Multiple sequence alignment - TraesCS3A01G423500

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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 TraesCS3A01G423500 chr3A 100.000 4487 0 0 1 4487 665968157 665963671 0.000000e+00 8287.0
1 TraesCS3A01G423500 chr3D 96.307 3168 87 11 750 3912 426440080 426443222 0.000000e+00 5175.0
2 TraesCS3A01G423500 chr3D 97.798 2952 61 3 965 3912 531367843 531364892 0.000000e+00 5088.0
3 TraesCS3A01G423500 chr3D 88.840 914 56 18 1 898 531368766 531367883 0.000000e+00 1081.0
4 TraesCS3A01G423500 chr3D 90.202 347 5 2 4170 4487 531364896 531364550 4.150000e-115 425.0
5 TraesCS3A01G423500 chr3D 89.490 314 10 9 4170 4460 426443218 426443531 4.240000e-100 375.0
6 TraesCS3A01G423500 chr3D 91.007 278 19 3 1 278 426439198 426439469 1.970000e-98 370.0
7 TraesCS3A01G423500 chr3D 85.284 299 21 7 106 389 426439545 426439835 2.040000e-73 287.0
8 TraesCS3A01G423500 chr3D 87.719 228 20 8 580 803 23088365 23088142 4.450000e-65 259.0
9 TraesCS3A01G423500 chr3D 97.959 49 1 0 460 508 426439855 426439903 8.000000e-13 86.1
10 TraesCS3A01G423500 chr3D 100.000 32 0 0 4456 4487 426444828 426444859 4.850000e-05 60.2
11 TraesCS3A01G423500 chr3B 97.951 2977 49 5 947 3912 702692632 702689657 0.000000e+00 5149.0
12 TraesCS3A01G423500 chr3B 85.828 628 58 13 276 899 702693247 702692647 4.890000e-179 638.0
13 TraesCS3A01G423500 chr3B 90.962 343 6 2 4170 4487 702689661 702689319 5.330000e-119 438.0
14 TraesCS3A01G423500 chr3B 91.244 217 16 2 63 278 702693493 702693279 4.390000e-75 292.0
15 TraesCS3A01G423500 chr3B 97.917 48 0 1 3866 3912 750356587 750356540 1.030000e-11 82.4
16 TraesCS3A01G423500 chr1D 93.277 2945 168 11 980 3912 391317203 391320129 0.000000e+00 4314.0
17 TraesCS3A01G423500 chr1D 90.545 275 22 2 3906 4180 331138318 331138588 1.190000e-95 361.0
18 TraesCS3A01G423500 chr1D 87.879 198 19 5 604 798 483524065 483523870 1.260000e-55 228.0
19 TraesCS3A01G423500 chr1A 93.020 2937 163 20 987 3912 493823624 493820719 0.000000e+00 4250.0
20 TraesCS3A01G423500 chr1B 94.815 2565 127 1 984 3548 531206272 531203714 0.000000e+00 3995.0
21 TraesCS3A01G423500 chr1B 85.492 386 25 12 3545 3912 531203604 531203232 1.520000e-99 374.0
22 TraesCS3A01G423500 chr4A 90.262 688 56 8 991 1668 590255595 590254909 0.000000e+00 889.0
23 TraesCS3A01G423500 chr4A 89.161 286 28 3 4204 4487 590254592 590254308 1.990000e-93 353.0
24 TraesCS3A01G423500 chr4A 86.364 330 30 7 3588 3903 590254915 590254587 3.320000e-91 346.0
25 TraesCS3A01G423500 chr4A 87.755 196 21 3 604 798 622198052 622197859 4.520000e-55 226.0
26 TraesCS3A01G423500 chrUn 98.446 386 6 0 3204 3589 480559231 480559616 0.000000e+00 680.0
27 TraesCS3A01G423500 chr4D 86.396 419 30 16 1252 1668 12419565 12419958 2.480000e-117 433.0
28 TraesCS3A01G423500 chr4D 89.851 335 25 6 3584 3911 12419948 12420280 5.370000e-114 422.0
29 TraesCS3A01G423500 chr4D 90.252 318 30 1 4170 4487 12420277 12420593 8.980000e-112 414.0
30 TraesCS3A01G423500 chr4D 91.481 270 20 1 3906 4175 275616759 275616493 7.090000e-98 368.0
31 TraesCS3A01G423500 chr4B 89.222 334 27 7 3585 3911 22753569 22753900 4.180000e-110 409.0
32 TraesCS3A01G423500 chr4B 89.011 182 19 1 4170 4351 22753897 22754077 1.620000e-54 224.0
33 TraesCS3A01G423500 chr4B 89.437 142 11 2 4346 4487 22804991 22805128 4.610000e-40 176.0
