Multiple sequence alignment - TraesCS3B01G192900

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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 TraesCS3B01G192900 chr3B 100.000 4688 0 0 1 4688 207290755 207295442 0.000000e+00 8658.0
1 TraesCS3B01G192900 chr3B 83.690 1214 175 16 1032 2239 207733649 207734845 0.000000e+00 1123.0
2 TraesCS3B01G192900 chr3B 82.473 1221 182 23 1032 2239 205775397 205776598 0.000000e+00 1040.0
3 TraesCS3B01G192900 chr3B 95.896 536 15 2 2293 2828 475438300 475438828 0.000000e+00 861.0
4 TraesCS3B01G192900 chr3B 80.868 1129 171 31 1054 2152 85108148 85107035 0.000000e+00 846.0
5 TraesCS3B01G192900 chr3A 95.299 2191 39 24 630 2795 163792655 163794806 0.000000e+00 3417.0
6 TraesCS3B01G192900 chr3A 84.885 1257 90 40 2812 3980 163794787 163796031 0.000000e+00 1177.0
7 TraesCS3B01G192900 chr3A 84.466 1133 161 12 1032 2161 164610944 164612064 0.000000e+00 1103.0
8 TraesCS3B01G192900 chr3A 93.513 632 28 2 1 632 163791853 163792471 0.000000e+00 928.0
9 TraesCS3B01G192900 chr3D 94.906 1963 61 14 842 2795 143948461 143950393 0.000000e+00 3035.0
10 TraesCS3B01G192900 chr3D 83.402 1211 174 17 1035 2239 148700253 148699064 0.000000e+00 1098.0
11 TraesCS3B01G192900 chr3D 90.456 723 49 8 1 723 143947350 143948052 0.000000e+00 935.0
12 TraesCS3B01G192900 chr3D 80.990 1131 193 13 1035 2154 148336790 148335671 0.000000e+00 878.0
13 TraesCS3B01G192900 chr3D 81.012 1127 170 27 1054 2152 55084928 55083818 0.000000e+00 856.0
14 TraesCS3B01G192900 chr3D 80.851 1128 170 34 1054 2152 55742239 55743349 0.000000e+00 845.0
15 TraesCS3B01G192900 chr3D 89.356 404 38 1 1 399 107079085 107078682 1.950000e-138 503.0
16 TraesCS3B01G192900 chr3D 89.500 400 38 1 1 396 316822946 316823345 1.950000e-138 503.0
17 TraesCS3B01G192900 chr3D 84.432 546 33 15 3027 3529 143950631 143951167 1.520000e-134 490.0
18 TraesCS3B01G192900 chr3D 92.857 224 6 3 2812 3025 143950374 143950597 2.720000e-82 316.0
19 TraesCS3B01G192900 chr3D 84.615 78 5 3 741 818 143948410 143948480 2.340000e-08 71.3
20 TraesCS3B01G192900 chr2B 95.915 710 24 5 3981 4688 23302105 23301399 0.000000e+00 1146.0
21 TraesCS3B01G192900 chrUn 94.385 748 30 4 2190 2933 73950791 73950052 0.000000e+00 1138.0
22 TraesCS3B01G192900 chrUn 88.079 453 34 12 3095 3529 73949529 73949079 1.930000e-143 520.0
23 TraesCS3B01G192900 chrUn 80.412 291 34 14 401 669 73962181 73961892 2.860000e-47 200.0
24 TraesCS3B01G192900 chrUn 95.745 94 4 0 2932 3025 73949891 73949798 8.120000e-33 152.0
25 TraesCS3B01G192900 chrUn 85.437 103 6 4 716 818 73960377 73960284 1.070000e-16 99.0
26 TraesCS3B01G192900 chr1A 95.077 711 30 5 3981 4688 581257310 581258018 0.000000e+00 1114.0
27 TraesCS3B01G192900 chr1A 94.655 711 33 5 3981 4688 563582234 563581526 0.000000e+00 1098.0
28 TraesCS3B01G192900 chr1A 93.863 717 40 4 3975 4688 536240012 536240727 0.000000e+00 1077.0
