Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 21 of 425
Found at i:5501972 original size:25 final size:25
Alignment explanation
Indices: 5501944--5501994 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5501934 TAATTTGAAA
*
5501944 AAACTTGCAAGAAGGGTATAGCAAG
1 AAACTTGCAAGAAGGGCATAGCAAG
* * *
5501969 AAACTTGTAGGAAGGGCATAGGAAG
1 AAACTTGCAAGAAGGGCATAGCAAG
5501994 A
1 A
5501995 GGGTTGGAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.31, T:0.16
Consensus pattern (25 bp):
AAACTTGCAAGAAGGGCATAGCAAG
Found at i:5503106 original size:14 final size:14
Alignment explanation
Indices: 5503089--5503125 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5503079 CACATACAAA
5503089 ACTAAATGGGTTTT
1 ACTAAATGGGTTTT
5503103 ACTAAATGGGTTTT
1 ACTAAATGGGTTTT
*
5503117 ACTAGATGG
1 ACTAAATGG
5503126 TGAGAGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.08, G:0.24, T:0.38
Consensus pattern (14 bp):
ACTAAATGGGTTTT
Found at i:5507675 original size:29 final size:25
Alignment explanation
Indices: 5507637--5507708 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 25
5507627 AAATAGTATC
*
5507637 AAAGAGAAATAAGATAAAAAGTAATTTAA
1 AAAGATAAATAAGATAAAAA-TAA---AA
5507666 AAAGATAAATAAAGATAAAAATAAAA
1 AAAGATAAAT-AAGATAAAAATAAAA
5507692 AAAGAT-AATAA-ATAAAA
1 AAAGATAAATAAGATAAAA
5507709 GTCTTCAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
23 6 0.15
24 2 0.05
25 3 0.07
26 8 0.20
29 12 0.29
30 10 0.24
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (25 bp):
AAAGATAAATAAGATAAAAATAAAA
Found at i:5507704 original size:17 final size:16
Alignment explanation
Indices: 5507665--5507708 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
5507655 AAGTAATTTA
*
5507665 AAAAGATAAATAAAGAT
1 AAAA-ATAAAAAAAGAT
5507682 AAAAATAAAAAAAGAT
1 AAAAATAAAAAAAGAT
5507698 AATAAATAAAA
1 AA-AAATAAAA
5507709 GTCTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAAAAGAT
Found at i:5510067 original size:40 final size:40
Alignment explanation
Indices: 5509876--5510060 Score: 236
Period size: 40 Copynumber: 4.7 Consensus size: 40
5509866 TCGAATGATG
* *
5509876 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
5509915 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
5509955 TTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5509995 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
5510036 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
5510061 AACGAGTAGC
Statistics
Matches: 132, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
39 25 0.19
40 105 0.80
41 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5510067 original size:80 final size:80
Alignment explanation
Indices: 5509876--5510093 Score: 236
Period size: 80 Copynumber: 2.8 Consensus size: 80
5509866 TCGAATGATG
* * **
5509876 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAGATCCGAAGGCATT
5509939 TGTGCGAGTTACTAAA
65 TGTGCGAGTTACTAAA
* *
5509955 TTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGAT-CCGAAGGCAT
5510018 TTGTGCGAGTTACTATAA
64 TTGTGCGAGTTACTA-AA
* ** *
5510036 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAA-ACTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGGTTAAGA-TCCGAAGG
5510094 TACGTGATTC
Statistics
Matches: 118, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
79 40 0.34
80 76 0.64
81 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGATCCGAAGGCATTT
GTGCGAGTTACTAAA
Found at i:5526403 original size:12 final size:11
Alignment explanation
Indices: 5526364--5526399 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
5526354 ATGACTAATG
5526364 ATAT-TAAAAT
1 ATATATAAAAT
5526374 ATATATAATAAT
1 ATATATAA-AAT
5526386 ATATATAAAAT
1 ATATATAAAAT
5526397 ATA
1 ATA
5526400 ATATTAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.17
11 9 0.38
12 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATATAAAAT
Found at i:5526616 original size:13 final size:14
Alignment explanation
Indices: 5526598--5526628 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
5526588 ATGTACGAAT
5526598 ATATACATATA-TA
1 ATATACATATATTA
5526611 ATATACATATATTA
1 ATATACATATATTA
5526625 ATAT
1 ATAT
5526629 TAATAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATACATATATTA
Found at i:5526728 original size:12 final size:12
Alignment explanation
Indices: 5526690--5526729 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
5526680 TGAAAATAAT
5526690 TAAT-ATATTAA
1 TAATAATATTAA
* *
5526701 TAAAAATACTAA
1 TAATAATATTAA
5526713 TAATAATATTAA
1 TAATAATATTAA
5526725 TAATA
1 TAATA
5526730 TGTAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:5528044 original size:20 final size:19
Alignment explanation
Indices: 5528016--5528053 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5528006 TTAATGGTAT
5528016 ATTAATAAAAATATAATTA
1 ATTAATAAAAATATAATTA
*
5528035 ATTAATTAAACATATAATT
1 ATTAA-TAAAAATATAATT
5528054 TTCTATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTAATAAAAATATAATTA
Found at i:5536082 original size:20 final size:20
Alignment explanation
Indices: 5536045--5536082 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5536035 AGTCTTTAAA
*
5536045 TTTTTAAATGATATAAATAT
1 TTTTTAAATAATATAAATAT
5536065 TTTTTAAATTAATA-AAAT
1 TTTTTAAA-TAATATAAAT
5536083 TATCATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTTAAATAATATAAATAT
Found at i:5538127 original size:16 final size:18
Alignment explanation
Indices: 5538106--5538138 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5538096 TGTTTTTGTC
5538106 ATTTTCT-G-ACAAAAAA
1 ATTTTCTAGTACAAAAAA
5538122 ATTTTCTAGTACAAAAA
1 ATTTTCTAGTACAAAAA
5538139 TTTACTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (18 bp):
ATTTTCTAGTACAAAAAA
Found at i:5546956 original size:24 final size:23
Alignment explanation
Indices: 5546909--5546958 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
5546899 AAATGGTAGC
*
5546909 AAAATAGTAAAAAAAATAACAAG
1 AAAATAGTAAAAAAAATAAAAAG
*
5546932 AAAATAGTAAAAAACAGTAAAAAG
1 AAAATAGTAAAAAA-AATAAAAAG
5546956 AAA
1 AAA
5546959 GCAAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.74, C:0.04, G:0.10, T:0.12
Consensus pattern (23 bp):
AAAATAGTAAAAAAAATAAAAAG
Found at i:5547945 original size:17 final size:17
Alignment explanation
Indices: 5547925--5547958 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5547915 AAATAGATTT
5547925 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
*
5547942 TTAATTAAAATTTTTAA
1 TTAATTAAAAATTTTAA
5547959 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:5560546 original size:19 final size:22
Alignment explanation
Indices: 5560522--5560566 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 22
5560512 AGTTGGTGAT
*
5560522 ATAATA-AACG-TTGTTAA-TA
1 ATAATAGAACGATTGTAAAGTA
5560541 ATAATAGAACGATTGTAAAGTA
1 ATAATAGAACGATTGTAAAGTA
5560563 ATAA
1 ATAA
5560567 GAAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 4 0.18
21 6 0.27
22 6 0.27
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.31
Consensus pattern (22 bp):
ATAATAGAACGATTGTAAAGTA
Found at i:5561691 original size:19 final size:20
Alignment explanation
Indices: 5561663--5561705 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
5561653 AAACTTACAA
5561663 ATAT-AAAAATTCA-TTATAT
1 ATATAAAAAATT-ATTTATAT
5561682 -TATAAAAAATTATTTATAT
1 ATATAAAAAATTATTTATAT
5561701 ATATA
1 ATATA
5561706 TTTTCTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.19
19 13 0.62
20 4 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATAAAAAATTATTTATAT
Found at i:5561715 original size:21 final size:21
Alignment explanation
Indices: 5561691--5561782 Score: 77
Period size: 22 Copynumber: 4.3 Consensus size: 21
5561681 TTATAAAAAA
5561691 TTAT-TTATATATATATTTTCT
1 TTATATTATAT-TATATTTTCT
*
5561712 TTATCTATATATTA-ATTTT-T
1 TTATAT-TATATTATATTTTCT
5561732 TTATATCT-TAATTATA-TTTCTT
1 TTATAT-TAT-ATTATATTTTC-T
*
5561754 TTATATTATATTATATTTTACG
1 TTATATTATATTATATTTT-CT
5561776 TTATATT
1 TTATATT
5561783 CATTCGATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 17
0.75 0.04 0.22
Matches are distributed among these distances:
19 1 0.02
20 14 0.24
21 17 0.29
22 21 0.36
23 6 0.10
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.64
Consensus pattern (21 bp):
TTATATTATATTATATTTTCT
Found at i:5561738 original size:22 final size:23
Alignment explanation
Indices: 5561696--5561772 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 23
5561686 AAAAATTATT
*
5561696 TATATA-TATATTTTCTT-TATC
1 TATATATTATATTTTTTTATATC
5561717 TATATATTA-ATTTTTTTATATC
1 TATATATTATATTTTTTTATATC
5561739 T-TA-ATTATATTTCTTTTATA--
1 TATATATTATATTT-TTTTATATC
5561759 T-TATATTATATTTT
1 TATATATTATATTTT
5561773 ACGTTATATT
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
20 8 0.16
21 28 0.56
22 14 0.28
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (23 bp):
TATATATTATATTTTTTTATATC
Found at i:5565205 original size:18 final size:18
Alignment explanation
Indices: 5565167--5565209 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
5565157 GATTAAATGA
5565167 ATTTATAATTTTATTAATT
1 ATTTATAATTTTA-TAATT
5565186 ATTTATAAATTTTA-AATT
