Multiple sequence alignment - TraesCS2D01G178900

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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 TraesCS2D01G178900 chr2D 100.000 5075 0 0 1 5075 122401628 122396554 0.000000e+00 9372.0
1 TraesCS2D01G178900 chr2D 77.211 588 97 21 4364 4940 26941132 26941693 4.930000e-80 309.0
2 TraesCS2D01G178900 chr2D 79.651 172 27 7 4638 4805 400373266 400373433 3.210000e-22 117.0
3 TraesCS2D01G178900 chr2A 94.919 2086 80 15 1023 3096 126649881 126647810 0.000000e+00 3241.0
4 TraesCS2D01G178900 chr2A 91.058 1163 58 24 3085 4213 126647783 126646633 0.000000e+00 1530.0
5 TraesCS2D01G178900 chr2A 93.353 662 33 7 4418 5073 126645971 126645315 0.000000e+00 968.0
6 TraesCS2D01G178900 chr2A 91.707 205 13 4 4213 4416 126646336 126646135 1.080000e-71 281.0
7 TraesCS2D01G178900 chr2A 84.579 214 32 1 4658 4871 731377914 731378126 1.430000e-50 211.0
8 TraesCS2D01G178900 chr2B 94.346 2087 96 13 1023 3096 175418326 175416249 0.000000e+00 3181.0
9 TraesCS2D01G178900 chr2B 91.422 1294 69 24 3090 4346 175416209 175414921 0.000000e+00 1736.0
10 TraesCS2D01G178900 chr2B 93.207 736 39 4 4344 5073 175414030 175413300 0.000000e+00 1072.0
11 TraesCS2D01G178900 chr2B 86.042 1003 73 30 9 968 175420685 175419707 0.000000e+00 1014.0
12 TraesCS2D01G178900 chr2B 79.326 445 79 13 4527 4965 737457665 737458102 2.970000e-77 300.0
13 TraesCS2D01G178900 chr2B 77.828 221 42 6 4583 4798 565036729 565036947 4.120000e-26 130.0
14 TraesCS2D01G178900 chr2B 84.677 124 19 0 1149 1272 5530284 5530407 1.920000e-24 124.0
15 TraesCS2D01G178900 chr2B 100.000 28 0 0 362 389 318311824 318311797 9.000000e-03 52.8
16 TraesCS2D01G178900 chr2B 100.000 28 0 0 362 389 683765326 683765299 9.000000e-03 52.8
17 TraesCS2D01G178900 chr1A 86.019 515 65 5 4405 4917 133410811 133411320 3.460000e-151 545.0
18 TraesCS2D01G178900 chr1B 84.016 513 78 3 4400 4909 186450374 186450885 1.640000e-134 490.0
19 TraesCS2D01G178900 chr6D 78.778 622 107 14 4359 4960 269234867 269235483 1.320000e-105 394.0
20 TraesCS2D01G178900 chr5D 86.111 288 36 4 4480 4767 547251462 547251179 1.770000e-79 307.0
21 TraesCS2D01G178900 chr5D 100.000 32 0 0 4525 4556 296999087 296999118 5.490000e-05 60.2
22 TraesCS2D01G178900 chr5D 100.000 28 0 0 528 555 245005297 245005270 9.000000e-03 52.8
23 TraesCS2D01G178900 chr6B 75.410 305 68 6 4612 4913 19037239 19036939 1.900000e-29 141.0
24 TraesCS2D01G178900 chr5A 73.121 346 63 16 4637 4977 7827892 7827572 4.180000e-16 97.1
25 TraesCS2D01G178900 chr4D 100.000 32 0 0 4525 4556 209865420 209865389 5.490000e-05 60.2
26 TraesCS2D01G178900 chr7B 77.885 104 13 9 362 459 334312196 334312097 7.100000e-04 56.5


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 TraesCS2D01G178900 chr2D 122396554 122401628 5074 True 9372.00 9372 100.00000 1 5075 1 chr2D.!!$R1 5074
1 TraesCS2D01G178900 chr2D 26941132 26941693 561 False 309.00 309 77.21100 4364 4940 1 chr2D.!!$F1 576
2 TraesCS2D01G178900 chr2A 126645315 126649881 4566 True 1505.00 3241 92.75925 1023 5073 4 chr2A.!!$R1 4050
3 TraesCS2D01G178900 chr2B 175413300 175420685 7385 True 1750.75 3181 91.25425 9 5073 4 chr2B.!!$R3 5064
4 TraesCS2D01G178900 chr1A 133410811 133411320 509 False 545.00 545 86.01900 4405 4917 1 chr1A.!!$F1 512
5 TraesCS2D01G178900 chr1B 186450374 186450885 511 False 490.00 490 84.01600 4400 4909 1 chr1B.!!$F1 509
6 TraesCS2D01G178900 chr6D 269234867 269235483 616 False 394.00 394 78.77800 4359 4960 1 chr6D.!!$F1 601

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
