Multiple sequence alignment - TraesCS2A01G326600

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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 TraesCS2A01G326600 chr2A 100.000 5998 0 0 585 6582 558088156 558094153 0.000000e+00 11077.0
1 TraesCS2A01G326600 chr2A 94.490 4646 198 25 1782 6383 556109582 556104951 0.000000e+00 7108.0
2 TraesCS2A01G326600 chr2A 94.052 1261 41 16 585 1819 556110894 556109642 0.000000e+00 1882.0
3 TraesCS2A01G326600 chr2A 81.601 1087 142 42 3361 4409 557400726 557401792 0.000000e+00 846.0
4 TraesCS2A01G326600 chr2A 80.747 1044 150 35 3392 4420 557319437 557320444 0.000000e+00 767.0
5 TraesCS2A01G326600 chr2A 82.209 860 122 18 3392 4240 557059009 557059848 0.000000e+00 712.0
6 TraesCS2A01G326600 chr2A 100.000 260 0 0 1 260 558087572 558087831 1.280000e-131 481.0
7 TraesCS2A01G326600 chr2A 96.047 253 7 1 1 253 556111142 556110893 6.140000e-110 409.0
8 TraesCS2A01G326600 chr2A 93.467 199 13 0 6384 6582 71972247 71972445 4.990000e-76 296.0
9 TraesCS2A01G326600 chr2A 95.946 74 2 1 6311 6383 558099876 558099949 1.160000e-22 119.0
10 TraesCS2A01G326600 chr2D 94.023 5856 231 56 592 6383 430382382 430388182 0.000000e+00 8765.0
11 TraesCS2A01G326600 chr2D 94.653 3123 110 23 1326 4429 429693674 429690590 0.000000e+00 4789.0
12 TraesCS2A01G326600 chr2D 94.109 1986 108 8 4403 6383 429690586 429688605 0.000000e+00 3011.0
13 TraesCS2A01G326600 chr2D 84.992 2532 259 61 3353 5858 429740480 429738044 0.000000e+00 2459.0
14 TraesCS2A01G326600 chr2D 91.483 1315 72 23 585 1878 429743239 429741944 0.000000e+00 1772.0
15 TraesCS2A01G326600 chr2D 90.085 706 39 15 602 1291 429694540 429693850 0.000000e+00 887.0
16 TraesCS2A01G326600 chr2D 84.652 847 114 12 3363 4199 429835761 429834921 0.000000e+00 830.0
17 TraesCS2A01G326600 chr2D 86.345 476 51 11 2517 2981 3093790 3093318 2.120000e-139 507.0
18 TraesCS2A01G326600 chr2D 82.487 571 65 17 1953 2495 429741933 429741370 9.990000e-128 468.0
19 TraesCS2A01G326600 chr2D 87.187 359 31 6 3008 3357 429741360 429741008 1.720000e-105 394.0
20 TraesCS2A01G326600 chr2D 93.478 230 15 0 1 230 429743774 429743545 6.320000e-90 342.0
21 TraesCS2A01G326600 chr2D 92.704 233 17 0 1 233 429694973 429694741 2.940000e-88 337.0
22 TraesCS2A01G326600 chr2D 93.981 216 13 0 1 216 430381777 430381992 1.770000e-85 327.0
23 TraesCS2A01G326600 chr2D 80.919 283 44 8 5048 5323 429834389 429834110 1.440000e-51 215.0
24 TraesCS2A01G326600 chr2D 91.270 126 10 1 5804 5928 2044028 2044153 3.160000e-38 171.0
25 TraesCS2A01G326600 chr2D 86.885 122 9 4 4303 4420 429924343 429924225 5.360000e-26 130.0
26 TraesCS2A01G326600 chr2D 88.542 96 11 0 4659 4754 429924044 429923949 4.170000e-22 117.0
27 TraesCS2A01G326600 chr2D 94.000 50 3 0 4817 4866 429834497 429834448 7.080000e-10 76.8
28 TraesCS2A01G326600 chr2B 93.634 3864 215 12 2525 6383 507194023 507190186 0.000000e+00 5744.0
29 TraesCS2A01G326600 chr2B 89.961 2281 179 26 3355 5608 506509283 506507026 0.000000e+00 2898.0
30 TraesCS2A01G326600 chr2B 89.360 1297 69 27 593 1857 507196287 507195028 0.000000e+00 1567.0
31 TraesCS2A01G326600 chr2B 94.502 582 24 3 1953 2533 507194959 507194385 0.000000e+00 891.0
32 TraesCS2A01G326600 chr2B 84.917 842 107 14 3364 4199 507410573 507409746 0.000000e+00 833.0
33 TraesCS2A01G326600 chr2B 80.722 1053 151 34 3392 4420 507756054 507755030 0.000000e+00 773.0
34 TraesCS2A01G326600 chr2B 91.728 544 27 7 1953 2495 506510749 506510223 0.000000e+00 739.0
35 TraesCS2A01G326600 chr2B 86.740 362 36 4 3008 3357 506510213 506509852 6.190000e-105 392.0
36 TraesCS2A01G326600 chr2B 81.922 437 26 21 1481 1884 506511160 506510744 2.960000e-83 320.0
37 TraesCS2A01G326600 chr2B 77.702 583 72 31 1304 1834 507506971 507506395 2.980000e-78 303.0
38 TraesCS2A01G326600 chr2B 88.710 186 12 4 1 177 507196827 507196642 1.110000e-52 219.0
39 TraesCS2A01G326600 chr2B 91.463 164 7 4 1713 1869 507412041 507411878 1.110000e-52 219.0
40 TraesCS2A01G326600 chr2B 81.287 171 21 9 5805 5968 34451574 34451408 1.930000e-25 128.0
41 TraesCS2A01G326600 chr2B 82.707 133 17 4 5805 5933 34527859 34527729 5.390000e-21 113.0
42 TraesCS2A01G326600 chr2B 90.411 73 6 1 4683 4754 507754824 507754752 1.950000e-15 95.3
43 TraesCS2A01G326600 chr2B 77.095 179 24 11 5161 5323 507409094 507408917 3.270000e-13 87.9
44 TraesCS2A01G326600 chr6D 86.382 492 53 11 2497 2978 28405943 28405456 5.850000e-145 525.0
45 TraesCS2A01G326600 chr6D 81.466 464 75 9 2519 2975 312817068 312817527 2.900000e-98 370.0
46 TraesCS2A01G326600 chr6D 81.690 142 21 5 5792 5929 402115204 402115344 5.390000e-21 113.0
47 TraesCS2A01G326600 chr7D 81.579 418 53 13 2502 2910 169441443 169441041 2.290000e-84 324.0
