Multiple sequence alignment - TraesCS2D01G205000

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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 TraesCS2D01G205000 chr2D 100.000 5532 0 0 1 5532 157013879 157019410 0.000000e+00 10216.0
1 TraesCS2D01G205000 chr2A 96.547 3475 83 17 810 4276 166825568 166829013 0.000000e+00 5718.0
2 TraesCS2D01G205000 chr2A 88.101 1185 82 24 4351 5496 166829012 166830176 0.000000e+00 1352.0
3 TraesCS2D01G205000 chr2A 100.000 32 0 0 1481 1512 16327267 16327298 5.980000e-05 60.2
4 TraesCS2D01G205000 chr2B 94.689 1657 65 12 786 2440 214530542 214532177 0.000000e+00 2551.0
5 TraesCS2D01G205000 chr2B 91.436 1191 81 15 3098 4273 214532871 214534055 0.000000e+00 1615.0
6 TraesCS2D01G205000 chr2B 85.012 1241 81 43 4350 5532 214534055 214535248 0.000000e+00 1164.0
7 TraesCS2D01G205000 chr2B 88.253 647 40 13 2466 3099 214532166 214532789 0.000000e+00 741.0
8 TraesCS2D01G205000 chr2B 83.942 274 39 2 1 269 282857828 282858101 1.980000e-64 257.0
9 TraesCS2D01G205000 chr4D 95.147 783 12 5 1 759 190496275 190497055 0.000000e+00 1212.0
10 TraesCS2D01G205000 chr4D 96.273 161 5 1 602 761 190493697 190493537 4.250000e-66 263.0
11 TraesCS2D01G205000 chr4B 92.465 783 36 4 1 760 644084576 644083794 0.000000e+00 1098.0
12 TraesCS2D01G205000 chr4B 96.855 159 4 1 602 759 644086270 644086428 1.180000e-66 265.0
13 TraesCS2D01G205000 chr4B 84.783 230 25 4 1 229 421703154 421703374 7.210000e-54 222.0
14 TraesCS2D01G205000 chr6B 93.097 565 17 3 217 759 159368861 159368297 0.000000e+00 808.0
15 TraesCS2D01G205000 chr6B 93.720 414 24 1 277 688 492217102 492217515 2.190000e-173 619.0
16 TraesCS2D01G205000 chr6B 92.328 378 8 8 1 357 492216748 492217125 8.210000e-143 518.0
17 TraesCS2D01G205000 chr6B 96.996 233 7 0 1 233 159369110 159368878 5.200000e-105 392.0
18 TraesCS2D01G205000 chr6B 97.500 160 3 1 602 760 159371446 159371605 7.060000e-69 272.0
19 TraesCS2D01G205000 chr6B 95.679 162 3 1 602 759 492212924 492212763 1.980000e-64 257.0
20 TraesCS2D01G205000 chr3D 94.328 476 22 4 298 769 267914628 267914154 0.000000e+00 725.0
21 TraesCS2D01G205000 chr3D 95.926 270 11 0 1 270 267914983 267914714 6.580000e-119 438.0
22 TraesCS2D01G205000 chr3D 85.401 274 35 2 1 269 41692915 41693188 4.220000e-71 279.0
23 TraesCS2D01G205000 chr3A 83.942 274 39 2 1 269 636681978 636681705 1.980000e-64 257.0
24 TraesCS2D01G205000 chr1B 86.522 230 21 3 1 229 569419183 569419403 1.540000e-60 244.0
25 TraesCS2D01G205000 chr7A 100.000 29 0 0 4315 4343 683484694 683484666 3.000000e-03 54.7


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 TraesCS2D01G205000 chr2D 157013879 157019410 5531 False 10216.00 10216 100.0000 1 5532 1 chr2D.!!$F1 5531
1 TraesCS2D01G205000 chr2A 166825568 166830176 4608 False 3535.00 5718 92.3240 810 5496 2 chr2A.!!$F2 4686
2 TraesCS2D01G205000 chr2B 214530542 214535248 4706 False 1517.75 2551 89.8475 786 5532 4 chr2B.!!$F2 4746
3 TraesCS2D01G205000 chr4D 190496275 190497055 780 False 1212.00 1212 95.1470 1 759 1 chr4D.!!$F1 758
4 TraesCS2D01G205000 chr4B 644083794 644084576 782 True 1098.00 1098 92.4650 1 760 1 chr4B.!!$R1 759
5 TraesCS2D01G205000 chr6B 159368297 159369110 813 True 600.00 808 95.0465 1 759 2 chr6B.!!$R2 758
6 TraesCS2D01G205000 chr6B 492216748 492217515 767 False 568.50 619 93.0240 1 688 2 chr6B.!!$F2 687