143 145 1.079336 GGAAGGTCGTGTGTAGGCC 60.079 63.158 0.00 0.00 0.00 5.19 F
1019 1104 0.250295 GCCCTTTTCAAAGTTGGCCC 60.250 55.000 0.00 0.00 37.37 5.80 F
1932 3314 0.385390 ACTGAAGCTGGCCGTTTTTG 59.615 50.000 0.00 0.00 0.00 2.44 F
2702 4089 0.458889 TTCGGTGGGATAAAGACGCG 60.459 55.000 3.53 3.53 0.00 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 3304 0.574922 CGAAAACTGCAAAAACGGCC 59.425 50.000 0.00 0.00 0.00 6.13 R
2973 4360 0.586319 TTGCCTTCTGTTTCGCTTCG 59.414 50.000 0.00 0.00 0.00 3.79 R
3610 5088 0.109723 AACCTTTTCAGCGGCTACCA 59.890 50.000 0.26 0.00 0.00 3.25 R
4219 6030 1.475682 CTATAGGATACCGGGCCGTTC 59.524 57.143 26.32 17.63 37.17 3.95 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
31 32 7.923344 CCTTTACAGTTCTATCGATGTCTCATT 59.077 37.037 8.54 0.00 0.00 2.57
32 33 8.634475 TTTACAGTTCTATCGATGTCTCATTG 57.366 34.615 8.54 0.82 0.00 2.82
82 84 5.334421 AGTAGAGCCTTCTTAACCTTGAGA 58.666 41.667 0.00 0.00 34.79 3.27
90 92 3.042682 TCTTAACCTTGAGACCCACACA 58.957 45.455 0.00 0.00 0.00 3.72
107 109 3.628942 CACACAGATAATGTCATGGGTGG 59.371 47.826 0.00 0.00 42.14 4.61
138 140 2.158813 AGTCATTTGGAAGGTCGTGTGT 60.159 45.455 0.00 0.00 0.00 3.72
139 141 3.070446 AGTCATTTGGAAGGTCGTGTGTA 59.930 43.478 0.00 0.00 0.00 2.90
141 143 2.536761 TTTGGAAGGTCGTGTGTAGG 57.463 50.000 0.00 0.00 0.00 3.18
143 145 1.079336 GGAAGGTCGTGTGTAGGCC 60.079 63.158 0.00 0.00 0.00 5.19
144 146 1.445582 GAAGGTCGTGTGTAGGCCG 60.446 63.158 0.00 0.00 0.00 6.13
145 147 2.830704 GAAGGTCGTGTGTAGGCCGG 62.831 65.000 0.00 0.00 0.00 6.13
191 193 6.939551 TCTTAACCTCGAGAAATTTACGTG 57.060 37.500 15.71 12.10 0.00 4.49
202 204 4.636648 AGAAATTTACGTGTGTGTTGTGGA 59.363 37.500 0.00 0.00 0.00 4.02
205 207 1.773410 TACGTGTGTGTTGTGGATCG 58.227 50.000 0.00 0.00 0.00 3.69
227 229 3.077556 ACTGGGCTCTAGTGGGCG 61.078 66.667 0.00 0.00 0.00 6.13
233 235 2.811101 CTCTAGTGGGCGGCTCTG 59.189 66.667 9.56 3.89 0.00 3.35
261 263 2.352715 GGGCTCAATGTAGCAACCAAAC 60.353 50.000 6.92 0.00 44.64 2.93
280 282 5.916883 CCAAACAACAACAATCTCTTAGCTG 59.083 40.000 0.00 0.00 0.00 4.24
349 378 5.128827 TCATCTAAAGCTAGGAACGTTGGAT 59.871 40.000 5.00 0.00 29.46 3.41
355 384 2.874457 GCTAGGAACGTTGGATGTTGGT 60.874 50.000 5.00 0.00 0.00 3.67
357 386 3.495434 AGGAACGTTGGATGTTGGTTA 57.505 42.857 5.00 0.00 0.00 2.85
358 387 4.028993 AGGAACGTTGGATGTTGGTTAT 57.971 40.909 5.00 0.00 0.00 1.89
361 390 2.790433 ACGTTGGATGTTGGTTATGCT 58.210 42.857 0.00 0.00 0.00 3.79
402 431 5.579564 GGTTCTCGACCTACTTAGATTGT 57.420 43.478 0.00 0.00 45.55 2.71
403 432 5.963594 GGTTCTCGACCTACTTAGATTGTT 58.036 41.667 0.00 0.00 45.55 2.83
529 560 8.268738 CGTTCAAGAAAAATCTTCATGGTTTTC 58.731 33.333 0.00 2.71 39.28 2.29
542 573 8.457261 TCTTCATGGTTTTCAAAAATTGTTTGG 58.543 29.630 0.00 0.00 0.00 3.28
543 574 7.928307 TCATGGTTTTCAAAAATTGTTTGGA 57.072 28.000 0.00 0.00 0.00 3.53
544 575 8.340618 TCATGGTTTTCAAAAATTGTTTGGAA 57.659 26.923 0.00 0.00 35.29 3.53
545 576 8.964772 TCATGGTTTTCAAAAATTGTTTGGAAT 58.035 25.926 0.00 0.00 36.70 3.01
546 577 9.583765 CATGGTTTTCAAAAATTGTTTGGAATT 57.416 25.926 0.00 0.00 36.70 2.17
632 663 8.039603 AGTTGTTTGGAATTTCAAAAAGTTCC 57.960 30.769 13.56 1.30 46.34 3.62
650 681 9.952030 AAAAGTTCCTGTTTCCAAAGAAAAATA 57.048 25.926 0.00 0.00 43.48 1.40
652 683 9.952030 AAGTTCCTGTTTCCAAAGAAAAATAAA 57.048 25.926 0.00 0.00 43.48 1.40
654 685 9.982291 GTTCCTGTTTCCAAAGAAAAATAAAAC 57.018 29.630 0.00 0.00 43.48 2.43
718 751 8.364142 TGTTTTCGAAATTTGTTCATTAGGGAT 58.636 29.630 12.12 0.00 0.00 3.85
725 758 8.546597 AAATTTGTTCATTAGGGATTTTTCCG 57.453 30.769 0.00 0.00 0.00 4.30
