Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015058.1 Kokia drynarioides strain JFW-HI SEQ_130102, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 830620
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 706 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:9636 original size:23 final size:21
Alignment explanation
Indices: 9610--9664 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
9600 ATTTTTCGGA
9610 TTTATAATTGTAATAATTAATAT
1 TTTATAATT-TAATAA-TAATAT
* *
9633 TTTAATAATTTAATCATCATAT
1 TTT-ATAATTTAATAATAATAT
*
9655 TTTATTATTT
1 TTTATAATTT
9665 TATTTATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 6 0.21
22 8 0.29
23 8 0.29
24 6 0.21
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTATAATTTAATAATAATAT
Found at i:27116 original size:35 final size:34
Alignment explanation
Indices: 27077--27186 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 34
27067 CCAAACTCAT
**
27077 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATTT-AAA
*
27112 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
*
27146 TTTAAATTTATTTTCAAATTTAAAATT-ATTATAAA
1 TTTAAATTTATTTT-AAATTTAAATTTAATT-TAAA
27181 TTTAAA
1 TTTAAA
27187 ATAAATAAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
34 20 0.30
35 47 0.70
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
Found at i:27120 original size:6 final size:6
Alignment explanation
Indices: 27109--27186 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
27099 ATTTGTTTTA
* *
27109 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
27155 -ATTTT CAAATTT AAAATT --ATTAT AAATTT AAA
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAA
27187 ATAAATAAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
4 2 0.04
5 14 0.25
6 34 0.60
7 7 0.12
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:27126 original size:11 final size:11
Alignment explanation
Indices: 27112--27167 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
27102 TGTTTTAAAA
27112 TTTAAATTTAT
1 TTTAAATTTAT
*
27123 TTTAAATTTAAA
1 TTTAAATTT-AT
*
27135 TTT-AATTTAAG
1 TTTAAATTT-AT
27146 TTTAAATTTAT
1 TTTAAATTTAT
27157 TTTCAAATTTA
1 TTT-AAATTTA
27168 AAATTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 23 0.59
12 16 0.41
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:27144 original size:52 final size:52
Alignment explanation
Indices: 27077--27186 Score: 166
Period size: 52 Copynumber: 2.1 Consensus size: 52
27067 CCAAACTCAT
* * * *
27077 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAATTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
* *
27129 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
27181 TTTAAA
1 TTTAAA
27187 ATAAATAAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
Found at i:27188 original size:17 final size:17
Alignment explanation
Indices: 27077--27186 Score: 141
Period size: 17 Copynumber: 6.4 Consensus size: 17
27067 CCAAACTCAT
27077 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
27095 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
27112 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
27129 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
27146 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
27164 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
27181 TTTAAA
1 TTTAAA
27187 ATAAATAAAG
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
17 53 0.65
18 28 0.35
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:27821 original size:13 final size:13
Alignment explanation
Indices: 27803--27827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27793 GCTCCATCTG
27803 TTTCCATTTATTA
1 TTTCCATTTATTA
27816 TTTCCATTTATT
1 TTTCCATTTATT
27828 TTCAATATCA
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:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTCCATTTATTA
Found at i:29055 original size:29 final size:29
Alignment explanation
Indices: 29011--29336 Score: 151
Period size: 29 Copynumber: 11.2 Consensus size: 29
29001 CATTTTTACC
* *
29011 CCTCAAAACTTCCAAAAATTCCATTTTGA
1 CCTCGAAACTTTCAAAAATTCCATTTTGA
*
29040 CCTCGAAACTTTCAAAAATTCCATTTTAA
1 CCTCGAAACTTTCAAAAATTCCATTTTGA
* *
29069 CC-CTAAAAC-TTCCAAAATTCCACTTTT-A
1 CCTC-GAAACTTTCAAAAATTCCA-TTTTGA
* * * *
29097 CCCCCG-ATC-TTCTAAAAATTTCATTTTTAA
1 -CCTCGAAACTTTC-AAAAATTCCA-TTTTGA
*
29127 CCTCGAAACTCTT--AAAATTCCATTTTTA
1 CCTCGAAACT-TTCAAAAATTCCATTTTGA
* * *
29155 CCCCTG-ATCTTCCAAAAATTCCATTTTCGA
1 CCTC-GAAACTTTCAAAAATTCCATTTT-GA
* * * *
29185 CCCCAAAACTTTC-AAAAGTCTCATTTTTA
1 CCTCGAAACTTTCAAAAATTC-CATTTTGA
* * *
29214 TCCTCG-AACTTCCAAAAAATCCATTTTGC
1 -CCTCGAAACTTTCAAAAATTCCATTTTGA
* * * *
29243 CCCCG-AA-TGTCCAAAAACTCTATTTTCGA
1 CCTCGAAACT-TTCAAAAATTCCATTTT-GA
* *
29272 CCTCGAAAC-TCCAAAAATTCCATTTTTA
1 CCTCGAAACTTTCAAAAATTCCATTTTGA
* * *
29300 CCCCG-AA-TGTCTAAAAATTCCATCTTTTAA
1 CCTCGAAACTTTC-AAAAATTCCA--TTTTGA
29330 CCTCGAA
1 CCTCGAA
29337 CTTCCCCAAA
Statistics
Matches: 229, Mismatches: 42, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
27 5 0.02
28 66 0.29
29 115 0.50
30 40 0.17
31 1 0.00
32 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
CCTCGAAACTTTCAAAAATTCCATTTTGA
Found at i:29084 original size:58 final size:56
Alignment explanation
Indices: 28994--29302 Score: 198
Period size: 58 Copynumber: 5.3 Consensus size: 56
28984 AAACTATCTG
* * *
28994 AAAATTACATTTTTACCCCTCAAAACTTCCAAAAATTCCATTTTGACCTCGAAACTTTCA
1 AAAATTCCA-TTTTAACCCT-AAAACTTCC-AAAATTCCATTTTGACCTCG-AACTTCCA
* * *
29054 AAAATTCCATTTTAACCCTAAAACTTCCAAAATTCCACTTTT-ACCCCCGATCTTCTA
1 AAAATTCCATTTTAACCCTAAAACTTCCAAAATTCCA-TTTTGA-CCTCGAACTTCCA
* * * * * *
29111 AAAATTTCATTTTTAA-CCTCGAAAC-TCTTAAAATTCCATTTTTACCCCTGATCTTCCA
1 AAAATTCCA-TTTTAACCCT-AAAACTTC-CAAAATTCCATTTTGACCTC-GAACTTCCA
* * * * *
29169 AAAATTCCATTTTCGACCCCAAAACTTTCAAAAGTCTCATTTTTATCCTCGAACTTCCA
1 AAAATTCCATTTT-AACCCTAAAACTTCCAAAATTC-CATTTTGA-CCTCGAACTTCCA
* * *** * *
29228 AAAAATCCATTTT-GCCCCCGAA-TGTCCAAAAACTCTATTTTCGACCTCGAAAC-TCCA
1 AAAATTCCATTTTAACCCTAAAACT-TCC-AAAATTCCATTTT-GACCTCG-AACTTCCA
*
29285 AAAATTCCATTTTTACCC
1 AAAATTCCATTTTAACCC
29303 CGAATGTCTA
Statistics
Matches: 203, Mismatches: 29, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
56 1 0.00
57 74 0.36
58 77 0.38
59 40 0.20
60 11 0.05
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (56 bp):
AAAATTCCATTTTAACCCTAAAACTTCCAAAATTCCATTTTGACCTCGAACTTCCA
Found at i:29255 original size:28 final size:28
Alignment explanation
Indices: 29021--29391 Score: 127
Period size: 29 Copynumber: 12.9 Consensus size: 28
29011 CCTCAAAACT
*
29021 TCCAAAAATTCCATTTTGACCTCGAAACT-
1 TCCAAAAATTCCATTTTGACCCCG-AA-TG
* * **
29050 TTCAAAAATTCCATTTTAACCCTAAAACT-
1 TCCAAAAATTCCATTTTGACCC-CGAA-TG
*
29079 TCC-AAAATTCCACTTTT-ACCCCCG-ATCT
1 TCCAAAAATTCCA-TTTTGA-CCCCGAAT-G
* * * * **
29107 TCTAAAAATTTCATTTTTAACCTCGAAAC
1 TCCAAAAATTCCA-TTTTGACCCCGAATG
** * *
29136 TCTTAAAATTCCATTTTTACCCCTG-ATCT
1 TCCAAAAATTCCATTTTGACCCC-GAAT-G
*
29165 TCCAAAAATTCCATTTTCGACCCCAAAACT-
1 TCCAAAAATTCCATTTT-GACCCC-GAA-TG
* * * *
29195 TTC-AAAAGTCTCATTTTTATCCTCGAACT-
1 TCCAAAAATTC-CATTTTGA-CCCCGAA-TG
* *
29224 TCCAAAAAATCCATTTTGCCCCCGAATG
1 TCCAAAAATTCCATTTTGACCCCGAATG
* * * **
29252 TCCAAAAACTCTATTTTCGACCTCGAAAC
1 TCCAAAAATTCCATTTT-GACCCCGAATG
*
29281 TCCAAAAATTCCATTTTTACCCCGAATG
1 TCCAAAAATTCCATTTTGACCCCGAATG
* * *
29309 TCTAAAAATTCCATCTTTTAACCTCGAACT-
1 TCCAAAAATTCCA--TTTTGACCCCGAA-TG
* * *
29339 TCCCCAAAATTACCATCTT-ACCCCGAAAG
1 T-CCAAAAATT-CCATTTTGACCCCGAATG
*
29368 TCC-AAAATTACCATTTTGCCCCCG
1 TCCAAAAATT-CCATTTTGACCCCG
29392 GGTATCTAAA
Statistics
Matches: 260, Mismatches: 57, Indels: 51
0.71 0.15 0.14
Matches are distributed among these distances:
26 1 0.00
27 15 0.06
28 68 0.26
29 124 0.48
30 39 0.15
31 9 0.03
32 4 0.02
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.32
Consensus pattern (28 bp):
TCCAAAAATTCCATTTTGACCCCGAATG
Found at i:29259 original size:145 final size:145
Alignment explanation
Indices: 28994--29303 Score: 360
Period size: 145 Copynumber: 2.1 Consensus size: 145