7 TraesCS2D01G205000 chr3D 267914154 267914983 829 True 581.50 725 95.1270 1 769 2 chr3D.!!$R1 768

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
783 942 0.036199 CCGGGTACAAACGATTCCCA 60.036 55.000 0.00 0.00 38.15 4.37 F
1470 1632 0.167470 TCGACGACATTGACGACCTC 59.833 55.000 15.06 2.12 31.55 3.85 F
1683 1845 0.730834 CTGACGCAGACAAGGACTCG 60.731 60.000 1.18 0.00 32.44 4.18 F
2181 2344 1.129998 CATTGCAGCCTGAAGAAGTCG 59.870 52.381 0.00 0.00 0.00 4.18 F
2575 2748 2.764572 TCTGTACCTTAGGCCAGCTTAC 59.235 50.000 5.01 0.00 0.00 2.34 F
4010 4275 0.106015 AGGCTTCAACCCACAAGCTT 60.106 50.000 0.00 0.00 43.89 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2135 0.991920 TCCCAATTCACCCCACTCTC 59.008 55.000 0.00 0.00 0.00 3.20 R
3327 3590 3.188667 CGCTTCCTCAAAAAGGTCCTTAC 59.811 47.826 4.04 0.00 46.32 2.34 R
3368 3631 6.488715 AGTTTAAGAGGAAGCTGAATCCATT 58.511 36.000 5.73 2.89 39.55 3.16 R
3992 4256 2.429927 AAGCTTGTGGGTTGAAGCC 58.570 52.632 6.44 6.44 44.79 4.35 R
4325 4601 0.178975 ACCTCCGTCCCAAAATGCAA 60.179 50.000 0.00 0.00 0.00 4.08 R
4874 5178 0.866427 CGGCAGACAGATCATGATGC 59.134 55.000 14.30 10.62 41.43 3.91 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 7.118390 GGATAGTGTGCTTATGCTTACTTATGG 59.882 40.741 12.83 0.00 40.48 2.74
99 100 2.854963 AGCATCAGTGACAAGCTTGAA 58.145 42.857 32.50 17.05 29.98 2.69
345 439 4.445453 TGCTGCCAGTTTCAGACATATAG 58.555 43.478 0.00 0.00 33.54 1.31
494 647 7.068593 TCACTTCTGGACAAAATTCAGACAAAT 59.931 33.333 0.00 0.00 37.28 2.32
630 784 0.661020 CAAAACCGGCGTCTCAAACT 59.339 50.000 6.01 0.00 0.00 2.66
657 812 1.076777 CGCCATCAGGGGGTGATTT 60.077 57.895 0.00 0.00 44.05 2.17
762 921 1.060698 GTATGTGGACTTCTTTCGCGC 59.939 52.381 0.00 0.00 0.00 6.86
763 922 1.626654 ATGTGGACTTCTTTCGCGCG 61.627 55.000 26.76 26.76 0.00 6.86
765 924 4.148645 GGACTTCTTTCGCGCGCC 62.149 66.667 27.95 14.43 0.00 6.53
778 937 2.816520 GCGCCGGGTACAAACGAT 60.817 61.111 2.18 0.00 0.00 3.73
779 938 2.392974 GCGCCGGGTACAAACGATT 61.393 57.895 2.18 0.00 0.00 3.34
780 939 1.711500 CGCCGGGTACAAACGATTC 59.289 57.895 2.18 0.00 0.00 2.52
781 940 1.698714 CGCCGGGTACAAACGATTCC 61.699 60.000 2.18 0.00 0.00 3.01
782 941 1.371337 GCCGGGTACAAACGATTCCC 61.371 60.000 2.18 0.00 35.22 3.97
783 942 0.036199 CCGGGTACAAACGATTCCCA 60.036 55.000 0.00 0.00 38.15 4.37
784 943 1.407712 CCGGGTACAAACGATTCCCAT 60.408 52.381 0.00 0.00 38.15 4.00
790 949 5.416639 GGGTACAAACGATTCCCATAAAACT 59.583 40.000 0.00 0.00 38.15 2.66
797 956 4.526650 ACGATTCCCATAAAACTTGGCTTT 59.473 37.500 0.00 0.00 32.60 3.51
805 965 5.221621 CCATAAAACTTGGCTTTTCCCTGAA 60.222 40.000 0.00 0.00 0.00 3.02
952 1114 3.958860 CCCGCCCCATCTCCATCC 61.959 72.222 0.00 0.00 0.00 3.51
1197 1359 3.552384 AACTCCAACGCCGACCCA 61.552 61.111 0.00 0.00 0.00 4.51
1470 1632 0.167470 TCGACGACATTGACGACCTC 59.833 55.000 15.06 2.12 31.55 3.85
1548 1710 1.519719 GCAGAAGGCTGGTCGAGAT 59.480 57.895 0.00 0.00 42.53 2.75
1593 1755 1.026718 GTGTAGGTGCTGGTGATGGC 61.027 60.000 0.00 0.00 0.00 4.40
1683 1845 0.730834 CTGACGCAGACAAGGACTCG 60.731 60.000 1.18 0.00 32.44 4.18
1833 1995 3.450457 AGGGAAAGTCAATGTTTGCAACA 59.550 39.130 0.00 0.88 46.94 3.33
1973 2135 9.767684 TCAGTTATGAATTAAAGTAATTGTGCG 57.232 29.630 0.00 0.00 38.42 5.34
2048 2211 4.823157 TGCAAAATTCAGAATCATGGGTG 58.177 39.130 0.00 0.00 0.00 4.61
2055 2218 4.212143 TCAGAATCATGGGTGAAGTGAG 57.788 45.455 0.00 0.00 38.01 3.51
2181 2344 1.129998 CATTGCAGCCTGAAGAAGTCG 59.870 52.381 0.00 0.00 0.00 4.18
