Multiple sequence alignment - TraesCS7D01G352700

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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 TraesCS7D01G352700 chr7D 100.000 3431 0 0 1 3431 454377267 454380697 0.000000e+00 6336.0
1 TraesCS7D01G352700 chr7D 86.788 1597 157 24 851 2425 454140427 454141991 0.000000e+00 1731.0
2 TraesCS7D01G352700 chr7D 80.255 157 31 0 1334 1490 454680631 454680475 6.010000e-23 119.0
3 TraesCS7D01G352700 chr7D 96.000 50 2 0 3328 3377 543628043 543628092 7.890000e-12 82.4
4 TraesCS7D01G352700 chr7B 95.437 2038 74 10 402 2438 478731819 478733838 0.000000e+00 3230.0
5 TraesCS7D01G352700 chr7B 87.300 1559 157 21 905 2447 478537140 478538673 0.000000e+00 1744.0
6 TraesCS7D01G352700 chr7B 81.818 770 102 18 2531 3289 478737801 478738543 2.260000e-171 612.0
7 TraesCS7D01G352700 chr7B 92.576 229 14 3 179 406 478730572 478730798 3.300000e-85 326.0
8 TraesCS7D01G352700 chr7B 86.139 202 21 5 2 196 478730040 478730241 9.650000e-51 211.0
9 TraesCS7D01G352700 chr7B 92.727 55 3 1 3323 3377 512761093 512761146 1.020000e-10 78.7
10 TraesCS7D01G352700 chr7A 90.540 2167 116 37 578 2711 543598205 543596095 0.000000e+00 2784.0
11 TraesCS7D01G352700 chr7A 88.632 1126 121 6 1331 2450 543615425 543614301 0.000000e+00 1363.0
12 TraesCS7D01G352700 chr7A 86.957 230 26 4 2961 3188 543594513 543594286 4.390000e-64 255.0
13 TraesCS7D01G352700 chr7A 80.892 157 30 0 1334 1490 543431412 543431568 1.290000e-24 124.0
14 TraesCS7D01G352700 chr3A 86.550 171 23 0 2027 2197 90294364 90294534 4.520000e-44 189.0
15 TraesCS7D01G352700 chr1A 83.415 205 27 7 2026 2225 130150332 130150534 2.100000e-42 183.0
16 TraesCS7D01G352700 chr1A 97.872 47 1 0 3331 3377 361354249 361354295 7.890000e-12 82.4
17 TraesCS7D01G352700 chr1A 92.857 56 3 1 3322 3377 498452660 498452714 2.840000e-11 80.5
18 TraesCS7D01G352700 chr3D 85.465 172 25 0 2026 2197 75947858 75948029 2.720000e-41 180.0
19 TraesCS7D01G352700 chr1D 83.770 191 25 6 2027 2214 118511602 118511789 3.520000e-40 176.0
20 TraesCS7D01G352700 chr3B 84.211 171 27 0 2027 2197 122827329 122827499 2.120000e-37 167.0
21 TraesCS7D01G352700 chr6D 96.078 51 2 0 3330 3380 428265016 428264966 2.190000e-12 84.2
22 TraesCS7D01G352700 chr2A 97.872 47 1 0 3331 3377 764259870 764259916 7.890000e-12 82.4
23 TraesCS7D01G352700 chr5B 94.231 52 3 0 3329 3380 489614778 489614727 2.840000e-11 80.5
24 TraesCS7D01G352700 chr6B 92.593 54 4 0 3327 3380 42582213 42582160 1.020000e-10 78.7
25 TraesCS7D01G352700 chr1B 94.118 51 3 0 3327 3377 611680419 611680469 1.020000e-10 78.7


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 TraesCS7D01G352700 chr7D 454377267 454380697 3430 False 6336.00 6336 100.0000 1 3431 1 chr7D.!!$F2 3430
1 TraesCS7D01G352700 chr7D 454140427 454141991 1564 False 1731.00 1731 86.7880 851 2425 1 chr7D.!!$F1 1574
2 TraesCS7D01G352700 chr7B 478537140 478538673 1533 False 1744.00 1744 87.3000 905 2447 1 chr7B.!!$F1 1542
3 TraesCS7D01G352700 chr7B 478730040 478738543 8503 False 1094.75 3230 88.9925 2 3289 4 chr7B.!!$F3 3287
4 TraesCS7D01G352700 chr7A 543594286 543598205 3919 True 1519.50 2784 88.7485 578 3188 2 chr7A.!!$R2 2610
5 TraesCS7D01G352700 chr7A 543614301 543615425 1124 True 1363.00 1363 88.6320 1331 2450 1 chr7A.!!$R1 1119

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
292 648 0.254178 ATGTGGGCTGAGATGTGTCC 59.746 55.0 0.0 0.0 0.0 4.02 F
444 1825 0.463116 GGGTGTGTTTGTCGGTCTGT 60.463 55.0 0.0 0.0 0.0 3.41 F
445 1826 0.935196 GGTGTGTTTGTCGGTCTGTC 59.065 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 3237 1.217244 GTACACCACGGAATCGGCT 59.783 57.895 0.00 0.00 41.39 5.52 R
2394 3810 1.067821 CTAGTGATGCCCTCGAGGAAC 59.932 57.143 33.39 23.36 38.24 3.62 R
2468 5117 1.135373 CGATAGTCTTGGTGCTGTCGT 60.135 52.381 0.00 0.00 40.04 4.34 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
19 20 0.405198 TTGTGGGTGATGATGTGCCT 59.595 50.000 0.00 0.00 0.00 4.75
20 21 1.284313 TGTGGGTGATGATGTGCCTA 58.716 50.000 0.00 0.00 0.00 3.93
29 30 0.747644 TGATGTGCCTATTGTGCCGG 60.748 55.000 0.00 0.00 0.00 6.13
40 42 4.832608 GTGCCGGGCCTAACCTCG 62.833 72.222 17.97 0.00 39.10 4.63
53 55 3.583086 CCTAACCTCGGGGACATATTCAT 59.417 47.826 9.33 0.00 36.25 2.57
66 68 8.695456 GGGGACATATTCATCATTAAGTTTGTT 58.305 33.333 0.00 0.00 0.00 2.83
107 109 9.947433 TTTGGATGCTAAATTCAAAAAGATGAT 57.053 25.926 0.00 0.00 0.00 2.45
108 110 9.590451 TTGGATGCTAAATTCAAAAAGATGATC 57.410 29.630 0.00 0.00 0.00 2.92
109 111 7.916977 TGGATGCTAAATTCAAAAAGATGATCG 59.083 33.333 0.00 0.00 0.00 3.69
113 120 9.119418 TGCTAAATTCAAAAAGATGATCGGATA 57.881 29.630 0.00 0.00 0.00 2.59
125 132 3.565516 TGATCGGATATCTTTCGAAGCG 58.434 45.455 2.05 0.00 36.49 4.68
153 161 4.992951 GCAAAGAGGAACAAATGCAAGAAT 59.007 37.500 0.00 0.00 34.10 2.40