29 TraesCS3B01G192900 chr1A 89.496 714 63 7 3985 4688 467235896 467236607 0.000000e+00 893.0
30 TraesCS3B01G192900 chr7D 92.697 712 45 5 3981 4687 33944214 33944923 0.000000e+00 1020.0
31 TraesCS3B01G192900 chr7D 92.416 712 47 5 3981 4687 33929312 33930021 0.000000e+00 1009.0
32 TraesCS3B01G192900 chr7D 87.317 410 47 1 1 405 170033795 170033386 9.190000e-127 464.0
33 TraesCS3B01G192900 chr4A 91.854 712 49 7 3981 4688 22718372 22719078 0.000000e+00 985.0
34 TraesCS3B01G192900 chr1D 89.430 719 62 11 3981 4688 3462005 3461290 0.000000e+00 894.0
35 TraesCS3B01G192900 chr1D 88.442 398 43 3 1 397 343188461 343188066 1.180000e-130 477.0
36 TraesCS3B01G192900 chr4B 96.828 536 9 1 2293 2828 507907879 507908406 0.000000e+00 889.0
37 TraesCS3B01G192900 chr2D 89.750 400 36 4 1 395 432128745 432129144 1.510000e-139 507.0
38 TraesCS3B01G192900 chr1B 88.972 399 39 1 1 394 374839425 374839823 5.450000e-134 488.0
39 TraesCS3B01G192900 chr1B 97.717 219 5 0 2581 2799 23740007 23739789 1.230000e-100 377.0
40 TraesCS3B01G192900 chr4D 88.206 407 40 2 2 403 338021804 338021401 3.280000e-131 479.0


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 TraesCS3B01G192900 chr3B 207290755 207295442 4687 False 8658.000000 8658 100.000000 1 4688 1 chr3B.!!$F2 4687
1 TraesCS3B01G192900 chr3B 207733649 207734845 1196 False 1123.000000 1123 83.690000 1032 2239 1 chr3B.!!$F3 1207
2 TraesCS3B01G192900 chr3B 205775397 205776598 1201 False 1040.000000 1040 82.473000 1032 2239 1 chr3B.!!$F1 1207
3 TraesCS3B01G192900 chr3B 475438300 475438828 528 False 861.000000 861 95.896000 2293 2828 1 chr3B.!!$F4 535
4 TraesCS3B01G192900 chr3B 85107035 85108148 1113 True 846.000000 846 80.868000 1054 2152 1 chr3B.!!$R1 1098
5 TraesCS3B01G192900 chr3A 163791853 163796031 4178 False 1840.666667 3417 91.232333 1 3980 3 chr3A.!!$F2 3979
6 TraesCS3B01G192900 chr3A 164610944 164612064 1120 False 1103.000000 1103 84.466000 1032 2161 1 chr3A.!!$F1 1129
7 TraesCS3B01G192900 chr3D 148699064 148700253 1189 True 1098.000000 1098 83.402000 1035 2239 1 chr3D.!!$R4 1204
8 TraesCS3B01G192900 chr3D 143947350 143951167 3817 False 969.460000 3035 89.453200 1 3529 5 chr3D.!!$F3 3528
9 TraesCS3B01G192900 chr3D 148335671 148336790 1119 True 878.000000 878 80.990000 1035 2154 1 chr3D.!!$R3 1119
10 TraesCS3B01G192900 chr3D 55083818 55084928 1110 True 856.000000 856 81.012000 1054 2152 1 chr3D.!!$R1 1098
11 TraesCS3B01G192900 chr3D 55742239 55743349 1110 False 845.000000 845 80.851000 1054 2152 1 chr3D.!!$F1 1098
12 TraesCS3B01G192900 chr2B 23301399 23302105 706 True 1146.000000 1146 95.915000 3981 4688 1 chr2B.!!$R1 707
13 TraesCS3B01G192900 chrUn 73949079 73950791 1712 True 603.333333 1138 92.736333 2190 3529 3 chrUn.!!$R1 1339
14 TraesCS3B01G192900 chr1A 581257310 581258018 708 False 1114.000000 1114 95.077000 3981 4688 1 chr1A.!!$F3 707
