Multiple sequence alignment - TraesCS3D01G470100

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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 TraesCS3D01G470100 chr3D 100.000 5940 0 0 1 5940 571996686 571990747 0.000000e+00 10970.0
1 TraesCS3D01G470100 chr3D 77.645 671 133 14 5271 5934 90262411 90261751 5.580000e-105 392.0
2 TraesCS3D01G470100 chr3D 82.262 389 47 12 4663 5049 573072880 573073248 3.460000e-82 316.0
3 TraesCS3D01G470100 chr3D 90.476 42 3 1 164 204 604863730 604863771 3.000000e-03 54.7
4 TraesCS3D01G470100 chr3B 91.718 5313 323 54 648 5917 762026028 762031266 0.000000e+00 7265.0
5 TraesCS3D01G470100 chr3B 83.333 432 51 15 4630 5054 762099953 762100370 4.340000e-101 379.0
6 TraesCS3D01G470100 chr3A 93.741 4649 220 44 659 5267 707082175 707086792 0.000000e+00 6907.0
7 TraesCS3D01G470100 chr3A 82.093 430 58 14 4630 5054 707093624 707094039 3.410000e-92 350.0
8 TraesCS3D01G470100 chr3A 87.552 241 8 6 7 225 571406008 571406248 5.910000e-65 259.0
9 TraesCS3D01G470100 chr5D 98.602 644 9 0 1 644 329260340 329259697 0.000000e+00 1140.0
10 TraesCS3D01G470100 chr1A 83.844 588 87 6 5351 5931 107468654 107469240 2.420000e-153 553.0
11 TraesCS3D01G470100 chr1A 93.333 90 6 0 518 607 164463128 164463217 3.730000e-27 134.0
12 TraesCS3D01G470100 chr1A 78.912 147 22 5 3749 3892 521258792 521258932 2.280000e-14 91.6
13 TraesCS3D01G470100 chr1B 82.765 586 94 7 5350 5931 161986948 161987530 3.170000e-142 516.0
14 TraesCS3D01G470100 chr1B 79.592 147 21 5 3749 3892 575711709 575711849 4.900000e-16 97.1
15 TraesCS3D01G470100 chr4B 78.293 668 142 3 5266 5931 622007149 622006483 1.530000e-115 427.0
16 TraesCS3D01G470100 chr4B 79.457 589 109 12 5349 5931 645310462 645311044 1.990000e-109 407.0
17 TraesCS3D01G470100 chr7D 78.434 677 128 15 5268 5934 227297064 227296396 5.500000e-115 425.0
18 TraesCS3D01G470100 chr7D 94.615 130 7 0 518 647 620312129 620312000 1.010000e-47 202.0
19 TraesCS3D01G470100 chr7D 97.727 88 2 0 558 645 488127607 488127694 1.030000e-32 152.0
20 TraesCS3D01G470100 chr5A 95.817 263 11 0 255 517 541940255 541939993 5.500000e-115 425.0
21 TraesCS3D01G470100 chr7B 79.504 605 114 10 5331 5931 627616349 627616947 7.120000e-114 422.0
22 TraesCS3D01G470100 chr7B 78.231 588 123 4 5334 5917 483025482 483026068 7.270000e-99 372.0
23 TraesCS3D01G470100 chr5B 79.500 600 114 9 5328 5922 381037482 381038077 9.210000e-113 418.0
24 TraesCS3D01G470100 chr5B 94.318 264 15 0 254 517 517197205 517196942 7.170000e-109 405.0
25 TraesCS3D01G470100 chr6A 92.889 225 16 0 1 225 548397926 548398150 1.600000e-85 327.0
26 TraesCS3D01G470100 chr2A 95.597 159 6 1 71 228 614567104 614566946 2.750000e-63 254.0
27 TraesCS3D01G470100 chr2A 87.083 240 9 7 7 224 718484218 718483979 9.880000e-63 252.0
28 TraesCS3D01G470100 chr6D 97.656 128 3 0 518 645 60392546 60392673 2.790000e-53 220.0
29 TraesCS3D01G470100 chr6D 79.787 188 27 8 1 181 153305058 153304875 6.250000e-25 126.0
