Multiple sequence alignment - TraesCS2A01G458000

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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 TraesCS2A01G458000 chr2A 100.000 3594 0 0 1 3594 705883728 705880135 0.000000e+00 6637.0
1 TraesCS2A01G458000 chr2A 81.762 488 48 16 723 1195 705919692 705919231 1.580000e-98 370.0
2 TraesCS2A01G458000 chr2A 83.166 398 52 11 1286 1681 705919045 705918661 2.050000e-92 350.0
3 TraesCS2A01G458000 chr2A 75.873 659 71 42 2198 2807 705918199 705917580 4.600000e-64 255.0
4 TraesCS2A01G458000 chr2A 100.000 41 0 0 3122 3162 705880562 705880522 3.850000e-10 76.8
5 TraesCS2A01G458000 chr2A 100.000 41 0 0 3167 3207 705880607 705880567 3.850000e-10 76.8
6 TraesCS2A01G458000 chr2B 90.938 949 42 20 763 1698 677857149 677856232 0.000000e+00 1236.0
7 TraesCS2A01G458000 chr2B 88.796 714 55 9 2161 2870 677852730 677852038 0.000000e+00 852.0
8 TraesCS2A01G458000 chr2B 86.386 830 41 22 2053 2833 677810140 677809334 0.000000e+00 841.0
9 TraesCS2A01G458000 chr2B 82.945 686 57 27 1254 1919 677811153 677810508 6.740000e-157 564.0
10 TraesCS2A01G458000 chr2B 86.406 434 27 18 763 1195 677811650 677811248 2.550000e-121 446.0
11 TraesCS2A01G458000 chr2B 82.341 487 43 20 724 1194 677880024 677879565 2.020000e-102 383.0
12 TraesCS2A01G458000 chr2B 77.164 543 73 30 2198 2727 677877562 677877058 5.910000e-68 268.0
13 TraesCS2A01G458000 chr2B 88.068 176 18 2 1425 1600 677879261 677879089 4.700000e-49 206.0
14 TraesCS2A01G458000 chr2B 80.078 256 22 19 3341 3594 677808879 677808651 2.870000e-36 163.0
15 TraesCS2A01G458000 chr2B 89.655 87 4 1 1603 1684 677878444 677878358 4.910000e-19 106.0
16 TraesCS2A01G458000 chr2B 93.443 61 3 1 3535 3594 677851482 677851422 4.940000e-14 89.8
17 TraesCS2A01G458000 chr2B 100.000 28 0 0 1253 1280 677879480 677879453 6.000000e-03 52.8
18 TraesCS2A01G458000 chr2D 85.515 787 66 29 2187 2954 565483990 565483233 0.000000e+00 778.0
19 TraesCS2A01G458000 chr2D 84.011 713 67 18 1278 1955 565484925 565484225 3.030000e-180 641.0
20 TraesCS2A01G458000 chr2D 84.962 399 32 11 724 1106 565517698 565517312 2.620000e-101 379.0
21 TraesCS2A01G458000 chr2D 86.957 345 21 11 763 1106 565485290 565484969 2.040000e-97 366.0
22 TraesCS2A01G458000 chr2D 94.570 221 12 0 1464 1684 565586544 565586324 3.440000e-90 342.0
23 TraesCS2A01G458000 chr2D 90.347 259 15 2 3346 3594 565480504 565480246 7.440000e-87 331.0
24 TraesCS2A01G458000 chr2D 92.760 221 16 0 1464 1684 565516788 565516568 1.610000e-83 320.0
25 TraesCS2A01G458000 chr2D 87.308 260 23 5 848 1106 565587268 565587018 4.540000e-74 289.0
26 TraesCS2A01G458000 chr2D 80.240 334 35 15 2509 2817 565585636 565585309 4.670000e-54 222.0
27 TraesCS2A01G458000 chr2D 86.364 176 12 7 2956 3127 565480984 565480817 7.930000e-42 182.0
28 TraesCS2A01G458000 chr2D 94.017 117 7 0 2198 2314 565516091 565515975 1.030000e-40 178.0
29 TraesCS2A01G458000 chr2D 93.162 117 8 0 2198 2314 565585949 565585833 4.770000e-39 172.0
30 TraesCS2A01G458000 chr2D 77.333 150 23 8 2455 2601 565515845 565515704 1.070000e-10 78.7
31 TraesCS2A01G458000 chr7D 86.356 601 76 1 1 595 343110331 343109731 0.000000e+00 651.0
32 TraesCS2A01G458000 chr4A 89.916 476 43 2 124 595 516372919 516372445 3.070000e-170 608.0
33 TraesCS2A01G458000 chr4A 95.200 125 6 0 4 128 516381772 516381648 7.870000e-47 198.0
34 TraesCS2A01G458000 chr6A 87.948 307 37 0 1 307 197778430 197778124 2.640000e-96 363.0
35 TraesCS2A01G458000 chrUn 96.296 108 4 0 997 1104 478858123 478858016 1.030000e-40 178.0
36 TraesCS2A01G458000 chr1A 96.296 108 4 0 997 1104 101335649 101335542 1.030000e-40 178.0
37 TraesCS2A01G458000 chr1A 90.323 124 12 0 1469 1592 364040070 364039947 2.870000e-36 163.0
38 TraesCS2A01G458000 chr1D 89.231 130 13 1 1469 1598 469890471 469890343 1.030000e-35 161.0


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 TraesCS2A01G458000 chr2A 705880135 705883728 3593 True 2263.533333 6637 100.00000 1 3594 3 chr2A.!!$R1 3593
1 TraesCS2A01G458000 chr2A 705917580 705919692 2112 True 325.000000 370 80.26700 723 2807 3 chr2A.!!$R2 2084
2 TraesCS2A01G458000 chr2B 677851422 677857149 5727 True 725.933333 1236 91.05900 763 3594 3 chr2B.!!$R2 2831
3 TraesCS2A01G458000 chr2B 677808651 677811650 2999 True 503.500000 841 83.95375 763 3594 4 chr2B.!!$R1 2831
4 TraesCS2A01G458000 chr2B 677877058 677880024 2966 True 203.160000 383 87.44560 724 2727 5 chr2B.!!$R3 2003
5 TraesCS2A01G458000 chr2D 565480246 565485290 5044 True 459.600000 778 86.63880 763 3594 5 chr2D.!!$R1 2831
6 TraesCS2A01G458000 chr2D 565585309 565587268 1959 True 256.250000 342 88.82000 848 2817 4 chr2D.!!$R3 1969
7 TraesCS2A01G458000 chr2D 565515704 565517698 1994 True 238.925000 379 87.26800 724 2601 4 chr2D.!!$R2 1877
8 TraesCS2A01G458000 chr7D 343109731 343110331 600 True 651.000000 651 86.35600 1 595 1 chr7D.!!$R1 594

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
338 345 0.044092 TGAGCCACCTATCCTCCCAA 59.956 55.0 0.00 0.0 0.00 4.12 F
