Multiple sequence alignment - TraesCS6B01G085200

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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 TraesCS6B01G085200 chr6B 100.000 4612 0 0 1 4612 62117997 62122608 0.000000e+00 8517.0
1 TraesCS6B01G085200 chr6B 79.163 1243 195 36 1354 2572 62081090 62082292 0.000000e+00 802.0
2 TraesCS6B01G085200 chr6B 78.562 737 103 25 1354 2055 77841342 77840626 7.090000e-118 435.0
3 TraesCS6B01G085200 chr6B 83.954 349 41 6 917 1253 62080749 62081094 2.070000e-83 320.0
4 TraesCS6B01G085200 chr6B 87.374 198 25 0 1027 1224 79275415 79275612 1.290000e-55 228.0
5 TraesCS6B01G085200 chr6B 86.145 166 19 2 4185 4348 62110569 62110732 4.740000e-40 176.0
6 TraesCS6B01G085200 chr6B 76.276 333 64 10 2157 2486 79554790 79554470 3.690000e-36 163.0
7 TraesCS6B01G085200 chr6B 76.347 334 59 15 2157 2486 79641118 79640801 1.330000e-35 161.0
8 TraesCS6B01G085200 chr6B 75.976 333 65 10 2157 2486 79437298 79436978 1.720000e-34 158.0
9 TraesCS6B01G085200 chr6B 88.430 121 10 3 4064 4184 62110394 62110510 4.810000e-30 143.0
10 TraesCS6B01G085200 chr6B 76.868 281 43 16 1442 1714 63713879 63714145 6.220000e-29 139.0
11 TraesCS6B01G085200 chr6B 81.657 169 23 5 4390 4551 60087254 60087087 2.890000e-27 134.0
12 TraesCS6B01G085200 chr6B 81.395 129 19 5 1422 1547 52360988 52360862 2.940000e-17 100.0
13 TraesCS6B01G085200 chr6B 87.654 81 7 2 2942 3019 62127452 62127372 1.770000e-14 91.6
14 TraesCS6B01G085200 chr6A 97.736 3268 60 6 1356 4612 34009595 34012859 0.000000e+00 5613.0
15 TraesCS6B01G085200 chr6A 94.675 338 16 1 918 1253 34009260 34009597 1.470000e-144 523.0
16 TraesCS6B01G085200 chr6A 79.817 327 53 12 66 385 573836811 573836491 4.640000e-55 226.0
17 TraesCS6B01G085200 chr6A 87.766 188 20 3 1032 1216 30137002 30136815 2.790000e-52 217.0
18 TraesCS6B01G085200 chr6A 72.833 600 119 26 1847 2430 30041010 30040439 1.030000e-36 165.0
19 TraesCS6B01G085200 chr6A 73.782 431 97 12 1994 2417 46062585 46063006 6.180000e-34 156.0
20 TraesCS6B01G085200 chr6A 75.075 333 68 10 2157 2486 46295439 46295119 1.730000e-29 141.0
21 TraesCS6B01G085200 chr6A 81.065 169 25 4 4390 4551 33184921 33184753 1.350000e-25 128.0
22 TraesCS6B01G085200 chr6A 75.862 232 34 15 1486 1706 32796548 32796328 1.060000e-16 99.0
23 TraesCS6B01G085200 chr6A 88.889 81 6 2 2942 3019 34031025 34030945 3.800000e-16 97.1
24 TraesCS6B01G085200 chr6A 80.153 131 23 3 3832 3962 47681700 47681573 1.370000e-15 95.3
25 TraesCS6B01G085200 chr6A 97.674 43 1 0 4570 4612 34006825 34006867 1.780000e-09 75.0
26 TraesCS6B01G085200 chr4B 97.933 919 16 2 1 919 187363334 187364249 0.000000e+00 1589.0
27 TraesCS6B01G085200 chr4D 78.556 1385 176 58 2653 3974 5545684 5544358 0.000000e+00 800.0
28 TraesCS6B01G085200 chr4D 79.792 673 103 23 1930 2577 5546378 5545714 4.210000e-125 459.0
29 TraesCS6B01G085200 chr4D 79.231 390 71 7 3 387 484124342 484123958 3.540000e-66 263.0
30 TraesCS6B01G085200 chr4D 83.404 235 32 5 3 232 387449449 387449681 1.300000e-50 211.0
31 TraesCS6B01G085200 chr5D 86.202 761 73 8 162 919 530867994 530868725 0.000000e+00 795.0
32 TraesCS6B01G085200 chr5D 91.463 164 13 1 1 164 530858876 530859038 1.670000e-54 224.0