34 TraesCS3A01G423500 chr5D 91.304 276 20 2 3906 4181 517961091 517961362 1.520000e-99 374.0
35 TraesCS3A01G423500 chr5D 83.003 353 50 8 539 889 531475426 531475082 1.210000e-80 311.0
36 TraesCS3A01G423500 chr5D 82.886 298 37 10 590 881 531470867 531470578 5.760000e-64 255.0
37 TraesCS3A01G423500 chr7A 92.075 265 18 1 3910 4174 646560186 646560447 1.970000e-98 370.0
38 TraesCS3A01G423500 chr7A 91.760 267 19 1 3910 4176 275561195 275561458 7.090000e-98 368.0
39 TraesCS3A01G423500 chr6D 91.176 272 19 3 3906 4176 247685267 247685534 9.170000e-97 364.0
40 TraesCS3A01G423500 chr2B 91.698 265 19 1 3910 4174 42029821 42029560 9.170000e-97 364.0
41 TraesCS3A01G423500 chr6A 91.418 268 17 4 3906 4173 235843648 235843387 3.300000e-96 363.0
42 TraesCS3A01G423500 chr5B 90.545 275 22 2 3902 4176 281946820 281946550 1.190000e-95 361.0
43 TraesCS3A01G423500 chr5B 85.333 300 38 5 592 889 669485886 669485591 5.640000e-79 305.0
44 TraesCS3A01G423500 chr5A 85.507 276 34 5 527 800 658600698 658600427 2.640000e-72 283.0
45 TraesCS3A01G423500 chr5A 81.481 162 24 6 3537 3695 450419360 450419518 1.310000e-25 128.0


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 TraesCS3A01G423500 chr3A 665963671 665968157 4486 True 8287.000000 8287 100.000000 1 4487 1 chr3A.!!$R1 4486
1 TraesCS3A01G423500 chr3D 531364550 531368766 4216 True 2198.000000 5088 92.280000 1 4487 3 chr3D.!!$R2 4486
2 TraesCS3A01G423500 chr3D 426439198 426444859 5661 False 1058.883333 5175 93.341167 1 4487 6 chr3D.!!$F1 4486
3 TraesCS3A01G423500 chr3B 702689319 702693493 4174 True 1629.250000 5149 91.496250 63 4487 4 chr3B.!!$R2 4424
4 TraesCS3A01G423500 chr1D 391317203 391320129 2926 False 4314.000000 4314 93.277000 980 3912 1 chr1D.!!$F2 2932
5 TraesCS3A01G423500 chr1A 493820719 493823624 2905 True 4250.000000 4250 93.020000 987 3912 1 chr1A.!!$R1 2925
6 TraesCS3A01G423500 chr1B 531203232 531206272 3040 True 2184.500000 3995 90.153500 984 3912 2 chr1B.!!$R1 2928
7 TraesCS3A01G423500 chr4A 590254308 590255595 1287 True 529.333333 889 88.595667 991 4487 3 chr4A.!!$R2 3496
8 TraesCS3A01G423500 chr4D 12419565 12420593 1028 False 423.000000 433 88.833000 1252 4487 3 chr4D.!!$F1 3235
9 TraesCS3A01G423500 chr4B 22753569 22754077 508 False 316.500000 409 89.116500 3585 4351 2 chr4B.!!$F2 766

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
405 701 0.237498 GTTGTGCCCAACGTAGAAGC 59.763 55.000 0.0 0.0 41.41 3.86 F
889 1225 1.038280 CGGCCCTAATTCGGTAGACT 58.962 55.000 0.0 0.0 0.00 3.24 F
1811 2169 1.153529 TGTGCTTGTCGTCGGTTGT 60.154 52.632 0.0 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 2075 1.134371 CCTCATCTCCCGGAAAACCTC 60.134 57.143 0.73 0.00 0.00 3.85 R
2612 2970 2.281484 GTTCTCGGGCCTGTGCAA 60.281 61.111 12.43 3.14 40.13 4.08 R
3511 3869 0.924823 ATCAATGAGCAGCTCCCCTT 59.075 50.000 20.16 7.94 0.00 3.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.880963 TTTGTGCTTACCAACTTGCC 57.119 45.000 0.00 0.00 0.00 4.52
27 28 1.993956 TGTGCTTACCAACTTGCCAT 58.006 45.000 0.00 0.00 0.00 4.40
44 45 5.247507 TGCCATGAGGAATTTAAATGACG 57.752 39.130 0.39 0.00 36.89 4.35
45 46 4.946772 TGCCATGAGGAATTTAAATGACGA 59.053 37.500 0.39 0.00 36.89 4.20
81 82 5.532406 AGCATCGTTATCCAGTAAAATGCAT 59.468 36.000 0.00 0.00 41.56 3.96
87 88 6.551736 GTTATCCAGTAAAATGCATGTTCGT 58.448 36.000 5.08 0.00 0.00 3.85
97 98 1.915614 GCATGTTCGTGCCCTCTGTG 61.916 60.000 5.78 0.00 39.18 3.66
