Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 54
Found at i:9318 original size:53 final size:53
Alignment explanation
Indices: 9247--9455 Score: 298
Period size: 52 Copynumber: 4.0 Consensus size: 53
9237 TCAGTTAAAT
* * *
9247 GCCTAACTGTGCACATTGGCAGAAATGTGTCAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
*
9300 GCCTAACTATGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * * *
9353 GCCTAACTGCGTA-ATTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* *
9405 GCCTAACTGTGCAT-TTAGTAGAAAGGT-TCCAATAATGCAAGTTAGATGAAA
1 GCCTAACTGTGCATATTGGCAGAAAGGTGT-CAATAATGCAAGTTAGATGAAA
9456 TGTTAAATAC
Statistics
Matches: 139, Mismatches: 15, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
52 80 0.58
53 59 0.42
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (53 bp):
GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
Found at i:9351 original size:27 final size:27
Alignment explanation
Indices: 9268--9353 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
9258 CACATTGGCA
* *
9268 GAAATGTGTCAATAATGTAAGTTAGAT
1 GAAAGGTGTCAATAATGCAAGTTAGAT
** *
9295 GAAAGGCCT-AACT-ATGCATA-TTGGCA-
1 GAAAGGTGTCAA-TAATGCA-AGTTAG-AT
9321 GAAAGGTGTCAATAATGCAAGTTAGAT
1 GAAAGGTGTCAATAATGCAAGTTAGAT
9348 GAAAGG
1 GAAAGG
9354 CCTAACTGCG
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
26 19 0.43
27 25 0.57
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (27 bp):
GAAAGGTGTCAATAATGCAAGTTAGAT
Found at i:9376 original size:105 final size:105
Alignment explanation
Indices: 9247--9455 Score: 323
Period size: 105 Copynumber: 2.0 Consensus size: 105
9237 TCAGTTAAAT
* * *
9247 GCCTAACTGTGCACATTGGCAGAAATGTGTCAATAATGTAAGTTAGATGAAAGGCCTAACTATGC
1 GCCTAACTGCGCACATTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTATGC
*
9312 ATATTGGCAGAAAGGTGT-CAATAATGCAAGTTAGATGAAAG
66 AT-TTAGCAGAAAGGT-TCCAATAATGCAAGTTAGATGAAAG
* *
9353 GCCTAACTGCGTA-ATTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGC
1 GCCTAACTGCGCACATTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTATGC
*
9417 ATTTAGTAGAAAGGTTCCAATAATGCAAGTTAGATGAAA
66 ATTTAGCAGAAAGGTTCCAATAATGCAAGTTAGATGAAA
9456 TGTTAAATAC
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
103 1 0.01
104 33 0.35
105 50 0.53
106 11 0.12
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (105 bp):
GCCTAACTGCGCACATTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTATGC
ATTTAGCAGAAAGGTTCCAATAATGCAAGTTAGATGAAAG
Found at i:9417 original size:26 final size:26
Alignment explanation
Indices: 9336--9417 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
9326 GTGTCAATAA
9336 TGCAAGTTAGATGAAAGGCCTAACTG
1 TGCAAGTTAGATGAAAGGCCTAACTG
* * * *
9362 CGTAA-TTGGCA-GAAATGTGCC-AA-TAA
1 TGCAAGTTAG-ATGAAA-G-GCCTAACT-G
9388 TGCAAGTTAGATGAAAGGCCTAACTG
1 TGCAAGTTAGATGAAAGGCCTAACTG
9414 TGCA
1 TGCA
9418 TTTAGTAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 16
0.62 0.12 0.25
Matches are distributed among these distances:
25 11 0.28
26 18 0.45
27 11 0.28
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (26 bp):
TGCAAGTTAGATGAAAGGCCTAACTG
Found at i:17789 original size:35 final size:35
Alignment explanation
Indices: 17743--17832 Score: 153
Period size: 35 Copynumber: 2.6 Consensus size: 35
17733 AACTCGAAGG
* *
17743 TTTTGTGTTTCAAGAGAAACATTTTCAAAGTTTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
*
17778 TTTTGTGTTTCATGAGAAACAATTTCAAAGGTTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
17813 TTTTGTGTTTCAAGAGAAAC
1 TTTTGTGTTTCAAGAGAAAC
17833 TGTCTCAAGG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.46
Consensus pattern (35 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
Found at i:18129 original size:203 final size:202
Alignment explanation
Indices: 17818--18362 Score: 666
Period size: 203 Copynumber: 2.7 Consensus size: 202
17808 GTTTTTTTTG
* * * * * *
17818 TGTTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGAGAAACATAATCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGA-GCAAAA-TTTATTTCAAGGGAAAGAT-TTCAATG-TT
** * * * * * * *
17883 GGTGTTTCAAGAGAAACTGTTTCAAGAGAGACAAAACTTTGTTTCAAAAGAAATTGTCTCAAGGG
62 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAAGGAAACTATCTCAAGAG
* ** *
17948 AGACGAAATTTGTTTCAAGGAAAACAG-ATTCAAAGATTT-TGTTTCAAGGGAAACTGTCTCAAG
127 AGACAAAATTCATTTCAAGGAAAA-AGTATTCAAAG-TTTATGTTTCAAGAGAAACTGTCTCAAG
*
18011 AGAGATAAAA-TT
190 AGAGACAAAATTT
* *
18023 TGTTTCAAGTGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATGGTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAG-CAAAATTTATTTCAAGGGAAA-GATTTCAATGTTTA
*
18088 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
64 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAAGGAAACTATCTCAAGAGAG
* * * * *
18153 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAG
129 ACAAAATTCATTTCAAGGAAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAG
18218 ACAAAATTT
194 ACAAAATTT
* * * * *
18227 TGTTTCAAGGGAAACTATCTCAAGAGAG-AAAATTCATTTCAAGGGAAACGTTTTTAATGTTTAT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGCAAAATTTATTTCAAGGGAAA-GATTTCAATGTTTAT
*
18291 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAAGGAAACTATCTCAAGCGAGA
65 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAAGGAAACTATCTCAAGAGAGA
*
18356 TAAAATT
130 CAAAATT
18363 TTCTTTAAAA
Statistics
Matches: 298, Mismatches: 37, Indels: 13
0.86 0.11 0.04
Matches are distributed among these distances:
202 105 0.35
203 114 0.38
204 48 0.16
205 31 0.10
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (202 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGCAAAATTTATTTCAAGGGAAAGATTTCAATGTTTATG
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAAGGAAACTATCTCAAGAGAGAC
AAAATTCATTTCAAGGAAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGAC
AAAATTT
Found at i:18159 original size:102 final size:102
Alignment explanation
Indices: 17818--18363 Score: 661
Period size: 102 Copynumber: 5.4 Consensus size: 102
17808 GTTTTTTTTG
* * * * * * * * *
17818 TGTTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGAGAAAC-ATAATCAAAGAT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTTATTTCAAGGGAAACGGT-TTCAATG-T
** * * *
17882 TGGTGTTTCAAGAGAAACTGTTTCAAGAGAGACAAAACTT
63 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
** * * * * * * * * *
17922 TGTTTCAAAAGAAATTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAACAGATTCAAAGATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAACGGTTTCAATG-TTT
* * *
17987 -TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA-TT
65 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * *
18023 TGTTTCAAGTGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATGGTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAACGGTTTCAATGTTTA
18088 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * *
18125 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAACGGTTTCAATGTTTA
18190 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * *
18227 TGTTTCAAGGGAAACTATCTCAAGAGAG--AAAATTCATTTCAAGGGAAACGTTTTTAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAACGGTTTCAATGTTTA
18290 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * *
18327 TGTTTCAAAGGAAACTATCTCAAGCGAGATAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT
18364 TCTTTAAAAA
Statistics
Matches: 401, Mismatches: 36, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
100 99 0.25
101 83 0.21
102 165 0.41
103 24 0.06
104 30 0.07
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAACGGTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:18513 original size:71 final size:75
Alignment explanation
Indices: 18381--18519 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 75
18371 AAATAGTCTA
* * *
18381 GAGTGAAATGAAATGCTTTCTTTCGAGTGAAAACGATCTCAGGCGAGACAAATCTTGTTTTAAGA
1 GAGTGAAATGAAATGCTTTCTTTCGAGTGAAAACGATCTCAAGCGAGACAAATCTTATTTTAAAA
18446 AAACAATCTT
66 AAACAATCTT
*
18456 GAGTGAAAT-AAAT-C-TTCTTTCGAGT-AAAAC-AGTCTCAAGTGAGACAAAGTC-TATTTTAA
1 GAGTGAAATGAAATGCTTTCTTTCGAGTGAAAACGA-TCTCAAGCGAGACAAA-TCTTATTTTAA
18515 AAAAA
64 AAAAA
18520 ATAATCTCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
70 1 0.02
71 30 0.52
72 13 0.22
73 1 0.02
74 4 0.07
75 9 0.16
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (75 bp):
GAGTGAAATGAAATGCTTTCTTTCGAGTGAAAACGATCTCAAGCGAGACAAATCTTATTTTAAAA
AAACAATCTT
Found at i:18539 original size:72 final size:72
Alignment explanation
Indices: 18382--18541 Score: 173
Period size: 72 Copynumber: 2.2 Consensus size: 72
18372 AATAGTCTAG
* * *
18382 AGTGAAATGAAATGCTTTCTTTCGAGTGAAAACGATCTCAGGCGAGACAAATCTTGTTTTAAGAA
1 AGTGAAAT-AAAT-C-TTCTTTCGAGTGAAAACGATCTCAAGCGAGACAAATCTTGTTTAAAAAA
**
18447 AACAATCTTG
63 AACAATCTCA
*
18457 AGTGAAATAAATCTTCTTTCGAGT-AAAAC-AGTCTCAAGTGAGACAAAGTCTAT-TTTAAAAAA
1 AGTGAAATAAATCTTCTTTCGAGTGAAAACGA-TCTCAAGCGAGACAAA-TCT-TGTTTAAAAAA
*
18519 AATAATCTCA
63 AACAATCTCA
*
18529 AGTGAGATAAATC
1 AGTGAAATAAATC
18542 ATCTGCATTA
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
70 1 0.01
71 19 0.26
72 40 0.54
73 2 0.03
74 4 0.05
75 8 0.11
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (72 bp):
AGTGAAATAAATCTTCTTTCGAGTGAAAACGATCTCAAGCGAGACAAATCTTGTTTAAAAAAAAC
AATCTCA
Found at i:20007 original size:183 final size:183
Alignment explanation
Indices: 19692--20045 Score: 582
Period size: 183 Copynumber: 1.9 Consensus size: 183
19682 ACCAAGTTTA
* * *
19692 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGTCTGATAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * *
19757 GCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGATTTCAAGTT
66 ACCAAGTGTCCAAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGACTTCAAGTT
* *
19822 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGAACAAATC
131 TCCTATATAACCAATTGCATTAGTGGAATAGCTCAGCTTTAGAGGAACAAATC
* * *
19875 ACTGAAGGGTTCATCTCATCATAAAGTCTTTGGCCTGACAAAAGCAGTGGAGTAAACACTGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
19940 ACCAAGTGTCCAAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCCTTCGAGTT
66 ACCAAGTGTCCAAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGACTTCAAGTT
*
20005 TCCTATATATCCAATTGCATTAGTGGAATAGCTCAGCTTTA
131 TCCTATATAACCAATTGCATTAGTGGAATAGCTCAGCTTTA
20046 CGGATTTAAT
Statistics
Matches: 157, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
183 157 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
ACCAAGTGTCCAAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGACTTCAAGTT
TCCTATATAACCAATTGCATTAGTGGAATAGCTCAGCTTTAGAGGAACAAATC
Found at i:25499 original size:20 final size:18
Alignment explanation
