Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 171 of 195
Found at i:28493436 original size:20 final size:18
Alignment explanation
Indices: 28493405--28493451 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 18
28493395 GTTAGTAATG
28493405 TAAAAGAAATAATATTATAAA
1 TAAAA-AAATAA-ATT-TAAA
28493426 TAAAAAAATAAATTTAAA
1 TAAAAAAATAAATTTAAA
*
28493444 CAAAAAAA
1 TAAAAAAA
28493452 GTTAATGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 11 0.44
19 3 0.12
20 6 0.24
21 5 0.20
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
TAAAAAAATAAATTTAAA
Found at i:28494086 original size:21 final size:22
Alignment explanation
Indices: 28494062--28494108 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
28494052 ACACCATGTG
28494062 TAAAAAAATATTATT-ATAACA
1 TAAAAAAATATTATTGATAACA
* *
28494083 T-AAATAATATTTTTGATAACA
1 TAAAAAAATATTATTGATAACA
28494104 TAAAA
1 TAAAA
28494109 GAATTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 11 0.50
21 8 0.36
22 3 0.14
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAAAAATATTATTGATAACA
Found at i:28494093 original size:20 final size:21
Alignment explanation
Indices: 28494068--28494107 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28494058 TGTGTAAAAA
28494068 AATATTATT-ATAACATAAAT
1 AATATTATTGATAACATAAAT
*
28494088 AATATTTTTGATAACATAAA
1 AATATTATTGATAACATAAA
28494108 AGAATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (21 bp):
AATATTATTGATAACATAAAT
Found at i:28495455 original size:16 final size:16
Alignment explanation
Indices: 28495434--28495468 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28495424 AAAAGATATT
* *
28495434 ATTGAAATGTAATAAA
1 ATTGAAACGTAAAAAA
28495450 ATTGAAACGTAAAAAA
1 ATTGAAACGTAAAAAA
28495466 ATT
1 ATT
28495469 AGTATTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.11, T:0.29
Consensus pattern (16 bp):
ATTGAAACGTAAAAAA
Found at i:28495502 original size:18 final size:20
Alignment explanation
Indices: 28495481--28495521 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
28495471 TATTATAAAT
28495481 AAAAATAACTG-TAAA-TAA
1 AAAAATAACTGTTAAAGTAA
*
28495499 AAAAATAAGTGTTAAAGTAA
1 AAAAATAACTGTTAAAGTAA
28495519 AAA
1 AAA
28495522 GATGAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 4 0.20
20 6 0.30
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (20 bp):
AAAAATAACTGTTAAAGTAA
Found at i:28495914 original size:926 final size:914
Alignment explanation
Indices: 28494061--28495991 Score: 1977
Period size: 926 Copynumber: 2.1 Consensus size: 914
28494051 AACACCATGT
* * *
28494061 GTAAAAAAATATTATTATAACATAAATAATATTTTTGATAACATAAAAGAATTATAAATAATTAA
1 GTAAAAAAATATTATTATAACATAAATAATACTTTTGACAACATAAAAGAATTATAAATAATAAA
* * * * *
28494126 TAATTAATAATTAAAAAAAAGTATTAGTATAAAAAAGTGAAAGTAATCATAATATTGATATTATT
66 TAAATAATAATTAAAAAAAAGTATTAATATAAAAAAGTGAAAGTAATCATAAAAATGATATCATT
* ** * * *
28494191 TGGTATAAAATGGTTAAAAATATTGTAACACTTTTAAGAAAAAAGTTATAGTACTTCTAAATATA
131 TAGTATAAAATGGTTAAAAATATCATAACACTTTTAAGAAAAAAGTTATAATAATTCTAAACATA
* *
28494256 ATGAAAAGTAACAATAAGCGTAAAAAGATATTATTAGAATATAAATAATTAAGTTGACAATATAA
196 ATGAAAAGTAACAACAAACGTAAAAAGATATTATTAGAATATAAATAATTAAGTTGACAATATAA
* ** ** * *
28494321 AATAACTATTAATACAAATAAAAAATAATTTTAAGTAAAAAGTTAAGAATTAATATAAAATAGTG
261 AAAAACTATTAATACAAATAAAAAATAATTTTAACAAAAAAAATAAGAATTAACATAAAATAGTA
* * * *
28494386 AGAATAATAATAAAATTGATATTATTTAACATAAAACAGTTAGAAGAATTGTTACACCTTAAGAA
326 AAAATAATAATAAAATTAATATTATTTAACATAAAACAGTTAGAAGAATCGTTACACCTTAAAAA
* * * *
28494451 AAAAATTGTAATAATTCTAAATGTAATGAAAATTAATAATAAATGTAAAAAGATATTATTAAAAT
391 AAAAATTGTAATAATTCTAAATGTAATGAAAAGTAACAACAAACGTAAAAAGATATTATTAAAAT
* * * *
28494516 GTAATAAATTGGTAACGTAGAAAAATTAGTATTATAAATAAAAAAACAATTCAATCAAAAAATAA
456 GTAATAAATTGGAAACGTAAAAAAATTAGTATTATAAATAAAAAAAC-ATTAAATAAAAAAATAA
* ** *
28494581 GTGTTAATGTAAACAAGTGAAAATAATTGTAAAATTGATATCATTTGGTGAAAAATATATTAAAA
520 GTGTTAAAGTAAACAAGTGAAAATAATCATAAAATTGATATAATTTGGTGAAAAATATATTAAAA
* * * *
28494646 GCATTGTAATACTTTAAGAAAAACTTGTGATAATTTTAAACATAATAAAAAATAACAACAAGTGC
585 GCATTGTAATACTTTAAGAAAAACATGTGATAATTCTAAACAAAATAAAAAATAACAACAAATGC
* * *
28494711 AAAAAATTTTAGGATAACATAAATATAAGTTGACAATATAAAAATATTATTATTATAAATAAAAA
650 AAAAAATTTTAGGATAACACAAATATAAATTGACAATATAAAAATATTATTATTATAAACAAAAA
* * *
28494776 ATAATTCTAAACAAAAAATACGTGTTACCATAAAAATATAAGAATAATTAAAAATTTAAAATTAT
715 ACAATTCTAAACAAAAAATACGTGTTAACATAAAAATATAAGAATAATTAAAAATTTAAAATAAT
** * * * * * * ** * *
28494841 TTGGTGTAAAATATATTACAATGTCATAATGTAATAATTGTAAAATTGGTGTCATATAATGTAAA
780 TTAATATAAAATATATTAAAATATCATAACGTAATAAATGTAAAATTAGTGAAAAATAATATAAA
* *
28494906 TTGGATTAAAAGCCTCATAACACCTTAATAAAAAATTATAATAATTCTAAATGTAACAAAAAGTA
845 TTGGATTAAAA--CTCATAACACCTTAAGAAAAAATTATAATAATTCTAAACGTAACAAAAAGTA
28494971 AGAACAA
908 AGAACAA
* * * * *
28494978 GTATAAAAAATATTATTGTAACATAAATAATACTTTTGGCAATATAAAATAATTATTAAT-ATAA
1 GTA-AAAAAATATTATTATAACATAAATAATACTTTTGACAACATAAAAGAATTATAAATAATAA
* *
28495042 ATAAATAATAATTCTAAACAAAAAAGTAAGTGTTAATATAAAAAATGTGAGAGTAATTATAAAAA
65 ATAAATAATAA-T-T-AA-AAAAAAGT-A---TTAATATAAAAAA-GTGAAAGTAATCATAAAAA
* *
28495107 TGATATCATTTAGTATAAAAT-GTTAGAAATATCATAATA-TCTTTAAG-AAAAAGTTATAATAA
121 TGATATCATTTAGTATAAAATGGTTAAAAATATCATAACACT-TTTAAGAAAAAAGTTATAATAA
* * * *
28495169 -TCTTAAACATAATGAAAGGTAGCAACAAACGTAAAAATATATTATTATAATATAAATAATTAAG
185 TTC-TAAACATAATGAAAAGTAACAACAAACGTAAAAAGATATTATTAGAATATAAATAATTAAG
* * * * *
28495233 TTGATAATGTAAAAAAATTATTATTACAAATAAAAAATAATTTTAAACAAAAAAAATAAGAGTTA
249 TTGACAATATAAAAAAACTATTAATACAAATAAAAAATAATTTT-AACAAAAAAAATAAGAATTA
* * ** ** *
28495298 ACATAAAATAGTAAAAATAATCATAAAATTAATATTATTTTATGTAAAATGGTTATAA-ATATCG
313 ACATAAAATAGTAAAAATAATAATAAAATTAATATTATTTAACATAAAACAGTTAGAAGA-ATCG
** * *
28495362 TTACATGTTAACAAAAAAAATTGTAATAATTTTAAATGTACTGAAAAGTAACAACAAACGTAAAA
377 TTACACCTTAA-AAAAAAAATTGTAATAATTCTAAATGTAATGAAAAGTAACAACAAACGTAAAA
*
28495427 AGATATTATTGAAATGTAATAAAATT-GAAACGTAAAAAAATTAGTATTATAAATAAAAATAAC-
441 AGATATTATTAAAATGTAAT-AAATTGGAAACGTAAAAAAATTAGTATTATAAATAAAAA-AACA
28495490 TGTAAATAAAAAAATAAGTGTTAAAGTAAA-AAGATGAAAATAATCATAAAATTCG-TATAATTT
504 T-TAAATAAAAAAATAAGTGTTAAAGTAAACAAG-TGAAAATAATCATAAAATT-GATATAATTT
** * ** ** * * *
28495553 GGTTTAAAATATGTTTGAAGTGTTGTGATAC-TTAAGAAAAAGATGTGATAATTCTAAATAAAAT
566 GGTGAAAAATATATTAAAAGCATTGTAATACTTTAAGAAAAACATGTGATAATTCTAAACAAAAT
** * * * * * * * *
28495617 AAAATGTAAGAACAAATGTAATAGATTTTATTG-TGACGCAAATAATTAAATTGATAATAT-AAA
631 AAAAAATAACAACAAATGCAAAAAATTTTA-GGATAACACAAAT-A-TAAATTGACAATATAAAA
* * * * * *
28495680 A-ATTATTATTATAAACAAAAAACAATTCTAAATCTAAAAATAAC-TGTTAATATGAAACTGTGA
693 ATATTATTATTATAAACAAAAAACAATTCTAAA-CAAAAAAT-ACGTGTTAACATAAAAATATAA
* ** * * **
28495743 GAATAGCTGT-AAAA-TTAGTATAATTTAATATAAAATGTGTTAAAAATATTGTAACGTAA-AAA
756 GAATA-AT-TAAAAATTTAAAATAATTTAATATAAAATATATT-AAAATATCATAACGTAATAAA
* * ** ** * * *
28495805 TGTAAGAA-TAGTCGAAAAATTAATAT-CATTTGATGTACTA-TTGTAATA-CTCTAAGGAAAAG
818 TGTAA-AATTAGT-GAAAAA-TAATATAAATTGGAT-TAAAACTCATAACACCT-TAAGAAAAAA
* * *
28495866 TTGTAATAATTCTAAACGTAATAAAGTA-TAAGAACAA
878 TTATAATAATTCTAAACGTAACAAA-AAGTAAGAACAA
* * ** * * * *
28495903 GCGTAAAAAAATATTATTTTAGCATAAATAATTA-AATTGATAACATAAAAAAATTAT-TATTAT
1 --GTAAAAAAATATTATTATAACATAAATAA-TACTTTTGACAACATAAAAGAATTATAAATAAT
*
28495966 AAATAAAAAAATAATTCAATAAAAAA
63 AAAT-AAATAATAATT-AA-AAAAAA
28495992 ACATTGTTTA
Statistics
Matches: 825, Mismatches: 150, Indels: 70
0.79 0.14 0.07
Matches are distributed among these distances:
917 16 0.02
918 50 0.06
919 1 0.00
920 2 0.00
921 8 0.01
922 1 0.00
923 2 0.00
924 110 0.13
925 251 0.30
926 311 0.38
927 64 0.08
928 9 0.01
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (914 bp):
GTAAAAAAATATTATTATAACATAAATAATACTTTTGACAACATAAAAGAATTATAAATAATAAA
TAAATAATAATTAAAAAAAAGTATTAATATAAAAAAGTGAAAGTAATCATAAAAATGATATCATT
TAGTATAAAATGGTTAAAAATATCATAACACTTTTAAGAAAAAAGTTATAATAATTCTAAACATA
ATGAAAAGTAACAACAAACGTAAAAAGATATTATTAGAATATAAATAATTAAGTTGACAATATAA
AAAAACTATTAATACAAATAAAAAATAATTTTAACAAAAAAAATAAGAATTAACATAAAATAGTA
AAAATAATAATAAAATTAATATTATTTAACATAAAACAGTTAGAAGAATCGTTACACCTTAAAAA
AAAAATTGTAATAATTCTAAATGTAATGAAAAGTAACAACAAACGTAAAAAGATATTATTAAAAT
GTAATAAATTGGAAACGTAAAAAAATTAGTATTATAAATAAAAAAACATTAAATAAAAAAATAAG
TGTTAAAGTAAACAAGTGAAAATAATCATAAAATTGATATAATTTGGTGAAAAATATATTAAAAG
CATTGTAATACTTTAAGAAAAACATGTGATAATTCTAAACAAAATAAAAAATAACAACAAATGCA
AAAAATTTTAGGATAACACAAATATAAATTGACAATATAAAAATATTATTATTATAAACAAAAAA
CAATTCTAAACAAAAAATACGTGTTAACATAAAAATATAAGAATAATTAAAAATTTAAAATAATT
TAATATAAAATATATTAAAATATCATAACGTAATAAATGTAAAATTAGTGAAAAATAATATAAAT
TGGATTAAAACTCATAACACCTTAAGAAAAAATTATAATAATTCTAAACGTAACAAAAAGTAAGA
ACAA
Found at i:28496180 original size:21 final size:20
Alignment explanation
Indices: 28496128--28496194 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
28496118 TATAAAAACA
*
28496128 TATTATTATAATGTAAATAAT
1 TATTATTATAA-GTAAAAAAT
*
28496149 TA-AATTGATAACGTAAAAAAT
1 TATTATT-ATAA-GTAAAAAAT
*
28496170 TATTATTATAAATAAAAAAT
1 TATTATTATAAGTAAAAAAT
*
28496190 AATTA
1 TATTA
28496195 CAAATTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 15 0.39
21 20 0.53
22 3 0.08
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (20 bp):
TATTATTATAAGTAAAAAAT
Found at i:28507137 original size:18 final size:18
Alignment explanation
Indices: 28507114--28507148 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28507104 AAATTCTATA
28507114 AAAAATT-TAAAAATTTTT
1 AAAAATTAT-AAAATTTTT
28507132 AAAAATTATAAAATTTT
1 AAAAATTATAAAATTTT
28507149 CGAAACAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAAATTATAAAATTTTT
Found at i:28507873 original size:20 final size:20
Alignment explanation
Indices: 28507832--28507875 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28507822 TAAAAACAAA
* *
28507832 TTTTAAAAGGTTGTAGAATT
1 TTTTAAAAGCTTGTAAAATT
28507852 TTTTAAAAGCTT-TAAAAGTT
1 TTTTAAAAGCTTGTAAAA-TT
28507872 TTTT
1 TTTT
28507876 TCTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (20 bp):
TTTTAAAAGCTTGTAAAATT
Found at i:28508018 original size:9 final size:9
Alignment explanation
Indices: 28508004--28508204 Score: 70
Period size: 10 Copynumber: 20.8 Consensus size: 9
28507994 AATATTTGTT
28508004 AATTTTTAA
1 AATTTTTAA
*
28508013 AATTTTTGATCG
1 AATTTTT-A--A
28508025 AATTTTTAGA
1 AATTTTTA-A
**
28508035 TTTTTTTATA
1 AATTTTTA-A
*
28508045 AA-TTATATA
1 AATTTTTA-A
*
28508054 AATTATTTAT
1 AATT-TTTAA
28508064 AA-TTTTAGA
1 AATTTTTA-A
*
28508073 AAATTTTAA
1 AATTTTTAA
*
28508082 AATTTTTTGA
1 AA-TTTTTAA
28508092 AA-TTTT-A
1 AATTTTTAA
28508099 AA-TTTTAA
1 AATTTTTAA
*
28508107 GATTTTTTAA
1 -AATTTTTAA
*
28508117 ATATTTTCAAA
1 A-ATTTT-TAA
*
28508128 AATATTTTAG
1 AAT-TTTTAA
*
28508138 AATTTTAAA
1 AATTTTTAA
28508147 ATATTTTTTAA
1 A-A-TTTTTAA
28508158 AATTTTTAA
1 AATTTTTAA
**
28508167 AATTCTAAAA
1 AATT-TTTAA
*
28508177 AATTTTAAA
1 AATTTTTAA
28508186 GAATCTTTTCAA
1 -AAT-TTTT-AA
28508198 AATTTTT
1 AATTTTT
28508205 TATTTTTTTG
Statistics
Matches: 146, Mismatches: 26, Indels: 39
0.69 0.12 0.18
Matches are distributed among these distances:
7 7 0.05
8 9 0.06
9 43 0.29
10 55 0.38
11 23 0.16
12 9 0.06
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (9 bp):
AATTTTTAA
Found at i:28508030 original size:21 final size:19
Alignment explanation
Indices: 28507988--28508032 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
28507978 CCTTTTTATA
*
28507988 TTTTAAAATATTTGTTAAT
1 TTTTAAAATATTTGTGAAT
*
28508007 TTTTAAAATTTTTGATCGAAT
1 TTTTAAAATATTTG-T-GAAT
