATACAAATAATAAT
1 ATAATATTATACAAATAAT-AT
* * *
20737956 ATAATATCATGCAATTAATAT
1 ATAATATTATACAAATAATAT
*
20737977 AAAATATTAT
1 ATAATATTAT
20737987 GTAAATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAATATTATACAAATAATAT
Found at i:20738181 original size:21 final size:20
Alignment explanation
Indices: 20738156--20738234 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 20
20738146 ATTAAAATAT
*
20738156 AAATATAAAAATAATATAACA
1 AAATA-AAAAATAAAATAACA
*
20738177 AAATAGAAAAATAAAATAAGA
1 AAATA-AAAAATAAAATAACA
* * *
20738198 AAAT-AAAAATCAAACAAAA
1 AAATAAAAAATAAAATAACA
*
20738217 AAATAAAAAAGAAAATAA
1 AAATAAAAAATAAAATAA
20738235 ACAAGAAAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
19 16 0.33
20 10 0.21
21 22 0.46
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (20 bp):
AAATAAAAAATAAAATAACA
Found at i:20738231 original size:12 final size:12
Alignment explanation
Indices: 20738176--20738243 Score: 57
Period size: 12 Copynumber: 5.3 Consensus size: 12
20738166 ATAATATAAC
*
20738176 AAAATAGAAAAAT
1 AAAATA-AAAAAG
*
20738189 AAAATAAGAAAATA
1 AAAATAA-AAAA-G
20738203 AAAATCAAACAAA-
1 AAAAT-AAA-AAAG
20738216 AAAATAAAAAAG
1 AAAATAAAAAAG
*
20738228 AAAATAAACAAG
1 AAAATAAAAAAG
20738240 AAAA
1 AAAA
20738244 GAAATGAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
11 3 0.06
12 19 0.40
13 15 0.31
14 6 0.12
15 5 0.10
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.10
Consensus pattern (12 bp):
AAAATAAAAAAG
Found at i:20738255 original size:24 final size:25
Alignment explanation
Indices: 20738189--20738247 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
20738179 ATAGAAAAAT
* *
20738189 AAAATAAGAAAATA-AAAATCAAAC
1 AAAAAAAGAAAAAAGAAAATCAAAC
*
20738213 AAAAAAATAAAAAAGAAAAT-AAAC
1 AAAAAAAGAAAAAAGAAAATCAAAC
*
20738237 AAGAAAAGAAA
1 AAAAAAAGAAA
20738248 TGAGAAAACC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.80, C:0.05, G:0.07, T:0.08
Consensus pattern (25 bp):
AAAAAAAGAAAAAAGAAAATCAAAC
Found at i:20739955 original size:22 final size:22
Alignment explanation
Indices: 20739915--20739982 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
20739905 ATCATGCAAA
* * *
20739915 ATAATATTATGCAAATAATAAT
1 ATAATATAATACAATTAATAAT
*
20739937 ATAATATCATACAATTAAT-AT
1 ATAATATAATACAATTAATAAT
* *
20739958 AAAATATAATGAAAATTAATTAAT
1 ATAATATAAT-ACAATTAA-TAAT
20739982 A
1 A
20739983 ATCATGAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
21 10 0.27
22 23 0.62
23 1 0.03
24 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.35
Consensus pattern (22 bp):
ATAATATAATACAATTAATAAT
Found at i:20741065 original size:17 final size:17
Alignment explanation
Indices: 20741043--20741080 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
20741033 ATAAATCACA
*
20741043 AAAATTGAATT-TAAATT
1 AAAATTAAATTGT-AATT
20741060 AAAATTAAATTGTAATT
1 AAAATTAAATTGTAATT
20741077 AAAA
1 AAAA
20741081 ATTTTGTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (17 bp):
AAAATTAAATTGTAATT
Found at i:20743652 original size:27 final size:27
Alignment explanation
Indices: 20743609--20743670 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
20743599 AGGTTGGGTA
*
20743609 GGTTGAGAATCTGGTTTTGAAGGGGCT
1 GGTTGAGAATCTAGTTTTGAAGGGGCT
*
20743636 GGTTGAGATTCTAGTTTTGAAGGGGCT
1 GGTTGAGAATCTAGTTTTGAAGGGGCT
20743663 GGTT-AGAA
1 GGTTGAGAA
20743671 AATTGGCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.21, C:0.06, G:0.39, T:0.34
Consensus pattern (27 bp):
GGTTGAGAATCTAGTTTTGAAGGGGCT
Found at i:20745790 original size:21 final size:21
Alignment explanation
