Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1171.1
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: 553655
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 33659 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:167064 original size:9 final size:9
Alignment explanation
Indices: 167050--167084 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
167040 TTATATTAAT
167050 TAAATAAAG
1 TAAATAAAG
167059 TAAATAAA-
1 TAAATAAAG
*
167067 TAAATAAAA
1 TAAATAAAG
167076 TAAATAAAG
1 TAAATAAAG
167085 ACAAATGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (9 bp):
TAAATAAAG
Found at i:167066 original size:13 final size:14
Alignment explanation
Indices: 167050--167084 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
167040 TTATATTAAT
167050 TAAATAAAGT-AAA
1 TAAATAAAGTAAAA
167063 TAAATAAA-TAAAA
1 TAAATAAAGTAAAA
167076 TAAATAAAG
1 TAAATAAAG
167085 ACAAATGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 19 0.95
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (14 bp):
TAAATAAAGTAAAA
Found at i:167228 original size:16 final size:16
Alignment explanation
Indices: 167180--167233 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
167170 ATTTACTATT
167180 TATAA-AAGATATTTA
1 TATAATAAGATATTTA
*
167195 T-TAATTAAG-TAATTA
1 TATAA-TAAGATATTTA
*
167210 TATTATAAGATATTTA
1 TATAATAAGATATTTA
167226 TATAATAA
1 TATAATAA
167234 ATAAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
14 3 0.10
15 11 0.35
16 17 0.55
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TATAATAAGATATTTA
Found at i:168967 original size:18 final size:18
Alignment explanation
Indices: 168911--169026 Score: 108
Period size: 18 Copynumber: 6.4 Consensus size: 18
168901 TAAATAAAGG
* * *
168911 TACTAAATACATGACTGC
1 TACTGAATAAATGACTGT
* * * *
168929 TATTGAATAATTAACTAT
1 TACTGAATAAATGACTGT
*
168947 TACTAAATAAATGACTGT
1 TACTGAATAAATGACTGT
168965 TACTGAATAAATGACTGT
1 TACTGAATAAATGACTGT
* *
168983 TATTGAATAACTGACTGT
1 TACTGAATAAATGACTGT
* *
169001 TACTGAACAATTGA-TCGT
1 TACTGAATAAATGACT-GT
169019 TACTGAAT
1 TACTGAAT
169027 GATATTGATA
Statistics
Matches: 78, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
17 1 0.01
18 77 0.99
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (18 bp):
TACTGAATAAATGACTGT
Found at i:169004 original size:54 final size:54
Alignment explanation
Indices: 168911--169026 Score: 135
Period size: 54 Copynumber: 2.1 Consensus size: 54
168901 TAAATAAAGG
* * * *
168911 TACTAAATACATGACTGCTATTGAATAATTAACTATTACTAAATAAATGA-CTGT
1 TACTGAATAAATGACTGCTATTGAATAACTAACTATTACTAAACAAATGATC-GT
* * * * *
168965 TACTGAATAAATGACTGTTATTGAATAACTGACTGTTACTGAACAATTGATCGT
1 TACTGAATAAATGACTGCTATTGAATAACTAACTATTACTAAACAAATGATCGT
169019 TACTGAAT
1 TACTGAAT
169027 GATATTGATA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 51 0.98
55 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (54 bp):
TACTGAATAAATGACTGCTATTGAATAACTAACTATTACTAAACAAATGATCGT
Found at i:176817 original size:16 final size:16
Alignment explanation
Indices: 176796--176829 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
176786 AATATATTGT
*
176796 AAAATGTATTTTTAAC
1 AAAATGTACTTTTAAC
176812 AAAATGTACTTTTAAC
1 AAAATGTACTTTTAAC
176828 AA
1 AA
176830 TTAAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (16 bp):
AAAATGTACTTTTAAC
Found at i:177532 original size:114 final size:113
Alignment explanation
Indices: 177300--177589 Score: 287
Period size: 114 Copynumber: 2.5 Consensus size: 113
177290 AGATGGAGCT
* * * * *
177300 TTAGCGGCGTTTTTAAAAAAGCGCCGCAATAGGTCGACCTTTAGCAGCG-TTTTTTAAAAACACC
1 TTAGCGGCGTTTTCAAAAAA-CGCCGCAATAGATCAAACTTTAGCGGCGTTTTTTTAAAAACACC
* * * * * **
177364 GCTAAAAGGTTAAGCAAAACGACATCATTTTACATGAGCTTCATTGGCA
65 GATAAAACGTTAAGCAAAACGACATCATTTTAAATGAACTTCAATGAAA
* * * * *
177413 GTAGCGGCGTTTTCCCAAAAACACCGCAATAGATCAAACTTTAGCGGCGTTTTTTTCTAAAACGC
1 TTAGCGGCGTTTT-CAAAAAACGCCGCAATAGATCAAACTTTAGCGGCGTTTTTTT-AAAAACAC
* * *
177478 CGAT-AAACGTTAAGCAAAACTACGTCGTTTTAAATGAACTTCAATGAAA
64 CGATAAAACGTTAAGCAAAACGACATCATTTTAAATGAACTTCAATGAAA
* * * * * *
177527 TTAGCGGCGCTTTACTAAAAACGCCACAATAGCTCACACTTTAGCGGCATTTTTGTTAAAAAC
1 TTAGCGGCG-TTTTCAAAAAACGCCGCAATAGATCAAACTTTAGCGGCGTTTTT-TTAAAAAC
177590 GTCGCTATAG
Statistics
Matches: 143, Mismatches: 29, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
113 35 0.24
114 94 0.66
115 14 0.10
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (113 bp):
TTAGCGGCGTTTTCAAAAAACGCCGCAATAGATCAAACTTTAGCGGCGTTTTTTTAAAAACACCG
ATAAAACGTTAAGCAAAACGACATCATTTTAAATGAACTTCAATGAAA
Found at i:177743 original size:156 final size:156
Alignment explanation
Indices: 177453--177745 Score: 378
Period size: 156 Copynumber: 1.9 Consensus size: 156
177443 AGATCAAACT
* * *
177453 TTAGCGGCGTTTTTTTCTAAAACGCCGATAAACGTTAAGCAAAACTACGTCGTTTTAAATGAACT
1 TTAGCGGCGTTTTTGTCAAAAACGCCGATAAACGTTAAGCAAAACTACGTCATTTTAAATGAACT
* *
177518 TCAATGAAATTAGCGGCGCTTTACTAAAAACGCCACAATAGCTCACACTTTAGCGGCATTTTTGT
66 TCAATGAAATTAGCGGCGCTTTACTAAAAACGCCACAATAGATCACACTTTAACGGCATTTTTGT
177583 TAAAAACGTCGCTATAGGTTGCTCCA
131 TAAAAACGTCGCTATAGGTTGCTCCA
* * ** * *
177609 TTAGCGGCGTTTTTGT-AAAAACGCCGCTAAAAGGTTAAGCAGCACGT-CGTCATTTTAAATTAG
1 TTAGCGGCGTTTTTGTCAAAAACGCCGAT-AAACGTTAAGCAAAAC-TACGTCATTTTAAATGAA
** * * *
177672 CTTCAATGGCATTAGCGGCGCTTTACTAAAAACGCCGCAATATATCA-ATCTTTAACGGCGTTTT
64 CTTCAATGAAATTAGCGGCGCTTTACTAAAAACGCCACAATAGATCACA-CTTTAACGGCATTTT
177736 T-TGTAAAAAC
128 TGT-TAAAAAC
177746 ACCGCGAAAA
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
155 12 0.10
156 104 0.89
157 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (156 bp):
TTAGCGGCGTTTTTGTCAAAAACGCCGATAAACGTTAAGCAAAACTACGTCATTTTAAATGAACT
TCAATGAAATTAGCGGCGCTTTACTAAAAACGCCACAATAGATCACACTTTAACGGCATTTTTGT
TAAAAACGTCGCTATAGGTTGCTCCA
Found at i:178430 original size:14 final size:14
Alignment explanation
Indices: 178404--178447 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
178394 TTTAAGGGTT
178404 ATGATTTAGGTTTG
1 ATGATTTAGGTTTG
* *
178418 ATGATTTATGTTTT
1 ATGATTTAGGTTTG
*
178432 ATGATTGAGGGTTTG
1 ATGATTTA-GGTTTG
178447 A
1 A
178448 GGTTTATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (14 bp):
ATGATTTAGGTTTG
Found at i:178496 original size:7 final size:7
Alignment explanation
Indices: 178486--178525 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
178476 AGGGTTGAAG
178486 GGTTAGT
1 GGTTAGT
178493 GGTTAGT
1 GGTTAGT
178500 GGTTAGT
1 GGTTAGT
178507 GG-TAGT
1 GGTTAGT
178513 GGTTAGT
1 GGTTAGT
178520 GGTTAG
1 GGTTAG
178526 GATTAAGGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.19
7 26 0.81
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.40
Consensus pattern (7 bp):
GGTTAGT
Found at i:178514 original size:13 final size:13
Alignment explanation
Indices: 178486--178522 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
178476 AGGGTTGAAG
178486 GGTTAGTGGTTAGT
1 GGTTAGTGG-TAGT
178500 GGTTAGTGGTAGT
1 GGTTAGTGGTAGT
178513 GGTTAGTGGT
1 GGTTAGTGGT
178523 TAGGATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.14, C:0.00, G:0.46, T:0.41
Consensus pattern (13 bp):
GGTTAGTGGTAGT
Found at i:179583 original size:16 final size:16
Alignment explanation
Indices: 179562--179613 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
179552 TTTGGTTCGC
179562 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
179578 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
179594 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
179610 TGTA
1 TGTA
179614 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:179660 original size:45 final size:44
Alignment explanation
Indices: 179594--179688 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
179584 GGATTAGAGG
* *
179594 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
179639 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
179683 TGTAAT
1 TGTAAT
179689 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:179871 original size:18 final size:17
Alignment explanation
Indices: 179850--179884 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
179840 TTATTATTTA
*
179850 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
179868 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
179885 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:179878 original size:28 final size:27
Alignment explanation
Indices: 179808--179880 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
179798 TTTATTATCA
*
179808 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
179836 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
179863 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
179881 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:179997 original size:144 final size:147
Alignment explanation
Indices: 179769--180040 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