148 149 2.426522 TGTGCTGGAGTATCAGTTTGC 58.573 47.619 0.00 0.00 36.25 3.68
169 170 8.795342 TTTGCAGTCAACAATGGCACATTTCT 62.795 38.462 0.00 0.00 35.69 2.52
221 222 8.675888 CGAACGAAATAACATGAATCATCAATG 58.324 33.333 0.00 0.00 39.49 2.82
270 272 6.910536 AGTGATCCAAAAATATGTCTCGTC 57.089 37.500 0.00 0.00 0.00 4.20
271 273 6.406370 AGTGATCCAAAAATATGTCTCGTCA 58.594 36.000 0.00 0.00 0.00 4.35
285 336 4.274950 TGTCTCGTCATATATCGTTGCTCA 59.725 41.667 0.00 0.00 0.00 4.26
340 392 1.202651 ACAGGAGGAAACCGACAACAG 60.203 52.381 0.00 0.00 34.73 3.16
389 685 6.093532 GTTCACAAAATTGAACCACAGTTG 57.906 37.500 4.91 0.00 46.60 3.16
405 701 0.237498 GTTGTGCCCAACGTAGAAGC 59.763 55.000 0.00 0.00 41.41 3.86
407 703 1.373748 GTGCCCAACGTAGAAGCGA 60.374 57.895 0.00 0.00 35.59 4.93
523 821 3.731431 TCAGGGGGCTACAAATAGAAGA 58.269 45.455 0.00 0.00 0.00 2.87
561 859 1.594331 GTTCACAAAGAAGCGAGGGT 58.406 50.000 0.00 0.00 36.78 4.34
803 1139 2.167900 GAGGTGGTACTAAACATCGGCT 59.832 50.000 0.00 0.00 0.00 5.52
823 1159 2.109126 GTCTGTTGCCATCCGCCTC 61.109 63.158 0.00 0.00 36.24 4.70
889 1225 1.038280 CGGCCCTAATTCGGTAGACT 58.962 55.000 0.00 0.00 0.00 3.24
936 1273 5.357032 GGGACATTTGGACTGTAATAACTGG 59.643 44.000 0.00 0.00 0.00 4.00
1554 1912 2.117858 TGCAAGCTGGGCCATGAA 59.882 55.556 6.72 0.00 0.00 2.57
1556 1914 2.277591 GCAAGCTGGGCCATGAACA 61.278 57.895 6.72 0.00 0.00 3.18
1770 2128 2.206576 AGATCAACCCCTTTGCACTC 57.793 50.000 0.00 0.00 34.88 3.51
1811 2169 1.153529 TGTGCTTGTCGTCGGTTGT 60.154 52.632 0.00 0.00 0.00 3.32
1840 2198 3.737559 AAGGTATCCATGCCTGTTCAA 57.262 42.857 0.00 0.00 42.38 2.69
2496 2854 8.752187 ACCATTGTAAGCAATTCACTTATTGAT 58.248 29.630 0.00 0.00 42.91 2.57
2523 2881 1.814394 GCAAAGTGTGGATGCATCAGA 59.186 47.619 27.25 11.10 39.81 3.27
2612 2970 4.139786 GGATATGCTGTTCATGGACATGT 58.860 43.478 7.44 0.00 39.72 3.21
3240 3598 6.569780 TGATACTAACGTAGTGTTGCATGAT 58.430 36.000 0.00 0.00 45.00 2.45
3320 3678 3.548770 CATATGGGCTTGTGATGACACT 58.451 45.455 0.00 0.00 46.07 3.55
3492 3850 4.041567 TGTGGTGACTATTGGTGATGTTCT 59.958 41.667 0.00 0.00 0.00 3.01
3788 4291 6.127925 TGAGCAAAGGTAAACATGCAATAGAG 60.128 38.462 0.00 0.00 41.18 2.43
3847 4354 6.493802 TGTATATGTACCCTCTCCAGAATGTC 59.506 42.308 0.00 0.00 0.00 3.06
3913 4425 7.191593 TGAAAAGGTAGAAAGGATAGTACCC 57.808 40.000 0.00 0.00 36.36 3.69
3914 4426 6.157471 TGAAAAGGTAGAAAGGATAGTACCCC 59.843 42.308 0.00 0.00 36.36 4.95
3915 4427 4.210611 AGGTAGAAAGGATAGTACCCCC 57.789 50.000 0.00 0.00 36.36 5.40
3916 4428 3.804228 AGGTAGAAAGGATAGTACCCCCT 59.196 47.826 0.00 0.00 36.36 4.79
3917 4429 4.140734 AGGTAGAAAGGATAGTACCCCCTC 60.141 50.000 0.00 0.00 36.36 4.30
3918 4430 3.347759 AGAAAGGATAGTACCCCCTCC 57.652 52.381 0.00 0.00 0.00 4.30
3919 4431 2.595380 AGAAAGGATAGTACCCCCTCCA 59.405 50.000 0.00 0.00 0.00 3.86
3920 4432 3.212397 AGAAAGGATAGTACCCCCTCCAT 59.788 47.826 0.00 0.00 0.00 3.41
3921 4433 3.745678 AAGGATAGTACCCCCTCCATT 57.254 47.619 0.00 0.00 0.00 3.16
3922 4434 3.277416 AGGATAGTACCCCCTCCATTC 57.723 52.381 0.00 0.00 0.00 2.67
3923 4435 2.157989 AGGATAGTACCCCCTCCATTCC 60.158 54.545 0.00 0.00 0.00 3.01
3924 4436 2.157989 GGATAGTACCCCCTCCATTCCT 60.158 54.545 0.00 0.00 0.00 3.36
3925 4437 3.599348 GATAGTACCCCCTCCATTCCTT 58.401 50.000 0.00 0.00 0.00 3.36
3926 4438 2.378308 AGTACCCCCTCCATTCCTTT 57.622 50.000 0.00 0.00 0.00 3.11
3927 4439 3.519370 AGTACCCCCTCCATTCCTTTA 57.481 47.619 0.00 0.00 0.00 1.85