48 TraesCS2A01G326600 chr6A 94.472 199 11 0 6384 6582 275231436 275231238 2.310000e-79 307.0
49 TraesCS2A01G326600 chr6A 94.472 199 11 0 6384 6582 308295367 308295169 2.310000e-79 307.0
50 TraesCS2A01G326600 chr6A 94.709 189 8 2 6384 6571 31086166 31086353 6.460000e-75 292.0
51 TraesCS2A01G326600 chr6A 92.611 203 14 1 6381 6582 303601881 303602083 2.320000e-74 291.0
52 TraesCS2A01G326600 chr5A 94.472 199 11 0 6384 6582 563213069 563213267 2.310000e-79 307.0
53 TraesCS2A01G326600 chr7A 92.683 205 11 4 6369 6571 510417450 510417652 6.460000e-75 292.0
54 TraesCS2A01G326600 chr4A 92.462 199 14 1 6384 6582 249670432 249670629 3.890000e-72 283.0
55 TraesCS2A01G326600 chr1A 92.462 199 14 1 6384 6582 137219538 137219735 3.890000e-72 283.0
56 TraesCS2A01G326600 chr3D 77.695 269 53 7 2487 2752 170775925 170776189 2.460000e-34 158.0
57 TraesCS2A01G326600 chr1B 84.375 128 15 5 5804 5929 178723197 178723321 3.220000e-23 121.0
58 TraesCS2A01G326600 chr4B 77.222 180 31 5 3135 3305 572914867 572914689 5.430000e-16 97.1


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 TraesCS2A01G326600 chr2A 558087572 558094153 6581 False 5779.000000 11077 100.000000 1 6582 2 chr2A.!!$F6 6581
1 TraesCS2A01G326600 chr2A 556104951 556111142 6191 True 3133.000000 7108 94.863000 1 6383 3 chr2A.!!$R1 6382
2 TraesCS2A01G326600 chr2A 557400726 557401792 1066 False 846.000000 846 81.601000 3361 4409 1 chr2A.!!$F4 1048
3 TraesCS2A01G326600 chr2A 557319437 557320444 1007 False 767.000000 767 80.747000 3392 4420 1 chr2A.!!$F3 1028
4 TraesCS2A01G326600 chr2A 557059009 557059848 839 False 712.000000 712 82.209000 3392 4240 1 chr2A.!!$F2 848
5 TraesCS2A01G326600 chr2D 430381777 430388182 6405 False 4546.000000 8765 94.002000 1 6383 2 chr2D.!!$F2 6382
6 TraesCS2A01G326600 chr2D 429688605 429694973 6368 True 2256.000000 4789 92.887750 1 6383 4 chr2D.!!$R2 6382
7 TraesCS2A01G326600 chr2D 429738044 429743774 5730 True 1087.000000 2459 87.925400 1 5858 5 chr2D.!!$R3 5857
8 TraesCS2A01G326600 chr2D 429834110 429835761 1651 True 373.933333 830 86.523667 3363 5323 3 chr2D.!!$R4 1960
9 TraesCS2A01G326600 chr2B 507190186 507196827 6641 True 2105.250000 5744 91.551500 1 6383 4 chr2B.!!$R5 6382
10 TraesCS2A01G326600 chr2B 506507026 506511160 4134 True 1087.250000 2898 87.587750 1481 5608 4 chr2B.!!$R4 4127
11 TraesCS2A01G326600 chr2B 507754752 507756054 1302 True 434.150000 773 85.566500 3392 4754 2 chr2B.!!$R7 1362
12 TraesCS2A01G326600 chr2B 507408917 507412041 3124 True 379.966667 833 84.491667 1713 5323 3 chr2B.!!$R6 3610
13 TraesCS2A01G326600 chr2B 507506395 507506971 576 True 303.000000 303 77.702000 1304 1834 1 chr2B.!!$R3 530

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
251 261 1.226974 CCTCCACGTGTAGCGATGG 60.227 63.158 15.65 4.57 44.77 3.51 F
1509 1733 1.277557 GTGGCAGAGGAGATGTCAGTT 59.722 52.381 0.00 0.00 31.84 3.16 F
1873 2323 0.178950 AGTGGAGACTGCTCTGGTCA 60.179 55.000 0.00 0.00 41.06 4.02 F
1910 2360 0.321298 TTGTTACAAGCTCTCGGCCC 60.321 55.000 0.00 0.00 43.05 5.80 F
2271 2792 0.322456 AATGGGCTTGCTCTGCGTTA 60.322 50.000 0.00 0.00 0.00 3.18 F
2272 2793 1.026718 ATGGGCTTGCTCTGCGTTAC 61.027 55.000 0.00 0.00 0.00 2.50 F
4131 5695 0.469917 CCAATGACATACCCTCCGCT 59.530 55.000 0.00 0.00 0.00 5.52 F
4946 6657 1.066858 CGTGTACCCTGAGATGCAACT 60.067 52.381 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 1958 0.737715 GCTCACGACATCTCGGCTTT 60.738 55.000 0.00 0.00 44.8 3.51 R
2843 3754 1.575419 TTCCCTTGCCTACCACGTAT 58.425 50.000 0.00 0.00 0.0 3.06 R
3409 4959 1.833630 TCCTGGCCACTGTGATAAGAG 59.166 52.381 9.86 0.00 0.0 2.85 R
3862 5416 2.486592 CCACCCTTTTATGACACCGTTC 59.513 50.000 0.00 0.00 0.0 3.95 R
4132 5696 0.178926 TACTGTTTGGGGGACGAGGA 60.179 55.000 0.00 0.00 0.0 3.71 R
4296 5921 6.671605 TCCCAATAATTCATCCACAGATCAA 58.328 36.000 0.00 0.00 0.0 2.57 R
5357 7113 0.035458 AACCAGCCTCTTCTCGTTGG 59.965 55.000 0.00 0.00 0.0 3.77 R
6392 8172 0.035458 AACTGAAGCTCCGGTCTTGG 59.965 55.000 14.63 10.22 0.0 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
50 51 3.118000 AGAGGACGGAAACTCAGGTTTTT 60.118 43.478 0.00 0.00 44.58 1.94
249 259 1.664321 GGTCCTCCACGTGTAGCGAT 61.664 60.000 15.65 0.00 44.77 4.58
251 261 1.226974 CCTCCACGTGTAGCGATGG 60.227 63.158 15.65 4.57 44.77 3.51
252 262 1.878522 CTCCACGTGTAGCGATGGC 60.879 63.158 15.65 0.00 44.77 4.40
1272 1329 2.368875 TGTTTCTGGTCTCCAACTCTCC 59.631 50.000 0.00 0.00 30.80 3.71
1438 1650 2.829043 TTCGGCGAGTGGTGGATTCG 62.829 60.000 10.46 0.00 36.90 3.34
1509 1733 1.277557 GTGGCAGAGGAGATGTCAGTT 59.722 52.381 0.00 0.00 31.84 3.16
1594 1831 2.652095 CGGCCAGGTTTCCCTCGTA 61.652 63.158 2.24 0.00 39.89 3.43
1618 1864 2.354188 GTGGCGGTGCGGTTTTTC 60.354 61.111 0.00 0.00 0.00 2.29