28984 AAACTATCTG
* * *
28994 AAAATTACATTTTTACCCCTCAAAACTTCCAAAAATTCCATTTTGACCTCGAAACTTTCAAAAAT
1 AAAATTCCATTTTTACCCCT-AAAACTTCCAAAAATTCCATTTTGACCCCAAAACTTTCAAAAAT
* * * *
29059 TCCATTTTAACCCTAAAACTTCCAAAATTCCACTTTTACCCCCGATCTTCTAAAAA-TTTCATTT
65 TCCATTTTAACCCTAAAACTTCCAAAAATCCACTTTTACCCCCGATCGTCCAAAAACTCT-ATTT
* **
29123 TTAACCTCGAAACTCTT
129 TCAACCTCGAAACTCCA
* * *
29140 AAAATTCCATTTTTACCCCT-GATCTTCCAAAAATTCCATTTTCGACCCCAAAACTTTC-AAAAG
1 AAAATTCCATTTTTACCCCTAAAACTTCCAAAAATTCCATTTT-GACCCCAAAACTTTCAAAAAT
* * ** *
29203 TCTCATTTTTATCCTCGAACTTCCAAAAAATCCA-TTTTGCCCCCGAAT-GTCCAAAAACTCTAT
65 TC-CATTTTAACCCTAAAACTTCC-AAAAATCCACTTTTACCCCCG-ATCGTCCAAAAACTCTAT
*
29266 TTTCGACCTCGAAACTCCA
127 TTTCAACCTCGAAACTCCA
29285 AAAATTCCATTTTTACCCC
1 AAAATTCCATTTTTACCCC
29304 GAATGTCTAA
Statistics
Matches: 140, Mismatches: 19, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
144 26 0.19
145 83 0.59
146 31 0.22
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (145 bp):
AAAATTCCATTTTTACCCCTAAAACTTCCAAAAATTCCATTTTGACCCCAAAACTTTCAAAAATT
CCATTTTAACCCTAAAACTTCCAAAAATCCACTTTTACCCCCGATCGTCCAAAAACTCTATTTTC
AACCTCGAAACTCCA
Found at i:31930 original size:59 final size:59
Alignment explanation
Indices: 31823--31986 Score: 215
Period size: 59 Copynumber: 2.8 Consensus size: 59
31813 ATTTGATATA
* * *
31823 TTTT-TTAATTTGATACCTAAACTTTTTTT-ACCCAATTTGATACTTGAACTTGACACT
1 TTTTCTTAATTTGGTACCTAAACTTTTTTTGACCCAATTTGGTACCTGAACTTGACACT
* * *
31880 TTTTCTTAATTTGGTACCCAAACTTTTTTTGACCCAATTTGGTACCTGAACTTGGCATT
1 TTTTCTTAATTTGGTACCTAAACTTTTTTTGACCCAATTTGGTACCTGAACTTGACACT
* * **
31939 TTTTCCTAATTTGGTACTTAAACTTTTTTTAGATTCAATTTGGTACCT
1 TTTTCTTAATTTGGTACCTAAACTTTTTTT-GACCCAATTTGGTACCT
31987 AAATTTATTA
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
57 4 0.04
58 23 0.25
59 51 0.55
60 15 0.16
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (59 bp):
TTTTCTTAATTTGGTACCTAAACTTTTTTTGACCCAATTTGGTACCTGAACTTGACACT
Found at i:31963 original size:31 final size:30
Alignment explanation
Indices: 31829--31963 Score: 84
Period size: 31 Copynumber: 4.6 Consensus size: 30
31819 TATATTTTTT
* *
31829 AATTTGATACCTAAACTT---TTTTTACCC
1 AATTTGGTACCTAAACTTGCATTTTTTCCC
* * * * **
31856 AATTTGATACTTGAACTTGACACTTTTTCTT
1 AATTTGGTACCTAAACTTG-CATTTTTTCCC
* *
31887 AATTTGGTACCCAAACTT---TTTTTGACCC
1 AATTTGGTACCTAAACTTGCATTTTT-TCCC
* *
31915 AATTTGGTACCTGAACTTGGCATTTTTTCCT
1 AATTTGGTACCTAAACTT-GCATTTTTTCCC
*
31946 AATTTGGTACTTAAACTT
1 AATTTGGTACCTAAACTT
31964 TTTTTAGATT
Statistics
Matches: 79, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
27 20 0.25
28 17 0.22
31 37 0.47
32 5 0.06
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.44
Consensus pattern (30 bp):
AATTTGGTACCTAAACTTGCATTTTTTCCC
Found at i:32251 original size:31 final size:31
Alignment explanation
Indices: 32190--32265 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
32180 GAACCCCAAA
* * *
32190 AAGTTTAAGTA-CAACTTTAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAATGTC
32220 AAGTTTAAGTACCAAATTAAAAAAAAATGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAATGTC
32251 AAGTTTAAGTACCAA
1 AAGTTTAAGTACCAA
32266 GCTGAACCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 11 0.26
31 31 0.74
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAATGTC
Found at i:32272 original size:89 final size:91
Alignment explanation
Indices: 32139--32327 Score: 224
Period size: 89 Copynumber: 2.1 Consensus size: 91
32129 AAAAGATTAG
* * * **
32139 GTACCAAATTAGGAAAAAGAGTCAAGTTCAAGTACCAAATTGAACCCCAAAA-AGTTTAAGTA-C
1 GTACCAAATTAGAAAAAAAAGTCAAGTTCAAGTACCAAACTGAACCAAAAAAGAGTTTAAGTACC
* *
32202 AACTTTAAAAAAA-GTGTCAAGTTTAA
66 AA-ATTAAAAAAACGTGTCAAGTTCAA
* * *
32228 GTACCAAATTA-AAAAAAAATGTCAAGTTTAAGTACCAAGCTGAACCAAAAAAGAGTTTAGGTAC
1 GTACCAAATTAGAAAAAAAA-GTCAAGTTCAAGTACCAAACTGAACCAAAAAAGAGTTTAAGTAC
* *
32292 CAAATTAAAAAAACGTGTTAAGTTCAG
65 CAAATTAAAAAAACGTGTCAAGTTCAA
32319 GTACCAAAT
1 GTACCAAAT
32328 ATTATATTAA
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
88 6 0.07
89 38 0.45
90 18 0.21
91 22 0.26
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (91 bp):
GTACCAAATTAGAAAAAAAAGTCAAGTTCAAGTACCAAACTGAACCAAAAAAGAGTTTAAGTACC
AAATTAAAAAAACGTGTCAAGTTCAA
Found at i:35333 original size:123 final size:123
Alignment explanation
Indices: 35129--35357 Score: 388
Period size: 123 Copynumber: 1.9 Consensus size: 123
35119 TTCTTTTTAT
* **
35129 TTTTTAAGTTCTGATAATTTTATGTATGTATAGGTGAAAACACGATAAAACAACATGGTAGCCCG
1 TTTTTAAGTTCTGATAATTTTACGTATGTATAGGTGAAAACACGATAAAACAACAACGTAGCCCG
* *
35194 TCTAGTTCAGTTGGTAGAGCGCAAGGCTCTTAACCTTGTGGGGTGGGCGTATTTCTTC
66 TCTAGCTCAGTCGGTAGAGCGCAAGGCTCTTAACCTTGTGGGGTGGGCGTATTTCTTC
*
35252 TTTTTAAGTTCTGATAATTTTACGTATGTATA-GTTATAAACACGATAAAACAACAACGTAGCCC
1 TTTTTAAGTTCTGATAATTTTACGTATGTATAGGTGA-AAACACGATAAAACAACAACGTAGCCC
35316 GTCTAGCTCAGTCGGTAGAGCGCAAGGCTCTTAACCTTGTGG
65 GTCTAGCTCAGTCGGTAGAGCGCAAGGCTCTTAACCTTGTGG
35358 TCGTGGGTTC
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
122 3 0.03
123 96 0.97
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (123 bp):
TTTTTAAGTTCTGATAATTTTACGTATGTATAGGTGAAAACACGATAAAACAACAACGTAGCCCG
TCTAGCTCAGTCGGTAGAGCGCAAGGCTCTTAACCTTGTGGGGTGGGCGTATTTCTTC
Found at i:36975 original size:31 final size:31
Alignment explanation
Indices: 36937--37008 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
36927 GTTAAAAAGA
*
36937 TTTAATTATTAGTATTTTTTAACAAGAGTAG
1 TTTAATTATTAGTATTTGTTAACAAGAGTAG
***
36968 TTTAATTATTAGTATTTGTTAATGGGAGTAG
1 TTTAATTATTAGTATTTGTTAACAAGAGTAG
36999 TTTAATTATT
1 TTTAATTATT
37009 GTTTTAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.51
Consensus pattern (31 bp):
TTTAATTATTAGTATTTGTTAACAAGAGTAG
Found at i:46944 original size:2 final size:2
Alignment explanation
Indices: 46939--46964 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46929 CATATATTGA
46939 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
46965 TTTAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55611 original size:21 final size:20
Alignment explanation
Indices: 55582--55630 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
55572 AATAATAAAA
* *
55582 TAAATAAATAATTCATGAAGT
1 TAAAAAAATAACTC-TGAAGT
* *
55603 TAAAAAAATAACTCTTAATT
1 TAAAAAAATAACTCTGAAGT
55623 TAAAAAAA
1 TAAAAAAA
55631 ATAAACGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (20 bp):
TAAAAAAATAACTCTGAAGT
Found at i:55641 original size:20 final size:21
Alignment explanation
Indices: 55604--55642 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
55594 TCATGAAGTT
* *
55604 AAAAAAATAACTCTTAATTTA
1 AAAAAAATAACACGTAATTTA
55625 AAAAAAATAA-ACGTAATT
1 AAAAAAATAACACGTAATT
55643 ATCTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAAAAATAACACGTAATTTA
Found at i:61547 original size:58 final size:59
Alignment explanation
Indices: 61480--61643 Score: 165
Period size: 60 Copynumber: 2.8 Consensus size: 59
61470 AATATTTGAT
* * **
61480 ACTTAAATTTGACATATTTTT-TTAATTTAGTATCTAAATTTTTTTGG-CCCAATTCGGT
1 ACTTGAATTTGACAT-TTTTTCTTAATTTAGTACCTAAATTTTTTTGGACCCAATTCGAC
* * * *
61538 ATTTGAATTTGA-TTCTTTTTCCTAATTT-GATACCTAAACTTTTTTTGGACCCAATTTGAC
1 ACTTGAATTTGACAT-TTTTTCTTAATTTAG-TACCTAAA-TTTTTTTGGACCCAATTCGAC
* *
61598 ACTTGAACTTGACATTTTTTCTTAATTTAGTACCTAAGCTTTTTTT
1 ACTTGAATTTGACATTTTTTCTTAATTTAGTACCTAA-ATTTTTTT
61644 AGGCTCATTT
Statistics
Matches: 85, Mismatches: 14, Indels: 12
0.77 0.13 0.11
Matches are distributed among these distances:
57 7 0.08
58 23 0.27
59 9 0.11
60 44 0.52
61 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.50
Consensus pattern (59 bp):
ACTTGAATTTGACATTTTTTCTTAATTTAGTACCTAAATTTTTTTGGACCCAATTCGAC
Found at i:63860 original size:9 final size:9
Alignment explanation
Indices: 63838--63881 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
63828 CATATTTTTT
63838 TAAATAATTA
1 TAAA-AATTA
*
63848 TAAAAAATA
1 TAAAAATTA
63857 TAAAAATTA
1 TAAAAATTA
*
63866 TTAAAATTA
1 TAAAAATTA
63875 TAGAAAA
1 TA-AAAA