3928 4440 4.035967 AGTACCCCCTCCATTCCTTTAT 57.964 45.455 0.00 0.00 0.00 1.40
3929 4441 5.179881 AGTACCCCCTCCATTCCTTTATA 57.820 43.478 0.00 0.00 0.00 0.98
3930 4442 5.749293 AGTACCCCCTCCATTCCTTTATAT 58.251 41.667 0.00 0.00 0.00 0.86
3931 4443 6.893396 AGTACCCCCTCCATTCCTTTATATA 58.107 40.000 0.00 0.00 0.00 0.86
3932 4444 7.326248 AGTACCCCCTCCATTCCTTTATATAA 58.674 38.462 0.00 0.00 0.00 0.98
3933 4445 6.720217 ACCCCCTCCATTCCTTTATATAAG 57.280 41.667 0.00 0.00 0.00 1.73
3934 4446 5.555941 ACCCCCTCCATTCCTTTATATAAGG 59.444 44.000 0.00 0.00 38.78 2.69
3935 4447 5.555941 CCCCCTCCATTCCTTTATATAAGGT 59.444 44.000 4.13 0.00 38.55 3.50
3936 4448 6.485171 CCCCTCCATTCCTTTATATAAGGTG 58.515 44.000 4.13 0.00 38.55 4.00
3937 4449 6.045577 CCCCTCCATTCCTTTATATAAGGTGT 59.954 42.308 4.13 2.81 38.55 4.16
3938 4450 7.238933 CCCCTCCATTCCTTTATATAAGGTGTA 59.761 40.741 4.13 3.09 38.55 2.90
3939 4451 8.836735 CCCTCCATTCCTTTATATAAGGTGTAT 58.163 37.037 4.13 4.58 38.55 2.29
3967 4479 6.683090 TTTTTCGAAAGTCAAACAAGTGTG 57.317 33.333 10.98 0.00 0.00 3.82
3968 4480 5.365403 TTTCGAAAGTCAAACAAGTGTGT 57.635 34.783 6.47 0.00 40.75 3.72
3969 4481 4.335082 TCGAAAGTCAAACAAGTGTGTG 57.665 40.909 0.00 0.00 38.27 3.82
3970 4482 3.749088 TCGAAAGTCAAACAAGTGTGTGT 59.251 39.130 1.62 0.00 38.27 3.72
3971 4483 4.214545 TCGAAAGTCAAACAAGTGTGTGTT 59.785 37.500 1.62 0.00 43.58 3.32
3977 4489 2.911819 AACAAGTGTGTGTTTGACCG 57.088 45.000 0.00 0.00 38.60 4.79
3978 4490 2.102070 ACAAGTGTGTGTTTGACCGA 57.898 45.000 0.00 0.00 36.31 4.69
3979 4491 2.006888 ACAAGTGTGTGTTTGACCGAG 58.993 47.619 0.00 0.00 36.31 4.63
3980 4492 2.006888 CAAGTGTGTGTTTGACCGAGT 58.993 47.619 0.00 0.00 0.00 4.18
3981 4493 2.396590 AGTGTGTGTTTGACCGAGTT 57.603 45.000 0.00 0.00 0.00 3.01
3982 4494 2.706890 AGTGTGTGTTTGACCGAGTTT 58.293 42.857 0.00 0.00 0.00 2.66
3983 4495 3.078837 AGTGTGTGTTTGACCGAGTTTT 58.921 40.909 0.00 0.00 0.00 2.43
3984 4496 3.504520 AGTGTGTGTTTGACCGAGTTTTT 59.495 39.130 0.00 0.00 0.00 1.94
4050 4562 8.812513 TCATTTGATCCATCATGAAAAGTAGT 57.187 30.769 0.00 0.00 36.56 2.73
4051 4563 9.246670 TCATTTGATCCATCATGAAAAGTAGTT 57.753 29.630 0.00 0.00 36.56 2.24
4052 4564 9.865321 CATTTGATCCATCATGAAAAGTAGTTT 57.135 29.630 0.00 0.00 36.56 2.66
4123 4635 7.722949 AATCTTGGTCAAACATTCATATGGT 57.277 32.000 2.13 0.00 36.01 3.55
4124 4636 7.722949 ATCTTGGTCAAACATTCATATGGTT 57.277 32.000 2.13 0.00 42.39 3.67
4132 4644 5.981088 AACATTCATATGGTTGACTTGCA 57.019 34.783 2.13 0.00 36.01 4.08
4133 4645 5.314923 ACATTCATATGGTTGACTTGCAC 57.685 39.130 2.13 0.00 36.01 4.57
4134 4646 4.142622 ACATTCATATGGTTGACTTGCACG 60.143 41.667 2.13 0.00 36.01 5.34
4135 4647 2.355197 TCATATGGTTGACTTGCACGG 58.645 47.619 2.13 0.00 0.00 4.94
4136 4648 2.027653 TCATATGGTTGACTTGCACGGA 60.028 45.455 2.13 0.00 0.00 4.69
4137 4649 2.552599 TATGGTTGACTTGCACGGAA 57.447 45.000 0.00 0.00 0.00 4.30
4138 4650 1.686355 ATGGTTGACTTGCACGGAAA 58.314 45.000 0.00 0.00 0.00 3.13
4139 4651 0.736053 TGGTTGACTTGCACGGAAAC 59.264 50.000 0.00 0.00 0.00 2.78
4140 4652 0.030235 GGTTGACTTGCACGGAAACC 59.970 55.000 11.74 11.74 0.00 3.27
4141 4653 0.736053 GTTGACTTGCACGGAAACCA 59.264 50.000 0.00 0.00 0.00 3.67
4142 4654 1.133407 GTTGACTTGCACGGAAACCAA 59.867 47.619 0.00 0.00 0.00 3.67
4143 4655 1.686355 TGACTTGCACGGAAACCAAT 58.314 45.000 0.00 0.00 0.00 3.16
4144 4656 2.852449 TGACTTGCACGGAAACCAATA 58.148 42.857 0.00 0.00 0.00 1.90