30 TraesCS3D01G470100 chr1D 79.612 206 31 8 1 200 35655276 35655476 2.890000e-28 137.0
31 TraesCS3D01G470100 chr1D 78.767 146 24 4 3749 3892 425674406 425674546 2.280000e-14 91.6
32 TraesCS3D01G470100 chr1D 78.082 146 25 4 3749 3892 425571257 425571397 1.060000e-12 86.1
33 TraesCS3D01G470100 chr1D 83.544 79 11 2 3818 3895 47988304 47988227 8.260000e-09 73.1
34 TraesCS3D01G470100 chr1D 84.000 75 12 0 3818 3892 460621151 460621225 8.260000e-09 73.1
35 TraesCS3D01G470100 chr2D 97.143 70 2 0 576 645 570060160 570060229 1.050000e-22 119.0
36 TraesCS3D01G470100 chrUn 78.912 147 22 5 3752 3895 7465003 7464863 2.280000e-14 91.6
37 TraesCS3D01G470100 chr2B 88.235 68 5 3 156 221 777296505 777296571 1.770000e-10 78.7


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 TraesCS3D01G470100 chr3D 571990747 571996686 5939 True 10970 10970 100.000 1 5940 1 chr3D.!!$R2 5939
1 TraesCS3D01G470100 chr3D 90261751 90262411 660 True 392 392 77.645 5271 5934 1 chr3D.!!$R1 663
2 TraesCS3D01G470100 chr3B 762026028 762031266 5238 False 7265 7265 91.718 648 5917 1 chr3B.!!$F1 5269
3 TraesCS3D01G470100 chr3A 707082175 707086792 4617 False 6907 6907 93.741 659 5267 1 chr3A.!!$F2 4608
4 TraesCS3D01G470100 chr5D 329259697 329260340 643 True 1140 1140 98.602 1 644 1 chr5D.!!$R1 643
5 TraesCS3D01G470100 chr1A 107468654 107469240 586 False 553 553 83.844 5351 5931 1 chr1A.!!$F1 580
6 TraesCS3D01G470100 chr1B 161986948 161987530 582 False 516 516 82.765 5350 5931 1 chr1B.!!$F1 581
7 TraesCS3D01G470100 chr4B 622006483 622007149 666 True 427 427 78.293 5266 5931 1 chr4B.!!$R1 665
8 TraesCS3D01G470100 chr4B 645310462 645311044 582 False 407 407 79.457 5349 5931 1 chr4B.!!$F1 582
9 TraesCS3D01G470100 chr7D 227296396 227297064 668 True 425 425 78.434 5268 5934 1 chr7D.!!$R1 666
10 TraesCS3D01G470100 chr7B 627616349 627616947 598 False 422 422 79.504 5331 5931 1 chr7B.!!$F2 600
11 TraesCS3D01G470100 chr7B 483025482 483026068 586 False 372 372 78.231 5334 5917 1 chr7B.!!$F1 583
12 TraesCS3D01G470100 chr5B 381037482 381038077 595 False 418 418 79.500 5328 5922 1 chr5B.!!$F1 594

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
644 645 1.000607 GGTTGGAAGGAAGCGTTTTCC 60.001 52.381 11.49 11.49 40.59 3.13 F
1250 1259 0.872451 TCTCGTGCGCGTTCTTTTCA 60.872 50.000 20.50 0.00 39.49 2.69 F
1774 1802 0.975040 AGAGCGGCTTCTCCATCAGT 60.975 55.000 2.97 0.00 33.66 3.41 F
2710 2738 1.065109 CATCATCGTGGTCGCGGTA 59.935 57.895 6.13 0.00 36.96 4.02 F
3983 4016 0.320073 CACTCCTTGTTTACGCCGGA 60.320 55.000 5.05 0.00 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2109 0.109913 ATGGTGAGCATGATGCCGAT 59.890 50.000 14.72 0.00 46.52 4.18 R
2461 2489 0.247460 TCAGCGTCTCCATCAGGTTG 59.753 55.000 0.00 0.00 35.89 3.77 R
3683 3711 1.065636 CCAAGAAGCAGAGCATGGAGA 60.066 52.381 0.00 0.00 0.00 3.71 R
4383 4428 0.396435 TGGTGATGAAGTTGTCGCCT 59.604 50.000 14.99 0.00 43.69 5.52 R