63882 GGATTTGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:64004 original size:31 final size:31
Alignment explanation
Indices: 63969--64027 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
63959 TTTTTGGTTC
63969 AATTTGGTA-CTCAAACTTGACACTTTTTCCT
1 AATTTGGTACCT-AAACTTGACACTTTTTCCT
64000 AATTTGGTACCTAAACTTGACACTTTTT
1 AATTTGGTACCTAAACTTGACACTTTTT
64028 TTTCAAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.42
Consensus pattern (31 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCT
Found at i:64321 original size:31 final size:30
Alignment explanation
Indices: 64274--64426 Score: 104
Period size: 31 Copynumber: 5.1 Consensus size: 30
64264 GAATCTAAAA
* *
64274 AAGTTTAGATACCAAATTAGGAAAAAATGCC
1 AAGTTTAGGTATCAAATTAGGAAAAAATG-C
*
64305 AAGTTCAGGTATCAAA-TAGGGTAAAAAA---
1 AAGTTTAGGTATCAAATTA-GG-AAAAAATGC
* * * *
64333 AAGTTTAAGTACCAAATTAAGAAAAAGTGTC
1 AAGTTTAGGTATCAAATTAGGAAAAAATG-C
*
64364 AAGTTTAGGTATCAAATTGGGTCAAAAAA---
1 AAGTTTAGGTATCAAATTAGG--AAAAAATGC
* * *
64393 AAGTTTAAGTACCAAATTAGGAAAAAGTGC
1 AAGTTTAGGTATCAAATTAGGAAAAAATGC
64423 AAGT
1 AAGT
64427 ACCAAATGTT
Statistics
Matches: 93, Mismatches: 17, Indels: 25
0.69 0.13 0.19
Matches are distributed among these distances:
27 10 0.11
28 14 0.15
29 20 0.22
30 6 0.06
31 32 0.34
32 6 0.06
33 5 0.05
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.24
Consensus pattern (30 bp):
AAGTTTAGGTATCAAATTAGGAAAAAATGC
Found at i:64417 original size:60 final size:59
Alignment explanation
Indices: 64249--64426 Score: 245
Period size: 59 Copynumber: 3.0 Consensus size: 59
64239 ATTTAATAAA
** * *
64249 TTTAGGTATCAAATTGAATC-TAAAAAAGTTT-AGATACCAAATTAGGAAAAAATGCCAAG
1 TTTAGGTATCAAATTGGGTCAAAAAAAAGTTTAAG-TACCAAATTAGGAAAAAGTG-CAAG
* * *
64308 TTCAGGTATCAAATAGGGT-AAAAAAAAGTTTAAGTACCAAATTAAGAAAAAGTGTCAAG
1 TTTAGGTATCAAATTGGGTCAAAAAAAAGTTTAAGTACCAAATTAGGAAAAAGTG-CAAG
64367 TTTAGGTATCAAATTGGGTCAAAAAAAAGTTTAAGTACCAAATTAGGAAAAAGTGCAAG
1 TTTAGGTATCAAATTGGGTCAAAAAAAAGTTTAAGTACCAAATTAGGAAAAAGTGCAAG
64426 T
1 T
64427 ACCAAATGTT
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
59 69 0.66
60 36 0.34
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (59 bp):
TTTAGGTATCAAATTGGGTCAAAAAAAAGTTTAAGTACCAAATTAGGAAAAAGTGCAAG
Found at i:70645 original size:13 final size:12
Alignment explanation
Indices: 70614--70644 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
70604 TATGTTTGAA
70614 TTTTTTTAAGGT
1 TTTTTTTAAGGT
70626 TTTTTTTAAGGT
1 TTTTTTTAAGGT
70638 TTTTTTT
1 TTTTTTT
70645 TTGTCCAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (12 bp):
TTTTTTTAAGGT
Found at i:72696 original size:3 final size:3
Alignment explanation
Indices: 72688--72712 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
72678 TTGAATCTGT
72688 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
72713 AGAGAAAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:74970 original size:26 final size:26
Alignment explanation
Indices: 74941--74997 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
74931 TTTGATCCTT
74941 ATTGATAT-AGTATGCTCTAAGGTAGC
1 ATTG-TATCAGTATGCTCTAAGGTAGC
* * *
74967 ATTGTTTCTGTATGCTCTGAGGTAGC
1 ATTGTATCAGTATGCTCTAAGGTAGC
*
74993 GTTGT
1 ATTGT
74998 TTCATTGGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.40
Consensus pattern (26 bp):
ATTGTATCAGTATGCTCTAAGGTAGC
Found at i:74998 original size:26 final size:26
Alignment explanation
Indices: 74950--75000 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
74940 TATTGATATA
74950 GTATGCTCTAAGGTAGCATTGTTTCT
1 GTATGCTCTAAGGTAGCATTGTTTCT
* *
74976 GTATGCTCTGAGGTAGCGTTGTTTC
1 GTATGCTCTAAGGTAGCATTGTTTC
75001 ATTGGTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (26 bp):
GTATGCTCTAAGGTAGCATTGTTTCT
Found at i:101163 original size:27 final size:28
Alignment explanation
Indices: 101133--101186 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
101123 AATTTTCAAC
*
101133 TTTTAAGGG-CCTCAA-TTTTTTTTTTAT
1 TTTTAAGGGTCC-CAACTTTATTTTTTAT
*
101160 TTTTACGGGTCCCAACTTTATTTTTTA
1 TTTTAAGGGTCCCAACTTTATTTTTTA
101187 CCAACTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.56
Consensus pattern (28 bp):
TTTTAAGGGTCCCAACTTTATTTTTTAT
Found at i:101192 original size:16 final size:18
Alignment explanation
Indices: 101171--101206 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
101161 TTTACGGGTC
101171 CCAAC-TTTATT-TTTTA
1 CCAACTTTTATTATTTTA
101187 CCAACTTTTATTATTTTA
1 CCAACTTTTATTATTTTA
101205 CC
1 CC
101207 TAGGGTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 6 0.33
18 7 0.39
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (18 bp):
CCAACTTTTATTATTTTA
Found at i:101631 original size:2 final size:2
Alignment explanation
Indices: 101624--101655 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
101614 CTTGGGAGTG
101624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
101656 CAAGAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102477 original size:7 final size:7
Alignment explanation
Indices: 102465--102507 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
102455 GGTGTCCACC
102465 ATATAAT
1 ATATAAT
102472 ATATAAT
1 ATATAAT
102479 ATATCATATT
1 ATAT-A-A-T
*
102489 ATATTAT
1 ATATAAT
102496 ATATAAT
1 ATATAAT
102503 ATATA
1 ATATA
102508 CTAGACAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 23 0.74
8 2 0.06
9 1 0.03
10 5 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (7 bp):
ATATAAT
Found at i:102497 original size:17 final size:17
Alignment explanation
Indices: 102471--102504 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
102461 CACCATATAA
*
102471 TATATAATATATCATAT
1 TATATAATATATAATAT
*
102488 TATATTATATATAATAT
1 TATATAATATATAATAT
102505 ATACTAGACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATAATATATAATAT
Found at i:102664 original size:18 final size:18
Alignment explanation
Indices: 102637--102680 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
102627 TTTAATGGTG
*
102637 TTTTACAATTTTTTTTAAT
1 TTTTA-AATTTTTTTAAAT
102656 TTTTAAATTTTTTTAAAT
1 TTTTAAATTTTTTTAAAT
*
102674 TTCTAAA
1 TTTTAAA
102681 AAAAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTAAATTTTTTTAAAT
Found at i:113895 original size:20 final size:20
Alignment explanation
Indices: 113864--113912 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
113854 GATAAATCAG
*
113864 ATTTTTTT-GTT-GATTTTT
1 ATTTTTTTAGTTGGATTTAT
113882 ATTATTTTTAGTTGGATTTAT
1 ATT-TTTTTAGTTGGATTTAT
113903 ATTTTTTTAG
1 ATTTTTTTAG
113913 GAAGAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 5 0.19
20 10 0.37
21 9 0.33
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.69
Consensus pattern (20 bp):
ATTTTTTTAGTTGGATTTAT
Found at i:114349 original size:14 final size:15
Alignment explanation
Indices: 114324--114352 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
114314 AGCCATTGCC
114324 CTTTTTTCTTTTTAA
1 CTTTTTTCTTTTTAA
114339 CTTTTTT-TTTTTAA
1 CTTTTTTCTTTTTAA
114353 GGGTTATGAT
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:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTTTCTTTTTAA
Found at i:115557 original size:21 final size:21
Alignment explanation
Indices: 115532--115586 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
115522 GTTAATTATT
115532 TTTATTTTCTTTAAATTAATA
1 TTTATTTTCTTTAAATTAATA
* *
115553 TTTATTTT-TTTCAATTTAATG
1 TTTATTTTCTTT-AAATTAATA
115574 TATTA-TTTCTTTA
1 T-TTATTTTCTTTA
115587 TTTTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 3 0.10
21 20 0.69
22 6 0.21
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTATTTTCTTTAAATTAATA
Found at i:116345 original size:29 final size:27
Alignment explanation
Indices: 116313--116379 Score: 62
Period size: 31 Copynumber: 2.3 Consensus size: 27
116303 TAAATCTCAA
*
116313 AATTATACATAAATTTTGATTTAATGTGC
1 AATTATACATAAATTTTGATTT--GGTGC
* **
116342 AATTGTATAGATGGATTTTGATTTGGTGC
1 AA-T-TATACATAAATTTTGATTTGGTGC
116371 AATTATACA
1 AATTATACA
116380 CATAATTGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 5 0.16
28 1 0.03
29 8 0.26
30 1 0.03
31 16 0.52