730 763 7.727181 TGTTCATTAGGGATTTTTCCGAAAAA 58.273 30.769 18.85 18.85 43.76 1.94
780 821 7.506296 AATCTTCACGTTTCAAAAAGTGTTC 57.494 32.000 17.13 0.00 44.86 3.18
781 822 6.249035 TCTTCACGTTTCAAAAAGTGTTCT 57.751 33.333 17.13 0.00 44.86 3.01
851 894 9.849166 AAATGTTTATTACAGTTAACCGGATTG 57.151 29.630 9.46 0.00 42.75 2.67
852 895 7.982761 TGTTTATTACAGTTAACCGGATTGT 57.017 32.000 9.46 0.95 31.68 2.71
918 961 2.795110 GCTGCTCGCTCCCTCTCAT 61.795 63.158 0.00 0.00 35.14 2.90
949 992 4.742201 CTACAGCGTGCACGGGCT 62.742 66.667 37.47 25.29 41.91 5.19
969 1012 3.646715 CCCTTCAAGACGCCCCCA 61.647 66.667 0.00 0.00 0.00 4.96
971 1014 2.359975 CTTCAAGACGCCCCCACC 60.360 66.667 0.00 0.00 0.00 4.61
972 1015 4.323477 TTCAAGACGCCCCCACCG 62.323 66.667 0.00 0.00 0.00 4.94
974 1017 4.760047 CAAGACGCCCCCACCGAG 62.760 72.222 0.00 0.00 0.00 4.63
989 1032 3.294493 GAGCAGGCGCCCAACAAA 61.294 61.111 26.15 0.00 39.83 2.83
990 1033 3.558099 GAGCAGGCGCCCAACAAAC 62.558 63.158 26.15 4.70 39.83 2.93
991 1034 3.910490 GCAGGCGCCCAACAAACA 61.910 61.111 26.15 0.00 0.00 2.83
992 1035 2.336088 CAGGCGCCCAACAAACAG 59.664 61.111 26.15 0.00 0.00 3.16
1012 1097 1.869774 GGCAACAGCCCTTTTCAAAG 58.130 50.000 0.00 0.00 42.80 2.77
1015 1100 2.609002 GCAACAGCCCTTTTCAAAGTTG 59.391 45.455 0.00 0.00 34.20 3.16
1016 1101 3.197265 CAACAGCCCTTTTCAAAGTTGG 58.803 45.455 0.00 0.00 34.20 3.77
1017 1102 1.138859 ACAGCCCTTTTCAAAGTTGGC 59.861 47.619 10.16 10.16 41.09 4.52
1018 1103 0.758734 AGCCCTTTTCAAAGTTGGCC 59.241 50.000 13.14 0.00 41.45 5.36
1019 1104 0.250295 GCCCTTTTCAAAGTTGGCCC 60.250 55.000 0.00 0.00 37.37 5.80
1021 1106 1.768275 CCCTTTTCAAAGTTGGCCCTT 59.232 47.619 0.00 0.00 34.20 3.95
1023 1108 3.244078 CCCTTTTCAAAGTTGGCCCTTAC 60.244 47.826 0.00 0.00 34.20 2.34
1025 1110 4.040339 CCTTTTCAAAGTTGGCCCTTACAT 59.960 41.667 0.00 0.00 34.20 2.29
1026 1111 4.599047 TTTCAAAGTTGGCCCTTACATG 57.401 40.909 0.00 0.00 0.00 3.21
1027 1112 3.237268 TCAAAGTTGGCCCTTACATGT 57.763 42.857 2.69 2.69 0.00 3.21
1028 1113 3.571590 TCAAAGTTGGCCCTTACATGTT 58.428 40.909 2.30 0.00 0.00 2.71
1029 1114 3.320541 TCAAAGTTGGCCCTTACATGTTG 59.679 43.478 2.30 0.00 0.00 3.33
1030 1115 2.969821 AGTTGGCCCTTACATGTTGA 57.030 45.000 2.30 0.00 0.00 3.18
1031 1116 2.514803 AGTTGGCCCTTACATGTTGAC 58.485 47.619 2.30 0.00 0.00 3.18
1032 1117 2.158534 AGTTGGCCCTTACATGTTGACA 60.159 45.455 2.30 0.00 0.00 3.58
1038 1123 2.039746 CCCTTACATGTTGACACCTCCA 59.960 50.000 2.30 0.00 0.00 3.86
1067 2437 1.588239 AGCCCATCTCATCAAGACCA 58.412 50.000 0.00 0.00 36.65 4.02
1146 2516 2.502492 CGCTCCCTCCCACATCGAT 61.502 63.158 0.00 0.00 0.00 3.59
1147 2517 1.832912 GCTCCCTCCCACATCGATT 59.167 57.895 0.00 0.00 0.00 3.34
1325 2695 2.106938 CGCGCCTCCATCTGCTAA 59.893 61.111 0.00 0.00 0.00 3.09
1333 2703 0.833287 TCCATCTGCTAACAGGAGGC 59.167 55.000 0.00 0.00 44.59 4.70
1522 2894 2.456840 CACCCCTCCCCCTTCTCT 59.543 66.667 0.00 0.00 0.00 3.10
1561 2933 3.632080 TCGCCGTGTGGGATTGGT 61.632 61.111 0.00 0.00 38.47 3.67
1590 2962 3.775316 AGTAGGATTCGGGATTCACTTGT 59.225 43.478 0.00 0.00 0.00 3.16
1665 3037 1.585006 GCGACCAACGAGGAGAAGA 59.415 57.895 5.70 0.00 45.77 2.87
1754 3126 0.963856 CCCCCAAGAAAAGTACCGCC 60.964 60.000 0.00 0.00 0.00 6.13
1783 3160 7.989170 TCAACTTGTCATAACTGATATGCTCAT 59.011 33.333 0.46 0.00 41.08 2.90
1821 3203 4.627611 CAGTATGCTGTATTGCTTTGCT 57.372 40.909 2.12 0.00 37.92 3.91
1822 3204 4.990257 CAGTATGCTGTATTGCTTTGCTT 58.010 39.130 2.12 0.00 37.92 3.91
1869 3251 2.852449 AGAGGGAGTATGGGATTTTGCA 59.148 45.455 0.00 0.00 0.00 4.08