155 163 6.218019 CAAAGAGGAACAAATGCAAGAATGA 58.782 36.000 0.00 0.00 0.00 2.57
158 166 7.707624 AGAGGAACAAATGCAAGAATGATAA 57.292 32.000 0.00 0.00 0.00 1.75
159 167 7.542025 AGAGGAACAAATGCAAGAATGATAAC 58.458 34.615 0.00 0.00 0.00 1.89
161 169 5.004726 GGAACAAATGCAAGAATGATAACGC 59.995 40.000 0.00 0.00 0.00 4.84
164 172 5.106197 ACAAATGCAAGAATGATAACGCTCA 60.106 36.000 0.00 0.00 0.00 4.26
173 181 3.179443 TGATAACGCTCACCCTCAATC 57.821 47.619 0.00 0.00 0.00 2.67
182 190 1.019673 CACCCTCAATCTGGCATTCG 58.980 55.000 0.00 0.00 0.00 3.34
209 565 6.410540 AGAAGAAATCTAGTAGGTGCAAAGG 58.589 40.000 0.00 0.00 36.32 3.11
210 566 4.518249 AGAAATCTAGTAGGTGCAAAGGC 58.482 43.478 0.00 0.00 41.68 4.35
232 588 3.864789 AGAAGGGTGGCTATAATGTGG 57.135 47.619 0.00 0.00 0.00 4.17
247 603 1.212751 GTGGAGGCGCAAATGGTTC 59.787 57.895 10.83 0.00 0.00 3.62
250 606 1.508088 GAGGCGCAAATGGTTCCAG 59.492 57.895 10.83 0.00 0.00 3.86
292 648 0.254178 ATGTGGGCTGAGATGTGTCC 59.746 55.000 0.00 0.00 0.00 4.02
298 654 2.489722 GGGCTGAGATGTGTCCTTTTTC 59.510 50.000 0.00 0.00 0.00 2.29
299 655 3.416156 GGCTGAGATGTGTCCTTTTTCT 58.584 45.455 0.00 0.00 0.00 2.52
301 657 4.320788 GGCTGAGATGTGTCCTTTTTCTTG 60.321 45.833 0.00 0.00 0.00 3.02
314 670 4.340950 CCTTTTTCTTGTGAAAGTGGGCTA 59.659 41.667 0.00 0.00 42.34 3.93
333 689 4.275936 GGCTAAGATGTGTGTTGTCTTTGT 59.724 41.667 0.00 0.00 34.33 2.83
343 699 5.675444 GTGTGTTGTCTTTGTCGTTGTATTC 59.325 40.000 0.00 0.00 0.00 1.75
362 718 5.568620 ATTCTTCTCAAGTTGTAGTGGGT 57.431 39.130 2.11 0.00 0.00 4.51
364 720 3.005472 TCTTCTCAAGTTGTAGTGGGTCG 59.995 47.826 2.11 0.00 0.00 4.79
379 735 1.500396 GTCGACGGGGTTTCATTGC 59.500 57.895 0.00 0.00 0.00 3.56
414 1795 5.081728 TCCAAGTGCTTAGAGGTTACAGTA 58.918 41.667 0.00 0.00 0.00 2.74
417 1798 7.398047 TCCAAGTGCTTAGAGGTTACAGTAATA 59.602 37.037 0.00 0.00 0.00 0.98
426 1807 9.590451 TTAGAGGTTACAGTAATATTTTGTCGG 57.410 33.333 8.15 0.00 0.00 4.79
434 1815 6.263617 ACAGTAATATTTTGTCGGGTGTGTTT 59.736 34.615 0.00 0.00 0.00 2.83
435 1816 6.580791 CAGTAATATTTTGTCGGGTGTGTTTG 59.419 38.462 0.00 0.00 0.00 2.93
437 1818 2.923605 TTTTGTCGGGTGTGTTTGTC 57.076 45.000 0.00 0.00 0.00 3.18
439 1820 1.090625 TTGTCGGGTGTGTTTGTCGG 61.091 55.000 0.00 0.00 0.00 4.79
440 1821 1.522130 GTCGGGTGTGTTTGTCGGT 60.522 57.895 0.00 0.00 0.00 4.69
441 1822 1.227321 TCGGGTGTGTTTGTCGGTC 60.227 57.895 0.00 0.00 0.00 4.79
442 1823 1.227438 CGGGTGTGTTTGTCGGTCT 60.227 57.895 0.00 0.00 0.00 3.85
443 1824 1.495584 CGGGTGTGTTTGTCGGTCTG 61.496 60.000 0.00 0.00 0.00 3.51
444 1825 0.463116 GGGTGTGTTTGTCGGTCTGT 60.463 55.000 0.00 0.00 0.00 3.41
445 1826 0.935196 GGTGTGTTTGTCGGTCTGTC 59.065 55.000 0.00 0.00 0.00 3.51
446 1827 1.472728 GGTGTGTTTGTCGGTCTGTCT 60.473 52.381 0.00 0.00 0.00 3.41
447 1828 2.277084 GTGTGTTTGTCGGTCTGTCTT 58.723 47.619 0.00 0.00 0.00 3.01
456 1837 2.028930 GTCGGTCTGTCTTTGTGATCCT 60.029 50.000 0.00 0.00 0.00 3.24
489 1870 3.823281 TTTGGCAGCATTTCATATGGG 57.177 42.857 2.13 0.00 0.00 4.00
514 1895 4.881920 AGCAAGTTTGTGACAGTTTTTGT 58.118 34.783 0.00 0.00 44.55 2.83
535 1916 9.710979 TTTTGTCTGATTTTCGTTAGTTAACTG 57.289 29.630 18.56 1.62 34.12 3.16
537 1918 6.425721 TGTCTGATTTTCGTTAGTTAACTGGG 59.574 38.462 18.56 7.15 34.12 4.45
571 1952 9.027129 GTTCGCCTTAATTAAAACTTTTTGACT 57.973 29.630 0.00 0.00 0.00 3.41
572 1953 8.791355 TCGCCTTAATTAAAACTTTTTGACTC 57.209 30.769 0.00 0.00 0.00 3.36
604 1985 2.502947 ACTGAATATGAGCAGCAGTCCA 59.497 45.455 0.00 0.00 35.02 4.02
718 2101 6.560253 ATTGGACTGTTATGTCTTCAACAC 57.440 37.500 0.00 0.00 41.75 3.32
767 2152 4.147322 GATGGACGCAACGCACCG 62.147 66.667 0.00 0.00 31.60 4.94
820 2207 1.752498 TCACACGTGACACAACCTAGT 59.248 47.619 25.01 0.00 34.14 2.57
825 2212 1.343465 CGTGACACAACCTAGTTCCCT 59.657 52.381 6.37 0.00 0.00 4.20
882 2272 2.297880 GGAACCATAAAAACCCACGCTT 59.702 45.455 0.00 0.00 0.00 4.68
1329 2727 3.148279 GTCGGGGAGCTCGTGGAT 61.148 66.667 7.83 0.00 0.00 3.41
1608 3006 4.746309 TCCACCGACCCGTCCGAT 62.746 66.667 0.00 0.00 0.00 4.18
1635 3033 1.197492 CACAGCGTGTACACTACCGTA 59.803 52.381 23.01 0.00 0.00 4.02
1743 3141 4.203076 GCGGTGGGAGCGTACGAT 62.203 66.667 21.65 14.36 41.74 3.73
2359 3775 2.409651 CGGTCGTAGAGGCTCTGC 59.590 66.667 26.95 23.90 36.95 4.26
2394 3810 3.608707 CGTCGGATCGTAATCTAAGGGTG 60.609 52.174 0.00 0.00 32.12 4.61
2468 5117 0.955428 GAAATGCGAGGCTGGACACA 60.955 55.000 0.00 0.00 0.00 3.72
2595 7881 3.005539 AGGGGCACGCATCTGTCT 61.006 61.111 0.00 0.00 46.88 3.41
2600 7886 0.740868 GGCACGCATCTGTCTTAGCA 60.741 55.000 0.00 0.00 0.00 3.49
2608 7894 3.616076 GCATCTGTCTTAGCAGTGTCAGT 60.616 47.826 0.00 0.00 37.70 3.41
2610 7896 3.222603 TCTGTCTTAGCAGTGTCAGTCA 58.777 45.455 0.00 0.00 37.70 3.41
2625 7911 1.059098 AGTCACCTGATTGCCTCACA 58.941 50.000 0.00 0.00 0.00 3.58
2639 7926 5.103290 TGCCTCACAATTCGTAAAGTTTC 57.897 39.130 0.00 0.00 0.00 2.78