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.43
Consensus pattern (27 bp):
AATTATACATAAATTTTGATTTGGTGC
Found at i:116948 original size:19 final size:18
Alignment explanation
Indices: 116916--116973 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
116906 AAAAATTAAT
*
116916 AATTAATTTTAAATACTA
1 AATTAAATTTAAATACTA
*
116934 AATTAAATCTTAAATAATA
1 AATTAAAT-TTAAATACTA
*
116953 AATTTAATTTAAATACTA
1 AATTAAATTTAAATACTA
116971 AAT
1 AAT
116974 GTTAAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 19 0.54
19 16 0.46
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTAAATTTAAATACTA
Found at i:123688 original size:9 final size:9
Alignment explanation
Indices: 123674--123706 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
123664 GATGTGCACT
123674 TTTTAGTAA
1 TTTTAGTAA
123683 TTTTAGTAA
1 TTTTAGTAA
123692 TTTTTA-TAA
1 -TTTTAGTAA
123701 TTTTAG
1 TTTTAG
123707 AAAAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.23
9 12 0.55
10 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (9 bp):
TTTTAGTAA
Found at i:131414 original size:28 final size:26
Alignment explanation
Indices: 131381--131444 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 26
131371 ACTACAGTTG
* *
131381 AAATTTTAAAATTAAAAGTAAAAAATTT
1 AAATTTTAAAAATAAAAAT-AAAAA-TT
*
131409 AAATTTTAAAAAATAAAAATTAAAATT
1 AAATTTT-AAAAATAAAAATAAAAATT
131436 AAATTTTAA
1 AAATTTTAA
131445 TTATACGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 2 0.06
27 9 0.28
28 11 0.34
29 10 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
AAATTTTAAAAATAAAAATAAAAATT
Found at i:137860 original size:4 final size:4
Alignment explanation
Indices: 137851--137934 Score: 68
Period size: 4 Copynumber: 20.8 Consensus size: 4
137841 ATGATCTAAG
* *
137851 AAAT AAAT AAAT AAAT AAAT AAAT -AA- AAAT GAAT ATAA- AAAT GATAGT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT -A-AAT
*
137899 ATAT AAAAT AAAT ACAA- AAAT AAAT AAAT AAAT AAA
1 AAAT -AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAA
137935 ACAAAGGACT
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
3 8 0.12
4 46 0.71
5 9 0.14
6 2 0.03
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:139319 original size:19 final size:19
Alignment explanation
Indices: 139295--139338 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
139285 TGAAAAGTTC
*
139295 AGGTTTGGGGCTTGTTTTT
1 AGGTTTGGGGCTTGTTGTT
139314 AGGTTT-GGGCTTGTTGTT
1 AGGTTTGGGGCTTGTTGTT
*
139332 GGGTTTG
1 AGGTTTG
139339 AGTCTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.05, C:0.05, G:0.41, T:0.50
Consensus pattern (19 bp):
AGGTTTGGGGCTTGTTGTT
Found at i:139396 original size:17 final size:18
Alignment explanation
Indices: 139374--139407 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
139364 GGTATTGGAC
139374 TTGGGTATTTTA-ATTTA
1 TTGGGTATTTTATATTTA
*
139391 TTGGGTCTTTTATATTT
1 TTGGGTATTTTATATTT
139408 TGTATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.62
Consensus pattern (18 bp):
TTGGGTATTTTATATTTA
Found at i:140022 original size:11 final size:11
Alignment explanation
Indices: 140008--140086 Score: 58
Period size: 10 Copynumber: 7.4 Consensus size: 11
139998 TTTCACTCAT
140008 TTTCTCTCAAA
1 TTTCTCTCAAA
*
140019 TTTCTCT-TAA
1 TTTCTCTCAAA
140029 TTTCTCTCTAAA
1 TTTCTCTC-AAA
* *
140041 TTTCACACAAA
1 TTTCTCTCAAA
*
140052 TTTCTTTCTAAA
1 TTTCTCTC-AAA
*
140064 --GCTCTCAAA
1 TTTCTCTCAAA
*
140073 ATTCTCT-AAA
1 TTTCTCTCAAA
140083 TTTC
1 TTTC
140087 ACACGAATCT
Statistics
Matches: 52, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
9 3 0.06
10 19 0.37
11 19 0.37
12 11 0.21
ACGTcount: A:0.29, C:0.24, G:0.01, T:0.46
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:142472 original size:19 final size:19
Alignment explanation
Indices: 142450--142487 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
142440 TATTTTTACC
142450 TTTAAATT-AAAAAGAAAAA
1 TTTAAATTGAAAAA-AAAAA
*
142469 TTTACATTGAAAAAAAAAA
1 TTTAAATTGAAAAAAAAAA
142488 CAAATAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (19 bp):
TTTAAATTGAAAAAAAAAA
Found at i:142597 original size:15 final size:14
Alignment explanation
Indices: 142539--142597 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
142529 GATAGGAAAA
142539 TAAATTATTAATTAAT
1 TAAATTA-TAATT-AT
**
142555 TAGTTTATAATTA-
1 TAAATTATAATTAT
*
142568 T-AATTATAATGAT
1 TAAATTATAATTAT
142581 TAAATTATAAATTAT
1 TAAATTAT-AATTAT
142596 TA
1 TA
142598 TTTTTATCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
12 8 0.24
13 2 0.06
14 7 0.21
15 12 0.35
16 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TAAATTATAATTAT
Found at i:143037 original size:20 final size:21
Alignment explanation
Indices: 142993--143044 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
142983 TATCAAAATT
142993 CTAATTTTAAAAACTCTAAACC
1 CTAA-TTTAAAAACTCTAAACC
143015 CTAATTTAAAAA-TCCTAAA-C
1 CTAATTTAAAAACT-CTAAACC
143035 CTAA-TTAAAA
1 CTAATTTAAAA
143045 CAAAAACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 13 0.45
22 4 0.14
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (21 bp):
CTAATTTAAAAACTCTAAACC
Found at i:143806 original size:16 final size:16
Alignment explanation
Indices: 143782--143813 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
143772 CCTTCGACTA
*
143782 TTTTGTCAAATTGATC
1 TTTTATCAAATTGATC
143798 TTTTATCAAATTGATC
1 TTTTATCAAATTGATC
143814 CAAAACAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.50
Consensus pattern (16 bp):
TTTTATCAAATTGATC
Found at i:144050 original size:29 final size:28
Alignment explanation
Indices: 144016--144093 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
144006 TTTACAGTTG
* * *
144016 AAATTTTAAAATTGAAAAGTAAAAAAATT
1 AAATTTTAAAAAT-AAAAATAAAAAAAAT
144045 AAATTTTTAAAAATAAAAATAAAAAAAAT
1 AAA-TTTTAAAAATAAAAATAAAAAAAAT
* *
144074 AAATTTCAAATATACAAAAT
1 AAATTTTAAAAATA-AAAAT
144094 TTATATAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 9 0.21
29 24 0.57
30 9 0.21
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (28 bp):
AAATTTTAAAAATAAAAATAAAAAAAAT
Found at i:144053 original size:30 final size:29
Alignment explanation
Indices: 144019--144079 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
144009 ACAGTTGAAA
* * *
144019 TTTTAAAATTGAAAAGTAAAAAAATTAAAT
1 TTTTAAAAAT-AAAAATAAAAAAAATAAAT
144049 TTTTAAAAATAAAAATAAAAAAAATAAAT
1 TTTTAAAAATAAAAATAAAAAAAATAAAT
144078 TT
1 TT
144080 CAAATATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (29 bp):
TTTTAAAAATAAAAATAAAAAAAATAAAT
Found at i:145320 original size:12 final size:11
Alignment explanation
Indices: 145299--145332 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
145289 ATTAAAATTA
145299 AATA-ATTTTT
1 AATATATTTTT
145309 AACTATATTTTT
1 AA-TATATTTTT
145321 AATATATTTTT
1 AATATATTTTT
145332 A
1 A
145333 GTATTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 12 0.55
12 8 0.36
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
AATATATTTTT
Found at i:145376 original size:27 final size:28
Alignment explanation
Indices: 145346--145404 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
145336 TTTTATATGT
145346 TTTTATCAAGT-TTAAT-AATTTTTAAAA
1 TTTTAT-AAGTATTAATGAATTTTTAAAA
* *
145373 TTTT-TATGTATTTATGAATTTTTAAAA
1 TTTTATAAGTATTAATGAATTTTTAAAA
145400 TTTTA
1 TTTTA
145405 ATTTATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 3 0.11
26 5 0.19
27 19 0.70
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTTATAAGTATTAATGAATTTTTAAAA
Found at i:150950 original size:2 final size:2
Alignment explanation
Indices: 150943--150971 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
150933 AAAGCTGGTG
150943 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
150972 AAATATACAC
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:158870 original size:36 final size:36
Alignment explanation
Indices: 158830--158922 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 36
158820 AATCAACATT
* * **
158830 TCCAGGCATGCCACCAGGCATTGCTCCAGGCATACC
1 TCCAGGAAAGCCACCAGGCATACCTCCAGGCATACC
* *