179759 ATGATTATTG
179769 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
179834 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
179899 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
179918 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
179980 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
180041 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:180015 original size:18 final size:17
Alignment explanation
Indices: 179994--180028 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
179984 TTATTATTAA
*
179994 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
180012 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
180029 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:184319 original size:35 final size:35
Alignment explanation
Indices: 184273--184340 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
184263 CTATTGCTTG
*
184273 TTATGTGAATTCTGTGCATCTTGTACGTGACTCTA
1 TTATGTGAATTCTGTGCATCATGTACGTGACTCTA
184308 TTATGTGAATTCTGTGCATCATGTACGTGACTC
1 TTATGTGAATTCTGTGCATCATGTACGTGACTC
184341 AATCAATCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (35 bp):
TTATGTGAATTCTGTGCATCATGTACGTGACTCTA
Found at i:184573 original size:42 final size:42
Alignment explanation
Indices: 184514--184598 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
184504 TTCTCCTCAC
*
184514 AATGGTCTTCATTAGGGTGACTGTTACTTACTGTCTTTCCCT
1 AATGGTCTTCATTAGGGTGACTGTTACTTACTATCTTTCCCT
184556 AATGGTCTTCATTAGGGTGACTGTTACTTACTATCTTTCCCT
1 AATGGTCTTCATTAGGGTGACTGTTACTTACTATCTTTCCCT
184598 A
1 A
184599 GAATTTTAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (42 bp):
AATGGTCTTCATTAGGGTGACTGTTACTTACTATCTTTCCCT
Found at i:186737 original size:23 final size:23
Alignment explanation
Indices: 186693--186738 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
186683 TTACCATTAT
**
186693 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTACGAGTATA
* *
186716 TATTTTTATTATGTACGGGTATA
1 TATTATTATTATGTACGAGTATA
186739 CCTATATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.54
Consensus pattern (23 bp):
TATTATTATTATGTACGAGTATA
Found at i:187006 original size:19 final size:19
Alignment explanation
Indices: 186971--187007 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
186961 ATATATTACC
**
186971 TAAATATTTTAGTATTATG
1 TAAATATTTTAACATTATG
186990 TAAATATTTTAACATTAT
1 TAAATATTTTAACATTAT
187008 ATTATATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
TAAATATTTTAACATTATG
Found at i:189214 original size:19 final size:20
Alignment explanation
Indices: 189174--189217 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
189164 GTTTCTTTTG
* *
189174 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
189193 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
189212 GCATTA
1 GCATTA
189218 GACTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:197561 original size:15 final size:15
Alignment explanation
Indices: 197541--197569 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
197531 GGAGTAGACC
197541 AGGTACGTTTTATTA
1 AGGTACGTTTTATTA
197556 AGGTACGTTTTATT
1 AGGTACGTTTTATT
197570 TCAAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
AGGTACGTTTTATTA
Found at i:198323 original size:53 final size:49
Alignment explanation
Indices: 198234--198338 Score: 129
Period size: 53 Copynumber: 2.1 Consensus size: 49
198224 GAAGGGCCAC
** *
198234 TTATAAATAATTTTATCAATATAATAATATTGATCATTGTTTAAATATA
1 TTATAAATAATTTTATCAATATAATAATATTGATCATTACTTAAATAAA
* *
198283 TTATAACTAATTTTTATCAAAATAGTATTAATATTGATCATTACTTAAATAAA
1 TTATAAATAA-TTTTATC--AATA-TAATAATATTGATCATTACTTAAATAAA
198336 TTA
1 TTA
198339 CATAACTCAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 9 0.19
50 7 0.15
52 4 0.09
53 27 0.57
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (49 bp):
TTATAAATAATTTTATCAATATAATAATATTGATCATTACTTAAATAAA
Found at i:207027 original size:44 final size:44
Alignment explanation
Indices: 206862--207111 Score: 257
Period size: 42 Copynumber: 5.7 Consensus size: 44
206852 ACTGGGCAAA
* * * *
206862 TTAGCGGTGTTTTTATAAAACAAGCGCCACTAAAGGTCCTGTTCT
1 TTAGCGGCGTTTTTCTAAAA-AAGCGCCGCTAAAAGTCCTGTTCT
* * *
206907 TTAACGGTGTTTTTCT--AAAAGCGCCGCTAAAAGTTCTGTTCT
1 TTAGCGGCGTTTTTCTAAAAAAGCGCCGCTAAAAGTCCTGTTCT
*
206949 TTAGCGGCGTTTTTCT--AAAAGCGCCGTTAAAAGTCCTCG-TCT
1 TTAGCGGCGTTTTTCTAAAAAAGCGCCGCTAAAAGTCCT-GTTCT
*
206991 TTAGCGGCGTTTTT-TAAAGAAAGCGCCGCTAAAAGTCCTGATCT
1 TTAGCGGCGTTTTTCTAAA-AAAGCGCCGCTAAAAGTCCTGTTCT
* * *
207035 TTAGCGACGTTTGTT-TAAAAAAACGCCGCTAAAAGTCCTGGTCT
1 TTAGCGGCGTTT-TTCTAAAAAAGCGCCGCTAAAAGTCCTGTTCT
*
207079 TCAGCGGCGCTTTTT-TCAAACAAA-CGCCGCTAA
1 TTAGCGGCG-TTTTTCT-AAA-AAAGCGCCGCTAA
207112 TTTTACCGGT
Statistics
Matches: 181, Mismatches: 15, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
41 1 0.01
42 71 0.39
43 5 0.03
44 66 0.36
45 35 0.19
46 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (44 bp):
TTAGCGGCGTTTTTCTAAAAAAGCGCCGCTAAAAGTCCTGTTCT
Found at i:207038 original size:86 final size:89
Alignment explanation
Indices: 206924--207111 Score: 251
Period size: 86 Copynumber: 2.1 Consensus size: 89
206914 TGTTTTTCTA
* * * * *
206924 AAAGCGCCGCTAAAAGTTCTGTTCTTTAGCGGCGTTT-TTCT-AAAAGCGCCGTTAAAAGTCCTC
1 AAAGCGCCGCTAAAAGTCCTGATCTTTAGCGACGTTTGTT-TAAAAAACGCCGCTAAAAGTCCTC
* *
206987 GTCTTTAGCGGCG-TTTTTT-AAAG
65 GTCTTCAGCGGCGCTTTTTTCAAAC
*
207010 AAAGCGCCGCTAAAAGTCCTGATCTTTAGCGACGTTTGTTTAAAAAAACGCCGCTAAAAGTCCTG
1 AAAGCGCCGCTAAAAGTCCTGATCTTTAGCGACGTTTGTTT-AAAAAACGCCGCTAAAAGTCCTC
207075 GTCTTCAGCGGCGCTTTTTTCAAAC
65 GTCTTCAGCGGCGCTTTTTTCAAAC
207100 AAA-CGCCGCTAA
1 AAAGCGCCGCTAA
207112 TTTTACCGGT
Statistics
Matches: 89, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
86 35 0.39
87 2 0.02
88 31 0.35
89 15 0.17
90 6 0.07
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (89 bp):
AAAGCGCCGCTAAAAGTCCTGATCTTTAGCGACGTTTGTTTAAAAAACGCCGCTAAAAGTCCTCG
TCTTCAGCGGCGCTTTTTTCAAAC
Found at i:215656 original size:21 final size:21
Alignment explanation
Indices: 215630--215673 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
215620 AATTAAGCAT
*
215630 TTGGTCTAAGTAAACTTTGAA
1 TTGGTCTAAGTAAACTTCGAA
*
215651 TTGGTCTAAGTCAACTTCGAA
1 TTGGTCTAAGTAAACTTCGAA
215672 TT
1 TT
215674 TAACCAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (21 bp):
TTGGTCTAAGTAAACTTCGAA
Found at i:217483 original size:23 final size:22
Alignment explanation
Indices: 217436--217486 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
217426 CATGGTTAAA
*
217436 TTTTTTTTATTAGTCTTTGTAT
1 TTTTTTTTATTAATCTTTGTAT
217458 TTTTATTTTATTAAT-TTTAGT-T
1 TTTT-TTTTATTAATCTTT-GTAT
217480 TTTTTTT
1 TTTTTTT
217487 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.12
22 12 0.46
23 11 0.42
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76
Consensus pattern (22 bp):
TTTTTTTTATTAATCTTTGTAT
Found at i:217700 original size:21 final size:19
Alignment explanation
Indices: 217675--217715 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
217665 TTTAGAATTT
217675 TAAAAATAAAAAATAATTAAA
1 TAAAAAT-AAAAA-AATTAAA
*
217696 TAAAAGTAAAAAAATTAAA
1 TAAAAATAAAAAAATTAAA
217715 T
1 T
217716 TCATAACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
TAAAAATAAAAAAATTAAA
Found at i:218881 original size:9 final size:9
Alignment explanation
Indices: 218851--218886 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
218841 CACCTATTTG
218851 TTATTTGAA
1 TTATTTGAA
*
218860 TTATTAGAA
1 TTATTTGAA
*
218869 TTATTTGAG
1 TTATTTGAA
218878 TTATTTGAA
1 TTATTTGAA
218887 AATTTAACTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (9 bp):
TTATTTGAA
Found at i:227262 original size:30 final size:29
Alignment explanation
Indices: 227228--227334 Score: 81
Period size: 31 Copynumber: 3.5 Consensus size: 29
227218 TTTAATTTGA
227228 TCAATTTTAGTTCTTATACTTTTGAATTGG
1 TCAATTTTAG-TCTTATACTTTTGAATTGG
* * *
227258 TCAATTTTAGCCCCTATACTTTTTGAATT-T
1 TCAATTTTAG-TCTTATAC-TTTTGAATTGG
* ** * *
227288 TGAAATTTTAAAACTTGTGCTTTTCGAATTGG
1 T-CAATTTT-AGTCTTATACTTTT-GAATTGG
227320 TCAATTTTAGTCTTA
1 TCAATTTTAGTCTTA
227335 ACCCAAATAG
Statistics
Matches: 57, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
30 25 0.44
31 30 0.53
32 2 0.04
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (29 bp):
TCAATTTTAGTCTTATACTTTTGAATTGG
Found at i:227285 original size:31 final size:30
Alignment explanation
Indices: 227228--227286 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
227218 TTTAATTTGA
** *
227228 TCAATTTTAGTTCTTATACTTTTGAATTGG
1 TCAATTTTAGCCCCTATACTTTTGAATTGG
227258 TCAATTTTAGCCCCTATACTTTTTGAATT
1 TCAATTTTAGCCCCTATAC-TTTTGAATT
227287 TTGAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (30 bp):
TCAATTTTAGCCCCTATACTTTTGAATTGG
Found at i:235674 original size:24 final size:25
Alignment explanation
Indices: 235647--235695 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
