Multiple sequence alignment - TraesCS1B01G474000

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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 TraesCS1B01G474000 chr1B 100.000 3208 0 0 1 3208 682002416 682005623 0.000000e+00 5925.0
1 TraesCS1B01G474000 chr1B 94.286 2310 79 10 236 2517 682026798 682024514 0.000000e+00 3485.0
2 TraesCS1B01G474000 chr1B 83.709 399 35 10 752 1137 680832128 680832509 1.830000e-92 350.0
3 TraesCS1B01G474000 chr1B 81.609 435 53 15 829 1242 680744488 680744060 5.130000e-88 335.0
4 TraesCS1B01G474000 chr1B 81.379 435 54 15 829 1242 682487962 682487534 2.390000e-86 329.0
5 TraesCS1B01G474000 chr1B 89.394 198 11 10 1 191 682065582 682065388 1.150000e-59 241.0
6 TraesCS1B01G474000 chr1B 82.101 257 24 11 928 1184 681834420 681834654 1.950000e-47 200.0
7 TraesCS1B01G474000 chr1B 85.714 126 11 2 1290 1408 681787920 681788045 3.360000e-25 126.0
8 TraesCS1B01G474000 chr1B 76.518 247 47 8 2060 2295 681837782 681838028 1.210000e-24 124.0
9 TraesCS1B01G474000 chr1B 83.784 111 10 5 1527 1635 681788249 681788353 7.320000e-17 99.0
10 TraesCS1B01G474000 chr1B 93.617 47 3 0 1091 1137 681787889 681787935 1.600000e-08 71.3
11 TraesCS1B01G474000 chr1D 90.185 1192 31 25 641 1805 489755657 489756789 0.000000e+00 1474.0
12 TraesCS1B01G474000 chr1D 90.385 1092 59 25 1820 2904 489756927 489757979 0.000000e+00 1393.0
13 TraesCS1B01G474000 chr1D 89.398 415 38 3 217 631 489755270 489755678 4.740000e-143 518.0
14 TraesCS1B01G474000 chr1D 82.207 444 41 17 758 1174 489781212 489781644 6.590000e-92 348.0
15 TraesCS1B01G474000 chr1D 82.540 315 28 12 824 1137 488589389 488589677 5.310000e-63 252.0
16 TraesCS1B01G474000 chr1D 79.254 429 37 27 1300 1721 490305726 490306109 5.310000e-63 252.0
17 TraesCS1B01G474000 chr1D 87.931 174 10 8 48 220 489755060 489755223 9.080000e-46 195.0
18 TraesCS1B01G474000 chr1D 78.090 356 44 23 1967 2305 489782661 489782999 9.080000e-46 195.0
19 TraesCS1B01G474000 chr1D 77.882 321 42 18 1139 1432 489301116 489300798 4.250000e-39 172.0
20 TraesCS1B01G474000 chr1D 77.882 321 42 18 1139 1432 489326237 489325919 4.250000e-39 172.0
21 TraesCS1B01G474000 chr1D 77.882 321 42 18 1139 1432 489434004 489433686 4.250000e-39 172.0
22 TraesCS1B01G474000 chr1D 91.667 120 9 1 1302 1420 489781950 489782069 7.120000e-37 165.0
23 TraesCS1B01G474000 chr1D 79.839 248 27 13 2192 2431 460302005 460301773 3.310000e-35 159.0
24 TraesCS1B01G474000 chr1D 83.803 142 13 7 1527 1663 488637946 488638082 3.360000e-25 126.0
25 TraesCS1B01G474000 chr1D 89.474 95 6 2 2859 2953 489757984 489758074 2.020000e-22 117.0
26 TraesCS1B01G474000 chr1D 78.832 137 25 2 1139 1271 489300938 489300802 4.410000e-14 89.8
27 TraesCS1B01G474000 chr1D 78.832 137 25 2 1139 1271 489326059 489325923 4.410000e-14 89.8
28 TraesCS1B01G474000 chr1D 78.832 137 25 2 1139 1271 489433826 489433690 4.410000e-14 89.8
29 TraesCS1B01G474000 chr1D 95.122 41 2 0 1548 1588 488589854 488589894 7.430000e-07 65.8
30 TraesCS1B01G474000 chr1D 89.796 49 3 2 673 721 368675967 368675921 9.610000e-06 62.1
31 TraesCS1B01G474000 chr1D 83.824 68 4 3 496 558 347395041 347395106 1.240000e-04 58.4
32 TraesCS1B01G474000 chr1A 90.190 316 19 2 825 1140 588389559 588389256 4.980000e-108 401.0
33 TraesCS1B01G474000 chr1A 81.122 196 33 4 1527 1721 587705068 587704876 1.540000e-33 154.0
34 TraesCS1B01G474000 chr1A 89.796 49 3 2 673 721 468411368 468411322 9.610000e-06 62.1
35 TraesCS1B01G474000 chr1A 89.796 49 3 2 673 721 468462539 468462493 9.610000e-06 62.1
36 TraesCS1B01G474000 chrUn 81.839 435 52 14 829 1242 9173681 9173253 1.100000e-89 340.0
37 TraesCS1B01G474000 chrUn 81.379 435 54 15 829 1242 205602734 205602306 2.390000e-86 329.0
38 TraesCS1B01G474000 chrUn 80.851 235 42 2 289 523 99878667 99878898 7.070000e-42 182.0
39 TraesCS1B01G474000 chrUn 95.556 90 4 0 1300 1389 9171798 9171709 9.280000e-31 145.0
40 TraesCS1B01G474000 chrUn 73.850 413 64 28 2054 2453 2243193 2243574 1.210000e-24 124.0
41 TraesCS1B01G474000 chr5A 83.111 225 36 2 298 522 552952893 552953115 1.510000e-48 204.0
42 TraesCS1B01G474000 chr5D 82.805 221 35 3 304 524 238910952 238910735 9.080000e-46 195.0
43 TraesCS1B01G474000 chr5D 79.310 145 19 6 3023 3164 348162944 348162808 1.230000e-14 91.6
44 TraesCS1B01G474000 chr7A 79.392 296 41 11 304 584 630485297 630485007 1.170000e-44 191.0
45 TraesCS1B01G474000 chr7A 79.392 296 41 11 304 584 631902405 631902695 1.170000e-44 191.0
46 TraesCS1B01G474000 chr7B 80.214 187 35 2 333 518 544443151 544442966 4.320000e-29 139.0
47 TraesCS1B01G474000 chr2A 78.166 229 43 7 298 524 621856169 621855946 4.320000e-29 139.0
