Multiple sequence alignment - TraesCS1D01G190400

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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 TraesCS1D01G190400 chr1D 100.000 4101 0 0 1 4101 262328612 262324512 0.000000e+00 7574.0
1 TraesCS1D01G190400 chr1D 96.597 911 26 1 2158 3063 459888818 459889728 0.000000e+00 1506.0
2 TraesCS1D01G190400 chr1D 89.706 1088 77 17 848 1926 459886675 459887736 0.000000e+00 1356.0
3 TraesCS1D01G190400 chr1D 89.567 786 58 10 3059 3834 459889843 459890614 0.000000e+00 976.0
4 TraesCS1D01G190400 chr1D 99.708 343 1 0 1 343 424678722 424679064 2.690000e-176 628.0
5 TraesCS1D01G190400 chr1D 99.417 343 2 0 1 343 275897838 275898180 1.250000e-174 623.0
6 TraesCS1D01G190400 chr1D 99.706 340 1 0 4 343 310888829 310888490 1.250000e-174 623.0
7 TraesCS1D01G190400 chr1D 99.417 343 2 0 1 343 365557746 365558088 1.250000e-174 623.0
8 TraesCS1D01G190400 chr1D 84.142 536 45 23 3273 3805 460144714 460145212 2.220000e-132 483.0
9 TraesCS1D01G190400 chr1D 95.582 249 11 0 3853 4101 82537576 82537824 2.300000e-107 399.0
10 TraesCS1D01G190400 chr1D 95.219 251 10 1 3853 4101 275168018 275168268 2.970000e-106 396.0
11 TraesCS1D01G190400 chr1D 94.841 252 10 2 3853 4101 46470414 46470665 1.380000e-104 390.0
12 TraesCS1D01G190400 chr1D 91.416 233 17 2 1919 2151 459887954 459888183 2.380000e-82 316.0
13 TraesCS1D01G190400 chr1D 95.276 127 5 1 712 837 154801052 154800926 2.500000e-47 200.0
14 TraesCS1D01G190400 chr1D 95.276 127 5 1 712 837 477843076 477843202 2.500000e-47 200.0
15 TraesCS1D01G190400 chr1D 94.531 128 5 2 712 837 442388516 442388643 3.230000e-46 196.0
16 TraesCS1D01G190400 chr2D 97.991 3385 53 10 728 4101 581824750 581828130 0.000000e+00 5860.0
17 TraesCS1D01G190400 chr2D 79.625 427 41 30 1224 1637 374343083 374342690 8.740000e-67 265.0
18 TraesCS1D01G190400 chr2D 94.615 130 4 2 711 837 42432326 42432197 8.990000e-47 198.0
19 TraesCS1D01G190400 chr2D 86.486 74 8 2 2985 3057 129924400 129924328 3.400000e-11 80.5
20 TraesCS1D01G190400 chr2D 87.324 71 7 2 2985 3054 370005001 370005070 3.400000e-11 80.5
21 TraesCS1D01G190400 chr1A 90.694 1268 86 15 898 2151 551601685 551602934 0.000000e+00 1659.0
22 TraesCS1D01G190400 chr1A 96.378 911 28 1 2158 3063 551603563 551604473 0.000000e+00 1495.0
23 TraesCS1D01G190400 chr1A 86.794 939 88 19 914 1841 379646397 379647310 0.000000e+00 1014.0
24 TraesCS1D01G190400 chr1A 88.619 782 65 14 3059 3831 551604588 551605354 0.000000e+00 929.0
25 TraesCS1D01G190400 chr1B 95.609 911 26 2 2158 3063 632000227 632001128 0.000000e+00 1448.0
26 TraesCS1D01G190400 chr1B 87.981 1065 73 34 862 1900 631998119 631999154 0.000000e+00 1206.0
27 TraesCS1D01G190400 chr1B 85.442 893 75 19 2200 3045 632021331 632022215 0.000000e+00 878.0
28 TraesCS1D01G190400 chr1B 89.034 611 39 12 3205 3807 632001495 632002085 0.000000e+00 732.0
29 TraesCS1D01G190400 chr1B 93.617 235 13 1 1919 2151 631999359 631999593 2.350000e-92 350.0
30 TraesCS1D01G190400 chr1B 85.756 344 28 10 3273 3616 632011514 632011836 1.090000e-90 344.0
31 TraesCS1D01G190400 chr1B 90.476 147 12 2 3059 3204 632001243 632001388 4.180000e-45 193.0
32 TraesCS1D01G190400 chr1B 86.719 128 12 4 3621 3748 632011891 632012013 1.990000e-28 137.0
33 TraesCS1D01G190400 chr5A 87.440 621 69 9 4 621 516730409 516729795 0.000000e+00 706.0
34 TraesCS1D01G190400 chr5A 87.857 140 14 2 1224 1362 557662636 557662773 1.180000e-35 161.0
35 TraesCS1D01G190400 chr5A 95.918 49 2 0 954 1002 609688604 609688652 3.400000e-11 80.5
36 TraesCS1D01G190400 chr5D 99.708 343 1 0 1 343 179586430 179586772 2.690000e-176 628.0
