Multiple sequence alignment - TraesCS2A01G250800

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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 TraesCS2A01G250800 chr2A 100.000 5145 0 0 1 5145 378854251 378849107 0.000000e+00 9502
1 TraesCS2A01G250800 chr2A 84.236 203 13 9 3164 3348 183787505 183787304 4.090000e-41 180
2 TraesCS2A01G250800 chr2A 80.292 137 24 3 2043 2177 711970081 711970216 3.280000e-17 100
3 TraesCS2A01G250800 chr2B 96.067 1068 33 6 1337 2402 356596281 356595221 0.000000e+00 1731
4 TraesCS2A01G250800 chr2B 94.762 1050 30 12 3341 4375 356595229 356594190 0.000000e+00 1611
5 TraesCS2A01G250800 chr2B 90.240 1250 48 19 1 1214 356597762 356596551 0.000000e+00 1565
6 TraesCS2A01G250800 chr2B 91.454 784 36 6 4365 5145 356583906 356583151 0.000000e+00 1048
7 TraesCS2A01G250800 chr2B 88.281 768 59 17 2605 3348 578991834 578992594 0.000000e+00 891
8 TraesCS2A01G250800 chr2B 91.954 87 6 1 3263 3348 559176038 559175952 2.520000e-23 121
9 TraesCS2A01G250800 chr2D 91.193 1249 39 28 1 1214 301820414 301819202 0.000000e+00 1631
10 TraesCS2A01G250800 chr2D 95.088 855 13 15 3341 4167 301817922 301817069 0.000000e+00 1319
11 TraesCS2A01G250800 chr2D 95.189 769 16 3 1634 2402 301818661 301817914 0.000000e+00 1195
12 TraesCS2A01G250800 chr2D 93.323 674 34 6 4479 5145 301763410 301762741 0.000000e+00 985
13 TraesCS2A01G250800 chr2D 87.273 770 67 18 2604 3352 380137214 380137973 0.000000e+00 850
14 TraesCS2A01G250800 chr2D 95.113 266 9 1 1337 1602 301818919 301818658 2.870000e-112 416
15 TraesCS2A01G250800 chr2D 94.737 209 8 2 4277 4483 301817036 301816829 6.430000e-84 322
16 TraesCS2A01G250800 chr2D 96.774 124 4 0 1217 1340 301819159 301819036 1.880000e-49 207
17 TraesCS2A01G250800 chr2D 82.308 130 21 2 2049 2177 572734003 572734131 1.510000e-20 111
18 TraesCS2A01G250800 chr7A 94.645 747 33 5 2604 3348 614733873 614733132 0.000000e+00 1151
19 TraesCS2A01G250800 chr7A 90.937 662 51 7 2604 3262 29429261 29428606 0.000000e+00 881
20 TraesCS2A01G250800 chr7A 95.187 187 8 1 2418 2604 614733913 614733728 1.400000e-75 294
21 TraesCS2A01G250800 chr7A 90.141 213 15 4 2401 2609 29429322 29429112 6.560000e-69 272
22 TraesCS2A01G250800 chr1D 89.323 768 52 15 2604 3348 448968421 448967661 0.000000e+00 937
23 TraesCS2A01G250800 chr1D 93.048 187 13 0 2418 2604 448968461 448968275 1.830000e-69 274
24 TraesCS2A01G250800 chr3A 89.207 769 49 16 2604 3348 182115898 182116656 0.000000e+00 929
25 TraesCS2A01G250800 chr3A 89.077 769 50 12 2604 3348 609669575 609670333 0.000000e+00 924
26 TraesCS2A01G250800 chr3A 93.583 187 12 0 2418 2604 182115858 182116044 3.920000e-71 279
27 TraesCS2A01G250800 chr3A 92.347 196 13 2 2410 2604 609669527 609669721 1.410000e-70 278
28 TraesCS2A01G250800 chr5A 88.182 770 60 16 2604 3349 110293688 110294450 0.000000e+00 889
29 TraesCS2A01G250800 chr5A 77.405 447 74 18 3687 4115 609871978 609872415 1.850000e-59 241
30 TraesCS2A01G250800 chr5D 87.906 769 61 17 2604 3348 401866712 401865952 0.000000e+00 876
31 TraesCS2A01G250800 chr5D 91.837 196 14 2 2411 2604 401866761 401866566 6.560000e-69 272
32 TraesCS2A01G250800 chr5D 78.670 436 73 18 3687 4115 488863900 488864322 6.560000e-69 272
33 TraesCS2A01G250800 chr7D 87.891 768 61 16 2605 3348 63050306 63049547 0.000000e+00 874
34 TraesCS2A01G250800 chr3D 85.176 769 51 26 2603 3348 290312597 290311869 0.000000e+00 730
35 TraesCS2A01G250800 chr3D 91.534 189 15 1 2415 2602 290312640 290312452 5.110000e-65 259
36 TraesCS2A01G250800 chr3D 90.426 94 8 1 3263 3356 448123409 448123317 7.000000e-24 122
37 TraesCS2A01G250800 chr7B 82.041 774 77 21 2604 3351 707864920 707864183 2.050000e-168 603
38 TraesCS2A01G250800 chr1A 79.372 732 75 32 2669 3354 393013936 393013235 3.650000e-121 446
39 TraesCS2A01G250800 chr1A 93.048 187 13 0 2418 2604 408812038 408811852 1.830000e-69 274
40 TraesCS2A01G250800 chr1A 91.623 191 15 1 2415 2604 131687611 131687421 3.950000e-66 263
41 TraesCS2A01G250800 chr4A 84.729 203 13 4 3164 3349 526274150 526274351 2.450000e-43 187


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 TraesCS2A01G250800 chr2A 378849107 378854251 5144 True 9502.000000 9502 100.000000 1 5145 1 chr2A.!!$R2 5144
1 TraesCS2A01G250800 chr2B 356594190 356597762 3572 True 1635.666667 1731 93.689667 1 4375 3 chr2B.!!$R3 4374
2 TraesCS2A01G250800 chr2B 356583151 356583906 755 True 1048.000000 1048 91.454000 4365 5145 1 chr2B.!!$R1 780
3 TraesCS2A01G250800 chr2B 578991834 578992594 760 False 891.000000 891 88.281000 2605 3348 1 chr2B.!!$F1 743