15 TraesCS3B01G192900 chr1A 563581526 563582234 708 True 1098.000000 1098 94.655000 3981 4688 1 chr1A.!!$R1 707
16 TraesCS3B01G192900 chr1A 536240012 536240727 715 False 1077.000000 1077 93.863000 3975 4688 1 chr1A.!!$F2 713
17 TraesCS3B01G192900 chr1A 467235896 467236607 711 False 893.000000 893 89.496000 3985 4688 1 chr1A.!!$F1 703
18 TraesCS3B01G192900 chr7D 33944214 33944923 709 False 1020.000000 1020 92.697000 3981 4687 1 chr7D.!!$F2 706
19 TraesCS3B01G192900 chr7D 33929312 33930021 709 False 1009.000000 1009 92.416000 3981 4687 1 chr7D.!!$F1 706
20 TraesCS3B01G192900 chr4A 22718372 22719078 706 False 985.000000 985 91.854000 3981 4688 1 chr4A.!!$F1 707
21 TraesCS3B01G192900 chr1D 3461290 3462005 715 True 894.000000 894 89.430000 3981 4688 1 chr1D.!!$R1 707
22 TraesCS3B01G192900 chr4B 507907879 507908406 527 False 889.000000 889 96.828000 2293 2828 1 chr4B.!!$F1 535

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
314 315 0.249489 GAGGTTCGTGCTATGCGGAT 60.249 55.000 0.00 0.0 0.0 4.18 F
558 559 0.332972 AAGGAGATGGCTTTGGACCC 59.667 55.000 0.00 0.0 0.0 4.46 F
940 1478 0.742505 GCCCCCTTAATAAACACGCC 59.257 55.000 0.00 0.0 0.0 5.68 F
941 1479 1.018910 CCCCCTTAATAAACACGCCG 58.981 55.000 0.00 0.0 0.0 6.46 F
1229 1791 1.157751 AACTTCCCCTCCGTCCTCA 59.842 57.895 0.00 0.0 0.0 3.86 F
1819 2384 2.256117 ACAAGAACCGTAGCAGCTTT 57.744 45.000 0.00 0.0 0.0 3.51 F
3250 4219 0.107081 TTGGAGAAGGAAAACGCGGA 59.893 50.000 12.47 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 2348 0.038067 TGTACATGTCCACGAACCGG 60.038 55.000 0.00 0.00 0.00 5.28 R
1819 2384 1.078637 GCTGATCTGTGCAGAGCCA 60.079 57.895 13.87 5.85 42.79 4.75 R
1917 2488 1.080501 CGAGTCGCCTTGAAGCTCA 60.081 57.895 0.00 0.00 0.00 4.26 R
2011 2582 1.299926 GTCGACGCTGAACAGGTGT 60.300 57.895 0.00 0.00 0.00 4.16 R
2907 3508 1.808945 GATGAAGGGCAACAGAGTGTG 59.191 52.381 0.00 0.00 39.74 3.82 R
3349 4319 0.328592 TCAGGTCACTCTAGCGGTCT 59.671 55.000 0.00 0.00 0.00 3.85 R
4635 5661 2.030540 TGCTTTTTCTGATGCTGACTGC 60.031 45.455 0.00 0.00 43.25 4.40 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
63 64 0.684805 GAGGGAAAGCTCGAGAGGGA 60.685 60.000 18.75 0.00 0.00 4.20
162 163 3.045492 GTCCCGCCGCTTTTTCGA 61.045 61.111 0.00 0.00 0.00 3.71
174 175 2.867429 CTTTTTCGAAGATGCGCCATT 58.133 42.857 4.18 0.00 35.04 3.16
219 220 4.322385 GCGCGGCGTTCACCTTTT 62.322 61.111 24.46 0.00 0.00 2.27
227 228 1.266718 GCGTTCACCTTTTCTGCATCA 59.733 47.619 0.00 0.00 0.00 3.07
238 239 0.967380 TCTGCATCACTCGAGCCTGA 60.967 55.000 13.61 10.43 0.00 3.86
314 315 0.249489 GAGGTTCGTGCTATGCGGAT 60.249 55.000 0.00 0.00 0.00 4.18
528 529 7.768582 AGATGTGATGGTCGTTATGAAATGTAA 59.231 33.333 0.00 0.00 0.00 2.41
529 530 7.302350 TGTGATGGTCGTTATGAAATGTAAG 57.698 36.000 0.00 0.00 0.00 2.34
530 531 7.100409 TGTGATGGTCGTTATGAAATGTAAGA 58.900 34.615 0.00 0.00 0.00 2.10
