Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 95 of 290
Found at i:29131568 original size:147 final size:148
Alignment explanation
Indices: 29131089--29131819 Score: 938
Period size: 147 Copynumber: 4.9 Consensus size: 148
29131079 ACGTGAGCCA
* * *
29131089 AGGCTCAACTCACCTT-TCGCAATATGAGTTGATTTTTTTTTG-AAAGTAGAATTTGAAAATACC
1 AGGCTCAACTCA-CTTCTCGCAATATGAGTTGA-TTTTTTTTGAAAAGCAGAAATTGAAATTACC
* * * * *
29131152 TCGGCGTGCCCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATT
64 TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTG-AAAAACAAAAATT
*
29131217 GAAATTACCTCAGCGTGTCTTG
127 GAAATTACCTCAGCGTGTCCTG
* **** *
29131239 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGGAATTGAA
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT---TTTGA-AAA--G--CAGAAATTGAA
* * * *
29131304 AATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGC
58 ATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT-TTGAAAAAC
* * ** *
29131369 AGAAATTGAAAATACCTCAATGTGTCTTG
120 AAAAATTGAAATTACCTCAGCGTGTCCTG
* *
29131398 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTCTTGAAAAGCAGAAATTGAAATTACCTC
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAGCAGAAATTGAAATTACCTC
* *
29131462 AGCGTGTCCTGAGGCCCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAA
66 AGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAA
29131527 TTACCTCAGCGTGTCCTG
131 TTACCTCAGCGTGTCCTG
* *
29131545 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTGACAA-CAGAAATTGAAATTACCT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTTTGAAAAGCAGAAATTGAAATTACCT
* *
29131609 CAGCGTCTCATGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAC-AAAATTGAA
65 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAA
29131673 ATTACCTCAGCGTGTCCTG
130 ATTACCTCAGCGTGTCCTG
* *
29131692 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTATTGACAAA--AG-AATTGAAATTACCT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGA-AAAGCAGAAATTGAAATTACCT
*
29131754 CAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTGAA
65 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAA
29131819 A
130 A
29131820 AAGGCTTAAC
Statistics
Matches: 518, Mismatches: 47, Indels: 36
0.86 0.08 0.06
Matches are distributed among these distances:
145 66 0.13
146 21 0.04
147 124 0.24
148 71 0.14
149 17 0.03
150 84 0.16
152 1 0.00
154 6 0.01
155 1 0.00
156 1 0.00
158 57 0.11
159 66 0.13
160 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (148 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAGCAGAAATTGAAATTACCTC
AGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAA
TTACCTCAGCGTGTCCTG
Found at i:29144747 original size:3 final size:3
Alignment explanation
Indices: 29144739--29144775 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
29144729 ACTAATGTAC
29144739 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29144776 TTGAAATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29145266 original size:11 final size:12
Alignment explanation
Indices: 29145252--29145289 Score: 62
Period size: 11 Copynumber: 3.3 Consensus size: 12
29145242 AAGAAAAAAA
29145252 GAAGAGAG-AGG
1 GAAGAGAGAAGG
29145263 GAAGAGAGAAGG
1 GAAGAGAGAAGG
29145275 G-AGAGAGAAGG
1 GAAGAGAGAAGG
29145286 GAAG
1 GAAG
29145290 GGGAAGGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:29145279 original size:22 final size:22
Alignment explanation
Indices: 29145254--29145297 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29145244 GAAAAAAAGA
29145254 AGAGAG-AGGGAAGAGAGAAGGG
1 AGAGAGAAGGGAAG-GAGAAGGG
*
29145276 AGAGAGAAGGGAAGGGGAAGGG
1 AGAGAGAAGGGAAGGAGAAGGG
29145298 GAATCCGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (22 bp):
AGAGAGAAGGGAAGGAGAAGGG
Found at i:29145401 original size:8 final size:8
Alignment explanation
Indices: 29145390--29145432 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
29145380 AAAAAATATT
29145390 TTTTTTTA
1 TTTTTTTA
29145398 TTTTTTTA
1 TTTTTTTA
* *
29145406 TGTTTATA
1 TTTTTTTA
29145414 CTTTTTTGTA
1 -TTTTTT-TA
29145424 TTTTTTTA
1 TTTTTTTA
29145432 T
1 T
29145433 ATATATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 17 0.59
9 10 0.34
10 2 0.07
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (8 bp):
TTTTTTTA
Found at i:29145850 original size:35 final size:35
Alignment explanation
Indices: 29145805--29145873 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
29145795 GGGTGTGTGA
29145805 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
29145840 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
29145874 AGAGGCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.51, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:29146786 original size:13 final size:13
Alignment explanation
Indices: 29146768--29146794 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29146758 TTAATTTACA
29146768 TTTGTCATTATAC
1 TTTGTCATTATAC
29146781 TTTGTCATTATAC
1 TTTGTCATTATAC
29146794 T
1 T
29146795 CTGAGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (13 bp):
TTTGTCATTATAC
Found at i:29148906 original size:41 final size:41
Alignment explanation
Indices: 29148831--29148908 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
29148821 ATAGTGATAT
*
29148831 TCGGGCTTTAAGCCTAGCAAGGATTGTGCTGGTGAATGTAA
1 TCGGGCTTTAAGCCTAGCAAGGATTGTGCCGGTGAATGTAA
* * *
29148872 TCGGGCTTTATGCCTAGC-AGGCTTATTGCCGGTGAAT
1 TCGGGCTTTAAGCCTAGCAAGGATT-GTGCCGGTGAAT
29148909 ATAAAATCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 5 0.16
41 27 0.84
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.31
Consensus pattern (41 bp):
TCGGGCTTTAAGCCTAGCAAGGATTGTGCCGGTGAATGTAA
Found at i:29150846 original size:17 final size:18
Alignment explanation
Indices: 29150824--29150864 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29150814 AAAATAAAAC
* *
29150824 ATTAAAAA-TATGTTTTA
1 ATTAAAAATTATCTTTAA
29150841 ATTAAAAATTATCTTTAA
1 ATTAAAAATTATCTTTAA
29150859 ATTAAA
1 ATTAAA
29150865 TAGAGAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTAAAAATTATCTTTAA
Found at i:29154288 original size:20 final size:20
Alignment explanation
Indices: 29154265--29154303 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29154255 CATGAAAAAA
*
29154265 GAGAAAATTCAAAAAATTAT
1 GAGAAAATTAAAAAAATTAT
29154285 GAGAAAATTAAAAAAATTA
1 GAGAAAATTAAAAAAATTA
29154304 ACAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (20 bp):
GAGAAAATTAAAAAAATTAT
Found at i:29160974 original size:18 final size:19
Alignment explanation
Indices: 29160951--29160986 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29160941 AACTTGGCAC
*
29160951 CATAA-TCATTTAATTTAA
1 CATAATTCAATTAATTTAA
29160969 CATAATTCAATTAATTTA
1 CATAATTCAATTAATTTA
29160987 CTAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (19 bp):
CATAATTCAATTAATTTAA
Found at i:29167053 original size:24 final size:24
Alignment explanation
Indices: 29167026--29167076 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
29167016 TGAAAAGCTT
* *
29167026 TAAACGTATAGACATGCGATGTGA
1 TAAACATATAGACATGCGATATGA
* * *
29167050 TAAATATATGGACATGTGATATGA
1 TAAACATATAGACATGCGATATGA
29167074 TAA
1 TAA
29167077 TTAAATTTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (24 bp):
TAAACATATAGACATGCGATATGA
Found at i:29173190 original size:27 final size:27
Alignment explanation
Indices: 29173160--29173237 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
29173150 GACTAATCGA
* *
29173160 GCCTTTCTCTGAGGCGCAAATGGTTGT
1 GCCTATCTCAGAGGCGCAAATGGTTGT
29173187 GCCTATCTCAGAGGCGCAAATGGTTGT
1 GCCTATCTCAGAGGCGCAAATGGTTGT
* * *
29173214 GCCTATCCCAGATGTGCAAATGGT
1 GCCTATCTCAGAGGCGCAAATGGT
29173238 GGGGCCCACA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (27 bp):
GCCTATCTCAGAGGCGCAAATGGTTGT
Found at i:29176679 original size:33 final size:33
Alignment explanation
Indices: 29176637--29176699 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
29176627 ATGAACTTGA
* *
29176637 GCCAGGAGGAGTGGAGTACGGCGATTGATATGG
1 GCCAGGAGGAGTGGAGTACGACGATAGATATGG
29176670 GCCAGGAGGAGTGGAGTACGACGATAGATA
1 GCCAGGAGGAGTGGAGTACGACGATAGATA
29176700 CAGGTCGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.13, G:0.43, T:0.16
Consensus pattern (33 bp):
GCCAGGAGGAGTGGAGTACGACGATAGATATGG
Found at i:29179218 original size:29 final size:30
Alignment explanation
Indices: 29179162--29179218 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
29179152 TAATACATAA