48 TraesCS1B01G474000 chr5B 78.947 114 10 5 3023 3124 689992858 689992747 7.430000e-07 65.8
49 TraesCS1B01G474000 chr4D 83.824 68 4 2 496 558 504323996 504323931 1.240000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G474000 chr1B 682002416 682005623 3207 False 5925.0 5925 100.0000 1 3208 1 chr1B.!!$F2 3207
1 TraesCS1B01G474000 chr1B 682024514 682026798 2284 True 3485.0 3485 94.2860 236 2517 1 chr1B.!!$R2 2281
2 TraesCS1B01G474000 chr1D 489755060 489758074 3014 False 739.4 1474 89.4746 48 2953 5 chr1D.!!$F5 2905
3 TraesCS1B01G474000 chr1D 489781212 489782999 1787 False 236.0 348 83.9880 758 2305 3 chr1D.!!$F6 1547
4 TraesCS1B01G474000 chrUn 9171709 9173681 1972 True 242.5 340 88.6975 829 1389 2 chrUn.!!$R2 560

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
664 719 0.255033 ATTAGGGCCGAAACCACCTC 59.745 55.000 2.36 0.0 34.59 3.85 F
1816 3362 7.304735 TGTGACTTGTTGATTTATACATGTGC 58.695 34.615 9.11 0.0 34.14 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 3547 0.250234 CACCGCCTTCATCTCCTCAA 59.750 55.0 0.0 0.0 0.0 3.02 R
2754 4485 0.187117 TGCACCTGTTTCCCCATGAA 59.813 50.0 0.0 0.0 0.0 2.57 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 5.885449 TTTGGAAAATGTCAAGGTCCATT 57.115 34.783 0.00 0.00 38.16 3.16
23 24 5.467035 TTGGAAAATGTCAAGGTCCATTC 57.533 39.130 0.00 0.00 38.16 2.67
24 25 4.739793 TGGAAAATGTCAAGGTCCATTCT 58.260 39.130 0.00 0.00 33.43 2.40
25 26 5.886609 TGGAAAATGTCAAGGTCCATTCTA 58.113 37.500 0.00 0.00 33.43 2.10
26 27 5.945784 TGGAAAATGTCAAGGTCCATTCTAG 59.054 40.000 0.00 0.00 33.43 2.43
27 28 6.180472 GGAAAATGTCAAGGTCCATTCTAGA 58.820 40.000 0.00 0.00 31.15 2.43
28 29 6.659242 GGAAAATGTCAAGGTCCATTCTAGAA 59.341 38.462 7.82 7.82 31.15 2.10
29 30 7.176690 GGAAAATGTCAAGGTCCATTCTAGAAA 59.823 37.037 9.71 0.00 31.15 2.52
30 31 8.477419 AAAATGTCAAGGTCCATTCTAGAAAA 57.523 30.769 9.71 0.00 31.15 2.29
31 32 8.477419 AAATGTCAAGGTCCATTCTAGAAAAA 57.523 30.769 9.71 0.00 31.15 1.94
79 80 9.931210 AGAAAAGAAAAAGTAACGACATAACAG 57.069 29.630 0.00 0.00 0.00 3.16
82 83 9.712359 AAAGAAAAAGTAACGACATAACAGAAC 57.288 29.630 0.00 0.00 0.00 3.01
84 85 9.754382 AGAAAAAGTAACGACATAACAGAACTA 57.246 29.630 0.00 0.00 0.00 2.24
138 139 2.738013 ACCGGTAAACTAGCACAGAC 57.262 50.000 4.49 0.00 0.00 3.51
173 174 6.470456 AAGAAGAAGAAAGGGGAATAACCT 57.530 37.500 0.00 0.00 40.96 3.50
177 178 4.606255 AGAAGAAAGGGGAATAACCTGGAA 59.394 41.667 0.00 0.00 38.63 3.53
214 215 3.194005 TCAGAGAAGGTTCGCAAAACT 57.806 42.857 0.00 0.00 32.29 2.66
267 318 7.275920 ACAAAAGGTGAGATATAACTAGCCTG 58.724 38.462 5.86 0.00 0.00 4.85
300 351 2.096220 TTAATTAGTGCGGGCGAACA 57.904 45.000 0.00 0.00 0.00 3.18
325 376 6.390504 TGTGGTTGGATAGTTATAGGAGGAT 58.609 40.000 0.00 0.00 0.00 3.24
328 379 7.894364 GTGGTTGGATAGTTATAGGAGGATAGA 59.106 40.741 0.00 0.00 0.00 1.98
360 411 2.341257 CTCATCAGGGTTCAAGTCGTG 58.659 52.381 0.00 0.00 0.00 4.35
406 457 7.657761 CGTTATATCTGGACTTATTTCAGGCTT 59.342 37.037 0.00 0.00 0.00 4.35
409 460 5.241403 TCTGGACTTATTTCAGGCTTTCA 57.759 39.130 0.00 0.00 0.00 2.69
538 589 2.185867 GGGCGTGCGTTCATAGGA 59.814 61.111 0.00 0.00 0.00 2.94
646 701 0.957395 CTCCGTTGAGTGCAAGCCAT 60.957 55.000 0.00 0.00 34.01 4.40
664 719 0.255033 ATTAGGGCCGAAACCACCTC 59.745 55.000 2.36 0.00 34.59 3.85
1816 3362 7.304735 TGTGACTTGTTGATTTATACATGTGC 58.695 34.615 9.11 0.00 34.14 4.57
1874 3547 2.975489 TGAAGAAGGAAGAGCTGGACTT 59.025 45.455 0.00 0.00 0.00 3.01
1875 3548 3.392616 TGAAGAAGGAAGAGCTGGACTTT 59.607 43.478 0.00 0.00 0.00 2.66
1892 3592 0.984230 TTTGAGGAGATGAAGGCGGT 59.016 50.000 0.00 0.00 0.00 5.68
1901 3601 4.299978 GAGATGAAGGCGGTGTTAGATAC 58.700 47.826 0.00 0.00 0.00 2.24
1945 3645 2.567615 GCAGGACCCTCTGTCTTTCTAA 59.432 50.000 0.00 0.00 43.89 2.10
2021 3740 8.472683 TTTTGTTTGTTTGACAGGAGTTTATG 57.527 30.769 0.00 0.00 0.00 1.90
2147 3869 0.642291 CACTTGTCTATGTCGCTGCG 59.358 55.000 17.25 17.25 0.00 5.18
2218 3940 5.014123 AGGAAAACCAGTGACTTATGATGGA 59.986 40.000 0.00 0.00 34.99 3.41
2411 4139 6.573664 AACTGTAGCTTGATGCAAACATAA 57.426 33.333 0.00 0.00 45.94 1.90
2452 4180 2.488937 CTGTCATGCATTGCTGGTGTTA 59.511 45.455 10.49 0.00 0.00 2.41
2455 4183 4.704057 TGTCATGCATTGCTGGTGTTATTA 59.296 37.500 10.49 0.00 0.00 0.98
2517 4245 7.731054 ACTTAGAAGTGTTCACTCTCTGAAAT 58.269 34.615 18.39 0.75 40.73 2.17
2562 4291 4.818546 CAGATCCTTTCACTTTGTGACTGT 59.181 41.667 0.00 0.00 42.60 3.55
2688 4419 4.937620 GTCTTGACCTATTCATTCTGCACA 59.062 41.667 0.00 0.00 32.84 4.57
2691 4422 6.317140 TCTTGACCTATTCATTCTGCACATTC 59.683 38.462 0.00 0.00 32.84 2.67