1695 1958 3.069158 AGTTCTCGGGAAAAAGAAGACGA 59.931 43.478 0.00 0.00 32.40 4.20
1700 1963 2.350484 CGGGAAAAAGAAGACGAAAGCC 60.350 50.000 0.00 0.00 0.00 4.35
1708 1971 1.921230 GAAGACGAAAGCCGAGATGTC 59.079 52.381 0.00 0.00 41.76 3.06
1710 1973 0.456312 GACGAAAGCCGAGATGTCGT 60.456 55.000 11.66 7.02 46.77 4.34
1760 2050 1.347097 GCCCGGTTTTACTCGTCGTC 61.347 60.000 0.00 0.00 0.00 4.20
1763 2056 0.998226 CGGTTTTACTCGTCGTCGCA 60.998 55.000 0.00 0.00 36.96 5.10
1873 2323 0.178950 AGTGGAGACTGCTCTGGTCA 60.179 55.000 0.00 0.00 41.06 4.02
1910 2360 0.321298 TTGTTACAAGCTCTCGGCCC 60.321 55.000 0.00 0.00 43.05 5.80
1942 2392 1.941325 CGGCCAAGGAGTAAGATGAC 58.059 55.000 2.24 0.00 0.00 3.06
2043 2522 1.275856 CCTCCATCTCTATCTGCCAGC 59.724 57.143 0.00 0.00 0.00 4.85
2270 2791 1.604593 AATGGGCTTGCTCTGCGTT 60.605 52.632 0.00 0.00 0.00 4.84
2271 2792 0.322456 AATGGGCTTGCTCTGCGTTA 60.322 50.000 0.00 0.00 0.00 3.18
2272 2793 1.026718 ATGGGCTTGCTCTGCGTTAC 61.027 55.000 0.00 0.00 0.00 2.50
2273 2794 2.740714 GGGCTTGCTCTGCGTTACG 61.741 63.158 0.00 0.00 0.00 3.18
2362 2887 4.022416 ACGTTGAAAATAGCAATGCAAGGA 60.022 37.500 8.35 0.00 36.06 3.36
2466 3003 7.780008 TTTTCTTCGAGTTAGTGAACATGAA 57.220 32.000 0.00 0.00 38.10 2.57
2762 3673 3.358707 TTTTGCAACAGAGCTGATGTG 57.641 42.857 0.00 1.06 36.01 3.21
2787 3698 4.558538 AAAGCTTGTCTAAGTTGCAGTG 57.441 40.909 0.00 0.00 36.27 3.66
2843 3754 6.094742 TGTTGTTGCAAGATGAAGTAAAGTGA 59.905 34.615 0.00 0.00 0.00 3.41
2961 3873 4.212913 GCGATCAGCCGGCAGAGA 62.213 66.667 31.54 23.21 40.81 3.10
3331 4309 7.748847 TCTTGCATTTACTTTTATTCTCGGTC 58.251 34.615 0.00 0.00 0.00 4.79
3385 4935 5.710513 TGATTTCTTGGAATCTTGTGGTG 57.289 39.130 3.63 0.00 37.04 4.17
3409 4959 3.611113 CACTTCATGCTTTGTATTGCAGC 59.389 43.478 0.00 0.00 42.74 5.25
3721 5275 3.659183 ACCAAGATGGATGGGAGAAAG 57.341 47.619 2.85 0.00 40.96 2.62
3829 5383 2.425668 TGATGTGCATTTCAGATGGCAG 59.574 45.455 0.00 0.00 36.86 4.85
4005 5562 1.657751 GATGAAAAGCACGGGGAGCC 61.658 60.000 0.00 0.00 0.00 4.70
4103 5667 3.117701 TCCATTTGCTGGGGAAATCGATA 60.118 43.478 0.00 0.00 45.98 2.92
4131 5695 0.469917 CCAATGACATACCCTCCGCT 59.530 55.000 0.00 0.00 0.00 5.52
4132 5696 1.134098 CCAATGACATACCCTCCGCTT 60.134 52.381 0.00 0.00 0.00 4.68
4519 6182 9.459640 CTATACATGAAAAATTTCTCTGCATGG 57.540 33.333 12.11 1.28 38.02 3.66
4569 6235 9.912634 CAAAAATATCAGAAGCTTTTAGTTCCA 57.087 29.630 0.00 0.00 0.00 3.53
4635 6306 4.104383 TCAAGCCTTCAAACTCCTTCAT 57.896 40.909 0.00 0.00 0.00 2.57
4775 6478 7.633193 AGTATTGTGTTGTCACCTTGTAAAA 57.367 32.000 0.00 0.00 43.26 1.52
4946 6657 1.066858 CGTGTACCCTGAGATGCAACT 60.067 52.381 0.00 0.00 0.00 3.16
4996 6707 2.227757 TTGCCCGACCCCAGAATGA 61.228 57.895 0.00 0.00 39.69 2.57
5028 6739 1.929494 TCCCATATGGCCTCTTGGTTT 59.071 47.619 16.97 0.00 35.27 3.27
5044 6755 1.523758 GTTTGCTGGAACCTCATCGT 58.476 50.000 0.00 0.00 0.00 3.73
5062 6773 1.068588 CGTATTCGAATGCCCTGGAGA 59.931 52.381 20.87 0.00 39.71 3.71
5067 6778 1.779025 CGAATGCCCTGGAGAATGCG 61.779 60.000 0.00 0.00 0.00 4.73
5092 6803 2.104451 CTGTCTGGCCTAGATGAATGCT 59.896 50.000 3.32 0.00 37.83 3.79
5166 6877 4.069232 CCTCTTGACGCGGAGGCA 62.069 66.667 12.47 0.00 41.92 4.75
5357 7113 2.125952 GGTTTTGATGCAGCGGCC 60.126 61.111 6.32 0.00 40.13 6.13
5445 7201 4.858692 CGATGCATGTCCGAGAAAATTTTT 59.141 37.500 2.46 0.00 0.00 1.94
5447 7203 5.452078 TGCATGTCCGAGAAAATTTTTCT 57.548 34.783 21.36 21.36 0.00 2.52
5451 7207 8.735315 TGCATGTCCGAGAAAATTTTTCTTATA 58.265 29.630 21.94 11.67 0.00 0.98
5499 7259 3.920412 GCTTGGCTATGTTTACTGTTTGC 59.080 43.478 0.00 0.00 0.00 3.68
5576 7337 7.147863 TGCATAGCCATGAAACTGATAAACAAT 60.148 33.333 0.00 0.00 33.67 2.71
5837 7610 5.636121 GTCCGATGACATGTGTTTAGTTACA 59.364 40.000 1.15 0.00 41.37 2.41
5931 7704 3.034721 TGTATTGTCCGGTCACTGTTC 57.965 47.619 0.00 0.00 0.00 3.18
5932 7705 2.365941 TGTATTGTCCGGTCACTGTTCA 59.634 45.455 0.00 0.00 0.00 3.18
5991 7764 1.025812 CGGTTTGCCACTTGTGGTTA 58.974 50.000 19.47 7.97 34.09 2.85
6000 7773 7.768807 TTGCCACTTGTGGTTATAATTACTT 57.231 32.000 19.47 0.00 0.00 2.24
6003 7776 8.952278 TGCCACTTGTGGTTATAATTACTTTAG 58.048 33.333 19.47 0.00 0.00 1.85
6095 7868 1.005805 ACATTAGCAATGCACCAGGGA 59.994 47.619 8.35 0.00 42.69 4.20
6178 7951 5.815740 CCCTTACACGCAGATAACAAATAGT 59.184 40.000 0.00 0.00 0.00 2.12
6179 7952 6.018994 CCCTTACACGCAGATAACAAATAGTC 60.019 42.308 0.00 0.00 0.00 2.59
6199 7972 3.735097 GGGAAAGCGGGCCCCTTA 61.735 66.667 21.62 0.00 38.45 2.69
6294 8071 8.232412 GGAATTAATCCTTTTTAGGGGGTCTAT 58.768 37.037 0.00 0.00 45.56 1.98
6390 8170 2.755836 ACACTCAAAATGTGTGACGC 57.244 45.000 16.67 0.00 45.57 5.19
6391 8171 1.333619 ACACTCAAAATGTGTGACGCC 59.666 47.619 16.67 0.00 45.57 5.68