* * * *
29179162 AATAATATTATAATATATAACTATTATTTT
1 AATAATATTATAATAAAAAAATAGTATTTT
29179192 AATAA-ATTATAATAAAAAAATAGTATT
1 AATAATATTATAATAAAAAAATAGTATT
29179219 ATATGATCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (30 bp):
AATAATATTATAATAAAAAAATAGTATTTT
Found at i:29182884 original size:40 final size:40
Alignment explanation
Indices: 29182840--29182918 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
29182830 AAAACACACC
29182840 AATTTGGCACCTAGTGCCTCATCGGAT-AATTCGAAGTAAT
1 AATTTGGCACCTAGTGCCTCATCGGATGAA-TCGAAGTAAT
* * * *
29182880 AATTTGTCACCTAGTGTCTTATCGGCTGAATCGAAGTAA
1 AATTTGGCACCTAGTGCCTCATCGGATGAATCGAAGTAA
29182919 ATTGGCACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (40 bp):
AATTTGGCACCTAGTGCCTCATCGGATGAATCGAAGTAAT
Found at i:29184029 original size:20 final size:19
Alignment explanation
Indices: 29183995--29184033 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
29183985 ATTAATAAGC
29183995 AATACATATTTTATTATTA
1 AATACATATTTTATTATTA
*
29184014 AATATATATGTTTATTATTA
1 AATACATAT-TTTATTATTA
29184034 TTACACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
AATACATATTTTATTATTA
Found at i:29186160 original size:11 final size:11
Alignment explanation
Indices: 29186144--29186169 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29186134 CATGACGCAC
29186144 AAAATAAAACT
1 AAAATAAAACT
29186155 AAAATAAAACT
1 AAAATAAAACT
29186166 AAAA
1 AAAA
29186170 AGCGAAAGTT
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:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAACT
Found at i:29187669 original size:30 final size:31
Alignment explanation
Indices: 29187633--29187716 Score: 127
Period size: 30 Copynumber: 2.7 Consensus size: 31
29187623 TCAATCTCAG
29187633 CATATACTGGGCCGAAGCCTTTAT-ATTATT
1 CATATACTGGGCCGAAGCCTTTATCATTATT
*
29187663 CATATACTGGGCTGAAGCCTTT-TCATTATT
1 CATATACTGGGCCGAAGCCTTTATCATTATT
*
29187693 CATATCACTAGGCCGAAGCCTTTA
1 CATAT-ACTGGGCCGAAGCCTTTA
29187717 CTGCAACAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
29 1 0.02
30 32 0.67
31 15 0.31
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.35
Consensus pattern (31 bp):
CATATACTGGGCCGAAGCCTTTATCATTATT
Found at i:29188019 original size:24 final size:26
Alignment explanation
Indices: 29187935--29188030 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
29187925 CTCTTTTAAT
* * *
29187935 AACTAGGGCAAAAGCCCTTTTTGATA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
29187961 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
29187987 AACTGGGGC-AAAGCCCTTTTCGGT-
1 AACTGGGGCAAAAGCCCTTTTCGGTA
*
29188011 AACTGGGGC-ATAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
29188031 GCACTTCCTC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
24 19 0.29
25 15 0.23
26 32 0.48
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (26 bp):
AACTGGGGCAAAAGCCCTTTTCGGTA
Found at i:29188191 original size:25 final size:25
Alignment explanation
Indices: 29188163--29188210 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29188153 ATAATTAAAC
* **
29188163 CCTAGAGGTAAAATGGTCATTTTTA
1 CCTAGAGGCAAAACAGTCATTTTTA
*
29188188 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGAGGCAAAACAGTCATTTT
29188211 CATATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (25 bp):
CCTAGAGGCAAAACAGTCATTTTTA
Found at i:29195487 original size:6 final size:6
Alignment explanation
Indices: 29195427--29195496 Score: 54
Period size: 6 Copynumber: 11.2 Consensus size: 6
29195417 TTATAGTAAT
* *
29195427 AAAAG- AAAA-A AAAAGA CAAAAGCA AAACGA AACAGAA AGAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA -AAAAG-A AAAAGA AAAAG-A A-AAAGA AAAAGA
*
29195477 AAAAGA GAAAGA AAGAAGA A
1 AAAAGA AAAAGA AA-AAGA A
29195497 CCCACGGCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 8 0.15
6 22 0.42
7 18 0.35
8 4 0.08
ACGTcount: A:0.76, C:0.06, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:29198358 original size:16 final size:17
Alignment explanation
Indices: 29198332--29198363 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29198322 AAATTTTTAA
29198332 AAAAGAATAAAATAAAT
1 AAAAGAATAAAATAAAT
29198349 AAAA-AATAAAATAAA
1 AAAAGAATAAAATAAA
29198364 ATCTGATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAAGAATAAAATAAAT
Found at i:29201741 original size:33 final size:31
Alignment explanation
Indices: 29201670--29201756 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 31
29201660 AATCAGATAA
* *
29201670 ATGGGCCTACACACCCGTGTGGCTTGCTCGT
1 ATGGGCCCACACACCCGTGTGGCTTACTCGT
* *
29201701 ATAGGCCCACACACCCAGTTTGGTCTTACTCGT
1 ATGGGCCCACACACCC-GTGTGG-CTTACTCGT
* **
29201734 GTGGGCCCACACGTCCGTGTGGC
1 ATGGGCCCACACACCCGTGTGGC
29201757 CCATATGCAT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
31 15 0.33
32 10 0.22
33 20 0.44
ACGTcount: A:0.15, C:0.33, G:0.28, T:0.24
Consensus pattern (31 bp):
ATGGGCCCACACACCCGTGTGGCTTACTCGT
Found at i:29202386 original size:20 final size:20
Alignment explanation
Indices: 29202337--29202397 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
29202327 GTGAAAAGGG
29202337 AATTTTTG-AAGAACAATAA
1 AATTTTTGAAAGAACAATAA
** *
29202356 AATTTAGGAAAGAA-AGTCAA
1 AATTTTTGAAAGAACAAT-AA
*
29202376 AATTTTTGAAA-AAGAATAA
1 AATTTTTGAAAGAACAATAA
29202395 AAT
1 AAT
29202398 AAATAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.56, C:0.03, G:0.13, T:0.28
Consensus pattern (20 bp):
AATTTTTGAAAGAACAATAA
Found at i:29202411 original size:16 final size:17
Alignment explanation
Indices: 29202385--29202416 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29202375 AAATTTTTGA
29202385 AAAAGAATAAAATAAAT
1 AAAAGAATAAAATAAAT
29202402 AAAA-AATAAAATAAA
1 AAAAGAATAAAATAAA
29202417 ATTTGATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAAGAATAAAATAAAT
Found at i:29207230 original size:50 final size:50
Alignment explanation
Indices: 29207106--29207354 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
29207096 GATAATAACA
* * ** * *
29207106 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
29207157 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
29207207 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
29207257 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
29207312 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
29207355 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:29207284 original size:100 final size:104
Alignment explanation
Indices: 29207105--29207354 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
29207095 TGATAATAAC
**
29207105 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
29207170 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
29207207 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
29207270 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
29207312 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
29207355 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:29207470 original size:13 final size:13
Alignment explanation
Indices: 29207449--29207480 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
29207439 GCTTGGATCA
*
29207449 TCATCAAATAAAT
1 TCATAAAATAAAT
29207462 TCATAAAATAAAT
1 TCATAAAATAAAT
29207475 TCATAA
1 TCATAA
29207481 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:29207727 original size:30 final size:30
Alignment explanation
Indices: 29207692--29207749 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
29207682 CCTCGACTCT
*
29207692 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
29207722 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
29207750 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:29220684 original size:3 final size:3
Alignment explanation
Indices: 29220676--29220704 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29220666 AAAGAACACA
29220676 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
29220705 TGTAAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29221719 original size:20 final size:20
Alignment explanation
Indices: 29221694--29221731 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29221684 ACTTAGAAGG
29221694 ACTTCTATAC-ATACAAGTCC
1 ACTTCTAT-CGATACAAGTCC
29221714 ACTTCTATCGATACAAGT
1 ACTTCTATCGATACAAGT
29221732 TTGCTTCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (20 bp):
ACTTCTATCGATACAAGTCC
Found at i:29225613 original size:20 final size:20
Alignment explanation