356 363 0.098025 AAAACAGTGTTGTGCGTCCG 59.902 50.0 9.79 0.0 37.67 4.79 F
1138 1191 0.169672 ACGACGAATCACTACACCCG 59.830 55.0 0.00 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 6037 0.038343 CATCAAACCCAGGCAAACCG 60.038 55.000 0.00 0.0 42.76 4.44 R
2323 7344 3.253188 ACCAAGAACGTGGACAATTGATG 59.747 43.478 13.59 0.0 41.65 3.07 R
3112 10656 0.613260 TCTACCTCATTGGCAGCGTT 59.387 50.000 0.00 0.0 40.22 4.84 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
22 23 1.678728 CGATGCCCATGTGTAGGTTGT 60.679 52.381 0.00 0.00 0.00 3.32
24 25 1.614996 TGCCCATGTGTAGGTTGTTG 58.385 50.000 0.00 0.00 0.00 3.33
27 28 1.804151 CCCATGTGTAGGTTGTTGTCG 59.196 52.381 0.00 0.00 0.00 4.35
28 29 2.549134 CCCATGTGTAGGTTGTTGTCGA 60.549 50.000 0.00 0.00 0.00 4.20
32 33 4.061357 TGTGTAGGTTGTTGTCGATGAA 57.939 40.909 0.00 0.00 0.00 2.57
34 35 4.056050 GTGTAGGTTGTTGTCGATGAACT 58.944 43.478 10.55 0.00 0.00 3.01
45 46 2.921754 GTCGATGAACTTTGTAGGACCG 59.078 50.000 0.00 0.00 0.00 4.79
51 52 3.056678 TGAACTTTGTAGGACCGCGAATA 60.057 43.478 8.23 0.00 0.00 1.75
80 87 1.302511 GGCTGACCTTGCCGAGAAA 60.303 57.895 0.00 0.00 41.03 2.52
84 91 0.320374 TGACCTTGCCGAGAAATCGT 59.680 50.000 0.00 0.00 0.00 3.73
115 122 2.100252 CCCATGACCATGCAAGTTGATC 59.900 50.000 7.16 0.00 37.49 2.92
116 123 2.100252 CCATGACCATGCAAGTTGATCC 59.900 50.000 7.16 0.00 37.49 3.36
128 135 0.320073 GTTGATCCGGTCGTTGTGGA 60.320 55.000 0.00 0.00 35.96 4.02
138 145 0.526211 TCGTTGTGGATCCAGAGTCG 59.474 55.000 16.81 20.87 0.00 4.18
149 156 0.817654 CCAGAGTCGTGCTATCCACA 59.182 55.000 0.00 0.00 44.91 4.17
164 171 1.580942 CACATGTGGCCAAACCTCG 59.419 57.895 18.51 0.00 40.22 4.63
175 182 2.846193 CCAAACCTCGAGAAACTGGAA 58.154 47.619 15.71 0.00 0.00 3.53
179 186 3.528597 ACCTCGAGAAACTGGAATAGC 57.471 47.619 15.71 0.00 0.00 2.97
183 190 1.855360 CGAGAAACTGGAATAGCGCTC 59.145 52.381 16.34 0.00 0.00 5.03
188 195 0.101399 ACTGGAATAGCGCTCTGTCG 59.899 55.000 16.34 1.60 0.00 4.35
195 202 0.808755 TAGCGCTCTGTCGTTCATGA 59.191 50.000 16.34 0.00 0.00 3.07
203 210 4.444838 TCGTTCATGACCGGGCCG 62.445 66.667 21.46 21.46 0.00 6.13
220 227 1.141665 CGACATCACGAGCCCATGA 59.858 57.895 0.00 0.00 35.09 3.07
223 230 1.947013 CATCACGAGCCCATGATGC 59.053 57.895 8.30 0.00 44.13 3.91
227 234 2.107750 CGAGCCCATGATGCGTCT 59.892 61.111 7.58 0.00 0.00 4.18
241 248 1.145803 GCGTCTTGTAAAGCTTCCGT 58.854 50.000 0.00 0.00 45.70 4.69
244 251 2.155155 CGTCTTGTAAAGCTTCCGTCAC 59.845 50.000 0.00 0.00 45.70 3.67
256 263 2.126618 CGTCACCGTTCTAGCGCA 60.127 61.111 11.47 0.00 0.00 6.09
257 264 2.434134 CGTCACCGTTCTAGCGCAC 61.434 63.158 11.47 0.00 0.00 5.34
261 268 2.273179 ACCGTTCTAGCGCACCTCA 61.273 57.895 11.47 0.00 0.00 3.86
263 270 0.872021 CCGTTCTAGCGCACCTCATC 60.872 60.000 11.47 0.00 0.00 2.92
281 288 1.675310 CCGCTTTGGCACCATCTCA 60.675 57.895 0.00 0.00 38.60 3.27
282 289 1.243342 CCGCTTTGGCACCATCTCAA 61.243 55.000 0.00 0.00 38.60 3.02
309 316 2.158249 AGAGGGGCTAGCTCATGTATCA 60.158 50.000 18.29 0.00 0.00 2.15
338 345 0.044092 TGAGCCACCTATCCTCCCAA 59.956 55.000 0.00 0.00 0.00 4.12
339 346 1.213296 GAGCCACCTATCCTCCCAAA 58.787 55.000 0.00 0.00 0.00 3.28
343 350 2.945890 GCCACCTATCCTCCCAAAACAG 60.946 54.545 0.00 0.00 0.00 3.16
356 363 0.098025 AAAACAGTGTTGTGCGTCCG 59.902 50.000 9.79 0.00 37.67 4.79
376 383 2.436115 GCCCACGGTCACCTTAGC 60.436 66.667 0.00 0.00 0.00 3.09
377 384 2.955881 GCCCACGGTCACCTTAGCT 61.956 63.158 0.00 0.00 0.00 3.32
379 386 1.671742 CCACGGTCACCTTAGCTGT 59.328 57.895 0.00 0.00 0.00 4.40
381 388 0.732880 CACGGTCACCTTAGCTGTCG 60.733 60.000 0.00 0.00 0.00 4.35
404 411 0.324943 GGTACAAGCCTCTTGCCTCA 59.675 55.000 6.49 0.00 42.71 3.86
410 417 2.507944 CCTCTTGCCTCATCGGGG 59.492 66.667 0.00 0.00 0.00 5.73
442 449 3.371034 TGAATTCCGTCCATGGTCTAGA 58.629 45.455 12.58 3.07 0.00 2.43
444 451 4.039245 TGAATTCCGTCCATGGTCTAGATC 59.961 45.833 12.58 0.00 0.00 2.75
446 453 1.142262 TCCGTCCATGGTCTAGATCGA 59.858 52.381 12.58 0.00 0.00 3.59
448 455 2.162608 CCGTCCATGGTCTAGATCGATC 59.837 54.545 17.91 17.91 0.00 3.69
466 473 2.148916 TCTGCTCGTTACAACCACAG 57.851 50.000 0.00 0.00 0.00 3.66
499 506 2.120909 GGGCCACATTCATCCACCG 61.121 63.158 4.39 0.00 0.00 4.94
502 509 1.996786 GCCACATTCATCCACCGCAG 61.997 60.000 0.00 0.00 0.00 5.18
521 528 1.748403 GTCTGTGACACTGAGCCCA 59.252 57.895 14.74 0.00 32.09 5.36
530 537 4.729918 CTGAGCCCACCTGCCCAC 62.730 72.222 0.00 0.00 0.00 4.61
545 552 1.178534 CCCACTTTGGTCGGCACAAT 61.179 55.000 0.00 0.00 35.17 2.71
547 554 0.667993 CACTTTGGTCGGCACAATGT 59.332 50.000 0.00 0.00 36.87 2.71
560 567 2.806019 GCACAATGTTTCCCATGCAACA 60.806 45.455 0.00 5.98 37.31 3.33
571 578 2.356075 TGCAACAGCGCATTTGCC 60.356 55.556 31.21 19.34 46.28 4.52
572 579 2.356075 GCAACAGCGCATTTGCCA 60.356 55.556 26.93 0.00 41.95 4.92
573 580 2.377310 GCAACAGCGCATTTGCCAG 61.377 57.895 26.93 6.29 41.95 4.85
595 602 1.453155 CCACCGTCTTCTTTCCCATG 58.547 55.000 0.00 0.00 0.00 3.66
596 603 1.003118 CCACCGTCTTCTTTCCCATGA 59.997 52.381 0.00 0.00 0.00 3.07
597 604 2.076863 CACCGTCTTCTTTCCCATGAC 58.923 52.381 0.00 0.00 0.00 3.06
