Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000178.1 Hibiscus syriacus cultivar Beakdansim tig00000313_pilon, 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: 178192
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:2520 original size:21 final size:21
Alignment explanation
Indices: 2473--2537 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2463 AAGACAATCA
* *
2473 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
2495 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
2515 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
2536 AG
1 AG
2538 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:2614 original size:32 final size:32
Alignment explanation
Indices: 2573--2633 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2563 AATAGATGGA
2573 GGTGAAAGAAG-TAGAGTGTTGAGGGGTGAAGT
1 GGTGAAAGAAGTTAGAGTGTT-AGGGGTGAAGT
* *
2605 GGTGAAAGAAGTTGGGGTGTTAGGGGTGA
1 GGTGAAAGAAGTTAGAGTGTTAGGGGTGA
2634 TATTAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.28, C:0.00, G:0.49, T:0.23
Consensus pattern (32 bp):
GGTGAAAGAAGTTAGAGTGTTAGGGGTGAAGT
Found at i:4896 original size:194 final size:195
Alignment explanation
Indices: 4550--5676 Score: 1808
Period size: 194 Copynumber: 5.9 Consensus size: 195
4540 ACATATGGCC
*
4550 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTC-ATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCA-ATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
4614 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
63 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
4679 AGAATATGTCTAAA-AAAGTGTCGACACTAATATAGTTTGTCGATATTTTTTTTCCAGAATGAAT
128 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTCGATA-TTTTTTTCCAGAATGAAT
4743 GGAA
192 GGAA
* *
4747 AACAGGATGCACCTATAAAGTGTCGATCC-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
1 AACAGGGTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
4811 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATT-TACCGGTTTTATGAGAGA
66 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
*
4875 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGG
131 ATATGTCTAAATAATGTGTCGACACTAATATAG-TT-TGTCGATATTTTTTTCCAGAATGAATGG
4940 AA
194 AA
4942 AACAGGGTTGCACCCATAAAGTGTCGATCC-ATATATAAAAGTGTCGATCCC-AAATCATCGAAC
1 AACAGGG-TGCACCCATAAAGTGTCGATCCAATATA-AAAAGTGTCGATCCCAAAATCATCGAAC
*
5005 CCAAAAGTATAAGGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTT-T----
64 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
5064 --ATATGTCTAAATAATGTG-CGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
129 GAATATGTCTAAATAATGTGTCGACACTAATATAG-TT-TGTCGATATTTTTTTCCAGAATGAAT
5126 GGAA
192 GGAA
*
5130 AACAGGGTGCACCCA-AAAGTGTAGATCCAATATAAAAAGTGTCGATCCCAAAA-CA-CGAACCC
1 AACAGGGTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
5192 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT-A-AGA
66 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
*
5255 ATA-GTCTAAATAATGTGTCGACACTAATATAGTTTGTGCGAT-TTTATTTCCAGAATGAATGGA
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGT-CGATATTTTTTTCCAGAATGAATGGA
5318 A
195 A
5319 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
5384 C-AAAGTATAATGTAATATGTAATTTTTTCAATCTAACCGGTACAA-TATACCGGTTTTATGTGA
65 CAAAAGTATAATGTAATATGTAA-TTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
5447 GAA-ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTCGATATTTTTTTCCAGAATGAATGG
129 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTCGATATTTTTTTCCAGAATGAATGG
5511 -A
194 AA
* *
5512 AACAGGGTGCATCCATAAAGTGTCGATCC-ATATATAAAGTGTCGATCCCAAAATCATCGAACCC
1 AACAGGGTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
5576 -AAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
66 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
* *
5639 ATATATCTAAATAATGTGTCGACACTAATAGAGTTTGT
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGT
5677 GTCGATACTA
Statistics
Matches: 881, Mismatches: 21, Indels: 62
0.91 0.02 0.06
Matches are distributed among these distances:
185 59 0.07
186 32 0.04
187 17 0.02
188 54 0.06
189 78 0.09
190 53 0.06
191 130 0.15
192 37 0.04
193 92 0.10
194 137 0.16
195 48 0.05
196 96 0.11
197 48 0.05
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (195 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTCGATATTTTTTTCCAGAATGAATGGAA
Found at i:7142 original size:6 final size:6
Alignment explanation
Indices: 7118--7197 Score: 61
Period size: 6 Copynumber: 13.3 Consensus size: 6
7108 AGCGGTCGCA
* * * * **
7118 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GAAGCT GGCGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * *
7166 GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
7198 TGATCCAAAC
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.38, C:0.07, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:7149 original size:24 final size:24
Alignment explanation
Indices: 7121--7167 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
7111 GGTCGCAGAA
7121 GATGAAGCTGACGATGAAGATGAC
1 GATGAAGCTGACGATGAAGATGAC
*
7145 GATGAAGCTGGCGATGAAGATGA
1 GATGAAGCTGACGATGAAGATGA
7168 TGACGATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.36, T:0.17
Consensus pattern (24 bp):
GATGAAGCTGACGATGAAGATGAC
Found at i:7178 original size:3 final size:3
Alignment explanation
Indices: 7157--7201 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
7147 TGAAGCTGGC
* * *
7157 GAT GAA GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
7202 CCAAACAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.38, C:0.02, G:0.33, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:7201 original size:12 final size:12
Alignment explanation
Indices: 7121--7197 Score: 73
Period size: 12 Copynumber: 6.4 Consensus size: 12
7111 GGTCGCAGAA
*
7121 GATGAAGCTGAC
1 GATGAAGATGAC
7133 GATGAAGATGAC
1 GATGAAGATGAC
* *
7145 GATGAAGCTGGC
1 GATGAAGATGAC
*
7157 GATGAAGATGAT
1 GATGAAGATGAC
* * *
7169 GACGATGATGAT
1 GATGAAGATGAC
* *
7181 GATGATGATGAA
1 GATGAAGATGAC
7193 GATGA
1 GATGA
7198 TGATCCAAAC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 55 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:9072 original size:182 final size:182
Alignment explanation
Indices: 8645--9161 Score: 844
Period size: 182 Copynumber: 2.9 Consensus size: 182
8635 CTTTCAACAT
** * * *
8645 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGT-TAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
8709 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAATTGGAAGAAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAATTGGAAGAAAA
* * *
8774 A--TGTCGATACGATTTAAAAAGGTGTCGACATTTACACATCGGAACCCATA
131 ATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
*
8824 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
*
8889 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATTTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA-ATTGGAAGAAA
8954 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAA-CCAGA
130 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
* * *
9006 TTTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
9071 GGTCTACAACCTATATCGATACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA-ATTGGAAGAAA
*
9136 AATGTGTCGATACCATTTAAAAAAGT
130 AATGTGTCGATACGATTTAAAAAAGT
9162 GTCAGTAATT
Statistics
Matches: 315, Mismatches: 19, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
179 32 0.10
180 78 0.25
181 13 0.04
182 151 0.48
183 41 0.13
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (182 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAATTGGAAGAAAA
ATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
Found at i:11637 original size:25 final size:25
Alignment explanation
Indices: 11603--11667 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
11593 TTATCATTAA
11603 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