Indices: 29225588--29225637 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
29225578 TGGCTTAAAA
29225588 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
29225608 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
29225625 GTGGTAGTGGATT
1 TTGGTAGTGGATT
29225638 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:29230251 original size:20 final size:20
Alignment explanation
Indices: 29230226--29230275 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
29230216 TGGCTTAAAA
29230226 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
29230246 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
29230263 GTGGTAGTGGATT
1 TTGGTAGTGGATT
29230276 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:29237922 original size:25 final size:25
Alignment explanation
Indices: 29237894--29237972 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
29237884 CTAATGGCCG
29237894 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
29237919 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
29237941 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
29237966 ATGTGAT
1 ATGTGAT
29237973 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:29237944 original size:47 final size:47
Alignment explanation
Indices: 29237878--29238300 Score: 665
Period size: 47 Copynumber: 9.1 Consensus size: 47
29237868 GAAATGATAG
29237878 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
29237925 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
29237972 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
29238019 TAAGGCCTAATAGCCGATGTGATGAATGTGAAA-TGTATATGTGT-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
29238064 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
29238111 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
29238158 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
29238205 TAAGGCCTAATGGCCGATGT--TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * * *
29238250 CAGGGCCGAGTGGCCAACGTGATGGATGCGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
29238297 TAAG
1 TAAG
29238301 TCTCGAAGGG
Statistics
Matches: 354, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
45 73 0.21
46 21 0.06
47 260 0.73
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:29238039 original size:94 final size:94
Alignment explanation
Indices: 29237878--29238300 Score: 656
Period size: 92 Copynumber: 4.5 Consensus size: 94
29237868 GAAATGATAG
* *
29237878 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
29237943 GTGATGAATGTGAAAGTGTATATATGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
*
29237972 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
*
29238037 GTGATGAATGTGAAA-TGTATATGTGT-A
66 GTGATGAATGTGAAAGTGTATATATGTGA
29238064 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
*
29238129 GTGATGAATGTGAAAGTGTATATATGTAA
66 GTGATGAATGTGAAAGTGTATATATGTGA
* *
29238158 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
29238223 GT--TGAATGTGAAAGTGTATATATGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * * * *
29238250 CAGGGCCGAGTGGCCAACGTGATGGATGCGAAAGTGCATAAATGTGATAAG
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
29238301 TCTCGAAGGG
Statistics
Matches: 308, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
92 145 0.47
93 20 0.06
94 143 0.46
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (94 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
GTGATGAATGTGAAAGTGTATATATGTGA
Found at i:29238041 original size:22 final size:22
Alignment explanation
Indices: 29238014--29238086 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
29238004 AGTGTATATG
29238014 TGTGATAAGGCCTAATAGCCGA
1 TGTGATAAGGCCTAATAGCCGA
* *** ***
29238036 TGTGATGAATGTGAAAT-GTATA
1 TGTGAT-AAGGCCTAATAGCCGA
29238058 TGTGTATAAGGCCTAATAGCCGA
1 TGTG-ATAAGGCCTAATAGCCGA
29238081 TGTGAT
1 TGTGAT
29238087 GAATGTGAAA
Statistics
Matches: 34, Mismatches: 14, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (22 bp):
TGTGATAAGGCCTAATAGCCGA
Found at i:29238192 original size:186 final size:185
Alignment explanation
Indices: 29237878--29238243 Score: 653
Period size: 186 Copynumber: 2.0 Consensus size: 185
29237868 GAAATGATAG
* *
29237878 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
*
29237943 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
*
29238008 TATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAA-TGTATATGTGTA
131 TATATATGTGATAAGGCCTAATAGCCGATGT--TGAATGTGAAAGTGTATATGTGTA
29238064 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
*
29238129 GTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
*
29238194 TATATATGTGATAAGGCCTAATGGCCGATGTTGAATGTGAAAGTGTATAT
131 TATATATGTGATAAGGCCTAATAGCCGATGTTGAATGTGAAAGTGTATAT
29238244 ATGTGACAGG
Statistics
Matches: 173, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
184 11 0.06
185 7 0.04
186 155 0.90
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (185 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
GTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
TATATATGTGATAAGGCCTAATAGCCGATGTTGAATGTGAAAGTGTATATGTGTA
Found at i:29238272 original size:139 final size:140
Alignment explanation
Indices: 29237878--29238300 Score: 663
Period size: 139 Copynumber: 3.0 Consensus size: 140
29237868 GAAATGATAG
29237878 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
29237943 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
66 GT-ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
*
29238008 TATATGTGTGA
130 TATATATGTGA
* * *
29238019 TAAGGCCTAATAGCCGATGTGATGAATGTGAAA-TGTATATGTGT-ATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
29238082 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
66 GT-ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
*
29238147 TATATATGTAA
130 TATATATGTGA
29238158 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * * * * * * * * *
29238223 GT-TGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGCGAAAGTGC
66 GTATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGT
*
29238287 ATAAATGTGA
131 ATATATGTGA
29238297 TAAG
1 TAAG
29238301 TCTCGAAGGG
Statistics
Matches: 260, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
139 188 0.72
140 20 0.08
141 52 0.20
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (140 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGT
ATATATGTGA
Found at i:29238285 original size:186 final size:185
Alignment explanation
Indices: 29237896--29238300 Score: 623
Period size: 186 Copynumber: 2.2 Consensus size: 185
29237886 AATGGCCGAT
*
29237896 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
* *
29237961 TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCC
66 TATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* * * * *
29238026 TAATAGCCGATGTGATGAATGTGAAATGTATATGTGTATAAGGCCTAATAGCCGAT
131 TAATAGCCGATGT-ATGAATGTGAAATGTATATATGTACAAGGCCGAATAGCCAAC
29238082 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
*
29238147 TATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
66 TATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* * * *
29238212 TAATGGCCGATGT-TGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAAC
131 TAATAGCCGATGTATGAATGTGAAA-TGTATATATGT-ACAAGGCCGAATAGCCAAC
* * * *
29238268 GTGATGGATGCGAAAGTGCATAAATGTGATAAG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAG
29238301 TCTCGAAGGG
Statistics
Matches: 200, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
184 11 0.05
185 10 0.05
186 179 0.89
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (185 bp):
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
TATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
TAATAGCCGATGTATGAATGTGAAATGTATATATGTACAAGGCCGAATAGCCAAC
Found at i:29238475 original size:37 final size:37
Alignment explanation
Indices: 29238419--29238497 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
29238409 CCGAGCTCTA
* *
29238419 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
29238456 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
29238493 AAGAC
1 AAGAC
29238498 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:29243584 original size:20 final size:20
Alignment explanation
Indices: 29243559--29243596 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29243549 TATTTAGGGA
29243559 AAAAATTTTCT-AAGTTTTGT
1 AAAAA-TTTCTAAAGTTTTGT
29243579 AAAAATTTCTAAAGTTTT
1 AAAAATTTCTAAAGTTTT
29243597 TGGTTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (20 bp):