1886 3268 3.788227 TGCATCTTTGGAGTAGTTGGT 57.212 42.857 0.00 0.00 0.00 3.67
1922 3304 3.201290 CAGCAGGGTTATACTGAAGCTG 58.799 50.000 0.00 0.00 41.64 4.24
1932 3314 0.385390 ACTGAAGCTGGCCGTTTTTG 59.615 50.000 0.00 0.00 0.00 2.44
1952 3334 4.764679 TGCAGTTTTCGTATGAATTGCT 57.235 36.364 20.59 9.27 37.28 3.91
1987 3369 1.363744 ATGTTACAGAGCAAGCGAGC 58.636 50.000 0.00 0.00 0.00 5.03
2005 3387 3.307242 CGAGCAACCTCTATTTCTTTCCG 59.693 47.826 0.00 0.00 35.90 4.30
2011 3393 6.183360 GCAACCTCTATTTCTTTCCGTCTAAC 60.183 42.308 0.00 0.00 0.00 2.34
2038 3420 8.374327 TGTGTTTTCCTACTTTCTTTAGCTAC 57.626 34.615 0.00 0.00 0.00 3.58
2056 3438 2.286365 ACGAAAGGCTGGATTTCCAA 57.714 45.000 0.18 0.00 46.97 3.53
2123 3505 4.654389 AAGGGATCCATGAATCCTGATC 57.346 45.455 15.23 5.01 44.06 2.92
2197 3579 3.063997 CGGGACACATTTTCTACATCTGC 59.936 47.826 0.00 0.00 0.00 4.26
2218 3600 7.999679 TCTGCATGGTCTAGAATTAATTTTGG 58.000 34.615 1.43 0.00 0.00 3.28
2271 3653 4.558226 ACCACTTGCATCTGTATCTTCA 57.442 40.909 0.00 0.00 0.00 3.02
2412 3794 6.910536 TTCTTTTCTTGAGTTCTGTCTGAC 57.089 37.500 0.00 0.00 0.00 3.51
2435 3817 6.362248 ACTACTTTCTTTTTCTGCCTTGGTA 58.638 36.000 0.00 0.00 0.00 3.25
2440 3822 7.724061 ACTTTCTTTTTCTGCCTTGGTATCTTA 59.276 33.333 0.00 0.00 0.00 2.10
2518 3900 1.207593 CAAACGGGAAGCTCTTGCG 59.792 57.895 0.00 0.00 45.42 4.85
2533 3915 3.997021 CTCTTGCGTCATACCTCAAACTT 59.003 43.478 0.00 0.00 0.00 2.66
2584 3966 5.805994 GCTACATGGTAGTCTTGAAGTACAC 59.194 44.000 0.00 0.00 35.76 2.90
2702 4089 0.458889 TTCGGTGGGATAAAGACGCG 60.459 55.000 3.53 3.53 0.00 6.01
2798 4185 8.443176 TGCCTATGATATCTTCTTGAATCCTTT 58.557 33.333 3.98 0.00 0.00 3.11
2845 4232 7.148573 GCACCATCCTATTTGTATGTCTATTCG 60.149 40.741 0.00 0.00 0.00 3.34
2913 4300 8.647796 TCAAATGTATATACACTGACCCCTTAG 58.352 37.037 17.69 0.00 39.30 2.18
2917 4304 6.557253 TGTATATACACTGACCCCTTAGCATT 59.443 38.462 11.62 0.00 0.00 3.56
2973 4360 8.226448 CAGGCATTTGATATATTCGAGAAACTC 58.774 37.037 0.00 0.00 0.00 3.01
3274 4752 7.136289 TCGATGTAGAAAAATGGGTGTTAAC 57.864 36.000 0.00 0.00 0.00 2.01
3427 4905 3.357166 ACTCCGCAGAATATCGAGTTC 57.643 47.619 5.45 5.45 0.00 3.01
3509 4987 8.208718 TGTTCAATTCATATTACTGCTGTACC 57.791 34.615 2.52 0.00 0.00 3.34
3525 5003 2.374170 TGTACCACCTCCTTTTCCTTCC 59.626 50.000 0.00 0.00 0.00 3.46
3533 5011 2.680339 CTCCTTTTCCTTCCGAATCAGC 59.320 50.000 0.00 0.00 0.00 4.26
3534 5012 2.039746 TCCTTTTCCTTCCGAATCAGCA 59.960 45.455 0.00 0.00 0.00 4.41
3610 5088 8.158132 AGATGAAGACTGCTATGATTGATGATT 58.842 33.333 0.00 0.00 0.00 2.57
3721 5199 5.068198 TGGAAGGTAGTGCGTAATTAGGTAG 59.932 44.000 7.00 0.00 0.00 3.18
3727 5205 7.723172 AGGTAGTGCGTAATTAGGTAGTTAGAT 59.277 37.037 8.57 0.00 0.00 1.98
3750 5228 3.804036 TGATTATTCTTCCCGCGTTCAT 58.196 40.909 4.92 0.00 0.00 2.57
3752 5230 2.684001 TATTCTTCCCGCGTTCATGT 57.316 45.000 4.92 0.00 0.00 3.21
3753 5231 1.369625 ATTCTTCCCGCGTTCATGTC 58.630 50.000 4.92 0.00 0.00 3.06
3754 5232 0.034198 TTCTTCCCGCGTTCATGTCA 59.966 50.000 4.92 0.00 0.00 3.58
3755 5233 0.034198 TCTTCCCGCGTTCATGTCAA 59.966 50.000 4.92 0.00 0.00 3.18
3756 5234 0.443869 CTTCCCGCGTTCATGTCAAG 59.556 55.000 4.92 0.00 0.00 3.02
3758 5236 0.034198 TCCCGCGTTCATGTCAAGAA 59.966 50.000 4.92 0.00 0.00 2.52
3759 5237 0.443869 CCCGCGTTCATGTCAAGAAG 59.556 55.000 4.92 0.00 0.00 2.85
3760 5238 0.443869 CCGCGTTCATGTCAAGAAGG 59.556 55.000 4.92 6.21 34.84 3.46
3764 5269 2.415512 GCGTTCATGTCAAGAAGGTACC 59.584 50.000 2.73 2.73 34.37 3.34
3781 5287 3.773119 GGTACCAGAAACTCAGGACCATA 59.227 47.826 7.15 0.00 29.93 2.74