28508028 TTTTA
1 TTTTA
28508033 GATTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 1 0.05
21 8 0.36
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (19 bp):
TTTTAAAATATTTGTGAAT
Found at i:28508084 original size:28 final size:29
Alignment explanation
Indices: 28508044--28508098 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
28508034 ATTTTTTTAT
28508044 AAATTATATAAATTATTT-ATAATTTTAGA
1 AAATTATATAAATTATTTGA-AATTTTAGA
* *
28508073 AAATTTTA-AAATTTTTTGAAATTTTA
1 AAATTATATAAATTATTTGAAATTTTA
28508099 AATTTTAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (29 bp):
AAATTATATAAATTATTTGAAATTTTAGA
Found at i:28508143 original size:29 final size:28
Alignment explanation
Indices: 28508111--28508203 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 28
28508101 TTTTAAGATT
*
28508111 TTTTAAATATTTTCAAAAATATTTTAGAA
1 TTTTAAATATTTTCAAAAAT-TTTTAAAA
**
28508140 TTTTAAAATATTTTTTAAAATTTTTAAAA
1 TTTT-AAATATTTTCAAAAATTTTTAAAA
* *
28508169 TTCTAAAAAATTTT-AAAGAATCTTTTCAAAA
1 TT-TTAAATATTTTCAAA-AAT-TTTT-AAAA
28508200 TTTT
1 TTTT
28508204 TTATTTTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
28 2 0.04
29 24 0.46
30 20 0.38
31 6 0.12
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (28 bp):
TTTTAAATATTTTCAAAAATTTTTAAAA
Found at i:28508155 original size:20 final size:20
Alignment explanation
Indices: 28508108--28508232 Score: 75
Period size: 20 Copynumber: 6.4 Consensus size: 20
28508098 AAATTTTAAG
28508108 ATTTTTTAAATATTTTCAAAA-
1 ATTTTTTAAA-ATTTT-AAAAT
* *
28508129 ATATTTTAGAATTTTAAAAT
1 ATTTTTTAAAATTTTAAAAT
*
28508149 ATTTTTTAAAATTTTTAAA-
1 ATTTTTTAAAATTTTAAAAT
* **
28508168 ATTCTAAAAAATTTTAAAGA-
1 ATTTTTTAAAATTTTAAA-AT
* **
28508188 ATCTTTTCAAAATTTT-TTAT
1 AT-TTTTTAAAATTTTAAAAT
*
28508208 -TTTTTTGAAA-TTTAAAA-
1 ATTTTTTAAAATTTTAAAAT
28508225 ATTTTTTA
1 ATTTTTTA
28508233 CTCTTTTTTA
Statistics
Matches: 79, Mismatches: 19, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
17 3 0.04
18 14 0.18
19 20 0.25
20 24 0.30
21 18 0.23
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTTTTAAAATTTTAAAAT
Found at i:28508226 original size:26 final size:28
Alignment explanation
Indices: 28508196--28508248 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
28508186 GAATCTTTTC
*
28508196 AAAATTTTTTA-T-TTTTTTGAAATTTA
1 AAAATTTTTTACTCTTTTTTAAAATTTA
28508222 AAAATTTTTTACTCTTTTTTAAAATTT
1 AAAATTTTTTACTCTTTTTTAAAATTT
28508249 TCTTTTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 11 0.46
27 1 0.04
28 12 0.50
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (28 bp):
AAAATTTTTTACTCTTTTTTAAAATTTA
Found at i:28508249 original size:10 final size:10
Alignment explanation
Indices: 28508076--28508249 Score: 66
Period size: 10 Copynumber: 18.2 Consensus size: 10
28508066 TTTTAGAAAA
28508076 TTTTAAAATT
1 TTTTAAAATT
*
28508086 TTTTGAAA--
1 TTTTAAAATT
28508094 TTTT-AAA--
1 TTTTAAAATT
*
28508101 TTTTAAGATT
1 TTTTAAAATT
28508111 TTTTAAATATT
1 TTTTAAA-ATT
** *
28508122 TTCAAAAATA
1 TTTTAAAATT
*
28508132 TTTTAGAA-T
1 TTTTAAAATT
*
28508141 TTTAAAATATT
1 TTTTAAA-ATT
28508152 TTTTAAAA-T
1 TTTTAAAATT
28508161 TTTTAAAA-T
1 TTTTAAAATT
* * *
28508170 TCTAAAAAAT
1 TTTTAAAATT
*
28508180 TTTAAAGAATCT
1 TTTTAA-AAT-T
*
28508192 TTTCAAAATT
1 TTTTAAAATT
*
28508202 TTTT--ATTT
1 TTTTAAAATT
*
28508210 TTTTGAAA--
1 TTTTAAAATT
*
28508218 TTTAAAAATT
1 TTTTAAAATT
***
28508228 TTTTACTCTT
1 TTTTAAAATT
28508238 TTTTAAAATT
1 TTTTAAAATT
28508248 TT
1 TT
28508250 CTTTTAATAT
Statistics
Matches: 121, Mismatches: 30, Indels: 26
0.68 0.17 0.15
Matches are distributed among these distances:
7 7 0.06
8 19 0.16
9 21 0.17
10 48 0.40
11 20 0.17
12 6 0.05
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:28508818 original size:9 final size:9
Alignment explanation
Indices: 28508804--28508954 Score: 51
Period size: 9 Copynumber: 16.0 Consensus size: 9
28508794 ATAATGTCTT
*
28508804 TTTTTTATA
1 TTTTTTAAA
28508813 TTTTTTAAA
1 TTTTTTAAA
28508822 TTTTTGATAGAA
1 TTTTT--TA-AA
28508834 -TTTTTAGAA
1 TTTTTTA-AA
28508843 TTCTTTTATAAA
1 -T-TTTT-TAAA
* *
28508855 TTATATAAAA
1 TT-TTTTAAA
28508865 TTTTTTATAA
1 TTTTTTA-AA
**
28508875 TTTTAAAAA
1 TTTTTTAAA
**
28508884 TTTTAAAAA
1 TTTTTTAAA
*
28508893 TTTTTTGAA
1 TTTTTTAAA
28508902 --TTTTAAA
1 TTTTTTAAA
** *
28508909 AATTTAAGAA
1 TTTTTTA-AA
28508919 TTTTTT-AA
1 TTTTTTAAA
28508927 TATTTTTAGAA
1 T-TTTTTA-AA
*
28508938 -TTTTAAAA
1 TTTTTTAAA
28508946 TTTTTTAAA
1 TTTTTTAAA
28508955 GAATTTTTAG
Statistics
Matches: 109, Mismatches: 17, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
7 6 0.06
8 5 0.05
9 59 0.54
10 18 0.17
11 11 0.10
12 8 0.07
13 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:28508856 original size:21 final size:18
Alignment explanation
Indices: 28508804--28508897 Score: 62
Period size: 18 Copynumber: 4.8 Consensus size: 18
28508794 ATAATGTCTT
*
28508804 TTTTTTATATTTTTTAAA
1 TTTTTTATAATTTTTAAA
*
28508822 TTTTTGATAGAATTTTTAGAA
1 TTTTT--TATAATTTTTA-AA
*
28508843 TTCTTTTATAAATTATATAAAA
1 TT-TTTTAT-AATT-T-TTAAA
*
28508865 TTTTTTATAATTTTAAAA
1 TTTTTTATAATTTTTAAA
* * *
28508883 ATTTTAAAAATTTTT
1 TTTTTTATAATTTTT
28508898 TGAATTTTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
18 21 0.34
19 1 0.02
20 15 0.25
21 14 0.23
22 8 0.13
23 2 0.03
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTTTATAATTTTTAAA
Found at i:28508876 original size:20 final size:20
Alignment explanation
Indices: 28508841--28508887 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
28508831 GAATTTTTAG
28508841 AATTCTTTTATAAATTATATAA
1 AATT-TTTTATAAATTATA-AA
*
28508863 AATTTTTTAT-AATTTTAAA
1 AATTTTTTATAAATTATAAA
28508882 AATTTT
1 AATTTT
28508888 AAAAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 6 0.25
21 6 0.25
22 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTTTTATAAATTATAAA
Found at i:28508887 original size:18 final size:18
Alignment explanation
Indices: 28508882--28508952 Score: 81
Period size: 18 Copynumber: 3.9 Consensus size: 18
28508872 TAATTTTAAA
*
28508882 AATTTTAAAAATTTTTTG
1 AATTTTAAAAATTTTTAG
*
28508900 AATTTTAAAAA-TTTAAG
1 AATTTTAAAAATTTTTAG
* *
28508917 AATTTTTTAATATTTTTAG
1 AA-TTTTAAAAATTTTTAG
*
28508936 AATTTTAAAATTTTTTA
1 AATTTTAAAAATTTTTA
28508953 AAGAATTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
17 6 0.14
18 30 0.70
19 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
AATTTTAAAAATTTTTAG
Found at i:28508890 original size:27 final size:26
Alignment explanation
Indices: 28508846--28508954 Score: 121
Period size: 27 Copynumber: 4.0 Consensus size: 26
28508836 TTTAGAATTC
*
28508846 TTTTATAAATTATATAAAATTTTTTATAA
1 TTTTAAAAATT-T-TAAAATTTTTTA-AA
*
28508875 TTTTAAAAATTTTAAAAATTTTTTGAA
1 TTTTAAAAATTTT-AAAATTTTTTAAA
28508902 TTTTAAAAA-TTTAAGAATTTTTTAATA
1 TTTTAAAAATTTTAA-AATTTTTTAA-A
* *
28508929 TTTTTAGAATTTTAAAATTTTTTAAA
1 TTTTAAAAATTTTAAAATTTTTTAAA
28508955 GAATTTTTAG
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
25 2 0.03
26 13 0.18
27 30 0.42
28 16 0.23
29 10 0.14
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (26 bp):
TTTTAAAAATTTTAAAATTTTTTAAA
Found at i:28508897 original size:19 final size:19
Alignment explanation
Indices: 28508846--28508981 Score: 66
Period size: 18 Copynumber: 7.2 Consensus size: 19
28508836 TTTAGAATTC
* *
28508846 TTTTATAAATTATATAAAAT
1 TTTTAAAAATTTTA-AAAAT
* *
28508866 TTTTTATAATTTTAAAAA-
1 TTTTAAAAATTTTAAAAAT
***
28508884 TTTTAAAAATTTTTTGAA-
1 TTTTAAAAATTTTAAAAAT
*
28508902 TTTTAAAAA-TTTAAGAAT
1 TTTTAAAAATTTTAAAAAT
* * * *
28508920 TTTTTAATATTTTTAGAA-
1 TTTTAAAAATTTTAAAAAT
*
28508938 TTTTAAAATTTTTTAAAGAAT
1 TTTTAAAA-ATTTTAAA-AAT
* *
28508959 TTTT-AGAATTCTAAAATAT
1 TTTTAAAAATTTTAAAA-AT
28508978 TTTT
1 TTTT
28508982 GGGAAATGTT
Statistics
Matches: 88, Mismatches: 22, Indels: 13
0.72 0.18 0.11
Matches are distributed among these distances:
17 6 0.07
18 36 0.41
19 28 0.32
20 14 0.16
21 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTAAAAATTTTAAAAAT
Found at i:28508966 original size:9 final size:9
Alignment explanation
Indices: 28508829--28508968 Score: 52
Period size: 9 Copynumber: 14.8 Consensus size: 9
28508819 AAATTTTTGA
28508829 TAGAATTTT
1 TAGAATTTT
28508838 TAGAATTCTTT
1 TAGAA-T-TTT
* *
28508849 TATAAATTATA
1 TA-GAATT-TT
*
28508860 TAAAATTTTT
1 TAGAA-TTTT
*
28508870 TATAATTTT
1 TAGAATTTT
* *
28508879 AAAAATTTT
1 TAGAATTTT
* *
28508888 AAAAATTTT
1 TAGAATTTT
*
28508897 TTGAA-TTT
1 TAGAATTTT
* *
28508905 TAAAAATTT
1 TAGAATTTT
*
28508914 AAGAATTTTT
1 TAGAA-TTTT
28508924 TA-ATATTTT
1 TAGA-ATTTT
28508933 TAGAA-TTT
1 TAGAATTTT
*
28508941 TAAAATTTTT
1 TAGAA-TTTT
28508951 TAAAGAATTTT
1 T--AGAATTTT
28508962 TAGAATT
1 TAGAATT
28508969 CTAAAATATT
Statistics
Matches: 101, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
8 13 0.13
9 47 0.47
10 20 0.20
11 16 0.16
12 5 0.05
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (9 bp):
TAGAATTTT
Found at i:28509396 original size:788 final size:795
Alignment explanation
Indices: 28508005--28509468 Score: 1804
Period size: 788 Copynumber: 1.8 Consensus size: 795
28507995 ATATTTGTTA
* *
28508005 ATTTTTAAAATTTTTGATCGAATTTTTAGATTTTTTTATAAATTATATAAATTATTTATAATTTT
1 ATTTTTAAAATTTTTGATAGAATTTTTAGATTCTTTTATAAATTATATAAATTATTTATAATTTT
*
28508070 AGAAAATTTTAAAATTTTTTGAAATTTTAAATTTTAAGATTTTTTAAATATTTTCAAAAATATTT
66 AGAAAATTTTAAAATTTTTTGAAATTTTAAAATTTAAGATTTTTT-AATA--TT----AATATTT
*
28508135 TAGAATTTTAAAATATTTTTTAAAATTTTTAAAATTCTAAAAAATTTTAAAGAATCTTTTCAAAA
124 TAGAATTTTAAAATATTTTTAAAAATTTTTAAAATTCTAAAAAATTTTAAAGAATCTTTTCAAAA
*
28508200 TTTTTTATTTTTTTGAAATTTAAAAATTTTTTACTCTTTTTTAAAATTTTCTTTTAATATTGATG
189 TTTTTTA----TTTGAAATTTAAAAATTTTTTACTCTTTTTTAAAATTTTCTTTTAATAATGATG
*
28508265 TTATATTAATGATGTGATGTTGATTAAATTTTTCTGACATATGTTAAACATTTTATTGGAAATTA
250 TTATATTAATGATGTGATGTTGATTAAATTTTTCTGACATATGTTAAACATTTTATTAGAAATTA
* ** * *
28508330 TATCATGTCTGTGTTTAGGGTTAACATATTAATAGTTGAGACAATTAACATACGAAAATATAGTT
315 TATCATATCAATATTTAGGGTTAACATATTAATAGTTGAGACAATTAACATACAAAAATATAGTT
*
28508395 TAAATATTTGATTAAAATTTTTTTATTATTTATCACATTAAAAAAAAAATCATAGTTTAAAGGTC
380 TAAATACTTGATTAAAATTTTTTTATTATTTATCACATTAAAAAAAAAATCATAGTTTAAAGGTC
* * * * **
28508460 AAATGAGATATTATTTCTTTTATAAATGATGTTTCAAATGATAATTTTTTTTTATTAAAATTTAC
445 AAAAGAGATATTATTCCTTTCACAAATGATGTTTCAAATGATAATTTTTTTAAATT-AAATTTAC
* *
28508525 TTGAAGTATAAAATTTTAGATGCATAAATTATAGAATCGAATTTATATATTATCATTTGATAGTG
509 TTGAAATATAAAATTTTAGATGAATAAATTATAGAATCGAATTTATATATTATCATTTGATAGTG
* *
28508590 GATGAAAAACTTATTTTGATCT-AAAAT-AAAAAGATAATTATAATATTAAAATTTTTTATCTCA
574 GATGAAAAACTTATTTTGATCTAAAAATAAAAAAGATAATTATAATATAAAAATTTTTAATCTCA
*
28508653 TTGCATGTTAATATAAAAATATAAAAATTTTATAACTTCGATGGTGCGAGGGCAACCTATTACTA
639 TTACATGTTAATA-AAAAA-ATAAAAATTTTATAACTTCGATGGTGCGAGGGCAACCTATTACTA
28508718 TTACTATTAATAATAAAAATTCTAAATTTTTTTTTAGATTTTTTTTCGATTTTTGGGATAATGTG
702 TTACTATTAATAATAAAAATTCTAAATTTTTTTTTAGATTTTTTTTCGATTTTTGGGATAATGTG
28508783 CCATTTTTGGGATAATGTCTTTTTTTTAT
767 CCATTTTTGGGATAATGTCTTTTTTTTAT
* *
28508812 ATTTTTTAAATTTTTGATAGAATTTTTAGAATTCTTTTATAAATTATATAAAATTTTTTATAATT
1 ATTTTTAAAATTTTTGATAGAATTTTTAG-ATTCTTTTATAAATTATAT-AAATTATTTATAATT
28508877 TTA-AAAATTTTAAAAATTTTTTG-AATTTTAAAAATTTAAGAATTTTTT-A-A-T-AT-TTTTA
64 TTAGAAAATTTT-AAAATTTTTTGAAATTTT-AAAATTTAAG-ATTTTTTAATATTAATATTTTA
* * *** * *
28508935 GAATTTTAAAAT-TTTTTAAAGAATTTTTAGAATTCTAAAATATTTTTGGGAAATGTTTT-AGAA
126 GAATTTTAAAATATTTTTAAA-AATTTTTAAAATTCTAAAAAATTTTAAAG-AATCTTTTCAAAA
* * * *