2575 2748 2.764572 TCTGTACCTTAGGCCAGCTTAC 59.235 50.000 5.01 0.00 0.00 2.34
2922 3096 6.741992 TGACTGTATGCTTGGTATTCTTTG 57.258 37.500 0.00 0.00 0.00 2.77
3047 3222 3.440522 GGAGGGTGCTCTTGTAAAATGAC 59.559 47.826 0.00 0.00 0.00 3.06
3055 3230 6.140737 GTGCTCTTGTAAAATGACGAAAACAG 59.859 38.462 0.00 0.00 0.00 3.16
3368 3631 4.394729 AGCGACTTTTGATGGTCCTTTTA 58.605 39.130 0.00 0.00 0.00 1.52
3402 3665 8.499967 CAGCTTCCTCTTAAACTCTTTTCTTAC 58.500 37.037 0.00 0.00 0.00 2.34
3404 3667 9.058174 GCTTCCTCTTAAACTCTTTTCTTACTT 57.942 33.333 0.00 0.00 0.00 2.24
3784 4048 5.045012 ACAGTGTGGCTCATATCATGAAT 57.955 39.130 0.00 0.00 39.11 2.57
3937 4201 4.455070 TCTATCGGAGGAGAAGAATCCA 57.545 45.455 0.00 0.00 42.26 3.41
3992 4256 1.163554 GCCAGCCTCAAAAGAGTGAG 58.836 55.000 0.00 0.00 43.98 3.51
4010 4275 0.106015 AGGCTTCAACCCACAAGCTT 60.106 50.000 0.00 0.00 43.89 3.74
4017 4282 1.542915 CAACCCACAAGCTTGGATCAG 59.457 52.381 29.18 15.29 39.24 2.90
4018 4283 0.610232 ACCCACAAGCTTGGATCAGC 60.610 55.000 29.18 0.00 39.24 4.26
4023 4288 3.635373 CCACAAGCTTGGATCAGCAATAT 59.365 43.478 29.18 1.60 42.84 1.28
4185 4456 5.874093 AGAATTCACTGTCTGAGGTTTCAT 58.126 37.500 8.44 0.00 31.68 2.57
4220 4496 4.804868 AATTGCATAAACATCCTGCACA 57.195 36.364 0.00 0.00 44.94 4.57
4224 4500 3.057386 TGCATAAACATCCTGCACAGTTG 60.057 43.478 0.00 0.00 40.75 3.16
4228 4504 2.346766 ACATCCTGCACAGTTGAACA 57.653 45.000 0.00 0.00 0.00 3.18
4266 4542 2.215942 ACTTGGTTAATCAGGTGGGC 57.784 50.000 2.17 0.00 0.00 5.36
4274 4550 4.042187 GGTTAATCAGGTGGGCTATCTCAT 59.958 45.833 0.00 0.00 0.00 2.90
4275 4551 5.248477 GGTTAATCAGGTGGGCTATCTCATA 59.752 44.000 0.00 0.00 0.00 2.15
4276 4552 4.899352 AATCAGGTGGGCTATCTCATAC 57.101 45.455 0.00 0.00 0.00 2.39
4277 4553 3.619900 TCAGGTGGGCTATCTCATACT 57.380 47.619 0.00 0.00 0.00 2.12
4278 4554 3.501349 TCAGGTGGGCTATCTCATACTC 58.499 50.000 0.00 0.00 0.00 2.59
4279 4555 2.564947 CAGGTGGGCTATCTCATACTCC 59.435 54.545 0.00 0.00 0.00 3.85
4280 4556 2.180086 AGGTGGGCTATCTCATACTCCA 59.820 50.000 0.00 0.00 0.00 3.86
4281 4557 3.177228 GGTGGGCTATCTCATACTCCAT 58.823 50.000 0.00 0.00 0.00 3.41
4282 4558 3.196685 GGTGGGCTATCTCATACTCCATC 59.803 52.174 0.00 0.00 0.00 3.51
4283 4559 3.196685 GTGGGCTATCTCATACTCCATCC 59.803 52.174 0.00 0.00 0.00 3.51
4284 4560 2.428890 GGGCTATCTCATACTCCATCCG 59.571 54.545 0.00 0.00 0.00 4.18
4285 4561 3.093057 GGCTATCTCATACTCCATCCGT 58.907 50.000 0.00 0.00 0.00 4.69
4286 4562 3.129638 GGCTATCTCATACTCCATCCGTC 59.870 52.174 0.00 0.00 0.00 4.79
4287 4563 3.129638 GCTATCTCATACTCCATCCGTCC 59.870 52.174 0.00 0.00 0.00 4.79
4288 4564 1.996798 TCTCATACTCCATCCGTCCC 58.003 55.000 0.00 0.00 0.00 4.46
4289 4565 1.216930 TCTCATACTCCATCCGTCCCA 59.783 52.381 0.00 0.00 0.00 4.37
4290 4566 2.039418 CTCATACTCCATCCGTCCCAA 58.961 52.381 0.00 0.00 0.00 4.12
4291 4567 2.434336 CTCATACTCCATCCGTCCCAAA 59.566 50.000 0.00 0.00 0.00 3.28
4292 4568 2.841266 TCATACTCCATCCGTCCCAAAA 59.159 45.455 0.00 0.00 0.00 2.44
4293 4569 3.458118 TCATACTCCATCCGTCCCAAAAT 59.542 43.478 0.00 0.00 0.00 1.82
4294 4570 4.656575 TCATACTCCATCCGTCCCAAAATA 59.343 41.667 0.00 0.00 0.00 1.40
4295 4571 3.277142 ACTCCATCCGTCCCAAAATAC 57.723 47.619 0.00 0.00 0.00 1.89
4296 4572 2.844348 ACTCCATCCGTCCCAAAATACT 59.156 45.455 0.00 0.00 0.00 2.12
4297 4573 3.265995 ACTCCATCCGTCCCAAAATACTT 59.734 43.478 0.00 0.00 0.00 2.24