Indices: 20745742--20745784 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
20745732 AGAAAAGTTA
**
20745742 AAAAAAAAACCCAAAAAACTC
1 AAAAAAATTCCCAAAAAACTC
20745763 AAAAAAATTCCCAAAAAACTC
1 AAAAAAATTCCCAAAAAACTC
20745784 A
1 A
20745785 GTAAAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.67, C:0.23, G:0.00, T:0.09
Consensus pattern (21 bp):
AAAAAAATTCCCAAAAAACTC
Found at i:20746179 original size:21 final size:22
Alignment explanation
Indices: 20746145--20746186 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
20746135 AAAATATCCA
*
20746145 CTTTGTTTCTTTTTCTACTTTC
1 CTTTATTTCTTTTTCTACTTTC
*
20746167 CTTTATTT-TTTTTTTACTTT
1 CTTTATTTCTTTTTCTACTTT
20746187 TGACTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (22 bp):
CTTTATTTCTTTTTCTACTTTC
Found at i:20746179 original size:22 final size:21
Alignment explanation
Indices: 20746145--20746186 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
20746135 AAAATATCCA
*
20746145 CTTTGTTTCTTTTTCTACTTTC
1 CTTTATTTCTTTTT-TACTTTC
*
20746167 CTTTATTTTTTTTTTACTTT
1 CTTTATTTCTTTTTTACTTT
20746187 TGACTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (21 bp):
CTTTATTTCTTTTTTACTTTC
Found at i:20746243 original size:12 final size:12
Alignment explanation
Indices: 20746223--20746261 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
20746213 ACAAAAATCG
*
20746223 AATCTAAATTAA
1 AATCAAAATTAA
20746235 AATCAAAATTAA
1 AATCAAAATTAA
*
20746247 AATCAAGATTAA
1 AATCAAAATTAA
20746259 AAT
1 AAT
20746262 TGAAATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (12 bp):
AATCAAAATTAA
Found at i:20746249 original size:18 final size:18
Alignment explanation
Indices: 20746228--20746283 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
20746218 AATCGAATCT
* *
20746228 AAATTAAAATCAAAATTA
1 AAATCAAAATTAAAATTA
* *
20746246 AAATCAAGATTAAAATTG
1 AAATCAAAATTAAAATTA
*
20746264 AAATC-AAATTACAATTA
1 AAATCAAAATTAAAATTA
20746281 AAA
1 AAA
20746284 ATTTTGGACT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATCAAAATTAAAATTA
Found at i:20746285 original size:18 final size:18
Alignment explanation
Indices: 20746239--20746283 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
20746229 AATTAAAATC
20746239 AAAATTAAAATCAAGATT
1 AAAATTAAAATCAAGATT
*
20746257 AAAATTGAAATCAA-ATT
1 AAAATTAAAATCAAGATT
*
20746274 ACAATTAAAA
1 AAAATTAAAA
20746284 ATTTTGGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (18 bp):
AAAATTAAAATCAAGATT
Found at i:20754379 original size:22 final size:21
Alignment explanation
Indices: 20754349--20754390 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20754339 AAAAATGGCA
20754349 GAAAACTAAAAAAATCAAATGT
1 GAAAACT-AAAAAATCAAATGT
* *
20754371 GAAAGCTAAAAACTCAAATG
1 GAAAACTAAAAAATCAAATG
20754391 CATTGAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (21 bp):
GAAAACTAAAAAATCAAATGT
Found at i:20755419 original size:20 final size:21
Alignment explanation
Indices: 20755391--20755445 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
20755381 TAAAAAATTA
20755391 TTTTT-TTTAATTAAT-TAAT
1 TTTTTATTTAATTAATATAAT
20755410 TTTTTATTT-A-TATATATAAT
1 TTTTTATTTAATTA-ATATAAT
*
20755430 TTTATATTTATATTAA
1 TTTTTATTTA-ATTAA
20755446 AAATATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
18 2 0.07
19 8 0.28
20 15 0.52
22 2 0.07
23 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTATTTAATTAATATAAT
Found at i:20755832 original size:1 final size:1
Alignment explanation
Indices: 20755826--20755853 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
20755816 CTCCATTGCT
20755826 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
