Multiple sequence alignment - TraesCS3B01G093400

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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 TraesCS3B01G093400 chr3B 100.000 5815 0 0 1 5815 62397533 62391719 0.000000e+00 10739
1 TraesCS3B01G093400 chr3B 88.318 214 24 1 3531 3743 62393793 62393580 7.480000e-64 255
2 TraesCS3B01G093400 chr3B 88.318 214 24 1 3741 3954 62394003 62393791 7.480000e-64 255
3 TraesCS3B01G093400 chr3D 93.627 5115 209 53 727 5770 39340112 39335044 0.000000e+00 7531
4 TraesCS3B01G093400 chr3D 92.632 285 14 4 373 650 39340669 39340385 2.520000e-108 403
5 TraesCS3B01G093400 chr3D 84.932 365 40 9 1 355 39341015 39340656 7.170000e-94 355
6 TraesCS3B01G093400 chr3D 89.202 213 17 4 3535 3743 39337095 39336885 1.610000e-65 261
7 TraesCS3B01G093400 chr3D 87.500 216 26 1 3741 3956 39337310 39337096 1.250000e-61 248
8 TraesCS3B01G093400 chr3A 92.926 3647 138 56 2184 5770 50750193 50746607 0.000000e+00 5195
9 TraesCS3B01G093400 chr3A 92.278 1839 81 18 373 2188 50752120 50750320 0.000000e+00 2553
10 TraesCS3B01G093400 chr3A 91.414 198 14 2 3548 3743 50748636 50748440 9.600000e-68 268
11 TraesCS3B01G093400 chr3A 88.940 217 21 2 3741 3956 50748864 50748650 1.240000e-66 265
12 TraesCS3B01G093400 chr2D 96.892 547 17 0 2537 3083 13706993 13707539 0.000000e+00 917
13 TraesCS3B01G093400 chr2D 96.667 90 3 0 3251 3340 208540141 208540230 3.630000e-32 150
14 TraesCS3B01G093400 chr2D 91.589 107 4 4 3246 3351 128890631 128890733 6.070000e-30 143
15 TraesCS3B01G093400 chr5B 92.381 105 4 3 3254 3357 184285349 184285248 4.700000e-31 147
16 TraesCS3B01G093400 chr2B 95.604 91 2 1 3250 3340 354879121 354879209 1.690000e-30 145
17 TraesCS3B01G093400 chr6A 90.179 112 8 2 3251 3362 584511449 584511341 6.070000e-30 143
18 TraesCS3B01G093400 chr1D 90.654 107 5 4 3246 3351 346659702 346659804 2.830000e-28 137
19 TraesCS3B01G093400 chr1A 89.286 112 9 2 3251 3362 505489870 505489762 2.830000e-28 137


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 TraesCS3B01G093400 chr3B 62391719 62397533 5814 True 3749.666667 10739 92.2120 1 5815 3 chr3B.!!$R1 5814
1 TraesCS3B01G093400 chr3D 39335044 39341015 5971 True 1759.600000 7531 89.5786 1 5770 5 chr3D.!!$R1 5769
2 TraesCS3B01G093400 chr3A 50746607 50752120 5513 True 2070.250000 5195 91.3895 373 5770 4 chr3A.!!$R1 5397
3 TraesCS3B01G093400 chr2D 13706993 13707539 546 False 917.000000 917 96.8920 2537 3083 1 chr2D.!!$F1 546

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
131 132 0.179004 AAACCATCAAGTCCCGCACA 60.179 50.000 0.00 0.0 0.00 4.57 F