531 532 7.768582 TGTGATGGTCGTTATGAAATGTAAGAT 59.231 33.333 0.00 0.00 0.00 2.40
532 533 8.064222 GTGATGGTCGTTATGAAATGTAAGATG 58.936 37.037 0.00 0.00 0.00 2.90
533 534 7.984617 TGATGGTCGTTATGAAATGTAAGATGA 59.015 33.333 0.00 0.00 0.00 2.92
534 535 8.731275 ATGGTCGTTATGAAATGTAAGATGAA 57.269 30.769 0.00 0.00 0.00 2.57
535 536 8.554835 TGGTCGTTATGAAATGTAAGATGAAA 57.445 30.769 0.00 0.00 0.00 2.69
536 537 9.173021 TGGTCGTTATGAAATGTAAGATGAAAT 57.827 29.630 0.00 0.00 0.00 2.17
537 538 9.438291 GGTCGTTATGAAATGTAAGATGAAATG 57.562 33.333 0.00 0.00 0.00 2.32
538 539 9.988350 GTCGTTATGAAATGTAAGATGAAATGT 57.012 29.630 0.00 0.00 0.00 2.71
558 559 0.332972 AAGGAGATGGCTTTGGACCC 59.667 55.000 0.00 0.00 0.00 4.46
623 624 5.533112 AGATAAGATCCTCTGGTCTTTGGA 58.467 41.667 0.00 0.00 36.23 3.53
886 1421 3.285215 CGATCGGACCCGGATCGT 61.285 66.667 22.64 0.00 40.64 3.73
887 1422 2.842256 CGATCGGACCCGGATCGTT 61.842 63.158 22.64 0.00 40.64 3.85
888 1423 1.007618 GATCGGACCCGGATCGTTC 60.008 63.158 0.73 4.74 40.25 3.95
889 1424 2.417649 GATCGGACCCGGATCGTTCC 62.418 65.000 0.73 2.15 40.25 3.62
890 1425 3.454573 CGGACCCGGATCGTTCCA 61.455 66.667 0.73 0.00 42.74 3.53
891 1426 2.499685 GGACCCGGATCGTTCCAG 59.500 66.667 0.73 5.77 42.74 3.86
892 1427 2.056223 GGACCCGGATCGTTCCAGA 61.056 63.158 0.73 0.00 42.74 3.86
931 1469 1.037579 GCTTTGCTCGCCCCCTTAAT 61.038 55.000 0.00 0.00 0.00 1.40
932 1470 1.749286 GCTTTGCTCGCCCCCTTAATA 60.749 52.381 0.00 0.00 0.00 0.98
934 1472 2.810870 TTGCTCGCCCCCTTAATAAA 57.189 45.000 0.00 0.00 0.00 1.40
935 1473 2.047002 TGCTCGCCCCCTTAATAAAC 57.953 50.000 0.00 0.00 0.00 2.01
936 1474 1.282447 TGCTCGCCCCCTTAATAAACA 59.718 47.619 0.00 0.00 0.00 2.83
938 1476 1.937899 CTCGCCCCCTTAATAAACACG 59.062 52.381 0.00 0.00 0.00 4.49
940 1478 0.742505 GCCCCCTTAATAAACACGCC 59.257 55.000 0.00 0.00 0.00 5.68
941 1479 1.018910 CCCCCTTAATAAACACGCCG 58.981 55.000 0.00 0.00 0.00 6.46
1229 1791 1.157751 AACTTCCCCTCCGTCCTCA 59.842 57.895 0.00 0.00 0.00 3.86
1271 1836 3.965026 CTCCTCCACGCCTCCCAGA 62.965 68.421 0.00 0.00 0.00 3.86
1569 2134 4.867599 CGCCTACCCGCTTCCGTC 62.868 72.222 0.00 0.00 0.00 4.79
1570 2135 4.525949 GCCTACCCGCTTCCGTCC 62.526 72.222 0.00 0.00 0.00 4.79
1571 2136 3.846430 CCTACCCGCTTCCGTCCC 61.846 72.222 0.00 0.00 0.00 4.46
1572 2137 4.203076 CTACCCGCTTCCGTCCCG 62.203 72.222 0.00 0.00 0.00 5.14
1819 2384 2.256117 ACAAGAACCGTAGCAGCTTT 57.744 45.000 0.00 0.00 0.00 3.51
1917 2488 6.098982 ACCTTCTCGGAGATCTTTAATGATGT 59.901 38.462 8.81 4.76 33.89 3.06
2011 2582 3.181422 TGGTCTACTTCTTCCTGGACAGA 60.181 47.826 0.00 0.00 0.00 3.41
2188 2776 6.092807 GCCCTCTTTGTAGATTCTTGTTACTG 59.907 42.308 0.00 0.00 0.00 2.74
2502 3097 7.658525 TGTATCCACTAATTTTGCCAATGAT 57.341 32.000 0.00 0.00 0.00 2.45
2793 3394 9.469097 AACATCTGTAGTATAGTTCTCACTTCT 57.531 33.333 0.00 0.00 34.06 2.85
2794 3395 9.469097 ACATCTGTAGTATAGTTCTCACTTCTT 57.531 33.333 0.00 0.00 34.06 2.52