2648 7935 7.796660 CACAATTCGTAAAGTTTCTCGATTTCA 59.203 33.333 13.73 3.44 32.54 2.69
2671 7958 4.385358 ACAAGGGCACAACAAGTTTTAG 57.615 40.909 0.00 0.00 0.00 1.85
2672 7959 3.767131 ACAAGGGCACAACAAGTTTTAGT 59.233 39.130 0.00 0.00 0.00 2.24
2674 7961 4.649088 AGGGCACAACAAGTTTTAGTTC 57.351 40.909 0.00 0.00 0.00 3.01
2676 7963 5.442391 AGGGCACAACAAGTTTTAGTTCTA 58.558 37.500 0.00 0.00 0.00 2.10
2678 7965 6.549736 AGGGCACAACAAGTTTTAGTTCTAAT 59.450 34.615 0.00 0.00 0.00 1.73
2679 7966 7.722285 AGGGCACAACAAGTTTTAGTTCTAATA 59.278 33.333 0.00 0.00 0.00 0.98
2680 7967 8.354426 GGGCACAACAAGTTTTAGTTCTAATAA 58.646 33.333 0.00 0.00 0.00 1.40
2708 7995 7.203218 TCTGAACTAATGATTTGATCGATCGT 58.797 34.615 20.03 9.01 0.00 3.73
2711 7998 7.491048 TGAACTAATGATTTGATCGATCGTTCA 59.509 33.333 23.66 23.66 35.16 3.18
2753 9333 9.862371 TTGAAACTTAAACTTGCTATTTTGTCA 57.138 25.926 0.00 0.00 0.00 3.58
2754 9334 9.296400 TGAAACTTAAACTTGCTATTTTGTCAC 57.704 29.630 0.00 0.00 0.00 3.67
2755 9335 9.516314 GAAACTTAAACTTGCTATTTTGTCACT 57.484 29.630 0.00 0.00 0.00 3.41
2756 9336 9.516314 AAACTTAAACTTGCTATTTTGTCACTC 57.484 29.630 0.00 0.00 0.00 3.51
2757 9337 8.220755 ACTTAAACTTGCTATTTTGTCACTCA 57.779 30.769 0.00 0.00 0.00 3.41
2758 9338 8.129211 ACTTAAACTTGCTATTTTGTCACTCAC 58.871 33.333 0.00 0.00 0.00 3.51
2759 9339 6.699575 AAACTTGCTATTTTGTCACTCACT 57.300 33.333 0.00 0.00 0.00 3.41
2760 9340 5.679734 ACTTGCTATTTTGTCACTCACTG 57.320 39.130 0.00 0.00 0.00 3.66
2772 9353 6.405278 TGTCACTCACTGATTCTGAAACTA 57.595 37.500 0.00 0.00 0.00 2.24
2785 9366 8.616942 TGATTCTGAAACTAACGATTTTGTTGA 58.383 29.630 0.00 0.00 31.99 3.18
2803 9384 3.034721 TGATCGCTCGTACCAAGTTTT 57.965 42.857 0.00 0.00 0.00 2.43
2895 9477 9.683069 AAGACTTCATCACAAAAACATGAATAC 57.317 29.630 0.00 0.00 36.26 1.89
3053 9676 2.680312 ATCCCACGTGATGACTTCTG 57.320 50.000 19.30 0.00 0.00 3.02
3075 9698 1.207089 GCCACCTACACACTGCTATGA 59.793 52.381 0.00 0.00 0.00 2.15
3086 9709 5.010516 ACACACTGCTATGATGTCTCTATCC 59.989 44.000 0.00 0.00 0.00 2.59
3105 9728 5.708877 ATCCTAGAGTAATTGCGGTCTAC 57.291 43.478 0.00 0.00 0.00 2.59
3115 9738 7.256286 AGTAATTGCGGTCTACAGTAACTAAG 58.744 38.462 0.00 0.00 0.00 2.18
3172 9796 2.401583 ATGCTTACGGTCTGATGCAA 57.598 45.000 0.00 0.00 34.07 4.08
3174 9798 1.001974 TGCTTACGGTCTGATGCAAGT 59.998 47.619 0.00 0.00 0.00 3.16
3188 9812 6.092122 TCTGATGCAAGTAATTTCCTACAACG 59.908 38.462 0.00 0.00 0.00 4.10
3193 9817 5.562113 GCAAGTAATTTCCTACAACGCACTT 60.562 40.000 0.00 0.00 0.00 3.16
3194 9818 5.607119 AGTAATTTCCTACAACGCACTTG 57.393 39.130 0.00 0.00 35.77 3.16
3195 9819 2.989422 ATTTCCTACAACGCACTTGC 57.011 45.000 0.00 0.00 32.41 4.01
3208 9832 2.859538 CGCACTTGCACTTTTGATGTTT 59.140 40.909 1.48 0.00 42.21 2.83
3209 9833 3.301963 CGCACTTGCACTTTTGATGTTTG 60.302 43.478 1.48 0.00 42.21 2.93
3211 9835 4.329528 GCACTTGCACTTTTGATGTTTGAA 59.670 37.500 0.00 0.00 41.59 2.69
3217 9841 4.151157 GCACTTTTGATGTTTGAAGCATCC 59.849 41.667 17.44 2.86 41.32 3.51
3218 9842 5.535333 CACTTTTGATGTTTGAAGCATCCT 58.465 37.500 17.44 0.00 41.32 3.24
3219 9843 5.987347 CACTTTTGATGTTTGAAGCATCCTT 59.013 36.000 17.44 0.00 41.32 3.36
3227 9851 5.312895 TGTTTGAAGCATCCTTGTAGCTAA 58.687 37.500 0.00 0.00 37.70 3.09
3249 9873 6.723131 AAATAAGCTAAAGTGAGGACGAAC 57.277 37.500 0.00 0.00 0.00 3.95
3250 9874 2.349297 AGCTAAAGTGAGGACGAACG 57.651 50.000 0.00 0.00 0.00 3.95
3251 9875 0.714439 GCTAAAGTGAGGACGAACGC 59.286 55.000 0.00 0.00 0.00 4.84
3259 9885 1.731709 TGAGGACGAACGCAATTCATG 59.268 47.619 0.00 0.00 37.12 3.07
3267 9893 2.202783 GCAATTCATGCGGCCACC 60.203 61.111 2.24 0.00 46.87 4.61
3275 9901 0.109319 CATGCGGCCACCTACAAAAC 60.109 55.000 2.24 0.00 0.00 2.43
3289 9915 6.364165 CACCTACAAAACAAGAAGAATGCATG 59.636 38.462 0.00 0.00 0.00 4.06
3290 9916 6.040842 ACCTACAAAACAAGAAGAATGCATGT 59.959 34.615 0.00 0.00 0.00 3.21
3291 9917 7.230510 ACCTACAAAACAAGAAGAATGCATGTA 59.769 33.333 0.00 0.00 0.00 2.29
3292 9918 8.081633 CCTACAAAACAAGAAGAATGCATGTAA 58.918 33.333 0.00 0.00 0.00 2.41
3293 9919 9.630098 CTACAAAACAAGAAGAATGCATGTAAT 57.370 29.630 0.00 0.00 0.00 1.89
3294 9920 8.891671 ACAAAACAAGAAGAATGCATGTAATT 57.108 26.923 0.00 0.00 0.00 1.40
3295 9921 9.979578 ACAAAACAAGAAGAATGCATGTAATTA 57.020 25.926 0.00 0.00 0.00 1.40
3298 9924 9.846248 AAACAAGAAGAATGCATGTAATTAGTC 57.154 29.630 0.00 0.00 0.00 2.59
3299 9925 8.798859 ACAAGAAGAATGCATGTAATTAGTCT 57.201 30.769 0.00 0.00 0.00 3.24
3300 9926 9.890629 ACAAGAAGAATGCATGTAATTAGTCTA 57.109 29.630 0.00 0.00 0.00 2.59
3316 9942 8.451908 AATTAGTCTATGTTCTTAATGTGGGC 57.548 34.615 0.00 0.00 0.00 5.36
3317 9943 4.781934 AGTCTATGTTCTTAATGTGGGCC 58.218 43.478 0.00 0.00 0.00 5.80
3318 9944 4.475016 AGTCTATGTTCTTAATGTGGGCCT 59.525 41.667 4.53 0.00 0.00 5.19
3319 9945 4.576463 GTCTATGTTCTTAATGTGGGCCTG 59.424 45.833 4.53 0.00 0.00 4.85