1517 1756 0.188587 ACATAGAGGGGATCGAGCCA 59.811 55.000 23.22 0.0 0.00 4.75 F
2706 3089 2.169330 TGCAATGCTCAATGCCACTAA 58.831 42.857 6.82 0.0 41.87 2.24 F
4610 5007 1.076332 GTAACGAAGATGCGGCTGTT 58.924 50.000 0.00 0.0 35.12 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1777 1.190984 CCATCAATGAAGCGATCGACG 59.809 52.381 21.57 0.0 45.66 5.12 R
2727 3110 2.034053 ACGGAGAAAATTTGAAGCGCAA 59.966 40.909 11.47 0.0 33.88 4.85 R
4667 5064 1.823610 ACCCGTTGTTCTAGACTAGCC 59.176 52.381 4.47 0.0 0.00 3.93 R
5510 5940 2.945008 TCAACACTCAGTTTCTTGCTGG 59.055 45.455 0.00 0.0 38.74 4.85 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
76 77 2.079925 GCATCCTCACCTTCTTGTCAC 58.920 52.381 0.00 0.00 0.00 3.67
121 122 6.998968 AAAAATGTGCAAGAAAACCATCAA 57.001 29.167 0.00 0.00 0.00 2.57
123 124 4.942761 ATGTGCAAGAAAACCATCAAGT 57.057 36.364 0.00 0.00 0.00 3.16
127 128 2.351738 GCAAGAAAACCATCAAGTCCCG 60.352 50.000 0.00 0.00 0.00 5.14
128 129 1.534729 AGAAAACCATCAAGTCCCGC 58.465 50.000 0.00 0.00 0.00 6.13
131 132 0.179004 AAACCATCAAGTCCCGCACA 60.179 50.000 0.00 0.00 0.00 4.57
154 155 4.823989 ACCTTTTGTTGAGAACATGAGAGG 59.176 41.667 0.00 0.00 41.79 3.69
157 158 3.969287 TGTTGAGAACATGAGAGGGAG 57.031 47.619 0.00 0.00 36.25 4.30
158 159 2.568956 TGTTGAGAACATGAGAGGGAGG 59.431 50.000 0.00 0.00 36.25 4.30
189 195 4.702131 GTCCTAAACTTGGCACAGATGATT 59.298 41.667 0.00 0.00 42.39 2.57
190 196 4.701651 TCCTAAACTTGGCACAGATGATTG 59.298 41.667 0.00 0.00 42.39 2.67
192 198 1.913778 ACTTGGCACAGATGATTGCA 58.086 45.000 0.00 0.00 42.39 4.08
194 200 2.829720 ACTTGGCACAGATGATTGCATT 59.170 40.909 0.00 0.00 42.39 3.56
221 231 9.679661 TTTTAATGTATTTCAGTCTATCTGGCA 57.320 29.630 0.00 0.00 43.76 4.92
226 236 7.661968 TGTATTTCAGTCTATCTGGCACTATC 58.338 38.462 0.00 0.00 43.76 2.08
228 238 3.149981 TCAGTCTATCTGGCACTATCCG 58.850 50.000 0.00 0.00 43.76 4.18
242 252 4.360563 CACTATCCGTTCAGTGGTATCAC 58.639 47.826 0.00 0.00 43.93 3.06
255 265 1.030457 GTATCACGTCCCCATCGACT 58.970 55.000 0.00 0.00 0.00 4.18
257 267 1.030457 ATCACGTCCCCATCGACTAC 58.970 55.000 0.00 0.00 0.00 2.73
277 287 7.305590 CGACTACGAGATATCTATAGCGACTTC 60.306 44.444 20.83 12.69 42.66 3.01
278 288 5.705813 ACGAGATATCTATAGCGACTTCG 57.294 43.478 15.98 9.53 43.27 3.79
282 292 6.183360 CGAGATATCTATAGCGACTTCGTCAA 60.183 42.308 4.89 0.00 42.22 3.18
286 296 6.994868 ATCTATAGCGACTTCGTCAATTTC 57.005 37.500 0.00 0.00 42.22 2.17
292 302 4.092091 AGCGACTTCGTCAATTTCAAGATC 59.908 41.667 0.00 0.00 42.22 2.75
297 307 5.577164 ACTTCGTCAATTTCAAGATCTACCG 59.423 40.000 0.00 0.00 0.00 4.02