AAAAATTTCTAAAGTTTTGT
Found at i:29245469 original size:137 final size:137
Alignment explanation
Indices: 29245219--29245487 Score: 414
Period size: 137 Copynumber: 2.0 Consensus size: 137
29245209 CGATTTAGGG
**
29245219 ATGAAATATATGTGATTGAATGTTTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAAT
1 ATGAAATATATGTGATTGAATGGCTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAAT
** *
29245284 ATTTCTAATTGTACGATAATACTTTGTAACCCTAATTCAACGATGGAGGCAGGTTAGGGGTGTTA
66 ATTTCTAATTGTACGATAATACTCCGTAACCCTAATTCAACGACGGAGGCAGGTTAGGGGTGTTA
29245349 CATTTAT
131 CATTTAT
* * *
29245356 ATGAAATGTATGTGATTGAATGGCTTATGATATATTTAAATTATTGAATGTTATGGTGTTTGAAT
1 ATGAAATATATGTGATTGAATGGCTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAAT
* * * *
29245421 ATTTTTTATTGTACGGTAATACTCCGTAACCCTAA-TCTAGCGACGGAGGCAGGTTAGGGGTGTT
66 ATTTCTAATTGTACGATAATACTCCGTAACCCTAATTC-AACGACGGAGGCAGGTTAGGGGTGTT
29245485 ACA
130 ACA
29245488 GTTCGAGTTT
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
136 2 0.02
137 117 0.98
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (137 bp):
ATGAAATATATGTGATTGAATGGCTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAAT
ATTTCTAATTGTACGATAATACTCCGTAACCCTAATTCAACGACGGAGGCAGGTTAGGGGTGTTA
CATTTAT
Found at i:29246004 original size:2 final size:2
Alignment explanation
Indices: 29245992--29246057 Score: 64
Period size: 2 Copynumber: 34.0 Consensus size: 2
29245982 AAAAAGACAA
* * * * *
29245992 AG AG AG A- AG AG AG AG GG AG AG GG GG GG AA AG AG AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
29246032 GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
29246058 TTGGAAATGA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29248057 original size:16 final size:16
Alignment explanation
Indices: 29248033--29248064 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29248023 ATTTGAAAGT
*
29248033 TTTATTTTTTTTATAA
1 TTTAATTTTTTTATAA
29248049 TTTAATTTTTTTATAA
1 TTTAATTTTTTTATAA
29248065 AATAACTTTA
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:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTAATTTTTTTATAA
Found at i:29248171 original size:23 final size:23
Alignment explanation
Indices: 29248145--29248188 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
29248135 TCAAATTGAC
29248145 TTTGATTCTACT-TATCAATAAAT
1 TTTGATTC-ACTATATCAATAAAT
*
29248168 TTTGATTCACTATGTCAATAA
1 TTTGATTCACTATATCAATAA
29248189 TTAAATCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (23 bp):
TTTGATTCACTATATCAATAAAT
Found at i:29248302 original size:31 final size:31
Alignment explanation
Indices: 29248211--29248307 Score: 90
Period size: 31 Copynumber: 3.1 Consensus size: 31
29248201 TTAAAACTTA
* * *
29248211 TTAATGAGTTAAATAAAAA-TATTTGAATAAT
1 TTAATAAGTAAAATAAAAACT-TTTCAATAAT
*
29248242 TAAATAAGTAAAATAAAAACTTTTCAATAAT
1 TTAATAAGTAAAATAAAAACTTTTCAATAAT
* * * *
29248273 TTAATAATTAAGATATAAA-TTTATTAATAAT
1 TTAATAAGTAAAATAAAAACTTT-TCAATAAT
29248304 TTAA
1 TTAA
29248308 AGAGTTAGTG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 3 0.05
31 51 0.93
32 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (31 bp):
TTAATAAGTAAAATAAAAACTTTTCAATAAT
Found at i:29251346 original size:42 final size:42
Alignment explanation
Indices: 29251287--29251372 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
29251277 TAATTAGGAC
29251287 AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAA
1 AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAA
* * *
29251329 AATAGTTCCCTTATTCTAATAAACTGCTAAAAGATAAAATAA
1 AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAA
29251371 AA
1 AA
29251373 ATATTCCTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (42 bp):
AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAA
Found at i:29251419 original size:19 final size:18
Alignment explanation
Indices: 29251397--29251436 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
29251387 TGAATAAAAC
*
29251397 TTATTTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
29251416 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
29251434 TTA
1 TTA
29251437 AAATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:29255734 original size:42 final size:42
Alignment explanation
Indices: 29255675--29255763 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
29255665 TCCTAATTAG
29255675 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
*
29255717 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
*
29255759 TAAAA
1 GAAAA
29255764 ATATTCCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.28
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
Found at i:29255784 original size:43 final size:42
Alignment explanation
Indices: 29255676--29255785 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
29255666 CCTAATTAGG
* * * *
29255676 AAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAG
1 AAAATAGTTCCCTGAATATAATAAACTACTAAAACATAAAAA
* * * *
29255718 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
1 AAAATAGTTCCCTGAATATAATAAACTACTAAAACATAAAA-A
29255761 AAAATA-TT-CCTAGAATATGAATAAA
1 AAAATAGTTCCCT-GAATAT-AATAAA
29255786 ACTTATTTAC
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
41 3 0.05
42 45 0.75
43 12 0.20
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (42 bp):
AAAATAGTTCCCTGAATATAATAAACTACTAAAACATAAAAA
Found at i:29255826 original size:18 final size:19
Alignment explanation
Indices: 29255788--29255827 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
29255778 TGAATAAAAC
*
29255788 TTATTTACCTAAATGAAAT
1 TTATCTACCTAAATGAAAT
29255807 TTATCTACCTAAAT-AAAT
1 TTATCTACCTAAATGAAAT
29255825 TTA
1 TTA
29255828 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (19 bp):
TTATCTACCTAAATGAAAT
Found at i:29267220 original size:36 final size:36
Alignment explanation
Indices: 29267173--29267247 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
29267163 CCTTGTCCAA
29267173 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
1 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
29267209 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
1 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
29267245 AAG
1 AAG
29267248 ATTCCATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (36 bp):
AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
Found at i:29279848 original size:15 final size:15
Alignment explanation
Indices: 29279830--29279858 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29279820 GACCACGACC
29279830 ATAGCCACCATGACT
1 ATAGCCACCATGACT
29279845 ATAGCCACCATGAC
1 ATAGCCACCATGAC
29279859 ACTGACCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (15 bp):
ATAGCCACCATGACT
Found at i:29283475 original size:43 final size:42
Alignment explanation
Indices: 29283352--29283476 Score: 151
Period size: 43 Copynumber: 2.9 Consensus size: 42
29283342 TGATTACATG
* * * *
29283352 TAAGACCATGTCTGGGACATTGGCATTGTATTGTGATTACGTG
1 TAAGACCATGTCTAGGACATTGGCATCGTA-TGTGATTTCGTA
* *
29283395 TAAGACCATGTCTAGGACATTGGTATCGTTATATGATTTCGTA
1 TAAGACCATGTCTAGGACATTGGCATCG-TATGTGATTTCGTA
* *
29283438 TAAGACCATGTCTAGGATAGTGGCATCGATATGTGATTT
1 TAAGACCATGTCTAGGACATTGGCATCG-TATGTGATTT
29283477 TCGAGTATCC
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
43 68 0.97
44 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (42 bp):
TAAGACCATGTCTAGGACATTGGCATCGTATGTGATTTCGTA
Found at i:29286700 original size:14 final size:15
Alignment explanation
Indices: 29286667--29286702 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
29286657 TCTAACCTTG
29286667 TTTAATATAGCATAT
1 TTTAATATAGCATAT
*
29286682 ATTAATATA-CATAT
1 TTTAATATAGCATAT
29286696 TTTAATA
1 TTTAATA
29286703 GCATGAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (15 bp):
TTTAATATAGCATAT
Found at i:29290649 original size:93 final size:92
Alignment explanation
Indices: 29290517--29290711 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
29290507 TTGATTTTAG
* *
29290517 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
29290581 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
29290609 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
29290674 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
29290702 CAAATTCATA
1 TAAATTCATA
29290712 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:29290769 original size:17 final size:17
Alignment explanation
