Multiple sequence alignment - TraesCS4A01G078100

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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 TraesCS4A01G078100 chr4A 100.000 5281 0 0 1 5281 78164203 78158923 0.000000e+00 9753
1 TraesCS4A01G078100 chr4B 90.571 3171 162 48 66 3155 488262774 488259660 0.000000e+00 4072
2 TraesCS4A01G078100 chr4B 92.260 801 21 11 3717 4492 488258974 488258190 0.000000e+00 1098
3 TraesCS4A01G078100 chr4B 91.743 327 14 9 3152 3468 488259628 488259305 4.850000e-120 442
4 TraesCS4A01G078100 chr4B 90.419 334 29 3 4942 5273 488257533 488257201 2.260000e-118 436
5 TraesCS4A01G078100 chr4B 96.087 230 9 0 3461 3690 488259252 488259023 4.990000e-100 375
6 TraesCS4A01G078100 chr4D 89.955 1991 123 35 193 2142 396437061 396435107 0.000000e+00 2497
7 TraesCS4A01G078100 chr4D 93.872 1028 39 8 3702 4715 396433421 396432404 0.000000e+00 1528
8 TraesCS4A01G078100 chr4D 88.995 836 48 22 2133 2941 396435026 396434208 0.000000e+00 994
9 TraesCS4A01G078100 chr4D 94.831 503 14 10 3156 3648 396434005 396433505 0.000000e+00 774
10 TraesCS4A01G078100 chr4D 89.121 239 22 3 4710 4944 396432288 396432050 1.440000e-75 294
11 TraesCS4A01G078100 chr4D 97.110 173 5 0 2983 3155 396434209 396434037 5.170000e-75 292
12 TraesCS4A01G078100 chr4D 91.228 171 15 0 5090 5260 396431424 396431254 3.180000e-57 233
13 TraesCS4A01G078100 chr4D 84.431 167 12 5 20 185 396437284 396437131 9.160000e-33 152
14 TraesCS4A01G078100 chr5D 84.511 1401 110 50 1799 3154 517418916 517417578 0.000000e+00 1286
15 TraesCS4A01G078100 chr1B 84.239 184 29 0 3462 3645 491040093 491039910 4.200000e-41 180
16 TraesCS4A01G078100 chr1D 83.696 184 30 0 3462 3645 366724585 366724768 1.950000e-39 174
17 TraesCS4A01G078100 chr1A 83.696 184 30 0 3462 3645 465453926 465453743 1.950000e-39 174
18 TraesCS4A01G078100 chr7B 90.217 92 8 1 2641 2732 296959534 296959624 9.290000e-23 119


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 TraesCS4A01G078100 chr4A 78158923 78164203 5280 True 9753.0 9753 100.000000 1 5281 1 chr4A.!!$R1 5280
1 TraesCS4A01G078100 chr4B 488257201 488262774 5573 True 1284.6 4072 92.216000 66 5273 5 chr4B.!!$R1 5207
2 TraesCS4A01G078100 chr4D 396431254 396437284 6030 True 845.5 2497 91.192875 20 5260 8 chr4D.!!$R1 5240
3 TraesCS4A01G078100 chr5D 517417578 517418916 1338 True 1286.0 1286 84.511000 1799 3154 1 chr5D.!!$R1 1355

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
64 65 0.251077 CCATATGCTCAGGGAAGGCC 60.251 60.000 0.0 0.0 0.00 5.19 F
706 772 0.663153 GCCGCATTGGGTCATTAGAC 59.337 55.000 0.0 0.0 44.21 2.59 F
1614 1705 0.969149 TGTTCACTCTGCATCGTCCT 59.031 50.000 0.0 0.0 0.00 3.85 F
2286 2527 1.483415 GGGCGTCTCACACCCTTTATA 59.517 52.381 0.0 0.0 37.49 0.98 F
2788 3065 0.179127 CTGAGGATCGACACATGCGT 60.179 55.000 0.0 0.0 38.61 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 1799 0.317938 CCGAGCTACCGCACATCTAC 60.318 60.0 0.00 0.0 39.10 2.59 R
1860 1979 0.588252 CAGGAGAACTGCAACAACCG 59.412 55.0 0.00 0.0 40.97 4.44 R
2773 3050 0.577269 GCTAACGCATGTGTCGATCC 59.423 55.0 13.23 0.0 35.78 3.36 R
4156 4589 0.037046 CTCCTGCATTGCCCAAAACC 60.037 55.0 6.12 0.0 0.00 3.27 R
4597 5111 0.386858 CCGATGTGACGAACGTGTCT 60.387 55.0 4.19 0.0 39.64 3.41 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
17 18 4.326255 GCCTTGGAGGACATGGTG 57.674 61.111 0.00 0.00 44.22 4.17
18 19 1.380302 GCCTTGGAGGACATGGTGT 59.620 57.895 0.00 0.00 44.22 4.16
19 20 0.251341 GCCTTGGAGGACATGGTGTT 60.251 55.000 0.00 0.00 44.22 3.32
20 21 1.826385 CCTTGGAGGACATGGTGTTC 58.174 55.000 0.00 0.00 37.67 3.18
21 22 1.352352 CCTTGGAGGACATGGTGTTCT 59.648 52.381 0.00 0.00 39.37 3.01
22 23 2.224867 CCTTGGAGGACATGGTGTTCTT 60.225 50.000 0.00 0.00 36.05 2.52
23 24 3.490348 CTTGGAGGACATGGTGTTCTTT 58.510 45.455 0.00 0.00 36.05 2.52
24 25 3.593442 TGGAGGACATGGTGTTCTTTT 57.407 42.857 0.00 0.00 36.05 2.27
25 26 3.221771 TGGAGGACATGGTGTTCTTTTG 58.778 45.455 0.00 0.00 36.05 2.44
26 27 3.117701 TGGAGGACATGGTGTTCTTTTGA 60.118 43.478 0.00 0.00 36.05 2.69