301 311 6.094464 TCGTCAATTTCAAGATCTACCGACTA 59.906 38.462 0.00 0.00 0.00 2.59
302 312 6.415280 CGTCAATTTCAAGATCTACCGACTAG 59.585 42.308 0.00 0.00 0.00 2.57
313 323 0.899720 ACCGACTAGGCCATTCGAAA 59.100 50.000 19.05 0.00 46.52 3.46
322 332 2.554032 AGGCCATTCGAAAGTGTTTCTG 59.446 45.455 5.01 0.00 37.52 3.02
324 334 2.552315 GCCATTCGAAAGTGTTTCTGGA 59.448 45.455 13.04 0.00 35.60 3.86
325 335 3.004315 GCCATTCGAAAGTGTTTCTGGAA 59.996 43.478 13.04 2.67 35.60 3.53
326 336 4.499019 GCCATTCGAAAGTGTTTCTGGAAA 60.499 41.667 13.04 0.00 35.60 3.13
328 338 5.687285 CCATTCGAAAGTGTTTCTGGAAAAG 59.313 40.000 0.00 0.00 35.60 2.27
419 430 0.397254 GAGGGAGATGGAGGAACGGA 60.397 60.000 0.00 0.00 0.00 4.69
446 457 1.676006 CCGAAGCCCATGGTTATTCAC 59.324 52.381 11.73 0.00 30.94 3.18
488 503 2.192979 CCCACCCACCCATCATCG 59.807 66.667 0.00 0.00 0.00 3.84
614 644 1.141657 CTATCCATCCACCACCACCAG 59.858 57.143 0.00 0.00 0.00 4.00
623 653 1.073199 CCACCACCAGAAGACACCC 59.927 63.158 0.00 0.00 0.00 4.61
801 1030 2.176273 CCTCGCCCTGCTCAAATCG 61.176 63.158 0.00 0.00 0.00 3.34
811 1040 1.688735 TGCTCAAATCGATCGATCCCT 59.311 47.619 29.48 12.85 33.08 4.20
812 1041 2.064762 GCTCAAATCGATCGATCCCTG 58.935 52.381 29.48 24.14 33.08 4.45
829 1060 0.877649 CTGATCGCCCCTGTCGATTG 60.878 60.000 0.00 0.00 45.44 2.67
862 1093 3.249189 AGCCCCGTGAGCTGGAAA 61.249 61.111 0.00 0.00 39.69 3.13
877 1108 0.392595 GGAAAGAAGTAGGTGCCCGG 60.393 60.000 0.00 0.00 0.00 5.73
880 1111 0.834687 AAGAAGTAGGTGCCCGGTGA 60.835 55.000 0.00 0.00 0.00 4.02
886 1117 4.041762 GGTGCCCGGTGATTCCCA 62.042 66.667 0.00 0.00 0.00 4.37
940 1172 4.147449 CCAGACCGCATCCGCTCA 62.147 66.667 0.00 0.00 35.30 4.26
947 1179 2.537560 CGCATCCGCTCACCCAATC 61.538 63.158 0.00 0.00 35.30 2.67
967 1199 1.133363 CGGCGCATCATTTTCCGTTG 61.133 55.000 10.83 0.00 35.75 4.10
972 1204 2.620242 GCATCATTTTCCGTTGCCAAT 58.380 42.857 0.00 0.00 0.00 3.16
973 1205 2.604462 GCATCATTTTCCGTTGCCAATC 59.396 45.455 0.00 0.00 0.00 2.67
974 1206 2.627863 TCATTTTCCGTTGCCAATCG 57.372 45.000 0.00 0.00 0.00 3.34
1336 1574 3.737172 ACGACGCCAGCAAATGCC 61.737 61.111 0.94 0.00 43.38 4.40
1347 1585 3.434319 AAATGCCTGCCGTGCTCG 61.434 61.111 0.14 0.14 0.00 5.03
1412 1650 5.879763 TCTGGATCAGACATTTTTCCTTGA 58.120 37.500 0.00 0.00 35.39 3.02
1446 1685 4.951715 CCTGACTGGAATGGATGATGAAAA 59.048 41.667 0.00 0.00 38.35 2.29
1449 1688 7.364408 CCTGACTGGAATGGATGATGAAAATTT 60.364 37.037 0.00 0.00 38.35 1.82
1517 1756 0.188587 ACATAGAGGGGATCGAGCCA 59.811 55.000 23.22 0.00 0.00 4.75