4145 4657 2.550606 TGACTTGCACGGAAACCAATAC 59.449 45.455 0.00 0.00 0.00 1.89
4146 4658 2.550606 GACTTGCACGGAAACCAATACA 59.449 45.455 0.00 0.00 0.00 2.29
4147 4659 2.292292 ACTTGCACGGAAACCAATACAC 59.708 45.455 0.00 0.00 0.00 2.90
4148 4660 1.240256 TGCACGGAAACCAATACACC 58.760 50.000 0.00 0.00 0.00 4.16
4149 4661 1.202830 TGCACGGAAACCAATACACCT 60.203 47.619 0.00 0.00 0.00 4.00
4150 4662 1.883926 GCACGGAAACCAATACACCTT 59.116 47.619 0.00 0.00 0.00 3.50
4151 4663 3.075884 GCACGGAAACCAATACACCTTA 58.924 45.455 0.00 0.00 0.00 2.69
4152 4664 3.692593 GCACGGAAACCAATACACCTTAT 59.307 43.478 0.00 0.00 0.00 1.73
4153 4665 4.877251 GCACGGAAACCAATACACCTTATA 59.123 41.667 0.00 0.00 0.00 0.98
4154 4666 5.529800 GCACGGAAACCAATACACCTTATAT 59.470 40.000 0.00 0.00 0.00 0.86
4155 4667 6.038936 GCACGGAAACCAATACACCTTATATT 59.961 38.462 0.00 0.00 0.00 1.28
4156 4668 7.636326 CACGGAAACCAATACACCTTATATTC 58.364 38.462 0.00 0.00 0.00 1.75
4157 4669 7.497909 CACGGAAACCAATACACCTTATATTCT 59.502 37.037 0.00 0.00 0.00 2.40
4158 4670 7.497909 ACGGAAACCAATACACCTTATATTCTG 59.502 37.037 0.00 0.00 0.00 3.02
4159 4671 7.041372 CGGAAACCAATACACCTTATATTCTGG 60.041 40.741 0.00 0.00 0.00 3.86
4160 4672 7.996644 GGAAACCAATACACCTTATATTCTGGA 59.003 37.037 0.00 0.00 0.00 3.86
4161 4673 9.403583 GAAACCAATACACCTTATATTCTGGAA 57.596 33.333 0.00 0.00 0.00 3.53
4162 4674 8.747538 AACCAATACACCTTATATTCTGGAAC 57.252 34.615 0.00 0.00 0.00 3.62
4163 4675 6.990349 ACCAATACACCTTATATTCTGGAACG 59.010 38.462 0.00 0.00 0.00 3.95
4164 4676 6.426937 CCAATACACCTTATATTCTGGAACGG 59.573 42.308 0.00 0.00 0.00 4.44
4165 4677 6.989155 ATACACCTTATATTCTGGAACGGA 57.011 37.500 0.00 0.00 45.11 4.69
4277 4795 4.609018 ACGCAACCGCAGAGCACT 62.609 61.111 0.00 0.00 38.40 4.40
4434 4975 8.853077 TTGTCATGATCAGTGAAGATTAAAGT 57.147 30.769 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.708322 TCTCTCTCGTCATTTAAATTCCTCATG 59.292 37.037 0.00 0.00 0.00 3.07
27 28 7.170393 TCTCTCTCGTCATTTAAATTCCTCA 57.830 36.000 0.00 0.00 0.00 3.86
81 82 2.280797 GCACAGAGGGCACGAACA 60.281 61.111 0.00 0.00 0.00 3.18
87 88 2.161855 CAGTTAAATGCACAGAGGGCA 58.838 47.619 0.00 0.00 46.66 5.36
97 98 7.915397 CCTCATGTAATTGTACCAGTTAAATGC 59.085 37.037 0.00 0.00 33.86 3.56
148 149 4.022589 AGAGAAATGTGCCATTGTTGACTG 60.023 41.667 1.80 0.00 0.00 3.51
169 170 9.553064 GATTAAGAGCATATTTGAAGGAGAAGA 57.447 33.333 0.00 0.00 0.00 2.87
170 171 8.494347 CGATTAAGAGCATATTTGAAGGAGAAG 58.506 37.037 0.00 0.00 0.00 2.85
175 176 7.042725 TCGTTCGATTAAGAGCATATTTGAAGG 60.043 37.037 0.00 0.00 0.00 3.46
221 222 7.878477 TTTGCTGCTAACATATACGGTATAC 57.122 36.000 9.92 0.00 0.00 1.47
227 228 6.771076 TCACTTTTTGCTGCTAACATATACG 58.229 36.000 0.00 0.00 0.00 3.06
302 353 6.990349 CCTCCTGTAACTTTTCTGAAACACTA 59.010 38.462 1.58 0.00 0.00 2.74
305 356 5.996644 TCCTCCTGTAACTTTTCTGAAACA 58.003 37.500 1.58 0.00 0.00 2.83
310 362 4.213482 CGGTTTCCTCCTGTAACTTTTCTG 59.787 45.833 0.00 0.00 0.00 3.02
312 364 4.212847 GTCGGTTTCCTCCTGTAACTTTTC 59.787 45.833 0.00 0.00 0.00 2.29
316 368 2.322658 TGTCGGTTTCCTCCTGTAACT 58.677 47.619 0.00 0.00 0.00 2.24
317 369 2.804527 GTTGTCGGTTTCCTCCTGTAAC 59.195 50.000 0.00 0.00 0.00 2.50
319 371 2.036733 CTGTTGTCGGTTTCCTCCTGTA 59.963 50.000 0.00 0.00 0.00 2.74
320 372 0.834612 TGTTGTCGGTTTCCTCCTGT 59.165 50.000 0.00 0.00 0.00 4.00
321 373 1.512926 CTGTTGTCGGTTTCCTCCTG 58.487 55.000 0.00 0.00 0.00 3.86