27 28 4.082125 GGAGGACATGGTGTTCTTTTGAT 58.918 43.478 0.00 0.00 36.05 2.57
52 53 7.745717 TGATAATAGTAATAGGGCCCATATGC 58.254 38.462 27.56 12.68 0.00 3.14
53 54 7.572485 TGATAATAGTAATAGGGCCCATATGCT 59.428 37.037 27.56 19.34 0.00 3.79
59 60 2.156098 GGGCCCATATGCTCAGGGA 61.156 63.158 19.95 0.00 45.80 4.20
60 61 1.719063 GGGCCCATATGCTCAGGGAA 61.719 60.000 19.95 0.00 45.80 3.97
64 65 0.251077 CCATATGCTCAGGGAAGGCC 60.251 60.000 0.00 0.00 0.00 5.19
99 100 3.246619 GCCTGAGAAAACGACTGTAGAG 58.753 50.000 0.00 0.00 0.00 2.43
136 137 2.669569 GCCTCTTGCACGAAGCCA 60.670 61.111 2.43 0.00 44.83 4.75
137 138 2.970974 GCCTCTTGCACGAAGCCAC 61.971 63.158 2.43 0.00 44.83 5.01
138 139 2.328099 CCTCTTGCACGAAGCCACC 61.328 63.158 0.00 0.00 44.83 4.61
222 285 3.763319 CGGTCGTTTGCCGTAGAG 58.237 61.111 0.00 0.00 43.84 2.43
234 297 2.683362 TGCCGTAGAGATGTGTGAGTAG 59.317 50.000 0.00 0.00 0.00 2.57
243 306 6.424032 AGAGATGTGTGAGTAGGTACATACA 58.576 40.000 19.01 0.77 40.91 2.29
291 354 1.099879 ATGCTCAGAGAAATGGCCGC 61.100 55.000 0.00 0.00 0.00 6.53
463 526 3.625897 GGCAAAGCCCAACACCCC 61.626 66.667 0.00 0.00 44.06 4.95
464 527 3.625897 GCAAAGCCCAACACCCCC 61.626 66.667 0.00 0.00 0.00 5.40
465 528 3.302344 CAAAGCCCAACACCCCCG 61.302 66.667 0.00 0.00 0.00 5.73
521 584 1.971167 TCATCGCCCCAAACAGCAC 60.971 57.895 0.00 0.00 0.00 4.40
540 603 3.303395 GCACTGCACTAATAAATCGCTCC 60.303 47.826 0.00 0.00 0.00 4.70
575 641 1.331756 CACGCAAATGCAGAGGTATCC 59.668 52.381 6.18 0.00 42.21 2.59
606 672 1.086696 GCAGCAGTAAATCGCTCCAA 58.913 50.000 0.00 0.00 35.96 3.53
612 678 4.218417 AGCAGTAAATCGCTCCAAATTGTT 59.782 37.500 0.00 0.00 31.16 2.83
620 686 1.938016 GCTCCAAATTGTTGCTGCCTG 60.938 52.381 0.00 0.00 33.01 4.85
639 705 1.286501 GCACAAACGCGGAGATATCA 58.713 50.000 12.47 0.00 0.00 2.15
647 713 1.665448 CGCGGAGATATCAGCTCACTG 60.665 57.143 10.67 0.00 45.95 3.66
664 730 1.915614 CTGATCACACGCCTGGCAAC 61.916 60.000 20.29 0.00 0.00 4.17
706 772 0.663153 GCCGCATTGGGTCATTAGAC 59.337 55.000 0.00 0.00 44.21 2.59
736 802 2.612212 CGTCCCCGATCAACTTAAATGG 59.388 50.000 0.00 0.00 35.63 3.16
822 901 2.737376 GCCGAGTCCACCAACGTC 60.737 66.667 0.00 0.00 0.00 4.34
954 1033 3.066190 TCGCCACCCTCCGTGTAG 61.066 66.667 0.00 0.00 41.26 2.74
1242 1330 4.335647 ACCTCCACGCCCAAGCAG 62.336 66.667 0.00 0.00 39.83 4.24
1565 1653 1.448717 GAGCACTCTTTCTCCCCGC 60.449 63.158 0.00 0.00 0.00 6.13
1591 1680 2.081725 TACCGCGTTGAATTGCAGTA 57.918 45.000 4.92 0.00 0.00 2.74
1599 1690 4.702392 CGTTGAATTGCAGTACTCTGTTC 58.298 43.478 0.00 0.00 43.05 3.18
1607 1698 2.288457 GCAGTACTCTGTTCACTCTGCA 60.288 50.000 8.95 0.00 43.83 4.41
1614 1705 0.969149 TGTTCACTCTGCATCGTCCT 59.031 50.000 0.00 0.00 0.00 3.85
1615 1706 2.164422 CTGTTCACTCTGCATCGTCCTA 59.836 50.000 0.00 0.00 0.00 2.94
1640 1731 3.000727 ACATGGTAGAAACGTAAGCAGC 58.999 45.455 0.00 0.00 45.62 5.25
1680 1771 8.079809 ACCTCAAGATTAACAAATTAAACGGTG 58.920 33.333 0.00 0.00 33.98 4.94
1712 1803 9.236006 ACGAAAGTTAACTACAGGATAAGTAGA 57.764 33.333 8.92 0.00 46.40 2.59
1743 1862 2.676342 GCTCGGGTAAGTAAATGTGTGG 59.324 50.000 0.00 0.00 0.00 4.17
1757 1876 2.790433 TGTGTGGATGGGTTAAAGCTC 58.210 47.619 0.00 0.00 0.00 4.09
1858 1977 4.127566 TGGGTAATTAGTCACGGTAAGC 57.872 45.455 0.00 0.00 0.00 3.09
1860 1979 2.537214 GGTAATTAGTCACGGTAAGCGC 59.463 50.000 0.00 0.00 0.00 5.92
1874 1993 2.662091 AAGCGCGGTTGTTGCAGTTC 62.662 55.000 24.43 0.00 0.00 3.01
1926 2047 3.572682 TCGTATACCTTGCCTGGTCATAG 59.427 47.826 0.72 0.00 41.22 2.23
1960 2089 3.570926 ATGAACTTGCATGCTTCTGTG 57.429 42.857 20.33 5.08 0.00 3.66
2058 2187 2.364324 GGTCTCCATTAGTCCGTGCATA 59.636 50.000 0.00 0.00 0.00 3.14
2126 2273 6.827586 AGATTGCCGTCATTTTAACCTTTA 57.172 33.333 0.00 0.00 0.00 1.85
2219 2460 4.680110 AGATTATCGTTTATGCCGAGTTCG 59.320 41.667 0.00 0.00 37.81 3.95
2272 2513 2.539476 CCAAATAAAATGCAGGGCGTC 58.461 47.619 0.00 0.00 0.00 5.19
2286 2527 1.483415 GGGCGTCTCACACCCTTTATA 59.517 52.381 0.00 0.00 37.49 0.98