Indices: 25457--25504 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
25447 TGATGTAATA
**
25457 GTATCGATACTAAGGTGG
1 GTATCGATACTAAGGAAG
25475 GTATCGATACTAAGAGAAAG
1 GTATCGATACTAAG-G-AAG
25495 GTATCGATAC
1 GTATCGATAC
25505 CATGGATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 14 0.54
19 1 0.04
20 11 0.42
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.25
Consensus pattern (18 bp):
GTATCGATACTAAGGAAG
Found at i:26206 original size:106 final size:105
Alignment explanation
Indices: 25997--26322 Score: 420
Period size: 106 Copynumber: 3.0 Consensus size: 105
25987 AAGAAAATTT
* ** * *
25997 AAAGGCCTAAATGCGCATATTGGCATAAAGGTGCCAATAATGCAAGTTACATGATCAGTTAAATG
1 AAAGGCCTAACTATGCA-ATTGGCAGAAAGGTGCCAATAATGCAAGTT--A-GAT--G--AAAGG
* *
26062 CCTAACTGTGCATATTGGCGGAAAGGTGTCAATAATGCAAGTTAGATT
58 CCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATG
* * *
26110 AAAGGCCTAACTATGCATATTGGCAGAAAGTTGTCAATAATGTAAGTTAGATGAAAGGCCTAACT
1 AAAGGCCTAACTATGCA-ATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACT
* *
26175 GTGCATATTGGTAAAAAGGTGTCAATAATGCAAGTTAGATG
65 GTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATG
* *
26216 AAAGGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTG
1 AAAGGCCTAACTATGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTG
* *
26281 TGCAT-TTGGCAGAAAGGTGACAATAAAGCAAGTTAGATG
66 TGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATG
26320 AAA
1 AAA
26323 TGTTAAATGT
Statistics
Matches: 192, Mismatches: 21, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
104 33 0.17
105 49 0.26
106 64 0.33
108 1 0.01
110 3 0.02
111 1 0.01
113 41 0.21
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.25
Consensus pattern (105 bp):
AAAGGCCTAACTATGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTG
TGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATG
Found at i:26233 original size:26 final size:26
Alignment explanation
Indices: 26203--26284 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
26193 GTGTCAATAA
26203 TGCAAGTTAGATGAAAGGCCTAACTG
1 TGCAAGTTAGATGAAAGGCCTAACTG
* *
26229 TGCAA-TT-GGTAGAAAGGTGCC-AA-TAA
1 TGCAAGTTAGAT-GAAA-G-GCCTAACT-G
26255 TGCAAGTTAGATGAAAGGCCTAACTG
1 TGCAAGTTAGATGAAAGGCCTAACTG
26281 TGCA
1 TGCA
26285 TTTGGCAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
24 2 0.05
25 10 0.23
26 20 0.45
27 10 0.23
28 2 0.05
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TGCAAGTTAGATGAAAGGCCTAACTG
Found at i:26259 original size:52 final size:53
Alignment explanation
Indices: 26061--26322 Score: 411
Period size: 53 Copynumber: 5.0 Consensus size: 53
26051 TCAGTTAAAT
* *
26061 GCCTAACTGTGCATATTGGCGGAAAGGTGTCAATAATGCAAGTTAGATTAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * *
26114 GCCTAACTATGCATATTGGCAGAAAGTTGTCAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* *
26167 GCCTAACTGTGCATATTGGTAAAAAGGTGTCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* *
26220 GCCTAACTGTGCA-ATTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* *
26272 GCCTAACTGTGCAT-TTGGCAGAAAGGTGACAATAAAGCAAGTTAGATGAAA
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
26323 TGTTAAATGT
Statistics
Matches: 193, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
52 84 0.44
53 109 0.56
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (53 bp):
GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
Found at i:29287 original size:15 final size:15
Alignment explanation
Indices: 29264--29299 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
29254 TGGTGAAGAA
29264 AAAAG-AAGATCAAG
1 AAAAGAAAGATCAAG
*
29278 AAAAGAAAGATGAAG
1 AAAAGAAAGATCAAG
29293 AAAAGAA
1 AAAAGAA
29300 TGAAATGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.69, C:0.03, G:0.22, T:0.06
Consensus pattern (15 bp):
AAAAGAAAGATCAAG
Found at i:29310 original size:15 final size:15
Alignment explanation
Indices: 29292--29321 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29282 GAAAGATGAA
*
29292 GAAAAGAATGAAATG
1 GAAAAGAATAAAATG
29307 GAAAAGAATAAAATG
1 GAAAAGAATAAAATG
29322 ATTGGTGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.13
Consensus pattern (15 bp):
GAAAAGAATAAAATG
Found at i:33940 original size:20 final size:20
Alignment explanation
Indices: 33915--33954 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
33905 ATCATTCCAA
33915 CATGCAAGCATCATCAAATT
1 CATGCAAGCATCATCAAATT
** *
33935 CATGCATTCATCTTCAAATT
1 CATGCAAGCATCATCAAATT
33955 TCATCTCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (20 bp):
CATGCAAGCATCATCAAATT
Found at i:36487 original size:21 final size:21
Alignment explanation
Indices: 36436--36487 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 21
36426 AATTCCAGTA
*
36436 TACTAAA-ATGGTATCGATAC
1 TACTAAATATAGTATCGATAC
*
36456 TA-T--ATACAGTATCGATAC
1 TACTAAATATAGTATCGATAC
36474 TACTAAATATAGTA
1 TACTAAATATAGTA
36488 GTATCGATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
17 1 0.04
18 13 0.52
19 2 0.08
20 2 0.08
21 7 0.28
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (21 bp):
TACTAAATATAGTATCGATAC
Found at i:41758 original size:5 final size:5
Alignment explanation
Indices: 41742--41800 Score: 57
Period size: 5 Copynumber: 11.8 Consensus size: 5
41732 GAACATAATA
* * * * *
41742 AAAAT AAGAT AAAAT AACAT AAAAGT AGAAT AAAAT -AAAT AATAT AATAT
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT
41792 AAAAT AAAA
1 AAAAT AAAA
41801 ATATTATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
4 4 0.09
5 36 0.82
6 4 0.09
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:42007 original size:2 final size:2
Alignment explanation
Indices: 41996--42030 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
41986 TCTTTCAAAG
41996 AT AT -T 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 AT
42031 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:42868 original size:12 final size:12
Alignment explanation
Indices: 42853--42898 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
42843 CGGTTTTTTT
*
42853 ACCGGATAAAAA
1 ACCGGTTAAAAA
42865 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
42880 ACCGGTTAAAAA
1 ACCGGTTAAAAA
42892 ACCGGTT
1 ACCGGTT
42899 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:42880 original size:15 final size:13
Alignment explanation
Indices: 42859--42899 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
42849 TTTTACCGGA
42859 TAAAAAACCGGTT
1 TAAAAAACCGGTT
42872 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
42886 TAAAAAACCGGTT
1 TAAAAAACCGGTT
42899 T
1 T
42900 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:45217 original size:21 final size:21
Alignment explanation
Indices: 45193--45232 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
45183 TTTATTTTAT
45193 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
45214 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
45233 AACTTAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:45281 original size:33 final size:33
Alignment explanation
Indices: 45227--45325 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
45217 TTTGTTTCAA
*
45227 TTATCGAACTT-AAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
45259 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
45292 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
45325 T
1 T
45326 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 11 0.18
33 51 0.82
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:45354 original size:13 final size:13
Alignment explanation
Indices: 45311--45365 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
45301 TTGGAAGTAT
45311 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
45324 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
45338 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
45351 TTAAGTATTTGAA
1 TTAAGTATTTCAA
45364 TT
1 TT
45366 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:45587 original size:21 final size:21
Alignment explanation
Indices: 45561--45617 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
45551 TGGAGCGTGG
*
45561 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
45582 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
45603 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
45618 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:45808 original size:15 final size:15
Alignment explanation
Indices: 45783--45838 Score: 76
Period size: 15 Copynumber: 3.6 Consensus size: 15
45773 ATCTGGAATA
*
45783 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
45798 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
45813 TTAAAAAACCGGTTTTT
1 TT--AAAACCGGTTTTT
45830 TTAAAACCG
1 TTAAAACCG
45839 AAACCGGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 22 0.61
17 14 0.39
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:45847 original size:21 final size:17
Alignment explanation
Indices: 45785--45835 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
45775 CTGGAATATT
*
45785 AAAATCGGTTTTTTT--
1 AAAACCGGTTTTTTTAA
*
45800 ATAACCGGTTTTTTTAA
1 AAAACCGGTTTTTTTAA
45817 AAAACCGGTTTTTTTAA
1 AAAACCGGTTTTTTTAA
45834 AA
1 AA
45836 CCGAAACCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 13 0.42
17 18 0.58
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (17 bp):
AAAACCGGTTTTTTTAA
Found at i:45956 original size:15 final size:17
Alignment explanation
Indices: 45930--45961 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
45920 TTCTATGGGA
45930 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
45946 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
45962 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:47003 original size:3 final size:3
Alignment explanation
Indices: 46995--47056 Score: 70
Period size: 3 Copynumber: 19.7 Consensus size: 3
46985 TTTATTTATG
* *
46995 ATA ATA ATA ATA ATA ATA ATA ATA CTTA ATA ATA ATA ATA CTTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -ATA ATA
*
47042 ATTA AAA ATA ATA AT
1 A-TA ATA ATA ATA AT
47057 CACTGGGCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
3 43 0.86
4 7 0.14
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:47026 original size:16 final size:16
Alignment explanation
Indices: 46995--47043 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
46985 TTTATTTATG
*
46995 ATAATAATA-ATAATA
1 ATAATAATACTTAATA
47010 ATAATAATACTTAATA
1 ATAATAATACTTAATA
47026 ATAATAATACTTAATA
1 ATAATAATACTTAATA
47042 AT
1 AT
47044 TAAAAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 9 0.28
16 23 0.72