322 374 0.396811 CCTGTTGTCGGTTTCCTCCT 59.603 55.000 0.00 0.00 0.00 3.69
323 375 1.235281 GCCTGTTGTCGGTTTCCTCC 61.235 60.000 0.00 0.00 0.00 4.30
324 376 0.250338 AGCCTGTTGTCGGTTTCCTC 60.250 55.000 0.00 0.00 0.00 3.71
340 392 2.192187 GCAGCTCCCTTATGCAGCC 61.192 63.158 0.00 0.00 39.75 4.85
389 685 0.947180 TTCGCTTCTACGTTGGGCAC 60.947 55.000 0.00 0.00 0.00 5.01
400 696 1.003580 TCCTCTTGGCAATTCGCTTCT 59.996 47.619 0.00 0.00 41.91 2.85
401 697 1.131315 GTCCTCTTGGCAATTCGCTTC 59.869 52.381 0.00 0.00 41.91 3.86
404 700 0.449388 CAGTCCTCTTGGCAATTCGC 59.551 55.000 0.00 0.00 41.28 4.70
405 701 1.813513 ACAGTCCTCTTGGCAATTCG 58.186 50.000 0.00 0.00 0.00 3.34
407 703 8.212259 AGATATATACAGTCCTCTTGGCAATT 57.788 34.615 0.00 0.00 0.00 2.32
523 821 4.222145 TGAACGCTTACAGATAGGTCCTTT 59.778 41.667 0.00 0.00 0.00 3.11
561 859 2.504175 GCCCTGGTATCTTACTTCCACA 59.496 50.000 0.00 0.00 0.00 4.17
729 1028 1.369091 CCCGCTTGCGACAGCTAAAT 61.369 55.000 16.99 0.00 45.42 1.40
904 1241 1.157276 CCAAATGTCCCAACCCCCA 59.843 57.895 0.00 0.00 0.00 4.96
905 1242 0.902984 GTCCAAATGTCCCAACCCCC 60.903 60.000 0.00 0.00 0.00 5.40
906 1243 0.114364 AGTCCAAATGTCCCAACCCC 59.886 55.000 0.00 0.00 0.00 4.95
907 1244 1.256812 CAGTCCAAATGTCCCAACCC 58.743 55.000 0.00 0.00 0.00 4.11
908 1245 1.995376 ACAGTCCAAATGTCCCAACC 58.005 50.000 0.00 0.00 0.00 3.77
909 1246 6.433093 AGTTATTACAGTCCAAATGTCCCAAC 59.567 38.462 0.00 0.00 32.02 3.77
910 1247 6.432783 CAGTTATTACAGTCCAAATGTCCCAA 59.567 38.462 0.00 0.00 32.02 4.12
911 1248 5.943416 CAGTTATTACAGTCCAAATGTCCCA 59.057 40.000 0.00 0.00 32.02 4.37
912 1249 5.357032 CCAGTTATTACAGTCCAAATGTCCC 59.643 44.000 0.00 0.00 32.02 4.46
913 1250 5.357032 CCCAGTTATTACAGTCCAAATGTCC 59.643 44.000 0.00 0.00 32.02 4.02
914 1251 6.093633 GTCCCAGTTATTACAGTCCAAATGTC 59.906 42.308 0.00 0.00 32.02 3.06
915 1252 5.944007 GTCCCAGTTATTACAGTCCAAATGT 59.056 40.000 0.00 0.00 34.62 2.71
947 1284 2.159627 CAGCGCACCGACTAGAATTTTT 59.840 45.455 11.47 0.00 0.00 1.94
948 1285 1.732259 CAGCGCACCGACTAGAATTTT 59.268 47.619 11.47 0.00 0.00 1.82
949 1286 1.359848 CAGCGCACCGACTAGAATTT 58.640 50.000 11.47 0.00 0.00 1.82
951 1288 1.519455 GCAGCGCACCGACTAGAAT 60.519 57.895 11.47 0.00 0.00 2.40
952 1289 2.126071 GCAGCGCACCGACTAGAA 60.126 61.111 11.47 0.00 0.00 2.10
953 1290 4.129737 GGCAGCGCACCGACTAGA 62.130 66.667 11.47 0.00 0.00 2.43
1249 1598 2.705821 CGCAGAAGAGGTCGAGGCT 61.706 63.158 0.00 0.00 0.00 4.58
1554 1912 1.597027 CCCGACAAAGGCGTTCTGT 60.597 57.895 6.65 6.65 0.00 3.41
1556 1914 1.301479 GACCCGACAAAGGCGTTCT 60.301 57.895 0.00 0.00 0.00 3.01
1717 2075 1.134371 CCTCATCTCCCGGAAAACCTC 60.134 57.143 0.73 0.00 0.00 3.85
1811 2169 2.749466 GCATGGATACCTTTGCCTAGCA 60.749 50.000 0.00 0.00 36.47 3.49
1840 2198 5.973565 GCTCAGCATCATAAAGCGTTTTTAT 59.026 36.000 1.60 2.14 35.48 1.40
2496 2854 3.762823 TGCATCCACACTTTGCATATGAA 59.237 39.130 6.97 0.00 41.18 2.57
2523 2881 5.587844 AGTTTCAAATATCTTGCGAGCATCT 59.412 36.000 0.00 0.00 0.00 2.90
2612 2970 2.281484 GTTCTCGGGCCTGTGCAA 60.281 61.111 12.43 3.14 40.13 4.08
3240 3598 4.579869 GAGCCTTTTGTTCCTCATCTACA 58.420 43.478 0.00 0.00 0.00 2.74
3492 3850 8.051468 TCCCCTTAATACATGAATGGACAATA 57.949 34.615 0.00 0.00 0.00 1.90
3511 3869 0.924823 ATCAATGAGCAGCTCCCCTT 59.075 50.000 20.16 7.94 0.00 3.95
3788 4291 1.784283 CGTTCATGAAAAACCGTTGGC 59.216 47.619 10.35 0.00 0.00 4.52