4 TraesCS2A01G250800 chr2D 301762741 301763410 669 True 985.000000 985 93.323000 4479 5145 1 chr2D.!!$R1 666
5 TraesCS2A01G250800 chr2D 380137214 380137973 759 False 850.000000 850 87.273000 2604 3352 1 chr2D.!!$F1 748
6 TraesCS2A01G250800 chr2D 301816829 301820414 3585 True 848.333333 1631 94.682333 1 4483 6 chr2D.!!$R2 4482
7 TraesCS2A01G250800 chr7A 614733132 614733913 781 True 722.500000 1151 94.916000 2418 3348 2 chr7A.!!$R2 930
8 TraesCS2A01G250800 chr7A 29428606 29429322 716 True 576.500000 881 90.539000 2401 3262 2 chr7A.!!$R1 861
9 TraesCS2A01G250800 chr1D 448967661 448968461 800 True 605.500000 937 91.185500 2418 3348 2 chr1D.!!$R1 930
10 TraesCS2A01G250800 chr3A 182115858 182116656 798 False 604.000000 929 91.395000 2418 3348 2 chr3A.!!$F1 930
11 TraesCS2A01G250800 chr3A 609669527 609670333 806 False 601.000000 924 90.712000 2410 3348 2 chr3A.!!$F2 938
12 TraesCS2A01G250800 chr5A 110293688 110294450 762 False 889.000000 889 88.182000 2604 3349 1 chr5A.!!$F1 745
13 TraesCS2A01G250800 chr5D 401865952 401866761 809 True 574.000000 876 89.871500 2411 3348 2 chr5D.!!$R1 937
14 TraesCS2A01G250800 chr7D 63049547 63050306 759 True 874.000000 874 87.891000 2605 3348 1 chr7D.!!$R1 743
15 TraesCS2A01G250800 chr3D 290311869 290312640 771 True 494.500000 730 88.355000 2415 3348 2 chr3D.!!$R2 933
16 TraesCS2A01G250800 chr7B 707864183 707864920 737 True 603.000000 603 82.041000 2604 3351 1 chr7B.!!$R1 747
17 TraesCS2A01G250800 chr1A 393013235 393013936 701 True 446.000000 446 79.372000 2669 3354 1 chr1A.!!$R2 685

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
720 741 0.855400 ATCCCCTTCCCCACCACAAT 60.855 55.0 0.00 0.0 0.00 2.71 F
723 744 1.509548 CCCTTCCCCACCACAATCCT 61.510 60.0 0.00 0.0 0.00 3.24 F
2505 2714 1.497161 AGCGATTTAGGCCAGGTACT 58.503 50.0 5.01 0.0 43.88 2.73 F
2522 2731 0.690762 ACTTGTACGTTGATGGGCCT 59.309 50.0 4.53 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2503 2712 0.690762 AGGCCCATCAACGTACAAGT 59.309 50.000 0.00 0.00 0.00 3.16 R
2511 2720 1.138859 GCCCATAAAAGGCCCATCAAC 59.861 52.381 0.00 0.00 45.16 3.18 R
3890 4326 0.755686 CTAGCTAGCCCAGGACAAGG 59.244 60.000 12.13 0.00 0.00 3.61 R
4195 4660 2.343544 GCAGTTACGTACGTAAGCCTTG 59.656 50.000 34.51 27.98 40.69 3.61 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
79 83 5.460419 GTGTCACAGAAGTACAGACTTGAAG 59.540 44.000 0.00 0.00 46.23 3.02
121 125 6.422100 GCTGACTGAGGTACATGTATTATGTG 59.578 42.308 9.18 1.60 33.76 3.21
171 175 3.004752 ACATTGACATGGGTTAGGCTC 57.995 47.619 0.00 0.00 34.27 4.70
219 223 6.405176 CGCATGACCAGCATTCTCTATCTATA 60.405 42.308 0.00 0.00 34.15 1.31
224 228 9.716531 TGACCAGCATTCTCTATCTATATTTTG 57.283 33.333 0.00 0.00 0.00 2.44
266 271 2.079925 GCTTTGAAGATTCTGGCGACT 58.920 47.619 0.00 0.00 0.00 4.18
290 295 6.779860 TGTTGAGGATGATGATGATGATGAT 58.220 36.000 0.00 0.00 0.00 2.45
291 296 6.655003 TGTTGAGGATGATGATGATGATGATG 59.345 38.462 0.00 0.00 0.00 3.07
292 297 6.620877 TGAGGATGATGATGATGATGATGA 57.379 37.500 0.00 0.00 0.00 2.92
293 298 7.200434 TGAGGATGATGATGATGATGATGAT 57.800 36.000 0.00 0.00 0.00 2.45
294 299 7.050377 TGAGGATGATGATGATGATGATGATG 58.950 38.462 0.00 0.00 0.00 3.07
296 301 6.069381 AGGATGATGATGATGATGATGATGGT 60.069 38.462 0.00 0.00 0.00 3.55
297 302 6.038714 GGATGATGATGATGATGATGATGGTG 59.961 42.308 0.00 0.00 0.00 4.17
298 303 4.700213 TGATGATGATGATGATGATGGTGC 59.300 41.667 0.00 0.00 0.00 5.01
299 304 4.093472 TGATGATGATGATGATGGTGCA 57.907 40.909 0.00 0.00 0.00 4.57
300 305 4.072131 TGATGATGATGATGATGGTGCAG 58.928 43.478 0.00 0.00 0.00 4.41
301 306 3.849563 TGATGATGATGATGGTGCAGA 57.150 42.857 0.00 0.00 0.00 4.26
302 307 4.367039 TGATGATGATGATGGTGCAGAT 57.633 40.909 0.00 0.00 0.00 2.90
303 308 5.492855 TGATGATGATGATGGTGCAGATA 57.507 39.130 0.00 0.00 0.00 1.98
304 309 6.062258 TGATGATGATGATGGTGCAGATAT 57.938 37.500 0.00 0.00 0.00 1.63
305 310 6.113411 TGATGATGATGATGGTGCAGATATC 58.887 40.000 0.00 0.00 0.00 1.63
306 311 5.492855 TGATGATGATGGTGCAGATATCA 57.507 39.130 5.32 9.18 35.52 2.15
307 312 6.062258 TGATGATGATGGTGCAGATATCAT 57.938 37.500 16.05 16.05 42.50 2.45
308 313 6.481643 TGATGATGATGGTGCAGATATCATT 58.518 36.000 16.78 6.66 40.56 2.57
349 354 2.649816 AGAAAGTAGCCCCAGGAAACAT 59.350 45.455 0.00 0.00 0.00 2.71
494 515 1.474320 CGAGGGGATAAATGTGGCGAA 60.474 52.381 0.00 0.00 0.00 4.70
594 615 2.587060 TCTCATCCATACAACCCCCT 57.413 50.000 0.00 0.00 0.00 4.79
595 616 2.408565 TCTCATCCATACAACCCCCTC 58.591 52.381 0.00 0.00 0.00 4.30
596 617 2.126882 CTCATCCATACAACCCCCTCA 58.873 52.381 0.00 0.00 0.00 3.86
597 618 2.713167 CTCATCCATACAACCCCCTCAT 59.287 50.000 0.00 0.00 0.00 2.90