2878 3479 4.082274 TCACGTGCTATTTTTCATGCAG 57.918 40.909 11.67 0.00 36.03 4.41
2907 3508 9.237846 GCTTGAAGCCAGATTATATTTGTAAAC 57.762 33.333 5.74 0.00 34.48 2.01
3025 3788 3.744660 ACGAAGAGTTTGGCTTCTTCAT 58.255 40.909 12.92 0.00 39.60 2.57
3037 3832 6.869206 TGGCTTCTTCATAAACTACTAGGT 57.131 37.500 0.00 0.00 0.00 3.08
3052 3996 8.870075 AACTACTAGGTATTACCGTATTAGGG 57.130 38.462 7.21 0.83 44.90 3.53
3092 4036 2.785540 TATCTGAGTGCATGTGCCAA 57.214 45.000 2.07 0.00 41.18 4.52
3102 4066 0.167470 CATGTGCCAACTCAGCTTCG 59.833 55.000 0.00 0.00 0.00 3.79
3180 4149 8.883731 CCAATTCTGGCTACTATAAATTATCCG 58.116 37.037 0.00 0.00 35.39 4.18
3240 4209 0.811281 GGATGCCGTTTTGGAGAAGG 59.189 55.000 0.00 0.00 42.00 3.46
3248 4217 2.381589 GTTTTGGAGAAGGAAAACGCG 58.618 47.619 3.53 3.53 33.63 6.01
3250 4219 0.107081 TTGGAGAAGGAAAACGCGGA 59.893 50.000 12.47 0.00 0.00 5.54
3290 4260 1.596408 TGCCGCTGCATCTCAACTA 59.404 52.632 0.00 0.00 44.23 2.24
3308 4278 5.890334 CAACTAGCCAAACTGAAGTTGAAA 58.110 37.500 7.56 0.00 46.29 2.69
3384 4354 2.902486 ACCTGAGCTTGTTGAGATCTGA 59.098 45.455 0.00 0.00 40.83 3.27
3473 4468 4.683942 GCATGTTACCGGATACCACCTTTA 60.684 45.833 9.46 0.00 0.00 1.85
3517 4512 2.760634 TTTAGACCGAGCATCAGCAA 57.239 45.000 0.00 0.00 45.49 3.91
3537 4532 3.375782 AAGATGTCTTTGCTTTGGTGC 57.624 42.857 0.00 0.00 30.82 5.01
3565 4560 4.080413 TCACCACTAAGGCATCATGAATCA 60.080 41.667 0.00 0.00 43.14 2.57
3588 4583 6.212791 TCAGCTATTAGACCTAACCAAGTTGT 59.787 38.462 1.45 0.00 0.00 3.32
3602 4597 6.415798 ACCAAGTTGTTGCAAATGTTTAAC 57.584 33.333 0.00 0.58 31.64 2.01
3605 4600 5.351948 AGTTGTTGCAAATGTTTAACCCT 57.648 34.783 0.00 0.00 0.00 4.34
3642 4637 4.137116 TGTATTGGTGACCTGTATGCTC 57.863 45.455 2.11 0.00 0.00 4.26
3717 4724 4.202151 GCAAAGGAGGTTGACAAATGAAGT 60.202 41.667 0.00 0.00 0.00 3.01
3743 4750 1.602311 AGAACTGCAGCAACTCCTTG 58.398 50.000 15.27 0.00 0.00 3.61
3747 4754 1.311859 CTGCAGCAACTCCTTGTGAA 58.688 50.000 0.00 0.00 0.00 3.18
3763 4770 8.340618 TCCTTGTGAATTGAAATAAAGAGAGG 57.659 34.615 0.00 0.00 0.00 3.69
3815 4822 7.065803 GGAATTTCTCATTCCATTAGTCAACGA 59.934 37.037 8.47 0.00 45.21 3.85
3817 4824 4.433615 TCTCATTCCATTAGTCAACGAGC 58.566 43.478 0.00 0.00 0.00 5.03
3824 4831 0.315886 TTAGTCAACGAGCCGAGCAA 59.684 50.000 1.50 0.00 0.00 3.91
3836 4843 2.523507 CGAGCAAGATCGCTGGCAG 61.524 63.158 10.94 10.94 43.92 4.85
3871 4883 2.202837 GACGACACCCGGCCATAC 60.203 66.667 2.24 0.00 41.44 2.39
3896 4908 1.686800 GGGTGCATGCCCCATCTTT 60.687 57.895 29.22 0.00 42.89 2.52
3906 4918 1.064017 GCCCCATCTTTGACCCATACA 60.064 52.381 0.00 0.00 0.00 2.29
3907 4919 2.424812 GCCCCATCTTTGACCCATACAT 60.425 50.000 0.00 0.00 0.00 2.29
3931 4943 3.436015 GCTAGAGCGTCTCCGACATTATA 59.564 47.826 0.00 0.00 35.63 0.98
3939 4951 3.069729 GTCTCCGACATTATAACAGGCCT 59.930 47.826 0.00 0.00 32.09 5.19