11628 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
11653 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
11668 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:12041 original size:23 final size:23
Alignment explanation
Indices: 12010--12072 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
12000 ATAGGTAAAC
*
12010 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
12033 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
12056 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
12073 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:12080 original size:23 final size:23
Alignment explanation
Indices: 12010--12082 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
12000 ATAGGTAAAC
* * **
12010 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
12033 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
12056 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
12079 ATAT
1 ATAT
12083 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:12280 original size:3 final size:3
Alignment explanation
Indices: 12274--12300 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12264 TATAAAATAT
12274 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
12301 AACCCAATTC
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:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:15779 original size:25 final size:25
Alignment explanation
Indices: 15745--15795 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
15735 ACAACAAATC
*
15745 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
15770 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
15795 A
1 A
15796 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:16204 original size:18 final size:18
Alignment explanation
Indices: 16183--16219 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16173 GTAATTGGAG
16183 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
16201 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
16219 T
1 T
16220 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:16227 original size:24 final size:24
Alignment explanation
Indices: 16175--16221 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
16165 TTTCATATGT
* *
16175 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
16199 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
16222 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:16520 original size:39 final size:39
Alignment explanation
Indices: 16477--16563 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
16467 TCCGATGCTC
*
16477 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
16516 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
16555 ATCAAAATC
1 ATCAAAATC
16564 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:16990 original size:23 final size:23
Alignment explanation
Indices: 16964--17036 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
16954 ATAGGTAAAC
*
16964 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
16987 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
17010 AAATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
17033 ATAT
1 ATAT
17037 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:17696 original size:333 final size:334
Alignment explanation
Indices: 17079--17719 Score: 1205
Period size: 333 Copynumber: 1.9 Consensus size: 334
17069 CATACTTTTT
17079 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
*
17144 TATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAA
66 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
*
17209 ATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
131 ATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
17274 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAA
196 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAA
*
17339 GAAGTATCGATCATTTTCATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
261 AAAGTATCGATCATTTTCATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
17404 TTGCAATGC
326 TTGCAATGC
17413 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
17478 TATAGGCGTCTAATGATTTA-TTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
66 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
*
17542 ATAATATTTTATAAAATATCAAAACAATC-AATAATTTTTTGTGTAAATGAAATTATTAAATTAA
131 ATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
*
17606 TATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTTAAA
196 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAAC-TTTAAA
*
17671 AAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAATA
260 AAAAGTATCGATCATTTTCATAAAAAGTATGGACACTTTCAATATAATA
17720 GGTAAACATA
Statistics
Matches: 300, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
332 91 0.30
333 124 0.41
334 85 0.28
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.39
Consensus pattern (334 bp):
TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
ATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAA
AAAGTATCGATCATTTTCATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
TTGCAATGC
Found at i:17758 original size:23 final size:23
Alignment explanation
Indices: 17727--17790 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
17717 ATAGGTAAAC
*
17727 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
17750 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
17773 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
17791 TGGTATATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:18336 original size:759 final size:764
Alignment explanation
Indices: 16671--18478 Score: 3408
Period size: 759 Copynumber: 2.4 Consensus size: 764
16661 TCAAGTGTTC
*
16671 TTAAGGTTATCCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
1 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
16736 TTTTTTACGTTACGATATATA-TATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATC
66 TTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATC
16800 AAAACAATCAAATAA-TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
131 AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
16864 AAACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAAGTATCGATCATTTTT
196 AAACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTT-AAAAAAAGTATCGATCATTTTT
16929 ATAAAAAGTATGGACACTTTC-A-ATAATAGGTAAACATATGATGTAATAGGTAGCGCTTATATA
260 ATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCGCTTATATA
16992 ATGTAATAGGTATCGTTTAAATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTT
325 ATGTAATAGGTATCGTTTAAATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTT
17057 TATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGT
390 TATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGT
17122 TTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATT
455 TTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTTCGTTACGA-ATATATT
17187 ATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGT
519 ATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGT
17252 GCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAA
584 GCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAA
17317 CATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTCATAAAAAGTATGGACACTTTCAATA
649 CATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTCATAAAAAGTATGGACACTTTCAATA
17382 TAATATAATGTAATAGGTAAATTTGCAATGCTCACTGTGGAAAACATTAAT
714 TAATATAATGTAATAGGTAAATTTGCAATGCTCACTGTGGAAAACATTAAT
17433 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
1 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
17498 -TTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATC
66 TTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATC
17562 AAAACAATC-AATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
131 AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
17626 AAACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTA
196 AAACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTA
17691 TAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCGCTTATATAA
261 TAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCGCTTATATAA
*
17756 TGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGG-TATATTGTAAAGTGTCTATCCTTTTT
326 TGTAATAGGTATCGTTTAAATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTT
17820 ATAAAAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTT
391 ATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTT
17884 TTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTTCGTTACG-ATATATTAT
456 TTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTTCGTTACGAATATATTAT
17948 TATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
521 TATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
18013 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACA
586 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACA
* *
18078 TAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC-A-ATA
651 TAAATTACATAACTTTAAAAGAAGTATCGATCATTTTCATAAAAAGTATGGACACTTTCAATATA
18141 ATATAATGTAATAGGTAAATTTGCAATGCTCACTGTGGAAAACATTAAT
716 ATATAATGTAATAGGTAAATTTGCAATGCTCACTGTGGAAAACATTAAT
18190 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
1 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
*
18255 TTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATT
66 TTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATC
* *
18320 AAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATG
131 AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
* *
18385 AAACACTATTAAAAAAAATTGAAACATAAATTACATAAC-TTTAAAAGAAA-TATCGATCCTTTT
196 AAACACTGTT-AAAAAAATTGAAACATAAATTACATAACTTTTAAAA-AAAGTATCGATCATTTT
18448 TATAAAAAGTATGGACACTTTCAATATAATA
259 TATAAAAAGTATGGACACTTTCAATATAATA
18479 TAATGTAATA
Statistics
Matches: 1029, Mismatches: 9, Indels: 19
0.97 0.01 0.02
Matches are distributed among these distances:
757 117 0.11
758 73 0.07
759 308 0.30
760 31 0.03
761 171 0.17
762 250 0.24
763 79 0.08
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (764 bp):
TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
TTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATC
AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
AAACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTA
TAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCGCTTATATAA
TGTAATAGGTATCGTTTAAATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTT
ATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTT
TTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTTCGTTACGAATATATTAT
TATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACA
TAAATTACATAACTTTAAAAGAAGTATCGATCATTTTCATAAAAAGTATGGACACTTTCAATATA
ATATAATGTAATAGGTAAATTTGCAATGCTCACTGTGGAAAACATTAAT
Found at i:18619 original size:332 final size:329
Alignment explanation
Indices: 17840--18505 Score: 1014
Period size: 332 Copynumber: 2.0 Consensus size: 329
17830 CCATACTTTT
** * * *
17840 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAA-TTAAGGTTATCTTTAAAATGAG-TGTAAGATATTAATCTAGTAAT
* * *
17905 TATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATTATT---ATTAAATTAAAAATTCTA
64 TATAAGCGTCTAATGATTTA-TTTGTACGTTACGATATA-TATTACGATTAAATTAAAAATTCTA
*
17967 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTA
127 AATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTA
*
18032 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
192 ATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
* *
18097 AGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAATATAATGTAATAGGTAAATT
257 AGAAATATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAATATAATGTAATAGATAAATT
*
18162 TGCAATGC
322 TGCAATAC
** * * *
18170 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAA-TTAAGGTTATCTTTAAAATGAG-TGTAAGATATTAATCTAGTAAT
* * **
18235 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
64 TATAAGCGTCTAATGATTTA-TTTGTACGTTACGATATATATTACGATTAAATTAAAAATTCTAA
*
18300 ATAATATTTTATAAAATATTAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
128 ATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
18365 TATTATAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAA
193 TATTATAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAA
18430 AGAAATATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGATAAA
257 AGAAATATCGATCCTTTTTATAAAAAGTATGGACACTTTC-A-ATAATATAATGTAATAGATAAA
18495 TTTGCAATAC
320 TTTGCAATAC
18505 T
1 T
18506 ATCGGTATAA
Statistics
Matches: 323, Mismatches: 7, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
329 4 0.01
330 103 0.32
332 111 0.34
333 73 0.23
334 1 0.00
335 31 0.10
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (329 bp):
TCACTGTGGAAAACATTAATTAAGGTTATCTTTAAAATGAGTGTAAGATATTAATCTAGTAATTA
TAAGCGTCTAATGATTTATTTGTACGTTACGATATATATTACGATTAAATTAAAAATTCTAAATA
ATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATAT
TATAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAA
ATATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAATATAATGTAATAGATAAATTTGCA
ATAC
Found at i:28434 original size:16 final size:16
Alignment explanation
Indices: 28410--28440 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28400 GATCAATGTC
*
28410 ACCATAAGATGATGCT
1 ACCAAAAGATGATGCT
28426 ACCAAAAGATGATGC
1 ACCAAAAGATGATGC
28441 CTTTTTAGAG
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:0.19, G:0.19, T:0.19
Consensus pattern (16 bp):
ACCAAAAGATGATGCT
Found at i:29007 original size:217 final size:217
Alignment explanation
Indices: 28622--29014 Score: 479
Period size: 217 Copynumber: 1.8 Consensus size: 217
28612 AAACAATAAT
* * *
28622 TTTCTCGAGAAGGTTAGGTTACTCGTGTTGATGAAGGTTCATGAGACCGATGTGTTTGATGAAGA
1 TTTCTCGAGAAGGTTAGGTTACTCATGTTGAAGAAGGTTCATGAGACCGATGGGTTTGATGAAGA
* * * * * * * **
28687 GTGAATTGGGCATAAAAACAAAATTTAGGAACCACGTCCACGACTGTAACAACAACAAACACATT
66 GTGAATTGAGAACAAAAACAAAATTCAGAAACCACGCCCACGACTGCAACAACAACAAACACACC
* * ** * *
28752 TCAATGACTTGTTTTTTCCGATTAACAGTTGGTTTGATGGAAGAAGATGACGCCACCAGAAGTGG
131 TCAATGACTTGTTTTTTCAGATCAACAACTGATTTGATGAAAGAAGATGACGCCACCAGAAGTGG
28817 ATACCTTTTTAGAAATGATCAG
196 ATACCTTTTTAGAAATGATCAG
* * * *
28839 TTTCTCGAGAAGGTTAGGTTACTCATGTTGAAGAAGGTTGATGAGATCGGTGGGTTTGATGGAGA
1 TTTCTCGAGAAGGTTAGGTTACTCATGTTGAAGAAGGTTCATGAGACCGATGGGTTTGATGAAGA
* * * * *
28904 GTGAATTGAGAACAAAAACAGAATTCATAAATCATGCCCACGACTGCAATAGA-AACAAACAC-C
66 GTGAATTGAGAACAAAAACAAAATTCAGAAACCACGCCCACGACTGCAACA-ACAACAAACACAC
28967 CTCGAACT-ACTTGTTTATTT-AGATCAACAACTGATTTGATGAAAGAAG
130 CTC-AA-TGACTTGTTT-TTTCAGATCAACAACTGATTTGATGAAAGAAG
29015 GTGATGCTTT
Statistics
Matches: 145, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
216 2 0.01
217 138 0.95
218 5 0.03
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (217 bp):
TTTCTCGAGAAGGTTAGGTTACTCATGTTGAAGAAGGTTCATGAGACCGATGGGTTTGATGAAGA
GTGAATTGAGAACAAAAACAAAATTCAGAAACCACGCCCACGACTGCAACAACAACAAACACACC
TCAATGACTTGTTTTTTCAGATCAACAACTGATTTGATGAAAGAAGATGACGCCACCAGAAGTGG
ATACCTTTTTAGAAATGATCAG
Found at i:30317 original size:48 final size:48
Alignment explanation
Indices: 30261--30357 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
30251 TTTGACTATG
30261 CGGTGGTGCTTTGTTAAGTCTTTCTACAATTAAAAGTTACAAAATAGT
1 CGGTGGTGCTTTGTTAAGTCTTTCTACAATTAAAAGTTACAAAATAGT
30309 CGGTGGTGCTTTGTTAAGTCTTTCTACAATTAAAAGTTACAAAATAGT
1 CGGTGGTGCTTTGTTAAGTCTTTCTACAATTAAAAGTTACAAAATAGT
30357 C
1 C
30358 ATATGACTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (48 bp):
CGGTGGTGCTTTGTTAAGTCTTTCTACAATTAAAAGTTACAAAATAGT
Found at i:32945 original size:26 final size:26
Alignment explanation
Indices: 32914--32972 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
32904 CGTTACTCAT
*
32914 CCGTCCGTCACGGGAAACACCACTCC
1 CCGTCCGCCACGGGAAACACCACTCC
*
32940 CCGTCCGCCACTGGAAACACCACTCC
1 CCGTCCGCCACGGGAAACACCACTCC
*
32966 CCATCCG
1 CCGTCCG
32973 ATGGGTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.22, C:0.49, G:0.17, T:0.12
