Multiple sequence alignment - TraesCS3B01G119500

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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 TraesCS3B01G119500 chr3B 100.000 4022 0 0 1 4022 89355328 89351307 0.000000e+00 7428
1 TraesCS3B01G119500 chr3B 89.287 3463 240 60 639 4022 89092679 89096089 0.000000e+00 4218
2 TraesCS3B01G119500 chr3B 83.573 347 28 18 1 335 89066002 89066331 8.450000e-77 298
3 TraesCS3B01G119500 chr3B 89.730 185 10 4 358 542 89071233 89071408 1.120000e-55 228
4 TraesCS3B01G119500 chr3A 88.571 3640 283 68 1 3582 66061400 66064964 0.000000e+00 4294
5 TraesCS3B01G119500 chr3D 91.530 2987 192 31 328 3260 56687725 56684746 0.000000e+00 4058
6 TraesCS3B01G119500 chr3D 86.783 802 53 24 3264 4022 56684557 56683766 0.000000e+00 845
7 TraesCS3B01G119500 chr3D 89.465 598 39 11 3265 3846 490682176 490681587 0.000000e+00 734
8 TraesCS3B01G119500 chr3D 93.939 165 9 1 172 336 56707471 56707308 8.630000e-62 248
9 TraesCS3B01G119500 chr3D 90.517 116 8 1 1 113 56707612 56707497 2.500000e-32 150
10 TraesCS3B01G119500 chr3D 86.885 122 10 4 1 117 56688291 56688171 9.070000e-27 132
11 TraesCS3B01G119500 chr3D 88.372 86 7 3 734 818 56689275 56689192 2.560000e-17 100
12 TraesCS3B01G119500 chr6D 89.632 598 38 11 3265 3846 18949973 18950562 0.000000e+00 739
13 TraesCS3B01G119500 chr5D 89.632 598 38 11 3265 3846 39667070 39666481 0.000000e+00 739
14 TraesCS3B01G119500 chr5D 89.632 598 38 11 3265 3846 53887638 53887049 0.000000e+00 739
15 TraesCS3B01G119500 chr2D 89.632 598 38 11 3265 3846 193902040 193902629 0.000000e+00 739
16 TraesCS3B01G119500 chr2D 89.632 598 38 11 3265 3846 465784067 465783478 0.000000e+00 739
17 TraesCS3B01G119500 chr1D 89.482 599 38 12 3265 3846 394221797 394221207 0.000000e+00 734
18 TraesCS3B01G119500 chr1D 89.465 598 39 11 3265 3846 428761414 428762003 0.000000e+00 734
19 TraesCS3B01G119500 chr1D 89.465 598 38 12 3265 3846 266861201 266860613 0.000000e+00 732
20 TraesCS3B01G119500 chr1D 89.130 598 40 12 3265 3846 42318903 42319491 0.000000e+00 721
21 TraesCS3B01G119500 chr1D 90.040 502 30 9 3265 3753 450297678 450297184 2.040000e-177 632
22 TraesCS3B01G119500 chr6B 71.618 1582 387 47 1129 2664 164372206 164373771 1.060000e-100 377


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 TraesCS3B01G119500 chr3B 89351307 89355328 4021 True 7428.00 7428 100.0000 1 4022 1 chr3B.!!$R1 4021
1 TraesCS3B01G119500 chr3B 89092679 89096089 3410 False 4218.00 4218 89.2870 639 4022 1 chr3B.!!$F3 3383
2 TraesCS3B01G119500 chr3A 66061400 66064964 3564 False 4294.00 4294 88.5710 1 3582 1 chr3A.!!$F1 3581
3 TraesCS3B01G119500 chr3D 56683766 56689275 5509 True 1283.75 4058 88.3925 1 4022 4 chr3D.!!$R2 4021
4 TraesCS3B01G119500 chr3D 490681587 490682176 589 True 734.00 734 89.4650 3265 3846 1 chr3D.!!$R1 581
5 TraesCS3B01G119500 chr6D 18949973 18950562 589 False 739.00 739 89.6320 3265 3846 1 chr6D.!!$F1 581
6 TraesCS3B01G119500 chr5D 39666481 39667070 589 True 739.00 739 89.6320 3265 3846 1 chr5D.!!$R1 581
7 TraesCS3B01G119500 chr5D 53887049 53887638 589 True 739.00 739 89.6320 3265 3846 1 chr5D.!!$R2 581
8 TraesCS3B01G119500 chr2D 193902040 193902629 589 False 739.00 739 89.6320 3265 3846 1 chr2D.!!$F1 581
9 TraesCS3B01G119500 chr2D 465783478 465784067 589 True 739.00 739 89.6320 3265 3846 1 chr2D.!!$R1 581