3794 5300 3.252701 CAGGACCATATGAATTCTGCAGC 59.747 47.826 9.47 0.00 0.00 5.25
3795 5301 3.117776 AGGACCATATGAATTCTGCAGCA 60.118 43.478 9.47 0.00 0.00 4.41
3799 5305 3.824443 CCATATGAATTCTGCAGCATCCA 59.176 43.478 9.47 0.00 0.00 3.41
3813 5319 4.730657 CAGCATCCAGTTCTGAATGTTTC 58.269 43.478 1.00 0.00 0.00 2.78
3822 5328 5.003804 AGTTCTGAATGTTTCCTATTGCGT 58.996 37.500 0.00 0.00 0.00 5.24
3858 5365 5.818136 TGCATTCTACCTGCACTTTAATC 57.182 39.130 0.00 0.00 44.30 1.75
3866 5373 4.455606 ACCTGCACTTTAATCCATAGAGC 58.544 43.478 0.00 0.00 0.00 4.09
3878 5385 2.171237 TCCATAGAGCTGGGTTCACATG 59.829 50.000 0.00 0.00 36.89 3.21
3884 5391 0.961019 GCTGGGTTCACATGCAAAGA 59.039 50.000 0.00 0.00 0.00 2.52
3930 5437 8.938906 GGACTTTGATTTTTATGTGCATTTCAT 58.061 29.630 0.00 0.00 0.00 2.57
3957 5464 5.324409 AGAAACCTGGCAGTTGATGATTTA 58.676 37.500 14.43 0.00 0.00 1.40
3993 5500 2.628696 TTTGGCATGTGCTCCGCTG 61.629 57.895 4.84 0.00 41.70 5.18
3998 5505 1.219124 CATGTGCTCCGCTGTAGGT 59.781 57.895 0.00 0.00 0.00 3.08
4007 5514 1.115467 CCGCTGTAGGTCAGGATTCT 58.885 55.000 0.00 0.00 43.78 2.40
4025 5532 3.944422 TCTGAAGTTGAAAGCGTGTTC 57.056 42.857 0.00 0.00 0.00 3.18
4034 5541 4.273005 TGAAAGCGTGTTCTGTTCTTTC 57.727 40.909 0.00 0.00 41.56 2.62
4036 5543 4.394920 TGAAAGCGTGTTCTGTTCTTTCTT 59.605 37.500 12.36 0.00 41.67 2.52
4038 5545 6.092944 TGAAAGCGTGTTCTGTTCTTTCTTTA 59.907 34.615 12.36 0.00 41.67 1.85
4144 5654 1.282248 CGATCGAACGGCTGTGTGTT 61.282 55.000 10.26 0.00 0.00 3.32
4184 5694 2.545731 GCAGTAGCTAAGAGCAACTCC 58.454 52.381 0.00 0.00 45.56 3.85
4195 5705 2.106683 GCAACTCCAACCGATCCCG 61.107 63.158 0.00 0.00 0.00 5.14
4258 6069 2.810164 AGAGGACTACTTTCGCTCCTT 58.190 47.619 0.00 0.00 33.00 3.36
4259 6070 2.494073 AGAGGACTACTTTCGCTCCTTG 59.506 50.000 0.00 0.00 33.00 3.61
4315 6128 7.919690 ACTTACCGGAGTAAAAACTTAAACAC 58.080 34.615 9.46 0.00 37.99 3.32
4402 7108 6.538742 CCAATTCTTCGCTAAGAGAACCAATA 59.461 38.462 0.55 0.00 42.60 1.90
4496 7366 5.296283 CGATCAATGCTTTCTCCATCTCTTT 59.704 40.000 0.00 0.00 0.00 2.52
4987 7879 2.223745 GAGAGGAGGACATACCGAGAC 58.776 57.143 0.00 0.00 44.74 3.36
5028 7920 2.768344 ATGCCCGGTTCGATCCCT 60.768 61.111 6.94 0.00 0.00 4.20
5032 7924 2.355986 CCCGGTTCGATCCCTGTCA 61.356 63.158 6.94 0.00 0.00 3.58
5047 7939 4.141274 TCCCTGTCAAATCTCTCCAAAACA 60.141 41.667 0.00 0.00 0.00 2.83
5074 7972 1.828832 GACTAGGTGCGTCGAATCTG 58.171 55.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 3.371917 CCCATGACATTATCTGTGTGGGT 60.372 47.826 13.45 0.00 46.22 4.51
90 92 3.788142 ACTTCCCACCCATGACATTATCT 59.212 43.478 0.00 0.00 0.00 1.98
107 109 4.301628 CTTCCAAATGACTTTGCACTTCC 58.698 43.478 0.00 0.00 40.39 3.46
138 140 1.830587 CTGCCATCATAGCCGGCCTA 61.831 60.000 26.15 15.46 45.63 3.93
139 141 3.170672 TGCCATCATAGCCGGCCT 61.171 61.111 26.15 13.52 45.63 5.19
141 143 2.670934 CCTGCCATCATAGCCGGC 60.671 66.667 21.89 21.89 46.43 6.13
143 145 1.302033 GGTCCTGCCATCATAGCCG 60.302 63.158 0.00 0.00 37.17 5.52
144 146 1.302033 CGGTCCTGCCATCATAGCC 60.302 63.158 0.00 0.00 36.97 3.93
145 147 0.320247 CTCGGTCCTGCCATCATAGC 60.320 60.000 0.00 0.00 36.97 2.97
156 158 2.168728 GAGGTTAAGAATGCTCGGTCCT 59.831 50.000 0.00 0.00 0.00 3.85
191 193 3.428870 CAGTCTAACGATCCACAACACAC 59.571 47.826 0.00 0.00 0.00 3.82
202 204 2.952978 CACTAGAGCCCAGTCTAACGAT 59.047 50.000 0.00 0.00 0.00 3.73
205 207 1.757699 CCCACTAGAGCCCAGTCTAAC 59.242 57.143 0.00 0.00 0.00 2.34
227 229 2.360475 AGCCCTTTTCGCAGAGCC 60.360 61.111 0.00 0.00 38.43 4.70
229 231 1.131883 CATTGAGCCCTTTTCGCAGAG 59.868 52.381 0.00 0.00 38.43 3.35