33 TraesCS6B01G085200 chr5D 92.424 66 5 0 2576 2641 241947541 241947606 1.370000e-15 95.3
34 TraesCS6B01G085200 chr5D 80.645 93 9 7 1604 1696 484568202 484568285 3.850000e-06 63.9
35 TraesCS6B01G085200 chrUn 80.250 1038 144 26 1354 2349 112594034 112595052 0.000000e+00 725.0
36 TraesCS6B01G085200 chrUn 78.610 734 102 25 1354 2052 265564866 265565579 7.090000e-118 435.0
37 TraesCS6B01G085200 chrUn 78.562 737 103 25 1354 2055 328345326 328344610 7.090000e-118 435.0
38 TraesCS6B01G085200 chrUn 84.701 268 20 6 4345 4612 112599026 112599272 9.910000e-62 248.0
39 TraesCS6B01G085200 chrUn 90.385 156 14 1 4064 4219 112598402 112598556 2.180000e-48 204.0
40 TraesCS6B01G085200 chrUn 72.691 498 112 15 1935 2423 27883828 27883346 1.340000e-30 145.0
41 TraesCS6B01G085200 chrUn 86.047 86 9 1 2934 3019 112597172 112597090 6.360000e-14 89.8
42 TraesCS6B01G085200 chrUn 74.667 225 41 12 1490 1706 27038980 27039196 8.220000e-13 86.1
43 TraesCS6B01G085200 chrUn 85.897 78 7 3 2942 3016 112650726 112650650 3.830000e-11 80.5
44 TraesCS6B01G085200 chr6D 95.026 382 15 1 4170 4551 28663499 28663122 8.540000e-167 597.0
45 TraesCS6B01G085200 chr6D 79.070 172 26 7 4387 4551 29229022 29229190 4.880000e-20 110.0
46 TraesCS6B01G085200 chr6D 90.667 75 4 2 2942 3013 28656485 28656559 3.800000e-16 97.1
47 TraesCS6B01G085200 chr6D 100.000 40 0 0 4573 4612 28660933 28660894 1.780000e-09 75.0
48 TraesCS6B01G085200 chr1B 82.576 396 54 12 532 919 570852470 570852082 7.390000e-88 335.0
49 TraesCS6B01G085200 chr1B 81.748 389 63 7 1 385 570853079 570852695 7.450000e-83 318.0
50 TraesCS6B01G085200 chr1B 92.537 67 5 0 2576 2642 68073412 68073478 3.800000e-16 97.1
51 TraesCS6B01G085200 chr4A 79.545 308 48 12 12 308 695909548 695909851 6.050000e-49 206.0
52 TraesCS6B01G085200 chr3A 99.099 111 1 0 1248 1358 308676027 308675917 2.810000e-47 200.0
53 TraesCS6B01G085200 chr3A 99.099 111 1 0 1245 1355 481522315 481522205 2.810000e-47 200.0
54 TraesCS6B01G085200 chr3A 98.214 112 2 0 1248 1359 152176486 152176375 3.640000e-46 196.0
55 TraesCS6B01G085200 chr3A 95.082 122 5 1 1237 1357 19299527 19299648 1.690000e-44 191.0
56 TraesCS6B01G085200 chr3A 91.667 72 6 0 2576 2647 34532514 34532443 2.940000e-17 100.0
57 TraesCS6B01G085200 chr7B 100.000 107 0 0 1249 1355 29313246 29313140 1.010000e-46 198.0
58 TraesCS6B01G085200 chr7B 95.902 122 4 1 1237 1357 586328567 586328688 3.640000e-46 196.0
59 TraesCS6B01G085200 chr7A 99.091 110 1 0 1248 1357 609518901 609519010 1.010000e-46 198.0
60 TraesCS6B01G085200 chr2A 95.000 120 6 0 1238 1357 16547056 16546937 6.090000e-44 189.0
61 TraesCS6B01G085200 chr2A 86.713 143 19 0 3 145 768255421 768255563 4.780000e-35 159.0
62 TraesCS6B01G085200 chr2A 93.750 64 4 0 2576 2639 186406064 186406001 3.800000e-16 97.1
63 TraesCS6B01G085200 chr2A 83.810 105 11 6 2033 2133 761200535 761200433 1.370000e-15 95.3
64 TraesCS6B01G085200 chr1A 95.000 120 6 0 1238 1357 587813147 587813028 6.090000e-44 189.0
65 TraesCS6B01G085200 chr2B 87.349 166 16 4 2763 2927 794107616 794107777 7.880000e-43 185.0
66 TraesCS6B01G085200 chr2B 88.462 156 13 4 2773 2927 794098616 794098767 2.830000e-42 183.0
67 TraesCS6B01G085200 chr1D 83.439 157 24 2 1 156 104214804 104214959 1.340000e-30 145.0