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATAATACTTAATA
Found at i:47056 original size:16 final size:16
Alignment explanation
Indices: 46995--47053 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
46985 TTTATTTATG
46995 ATAATAATAA-TAATA
1 ATAATAATAATTAATA
*
47010 ATAATAATACTTAATA
1 ATAATAATAATTAATA
*
47026 ATAATAATACTTAATA
1 ATAATAATAATTAATA
*
47042 ATTAAAAATAAT
1 A-TAATAATAAT
47054 AATCACTGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
15 9 0.23
16 22 0.56
17 8 0.21
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATAATAATTAATA
Found at i:53393 original size:23 final size:23
Alignment explanation
Indices: 53355--53422 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
53345 GCATTGTACG
*
53355 TTTTCATTTGTCTTTATGGCACA
1 TTTTCATCTGTCTTTATGGCACA
* *
53378 TTTTCATCTGTTTTTATGGCACG
1 TTTTCATCTGTCTTTATGGCACA
* * *
53401 TTTTCATATGCCTTCATGGCAC
1 TTTTCATCTGTCTTTATGGCAC
53423 TATATGATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.49
Consensus pattern (23 bp):
TTTTCATCTGTCTTTATGGCACA
Found at i:53747 original size:23 final size:23
Alignment explanation
Indices: 53694--53799 Score: 88
Period size: 23 Copynumber: 4.6 Consensus size: 23
53684 TCAACATGTA
* * * *
53694 TGTCTGTATGACATGTTTTAATC
1 TGTCTTTATGGCACGTTTTCATC
* * *
53717 TG-CATTTATAGTACGTTTTCATT
1 TGTC-TTTATGGCACGTTTTCATC
*
53740 TGTCTTTATGGCACATTTTCATC
1 TGTCTTTATGGCACGTTTTCATC
* *
53763 TGTTTTTATGGCACGTTTTCATA
1 TGTCTTTATGGCACGTTTTCATC
* *
53786 TGCCTTCATGGCAC
1 TGTCTTTATGGCAC
53800 ACTTTCTTTT
Statistics
Matches: 64, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
22 1 0.02
23 62 0.97
24 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTCTTTATGGCACGTTTTCATC
Found at i:53805 original size:23 final size:23
Alignment explanation
Indices: 53732--53815 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
53722 TTATAGTACG
*
53732 TTTTCATTTGTCTTTATGGCACA
1 TTTTCATATGTCTTTATGGCACA
* * *
53755 TTTTCATCTGTTTTTATGGCACG
1 TTTTCATATGTCTTTATGGCACA
* *
53778 TTTTCATATGCCTTCATGGCACA
1 TTTTCATATGTCTTTATGGCACA
* * *
53801 CTTTCTTTTGTCTTT
1 TTTTCATATGTCTTT
53816 TGACATATTT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.14, C:0.20, G:0.13, T:0.52
Consensus pattern (23 bp):
TTTTCATATGTCTTTATGGCACA
Found at i:56195 original size:55 final size:55
Alignment explanation
Indices: 56111--56296 Score: 320
Period size: 55 Copynumber: 3.4 Consensus size: 55
56101 CCTTAGAATT
56111 AGGGGGAATT-AGAATCCAATTCCACCACTTTCCCATGTTTGGTTCAAGTTTTCAA
1 AGGGGGAATTGA-AATCCAATTCCACCACTTTCCCATGTTTGGTTCAAGTTTTCAA
56166 AGGGGGAATTGAAATCCAATTCCACCACTTTCCCATGTTTGGTTCAAGTTTTCAA
1 AGGGGGAATTGAAATCCAATTCCACCACTTTCCCATGTTTGGTTCAAGTTTTCAA
* *
56221 AGGGAGAATTGAAATCCAATCCCACCACTTTCCCATGTTTGGTTCAAGTTTTCAA
1 AGGGGGAATTGAAATCCAATTCCACCACTTTCCCATGTTTGGTTCAAGTTTTCAA
* *
56276 AGGGGAAATTGAAATCTAATT
1 AGGGGGAATTGAAATCCAATT
56297 TCATCAAGGG
Statistics
Matches: 124, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
55 123 0.99
56 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (55 bp):
AGGGGGAATTGAAATCCAATTCCACCACTTTCCCATGTTTGGTTCAAGTTTTCAA
Found at i:56499 original size:28 final size:28
Alignment explanation
Indices: 56468--56553 Score: 113
Period size: 28 Copynumber: 3.1 Consensus size: 28
56458 TATCGGGTTT
56468 GGGTCTGGTTTTTTTAAGTTTGATATTC
1 GGGTCTGGTTTTTTTAAGTTTGATATTC
* *
56496 GGGT-TGAGCTTTTTTAAGTGTGATATTC
1 GGGTCTG-GTTTTTTTAAGTTTGATATTC
*
56524 GGGTCGGGTTTTTTTAAGTGTT-ATATTC
1 GGGTCTGGTTTTTTTAAGT-TTGATATTC
56552 GG
1 GG
56554 TCGGGTTCGG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.04
28 46 0.92
29 2 0.04
ACGTcount: A:0.15, C:0.07, G:0.29, T:0.49
Consensus pattern (28 bp):
GGGTCTGGTTTTTTTAAGTTTGATATTC
Found at i:57188 original size:18 final size:18
Alignment explanation
Indices: 57150--57201 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
57140 GTTTCAGATT
57150 CATATTCCAATT-CCT-A
1 CATATTCCAATTCCCTCA
57166 CATATTCCAATTCCCTCA
1 CATATTCCAATTCCCTCA
* *
57184 CATATTCTAATTCTCTCA
1 CATATTCCAATTCCCTCA
57202 GAAACATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.38
17 3 0.09
18 17 0.53
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (18 bp):
CATATTCCAATTCCCTCA
Found at i:59631 original size:6 final size:6
Alignment explanation
Indices: 59620--59657 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
59610 CTTGTTTCCT
59620 TAACCC TAACCC TAACCC TAACCC TAACCC TAACCC TA
1 TAACCC TAACCC TAACCC TAACCC TAACCC TAACCC TA
59658 CCACCAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.18
Consensus pattern (6 bp):
TAACCC
Found at i:62009 original size:54 final size:54
Alignment explanation
Indices: 61951--62131 Score: 220
Period size: 54 Copynumber: 3.4 Consensus size: 54
61941 AATGCACCCG
* *
61951 TAGTGCCCATACAGTTATTCATAAACATATTATGAA-TCTCGTGGTTTGCACACA
1 TAGTGCCGAAACAGTTATTCATAAACATATTATGAATTC-CGTGGTTTGCACACA
* *
62005 TAGTGCTGAAACGGTTATTCATAAACATATTATGAATTCCGTGGTTTGCACACA
1 TAGTGCCGAAACAGTTATTCATAAACATATTATGAATTCCGTGGTTTGCACACA
* ** ** *** *
62059 TAGTGCCGAAACTGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACT
1 TAGTGCCGAAACAGTTATTCATAAACATATTATGAATTCCGTGGTTTGCACACA
*
62113 TAGTGCCGAAACGGTTATT
1 TAGTGCCGAAACAGTTATT
62132 ATCCACGTAG
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
54 109 0.98
55 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (54 bp):
TAGTGCCGAAACAGTTATTCATAAACATATTATGAATTCCGTGGTTTGCACACA
Found at i:62193 original size:107 final size:108
Alignment explanation
Indices: 61997--62333 Score: 453
Period size: 107 Copynumber: 3.1 Consensus size: 108
61987 TCTCGTGGTT
* * ** ** *** *
61997 TGCACACATAGTGCTGAAACGGTTATTCATAAACATATTATGAATTCCGTGGTTTGCACACATAG
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAG
* *
62062 TGCCGAAACTGTTATTCATCCACATAGGATGAATTCCGTGAAA
66 TGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* *
62105 TGCACACTTAGTGCCGAAACGGTTATT-ATCCACGTAGGATGAATTCTGTGAAATGCACACTTAG
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAG
*
62169 TGCAAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
66 TGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
** * * * *
62212 -AAAAACTTAGTGTCGAAACGGTTATTCATCCACTTAGGATGAATTCCGTGAAACGCACACTTAG
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAG
**
62276 TGCCAAAACGGTTATTCATCCACATAGGATGAATTATGTGAAA
66 TGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
62319 TGCACACTTAGTGCC
1 TGCACACTTAGTGCC
62334 TATTTGGTAA
Statistics
Matches: 198, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
106 22 0.11
107 141 0.71
108 35 0.18
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (108 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAG
TGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:62297 original size:54 final size:54
Alignment explanation
Indices: 61997--62333 Score: 444
Period size: 54 Copynumber: 6.3 Consensus size: 54
61987 TCTCGTGGTT
* * ** ** ***
61997 TGCACACATAGTGCTGAAACGGTTATTCATAAACATATTATGAATTCCGTGGTT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* *
62051 TGCACACATAGTGCCGAAACTGTTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* *
62105 TGCACACTTAGTGCCGAAACGGTTATT-ATCCACGTAGGATGAATTCTGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
**
62158 TGCACACTTAGTGCAAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
** * * *
62212 -AAAAACTTAGTGTCGAAACGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * **
62265 CGCACACTTAGTGCCAAAACGGTTATTCATCCACATAGGATGAATTATGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
62319 TGCACACTTAGTGCC
1 TGCACACTTAGTGCC
62334 TATTTGGTAA
Statistics
Matches: 248, Mismatches: 33, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
53 95 0.38
54 153 0.62
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:68802 original size:54 final size:54
Alignment explanation
Indices: 68776--69006 Score: 354
Period size: 54 Copynumber: 4.3 Consensus size: 54
68766 TTCCATGGTT
* *
68776 TGCACACATAGTGCCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
68830 TGCACACTTAGTGCCGAAATGGTTATTCATCCACATATGATGAATTCTGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
*
68884 TGCAAACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* ** * * *
68938 TGCACACGTAGTGCTAAAACAGTTATTCATTCACATAGGATGAATTCCGTAAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
68992 TGCACACTTAGTGCC
1 TGCACACTTAGTGCC
69007 TATTTGGTAA
Statistics
Matches: 159, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 159 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:69401 original size:19 final size:21
Alignment explanation
Indices: 69348--69401 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
69338 TACCCATACC
69348 ATGGTATCAATACTACCACATT
1 ATGGTATCAATACTACCACA-T
* * *
69370 ATGGTACCGATACTA-CGC-T
1 ATGGTATCAATACTACCACAT
69389 ATGGTATCAATAC
1 ATGGTATCAATAC
69402 CATTTTTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 12 0.44
21 2 0.07
22 13 0.48
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (21 bp):
ATGGTATCAATACTACCACAT
Found at i:70240 original size:16 final size:16
Alignment explanation
Indices: 70219--70258 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
70209 TTTAATCGAA
70219 TAAATCCTACTATTTT
1 TAAATCCTACTATTTT
70235 TAAATCCTACTATTTT
1 TAAATCCTACTATTTT
70251 TAAATCCT
1 TAAATCCT
70259 TTCAATAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATCCTACTATTTT
Found at i:75257 original size:16 final size:17
Alignment explanation
Indices: 75231--75287 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 17
75221 TTTCCATTTA
75231 AATAGAATATAAATTCTT
1 AATA-AATATAAATTCTT
75249 AATAATATATTTAAATT-TT
1 AATAA-ATA--TAAATTCTT
*
75268 AATTGAATATAAATTCTT
1 AA-TAAATATAAATTCTT
75286 AA
1 AA
75288 ATAATAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
17 7 0.21
18 11 0.33
19 7 0.21
20 8 0.24
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (17 bp):
AATAAATATAAATTCTT
Found at i:75283 original size:37 final size:37
Alignment explanation
Indices: 75122--75293 Score: 170
Period size: 37 Copynumber: 4.6 Consensus size: 37
75112 TATTCCAATC
**
75122 GAATATAAATT-TGTAATAATATATTCGTATTTTAATT
1 GAATATAAATTCT-TAATAATATATTTATATTTTAATT
* *
75159 GAATATAAATTCATAAATAATATATTTATA-TTTAATC
1 GAATATAAATTC-TTAATAATATATTTATATTTTAATT
* * ** * *
75196 AAATATAAATT-TATAAGTAAATGTATTTCCATTTAAATA
1 GAATATAAATTCT-TAA-T-AATATATTTATATTTTAATT
*
75235 GAATATAAATTCTTAATAATATATTTAAATTTTAATT
1 GAATATAAATTCTTAATAATATATTTATATTTTAATT
75272 GAATATAAATTCTTAAATAATA
1 GAATATAAATTCTT-AATAATA
75294 AAATATTATC
Statistics
Matches: 110, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