Indices: 29290744--29290777 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29290734 ATAATTTTAA
*
29290744 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
29290761 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
29290778 TATGTATAAT
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:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:29290851 original size:54 final size:54
Alignment explanation
Indices: 29290793--29290971 Score: 137
Period size: 54 Copynumber: 3.1 Consensus size: 54
29290783 ATAATCATAT
29290793 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * *
29290847 ATTATAAATTTTAATTATATT-ATATTTAATAATAATTATGTTATTTTA-TATTTTACAGTATCA
1 ATTAT-GA-TTTGAGTAAATTCATA--TAAGAAT-ATTA-ATTA-TTAAGAATTTT--A-T-T-A
29290910 TA
54 -A
*
29290912 TATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
29290967 ATTAT
1 ATTAT
29290972 ATATTTTAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 10 0.11
57 7 0.08
58 5 0.05
59 9 0.10
60 6 0.07
61 9 0.10
62 5 0.05
63 7 0.08
64 10 0.11
65 4 0.04
66 5 0.05
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:29290868 original size:18 final size:17
Alignment explanation
Indices: 29290836--29290870 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29290826 AATTATTAAG
29290836 AATTTTATTAAATTATA
1 AATTTTATTAAATTATA
*
29290853 AATTTTAATTATATTATA
1 AATTTT-ATTAAATTATA
29290871 TTTAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTTATTAAATTATA
Found at i:29290910 original size:120 final size:120
Alignment explanation
Indices: 29290786--29291008 Score: 410
Period size: 120 Copynumber: 1.9 Consensus size: 120
29290776 ATTATGTATA
29290786 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
* *
29290851 TAAATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGT
66 TAAATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
*
29290906 ATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
*
29290971 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 TAAATTTTAATTAAAATATATTTAATAATAATTATGTT
29291009 TAAATATGAT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 99 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
TAAATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
Found at i:29290985 original size:18 final size:17
Alignment explanation
Indices: 29290957--29290991 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29290947 ATTATTAAGA
*
29290957 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29290974 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29290992 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29291104 original size:144 final size:147
Alignment explanation
Indices: 29290945--29291216 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
29290935 ATAAGAATAT
*
29290945 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
29291010 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
29291072 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
29291089 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
29291154 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
29291217 CAATAATCAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 91 0.75
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:29291129 original size:18 final size:17
Alignment explanation
Indices: 29291101--29291135 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29291091 ATTATTAAGA
*
29291101 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29291118 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29291136 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29291346 original size:44 final size:45
Alignment explanation
Indices: 29291297--29291391 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
29291287 TTACACCTCT
* *
29291297 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
29291341 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
29291386 ATTACA
1 ATTACA
29291392 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:29291391 original size:16 final size:16
Alignment explanation
Indices: 29291370--29291402 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29291360 TTGATTTGCT
*
29291370 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
29291386 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
29291402 A
1 A
29291403 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:29291412 original size:21 final size:21
Alignment explanation
Indices: 29291383--29291425 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
29291373 ACACCTCTAT
*
29291383 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
29291404 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
29291425 T
1 T
29291426 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:29291633 original size:58 final size:60
Alignment explanation
Indices: 29291564--29291678 Score: 153
Period size: 58 Copynumber: 1.9 Consensus size: 60
29291554 ATTTTTTACT
* *
29291564 CAATTTAGTACCTGAACTTGACA-CTTTTTTCTAATTTAGTATCTAA-TTTTTTTTCTCC
1 CAATTTAGTACCTAAACTTGACATCTTTTTTCTAATTTAGTACCTAAGTTTTTTTTCTCC
* * * *
29291622 CAATTTGGTACCTAAACTTGGCATTTTTTTTTCTAATTTGGTACCTAAGTTTTTTTT
1 CAATTTAGTACCTAAACTTGACA-TCTTTTTTCTAATTTAGTACCTAAGTTTTTTTT
29291679 AGGTTCAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 20 0.42
60 20 0.42
61 8 0.17
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.51
Consensus pattern (60 bp):
CAATTTAGTACCTAAACTTGACATCTTTTTTCTAATTTAGTACCTAAGTTTTTTTTCTCC
Found at i:29291696 original size:62 final size:58
Alignment explanation
Indices: 29291562--29291699 Score: 152
Period size: 58 Copynumber: 2.3 Consensus size: 58
29291552 CTATTTTTTA
* * *
29291562 CTCAATTTAGTACCTGAACTTGACACTTTTTTCTAATTTAGTATCTAATTTTTTTTCT
1 CTCAATTTGGTACCTAAACTTGACACTTTTTTCTAATTTAGTACCTAATTTTTTTTCT
* * * * *
29291620 CCCAATTTGGTACCTAAACTTGGCATTTTTTTTTCTAATTTGGTACCTAAGTTTTTTTTAGGT
1 CTCAATTTGGTACCTAAACTTGACA--CTTTTTTCTAATTTAGTACCTAA-TTTTTTTT--CT
29291683 -TCAATTTGGTACCTAAA
1 CTCAATTTGGTACCTAAA
29291700 TTTATTAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
58 21 0.32
60 20 0.30
61 8 0.12
62 16 0.24
63 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.49
Consensus pattern (58 bp):
CTCAATTTGGTACCTAAACTTGACACTTTTTTCTAATTTAGTACCTAATTTTTTTTCT
Found at i:29292171 original size:31 final size:30
Alignment explanation
Indices: 29292119--29292240 Score: 147
Period size: 31 Copynumber: 3.9 Consensus size: 30
29292109 AAAAGATTAA
* *
29292119 GTACCAACTTAAGAAAAAAGTGTCAAGTTTAG
1 GTACCAAATT-AGGAAAAAGTGTCAAGTTT-G
29292151 GTACCAAATTAGGAAAAAGTGT-ATAGTTTG
1 GTACCAAATTAGGAAAAAGTGTCA-AGTTTG
*
29292181 AGTACCAAATTAGGAAAAACTGTCAAGTTTGG
1 -GTACCAAATTAGGAAAAAGTGTCAAGTTT-G
* *
29292213 GTGCCAAATTAGGAAAAAGTATCAAGTT
1 GTACCAAATTAGGAAAAAGTGTCAAGTT
29292241 CATATACCAA
Statistics
Matches: 80, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
30 2 0.03
31 67 0.84
32 11 0.14
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (30 bp):
GTACCAAATTAGGAAAAAGTGTCAAGTTTG
Found at i:29292397 original size:15 final size:14
Alignment explanation
Indices: 29292361--29292399 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
29292351 GAATTTAGAT
29292361 TTTAAAATTTTTTA
1 TTTAAAATTTTTTA
*
29292375 TTTGAAATTTTTTA
1 TTTAAAATTTTTTA
29292389 TTTATAAATTT
1 TTTA-AAATTT
29292400 ATAATTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (14 bp):
TTTAAAATTTTTTA
Found at i:29292524 original size:12 final size:12
Alignment explanation
Indices: 29292507--29292532 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29292497 TAAATTCAAG
29292507 TTTTAAAATTAT
1 TTTTAAAATTAT
29292519 TTTTAAAATTAT
1 TTTTAAAATTAT
29292531 TT
1 TT
29292533 ATTTATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTAAAATTAT
Found at i:29293353 original size:82 final size:82
Alignment explanation
Indices: 29293216--29293366 Score: 284
Period size: 82 Copynumber: 1.8 Consensus size: 82
29293206 ACGAATTCTA
*
29293216 GAAAACATAACAAACAAAGTTCAAATGAATTTGTGAGTTACTAATATAACATACCATTTATGAAT
1 GAAAACATAACAAACAAAGTTCAAATGAATTAGTGAGTTACTAATATAACATACCATTTATGAAT
29293281 TTATGAATTTATACCTG
66 TTATGAATTTATACCTG
*
29293298 GAAAACATAACAAACTAAGTTCAAATGAATTAGTGAGTTACTAATATAACATACCATTTATGAAT
1 GAAAACATAACAAACAAAGTTCAAATGAATTAGTGAGTTACTAATATAACATACCATTTATGAAT
29293363 TTAT
66 TTAT
29293367 AAGTTAGAAC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (82 bp):
GAAAACATAACAAACAAAGTTCAAATGAATTAGTGAGTTACTAATATAACATACCATTTATGAAT