68 TraesCS6B01G085200 chr1D 94.030 67 4 0 2576 2642 48391398 48391464 8.160000e-18 102.0
69 TraesCS6B01G085200 chr5A 93.939 66 4 0 2576 2641 311937072 311937137 2.940000e-17 100.0
70 TraesCS6B01G085200 chr3B 91.667 72 6 0 2576 2647 42630883 42630812 2.940000e-17 100.0
71 TraesCS6B01G085200 chr3D 92.537 67 5 0 2576 2642 426451924 426451858 3.800000e-16 97.1
72 TraesCS6B01G085200 chr2D 97.222 36 1 0 1486 1521 63542785 63542750 1.390000e-05 62.1


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 TraesCS6B01G085200 chr6B 62117997 62122608 4611 False 8517.000000 8517 100.0000 1 4612 1 chr6B.!!$F1 4611
1 TraesCS6B01G085200 chr6B 62080749 62082292 1543 False 561.000000 802 81.5585 917 2572 2 chr6B.!!$F4 1655
2 TraesCS6B01G085200 chr6B 77840626 77841342 716 True 435.000000 435 78.5620 1354 2055 1 chr6B.!!$R4 701
3 TraesCS6B01G085200 chr6A 34006825 34012859 6034 False 2070.333333 5613 96.6950 918 4612 3 chr6A.!!$F2 3694
4 TraesCS6B01G085200 chr4B 187363334 187364249 915 False 1589.000000 1589 97.9330 1 919 1 chr4B.!!$F1 918
5 TraesCS6B01G085200 chr4D 5544358 5546378 2020 True 629.500000 800 79.1740 1930 3974 2 chr4D.!!$R2 2044
6 TraesCS6B01G085200 chr5D 530867994 530868725 731 False 795.000000 795 86.2020 162 919 1 chr5D.!!$F4 757
7 TraesCS6B01G085200 chrUn 265564866 265565579 713 False 435.000000 435 78.6100 1354 2052 1 chrUn.!!$F2 698
8 TraesCS6B01G085200 chrUn 328344610 328345326 716 True 435.000000 435 78.5620 1354 2055 1 chrUn.!!$R4 701
9 TraesCS6B01G085200 chrUn 112594034 112599272 5238 False 392.333333 725 85.1120 1354 4612 3 chrUn.!!$F3 3258
10 TraesCS6B01G085200 chr6D 28660894 28663499 2605 True 336.000000 597 97.5130 4170 4612 2 chr6D.!!$R1 442
11 TraesCS6B01G085200 chr1B 570852082 570853079 997 True 326.500000 335 82.1620 1 919 2 chr1B.!!$R1 918

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
943 2462 0.955428 GCGATTCAAGTCCACAGCCA 60.955 55.0 0.00 0.00 0.00 4.75 F
1263 2796 0.107017 TACCTACTCCCTCCGTTCGG 60.107 60.0 4.74 4.74 0.00 4.30 F
1653 3204 0.109781 CCGACAATCAACAAAGCCGG 60.110 55.0 0.00 0.00 0.00 6.13 F
1699 3250 0.968405 GACCGGCGTATGGGGTAATA 59.032 55.0 6.01 0.00 33.28 0.98 F
1735 3286 1.201343 GATTCAGTCCGAGCTTACGC 58.799 55.0 0.00 0.00 0.00 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 3681 4.869861 GCAAATTATTGTCCTCGGCAAATT 59.130 37.500 0.00 0.0 38.85 1.82 R
3055 6266 4.806775 TGAATTTGAAACGAACTCGACAGA 59.193 37.500 6.05 0.0 43.02 3.41 R
3059 6270 9.672086 ATTTTTATGAATTTGAAACGAACTCGA 57.328 25.926 6.05 0.0 43.02 4.04 R
3402 6633 9.959749 GAAACAGATAAACAAAACCACATCTAA 57.040 29.630 0.00 0.0 0.00 2.10 R
3782 7051 3.312421 CAGCAAACAAAAGAGAAGGACGA 59.688 43.478 0.00 0.0 0.00 4.20 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
568 650 4.388804 CCTCCCCTACTACCTGGTTCTTAT 60.389 50.000 3.84 0.00 0.00 1.73
653 738 3.509967 TCTTCGCTTGGTACATCTCTTCA 59.490 43.478 0.00 0.00 39.30 3.02
691 777 2.278330 CCCTGTTTGCTCCCCTTGC 61.278 63.158 0.00 0.00 0.00 4.01
883 969 5.475719 CACAACTATAACAGAAGTCGGGAA 58.524 41.667 0.00 0.00 0.00 3.97
884 970 5.577164 CACAACTATAACAGAAGTCGGGAAG 59.423 44.000 0.00 0.00 0.00 3.46
919 1005 9.383519 GTATGTGAATGAGACAATCTTTTCCTA 57.616 33.333 0.00 0.00 0.00 2.94
921 1007 8.272545 TGTGAATGAGACAATCTTTTCCTATG 57.727 34.615 0.00 0.00 0.00 2.23