2287 2528 2.093341 GGGCGTCTCACACCCTTTATAA 60.093 50.000 0.00 0.00 37.49 0.98
2289 2530 4.202284 GGGCGTCTCACACCCTTTATAATA 60.202 45.833 0.00 0.00 37.49 0.98
2292 2533 7.156673 GGCGTCTCACACCCTTTATAATATTA 58.843 38.462 0.00 0.00 0.00 0.98
2293 2534 7.822822 GGCGTCTCACACCCTTTATAATATTAT 59.177 37.037 12.51 12.51 0.00 1.28
2370 2619 5.069251 TGAACCAAATTAATTGAACCCGTGT 59.931 36.000 0.39 0.00 41.85 4.49
2371 2620 6.264744 TGAACCAAATTAATTGAACCCGTGTA 59.735 34.615 0.39 0.00 41.85 2.90
2372 2621 6.016213 ACCAAATTAATTGAACCCGTGTAC 57.984 37.500 0.39 0.00 41.85 2.90
2373 2622 5.771165 ACCAAATTAATTGAACCCGTGTACT 59.229 36.000 0.39 0.00 41.85 2.73
2374 2623 6.090129 CCAAATTAATTGAACCCGTGTACTG 58.910 40.000 0.39 0.00 41.85 2.74
2375 2624 6.294286 CCAAATTAATTGAACCCGTGTACTGT 60.294 38.462 0.39 0.00 41.85 3.55
2376 2625 7.094720 CCAAATTAATTGAACCCGTGTACTGTA 60.095 37.037 0.39 0.00 41.85 2.74
2377 2626 6.973229 ATTAATTGAACCCGTGTACTGTAC 57.027 37.500 10.98 10.98 0.00 2.90
2451 2703 5.630061 ACATTGCTTTTGTTTTCTTTGTGC 58.370 33.333 0.00 0.00 0.00 4.57
2521 2785 4.303086 GTGATGGCACGTACTAGTATGT 57.697 45.455 19.96 19.96 34.94 2.29
2522 2786 5.428496 GTGATGGCACGTACTAGTATGTA 57.572 43.478 24.00 12.02 33.83 2.29
2523 2787 6.010294 GTGATGGCACGTACTAGTATGTAT 57.990 41.667 24.00 15.74 33.83 2.29
2524 2788 6.084925 GTGATGGCACGTACTAGTATGTATC 58.915 44.000 24.00 21.88 33.83 2.24
2525 2789 5.182570 TGATGGCACGTACTAGTATGTATCC 59.817 44.000 24.00 24.51 33.83 2.59
2536 2800 9.682465 GTACTAGTATGTATCCATCCATCTACA 57.318 37.037 5.75 0.00 32.29 2.74
2550 2814 4.785301 CCATCTACATGGTTGGTTGAGAT 58.215 43.478 0.00 0.00 44.46 2.75
2620 2892 6.349694 GGATGCCCTTACTTTCAAGAAAAGAG 60.350 42.308 4.64 0.00 46.18 2.85
2637 2909 5.921962 AAAGAGAAAGCAACAGAAAAGGT 57.078 34.783 0.00 0.00 0.00 3.50
2666 2938 3.250280 GTGACCGAACTTTCCTCCTTTTC 59.750 47.826 0.00 0.00 0.00 2.29
2726 3003 4.384208 GGTAGTATGTGCCATCTTTGGAGT 60.384 45.833 0.00 0.00 46.92 3.85
2773 3050 1.520120 ACGCACATGGATCGCTGAG 60.520 57.895 0.00 0.00 0.00 3.35
2788 3065 0.179127 CTGAGGATCGACACATGCGT 60.179 55.000 0.00 0.00 38.61 5.24
2848 3125 5.048713 ACGGGTTCAGAAATCAGAATGTTTC 60.049 40.000 0.00 0.00 36.81 2.78
2884 3161 1.391485 CGAACAGCATCTTTCAGGTCG 59.609 52.381 0.00 0.00 0.00 4.79
2893 3170 4.753233 CATCTTTCAGGTCGTTCAGAGAT 58.247 43.478 0.00 0.00 0.00 2.75
2912 3194 6.496565 CAGAGATCCCACTCCATAAGTAATCT 59.503 42.308 0.00 0.00 36.07 2.40
2913 3195 7.671819 CAGAGATCCCACTCCATAAGTAATCTA 59.328 40.741 0.00 0.00 36.07 1.98
2914 3196 7.893302 AGAGATCCCACTCCATAAGTAATCTAG 59.107 40.741 0.00 0.00 36.07 2.43
2915 3197 6.957020 AGATCCCACTCCATAAGTAATCTAGG 59.043 42.308 0.00 0.00 36.07 3.02
2916 3198 6.289482 TCCCACTCCATAAGTAATCTAGGA 57.711 41.667 0.00 0.00 36.07 2.94
2917 3199 6.315714 TCCCACTCCATAAGTAATCTAGGAG 58.684 44.000 0.00 0.00 46.18 3.69
2935 3217 7.739825 TCTAGGAGTAGATGATTTGAAATGGG 58.260 38.462 0.00 0.00 29.69 4.00
2955 3237 3.753797 GGGACAGTGAGGATTTGAAGAAC 59.246 47.826 0.00 0.00 0.00 3.01
2963 3245 5.117592 GTGAGGATTTGAAGAACATTTTGCG 59.882 40.000 0.00 0.00 0.00 4.85
2966 3248 4.376311 GGATTTGAAGAACATTTTGCGCAC 60.376 41.667 11.12 0.00 0.00 5.34
2967 3249 1.752753 TGAAGAACATTTTGCGCACG 58.247 45.000 11.12 0.86 0.00 5.34
2980 3262 0.803768 GCGCACGTGATCAGAGATGT 60.804 55.000 22.23 0.00 0.00 3.06
2981 3263 0.919300 CGCACGTGATCAGAGATGTG 59.081 55.000 22.23 1.73 33.06 3.21
2987 3269 3.068732 ACGTGATCAGAGATGTGGTATGG 59.931 47.826 0.00 0.00 0.00 2.74
3002 3284 5.583061 TGTGGTATGGTCTTATTAACAAGCG 59.417 40.000 0.00 0.00 0.00 4.68
3047 3329 5.810080 TTGGTTTTGTAATTTGTAGGGGG 57.190 39.130 0.00 0.00 0.00 5.40
3376 3710 3.727227 CGTTTCCGTTTCTGTTTAAAGCC 59.273 43.478 0.00 0.00 0.00 4.35
3445 3783 3.008049 AGACACCCACTGATTCTGTTACC 59.992 47.826 0.00 0.00 0.00 2.85
3475 3872 9.624697 TTCTATTGTGAATTTTGTTGCAGTATC 57.375 29.630 0.00 0.00 0.00 2.24
3478 3875 3.297979 GTGAATTTTGTTGCAGTATCGCG 59.702 43.478 0.00 0.00 33.35 5.87
3541 3938 2.479566 TCAAGTCCAGCAACATCCTC 57.520 50.000 0.00 0.00 0.00 3.71