598 619 2.711009 TCATCCATACAACCCCCTCATC 59.289 50.000 0.00 0.00 0.00 2.92
599 620 2.587060 TCCATACAACCCCCTCATCT 57.413 50.000 0.00 0.00 0.00 2.90
600 621 2.408565 TCCATACAACCCCCTCATCTC 58.591 52.381 0.00 0.00 0.00 2.75
607 628 1.619298 ACCCCCTCATCTCTCTCTCT 58.381 55.000 0.00 0.00 0.00 3.10
611 632 2.713167 CCCCTCATCTCTCTCTCTCTCT 59.287 54.545 0.00 0.00 0.00 3.10
621 642 3.008923 TCTCTCTCTCTCTCTCAACTGCA 59.991 47.826 0.00 0.00 0.00 4.41
649 670 5.622770 ATTCTCCGTTGTATTGTTTGTCC 57.377 39.130 0.00 0.00 0.00 4.02
720 741 0.855400 ATCCCCTTCCCCACCACAAT 60.855 55.000 0.00 0.00 0.00 2.71
723 744 1.509548 CCCTTCCCCACCACAATCCT 61.510 60.000 0.00 0.00 0.00 3.24
885 921 5.657470 TCTTTCTTTGTCTTGATCGTGTG 57.343 39.130 0.00 0.00 0.00 3.82
916 956 2.422276 GTGTTTCACCCACTTGCATC 57.578 50.000 0.00 0.00 0.00 3.91
930 974 7.121315 ACCCACTTGCATCTAGTAATTTTCTTC 59.879 37.037 0.00 0.00 0.00 2.87
1152 1196 2.352422 CTGTAAGCTGCCTGCCCA 59.648 61.111 0.00 0.00 44.23 5.36
1153 1197 1.748122 CTGTAAGCTGCCTGCCCAG 60.748 63.158 0.00 0.00 44.23 4.45
1214 1258 4.737765 TCTGTTTTGTTTGTAGAAATGCGC 59.262 37.500 0.00 0.00 0.00 6.09
1215 1259 4.677584 TGTTTTGTTTGTAGAAATGCGCT 58.322 34.783 9.73 0.00 0.00 5.92
1285 1369 2.791560 CGCATCTAATTCACCAGAGACG 59.208 50.000 0.00 0.00 0.00 4.18
1296 1380 6.525578 TTCACCAGAGACGACAAACTATAT 57.474 37.500 0.00 0.00 0.00 0.86
1325 1409 6.610741 AATTAAAGAGGACGATTCTGATGC 57.389 37.500 0.00 0.00 0.00 3.91
1366 1570 6.910536 ATAGGTTGCTCAAGTAATTTCTCG 57.089 37.500 0.00 0.00 0.00 4.04
1399 1603 7.286775 CCTTTCAGAGCTAGACTTACTAATCCT 59.713 40.741 0.00 0.00 0.00 3.24
1431 1635 5.083533 TGATTTACCCATCATTGTTTGCC 57.916 39.130 0.00 0.00 0.00 4.52
1439 1643 4.128643 CCATCATTGTTTGCCTGTGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
1524 1728 2.652590 GGATTCAAGCTCTCAATGCCT 58.347 47.619 0.00 0.00 0.00 4.75
1592 1796 5.410924 TGGTATTGTCTCTCTGAAATGTCG 58.589 41.667 0.00 0.00 0.00 4.35
1607 1811 6.676950 TGAAATGTCGTTTGATTGTGCTTAT 58.323 32.000 0.00 0.00 0.00 1.73
1608 1812 7.811653 TGAAATGTCGTTTGATTGTGCTTATA 58.188 30.769 0.00 0.00 0.00 0.98
1610 1814 9.929722 GAAATGTCGTTTGATTGTGCTTATATA 57.070 29.630 0.00 0.00 0.00 0.86
1853 2058 4.256920 TGAGGTGCTAAAGAAAGATGCTC 58.743 43.478 0.00 0.00 0.00 4.26
2012 2217 7.117523 CCTTGTCTCTCTCATTTTGTTACTCAG 59.882 40.741 0.00 0.00 0.00 3.35
2181 2386 4.141711 GCTGATATCAAGAACAGGTACCCA 60.142 45.833 8.74 0.00 0.00 4.51
2407 2612 5.483685 TGGACCAGGTGCATAATCTATAC 57.516 43.478 10.31 0.00 0.00 1.47
2414 2619 9.507381 ACCAGGTGCATAATCTATACCTATATT 57.493 33.333 0.00 0.00 39.63 1.28
2457 2666 8.185506 AGGAAATAGGTATTTTTCGTTTGGTT 57.814 30.769 0.00 0.00 36.13 3.67
2458 2667 8.644216 AGGAAATAGGTATTTTTCGTTTGGTTT 58.356 29.630 0.00 0.00 36.13 3.27
2459 2668 9.911138 GGAAATAGGTATTTTTCGTTTGGTTTA 57.089 29.630 0.00 0.00 36.13 2.01
2463 2672 6.973843 AGGTATTTTTCGTTTGGTTTAGTCC 58.026 36.000 0.00 0.00 0.00 3.85
2464 2673 6.774170 AGGTATTTTTCGTTTGGTTTAGTCCT 59.226 34.615 0.00 0.00 0.00 3.85
2465 2674 7.286087 AGGTATTTTTCGTTTGGTTTAGTCCTT 59.714 33.333 0.00 0.00 0.00 3.36
2466 2675 7.922278 GGTATTTTTCGTTTGGTTTAGTCCTTT 59.078 33.333 0.00 0.00 0.00 3.11
2467 2676 9.304731 GTATTTTTCGTTTGGTTTAGTCCTTTT 57.695 29.630 0.00 0.00 0.00 2.27
2468 2677 7.815398 TTTTTCGTTTGGTTTAGTCCTTTTC 57.185 32.000 0.00 0.00 0.00 2.29
2469 2678 4.799419 TCGTTTGGTTTAGTCCTTTTCG 57.201 40.909 0.00 0.00 0.00 3.46
2470 2679 4.190772 TCGTTTGGTTTAGTCCTTTTCGT 58.809 39.130 0.00 0.00 0.00 3.85
2471 2680 4.635324 TCGTTTGGTTTAGTCCTTTTCGTT 59.365 37.500 0.00 0.00 0.00 3.85
2472 2681 5.123661 TCGTTTGGTTTAGTCCTTTTCGTTT 59.876 36.000 0.00 0.00 0.00 3.60
2473 2682 5.228427 CGTTTGGTTTAGTCCTTTTCGTTTG 59.772 40.000 0.00 0.00 0.00 2.93
2474 2683 4.904253 TGGTTTAGTCCTTTTCGTTTGG 57.096 40.909 0.00 0.00 0.00 3.28
2475 2684 3.067040 TGGTTTAGTCCTTTTCGTTTGGC 59.933 43.478 0.00 0.00 0.00 4.52
2476 2685 3.317149 GGTTTAGTCCTTTTCGTTTGGCT 59.683 43.478 0.00 0.00 0.00 4.75
2477 2686 4.202080 GGTTTAGTCCTTTTCGTTTGGCTT 60.202 41.667 0.00 0.00 0.00 4.35
2478 2687 5.008911 GGTTTAGTCCTTTTCGTTTGGCTTA 59.991 40.000 0.00 0.00 0.00 3.09
2479 2688 5.678132 TTAGTCCTTTTCGTTTGGCTTAC 57.322 39.130 0.00 0.00 0.00 2.34
2480 2689 3.547746 AGTCCTTTTCGTTTGGCTTACA 58.452 40.909 0.00 0.00 0.00 2.41
2481 2690 3.314357 AGTCCTTTTCGTTTGGCTTACAC 59.686 43.478 0.00 0.00 0.00 2.90
2482 2691 3.065648 GTCCTTTTCGTTTGGCTTACACA 59.934 43.478 0.00 0.00 0.00 3.72
2483 2692 3.886505 TCCTTTTCGTTTGGCTTACACAT 59.113 39.130 0.00 0.00 0.00 3.21
2484 2693 4.339814 TCCTTTTCGTTTGGCTTACACATT 59.660 37.500 0.00 0.00 0.00 2.71