598 605 1.337823 ACCGTCTTCTTTCCCATGACG 60.338 52.381 0.00 0.00 46.55 4.35
599 606 1.359848 CGTCTTCTTTCCCATGACGG 58.640 55.000 0.00 0.00 44.29 4.79
600 607 1.067142 CGTCTTCTTTCCCATGACGGA 60.067 52.381 0.00 0.00 44.29 4.69
601 608 2.622436 GTCTTCTTTCCCATGACGGAG 58.378 52.381 0.00 0.00 36.56 4.63
616 623 3.965292 ACGGAGTGTATAGTCATGTCG 57.035 47.619 0.00 0.00 42.51 4.35
617 624 3.276857 ACGGAGTGTATAGTCATGTCGT 58.723 45.455 0.00 0.00 42.51 4.34
618 625 4.445453 ACGGAGTGTATAGTCATGTCGTA 58.555 43.478 0.00 0.00 42.51 3.43
619 626 4.510711 ACGGAGTGTATAGTCATGTCGTAG 59.489 45.833 0.00 0.00 42.51 3.51
620 627 4.510711 CGGAGTGTATAGTCATGTCGTAGT 59.489 45.833 0.00 0.00 0.00 2.73
621 628 5.693555 CGGAGTGTATAGTCATGTCGTAGTA 59.306 44.000 0.00 0.00 0.00 1.82
622 629 6.368243 CGGAGTGTATAGTCATGTCGTAGTAT 59.632 42.308 0.00 0.00 0.00 2.12
623 630 7.095313 CGGAGTGTATAGTCATGTCGTAGTATT 60.095 40.741 0.00 0.00 0.00 1.89
624 631 8.566260 GGAGTGTATAGTCATGTCGTAGTATTT 58.434 37.037 0.00 0.00 0.00 1.40
625 632 9.947669 GAGTGTATAGTCATGTCGTAGTATTTT 57.052 33.333 0.00 0.00 0.00 1.82
679 686 9.864034 AAAAATTAGATATCGTTTGCTATCGTG 57.136 29.630 0.00 0.00 30.31 4.35
680 687 8.812147 AAATTAGATATCGTTTGCTATCGTGA 57.188 30.769 0.00 0.00 30.31 4.35
681 688 8.812147 AATTAGATATCGTTTGCTATCGTGAA 57.188 30.769 0.00 0.00 30.31 3.18
682 689 8.812147 ATTAGATATCGTTTGCTATCGTGAAA 57.188 30.769 0.00 0.00 30.31 2.69
683 690 8.812147 TTAGATATCGTTTGCTATCGTGAAAT 57.188 30.769 0.00 0.00 30.31 2.17
684 691 7.715265 AGATATCGTTTGCTATCGTGAAATT 57.285 32.000 0.00 0.00 30.31 1.82
685 692 8.142994 AGATATCGTTTGCTATCGTGAAATTT 57.857 30.769 0.00 0.00 30.31 1.82
686 693 8.064222 AGATATCGTTTGCTATCGTGAAATTTG 58.936 33.333 0.00 0.00 30.31 2.32
687 694 5.351233 TCGTTTGCTATCGTGAAATTTGT 57.649 34.783 0.00 0.00 0.00 2.83
688 695 6.469139 TCGTTTGCTATCGTGAAATTTGTA 57.531 33.333 0.00 0.00 0.00 2.41
689 696 7.067532 TCGTTTGCTATCGTGAAATTTGTAT 57.932 32.000 0.00 0.00 0.00 2.29
690 697 7.523219 TCGTTTGCTATCGTGAAATTTGTATT 58.477 30.769 0.00 0.00 0.00 1.89
691 698 8.018520 TCGTTTGCTATCGTGAAATTTGTATTT 58.981 29.630 0.00 0.00 36.68 1.40
692 699 8.635124 CGTTTGCTATCGTGAAATTTGTATTTT 58.365 29.630 0.00 0.00 34.16 1.82
693 700 9.726034 GTTTGCTATCGTGAAATTTGTATTTTG 57.274 29.630 0.00 0.00 34.16 2.44
694 701 9.684448 TTTGCTATCGTGAAATTTGTATTTTGA 57.316 25.926 0.00 0.00 34.16 2.69
695 702 8.894409 TGCTATCGTGAAATTTGTATTTTGAG 57.106 30.769 0.00 0.00 34.16 3.02
696 703 8.511321 TGCTATCGTGAAATTTGTATTTTGAGT 58.489 29.630 0.00 0.00 34.16 3.41
697 704 9.341899 GCTATCGTGAAATTTGTATTTTGAGTT 57.658 29.630 0.00 0.00 34.16 3.01
700 707 8.918961 TCGTGAAATTTGTATTTTGAGTTTGT 57.081 26.923 0.00 0.00 34.16 2.83
701 708 8.802856 TCGTGAAATTTGTATTTTGAGTTTGTG 58.197 29.630 0.00 0.00 34.16 3.33
702 709 8.591312 CGTGAAATTTGTATTTTGAGTTTGTGT 58.409 29.630 0.00 0.00 34.16 3.72
705 712 9.209297 GAAATTTGTATTTTGAGTTTGTGTTGC 57.791 29.630 0.00 0.00 34.16 4.17
706 713 6.654793 TTTGTATTTTGAGTTTGTGTTGCC 57.345 33.333 0.00 0.00 0.00 4.52
707 714 4.688021 TGTATTTTGAGTTTGTGTTGCCC 58.312 39.130 0.00 0.00 0.00 5.36
708 715 4.404073 TGTATTTTGAGTTTGTGTTGCCCT 59.596 37.500 0.00 0.00 0.00 5.19
709 716 5.594725 TGTATTTTGAGTTTGTGTTGCCCTA 59.405 36.000 0.00 0.00 0.00 3.53
710 717 5.606348 ATTTTGAGTTTGTGTTGCCCTAA 57.394 34.783 0.00 0.00 0.00 2.69
711 718 5.606348 TTTTGAGTTTGTGTTGCCCTAAT 57.394 34.783 0.00 0.00 0.00 1.73
712 719 6.716934 TTTTGAGTTTGTGTTGCCCTAATA 57.283 33.333 0.00 0.00 0.00 0.98
713 720 6.909550 TTTGAGTTTGTGTTGCCCTAATAT 57.090 33.333 0.00 0.00 0.00 1.28
714 721 6.509418 TTGAGTTTGTGTTGCCCTAATATC 57.491 37.500 0.00 0.00 0.00 1.63
715 722 5.565509 TGAGTTTGTGTTGCCCTAATATCA 58.434 37.500 0.00 0.00 0.00 2.15
716 723 5.414454 TGAGTTTGTGTTGCCCTAATATCAC 59.586 40.000 0.00 0.00 0.00 3.06
717 724 5.570320 AGTTTGTGTTGCCCTAATATCACT 58.430 37.500 0.00 0.00 0.00 3.41
718 725 6.717289 AGTTTGTGTTGCCCTAATATCACTA 58.283 36.000 0.00 0.00 0.00 2.74
719 726 7.172342 AGTTTGTGTTGCCCTAATATCACTAA 58.828 34.615 0.00 0.00 0.00 2.24
720 727 7.834181 AGTTTGTGTTGCCCTAATATCACTAAT 59.166 33.333 0.00 0.00 0.00 1.73
721 728 8.466798 GTTTGTGTTGCCCTAATATCACTAATT 58.533 33.333 0.00 0.00 0.00 1.40
722 729 9.688091 TTTGTGTTGCCCTAATATCACTAATTA 57.312 29.630 0.00 0.00 0.00 1.40
728 735 8.877864 TGCCCTAATATCACTAATTAAATGGG 57.122 34.615 0.00 0.00 30.41 4.00
742 749 1.184970 AATGGGCCGGTTCAACAAGG 61.185 55.000 1.90 0.00 0.00 3.61
749 756 0.248866 CGGTTCAACAAGGGTGCAAC 60.249 55.000 0.00 0.00 0.00 4.17
755 762 2.952978 TCAACAAGGGTGCAACGTTTAT 59.047 40.909 7.02 0.00 38.12 1.40
756 763 4.135306 TCAACAAGGGTGCAACGTTTATA 58.865 39.130 7.02 0.00 38.12 0.98
759 766 6.430308 TCAACAAGGGTGCAACGTTTATATAA 59.570 34.615 7.02 0.00 38.12 0.98
760 767 6.431198 ACAAGGGTGCAACGTTTATATAAG 57.569 37.500 7.02 0.00 38.12 1.73
761 768 6.174760 ACAAGGGTGCAACGTTTATATAAGA 58.825 36.000 7.02 0.00 38.12 2.10
771 779 7.254795 GCAACGTTTATATAAGAGGACAGCATT 60.255 37.037 0.00 0.00 0.00 3.56