235637 GCTTTTTTAT
*
235647 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
235671 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
235696 AAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:235688 original size:25 final size:23
Alignment explanation
Indices: 235659--235723 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 23
235649 AATAAAAAAC
*
235659 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
235684 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
235705 -TTAAAACA-AAAAACAAATA
1 TTTAAAACATAAAAACAAATA
235724 AAAAATAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 10 0.26
20 8 0.21
21 1 0.03
23 5 0.13
24 3 0.08
25 11 0.29
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:235718 original size:19 final size:20
Alignment explanation
Indices: 235685--235723 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
235675 TCAAATACAT
235685 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
235705 TTAAAACA-AAAAACAAATA
1 TTAAAACATAAAAACAAATA
235724 AAAAATAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:239712 original size:15 final size:16
Alignment explanation
Indices: 239694--239724 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
239684 GTATAATTGA
239694 AAATTAAATTT-AAAT
1 AAATTAAATTTGAAAT
239709 AAATTAAATTTGAAAT
1 AAATTAAATTTGAAAT
239725 TTAACTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AAATTAAATTTGAAAT
Found at i:240181 original size:21 final size:21
Alignment explanation
Indices: 240157--240224 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
240147 TTTAATAGTT
240157 TATATTTTTATAAATTTTAAA
1 TATATTTTTATAAATTTTAAA
* *
240178 TATAATTTTAT-TATTTTAATA
1 TATATTTTTATAAATTTTAA-A
*
240199 GTTTATATCTTTATAAATTTTAAA
1 ---TATATTTTTATAAATTTTAAA
240223 TA
1 TA
240225 GTTAAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
20 7 0.19
21 13 0.35
24 10 0.27
25 7 0.19
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (21 bp):
TATATTTTTATAAATTTTAAA
Found at i:240185 original size:45 final size:45
Alignment explanation
Indices: 240130--240224 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
240120 ACTATAATAA
*
240130 AAATATAATTTTATTATTTTAATAGTTTATATTTTTATAAATTTT
1 AAATATAATTTTATTATTTTAATAGTTTATATCTTTATAAATTTT
240175 AAATATAATTTTATTATTTTAATAGTTTATATCTTTATAAATTTT
1 AAATATAATTTTATTATTTTAATAGTTTATATCTTTATAAATTTT
240220 AAATA
1 AAATA
240225 GTTAAATTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (45 bp):
AAATATAATTTTATTATTTTAATAGTTTATATCTTTATAAATTTT
Found at i:240271 original size:32 final size:32
Alignment explanation
Indices: 240208--240273 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
240198 AGTTTATATC
* * *
240208 TTTATAAATTTTAAATAGTTAAATTTTAAAAT
1 TTTATAAATTATAAATACTTAAATTTGAAAAT
*
240240 TTTATAAATTATACCATACTTAAA-TTGAAAAT
1 TTTATAAATTATA-AATACTTAAATTTGAAAAT
240272 TT
1 TT
240274 ACCACTGCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (32 bp):
TTTATAAATTATAAATACTTAAATTTGAAAAT
Found at i:245224 original size:10 final size:11
Alignment explanation
Indices: 245208--245239 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
245198 CTTAAAAAGG
245208 AGAAAAAAAAA
1 AGAAAAAAAAA
245219 AGAAAAAAAAA
1 AGAAAAAAAAA
245230 AGAAGAAAAA
1 AGAA-AAAAA
245240 CTTAGAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:259730 original size:16 final size:16
Alignment explanation
Indices: 259709--259754 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
259699 TGCAACAACC
259709 AAGAAATATTATAAAG
1 AAGAAATATTATAAAG
* *
259725 AAGAAAAAGTTAAAAAG
1 AAGAAATA-TTATAAAG
*
259742 CAGAAATATTATA
1 AAGAAATATTATA
259755 CTAACCAAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.63, C:0.02, G:0.13, T:0.22
Consensus pattern (16 bp):
AAGAAATATTATAAAG
Found at i:270502 original size:19 final size:19
Alignment explanation
Indices: 270461--270500 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
270451 TTGTAGGTGG
270461 AAATTTATTTATCTAAATA
1 AAATTTATTTATCTAAATA
270480 AAATTTATATT-T-TAAATA
1 AAATTTAT-TTATCTAAATA
270498 AAA
1 AAA
270501 ATATTTATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 9 0.45
20 2 0.10
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTTATTTATCTAAATA
Found at i:285808 original size:16 final size:16
Alignment explanation
Indices: 285769--285810 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
285759 ATAATAAAAA
*
285769 TATAATTTTATTATTTT
1 TATAAGTTT-TTATTTT
*
285786 AAT-AGTTTTTATTTT
1 TATAAGTTTTTATTTT
285801 TATAAGTTTT
1 TATAAGTTTT
285811 AAAGGATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.43
16 10 0.48
17 2 0.10
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (16 bp):
TATAAGTTTTTATTTT
Found at i:287197 original size:17 final size:16
Alignment explanation
Indices: 287159--287192 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
287149 AGGTTTGAAA
287159 TTTTTAATTAATTAAAT
1 TTTTTAATTAA-TAAAT
287176 TTTTTAATTAA-AAAT
1 TTTTTAATTAATAAAT
287191 TT
1 TT
287193 ATTTTCATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
17 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTAATTAATAAAT
Found at i:291215 original size:2 final size:2
Alignment explanation
Indices: 291208--291336 Score: 258
Period size: 2 Copynumber: 64.5 Consensus size: 2
291198 TCTTGTTGTT
291208 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
291250 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
291292 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
291334 GA G
1 GA G
291337 GTTAAAATGA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 127 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:295978 original size:22 final size:21
Alignment explanation
Indices: 295952--295995 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
295942 TCAAAGAAAG
295952 AGAAAAAAAGATACCAGAAAAA
1 AGAAAAAAA-ATACCAGAAAAA
* * *
295974 AGAAACAAATTACCAGTAAAA
1 AGAAAAAAAATACCAGAAAAA
295995 A
1 A
295996 TAAATGAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.09
Consensus pattern (21 bp):
AGAAAAAAAATACCAGAAAAA
Found at i:298197 original size:12 final size:13
Alignment explanation
Indices: 298180--298209 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
298170 TACGAAATAA
298180 AAATTTAAA-ATC
1 AAATTTAAATATC
298192 AAATTTAAATATC
1 AAATTTAAATATC
298205 AAATT
1 AAATT
298210 ATGACAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
AAATTTAAATATC
Found at i:303981 original size:70 final size:70
Alignment explanation
Indices: 303888--304027 Score: 235
Period size: 70 Copynumber: 2.0 Consensus size: 70
303878 TTTACAATCT
* * * *
303888 TTCAAAAATATCTTATTGGAATAATGAAAGATTAATCTTTGTTCCCTTTAACAAACACCGTCCAT
1 TTCAAAAATATCCTATTAGAATAATGAAAGAGTAATCTTTGTTCCCTTTAACAAACACCATCCAT
303953 AATGA
66 AATGA
*
303958 TTCAAAAATATCCTATTAGAATAATGAAAGAGTAATCTTTGTTCCCTTTAACAAACACCATCGAT
1 TTCAAAAATATCCTATTAGAATAATGAAAGAGTAATCTTTGTTCCCTTTAACAAACACCATCCAT
304023 AATGA
66 AATGA
304028 ACATAACAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (70 bp):
TTCAAAAATATCCTATTAGAATAATGAAAGAGTAATCTTTGTTCCCTTTAACAAACACCATCCAT
AATGA
Found at i:304754 original size:11 final size:11
Alignment explanation
Indices: 304738--304771 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
304728 AAATATTTTA
304738 TATTTAATATT
1 TATTTAATATT
304749 TATTTAATATT
1 TATTTAATATT
* *
304760 AATTTGATATT
1 TATTTAATATT
304771 T
1 T
304772 GTCAATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (11 bp):
TATTTAATATT
Found at i:305781 original size:18 final size:17
Alignment explanation
Indices: 305740--305774 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
305730 TCTTTAAGAA
305740 GAAAAAAATACTCAAAC
1 GAAAAAAATACTCAAAC
305757 GAAAAAAATACTCAAAC
1 GAAAAAAATACTCAAAC
305774 G
1 G
305775 GTAAAAAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.63, C:0.17, G:0.09, T:0.11
Consensus pattern (17 bp):
GAAAAAAATACTCAAAC
Found at i:313417 original size:6 final size:6
Alignment explanation
Indices: 313406--313439 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
313396 TTCAGAAAAC
313406 AATAAA AATAAAA AATAAAA AATAAA AATAAA AA
1 AATAAA AAT-AAA AAT-AAA AATAAA AATAAA AA
313440 CCAATCTGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 14 0.52
7 13 0.48
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:313421 original size:7 final size:7
Alignment explanation
Indices: 313409--313439 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
313399 AGAAAACAAT
313409 AAAAATA
1 AAAAATA
313416 AAAAATA
1 AAAAATA
313423 AAAAAT-
1 AAAAATA
313429 AAAAATA
1 AAAAATA
313436 AAAA
1 AAAA
313440 CCAATCTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:313424 original size:13 final size:12
Alignment explanation
Indices: 313401--313439 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
313391 TCCCTTTCAG
*
313401 AAAACAATAAAA
1 AAAAAAATAAAA