4298 4574 4.472108 ACTCCATCCGTCCCAAAATACTTA 59.528 41.667 0.00 0.00 0.00 2.24
4299 4575 5.132144 ACTCCATCCGTCCCAAAATACTTAT 59.868 40.000 0.00 0.00 0.00 1.73
4300 4576 6.328148 ACTCCATCCGTCCCAAAATACTTATA 59.672 38.462 0.00 0.00 0.00 0.98
4301 4577 7.139287 TCCATCCGTCCCAAAATACTTATAA 57.861 36.000 0.00 0.00 0.00 0.98
4302 4578 7.221450 TCCATCCGTCCCAAAATACTTATAAG 58.779 38.462 11.05 11.05 0.00 1.73
4303 4579 7.071447 TCCATCCGTCCCAAAATACTTATAAGA 59.929 37.037 19.38 3.51 0.00 2.10
4304 4580 7.172703 CCATCCGTCCCAAAATACTTATAAGAC 59.827 40.741 19.38 2.94 0.00 3.01
4305 4581 7.185318 TCCGTCCCAAAATACTTATAAGACA 57.815 36.000 19.38 6.73 0.00 3.41
4306 4582 7.622713 TCCGTCCCAAAATACTTATAAGACAA 58.377 34.615 19.38 4.65 0.00 3.18
4307 4583 8.269317 TCCGTCCCAAAATACTTATAAGACAAT 58.731 33.333 19.38 6.69 0.00 2.71
4308 4584 8.899771 CCGTCCCAAAATACTTATAAGACAATT 58.100 33.333 19.38 11.74 0.00 2.32
4328 4604 7.249858 ACAATTTTTGACAAAAATGGTCTTGC 58.750 30.769 29.05 0.00 46.82 4.01
4329 4605 6.998968 ATTTTTGACAAAAATGGTCTTGCA 57.001 29.167 29.31 7.30 46.30 4.08
4330 4606 6.998968 TTTTTGACAAAAATGGTCTTGCAT 57.001 29.167 19.67 0.00 35.57 3.96
4331 4607 6.998968 TTTTGACAAAAATGGTCTTGCATT 57.001 29.167 10.92 0.00 36.26 3.56
4332 4608 6.998968 TTTGACAAAAATGGTCTTGCATTT 57.001 29.167 0.00 0.00 36.26 2.32
4333 4609 6.998968 TTGACAAAAATGGTCTTGCATTTT 57.001 29.167 0.00 0.00 41.18 1.82
4334 4610 6.360844 TGACAAAAATGGTCTTGCATTTTG 57.639 33.333 14.68 14.68 39.87 2.44
4335 4611 5.296283 TGACAAAAATGGTCTTGCATTTTGG 59.704 36.000 18.53 8.48 39.87 3.28
4336 4612 4.579753 ACAAAAATGGTCTTGCATTTTGGG 59.420 37.500 18.53 7.46 39.87 4.12
4337 4613 4.703379 AAAATGGTCTTGCATTTTGGGA 57.297 36.364 0.00 0.00 38.91 4.37
4338 4614 3.683365 AATGGTCTTGCATTTTGGGAC 57.317 42.857 0.00 0.00 0.00 4.46
4339 4615 0.958091 TGGTCTTGCATTTTGGGACG 59.042 50.000 0.00 0.00 0.00 4.79
4340 4616 0.243636 GGTCTTGCATTTTGGGACGG 59.756 55.000 0.00 0.00 0.00 4.79
4341 4617 1.243902 GTCTTGCATTTTGGGACGGA 58.756 50.000 0.00 0.00 0.00 4.69
4342 4618 1.200020 GTCTTGCATTTTGGGACGGAG 59.800 52.381 0.00 0.00 0.00 4.63
4343 4619 0.527565 CTTGCATTTTGGGACGGAGG 59.472 55.000 0.00 0.00 0.00 4.30
4344 4620 0.178975 TTGCATTTTGGGACGGAGGT 60.179 50.000 0.00 0.00 0.00 3.85
4345 4621 0.693622 TGCATTTTGGGACGGAGGTA 59.306 50.000 0.00 0.00 0.00 3.08
4346 4622 1.339631 TGCATTTTGGGACGGAGGTAG 60.340 52.381 0.00 0.00 0.00 3.18
4347 4623 1.339727 GCATTTTGGGACGGAGGTAGT 60.340 52.381 0.00 0.00 0.00 2.73
4348 4624 2.093341 GCATTTTGGGACGGAGGTAGTA 60.093 50.000 0.00 0.00 0.00 1.82
4366 4642 9.122779 GAGGTAGTACTAGTTATGTTCTCACAT 57.877 37.037 1.87 0.00 46.07 3.21
4410 4686 2.749621 GGGTAACAGAGGCAAATCACTG 59.250 50.000 0.00 0.00 39.74 3.66
4417 4693 0.963962 AGGCAAATCACTGTGCTTGG 59.036 50.000 18.11 8.86 40.70 3.61
4442 4718 1.728971 GGATTCACTGTCTCACTTGCG 59.271 52.381 0.00 0.00 0.00 4.85
4463 4739 3.506067 CGTGGAAACTAATTTTGCTCCCT 59.494 43.478 0.00 0.00 36.51 4.20
4556 4835 1.339610 GCCCACTGCATTACAACAACA 59.660 47.619 0.00 0.00 40.77 3.33
4561 4840 5.050227 CCCACTGCATTACAACAACAAATTG 60.050 40.000 0.00 0.00 41.98 2.32
4608 4888 6.780457 AGTTTGGATGAAGATACAAATGGG 57.220 37.500 0.00 0.00 43.07 4.00
4611 4891 4.209538 TGGATGAAGATACAAATGGGCAG 58.790 43.478 0.00 0.00 0.00 4.85
4616 4896 4.467082 TGAAGATACAAATGGGCAGCAATT 59.533 37.500 0.00 0.00 0.00 2.32
4617 4897 5.046448 TGAAGATACAAATGGGCAGCAATTT 60.046 36.000 0.00 0.00 0.00 1.82