10 TraesCS3B01G119500 chr1D 394221207 394221797 590 True 734.00 734 89.4820 3265 3846 1 chr1D.!!$R2 581
11 TraesCS3B01G119500 chr1D 428761414 428762003 589 False 734.00 734 89.4650 3265 3846 1 chr1D.!!$F2 581
12 TraesCS3B01G119500 chr1D 266860613 266861201 588 True 732.00 732 89.4650 3265 3846 1 chr1D.!!$R1 581
13 TraesCS3B01G119500 chr1D 42318903 42319491 588 False 721.00 721 89.1300 3265 3846 1 chr1D.!!$F1 581
14 TraesCS3B01G119500 chr6B 164372206 164373771 1565 False 377.00 377 71.6180 1129 2664 1 chr6B.!!$F1 1535

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
438 1771 0.108472 GTACACTCCGGTACTTGGCC 60.108 60.000 0.00 0.0 40.34 5.36 F
549 1910 1.064758 ACCAACAGAAGTGCCAACAGA 60.065 47.619 0.00 0.0 0.00 3.41 F
1548 2961 0.457035 GCACCGGGTACTACGATGAA 59.543 55.000 6.32 0.0 0.00 2.57 F
2250 3672 0.604243 TGCTTGGTTATTGCCGACGT 60.604 50.000 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 2961 0.909610 TGTTGAAGGATCCGCTCCCT 60.910 55.0 5.98 0.00 46.27 4.20 R
2500 3928 0.246360 TCAGTGCCATGGTCGTACAG 59.754 55.0 14.67 5.28 0.00 2.74 R
2736 4164 0.179124 GCAGTCTCGGATCCACAGTC 60.179 60.0 13.41 4.78 0.00 3.51 R
3823 5488 0.179108 AACCGAAGCTAGCGATGGTC 60.179 55.0 22.42 10.52 0.00 4.02 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
21 1005 4.946784 GTTGATTTCGTCCAATGCTAGT 57.053 40.909 0.00 0.00 0.00 2.57
22 1006 4.898370 GTTGATTTCGTCCAATGCTAGTC 58.102 43.478 0.00 0.00 0.00 2.59
24 1008 4.832248 TGATTTCGTCCAATGCTAGTCTT 58.168 39.130 0.00 0.00 0.00 3.01
53 1042 0.560688 ACCCATCTCTCTCCTCCCTC 59.439 60.000 0.00 0.00 0.00 4.30
54 1043 0.859760 CCCATCTCTCTCCTCCCTCT 59.140 60.000 0.00 0.00 0.00 3.69
73 1062 4.321527 CCTCTGCTTTCACATTTTTCCTCC 60.322 45.833 0.00 0.00 0.00 4.30
82 1071 8.713708 TTTCACATTTTTCCTCCCATACTTTA 57.286 30.769 0.00 0.00 0.00 1.85
128 1117 2.114670 CGCCATGGGTTAGCCACAG 61.115 63.158 15.13 0.80 36.17 3.66
129 1118 1.302949 GCCATGGGTTAGCCACAGA 59.697 57.895 15.13 0.00 36.17 3.41
130 1119 0.749454 GCCATGGGTTAGCCACAGAG 60.749 60.000 15.13 0.00 36.17 3.35
134 1123 1.561643 TGGGTTAGCCACAGAGAGAG 58.438 55.000 0.00 0.00 36.17 3.20
139 1128 4.406003 GGGTTAGCCACAGAGAGAGAAATA 59.594 45.833 0.00 0.00 36.17 1.40
148 1137 2.032799 AGAGAGAGAAATAGCTGTCGCG 59.967 50.000 0.00 0.00 42.32 5.87
158 1147 1.171308 AGCTGTCGCGGTAGACTTTA 58.829 50.000 6.13 0.00 41.47 1.85
159 1148 1.132643 AGCTGTCGCGGTAGACTTTAG 59.867 52.381 6.13 0.00 41.47 1.85
160 1149 1.131883 GCTGTCGCGGTAGACTTTAGA 59.868 52.381 6.13 0.00 41.47 2.10
162 1151 2.419324 CTGTCGCGGTAGACTTTAGACT 59.581 50.000 6.13 0.00 41.47 3.24
163 1152 2.816087 TGTCGCGGTAGACTTTAGACTT 59.184 45.455 6.13 0.00 41.47 3.01
167 1156 6.032717 GTCGCGGTAGACTTTAGACTTTTAT 58.967 40.000 6.13 0.00 38.09 1.40
168 1157 6.196168 GTCGCGGTAGACTTTAGACTTTTATC 59.804 42.308 6.13 0.00 38.09 1.75
169 1158 6.032094 CGCGGTAGACTTTAGACTTTTATCA 58.968 40.000 0.00 0.00 0.00 2.15
177 1166 9.699703 AGACTTTAGACTTTTATCAGAGACAAC 57.300 33.333 0.00 0.00 0.00 3.32
184 1173 8.261522 AGACTTTTATCAGAGACAACCTATTCC 58.738 37.037 0.00 0.00 0.00 3.01
216 1205 5.067153 CCCATTTGACTCTACAAACAACACA 59.933 40.000 0.00 0.00 41.49 3.72
226 1215 4.836125 ACAAACAACACATCCATCAGTC 57.164 40.909 0.00 0.00 0.00 3.51
232 1221 1.836166 ACACATCCATCAGTCTGGGAG 59.164 52.381 0.00 0.00 36.89 4.30
234 1223 0.835276 CATCCATCAGTCTGGGAGCA 59.165 55.000 0.00 0.00 36.89 4.26
275 1264 2.181021 GCGAGGTAGGTGTCCACG 59.819 66.667 0.00 0.00 40.78 4.94