35 1 0.01
36 2 0.02
37 57 0.52
38 30 0.27
39 19 0.17
40 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (37 bp):
GAATATAAATTCTTAATAATATATTTATATTTTAATT
Found at i:83817 original size:2 final size:2
Alignment explanation
Indices: 83810--83851 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
83800 TAAATATTTG
83810 AT AT AT AT 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 AT AT AT AT
83852 TATTTCTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86068 original size:12 final size:12
Alignment explanation
Indices: 86051--86084 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
86041 GAAAATAAAG
86051 AAAACTTAATGT
1 AAAACTTAATGT
*
86063 AAAACTTGATGT
1 AAAACTTAATGT
86075 AAAAC-TAATG
1 AAAACTTAATG
86085 GCCCTAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (12 bp):
AAAACTTAATGT
Found at i:87775 original size:24 final size:24
Alignment explanation
Indices: 87743--87796 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
87733 GCGGCTATCA
87743 ATGAAAGGTCGGTAGATTTCACAG
1 ATGAAAGGTCGGTAGATTTCACAG
87767 ATGAAAGGTCGGTAGATTTCACAG
1 ATGAAAGGTCGGTAGATTTCACAG
87791 ATGAAA
1 ATGAAA
87797 TAAAATAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.24
Consensus pattern (24 bp):
ATGAAAGGTCGGTAGATTTCACAG
Found at i:97581 original size:90 final size:91
Alignment explanation
Indices: 97473--97643 Score: 290
Period size: 90 Copynumber: 1.9 Consensus size: 91
97463 AATATTTATA
* *
97473 TTCAATTACTTAAATATAGATTTAATTAATTTGAAATAAT-AAAATCCCTAATAAGATTAAGGTA
1 TTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATAAGATTAAGGTA
97537 ACTTGGATATAAAAGGATTATTAAAT
66 ACTTGGATATAAAAGGATTATTAAAT
* *
97563 TTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGATTAGGGTA
1 TTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATAAGATTAAGGTA
*
97628 ACTTGGCTATAAAAGG
66 ACTTGGATATAAAAGG
97644 GTGTGTTAGG
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 39 0.52
91 36 0.48
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (91 bp):
TTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATAAGATTAAGGTA
ACTTGGATATAAAAGGATTATTAAAT
Found at i:107727 original size:20 final size:20
Alignment explanation
Indices: 107683--107720 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
107673 GTTCACGTAG
* *
107683 ATCTATCTTAATTCTCTCAT
1 ATCTATCTTAATTATATCAT
107703 ATCTATCTTAATTATATC
1 ATCTATCTTAATTATATC
107721 GAATCTAAGA
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:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (20 bp):
ATCTATCTTAATTATATCAT
Found at i:111993 original size:56 final size:57
Alignment explanation
Indices: 111926--112040 Score: 223
Period size: 56 Copynumber: 2.0 Consensus size: 57
111916 CCTCAAAAAT
111926 AAGAAAACATAAAATTTAAAGGAAACGGATATAATTGTCACATAACTGTT-AGAGAG
1 AAGAAAACATAAAATTTAAAGGAAACGGATATAATTGTCACATAACTGTTAAGAGAG
111982 AAGAAAACATAAAATTTAAAGGAAACGGATATAATTGTCACATAACTGTTAAGAGAG
1 AAGAAAACATAAAATTTAAAGGAAACGGATATAATTGTCACATAACTGTTAAGAGAG
112039 AA
1 AA
112041 AGGGAAGATA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 50 0.86
57 8 0.14
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (57 bp):
AAGAAAACATAAAATTTAAAGGAAACGGATATAATTGTCACATAACTGTTAAGAGAG
Found at i:113718 original size:2 final size:2
Alignment explanation
Indices: 113711--113761 Score: 70
Period size: 2 Copynumber: 25.5 Consensus size: 2
113701 ACATAAAGTA
113711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113751 CAT GAT AT AT A
1 -AT -AT AT AT A
113762 ATTAATAAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
1 2 0.04
2 39 0.87
3 4 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:115366 original size:3 final size:3
Alignment explanation
Indices: 115358--115385 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
115348 AATATAAGAA
115358 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
115386 TAAAACCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:115775 original size:20 final size:20
Alignment explanation
Indices: 115750--115794 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
115740 CTTCTTGCCC
115750 GAAGGTCTTATAGATGGCCT
1 GAAGGTCTTATAGATGGCCT
115770 GAAGGTCTTATAGATGGCCT
1 GAAGGTCTTATAGATGGCCT
115790 GAAGG
1 GAAGG
115795 GCTTGTCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.13, G:0.33, T:0.27
Consensus pattern (20 bp):
GAAGGTCTTATAGATGGCCT
Found at i:116229 original size:258 final size:257
Alignment explanation
Indices: 115771--117381 Score: 1958
Period size: 258 Copynumber: 6.3 Consensus size: 257
115761 AGATGGCCTG
* * * * * * * *
115771 AAGGTCTTATAGATGGCCTGAAGGGCTTGTCATCTTACTCGAAAGACTGACATATGACCTGAAAG
1 AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACC-CAAGG
* * * *
115836 ATTTAATCATCATTCTTGAAAGACTTACTGATGGCCCGAAGGACTAACCAATTTTGGAAATTGTT
65 ATTTAATCATCATGCTCGAAAGACTTACTGATGG-CCGAAGGACTTACCAATTTTGGAAATAGTT
* *
115901 TACTAGGTAATAAACTTTGGAAATCGCTTTCTTACTTTTC-AAAATTATCATTTTTTGAAAATAC
129 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATT-TCATTTTCTGAAAATAC
*
115965 TAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCAAATTATCATATGAAATCATCTTGCCCA
193 TAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAATCATCTTGCCCA
* *
116030 AAGGTCTTATAGATGGTCAGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCAAGGG
1 AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCAA-GG
* * **
116095 ATTTAATCATCATGCTCGAAAGACTTCCTGAT-GCTCGAAGGACTTTCCAATTTTTTAAATAGTT
65 ATTTAATCATCATGCTCGAAAGACTTACTGATGGC-CGAAGGACTTACCAATTTTGGAAATAGTT
** * * *
116159 TACTAGGTAAGAAACTTTGGAAATAACTTTCTTATTTTTCAAAACTTTCATTTTATGAAAATACT
129 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACT
* * *
116224 AAATGAGAAACTTTGAAAATCGTTTTCTCATTTTTCAAATTGTCATATGAAATCATCTTTCCCA
194 AAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAATCATCTTGCCCA
* * **
116288 AAGGTCTTATAGATTGCCTGAAGGACTTATCATCTTGCTCGAAAGACTGGCAGATGACCCGAAGG
1 AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCC-AAGG
* *
116353 ATTT-A--ATCATGCTCGAAAGATTTACTGAT-GTCGAAGGACTTACCAATTTTGGAAATAGTTT
65 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCGAAGGACTTACCAATTTTGGAAATAGTTT
116414 ACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTC-GAAAAATACT
130 ACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTG-AAAATACT
* * * * * *
116478 AAATGATAAACTTTG-AAAGCACTTTCTCATTTTTCAAATTATCACT-TGAAAGCATCTTGGCCG
194 AAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCA-TATGAAATCATCTTGCCCA
* * * * * * * *
116541 AAGGTCTTATAGATGGCCCGAAGGAATTATTATTTTGCTTGAAAGATTGAC-GAATGAGCCGAAT
1 AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAG-ATGA-CCCAAG
* *
116605 GATATAATCATCATGCTCGAACA-ACTTATTGATGGCCCGAAGGACTTACCAATTTTGGAAATAG
64 GATTTAATCATCATGCTCGAA-AGACTTACTGATGG-CCGAAGGACTTACCAATTTTGGAAATAG
* * ** **
116669 TTTACTAGCTAAGAAACTTTGGAAATCGCTTTCTCACTTTT-AAAAAAATCATTTTCTTTAAATA
127 TTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATA
* ** * * * *
116733 CTAAA-CAGGAAAAGTTCAAAATTGCTTTCTTATTTTTCAAATTATCATATAAAATCATCTTGCC
192 CTAAATGA-GAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAATCATCTTGCC
*
116797 CG
256 CA
* * * * ** * *
116799 AAGGTCTTACAAATGGCCCGAATGACTTGTCATCTTTATCGAAAGATTAACAGATGACTCAAAGG
1 AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGAC-CCAAGG
* * * *
116864 ATGTAATCATCATGCTCTAAAGGCTTATTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTT
65 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCC-GAAGGACTTACCAATTTTGGAAATAGTT
* * *
116929 TACTAGGTAAGAAAATTTGGAAATCACTTTCTTACTTTCCAAAAATTTCATTTTCTGAAAATACT
129 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACT
* * * * * * * *
116994 ATATGTGAAACTTTGAAAACCGCTTTCTGATTTTTTAAAATATAATATGAAATCATCTTGTCCA
194 AAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAATCATCTTGCCCA
* * *
117058 AGGGTATTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAA-ATCTGAA-AGATGGCCCAAA
1 AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA-CT-AACAGATGACCC-AA
* * * *
117121 AGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCAAAGACTTACCAATTTTGGAAATAGT
63 GGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCGAAGGACTTACCAATTTTGGAAATAGT
* * *
117186 TTACTAGGTAAGAAACTTTGGAAATTGTTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAATAC
128 TTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATAC
* * * *
117251 TAAATGAGAAACTTTGAAAAGCGCTTTCTCATTTTTTAAATTATCACAAGAAAGT-ATCTTGCCC
193 TAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAA-TCATCTTGCCC
*
117315 G
257 A
** * **
117316 AAGGTCTTATAGATGGCCCGAATAACTTATCATCTTGCTCGAAAGACTTATTGATGACCCGAAGG
1 AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCC-AAGG
117381 A
65 A
117382 GTTACCAATG
Statistics
Matches: 1154, Mismatches: 168, Indels: 61
0.83 0.12 0.04
Matches are distributed among these distances:
252 1 0.00
253 92 0.08
254 102 0.09
255 23 0.02
256 21 0.02
257 38 0.03
258 637 0.55
259 238 0.21
260 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (257 bp):
AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCAAGGA
TTTAATCATCATGCTCGAAAGACTTACTGATGGCCGAAGGACTTACCAATTTTGGAAATAGTTTA
CTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACTAA
ATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAATCATCTTGCCCA
Found at i:120249 original size:23 final size:23
Alignment explanation
Indices: 120223--120276 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
120213 CAAGAAAATA
120223 TGTTCCTCACTATCGTCTTCTTG
1 TGTTCCTCACTATCGTCTTCTTG
*
120246 TGTTCCTCACTGTCGTCTTCTTG
1 TGTTCCTCACTATCGTCTTCTTG
120269 TGTTCCTC
1 TGTTCCTC
120277 TAACCTTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.06, C:0.31, G:0.15, T:0.48
Consensus pattern (23 bp):
TGTTCCTCACTATCGTCTTCTTG
Found at i:153009 original size:16 final size:16
Alignment explanation
Indices: 152988--153019 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
152978 TGGATGCTCC
152988 AGGGTAGGTTGTCATT
1 AGGGTAGGTTGTCATT
153004 AGGGTAGGTTGTCATT
1 AGGGTAGGTTGTCATT
153020 CTCGACGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.38, T:0.38
Consensus pattern (16 bp):
AGGGTAGGTTGTCATT
Found at i:155143 original size:21 final size:20
Alignment explanation
Indices: 155096--155166 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
155086 TACAAGGAAG
* * *
155096 ATAATAAAATGATAAGAATT
1 ATAATAAAATAATAATAATA
*
155116 ATTATAAAAGTAATAATAATA
1 ATAATAAAA-TAATAATAATA
*
155137 ATAATAAAATAA-ATTAATA
1 ATAATAAAATAATAATAATA
155156 AGCTAATAAAA
1 A--TAATAAAA
155167 AACCATAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 7 0.17
