Multiple sequence alignment - TraesCS1B01G236100

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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 TraesCS1B01G236100 chr1B 100.000 4704 0 0 1 4704 423210936 423206233 0.000000e+00 8687
1 TraesCS1B01G236100 chr1B 85.936 2702 362 12 995 3691 67683215 67680527 0.000000e+00 2868
2 TraesCS1B01G236100 chr1B 80.344 1104 183 9 1803 2904 67053752 67052681 0.000000e+00 806
3 TraesCS1B01G236100 chr1D 97.778 4005 61 9 1 3985 312974496 312970500 0.000000e+00 6878
4 TraesCS1B01G236100 chr1D 86.010 2702 360 12 995 3691 48024252 48021564 0.000000e+00 2880
5 TraesCS1B01G236100 chr1D 81.703 1104 193 6 1802 2904 47329715 47328620 0.000000e+00 911
6 TraesCS1B01G236100 chr1D 97.166 494 14 0 4211 4704 312970388 312969895 0.000000e+00 835
7 TraesCS1B01G236100 chr1D 79.054 740 113 23 2956 3684 47328610 47327902 1.980000e-128 470
8 TraesCS1B01G236100 chr1A 96.127 4028 119 17 4 3996 392530843 392526818 0.000000e+00 6540
9 TraesCS1B01G236100 chr1A 86.373 2451 328 5 995 3440 47826769 47824320 0.000000e+00 2671
10 TraesCS1B01G236100 chr1A 82.009 1095 188 8 1803 2893 47211649 47210560 0.000000e+00 922
11 TraesCS1B01G236100 chr1A 96.829 410 13 0 4295 4704 392526614 392526205 0.000000e+00 686
12 TraesCS1B01G236100 chr1A 82.969 458 71 3 2956 3413 47210539 47210089 1.580000e-109 407
13 TraesCS1B01G236100 chr5D 72.911 1484 331 52 1005 2460 42555298 42556738 9.290000e-122 448
14 TraesCS1B01G236100 chr5D 72.043 1488 343 48 1005 2460 52617302 52615856 4.440000e-100 375
15 TraesCS1B01G236100 chr5B 72.267 1482 340 51 1005 2458 37059787 37058349 1.230000e-105 394
16 TraesCS1B01G236100 chr5B 71.602 1486 353 47 1005 2460 55625208 55623762 4.510000e-90 342
17 TraesCS1B01G236100 chr3B 71.824 1409 307 62 1957 3332 564319098 564320449 2.110000e-83 320
18 TraesCS1B01G236100 chr3D 71.927 1375 289 53 1990 3332 432135136 432136445 1.270000e-80 311


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 TraesCS1B01G236100 chr1B 423206233 423210936 4703 True 8687.0 8687 100.0000 1 4704 1 chr1B.!!$R3 4703
1 TraesCS1B01G236100 chr1B 67680527 67683215 2688 True 2868.0 2868 85.9360 995 3691 1 chr1B.!!$R2 2696
2 TraesCS1B01G236100 chr1B 67052681 67053752 1071 True 806.0 806 80.3440 1803 2904 1 chr1B.!!$R1 1101
3 TraesCS1B01G236100 chr1D 312969895 312974496 4601 True 3856.5 6878 97.4720 1 4704 2 chr1D.!!$R3 4703
4 TraesCS1B01G236100 chr1D 48021564 48024252 2688 True 2880.0 2880 86.0100 995 3691 1 chr1D.!!$R1 2696
5 TraesCS1B01G236100 chr1D 47327902 47329715 1813 True 690.5 911 80.3785 1802 3684 2 chr1D.!!$R2 1882
6 TraesCS1B01G236100 chr1A 392526205 392530843 4638 True 3613.0 6540 96.4780 4 4704 2 chr1A.!!$R3 4700
7 TraesCS1B01G236100 chr1A 47824320 47826769 2449 True 2671.0 2671 86.3730 995 3440 1 chr1A.!!$R1 2445
8 TraesCS1B01G236100 chr1A 47210089 47211649 1560 True 664.5 922 82.4890 1803 3413 2 chr1A.!!$R2 1610
9 TraesCS1B01G236100 chr5D 42555298 42556738 1440 False 448.0 448 72.9110 1005 2460 1 chr5D.!!$F1 1455
10 TraesCS1B01G236100 chr5D 52615856 52617302 1446 True 375.0 375 72.0430 1005 2460 1 chr5D.!!$R1 1455
11 TraesCS1B01G236100 chr5B 37058349 37059787 1438 True 394.0 394 72.2670 1005 2458 1 chr5B.!!$R1 1453
