Multiple sequence alignment - TraesCS2D01G170300

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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 TraesCS2D01G170300 chr2D 100.000 4055 0 0 1 4055 114524033 114519979 0.000000e+00 7489.0
1 TraesCS2D01G170300 chr2D 80.000 155 25 3 3379 3533 572791893 572791745 4.290000e-20 110.0
2 TraesCS2D01G170300 chr2A 96.155 2809 92 10 829 3633 115718674 115715878 0.000000e+00 4575.0
3 TraesCS2D01G170300 chr2A 92.652 313 12 5 3751 4055 115715876 115715567 1.340000e-119 440.0
4 TraesCS2D01G170300 chr2A 85.432 405 45 13 54 454 115719310 115718916 3.770000e-110 409.0
5 TraesCS2D01G170300 chr2A 90.164 305 22 5 7 306 115719952 115719651 1.370000e-104 390.0
6 TraesCS2D01G170300 chr2A 85.878 262 21 9 535 792 115718908 115718659 8.640000e-67 265.0
7 TraesCS2D01G170300 chr2A 86.784 227 14 8 307 526 115719524 115719307 5.240000e-59 239.0
8 TraesCS2D01G170300 chr2A 93.701 127 7 1 3625 3750 606523678 606523804 5.350000e-44 189.0
9 TraesCS2D01G170300 chr2B 97.269 2600 70 1 831 3429 164906850 164904251 0.000000e+00 4407.0
10 TraesCS2D01G170300 chr2B 91.028 457 33 7 341 792 164907290 164906837 9.640000e-171 610.0
11 TraesCS2D01G170300 chr2B 94.828 290 11 2 3749 4037 164903960 164903674 2.220000e-122 449.0
12 TraesCS2D01G170300 chr2B 88.742 302 25 5 1 296 164907589 164907291 1.070000e-95 361.0
13 TraesCS2D01G170300 chr2B 93.237 207 13 1 3428 3634 164904164 164903959 1.830000e-78 303.0
14 TraesCS2D01G170300 chr2B 95.238 126 5 1 3630 3755 518048322 518048446 8.890000e-47 198.0
15 TraesCS2D01G170300 chrUn 86.695 233 23 4 3784 4012 42851115 42850887 6.730000e-63 252.0
16 TraesCS2D01G170300 chrUn 86.695 233 23 4 3784 4012 331603456 331603684 6.730000e-63 252.0
17 TraesCS2D01G170300 chr5B 86.266 233 27 2 3784 4012 547543331 547543562 8.700000e-62 248.0
18 TraesCS2D01G170300 chr5B 80.583 206 31 7 3336 3539 547542898 547543096 2.520000e-32 150.0
19 TraesCS2D01G170300 chr5B 73.177 384 56 32 165 529 210790240 210789885 1.200000e-15 95.3
20 TraesCS2D01G170300 chr3B 85.837 233 25 3 3784 4012 612031930 612032158 1.460000e-59 241.0
21 TraesCS2D01G170300 chr3B 80.976 205 32 5 3336 3539 612031508 612031706 5.430000e-34 156.0
22 TraesCS2D01G170300 chr3B 84.211 57 6 2 298 353 341018387 341018333 7.000000e-03 52.8
23 TraesCS2D01G170300 chr6B 96.694 121 4 0 3633 3753 231349958 231349838 6.870000e-48 202.0
24 TraesCS2D01G170300 chr6B 84.211 57 6 2 298 353 657586975 657587029 7.000000e-03 52.8
25 TraesCS2D01G170300 chr6D 95.968 124 3 2 3632 3755 17055003 17055124 2.470000e-47 200.0
26 TraesCS2D01G170300 chr6D 85.714 56 7 1 298 353 152772555 152772609 1.570000e-04 58.4
27 TraesCS2D01G170300 chr7D 94.574 129 6 1 3629 3757 301329621 301329748 8.890000e-47 198.0
28 TraesCS2D01G170300 chr7D 90.769 65 6 0 3949 4013 306457294 306457358 2.010000e-13 87.9
29 TraesCS2D01G170300 chr7D 85.714 56 7 1 298 353 153425239 153425185 1.570000e-04 58.4
30 TraesCS2D01G170300 chr7B 94.574 129 6 1 3624 3751 81424979 81425107 8.890000e-47 198.0
31 TraesCS2D01G170300 chr4D 96.610 118 4 0 3633 3750 367720887 367720770 3.200000e-46 196.0
32 TraesCS2D01G170300 chr4D 94.400 125 6 1 3633 3756 55352441 55352565 1.490000e-44 191.0