313 1302 1.172180 CCTTGGTGTTGTGCGGATGT 61.172 55.000 0.00 0.00 0.00 3.06
325 1655 0.250901 GCGGATGTGGATGCCCTTAT 60.251 55.000 0.00 0.00 0.00 1.73
326 1656 1.819305 GCGGATGTGGATGCCCTTATT 60.819 52.381 0.00 0.00 0.00 1.40
352 1682 4.163268 AGAGGATGAAGAAAACTCTAGGCC 59.837 45.833 0.00 0.00 36.80 5.19
357 1687 7.001073 GGATGAAGAAAACTCTAGGCCATATT 58.999 38.462 5.01 0.00 0.00 1.28
398 1731 2.347490 CCGGACCACCTCAGGTTG 59.653 66.667 0.00 0.00 43.38 3.77
403 1736 0.603975 GACCACCTCAGGTTGAGCAC 60.604 60.000 0.83 0.00 42.98 4.40
431 1764 2.028839 CCAACACATGTACACTCCGGTA 60.029 50.000 0.00 0.00 0.00 4.02
438 1771 0.108472 GTACACTCCGGTACTTGGCC 60.108 60.000 0.00 0.00 40.34 5.36
542 1903 4.153117 CAGACTTATCACCAACAGAAGTGC 59.847 45.833 0.00 0.00 33.90 4.40
543 1904 3.412386 ACTTATCACCAACAGAAGTGCC 58.588 45.455 0.00 0.00 33.90 5.01
544 1905 3.181445 ACTTATCACCAACAGAAGTGCCA 60.181 43.478 0.00 0.00 33.90 4.92
545 1906 2.363306 ATCACCAACAGAAGTGCCAA 57.637 45.000 0.00 0.00 33.90 4.52
546 1907 1.388547 TCACCAACAGAAGTGCCAAC 58.611 50.000 0.00 0.00 33.90 3.77
547 1908 1.102154 CACCAACAGAAGTGCCAACA 58.898 50.000 0.00 0.00 0.00 3.33
548 1909 1.066002 CACCAACAGAAGTGCCAACAG 59.934 52.381 0.00 0.00 0.00 3.16
549 1910 1.064758 ACCAACAGAAGTGCCAACAGA 60.065 47.619 0.00 0.00 0.00 3.41
550 1911 2.023673 CCAACAGAAGTGCCAACAGAA 58.976 47.619 0.00 0.00 0.00 3.02
551 1912 2.426738 CCAACAGAAGTGCCAACAGAAA 59.573 45.455 0.00 0.00 0.00 2.52
552 1913 3.489738 CCAACAGAAGTGCCAACAGAAAG 60.490 47.826 0.00 0.00 0.00 2.62
553 1914 3.281727 ACAGAAGTGCCAACAGAAAGA 57.718 42.857 0.00 0.00 0.00 2.52
554 1915 3.825328 ACAGAAGTGCCAACAGAAAGAT 58.175 40.909 0.00 0.00 0.00 2.40
555 1916 3.567164 ACAGAAGTGCCAACAGAAAGATG 59.433 43.478 0.00 0.00 0.00 2.90
556 1917 3.567164 CAGAAGTGCCAACAGAAAGATGT 59.433 43.478 0.00 0.00 33.96 3.06
557 1918 4.756642 CAGAAGTGCCAACAGAAAGATGTA 59.243 41.667 0.00 0.00 31.70 2.29
558 1919 4.757149 AGAAGTGCCAACAGAAAGATGTAC 59.243 41.667 0.00 0.00 31.70 2.90
559 1920 4.357918 AGTGCCAACAGAAAGATGTACT 57.642 40.909 0.00 0.00 31.70 2.73
560 1921 5.483685 AGTGCCAACAGAAAGATGTACTA 57.516 39.130 0.00 0.00 31.70 1.82
561 1922 5.482908 AGTGCCAACAGAAAGATGTACTAG 58.517 41.667 0.00 0.00 31.70 2.57
562 1923 5.012148 AGTGCCAACAGAAAGATGTACTAGT 59.988 40.000 0.00 0.00 31.70 2.57
563 1924 5.120830 GTGCCAACAGAAAGATGTACTAGTG 59.879 44.000 5.39 0.00 31.70 2.74
588 1949 6.054860 ACACATGCTATTCTACTTTCTGGT 57.945 37.500 0.00 0.00 0.00 4.00
621 1995 3.459063 CGGAGTCGGAGGGGGAAC 61.459 72.222 0.00 0.00 0.00 3.62
662 2036 1.741770 GCCTAGTGGTTGCCGTCTG 60.742 63.158 0.00 0.00 35.27 3.51
738 2112 5.831702 GGGAGACGAACTTTCAGTATCTA 57.168 43.478 0.00 0.00 0.00 1.98
766 2140 4.342092 AGAAAATTGAACCTGTTGGACCAG 59.658 41.667 0.00 0.00 37.04 4.00
770 2144 1.239347 GAACCTGTTGGACCAGCTTC 58.761 55.000 9.95 1.80 37.04 3.86
772 2146 1.303643 CCTGTTGGACCAGCTTCCC 60.304 63.158 9.95 0.00 34.33 3.97
773 2147 1.672356 CTGTTGGACCAGCTTCCCG 60.672 63.158 9.95 0.00 34.33 5.14
788 2162 4.160635 CCGTTCGATTGCACCCGC 62.161 66.667 2.33 0.00 39.24 6.13
804 2178 1.609061 CCCGCAGATGGTGATGTATCC 60.609 57.143 0.00 0.00 0.00 2.59
805 2179 1.345741 CCGCAGATGGTGATGTATCCT 59.654 52.381 0.00 0.00 0.00 3.24
806 2180 2.611473 CCGCAGATGGTGATGTATCCTC 60.611 54.545 0.00 0.00 0.00 3.71
815 2190 3.551863 GGTGATGTATCCTCTCTTGCGAG 60.552 52.174 0.00 0.00 38.67 5.03