37 TraesCS1D01G190400 chr5D 95.618 251 9 2 3853 4101 282226077 282226327 6.390000e-108 401.0
38 TraesCS1D01G190400 chr5D 87.324 71 7 2 2985 3054 259634120 259634189 3.400000e-11 80.5
39 TraesCS1D01G190400 chr3D 99.708 343 1 0 1 343 396163882 396163540 2.690000e-176 628.0
40 TraesCS1D01G190400 chr3D 94.242 330 14 4 344 671 498649214 498648888 2.200000e-137 499.0
41 TraesCS1D01G190400 chr3D 94.495 327 11 5 343 667 147003042 147002721 7.920000e-137 497.0
42 TraesCS1D01G190400 chr3D 96.000 250 9 1 3853 4101 597704561 597704312 4.940000e-109 405.0
43 TraesCS1D01G190400 chr3D 95.276 127 5 1 712 837 385702607 385702481 2.500000e-47 200.0
44 TraesCS1D01G190400 chr3D 86.486 74 8 2 2985 3057 119268041 119267969 3.400000e-11 80.5
45 TraesCS1D01G190400 chr3D 87.324 71 7 2 2985 3054 133676204 133676273 3.400000e-11 80.5
46 TraesCS1D01G190400 chr4D 99.417 343 2 0 1 343 138269382 138269040 1.250000e-174 623.0
47 TraesCS1D01G190400 chr4D 99.706 340 1 0 4 343 220911738 220911399 1.250000e-174 623.0
48 TraesCS1D01G190400 chr4D 94.260 331 13 5 343 671 411367679 411368005 6.120000e-138 501.0
49 TraesCS1D01G190400 chr4D 93.921 329 15 3 344 671 493192024 493191700 3.680000e-135 492.0
50 TraesCS1D01G190400 chr4D 94.172 326 12 6 344 669 485735803 485735485 1.320000e-134 490.0
51 TraesCS1D01G190400 chr4D 95.618 251 9 2 3853 4101 131746436 131746686 6.390000e-108 401.0
52 TraesCS1D01G190400 chr4D 95.200 250 11 1 3853 4101 500904069 500903820 1.070000e-105 394.0
53 TraesCS1D01G190400 chr7D 94.545 330 13 4 343 671 239701955 239701630 4.730000e-139 505.0
54 TraesCS1D01G190400 chr7D 93.939 330 17 3 344 671 565032959 565032631 2.850000e-136 496.0
55 TraesCS1D01G190400 chr7D 96.400 250 7 2 3853 4101 242115716 242115468 1.060000e-110 411.0
56 TraesCS1D01G190400 chr7D 96.386 249 9 0 3853 4101 562559273 562559025 1.060000e-110 411.0
57 TraesCS1D01G190400 chr7D 96.000 250 9 1 3853 4101 103974521 103974272 4.940000e-109 405.0
58 TraesCS1D01G190400 chr7D 96.000 250 9 1 3853 4101 519061200 519061449 4.940000e-109 405.0
59 TraesCS1D01G190400 chr7D 95.385 130 6 0 708 837 213342370 213342499 1.490000e-49 207.0
60 TraesCS1D01G190400 chr7D 86.486 74 8 2 2985 3057 55627850 55627778 3.400000e-11 80.5
61 TraesCS1D01G190400 chr6D 94.529 329 15 3 344 671 425516645 425516971 4.730000e-139 505.0
62 TraesCS1D01G190400 chr6D 96.000 250 9 1 3853 4101 19768636 19768885 4.940000e-109 405.0
63 TraesCS1D01G190400 chr6D 95.600 250 10 1 3853 4101 40660653 40660404 2.300000e-107 399.0
64 TraesCS1D01G190400 chr6D 95.600 250 10 1 3853 4101 313406968 313406719 2.300000e-107 399.0
65 TraesCS1D01G190400 chr6D 95.582 249 11 0 3853 4101 443668783 443668535 2.300000e-107 399.0
66 TraesCS1D01G190400 chr6D 94.821 251 8 3 3853 4101 46403522 46403769 1.790000e-103 387.0
67 TraesCS1D01G190400 chr6D 94.422 251 12 2 3853 4101 250861196 250860946 6.430000e-103 385.0
68 TraesCS1D01G190400 chr6D 94.422 251 12 2 3853 4101 384350135 384350385 6.430000e-103 385.0
69 TraesCS1D01G190400 chr6D 94.531 128 5 2 712 837 27776495 27776622 3.230000e-46 196.0
70 TraesCS1D01G190400 chr6D 94.531 128 5 2 712 837 242939730 242939857 3.230000e-46 196.0
71 TraesCS1D01G190400 chr6D 85.093 161 12 6 1224 1383 234472725 234472874 1.970000e-33 154.0
72 TraesCS1D01G190400 chrUn 94.821 251 11 2 3853 4101 114642026 114642276 1.380000e-104 390.0
73 TraesCS1D01G190400 chrUn 94.000 250 14 1 3853 4101 90683856 90683607 1.080000e-100 377.0
74 TraesCS1D01G190400 chrUn 94.000 250 14 1 3853 4101 102178324 102178075 1.080000e-100 377.0
75 TraesCS1D01G190400 chrUn 92.063 252 17 2 3853 4101 95377575 95377826 6.520000e-93 351.0
76 TraesCS1D01G190400 chrUn 93.333 240 12 4 3853 4089 105356013 105356251 6.520000e-93 351.0