33 TraesCS2D01G170300 chr1A 90.411 146 9 5 3628 3769 208212526 208212670 1.920000e-43 187.0
34 TraesCS2D01G170300 chr1A 96.774 31 1 0 3261 3291 563758035 563758005 7.000000e-03 52.8
35 TraesCS2D01G170300 chr5D 82.667 75 7 4 316 386 256176782 256176854 1.220000e-05 62.1
36 TraesCS2D01G170300 chr5D 85.714 56 7 1 298 353 216030549 216030495 1.570000e-04 58.4
37 TraesCS2D01G170300 chr5D 100.000 31 0 0 3263 3293 429503344 429503314 1.570000e-04 58.4
38 TraesCS2D01G170300 chr4A 100.000 29 0 0 3263 3291 550171154 550171182 2.000000e-03 54.7
39 TraesCS2D01G170300 chr1D 100.000 29 0 0 3263 3291 206082138 206082110 2.000000e-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 TraesCS2D01G170300 chr2D 114519979 114524033 4054 True 7489 7489 100.000000 1 4055 1 chr2D.!!$R1 4054
1 TraesCS2D01G170300 chr2A 115715567 115719952 4385 True 1053 4575 89.510833 7 4055 6 chr2A.!!$R1 4048
2 TraesCS2D01G170300 chr2B 164903674 164907589 3915 True 1226 4407 93.020800 1 4037 5 chr2B.!!$R1 4036

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
943 1482 2.607771 GCGTGTCCACTTAACCTAACGA 60.608 50.0 0.0 0.0 31.76 3.85 F
1695 2236 0.978146 AGGCTACCACGCTCCTTGAT 60.978 55.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 2872 1.602851 GTGCAGATATCAGGCTTGCAG 59.397 52.381 14.80 0.00 0.00 4.41 R
3652 4293 0.312102 GGGACAAGCTTGTGACAAGC 59.688 55.000 35.84 35.84 42.43 4.01 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
355 490 9.995003 AGTCATATTATCTCCTCTCATTTTGTC 57.005 33.333 0.00 0.00 0.00 3.18
368 503 9.740239 CCTCTCATTTTGTCATATGGTTAATTG 57.260 33.333 2.13 2.52 0.00 2.32
458 598 7.935755 TCCATTGGAGATGTCATTTTATCTCTC 59.064 37.037 0.00 5.45 45.43 3.20
497 637 5.894807 ACGAGCCAGATCCAATTTAAAATG 58.105 37.500 0.00 0.00 0.00 2.32
746 1283 7.086376 TCTGAAAATCATAGCAGCTCAAAAAC 58.914 34.615 0.00 0.00 0.00 2.43
751 1288 8.922058 AAATCATAGCAGCTCAAAAACTATTG 57.078 30.769 0.00 0.00 0.00 1.90
943 1482 2.607771 GCGTGTCCACTTAACCTAACGA 60.608 50.000 0.00 0.00 31.76 3.85
1692 2233 2.711922 CGAGGCTACCACGCTCCTT 61.712 63.158 0.00 0.00 30.30 3.36
1695 2236 0.978146 AGGCTACCACGCTCCTTGAT 60.978 55.000 0.00 0.00 0.00 2.57
1819 2360 3.307339 GGACAGGATGATGATAAGAGGCC 60.307 52.174 0.00 0.00 39.69 5.19
2134 2675 3.421844 GATAAGGGTTGTGCTCCAAACT 58.578 45.455 5.01 0.00 40.79 2.66
2241 2782 4.082354 GCAAATGGCTTGAGTCTGAATTCT 60.082 41.667 7.05 0.00 40.25 2.40
2331 2872 2.677337 GCAAGAGATGAAGAGTGAAGGC 59.323 50.000 0.00 0.00 0.00 4.35
2547 3088 5.049060 TGAAATGGTACTTCATGGTTGTTCG 60.049 40.000 0.00 0.00 0.00 3.95
2565 3106 4.151689 TGTTCGCTTGATGTTGTTAGCTAC 59.848 41.667 0.00 0.00 0.00 3.58
2591 3132 2.421424 GTCTGATTAAAGCCCTGTGCAG 59.579 50.000 0.00 0.00 44.83 4.41
2730 3271 1.403323 CGTGATGCACTAGAGCTCTCA 59.597 52.381 22.17 12.67 34.99 3.27
3009 3550 6.208402 GGGGAATTATGGTGCAAAATTTTGTT 59.792 34.615 27.13 13.90 40.24 2.83
3198 3741 6.213802 TGACCTGGTATGTATGTTTCCTGTTA 59.786 38.462 0.00 0.00 0.00 2.41
3295 3849 1.789751 CGTGCAATGCATGTCTCGT 59.210 52.632 18.55 0.00 41.91 4.18
3296 3850 0.166597 CGTGCAATGCATGTCTCGTT 59.833 50.000 18.55 0.00 41.91 3.85
3297 3851 1.393196 CGTGCAATGCATGTCTCGTTA 59.607 47.619 18.55 0.00 41.91 3.18
3298 3852 2.535534 CGTGCAATGCATGTCTCGTTAG 60.536 50.000 18.55 0.00 41.91 2.34