870 2245 6.514947 ACTCTCAGTAGTACTAGTACATCGG 58.485 44.000 29.87 21.79 38.48 4.18
898 2273 1.636148 ATCATGGGCAGTTGTTTGCT 58.364 45.000 0.00 0.00 43.57 3.91
903 2278 1.133945 TGGGCAGTTGTTTGCTACTGA 60.134 47.619 11.97 0.00 46.43 3.41
990 2377 8.773033 AATATCATAATCTTTTCCTTGCCAGT 57.227 30.769 0.00 0.00 0.00 4.00
1041 2436 1.568504 TCTTCCTCCTACACGCCATT 58.431 50.000 0.00 0.00 0.00 3.16
1051 2446 1.194781 ACACGCCATTCCACTCCTCT 61.195 55.000 0.00 0.00 0.00 3.69
1061 2456 3.260269 TCCACTCCTCTTCCTTCTTCA 57.740 47.619 0.00 0.00 0.00 3.02
1119 2517 3.743396 GCTTCCTATACAATGGCTTCTCG 59.257 47.826 0.00 0.00 0.00 4.04
1533 2946 4.715523 TTGCAGGCCTACCGCACC 62.716 66.667 15.40 0.00 42.47 5.01
1548 2961 0.457035 GCACCGGGTACTACGATGAA 59.543 55.000 6.32 0.00 0.00 2.57
1584 3006 3.650942 TCAACAACCTGACCCTTATCAGT 59.349 43.478 2.35 0.00 43.99 3.41
1794 3216 1.374758 CGTTCTCGGCTGGAGCTTT 60.375 57.895 0.00 0.00 42.82 3.51
1800 3222 2.345760 CGGCTGGAGCTTTGCCATT 61.346 57.895 20.31 0.00 46.39 3.16
1935 3357 2.224209 CGTCCTTGTAGTGGGAACTGTT 60.224 50.000 0.00 0.00 33.01 3.16
1945 3367 4.848357 AGTGGGAACTGTTATCATTCTGG 58.152 43.478 0.00 0.00 0.00 3.86
1956 3378 5.009110 TGTTATCATTCTGGTTGTTCGCAAA 59.991 36.000 0.00 0.00 39.04 3.68
1986 3408 3.394836 AGGGAGCTGCGGGAAGAC 61.395 66.667 0.00 0.00 0.00 3.01
2010 3432 1.451387 GGTCGATTTCGGGCCACAT 60.451 57.895 4.39 0.00 40.29 3.21
2043 3465 2.267045 GGACCTGTTCCATGCAACC 58.733 57.895 0.00 0.00 45.10 3.77
2111 3533 2.764572 AGGTATACAAAGGGACACTCCG 59.235 50.000 5.01 0.00 37.43 4.63
2238 3660 2.203538 CTTGTGCCCCTGCTTGGT 60.204 61.111 0.00 0.00 38.71 3.67
2250 3672 0.604243 TGCTTGGTTATTGCCGACGT 60.604 50.000 0.00 0.00 0.00 4.34
2310 3732 4.944619 TGGTAGCCTCAATCAGTATCTG 57.055 45.455 0.00 0.00 0.00 2.90
2355 3783 2.573915 ACTGAATTGGGAGGAGAGGTTC 59.426 50.000 0.00 0.00 0.00 3.62
2370 3798 5.248380 AGAGGTTCCATATTATCAAGGGC 57.752 43.478 0.00 0.00 0.00 5.19
2376 3804 2.412870 CATATTATCAAGGGCGTCGCA 58.587 47.619 20.50 0.00 0.00 5.10
2500 3928 2.147150 GTGACTTTGGTCTCTCAAGGC 58.853 52.381 0.00 0.00 42.54 4.35
2570 3998 1.113517 GGATACCTGGCGCCTGAGTA 61.114 60.000 32.43 28.21 0.00 2.59
2574 4002 2.202623 CTGGCGCCTGAGTACGTC 60.203 66.667 29.70 0.00 0.00 4.34
2576 4004 3.755628 GGCGCCTGAGTACGTCCA 61.756 66.667 22.15 0.00 0.00 4.02
2593 4021 3.965258 ACACGGGCAAGGCATCCA 61.965 61.111 0.00 0.00 0.00 3.41
2605 4033 1.591703 GCATCCACTCTGACGGACA 59.408 57.895 0.00 0.00 33.05 4.02
2736 4164 0.179100 ACAACGGATCGCTCATGGAG 60.179 55.000 0.00 0.00 0.00 3.86
2739 4167 0.753479 ACGGATCGCTCATGGAGACT 60.753 55.000 0.00 0.00 0.00 3.24
2847 4275 3.372730 GCAAGGCCCACAATGCGA 61.373 61.111 0.00 0.00 0.00 5.10
2850 4278 1.304381 AAGGCCCACAATGCGACAT 60.304 52.632 0.00 0.00 0.00 3.06
2904 4332 1.339438 CCAGAGCTAACACCAGCACAT 60.339 52.381 0.00 0.00 44.35 3.21
3001 4429 2.494073 ACGAGTTTTGCCACTTTTTCCA 59.506 40.909 0.00 0.00 0.00 3.53
3002 4430 3.115554 CGAGTTTTGCCACTTTTTCCAG 58.884 45.455 0.00 0.00 0.00 3.86
3006 4434 1.039856 TTGCCACTTTTTCCAGCCTC 58.960 50.000 0.00 0.00 0.00 4.70
3027 4455 5.599732 CTCTCAGGAGGAAGATAACACATG 58.400 45.833 0.00 0.00 36.03 3.21
3042 4470 4.614555 ACACATGCATATACGGTGTTTG 57.385 40.909 12.57 0.00 39.48 2.93
3050 4478 5.648526 TGCATATACGGTGTTTGGTGTTATT 59.351 36.000 0.00 0.00 0.00 1.40
3060 4489 6.199393 GTGTTTGGTGTTATTGTGTCTCTTC 58.801 40.000 0.00 0.00 0.00 2.87