943 2462 0.955428 GCGATTCAAGTCCACAGCCA 60.955 55.000 0.00 0.00 0.00 4.75
1054 2587 2.879233 GCGGGTCCACTGGAGAACA 61.879 63.158 0.00 0.00 29.39 3.18
1220 2753 0.322546 CCCCTCCTCGGTTTCTTTGG 60.323 60.000 0.00 0.00 0.00 3.28
1225 2758 3.343617 CTCCTCGGTTTCTTTGGCAATA 58.656 45.455 0.00 0.00 0.00 1.90
1248 2781 2.764547 GGCCGCTCCTTCCTACCT 60.765 66.667 0.00 0.00 0.00 3.08
1249 2782 1.457079 GGCCGCTCCTTCCTACCTA 60.457 63.158 0.00 0.00 0.00 3.08
1250 2783 1.740905 GCCGCTCCTTCCTACCTAC 59.259 63.158 0.00 0.00 0.00 3.18
1251 2784 0.756070 GCCGCTCCTTCCTACCTACT 60.756 60.000 0.00 0.00 0.00 2.57
1252 2785 1.320507 CCGCTCCTTCCTACCTACTC 58.679 60.000 0.00 0.00 0.00 2.59
1253 2786 1.320507 CGCTCCTTCCTACCTACTCC 58.679 60.000 0.00 0.00 0.00 3.85
1254 2787 1.707106 GCTCCTTCCTACCTACTCCC 58.293 60.000 0.00 0.00 0.00 4.30
1255 2788 1.218450 GCTCCTTCCTACCTACTCCCT 59.782 57.143 0.00 0.00 0.00 4.20
1256 2789 2.753846 GCTCCTTCCTACCTACTCCCTC 60.754 59.091 0.00 0.00 0.00 4.30
1257 2790 1.858246 TCCTTCCTACCTACTCCCTCC 59.142 57.143 0.00 0.00 0.00 4.30
1258 2791 1.479021 CCTTCCTACCTACTCCCTCCG 60.479 61.905 0.00 0.00 0.00 4.63
1259 2792 1.214923 CTTCCTACCTACTCCCTCCGT 59.785 57.143 0.00 0.00 0.00 4.69
1260 2793 1.302907 TCCTACCTACTCCCTCCGTT 58.697 55.000 0.00 0.00 0.00 4.44
1261 2794 1.213926 TCCTACCTACTCCCTCCGTTC 59.786 57.143 0.00 0.00 0.00 3.95
1262 2795 1.307097 CTACCTACTCCCTCCGTTCG 58.693 60.000 0.00 0.00 0.00 3.95
1263 2796 0.107017 TACCTACTCCCTCCGTTCGG 60.107 60.000 4.74 4.74 0.00 4.30
1264 2797 1.077212 CCTACTCCCTCCGTTCGGA 60.077 63.158 13.34 13.34 0.00 4.55
1265 2798 0.682209 CCTACTCCCTCCGTTCGGAA 60.682 60.000 14.79 0.04 33.41 4.30
1266 2799 1.400737 CTACTCCCTCCGTTCGGAAT 58.599 55.000 14.79 2.09 33.41 3.01
1267 2800 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
1268 2801 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
1269 2802 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1270 2803 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1271 2804 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
1272 2805 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
1273 2806 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
1274 2807 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
1275 2808 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
1276 2809 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
1277 2810 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
1278 2811 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
1279 2812 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
1280 2813 4.430908 GTTCGGAATTACTTGTCTCGGAT 58.569 43.478 0.00 0.00 0.00 4.18
1281 2814 5.585390 GTTCGGAATTACTTGTCTCGGATA 58.415 41.667 0.00 0.00 0.00 2.59
1282 2815 6.214399 GTTCGGAATTACTTGTCTCGGATAT 58.786 40.000 0.00 0.00 0.00 1.63
1283 2816 5.769367 TCGGAATTACTTGTCTCGGATATG 58.231 41.667 0.00 0.00 0.00 1.78
1284 2817 4.923871 CGGAATTACTTGTCTCGGATATGG 59.076 45.833 0.00 0.00 0.00 2.74
1285 2818 5.278808 CGGAATTACTTGTCTCGGATATGGA 60.279 44.000 0.00 0.00 0.00 3.41
1286 2819 6.572509 CGGAATTACTTGTCTCGGATATGGAT 60.573 42.308 0.00 0.00 0.00 3.41
1287 2820 6.591834 GGAATTACTTGTCTCGGATATGGATG 59.408 42.308 0.00 0.00 0.00 3.51