TTATGAATTTATACCTG
Found at i:29297235 original size:38 final size:38
Alignment explanation
Indices: 29297173--29297247 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
29297163 TTTAAAATTT
*
29297173 TAAAAATTAAAAAAAATTGAAAAAAATATATTTAAAAAG
1 TAAAAAGTAAAAAAAATTGAAAAAAA-ATATTTAAAAAG
*
29297212 TAAAAAGT-AAAAAAATT-ATAAAAAAATATTTTAAAA
1 TAAAAAGTAAAAAAAATTGA-AAAAAAATATTTAAAAA
29297248 TTTTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 11 0.33
38 15 0.45
39 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (38 bp):
TAAAAAGTAAAAAAAATTGAAAAAAAATATTTAAAAAG
Found at i:29297255 original size:39 final size:39
Alignment explanation
Indices: 29297162--29297256 Score: 122
Period size: 39 Copynumber: 2.4 Consensus size: 39
29297152 TTAATTAATT
*
29297162 TTTTAAAATTTTAAAAATTAAAAAAAATTGAAAAAAATA
1 TTTTAAAATTTTAAAAAGTAAAAAAAATTGAAAAAAATA
** *
29297201 TATTTAAAA-AGTAAAAAGT-AAAAAAATTATAAAAAAATA
1 T-TTTAAAATTTTAAAAAGTAAAAAAAATT-GAAAAAAATA
29297240 TTTTAAAATTTTAAAAA
1 TTTTAAAATTTTAAAAA
29297257 TTAATTAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
38 16 0.34
39 24 0.51
40 7 0.15
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (39 bp):
TTTTAAAATTTTAAAAAGTAAAAAAAATTGAAAAAAATA
Found at i:29297745 original size:6 final size:6
Alignment explanation
Indices: 29297727--29297758 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
29297717 CTTCAAATTA
29297727 TCCTTT ATCCTTT TCCTTT TCCTTT TCCTTT T
1 TCCTTT -TCCTTT TCCTTT TCCTTT TCCTTT T
29297759 ATGGTCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (6 bp):
TCCTTT
Found at i:29302861 original size:21 final size:22
Alignment explanation
Indices: 29302813--29302863 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
29302803 TAACATAATT
29302813 TATTTT-A-AAATTTTTATTGA
1 TATTTTAACAAATTTTTATTGA
*
29302833 TGTTTTAACAAATTTTT-TT-A
1 TATTTTAACAAATTTTTATTGA
29302853 TATTATTAACA
1 TATT-TTAACA
29302864 CATAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 8 0.31
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (22 bp):
TATTTTAACAAATTTTTATTGA
Found at i:29309846 original size:21 final size:20
Alignment explanation
Indices: 29309805--29309846 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
29309795 ACAATTGTAA
*
29309805 TTTCATTTATTAAACATTAT
1 TTTCATTTATAAAACATTAT
*
29309825 TTTCATTTAATAAAATATTAT
1 TTTCATTT-ATAAAACATTAT
29309846 T
1 T
29309847 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTCATTTATAAAACATTAT
Found at i:29314012 original size:2 final size:2
Alignment explanation
Indices: 29314005--29314031 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29313995 AAACCCCGGG
29314005 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 A
29314032 AGAGAGAGTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29318851 original size:38 final size:40
Alignment explanation
Indices: 29318782--29318870 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 40
29318772 TGAAAAGTAT
29318782 TTATATTAAAAAAATCAACCATAAATATAATAAATGTCTTA
1 TTATATTAAAAAAATCAA-CATAAATATAATAAATGTCTTA
* * * *
29318823 TTATATTAAAAACAT-AA-ATAAATATAATAATTTTTTTA
1 TTATATTAAAAAAATCAACATAAATATAATAAATGTCTTA
*
29318861 TTGTATTAAA
1 TTATATTAAA
29318871 TATAATTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 27 0.63
40 2 0.05
41 14 0.33
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (40 bp):
TTATATTAAAAAAATCAACATAAATATAATAAATGTCTTA
Found at i:29319858 original size:7 final size:7
Alignment explanation
Indices: 29319846--29319877 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
29319836 AATAAAACGA
29319846 TTTTCTT
1 TTTTCTT
29319853 TTTTCTT
1 TTTTCTT
29319860 TTTTCTT
1 TTTTCTT
29319867 TTTTCTT
1 TTTTCTT
29319874 TTTT
1 TTTT
29319878 TGTTTCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:29320455 original size:14 final size:14
Alignment explanation
Indices: 29320436--29320475 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29320426 TTGATTGCCA
29320436 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
29320450 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
29320464 GGAAAATGTTTT
1 GTAAAATGTTTT
29320476 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:29320484 original size:20 final size:20
Alignment explanation
Indices: 29320459--29320497 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29320449 CGTAAAATGA
*
29320459 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
29320479 TTTCTGTAAAATGATTTAC
1 TTTCTGGAAAATGATTTAC
29320498 CAGAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:29325945 original size:6 final size:6
Alignment explanation
Indices: 29325934--29325974 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
29325924 ATTATATATA
* *
29325934 TTTATT TTTATT TTTATT TTTATT TTTATA TTTATA TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
29325975 ATTAAATTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:29325957 original size:18 final size:18
Alignment explanation
Indices: 29325930--29325974 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
29325920 AATTATTATA
*
29325930 TATATTTATTTTTATTTT
1 TATATTTATTTTTATATT
*
29325948 TATTTTTATTTTTATATT
1 TATATTTATTTTTATATT
29325966 TATATTTAT
1 TATATTTAT
29325975 ATTAAATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TATATTTATTTTTATATT
Found at i:29325975 original size:6 final size:6
Alignment explanation
Indices: 29325930--29325977 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
29325920 AATTATTATA
* * * *
29325930 TATATT TATTTT TATTTT TATTTT TATTTT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
29325978 AAATTACTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (6 bp):
TATATT
Found at i:29327069 original size:48 final size:47
Alignment explanation
Indices: 29327007--29327134 Score: 152
Period size: 48 Copynumber: 2.7 Consensus size: 47
29326997 GTGCGAGTGA
* *
29327007 TACCTTGATTTGGCTGTGGGCCATGGTATAGGTATTTCAGAGAGGAGT
1 TACCTTGATTTGGCTGTGGGCCATGGTATAGGTA-ATCAGAGAGAAGT
* * * * *
29327055 TACCTTGATTTGGCTGTAGGCCATGTTATAGGTAATCCGGGATAAGT
1 TACCTTGATTTGGCTGTGGGCCATGGTATAGGTAATCAGAGAGAAGT
*
29327102 TACCTTGATTTGG-T-TAGGGCCTTGGTATAGGTA
1 TACCTTGATTTGGCTGT-GGGCCATGGTATAGGTA
29327135 CTTATCGATT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
45 1 0.01
46 15 0.22
47 21 0.30
48 32 0.46
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.35
Consensus pattern (47 bp):
TACCTTGATTTGGCTGTGGGCCATGGTATAGGTAATCAGAGAGAAGT
Found at i:29334245 original size:48 final size:46
Alignment explanation
Indices: 29334179--29334305 Score: 139
Period size: 48 Copynumber: 2.7 Consensus size: 46
29334169 CGAATGATAT
* *
29334179 CTTGATTTGGATATGGGCCATGGTATAGGTATTTCAGAGAGGAA-TTAC
1 CTTGATTTGGCTA-GGGCCATGGTATAGGTA-CTCAGAGA-GAAGTTAC
* * * *
29334227 CTTGATTTGGCTACGGGCCATGTTATAGGTACTCCGGGATAAGTTAC
1 CTTGATTTGGCTA-GGGCCATGGTATAGGTACTCAGAGAGAAGTTAC
* *
29334274 ATTGATTTGGCTATGGCCATGGTATAGGTACT
1 CTTGATTTGGCTAGGGCCATGGTATAGGTACT
29334306 TATCGATTGT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 19 0.28
47 21 0.31
48 28 0.41
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (46 bp):
CTTGATTTGGCTAGGGCCATGGTATAGGTACTCAGAGAGAAGTTAC
Found at i:29335688 original size:27 final size:26
Alignment explanation
Indices: 29335658--29335719 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
29335648 AGATAATTAA
29335658 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
29335685 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
29335712 AATAAAAT
1 AATAAAAT
29335720 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:29336303 original size:11 final size:11
Alignment explanation
Indices: 29336289--29336317 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29336279 TTAGTACTTA
29336289 TTTTTTTT-TC
1 TTTTTTTTCTC
29336299 TTTTTTTTCTC
1 TTTTTTTTCTC
29336310 TTTTTTTT
1 TTTTTTTT
29336318 ATTATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:29338893 original size:6 final size:5
Alignment explanation
Indices: 29338837--29338901 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
29338827 GAATTTTATT
* * * * *
29338837 AATAT AATAA AAT-A ATTAAA AACAA AACAA AACAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AAT-AA AATAA AATAA AATAA AATAA AATAA AATAA
29338887 TAATAA TAATAA AAT
1 -AATAA -AATAA AAT
29338902 TTAAAATTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
4 3 0.06
5 36 0.69
6 13 0.25