2485 2694 5.531659 TCCTTTTCGTTTGGCTTACACATTA 59.468 36.000 0.00 0.00 0.00 1.90
2486 2695 6.039493 TCCTTTTCGTTTGGCTTACACATTAA 59.961 34.615 0.00 0.00 0.00 1.40
2487 2696 6.362283 CCTTTTCGTTTGGCTTACACATTAAG 59.638 38.462 0.00 0.00 0.00 1.85
2488 2697 4.413495 TCGTTTGGCTTACACATTAAGC 57.587 40.909 7.37 7.37 46.64 3.09
2497 2706 5.205565 GCTTACACATTAAGCGATTTAGGC 58.794 41.667 0.00 0.00 40.19 3.93
2498 2707 5.744666 TTACACATTAAGCGATTTAGGCC 57.255 39.130 0.00 0.00 0.00 5.19
2499 2708 3.616219 ACACATTAAGCGATTTAGGCCA 58.384 40.909 5.01 0.00 0.00 5.36
2500 2709 3.627577 ACACATTAAGCGATTTAGGCCAG 59.372 43.478 5.01 0.00 0.00 4.85
2501 2710 3.003689 CACATTAAGCGATTTAGGCCAGG 59.996 47.826 5.01 0.00 0.00 4.45
2502 2711 3.214328 CATTAAGCGATTTAGGCCAGGT 58.786 45.455 5.01 0.00 0.00 4.00
2503 2712 4.141574 ACATTAAGCGATTTAGGCCAGGTA 60.142 41.667 5.01 0.00 0.00 3.08
2504 2713 2.327200 AAGCGATTTAGGCCAGGTAC 57.673 50.000 5.01 0.00 0.00 3.34
2505 2714 1.497161 AGCGATTTAGGCCAGGTACT 58.503 50.000 5.01 0.00 43.88 2.73
2506 2715 1.838077 AGCGATTTAGGCCAGGTACTT 59.162 47.619 5.01 0.00 34.60 2.24
2507 2716 1.940613 GCGATTTAGGCCAGGTACTTG 59.059 52.381 5.01 0.00 34.60 3.16
2508 2717 2.679930 GCGATTTAGGCCAGGTACTTGT 60.680 50.000 5.01 0.00 34.60 3.16
2509 2718 3.431207 GCGATTTAGGCCAGGTACTTGTA 60.431 47.826 5.01 0.00 34.60 2.41
2510 2719 4.117685 CGATTTAGGCCAGGTACTTGTAC 58.882 47.826 5.01 2.55 34.60 2.90
2511 2720 3.598019 TTTAGGCCAGGTACTTGTACG 57.402 47.619 5.01 0.00 34.60 3.67
2512 2721 2.220653 TAGGCCAGGTACTTGTACGT 57.779 50.000 5.01 0.00 34.60 3.57
2513 2722 1.345063 AGGCCAGGTACTTGTACGTT 58.655 50.000 5.01 0.00 34.60 3.99
2514 2723 1.001633 AGGCCAGGTACTTGTACGTTG 59.998 52.381 5.01 5.56 34.60 4.10
2515 2724 1.001181 GGCCAGGTACTTGTACGTTGA 59.999 52.381 0.00 0.00 34.60 3.18
2516 2725 2.354403 GGCCAGGTACTTGTACGTTGAT 60.354 50.000 0.00 0.00 34.60 2.57
2517 2726 2.671396 GCCAGGTACTTGTACGTTGATG 59.329 50.000 4.10 4.71 34.60 3.07
2518 2727 3.259064 CCAGGTACTTGTACGTTGATGG 58.741 50.000 4.10 8.44 34.60 3.51
2519 2728 3.259064 CAGGTACTTGTACGTTGATGGG 58.741 50.000 0.00 0.00 34.60 4.00
2520 2729 2.004733 GGTACTTGTACGTTGATGGGC 58.995 52.381 0.00 0.00 0.00 5.36
2521 2730 2.004733 GTACTTGTACGTTGATGGGCC 58.995 52.381 0.00 0.00 0.00 5.80
2522 2731 0.690762 ACTTGTACGTTGATGGGCCT 59.309 50.000 4.53 0.00 0.00 5.19
2523 2732 1.073284 ACTTGTACGTTGATGGGCCTT 59.927 47.619 4.53 0.00 0.00 4.35
2524 2733 2.159382 CTTGTACGTTGATGGGCCTTT 58.841 47.619 4.53 0.00 0.00 3.11
2525 2734 2.279935 TGTACGTTGATGGGCCTTTT 57.720 45.000 4.53 0.00 0.00 2.27
2526 2735 3.420300 TGTACGTTGATGGGCCTTTTA 57.580 42.857 4.53 0.00 0.00 1.52
2527 2736 3.958018 TGTACGTTGATGGGCCTTTTAT 58.042 40.909 4.53 0.00 0.00 1.40
2528 2737 3.692101 TGTACGTTGATGGGCCTTTTATG 59.308 43.478 4.53 0.00 0.00 1.90
2529 2738 2.099405 ACGTTGATGGGCCTTTTATGG 58.901 47.619 4.53 0.00 0.00 2.74
2530 2739 1.408702 CGTTGATGGGCCTTTTATGGG 59.591 52.381 4.53 0.00 0.00 4.00
2544 2753 6.984474 GCCTTTTATGGGCTTTTATAGAAACC 59.016 38.462 0.00 0.00 45.57 3.27
2545 2754 7.200455 CCTTTTATGGGCTTTTATAGAAACCG 58.800 38.462 0.00 0.00 0.00 4.44
2546 2755 7.147966 CCTTTTATGGGCTTTTATAGAAACCGT 60.148 37.037 0.00 0.00 0.00 4.83
2547 2756 6.687081 TTATGGGCTTTTATAGAAACCGTG 57.313 37.500 0.00 0.00 0.00 4.94
2548 2757 4.289238 TGGGCTTTTATAGAAACCGTGA 57.711 40.909 0.00 0.00 0.00 4.35
2549 2758 4.653868 TGGGCTTTTATAGAAACCGTGAA 58.346 39.130 0.00 0.00 0.00 3.18
2550 2759 5.071370 TGGGCTTTTATAGAAACCGTGAAA 58.929 37.500 0.00 0.00 0.00 2.69
2551 2760 5.535406 TGGGCTTTTATAGAAACCGTGAAAA 59.465 36.000 0.00 0.00 0.00 2.29
2552 2761 6.040616 TGGGCTTTTATAGAAACCGTGAAAAA 59.959 34.615 0.00 0.00 0.00 1.94
2553 2762 7.094631 GGGCTTTTATAGAAACCGTGAAAAAT 58.905 34.615 0.00 0.00 0.00 1.82
2554 2763 8.245491 GGGCTTTTATAGAAACCGTGAAAAATA 58.755 33.333 0.00 0.00 0.00 1.40
2555 2764 9.628746 GGCTTTTATAGAAACCGTGAAAAATAA 57.371 29.630 0.00 0.00 0.00 1.40
2584 2793 9.829507 AAGTCAAAATAAATCAACATTGTGGAA 57.170 25.926 0.00 0.00 0.00 3.53
2585 2794 9.829507 AGTCAAAATAAATCAACATTGTGGAAA 57.170 25.926 0.00 0.00 0.00 3.13
2594 2803 8.954950 AATCAACATTGTGGAAATTAAACACA 57.045 26.923 0.00 5.87 42.77 3.72
2595 2804 9.558396 AATCAACATTGTGGAAATTAAACACAT 57.442 25.926 0.00 0.90 43.75 3.21
2596 2805 8.362860 TCAACATTGTGGAAATTAAACACATG 57.637 30.769 9.63 11.29 43.75 3.21
2597 2806 8.200120 TCAACATTGTGGAAATTAAACACATGA 58.800 29.630 0.00 8.10 43.75 3.07
2598 2807 7.945033 ACATTGTGGAAATTAAACACATGAC 57.055 32.000 0.00 0.00 43.75 3.06
2599 2808 6.928492 ACATTGTGGAAATTAAACACATGACC 59.072 34.615 0.00 0.00 43.75 4.02