3320 9946 1.544724 TGTTCTTAATGTGGGCCTGC 58.455 50.000 4.53 0.00 0.00 4.85
3321 9947 1.202989 TGTTCTTAATGTGGGCCTGCA 60.203 47.619 4.53 4.23 0.00 4.41
3322 9948 2.102578 GTTCTTAATGTGGGCCTGCAT 58.897 47.619 4.53 6.72 0.00 3.96
3323 9949 3.287222 GTTCTTAATGTGGGCCTGCATA 58.713 45.455 4.53 0.00 0.00 3.14
3324 9950 3.213206 TCTTAATGTGGGCCTGCATAG 57.787 47.619 4.53 5.25 0.00 2.23
3325 9951 2.509548 TCTTAATGTGGGCCTGCATAGT 59.490 45.455 4.53 0.00 0.00 2.12
3326 9952 3.053693 TCTTAATGTGGGCCTGCATAGTT 60.054 43.478 4.53 0.00 0.00 2.24
3327 9953 4.165180 TCTTAATGTGGGCCTGCATAGTTA 59.835 41.667 4.53 0.00 0.00 2.24
3328 9954 3.380471 AATGTGGGCCTGCATAGTTAA 57.620 42.857 4.53 0.00 0.00 2.01
3329 9955 2.889170 TGTGGGCCTGCATAGTTAAA 57.111 45.000 4.53 0.00 0.00 1.52
3330 9956 3.380471 TGTGGGCCTGCATAGTTAAAT 57.620 42.857 4.53 0.00 0.00 1.40
3331 9957 4.511786 TGTGGGCCTGCATAGTTAAATA 57.488 40.909 4.53 0.00 0.00 1.40
3332 9958 4.204012 TGTGGGCCTGCATAGTTAAATAC 58.796 43.478 4.53 0.00 0.00 1.89
3333 9959 4.080015 TGTGGGCCTGCATAGTTAAATACT 60.080 41.667 4.53 0.00 41.04 2.12
3334 9960 4.515567 GTGGGCCTGCATAGTTAAATACTC 59.484 45.833 4.53 0.00 38.33 2.59
3335 9961 4.072839 GGGCCTGCATAGTTAAATACTCC 58.927 47.826 0.84 0.00 38.33 3.85
3336 9962 4.072839 GGCCTGCATAGTTAAATACTCCC 58.927 47.826 0.00 0.00 38.33 4.30
3337 9963 4.202472 GGCCTGCATAGTTAAATACTCCCT 60.202 45.833 0.00 0.00 38.33 4.20
3338 9964 4.998033 GCCTGCATAGTTAAATACTCCCTC 59.002 45.833 0.00 0.00 38.33 4.30
3339 9965 5.552178 CCTGCATAGTTAAATACTCCCTCC 58.448 45.833 0.00 0.00 38.33 4.30
3340 9966 5.209818 TGCATAGTTAAATACTCCCTCCG 57.790 43.478 0.00 0.00 38.33 4.63
3341 9967 4.652421 TGCATAGTTAAATACTCCCTCCGT 59.348 41.667 0.00 0.00 38.33 4.69
3342 9968 5.221382 TGCATAGTTAAATACTCCCTCCGTC 60.221 44.000 0.00 0.00 38.33 4.79
3343 9969 5.780984 CATAGTTAAATACTCCCTCCGTCC 58.219 45.833 0.00 0.00 38.33 4.79
3344 9970 2.692041 AGTTAAATACTCCCTCCGTCCG 59.308 50.000 0.00 0.00 28.23 4.79
3345 9971 2.689983 GTTAAATACTCCCTCCGTCCGA 59.310 50.000 0.00 0.00 0.00 4.55
3346 9972 1.856629 AAATACTCCCTCCGTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
3347 9973 1.856629 AATACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
3348 9974 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
3349 9975 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
3350 9976 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
3351 9977 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
3352 9978 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
3353 9979 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
3354 9980 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
3355 9981 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
3356 9982 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
3357 9983 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
3358 9984 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
3359 9985 1.314730 GTCCGAAAAAGCTTGTCCCA 58.685 50.000 0.00 0.00 0.00 4.37
3360 9986 1.679153 GTCCGAAAAAGCTTGTCCCAA 59.321 47.619 0.00 0.00 0.00 4.12
3361 9987 2.100087 GTCCGAAAAAGCTTGTCCCAAA 59.900 45.455 0.00 0.00 0.00 3.28
3362 9988 2.100087 TCCGAAAAAGCTTGTCCCAAAC 59.900 45.455 0.00 0.00 0.00 2.93
3363 9989 2.100749 CCGAAAAAGCTTGTCCCAAACT 59.899 45.455 0.00 0.00 0.00 2.66
3364 9990 3.430236 CCGAAAAAGCTTGTCCCAAACTT 60.430 43.478 0.00 0.00 0.00 2.66
3365 9991 4.202070 CCGAAAAAGCTTGTCCCAAACTTA 60.202 41.667 0.00 0.00 0.00 2.24
3366 9992 5.508994 CCGAAAAAGCTTGTCCCAAACTTAT 60.509 40.000 0.00 0.00 0.00 1.73
3367 9993 5.983118 CGAAAAAGCTTGTCCCAAACTTATT 59.017 36.000 0.00 0.00 0.00 1.40
3368 9994 6.478673 CGAAAAAGCTTGTCCCAAACTTATTT 59.521 34.615 0.00 0.00 0.00 1.40
3369 9995 7.306574 CGAAAAAGCTTGTCCCAAACTTATTTC 60.307 37.037 0.00 0.55 0.00 2.17
3370 9996 6.731292 AAAGCTTGTCCCAAACTTATTTCT 57.269 33.333 0.00 0.00 0.00 2.52
3371 9997 5.966742 AGCTTGTCCCAAACTTATTTCTC 57.033 39.130 0.00 0.00 0.00 2.87
3372 9998 5.385198 AGCTTGTCCCAAACTTATTTCTCA 58.615 37.500 0.00 0.00 0.00 3.27
3373 9999 5.833131 AGCTTGTCCCAAACTTATTTCTCAA 59.167 36.000 0.00 0.00 0.00 3.02
3374 10000 6.323739 AGCTTGTCCCAAACTTATTTCTCAAA 59.676 34.615 0.00 0.00 0.00 2.69
3375 10001 7.015584 AGCTTGTCCCAAACTTATTTCTCAAAT 59.984 33.333 0.00 0.00 34.90 2.32
3376 10002 7.116805 GCTTGTCCCAAACTTATTTCTCAAATG 59.883 37.037 0.00 0.00 32.38 2.32
3377 10003 7.595819 TGTCCCAAACTTATTTCTCAAATGT 57.404 32.000 0.00 0.00 32.38 2.71
3378 10004 8.698973 TGTCCCAAACTTATTTCTCAAATGTA 57.301 30.769 0.00 0.00 32.38 2.29
3379 10005 9.308000 TGTCCCAAACTTATTTCTCAAATGTAT 57.692 29.630 0.00 0.00 32.38 2.29
3382 10008 9.289303 CCCAAACTTATTTCTCAAATGTATTCG 57.711 33.333 0.00 0.00 32.38 3.34
3383 10009 9.289303 CCAAACTTATTTCTCAAATGTATTCGG 57.711 33.333 0.00 0.00 32.38 4.30
3387 10013 9.667107 ACTTATTTCTCAAATGTATTCGGAAGA 57.333 29.630 0.00 0.00 33.08 2.87