5621 5683 0.322187 TCGATCTGACGTCCACCAGA 60.322 55.000 14.12 10.17 42.78 3.86 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
181 182 1.297893 GATGCTTCATCGCAACGCC 60.298 57.895 0.00 0.00 44.06 5.68
206 207 4.785453 CCCCTCTGCTTCACCGGC 62.785 72.222 0.00 0.00 0.00 6.13
230 231 4.722700 AGCCCCGCATCGCAACTT 62.723 61.111 0.00 0.00 0.00 2.66
561 562 1.826096 GGAGGAAGAGAGTTAAGCGGT 59.174 52.381 0.00 0.00 0.00 5.68
644 645 1.000607 GGTTGGAAGGAAGCGTTTTCC 60.001 52.381 11.49 11.49 40.59 3.13
645 646 1.679153 GTTGGAAGGAAGCGTTTTCCA 59.321 47.619 18.81 13.03 46.33 3.53
646 647 2.060050 TGGAAGGAAGCGTTTTCCAA 57.940 45.000 18.81 3.68 45.36 3.53
647 648 2.593026 TGGAAGGAAGCGTTTTCCAAT 58.407 42.857 18.81 9.95 45.36 3.16
648 649 3.757270 TGGAAGGAAGCGTTTTCCAATA 58.243 40.909 18.81 4.27 45.36 1.90
649 650 4.340617 TGGAAGGAAGCGTTTTCCAATAT 58.659 39.130 18.81 6.10 45.36 1.28
650 651 4.398044 TGGAAGGAAGCGTTTTCCAATATC 59.602 41.667 18.81 12.27 45.36 1.63
651 652 4.640647 GGAAGGAAGCGTTTTCCAATATCT 59.359 41.667 18.81 0.00 41.00 1.98
652 653 5.125578 GGAAGGAAGCGTTTTCCAATATCTT 59.874 40.000 18.81 6.92 41.00 2.40
653 654 6.317893 GGAAGGAAGCGTTTTCCAATATCTTA 59.682 38.462 18.81 0.00 41.00 2.10
654 655 7.148137 GGAAGGAAGCGTTTTCCAATATCTTAA 60.148 37.037 18.81 0.00 41.00 1.85
655 656 7.321745 AGGAAGCGTTTTCCAATATCTTAAG 57.678 36.000 18.81 0.00 41.00 1.85
656 657 7.110155 AGGAAGCGTTTTCCAATATCTTAAGA 58.890 34.615 18.81 7.82 41.00 2.10
657 658 7.775561 AGGAAGCGTTTTCCAATATCTTAAGAT 59.224 33.333 21.28 21.28 41.00 2.40
754 759 5.394553 CCAAAGAAGAAATATTCTGGCCCAC 60.395 44.000 0.00 0.00 39.47 4.61
883 889 5.928839 CAGAATACCATGGAAATAGGACTCG 59.071 44.000 21.47 0.00 0.00 4.18
884 890 2.622064 ACCATGGAAATAGGACTCGC 57.378 50.000 21.47 0.00 0.00 5.03
888 894 3.535561 CATGGAAATAGGACTCGCAGTT 58.464 45.455 0.00 0.00 0.00 3.16
900 906 1.531149 CTCGCAGTTTCCAACGTTCAT 59.469 47.619 0.00 0.00 36.23 2.57
917 923 4.201990 CGTTCATACGCTTCCTAGGTAGTT 60.202 45.833 16.04 7.01 41.41 2.24
944 950 4.830600 GGGATAGAGAAGAAGTGTAGGGAG 59.169 50.000 0.00 0.00 0.00 4.30
947 953 3.976015 AGAGAAGAAGTGTAGGGAGAGG 58.024 50.000 0.00 0.00 0.00 3.69
976 982 6.093771 ACTGCAAGAGAGTTGATCAATCAATC 59.906 38.462 12.12 7.94 42.63 2.67
1041 1047 3.588842 AGTCCATGGATTTCCTCAAGACA 59.411 43.478 19.62 0.00 36.82 3.41
1146 1152 2.436646 CGCTTTCGCATGGTCCCT 60.437 61.111 0.00 0.00 35.30 4.20
1207 1216 2.651455 ACATCCAGGTTCGTCGATCTA 58.349 47.619 0.00 0.00 0.00 1.98
1224 1233 7.416817 GTCGATCTATCCATCTGATGATACAG 58.583 42.308 18.92 9.89 39.02 2.74
1225 1234 7.066887 GTCGATCTATCCATCTGATGATACAGT 59.933 40.741 18.92 1.27 38.79 3.55
1236 1245 4.381411 TGATGATACAGTCTCGATCTCGT 58.619 43.478 0.00 0.00 40.80 4.18
1237 1246 4.212214 TGATGATACAGTCTCGATCTCGTG 59.788 45.833 0.00 0.00 40.80 4.35
1247 1256 1.674611 CGATCTCGTGCGCGTTCTTT 61.675 55.000 20.50 1.31 39.49 2.52
1250 1259 0.872451 TCTCGTGCGCGTTCTTTTCA 60.872 50.000 20.50 0.00 39.49 2.69
1257 1266 1.557443 CGCGTTCTTTTCAGCCGAGT 61.557 55.000 0.00 0.00 0.00 4.18