3299 3853 2.672874 GTGCAATGCATGTCTCGTTAGA 59.327 45.455 12.38 0.00 41.91 2.10
3300 3854 3.125146 GTGCAATGCATGTCTCGTTAGAA 59.875 43.478 12.38 0.00 41.91 2.10
3301 3855 3.750652 TGCAATGCATGTCTCGTTAGAAA 59.249 39.130 2.72 0.00 31.71 2.52
3302 3856 4.395854 TGCAATGCATGTCTCGTTAGAAAT 59.604 37.500 2.72 0.00 31.71 2.17
3303 3857 5.106197 TGCAATGCATGTCTCGTTAGAAATT 60.106 36.000 2.72 0.00 31.71 1.82
3304 3858 5.453587 GCAATGCATGTCTCGTTAGAAATTC 59.546 40.000 0.00 0.00 32.16 2.17
3305 3859 4.840401 TGCATGTCTCGTTAGAAATTCG 57.160 40.909 0.00 0.00 32.16 3.34
3317 3871 7.672738 TCGTTAGAAATTCGCTAGAAATCAAC 58.327 34.615 0.00 0.00 40.15 3.18
3381 3935 1.790755 ACGTGATCTAAAGTGCGCAA 58.209 45.000 14.00 0.00 0.00 4.85
3407 3961 6.592220 TGATTTACTGTACATTGCACGTACAT 59.408 34.615 22.24 16.28 45.97 2.29
3440 4081 9.832445 TTTAAATCTTGATGGGATGTAGTACTC 57.168 33.333 0.00 0.00 0.00 2.59
3516 4157 8.306038 CAAATCAAGAATCTTAATGAACACCCA 58.694 33.333 0.00 0.00 0.00 4.51
3526 4167 8.877864 TCTTAATGAACACCCATAACATTTCT 57.122 30.769 0.00 0.00 33.99 2.52
3539 4180 3.228188 ACATTTCTCCCTTGTTGAGCA 57.772 42.857 0.00 0.00 0.00 4.26
3593 4234 5.909417 TCTATGGGGCATATCAGATCATCAT 59.091 40.000 0.00 0.00 0.00 2.45
3595 4236 5.625568 TGGGGCATATCAGATCATCATAG 57.374 43.478 0.00 0.00 0.00 2.23
3641 4282 7.800300 AGGTAGAATAAATCATACTCCCTCC 57.200 40.000 0.00 0.00 0.00 4.30
3642 4283 6.437793 AGGTAGAATAAATCATACTCCCTCCG 59.562 42.308 0.00 0.00 0.00 4.63
3643 4284 6.210984 GGTAGAATAAATCATACTCCCTCCGT 59.789 42.308 0.00 0.00 0.00 4.69
3644 4285 6.347859 AGAATAAATCATACTCCCTCCGTC 57.652 41.667 0.00 0.00 0.00 4.79
3645 4286 5.246429 AGAATAAATCATACTCCCTCCGTCC 59.754 44.000 0.00 0.00 0.00 4.79
3646 4287 1.329256 AATCATACTCCCTCCGTCCG 58.671 55.000 0.00 0.00 0.00 4.79
3647 4288 0.477204 ATCATACTCCCTCCGTCCGA 59.523 55.000 0.00 0.00 0.00 4.55
3648 4289 0.256752 TCATACTCCCTCCGTCCGAA 59.743 55.000 0.00 0.00 0.00 4.30
3649 4290 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
3650 4291 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
3651 4292 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
3652 4293 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
3653 4294 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
3654 4295 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
3655 4296 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
3656 4297 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
3657 4298 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
3658 4299 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
3659 4300 0.941542 CCGTCCGAAAAAGCTTGTCA 59.058 50.000 0.00 0.00 0.00 3.58
3660 4301 1.333791 CCGTCCGAAAAAGCTTGTCAC 60.334 52.381 0.00 0.00 0.00 3.67
3661 4302 1.329292 CGTCCGAAAAAGCTTGTCACA 59.671 47.619 0.00 0.00 0.00 3.58
3662 4303 2.223157 CGTCCGAAAAAGCTTGTCACAA 60.223 45.455 0.00 0.00 0.00 3.33
3663 4304 3.363178 GTCCGAAAAAGCTTGTCACAAG 58.637 45.455 13.67 13.67 0.00 3.16
3664 4305 2.119457 CCGAAAAAGCTTGTCACAAGC 58.881 47.619 31.68 31.68 43.31 4.01
3670 4311 3.853623 GCTTGTCACAAGCTTGTCC 57.146 52.632 31.50 21.35 39.91 4.02
3671 4312 0.312102 GCTTGTCACAAGCTTGTCCC 59.688 55.000 31.50 21.01 39.91 4.46
3672 4313 1.972872 CTTGTCACAAGCTTGTCCCT 58.027 50.000 28.97 5.19 39.91 4.20