796 805 2.045926 CCAGAAGCCCAGAACCGG 60.046 66.667 0.00 0.00 0.00 5.28
800 809 4.660938 AAGCCCAGAACCGGTGCC 62.661 66.667 8.52 2.89 0.00 5.01
902 929 3.984193 CTCCCTTGGCTCCCTTGCG 62.984 68.421 0.00 0.00 0.00 4.85
974 1012 2.482333 CCGGCGAGAGGAGAACGAT 61.482 63.158 9.30 0.00 0.00 3.73
975 1013 1.009449 CGGCGAGAGGAGAACGATC 60.009 63.158 0.00 0.00 0.00 3.69
976 1014 1.009449 GGCGAGAGGAGAACGATCG 60.009 63.158 14.88 14.88 35.77 3.69
977 1015 1.437772 GGCGAGAGGAGAACGATCGA 61.438 60.000 24.34 0.00 35.00 3.59
991 1029 2.824489 TCGAGAGCCATCGAGCGT 60.824 61.111 6.76 0.00 46.20 5.07
1113 1151 7.541074 TCCAGGACAAGGAAGGTACATATATA 58.459 38.462 0.00 0.00 30.71 0.86
1134 1184 3.629438 TGTGAACGACGAATCACTACA 57.371 42.857 26.44 13.04 44.86 2.74
1138 1191 0.169672 ACGACGAATCACTACACCCG 59.830 55.000 0.00 0.00 0.00 5.28
1245 1314 6.150307 TGTTGTTGCTCTTCTTGTTCTTGTTA 59.850 34.615 0.00 0.00 0.00 2.41
1281 1456 1.211457 AGCATCCTCCATGTTGTCTCC 59.789 52.381 0.00 0.00 34.56 3.71
1284 1463 2.940514 TCCTCCATGTTGTCTCCCTA 57.059 50.000 0.00 0.00 0.00 3.53
1369 1554 0.586319 CTGTGTGTTAACCTGCCGTG 59.414 55.000 2.48 0.00 0.00 4.94
1387 1578 3.065371 CCGTGGGATATGCTTCTTGTTTC 59.935 47.826 0.00 0.00 0.00 2.78
1443 1731 3.382048 AAGGGACGAACTAACTGTGTC 57.618 47.619 0.00 0.00 0.00 3.67
1457 1745 3.574614 ACTGTGTCAGTTTGTGTTTTGC 58.425 40.909 0.00 0.00 42.59 3.68
1569 1882 1.153997 GGAGTCGACGCTTCACCTC 60.154 63.158 18.88 4.01 0.00 3.85
1705 5750 5.357878 GCAGATCATGGATTGTGACCTTTTA 59.642 40.000 0.00 0.00 0.00 1.52
1763 5871 7.220740 TGTGTAGATAAATGTGTCCTTGTTGA 58.779 34.615 0.00 0.00 0.00 3.18
1805 5953 8.546083 AATAGATAGTCAGACAGAGGTTGATT 57.454 34.615 2.66 0.00 0.00 2.57
1811 5959 1.066573 AGACAGAGGTTGATTGAGGCG 60.067 52.381 0.00 0.00 0.00 5.52
1827 5975 1.372087 GGCGCCTCTCACCTTCAATG 61.372 60.000 22.15 0.00 0.00 2.82
1853 6028 9.831054 GTTAATAGATTGTAATTCGAACTCACG 57.169 33.333 0.00 0.00 0.00 4.35
1862 6037 0.662374 TCGAACTCACGAGCGGTTTC 60.662 55.000 0.00 0.00 37.37 2.78
1879 6054 0.395862 TTCGGTTTGCCTGGGTTTGA 60.396 50.000 0.00 0.00 0.00 2.69
2043 6517 8.694975 ATGTAAGATCACATGAATATAGCGAC 57.305 34.615 0.00 0.00 37.74 5.19
2081 6606 5.039333 GCATGGTTGCTTTATGATCTTGAC 58.961 41.667 0.00 0.00 45.77 3.18
2086 6616 8.158169 TGGTTGCTTTATGATCTTGACATATC 57.842 34.615 0.00 0.00 31.64 1.63
2110 6645 8.563123 TCTATGAGTACTCTTCTCGAAAGAAA 57.437 34.615 23.01 0.00 40.95 2.52
2116 6651 9.800299 GAGTACTCTTCTCGAAAGAAATTTTTC 57.200 33.333 15.91 0.00 40.95 2.29
2209 7202 3.684103 AGTTTTTCGTCATTGCGTTGA 57.316 38.095 0.00 0.00 0.00 3.18
2388 7423 4.685575 GCCTTCTCTTGAGCAATATGTCCT 60.686 45.833 0.00 0.00 0.00 3.85
2472 7508 7.589395 AGTTGTCGTGCAAAATAATTACATGA 58.411 30.769 0.00 0.00 39.03 3.07
2538 7585 9.990360 TTTTGTTCTGATAATTTTTACCCTTCC 57.010 29.630 0.00 0.00 0.00 3.46
2601 7648 2.098117 GGAGCGATTCTTGAACATTGGG 59.902 50.000 0.00 0.00 0.00 4.12
2702 7755 2.917971 GCTAAATCGTCTAGCGCCATAG 59.082 50.000 2.29 0.00 41.07 2.23
2752 7826 8.528643 TCCGGAGTTTGAACCTATGTATATATG 58.471 37.037 0.00 0.00 0.00 1.78
2753 7827 7.277981 CCGGAGTTTGAACCTATGTATATATGC 59.722 40.741 0.00 0.00 0.00 3.14
2754 7828 8.035394 CGGAGTTTGAACCTATGTATATATGCT 58.965 37.037 2.37 0.00 0.00 3.79
2755 7829 9.726438 GGAGTTTGAACCTATGTATATATGCTT 57.274 33.333 2.37 0.00 0.00 3.91
2867 7945 3.660501 AGCTGTTTGTATCGACACTCA 57.339 42.857 0.00 0.00 34.48 3.41
2935 8222 4.213482 AGTCATTTCTTTTTCGGGTTCTCG 59.787 41.667 0.00 0.00 0.00 4.04
2954 8241 3.808728 TCGAAGGCTCCAAAATATCCTG 58.191 45.455 0.00 0.00 0.00 3.86
2956 8243 4.103153 TCGAAGGCTCCAAAATATCCTGAT 59.897 41.667 0.00 0.00 0.00 2.90
2957 8244 4.214971 CGAAGGCTCCAAAATATCCTGATG 59.785 45.833 0.00 0.00 0.00 3.07
2958 8245 5.380043 GAAGGCTCCAAAATATCCTGATGA 58.620 41.667 0.00 0.00 0.00 2.92
2990 10530 1.546323 CCCAAGCATGCCCATAGTAGG 60.546 57.143 15.66 4.81 0.00 3.18
3065 10605 3.316868 CCATTACCAAACACGGAAACACT 59.683 43.478 0.00 0.00 0.00 3.55
3095 10635 3.584294 ACGGTAGCCCTATCCATTAGTT 58.416 45.455 0.00 0.00 0.00 2.24
3112 10656 3.386768 AGTTTAGCGAGCTCAAACTCA 57.613 42.857 19.63 2.38 37.87 3.41
3122 10666 0.662619 CTCAAACTCAACGCTGCCAA 59.337 50.000 0.00 0.00 0.00 4.52
3123 10667 1.267806 CTCAAACTCAACGCTGCCAAT 59.732 47.619 0.00 0.00 0.00 3.16
3126 10670 0.877071 AACTCAACGCTGCCAATGAG 59.123 50.000 17.31 17.31 43.79 2.90
3127 10671 0.957395 ACTCAACGCTGCCAATGAGG 60.957 55.000 20.79 9.01 42.76 3.86
3128 10672 0.957395 CTCAACGCTGCCAATGAGGT 60.957 55.000 13.24 0.00 40.61 3.85
3129 10673 0.323302 TCAACGCTGCCAATGAGGTA 59.677 50.000 0.00 0.00 40.61 3.08
3138 10682 3.754965 TGCCAATGAGGTAGATATTGCC 58.245 45.455 0.00 0.00 40.61 4.52
3139 10683 2.744202 GCCAATGAGGTAGATATTGCCG 59.256 50.000 0.00 0.00 40.61 5.69
3141 10685 2.744202 CAATGAGGTAGATATTGCCGCC 59.256 50.000 0.00 0.00 36.53 6.13
3142 10686 1.717032 TGAGGTAGATATTGCCGCCT 58.283 50.000 0.00 0.00 36.53 5.52
3143 10687 1.618837 TGAGGTAGATATTGCCGCCTC 59.381 52.381 0.00 0.00 41.92 4.70
3144 10688 1.618837 GAGGTAGATATTGCCGCCTCA 59.381 52.381 0.00 0.00 41.39 3.86