1288 2821 6.672266 ATTACTTGTCTCGGATATGGATGT 57.328 37.500 0.00 0.00 0.00 3.06
1289 2822 7.776618 ATTACTTGTCTCGGATATGGATGTA 57.223 36.000 0.00 0.00 0.00 2.29
1290 2823 7.776618 TTACTTGTCTCGGATATGGATGTAT 57.223 36.000 0.00 0.00 0.00 2.29
1291 2824 6.274157 ACTTGTCTCGGATATGGATGTATC 57.726 41.667 0.00 0.00 0.00 2.24
1292 2825 6.013379 ACTTGTCTCGGATATGGATGTATCT 58.987 40.000 0.00 0.00 32.78 1.98
1293 2826 7.175797 ACTTGTCTCGGATATGGATGTATCTA 58.824 38.462 0.00 0.00 32.78 1.98
1294 2827 7.338196 ACTTGTCTCGGATATGGATGTATCTAG 59.662 40.741 0.00 0.00 32.78 2.43
1295 2828 6.958767 TGTCTCGGATATGGATGTATCTAGA 58.041 40.000 0.00 0.00 32.78 2.43
1296 2829 7.402862 TGTCTCGGATATGGATGTATCTAGAA 58.597 38.462 0.00 0.00 31.35 2.10
1297 2830 7.337184 TGTCTCGGATATGGATGTATCTAGAAC 59.663 40.741 0.00 0.00 31.35 3.01
1298 2831 7.554835 GTCTCGGATATGGATGTATCTAGAACT 59.445 40.741 0.00 0.00 31.35 3.01
1299 2832 8.769359 TCTCGGATATGGATGTATCTAGAACTA 58.231 37.037 0.00 0.00 32.78 2.24
1300 2833 9.397280 CTCGGATATGGATGTATCTAGAACTAA 57.603 37.037 0.00 0.00 32.78 2.24
1301 2834 9.749340 TCGGATATGGATGTATCTAGAACTAAA 57.251 33.333 0.00 0.00 32.78 1.85
1327 2860 9.664332 AATACATCTAGATACATCCATTTCTGC 57.336 33.333 4.54 0.00 0.00 4.26
1328 2861 6.162079 ACATCTAGATACATCCATTTCTGCG 58.838 40.000 4.54 0.00 0.00 5.18
1329 2862 6.015095 ACATCTAGATACATCCATTTCTGCGA 60.015 38.462 4.54 0.00 0.00 5.10
1330 2863 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
1331 2864 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
1332 2865 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
1333 2866 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
1334 2867 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
1335 2868 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
1336 2869 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
1337 2870 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
1338 2871 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
1339 2872 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
1340 2873 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
1341 2874 4.155826 CCATTTCTGCGACAAGTAATTCCA 59.844 41.667 0.00 0.00 0.00 3.53
1342 2875 5.335583 CCATTTCTGCGACAAGTAATTCCAA 60.336 40.000 0.00 0.00 0.00 3.53
1343 2876 5.759506 TTTCTGCGACAAGTAATTCCAAA 57.240 34.783 0.00 0.00 0.00 3.28
1344 2877 4.742438 TCTGCGACAAGTAATTCCAAAC 57.258 40.909 0.00 0.00 0.00 2.93
1345 2878 3.185594 TCTGCGACAAGTAATTCCAAACG 59.814 43.478 0.00 0.00 0.00 3.60
1346 2879 2.224549 TGCGACAAGTAATTCCAAACGG 59.775 45.455 0.00 0.00 0.00 4.44
1347 2880 2.481185 GCGACAAGTAATTCCAAACGGA 59.519 45.455 0.00 0.00 0.00 4.69
1348 2881 3.424433 GCGACAAGTAATTCCAAACGGAG 60.424 47.826 0.00 0.00 32.88 4.63
1349 2882 3.124636 CGACAAGTAATTCCAAACGGAGG 59.875 47.826 0.00 0.00 32.88 4.30
1350 2883 3.418047 ACAAGTAATTCCAAACGGAGGG 58.582 45.455 0.00 0.00 32.88 4.30
1351 2884 3.073356 ACAAGTAATTCCAAACGGAGGGA 59.927 43.478 0.00 0.00 32.88 4.20
1352 2885 3.629142 AGTAATTCCAAACGGAGGGAG 57.371 47.619 0.00 0.00 34.02 4.30
1381 2914 4.752879 CGCCCAATCGTGTCCCGT 62.753 66.667 0.00 0.00 37.94 5.28
1650 3201 2.319472 GAAGCCGACAATCAACAAAGC 58.681 47.619 0.00 0.00 0.00 3.51
1653 3204 0.109781 CCGACAATCAACAAAGCCGG 60.110 55.000 0.00 0.00 0.00 6.13