6392 8172 0.951558 ACTCAAAATGTGTGACGCCC 59.048 50.000 0.00 0.00 0.00 6.13
6393 8173 0.240945 CTCAAAATGTGTGACGCCCC 59.759 55.000 0.00 0.00 0.00 5.80
6394 8174 0.466372 TCAAAATGTGTGACGCCCCA 60.466 50.000 0.00 0.00 0.00 4.96
6395 8175 0.387202 CAAAATGTGTGACGCCCCAA 59.613 50.000 0.00 0.00 0.00 4.12
6396 8176 0.673437 AAAATGTGTGACGCCCCAAG 59.327 50.000 0.00 0.00 0.00 3.61
6397 8177 0.179004 AAATGTGTGACGCCCCAAGA 60.179 50.000 0.00 0.00 0.00 3.02
6398 8178 0.889186 AATGTGTGACGCCCCAAGAC 60.889 55.000 0.00 0.00 0.00 3.01
6399 8179 2.668550 GTGTGACGCCCCAAGACC 60.669 66.667 0.00 0.00 0.00 3.85
6400 8180 4.308458 TGTGACGCCCCAAGACCG 62.308 66.667 0.00 0.00 0.00 4.79
6403 8183 4.452733 GACGCCCCAAGACCGGAG 62.453 72.222 9.46 0.00 0.00 4.63
6406 8186 4.035102 GCCCCAAGACCGGAGCTT 62.035 66.667 9.46 8.67 0.00 3.74
6407 8187 2.269241 CCCCAAGACCGGAGCTTC 59.731 66.667 9.46 0.00 0.00 3.86
6408 8188 2.592993 CCCCAAGACCGGAGCTTCA 61.593 63.158 9.46 0.00 0.00 3.02
6409 8189 1.078848 CCCAAGACCGGAGCTTCAG 60.079 63.158 9.46 5.05 0.00 3.02
6410 8190 1.674057 CCAAGACCGGAGCTTCAGT 59.326 57.895 9.46 0.00 0.00 3.41
6411 8191 0.035458 CCAAGACCGGAGCTTCAGTT 59.965 55.000 9.46 0.00 0.00 3.16
6412 8192 1.151668 CAAGACCGGAGCTTCAGTTG 58.848 55.000 9.46 0.00 0.00 3.16
6413 8193 0.603975 AAGACCGGAGCTTCAGTTGC 60.604 55.000 9.46 0.00 0.00 4.17
6414 8194 2.032681 ACCGGAGCTTCAGTTGCC 59.967 61.111 9.46 0.00 0.00 4.52
6415 8195 2.348998 CCGGAGCTTCAGTTGCCT 59.651 61.111 0.00 0.00 0.00 4.75
6416 8196 1.302832 CCGGAGCTTCAGTTGCCTT 60.303 57.895 0.00 0.00 0.00 4.35
6417 8197 1.301677 CCGGAGCTTCAGTTGCCTTC 61.302 60.000 0.00 0.00 0.00 3.46
6418 8198 1.301677 CGGAGCTTCAGTTGCCTTCC 61.302 60.000 0.00 0.00 0.00 3.46
6419 8199 0.250901 GGAGCTTCAGTTGCCTTCCA 60.251 55.000 0.00 0.00 0.00 3.53
6420 8200 1.163554 GAGCTTCAGTTGCCTTCCAG 58.836 55.000 0.00 0.00 0.00 3.86
6421 8201 0.251077 AGCTTCAGTTGCCTTCCAGG 60.251 55.000 0.00 0.00 38.80 4.45
6422 8202 1.246737 GCTTCAGTTGCCTTCCAGGG 61.247 60.000 0.00 0.00 35.37 4.45
6423 8203 0.111253 CTTCAGTTGCCTTCCAGGGT 59.889 55.000 0.00 0.00 35.37 4.34
6424 8204 0.555769 TTCAGTTGCCTTCCAGGGTT 59.444 50.000 0.00 0.00 35.37 4.11
6425 8205 0.555769 TCAGTTGCCTTCCAGGGTTT 59.444 50.000 0.00 0.00 35.37 3.27
6426 8206 0.961753 CAGTTGCCTTCCAGGGTTTC 59.038 55.000 0.00 0.00 35.37 2.78
6427 8207 0.178961 AGTTGCCTTCCAGGGTTTCC 60.179 55.000 0.00 0.00 35.37 3.13
6428 8208 1.228429 TTGCCTTCCAGGGTTTCCG 60.228 57.895 0.00 0.00 35.37 4.30
6429 8209 2.361230 GCCTTCCAGGGTTTCCGG 60.361 66.667 0.00 0.00 35.37 5.14
6431 8211 2.535331 CCTTCCAGGGTTTCCGGGT 61.535 63.158 0.00 0.00 46.69 5.28
6432 8212 1.458927 CTTCCAGGGTTTCCGGGTT 59.541 57.895 0.00 0.00 46.69 4.11
6433 8213 0.178973 CTTCCAGGGTTTCCGGGTTT 60.179 55.000 0.00 0.00 46.69 3.27
6434 8214 0.178984 TTCCAGGGTTTCCGGGTTTC 60.179 55.000 0.00 0.00 46.69 2.78
6435 8215 1.063654 TCCAGGGTTTCCGGGTTTCT 61.064 55.000 0.00 0.00 46.69 2.52
6436 8216 0.608308 CCAGGGTTTCCGGGTTTCTC 60.608 60.000 0.00 0.00 42.50 2.87
6437 8217 0.608308 CAGGGTTTCCGGGTTTCTCC 60.608 60.000 0.00 0.00 38.33 3.71
6444 8224 4.449391 CGGGTTTCTCCGTGTGTT 57.551 55.556 0.00 0.00 44.60 3.32
6445 8225 2.697819 CGGGTTTCTCCGTGTGTTT 58.302 52.632 0.00 0.00 44.60 2.83
6446 8226 0.584876 CGGGTTTCTCCGTGTGTTTC 59.415 55.000 0.00 0.00 44.60 2.78
6447 8227 1.670791 GGGTTTCTCCGTGTGTTTCA 58.329 50.000 0.00 0.00 37.00 2.69
6448 8228 2.227194 GGGTTTCTCCGTGTGTTTCAT 58.773 47.619 0.00 0.00 37.00 2.57
6449 8229 2.621526 GGGTTTCTCCGTGTGTTTCATT 59.378 45.455 0.00 0.00 37.00 2.57
6450 8230 3.067601 GGGTTTCTCCGTGTGTTTCATTT 59.932 43.478 0.00 0.00 37.00 2.32
6451 8231 4.440940 GGGTTTCTCCGTGTGTTTCATTTT 60.441 41.667 0.00 0.00 37.00 1.82
6452 8232 5.106442 GGTTTCTCCGTGTGTTTCATTTTT 58.894 37.500 0.00 0.00 0.00 1.94
6453 8233 5.005299 GGTTTCTCCGTGTGTTTCATTTTTG 59.995 40.000 0.00 0.00 0.00 2.44
6454 8234 3.701241 TCTCCGTGTGTTTCATTTTTGC 58.299 40.909 0.00 0.00 0.00 3.68
6455 8235 3.380004 TCTCCGTGTGTTTCATTTTTGCT 59.620 39.130 0.00 0.00 0.00 3.91
6456 8236 4.111916 CTCCGTGTGTTTCATTTTTGCTT 58.888 39.130 0.00 0.00 0.00 3.91
6457 8237 3.862267 TCCGTGTGTTTCATTTTTGCTTG 59.138 39.130 0.00 0.00 0.00 4.01
6458 8238 3.543852 CCGTGTGTTTCATTTTTGCTTGC 60.544 43.478 0.00 0.00 0.00 4.01
6459 8239 3.306703 CGTGTGTTTCATTTTTGCTTGCT 59.693 39.130 0.00 0.00 0.00 3.91
6460 8240 4.548726 CGTGTGTTTCATTTTTGCTTGCTC 60.549 41.667 0.00 0.00 0.00 4.26
6461 8241 3.870419 TGTGTTTCATTTTTGCTTGCTCC 59.130 39.130 0.00 0.00 0.00 4.70
6462 8242 4.122046 GTGTTTCATTTTTGCTTGCTCCT 58.878 39.130 0.00 0.00 0.00 3.69
6463 8243 4.571984 GTGTTTCATTTTTGCTTGCTCCTT 59.428 37.500 0.00 0.00 0.00 3.36
6464 8244 5.065090 GTGTTTCATTTTTGCTTGCTCCTTT 59.935 36.000 0.00 0.00 0.00 3.11