1 ATTTAT-AATTTTATAATT
5565204 ATTTAT
1 ATTTAT
5565210 TTGATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
19 6 0.26
20 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTATAATTTTATAATT
Found at i:5567884 original size:46 final size:46
Alignment explanation
Indices: 5567831--5567998 Score: 200
Period size: 46 Copynumber: 3.6 Consensus size: 46
5567821 TATTTGGACA
5567831 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5567877 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
5567922 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5567970 TCAGAACTCGTTCAGTTGAATCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
5567999 GAGAGATGTA
Statistics
Matches: 102, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 54 0.53
47 28 0.27
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5567946 original size:47 final size:47
Alignment explanation
Indices: 5567877--5568045 Score: 186
Period size: 47 Copynumber: 3.6 Consensus size: 47
5567867 GATGCGAATG
5567877 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
* * * *
5567924 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCA
* * * *
5567970 TCAGAACTCGTTCAGTTGAATCCGAGTTCGAGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
*
5568017 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
5568046 ACTTATGGGC
Statistics
Matches: 97, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 2 0.02
46 25 0.26
47 53 0.55
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:5567988 original size:93 final size:93
Alignment explanation
Indices: 5567829--5568053 Score: 405
Period size: 93 Copynumber: 2.4 Consensus size: 93
5567819 GATATTTGGA
* * *
5567829 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCAGAACTCGTTCAGTT
* *
5567894 GAGTCCGAGTTCGTGAGATGTAACTAGG
66 GAATCCGAGTTCGAGAGATGTAACTAGG
5567922 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCAGAACTCGTTCAGTT
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCAGAACTCGTTCAGTT
5567987 GAATCCGAGTTCGAGAGATGTAACTAGG
66 GAATCCGAGTTCGAGAGATGTAACTAGG
5568015 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5568054 GCGGGTTACA
Statistics
Matches: 127, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 127 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCAGAACTCGTTCAGTT
GAATCCGAGTTCGAGAGATGTAACTAGG
Found at i:5569899 original size:27 final size:27
Alignment explanation
Indices: 5569869--5569926 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
5569859 CCTTCGAATA
5569869 GTAAAATTTTATTTAATTATTTTTAAT
1 GTAAAATTTTATTTAATTATTTTTAAT
5569896 GTAAAATTTTATTTAATTATTTTTAAT
1 GTAAAATTTTATTTAATTATTTTTAAT
5569923 GTAA
1 GTAA
5569927 TAATAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (27 bp):
GTAAAATTTTATTTAATTATTTTTAAT
Found at i:5582108 original size:18 final size:18
Alignment explanation
Indices: 5582067--5582110 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
5582057 AAAAATTATA
*
5582067 AAAAAATTAAAATAAATTT
1 AAAAAATCAAAAT-AATTT
5582086 AAAAAATCAAAAT-ATTT
1 AAAAAATCAAAATAATTT
5582103 ATAAAAAT
1 A-AAAAAT
5582111 TTCTAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAAATCAAAATAATTT
Found at i:5582741 original size:20 final size:19
Alignment explanation
Indices: 5582716--5582770 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
5582706 ATTTTTTTAA
5582716 TAAAAAATAATTTACTTTTC
1 TAAAAAATAATTTA-TTTTC
*
5582736 TAAAAATTATAATTTATTTTT
1 TAAAAA--ATAATTTATTTTC
5582757 TAAAAAAATAATTT
1 T-AAAAAATAATTT
5582771 TACTATTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 13 0.42
21 5 0.16
22 13 0.42
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAAAATAATTTATTTTC
Found at i:5582747 original size:22 final size:20
Alignment explanation
Indices: 5582717--5582770 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
5582707 TTTTTTTAAT
5582717 AAAAAATAATTTACTTTTCTA
1 AAAAAATAATTTA-TTTTCTA
* *
5582738 AAAATTATAATTTATTTTTTA
1 AAAA-AATAATTTATTTTCTA
5582759 AAAAAATAATTT
1 AAAAAATAATTT
5582771 TACTATTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.24
21 14 0.48
22 8 0.28
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAAAATAATTTATTTTCTA
Found at i:5587136 original size:20 final size:20
Alignment explanation
Indices: 5587111--5587154 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
5587101 TATACTTAAT
5587111 TTTATTCTTATAAAGTTCAA
1 TTTATTCTTATAAAGTTCAA
5587131 TTTATTCTTATAAAGTTCAA
1 TTTATTCTTATAAAGTTCAA
5587151 TTTA
1 TTTA
5587155 GACTTCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTATTCTTATAAAGTTCAA
Found at i:5587627 original size:16 final size:18
Alignment explanation
Indices: 5587592--5587627 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5587582 ATAAAATCAT
5587592 TTAAATAAGTTTTATAAC
1 TTAAATAAGTTTTATAAC
5587610 TTAAATAA-TTTT-TAAC
1 TTAAATAAGTTTTATAAC
5587626 TT
1 TT
5587628 TCTACAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (18 bp):
TTAAATAAGTTTTATAAC
Found at i:5588763 original size:18 final size:18
Alignment explanation
Indices: 5588740--5588777 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
5588730 TTATCGTCAC
5588740 CTAATCTCCTTTGAACCT
1 CTAATCTCCTTTGAACCT
5588758 CTAATCTCCTTTGAACCT
1 CTAATCTCCTTTGAACCT
5588776 CT
1 CT
5588778 GCAACACTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.34, G:0.05, T:0.39
Consensus pattern (18 bp):
CTAATCTCCTTTGAACCT
Found at i:5590127 original size:15 final size:14
Alignment explanation
Indices: 5590104--5590133 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5590094 CTTACCTATA
5590104 TTTTTACTTGAAAT
1 TTTTTACTTGAAAT
5590118 TTTTTCACTTGAAAT
1 TTTTT-ACTTGAAAT
5590133 T
1 T
5590134 AATCATTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTTTACTTGAAAT
Found at i:5597794 original size:13 final size:13
Alignment explanation
Indices: 5597757--5597799 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 13
5597747 TAATTTTTTT
5597757 TTTTAATTTTTAAAA
1 TTTT-ATTTTT-AAA
5597772 TGTCTTATTTTTAAA
1 T-T-TTATTTTTAAA
5597787 TTTTATTTTTAAA
1 TTTTATTTTTAAA
5597800 AATTAAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.42
14 1 0.04
15 5 0.19
16 7 0.27
17 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (13 bp):
TTTTATTTTTAAA
Found at i:5603265 original size:17 final size:17
Alignment explanation
Indices: 5603237--5603272 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
5603227 GTAGTTGAAC
5603237 TTATTTTTATAA-TTAT
1 TTATTTTTATAATTTAT
5603253 TTATTTTTAATAATTTAT
1 TTATTTTT-ATAATTTAT
5603271 TT
1 TT
5603273 GCTTTGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTTTTATAATTTAT
Found at i:5604326 original size:18 final size:18
Alignment explanation
Indices: 5604272--5604345 Score: 53
Period size: 19 Copynumber: 3.9 Consensus size: 18
5604262 TTTTTTCTTT
* *
5604272 ATAATTTTCTAGTATTTT-
1 ATAATTTTTTAAT-TTTTA
*
5604290 ATATATTTTTCTAAATTTTA
1 ATA-ATTTTT-TAATTTTTA
5604310 ATAATTTTTTAATTTTTA
1 ATAATTTTTTAATTTTTA
*
5604328 TGTTAA-TTTTTAATTTTT
1 --ATAATTTTTTAATTTTT
5604346 TTAATTTTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 11 0.24
19 27 0.59
20 8 0.17
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
ATAATTTTTTAATTTTTA
Found at i:5604326 original size:28 final size:28
Alignment explanation
Indices: 5604286--5604353 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
5604276 TTTTCTAGTA
5604286 TTTTATATATTTT-TCTAAA-TTTTAATAATT
1 TTTTA-AT-TTTTATCTAAATTTTTAAT--TT
* *
5604316 TTTTAATTTTTATGTTAATTTTTAATTT
1 TTTTAATTTTTATCTAAATTTTTAATTT
5604344 TTTTAATTTT
1 TTTTAATTTT
5604354 CAGAATCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 16 0.47
29 6 0.18
30 12 0.35
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (28 bp):
TTTTAATTTTTATCTAAATTTTTAATTT
Found at i:5607963 original size:3 final size:3
Alignment explanation
Indices: 5607955--5607995 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5607945 CAAATTTTAT
5607955 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5607996 GAAACTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5609739 original size:20 final size:21
Alignment explanation
Indices: 5609701--5609742 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5609691 AGTTGATATT
*
5609701 AATTTTCATAAAAATATAAAA
1 AATTTTAATAAAAATATAAAA
5609722 AATTTTAATAAAAA-ATAAAA
1 AATTTTAATAAAAATATAAAA
5609742 A
1 A
5609743 TTTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTTTAATAAAAATATAAAA
Found at i:5611615 original size:7 final size:7
Alignment explanation
Indices: 5611603--5611628 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5611593 TCATAAGTTT
5611603 TAAAATA
1 TAAAATA
5611610 TAAAATA
1 TAAAATA
5611617 TAAAATA
1 TAAAATA
5611624 TAAAA
1 TAAAA
5611629 ACTTTAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAATA
Found at i:5617491 original size:2 final size:2
Alignment explanation
Indices: 5617478--5617514 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5617468 TATTTACATA
*
5617478 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5617515 AAACAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5617663 original size:33 final size:33
Alignment explanation
