Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 131 of 172
Found at i:43608613 original size:44 final size:42
Alignment explanation
Indices: 43608329--43608701 Score: 213
Period size: 44 Copynumber: 8.6 Consensus size: 42
43608319 GTTTATTATA
* * **
43608329 CAGG-TCTTATCTCCCTGAGAATACAGTGGAACAGACCAAAG
1 CAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
* *
43608370 AATTTCA-GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG
1 -----CAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
* * * * *
43608416 ATAGTAATCCTATCTCCTTGAGATTACAATGGAGCAGATT-AA-
1 -CAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
* * * * * *
43608458 -AGGATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACAT
1 CAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAG
** **
43608499 CAGG-TCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAG
1 CAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
* * *
43608540 AATTTCGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAG
1 CA----GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
* **
43608586 CCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG
1 -CAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
** * * *
43608630 ACACTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATA
1 -CAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATT-AAA-G
* * *
43608675 AAGGATCTTATCTCTCTGAGGTTACAG
1 CAGGATCTTATCTCCCTGAGATTACAG
43608702 CAGAGTAGAT
Statistics
Matches: 254, Mismatches: 54, Indels: 40
0.73 0.16 0.11
Matches are distributed among these distances:
38 1 0.00
39 25 0.10
40 3 0.01
41 29 0.11
42 6 0.02
43 31 0.12
44 89 0.35
45 3 0.01
46 66 0.26
47 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
CAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
Found at i:43608643 original size:87 final size:87
Alignment explanation
Indices: 43608552--43608713 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
43608542 TTTCGGATCT
* * * *
43608552 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCTGAGATTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCTGAGATTACAGC
*
43608616 GGAGCAGATCGAAGACACTATCC
65 AGAGCAGATCGAAGACACTATCC
* * * *
43608639 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
*
43608704 GAGTAGATCG
66 GAGCAGATCG
43608714 CATCAAGTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 62 0.97
88 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
GAGCAGATCGAAGACACTATCC
Found at i:43608817 original size:218 final size:213
Alignment explanation
Indices: 43608376--43608817 Score: 462
Period size: 218 Copynumber: 2.0 Consensus size: 213
43608366 AAAGAATTTC
* * *
43608376 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
* *
43608441 ACAATGGAGCAGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCAGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
* * ** * * *
43608506 TATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCGGATCTTATCTCCCTGAGGTTACAG
131 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAAATAAGGA-CGTATCTCCCTAAAGTTACAG
* *** *
43608571 TGGAGCAGATTGAAGCCAG
195 CGGAGCAGACAAAAGACAG
*
43608590 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGA-T
* * * * *
43608653 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATC
65 TACAATGGAGCAGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATC
* * * *
43608718 AAGTCTTATTTCCCTGAAGA-TGCAGTGGAACAGACTGAAA-ACAATAAGG-CGTGTCTCCCTAA
125 AAGTCTTATCTCCCTG-AGATTACAGTGGAACAGAC-CAAAGA-AATAAGGACGTATCTCCCTAA
** * *
43608780 AGTTGTAGCGGAGCGGACAAAAGATAG
187 AGTTACAGCGGAGCAGACAAAAGACAG
*
43608807 TGATTCTTATC
1 AGA-TCTTATC
43608818 ATGTCTAATC
Statistics
Matches: 186, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
212 1 0.01
213 27 0.15
214 43 0.23
217 29 0.16
218 76 0.41
219 10 0.05
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (213 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
ACAATGGAGCAGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAAATAAGGACGTATCTCCCTAAAGTTACAGC
GGAGCAGACAAAAGACAG
Found at i:43609288 original size:15 final size:16
Alignment explanation
Indices: 43609268--43609297 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43609258 CTAACAAAAG
43609268 AACCCAAT-ACCCACA
1 AACCCAATAACCCACA
43609283 AACCCAATAACCCAC
1 AACCCAATAACCCAC
43609298 CTAAACACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.47, G:0.00, T:0.07
Consensus pattern (16 bp):
AACCCAATAACCCACA
Found at i:43610160 original size:16 final size:16
Alignment explanation
Indices: 43610132--43610164 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43610122 TACACTCATG
43610132 TATATGTTTTATATTT
1 TATATGTTTTATATTT
43610148 TATA-GTTTATATATTT
1 TATATGTTT-TATATTT
43610164 T
1 T
43610165 CTTTGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
TATATGTTTTATATTT
Found at i:43611397 original size:25 final size:26
Alignment explanation
Indices: 43611367--43611431 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
43611357 TATAAACGGT
43611367 AAGCTCCA-CCGAGCTAAATAATGGG
1 AAGCTCCATCCGAGCTAAATAATGGG
** *
43611392 AAGCT-CATGTGAGCTGAATAATGGG
1 AAGCTCCATCCGAGCTAAATAATGGG
*
43611417 AAGCT-CATGCGAGCT
1 AAGCTCCATCCGAGCT
43611432 GAGTATCAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 2 0.06
25 33 0.94
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (26 bp):
AAGCTCCATCCGAGCTAAATAATGGG
Found at i:43611432 original size:25 final size:25
Alignment explanation
Indices: 43611376--43611433 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
43611366 TAAGCTCCAC
*
43611376 CGAGCTAAATAATGGGAAGCTCATG
1 CGAGCTGAATAATGGGAAGCTCATG
*
43611401 TGAGCTGAATAATGGGAAGCTCATG
1 CGAGCTGAATAATGGGAAGCTCATG
43611426 CGAGCTGA
1 CGAGCTGA
43611434 GTATCAGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.21
Consensus pattern (25 bp):
CGAGCTGAATAATGGGAAGCTCATG
Found at i:43618159 original size:27 final size:25
Alignment explanation
Indices: 43618121--43618237 Score: 121
Period size: 27 Copynumber: 4.4 Consensus size: 25
43618111 GACTTTTTAC
43618121 TTTAAACTATTTTATTATATATTATTT
1 TTTAAACT-TTTT-TTATATATTATTT
* *
43618148 TTTAAA-TTATTTTATATATGATCTAT
1 TTTAAACTTTTTTTATATATTAT-T-T
*
43618174 TTT-AAGTTTTTTTATATATTATTTAT
1 TTTAAACTTTTTTTATATATTA-TT-T
43618200 TTTAAACTTTTTTTATATATTATTT
1 TTTAAACTTTTTTTATATATTATTT
43618225 ATTTCAAACTTTT
1 -TTT-AAACTTTT
43618238 ACATATGTTA
Statistics
Matches: 78, Mismatches: 5, Indels: 14
0.80 0.05 0.14
Matches are distributed among these distances:
24 10 0.13
25 7 0.09
26 29 0.37
27 32 0.41
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (25 bp):
TTTAAACTTTTTTTATATATTATTT
Found at i:43618214 original size:53 final size:50
Alignment explanation
Indices: 43618130--43618228 Score: 135
Period size: 53 Copynumber: 1.9 Consensus size: 50
43618120 CTTTAAACTA
43618130 TTTTATTATATATTATTTTTTAAATTATTTTATATATGATCTATTTTAAG
1 TTTTATTATATATTATTTTTTAAATTATTTTATATATGATCTATTTTAAG
* * * *
43618180 TTTTTTTATATATTATTTATTTTAAACTTTTTTTATATATTATTTATTT
1 TTTTATTATATATTA-TT-TTTTAAA-TTATTTTATATATGATCTATTT
43618229 CAAACTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
50 14 0.33
51 2 0.05
52 7 0.17
53 19 0.45
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (50 bp):
TTTTATTATATATTATTTTTTAAATTATTTTATATATGATCTATTTTAAG
Found at i:43618237 original size:26 final size:26
Alignment explanation
Indices: 43618116--43618256 Score: 126
Period size: 26 Copynumber: 5.3 Consensus size: 26
43618106 TCCTTGACTT
*
43618116 TTTACTTTAAACTATTTTATTATATATTA
1 TTTATTTTAAAC--TTTT-TTATATATTA
*
43618145 -TT-TTTTAAA-TTATTTTATATATGA
1 TTTATTTTAAACTT-TTTTATATATTA
* **
43618169 TCTATTTTAAGTTTTTTTATATATTA
1 TTTATTTTAAACTTTTTTATATATTA
43618195 TTTATTTTAAACTTTTTTTATATATTA
1 TTTATTTTAAAC-TTTTTTATATATTA
* ** *
43618222 TTTATTTCAAACTTTTACATATGTTA
1 TTTATTTTAAACTTTTTTATATATTA
*
43618248 TCTATTTTA
1 TTTATTTTA
43618257 TATATTATTT
Statistics
Matches: 93, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
24 11 0.12
25 3 0.03
26 44 0.47
27 33 0.35
28 2 0.02
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTATTTTAAACTTTTTTATATATTA
Found at i:43618254 original size:53 final size:52
Alignment explanation
Indices: 43618137--43618266 Score: 129
Period size: 53 Copynumber: 2.5 Consensus size: 52
43618127 CTATTTTATT
* ** **
43618137 ATATATTAT-T-TTTTAAATTATTTTATATATGATCTATTTTAAGTTTTTTT
1 ATATATTATCTATTTTAAATTATTTTATATATGATCTATTTCAAACTTTTAC
* * * *
43618187 ATATATTATTTATTTTAAACTTTTTTTATATATTATTTATTTCAAACTTTTAC
1 ATATATTATCTATTTTAAA-TTATTTTATATATGATCTATTTCAAACTTTTAC
*
43618240 ATATGTTATCTATTTTATATATTATTT
1 ATATATTATCTATTTTA-A-ATTATTT
43618267 AGTTTAAACT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
50 9 0.14
51 1 0.02
52 7 0.11
53 40 0.62
54 6 0.09
55 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (52 bp):
ATATATTATCTATTTTAAATTATTTTATATATGATCTATTTCAAACTTTTAC
Found at i:43618257 original size:42 final size:42
Alignment explanation
Indices: 43618205--43618297 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
43618195 TTTATTTTAA
*
43618205 ACTTTTTTTATATATTATTTA-TTTCAAACT-TTTACATATGTT
1 ACTTATTTTATATATTATTTAGTTT-AAACTGTTT-CATATGTT
*
43618247 A-TCTATTTTATATATTATTTAGTTTAAACTGTTTTATATGTT
1 ACT-TATTTTATATATTATTTAGTTTAAACTGTTTCATATGTT
43618289 ACTTATTTT
1 ACTTATTTT
43618298 TAAAAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
41 1 0.02
42 37 0.82
43 7 0.16
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (42 bp):
ACTTATTTTATATATTATTTAGTTTAAACTGTTTCATATGTT
Found at i:43618373 original size:26 final size:25
Alignment explanation
Indices: 43618344--43618972 Score: 173
Period size: 26 Copynumber: 25.4 Consensus size: 25
43618334 TATATATGAT
*
43618344 TTTTAAATTGTTTTATATATTATCTA
1 TTTTAAATT-TTTTATATATTATTTA
*
43618370 TTTTAAGTTTTTTTATATATTATTTA
1 TTTTAA-ATTTTTTATATATTATTTA
43618396 TTTTAAACTTTTTTATATATTATTTA
1 TTTTAAA-TTTTTTATATATTATTTA
* * *
43618422 TTTCAAA-CTTTTACATA--ATTTA
1 TTTTAAATTTTTTATATATTATTTA
* *
43618444 -TCT--ATTTTATATATTATCTAGTTTA
1 TTTTAAATTTTTTATA-TAT-TA-TTTA
* * * *
43618469 ----AACTGTTTTATATGTTACTTATT
1 TTTTAAATTTTTTATATATTA-TT-TA
***** * *
43618492 TTTTAAAAAAAAT-TATATTGTATA
1 TTTTAAATTTTTTATATATTATTTA
* *
43618516 TTTGAAACTGTTTTAT-TA-TATATTA
1 TTTTAAA-TTTTTTATATATTAT-TTA
*
43618541 TTTTTAAATTATTTTATATATTATCTA
1 -TTTTAAATT-TTTTATATATTATTTA
*
43618568 TTTTAAGTTTTTTTTATATATTATTTA
1 TTTTAA--ATTTTTTATATATTATTTA
43618595 TTTTAAACCTTTTTTTTCATATATTATTTA
1 TTTTAAA----TTTTTT-ATATATTATTTA
* * ** *
43618625 TGTCAAACTTTTACATATGTTATTTA
1 TTTTAAA-TTTTTTATATATTATTTA
* *
43618651 TTTT--A-TATAT-TAT-TTAGTTTA
1 TTTTAAATTTTTTATATATTA-TTTA
* * * *
43618672 ----AACTGTTTTATATGTTACTTA
1 TTTTAAATTTTTTATATATTATTTA
***** * *
43618693 TTTTAAAAAAAAT-TATATTGTATA
1 TTTTAAATTTTTTATATATTATTTA
*
43618717 TTTGAAATTGTTTTAT-TA-TATATTA
1 TTTTAAATT-TTTTATATATTAT-TTA
* *
43618742 TTTTTAAATTATTTATATATTATCTA
1 -TTTTAAATTTTTTATATATTATTTA
* *
43618768 TTTTAAGTTTTTTTATATATTATGTA
1 TTTTAA-ATTTTTTATATATTATTTA
43618794 TTTTAAACCTTTTTTTTCATATATTATTTA
1 TTTTAAA----TTTTTT-ATATATTATTTA
* * * *
43618824 TTTCAAA-CTTTTACATA-T-GTTA
1 TTTTAAATTTTTTATATATTATTTA
43618846 --TT--ATTTTTTATATATTATTTA
1 TTTTAAATTTTTTATATATTATTTA
* * *
43618867 GTTTAAACTGTTTTATATGTTATTTA
1 TTTTAAA-TTTTTTATATATTATTTA
*
43618893 TTTTAAAATTTTTATAT-TGTA--TA
1 TTTTAAATTTTTTATATAT-TATTTA
* *
43618916 TTTGAAACTGTTTTAT-TATTATTTA
1 TTTTAAA-TTTTTTATATATTATTTA
* *
43618941 TTATAAGTTTTTT-T-TATTATTTA
1 TTTTAAATTTTTTATATATTATTTA
*
43618964 TTTGAAATT
1 TTTTAAATT
43618973 GTCCTATTAT
Statistics
Matches: 434, Mismatches: 105, Indels: 131
0.65 0.16 0.20
Matches are distributed among these distances:
18 1 0.00
19 9 0.02
20 12 0.03
21 19 0.04
22 18 0.04
23 33 0.08
24 58 0.13
25 51 0.12
26 145 0.33
27 37 0.09
28 5 0.01
29 12 0.03
30 34 0.08
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTTAAATTTTTTATATATTATTTA
Found at i:43618379 original size:49 final size:51