1556 1795 2.389059 CTCGTCGATCGCTTCATTGAT 58.611 47.619 11.09 0.00 39.67 2.57
1640 1879 5.918608 AGCAAAGTGATATACGAGGATGTT 58.081 37.500 0.00 0.00 0.00 2.71
2023 2271 3.700539 TCACCATGGCAACCTATGAAATG 59.299 43.478 13.04 0.00 0.00 2.32
2091 2339 8.036575 TGCCGCTAGAACTTTTTCTACTAAATA 58.963 33.333 0.00 0.00 42.44 1.40
2706 3089 2.169330 TGCAATGCTCAATGCCACTAA 58.831 42.857 6.82 0.00 41.87 2.24
2745 3128 8.859156 TGTTATTATTGCGCTTCAAATTTTCTC 58.141 29.630 9.73 0.00 38.34 2.87
2747 3130 2.330231 TGCGCTTCAAATTTTCTCCG 57.670 45.000 9.73 0.00 0.00 4.63
2890 3277 2.507471 GTTTCTCCCTGGTCCTCATCAT 59.493 50.000 0.00 0.00 0.00 2.45
2998 3385 2.899900 GCCCAAAAAGGATCTTGAGGTT 59.100 45.455 0.00 0.00 41.22 3.50
3039 3426 9.073475 TGCCATACAGTCTTAACAGTAAAATTT 57.927 29.630 0.00 0.00 32.01 1.82
3240 3627 2.086094 TGATTGCGATGCTCACATGTT 58.914 42.857 0.00 0.00 36.35 2.71
3241 3628 2.159490 TGATTGCGATGCTCACATGTTG 60.159 45.455 0.00 0.00 36.35 3.33
3242 3629 1.521580 TTGCGATGCTCACATGTTGA 58.478 45.000 0.00 0.00 36.35 3.18
3243 3630 1.741528 TGCGATGCTCACATGTTGAT 58.258 45.000 0.00 0.00 36.35 2.57
3244 3631 1.399089 TGCGATGCTCACATGTTGATG 59.601 47.619 0.00 0.00 36.35 3.07
3245 3632 1.399440 GCGATGCTCACATGTTGATGT 59.601 47.619 0.00 0.00 44.08 3.06
3249 3636 4.093261 CGATGCTCACATGTTGATGTTGTA 59.907 41.667 0.00 0.00 41.12 2.41
3373 3760 9.545105 AAAAATTCAAGATTAAGCATCAACACA 57.455 25.926 0.00 0.00 33.75 3.72
3374 3761 9.545105 AAAATTCAAGATTAAGCATCAACACAA 57.455 25.926 0.00 0.00 33.75 3.33
3375 3762 9.545105 AAATTCAAGATTAAGCATCAACACAAA 57.455 25.926 0.00 0.00 33.75 2.83
3376 3763 7.928908 TTCAAGATTAAGCATCAACACAAAC 57.071 32.000 0.00 0.00 33.75 2.93
3377 3764 7.036996 TCAAGATTAAGCATCAACACAAACA 57.963 32.000 0.00 0.00 33.75 2.83
3378 3765 7.487484 TCAAGATTAAGCATCAACACAAACAA 58.513 30.769 0.00 0.00 33.75 2.83
3379 3766 7.648908 TCAAGATTAAGCATCAACACAAACAAG 59.351 33.333 0.00 0.00 33.75 3.16
3421 3808 7.514721 TGTCTTAACTAAGAAATGTCCTTGGT 58.485 34.615 0.75 0.00 43.30 3.67
3452 3839 2.031120 TGTCCAGTTTCTTTTGGCCAG 58.969 47.619 5.11 0.00 34.38 4.85
3479 3866 3.634910 GGACTTTGTTTGTTGGCTTCCTA 59.365 43.478 0.00 0.00 0.00 2.94
3626 4013 6.092533 AGTTTTCTTTGTTTTGTGAAGGCATG 59.907 34.615 0.00 0.00 0.00 4.06
3778 4167 9.780186 AGCTATAGGAAATTAAGTGATGTAACC 57.220 33.333 1.04 0.00 0.00 2.85
3786 4175 5.699097 TTAAGTGATGTAACCTTGGTTGC 57.301 39.130 14.67 13.60 0.00 4.17
3801 4190 4.226113 TGGTTGCGTTGTTTACCATAAC 57.774 40.909 0.00 0.00 35.82 1.89
3871 4260 3.838317 ACTGCCACCTGTTATCTGAAGTA 59.162 43.478 0.00 0.00 0.00 2.24