3959 4971 4.436332 CCTGAGGGCAATCTTTAATTTGC 58.564 43.478 8.86 8.86 45.82 3.68
3972 4984 4.718940 TTAATTTGCAAAGGGCTAGAGC 57.281 40.909 18.19 0.00 45.15 4.09
3985 4997 4.969359 AGGGCTAGAGCTTTAGGATGTAAA 59.031 41.667 12.84 0.00 41.70 2.01
4007 5019 2.270352 TTGATCTGGTGGAAGCGTTT 57.730 45.000 0.00 0.00 36.92 3.60
4054 5067 8.660373 GTTGTGTTTATTTATGAGAGACAGGAG 58.340 37.037 0.00 0.00 0.00 3.69
4118 5135 2.305928 ACATCGATGAGGAGACAGAGG 58.694 52.381 31.33 0.47 0.00 3.69
4162 5183 8.696374 CAGATAGAGGGTTTAGATTACAACAGA 58.304 37.037 0.00 0.00 0.00 3.41
4163 5184 9.268282 AGATAGAGGGTTTAGATTACAACAGAA 57.732 33.333 0.00 0.00 0.00 3.02
4238 5261 8.469309 AAATTTCTCTTGAACTCCTCAAATGA 57.531 30.769 0.00 0.00 43.54 2.57
4288 5311 4.794311 TCTGCCAATTGATCCTTGGATA 57.206 40.909 22.13 12.13 44.95 2.59
4314 5338 9.892130 AGAATGAACCGTATCTCTAATTTCTTT 57.108 29.630 0.00 0.00 0.00 2.52
4382 5406 1.337167 GGTTCTGGCATGGAAAACTGC 60.337 52.381 0.00 0.00 37.66 4.40
4635 5661 2.099756 TCTGTCATCACTACATCCTGCG 59.900 50.000 0.00 0.00 0.00 5.18
4668 5694 3.725740 CAGAAAAAGCACTAACAAGCGTG 59.274 43.478 0.00 0.00 35.48 5.34
4671 5697 1.512926 AAGCACTAACAAGCGTGGAG 58.487 50.000 4.26 3.50 35.48 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 1.789576 AACTCCCGCCACCATTTCCT 61.790 55.000 0.00 0.00 0.00 3.36
102 103 3.314357 CGATTCGGTCGCCCTATATATCA 59.686 47.826 0.00 0.00 44.33 2.15
218 219 0.108472 CAGGCTCGAGTGATGCAGAA 60.108 55.000 15.13 0.00 0.00 3.02
219 220 0.967380 TCAGGCTCGAGTGATGCAGA 60.967 55.000 15.13 0.00 0.00 4.26
264 265 3.878667 GCCTGGCCCGCTAGGAAT 61.879 66.667 22.01 0.00 46.11 3.01
314 315 5.764487 TGATGCATGTGTTTACTGTTTGA 57.236 34.783 2.46 0.00 0.00 2.69
528 529 5.643421 AGCCATCTCCTTACATTTCATCT 57.357 39.130 0.00 0.00 0.00 2.90
529 530 6.460676 CCAAAGCCATCTCCTTACATTTCATC 60.461 42.308 0.00 0.00 0.00 2.92
530 531 5.361857 CCAAAGCCATCTCCTTACATTTCAT 59.638 40.000 0.00 0.00 0.00 2.57
531 532 4.706476 CCAAAGCCATCTCCTTACATTTCA 59.294 41.667 0.00 0.00 0.00 2.69
532 533 4.949856 TCCAAAGCCATCTCCTTACATTTC 59.050 41.667 0.00 0.00 0.00 2.17
533 534 4.706962 GTCCAAAGCCATCTCCTTACATTT 59.293 41.667 0.00 0.00 0.00 2.32
534 535 4.273318 GTCCAAAGCCATCTCCTTACATT 58.727 43.478 0.00 0.00 0.00 2.71
535 536 3.372025 GGTCCAAAGCCATCTCCTTACAT 60.372 47.826 0.00 0.00 0.00 2.29
536 537 2.026262 GGTCCAAAGCCATCTCCTTACA 60.026 50.000 0.00 0.00 0.00 2.41
537 538 2.644676 GGTCCAAAGCCATCTCCTTAC 58.355 52.381 0.00 0.00 0.00 2.34
538 539 1.564348 GGGTCCAAAGCCATCTCCTTA 59.436 52.381 0.00 0.00 42.92 2.69
539 540 0.332972 GGGTCCAAAGCCATCTCCTT 59.667 55.000 0.00 0.00 42.92 3.36
558 559 1.133025 GTTTGAATGTGATCCCGGCAG 59.867 52.381 0.00 0.00 0.00 4.85
623 624 9.190317 GGAAATAAAGTCAGGGATTAACTCATT 57.810 33.333 0.00 0.00 0.00 2.57
842 1377 2.656646 TGACGCAATCAGTCGGCT 59.343 55.556 0.00 0.00 41.24 5.52
885 1420 1.084370 CGGAATGGCTCGTCTGGAAC 61.084 60.000 0.00 0.00 0.00 3.62