Alignment explanation
Indices: 43618326--43618424 Score: 132
Period size: 52 Copynumber: 2.0 Consensus size: 51
43618316 TATTTGAAAC
43618326 AGTTTTGTTATATATGA-T-TTTTAAA-TTGTTTTATATATTATCTATTTTA
1 AGTTTTGTTATATATGATTATTTTAAACTT-TTTTATATATTATCTATTTTA
* * *
43618375 AGTTTTTTTATATATTATTTATTTTAAACTTTTTTATATATTATTTATTT
1 AGTTTTGTTATATATGA-TTATTTTAAACTTTTTTATATATTATCTATTT
43618425 CAAACTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
49 15 0.35
51 1 0.02
52 25 0.58
53 2 0.05
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (51 bp):
AGTTTTGTTATATATGATTATTTTAAACTTTTTTATATATTATCTATTTTA
Found at i:43618561 original size:23 final size:24
Alignment explanation
Indices: 43618531--43618593 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 24
43618521 AACTGTTTTA
43618531 TTATATATTATTTTTAA-ATTATT
1 TTATATATTATTTTTAAGATTATT
* *
43618554 TTATATATTATCTATTTTAAGTTTTTT
1 TTATATATTA--T-TTTTAAGATTATT
43618581 TTATATATTATTT
1 TTATATATTATTT
43618594 ATTTTAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 10 0.29
24 2 0.06
25 2 0.06
26 6 0.18
27 14 0.41
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
TTATATATTATTTTTAAGATTATT
Found at i:43618611 original size:30 final size:27
Alignment explanation
Indices: 43618552--43618625 Score: 103
Period size: 27 Copynumber: 2.6 Consensus size: 27
43618542 TTTTAAATTA
*
43618552 TTTTATATATTATCTATTTTAAGTTTT
1 TTTTATATATTATTTATTTTAAGTTTT
*
43618579 TTTTATATATTATTTATTTTAAACCTTTT
1 TTTTATATATTATTTATTTT-AA-GTTTT
43618608 TTTTCATATATTATTTAT
1 TTTT-ATATATTATTTAT
43618626 GTCAAACTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
27 19 0.45
28 2 0.05
29 8 0.19
30 13 0.31
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.66
Consensus pattern (27 bp):
TTTTATATATTATTTATTTTAAGTTTT
Found at i:43618659 original size:42 final size:42
Alignment explanation
Indices: 43618608--43618697 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
43618598 TAAACCTTTT
*
43618608 TTTTCATATATTATTTA-TGTCAAACT-TTTACATATGTTATTTA
1 TTTT-ATATATTATTTAGT-TCAAACTGTTT-CATATGTTACTTA
* *
43618651 TTTTATATATTATTTAGTTTAAACTGTTTTATATGTTACTTA
1 TTTTATATATTATTTAGTTCAAACTGTTTCATATGTTACTTA
43618693 TTTTA
1 TTTTA
43618698 AAAAAAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 34 0.81
43 8 0.19
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.59
Consensus pattern (42 bp):
TTTTATATATTATTTAGTTCAAACTGTTTCATATGTTACTTA
Found at i:43618834 original size:29 final size:29
Alignment explanation
Indices: 43618775--43618835 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
43618765 CTATTTTAAG
*
43618775 TTTTTTTATATATTATGTATTTTAAACCT
1 TTTTTTTATATATTATGTATTTCAAACCT
*
43618804 TTTTTTTCATATATTATTTATTTCAAA-CT
1 TTTTTTT-ATATATTATGTATTTCAAACCT
43618833 TTT
1 TTT
43618836 ACATATGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (29 bp):
TTTTTTTATATATTATGTATTTCAAACCT
Found at i:43618835 original size:25 final size:23
Alignment explanation
Indices: 43618732--43619014 Score: 84
Period size: 26 Copynumber: 11.7 Consensus size: 23
43618722 AATTGTTTTA
*
43618732 TTATATATTA-TT-TTTAAATTAT
1 TTATATATTATTTATTTAAACT-T
* **
43618754 TTATATATTATCTATTTTAAGTTTTT
1 TTATATATTATTTA-TTTAA--ACTT
*
43618780 TTATATATTATGTATTTTAAACCTTTTTT
1 TTATATATTATTTA-TTTAAA-C----TT
43618809 TTCATATATTATTTATTTCAAACTT
1 TT-ATATATTATTTATTT-AAACTT
* * **
43618834 TTACATA-T-GTTA-TT-ATTTT
1 TTATATATTATTTATTTAAACTT
43618853 TTATATATTATTTAGTTTAAACTGTT
1 TTATATATTATTTA-TTTAAAC--TT
* *
43618879 TTATATGTTATTTATTTTAAAATT
1 TTATATATTATTTA-TTTAAACTT
* *
43618903 TT-TATATTGTATATTTGAAACTGT
1 TTATATATTATTTATTT-AAACT-T
*
43618927 TT-TATTATTATTTA-TTATAAGTT
1 TTATA-TATTATTTATTTA-AACTT
* *
43618950 TTTTTTATTATTTATTTGAAA-TT
1 TTATATATTATTTATTT-AAACTT
* ** *
43618973 GT-CCTATTATTTTTTTCAAAACGTT
1 TTATATATTATTTATTT--AAAC-TT
*
43618998 TTATAAATTATTTATTT
1 TTATATATTATTTATTT
43619015 TAAAATATTA
Statistics
Matches: 196, Mismatches: 35, Indels: 56
0.68 0.12 0.20
Matches are distributed among these distances:
19 9 0.05
20 1 0.01
21 5 0.03
22 27 0.14
23 35 0.18
24 24 0.12
25 20 0.10
26 51 0.26
27 2 0.01
29 8 0.04
30 14 0.07
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (23 bp):
TTATATATTATTTATTTAAACTT
Found at i:43618838 original size:199 final size:197
Alignment explanation
Indices: 43618124--43618938 Score: 1318
Period size: 199 Copynumber: 4.1 Consensus size: 197
43618114 TTTTTACTTT
* *
43618124 AAACTATTTTATTATATATTATTTTTTAAATTATTTTATATATGATCTATTTTAAGTTTTTTTAT
1 AAACTGTTTTATTATATATTA-TTTTTAAATTATTTTATATATTATCTATTTTAAGTTTTTTTAT
43618189 ATATTATTTATTTTAAACTTTTTTTATATATTATTTATTTCAAACTTTTACATATGTTATCTATT
65 ATATTATTTATTTTAAACTTTTTTTATATATTATTTATTTCAAACTTTTACATATGTTATCTATT
* *
43618254 TTATATATTATTTAGTTTAAACTGTTTTATATGTTACTTATTTTTAAAAAAATTATTTTGTATAT
130 TTATATATTATTTAGTTTAAACTGTTTTATATGTTACTTATTTTAAAAAAAATTATATTGTATAT
43618319 TTG
195 TTG
* * * *
43618322 AAACAGTTTTGTTATATATGATTTTTAAATTGTTTTATATATTATCTATTTTAAGTTTTTTTATA
1 AAACTGTTTTATTATATATTATTTTTAAATTATTTTATATATTATCTATTTTAAGTTTTTTTATA
43618387 TATTATTTATTTTAAAC-TTTTTTATATATTATTTATTTCAAACTTTTACATAAT-TTATCTATT
66 TATTATTTATTTTAAACTTTTTTTATATATTATTTATTTCAAACTTTTACAT-ATGTTATCTATT
*
43618450 TTATATATTATCTAGTTTAAACTGTTTTATATGTTACTTATTTTTTAAAAAAAATTATATTGTAT
130 TTATATATTATTTAGTTTAAACTGTTTTATATGTTACTTA--TTTTAAAAAAAATTATATTGTAT
43618515 ATTTG
193 ATTTG
43618520 AAACTGTTTTATTATATATTATTTTTAAATTATTTTATATATTATCTATTTTAAGTTTTTTTTAT
1 AAACTGTTTTATTATATATTATTTTTAAATTATTTTATATATTATCTATTTTAAG-TTTTTTTAT
* *
43618585 ATATTATTTATTTTAAACCTTTTTTTTCATATATTATTTATGTCAAACTTTTACATATGTTATTT
65 ATATTATTTATTTTAAA-C-TTTTTTT-ATATATTATTTATTTCAAACTTTTACATATGTTATCT
43618650 ATTTTATATATTATTTAGTTTAAACTGTTTTATATGTTACTTATTTTAAAAAAAATTATATTGTA
127 ATTTTATATATTATTTAGTTTAAACTGTTTTATATGTTACTTATTTTAAAAAAAATTATATTGTA
43618715 TATTTG
192 TATTTG
*
43618721 AAATTGTTTTATTATATATTATTTTTAAATTA-TTTATATATTATCTATTTTAAGTTTTTTTATA
1 AAACTGTTTTATTATATATTATTTTTAAATTATTTTATATATTATCTATTTTAAGTTTTTTTATA
*
43618785 TATTATGTATTTTAAACCTTTTTTTTCATATATTATTTATTTCAAACTTTTACATATGTTAT-TA
66 TATTATTTATTTTAAA-C-TTTTTTT-ATATATTATTTATTTCAAACTTTTACATATGTTATCTA
* ***
43618849 TTTTTTATATATTATTTAGTTTAAACTGTTTTATATGTTATTTATTTT-AAAATTTTTATATTGT
128 --TTTTATATATTATTTAGTTTAAACTGTTTTATATGTTACTTATTTTAAAAAAAATTATATTGT
43618913 ATATTTG
191 ATATTTG
43618920 AAACTGTTTTATTAT-TATT
1 AAACTGTTTTATTATATATT
43618939 TATTATAAGT
Statistics
Matches: 582, Mismatches: 24, Indels: 22
0.93 0.04 0.04
Matches are distributed among these distances:
196 82 0.14
197 61 0.10
198 100 0.17
199 130 0.22
200 68 0.12
201 59 0.10
202 8 0.01
203 74 0.13
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (197 bp):
AAACTGTTTTATTATATATTATTTTTAAATTATTTTATATATTATCTATTTTAAGTTTTTTTATA
TATTATTTATTTTAAACTTTTTTTATATATTATTTATTTCAAACTTTTACATATGTTATCTATTT
TATATATTATTTAGTTTAAACTGTTTTATATGTTACTTATTTTAAAAAAAATTATATTGTATATT
TG
Found at i:43618859 original size:43 final size:45
Alignment explanation
Indices: 43618805--43618896 Score: 129
Period size: 43 Copynumber: 2.1 Consensus size: 45
43618795 TTTAAACCTT
43618805 TTTTTTCATATATTATTTA-TTTCAAACT-TTTACATATGTTA-TTA
1 TTTTTTCATATATTATTTAGTTT-AAACTGTTT-CATATGTTATTTA
*
43618849 TTTTTT-ATATATTATTTAGTTTAAACTGTTTTATATGTTATTTA
1 TTTTTTCATATATTATTTAGTTTAAACTGTTTCATATGTTATTTA
43618893 TTTT
1 TTTT
43618897 AAAATTTTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
43 25 0.57
44 19 0.43
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.63
Consensus pattern (45 bp):
TTTTTTCATATATTATTTAGTTTAAACTGTTTCATATGTTATTTA
Found at i:43618966 original size:48 final size:49
Alignment explanation
Indices: 43618848--43618970 Score: 142
Period size: 48 Copynumber: 2.5 Consensus size: 49
43618838 ATATGTTATT
* *
43618848 ATTTTTTATATATTATTTAGTTT-AAACTGTTTTATATGTTATTTATTTTAA
1 ATTTTTT-T-TATTATTTA-TTTGAAACTGTTTTATATATTATTTATTATAA
* * * *
43618899 AATTTTTATATTGTATATTTGAAACTGTTTTAT-TATTATTTATTATAA
1 ATTTTTTTTATTATTTATTTGAAACTGTTTTATATATTATTTATTATAA
*
43618947 GTTTTTTTTATTATTTATTTGAAA
1 ATTTTTTTTATTATTTATTTGAAA
43618971 TTGTCCTATT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
48 35 0.58
49 19 0.32
51 6 0.10
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.62
Consensus pattern (49 bp):
ATTTTTTTTATTATTTATTTGAAACTGTTTTATATATTATTTATTATAA
Found at i:43619057 original size:18 final size:19
Alignment explanation
Indices: 43619030--43619069 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
43619020 TATTATTTAC
43619030 TTTAAATTTTTTTATA-TA
1 TTTAAATTTTTTTATATTA
*
43619048 TTTAATTTTTTTTATATTA
1 TTTAAATTTTTTTATATTA
43619067 TTT
1 TTT
43619070 TGTTTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTAAATTTTTTTATATTA
Found at i:43625659 original size:15 final size:16
Alignment explanation
Indices: 43625634--43625674 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
43625624 TACTTCACTT
* *
43625634 AAAAAAAAAGAGAAAG
1 AAAAGAAAAGAAAAAG
43625650 -AAAGAAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
43625665 AAAAGAAAAG
1 AAAAGAAAAG
43625675 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:43625662 original size:20 final size:20
Alignment explanation
Indices: 43625634--43625672 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
43625624 TACTTCACTT
43625634 AAAAAAAAAGAGAAAGAAAGA
1 AAAAAAAAAGA-AAAGAAAGA
*
43625655 AAAGAAAAAGAAAAGAAA
1 AAAAAAAAAGAAAAGAAA
43625673 AGGGAGAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAAAAGAAAGA
Found at i:43625666 original size:11 final size:11
Alignment explanation
Indices: 43625634--43625673 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
43625624 TACTTCACTT
43625634 AAAA-AAAAAG
1 AAAAGAAAAAG
43625644 AGAAAG--AAAG
1 A-AAAGAAAAAG
43625654 AAAAGAAAAAG
1 AAAAGAAAAAG
43625665 AAAAGAAAA
1 AAAAGAAAA
43625674 GGGAGAGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.15
10 6 0.23
11 16 0.62
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:43626187 original size:22 final size:23
Alignment explanation
Indices: 43626162--43626207 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
43626152 CAACCAAATC
43626162 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
43626184 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
43626207 A
1 A
43626208 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:43626213 original size:23 final size:23
Alignment explanation
Indices: 43626169--43626213 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
43626159 ATCAATTCAA
*
43626169 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
43626192 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
43626214 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:43628479 original size:107 final size:107
Alignment explanation
Indices: 43628293--43628507 Score: 412
Period size: 107 Copynumber: 2.0 Consensus size: 107
43628283 GTGCAAAAAT
* *
43628293 GATGAAATACCAGCTTAGAGAACCCTCCTATGGCGTTTTTAGCTGCTGGAATTGGAGAGAAATGA
1 GATGAAATACCAGCTTAGAGAACCCTCCTATGGCATTTTTAGCTGCTGGAATTGAAGAGAAATGA
43628358 AGAGAAATCTAGATATTTCCTATTTAGTCCTAGCTTTATTTA
66 AGAGAAATCTAGATATTTCCTATTTAGTCCTAGCTTTATTTA
43628400 GATGAAATACCAGCTTAGAGAACCCTCCTATGGCATTTTTAGCTGCTGGAATTGAAGAGAAATGA
1 GATGAAATACCAGCTTAGAGAACCCTCCTATGGCATTTTTAGCTGCTGGAATTGAAGAGAAATGA
43628465 AGAGAAATCTAGATATTTCCTATTTAGTCCTAGCTTTATTTA
66 AGAGAAATCTAGATATTTCCTATTTAGTCCTAGCTTTATTTA
43628507 G
1 G
43628508 TTAATTTTGC
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 106 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (107 bp):
GATGAAATACCAGCTTAGAGAACCCTCCTATGGCATTTTTAGCTGCTGGAATTGAAGAGAAATGA
AGAGAAATCTAGATATTTCCTATTTAGTCCTAGCTTTATTTA
Found at i:43629848 original size:46 final size:45
Alignment explanation
Indices: 43629789--43629903 Score: 140
Period size: 46 Copynumber: 2.5 Consensus size: 45
43629779 GCCATAATCT
*