2600 2809 6.723298 TTGTGGAAATTAAACACATGACCT 57.277 33.333 0.00 0.00 43.75 3.85
2601 2810 6.325919 TGTGGAAATTAAACACATGACCTC 57.674 37.500 0.00 0.00 39.92 3.85
2602 2811 5.242838 TGTGGAAATTAAACACATGACCTCC 59.757 40.000 0.00 0.00 39.92 4.30
3062 3457 9.561069 AAAGATCTGTAGACTTAAATGTGTTGT 57.439 29.630 0.00 0.00 0.00 3.32
3236 3637 3.955771 ACACGACTAAATTGCAACGTT 57.044 38.095 0.00 1.33 31.82 3.99
3531 3957 8.475639 TCTTACTTGAACTTGACAACTAACTCT 58.524 33.333 0.00 0.00 0.00 3.24
3582 4008 2.740981 GTGGCTCTGAACTGAAGATGTG 59.259 50.000 0.00 0.00 0.00 3.21
3590 4016 2.191128 ACTGAAGATGTGGCCTTGTC 57.809 50.000 3.32 0.00 0.00 3.18
3950 4407 2.493035 TGATATTAGGTGTGCATGGCG 58.507 47.619 0.00 0.00 0.00 5.69
4167 4624 0.168128 GGAACCAAATCAAGTCGGCG 59.832 55.000 0.00 0.00 0.00 6.46
4195 4660 1.226888 GGCGGCCGTATATCGATCC 60.227 63.158 28.70 12.21 42.86 3.36
4202 4667 2.353803 GCCGTATATCGATCCAAGGCTT 60.354 50.000 21.20 0.00 42.86 4.35
4214 4679 2.819608 TCCAAGGCTTACGTACGTAACT 59.180 45.455 31.35 25.12 35.88 2.24
4219 4684 2.280708 GGCTTACGTACGTAACTGCATG 59.719 50.000 34.13 25.43 35.09 4.06
4225 4690 7.842609 TTACGTACGTAACTGCATGGATGCA 62.843 44.000 31.35 13.50 46.12 3.96
4328 4794 3.869832 GTGATATGGCATGGATCGATCAG 59.130 47.826 25.93 15.87 0.00 2.90
4451 4919 4.077184 TCTACCGGCCGCCAACAG 62.077 66.667 22.85 7.58 0.00 3.16
4540 5008 7.487189 CCAATCTCATGCTTGAAAATACAAGTC 59.513 37.037 3.65 0.00 45.98 3.01
4560 5028 8.695456 ACAAGTCTCAAGAACAAAAATAACCAT 58.305 29.630 0.00 0.00 0.00 3.55
4569 5037 8.292444 AGAACAAAAATAACCATATGCTAGCA 57.708 30.769 21.85 21.85 0.00 3.49
4601 5070 3.614630 CGTATGTGTCTTTAACCACCGGA 60.615 47.826 9.46 0.00 0.00 5.14
4612 5081 1.293062 ACCACCGGACTAGGACTAGA 58.707 55.000 9.46 0.00 36.97 2.43
4623 5092 0.397816 AGGACTAGAAGGGCATCGCT 60.398 55.000 0.00 0.00 0.00 4.93
4773 5242 4.821589 GCTCCCTGACGAAGCGGG 62.822 72.222 0.00 0.00 39.41 6.13
4830 5299 0.384669 GCTGGCTTGGATTCTGATGC 59.615 55.000 0.00 0.00 0.00 3.91
4987 5463 2.191802 TGCGCACACATTTCAAACAAG 58.808 42.857 5.66 0.00 0.00 3.16
5090 5567 7.252612 TCTGGTTGTCTATTTTGTATGGAGA 57.747 36.000 0.00 0.00 0.00 3.71
5095 5572 6.985188 TGTCTATTTTGTATGGAGACTTGC 57.015 37.500 0.00 0.00 37.89 4.01
5130 5608 9.162764 TGACTAATTGCTTAATTAAGTCAGACC 57.837 33.333 22.94 8.68 33.34 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.357878 GCACTTCATTTACCATCTCCAATGA 59.642 40.000 0.00 0.00 34.54 2.57
12 13 6.012658 TGTTTGCACTTCATTTACCATCTC 57.987 37.500 0.00 0.00 0.00 2.75
121 125 0.670162 TGGCTGCTTTGACTTCTTGC 59.330 50.000 0.00 0.00 0.00 4.01
171 175 8.543774 TGCGACCAACAATTAAAGTTATTTTTG 58.456 29.630 0.00 0.00 0.00 2.44
194 198 2.229675 TAGAGAATGCTGGTCATGCG 57.770 50.000 0.00 0.00 35.77 4.73
224 228 7.269477 AGCCAGCTTCATCAGTTATTAATTC 57.731 36.000 0.00 0.00 0.00 2.17
243 247 1.131883 CGCCAGAATCTTCAAAGCCAG 59.868 52.381 0.00 0.00 0.00 4.85
266 271 6.182507 TCATCATCATCATCATCCTCAACA 57.817 37.500 0.00 0.00 0.00 3.33
290 295 7.455891 AGACAATAATGATATCTGCACCATCA 58.544 34.615 3.98 3.35 33.47 3.07
291 296 7.918536 AGACAATAATGATATCTGCACCATC 57.081 36.000 3.98 0.00 0.00 3.51
292 297 7.722728 ACAAGACAATAATGATATCTGCACCAT 59.277 33.333 3.98 0.00 0.00 3.55
293 298 7.056006 ACAAGACAATAATGATATCTGCACCA 58.944 34.615 3.98 0.00 0.00 4.17
294 299 7.443575 AGACAAGACAATAATGATATCTGCACC 59.556 37.037 3.98 0.00 0.00 5.01
296 301 7.658982 GGAGACAAGACAATAATGATATCTGCA 59.341 37.037 3.98 0.00 0.00 4.41
297 302 7.658982 TGGAGACAAGACAATAATGATATCTGC 59.341 37.037 3.98 0.00 37.44 4.26
336 341 0.038166 TCAGACATGTTTCCTGGGGC 59.962 55.000 11.83 0.00 0.00 5.80
349 354 0.615331 GATCAGGGGTGCTTCAGACA 59.385 55.000 0.00 0.00 0.00 3.41
494 515 2.311841 CAACCCTCCCTTCCCTACAAAT 59.688 50.000 0.00 0.00 0.00 2.32
594 615 5.426509 AGTTGAGAGAGAGAGAGAGAGATGA 59.573 44.000 0.00 0.00 0.00 2.92
595 616 5.526479 CAGTTGAGAGAGAGAGAGAGAGATG 59.474 48.000 0.00 0.00 0.00 2.90
596 617 5.678583 CAGTTGAGAGAGAGAGAGAGAGAT 58.321 45.833 0.00 0.00 0.00 2.75
597 618 4.623886 GCAGTTGAGAGAGAGAGAGAGAGA 60.624 50.000 0.00 0.00 0.00 3.10
598 619 3.624861 GCAGTTGAGAGAGAGAGAGAGAG 59.375 52.174 0.00 0.00 0.00 3.20
599 620 3.008923 TGCAGTTGAGAGAGAGAGAGAGA 59.991 47.826 0.00 0.00 0.00 3.10
600 621 3.127548 GTGCAGTTGAGAGAGAGAGAGAG 59.872 52.174 0.00 0.00 0.00 3.20
607 628 6.705302 AGAATAATTGTGCAGTTGAGAGAGA 58.295 36.000 0.00 0.00 0.00 3.10
611 632 4.631377 CGGAGAATAATTGTGCAGTTGAGA 59.369 41.667 0.00 0.00 0.00 3.27
621 642 8.573035 ACAAACAATACAACGGAGAATAATTGT 58.427 29.630 0.00 0.00 37.60 2.71
649 670 0.592637 TCAAGGTTTCTGTGCATGCG 59.407 50.000 14.09 0.00 0.00 4.73
720 741 3.844804 GGAAGGAAGGAAGGAACTAAGGA 59.155 47.826 0.00 0.00 38.49 3.36