233 235 1.202188 GCTACATTGAGCCCTTTTCGC 60.202 52.381 0.00 0.00 36.38 4.70
238 240 1.075374 TGGTTGCTACATTGAGCCCTT 59.925 47.619 0.00 0.00 42.11 3.95
327 356 5.104900 ACATCCAACGTTCCTAGCTTTAGAT 60.105 40.000 0.00 0.00 0.00 1.98
329 358 4.504858 ACATCCAACGTTCCTAGCTTTAG 58.495 43.478 0.00 0.00 0.00 1.85
342 371 3.848272 AAGCATAACCAACATCCAACG 57.152 42.857 0.00 0.00 0.00 4.10
349 378 3.070302 GGTTCCCAAAAGCATAACCAACA 59.930 43.478 0.00 0.00 39.51 3.33
355 384 6.134535 TCTAGAAGGTTCCCAAAAGCATAA 57.865 37.500 0.00 0.00 0.00 1.90
357 386 4.657814 TCTAGAAGGTTCCCAAAAGCAT 57.342 40.909 0.00 0.00 0.00 3.79
358 387 4.398319 CTTCTAGAAGGTTCCCAAAAGCA 58.602 43.478 22.67 0.00 34.87 3.91
549 580 9.671279 ACAGATTTTGAGAAAGGAAACATTTTT 57.329 25.926 0.00 0.00 0.00 1.94
550 581 9.671279 AACAGATTTTGAGAAAGGAAACATTTT 57.329 25.926 0.00 0.00 0.00 1.82
551 582 9.671279 AAACAGATTTTGAGAAAGGAAACATTT 57.329 25.926 0.00 0.00 0.00 2.32
553 584 9.750125 GTAAACAGATTTTGAGAAAGGAAACAT 57.250 29.630 0.00 0.00 0.00 2.71
592 623 6.986817 TCCAAACAACTTTTGAAAACACAGAA 59.013 30.769 0.00 0.00 0.00 3.02
594 625 6.777526 TCCAAACAACTTTTGAAAACACAG 57.222 33.333 0.00 0.00 0.00 3.66
694 727 9.771534 AAATCCCTAATGAACAAATTTCGAAAA 57.228 25.926 15.66 0.00 0.00 2.29
725 758 6.710692 ATCCTTGTGAATGCGAAATTTTTC 57.289 33.333 0.00 0.00 0.00 2.29
755 796 8.455682 AGAACACTTTTTGAAACGTGAAGATTA 58.544 29.630 16.78 0.00 39.64 1.75
759 800 8.442605 TTTAGAACACTTTTTGAAACGTGAAG 57.557 30.769 16.78 0.59 39.64 3.02
825 868 9.849166 CAATCCGGTTAACTGTAATAAACATTT 57.151 29.630 13.35 0.00 37.50 2.32
833 876 6.938507 TGTAGACAATCCGGTTAACTGTAAT 58.061 36.000 13.35 4.00 0.00 1.89
834 877 6.343716 TGTAGACAATCCGGTTAACTGTAA 57.656 37.500 13.35 1.73 0.00 2.41
851 894 1.932277 GCGGGCGCTTATTGTAGAC 59.068 57.895 7.64 0.00 38.26 2.59
852 895 4.431035 GCGGGCGCTTATTGTAGA 57.569 55.556 7.64 0.00 38.26 2.59
946 989 2.747855 CGTCTTGAAGGGCCAGCC 60.748 66.667 6.18 0.00 0.00 4.85
957 1000 4.760047 CTCGGTGGGGGCGTCTTG 62.760 72.222 0.00 0.00 0.00 3.02
972 1015 3.294493 TTTGTTGGGCGCCTGCTC 61.294 61.111 28.56 10.32 44.05 4.26
973 1016 3.605664 GTTTGTTGGGCGCCTGCT 61.606 61.111 28.56 0.00 42.25 4.24
974 1017 3.846602 CTGTTTGTTGGGCGCCTGC 62.847 63.158 28.56 16.83 41.71 4.85
975 1018 2.336088 CTGTTTGTTGGGCGCCTG 59.664 61.111 28.56 0.00 0.00 4.85
977 1020 3.989787 CCCTGTTTGTTGGGCGCC 61.990 66.667 21.18 21.18 36.61 6.53
981 1024 0.104671 CTGTTGCCCTGTTTGTTGGG 59.895 55.000 0.00 0.00 46.00 4.12
983 1026 2.976271 GCTGTTGCCCTGTTTGTTG 58.024 52.632 0.00 0.00 0.00 3.33
994 1037 2.602257 ACTTTGAAAAGGGCTGTTGC 57.398 45.000 7.65 0.00 40.31 4.17
995 1038 3.197265 CCAACTTTGAAAAGGGCTGTTG 58.803 45.455 7.65 0.00 40.31 3.33
1012 1097 2.030274 GTGTCAACATGTAAGGGCCAAC 60.030 50.000 6.18 3.87 0.00 3.77
1015 1100 1.173913 GGTGTCAACATGTAAGGGCC 58.826 55.000 0.00 0.00 0.00 5.80
1016 1101 2.084546 GAGGTGTCAACATGTAAGGGC 58.915 52.381 0.00 0.00 0.00 5.19
1017 1102 2.039746 TGGAGGTGTCAACATGTAAGGG 59.960 50.000 0.00 0.00 0.00 3.95
1018 1103 3.417069 TGGAGGTGTCAACATGTAAGG 57.583 47.619 0.00 0.00 0.00 2.69
1019 1104 4.578871 TGATGGAGGTGTCAACATGTAAG 58.421 43.478 0.00 0.00 0.00 2.34
1021 1106 4.632327 TTGATGGAGGTGTCAACATGTA 57.368 40.909 0.00 0.00 29.93 2.29
1023 1108 5.415389 TGTATTTGATGGAGGTGTCAACATG 59.585 40.000 0.00 0.00 34.34 3.21
1025 1110 4.979335 TGTATTTGATGGAGGTGTCAACA 58.021 39.130 0.00 0.00 34.34 3.33
1026 1111 5.619981 GCTTGTATTTGATGGAGGTGTCAAC 60.620 44.000 0.00 0.00 34.34 3.18
1027 1112 4.458989 GCTTGTATTTGATGGAGGTGTCAA 59.541 41.667 0.00 0.00 32.86 3.18