43629789 TTATCTCCCTGAAGTTGCAGTGGAGTAGGATAAAAATACACAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGATAAAAATA-ACAAACC
* * * * * *
43629835 TTATCTCCTTGAAGTTGCAGTGGAGCAGGTTGAAGATAGCAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGATAAAAATAACAAACC
* *
43629880 TTTTTTCCCTGAAGTTGCAGTGGA
1 TTATCTCCCTGAAGTTGCAGTGGA
43629904 ATAGATTACG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
45 26 0.44
46 33 0.56
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (45 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGGATAAAAATAACAAACC
Found at i:43630119 original size:190 final size:193
Alignment explanation
Indices: 43629784--43630142 Score: 447
Period size: 190 Copynumber: 1.9 Consensus size: 193
43629774 TCGAAGCCAT
* *
43629784 AATCTTTATCTCCCTGAAGTTGCAGTGGAGTAGGATAAAAATACACAAACCTTATCTCCTTGAAG
1 AATCTTTATCTCCCTGAAGTTGCAGTGGAGTAGGATAAAAATACACAAACCTTATCTCCCTAAAG
* * ** * * * * * **
43629849 TTGCAGTGGAGCAGGTTGAAGATAGCAAATCTTTTTTCCCTGAAGTTGCAGTGGAATAGATTACG
66 TTGCAGAGGAGCAGATTGAAGATAAAAAATATTATCTCCCTGAAGTTGCAGTAGAATAAATTAAA
* **
43629914 GCTATAAGTCACAAATCTTATACCT-CTAAAGTTGCAGTAGGTCAGATCAAATCTATTATGGCG
131 GCTACAAACCACAAATCTTAT-CCTCCTAAAGTTGCAGTAGGTCAGATCAAATCTATTATGGCG
* * * **
43629977 AATC-TTATCTCCCTGAAGTTGCAGTGGAGTA-GATAGAAA-CCACTAGTCTTATCTCCCTAAAG
1 AATCTTTATCTCCCTGAAGTTGCAGTGGAGTAGGATAAAAATACACAAACCTTATCTCCCTAAAG
* * *
43630039 TTGCAGAGGAGTAGATTGAAGATAAAAAATATTATCTCTCTGAAGTTGCAGTAGAGTAAATTAAA
66 TTGCAGAGGAGCAGATTGAAGATAAAAAATATTATCTCCCTGAAGTTGCAGTAGAATAAATTAAA
* *
43630104 GCTACAAACCACAAATCTTATCTTCCTGAAGTTGCAGTA
131 GCTACAAACCACAAATCTTATCCTCCTAAAGTTGCAGTA
43630143 AAGAAGATTG
Statistics
Matches: 139, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
189 2 0.01
190 99 0.71
191 7 0.05
192 27 0.19
193 4 0.03
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (193 bp):
AATCTTTATCTCCCTGAAGTTGCAGTGGAGTAGGATAAAAATACACAAACCTTATCTCCCTAAAG
TTGCAGAGGAGCAGATTGAAGATAAAAAATATTATCTCCCTGAAGTTGCAGTAGAATAAATTAAA
GCTACAAACCACAAATCTTATCCTCCTAAAGTTGCAGTAGGTCAGATCAAATCTATTATGGCG
Found at i:43630157 original size:51 final size:51
Alignment explanation
Indices: 43630065--43630161 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
43630055 TGAAGATAAA
*
43630065 AAATATTATCTCTCTGAAGTTGCAGTAGAGTAAATTAAAGCTACAAACCAC
1 AAATATTATCTCTCTGAAGTTGCAGTAAAGTAAATTAAAGCTACAAACCAC
* *
43630116 AAATCTTATCT-TCCTGAAGTTGCAGTAAAG-AAGATTGAAGCTACAA
1 AAATATTATCTCT-CTGAAGTTGCAGTAAAGTAA-ATTAAAGCTACAA
43630162 GTCTAATCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
50 3 0.07
51 38 0.93
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.28
Consensus pattern (51 bp):
AAATATTATCTCTCTGAAGTTGCAGTAAAGTAAATTAAAGCTACAAACCAC
Found at i:43630434 original size:16 final size:15
Alignment explanation
Indices: 43630393--43630426 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
43630383 CCCAGTTTAT
*
43630393 AAAATAAAA-CCCAA
1 AAAATAAAAGTCCAA
43630407 AAAATAAAAGTCCAA
1 AAAATAAAAGTCCAA
43630422 AAAAT
1 AAAAT
43630427 GAATAGTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.71, C:0.15, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAATAAAAGTCCAA
Found at i:43631780 original size:26 final size:26
Alignment explanation
Indices: 43631676--43632006 Score: 176
Period size: 26 Copynumber: 12.3 Consensus size: 26
43631666 TCTTTGACTT
* *
43631676 TTTACTTTAAACTGTTTTATTATATT-
1 TTTATTTTAAACTTTTTTA-TATATTA
* *
43631702 TTATTTTTTGAA-TTGTTTTATATATTA
1 TT-TATTTTAAACTT-TTTTATATATTA
* * **
43631729 TCTATTTTTAGTTTTTTTATATATTA
1 TTTATTTTAAACTTTTTTATATATTA
*
43631755 TATATTTTAAACTTTTTTATATATTA
1 TTTATTTTAAACTTTTTTATATATTA
*
43631781 TTTATTTCAAACTTTTATCTATTTTATATATTA
1 TTTATTTTAAAC-----T-T-TTTTATATATTA
* * *
43631814 TTTAGTTTAAACTGTTTTATATGTTA
1 TTTATTTTAAACTTTTTTATATATTA
* * ****
43631840 CTTATTTAAAAAAAATTTATAT-TGTA
1 TTTATTTTAAACTTTTTTATATAT-TA
*
43631866 --TATTTGAAACTGTTTTGT-TATA-TA
1 TTTATTTTAAACT-TTTT-TATATATTA
43631890 -TTATTTTTAAA-TTATTTTATATATTA
1 TTTA-TTTTAAACTT-TTTTATATATTA
* **
43631916 TCTATTTTAATTTCTTTTTATATATTA
1 TTTATTTTAAACT-TTTTTATATATTA
43631943 TTTATTTTAAACCTTTTTTTCATATATTA
1 TTTATTTTAAA-C-TTTTTT-ATATATTA
* ** * *
43631972 TTTATTTCAAACTTTTACATATGTTT
1 TTTATTTTAAACTTTTTTATATATTA
43631998 TTTATTTTA
1 TTTATTTTA
43632007 TATTTTATTT
Statistics
Matches: 237, Mismatches: 42, Indels: 52
0.72 0.13 0.16
Matches are distributed among these distances:
24 12 0.05
25 16 0.07
26 116 0.49
27 42 0.18
28 8 0.03
29 19 0.08
31 1 0.00
32 1 0.00
33 22 0.09
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (26 bp):
TTTATTTTAAACTTTTTTATATATTA
Found at i:43631868 original size:59 final size:58
Alignment explanation
Indices: 43631746--43631868 Score: 131
Period size: 59 Copynumber: 2.1 Consensus size: 58
43631736 TTAGTTTTTT
* * * * ** *
43631746 TATATATTATATATTTTAAACTTTTTTATATATTATTTATTTCAAACTTTTATCTATTT
1 TATATATTATATAGTTTAAACTGTTTTATATATTACTTATTTAAAAAATTTA-CTATTG
* *
43631805 TATATATTATTTAGTTTAAACTGTTTTATATGTTACTTATTTAAAAAAAATTTA-TATTG
1 TATATATTATATAGTTTAAACTGTTTTATATATTACTTATTT--AAAAAATTTACTATTG
43631864 TATAT
1 TATAT
43631869 TTGAAACTGT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 46 0.87
61 7 0.13
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (58 bp):
TATATATTATATAGTTTAAACTGTTTTATATATTACTTATTTAAAAAATTTACTATTG
Found at i:43631921 original size:16 final size:16
Alignment explanation
Indices: 43631902--43631951 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
43631892 ATTTTTAAAT
43631902 TATTTTATATATTATC
1 TATTTTATATATTATC
43631918 TA-TTT-TA-ATT-TC
1 TATTTTATATATTATC
*
43631930 T-TTTTATATATTATT
1 TATTTTATATATTATC
43631945 TATTTTA
1 TATTTTA
43631952 AACCTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
12 6 0.21
13 5 0.18
14 5 0.18
15 5 0.18
16 7 0.25
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTATATATTATC
Found at i:43631922 original size:27 final size:26
Alignment explanation
Indices: 43631878--43632018 Score: 117
Period size: 27 Copynumber: 5.3 Consensus size: 26
43631868 TTTGAAACTG
*
43631878 TTTTGTTATATATTA--T-TTTTAAA
1 TTTTTTTATATATTATTTATTTTAAA
* * *
43631901 TTATTTTATATATTATCTATTTTAAT
1 TTTTTTTATATATTATTTATTTTAAA
43631927 TTCTTTTTATATATTATTTATTTTAAA
1 TT-TTTTTATATATTATTTATTTTAAA
*
43631954 CCTTTTTTTCATATATTATTTATTTCAAA
1 --TTTTTTT-ATATATTATTTATTTTAAA
* ** * * *
43631983 CTTTTACATATGTTTTTTATTTTATA
1 TTTTTTTATATATTATTTATTTTAAA
43632009 TTTTATTTAT
1 TTTT-TTTAT
43632019 TTGAAACTGT
Statistics
Matches: 93, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
23 13 0.14
25 1 0.01
26 26 0.28
27 28 0.30
28 5 0.05
29 20 0.22
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTTTTTATATATTATTTATTTTAAA
Found at i:43637063 original size:15 final size:15
Alignment explanation
Indices: 43637043--43637074 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43637033 AATAAAAAAA
43637043 ATTATAAATTAATAT
1 ATTATAAATTAATAT
*
43637058 ATTATAGATTAATAT
1 ATTATAAATTAATAT
43637073 AT
1 AT
43637075 AGTAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATTATAAATTAATAT
Found at i:43637170 original size:23 final size:22
Alignment explanation
Indices: 43637135--43637199 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
43637125 TCCTTCAAAA
43637135 ATAATAAAATTATAAATTAATAT
1 ATAA-AAAATTATAAATTAATAT
** * *
43637158 ATAAAAAACTTATATTTTATTTT
1 ATAAAAAA-TTATAAATTAATAT
43637181 ATAAAAAAATTAT-AATTAA
1 AT-AAAAAATTATAAATTAA
43637200 ATTTCGTCGT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
22 7 0.21
23 20 0.61
24 6 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAAAAATTATAAATTAATAT
Found at i:43640133 original size:30 final size:31
Alignment explanation
Indices: 43640074--43640137 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
43640064 ACTTAATAAG
43640074 CAAATGCCTCTAAAATAATTAAAAAAATTAA
1 CAAATGCCTCTAAAATAATTAAAAAAATTAA
* *
43640105 CAAATGCCTTTAAAATAA-TAACAAAATTAA
1 CAAATGCCTCTAAAATAATTAAAAAAATTAA
43640135 CAA
1 CAA
43640138 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (31 bp):
CAAATGCCTCTAAAATAATTAAAAAAATTAA
Found at i:43640180 original size:11 final size:11
Alignment explanation
Indices: 43640166--43640213 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
43640156 ATATCCAAAT
*
43640166 AATAATAACAA
1 AATAATAGCAA
*
43640177 AATAGTAGCAA
1 AATAATAGCAA
* *
43640188 CATAATAGTAA
1 AATAATAGCAA
*
43640199 AATAGTAGCAA
1 AATAATAGCAA
43640210 AATA
1 AATA
43640214 GAGAGAAAAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.21
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:43640192 original size:22 final size:22
Alignment explanation
Indices: 43640167--43640209 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
43640157 TATCCAAATA
43640167 ATAATAACAAAATAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
**
43640189 ATAATAGTAAAATAGTAGCAA
1 ATAATAACAAAATAGTAGCAA
43640210 AATAGAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:43640214 original size:11 final size:11
Alignment explanation
Indices: 43640174--43640214 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
43640164 ATAATAATAA
43640174 CAAAATAGTAG
1 CAAAATAGTAG
* *
43640185 CAACATAATAG
1 CAAAATAGTAG
*
43640196 TAAAATAGTAG
1 CAAAATAGTAG
43640207 CAAAATAG
1 CAAAATAG
43640215 AGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:43640222 original size:22 final size:22
Alignment explanation
Indices: 43640175--43640222 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43640165 TAATAATAAC
* *
43640175 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
43640197 AAAATAGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
43640219 AAAA
1 AAAA
43640223 CAACAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:43647611 original size:72 final size:72
Alignment explanation
Indices: 43647493--43647678 Score: 275
Period size: 72 Copynumber: 2.6 Consensus size: 72
43647483 ATCTTAAAAA
* *
43647493 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* *
43647558 TATTTTTC
66 T-GTTGTC
* *
43647566 -AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
43647630 TGTTGTC
66 TGTTGTC
*
43647637 AAAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAG
1 --AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAG
43647679 TTCACATGTT
Statistics
Matches: 101, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
71 4 0.04
72 61 0.60
74 36 0.36
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGTTGTC
Found at i:43647886 original size:74 final size:74
Alignment explanation
Indices: 43647783--43648252 Score: 457
Period size: 74 Copynumber: 6.2 Consensus size: 74
43647773 TGCCAACCTG
* *
43647783 TTCAATTTATG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
1 TTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
43647847 TGAGGTAATT
66 TGAGGT-ATT
*
43647857 TT-AATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
1 TTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
43647921 TGAGGTAATT
66 TGAGGT-ATT
* * *
43647931 TT-AATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGGCACGC
1 TTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
*
43647995 CGAGGTATT
66 TGAGGTATT
* * **** * * * *
43648004 TTCAAATTCTACTTTAAAAAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCT-TGGCTCAC
1 TTCAATTTCT-GTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC
* *
43648068 G-TGTTGAGTCACT
64 GCTG-AG-GT-ATT
** *
43648081 TTCAATTTCTGTTTTTATGTCTGTTTTCTAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
1 TTCAATTTCTG-TTTT-T-TC------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* * *
43648146 GGGGCACGATGAGGTATT
57 AGGACACGCTGAGGTATT
* ** * * *
43648164 TTCAATTACTG-TTTGGCAAAAACCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGC
1 TTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
*
43648228 TGATGTATT
66 TGAGGTATT
*
43648237 TTCCATTTCTGTTTTT
1 TTCAATTTCTGTTTTT
43648253 CAATTTATGT
Statistics
Matches: 326, Mismatches: 51, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