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:29345376 original size:27 final size:26
Alignment explanation
Indices: 29345346--29345407 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
29345336 AGATAATTAA
29345346 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
29345373 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
29345400 AATAAAAT
1 AATAAAAT
29345408 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:29347414 original size:19 final size:18
Alignment explanation
Indices: 29347387--29347423 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
29347377 TAATTAAAGG
29347387 GGTTAATTTTTTTAAAATT
1 GGTTAA-TTTTTTAAAATT
*
29347406 GGTTTATTTTTTAAAATT
1 GGTTAATTTTTTAAAATT
29347424 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (18 bp):
GGTTAATTTTTTAAAATT
Found at i:29348932 original size:18 final size:18
Alignment explanation
Indices: 29348909--29349191 Score: 169
Period size: 18 Copynumber: 15.3 Consensus size: 18
29348899 GAATAATTAT
29348909 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
29348927 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
29348945 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
29348963 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
29348989 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
*
29349007 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
29349024 ATATTCAGTAACTATTAAG
1 TTATTCAGTAAC-AGTCAG
*
29349043 TTATTCAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* *
29349060 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
29349079 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
29349097 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
29349115 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
29349133 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
29349151 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
29349169 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
29349187 TTATT
1 TTATT
29349192 TTATACCTTT
Statistics
Matches: 202, Mismatches: 47, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
17 17 0.08
18 151 0.75
19 18 0.09
21 2 0.01
22 1 0.00
23 2 0.01
26 11 0.05
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:29348951 original size:36 final size:36
Alignment explanation
Indices: 29348909--29349191 Score: 196
Period size: 36 Copynumber: 7.6 Consensus size: 36
29348899 GAATAATTAT
* *
29348909 TTATTCAGTAACAGTCAGTTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * * * *
29348945 TTATTCAATAATAACCAGTTATTCAGTATCGATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* *
29348981 TTGATCGGTTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA
1 TT-A-----T-T-CAGTAACAATCAGTTATTCAGTAACAATCA-A
* * * *
29349025 -TATTCAGTAACTATTAAGTTATTCAGTAGCAGTC-A
1 TTATTCAGTAAC-AATCAGTTATTCAGTAACAATCAA
* **
29349060 TTCATTCAGTGACAATCAGTTATTCAGTAATGATCAA
1 TT-ATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * *
29349097 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATC-AA
* * * * * *
29349134 -TATCCAGTAACAGTCAATTATCCGGTAACAGTCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
*
29349169 TTATTCAGTAATAATCAGTTATT
1 TTATTCAGTAACAATCAGTTATT
29349192 TTATACCTTT
Statistics
Matches: 188, Mismatches: 43, Indels: 32
0.71 0.16 0.12
Matches are distributed among these distances:
35 10 0.05
36 132 0.70
37 19 0.10
42 2 0.01
43 6 0.03
44 19 0.10
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (36 bp):
TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
Found at i:29349124 original size:72 final size:71
Alignment explanation
Indices: 29348990--29349191 Score: 228
Period size: 72 Copynumber: 2.8 Consensus size: 71
29348980 ATTGATCGGT
* * *
29348990 TATCCAGTAACAGTCAATTATTCAGTAAAATCAGA-TATTCAGTAACTATTAAGTTATTCAGTAG
1 TATCCAGTAACAATCAATTATTCAGTAAAATCA-ATTATTCAGTAA-TATTCAGTTATTCAGTAA
*
29349054 CAGTC-AT
64 CAGTCTAA
* * * *
29349061 TCATTCAGTGACAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTCAGTTATTCAGTAA
1 T-ATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATTCAGTAA
29349126 CAGTCTAA
64 CAGTCTAA
* * * * *
29349134 TATCCAGTAACAGTCAATTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATT
29349192 TTATACCTTT
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
71 1 0.01
72 92 0.84
73 16 0.15
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (71 bp):
TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAATATTCAGTTATTCAGTAACA
GTCTAA
Found at i:29349416 original size:45 final size:45
Alignment explanation
Indices: 29349359--29349643 Score: 428
Period size: 45 Copynumber: 6.3 Consensus size: 45
29349349 ATCTAGAATA
* * *
29349359 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTG-CTGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGTC-GAATCG
*
29349404 ATAACGGTAACAGTAACAATATTCGACACACAAAGTGTCGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGTCGAATCG
* *
29349449 GTAACGGTAACAGTAACAATATTCGACACACACAGTGCCGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGTCGAATCG
*
29349494 GCAACGGTAACAGTAACAATATTCGACACACAAAGTGTCGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGTCGAATCG
*
29349539 GTAACGGTAGCAGTAACAATATTCGACACACAAAGTGTCGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGTCGAATCG
* * * *
29349584 GTAACAGTAGCAGTAACAATATTCGACACACAAAGTGCCGAATCA
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGTCGAATCG
* *
29349629 GTAACAGTAGCAGTA
1 GTAACGGTAACAGTA
29349644 GCGGTAACAG
Statistics
Matches: 224, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 223 1.00
46 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (45 bp):
GTAACGGTAACAGTAACAATATTCGACACACAAAGTGTCGAATCG
Found at i:29349823 original size:16 final size:16
Alignment explanation
Indices: 29349794--29349831 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
29349784 TAATTCACTT
29349794 TTCAATTTTCAATTAA
1 TTCAATTTTCAATTAA
29349810 TTCATATTTT-AATTAA
1 TTCA-ATTTTCAATTAA
29349826 TT-AATT
1 TTCAATT
29349832 ATATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.14
15 1 0.05
16 12 0.57
17 5 0.24
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (16 bp):
TTCAATTTTCAATTAA
Found at i:29349823 original size:23 final size:23
Alignment explanation
Indices: 29349783--29349848 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
29349773 AATAGGGTAT
*
29349783 TTAATTCACT-TTTCAATTTTCAA
1 TTAATTCA-TATTTTAATTTTCAA
29349806 TTAATTCATATTTTAA--TT-AA
1 TTAATTCATATTTTAATTTTCAA
*
29349826 TTAATT-ATATTTT-TTTTTCAA
1 TTAATTCATATTTTAATTTTCAA
29349847 TT
1 TT
29349849 CAATATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 7 0.19
20 10 0.27
21 6 0.16
22 1 0.03
23 13 0.35
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (23 bp):
TTAATTCATATTTTAATTTTCAA
Found at i:29351305 original size:9 final size:9
Alignment explanation
Indices: 29351287--29351321 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
29351277 TTTCTTTTTC
*
29351287 ATTTCTTTT
1 ATTTCATTT
29351296 ATTTCATTT
1 ATTTCATTT
29351305 ATTTC-TTT
1 ATTTCATTT
29351313 ATTTCATTT
1 ATTTCATTT
29351322 CTTTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTCATTT
Found at i:29351313 original size:17 final size:18
Alignment explanation
Indices: 29351287--29351333 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
29351277 TTTCTTTTTC
29351287 ATTTCTTTTATTTCATTT
1 ATTTCTTTTATTTCATTT
29351305 ATTTC-TTTATTTCATTT
1 ATTTCTTTTATTTCATTT
* *
29351322 CTTTATTTTATT
1 ATTTCTTTTATT
29351334 ATTAAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTCTTTTATTTCATTT
Found at i:29351323 original size:13 final size:13
Alignment explanation
Indices: 29351287--29351329 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
29351277 TTTCTTTTTC
* *
29351287 ATTTCTTTTATTT
1 ATTTCATTTCTTT
29351300 CATTT-ATTTCTTT
1 -ATTTCATTTCTTT
29351313 ATTTCATTTCTTT
1 ATTTCATTTCTTT
29351326 ATTT
1 ATTT
29351330 TATTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTCATTTCTTT
Found at i:29351384 original size:20 final size:20
Alignment explanation
Indices: 29351355--29351392 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29351345 ATAATATTTA
* *
29351355 TTATTTATACATGTGTATAT
1 TTATTAATACATATGTATAT
29351375 TTATTAATACATATGTAT
1 TTATTAATACATATGTAT
29351393 TAATTTATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (20 bp):
TTATTAATACATATGTATAT
Found at i:29351459 original size:16 final size:16
Alignment explanation