3663 4060 1.810030 GCGTCCGGTTCAGTCCATC 60.810 63.158 0.00 0.00 0.00 3.51
3673 4072 2.015456 TCAGTCCATCCCGCTCATAT 57.985 50.000 0.00 0.00 0.00 1.78
3690 4089 5.178996 GCTCATATTTGCATCACTCGATTCT 59.821 40.000 0.00 0.00 0.00 2.40
3691 4090 6.535274 TCATATTTGCATCACTCGATTCTG 57.465 37.500 0.00 0.00 0.00 3.02
3692 4091 6.282930 TCATATTTGCATCACTCGATTCTGA 58.717 36.000 0.00 0.00 0.00 3.27
3696 4095 3.865446 TGCATCACTCGATTCTGAACAT 58.135 40.909 0.00 0.00 0.00 2.71
3697 4096 4.256110 TGCATCACTCGATTCTGAACATT 58.744 39.130 0.00 0.00 0.00 2.71
3698 4097 4.696877 TGCATCACTCGATTCTGAACATTT 59.303 37.500 0.00 0.00 0.00 2.32
3699 4098 5.181811 TGCATCACTCGATTCTGAACATTTT 59.818 36.000 0.00 0.00 0.00 1.82
4081 4514 1.445410 TACGCACGCACTCCATCAC 60.445 57.895 0.00 0.00 0.00 3.06
4113 4546 4.941325 CATGCATGCATCATACTCCTAC 57.059 45.455 30.07 0.00 33.90 3.18
4114 4547 4.320870 CATGCATGCATCATACTCCTACA 58.679 43.478 30.07 0.00 33.90 2.74
4115 4548 4.628963 TGCATGCATCATACTCCTACAT 57.371 40.909 18.46 0.00 0.00 2.29
4116 4549 5.743636 TGCATGCATCATACTCCTACATA 57.256 39.130 18.46 0.00 0.00 2.29
4117 4550 5.727434 TGCATGCATCATACTCCTACATAG 58.273 41.667 18.46 0.00 0.00 2.23
4118 4551 5.114780 GCATGCATCATACTCCTACATAGG 58.885 45.833 14.21 0.00 45.02 2.57
4119 4552 4.808414 TGCATCATACTCCTACATAGGC 57.192 45.455 0.00 0.00 43.31 3.93
4120 4553 4.420206 TGCATCATACTCCTACATAGGCT 58.580 43.478 0.00 0.00 43.31 4.58
4121 4554 4.840680 TGCATCATACTCCTACATAGGCTT 59.159 41.667 0.00 0.00 43.31 4.35
4122 4555 5.174395 GCATCATACTCCTACATAGGCTTG 58.826 45.833 0.00 0.00 43.31 4.01
4123 4556 5.047021 GCATCATACTCCTACATAGGCTTGA 60.047 44.000 0.00 1.79 43.31 3.02
4124 4557 6.393990 CATCATACTCCTACATAGGCTTGAC 58.606 44.000 0.00 0.00 43.31 3.18
4125 4558 4.833380 TCATACTCCTACATAGGCTTGACC 59.167 45.833 0.00 0.00 43.31 4.02
4126 4559 3.116096 ACTCCTACATAGGCTTGACCA 57.884 47.619 0.00 0.00 43.31 4.02
4141 4574 4.582869 CTTGACCAGAGGTGAATGAATCA 58.417 43.478 0.00 0.00 35.25 2.57
4326 4777 1.542472 CCGGGGTGGTGTACATTTTTC 59.458 52.381 0.00 0.00 0.00 2.29
4389 4840 7.088272 AGTATTGCATGATTAATACGAGCGTA 58.912 34.615 5.12 5.12 42.01 4.42
4424 4875 8.761575 TTTTATCTTTTGTAGTAGTACCGTGG 57.238 34.615 5.26 0.00 0.00 4.94
4537 5050 4.067896 CCAAACCCCTCATCGATTCTATG 58.932 47.826 0.00 0.00 0.00 2.23
4553 5066 1.611977 CTATGTGTCCGGGCTATTCGA 59.388 52.381 7.97 0.00 0.00 3.71
4656 5170 1.464608 CCAAAACTCATCGACATGCGT 59.535 47.619 8.91 0.00 41.80 5.24
4737 5372 0.181587 TCTTTCTTCACGGGTGGCAA 59.818 50.000 0.00 0.00 0.00 4.52
4750 5385 2.164422 GGGTGGCAACTTAGCTTCAATC 59.836 50.000 0.97 0.00 37.61 2.67
4763 5398 2.923605 GCTTCAATCGTGCATGTGCTTT 60.924 45.455 5.68 0.00 42.66 3.51
4804 5439 8.510243 TCTTCATTAGCTTTTCATGCTCATAA 57.490 30.769 0.00 0.00 41.46 1.90
4805 5440 8.618677 TCTTCATTAGCTTTTCATGCTCATAAG 58.381 33.333 0.00 0.00 41.46 1.73
4806 5441 7.268199 TCATTAGCTTTTCATGCTCATAAGG 57.732 36.000 0.00 0.00 41.46 2.69
4808 5445 6.932356 TTAGCTTTTCATGCTCATAAGGAG 57.068 37.500 0.00 0.00 46.93 3.69
4878 5517 1.737838 TCAATGGGTGTCTCGAATGC 58.262 50.000 0.00 0.00 0.00 3.56
4881 5520 1.742761 ATGGGTGTCTCGAATGCTTG 58.257 50.000 0.00 0.00 0.00 4.01
4883 5522 1.421485 GGTGTCTCGAATGCTTGCG 59.579 57.895 0.00 0.00 0.00 4.85
4884 5523 1.291877 GGTGTCTCGAATGCTTGCGT 61.292 55.000 0.00 0.00 0.00 5.24
4891 5530 0.438445 CGAATGCTTGCGTCTCGAAA 59.562 50.000 11.16 0.00 0.00 3.46
4908 5547 2.288273 CGAAAGTCTCCACGACCTCTTT 60.288 50.000 0.00 0.00 43.91 2.52
4911 5550 2.599677 AGTCTCCACGACCTCTTTCTT 58.400 47.619 0.00 0.00 43.91 2.52
4946 5620 6.969043 TCAGTATAACATTCCCACCTTTGAT 58.031 36.000 0.00 0.00 0.00 2.57
4957 5631 1.920574 CACCTTTGATGACTCGTAGCG 59.079 52.381 0.00 0.00 0.00 4.26
4966 5640 1.396543 GACTCGTAGCGCAACGTCAG 61.397 60.000 11.47 0.00 43.31 3.51
4981 5655 4.650754 ACGTCAGGGTCAAGATATACAC 57.349 45.455 0.00 0.00 0.00 2.90
5006 5680 4.562082 TCACTCAATTTATCGGAACACGT 58.438 39.130 0.00 0.00 44.69 4.49
5021 5695 2.055299 ACGTAGTGGGGTCTTGGTG 58.945 57.895 0.00 0.00 42.51 4.17