12 TraesCS1B01G236100 chr5B 55623762 55625208 1446 True 342.0 342 71.6020 1005 2460 1 chr5B.!!$R2 1455
13 TraesCS1B01G236100 chr3B 564319098 564320449 1351 False 320.0 320 71.8240 1957 3332 1 chr3B.!!$F1 1375
14 TraesCS1B01G236100 chr3D 432135136 432136445 1309 False 311.0 311 71.9270 1990 3332 1 chr3D.!!$F1 1342

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
557 589 1.340502 GCCTCTTTAGCTTGGCTCCTT 60.341 52.381 0.00 0.0 41.92 3.36 F
823 856 3.057734 ACACTAAGCTACGTGAAACTGC 58.942 45.455 18.82 0.0 35.23 4.40 F
2212 2272 1.074566 CCCTTGAGAAACTTGCTCCCT 59.925 52.381 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2272 1.122632 TCAAGTCCGGCCTGTACCAA 61.123 55.0 0.0 0.00 0.0 3.67 R
2904 2982 0.523072 CAAAATCTGGACCTGTGGCG 59.477 55.0 0.0 0.00 0.0 5.69 R
4066 4169 0.110644 CTCCAGCAAAACGTTCGAGC 60.111 55.0 0.0 6.35 0.0 5.03 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
176 187 5.647589 CCTATATACGCATCGGAGCTTTAA 58.352 41.667 0.00 0.00 0.00 1.52
279 301 1.488527 CTTAGCTCGCCGTGGATTAC 58.511 55.000 0.00 0.00 0.00 1.89
357 379 6.666546 GGTCCTGGTAGTGTAGGCATATATTA 59.333 42.308 0.00 0.00 34.00 0.98
362 384 7.711557 TGGTAGTGTAGGCATATATTACCCTA 58.288 38.462 19.23 4.28 35.66 3.53
418 446 3.270027 TGCATGTGGTAGCATTAGTCAC 58.730 45.455 0.00 0.00 35.51 3.67
419 447 3.270027 GCATGTGGTAGCATTAGTCACA 58.730 45.455 0.00 0.00 41.64 3.58
421 449 4.507710 CATGTGGTAGCATTAGTCACAGT 58.492 43.478 0.00 0.00 40.89 3.55
528 559 6.428159 CCTCATGAATACCTAGTTATTGTGGC 59.572 42.308 0.00 0.00 0.00 5.01
557 589 1.340502 GCCTCTTTAGCTTGGCTCCTT 60.341 52.381 0.00 0.00 41.92 3.36
575 607 9.528489 TGGCTCCTTAATCAAATAAACTTAACT 57.472 29.630 0.00 0.00 0.00 2.24
713 746 3.193267 TGGTAGATGTTTTTGCATCCTGC 59.807 43.478 0.00 0.00 44.58 4.85
823 856 3.057734 ACACTAAGCTACGTGAAACTGC 58.942 45.455 18.82 0.00 35.23 4.40
921 956 4.515191 TCCTTAAATGTTGCTGACTGACAC 59.485 41.667 0.00 0.00 0.00 3.67
922 957 4.275689 CCTTAAATGTTGCTGACTGACACA 59.724 41.667 0.00 0.00 0.00 3.72
2212 2272 1.074566 CCCTTGAGAAACTTGCTCCCT 59.925 52.381 0.00 0.00 0.00 4.20
2904 2982 1.135286 GCCATTGGTGCTCTTGCTTAC 60.135 52.381 4.26 0.00 40.48 2.34
3219 3304 2.285024 GCCAATGCTTCAAGGGGCA 61.285 57.895 0.00 0.00 41.02 5.36
3413 3498 2.832129 TCTACAAAGATCGGAGCAGGTT 59.168 45.455 0.00 0.00 0.00 3.50
3414 3499 1.813513 ACAAAGATCGGAGCAGGTTG 58.186 50.000 0.00 0.00 0.00 3.77
3438 3523 7.765307 TGATGTCATTTCTATTGCCTTTCTTC 58.235 34.615 0.00 0.00 0.00 2.87
3442 3527 8.641541 TGTCATTTCTATTGCCTTTCTTCTTTT 58.358 29.630 0.00 0.00 0.00 2.27
3443 3528 8.919661 GTCATTTCTATTGCCTTTCTTCTTTTG 58.080 33.333 0.00 0.00 0.00 2.44
3445 3530 9.264719 CATTTCTATTGCCTTTCTTCTTTTGTT 57.735 29.630 0.00 0.00 0.00 2.83
3447 3532 9.744468 TTTCTATTGCCTTTCTTCTTTTGTTAC 57.256 29.630 0.00 0.00 0.00 2.50
3475 3562 3.526899 TGGGTGATTGGTTCTCTTCCTA 58.473 45.455 0.00 0.00 0.00 2.94
3526 3615 1.347707 AGGGATGAGAGCGTGACAAAA 59.652 47.619 0.00 0.00 0.00 2.44
3734 3831 2.717580 TCTTGCGTCGTCTGTTATGT 57.282 45.000 0.00 0.00 0.00 2.29
3842 3945 5.171476 AGGAACATTGTCGTAGATGTCTTG 58.829 41.667 0.00 0.00 40.67 3.02
3968 4071 4.449743 TGTATTCTACTCGTTTGTGTTGCC 59.550 41.667 0.00 0.00 0.00 4.52
3978 4081 3.308530 GTTTGTGTTGCCTACTTGCATC 58.691 45.455 0.00 0.00 41.70 3.91