886 1421 1.218047 CGGAATGGCTCGTCTGGAA 59.782 57.895 0.00 0.00 0.00 3.53
887 1422 2.892640 CGGAATGGCTCGTCTGGA 59.107 61.111 0.00 0.00 0.00 3.86
888 1423 2.892425 GCGGAATGGCTCGTCTGG 60.892 66.667 0.00 0.00 0.00 3.86
889 1424 2.185350 AGCGGAATGGCTCGTCTG 59.815 61.111 0.00 0.00 39.61 3.51
931 1469 0.518195 GCTTAAAGGCGGCGTGTTTA 59.482 50.000 9.37 10.06 0.00 2.01
932 1470 1.284715 GCTTAAAGGCGGCGTGTTT 59.715 52.632 9.37 11.11 0.00 2.83
934 1472 3.053896 GGCTTAAAGGCGGCGTGT 61.054 61.111 9.37 0.00 0.00 4.49
935 1473 2.332654 AAGGCTTAAAGGCGGCGTG 61.333 57.895 9.37 0.00 46.58 5.34
936 1474 2.033602 AAGGCTTAAAGGCGGCGT 59.966 55.556 9.37 0.00 46.58 5.68
938 1476 0.817654 AATCAAGGCTTAAAGGCGGC 59.182 50.000 0.00 0.00 46.58 6.53
940 1478 3.848272 TTCAATCAAGGCTTAAAGGCG 57.152 42.857 0.00 0.00 46.58 5.52
941 1479 4.021104 AGGTTTCAATCAAGGCTTAAAGGC 60.021 41.667 0.00 0.00 41.73 4.35
1024 1562 1.220169 CCATCTCGGCTCTGAATGCG 61.220 60.000 0.00 0.00 0.00 4.73
1774 2339 4.699522 ACGAACCGGAGCTTGCCC 62.700 66.667 9.46 0.00 0.00 5.36
1783 2348 0.038067 TGTACATGTCCACGAACCGG 60.038 55.000 0.00 0.00 0.00 5.28
1819 2384 1.078637 GCTGATCTGTGCAGAGCCA 60.079 57.895 13.87 5.85 42.79 4.75
1917 2488 1.080501 CGAGTCGCCTTGAAGCTCA 60.081 57.895 0.00 0.00 0.00 4.26
1960 2531 2.281345 CTGGGATGGATGAGCGCC 60.281 66.667 2.29 0.00 0.00 6.53
2011 2582 1.299926 GTCGACGCTGAACAGGTGT 60.300 57.895 0.00 0.00 0.00 4.16
2188 2776 4.278419 ACCATTTCCAGTCACTAAACAAGC 59.722 41.667 0.00 0.00 0.00 4.01
2285 2880 9.753674 TCTCTCCCACAACTTAATAATCAAATT 57.246 29.630 0.00 0.00 0.00 1.82
2290 2885 6.768381 CCCTTCTCTCCCACAACTTAATAATC 59.232 42.308 0.00 0.00 0.00 1.75
2878 3479 7.260603 ACAAATATAATCTGGCTTCAAGCAAC 58.739 34.615 12.53 0.00 44.75 4.17
2907 3508 1.808945 GATGAAGGGCAACAGAGTGTG 59.191 52.381 0.00 0.00 39.74 3.82
3000 3763 4.067972 AGAAGCCAAACTCTTCGTAACA 57.932 40.909 0.00 0.00 43.40 2.41
3092 4036 5.386958 TGTTACACTAATCGAAGCTGAGT 57.613 39.130 0.00 0.00 0.00 3.41
3102 4066 7.550906 AGCATCTCCTCTTTTGTTACACTAATC 59.449 37.037 0.00 0.00 0.00 1.75
3171 4138 7.390718 GCATAAGGATAACAGGACGGATAATTT 59.609 37.037 0.00 0.00 0.00 1.82
3180 4149 2.143925 GCCGCATAAGGATAACAGGAC 58.856 52.381 0.00 0.00 0.00 3.85
3191 4160 4.457810 CAAATAGATTGACGCCGCATAAG 58.542 43.478 0.00 0.00 41.85 1.73
3240 4209 2.981400 TGATTTCCTTCCGCGTTTTC 57.019 45.000 4.92 0.00 0.00 2.29
3248 4217 6.254281 TCAACGATTTCTTGATTTCCTTCC 57.746 37.500 0.00 0.00 0.00 3.46
3250 4219 6.095377 GCATCAACGATTTCTTGATTTCCTT 58.905 36.000 0.00 0.00 36.42 3.36
3290 4260 3.004734 CCGATTTCAACTTCAGTTTGGCT 59.995 43.478 0.00 0.00 35.83 4.75
3349 4319 0.328592 TCAGGTCACTCTAGCGGTCT 59.671 55.000 0.00 0.00 0.00 3.85
3350 4320 0.736053 CTCAGGTCACTCTAGCGGTC 59.264 60.000 0.00 0.00 0.00 4.79
3351 4321 1.316706 GCTCAGGTCACTCTAGCGGT 61.317 60.000 0.00 0.00 0.00 5.68
3352 4322 1.034838 AGCTCAGGTCACTCTAGCGG 61.035 60.000 0.00 0.00 37.67 5.52