28508998 -TTTTTA-TTGAAAATTTCAAAATTTTTTGATTTTTTTTTGAAATTATT-TTTTAATAATGATGT
189 TTTTTTATTTG-AAATTTAAAAATTTTTT-ACTCTTTTTTAAAATT-TTCTTTTAATAATGATGT
* * * * *
28509060 TGTATTGATGATGTGATG-TGATTAAATTTTT-TGACTTATG-T-CA-ATGTTTATTATATAATT
251 TATATTAATGATGTGATGTTGATTAAATTTTTCTGACATATGTTAAACAT-TTTATTAGA-AATT
* * * *
28509120 ATATCATATCAATATTTAGGGTTAACGATGTTAAT-GATTGAGATAATTAATATATAAAAATATA
314 ATATCATATCAATATTTAGGGTTAAC-ATATTAATAG-TTGAGACAATTAACATACAAAAATAT-
**
28509184 AG-TTAAATACTTGATTAGAAA-TTTTTT-TTATTTATCACA-TAAAAAATGTAAT-A-A-TTT-
376 AGTTTAAATACTTGATTA-AAATTTTTTTATTATTTATCACATTAAAAAA-AAAATCATAGTTTA
** *
28509241 AAGTGTCAAACAG-GATATTATTCCTTTCACAGGTGATGTTTCATATGATAATTTTTTTAAAACT
439 AAG-GTCAAA-AGAGATATTATTCCTTTCACAAATGATGTTTCAAATGATAATTTTTTT-AAA-T
** * * * * *
28509305 T-TTTTTA-TTGAAATTTACTTAATTTTAGATGAATGAATTGTAGAATTGAATTTATATA-TATC
500 TAAATTTACTTGAAATATA--AAATTTTAGATGAATAAATTATAGAATCGAATTTATATATTATC
* ** * *
28509367 TTTTGATAGTTTATGACAAACTTATTTTGATTTAAAAATAAAAAAGATAATTATAATATAAAAAT
563 ATTTGATAGTGGATGAAAAACTTATTTTGATCTAAAAATAAAAAAGATAATTATAATATAAAAAT
*
28509432 TTTTAATCTTATTACATGTTAATAAAAAAATAAAAAT
628 TTTTAATCTCATTACATGTTAATAAAAAAATAAAAAT
28509469 ATATAAAAAA
Statistics
Matches: 569, Mismatches: 63, Indels: 69
0.81 0.09 0.10
Matches are distributed among these distances:
787 11 0.02
788 92 0.16
789 49 0.09
790 63 0.11
791 43 0.08
792 60 0.11
793 34 0.06
794 43 0.08
795 2 0.00
797 13 0.02
798 44 0.08
799 9 0.02
804 1 0.00
807 28 0.05
808 33 0.06
809 37 0.07
810 7 0.01
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (795 bp):
ATTTTTAAAATTTTTGATAGAATTTTTAGATTCTTTTATAAATTATATAAATTATTTATAATTTT
AGAAAATTTTAAAATTTTTTGAAATTTTAAAATTTAAGATTTTTTAATATTAATATTTTAGAATT
TTAAAATATTTTTAAAAATTTTTAAAATTCTAAAAAATTTTAAAGAATCTTTTCAAAATTTTTTA
TTTGAAATTTAAAAATTTTTTACTCTTTTTTAAAATTTTCTTTTAATAATGATGTTATATTAATG
ATGTGATGTTGATTAAATTTTTCTGACATATGTTAAACATTTTATTAGAAATTATATCATATCAA
TATTTAGGGTTAACATATTAATAGTTGAGACAATTAACATACAAAAATATAGTTTAAATACTTGA
TTAAAATTTTTTTATTATTTATCACATTAAAAAAAAAATCATAGTTTAAAGGTCAAAAGAGATAT
TATTCCTTTCACAAATGATGTTTCAAATGATAATTTTTTTAAATTAAATTTACTTGAAATATAAA
ATTTTAGATGAATAAATTATAGAATCGAATTTATATATTATCATTTGATAGTGGATGAAAAACTT
ATTTTGATCTAAAAATAAAAAAGATAATTATAATATAAAAATTTTTAATCTCATTACATGTTAAT
AAAAAAATAAAAATTTTATAACTTCGATGGTGCGAGGGCAACCTATTACTATTACTATTAATAAT
AAAAATTCTAAATTTTTTTTTAGATTTTTTTTCGATTTTTGGGATAATGTGCCATTTTTGGGATA
ATGTCTTTTTTTTAT
Found at i:28509529 original size:798 final size:797
Alignment explanation
Indices: 28508005--28509538 Score: 1773
Period size: 798 Copynumber: 1.9 Consensus size: 797
28507995 ATATTTGTTA
* *
28508005 ATTTTTAAAATTTTTGATCGAATTTTTAGATTTTTTTATAAATTATATAAATTATTTATAATTTT
1 ATTTTTAAAATTTTTGATAGAATTTTTAGATTCTTTTATAAATTATATAAATTATTTATAATTTT
*
28508070 AGAAAATTTTAAAATTTTTTGAAATTTTAAATTTTAAGATTTTTTAAATATTTTCAAAAATATTT
66 AGAAAATTTTAAAATTTTTTGAAATTTTAAAATTTAAGATTTTTT-AATA--TT----AATATTT
*
28508135 TAGAATTTTAAAATATTTTTTAAAATTTTTAAAATTCTAAAAAATTTTAAAGAATCTTTTCAAAA
124 TAGAATTTTAAAATATTTTTAAAAATTTTTAAAATTCTAAAAAATTTTAAAGAATCTTTTCAAAA
*
28508200 TTTTTTATTTTTTTGAAATTTAAAAATTTTTTACTCTTTTTTAAAATTTTCTTTTAATATTGATG
189 TTTTTTA----TTTGAAATTTAAAAATTTTTTACTCTTTTTTAAAATTTTCTTTTAATAATGATG
*
28508265 TTATATTAATGATGTGATGTTGATTAAATTTTTCTGACATATGTTAAACATTTTATTGGAAATTA
250 TTATATTAATGATGTGATGTTGATTAAATTTTTCTGACATATGTTAAACATTTTATTAGAAATTA
* ** * *
28508330 TATCATGTCTGTGTTTAGGGTTAACATATTAATAGTTGAGACAATTAACATACGAAAATATAGTT
315 TATCATATCAATATTTAGGGTTAACATATTAATAGTTGAGACAATTAACATACAAAAATATAGTT
*
28508395 TAAATATTTGATTAAAATTTTTTTATTATTTATCACATTAAAAAAAAAATCATAGTTTAAAGGTC
380 TAAATACTTGATTAAAATTTTTTTATTATTTATCACATTAAAAAAAAAATCATAGTTTAAAGGTC
* * * * **
28508460 AAATGAGATATTATTTCTTTTATAAATGATGTTTCAAATGATAATTTTTTTTTATTAAAATTTAC
445 AAAAGAGATATTATTCCTTTCACAAATGATGTTTCAAATGATAATTTTTTTAAATT-AAATTTAC
* *
28508525 TTGAAGTATAAAATTTTAGATGCATAAATTATAGAATCGAATTTATATATTATCATTTGATAGTG
509 TTGAAATATAAAATTTTAGATGAATAAATTATAGAATCGAATTTATATATTATCATTTGATAGTG
* *
28508590 GATGAAAAACTTATTTTGATCTAAAATAAAAAGATAATTATAATATTAAAATTTTTTATCTCATT
574 GATGAAAAACTTATTTTGATCTAAAATAAAAAGATAATTATAATATAAAAATTTTTAATCTCATT
* ** * * ** * *
28508655 GCATGTTAATATAAAAATATAAAAATTTTATAACTTCGATGGTGCGAGGGCAACCTATTACTATT
639 ACATGTTAATATAAAAATATAAAAAACTTATAACCTCGATGATGCGAAAGCAACCTACTACTACT
*
28508720 ACTATTAATAAT-A-AAAATTCTAAATTTTTTTTTAGATTTTTTTTCGATTTTTGGGATAATGTG
704 ACTAATAATAATCATAAAATTCTAAATTTTTTTTTAGATTTTTTTTCGATTTTTGGGATAATGTG
28508783 CCATTTTTGGGATAATGTCTTTTTTTTAT
769 CCATTTTTGGGATAATGTCTTTTTTTTAT
* *
28508812 ATTTTTTAAATTTTTGATAGAATTTTTAGAATTCTTTTATAAATTATATAAAATTTTTTATAATT
1 ATTTTTAAAATTTTTGATAGAATTTTTAG-ATTCTTTTATAAATTATAT-AAATTATTTATAATT
28508877 TTA-AAAATTTTAAAAATTTTTTG-AATTTTAAAAATTTAAGAATTTTTT-A-A-T-AT-TTTTA
64 TTAGAAAATTTT-AAAATTTTTTGAAATTTT-AAAATTTAAG-ATTTTTTAATATTAATATTTTA
* * *** * *
28508935 GAATTTTAAAAT-TTTTTAAAGAATTTTTAGAATTCTAAAATATTTTTGGGAAATGTTTT-AGAA
126 GAATTTTAAAATATTTTTAAA-AATTTTTAAAATTCTAAAAAATTTTAAAG-AATCTTTTCAAAA
* * * *
28508998 -TTTTTA-TTGAAAATTTCAAAATTTTTTGATTTTTTTTTGAAATTATT-TTTTAATAATGATGT
189 TTTTTTATTTG-AAATTTAAAAATTTTTT-ACTCTTTTTTAAAATT-TTCTTTTAATAATGATGT
* * * * *
28509060 TGTATTGATGATGTGATG-TGATTAAATTTTT-TGACTTATG-T-CA-ATGTTTATTATATAATT
251 TATATTAATGATGTGATGTTGATTAAATTTTTCTGACATATGTTAAACAT-TTTATTAGA-AATT
* * * *
28509120 ATATCATATCAATATTTAGGGTTAACGATGTTAAT-GATTGAGATAATTAATATATAAAAATATA
314 ATATCATATCAATATTTAGGGTTAAC-ATATTAATAG-TTGAGACAATTAACATACAAAAATAT-
**
28509184 AG-TTAAATACTTGATTAGAAA-TTTTTT-TTATTTATCACA-TAAAAAATGTAAT-A-A-TTT-
376 AGTTTAAATACTTGATTA-AAATTTTTTTATTATTTATCACATTAAAAAA-AAAATCATAGTTTA
** *
28509241 AAGTGTCAAACAG-GATATTATTCCTTTCACAGGTGATGTTTCATATGATAATTTTTTTAAAACT
439 AAG-GTCAAA-AGAGATATTATTCCTTTCACAAATGATGTTTCAAATGATAATTTTTTT-AAA-T
** * * * * *
28509305 T-TTTTTA-TTGAAATTTACTTAATTTTAGATGAATGAATTGTAGAATTGAATTTATATA-TATC
500 TAAATTTACTTGAAATATA--AAATTTTAGATGAATAAATTATAGAATCGAATTTATATATTATC
* ** * *
28509367 TTTTGATAGTTTATGACAAACTTATTTTGATTTAAAAATAAAAAAGATAATTATAATATAAAAAT
563 ATTTGATAGTGGATGAAAAACTTATTTTGATCT-AAAAT-AAAAAGATAATTATAATATAAAAAT
* *
28509432 TTTTAATCTTATTACATGTTAATAAAAAAATAAAAATATATAAAAAACTTATATCCTCGATGATG
626 TTTTAATCTCATTACATGTTAAT------AT-AAAA-ATATAAAAAACTTATAACCTCGATGATG
*
28509497 CGAAAGCAATCTACTACTACTACTAATAATAATCATAAAATT
683 CGAAAGCAACCTACTACTACTACTAATAATAATCATAAAATT
28509539 TTTAATATTA
Statistics
Matches: 618, Mismatches: 74, Indels: 77
0.80 0.10 0.10
Matches are distributed among these distances:
787 11 0.02
788 84 0.14
789 44 0.07
790 62 0.10
791 43 0.07
792 60 0.10
793 34 0.06
794 43 0.07
795 2 0.00
796 2 0.00
797 17 0.03
798 94 0.15
799 10 0.02
800 6 0.01
804 1 0.00
807 28 0.05
808 33 0.05
809 37 0.06
810 7 0.01
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (797 bp):
ATTTTTAAAATTTTTGATAGAATTTTTAGATTCTTTTATAAATTATATAAATTATTTATAATTTT
AGAAAATTTTAAAATTTTTTGAAATTTTAAAATTTAAGATTTTTTAATATTAATATTTTAGAATT
TTAAAATATTTTTAAAAATTTTTAAAATTCTAAAAAATTTTAAAGAATCTTTTCAAAATTTTTTA
TTTGAAATTTAAAAATTTTTTACTCTTTTTTAAAATTTTCTTTTAATAATGATGTTATATTAATG
ATGTGATGTTGATTAAATTTTTCTGACATATGTTAAACATTTTATTAGAAATTATATCATATCAA
TATTTAGGGTTAACATATTAATAGTTGAGACAATTAACATACAAAAATATAGTTTAAATACTTGA
TTAAAATTTTTTTATTATTTATCACATTAAAAAAAAAATCATAGTTTAAAGGTCAAAAGAGATAT
TATTCCTTTCACAAATGATGTTTCAAATGATAATTTTTTTAAATTAAATTTACTTGAAATATAAA
ATTTTAGATGAATAAATTATAGAATCGAATTTATATATTATCATTTGATAGTGGATGAAAAACTT
ATTTTGATCTAAAATAAAAAGATAATTATAATATAAAAATTTTTAATCTCATTACATGTTAATAT
AAAAATATAAAAAACTTATAACCTCGATGATGCGAAAGCAACCTACTACTACTACTAATAATAAT
CATAAAATTCTAAATTTTTTTTTAGATTTTTTTTCGATTTTTGGGATAATGTGCCATTTTTGGGA
TAATGTCTTTTTTTTAT
Found at i:28527201 original size:10 final size:10
Alignment explanation
Indices: 28527182--28527212 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28527172 TAAGTGCAAA
*
28527182 GGTAAATGGT
1 GGTAAGTGGT
28527192 GGTAAGTGGT
1 GGTAAGTGGT
28527202 GGTAAGTGGT
1 GGTAAGTGGT
28527212 G
1 G
28527213 AAGTAAGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.48, T:0.29
Consensus pattern (10 bp):
GGTAAGTGGT
Found at i:28528482 original size:48 final size:47
Alignment explanation
Indices: 28528423--28528621 Score: 147
Period size: 47 Copynumber: 4.1 Consensus size: 47
28528413 AAAATAAGTA
* *
28528423 ATAAAA-A-TGTTTTCCTAAAAAATAGGAAAATTATTAGAAGGAATAG
1 ATAAAAGAGTGTTTTCCTAAAAAATA-GAAAATTATTAAAAGAAATAG
* * *
28528469 ATAAAAGAGTGTTTTCGTAAAAAAAAAAAAATGAAAATTAATAAAAGAAATAG
1 ATAAAAGAGTGTTTTCCT-----AAAAAATA-GAAAATTATTAAAAGAAATAG
* * * *
28528522 TTAATAGGAGTATTTTTCTAAAAAATAGAAGAATTATTAAAAGAAATA-
1 ATAA-AAGAGTGTTTTCCTAAAAAATAGAA-AATTATTAAAAGAAATAG
* * *
28528570 AGTAAAGGAGTG-TTTCGTAAAAAATAAGAAAACTATTAAAA-ATAATAG
1 A-TAAAAGAGTGTTTTCCTAAAAAAT-AGAAAATTATTAAAAGA-AATAG
28528618 ATAA
1 ATAA
28528622 TAAAAATGTT
Statistics
Matches: 122, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
46 7 0.06
47 29 0.24
48 22 0.18
49 26 0.21
53 28 0.23
54 10 0.08
ACGTcount: A:0.56, C:0.03, G:0.14, T:0.27
Consensus pattern (47 bp):
ATAAAAGAGTGTTTTCCTAAAAAATAGAAAATTATTAAAAGAAATAG
Found at i:28534661 original size:55 final size:54
Alignment explanation
Indices: 28534594--28534702 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 54
28534584 GAGAGTTGAG
* *
28534594 TAAGTTTGGCAAAAATCT-TCAAAAGTCTCTCAATGAACTGAAGAAACTCCTATTT
1 TAAGTTTAGCAAAAATCTCT-AAAAGTCTCTCAATAAACT-AAGAAACTCCTATTT
* * *
28534649 TAAGTTTAGCAAAAGTCTCTAAAAGTCTCTCAATAAACTAAGGAACTCTTATTT
1 TAAGTTTAGCAAAAATCTCTAAAAGTCTCTCAATAAACTAAGAAACTCCTATTT
28534703 ATAGGTCTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
54 13 0.27
55 34 0.71
56 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (54 bp):
TAAGTTTAGCAAAAATCTCTAAAAGTCTCTCAATAAACTAAGAAACTCCTATTT
Found at i:28535563 original size:26 final size:26
Alignment explanation
Indices: 28535534--28535591 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
28535524 TGAAAGAAAA
*
28535534 AAATTTATATATATATTTGTGGGTGT
1 AAATGTATATATATATTTGTGGGTGT
*
28535560 AAATGTGTATATATATTTGTGGGTGT
1 AAATGTATATATATATTTGTGGGTGT
28535586 AAATGT
1 AAATGT
28535592 GTGGATTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (26 bp):
AAATGTATATATATATTTGTGGGTGT
Found at i:28535594 original size:28 final size:26
Alignment explanation
Indices: 28535541--28535593 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28535531 AAAAAATTTA
28535541 TATATATATTTGTGGGTGTAAATGTG
1 TATATATATTTGTGGGTGTAAATGTG
28535567 TATATATATTTGTGGGTGTAAATGTG
1 TATATATATTTGTGGGTGTAAATGTG
28535593 T
1 T
28535594 GGATTCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (26 bp):
TATATATATTTGTGGGTGTAAATGTG
Found at i:28536802 original size:17 final size:17
Alignment explanation
Indices: 28536780--28536820 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
28536770 TCTCTTTTTT
28536780 TTTTTTTA-CTATTTGA
1 TTTTTTTAGCTATTTGA
28536796 CTTTTTTTAGGCTATTTGA
1 -TTTTTTTA-GCTATTTGA
28536815 TTTTTT
1 TTTTTT
28536821 ATTTTTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 6 0.27
19 8 0.36
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (17 bp):
TTTTTTTAGCTATTTGA
Found at i:28536802 original size:18 final size:18
Alignment explanation
Indices: 28536779--28536820 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
28536769 CTCTCTTTTT
28536779 TTTTTTTTA-CTATTTGA
1 TTTTTTTTAGCTATTTGA
*
28536796 CTTTTTTTAGGCTATTTGA
1 TTTTTTTTA-GCTATTTGA
28536815 TTTTTT
1 TTTTTT
28536821 ATTTTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.14, C:0.07, G:0.10, T:0.69
Consensus pattern (18 bp):