158866 TCCAGGAAAGCCTCCAGGCATACCTCCGGGCATACC
1 TCCAGGAAAGCCACCAGGCATACCTCCAGGCATACC
* *
158902 TCC-GGTAAAACCCCCAGGCAT
1 TCCAGG-AAAGCCACCAGGCAT
158923 TCCACCTGGA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 2 0.04
36 46 0.96
ACGTcount: A:0.25, C:0.39, G:0.22, T:0.15
Consensus pattern (36 bp):
TCCAGGAAAGCCACCAGGCATACCTCCAGGCATACC
Found at i:158906 original size:12 final size:12
Alignment explanation
Indices: 158830--158904 Score: 80
Period size: 12 Copynumber: 6.2 Consensus size: 12
158820 AATCAACATT
*
158830 TCCAGGCATGCC
1 TCCAGGCATACC
* **
158842 ACCAGGCATTGC
1 TCCAGGCATACC
158854 TCCAGGCATACC
1 TCCAGGCATACC
*
158866 TCCAGG-AAAGCC
1 TCCAGGCATA-CC
158878 TCCAGGCATACC
1 TCCAGGCATACC
*
158890 TCCGGGCATACC
1 TCCAGGCATACC
158902 TCC
1 TCC
158905 GGTAAAACCC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
11 2 0.04
12 48 0.92
13 2 0.04
ACGTcount: A:0.23, C:0.40, G:0.21, T:0.16
Consensus pattern (12 bp):
TCCAGGCATACC
Found at i:163794 original size:3 final size:3
Alignment explanation
Indices: 163786--163816 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
163776 AAATAAAACG
163786 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
163817 TGTTTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:170692 original size:30 final size:29
Alignment explanation
Indices: 170637--170710 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 29
170627 GATTTAATGT
* *
170637 GTAATTTTATATATGAACATTGATTTTAC
1 GTAATTTTATACATGAACATTGATTTGAC
** **
170666 GTAATTTTATACATGTAATTTTGATTTGGT
1 GTAATTTTATACATG-AACATTGATTTGAC
170696 GTAATTTTCATACAT
1 GTAATTTT-ATACAT
170711 TATTAAAACA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 14 0.38
30 17 0.46
31 6 0.16
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (29 bp):
GTAATTTTATACATGAACATTGATTTGAC
Found at i:171180 original size:29 final size:29
Alignment explanation
Indices: 171121--171206 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
171111 AGGAGAATTG
* **
171121 AAATTAAATTATATATTTTTATGATAAT-A
1 AAATTAAATT-TATATTTTTATAATTTTAA
*
171150 AAATTATAATTTATATTTTAATAATTTTAA
1 AAATTA-AATTTATATTTTTATAATTTTAA
*
171180 AAGATTAAATTTA-ATTTTTATCATTTT
1 AA-ATTAAATTTATATTTTTATAATTTT
171207 TGAGAAGTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
29 31 0.65
30 13 0.27
31 4 0.08
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (29 bp):
AAATTAAATTTATATTTTTATAATTTTAA
Found at i:173303 original size:17 final size:17
Alignment explanation
Indices: 173281--173352 Score: 56
Period size: 19 Copynumber: 4.0 Consensus size: 17
173271 GTGATTTGTG
173281 GTAAAAAATTATAAAAA
1 GTAAAAAATTATAAAAA
*
173298 GT-AAAAATCAATAAAAA
1 GTAAAAAAT-TATAAAAA
* *
173315 TTAGAAAAAAATATAAAAA
1 GT--AAAAAATTATAAAAA
*
173334 ATATAAAAATTTATAAAAA
1 GTA-AAAAA-TTATAAAAA
173353 TCATAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
16 6 0.14
17 11 0.26
18 5 0.12
19 16 0.37
20 5 0.12
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (17 bp):
GTAAAAAATTATAAAAA
Found at i:173312 original size:10 final size:9
Alignment explanation
Indices: 173299--173369 Score: 56
Period size: 9 Copynumber: 7.6 Consensus size: 9
173289 TTATAAAAAG
173299 TAAAAATCAA
1 TAAAAAT-AA
173309 TAAAAATTAGA
1 TAAAAA-TA-A
*
173320 AAAAAAT-A
1 TAAAAATAA
173328 TAAAAA-ATA
1 TAAAAATA-A
*
173337 TAAAAATTTA
1 TAAAAA-TAA
*
173347 TAAAAATCA
1 TAAAAATAA
173356 TAAAAATAA
1 TAAAAATAA
173365 TAAAA
1 TAAAA
173370 TGCATCAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
8 6 0.12
9 22 0.44
10 15 0.30
11 7 0.14
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (9 bp):
TAAAAATAA
Found at i:173332 original size:9 final size:9
Alignment explanation
Indices: 173320--173361 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
173310 AAAAATTAGA
173320 AAAAAATAT
1 AAAAAATAT
173329 AAAAAATAT
1 AAAAAATAT
*
173338 -AAAAATTT
1 AAAAAATAT
173346 ATAAAAATCAT
1 A-AAAAAT-AT
173357 AAAAA
1 AAAAA
173362 TAATAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 7 0.25
9 9 0.32
10 10 0.36
11 2 0.07
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAAATAT
Found at i:173339 original size:28 final size:28
Alignment explanation
Indices: 173299--173369 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
173289 TTATAAAAAG
173299 TAAAAATCAATAAAAATTAGAAAAAAAT-A
1 TAAAAAT-AATAAAAATT-GAAAAAAATCA
* *
173328 TAAAAA-ATATAAAAATTTATAAAAATCA
1 TAAAAATA-ATAAAAATTGAAAAAAATCA
173356 TAAAAATAATAAAA
1 TAAAAATAATAAAA
173370 TGCATCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 8 0.22
28 22 0.59
29 7 0.19
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (28 bp):
TAAAAATAATAAAAATTGAAAAAAATCA
Found at i:173358 original size:19 final size:17
Alignment explanation
Indices: 173321--173369 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
173311 AAAATTAGAA
173321 AAAAATATAAAAAATAT
1 AAAAATATAAAAAATAT
*
173338 AAAAATTTATAAAAATCAT
1 AAAAATATA-AAAAAT-AT
173357 AAAAATAATAAAA
1 AAAAAT-ATAAAA
173370 TGCATCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 8 0.30
18 6 0.22
19 11 0.41
20 2 0.07
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATATAAAAAATAT
Found at i:174002 original size:2 final size:2
Alignment explanation
Indices: 173997--174022 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
173987 AATCATAGAC
173997 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
174023 AAATGGAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:177770 original size:32 final size:34
Alignment explanation
Indices: 177724--177810 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 34
177714 TTTATAGAAC
* * *
177724 AAAAAAGAGTAAGAAAAAA-TAATAAAATA-AGAG
1 AAAAAA-AGAAAGAAAAAAGGAAGAAAATACAGAG
*
177757 AAAAAAAGAAAGAAAAAAGGAAGAAGATACAGAG
1 AAAAAAAGAAAGAAAAAAGGAAGAAAATACAGAG
177791 AAAAGAAAGAAAGAGAAAAA
1 AAAA-AAAGAAAGA-AAAAA
177811 AATGGGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
32 11 0.24
33 13 0.28
34 8 0.17
35 9 0.20
36 5 0.11
ACGTcount: A:0.74, C:0.01, G:0.20, T:0.06
Consensus pattern (34 bp):
AAAAAAAGAAAGAAAAAAGGAAGAAAATACAGAG
Found at i:182232 original size:2 final size:2
Alignment explanation
Indices: 182225--182251 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
182215 TGAATTGTAT
182225 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
182252 TAAATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:182688 original size:9 final size:9
Alignment explanation
Indices: 182655--182688 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
182645 CTTAAATTTT
182655 AAAATTAAA
1 AAAATTAAA
*
182664 AAAAATAATA
1 AAAATTAA-A
182674 AAAATTAAA
1 AAAATTAAA
182683 AAAATT
1 AAAATT
182689 GAATTCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATTAAA
Found at i:193641 original size:21 final size:23
Alignment explanation
Indices: 193601--193645 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
193591 AATTTAACAA
193601 TTTTAATTTTTAAAAGTATTTTT
1 TTTTAATTTTTAAAAGTATTTTT
*
193624 TTTTAA-TTTTAATA-TATTTTT
1 TTTTAATTTTTAAAAGTATTTTT
193645 T
1 T
193646 AAAATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 7 0.33
23 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTAATTTTTAAAAGTATTTTT
Found at i:195453 original size:7 final size:7
Alignment explanation
Indices: 195443--195550 Score: 147
Period size: 7 Copynumber: 16.1 Consensus size: 7
195433 NNNNNTTCCC
*
195443 CCTTCCT
1 CCTTTCT
195450 CCTTTCT
1 CCTTTCT
195457 CCTTTCT
1 CCTTTCT
195464 CCTTTCT
1 CCTTTCT
195471 CCTTTCT
1 CCTTTCT
195478 CCTTTC-
1 CCTTTCT
195484 CC-TTCT
1 CCTTTCT
195490 CC-TTCT
1 CCTTTCT
195496 CC-TTCT
1 CCTTTCT
195502 CC-TTCT
1 CCTTTCT
195508 CCCTTTCT
1 -CCTTTCT
195516 CCTTTCT
1 CCTTTCT
*
195523 CCTTTCC
1 CCTTTCT
195530 CCTTTCT
1 CCTTTCT
195537 CCTTTC-
1 CCTTTCT
195543 CCTTTCT
1 CCTTTCT
195550 C
1 C
195551 GTTTTCAATT
Statistics
Matches: 94, Mismatches: 3, Indels: 8
0.90 0.03 0.08
Matches are distributed among these distances:
5 3 0.03
6 26 0.28
7 61 0.65
8 4 0.04
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (7 bp):
CCTTTCT
Found at i:198001 original size:32 final size:33