20 11 0.26
21 24 0.57
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (20 bp):
ATAATAAAATAATAATAATA
Found at i:157571 original size:3 final size:3
Alignment explanation
Indices: 157565--157684 Score: 186
Period size: 3 Copynumber: 39.7 Consensus size: 3
157555 GTTGTTGTTG
157565 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
157613 TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
157661 TTA CTA ATA TTA TTC TTCA TTA TT
1 TTA TTA TTA TTA TTA TT-A TTA TT
157685 TTCAGGTTAC
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
3 106 0.98
4 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:160917 original size:16 final size:17
Alignment explanation
Indices: 160893--160925 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
160883 TCTTGAAAAT
*
160893 AAAGTATGTC-GGGTAG
1 AAAGCATGTCTGGGTAG
160909 AAAGCATGTCTGGGTAG
1 AAAGCATGTCTGGGTAG
160926 GATTGCTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.30, C:0.09, G:0.36, T:0.24
Consensus pattern (17 bp):
AAAGCATGTCTGGGTAG
Found at i:181497 original size:19 final size:19
Alignment explanation
Indices: 181473--181510 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
181463 TATTGACCAT
181473 ACCTGAACCATTGACTTTG
1 ACCTGAACCATTGACTTTG
* *
181492 ACCTGACCCGTTGACTTTG
1 ACCTGAACCATTGACTTTG
181511 GTCAGAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (19 bp):
ACCTGAACCATTGACTTTG
Found at i:181535 original size:21 final size:21
Alignment explanation
Indices: 181510--181574 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
181500 CGTTGACTTT
181510 GGTCAGA-GTTAACTATTGACC
1 GGTCAGACGTTAACT-TTGACC
*
181531 GGTCAGACCGTTAACTTTGACT
1 GGTCAGA-CGTTAACTTTGACC
* * *
181553 TGTCTGATCGTTGACTTTGACC
1 GGTCAGA-CGTTAACTTTGACC
181575 AAAAAAGTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 7 0.19
22 22 0.61
23 7 0.19
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.34
Consensus pattern (21 bp):
GGTCAGACGTTAACTTTGACC
Found at i:181543 original size:23 final size:20
Alignment explanation
Indices: 181510--181551 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 20
181500 CGTTGACTTT
181510 GGTCAGAGTTAACTATTGACC
1 GGTCAGAGTTAACT-TTGACC
181531 GGTCAGACCGTTAACTTTGAC
1 GGTCAGA--GTTAACTTTGAC
181552 TTGTCTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (20 bp):
GGTCAGAGTTAACTTTGACC
Found at i:186227 original size:15 final size:15
Alignment explanation
Indices: 186209--186258 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
186199 AAAAAATAAC
186209 AGTTAATAATTAATA
1 AGTTAATAATTAATA
*
186224 AGTTAGTAATT-ATCA
1 AGTTAATAATTAAT-A
*
186239 AGTTAGA-AATTAGTA
1 AGTTA-ATAATTAATA
186254 AGTTA
1 AGTTA
186259 GAGTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.07
15 26 0.90
16 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (15 bp):
AGTTAATAATTAATA
Found at i:186259 original size:15 final size:14
Alignment explanation
Indices: 186216--186260 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
186206 AACAGTTAAT
*
186216 AATTAATAAGTTAGT
1 AATT-ATAAGTTAGA
186231 AATTATCAAGTTAGA
1 AATTAT-AAGTTAGA
186246 AATTAGTAAGTTAGA
1 AATTA-TAAGTTAGA
186261 GTTTATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 2 0.07
15 24 0.89
16 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.36
Consensus pattern (14 bp):
AATTATAAGTTAGA
Found at i:188580 original size:2 final size:2
Alignment explanation
Indices: 188575--188622 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
188565 ACACACACAC
188575 AT AT AT AT 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 AT AT AT AT
188617 AT AT AT
1 AT AT AT
188623 TATTTTTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:189774 original size:19 final size:19
Alignment explanation
Indices: 189740--189786 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
189730 AGTATTTTGT
*
189740 TTTTATTTTTCTTTATTTTC
1 TTTTATTTTTCGTTA-TTTC
189760 TTTTATTTTT-GTTATTTC
1 TTTTATTTTTCGTTATTTC
189778 TTTTGATTT
1 TTTT-ATTT
189787 CGATTCTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 7 0.28
20 10 0.40
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.79
Consensus pattern (19 bp):
TTTTATTTTTCGTTATTTC
Found at i:189834 original size:23 final size:22
Alignment explanation
Indices: 189808--189856 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
189798 GCGCTTTATT
*
189808 TTTTATTC-TTTTTATTATCTTTG
1 TTTTATTCATTATT-TTAT-TTTG
*
189831 TTTTTTTCATTATTTTATTTTG
1 TTTTATTCATTATTTTATTTTG
189853 TTTT
1 TTTT
189857 GTTTTTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 11 0.48
24 4 0.17
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.78
Consensus pattern (22 bp):
TTTTATTCATTATTTTATTTTG
Found at i:189908 original size:27 final size:26
Alignment explanation
Indices: 189816--189904 Score: 69
Period size: 26 Copynumber: 3.4 Consensus size: 26
189806 TTTTTTATTC
* *
189816 TTTTTATTATCTTTGTTTTTTTCATTA
1 TTTTTATT-TATTTGTTTTTTTCGTTA
189843 -TTTTATTT-TGTT-TTGTTTTTCTGTT-
1 TTTTTATTTAT-TTGTT-TTTTTC-GTTA
* *
189868 TCTTTAGGTTATTTGTTTTTTTCGTTA
1 TTTTTA-TTTATTTGTTTTTTTCGTTA
189895 TTTTTATTTA
1 TTTTTATTTA
189905 ATTTACTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
24 3 0.06
25 9 0.18
26 19 0.39
27 15 0.31
28 3 0.06
ACGTcount: A:0.11, C:0.06, G:0.09, T:0.74
Consensus pattern (26 bp):
TTTTTATTTATTTGTTTTTTTCGTTA
Found at i:196886 original size:16 final size:16
Alignment explanation
Indices: 196862--196907 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
196852 CAGTTTTCTT
*
196862 ATTCCATTTCTTTTGA
1 ATTCTATTTCTTTTGA
196878 ATTCTATTTCTTTTGA
1 ATTCTATTTCTTTTGA
196894 ATTCTATTTCTTTT
1 ATTCTATTTCTTTT
196908 CTTTTCTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.17, C:0.15, G:0.04, T:0.63
Consensus pattern (16 bp):
ATTCTATTTCTTTTGA
Found at i:200442 original size:13 final size:13
Alignment explanation
Indices: 200424--200451 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
200414 TCGATGCACT
200424 TGATTCAATCGAA
1 TGATTCAATCGAA
200437 TGATTCAATCGAA
1 TGATTCAATCGAA
200450 TG
1 TG
200452 CTACACCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (13 bp):
TGATTCAATCGAA
Found at i:201757 original size:21 final size:22
Alignment explanation
Indices: 201731--201788 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
201721 CAAAAATTCT
201731 TGAATAAATGCAAATGCAAA-A
1 TGAATAAATGCAAATGCAAATA
* *
201752 TGAATAGATGCAAATGTAAATA
1 TGAATAAATGCAAATGCAAATA
*
201774 TGAATGAAATACAAA
1 TGAAT-AAATGCAAA
201789 AGGTATTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 18 0.58
22 6 0.19
23 7 0.23
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.22
Consensus pattern (22 bp):
TGAATAAATGCAAATGCAAATA
Found at i:203140 original size:24 final size:22
Alignment explanation
Indices: 203101--203167 Score: 57
Period size: 24 Copynumber: 3.0 Consensus size: 22
203091 AACTATATTT
203101 TTTTCAAAAACT--TTATAATAGG
1 TTTT-AAAAACTAATTATAATA-G
* *
203123 TTTTCAAAACTATATTATATATAT
1 TTTTAAAAACTA-ATTATA-ATAG
*
203147 TTTTAAAAACTAAATATAATA
1 TTTTAAAAACTAATTATAATA
203168 TATATTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 6 0.16
22 7 0.19
23 5 0.14
24 16 0.43
25 3 0.08
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (22 bp):
TTTTAAAAACTAATTATAATAG
Found at i:203168 original size:24 final size:24
Alignment explanation
Indices: 203123--203173 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
203113 TTATAATAGG
* *
203123 TTTTCAAAACTATATTATATATAT
1 TTTTAAAAACTAAATTATATATAT
203147 TTTTAAAAACTAAATATAATATATAT
1 TTTTAAAAACTAAAT-T-ATATATAT
203173 T
1 T
203174 ATATATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 13 0.57
25 1 0.04
26 9 0.39
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTTAAAAACTAAATTATATATAT
Found at i:203213 original size:20 final size:19
Alignment explanation
Indices: 203169--203217 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
203159 AATATAATAT
* **
203169 ATATTATATATTTGAAATT
1 ATATTATATATTTCAAAAA
203188 ATATTATATATTTTCAAAAA
1 ATATTATATA-TTTCAAAAA
203208 ATATTATATA
1 ATATTATATA
203218 ACATGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATTATATATTTCAAAAA
Found at i:211917 original size:32 final size:29
Alignment explanation
Indices: 211852--211931 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
211842 AGTGGACCTC
*
211852 TAATAATAAATATTAGAAAAAATAACTCA
1 TAATAATAAATATTAGAAAAAATAAATCA
* * *
211881 TAATAATAAATATTGGAGAAATATTAAATCCT
1 TAATAATAAATATT--AGAAAAAATAAAT-CA
*
211913 TAATAACAAATATTA-AAAA
1 TAATAATAAATATTAGAAAA
211932 TAATTGGGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 17 0.40
30 1 0.02
31 10 0.24
32 14 0.33
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.30
Consensus pattern (29 bp):
TAATAATAAATATTAGAAAAAATAAATCA
Found at i:214128 original size:133 final size:134
Alignment explanation
Indices: 213917--214304 Score: 397
Period size: 133 Copynumber: 2.8 Consensus size: 134
213907 TTATATTTCC
* * *
213917 AAAAA-ATATATTAATACATTTTCAAAAACTATTTTTAAAAACTATATTATATATGTTTTCAAAA
1 AAAAATATATACT-ATACGTTTTC-AAAATTA-TTTTAAAAACTATA-TATATATGTTTTCAAAA
213981 CCGTTTTAAAAACTATATATTATACATTCTCAAAACTATTTTAAAAAC-TA-TACACGTTTTCAA
62 CCGTTTTAAAAACTATATATTATACATT-TCAAAACTATTTTAAAAACATATTACACGTTTTCAA
*
214044 AATTATTTT
126 AATTATCTT
* * *
214053 AAAAA-CTATAGTATACGTTTTCAAAATTATTTAAAAAACTATATACTATATGTTTTCAAAACCG
1 AAAAATATATACTATACGTTTTCAAAATTATTTTAAAAACTATATA-TATATGTTTTCAAAACCG
* * *
214117 TTTTAAAAACTATATATTATACCTTTTCAAAACTATTTTTTAAAAAAACTATATATTATATGTTT
65 TTTTAAAAACTATATATTATA-CATTTCAAAACTA--TTTT--AAAAAC---ATATTACACGTTT
214182 TCAAAATTATCTT
122 TCAAAATTATCTT
* ** *
214195 AAAAATTATATACTATATGTTTTCAAAATCGTTTTAAAAACTATATATTATATGTTTTTAAAAGT
1 AAAAA-TATATACTATACGTTTTCAAAATTATTTTAAAAACTATATA-TATATGTTTTCAAAA--
** * *
214260 AAGTTTCCAAAAACTATATATTATATATTTCAAAAGCTATATTTA
62 CCGTTT-TAAAAACTATATATTATACATTTCAAAA-CTAT-TTTA
214305 TTATATATAC
Statistics
Matches: 212, Mismatches: 22, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
132 2 0.01
133 61 0.29
134 9 0.04
135 13 0.06
136 10 0.05
137 6 0.03
141 2 0.01
142 24 0.11
144 49 0.23
145 1 0.00
146 15 0.07
147 20 0.09
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (134 bp):
AAAAATATATACTATACGTTTTCAAAATTATTTTAAAAACTATATATATATGTTTTCAAAACCGT
TTTAAAAACTATATATTATACATTTCAAAACTATTTTAAAAACATATTACACGTTTTCAAAATTA
TCTT
Found at i:214181 original size:74 final size:72
Alignment explanation
Indices: 214036--214284 Score: 235
Period size: 74 Copynumber: 3.5 Consensus size: 72
214026 AACTATACAC
* * *
214036 GTTTTCAAAATTA-TTTTAAAAAC--TATAGTATACGTTTTC-AAA-ATTATTTAAAAAACTATA