73 67 0.21
74 142 0.44
75 42 0.13
76 2 0.01
77 14 0.04
79 1 0.00
81 3 0.01
83 12 0.04
84 2 0.01
85 37 0.11
86 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (74 bp):
TTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTATT
Found at i:43648530 original size:15 final size:16
Alignment explanation
Indices: 43648499--43648532 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43648489 CGCTGAGATA
*
43648499 TTTTCAATTTTTCGCT
1 TTTTCAATTTATCGCT
43648515 TTTTCAATTTAT-GCT
1 TTTTCAATTTATCGCT
43648530 TTT
1 TTT
43648533 CAAATTCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTTCAATTTATCGCT
Found at i:43648651 original size:74 final size:75
Alignment explanation
Indices: 43648549--43648883 Score: 410
Period size: 74 Copynumber: 4.5 Consensus size: 75
43648539 CTACTTTTCC
* * * *
43648549 AAAATCAGCTCATATTGCAAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
43648614 G-TTGTCAAA
66 GCTTGTCAAA
* * * ** *
43648623 AAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* *
43648688 GCTTTTCAAG
66 GCTTGTCAAA
* * * *
43648698 AAAATCAACTCATATTGA-GAGATGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAATCAACTCATATT-ACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
*
43648762 TGCTTTTC--A
65 TGCTTGTCAAA
* * * * *
43648771 AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGACACGCCGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
43648836 G-TTGTCAAA
66 GCTTGTCAAA
* *
43648845 AAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAG
1 AAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCAG
43648884 TTCACATGTT
Statistics
Matches: 226, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
72 4 0.02
73 56 0.25
74 92 0.41
75 73 0.32
76 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (75 bp):
AAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GCTTGTCAAA
Found at i:43650102 original size:197 final size:198
Alignment explanation
Indices: 43649741--43650138 Score: 728
Period size: 197 Copynumber: 2.0 Consensus size: 198
43649731 GGCAAGAAAT
*
43649741 TTAAAAAATATTGTATTGAAATGGCTATAAATGTCAGATCTGAATGTAATAGAGAGGGGATTTTT
1 TTAAAAAATATTGTATTGAAATGGCTATAAATGCCAGATCTGAATGTAATAGAGAGGGGA---TT
43649806 ATTTTTTTTTGGAGATTTCAAAGGGAAGAATCGGTTGTATTTTGGGGGGACCCTTTTTTTCTCTT
63 ATTTTTTTTTGGAGATTTCAAAGGGAAGAATCGGTTGTATTTTGGGGGGACCCTTTTTTTCTCTT
43649871 CTCTCTTTCGATTTCTTAACCAAAAAGCAAACAATTGATATCCGAAATACTACGATCTTAACATC
128 CTCTCTTTCGATTTCTTAACCAAAAAGCAAACAATTGATATCCGAAATACTACGATCTTAACATC
43649936 AAAAGG
193 AAAAGG
43649942 TTAAAAAATATTGTATTGAAATGGCTATAAATGCCAGATCTGAATGTAATAGAGAGGGGA-T-TT
1 TTAAAAAATATTGTATTGAAATGGCTATAAATGCCAGATCTGAATGTAATAGAGAGGGGATTATT
43650005 TTTTTTTGGAGATTTCAAAGGGAAGAATCGGTTGTATTTTGGGGGGGACCCTTTTTTTCTCTTCT
66 TTTTTTTGGAGATTTCAAAGGGAAGAATCGGTTGTATTTT-GGGGGGACCCTTTTTTTCTCTTCT
*
43650070 CTCTTTCGATTTCTTAACCAAAAAGTAAACAATTGATATCCGAAATACTACGATCTTAACATCAA
130 CTCTTTCGATTTCTTAACCAAAAAGCAAACAATTGATATCCGAAATACTACGATCTTAACATCAA
43650135 AAGG
195 AAGG
43650139 CAGAGATTCG
Statistics
Matches: 194, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
196 42 0.22
197 93 0.48
201 59 0.30
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (198 bp):
TTAAAAAATATTGTATTGAAATGGCTATAAATGCCAGATCTGAATGTAATAGAGAGGGGATTATT
TTTTTTTGGAGATTTCAAAGGGAAGAATCGGTTGTATTTTGGGGGGACCCTTTTTTTCTCTTCTC
TCTTTCGATTTCTTAACCAAAAAGCAAACAATTGATATCCGAAATACTACGATCTTAACATCAAA
AGG
Found at i:43656741 original size:75 final size:74
Alignment explanation
Indices: 43656482--43657244 Score: 743
Period size: 75 Copynumber: 10.0 Consensus size: 74
43656472 CATCTTAAAA
** *
43656482 AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
* *
43656547 TTATTTTTC
66 CTGTTTTTC
* *
43656556 --AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
*
43656619 CTG-TTGTC
66 CTGTTTTTC
* * **
43656627 AAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATT
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
*
43656692 TCTGCTTTTC
65 TCTGTTTTTC
* **
43656702 AAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATT
1 AA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
*
43656767 TCTGCTTTTC
65 TCTGTTTTTC
* *
43656777 AAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 AA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA--
43656842 CCTGTTCAATTTATGTTTTTC
63 --T-TTC------TGTTTTTC
*
43656863 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTT-AATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTTCAATT
43656926 TCTGTTTTTTC
65 TCTG-TTTTTC
* * * * *
43656937 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGGCACGCCGAGGTATTTTCAAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
* ***
43657001 CTACTTTAAA
66 CT-GTTTTTC
* * * * * *
43657011 AAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCT-TGGCTCACG-TGTTGAGTCACTTTCA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTG-AG-GT-ATTTTCA
43657074 ATTTCTGTTTTTATGTC
62 ATTTCTG--TTT-T-TC
*** * * * *
43657091 TGTTTTCTAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGATGAGGTATTTTC
1 -----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
* **
43657156 AATTACTGTTTGGC
61 AATTTCTGTTTTTC
* * * * *
43657170 -AAAAACCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGATGTATTTTCCATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
43657234 CTGTTTTTC
66 CTGTTTTTC
43657243 AA
1 AA
43657245 TTTATGTTTT
Statistics
Matches: 585, Mismatches: 67, Indels: 74
0.81 0.09 0.10
Matches are distributed among these distances:
71 4 0.01
72 61 0.10
73 66 0.11
74 129 0.22
75 176 0.30
76 2 0.00
77 11 0.02
78 3 0.01
79 5 0.01
80 4 0.01
81 3 0.01
83 12 0.02
84 55 0.09
85 43 0.07
86 11 0.02
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (74 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
CTGTTTTTC
Found at i:43657001 original size:159 final size:161
Alignment explanation
Indices: 43656685--43657827 Score: 571
Period size: 149 Copynumber: 7.0 Consensus size: 161
43656675 TTGAGGTATT
*
43656685 TTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
1 TTCAATTTATGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
*
43656750 TTGAGGTATTTTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
66 CTGAGGTATTTTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
**
43656815 TCAAGACACGTTGAGGTATTTTCAATTCCTG
131 TCAAGACACGCCGAGGTATTTTCAATTCCTG
* *
43656846 TTCAATTTATGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
1 TTCAATTTATGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
*
43656909 CTGAGGTAATTTT-AATTTCTGTTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAG
66 CTGAGGT-ATTTTCAATTTCTG-CTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* ** * *
43656971 TCTCGGGGCACGCCGAGGTATTTTCAA-----A
129 CCTCAAGACACGCCGAGGTATTTTCAATTCCTG
** * * * * * *
43656999 TTC----TA--CTTTAAAAAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCT--TGGCTCA
1 TTCAATTTATGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
* * * * * *
43657056 CGTGTTGAGTCACTTTCAATTTCTG-TTTTTATGTCTGTTTTCTAAATCAACTCATATTGCAAGA
66 C-TG-AG-GT-ATTTTCAATTTCTGCTTTTCA----AG-----AAAATCAACTCATATTGCGAGA
** * ** *
43657120 GGTGAGTTGAGCCTCGGGGCACGATGAGGTATTTTCAATTACTG
118 GGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTCAATTCCTG
* * * * **
43657164 ------TT-TG----GC-A-AAAACCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATG
1 TTCAATTTATGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
* * * * *
43657216 CTGATGTATTTTCCATTTCTGTTTTTCAATTTATGTTTTCAAAAATCAATTCATATTGCTAGAGG
66 CTGAGGTATTTTCAATTTCTGCTTTTC-A---A-G------AAAATCAACTCATATTGCGAGAGG
* * * * ** *
43657281 TGAATGGAGCCTCAGGTCATACGCCGAGGTATTTTCAATAGATGTTTT
120 TGAGTTGAGCCTCAAG--ACACGCCGAGGTATTTTCAAT---T-CCTG
* ** * * * **
43657329 TTCCAACTCCTGCTTCTCAAAAAAAAAATTTTTAACTCATATTGCGAGAAATGAGTTGAGCCTCA
1 TT-CAATTTATGCTTTTC---AAGAAAA---TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
** * *
43657394 AGACACGTTGAGGTATTTTCAAGTTCTGCTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTG
59 AGACACACTGAGGTATTTTCAATTTCTGCTTTTC--AAGAAAATCAACTCATATTGCGAGAGGTG
* * * * *
43657459 AGTTGAGCCTC-GGCTCGCACGCTGAGATATTTTCAATTTTTCGCTTT
122 AGTTGAGCCTCAAG---ACACGCCGAGGTATTTTCAA---TTC-C-TG
* * * **
43657506 TTCAATTTATGCTTTTCAAATTCTACTTTTCCAAAATCAGCTCATATTGCAAGAAATGAGTTGAG
1 TTCAATTTATGCTTTTC--A----A------GAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* * * * * * *
43657571 CCTCAGGACACGCTGAGGTAATTTCAATTTCTG-TTGTCAAAAAAATCAATTCATATTACGAGAG
54 CCTCAAGACACACTGAGGTATTTTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAG
***
43657635 GTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAA----T-
119 GTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTCAATTCCTG
* * *
43657673 TTC------TGCTTTTCAAGAAAATCAACTCATATTGAGAGATGTGAGTTGAGCCTCAAGACACG
1 TTCAATTTATGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
* * **
43657732 TTGAGGTATTTTCAATTTCTGCTTTTC-A-AAATTCAACTCATATTGCGAGAAATGAGTTGAGCC
66 CTGAGGTATTTTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
** * *
43657795 TCGGGACACGCCGAGGTAATTTCAATTTCTG
131 TCAAGACACGCCGAGGTATTTTCAATTCCTG
43657826 TT
1 TT
43657828 GTCAAAAAAA
Statistics
Matches: 767, Mismatches: 132, Indels: 174
0.71 0.12 0.16
Matches are distributed among these distances:
147 7 0.01
148 52 0.07
149 100 0.13
150 10 0.01
151 8 0.01
152 1 0.00
153 5 0.01
155 1 0.00
156 12 0.02
157 7 0.01
158 88 0.11
159 100 0.13
160 69 0.09
161 40 0.05
163 1 0.00
164 1 0.00
165 1 0.00
167 3 0.00
168 1 0.00
172 1 0.00
173 2 0.00
175 5 0.01
176 63 0.08
177 21 0.03
179 40 0.05
180 1 0.00
181 5 0.01
182 59 0.08
183 1 0.00
185 60 0.08
186 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (161 bp):
TTCAATTTATGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
CTGAGGTATTTTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
TCAAGACACGCCGAGGTATTTTCAATTCCTG
Found at i:43657025 original size:233 final size:227
Alignment explanation
Indices: 43656483--43657235 Score: 814
Period size: 233 Copynumber: 3.3 Consensus size: 227
43656473 ATCTTAAAAA
** * *
43656483 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
*** * *
43656548 TA-TTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT
66 TACTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTAATT
* *** *
43656612 TCAA---T-TTCTGT-TG--TCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAG
131 TCAATTCTGTTCTTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG
*
43656670 ACAC-ATTGAGGTATTTTCAATTTCTGCTTTTC
196 ACACGA-TGAGGTATTTTCAATTTCTGTTTTTC
* **
43656702 AAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATT
1 -A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
* * *
43656767 TCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGT
64 TCTAC-TTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGT
*
43656832 ATTTTCAATTCCTGTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
127 AATTTCAATT-CTGTTC--TTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
*
43656897 CCTCAAGACACGCTGAGGTAATTTT-AATTTCTGTTTTTTC
189 CCTCAAGACACGATGAGGT-ATTTTCAATTTCTG-TTTTTC
* * * * *
43656937 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGGCACGCCGAGGTATTTTCAAATTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* * * *
43657002 TACTTTAAAAAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCT-TGGCTCACGTGTTGA-G
66 TACTTT--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC--GTTGAGG
* * *
43657065 TCACTTTCAATTTCTGTT-TTTATGTCTGTTTTC-TAAATCAACTCATATTGCAAGAGGTGAGTT
126 T-AATTTCAA-TTCTGTTCTTTATG--T-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
** * * **
43657128 GAGCCTCGGGGCACGATGAGGTATTTTCAATTACTGTTTGGC
186 GAGCCTCAAGACACGATGAGGTATTTTCAATTTCTGTTTTTC
* * * * *
43657170 AAAAACCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGATGTATTTTCCATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
43657235 T
66 T
43657236 GTTTTTCAAT
Statistics
Matches: 448, Mismatches: 58, Indels: 41
