Multiple sequence alignment - TraesCS6A01G270300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G270300 chr6A 100.000 4951 0 0 1 4951 496572012 496576962 0.000000e+00 9143.0
1 TraesCS6A01G270300 chr6A 79.394 660 101 16 4307 4935 570490740 570490085 2.740000e-117 433.0
2 TraesCS6A01G270300 chr6A 82.974 417 57 13 2496 2904 94170771 94171181 1.010000e-96 364.0
3 TraesCS6A01G270300 chr6A 77.689 623 71 37 1004 1572 496830449 496831057 8.000000e-83 318.0
4 TraesCS6A01G270300 chr6A 78.675 483 65 21 3015 3460 496832692 496833173 2.260000e-73 287.0
5 TraesCS6A01G270300 chr6A 78.730 315 36 19 3610 3921 496833350 496833636 1.090000e-41 182.0
6 TraesCS6A01G270300 chr6B 87.332 2684 207 56 2326 4939 534228912 534231532 0.000000e+00 2950.0
7 TraesCS6A01G270300 chr6B 89.662 1006 71 21 710 1700 534227924 534228911 0.000000e+00 1251.0
8 TraesCS6A01G270300 chr6B 85.165 728 29 27 1 708 534225869 534226537 0.000000e+00 673.0
9 TraesCS6A01G270300 chr6B 78.855 681 108 20 4293 4939 678532965 678533643 1.270000e-115 427.0
10 TraesCS6A01G270300 chr6B 80.783 562 60 27 1004 1534 534510506 534511050 3.590000e-106 396.0
11 TraesCS6A01G270300 chr6B 88.166 338 29 7 1821 2148 534511397 534511733 4.650000e-105 392.0
12 TraesCS6A01G270300 chr6B 75.395 760 124 46 2981 3711 534513492 534514217 4.810000e-80 309.0
13 TraesCS6A01G270300 chr6B 88.652 141 13 3 3784 3921 534514265 534514405 8.520000e-38 169.0
14 TraesCS6A01G270300 chr6D 89.174 2023 115 53 516 2492 346839251 346837287 0.000000e+00 2427.0
15 TraesCS6A01G270300 chr6D 88.469 1986 133 34 3024 4934 346837092 346835128 0.000000e+00 2311.0
16 TraesCS6A01G270300 chr6D 77.602 884 118 51 1004 1831 346703309 346702450 3.490000e-126 462.0
17 TraesCS6A01G270300 chr6D 89.157 332 31 4 1833 2161 346702314 346701985 4.610000e-110 409.0
18 TraesCS6A01G270300 chr6D 82.872 397 58 8 4545 4935 38340560 38340952 1.020000e-91 348.0
19 TraesCS6A01G270300 chr6D 91.469 211 12 3 305 515 346841085 346840881 8.110000e-73 285.0
20 TraesCS6A01G270300 chr6D 74.548 774 125 37 2986 3716 346700877 346700133 6.320000e-69 272.0
21 TraesCS6A01G270300 chr6D 92.517 147 8 3 1 145 346841331 346841186 1.810000e-49 207.0
22 TraesCS6A01G270300 chr6D 89.831 118 6 3 2914 3029 346837285 346837172 3.990000e-31 147.0
23 TraesCS6A01G270300 chr4A 80.000 675 105 19 4307 4951 733887336 733886662 5.800000e-129 472.0
24 TraesCS6A01G270300 chr4A 79.897 582 83 22 4308 4857 691505947 691505368 3.590000e-106 396.0
25 TraesCS6A01G270300 chr4A 83.448 435 55 14 2490 2910 602255933 602255502 6.010000e-104 388.0
26 TraesCS6A01G270300 chr4A 78.947 399 67 14 2471 2862 647562926 647563314 6.360000e-64 255.0
27 TraesCS6A01G270300 chr7D 85.714 427 45 10 2494 2910 118160181 118159761 2.120000e-118 436.0
28 TraesCS6A01G270300 chr2D 86.019 422 42 10 2494 2910 65684095 65684504 2.120000e-118 436.0
29 TraesCS6A01G270300 chr2D 82.984 429 61 12 2491 2910 5330215 5330640 1.300000e-100 377.0
30 TraesCS6A01G270300 chr2B 78.838 671 108 22 4302 4939 787077487 787078156 5.930000e-114 422.0
31 TraesCS6A01G270300 chr2B 83.450 429 56 14 2494 2910 697508381 697507956 7.770000e-103 385.0
32 TraesCS6A01G270300 chr2B 77.847 641 110 19 4302 4916 154596863 154597497 7.830000e-98 368.0
33 TraesCS6A01G270300 chr2B 83.333 396 56 8 4545 4934 522824930 522824539 1.690000e-94 357.0
34 TraesCS6A01G270300 chr2B 77.178 241 49 4 4293 4527 154498790 154498550 8.640000e-28 135.0
35 TraesCS6A01G270300 chr1D 79.027 658 106 17 4312 4939 1816152 1816807 5.930000e-114 422.0
36 TraesCS6A01G270300 chr1D 82.629 426 61 10 2491 2910 29882792 29883210 1.010000e-96 364.0
37 TraesCS6A01G270300 chr1D 82.152 409 65 5 4545 4948 350619012 350619417 1.320000e-90 344.0
38 TraesCS6A01G270300 chr1D 76.936 581 93 20 4307 4853 476374711 476374138 4.850000e-75 292.0
39 TraesCS6A01G270300 chr1D 76.127 377 59 18 4302 4647 6323709 6324085 8.520000e-38 169.0
40 TraesCS6A01G270300 chr1B 82.629 426 63 10 2494 2911 368712219 368711797 2.820000e-97 366.0
41 TraesCS6A01G270300 chr1B 75.578 606 102 29 4307 4877 9907834 9908428 1.770000e-64 257.0
42 TraesCS6A01G270300 chr3B 77.231 650 107 25 4302 4916 383471948 383472591 4.750000e-90 342.0
43 TraesCS6A01G270300 chr2A 79.830 352 60 11 2464 2808 16067407 16067754 3.830000e-61 246.0
44 TraesCS6A01G270300 chr2A 93.382 136 9 0 1969 2104 34661732 34661597 8.400000e-48 202.0
45 TraesCS6A01G270300 chr1A 83.516 91 12 3 4135 4223 516590062 516590151 1.140000e-11 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G270300 chr6A 496572012 496576962 4950 False 9143.000000 9143 100.000000 1 4951 1 chr6A.!!$F2 4950
1 TraesCS6A01G270300 chr6A 570490085 570490740 655 True 433.000000 433 79.394000 4307 4935 1 chr6A.!!$R1 628
2 TraesCS6A01G270300 chr6A 496830449 496833636 3187 False 262.333333 318 78.364667 1004 3921 3 chr6A.!!$F3 2917
3 TraesCS6A01G270300 chr6B 534225869 534231532 5663 False 1624.666667 2950 87.386333 1 4939 3 chr6B.!!$F2 4938