1326 1337 4.685575 GCATGGCTCCTGATCTAGAAACTT 60.686 45.833 0.00 0.00 0.00 2.66
1333 1344 9.785982 GGCTCCTGATCTAGAAACTTATTAATT 57.214 33.333 0.00 0.00 0.00 1.40
1393 1405 2.616960 GCAGTTACGTGGATCACATCA 58.383 47.619 0.00 0.00 33.40 3.07
1400 1412 3.308820 CGTGGATCACATCAATCAACG 57.691 47.619 0.00 0.00 42.35 4.10
1403 1415 2.419673 TGGATCACATCAATCAACGTGC 59.580 45.455 0.00 0.00 0.00 5.34
1415 1441 3.699779 TCAACGTGCAATTTGTTAGCA 57.300 38.095 8.09 0.00 35.63 3.49
1418 1444 5.763088 TCAACGTGCAATTTGTTAGCAATA 58.237 33.333 8.09 0.00 40.35 1.90
1443 1471 5.049543 GCTCTGCAATAGATTGAGATTGACC 60.050 44.000 6.43 0.00 40.14 4.02
1446 1474 4.811024 TGCAATAGATTGAGATTGACCGTC 59.189 41.667 6.43 0.00 40.14 4.79
1511 1539 6.016276 GTCTTGACCAGGCTTAAATTTTCTCA 60.016 38.462 0.00 0.00 0.00 3.27
1532 1560 4.768448 TCATCTGATGTTTGGTTGCATCTT 59.232 37.500 16.66 0.00 41.33 2.40
1535 1563 4.022935 TCTGATGTTTGGTTGCATCTTCAC 60.023 41.667 0.00 0.00 41.33 3.18
1600 1628 3.622612 TGCAGTTCATCGATGGTATGTTG 59.377 43.478 24.61 14.75 0.00 3.33
1621 1649 2.359850 TGCATCACCGGCAACCTC 60.360 61.111 0.00 0.00 38.54 3.85
1774 1802 0.975040 AGAGCGGCTTCTCCATCAGT 60.975 55.000 2.97 0.00 33.66 3.41
2308 2336 1.315257 ACGGGCTGTTCATTGATGGC 61.315 55.000 0.00 0.00 0.00 4.40
2413 2441 4.643387 ACCAAGGTGCAGGACGGC 62.643 66.667 0.00 0.00 0.00 5.68
2530 2558 2.551270 GTGAAGCTCAACGGCGTG 59.449 61.111 15.70 8.32 37.29 5.34
2710 2738 1.065109 CATCATCGTGGTCGCGGTA 59.935 57.895 6.13 0.00 36.96 4.02
2818 2846 4.760047 GCGTGCGAGACCATGGGT 62.760 66.667 18.09 1.90 39.44 4.51
3010 3038 3.997064 CTTCCAGTGCTCCGGCTCG 62.997 68.421 0.00 0.00 39.59 5.03
3676 3704 4.323553 AATCCAGGCACGTATCTTCTAC 57.676 45.455 0.00 0.00 0.00 2.59
3683 3711 3.431766 GGCACGTATCTTCTACCACCATT 60.432 47.826 0.00 0.00 0.00 3.16
3701 3729 3.280295 CATTCTCCATGCTCTGCTTCTT 58.720 45.455 0.00 0.00 0.00 2.52
3720 3748 1.808411 TGGAAGAAGTTGATGCCGAC 58.192 50.000 0.00 0.00 0.00 4.79
3938 3971 1.269831 CGTACTGCCCTGCTATCTTCC 60.270 57.143 0.00 0.00 0.00 3.46
3939 3972 1.762957 GTACTGCCCTGCTATCTTCCA 59.237 52.381 0.00 0.00 0.00 3.53
3952 3985 4.994217 GCTATCTTCCACTCTTCCTTATGC 59.006 45.833 0.00 0.00 0.00 3.14
3954 3987 3.181329 TCTTCCACTCTTCCTTATGCCA 58.819 45.455 0.00 0.00 0.00 4.92
3973 4006 3.810743 GCCAATGAGGTTACACTCCTTGT 60.811 47.826 13.17 0.00 39.77 3.16
3976 4009 6.001460 CCAATGAGGTTACACTCCTTGTTTA 58.999 40.000 13.17 0.00 39.77 2.01
3979 4012 3.396560 AGGTTACACTCCTTGTTTACGC 58.603 45.455 0.00 0.00 39.91 4.42
3980 4013 2.481568 GGTTACACTCCTTGTTTACGCC 59.518 50.000 0.00 0.00 39.91 5.68
3981 4014 2.068837 TACACTCCTTGTTTACGCCG 57.931 50.000 0.00 0.00 39.91 6.46
3983 4016 0.320073 CACTCCTTGTTTACGCCGGA 60.320 55.000 5.05 0.00 0.00 5.14
4146 4185 2.894126 ACTCATGGTGAACTTCGTCTCT 59.106 45.455 0.00 0.00 0.00 3.10
4163 4202 4.679106 CGTCTCTGCATCTTTCACAGGTAT 60.679 45.833 0.00 0.00 32.19 2.73
4167 4209 5.664457 TCTGCATCTTTCACAGGTATACAG 58.336 41.667 5.01 0.00 32.19 2.74