1028 1113 4.009675 GCTTGTATTTGATGGAGGTGTCA 58.990 43.478 0.00 0.00 0.00 3.58
1029 1114 3.378427 GGCTTGTATTTGATGGAGGTGTC 59.622 47.826 0.00 0.00 0.00 3.67
1030 1115 3.356290 GGCTTGTATTTGATGGAGGTGT 58.644 45.455 0.00 0.00 0.00 4.16
1031 1116 2.689983 GGGCTTGTATTTGATGGAGGTG 59.310 50.000 0.00 0.00 0.00 4.00
1032 1117 2.311542 TGGGCTTGTATTTGATGGAGGT 59.688 45.455 0.00 0.00 0.00 3.85
1038 1123 5.698104 TGATGAGATGGGCTTGTATTTGAT 58.302 37.500 0.00 0.00 0.00 2.57
1133 2503 2.017049 GGTTGAAATCGATGTGGGAGG 58.983 52.381 0.00 0.00 0.00 4.30
1246 2616 2.438021 CGGAGATTGGTTGGGGAGAATA 59.562 50.000 0.00 0.00 0.00 1.75
1522 2894 1.228769 AGTCGAGGTGGTGGCTACA 60.229 57.895 1.52 0.00 0.00 2.74
1552 2924 6.590656 ATCCTACTAATTCAACCAATCCCA 57.409 37.500 0.00 0.00 0.00 4.37
1561 2933 6.990349 GTGAATCCCGAATCCTACTAATTCAA 59.010 38.462 0.00 0.00 34.67 2.69
1665 3037 3.779444 TCAAGGTGGACAGTATCAGAGT 58.221 45.455 0.00 0.00 0.00 3.24
1754 3126 7.279536 AGCATATCAGTTATGACAAGTTGAGTG 59.720 37.037 10.54 0.00 40.22 3.51
1783 3160 2.378038 ACTGTGCAGCAAGAGGAAAAA 58.622 42.857 0.00 0.00 0.00 1.94
1818 3200 6.542735 ACATACTAGTGTAGAATCGAGAAGCA 59.457 38.462 5.39 0.00 31.51 3.91
1819 3201 6.961576 ACATACTAGTGTAGAATCGAGAAGC 58.038 40.000 5.39 0.00 31.51 3.86
1869 3251 7.496346 TTATCTGACCAACTACTCCAAAGAT 57.504 36.000 0.00 0.00 0.00 2.40
1886 3268 4.660303 ACCCTGCTGTATCCAATTATCTGA 59.340 41.667 0.00 0.00 0.00 3.27
1914 3296 0.940991 GCAAAAACGGCCAGCTTCAG 60.941 55.000 2.24 0.00 0.00 3.02
1922 3304 0.574922 CGAAAACTGCAAAAACGGCC 59.425 50.000 0.00 0.00 0.00 6.13
1932 3314 4.475944 ACAGCAATTCATACGAAAACTGC 58.524 39.130 0.00 0.00 34.88 4.40
1952 3334 6.379988 TCTGTAACATAAGCAGTCCTGATACA 59.620 38.462 0.00 0.00 0.00 2.29
1987 3369 6.313164 GGTTAGACGGAAAGAAATAGAGGTTG 59.687 42.308 0.00 0.00 0.00 3.77
2005 3387 6.990939 AGAAAGTAGGAAAACACAGGTTAGAC 59.009 38.462 0.00 0.00 35.82 2.59
2011 3393 6.486993 AGCTAAAGAAAGTAGGAAAACACAGG 59.513 38.462 0.00 0.00 0.00 4.00
2237 3619 9.590451 CAGATGCAAGTGGTAATATCAAATTTT 57.410 29.630 0.00 0.00 0.00 1.82
2296 3678 7.468357 GCTGAATTGTTTCTATGAGCTAGCAAT 60.468 37.037 18.83 12.57 32.78 3.56
2401 3783 8.331742 CAGAAAAAGAAAGTAGTCAGACAGAAC 58.668 37.037 2.66 0.00 0.00 3.01
2412 3794 5.774498 ACCAAGGCAGAAAAAGAAAGTAG 57.226 39.130 0.00 0.00 0.00 2.57
2435 3817 7.776107 TCTTTGTCGTCATTCTCTGATAAGAT 58.224 34.615 0.00 0.00 35.97 2.40
2440 3822 5.651387 TCTCTTTGTCGTCATTCTCTGAT 57.349 39.130 0.00 0.00 35.97 2.90
2518 3900 4.816925 GCAGGGATAAGTTTGAGGTATGAC 59.183 45.833 0.00 0.00 0.00 3.06
2533 3915 3.439154 TGCAGGAAAATTTGCAGGGATA 58.561 40.909 0.00 0.00 44.72 2.59
2798 4185 5.350091 GTGCAAACAAAGCAGTTTCCTTAAA 59.650 36.000 0.00 0.00 43.63 1.52
2845 4232 7.858583 AGTGTTCATTTAAGTTCCGTTACTTC 58.141 34.615 3.03 0.00 39.08 3.01
2852 4239 7.510630 CACTAGAAGTGTTCATTTAAGTTCCG 58.489 38.462 0.00 0.00 41.19 4.30
2913 4300 6.400727 GCAAACAAAGATGACAAGATCAATGC 60.401 38.462 0.00 0.00 41.93 3.56
2917 4304 4.583907 TGGCAAACAAAGATGACAAGATCA 59.416 37.500 0.00 0.00 43.13 2.92
2973 4360 0.586319 TTGCCTTCTGTTTCGCTTCG 59.414 50.000 0.00 0.00 0.00 3.79
2982 4369 2.226962 AATGATGGCTTGCCTTCTGT 57.773 45.000 22.35 12.19 0.00 3.41
3221 4698 3.820467 CCACAGTGCATAAAGTTCCAAGA 59.180 43.478 0.00 0.00 0.00 3.02
3274 4752 5.692613 ATTTTGCCAAAACCATGAACATG 57.307 34.783 4.45 7.70 33.98 3.21
3427 4905 2.985139 CCAGTCATCATCGTCATCATCG 59.015 50.000 0.00 0.00 0.00 3.84
3505 4983 2.614734 CGGAAGGAAAAGGAGGTGGTAC 60.615 54.545 0.00 0.00 0.00 3.34
3509 4987 2.561478 TTCGGAAGGAAAAGGAGGTG 57.439 50.000 0.00 0.00 0.00 4.00