4618 4898 6.154192 TGAAGATACAAATGGGCAGCAATTTA 59.846 34.615 5.27 0.00 0.00 1.40
4619 4899 6.152932 AGATACAAATGGGCAGCAATTTAG 57.847 37.500 5.27 4.00 0.00 1.85
4620 4900 5.893255 AGATACAAATGGGCAGCAATTTAGA 59.107 36.000 5.27 0.00 0.00 2.10
4622 4902 4.824289 ACAAATGGGCAGCAATTTAGAAG 58.176 39.130 5.27 0.00 0.00 2.85
4623 4903 3.531934 AATGGGCAGCAATTTAGAAGC 57.468 42.857 0.00 0.00 0.00 3.86
4624 4904 2.220653 TGGGCAGCAATTTAGAAGCT 57.779 45.000 0.00 0.00 39.63 3.74
4666 4946 3.733024 TCAATGCCTACGTTTTTAGCG 57.267 42.857 0.00 0.00 0.00 4.26
4669 4949 0.320946 TGCCTACGTTTTTAGCGGCT 60.321 50.000 7.98 7.98 38.33 5.52
4690 4970 2.689471 TGTGCTGAATGCTTCTTTGTGT 59.311 40.909 0.00 0.00 43.37 3.72
4764 5048 8.353423 ACATGGTGAATATGTTAAAAGCTTCT 57.647 30.769 0.00 0.00 35.32 2.85
4783 5068 5.183904 GCTTCTATTGCCTCTCAAAGGAAAA 59.816 40.000 0.00 0.00 46.48 2.29
4784 5069 6.294731 GCTTCTATTGCCTCTCAAAGGAAAAA 60.295 38.462 0.00 0.00 46.48 1.94
4785 5070 6.824305 TCTATTGCCTCTCAAAGGAAAAAG 57.176 37.500 0.00 0.00 46.48 2.27
4786 5071 4.879197 ATTGCCTCTCAAAGGAAAAAGG 57.121 40.909 0.00 0.00 46.48 3.11
4788 5073 4.655649 ATTGCCTCTCAAAGGAAAAAGGTT 59.344 37.500 0.00 0.00 46.48 3.50
4790 5075 8.369704 ATTGCCTCTCAAAGGAAAAAGGTTGG 62.370 42.308 0.00 0.00 46.48 3.77
4791 5076 3.982475 CTCTCAAAGGAAAAAGGTTGGC 58.018 45.455 0.00 0.00 0.00 4.52
4869 5173 1.850441 GCGCTGCAAAAGAAGCATATG 59.150 47.619 0.00 0.00 41.82 1.78
4870 5174 1.850441 CGCTGCAAAAGAAGCATATGC 59.150 47.619 20.36 20.36 41.82 3.14
4898 5206 2.887568 GATCTGTCTGCCGGTGCG 60.888 66.667 1.90 0.00 41.78 5.34
4916 5224 1.264826 GCGCAAGAAAAGACGGGTAAA 59.735 47.619 0.30 0.00 43.02 2.01
4918 5226 3.743886 CGCAAGAAAAGACGGGTAAATC 58.256 45.455 0.00 0.00 43.02 2.17
4986 5297 4.695231 CCAGTCGCCGTCGTCGTT 62.695 66.667 0.71 0.00 36.96 3.85
5017 5328 1.810030 GCTGTCGTCCGACCATTCC 60.810 63.158 16.39 0.00 43.97 3.01
5106 5430 1.656652 AGCATGCGTACAATGTCCTC 58.343 50.000 13.01 0.00 0.00 3.71
5120 5444 4.717328 ATGTCCTCCCCCTATATGATGA 57.283 45.455 0.00 0.00 0.00 2.92
5121 5445 4.717328 TGTCCTCCCCCTATATGATGAT 57.283 45.455 0.00 0.00 0.00 2.45
5122 5446 4.365368 TGTCCTCCCCCTATATGATGATG 58.635 47.826 0.00 0.00 0.00 3.07
5123 5447 4.202934 TGTCCTCCCCCTATATGATGATGT 60.203 45.833 0.00 0.00 0.00 3.06
5297 5630 1.952133 TTCACCTGCACGTACGCAC 60.952 57.895 16.72 8.27 36.86 5.34
5356 5689 1.226547 GCGACGAGAGAGAGCCAAG 60.227 63.158 0.00 0.00 0.00 3.61
5439 5776 1.832167 GCCGAGAGCTGGGAGAGAT 60.832 63.158 2.47 0.00 38.99 2.75
5490 5827 1.213013 GACGAGCCGTGTGATCTGT 59.787 57.895 4.94 0.00 41.37 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 0.321564 TGCTACACATCACCACTGCC 60.322 55.000 0.00 0.00 0.00 4.85
345 439 5.132897 TGTCCAAATTGCATAAACCTGAC 57.867 39.130 0.00 0.00 0.00 3.51
630 784 0.322997 CCCTGATGGCGTTTTGGGTA 60.323 55.000 4.95 0.00 0.00 3.69
657 812 2.050918 TGGACTGTCCAATACCACACA 58.949 47.619 26.54 0.00 45.00 3.72
762 921 1.698714 GGAATCGTTTGTACCCGGCG 61.699 60.000 0.00 0.00 0.00 6.46
763 922 1.371337 GGGAATCGTTTGTACCCGGC 61.371 60.000 0.00 0.00 0.00 6.13
765 924 2.032680 ATGGGAATCGTTTGTACCCG 57.967 50.000 0.00 0.00 43.04 5.28
768 927 6.804783 CCAAGTTTTATGGGAATCGTTTGTAC 59.195 38.462 0.00 0.00 34.15 2.90
769 928 6.570764 GCCAAGTTTTATGGGAATCGTTTGTA 60.571 38.462 0.00 0.00 38.44 2.41
770 929 5.778862 CCAAGTTTTATGGGAATCGTTTGT 58.221 37.500 0.00 0.00 34.15 2.83