4 TraesCS6A01G270300 chr6B 678532965 678533643 678 False 427.000000 427 78.855000 4293 4939 1 chr6B.!!$F1 646
5 TraesCS6A01G270300 chr6B 534510506 534514405 3899 False 316.500000 396 83.249000 1004 3921 4 chr6B.!!$F3 2917
6 TraesCS6A01G270300 chr6D 346835128 346841331 6203 True 1075.400000 2427 90.292000 1 4934 5 chr6D.!!$R2 4933
7 TraesCS6A01G270300 chr6D 346700133 346703309 3176 True 381.000000 462 80.435667 1004 3716 3 chr6D.!!$R1 2712
8 TraesCS6A01G270300 chr4A 733886662 733887336 674 True 472.000000 472 80.000000 4307 4951 1 chr4A.!!$R3 644
9 TraesCS6A01G270300 chr4A 691505368 691505947 579 True 396.000000 396 79.897000 4308 4857 1 chr4A.!!$R2 549
10 TraesCS6A01G270300 chr2B 787077487 787078156 669 False 422.000000 422 78.838000 4302 4939 1 chr2B.!!$F2 637
11 TraesCS6A01G270300 chr2B 154596863 154597497 634 False 368.000000 368 77.847000 4302 4916 1 chr2B.!!$F1 614
12 TraesCS6A01G270300 chr1D 1816152 1816807 655 False 422.000000 422 79.027000 4312 4939 1 chr1D.!!$F1 627
13 TraesCS6A01G270300 chr1D 476374138 476374711 573 True 292.000000 292 76.936000 4307 4853 1 chr1D.!!$R1 546
14 TraesCS6A01G270300 chr1B 9907834 9908428 594 False 257.000000 257 75.578000 4307 4877 1 chr1B.!!$F1 570
15 TraesCS6A01G270300 chr3B 383471948 383472591 643 False 342.000000 342 77.231000 4302 4916 1 chr3B.!!$F1 614

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
805 3859 0.032017 GGGAGGGAGCTAGAGAACCA 60.032 60.0 0.0 0.0 0.0 3.67 F
2019 5401 0.543277 CAAGGATGTGGCAGGCTCTA 59.457 55.0 0.0 0.0 0.0 2.43 F
2516 7321 0.890683 AATTGCTTTTCGAGGCTGGG 59.109 50.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2649 7456 0.109597 GCACAGCCCTCATTTCAACG 60.110 55.0 0.00 0.00 0.0 4.10 R
3551 9117 0.119155 TGGTCCCTGAATCCTGAGGT 59.881 55.0 0.00 0.00 0.0 3.85 R
4245 9843 0.829333 CTGGATGTGGCTAGCTCAGT 59.171 55.0 15.72 3.04 0.0 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.109272 ACGTGACATGAGGTACAGCG 60.109 55.000 0.00 0.00 0.00 5.18
111 130 0.874607 CCGCCATAGTACGCTTGGTC 60.875 60.000 11.71 5.44 32.90 4.02
165 184 3.814625 GGGAAGAGATGAACCCTGATTC 58.185 50.000 0.00 0.00 39.28 2.52
166 185 3.457749 GGGAAGAGATGAACCCTGATTCT 59.542 47.826 0.00 0.00 39.28 2.40
167 186 4.080072 GGGAAGAGATGAACCCTGATTCTT 60.080 45.833 0.00 0.00 39.28 2.52
168 187 5.122519 GGAAGAGATGAACCCTGATTCTTC 58.877 45.833 3.42 3.42 38.71 2.87
169 188 5.104569 GGAAGAGATGAACCCTGATTCTTCT 60.105 44.000 10.14 4.19 42.63 2.85
170 189 6.385766 AAGAGATGAACCCTGATTCTTCTT 57.614 37.500 5.65 1.94 41.00 2.52
171 190 5.988287 AGAGATGAACCCTGATTCTTCTTC 58.012 41.667 5.65 0.00 41.00 2.87
172 191 5.725822 AGAGATGAACCCTGATTCTTCTTCT 59.274 40.000 5.65 0.00 41.00 2.85
173 192 6.215227 AGAGATGAACCCTGATTCTTCTTCTT 59.785 38.462 5.65 0.00 41.00 2.52
174 193 6.179040 AGATGAACCCTGATTCTTCTTCTTG 58.821 40.000 0.00 0.00 39.03 3.02
175 194 5.567037 TGAACCCTGATTCTTCTTCTTGA 57.433 39.130 0.00 0.00 0.00 3.02
176 195 5.555017 TGAACCCTGATTCTTCTTCTTGAG 58.445 41.667 0.00 0.00 0.00 3.02
177 196 5.307976 TGAACCCTGATTCTTCTTCTTGAGA 59.692 40.000 0.00 0.00 0.00 3.27
178 197 5.832539 ACCCTGATTCTTCTTCTTGAGAA 57.167 39.130 0.00 0.00 42.03 2.87
179 198 6.192970 ACCCTGATTCTTCTTCTTGAGAAA 57.807 37.500 0.00 0.00 43.56 2.52
180 199 6.000840 ACCCTGATTCTTCTTCTTGAGAAAC 58.999 40.000 0.00 0.00 43.56 2.78
181 200 6.000219 CCCTGATTCTTCTTCTTGAGAAACA 59.000 40.000 0.00 0.00 43.56 2.83
182 201 6.149142 CCCTGATTCTTCTTCTTGAGAAACAG 59.851 42.308 13.25 13.25 43.56 3.16
187 206 5.295950 TCTTCTTCTTGAGAAACAGCTCTG 58.704 41.667 0.00 0.00 43.56 3.35
189 208 3.389329 TCTTCTTGAGAAACAGCTCTGGT 59.611 43.478 1.66 0.00 35.91 4.00
209 228 4.283978 TGGTTGAACCGTTCTACTCCATTA 59.716 41.667 20.41 3.86 42.58 1.90
210 229 4.868734 GGTTGAACCGTTCTACTCCATTAG 59.131 45.833 20.41 0.00 36.02 1.73
233 252 5.824624 AGTATATGCAAACCACAGATTCCAG 59.175 40.000 0.00 0.00 0.00 3.86
234 253 2.655090 TGCAAACCACAGATTCCAGA 57.345 45.000 0.00 0.00 0.00 3.86
264 283 4.938226 AGAATTTCCTTGCTACTTTCTCCG 59.062 41.667 0.00 0.00 0.00 4.63
298 317 6.282930 TGCCTTTCCATTTTCTTTTCTGAAG 58.717 36.000 0.00 0.00 0.00 3.02
299 318 6.098124 TGCCTTTCCATTTTCTTTTCTGAAGA 59.902 34.615 0.00 0.00 0.00 2.87
300 319 6.644181 GCCTTTCCATTTTCTTTTCTGAAGAG 59.356 38.462 1.71 1.71 0.00 2.85
301 320 7.470563 GCCTTTCCATTTTCTTTTCTGAAGAGA 60.471 37.037 6.55 6.55 0.00 3.10
302 321 8.583296 CCTTTCCATTTTCTTTTCTGAAGAGAT 58.417 33.333 10.96 0.00 0.00 2.75
303 322 9.623350 CTTTCCATTTTCTTTTCTGAAGAGATC 57.377 33.333 10.96 0.00 0.00 2.75
304 323 8.930846 TTCCATTTTCTTTTCTGAAGAGATCT 57.069 30.769 10.96 0.00 0.00 2.75
305 324 8.558973 TCCATTTTCTTTTCTGAAGAGATCTC 57.441 34.615 15.29 15.29 0.00 2.75
306 325 8.381636 TCCATTTTCTTTTCTGAAGAGATCTCT 58.618 33.333 19.92 19.92 42.75 3.10
323 342 9.165035 AGAGATCTCTTTTCTGAATGTTTCATC 57.835 33.333 19.92 0.00 36.33 2.92
333 352 4.085733 TGAATGTTTCATCCGTTCCCATT 58.914 39.130 0.00 0.00 34.08 3.16