5054 5729 4.141135 TGGAGAAGGTTTAACAATGTGGGA 60.141 41.667 0.00 0.00 0.00 4.37
5163 6282 5.791336 TGAACTCTACATATCTCCGCATT 57.209 39.130 0.00 0.00 0.00 3.56
5240 6359 7.807977 TTATTTTCAGAGCATATGGAAGGAC 57.192 36.000 4.56 0.00 0.00 3.85
5241 6360 5.441718 TTTTCAGAGCATATGGAAGGACT 57.558 39.130 4.56 0.00 0.00 3.85
5257 6376 8.350852 TGGAAGGACTACAAAGTAAAAACAAA 57.649 30.769 0.00 0.00 35.56 2.83
5273 6392 7.835634 AAAAACAAAAATTACATCCACACGT 57.164 28.000 0.00 0.00 0.00 4.49
5274 6393 7.835634 AAAACAAAAATTACATCCACACGTT 57.164 28.000 0.00 0.00 0.00 3.99
5275 6394 7.835634 AAACAAAAATTACATCCACACGTTT 57.164 28.000 0.00 0.00 0.00 3.60
5276 6395 6.820470 ACAAAAATTACATCCACACGTTTG 57.180 33.333 0.00 0.00 0.00 2.93
5277 6396 6.565234 ACAAAAATTACATCCACACGTTTGA 58.435 32.000 2.58 0.00 0.00 2.69
5278 6397 6.474102 ACAAAAATTACATCCACACGTTTGAC 59.526 34.615 2.58 0.00 0.00 3.18
5279 6398 5.759506 AAATTACATCCACACGTTTGACA 57.240 34.783 2.58 0.00 0.00 3.58
5280 6399 5.957842 AATTACATCCACACGTTTGACAT 57.042 34.783 2.58 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.251341 AACACCATGTCCTCCAAGGC 60.251 55.000 0.00 0.00 35.23 4.35
2 3 2.867109 AGAACACCATGTCCTCCAAG 57.133 50.000 0.00 0.00 0.00 3.61
5 6 3.486383 TCAAAAGAACACCATGTCCTCC 58.514 45.455 0.00 0.00 0.00 4.30
8 9 5.649782 ATCATCAAAAGAACACCATGTCC 57.350 39.130 0.00 0.00 0.00 4.02
9 10 9.941664 CTATTATCATCAAAAGAACACCATGTC 57.058 33.333 0.00 0.00 0.00 3.06
10 11 9.466497 ACTATTATCATCAAAAGAACACCATGT 57.534 29.630 0.00 0.00 0.00 3.21
19 20 9.959721 GGCCCTATTACTATTATCATCAAAAGA 57.040 33.333 0.00 0.00 0.00 2.52
20 21 9.178758 GGGCCCTATTACTATTATCATCAAAAG 57.821 37.037 17.04 0.00 0.00 2.27
21 22 8.674173 TGGGCCCTATTACTATTATCATCAAAA 58.326 33.333 25.70 0.00 0.00 2.44
22 23 8.225863 TGGGCCCTATTACTATTATCATCAAA 57.774 34.615 25.70 0.00 0.00 2.69
23 24 7.822749 TGGGCCCTATTACTATTATCATCAA 57.177 36.000 25.70 0.00 0.00 2.57
24 25 9.689008 ATATGGGCCCTATTACTATTATCATCA 57.311 33.333 25.70 0.00 0.00 3.07
25 26 9.950496 CATATGGGCCCTATTACTATTATCATC 57.050 37.037 25.70 0.00 0.00 2.92
26 27 8.386264 GCATATGGGCCCTATTACTATTATCAT 58.614 37.037 25.70 4.91 0.00 2.45
27 28 7.572485 AGCATATGGGCCCTATTACTATTATCA 59.428 37.037 25.70 0.00 0.00 2.15
39 40 0.842030 CCCTGAGCATATGGGCCCTA 60.842 60.000 25.70 13.40 33.88 3.53
52 53 2.581354 CTCACGGCCTTCCCTGAG 59.419 66.667 0.00 0.00 34.67 3.35
53 54 3.706373 GCTCACGGCCTTCCCTGA 61.706 66.667 0.00 0.00 34.27 3.86
107 108 1.898574 AAGAGGCAACACGGGCTTG 60.899 57.895 0.00 0.00 44.62 4.01
129 130 1.153745 CTCTCCTTCGGTGGCTTCG 60.154 63.158 0.00 0.00 0.00 3.79
130 131 1.448717 GCTCTCCTTCGGTGGCTTC 60.449 63.158 0.00 0.00 0.00 3.86
131 132 1.915769 AGCTCTCCTTCGGTGGCTT 60.916 57.895 0.00 0.00 0.00 4.35
133 134 2.125350 CAGCTCTCCTTCGGTGGC 60.125 66.667 0.00 0.00 0.00 5.01
134 135 0.321671 TTTCAGCTCTCCTTCGGTGG 59.678 55.000 0.00 0.00 0.00 4.61
135 136 2.275318 GATTTCAGCTCTCCTTCGGTG 58.725 52.381 0.00 0.00 0.00 4.94
136 137 1.902508 TGATTTCAGCTCTCCTTCGGT 59.097 47.619 0.00 0.00 0.00 4.69
137 138 2.548875 CTGATTTCAGCTCTCCTTCGG 58.451 52.381 0.00 0.00 37.15 4.30
222 285 6.319152 ACTCTGTATGTACCTACTCACACATC 59.681 42.308 9.35 0.00 33.78 3.06
274 337 2.476320 GGCGGCCATTTCTCTGAGC 61.476 63.158 15.62 0.00 0.00 4.26
278 341 4.129148 GGGGGCGGCCATTTCTCT 62.129 66.667 30.95 0.00 0.00 3.10
291 354 1.142314 CATTTGATTGCGCAGGGGG 59.858 57.895 11.31 0.00 0.00 5.40
350 413 0.761702 TAGATCCGGGCCCACCTTAC 60.762 60.000 24.92 7.59 36.97 2.34
351 414 0.471211 CTAGATCCGGGCCCACCTTA 60.471 60.000 24.92 6.22 36.97 2.69
502 565 1.971167 TGCTGTTTGGGGCGATGAC 60.971 57.895 0.00 0.00 0.00 3.06
508 571 3.225798 TGCAGTGCTGTTTGGGGC 61.226 61.111 17.60 0.00 0.00 5.80
521 584 4.371786 TCTGGAGCGATTTATTAGTGCAG 58.628 43.478 0.00 0.00 0.00 4.41
540 603 2.887568 GTGGGCAGTCGCGATCTG 60.888 66.667 24.87 24.87 39.92 2.90
584 650 2.165282 GAGCGATTTACTGCTGCAAC 57.835 50.000 3.02 0.00 42.60 4.17
620 686 1.258982 CTGATATCTCCGCGTTTGTGC 59.741 52.381 4.92 0.00 0.00 4.57