3145 10689 2.037251 GAGGTAGATATTGCCGCCTCAA 59.963 50.000 0.00 0.00 41.39 3.02
3147 10691 3.118038 AGGTAGATATTGCCGCCTCAAAA 60.118 43.478 0.00 0.00 36.53 2.44
3148 10692 3.630312 GGTAGATATTGCCGCCTCAAAAA 59.370 43.478 0.00 0.00 0.00 1.94
3149 10693 4.278419 GGTAGATATTGCCGCCTCAAAAAT 59.722 41.667 0.00 0.00 0.00 1.82
3150 10694 5.472137 GGTAGATATTGCCGCCTCAAAAATA 59.528 40.000 0.00 0.00 0.00 1.40
3151 10695 6.151144 GGTAGATATTGCCGCCTCAAAAATAT 59.849 38.462 0.00 0.00 0.00 1.28
3153 10697 5.536161 AGATATTGCCGCCTCAAAAATATGT 59.464 36.000 0.00 0.00 0.00 2.29
3154 10698 2.937469 TGCCGCCTCAAAAATATGTG 57.063 45.000 0.00 0.00 0.00 3.21
3156 10700 2.822561 TGCCGCCTCAAAAATATGTGAA 59.177 40.909 0.00 0.00 0.00 3.18
3157 10701 3.256879 TGCCGCCTCAAAAATATGTGAAA 59.743 39.130 0.00 0.00 0.00 2.69
3158 10702 4.081752 TGCCGCCTCAAAAATATGTGAAAT 60.082 37.500 0.00 0.00 0.00 2.17
3252 10902 4.020617 CCGTGCCAAGCTCCTGGA 62.021 66.667 8.71 0.00 38.96 3.86
3287 10954 0.536006 AGCTTGACTTGCAGGTCCAC 60.536 55.000 24.44 14.21 35.54 4.02
3305 10972 0.661020 ACAGCCAGTGTTTTACGTGC 59.339 50.000 0.00 0.00 34.94 5.34
3342 11010 4.309099 TGCTCCATCTTTGCAAAAATGTC 58.691 39.130 21.01 11.84 33.48 3.06
3343 11011 4.202233 TGCTCCATCTTTGCAAAAATGTCA 60.202 37.500 21.01 13.82 33.48 3.58
3344 11012 4.387862 GCTCCATCTTTGCAAAAATGTCAG 59.612 41.667 21.01 16.98 0.00 3.51
3369 11070 2.632987 AAAAACACCCTGTAGCTCGT 57.367 45.000 0.00 0.00 0.00 4.18
3391 11092 3.139077 CCTTAGAAAAACCGTGCTCAGT 58.861 45.455 0.00 0.00 0.00 3.41
3394 11095 2.213499 AGAAAAACCGTGCTCAGTGAG 58.787 47.619 16.21 16.21 0.00 3.51
3582 11294 2.165234 GGAGGGAGCTTGAGATTTTTGC 59.835 50.000 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.287238 ACAAAGTTCATCGACAACAACC 57.713 40.909 10.81 0.00 0.00 3.77
22 23 4.312443 GGTCCTACAAAGTTCATCGACAA 58.688 43.478 0.00 0.00 0.00 3.18
24 25 2.921754 CGGTCCTACAAAGTTCATCGAC 59.078 50.000 0.00 0.00 0.00 4.20
27 28 1.659098 CGCGGTCCTACAAAGTTCATC 59.341 52.381 0.00 0.00 0.00 2.92
28 29 1.274167 TCGCGGTCCTACAAAGTTCAT 59.726 47.619 6.13 0.00 0.00 2.57
32 33 3.454375 CATATTCGCGGTCCTACAAAGT 58.546 45.455 6.13 0.00 0.00 2.66
34 35 2.828877 CCATATTCGCGGTCCTACAAA 58.171 47.619 6.13 0.00 0.00 2.83
80 87 2.366916 GTCATGGGAGAAGGATGACGAT 59.633 50.000 0.00 0.00 37.37 3.73
84 91 2.268796 TGGTCATGGGAGAAGGATGA 57.731 50.000 0.00 0.00 0.00 2.92
115 122 1.447838 CTGGATCCACAACGACCGG 60.448 63.158 11.44 0.00 0.00 5.28
116 123 0.458543 CTCTGGATCCACAACGACCG 60.459 60.000 11.44 0.00 0.00 4.79
128 135 1.683917 GTGGATAGCACGACTCTGGAT 59.316 52.381 0.00 0.00 0.00 3.41
149 156 0.400213 TTCTCGAGGTTTGGCCACAT 59.600 50.000 13.56 0.00 40.61 3.21
164 171 2.863137 CAGAGCGCTATTCCAGTTTCTC 59.137 50.000 11.50 0.00 0.00 2.87
175 182 1.405463 TCATGAACGACAGAGCGCTAT 59.595 47.619 11.50 3.14 33.86 2.97
179 186 1.406219 CGGTCATGAACGACAGAGCG 61.406 60.000 28.97 5.59 45.97 5.03
183 190 2.100631 GCCCGGTCATGAACGACAG 61.101 63.158 33.84 21.59 45.97 3.51
188 195 2.818274 GTCGGCCCGGTCATGAAC 60.818 66.667 1.90 0.00 0.00 3.18
203 210 3.694364 ATCATGGGCTCGTGATGTC 57.306 52.632 20.68 0.00 45.15 3.06
220 227 1.732259 CGGAAGCTTTACAAGACGCAT 59.268 47.619 0.00 0.00 0.00 4.73
223 230 2.155155 GTGACGGAAGCTTTACAAGACG 59.845 50.000 0.00 0.13 0.00 4.18
241 248 2.209064 GAGGTGCGCTAGAACGGTGA 62.209 60.000 9.73 0.00 0.00 4.02
244 251 0.872021 GATGAGGTGCGCTAGAACGG 60.872 60.000 9.73 0.00 0.00 4.44
256 263 1.675641 GTGCCAAAGCGGATGAGGT 60.676 57.895 0.00 0.00 44.31 3.85
257 264 2.409870 GGTGCCAAAGCGGATGAGG 61.410 63.158 0.00 0.00 44.31 3.86
261 268 0.749454 GAGATGGTGCCAAAGCGGAT 60.749 55.000 0.00 0.00 44.31 4.18
263 270 1.243342 TTGAGATGGTGCCAAAGCGG 61.243 55.000 0.00 0.00 44.31 5.52
281 288 2.046292 GAGCTAGCCCCTCTCATCTTT 58.954 52.381 12.13 0.00 0.00 2.52
282 289 1.062581 TGAGCTAGCCCCTCTCATCTT 60.063 52.381 12.13 0.00 32.48 2.40
293 300 5.355596 GGATACATGATACATGAGCTAGCC 58.644 45.833 12.13 3.49 0.00 3.93
309 316 1.204146 AGGTGGCTCAACGGATACAT 58.796 50.000 0.00 0.00 0.00 2.29
338 345 1.022451 ACGGACGCACAACACTGTTT 61.022 50.000 0.00 0.00 31.64 2.83
339 346 1.426041 GACGGACGCACAACACTGTT 61.426 55.000 0.00 0.00 31.64 3.16
356 363 2.830704 CTAAGGTGACCGTGGGCGAC 62.831 65.000 0.00 0.00 41.33 5.19
364 371 1.805945 GCGACAGCTAAGGTGACCG 60.806 63.158 0.00 0.00 41.01 4.79
365 372 4.187056 GCGACAGCTAAGGTGACC 57.813 61.111 0.00 0.00 41.01 4.02
376 383 0.320771 AGGCTTGTACCAAGCGACAG 60.321 55.000 19.37 0.00 43.89 3.51
377 384 0.320421 GAGGCTTGTACCAAGCGACA 60.320 55.000 19.37 0.00 43.89 4.35
379 386 0.685097 AAGAGGCTTGTACCAAGCGA 59.315 50.000 19.37 0.00 43.89 4.93
381 388 0.523519 GCAAGAGGCTTGTACCAAGC 59.476 55.000 18.24 18.24 42.30 4.01
395 402 2.721167 CGTCCCCGATGAGGCAAGA 61.721 63.158 0.00 0.00 39.21 3.02
404 411 0.613853 TCAAGTTCTCCGTCCCCGAT 60.614 55.000 0.00 0.00 35.63 4.18
413 420 3.053831 TGGACGGAATTCAAGTTCTCC 57.946 47.619 7.93 5.40 0.00 3.71
414 421 3.375299 CCATGGACGGAATTCAAGTTCTC 59.625 47.826 5.56 2.56 0.00 2.87
419 426 2.991250 AGACCATGGACGGAATTCAAG 58.009 47.619 21.47 3.20 0.00 3.02