362 381 4.503817 GGCAGAAAGAAAAGAAAATGGGCT 60.504 41.667 0.00 0.00 0.00 5.19
366 385 3.923017 AGAAAAGAAAATGGGCTGACG 57.077 42.857 0.00 0.00 0.00 4.35
372 391 2.489329 AGAAAATGGGCTGACGTTCATG 59.511 45.455 0.00 0.00 0.00 3.07
378 397 1.499056 GCTGACGTTCATGGCACTG 59.501 57.895 0.00 0.00 0.00 3.66
380 399 0.952497 CTGACGTTCATGGCACTGCT 60.952 55.000 0.00 0.00 0.00 4.24
382 401 1.959899 GACGTTCATGGCACTGCTCG 61.960 60.000 0.00 1.37 0.00 5.03
411 430 2.391389 GGACTTTTGCGAGGCGGAG 61.391 63.158 0.00 0.00 0.00 4.63
464 483 0.100503 CCGCAGCTTTTTAATCCCCG 59.899 55.000 0.00 0.00 0.00 5.73
475 494 6.035975 GCTTTTTAATCCCCGTCATTCATTTG 59.964 38.462 0.00 0.00 0.00 2.32
563 2211 1.929836 GCAGAGGCGTTGATTACTGAG 59.070 52.381 0.00 0.00 0.00 3.35
581 2229 2.059541 GAGTTACTGACGCACAAGGAC 58.940 52.381 0.00 0.00 0.00 3.85
582 2230 0.782384 GTTACTGACGCACAAGGACG 59.218 55.000 0.00 0.00 0.00 4.79
583 2231 0.386476 TTACTGACGCACAAGGACGT 59.614 50.000 0.00 0.00 46.91 4.34
584 2232 1.237533 TACTGACGCACAAGGACGTA 58.762 50.000 0.00 0.00 43.71 3.57
672 2320 2.642700 CCGGCGTGGAAAAACAGG 59.357 61.111 6.01 0.00 42.00 4.00
708 2356 2.512286 GGCACAGCAGCTCGCATA 60.512 61.111 14.05 0.00 46.13 3.14
750 3783 2.870161 CGACGTCGCTCTGTTCGG 60.870 66.667 26.59 0.00 0.00 4.30
751 3784 3.173240 GACGTCGCTCTGTTCGGC 61.173 66.667 0.00 0.00 0.00 5.54
768 3822 4.150454 CCTCGGCCCTCTCTCCCT 62.150 72.222 0.00 0.00 0.00 4.20
769 3823 2.837291 CTCGGCCCTCTCTCCCTG 60.837 72.222 0.00 0.00 0.00 4.45
772 3826 3.478274 GGCCCTCTCTCCCTGCTG 61.478 72.222 0.00 0.00 0.00 4.41
774 3828 2.686470 CCCTCTCTCCCTGCTGCA 60.686 66.667 0.88 0.88 0.00 4.41
777 3831 2.284478 TCTCTCCCTGCTGCAGCT 60.284 61.111 36.61 0.00 42.66 4.24
795 3849 2.270527 GCACAAGAGGGAGGGAGC 59.729 66.667 0.00 0.00 0.00 4.70
796 3850 2.297129 GCACAAGAGGGAGGGAGCT 61.297 63.158 0.00 0.00 0.00 4.09
797 3851 0.978146 GCACAAGAGGGAGGGAGCTA 60.978 60.000 0.00 0.00 0.00 3.32
798 3852 1.118838 CACAAGAGGGAGGGAGCTAG 58.881 60.000 0.00 0.00 0.00 3.42
799 3853 1.011595 ACAAGAGGGAGGGAGCTAGA 58.988 55.000 0.00 0.00 0.00 2.43
801 3855 1.216678 CAAGAGGGAGGGAGCTAGAGA 59.783 57.143 0.00 0.00 0.00 3.10
802 3856 1.614449 AGAGGGAGGGAGCTAGAGAA 58.386 55.000 0.00 0.00 0.00 2.87
803 3857 1.216930 AGAGGGAGGGAGCTAGAGAAC 59.783 57.143 0.00 0.00 0.00 3.01
804 3858 0.263468 AGGGAGGGAGCTAGAGAACC 59.737 60.000 0.00 0.00 0.00 3.62
805 3859 0.032017 GGGAGGGAGCTAGAGAACCA 60.032 60.000 0.00 0.00 0.00 3.67
806 3860 1.622725 GGGAGGGAGCTAGAGAACCAA 60.623 57.143 0.00 0.00 0.00 3.67
834 3888 0.930742 CGAGATTAGCACGAGACGGC 60.931 60.000 0.00 0.00 31.96 5.68
835 3889 0.930742 GAGATTAGCACGAGACGGCG 60.931 60.000 4.80 4.80 34.54 6.46
836 3890 1.944676 GATTAGCACGAGACGGCGG 60.945 63.158 13.24 0.00 35.12 6.13
837 3891 4.789075 TTAGCACGAGACGGCGGC 62.789 66.667 13.24 8.92 35.12 6.53
893 3962 1.753470 CCTCCTCCATGGCTAGCTG 59.247 63.158 15.72 5.79 35.26 4.24
903 3972 3.185155 GCTAGCTGCCTGTTGCTG 58.815 61.111 7.70 0.00 42.00 4.41
904 3973 1.673665 GCTAGCTGCCTGTTGCTGT 60.674 57.895 7.70 0.00 42.00 4.40
905 3974 1.239968 GCTAGCTGCCTGTTGCTGTT 61.240 55.000 7.70 0.00 42.00 3.16
906 3975 1.945819 GCTAGCTGCCTGTTGCTGTTA 60.946 52.381 7.70 0.00 42.00 2.41
908 3977 1.211190 GCTGCCTGTTGCTGTTAGC 59.789 57.895 0.00 0.00 42.82 3.09
909 3978 1.878775 CTGCCTGTTGCTGTTAGCC 59.121 57.895 0.00 0.00 41.51 3.93
910 3979 1.915614 CTGCCTGTTGCTGTTAGCCG 61.916 60.000 0.00 0.00 41.51 5.52
911 3980 2.690778 GCCTGTTGCTGTTAGCCGG 61.691 63.158 0.00 0.00 41.51 6.13
912 3981 1.302511 CCTGTTGCTGTTAGCCGGT 60.303 57.895 1.90 0.00 41.51 5.28
913 3982 0.889186 CCTGTTGCTGTTAGCCGGTT 60.889 55.000 1.90 0.00 41.51 4.44
914 3983 1.609580 CCTGTTGCTGTTAGCCGGTTA 60.610 52.381 1.90 0.00 41.51 2.85
915 3984 2.356135 CTGTTGCTGTTAGCCGGTTAT 58.644 47.619 1.90 0.00 41.51 1.89
916 3985 3.527533 CTGTTGCTGTTAGCCGGTTATA 58.472 45.455 1.90 0.00 41.51 0.98
919 3988 5.860611 TGTTGCTGTTAGCCGGTTATATAT 58.139 37.500 1.90 0.00 41.51 0.86
946 4015 1.928868 CTTCCCTGACCCTTGCATTT 58.071 50.000 0.00 0.00 0.00 2.32
949 4018 1.315257 CCCTGACCCTTGCATTTCCG 61.315 60.000 0.00 0.00 0.00 4.30
967 4036 3.104512 TCCGCCATTTCTTCCTTCTCTA 58.895 45.455 0.00 0.00 0.00 2.43
976 4045 2.678836 TCTTCCTTCTCTAGCTCGTTCG 59.321 50.000 0.00 0.00 0.00 3.95
1020 4089 2.747855 GGGGACGGAAGCAAGCTG 60.748 66.667 0.00 0.00 0.00 4.24
1101 4179 2.789092 CGTGGACATTACCTACGTCGAC 60.789 54.545 5.18 5.18 35.71 4.20
1192 4291 2.159043 AGCCTGACGTATGATTCTGTGG 60.159 50.000 0.00 0.00 0.00 4.17
1292 4397 6.817765 TGGTTCATTTTGAGGTCAGTTATC 57.182 37.500 0.00 0.00 0.00 1.75
1320 4433 2.607187 CTCGGAGCACGTACAGAATTT 58.393 47.619 0.00 0.00 44.69 1.82
1333 4455 3.242011 ACAGAATTTGGTGCCAAGGAAT 58.758 40.909 3.72 0.00 37.24 3.01
1339 4463 2.530460 TGGTGCCAAGGAATATGCTT 57.470 45.000 0.00 0.00 0.00 3.91
1352 4476 5.365025 AGGAATATGCTTAGCTCAACTCTGA 59.635 40.000 5.60 0.00 0.00 3.27
1434 4566 4.382320 TCGCACACCCGGTTAGGC 62.382 66.667 0.00 0.00 39.21 3.93