2693 4424 5.121380 ACCTATTCATTCTGCACATTCCT 57.879 39.130 0.00 0.00 0.00 3.36
2695 4426 5.954150 ACCTATTCATTCTGCACATTCCTTT 59.046 36.000 0.00 0.00 0.00 3.11
2696 4427 6.438425 ACCTATTCATTCTGCACATTCCTTTT 59.562 34.615 0.00 0.00 0.00 2.27
2699 4430 9.674824 CTATTCATTCTGCACATTCCTTTTATC 57.325 33.333 0.00 0.00 0.00 1.75
2700 4431 7.465353 TTCATTCTGCACATTCCTTTTATCA 57.535 32.000 0.00 0.00 0.00 2.15
2702 4433 4.970662 TCTGCACATTCCTTTTATCAGC 57.029 40.909 0.00 0.00 0.00 4.26
2703 4434 4.334552 TCTGCACATTCCTTTTATCAGCA 58.665 39.130 0.00 0.00 0.00 4.41
2705 4436 3.825585 TGCACATTCCTTTTATCAGCACA 59.174 39.130 0.00 0.00 0.00 4.57
2706 4437 4.168760 GCACATTCCTTTTATCAGCACAC 58.831 43.478 0.00 0.00 0.00 3.82
2707 4438 4.321156 GCACATTCCTTTTATCAGCACACA 60.321 41.667 0.00 0.00 0.00 3.72
2708 4439 5.622914 GCACATTCCTTTTATCAGCACACAT 60.623 40.000 0.00 0.00 0.00 3.21
2709 4440 5.803461 CACATTCCTTTTATCAGCACACATG 59.197 40.000 0.00 0.00 0.00 3.21
2710 4441 5.711506 ACATTCCTTTTATCAGCACACATGA 59.288 36.000 0.00 0.00 0.00 3.07
2711 4442 5.885230 TTCCTTTTATCAGCACACATGAG 57.115 39.130 0.00 0.00 0.00 2.90
2712 4443 4.264253 TCCTTTTATCAGCACACATGAGG 58.736 43.478 0.00 0.00 0.00 3.86
2713 4444 4.012374 CCTTTTATCAGCACACATGAGGT 58.988 43.478 0.00 0.00 0.00 3.85
2715 4446 5.647658 CCTTTTATCAGCACACATGAGGTTA 59.352 40.000 0.00 0.00 0.00 2.85
2717 4448 3.988976 ATCAGCACACATGAGGTTACT 57.011 42.857 0.00 0.00 0.00 2.24
2718 4449 3.319137 TCAGCACACATGAGGTTACTC 57.681 47.619 0.00 0.00 44.23 2.59
2732 4463 6.215495 GAGGTTACTCATTTAGCACTCTCT 57.785 41.667 0.00 0.00 43.41 3.10
2744 4475 3.733337 AGCACTCTCTTACAAACCTGTG 58.267 45.455 0.00 0.00 36.96 3.66
2754 4485 5.359576 TCTTACAAACCTGTGCAGTTCAAAT 59.640 36.000 0.00 0.00 36.96 2.32
2763 4494 2.562298 GTGCAGTTCAAATTCATGGGGA 59.438 45.455 0.00 0.00 0.00 4.81
2801 4532 3.745723 GGAGCAACCTTTCCCTTCA 57.254 52.632 0.00 0.00 35.41 3.02
2802 4533 1.995376 GGAGCAACCTTTCCCTTCAA 58.005 50.000 0.00 0.00 35.41 2.69
2803 4534 2.316108 GGAGCAACCTTTCCCTTCAAA 58.684 47.619 0.00 0.00 35.41 2.69
2804 4535 2.899900 GGAGCAACCTTTCCCTTCAAAT 59.100 45.455 0.00 0.00 35.41 2.32
2805 4536 3.324846 GGAGCAACCTTTCCCTTCAAATT 59.675 43.478 0.00 0.00 35.41 1.82
2806 4537 4.526650 GGAGCAACCTTTCCCTTCAAATTA 59.473 41.667 0.00 0.00 35.41 1.40
2807 4538 5.336770 GGAGCAACCTTTCCCTTCAAATTAG 60.337 44.000 0.00 0.00 35.41 1.73
2808 4539 5.147767 AGCAACCTTTCCCTTCAAATTAGT 58.852 37.500 0.00 0.00 0.00 2.24
2809 4540 5.011023 AGCAACCTTTCCCTTCAAATTAGTG 59.989 40.000 0.00 0.00 0.00 2.74
2810 4541 5.230182 CAACCTTTCCCTTCAAATTAGTGC 58.770 41.667 0.00 0.00 0.00 4.40
2811 4542 4.479158 ACCTTTCCCTTCAAATTAGTGCA 58.521 39.130 0.00 0.00 0.00 4.57
2812 4543 4.524328 ACCTTTCCCTTCAAATTAGTGCAG 59.476 41.667 0.00 0.00 0.00 4.41
2813 4544 4.082026 CCTTTCCCTTCAAATTAGTGCAGG 60.082 45.833 0.00 0.00 32.26 4.85
2814 4545 2.446435 TCCCTTCAAATTAGTGCAGGC 58.554 47.619 0.00 0.00 31.21 4.85
2815 4546 1.478105 CCCTTCAAATTAGTGCAGGCC 59.522 52.381 0.00 0.00 31.21 5.19
2816 4547 2.170166 CCTTCAAATTAGTGCAGGCCA 58.830 47.619 5.01 0.00 0.00 5.36
2817 4548 2.762327 CCTTCAAATTAGTGCAGGCCAT 59.238 45.455 5.01 0.00 0.00 4.40
2818 4549 3.181483 CCTTCAAATTAGTGCAGGCCATC 60.181 47.826 5.01 0.00 0.00 3.51
2819 4550 3.370840 TCAAATTAGTGCAGGCCATCT 57.629 42.857 5.01 0.00 0.00 2.90
2820 4551 4.502105 TCAAATTAGTGCAGGCCATCTA 57.498 40.909 5.01 0.00 0.00 1.98
2821 4552 4.854173 TCAAATTAGTGCAGGCCATCTAA 58.146 39.130 5.01 8.36 0.00 2.10
2825 4556 2.584835 AGTGCAGGCCATCTAACAAA 57.415 45.000 5.01 0.00 0.00 2.83
2842 4573 7.572759 TCTAACAAATGCTAAACAAGAGAACG 58.427 34.615 0.00 0.00 0.00 3.95
2865 4597 5.853282 CGCTGGAAGTTTGTTCTAGATTTTG 59.147 40.000 0.00 0.00 35.30 2.44
2866 4598 5.631096 GCTGGAAGTTTGTTCTAGATTTTGC 59.369 40.000 0.00 0.00 35.30 3.68
2867 4599 5.757886 TGGAAGTTTGTTCTAGATTTTGCG 58.242 37.500 0.00 0.00 0.00 4.85
2868 4600 5.529430 TGGAAGTTTGTTCTAGATTTTGCGA 59.471 36.000 0.00 0.00 0.00 5.10
2869 4601 6.206634 TGGAAGTTTGTTCTAGATTTTGCGAT 59.793 34.615 0.00 0.00 0.00 4.58
2870 4602 6.743172 GGAAGTTTGTTCTAGATTTTGCGATC 59.257 38.462 0.00 0.00 0.00 3.69
2875 4650 8.656849 GTTTGTTCTAGATTTTGCGATCTTCTA 58.343 33.333 0.00 0.00 37.54 2.10
2944 4719 6.016527 CCTCCAATCCATATCAATTGTCACTG 60.017 42.308 5.13 0.00 32.20 3.66
2945 4720 6.425735 TCCAATCCATATCAATTGTCACTGT 58.574 36.000 5.13 0.00 32.20 3.55
2953 4728 7.653713 CCATATCAATTGTCACTGTAGGTAGTC 59.346 40.741 5.13 0.00 0.00 2.59
2954 4729 6.859112 ATCAATTGTCACTGTAGGTAGTCT 57.141 37.500 5.13 0.00 0.00 3.24
2955 4730 6.665992 TCAATTGTCACTGTAGGTAGTCTT 57.334 37.500 5.13 0.00 0.00 3.01