3673 4314 1.876156 CTTGTCACAAGCTTGTCCCTC 59.124 52.381 28.97 18.08 39.91 4.30
3674 4315 0.836606 TGTCACAAGCTTGTCCCTCA 59.163 50.000 28.97 20.16 39.91 3.86
3675 4316 1.211703 TGTCACAAGCTTGTCCCTCAA 59.788 47.619 28.97 9.18 39.91 3.02
3676 4317 2.297701 GTCACAAGCTTGTCCCTCAAA 58.702 47.619 28.97 6.30 39.91 2.69
3677 4318 2.887152 GTCACAAGCTTGTCCCTCAAAT 59.113 45.455 28.97 1.52 39.91 2.32
3678 4319 2.886523 TCACAAGCTTGTCCCTCAAATG 59.113 45.455 28.97 14.50 39.91 2.32
3679 4320 2.029649 CACAAGCTTGTCCCTCAAATGG 60.030 50.000 28.97 10.25 39.91 3.16
3680 4321 2.158475 ACAAGCTTGTCCCTCAAATGGA 60.158 45.455 26.36 0.00 36.50 3.41
3681 4322 3.094572 CAAGCTTGTCCCTCAAATGGAT 58.905 45.455 18.65 0.00 35.48 3.41
3682 4323 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
3683 4324 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
3684 4325 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
3685 4326 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
3686 4327 4.276926 GCTTGTCCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.48 2.24
3687 4328 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
3688 4329 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
3689 4330 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
3690 4331 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
3691 4332 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
3692 4333 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
3693 4334 5.221803 CCCTCAAATGGATGTATCTAGCACT 60.222 44.000 0.00 0.00 0.00 4.40
3694 4335 6.014242 CCCTCAAATGGATGTATCTAGCACTA 60.014 42.308 0.00 0.00 0.00 2.74
3695 4336 7.445121 CCTCAAATGGATGTATCTAGCACTAA 58.555 38.462 0.00 0.00 0.00 2.24
3696 4337 7.601886 CCTCAAATGGATGTATCTAGCACTAAG 59.398 40.741 0.00 0.00 0.00 2.18
3697 4338 8.023021 TCAAATGGATGTATCTAGCACTAAGT 57.977 34.615 0.00 0.00 0.00 2.24
3698 4339 8.486210 TCAAATGGATGTATCTAGCACTAAGTT 58.514 33.333 0.00 0.00 0.00 2.66
3699 4340 8.554528 CAAATGGATGTATCTAGCACTAAGTTG 58.445 37.037 0.00 0.00 0.00 3.16
3700 4341 7.603180 ATGGATGTATCTAGCACTAAGTTGA 57.397 36.000 0.00 0.00 0.00 3.18
3701 4342 7.603180 TGGATGTATCTAGCACTAAGTTGAT 57.397 36.000 0.00 0.00 0.00 2.57
3702 4343 7.436933 TGGATGTATCTAGCACTAAGTTGATG 58.563 38.462 0.00 0.00 0.00 3.07
3703 4344 6.367422 GGATGTATCTAGCACTAAGTTGATGC 59.633 42.308 5.30 5.30 39.74 3.91
3713 4354 7.344910 GCACTAAGTTGATGCTAGATACATC 57.655 40.000 0.00 0.00 43.46 3.06
3714 4355 6.367422 GCACTAAGTTGATGCTAGATACATCC 59.633 42.308 0.00 0.00 42.68 3.51
3715 4356 7.436933 CACTAAGTTGATGCTAGATACATCCA 58.563 38.462 0.00 0.00 42.68 3.41
3716 4357 8.093307 CACTAAGTTGATGCTAGATACATCCAT 58.907 37.037 0.00 0.00 42.68 3.41
3717 4358 8.654997 ACTAAGTTGATGCTAGATACATCCATT 58.345 33.333 0.00 0.00 42.68 3.16
3718 4359 9.499479 CTAAGTTGATGCTAGATACATCCATTT 57.501 33.333 0.00 0.00 42.68 2.32
3719 4360 7.741027 AGTTGATGCTAGATACATCCATTTG 57.259 36.000 0.00 0.00 42.68 2.32
3720 4361 7.512130 AGTTGATGCTAGATACATCCATTTGA 58.488 34.615 0.00 0.00 42.68 2.69
3721 4362 7.660617 AGTTGATGCTAGATACATCCATTTGAG 59.339 37.037 0.00 0.00 42.68 3.02
3722 4363 6.470278 TGATGCTAGATACATCCATTTGAGG 58.530 40.000 0.00 0.00 42.68 3.86
3723 4364 5.233083 TGCTAGATACATCCATTTGAGGG 57.767 43.478 0.00 0.00 0.00 4.30