4175 4217 7.152645 TCTTTCACAGGTATACAGAACTGAAC 58.847 38.462 12.19 4.05 35.08 3.18
4196 4238 4.074970 ACCTCCATTGATTCTTGACACAC 58.925 43.478 0.00 0.00 0.00 3.82
4204 4246 2.910688 TTCTTGACACACAGGGTCTC 57.089 50.000 0.74 0.00 36.26 3.36
4232 4274 7.155328 CCATGTCCTGGTATTCTATCAAGTAC 58.845 42.308 0.00 0.00 40.49 2.73
4425 4470 0.460109 TCATGTGGAGGAACATCGCG 60.460 55.000 0.00 0.00 38.75 5.87
4591 4640 4.911610 CACACAAGATCGAAACACAAATCC 59.088 41.667 0.00 0.00 0.00 3.01
4627 4677 4.202172 TGACACTTTCACCTTGTGACGATA 60.202 41.667 0.00 0.00 42.60 2.92
4668 4718 1.045911 AGCCGGGAGATGGAGAAGAC 61.046 60.000 2.18 0.00 0.00 3.01
4864 4914 0.549950 CCATCCTCAAGTGCATCCCT 59.450 55.000 0.00 0.00 0.00 4.20
4867 4917 1.067295 TCCTCAAGTGCATCCCTGTT 58.933 50.000 0.00 0.00 0.00 3.16
4944 4994 1.225745 CGAGCGCCGTGTGATTTTC 60.226 57.895 2.29 0.00 0.00 2.29
4959 5009 5.811613 TGTGATTTTCAAGACTTTTTGCTGG 59.188 36.000 0.00 0.00 0.00 4.85
4999 5052 9.521503 GAAGAGGAAAATATGTTAATCCTTTGC 57.478 33.333 9.81 1.89 40.53 3.68
5028 5081 0.599558 TTGCATGCAGCTTCAGTTCC 59.400 50.000 21.50 0.00 45.94 3.62
5046 5099 2.652530 GTGTAGGACGTGCCGGAA 59.347 61.111 5.05 0.00 43.43 4.30
5059 5112 2.469516 CCGGAACATACTTGCGGCC 61.470 63.158 0.00 0.00 45.72 6.13
5070 5123 1.001020 TTGCGGCCATGACCATTCT 60.001 52.632 2.24 0.00 0.00 2.40
5136 5189 5.289434 GCTTTCTAGCCAAACATTGTTATGC 59.711 40.000 12.75 12.75 41.74 3.14
5142 5195 6.243811 AGCCAAACATTGTTATGCATTTTG 57.756 33.333 19.34 7.63 35.03 2.44
5143 5196 5.996513 AGCCAAACATTGTTATGCATTTTGA 59.003 32.000 19.34 0.00 35.03 2.69
5223 5276 9.415008 TCACTAATAGAGAGATGAGTTTTAGCT 57.585 33.333 0.00 0.00 0.00 3.32
5233 5286 4.967084 TGAGTTTTAGCTACACCAAGGA 57.033 40.909 0.00 0.00 0.00 3.36
5293 5349 5.568685 GAGCATCTACAGACAGACTACAA 57.431 43.478 0.00 0.00 0.00 2.41
5297 5353 6.647067 AGCATCTACAGACAGACTACAAAAAC 59.353 38.462 0.00 0.00 0.00 2.43
5310 5366 2.572290 ACAAAAACCCGACCTCTCAAG 58.428 47.619 0.00 0.00 0.00 3.02
5428 5485 6.262944 TCAAATCCATACTATGACATGCAACC 59.737 38.462 0.00 0.00 0.00 3.77
5439 5498 2.541762 GACATGCAACCTAGCGATCTTC 59.458 50.000 0.00 0.00 37.31 2.87
5445 5504 3.002791 CAACCTAGCGATCTTCAAGCAA 58.997 45.455 0.00 0.00 0.00 3.91
5512 5574 2.487934 CTTCAGAGTGTTGGTCCAGTG 58.512 52.381 0.00 0.00 0.00 3.66
5516 5578 2.597510 GTGTTGGTCCAGTGGCCC 60.598 66.667 16.97 11.06 0.00 5.80
5557 5619 2.357034 CACGCACCGGCTTACTGT 60.357 61.111 0.00 0.00 38.10 3.55
5565 5627 2.230508 CACCGGCTTACTGTACTCAAGA 59.769 50.000 0.00 0.00 0.00 3.02
5687 5752 1.447838 GACATCCACCATGACGCGT 60.448 57.895 13.85 13.85 36.21 6.01
5688 5753 1.695893 GACATCCACCATGACGCGTG 61.696 60.000 20.70 4.12 36.21 5.34
5784 5849 4.103103 CTGTCGCCGTCTCTCGCA 62.103 66.667 0.00 0.00 38.35 5.10
5802 5868 4.749310 CTCGCTGCCTCGCAAGGT 62.749 66.667 0.00 0.00 45.34 3.50
5824 5891 2.281484 ACGCTCCGCCATGTTTGT 60.281 55.556 0.00 0.00 0.00 2.83
5831 5898 0.309302 CCGCCATGTTTGTGTCGAAA 59.691 50.000 0.00 0.00 0.00 3.46