2956 4731 6.455647 TCAATTGTCACTGTAGGTAGTCTTG 58.544 40.000 5.13 0.00 0.00 3.02
2957 4732 6.041637 TCAATTGTCACTGTAGGTAGTCTTGT 59.958 38.462 5.13 0.00 0.00 3.16
2958 4733 5.449107 TTGTCACTGTAGGTAGTCTTGTC 57.551 43.478 0.00 0.00 0.00 3.18
2959 4734 4.726583 TGTCACTGTAGGTAGTCTTGTCT 58.273 43.478 0.00 0.00 0.00 3.41
2960 4735 5.138276 TGTCACTGTAGGTAGTCTTGTCTT 58.862 41.667 0.00 0.00 0.00 3.01
2961 4736 5.009710 TGTCACTGTAGGTAGTCTTGTCTTG 59.990 44.000 0.00 0.00 0.00 3.02
2962 4737 5.241064 GTCACTGTAGGTAGTCTTGTCTTGA 59.759 44.000 0.00 0.00 0.00 3.02
2963 4738 5.241064 TCACTGTAGGTAGTCTTGTCTTGAC 59.759 44.000 0.00 0.00 34.88 3.18
2964 4739 5.009710 CACTGTAGGTAGTCTTGTCTTGACA 59.990 44.000 0.00 0.00 36.94 3.58
2965 4740 5.775701 ACTGTAGGTAGTCTTGTCTTGACAT 59.224 40.000 4.18 0.00 36.94 3.06
2966 4741 6.025749 TGTAGGTAGTCTTGTCTTGACATG 57.974 41.667 4.18 7.23 36.94 3.21
2967 4742 5.538813 TGTAGGTAGTCTTGTCTTGACATGT 59.461 40.000 0.00 0.00 36.94 3.21
2968 4743 5.552870 AGGTAGTCTTGTCTTGACATGTT 57.447 39.130 0.00 8.24 36.94 2.71
2969 4744 5.542779 AGGTAGTCTTGTCTTGACATGTTC 58.457 41.667 0.00 9.74 36.94 3.18
2970 4745 5.070446 AGGTAGTCTTGTCTTGACATGTTCA 59.930 40.000 0.00 0.00 36.94 3.18
2971 4746 5.934625 GGTAGTCTTGTCTTGACATGTTCAT 59.065 40.000 0.00 4.73 36.94 2.57
2972 4747 6.428159 GGTAGTCTTGTCTTGACATGTTCATT 59.572 38.462 0.00 0.00 36.94 2.57
2973 4748 6.551385 AGTCTTGTCTTGACATGTTCATTC 57.449 37.500 0.00 0.00 36.94 2.67
2974 4749 6.294473 AGTCTTGTCTTGACATGTTCATTCT 58.706 36.000 0.00 4.98 36.94 2.40
2975 4750 6.204301 AGTCTTGTCTTGACATGTTCATTCTG 59.796 38.462 0.00 0.00 36.94 3.02
2976 4751 4.754372 TGTCTTGACATGTTCATTCTGC 57.246 40.909 0.00 0.00 32.84 4.26
2977 4752 4.136051 TGTCTTGACATGTTCATTCTGCA 58.864 39.130 0.00 0.00 32.84 4.41
2978 4753 4.763279 TGTCTTGACATGTTCATTCTGCAT 59.237 37.500 0.00 0.00 32.84 3.96
2979 4754 5.093457 GTCTTGACATGTTCATTCTGCATG 58.907 41.667 0.00 0.00 43.84 4.06
2984 4759 4.713824 CATGTTCATTCTGCATGTTCCT 57.286 40.909 0.00 0.00 36.28 3.36
2985 4760 5.068234 CATGTTCATTCTGCATGTTCCTT 57.932 39.130 0.00 0.00 36.28 3.36
2986 4761 5.475719 CATGTTCATTCTGCATGTTCCTTT 58.524 37.500 0.00 0.00 36.28 3.11
2987 4762 5.534207 TGTTCATTCTGCATGTTCCTTTT 57.466 34.783 0.00 0.00 34.06 2.27
2988 4763 6.647334 TGTTCATTCTGCATGTTCCTTTTA 57.353 33.333 0.00 0.00 34.06 1.52
2989 4764 7.230849 TGTTCATTCTGCATGTTCCTTTTAT 57.769 32.000 0.00 0.00 34.06 1.40
2990 4765 7.315142 TGTTCATTCTGCATGTTCCTTTTATC 58.685 34.615 0.00 0.00 34.06 1.75
2991 4766 7.039853 TGTTCATTCTGCATGTTCCTTTTATCA 60.040 33.333 0.00 0.00 34.06 2.15
2992 4767 7.092137 TCATTCTGCATGTTCCTTTTATCAG 57.908 36.000 0.00 0.00 34.06 2.90
2993 4768 4.970662 TCTGCATGTTCCTTTTATCAGC 57.029 40.909 0.00 0.00 0.00 4.26
2994 4769 4.334552 TCTGCATGTTCCTTTTATCAGCA 58.665 39.130 0.00 0.00 0.00 4.41
2995 4770 4.156556 TCTGCATGTTCCTTTTATCAGCAC 59.843 41.667 0.00 0.00 0.00 4.40
2996 4771 3.825585 TGCATGTTCCTTTTATCAGCACA 59.174 39.130 0.00 0.00 0.00 4.57
2997 4772 4.280425 TGCATGTTCCTTTTATCAGCACAA 59.720 37.500 0.00 0.00 0.00 3.33
2998 4773 5.221402 TGCATGTTCCTTTTATCAGCACAAA 60.221 36.000 0.00 0.00 0.00 2.83
2999 4774 5.870978 GCATGTTCCTTTTATCAGCACAAAT 59.129 36.000 0.00 0.00 0.00 2.32
3000 4775 6.183360 GCATGTTCCTTTTATCAGCACAAATG 60.183 38.462 0.00 0.00 0.00 2.32
3001 4776 6.647334 TGTTCCTTTTATCAGCACAAATGA 57.353 33.333 0.00 0.00 0.00 2.57
3002 4777 6.680810 TGTTCCTTTTATCAGCACAAATGAG 58.319 36.000 0.00 0.00 0.00 2.90
3003 4778 5.902613 TCCTTTTATCAGCACAAATGAGG 57.097 39.130 0.00 0.00 0.00 3.86
3004 4779 5.324409 TCCTTTTATCAGCACAAATGAGGT 58.676 37.500 0.00 0.00 0.00 3.85
3005 4780 5.774690 TCCTTTTATCAGCACAAATGAGGTT 59.225 36.000 0.00 0.00 0.00 3.50
3006 4781 6.945435 TCCTTTTATCAGCACAAATGAGGTTA 59.055 34.615 0.00 0.00 0.00 2.85
3007 4782 7.615365 TCCTTTTATCAGCACAAATGAGGTTAT 59.385 33.333 0.00 0.00 0.00 1.89
3008 4783 8.253113 CCTTTTATCAGCACAAATGAGGTTATT 58.747 33.333 0.00 0.00 0.00 1.40
3009 4784 9.294030 CTTTTATCAGCACAAATGAGGTTATTC 57.706 33.333 0.00 0.00 0.00 1.75
3010 4785 7.936496 TTATCAGCACAAATGAGGTTATTCA 57.064 32.000 0.00 0.00 0.00 2.57
3011 4786 8.523915 TTATCAGCACAAATGAGGTTATTCAT 57.476 30.769 0.00 0.00 39.42 2.57
3012 4787 6.839124 TCAGCACAAATGAGGTTATTCATT 57.161 33.333 0.00 0.00 46.81 2.57
3021 4796 6.949352 ATGAGGTTATTCATTTAGCACTGG 57.051 37.500 0.00 0.00 34.17 4.00
3022 4797 6.061022 TGAGGTTATTCATTTAGCACTGGA 57.939 37.500 0.00 0.00 0.00 3.86
3023 4798 6.480763 TGAGGTTATTCATTTAGCACTGGAA 58.519 36.000 0.00 0.00 0.00 3.53
3024 4799 6.945435 TGAGGTTATTCATTTAGCACTGGAAA 59.055 34.615 0.00 0.00 0.00 3.13