313413 ATAAAAAATAAAA
1 A-AAAAAATAAAA
313426 AATAAAAATAAAA
1 AA-AAAAATAAAA
313439 A
1 A
313440 CCAATCTGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 2 0.08
13 22 0.92
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAATAAAA
Found at i:324590 original size:3 final size:3
Alignment explanation
Indices: 324582--324620 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
324572 TTTAGTGTGC
*
324582 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
324621 CCGAAGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:326302 original size:12 final size:12
Alignment explanation
Indices: 326272--326311 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
326262 CAATCTAGGA
326272 TTAGAATTT-GAT
1 TTAG-ATTTCGAT
*
326284 TTTGATTTCGAT
1 TTAGATTTCGAT
326296 TTAGATTTCGAT
1 TTAGATTTCGAT
326308 TTAG
1 TTAG
326312 GGTTATTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.25, C:0.05, G:0.17, T:0.53
Consensus pattern (12 bp):
TTAGATTTCGAT
Found at i:326504 original size:48 final size:48
Alignment explanation
Indices: 326452--326657 Score: 126
Period size: 48 Copynumber: 4.3 Consensus size: 48
326442 TTGATGTGTT
326452 TGTATCTGCCATTGTATGAATGTCATTATCAAACTGATCTTTATTGTG
1 TGTATCTGCCATTGTATGAATGTCATTATCAAACTGATCTTTATTGTG
* * * * * *
326500 TGTATCCGTCATTGTTTGTATCTGTCATTGTAT-GAA-TGCCA-CTGTA-T-TG
1 TGTATCTGCCATTGTATG-A-ATGTCA-T-TATCAAACTG--ATCTTTATTGTG
* * * ** * *
326549 TG--TCTGCCATTGT-TTAAGGTTATT-TCAATTTTTAT-TTTGATGTGTT
1 TGTATCTGCCATTGTATGAATGTCATTATCAA-ACTGATCTTT-AT-TGTG
* *
326595 TGTATCTGCCATTCTATGAATGCCATTATCAAACTGATCTTTATTGTG
1 TGTATCTGCCATTGTATGAATGTCATTATCAAACTGATCTTTATTGTG
326643 TGTATCTGCCATTGT
1 TGTATCTGCCATTGT
326658 TTGTATCTGT
Statistics
Matches: 112, Mismatches: 27, Indels: 38
0.63 0.15 0.21
Matches are distributed among these distances:
41 1 0.01
42 5 0.04
43 2 0.02
44 4 0.04
45 2 0.02
46 4 0.04
47 9 0.08
48 42 0.38
49 17 0.15
50 15 0.13
51 7 0.06
52 4 0.04
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (48 bp):
TGTATCTGCCATTGTATGAATGTCATTATCAAACTGATCTTTATTGTG
Found at i:326519 original size:16 final size:16
Alignment explanation
Indices: 326494--326530 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
326484 ACTGATCTTT
326494 ATTGTGTGTATCCGTC
1 ATTGTGTGTATCCGTC
* *
326510 ATTGTTTGTATCTGTC
1 ATTGTGTGTATCCGTC
326526 ATTGT
1 ATTGT
326531 ATGAATGCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (16 bp):
ATTGTGTGTATCCGTC
Found at i:326572 original size:143 final size:143
Alignment explanation
Indices: 326401--326683 Score: 512
Period size: 143 Copynumber: 2.0 Consensus size: 143
326391 ATGTGTACTA
* *
326401 TATTGTGTCTGCCATTGTTTAAGGTTATTTCGATTTTGATTTTGATGTGTTTGTATCTGCCATTG
1 TATTGTGTCTGCCATTGTTTAAGGTTATTTCAATTTTGATTTTGATGTGTTTGTATCTGCCATTC
* *
326466 TATGAATGTCATTATCAAACTGATCTTTATTGTGTGTATCCGTCATTGTTTGTATCTGTCATTGT
66 TATGAATGCCATTATCAAACTGATCTTTATTGTGTGTATCCGCCATTGTTTGTATCTGTCATTGT
326531 ATGAATGCCACTG
131 ATGAATGCCACTG
*
326544 TATTGTGTCTGCCATTGTTTAAGGTTATTTCAATTTTTATTTTGATGTGTTTGTATCTGCCATTC
1 TATTGTGTCTGCCATTGTTTAAGGTTATTTCAATTTTGATTTTGATGTGTTTGTATCTGCCATTC
*
326609 TATGAATGCCATTATCAAACTGATCTTTATTGTGTGTATCTGCCATTGTTTGTATCTGTCATTGT
66 TATGAATGCCATTATCAAACTGATCTTTATTGTGTGTATCCGCCATTGTTTGTATCTGTCATTGT
326674 ATGAATGCCA
131 ATGAATGCCA
326684 TTATCAAACT
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
143 134 1.00
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (143 bp):
TATTGTGTCTGCCATTGTTTAAGGTTATTTCAATTTTGATTTTGATGTGTTTGTATCTGCCATTC
TATGAATGCCATTATCAAACTGATCTTTATTGTGTGTATCCGCCATTGTTTGTATCTGTCATTGT
ATGAATGCCACTG
Found at i:326662 original size:16 final size:16
Alignment explanation
Indices: 326637--326673 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
326627 ACTGATCTTT
326637 ATTGTGTGTATCTGCC
1 ATTGTGTGTATCTGCC
* *
326653 ATTGTTTGTATCTGTC
1 ATTGTGTGTATCTGCC
326669 ATTGT
1 ATTGT
326674 ATGAATGCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (16 bp):
ATTGTGTGTATCTGCC
Found at i:326665 original size:64 final size:64
Alignment explanation
Indices: 326591--326721 Score: 235
Period size: 64 Copynumber: 2.0 Consensus size: 64
326581 TATTTTGATG
*
326591 TGTTTGTATCTGCCATTCTATGAATGCCATTATCAAACTGATCTTTATTGTGTGTATCTGCCAT
1 TGTTTGTATCTGCCATTCTATGAATGCCATTATCAAACTGATCTTTATTGTGTATATCTGCCAT
* *
326655 TGTTTGTATCTGTCATTGTATGAATGCCATTATCAAACTGATCTTTATTGTGTATATCTGCCAT
1 TGTTTGTATCTGCCATTCTATGAATGCCATTATCAAACTGATCTTTATTGTGTATATCTGCCAT
326719 TGT
1 TGT
326722 ATGAATGTCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (64 bp):
TGTTTGTATCTGCCATTCTATGAATGCCATTATCAAACTGATCTTTATTGTGTATATCTGCCAT
Found at i:326717 original size:34 final size:34
Alignment explanation
Indices: 326615--326719 Score: 89
Period size: 34 Copynumber: 3.2 Consensus size: 34
326605 ATTCTATGAA
*
326615 TGCCATTATCAAACTGATCTTTATTGTGTGTATC
1 TGCCATTATCAAACTGATCTTTATTGTGTATATC
* * * *
326649 TGCCATTGT----TTGTATCTGTCA-T-TGTATGA-A
1 TGCCATTATCAAACTG-ATCT-TTATTGTGTAT-ATC
326679 TGCCATTATCAAACTGATCTTTATTGTGTATATC
1 TGCCATTATCAAACTGATCTTTATTGTGTATATC
326713 TGCCATT
1 TGCCATT
326720 GTATGAATGT
Statistics
Matches: 52, Mismatches: 9, Indels: 20
0.64 0.11 0.25
Matches are distributed among these distances:
30 14 0.27
31 6 0.12
32 4 0.08
33 6 0.12
34 22 0.42
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (34 bp):
TGCCATTATCAAACTGATCTTTATTGTGTATATC
Found at i:326724 original size:48 final size:48
Alignment explanation
Indices: 326661--326769 Score: 182
Period size: 48 Copynumber: 2.3 Consensus size: 48
326651 CCATTGTTTG
*
326661 TATCTGTCATTGTATGAATGCCATTATCAAACTGATCTTTATTGTGTA
1 TATCTGCCATTGTATGAATGCCATTATCAAACTGATCTTTATTGTGTA
* * *
326709 TATCTGCCATTGTATGAATGTCATTATCAAATTGATGTTTATTGTGTA
1 TATCTGCCATTGTATGAATGCCATTATCAAACTGATCTTTATTGTGTA
326757 TATCTGCCATTGT
1 TATCTGCCATTGT
326770 TTGTATCTGC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.45
Consensus pattern (48 bp):
TATCTGCCATTGTATGAATGCCATTATCAAACTGATCTTTATTGTGTA
Found at i:326753 original size:112 final size:110
Alignment explanation
Indices: 326597--326831 Score: 335
Period size: 112 Copynumber: 2.1 Consensus size: 110
326587 GATGTGTTTG
* *
326597 TATCTGCCATTCTATGAATGCCATTATCAAACTGATCTTTATTGTGTGTATCTGCCATTGTTTGT
1 TATCTGCCATTGTATGAATGCCATTATCAAACTGATCTTTATTGTGTATATCTGCCATTGTTTGT
* ** *
326662 ATCTGTCATTGTATGAATGCCATTATCAAACTGATCTTTATTGTGTA
66 ATCTGCCATTAAAT-AAT-ACATTATCAAACTGATCTTTATTGTGTA
* * *
326709 TATCTGCCATTGTATGAATGTCATTATCAAATTGATGTTTATTGTGTATATCTGCCATTGTTTGT
1 TATCTGCCATTGTATGAATGCCATTATCAAACTGATCTTTATTGTGTATATCTGCCATTGTTTGT
* * *
326774 ATCTGCCATTAAATTATACATTATTAAACTGATGTTTATTGTGTA
66 ATCTGCCATTAAATAATACATTATCAAACTGATCTTTATTGTGTA
*
326819 TATCTGTCATTGT
1 TATCTGCCATTGT
326832 TTGTATCCAG
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
110 37 0.34
111 2 0.02
112 71 0.65
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (110 bp):
TATCTGCCATTGTATGAATGCCATTATCAAACTGATCTTTATTGTGTATATCTGCCATTGTTTGT
ATCTGCCATTAAATAATACATTATCAAACTGATCTTTATTGTGTA
Found at i:327133 original size:15 final size:15
Alignment explanation
Indices: 327113--327156 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
327103 GAAGAAAATA
327113 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
*
327128 TGTCTGGTAGTGAAG
1 TGTCTGGTAGTGATG
*
327143 TATCTGGTAGTGAT
1 TGTCTGGTAGTGAT
327157 AGTGATGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.18, C:0.07, G:0.36, T:0.39
Consensus pattern (15 bp):
TGTCTGGTAGTGATG
Found at i:328868 original size:43 final size:43
Alignment explanation
Indices: 328766--328943 Score: 213
Period size: 43 Copynumber: 4.2 Consensus size: 43
328756 TTGTTGATCA
* * * *
328766 CATGCAGTGATTGTTGGAAAGCTATTGAGT-TTTTTTAATATG
1 CATGCAATGATAGTTGGAAAGCTGTTGACTATTTTTTAATATG
* * *
328808 TATGCAGTGATTA-TTGGAAAGTTGTTGACTATTTTTTAATATG
1 CATGCAATGA-TAGTTGGAAAGCTGTTGACTATTTTTTAATATG
328851 CATGCAATGATAGTTGGAAAGCTGTTGACTATTTTTTAATATG
1 CATGCAATGATAGTTGGAAAGCTGTTGACTATTTTTTAATATG
* * *
328894 CATGCAATGATTGTTGG--TG-TGTTGCCTATTTTTTAATATG
1 CATGCAATGATAGTTGGAAAGCTGTTGACTATTTTTTAATATG
*
328934 CATGCGATGA
1 CATGCAATGA
328944 GTTTTTTTTA
Statistics
Matches: 121, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
40 29 0.24
41 1 0.01
42 25 0.21
43 66 0.55
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43
Consensus pattern (43 bp):
CATGCAATGATAGTTGGAAAGCTGTTGACTATTTTTTAATATG
Found at i:328935 original size:83 final size:84
Alignment explanation
Indices: 328766--328943 Score: 234
Period size: 83 Copynumber: 2.1 Consensus size: 84
328756 TTGTTGATCA
* * * * *
328766 CATGCAGTGATTGTTGGAAAGCTATTGAGTTTTTTTAATATGTATGCAGTGATTATTGGAAAGTT
1 CATGCAATGATAGTTGGAAAGCTATTGACTTTTTTTAATATGCATGCAATGATTATTGG-AAGTT
328831 GTTGACTATTTTTTAATATG
65 GTTGACTATTTTTTAATATG
* * *
328851 CATGCAATGATAGTTGGAAAGCTGTTGACTATTTTTTAATATGCATGCAATGATTGTTGG-TG-T