627 693 0.595588 AGTGAGCTGATATCTCCGCG 59.404 55.000 0.00 0.00 36.79 6.46
639 705 1.079543 GGCGTGTGATCAGTGAGCT 60.080 57.895 10.19 0.00 0.00 4.09
647 713 2.690778 GGTTGCCAGGCGTGTGATC 61.691 63.158 7.03 0.00 0.00 2.92
648 714 2.672996 GGTTGCCAGGCGTGTGAT 60.673 61.111 7.03 0.00 0.00 3.06
649 715 3.872603 AGGTTGCCAGGCGTGTGA 61.873 61.111 7.03 0.00 0.00 3.58
654 720 1.213537 CATTTCAGGTTGCCAGGCG 59.786 57.895 7.03 0.00 0.00 5.52
655 721 0.037975 CACATTTCAGGTTGCCAGGC 60.038 55.000 3.66 3.66 0.00 4.85
736 802 3.059051 GCATTGATTTCTGGAGATCGAGC 60.059 47.826 0.00 0.00 0.00 5.03
778 857 1.269703 GGACCCCGTCCCATTACTGT 61.270 60.000 0.00 0.00 46.19 3.55
779 858 1.525442 GGACCCCGTCCCATTACTG 59.475 63.158 0.00 0.00 46.19 2.74
822 901 1.497722 GTTTTCTTCGCTCCCGCTG 59.502 57.895 0.00 0.00 0.00 5.18
841 920 5.582269 CCTGCGTTATATGGAGTTATGATGG 59.418 44.000 0.00 0.00 0.00 3.51
1094 1182 4.180946 CGACGAGGAGCAGGACGG 62.181 72.222 0.00 0.00 0.00 4.79
1242 1330 1.516603 GACCTCGGCGTACTTCTGC 60.517 63.158 6.85 0.00 0.00 4.26
1377 1465 3.813724 CAGCCCATCTCCACCCCC 61.814 72.222 0.00 0.00 0.00 5.40
1464 1552 4.208686 GTGCCGTAGCCTCCCTCG 62.209 72.222 0.00 0.00 38.69 4.63
1565 1653 1.153353 ATTCAACGCGGTAACAGTGG 58.847 50.000 12.47 0.00 0.00 4.00
1577 1666 4.211164 TGAACAGAGTACTGCAATTCAACG 59.789 41.667 0.00 0.00 46.95 4.10
1591 1680 1.615883 ACGATGCAGAGTGAACAGAGT 59.384 47.619 0.00 0.00 0.00 3.24
1599 1690 3.128764 TGTTAGTAGGACGATGCAGAGTG 59.871 47.826 1.30 0.00 0.00 3.51
1607 1698 6.459298 CGTTTCTACCATGTTAGTAGGACGAT 60.459 42.308 19.74 0.00 43.00 3.73
1614 1705 6.923012 TGCTTACGTTTCTACCATGTTAGTA 58.077 36.000 0.00 0.00 0.00 1.82
1615 1706 5.786311 TGCTTACGTTTCTACCATGTTAGT 58.214 37.500 0.00 0.00 0.00 2.24
1667 1758 6.556146 TTCGTTTTGACACCGTTTAATTTG 57.444 33.333 0.00 0.00 0.00 2.32
1680 1771 7.237920 TCCTGTAGTTAACTTTCGTTTTGAC 57.762 36.000 14.49 2.97 34.59 3.18
1707 1798 0.663688 CGAGCTACCGCACATCTACT 59.336 55.000 0.00 0.00 39.10 2.57
1708 1799 0.317938 CCGAGCTACCGCACATCTAC 60.318 60.000 0.00 0.00 39.10 2.59
1710 1801 2.786495 CCCGAGCTACCGCACATCT 61.786 63.158 0.00 0.00 39.10 2.90
1711 1802 1.731433 TACCCGAGCTACCGCACATC 61.731 60.000 0.00 0.00 39.10 3.06
1712 1803 1.324740 TTACCCGAGCTACCGCACAT 61.325 55.000 0.00 0.00 39.10 3.21
1743 1862 1.739067 ACTGCGAGCTTTAACCCATC 58.261 50.000 0.00 0.00 0.00 3.51
1757 1876 3.857665 CCACATAGTTGTACAGTACTGCG 59.142 47.826 22.90 0.12 33.76 5.18
1858 1977 1.082756 GAGAACTGCAACAACCGCG 60.083 57.895 0.00 0.00 0.00 6.46
1860 1979 0.588252 CAGGAGAACTGCAACAACCG 59.412 55.000 0.00 0.00 40.97 4.44
1874 1993 2.281761 AAGCCACGCCAACAGGAG 60.282 61.111 0.00 0.00 0.00 3.69
1926 2047 4.600032 CAAGTTCATTTTTGCCCTTTTGC 58.400 39.130 0.00 0.00 0.00 3.68
1960 2089 4.283467 AGGACAAATTGGGCCTTTAACTTC 59.717 41.667 0.00 0.00 0.00 3.01
2058 2187 6.003950 ACTTGCTGTGACTAATTACCAACAT 58.996 36.000 0.00 0.00 0.00 2.71
2126 2273 5.937540 GCCACAAGTTTATTTTGCCCTTAAT 59.062 36.000 0.00 0.00 0.00 1.40
2219 2460 7.020010 GTCAAATGACATCACAAGATTCTGAC 58.980 38.462 8.63 0.00 44.18 3.51
2292 2533 6.543465 CCCTATCAATAATCACACACACACAT 59.457 38.462 0.00 0.00 0.00 3.21
2293 2534 5.879777 CCCTATCAATAATCACACACACACA 59.120 40.000 0.00 0.00 0.00 3.72
2370 2619 9.201127 CGATAGTGCTGTATAACTAGTACAGTA 57.799 37.037 20.27 15.47 46.75 2.74
2371 2620 8.085720 CGATAGTGCTGTATAACTAGTACAGT 57.914 38.462 20.27 8.07 46.75 3.55
2444 2696 0.820074 TGTGTAACCGGGGCACAAAG 60.820 55.000 20.44 0.00 39.76 2.77
2451 2703 2.093181 TCTCAATCATGTGTAACCGGGG 60.093 50.000 6.32 0.00 34.36 5.73
2536 2800 4.916041 TCTCAAGATCTCAACCAACCAT 57.084 40.909 0.00 0.00 0.00 3.55
2550 2814 1.201647 GACGGACGGACAATCTCAAGA 59.798 52.381 0.00 0.00 0.00 3.02
2620 2892 4.441087 CGCTTTACCTTTTCTGTTGCTTTC 59.559 41.667 0.00 0.00 0.00 2.62
2666 2938 8.159447 TGATTGGATATTTGTAGGATCAGGAAG 58.841 37.037 0.00 0.00 0.00 3.46
2726 3003 8.888579 TTTGGTTCACTTCAAAGTTAAAACAA 57.111 26.923 11.45 11.45 37.18 2.83
2773 3050 0.577269 GCTAACGCATGTGTCGATCC 59.423 55.000 13.23 0.00 35.78 3.36