3025 4800 7.615365 TGAGGTTATTCATTTAGCACTGGAAAT 59.385 33.333 0.00 0.00 0.00 2.17
3026 4801 7.775120 AGGTTATTCATTTAGCACTGGAAATG 58.225 34.615 0.00 0.00 42.09 2.32
3027 4802 6.476706 GGTTATTCATTTAGCACTGGAAATGC 59.523 38.462 3.08 0.00 41.03 3.56
3035 4810 3.795623 GCACTGGAAATGCTGAATGAT 57.204 42.857 0.00 0.00 40.08 2.45
3036 4811 3.444916 GCACTGGAAATGCTGAATGATG 58.555 45.455 0.00 0.00 40.08 3.07
3037 4812 3.737047 GCACTGGAAATGCTGAATGATGG 60.737 47.826 0.00 0.00 40.08 3.51
3038 4813 3.697542 CACTGGAAATGCTGAATGATGGA 59.302 43.478 0.00 0.00 0.00 3.41
3039 4814 3.698040 ACTGGAAATGCTGAATGATGGAC 59.302 43.478 0.00 0.00 0.00 4.02
3040 4815 2.684374 TGGAAATGCTGAATGATGGACG 59.316 45.455 0.00 0.00 0.00 4.79
3041 4816 2.945008 GGAAATGCTGAATGATGGACGA 59.055 45.455 0.00 0.00 0.00 4.20
3042 4817 3.003068 GGAAATGCTGAATGATGGACGAG 59.997 47.826 0.00 0.00 0.00 4.18
3043 4818 1.590932 ATGCTGAATGATGGACGAGC 58.409 50.000 0.00 0.00 0.00 5.03
3044 4819 0.538584 TGCTGAATGATGGACGAGCT 59.461 50.000 0.00 0.00 0.00 4.09
3045 4820 1.216122 GCTGAATGATGGACGAGCTC 58.784 55.000 2.73 2.73 0.00 4.09
3046 4821 1.863267 CTGAATGATGGACGAGCTCC 58.137 55.000 8.47 0.00 39.97 4.70
3052 4827 3.621225 TGGACGAGCTCCATGGAG 58.379 61.111 33.73 33.73 44.99 3.86
3123 4898 8.902540 AATATTACACACGTTCATATGGATGT 57.097 30.769 2.73 2.73 34.41 3.06
3124 4899 9.990360 AATATTACACACGTTCATATGGATGTA 57.010 29.630 8.60 0.07 34.41 2.29
3128 4903 9.990360 TTACACACGTTCATATGGATGTATATT 57.010 29.630 8.60 0.00 34.41 1.28
3169 4944 8.797350 TTGAAGATCATATACATTATGGCAGG 57.203 34.615 0.00 0.00 0.00 4.85
3170 4945 8.149631 TGAAGATCATATACATTATGGCAGGA 57.850 34.615 0.00 0.00 0.00 3.86
3171 4946 8.262933 TGAAGATCATATACATTATGGCAGGAG 58.737 37.037 0.00 0.00 0.00 3.69
3172 4947 6.590068 AGATCATATACATTATGGCAGGAGC 58.410 40.000 0.00 0.00 41.10 4.70
3173 4948 6.386342 AGATCATATACATTATGGCAGGAGCT 59.614 38.462 0.00 0.00 41.70 4.09
3174 4949 7.566509 AGATCATATACATTATGGCAGGAGCTA 59.433 37.037 0.00 0.00 41.70 3.32
3175 4950 6.878317 TCATATACATTATGGCAGGAGCTAC 58.122 40.000 0.00 0.00 41.70 3.58
3176 4951 6.440328 TCATATACATTATGGCAGGAGCTACA 59.560 38.462 0.00 0.00 41.70 2.74
3177 4952 3.199880 ACATTATGGCAGGAGCTACAC 57.800 47.619 0.00 0.00 41.70 2.90
3178 4953 2.505407 ACATTATGGCAGGAGCTACACA 59.495 45.455 0.00 0.00 41.70 3.72
3179 4954 3.054434 ACATTATGGCAGGAGCTACACAA 60.054 43.478 0.00 0.00 41.70 3.33
3180 4955 3.712016 TTATGGCAGGAGCTACACAAA 57.288 42.857 0.00 0.00 41.70 2.83
3181 4956 2.584835 ATGGCAGGAGCTACACAAAA 57.415 45.000 0.00 0.00 41.70 2.44
3182 4957 2.356665 TGGCAGGAGCTACACAAAAA 57.643 45.000 0.00 0.00 41.70 1.94
3200 4975 3.521524 AAAAGAGACAATCGTCAACGC 57.478 42.857 0.00 0.00 45.23 4.84
3201 4976 2.148916 AAGAGACAATCGTCAACGCA 57.851 45.000 0.00 0.00 45.23 5.24
3202 4977 2.370281 AGAGACAATCGTCAACGCAT 57.630 45.000 0.00 0.00 45.23 4.73
3203 4978 2.688507 AGAGACAATCGTCAACGCATT 58.311 42.857 0.00 0.00 45.23 3.56
3204 4979 3.067106 AGAGACAATCGTCAACGCATTT 58.933 40.909 0.00 0.00 45.23 2.32
3205 4980 3.498397 AGAGACAATCGTCAACGCATTTT 59.502 39.130 0.00 0.00 45.23 1.82
3206 4981 3.810373 AGACAATCGTCAACGCATTTTC 58.190 40.909 0.00 2.70 45.23 2.29
3207 4982 3.249799 AGACAATCGTCAACGCATTTTCA 59.750 39.130 0.00 0.00 45.23 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.602145 AGAATGGACCTTGACATTTTCCAAA 59.398 36.000 4.11 0.00 39.77 3.28
1 2 5.147032 AGAATGGACCTTGACATTTTCCAA 58.853 37.500 4.11 0.00 39.77 3.53
2 3 4.739793 AGAATGGACCTTGACATTTTCCA 58.260 39.130 0.00 2.76 40.61 3.53
3 4 6.180472 TCTAGAATGGACCTTGACATTTTCC 58.820 40.000 0.00 0.00 37.43 3.13
4 5 7.687941 TTCTAGAATGGACCTTGACATTTTC 57.312 36.000 0.00 0.00 37.43 2.29
5 6 8.477419 TTTTCTAGAATGGACCTTGACATTTT 57.523 30.769 5.89 0.00 37.43 1.82
6 7 8.477419 TTTTTCTAGAATGGACCTTGACATTT 57.523 30.769 5.89 0.00 37.43 2.32
96 97 9.908152 CGGTTTTCTTTTTGTTCCTTCTATTAT 57.092 29.630 0.00 0.00 0.00 1.28
102 103 4.751060 ACCGGTTTTCTTTTTGTTCCTTC 58.249 39.130 0.00 0.00 0.00 3.46
150 151 6.249192 CAGGTTATTCCCCTTTCTTCTTCTT 58.751 40.000 0.00 0.00 36.75 2.52
151 152 5.281245 CCAGGTTATTCCCCTTTCTTCTTCT 60.281 44.000 0.00 0.00 36.75 2.85
152 153 4.950475 CCAGGTTATTCCCCTTTCTTCTTC 59.050 45.833 0.00 0.00 36.75 2.87
173 174 1.774254 TGCTTCAGAAGGTTCCTTCCA 59.226 47.619 23.02 13.35 42.30 3.53
214 215 0.967887 AGAAGCACTCGCCTCTAGCA 60.968 55.000 0.00 0.00 44.04 3.49
284 335 0.392461 ACATGTTCGCCCGCACTAAT 60.392 50.000 0.00 0.00 0.00 1.73
300 351 6.390504 TCCTCCTATAACTATCCAACCACAT 58.609 40.000 0.00 0.00 0.00 3.21
325 376 2.110721 TGATGAGCTAGGGATGCCTCTA 59.889 50.000 10.00 0.00 0.00 2.43
328 379 1.350071 CTGATGAGCTAGGGATGCCT 58.650 55.000 11.82 11.82 0.00 4.75