3090 4543 9.410556 TGTTAAAATATCTGCTTTCTTTCTTGC 57.589 29.630 0.00 0.00 0.00 4.01
3092 4545 5.886960 AATATCTGCTTTCTTTCTTGCGT 57.113 34.783 0.00 0.00 0.00 5.24
3097 4550 6.795098 TCTGCTTTCTTTCTTGCGTATTTA 57.205 33.333 0.00 0.00 0.00 1.40
3155 4610 5.416326 ACGCTAGCTAGGGAGTATATCAAAG 59.584 44.000 36.37 4.79 39.31 2.77
3183 4638 8.958119 TTACTTCACTTCAAATGTTACTCTGT 57.042 30.769 0.00 0.00 0.00 3.41
3260 4715 5.485353 TCTTCTACATGGTTCCAGTCTGAAT 59.515 40.000 0.00 0.00 0.00 2.57
3261 4716 5.089970 TCTACATGGTTCCAGTCTGAATG 57.910 43.478 0.00 0.00 0.00 2.67
3275 4915 7.044181 CCAGTCTGAATGTAGTACATGTGAAT 58.956 38.462 16.46 10.93 37.97 2.57
3323 4963 4.320608 TTGTGCTTGTTTGGAATTCCTC 57.679 40.909 24.73 15.05 36.82 3.71
3334 4974 6.183360 TGTTTGGAATTCCTCTGAGAAACAAC 60.183 38.462 25.00 13.74 36.82 3.32
3338 4978 3.386768 TTCCTCTGAGAAACAACGAGG 57.613 47.619 6.17 0.00 40.29 4.63
3412 5052 2.552743 GCCTTTGGGTCAGTTTGAGTAC 59.447 50.000 0.00 0.00 34.45 2.73
3483 5123 6.814076 CGAAGCTACAACTTATTAGGACTG 57.186 41.667 0.00 0.00 0.00 3.51
3506 5146 3.630312 CCCCAAATCGTACGGATTGAATT 59.370 43.478 25.40 12.04 44.59 2.17
3517 5157 8.810427 TCGTACGGATTGAATTAATTGTACTTC 58.190 33.333 16.52 0.00 38.00 3.01
3534 5174 2.802816 ACTTCAAGTGTCGATCTTGTGC 59.197 45.455 22.94 0.00 41.78 4.57
3606 5246 0.741927 CTGCTCGCCACACATCATCA 60.742 55.000 0.00 0.00 0.00 3.07
3642 5282 6.015180 GTGGATATTGCCAAATATGTGGACAT 60.015 38.462 16.77 8.59 41.65 3.06
3647 5287 4.854173 TGCCAAATATGTGGACATAGTGT 58.146 39.130 16.77 0.00 41.58 3.55
3661 5314 5.220854 GGACATAGTGTTGGAATTCAATCCG 60.221 44.000 7.93 0.00 42.76 4.18
3711 5372 7.318141 AGTTTGATGCCATTGTTCTTTATGAG 58.682 34.615 0.00 0.00 0.00 2.90
3844 5509 0.876342 CCATCGCTAGCTTCGGTTCC 60.876 60.000 13.93 0.00 0.00 3.62
3846 5511 0.103208 ATCGCTAGCTTCGGTTCCTG 59.897 55.000 13.93 0.00 0.00 3.86
3847 5512 1.215647 CGCTAGCTTCGGTTCCTGT 59.784 57.895 13.93 0.00 0.00 4.00
3872 5560 7.849804 TTAGTGCAAAATCTCTGACCTAATC 57.150 36.000 0.00 0.00 0.00 1.75
3889 5577 4.455137 CAGGATCCCCCACCCCCT 62.455 72.222 8.55 0.00 37.41 4.79
3918 5606 0.107654 GATGCAGCGGGAAACTAGGT 60.108 55.000 0.00 0.00 0.00 3.08
3923 5611 1.129058 AGCGGGAAACTAGGTATGGG 58.871 55.000 0.00 0.00 0.00 4.00
3957 5645 2.055042 CGACTGGGGAGGGAGAGTG 61.055 68.421 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 990 4.381612 CCACTAAGACTAGCATTGGACGAA 60.382 45.833 0.00 0.00 0.00 3.85
9 993 4.434520 GTCCACTAAGACTAGCATTGGAC 58.565 47.826 2.29 2.29 39.63 4.02
20 1004 1.136500 GATGGGTCGGTCCACTAAGAC 59.864 57.143 0.00 0.00 39.97 3.01
21 1005 1.006758 AGATGGGTCGGTCCACTAAGA 59.993 52.381 0.00 0.00 39.97 2.10
22 1006 1.409427 GAGATGGGTCGGTCCACTAAG 59.591 57.143 0.00 0.00 39.97 2.18
24 1008 0.629596 AGAGATGGGTCGGTCCACTA 59.370 55.000 0.00 0.00 39.97 2.74
53 1042 3.321682 TGGGAGGAAAAATGTGAAAGCAG 59.678 43.478 0.00 0.00 0.00 4.24
54 1043 3.303938 TGGGAGGAAAAATGTGAAAGCA 58.696 40.909 0.00 0.00 0.00 3.91
73 1062 4.618227 GCTGCAGTTTTGGGTAAAGTATGG 60.618 45.833 16.64 0.00 0.00 2.74
82 1071 2.051941 CATGGCTGCAGTTTTGGGT 58.948 52.632 16.64 0.00 0.00 4.51
128 1117 2.380660 CGCGACAGCTATTTCTCTCTC 58.619 52.381 0.00 0.00 42.32 3.20
129 1118 1.066303 CCGCGACAGCTATTTCTCTCT 59.934 52.381 8.23 0.00 42.32 3.10
130 1119 1.202313 ACCGCGACAGCTATTTCTCTC 60.202 52.381 8.23 0.00 42.32 3.20
134 1123 2.117910 GTCTACCGCGACAGCTATTTC 58.882 52.381 8.23 0.00 42.32 2.17