Consensus pattern (26 bp):
CCGTCCGCCACGGGAAACACCACTCC
Found at i:33305 original size:117 final size:117
Alignment explanation
Indices: 33157--33403 Score: 433
Period size: 117 Copynumber: 2.1 Consensus size: 117
33147 ATATATAGAG
* *
33157 AGAGAGAGAGAGATAAATACCTAAAATTTAAGGTAAA-ATTTTTGTATTTATTTTAAATAAAAAA
1 AGAGAGAGAGAGATAAACAACTAAAATTTAAGGTAAATATTTTTGTATTTATTTTAAAT-AAAAA
33221 AATTAGACACTAAAAATTAATATAAATATAATTTAGACACCTATTAAACTAAA
65 AATTAGACACTAAAAATTAATATAAATATAATTTAGACACCTATTAAACTAAA
*
33274 AGAGAGAGAGAGATAAACAACTAAAATTTAAGGTAAATTTTTTTGTATTTATTTTAAATAAAAAA
1 AGAGAGAGAGAGATAAACAACTAAAATTTAAGGTAAATATTTTTGTATTTATTTTAAATAAAAAA
*
33339 ATTAGAGACTAAAAATTAATATAAATATAATTTAGACACCTATTAAACTAAA
66 ATTAGACACTAAAAATTAATATAAATATAATTTAGACACCTATTAAACTAAA
*
33391 ATAGAGAGAGAGA
1 AGAGAGAGAGAGA
33404 GAGGAACTGT
Statistics
Matches: 124, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
117 104 0.84
118 20 0.16
ACGTcount: A:0.52, C:0.06, G:0.11, T:0.31
Consensus pattern (117 bp):
AGAGAGAGAGAGATAAACAACTAAAATTTAAGGTAAATATTTTTGTATTTATTTTAAATAAAAAA
ATTAGACACTAAAAATTAATATAAATATAATTTAGACACCTATTAAACTAAA
Found at i:41272 original size:2 final size:2
Alignment explanation
Indices: 41265--41294 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41255 TTAATCAACA
41265 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
41295 CCACCATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44536 original size:2 final size:2
Alignment explanation
Indices: 44529--44562 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
44519 ATATAATTAA
44529 AT 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 AT
44563 TTTAATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45665 original size:20 final size:20
Alignment explanation
Indices: 45640--45678 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
45630 ATCACTTTGA
45640 TTTATT-TTATTAATAATATT
1 TTTATTATT-TTAATAATATT
45660 TTTATTATTTTAATAATAT
1 TTTATTATTTTAATAATAT
45679 ATAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATTATTTTAATAATATT
Found at i:46489 original size:21 final size:21
Alignment explanation
Indices: 46460--46512 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
46450 ATTCTGACTA
46460 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
*
46481 TCGCGTTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
*
46502 TCGCAATGCGA
1 TCGCATTGCGA
46513 ATACATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:46527 original size:20 final size:20
Alignment explanation
Indices: 46502--46597 Score: 92
Period size: 20 Copynumber: 4.8 Consensus size: 20
46492 TTTCCCAAAT
46502 TCGCAATGCGAATACATA-AA
1 TCGCAATGCGAATAC-TACAA
*
46522 TCGCAATACGAATACGTA-AA
1 TCGCAATGCGAATAC-TACAA
*
46542 TCGCAATGCGAAT-CTGACTA
1 TCGCAATGCGAATACT-ACAA
*
46562 TCGCAATGCGAAT-CTGACTA
1 TCGCAATGCGAATACT-ACAA
46582 TCGCAATGCGATATAC
1 TCGCAATGCGA-ATAC
46598 ATAGCGCCAT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
18 1 0.01
19 2 0.03
20 62 0.91
21 2 0.03
22 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACTACAA
Found at i:49229 original size:18 final size:18
Alignment explanation
Indices: 49206--49240 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49196 TTCCATCCGG
*
49206 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
49224 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
49241 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:50556 original size:13 final size:13
Alignment explanation
Indices: 50538--50566 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
50528 GCGGTCAACG
50538 GTCAACGGGTCGA
1 GTCAACGGGTCGA
50551 GTCAACGGGTCGA
1 GTCAACGGGTCGA
50564 GTC
1 GTC
50567 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.38, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:50572 original size:18 final size:17
Alignment explanation
Indices: 50545--50632 Score: 84
Period size: 18 Copynumber: 5.5 Consensus size: 17
50535 ACGGTCAACG
*
50545 GGTCGAGTCAACGGGTC
1 GGTCGGGTCAACGGGTC
50562 GAGTCGGGTCAAC--G--
1 G-GTCGGGTCAACGGGTC
50576 GGTCGGGTCAACGGGTC
1 GGTCGGGTCAACGGGTC
50593 GGGTCGGGTCAAC--G--
1 -GGTCGGGTCAACGGGTC
50607 GGTCGGGTCAACGGGTC
1 GGTCGGGTCAACGGGTC
50624 GGGTCGGGT
1 -GGTCGGGT
50633 TGTGACCGGT
Statistics
Matches: 59, Mismatches: 1, Indels: 21
0.73 0.01 0.26
Matches are distributed among these distances:
13 23 0.39
14 1 0.02
15 2 0.03
16 2 0.03
17 1 0.02
18 30 0.51
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.17
Consensus pattern (17 bp):
GGTCGGGTCAACGGGTC
Found at i:50575 original size:31 final size:31
Alignment explanation
Indices: 50537--50632 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
50527 GGCGGTCAAC
* *
50537 GGTCAACGGGTCGAGTCAACGGGTCGAGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
50568 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
50599 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
50630 GGT
1 GGT
50633 TGTGACCGGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:50580 original size:13 final size:13
Alignment explanation
Indices: 50564--50628 Score: 85
Period size: 13 Copynumber: 4.6 Consensus size: 13
50554 AACGGGTCGA
50564 GTCGGGTCAACGG
1 GTCGGGTCAACGG
50577 GTCGGGTCAACGGGTCGG
1 GTCGGGTCAA-----CGG
50595 GTCGGGTCAACGG
1 GTCGGGTCAACGG
50608 GTCGGGTCAACGG
1 GTCGGGTCAACGG
50621 GTCGGGTC
1 GTCGGGTC
50629 GGGTTGTGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
13 34 0.72
18 13 0.28
ACGTcount: A:0.12, C:0.23, G:0.48, T:0.17
Consensus pattern (13 bp):
GTCGGGTCAACGG
Found at i:51773 original size:20 final size:20
Alignment explanation
Indices: 51748--51794 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
51738 CAACGAGTGA
51748 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCAAAAATGACT
* * **
51768 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCAAAAATGACT
51788 ATCGCAA
1 ATCGCAA
51795 TGCGATTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCAAAAATGACT
Found at i:51811 original size:19 final size:20
Alignment explanation
Indices: 51765--51805 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
51755 CGCAAAAATG
*
51765 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAATTTC
*
51785 ACTATCGCAATGCGATTTTC
1 ACTATCGCAATGCGAATTTC
51805 A
1 A
51806 TTTCGCGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (20 bp):
ACTATCGCAATGCGAATTTC
Found at i:51832 original size:20 final size:20
Alignment explanation
Indices: 51807--51859 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
51797 CGATTTTCAT
51807 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
51827 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
51847 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
51860 TTAAAGTGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:53849 original size:74 final size:78
Alignment explanation
Indices: 53728--53897 Score: 249
Period size: 74 Copynumber: 2.2 Consensus size: 78
53718 AGAATAGTTT
* *
53728 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCACAA-CG-AGA-GA-ATCG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCACAAGCGAAAATAACATCG
*
53789 CAATGCGAAAATG
66 CAAAGCGAAAATG
*
53802 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCACAATGCGAAAATAACTAT
1 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCACAA-GCGAAAATAAC-AT
*
53867 CGCAAAGCGAAATTG
64 CGCAAAGCGAAAATG
53882 ACTATCGCAATGCGAA
1 ACTATCGCAATGCGAA
53898 TTTAACTATC
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
74 49 0.58
76 2 0.02
77 2 0.02
78 1 0.01
80 31 0.36
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (78 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCACAAGCGAAAATAACATCG
CAAAGCGAAAATG
Found at i:53908 original size:20 final size:20
Alignment explanation
Indices: 53728--53897 Score: 235
Period size: 20 Copynumber: 8.8 Consensus size: 20
53718 AGAATAGTTT