3996 4099 2.133281 TCCATGCTATGTTGCTGCTT 57.867 45.000 0.00 0.00 0.00 3.91
3997 4100 1.746787 TCCATGCTATGTTGCTGCTTG 59.253 47.619 0.00 0.00 0.00 4.01
3998 4101 1.202371 CCATGCTATGTTGCTGCTTGG 60.202 52.381 0.00 0.00 42.61 3.61
3999 4102 1.475280 CATGCTATGTTGCTGCTTGGT 59.525 47.619 0.00 0.00 0.00 3.67
4000 4103 0.883153 TGCTATGTTGCTGCTTGGTG 59.117 50.000 0.00 0.00 0.00 4.17
4001 4104 0.171903 GCTATGTTGCTGCTTGGTGG 59.828 55.000 0.00 0.00 0.00 4.61
4002 4105 1.538047 CTATGTTGCTGCTTGGTGGT 58.462 50.000 0.00 0.00 0.00 4.16
4003 4106 2.710377 CTATGTTGCTGCTTGGTGGTA 58.290 47.619 0.00 0.00 0.00 3.25
4004 4107 1.247567 ATGTTGCTGCTTGGTGGTAC 58.752 50.000 0.00 0.00 0.00 3.34
4005 4108 0.106967 TGTTGCTGCTTGGTGGTACA 60.107 50.000 0.00 0.00 0.00 2.90
4006 4109 1.247567 GTTGCTGCTTGGTGGTACAT 58.752 50.000 0.00 0.00 44.52 2.29
4007 4110 1.613437 GTTGCTGCTTGGTGGTACATT 59.387 47.619 0.00 0.00 44.52 2.71
4008 4111 1.246649 TGCTGCTTGGTGGTACATTG 58.753 50.000 0.00 0.00 44.52 2.82
4009 4112 1.247567 GCTGCTTGGTGGTACATTGT 58.752 50.000 0.00 0.00 44.52 2.71
4010 4113 1.613437 GCTGCTTGGTGGTACATTGTT 59.387 47.619 0.00 0.00 44.52 2.83
4011 4114 2.351738 GCTGCTTGGTGGTACATTGTTC 60.352 50.000 0.00 0.00 44.52 3.18
4012 4115 3.149196 CTGCTTGGTGGTACATTGTTCT 58.851 45.455 0.00 0.00 44.52 3.01
4013 4116 3.561143 TGCTTGGTGGTACATTGTTCTT 58.439 40.909 0.00 0.00 44.52 2.52
4014 4117 4.720046 TGCTTGGTGGTACATTGTTCTTA 58.280 39.130 0.00 0.00 44.52 2.10
4015 4118 5.321102 TGCTTGGTGGTACATTGTTCTTAT 58.679 37.500 0.00 0.00 44.52 1.73
4016 4119 5.414454 TGCTTGGTGGTACATTGTTCTTATC 59.586 40.000 0.00 0.00 44.52 1.75
4017 4120 5.447279 GCTTGGTGGTACATTGTTCTTATCG 60.447 44.000 0.00 0.00 44.52 2.92
4018 4121 5.408880 TGGTGGTACATTGTTCTTATCGA 57.591 39.130 0.00 0.00 44.52 3.59
4019 4122 5.984725 TGGTGGTACATTGTTCTTATCGAT 58.015 37.500 2.16 2.16 44.52 3.59
4020 4123 6.046593 TGGTGGTACATTGTTCTTATCGATC 58.953 40.000 0.00 0.00 44.52 3.69
4021 4124 5.175126 GGTGGTACATTGTTCTTATCGATCG 59.825 44.000 9.36 9.36 44.52 3.69
4022 4125 5.747197 GTGGTACATTGTTCTTATCGATCGT 59.253 40.000 15.94 5.23 44.52 3.73
4023 4126 5.975344 TGGTACATTGTTCTTATCGATCGTC 59.025 40.000 15.94 0.00 0.00 4.20
4024 4127 6.183360 TGGTACATTGTTCTTATCGATCGTCT 60.183 38.462 15.94 6.60 0.00 4.18
4025 4128 6.360148 GGTACATTGTTCTTATCGATCGTCTC 59.640 42.308 15.94 1.28 0.00 3.36
4026 4129 5.282510 ACATTGTTCTTATCGATCGTCTCC 58.717 41.667 15.94 0.00 0.00 3.71
4027 4130 3.604065 TGTTCTTATCGATCGTCTCCG 57.396 47.619 15.94 1.68 0.00 4.63
4028 4131 2.286831 TGTTCTTATCGATCGTCTCCGC 60.287 50.000 15.94 2.53 0.00 5.54
4029 4132 1.880271 TCTTATCGATCGTCTCCGCT 58.120 50.000 15.94 0.00 0.00 5.52
4030 4133 1.531578 TCTTATCGATCGTCTCCGCTG 59.468 52.381 15.94 0.00 0.00 5.18
4031 4134 0.591659 TTATCGATCGTCTCCGCTGG 59.408 55.000 15.94 0.00 0.00 4.85
4032 4135 0.534427 TATCGATCGTCTCCGCTGGT 60.534 55.000 15.94 0.00 0.00 4.00
4033 4136 0.534427 ATCGATCGTCTCCGCTGGTA 60.534 55.000 15.94 0.00 0.00 3.25
4034 4137 0.745486 TCGATCGTCTCCGCTGGTAA 60.745 55.000 15.94 0.00 0.00 2.85
4035 4138 0.317103 CGATCGTCTCCGCTGGTAAG 60.317 60.000 7.03 0.00 0.00 2.34
4036 4139 0.739561 GATCGTCTCCGCTGGTAAGT 59.260 55.000 0.00 0.00 0.00 2.24
4037 4140 1.134560 GATCGTCTCCGCTGGTAAGTT 59.865 52.381 0.00 0.00 0.00 2.66