1 CATGCAATGATAGTTGGAAAGCTATTGACT-TTTTTTAATATGCATGCAATGATTATTGGAAGTT
*
328914 GTTGCCTATTTTTTAATATG
65 GTTGACTATTTTTTAATATG
*
328934 CATGCGATGA
1 CATGCAATGA
328944 GTTTTTTTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
83 29 0.35
84 1 0.01
85 26 0.32
86 26 0.32
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43
Consensus pattern (84 bp):
CATGCAATGATAGTTGGAAAGCTATTGACTTTTTTTAATATGCATGCAATGATTATTGGAAGTTG
TTGACTATTTTTTAATATG
Found at i:329623 original size:22 final size:21
Alignment explanation
Indices: 329598--329644 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
329588 AAGTTGGTGT
329598 CCAAACCTAGCAAGAGGCTACC
1 CCAAACC-AGCAAGAGGCTACC
** *
329620 CCAAGTCAGCAAGAGGGTACC
1 CCAAACCAGCAAGAGGCTACC
329641 CCAA
1 CCAA
329645 CTCAACAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.36, C:0.34, G:0.21, T:0.09
Consensus pattern (21 bp):
CCAAACCAGCAAGAGGCTACC
Found at i:329630 original size:21 final size:21
Alignment explanation
Indices: 329606--329653 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
329596 GTCCAAACCT
*
329606 AGCAAGAGGCTACCCCAAGTC
1 AGCAAGAGGCTACCCCAACTC
*
329627 AGCAAGAGGGTACCCCAACTC
1 AGCAAGAGGCTACCCCAACTC
*
329648 AACAAG
1 AGCAAG
329654 GTGCCCCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.31, G:0.23, T:0.08
Consensus pattern (21 bp):
AGCAAGAGGCTACCCCAACTC
Found at i:330166 original size:56 final size:56
Alignment explanation
Indices: 330075--330186 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 56
330065 TTATCATATT
* *
330075 ATTTGTTATCCAACTGTTATCTTTTCTAACTAGCAGCCATGTATACCAACTGTTAA
1 ATTTGTTATCCAACTGTTATCTTTTCTAACCAGCAGCCATGTATACCAAATGTTAA
*
330131 ATTTGTATAT-CAATTGTTATCTTTTCTAACCAGCAGCCATGTATACCAAATGTTAA
1 ATTTGT-TATCCAACTGTTATCTTTTCTAACCAGCAGCCATGTATACCAAATGTTAA
330187 GCAATTTGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
56 49 0.94
57 3 0.06
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (56 bp):
ATTTGTTATCCAACTGTTATCTTTTCTAACCAGCAGCCATGTATACCAAATGTTAA
Found at i:330767 original size:20 final size:23
Alignment explanation
Indices: 330742--330788 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
330732 TATCCATTTT
330742 TTCTCTT-CTCCTT-T-TTCTTC
1 TTCTCTTCCTCCTTCTCTTCTTC
*
330762 TTCTCTTCCTGCTTCTCTTCTTC
1 TTCTCTTCCTCCTTCTCTTCTTC
330785 TTCT
1 TTCT
330789 TTTTTTCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 5 0.22
22 1 0.04
23 10 0.43
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (23 bp):
TTCTCTTCCTCCTTCTCTTCTTC
Found at i:333429 original size:51 final size:50
Alignment explanation
Indices: 333354--333454 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 50
333344 CTTCTCCTTA
* * *
333354 CTTATCTTACATCACTTGTTTTGAAACACACAACATT-TGCAAAGCTAAAGC
1 CTTATCCTACATCACTCGTTTTGAAACA-A-AAAATTCTGCAAAGCTAAAGC
333405 CTTATCCTACATCACTCGTTTTGAAACAAAAAATTGCTGCAAAGCTAAAG
1 CTTATCCTACATCACTCGTTTTGAAACAAAAAATT-CTGCAAAGCTAAAG
333455 TATCCATTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
49 5 0.11
50 1 0.02
51 39 0.87
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.30
Consensus pattern (50 bp):
CTTATCCTACATCACTCGTTTTGAAACAAAAAATTCTGCAAAGCTAAAGC
Found at i:334950 original size:19 final size:20
Alignment explanation
Indices: 334905--334950 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
334895 GAGTTCTATA
334905 TAAAAATTATAAAAAAACCT
1 TAAAAATTATAAAAAAACCT
* *
334925 T-ACAATTATAAAAAAA-TT
1 TAAAAATTATAAAAAAACCT
334943 TAAAAATT
1 TAAAAATT
334951 CTATATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 2 0.09
19 19 0.86
20 1 0.05
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAATTATAAAAAAACCT
Found at i:335713 original size:13 final size:13
Alignment explanation
Indices: 335695--335755 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
335685 CTTAAATTTT
335695 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* * *
335708 TCAAAAGTATTTT
1 TCAAAAGCACTTC
* *
335721 TCCATAGCACTTC
1 TCAAAAGCACTTC
* *
335734 TCAAAAGCAATTT
1 TCAAAAGCACTTC
335747 TCAAAAGCA
1 TCAAAAGCA
335756 TTGCCAAACT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:335721 original size:26 final size:26
Alignment explanation
Indices: 335690--335755 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
335680 AAACACTTAA
*
335690 ATTTTTCAAAAGCACTTCTCAAAAGT
1 ATTTTTCAAAAGCACTTCTCAAAAGC
* *
335716 ATTTTTCCATAGCACTTCTCAAAAGC
1 ATTTTTCAAAAGCACTTCTCAAAAGC
*
335742 AATTTTCAAAAGCA
1 ATTTTTCAAAAGCA
335756 TTGCCAAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (26 bp):
ATTTTTCAAAAGCACTTCTCAAAAGC
Found at i:342806 original size:16 final size:18
Alignment explanation
Indices: 342771--342810 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
342761 GAATACTTAT
342771 TAAAATAAAATATAAGAG
1 TAAAATAAAATATAAGAG
342789 TAAAATAAAATA-AA-AG
1 TAAAATAAAATATAAGAG
342805 TAAAAT
1 TAAAAT
342811 TCATATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
TAAAATAAAATATAAGAG
Found at i:347788 original size:21 final size:22
Alignment explanation
Indices: 347759--347805 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
347749 CAGAAGGAGT
*
347759 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
347781 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
347802 GAGT
1 GAGT
347806 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:357373 original size:14 final size:15
Alignment explanation
Indices: 357347--357375 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
357337 GATTTAGCAC
357347 TTGAAGTAAACGGGA
1 TTGAAGTAAACGGGA
357362 TTGAAG-AAACGGGA
1 TTGAAGTAAACGGGA
357376 GGACGTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.07, G:0.34, T:0.17
Consensus pattern (15 bp):
TTGAAGTAAACGGGA
Found at i:361297 original size:9 final size:9
Alignment explanation
Indices: 361283--361314 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
361273 AACTTGGTGC
361283 ATTTTGTTT
1 ATTTTGTTT
361292 ATTTTGTTT
1 ATTTTGTTT
361301 ATTTTGTTT
1 ATTTTGTTT
361310 ATTTT
1 ATTTT
361315 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:365759 original size:9 final size:9
Alignment explanation
Indices: 365745--365776 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
365735 AACTTGGTGC
365745 ATTTTGTTT
1 ATTTTGTTT
365754 ATTTTGTTT
1 ATTTTGTTT
365763 ATTTTGTTT
1 ATTTTGTTT
365772 ATTTT
1 ATTTT
365777 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:368454 original size:15 final size:16
Alignment explanation
Indices: 368428--368462 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
368418 AAGAGAGAGA
368428 AAAACAAACACTCAAC
1 AAAACAAACACTCAAC
368444 AAAAC-AACACTCAAC
1 AAAACAAACACTCAAC
368459 AAAA
1 AAAA
368463 TTACATCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.66, C:0.29, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAACAAACACTCAAC
Found at i:368507 original size:44 final size:44
Alignment explanation
Indices: 368444--368537 Score: 188
Period size: 44 Copynumber: 2.1 Consensus size: 44
368434 AACACTCAAC
368444 AAAACAACACTCAACAAAATTACATCTGCAATTAGATCGATAAG
1 AAAACAACACTCAACAAAATTACATCTGCAATTAGATCGATAAG
368488 AAAACAACACTCAACAAAATTACATCTGCAATTAGATCGATAAG
1 AAAACAACACTCAACAAAATTACATCTGCAATTAGATCGATAAG
368532 AAAACA
1 AAAACA
368538 TACTCTTACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.52, C:0.20, G:0.09, T:0.19
Consensus pattern (44 bp):
AAAACAACACTCAACAAAATTACATCTGCAATTAGATCGATAAG
Found at i:372047 original size:21 final size:21
Alignment explanation
Indices: 372023--372064 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
372013 GTTACCCTTG
*
372023 ATTATAAGTTTTAATAATTTT
1 ATTATAAGTTCTAATAATTTT
* *
372044 ATTATAGGTTCTAATTATTTT
1 ATTATAAGTTCTAATAATTTT
372065 TTTTGACATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
ATTATAAGTTCTAATAATTTT
Found at i:373179 original size:16 final size:17
Alignment explanation
Indices: 373158--373200 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
373148 TTGAGACAAG
373158 AATAAATTT-TTAATTA
1 AATAAATTTATTAATTA
373174 AATAAATTTAATTAATTA
1 AATAAATTT-ATTAATTA
373192 AA-AAATTTA
1 AATAAATTTA
373201 AATTAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.40
17 6 0.24
18 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAAATTTATTAATTA
Found at i:373190 original size:18 final size:18
Alignment explanation
Indices: 373158--373208 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
373148 TTGAGACAAG
373158 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
373174 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
373192 AA-AAATTTAAATTAATT
1 AATAAATTT-AATTAATT
373209 TGGAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.28
17 6 0.19
18 17 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:376808 original size:27 final size:28
Alignment explanation
Indices: 376772--376831 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
376762 TATTTTTATT