1 GTTTTCAAAA-AAGTTTTAAAAACTATATATTATACGTTTTCAAAATATTTTTTAAAAAACTATA
*
214096 TACTATAT
65 TATTATAT
** *
214104 GTTTTCAAAACCGTTTTAAAAACTATATATTATACCTTTTCAAAACTATTTTTTAAAAAAACTAT
1 GTTTTCAAAAAAGTTTTAAAAACTATATATTATACGTTTTCAAAA-TATTTTTT-AAAAAACTAT
214169 ATATTATAT
64 ATATTATAT
* * * * * **
214178 GTTTTCAAAATTA-TCTTAAAAATTATATACTATATGTTTTCAAAAT-CGTTTT-AAAAACTATA
1 GTTTTCAAAA-AAGTTTTAAAAACTATATATTATACGTTTTCAAAATATTTTTTAAAAAACTATA
214240 TATTATAT
65 TATTATAT
* *
214248 GTTTTTAAAAGTAAGTTTCCAAAAACTATATATTATA
1 GTTTTCAAAA--AAGTTT-TAAAAACTATATATTATA
214285 TATTTCAAAA
Statistics
Matches: 149, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
68 20 0.13
70 41 0.28
71 5 0.03
72 6 0.04
73 22 0.15
74 55 0.37
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (72 bp):
GTTTTCAAAAAAGTTTTAAAAACTATATATTATACGTTTTCAAAATATTTTTTAAAAAACTATAT
ATTATAT
Found at i:214205 original size:109 final size:105
Alignment explanation
Indices: 213922--214294 Score: 363
Period size: 109 Copynumber: 3.5 Consensus size: 105
213912 TTTCCAAAAA
* * *
213922 ATATATTAATACATTTTCAAAAACTATTTTTAAAAACTATAT-TATATATGTTTTCAAAACCGT-
1 ATATATT-ATACGTTTTC-AAAACTAATTTTAAAAACTATATAT-TATATGTTTTCAAAA--TTA
* ** * **
213985 TTTAAAAACTATATATTATACATTCTCAAAACTATTTTAAAAAC-
61 TTTAAAAACTATATACTATATGTTTTCAAAACCGTTTTAAAAACT
* * * *
214029 ---TA-TACACGTTTTCAAAA-TTATTTTAAAAAC--TATAGTATACGTTTTCAAAATTATTTAA
1 ATATATTATACGTTTTCAAAACTAATTTTAAAAACTATATATTATATGTTTTCAAAATTATTT-A
214087 AAAACTATATACTATATGTTTTCAAAACCGTTTTAAAAACT
65 AAAACTATATACTATATGTTTTCAAAACCGTTTTAAAAACT
* *
214128 ATATATTATACCTTTTCAAAACTATTTTTTAAAAAAACTATATATTATATGTTTTCAAAATTATC
1 ATATATTATACGTTTTCAAAACTA-ATTTT--AAAAACTATATATTATATGTTTTCAAAATTAT-
* *
214193 TTAAAAATTATATACTATATGTTTTCAAAATCGTTTTAAAAACT
62 TTAAAAACTATATACTATATGTTTTCAAAACCGTTTTAAAAACT
* * * * *
214237 ATATATTATATGTTTTTAAAAGTAAGTTTCCAAAAACTATATATTATAT-ATTTCAAAA
1 ATATATTATACGTTTTCAAAACTAA-TTT-TAAAAACTATATATTATATGTTTTCAAAA
214295 GCTATATTTA
Statistics
Matches: 221, Mismatches: 28, Indels: 34
0.78 0.10 0.12
Matches are distributed among these distances:
96 1 0.00
97 3 0.01
98 52 0.24
100 11 0.05
101 4 0.02
102 10 0.05
103 14 0.06
104 3 0.01
105 4 0.02
107 14 0.06
108 18 0.08
109 85 0.38
110 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.42
Consensus pattern (105 bp):
ATATATTATACGTTTTCAAAACTAATTTTAAAAACTATATATTATATGTTTTCAAAATTATTTAA
AAACTATATACTATATGTTTTCAAAACCGTTTTAAAAACT
Found at i:214241 original size:35 final size:35
Alignment explanation
Indices: 213935--214294 Score: 292
Period size: 35 Copynumber: 10.3 Consensus size: 35
213925 TATTAATACA
*
213935 TTTTCAAAAACTATTTTTAAAAACTATAT-TATATATG
1 TTTTCAAAATC-A-TTTTAAAAACTATATAT-TATATG
* * **
213972 TTTTCAAAACCGTTTTAAAAACTATATATTATACA
1 TTTTCAAAATCATTTTAAAAACTATATATTATATG
* * *
214007 TTCTCAAAA-CTATTTTAAAAAC----TA-TACACG
1 TTTTCAAAATC-ATTTTAAAAACTATATATTATATG
* * *
214037 TTTTCAAAATTATTTTAAAAAC--TATAGTATACG
1 TTTTCAAAATCATTTTAAAAACTATATATTATATG
* * *
214070 TTTTCAAAATTATTTAAAAAACTATATACTATATG
1 TTTTCAAAATCATTTTAAAAACTATATATTATATG
* * **
214105 TTTTCAAAACCGTTTTAAAAACTATATATTATACC
1 TTTTCAAAATCATTTTAAAAACTATATATTATATG
214140 TTTTCAAAA-CTATTTTTTAAAAAAACTATATATTATATG
1 TTTTCAAAATC-A--TTTT--AAAAACTATATATTATATG
* * * *
214179 TTTTCAAAATTATCTTAAAAATTATATACTATATG
1 TTTTCAAAATCATTTTAAAAACTATATATTATATG
*
214214 TTTTCAAAATCGTTTTAAAAACTATATATTATATG
1 TTTTCAAAATCATTTTAAAAACTATATATTATATG
* * *
214249 TTTTTAAAAGTAAGTTTCCAAAAACTATATATTATAT-
1 TTTTCAAAA-TCA-TTT-TAAAAACTATATATTATATG
*
214286 ATTTCAAAA
1 TTTTCAAAA
214295 GCTATATTTA
Statistics
Matches: 267, Mismatches: 39, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
30 23 0.09
31 2 0.01
32 2 0.01
33 26 0.10
34 2 0.01
35 138 0.52
36 2 0.01
37 27 0.10
38 18 0.07
39 27 0.10
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (35 bp):
TTTTCAAAATCATTTTAAAAACTATATATTATATG
Found at i:214294 original size:23 final size:24
Alignment explanation
Indices: 214267--214312 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
214257 AGTAAGTTTC
214267 CAAAAACTATA-TATTATATATTT
1 CAAAAACTATATTATTATATATTT
*
214290 CAAAAGCTATATTTATTATATAT
1 CAAAAACTATA-TTATTATATAT
214313 ACTATGCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
25 10 0.50
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (24 bp):
CAAAAACTATATTATTATATATTT
Found at i:214776 original size:2 final size:2
Alignment explanation
Indices: 214769--214801 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
214759 TCTAATCATA
214769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
214802 GTTATGTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:220154 original size:3 final size:3
Alignment explanation
Indices: 220146--220206 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
220136 CACAAACATC
220146 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
220194 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
220207 CACTAAATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:220900 original size:15 final size:12
Alignment explanation
Indices: 220875--220919 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 12
220865 TTTAGTTATA
220875 TTATATATTAAT
1 TTATATATTAAT
220887 TTATGAAGTATTAAT
1 TTAT--A-TATTAAT
220902 ATTATATATTAAT
1 -TTATATATTAAT
220915 TTATA
1 TTATA
220920 ACATTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 9 0.31
13 7 0.24
14 2 0.07
15 7 0.24
16 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (12 bp):
TTATATATTAAT
Found at i:220925 original size:13 final size:13
Alignment explanation
Indices: 220875--220929 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 13
220865 TTTAGTTATA
220875 TTAT-ATATTAAT
1 TTATAATATTAAT
220887 TTATGAAGTATTAAT
1 TTAT-AA-TATTAAT
220902 ATTAT-ATATTAAT
1 -TTATAATATTAAT
*
220915 TTATAACATT-AT
1 TTATAATATTAAT
220927 TTA
1 TTA
220930 GGTGTTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 13 0.35
13 11 0.30
14 2 0.05
15 7 0.19
16 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (13 bp):
TTATAATATTAAT
Found at i:234769 original size:8 final size:8
Alignment explanation
Indices: 234737--234811 Score: 52
Period size: 8 Copynumber: 9.5 Consensus size: 8
234727 GCTTGAAGAA
*
234737 AAAAAAGG
1 AAAAAATG
*
234745 AACAAAT-
1 AAAAAATG
234752 AAAAAGATG
1 AAAAA-ATG
234761 AAAAAATG
1 AAAAAATG
234769 -AAAAA-G
1 AAAAAATG
234775 AAAAAAATG
1 -AAAAAATG
234784 ATGAAAAA--
1 A--AAAAATG
*
234792 AAGAAATG
1 AAAAAATG
234800 AAAAAATG
1 AAAAAATG
234808 AAAA
1 AAAA
234812 GAGAAAAAGG
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
6 5 0.09
7 9 0.17
8 28 0.53
9 6 0.11
10 5 0.09
ACGTcount: A:0.75, C:0.01, G:0.15, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:234780 original size:25 final size:25
Alignment explanation
Indices: 234752--234805 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
234742 AGGAACAAAT
*
234752 AAAAA-GATGAAAAAATGAAAAAGAA
1 AAAAATGATGAAAAAAAG-AAAAGAA
*
234777 AAAAATGATGAAAAAAAGAAATGAA
1 AAAAATGATGAAAAAAAGAAAAGAA
234802 AAAA
1 AAAA
234806 TGAAAAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (25 bp):
AAAAATGATGAAAAAAAGAAAAGAA
Found at i:234781 original size:26 final size:25
Alignment explanation
Indices: 234752--234805 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
234742 AGGAACAAAT
*
234752 AAAAAGATGAAAAAATGAAAAAGAAA
1 AAAAAGATGAAAAAAAG-AAAAGAAA
* *
234778 AAAATGATGAAAAAAAGAAATGAAA
1 AAAAAGATGAAAAAAAGAAAAGAAA
234803 AAA
1 AAA
234806 TGAAAAGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (25 bp):
AAAAAGATGAAAAAAAGAAAAGAAA
Found at i:235941 original size:91 final size:90
Alignment explanation
Indices: 235827--235994 Score: 275
Period size: 92 Copynumber: 1.9 Consensus size: 90
235817 TGAGGGATTG
*
235827 ACATTTTCAGGAGAGTTCATAATGAGAATAACTCATCCAAC-GAGGAAGAAGAAGTTCATAATGA
1 ACATTTTCAGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGA
235891 GAAGAACTTGTTCAACTTCGCATCA
66 GAAGAACTTGTTCAACTTCGCATCA
* *
235916 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTTC-A-GGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAAT
*
235981 GAGAAGAGCTTGTT
64 GAGAAGAACTTGTT
235995 TGACCTATCA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
89 8 0.11
90 1 0.01
91 30 0.42
92 33 0.46
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (90 bp):
ACATTTTCAGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACTTCGCATCA
Found at i:236094 original size:19 final size:19
Alignment explanation
Indices: 236070--236125 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
236060 AATGAAGAGT
236070 TCATAATGAGAAGAACTCA
1 TCATAATGAGAAGAACTCA
* *
236089 TCATAA--AGGAGAGAGT--
1 TCATAATGAGAAGA-ACTCA
236105 TCATAATGAGAAGAACTCA
1 TCATAATGAGAAGAACTCA
236124 TC
1 TC
236126 CAACAAGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
16 6 0.21
17 7 0.25
18 7 0.25
19 8 0.29
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (19 bp):
TCATAATGAGAAGAACTCA
Found at i:236111 original size:35 final size:38
Alignment explanation
Indices: 236063--236155 Score: 140
Period size: 35 Copynumber: 2.5 Consensus size: 38
236053 CATTTCCAAT
236063 GAAGAGTTCATAATGAGAAGAACTCAT-CATA-AA-GGA
1 GAAGAGTTCATAATGAGAAGAACTCATCCA-ACAAGGGA
236099 G-AGAGTTCATAATGAGAAGAACTCATCCAACAAGGGA
1 GAAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGA
236136 GAAGGAGTTCATAATGAGAA
1 GAA-GAGTTCATAATGAGAA
236156 TAATTTGTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
35 26 0.50
36 5 0.10
37 4 0.08
38 1 0.02
39 16 0.31
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.18
Consensus pattern (38 bp):
GAAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGA
Found at i:243132 original size:13 final size:13
Alignment explanation
Indices: 243102--243153 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
243092 GTCATAAATC
*
243102 TATGACGCGCATT
1 TATGACACGCATT
* *
243115 GATGACACGTATT
1 TATGACACGCATT
* *
243128 TATGACTCACATT
1 TATGACACGCATT
*
243141 TATGACGCGCATT
1 TATGACACGCATT
243154 GAGCGTCATT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:247377 original size:22 final size:22
Alignment explanation
Indices: 247352--247394 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
247342 TATGTTGTAC
247352 TAATCATATATGT-ATGATTATT
1 TAAT-ATATATGTGATGATTATT
* *
247374 TAATATGTATGTGGTGATTAT
1 TAATATATATGTGATGATTAT
247395 CAAATAGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAATATATATGTGATGATTATT
Found at i:247459 original size:54 final size:54
Alignment explanation
Indices: 247401--247849 Score: 594