3389 10015 6.985188 TTTCTCAAATGTATTCGGAAGAGG 57.015 37.500 0.00 0.00 43.69 3.69
3390 10016 5.023533 TCTCAAATGTATTCGGAAGAGGG 57.976 43.478 0.00 0.00 43.69 4.30
3391 10017 4.714802 TCTCAAATGTATTCGGAAGAGGGA 59.285 41.667 0.00 0.00 43.69 4.20
3392 10018 5.023533 TCAAATGTATTCGGAAGAGGGAG 57.976 43.478 0.00 0.00 43.69 4.30
3393 10019 4.469945 TCAAATGTATTCGGAAGAGGGAGT 59.530 41.667 0.00 0.00 43.69 3.85
3394 10020 5.659525 TCAAATGTATTCGGAAGAGGGAGTA 59.340 40.000 0.00 0.00 43.69 2.59
3395 10021 6.155565 TCAAATGTATTCGGAAGAGGGAGTAA 59.844 38.462 0.00 0.00 43.69 2.24
3396 10022 6.749036 AATGTATTCGGAAGAGGGAGTAAT 57.251 37.500 0.00 0.00 43.69 1.89
3397 10023 7.850935 AATGTATTCGGAAGAGGGAGTAATA 57.149 36.000 0.00 0.00 43.69 0.98
3398 10024 8.437274 AATGTATTCGGAAGAGGGAGTAATAT 57.563 34.615 0.00 0.00 43.69 1.28
3399 10025 7.850935 TGTATTCGGAAGAGGGAGTAATATT 57.149 36.000 0.00 0.00 43.69 1.28
3400 10026 8.258850 TGTATTCGGAAGAGGGAGTAATATTT 57.741 34.615 0.00 0.00 43.69 1.40
3401 10027 8.148351 TGTATTCGGAAGAGGGAGTAATATTTG 58.852 37.037 0.00 0.00 43.69 2.32
3402 10028 6.555463 TTCGGAAGAGGGAGTAATATTTGT 57.445 37.500 0.00 0.00 43.69 2.83
3403 10029 6.555463 TCGGAAGAGGGAGTAATATTTGTT 57.445 37.500 0.00 0.00 34.84 2.83
3404 10030 7.664552 TCGGAAGAGGGAGTAATATTTGTTA 57.335 36.000 0.00 0.00 34.84 2.41
3405 10031 7.723324 TCGGAAGAGGGAGTAATATTTGTTAG 58.277 38.462 0.00 0.00 34.84 2.34
3406 10032 7.343833 TCGGAAGAGGGAGTAATATTTGTTAGT 59.656 37.037 0.00 0.00 34.84 2.24
3407 10033 8.636213 CGGAAGAGGGAGTAATATTTGTTAGTA 58.364 37.037 0.00 0.00 0.00 1.82
3412 10038 8.953368 AGGGAGTAATATTTGTTAGTAAACCG 57.047 34.615 0.00 0.00 34.49 4.44
3413 10039 7.989170 AGGGAGTAATATTTGTTAGTAAACCGG 59.011 37.037 0.00 0.00 34.49 5.28
3414 10040 7.986889 GGGAGTAATATTTGTTAGTAAACCGGA 59.013 37.037 9.46 0.00 34.49 5.14
3415 10041 9.551734 GGAGTAATATTTGTTAGTAAACCGGAT 57.448 33.333 9.46 0.00 34.49 4.18
3421 10047 6.746745 TTTGTTAGTAAACCGGATCAATCC 57.253 37.500 9.46 0.00 37.28 3.01
3422 10048 5.687166 TGTTAGTAAACCGGATCAATCCT 57.313 39.130 9.46 0.00 38.13 3.24
3423 10049 6.057321 TGTTAGTAAACCGGATCAATCCTT 57.943 37.500 9.46 0.00 38.13 3.36
3424 10050 7.185318 TGTTAGTAAACCGGATCAATCCTTA 57.815 36.000 9.46 0.00 38.13 2.69
3425 10051 7.798071 TGTTAGTAAACCGGATCAATCCTTAT 58.202 34.615 9.46 0.00 38.13 1.73
3426 10052 8.269317 TGTTAGTAAACCGGATCAATCCTTATT 58.731 33.333 9.46 2.40 38.13 1.40
3427 10053 9.768662 GTTAGTAAACCGGATCAATCCTTATTA 57.231 33.333 9.46 1.58 44.93 0.98
3430 10056 9.862149 AGTAAACCGGATCAATCCTTATTATTT 57.138 29.630 9.46 0.00 44.93 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.405198 AGGCACATCATCACCCACAA 59.595 50.000 0.00 0.00 0.00 3.33
17 18 0.818040 GTTAGGCCCGGCACAATAGG 60.818 60.000 12.58 0.00 0.00 2.57
19 20 1.225148 GGTTAGGCCCGGCACAATA 59.775 57.895 12.58 0.00 0.00 1.90
20 21 2.044352 GGTTAGGCCCGGCACAAT 60.044 61.111 12.58 0.00 0.00 2.71
29 30 0.761702 TATGTCCCCGAGGTTAGGCC 60.762 60.000 0.00 0.00 37.58 5.19
40 42 8.237811 ACAAACTTAATGATGAATATGTCCCC 57.762 34.615 0.00 0.00 0.00 4.81
97 99 8.662781 TTCGAAAGATATCCGATCATCTTTTT 57.337 30.769 15.90 0.68 46.43 1.94
100 102 5.866633 GCTTCGAAAGATATCCGATCATCTT 59.133 40.000 0.00 1.20 42.03 2.40
102 104 4.264145 CGCTTCGAAAGATATCCGATCATC 59.736 45.833 0.00 0.00 41.60 2.92
104 106 3.004419 ACGCTTCGAAAGATATCCGATCA 59.996 43.478 0.00 0.00 41.60 2.92
105 107 3.566523 ACGCTTCGAAAGATATCCGATC 58.433 45.455 0.00 0.00 41.60 3.69
107 109 4.556942 TTACGCTTCGAAAGATATCCGA 57.443 40.909 0.00 0.00 41.60 4.55
108 110 4.433022 GCATTACGCTTCGAAAGATATCCG 60.433 45.833 0.00 0.00 41.60 4.18
109 111 4.447724 TGCATTACGCTTCGAAAGATATCC 59.552 41.667 0.00 0.00 43.06 2.59
113 120 4.391830 TCTTTGCATTACGCTTCGAAAGAT 59.608 37.500 0.00 0.00 43.06 2.40
117 124 2.415168 CCTCTTTGCATTACGCTTCGAA 59.585 45.455 0.00 0.00 43.06 3.71
125 132 5.229423 TGCATTTGTTCCTCTTTGCATTAC 58.771 37.500 0.00 0.00 35.36 1.89
153 161 2.766263 AGATTGAGGGTGAGCGTTATCA 59.234 45.455 0.00 0.00 0.00 2.15
155 163 2.158900 CCAGATTGAGGGTGAGCGTTAT 60.159 50.000 0.00 0.00 0.00 1.89
158 166 1.599047 CCAGATTGAGGGTGAGCGT 59.401 57.895 0.00 0.00 0.00 5.07
159 167 1.817099 GCCAGATTGAGGGTGAGCG 60.817 63.158 0.00 0.00 0.00 5.03
161 169 2.295885 GAATGCCAGATTGAGGGTGAG 58.704 52.381 0.00 0.00 0.00 3.51
164 172 0.749454 GCGAATGCCAGATTGAGGGT 60.749 55.000 0.00 0.00 33.98 4.34
173 181 2.995466 TTTCTTCTTGCGAATGCCAG 57.005 45.000 0.00 0.00 41.78 4.85
182 190 5.178797 TGCACCTACTAGATTTCTTCTTGC 58.821 41.667 0.00 0.00 35.79 4.01
209 565 3.316308 CACATTATAGCCACCCTTCTTGC 59.684 47.826 0.00 0.00 0.00 4.01
210 566 3.885297 CCACATTATAGCCACCCTTCTTG 59.115 47.826 0.00 0.00 0.00 3.02
220 576 0.250295 TGCGCCTCCACATTATAGCC 60.250 55.000 4.18 0.00 0.00 3.93
232 588 1.508088 CTGGAACCATTTGCGCCTC 59.492 57.895 4.18 0.00 0.00 4.70