53728 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
53748 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
53768 ACTATCACAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
53784 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
53802 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
53822 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
53842 ACTATCACAATGCGAAAATA
1 ACTATCGCAATGCGAAAATG
* *
53862 ACTATCGCAAAGCGAAATTG
1 ACTATCGCAATGCGAAAATG
53882 ACTATCGCAATGCGAA
1 ACTATCGCAATGCGAA
53898 TTTAACTATC
Statistics
Matches: 132, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
14 6 0.05
16 4 0.03
17 4 0.03
18 4 0.03
20 114 0.86
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:54070 original size:20 final size:20
Alignment explanation
Indices: 54045--54131 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
54035 GATTCTCTCG
**
54045 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
54065 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCATTTTCGCA
54085 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
54105 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
54125 TTGCGAT
1 TTGCGAT
54132 TTTAAGTTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:54647 original size:18 final size:19
Alignment explanation
Indices: 54608--54649 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
54598 CTCATCTGTC
54608 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
54629 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
54647 ATC
1 ATC
54650 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:54679 original size:21 final size:21
Alignment explanation
Indices: 54655--54713 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
54645 CTATCATCCC
54655 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* * * *
54676 TCAAGAGGCCACTGCCATCGT
1 TCAAGAGTCCCCTCCCACCGT
*
54697 TGAAGACGT-CCCTCCCA
1 TCAAGA-GTCCCCTCCCA
54714 ACATTCTAGA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.22, C:0.41, G:0.19, T:0.19
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:56301 original size:40 final size:40
Alignment explanation
Indices: 56236--56312 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
56226 CGATTTTCAT
* **
56236 TTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCACA
1 TTTCGCATTGCGATTCACTCATTGCGATAGTCATTTCACA
** *
56276 TTTCGCATTGCGATTTTCTTATTGCGATAGTCATTTC
1 TTTCGCATTGCGATTCACTCATTGCGATAGTCATTTC
56313 CGCATTGCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (40 bp):
TTTCGCATTGCGATTCACTCATTGCGATAGTCATTTCACA
Found at i:56319 original size:20 final size:20
Alignment explanation
Indices: 56296--56363 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
56286 CGATTTTCTT
56296 ATTGCGATAGTCATTTCCGC
1 ATTGCGATAGTCATTTCCGC
*
56316 ATTGCGATAGTCATTTCCGT
1 ATTGCGATAGTCATTTCCGC
*
56336 GTTGCGATAGTCATATT-CGC
1 ATTGCGATAGTCAT-TTCCGC
56356 ATTGCGAT
1 ATTGCGAT
56364 TTCCGCGTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (20 bp):
ATTGCGATAGTCATTTCCGC
Found at i:58603 original size:3 final size:3
Alignment explanation
Indices: 58595--58633 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
58585 CTTTGGGGAT
* *
58595 TTC TTC TTC TTC TTC TTT TTC TTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
58634 AGTGTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:58610 original size:12 final size:12
Alignment explanation
Indices: 58595--58633 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
58585 CTTTGGGGAT
*
58595 TTCTTCTTCTTC
1 TTCTTTTTCTTC
58607 TTCTTTTTCTTC
1 TTCTTTTTCTTC
58619 TTCTTTTTCTTC
1 TTCTTTTTCTTC
58631 TTC
1 TTC
58634 AGTGTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:58843 original size:24 final size:24
Alignment explanation
Indices: 58809--58862 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
58799 CTGAAAAATA
58809 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
58833 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
58857 ATCAAA
1 ATCAAA
58863 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:58876 original size:24 final size:24
Alignment explanation
Indices: 58809--58876 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
58799 CTGAAAAATA
* * *
58809 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
58833 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
58857 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
58877 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:59746 original size:20 final size:20
Alignment explanation
Indices: 59723--59989 Score: 310
Period size: 20 Copynumber: 13.3 Consensus size: 20
59713 CAGAATCTCG
*
59723 TTGCGATTTACAAATTCGCA
1 TTGCGATTTACGAATTCGCA
*
59743 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGAATTCGCA
* *
59763 TTACGATTTACGTAA-TCGTA
1 TTGCGATTTACG-AATTCGCA
*
59783 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGAATTCGCA
59803 TTGCGATTTACGTAA-TCGCA
1 TTGCGATTTACG-AATTCGCA
*
59823 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGAATTCGCA
* *
59843 TTACGATTTACGTAA-TCGTA
1 TTGCGATTTACG-AATTCGCA
*
59863 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGAATTCGCA
59883 TTGCGATTTACGTAA-TCGCA
1 TTGCGATTTACG-AATTCGCA
*
59903 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGAATTCGCA
59923 TTGCGATTTACGTAA-TCGCA
1 TTGCGATTTACG-AATTCGCA
* * * *
59943 TTGCGATTTTCCAAATTTGCG
1 TTGCGA-TTTACGAATTCGCA
*
59964 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGAATTCGCA
59984 TTGCGA
1 TTGCGA
59990 ATTAGGAAAA
Statistics
Matches: 208, Mismatches: 28, Indels: 22
0.81 0.11 0.09
Matches are distributed among these distances:
19 4 0.02
20 186 0.89
21 18 0.09
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGAATTCGCA
Found at i:59770 original size:40 final size:40
Alignment explanation
Indices: 59723--59989 Score: 410
Period size: 40 Copynumber: 6.7 Consensus size: 40
59713 CAGAATCTCG
*
59723 TTGCGATTTAC-AAATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAA-TCGCATTGCGATTTACGTATTCGCA
* *
59763 TTACGATTTACGTAATCGTATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
59803 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
* *
59843 TTACGATTTACGTAATCGTATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
59883 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
* ** * *
59923 TTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTTGCG
1 TTGCGATTTACGTAATCGCATTGCGA-TTTACGTATTCGCA
*
59964 TTGCGATTTACGTATTCGCATTGCGA
1 TTGCGATTTACGTAATCGCATTGCGA
59990 ATTAGGAAAA
Statistics
Matches: 210, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
40 174 0.83
41 36 0.17
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
Found at i:60010 original size:21 final size:21
Alignment explanation
Indices: 59986--60031 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
59976 TATTCGCATT
59986 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
60007 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
60028 GCGA
1 GCGA
60032 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:60992 original size:32 final size:32
Alignment explanation
Indices: 60915--61129 Score: 170
Period size: 32 Copynumber: 6.5 Consensus size: 32
60905 TTTTCACCCT
*
60915 AAACCCGACTCCGACCCAAATATCACACTTAAA
1 AAACCCGAC-CCGACCCGAATATCACACTTAAA
* * *
60948 AAAACCGA-CCGACCTGAATATCACACTTTAA
1 AAACCCGACCCGACCCGAATATCACACTTAAA
*
60979 AAACCCAACCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACCCGAATATCACACTT-AAA
* *****
61012 AAACCCGACCCGACCCGATCCTGATTTTTTTTAAAA
1 AAACCCGACCCGACCCGA--AT-ATCACACTT-AAA
61048 AAACCCGACCTGAACCTGACCCGAATATCACACTTAAA
1 AAACCCGA-C----CC-GACCCGAATATCACACTTAAA
*
61086 AAA----ACCCGACCCGAATATCAAACTTAAA
1 AAACCCGACCCGACCCGAATATCACACTTAAA
*
61114 AAACCTGACCCGACCC
1 AAACCCGACCCGACCC
61130 AACCCGAACC
Statistics
Matches: 145, Mismatches: 22, Indels: 31
0.73 0.11 0.16
Matches are distributed among these distances:
28 23 0.16