Indices: 29351438--29351479 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
29351428 TATTTAATTA
29351438 ATTAATATAAAATAAT
1 ATTAATATAAAATAAT
29351454 ATTAATATAAAATAAT
1 ATTAATATAAAATAAT
29351470 ATTAATATAA
1 ATTAATATAA
29351480 TATACTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTAATATAAAATAAT
Found at i:29351480 original size:5 final size:5
Alignment explanation
Indices: 29351432--29351483 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
29351422 TTTATTTATT
* *
29351432 TAAT- TAAT- TAATA TAAAA TAATA TTAATA TAAAA TAATA TTAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA -TAATA TAATA TAATA -TAATA TAATA
29351482 TA
1 TA
29351484 CTTTAATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
4 8 0.20
5 23 0.56
6 10 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:29352582 original size:14 final size:14
Alignment explanation
Indices: 29352563--29352622 Score: 77
Period size: 14 Copynumber: 4.4 Consensus size: 14
29352553 TGTTTCATTG
29352563 AAAATGATTTTTGA
1 AAAATGATTTTTGA
**
29352577 AAAATGATCATTG-
1 AAAATGATTTTTGA
29352590 AAAATGATTTTTGA
1 AAAATGATTTTTGA
* *
29352604 AAAATAATTTCTGA
1 AAAATGATTTTTGA
29352618 AAAAT
1 AAAAT
29352623 AACTTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
13 11 0.28
14 28 0.72
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.37
Consensus pattern (14 bp):
AAAATGATTTTTGA
Found at i:29352595 original size:27 final size:27
Alignment explanation
Indices: 29352557--29352608 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
29352547 TTAGTTTGTT
29352557 TCATTGAAAATGATTTTTGAAAAATGA
1 TCATTGAAAATGATTTTTGAAAAATGA
29352584 TCATTGAAAATGATTTTTGAAAAAT
1 TCATTGAAAATGATTTTTGAAAAAT
29352609 AATTTCTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.38
Consensus pattern (27 bp):
TCATTGAAAATGATTTTTGAAAAATGA
Found at i:29353182 original size:14 final size:13
Alignment explanation
Indices: 29353154--29353189 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
29353144 ATATTTATAT
29353154 TTATTAAAA-TTA
1 TTATTAAAATTTA
29353166 TTACTTAAAATTTA
1 TTA-TTAAAATTTA
29353180 TTATTAAAAT
1 TTATTAAAAT
29353190 AAAATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 13 0.59
14 6 0.27
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATTAAAATTTA
Found at i:29353330 original size:13 final size:12
Alignment explanation
Indices: 29353276--29353327 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
29353266 TATAATATTT
29353276 TAATAATTTTAA
1 TAATAATTTTAA
* *
29353288 T-TTTATTTTAA
1 TAATAATTTTAA
29353299 TAATAAATTTTAA
1 TAAT-AATTTTAA
29353312 GTAATAATTTTAA
1 -TAATAATTTTAA
29353325 TAA
1 TAA
29353328 ATATAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 9 0.27
12 5 0.15
13 15 0.45
14 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
TAATAATTTTAA
Found at i:29354532 original size:55 final size:56
Alignment explanation
Indices: 29354466--29354578 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 56
29354456 TAATCAATTT
*
29354466 TGAGTGTTG-TTTTTTTTTTATATGAAAGGAATGAAGATAAGGACAATAGGAAAGG
1 TGAGTGTTGTTTTTTTTTTTATATGAAAGGAATGAAGATAAGGAAAATAGGAAAGG
29354521 TGAGTGTTGTTTTTTTTTTTTATATGAAAGGAATGAAGATAAGGAAAATAGGAAAGG
1 TGAGTGTTG-TTTTTTTTTTTATATGAAAGGAATGAAGATAAGGAAAATAGGAAAGG
29354578 T
1 T
29354579 AATCATTTTC
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
55 9 0.16
57 46 0.84
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.36
Consensus pattern (56 bp):
TGAGTGTTGTTTTTTTTTTTATATGAAAGGAATGAAGATAAGGAAAATAGGAAAGG
Found at i:29356269 original size:17 final size:18
Alignment explanation
Indices: 29356237--29356274 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
29356227 GCAAAACGTG
*
29356237 CCACACGTGTATGTT-AC
1 CCACACGTGTAGGTTAAC
*
29356254 CCACACGTGTCGGTTAAC
1 CCACACGTGTAGGTTAAC
29356272 CCA
1 CCA
29356275 TGCACTGTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (18 bp):
CCACACGTGTAGGTTAAC
Found at i:29359845 original size:15 final size:15
Alignment explanation
Indices: 29359825--29359857 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29359815 CTGAAGGTTA
29359825 ACTTGTTTTGAGAAT
1 ACTTGTTTTGAGAAT
*
29359840 ACTTGTTTTGAGAGT
1 ACTTGTTTTGAGAAT
29359855 ACT
1 ACT
29359858 AACTGATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.45
Consensus pattern (15 bp):
ACTTGTTTTGAGAAT
Found at i:29367559 original size:12 final size:12
Alignment explanation
Indices: 29367542--29367573 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
29367532 GTTTTTACCC
29367542 AATTTCTTCAAT
1 AATTTCTTCAAT
29367554 AATTTCTTCAAT
1 AATTTCTTCAAT
29367566 AATTTCTT
1 AATTTCTT
29367574 TTTCTAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTCTTCAAT
Found at i:29367635 original size:25 final size:27
Alignment explanation
Indices: 29367601--29367652 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
29367591 AATCGGTAAA
*
29367601 ATTTTTCTATCA-AT-ATTTTCATACG
1 ATTTTCCTATCATATAATTTTCATACG
29367626 ATTTTCCTATCATATCAATTTTCATAC
1 ATTTTCCTATCATAT-AATTTTCATAC
29367653 AAAAATATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 2 0.09
28 10 0.43
ACGTcount: A:0.29, C:0.19, G:0.02, T:0.50
Consensus pattern (27 bp):
ATTTTCCTATCATATAATTTTCATACG
Found at i:29385519 original size:21 final size:21
Alignment explanation
Indices: 29385493--29385533 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29385483 AGACGAGCAA
* *
29385493 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
29385514 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
29385534 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:29391487 original size:47 final size:47
Alignment explanation
Indices: 29391421--29391544 Score: 144
Period size: 47 Copynumber: 2.6 Consensus size: 47
29391411 TTACATAATA
* * * *
29391421 ATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCTC-ACTG
1 ATGCCATATCCCAGATATGGTCTTACACAGT-AGCACATATCACAAC-G
* * *
29391468 ATGTCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAACG
1 ATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAACG
*
29391515 ATGCCATATCCCAGATATGGTCTTATACAG
1 ATGCCATATCCCAGATATGGTCTTACACAG
29391545 AAATCACTTG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 63 0.94
48 4 0.06
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (47 bp):
ATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAACG
Found at i:29391603 original size:31 final size:31
Alignment explanation
Indices: 29391568--29391838 Score: 389
Period size: 31 Copynumber: 8.7 Consensus size: 31
29391558 CTTGTCACTT
* *
29391568 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** *
29391599 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** *
29391630 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
29391661 GTAGCCGGAGCTACCACTTTTCACTGGTCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
29391692 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
29391723 GTAGCCGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
29391754 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
29391785 GTAGCTGAAACTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
29391816 GTAGCTGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
29391839 GTTGTCATTT
Statistics
Matches: 222, Mismatches: 18, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 222 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:29391922 original size:50 final size:51
Alignment explanation
Indices: 29391816--29391944 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
29391806 CACTGATCAG
* * * * * *
29391816 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTGCCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGCCATTAATCAGATAAGT
29391867 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCC-TTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTG-CCATTAATCAGATAAGT
29391917 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
29391945 TTCCATGGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 45 0.64
51 25 0.36
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTGCCATTAATCAGATAAGT
Found at i:29398139 original size:19 final size:20
Alignment explanation
Indices: 29398115--29398157 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
29398105 TTTCTTTAAA
*
29398115 AAAAATCAGAACTTT-TTTT
1 AAAAATCAAAACTTTATTTT
29398134 AAAAATCAAAACTTTATTTT
1 AAAAATCAAAACTTTATTTT
29398154 AAAA
1 AAAA
29398158 TAGTTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAATCAAAACTTTATTTT
Done.