6465 8245 5.647225 TGTTTCATTTTTGCTTGCTCCTTTT 59.353 32.000 0.00 0.00 0.00 2.27
6466 8246 6.820656 TGTTTCATTTTTGCTTGCTCCTTTTA 59.179 30.769 0.00 0.00 0.00 1.52
6467 8247 7.498570 TGTTTCATTTTTGCTTGCTCCTTTTAT 59.501 29.630 0.00 0.00 0.00 1.40
6468 8248 8.344831 GTTTCATTTTTGCTTGCTCCTTTTATT 58.655 29.630 0.00 0.00 0.00 1.40
6469 8249 8.449251 TTCATTTTTGCTTGCTCCTTTTATTT 57.551 26.923 0.00 0.00 0.00 1.40
6470 8250 8.449251 TCATTTTTGCTTGCTCCTTTTATTTT 57.551 26.923 0.00 0.00 0.00 1.82
6471 8251 8.901793 TCATTTTTGCTTGCTCCTTTTATTTTT 58.098 25.926 0.00 0.00 0.00 1.94
6472 8252 8.960075 CATTTTTGCTTGCTCCTTTTATTTTTG 58.040 29.630 0.00 0.00 0.00 2.44
6473 8253 5.671742 TTGCTTGCTCCTTTTATTTTTGC 57.328 34.783 0.00 0.00 0.00 3.68
6474 8254 4.701765 TGCTTGCTCCTTTTATTTTTGCA 58.298 34.783 0.00 0.00 0.00 4.08
6475 8255 5.307204 TGCTTGCTCCTTTTATTTTTGCAT 58.693 33.333 0.00 0.00 0.00 3.96
6476 8256 5.764192 TGCTTGCTCCTTTTATTTTTGCATT 59.236 32.000 0.00 0.00 0.00 3.56
6477 8257 6.081693 GCTTGCTCCTTTTATTTTTGCATTG 58.918 36.000 0.00 0.00 0.00 2.82
6478 8258 5.610235 TGCTCCTTTTATTTTTGCATTGC 57.390 34.783 0.46 0.46 0.00 3.56
6479 8259 5.061853 TGCTCCTTTTATTTTTGCATTGCA 58.938 33.333 7.38 7.38 36.47 4.08
6480 8260 5.706369 TGCTCCTTTTATTTTTGCATTGCAT 59.294 32.000 12.95 0.00 38.76 3.96
6481 8261 6.128227 TGCTCCTTTTATTTTTGCATTGCATC 60.128 34.615 12.95 0.00 38.76 3.91
6482 8262 6.128227 GCTCCTTTTATTTTTGCATTGCATCA 60.128 34.615 12.95 0.00 38.76 3.07
6483 8263 7.414762 GCTCCTTTTATTTTTGCATTGCATCAT 60.415 33.333 12.95 7.46 38.76 2.45
6484 8264 7.753659 TCCTTTTATTTTTGCATTGCATCATG 58.246 30.769 12.95 0.00 38.76 3.07
6485 8265 7.390996 TCCTTTTATTTTTGCATTGCATCATGT 59.609 29.630 12.95 1.14 38.76 3.21
6486 8266 7.694784 CCTTTTATTTTTGCATTGCATCATGTC 59.305 33.333 12.95 0.00 38.76 3.06
6487 8267 7.668525 TTTATTTTTGCATTGCATCATGTCA 57.331 28.000 12.95 0.00 38.76 3.58
6488 8268 7.851387 TTATTTTTGCATTGCATCATGTCAT 57.149 28.000 12.95 1.42 38.76 3.06
6489 8269 6.751514 ATTTTTGCATTGCATCATGTCATT 57.248 29.167 12.95 0.00 38.76 2.57
6490 8270 7.851387 ATTTTTGCATTGCATCATGTCATTA 57.149 28.000 12.95 0.00 38.76 1.90
6491 8271 7.851387 TTTTTGCATTGCATCATGTCATTAT 57.149 28.000 12.95 0.00 38.76 1.28
6492 8272 6.836577 TTTGCATTGCATCATGTCATTATG 57.163 33.333 12.95 3.04 38.76 1.90
6493 8273 4.303282 TGCATTGCATCATGTCATTATGC 58.697 39.130 20.48 20.48 44.94 3.14
6494 8274 3.678072 GCATTGCATCATGTCATTATGCC 59.322 43.478 23.09 9.02 44.26 4.40
6495 8275 4.797933 GCATTGCATCATGTCATTATGCCA 60.798 41.667 23.09 15.88 44.26 4.92
6496 8276 5.478407 CATTGCATCATGTCATTATGCCAT 58.522 37.500 23.09 17.13 44.26 4.40
6497 8277 4.776795 TGCATCATGTCATTATGCCATC 57.223 40.909 23.09 3.41 44.26 3.51
6498 8278 4.145807 TGCATCATGTCATTATGCCATCA 58.854 39.130 23.09 7.36 44.26 3.07
6499 8279 4.770010 TGCATCATGTCATTATGCCATCAT 59.230 37.500 23.09 0.00 44.26 2.45
6500 8280 5.946972 TGCATCATGTCATTATGCCATCATA 59.053 36.000 23.09 6.47 44.26 2.15
6501 8281 6.605594 TGCATCATGTCATTATGCCATCATAT 59.394 34.615 23.09 0.00 44.26 1.78
6502 8282 7.139392 GCATCATGTCATTATGCCATCATATC 58.861 38.462 17.68 0.00 40.06 1.63
6503 8283 7.201785 GCATCATGTCATTATGCCATCATATCA 60.202 37.037 17.68 0.00 40.06 2.15
6504 8284 8.850156 CATCATGTCATTATGCCATCATATCAT 58.150 33.333 0.00 0.00 35.30 2.45
6505 8285 8.817092 TCATGTCATTATGCCATCATATCATT 57.183 30.769 0.00 0.00 35.30 2.57
6506 8286 9.908747 TCATGTCATTATGCCATCATATCATTA 57.091 29.630 0.00 0.00 35.30 1.90
6516 8296 8.959705 TGCCATCATATCATTAATTTTTGCAA 57.040 26.923 0.00 0.00 0.00 4.08
6517 8297 8.828644 TGCCATCATATCATTAATTTTTGCAAC 58.171 29.630 0.00 0.00 0.00 4.17
6518 8298 9.048446 GCCATCATATCATTAATTTTTGCAACT 57.952 29.630 0.00 0.00 0.00 3.16
6534 8314 8.649973 TTTTGCAACTCAAATAAATAAACCGT 57.350 26.923 0.00 0.00 43.53 4.83
6535 8315 9.745880 TTTTGCAACTCAAATAAATAAACCGTA 57.254 25.926 0.00 0.00 43.53 4.02
6536 8316 9.915629 TTTGCAACTCAAATAAATAAACCGTAT 57.084 25.926 0.00 0.00 39.58 3.06
6537 8317 8.903570 TGCAACTCAAATAAATAAACCGTATG 57.096 30.769 0.00 0.00 0.00 2.39
6538 8318 8.731605 TGCAACTCAAATAAATAAACCGTATGA 58.268 29.630 0.00 0.00 0.00 2.15
6539 8319 9.562583 GCAACTCAAATAAATAAACCGTATGAA 57.437 29.630 0.00 0.00 0.00 2.57
6550 8330 2.882927 CCGTATGAATCTTCGGTCCA 57.117 50.000 0.00 0.00 38.45 4.02
6551 8331 3.386768 CCGTATGAATCTTCGGTCCAT 57.613 47.619 0.00 0.00 38.45 3.41
6552 8332 3.728845 CCGTATGAATCTTCGGTCCATT 58.271 45.455 0.00 0.00 38.45 3.16
6553 8333 4.127171 CCGTATGAATCTTCGGTCCATTT 58.873 43.478 0.00 0.00 38.45 2.32
6554 8334 5.294356 CCGTATGAATCTTCGGTCCATTTA 58.706 41.667 0.00 0.00 38.45 1.40
6555 8335 5.756347 CCGTATGAATCTTCGGTCCATTTAA 59.244 40.000 0.00 0.00 38.45 1.52
6556 8336 6.259167 CCGTATGAATCTTCGGTCCATTTAAA 59.741 38.462 0.00 0.00 38.45 1.52