TTTTTTTTAGCTATTTGA
Found at i:28540602 original size:5 final size:6
Alignment explanation
Indices: 28540588--28540698 Score: 68
Period size: 6 Copynumber: 17.3 Consensus size: 6
28540578 CCTAATGGGC
*
28540588 TTTTAT TTTTAT TTTCAT TATTTAAT ATATATT-T TTTTAT TTTTAT TTTTA-
1 TTTTAT TTTTAT TTTTAT T-TTT-AT -T-T-TTAT TTTTAT TTTTAT TTTTAT
* *
28540639 TTTTAT CTATTAATAT TTTTAT TATTTA- -TCTAC TTTTAT TTTTAT TTTTAT
1 TTTTAT -T-TT--TAT TTTTAT T-TTTAT TTTTAT TTTTAT TTTTAT TTTTAT
28540690 TATTTAT TT
1 T-TTTAT TT
28540699 CTTTTATTTA
Statistics
Matches: 86, Mismatches: 5, Indels: 28
0.72 0.04 0.24
Matches are distributed among these distances:
4 3 0.03
5 7 0.08
6 46 0.53
7 14 0.16
8 7 0.08
9 4 0.05
10 5 0.06
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTAT
Found at i:28540658 original size:34 final size:33
Alignment explanation
Indices: 28540588--28540667 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 33
28540578 CCTAATGGGC
*
28540588 TTTTATTTTTATTTTCATTATTTAATATATATTT
1 TTTTATTTTTATTTTCATTATCTAATATATA-TT
* *
28540622 TTTTATTTTTATTTTTATTTTATCTATTA-ATA-T
1 TTTTATTTTTATTTTCA--TTATCTAATATATATT
28540655 TTTTATTATTTAT
1 TTTTATT-TTTAT
28540668 CTACTTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
33 8 0.20
34 21 0.52
35 3 0.08
36 8 0.20
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (33 bp):
TTTTATTTTTATTTTCATTATCTAATATATATT
Found at i:28540660 original size:16 final size:15
Alignment explanation
Indices: 28540639--28540737 Score: 53
Period size: 16 Copynumber: 6.4 Consensus size: 15
28540629 TTTATTTTTA
28540639 TTTTATCTATTAATAT
1 TTTTAT-TATTAATAT
* *
28540655 TTTTATTATTTATCTAC
1 TTTTATTA-TTA-ATAT
28540672 TTTTATT-TT--TAT
1 TTTTATTATTAATAT
* *
28540684 TTTTATTATTTATTT
1 TTTTATTATTAATAT
*
28540699 CTTTTATTTATCT-ATTT
1 -TTTTA-TTAT-TAATAT
28540716 TTTTATCTATTAATAT
1 TTTTAT-TATTAATAT
*
28540732 ATTTAT
1 TTTTAT
28540738 CTTTTTATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
12 9 0.13
13 2 0.03
15 8 0.12
16 30 0.45
17 17 0.25
18 1 0.01
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATTATTAATAT
Found at i:28540670 original size:23 final size:20
Alignment explanation
Indices: 28540589--28540719 Score: 101
Period size: 20 Copynumber: 6.4 Consensus size: 20
28540579 CTAATGGGCT
*
28540589 TTTATTTTTATTTTCAT-TA
1 TTTATTTTTATTTTTATCTA
* * * * *
28540608 TTTAATATATATTTTTTTATT
1 TTT-ATTTTTATTTTTATCTA
28540629 TTTATTTTTA-TTTTATCTA
1 TTTATTTTTATTTTTATCTA
28540648 TTAATATTTTTATTATTTATCTA
1 TT--TATTTTTATT-TTTATCTA
28540671 CTTTTATTTTTATTTTTAT-TA
1 --TTTATTTTTATTTTTATCTA
28540692 TTTATTTCTT-TTATTTATCTA
1 TTTATTT-TTATT-TTTATCTA
28540713 TTT-TTTT
1 TTTATTTT
28540720 ATCTATTAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
19 21 0.23
20 25 0.27
21 19 0.21
22 6 0.07
23 18 0.20
25 2 0.02
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTTTTATTTTTATCTA
Found at i:28540716 original size:29 final size:28
Alignment explanation
Indices: 28540587--28540727 Score: 123
Period size: 29 Copynumber: 5.0 Consensus size: 28
28540577 CCCTAATGGG
*
28540587 CTTTTATTTTTATTTTCATTATTTAATATA
1 CTTTTATTTTTATTTTTATTATTT-AT-TA
*
28540617 -TATT-TTTTTATTTTTATT-TTTATT-
1 CTTTTATTTTTATTTTTATTATTTATTA
**
28540641 -TTATCTATTAATATTTTTATTATTTATCTA
1 CTT-T-TATTTTTATTTTTATTATTTAT-TA
*
28540671 CTTTTATTTTTATTTTTATTATTTATTT
1 CTTTTATTTTTATTTTTATTATTTATTA
*
28540699 CTTTTATTTATCTATTTTT-TTATCTATTA
1 CTTTTATTT-T-TATTTTTATTATTTATTA
28540728 ATATATTTAT
Statistics
Matches: 92, Mismatches: 10, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
24 1 0.01
25 2 0.02
26 3 0.03
27 15 0.16
28 28 0.30
29 33 0.36
30 8 0.09
31 2 0.02
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.72
Consensus pattern (28 bp):
CTTTTATTTTTATTTTTATTATTTATTA
Found at i:28540721 original size:44 final size:43
Alignment explanation
Indices: 28540588--28540717 Score: 132
Period size: 42 Copynumber: 3.1 Consensus size: 43
28540578 CCTAATGGGC
* *
28540588 TTTTATTTTTATTTTCAT-TATT-TAATATATATT-TTT-T-TAT
1 TTTTATTTTTATTTT-ATCTATTAT-ATTTTTATTATTTATCTAT
*
28540628 TTTTATTTTTATTTTATCTATTAATATTTTTATTATTTATCTAC
1 TTTTATTTTTATTTTATCTATT-ATATTTTTATTATTTATCTAT
28540672 TTTTATTTTTATTTTTAT-TATT-TATTTCTT-TTATTTATCTAT
1 TTTTATTTTTA-TTTTATCTATTATATTT-TTATTATTTATCTAT
28540714 TTTT
1 TTTT
28540718 TTATCTATTA
Statistics
Matches: 78, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.03
40 19 0.24
41 7 0.09
42 24 0.31
43 3 0.04
44 17 0.22
45 6 0.08
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (43 bp):
TTTTATTTTTATTTTATCTATTATATTTTTATTATTTATCTAT
Found at i:28540722 original size:12 final size:13
Alignment explanation
Indices: 28540660--28540747 Score: 65
Period size: 13 Copynumber: 6.5 Consensus size: 13
28540650 AATATTTTTA
28540660 TTATTTATCTACTT
1 TTATTTATCTA-TT
*
28540674 TTATTTTTAT-TTTT
1 TTA--TTTATCTATT
* *
28540688 ATTATTTATTTCTT
1 -TTATTTATCTATT
28540702 TTATTTATCTATT
1 TTATTTATCTATT
28540715 TT-TTTATCTATT
1 TTATTTATCTATT
28540727 AATATATTTATCT-TT
1 --T-TATTTATCTATT
28540742 TTATTT
1 TTATTT
28540748 TGATTAATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
12 15 0.24
13 19 0.31
14 9 0.15
15 7 0.11
16 12 0.19
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTATCTATT
Found at i:28540727 original size:77 final size:78
Alignment explanation
Indices: 28540594--28540737 Score: 202
Period size: 77 Copynumber: 1.9 Consensus size: 78
28540584 GGGCTTTTAT
* * *
28540594 TTTTATTTTCATTATTTAATATATATTTTTTTATTTTTATTTTTATTTTATCTATTAATATTTTT
1 TTTTATTTTCATTATTTAATATATATTTTTTTATTTATATATTTATTTTATCTATTAATATATTT
28540659 ATTATTTATCTAC
66 ATTATTTATCTAC
* * * *
28540672 TTTTATTTTTATT-TTTATTATTTATTTCTTTTATTTATCTATTT-TTTTATCTATTAATATATT
1 TTTTATTTTCATTATTTAATATATATTT-TTTTATTTATATATTTATTTTATCTATTAATATATT
28540735 TAT
65 TAT
28540738 CTTTTTATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
77 33 0.57
78 25 0.43
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (78 bp):
TTTTATTTTCATTATTTAATATATATTTTTTTATTTATATATTTATTTTATCTATTAATATATTT
ATTATTTATCTAC
Found at i:28541550 original size:3 final size:3
Alignment explanation
Indices: 28541537--28541586 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
28541527 GTTCTCAAGT
28541537 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28541584 TTA
1 TTA
28541587 GATTAGATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28541616 original size:6 final size:6
Alignment explanation
Indices: 28541605--28541633 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
28541595 TTGTTTAATA
28541605 TATTTT TATTTT TATTTT TATTTT TATTT
1 TATTTT TATTTT TATTTT TATTTT TATTT
28541634 AAATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:28541767 original size:45 final size:46
Alignment explanation
Indices: 28541716--28541807 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
28541706 AAAGGATTTT
*
28541716 TGAGGAAAAGCTGAAAGTATC-AATTTTTCTTGAAAATAAGCTTTC
1 TGAGGAAAAGCTAAAAGTATCAAATTTTTCTTGAAAATAAGCTTTC
* * *
28541761 TGAGGAAAAGTTAAAAGTATCAAATTTTTTTTTAAAATAAGCTTTC
1 TGAGGAAAAGCTAAAAGTATCAAATTTTTCTTGAAAATAAGCTTTC
28541807 T
1 T
28541808 AAAAAAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 19 0.45
46 23 0.55
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (46 bp):
TGAGGAAAAGCTAAAAGTATCAAATTTTTCTTGAAAATAAGCTTTC
Found at i:28541844 original size:108 final size:103
Alignment explanation
Indices: 28541658--28541862 Score: 257
Period size: 108 Copynumber: 1.9 Consensus size: 103
28541648 AAAATATTTT
* * * *
28541658 TGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATGAGCTTTCTAAAAAGGATTTTTGAGGAA
1 TGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATAAGCTTTCTAAAAAAGATTTTTGAGAAA
* * *
28541723 AAGCTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
66 AAGCTGAAAGTATCAATTCTCCTTAAAAATAAGCTTTC
** * *
28541761 TGAGGAAAAGTTAAAAGTATCAAATTTTTTTTTAAAATAAGCTTTCTAAAAAAAATATATTTTTG
1 TGAGGAAAAGTTAAAAGTATC-AATTTTCCTTGAAAATAAGCTTTCT---AAAAA-AGATTTTTG
*
28541826 AGAAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAA
61 AGAAAAAGCTGAAAGTATCAATTCTCCTTAAAAATAA
28541863 ATTTTCAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
103 20 0.24
104 21 0.25
107 5 0.06
108 39 0.46
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (103 bp):
TGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATAAGCTTTCTAAAAAAGATTTTTGAGAAA
AAGCTGAAAGTATCAATTCTCCTTAAAAATAAGCTTTC
Found at i:28541886 original size:58 final size:58
Alignment explanation
Indices: 28541811--28542142 Score: 359
Period size: 58 Copynumber: 5.7 Consensus size: 58
28541801 GCTTTCTAAA
* *
28541811 AAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAATTTTC
1 AAAAATAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * * *
28541869 AAAAATAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTAGAAACAAGTTTTT
1 AAAAATAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * ** * *
28541927 AAAAGT-GAATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTCCTCGAAATTAAAAGTTTC
1 AAAAATAG-ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
* * * * *
28541985 AAAAAAATATTTTTGAAAAAAAGTTGAACGTATCAATTTTCCTTAAAAATAAGTTTTC
1 AAAAATAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * * *
28542043 AAAAATGGGA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAGTTTTC
1 AAAAAT-AGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTTC
* *
28542102 AAAAA-A-ATATTTTGGGAAAAAATTGAAAGTATCAATTTTCC
1 AAAAATAGAT-TTTTGAGAAAAAGTTGAAAGTATCAATTTTCC
28542143 CTTTACAAAA
Statistics
Matches: 222, Mismatches: 44, Indels: 16
0.79 0.16 0.06
Matches are distributed among these distances:
56 1 0.00
57 8 0.04
58 192 0.86
59 21 0.09
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (58 bp):
AAAAATAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:28541965 original size:27 final size:27
Alignment explanation
Indices: 28541819--28541965 Score: 77
Period size: 27 Copynumber: 5.1 Consensus size: 27
28541809 AAAAAAATAT
28541819 ATTTTTGAGAAAAAGTTGAAAGTATCA
1 ATTTTTGAGAAAAAGTTGAAAGTATCA
* * * * *
28541846 ATTCTCCTTAAAAATAAATTTTCAAA-AAT-A
1 ATT-T--TTGAGAA-AAA-GTTGAAAGTATCA
28541876 GATTTTTGAGAAAAAGTTGAAAGTATCA
1 -ATTTTTGAGAAAAAGTTGAAAGTATCA
* * *
28541904 ATTTTCTTTAGAAACAAGTTTTTAAA--AGTGA
1 A-TTT-TTGAGAAA-AAG--TTGAAAGTA-TCA
*
28541935 ATTTTTGAGGAAAAGTTGAAAGTATCA
1 ATTTTTGAGAAAAAGTTGAAAGTATCA
28541962 ATTT
1 ATTT
28541966 CCTCGAAATT
Statistics
Matches: 87, Mismatches: 17, Indels: 32
0.64 0.12 0.24
Matches are distributed among these distances:
26 10 0.11
27 15 0.17
28 14 0.16
29 13 0.15
30 14 0.16
31 11 0.13
32 10 0.11
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (27 bp):
ATTTTTGAGAAAAAGTTGAAAGTATCA
Found at i:28541985 original size:116 final size:114
Alignment explanation
Indices: 28541819--28542142 Score: 409
Period size: 116 Copynumber: 2.8 Consensus size: 114
28541809 AAAAAAATAT
* * * *
28541819 ATTTTTGAGAAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAATTTTCAAAAATAGATTTTTG
1 ATTTTTGAGGAAAAGTTGAAAGTATCAATT-TCCTTGAAATTAAAGTTTCAAAAA-A-ATTTTTG
* * * *
28541884 AGAAAAAGTTGAAAGTATCAATTTTCTTTAGAAACAAGTTTTTAAAAGT-GA
63 AGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAGTTTTCAAAAATGGA
*
28541935 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTCCTCGAAATTAAAAGTTTCAAAAAAATATTTTTG
1 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTCCTTGAAATT-AAAGTTTC-AAAAAA-ATTTTTG
* * * *
28542000 AAAAAAAGTTGAACGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAATGGG
63 AGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAGTTTTCAAAAATGGA
*
28542052 A-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAGTTTTCAAAAAAATATTTTG
1 ATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTCCTTGAAATTAAAG-TTTCAAAAAAAT-TTTTG
* *
28542116 GGAAAAAATTGAAAGTATCAATTTTCC
63 AGAAAAAGTTGAAAGTATCAATTTTCC
28542143 CTTTACAAAA
Statistics
Matches: 182, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
115 10 0.05
116 150 0.82
117 22 0.12
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (114 bp):
ATTTTTGAGGAAAAGTTGAAAGTATCAATTTCCTTGAAATTAAAGTTTCAAAAAAATTTTTGAGA
AAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAGTTTTCAAAAATGGA
Found at i:28542130 original size:174 final size:174
Alignment explanation
Indices: 28541810--28542139 Score: 465
Period size: 174 Copynumber: 1.9 Consensus size: 174
28541800 AGCTTTCTAA
*
28541810 AAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAATTTTCAAAAAT
1 AAAAAATATATTTTTGAAAAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAATTTTCAAAAAT
* * *
28541875 AGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTAGAAACAAGTTTTTAAAAGTGAATTTT
66 AGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTAGAAAAAAGTTTTCAAAAG-AAATTTT
*
28541940 TGAGGAAAAGTTGAAAGTATCAATTTCCTCGAAATTAAAAGTTTC
130 TGAGGAAAAATTGAAAGTATCAATTTCCTCGAAATTAAAAGTTTC
* * *
28541985 AAAAAA-ATATTTTTGAAAAAAAGTTGAACGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAAT
1 AAAAAATATATTTTTGAAAAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAATTTTCAAAAAT
* *
28542049 GGGA-TTTTGAGGAAAAGTTGAAAGTATCAATTTT-TCTT-GAAATTAAAGTTTTCAAAA-AAAT
66 -AGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCT-TTAGAAA--AAAGTTTTCAAAAGAAAT
28542110 ATTTTG-GGAAAAAATTGAAAGTATCAATTT
127 -TTTTGAGG-AAAAATTGAAAGTATCAATTT
28542140 TCCCTTTACA
Statistics
Matches: 139, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
173 10 0.07
174 110 0.79
175 19 0.14
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (174 bp):
AAAAAATATATTTTTGAAAAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAATTTTCAAAAAT
AGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTAGAAAAAAGTTTTCAAAAGAAATTTTT
GAGGAAAAATTGAAAGTATCAATTTCCTCGAAATTAAAAGTTTC
Found at i:28546113 original size:14 final size:14
Alignment explanation
Indices: 28546106--28546138 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28546096 AAAAAAATGG
28546106 AGAAAAAAAAAGAA
1 AGAAAAAAAAAGAA
*
28546120 AGAAAAAAAATGAA
1 AGAAAAAAAAAGAA
28546134 A-AAAA
1 AGAAAA
28546139 GATTCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (14 bp):
AGAAAAAAAAAGAA
Found at i:28547367 original size:22 final size:22
Alignment explanation
Indices: 28547342--28547397 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
28547332 AATTCAAATA
28547342 AGAATCTTTGAGTTTCGAACTG
1 AGAATCTTTGAGTTTCGAACTG
28547364 AGAATCTTTGAGTTTCGAACTG
1 AGAATCTTTGAGTTTCGAACTG
28547386 AGAATCTTTGAG
1 AGAATCTTTGAG
28547398 GAGTGAAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (22 bp):
AGAATCTTTGAGTTTCGAACTG
Found at i:28548027 original size:42 final size:42
Alignment explanation
Indices: 28547917--28548627 Score: 741
Period size: 42 Copynumber: 17.0 Consensus size: 42
28547907 TTAAGGAGTA
* * * * **
28547917 ATTTATTTTTC-AAAGTTGTGGTGCCT-TTATTTAGAGGAGTA
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGA-TTAGAGGAGCC
** * * **
28547958 ATTTAC-TTTCTAAAAGTTGAGGTGCCTCTGTTTAGAGGAGTA
1 ATTTACTTTTC-AAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
** * *
28548000 ATTTACTTTTCAAAAGTCATTGAGCCTCTGATTATATGAGCC
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
* * * *
28548042 ATTTACTTTTCAAAAGTTATTGAGCTTCTGATTAGAAGAGTC
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
* *
28548084 ATTTACTTTCCAAAAGTCGTTGAGCCTCTGATTAG-GGAAGCC
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGG-AGCC
*
28548126 ATTTATTTTTTCAAAA-TTGTTGAGCCTCTGATTAGAGGAGCC
1 ATTTA-CTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
*
28548168 ATTTACTTTTC-AAAGTTGTTGAGCCTCGGATTAGAGGAGCC
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
* * * * *
28548209 ATTTAGTTTTCAAAAGTCGTTGAGCCTCTTATTAGAAGAGCTTT
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGC--C
* *
28548253 AGTTA-TTTTC-AAAGTTGTTGAGCCTCTGATAAGAGGAGCC
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
**
28548293 ATTTACTTTTCAAAAGTCATTGAGCCTCTGATTAGAGGAG-C
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
* ***
28548334 -TTTAGTTTTTTTTTAAGTTGTTGAGCCTCTGATTAGAGGAGCC
1 ATTTA--CTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
* *
28548377 ATTTACTTTTC-AAAGTTGTTGAGCCTCTGATTAAATGAGCC
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
* * *
28548418 ATTTATTTTTTC-AAAGTCGTTGAGCTTCTGATTAGAGGAGCC
1 ATTTA-CTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
*
28548460 ATTTACTTTTC-AAAGTTGTTGAGCCTCTGATTAGAGAAGCC
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
* *
28548501 ATTTATTTTTTC-AAAGTTGTTGAGCCTCTGATTAGAGGAGCA
1 ATTTA-CTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
* * * *
28548543 ACTTATTTTTCCAAAA-TCGTTGAGCCTCTAATTAGAGGAGCC
1 ATTTACTTTT-CAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
* *
28548585 TTGTTTATTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGC
1 --ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGC
28548628 TTTGTTTATG
Statistics
Matches: 569, Mismatches: 77, Indels: 45
0.82 0.11 0.07
Matches are distributed among these distances:
40 15 0.03
41 126 0.22
42 360 0.63
43 29 0.05
44 39 0.07
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (42 bp):
ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
Found at i:28548243 original size:125 final size:125
Alignment explanation
Indices: 28548019--28548621 Score: 727
Period size: 125 Copynumber: 4.8 Consensus size: 125
28548009 TCAAAAGTCA
* * ** * * *
28548019 TTGAGCCTCTGATTATATGAGCCATTTACTTTTCAAAAGTTATTGAGCTTCTGATTAGAAGAGTC
1 TTGAGCCTCTGATTAGAGGAGCCATTTACTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGCC
* * *
28548084 ATTTACTTTCCAAAAGTCGTTGAGCCTCTGATTAGGGAAGCCATTTATTTTTTCAAAATTG
65 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGGGAAGCCATTTATTTTTTCAAAGTTG
* *
28548145 TTGAGCCTCTGATTAGAGGAGCCATTTACTTTTCAAAGTTGTTGAGCCTCGGATTAGAGGAGCCA
1 TTGAGCCTCTGATTAGAGGAGCCATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
* * * *
28548210 TTTAGTTTTCAAAAGTCGTTGAGCCTCTTATTA--GAAGAGC-TTTAGTTATTTTCAAAGTTG
66 TTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGGGAAG-CCATTTA-TT-TTTTCAAAGTTG
* *
28548270 TTGAGCCTCTGATAAGAGGAGCCATTTACTTTTCAAAAGTCATTGAGCCTCTGATTAGAGGAG-C
1 TTGAGCCTCTGATTAGAGGAGCCATTTACTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGCC
* *** *
28548334 -TTTAGTTTTTTTTTAAGTTGTTGAGCCTCTGATTAGAGG-AGCCATTTA-CTTTTCAAAGTTG
65 ATTTA--CTTTTCAAAAGTTGTTGAGCCTCTGATTAG-GGAAGCCATTTATTTTTTCAAAGTTG
* * * *
28548395 TTGAGCCTCTGATTAAATGAGCCATTTATTTTTTCAAAGTCGTTGAGCTTCTGATTAGAGGAGCC
1 TTGAGCCTCTGATTAGAGGAGCCATTTA-CTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
*
28548460 ATTTACTTTTC-AAAGTTGTTGAGCCTCTGATTAGAGAAGCCATTTATTTTTTCAAAGTTG
65 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGGGAAGCCATTTATTTTTTCAAAGTTG
* * * * *
28548520 TTGAGCCTCTGATTAGAGGAGCAACTTATTTTTCCAAAATCGTTGAGCCTCTAATTAGAGGAGCC
1 TTGAGCCTCTGATTAGAGGAGCCATTTACTTTT-CAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
* *
28548585 TTGTTTATTTTTCAAAAGTTGTTGAGCCTCTGATTAG
65 --ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAG
28548622 AGGAGCTTTG
Statistics
Matches: 414, Mismatches: 44, Indels: 36
0.84 0.09 0.07
Matches are distributed among these distances:
123 9 0.02
124 43 0.10
125 232 0.56
126 86 0.21
127 14 0.03
128 29 0.07
129 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (125 bp):
TTGAGCCTCTGATTAGAGGAGCCATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
TTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGGGAAGCCATTTATTTTTTCAAAGTTG
Found at i:28548705 original size:5 final size:5
Alignment explanation
Indices: 28548691--28548744 Score: 55
Period size: 5 Copynumber: 11.6 Consensus size: 5
28548681 AAATTTTAAC
*
28548691 AAAC- AAACA AAAC- AAA-A AAACA AAACA AAACA AAA-A AAATAA AAACA
1 AAACA AAACA AAACA AAACA AAACA AAACA AAACA AAACA AAA-CA AAACA
28548738 AAA-A AAA
1 AAACA AAA
28548745 GTGTCAAGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
4 18 0.41
5 22 0.50
6 4 0.09
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (5 bp):
AAACA
Found at i:28548718 original size:18 final size:17
Alignment explanation
Indices: 28548691--28548743 Score: 74
Period size: 18 Copynumber: 3.2 Consensus size: 17
28548681 AAATTTTAAC
28548691 AAACAAACAAAACAAAA
1 AAACAAACAAAACAAAA
28548708 AAACAAAACAAAACAAAA
1 AAAC-AAACAAAACAAAA
*
28548726 AAA-ATA-AAAACAAAA
1 AAACAAACAAAACAAAA
28548741 AAA
1 AAA
28548744 AGTGTCAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
15 12 0.35
16 2 0.06
17 4 0.12
18 16 0.47
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (17 bp):
AAACAAACAAAACAAAA
Found at i:28548741 original size:13 final size:13
Alignment explanation
Indices: 28548688--28548744 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
28548678 TAAAAATTTT
*
28548688 AACAAACAAACAA
1 AACAAAAAAACAA
28548701 AACAAAAAAACAA
1 AACAAAAAAACAA
28548714 AACAAAACAAA-AA
1 AACAAAA-AAACAA
*
28548727 AA-ATAAAAACAA
1 AACAAAAAAACAA
28548739 AA-AAAA
1 AACAAAA
28548745 GTGTCAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 3 0.08
12 10 0.26
13 23 0.59
14 3 0.08
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (13 bp):
AACAAAAAAACAA
Found at i:28548744 original size:18 final size:17
Alignment explanation
Indices: 28548695--28548744 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
28548685 TTTAACAAAC
*
28548695 AAACAAAACAAAAAAACA
1 AAACAAAA-AAAAAAAAA
28548713 AAACAAAACAAAAAAAATAA
1 AAAC-AAA-AAAAAAAA-AA
28548733 AAACAAAAAAAA
1 AAACAAAAAAAA
28548745 GTGTCAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 9 0.32
19 13 0.46
20 6 0.21
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (17 bp):
AAACAAAAAAAAAAAAA
Found at i:28548978 original size:34 final size:33
Alignment explanation
Indices: 28548935--28549008 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 33
28548925 TCCAATTGGC
28548935 TTTTATTTTTATTTTCAT-TATTTAATATATTT-AT
1 TTTTATTTTTATTTT-ATCTA-TTAATAT-TTTCAT
28548969 TTTTATTTTTATTTTATCTATTAATATTTTCAT
1 TTTTATTTTTATTTTATCTATTAATATTTTCAT
28549002 TATTTAT
1 T-TTTAT
28549009 CTACTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
32 3 0.08
33 12 0.32
34 22 0.59
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (33 bp):
TTTTATTTTTATTTTATCTATTAATATTTTCAT
Found at i:28548985 original size:5 final size:6
Alignment explanation
Indices: 28548935--28548983 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
28548925 TCCAATTGGC
*
28548935 TTTTAT TTTTAT TTTCAT TATTTAAT ATATTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT T-TTT-AT -T-TTTAT TTTTAT TTTTAT TTT
28548984 ATCTATTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 26 0.68
7 3 0.08
8 4 0.11
9 5 0.13
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:28549003 original size:49 final size:52
Alignment explanation
Indices: 28548944--28549043 Score: 136
Period size: 49 Copynumber: 2.0 Consensus size: 52
28548934 CTTTTATTTT
*
28548944 TATTTTCATTATTTAATATA-TTTATTT-TTATTTTTA-T-TTTATCTATTAA
1 TATTTTCATTATTT-ATATACTTTATTTATTATTATTATTATTTATCTATTAA
*
28548993 TATTTTCATTATTTATCTACTTTTATTTATTATTATTATTATTTATCTATT