Alignment explanation
Indices: 197952--198023 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
197942 AGTTTTCTTG
197952 AAATATTTTCAGGAAATTTG-T-CAAACA-ATAAA
1 AAATATTTTCAGGAAA-TTGATCCAAACATA-AAA
*
197984 AAATATTTTACA-TAAATTGATCCAAACATAAAA
1 AAATATTTT-CAGGAAATTGATCCAAACATAAAA
198017 AAATATT
1 AAATATT
198024 AAATTTTCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
31 3 0.09
32 13 0.37
33 18 0.51
34 1 0.03
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.32
Consensus pattern (33 bp):
AAATATTTTCAGGAAATTGATCCAAACATAAAA
Found at i:209954 original size:26 final size:24
Alignment explanation
Indices: 209909--209956 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
209899 AGAGAAATGT
*
209909 AAATGTGATATATGAAATTATGAG
1 AAATGTGATATAAGAAATTATGAG
*
209933 AAATGATGAATATAAGAGATTATG
1 AAATG-TG-ATATAAGAAATTATG
209957 TCCATGTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 2 0.10
26 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (24 bp):
AAATGTGATATAAGAAATTATGAG
Found at i:210051 original size:23 final size:21
Alignment explanation
Indices: 210019--210168 Score: 84
Period size: 23 Copynumber: 6.5 Consensus size: 21
210009 ACGCTAGCGC
*
210019 GCTTATTGTTTAGCACTGTGTGT
1 GCTTACTGTTT-GCACT-TGTGT
210042 GCTTACTGTTTTGCACTTCGTGT
1 GCTTACTG-TTTGCACTT-GTGT
*
210065 GCTTACTGTTTCGCACCTCGTGT
1 GCTTACTGTTT-GCA-CTTGTGT
* * *
210088 GCCTACTGATTTGCGCTATGTGC
1 GCTTACTG-TTTGCACT-TGTGT
* * * *
210111 GCCTAGTGATTGTACTGTGTGT
1 GCTTACTGTTTGCACT-TGTGT
*
210133 GCTTATTGTTTCCCCAGCACTTGTGT
1 GCTTACTGTTT-----GCACTTGTGT
210159 GCTTACTGTT
1 GCTTACTGTT
210169 AAGTACTTCG
Statistics
Matches: 99, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
22 23 0.23
23 50 0.51
24 8 0.08
26 14 0.14
27 4 0.04
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.43
Consensus pattern (21 bp):
GCTTACTGTTTGCACTTGTGT
Found at i:212160 original size:19 final size:19
Alignment explanation
Indices: 212128--212166 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
212118 TTTTTATGAA
*
212128 TTTTTCATATATTTTAAAT
1 TTTTTCATAAATTTTAAAT
*
212147 TTTTTTATAAATTTTAAAT
1 TTTTTCATAAATTTTAAAT
212166 T
1 T
212167 AATTATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTCATAAATTTTAAAT
Found at i:214922 original size:24 final size:24
Alignment explanation
Indices: 214894--214948 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
214884 ATAAATTGAA
*
214894 TAAAAATACATTAAAAT-ATTAATT
1 TAAAAATACA-AAAAATAATTAATT
*
214918 TAAAAATATAAAAAATAATTAATT
1 TAAAAATACAAAAAATAATTAATT
*
214942 TATAAAT
1 TAAAAAT
214949 TAATATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAAAATACAAAAAATAATTAATT
Found at i:214996 original size:17 final size:18
Alignment explanation
Indices: 214974--215007 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
214964 GTTAAATTAT
*
214974 TTTTTATATTT-TAAATA
1 TTTTTAAATTTCTAAATA
214991 TTTTTAAATTTCTAAAT
1 TTTTTAAATTTCTAAAT
215008 TTTAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTAAATTTCTAAATA
Found at i:216042 original size:20 final size:19
Alignment explanation
Indices: 216017--216079 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 19
216007 AATTTAAAAA
216017 AAAAATCAATAATAATTTTT
1 AAAAATCAA-AATAATTTTT
*
216037 AAAAATTGAAAATAA-TTTT
1 AAAAA-TCAAAATAATTTTT
*
216056 -AAAATCTAAAAT-ATTTAT
1 AAAAATC-AAAATAATTTTT
216074 AAAAAT
1 AAAAAT
216080 TCTAAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.06
18 12 0.33
19 9 0.25
20 10 0.28
21 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAATCAAAATAATTTTT
Found at i:216085 original size:20 final size:20
Alignment explanation
Indices: 216027--216085 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
216017 AAAAATCAAT
*
216027 AATAATTTTTAAAAATT-GAA
1 AATAA-TTTTAAAAATTCTAA
216047 AATAATTTT-AAAA-TCTAA
1 AATAATTTTAAAAATTCTAA
216065 AAT-ATTTATAAAAATTCTAA
1 AATAATTT-TAAAAATTCTAA
216085 A
1 A
216086 TTTTGTAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.15
18 10 0.29
19 8 0.24
20 11 0.32
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (20 bp):
AATAATTTTAAAAATTCTAA
Found at i:216147 original size:20 final size:21
Alignment explanation
Indices: 216097--216137 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
216087 TTTGTAGTTC
*
216097 TAAAAAAAT-TATAAAATTTT
1 TAAAAATATATATAAAATTTT
216117 TAAAAATATATATAAAATTTT
1 TAAAAATATATATAAAATTTT
216138 GAATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAATATATATAAAATTTT
Found at i:219223 original size:67 final size:59
Alignment explanation
Indices: 219126--219274 Score: 167
Period size: 67 Copynumber: 2.4 Consensus size: 59
219116 TTTATATTCT
*
219126 TAAA-AAAAA-AAAAAAAAAATAATATTATTTTACACTTATTTATTTATATTAATATAATAATGA
1 TAAATAAAAATAAAAAAAAAATAATATTATTTT--A--TATTTATTTATATT--TATAAAAAT-A
219189 A
59 A
* *
219190 TAAATAAATAATAAAATAAAATTAATATTATTTTATATTTATTTATATTTATAAAAATAA
1 TAAATAAA-AATAAAAAAAAAATAATATTATTTTATATTTATTTATATTTATAAAAATAA
*
219250 TAAATAAAAATAATAAGAAAAATAA
1 TAAATAAAAATAA-AAAAAAAATAA
219275 AATTGGGTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
59 5 0.07
60 19 0.25
61 8 0.11
63 14 0.18
64 4 0.05
65 4 0.05
66 2 0.03
67 20 0.26
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (59 bp):
TAAATAAAAATAAAAAAAAAATAATATTATTTTATATTTATTTATATTTATAAAAATAA
Found at i:219258 original size:13 final size:12
Alignment explanation
Indices: 219240--219274 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
219230 ATTTATATTT
219240 ATAAAAATAATAA
1 ATAAAAATAAT-A
219253 ATAAAAATAATA
1 ATAAAAATAATA
*
219265 AGAAAAATAA
1 ATAAAAATAA
219275 AATTGGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:230804 original size:31 final size:31
Alignment explanation
Indices: 230735--230809 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
230725 ATTTTATCCA
* *
230735 AGGTCATTTAATTATTAGCAAGTTTATATTT
1 AGGTCATTAAATTATTAGAAAGTTTATATTT
* * *
230766 TGCTCATTAAATTATTTA-AAAGTTTTTATTT
1 AGGTCATTAAATTA-TTAGAAAGTTTATATTT
*
230797 AGGTCATTGAATT
1 AGGTCATTAAATT
230810 GTTAAATTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (31 bp):
AGGTCATTAAATTATTAGAAAGTTTATATTT
Found at i:272137 original size:23 final size:24
Alignment explanation
Indices: 272094--272145 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
272084 AGTAAGATTT
272094 TGAATTATTAATAAAAAACAATAA
1 TGAATTATTAATAAAAAACAATAA
272118 TGAATTATTAAT-AAAAACAATAA
1 TGAATTATTAATAAAAAACAATAA
272141 T-AATT
1 TGAATT
272146 TTTTTAGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 4 0.14
23 12 0.43
24 12 0.43
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (24 bp):
TGAATTATTAATAAAAAACAATAA
Found at i:274033 original size:19 final size:19
Alignment explanation
Indices: 273995--274040 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
273985 TAGTATATTT
*
273995 TTTAAAGTTTATGAATTAA
1 TTTAAAGTTTATGAAATAA
274014 TTTAAAGTTTA-GATAATAA
1 TTTAAAGTTTATGA-AATAA
*
274033 TTTGAAGT
1 TTTAAAGT
274041 AAAATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (19 bp):
TTTAAAGTTTATGAAATAA
Found at i:275850 original size:22 final size:21
Alignment explanation
Indices: 275822--275863 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
275812 ATATTATAAT
275822 AATATTATAATATAAAATAAAA
1 AATATTATAATA-AAAATAAAA
*
275844 AATATTATACTAAAAATAAA
1 AATATTATAATAAAAATAAA
275864 CATCCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AATATTATAATAAAAATAAAA
Found at i:276685 original size:17 final size:17
Alignment explanation
Indices: 276655--276692 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
276645 GTGTGAAATT
276655 TAATCATTTTATTAAAA
1 TAATCATTTTATTAAAA
*
276672 TAAT-ATTTTAATTAAGA
1 TAATCATTTT-ATTAAAA
276689 TAAT
1 TAAT
276693 TTTCATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TAATCATTTTATTAAAA
Found at i:288644 original size:3 final size:3
Alignment explanation
Indices: 288636--288671 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
288626 ACAAGTACTT
288636 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