3610 5088 0.109723 AACCTTTTCAGCGGCTACCA 59.890 50.000 0.26 0.00 0.00 3.25
3721 5199 6.812160 ACGCGGGAAGAATAATCATATCTAAC 59.188 38.462 12.47 0.00 0.00 2.34
3727 5205 4.951254 TGAACGCGGGAAGAATAATCATA 58.049 39.130 12.47 0.00 0.00 2.15
3750 5228 4.407621 TGAGTTTCTGGTACCTTCTTGACA 59.592 41.667 14.36 3.81 0.00 3.58
3752 5230 4.040461 CCTGAGTTTCTGGTACCTTCTTGA 59.960 45.833 14.36 1.04 31.65 3.02
3753 5231 4.040461 TCCTGAGTTTCTGGTACCTTCTTG 59.960 45.833 14.36 0.00 36.89 3.02
3754 5232 4.040584 GTCCTGAGTTTCTGGTACCTTCTT 59.959 45.833 14.36 0.00 36.89 2.52
3755 5233 3.579151 GTCCTGAGTTTCTGGTACCTTCT 59.421 47.826 14.36 4.20 36.89 2.85
3756 5234 3.306849 GGTCCTGAGTTTCTGGTACCTTC 60.307 52.174 14.36 2.29 36.89 3.46
3758 5236 2.258109 GGTCCTGAGTTTCTGGTACCT 58.742 52.381 14.36 0.00 36.89 3.08
3759 5237 1.975680 TGGTCCTGAGTTTCTGGTACC 59.024 52.381 4.43 4.43 36.89 3.34
3760 5238 3.983044 ATGGTCCTGAGTTTCTGGTAC 57.017 47.619 2.53 0.00 36.89 3.34
3764 5269 7.012138 CAGAATTCATATGGTCCTGAGTTTCTG 59.988 40.741 8.44 13.85 37.25 3.02
3781 5287 3.014304 ACTGGATGCTGCAGAATTCAT 57.986 42.857 16.62 10.12 38.14 2.57
3795 5301 6.096001 GCAATAGGAAACATTCAGAACTGGAT 59.904 38.462 1.93 0.00 0.00 3.41
3799 5305 5.003804 ACGCAATAGGAAACATTCAGAACT 58.996 37.500 0.00 0.00 0.00 3.01
3839 5345 8.034313 TCTATGGATTAAAGTGCAGGTAGAAT 57.966 34.615 0.00 0.00 0.00 2.40
3840 5346 7.432148 TCTATGGATTAAAGTGCAGGTAGAA 57.568 36.000 0.00 0.00 0.00 2.10
3842 5348 5.698545 GCTCTATGGATTAAAGTGCAGGTAG 59.301 44.000 0.00 0.00 31.73 3.18
3844 5350 4.164988 AGCTCTATGGATTAAAGTGCAGGT 59.835 41.667 0.00 0.00 33.36 4.00
3845 5351 4.514441 CAGCTCTATGGATTAAAGTGCAGG 59.486 45.833 0.00 0.00 33.36 4.85
3850 5357 5.191722 TGAACCCAGCTCTATGGATTAAAGT 59.808 40.000 0.00 0.00 43.57 2.66
3858 5365 2.569059 CATGTGAACCCAGCTCTATGG 58.431 52.381 0.00 0.00 40.29 2.74
3866 5373 3.731652 TTTCTTTGCATGTGAACCCAG 57.268 42.857 0.00 0.00 0.00 4.45
3910 5417 9.708092 TCTTCAATGAAATGCACATAAAAATCA 57.292 25.926 0.00 0.00 0.00 2.57
3918 5425 5.929992 CAGGTTTCTTCAATGAAATGCACAT 59.070 36.000 0.00 0.00 38.09 3.21
3930 5437 3.011566 TCAACTGCCAGGTTTCTTCAA 57.988 42.857 0.00 0.00 0.00 2.69
3931 5438 2.727123 TCAACTGCCAGGTTTCTTCA 57.273 45.000 0.00 0.00 0.00 3.02
3957 5464 4.615912 GCCAAACATAACGATGTGAGCTTT 60.616 41.667 0.00 0.00 45.93 3.51
3998 5505 3.748048 CGCTTTCAACTTCAGAATCCTGA 59.252 43.478 0.00 0.00 46.95 3.86
4007 5514 3.006940 ACAGAACACGCTTTCAACTTCA 58.993 40.909 0.00 0.00 0.00 3.02
4046 5556 3.525609 TCCAAGCCACCACAAGGAATATA 59.474 43.478 0.00 0.00 38.69 0.86
4144 5654 1.611410 CCTGTCATGCTTGCCAGTACA 60.611 52.381 9.44 1.32 26.55 2.90
4184 5694 2.623889 AGAGATTAGACGGGATCGGTTG 59.376 50.000 0.00 0.00 41.39 3.77
4219 6030 1.475682 CTATAGGATACCGGGCCGTTC 59.524 57.143 26.32 17.63 37.17 3.95
4315 6128 7.700234 TCGATGGACCAAAAATAAATGAATTCG 59.300 33.333 0.00 0.00 0.00 3.34
4437 7305 5.992217 AGCAGTTAAGGAAGTAGTGTTTCTG 59.008 40.000 0.00 0.00 0.00 3.02
4496 7366 8.934023 AGGGAAAAGAAACAATGTAGTCAATA 57.066 30.769 0.00 0.00 0.00 1.90
4718 7609 6.445475 TCTTCAAATTCATCGCAATGTGAAA 58.555 32.000 0.00 0.00 38.82 2.69
5000 7892 3.461773 CGGGCATCCACCTCGAGT 61.462 66.667 12.31 0.00 0.00 4.18
5028 7920 4.447290 TCGTGTTTTGGAGAGATTTGACA 58.553 39.130 0.00 0.00 0.00 3.58
5032 7924 3.191371 GCCATCGTGTTTTGGAGAGATTT 59.809 43.478 0.00 0.00 34.81 2.17
5047 7939 2.494918 GCACCTAGTCGCCATCGT 59.505 61.111 0.00 0.00 36.96 3.73


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

AutoCloner maintained by Alex Coulton.