6557 8337 7.123830 CGTATGAATCTTCGGTCCATTTAAAC 58.876 38.462 0.00 0.00 0.00 2.01
6558 8338 5.890424 TGAATCTTCGGTCCATTTAAACC 57.110 39.130 0.00 0.00 0.00 3.27
6564 8344 2.793288 GGTCCATTTAAACCGAGGGA 57.207 50.000 0.00 0.00 0.00 4.20
6565 8345 3.076079 GGTCCATTTAAACCGAGGGAA 57.924 47.619 0.00 0.00 0.00 3.97
6566 8346 3.628008 GGTCCATTTAAACCGAGGGAAT 58.372 45.455 0.00 0.00 0.00 3.01
6567 8347 4.021229 GGTCCATTTAAACCGAGGGAATT 58.979 43.478 0.00 0.00 0.00 2.17
6568 8348 4.097437 GGTCCATTTAAACCGAGGGAATTC 59.903 45.833 0.00 0.00 0.00 2.17
6569 8349 4.703093 GTCCATTTAAACCGAGGGAATTCA 59.297 41.667 7.93 0.00 0.00 2.57
6570 8350 4.703093 TCCATTTAAACCGAGGGAATTCAC 59.297 41.667 7.93 3.01 0.00 3.18
6571 8351 4.461081 CCATTTAAACCGAGGGAATTCACA 59.539 41.667 11.02 0.00 0.00 3.58
6572 8352 5.127031 CCATTTAAACCGAGGGAATTCACAT 59.873 40.000 11.02 0.00 0.00 3.21
6573 8353 6.320164 CCATTTAAACCGAGGGAATTCACATA 59.680 38.462 11.02 0.00 0.00 2.29
6574 8354 7.147983 CCATTTAAACCGAGGGAATTCACATAA 60.148 37.037 11.02 0.00 0.00 1.90
6575 8355 7.948034 TTTAAACCGAGGGAATTCACATAAT 57.052 32.000 11.02 0.00 0.00 1.28
6576 8356 5.835113 AAACCGAGGGAATTCACATAATG 57.165 39.130 11.02 0.00 0.00 1.90
6577 8357 4.771114 ACCGAGGGAATTCACATAATGA 57.229 40.909 11.02 0.00 34.65 2.57
6578 8358 4.708177 ACCGAGGGAATTCACATAATGAG 58.292 43.478 11.02 0.00 38.99 2.90
6579 8359 4.164221 ACCGAGGGAATTCACATAATGAGT 59.836 41.667 11.02 0.00 38.99 3.41
6580 8360 5.126067 CCGAGGGAATTCACATAATGAGTT 58.874 41.667 11.02 0.00 39.80 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.209048 TGCTTCTTTAGGGATAAGTATTCAGTA 57.791 33.333 0.00 0.00 0.00 2.74
91 92 5.525745 TGAGTGTCTTCTTTTGCGTAATTCA 59.474 36.000 0.00 0.00 0.00 2.57
590 614 1.585002 GTTGCGAAAACTGCGTGCA 60.585 52.632 0.00 0.00 34.24 4.57
1272 1329 1.309499 AAGGACAGAGAGGACGAGCG 61.309 60.000 0.00 0.00 0.00 5.03
1301 1365 0.956633 TCCAGAGCAGCAGCAAAAAG 59.043 50.000 3.17 0.00 45.49 2.27
1393 1605 3.447025 GACGCCCCTCCGGATGAAG 62.447 68.421 3.57 0.00 0.00 3.02
1438 1650 2.561037 CCTCCAAAACCACGCACCC 61.561 63.158 0.00 0.00 0.00 4.61
1509 1733 0.820226 CTCACTCATCGCTCCCTCAA 59.180 55.000 0.00 0.00 0.00 3.02
1618 1864 1.743394 GCCATCGTAGTCCCAAAAAGG 59.257 52.381 0.00 0.00 37.03 3.11
1654 1904 2.564947 ACTTCACTGCTTCCTTCGAGAT 59.435 45.455 0.00 0.00 0.00 2.75
1695 1958 0.737715 GCTCACGACATCTCGGCTTT 60.738 55.000 0.00 0.00 44.80 3.51
1873 2323 1.802960 CAACAGAAGCATCTTCGCTGT 59.197 47.619 0.00 0.00 42.89 4.40
1910 2360 1.895020 TTGGCCGCTACCACTACCAG 61.895 60.000 0.00 0.00 40.19 4.00
1942 2392 1.209504 TCTGCAATTTCTCTACCCCCG 59.790 52.381 0.00 0.00 0.00 5.73
2043 2522 6.575201 GCAGAAGAGTTGTGAATAAGTTTTCG 59.425 38.462 0.00 0.00 32.41 3.46
2270 2791 5.311265 TCAGAAGAAACAGGAGAGTACGTA 58.689 41.667 0.00 0.00 0.00 3.57
2271 2792 4.142790 TCAGAAGAAACAGGAGAGTACGT 58.857 43.478 0.00 0.00 0.00 3.57
2272 2793 4.768130 TCAGAAGAAACAGGAGAGTACG 57.232 45.455 0.00 0.00 0.00 3.67
2362 2887 9.986833 GATTAACACTTGTTTGCAAATCTTTTT 57.013 25.926 16.21 7.50 39.31 1.94
2448 2984 7.348080 AGGATATTCATGTTCACTAACTCGA 57.652 36.000 0.00 0.00 36.51 4.04
2466 3003 7.639113 TTTAAAGCCAACGAATCAAGGATAT 57.361 32.000 0.00 0.00 0.00 1.63
2689 3597 8.882415 AAAAATCTACGACAAGAACTCTGTTA 57.118 30.769 0.00 0.00 0.00 2.41
2843 3754 1.575419 TTCCCTTGCCTACCACGTAT 58.425 50.000 0.00 0.00 0.00 3.06
3011 3936 9.607333 TCAGTTCTAGGTTCAATCATAGGATAT 57.393 33.333 0.00 0.00 32.09 1.63
3012 3937 9.083422 CTCAGTTCTAGGTTCAATCATAGGATA 57.917 37.037 0.00 0.00 32.09 2.59
3013 3938 7.786943 TCTCAGTTCTAGGTTCAATCATAGGAT 59.213 37.037 0.00 0.00 34.43 3.24
3014 3939 7.126061 TCTCAGTTCTAGGTTCAATCATAGGA 58.874 38.462 0.00 0.00 0.00 2.94
3015 3940 7.353414 TCTCAGTTCTAGGTTCAATCATAGG 57.647 40.000 0.00 0.00 0.00 2.57
3017 3942 9.868160 TCTATCTCAGTTCTAGGTTCAATCATA 57.132 33.333 0.00 0.00 0.00 2.15
3034 3959 4.511527 ACACAAACAGGCATCTATCTCAG 58.488 43.478 0.00 0.00 0.00 3.35
3307 4285 6.967199 GGACCGAGAATAAAAGTAAATGCAAG 59.033 38.462 0.00 0.00 0.00 4.01
3409 4959 1.833630 TCCTGGCCACTGTGATAAGAG 59.166 52.381 9.86 0.00 0.00 2.85
3736 5290 9.676195 CCAACATCGTATGCATTTGATATTTTA 57.324 29.630 3.54 0.00 0.00 1.52
3806 5360 2.793585 GCCATCTGAAATGCACATCACG 60.794 50.000 0.00 0.00 0.00 4.35
3862 5416 2.486592 CCACCCTTTTATGACACCGTTC 59.513 50.000 0.00 0.00 0.00 3.95
4103 5667 3.053917 GGGTATGTCATTGGGGTTGTAGT 60.054 47.826 0.00 0.00 0.00 2.73
4131 5695 1.057851 ACTGTTTGGGGGACGAGGAA 61.058 55.000 0.00 0.00 0.00 3.36
4132 5696 0.178926 TACTGTTTGGGGGACGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
4296 5921 6.671605 TCCCAATAATTCATCCACAGATCAA 58.328 36.000 0.00 0.00 0.00 2.57
4519 6182 3.929610 GAGACTGTTGGATGCACTCTTAC 59.070 47.826 0.00 0.00 0.00 2.34