2788 3065 3.399330 GGATATTTACGGCTGCTGCTAA 58.601 45.455 15.64 4.47 39.59 3.09
2848 3125 1.602377 GTTCGTTGGAACCTCAACAGG 59.398 52.381 8.19 0.00 45.48 4.00
2884 3161 4.407296 ACTTATGGAGTGGGATCTCTGAAC 59.593 45.833 0.00 0.00 37.17 3.18
2893 3170 6.125860 ACTCCTAGATTACTTATGGAGTGGGA 60.126 42.308 11.11 0.00 42.42 4.37
2912 3194 7.127186 TGTCCCATTTCAAATCATCTACTCCTA 59.873 37.037 0.00 0.00 0.00 2.94
2913 3195 6.069440 TGTCCCATTTCAAATCATCTACTCCT 60.069 38.462 0.00 0.00 0.00 3.69
2914 3196 6.122277 TGTCCCATTTCAAATCATCTACTCC 58.878 40.000 0.00 0.00 0.00 3.85
2915 3197 6.825721 ACTGTCCCATTTCAAATCATCTACTC 59.174 38.462 0.00 0.00 0.00 2.59
2916 3198 6.600822 CACTGTCCCATTTCAAATCATCTACT 59.399 38.462 0.00 0.00 0.00 2.57
2917 3199 6.599244 TCACTGTCCCATTTCAAATCATCTAC 59.401 38.462 0.00 0.00 0.00 2.59
2935 3217 6.566197 AATGTTCTTCAAATCCTCACTGTC 57.434 37.500 0.00 0.00 0.00 3.51
2955 3237 1.136000 TCTGATCACGTGCGCAAAATG 60.136 47.619 14.00 11.36 0.00 2.32
2963 3245 1.284657 CCACATCTCTGATCACGTGC 58.715 55.000 11.67 0.00 0.00 5.34
2966 3248 3.068732 ACCATACCACATCTCTGATCACG 59.931 47.826 0.00 0.00 0.00 4.35
2967 3249 4.343526 AGACCATACCACATCTCTGATCAC 59.656 45.833 0.00 0.00 0.00 3.06
2980 3262 5.120399 CCGCTTGTTAATAAGACCATACCA 58.880 41.667 15.41 0.00 0.00 3.25
2981 3263 4.514066 CCCGCTTGTTAATAAGACCATACC 59.486 45.833 15.41 0.00 0.00 2.73
2987 3269 5.353123 TCAACATCCCGCTTGTTAATAAGAC 59.647 40.000 15.41 6.30 35.61 3.01
3002 3284 4.272489 TCCAACATTCAGATCAACATCCC 58.728 43.478 0.00 0.00 0.00 3.85
3047 3329 4.400961 AACTCCTGCTCGGCCTGC 62.401 66.667 0.00 5.84 0.00 4.85
3062 3344 1.609072 GCTTCAACCTCCACCTTGAAC 59.391 52.381 0.00 0.00 33.73 3.18
3173 3490 1.467713 GCTACCACACGCTACTCAGTC 60.468 57.143 0.00 0.00 0.00 3.51
3376 3710 2.738846 GCCATATGATTAGTGTGAGCGG 59.261 50.000 3.65 0.00 0.00 5.52
3445 3783 8.523523 TGCAACAAAATTCACAATAGAAGATG 57.476 30.769 0.00 0.00 0.00 2.90
3475 3872 3.179265 CCCTCGTGCAAGTACGCG 61.179 66.667 3.53 3.53 43.40 6.01
3478 3875 1.741770 CAGCCCCTCGTGCAAGTAC 60.742 63.158 0.00 0.00 0.00 2.73
3541 3938 2.171003 GGGTTCCATTTCTTGTCCAGG 58.829 52.381 0.00 0.00 0.00 4.45
3650 4047 2.511600 GCGGGATGGACTGAACCG 60.512 66.667 0.00 0.00 46.78 4.44
3657 4054 1.537202 GCAAATATGAGCGGGATGGAC 59.463 52.381 0.00 0.00 0.00 4.02
3663 4060 2.224606 AGTGATGCAAATATGAGCGGG 58.775 47.619 0.00 0.00 0.00 6.13
3673 4072 4.064388 TGTTCAGAATCGAGTGATGCAAA 58.936 39.130 0.00 0.00 31.86 3.68
3690 4089 6.995091 CCACCCCAAAAGAAATAAAATGTTCA 59.005 34.615 0.00 0.00 0.00 3.18
3691 4090 6.429692 CCCACCCCAAAAGAAATAAAATGTTC 59.570 38.462 0.00 0.00 0.00 3.18
3692 4091 6.126332 ACCCACCCCAAAAGAAATAAAATGTT 60.126 34.615 0.00 0.00 0.00 2.71
3696 4095 4.445019 GCACCCACCCCAAAAGAAATAAAA 60.445 41.667 0.00 0.00 0.00 1.52
3697 4096 3.071747 GCACCCACCCCAAAAGAAATAAA 59.928 43.478 0.00 0.00 0.00 1.40
3698 4097 2.635427 GCACCCACCCCAAAAGAAATAA 59.365 45.455 0.00 0.00 0.00 1.40
3699 4098 2.252714 GCACCCACCCCAAAAGAAATA 58.747 47.619 0.00 0.00 0.00 1.40
3848 4275 1.128188 ACTCCACCAGGTTCACCTCC 61.128 60.000 0.00 0.00 46.65 4.30
4016 4443 2.012237 GAGCATGTGCACGATCTGG 58.988 57.895 13.13 0.00 45.16 3.86
4081 4514 3.454573 ATGCATGCTGCCGTTGGG 61.455 61.111 20.33 0.00 44.23 4.12
4099 4532 5.047021 TCAAGCCTATGTAGGAGTATGATGC 60.047 44.000 10.25 0.00 46.63 3.91
4100 4533 6.393990 GTCAAGCCTATGTAGGAGTATGATG 58.606 44.000 10.25 0.00 46.63 3.07
4101 4534 5.482175 GGTCAAGCCTATGTAGGAGTATGAT 59.518 44.000 10.25 0.00 46.63 2.45
4102 4535 4.833380 GGTCAAGCCTATGTAGGAGTATGA 59.167 45.833 10.25 5.20 46.63 2.15
4103 4536 4.588951 TGGTCAAGCCTATGTAGGAGTATG 59.411 45.833 10.25 3.16 46.63 2.39
4104 4537 4.816126 TGGTCAAGCCTATGTAGGAGTAT 58.184 43.478 10.25 0.00 46.63 2.12
4105 4538 4.079385 TCTGGTCAAGCCTATGTAGGAGTA 60.079 45.833 10.25 0.00 46.63 2.59
4107 4540 3.300388 TCTGGTCAAGCCTATGTAGGAG 58.700 50.000 10.25 0.00 46.63 3.69
4108 4541 3.300388 CTCTGGTCAAGCCTATGTAGGA 58.700 50.000 10.25 0.00 46.63 2.94