1699 3250 0.968405 GACCGGCGTATGGGGTAATA 59.032 55.000 6.01 0.00 33.28 0.98
1706 3257 4.382685 CGGCGTATGGGGTAATATCATCTT 60.383 45.833 0.00 0.00 0.00 2.40
1707 3258 5.116882 GGCGTATGGGGTAATATCATCTTC 58.883 45.833 0.00 0.00 0.00 2.87
1708 3259 5.104900 GGCGTATGGGGTAATATCATCTTCT 60.105 44.000 0.00 0.00 0.00 2.85
1715 3266 7.226441 TGGGGTAATATCATCTTCTCAACATG 58.774 38.462 0.00 0.00 0.00 3.21
1735 3286 1.201343 GATTCAGTCCGAGCTTACGC 58.799 55.000 0.00 0.00 0.00 4.42
1753 3304 1.375396 CACGACCTTCCCATCGCAA 60.375 57.895 0.00 0.00 42.12 4.85
2375 3959 8.797266 AAGCTAACAATTTTAAGTAGTGTTGC 57.203 30.769 12.75 12.96 34.43 4.17
2869 6062 4.901197 TCAGTGTAGTTTATCCCAAGCA 57.099 40.909 0.00 0.00 0.00 3.91
3782 7051 3.763897 GCTTCCCATTTACTTCCACATGT 59.236 43.478 0.00 0.00 0.00 3.21
4033 7303 1.726791 CGTGTCTGCATTTAGAAGCGT 59.273 47.619 0.00 0.00 0.00 5.07
4281 7849 9.903682 AAAACTTCATATGAAACAAGTGATCAG 57.096 29.630 18.47 5.50 33.07 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
568 650 8.974060 ACAAGTCCTCTCAAATTAAAACAGTA 57.026 30.769 0.00 0.00 0.00 2.74
653 738 4.778143 GCGATGGGCCGTTCTGGT 62.778 66.667 0.00 0.00 41.21 4.00
691 777 5.127194 TCTGGTCAAGCAATAGTACAGGTAG 59.873 44.000 0.00 0.00 0.00 3.18
883 969 6.768381 TGTCTCATTCACATACGAGTATCTCT 59.232 38.462 0.00 0.00 0.00 3.10
884 970 6.960468 TGTCTCATTCACATACGAGTATCTC 58.040 40.000 0.00 0.00 0.00 2.75
919 1005 2.485426 CTGTGGACTTGAATCGCAACAT 59.515 45.455 0.00 0.00 31.96 2.71
920 1006 1.872952 CTGTGGACTTGAATCGCAACA 59.127 47.619 0.00 0.00 31.96 3.33
921 1007 1.400242 GCTGTGGACTTGAATCGCAAC 60.400 52.381 0.00 0.00 31.96 4.17
943 2462 2.668144 TCTTTTCGGGGAAATGGTGT 57.332 45.000 4.74 0.00 31.34 4.16
1220 2753 1.569479 GGAGCGGCCGAGATTATTGC 61.569 60.000 33.48 7.47 0.00 3.56
1225 2758 2.501610 GAAGGAGCGGCCGAGATT 59.498 61.111 33.48 17.33 43.43 2.40
1248 2781 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
1249 2782 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
1250 2783 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
1251 2784 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
1252 2785 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
1253 2786 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
1254 2787 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
1255 2788 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
1256 2789 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
1257 2790 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
1258 2791 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
1259 2792 4.730949 ATCCGAGACAAGTAATTCCGAA 57.269 40.909 0.00 0.00 0.00 4.30
1260 2793 5.278808 CCATATCCGAGACAAGTAATTCCGA 60.279 44.000 0.00 0.00 0.00 4.55
1261 2794 4.923871 CCATATCCGAGACAAGTAATTCCG 59.076 45.833 0.00 0.00 0.00 4.30
1262 2795 6.097915 TCCATATCCGAGACAAGTAATTCC 57.902 41.667 0.00 0.00 0.00 3.01
1263 2796 7.155328 ACATCCATATCCGAGACAAGTAATTC 58.845 38.462 0.00 0.00 0.00 2.17
1264 2797 7.067496 ACATCCATATCCGAGACAAGTAATT 57.933 36.000 0.00 0.00 0.00 1.40
1265 2798 6.672266 ACATCCATATCCGAGACAAGTAAT 57.328 37.500 0.00 0.00 0.00 1.89
1266 2799 7.670140 AGATACATCCATATCCGAGACAAGTAA 59.330 37.037 0.00 0.00 32.76 2.24