Indices: 5617623--5617686 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
5617613 ATATATACGT
* *
5617623 AATATAGTA-CTAAGAATATATATATACATATAC
1 AATATAGTATCTAAAAATATATACATA-ATATAC
*
5617656 AATATAGTATTTAAAAATATATACATAATAT
1 AATATAGTATCTAAAAATATATACATAATAT
5617687 TTACATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 13 0.48
34 14 0.52
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (33 bp):
AATATAGTATCTAAAAATATATACATAATATAC
Found at i:5617689 original size:21 final size:23
Alignment explanation
Indices: 5617663--5617717 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
5617653 TACAATATAG
*
5617663 TATTTAAAAATATAT-ACAT-AA
1 TATTTAAAAATATATAAAATAAA
* *
5617684 TATTTACATATATATAAAATAAA
1 TATTTAAAAATATATAAAATAAA
*
5617707 TATTGAAAAAT
1 TATTTAAAAAT
5617718 GTATGCACAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 13 0.50
22 3 0.12
23 10 0.38
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (23 bp):
TATTTAAAAATATATAAAATAAA
Found at i:5617697 original size:36 final size:34
Alignment explanation
Indices: 5617597--5617697 Score: 89
Period size: 36 Copynumber: 2.9 Consensus size: 34
5617587 GGGGTAAAAA
* * *
5617597 TAAATATATACACATAATATATACGTAATATAGTAC
1 TAAAAATATATACATAATAT-TACAT-ATATAGTAC
* * *
5617633 TAAGAATATATATATACATA-TACA-ATATAGTATT
1 TAAAAATATATACATA-ATATTACATATATAGTA-C
5617667 TAAAAATATATACATAATATTTACATATATA
1 TAAAAATATATACATAATA-TTACATATATA
5617698 TAAAATAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
33 11 0.21
34 14 0.27
35 7 0.13
36 17 0.33
37 3 0.06
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (34 bp):
TAAAAATATATACATAATATTACATATATAGTAC
Found at i:5618204 original size:25 final size:26
Alignment explanation
Indices: 5618170--5618278 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
5618160 TGATACAAAT
5618170 TGATAATAGGTTA-GTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
5618195 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5618221 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5618247 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
5618273 TGATAA
1 TGATAA
5618279 GAATTTCATG
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
25 13 0.16
26 64 0.81
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:5619755 original size:27 final size:26
Alignment explanation
Indices: 5619714--5619787 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
5619704 AAAAGTAGCT
* * *
5619714 AAATTACTATAATACCCCTATGTATGA
1 AAATTACTGTTATACCCCTAGGTAT-A
*
5619741 AAATTACTGTTATACCCCTAGGTGTA
1 AAATTACTGTTATACCCCTAGGTATA
*
5619767 AAATTACCGTTATA-CCCTAGG
1 AAATTACTGTTATACCCCTAGG
5619788 GTTAATTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 7 0.17
26 14 0.33
27 21 0.50
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGGTATA
Found at i:5619778 original size:26 final size:27
Alignment explanation
Indices: 5619725--5619787 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
5619715 AATTACTATA
* *
5619725 ATACCCCTATGTATGAAAATTACTGTT
1 ATACCCCTAGGTATGAAAATTACCGTT
*
5619752 ATACCCCTAGGTGT-AAAATTACCGTT
1 ATACCCCTAGGTATGAAAATTACCGTT
5619778 ATA-CCCTAGG
1 ATACCCCTAGG
5619788 GTTAATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 7 0.21
26 14 0.42
27 12 0.36
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (27 bp):
ATACCCCTAGGTATGAAAATTACCGTT
Found at i:5619953 original size:26 final size:26
Alignment explanation
Indices: 5619888--5620002 Score: 142
Period size: 27 Copynumber: 4.3 Consensus size: 26
5619878 TGGAGGAAGC
* *
5619888 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
5619915 GATCTGGTGGCTCTGCCACATATAT-T
1 GTTCTGGTGGCTCTGCCACAT-TATCT
5619941 GTTCTGGTGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* *
5619968 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
5619995 GTTCTGGT
1 GTTCTGGT
5620003 AGCCATGCTG
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
26 29 0.37
27 34 0.44
28 15 0.19
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:5619998 original size:54 final size:53
Alignment explanation
Indices: 5619888--5620002 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 53
5619878 TGGAGGAAGC
*
5619888 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATT
* * * *
5619941 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATAT-T
5619995 GTTCTGGT
1 GTTCTGGT
5620003 AGCCATGCTG
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
53 28 0.51
54 27 0.49
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (53 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATT
Found at i:5620085 original size:19 final size:22
Alignment explanation
Indices: 5620061--5620100 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
5620051 CTCCCCACAT
5620061 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
5620080 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
5620101 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:5624939 original size:26 final size:26
Alignment explanation
Indices: 5624877--5624985 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5624867 TGATACAAAT
5624877 TGATAATAGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5624902 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5624928 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5624954 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
5624980 TGATAA
1 TGATAA
5624986 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
25 21 0.26
26 59 0.74
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:5626467 original size:28 final size:26
Alignment explanation
Indices: 5626425--5626499 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
5626415 AAAAGTAGCT
* * *
5626425 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGCA
*
5626453 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGCA
*
5626479 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
5626500 GGTTAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.55
27 1 0.02
28 18 0.43
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.31
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGCA
Found at i:5626644 original size:27 final size:27
Alignment explanation
Indices: 5626603--5626715 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
5626593 GAGGAAGCGT
*
5626603 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5626630 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5626657 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
5626685 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
5626711 TCTGG
1 TCTGG
5626716 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:5626708 original size:54 final size:54
Alignment explanation
Indices: 5626601--5626715 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
5626591 TGGAGGAAGC
*
5626601 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
5626655 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
5626709 GTTCTGG
1 GTTCTGG
5626716 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:5626801 original size:19 final size:22
Alignment explanation
Indices: 5626777--5626816 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
5626767 CTCCCCACAC
5626777 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
5626796 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
5626817 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:5628138 original size:3 final size:3
Alignment explanation
Indices: 5628132--5628178 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
5628122 TTATACAAAT
* **
5628132 ATA ATA ATA ATTA ATA ATA ATA ATA ACA ATA ATA GCA ATA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5628178 A
1 A
5628179 AGATACAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:5632929 original size:27 final size:27
Alignment explanation
Indices: 5632899--5632963 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
5632889 TATATATAAC
5632899 TAACAGATT-AAATATTGCTTAACACAA
1 TAACA-ATTCAAATATTGCTTAACACAA
* *
5632926 TAACATTTCAAATATTGTTTAACACAA
1 TAACAATTCAAATATTGCTTAACACAA
5632953 TTAA-AATTCAA
1 -TAACAATTCAA
5632964 TTAAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 2 0.06
27 28 0.85
28 3 0.09
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (27 bp):
TAACAATTCAAATATTGCTTAACACAA
Found at i:5633756 original size:2 final size:2
Alignment explanation
Indices: 5633749--5633777 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5633739 AATATGCTTC
5633749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5633778 AATACTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5637509 original size:32 final size:32
Alignment explanation
Indices: 5637473--5637538 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
5637463 AATACTCTAC
*
5637473 AAGCTTGCCAAAAACTTAGTGCATTTTACATT
1 AAGCTTGCCAAAAACTTAGTACATTTTACATT
*
5637505 AAGCTTGTCAAAAACTTAGTACATTTTACATT
1 AAGCTTGCCAAAAACTTAGTACATTTTACATT
5637537 AA
1 AA
5637539 TTTTCTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (32 bp):
AAGCTTGCCAAAAACTTAGTACATTTTACATT
Found at i:5641945 original size:32 final size:32
Alignment explanation