4564 6230 8.243426 TGTTAAGCATTGATCTTTGTATGGAAC 58.757 33.333 0.00 0.00 0.00 3.62
4572 6241 9.552114 CTCTAAGTTGTTAAGCATTGATCTTTG 57.448 33.333 0.00 0.00 0.00 2.77
4786 6496 3.655615 AACAGTTTACAAGGTCACCCA 57.344 42.857 0.00 0.00 0.00 4.51
4946 6657 1.817740 CGTCCAGGCCAAGAGGAAAAA 60.818 52.381 5.01 0.00 36.89 1.94
5028 6739 2.481276 CGAATACGATGAGGTTCCAGCA 60.481 50.000 0.00 0.00 42.66 4.41
5044 6755 3.743521 CATTCTCCAGGGCATTCGAATA 58.256 45.455 10.97 0.00 0.00 1.75
5082 6793 0.806868 CGTGTGGCAAGCATTCATCT 59.193 50.000 0.00 0.00 0.00 2.90
5312 7047 1.905215 CCAGAAGATGTCCTGTGACCT 59.095 52.381 0.00 0.00 41.01 3.85
5317 7052 2.702093 CCCCCAGAAGATGTCCTGT 58.298 57.895 0.00 0.00 0.00 4.00
5357 7113 0.035458 AACCAGCCTCTTCTCGTTGG 59.965 55.000 0.00 0.00 0.00 3.77
5445 7201 3.244215 CGGCAAGCTCCAGGATTATAAGA 60.244 47.826 0.00 0.00 0.00 2.10
5447 7203 2.703536 TCGGCAAGCTCCAGGATTATAA 59.296 45.455 0.00 0.00 0.00 0.98
5451 7207 0.465097 CATCGGCAAGCTCCAGGATT 60.465 55.000 0.00 0.00 0.00 3.01
5576 7337 7.455641 TCAAACACTTTTGAGGAACAAACTA 57.544 32.000 0.00 0.00 45.08 2.24
5739 7504 1.597742 AATATGCTACAAGGGCAGCG 58.402 50.000 0.00 0.00 43.15 5.18
5837 7610 9.371136 CATATTATTCTCATGCAACGTACCTAT 57.629 33.333 0.00 0.00 0.00 2.57
5914 7687 2.426522 CATGAACAGTGACCGGACAAT 58.573 47.619 9.46 4.09 0.00 2.71
5931 7704 0.942252 CGCATCCAGACACATCCATG 59.058 55.000 0.00 0.00 0.00 3.66
5932 7705 0.543277 ACGCATCCAGACACATCCAT 59.457 50.000 0.00 0.00 0.00 3.41
6000 7773 6.772233 TGCTATATGAAAAATGCTCTGGCTAA 59.228 34.615 0.00 0.00 39.59 3.09
6003 7776 5.218139 GTGCTATATGAAAAATGCTCTGGC 58.782 41.667 0.00 0.00 39.26 4.85
6095 7868 2.429610 ACTTGAGTGGAGTACGTGTGTT 59.570 45.455 0.00 0.00 0.00 3.32
6199 7972 4.567159 GCATCGATTCTAAAACGAGAAGGT 59.433 41.667 0.00 0.00 38.80 3.50
6284 8057 5.280727 GCTAGCATTAATTCATAGACCCCCT 60.281 44.000 10.63 0.00 0.00 4.79
6285 8058 4.944317 GCTAGCATTAATTCATAGACCCCC 59.056 45.833 10.63 0.00 0.00 5.40
6290 8066 5.161358 CGGACGCTAGCATTAATTCATAGA 58.839 41.667 16.45 0.00 0.00 1.98
6294 8071 2.159014 ACCGGACGCTAGCATTAATTCA 60.159 45.455 16.45 0.00 0.00 2.57
6327 8104 8.217111 TCATGTTATGTGAGGCCATTTAGAATA 58.783 33.333 5.01 0.00 0.00 1.75
6383 8163 4.308458 CGGTCTTGGGGCGTCACA 62.308 66.667 0.00 0.00 0.00 3.58
6386 8166 4.452733 CTCCGGTCTTGGGGCGTC 62.453 72.222 0.00 0.00 0.00 5.19
6390 8170 2.269241 GAAGCTCCGGTCTTGGGG 59.731 66.667 14.63 0.00 0.00 4.96
6391 8171 1.078848 CTGAAGCTCCGGTCTTGGG 60.079 63.158 14.63 5.47 0.00 4.12
6392 8172 0.035458 AACTGAAGCTCCGGTCTTGG 59.965 55.000 14.63 10.22 0.00 3.61
6393 8173 1.151668 CAACTGAAGCTCCGGTCTTG 58.848 55.000 14.63 5.94 0.00 3.02
6394 8174 0.603975 GCAACTGAAGCTCCGGTCTT 60.604 55.000 0.00 6.37 0.00 3.01
6395 8175 1.004440 GCAACTGAAGCTCCGGTCT 60.004 57.895 0.00 0.00 0.00 3.85
6396 8176 2.035442 GGCAACTGAAGCTCCGGTC 61.035 63.158 0.00 0.00 0.00 4.79
6397 8177 2.032681 GGCAACTGAAGCTCCGGT 59.967 61.111 0.00 0.00 0.00 5.28
6414 8194 0.178973 AAACCCGGAAACCCTGGAAG 60.179 55.000 0.73 0.00 44.44 3.46
6415 8195 0.178984 GAAACCCGGAAACCCTGGAA 60.179 55.000 0.73 0.00 44.44 3.53
6416 8196 1.063654 AGAAACCCGGAAACCCTGGA 61.064 55.000 0.73 0.00 44.44 3.86
6417 8197 0.608308 GAGAAACCCGGAAACCCTGG 60.608 60.000 0.73 0.00 41.19 4.45
6418 8198 0.608308 GGAGAAACCCGGAAACCCTG 60.608 60.000 0.73 0.00 0.00 4.45
6419 8199 1.765727 GGAGAAACCCGGAAACCCT 59.234 57.895 0.73 0.00 0.00 4.34
6420 8200 1.673337 CGGAGAAACCCGGAAACCC 60.673 63.158 0.73 0.00 45.43 4.11
6421 8201 3.976758 CGGAGAAACCCGGAAACC 58.023 61.111 0.73 0.00 45.43 3.27
6428 8208 1.670791 TGAAACACACGGAGAAACCC 58.329 50.000 0.00 0.00 34.64 4.11
6429 8209 3.982576 AATGAAACACACGGAGAAACC 57.017 42.857 0.00 0.00 0.00 3.27
6430 8210 5.500131 GCAAAAATGAAACACACGGAGAAAC 60.500 40.000 0.00 0.00 0.00 2.78
6431 8211 4.564769 GCAAAAATGAAACACACGGAGAAA 59.435 37.500 0.00 0.00 0.00 2.52
6432 8212 4.109050 GCAAAAATGAAACACACGGAGAA 58.891 39.130 0.00 0.00 0.00 2.87
6433 8213 3.380004 AGCAAAAATGAAACACACGGAGA 59.620 39.130 0.00 0.00 0.00 3.71
6434 8214 3.705604 AGCAAAAATGAAACACACGGAG 58.294 40.909 0.00 0.00 0.00 4.63
6435 8215 3.791973 AGCAAAAATGAAACACACGGA 57.208 38.095 0.00 0.00 0.00 4.69
6436 8216 3.543852 GCAAGCAAAAATGAAACACACGG 60.544 43.478 0.00 0.00 0.00 4.94
6437 8217 3.306703 AGCAAGCAAAAATGAAACACACG 59.693 39.130 0.00 0.00 0.00 4.49
6438 8218 4.260334 GGAGCAAGCAAAAATGAAACACAC 60.260 41.667 0.00 0.00 0.00 3.82
6439 8219 3.870419 GGAGCAAGCAAAAATGAAACACA 59.130 39.130 0.00 0.00 0.00 3.72
6440 8220 4.122046 AGGAGCAAGCAAAAATGAAACAC 58.878 39.130 0.00 0.00 0.00 3.32
6441 8221 4.405116 AGGAGCAAGCAAAAATGAAACA 57.595 36.364 0.00 0.00 0.00 2.83
6442 8222 5.739752 AAAGGAGCAAGCAAAAATGAAAC 57.260 34.783 0.00 0.00 0.00 2.78