723 744 2.917600 GGGGAAGGAAGGAAGGAACTAA 59.082 50.000 0.00 0.00 38.49 2.24
930 974 4.398673 AGGCGTAGTTAGTTACCTGAAGAG 59.601 45.833 0.00 0.00 0.00 2.85
947 991 3.749088 CCATACAAACAACAAGAGGCGTA 59.251 43.478 0.00 0.00 0.00 4.42
996 1040 5.047872 TGTGACATTGGTGATCTCCATTTTG 60.048 40.000 16.93 15.83 37.33 2.44
1044 1088 4.162320 TCGTAGATCATCTTGGGAAGCTTT 59.838 41.667 0.00 0.00 0.00 3.51
1152 1196 1.073923 AGAAAACGTCAAGGATGGGCT 59.926 47.619 0.00 0.00 0.00 5.19
1153 1197 1.534729 AGAAAACGTCAAGGATGGGC 58.465 50.000 0.00 0.00 0.00 5.36
1154 1198 2.488153 GGAAGAAAACGTCAAGGATGGG 59.512 50.000 0.00 0.00 0.00 4.00
1155 1199 2.488153 GGGAAGAAAACGTCAAGGATGG 59.512 50.000 0.00 0.00 0.00 3.51
1156 1200 3.058224 GTGGGAAGAAAACGTCAAGGATG 60.058 47.826 0.00 0.00 0.00 3.51
1214 1258 2.747446 CCCCGAAATTCAGTTGGTACAG 59.253 50.000 0.00 0.00 42.39 2.74
1215 1259 2.106857 ACCCCGAAATTCAGTTGGTACA 59.893 45.455 0.00 0.00 0.00 2.90
1296 1380 7.768582 TCAGAATCGTCCTCTTTAATTATTGCA 59.231 33.333 0.00 0.00 0.00 4.08
1366 1570 6.648879 AGTCTAGCTCTGAAAGGATGTATC 57.351 41.667 0.00 0.00 0.00 2.24
1399 1603 9.613428 CAATGATGGGTAAATCAGAAGTACTAA 57.387 33.333 0.00 0.00 39.84 2.24
1407 1611 5.105392 GGCAAACAATGATGGGTAAATCAGA 60.105 40.000 0.00 0.00 39.84 3.27
1431 1635 1.877443 CGGAACCTACCCAAAACACAG 59.123 52.381 0.00 0.00 0.00 3.66
1524 1728 2.158475 GGCAGTGGGGGAAATCATGATA 60.158 50.000 9.04 0.00 0.00 2.15
1614 1818 7.011382 CCTACAACCTTATATACTCCCAGAGT 58.989 42.308 2.38 2.38 45.54 3.24
1615 1819 7.239438 TCCTACAACCTTATATACTCCCAGAG 58.761 42.308 0.00 0.00 35.52 3.35
1616 1820 7.170554 TCCTACAACCTTATATACTCCCAGA 57.829 40.000 0.00 0.00 0.00 3.86
1617 1821 7.850935 TTCCTACAACCTTATATACTCCCAG 57.149 40.000 0.00 0.00 0.00 4.45
1618 1822 8.808240 AATTCCTACAACCTTATATACTCCCA 57.192 34.615 0.00 0.00 0.00 4.37
1631 1835 6.649141 GGAACCATTTCAAAATTCCTACAACC 59.351 38.462 4.61 0.00 32.80 3.77
2012 2217 4.883585 TGAACTATGATCATTCACAAGCCC 59.116 41.667 14.65 1.29 33.85 5.19
2316 2521 2.419667 GCAAAACAAATCTGCAGCCAT 58.580 42.857 9.47 0.00 36.09 4.40
2377 2582 1.470996 GCACCTGGTCCATTTTGCCA 61.471 55.000 0.00 0.00 0.00 4.92
2380 2585 4.403432 AGATTATGCACCTGGTCCATTTTG 59.597 41.667 8.85 0.00 0.00 2.44
2446 2655 5.123661 ACGAAAAGGACTAAACCAAACGAAA 59.876 36.000 0.00 0.00 0.00 3.46
2449 2658 4.541085 ACGAAAAGGACTAAACCAAACG 57.459 40.909 0.00 0.00 0.00 3.60
2457 2666 5.007921 GTGTAAGCCAAACGAAAAGGACTAA 59.992 40.000 0.00 0.00 0.00 2.24
2458 2667 4.512571 GTGTAAGCCAAACGAAAAGGACTA 59.487 41.667 0.00 0.00 0.00 2.59
2459 2668 3.314357 GTGTAAGCCAAACGAAAAGGACT 59.686 43.478 0.00 0.00 0.00 3.85
2460 2669 3.065648 TGTGTAAGCCAAACGAAAAGGAC 59.934 43.478 0.00 0.00 0.00 3.85
2461 2670 3.280295 TGTGTAAGCCAAACGAAAAGGA 58.720 40.909 0.00 0.00 0.00 3.36
2462 2671 3.701532 TGTGTAAGCCAAACGAAAAGG 57.298 42.857 0.00 0.00 0.00 3.11
2463 2672 6.129194 GCTTAATGTGTAAGCCAAACGAAAAG 60.129 38.462 6.80 0.00 42.88 2.27
2464 2673 5.688176 GCTTAATGTGTAAGCCAAACGAAAA 59.312 36.000 6.80 0.00 42.88 2.29
2465 2674 5.216648 GCTTAATGTGTAAGCCAAACGAAA 58.783 37.500 6.80 0.00 42.88 3.46
2466 2675 4.611807 CGCTTAATGTGTAAGCCAAACGAA 60.612 41.667 11.43 0.00 45.09 3.85
2467 2676 3.120477 CGCTTAATGTGTAAGCCAAACGA 60.120 43.478 11.43 0.00 45.09 3.85
2468 2677 3.120477 TCGCTTAATGTGTAAGCCAAACG 60.120 43.478 11.43 0.00 45.09 3.60
2469 2678 4.413495 TCGCTTAATGTGTAAGCCAAAC 57.587 40.909 11.43 0.00 45.09 2.93
2470 2679 5.637006 AATCGCTTAATGTGTAAGCCAAA 57.363 34.783 11.43 0.33 45.09 3.28
2471 2680 5.637006 AAATCGCTTAATGTGTAAGCCAA 57.363 34.783 11.43 2.43 45.09 4.52
2472 2681 5.295787 CCTAAATCGCTTAATGTGTAAGCCA 59.704 40.000 11.43 0.82 45.09 4.75
2473 2682 5.748592 CCTAAATCGCTTAATGTGTAAGCC 58.251 41.667 11.43 0.00 45.09 4.35
2474 2683 5.205565 GCCTAAATCGCTTAATGTGTAAGC 58.794 41.667 7.83 7.83 44.61 3.09
2475 2684 5.295787 TGGCCTAAATCGCTTAATGTGTAAG 59.704 40.000 3.32 0.00 0.00 2.34
2476 2685 5.186942 TGGCCTAAATCGCTTAATGTGTAA 58.813 37.500 3.32 0.00 0.00 2.41
2477 2686 4.771903 TGGCCTAAATCGCTTAATGTGTA 58.228 39.130 3.32 0.00 0.00 2.90
2478 2687 3.616219 TGGCCTAAATCGCTTAATGTGT 58.384 40.909 3.32 0.00 0.00 3.72
2479 2688 3.003689 CCTGGCCTAAATCGCTTAATGTG 59.996 47.826 3.32 0.00 0.00 3.21
2480 2689 3.214328 CCTGGCCTAAATCGCTTAATGT 58.786 45.455 3.32 0.00 0.00 2.71
2481 2690 3.214328 ACCTGGCCTAAATCGCTTAATG 58.786 45.455 3.32 0.00 0.00 1.90
2482 2691 3.577805 ACCTGGCCTAAATCGCTTAAT 57.422 42.857 3.32 0.00 0.00 1.40
2483 2692 3.453353 AGTACCTGGCCTAAATCGCTTAA 59.547 43.478 3.32 0.00 0.00 1.85
2484 2693 3.036091 AGTACCTGGCCTAAATCGCTTA 58.964 45.455 3.32 0.00 0.00 3.09