458 509 8.564574 TCTTGATATTTTACAAAGTCACCACAC 58.435 33.333 0.00 0.00 0.00 3.82
538 589 5.521906 AGTCACTCGCATACACTCATATT 57.478 39.130 0.00 0.00 0.00 1.28
594 646 7.578203 CCCTATTGGTTATCTTCCTTCTTCTT 58.422 38.462 0.00 0.00 0.00 2.52
646 701 1.681076 GAGGTGGTTTCGGCCCTAA 59.319 57.895 0.00 0.00 0.00 2.69
660 715 4.777463 TCTTCGTTCTTTTTCTTGGAGGT 58.223 39.130 0.00 0.00 0.00 3.85
664 719 4.735338 GCACTTCTTCGTTCTTTTTCTTGG 59.265 41.667 0.00 0.00 0.00 3.61
723 781 2.451493 TGGGGGAAGAAGTGGGCA 60.451 61.111 0.00 0.00 0.00 5.36
787 865 3.479269 GTTCGCCGCTTCCTGTCG 61.479 66.667 0.00 0.00 0.00 4.35
788 866 3.479269 CGTTCGCCGCTTCCTGTC 61.479 66.667 0.00 0.00 0.00 3.51
1874 3547 0.250234 CACCGCCTTCATCTCCTCAA 59.750 55.000 0.00 0.00 0.00 3.02
1875 3548 0.904865 ACACCGCCTTCATCTCCTCA 60.905 55.000 0.00 0.00 0.00 3.86
1892 3592 1.470285 GCTCCGCCAACGTATCTAACA 60.470 52.381 0.00 0.00 37.70 2.41
1901 3601 2.187599 CTTTTGGAGCTCCGCCAACG 62.188 60.000 27.43 13.60 42.55 4.10
1945 3645 8.922676 CAAGTAACTTTGTATCTTCACGTACAT 58.077 33.333 0.00 0.00 31.48 2.29
2093 3812 2.171659 TCCAACAACCACAGTCTTAGCA 59.828 45.455 0.00 0.00 0.00 3.49
2147 3869 1.595109 GCCACCAAAAGCAACAGCC 60.595 57.895 0.00 0.00 0.00 4.85
2188 3910 4.086706 AGTCACTGGTTTTCCTTGGTAG 57.913 45.455 0.00 0.00 41.38 3.18
2357 4085 9.196139 GCATAACCTACTGGAATAGATAGATCT 57.804 37.037 0.00 0.00 37.73 2.75
2411 4139 3.561310 CAGTACGATACAAGCCATGCAAT 59.439 43.478 0.00 0.00 0.00 3.56
2517 4245 4.575236 TGTTACAAGGCGTCACACAATTAA 59.425 37.500 0.00 0.00 26.58 1.40
2658 4389 5.957771 ATGAATAGGTCAAGACAAGCCTA 57.042 39.130 2.29 0.00 40.50 3.93
2659 4390 4.851639 ATGAATAGGTCAAGACAAGCCT 57.148 40.909 2.29 0.00 40.50 4.58
2666 4397 5.164620 TGTGCAGAATGAATAGGTCAAGA 57.835 39.130 0.00 0.00 40.50 3.02
2688 4419 5.359009 CCTCATGTGTGCTGATAAAAGGAAT 59.641 40.000 0.00 0.00 0.00 3.01
2691 4422 4.012374 ACCTCATGTGTGCTGATAAAAGG 58.988 43.478 0.00 0.00 0.00 3.11
2693 4424 6.237901 AGTAACCTCATGTGTGCTGATAAAA 58.762 36.000 0.00 0.00 0.00 1.52
2695 4426 5.046663 TGAGTAACCTCATGTGTGCTGATAA 60.047 40.000 0.00 0.00 42.80 1.75
2696 4427 4.466015 TGAGTAACCTCATGTGTGCTGATA 59.534 41.667 0.00 0.00 42.80 2.15
2699 4430 3.044235 TGAGTAACCTCATGTGTGCTG 57.956 47.619 0.00 0.00 42.80 4.41
2709 4440 6.215495 AGAGAGTGCTAAATGAGTAACCTC 57.785 41.667 0.00 0.00 38.27 3.85
2710 4441 6.613153 AAGAGAGTGCTAAATGAGTAACCT 57.387 37.500 0.00 0.00 0.00 3.50
2711 4442 7.321153 TGTAAGAGAGTGCTAAATGAGTAACC 58.679 38.462 0.00 0.00 0.00 2.85
2712 4443 8.758633 TTGTAAGAGAGTGCTAAATGAGTAAC 57.241 34.615 0.00 0.00 0.00 2.50
2713 4444 9.204570 GTTTGTAAGAGAGTGCTAAATGAGTAA 57.795 33.333 0.00 0.00 0.00 2.24
2715 4446 6.651225 GGTTTGTAAGAGAGTGCTAAATGAGT 59.349 38.462 0.00 0.00 0.00 3.41
2717 4448 6.650807 CAGGTTTGTAAGAGAGTGCTAAATGA 59.349 38.462 0.00 0.00 0.00 2.57
2718 4449 6.428159 ACAGGTTTGTAAGAGAGTGCTAAATG 59.572 38.462 0.00 0.00 35.25 2.32
2720 4451 5.758296 CACAGGTTTGTAAGAGAGTGCTAAA 59.242 40.000 0.00 0.00 35.25 1.85
2721 4452 5.297547 CACAGGTTTGTAAGAGAGTGCTAA 58.702 41.667 0.00 0.00 35.25 3.09
2722 4453 4.799586 GCACAGGTTTGTAAGAGAGTGCTA 60.800 45.833 0.00 0.00 45.41 3.49
2723 4454 3.733337 CACAGGTTTGTAAGAGAGTGCT 58.267 45.455 0.00 0.00 35.25 4.40
2724 4455 2.224314 GCACAGGTTTGTAAGAGAGTGC 59.776 50.000 0.00 0.00 43.27 4.40
2725 4456 3.466836 TGCACAGGTTTGTAAGAGAGTG 58.533 45.455 0.00 0.00 35.25 3.51
2726 4457 3.134804 ACTGCACAGGTTTGTAAGAGAGT 59.865 43.478 2.21 0.00 35.25 3.24
2727 4458 3.733337 ACTGCACAGGTTTGTAAGAGAG 58.267 45.455 2.21 0.00 35.25 3.20
2728 4459 3.838244 ACTGCACAGGTTTGTAAGAGA 57.162 42.857 2.21 0.00 35.25 3.10
2729 4460 3.876914 TGAACTGCACAGGTTTGTAAGAG 59.123 43.478 2.21 0.00 35.25 2.85
2730 4461 3.879998 TGAACTGCACAGGTTTGTAAGA 58.120 40.909 2.21 0.00 35.25 2.10
2731 4462 4.630894 TTGAACTGCACAGGTTTGTAAG 57.369 40.909 2.21 0.00 35.25 2.34
2732 4463 5.590530 ATTTGAACTGCACAGGTTTGTAA 57.409 34.783 2.21 0.00 35.25 2.41
2744 4475 3.959535 TTCCCCATGAATTTGAACTGC 57.040 42.857 0.00 0.00 0.00 4.40
2754 4485 0.187117 TGCACCTGTTTCCCCATGAA 59.813 50.000 0.00 0.00 0.00 2.57
2763 4494 5.660460 CTCCTTTTTAAGTTGCACCTGTTT 58.340 37.500 0.00 0.00 0.00 2.83
2801 4532 4.599041 TGTTAGATGGCCTGCACTAATTT 58.401 39.130 3.32 0.00 0.00 1.82
2802 4533 4.235079 TGTTAGATGGCCTGCACTAATT 57.765 40.909 3.32 0.00 0.00 1.40
2803 4534 3.931907 TGTTAGATGGCCTGCACTAAT 57.068 42.857 3.32 0.00 0.00 1.73
2804 4535 3.712016 TTGTTAGATGGCCTGCACTAA 57.288 42.857 3.32 5.91 0.00 2.24
2805 4536 3.712016 TTTGTTAGATGGCCTGCACTA 57.288 42.857 3.32 0.00 0.00 2.74