771 930 4.625311 GCCAAGTTTTATGGGAATCGTTTG 59.375 41.667 0.00 0.00 38.44 2.93
772 931 4.526650 AGCCAAGTTTTATGGGAATCGTTT 59.473 37.500 0.00 0.00 38.44 3.60
773 932 4.086457 AGCCAAGTTTTATGGGAATCGTT 58.914 39.130 0.00 0.00 38.44 3.85
774 933 3.697166 AGCCAAGTTTTATGGGAATCGT 58.303 40.909 0.00 0.00 38.44 3.73
775 934 4.718940 AAGCCAAGTTTTATGGGAATCG 57.281 40.909 0.00 0.00 38.44 3.34
776 935 5.874810 GGAAAAGCCAAGTTTTATGGGAATC 59.125 40.000 0.00 0.00 38.44 2.52
777 936 5.280470 GGGAAAAGCCAAGTTTTATGGGAAT 60.280 40.000 0.00 0.00 38.44 3.01
778 937 4.041075 GGGAAAAGCCAAGTTTTATGGGAA 59.959 41.667 0.00 0.00 38.44 3.97
779 938 3.580895 GGGAAAAGCCAAGTTTTATGGGA 59.419 43.478 0.00 0.00 38.44 4.37
780 939 3.582647 AGGGAAAAGCCAAGTTTTATGGG 59.417 43.478 0.00 0.00 38.44 4.00
781 940 4.283212 TCAGGGAAAAGCCAAGTTTTATGG 59.717 41.667 0.00 0.00 41.08 2.74
782 941 5.467035 TCAGGGAAAAGCCAAGTTTTATG 57.533 39.130 0.00 0.00 38.95 1.90
783 942 6.493189 TTTCAGGGAAAAGCCAAGTTTTAT 57.507 33.333 0.00 0.00 38.95 1.40
784 943 5.941555 TTTCAGGGAAAAGCCAAGTTTTA 57.058 34.783 0.00 0.00 38.95 1.52
866 1028 2.636412 CGGCCACGACTCCTCTCAA 61.636 63.158 2.24 0.00 44.60 3.02
893 1055 3.368531 GCTTTCTGACACGGGAATACTCT 60.369 47.826 0.00 0.00 0.00 3.24
938 1100 3.958860 CGGGGATGGAGATGGGGC 61.959 72.222 0.00 0.00 0.00 5.80
939 1101 2.448542 ACGGGGATGGAGATGGGG 60.449 66.667 0.00 0.00 0.00 4.96
941 1103 1.476007 GGAGACGGGGATGGAGATGG 61.476 65.000 0.00 0.00 0.00 3.51
942 1104 2.053618 GGAGACGGGGATGGAGATG 58.946 63.158 0.00 0.00 0.00 2.90
1449 1611 0.914551 GGTCGTCAATGTCGTCGATG 59.085 55.000 0.00 0.00 34.93 3.84
1470 1632 1.039785 TCTGCCCCTCTGTCATCTCG 61.040 60.000 0.00 0.00 0.00 4.04
1683 1845 4.024048 TCAAACTTGGTCTTCATTCGCTTC 60.024 41.667 0.00 0.00 0.00 3.86
1833 1995 2.557805 CGCGCACACTGCTTGAAT 59.442 55.556 8.75 0.00 42.25 2.57
1954 2116 7.360861 CCACTCTCGCACAATTACTTTAATTCA 60.361 37.037 0.00 0.00 36.29 2.57
1973 2135 0.991920 TCCCAATTCACCCCACTCTC 59.008 55.000 0.00 0.00 0.00 3.20
2048 2211 3.931578 ACACAATAGCACTCCTCACTTC 58.068 45.455 0.00 0.00 0.00 3.01
2055 2218 7.321153 TCTTAAGTTCTACACAATAGCACTCC 58.679 38.462 1.63 0.00 0.00 3.85
2181 2344 9.010029 TCAGTTTTCCATTCCAAAATACTCTAC 57.990 33.333 0.00 0.00 0.00 2.59
2262 2425 5.716228 TCCGGTTACCACTATTTTAGTCTCA 59.284 40.000 0.00 0.00 36.76 3.27
2479 2642 7.119699 TCGTTGAATCTCTAGCAAATGTGATTT 59.880 33.333 0.00 0.00 29.95 2.17
2626 2800 7.858012 ACTAGGAAGTAGCATGTCTACCATGTA 60.858 40.741 18.00 8.84 46.98 2.29
3327 3590 3.188667 CGCTTCCTCAAAAAGGTCCTTAC 59.811 47.826 4.04 0.00 46.32 2.34
3368 3631 6.488715 AGTTTAAGAGGAAGCTGAATCCATT 58.511 36.000 5.73 2.89 39.55 3.16
3402 3665 8.461249 AATGAGAAAGTGAATCCATGGATAAG 57.539 34.615 27.54 0.00 33.97 1.73
3404 3667 9.919416 TTTAATGAGAAAGTGAATCCATGGATA 57.081 29.630 27.54 10.53 33.97 2.59
3405 3668 8.827832 TTTAATGAGAAAGTGAATCCATGGAT 57.172 30.769 22.15 22.15 36.23 3.41
3406 3669 8.108999 TCTTTAATGAGAAAGTGAATCCATGGA 58.891 33.333 18.88 18.88 37.62 3.41
3937 4201 2.841442 CCTCAGAAGGACCTTTCGTT 57.159 50.000 8.49 0.00 46.67 3.85
3979 4243 5.812436 GGGTTGAAGCCTCACTCTTTTGAG 61.812 50.000 6.10 0.00 41.51 3.02
3992 4256 2.429927 AAGCTTGTGGGTTGAAGCC 58.570 52.632 6.44 6.44 44.79 4.35
4010 4275 5.139727 CCCCAAACTTATATTGCTGATCCA 58.860 41.667 0.00 0.00 0.00 3.41
4017 4282 6.099341 CACAAAGACCCCAAACTTATATTGC 58.901 40.000 0.00 0.00 0.00 3.56