250 606 3.501349 TGCATCCTAGAGAGGTGTATCC 58.499 50.000 0.00 0.00 44.19 2.59
260 616 1.952296 GCCCACATTTGCATCCTAGAG 59.048 52.381 0.00 0.00 0.00 2.43
292 648 4.391405 AGCCCACTTTCACAAGAAAAAG 57.609 40.909 0.00 0.00 42.78 2.27
298 654 4.074970 ACATCTTAGCCCACTTTCACAAG 58.925 43.478 0.00 0.00 35.92 3.16
299 655 3.820467 CACATCTTAGCCCACTTTCACAA 59.180 43.478 0.00 0.00 0.00 3.33
301 657 3.189287 CACACATCTTAGCCCACTTTCAC 59.811 47.826 0.00 0.00 0.00 3.18
314 670 3.938963 ACGACAAAGACAACACACATCTT 59.061 39.130 0.00 0.00 34.11 2.40
333 689 7.381408 CACTACAACTTGAGAAGAATACAACGA 59.619 37.037 0.00 0.00 0.00 3.85
343 699 3.005472 TCGACCCACTACAACTTGAGAAG 59.995 47.826 0.00 0.00 0.00 2.85
362 718 0.953471 CAGCAATGAAACCCCGTCGA 60.953 55.000 0.00 0.00 0.00 4.20
364 720 1.133025 CATCAGCAATGAAACCCCGTC 59.867 52.381 0.00 0.00 37.59 4.79
379 735 3.079578 AGCACTTGGATCACAACATCAG 58.920 45.455 0.00 0.00 34.76 2.90
414 1795 5.523438 ACAAACACACCCGACAAAATATT 57.477 34.783 0.00 0.00 0.00 1.28
417 1798 2.223386 CGACAAACACACCCGACAAAAT 60.223 45.455 0.00 0.00 0.00 1.82
425 1806 0.463116 ACAGACCGACAAACACACCC 60.463 55.000 0.00 0.00 0.00 4.61
426 1807 0.935196 GACAGACCGACAAACACACC 59.065 55.000 0.00 0.00 0.00 4.16
434 1815 2.288825 GGATCACAAAGACAGACCGACA 60.289 50.000 0.00 0.00 0.00 4.35
435 1816 2.028930 AGGATCACAAAGACAGACCGAC 60.029 50.000 0.00 0.00 0.00 4.79
437 1818 2.289072 ACAGGATCACAAAGACAGACCG 60.289 50.000 0.00 0.00 0.00 4.79
439 1820 3.070018 CCACAGGATCACAAAGACAGAC 58.930 50.000 0.00 0.00 0.00 3.51
440 1821 2.550855 GCCACAGGATCACAAAGACAGA 60.551 50.000 0.00 0.00 0.00 3.41
441 1822 1.808945 GCCACAGGATCACAAAGACAG 59.191 52.381 0.00 0.00 0.00 3.51
442 1823 1.421268 AGCCACAGGATCACAAAGACA 59.579 47.619 0.00 0.00 0.00 3.41
443 1824 2.079925 GAGCCACAGGATCACAAAGAC 58.920 52.381 0.00 0.00 38.12 3.01
444 1825 1.003580 GGAGCCACAGGATCACAAAGA 59.996 52.381 3.53 0.00 40.28 2.52
445 1826 1.271543 TGGAGCCACAGGATCACAAAG 60.272 52.381 3.53 0.00 40.28 2.77
446 1827 0.770499 TGGAGCCACAGGATCACAAA 59.230 50.000 3.53 0.00 40.28 2.83
447 1828 0.036732 GTGGAGCCACAGGATCACAA 59.963 55.000 14.53 0.00 45.53 3.33
489 1870 3.764885 AACTGTCACAAACTTGCTCAC 57.235 42.857 0.00 0.00 0.00 3.51
514 1895 5.410439 GCCCAGTTAACTAACGAAAATCAGA 59.590 40.000 8.04 0.00 40.96 3.27
516 1897 5.064558 TGCCCAGTTAACTAACGAAAATCA 58.935 37.500 8.04 0.00 40.96 2.57
522 1903 1.621814 AGCTGCCCAGTTAACTAACGA 59.378 47.619 8.04 0.00 40.96 3.85
528 1909 1.807142 GAACAGAGCTGCCCAGTTAAC 59.193 52.381 0.00 0.00 0.00 2.01
537 1918 1.373570 ATTAAGGCGAACAGAGCTGC 58.626 50.000 0.00 0.00 34.52 5.25
571 1952 6.876789 TGCTCATATTCAGTCTTTTTAACGGA 59.123 34.615 0.00 0.00 0.00 4.69
572 1953 7.072177 TGCTCATATTCAGTCTTTTTAACGG 57.928 36.000 0.00 0.00 0.00 4.44
728 2111 5.500234 TCCATTGGTTCATAAAGAGTCCAG 58.500 41.667 1.86 0.00 34.94 3.86
760 2145 4.412933 CCGTTCATATCGGTGCGT 57.587 55.556 0.00 0.00 42.62 5.24
767 2152 0.390124 TACGCCCCACCGTTCATATC 59.610 55.000 0.00 0.00 42.20 1.63
806 2192 3.613432 CGTAGGGAACTAGGTTGTGTCAC 60.613 52.174 0.00 0.00 45.49 3.67
825 2212 1.937278 TGTTTGACGAAACAGCCGTA 58.063 45.000 0.00 0.00 45.26 4.02
1608 3006 2.159014 AGTGTACACGCTGTGGAAGAAA 60.159 45.455 19.93 0.00 37.94 2.52
1839 3237 1.217244 GTACACCACGGAATCGGCT 59.783 57.895 0.00 0.00 41.39 5.52
2359 3775 2.809601 CGACGAGCCACCTTTCCG 60.810 66.667 0.00 0.00 0.00 4.30
2394 3810 1.067821 CTAGTGATGCCCTCGAGGAAC 59.932 57.143 33.39 23.36 38.24 3.62
2468 5117 1.135373 CGATAGTCTTGGTGCTGTCGT 60.135 52.381 0.00 0.00 40.04 4.34
2568 7854 2.040544 CGTGCCCCTGCGAATTTCT 61.041 57.895 0.00 0.00 41.78 2.52
2608 7894 2.885135 ATTGTGAGGCAATCAGGTGA 57.115 45.000 0.00 0.00 43.86 4.02
2610 7896 2.086869 CGAATTGTGAGGCAATCAGGT 58.913 47.619 0.00 0.00 46.29 4.00
2625 7911 9.166126 GTTTGAAATCGAGAAACTTTACGAATT 57.834 29.630 0.00 0.00 38.22 2.17
2637 7924 3.004315 GTGCCCTTGTTTGAAATCGAGAA 59.996 43.478 0.00 0.00 0.00 2.87
2639 7926 2.293122 TGTGCCCTTGTTTGAAATCGAG 59.707 45.455 0.00 0.00 0.00 4.04
2648 7935 3.694043 AAACTTGTTGTGCCCTTGTTT 57.306 38.095 0.00 0.00 0.00 2.83
2682 7969 7.706607 ACGATCGATCAAATCATTAGTTCAGAA 59.293 33.333 24.34 0.00 0.00 3.02
2684 7971 7.400158 ACGATCGATCAAATCATTAGTTCAG 57.600 36.000 24.34 5.39 0.00 3.02
2685 7972 7.491048 TGAACGATCGATCAAATCATTAGTTCA 59.509 33.333 23.67 23.95 40.10 3.18
2686 7973 7.841486 TGAACGATCGATCAAATCATTAGTTC 58.159 34.615 23.67 22.10 35.18 3.01
2687 7974 7.770801 TGAACGATCGATCAAATCATTAGTT 57.229 32.000 23.67 15.78 0.00 2.24
2688 7975 7.953158 ATGAACGATCGATCAAATCATTAGT 57.047 32.000 28.31 9.00 30.98 2.24
2699 7986 5.920840 TGAATCTTGGTATGAACGATCGATC 59.079 40.000 24.34 20.58 0.00 3.69
2700 7987 5.842907 TGAATCTTGGTATGAACGATCGAT 58.157 37.500 24.34 10.66 0.00 3.59
2708 7995 7.939039 AGTTTCAACTCTGAATCTTGGTATGAA 59.061 33.333 0.00 0.00 41.22 2.57