2806 4537 2.584835 TTTGTTAGATGGCCTGCACT 57.415 45.000 3.32 0.33 0.00 4.40
2807 4538 2.736400 GCATTTGTTAGATGGCCTGCAC 60.736 50.000 3.32 0.00 0.00 4.57
2808 4539 1.477700 GCATTTGTTAGATGGCCTGCA 59.522 47.619 3.32 0.00 0.00 4.41
2809 4540 1.753073 AGCATTTGTTAGATGGCCTGC 59.247 47.619 3.32 0.36 0.00 4.85
2810 4541 5.105797 TGTTTAGCATTTGTTAGATGGCCTG 60.106 40.000 3.32 0.00 0.00 4.85
2811 4542 5.016173 TGTTTAGCATTTGTTAGATGGCCT 58.984 37.500 3.32 0.00 0.00 5.19
2812 4543 5.323371 TGTTTAGCATTTGTTAGATGGCC 57.677 39.130 0.00 0.00 0.00 5.36
2813 4544 6.620678 TCTTGTTTAGCATTTGTTAGATGGC 58.379 36.000 0.00 0.00 0.00 4.40
2814 4545 8.044060 TCTCTTGTTTAGCATTTGTTAGATGG 57.956 34.615 0.00 0.00 0.00 3.51
2815 4546 9.334693 GTTCTCTTGTTTAGCATTTGTTAGATG 57.665 33.333 0.00 0.00 0.00 2.90
2816 4547 8.230486 CGTTCTCTTGTTTAGCATTTGTTAGAT 58.770 33.333 0.00 0.00 0.00 1.98
2817 4548 7.572759 CGTTCTCTTGTTTAGCATTTGTTAGA 58.427 34.615 0.00 0.00 0.00 2.10
2818 4549 6.303259 GCGTTCTCTTGTTTAGCATTTGTTAG 59.697 38.462 0.00 0.00 0.00 2.34
2819 4550 6.017440 AGCGTTCTCTTGTTTAGCATTTGTTA 60.017 34.615 0.00 0.00 0.00 2.41
2820 4551 4.976116 GCGTTCTCTTGTTTAGCATTTGTT 59.024 37.500 0.00 0.00 0.00 2.83
2821 4552 4.275936 AGCGTTCTCTTGTTTAGCATTTGT 59.724 37.500 0.00 0.00 0.00 2.83
2825 4556 2.744202 CCAGCGTTCTCTTGTTTAGCAT 59.256 45.455 0.00 0.00 0.00 3.79
2842 4573 5.631096 GCAAAATCTAGAACAAACTTCCAGC 59.369 40.000 0.00 0.00 0.00 4.85
2912 4687 7.594849 ATTGATATGGATTGGAGGGAGTATT 57.405 36.000 0.00 0.00 0.00 1.89
2923 4698 7.500227 ACCTACAGTGACAATTGATATGGATTG 59.500 37.037 13.59 6.23 38.79 2.67
2924 4699 7.577303 ACCTACAGTGACAATTGATATGGATT 58.423 34.615 13.59 0.00 0.00 3.01
2933 4708 6.223852 ACAAGACTACCTACAGTGACAATTG 58.776 40.000 3.24 3.24 0.00 2.32
2944 4719 6.026947 ACATGTCAAGACAAGACTACCTAC 57.973 41.667 11.85 0.00 45.41 3.18
2945 4720 6.266786 TGAACATGTCAAGACAAGACTACCTA 59.733 38.462 11.85 0.00 45.41 3.08
2953 4728 5.152097 GCAGAATGAACATGTCAAGACAAG 58.848 41.667 7.02 5.44 41.74 3.16
2954 4729 4.579753 TGCAGAATGAACATGTCAAGACAA 59.420 37.500 7.02 0.00 41.74 3.18
2955 4730 4.136051 TGCAGAATGAACATGTCAAGACA 58.864 39.130 5.24 5.24 42.42 3.41
2956 4731 4.754372 TGCAGAATGAACATGTCAAGAC 57.246 40.909 0.00 0.00 40.50 3.01
2957 4732 4.763279 ACATGCAGAATGAACATGTCAAGA 59.237 37.500 0.00 0.00 43.26 3.02
2958 4733 5.055642 ACATGCAGAATGAACATGTCAAG 57.944 39.130 0.00 0.00 43.26 3.02
2959 4734 5.456548 AACATGCAGAATGAACATGTCAA 57.543 34.783 0.00 0.00 45.04 3.18
2960 4735 4.082625 GGAACATGCAGAATGAACATGTCA 60.083 41.667 0.00 0.00 45.04 3.58
2961 4736 4.157289 AGGAACATGCAGAATGAACATGTC 59.843 41.667 0.00 0.00 45.04 3.06
2962 4737 4.084287 AGGAACATGCAGAATGAACATGT 58.916 39.130 0.00 0.00 46.83 3.21
2963 4738 4.713824 AGGAACATGCAGAATGAACATG 57.286 40.909 0.00 0.00 40.80 3.21
2964 4739 5.733620 AAAGGAACATGCAGAATGAACAT 57.266 34.783 0.00 0.00 39.69 2.71
2965 4740 5.534207 AAAAGGAACATGCAGAATGAACA 57.466 34.783 0.00 0.00 39.69 3.18
2966 4741 7.315142 TGATAAAAGGAACATGCAGAATGAAC 58.685 34.615 0.00 0.00 39.69 3.18
2967 4742 7.465353 TGATAAAAGGAACATGCAGAATGAA 57.535 32.000 0.00 0.00 39.69 2.57
2968 4743 6.405065 GCTGATAAAAGGAACATGCAGAATGA 60.405 38.462 0.00 0.00 39.69 2.57
2969 4744 5.747197 GCTGATAAAAGGAACATGCAGAATG 59.253 40.000 0.00 0.00 42.48 2.67
2970 4745 5.419788 TGCTGATAAAAGGAACATGCAGAAT 59.580 36.000 0.00 0.00 0.00 2.40
2971 4746 4.766373 TGCTGATAAAAGGAACATGCAGAA 59.234 37.500 0.00 0.00 0.00 3.02
2972 4747 4.156556 GTGCTGATAAAAGGAACATGCAGA 59.843 41.667 0.00 0.00 0.00 4.26
2973 4748 4.082625 TGTGCTGATAAAAGGAACATGCAG 60.083 41.667 0.00 0.00 0.00 4.41
2974 4749 3.825585 TGTGCTGATAAAAGGAACATGCA 59.174 39.130 0.00 0.00 0.00 3.96
2975 4750 4.439305 TGTGCTGATAAAAGGAACATGC 57.561 40.909 0.00 0.00 0.00 4.06
2976 4751 7.092079 TCATTTGTGCTGATAAAAGGAACATG 58.908 34.615 0.00 0.00 0.00 3.21
2977 4752 7.230849 TCATTTGTGCTGATAAAAGGAACAT 57.769 32.000 0.00 0.00 0.00 2.71
2978 4753 6.294675 CCTCATTTGTGCTGATAAAAGGAACA 60.295 38.462 0.00 0.00 0.00 3.18
2979 4754 6.095377 CCTCATTTGTGCTGATAAAAGGAAC 58.905 40.000 0.00 0.00 0.00 3.62
2980 4755 5.774690 ACCTCATTTGTGCTGATAAAAGGAA 59.225 36.000 0.00 0.00 0.00 3.36
2981 4756 5.324409 ACCTCATTTGTGCTGATAAAAGGA 58.676 37.500 0.00 0.00 0.00 3.36
2982 4757 5.649782 ACCTCATTTGTGCTGATAAAAGG 57.350 39.130 0.00 0.00 0.00 3.11
2983 4758 9.294030 GAATAACCTCATTTGTGCTGATAAAAG 57.706 33.333 0.00 0.00 0.00 2.27
2984 4759 8.801299 TGAATAACCTCATTTGTGCTGATAAAA 58.199 29.630 0.00 0.00 0.00 1.52
2985 4760 8.347004 TGAATAACCTCATTTGTGCTGATAAA 57.653 30.769 0.00 0.00 0.00 1.40
2986 4761 7.936496 TGAATAACCTCATTTGTGCTGATAA 57.064 32.000 0.00 0.00 0.00 1.75