430 437 2.822561 GCAGATCGATCTAGACCATGGA 59.177 50.000 26.87 0.00 34.85 3.41
446 453 2.688507 CTGTGGTTGTAACGAGCAGAT 58.311 47.619 0.00 0.00 0.00 2.90
448 455 0.512952 GCTGTGGTTGTAACGAGCAG 59.487 55.000 0.00 0.00 0.00 4.24
457 464 2.186826 GCGAAGTGGCTGTGGTTGT 61.187 57.895 0.00 0.00 0.00 3.32
461 468 1.165907 TTCAAGCGAAGTGGCTGTGG 61.166 55.000 0.00 0.00 43.93 4.17
466 473 3.267974 CCCTTCAAGCGAAGTGGC 58.732 61.111 1.86 0.00 46.19 5.01
482 489 2.774799 GCGGTGGATGAATGTGGCC 61.775 63.158 0.00 0.00 0.00 5.36
499 506 0.948141 GCTCAGTGTCACAGACCTGC 60.948 60.000 5.62 0.00 33.82 4.85
502 509 1.004440 GGGCTCAGTGTCACAGACC 60.004 63.158 5.62 2.35 0.00 3.85
505 512 1.302033 GGTGGGCTCAGTGTCACAG 60.302 63.158 5.62 0.00 32.29 3.66
507 514 1.302033 CAGGTGGGCTCAGTGTCAC 60.302 63.158 0.00 0.00 0.00 3.67
530 537 2.393764 GAAACATTGTGCCGACCAAAG 58.606 47.619 0.00 0.00 0.00 2.77
545 552 1.659233 CGCTGTTGCATGGGAAACA 59.341 52.632 0.00 0.00 40.34 2.83
547 554 2.198969 TGCGCTGTTGCATGGGAAA 61.199 52.632 9.73 0.00 40.62 3.13
570 577 2.411765 AAAGAAGACGGTGGGGCTGG 62.412 60.000 0.00 0.00 0.00 4.85
571 578 0.955919 GAAAGAAGACGGTGGGGCTG 60.956 60.000 0.00 0.00 0.00 4.85
572 579 1.375326 GAAAGAAGACGGTGGGGCT 59.625 57.895 0.00 0.00 0.00 5.19
573 580 1.674651 GGAAAGAAGACGGTGGGGC 60.675 63.158 0.00 0.00 0.00 5.80
595 602 3.311871 ACGACATGACTATACACTCCGTC 59.688 47.826 0.00 0.00 0.00 4.79
596 603 3.276857 ACGACATGACTATACACTCCGT 58.723 45.455 0.00 0.00 0.00 4.69
597 604 3.965292 ACGACATGACTATACACTCCG 57.035 47.619 0.00 0.00 0.00 4.63
598 605 7.670009 ATACTACGACATGACTATACACTCC 57.330 40.000 0.00 0.00 0.00 3.85
599 606 9.947669 AAAATACTACGACATGACTATACACTC 57.052 33.333 0.00 0.00 0.00 3.51
653 660 9.864034 CACGATAGCAAACGATATCTAATTTTT 57.136 29.630 0.34 0.00 42.67 1.94
654 661 9.256477 TCACGATAGCAAACGATATCTAATTTT 57.744 29.630 0.34 0.00 42.67 1.82
655 662 8.812147 TCACGATAGCAAACGATATCTAATTT 57.188 30.769 0.34 0.00 42.67 1.82
656 663 8.812147 TTCACGATAGCAAACGATATCTAATT 57.188 30.769 0.34 0.00 42.67 1.40
657 664 8.812147 TTTCACGATAGCAAACGATATCTAAT 57.188 30.769 0.34 0.00 42.67 1.73
658 665 8.812147 ATTTCACGATAGCAAACGATATCTAA 57.188 30.769 0.34 0.00 42.67 2.10
659 666 8.812147 AATTTCACGATAGCAAACGATATCTA 57.188 30.769 0.34 0.00 42.67 1.98
660 667 7.715265 AATTTCACGATAGCAAACGATATCT 57.285 32.000 0.34 0.00 42.67 1.98
661 668 7.850982 ACAAATTTCACGATAGCAAACGATATC 59.149 33.333 0.00 0.00 42.67 1.63
662 669 7.693952 ACAAATTTCACGATAGCAAACGATAT 58.306 30.769 0.00 0.00 42.67 1.63
663 670 7.067532 ACAAATTTCACGATAGCAAACGATA 57.932 32.000 0.00 0.00 42.67 2.92
664 671 5.938322 ACAAATTTCACGATAGCAAACGAT 58.062 33.333 0.00 0.00 42.67 3.73
665 672 5.351233 ACAAATTTCACGATAGCAAACGA 57.649 34.783 0.00 0.00 42.67 3.85
666 673 7.719689 AATACAAATTTCACGATAGCAAACG 57.280 32.000 0.00 0.00 42.67 3.60
667 674 9.726034 CAAAATACAAATTTCACGATAGCAAAC 57.274 29.630 0.00 0.00 34.90 2.93
668 675 9.684448 TCAAAATACAAATTTCACGATAGCAAA 57.316 25.926 0.00 0.00 34.90 3.68
669 676 9.340695 CTCAAAATACAAATTTCACGATAGCAA 57.659 29.630 0.00 0.00 34.90 3.91
670 677 8.511321 ACTCAAAATACAAATTTCACGATAGCA 58.489 29.630 0.00 0.00 34.90 3.49
671 678 8.895932 ACTCAAAATACAAATTTCACGATAGC 57.104 30.769 0.00 0.00 34.90 2.97
674 681 9.528018 ACAAACTCAAAATACAAATTTCACGAT 57.472 25.926 0.00 0.00 34.12 3.73
675 682 8.802856 CACAAACTCAAAATACAAATTTCACGA 58.197 29.630 0.00 0.00 34.12 4.35
676 683 8.591312 ACACAAACTCAAAATACAAATTTCACG 58.409 29.630 0.00 0.00 34.12 4.35
679 686 9.209297 GCAACACAAACTCAAAATACAAATTTC 57.791 29.630 0.00 0.00 34.12 2.17
680 687 8.180920 GGCAACACAAACTCAAAATACAAATTT 58.819 29.630 0.00 0.00 36.87 1.82
681 688 7.201688 GGGCAACACAAACTCAAAATACAAATT 60.202 33.333 0.00 0.00 39.74 1.82
682 689 6.259829 GGGCAACACAAACTCAAAATACAAAT 59.740 34.615 0.00 0.00 39.74 2.32
683 690 5.582665 GGGCAACACAAACTCAAAATACAAA 59.417 36.000 0.00 0.00 39.74 2.83
684 691 5.105146 AGGGCAACACAAACTCAAAATACAA 60.105 36.000 0.00 0.00 39.74 2.41
685 692 4.404073 AGGGCAACACAAACTCAAAATACA 59.596 37.500 0.00 0.00 39.74 2.29
686 693 4.944048 AGGGCAACACAAACTCAAAATAC 58.056 39.130 0.00 0.00 39.74 1.89
687 694 6.716934 TTAGGGCAACACAAACTCAAAATA 57.283 33.333 0.00 0.00 39.74 1.40
688 695 5.606348 TTAGGGCAACACAAACTCAAAAT 57.394 34.783 0.00 0.00 39.74 1.82
689 696 5.606348 ATTAGGGCAACACAAACTCAAAA 57.394 34.783 0.00 0.00 39.74 2.44
690 697 6.491745 TGATATTAGGGCAACACAAACTCAAA 59.508 34.615 0.00 0.00 39.74 2.69
691 698 6.007076 TGATATTAGGGCAACACAAACTCAA 58.993 36.000 0.00 0.00 39.74 3.02
692 699 5.414454 GTGATATTAGGGCAACACAAACTCA 59.586 40.000 0.00 0.00 39.74 3.41
693 700 5.648092 AGTGATATTAGGGCAACACAAACTC 59.352 40.000 0.00 0.00 39.74 3.01
694 701 5.570320 AGTGATATTAGGGCAACACAAACT 58.430 37.500 0.00 0.00 39.74 2.66
695 702 5.897377 AGTGATATTAGGGCAACACAAAC 57.103 39.130 0.00 0.00 39.74 2.93
696 703 8.588290 AATTAGTGATATTAGGGCAACACAAA 57.412 30.769 0.00 0.00 39.74 2.83
697 704 9.688091 TTAATTAGTGATATTAGGGCAACACAA 57.312 29.630 0.00 0.00 39.74 3.33