0.82 0.11 0.07
Matches are distributed among these distances:
220 1 0.00
221 58 0.13
223 3 0.01
224 56 0.12
228 1 0.00
229 3 0.01
231 2 0.00
232 12 0.03
233 162 0.36
234 116 0.26
235 32 0.07
236 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (227 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TACTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTAATT
TCAATTCTGTTCTTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG
ACACGATGAGGTATTTTCAATTTCTGTTTTTC
Found at i:43657225 original size:73 final size:73
Alignment explanation
Indices: 43657103--43657239 Score: 193
Period size: 73 Copynumber: 1.9 Consensus size: 73
43657093 TTTTCTAAAT
* * *
43657103 CAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGATGAGGTATTTTCAATTACTGTTTG
1 CAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTATTTTCAATTACTGTTTG
43657168 GCAAAAAC
66 GCAAAAAC
* * * * * *
43657176 CAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGATGTATTTTCCATTTCTGTTT
1 CAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTATTTTCAATTACTGTTT
43657240 TTCAATTTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 55 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (73 bp):
CAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTATTTTCAATTACTGTTTG
GCAAAAAC
Found at i:43657519 original size:15 final size:16
Alignment explanation
Indices: 43657488--43657521 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43657478 CGCTGAGATA
*
43657488 TTTTCAATTTTTCGCT
1 TTTTCAATTTATCGCT
43657504 TTTTCAATTTAT-GCT
1 TTTTCAATTTATCGCT
43657519 TTT
1 TTT
43657522 CAAATTCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTTCAATTTATCGCT
Found at i:43657640 original size:74 final size:75
Alignment explanation
Indices: 43657538--43657872 Score: 410
Period size: 74 Copynumber: 4.5 Consensus size: 75
43657528 CTACTTTTCC
* * * *
43657538 AAAATCAGCTCATATTGCAAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
43657603 G-TTGTCAAA
66 GCTTGTCAAA
* * * ** *
43657612 AAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* *
43657677 GCTTTTCAAG
66 GCTTGTCAAA
* * * *
43657687 AAAATCAACTCATATTGA-GAGATGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAATCAACTCATATT-ACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
*
43657751 TGCTTTTC--A
65 TGCTTGTCAAA
* * * * *
43657760 AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGACACGCCGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
43657825 G-TTGTCAAA
66 GCTTGTCAAA
* *
43657834 AAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAG
1 AAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCAG
43657873 TTCACATGTT
Statistics
Matches: 226, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
72 4 0.02
73 56 0.25
74 92 0.41
75 73 0.32
76 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (75 bp):
AAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GCTTGTCAAA
Found at i:43659009 original size:17 final size:17
Alignment explanation
Indices: 43658989--43659050 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 17
43658979 ATTTTTATAA
*
43658989 TTTTATACTTTTTAATT
1 TTTTATAATTTTTAATT
* ***
43659006 TTTTTTAAAAATTAATT
1 TTTTATAATTTTTAATT
* *
43659023 TTATATATTTTTTAATT
1 TTTTATAATTTTTAATT
43659040 TTTTA-AATTTT
1 TTTTATAATTTT
43659051 CAAAAAATTT
Statistics
Matches: 32, Mismatches: 13, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
16 5 0.16
17 27 0.84
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATAATTTTTAATT
Found at i:43662938 original size:47 final size:47
Alignment explanation
Indices: 43662869--43663009 Score: 264
Period size: 47 Copynumber: 3.0 Consensus size: 47
43662859 GGAAGTTTGA
*
43662869 TGGACATGCCACATCTCCTACTCATTTTATTAAATACTTCATACATT
1 TGGACATGCCACAGCTCCTACTCATTTTATTAAATACTTCATACATT
43662916 TGGACATGCCACAGCTCCTACTCATTTTATTAAATACTTCATACATT
1 TGGACATGCCACAGCTCCTACTCATTTTATTAAATACTTCATACATT
*
43662963 TGGACATGCCACAGCTCCTACTCATTTTATTAAATAATTCATACATT
1 TGGACATGCCACAGCTCCTACTCATTTTATTAAATACTTCATACATT
43663010 CTGTTGTCTT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 92 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (47 bp):
TGGACATGCCACAGCTCCTACTCATTTTATTAAATACTTCATACATT
Found at i:43667538 original size:29 final size:30
Alignment explanation
Indices: 43667506--43667579 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
43667496 TAATATCATT
* * *
43667506 TTATATTTATATATTACATATATAAA-TAA
1 TTATATTTATTTATTACAAAAATAAATTAA
* *
43667535 TTATATTTATTTAATATAAAAATAAATTAA
1 TTATATTTATTTATTACAAAAATAAATTAA
43667565 -TATATTTATTTATTA
1 TTATATTTATTTATTA
43667580 TTAAATTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 35 0.92
30 3 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
TTATATTTATTTATTACAAAAATAAATTAA
Found at i:43667570 original size:25 final size:26
Alignment explanation
Indices: 43667513--43667572 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
43667503 ATTTTATATT
*
43667513 TATATA-TTACATATATAAATAATTA
1 TATATATTTACATATAAAAATAATTA
*
43667538 TATTTATTTA-ATATAAAAATAAATTA
1 TATATATTTACATATAAAAAT-AATTA
43667564 -ATATATTTA
1 TATATATTTA
43667573 TTTATTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 22 0.73
26 8 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TATATATTTACATATAAAAATAATTA
Found at i:43667589 original size:29 final size:29
Alignment explanation
Indices: 43667509--43667589 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
43667499 TATCATTTTA
43667509 TATTTATATATTACATATATAAATAATTATATT
1 TATTTAT-TATTA-A-AT-TAAATAATTATATT
* * *
43667542 TATTTAATATAAAAATAAATTAA-TATATT
1 TATTTATTATTAAATTAAA-TAATTATATT
43667571 TATTTATTATTAAATTAAA
1 TATTTATTATTAAATTAAA
43667590 ATTTACCTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
29 26 0.63
30 4 0.10
31 1 0.02
32 4 0.10
33 6 0.15
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
TATTTATTATTAAATTAAATAATTATATT
Found at i:43670790 original size:18 final size:20
Alignment explanation
Indices: 43670753--43670792 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
43670743 CCATTTTTAG
*
43670753 TTAATCAAACTTCTTATTTC
1 TTAATCAAAATTCTTATTTC
43670773 TTAAT-AAAATTC-TATTTC
1 TTAATCAAAATTCTTATTTC
43670791 TT
1 TT
43670793 TTGAGGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATCAAAATTCTTATTTC
Found at i:43675752 original size:18 final size:18
Alignment explanation
Indices: 43675729--43675821 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
43675719 CCCAACTACT
*
43675729 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
43675747 GTATACATGAATAGTACC
1 GTATACGTGAATAGTACC
*
43675765 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* * *
43675783 ATATACATGAATAGTGCC
1 GTATACGTGAATAGTACC
43675801 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
43675819 GTA
1 GTA
43675822 AACGGTCGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:43675781 original size:36 final size:36
Alignment explanation
Indices: 43675730--43675821 Score: 148
Period size: 36 Copynumber: 2.6 Consensus size: 36
43675720 CCAACTACTG
*
43675730 TATACGTGAACAGTACCGTATACATGAATAGTACCA
1 TATACGTGAATAGTACCGTATACATGAATAGTACCA
* * *
43675766 TATACGTGAATAGTACCATATACATGAATAGTGCCG
1 TATACGTGAATAGTACCGTATACATGAATAGTACCA
43675802 TATACGTGAATAGTACCGTA
1 TATACGTGAATAGTACCGTA
43675822 AACGGTCGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (36 bp):
TATACGTGAATAGTACCGTATACATGAATAGTACCA
Found at i:43681335 original size:12 final size:12
Alignment explanation
Indices: 43681320--43681346 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43681310 ATAAACATAA
43681320 ATAATATATATG
1 ATAATATATATG
43681332 ATAATATATATG
1 ATAATATATATG
43681344 ATA
1 ATA
43681347 TACAAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (12 bp):
ATAATATATATG
Found at i:43681564 original size:20 final size:21
Alignment explanation
Indices: 43681523--43681565 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
43681513 AATAATTTAT
*
43681523 AAATATATATAATACAAGTAA
1 AAATATATATAATACAAATAA
43681544 AAATATA-ATAATA-ATAATAA
1 AAATATATATAATACA-AATAA
43681564 AA
1 AA
43681566 TAATGATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 12 0.60
21 7 0.35
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
AAATATATATAATACAAATAA
Found at i:43681648 original size:25 final size:23
Alignment explanation
Indices: 43681605--43681655 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
43681595 AAAATAATAG
43681605 ATAAT-AAATAATATTAATATAT
1 ATAATAAAATAATATTAATATAT
*
43681627 ATAATAAAATAATCTTACA-ATAT
1 ATAATAAAATAATATTA-ATATAT
43681650 ATAATA
1 ATAATA
43681656 TAAAAGTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 20 0.77
24 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAATAAAATAATATTAATATAT
Found at i:43682507 original size:20 final size:21
Alignment explanation
Indices: 43682466--43682508 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
43682456 AATAATTTAT
*
43682466 AAATATATATAATACAAGTAA
1 AAATATATATAATACAAATAA
43682487 AAATATA-ATAATA-ATAATAA
1 AAATATATATAATACA-AATAA
43682507 AA
1 AA
43682509 TAATGATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 12 0.60
21 7 0.35
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
AAATATATATAATACAAATAA
Found at i:43682591 original size:25 final size:23
Alignment explanation
Indices: 43682548--43682598 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
43682538 AAAATAATAG
43682548 ATAAT-AAATAATATTAATATAT
1 ATAATAAAATAATATTAATATAT
*
43682570 ATAATAAAATAATCTTACA-ATAT
1 ATAATAAAATAATATTA-ATATAT
43682593 ATAATA
1 ATAATA
43682599 TAAAAGTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 20 0.77
24 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAATAAAATAATATTAATATAT
Found at i:43682695 original size:943 final size:946
Alignment explanation
Indices: 43680867--43682760 Score: 3609
Period size: 943 Copynumber: 2.0 Consensus size: 946
43680857 AGTAATAATT
*
43680867 AAAAACAATGCATAATATACAACGAAGTAATACAATATCAATGTACATGTTCATAAAATGTAATA
1 AAAAACAATGCATAATATACAACAAAGTAATACAATATCAATGTACATGTTCATAAAATGTAATA
*
43680932 TCAAATAATAAATATAAAATGACATTTAGCACATGATATATGCAATATAAAAATAAAATGAAATG
66 TCAAATAATAAATATAAAATGACATTTAGCACAAGATATATGCAATATAAAAATAAAATGAAATG
43680997 AGCAATTGTTAACAAAATATACATATAATACAAATAAAACATGATATTTAATAATAATTTTAAAA
131 AGCAATTGTTAACAAAATATACATATAATACAAATAAAACATGATATTTAATAATAATTTTAAAA
43681062 TAGTATTTAATATACAATATATATATTAACAAAATATTTATAAAAGAATAATAATTATATATATA
196 TAGTATTTAATATACAATATATATATTAACAAAATATTTATAAAAGAATAATAATTATATATATA
*
43681127 AAATATATTGGTTTAAAAGTATGTAAAAGAACTTATAAAACAACACATAATATAAAAAAATATTA
261 AAATATATTAGTTTAAAAGTATGTAAAAGAACTTATAAAACAACACATAATATAAAAAAATATTA
* *
43681192 TTTAAAATAAAATTAAACATAATAATTAATTAATTAATAATTTAATATGAGTACAATATGAGTTA
326 TTTAAAATAAAATTAAACATAATAAATAATTAATTAATAATTTAACATGAGTACAATATGAGTTA
43681257 AAAATATAATTTAATTTACAAATTTTAAAATTATGAATAATATAAGGAATAATATAAACATAAAT
391 AAAATATAATTTAATTTACAAATTTTAAAATTATGAATAATATAAGGAATAATATAAACATAAAT
43681322 AATATATATGATAATATATATGATATACAAAACATATATAAAAAAAAAGAAAAATAATAAGTAAT
456 AATATATATGATAATATATATGATATACAAAACATATAT-AAAAAAAAGAAAAATAATAAGTAAT
* *
43681387 ATAGGATAAAAATAAAAATATAATAAATTTTATATAATAAAATATAATTTAAATATATAGGAAAT
520 ATAGAATAAAAATAAAAATATAATAAATGTTATATAATAAAATATAATTTAAATATATAGGAAAT
* *
43681452 AAGAAATATAATAGATATAATATAAAATAATGAAAGTATATATGTAAAAACAATATATATAAATA
585 AAGAAATATAATACAGATAATATAAAATAATGAAAGTATATATGTAAAAACAATATATATAAATA
43681517 ATTTATAAATATATATAATACAAGTAAAAATATAATAATAATAATAAAATAATGATGCAAAATAA
650 ATTTATAAATATATATAATACAAGTAAAAATATAATAATAATAATAAAATAATGATGCAAAATAA
43681582 TAATAATTTGTGAAAAATAATAGATAATAAATAATATTAATATATATAATAAAATAATCTTACAA
715 TAATAATTTGTGAAAAATAATAGATAATAAATAATATTAATATATATAATAAAATAATCTTACAA
43681647 TATATAATATAAAAGTAAGGTTAAAAAAAACAAATTACAATATATGAAATATATATATAATAATA
780 TATATAATATAAAAGTAAGGTTAAAAAAAACAAATTACAATATATGAAATATATATATAATAATA