1517 4649 4.820894 ACAACCCAGGTATACTTCAGTC 57.179 45.455 2.25 0.00 0.00 3.51
1575 4707 5.189928 TGCTTCTCTTTGTCAGGTTTGTAA 58.810 37.500 0.00 0.00 0.00 2.41
1576 4708 5.827797 TGCTTCTCTTTGTCAGGTTTGTAAT 59.172 36.000 0.00 0.00 0.00 1.89
1577 4709 6.995686 TGCTTCTCTTTGTCAGGTTTGTAATA 59.004 34.615 0.00 0.00 0.00 0.98
1636 4801 2.032117 TCTTGTGCTTAATGTGTGTGCG 60.032 45.455 0.00 0.00 0.00 5.34
1737 4902 2.668457 CGACAAGGAAGAAGTTGATCCG 59.332 50.000 0.00 0.00 38.31 4.18
1800 4969 0.727398 GCATTACTGCCGGTCTGAAC 59.273 55.000 1.90 0.00 42.88 3.18
1813 4982 3.002348 CGGTCTGAACTGAGGTTTTTGTC 59.998 47.826 0.00 0.00 35.58 3.18
1816 4985 5.220873 GGTCTGAACTGAGGTTTTTGTCTTC 60.221 44.000 0.00 0.00 35.58 2.87
1899 5270 2.697751 AGTTATGGAAGATCTGCTCGCT 59.302 45.455 0.00 0.00 0.00 4.93
1967 5349 1.194218 TGCCTAGCATGTGACTAGCA 58.806 50.000 0.00 0.00 36.58 3.49
1971 5353 3.629398 GCCTAGCATGTGACTAGCAAAAT 59.371 43.478 0.00 0.00 36.58 1.82
1980 5362 5.304778 TGTGACTAGCAAAATTGTAGCAGA 58.695 37.500 0.00 0.00 0.00 4.26
2019 5401 0.543277 CAAGGATGTGGCAGGCTCTA 59.457 55.000 0.00 0.00 0.00 2.43
2064 5446 5.109903 GGATTAACTTCGATACTGCACTGT 58.890 41.667 0.00 0.00 0.00 3.55
2106 5488 2.102161 GCGGCGGCCAATGTTAAG 59.898 61.111 20.71 0.45 0.00 1.85
2124 5506 0.964358 AGTGCCTTTCTGATGCTGGC 60.964 55.000 0.00 0.00 43.49 4.85
2153 5535 6.941857 TCATCAATGTGTAAGGCAGTACTAA 58.058 36.000 0.00 0.00 0.00 2.24
2154 5536 7.564793 TCATCAATGTGTAAGGCAGTACTAAT 58.435 34.615 0.00 0.00 0.00 1.73
2212 6312 1.682854 CTGCTTTTGCCACTTTGGAGA 59.317 47.619 0.00 0.00 46.87 3.71
2213 6313 2.298163 CTGCTTTTGCCACTTTGGAGAT 59.702 45.455 0.00 0.00 46.87 2.75
2214 6314 3.495331 TGCTTTTGCCACTTTGGAGATA 58.505 40.909 0.00 0.00 46.87 1.98
2215 6315 4.088634 TGCTTTTGCCACTTTGGAGATAT 58.911 39.130 0.00 0.00 46.87 1.63
2216 6316 5.260424 TGCTTTTGCCACTTTGGAGATATA 58.740 37.500 0.00 0.00 46.87 0.86
2217 6317 5.125417 TGCTTTTGCCACTTTGGAGATATAC 59.875 40.000 0.00 0.00 46.87 1.47
2218 6318 5.358160 GCTTTTGCCACTTTGGAGATATACT 59.642 40.000 0.00 0.00 40.96 2.12
2219 6319 6.542370 GCTTTTGCCACTTTGGAGATATACTA 59.458 38.462 0.00 0.00 40.96 1.82
2220 6320 7.254932 GCTTTTGCCACTTTGGAGATATACTAG 60.255 40.741 0.00 0.00 40.96 2.57
2221 6321 5.808366 TGCCACTTTGGAGATATACTAGG 57.192 43.478 0.00 0.00 40.96 3.02
2222 6322 4.040461 TGCCACTTTGGAGATATACTAGGC 59.960 45.833 0.00 0.00 40.96 3.93
2223 6323 4.040461 GCCACTTTGGAGATATACTAGGCA 59.960 45.833 0.00 0.00 40.96 4.75
2224 6324 5.280215 GCCACTTTGGAGATATACTAGGCAT 60.280 44.000 0.00 0.00 40.96 4.40
2225 6325 6.745474 GCCACTTTGGAGATATACTAGGCATT 60.745 42.308 0.00 0.00 40.96 3.56
2226 6326 6.652481 CCACTTTGGAGATATACTAGGCATTG 59.348 42.308 0.00 0.00 40.96 2.82
2227 6327 6.148480 CACTTTGGAGATATACTAGGCATTGC 59.852 42.308 0.00 0.00 0.00 3.56
2228 6328 5.823861 TTGGAGATATACTAGGCATTGCA 57.176 39.130 11.39 0.00 0.00 4.08
2252 7046 7.325338 GCAATATATAGAAGAAAGTACGTCGCA 59.675 37.037 0.00 0.00 0.00 5.10
2267 7061 8.589335 AGTACGTCGCATTTCTGAATAATTAT 57.411 30.769 0.00 0.00 0.00 1.28
2507 7312 4.237349 TCAGGACCGAAAATTGCTTTTC 57.763 40.909 1.96 1.96 44.45 2.29
2516 7321 0.890683 AATTGCTTTTCGAGGCTGGG 59.109 50.000 0.00 0.00 0.00 4.45
2517 7322 1.598701 ATTGCTTTTCGAGGCTGGGC 61.599 55.000 0.00 0.00 0.00 5.36
2518 7323 2.360475 GCTTTTCGAGGCTGGGCT 60.360 61.111 0.00 0.00 0.00 5.19
2520 7325 1.746991 CTTTTCGAGGCTGGGCTCC 60.747 63.158 16.57 2.08 0.00 4.70
2521 7326 2.469465 CTTTTCGAGGCTGGGCTCCA 62.469 60.000 16.57 3.17 0.00 3.86
2523 7328 2.541547 TTTCGAGGCTGGGCTCCATG 62.542 60.000 16.57 5.19 30.82 3.66
2524 7329 4.559063 CGAGGCTGGGCTCCATGG 62.559 72.222 16.57 4.97 30.82 3.66
2528 7333 3.092511 GCTGGGCTCCATGGAGGA 61.093 66.667 36.92 7.69 46.75 3.71
2562 7367 9.274206 TGCAAAATTCAAAATTCATCAGATTCA 57.726 25.926 0.00 0.00 0.00 2.57
2621 7428 8.220559 GCAGATATACATGGGGGAATAATGTAT 58.779 37.037 11.15 11.15 45.15 2.29
2665 7638 4.701956 AAATACGTTGAAATGAGGGCTG 57.298 40.909 0.00 0.00 0.00 4.85
2666 7639 2.851263 TACGTTGAAATGAGGGCTGT 57.149 45.000 0.00 0.00 0.00 4.40
2770 7752 7.074502 GTCGCATTTCAAGATATTTCATCCTC 58.925 38.462 0.00 0.00 0.00 3.71
2783 7765 9.321562 GATATTTCATCCTCAATTTTTGCACAT 57.678 29.630 0.00 0.00 0.00 3.21
2921 8258 3.258622 AGGCCCTACTCGACAATATAAGC 59.741 47.826 0.00 0.00 0.00 3.09
2975 8326 6.588348 TCAGTAACAATATCTCATGTTGCG 57.412 37.500 1.66 0.00 43.88 4.85
3006 8361 9.942850 AAAATAAAATGCTTTGCACCTATACTT 57.057 25.926 0.00 0.00 43.04 2.24
3029 8479 9.062524 ACTTATTATGCTGTTTTGTCTTGTACA 57.937 29.630 0.00 0.00 35.88 2.90
3155 8620 3.181447 ACAATGCACATCTAGGGATCAGG 60.181 47.826 0.00 0.00 0.00 3.86
3178 8644 5.356426 GTTGCACTCCCTTACAAAAACATT 58.644 37.500 0.00 0.00 0.00 2.71
3304 8794 7.933577 TCAGATATAAACCATTTCTACCTGCAG 59.066 37.037 6.78 6.78 0.00 4.41
3324 8815 3.187227 CAGTATGCTTGACAGTTGACACC 59.813 47.826 0.00 0.00 0.00 4.16
3342 8841 1.039233 CCACCATCCATCAAGGCACC 61.039 60.000 0.00 0.00 37.29 5.01