3847 4354 7.654923 AGCCTTTTGCATTTTCTCTAAAGAAAG 59.345 33.333 5.10 0.00 46.05 2.62
3912 4424 6.045577 ACACCTTATATAAAGGAATGGAGGGG 59.954 42.308 10.67 5.38 39.81 4.79
3913 4425 7.091533 ACACCTTATATAAAGGAATGGAGGG 57.908 40.000 10.67 4.11 39.81 4.30
3944 4456 6.143118 CACACACTTGTTTGACTTTCGAAAAA 59.857 34.615 12.41 0.49 31.66 1.94
3945 4457 5.627367 CACACACTTGTTTGACTTTCGAAAA 59.373 36.000 12.41 0.00 31.66 2.29
3946 4458 5.150683 CACACACTTGTTTGACTTTCGAAA 58.849 37.500 10.71 10.71 31.66 3.46
3947 4459 4.214545 ACACACACTTGTTTGACTTTCGAA 59.785 37.500 2.56 0.00 31.66 3.71
3948 4460 3.749088 ACACACACTTGTTTGACTTTCGA 59.251 39.130 2.56 0.00 31.66 3.71
3949 4461 4.078363 ACACACACTTGTTTGACTTTCG 57.922 40.909 2.56 0.00 31.66 3.46
3958 4470 2.418628 CTCGGTCAAACACACACTTGTT 59.581 45.455 0.00 0.00 41.62 2.83
3959 4471 2.006888 CTCGGTCAAACACACACTTGT 58.993 47.619 0.00 0.00 35.84 3.16
3960 4472 2.006888 ACTCGGTCAAACACACACTTG 58.993 47.619 0.00 0.00 0.00 3.16
3961 4473 2.396590 ACTCGGTCAAACACACACTT 57.603 45.000 0.00 0.00 0.00 3.16
3962 4474 2.396590 AACTCGGTCAAACACACACT 57.603 45.000 0.00 0.00 0.00 3.55
3963 4475 3.481112 AAAACTCGGTCAAACACACAC 57.519 42.857 0.00 0.00 0.00 3.82
4024 4536 9.417561 ACTACTTTTCATGATGGATCAAATGAT 57.582 29.630 0.00 0.00 40.69 2.45
4025 4537 8.812513 ACTACTTTTCATGATGGATCAAATGA 57.187 30.769 0.00 0.00 40.69 2.57
4026 4538 9.865321 AAACTACTTTTCATGATGGATCAAATG 57.135 29.630 0.00 0.00 40.69 2.32
4097 4609 9.425248 ACCATATGAATGTTTGACCAAGATTAT 57.575 29.630 3.65 0.00 28.47 1.28
4098 4610 8.821686 ACCATATGAATGTTTGACCAAGATTA 57.178 30.769 3.65 0.00 28.47 1.75
4099 4611 7.722949 ACCATATGAATGTTTGACCAAGATT 57.277 32.000 3.65 0.00 31.00 2.40
4100 4612 7.396907 TCAACCATATGAATGTTTGACCAAGAT 59.603 33.333 3.65 0.00 38.97 2.40
4101 4613 6.718912 TCAACCATATGAATGTTTGACCAAGA 59.281 34.615 3.65 0.00 38.97 3.02
4102 4614 6.923012 TCAACCATATGAATGTTTGACCAAG 58.077 36.000 3.65 0.00 38.97 3.61
4103 4615 6.907853 TCAACCATATGAATGTTTGACCAA 57.092 33.333 3.65 0.00 38.97 3.67
4107 4619 6.015603 TGCAAGTCAACCATATGAATGTTTGA 60.016 34.615 3.65 2.45 40.85 2.69
4108 4620 6.089820 GTGCAAGTCAACCATATGAATGTTTG 59.910 38.462 3.65 11.78 36.97 2.93
4109 4621 6.158598 GTGCAAGTCAACCATATGAATGTTT 58.841 36.000 3.65 0.57 0.00 2.83
4110 4622 5.619757 CGTGCAAGTCAACCATATGAATGTT 60.620 40.000 3.65 0.00 0.00 2.71
4111 4623 4.142622 CGTGCAAGTCAACCATATGAATGT 60.143 41.667 3.65 0.00 0.00 2.71
4112 4624 4.345288 CGTGCAAGTCAACCATATGAATG 58.655 43.478 3.65 2.85 0.00 2.67
4113 4625 3.378112 CCGTGCAAGTCAACCATATGAAT 59.622 43.478 3.65 0.00 0.00 2.57
4114 4626 2.746904 CCGTGCAAGTCAACCATATGAA 59.253 45.455 3.65 0.00 0.00 2.57
4115 4627 2.027653 TCCGTGCAAGTCAACCATATGA 60.028 45.455 3.65 0.00 0.00 2.15
4116 4628 2.355197 TCCGTGCAAGTCAACCATATG 58.645 47.619 0.00 0.00 0.00 1.78
4117 4629 2.779755 TCCGTGCAAGTCAACCATAT 57.220 45.000 0.00 0.00 0.00 1.78
4118 4630 2.550606 GTTTCCGTGCAAGTCAACCATA 59.449 45.455 0.00 0.00 0.00 2.74
4119 4631 1.336755 GTTTCCGTGCAAGTCAACCAT 59.663 47.619 0.00 0.00 0.00 3.55
4120 4632 0.736053 GTTTCCGTGCAAGTCAACCA 59.264 50.000 0.00 0.00 0.00 3.67
4121 4633 0.030235 GGTTTCCGTGCAAGTCAACC 59.970 55.000 12.37 12.37 0.00 3.77
4122 4634 0.736053 TGGTTTCCGTGCAAGTCAAC 59.264 50.000 0.00 1.08 0.00 3.18
4123 4635 1.464734 TTGGTTTCCGTGCAAGTCAA 58.535 45.000 0.00 0.00 0.00 3.18