288672 AAACTTATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:293914 original size:9 final size:9
Alignment explanation
Indices: 293898--293927 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
293888 AGTTGATTCG
293898 AATAACTCA
1 AATAACTCA
*
293907 ATTAACTCA
1 AATAACTCA
293916 AATAACTCA
1 AATAACTCA
293925 AAT
1 AAT
293928 TATTTAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (9 bp):
AATAACTCA
Found at i:300670 original size:5 final size:6
Alignment explanation
Indices: 300655--300679 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
300645 CAAAGCTTGA
300655 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
300680 GACCGGCGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:317076 original size:11 final size:10
Alignment explanation
Indices: 317052--317077 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
317042 AAAGGTTGAC
317052 AAAAATCTTT
1 AAAAATCTTT
317062 AAAAATCTTT
1 AAAAATCTTT
317072 AAAAAT
1 AAAAAT
317078 AATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAATCTTT
Found at i:317171 original size:24 final size:24
Alignment explanation
Indices: 317101--317191 Score: 76
Period size: 24 Copynumber: 3.7 Consensus size: 24
317091 TAAAATTTTG
317101 TAAAAATTATTAAAATATTAAAAACAT
1 TAAAAATTATTAAAA-A-TAAAAA-AT
* ****
317128 TAAAAATTGTTATTTTTAAAAAAT
1 TAAAAATTATTAAAAATAAAAAAT
**
317152 TAAAAATTATTAAAAATAAAATTT
1 TAAAAATTATTAAAAATAAAAAAT
317176 GTAAAAA-TATTAAAAA
1 -TAAAAATTATTAAAAA
317192 AAAGTGTTCT
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
24 28 0.55
25 12 0.24
27 11 0.22
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (24 bp):
TAAAAATTATTAAAAATAAAAAAT
Found at i:317188 original size:34 final size:34
Alignment explanation
Indices: 317112--317191 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
317102 AAAAATTATT
*** *
317112 AAAATATTAAAAACATTAAAAATTGTTATTTTTA
1 AAAATATTAAAAACATTAAAAATTAAAATTTGTA
*
317146 AAAA-ATTAAAAATTATTAAAAA-TAAAATTTGTA
1 AAAATATTAAAAA-CATTAAAAATTAAAATTTGTA
317179 AAAATATTAAAAA
1 AAAATATTAAAAA
317192 AAAGTGTTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
33 19 0.49
34 20 0.51
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (34 bp):
AAAATATTAAAAACATTAAAAATTAAAATTTGTA
Found at i:318023 original size:18 final size:19
Alignment explanation
Indices: 317975--318024 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
317965 TATTATTTAA
317975 AAATTTAGATATTGCGTTAG
1 AAATTTA-ATATTGCGTTAG
* *
317995 AAATATTAATATT-TGTTAT
1 AAAT-TTAATATTGCGTTAG
318014 AAATTTAATAT
1 AAATTTAATAT
318025 CATAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 7 0.26
19 8 0.30
20 9 0.33
21 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (19 bp):
AAATTTAATATTGCGTTAG
Found at i:319208 original size:16 final size:16
Alignment explanation
Indices: 319187--319217 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
319177 TCTCTCTCCC
*
319187 AAATCAATTTATTTTA
1 AAATCAATCTATTTTA
319203 AAATCAATCTATTTT
1 AAATCAATCTATTTT
319218 GCCAAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATCAATCTATTTTA
Found at i:319720 original size:22 final size:22
Alignment explanation
Indices: 319695--319738 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
319685 TGACTACTGA
* *
319695 TTAAGATAAACACATTTCAATT
1 TTAAAATAAACACATCTCAATT
*
319717 TTAAAATAATCACATCTCAATT
1 TTAAAATAAACACATCTCAATT
319739 GATTTATAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.36
Consensus pattern (22 bp):
TTAAAATAAACACATCTCAATT
Found at i:320864 original size:96 final size:96
Alignment explanation
Indices: 320680--320871 Score: 255
Period size: 96 Copynumber: 2.0 Consensus size: 96
320670 TTTTTGGGAA
* * * *
320680 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAATATTTTA
1 AAGGATATTCGATTATCTCGATTAGAAGAAAAATTGCACATAGTAAGTTAAGGCACAATATTTTA
*
320745 GAATCGAAGATAATGAAACATTGCCTCGATT
66 GAATCGAAGATAATAAAACATTGCCTCGATT
* * *
320776 AAGGGTATTCGATTATTTCGATTAGAAGAAAAATTGCACATAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTAGAAGAAAAATTGCACATAGTAAGTTAAGGCACAATATTTTA
*
320840 GAAACTCGAA-ATAA-AATAATATTGCCTCGATT
66 G-AA-TCGAAGATAATAA-AACATTGCCTCGATT
320872 TTAAAGTTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
95 7 0.08
96 72 0.86
97 5 0.06
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTAGAAGAAAAATTGCACATAGTAAGTTAAGGCACAATATTTTA
GAATCGAAGATAATAAAACATTGCCTCGATT
Found at i:321167 original size:29 final size:30
Alignment explanation
Indices: 321112--321328 Score: 202
Period size: 29 Copynumber: 7.3 Consensus size: 30
321102 GCAAAATGGT
321112 AATTTTTGGAAAG-TTCGAGGGTAAAAATGA
1 AATTTTT-GAAAGTTTCGAGGGTAAAAATGA
* *
321142 AAATTTTGAAAGTTTTGAGGGTAAAAAATGGA
1 AATTTTTGAAAGTTTCGAGGGT-AAAAAT-GA
* * *
321174 ACTTTTTG-AAGTTTTG-GGGTAAAAATGG
1 AATTTTTGAAAGTTTCGAGGGTAAAAATGA
* *
321202 AATTTTTGGAAG-TTCGTGGGTAAAAATGA
1 AATTTTTGAAAGTTTCGAGGGTAAAAATGA
* * *
321231 AATTTTTCAAAGTTTCGA-GATCAAAAATGG
1 AATTTTTGAAAGTTTCGAGGGT-AAAAATGA
321261 AATTTTTGAAAGTTTCGA-GGTCAAAAAT-A
1 AATTTTTGAAAGTTTCGAGGGT-AAAAATGA
*
321290 GAA-TTTTGGAAGTTT--AGTGGTAAAAATGA
1 -AATTTTTGAAAGTTTCGAG-GGTAAAAATGA
321319 AATTTTTGAA
1 AATTTTTGAA
321329 TAATTTAGGG
Statistics
Matches: 157, Mismatches: 18, Indels: 25
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.01
28 19 0.12
29 58 0.37
30 57 0.36
31 14 0.09
32 8 0.05
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.35
Consensus pattern (30 bp):
AATTTTTGAAAGTTTCGAGGGTAAAAATGA
Found at i:321302 original size:88 final size:89
Alignment explanation
Indices: 321112--321325 Score: 274
Period size: 88 Copynumber: 2.4 Consensus size: 89
321102 GCAAAATGGT
* * * * *
321112 AATTTTTGGAAAGTTCGAGGGTAAAAATGAAAATTTTGAAAGTTTTGAGGGTAAAAAATGGAACT
1 AATTTTTGG-AAGTTCGTGGGTAAAAATGAAATTTTTCAAAGTTTCGAGGATAAAAAATGGAACT
* * *
321177 TTTTGAAGTTTTGGGGTAAAAATGG
65 TTTTGAAGTTTCGAGGTAAAAATAG
*
321202 AATTTTTGGAAGTTCGTGGGTAAAAATGAAATTTTTCAAAGTTTCGA-GATCAAAAATGGAA-TT
1 AATTTTTGGAAGTTCGTGGGTAAAAATGAAATTTTTCAAAGTTTCGAGGATAAAAAATGGAACTT
321265 TTTGAAAGTTTCGAGGTCAAAAATAG
66 TTTG-AAGTTTCGAGGT-AAAAATAG
*
321291 AA-TTTTGGAAGTTTAGT-GGTAAAAATGAAATTTTT
1 AATTTTTGGAAG-TTCGTGGGTAAAAATGAAATTTTT
321326 GAATAATTTA
Statistics
Matches: 111, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
87 6 0.05
88 49 0.44
89 47 0.42
90 9 0.08
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (89 bp):
AATTTTTGGAAGTTCGTGGGTAAAAATGAAATTTTTCAAAGTTTCGAGGATAAAAAATGGAACTT
TTTGAAGTTTCGAGGTAAAAATAG
Found at i:322377 original size:15 final size:15
Alignment explanation
Indices: 322326--322381 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
322316 GTAAGGCAAT
*
322326 TATTATTATTAAAAAC
1 TATTATTATT-AATAC
*
322342 GTCATTATTATT-ATAGA
1 -T-ATTATTATTAATA-C
322359 TATTATTATTAATAC
1 TATTATTATTAATAC
322374 TATTATTA
1 TATTATTA
322382 CATACGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 17 0.52
16 6 0.18
17 1 0.03
18 9 0.27
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (15 bp):
TATTATTATTAATAC
Found at i:323067 original size:17 final size:17
Alignment explanation
Indices: 323033--323120 Score: 106
Period size: 17 Copynumber: 5.0 Consensus size: 17
323023 TATAATAAGT
*
323033 TTTAAATATAAATCTAAA
1 TTTAAA-ATAAATTTAAA
*
323051 TTTAAATTAAATTTAAA
1 TTTAAAATAAATTTAAA
323068 TTTTAAAATAAATTTAAA
1 -TTTAAAATAAATTTAAA
*
323086 TTTAAAATCAATTT-AA
1 TTTAAAATAAATTTAAA
323102 TCTTAAAATAAATCTTAAA
1 T-TTAAAATAAAT-TTAAA
323121 ATGAGTTTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
16 3 0.05
17 32 0.52
18 24 0.39
19 2 0.03
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:323074 original size:7 final size:6
Alignment explanation
Indices: 323033--323091 Score: 68
Period size: 6 Copynumber: 10.0 Consensus size: 6
323023 TATAATAAGT
* * *
323033 TTTAAA TATAAA TCTAAA TTTAAA -TTAAA TTTAAA TTTTAAA -ATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA
323080 TTTAAA TTTAAA
1 TTTAAA TTTAAA
323092 ATCAATTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 9 0.20
6 30 0.67
7 6 0.13
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:324117 original size:46 final size:47