Indices: 5641907--5641973 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
5641897 ACAAACATAC
* *
5641907 AAAGTAATAATTAAATAATGTATGATATACAA
1 AAAGTAATAATTAAATAATGCATGACATACAA
5641939 AAAGTAATAATTAAATAATGCATGACATACAA
1 AAAGTAATAATTAAATAATGCATGACATACAA
5641971 AAA
1 AAA
5641974 AGAGTAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (32 bp):
AAAGTAATAATTAAATAATGCATGACATACAA
Found at i:5642189 original size:22 final size:23
Alignment explanation
Indices: 5642164--5642219 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
5642154 TTTGCTATAC
* *
5642164 AATATATAAAACATAATAACAA-
1 AATATATAAAAAAGAATAACAAT
* *
5642186 AATATTTAAAAAAGAATAATAAT
1 AATATATAAAAAAGAATAACAAT
*
5642209 TATATATAAAA
1 AATATATAAAA
5642220 TATATTGGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (23 bp):
AATATATAAAAAAGAATAACAAT
Found at i:5642547 original size:18 final size:19
Alignment explanation
Indices: 5642494--5642548 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 19
5642484 AATAAATGTT
*
5642494 ATATAATAAGATATAATTTAA
1 ATATAAT-AGATATAA-TGAA
*
5642515 ATAT-ATAGGAAATAA-GAA
1 ATATAATA-GATATAATGAA
5642533 ATATAATAGATATAAT
1 ATATAATAGATATAAT
5642549 ATAAAACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
18 12 0.43
19 4 0.14
20 8 0.29
21 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (19 bp):
ATATAATAGATATAATGAA
Found at i:5642631 original size:3 final size:3
Alignment explanation
Indices: 5642623--5642708 Score: 58
Period size: 3 Copynumber: 28.7 Consensus size: 3
5642613 CAAGTAAATT
* *
5642623 ATA ATA ATA AT- ATA A-A GATA ATA ATA ATA ATA ATTT GTGA A-A A-A
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA A-TA AT-A ATA ATA
5642667 ATA ATA TATA ATAA ATA ATA ATA AT- ATA TATA ATA A-A ATA AT
1 ATA ATA -ATA AT-A ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT
5642709 CTTATAATGT
Statistics
Matches: 68, Mismatches: 4, Indels: 22
0.72 0.04 0.23
Matches are distributed among these distances:
2 11 0.16
3 46 0.68
4 11 0.16
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5642688 original size:17 final size:17
Alignment explanation
Indices: 5642579--5642702 Score: 57
Period size: 15 Copynumber: 7.3 Consensus size: 17
5642569 ATGTAAGAAC
*
5642579 AATATATATATAAATAATT
1 AATA-ATATAT-AATAAAT
*
5642598 AATAAATATATAATGCAAGT
1 AAT-AATATATAAT--AAAT
*
5642618 AA-ATTATAATAATAATAT
1 AATAATAT-ATAATAA-AT
5642636 AA-AGATA-ATAAT-AAT
1 AATA-ATATATAATAAAT
* * *
5642651 AATAATTTGTGA-AAA-
1 AATAATATATAATAAAT
5642666 AATAATATATAATAAAT
1 AATAATATATAATAAAT
*
5642683 AATAATA-AT-ATATAT
1 AATAATATATAATAAAT
5642698 AATAA
1 AATAA
5642703 AATAATCTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
15 25 0.30
16 11 0.13
17 14 0.17
18 11 0.13
19 16 0.19
20 6 0.07
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (17 bp):
AATAATATATAATAAAT
Found at i:5642691 original size:20 final size:20
Alignment explanation
Indices: 5642623--5642708 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
5642613 CAAGTAAATT
*
5642623 ATAATAATAATATA-AAGATA
1 ATAATAATAATATATAATA-A
** *
5642643 ATAATAATAATA-ATTTGTGA
1 ATAATAATAATATA-TAATAA
5642663 A-AA-AATAATATATAATAA
1 ATAATAATAATATATAATAA
5642681 ATAATAATAATATAT-AT-A
1 ATAATAATAATATATAATAA
5642699 ATAA-AATAAT
1 ATAATAATAAT
5642709 CTTATAATGT
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
17 6 0.11
18 16 0.30
19 8 0.15
20 24 0.44
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
ATAATAATAATATATAATAA
Found at i:5642706 original size:17 final size:18
Alignment explanation
Indices: 5642582--5642708 Score: 81
Period size: 17 Copynumber: 7.1 Consensus size: 18
5642572 TAAGAACAAT
5642582 ATATATATAAATAATTAATA
1 ATATATAT-AATAA-TAATA
* *
5642602 A-ATATATAATGCA-AGTA
1 ATATATATAAT-AATAATA
5642619 A-AT-TATAATAATAAT-
1 ATATATATAATAATAATA
* *
5642634 ATAAAGATAATAATAATA
1 ATATATATAATAATAATA
* *
5642652 ATAATTTGTGAA-AA-AATA
1 AT-ATATAT-AATAATAATA
5642670 ATATATAATAAATAATAATA
1 ATATAT-AT-AATAATAATA
5642690 ATATATATAATAA-AATA
1 ATATATATAATAATAATA
5642707 AT
1 AT
5642709 CTTATAATGT
Statistics
Matches: 84, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
15 2 0.02
16 9 0.11
17 26 0.31
18 19 0.23
19 15 0.18
20 13 0.15
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.35
Consensus pattern (18 bp):
ATATATATAATAATAATA
Found at i:5642714 original size:20 final size:22
Alignment explanation
Indices: 5642579--5642702 Score: 54
Period size: 23 Copynumber: 5.1 Consensus size: 22
5642569 ATGTAAGAAC
5642579 AATATATAT-ATAAATAATTAAT
1 AATATATATAATAAATAA-TAAT
*
5642601 AAATATATAATGCAAGTAAATTATAAT
1 -AATATAT-AT--AA-TAAATAATAAT
*
5642628 AATA-ATATAAAGATAATAATAAT
1 AATATATAT-AATA-AATAATAAT
* * *
5642651 AATAATTTGTGAAAAAATAATATAT
1 AAT-ATATAT-AATAAATAATA-AT
*
5642676 AATAAATAATAATAATATATATAAT
1 AATATAT-ATAATAA-ATA-ATAAT
5642701 AA
1 AA
5642703 AATAATCTTA
Statistics
Matches: 77, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
22 1 0.01
23 20 0.26
24 18 0.23
25 20 0.26
26 7 0.09
27 5 0.06
28 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (22 bp):
AATATATATAATAAATAATAAT
Found at i:5642716 original size:38 final size:34
Alignment explanation
Indices: 5642640--5642708 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 34
5642630 TAATATAAAG
*
5642640 ATAATAATAATAATAATTTGTGAAAAAATAATAT
1 ATAATAATAATAATAATTTATGAAAAAATAATAT
5642674 ATAATAAATAATAATAATATATAT-AATAAAATAAT
1 ATAAT-AATAATAATAAT-T-TATGAA-AAAATAAT
5642709 CTTATAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 5 0.17
35 12 0.40
36 3 0.10
37 10 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (34 bp):
ATAATAATAATAATAATTTATGAAAAAATAATAT
Found at i:5642798 original size:20 final size:22
Alignment explanation
Indices: 5642757--5642798 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
5642747 AACAAATAAA
*
5642757 AATATATAAAATATATATATAG
1 AATATATAAAATATAAATATAG
5642779 AATA-ATAAAA-ATAAATATAG
1 AATATATAAAATATAAATATAG
5642799 GGCTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 6 0.32
22 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
AATATATAAAATATAAATATAG
Found at i:5656821 original size:18 final size:18
Alignment explanation
Indices: 5656798--5656871 Score: 105
Period size: 18 Copynumber: 4.2 Consensus size: 18
5656788 CCCAACTATT
*
5656798 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
5656816 GTATACGTGAATAGT-TC
1 GTATACGTGAATAGTACC
* *
5656833 GTATATGTGAATAGTACT
1 GTATACGTGAATAGTACC
5656851 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
5656869 GTA
1 GTA
5656872 AACGATCGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
17 15 0.31
18 33 0.69
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:5656849 original size:35 final size:35
Alignment explanation
Indices: 5656798--5656865 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
5656788 CCCAACTATT
5656798 GTATACGTGAACAGTACCGTATACGTGAATAGTTC
1 GTATACGTGAACAGTACCGTATACGTGAATAGTTC
* * *
5656833 GTATATGTGAATAGTACTGTATACGTGAATAGT
1 GTATACGTGAACAGTACCGTATACGTGAATAGT
5656866 ACCGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (35 bp):
GTATACGTGAACAGTACCGTATACGTGAATAGTTC
Found at i:5659080 original size:16 final size:15
Alignment explanation
Indices: 5659037--5659082 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
5659027 AGGCCCATTC
5659037 ATATTATTTTATTTTA
1 ATATT-TTTTATTTTA
*
5659053 ATATTTAATTATTTTA
1 ATATTT-TTTATTTTA
5659069 TATATTTTTTATTT
1 -ATATTTTTTATTT
5659083 ATTGAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 19 0.73
17 6 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATATTTTTTATTTTA
Found at i:5662035 original size:2 final size:2
Alignment explanation
Indices: 5662028--5662092 Score: 89
Period size: 2 Copynumber: 33.5 Consensus size: 2
5662018 TAATATCATC
5662028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
5662069 TA TA CA TG TA TA T- TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5662093 TCCTTTTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5673285 original size:4 final size:4
Alignment explanation
Indices: 5673276--5673311 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
5673266 TACTTCGCCT
* *
5673276 AAAG AAAG AAAG AAAG AAAG AAAA AAAA AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
5673312 GCCAGGGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:5676808 original size:2 final size:2
Alignment explanation
Indices: 5676801--5676850 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
5676791 TTAATATCTC
* *
5676801 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AC AT GT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5676841 AT GT AT AT AT
1 AT AT AT AT AT
5676851 TCCTTTTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5676816 original size:19 final size:17
Alignment explanation
Indices: 5676804--5676850 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
5676794 ATATCTCATA
5676804 TATATATATATATATAT
1 TATATATATATATATAT
*
5676821 TATATATATACATGTATAT
1 TATATATAT--ATATATAT
*
5676840 TATGTATATAT
1 TATATATATAT
5676851 TCCTTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
19 15 0.58