29 2 0.01
31 26 0.18
32 28 0.19
33 27 0.19
34 1 0.01
35 1 0.01
36 16 0.11
37 1 0.01
38 6 0.04
39 4 0.03
40 1 0.01
41 2 0.01
42 7 0.05
ACGTcount: A:0.40, C:0.34, G:0.09, T:0.17
Consensus pattern (32 bp):
AAACCCGACCCGACCCGAATATCACACTTAAA
Found at i:61123 original size:27 final size:28
Alignment explanation
Indices: 61060--61126 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
61050 ACCCGACCTG
*
61060 AACCTGACCCGAATATCACACTTAAAAA
1 AACCTGACCCGAATATCAAACTTAAAAA
*
61088 AACCCGACCCGAATATCAAACTT-AAAA
1 AACCTGACCCGAATATCAAACTTAAAAA
61115 AACCTGACCCGA
1 AACCTGACCCGA
61127 CCCAACCCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 15 0.42
28 21 0.58
ACGTcount: A:0.45, C:0.31, G:0.09, T:0.15
Consensus pattern (28 bp):
AACCTGACCCGAATATCAAACTTAAAAA
Found at i:61135 original size:107 final size:106
Alignment explanation
Indices: 60958--61159 Score: 275
Period size: 107 Copynumber: 1.9 Consensus size: 106
60948 AAAACCGACC
* *
60958 GACCTGAATATCACACTTTAAAAACCCAACCCGACCCGAATATCACACTTAAAAAAACCCGACCC
1 GACCCGAATATCACACTTTAAAAA--CAACCCGACCCGAATATCAAACTTAAAAAAACCCGACCC
* * *
61023 GACCCGATCCTGA-TTTTTTTTAAAAAAACCCGACCTGAACCT
64 AACCCGAACCCGATTTTTTTTTAAAAAAACCCGACCTGAACCT
61065 GACCCGAATATCACAC-TTAAAAA-AACCCGACCCGAATATCAAACTTAAAAAACCTGACCCGAC
1 GACCCGAATATCACACTTTAAAAACAACCCGACCCGAATATCAAACTTAAAAAA----ACCCGAC
61128 CCAACCCGAACCCGATTTTTTTTTTAAAAAAA
62 CCAACCCGAACCCGA-TTTTTTTTTAAAAAAA
61160 ATCCTACCTA
Statistics
Matches: 84, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
103 28 0.33
106 7 0.08
107 34 0.40
109 15 0.18
ACGTcount: A:0.40, C:0.31, G:0.09, T:0.20
Consensus pattern (106 bp):
GACCCGAATATCACACTTTAAAAACAACCCGACCCGAATATCAAACTTAAAAAAACCCGACCCAA
CCCGAACCCGATTTTTTTTTAAAAAAACCCGACCTGAACCT
Found at i:63850 original size:14 final size:15
Alignment explanation
Indices: 63831--63859 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
63821 CATCTATAAT
63831 CATAAC-AAAATATG
1 CATAACTAAAATATG
63845 CATAACTAAAATATG
1 CATAACTAAAATATG
63860 ATTCATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (15 bp):
CATAACTAAAATATG
Found at i:63930 original size:47 final size:47
Alignment explanation
Indices: 63876--64014 Score: 122
Period size: 47 Copynumber: 3.2 Consensus size: 47
63866 ATATAAGTGG
63876 TACAAATTGCACGGTTATAACGATTGAATTGTAGCTTCAAAGGATGC
1 TACAAATTGCACGGTTATAACGATTGAATTGTAGCTTCAAAGGATGC
* * * **
63923 TACAAATTGCAATGG-TACCAAC----G-A---T-GCCT-AAACCAT-C
1 TACAAATTGC-ACGGTTA-TAACGATTGAATTGTAGCTTCAAAGGATGC
*
63960 AACAAATTGCACGGTTATAACGATTGAATTGTAGCTTCAAAGGATGC
1 TACAAATTGCACGGTTATAACGATTGAATTGTAGCTTCAAAGGATGC
64007 TACAAATT
1 TACAAATT
64015 CAGCCTCCAT
Statistics
Matches: 66, Mismatches: 12, Indels: 28
0.62 0.11 0.26
Matches are distributed among these distances:
36 6 0.09
37 12 0.18
38 5 0.08
39 3 0.05
40 2 0.03
41 1 0.02
43 1 0.02
44 2 0.03
45 3 0.05
46 5 0.08
47 20 0.30
48 6 0.09
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (47 bp):
TACAAATTGCACGGTTATAACGATTGAATTGTAGCTTCAAAGGATGC
Found at i:65068 original size:15 final size:15
Alignment explanation
Indices: 65039--65079 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
65029 AACCATGTCT
65039 AATCCT-AAA-ATCA
1 AATCCTAAAACATCA
65052 AATCCTAAAACATCA
1 AATCCTAAAACATCA
65067 AA-CCTAGAAACAT
1 AATCCTA-AAACAT
65080 AAACAAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.24
14 7 0.28
15 12 0.48
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (15 bp):
AATCCTAAAACATCA
Found at i:65973 original size:40 final size:40
Alignment explanation
Indices: 65918--66002 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
65908 GATTGAAGTA
*
65918 GTATCGATATTGATGTGGAGGTATTGACACCAAGAGTAAG
1 GTATCAATATTGATGTGGAGGTATTGACACCAAGAGTAAG
65958 GTATCAATATTGATGTGGAGGTATTGACACCAAGAGTAAG
1 GTATCAATATTGATGTGGAGGTATTGACACCAAGAGTAAG
65998 GTATC
1 GTATC
66003 GATACTGTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (40 bp):
GTATCAATATTGATGTGGAGGTATTGACACCAAGAGTAAG
Found at i:66494 original size:15 final size:15
Alignment explanation
Indices: 66474--66508 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
66464 TTATTAGTAT
66474 GTGAATACGTTATAC
1 GTGAATACGTTATAC
**
66489 GTGAATGTGTTATAC
1 GTGAATACGTTATAC
66504 GTGAA
1 GTGAA
66509 AATGTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (15 bp):
GTGAATACGTTATAC
Found at i:66518 original size:17 final size:15
Alignment explanation
Indices: 66482--66554 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
66472 ATGTGAATAC
66482 GTTATACGTGAATGT
1 GTTATACGTGAATGT
**
66497 GTTATACGTGAAAAT
1 GTTATACGTGAATGT
* *
66512 GTTTTATGTGAA-GAT
1 GTTATACGTGAATG-T
* *
66527 GTTCTATGTGAATGT
1 GTTATACGTGAATGT
* *
66542 GGTATATGTGAAT
1 GTTATACGTGAAT
66555 AAATGATATT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 47 0.98
16 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.26, T:0.41
Consensus pattern (15 bp):
GTTATACGTGAATGT
Found at i:66851 original size:13 final size:13
Alignment explanation
Indices: 66833--66857 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66823 TTCATTATGA
66833 AATATGAATTTTC
1 AATATGAATTTTC
66846 AATATGAATTTT
1 AATATGAATTTT
66858 TTTTGTATAA
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:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
AATATGAATTTTC
Found at i:67852 original size:237 final size:236
Alignment explanation
Indices: 67431--67906 Score: 801
Period size: 237 Copynumber: 2.0 Consensus size: 236
67421 GACCTTAAGA
*
67431 TCTTCCCTTTGCCTTGCATTCTCTTGCAAGAGCATGACCTTAGTATCCGAAAGAGACCATTTTCC
1 TCTTCCCTTTGCCTTGAATTCTCTTGCAAGAGCATGACCTTAGTATCCGAAAGAGACCATTTTCC
* *
67496 TTAAGTTGGTTGTATGTTCACTGAAATTGATTGAAATCATCACCCTTACATGATTTCAGCATGAA
66 TTAAGTTGGTTGTATGTTCACTGAAATTGATTGAAATCAACACCCTTACATGATTTCAGCACGAA
* * *
67561 CTCAACCAATACCCTCTCACCAAGATCCATATCCAAATTTTTAAGTATGTTGTAGGTATCCACCA
131 CTCAACCAATACCCTCTCACAAAAATCCATATCCAAAATTTTAAGTATGTTGTAGGTATCCACCA
* *
67626 TATGAATAATGTGTTTTTCCGTTGACTGATCTATAGTGTAC
196 TATGAATAATGTGTTTTTCCATTGACTGAGCTATAGTGTAC
* *
67667 TCTTCCCTTTGCCTTGAATTCTCTTGCAAGAGCATGTCCTTTGTATCCGAAAGAGACCAGTTTTC
1 TCTTCCCTTTGCCTTGAATTCTCTTGCAAGAGCATGACCTTAGTATCCGAAAGAGACCA-TTTTC
* *
67732 CTTAAGTTGGTTGTATGTTCATTGAAATTGATTGAAATCAACACCCTTACATGATTTCAGGACGA
65 CTTAAGTTGGTTGTATGTTCACTGAAATTGATTGAAATCAACACCCTTACATGATTTCAGCACGA
*
67797 ACTCAACCAATACCCTCTCACAAAAATCCATATCCAAAATTTTAAGT-TGGTTGTAGGTATTCAC
130 ACTCAACCAATACCCTCTCACAAAAATCCATATCCAAAATTTTAAGTAT-GTTGTAGGTATCCAC
*
67861 CATATGAGTAATGTGTTTTTCCATTGACTGAGCTATAGTGTAC
194 CATATGAATAATGTGTTTTTCCATTGACTGAGCTATAGTGTAC
67904 TCT
1 TCT
67907 CTATTAGATA
Statistics
Matches: 224, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
236 57 0.25
237 167 0.75
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (236 bp):
TCTTCCCTTTGCCTTGAATTCTCTTGCAAGAGCATGACCTTAGTATCCGAAAGAGACCATTTTCC
TTAAGTTGGTTGTATGTTCACTGAAATTGATTGAAATCAACACCCTTACATGATTTCAGCACGAA
CTCAACCAATACCCTCTCACAAAAATCCATATCCAAAATTTTAAGTATGTTGTAGGTATCCACCA
TATGAATAATGTGTTTTTCCATTGACTGAGCTATAGTGTAC
Found at i:68908 original size:36 final size:35
Alignment explanation
Indices: 68853--68921 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
68843 TTGCAACTTC
*
68853 AATAAGAAAATACCTAAATTTCTTATGAAACCTTT
1 AATAAGAAAATACCCAAATTTCTTATGAAACCTTT
*
68888 AATAAGAAAAATACCCAAATTTTTTATGAAACCT
1 AATAAG-AAAATACCCAAATTTCTTATGAAACCT
68922 AAATTGGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (35 bp):
AATAAGAAAATACCCAAATTTCTTATGAAACCTTT
Found at i:71106 original size:15 final size:15
Alignment explanation
Indices: 71086--71116 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
71076 AATTAGGTTT
71086 ACTATAGGGACAAAA
1 ACTATAGGGACAAAA
71101 ACTATAGGGACAAAA
1 ACTATAGGGACAAAA
71116 A
1 A
71117 TGACCCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.19, T:0.13
Consensus pattern (15 bp):
ACTATAGGGACAAAA
Found at i:74856 original size:24 final size:24