3505 9029 2.561478 ACTGCATTTTACTGACGGGT 57.439 45.000 0.00 0.00 0.00 5.28
3506 9030 2.423577 ACTGCATTTTACTGACGGGTC 58.576 47.619 0.00 0.00 0.00 4.46
3526 9063 2.305635 TCAGCCATGAACCTGTGTGTAT 59.694 45.455 0.00 0.00 30.61 2.29
3529 9066 3.263170 AGCCATGAACCTGTGTGTATGTA 59.737 43.478 0.00 0.00 0.00 2.29
3538 9075 8.973182 TGAACCTGTGTGTATGTATATTCAGTA 58.027 33.333 0.00 0.00 0.00 2.74
3551 9117 8.528044 TGTATATTCAGTACTGTGTATGTCCA 57.472 34.615 21.99 14.69 0.00 4.02
3552 9118 8.410912 TGTATATTCAGTACTGTGTATGTCCAC 58.589 37.037 21.99 14.67 35.86 4.02
3554 9120 3.774734 TCAGTACTGTGTATGTCCACCT 58.225 45.455 21.99 0.00 34.35 4.00
3592 9158 1.821332 CCTGGAAGCAATCGAGGCC 60.821 63.158 8.11 0.00 45.59 5.19
3817 9399 2.208132 TCTGACGAGAGCTCCTTCTT 57.792 50.000 10.93 0.00 0.00 2.52
3821 9403 2.230025 TGACGAGAGCTCCTTCTTTCTG 59.770 50.000 10.93 0.04 0.00 3.02
3823 9405 2.029470 ACGAGAGCTCCTTCTTTCTGTG 60.029 50.000 10.93 0.00 0.00 3.66
3936 9520 1.466167 CCTGCCATGTCTTCAAGAACG 59.534 52.381 0.00 0.00 0.00 3.95
3954 9538 2.033194 GCCTCCCACACGTAGCAAC 61.033 63.158 0.00 0.00 0.00 4.17
3995 9579 5.454554 CGTACTACTGTTACCATTGATCACG 59.545 44.000 0.00 0.00 0.00 4.35
4010 9594 7.166307 CCATTGATCACGTTATTGTTGCTATTG 59.834 37.037 0.00 0.00 0.00 1.90
4025 9609 2.536803 GCTATTGCATTTGATTGGTGCG 59.463 45.455 0.00 0.00 41.61 5.34
4100 9684 9.573133 CCATTGATTTTGTTTACAGGAATAGTC 57.427 33.333 0.00 0.00 0.00 2.59
4128 9712 4.866508 AATGTCGACTGAGACTTGGTTA 57.133 40.909 17.92 0.00 41.47 2.85
4129 9713 5.407407 AATGTCGACTGAGACTTGGTTAT 57.593 39.130 17.92 0.00 41.47 1.89
4130 9714 4.174411 TGTCGACTGAGACTTGGTTATG 57.826 45.455 17.92 0.00 41.47 1.90
4131 9715 3.572682 TGTCGACTGAGACTTGGTTATGT 59.427 43.478 17.92 0.00 41.47 2.29
4132 9716 4.167268 GTCGACTGAGACTTGGTTATGTC 58.833 47.826 8.70 0.00 38.09 3.06
4133 9717 3.192844 TCGACTGAGACTTGGTTATGTCC 59.807 47.826 0.00 0.00 32.86 4.02
4134 9718 3.056821 CGACTGAGACTTGGTTATGTCCA 60.057 47.826 0.00 0.00 32.86 4.02
4135 9719 4.560716 CGACTGAGACTTGGTTATGTCCAA 60.561 45.833 0.00 0.00 44.03 3.53
4142 9726 3.328382 TTGGTTATGTCCAAGTCTCGG 57.672 47.619 0.00 0.00 41.79 4.63
4143 9727 2.253610 TGGTTATGTCCAAGTCTCGGT 58.746 47.619 0.00 0.00 34.24 4.69
4245 9843 2.031944 CACTTGAAGTCTCAGTCGTCGA 60.032 50.000 0.00 0.00 31.69 4.20
4260 9858 0.457851 GTCGACTGAGCTAGCCACAT 59.542 55.000 12.13 0.00 0.00 3.21
4300 9902 5.069914 TGAAGATGCCGGCTTCTAAACTATA 59.930 40.000 36.69 18.93 41.71 1.31
4305 9907 7.502561 AGATGCCGGCTTCTAAACTATATTTTT 59.497 33.333 36.03 12.95 0.00 1.94
4368 9970 1.065928 GCCATCTAGACACCGACCG 59.934 63.158 0.00 0.00 0.00 4.79
4492 10097 2.280797 GTGTGTCGCCTGCCTTCA 60.281 61.111 0.00 0.00 0.00 3.02
4518 10137 2.228822 CACCAGAGGAAAAATTGACGGG 59.771 50.000 0.00 0.00 0.00 5.28
4530 10149 1.185618 TTGACGGGTCACCTCCTCAG 61.186 60.000 0.04 0.00 39.66 3.35
4552 10184 1.293924 GAGCTTGACGCATATGCAGT 58.706 50.000 26.52 22.97 42.61 4.40
4568 10200 4.966965 TGCAGTTTTACGAACCTTCAAA 57.033 36.364 0.00 0.00 0.00 2.69
4596 10231 2.806434 ACCAATAGTGAAGCCATTGCA 58.194 42.857 0.00 0.00 41.13 4.08
4649 10288 0.689080 ACGCCATCCTCCAGATCTGT 60.689 55.000 21.11 0.00 30.59 3.41
4724 10363 4.112634 ACCACAAACCCAGTACATGATT 57.887 40.909 0.00 0.00 0.00 2.57
4831 10474 1.733041 CGATGTCACACGGCGAAGT 60.733 57.895 16.62 9.17 0.00 3.01
4895 10538 4.693566 CGCCATCCTTACTTGAACAAACTA 59.306 41.667 0.00 0.00 0.00 2.24
4911 10554 7.505585 TGAACAAACTAGTTTCCAAATCCATCT 59.494 33.333 18.00 0.00 0.00 2.90
4939 10582 2.247437 GGACCAATCGCCTCATCGC 61.247 63.158 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.949847 CTGCTACCAGCGCTGTACCT 61.950 60.000 33.75 16.45 46.26 3.08
27 28 1.449246 CTGTGGCTCTGCTACCAGC 60.449 63.158 3.76 0.00 39.28 4.85
142 161 2.921221 TCAGGGTTCATCTCTTCCCTT 58.079 47.619 0.00 0.00 46.99 3.95
144 163 3.457749 AGAATCAGGGTTCATCTCTTCCC 59.542 47.826 0.00 0.00 40.16 3.97
145 164 4.769345 AGAATCAGGGTTCATCTCTTCC 57.231 45.455 0.00 0.00 0.00 3.46
149 168 5.988287 AGAAGAAGAATCAGGGTTCATCTC 58.012 41.667 1.01 0.00 35.72 2.75
158 177 6.348376 GCTGTTTCTCAAGAAGAAGAATCAGG 60.348 42.308 17.94 6.72 44.69 3.86
162 181 6.427547 CAGAGCTGTTTCTCAAGAAGAAGAAT 59.572 38.462 0.00 0.00 44.69 2.40
165 184 4.451774 CCAGAGCTGTTTCTCAAGAAGAAG 59.548 45.833 0.00 0.00 44.69 2.85
166 185 4.141620 ACCAGAGCTGTTTCTCAAGAAGAA 60.142 41.667 0.00 0.00 42.35 2.52
167 186 3.389329 ACCAGAGCTGTTTCTCAAGAAGA 59.611 43.478 0.00 0.00 35.21 2.87
168 187 3.737850 ACCAGAGCTGTTTCTCAAGAAG 58.262 45.455 0.00 0.00 35.21 2.85
169 188 3.845781 ACCAGAGCTGTTTCTCAAGAA 57.154 42.857 0.00 0.00 35.59 2.52
170 189 3.134623 TCAACCAGAGCTGTTTCTCAAGA 59.865 43.478 0.00 0.00 35.59 3.02
171 190 3.470709 TCAACCAGAGCTGTTTCTCAAG 58.529 45.455 0.00 0.00 35.59 3.02
172 191 3.558931 TCAACCAGAGCTGTTTCTCAA 57.441 42.857 0.00 0.00 35.59 3.02
173 192 3.206150 GTTCAACCAGAGCTGTTTCTCA 58.794 45.455 0.00 0.00 35.59 3.27