1 TATTTTCATTATTTATATAC-TTTATTTATTATTATTATTATTTATCTATT
28549044 TCTTTTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
48 4 0.09
49 14 0.32
50 7 0.16
51 8 0.18
52 1 0.02
53 10 0.23
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (52 bp):
TATTTTCATTATTTATATACTTTATTTATTATTATTATTATTTATCTATTAA
Found at i:28549017 original size:33 final size:30
Alignment explanation
Indices: 28548965--28549041 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
28548955 TTTAATATAT
*
28548965 TTATTTTTATTT-T-TA-TTTTATCTATTAA
1 TTATTATTATTTATCTACTTTTATCTATT-A
* *
28548993 TATTTTCATTATTTATCTACTTTTATTTATTA
1 T-TATT-ATTATTTATCTACTTTTATCTATTA
28549025 TTATTATTATTTATCTA
1 TTATTATTATTTATCTA
28549042 TTTCTTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.03
29 3 0.08
30 18 0.45
31 4 0.10
32 4 0.10
33 10 0.25
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (30 bp):
TTATTATTATTTATCTACTTTTATCTATTA
Found at i:28549031 original size:23 final size:21
Alignment explanation
Indices: 28548969--28549036 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 21
28548959 ATATATTTAT
28548969 TTTTATTTTTATT-TTATCTA
1 TTTTATTTTTATTATTATCTA
* *
28548989 TTAATATTTTCATTATTTATCTA
1 TT-TTATTTTTATTA-TTATCTA
28549012 CTTTTATTTATTATTATTAT-TA
1 -TTTTATTT-TTATTATTATCTA
28549034 TTT
1 TTT
28549037 ATCTATTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
20 2 0.05
21 12 0.31
22 2 0.05
23 16 0.41
24 7 0.18
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTATTTTTATTATTATCTA
Found at i:28549957 original size:6 final size:6
Alignment explanation
Indices: 28549946--28550027 Score: 73
Period size: 6 Copynumber: 13.8 Consensus size: 6
28549936 TTTAATATAT
* * *
28549946 TTTTTA TTTTTA -TTTT- GTTTTA TTCTTA TTTTTAA TTTATTT TTCTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT-A TTT-TTA TT-TTTA
*
28549995 TTTTTA TTTTCA TTTTTA -TTTTA -TTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
28550028 TTAAATAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
5 18 0.29
6 32 0.51
7 10 0.16
8 3 0.05
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:28549974 original size:22 final size:21
Alignment explanation
Indices: 28549949--28550029 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 21
28549939 AATATATTTT
28549949 TTATTTTTATTTTGTTTTATTC
1 TTATTTTTATTTT-TTTTATTC
* *
28549971 TTATTTTTAATTTATTT-TTC
1 TTATTTTTATTTTTTTTATTC
28549991 TTTATTTTTATTTTCATTTTTATT-
1 -TTATTTTTA-TTT--TTTTTATTC
28550015 TTA-TTTTATTTTTTT
1 TTATTTTTATTTTTTT
28550030 AAATAAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
19 4 0.08
20 3 0.06
21 15 0.30
22 19 0.38
23 3 0.06
24 4 0.08
25 2 0.04
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.79
Consensus pattern (21 bp):
TTATTTTTATTTTTTTTATTC
Found at i:28549977 original size:27 final size:26
Alignment explanation
Indices: 28549947--28550024 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 26
28549937 TTAATATATT
28549947 TTTTATTTTTATTTTGTTTTATTCTTA
1 TTTTATTTTTATTTT-TTTTATTCTTA
* *
28549974 TTTT-TAATTTATTTTTCTTTATTTTTA
1 TTTTAT-TTTTATTTTT-TTTATTCTTA
28550001 TTTTCATTTTTATTTTATTTTATT
1 TTTT-ATTTTTATTTT-TTTTATT
28550025 TTTTTAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
26 2 0.05
27 25 0.58
28 14 0.33
29 2 0.05
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.78
Consensus pattern (26 bp):
TTTTATTTTTATTTTTTTTATTCTTA
Found at i:28549985 original size:33 final size:32
Alignment explanation
Indices: 28549948--28550029 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 32
28549938 TAATATATTT
28549948 TTTATTTTTATTTTGTTTTATTCTT-ATTTTTAA
1 TTTATTTTTATTTT-TTTTATT-TTCATTTTTAA
* *
28549981 TTTATTTTTCTTTATTTTTATTTTCATTTTTAT
1 TTTATTTTTATTT-TTTTTATTTTCATTTTTAA
28550014 TTTA-TTTTATTTTTTT
1 TTTATTTTTATTTTTTT
28550030 AAATAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 4 0.09
32 9 0.20
33 30 0.68
34 1 0.02
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.79
Consensus pattern (32 bp):
TTTATTTTTATTTTTTTTATTTTCATTTTTAA
Found at i:28550112 original size:58 final size:58
Alignment explanation
Indices: 28550041--28550374 Score: 417
Period size: 58 Copynumber: 5.7 Consensus size: 58
28550031 AATAAAATTC
*
28550041 AAAAGAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
1 AAAA-AATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
**
28550100 AAAAAGGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
1 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
*
28550158 AAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
1 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
* *
28550216 AAAAAAAATATATTTTTG-GAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAG-TTT-T
1 ---AAAAA-ATATTTTTGAG-AAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
* * * * * *
28550276 CAAAAATGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTT-TTTCGAAATTAAAGTTTTCA
1 AAAAAAT--ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTT-GAAAAT-AAGCTTTCT
* *
28550337 AAAAAATATTTTCGA-AAAAAATTGAAAGTATCAATTTT
1 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTT
28550375 TTCTGTACAA
Statistics
Matches: 242, Mismatches: 21, Indels: 25
0.84 0.07 0.09
Matches are distributed among these distances:
56 2 0.01
57 6 0.02
58 159 0.66
59 14 0.06
60 4 0.02
61 15 0.06
62 42 0.17
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (58 bp):
AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
Found at i:28550144 original size:30 final size:30
Alignment explanation
Indices: 28550110--28550202 Score: 81
Period size: 29 Copynumber: 3.2 Consensus size: 30
28550100 AAAAAGGATT
28550110 TTTGAGAAAAAGTTGAAAGTATCAATTTTC
1 TTTGAGAAAAAGTTGAAAGTATCAATTTTC
* *
28550140 TTTGA-AAATAAGCTTTCTAAA--A--AATATT-
1 TTTGAGAAA-AAG--TT-GAAAGTATCAATTTTC
*
28550168 TTTGAGAAAAAATTGAAAGTATCAATTTTC
1 TTTGAGAAAAAGTTGAAAGTATCAATTTTC
28550198 TTTGA
1 TTTGA
28550203 AAATAAGCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 20
0.66 0.07 0.27
Matches are distributed among these distances:
25 3 0.06
26 2 0.04
27 1 0.02
28 7 0.15
29 16 0.33
30 13 0.27
31 1 0.02
32 2 0.04
33 3 0.06
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (30 bp):
TTTGAGAAAAAGTTGAAAGTATCAATTTTC
Found at i:28550358 original size:178 final size:178
Alignment explanation
Indices: 28550047--28550374 Score: 520
Period size: 178 Copynumber: 1.8 Consensus size: 178
28550037 ATTCAAAAGA
*
28550047 ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCTAAAAAGGATTTT
1 ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTCTAAAAAGGATTTT
* *
28550112 TGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCTAAAAAATATTTTTGAGAAA
66 TGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCAAAAAAATATTTTCGAGAAA
28550177 AAATTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCTAAAAAAAAT
131 AAATTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCTAAAAAAAAT
* *
28550225 ATATTTTTG-GAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC-AAAAATGGGTT
1 ATATTTTTGAG-AAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTCTAAAAA-GGATT
* * *
28550288 TTTGAGGAAAAGTTGAAAGTATCAATTTT-TTTCGAAATTAAAGTTTTCAAAAAAATATTTTCGA
64 TTTGAGAAAAAGTTGAAAGTATCAATTTTCTTT-GAAAAT-AAGCTTTCAAAAAAATATTTTCGA
28550352 -AAAAAATTGAAAGTATCAATTTT
127 GAAAAAATTGAAAGTATCAATTTT
28550375 TTCTGTACAA
Statistics
Matches: 138, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
177 9 0.07
178 108 0.78
179 21 0.15
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (178 bp):
ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTCTAAAAAGGATTTT
TGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCAAAAAAATATTTTCGAGAAA
AAATTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCTAAAAAAAAT
Found at i:28553128 original size:14 final size:14
Alignment explanation
Indices: 28553109--28553150 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
28553099 TCAAAATCCA
28553109 ATTTTATT-TTTATT
1 ATTTTATTATTT-TT
28553123 ATTTTATTATTTTT
1 ATTTTATTATTTTT
*
28553137 ATTGTTCTTATTTT
1 ATT-TTATTATTTT
28553151 CGTTATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (14 bp):
ATTTTATTATTTTT
Found at i:28555301 original size:16 final size:17
Alignment explanation
Indices: 28555259--28555302 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
28555249 TTATTCATAG
*
28555259 ATAATTAT-ATTATTAC
1 ATAATTATAAATATTAC
28555275 ATAACTTATAAATATTA-
1 ATAA-TTATAAATATTAC
28555292 ATAATTATAAA
1 ATAATTATAAA
28555303 AGTAAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 11 0.44
17 8 0.32
18 6 0.24
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATTATAAATATTAC
Found at i:28555399 original size:16 final size:17
Alignment explanation
Indices: 28555380--28555417 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
28555370 GGAGAAAAGA
28555380 TTTTT-AATACAAAATT
1 TTTTTCAATACAAAATT
28555396 TTTTTCAATACAAAATT
1 TTTTTCAATACAAAATT
28555413 TTTTT
1 TTTTT
28555418 TATTTGAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTCAATACAAAATT
Found at i:28563202 original size:13 final size:13
Alignment explanation
Indices: 28563184--28563210 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28563174 TTACGCAAAA
28563184 TCAAATCCATCTC
1 TCAAATCCATCTC
28563197 TCAAATCCATCTC
1 TCAAATCCATCTC
28563210 T
1 T
28563211 TATGCCACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (13 bp):
TCAAATCCATCTC
Found at i:28566544 original size:19 final size:19
Alignment explanation
Indices: 28566522--28566589 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
28566512 TTTTTATTTC
28566522 TTTTGTATTATTTTTGGTA
1 TTTTGTATTATTTTTGGTA
28566541 TTTTGTATTATTTTT-GT-
1 TTTTGTATTATTTTTGGTA
* **
28566558 TTTT-T-TTATATTTCATA
1 TTTTGTATTATTTTTGGTA
28566575 TTTTGTATT-TTTTTG
1 TTTTGTATTATTTTTG
28566590 TCTAGACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
15 7 0.17
16 2 0.05
17 8 0.20
18 7 0.17
19 17 0.41
ACGTcount: A:0.15, C:0.01, G:0.10, T:0.74
Consensus pattern (19 bp):
TTTTGTATTATTTTTGGTA
Found at i:28566564 original size:10 final size:11
Alignment explanation
Indices: 28566522--28566590 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
28566512 TTTTTATTTC
28566522 TTTTGTATTAT
1 TTTTGTATTAT
*
28566533 TTTTG--GTA-
1 TTTTGTATTAT
28566541 TTTTGTATTAT
1 TTTTGTATTAT
28566552 TTTTGT-TT-T
1 TTTTGTATTAT
*
28566561 TTTTATATTTCAT
1 TTTTGTA-TT-AT
28566574 ATTTTGTATT-T
1 -TTTTGTATTAT
28566585 TTTTGT
1 TTTTGT
28566591 CTAGACAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
8 5 0.11
9 8 0.17
10 10 0.22
11 14 0.30
13 3 0.07
14 6 0.13
ACGTcount: A:0.14, C:0.01, G:0.10, T:0.74
Consensus pattern (11 bp):
TTTTGTATTAT
Found at i:28568012 original size:21 final size:20
Alignment explanation
Indices: 28567987--28568053 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
28567977 CATCCTCAAT
28567987 TTTTTTTGTTTTATTTTTTTA
1 TTTTTTTG-TTTATTTTTTTA
*
28568008 TTTTTTTG--TATTTTTTTG
1 TTTTTTTGTTTATTTTTTTA
* *
28568026 GTATTTTGTATTATTTTTTGT-
1 TTTTTTTGT-TTATTTTTT-TA
28568047 TTTTTTT
1 TTTTTTT
28568054 TAATTTCGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 15 0.41
21 21 0.57
22 1 0.03
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (20 bp):
TTTTTTTGTTTATTTTTTTA
Found at i:28568013 original size:10 final size:10
Alignment explanation
Indices: 28567985--28568054 Score: 52
Period size: 10 Copynumber: 6.8 Consensus size: 10
28567975 GCCATCCTCA
28567985 ATTTTTTTTGT
1 ATTTTTTTT-T
*
28567996 TTTATTTTTTT
1 ATT-TTTTTTT
*
28568007 ATTTTTTTGT
1 ATTTTTTTTT
*
28568017 ATTTTTTTGGT