Alignment explanation
Indices: 74828--74884 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
74818 ATTGGAATCC
74828 AATTCCATCAAGGGAGGGAAAGTA
1 AATTCCATCAAGGGAGGGAAAGTA
*
74852 AATTCCATAAAGGGAGGGAAAGTA
1 AATTCCATCAAGGGAGGGAAAGTA
*
74876 AATTACATC
1 AATTCCATC
74885 CATAACATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (24 bp):
AATTCCATCAAGGGAGGGAAAGTA
Found at i:75039 original size:38 final size:37
Alignment explanation
Indices: 74987--75081 Score: 118
Period size: 37 Copynumber: 2.5 Consensus size: 37
74977 TTTAAAAAAA
* *
74987 ATTTGGGATAGGGTCGGGTCGGGTTTTTTTAAGTTTGAT
1 ATTTGGG-TCGGGTCGGGTC-GGTTTTTTTAAGTGTGAT
* *
75026 ATTTGGGTCGGGTCGAGTCTGTTTTTTTAAGTGTGAT
1 ATTTGGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGAT
*
75063 ATTCGGGTCGGGTTCGGGT
1 ATTTGGGTCGGG-TCGGGT
75082 TTAGGGTGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
37 27 0.55
38 15 0.31
39 7 0.14
ACGTcount: A:0.13, C:0.08, G:0.37, T:0.42
Consensus pattern (37 bp):
ATTTGGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGAT
Found at i:75823 original size:12 final size:12
Alignment explanation
Indices: 75806--75830 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75796 ATGTAACACA
75806 TCCTGCAGAACC
1 TCCTGCAGAACC
75818 TCCTGCAGAACC
1 TCCTGCAGAACC
75830 T
1 T
75831 TCAGCTGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (12 bp):
TCCTGCAGAACC
Found at i:90307 original size:15 final size:15
Alignment explanation
Indices: 90285--90327 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
90275 GACACACCTA
90285 GATGATGATGATGGG
1 GATGATGATGATGGG
* *
90300 GGTGATGATGACGGG
1 GATGATGATGATGGG
90315 GATGATGATGATG
1 GATGATGATGATG
90328 ATGATACTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.47, T:0.26
Consensus pattern (15 bp):
GATGATGATGATGGG
Found at i:106303 original size:24 final size:23
Alignment explanation
Indices: 106276--106349 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 23
106266 TTGATCATGT
106276 TACCTTAATTGGGATTTTAGGGGA
1 TACCTTAATT-GGATTTTAGGGGA
* ** * *
106300 TACCTTAATATGAACGTAATGGGA
1 TACCTTAAT-TGGATTTTAGGGGA
*
106324 TATCTTAATTAGGATTTTAGGGGA
1 TACCTTAATT-GGATTTTAGGGGA
106348 TA
1 TA
106350 TTTTATGGTG
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
23 1 0.03
24 35 0.95
25 1 0.03
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.36
Consensus pattern (23 bp):
TACCTTAATTGGATTTTAGGGGA
Found at i:124377 original size:39 final size:39
Alignment explanation
Indices: 124334--124431 Score: 151
Period size: 39 Copynumber: 2.5 Consensus size: 39
124324 GAATTACAAA
124334 TTTAGATTAACTATAACTTTATCCTATTTGATTTGGTAG
1 TTTAGATTAACTATAACTTTATCCTATTTGATTTGGTAG
** * *
124373 TTTAGATTAACTATAACTCAATCTTGTTTGATTTGGTAG
1 TTTAGATTAACTATAACTTTATCCTATTTGATTTGGTAG
*
124412 TTTAGATTAACTATATCTTT
1 TTTAGATTAACTATAACTTT
124432 TTATTTTCTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (39 bp):
TTTAGATTAACTATAACTTTATCCTATTTGATTTGGTAG
Found at i:134667 original size:2 final size:2
Alignment explanation
Indices: 134662--134687 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
134652 TCTCTCTCTG
134662 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
134688 ATCCAGTTCT
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):
TA
Found at i:148949 original size:661 final size:661
Alignment explanation
Indices: 147687--149016 Score: 2084
Period size: 661 Copynumber: 2.0 Consensus size: 661
147677 AAGATATAAT
* *** * *
147687 CCCTTAGGGGGTGTTTGGATTGGGGAATGTGGGATTCCCATGGGAATGGAATCCACATTCCCCCG
1 CCCTTAGGGGATGTTTGGATCAAGGAATGTGGGATTCCCATGGGAATAGAATCCACATTCCCACG
* * * *
147752 TTTGGTTAGCCCGGGAATCCTATTCCCGGTAATGTAAGATTACCAATAGTGGATTTTTTGGGGTA
66 CTTGGTTAGACCGGGAATCCTATTCCCGGTAATGTAAGATTACCAATAGTAGATTTTTTGAGGTA
*
147817 TATTACCGGGAATGTCATTACCTCCATTTCCTTAGGTATTGTTGGATTACCGGCGTTTTGGACTA
131 TATTACCGGGAATATCATTACCTCCATTTCCTTAGGTATTGTTGGATTACCGGCGTTTTGGACTA
* *
147882 AAATGCCCTTAAATTTTTATTTTTTTTCAAAAATATATTTATTCTGTCATCGAATAATAAAAATT
196 AAATGCCCTTAAA-TTTTATTTTTCTTCAAAAATATACTTATTCTGTCATCGAATAATAAAAATT
* * *
147947 TTACGAATGTTAAATTACAAATTTATCCTTAAATTATTTTAGATTTACAAAAAAAAATCTATAAT
260 CTACGAAGGTTAAATTACAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAATCTATAAT
* * *
148012 TAAAATTTTATATAAAGTTCAAGGGTTTAAATAAAATTTTACCCTTTCATTAAACTTTTTTTTAT
325 TAAAATTTTATATAAAGTTCAAGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATAT
*
148077 TTTTAATTTTGTAAAAAATATATAAATATTATGAATTTAATTTTTTTAAAGAAAATATATAAATA
390 TTTCAATTTTGTAAAAAATATATAAATATTATGAATTTAATTTTTTTAAAGAAAATATATAAATA
* *
148142 TTTTCCAACTTGTAATATTACACAAATATATAATTAGGACAATTTGGTCAAATATACATTCCAAT
455 TTTTCCAACTTGTAATA-TAAACAAATATATAATAAGGACAATTTGGTCAAATATACATTCCAAT
*
148207 AATCTTTTATTCCTTTAACCAAACACGGTAATCTTACATTCCTGCTAAGCCAACCAAACACAAAA
519 AATCTTTTATTCCTTTAACCAAACACGGTAATCTTACATTCCTGCTAAACCAACCAAACACAAAA
**
148272 TACAACATTCCCAGTAATGC-TATTCCTTGGTAATCTTACATTCCCACTGGTAATCTTATATTCC
584 TACAACATTCCCAGTAAT-CATATTCCCAGGTAATCTTACATTCCCACTGGTAATCTTATATTCC
*
148336 GTGAACCAAACGCA
648 GTGAACCAAACACA
* *
148350 CCCTTAGGGGATGTTTGGATCAAGGAATGTGGGATTCTCATGGGAATAGAATCCACATTCCCATG
1 CCCTTAGGGGATGTTTGGATCAAGGAATGTGGGATTCCCATGGGAATAGAATCCACATTCCCACG
* *** * *
148415 CTTGGTT-GATCGGGAAT-CTCATTCCCGGTAATGTTTTATTATCAATAGTAGATTTTTTTAGGT
66 CTTGGTTAGACCGGGAATCCT-ATTCCCGGTAATGTAAGATTACCAATAGTAGATTTTTTGAGGT
* * *
148478 ATATTACCGGGAATATCATTACCTCCCTTTCCTTAGGTATTGTTGGATTACTGGCTTTTTGGACT
130 ATATTACCGGGAATATCATTACCTCCATTTCCTTAGGTATTGTTGGATTACCGGCGTTTTGGACT
* * *
148543 AAAATGCCCTT-AA-TTT-TTTTTCTTCAAAAATATCCTTCTTCTGTCATTGAATAATAAAAATT
195 AAAATGCCCTTAAATTTTATTTTTCTTCAAAAATATACTTATTCTGTCATCGAATAATAAAAATT
*
148605 CTACGAAGGTTAAATTATAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAAATCTATAA
260 CTACGAAGGTTAAATTACAAATTTATCCTTAAACTATTTTAGATTTAC-AAAAAAAAATCTATAA
* *
148670 TTAAAATTTTATATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATA
324 TTAAAATTTTATATAAAGTTCAAGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATA
*
148735 TTTTCAATTTTGTAAAAAATATATATGTAAATTTTATGAATTCTAA-TTTTTTAAAGAAAATATA
389 TTTTCAATTTTGT-AAAAA-ATATA--TAAATATTATGAATT-TAATTTTTTTAAAGAAAATATA
148799 TAAATATTTTCCAACTTGTTAA-A-AAACAAATATATAATAAGGACAATTTGGTCAAATATACAT
449 TAAATATTTTCCAACTTG-TAATATAAACAAATATATAATAAGGACAATTTGGTCAAATATACAT
*
148862 TTCAATAATCTTTTATTCCTTTAACCAAACACGGTAATCTTACATTCCTGCTAAACCAACCAAAC
513 TCCAATAATCTTTTATTCCTTTAACCAAACACGGTAATCTTACATTCCTGCTAAACCAACCAAAC
*
148927 ACAAAATACAACATTTCCAGTAATCATATTCCCAGGTAATCTTACATTCCCACTGGTAATCTTAT
578 ACAAAATACAACATTCCCAGTAATCATATTCCCAGGTAATCTTACATTCCCACTGGTAATCTTAT
148992 ATTCCGTGAACCAAACACA
643 ATTCCGTGAACCAAACACA
149011 CCCTTA
1 CCCTTA
149017 AAGTTTGGAA
Statistics
Matches: 612, Mismatches: 46, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
658 85 0.14
659 91 0.15
660 6 0.01
661 194 0.32
662 116 0.19
663 114 0.19
664 6 0.01
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (661 bp):
CCCTTAGGGGATGTTTGGATCAAGGAATGTGGGATTCCCATGGGAATAGAATCCACATTCCCACG
CTTGGTTAGACCGGGAATCCTATTCCCGGTAATGTAAGATTACCAATAGTAGATTTTTTGAGGTA
TATTACCGGGAATATCATTACCTCCATTTCCTTAGGTATTGTTGGATTACCGGCGTTTTGGACTA
AAATGCCCTTAAATTTTATTTTTCTTCAAAAATATACTTATTCTGTCATCGAATAATAAAAATTC
TACGAAGGTTAAATTACAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAATCTATAATT
AAAATTTTATATAAAGTTCAAGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATT
TTCAATTTTGTAAAAAATATATAAATATTATGAATTTAATTTTTTTAAAGAAAATATATAAATAT
TTTCCAACTTGTAATATAAACAAATATATAATAAGGACAATTTGGTCAAATATACATTCCAATAA
TCTTTTATTCCTTTAACCAAACACGGTAATCTTACATTCCTGCTAAACCAACCAAACACAAAATA
CAACATTCCCAGTAATCATATTCCCAGGTAATCTTACATTCCCACTGGTAATCTTATATTCCGTG
AACCAAACACA
Found at i:148977 original size:18 final size:19
Alignment explanation
Indices: 148954--148996 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
148944 CAGTAATCAT
148954 ATTCCCA-GGTAATCTTAC
1 ATTCCCACGGTAATCTTAC
*