4018 4283 7.227049 ACACAAAGACCCCAAACTTATATTG 57.773 36.000 0.00 0.00 0.00 1.90
4023 4288 6.607019 AGATTACACAAAGACCCCAAACTTA 58.393 36.000 0.00 0.00 0.00 2.24
4153 4424 4.940046 CAGACAGTGAATTCTATTGGCACT 59.060 41.667 7.05 0.00 40.17 4.40
4156 4427 4.574013 CCTCAGACAGTGAATTCTATTGGC 59.426 45.833 7.05 4.73 33.60 4.52
4220 4496 2.175202 TGCCAACACCTTTGTTCAACT 58.825 42.857 0.00 0.00 44.57 3.16
4224 4500 2.276201 GGTTTGCCAACACCTTTGTTC 58.724 47.619 2.78 0.00 44.57 3.18
4266 4542 3.697045 GGGACGGATGGAGTATGAGATAG 59.303 52.174 0.00 0.00 0.00 2.08
4274 4550 4.035112 AGTATTTTGGGACGGATGGAGTA 58.965 43.478 0.00 0.00 0.00 2.59
4275 4551 2.844348 AGTATTTTGGGACGGATGGAGT 59.156 45.455 0.00 0.00 0.00 3.85
4276 4552 3.560636 AGTATTTTGGGACGGATGGAG 57.439 47.619 0.00 0.00 0.00 3.86
4277 4553 5.640158 ATAAGTATTTTGGGACGGATGGA 57.360 39.130 0.00 0.00 0.00 3.41
4278 4554 7.172703 GTCTTATAAGTATTTTGGGACGGATGG 59.827 40.741 12.19 0.00 0.00 3.51
4279 4555 7.713507 TGTCTTATAAGTATTTTGGGACGGATG 59.286 37.037 12.19 0.00 0.00 3.51
4280 4556 7.798071 TGTCTTATAAGTATTTTGGGACGGAT 58.202 34.615 12.19 0.00 0.00 4.18
4281 4557 7.185318 TGTCTTATAAGTATTTTGGGACGGA 57.815 36.000 12.19 0.00 0.00 4.69
4282 4558 7.852971 TTGTCTTATAAGTATTTTGGGACGG 57.147 36.000 12.19 0.00 0.00 4.79
4303 4579 7.094463 TGCAAGACCATTTTTGTCAAAAATTGT 60.094 29.630 27.72 27.72 46.01 2.71
4304 4580 7.249147 TGCAAGACCATTTTTGTCAAAAATTG 58.751 30.769 26.49 24.85 46.01 2.32
4305 4581 7.388460 TGCAAGACCATTTTTGTCAAAAATT 57.612 28.000 26.49 17.05 46.01 1.82
4307 4583 6.998968 ATGCAAGACCATTTTTGTCAAAAA 57.001 29.167 22.32 22.32 43.76 1.94
4308 4584 6.998968 AATGCAAGACCATTTTTGTCAAAA 57.001 29.167 6.65 6.65 36.30 2.44
4309 4585 6.998968 AAATGCAAGACCATTTTTGTCAAA 57.001 29.167 0.00 0.00 41.32 2.69
4317 4593 3.554752 CGTCCCAAAATGCAAGACCATTT 60.555 43.478 0.00 0.00 44.81 2.32
4318 4594 2.029110 CGTCCCAAAATGCAAGACCATT 60.029 45.455 0.00 0.00 37.03 3.16
4319 4595 1.545582 CGTCCCAAAATGCAAGACCAT 59.454 47.619 0.00 0.00 0.00 3.55
4320 4596 0.958091 CGTCCCAAAATGCAAGACCA 59.042 50.000 0.00 0.00 0.00 4.02
4321 4597 0.243636 CCGTCCCAAAATGCAAGACC 59.756 55.000 0.00 0.00 0.00 3.85
4322 4598 1.200020 CTCCGTCCCAAAATGCAAGAC 59.800 52.381 0.00 0.00 0.00 3.01
4323 4599 1.533625 CTCCGTCCCAAAATGCAAGA 58.466 50.000 0.00 0.00 0.00 3.02
4324 4600 0.527565 CCTCCGTCCCAAAATGCAAG 59.472 55.000 0.00 0.00 0.00 4.01
4325 4601 0.178975 ACCTCCGTCCCAAAATGCAA 60.179 50.000 0.00 0.00 0.00 4.08
4326 4602 0.693622 TACCTCCGTCCCAAAATGCA 59.306 50.000 0.00 0.00 0.00 3.96
4327 4603 1.339727 ACTACCTCCGTCCCAAAATGC 60.340 52.381 0.00 0.00 0.00 3.56
4328 4604 2.781681 ACTACCTCCGTCCCAAAATG 57.218 50.000 0.00 0.00 0.00 2.32
4329 4605 3.447950 AGTACTACCTCCGTCCCAAAAT 58.552 45.455 0.00 0.00 0.00 1.82
4330 4606 2.893424 AGTACTACCTCCGTCCCAAAA 58.107 47.619 0.00 0.00 0.00 2.44
4331 4607 2.610438 AGTACTACCTCCGTCCCAAA 57.390 50.000 0.00 0.00 0.00 3.28
4332 4608 2.578021 ACTAGTACTACCTCCGTCCCAA 59.422 50.000 0.00 0.00 0.00 4.12
4333 4609 2.200081 ACTAGTACTACCTCCGTCCCA 58.800 52.381 0.00 0.00 0.00 4.37
4334 4610 3.289407 AACTAGTACTACCTCCGTCCC 57.711 52.381 0.00 0.00 0.00 4.46
4335 4611 5.372373 ACATAACTAGTACTACCTCCGTCC 58.628 45.833 0.00 0.00 0.00 4.79
4336 4612 6.765512 AGAACATAACTAGTACTACCTCCGTC 59.234 42.308 0.00 0.00 0.00 4.79
4337 4613 6.657875 AGAACATAACTAGTACTACCTCCGT 58.342 40.000 0.00 0.00 0.00 4.69