Alignment explanation
Indices: 324047--324136 Score: 137
Period size: 46 Copynumber: 1.9 Consensus size: 47
324037 ATTCGAATAA
* *
324047 AAAAATGTAAAACTACGTCGTTTTGATAAATGTTTACCTATTAAGTT
1 AAAAATGTAAAACTACGTCATTTTGATAAATGATTACCTATTAAGTT
* *
324094 AAAAA-GTAAAATTATGTCATTTTGATAAATGATTACCTATTAA
1 AAAAATGTAAAACTACGTCATTTTGATAAATGATTACCTATTAA
324137 ACCATTATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 34 0.87
47 5 0.13
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (47 bp):
AAAAATGTAAAACTACGTCATTTTGATAAATGATTACCTATTAAGTT
Found at i:329802 original size:30 final size:30
Alignment explanation
Indices: 329768--329826 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
329758 CTTAACAAGC
* *
329768 AAATGTCTCTAAAATAGTAACAAAATTAAT
1 AAATGCCTCTAAAATAATAACAAAATTAAT
329798 AAATGCCTCTAAAATAATAACAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
329827 CAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAT
Found at i:330000 original size:11 final size:11
Alignment explanation
Indices: 329984--330009 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
329974 TTTTGTCCTT
329984 AAAACACTAAG
1 AAAACACTAAG
329995 AAAACACTAAG
1 AAAACACTAAG
330006 AAAA
1 AAAA
330010 AATGCCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.15, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAACACTAAG
Found at i:338496 original size:22 final size:23
Alignment explanation
Indices: 338451--338499 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
338441 TTAGCGCTCG
* *
338451 CTCCGTTTAGCACTTTGTGTGCT
1 CTCCATTTAGCACGTTGTGTGCT
338474 CTCCATTTAGCACGTT-TGTGCT
1 CTCCATTTAGCACGTTGTGTGCT
338496 CTCC
1 CTCC
338500 GTTCATTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.10, C:0.31, G:0.18, T:0.41
Consensus pattern (23 bp):
CTCCATTTAGCACGTTGTGTGCT
Found at i:339422 original size:46 final size:47
Alignment explanation
Indices: 339372--339460 Score: 171
Period size: 46 Copynumber: 1.9 Consensus size: 47
339362 TTCAAATCTC
339372 AATATAAAAAAACCGATCAAGTTCAAATATTAACTTA-AAAAATCCT
1 AATATAAAAAAACCGATCAAGTTCAAATATTAACTTAGAAAAATCCT
339418 AATATAAAAAAACCGATCAAGTTCAAATATTAACTTAGAAAAA
1 AATATAAAAAAACCGATCAAGTTCAAATATTAACTTAGAAAAA
339461 AGATTCAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 37 0.88
47 5 0.12
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.25
Consensus pattern (47 bp):
AATATAAAAAAACCGATCAAGTTCAAATATTAACTTAGAAAAATCCT
Found at i:344199 original size:25 final size:24
Alignment explanation
Indices: 344144--344190 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
344134 TAATCACGTC
*
344144 ATTTTTTAATAATAAAAATGAATG
1 ATTTTTTAATAATAAAAATCAATG
344168 ATATTTTTAATAA-AAAAATCAAT
1 AT-TTTTTAATAATAAAAATCAAT
344191 TTACTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (24 bp):
ATTTTTTAATAATAAAAATCAATG
Found at i:344247 original size:31 final size:30
Alignment explanation
Indices: 344176--344247 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 30
344166 TGATATTTTT
*
344176 AATAAAAAAATCAATTTACTTTTTAATCTA
1 AATAAAAAAATCAATTAACTTTTTAATCTA
* * * * *
344206 ACATACAAAAATTAATTAATTATTTTTATTTA
1 A-ATAAAAAAATCAATTAACT-TTTTAATCTA
344238 AATAAAAAAA
1 AATAAAAAAA
344248 CAAAATACAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
30 1 0.03
31 23 0.70
32 9 0.27
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (30 bp):
AATAAAAAAATCAATTAACTTTTTAATCTA
Found at i:344794 original size:8 final size:8
Alignment explanation
Indices: 344781--344818 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
344771 GTAGTTTATC
344781 AAATATTA
1 AAATATTA
344789 AAATATTA
1 AAATATTA
344797 AAATA-TA
1 AAATATTA
344804 AAAT-TCTA
1 AAATAT-TA
344812 AAATATT
1 AAATATT
344819 TATAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 6 0.22
8 20 0.74
9 1 0.04
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (8 bp):
AAATATTA
Found at i:345641 original size:20 final size:24
Alignment explanation
Indices: 345601--345662 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 24
345591 TCTAAAAAAC
* *
345601 TAAAAATATTAAAATTCATAATTTATTT
1 TAAAAA-ATTATAATT-ATAA-TTA-TA
345629 TAAAAAATTATAATTATAATTATA
1 TAAAAAATTATAATTATAATTATA
345653 TAAAAAATTA
1 TAAAAAATTA
345663 AAAATCATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 11 0.34
25 3 0.09
26 4 0.12
27 8 0.25
28 6 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAAAATTATAATTATAATTATA
Found at i:347512 original size:34 final size:34
Alignment explanation
Indices: 347469--347539 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
347459 AGAAGCAAAC
347469 ATATTCCATATCCTTTTTCTTCAGTTCAGTGGGA
1 ATATTCCATATCCTTTTTCTTCAGTTCAGTGGGA
347503 ATATTCCATATCCTTTTTCTTCAGTTCAGTGGGA
1 ATATTCCATATCCTTTTTCTTCAGTTCAGTGGGA
347537 ATA
1 ATA
347540 CTCCTTTCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.44
Consensus pattern (34 bp):
ATATTCCATATCCTTTTTCTTCAGTTCAGTGGGA
Found at i:347546 original size:28 final size:30
Alignment explanation
Indices: 347478--347546 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 30
347468 CATATTCCAT
347478 ATCCTTTTTCTTCAGTTCAGTGGGAATATTCC
1 ATCCTTTTTCTTCAGTTCAGTGGGAATA-T-C
347510 ATATCCTTTTTCTTCAGTTCAGTGGGAATA-C
1 --ATCCTTTTTCTTCAGTTCAGTGGGAATATC
347541 -TCCTTT
1 ATCCTTT
347547 CACTTTCTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
28 6 0.17
31 1 0.03
34 28 0.80
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (30 bp):
ATCCTTTTTCTTCAGTTCAGTGGGAATATC
Found at i:355309 original size:2 final size:2
Alignment explanation
Indices: 355302--355332 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
355292 AAATAAATAA
*
355302 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
355333 ATTTAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:357543 original size:31 final size:31
Alignment explanation
Indices: 357480--357543 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
357470 TGACCACTAG
**
357480 TTATATATTTTTAAATTTCTATTTTTTGAGA
1 TTATATATTTTTAAATTTCTATTGATTGAGA
357511 TTATATATCTTTTAAATTT-TAATTGATT-AGA
1 TTATATAT-TTTTAAATTTCT-ATTGATTGAGA
357542 TT
1 TT
357544 CTAATATCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.59
Consensus pattern (31 bp):
TTATATATTTTTAAATTTCTATTGATTGAGA
Found at i:358335 original size:37 final size:37
Alignment explanation
Indices: 358285--358359 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
358275 CAGAACGAGG
358285 TTAGTTTTAGACTCCAATCCCTAATAATTCACTAAAT
1 TTAGTTTTAGACTCCAATCCCTAATAATTCACTAAAT
358322 TTAGTTTTAGACTCCAATCCCTAATAATTCACTAAAT
1 TTAGTTTTAGACTCCAATCCCTAATAATTCACTAAAT
358359 T
1 T
358360 AAAATTGTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (37 bp):
TTAGTTTTAGACTCCAATCCCTAATAATTCACTAAAT
Found at i:370553 original size:2 final size:2
Alignment explanation
Indices: 370548--370576 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
370538 AAAATATTAA
370548 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
370577 AATGTAACAC
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:375593 original size:3 final size:3
Alignment explanation
Indices: 375585--375611 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
375575 CCGCCAATGA
375585 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
375612 TAGATTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:379005 original size:2 final size:2
Alignment explanation
Indices: 378993--379027 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
378983 GTAGAAAAGC
378993 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
379028 TTTCTGTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:380131 original size:12 final size:12
Alignment explanation
Indices: 380114--380151 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
380104 ACATTGTTCC
380114 CATCCTCGTCCT
1 CATCCTCGTCCT
380126 CATCCTCGTCCT
1 CATCCTCGTCCT
380138 CATCCTCGTCCT
1 CATCCTCGTCCT
380150 CA
1 CA
380152 ACCAACTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.11, C:0.50, G:0.08, T:0.32
Consensus pattern (12 bp):
CATCCTCGTCCT
Done.