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:5679089 original size:17 final size:18
Alignment explanation
Indices: 5679067--5679101 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5679057 TTATATATTC
*
5679067 TTATAATTAAAT-TTTTG
1 TTATAAATAAATATTTTG
5679084 TTATAAATAAATATTTTG
1 TTATAAATAAATATTTTG
5679102 GGTACAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
TTATAAATAAATATTTTG
Found at i:5680349 original size:22 final size:22
Alignment explanation
Indices: 5680305--5680356 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
5680295 AATAATAAAA
5680305 ATAAAT-TTAATTATAAAATAT
1 ATAAATATTAATTATAAAATAT
5680326 ATAAATATTAA-TATAAAATAAT
1 ATAAATATTAATTATAAAAT-AT
*
5680348 ATTAATATT
1 ATAAATATT
5680357 TTGTTATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAATATTAATTATAAAATAT
Found at i:5686165 original size:29 final size:30
Alignment explanation
Indices: 5686107--5686171 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
5686097 ATTTTCTTCC
**
5686107 CTTTTTCAATTTTTAAAGTAGTTTTCTATA
1 CTTTTTCAATTTTTAAAGTAGCCTTCTATA
5686137 -TTTTTC-ATTTGTTAAAGTTAGCCTT-TATA
1 CTTTTTCAATTT-TTAAAG-TAGCCTTCTATA
5686166 CTTTTT
1 CTTTTT
5686172 TTTAAACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
28 4 0.13
29 16 0.53
30 10 0.33
ACGTcount: A:0.23, C:0.11, G:0.08, T:0.58
Consensus pattern (30 bp):
CTTTTTCAATTTTTAAAGTAGCCTTCTATA
Found at i:5686341 original size:22 final size:21
Alignment explanation
Indices: 5686315--5686363 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
5686305 AAGGAAATTT
5686315 AAAATAACATAAAA-GAAAATA
1 AAAATAACATAAAATGAAAA-A
* *
5686336 ATAAATTACTTAAAATGAAAAA
1 A-AAATAACATAAAATGAAAAA
5686358 AAAATA
1 AAAATA
5686364 TAAAGACCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 5 0.22
22 13 0.57
23 5 0.22
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAATAACATAAAATGAAAAA
Found at i:5693215 original size:37 final size:37
Alignment explanation
Indices: 5693165--5693242 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
5693155 CAACGAAGTG
5693165 TTAAAAGAAAGAGAAAATGGACTATAACACCTAAATT
1 TTAAAAGAAAGAGAAAATGGACTATAACACCTAAATT
5693202 TTAAAAGAAAGAGAAAATGGACTATAACACCTAAATT
1 TTAAAAGAAAGAGAAAATGGACTATAACACCTAAATT
5693239 TTAA
1 TTAA
5693243 CTTACTCGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (37 bp):
TTAAAAGAAAGAGAAAATGGACTATAACACCTAAATT
Found at i:5704211 original size:14 final size:15
Alignment explanation
Indices: 5704184--5704212 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5704174 AATTTTATGA
5704184 ATTTCATGATGTGTT
1 ATTTCATGATGTGTT
5704199 ATTTCAT-ATGTGTT
1 ATTTCATGATGTGTT
5704213 GATGATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (15 bp):
ATTTCATGATGTGTT
Found at i:5704405 original size:50 final size:51
Alignment explanation
Indices: 5704328--5704456 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
5704318 GACCATGGCA
5704328 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
5704379 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
5704429 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
5704457 CTGATCAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:5704470 original size:31 final size:31
Alignment explanation
Indices: 5704432--5704609 Score: 268
Period size: 31 Copynumber: 5.8 Consensus size: 31
5704422 ACAAATGACA
*
5704432 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
5704463 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
5704494 AGTGAAAAGTGGTAGTTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
5704525 AGTGAAAAGTGGTAGCTCCAGCAACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
5704556 TGTGAAAA-TGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
5704586 AGTGAATAGTGGTAGCTTCGGCTA
1 AGTGAAAAGTGGTAGCTTCGGCTA
5704610 TAAGTGACAA
Statistics
Matches: 133, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
30 26 0.20
31 107 0.80
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:5704599 original size:92 final size:93
Alignment explanation
Indices: 5704432--5704609 Score: 286
Period size: 92 Copynumber: 1.9 Consensus size: 93
5704422 ACAAATGACA
* * * *
5704432 AGTGAAAAGTGGTAGCTTCAGCTACCTGATCAGTGAAAAGTGGTAGCTTCTGCTACCTGATCAGT
1 AGTGAAAAGTGGTAGCTCCAGCAACCTGATCAGTGAAAAGTGGTAGCTCCGGCTACCTGATCAGT
*
5704497 GAAAAGTGGTAGTTTCGGCTACCTGATC
66 GAAAAGTGGTAGCTTCGGCTACCTGATC
*
5704525 AGTGAAAAGTGGTAGCTCCAGCAACCTGATCTGTGAAAA-TGGTAGCTCCGGCTACCTGATCAGT
1 AGTGAAAAGTGGTAGCTCCAGCAACCTGATCAGTGAAAAGTGGTAGCTCCGGCTACCTGATCAGT
*
5704589 GAATAGTGGTAGCTTCGGCTA
66 GAAAAGTGGTAGCTTCGGCTA
5704610 TAAGTGACAA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 42 0.54
93 36 0.46
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (93 bp):
AGTGAAAAGTGGTAGCTCCAGCAACCTGATCAGTGAAAAGTGGTAGCTCCGGCTACCTGATCAGT
GAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:5704753 original size:46 final size:49
Alignment explanation
Indices: 5704639--5704799 Score: 163
Period size: 47 Copynumber: 3.4 Consensus size: 49
5704629 GATTTCCGTA
* * * * * * *
5704639 TAAGACCATATCTGGGATATGGCATCGGTGT-A-ATATATG-CTACTATA
1 TAAGACCATAGCTGGGCTATGGCATCGATATGAGATATATGATTAC-GTG
* * * *
5704686 TAAGACCATATCTGGGATATGGCATC-A-GTGAGATATGTGATT-CGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGAGATATATGATTACGTG
*
5704732 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATATGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGAGATATATGATTACGTG
5704781 TAAGACCATAGCTGGGCTA
1 TAAGACCATAGCTGGGCTA
5704800 CGACGTCGAT
Statistics
Matches: 98, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
45 2 0.02
46 26 0.27
47 34 0.35
48 13 0.13
49 23 0.23
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (49 bp):
TAAGACCATAGCTGGGCTATGGCATCGATATGAGATATATGATTACGTG
Found at i:5704809 original size:49 final size:48
Alignment explanation
Indices: 5704717--5704811 Score: 145
Period size: 49 Copynumber: 2.0 Consensus size: 48
5704707 GCATCAGTGA
* * *
5704717 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATGT
1 GATATATGATTCGTGTAAGACCATAGCTGGGCTACGACATCGATATGT
*
5704765 GATATATGATTACGTGTAAGACCATAGCTGGGCTACGACGTCGATAT
1 GATATATGATT-CGTGTAAGACCATAGCTGGGCTACGACATCGATAT
5704812 ATGAAGATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 10 0.24
49 32 0.76
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (48 bp):
GATATATGATTCGTGTAAGACCATAGCTGGGCTACGACATCGATATGT
Found at i:5706428 original size:21 final size:22
Alignment explanation
Indices: 5706404--5706452 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
5706394 GTAATACATG
5706404 TATTAGATATTA-AAAA-ATATT
1 TATTA-ATATTATAAAAGATATT
*
5706425 TATT-ATTTTATAAAAGATATT
1 TATTAATATTATAAAAGATATT
5706446 TATTAAT
1 TATTAAT
5706453 TAAATAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 4 0.17
21 13 0.54
22 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (22 bp):
TATTAATATTATAAAAGATATT
Found at i:5706456 original size:18 final size:19
Alignment explanation
Indices: 5706410--5706469 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 19
5706400 CATGTATTAG
5706410 ATATTAAAAAATATTTATT
1 ATATTAAAAAATATTTATT
*
5706429 ATTTTATAAAAGATATTTATT
1 ATATTA-AAAA-ATATTTATT
* *
5706450 A-ATTAAATAAT-TATATT
1 ATATTAAAAAATATTTATT
5706467 ATA
1 ATA
5706470 AGATTTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
17 6 0.18
18 3 0.09
19 8 0.24
20 7 0.21
21 10 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATATTAAAAAATATTTATT
Found at i:5708721 original size:46 final size:46
Alignment explanation
Indices: 5708660--5708890 Score: 327
Period size: 46 Copynumber: 5.0 Consensus size: 46
5708650 AGTGTGCTCT
* *
5708660 CTGAAATGAAGTGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
5708706 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
5708752 CTGATATAAAATGTGTAAAACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
5708798 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** ** *
5708844 ATGATGGGAAAATGAATAAAACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
5708891 ATGACAGAAA
Statistics
Matches: 169, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 132 0.78
47 37 0.22
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:5708914 original size:93 final size:92
Alignment explanation
Indices: 5708679--5708940 Score: 346
Period size: 93 Copynumber: 2.8 Consensus size: 92
5708669 AGTGTGTAAG
* * *
5708679 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
1 ACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATGGTTGAAAGATACC
* * **
5708744 ATGGCAACCTGATATAAAATGTGTAAA
66 ATGGCAACATGATAGAAAATGAATAAA
* *
5708771 ACCATGGTTGAAAGATACCATGGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAGATACC
1 ACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATGGTTGAAAGATACC
*
5708836 ATGGCAACATGATGGGAAAATGAATAAA
66 ATGGCAACATGAT-AGAAAATGAATAAA
* * * * *
5708864 ACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAACGAGCAAAACCATAGTTGAAAGATAT
1 ACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAGTAAGACCATGGTTGAAAGATAC
* *
5708928 TATGGCATCATGA
65 CATGGCAACATGA
5708941 CGAAGATAAA
Statistics
Matches: 150, Mismatches: 18, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