2711 7998 9.793259 TTAAGTTTCAACTCTGAATCTTGGTAT 57.207 29.630 16.16 0.00 45.15 2.73
2742 9322 6.369890 TCAGAATCAGTGAGTGACAAAATAGC 59.630 38.462 0.00 0.00 38.28 2.97
2752 9332 5.920840 TCGTTAGTTTCAGAATCAGTGAGTG 59.079 40.000 0.00 0.00 0.00 3.51
2753 9333 6.085555 TCGTTAGTTTCAGAATCAGTGAGT 57.914 37.500 0.00 0.00 0.00 3.41
2754 9334 7.588143 AATCGTTAGTTTCAGAATCAGTGAG 57.412 36.000 0.00 0.00 0.00 3.51
2755 9335 7.962964 AAATCGTTAGTTTCAGAATCAGTGA 57.037 32.000 0.00 0.00 0.00 3.41
2756 9336 8.070171 ACAAAATCGTTAGTTTCAGAATCAGTG 58.930 33.333 0.00 0.00 0.00 3.66
2757 9337 8.154649 ACAAAATCGTTAGTTTCAGAATCAGT 57.845 30.769 0.00 0.00 0.00 3.41
2758 9338 8.895845 CAACAAAATCGTTAGTTTCAGAATCAG 58.104 33.333 0.00 0.00 0.00 2.90
2759 9339 8.616942 TCAACAAAATCGTTAGTTTCAGAATCA 58.383 29.630 0.00 0.00 0.00 2.57
2760 9340 9.612620 ATCAACAAAATCGTTAGTTTCAGAATC 57.387 29.630 0.00 0.00 0.00 2.52
2772 9353 2.478894 ACGAGCGATCAACAAAATCGTT 59.521 40.909 0.00 1.32 45.93 3.85
2785 9366 5.467735 ACTTTTAAAACTTGGTACGAGCGAT 59.532 36.000 0.00 0.00 0.00 4.58
2863 9444 8.824159 TGTTTTTGTGATGAAGTCTTTCAAAA 57.176 26.923 0.00 0.00 45.82 2.44
2983 9605 2.038557 AGGATTTGTAGCACGAAGGTGT 59.961 45.455 0.00 0.00 46.13 4.16
2989 9612 1.480954 GGGAGAGGATTTGTAGCACGA 59.519 52.381 0.00 0.00 0.00 4.35
3053 9676 0.895530 TAGCAGTGTGTAGGTGGCTC 59.104 55.000 0.00 0.00 33.10 4.70
3086 9709 5.502153 ACTGTAGACCGCAATTACTCTAG 57.498 43.478 0.00 0.00 0.00 2.43
3097 9720 5.246145 ACATCTTAGTTACTGTAGACCGC 57.754 43.478 0.00 0.00 0.00 5.68
3156 9780 6.422776 AAATTACTTGCATCAGACCGTAAG 57.577 37.500 0.00 0.00 0.00 2.34
3160 9784 3.941483 AGGAAATTACTTGCATCAGACCG 59.059 43.478 0.00 0.00 0.00 4.79
3172 9796 4.083484 GCAAGTGCGTTGTAGGAAATTACT 60.083 41.667 1.04 0.00 38.55 2.24
3174 9798 3.815962 TGCAAGTGCGTTGTAGGAAATTA 59.184 39.130 0.00 0.00 45.83 1.40
3188 9812 3.864583 TCAAACATCAAAAGTGCAAGTGC 59.135 39.130 0.00 0.00 42.50 4.40
3193 9817 4.120792 TGCTTCAAACATCAAAAGTGCA 57.879 36.364 0.00 0.00 0.00 4.57
3194 9818 4.151157 GGATGCTTCAAACATCAAAAGTGC 59.849 41.667 3.24 0.00 44.68 4.40
3195 9819 5.535333 AGGATGCTTCAAACATCAAAAGTG 58.465 37.500 3.24 0.00 44.68 3.16
3208 9832 6.260936 GCTTATTTAGCTACAAGGATGCTTCA 59.739 38.462 0.00 0.00 46.77 3.02
3209 9833 6.663565 GCTTATTTAGCTACAAGGATGCTTC 58.336 40.000 0.00 0.00 46.77 3.86
3227 9851 4.863131 CGTTCGTCCTCACTTTAGCTTATT 59.137 41.667 0.00 0.00 0.00 1.40
3239 9863 1.731709 CATGAATTGCGTTCGTCCTCA 59.268 47.619 0.00 0.00 39.80 3.86
3241 9865 0.447801 GCATGAATTGCGTTCGTCCT 59.552 50.000 0.00 0.00 42.54 3.85
3251 9875 0.381801 GTAGGTGGCCGCATGAATTG 59.618 55.000 19.98 0.00 0.00 2.32
3259 9885 0.039527 CTTGTTTTGTAGGTGGCCGC 60.040 55.000 8.12 8.12 0.00 6.53
3262 9888 4.911514 TTCTTCTTGTTTTGTAGGTGGC 57.088 40.909 0.00 0.00 0.00 5.01
3263 9889 5.221224 TGCATTCTTCTTGTTTTGTAGGTGG 60.221 40.000 0.00 0.00 0.00 4.61
3264 9890 5.830912 TGCATTCTTCTTGTTTTGTAGGTG 58.169 37.500 0.00 0.00 0.00 4.00
3267 9893 9.630098 ATTACATGCATTCTTCTTGTTTTGTAG 57.370 29.630 0.00 0.00 0.00 2.74
3290 9916 9.555727 GCCCACATTAAGAACATAGACTAATTA 57.444 33.333 0.00 0.00 0.00 1.40
3291 9917 7.502561 GGCCCACATTAAGAACATAGACTAATT 59.497 37.037 0.00 0.00 0.00 1.40
3292 9918 6.998673 GGCCCACATTAAGAACATAGACTAAT 59.001 38.462 0.00 0.00 0.00 1.73
3293 9919 6.157994 AGGCCCACATTAAGAACATAGACTAA 59.842 38.462 0.00 0.00 0.00 2.24
3294 9920 5.665812 AGGCCCACATTAAGAACATAGACTA 59.334 40.000 0.00 0.00 0.00 2.59
3295 9921 4.475016 AGGCCCACATTAAGAACATAGACT 59.525 41.667 0.00 0.00 0.00 3.24
3296 9922 4.576463 CAGGCCCACATTAAGAACATAGAC 59.424 45.833 0.00 0.00 0.00 2.59
3297 9923 4.780815 CAGGCCCACATTAAGAACATAGA 58.219 43.478 0.00 0.00 0.00 1.98
3298 9924 3.316308 GCAGGCCCACATTAAGAACATAG 59.684 47.826 0.00 0.00 0.00 2.23
3299 9925 3.287222 GCAGGCCCACATTAAGAACATA 58.713 45.455 0.00 0.00 0.00 2.29
3300 9926 2.102578 GCAGGCCCACATTAAGAACAT 58.897 47.619 0.00 0.00 0.00 2.71
3301 9927 1.202989 TGCAGGCCCACATTAAGAACA 60.203 47.619 0.00 0.00 0.00 3.18
3302 9928 1.544724 TGCAGGCCCACATTAAGAAC 58.455 50.000 0.00 0.00 0.00 3.01
3303 9929 2.530460 ATGCAGGCCCACATTAAGAA 57.470 45.000 0.00 0.00 0.00 2.52
3304 9930 2.509548 ACTATGCAGGCCCACATTAAGA 59.490 45.455 12.96 0.00 0.00 2.10
3305 9931 2.936202 ACTATGCAGGCCCACATTAAG 58.064 47.619 12.96 8.27 0.00 1.85
3306 9932 3.380471 AACTATGCAGGCCCACATTAA 57.620 42.857 12.96 0.00 0.00 1.40
3307 9933 4.511786 TTAACTATGCAGGCCCACATTA 57.488 40.909 12.96 0.00 0.00 1.90
3308 9934 3.380471 TTAACTATGCAGGCCCACATT 57.620 42.857 12.96 0.02 0.00 2.71
3309 9935 3.380471 TTTAACTATGCAGGCCCACAT 57.620 42.857 12.40 12.40 0.00 3.21
3310 9936 2.889170 TTTAACTATGCAGGCCCACA 57.111 45.000 0.00 0.00 0.00 4.17
3311 9937 4.461198 AGTATTTAACTATGCAGGCCCAC 58.539 43.478 0.00 0.00 36.36 4.61
3312 9938 4.445735 GGAGTATTTAACTATGCAGGCCCA 60.446 45.833 0.00 0.00 39.07 5.36