4038 4141 1.825090 TCGTCTCCGCTGGTAAGTTA 58.175 50.000 0.00 0.00 0.00 2.24
4039 4142 2.372264 TCGTCTCCGCTGGTAAGTTAT 58.628 47.619 0.00 0.00 0.00 1.89
4040 4143 2.756760 TCGTCTCCGCTGGTAAGTTATT 59.243 45.455 0.00 0.00 0.00 1.40
4041 4144 3.114065 CGTCTCCGCTGGTAAGTTATTC 58.886 50.000 0.00 0.00 0.00 1.75
4042 4145 3.181489 CGTCTCCGCTGGTAAGTTATTCT 60.181 47.826 0.00 0.00 0.00 2.40
4043 4146 4.677250 CGTCTCCGCTGGTAAGTTATTCTT 60.677 45.833 0.00 0.00 39.89 2.52
4044 4147 5.176592 GTCTCCGCTGGTAAGTTATTCTTT 58.823 41.667 0.00 0.00 37.56 2.52
4045 4148 6.335777 GTCTCCGCTGGTAAGTTATTCTTTA 58.664 40.000 0.00 0.00 37.56 1.85
4046 4149 6.985059 GTCTCCGCTGGTAAGTTATTCTTTAT 59.015 38.462 0.00 0.00 37.56 1.40
4047 4150 7.169476 GTCTCCGCTGGTAAGTTATTCTTTATC 59.831 40.741 0.00 0.00 37.56 1.75
4048 4151 7.069578 TCTCCGCTGGTAAGTTATTCTTTATCT 59.930 37.037 0.00 0.00 37.56 1.98
4049 4152 6.984474 TCCGCTGGTAAGTTATTCTTTATCTG 59.016 38.462 0.00 0.00 37.56 2.90
4050 4153 6.761714 CCGCTGGTAAGTTATTCTTTATCTGT 59.238 38.462 0.00 0.00 37.56 3.41
4051 4154 7.280205 CCGCTGGTAAGTTATTCTTTATCTGTT 59.720 37.037 0.00 0.00 37.56 3.16
4052 4155 8.328864 CGCTGGTAAGTTATTCTTTATCTGTTC 58.671 37.037 0.00 0.00 37.56 3.18
4053 4156 8.613482 GCTGGTAAGTTATTCTTTATCTGTTCC 58.387 37.037 0.00 0.00 37.56 3.62
4054 4157 9.667107 CTGGTAAGTTATTCTTTATCTGTTCCA 57.333 33.333 0.00 0.00 37.56 3.53
4059 4162 9.807921 AAGTTATTCTTTATCTGTTCCAAGGAA 57.192 29.630 0.00 0.00 31.57 3.36
4060 4163 9.981460 AGTTATTCTTTATCTGTTCCAAGGAAT 57.019 29.630 4.63 0.00 36.45 3.01
4064 4167 8.477419 TTCTTTATCTGTTCCAAGGAATTTGT 57.523 30.769 4.63 0.00 36.45 2.83
4065 4168 8.110860 TCTTTATCTGTTCCAAGGAATTTGTC 57.889 34.615 4.63 0.00 36.45 3.18
4066 4169 6.494893 TTATCTGTTCCAAGGAATTTGTCG 57.505 37.500 4.63 0.00 36.45 4.35
4067 4170 2.552315 TCTGTTCCAAGGAATTTGTCGC 59.448 45.455 4.63 0.00 36.45 5.19
4068 4171 2.554032 CTGTTCCAAGGAATTTGTCGCT 59.446 45.455 4.63 0.00 36.45 4.93
4069 4172 2.552315 TGTTCCAAGGAATTTGTCGCTC 59.448 45.455 4.63 0.00 36.45 5.03
4070 4173 1.438651 TCCAAGGAATTTGTCGCTCG 58.561 50.000 0.00 0.00 34.87 5.03
4071 4174 1.001520 TCCAAGGAATTTGTCGCTCGA 59.998 47.619 0.00 0.00 34.87 4.04
4072 4175 1.804151 CCAAGGAATTTGTCGCTCGAA 59.196 47.619 0.00 0.00 34.87 3.71
4073 4176 2.412847 CCAAGGAATTTGTCGCTCGAAC 60.413 50.000 0.00 0.00 34.87 3.95
4074 4177 1.068474 AGGAATTTGTCGCTCGAACG 58.932 50.000 0.82 0.82 0.00 3.95
4075 4178 0.788391 GGAATTTGTCGCTCGAACGT 59.212 50.000 8.23 0.00 0.00 3.99
4076 4179 1.193874 GGAATTTGTCGCTCGAACGTT 59.806 47.619 8.23 0.00 0.00 3.99
4077 4180 2.349155 GGAATTTGTCGCTCGAACGTTT 60.349 45.455 8.23 0.00 0.00 3.60
4078 4181 3.285745 GAATTTGTCGCTCGAACGTTTT 58.714 40.909 8.23 0.00 0.00 2.43
4079 4182 2.079941 TTTGTCGCTCGAACGTTTTG 57.920 45.000 8.23 0.00 0.00 2.44
4080 4183 0.315544 TTGTCGCTCGAACGTTTTGC 60.316 50.000 8.23 6.64 0.00 3.68
4081 4184 1.149361 TGTCGCTCGAACGTTTTGCT 61.149 50.000 8.23 0.00 0.00 3.91
4082 4185 0.718220 GTCGCTCGAACGTTTTGCTG 60.718 55.000 8.23 4.79 0.00 4.41
4083 4186 1.438710 CGCTCGAACGTTTTGCTGG 60.439 57.895 0.46 0.00 0.00 4.85
4084 4187 1.827315 CGCTCGAACGTTTTGCTGGA 61.827 55.000 0.46 0.00 0.00 3.86
4085 4188 0.110644 GCTCGAACGTTTTGCTGGAG 60.111 55.000 0.46 4.40 0.00 3.86
4086 4189 1.497991 CTCGAACGTTTTGCTGGAGA 58.502 50.000 0.46 0.00 0.00 3.71