1267 2800 7.175797 AGATACATCCATATCCGAGACAAGTA 58.824 38.462 0.00 0.00 32.76 2.24
1268 2801 6.013379 AGATACATCCATATCCGAGACAAGT 58.987 40.000 0.00 0.00 32.76 3.16
1269 2802 6.522625 AGATACATCCATATCCGAGACAAG 57.477 41.667 0.00 0.00 32.76 3.16
1270 2803 7.402862 TCTAGATACATCCATATCCGAGACAA 58.597 38.462 0.00 0.00 32.76 3.18
1271 2804 6.958767 TCTAGATACATCCATATCCGAGACA 58.041 40.000 0.00 0.00 32.76 3.41
1272 2805 7.554835 AGTTCTAGATACATCCATATCCGAGAC 59.445 40.741 0.00 0.00 32.76 3.36
1273 2806 7.634718 AGTTCTAGATACATCCATATCCGAGA 58.365 38.462 0.00 0.00 32.76 4.04
1274 2807 7.873719 AGTTCTAGATACATCCATATCCGAG 57.126 40.000 0.00 0.00 32.76 4.63
1275 2808 9.749340 TTTAGTTCTAGATACATCCATATCCGA 57.251 33.333 0.00 0.00 32.76 4.55
1301 2834 9.664332 GCAGAAATGGATGTATCTAGATGTATT 57.336 33.333 15.79 4.32 0.00 1.89
1302 2835 7.978414 CGCAGAAATGGATGTATCTAGATGTAT 59.022 37.037 15.79 9.11 0.00 2.29
1303 2836 7.176690 TCGCAGAAATGGATGTATCTAGATGTA 59.823 37.037 15.79 4.44 0.00 2.29
1304 2837 6.015095 TCGCAGAAATGGATGTATCTAGATGT 60.015 38.462 15.79 1.25 0.00 3.06
1305 2838 6.309980 GTCGCAGAAATGGATGTATCTAGATG 59.690 42.308 15.79 0.00 39.69 2.90
1306 2839 6.015095 TGTCGCAGAAATGGATGTATCTAGAT 60.015 38.462 10.73 10.73 39.69 1.98
1307 2840 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
1308 2841 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
1309 2842 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
1310 2843 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
1311 2844 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
1312 2845 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
1313 2846 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
1314 2847 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
1315 2848 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
1316 2849 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
1317 2850 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
1318 2851 4.155826 TGGAATTACTTGTCGCAGAAATGG 59.844 41.667 0.00 0.00 39.69 3.16
1319 2852 5.295431 TGGAATTACTTGTCGCAGAAATG 57.705 39.130 0.00 0.00 39.69 2.32
1320 2853 5.957842 TTGGAATTACTTGTCGCAGAAAT 57.042 34.783 0.00 0.00 39.69 2.17
1321 2854 5.516090 GTTTGGAATTACTTGTCGCAGAAA 58.484 37.500 0.00 0.00 39.69 2.52
1322 2855 4.319190 CGTTTGGAATTACTTGTCGCAGAA 60.319 41.667 0.00 0.00 39.69 3.02
1323 2856 3.185594 CGTTTGGAATTACTTGTCGCAGA 59.814 43.478 0.00 0.00 0.00 4.26
1324 2857 3.479006 CGTTTGGAATTACTTGTCGCAG 58.521 45.455 0.00 0.00 0.00 5.18
1325 2858 2.224549 CCGTTTGGAATTACTTGTCGCA 59.775 45.455 0.00 0.00 37.49 5.10
1326 2859 2.481185 TCCGTTTGGAATTACTTGTCGC 59.519 45.455 0.00 0.00 42.85 5.19
1327 2860 3.124636 CCTCCGTTTGGAATTACTTGTCG 59.875 47.826 0.00 0.00 45.87 4.35
1328 2861 3.439129 CCCTCCGTTTGGAATTACTTGTC 59.561 47.826 0.00 0.00 45.87 3.18
1329 2862 3.073356 TCCCTCCGTTTGGAATTACTTGT 59.927 43.478 0.00 0.00 45.87 3.16
1330 2863 3.681593 TCCCTCCGTTTGGAATTACTTG 58.318 45.455 0.00 0.00 45.87 3.16
1331 2864 3.329814 ACTCCCTCCGTTTGGAATTACTT 59.670 43.478 0.00 0.00 45.87 2.24
1332 2865 2.910977 ACTCCCTCCGTTTGGAATTACT 59.089 45.455 0.00 0.00 45.87 2.24
1333 2866 3.345508 ACTCCCTCCGTTTGGAATTAC 57.654 47.619 0.00 0.00 45.87 1.89
1334 2867 4.098894 AGTACTCCCTCCGTTTGGAATTA 58.901 43.478 0.00 0.00 45.87 1.40