3724 4365 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
3725 4366 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
3726 4367 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
3727 4368 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
3728 4369 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
3729 4370 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
3730 4371 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
3731 4372 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
3732 4373 3.243359 TCCATTTGAGGGACAAGCTTT 57.757 42.857 0.00 0.00 39.77 3.51
3733 4374 3.575805 TCCATTTGAGGGACAAGCTTTT 58.424 40.909 0.00 0.00 39.77 2.27
3734 4375 3.966665 TCCATTTGAGGGACAAGCTTTTT 59.033 39.130 0.00 0.00 39.77 1.94
3735 4376 4.039124 TCCATTTGAGGGACAAGCTTTTTC 59.961 41.667 0.00 0.00 39.77 2.29
3736 4377 3.708563 TTTGAGGGACAAGCTTTTTCG 57.291 42.857 0.00 0.00 39.77 3.46
3737 4378 1.604604 TGAGGGACAAGCTTTTTCGG 58.395 50.000 0.00 0.00 0.00 4.30
3738 4379 1.142060 TGAGGGACAAGCTTTTTCGGA 59.858 47.619 0.00 0.00 0.00 4.55
3739 4380 1.535896 GAGGGACAAGCTTTTTCGGAC 59.464 52.381 0.00 0.00 0.00 4.79
3740 4381 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
3741 4382 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
3742 4383 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
3743 4384 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
3744 4385 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
3745 4386 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
3746 4387 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
3747 4388 1.019805 GCTTTTTCGGACGGAGGGAG 61.020 60.000 0.00 0.00 0.00 4.30
3748 4389 0.320697 CTTTTTCGGACGGAGGGAGT 59.679 55.000 0.00 0.00 0.00 3.85
3749 4390 1.547372 CTTTTTCGGACGGAGGGAGTA 59.453 52.381 0.00 0.00 0.00 2.59
3782 4424 8.981724 TCTCATAATATTATGACAACTACGGC 57.018 34.615 27.09 0.00 43.25 5.68
3962 4612 6.158598 GGTTCTGATCAAAAGCAGCAATTAA 58.841 36.000 6.09 0.00 38.82 1.40
4021 4671 6.976925 AGCAAATATATTTCAGTTGCAGCTTC 59.023 34.615 17.20 0.00 45.47 3.86
4022 4672 6.753279 GCAAATATATTTCAGTTGCAGCTTCA 59.247 34.615 7.76 0.00 43.17 3.02
4023 4673 7.437267 GCAAATATATTTCAGTTGCAGCTTCAT 59.563 33.333 7.76 0.00 43.17 2.57
4038 4688 8.146479 TGCAGCTTCATACACAAAGAATATAG 57.854 34.615 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 122 5.175673 GTGTGCAAGTTTCTGGATTTTTAGC 59.824 40.000 0.00 0.00 0.00 3.09
319 454 8.027524 AGGAGATAATATGACTTCTCTGCAAA 57.972 34.615 0.00 0.00 35.90 3.68
322 457 7.176515 TGAGAGGAGATAATATGACTTCTCTGC 59.823 40.741 15.25 9.88 43.89 4.26
323 458 8.634335 TGAGAGGAGATAATATGACTTCTCTG 57.366 38.462 15.25 0.00 43.89 3.35
324 459 9.827198 AATGAGAGGAGATAATATGACTTCTCT 57.173 33.333 12.02 12.02 45.73 3.10
374 512 8.757877 TGCATTTAGAGGCCATTTAAGTATTTT 58.242 29.630 5.01 0.00 0.00 1.82
376 514 7.896383 TGCATTTAGAGGCCATTTAAGTATT 57.104 32.000 5.01 0.00 0.00 1.89
377 515 7.896383 TTGCATTTAGAGGCCATTTAAGTAT 57.104 32.000 5.01 0.00 0.00 2.12
380 518 9.768662 ATTATTTGCATTTAGAGGCCATTTAAG 57.231 29.630 5.01 0.00 0.00 1.85
458 598 5.116180 TGGCTCGTATTCAAATTACAGAGG 58.884 41.667 0.00 0.00 0.00 3.69
475 615 4.741676 GCATTTTAAATTGGATCTGGCTCG 59.258 41.667 11.07 0.00 0.00 5.03
663 1200 5.735285 TTCCAAACCATGTGATGCAAATA 57.265 34.783 0.00 0.00 0.00 1.40