3911 4300 2.093306 TCCACGCACAAAGATACAGG 57.907 50.000 0.00 0.00 0.00 4.00
3912 4301 1.346395 TCCACGCACAAAGATACAGGT 59.654 47.619 0.00 0.00 0.00 4.00
3972 4363 7.950124 TGTGAAGGGAAAGGAAAGAAATAAGAT 59.050 33.333 0.00 0.00 0.00 2.40
4052 4443 6.154203 TGTTTTGATTGCATAGTGGTGAAA 57.846 33.333 0.00 0.00 0.00 2.69
4053 4444 6.577103 TGTTTTGATTGCATAGTGGTGAAAA 58.423 32.000 0.00 0.00 0.00 2.29
4057 4448 6.343716 TGATTGCATAGTGGTGAAAACATT 57.656 33.333 0.00 0.00 0.00 2.71
4074 4465 9.838339 TGAAAACATTTTTAATTTCCTAAGGCA 57.162 25.926 0.00 0.00 32.21 4.75
4088 4479 9.652114 ATTTCCTAAGGCATTATTCTTGAATCT 57.348 29.630 0.00 0.00 0.00 2.40
4089 4480 8.455903 TTCCTAAGGCATTATTCTTGAATCTG 57.544 34.615 0.00 1.32 0.00 2.90
4090 4481 7.577303 TCCTAAGGCATTATTCTTGAATCTGT 58.423 34.615 0.00 0.00 0.00 3.41
4091 4482 7.500227 TCCTAAGGCATTATTCTTGAATCTGTG 59.500 37.037 0.00 0.07 0.00 3.66
4092 4483 7.500227 CCTAAGGCATTATTCTTGAATCTGTGA 59.500 37.037 0.00 0.00 0.00 3.58
4093 4484 6.690194 AGGCATTATTCTTGAATCTGTGAC 57.310 37.500 0.00 0.83 0.00 3.67
4094 4485 6.421485 AGGCATTATTCTTGAATCTGTGACT 58.579 36.000 0.00 2.90 0.00 3.41
4095 4486 6.888632 AGGCATTATTCTTGAATCTGTGACTT 59.111 34.615 0.00 0.00 0.00 3.01
4096 4487 8.049117 AGGCATTATTCTTGAATCTGTGACTTA 58.951 33.333 0.00 0.00 0.00 2.24
4105 4496 7.719193 TCTTGAATCTGTGACTTAAACCAATCA 59.281 33.333 0.00 0.00 0.00 2.57
4172 4563 2.882761 GTCAAGTTTGTCCTTGGTACCC 59.117 50.000 10.07 0.00 41.72 3.69
4190 4586 5.785940 GGTACCCACTTCATAGGATCCTAAT 59.214 44.000 25.20 11.16 31.73 1.73
4312 4709 7.124471 CGTGATTGATTGAGAATGCTCTTTAG 58.876 38.462 1.43 0.00 41.84 1.85
4437 4834 5.593095 ACCCAGACTTTTACTTTTTCCACTC 59.407 40.000 0.00 0.00 0.00 3.51
4610 5007 1.076332 GTAACGAAGATGCGGCTGTT 58.924 50.000 0.00 0.00 35.12 3.16
4667 5064 4.757594 AGTTGAAGCTAGATTCTGAGCAG 58.242 43.478 20.62 0.00 41.36 4.24
4673 5070 2.627699 GCTAGATTCTGAGCAGGCTAGT 59.372 50.000 16.53 0.00 38.62 2.57
4757 5154 3.306502 CCGGCCTAACTTTCTGTCTGTAA 60.307 47.826 0.00 0.00 0.00 2.41
4758 5155 4.312443 CGGCCTAACTTTCTGTCTGTAAA 58.688 43.478 0.00 0.00 0.00 2.01
4840 5237 4.338682 CAGATGGTCCCTAGTGTGTAGTAC 59.661 50.000 0.00 0.00 0.00 2.73
4849 5246 3.515330 AGTGTGTAGTACCCATAACGC 57.485 47.619 0.00 0.00 0.00 4.84
4914 5328 0.260523 GAGGAGGGAGGTGCTCTAGT 59.739 60.000 0.00 0.00 32.39 2.57
4917 5331 2.033372 GGAGGGAGGTGCTCTAGTAAC 58.967 57.143 0.00 0.00 0.00 2.50
4957 5374 2.350772 CCAACCACTTGAATTCTGTCGC 60.351 50.000 7.05 0.00 0.00 5.19
4969 5386 1.063327 CTGTCGCGGCACAAACAAA 59.937 52.632 10.57 0.00 0.00 2.83