5834 5901 2.095768 CGCCATGTTTGTGTCGAAAGAT 60.096 45.455 0.00 0.00 45.19 2.40
5854 5921 1.904771 CCCATGCGTTCACCTCCTA 59.095 57.895 0.00 0.00 0.00 2.94
5857 5924 1.645034 CATGCGTTCACCTCCTACTG 58.355 55.000 0.00 0.00 0.00 2.74
5934 6002 3.285371 CGCCTTCGGTGAGGTAGT 58.715 61.111 3.06 0.00 39.11 2.73
5935 6003 1.590147 CGCCTTCGGTGAGGTAGTT 59.410 57.895 3.06 0.00 39.11 2.24
5936 6004 0.736325 CGCCTTCGGTGAGGTAGTTG 60.736 60.000 3.06 0.00 39.11 3.16
5937 6005 0.320697 GCCTTCGGTGAGGTAGTTGT 59.679 55.000 3.06 0.00 39.11 3.32
5938 6006 1.939838 GCCTTCGGTGAGGTAGTTGTG 60.940 57.143 3.06 0.00 39.11 3.33
5939 6007 1.616865 CCTTCGGTGAGGTAGTTGTGA 59.383 52.381 0.00 0.00 31.89 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
422 423 4.404654 CAAGAACAAGGGCGCCGC 62.405 66.667 22.54 13.90 0.00 6.53
525 526 0.682292 CTCCCTTATCTCTTCCGCCC 59.318 60.000 0.00 0.00 0.00 6.13
665 666 6.215636 TCCCTGTCTAAAGCCTAAGAATTCTT 59.784 38.462 23.53 23.53 39.85 2.52
676 677 1.286248 TTCCCTCCCTGTCTAAAGCC 58.714 55.000 0.00 0.00 0.00 4.35
677 678 2.239907 ACATTCCCTCCCTGTCTAAAGC 59.760 50.000 0.00 0.00 0.00 3.51
678 679 4.443598 GCTACATTCCCTCCCTGTCTAAAG 60.444 50.000 0.00 0.00 0.00 1.85
679 680 3.454812 GCTACATTCCCTCCCTGTCTAAA 59.545 47.826 0.00 0.00 0.00 1.85
680 681 3.039011 GCTACATTCCCTCCCTGTCTAA 58.961 50.000 0.00 0.00 0.00 2.10
681 682 2.023404 TGCTACATTCCCTCCCTGTCTA 60.023 50.000 0.00 0.00 0.00 2.59
682 683 1.273838 TGCTACATTCCCTCCCTGTCT 60.274 52.381 0.00 0.00 0.00 3.41
683 684 1.204146 TGCTACATTCCCTCCCTGTC 58.796 55.000 0.00 0.00 0.00 3.51
686 687 1.840635 GAGTTGCTACATTCCCTCCCT 59.159 52.381 0.13 0.00 0.00 4.20
731 736 5.420104 AGTGGGCCAGAATATTTCTTCTTTG 59.580 40.000 6.40 0.00 38.11 2.77
812 818 1.921243 CGGTTCACATCGCACAGATA 58.079 50.000 0.00 0.00 37.52 1.98
883 889 2.834689 CGTATGAACGTTGGAAACTGC 58.165 47.619 5.00 0.00 46.99 4.40
900 906 2.684881 CCGAAACTACCTAGGAAGCGTA 59.315 50.000 17.98 0.00 0.00 4.42
917 923 3.709587 ACACTTCTTCTCTATCCCCGAA 58.290 45.455 0.00 0.00 0.00 4.30
944 950 1.153667 CTCTCTTGCAGTCCGCCTC 60.154 63.158 0.00 0.00 41.33 4.70
947 953 0.319900 TCAACTCTCTTGCAGTCCGC 60.320 55.000 0.00 0.00 42.89 5.54
1207 1216 5.320277 TCGAGACTGTATCATCAGATGGAT 58.680 41.667 10.67 5.73 38.63 3.41
1224 1233 3.013990 CGCGCACGAGATCGAGAC 61.014 66.667 8.75 0.00 43.93 3.36
1225 1234 2.898087 GAACGCGCACGAGATCGAGA 62.898 60.000 5.73 0.00 43.93 4.04
1236 1245 2.637025 GGCTGAAAAGAACGCGCA 59.363 55.556 5.73 0.00 0.00 6.09
1237 1246 2.499732 CGGCTGAAAAGAACGCGC 60.500 61.111 5.73 0.00 0.00 6.86
1250 1259 0.905357 ATCAACCAGCTAACTCGGCT 59.095 50.000 0.00 0.00 41.07 5.52
1257 1266 2.170607 GGGCAGTAGATCAACCAGCTAA 59.829 50.000 0.00 0.00 0.00 3.09
1263 1272 0.253044 TGCAGGGCAGTAGATCAACC 59.747 55.000 0.00 0.00 33.32 3.77
1333 1344 9.806203 CAAGATCAATTGCAACTAATTAATCCA 57.194 29.630 0.00 0.00 28.85 3.41
1352 1363 0.179111 GTCCACGCGGATCAAGATCA 60.179 55.000 12.47 0.00 45.33 2.92
1353 1364 1.209275 CGTCCACGCGGATCAAGATC 61.209 60.000 12.47 1.40 45.33 2.75