139 1128 1.132643 CTAAAGTCTACCGCGACAGCT 59.867 52.381 8.23 3.01 42.32 4.24
148 1137 9.791820 GTCTCTGATAAAAGTCTAAAGTCTACC 57.208 37.037 0.00 0.00 0.00 3.18
158 1147 8.261522 GGAATAGGTTGTCTCTGATAAAAGTCT 58.738 37.037 0.00 0.00 0.00 3.24
159 1148 7.222999 CGGAATAGGTTGTCTCTGATAAAAGTC 59.777 40.741 0.00 0.00 0.00 3.01
160 1149 7.042335 CGGAATAGGTTGTCTCTGATAAAAGT 58.958 38.462 0.00 0.00 0.00 2.66
162 1151 5.815740 GCGGAATAGGTTGTCTCTGATAAAA 59.184 40.000 0.00 0.00 0.00 1.52
163 1152 5.105106 TGCGGAATAGGTTGTCTCTGATAAA 60.105 40.000 0.00 0.00 0.00 1.40
167 1156 2.166459 CTGCGGAATAGGTTGTCTCTGA 59.834 50.000 0.00 0.00 0.00 3.27
168 1157 2.544685 CTGCGGAATAGGTTGTCTCTG 58.455 52.381 0.00 0.00 0.00 3.35
169 1158 1.482593 CCTGCGGAATAGGTTGTCTCT 59.517 52.381 0.00 0.00 0.00 3.10
177 1166 2.203209 GGGTGCCTGCGGAATAGG 60.203 66.667 0.00 0.00 38.39 2.57
180 1169 1.305213 AAATGGGTGCCTGCGGAAT 60.305 52.632 0.00 0.00 0.00 3.01
184 1173 1.926511 GAGTCAAATGGGTGCCTGCG 61.927 60.000 0.00 0.00 0.00 5.18
195 1184 6.545666 TGGATGTGTTGTTTGTAGAGTCAAAT 59.454 34.615 0.00 0.00 39.09 2.32
216 1205 1.698532 GATGCTCCCAGACTGATGGAT 59.301 52.381 3.32 0.20 43.57 3.41
226 1215 2.124570 CGGGTTGGATGCTCCCAG 60.125 66.667 15.43 7.01 41.12 4.45
232 1221 1.077787 TCCATGTCGGGTTGGATGC 60.078 57.895 0.00 0.00 37.10 3.91
234 1223 0.541863 GTCTCCATGTCGGGTTGGAT 59.458 55.000 0.00 0.00 41.09 3.41
259 1248 1.975407 ACCGTGGACACCTACCTCG 60.975 63.158 0.00 0.00 41.85 4.63
275 1264 4.910585 CCGGGCCATCGCTACACC 62.911 72.222 4.39 0.00 34.44 4.16
313 1302 3.664320 TCCTCTACAATAAGGGCATCCA 58.336 45.455 0.00 0.00 33.21 3.41
325 1655 7.579723 GCCTAGAGTTTTCTTCATCCTCTACAA 60.580 40.741 0.00 0.00 34.51 2.41
326 1656 6.127310 GCCTAGAGTTTTCTTCATCCTCTACA 60.127 42.308 0.00 0.00 34.51 2.74
352 1682 3.755965 TGCACCGCACAAGTAAATATG 57.244 42.857 0.00 0.00 31.71 1.78
357 1687 1.578926 GCATGCACCGCACAAGTAA 59.421 52.632 14.21 0.00 43.04 2.24
398 1731 3.181487 ACATGTGTTGGACTTTTGTGCTC 60.181 43.478 0.00 0.00 41.62 4.26
403 1736 5.499139 AGTGTACATGTGTTGGACTTTTG 57.501 39.130 9.11 0.00 40.17 2.44
556 1917 8.975663 AGTAGAATAGCATGTGTACACTAGTA 57.024 34.615 25.60 12.61 0.00 1.82
557 1918 7.883391 AGTAGAATAGCATGTGTACACTAGT 57.117 36.000 25.60 9.82 0.00 2.57
558 1919 9.239002 GAAAGTAGAATAGCATGTGTACACTAG 57.761 37.037 25.60 18.28 0.00 2.57
559 1920 8.967918 AGAAAGTAGAATAGCATGTGTACACTA 58.032 33.333 25.60 13.17 0.00 2.74
560 1921 7.761704 CAGAAAGTAGAATAGCATGTGTACACT 59.238 37.037 25.60 9.01 0.00 3.55
561 1922 7.010552 CCAGAAAGTAGAATAGCATGTGTACAC 59.989 40.741 19.36 19.36 0.00 2.90
562 1923 7.041721 CCAGAAAGTAGAATAGCATGTGTACA 58.958 38.462 0.00 0.00 0.00 2.90
563 1924 7.042335 ACCAGAAAGTAGAATAGCATGTGTAC 58.958 38.462 0.00 0.00 0.00 2.90
588 1949 6.095860 TCCGACTCCGAAAGTAGAATATCAAA 59.904 38.462 0.00 0.00 38.74 2.69
598 1959 0.682209 CCCCTCCGACTCCGAAAGTA 60.682 60.000 0.00 0.00 38.74 2.24
600 1961 2.722201 CCCCCTCCGACTCCGAAAG 61.722 68.421 0.00 0.00 38.22 2.62
601 1962 2.682494 CCCCCTCCGACTCCGAAA 60.682 66.667 0.00 0.00 38.22 3.46
602 1963 3.228243 TTCCCCCTCCGACTCCGAA 62.228 63.158 0.00 0.00 38.22 4.30
642 2016 1.741770 GACGGCAACCACTAGGCAG 60.742 63.158 0.00 0.00 39.06 4.85
692 2066 2.486592 TCGACGCTGAAGTCTGAACATA 59.513 45.455 0.00 0.00 38.90 2.29
738 2112 5.660864 TCCAACAGGTTCAATTTTCTTCCTT 59.339 36.000 0.00 0.00 0.00 3.36