174 193 2.550180 GGTTCAACCAGAGCTGTTTCTC 59.450 50.000 0.01 0.00 38.42 2.87
175 194 2.576615 GGTTCAACCAGAGCTGTTTCT 58.423 47.619 0.01 0.00 38.42 2.52
176 195 1.264288 CGGTTCAACCAGAGCTGTTTC 59.736 52.381 7.52 0.00 38.47 2.78
177 196 1.308998 CGGTTCAACCAGAGCTGTTT 58.691 50.000 7.52 0.00 38.47 2.83
178 197 0.180406 ACGGTTCAACCAGAGCTGTT 59.820 50.000 7.52 0.00 43.59 3.16
179 198 1.830145 ACGGTTCAACCAGAGCTGT 59.170 52.632 7.52 0.00 41.60 4.40
180 199 0.868406 GAACGGTTCAACCAGAGCTG 59.132 55.000 15.70 0.00 38.47 4.24
181 200 0.759346 AGAACGGTTCAACCAGAGCT 59.241 50.000 21.86 0.00 38.47 4.09
182 201 2.067013 GTAGAACGGTTCAACCAGAGC 58.933 52.381 21.86 0.00 38.47 4.09
187 206 2.825861 TGGAGTAGAACGGTTCAACC 57.174 50.000 21.86 17.30 34.05 3.77
189 208 5.733620 ACTAATGGAGTAGAACGGTTCAA 57.266 39.130 21.86 2.01 36.27 2.69
209 228 5.754782 TGGAATCTGTGGTTTGCATATACT 58.245 37.500 0.00 0.00 0.00 2.12
210 229 5.822519 TCTGGAATCTGTGGTTTGCATATAC 59.177 40.000 0.00 0.00 0.00 1.47
233 252 8.648557 AAGTAGCAAGGAAATTCTTGTTTTTC 57.351 30.769 8.27 0.00 44.26 2.29
234 253 9.098355 GAAAGTAGCAAGGAAATTCTTGTTTTT 57.902 29.630 8.27 2.50 44.26 1.94
298 317 8.397148 GGATGAAACATTCAGAAAAGAGATCTC 58.603 37.037 15.29 15.29 43.98 2.75
299 318 7.065563 CGGATGAAACATTCAGAAAAGAGATCT 59.934 37.037 0.00 0.00 43.98 2.75
300 319 7.148340 ACGGATGAAACATTCAGAAAAGAGATC 60.148 37.037 0.00 0.00 43.98 2.75
301 320 6.656693 ACGGATGAAACATTCAGAAAAGAGAT 59.343 34.615 0.00 0.00 43.98 2.75
302 321 5.997746 ACGGATGAAACATTCAGAAAAGAGA 59.002 36.000 0.00 0.00 43.98 3.10
303 322 6.246420 ACGGATGAAACATTCAGAAAAGAG 57.754 37.500 0.00 0.00 43.98 2.85
304 323 6.293955 GGAACGGATGAAACATTCAGAAAAGA 60.294 38.462 0.00 0.00 43.98 2.52
305 324 5.858581 GGAACGGATGAAACATTCAGAAAAG 59.141 40.000 0.00 0.00 43.98 2.27
306 325 5.278758 GGGAACGGATGAAACATTCAGAAAA 60.279 40.000 0.00 0.00 43.98 2.29
307 326 4.217550 GGGAACGGATGAAACATTCAGAAA 59.782 41.667 0.00 0.00 43.98 2.52
308 327 3.756434 GGGAACGGATGAAACATTCAGAA 59.244 43.478 0.00 0.00 43.98 3.02
309 328 3.244735 TGGGAACGGATGAAACATTCAGA 60.245 43.478 0.00 0.00 43.98 3.27
310 329 3.081061 TGGGAACGGATGAAACATTCAG 58.919 45.455 0.00 0.00 43.98 3.02
311 330 3.147553 TGGGAACGGATGAAACATTCA 57.852 42.857 0.00 0.00 45.01 2.57
312 331 4.718940 AATGGGAACGGATGAAACATTC 57.281 40.909 0.00 0.00 0.00 2.67
313 332 5.011533 TGAAAATGGGAACGGATGAAACATT 59.988 36.000 0.00 0.00 0.00 2.71
314 333 4.526262 TGAAAATGGGAACGGATGAAACAT 59.474 37.500 0.00 0.00 0.00 2.71
323 342 0.894141 TGCCATGAAAATGGGAACGG 59.106 50.000 6.86 0.00 39.16 4.44
333 352 7.227116 CCATTTTCTTTTCTTTCTGCCATGAAA 59.773 33.333 0.00 0.00 35.07 2.69
347 366 3.643159 ACGTCAGCCCATTTTCTTTTC 57.357 42.857 0.00 0.00 0.00 2.29
362 381 0.950555 GAGCAGTGCCATGAACGTCA 60.951 55.000 12.58 0.00 0.00 4.35
366 385 3.044059 GCCGAGCAGTGCCATGAAC 62.044 63.158 12.58 0.00 0.00 3.18
464 483 2.424956 GGGGTGAGCTCAAATGAATGAC 59.575 50.000 20.19 1.96 0.00 3.06
563 2211 0.782384 CGTCCTTGTGCGTCAGTAAC 59.218 55.000 0.00 0.00 0.00 2.50
582 2230 2.279937 CTTTTGGCTCGCTCGCGTAC 62.280 60.000 5.77 4.65 40.74 3.67
583 2231 2.048970 TTTTGGCTCGCTCGCGTA 60.049 55.556 5.77 0.00 40.74 4.42
584 2232 3.414700 CTTTTGGCTCGCTCGCGT 61.415 61.111 5.77 0.00 40.74 6.01
708 2356 1.028868 GCTTCGAGCTTCCCAATGCT 61.029 55.000 0.00 0.00 42.82 3.79
751 3784 4.150454 AGGGAGAGAGGGCCGAGG 62.150 72.222 0.00 0.00 0.00 4.63
756 3810 4.173924 GCAGCAGGGAGAGAGGGC 62.174 72.222 0.00 0.00 0.00 5.19
757 3811 2.686470 TGCAGCAGGGAGAGAGGG 60.686 66.667 0.00 0.00 0.00 4.30
758 3812 2.901813 CTGCAGCAGGGAGAGAGG 59.098 66.667 15.35 0.00 37.05 3.69
761 3815 2.125065 CAGCTGCAGCAGGGAGAG 60.125 66.667 38.24 15.70 45.16 3.20
772 3826 2.033141 TCCCTCTTGTGCAGCTGC 59.967 61.111 31.89 31.89 42.50 5.25
774 3828 2.600729 CCCTCCCTCTTGTGCAGCT 61.601 63.158 0.00 0.00 0.00 4.24
777 3831 2.596851 GCTCCCTCCCTCTTGTGCA 61.597 63.158 0.00 0.00 0.00 4.57
795 3849 0.108138 CAGCCGGGTTGGTTCTCTAG 60.108 60.000 1.64 0.00 41.21 2.43
796 3850 1.980052 CAGCCGGGTTGGTTCTCTA 59.020 57.895 1.64 0.00 41.21 2.43
797 3851 2.750350 CAGCCGGGTTGGTTCTCT 59.250 61.111 1.64 0.00 41.21 3.10
798 3852 3.056328 GCAGCCGGGTTGGTTCTC 61.056 66.667 13.02 0.00 41.21 2.87
803 3857 2.587322 TAATCTCGCAGCCGGGTTGG 62.587 60.000 13.02 0.00 42.50 3.77
804 3858 1.153449 TAATCTCGCAGCCGGGTTG 60.153 57.895 1.64 6.50 36.05 3.77
805 3859 1.144057 CTAATCTCGCAGCCGGGTT 59.856 57.895 1.64 0.00 36.05 4.11
806 3860 2.815308 CTAATCTCGCAGCCGGGT 59.185 61.111 0.00 0.00 36.05 5.28
835 3889 3.068729 GAATGGAAGCCGGCAAGCC 62.069 63.158 31.54 25.48 0.00 4.35
836 3890 2.491621 GAATGGAAGCCGGCAAGC 59.508 61.111 31.54 16.99 0.00 4.01
837 3891 1.678635 TGGAATGGAAGCCGGCAAG 60.679 57.895 31.54 0.00 0.00 4.01
838 3892 1.976474 GTGGAATGGAAGCCGGCAA 60.976 57.895 31.54 11.73 0.00 4.52
839 3893 2.361104 GTGGAATGGAAGCCGGCA 60.361 61.111 31.54 8.23 0.00 5.69
840 3894 3.140814 GGTGGAATGGAAGCCGGC 61.141 66.667 21.89 21.89 0.00 6.13