4087 4190 1.864711 CTCGAACGTTTTGCTGGAGAA 59.135 47.619 0.46 0.00 0.00 2.87
4088 4191 2.281517 TCGAACGTTTTGCTGGAGAAA 58.718 42.857 0.46 0.00 0.00 2.52
4109 4212 0.681733 TGTCTCTTCTGCAGGGTGTC 59.318 55.000 15.13 6.87 0.00 3.67
4117 4221 4.664677 GCAGGGTGTCGTGCGAGT 62.665 66.667 0.00 0.00 43.44 4.18
4144 4248 4.694233 CAGCCGCTGCACTCAGGT 62.694 66.667 7.61 0.00 40.65 4.00
4145 4249 4.694233 AGCCGCTGCACTCAGGTG 62.694 66.667 2.05 0.00 45.53 4.00
4158 4262 2.368875 ACTCAGGTGGTCTGGTTACAAG 59.631 50.000 0.00 0.00 43.53 3.16
4166 4270 3.515502 TGGTCTGGTTACAAGATCTGGAG 59.484 47.826 3.42 0.00 0.00 3.86
4172 4276 5.551233 TGGTTACAAGATCTGGAGAAACTG 58.449 41.667 3.42 0.00 0.00 3.16
4173 4277 5.071788 TGGTTACAAGATCTGGAGAAACTGT 59.928 40.000 3.42 0.67 0.00 3.55
4175 4279 6.590677 GGTTACAAGATCTGGAGAAACTGTAC 59.409 42.308 3.42 0.00 0.00 2.90
4177 4281 6.174720 ACAAGATCTGGAGAAACTGTACAA 57.825 37.500 3.42 0.00 0.00 2.41
4179 4283 5.413309 AGATCTGGAGAAACTGTACAAGG 57.587 43.478 0.00 0.00 0.00 3.61
4180 4284 4.841246 AGATCTGGAGAAACTGTACAAGGT 59.159 41.667 0.00 0.00 0.00 3.50
4181 4285 4.336889 TCTGGAGAAACTGTACAAGGTG 57.663 45.455 0.00 0.00 0.00 4.00
4184 4288 3.181458 TGGAGAAACTGTACAAGGTGGTC 60.181 47.826 0.00 0.00 0.00 4.02
4185 4289 3.071167 GGAGAAACTGTACAAGGTGGTCT 59.929 47.826 0.00 0.00 0.00 3.85
4187 4291 5.112129 AGAAACTGTACAAGGTGGTCTTT 57.888 39.130 0.00 0.00 32.41 2.52
4189 4293 6.838382 AGAAACTGTACAAGGTGGTCTTTAT 58.162 36.000 0.00 0.00 32.41 1.40
4190 4294 7.287810 AGAAACTGTACAAGGTGGTCTTTATT 58.712 34.615 0.00 0.00 32.41 1.40
4191 4295 7.778382 AGAAACTGTACAAGGTGGTCTTTATTT 59.222 33.333 0.00 0.00 32.41 1.40
4192 4296 7.506328 AACTGTACAAGGTGGTCTTTATTTC 57.494 36.000 0.00 0.00 32.41 2.17
4194 4298 7.231467 ACTGTACAAGGTGGTCTTTATTTCAT 58.769 34.615 0.00 0.00 32.41 2.57
4195 4299 7.390718 ACTGTACAAGGTGGTCTTTATTTCATC 59.609 37.037 0.00 0.00 32.41 2.92
4196 4300 6.657541 TGTACAAGGTGGTCTTTATTTCATCC 59.342 38.462 0.00 0.00 32.41 3.51
4197 4301 5.640147 ACAAGGTGGTCTTTATTTCATCCA 58.360 37.500 0.00 0.00 32.41 3.41
4199 4303 6.553100 ACAAGGTGGTCTTTATTTCATCCAAA 59.447 34.615 0.00 0.00 32.41 3.28
4200 4304 7.235399 ACAAGGTGGTCTTTATTTCATCCAAAT 59.765 33.333 0.00 0.00 34.63 2.32
4202 4306 8.293699 AGGTGGTCTTTATTTCATCCAAATAC 57.706 34.615 0.00 0.00 36.79 1.89
4203 4307 7.893302 AGGTGGTCTTTATTTCATCCAAATACA 59.107 33.333 0.00 0.00 36.79 2.29
4204 4308 7.973944 GGTGGTCTTTATTTCATCCAAATACAC 59.026 37.037 0.00 0.00 36.79 2.90
4205 4309 8.519526 GTGGTCTTTATTTCATCCAAATACACA 58.480 33.333 0.00 0.00 36.79 3.72
4206 4310 9.253832 TGGTCTTTATTTCATCCAAATACACAT 57.746 29.630 0.00 0.00 36.79 3.21
4285 4421 2.124403 CCATCAGGGTGCAGCTCC 60.124 66.667 16.65 4.78 0.00 4.70
4286 4422 2.672908 CATCAGGGTGCAGCTCCA 59.327 61.111 16.65 0.00 0.00 3.86
4416 4552 2.513204 CTCGCCACCTCTGCCATG 60.513 66.667 0.00 0.00 0.00 3.66
4461 4597 1.003839 GGTGCAGGACCGAATCACA 60.004 57.895 0.00 0.00 34.02 3.58
4548 4684 2.686470 CTCAGCTGCCTCTCCCCA 60.686 66.667 9.47 0.00 0.00 4.96
4668 4804 2.888863 CTCTCCCTGTCGGACAGC 59.111 66.667 28.50 0.00 44.63 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 187 0.617820 CTGGCCTACCACTACCAGGT 60.618 60.000 3.32 0.00 44.90 4.00