376772 TGTTTCAAA-TTACATTTTAATCACTTA
1 TGTTTCAAAGTTACATTTTAATCACTTA
* * *
376799 TGTTTGAAATGTTATATTTTAGTCACTTA
1 TGTTTCAAA-GTTACATTTTAATCACTTA
376828 TGTT
1 TGTT
376832 ATCATTTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.29
29 20 0.71
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (28 bp):
TGTTTCAAAGTTACATTTTAATCACTTA
Found at i:381734 original size:26 final size:26
Alignment explanation
Indices: 381701--381755 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
381691 GGTTATTAAC
381701 TTAGTTAACTAATAATTAACTATACT
1 TTAGTTAACTAATAATTAACTATACT
381727 TTAGTTAACTAATAATTAACTATACT
1 TTAGTTAACTAATAATTAACTATACT
381753 TTA
1 TTA
381756 ATAATAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.44
Consensus pattern (26 bp):
TTAGTTAACTAATAATTAACTATACT
Found at i:382844 original size:88 final size:88
Alignment explanation
Indices: 382662--382859 Score: 222
Period size: 88 Copynumber: 2.2 Consensus size: 88
382652 CTAATATACC
* *
382662 ATCAATATACCAG-TTCCATAAACATAAGCCATCAAATTAAAGACATTTTTTCCATCATGATCAA
1 ATCAATATACCAGTTTCCATAAACACAAGCCATCAAATTAAAGACA--TTTTCCATCATGACCAA
* * *
382726 ATATTCAATTTACACCTAATATGCG
64 ATATTCAATATACAACAAATATGCG
* * * *
382751 ATCAATATACCAGTTTCCCATAAACACAAGCCATTC-AATTCAAGACA-TTTCTATTATGGCCAA
1 ATCAATATACCAGTTT-CCATAAACACAAGCCA-TCAAATTAAAGACATTTTCCATCATGACCAA
*
382814 ATATTCAATATACAACAAATATGCT
64 ATATTCAATATACAACAAATATGCG
* *
382839 ATCAATAAACCAATTTTCCAT
1 ATCAATATACC-AGTTTCCAT
382860 TTTTATCATT
Statistics
Matches: 93, Mismatches: 12, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
88 47 0.51
89 17 0.18
90 2 0.02
91 25 0.27
92 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (88 bp):
ATCAATATACCAGTTTCCATAAACACAAGCCATCAAATTAAAGACATTTTCCATCATGACCAAAT
ATTCAATATACAACAAATATGCG
Found at i:386677 original size:62 final size:62
Alignment explanation
Indices: 386583--386702 Score: 240
Period size: 62 Copynumber: 1.9 Consensus size: 62
386573 TAATATATCC
386583 TTTTTTGTGAAGTAGCTAACTAAAATTAATGGTAGTTTAGAAAGGTTTGATGTTCACACCCT
1 TTTTTTGTGAAGTAGCTAACTAAAATTAATGGTAGTTTAGAAAGGTTTGATGTTCACACCCT
386645 TTTTTTGTGAAGTAGCTAACTAAAATTAATGGTAGTTTAGAAAGGTTTGATGTTCACA
1 TTTTTTGTGAAGTAGCTAACTAAAATTAATGGTAGTTTAGAAAGGTTTGATGTTCACA
386703 GCTTTGGCCC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (62 bp):
TTTTTTGTGAAGTAGCTAACTAAAATTAATGGTAGTTTAGAAAGGTTTGATGTTCACACCCT
Found at i:396713 original size:66 final size:66
Alignment explanation
Indices: 396607--396985 Score: 616
Period size: 66 Copynumber: 5.7 Consensus size: 66
396597 CAGGTTGACC
* *
396607 TTGAGGAATCAAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTACAAAAGATGCAACTTGAG
1 TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
396672 T
66 T
* * *
396673 TTGAGGAATCCAAGAAAA-AGGAAAGTGCAAGGTTTGAATCTAATTTGCAAAAGAAGGAACTTGA
1 TTGAGGAATCCAA-AAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGA
396737 GT
65 GT
* *
396739 TTGAGGAATCCAAAAAACAGGAAAGTGAAAGGTTTGAATCTACTTTGCACAAGATGCAACTTGAG
1 TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
396804 T
66 T
* * * *
396805 TTGAGGAATCCAAGAAACAGGAAAGTGAAAGGTTTGAATCTACTTTCCACAAGATGCAACTTGAG
1 TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
396870 T
66 T
**
396871 TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTACGCAAAAGATGCAACTTGAG
1 TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
396936 T
66 T
*
396937 TTGAGGAATCCAAAAAACAGGAAAGAGCAAGGTTTGAATCTACTTTGCA
1 TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCA
396986 CAGAAAGGAA
Statistics
Matches: 290, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
65 4 0.01
66 282 0.97
67 4 0.01
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (66 bp):
TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
T
Found at i:397033 original size:21 final size:21
Alignment explanation
Indices: 396994--397045 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
396984 CACAGAAAGG
* * *
396994 AACTTCAGTTTCAGCAACTGC
1 AACTTGAGTTGCAGAAACTGC
*
397015 AATTTGAGTTGCAGAAACTGC
1 AACTTGAGTTGCAGAAACTGC
*
397036 AGCTTGAGTT
1 AACTTGAGTT
397046 TGAGGAATCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (21 bp):
AACTTGAGTTGCAGAAACTGC
Found at i:397129 original size:66 final size:66
Alignment explanation
Indices: 397038--397184 Score: 249
Period size: 66 Copynumber: 2.2 Consensus size: 66
397028 GAAACTGCAG
*
397038 CTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTTTGCACAAGAAGGA
1 CTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTTTGCACAAGAAGGA
397103 A
66 A
* * * *
397104 CTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGCAACATTTGAATCTACTTTGTACAAGAAGGA
1 CTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTTTGCACAAGAAGGA
397169 A
66 A
397170 CTTGAGTTTCAGGAA
1 CTTGAGTTTCAGGAA
397185 CTGCAAGTTG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 76 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (66 bp):
CTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTTTGCACAAGAAGGA
A
Found at i:397154 original size:174 final size:174
Alignment explanation
Indices: 396858--397226 Score: 524
Period size: 174 Copynumber: 2.1 Consensus size: 174
396848 TTTCCACAAG
* * *** *
396858 ATGCAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTACGCAAAA
1 ATGCAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTACGCAAAA
* * **
396923 GATGCAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGCAAGGTTTGAATCTACTTTGCAC-
66 GAAGCAACTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGCAACATTTGAATCTACTTTGCACA
*
396987 AGAAAGGAACTTCAGTTTCAGCAACTGCAATTTGAGTTGCAGAAA
131 AG-AAGGAACTTCAGTTTCAGCAACTGCAAGTTGAGTTGCAGAAA
* * ** *
397032 CTGCAGCTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTTTGCACAA
1 ATGCAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTACGCAAAA
* *
397097 GAAGGAACTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGCAACATTTGAATCTACTTTGTACA
66 GAAGCAACTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGCAACATTTGAATCTACTTTGCACA
* * *
397162 AGAAGGAACTTGAGTTTCAGGAACTGCAAGTTGAGTTTCAGAAA
131 AGAAGGAACTTCAGTTTCAGCAACTGCAAGTTGAGTTGCAGAAA
*
397206 ATGCAACTTGAGCTTGAGGAA
1 ATGCAACTTGAGTTTGAGGAA
397227 ACAAAAGAGT
Statistics
Matches: 170, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
174 168 0.99
175 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (174 bp):
ATGCAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTACGCAAAA
GAAGCAACTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGCAACATTTGAATCTACTTTGCACA
AGAAGGAACTTCAGTTTCAGCAACTGCAAGTTGAGTTGCAGAAA
Found at i:397197 original size:21 final size:21
Alignment explanation
Indices: 397168--397227 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
397158 TACAAGAAGG
*
397168 AACTTGAGTTTCAGGAACTGC
1 AACTTGAGTTTCAGGAAATGC
* *
397189 AAGTTGAGTTTCAGAAAATGC
1 AACTTGAGTTTCAGGAAATGC
* *
397210 AACTTGAGCTTGAGGAAA
1 AACTTGAGTTTCAGGAAA
397228 CAAAAGAGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (21 bp):
AACTTGAGTTTCAGGAAATGC
Found at i:398009 original size:33 final size:33
Alignment explanation
Indices: 397961--398089 Score: 222
Period size: 33 Copynumber: 3.9 Consensus size: 33
397951 CAGGAGATCC
* * *
397961 CCGTTGTTGACGATGAATCAATGAATAAACCTA
1 CCGTTATTGAAGATGAATCAATGAATAAACATA
397994 CCGTTATTGAAGATGAATCAATGAATAAACATA
1 CCGTTATTGAAGATGAATCAATGAATAAACATA
398027 CCGTTATTGAAGATGAATCAATGAATAAACATA
1 CCGTTATTGAAGATGAATCAATGAATAAACATA
*
398060 CCGTTATTGATGATGAATCAATGAATAAAC
1 CCGTTATTGAAGATGAATCAATGAATAAAC
398090 TTACTCCTGA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 92 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (33 bp):
CCGTTATTGAAGATGAATCAATGAATAAACATA
Found at i:398664 original size:347 final size:347
Alignment explanation
Indices: 398029--398878 Score: 1468
Period size: 347 Copynumber: 2.4 Consensus size: 347
398019 TAAACATACC
* *
398029 GTTATTGAAGATGAATCAATGAATAAACATACCGTTATTGATGATGAATCAATGAATAAACTTAC
1 GTTATTGAA-ATGAATCAATGAATAAACCTACCGTTATTGACGATGAATCAATGAATAAACTTAC
* *
398094 TCCTGAAAATGAACAGCTGAAGGTATTGTTAGACATTTGTTGCTTCAAATACTATCTCAGGTTTG
65 TGCTGAAAATGAACAGCTGAAGGTATTGTTAGACATTTGTTGCTTCGAATACTATCTCAGGTTTG
*
398159 ACTAAAGGCTTTCTTGATGTCATTTGGAAAAAAGATTTTGGACATGGGAGCTGAGGACCAGAAAC
130 ACTAAAGGCTTTCTTGATGTCATTTGAAAAAAAGATTTTGGACATGGGAGCTGAGGACCAGAAAC
* * *
398224 CACAGCAGCAGGCCATGCTGAGTTCACTGAGTACTACCATTTCAGAGGTGACATCTGCAGTAAGA
195 CACAGCAGCAGGCCATGCCGAGTTCACTGAGTACAACCATGTCAGAGGTGACATCTGCAGTAAGA
*
398289 TATATCTCAACATTCTTTCCTTTTA-TTTTATTGAGTAGAATTATTCTTTCCTTATCTCAACAAG
260 TATATCTCAACATTCTTTCCTTTTATTTTTATTGAGTAGAATGATTCTTTCCTTATCTCAACAAG
398353 TTCCTGTGGTTCAGGAGATCCCT
325 TTCCTGTGGTTCAGGAGATCCCT
*
398376 GTTATTGAGAATGAATCAATGAATAAACCTACCGTTAATGACGATGAATCAATGAATAAACTTAC
1 GTTATTGA-AATGAATCAATGAATAAACCTACCGTTATTGACGATGAATCAATGAATAAACTTAC
*
398441 TGCTGAAAAAGAACAGCTGAAGGTATTGTTAGACATTTGTTGCTTCGAATACTATCTCAGGTTTG