820 1358 9.723601 CCCAAAAGATTTCAAATTTATCCTCAA 57.276 29.630 0.00 0.00 0.00 3.02
821 1359 9.099071 TCCCAAAAGATTTCAAATTTATCCTCA 57.901 29.630 0.00 0.00 0.00 3.86
823 1361 9.895138 CATCCCAAAAGATTTCAAATTTATCCT 57.105 29.630 0.00 0.00 0.00 3.24
824 1362 9.671279 ACATCCCAAAAGATTTCAAATTTATCC 57.329 29.630 0.00 0.00 0.00 2.59
828 1366 9.844257 TGTAACATCCCAAAAGATTTCAAATTT 57.156 25.926 0.00 0.00 0.00 1.82
829 1367 9.271828 GTGTAACATCCCAAAAGATTTCAAATT 57.728 29.630 0.00 0.00 36.32 1.82
943 1482 4.717279 TTTTTCACTTACTAGGCCCAGT 57.283 40.909 9.37 9.37 0.00 4.00
1695 2236 1.561076 CACCCCATGAGGAACATCTCA 59.439 52.381 0.00 0.00 46.32 3.27
2134 2675 3.762288 AGCAAGATCGTGTAGGTCACTAA 59.238 43.478 10.41 0.00 44.16 2.24
2241 2782 8.579006 GCATAAATCATTCCATTGTATCCTTGA 58.421 33.333 0.00 0.00 0.00 3.02
2308 2849 3.683822 CCTTCACTCTTCATCTCTTGCAC 59.316 47.826 0.00 0.00 0.00 4.57
2331 2872 1.602851 GTGCAGATATCAGGCTTGCAG 59.397 52.381 14.80 0.00 0.00 4.41
2403 2944 9.619316 TCAACCAAATTTTCAAATAGATACACG 57.381 29.630 0.00 0.00 0.00 4.49
2514 3055 5.782047 TGAAGTACCATTTCATTTGCAAGG 58.218 37.500 0.00 0.00 30.03 3.61
2565 3106 4.019174 ACAGGGCTTTAATCAGACCATTG 58.981 43.478 1.83 0.00 46.00 2.82
2591 3132 3.397482 CTCCGATCAACATTCCCATCTC 58.603 50.000 0.00 0.00 0.00 2.75
2628 3169 8.918116 GGCTTAATTCCCTTTTCTATCATTTCT 58.082 33.333 0.00 0.00 0.00 2.52
2730 3271 3.832490 GCCCTTGGTTTAACATCTCCTTT 59.168 43.478 0.00 0.00 0.00 3.11
3036 3577 5.332743 AGAAATTAATGCCCTTCAACCTCA 58.667 37.500 0.00 0.00 0.00 3.86
3296 3850 9.773328 CAAATGTTGATTTCTAGCGAATTTCTA 57.227 29.630 0.00 0.00 28.65 2.10
3297 3851 8.514594 TCAAATGTTGATTTCTAGCGAATTTCT 58.485 29.630 0.00 0.00 34.08 2.52
3298 3852 8.673626 TCAAATGTTGATTTCTAGCGAATTTC 57.326 30.769 0.00 0.00 34.08 2.17
3299 3853 9.643693 ATTCAAATGTTGATTTCTAGCGAATTT 57.356 25.926 0.00 0.00 39.84 1.82
3366 3920 6.630443 CAGTAAATCATTGCGCACTTTAGATC 59.370 38.462 11.12 0.00 0.00 2.75
3371 3925 4.503741 ACAGTAAATCATTGCGCACTTT 57.496 36.364 11.12 10.49 0.00 2.66
3373 3927 4.000325 TGTACAGTAAATCATTGCGCACT 59.000 39.130 11.12 0.00 0.00 4.40
3407 3961 6.522625 TCCCATCAAGATTTAAATTCGCAA 57.477 33.333 1.43 0.00 0.00 4.85
3488 4129 9.346725 GGTGTTCATTAAGATTCTTGATTTGTC 57.653 33.333 9.22 0.00 0.00 3.18
3516 4157 5.324409 TGCTCAACAAGGGAGAAATGTTAT 58.676 37.500 0.00 0.00 35.63 1.89
3526 4167 6.723977 AGGTATTTTATTTGCTCAACAAGGGA 59.276 34.615 0.00 0.00 40.06 4.20
3555 4196 1.270518 CCATAGAGGCGTCTGGATTGG 60.271 57.143 18.96 14.88 33.84 3.16
3634 4275 1.019805 GCTTTTTCGGACGGAGGGAG 61.020 60.000 0.00 0.00 0.00 4.30
3635 4276 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
3636 4277 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
3637 4278 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
3638 4279 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
3639 4280 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
3640 4281 0.941542 TGACAAGCTTTTTCGGACGG 59.058 50.000 0.00 0.00 0.00 4.79
3641 4282 1.329292 TGTGACAAGCTTTTTCGGACG 59.671 47.619 0.00 0.00 0.00 4.79
3642 4283 3.363178 CTTGTGACAAGCTTTTTCGGAC 58.637 45.455 12.89 0.00 0.00 4.79
3643 4284 2.223479 GCTTGTGACAAGCTTTTTCGGA 60.223 45.455 35.54 0.00 40.01 4.55