92 74 0.49
93 76 0.51
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (92 bp):
ACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATGGTTGAAAGATACC
ATGGCAACATGATAGAAAATGAATAAA
Found at i:5708920 original size:46 final size:46
Alignment explanation
Indices: 5708674--5708941 Score: 306
Period size: 46 Copynumber: 5.8 Consensus size: 46
5708664 AATGAAGTGT
* * * *
5708674 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAATGT
1 GTAAAACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGA
* * * * *
5708720 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGT
1 GTAAAACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGA
*
5708766 GTAAAACCATGGTTGAAAGATACCATGGCAACGTGACATG-AAATGA
1 GTAAAACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGA
* * **
5708812 ATAAGACCATGGTTGAAAGATACCATGGCAACATGATGGGAAAATGA
1 GTAAAACCATGGTTGAAAGATACCATGGCAACATGA-CAGAAAATGA
* *
5708859 ATAAAACCATGGTTGAAAGATACCATGGCAACATGACAGAAAACGA
1 GTAAAACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGA
* * ** *
5708905 GCAAAACCATAGTTGAAAGATATTATGGCATCATGAC
1 GTAAAACCATGGTTGAAAGATACCATGGCAACATGAC
5708942 GAAGATAAAT
Statistics
Matches: 197, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
46 156 0.79
47 41 0.21
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.21
Consensus pattern (46 bp):
GTAAAACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGA
Found at i:5711406 original size:53 final size:52
Alignment explanation
Indices: 5711327--5711429 Score: 154
Period size: 53 Copynumber: 2.0 Consensus size: 52
5711317 GAAGGAAAAG
*
5711327 ATGTGATATGTACTTCCGTATAAGACCATAGCTGGGTTATGGCATCGGTACA
1 ATGTGATATGTACTTCCGTATAAGACCATAGCTGGGATATGGCATCGGTACA
* *
5711379 ATGTGATAATGTGA-TTTCGTATAAGACCATATCTGGGATATGGCATCGGTA
1 ATGTGAT-ATGT-ACTTCCGTATAAGACCATAGCTGGGATATGGCATCGGTA
5711430 TGATATGTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 7 0.15
53 38 0.83
54 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (52 bp):
ATGTGATATGTACTTCCGTATAAGACCATAGCTGGGATATGGCATCGGTACA
Found at i:5711468 original size:46 final size:50
Alignment explanation
Indices: 5711340--5711454 Score: 148
Period size: 53 Copynumber: 2.3 Consensus size: 50
5711330 TGATATGTAC
*
5711340 TTCCGTATAAGACCATAGCTGGGTTATGGCATCGGTACAATGTGATAATGTGA
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGGT--AA-GTGATAATGTGA
* *
5711393 TTTCGTATAAGACCATATCTGGGATATGGCATCGGT-A-TGAT-ATGTGA
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGGTAAGTGATAATGTGA
5711440 -TCCGTATAAGACCAT
1 TTCCGTATAAGACCAT
5711455 GACAGGGCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
46 14 0.24
47 6 0.10
48 4 0.07
50 1 0.02
53 33 0.57
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (50 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCATCGGTAAGTGATAATGTGA
Found at i:5711484 original size:46 final size:47
Alignment explanation
Indices: 5711330--5711474 Score: 134
Period size: 53 Copynumber: 3.0 Consensus size: 47
5711320 GGAAAAGATG
* * *
5711330 TGATATGT-ACTTCCGTATAAGACCATAGCTGGGTTATGGCATCGGTACAA
1 TGATATGTGA-TTCCGTATAAGACCATATCAGGGATATGGCATCGGT---A
* *
5711380 TGTGATAATGTGATTTCGTATAAGACCATATCTGGGATATGGCATCGGTA
1 --TGAT-ATGTGATTCCGTATAAGACCATATCAGGGATATGGCATCGGTA
* *
5711430 TGATATGTGA-TCCGTATAAGACCATGA-CAGGGCTATGGCTTCGGT
1 TGATATGTGATTCCGTATAAGACCAT-ATCAGGGATATGGCATCGGT
5711475 GTGTGATGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
46 29 0.35
47 7 0.08
48 4 0.05
50 1 0.01
52 4 0.05
53 37 0.45
54 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (47 bp):
TGATATGTGATTCCGTATAAGACCATATCAGGGATATGGCATCGGTA
Found at i:5712477 original size:31 final size:32
Alignment explanation
Indices: 5712433--5712497 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
5712423 ATATAAAGTG
* *
5712433 AACATATACAATATATATTAGA-AATACTA-AT
1 AACATAAAAAATATATATTA-ATAATACTACAT
5712464 AACATAAAAAATATATATTAATAATACTACAT
1 AACATAAAAAATATATATTAATAATACTACAT
5712496 AA
1 AA
5712498 ATATGTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 1 0.03
31 25 0.83
32 4 0.13
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (32 bp):
AACATAAAAAATATATATTAATAATACTACAT
Found at i:5712551 original size:22 final size:22
Alignment explanation
Indices: 5712503--5712544 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5712493 CATAAATATG
5712503 TACAT-AT-ATATTAAAATAAA
1 TACATAATAATATTAAAATAAA
5712523 TACATAATAATATTAAAATAAA
1 TACATAATAATATTAAAATAAA
5712545 ATAATAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
TACATAATAATATTAAAATAAA
Found at i:5712635 original size:19 final size:18
Alignment explanation
Indices: 5712597--5712634 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5712587 TATAACGATG
5712597 TATGAAAATAATACTATA
1 TATGAAAATAATACTATA
5712615 TATGAAAAGT-ATA-TATA
1 TATGAAAA-TAATACTATA
5712632 TAT
1 TAT
5712635 ACCCATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 11 0.58
19 1 0.05
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.37
Consensus pattern (18 bp):
TATGAAAATAATACTATA
Found at i:5712737 original size:31 final size:31
Alignment explanation
Indices: 5712694--5712753 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
5712684 GATAAAATAG
* *
5712694 ATATAATAATATATACATAATATGGTATTAA
1 ATATAATAATATATACATAACATAGTATTAA
*
5712725 ATAT-ATATATATATATATAACATAGTATT
1 ATATAATA-ATATATACATAACATAGTATT
5712754 CAAGAATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (31 bp):
ATATAATAATATATACATAACATAGTATTAA
Found at i:5712856 original size:11 final size:9
Alignment explanation
Indices: 5712830--5712889 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
5712820 TAACATTAAA
5712830 AAAATATAT
1 AAAATATAT
5712839 AAAATATAT
1 AAAATATAT
*
5712848 ACAATATAT
1 AAAATATAT
* *
5712857 ACATATATTT
1 A-AAATATAT
5712867 AGAAATGATA-
1 A-AAAT-ATAT
*
5712877 ATAATATAT
1 AAAATATAT
5712886 AAAA
1 AAAA
5712890 AAAACTATTC
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
8 3 0.08
9 24 0.62
10 10 0.26
11 2 0.05
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAATATAT
Found at i:5713030 original size:19 final size:21
Alignment explanation
Indices: 5712949--5713096 Score: 74
Period size: 21 Copynumber: 7.0 Consensus size: 21
5712939 ATGATGTTAG
* *
5712949 AAATATACA-ATATAATATTAG
1 AAATATACATA-ATAATATAAA
*
5712970 AAATATACAT-ACAATAGTACAA
1 AAATATACATAATAATA-TA-AA
*
5712992 AAGATATATAACTAATAATATTAAA
1 AA-ATATA-CA-TAATAATA-TAAA
*
5713017 ATATATACATAATAATATAAA
1 AAATATACATAATAATATAAA
* *
5713038 AAATATA-ATATTAA-A-AAC
1 AAATATACATAATAATATAAA
* * * *
5713056 ATATATGCATAACATATATGAA
1 AAATATACATAATA-ATATAAA
*
5713078 AAATATATAT-ATAATATAA
1 AAATATACATAATAATATAA
5713097 TATTAAAATA
Statistics
Matches: 94, Mismatches: 22, Indels: 23
0.68 0.16 0.17
Matches are distributed among these distances:
18 7 0.07
19 5 0.05
20 17 0.18
21 23 0.24
22 19 0.20
23 6 0.06
24 6 0.06
25 4 0.04
26 7 0.07
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (21 bp):
AAATATACATAATAATATAAA
Found at i:5713047 original size:17 final size:16
Alignment explanation
Indices: 5713023--5713060 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
5713013 TAAAATATAT
5713023 ACATAATAATA-TAAAA
1 ACAT-ATAATATTAAAA
5713039 A-ATATAATATTAAAA
1 ACATATAATATTAAAA
5713054 ACATATA
1 ACATATA
5713061 TGCATAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
15 8 0.40
16 6 0.30
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (16 bp):
ACATATAATATTAAAA
Found at i:5713060 original size:39 final size:37
Alignment explanation
Indices: 5713006--5713089 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 37
5712996 TATATAACTA
*
5713006 ATAATATTAAAATATATACATAATA-ATATAAAAAAT
1 ATAATATTAAAATATATACATAACATATATAAAAAAT
* *
5713042 ATAATATTAAAAACATATATGCATAACATATATGAAAAAT
1 ATAATATT--AAA-ATATATACATAACATATATAAAAAAT
5713082 ATATATAT
1 ATA-ATAT
5713090 AATATAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
36 8 0.20
38 3 0.08
39 12 0.30
40 13 0.32
41 4 0.10
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (37 bp):
ATAATATTAAAATATATACATAACATATATAAAAAAT
Found at i:5713061 original size:13 final size:13
Alignment explanation
Indices: 5713031--5713087 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
5713021 ATACATAATA
* *
5713031 ATATAAAAAATAT
1 ATATGAAAAACAT
*
5713044 AATATTAAAAACAT
1 -ATATGAAAAACAT
* *
5713058 ATATGCATAACAT
1 ATATGAAAAACAT
*
5713071 ATATGAAAAATAT
1 ATATGAAAAACAT
5713084 ATAT
1 ATAT
5713088 ATAATATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
13 24 0.69
14 11 0.31
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.32
Consensus pattern (13 bp):
ATATGAAAAACAT
Found at i:5713104 original size:24 final size:24
Alignment explanation
Indices: 5713039--5713119 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 24
5713029 TAATATAAAA
*
5713039 AATATAATATTAAAAACATATATGCAT
1 AATATAATATT-AAAATATATAT--AT
* *
5713066 AACAT-ATATGAAAAATATATATAT
1 AATATAATAT-TAAAATATATATAT
* *
5713090 AATATAATATTAAAATATTTACAT
1 AATATAATATTAAAATATATATAT
5713114 AATATA
1 AATATA
5713120 TACATATTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