841 3895 1.750399 CTGGTGGAATGGAAGCCGG 60.750 63.158 0.00 0.00 0.00 6.13
850 3904 1.299976 GGAGCGAACCTGGTGGAAT 59.700 57.895 0.00 0.00 37.04 3.01
871 3925 0.835543 CTAGCCATGGAGGAGGGAGG 60.836 65.000 18.40 0.00 41.22 4.30
893 3962 2.690778 CCGGCTAACAGCAACAGGC 61.691 63.158 0.00 0.00 44.75 4.85
901 3970 6.145534 CACACACATATATAACCGGCTAACAG 59.854 42.308 0.00 0.00 0.00 3.16
902 3971 5.986741 CACACACATATATAACCGGCTAACA 59.013 40.000 0.00 0.00 0.00 2.41
903 3972 5.107220 GCACACACATATATAACCGGCTAAC 60.107 44.000 0.00 0.00 0.00 2.34
904 3973 4.992319 GCACACACATATATAACCGGCTAA 59.008 41.667 0.00 0.00 0.00 3.09
905 3974 4.282449 AGCACACACATATATAACCGGCTA 59.718 41.667 0.00 0.00 0.00 3.93
906 3975 3.071023 AGCACACACATATATAACCGGCT 59.929 43.478 0.00 0.00 0.00 5.52
908 3977 4.451096 GGAAGCACACACATATATAACCGG 59.549 45.833 0.00 0.00 0.00 5.28
909 3978 4.451096 GGGAAGCACACACATATATAACCG 59.549 45.833 0.00 0.00 0.00 4.44
910 3979 5.470098 CAGGGAAGCACACACATATATAACC 59.530 44.000 0.00 0.00 0.00 2.85
911 3980 6.202954 GTCAGGGAAGCACACACATATATAAC 59.797 42.308 0.00 0.00 0.00 1.89
912 3981 6.288294 GTCAGGGAAGCACACACATATATAA 58.712 40.000 0.00 0.00 0.00 0.98
913 3982 5.221641 GGTCAGGGAAGCACACACATATATA 60.222 44.000 0.00 0.00 0.00 0.86
914 3983 4.444876 GGTCAGGGAAGCACACACATATAT 60.445 45.833 0.00 0.00 0.00 0.86
915 3984 3.118408 GGTCAGGGAAGCACACACATATA 60.118 47.826 0.00 0.00 0.00 0.86
916 3985 2.356125 GGTCAGGGAAGCACACACATAT 60.356 50.000 0.00 0.00 0.00 1.78
919 3988 1.148273 GGTCAGGGAAGCACACACA 59.852 57.895 0.00 0.00 0.00 3.72
946 4015 1.909302 AGAGAAGGAAGAAATGGCGGA 59.091 47.619 0.00 0.00 0.00 5.54
949 4018 4.126437 GAGCTAGAGAAGGAAGAAATGGC 58.874 47.826 0.00 0.00 0.00 4.40
986 4055 2.825836 CCATTCCCGTGGCTGAGC 60.826 66.667 0.00 0.00 31.43 4.26
1192 4291 2.225963 CCCGTCCAGACATACTACGATC 59.774 54.545 0.00 0.00 33.88 3.69
1216 4321 1.760875 GAGATGGTACGCAGGGGGA 60.761 63.158 0.00 0.00 0.00 4.81
1292 4397 3.423154 GTGCTCCGAGCGGGTTTG 61.423 66.667 15.58 0.00 46.26 2.93
1320 4433 2.530460 AAGCATATTCCTTGGCACCA 57.470 45.000 0.00 0.00 0.00 4.17
1333 4455 4.813161 GCATTCAGAGTTGAGCTAAGCATA 59.187 41.667 0.00 0.00 34.15 3.14
1339 4463 6.579666 AAATTTGCATTCAGAGTTGAGCTA 57.420 33.333 0.00 0.00 34.15 3.32
1352 4476 1.297456 CCGCCGCCAAAATTTGCATT 61.297 50.000 0.00 0.00 0.00 3.56
1517 4649 1.377725 GTGATGGCCAGGTGGTGAG 60.378 63.158 13.05 0.00 37.57 3.51
1636 4801 6.385033 AGTCTATTCTTTGTCAAATTGCAGC 58.615 36.000 0.00 0.00 0.00 5.25
1713 4878 1.140052 TCAACTTCTTCCTTGTCGCCA 59.860 47.619 0.00 0.00 0.00 5.69
1737 4902 0.464554 GCTTGGAGTATGGGCTCACC 60.465 60.000 0.00 0.00 37.24 4.02
1800 4969 7.706179 TGCAAAATTAGAAGACAAAAACCTCAG 59.294 33.333 0.00 0.00 0.00 3.35
1813 4982 8.509690 TCTCTGTCAAGATTGCAAAATTAGAAG 58.490 33.333 1.71 0.00 0.00 2.85
1816 4985 8.077991 TGTTCTCTGTCAAGATTGCAAAATTAG 58.922 33.333 1.71 0.00 0.00 1.73
1899 5270 8.203485 ACATTTTCAGCTTTGTTCATTCCTTTA 58.797 29.630 0.00 0.00 0.00 1.85
1965 5347 7.486232 GGAAATTAGAGTCTGCTACAATTTTGC 59.514 37.037 1.86 0.00 32.72 3.68
1967 5349 8.870075 AGGAAATTAGAGTCTGCTACAATTTT 57.130 30.769 1.86 0.00 32.72 1.82
1971 5353 5.721960 AGGAGGAAATTAGAGTCTGCTACAA 59.278 40.000 1.86 0.00 0.00 2.41
1980 5362 5.478332 CCTTGCAAAAGGAGGAAATTAGAGT 59.522 40.000 0.00 0.00 42.62 3.24
2019 5401 2.094675 CCAGCAGAACATCCCGAAATT 58.905 47.619 0.00 0.00 0.00 1.82
2064 5446 3.264947 CAGAAGCCGATGAAATCTGTCA 58.735 45.455 0.00 0.00 42.58 3.58
2106 5488 1.509923 GCCAGCATCAGAAAGGCAC 59.490 57.895 0.00 0.00 44.59 5.01
2124 5506 5.413833 ACTGCCTTACACATTGATGAAGAAG 59.586 40.000 0.00 0.00 0.00 2.85
2161 5543 3.963476 TTTCCTTTTCTCCCAACTGGA 57.037 42.857 0.00 0.00 42.41 3.86
2219 6319 8.930846 ACTTTCTTCTATATATTGCAATGCCT 57.069 30.769 22.27 8.95 0.00 4.75
2221 6321 9.746711 CGTACTTTCTTCTATATATTGCAATGC 57.253 33.333 22.27 0.00 0.00 3.56
2224 6324 9.177304 CGACGTACTTTCTTCTATATATTGCAA 57.823 33.333 0.00 0.00 0.00 4.08
2225 6325 7.325338 GCGACGTACTTTCTTCTATATATTGCA 59.675 37.037 0.00 0.00 0.00 4.08
2226 6326 7.325338 TGCGACGTACTTTCTTCTATATATTGC 59.675 37.037 0.00 0.00 0.00 3.56
2227 6327 8.723777 TGCGACGTACTTTCTTCTATATATTG 57.276 34.615 0.00 0.00 0.00 1.90
2228 6328 9.909644 AATGCGACGTACTTTCTTCTATATATT 57.090 29.630 0.00 0.00 0.00 1.28
2249 7043 9.520204 ACAAGGAAATAATTATTCAGAAATGCG 57.480 29.630 11.08 0.00 0.00 4.73
2267 7061 4.781775 TGGGAAGTGTTAGACAAGGAAA 57.218 40.909 0.00 0.00 0.00 3.13
2285 7079 5.684704 TCCTGTAGAGCAAATTAAGATGGG 58.315 41.667 0.00 0.00 0.00 4.00
2286 7080 6.261826 CCTTCCTGTAGAGCAAATTAAGATGG 59.738 42.308 0.00 0.00 0.00 3.51
2507 7312 4.559063 CCATGGAGCCCAGCCTCG 62.559 72.222 5.56 0.00 36.75 4.63
2523 7328 6.907877 TTTGAATTTTGCAAAAGGAGTCCTCC 60.908 38.462 27.08 5.13 38.81 4.30
2524 7329 5.200368 TGAATTTTGCAAAAGGAGTCCTC 57.800 39.130 27.08 15.00 30.89 3.71
2528 7333 8.278729 TGAATTTTGAATTTTGCAAAAGGAGT 57.721 26.923 27.08 13.80 45.18 3.85