43681712 AAAATAAATATATAGGGCTAAATTTAAAGCTCAGCAAAATTACTAGGCGAATTCAAAAGAAGTAG
845 AAAATAAATATATAGGGCTAAATTTAAAGCTCAGCAAAATTACTAGGCGAATTCAAAAGAAGTAG
43681777 AACTGAATTTAGGTCCTAATTAAAACGCGCGC-AAAC
910 AACTGAATTTAGGTCCTAATTAAAACGCGCGCAAAAC
*
43681813 AAAAACAATGCATAGTATACAACAAAGTAATACAATATCAATGTACATGTTCATAAAATGTAATA
1 AAAAACAATGCATAATATACAACAAAGTAATACAATATCAATGTACATGTTCATAAAATGTAATA
43681878 TCAAATAATAAATATAAAATGACATTTAGCACAAGATATATGCAATATAAAAATAAAATGAAATG
66 TCAAATAATAAATATAAAATGACATTTAGCACAAGATATATGCAATATAAAAATAAAATGAAATG
43681943 AGCAATTGTTAACAAAATATACATATAATACAAATAAAACATGATATTTAATAATAATTTTAAAA
131 AGCAATTGTTAACAAAATATACATATAATACAAATAAAACATGATATTTAATAATAATTTTAAAA
43682008 TAGTATTTAATATACAATATATATATTAACAAAATATTTATAAAAGAATAATAATTATATATATA
196 TAGTATTTAATATACAATATATATATTAACAAAATATTTATAAAAGAATAATAATTATATATATA
43682073 AAATATATTAGTTTAAAAGTATGTAAAAGAACTTATAAAACAACACATAATAT-AAAAAATATTA
261 AAATATATTAGTTTAAAAGTATGTAAAAGAACTTATAAAACAACACATAATATAAAAAAATATTA
*
43682137 TTTAAAATAAAA-TAATACATAATAAATAATTAATTAATAATTTAACATGAGTATAATATGAGTT
326 TTTAAAATAAAATTAA-ACATAATAAATAATTAATTAATAATTTAACATGAGTACAATATGAGTT
*
43682201 AAAAATATAATTTAATTTACAAATTTTAAAATTATGAATAATATAATGAATAATATAAACATAAA
390 AAAAATATAATTTAATTTACAAATTTTAAAATTATGAATAATATAAGGAATAATATAAACATAAA
*
43682266 TAATATA-ATAGATAATATATATGATATACATAACATATAT-AAAAAAAGAAAAATAATAAGTAA
455 TAATATATAT-GATAATATATATGATATACAAAACATATATAAAAAAAAGAAAAATAATAAGTAA
43682329 TATAGAATAAAAATAAAAATATAATAAATGTTATATAATAAAATATAATTTAAATATATAGGAAA
519 TATAGAATAAAAATAAAAATATAATAAATGTTATATAATAAAATATAATTTAAATATATAGGAAA
43682394 TAAGAAATATAATACAGATAATATAAAATAATGAAAGTATATATGTAAAAACAATATATATAAAT
584 TAAGAAATATAATACAGATAATATAAAATAATGAAAGTATATATGTAAAAACAATATATATAAAT
43682459 AATTTATAAATATATATAATACAAGTAAAAATATAATAATAATAATAAAATAATGATGCAAAATA
649 AATTTATAAATATATATAATACAAGTAAAAATATAATAATAATAATAAAATAATGATGCAAAATA
43682524 ATAATAATTTGTGAAAAATAATAGATAATAAATAATATTAATATATATAATAAAATAATCTTACA
714 ATAATAATTTGTGAAAAATAATAGATAATAAATAATATTAATATATATAATAAAATAATCTTACA
43682589 ATATATAATATAAAAGTAAGGTTAAAAAAAACAAATTACAATATATGAAATATATATATAATAAT
779 ATATATAATATAAAAGTAAGGTTAAAAAAAACAAATTACAATATATGAAATATATATATAATAAT
43682654 AAAAATAAATATATAGGGCTAAATTTAAAGCTCAGCAAAATTACTAGGCGAATTCAAAAGAAGTA
844 AAAAATAAATATATAGGGCTAAATTTAAAGCTCAGCAAAATTACTAGGCGAATTCAAAAGAAGTA
43682719 GAACTGAATTTAGGTCCTAATTAAAACGCGCGCAAAAC
909 GAACTGAATTTAGGTCCTAATTAAAACGCGCGCAAAAC
43682757 AAAA
1 AAAA
43682761 GGGACTCATT
Statistics
Matches: 932, Mismatches: 13, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
943 442 0.47
944 13 0.01
945 168 0.18
946 309 0.33
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (946 bp):
AAAAACAATGCATAATATACAACAAAGTAATACAATATCAATGTACATGTTCATAAAATGTAATA
TCAAATAATAAATATAAAATGACATTTAGCACAAGATATATGCAATATAAAAATAAAATGAAATG
AGCAATTGTTAACAAAATATACATATAATACAAATAAAACATGATATTTAATAATAATTTTAAAA
TAGTATTTAATATACAATATATATATTAACAAAATATTTATAAAAGAATAATAATTATATATATA
AAATATATTAGTTTAAAAGTATGTAAAAGAACTTATAAAACAACACATAATATAAAAAAATATTA
TTTAAAATAAAATTAAACATAATAAATAATTAATTAATAATTTAACATGAGTACAATATGAGTTA
AAAATATAATTTAATTTACAAATTTTAAAATTATGAATAATATAAGGAATAATATAAACATAAAT
AATATATATGATAATATATATGATATACAAAACATATATAAAAAAAAGAAAAATAATAAGTAATA
TAGAATAAAAATAAAAATATAATAAATGTTATATAATAAAATATAATTTAAATATATAGGAAATA
AGAAATATAATACAGATAATATAAAATAATGAAAGTATATATGTAAAAACAATATATATAAATAA
TTTATAAATATATATAATACAAGTAAAAATATAATAATAATAATAAAATAATGATGCAAAATAAT
AATAATTTGTGAAAAATAATAGATAATAAATAATATTAATATATATAATAAAATAATCTTACAAT
ATATAATATAAAAGTAAGGTTAAAAAAAACAAATTACAATATATGAAATATATATATAATAATAA
AAATAAATATATAGGGCTAAATTTAAAGCTCAGCAAAATTACTAGGCGAATTCAAAAGAAGTAGA
ACTGAATTTAGGTCCTAATTAAAACGCGCGCAAAAC
Found at i:43683209 original size:20 final size:21
Alignment explanation
Indices: 43683168--43683210 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
43683158 AATAATTTAT
*
43683168 AAATATATATAATACAAGTAA
1 AAATATATATAATACAAATAA
43683189 AAATATA-ATAATA-ATAATAA
1 AAATATATATAATACA-AATAA
43683209 AA
1 AA
43683211 TAATGATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 12 0.60
21 7 0.35
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
AAATATATATAATACAAATAA
Found at i:43683293 original size:25 final size:23
Alignment explanation
Indices: 43683250--43683300 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
43683240 AAAATAATAG
43683250 ATAAT-AAATAATATTAATATAT
1 ATAATAAAATAATATTAATATAT
*
43683272 ATAATAAAATAATCTTACA-ATAT
1 ATAATAAAATAATATTA-ATATAT
43683295 ATAATA
1 ATAATA
43683301 TAAAAGTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 20 0.77
24 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAATAAAATAATATTAATATAT
Found at i:43683572 original size:702 final size:702
Alignment explanation
Indices: 43682230--43683638 Score: 2818
Period size: 702 Copynumber: 2.0 Consensus size: 702
43682220 CAAATTTTAA
43682230 AATTATGAATAATATAATGAATAATATAAACATAAATAATATAATAGATAATATATATGATATAC
1 AATTATGAATAATATAATGAATAATATAAACATAAATAATATAATAGATAATATATATGATATAC
43682295 ATAACATATATAAAAAAAGAAAAATAATAAGTAATATAGAATAAAAATAAAAATATAATAAATGT
66 ATAACATATATAAAAAAAGAAAAATAATAAGTAATATAGAATAAAAATAAAAATATAATAAATGT
43682360 TATATAATAAAATATAATTTAAATATATAGGAAATAAGAAATATAATACAGATAATATAAAATAA
131 TATATAATAAAATATAATTTAAATATATAGGAAATAAGAAATATAATACAGATAATATAAAATAA
43682425 TGAAAGTATATATGTAAAAACAATATATATAAATAATTTATAAATATATATAATACAAGTAAAAA
196 TGAAAGTATATATGTAAAAACAATATATATAAATAATTTATAAATATATATAATACAAGTAAAAA
43682490 TATAATAATAATAATAAAATAATGATGCAAAATAATAATAATTTGTGAAAAATAATAGATAATAA
261 TATAATAATAATAATAAAATAATGATGCAAAATAATAATAATTTGTGAAAAATAATAGATAATAA
43682555 ATAATATTAATATATATAATAAAATAATCTTACAATATATAATATAAAAGTAAGGTTAAAAAAAA
326 ATAATATTAATATATATAATAAAATAATCTTACAATATATAATATAAAAGTAAGGTTAAAAAAAA
43682620 CAAATTACAATATATGAAATATATATATAATAATAAAAATAAATATATAGGGCTAAATTTAAAGC
391 CAAATTACAATATATGAAATATATATATAATAATAAAAATAAATATATAGGGCTAAATTTAAAGC
43682685 TCAGCAAAATTACTAGGCGAATTCAAAAGAAGTAGAACTGAATTTAGGTCCTAATTAAAACGCGC
456 TCAGCAAAATTACTAGGCGAATTCAAAAGAAGTAGAACTGAATTTAGGTCCTAATTAAAACGCGC
43682750 GCAAAACAAAAGGGACTCATTGGGCAAATTTCCCTATTCCCAAAATGACTGCGTTTTAAACTTGG
521 GCAAAACAAAAGGGACTCATTGGGCAAATTTCCCTATTCCCAAAATGACTGCGTTTTAAACTTGG
43682815 ACTTAAAGCAGCTACTTCAGGGATTAAATCACAACTGAGACAAAATATTAGGGTTAAATCATAAA
586 ACTTAAAGCAGCTACTTCAGGGATTAAATCACAACTGAGACAAAATATTAGGGTTAAATCATAAA
43682880 TAAAATAAAACTTAATTGTAAACACAAAAAAGGATAGAAGGATCAATTGGGT
651 TAAAATAAAACTTAATTGTAAACACAAAAAAGGATAGAAGGATCAATTGGGT
43682932 AATTATGAATAATATAATGAATAATATAAACATAAATAATATAATAGATAATATATATGATATAC
1 AATTATGAATAATATAATGAATAATATAAACATAAATAATATAATAGATAATATATATGATATAC
43682997 ATAACATATATAAAAAAAGAAAAATAATAAGTAATATAGAATAAAAATAAAAATATAATAAATGT
66 ATAACATATATAAAAAAAGAAAAATAATAAGTAATATAGAATAAAAATAAAAATATAATAAATGT
43683062 TATATAATAAAATATAATTTAAATATATAGGAAATAAGAAATATAATACAGATAATATAAAATAA
131 TATATAATAAAATATAATTTAAATATATAGGAAATAAGAAATATAATACAGATAATATAAAATAA
43683127 TGAAAGTATATATGTAAAAACAATATATATAAATAATTTATAAATATATATAATACAAGTAAAAA
196 TGAAAGTATATATGTAAAAACAATATATATAAATAATTTATAAATATATATAATACAAGTAAAAA
43683192 TATAATAATAATAATAAAATAATGATGCAAAATAATAATAATTTGTGAAAAATAATAGATAATAA
261 TATAATAATAATAATAAAATAATGATGCAAAATAATAATAATTTGTGAAAAATAATAGATAATAA
43683257 ATAATATTAATATATATAATAAAATAATCTTACAATATATAATATAAAAGTAAGGTTAAAAAAAA
326 ATAATATTAATATATATAATAAAATAATCTTACAATATATAATATAAAAGTAAGGTTAAAAAAAA
43683322 CAAATTACAATATATGAAATATATATATAATAATAAAAATAAATATATAGGGCTAAATTTAAAGC
391 CAAATTACAATATATGAAATATATATATAATAATAAAAATAAATATATAGGGCTAAATTTAAAGC
43683387 TCAGCAAAATTACTAGGCGAATTCAAAAGAAGTAGAACTGAATTTAGGTCCTAATTAAAACGCGC
456 TCAGCAAAATTACTAGGCGAATTCAAAAGAAGTAGAACTGAATTTAGGTCCTAATTAAAACGCGC
43683452 GCAAAACAAAAGGGACTCATTGGGCAAATTTCCCTATTCCCAAAATGACTGCGTTTTAAACTTGG
521 GCAAAACAAAAGGGACTCATTGGGCAAATTTCCCTATTCCCAAAATGACTGCGTTTTAAACTTGG
43683517 ACTTAAAGCAGCTACTTCAGGGATTAAATCACAACTGAGACAAAATATTAGGGTTAAATCATAAA
586 ACTTAAAGCAGCTACTTCAGGGATTAAATCACAACTGAGACAAAATATTAGGGTTAAATCATAAA
43683582 TAAAATAAAACTTAATTGTAAACACAAAAAAGGATAGAAGGATCAATTGGGT
651 TAAAATAAAACTTAATTGTAAACACAAAAAAGGATAGAAGGATCAATTGGGT
43683634 AATTA
1 AATTA
43683639 ACCCAATCCT
Statistics
Matches: 707, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
702 707 1.00
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (702 bp):
AATTATGAATAATATAATGAATAATATAAACATAAATAATATAATAGATAATATATATGATATAC
ATAACATATATAAAAAAAGAAAAATAATAAGTAATATAGAATAAAAATAAAAATATAATAAATGT
TATATAATAAAATATAATTTAAATATATAGGAAATAAGAAATATAATACAGATAATATAAAATAA
TGAAAGTATATATGTAAAAACAATATATATAAATAATTTATAAATATATATAATACAAGTAAAAA
TATAATAATAATAATAAAATAATGATGCAAAATAATAATAATTTGTGAAAAATAATAGATAATAA
ATAATATTAATATATATAATAAAATAATCTTACAATATATAATATAAAAGTAAGGTTAAAAAAAA
CAAATTACAATATATGAAATATATATATAATAATAAAAATAAATATATAGGGCTAAATTTAAAGC
TCAGCAAAATTACTAGGCGAATTCAAAAGAAGTAGAACTGAATTTAGGTCCTAATTAAAACGCGC
GCAAAACAAAAGGGACTCATTGGGCAAATTTCCCTATTCCCAAAATGACTGCGTTTTAAACTTGG
ACTTAAAGCAGCTACTTCAGGGATTAAATCACAACTGAGACAAAATATTAGGGTTAAATCATAAA
TAAAATAAAACTTAATTGTAAACACAAAAAAGGATAGAAGGATCAATTGGGT
Found at i:43684635 original size:17 final size:17
Alignment explanation
Indices: 43684613--43684656 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
43684603 TTATAATTGT
43684613 AATGGGTCCAGGGTGTA
1 AATGGGTCCAGGGTGTA
** *
43684630 AATGGGTTAAGGTTGTA
1 AATGGGTCCAGGGTGTA
*
43684647 AGTGGGTCCA
1 AATGGGTCCA
43684657 CTGGGTAGCT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.39, T:0.27
Consensus pattern (17 bp):
AATGGGTCCAGGGTGTA
Found at i:43687773 original size:30 final size:30
Alignment explanation
Indices: 43687739--43687800 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
43687729 ATGAGTGAAT
43687739 GTTTGAGTCCTAAGTGAGCTTCCAAAAATG
1 GTTTGAGTCCTAAGTGAGCTTCCAAAAATG
43687769 GTTTGAGTCCTAAGTGAGCTTCCAAAAATG
1 GTTTGAGTCCTAAGTGAGCTTCCAAAAATG
43687799 GT
1 GT
43687801 GAAATCGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (30 bp):
GTTTGAGTCCTAAGTGAGCTTCCAAAAATG
Found at i:43687894 original size:5 final size:5
Alignment explanation
Indices: 43687886--43687926 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
43687876 TAACTTAATA
43687886 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
43687927 TATAAAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:43693430 original size:24 final size:24
Alignment explanation
Indices: 43693403--43693448 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
43693393 ATTAAATAAG
43693403 TTTTAAGTATTTT-ATTTATTTTAT
1 TTTTAAG-ATTTTAATTTATTTTAT
*
43693427 TTTTAAGATTTTAATTTTTTTT
1 TTTTAAGATTTTAATTTATTTT
43693449 GTTTGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTTAAGATTTTAATTTATTTTAT
Found at i:43700531 original size:13 final size:13
Alignment explanation
Indices: 43700513--43700541 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
43700503 GGTTGTTTAT
43700513 TAAACTAATTAAC
1 TAAACTAATTAAC
43700526 TAAACTAATTAAC
1 TAAACTAATTAAC
43700539 TAA
1 TAA
43700542 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:43709371 original size:252 final size:252
Alignment explanation
Indices: 43708926--43709428 Score: 997
Period size: 252 Copynumber: 2.0 Consensus size: 252
43708916 GAAAAAGACT
43708926 TAAAGAAAAGTATTTGATAAAGACGACACCCAATGAGGAATACCTAGATTTCACTTGTTATCTGA
1 TAAAGAAAAGTATTTGATAAAGACGACACCCAATGAGGAATACCTAGATTTCACTTGTTATCTGA
43708991 CTCTGAACCAGACGATTTATTCACTTGACTTGATCCGTGAGACTCCCTAACATATATTATTATCT
66 CTCTGAACCAGACGATTTATTCACTTGACTTGATCCGTGAGACTCCCTAACATATATTATTATCT
*
43709056 CTTTCGAGACTAATAATGTCTAACCCTCAGTTGAATTAATTAAAATCTATTTCTTAATTAAAACC
131 CTTTCGAGACTAATAACGTCTAACCCTCAGTTGAATTAATTAAAATCTATTTCTTAATTAAAACC
43709121 CCTAGGGAAGCAGTAAATCGATCTATGGACTCCTATATTAGGTTTCACCCTAATCCA
196 CCTAGGGAAGCAGTAAATCGATCTATGGACTCCTATATTAGGTTTCACCCTAATCCA
43709178 TAAAGAAAAGTATTTGATAAAGACGACACCCAATGAGGAATACCTAGATTTCACTTGTTATCTGA
1 TAAAGAAAAGTATTTGATAAAGACGACACCCAATGAGGAATACCTAGATTTCACTTGTTATCTGA
43709243 CTCTGAACCAGACGATTTATTCACTTGACTTGATCCGTGAGACTCCCTAACATATATTATTATCT