2485 2694 1.838077 AGTACCTGGCCTAAATCGCTT 59.162 47.619 3.32 0.00 0.00 4.68
2486 2695 1.497161 AGTACCTGGCCTAAATCGCT 58.503 50.000 3.32 0.00 0.00 4.93
2487 2696 1.940613 CAAGTACCTGGCCTAAATCGC 59.059 52.381 3.32 0.00 0.00 4.58
2488 2697 3.261981 ACAAGTACCTGGCCTAAATCG 57.738 47.619 3.32 0.00 0.00 3.34
2489 2698 4.117685 CGTACAAGTACCTGGCCTAAATC 58.882 47.826 3.32 0.00 32.61 2.17
2490 2699 3.516700 ACGTACAAGTACCTGGCCTAAAT 59.483 43.478 3.32 0.00 32.61 1.40
2491 2700 2.899256 ACGTACAAGTACCTGGCCTAAA 59.101 45.455 3.32 0.00 32.61 1.85
2492 2701 2.528564 ACGTACAAGTACCTGGCCTAA 58.471 47.619 3.32 0.00 32.61 2.69
2493 2702 2.220653 ACGTACAAGTACCTGGCCTA 57.779 50.000 3.32 0.00 32.61 3.93
2494 2703 1.001633 CAACGTACAAGTACCTGGCCT 59.998 52.381 3.32 0.00 32.61 5.19
2495 2704 1.001181 TCAACGTACAAGTACCTGGCC 59.999 52.381 0.00 0.00 32.61 5.36
2496 2705 2.443887 TCAACGTACAAGTACCTGGC 57.556 50.000 4.89 0.00 32.61 4.85
2497 2706 3.259064 CCATCAACGTACAAGTACCTGG 58.741 50.000 4.89 0.00 32.61 4.45
2498 2707 3.259064 CCCATCAACGTACAAGTACCTG 58.741 50.000 4.89 3.45 32.61 4.00
2499 2708 2.354403 GCCCATCAACGTACAAGTACCT 60.354 50.000 4.89 0.00 32.61 3.08
2500 2709 2.004733 GCCCATCAACGTACAAGTACC 58.995 52.381 4.89 0.00 32.61 3.34
2501 2710 2.004733 GGCCCATCAACGTACAAGTAC 58.995 52.381 0.00 0.29 0.00 2.73
2502 2711 1.903860 AGGCCCATCAACGTACAAGTA 59.096 47.619 0.00 0.00 0.00 2.24
2503 2712 0.690762 AGGCCCATCAACGTACAAGT 59.309 50.000 0.00 0.00 0.00 3.16
2504 2713 1.821216 AAGGCCCATCAACGTACAAG 58.179 50.000 0.00 0.00 0.00 3.16
2505 2714 2.279935 AAAGGCCCATCAACGTACAA 57.720 45.000 0.00 0.00 0.00 2.41
2506 2715 2.279935 AAAAGGCCCATCAACGTACA 57.720 45.000 0.00 0.00 0.00 2.90
2507 2716 3.066203 CCATAAAAGGCCCATCAACGTAC 59.934 47.826 0.00 0.00 0.00 3.67
2508 2717 3.283751 CCATAAAAGGCCCATCAACGTA 58.716 45.455 0.00 0.00 0.00 3.57
2509 2718 2.099405 CCATAAAAGGCCCATCAACGT 58.901 47.619 0.00 0.00 0.00 3.99
2510 2719 1.408702 CCCATAAAAGGCCCATCAACG 59.591 52.381 0.00 0.00 0.00 4.10
2511 2720 1.138859 GCCCATAAAAGGCCCATCAAC 59.861 52.381 0.00 0.00 45.16 3.18
2512 2721 1.494960 GCCCATAAAAGGCCCATCAA 58.505 50.000 0.00 0.00 45.16 2.57
2513 2722 3.222287 GCCCATAAAAGGCCCATCA 57.778 52.632 0.00 0.00 45.16 3.07
2520 2729 7.147966 ACGGTTTCTATAAAAGCCCATAAAAGG 60.148 37.037 0.00 0.00 0.00 3.11
2521 2730 7.700656 CACGGTTTCTATAAAAGCCCATAAAAG 59.299 37.037 0.00 0.00 0.00 2.27
2522 2731 7.393796 TCACGGTTTCTATAAAAGCCCATAAAA 59.606 33.333 0.00 0.00 0.00 1.52
2523 2732 6.885376 TCACGGTTTCTATAAAAGCCCATAAA 59.115 34.615 0.00 0.00 0.00 1.40
2524 2733 6.416415 TCACGGTTTCTATAAAAGCCCATAA 58.584 36.000 0.00 0.00 0.00 1.90
2525 2734 5.991861 TCACGGTTTCTATAAAAGCCCATA 58.008 37.500 0.00 0.00 0.00 2.74
2526 2735 4.850680 TCACGGTTTCTATAAAAGCCCAT 58.149 39.130 0.00 0.00 0.00 4.00
2527 2736 4.289238 TCACGGTTTCTATAAAAGCCCA 57.711 40.909 0.00 0.00 0.00 5.36
2528 2737 5.632244 TTTCACGGTTTCTATAAAAGCCC 57.368 39.130 0.00 0.00 0.00 5.19
2529 2738 9.628746 TTATTTTTCACGGTTTCTATAAAAGCC 57.371 29.630 0.00 0.00 0.00 4.35
2558 2767 9.829507 TTCCACAATGTTGATTTATTTTGACTT 57.170 25.926 0.00 0.00 0.00 3.01
2559 2768 9.829507 TTTCCACAATGTTGATTTATTTTGACT 57.170 25.926 0.00 0.00 0.00 3.41
2568 2777 9.388506 TGTGTTTAATTTCCACAATGTTGATTT 57.611 25.926 0.00 0.00 36.25 2.17
2569 2778 8.954950 TGTGTTTAATTTCCACAATGTTGATT 57.045 26.923 0.00 0.00 36.25 2.57
2570 2779 8.991026 CATGTGTTTAATTTCCACAATGTTGAT 58.009 29.630 8.11 0.00 41.91 2.57
2571 2780 8.200120 TCATGTGTTTAATTTCCACAATGTTGA 58.800 29.630 8.11 5.64 41.91 3.18
2572 2781 8.274939 GTCATGTGTTTAATTTCCACAATGTTG 58.725 33.333 8.11 0.00 41.91 3.33
2573 2782 7.440856 GGTCATGTGTTTAATTTCCACAATGTT 59.559 33.333 8.11 0.00 41.91 2.71
2574 2783 6.928492 GGTCATGTGTTTAATTTCCACAATGT 59.072 34.615 8.11 0.00 41.91 2.71
2575 2784 7.153985 AGGTCATGTGTTTAATTTCCACAATG 58.846 34.615 8.11 7.63 41.91 2.82
2576 2785 7.301868 AGGTCATGTGTTTAATTTCCACAAT 57.698 32.000 8.11 0.00 41.91 2.71
2577 2786 6.239176 GGAGGTCATGTGTTTAATTTCCACAA 60.239 38.462 8.11 0.00 41.91 3.33
2578 2787 5.242838 GGAGGTCATGTGTTTAATTTCCACA 59.757 40.000 6.89 6.89 42.70 4.17
2579 2788 5.476945 AGGAGGTCATGTGTTTAATTTCCAC 59.523 40.000 0.00 0.00 0.00 4.02
2580 2789 5.640147 AGGAGGTCATGTGTTTAATTTCCA 58.360 37.500 0.00 0.00 0.00 3.53
2581 2790 6.590234 AAGGAGGTCATGTGTTTAATTTCC 57.410 37.500 0.00 0.00 0.00 3.13
2582 2791 8.336801 ACTAAGGAGGTCATGTGTTTAATTTC 57.663 34.615 0.00 0.00 0.00 2.17
2583 2792 7.393515 GGACTAAGGAGGTCATGTGTTTAATTT 59.606 37.037 0.00 0.00 35.61 1.82
2584 2793 6.884836 GGACTAAGGAGGTCATGTGTTTAATT 59.115 38.462 0.00 0.00 35.61 1.40