24 23 0.51
25 4 0.09
26 14 0.31
27 4 0.09
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
AATATAATATTAAAATATATATAT
Found at i:5713203 original size:3 final size:3
Alignment explanation
Indices: 5713195--5713254 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
5713185 ATATAGTAAC
*
5713195 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5713243 AAT AAT AAT AAT
1 AAT AAT AAT AAT
5713255 GATGATGATG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5713208 original size:12 final size:12
Alignment explanation
Indices: 5713175--5713253 Score: 101
Period size: 12 Copynumber: 6.8 Consensus size: 12
5713165 ATATACATAC
5713175 ATAATAA-AAC-
1 ATAATAATAACA
*
5713185 AT-ATAGTAACA
1 ATAATAATAACA
5713196 ATAATAATAACA
1 ATAATAATAACA
*
5713208 ATAATAATAATA
1 ATAATAATAACA
*
5713220 ATAATAATAATA
1 ATAATAATAACA
*
5713232 ATAATAATAATA
1 ATAATAATAACA
5713244 ATAATAATAA
1 ATAATAATAA
5713254 TGATGATGAT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
9 3 0.05
10 5 0.08
11 2 0.03
12 53 0.84
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (12 bp):
ATAATAATAACA
Found at i:5713910 original size:14 final size:15
Alignment explanation
Indices: 5713891--5713919 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5713881 CGAAAAGGTG
5713891 TATTTTTT-TATTTT
1 TATTTTTTATATTTT
5713905 TATTTTTTATATTTT
1 TATTTTTTATATTTT
5713920 AATATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TATTTTTTATATTTT
Found at i:5714960 original size:26 final size:26
Alignment explanation
Indices: 5714923--5715058 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
5714913 TGATACAAAT
*
5714923 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5714949 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5714975 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5715001 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5715027 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5715053 TGATAA
1 TGATAA
5715059 GAATATCATG
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 106 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5717830 original size:23 final size:25
Alignment explanation
Indices: 5717804--5717850 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5717794 TATCATTCAT
*
5717804 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
5717827 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
5717851 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:5718171 original size:46 final size:45
Alignment explanation
Indices: 5718111--5718544 Score: 516
Period size: 46 Copynumber: 10.0 Consensus size: 45
5718101 TTTGACGTGA
* * * * *
5718111 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
** * *
5718157 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTTATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTA--TCAGGT
*
5718203 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
5718249 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
*
5718295 TGCCATGGTATCTTTCAACCATGGTCTT-----TTAC-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
* *
5718333 TACCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
5718379 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
*
5718417 TTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
5718463 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
5718501 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAG
5718545 AGAGCACACT
Statistics
Matches: 341, Mismatches: 19, Indels: 56
0.82 0.05 0.13
Matches are distributed among these distances:
38 97 0.28
39 3 0.01
40 6 0.02
41 5 0.01
43 5 0.01
44 10 0.03
45 3 0.01
46 208 0.61
47 2 0.01
48 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:5718341 original size:38 final size:38
Alignment explanation
Indices: 5718290--5718528 Score: 262
Period size: 38 Copynumber: 5.9 Consensus size: 38
5718280 CATTTCATAT
5718290 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTTTACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTTTACA
* *
5718328 CAGGTTACCATGGTATCTTTCAACCATGGTCTTACATATTTCATA
1 CAGGTTGCCATGGTATCTTTCAACCATGG---T-C-T-TTT-ACA
**
5718373 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTTTTACA
* *
5718412 CAGGTTTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTC-T-----TTT-ACA
**
5718457 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTTTTACA
5718496 CAGGTTGCCATGGTATCTTTCAACCATGGTCTT
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTT
5718529 ACACATTTCA
Statistics
Matches: 171, Mismatches: 14, Indels: 32
0.79 0.06 0.15
Matches are distributed among these distances:
38 91 0.53
39 5 0.03
40 2 0.01
41 2 0.01
42 2 0.01
43 2 0.01
44 4 0.02
45 5 0.03
46 58 0.34
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTTTACA
Found at i:5718385 original size:84 final size:84
Alignment explanation
Indices: 5718244--5718544 Score: 557
Period size: 84 Copynumber: 3.6 Consensus size: 84
5718234 CATCTCATAT
5718244 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
**
5718309 TCAACCATGGTCTTTTACA
66 TCAACCATGGTCTTACACA
* *
5718328 CAGGTTACCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAGGTTGCCATGGTATCTT
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
5718393 TCAACCATGGTCTTACACA
66 TCAACCATGGTCTTACACA
*
5718412 CAGGTTTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
5718477 TCAACCATGGTCTTACACA
66 TCAACCATGGTCTTACACA
5718496 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5718545 AGAGCACACT
Statistics
Matches: 210, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 210 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (84 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
TCAACCATGGTCTTACACA
Found at i:5718480 original size:168 final size:172
Alignment explanation
Indices: 5718159--5718544 Score: 604
Period size: 168 Copynumber: 2.2 Consensus size: 172
5718149 TATCATGTTG
* * *
5718159 CCATGGTATCTTTCAACCATGGTCTTATTC-T-TTTTATGTCACGTTGCCATGGTATCTTTCAAC
1 CCATGGTATCTTTCAACCATGGTCTTA--CATATTTCATATCAGGTTGCCATGGTATCTTTCAAC
5718222 CATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
64 CATGGTCTTA-ACA--TCA-ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
**
5718287 TATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTTTACACAGGTTA
125 TATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACAGGTTA
5718335 CCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
1 CCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
*
5718400 TGGTCTT-ACA-C-A-CAGGTTTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
66 TGGTCTTAACATCAATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
*
5718461 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAGGTTG
131 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAGGTTA
*
5718503 CCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 CCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAG
5718545 AGAGCACACT
Statistics
Matches: 200, Mismatches: 8, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
168 128 0.64
169 1 0.00
171 1 0.00
174 4 0.02
175 1 0.00
176 65 0.32
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.37
Consensus pattern (172 bp):
CCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
TGGTCTTAACATCAATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAGGTTA
Found at i:5722010 original size:20 final size:20
Alignment explanation
Indices: 5721985--5722042 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
5721975 TGCCCATGGG
*
5721985 CAGGCCACACGGGCATGTTC
1 CAGGCCACACGGGCATGTCC
*
5722005 CAGGCCACACGGGCGTGTCC
1 CAGGCCACACGGGCATGTCC
5722025 CAGGCCACACGGGCATGT
1 CAGGCCACACGGGCATGT
5722043 GCCCCTATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.36, G:0.33, T:0.12
Consensus pattern (20 bp):
CAGGCCACACGGGCATGTCC
Found at i:5724097 original size:52 final size:52
Alignment explanation
Indices: 5724027--5724130 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
5724017 AACCTAAATA
*
5724027 TTGTATAATTTGATTTTTTTTCAGTTTTATTTTATTTGGGACATTAAATTTT
1 TTGTATAATTTGATTTTTTTTAAGTTTTATTTTATTTGGGACATTAAATTTT
5724079 TTGTATAATTTGATTTTTTTTAAGTTTTATTTTATTTGGGACATTAAATTTT
1 TTGTATAATTTGATTTTTTTTAAGTTTTATTTTATTTGGGACATTAAATTTT
5724131 AGTTTTAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.62
Consensus pattern (52 bp):
TTGTATAATTTGATTTTTTTTAAGTTTTATTTTATTTGGGACATTAAATTTT
Found at i:5726972 original size:12 final size:13
Alignment explanation
Indices: 5726949--5726973 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5726939 GTTAAACCTG
5726949 GATGGAAAAAAAA
1 GATGGAAAAAAAA
5726962 GATGGAAAAAAA
1 GATGGAAAAAAA
5726974 TTTTACATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (13 bp):
GATGGAAAAAAAA
Found at i:5732666 original size:39 final size:39
Alignment explanation
Indices: 5732623--5732755 Score: 167
Period size: 39 Copynumber: 3.4 Consensus size: 39
5732613 GGTCTTTAAC
** *
5732623 CCGGATATTTTTCCAACACGTAGCCTGCAGACCTCAAGT
1 CCGGATATTTTTCCAACATATAGCCTGCAGACCTCATGT
* * * * * *
5732662 CCGGATATATTTCTAGCATATAGCCTGCGGATCTCATCT
1 CCGGATATTTTTCCAACATATAGCCTGCAGACCTCATGT
* *
5732701 CCGGATATTTTTCCAGCATATAGCCTGCTGACCTCATGT