4109 4542 2.366916 CCTCTGGTCAAGCCTATGTAGG 59.633 54.545 1.57 1.57 46.42 3.18
4110 4543 3.034635 ACCTCTGGTCAAGCCTATGTAG 58.965 50.000 0.00 0.00 38.35 2.74
4111 4544 2.766263 CACCTCTGGTCAAGCCTATGTA 59.234 50.000 0.00 0.00 38.35 2.29
4112 4545 1.556911 CACCTCTGGTCAAGCCTATGT 59.443 52.381 0.00 0.00 38.35 2.29
4113 4546 1.833630 TCACCTCTGGTCAAGCCTATG 59.166 52.381 0.00 0.00 38.35 2.23
4114 4547 2.254152 TCACCTCTGGTCAAGCCTAT 57.746 50.000 0.00 0.00 38.35 2.57
4115 4548 2.024176 TTCACCTCTGGTCAAGCCTA 57.976 50.000 0.00 0.00 38.35 3.93
4116 4549 1.004044 CATTCACCTCTGGTCAAGCCT 59.996 52.381 0.00 0.00 38.35 4.58
4117 4550 1.003580 TCATTCACCTCTGGTCAAGCC 59.996 52.381 0.00 0.00 31.02 4.35
4118 4551 2.479566 TCATTCACCTCTGGTCAAGC 57.520 50.000 0.00 0.00 31.02 4.01
4119 4552 4.582869 TGATTCATTCACCTCTGGTCAAG 58.417 43.478 0.00 0.00 31.02 3.02
4120 4553 4.639078 TGATTCATTCACCTCTGGTCAA 57.361 40.909 0.00 0.00 31.02 3.18
4121 4554 4.849813 ATGATTCATTCACCTCTGGTCA 57.150 40.909 0.00 0.00 37.11 4.02
4122 4555 5.747951 GAATGATTCATTCACCTCTGGTC 57.252 43.478 26.99 3.78 46.50 4.02
4141 4574 4.396478 CCCAAAACCAAAACCAAAACGAAT 59.604 37.500 0.00 0.00 0.00 3.34
4144 4577 2.159503 GCCCAAAACCAAAACCAAAACG 60.160 45.455 0.00 0.00 0.00 3.60
4150 4583 1.336440 GCATTGCCCAAAACCAAAACC 59.664 47.619 0.00 0.00 0.00 3.27
4155 4588 0.762082 TCCTGCATTGCCCAAAACCA 60.762 50.000 6.12 0.00 0.00 3.67
4156 4589 0.037046 CTCCTGCATTGCCCAAAACC 60.037 55.000 6.12 0.00 0.00 3.27
4326 4777 3.726291 ACCAAACCAAAGGAATGAACG 57.274 42.857 0.00 0.00 0.00 3.95
4470 4921 3.691609 GGCTCCAAGTCAAAGACTAATGG 59.308 47.826 10.30 10.30 42.59 3.16
4475 4926 3.243724 ACTAGGCTCCAAGTCAAAGACT 58.756 45.455 0.00 0.00 45.64 3.24
4537 5050 0.804933 GTGTCGAATAGCCCGGACAC 60.805 60.000 0.73 2.45 36.59 3.67
4553 5066 0.848735 ATGAGCTGCATATGGGGTGT 59.151 50.000 4.56 0.00 34.82 4.16
4577 5090 3.258372 TCTGAATGTCCCATATACGCTCC 59.742 47.826 0.00 0.00 0.00 4.70
4579 5092 3.641436 TGTCTGAATGTCCCATATACGCT 59.359 43.478 0.00 0.00 0.00 5.07
4594 5108 2.390938 GATGTGACGAACGTGTCTGAA 58.609 47.619 4.19 0.00 39.64 3.02
4595 5109 1.662026 CGATGTGACGAACGTGTCTGA 60.662 52.381 4.19 0.00 39.64 3.27
4597 5111 0.386858 CCGATGTGACGAACGTGTCT 60.387 55.000 4.19 0.00 39.64 3.41
4605 5119 1.333931 GCTATCTGTCCGATGTGACGA 59.666 52.381 0.00 0.00 38.11 4.20
4729 5364 1.616159 TTGAAGCTAAGTTGCCACCC 58.384 50.000 0.00 0.00 0.00 4.61
4737 5372 3.125829 CACATGCACGATTGAAGCTAAGT 59.874 43.478 0.00 0.00 0.00 2.24
4750 5385 2.046313 GAGAAACAAAGCACATGCACG 58.954 47.619 6.64 0.00 45.16 5.34
4763 5398 7.041098 GCTAATGAAGAAACAAGAGGAGAAACA 60.041 37.037 0.00 0.00 0.00 2.83
4840 5479 7.147863 CCCATTGAAGATGATTGTGAACCAATA 60.148 37.037 0.00 0.00 43.87 1.90
4881 5520 1.066114 CGTGGAGACTTTCGAGACGC 61.066 60.000 0.00 0.00 0.00 5.19
4883 5522 1.966422 GTCGTGGAGACTTTCGAGAC 58.034 55.000 0.00 0.00 46.13 3.36
4891 5530 4.874459 CCAAGAAAGAGGTCGTGGAGACT 61.874 52.174 1.44 0.00 46.57 3.24
4908 5547 5.724370 TGTTATACTGATGAAGACCCCAAGA 59.276 40.000 0.00 0.00 0.00 3.02
4911 5550 6.409234 GGAATGTTATACTGATGAAGACCCCA 60.409 42.308 0.00 0.00 0.00 4.96
4946 5620 1.441515 GACGTTGCGCTACGAGTCA 60.442 57.895 41.88 3.15 43.99 3.41
4957 5631 2.380084 TATCTTGACCCTGACGTTGC 57.620 50.000 0.00 0.00 0.00 4.17
4966 5640 6.640518 TGAGTGAAAGTGTATATCTTGACCC 58.359 40.000 0.00 0.00 0.00 4.46
4981 5655 6.015504 CGTGTTCCGATAAATTGAGTGAAAG 58.984 40.000 0.00 0.00 39.56 2.62
5006 5680 1.946984 CCTACACCAAGACCCCACTA 58.053 55.000 0.00 0.00 0.00 2.74
5021 5695 3.636153 AACCTTCTCCATCTTGCCTAC 57.364 47.619 0.00 0.00 0.00 3.18
5054 5729 4.538490 TGTTTGGGATGGACTATGTTACCT 59.462 41.667 0.00 0.00 0.00 3.08
5120 6239 8.963725 AGTTCATCTTCAGATATGATGCAAAAA 58.036 29.630 0.00 0.00 38.84 1.94
5122 6241 7.991460 AGAGTTCATCTTCAGATATGATGCAAA 59.009 33.333 0.00 0.00 38.84 3.68
5224 6343 5.426833 ACTTTGTAGTCCTTCCATATGCTCT 59.573 40.000 0.00 0.00 0.00 4.09
5257 6376 5.759506 TGTCAAACGTGTGGATGTAATTT 57.240 34.783 5.75 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.