66 CTCTGAACCAGACGATTTATTCACTTGACTTGATCCGTGAGACTCCCTAACATATATTATTATCT
43709308 CTTTCGAGACTAATAACGTCTAACCCTCAGTTGAATTAATTAAAATCTATTTCTTAATTAAAACC
131 CTTTCGAGACTAATAACGTCTAACCCTCAGTTGAATTAATTAAAATCTATTTCTTAATTAAAACC
43709373 CCTAGGGAAGCAGTAAATCGATCTATGGACTCCTATATTAGGTTTCACCCTAATCC
196 CCTAGGGAAGCAGTAAATCGATCTATGGACTCCTATATTAGGTTTCACCCTAATCC
43709429 GGTAAAATCT
Statistics
Matches: 250, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
252 250 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (252 bp):
TAAAGAAAAGTATTTGATAAAGACGACACCCAATGAGGAATACCTAGATTTCACTTGTTATCTGA
CTCTGAACCAGACGATTTATTCACTTGACTTGATCCGTGAGACTCCCTAACATATATTATTATCT
CTTTCGAGACTAATAACGTCTAACCCTCAGTTGAATTAATTAAAATCTATTTCTTAATTAAAACC
CCTAGGGAAGCAGTAAATCGATCTATGGACTCCTATATTAGGTTTCACCCTAATCCA
Found at i:43711134 original size:18 final size:18
Alignment explanation
Indices: 43711111--43711161 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
43711101 ATTTATTTTC
43711111 TTTCTATTATATTAATAT
1 TTTCTATTATATTAATAT
43711129 TTTCTA-T-TA-TAAT-T
1 TTTCTATTATATTAATAT
*
43711143 TTTCTATTATATTAGTAT
1 TTTCTATTATATTAATAT
43711161 T
1 T
43711162 AGATTAGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 7 0.25
15 5 0.18
16 4 0.14
17 4 0.14
18 8 0.29
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTCTATTATATTAATAT
Found at i:43711147 original size:14 final size:15
Alignment explanation
Indices: 43711123--43711153 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
43711113 TCTATTATAT
43711123 TAATATTTTCTATTA
1 TAATATTTTCTATTA
43711138 TAAT-TTTTCTATTA
1 TAATATTTTCTATTA
43711152 TA
1 TA
43711154 TTAGTATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATATTTTCTATTA
Found at i:43711167 original size:11 final size:11
Alignment explanation
Indices: 43711147--43711199 Score: 76
Period size: 11 Copynumber: 5.1 Consensus size: 11
43711137 ATAATTTTTC
*
43711147 TATTATATTAG
1 TATTAGATTAG
43711158 TATTAGATTAG
1 TATTAGATTAG
43711169 TATTAG-TTAG
1 TATTAGATTAG
43711179 -ATTAGATTAG
1 TATTAGATTAG
43711189 TATTAG-TTAG
1 TATTAGATTAG
43711199 T
1 T
43711200 GATCCCGGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
9 5 0.13
10 13 0.33
11 21 0.54
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (11 bp):
TATTAGATTAG
Found at i:43711184 original size:20 final size:21
Alignment explanation
Indices: 43711154--43711199 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
43711144 TTCTATTATA
43711154 TTAGTATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
43711175 TTAG-ATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
43711195 TTAGT
1 TTAGT
43711200 GATCCCGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (21 bp):
TTAGTATTAGATTAGTATTAG
Found at i:43711198 original size:15 final size:14
Alignment explanation
Indices: 43711160--43711189 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
43711150 TATATTAGTA
43711160 TTAGATTAGTATTAG
1 TTAGATTAG-ATTAG
43711175 TTAGATTAGATTAG
1 TTAGATTAGATTAG
43711189 T
1 T
43711190 ATTAGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (14 bp):
TTAGATTAGATTAG
Found at i:43714631 original size:3 final size:3
Alignment explanation
Indices: 43714623--43714653 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
43714613 AATAGATACA
43714623 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
43714654 AAATAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:43732058 original size:12 final size:12
Alignment explanation
Indices: 43732041--43732065 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43732031 TGAACCAATG
43732041 TGAATTATTTTT
1 TGAATTATTTTT
43732053 TGAATTATTTTT
1 TGAATTATTTTT
43732065 T
1 T
43732066 TTCTTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TGAATTATTTTT
Found at i:43732759 original size:15 final size:14
Alignment explanation
Indices: 43732724--43732762 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
43732714 TTAGATTTAA
43732724 AATTTAATTTATAT
1 AATTTAATTTATAT
43732738 -ATATTAATTTAATAT
1 AAT-TTAATTT-ATAT
43732753 AATTTAATTT
1 AATTTAATTT
43732763 CTTTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.09
14 7 0.32
15 11 0.50
16 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATTTAATTTATAT
Found at i:43739917 original size:20 final size:18
Alignment explanation
Indices: 43739894--43739944 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
43739884 TTAAATATTT
43739894 TTATATTATTAAATTATATA
1 TTATATTATTAAATT-TA-A
* *
43739914 TTATGTTATTACATTTAA
1 TTATATTATTAAATTTAA
43739932 TATATATTATTAA
1 T-TATATTATTAA
43739945 CCCTAAGCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 11 0.42
20 13 0.50
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TTATATTATTAAATTTAA
Found at i:43748876 original size:30 final size:30
Alignment explanation
Indices: 43748816--43748878 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
43748806 AATGGTGGTT
* * *
43748816 AAACATGTATTAGATGATAATGTAAAAAAA
1 AAACATATATTAGATAATAATGCAAAAAAA
**
43748846 AAACATATATTAGATAATAATGCACTAAAA
1 AAACATATATTAGATAATAATGCAAAAAAA
43748876 AAA
1 AAA
43748879 TAATAGAGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.59, C:0.06, G:0.10, T:0.25
Consensus pattern (30 bp):
AAACATATATTAGATAATAATGCAAAAAAA
Found at i:43750118 original size:26 final size:26
Alignment explanation
Indices: 43750083--43750136 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
43750073 TTTGTATGTG
43750083 TATTTAAAATATTTTACATATAAAAA
1 TATTTAAAATATTTTACATATAAAAA
*
43750109 TATTTGAAATATTTTACATATAAAAA
1 TATTTAAAATATTTTACATATAAAAA
43750135 TA
1 TA
43750137 ACAATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (26 bp):
TATTTAAAATATTTTACATATAAAAA
Found at i:43754773 original size:69 final size:69
Alignment explanation
Indices: 43754662--43754801 Score: 253
Period size: 69 Copynumber: 2.0 Consensus size: 69
43754652 TATTTTGATA
43754662 TTGATGAATATCTATTTAATAAAATATTCATAATACTTTTCATAAAATGTCTATTGGTAGATAAT
1 TTGATGAATATCTATTTAATAAAATATTCATAATACTTTTCATAAAATGTCTATTGGTAGATAAT
43754727 ATGT
66 ATGT
* * *
43754731 TTGATGAATATCTATTTAATAAAATATTCATAATATTTTTCATAAAATGTTTATTTGTAGATAAT
1 TTGATGAATATCTATTTAATAAAATATTCATAATACTTTTCATAAAATGTCTATTGGTAGATAAT
43754796 ATGT
66 ATGT
43754800 TT
1 TT
43754802 TGTTAAAACT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (69 bp):
TTGATGAATATCTATTTAATAAAATATTCATAATACTTTTCATAAAATGTCTATTGGTAGATAAT
ATGT
Found at i:43763170 original size:5 final size:5
Alignment explanation
Indices: 43763160--43763187 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
43763150 GATGCCAACC
43763160 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
43763188 GATTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:43763535 original size:39 final size:39
Alignment explanation
Indices: 43763480--43763648 Score: 189
Period size: 39 Copynumber: 4.2 Consensus size: 39
43763470 TTTAAATTAC
* *
43763480 AAATTTTGAACCAGGATTAAAAATAAAATAT-AACCAGAT
1 AAATTTAGAAACAGGATTAAAAATAAAATATGAA-CAGAT
* *
43763519 AAATTTAGAAATAGGATTAAAAATAAAATATGAATAGAT
1 AAATTTAGAAACAGGATTAAAAATAAAATATGAACAGAT
* * *
43763558 AAATTTAGAAGCAGGATTAAAAATAAATTATGAACATAT
1 AAATTTAGAAACAGGATTAAAAATAAAATATGAACAGAT
*
43763597 ACAAATAATTTAGAAACAAGATTAAAAATAAAATATGAACAG-T
1 ----A-AATTTAGAAACAGGATTAAAAATAAAATATGAACAGAT
43763640 AAAATTTAG
1 -AAATTTAG
43763649 GCTCGAAATT
Statistics
Matches: 111, Mismatches: 13, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
39 73 0.66
40 4 0.04
43 2 0.02
44 32 0.29
ACGTcount: A:0.57, C:0.05, G:0.11, T:0.27
Consensus pattern (39 bp):
AAATTTAGAAACAGGATTAAAAATAAAATATGAACAGAT
Found at i:43763625 original size:23 final size:23
Alignment explanation
Indices: 43763559--43763627 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
43763549 TGAATAGATA
* *
43763559 AATTTAGAAGCAGGATTAAAAAT
1 AATTTAGAAACAAGATTAAAAAT
* * *
43763582 AAATTATG-AAC-ATA-TACAAAT
1 AATTTA-GAAACAAGATTAAAAAT
43763603 AATTTAGAAACAAGATTAAAAAT
1 AATTTAGAAACAAGATTAAAAAT
43763626 AA
1 AA
43763628 AATATGAACA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 3 0.09
23 15 0.44
24 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (23 bp):
AATTTAGAAACAAGATTAAAAAT
Found at i:43766610 original size:26 final size:26
Alignment explanation
Indices: 43766581--43766688 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
43766571 TGGTACAAAT
43766581 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
43766607 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
43766633 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
43766659 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
43766685 TGAT
1 TGAT
43766689 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:43776018 original size:21 final size:22
Alignment explanation
Indices: 43775981--43776024 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
43775971 TTTTTCATTG
*
43775981 TCTTCTGCTTCTCCATTTGTTT
1 TCTTCTGCTTCTCCATTTCTTT
*
43776003 TCTTCT-CTTCTTCATTTCTTT
1 TCTTCTGCTTCTCCATTTCTTT
43776024 T
1 T
43776025 AACGTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.05, C:0.27, G:0.05, T:0.64
Consensus pattern (22 bp):
TCTTCTGCTTCTCCATTTCTTT
Found at i:43776855 original size:16 final size:16
Alignment explanation
Indices: 43776833--43776900 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
43776823 TTTGGTTCGC
43776833 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
43776849 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
43776865 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
43776881 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
43776897 TGTA
1 TGTA
43776901 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.25, C:0.01, G:0.37, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:43776965 original size:44 final size:45
Alignment explanation
Indices: 43776881--43776971 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
43776871 GGATTAGAGG
* * *
43776881 TGTATTGGATTAGAGGTGTAATAGCTAATCCATTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCATTGTTTGGTTGAA
*
43776926 TGTAATGGAATAGAGGCGTAATAG-TAAT-CTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCAT-TGTTTGGTTGAA
43776970 TG
1 TG
43776972 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 2 0.05
44 18 0.44
45 21 0.51
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.38
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCATTGTTTGGTTGAA
Found at i:43777157 original size:18 final size:17
Alignment explanation
Indices: 43777136--43777170 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43777126 TTATTATTAA
*
43777136 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
43777154 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
43777171 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:43777277 original size:18 final size:17
Alignment explanation
Indices: 43777256--43777290 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43777246 TTATTATTAA
*
43777256 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
43777274 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
43777291 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:43777332 original size:120 final size:120
Alignment explanation
Indices: 43777119--43777536 Score: 712
Period size: 120 Copynumber: 3.4 Consensus size: 120
43777109 ATCATATTTA
43777119 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
43777184 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
43777239 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
43777304 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
43777359 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* * * * *
43777424 TATTCTTATATGAATTTACTCAAATCATAATATATTATATGATACTATAAAAGATAATTT
66 TATTCTTATATTAATTTACTGAAATC---ATA-A-TATATGATACTGTAAAATATAAATT
* *
43777484 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 -AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