3644 4285 2.119457 GCTTGTGACAAGCTTTTTCGG 58.881 47.619 35.54 7.02 40.01 4.30
3652 4293 0.312102 GGGACAAGCTTGTGACAAGC 59.688 55.000 35.84 35.84 42.43 4.01
3653 4294 1.876156 GAGGGACAAGCTTGTGACAAG 59.124 52.381 35.67 20.42 42.43 3.16
3654 4295 1.211703 TGAGGGACAAGCTTGTGACAA 59.788 47.619 35.67 16.62 42.43 3.18
3655 4296 0.836606 TGAGGGACAAGCTTGTGACA 59.163 50.000 35.67 23.64 42.43 3.58
3656 4297 1.967319 TTGAGGGACAAGCTTGTGAC 58.033 50.000 35.67 25.69 42.43 3.67
3657 4298 2.727123 TTTGAGGGACAAGCTTGTGA 57.273 45.000 35.67 11.68 42.43 3.58
3658 4299 2.029649 CCATTTGAGGGACAAGCTTGTG 60.030 50.000 35.67 17.46 42.43 3.33
3659 4300 2.158475 TCCATTTGAGGGACAAGCTTGT 60.158 45.455 31.57 31.57 45.65 3.16
3660 4301 2.517959 TCCATTTGAGGGACAAGCTTG 58.482 47.619 24.84 24.84 39.77 4.01
3661 4302 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
3662 4303 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
3663 4304 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
3664 4305 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
3665 4306 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
3666 4307 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
3667 4308 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
3668 4309 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
3669 4310 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
3670 4311 5.862845 AGTGCTAGATACATCCATTTGAGG 58.137 41.667 0.00 0.00 0.00 3.86
3671 4312 8.147058 ACTTAGTGCTAGATACATCCATTTGAG 58.853 37.037 0.00 0.00 0.00 3.02
3672 4313 8.023021 ACTTAGTGCTAGATACATCCATTTGA 57.977 34.615 0.00 0.00 0.00 2.69
3673 4314 8.554528 CAACTTAGTGCTAGATACATCCATTTG 58.445 37.037 0.00 0.00 0.00 2.32
3674 4315 8.486210 TCAACTTAGTGCTAGATACATCCATTT 58.514 33.333 0.00 0.00 0.00 2.32
3675 4316 8.023021 TCAACTTAGTGCTAGATACATCCATT 57.977 34.615 0.00 0.00 0.00 3.16
3676 4317 7.603180 TCAACTTAGTGCTAGATACATCCAT 57.397 36.000 0.00 0.00 0.00 3.41
3677 4318 7.436933 CATCAACTTAGTGCTAGATACATCCA 58.563 38.462 0.00 0.00 0.00 3.41
3678 4319 6.367422 GCATCAACTTAGTGCTAGATACATCC 59.633 42.308 0.00 0.00 36.02 3.51
3679 4320 7.151308 AGCATCAACTTAGTGCTAGATACATC 58.849 38.462 0.00 0.00 46.54 3.06
3680 4321 7.060383 AGCATCAACTTAGTGCTAGATACAT 57.940 36.000 0.00 0.00 46.54 2.29
3681 4322 6.471233 AGCATCAACTTAGTGCTAGATACA 57.529 37.500 0.00 0.00 46.54 2.29
3687 4328 7.582667 TGTATCTAGCATCAACTTAGTGCTA 57.417 36.000 6.20 6.20 46.54 3.49
3689 4330 6.367422 GGATGTATCTAGCATCAACTTAGTGC 59.633 42.308 9.99 0.00 43.17 4.40
3690 4331 7.436933 TGGATGTATCTAGCATCAACTTAGTG 58.563 38.462 9.99 0.00 43.17 2.74
3691 4332 7.603180 TGGATGTATCTAGCATCAACTTAGT 57.397 36.000 9.99 0.00 43.17 2.24
3692 4333 9.499479 AAATGGATGTATCTAGCATCAACTTAG 57.501 33.333 9.99 0.00 43.17 2.18
3693 4334 9.276590 CAAATGGATGTATCTAGCATCAACTTA 57.723 33.333 9.99 0.00 43.17 2.24
3694 4335 7.994911 TCAAATGGATGTATCTAGCATCAACTT 59.005 33.333 9.99 0.00 43.17 2.66
3695 4336 7.512130 TCAAATGGATGTATCTAGCATCAACT 58.488 34.615 9.99 0.00 43.17 3.16
3696 4337 7.094890 CCTCAAATGGATGTATCTAGCATCAAC 60.095 40.741 9.99 0.00 43.17 3.18
3697 4338 6.938596 CCTCAAATGGATGTATCTAGCATCAA 59.061 38.462 9.99 0.98 43.17 2.57
3698 4339 6.470278 CCTCAAATGGATGTATCTAGCATCA 58.530 40.000 9.99 0.00 43.17 3.07