219 237 4.281435 TCGAACCAACTTGGACACAGTATA 59.719 41.667 15.14 0.00 40.96 1.47
223 241 1.597663 GTCGAACCAACTTGGACACAG 59.402 52.381 15.14 1.76 40.96 3.66
279 301 5.693555 TCAACAGCGCTAGATCAATTCATAG 59.306 40.000 10.99 0.00 0.00 2.23
357 379 5.625568 AGAACACAAAGTTACAGTAGGGT 57.374 39.130 0.00 0.00 41.51 4.34
362 384 8.747538 AGGAAATAAGAACACAAAGTTACAGT 57.252 30.769 0.00 0.00 41.51 3.55
375 397 7.771183 TGCATGGACAATTAGGAAATAAGAAC 58.229 34.615 0.00 0.00 0.00 3.01
418 446 7.741027 ACAGCCAGATAAATTATGATGACTG 57.259 36.000 8.53 8.53 0.00 3.51
419 447 8.874156 TCTACAGCCAGATAAATTATGATGACT 58.126 33.333 0.00 0.00 0.00 3.41
421 449 9.494271 GTTCTACAGCCAGATAAATTATGATGA 57.506 33.333 0.00 0.00 0.00 2.92
528 559 2.973945 AGCTAAAGAGGCTAAACACCG 58.026 47.619 0.00 0.00 38.36 4.94
575 607 3.517901 AGTTACAAAGGATCCGACCATGA 59.482 43.478 5.98 0.00 0.00 3.07
921 956 4.848357 ACAAATATGGGAGGAACAGACTG 58.152 43.478 0.00 0.00 0.00 3.51
922 957 4.785376 AGACAAATATGGGAGGAACAGACT 59.215 41.667 0.00 0.00 0.00 3.24
2212 2272 1.122632 TCAAGTCCGGCCTGTACCAA 61.123 55.000 0.00 0.00 0.00 3.67
2904 2982 0.523072 CAAAATCTGGACCTGTGGCG 59.477 55.000 0.00 0.00 0.00 5.69
3219 3304 3.181483 CCAAAACAACAAGAAGCTCAGCT 60.181 43.478 0.00 0.00 42.56 4.24
3413 3498 7.613022 AGAAGAAAGGCAATAGAAATGACATCA 59.387 33.333 0.00 0.00 0.00 3.07
3414 3499 7.994194 AGAAGAAAGGCAATAGAAATGACATC 58.006 34.615 0.00 0.00 0.00 3.06
3438 3523 7.545265 CCAATCACCCATGTAATGTAACAAAAG 59.455 37.037 0.00 0.00 44.81 2.27
3442 3527 5.575157 ACCAATCACCCATGTAATGTAACA 58.425 37.500 0.00 0.00 44.81 2.41
3443 3528 6.377146 AGAACCAATCACCCATGTAATGTAAC 59.623 38.462 0.00 0.00 44.81 2.50
3445 3530 6.069673 AGAGAACCAATCACCCATGTAATGTA 60.070 38.462 0.00 0.00 44.81 2.29
3446 3531 4.934356 AGAACCAATCACCCATGTAATGT 58.066 39.130 0.00 0.00 44.81 2.71
3447 3532 5.195940 AGAGAACCAATCACCCATGTAATG 58.804 41.667 0.00 0.00 46.21 1.90
3504 3593 1.142748 GTCACGCTCTCATCCCTGG 59.857 63.158 0.00 0.00 0.00 4.45
3526 3615 1.600076 CAGGACAGCAACTGCAGCT 60.600 57.895 15.27 2.71 45.16 4.24
3734 3831 3.937706 CAGCAACAAAACCAAACATCCAA 59.062 39.130 0.00 0.00 0.00 3.53
3805 3908 2.578786 TGTTCCTACGACTGACTGACA 58.421 47.619 0.00 0.00 0.00 3.58
3842 3945 7.807907 CAGACTGAAAATAATAAACCACCACAC 59.192 37.037 0.00 0.00 0.00 3.82
3978 4081 1.202371 CCAAGCAGCAACATAGCATGG 60.202 52.381 0.00 0.00 40.20 3.66
3988 4091 1.612950 CAATGTACCACCAAGCAGCAA 59.387 47.619 0.00 0.00 0.00 3.91
3996 4099 5.408880 TCGATAAGAACAATGTACCACCA 57.591 39.130 0.00 0.00 0.00 4.17
3997 4100 5.175126 CGATCGATAAGAACAATGTACCACC 59.825 44.000 10.26 0.00 0.00 4.61
3998 4101 5.747197 ACGATCGATAAGAACAATGTACCAC 59.253 40.000 24.34 0.00 0.00 4.16
3999 4102 5.898174 ACGATCGATAAGAACAATGTACCA 58.102 37.500 24.34 0.00 0.00 3.25
4000 4103 6.207213 AGACGATCGATAAGAACAATGTACC 58.793 40.000 24.34 0.00 0.00 3.34
4001 4104 6.360148 GGAGACGATCGATAAGAACAATGTAC 59.640 42.308 24.34 0.00 0.00 2.90
4002 4105 6.436261 GGAGACGATCGATAAGAACAATGTA 58.564 40.000 24.34 0.00 0.00 2.29
4003 4106 5.282510 GGAGACGATCGATAAGAACAATGT 58.717 41.667 24.34 0.00 0.00 2.71
4004 4107 5.814314 GGAGACGATCGATAAGAACAATG 57.186 43.478 24.34 0.00 0.00 2.82
4021 4124 4.388378 AGAATAACTTACCAGCGGAGAC 57.612 45.455 1.50 0.00 0.00 3.36
4022 4125 5.416271 AAAGAATAACTTACCAGCGGAGA 57.584 39.130 1.50 0.00 37.93 3.71