1335 2868 2.910977 AGTACTCCCTCCGTTTGGAATT 59.089 45.455 0.00 0.00 45.87 2.17
1336 2869 2.500504 GAGTACTCCCTCCGTTTGGAAT 59.499 50.000 12.13 0.00 45.87 3.01
1337 2870 1.897802 GAGTACTCCCTCCGTTTGGAA 59.102 52.381 12.13 0.00 45.87 3.53
1338 2871 1.076677 AGAGTACTCCCTCCGTTTGGA 59.923 52.381 19.38 0.00 43.88 3.53
1339 2872 1.204941 CAGAGTACTCCCTCCGTTTGG 59.795 57.143 19.38 0.00 31.53 3.28
1340 2873 1.204941 CCAGAGTACTCCCTCCGTTTG 59.795 57.143 19.38 8.23 31.53 2.93
1341 2874 1.076677 TCCAGAGTACTCCCTCCGTTT 59.923 52.381 19.38 0.00 31.53 3.60
1342 2875 0.702902 TCCAGAGTACTCCCTCCGTT 59.297 55.000 19.38 0.00 31.53 4.44
1343 2876 0.256464 CTCCAGAGTACTCCCTCCGT 59.744 60.000 19.38 0.00 31.53 4.69
1344 2877 0.466555 CCTCCAGAGTACTCCCTCCG 60.467 65.000 19.38 4.75 31.53 4.63
1345 2878 0.757561 GCCTCCAGAGTACTCCCTCC 60.758 65.000 19.38 0.11 31.53 4.30
1346 2879 1.104577 CGCCTCCAGAGTACTCCCTC 61.105 65.000 19.38 2.69 0.00 4.30
1347 2880 1.076632 CGCCTCCAGAGTACTCCCT 60.077 63.158 19.38 0.00 0.00 4.20
1348 2881 2.787567 GCGCCTCCAGAGTACTCCC 61.788 68.421 19.38 0.00 0.00 4.30
1349 2882 2.787567 GGCGCCTCCAGAGTACTCC 61.788 68.421 22.15 1.96 34.01 3.85
1350 2883 2.787567 GGGCGCCTCCAGAGTACTC 61.788 68.421 28.56 15.41 36.21 2.59
1351 2884 2.760385 GGGCGCCTCCAGAGTACT 60.760 66.667 28.56 0.00 36.21 2.73
1352 2885 1.972660 ATTGGGCGCCTCCAGAGTAC 61.973 60.000 28.56 6.48 38.17 2.73
1381 2914 4.082523 CAAGGAGAAGCGCCCGGA 62.083 66.667 0.73 0.00 0.00 5.14
1534 3070 3.145551 CTCCGGATCGAACCCCGT 61.146 66.667 3.57 0.00 43.93 5.28
1595 3146 0.967380 GACCACCTGGAAATGCTGGG 60.967 60.000 0.00 0.00 38.94 4.45
1602 3153 1.073284 GCTACCAAGACCACCTGGAAA 59.927 52.381 0.00 0.00 38.94 3.13
1632 3183 0.598065 GGCTTTGTTGATTGTCGGCT 59.402 50.000 0.00 0.00 0.00 5.52
1634 3185 0.109781 CCGGCTTTGTTGATTGTCGG 60.110 55.000 0.00 0.00 0.00 4.79
1641 3192 1.440938 CGAACACCCGGCTTTGTTGA 61.441 55.000 16.43 0.00 36.06 3.18
1653 3204 1.205820 GTAAACGCAGGCGAACACC 59.794 57.895 21.62 0.33 42.83 4.16
1699 3250 6.660800 ACTGAATCCATGTTGAGAAGATGAT 58.339 36.000 0.00 0.00 34.30 2.45
1715 3266 1.841450 CGTAAGCTCGGACTGAATCC 58.159 55.000 0.00 0.00 45.20 3.01
1729 3280 0.108329 ATGGGAAGGTCGTGCGTAAG 60.108 55.000 0.00 0.00 43.44 2.34
1735 3286 0.744414 ATTGCGATGGGAAGGTCGTG 60.744 55.000 0.00 0.00 0.00 4.35
1739 3290 2.442236 ATCAATTGCGATGGGAAGGT 57.558 45.000 0.00 0.00 0.00 3.50
2108 3681 4.869861 GCAAATTATTGTCCTCGGCAAATT 59.130 37.500 0.00 0.00 38.85 1.82
2375 3959 6.864685 TCAAGCAGCAAAAGAAATAAGTGATG 59.135 34.615 0.00 0.00 0.00 3.07
2869 6062 7.054124 TCAACTTCCATCTGTTAAGTGTCTTT 58.946 34.615 0.00 0.00 33.85 2.52
3055 6266 4.806775 TGAATTTGAAACGAACTCGACAGA 59.193 37.500 6.05 0.00 43.02 3.41
3059 6270 9.672086 ATTTTTATGAATTTGAAACGAACTCGA 57.328 25.926 6.05 0.00 43.02 4.04
3402 6633 9.959749 GAAACAGATAAACAAAACCACATCTAA 57.040 29.630 0.00 0.00 0.00 2.10
3782 7051 3.312421 CAGCAAACAAAAGAGAAGGACGA 59.688 43.478 0.00 0.00 0.00 4.20
3988 7258 6.237901 AGCATATCGCACAAATAGGGAATTA 58.762 36.000 0.00 0.00 46.13 1.40
4033 7303 9.474313 AAGCAACAAAATAAATCATACTCCCTA 57.526 29.630 0.00 0.00 0.00 3.53
4281 7849 8.893219 TTATGGTGAATCTAATCATGTCAGTC 57.107 34.615 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.