77 TraesCS1D01G190400 chrUn 93.966 232 11 3 3853 4083 69183286 69183057 8.440000e-92 348.0
78 TraesCS1D01G190400 chrUn 95.392 217 8 2 3886 4101 89267473 89267688 1.090000e-90 344.0
79 TraesCS1D01G190400 chrUn 91.600 250 20 1 3853 4101 305484567 305484816 1.090000e-90 344.0
80 TraesCS1D01G190400 chrUn 91.235 251 20 2 3853 4101 69938125 69938375 1.410000e-89 340.0
81 TraesCS1D01G190400 chrUn 91.304 253 16 6 3853 4101 104978459 104978209 1.410000e-89 340.0
82 TraesCS1D01G190400 chr4A 90.062 161 13 2 1224 1383 22639062 22639220 5.370000e-49 206.0
83 TraesCS1D01G190400 chr4A 89.167 120 11 2 1247 1365 517573271 517573153 9.180000e-32 148.0
84 TraesCS1D01G190400 chr3A 77.123 424 54 29 1224 1637 734197332 734196942 5.370000e-49 206.0
85 TraesCS1D01G190400 chr5B 88.415 164 16 2 1221 1383 4574508 4574669 1.160000e-45 195.0
86 TraesCS1D01G190400 chr5B 93.478 46 3 0 957 1002 593360996 593361041 7.360000e-08 69.4
87 TraesCS1D01G190400 chr7A 90.833 120 10 1 1247 1365 187795767 187795648 4.240000e-35 159.0
88 TraesCS1D01G190400 chr4B 95.918 49 2 0 954 1002 564753044 564752996 3.400000e-11 80.5
89 TraesCS1D01G190400 chr4B 95.652 46 2 0 957 1002 652315143 652315188 1.580000e-09 75.0


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 TraesCS1D01G190400 chr1D 262324512 262328612 4100 True 7574.0 7574 100.0000 1 4101 1 chr1D.!!$R2 4100
1 TraesCS1D01G190400 chr1D 459886675 459890614 3939 False 1038.5 1506 91.8215 848 3834 4 chr1D.!!$F10 2986
2 TraesCS1D01G190400 chr2D 581824750 581828130 3380 False 5860.0 5860 97.9910 728 4101 1 chr2D.!!$F2 3373
3 TraesCS1D01G190400 chr1A 551601685 551605354 3669 False 1361.0 1659 91.8970 898 3831 3 chr1A.!!$F2 2933
4 TraesCS1D01G190400 chr1A 379646397 379647310 913 False 1014.0 1014 86.7940 914 1841 1 chr1A.!!$F1 927
5 TraesCS1D01G190400 chr1B 632021331 632022215 884 False 878.0 878 85.4420 2200 3045 1 chr1B.!!$F1 845
6 TraesCS1D01G190400 chr1B 631998119 632002085 3966 False 785.8 1448 91.3434 862 3807 5 chr1B.!!$F2 2945
7 TraesCS1D01G190400 chr5A 516729795 516730409 614 True 706.0 706 87.4400 4 621 1 chr5A.!!$R1 617

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
499 501 0.459585 CACGGTGCGCCACTAGTAAT 60.460 55.0 18.18 0.0 34.4 1.89 F
1235 1247 0.249238 GCGGCGATCTGAATCTGACT 60.249 55.0 12.98 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2281 5.472137 TGGTACTGAAATGCTAAGTTGAACC 59.528 40.000 0.00 0.0 0.0 3.62 R
3169 4247 3.827008 AGATCTTTCATTCAGCGGCTA 57.173 42.857 0.26 0.0 0.0 3.93 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 7.051000 AGAAAGATCAATCTAGTAGGCCAAAC 58.949 38.462 5.01 2.07 35.76 2.93
69 70 4.929146 ATCTAGTAGGCCAAACCAAACT 57.071 40.909 5.01 0.00 43.14 2.66
97 98 7.672983 AATTCGAAGAGACTTGCAAAGATAA 57.327 32.000 3.35 0.00 43.32 1.75
99 100 5.408604 TTCGAAGAGACTTGCAAAGATAACC 59.591 40.000 0.00 0.00 43.32 2.85
195 196 1.068474 GGATCTCGACAAACACACCG 58.932 55.000 0.00 0.00 0.00 4.94
201 202 1.199327 TCGACAAACACACCGCAAAAA 59.801 42.857 0.00 0.00 0.00 1.94
202 203 1.581602 CGACAAACACACCGCAAAAAG 59.418 47.619 0.00 0.00 0.00 2.27
204 205 2.851824 GACAAACACACCGCAAAAAGAG 59.148 45.455 0.00 0.00 0.00 2.85
229 231 8.356657 AGTTACATCGAATAGATCTCCAAGAAG 58.643 37.037 0.00 0.00 37.52 2.85
254 256 6.531503 TCGAGGAGAACTTTGTATTGAGAT 57.468 37.500 0.00 0.00 0.00 2.75
255 257 6.565234 TCGAGGAGAACTTTGTATTGAGATC 58.435 40.000 0.00 0.00 0.00 2.75
257 259 6.627087 AGGAGAACTTTGTATTGAGATCCA 57.373 37.500 0.00 0.00 0.00 3.41
269 271 8.316497 TGTATTGAGATCCAAAGAGAGAGAAT 57.684 34.615 1.49 0.00 38.43 2.40
298 300 6.405953 CCATCTAGCTAATAACTATGGACCCG 60.406 46.154 0.00 0.00 0.00 5.28