3353 4323 0.814457 AAGCTCAGGTCACTCTAGCG 59.186 55.000 0.00 0.00 37.67 4.26
3354 4324 1.548269 ACAAGCTCAGGTCACTCTAGC 59.452 52.381 0.00 0.00 34.47 3.42
3355 4325 3.256879 TCAACAAGCTCAGGTCACTCTAG 59.743 47.826 0.00 0.00 0.00 2.43
3356 4326 3.230976 TCAACAAGCTCAGGTCACTCTA 58.769 45.455 0.00 0.00 0.00 2.43
3414 4408 6.398234 CTCTCTAGCAAAGCCTACAAGATA 57.602 41.667 0.00 0.00 0.00 1.98
3473 4468 6.380079 AAGATCAACAAGTTCAGGGATACT 57.620 37.500 0.00 0.00 0.00 2.12
3517 4512 2.694628 TGCACCAAAGCAAAGACATCTT 59.305 40.909 0.00 0.00 42.46 2.40
3537 4532 5.999600 TCATGATGCCTTAGTGGTGATTATG 59.000 40.000 0.00 0.00 38.35 1.90
3565 4560 6.622427 ACAACTTGGTTAGGTCTAATAGCT 57.378 37.500 0.00 0.00 39.81 3.32
3622 4617 3.467803 GGAGCATACAGGTCACCAATAC 58.532 50.000 0.00 0.00 46.51 1.89
3671 4666 5.687828 CAGAGCTCACTCAATTTTCACTTC 58.312 41.667 17.77 0.00 46.09 3.01
3717 4724 0.532640 TTGCTGCAGTTCTTCGCTCA 60.533 50.000 16.64 0.00 0.00 4.26
3783 4790 4.402616 TGGAATGAGAAATTCCCAGGTT 57.597 40.909 13.22 0.00 45.27 3.50
3785 4792 6.131961 ACTAATGGAATGAGAAATTCCCAGG 58.868 40.000 13.22 5.29 45.27 4.45
3793 4800 5.351465 GCTCGTTGACTAATGGAATGAGAAA 59.649 40.000 0.00 0.00 35.56 2.52
3804 4811 0.530744 TGCTCGGCTCGTTGACTAAT 59.469 50.000 0.00 0.00 0.00 1.73
3808 4815 0.737715 ATCTTGCTCGGCTCGTTGAC 60.738 55.000 0.00 0.00 0.00 3.18
3815 4822 2.202851 CAGCGATCTTGCTCGGCT 60.203 61.111 0.00 0.00 45.23 5.52
3817 4824 3.267860 GCCAGCGATCTTGCTCGG 61.268 66.667 0.00 0.00 45.23 4.63
3824 4831 1.023513 GTCTTTGCTGCCAGCGATCT 61.024 55.000 12.80 0.00 46.26 2.75
3836 4843 2.278330 CCCTTGCCCAGGTCTTTGC 61.278 63.158 0.00 0.00 42.02 3.68
3896 4908 1.613925 GCTCTAGCGATGTATGGGTCA 59.386 52.381 0.00 0.00 0.00 4.02
3949 4961 5.105063 GCTCTAGCCCTTTGCAAATTAAAG 58.895 41.667 13.23 7.26 44.83 1.85
3954 4966 2.521547 AGCTCTAGCCCTTTGCAAAT 57.478 45.000 13.23 0.00 44.83 2.32
3959 4971 3.914426 TCCTAAAGCTCTAGCCCTTTG 57.086 47.619 14.14 7.20 43.38 2.77
3964 4976 6.163135 TCTTTACATCCTAAAGCTCTAGCC 57.837 41.667 0.00 0.00 43.38 3.93
3972 4984 8.834465 CACCAGATCAATCTTTACATCCTAAAG 58.166 37.037 0.00 0.00 34.22 1.85
3985 4997 1.556911 ACGCTTCCACCAGATCAATCT 59.443 47.619 0.00 0.00 37.72 2.40
4118 5135 6.932400 TCTATCTGAACTTCTCTCGTATCCTC 59.068 42.308 0.00 0.00 0.00 3.71
4162 5183 8.803235 GGAGGGTGTTAGAATTCTGTTTAAATT 58.197 33.333 18.47 0.00 0.00 1.82
4163 5184 7.396339 GGGAGGGTGTTAGAATTCTGTTTAAAT 59.604 37.037 18.47 0.00 0.00 1.40
4288 5311 9.892130 AAAGAAATTAGAGATACGGTTCATTCT 57.108 29.630 0.00 0.00 0.00 2.40
4314 5338 4.316205 TGTACGAGAAAGAGTTGCTGAA 57.684 40.909 0.00 0.00 0.00 3.02
4382 5406 5.694006 GGTGCTACTTATCTGTCTGCTAATG 59.306 44.000 0.00 0.00 0.00 1.90
4635 5661 2.030540 TGCTTTTTCTGATGCTGACTGC 60.031 45.455 0.00 0.00 43.25 4.40


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

AutoCloner maintained by Alex Coulton.