65 TGCTGAAAATGAACAGCTGAAGGTATTGTTAGACATTTGTTGCTTCGAATACTATCTCAGGTTTG
398506 ACTAAAGGCTTTCTTGATGTCATTTGAAAAAAAGATTTTGGACATGGGAGCTGAGGACCAGAAAC
130 ACTAAAGGCTTTCTTGATGTCATTTGAAAAAAAGATTTTGGACATGGGAGCTGAGGACCAGAAAC
*
398571 CACAGCAGCTGGCCATGCCGAGTTCACTGAGTACAACCATGTCAGAGGTGACATCTGCAGTAAGA
195 CACAGCAGCAGGCCATGCCGAGTTCACTGAGTACAACCATGTCAGAGGTGACATCTGCAGTAAGA
*
398636 TATATCTCAACATTCTTTCCTTTTATTTTTATTGAGTAGAATGATTCTTTCGTTATCTCAACAAG
260 TATATCTCAACATTCTTTCCTTTTATTTTTATTGAGTAGAATGATTCTTTCCTTATCTCAACAAG
398701 TTCCTGTGGTTCAGGAGATCCCT
325 TTCCTGTGGTTCAGGAGATCCCT
* * * *
398724 GTTATTGACAATGAATCAATGAATAAACCTACCGTTATTGACGATGGATCAATAAATAGACTTAT
1 GTTATTGA-AATGAATCAATGAATAAACCTACCGTTATTGACGATGAATCAATGAATAAACTTAC
* * * * *
398789 TGCTGAAAATGAGCAGCTGAAGGTATTGTTAGATATTTTTTGCTTCGAATACTATCTTAGTTTTG
65 TGCTGAAAATGAACAGCTGAAGGTATTGTTAGACATTTGTTGCTTCGAATACTATCTCAGGTTTG
398854 ACTAAAGGCTTTCTTGATGTCATTT
130 ACTAAAGGCTTTCTTGATGTCATTT
398879 TTAAACTTGG
Statistics
Matches: 476, Mismatches: 25, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
347 272 0.57
348 204 0.43
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (347 bp):
GTTATTGAAATGAATCAATGAATAAACCTACCGTTATTGACGATGAATCAATGAATAAACTTACT
GCTGAAAATGAACAGCTGAAGGTATTGTTAGACATTTGTTGCTTCGAATACTATCTCAGGTTTGA
CTAAAGGCTTTCTTGATGTCATTTGAAAAAAAGATTTTGGACATGGGAGCTGAGGACCAGAAACC
ACAGCAGCAGGCCATGCCGAGTTCACTGAGTACAACCATGTCAGAGGTGACATCTGCAGTAAGAT
ATATCTCAACATTCTTTCCTTTTATTTTTATTGAGTAGAATGATTCTTTCCTTATCTCAACAAGT
TCCTGTGGTTCAGGAGATCCCT
Found at i:406258 original size:14 final size:14
Alignment explanation
Indices: 406241--406277 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
406231 ATATTTACAA
*
406241 TATTATCTATTATG
1 TATTATATATTATG
406255 TATTATATATTATG
1 TATTATATATTATG
406269 TATT-TATAT
1 TATTATATAT
406278 AATTTCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (14 bp):
TATTATATATTATG
Found at i:410458 original size:2 final size:2
Alignment explanation
Indices: 410451--410484 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
410441 AATAAATATA
410451 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
410485 TTAAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:416022 original size:20 final size:20
Alignment explanation
Indices: 415999--416037 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
415989 TAAATGTGTT
*
415999 AAAATTATTAATTAAAATAA
1 AAAAATATTAATTAAAATAA
**
416019 AAAAATATTTTTTAAAATA
1 AAAAATATTAATTAAAATA
416038 CTAATTACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATATTAATTAAAATAA
Found at i:418380 original size:13 final size:12
Alignment explanation
Indices: 418361--418433 Score: 62
Period size: 13 Copynumber: 6.0 Consensus size: 12
418351 TCCAACAACT
418361 TCACTAAACCAC
1 TCACTAAACCAC
418373 TACACTAAACCAC
1 T-CACTAAACCAC
418386 TCTACTAAACCA-
1 TC-ACTAAACCAC
*
418398 TC-C-CAACCAC
1 TCACTAAACCAC
* *
418408 CCTACTAAATCAC
1 TC-ACTAAACCAC
418421 TCCACTAAACCAC
1 T-CACTAAACCAC
418434 ACCAACCACT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
9 5 0.10
10 2 0.04
12 5 0.10
13 35 0.73
14 1 0.02
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.18
Consensus pattern (12 bp):
TCACTAAACCAC
Found at i:418406 original size:35 final size:35
Alignment explanation
Indices: 418367--418448 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 35
418357 AACTTCACTA
* *
418367 AACCACTACACTAAACCACTCTACTAAACCATC-CC
1 AACCACTCCACTAAACCACTCCACTAAACCA-CACC
*
418402 AACCAC-CCTACTAAATCACTCCACTAAACCACACC
1 AACCACTCC-ACTAAACCACTCCACTAAACCACACC
418437 AACCACTCCACT
1 AACCACTCCACT
418449 TGCCTACAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 2 0.05
35 37 0.90
36 2 0.05
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.16
Consensus pattern (35 bp):
AACCACTCCACTAAACCACTCCACTAAACCACACC
Found at i:418843 original size:3 final size:3
Alignment explanation
Indices: 418830--418908 Score: 60
Period size: 3 Copynumber: 26.3 Consensus size: 3
418820 GTTGAGAGAT
* *
418830 TTA TT- TTA TTA TTA TT- TTT TTA CTA TTA TT- TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
418873 TTA TT- TCTCA TGTA TATA TTA TTA TTA -TA TTA TTA T
1 TTA TTA T-T-A T-TA T-TA TTA TTA TTA TTA TTA TTA T
418909 ATCATTATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
2 8 0.13
3 47 0.75
4 6 0.10
5 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:418915 original size:11 final size:10
Alignment explanation
Indices: 418853--418916 Score: 51
Period size: 11 Copynumber: 6.3 Consensus size: 10
418843 ATTTTTTTAC
*
418853 TATTATTTA-
1 TATTATATAT
418862 TATTAT-TAT
1 TATTATATAT
* *
418871 TATTATTTCT
1 TATTATATAT
*
418881 CATGTATATAT
1 TAT-TATATAT
418892 TATTATTATAT
1 TATTA-TATAT
418903 TATTATATCAT
1 TATTATAT-AT
418914 TAT
1 TAT
418917 ATCCAACCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
8 2 0.04
9 12 0.27
10 9 0.20
11 22 0.49
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (10 bp):
TATTATATAT
Found at i:418917 original size:29 final size:29
Alignment explanation
Indices: 418835--418918 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
418825 GAGATTTATT
* * *
418835 TTATTATTATTTTTTTACTATTATT-TATA
1 TTATTATTATATTATTA-TATCATTATATA
*
418864 TTATTA-T-TATTATT-TCTCATGTATATA
1 TTATTATTATATTATTATATCAT-TATATA
418891 TTATTATTATATTATTATATCATTATAT
1 TTATTATTATATTATTATATCATTATAT
418919 CCAACCCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
25 4 0.09
26 1 0.02
27 15 0.33
28 2 0.04
29 18 0.40
30 5 0.11
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (29 bp):
TTATTATTATATTATTATATCATTATATA
Found at i:422112 original size:89 final size:89
Alignment explanation
Indices: 421948--422359 Score: 689
Period size: 89 Copynumber: 4.6 Consensus size: 89
421938 NNNNNNNNNN
* *
421948 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAGAGCAGAAATTGGAAAGCAGAAATT
1 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATT
422013 GAAAATACCTCAGCGTGCCCTGAGG
65 GAAAATACCTCAGCGTGCCCTGAGG
* *
422038 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAAAAATTGAAAAACATAAATTG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTG
* *
422103 AAATTACCTCAGCGTGTCCTGAGG
66 AAAATACCTCAGCGTGCCCTGAGG
* * *
422127 CTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAGAGCAGAAATTGGAAAACAGAAATCG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTG
422192 AAAATACCTCAGCGTGCCCTGAGG
66 AAAATACCTCAGCGTGCCCTGAGG
*
422216 CTCAACTCGCCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTG
* * *
422281 AAATTACCTCAGCGTGTCTTGAGG
66 AAAATACCTCAGCGTGCCCTGAGG
*
422305 CTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAGAGCAGAAATTGAAAA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAA
422360 TACCTCAGCT
Statistics
Matches: 300, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
89 271 0.90
90 29 0.10
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (89 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTG
AAAATACCTCAGCGTGCCCTGAGG
Found at i:424495 original size:79 final size:79
Alignment explanation
Indices: 424364--424524 Score: 322
Period size: 79 Copynumber: 2.0 Consensus size: 79
424354 TGAAGCCAAC
424364 ATGGCCAGGGCATCAGCTAACTGGTTTTCTTCTCATGGGAAGTAATTAAAAGTTATTTCTTCGAA
1 ATGGCCAGGGCATCAGCTAACTGGTTTTCTTCTCATGGGAAGTAATTAAAAGTTATTTCTTCGAA
424429 TTCTTTAATCAATT
66 TTCTTTAATCAATT
424443 ATGGCCAGGGCATCAGCTAACTGGTTTTCTTCTCATGGGAAGTAATTAAAAGTTATTTCTTCGAA
1 ATGGCCAGGGCATCAGCTAACTGGTTTTCTTCTCATGGGAAGTAATTAAAAGTTATTTCTTCGAA
424508 TTCTTTAATCAATT
66 TTCTTTAATCAATT
424522 ATG
1 ATG
424525 CCACTAGGTC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (79 bp):
ATGGCCAGGGCATCAGCTAACTGGTTTTCTTCTCATGGGAAGTAATTAAAAGTTATTTCTTCGAA
TTCTTTAATCAATT
Found at i:432519 original size:102 final size:102
Alignment explanation
Indices: 432343--432544 Score: 404
Period size: 102 Copynumber: 2.0 Consensus size: 102
432333 ATACAGACAG
432343 AAAAAATTATGGAAAATTTAACGAATCAAACTACCCAAATCTAGTTTATTAAATAGACCCAATCC
1 AAAAAATTATGGAAAATTTAACGAATCAAACTACCCAAATCTAGTTTATTAAATAGACCCAATCC
432408 CCTTGTATAGAAAGTGAAAATGCAAAAGGCAAGAGAA
66 CCTTGTATAGAAAGTGAAAATGCAAAAGGCAAGAGAA
432445 AAAAAATTATGGAAAATTTAACGAATCAAACTACCCAAATCTAGTTTATTAAATAGACCCAATCC
1 AAAAAATTATGGAAAATTTAACGAATCAAACTACCCAAATCTAGTTTATTAAATAGACCCAATCC
432510 CCTTGTATAGAAAGTGAAAATGCAAAAGGCAAGAG
66 CCTTGTATAGAAAGTGAAAATGCAAAAGGCAAGAG
432545 GCGTTCCTCC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (102 bp):
AAAAAATTATGGAAAATTTAACGAATCAAACTACCCAAATCTAGTTTATTAAATAGACCCAATCC
CCTTGTATAGAAAGTGAAAATGCAAAAGGCAAGAGAA
Found at i:434387 original size:30 final size:30
Alignment explanation
Indices: 434353--434443 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
434343 AATGGAGCAA
* *
434353 GTGTGGCTAGTGGATTTGGTGGTAGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
434383 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