6443 8223 8.449251 AATAAAAGGAGCAAGCAAAAATGAAA 57.551 26.923 0.00 0.00 0.00 2.69
6444 8224 8.449251 AAATAAAAGGAGCAAGCAAAAATGAA 57.551 26.923 0.00 0.00 0.00 2.57
6445 8225 8.449251 AAAATAAAAGGAGCAAGCAAAAATGA 57.551 26.923 0.00 0.00 0.00 2.57
6446 8226 8.960075 CAAAAATAAAAGGAGCAAGCAAAAATG 58.040 29.630 0.00 0.00 0.00 2.32
6447 8227 7.648908 GCAAAAATAAAAGGAGCAAGCAAAAAT 59.351 29.630 0.00 0.00 0.00 1.82
6448 8228 6.971756 GCAAAAATAAAAGGAGCAAGCAAAAA 59.028 30.769 0.00 0.00 0.00 1.94
6449 8229 6.094603 TGCAAAAATAAAAGGAGCAAGCAAAA 59.905 30.769 0.00 0.00 0.00 2.44
6450 8230 5.587844 TGCAAAAATAAAAGGAGCAAGCAAA 59.412 32.000 0.00 0.00 0.00 3.68
6451 8231 5.121811 TGCAAAAATAAAAGGAGCAAGCAA 58.878 33.333 0.00 0.00 0.00 3.91
6452 8232 4.701765 TGCAAAAATAAAAGGAGCAAGCA 58.298 34.783 0.00 0.00 0.00 3.91
6453 8233 5.868043 ATGCAAAAATAAAAGGAGCAAGC 57.132 34.783 0.00 0.00 33.91 4.01
6454 8234 6.081693 GCAATGCAAAAATAAAAGGAGCAAG 58.918 36.000 0.00 0.00 33.91 4.01
6455 8235 5.530171 TGCAATGCAAAAATAAAAGGAGCAA 59.470 32.000 5.01 0.00 34.76 3.91
6456 8236 5.061853 TGCAATGCAAAAATAAAAGGAGCA 58.938 33.333 5.01 0.00 34.76 4.26
6457 8237 5.610235 TGCAATGCAAAAATAAAAGGAGC 57.390 34.783 5.01 0.00 34.76 4.70
6458 8238 7.367159 TGATGCAATGCAAAAATAAAAGGAG 57.633 32.000 13.45 0.00 43.62 3.69
6459 8239 7.390996 ACATGATGCAATGCAAAAATAAAAGGA 59.609 29.630 13.45 0.00 43.62 3.36
6460 8240 7.531716 ACATGATGCAATGCAAAAATAAAAGG 58.468 30.769 13.45 0.00 43.62 3.11
6461 8241 8.231161 TGACATGATGCAATGCAAAAATAAAAG 58.769 29.630 13.45 0.00 43.62 2.27
6462 8242 8.095937 TGACATGATGCAATGCAAAAATAAAA 57.904 26.923 13.45 0.00 43.62 1.52
6463 8243 7.668525 TGACATGATGCAATGCAAAAATAAA 57.331 28.000 13.45 0.00 43.62 1.40
6464 8244 7.851387 ATGACATGATGCAATGCAAAAATAA 57.149 28.000 13.45 0.00 43.62 1.40
6465 8245 7.851387 AATGACATGATGCAATGCAAAAATA 57.149 28.000 13.45 0.00 43.62 1.40
6466 8246 6.751514 AATGACATGATGCAATGCAAAAAT 57.248 29.167 13.45 3.29 43.62 1.82
6467 8247 7.677511 GCATAATGACATGATGCAATGCAAAAA 60.678 33.333 26.74 0.59 43.62 1.94
6468 8248 6.238239 GCATAATGACATGATGCAATGCAAAA 60.238 34.615 26.74 3.51 43.62 2.44
6469 8249 5.235401 GCATAATGACATGATGCAATGCAAA 59.765 36.000 26.74 3.94 43.62 3.68
6470 8250 4.747605 GCATAATGACATGATGCAATGCAA 59.252 37.500 26.74 0.00 43.62 4.08
6471 8251 4.303282 GCATAATGACATGATGCAATGCA 58.697 39.130 26.74 11.44 44.35 3.96
6472 8252 3.678072 GGCATAATGACATGATGCAATGC 59.322 43.478 30.56 15.22 46.29 3.56
6473 8253 4.877282 TGGCATAATGACATGATGCAATG 58.123 39.130 30.56 11.47 46.29 2.82
6474 8254 5.738619 ATGGCATAATGACATGATGCAAT 57.261 34.783 30.56 25.01 46.11 3.56
6490 8270 9.562408 TTGCAAAAATTAATGATATGATGGCAT 57.438 25.926 0.00 0.00 38.54 4.40
6491 8271 8.828644 GTTGCAAAAATTAATGATATGATGGCA 58.171 29.630 0.00 0.00 0.00 4.92
6492 8272 9.048446 AGTTGCAAAAATTAATGATATGATGGC 57.952 29.630 0.00 0.00 0.00 4.40
6511 8291 9.347934 CATACGGTTTATTTATTTGAGTTGCAA 57.652 29.630 0.00 0.00 33.88 4.08
6512 8292 8.731605 TCATACGGTTTATTTATTTGAGTTGCA 58.268 29.630 0.00 0.00 0.00 4.08
6513 8293 9.562583 TTCATACGGTTTATTTATTTGAGTTGC 57.437 29.630 0.00 0.00 0.00 4.17
6532 8312 6.838198 TTAAATGGACCGAAGATTCATACG 57.162 37.500 0.00 0.00 0.00 3.06
6533 8313 7.415229 GGTTTAAATGGACCGAAGATTCATAC 58.585 38.462 0.00 0.00 0.00 2.39
6534 8314 7.562454 GGTTTAAATGGACCGAAGATTCATA 57.438 36.000 0.00 0.00 0.00 2.15
6535 8315 6.451064 GGTTTAAATGGACCGAAGATTCAT 57.549 37.500 0.00 0.00 0.00 2.57
6536 8316 5.890424 GGTTTAAATGGACCGAAGATTCA 57.110 39.130 0.00 0.00 0.00 2.57
6545 8325 2.793288 TCCCTCGGTTTAAATGGACC 57.207 50.000 0.00 0.00 0.00 4.46
6546 8326 4.703093 TGAATTCCCTCGGTTTAAATGGAC 59.297 41.667 2.27 0.00 0.00 4.02
6547 8327 4.703093 GTGAATTCCCTCGGTTTAAATGGA 59.297 41.667 2.27 0.00 0.00 3.41
6548 8328 4.461081 TGTGAATTCCCTCGGTTTAAATGG 59.539 41.667 2.27 0.00 0.00 3.16
6549 8329 5.637006 TGTGAATTCCCTCGGTTTAAATG 57.363 39.130 2.27 0.00 0.00 2.32
6550 8330 7.948034 TTATGTGAATTCCCTCGGTTTAAAT 57.052 32.000 2.27 0.00 0.00 1.40
6551 8331 7.612244 TCATTATGTGAATTCCCTCGGTTTAAA 59.388 33.333 2.27 0.00 32.78 1.52
6552 8332 7.113437 TCATTATGTGAATTCCCTCGGTTTAA 58.887 34.615 2.27 0.00 32.78 1.52
6553 8333 6.654959 TCATTATGTGAATTCCCTCGGTTTA 58.345 36.000 2.27 0.00 32.78 2.01
6554 8334 5.505780 TCATTATGTGAATTCCCTCGGTTT 58.494 37.500 2.27 0.00 32.78 3.27
6555 8335 5.110814 TCATTATGTGAATTCCCTCGGTT 57.889 39.130 2.27 0.00 32.78 4.44
6556 8336 4.164221 ACTCATTATGTGAATTCCCTCGGT 59.836 41.667 2.27 0.00 36.14 4.69
6557 8337 4.708177 ACTCATTATGTGAATTCCCTCGG 58.292 43.478 2.27 0.00 36.14 4.63
6558 8338 6.292389 GAACTCATTATGTGAATTCCCTCG 57.708 41.667 2.27 0.00 37.16 4.63


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

AutoCloner maintained by Alex Coulton.