2585 2794 6.215636 AGGACTAAGGAGGTCATGTGTTTAAT 59.784 38.462 0.00 0.00 35.61 1.40
2586 2795 5.546499 AGGACTAAGGAGGTCATGTGTTTAA 59.454 40.000 0.00 0.00 35.61 1.52
2587 2796 5.091552 AGGACTAAGGAGGTCATGTGTTTA 58.908 41.667 0.00 0.00 35.61 2.01
2588 2797 3.910627 AGGACTAAGGAGGTCATGTGTTT 59.089 43.478 0.00 0.00 35.61 2.83
2589 2798 3.521727 AGGACTAAGGAGGTCATGTGTT 58.478 45.455 0.00 0.00 35.61 3.32
2590 2799 3.191888 AGGACTAAGGAGGTCATGTGT 57.808 47.619 0.00 0.00 35.61 3.72
2591 2800 3.772025 AGAAGGACTAAGGAGGTCATGTG 59.228 47.826 0.00 0.00 35.61 3.21
2592 2801 4.027437 GAGAAGGACTAAGGAGGTCATGT 58.973 47.826 0.00 0.00 35.61 3.21
2593 2802 3.067461 CGAGAAGGACTAAGGAGGTCATG 59.933 52.174 0.00 0.00 35.61 3.07
2594 2803 3.292460 CGAGAAGGACTAAGGAGGTCAT 58.708 50.000 0.00 0.00 35.61 3.06
2595 2804 2.041350 ACGAGAAGGACTAAGGAGGTCA 59.959 50.000 0.00 0.00 35.61 4.02
2596 2805 2.725637 ACGAGAAGGACTAAGGAGGTC 58.274 52.381 0.00 0.00 0.00 3.85
2597 2806 2.903375 ACGAGAAGGACTAAGGAGGT 57.097 50.000 0.00 0.00 0.00 3.85
2598 2807 3.368531 CCAAACGAGAAGGACTAAGGAGG 60.369 52.174 0.00 0.00 0.00 4.30
2599 2808 3.851098 CCAAACGAGAAGGACTAAGGAG 58.149 50.000 0.00 0.00 0.00 3.69
2600 2809 2.028385 GCCAAACGAGAAGGACTAAGGA 60.028 50.000 0.00 0.00 0.00 3.36
2601 2810 2.028020 AGCCAAACGAGAAGGACTAAGG 60.028 50.000 0.00 0.00 0.00 2.69
2602 2811 3.320673 AGCCAAACGAGAAGGACTAAG 57.679 47.619 0.00 0.00 0.00 2.18
3048 3442 7.811117 TTTAGTAGCCACAACACATTTAAGT 57.189 32.000 0.00 0.00 0.00 2.24
3060 3455 8.927675 TTCCTTTTTCTAATTTAGTAGCCACA 57.072 30.769 3.45 0.00 0.00 4.17
3062 3457 8.387813 TCCTTCCTTTTTCTAATTTAGTAGCCA 58.612 33.333 3.45 0.00 0.00 4.75
3269 3693 2.631160 TGTCTCACAACATCGGGTTT 57.369 45.000 0.00 0.00 37.72 3.27
3383 3808 4.040706 AGAGATCCCATGAGAATTCAGAGC 59.959 45.833 8.44 0.00 36.61 4.09
3467 3892 3.007614 GGTTTACCTTCCAGCTCAGTGTA 59.992 47.826 0.00 0.00 0.00 2.90
3582 4008 2.045926 ATCCTGCACGACAAGGCC 60.046 61.111 0.00 0.00 0.00 5.19
3590 4016 1.915614 GCCACTTCACATCCTGCACG 61.916 60.000 0.00 0.00 0.00 5.34
3866 4292 1.202475 TGCACTGCACTTACGAAGACA 60.202 47.619 0.00 0.00 31.71 3.41
3890 4326 0.755686 CTAGCTAGCCCAGGACAAGG 59.244 60.000 12.13 0.00 0.00 3.61
4195 4660 2.343544 GCAGTTACGTACGTAAGCCTTG 59.656 50.000 34.51 27.98 40.69 3.61
4202 4667 3.697982 CATCCATGCAGTTACGTACGTA 58.302 45.455 23.60 23.60 0.00 3.57
4231 4696 8.658609 GTCCAAAATTAATTACACTACGTAGCA 58.341 33.333 22.40 5.30 0.00 3.49
4232 4697 7.842721 CGTCCAAAATTAATTACACTACGTAGC 59.157 37.037 22.40 0.00 0.00 3.58
4233 4698 8.323140 CCGTCCAAAATTAATTACACTACGTAG 58.677 37.037 20.97 20.97 0.00 3.51
4234 4699 7.277539 CCCGTCCAAAATTAATTACACTACGTA 59.722 37.037 0.01 0.00 0.00 3.57
4235 4700 6.092533 CCCGTCCAAAATTAATTACACTACGT 59.907 38.462 0.01 0.00 0.00 3.57
4236 4701 6.313411 TCCCGTCCAAAATTAATTACACTACG 59.687 38.462 0.01 8.21 0.00 3.51
4237 4702 7.614124 TCCCGTCCAAAATTAATTACACTAC 57.386 36.000 0.01 0.00 0.00 2.73
4350 4816 6.431198 TTCTTTTGCGAGGAATAATGTACC 57.569 37.500 0.00 0.00 0.00 3.34
4413 4881 7.763071 GGTAGAGTAACTTGTTCGTTGGATAAT 59.237 37.037 0.00 0.00 0.00 1.28
4451 4919 7.387643 ACTAGTTAGTTTCTTGGAGATCAACC 58.612 38.462 0.00 0.00 31.13 3.77
4569 5037 3.936372 AGACACATACGTACAGTGCTT 57.064 42.857 22.79 12.69 36.76 3.91
4572 5040 5.921976 TGGTTAAAGACACATACGTACAGTG 59.078 40.000 21.78 21.78 39.12 3.66
4575 5043 5.229423 GGTGGTTAAAGACACATACGTACA 58.771 41.667 0.00 0.00 39.31 2.90
4576 5044 4.324402 CGGTGGTTAAAGACACATACGTAC 59.676 45.833 0.00 0.00 39.31 3.67
4577 5045 4.484236 CGGTGGTTAAAGACACATACGTA 58.516 43.478 0.00 0.00 39.31 3.57
4578 5046 3.319755 CGGTGGTTAAAGACACATACGT 58.680 45.455 0.00 0.00 39.31 3.57
4579 5047 2.669434 CCGGTGGTTAAAGACACATACG 59.331 50.000 0.00 0.00 39.31 3.06
4580 5048 3.681417 GTCCGGTGGTTAAAGACACATAC 59.319 47.826 0.00 0.00 39.31 2.39
4581 5049 3.579586 AGTCCGGTGGTTAAAGACACATA 59.420 43.478 0.00 0.00 39.31 2.29
4582 5050 2.370849 AGTCCGGTGGTTAAAGACACAT 59.629 45.455 0.00 0.00 39.31 3.21
4583 5051 1.764134 AGTCCGGTGGTTAAAGACACA 59.236 47.619 0.00 0.00 39.31 3.72
4601 5070 2.588620 CGATGCCCTTCTAGTCCTAGT 58.411 52.381 1.49 0.00 34.84 2.57
4773 5242 0.109597 CTCCATTGTTGGCTTCACGC 60.110 55.000 0.00 0.00 43.29 5.34
4784 5253 1.805428 GCAACGTTGGGCTCCATTGT 61.805 55.000 28.33 0.00 31.53 2.71
5022 5499 7.816513 TCGCACCAAAAATCAAAATGATTATGA 59.183 29.630 15.05 0.00 45.57 2.15
5090 5567 3.876309 TTAGTCAGAAAAGGGGCAAGT 57.124 42.857 0.00 0.00 0.00 3.16
5095 5572 6.834168 TTAAGCAATTAGTCAGAAAAGGGG 57.166 37.500 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.