2643 7450 5.123186 CACAGCCCTCATTTCAACGTATTTA 59.877 40.000 0.00 0.00 0.00 1.40
2649 7456 0.109597 GCACAGCCCTCATTTCAACG 60.110 55.000 0.00 0.00 0.00 4.10
2882 8212 0.955919 CCTTTTGGTGACCGAGCTCC 60.956 60.000 8.47 0.00 34.07 4.70
2921 8258 1.939934 TGCCACAGTTTGAACTCGAAG 59.060 47.619 0.00 0.00 37.08 3.79
3005 8360 9.838975 CATGTACAAGACAAAACAGCATAATAA 57.161 29.630 0.00 0.00 42.78 1.40
3006 8361 9.225436 TCATGTACAAGACAAAACAGCATAATA 57.775 29.630 0.00 0.00 42.78 0.98
3007 8362 8.109705 TCATGTACAAGACAAAACAGCATAAT 57.890 30.769 0.00 0.00 42.78 1.28
3029 8479 6.205853 ACGGTATTTGTACACAACACAATCAT 59.794 34.615 0.00 0.00 38.00 2.45
3065 8519 5.088739 GTGCACGAAGATGGTAAATTCTTG 58.911 41.667 0.00 0.00 32.46 3.02
3155 8620 4.379339 TGTTTTTGTAAGGGAGTGCAAC 57.621 40.909 0.00 0.00 0.00 4.17
3178 8644 0.828762 AGGCACTGCATCCAAGCAAA 60.829 50.000 2.82 0.00 45.13 3.68
3304 8794 3.058914 GTGGTGTCAACTGTCAAGCATAC 60.059 47.826 0.00 0.00 0.00 2.39
3324 8815 0.323633 TGGTGCCTTGATGGATGGTG 60.324 55.000 0.00 0.00 38.35 4.17
3342 8841 5.149273 CACGTGGAAACAGAATCAAGATTG 58.851 41.667 7.95 0.00 44.46 2.67
3350 8868 1.234615 CGGGCACGTGGAAACAGAAT 61.235 55.000 18.88 0.00 44.46 2.40
3505 9029 0.473755 ACACACAGGTTCATGGCTGA 59.526 50.000 0.00 0.00 0.00 4.26
3506 9030 2.183478 TACACACAGGTTCATGGCTG 57.817 50.000 0.00 0.00 0.00 4.85
3510 9034 8.661352 TGAATATACATACACACAGGTTCATG 57.339 34.615 0.00 0.00 0.00 3.07
3526 9063 8.410912 GTGGACATACACAGTACTGAATATACA 58.589 37.037 29.30 18.36 40.99 2.29
3529 9066 6.611642 AGGTGGACATACACAGTACTGAATAT 59.388 38.462 29.30 20.37 43.08 1.28
3538 9075 1.902508 CCTGAGGTGGACATACACAGT 59.097 52.381 0.00 0.00 43.08 3.55
3548 9114 0.417437 TCCCTGAATCCTGAGGTGGA 59.583 55.000 0.00 0.00 40.82 4.02
3551 9117 0.119155 TGGTCCCTGAATCCTGAGGT 59.881 55.000 0.00 0.00 0.00 3.85
3552 9118 1.516110 ATGGTCCCTGAATCCTGAGG 58.484 55.000 0.00 0.00 0.00 3.86
3554 9120 2.242196 GGAAATGGTCCCTGAATCCTGA 59.758 50.000 0.00 0.00 41.10 3.86
3699 9265 1.282875 GCGAGGGTGTTCACTTTGC 59.717 57.895 2.98 4.29 0.00 3.68
3817 9399 1.318576 TCTCTGCGACAGACACAGAA 58.681 50.000 5.59 0.00 39.79 3.02
3821 9403 2.189342 GCTATTCTCTGCGACAGACAC 58.811 52.381 5.59 0.00 35.39 3.67
3823 9405 2.568696 TGCTATTCTCTGCGACAGAC 57.431 50.000 5.59 0.00 35.39 3.51
3936 9520 2.033194 GTTGCTACGTGTGGGAGGC 61.033 63.158 0.00 0.00 0.00 4.70
3954 9538 3.497932 GAAGCGAGGCTGCTGCAG 61.498 66.667 24.80 24.80 46.60 4.41
4010 9594 2.160221 CGGCGCACCAATCAAATGC 61.160 57.895 10.83 0.00 34.57 3.56
4100 9684 4.489810 AGTCTCAGTCGACATTTAGCAAG 58.510 43.478 19.50 3.12 36.38 4.01
4128 9712 1.482593 GATCCACCGAGACTTGGACAT 59.517 52.381 16.24 3.88 44.80 3.06
4129 9713 0.895530 GATCCACCGAGACTTGGACA 59.104 55.000 16.24 0.00 44.80 4.02
4130 9714 1.187087 AGATCCACCGAGACTTGGAC 58.813 55.000 16.24 1.73 44.80 4.02
4131 9715 2.820728 TAGATCCACCGAGACTTGGA 57.179 50.000 16.24 6.27 46.06 3.53
4132 9716 5.620205 CGAATATAGATCCACCGAGACTTGG 60.620 48.000 7.25 7.25 0.00 3.61
4133 9717 5.048643 ACGAATATAGATCCACCGAGACTTG 60.049 44.000 0.00 0.00 0.00 3.16
4134 9718 5.048643 CACGAATATAGATCCACCGAGACTT 60.049 44.000 0.00 0.00 0.00 3.01
4135 9719 4.456222 CACGAATATAGATCCACCGAGACT 59.544 45.833 0.00 0.00 0.00 3.24
4136 9720 4.454847 TCACGAATATAGATCCACCGAGAC 59.545 45.833 0.00 0.00 0.00 3.36
4137 9721 4.648651 TCACGAATATAGATCCACCGAGA 58.351 43.478 0.00 0.00 0.00 4.04
4138 9722 4.695928 TCTCACGAATATAGATCCACCGAG 59.304 45.833 0.00 0.00 0.00 4.63
4139 9723 4.648651 TCTCACGAATATAGATCCACCGA 58.351 43.478 0.00 0.00 0.00 4.69
4140 9724 5.355630 AGATCTCACGAATATAGATCCACCG 59.644 44.000 8.27 0.00 44.39 4.94
4141 9725 6.767524 AGATCTCACGAATATAGATCCACC 57.232 41.667 8.27 0.00 44.39 4.61
4142 9726 6.529829 GCAAGATCTCACGAATATAGATCCAC 59.470 42.308 0.00 0.00 44.39 4.02
4143 9727 6.209391 TGCAAGATCTCACGAATATAGATCCA 59.791 38.462 0.00 0.00 44.39 3.41
4245 9843 0.829333 CTGGATGTGGCTAGCTCAGT 59.171 55.000 15.72 3.04 0.00 3.41
4248 9846 0.833287 TTCCTGGATGTGGCTAGCTC 59.167 55.000 15.72 8.97 0.00 4.09
4260 9858 5.415701 GCATCTTCACTTGTTATTTCCTGGA 59.584 40.000 0.00 0.00 0.00 3.86
4368 9970 2.920490 TGTTGTCTTTTCAGTTTTGCGC 59.080 40.909 0.00 0.00 0.00 6.09
4437 10040 3.558033 AGGGTTTCTTCGGTTTTGCTTA 58.442 40.909 0.00 0.00 0.00 3.09
4444 10047 5.066893 GTGAAGTTAAAGGGTTTCTTCGGTT 59.933 40.000 0.00 0.00 37.78 4.44
4492 10097 2.629617 CAATTTTTCCTCTGGTGGTGCT 59.370 45.455 0.00 0.00 0.00 4.40
4552 10184 7.190871 GTGAGTCATTTTGAAGGTTCGTAAAA 58.809 34.615 0.00 0.00 0.00 1.52
4596 10231 1.279271 CCCCGGTCTGATTCTTCAACT 59.721 52.381 0.00 0.00 0.00 3.16
4649 10288 2.111384 GACTTAGTCATGCAGGGGAGA 58.889 52.381 7.59 0.00 32.09 3.71
4815 10457 1.374252 GGACTTCGCCGTGTGACAT 60.374 57.895 0.00 0.00 0.00 3.06
4895 10538 5.147032 TGGTTTGAGATGGATTTGGAAACT 58.853 37.500 0.00 0.00 0.00 2.66
4911 10554 2.639065 GCGATTGGTCCTATGGTTTGA 58.361 47.619 0.00 0.00 0.00 2.69


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.