321 323 4.868314 AGGTCTGTGGTAAACTACTCAC 57.132 45.455 0.00 0.00 33.39 3.51
322 324 4.220724 AGGTCTGTGGTAAACTACTCACA 58.779 43.478 0.00 0.00 37.45 3.58
324 326 4.202182 GGTCTGTGGTAAACTACTCACACA 60.202 45.833 0.00 0.00 36.02 3.72
338 340 0.463204 CACACATCATCGGAGAGGCT 59.537 55.000 0.00 0.00 43.63 4.58
370 372 8.011290 ACTACTAGGAAAAGGGCTATAGATGAA 58.989 37.037 3.21 0.00 0.00 2.57
384 386 6.881065 GCTATAGATGAAATGGCCACTAATGA 59.119 38.462 8.16 0.00 0.00 2.57
385 387 7.065563 GCTATAGATGAAATGGCCACTAATGAG 59.934 40.741 8.16 4.70 0.00 2.90
392 394 2.785868 GCCACTAATGAGGCACCAG 58.214 57.895 0.00 0.00 46.92 4.00
419 421 2.230508 TGGTGCGCCACTACTATATAGC 59.769 50.000 16.89 0.00 40.46 2.97
421 423 3.502920 GTGCGCCACTACTATATAGCAG 58.497 50.000 4.18 8.96 33.84 4.24
454 456 1.796151 CTGGTGCGCCATTAGTGTG 59.204 57.895 21.54 1.70 45.05 3.82
455 457 0.673333 CTGGTGCGCCATTAGTGTGA 60.673 55.000 21.54 0.00 45.05 3.58
458 460 1.135689 GGTGCGCCATTAGTGTGAAAG 60.136 52.381 12.58 0.00 34.09 2.62
459 461 1.804151 GTGCGCCATTAGTGTGAAAGA 59.196 47.619 4.18 0.00 0.00 2.52
460 462 1.804151 TGCGCCATTAGTGTGAAAGAC 59.196 47.619 4.18 0.00 0.00 3.01
499 501 0.459585 CACGGTGCGCCACTAGTAAT 60.460 55.000 18.18 0.00 34.40 1.89
500 502 0.459585 ACGGTGCGCCACTAGTAATG 60.460 55.000 18.18 0.00 34.40 1.90
506 508 4.142469 GGTGCGCCACTAGTAATGAATTTT 60.142 41.667 12.58 0.00 34.40 1.82
542 544 5.378292 TTTTCAAACATACTAATGGCGCA 57.622 34.783 10.83 0.00 37.43 6.09
543 545 4.349663 TTCAAACATACTAATGGCGCAC 57.650 40.909 10.83 0.00 37.43 5.34
544 546 2.680841 TCAAACATACTAATGGCGCACC 59.319 45.455 10.83 0.00 37.43 5.01
556 558 4.935495 CGCACCAGGGCACAGTGT 62.935 66.667 10.45 0.00 33.96 3.55
557 559 3.289834 GCACCAGGGCACAGTGTG 61.290 66.667 19.27 19.27 36.51 3.82
570 572 4.928661 CACAGTGTGCCATTACTAGTTC 57.071 45.455 10.97 0.00 0.00 3.01
571 573 4.569943 CACAGTGTGCCATTACTAGTTCT 58.430 43.478 10.97 0.00 0.00 3.01
572 574 5.720202 CACAGTGTGCCATTACTAGTTCTA 58.280 41.667 10.97 0.00 0.00 2.10
573 575 6.163476 CACAGTGTGCCATTACTAGTTCTAA 58.837 40.000 10.97 0.00 0.00 2.10
574 576 6.090898 CACAGTGTGCCATTACTAGTTCTAAC 59.909 42.308 10.97 0.00 0.00 2.34
575 577 6.014499 ACAGTGTGCCATTACTAGTTCTAACT 60.014 38.462 0.00 0.39 42.91 2.24
576 578 7.177921 ACAGTGTGCCATTACTAGTTCTAACTA 59.822 37.037 0.00 2.76 40.37 2.24
587 589 4.730949 AGTTCTAACTAGTAATGGCGCA 57.269 40.909 10.83 0.00 37.52 6.09
588 590 4.430908 AGTTCTAACTAGTAATGGCGCAC 58.569 43.478 10.83 0.00 37.52 5.34
589 591 3.447918 TCTAACTAGTAATGGCGCACC 57.552 47.619 10.83 0.00 0.00 5.01
590 592 7.078031 AGTTCTAACTAGTAATGGCGCACCA 62.078 44.000 10.83 0.00 44.04 4.17
591 593 8.781050 AGTTCTAACTAGTAATGGCGCACCAG 62.781 46.154 10.83 0.00 43.47 4.00
600 602 2.187946 GCGCACCAGCCTCATAGT 59.812 61.111 0.30 0.00 37.52 2.12
601 603 2.176273 GCGCACCAGCCTCATAGTG 61.176 63.158 0.30 0.00 37.52 2.74
603 605 2.176273 GCACCAGCCTCATAGTGCG 61.176 63.158 0.00 0.00 45.28 5.34
604 606 2.176273 CACCAGCCTCATAGTGCGC 61.176 63.158 0.00 0.00 0.00 6.09
605 607 2.590007 CCAGCCTCATAGTGCGCC 60.590 66.667 4.18 0.00 0.00 6.53
606 608 2.187685 CAGCCTCATAGTGCGCCA 59.812 61.111 4.18 0.00 0.00 5.69
607 609 2.176273 CAGCCTCATAGTGCGCCAC 61.176 63.158 4.18 3.02 34.10 5.01
676 678 2.330231 CACCATTAGTGTTTGCGGTG 57.670 50.000 0.00 0.00 41.93 4.94
677 679 1.606668 CACCATTAGTGTTTGCGGTGT 59.393 47.619 0.00 0.00 41.93 4.16
678 680 1.606668 ACCATTAGTGTTTGCGGTGTG 59.393 47.619 0.00 0.00 0.00 3.82
679 681 1.665735 CCATTAGTGTTTGCGGTGTGC 60.666 52.381 0.00 0.00 46.70 4.57
680 682 0.596082 ATTAGTGTTTGCGGTGTGCC 59.404 50.000 0.00 0.00 45.60 5.01
681 683 1.448922 TTAGTGTTTGCGGTGTGCCC 61.449 55.000 0.00 0.00 45.60 5.36