4023 4126 7.169982 CAGATAAAGAATAACTTACCAGCGGAG 59.830 40.741 1.50 0.00 37.93 4.63
4024 4127 6.984474 CAGATAAAGAATAACTTACCAGCGGA 59.016 38.462 1.50 0.00 37.93 5.54
4025 4128 6.761714 ACAGATAAAGAATAACTTACCAGCGG 59.238 38.462 0.00 0.00 37.93 5.52
4026 4129 7.772332 ACAGATAAAGAATAACTTACCAGCG 57.228 36.000 0.00 0.00 37.93 5.18
4027 4130 8.613482 GGAACAGATAAAGAATAACTTACCAGC 58.387 37.037 0.00 0.00 37.93 4.85
4028 4131 9.667107 TGGAACAGATAAAGAATAACTTACCAG 57.333 33.333 0.00 0.00 37.93 4.00
4033 4136 9.807921 TTCCTTGGAACAGATAAAGAATAACTT 57.192 29.630 0.00 0.00 42.39 2.66
4034 4137 9.981460 ATTCCTTGGAACAGATAAAGAATAACT 57.019 29.630 4.00 0.00 42.39 2.24
4038 4141 9.093458 ACAAATTCCTTGGAACAGATAAAGAAT 57.907 29.630 4.00 0.00 42.39 2.40
4039 4142 8.477419 ACAAATTCCTTGGAACAGATAAAGAA 57.523 30.769 4.00 0.00 42.39 2.52
4040 4143 7.094805 CGACAAATTCCTTGGAACAGATAAAGA 60.095 37.037 4.00 0.00 42.39 2.52
4041 4144 7.023575 CGACAAATTCCTTGGAACAGATAAAG 58.976 38.462 4.00 0.00 42.39 1.85
4042 4145 6.569610 GCGACAAATTCCTTGGAACAGATAAA 60.570 38.462 4.00 0.00 42.39 1.40
4043 4146 5.106317 GCGACAAATTCCTTGGAACAGATAA 60.106 40.000 4.00 0.00 42.39 1.75
4044 4147 4.394920 GCGACAAATTCCTTGGAACAGATA 59.605 41.667 4.00 0.00 42.39 1.98
4045 4148 3.191371 GCGACAAATTCCTTGGAACAGAT 59.809 43.478 4.00 0.00 42.39 2.90
4046 4149 2.552315 GCGACAAATTCCTTGGAACAGA 59.448 45.455 4.00 0.00 42.39 3.41
4047 4150 2.554032 AGCGACAAATTCCTTGGAACAG 59.446 45.455 4.00 0.81 42.39 3.16
4048 4151 2.552315 GAGCGACAAATTCCTTGGAACA 59.448 45.455 4.00 0.00 39.56 3.18
4049 4152 2.412847 CGAGCGACAAATTCCTTGGAAC 60.413 50.000 4.00 0.00 39.56 3.62
4050 4153 1.804151 CGAGCGACAAATTCCTTGGAA 59.196 47.619 4.43 4.43 39.56 3.53
4051 4154 1.001520 TCGAGCGACAAATTCCTTGGA 59.998 47.619 0.00 0.00 39.56 3.53
4052 4155 1.438651 TCGAGCGACAAATTCCTTGG 58.561 50.000 0.00 0.00 39.56 3.61
4053 4156 2.721797 CGTTCGAGCGACAAATTCCTTG 60.722 50.000 17.32 0.00 41.19 3.61
4054 4157 1.459592 CGTTCGAGCGACAAATTCCTT 59.540 47.619 17.32 0.00 0.00 3.36
4055 4158 1.068474 CGTTCGAGCGACAAATTCCT 58.932 50.000 17.32 0.00 0.00 3.36
4056 4159 0.788391 ACGTTCGAGCGACAAATTCC 59.212 50.000 28.55 0.00 35.59 3.01
4057 4160 2.572173 AACGTTCGAGCGACAAATTC 57.428 45.000 28.55 0.00 35.59 2.17
4058 4161 3.033185 CAAAACGTTCGAGCGACAAATT 58.967 40.909 28.55 8.65 35.59 1.82
4059 4162 2.635444 CAAAACGTTCGAGCGACAAAT 58.365 42.857 28.55 1.84 35.59 2.32
4060 4163 1.852861 GCAAAACGTTCGAGCGACAAA 60.853 47.619 28.55 0.00 35.59 2.83
4061 4164 0.315544 GCAAAACGTTCGAGCGACAA 60.316 50.000 28.55 0.00 35.59 3.18
4062 4165 1.149361 AGCAAAACGTTCGAGCGACA 61.149 50.000 28.55 0.00 35.59 4.35
4063 4166 0.718220 CAGCAAAACGTTCGAGCGAC 60.718 55.000 28.55 11.23 35.59 5.19
4064 4167 1.562691 CAGCAAAACGTTCGAGCGA 59.437 52.632 28.55 0.00 35.59 4.93
4065 4168 1.438710 CCAGCAAAACGTTCGAGCG 60.439 57.895 20.50 20.50 37.94 5.03
4066 4169 0.110644 CTCCAGCAAAACGTTCGAGC 60.111 55.000 0.00 6.35 0.00 5.03
4067 4170 1.497991 TCTCCAGCAAAACGTTCGAG 58.502 50.000 0.00 0.54 0.00 4.04
4068 4171 1.942677 TTCTCCAGCAAAACGTTCGA 58.057 45.000 0.00 0.00 0.00 3.71
4069 4172 2.748461 TTTCTCCAGCAAAACGTTCG 57.252 45.000 0.00 0.00 0.00 3.95
4070 4173 4.359706 ACATTTTCTCCAGCAAAACGTTC 58.640 39.130 0.00 0.00 0.00 3.95