2987 4762 8.523915 AATGAATAACCTCATTTGTGCTGATA 57.476 30.769 0.00 0.00 42.16 2.15
2988 4763 7.414222 AATGAATAACCTCATTTGTGCTGAT 57.586 32.000 0.00 0.00 42.16 2.90
2989 4764 6.839124 AATGAATAACCTCATTTGTGCTGA 57.161 33.333 0.00 0.00 42.16 4.26
2997 4772 7.118723 TCCAGTGCTAAATGAATAACCTCATT 58.881 34.615 0.00 0.00 45.82 2.57
2998 4773 6.662755 TCCAGTGCTAAATGAATAACCTCAT 58.337 36.000 0.00 0.00 37.66 2.90
2999 4774 6.061022 TCCAGTGCTAAATGAATAACCTCA 57.939 37.500 0.00 0.00 0.00 3.86
3000 4775 7.391148 TTTCCAGTGCTAAATGAATAACCTC 57.609 36.000 0.00 0.00 0.00 3.85
3001 4776 7.631377 GCATTTCCAGTGCTAAATGAATAACCT 60.631 37.037 23.13 0.00 42.90 3.50
3002 4777 6.476706 GCATTTCCAGTGCTAAATGAATAACC 59.523 38.462 23.13 8.68 42.90 2.85
3003 4778 7.455331 GCATTTCCAGTGCTAAATGAATAAC 57.545 36.000 23.13 9.16 42.90 1.89
3015 4790 3.444916 CATCATTCAGCATTTCCAGTGC 58.555 45.455 0.00 0.00 42.81 4.40
3016 4791 3.697542 TCCATCATTCAGCATTTCCAGTG 59.302 43.478 0.00 0.00 0.00 3.66
3017 4792 3.698040 GTCCATCATTCAGCATTTCCAGT 59.302 43.478 0.00 0.00 0.00 4.00
3018 4793 3.242969 CGTCCATCATTCAGCATTTCCAG 60.243 47.826 0.00 0.00 0.00 3.86
3019 4794 2.684374 CGTCCATCATTCAGCATTTCCA 59.316 45.455 0.00 0.00 0.00 3.53
3020 4795 2.945008 TCGTCCATCATTCAGCATTTCC 59.055 45.455 0.00 0.00 0.00 3.13
3021 4796 3.547613 GCTCGTCCATCATTCAGCATTTC 60.548 47.826 0.00 0.00 0.00 2.17
3022 4797 2.357009 GCTCGTCCATCATTCAGCATTT 59.643 45.455 0.00 0.00 0.00 2.32
3023 4798 1.945394 GCTCGTCCATCATTCAGCATT 59.055 47.619 0.00 0.00 0.00 3.56
3024 4799 1.140452 AGCTCGTCCATCATTCAGCAT 59.860 47.619 0.00 0.00 0.00 3.79
3025 4800 0.538584 AGCTCGTCCATCATTCAGCA 59.461 50.000 0.00 0.00 0.00 4.41
3026 4801 1.216122 GAGCTCGTCCATCATTCAGC 58.784 55.000 0.00 0.00 0.00 4.26
3027 4802 1.863267 GGAGCTCGTCCATCATTCAG 58.137 55.000 7.83 0.00 46.10 3.02
3097 4872 9.337396 ACATCCATATGAACGTGTGTAATATTT 57.663 29.630 3.65 0.00 36.54 1.40
3098 4873 8.902540 ACATCCATATGAACGTGTGTAATATT 57.097 30.769 3.65 0.00 36.54 1.28
3102 4877 9.990360 AATATACATCCATATGAACGTGTGTAA 57.010 29.630 3.65 0.00 36.54 2.41
3143 4918 9.234827 CCTGCCATAATGTATATGATCTTCAAA 57.765 33.333 0.00 0.00 0.00 2.69
3144 4919 8.605065 TCCTGCCATAATGTATATGATCTTCAA 58.395 33.333 0.00 0.00 0.00 2.69
3145 4920 8.149631 TCCTGCCATAATGTATATGATCTTCA 57.850 34.615 0.00 0.00 0.00 3.02
3146 4921 7.226325 GCTCCTGCCATAATGTATATGATCTTC 59.774 40.741 0.00 0.00 0.00 2.87
3147 4922 7.052873 GCTCCTGCCATAATGTATATGATCTT 58.947 38.462 0.00 0.00 0.00 2.40
3148 4923 6.386342 AGCTCCTGCCATAATGTATATGATCT 59.614 38.462 0.00 0.00 40.80 2.75
3149 4924 6.590068 AGCTCCTGCCATAATGTATATGATC 58.410 40.000 0.00 0.00 40.80 2.92
3150 4925 6.572182 AGCTCCTGCCATAATGTATATGAT 57.428 37.500 0.00 0.00 40.80 2.45
3151 4926 6.440328 TGTAGCTCCTGCCATAATGTATATGA 59.560 38.462 0.00 0.00 40.80 2.15
3152 4927 6.536582 GTGTAGCTCCTGCCATAATGTATATG 59.463 42.308 0.00 0.00 40.80 1.78
3153 4928 6.213397 TGTGTAGCTCCTGCCATAATGTATAT 59.787 38.462 0.00 0.00 40.80 0.86
3154 4929 5.542251 TGTGTAGCTCCTGCCATAATGTATA 59.458 40.000 0.00 0.00 40.80 1.47
3155 4930 4.347876 TGTGTAGCTCCTGCCATAATGTAT 59.652 41.667 0.00 0.00 40.80 2.29
3156 4931 3.709141 TGTGTAGCTCCTGCCATAATGTA 59.291 43.478 0.00 0.00 40.80 2.29
3157 4932 2.505407 TGTGTAGCTCCTGCCATAATGT 59.495 45.455 0.00 0.00 40.80 2.71
3158 4933 3.198409 TGTGTAGCTCCTGCCATAATG 57.802 47.619 0.00 0.00 40.80 1.90
3159 4934 3.931907 TTGTGTAGCTCCTGCCATAAT 57.068 42.857 0.00 0.00 40.80 1.28
3160 4935 3.712016 TTTGTGTAGCTCCTGCCATAA 57.288 42.857 0.00 0.00 40.80 1.90
3161 4936 3.712016 TTTTGTGTAGCTCCTGCCATA 57.288 42.857 0.00 0.00 40.80 2.74
3162 4937 2.584835 TTTTGTGTAGCTCCTGCCAT 57.415 45.000 0.00 0.00 40.80 4.40
3163 4938 2.356665 TTTTTGTGTAGCTCCTGCCA 57.643 45.000 0.00 0.00 40.80 4.92
3179 4954 3.311322 TGCGTTGACGATTGTCTCTTTTT 59.689 39.130 14.27 0.00 45.70 1.94
3180 4955 2.869801 TGCGTTGACGATTGTCTCTTTT 59.130 40.909 14.27 0.00 45.70 2.27
3181 4956 2.479837 TGCGTTGACGATTGTCTCTTT 58.520 42.857 14.27 0.00 45.70 2.52
3182 4957 2.148916 TGCGTTGACGATTGTCTCTT 57.851 45.000 14.27 0.00 45.70 2.85
3183 4958 2.370281 ATGCGTTGACGATTGTCTCT 57.630 45.000 14.27 0.00 45.70 3.10
3184 4959 3.455619 AAATGCGTTGACGATTGTCTC 57.544 42.857 14.27 6.70 45.70 3.36
3185 4960 3.249799 TGAAAATGCGTTGACGATTGTCT 59.750 39.130 14.27 0.00 45.70 3.41
3186 4961 3.550561 TGAAAATGCGTTGACGATTGTC 58.449 40.909 7.85 6.11 45.71 3.18
3187 4962 3.617540 TGAAAATGCGTTGACGATTGT 57.382 38.095 7.85 0.15 43.02 2.71


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

AutoCloner maintained by Alex Coulton.