682 684 2.332312 TAGTGTTTGCGGTGTGCCCT 62.332 55.000 0.00 0.00 45.60 5.19
683 685 3.215568 TGTTTGCGGTGTGCCCTG 61.216 61.111 0.00 0.00 45.60 4.45
684 686 2.904866 GTTTGCGGTGTGCCCTGA 60.905 61.111 0.00 0.00 45.60 3.86
685 687 2.115052 TTTGCGGTGTGCCCTGAT 59.885 55.556 0.00 0.00 45.60 2.90
686 688 2.267351 TTTGCGGTGTGCCCTGATG 61.267 57.895 0.00 0.00 45.60 3.07
692 694 4.429522 TGTGCCCTGATGCGCCAT 62.430 61.111 4.18 0.00 41.01 4.40
693 695 3.142838 GTGCCCTGATGCGCCATT 61.143 61.111 4.18 0.00 35.74 3.16
694 696 1.823470 GTGCCCTGATGCGCCATTA 60.823 57.895 4.18 0.00 35.74 1.90
695 697 1.526686 TGCCCTGATGCGCCATTAG 60.527 57.895 4.18 4.82 0.00 1.73
696 698 1.526917 GCCCTGATGCGCCATTAGT 60.527 57.895 4.18 0.00 0.00 2.24
697 699 1.789078 GCCCTGATGCGCCATTAGTG 61.789 60.000 4.18 0.00 0.00 2.74
698 700 0.464373 CCCTGATGCGCCATTAGTGT 60.464 55.000 4.18 0.00 0.00 3.55
699 701 1.202639 CCCTGATGCGCCATTAGTGTA 60.203 52.381 4.18 0.00 0.00 2.90
700 702 2.550855 CCCTGATGCGCCATTAGTGTAT 60.551 50.000 4.18 0.00 33.58 2.29
701 703 2.481568 CCTGATGCGCCATTAGTGTATG 59.518 50.000 4.18 0.00 30.74 2.39
702 704 2.481568 CTGATGCGCCATTAGTGTATGG 59.518 50.000 4.18 0.00 46.46 2.74
709 711 1.599071 CCATTAGTGTATGGCGCACTG 59.401 52.381 10.83 0.00 45.59 3.66
710 712 2.549926 CATTAGTGTATGGCGCACTGA 58.450 47.619 10.83 0.00 45.59 3.41
711 713 2.979814 TTAGTGTATGGCGCACTGAT 57.020 45.000 10.83 0.00 45.59 2.90
712 714 2.223537 TAGTGTATGGCGCACTGATG 57.776 50.000 10.83 0.00 45.59 3.07
713 715 6.595237 CATTAGTGTATGGCGCACTGATGC 62.595 50.000 19.74 0.00 46.32 3.91
722 724 2.397751 GCACTGATGCGCCATTAGT 58.602 52.632 4.18 8.14 43.33 2.24
724 726 1.372582 CACTGATGCGCCATTAGTGT 58.627 50.000 23.77 7.33 46.41 3.55
725 727 1.739466 CACTGATGCGCCATTAGTGTT 59.261 47.619 23.77 3.49 46.41 3.32
726 728 2.162208 CACTGATGCGCCATTAGTGTTT 59.838 45.455 23.77 3.24 46.41 2.83
733 735 5.539582 TGCGCCATTAGTGTTTAAACTAG 57.460 39.130 18.72 0.00 34.24 2.57
744 746 5.084055 GTGTTTAAACTAGTAATGGCGCAC 58.916 41.667 18.72 0.00 0.00 5.34
745 747 4.998672 TGTTTAAACTAGTAATGGCGCACT 59.001 37.500 18.72 6.53 0.00 4.40
746 748 5.106869 TGTTTAAACTAGTAATGGCGCACTG 60.107 40.000 18.72 1.89 0.00 3.66
747 749 2.762535 AACTAGTAATGGCGCACTGT 57.237 45.000 10.83 2.52 0.00 3.55
749 751 0.652592 CTAGTAATGGCGCACTGTGC 59.347 55.000 22.38 22.38 40.69 4.57
766 768 1.526917 GCCCTGATGCGCCATTAGT 60.527 57.895 4.18 0.00 0.00 2.24
767 769 1.789078 GCCCTGATGCGCCATTAGTG 61.789 60.000 4.18 0.00 0.00 2.74
768 770 0.464373 CCCTGATGCGCCATTAGTGT 60.464 55.000 4.18 0.00 0.00 3.55
826 828 1.211949 AGGTGCGCCATTAGTAACCAT 59.788 47.619 20.59 0.00 37.19 3.55
877 879 0.547712 CCTCCTCCCTTTCCCAGTCA 60.548 60.000 0.00 0.00 0.00 3.41
1235 1247 0.249238 GCGGCGATCTGAATCTGACT 60.249 55.000 12.98 0.00 0.00 3.41
2522 3438 4.330944 TTTCTCTTACCACGACACACAT 57.669 40.909 0.00 0.00 0.00 3.21
2578 3494 9.104713 AGGGGACTGAAGAATCAAATAAATTTT 57.895 29.630 0.00 0.00 41.13 1.82
2760 3691 3.144506 CTGGCAACTCTGAAGAACATGT 58.855 45.455 0.00 0.00 37.61 3.21
3071 4145 7.583625 TCACTCTTCTCCCTGTATCATACTTA 58.416 38.462 0.00 0.00 0.00 2.24
3169 4247 6.721318 TCATTAACTAGCCTGAATTTGGACT 58.279 36.000 3.03 2.90 0.00 3.85
3462 4648 7.277174 TCGTCTCATCTGTGTAATATCATGT 57.723 36.000 0.00 0.00 0.00 3.21
3543 4729 4.694509 GCCTGATGGATGTCTGATTGTATC 59.305 45.833 0.00 0.00 34.57 2.24
3931 5128 1.676006 GCGCCATTAGTATGCCAAAGT 59.324 47.619 0.00 0.00 0.00 2.66
3949 5146 5.412594 CCAAAGTATACTAATGGCGCATCAT 59.587 40.000 19.30 0.46 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.082081 TGCTTAGCTTTGGGTTCAATCATG 60.082 41.667 5.60 0.00 32.28 3.07