1 ATTTTTTT-TT
* *
28568028 ATTTTGTATT
1 ATTTTTTTTT
*
28568038 ATTTTTTGTT
1 ATTTTTTTTT
28568048 -TTTTTTT
1 ATTTTTTT
28568055 AATTTCGTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.12
10 23 0.48
11 13 0.27
12 6 0.12
ACGTcount: A:0.10, C:0.00, G:0.09, T:0.81
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:28568019 original size:18 final size:17
Alignment explanation
Indices: 28567986--28568051 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 17
28567976 CCATCCTCAA
*
28567986 TTTTTTTTGTTT-TATT
1 TTTTTTTTTTTTGTATT
28568002 TTTTTATTTTTTTGTATT
1 TTTTT-TTTTTTTGTATT
* *
28568020 TTTTTGGTATTTTGTATT
1 TTTTT-TTTTTTTGTATT
28568038 ATTTTTTGTTTTTT
1 -TTTTTT-TTTTTT
28568052 TTTAATTTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 5 0.12
17 6 0.15
18 19 0.47
19 10 0.25
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTTTGTATT
Found at i:28568059 original size:18 final size:19
Alignment explanation
Indices: 28567989--28568059 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 19
28567979 TCCTCAATTT
* *
28567989 TTTTTGTTTTATTTTTTTA
1 TTTTTGTTTTAATTTTTTG
* *
28568008 TTTTT-TTGTATTTTTTTGG
1 TTTTTGTTTTAATTTTTT-G
*
28568027 TATTTTGTATT-ATTTTTTG
1 T-TTTTGTTTTAATTTTTTG
28568046 TTTTT-TTTTAATTT
1 TTTTTGTTTTAATTT
28568060 CGTATTCTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
17 3 0.07
18 19 0.45
19 8 0.19
20 10 0.24
21 2 0.05
ACGTcount: A:0.11, C:0.00, G:0.08, T:0.80
Consensus pattern (19 bp):
TTTTTGTTTTAATTTTTTG
Found at i:28577576 original size:35 final size:35
Alignment explanation
Indices: 28577530--28577600 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
28577520 ACAGATTATG
28577530 TATCAAATCAGGATCAATTTCCTGAGTTATTGGGA
1 TATCAAATCAGGATCAATTTCCTGAGTTATTGGGA
* * *
28577565 TATCAAATCAGGATCACTTTCCTGATTTGTTGGGA
1 TATCAAATCAGGATCAATTTCCTGAGTTATTGGGA
28577600 T
1 T
28577601 TTATATTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (35 bp):
TATCAAATCAGGATCAATTTCCTGAGTTATTGGGA
Found at i:28578711 original size:22 final size:22
Alignment explanation
Indices: 28578685--28578728 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28578675 TGTATATTTA
*
28578685 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
28578707 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
28578729 AAAAAAAAAA
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:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:28582659 original size:22 final size:22
Alignment explanation
Indices: 28582633--28582676 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28582623 TGTATATTTA
*
28582633 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
28582655 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
28582677 AAAAAAAAAA
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:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:28585506 original size:35 final size:35
Alignment explanation
Indices: 28585460--28585530 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
28585450 ACAGATTATG
28585460 TATCAAATCAGGATCAATTTCCTGATTTGCTGGGA
1 TATCAAATCAGGATCAATTTCCTGATTTGCTGGGA
* *
28585495 TATCAAATCAGGATCACTTTCCTGATTTGTTGGGA
1 TATCAAATCAGGATCAATTTCCTGATTTGCTGGGA
28585530 T
1 T
28585531 TTATATTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (35 bp):
TATCAAATCAGGATCAATTTCCTGATTTGCTGGGA
Found at i:28589230 original size:2 final size:2
Alignment explanation
Indices: 28589225--28589251 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28589215 TATATATAAC
28589225 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
28589252 ATAATAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:28600278 original size:2 final size:2
Alignment explanation
Indices: 28600267--28600303 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
28600257 GAATAAAACC
28600267 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28600304 CGAGTACCGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28601287 original size:17 final size:18
Alignment explanation
Indices: 28601259--28601292 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
28601249 ATCTCTATCG
28601259 AATATGAATATAAAAATA
1 AATATGAATATAAAAATA
28601277 AATAT-AATATAAAAAT
1 AATATGAATATAAAAAT
28601293 TTAAAGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AATATGAATATAAAAATA
Found at i:28610333 original size:18 final size:20
Alignment explanation
Indices: 28610296--28610336 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28610286 TTTGAGTTTC
*
28610296 TTTCCTTTTTCTTTTCCTTT
1 TTTCCTTTGTCTTTTCCTTT
28610316 TTTCCTTTGT-TTTT-CTTT
1 TTTCCTTTGTCTTTTCCTTT
28610334 TTT
1 TTT
28610337 TTTTTTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
20 9 0.45
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTCCTTTGTCTTTTCCTTT
Found at i:28620750 original size:15 final size:15
Alignment explanation
Indices: 28620730--28620760 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28620720 AAAAAGACAG
28620730 ATCATCTCCACTAGC
1 ATCATCTCCACTAGC
28620745 ATCATCTCCACTAGC
1 ATCATCTCCACTAGC
28620760 A
1 A
28620761 CAATTGGCCC
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:0.29, C:0.39, G:0.06, T:0.26
Consensus pattern (15 bp):
ATCATCTCCACTAGC
Found at i:28625098 original size:2 final size:2
Alignment explanation
Indices: 28625091--28625120 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28625081 ACCAAATAAG
28625091 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
28625121 CAAGAAATAA
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):
TA
Found at i:28626727 original size:21 final size:19
Alignment explanation
Indices: 28626671--28626728 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 19
28626661 CAAAAATATT
28626671 AAAAATCTAAAAAGTTAATA
1 AAAAATCTAAAAA-TTAATA
*
28626691 AAAAATTTTAAAAAATTCAAATA
1 AAAAA-TCT-AAAAATT--AATA
28626714 AAAAATCTAAAAATT
1 AAAAATCTAAAAATT
28626729 TTTTAACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 5 0.16
21 11 0.34
22 7 0.22
23 9 0.28
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAATCTAAAAATTAATA
Found at i:28626831 original size:11 final size:10
Alignment explanation
Indices: 28626772--28626906 Score: 64
Period size: 10 Copynumber: 13.6 Consensus size: 10
28626762 AAACAATTCT
*
28626772 AAAATTCTAA
1 AAAATTTTAA
*
28626782 AAAATTTCCAA
1 AAAATTT-TAA
*
28626793 AAAATTTTTCA
1 AAAA-TTTTAA
* *
28626804 AACA-TTCAA
1 AAAATTTTAA
28626813 AAAATTTTAA
1 AAAATTTTAA
28626823 AAGAATTTTAA
1 AA-AATTTTAA
*** **
28626834 ATTTTTTTGT
1 AAAATTTTAA
**
28626844 AAAA-TCCAA
1 AAAATTTTAA
28626853 AAAATTTT-A
1 AAAATTTTAA
*
28626862 AAAATTCTAA
1 AAAATTTTAA
* *
28626872 AAACTTTTTA
1 AAAATTTTAA
28626882 AAAATTTT--
1 AAAATTTTAA
28626890 AAAATTTCTAA
1 AAAATTT-TAA
28626901 AAAATT
1 AAAATT
28626907 AAAAAATAAT
Statistics
Matches: 88, Mismatches: 28, Indels: 17
0.66 0.21 0.13
Matches are distributed among these distances:
8 7 0.08
9 20 0.23
10 33 0.38
11 25 0.28
12 3 0.03
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:28626864 original size:9 final size:9
Alignment explanation
Indices: 28626852--28626913 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
28626842 GTAAAATCCA
28626852 AAAAATTTT
1 AAAAATTTT
*
28626861 AAAAATTCT
1 AAAAATTTT
28626870 AAAAACTTTTT
1 AAAAA--TTTT
28626881 AAAAATTTT
1 AAAAATTTT
28626890 -AAAATTTCT
1 AAAAATTT-T
* *
28626899 AAAAAATTA
1 AAAAATTTT
28626908 AAAAAT
1 AAAAAT
28626914 AATTAAGGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 7 0.16
9 23 0.52
10 6 0.14
11 8 0.18
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:28627062 original size:37 final size:36
Alignment explanation
Indices: 28627022--28627108 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 36
28627012 AATTATGATT
28627022 TTTTTTAT-AATTTATAAAAGTATTTCA-TATTTTTC-A
1 TTTTTTATAAATTTA-AAAA--ATTTCATTATTTTTCTA
*
28627058 TTTTTTATAAATTTAAAAAATTTTATTATTTTTCTAA
1 TTTTTTATAAATTTAAAAAATTTCATTATTTTTCT-A
*
28627095 TTTTTTAAAAATTT
1 TTTTTTATAAATTT
28627109 TTAGAACTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 5 0.11
35 8 0.18
36 12 0.27
37 20 0.44
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (36 bp):
TTTTTTATAAATTTAAAAAATTTCATTATTTTTCTA
Found at i:28627157 original size:10 final size:10
Alignment explanation
Indices: 28627093--28627149 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
28627083 TTATTTTTCT
*
28627093 AATTTTTTAA
1 AATTTTTTAG
*
28627103 AAATTTTTAG
1 AATTTTTTAG
*
28627113 AACTTTTTAG
1 AATTTTTTAG
**
28627123 AAGGTTTT--
1 AATTTTTTAG
28627131 AATTTTTTAG
1 AATTTTTTAG
28627141 AATTTTTTA
1 AATTTTTTA
28627150 AATATTTTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 6 0.16
10 32 0.84
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (10 bp):
AATTTTTTAG
Found at i:28627219 original size:26 final size:25
Alignment explanation
Indices: 28627172--28627220 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
28627162 AATTTTAAAA
* **
28627172 AAAAATTTGAATATTTAAAAAAATT
1 AAAATTTTGAATATTTTTAAAAATT
28627197 AAAATTTTAGAATATTTTTAAAAA
1 AAAATTTT-GAATATTTTTAAAAA
28627221 GTTTTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
AAAATTTTGAATATTTTTAAAAATT
Found at i:28627351 original size:20 final size:20
Alignment explanation
Indices: 28627326--28627370 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
28627316 AAAAAATTAT
*
28627326 AATTTTTCA-AAAATTTTAG
1 AATTTTTTAGAAAATTTTAG
**
28627345 AATTTTTTAGAATGTTTTAG
1 AATTTTTTAGAAAATTTTAG
28627365 AATTTT
1 AATTTT
28627371 AATTTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (20 bp):
AATTTTTTAGAAAATTTTAG
Found at i:28627352 original size:10 final size:10
Alignment explanation
Indices: 28627339--28627370 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
28627329 TTTTCAAAAA
28627339 TTTTAGAATT
1 TTTTAGAATT
*
28627349 TTTTAGAATG
1 TTTTAGAATT
28627359 TTTTAGAATT
1 TTTTAGAATT
28627369 TT
1 TT
28627371 AATTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (10 bp):
TTTTAGAATT
Found at i:28627427 original size:27 final size:28
Alignment explanation
Indices: 28627379--28627434 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
28627369 TTAATTTTAA
*
28627379 ATTTTTTGAGAAACTTTAAAAAGTTTTT
1 ATTTTTTGAGAAACTTTAAAAACTTTTT
* * *
28627407 ATTTTTTTAG-AATTTTTAAAACTTTTT
1 ATTTTTTGAGAAACTTTAAAAACTTTTT
28627434 A
1 A
28627435 AATTATGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (28 bp):
ATTTTTTGAGAAACTTTAAAAACTTTTT
Found at i:28627533 original size:9 final size:9
Alignment explanation
Indices: 28627519--28627647 Score: 71
Period size: 9 Copynumber: 13.6 Consensus size: 9
28627509 ATTTTTCAAA
28627519 AATTTTTAG
1 AATTTTTAG
*
28627528 AATTTTTGG
1 AATTTTTAG
28627537 AATGTTTT-G
1 AAT-TTTTAG
28627546 AATTTTTTCTAG
1 AA--TTTT-TAG
*
28627558 AATTTTTAA
1 AATTTTTAG
*
28627567 AAATTTTAG
1 AATTTTTAG
* **
28627576 GATTTTTTT
1 AATTTTTAG
* *
28627585 AAGTGTTTAC
1 AA-TTTTTAG
*
28627595 AATTTTTTTG
1 AA-TTTTTAG
*
28627605 AAGTTTTTAA
1 AA-TTTTTAG
28627615 AATTTTTAG
1 AATTTTTAG
* *
28627624 AAAATTTTAA
1 -AATTTTTAG
28627634 AATTTTTAG
1 AATTTTTAG
28627643 AATTT
1 AATTT
28627648 AAAAAAAAAA
Statistics
Matches: 89, Mismatches: 24, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
9 47 0.53
10 37 0.42
11 2 0.02
12 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.55
Consensus pattern (9 bp):
AATTTTTAG
Found at i:28627601 original size:20 final size:20
Alignment explanation
Indices: 28627577--28627621 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
28627567 AAATTTTAGG
*