20755854 CCTTGCTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20756314 original size:27 final size:27
Alignment explanation
Indices: 20756284--20756350 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 27
20756274 TTAAGAGTAG
* *
20756284 ATAAATTATTAAATTT-TTTATATTAAA
1 ATAAATTATTAAATTTAATAAT-TTAAA
*
20756311 ATAAAATATATTATATTTAATAATTTAAA
1 AT-AAAT-TATTAAATTTAATAATTTAAA
*
20756340 ATAAATAATTA
1 ATAAATTATTA
20756351 TAAATTATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 6 0.18
28 8 0.24
29 16 0.48
30 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAAATTATTAAATTTAATAATTTAAA
Found at i:20780994 original size:28 final size:28
Alignment explanation
Indices: 20780954--20781031 Score: 104
Period size: 27 Copynumber: 2.8 Consensus size: 28
20780944 TTTGGTTAAG
* *
20780954 AATGATTGTTTGAAATCTTATAAGTGCA
1 AATGATTGTTTGAAATCTTACAAGGGCA
*
20780982 AATGATTGTTTG-AATTTTACAAGGGCA
1 AATGATTGTTTGAAATCTTACAAGGGCA
* *
20781009 AAAGATTGGTTGAAATCTTACAA
1 AATGATTGTTTGAAATCTTACAA
20781032 ATAATGATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 22 0.51
28 21 0.49
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (28 bp):
AATGATTGTTTGAAATCTTACAAGGGCA
Found at i:20783469 original size:15 final size:15
Alignment explanation
Indices: 20783449--20783477 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20783439 TGAGATGGAT
20783449 CATATATGGTTAGAC
1 CATATATGGTTAGAC
20783464 CATATATGGTTAGA
1 CATATATGGTTAGA
20783478 AAGCTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (15 bp):
CATATATGGTTAGAC
Found at i:20787927 original size:26 final size:26
Alignment explanation
Indices: 20787875--20787939 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
20787865 AGGGTTTGGT
* * * *
20787875 AATGAAGGCCT-AAATAGGATTCGAC
1 AATGAATGCCTAAAATAGAAGTCAAC
20787900 AATGAATGCCTAAAATAGAAGTCAAC
1 AATGAATGCCTAAAATAGAAGTCAAC
20787926 AATGAATG-CTAAAA
1 AATGAATGCCTAAAA
20787940 ATTTTACTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 16 0.46
26 19 0.54
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (26 bp):
AATGAATGCCTAAAATAGAAGTCAAC
Found at i:20788197 original size:22 final size:22
Alignment explanation
Indices: 20788159--20788202 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
20788149 TTTTTTATCC
*
20788159 TTAATTTTAGGGATACAAATAT
1 TTAATTCTAGGGATACAAATAT
20788181 TTAATTCTAGAGG-TACAAATAT
1 TTAATTCTAG-GGATACAAATAT
20788203 ATATATACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.39
Consensus pattern (22 bp):
TTAATTCTAGGGATACAAATAT
Found at i:20792672 original size:2 final size:2
Alignment explanation
Indices: 20792665--20792692 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20792655 TCAATTAGTA
20792665 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
20792693 TTCACGACAA
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:20806542 original size:21 final size:22
Alignment explanation
Indices: 20806517--20806562 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
20806507 TAAATATTAA
*
20806517 TAAATAATAATGGTTTT-AAAT
1 TAAATAATAATGATTTTAAAAT
20806538 TAAATAATAATGATTTTAAAAT
1 TAAATAATAATGATTTTAAAAT
20806560 TAA
1 TAA
20806563 TTTTTTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
TAAATAATAATGATTTTAAAAT
Found at i:20815030 original size:2 final size:2
Alignment explanation
Indices: 20815018--20815050 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
20815008 GGATGGATAG
*
20815018 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
20815051 CAGAAGCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Done.