1 2 4.082026 GTGCTTAGCTTTGGGTTCAATCAT 60.082 41.667 5.60 0.00 32.28 2.45
2 3 3.255642 GTGCTTAGCTTTGGGTTCAATCA 59.744 43.478 5.60 0.00 32.28 2.57
9 10 2.553247 GGAGAAGTGCTTAGCTTTGGGT 60.553 50.000 5.60 0.00 0.00 4.51
20 21 1.074405 TCTTGCAATGGGAGAAGTGCT 59.926 47.619 0.00 0.00 37.87 4.40
63 64 7.459486 CAAGTCTCTTCGAATTATCAGTTTGG 58.541 38.462 0.00 0.00 0.00 3.28
69 70 6.873605 TCTTTGCAAGTCTCTTCGAATTATCA 59.126 34.615 0.00 0.00 0.00 2.15
155 156 5.445069 TCCGATGAATTGTGGGTTTATGAT 58.555 37.500 0.00 0.00 0.00 2.45
184 185 2.230266 ACTCTTTTTGCGGTGTGTTTGT 59.770 40.909 0.00 0.00 0.00 2.83
195 196 8.821894 AGATCTATTCGATGTAACTCTTTTTGC 58.178 33.333 0.00 0.00 30.84 3.68
201 202 7.721842 TCTTGGAGATCTATTCGATGTAACTCT 59.278 37.037 0.00 0.00 30.84 3.24
202 203 7.877003 TCTTGGAGATCTATTCGATGTAACTC 58.123 38.462 0.00 0.00 30.84 3.01
204 205 8.353684 TCTTCTTGGAGATCTATTCGATGTAAC 58.646 37.037 0.00 0.00 30.84 2.50
222 224 4.464069 AAGTTCTCCTCGATCTTCTTGG 57.536 45.455 0.00 0.00 27.88 3.61
229 231 6.565234 TCTCAATACAAAGTTCTCCTCGATC 58.435 40.000 0.00 0.00 0.00 3.69
254 256 5.664908 AGATGGCTTATTCTCTCTCTTTGGA 59.335 40.000 0.00 0.00 0.00 3.53
255 257 5.927819 AGATGGCTTATTCTCTCTCTTTGG 58.072 41.667 0.00 0.00 0.00 3.28
257 259 6.554605 AGCTAGATGGCTTATTCTCTCTCTTT 59.445 38.462 0.00 0.00 39.86 2.52
269 271 8.750298 GTCCATAGTTATTAGCTAGATGGCTTA 58.250 37.037 0.00 0.00 42.97 3.09
298 300 5.221382 TGTGAGTAGTTTACCACAGACCTTC 60.221 44.000 0.00 0.00 36.02 3.46
321 323 2.353505 CCATAGCCTCTCCGATGATGTG 60.354 54.545 0.00 0.00 0.00 3.21
322 324 1.898472 CCATAGCCTCTCCGATGATGT 59.102 52.381 0.00 0.00 0.00 3.06
324 326 0.901124 GCCATAGCCTCTCCGATGAT 59.099 55.000 0.00 0.00 0.00 2.45
338 340 3.135895 GCCCTTTTCCTAGTAGTGCCATA 59.864 47.826 0.00 0.00 0.00 2.74
384 386 3.580084 ACCACATGTCTGGTGCCT 58.420 55.556 7.18 0.00 43.38 4.75
408 410 3.502920 GTGCGCCACTGCTATATAGTAG 58.497 50.000 22.10 22.10 41.13 2.57
411 413 1.000843 TGGTGCGCCACTGCTATATAG 59.999 52.381 16.89 5.30 40.46 1.31
454 456 1.130561 GGTGCGCCATTAGTGTCTTTC 59.869 52.381 12.58 0.00 34.09 2.62
455 457 1.165270 GGTGCGCCATTAGTGTCTTT 58.835 50.000 12.58 0.00 34.09 2.52
458 460 0.391130 TCTGGTGCGCCATTAGTGTC 60.391 55.000 21.54 0.00 45.05 3.67
459 461 0.673644 GTCTGGTGCGCCATTAGTGT 60.674 55.000 21.54 0.00 45.05 3.55
460 462 0.673333 TGTCTGGTGCGCCATTAGTG 60.673 55.000 21.54 7.89 45.05 2.74
476 478 3.851845 TAGTGGCGCACCGTGTGTC 62.852 63.158 10.83 9.79 39.70 3.67
478 480 2.480853 TACTAGTGGCGCACCGTGTG 62.481 60.000 10.83 7.76 39.70 3.82
479 481 1.808531 TTACTAGTGGCGCACCGTGT 61.809 55.000 10.83 4.70 39.70 4.49
481 483 0.459585 CATTACTAGTGGCGCACCGT 60.460 55.000 10.83 8.47 39.70 4.83
519 521 5.631512 GTGCGCCATTAGTATGTTTGAAAAA 59.368 36.000 4.18 0.00 0.00 1.94
520 522 5.157781 GTGCGCCATTAGTATGTTTGAAAA 58.842 37.500 4.18 0.00 0.00 2.29
521 523 4.380023 GGTGCGCCATTAGTATGTTTGAAA 60.380 41.667 12.58 0.00 34.09 2.69
522 524 3.127895 GGTGCGCCATTAGTATGTTTGAA 59.872 43.478 12.58 0.00 34.09 2.69
523 525 2.680841 GGTGCGCCATTAGTATGTTTGA 59.319 45.455 12.58 0.00 34.09 2.69
524 526 2.421775 TGGTGCGCCATTAGTATGTTTG 59.578 45.455 16.89 0.00 40.46 2.93
525 527 2.682856 CTGGTGCGCCATTAGTATGTTT 59.317 45.455 21.54 0.00 45.05 2.83
526 528 2.288666 CTGGTGCGCCATTAGTATGTT 58.711 47.619 21.54 0.00 45.05 2.71
527 529 1.475034 CCTGGTGCGCCATTAGTATGT 60.475 52.381 21.54 0.00 45.05 2.29
528 530 1.229428 CCTGGTGCGCCATTAGTATG 58.771 55.000 21.54 5.92 45.05 2.39
529 531 0.108585 CCCTGGTGCGCCATTAGTAT 59.891 55.000 21.54 0.00 45.05 2.12
530 532 1.524961 CCCTGGTGCGCCATTAGTA 59.475 57.895 21.54 0.00 45.05 1.82
531 533 2.272146 CCCTGGTGCGCCATTAGT 59.728 61.111 21.54 0.00 45.05 2.24