28627577 ATTTTTTT-AAGTGTTTACA
1 ATTTTTTTGAAGTGTTTAAA
*
28627596 ATTTTTTTGAAGTTTTTAAA
1 ATTTTTTTGAAGTGTTTAAA
28627616 ATTTTT
1 ATTTTT
28627622 AGAAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (20 bp):
ATTTTTTTGAAGTGTTTAAA
Found at i:28627647 original size:48 final size:48
Alignment explanation
Indices: 28627508--28627647 Score: 124
Period size: 48 Copynumber: 2.9 Consensus size: 48
28627498 AAAAATTTAT
**
28627508 AATTTTTCAAAAATTTTTAGAATTTTTGGAATGTTTT-GAATTTTTTCTAG
1 AATTTTT--AAAATTTTTAGAATTTTTAAAAT-TTTTAGAATTTTTTCTAG
* * * * * *
28627558 AATTTTTAAAAATTTTAGGATTTTTTTAAGTGTTTACAATTTTTT-T-G
1 AATTTTTAAAATTTTTA-GAATTTTTAAAATTTTTAGAATTTTTTCTAG
*
28627605 AAGTTTTTAAAATTTTTAGAAAATTTTAAAATTTTTAGAATTT
1 AA-TTTTTAAAATTTTTAG-AATTTTTAAAATTTTTAGAATTT
28627648 AAAAAAAAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
47 4 0.06
48 44 0.61
49 17 0.24
50 7 0.10
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (48 bp):
AATTTTTAAAATTTTTAGAATTTTTAAAATTTTTAGAATTTTTTCTAG
Found at i:28627700 original size:21 final size:19
Alignment explanation
Indices: 28627674--28627718 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
28627664 TTTTTAATAT
28627674 TTTTTAAGAATTTTATTTTAA
1 TTTTTAAG-ATTTT-TTTTAA
*
28627695 TTTTTATGATTTTTTTTAA
1 TTTTTAAGATTTTTTTTAA
28627714 TTTTT
1 TTTTT
28627719 TTATGCTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
20 5 0.22
21 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTTTAAGATTTTTTTTAA
Found at i:28627719 original size:21 final size:22
Alignment explanation
Indices: 28627664--28627723 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
28627654 AAAATTAAAA
*
28627664 TTTTTAATATTTTTTAAGAATTT
1 TTTTTAAT-TTTTTTATGAATTT
28627687 TATTTTAA--TTTTTATG-ATTT
1 T-TTTTAATTTTTTTATGAATTT
28627707 TTTTTAATTTTTTTATG
1 TTTTTAATTTTTTTATG
28627724 CTAATATGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 6 0.18
20 5 0.15
21 15 0.45
23 1 0.03
24 6 0.18
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTTTAATTTTTTTATGAATTT
Found at i:28627897 original size:26 final size:24
Alignment explanation
Indices: 28627855--28627914 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
28627845 AAACGATTTG
* *
28627855 AAAA-TTTATATAATAATGTGATAAA
1 AAAATTTTAAATAATAATATG--AAA
* *
28627880 AAAATTTTAAATATTAATATGACA
1 AAAATTTTAAATAATAATATGAAA
28627904 AAAATTTTAAA
1 AAAATTTTAAA
28627915 ATTCTAAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 13 0.43
25 4 0.13
26 13 0.43
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (24 bp):
AAAATTTTAAATAATAATATGAAA
Found at i:28643772 original size:29 final size:26
Alignment explanation
Indices: 28643739--28643815 Score: 64
Period size: 29 Copynumber: 2.8 Consensus size: 26
28643729 ATTTTTGTAG
28643739 AAATATTAATAAAATTTTTATTGATAAA
1 AAATATTAATAAAATTTTTATT-AT-AA
** * **
28643767 TAAATATCGATCAAATTTAAATTATAA
1 -AAATATTAATAAAATTTTTATTATAA
*
28643794 AAATATTTATAATAATTTTTAT
1 AAATATTAATAA-AATTTTTAT
28643816 ATATTTATTT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
26 9 0.24
27 9 0.24
28 2 0.05
29 17 0.46
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (26 bp):
AAATATTAATAAAATTTTTATTATAA
Found at i:28651672 original size:67 final size:67
Alignment explanation
Indices: 28651564--28651731 Score: 291
Period size: 67 Copynumber: 2.5 Consensus size: 67
28651554 CATTTAGACT
28651564 TGCAAACTTAAGAACTCTACATGAGCCTTAGATAGCCTTAGATTCATAATAAAATGAGTCCACTT
1 TGCAAACTTAAGAACTCTACATGAGCCTTAGATAGCCTTAGATTCATAATAAAATGAGTCCACTT
28651629 AA
66 AA
*
28651631 TGCAAACTTAAGAACTCTACATGAGCCTTAGATAGCCTTAGATTCATAATAAAATGAGTCCATTT
1 TGCAAACTTAAGAACTCTACATGAGCCTTAGATAGCCTTAGATTCATAATAAAATGAGTCCACTT
*
28651696 GA
66 AA
**
28651698 TGGGAACTTAAGAACTCTACATGGAGCCTTAGAT
1 TGCAAACTTAAGAACTCTACAT-GAGCCTTAGAT
28651732 TCATAATAAA
Statistics
Matches: 96, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 85 0.89
68 11 0.11
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (67 bp):
TGCAAACTTAAGAACTCTACATGAGCCTTAGATAGCCTTAGATTCATAATAAAATGAGTCCACTT
AA
Found at i:28652964 original size:2 final size:2
Alignment explanation
Indices: 28652959--28652998 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
28652949 GAGAGATCAT
*
28652959 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G GG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
28652999 AATAAACAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28655697 original size:29 final size:29
Alignment explanation
Indices: 28655606--28655697 Score: 141
Period size: 29 Copynumber: 3.2 Consensus size: 29
28655596 TTTCTCATTG
28655606 AATTTT-TTTTTTCAATCGCAGCTACAAT
1 AATTTTATTTTTTCAATCGCAGCTACAAT
* *
28655634 AATTTAATTTTTTCAATCGCAGCCACAAT
1 AATTTTATTTTTTCAATCGCAGCTACAAT
* *
28655663 AATTTTATTTTTTCAATCGTAGCTATAAT
1 AATTTTATTTTTTCAATCGCAGCTACAAT
28655692 AATTTT
1 AATTTT
28655698 TATTACTGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 5 0.09
29 52 0.91
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.47
Consensus pattern (29 bp):
AATTTTATTTTTTCAATCGCAGCTACAAT
Found at i:28656760 original size:22 final size:23
Alignment explanation
Indices: 28656735--28656788 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
28656725 TATAAAATTA
*
28656735 ATATAAAATAAA-TATAATATAT
1 ATATAAAACAAATTATAATATAT
* * *
28656757 ATATATATACAAATTATTATATCT
1 ATATA-AAACAAATTATAATATAT
28656781 ATATAAAA
1 ATATAAAA
28656789 GAAGTGAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 5 0.20
23 7 0.28
24 13 0.52
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATAAAACAAATTATAATATAT
Found at i:28656762 original size:24 final size:23
Alignment explanation
Indices: 28656735--28656788 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
28656725 TATAAAATTA
*
28656735 ATATAAAATAAATATAATATATAT
1 ATATAAAACAAAT-TAATATATAT
* * *
28656759 ATAT-ATACAAATTATTATATCT
1 ATATAAAACAAATTAATATATAT
28656781 ATATAAAA
1 ATATAAAA
28656789 GAAGTGAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 12 0.50
23 8 0.33
24 4 0.17
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATAAAACAAATTAATATATAT
Found at i:28658465 original size:19 final size:19
Alignment explanation
Indices: 28658400--28658470 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
28658390 ACATACTATA
*
28658400 AATAAACACAAATAACACT
1 AATATACACAAATAACACT
* *
28658419 AATTTATACAAATAA-ACAT
1 AATATACACAAATAACAC-T
* * *
28658438 GATACACACGAATAACACT
1 AATATACACAAATAACACT
28658457 AATATACACAAATA
1 AATATACACAAATA
28658471 CATAGCAGAT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
18 2 0.05
19 35 0.90
20 2 0.05
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (19 bp):
AATATACACAAATAACACT
Found at i:28663735 original size:20 final size:20
Alignment explanation
Indices: 28663712--28663750 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28663702 CATATATCAT
* *
28663712 GTCAATAAGAATTATATCGC
1 GTCAACAAGAATAATATCGC
*
28663732 GTCAACATGAATAATATCG
1 GTCAACAAGAATAATATCG
28663751 TGTCGATACG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
GTCAACAAGAATAATATCGC
Found at i:28665458 original size:17 final size:18
Alignment explanation
Indices: 28665436--28665469 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28665426 TTTAATTAAA
28665436 TTTTTA-TATTTAAATTT
1 TTTTTATTATTTAAATTT
*
28665453 TTTTTATTATTTTAATT
1 TTTTTATTATTTAAATT
28665470 AATAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATTATTTAAATTT
Found at i:28665661 original size:19 final size:18
Alignment explanation
Indices: 28665637--28665678 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
28665627 AATCGAATTT
*
28665637 AAATTAAATATCAAACTTC
1 AAATTAAAAATCAAAC-TC
*
28665656 AAATTAAAAATTAAACTC
1 AAATTAAAAATCAAACTC
28665674 AAATT
1 AAATT
28665679 TTTTACTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATTAAAAATCAAACTC
Found at i:28670700 original size:22 final size:22
Alignment explanation
Indices: 28670652--28670701 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
28670642 ATTTTTATTT
* *
28670652 TTATTTTTATTAAAATTTTATA
1 TTATTATTATTAAAATTTTAAA
* *
28670674 CTATTATTGTTAAAATTTTAAA
1 TTATTATTATTAAAATTTTAAA
28670696 TTATTA
1 TTATTA
28670702 ATTTTATATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATTATTATTAAAATTTTAAA
Found at i:28670700 original size:38 final size:39
Alignment explanation
Indices: 28670665--28670736 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 39
28670655 TTTTTATTAA
*
28670665 AATTTTATACTAT-T-ATTGT-TAAAATTTTAAATTATT
1 AATTTTATACTATCTCATTGTATAAAATTTAAAATTATT
* *
28670701 AATTTTATATTATCTCATTGTATAATATTTAAAATT
1 AATTTTATACTATCTCATTGTATAAAATTTAAAATT
28670737 GACGGATCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 12 0.40
37 1 0.03
38 5 0.17
39 12 0.40
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (39 bp):
AATTTTATACTATCTCATTGTATAAAATTTAAAATTATT
Found at i:28679620 original size:29 final size:27
Alignment explanation
Indices: 28679582--28679644 Score: 108
Period size: 29 Copynumber: 2.3 Consensus size: 27
28679572 GCACCAAAAA
28679582 AAAAAAAATTATACTTTTATGAAAAATAT
1 AAAAAAAATTATACTTTTATG-AAAAT-T
28679611 AAAAAAAATTATACTTTTATGAAAATT
1 AAAAAAAATTATACTTTTATGAAAATT
28679638 AAAAAAA
1 AAAAAAA
28679645 TAATAATTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 8 0.24
28 5 0.15
29 21 0.62
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (27 bp):
AAAAAAAATTATACTTTTATGAAAATT
Found at i:28682547 original size:15 final size:15
Alignment explanation
Indices: 28682522--28682558 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
28682512 TCAGGAGGTG
28682522 AGAATGATGAAGAAGA
1 AGAA-GATGAAGAAGA
*
28682538 GGAAGATGAAGAAGA
1 AGAAGATGAAGAAGA
28682553 AGAAGA
1 AGAAGA
28682559 AGTGAAACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 16 0.84
16 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.08
Consensus pattern (15 bp):
AGAAGATGAAGAAGA
Found at i:28691335 original size:23 final size:24
Alignment explanation
Indices: 28691288--28691342 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
28691278 AAATATATGT
*
28691288 TTTAT-TATTCATTTAATTTTATA
1 TTTATATATTCATTTAAATTTATA
28691311 TTTATATATT-ATTTAAA-TTATTA
1 TTTATATATTCATTTAAATTTA-TA
28691334 TTTA-ATATT
1 TTTATATATT
28691343 TTAATTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 8 0.28
23 17 0.59
24 4 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTATATATTCATTTAAATTTATA
Found at i:28691342 original size:19 final size:19
Alignment explanation
Indices: 28691291--28691348 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
28691281 TATATGTTTT
*
28691291 ATTATTCATTTAAT-TTTAT
1 ATTATT-ATTTAATATTTAA
* *
28691310 A-T-TTATATATTATTTAA
1 ATTATTATTTAATATTTAA
*
28691327 ATTATTATTTAATATTTTA
1 ATTATTATTTAATATTTAA
28691346 ATT
1 ATT
28691349 TAATAAATCC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 5 0.17
17 7 0.23
18 2 0.07
19 16 0.53
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTATTTAATATTTAA
Found at i:28691351 original size:13 final size:12
Alignment explanation
Indices: 28691298--28691353 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
28691288 TTTATTATTC
28691298 ATTTAAT-TTTAT
1 ATTTAATATTT-T
*
28691310 ATTT-ATATATT
1 ATTTAATATTTT
28691321 ATTTAA-ATTATT
1 ATTTAATATT-TT
28691333 ATTTAATATTTT
1 ATTTAATATTTT
28691345 AATTTAATA
1 -ATTTAATA
28691354 AATCCACGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
11 9 0.24
12 17 0.46
13 11 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTAATATTTT
Done.