766 2140 1.134694 GTGCAATCGAACGGGAAGC 59.865 57.895 0.00 0.00 0.00 3.86
770 2144 3.496131 CGGGTGCAATCGAACGGG 61.496 66.667 4.17 0.00 0.00 5.28
788 2162 5.539979 CAAGAGAGGATACATCACCATCTG 58.460 45.833 0.00 0.00 41.41 2.90
850 2225 5.284864 CGACCGATGTACTAGTACTACTGA 58.715 45.833 28.56 12.50 37.00 3.41
852 2227 4.054671 GCGACCGATGTACTAGTACTACT 58.945 47.826 28.56 16.08 37.00 2.57
853 2228 3.121194 CGCGACCGATGTACTAGTACTAC 60.121 52.174 28.56 21.14 35.30 2.73
854 2229 3.052745 CGCGACCGATGTACTAGTACTA 58.947 50.000 28.56 17.69 35.30 1.82
855 2230 1.863454 CGCGACCGATGTACTAGTACT 59.137 52.381 28.56 16.82 35.30 2.73
858 2233 1.372582 TTCGCGACCGATGTACTAGT 58.627 50.000 9.15 0.00 43.97 2.57
859 2234 2.463553 TTTCGCGACCGATGTACTAG 57.536 50.000 9.15 0.00 43.97 2.57
870 2245 0.248215 CTGCCCATGATTTTCGCGAC 60.248 55.000 9.15 0.00 0.00 5.19
898 2273 1.140161 GTATGTGCGCCCGTCAGTA 59.860 57.895 4.18 0.00 0.00 2.74
903 2278 4.386951 TGCTGTATGTGCGCCCGT 62.387 61.111 4.18 0.00 0.00 5.28
971 2357 4.347607 AGCACTGGCAAGGAAAAGATTAT 58.652 39.130 0.00 0.00 44.61 1.28
990 2377 2.895680 GGAGCCATGTCTCGAGCA 59.104 61.111 7.81 9.81 33.98 4.26
1041 2436 2.900546 GTGAAGAAGGAAGAGGAGTGGA 59.099 50.000 0.00 0.00 0.00 4.02
1051 2446 1.133823 TGCAGCAAGGTGAAGAAGGAA 60.134 47.619 3.05 0.00 0.00 3.36
1061 2456 1.181098 GGTTGTGGATGCAGCAAGGT 61.181 55.000 3.51 0.00 0.00 3.50
1467 2880 1.593196 CGTGGTTGTTGTCCATGTCT 58.407 50.000 0.00 0.00 37.25 3.41
1533 2946 1.607628 CTCCCTTCATCGTAGTACCCG 59.392 57.143 0.00 0.00 0.00 5.28
1548 2961 0.909610 TGTTGAAGGATCCGCTCCCT 60.910 55.000 5.98 0.00 46.27 4.20
1584 3006 2.269520 ATACCTGCATCGCCTTGCCA 62.270 55.000 3.31 0.00 42.06 4.92
1673 3095 1.004440 GACGAAAGCAGTGGCCTCT 60.004 57.895 3.32 1.65 42.56 3.69
1767 3189 1.741770 GCCGAGAACGCAGTGGATT 60.742 57.895 0.00 0.00 45.00 3.01
1800 3222 2.597340 GCAGGAGCAGGGCCATTA 59.403 61.111 6.18 0.00 41.58 1.90
1935 3357 5.471797 TCTTTTGCGAACAACCAGAATGATA 59.528 36.000 0.00 0.00 34.30 2.15
1945 3367 3.964909 ACCTGAATCTTTTGCGAACAAC 58.035 40.909 0.00 0.00 34.87 3.32
1956 3378 2.503356 CAGCTCCCTGTACCTGAATCTT 59.497 50.000 0.00 0.00 34.31 2.40
1986 3408 1.144057 CCCGAAATCGACCTCCCAG 59.856 63.158 4.04 0.00 43.02 4.45
2010 3432 0.974383 GGTCCTTGAAGGAGAACCGA 59.026 55.000 15.46 0.00 46.90 4.69
2043 3465 4.224715 GTTCTTTTCCTTGAACCCTTCG 57.775 45.455 0.00 0.00 37.26 3.79
2111 3533 3.706698 GCCACTTTCAGTTTGGACTTTC 58.293 45.455 0.00 0.00 32.54 2.62
2238 3660 3.316071 TCACCTTTACGTCGGCAATAA 57.684 42.857 0.00 0.00 0.00 1.40
2250 3672 9.191479 TCATAAACCAAAAGAAGTTCACCTTTA 57.809 29.630 5.50 0.00 32.81 1.85
2310 3732 1.740025 GGCTTGCCATCTTCACAGTAC 59.260 52.381 6.79 0.00 0.00 2.73
2355 3783 1.732259 GCGACGCCCTTGATAATATGG 59.268 52.381 9.14 0.00 0.00 2.74
2376 3804 3.335579 GTGAAGGTAGAACAAGCCGAAT 58.664 45.455 0.00 0.00 0.00 3.34
2500 3928 0.246360 TCAGTGCCATGGTCGTACAG 59.754 55.000 14.67 5.28 0.00 2.74
2570 3998 4.619227 CCTTGCCCGTGTGGACGT 62.619 66.667 0.00 0.00 44.54 4.34
2574 4002 3.443045 GATGCCTTGCCCGTGTGG 61.443 66.667 0.00 0.00 37.09 4.17
2576 4004 3.965258 TGGATGCCTTGCCCGTGT 61.965 61.111 0.00 0.00 0.00 4.49
2593 4021 1.202639 TGCAAACATGTCCGTCAGAGT 60.203 47.619 0.00 0.00 0.00 3.24
2694 4122 1.409064 CAGCGCTCTATAACCCAGTCA 59.591 52.381 7.13 0.00 0.00 3.41
2736 4164 0.179124 GCAGTCTCGGATCCACAGTC 60.179 60.000 13.41 4.78 0.00 3.51
2739 4167 2.885113 CGCAGTCTCGGATCCACA 59.115 61.111 13.41 0.00 0.00 4.17