532 534 3.211963 GCCCTGGTGCGCCATTAG 61.212 66.667 21.54 12.51 45.05 1.73
533 535 4.040426 TGCCCTGGTGCGCCATTA 62.040 61.111 21.54 3.56 45.05 1.90
539 541 4.935495 ACACTGTGCCCTGGTGCG 62.935 66.667 7.90 0.00 34.70 5.34
540 542 3.289834 CACACTGTGCCCTGGTGC 61.290 66.667 7.90 0.00 34.70 5.01
549 551 8.005007 AGTTAGAACTAGTAATGGCACACTGTG 61.005 40.741 12.56 6.19 38.49 3.66
550 552 6.014499 AGTTAGAACTAGTAATGGCACACTGT 60.014 38.462 12.56 6.96 38.49 3.55
551 553 6.398918 AGTTAGAACTAGTAATGGCACACTG 58.601 40.000 12.56 6.46 38.49 3.66
552 554 6.607004 AGTTAGAACTAGTAATGGCACACT 57.393 37.500 8.47 8.47 38.49 3.55
564 566 7.224000 GGTGCGCCATTACTAGTTAGAACTAG 61.224 46.154 22.30 22.30 46.85 2.57
565 567 5.450965 GGTGCGCCATTACTAGTTAGAACTA 60.451 44.000 12.58 2.30 36.21 2.24
566 568 4.430908 GTGCGCCATTACTAGTTAGAACT 58.569 43.478 4.18 0.00 42.91 3.01
567 569 3.554731 GGTGCGCCATTACTAGTTAGAAC 59.445 47.826 12.58 0.00 34.09 3.01
568 570 3.196039 TGGTGCGCCATTACTAGTTAGAA 59.804 43.478 16.89 0.00 40.46 2.10
569 571 2.761767 TGGTGCGCCATTACTAGTTAGA 59.238 45.455 16.89 0.00 40.46 2.10
570 572 3.123804 CTGGTGCGCCATTACTAGTTAG 58.876 50.000 21.54 0.00 45.05 2.34
571 573 2.740580 GCTGGTGCGCCATTACTAGTTA 60.741 50.000 21.54 0.00 45.05 2.24
572 574 2.012051 GCTGGTGCGCCATTACTAGTT 61.012 52.381 21.54 0.00 45.05 2.24
573 575 0.462047 GCTGGTGCGCCATTACTAGT 60.462 55.000 21.54 0.00 45.05 2.57
574 576 2.311294 GCTGGTGCGCCATTACTAG 58.689 57.895 21.54 8.11 45.05 2.57
575 577 4.532490 GCTGGTGCGCCATTACTA 57.468 55.556 21.54 0.00 45.05 1.82
583 585 2.176273 CACTATGAGGCTGGTGCGC 61.176 63.158 0.00 0.00 40.82 6.09
584 586 2.176273 GCACTATGAGGCTGGTGCG 61.176 63.158 13.02 0.00 43.91 5.34
585 587 3.819188 GCACTATGAGGCTGGTGC 58.181 61.111 13.02 13.02 45.93 5.01
586 588 2.176273 GCGCACTATGAGGCTGGTG 61.176 63.158 0.30 0.00 0.00 4.17
587 589 2.187946 GCGCACTATGAGGCTGGT 59.812 61.111 0.30 0.00 0.00 4.00
588 590 2.590007 GGCGCACTATGAGGCTGG 60.590 66.667 10.83 0.00 39.50 4.85
589 591 2.176273 GTGGCGCACTATGAGGCTG 61.176 63.158 10.83 0.00 42.83 4.85
590 592 1.043116 TAGTGGCGCACTATGAGGCT 61.043 55.000 10.83 0.00 43.46 4.58
591 593 0.876342 GTAGTGGCGCACTATGAGGC 60.876 60.000 18.30 0.00 46.56 4.70
592 594 0.747255 AGTAGTGGCGCACTATGAGG 59.253 55.000 18.30 0.00 46.56 3.86
593 595 3.924918 ATAGTAGTGGCGCACTATGAG 57.075 47.619 15.13 0.00 46.56 2.90
594 596 4.665833 AAATAGTAGTGGCGCACTATGA 57.334 40.909 16.23 10.75 46.56 2.15
595 597 5.734855 AAAAATAGTAGTGGCGCACTATG 57.265 39.130 16.23 0.00 46.56 2.23
624 626 2.515912 GTGCGCCATTACTAGTTTTGC 58.484 47.619 4.18 0.00 0.00 3.68
648 650 0.523072 CACTAATGGTGCACTGTGCC 59.477 55.000 28.17 19.06 44.23 5.01
658 660 1.606668 CACACCGCAAACACTAATGGT 59.393 47.619 0.00 0.00 0.00 3.55
659 661 1.665735 GCACACCGCAAACACTAATGG 60.666 52.381 0.00 0.00 41.79 3.16
660 662 1.665735 GGCACACCGCAAACACTAATG 60.666 52.381 0.00 0.00 45.17 1.90
661 663 0.596082 GGCACACCGCAAACACTAAT 59.404 50.000 0.00 0.00 45.17 1.73
662 664 1.448922 GGGCACACCGCAAACACTAA 61.449 55.000 0.00 0.00 45.17 2.24
663 665 1.894756 GGGCACACCGCAAACACTA 60.895 57.895 0.00 0.00 45.17 2.74
664 666 3.216292 GGGCACACCGCAAACACT 61.216 61.111 0.00 0.00 45.17 3.55
665 667 3.216292 AGGGCACACCGCAAACAC 61.216 61.111 0.00 0.00 46.96 3.32
666 668 2.974692 ATCAGGGCACACCGCAAACA 62.975 55.000 0.00 0.00 46.96 2.83
667 669 2.268076 ATCAGGGCACACCGCAAAC 61.268 57.895 0.00 0.00 46.96 2.93
668 670 2.115052 ATCAGGGCACACCGCAAA 59.885 55.556 0.00 0.00 46.96 3.68
669 671 2.672651 CATCAGGGCACACCGCAA 60.673 61.111 0.00 0.00 46.96 4.85
679 681 0.464373 ACACTAATGGCGCATCAGGG 60.464 55.000 10.83 3.77 0.00 4.45
680 682 2.238942 TACACTAATGGCGCATCAGG 57.761 50.000 10.83 0.00 0.00 3.86