434413 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
434443 G
1 G
434444 CTAAGATTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.21, C:0.03, G:0.48, T:0.27
Consensus pattern (30 bp):
GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
Found at i:434396 original size:60 final size:60
Alignment explanation
Indices: 434323--434443 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 60
434313 AGAAGGACAA
* * *
434323 GTGTGGTTAGTGGAGTAGGTAATGGAGCAA-GTGTGGCTAGTGGATTTGGTGGTAGAAAAG
1 GTGTGGCTAGTGGAGTAGGTAATGGA-AAAGGTGTGGCTAGTGGAGTTGGTGGTAGAAAAG
* ** *
434383 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTAGGTAATGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTAGAAAAG
434443 G
1 G
434444 CTAAGATTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
59 2 0.04
60 51 0.96
ACGTcount: A:0.22, C:0.03, G:0.47, T:0.27
Consensus pattern (60 bp):
GTGTGGCTAGTGGAGTAGGTAATGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTAGAAAAG
Found at i:438954 original size:19 final size:19
Alignment explanation
Indices: 438932--438978 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
438922 CTTCCTTTCT
*
438932 TTTGCATT-CATTCCATACA
1 TTTGCATTACATTACA-ACA
438951 TTTGCATTACATTACAACA
1 TTTGCATTACATTACAACA
*
438970 TCTGCATTA
1 TTTGCATTA
438979 AACTTTCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (19 bp):
TTTGCATTACATTACAACA
Found at i:439978 original size:32 final size:32
Alignment explanation
Indices: 439942--440006 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
439932 TGTATGCATT
439942 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
439974 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
440006 T
1 T
440007 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:445194 original size:13 final size:14
Alignment explanation
Indices: 445176--445215 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
445166 AGAGAGCCCT
*
445176 ACAAAAAACAC-AC
1 ACAAAAAACACAAA
445189 ACAAAAAA-ACAAA
1 ACAAAAAACACAAA
445202 ACAAAAAACA-AAA
1 ACAAAAAACACAAA
445215 A
1 A
445216 ATTCTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.08
13 21 0.88
14 1 0.04
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (14 bp):
ACAAAAAACACAAA
Found at i:445207 original size:12 final size:12
Alignment explanation
Indices: 445176--445214 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
445166 AGAGAGCCCT
*
445176 ACAAAAAACACAC
1 ACAAAAAACA-AA
445189 ACAAAAAAACAAA
1 AC-AAAAAACAAA
445202 ACAAAAAACAAA
1 ACAAAAAACAAA
445214 A
1 A
445215 AATTCTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 11 0.46
13 5 0.21
14 8 0.33
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (12 bp):
ACAAAAAACAAA
Found at i:445648 original size:53 final size:52
Alignment explanation
Indices: 445549--445652 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 52
445539 GTCCAAATAA
* * * *
445549 ATTTTCTTCTTATTACATTGCTATCTTTGATTAAATCATTCGTTTTGAGTTG
1 ATTTCCTTCTTATTACATTGCAATCTTTGATTAAATCATCCATTTTGAGTTG
* * *
445601 ATTTCCTTCTTATTGCATTTGCAATCTTTGATTAATTTATCCATTTTGAGTT
1 ATTTCCTTCTTATTACA-TTGCAATCTTTGATTAAATCATCCATTTTGAGTT
445653 ATGCTCCTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 15 0.34
53 29 0.66
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (52 bp):
ATTTCCTTCTTATTACATTGCAATCTTTGATTAAATCATCCATTTTGAGTTG
Found at i:446914 original size:205 final size:205
Alignment explanation
Indices: 446550--447035 Score: 747
Period size: 205 Copynumber: 2.4 Consensus size: 205
446540 ATCAGGCGGA
* *
446550 GAGCAGATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
1 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
* *
446615 TTGGCATTTCTGTATTGTCAGAGAACAAATCGAAGTCTAGTATCTCCACTTCAATGGAAGGCAGA
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCAATGGAAGGCAGA
* * *
446680 CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGCTTGGCATCCTTG
131 CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGCTTGCCATCCTTG
446745 TGCTTACAAT
196 TGCTTACAAT
* * * *
446755 GAGCAAATCGAAGACATAGCTAATTTGGCTTTCACGTGCTTACGTTAAAGCAAATCTAATATGAT
1 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
* * * * * *
446820 TTGGCATCTCTGTATTGTTAGAGAACAAATTGAAGTCTGGCATCTCCACTTCGATGGAGGGTAGA
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCAATGGAAGGCAGA
* *
446885 CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAATATGGTTTGCCATCCTTG
131 CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGCTTGCCATCCTTG
446950 TGCTTACAAT
196 TGCTTACAAT
* * * * *
446960 GAGCAAATCGAAGACATAGTTGATTTCGCTTTCACGTGTTTATGTTGAAGCAAATCCAAGATAAT
1 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
*
447025 TTGGCGTCTCT
66 TTGGCATCTCT
447036 ATGCGGCGGA
Statistics
Matches: 252, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
205 252 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (205 bp):
GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCAATGGAAGGCAGA
CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGCTTGCCATCCTTG
TGCTTACAAT
Found at i:447128 original size:44 final size:44
Alignment explanation
Indices: 447046--447299 Score: 221
Period size: 44 Copynumber: 5.8 Consensus size: 44
447036 ATGCGGCGGA
* * * * *
447046 GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGT
1 GAACAGATCGAAGATAGCAGATATGGCATCCCTGTGCTTACAGG
** *
447090 GAAGCAGATCGAAGATTTCAG-TATGGCATCCCTGTGCTTATAGG
1 GAA-CAGATCGAAGATAGCAGATATGGCATCCCTGTGCTTACAGG
* * * * *
447134 GAACA-AGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGG
1 GAACAGA-TCGAAGATAGCAGATATGGCATCCCTGTGCTTACAGG
* * * *
447178 GAACAGATCGAAGATAGCAGATCTGACATTCTTGTGCTTAC-GG
1 GAACAGATCGAAGATAGCAGATATGGCATCCCTGTGCTTACAGG
** * *
447221 TGAAGCAGATCGAAGATTTCAG-CATGGCATCCCTGTGCTTATAGG
1 -GAA-CAGATCGAAGATAGCAGATATGGCATCCCTGTGCTTACAGG
* *
447266 GAACA-AGTTGAAGATAGCAGATTTGGCATCCCTG
1 GAACAGA-TCGAAGATAGCAGATATGGCATCCCTG
447300 NNNNNNNNNN
Statistics
Matches: 166, Mismatches: 35, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
42 2 0.01
43 24 0.14
44 108 0.65
45 32 0.19
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
GAACAGATCGAAGATAGCAGATATGGCATCCCTGTGCTTACAGG
Found at i:447202 original size:132 final size:132
Alignment explanation
Indices: 447046--447299 Score: 454
Period size: 132 Copynumber: 1.9 Consensus size: 132
447036 ATGCGGCGGA
447046 GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATTTCAG
1 GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATTTCAG
*
447111 TATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATA
66 CATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATA
447176 GG
131 GG
* * *
447178 GAACAGATCGAAGATAGCAGATCTGACATTCTTGTGCTTACGGTGAAGCAGATCGAAGATTTCAG
1 GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATTTCAG
* *
447243 CATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTG
66 CATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTG
447300 NNNNNNNNNN
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 116 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATTTCAG
CATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATA
GG
Found at i:451067 original size:15 final size:14
Alignment explanation
Indices: 451047--451096 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
451037 TATTTAGGCA
451047 ATTTTTGAAGTTTTG
1 ATTTTTGAA-TTTTG
* * *
451062 ATTTTTTATTTTTT
1 ATTTTTGAATTTTG
451076 ATTTTTGAATTTTG
1 ATTTTTGAATTTTG
451090 ACTTTTT
1 A-TTTTT
451097 TGTTTTTGGG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.18, C:0.02, G:0.10, T:0.70
Consensus pattern (14 bp):
ATTTTTGAATTTTG
Found at i:451080 original size:29 final size:29
Alignment explanation
Indices: 451047--451103 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
451037 TATTTAGGCA
451047 ATTTTTGAAGTTTTGA-TTTTTTATTTTTT
1 ATTTTTGAA-TTTTGACTTTTTTATTTTTT
*
451076 ATTTTTGAATTTTGACTTTTTTGTTTTT
1 ATTTTTGAATTTTGACTTTTTTATTTTT
451104 GGGTTCGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.16, C:0.02, G:0.11, T:0.72
Consensus pattern (29 bp):
ATTTTTGAATTTTGACTTTTTTATTTTTT
Found at i:451095 original size:22 final size:21
Alignment explanation
Indices: 451057--451104 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
451047 ATTTTTGAAG
* *
451057 TTTTGATTTTTTATTTTTTAT
1 TTTTGAATTTTGATTTTTTAT
*
451078 TTTTGAATTTTGACTTTTTTGT
1 TTTTGAATTTTGA-TTTTTTAT
451100 TTTTG
1 TTTTG
451105 GGTTCGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.75
Consensus pattern (21 bp):
TTTTGAATTTTGATTTTTTAT
Found at i:461524 original size:19 final size:19
Alignment explanation
Indices: 461497--461533 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
461487 TATTATTACC
*
461497 AATTTAGTTAATTTTAATT
1 AATTCAGTTAATTTTAATT
461516 AATTCAGTTAATTTTAAT
1 AATTCAGTTAATTTTAAT
461534 CTGATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (19 bp):
AATTCAGTTAATTTTAATT
Done.