1 CCGGATATTTTTCCAACATATAGCCTGCAGACCTCATGT
5732740 CCGGATATTTTTCCAA
1 CCGGATATTTTTCCAA
5732756 TCTCATATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAACATATAGCCTGCAGACCTCATGT
Found at i:5732734 original size:78 final size:77
Alignment explanation
Indices: 5732597--5732752 Score: 206
Period size: 78 Copynumber: 2.0 Consensus size: 77
5732587 GAATACATTA
* * *
5732597 CTAGCATAAGCCTGCGGGTCTTTAACCCGGATATTTTTCCAACACGTAGCCTGCAGACCTCAAGT
1 CTAGCATAAGCCTGCGGATCTTCAACCCGGATATTTTTCCAACACATAGCCTGCAGACCTCAAGT
5732662 CCGGATATATTT
66 CCGGATATATTT
* * * * *
5732674 CTAGCATATAGCCTGCGGATC-TCATCTCCGGATATTTTTCCAGCATATAGCCTGCTGACCTCAT
1 CTAGCATA-AGCCTGCGGATCTTCAAC-CCGGATATTTTTCCAACACATAGCCTGCAGACCTCAA
*
5732738 GTCCGGATATTTTT
64 GTCCGGATATATTT
5732752 C
1 C
5732753 CAATCTCATA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
77 11 0.16
78 57 0.84
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (77 bp):
CTAGCATAAGCCTGCGGATCTTCAACCCGGATATTTTTCCAACACATAGCCTGCAGACCTCAAGT
CCGGATATATTT
Found at i:5737911 original size:382 final size:382
Alignment explanation
Indices: 5737205--5737973 Score: 1511
Period size: 382 Copynumber: 2.0 Consensus size: 382
5737195 TCTATAACCA
5737205 CAACTACAAACCGGTCCAAATACTGCCTGAAAATTTGGTTCATCAAATCCATAAATACTGCAAGG
1 CAACTACAAACCGGTCCAAATACTGCCTGAAAATTTGGTTCATCAAATCCATAAATACTGCAAGG
*
5737270 GCATTAGTGAGTCAAAACGGCATCACTAAGAACTCATAGTGACCGTATCTCATTTTGAAAGCAGT
66 GCATTAGCGAGTCAAAACGGCATCACTAAGAACTCATAGTGACCGTATCTCATTTTGAAAGCAGT
5737335 TTTAGGTATATCTGAATCTCGAACTCGCAACTGATAATAACCCGATCTCAAATCTATCTTTGAAA
131 TTTAGGTATATCTGAATCTCGAACTCGCAACTGATAATAACCCGATCTCAAATCTATCTTTGAAA
5737400 ACACTGAAGCTCCCTTCAGCTGATCAAACAAATCATCAATACGCGGTAACGGATATTTATTCTTT
196 ACACTGAAGCTCCCTTCAGCTGATCAAACAAATCATCAATACGCGGTAACGGATATTTATTCTTT
5737465 ATCGTCACTTTATTCAACTGACGATAGTCGATGCACAATCTCATGGTTCTGTCCATCTTTTTCAC
261 ATCGTCACTTTATTCAACTGACGATAGTCGATGCACAATCTCATGGTTCTGTCCATCTTTTTCAC
5737530 GAACAATACTGGTGCACCCCAAGGTGAGAAACTCGGTCGAGCGAAACCTCTATCCGT
326 GAACAATACTGGTGCACCCCAAGGTGAGAAACTCGGTCGAGCGAAACCTCTATCCGT
*
5737587 CAACTACAAACCGGTCTAAATACTGCCTGAAAATTTGGTTCATCAAATCCATAAATACTGCAAGG
1 CAACTACAAACCGGTCCAAATACTGCCTGAAAATTTGGTTCATCAAATCCATAAATACTGCAAGG
5737652 GCATTAGCGAGTCAAAACGGCATCACTAAGAACTCATAGTGACCGTATCTCATTTTGAAAGCAGT
66 GCATTAGCGAGTCAAAACGGCATCACTAAGAACTCATAGTGACCGTATCTCATTTTGAAAGCAGT
5737717 TTTAGGTATATCTGAATCTCGAACTCGCAACTGATAATAACCCGATCTCAAATCTATCTTTGAAA
131 TTTAGGTATATCTGAATCTCGAACTCGCAACTGATAATAACCCGATCTCAAATCTATCTTTGAAA
5737782 ACACTGAAGCTCCCTTCAGCTGATCAAACAAATCATCAATACGCGGTAACGGATATTTATTCTTT
196 ACACTGAAGCTCCCTTCAGCTGATCAAACAAATCATCAATACGCGGTAACGGATATTTATTCTTT
*
5737847 ATCGTCACTTTATTCAACTGACGATAGTCGATGCACAATCTCATGGTTTTGTCCATCTTTTTCAC
261 ATCGTCACTTTATTCAACTGACGATAGTCGATGCACAATCTCATGGTTCTGTCCATCTTTTTCAC
5737912 GAACAATACTGGTGCACCCCAAGGTGAGAAACTCGGTCGAGCGAAACCTCTATCCGT
326 GAACAATACTGGTGCACCCCAAGGTGAGAAACTCGGTCGAGCGAAACCTCTATCCGT
5737969 CAACT
1 CAACT
5737974 CTTGCAACTG
Statistics
Matches: 384, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
382 384 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (382 bp):
CAACTACAAACCGGTCCAAATACTGCCTGAAAATTTGGTTCATCAAATCCATAAATACTGCAAGG
GCATTAGCGAGTCAAAACGGCATCACTAAGAACTCATAGTGACCGTATCTCATTTTGAAAGCAGT
TTTAGGTATATCTGAATCTCGAACTCGCAACTGATAATAACCCGATCTCAAATCTATCTTTGAAA
ACACTGAAGCTCCCTTCAGCTGATCAAACAAATCATCAATACGCGGTAACGGATATTTATTCTTT
ATCGTCACTTTATTCAACTGACGATAGTCGATGCACAATCTCATGGTTCTGTCCATCTTTTTCAC
GAACAATACTGGTGCACCCCAAGGTGAGAAACTCGGTCGAGCGAAACCTCTATCCGT
Found at i:5743971 original size:43 final size:44
Alignment explanation
Indices: 5743910--5744372 Score: 204
Period size: 45 Copynumber: 10.4 Consensus size: 44
5743900 TATCATAAGC
5743910 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AAATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAATACCAGAT
* * ***
5743953 CTTATCTTCACTGAGCAGGAGTGAAGCA-GATCAAATTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAA--TACCAG-AT
** * ** *
5743999 CTTATCTCTACGTACTG-GC--GA-TGGAGCAGATTCCAATCATAAG-C
1 CTTATCT-T-C--ACTGAGCAGGAGTGGAGCAGGCTCAAAT-ACCAGAT
5744043 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AAATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAATACCAGAT
* * * ***
5744086 CTTATCTTCACTGAGCAGGGGTGAAGCA-GATCAAATTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAA--TACCAG-AT
* * * * * *
5744132 CTTATCTCCAC-GTA-CCGGCGATGGAGCAGGTTCCAATCATCA-A-
1 CTTATCTTCACTG-AGCAGGAG-TGGAGCAGGCTCAAAT-ACCAGAT
* *
5744175 CTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAAAT
1 C-TTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAA-ATACCAGAT
* * * * ***
5744221 CTTATCTTCATTGAGCAGGAGTGAAGCA-GATCGAATTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTC-AA-ATACCAG-AT
* * * ** * * *
5744267 CTTATCTCCAC-GTA-CCGGCGATGGAGCAGATTCCAATCATCAGCT
1 CTTATCTTCACTG-AGCAGGAG-TGGAGCAGGCTCAAAT-ACCAGAT
* * *
5744312 -TTATCTTTACTGAGCAGGAATGGAGCAGGCTAAATATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAA-ATACCAGAT
*
5744356 CTTATCTTCATTGAGCA
1 CTTATCTTCACTGAGCA
5744373 AGAGCGGATC
Statistics
Matches: 305, Mismatches: 76, Indels: 76
0.67 0.17 0.17
Matches are distributed among these distances:
40 4 0.01
41 2 0.01
42 8 0.03
43 66 0.22
44 67 0.22
45 78 0.26
46 59 0.19
47 14 0.05
48 1 0.00
49 2 0.01
50 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (44 bp):
CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAATACCAGAT
Found at i:5744139 original size:133 final size:135
Alignment explanation
Indices: 5743901--5744372 Score: 783
Period size: 133 Copynumber: 3.5 Consensus size: 135
5743891 GATTATAGAT
5743901 ATCATAAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AA-ATACCAGATCTTATCTTCAC
1 ATCATAAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAC
* *
5743964 TGAGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCTACGTACTGGCGATGGAGCAGA
66 TGAGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
5744029 TTCCA
131 TTCCA
5744034 ATCATAAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AA-ATACCAGATCTTATCTTCAC
1 ATCATAAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAC
* *
5744097 TGAGCAGGGGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGG
66 TGAGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
5744162 TTCCA
131 TTCCA
* *
5744167 ATCATCAA-CTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAAATCTTATCTTCA
1 ATCAT-AAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCA
* *
5744231 TTGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAG
65 CTGAGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAG
5744296 ATTCCA
130 ATTCCA
* * * * *
5744302 ATCATCAGCTTTATCTTTACTGAGCAGGAATGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
1 ATCATAAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAC
5744367 TGAGCA
66 TGAGCA
5744373 AGAGCGGATC
Statistics
Matches: 321, Mismatches: 14, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
133 166 0.52
134 5 0.02
135 150 0.47
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (135 bp):
ATCATAAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAC
TGAGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
TTCCA
Found at i:5744371 original size:45 final size:46
Alignment explanation
Indices: 5743910--5744372 Score: 174
Period size: 44 Copynumber: 10.4 Consensus size: 46
5743900 TATCATAAGC
*
5743910 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCT--AA-ATACCAGAT
1 CTTATCTTCACTGAGCAGGAATGGAGCAGGCTCAAATATACCAGAT
* * * * ***
5743953 CTTATCTTCACTGAGCAGGAGTGAAGCA-GATCAAATTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAATGGAGCAGGCTCAAATATACCAG-AT
** * *
5743999 CTTATCTCTACGTACTG-GC--G-ATGGAGCAGATTCCAATCATA--AG-C
1 CTTATCT-T-C--ACTGAGCAGGAATGGAGCAGGCTCAAAT-ATACCAGAT
*
5744043 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCT--AA-ATACCAGAT
1 CTTATCTTCACTGAGCAGGAATGGAGCAGGCTCAAATATACCAGAT
** * * * ***
5744086 CTTATCTTCACTGAGCAGGGGTGAAGCA-GATCAAATTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAATGGAGCAGGCTCAAATATACCAG-AT
* * * * *
5744132 CTTATCTCCAC-GTA-CCGGCGATGGAGCAGGTTCCAATCAT--CA-A-
1 CTTATCTTCACTG-AGCAGG-AATGGAGCAGGCTCAAAT-ATACCAGAT
* *
5744175 CTTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AAATATACCAAAT
1 C-TTATCTTCACTGAGCAGGAATGGAGCAGGCTCAAATATACCAGAT
* * * * * * ***
5744221 CTTATCTTCATTGAGCAGGAGTGAAGCA-GATCGAATTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAATGGAGCAGGCTCAAATATACCAG-AT
* * * ** * *
5744267 CTTATCTCCAC-GTA-CCGGCGATGGAGCAGATTCCAATCAT--CAGCT
1 CTTATCTTCACTG-AGCAGG-AATGGAGCAGGCTCAAAT-ATACCAGAT
*
5744312 -TTATCTTTACTGAGCAGGAATGGAGCAGGCT-AAATATACCAGAT
1 CTTATCTTCACTGAGCAGGAATGGAGCAGGCTCAAATATACCAGAT
*
5744356 CTTATCTTCATTGAGCA
1 CTTATCTTCACTGAGCA
5744373 AGAGCGGATC
Statistics
Matches: 307, Mismatches: 70, Indels: 84
0.67 0.15 0.18
Matches are distributed among these distances:
40 7 0.02
41 2 0.01
42 13 0.04
43 62 0.20
44 68 0.22
45 68 0.22
46 59 0.19
47 18 0.06
48 4 0.01
49 2 0.01
50 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (46 bp):
CTTATCTTCACTGAGCAGGAATGGAGCAGGCTCAAATATACCAGAT
Done.