681 683 2.481568 CCATACACTAATGGCGCATCAG 59.518 50.000 10.83 2.55 40.07 2.90
682 684 2.493035 CCATACACTAATGGCGCATCA 58.507 47.619 10.83 0.00 40.07 3.07
689 691 1.599071 CAGTGCGCCATACACTAATGG 59.401 52.381 4.18 0.00 46.44 3.16
690 692 2.549926 TCAGTGCGCCATACACTAATG 58.450 47.619 4.18 0.00 46.44 1.90
691 693 2.979814 TCAGTGCGCCATACACTAAT 57.020 45.000 4.18 0.00 46.44 1.73
692 694 2.549926 CATCAGTGCGCCATACACTAA 58.450 47.619 4.18 0.00 46.44 2.24
693 695 1.806247 GCATCAGTGCGCCATACACTA 60.806 52.381 4.18 0.00 46.44 2.74
695 697 1.353103 GCATCAGTGCGCCATACAC 59.647 57.895 4.18 0.00 42.28 2.90
696 698 3.812203 GCATCAGTGCGCCATACA 58.188 55.556 4.18 0.00 42.28 2.29
705 707 1.372582 ACACTAATGGCGCATCAGTG 58.627 50.000 21.62 21.62 41.83 3.66
706 708 2.113860 AACACTAATGGCGCATCAGT 57.886 45.000 10.83 3.28 0.00 3.41
707 709 4.614555 TTAAACACTAATGGCGCATCAG 57.385 40.909 10.83 2.55 0.00 2.90
708 710 4.457603 AGTTTAAACACTAATGGCGCATCA 59.542 37.500 20.06 0.00 0.00 3.07
709 711 4.981794 AGTTTAAACACTAATGGCGCATC 58.018 39.130 20.06 0.00 0.00 3.91
710 712 5.646360 ACTAGTTTAAACACTAATGGCGCAT 59.354 36.000 20.06 0.00 0.00 4.73
711 713 4.998672 ACTAGTTTAAACACTAATGGCGCA 59.001 37.500 20.06 0.00 0.00 6.09
712 714 5.541098 ACTAGTTTAAACACTAATGGCGC 57.459 39.130 20.06 0.00 0.00 6.53
713 715 8.120465 CCATTACTAGTTTAAACACTAATGGCG 58.880 37.037 27.66 16.85 36.39 5.69
714 716 7.913821 GCCATTACTAGTTTAAACACTAATGGC 59.086 37.037 35.66 35.66 46.39 4.40
715 717 8.120465 CGCCATTACTAGTTTAAACACTAATGG 58.880 37.037 30.53 30.53 40.48 3.16
716 718 7.638683 GCGCCATTACTAGTTTAAACACTAATG 59.361 37.037 20.06 21.08 0.00 1.90
717 719 7.334921 TGCGCCATTACTAGTTTAAACACTAAT 59.665 33.333 20.06 13.12 0.00 1.73
718 720 6.649973 TGCGCCATTACTAGTTTAAACACTAA 59.350 34.615 20.06 11.63 0.00 2.24
719 721 6.091169 GTGCGCCATTACTAGTTTAAACACTA 59.909 38.462 20.06 4.14 0.00 2.74
720 722 4.998672 TGCGCCATTACTAGTTTAAACACT 59.001 37.500 20.06 3.08 0.00 3.55
721 723 5.084055 GTGCGCCATTACTAGTTTAAACAC 58.916 41.667 20.06 1.55 0.00 3.32
722 724 4.998672 AGTGCGCCATTACTAGTTTAAACA 59.001 37.500 20.06 5.82 0.00 2.83
723 725 5.106830 ACAGTGCGCCATTACTAGTTTAAAC 60.107 40.000 10.47 10.47 0.00 2.01
724 726 4.998672 ACAGTGCGCCATTACTAGTTTAAA 59.001 37.500 4.18 0.00 0.00 1.52
725 727 4.390603 CACAGTGCGCCATTACTAGTTTAA 59.609 41.667 4.18 0.00 0.00 1.52
726 728 3.930229 CACAGTGCGCCATTACTAGTTTA 59.070 43.478 4.18 0.00 0.00 2.01
749 751 0.464373 ACACTAATGGCGCATCAGGG 60.464 55.000 10.83 3.77 0.00 4.45
751 753 3.492421 AAAACACTAATGGCGCATCAG 57.508 42.857 10.83 2.55 0.00 2.90
752 754 3.932545 AAAAACACTAATGGCGCATCA 57.067 38.095 10.83 0.00 0.00 3.07
826 828 9.184523 CCTTCCACATTTTCATATTAGTAACCA 57.815 33.333 0.00 0.00 0.00 3.67
858 860 0.547712 TGACTGGGAAAGGGAGGAGG 60.548 60.000 0.00 0.00 0.00 4.30
877 879 0.547954 GGGGGAGGAGGACAGAACTT 60.548 60.000 0.00 0.00 0.00 2.66
2005 2281 5.472137 TGGTACTGAAATGCTAAGTTGAACC 59.528 40.000 0.00 0.00 0.00 3.62
2578 3494 4.827284 TCTACGCATCTCATATTCCTGACA 59.173 41.667 0.00 0.00 0.00 3.58
2760 3691 4.318332 GCAACCTCATTCATATCCGATGA 58.682 43.478 0.00 0.00 0.00 2.92
3071 4145 4.957296 CTTGTAAAGGTAGGCGGTGATAT 58.043 43.478 0.00 0.00 41.27 1.63
3134 4210 4.572795 GGCTAGTTAATGAAGTGAAGGAGC 59.427 45.833 0.00 0.00 0.00 4.70
3169 4247 3.827008 AGATCTTTCATTCAGCGGCTA 57.173 42.857 0.26 0.00 0.00 3.93
3873 5068 7.842982 TGCGCCATTAGTATGTATATTAGGAA 58.157 34.615 4.18 0.00 0.00 3.36
3874 5069 7.412853 TGCGCCATTAGTATGTATATTAGGA 57.587 36.000 4.18 0.00 0.00 2.94
3931 5128 3.430236 CGGGATGATGCGCCATTAGTATA 60.430 47.826 4.18 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.