Period size: 54 Copynumber: 8.3 Consensus size: 54
247391 TTATCAAATA
* *
247401 GGCACTAAGTGTGCATCTT-ACGGAATTTATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAT-TTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
*
247455 GGCACTAAGTGTGCATTTTACGAAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
247509 GACACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * * *
247563 GGCACTAAGTGTGCATTTTACTAAATTTATCATATTTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
** *
247617 GGCACTAAGTGTTTATTTCACGAAATTCATCCTATATGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
* *
247671 GGCACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
* *
247725 GGCACTAAGTGTGCATTTCACAAAATTCATCCTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
* * * ** ** * * *
247779 GACACTAAGTGTGCATTTCATGGAATTCATAATATGTTCATGAATAACTGTATG
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
* *
247833 GGCACTACGGGTGCATT
1 GGCACTAAGTGTGCATT
247850 ATAAAGAAAT
Statistics
Matches: 347, Mismatches: 47, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
53 2 0.01
54 345 0.99
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:251728 original size:20 final size:20
Alignment explanation
Indices: 251679--251750 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
251669 TGATTCAATC
*
251679 GGTATCGATACAGAAGGG--
1 GGTATCGATACCGAAGGGAA
251697 GGACTATCGATACCGAAGGGAA
1 GG--TATCGATACCGAAGGGAA
* *
251719 GGTATTGATACCTAAGGGAA
1 GGTATCGATACCGAAGGGAA
251739 GGTATCGATACC
1 GGTATCGATACC
251751 ATTCAAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.04
20 42 0.91
22 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.32, T:0.19
Consensus pattern (20 bp):
GGTATCGATACCGAAGGGAA
Found at i:251825 original size:22 final size:23
Alignment explanation
Indices: 251794--251837 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
251784 CATAGCATAA
*
251794 TATCAGTACCATAGTA-TGGTAG
1 TATCAATACCATAGTATTGGTAG
*
251816 TATCAATACCATGGTATTGGTA
1 TATCAATACCATAGTATTGGTA
251838 TAGATATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (23 bp):
TATCAATACCATAGTATTGGTAG
Found at i:252228 original size:54 final size:54
Alignment explanation
Indices: 252171--252725 Score: 779
Period size: 54 Copynumber: 10.3 Consensus size: 54
252161 ATCAAATAGA
* * * * ** **
252171 CACTAAATATGCATTTTACGGAATTCATCTTATGTGGATGAATAGTCGTTTCAA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* * *
252225 CACTAAGTGTGTATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* * *
252279 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGACGAATAATCATTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
252333 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
*
252387 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* * *
252441 CACTAAGTGTTCATTTCACGGAATTTATCCTATGTGGATGAATAACCTTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* * *
252495 TACTACGTGTGCATTTCACGGAATTCATCCTATGTGGATAAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* *
252549 CACTAAGTGTGCATTTCACGGAATTCATCATATGTGAATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
*
252603 CACTAAGTGTGCATTTCACGGAATTCATCCTACT-TGGATAAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTA-TGTGGATGAATAACCGTTTCGG
* * ** ** * * *
252657 CACTAAGTGTGTATTTCACGAAATTCATAATATGTTCATAAATAACCGTATGGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* *
252711 CACTACGAGTGCATT
1 CACTAAGTGTGCATT
252726 ATAAAGAAAT
Statistics
Matches: 453, Mismatches: 46, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
53 1 0.00
54 451 1.00
55 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
Found at i:266191 original size:34 final size:34
Alignment explanation
Indices: 266143--266211 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 34
266133 TTATGTTTTC
*
266143 TTGGATTTTCAAACTTGGATTGAT-TTTGATGTTT
1 TTGGATTTTCAAACTT-GATGGATGTTTGATGTTT
*
266177 TTGGATGTTT-AAACTTGATGGTTGTTTGATGTTT
1 TTGGAT-TTTCAAACTTGATGGATGTTTGATGTTT
266211 T
1 T
266212 GAACTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.16
34 23 0.74
35 3 0.10
ACGTcount: A:0.19, C:0.04, G:0.23, T:0.54
Consensus pattern (34 bp):
TTGGATTTTCAAACTTGATGGATGTTTGATGTTT
Found at i:266920 original size:20 final size:20
Alignment explanation
Indices: 266891--266928 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
266881 TTTAAGAGTG
266891 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
266911 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
266929 TAATGTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:267038 original size:46 final size:45
Alignment explanation
Indices: 266948--267038 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
266938 AAACATCAAA
* *
266948 TGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAG
266993 TGCATTTGATGCATCGATGCA-AAAGGCCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAA--CCATGCATCGATGCACTCAG
267039 GTTTTTTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
44 2 0.05
45 20 0.48
46 20 0.48
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.26
Consensus pattern (45 bp):
TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAG
Found at i:267321 original size:10 final size:11
Alignment explanation
Indices: 267306--267355 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
267296 AATAACAAGA
267306 AACA-AGAATC
1 AACAGAGAATC
267316 AACA-AGAATC
1 AACAGAGAATC
*
267326 AAGAGAGAATC
1 AACAGAGAATC
*
267337 AAGAGAGAATC
1 AACAGAGAATC
267348 AA-AGAGAA
1 AACAGAGAA
267356 AGCATCAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
10 19 0.50
11 19 0.50
ACGTcount: A:0.60, C:0.12, G:0.20, T:0.08
Consensus pattern (11 bp):
AACAGAGAATC
Found at i:267335 original size:21 final size:21
Alignment explanation
Indices: 267310--267355 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
267300 ACAAGAAACA
267310 AGAATCAACA-AGAATCAAGAG
1 AGAATCAACAGAGAATCAA-AG
*
267331 AGAATCAAGAGAGAATCAAAG
1 AGAATCAACAGAGAATCAAAG
267352 AGAA
1 AGAA
267356 AGCATCAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.59, C:0.11, G:0.22, T:0.09
Consensus pattern (21 bp):
AGAATCAACAGAGAATCAAAG
Found at i:267336 original size:11 final size:11
Alignment explanation
Indices: 267310--267355 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
267300 ACAAGAAACA
*
267310 AGAATCAACA-
1 AGAATCAAGAG
267320 AGAATCAAGAG
1 AGAATCAAGAG
267331 AGAATCAAGAG
1 AGAATCAAGAG
267342 AGAATCAA-AG
1 AGAATCAAGAG
267352 AGAA
1 AGAA
267356 AGCATCAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
10 15 0.44
11 19 0.56
ACGTcount: A:0.59, C:0.11, G:0.22, T:0.09
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:268365 original size:38 final size:38
Alignment explanation
Indices: 268239--268379 Score: 185
Period size: 39 Copynumber: 3.7 Consensus size: 38
268229 TAAGGACTTA
*
268239 TTACCCT-ATGCACAAAGCAGAGGAGTCTGCAGTAAGGTC
1 TTACCCTGA-GCACAAAGCAGAGGAGT-TGCAGTAAGGAC
* * *
268278 TTATCCTGTGCACAAAGCAGAGGAGCTTGCAGTAACGAC
1 TTACCCTGAGCACAAAGCAGAGGAG-TTGCAGTAAGGAC
* *
268317 TTACCCTGAGCACAAAGCCGAGGAGTTGCGGTAAGGAC
1 TTACCCTGAGCACAAAGCAGAGGAGTTGCAGTAAGGAC
*
268355 TTACCCTGAGCACAAAGCCGAGGAG
1 TTACCCTGAGCACAAAGCAGAGGAG
268380 CCTGCGAAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
38 36 0.40
39 54 0.59
40 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (38 bp):
TTACCCTGAGCACAAAGCAGAGGAGTTGCAGTAAGGAC
Found at i:274631 original size:2 final size:2
Alignment explanation
Indices: 274624--274726 Score: 197
Period size: 2 Copynumber: 51.5 Consensus size: 2
274614 AAAATATGGA
274624 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
274666 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
274708 AC AC AC AC AC AT AC AC AC A
1 AC AC AC AC AC AC AC AC AC A
274727 TAGAGGACTA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 99 1.00
ACGTcount: A:0.50, C:0.49, G:0.00, T:0.01
Consensus pattern (2 bp):
AC
Found at i:274884 original size:28 final size:28
Alignment explanation
Indices: 274823--274890 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
274813 AAAAGCTCAA
** *
274823 AAAATTAAAGTAAATAAAATGTAAGGACT
1 AAAATTAAA-TAAATAAAATAAAAGGAAT
274852 AAAATTAAATAAATAAAAATAAAAGGAAT
1 AAAATTAAATAAAT-AAAATAAAAGGAAT
*
274881 AAATTTAAAT
1 AAAATTAAAT
274891 GTGCATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.25
Consensus pattern (28 bp):
AAAATTAAATAAATAAAATAAAAGGAAT
Found at i:274960 original size:29 final size:29
Alignment explanation
Indices: 274921--274987 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
274911 AAGTAAAAGA
*
274921 GCAATAAAAATAAAATATTAGTA-TTAATAT
1 GCAAT-AAAATAAAA-ATTAATAGTTAATAT
* *
274951 GCAATAAAATGAAAGTTAATAGTTAATAT
1 GCAATAAAATAAAAATTAATAGTTAATAT
*
274980 GAAATAAA
1 GCAATAAA
274988 TAACATAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.16
29 22 0.69
30 5 0.16
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (29 bp):
GCAATAAAATAAAAATTAATAGTTAATAT
Found at i:277194 original size:45 final size:45
Alignment explanation
Indices: 277121--277372 Score: 337
Period size: 45 Copynumber: 5.6 Consensus size: 45
277111 CATTATTTTT
* *
277121 ATTTATGGCATCATTTC-TGCCTTTAATGCACAATTGTGCATTTC
1 ATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGCATTTC
* * *
277165 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTTTGCATTTC
1 ATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGCATTTC
* ** * * *
277210 ATTTATGACATCCCTTCATGACTTTAATGCACCGTTATGTATTTC
1 ATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGCATTTC
* * *
277255 ATTTATGGCATCATTTCATACCTTTAATGCATCGA-TATACATTTC
1 ATTTATGGCATCATTTCATGCCTTTAATGCA-CCATTATGCATTTC
277300 ATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGCATTTC
1 ATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGCATTTC
* *
277345 ATATATGGCCTCATTTCATGCCTTTAAT
1 ATTTATGGCATCATTTCATGCCTTTAAT
277373 TTATGACATC
Statistics
Matches: 182, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
44 18 0.10
45 163 0.90
46 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.43
Consensus pattern (45 bp):
ATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGCATTTC
Found at i:277280 original size:21 final size:21
Alignment explanation
Indices: 277256--277325 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
277246 ATGTATTTCA
277256 TTTATGGCATCATTTCATACC
1 TTTATGGCATCATTTCATACC
* * *
277277 TTTAAT-GCATCGATATACATTTCA
1 TTT-ATGGCATC-AT-TTCA-TACC
*
277301 TTTATGGCATCATTTCATGCC
1 TTTATGGCATCATTTCATACC
277322 TTTA
1 TTTA
277326 ATGCACCATT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
21 14 0.37
22 7 0.18
23 7 0.18
24 10 0.26