1373 1385 2.616960 TGATGTGATCCACGTAACTGC 58.383 47.619 0.00 0.00 37.14 4.40
1393 1405 4.615949 TGCTAACAAATTGCACGTTGATT 58.384 34.783 14.02 7.99 0.00 2.57
1415 1441 8.155510 TCAATCTCAATCTATTGCAGAGCTATT 58.844 33.333 0.00 0.00 36.48 1.73
1418 1444 5.759273 GTCAATCTCAATCTATTGCAGAGCT 59.241 40.000 0.00 0.00 36.48 4.09
1422 1448 4.813161 ACGGTCAATCTCAATCTATTGCAG 59.187 41.667 0.00 0.00 37.68 4.41
1423 1449 4.769688 ACGGTCAATCTCAATCTATTGCA 58.230 39.130 0.00 0.00 37.68 4.08
1433 1459 3.305813 GGTTACACAGACGGTCAATCTCA 60.306 47.826 11.27 0.00 0.00 3.27
1443 1471 1.973138 CCACGTAGGTTACACAGACG 58.027 55.000 0.00 0.00 39.37 4.18
1511 1539 4.768448 TGAAGATGCAACCAAACATCAGAT 59.232 37.500 5.84 0.00 44.16 2.90
1532 1560 2.325583 ACACGAAGCTTTTCCTGTGA 57.674 45.000 17.65 0.00 0.00 3.58
1535 1563 2.882742 GCTACACGAAGCTTTTCCTG 57.117 50.000 0.00 0.00 39.50 3.86
1552 1580 0.814457 CCTTCTGCACGTAGAGAGCT 59.186 55.000 0.00 0.00 0.00 4.09
1600 1628 2.359850 TTGCCGGTGATGCAGACC 60.360 61.111 1.90 7.50 40.35 3.85
1621 1649 7.601705 ATCAAACTAATGGGATGTTTATGGG 57.398 36.000 0.00 0.00 33.31 4.00
2081 2109 0.109913 ATGGTGAGCATGATGCCGAT 59.890 50.000 14.72 0.00 46.52 4.18
2308 2336 1.322637 TCGTCGACGATGAACGAGTAG 59.677 52.381 34.97 4.19 44.22 2.57
2413 2441 3.842923 ACCAGCATCCTCGCCGAG 61.843 66.667 7.25 7.25 0.00 4.63
2461 2489 0.247460 TCAGCGTCTCCATCAGGTTG 59.753 55.000 0.00 0.00 35.89 3.77
2818 2846 2.437180 CAGATGCAGCTGGCCGAA 60.437 61.111 24.22 0.00 43.89 4.30
3299 3327 2.605366 GCTTCATGTAGTTCTTCTCCGC 59.395 50.000 1.02 0.00 0.00 5.54
3676 3704 1.676746 CAGAGCATGGAGAATGGTGG 58.323 55.000 0.00 0.00 46.95 4.61
3683 3711 1.065636 CCAAGAAGCAGAGCATGGAGA 60.066 52.381 0.00 0.00 0.00 3.71
3701 3729 1.808411 GTCGGCATCAACTTCTTCCA 58.192 50.000 0.00 0.00 0.00 3.53
3739 3769 3.490759 CGCCATCACCTGCACGAC 61.491 66.667 0.00 0.00 0.00 4.34
3938 3971 3.881688 CCTCATTGGCATAAGGAAGAGTG 59.118 47.826 4.74 0.00 0.00 3.51
3939 3972 3.525199 ACCTCATTGGCATAAGGAAGAGT 59.475 43.478 14.95 0.00 40.22 3.24
3954 3987 5.699458 CGTAAACAAGGAGTGTAACCTCATT 59.301 40.000 0.00 0.00 40.60 2.57
3973 4006 1.669760 CAACCTGCTCCGGCGTAAA 60.670 57.895 6.01 0.00 42.25 2.01
3979 4012 3.058160 CTTGGCAACCTGCTCCGG 61.058 66.667 0.00 0.00 44.28 5.14
3980 4013 3.058160 CCTTGGCAACCTGCTCCG 61.058 66.667 0.00 0.00 44.28 4.63
3981 4014 1.676967 CTCCTTGGCAACCTGCTCC 60.677 63.158 0.00 0.00 44.28 4.70
3983 4016 0.538287 GTTCTCCTTGGCAACCTGCT 60.538 55.000 0.00 0.00 44.28 4.24
4134 4173 8.241642 CTGTGAAAGATGCAGAGACGAAGTTC 62.242 46.154 0.00 0.00 34.42 3.01
4146 4185 5.675684 TCTGTATACCTGTGAAAGATGCA 57.324 39.130 0.00 0.00 0.00 3.96
4163 4202 5.762179 ATCAATGGAGGTTCAGTTCTGTA 57.238 39.130 0.00 0.00 0.00 2.74
4167 4209 5.707298 TCAAGAATCAATGGAGGTTCAGTTC 59.293 40.000 0.00 0.00 0.00 3.01
4175 4217 4.074259 TGTGTGTCAAGAATCAATGGAGG 58.926 43.478 0.00 0.00 0.00 4.30
4196 4238 1.222936 GGACATGGCAGAGACCCTG 59.777 63.158 0.00 0.00 45.67 4.45