43777537 TAAAATAATT
Statistics
Matches: 285, Mismatches: 7, Indels: 7
0.95 0.02 0.02
Matches are distributed among these distances:
120 209 0.73
123 3 0.01
124 1 0.00
125 70 0.25
126 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:43777397 original size:18 final size:17
Alignment explanation
Indices: 43777376--43777410 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43777366 TTATTATTAA
*
43777376 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
43777394 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
43777411 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:43778320 original size:13 final size:13
Alignment explanation
Indices: 43778302--43778331 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
43778292 CAATCAGCTA
43778302 AATTCAGAAAAAC
1 AATTCAGAAAAAC
43778315 AATTCAGAAAAAC
1 AATTCAGAAAAAC
43778328 AATT
1 AATT
43778332 ACATGACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:43781224 original size:15 final size:15
Alignment explanation
Indices: 43781201--43781242 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
43781191 CTCGGCTTTT
*
43781201 TTCTCCTCGGCTGGC
1 TTCTTCTCGGCTGGC
*
43781216 TTTTTCTCGGCTGGC
1 TTCTTCTCGGCTGGC
43781231 TTCTTCTCGGCT
1 TTCTTCTCGGCT
43781243 TTGGGTGCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.24, T:0.43
Consensus pattern (15 bp):
TTCTTCTCGGCTGGC
Found at i:43782452 original size:3 final size:3
Alignment explanation
Indices: 43782444--43782478 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
43782434 GGGGAGAGTG
43782444 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
43782479 CTATATACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:43782554 original size:20 final size:20
Alignment explanation
Indices: 43782529--43782632 Score: 66
Period size: 20 Copynumber: 5.0 Consensus size: 20
43782519 AACGTAATAG
43782529 TATTTTTATTATTTTATTAT
1 TATTTTTATTATTTTATTAT
* * *
43782549 TATTTTCACCT-TTTTATTAC
1 TATTTTTA-TTATTTTATTAT
* *
43782569 TATTATTATTAACCTATTATTAT
1 TATTTTTATT-A--TTTTATTAT
* * * *
43782592 TATTTTTATTAATATAGTGT
1 TATTTTTATTATTTTATTAT
*
43782612 TATTTTCTTTTATTTTATTAT
1 TATTTT-TATTATTTTATTAT
43782633 CATTATTAAC
Statistics
Matches: 59, Mismatches: 19, Indels: 11
0.66 0.21 0.12
Matches are distributed among these distances:
19 1 0.02
20 31 0.53
21 10 0.17
22 1 0.02
23 16 0.27
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTTTTATTATTTTATTAT
Found at i:43784042 original size:21 final size:20
Alignment explanation
Indices: 43784008--43784049 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
43783998 ATAATAGTCT
*
43784008 ATTAAAAAATTACAAGCCCA
1 ATTAAAAAAGTACAAGCCCA
43784028 ATTAACAAAAGTACAAGCCCA
1 ATTAA-AAAAGTACAAGCCCA
43784049 A
1 A
43784050 AATACAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (20 bp):
ATTAAAAAAGTACAAGCCCA
Found at i:43785912 original size:154 final size:154
Alignment explanation
Indices: 43785632--43785942 Score: 559
Period size: 154 Copynumber: 2.0 Consensus size: 154
43785622 TTTAAATTGA
* * *
43785632 TTTTACTTGCATTTTATTGCTTAAATTATAGAAATACCTCTGAGCTTCATTGCTTAGCGTACAAT
1 TTTTACTTGCATTTTATTGCTTAAATTATAGAAATACCTCCGAGCTTCATTACTCAGCGTACAAT
43785697 TTGTTTTCTTCATGCATAGGTACAATAGATCCTCAATAGATCAAGCAGAGTTTCAACATCCAGAA
66 TTGTTTTCTTCATGCATAGGTACAATAGATCCTCAATAGATCAAGCAGAGTTTCAACATCCAGAA
*
43785762 ATCGATTCCCAACTCAACAAAGTT
131 ATCAATTCCCAACTCAACAAAGTT
43785786 TTTTACTTGCATTTTATTGCTTAAATTATAGAAATACCTCCGAGCTTCATTACTCAGCGTACAAT
1 TTTTACTTGCATTTTATTGCTTAAATTATAGAAATACCTCCGAGCTTCATTACTCAGCGTACAAT
* * *
43785851 TTGTTTTCTTCGTGCATAGGTACAGTAGATCCTCGATAGATCAAGCAGAGTTTCAACATCCAGAA
66 TTGTTTTCTTCATGCATAGGTACAATAGATCCTCAATAGATCAAGCAGAGTTTCAACATCCAGAA
43785916 ATCAATTCCCAACTCAACAAAGTT
131 ATCAATTCCCAACTCAACAAAGTT
43785940 TTT
1 TTT
43785943 ATGCATTTTT
Statistics
Matches: 150, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
154 150 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (154 bp):
TTTTACTTGCATTTTATTGCTTAAATTATAGAAATACCTCCGAGCTTCATTACTCAGCGTACAAT
TTGTTTTCTTCATGCATAGGTACAATAGATCCTCAATAGATCAAGCAGAGTTTCAACATCCAGAA
ATCAATTCCCAACTCAACAAAGTT
Found at i:43788023 original size:15 final size:15
Alignment explanation
Indices: 43788003--43788035 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
43787993 TGGCACCCAA
*
43788003 AGCCGAGAAGAAGCC
1 AGCCGAGAAAAAGCC
43788018 AGCCGAGAAAAAGCC
1 AGCCGAGAAAAAGCC
43788033 AGC
1 AGC
43788036 TGAGGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.27, G:0.30, T:0.00
Consensus pattern (15 bp):
AGCCGAGAAAAAGCC
Found at i:43795714 original size:26 final size:26
Alignment explanation
Indices: 43795683--43795790 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
43795673 TGAAATGCCC
*
43795683 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
43795709 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
43795735 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
43795761 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
43795787 ATCA
1 ATCA
43795791 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:43797458 original size:19 final size:21
Alignment explanation
Indices: 43797434--43797473 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43797424 TCAGAGTTCT
*
43797434 TCGG-AACACA-AATTCTTTC
1 TCGGAAACACAGAACTCTTTC
43797453 TCGGAAACACAGAACTCTTTC
1 TCGGAAACACAGAACTCTTTC
43797474 ACCATCTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 8 0.44
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (21 bp):
TCGGAAACACAGAACTCTTTC
Found at i:43801756 original size:26 final size:26
Alignment explanation
Indices: 43801720--43801775 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
43801710 NNNNNNNNNN
*
43801720 ATCATGGAACATTTACCTAGCCCATT
1 ATCATGGAACATTTACCTAACCCATT
43801746 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
43801772 ATCA
1 ATCA
43801776 ATTTGTACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.27, G:0.09, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:43802317 original size:68 final size:69
Alignment explanation
Indices: 43802244--43802378 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 69
43802234 TTTAATAGAT
* * * * * *
43802244 TTAATATTAAATTTAATTTGATACTTATTTTGAT-AGTATTTTGTTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATATAATACTTATCTTCATAAGTATTATATTAATTTAATATTAAAGTGAT
43802308 TATC
66 TATC
* *
43802312 TTAATATTAAATTTACTATAATATTTATCTTCATAAGTATTATATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATATAATACTTATCTTCATAAGTATTATATTAATTTAATATTAAAGTGAT
43802377 TA
66 TA
43802379 AATTTAATTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 28 0.48
69 30 0.52
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.51
Consensus pattern (69 bp):
TTAATATTAAATTTAATATAATACTTATCTTCATAAGTATTATATTAATTTAATATTAAAGTGAT
TATC
Found at i:43811787 original size:33 final size:33
Alignment explanation
Indices: 43811745--43811814 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
43811735 ATTGAACCCT
43811745 ATATTATTATATTTCATAGAATTTAAATTCAAG
1 ATATTATTATATTTCATAGAATTTAAATTCAAG
43811778 ATATTATTATATTTCATAGAATTTAAATTCAAG
1 ATATTATTATATTTCATAGAATTTAAATTCAAG
43811811 -TATT
1 ATATT
43811815 CTTTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 4 0.11
33 33 0.89
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (33 bp):
ATATTATTATATTTCATAGAATTTAAATTCAAG
Found at i:43816945 original size:22 final size:23
Alignment explanation
Indices: 43816919--43816964 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
43816909 CAACCGAACC
43816919 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
43816941 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
43816964 A
1 A
43816965 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:43816970 original size:23 final size:23
Alignment explanation
Indices: 43816926--43816970 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
43816916 ACCAATTCAA
*
43816926 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
43816949 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
43816971 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:43825466 original size:23 final size:25
Alignment explanation
Indices: 43825424--43825483 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
43825414 ATAATAATAC
43825424 TAATATAATAAATGTAATAGTGAT-AA
1 TAATATAATAAATG-AATAGT-ATGAA
43825450 TAATATAAT-AATG-ATAGTATGAA
1 TAATATAATAAATGAATAGTATGAA
43825473 TAATAT-ATAAA
1 TAATATAATAAA
43825484 AAAAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.12
23 15 0.47
25 4 0.12
26 9 0.28
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (25 bp):
TAATATAATAAATGAATAGTATGAA
Found at i:43825475 original size:26 final size:27
Alignment explanation
Indices: 43825419--43825482 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
43825409 TAGCAATAAT
*
43825419 AATACTAATATAATAAATGTAATAGTG
1 AATAATAATATAATAAATGTAATAGTG
*
43825446 -ATAATAATATAAT-AATGATAGTA-TG
1 AATAATAATATAATAAATG-TAATAGTG
43825471 AATAAT-ATATAA
1 AATAATAATATAA
43825483 AAAAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 12 0.36
26 21 0.64
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (27 bp):
AATAATAATATAATAAATGTAATAGTG
Found at i:43825613 original size:3 final size:3
Alignment explanation
Indices: 43825605--43825656 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
43825595 ATACACTAAC
* * ** *
43825605 ATA ATA ATA ATT ATA ATA ATA CTA GCA ATA ATA ATA ATTA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
43825651 ATA ATA
1 ATA ATA
43825657 TATACACAAC
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:43825652 original size:16 final size:16
Alignment explanation
Indices: 43825617--43825656 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
43825607 AATAATAATT
43825617 ATAATAAT-ACTAGCA
1 ATAATAATAACTAGCA
* *
43825632 ATAATAATAATTAGTA
1 ATAATAATAACTAGCA
43825648 ATAATAATA
1 ATAATAATA
43825657 TATACACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
ATAATAATAACTAGCA
Found at i:43825768 original size:262 final size:262
Alignment explanation
Indices: 43825485--43826009 Score: 1034
Period size: 262 Copynumber: 2.0 Consensus size: 262
43825475 ATATATAAAA
43825485 AAAAATAATGATATAATAATAACAATATTAAAATAAAAAAGCTACTATAATAAAAATGTTAAAAT
1 AAAAATAATGATATAATAATAACAATATTAAAATAAAAAAGCTACTATAATAAAAATGTTAAAAT
43825550 AAAGTAATAAAAACATTGCTACATATATATATACGTACATAAAATATACACTAACATAATAATAA
66 AAAGTAATAAAAACATTGCTACATATATATATACGTACATAAAATATACACTAACATAATAATAA
43825615 TTATAATAATACTAGCAATAATAATAATTAGTAATAATAATATATACACAACATGGTATTT-AAA
131 TTATAATAATACTAGCAATAATAATAATTAGTAATAATAATATATACACAACATGGTATTTAAAA
43825679 AAAATAAAAAATAAAATATATATATAATAGTATTTAAGAATATATACATAAGATGATATAAAATA
196 AAAAT-AAAAATAAAATATATATATAATAGTATTTAAGAATATATACATAAGATGATATAAAATA
43825744 CAT
260 CAT
43825747 AAAAATAATGATATAATAATAACAATATTAAAATAAAAAAGCTACTATAATAAAAATGTTAAAAT
1 AAAAATAATGATATAATAATAACAATATTAAAATAAAAAAGCTACTATAATAAAAATGTTAAAAT
43825812 AAAGTAATAAAAACATTGCTACATATATATATACGTACATAAAATATACACTAACATAATAATAA
66 AAAGTAATAAAAACATTGCTACATATATATATACGTACATAAAATATACACTAACATAATAATAA
43825877 TTATAATAATACTAGCAATAATAATAATTAGTAATAATAATATATACACAACATGGTATTTAAAA
131 TTATAATAATACTAGCAATAATAATAATTAGTAATAATAATATATACACAACATGGTATTTAAAA
43825942 AAAATAAAAATAAAATATATATATAATAGTATTTAAGAATATATACATAAGATGATATAAAATAC
196 AAAATAAAAATAAAATATATATATAATAGTATTTAAGAATATATACATAAGATGATATAAAATAC
43826007 AT
261 AT
43826009 A
1 A
43826010 CATGGAATAA
Statistics
Matches: 262, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
262 254 0.97
263 8 0.03
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (262 bp):
AAAAATAATGATATAATAATAACAATATTAAAATAAAAAAGCTACTATAATAAAAATGTTAAAAT
AAAGTAATAAAAACATTGCTACATATATATATACGTACATAAAATATACACTAACATAATAATAA
TTATAATAATACTAGCAATAATAATAATTAGTAATAATAATATATACACAACATGGTATTTAAAA
AAAATAAAAATAAAATATATATATAATAGTATTTAAGAATATATACATAAGATGATATAAAATAC
AT
Done.