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (21 bp):
TTTATGGCATCATTTCATACC
Found at i:277383 original size:71 final size:71
Alignment explanation
Indices: 277300--277443 Score: 243
Period size: 71 Copynumber: 2.0 Consensus size: 71
277290 TATACATTTC
* *
277300 ATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGCATTTCATATATGGCCTCATTTCATG
1 ATTTATGACATCATTTCATGCCTTTAATGCACCATTATGCATTTCATATATGGCATCATTTCATG
277365 CCTTTA
66 CCTTTA
* * *
277371 ATTTATGACATCATTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG
1 ATTTATGACATCATTTCATGCCTTTAATGCACCATTATGCATTTCATATATGGCATCATTTCATG
277436 CCTTTA
66 CCTTTA
277442 AT
1 AT
277444 GCACCGTTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (71 bp):
ATTTATGACATCATTTCATGCCTTTAATGCACCATTATGCATTTCATATATGGCATCATTTCATG
CCTTTA
Found at i:277398 original size:161 final size:161
Alignment explanation
Indices: 277210--277512 Score: 498
Period size: 161 Copynumber: 1.9 Consensus size: 161
277200 TTTGCATTTC
* *
277210 ATTTATGACATCCCTTCATGACTTTAATGCACCGTTATGTATTTCATTTATGGCATCATTTCATA
1 ATTTATGACATCACTTCATGACTTTAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATA
* *
277275 CCTTTAATGCATCGATATACATTTCATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGC
66 CCTTTAATGCACCGATATACATTTAATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGC
277340 ATTTCATATATGGCCTCATTTCATGCCTTTA
131 ATTTCATATATGGCCTCATTTCATGCCTTTA
* * * *
277371 ATTTATGACATCATTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG
1 ATTTATGACATCACTTCATGACTTTAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATA
* * *
277436 CCTTTAATGCACCGTTATACATTTAATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
66 CCTTTAATGCACCGATATACATTTAATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGC
*
277501 ATTTCATTTATG
131 ATTTCATATATG
277513 TAATGAAAAC
Statistics
Matches: 130, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
161 130 1.00
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (161 bp):
ATTTATGACATCACTTCATGACTTTAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATA
CCTTTAATGCACCGATATACATTTAATTTATGGCATCATTTCATGCCTTTAATGCACCATTATGC
ATTTCATATATGGCCTCATTTCATGCCTTTA
Found at i:277414 original size:116 final size:116
Alignment explanation
Indices: 277255--277488 Score: 360
Period size: 116 Copynumber: 2.0 Consensus size: 116
277245 TATGTATTTC
* *
277255 ATTTATGGCATCATTTCATACCTTTAATGCATCGATATACATTTCATTTATGGCATCATTTCATG
1 ATTTATGACATCATTTCATACCTTTAATGCACCGATATACATTTCATTTATGGCATCATTTCATG
* * *
277320 CCTTTAATGCACCATTATGCATTTCATATATGGCCTCATTTCATGCCTTTA
66 CCTTTAATGCACCATTATACATTTAATATATGGCATCATTTCATGCCTTTA
* * * *
277371 ATTTATGACATCATTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG
1 ATTTATGACATCATTTCATACCTTTAATGCACCGATATACATTTCATTTATGGCATCATTTCATG
* * *
277436 CCTTTAATGCACCGTTATACATTTAATTTATGGCATCCTTTCATGCCTTTA
66 CCTTTAATGCACCATTATACATTTAATATATGGCATCATTTCATGCCTTTA
277487 AT
1 AT
277489 GCACCGTTAT
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
116 106 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.43
Consensus pattern (116 bp):
ATTTATGACATCATTTCATACCTTTAATGCACCGATATACATTTCATTTATGGCATCATTTCATG
CCTTTAATGCACCATTATACATTTAATATATGGCATCATTTCATGCCTTTA
Found at i:277435 original size:45 final size:45
Alignment explanation
Indices: 277362--277512 Score: 248
Period size: 45 Copynumber: 3.4 Consensus size: 45
277352 GCCTCATTTC
* * *
277362 ATGCCTTTAATTTATGACATCATTTCATGCCTTTAATGCACCGTT
1 ATGCATTTAATTTATGGCATCCTTTCATGCCTTTAATGCACCGTT
*
277407 ATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTT
1 ATGCATTTAATTTATGGCATCCTTTCATGCCTTTAATGCACCGTT
*
277452 ATACATTTAATTTATGGCATCCTTTCATGCCTTTAATGCACCGTT
1 ATGCATTTAATTTATGGCATCCTTTCATGCCTTTAATGCACCGTT
*
277497 ATGCATTTCATTTATG
1 ATGCATTTAATTTATG
277513 TAATGAAAAC
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 98 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (45 bp):
ATGCATTTAATTTATGGCATCCTTTCATGCCTTTAATGCACCGTT
Found at i:278018 original size:95 final size:96
Alignment explanation
Indices: 277875--278074 Score: 255
Period size: 95 Copynumber: 2.1 Consensus size: 96
277865 CCCTACCATG
277875 GTATCGATACTTCTACACTATGGTATCGATACGCCCTTCTAGTATCGATACCATTTCT-ACATTA
1 GTATCGATACTTCTACACTATGGTATCGATACGCCCTTCTAGTATCGATACCATTT-TGACATTA
* * *
277939 TGTAATTC-ATGGTATCGATACCTTTCTCTTA
65 TGGAATTCTATGATATCGATACATTTCTCTTA
* * * *
277970 GTATCGATACTTCTATATTATGGTA-CGGATACTCCCTT-TCAGTATCGATACCATTTTGATATT
1 GTATCGATACTTCTACACTATGGTATC-GATACGCCCTTCT-AGTATCGATACCATTTTGACATT
* * *
278033 CTGGAATTCTCTGATATCGATACATTTCTCTTG
64 ATGGAATTCTATGATATCGATACATTTCTCTTA
278066 GTATCGATA
1 GTATCGATA
278075 TCCACAGTAG
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
94 3 0.03
95 60 0.66
96 28 0.31
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (96 bp):
GTATCGATACTTCTACACTATGGTATCGATACGCCCTTCTAGTATCGATACCATTTTGACATTAT
GGAATTCTATGATATCGATACATTTCTCTTA
Found at i:279763 original size:174 final size:174
Alignment explanation
Indices: 279473--279817 Score: 467
Period size: 174 Copynumber: 2.0 Consensus size: 174
279463 GATTTAAATG
* * * *
279473 AGAAACTTTGAAAATCGCTTTCTCATTTTTTTGAAAATCACGTGAAAACATCCTGCTCGAAGATC
1 AGAAACTCTGAAAATCGCTTTCTCATTTTTTCGAAAATCACATGAAAACATCCTGCCCGAAGATC
* * * * *
279538 TTATGAATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAGTTATAGATGACCCAAAGGATTTAA
66 TAATGAATGACCCGAAGGACTTATCATATTGCTCGAAAGACTTATAGATGACCCAAAGGATTAAA
*
279603 GAATCATGCTCGAAAA-ACTTGCTGATGGCCCGAAGGACTTAGTA
131 GAATCATGCTC-AAAAGACTTACTGATGGCCCGAAGGACTTAGTA
* * * * * *
279647 AGAAACTCTGGAAATTGTTTTCTCATTTTTTCGAAAATCATATGAAAACATCTTGCCCGAAGGTC
1 AGAAACTCTGAAAATCGCTTTCTCATTTTTTCGAAAATCACATGAAAACATCCTGCCCGAAGATC
* * * * * *
279712 TAATGGATGACCTGAATGACTTATCATATTTCTCGAAAGACTTATAGATGACTCGAAGGATTAAA
66 TAATGAATGACCCGAAGGACTTATCATATTGCTCGAAAGACTTATAGATGACCCAAAGGATTAAA
*
279777 GCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTA
131 GAATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTA
279818 CTCATCAAGA
Statistics
Matches: 147, Mismatches: 23, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
173 4 0.03
174 143 0.97
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (174 bp):
AGAAACTCTGAAAATCGCTTTCTCATTTTTTCGAAAATCACATGAAAACATCCTGCCCGAAGATC
TAATGAATGACCCGAAGGACTTATCATATTGCTCGAAAGACTTATAGATGACCCAAAGGATTAAA
GAATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTAGTA
Found at i:279997 original size:53 final size:53
Alignment explanation
Indices: 279878--280225 Score: 457
Period size: 53 Copynumber: 6.6 Consensus size: 53
279868 TTACAGTTAT
* *
279878 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTC-TACAAAAATTCATTTAAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTC--AAATTCATTTGAAAA
* * * *
279932 TATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTCCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* *
279985 CATCAAGAAACCCCTAAAACTTAGGCTTATCTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * * * * *
280038 CGTCAAGAAACCCGTAAAAATCAGACTTAG-TTTTTTCAAATTAATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * *
280090 CATCAAGAAACCCCTAAAAATTAGCCTTAGCTTCTTTTAAATTCAATTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * * * *
280143 CATCAAGAAACTCCTAAAAATTAGGCTTAGTTTCTTTTAAATTTATTTTAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
*
280196 CATTAAGAAACCCCTAAAAATTAGGCTTAG
1 CATCAAGAAACCCCTAAAAATTAGGCTTAG
280226 TTTAAATAAA
Statistics
Matches: 257, Mismatches: 35, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
52 46 0.18
53 178 0.69
54 31 0.12
55 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.30
Consensus pattern (53 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
Found at i:280108 original size:105 final size:104
Alignment explanation
Indices: 279878--280225 Score: 455
Period size: 105 Copynumber: 3.3 Consensus size: 104
279868 TTACAGTTAT
* * *
279878 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTC-TACAAAAATTCATTTAAAAATATCAAGAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTC--AAATTCATTTGAAAACATCAAGAAA
* * * *
279942 CCCCTGAAAATCAGGCTTAGCTTCTTCCAAATTCATTTGAAAA
64 -CCCTAAAAATCAGGCTTAG-TTTTTTCAAATTAATTTGAAAA
* * *
279985 CATCAAGAAACCCCTAAAACTTAGGCTTATCTTCTTTCAAATTCATTTGAAAACGTCAAGAAACC
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACC
*
280050 CGTAAAAATCAGACTTAGTTTTTTCAAATTAATTTGAAAA
66 C-TAAAAATCAGGCTTAGTTTTTTCAAATTAATTTGAAAA
* * *
280090 CATCAAGAAACCCCTAAAAATTAGCCTTAGCTTCTTTTAAATTCAATTGAAAACATCAAGAAACT
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAAC-
* * * *
280155 CCTAAAAATTAGGCTTAGTTTCTTTTAAATTTATTTTAAAA
65 CCTAAAAATCAGGCTTAGTTT-TTTCAAATTAATTTGAAAA
*
280196 CATTAAGAAACCCCTAAAAATTAGGCTTAG
1 CATCAAGAAACCCCTAAAAATTAGGCTTAG
280226 TTTAAATAAA
Statistics
Matches: 213, Mismatches: 24, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
105 97 0.46
106 82 0.38
107 32 0.15
108 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.30
Consensus pattern (104 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACC
CTAAAAATCAGGCTTAGTTTTTTCAAATTAATTTGAAAA
Found at i:280119 original size:158 final size:159
Alignment explanation
Indices: 279878--280228 Score: 472
Period size: 158 Copynumber: 2.2 Consensus size: 159
279868 TTACAGTTAT
* * *
279878 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTACAAAAATTCATTTAAAAATATCAAGAAAC
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTAC-AAAATTAATTTAAAAACATCAAGAAAC
* * * *
279943 CCCTGAAAATCAGGCTTAGCTTCTTCCAAATTCATTTGAAAACATCAAGAAACCCCTAAAACTTA
65 CCCTAAAAATCAGCCTTAGCTTCTTCCAAATTCAATTGAAAACATCAAGAAACCCCTAAAAATTA
280008 GGCTTA-TCTTCTTTCAAATTCATTTGAAAA
130 GGCTTAGT-TTCTTTCAAATTCATTTGAAAA
* * * * * * *
280038 CGTCAAGAAACCCGTAAAAATCAGACTTAGTTTTTTC-AAATTAATTTGAAAACATCAAGAAACC
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTACAAAATTAATTTAAAAACATCAAGAAACC
* ** *
280102 CCTAAAAATTAGCCTTAGCTTCTTTTAAATTCAATTGAAAACATCAAGAAACTCCTAAAAATTAG
66 CCTAAAAATCAGCCTTAGCTTCTTCCAAATTCAATTGAAAACATCAAGAAACCCCTAAAAATTAG
* * *
280167 GCTTAGTTTCTTTTAAATTTATTTTAAAA
131 GCTTAGTTTCTTTCAAATTCATTTGAAAA
*
280196 CATTAAGAAACCCCTAAAAATTAGGCTTAGTTT
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTT
280229 AAATAAAGGA
Statistics
Matches: 164, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
158 133 0.81
159 1 0.01
160 30 0.18
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (159 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTACAAAATTAATTTAAAAACATCAAGAAACC
CCTAAAAATCAGCCTTAGCTTCTTCCAAATTCAATTGAAAACATCAAGAAACCCCTAAAAATTAG
GCTTAGTTTCTTTCAAATTCATTTGAAAA
Done.