4211 4253 7.595502 CGAATGTACTTGATAGAATACCAGGAC 59.404 40.741 0.00 0.00 0.00 3.85
4383 4428 0.396435 TGGTGATGAAGTTGTCGCCT 59.604 50.000 14.99 0.00 43.69 5.52
4425 4470 1.153005 CTGGAAGATGCTCTGGCCC 60.153 63.158 0.00 0.00 34.07 5.80
4591 4640 6.430451 GTGAAAGTGTCAGTACAAATTCAGG 58.570 40.000 0.00 0.00 40.39 3.86
4603 4652 2.285220 CGTCACAAGGTGAAAGTGTCAG 59.715 50.000 0.00 0.00 44.49 3.51
4627 4677 1.410004 TCACCTCGTTGAAGACCTGT 58.590 50.000 0.00 0.00 0.00 4.00
4668 4718 1.970917 GATGCCGCTGAAGACGTTGG 61.971 60.000 0.00 0.00 0.00 3.77
4847 4897 1.293062 ACAGGGATGCACTTGAGGAT 58.707 50.000 0.00 0.00 0.00 3.24
4944 4994 4.747810 AGAAACACCAGCAAAAAGTCTTG 58.252 39.130 0.00 0.00 0.00 3.02
4999 5052 1.652124 GCTGCATGCAAAGATCGTTTG 59.348 47.619 22.88 6.86 42.31 2.93
5046 5099 0.748005 GGTCATGGCCGCAAGTATGT 60.748 55.000 0.00 0.00 0.00 2.29
5059 5112 6.114089 ACTCAAATCTCTCAGAATGGTCATG 58.886 40.000 0.00 0.00 36.16 3.07
5070 5123 7.770433 TGACAAGAAAGAAACTCAAATCTCTCA 59.230 33.333 0.00 0.00 0.00 3.27
5158 5211 5.450592 TGATAAGCAACTGCATTTGTCAA 57.549 34.783 17.00 4.53 45.16 3.18
5162 5215 8.130469 TGTATACATGATAAGCAACTGCATTTG 58.870 33.333 12.16 12.16 45.16 2.32
5163 5216 8.131100 GTGTATACATGATAAGCAACTGCATTT 58.869 33.333 9.18 0.00 45.16 2.32
5167 5220 6.603237 TGTGTATACATGATAAGCAACTGC 57.397 37.500 9.18 0.00 42.49 4.40
5223 5276 2.375174 AGCAACAATCCTCCTTGGTGTA 59.625 45.455 4.03 0.00 44.09 2.90
5233 5286 6.098266 AGTTTTGGACTTTTAGCAACAATCCT 59.902 34.615 0.00 0.00 33.92 3.24
5285 5341 2.970640 AGAGGTCGGGTTTTTGTAGTCT 59.029 45.455 0.00 0.00 0.00 3.24
5290 5346 2.572290 CTTGAGAGGTCGGGTTTTTGT 58.428 47.619 0.00 0.00 0.00 2.83
5291 5347 1.266989 GCTTGAGAGGTCGGGTTTTTG 59.733 52.381 0.00 0.00 0.00 2.44
5293 5349 0.602905 CGCTTGAGAGGTCGGGTTTT 60.603 55.000 0.00 0.00 0.00 2.43
5418 5475 2.231215 AGATCGCTAGGTTGCATGTC 57.769 50.000 0.00 0.00 0.00 3.06
5428 5485 2.935201 AGCTTTGCTTGAAGATCGCTAG 59.065 45.455 0.00 0.00 33.89 3.42
5439 5498 1.208614 GCTGGACGAGCTTTGCTTG 59.791 57.895 1.67 5.35 45.21 4.01
5485 5546 1.546323 CCAACACTCTGAAGGGTGCAT 60.546 52.381 10.29 0.00 38.55 3.96
5512 5574 2.517875 TACTCTACCTCGCGGGCC 60.518 66.667 6.13 0.00 39.10 5.80
5516 5578 1.173444 ATGCCCTACTCTACCTCGCG 61.173 60.000 0.00 0.00 0.00 5.87
5552 5614 3.353557 AGGCGATGTCTTGAGTACAGTA 58.646 45.455 0.00 0.00 0.00 2.74
5557 5619 2.427453 GGAGAAGGCGATGTCTTGAGTA 59.573 50.000 0.00 0.00 0.00 2.59
5565 5627 1.153086 GCATGGGAGAAGGCGATGT 60.153 57.895 0.00 0.00 0.00 3.06
5621 5683 0.322187 TCGATCTGACGTCCACCAGA 60.322 55.000 14.12 10.17 42.78 3.86
5784 5849 4.749310 CCTTGCGAGGCAGCGAGT 62.749 66.667 7.18 0.00 44.98 4.18
5824 5891 1.368345 CGCATGGGCATCTTTCGACA 61.368 55.000 0.00 0.00 41.24 4.35
5831 5898 1.750399 GGTGAACGCATGGGCATCT 60.750 57.895 10.10 0.00 41.24 2.90
5834 5901 2.359850 GAGGTGAACGCATGGGCA 60.360 61.111 10.10 0.00 41.24 5.36


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

AutoCloner maintained by Alex Coulton.