2808 4236 2.906354 CTAGTAAAAGGGTGCGAGCAT 58.094 47.619 0.00 0.00 0.00 3.79
2847 4275 1.824852 TCGAGGTACTGCATGACATGT 59.175 47.619 16.62 0.00 41.55 3.21
2850 4278 1.204704 CCTTCGAGGTACTGCATGACA 59.795 52.381 0.00 0.00 41.55 3.58
2904 4332 2.086869 GCCTGCATAGTGAAGCTGAAA 58.913 47.619 0.00 0.00 32.24 2.69
2964 4392 5.421212 AACTCGTCGATAACTGAGGATAC 57.579 43.478 0.00 0.00 34.73 2.24
3006 4434 4.125703 GCATGTGTTATCTTCCTCCTGAG 58.874 47.826 0.00 0.00 0.00 3.35
3024 4452 3.376859 ACACCAAACACCGTATATGCATG 59.623 43.478 10.16 0.00 0.00 4.06
3027 4455 5.744666 ATAACACCAAACACCGTATATGC 57.255 39.130 0.00 0.00 0.00 3.14
3042 4470 5.934625 ACATCTGAAGAGACACAATAACACC 59.065 40.000 0.00 0.00 0.00 4.16
3072 4501 6.985188 AATACGCAAGAAAGAAAGCAGATA 57.015 33.333 0.00 0.00 43.62 1.98
3077 4506 6.738649 CAGACTAAATACGCAAGAAAGAAAGC 59.261 38.462 0.00 0.00 43.62 3.51
3081 4510 6.032956 TCCAGACTAAATACGCAAGAAAGA 57.967 37.500 0.00 0.00 43.62 2.52
3133 4586 7.654022 ATCTTTGATATACTCCCTAGCTAGC 57.346 40.000 15.74 6.62 0.00 3.42
3171 4626 9.809096 CTGAACATAGACATACAGAGTAACATT 57.191 33.333 0.00 0.00 0.00 2.71
3237 4692 4.808414 TCAGACTGGAACCATGTAGAAG 57.192 45.455 1.81 0.00 0.00 2.85
3275 4915 8.402472 ACAGAAACTTCGTGTAAAATTCATGAA 58.598 29.630 11.26 11.26 38.13 2.57
3323 4963 2.544267 GTGAACCCTCGTTGTTTCTCAG 59.456 50.000 0.00 0.00 30.30 3.35
3338 4978 7.254455 CGATGTAATCCATTCAGTTAGTGAACC 60.254 40.741 4.46 0.00 43.83 3.62
3412 5052 3.447586 ACGCCACTGCCACCTATATATAG 59.552 47.826 12.18 12.18 0.00 1.31
3440 5080 3.265995 TCGCCCCTCCTAAGATTTCTTTT 59.734 43.478 0.00 0.00 37.40 2.27
3474 5114 1.564348 ACGATTTGGGGCAGTCCTAAT 59.436 47.619 0.00 0.00 35.84 1.73
3483 5123 0.661020 CAATCCGTACGATTTGGGGC 59.339 55.000 18.76 0.00 39.28 5.80
3506 5146 7.870954 ACAAGATCGACACTTGAAGTACAATTA 59.129 33.333 28.68 0.00 44.92 1.40
3517 5157 1.195448 GGTGCACAAGATCGACACTTG 59.805 52.381 20.43 23.59 46.69 3.16
3534 5174 8.586570 TTTGTAGAATTGCAAAGTTTATGGTG 57.413 30.769 1.71 0.00 34.57 4.17
3606 5246 5.765510 TGGCAATATCCACCTAATCAAAGT 58.234 37.500 0.00 0.00 0.00 2.66
3642 5282 4.900684 TGACGGATTGAATTCCAACACTA 58.099 39.130 2.27 0.00 37.63 2.74
3647 5287 7.065803 GTCTTATTCTGACGGATTGAATTCCAA 59.934 37.037 2.27 0.00 39.41 3.53
3661 5314 9.604626 CTCAAACAATTGAAGTCTTATTCTGAC 57.395 33.333 13.59 0.00 44.64 3.51
3817 5481 1.226974 GCTAGCGATGGTCAAGCGA 60.227 57.895 0.00 0.00 35.78 4.93
3819 5483 0.933796 GAAGCTAGCGATGGTCAAGC 59.066 55.000 9.55 0.00 0.00 4.01
3822 5487 1.320344 ACCGAAGCTAGCGATGGTCA 61.320 55.000 18.34 0.00 0.00 4.02
3823 5488 0.179108 AACCGAAGCTAGCGATGGTC 60.179 55.000 22.42 10.52 0.00 4.02
3844 5509 5.471456 AGGTCAGAGATTTTGCACTAAACAG 59.529 40.000 0.00 0.00 0.00 3.16
3846 5511 5.948992 AGGTCAGAGATTTTGCACTAAAC 57.051 39.130 0.00 0.00 0.00 2.01
3847 5512 7.882791 TGATTAGGTCAGAGATTTTGCACTAAA 59.117 33.333 0.00 0.00 31.80 1.85
3872 5560 3.047904 TAGGGGGTGGGGGATCCTG 62.048 68.421 12.58 0.00 36.20 3.86
3889 5577 4.948341 TCCCGCTGCATCTTAATTAGTA 57.052 40.909 0.00 0.00 0.00 1.82
3918 5606 6.328148 AGTCGGTAATTTTATCCAGTCCCATA 59.672 38.462 0.00 0.00 0.00 2.74
3923 5611 4.814771 CCCAGTCGGTAATTTTATCCAGTC 59.185 45.833 0.00 0.00 0.00 3.51
3957 5645 1.375098 GGTGAGCAGCAAGAGCATCC 61.375 60.000 0.00 0.00 45.49 3.51


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

AutoCloner maintained by Alex Coulton.