4124 4636 1.686355 ATTGGTTTCCGTGCAAGTCA 58.314 45.000 0.00 0.00 0.00 3.41
4125 4637 2.550606 TGTATTGGTTTCCGTGCAAGTC 59.449 45.455 0.00 0.00 0.00 3.01
4126 4638 2.292292 GTGTATTGGTTTCCGTGCAAGT 59.708 45.455 0.00 0.00 0.00 3.16
4127 4639 2.351350 GGTGTATTGGTTTCCGTGCAAG 60.351 50.000 0.00 0.00 0.00 4.01
4128 4640 1.609555 GGTGTATTGGTTTCCGTGCAA 59.390 47.619 0.00 0.00 0.00 4.08
4129 4641 1.202830 AGGTGTATTGGTTTCCGTGCA 60.203 47.619 0.00 0.00 0.00 4.57
4130 4642 1.530323 AGGTGTATTGGTTTCCGTGC 58.470 50.000 0.00 0.00 0.00 5.34
4131 4643 7.497909 AGAATATAAGGTGTATTGGTTTCCGTG 59.502 37.037 0.00 0.00 0.00 4.94
4132 4644 7.497909 CAGAATATAAGGTGTATTGGTTTCCGT 59.502 37.037 0.00 0.00 0.00 4.69
4133 4645 7.041372 CCAGAATATAAGGTGTATTGGTTTCCG 60.041 40.741 0.00 0.00 0.00 4.30
4134 4646 7.996644 TCCAGAATATAAGGTGTATTGGTTTCC 59.003 37.037 0.00 0.00 0.00 3.13
4135 4647 8.974060 TCCAGAATATAAGGTGTATTGGTTTC 57.026 34.615 0.00 0.00 0.00 2.78
4136 4648 9.185680 GTTCCAGAATATAAGGTGTATTGGTTT 57.814 33.333 0.00 0.00 0.00 3.27
4137 4649 7.497909 CGTTCCAGAATATAAGGTGTATTGGTT 59.502 37.037 0.00 0.00 0.00 3.67
4138 4650 6.990349 CGTTCCAGAATATAAGGTGTATTGGT 59.010 38.462 0.00 0.00 0.00 3.67
4139 4651 6.426937 CCGTTCCAGAATATAAGGTGTATTGG 59.573 42.308 0.00 0.00 0.00 3.16
4140 4652 7.214381 TCCGTTCCAGAATATAAGGTGTATTG 58.786 38.462 0.00 0.00 0.00 1.90
4141 4653 7.369551 TCCGTTCCAGAATATAAGGTGTATT 57.630 36.000 0.00 0.00 0.00 1.89
4142 4654 6.014499 CCTCCGTTCCAGAATATAAGGTGTAT 60.014 42.308 0.00 0.00 0.00 2.29
4143 4655 5.303589 CCTCCGTTCCAGAATATAAGGTGTA 59.696 44.000 0.00 0.00 0.00 2.90
4144 4656 4.101119 CCTCCGTTCCAGAATATAAGGTGT 59.899 45.833 0.00 0.00 0.00 4.16
4145 4657 4.503296 CCCTCCGTTCCAGAATATAAGGTG 60.503 50.000 0.00 0.00 0.00 4.00
4146 4658 3.646637 CCCTCCGTTCCAGAATATAAGGT 59.353 47.826 0.00 0.00 0.00 3.50
4147 4659 3.901844 TCCCTCCGTTCCAGAATATAAGG 59.098 47.826 0.00 0.00 0.00 2.69
4148 4660 4.589374 ACTCCCTCCGTTCCAGAATATAAG 59.411 45.833 0.00 0.00 0.00 1.73
4149 4661 4.553678 ACTCCCTCCGTTCCAGAATATAA 58.446 43.478 0.00 0.00 0.00 0.98
4150 4662 4.194678 ACTCCCTCCGTTCCAGAATATA 57.805 45.455 0.00 0.00 0.00 0.86
4151 4663 3.047695 ACTCCCTCCGTTCCAGAATAT 57.952 47.619 0.00 0.00 0.00 1.28
4152 4664 2.544844 ACTCCCTCCGTTCCAGAATA 57.455 50.000 0.00 0.00 0.00 1.75
4153 4665 2.544844 TACTCCCTCCGTTCCAGAAT 57.455 50.000 0.00 0.00 0.00 2.40
4154 4666 2.544844 ATACTCCCTCCGTTCCAGAA 57.455 50.000 0.00 0.00 0.00 3.02
4155 4667 3.294214 GTTATACTCCCTCCGTTCCAGA 58.706 50.000 0.00 0.00 0.00 3.86
4156 4668 2.364647 GGTTATACTCCCTCCGTTCCAG 59.635 54.545 0.00 0.00 0.00 3.86
4157 4669 2.391678 GGTTATACTCCCTCCGTTCCA 58.608 52.381 0.00 0.00 0.00 3.53
4158 4670 1.690893 GGGTTATACTCCCTCCGTTCC 59.309 57.143 5.24 0.00 41.58 3.62
4159 4671 2.364647 CTGGGTTATACTCCCTCCGTTC 59.635 54.545 11.93 0.00 44.84 3.95
4160 4672 2.395619 CTGGGTTATACTCCCTCCGTT 58.604 52.381 11.93 0.00 44.84 4.44
4161 4673 1.412649 CCTGGGTTATACTCCCTCCGT 60.413 57.143 11.93 0.00 44.84 4.69
4162 4674 1.133262 TCCTGGGTTATACTCCCTCCG 60.133 57.143 11.93 3.24 44.84 4.63
4163 4675 2.610873 CTCCTGGGTTATACTCCCTCC 58.389 57.143 11.93 0.00 44.84 4.30
4164 4676 2.610873 CCTCCTGGGTTATACTCCCTC 58.389 57.143 11.93 0.00 44.84 4.30
4165 4677 2.797285 CCTCCTGGGTTATACTCCCT 57.203 55.000 11.93 0.00 44.84 4.20
4434 4975 4.219115 TCATAGCCAAAACAACCCTTTCA 58.781 39.130 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.