3699 4340 5.879223 CCCTCAAATGGATGTATCTAGCATC 59.121 44.000 1.37 1.37 41.30 3.91
3700 4341 5.549228 TCCCTCAAATGGATGTATCTAGCAT 59.451 40.000 0.00 0.00 0.00 3.79
3701 4342 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
3702 4343 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
3703 4344 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
3704 4345 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
3705 4346 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
3706 4347 4.276926 GCTTGTCCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.48 2.24
3707 4348 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
3708 4349 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
3709 4350 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
3710 4351 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
3711 4352 3.463048 AAGCTTGTCCCTCAAATGGAT 57.537 42.857 0.00 0.00 35.48 3.41
3712 4353 2.978156 AAGCTTGTCCCTCAAATGGA 57.022 45.000 0.00 0.00 35.48 3.41
3713 4354 4.309933 GAAAAAGCTTGTCCCTCAAATGG 58.690 43.478 0.00 0.00 35.48 3.16
3714 4355 3.983344 CGAAAAAGCTTGTCCCTCAAATG 59.017 43.478 0.00 0.00 35.48 2.32
3715 4356 3.005791 CCGAAAAAGCTTGTCCCTCAAAT 59.994 43.478 0.00 0.00 35.48 2.32
3716 4357 2.360801 CCGAAAAAGCTTGTCCCTCAAA 59.639 45.455 0.00 0.00 35.48 2.69
3717 4358 1.953686 CCGAAAAAGCTTGTCCCTCAA 59.046 47.619 0.00 0.00 34.61 3.02
3718 4359 1.142060 TCCGAAAAAGCTTGTCCCTCA 59.858 47.619 0.00 0.00 0.00 3.86
3719 4360 1.535896 GTCCGAAAAAGCTTGTCCCTC 59.464 52.381 0.00 0.00 0.00 4.30
3720 4361 1.605753 GTCCGAAAAAGCTTGTCCCT 58.394 50.000 0.00 0.00 0.00 4.20
3721 4362 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
3722 4363 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
3723 4364 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
3724 4365 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
3725 4366 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
3726 4367 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
3727 4368 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
3728 4369 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
3729 4370 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
3730 4371 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
3731 4372 1.631405 TTACTCCCTCCGTCCGAAAA 58.369 50.000 0.00 0.00 0.00 2.29
3732 4373 1.856629 ATTACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
3733 4374 2.734755 TATTACTCCCTCCGTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
3734 4375 2.965671 ATATTACTCCCTCCGTCCGA 57.034 50.000 0.00 0.00 0.00 4.55
3735 4376 5.418209 AGAAATATATTACTCCCTCCGTCCG 59.582 44.000 0.00 0.00 0.00 4.79
3736 4377 6.436532 TGAGAAATATATTACTCCCTCCGTCC 59.563 42.308 0.00 0.00 0.00 4.79
3737 4378 7.463961 TGAGAAATATATTACTCCCTCCGTC 57.536 40.000 0.00 0.00 0.00 4.79
3738 4379 9.543231 TTATGAGAAATATATTACTCCCTCCGT 57.457 33.333 0.00 0.00 0.00 4.69
3770 4412 0.973632 ATGGTGAGCCGTAGTTGTCA 59.026 50.000 0.00 0.00 37.67 3.58
3775 4417 4.081087 AGTTAAATGATGGTGAGCCGTAGT 60.081 41.667 0.00 0.00 37.67 2.73
3823 4473 1.282157 AGCTATGGAGGTGGTGTTTCC 59.718 52.381 0.00 0.00 30.28 3.13
4023 4673 9.582431 GTGCACTCTTACTATATTCTTTGTGTA 57.418 33.333 10.32 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.