4071 4174 4.097892 AGACATTTTCTCCAGCAAAACGTT 59.902 37.500 0.00 0.00 0.00 3.99
4072 4175 3.632145 AGACATTTTCTCCAGCAAAACGT 59.368 39.130 0.00 0.00 0.00 3.99
4073 4176 4.222114 GAGACATTTTCTCCAGCAAAACG 58.778 43.478 0.00 0.00 44.74 3.60
4084 4187 3.073650 ACCCTGCAGAAGAGACATTTTCT 59.926 43.478 17.39 0.00 37.23 2.52
4085 4188 3.190118 CACCCTGCAGAAGAGACATTTTC 59.810 47.826 17.39 0.00 0.00 2.29
4086 4189 3.152341 CACCCTGCAGAAGAGACATTTT 58.848 45.455 17.39 0.00 0.00 1.82
4087 4190 2.107204 ACACCCTGCAGAAGAGACATTT 59.893 45.455 17.39 0.00 0.00 2.32
4088 4191 1.701847 ACACCCTGCAGAAGAGACATT 59.298 47.619 17.39 0.00 0.00 2.71
4127 4231 4.694233 ACCTGAGTGCAGCGGCTG 62.694 66.667 25.21 25.21 40.91 4.85
4128 4232 4.694233 CACCTGAGTGCAGCGGCT 62.694 66.667 10.92 0.00 40.91 5.52
4130 4234 4.320456 ACCACCTGAGTGCAGCGG 62.320 66.667 0.00 0.00 43.09 5.52
4131 4235 2.740055 GACCACCTGAGTGCAGCG 60.740 66.667 0.00 0.00 43.09 5.18
4132 4236 1.670406 CAGACCACCTGAGTGCAGC 60.670 63.158 0.00 0.00 45.78 5.25
4133 4237 1.004080 CCAGACCACCTGAGTGCAG 60.004 63.158 0.00 0.00 45.78 4.41
4140 4244 3.261897 AGATCTTGTAACCAGACCACCTG 59.738 47.826 0.00 0.00 42.55 4.00
4144 4248 3.515502 CTCCAGATCTTGTAACCAGACCA 59.484 47.826 0.00 0.00 0.00 4.02
4145 4249 3.769844 TCTCCAGATCTTGTAACCAGACC 59.230 47.826 0.00 0.00 0.00 3.85
4158 4262 4.932200 CACCTTGTACAGTTTCTCCAGATC 59.068 45.833 0.00 0.00 0.00 2.75
4166 4270 7.506328 AATAAAGACCACCTTGTACAGTTTC 57.494 36.000 0.00 0.00 34.79 2.78
4172 4276 6.657541 TGGATGAAATAAAGACCACCTTGTAC 59.342 38.462 0.00 0.00 34.79 2.90
4173 4277 6.785076 TGGATGAAATAAAGACCACCTTGTA 58.215 36.000 0.00 0.00 34.79 2.41
4175 4279 6.588719 TTGGATGAAATAAAGACCACCTTG 57.411 37.500 0.00 0.00 34.79 3.61
4177 4281 7.893302 TGTATTTGGATGAAATAAAGACCACCT 59.107 33.333 0.00 0.00 38.09 4.00
4179 4283 8.519526 TGTGTATTTGGATGAAATAAAGACCAC 58.480 33.333 0.00 0.00 38.09 4.16
4180 4284 8.642935 TGTGTATTTGGATGAAATAAAGACCA 57.357 30.769 0.00 0.00 38.09 4.02
4184 4288 9.169468 GCGTATGTGTATTTGGATGAAATAAAG 57.831 33.333 0.00 0.00 38.09 1.85
4185 4289 8.678199 TGCGTATGTGTATTTGGATGAAATAAA 58.322 29.630 0.00 0.00 38.09 1.40
4187 4291 7.497579 AGTGCGTATGTGTATTTGGATGAAATA 59.502 33.333 0.00 0.00 35.74 1.40
4189 4293 5.645929 AGTGCGTATGTGTATTTGGATGAAA 59.354 36.000 0.00 0.00 0.00 2.69
4190 4294 5.064579 CAGTGCGTATGTGTATTTGGATGAA 59.935 40.000 0.00 0.00 0.00 2.57
4191 4295 4.570369 CAGTGCGTATGTGTATTTGGATGA 59.430 41.667 0.00 0.00 0.00 2.92
4192 4296 4.786292 GCAGTGCGTATGTGTATTTGGATG 60.786 45.833 0.00 0.00 0.00 3.51
4194 4298 2.675844 GCAGTGCGTATGTGTATTTGGA 59.324 45.455 0.00 0.00 0.00 3.53
4195 4299 3.051606 GCAGTGCGTATGTGTATTTGG 57.948 47.619 0.00 0.00 0.00 3.28
4209 4345 0.593128 AACAGTTGGAATCGCAGTGC 59.407 50.000 4.58 4.58 0.00 4.40
4231 4367 2.606717 TGCTACAGTGAGTTCGTACG 57.393 50.000 9.53 9.53 0.00 3.67
4285 4421 2.864114 CCACCTGAAGATGGCACTG 58.136 57.895 0.00 0.00 0.00 3.66
4461 4597 2.426023 GTCAACAGGCTGGACGGT 59.574 61.111 20.34 0.00 0.00 4.83
4513 4649 1.987855 GGGACGTGATGGACCCTGA 60.988 63.158 0.00 0.00 39.28 3.86
4668 4804 4.463879 CTGCAGTCCCTCCTGGCG 62.464 72.222 5.25 0.00 32.92 5.69


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

AutoCloner maintained by Alex Coulton.