698 705 9.688091 TTTAATTAGTGATATTAGGGCAACACA 57.312 29.630 0.00 0.00 39.74 3.72
702 709 9.308000 CCCATTTAATTAGTGATATTAGGGCAA 57.692 33.333 0.00 0.00 0.00 4.52
703 710 7.396055 GCCCATTTAATTAGTGATATTAGGGCA 59.604 37.037 0.00 0.00 41.51 5.36
704 711 7.147897 GGCCCATTTAATTAGTGATATTAGGGC 60.148 40.741 0.00 0.00 41.35 5.19
705 712 7.067008 CGGCCCATTTAATTAGTGATATTAGGG 59.933 40.741 0.00 0.00 0.00 3.53
706 713 7.067008 CCGGCCCATTTAATTAGTGATATTAGG 59.933 40.741 0.00 0.00 0.00 2.69
707 714 7.610305 ACCGGCCCATTTAATTAGTGATATTAG 59.390 37.037 0.00 0.00 0.00 1.73
708 715 7.463431 ACCGGCCCATTTAATTAGTGATATTA 58.537 34.615 0.00 0.00 0.00 0.98
709 716 6.311735 ACCGGCCCATTTAATTAGTGATATT 58.688 36.000 0.00 0.00 0.00 1.28
710 717 5.887754 ACCGGCCCATTTAATTAGTGATAT 58.112 37.500 0.00 0.00 0.00 1.63
711 718 5.313280 ACCGGCCCATTTAATTAGTGATA 57.687 39.130 0.00 0.00 0.00 2.15
712 719 4.178956 ACCGGCCCATTTAATTAGTGAT 57.821 40.909 0.00 0.00 0.00 3.06
713 720 3.655615 ACCGGCCCATTTAATTAGTGA 57.344 42.857 0.00 0.00 0.00 3.41
714 721 3.697045 TGAACCGGCCCATTTAATTAGTG 59.303 43.478 0.00 0.00 0.00 2.74
715 722 3.970842 TGAACCGGCCCATTTAATTAGT 58.029 40.909 0.00 0.00 0.00 2.24
716 723 4.158764 TGTTGAACCGGCCCATTTAATTAG 59.841 41.667 0.00 0.00 0.00 1.73
717 724 4.087182 TGTTGAACCGGCCCATTTAATTA 58.913 39.130 0.00 0.00 0.00 1.40
718 725 2.900546 TGTTGAACCGGCCCATTTAATT 59.099 40.909 0.00 0.00 0.00 1.40
719 726 2.530701 TGTTGAACCGGCCCATTTAAT 58.469 42.857 0.00 0.00 0.00 1.40
720 727 1.996798 TGTTGAACCGGCCCATTTAA 58.003 45.000 0.00 0.00 0.00 1.52
721 728 1.889829 CTTGTTGAACCGGCCCATTTA 59.110 47.619 0.00 0.00 0.00 1.40
722 729 0.678950 CTTGTTGAACCGGCCCATTT 59.321 50.000 0.00 0.00 0.00 2.32
728 735 3.039134 CACCCTTGTTGAACCGGC 58.961 61.111 0.00 0.00 0.00 6.13
742 749 5.813672 TGTCCTCTTATATAAACGTTGCACC 59.186 40.000 0.00 0.00 0.00 5.01
749 756 6.089551 CCGAATGCTGTCCTCTTATATAAACG 59.910 42.308 0.00 0.00 0.00 3.60
755 762 2.037251 GGCCGAATGCTGTCCTCTTATA 59.963 50.000 0.00 0.00 40.92 0.98
756 763 1.202698 GGCCGAATGCTGTCCTCTTAT 60.203 52.381 0.00 0.00 40.92 1.73
759 766 2.586792 GGCCGAATGCTGTCCTCT 59.413 61.111 0.00 0.00 40.92 3.69
760 767 2.892425 CGGCCGAATGCTGTCCTC 60.892 66.667 24.07 0.00 41.73 3.71
800 809 3.507009 GACTCGGTCGGGACTCGG 61.507 72.222 0.00 0.00 39.77 4.63
820 833 2.985847 GTGGCCGCCAAGAAGCTT 60.986 61.111 15.39 0.00 34.18 3.74
974 1012 1.523032 TACGCTCGATGGCTCTCGA 60.523 57.895 11.24 11.24 44.85 4.04
975 1013 1.369448 GTACGCTCGATGGCTCTCG 60.369 63.158 0.00 4.05 39.99 4.04
976 1014 1.369448 CGTACGCTCGATGGCTCTC 60.369 63.158 0.52 0.00 0.00 3.20
977 1015 2.716244 CGTACGCTCGATGGCTCT 59.284 61.111 0.52 0.00 0.00 4.09
989 1027 0.855349 GATCTGCATCTTGCCGTACG 59.145 55.000 8.69 8.69 44.23 3.67
991 1029 2.988010 AAGATCTGCATCTTGCCGTA 57.012 45.000 1.73 0.00 46.06 4.02
1113 1151 3.918591 GTGTAGTGATTCGTCGTTCACAT 59.081 43.478 23.27 14.99 43.72 3.21
1134 1184 2.633557 TAGAGGGGAAGAGGCGGGT 61.634 63.158 0.00 0.00 0.00 5.28
1138 1191 1.707106 GGTAGTAGAGGGGAAGAGGC 58.293 60.000 0.00 0.00 0.00 4.70
1245 1314 6.185114 AGGATGCTAGCTATGAAGAACAAT 57.815 37.500 17.23 0.00 0.00 2.71
1281 1456 8.951243 AGCAGAAAAGTTTTTATCTAGCTTAGG 58.049 33.333 1.64 0.00 0.00 2.69
1313 1492 3.640029 CCGGTCCAAAGCTATCTAACCTA 59.360 47.826 0.00 0.00 0.00 3.08
1369 1554 7.009540 CGATTTTTGAAACAAGAAGCATATCCC 59.990 37.037 0.00 0.00 0.00 3.85
1423 1711 2.696707 TGACACAGTTAGTTCGTCCCTT 59.303 45.455 0.00 0.00 0.00 3.95
1443 1731 5.156355 CCTATAGCAGCAAAACACAAACTG 58.844 41.667 0.00 0.00 0.00 3.16
1685 2645 7.781324 AAAGTAAAAGGTCACAATCCATGAT 57.219 32.000 0.00 0.00 0.00 2.45
1785 5933 5.128499 CCTCAATCAACCTCTGTCTGACTAT 59.872 44.000 9.51 0.00 0.00 2.12
1789 5937 2.027745 GCCTCAATCAACCTCTGTCTGA 60.028 50.000 0.00 0.00 0.00 3.27
1792 5940 1.363744 CGCCTCAATCAACCTCTGTC 58.636 55.000 0.00 0.00 0.00 3.51
1811 5959 6.349300 TCTATTAACATTGAAGGTGAGAGGC 58.651 40.000 0.00 0.00 0.00 4.70
1827 5975 9.831054 CGTGAGTTCGAATTACAATCTATTAAC 57.169 33.333 0.00 0.00 0.00 2.01
1853 6028 2.254350 GGCAAACCGAAACCGCTC 59.746 61.111 0.00 0.00 0.00 5.03
1862 6037 0.038343 CATCAAACCCAGGCAAACCG 60.038 55.000 0.00 0.00 42.76 4.44
1879 6054 8.195436 CCATTGTTCATAGAAAGAAATCAGCAT 58.805 33.333 0.00 0.00 0.00 3.79
1910 6087 4.672587 TCTACATGCCAACCATCTAGTC 57.327 45.455 0.00 0.00 29.71 2.59
1923 6183 7.094634 CCACACCCTAATTAATGATCTACATGC 60.095 40.741 0.00 0.00 39.39 4.06
1993 6467 9.729281 ATGTAGATCCATGCAAAATTTTCTTTT 57.271 25.926 0.00 0.00 0.00 2.27
1994 6468 9.158233 CATGTAGATCCATGCAAAATTTTCTTT 57.842 29.630 0.00 0.00 36.15 2.52
1995 6469 8.316214 ACATGTAGATCCATGCAAAATTTTCTT 58.684 29.630 10.76 0.00 44.88 2.52
1996 6470 7.844009 ACATGTAGATCCATGCAAAATTTTCT 58.156 30.769 10.76 0.00 44.88 2.52
1997 6471 9.585099 TTACATGTAGATCCATGCAAAATTTTC 57.415 29.630 5.56 0.00 44.88 2.29
1998 6472 9.590451 CTTACATGTAGATCCATGCAAAATTTT 57.410 29.630 5.56 0.00 44.88 1.82
1999 6473 8.970020 TCTTACATGTAGATCCATGCAAAATTT 58.030 29.630 5.56 0.00 44.88 1.82