4338 4614 6.765036 TGAGAACATAACTAGTACTACCTCCG 59.235 42.308 0.00 0.00 0.00 4.63
4339 4615 7.555554 TGTGAGAACATAACTAGTACTACCTCC 59.444 40.741 0.00 0.00 0.00 4.30
4340 4616 8.503458 TGTGAGAACATAACTAGTACTACCTC 57.497 38.462 0.00 0.33 0.00 3.85
4366 4642 6.042093 CCCAAGTAGCCAAGTCTGATCTATTA 59.958 42.308 0.00 0.00 0.00 0.98
4410 4686 2.746362 CAGTGAATCCTCTTCCAAGCAC 59.254 50.000 0.00 0.00 0.00 4.40
4417 4693 4.799564 AGTGAGACAGTGAATCCTCTTC 57.200 45.455 0.00 0.00 0.00 2.87
4442 4718 4.082190 GGAGGGAGCAAAATTAGTTTCCAC 60.082 45.833 0.00 0.00 0.00 4.02
4561 4840 7.860872 ACTTCGTTCTTGTGATTTGGAAATTAC 59.139 33.333 1.14 1.14 35.97 1.89
4578 4857 6.464222 TGTATCTTCATCCAAACTTCGTTCT 58.536 36.000 0.00 0.00 0.00 3.01
4597 4877 6.147864 TCTAAATTGCTGCCCATTTGTATC 57.852 37.500 14.07 0.00 0.00 2.24
4600 4880 4.824289 CTTCTAAATTGCTGCCCATTTGT 58.176 39.130 14.07 0.00 0.00 2.83
4636 4916 2.565841 GTAGGCATTGATGTCTCCACC 58.434 52.381 0.65 0.00 42.67 4.61
4647 4927 2.780993 CCGCTAAAAACGTAGGCATTG 58.219 47.619 0.00 0.00 0.00 2.82
4690 4970 0.253894 CCATGGAGCCTGACATCACA 59.746 55.000 5.56 0.00 0.00 3.58
4764 5048 5.393866 ACCTTTTTCCTTTGAGAGGCAATA 58.606 37.500 0.00 0.00 45.87 1.90
4767 5052 3.312736 ACCTTTTTCCTTTGAGAGGCA 57.687 42.857 0.00 0.00 45.87 4.75
4783 5068 6.478512 TCAAGTAAGAAATTTGCCAACCTT 57.521 33.333 0.00 0.00 0.00 3.50
4784 5069 6.267471 TCATCAAGTAAGAAATTTGCCAACCT 59.733 34.615 0.00 0.00 0.00 3.50
4785 5070 6.454795 TCATCAAGTAAGAAATTTGCCAACC 58.545 36.000 0.00 0.00 0.00 3.77
4786 5071 7.945033 TTCATCAAGTAAGAAATTTGCCAAC 57.055 32.000 0.00 0.00 0.00 3.77
4788 5073 7.495901 TGTTTCATCAAGTAAGAAATTTGCCA 58.504 30.769 0.00 0.00 34.23 4.92
4790 5075 8.579682 ACTGTTTCATCAAGTAAGAAATTTGC 57.420 30.769 0.00 0.00 34.23 3.68
4869 5173 3.186817 GCAGACAGATCATGATGCTAAGC 59.813 47.826 14.30 6.41 40.05 3.09
4870 5174 3.747010 GGCAGACAGATCATGATGCTAAG 59.253 47.826 14.30 0.63 41.68 2.18
4871 5175 3.736720 GGCAGACAGATCATGATGCTAA 58.263 45.455 14.30 0.00 41.68 3.09
4872 5176 2.288640 CGGCAGACAGATCATGATGCTA 60.289 50.000 14.30 0.00 41.68 3.49
4874 5178 0.866427 CGGCAGACAGATCATGATGC 59.134 55.000 14.30 10.62 41.43 3.91
4898 5206 4.215613 ACAGATTTACCCGTCTTTTCTTGC 59.784 41.667 0.00 0.00 0.00 4.01
4916 5224 3.314553 CCGTCAACAAACGTAGACAGAT 58.685 45.455 0.00 0.00 41.01 2.90
4918 5226 1.191647 GCCGTCAACAAACGTAGACAG 59.808 52.381 0.00 0.00 41.01 3.51
5106 5430 4.688045 GCATGGACATCATCATATAGGGGG 60.688 50.000 0.00 0.00 32.92 5.40
5120 5444 2.289195 CCAAGTTGCTTTGCATGGACAT 60.289 45.455 5.09 0.00 38.16 3.06
5121 5445 1.068895 CCAAGTTGCTTTGCATGGACA 59.931 47.619 5.09 0.00 38.16 4.02
5122 5446 1.069049 ACCAAGTTGCTTTGCATGGAC 59.931 47.619 15.00 2.04 38.16 4.02
5123 5447 1.412079 ACCAAGTTGCTTTGCATGGA 58.588 45.000 15.00 0.00 38.16 3.41
5188 5515 3.256960 GTGGCTTCTCCCCCACCA 61.257 66.667 0.00 0.00 44.48 4.17
5245 5578 1.372087 GCCTTCTCAAGATGGTGGCG 61.372 60.000 12.14 0.00 40.40 5.69
5279 5612 2.417936 TGCGTACGTGCAGGTGAA 59.582 55.556 21.78 0.00 40.62 3.18
5305 5638 1.739562 GCAGGAGCTCACTTGGACG 60.740 63.158 17.19 0.00 37.91 4.79
5309 5642 4.785767 TGTGCAGGAGCTCACTTG 57.214 55.556 17.19 11.54 39.15 3.16
5434 5771 2.038837 TGTCGTCGTCGGCATCTCT 61.039 57.895 5.00 0.00 46.84 3.10
5470 5807 2.178521 GATCACACGGCTCGTCGT 59.821 61.111 0.00 0.00 44.91 4.34


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

AutoCloner maintained by Alex Coulton.