148972 ATTCCCACTGGTAATCTTAT
1 ATTCCCAC-GGTAATCTTAC
148992 ATTCC
1 ATTCC
148997 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCCACGGTAATCTTAC
Found at i:149230 original size:20 final size:19
Alignment explanation
Indices: 149191--149230 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
149181 AATGAGCTTG
* *
149191 GGTTTGTGTTTTGGTGATA
1 GGTTTGTGTGTAGGTGATA
149210 GGTTTGTGTGTAGGTTGATA
1 GGTTTGTGTGTAGG-TGATA
149230 G
1 G
149231 ATATCAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.47
Consensus pattern (19 bp):
GGTTTGTGTGTAGGTGATA
Found at i:166593 original size:16 final size:16
Alignment explanation
Indices: 166569--166602 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
166559 TATCGTCGAC
*
166569 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
166585 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
166601 CG
1 CG
166603 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:168805 original size:21 final size:21
Alignment explanation
Indices: 168775--168844 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
168765 GATTTATATA
*
168775 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
** * *
168796 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCGAAG
168817 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
168836 TTCGCGTTG
1 TTCGCGTTG
168845 TGATTTATTC
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
19 15 0.39
21 23 0.61
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:168829 original size:40 final size:42
Alignment explanation
Indices: 168781--168873 Score: 154
Period size: 40 Copynumber: 2.3 Consensus size: 42
168771 TATATTCGCA
168781 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
168821 TTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
168863 TTGCGATAGTC
1 TTGCGATAGTC
168874 CAAAATCGCA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 26 0.53
41 2 0.04
42 21 0.43
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:168978 original size:6 final size:6
Alignment explanation
Indices: 168967--169003 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
168957 CACGTATTAT
*
168967 CACGAC CACGAC CACGAC CACGAC CACAAC CACGAC C
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC C
169004 CGAGACGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.51, G:0.14, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:169654 original size:21 final size:21
Alignment explanation
Indices: 169625--170085 Score: 197
Period size: 21 Copynumber: 22.4 Consensus size: 21
169615 ATTTTGGACT
*
169625 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTCGAATAA
* * *
169646 ATTGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTCGAATAA
* *
169667 ATCGCAACAAATTTGGAATAA
1 ATCGCAACGAATTTCGAATAA
* *
169688 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTCGAATAA
* *
169709 ATTGCAACGAATTTAGAATAA
1 ATCGCAACGAATTTCGAATAA
* *
169730 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTCGAATAA
*
169751 ATCGCAACGAATTT-GGA-AA
1 ATCGCAACGAATTTCGAATAA
* *
169770 ATCGCAACGAACTTCGACT--
1 ATCGCAACGAATTTCGAATAA
*
169789 ATCGCAACGAATTT-GGA-AA
1 ATCGCAACGAATTTCGAATAA
*
169808 ATCGCAACGCGAACTTC-AACT--
1 ATCGCAA--CGAATTTCGAA-TAA
*
169829 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTCGAATAA
* * *
169850 ATCACAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTCGAATAA
*
169871 ATCGCAACGAATTT-GGA-AA
1 ATCGCAACGAATTTCGAATAA
* *
169890 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTCGAATAA
* *
169911 ATCGCAATGAATTT-GGA-AA
1 ATCGCAACGAATTTCGAATAA
* *
169930 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTCGAATAA
*
169951 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTCGAATAA
* *
169972 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTCGAATAA
*
169993 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTCGAATAA
* *
170014 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTCGAATAA
* *
170035 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAATTTCGAATAA
* *
170056 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAATTTCGAATAA
*
170077 ATCGTAACG
1 ATCGCAACG
170086 CAAACTTCGA
Statistics
Matches: 324, Mismatches: 68, Indels: 96
0.66 0.14 0.20
Matches are distributed among these distances:
18 4 0.01
19 116 0.36
20 3 0.01
21 146 0.45
22 2 0.01
23 53 0.16
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTCGAATAA
Found at i:169680 original size:42 final size:42
Alignment explanation
Indices: 169621--170064 Score: 746
Period size: 42 Copynumber: 10.8 Consensus size: 42
169611 TGCGATTTTG
*
169621 GACTATCGCAACGAATTTGGAATAAATTGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
169663 GACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
169705 GACTATTGCAACGAATTTAGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
169747 GACTATCGCAACGAATTTGG-A-AAATCGCAA--CGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
169785 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
169825 AACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
169867 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
169907 GACTATCGCAATGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
169947 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
169989 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
170031 GACTATCGCAACGAACTTGGAATAAATCGCAACG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACG
170065 AACTTGGAAT
Statistics
Matches: 382, Mismatches: 14, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
38 38 0.10
40 112 0.29
41 4 0.01
42 228 0.60
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:169962 original size:122 final size:126
Alignment explanation
Indices: 169621--170064 Score: 746
Period size: 122 Copynumber: 3.6 Consensus size: 126
169611 TGCGATTTTG
* *
169621 GACTATCGCAACGAATTTGGAATAAATTGCAACGCGAACTTCGACTATCGCAACAAATTTGGAAT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
* *
169686 AAATCGCAACGCGAACTTCGACTATTGCAACGAATTTAGAATAAATCGCAACGCGAACTTC
66 AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
169747 GACTATCGCAACGAATTTGG-A-AAATCGCAA--CGAACTTCGACTATCGCAACGAATTTGG-A-
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
* *
169806 AAATCGCAACGCGAACTTCAACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTC
66 AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
169867 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACTATCGCAATGAATTTGG-A-
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
169928 AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
66 AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
169989 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
170054 AAATCGCAACG
66 AAATCGCAACG
170065 AACTTGGAAT
Statistics
Matches: 301, Mismatches: 11, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
120 87 0.29
121 1 0.00
122 134 0.45
123 1 0.00
124 45 0.15
125 2 0.01
126 31 0.10
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (126 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:174796 original size:28 final size:29
Alignment explanation
Indices: 174763--174817 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
174753 AAAGTCTATT
174763 TTTTAAAATAATATTT-TATTTTAAAATA
1 TTTTAAAATAATATTTATATTTTAAAATA
*
174791 TTTTAAAATAATATTTATTTTTTAAAA
1 TTTTAAAATAATATTTATATTTTAAAA
174818 AATATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTTAAAATAATATTTATATTTTAAAATA
Found at i:175371 original size:16 final size:16
Alignment explanation
Indices: 175323--175373 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
175313 ATGTCTATCC
*
175323 TAATTTCAATCTTCTTA
1 TAATTTTAATCTT-TTA
*
175340 -AATTTTAATATTTTA
1 TAATTTTAATCTTTTA
175355 TAATTTT-ATCTTATTA
1 TAATTTTAATCTT-TTA
175371 TAA
1 TAA
175374 AATATTTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 7 0.24
16 22 0.76
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATTTTAATCTTTTA
Done.