3313 9939 4.072839 GGAGTATTTAACTATGCAGGCCC 58.927 47.826 0.00 0.00 39.07 5.80
3314 9940 4.072839 GGGAGTATTTAACTATGCAGGCC 58.927 47.826 0.00 0.00 39.07 5.19
3315 9941 4.974399 AGGGAGTATTTAACTATGCAGGC 58.026 43.478 0.00 0.00 39.07 4.85
3316 9942 5.552178 GGAGGGAGTATTTAACTATGCAGG 58.448 45.833 0.00 0.00 39.07 4.85
3317 9943 5.221461 ACGGAGGGAGTATTTAACTATGCAG 60.221 44.000 0.00 0.00 39.07 4.41
3318 9944 4.652421 ACGGAGGGAGTATTTAACTATGCA 59.348 41.667 0.00 0.00 39.07 3.96
3319 9945 5.211174 ACGGAGGGAGTATTTAACTATGC 57.789 43.478 0.00 0.00 39.07 3.14
3320 9946 5.564259 CGGACGGAGGGAGTATTTAACTATG 60.564 48.000 0.00 0.00 39.07 2.23
3321 9947 4.522022 CGGACGGAGGGAGTATTTAACTAT 59.478 45.833 0.00 0.00 39.07 2.12
3322 9948 3.885297 CGGACGGAGGGAGTATTTAACTA 59.115 47.826 0.00 0.00 39.07 2.24
3323 9949 2.692041 CGGACGGAGGGAGTATTTAACT 59.308 50.000 0.00 0.00 42.80 2.24
3324 9950 2.689983 TCGGACGGAGGGAGTATTTAAC 59.310 50.000 0.00 0.00 0.00 2.01
3325 9951 3.017048 TCGGACGGAGGGAGTATTTAA 57.983 47.619 0.00 0.00 0.00 1.52
3326 9952 2.734755 TCGGACGGAGGGAGTATTTA 57.265 50.000 0.00 0.00 0.00 1.40
3327 9953 1.856629 TTCGGACGGAGGGAGTATTT 58.143 50.000 0.00 0.00 0.00 1.40
3328 9954 1.856629 TTTCGGACGGAGGGAGTATT 58.143 50.000 0.00 0.00 0.00 1.89
3329 9955 1.856629 TTTTCGGACGGAGGGAGTAT 58.143 50.000 0.00 0.00 0.00 2.12
3330 9956 1.547372 CTTTTTCGGACGGAGGGAGTA 59.453 52.381 0.00 0.00 0.00 2.59
3331 9957 0.320697 CTTTTTCGGACGGAGGGAGT 59.679 55.000 0.00 0.00 0.00 3.85
3332 9958 1.019805 GCTTTTTCGGACGGAGGGAG 61.020 60.000 0.00 0.00 0.00 4.30
3333 9959 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
3334 9960 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
3335 9961 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
3336 9962 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
3337 9963 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
3338 9964 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
3339 9965 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
3340 9966 1.314730 TGGGACAAGCTTTTTCGGAC 58.685 50.000 0.00 0.00 31.92 4.79
3341 9967 3.811031 TGGGACAAGCTTTTTCGGA 57.189 47.368 0.00 0.00 31.92 4.55
3353 9979 7.595819 ACATTTGAGAAATAAGTTTGGGACA 57.404 32.000 0.00 0.00 0.00 4.02
3356 9982 9.289303 CGAATACATTTGAGAAATAAGTTTGGG 57.711 33.333 0.00 0.00 0.00 4.12
3357 9983 9.289303 CCGAATACATTTGAGAAATAAGTTTGG 57.711 33.333 0.00 0.00 0.00 3.28
3361 9987 9.667107 TCTTCCGAATACATTTGAGAAATAAGT 57.333 29.630 0.00 0.00 0.00 2.24
3363 9989 9.109393 CCTCTTCCGAATACATTTGAGAAATAA 57.891 33.333 0.00 0.00 0.00 1.40
3364 9990 7.715249 CCCTCTTCCGAATACATTTGAGAAATA 59.285 37.037 0.00 0.00 0.00 1.40
3365 9991 6.543831 CCCTCTTCCGAATACATTTGAGAAAT 59.456 38.462 0.00 0.00 0.00 2.17
3366 9992 5.880332 CCCTCTTCCGAATACATTTGAGAAA 59.120 40.000 0.00 0.00 0.00 2.52
3367 9993 5.188948 TCCCTCTTCCGAATACATTTGAGAA 59.811 40.000 0.00 0.00 0.00 2.87
3368 9994 4.714802 TCCCTCTTCCGAATACATTTGAGA 59.285 41.667 0.00 0.00 0.00 3.27
3369 9995 5.023533 TCCCTCTTCCGAATACATTTGAG 57.976 43.478 0.00 0.00 0.00 3.02
3370 9996 4.469945 ACTCCCTCTTCCGAATACATTTGA 59.530 41.667 0.00 0.00 0.00 2.69
3371 9997 4.770795 ACTCCCTCTTCCGAATACATTTG 58.229 43.478 0.00 0.00 0.00 2.32
3372 9998 6.555463 TTACTCCCTCTTCCGAATACATTT 57.445 37.500 0.00 0.00 0.00 2.32
3373 9999 6.749036 ATTACTCCCTCTTCCGAATACATT 57.251 37.500 0.00 0.00 0.00 2.71
3374 10000 8.437274 AATATTACTCCCTCTTCCGAATACAT 57.563 34.615 0.00 0.00 0.00 2.29
3375 10001 7.850935 AATATTACTCCCTCTTCCGAATACA 57.149 36.000 0.00 0.00 0.00 2.29
3376 10002 8.148999 ACAAATATTACTCCCTCTTCCGAATAC 58.851 37.037 0.00 0.00 0.00 1.89
3377 10003 8.258850 ACAAATATTACTCCCTCTTCCGAATA 57.741 34.615 0.00 0.00 0.00 1.75
3378 10004 7.138054 ACAAATATTACTCCCTCTTCCGAAT 57.862 36.000 0.00 0.00 0.00 3.34
3379 10005 6.555463 ACAAATATTACTCCCTCTTCCGAA 57.445 37.500 0.00 0.00 0.00 4.30
3380 10006 6.555463 AACAAATATTACTCCCTCTTCCGA 57.445 37.500 0.00 0.00 0.00 4.55
3381 10007 7.498443 ACTAACAAATATTACTCCCTCTTCCG 58.502 38.462 0.00 0.00 0.00 4.30
3386 10012 9.038803 CGGTTTACTAACAAATATTACTCCCTC 57.961 37.037 0.00 0.00 35.92 4.30
3387 10013 7.989170 CCGGTTTACTAACAAATATTACTCCCT 59.011 37.037 0.00 0.00 35.92 4.20
3388 10014 7.986889 TCCGGTTTACTAACAAATATTACTCCC 59.013 37.037 0.00 0.00 35.92 4.30
3389 10015 8.947055 TCCGGTTTACTAACAAATATTACTCC 57.053 34.615 0.00 0.00 35.92 3.85
3395 10021 9.063615 GGATTGATCCGGTTTACTAACAAATAT 57.936 33.333 0.00 0.00 37.19 1.28
3396 10022 8.441312 GGATTGATCCGGTTTACTAACAAATA 57.559 34.615 0.00 0.00 37.19 1.40
3397 10023 7.329588 GGATTGATCCGGTTTACTAACAAAT 57.670 36.000 0.00 0.00 37.19 2.32
3398 10024 6.746745 GGATTGATCCGGTTTACTAACAAA 57.253 37.500 0.00 0.00 37.19 2.83


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

AutoCloner maintained by Alex Coulton.