2000 6474 8.523915 TCTTACATGTAGATCCATGCAAAATT 57.476 30.769 5.56 0.00 44.88 1.82
2001 6475 8.701908 ATCTTACATGTAGATCCATGCAAAAT 57.298 30.769 5.56 0.00 44.88 1.82
2002 6476 7.774625 TGATCTTACATGTAGATCCATGCAAAA 59.225 33.333 25.84 13.10 44.88 2.44
2003 6477 7.227314 GTGATCTTACATGTAGATCCATGCAAA 59.773 37.037 25.84 13.54 44.88 3.68
2004 6478 6.707608 GTGATCTTACATGTAGATCCATGCAA 59.292 38.462 25.84 13.97 44.88 4.08
2005 6479 6.183360 TGTGATCTTACATGTAGATCCATGCA 60.183 38.462 25.84 19.99 44.88 3.96
2006 6480 6.226052 TGTGATCTTACATGTAGATCCATGC 58.774 40.000 25.84 18.70 44.88 4.06
2028 6502 8.847196 TGTTAGTCTTAGTCGCTATATTCATGT 58.153 33.333 0.00 0.00 0.00 3.21
2040 6514 4.268644 CCATGCACATGTTAGTCTTAGTCG 59.731 45.833 9.63 0.00 37.11 4.18
2043 6517 5.872635 CAACCATGCACATGTTAGTCTTAG 58.127 41.667 9.63 0.00 37.11 2.18
2086 6616 9.796120 AATTTCTTTCGAGAAGAGTACTCATAG 57.204 33.333 24.44 10.39 34.47 2.23
2110 6645 6.210185 AGAGTGCTAGATTGGCAAAGAAAAAT 59.790 34.615 3.01 0.00 41.54 1.82
2116 6651 4.764172 ACTAGAGTGCTAGATTGGCAAAG 58.236 43.478 3.01 0.00 45.71 2.77
2174 6741 9.047371 TGACGAAAAACTTAGATATGTCACAAA 57.953 29.630 0.00 0.00 0.00 2.83
2175 6742 8.596271 TGACGAAAAACTTAGATATGTCACAA 57.404 30.769 0.00 0.00 0.00 3.33
2184 6755 5.607119 ACGCAATGACGAAAAACTTAGAT 57.393 34.783 4.30 0.00 36.70 1.98
2323 7344 3.253188 ACCAAGAACGTGGACAATTGATG 59.747 43.478 13.59 0.00 41.65 3.07
2388 7423 6.978659 CCAAGAACGACTCTAAGCATACAATA 59.021 38.462 0.00 0.00 32.46 1.90
2538 7585 6.601217 CCTCTTCTTTTCCCTTATCTGAAAGG 59.399 42.308 10.04 10.04 44.87 3.11
2702 7755 5.940470 ACTGGACAAAACTGACTCCAATATC 59.060 40.000 0.00 0.00 32.30 1.63
2859 7937 4.742201 CCGGGTGCCTGAGTGTCG 62.742 72.222 0.00 0.00 0.00 4.35
2867 7945 3.164269 CCTATCTGCCGGGTGCCT 61.164 66.667 2.18 0.00 40.16 4.75
2878 7956 7.181125 CCTATAGTGGGCAGATTTAACCTATCT 59.819 40.741 0.00 0.00 32.66 1.98
2935 8222 5.380043 TCATCAGGATATTTTGGAGCCTTC 58.620 41.667 0.00 0.00 0.00 3.46
2990 10530 3.006859 ACTTTTGCTTTCCCTAATGGTGC 59.993 43.478 0.00 0.00 34.77 5.01
3095 10635 2.058798 CGTTGAGTTTGAGCTCGCTAA 58.941 47.619 9.64 0.23 38.28 3.09
3112 10656 0.613260 TCTACCTCATTGGCAGCGTT 59.387 50.000 0.00 0.00 40.22 4.84
3122 10666 2.234908 GAGGCGGCAATATCTACCTCAT 59.765 50.000 13.08 0.00 42.64 2.90
3123 10667 1.618837 GAGGCGGCAATATCTACCTCA 59.381 52.381 13.08 0.00 42.64 3.86
3126 10670 2.543777 TTGAGGCGGCAATATCTACC 57.456 50.000 13.08 0.00 0.00 3.18
3127 10671 4.893424 TTTTTGAGGCGGCAATATCTAC 57.107 40.909 13.08 0.00 0.00 2.59
3128 10672 6.714810 ACATATTTTTGAGGCGGCAATATCTA 59.285 34.615 13.08 0.00 0.00 1.98
3129 10673 5.536161 ACATATTTTTGAGGCGGCAATATCT 59.464 36.000 13.08 0.00 0.00 1.98
3131 10675 5.301551 TCACATATTTTTGAGGCGGCAATAT 59.698 36.000 13.08 8.63 0.00 1.28
3132 10676 4.642437 TCACATATTTTTGAGGCGGCAATA 59.358 37.500 13.08 6.45 0.00 1.90
3133 10677 3.446873 TCACATATTTTTGAGGCGGCAAT 59.553 39.130 13.08 4.08 0.00 3.56
3134 10678 2.822561 TCACATATTTTTGAGGCGGCAA 59.177 40.909 13.08 0.00 0.00 4.52
3135 10679 2.441410 TCACATATTTTTGAGGCGGCA 58.559 42.857 13.08 0.00 0.00 5.69
3136 10680 3.502191 TTCACATATTTTTGAGGCGGC 57.498 42.857 0.00 0.00 0.00 6.53
3137 10681 6.098679 TCAATTTCACATATTTTTGAGGCGG 58.901 36.000 0.00 0.00 0.00 6.13
3138 10682 7.579589 TTCAATTTCACATATTTTTGAGGCG 57.420 32.000 0.00 0.00 0.00 5.52
3139 10683 8.323140 CGATTCAATTTCACATATTTTTGAGGC 58.677 33.333 0.00 0.00 0.00 4.70
3147 10691 8.906867 ACCTCATTCGATTCAATTTCACATATT 58.093 29.630 0.00 0.00 0.00 1.28
3148 10692 8.455903 ACCTCATTCGATTCAATTTCACATAT 57.544 30.769 0.00 0.00 0.00 1.78
3149 10693 7.864108 ACCTCATTCGATTCAATTTCACATA 57.136 32.000 0.00 0.00 0.00 2.29
3150 10694 6.764308 ACCTCATTCGATTCAATTTCACAT 57.236 33.333 0.00 0.00 0.00 3.21
3151 10695 7.102993 TCTACCTCATTCGATTCAATTTCACA 58.897 34.615 0.00 0.00 0.00 3.58
3156 10700 8.725148 GCAATATCTACCTCATTCGATTCAATT 58.275 33.333 0.00 0.00 0.00 2.32
3157 10701 7.335422 GGCAATATCTACCTCATTCGATTCAAT 59.665 37.037 0.00 0.00 0.00 2.57
3158 10702 6.650807 GGCAATATCTACCTCATTCGATTCAA 59.349 38.462 0.00 0.00 0.00 2.69
3228 10878 0.108138 GAGCTTGGCACGGTGATAGT 60.108 55.000 13.29 0.00 0.00 2.12
3234 10884 4.335647 CCAGGAGCTTGGCACGGT 62.336 66.667 0.00 0.00 0.00 4.83
3252 10902 4.379243 CTGGAGCCGGAGTTGCGT 62.379 66.667 5.05 0.00 0.00 5.24
3287 10954 0.944386 AGCACGTAAAACACTGGCTG 59.056 50.000 0.00 0.00 0.00 4.85
3302 10969 1.934399 GCAGATCCGAGCTATCAGCAC 60.934 57.143 7.30 0.00 45.56 4.40
3305 10972 1.202114 GGAGCAGATCCGAGCTATCAG 59.798 57.143 5.05 0.00 42.04 2.90
3359 11060 4.626172 GGTTTTTCTAAGGACGAGCTACAG 59.374 45.833 0.00 0.00 0.00 2.74
3369 11070 3.181458 ACTGAGCACGGTTTTTCTAAGGA 60.181 43.478 0.00 0.00 30.63 3.36
3391 11092 8.629158 AGTAAGTGTTGAAAATATTTGTGCTCA 58.371 29.630 0.39 0.00 0.00 4.26
3503 11212 6.072175 TGGCACTAACAAATTCCAGAATGTAC 60.072 38.462 0.00 0.00 0.00 2.90
3504 11213 6.007076 TGGCACTAACAAATTCCAGAATGTA 58.993 36.000 0.00 0.00 0.00 2.29
3519 11230 4.689612 TCCCTATCATCTTGGCACTAAC 57.310 45.455 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.