4970 5387 0.317770 CTGTCGCGGCACAAACAAAT 60.318 50.000 10.57 0.00 0.00 2.32
4992 5409 1.788067 AAACAAGGCCGCGTTGTACC 61.788 55.000 26.80 2.99 40.76 3.34
5065 5482 0.116143 AGCTCCCTGTGGTCTTCTCT 59.884 55.000 0.00 0.00 0.00 3.10
5068 5485 1.824230 CTCCCTGTGGTCTTCTCTCAG 59.176 57.143 0.00 0.00 0.00 3.35
5070 5487 1.265236 CCTGTGGTCTTCTCTCAGCT 58.735 55.000 0.00 0.00 0.00 4.24
5081 5498 4.813161 TCTTCTCTCAGCTTGAAACAACAG 59.187 41.667 0.00 0.00 0.00 3.16
5135 5552 1.299541 GCATGTTGAATCCGACCGAT 58.700 50.000 0.00 0.00 0.00 4.18
5148 5565 2.029649 CCGACCGATCCCGTTGTATATT 60.030 50.000 0.00 0.00 0.00 1.28
5163 5580 9.480538 CCGTTGTATATTAACAATAACACACAC 57.519 33.333 0.00 0.00 41.18 3.82
5171 5588 8.641499 ATTAACAATAACACACACAAAACTGG 57.359 30.769 0.00 0.00 0.00 4.00
5205 5622 5.221880 CCATTTCGCTTGAATTTTCTGTCA 58.778 37.500 0.00 0.00 0.00 3.58
5251 5668 7.571071 ATCATGGTCATAATCAGGAATCTCT 57.429 36.000 0.00 0.00 0.00 3.10
5255 5672 9.217278 CATGGTCATAATCAGGAATCTCTAAAG 57.783 37.037 0.00 0.00 0.00 1.85
5280 5697 8.478066 AGTAAAGTCAGCAAGAAGGAAAAATTT 58.522 29.630 0.00 0.00 0.00 1.82
5408 5833 4.680171 AAAGTAGGAAAACGTGCTATGC 57.320 40.909 0.00 0.00 32.10 3.14
5442 5867 4.693566 TCGTTTGAGTTTTCTGTGAGTTGT 59.306 37.500 0.00 0.00 0.00 3.32
5603 6048 3.883489 GCGCTCTGGGGATTAAAAAGTAT 59.117 43.478 0.00 0.00 0.00 2.12
5604 6049 4.261197 GCGCTCTGGGGATTAAAAAGTATG 60.261 45.833 0.00 0.00 0.00 2.39
5673 6132 0.976641 AGCAGCAGCAGGTTGTACTA 59.023 50.000 3.17 0.00 45.49 1.82
5682 6141 5.009010 GCAGCAGGTTGTACTATTTATGCAT 59.991 40.000 3.79 3.79 34.93 3.96
5683 6142 6.432936 CAGCAGGTTGTACTATTTATGCATG 58.567 40.000 10.16 0.00 34.93 4.06
5733 6202 1.335597 CGCCAGTAGTTCTCGTGTTGA 60.336 52.381 0.00 0.00 0.00 3.18
5750 6219 3.932710 TGTTGATCTGACCGAACTAATGC 59.067 43.478 0.00 0.00 0.00 3.56
5771 6240 3.753272 GCATCTCCAGAACAAAGTGCTTA 59.247 43.478 0.00 0.00 0.00 3.09
5772 6241 4.216257 GCATCTCCAGAACAAAGTGCTTAA 59.784 41.667 0.00 0.00 0.00 1.85
5773 6242 5.105997 GCATCTCCAGAACAAAGTGCTTAAT 60.106 40.000 0.00 0.00 0.00 1.40
5774 6243 6.571150 GCATCTCCAGAACAAAGTGCTTAATT 60.571 38.462 0.00 0.00 0.00 1.40
5775 6244 7.362056 GCATCTCCAGAACAAAGTGCTTAATTA 60.362 37.037 0.00 0.00 0.00 1.40
5776 6245 7.672983 TCTCCAGAACAAAGTGCTTAATTAG 57.327 36.000 0.00 0.00 0.00 1.73
5792 6261 8.348983 GCTTAATTAGCGTTGTATTAGACTGA 57.651 34.615 0.00 0.00 40.71 3.41
5793 6262 8.814235 GCTTAATTAGCGTTGTATTAGACTGAA 58.186 33.333 0.00 0.00 40.71 3.02
5796 6265 8.997621 AATTAGCGTTGTATTAGACTGAAGAA 57.002 30.769 0.00 0.00 0.00 2.52
5797 6266 7.807687 TTAGCGTTGTATTAGACTGAAGAAC 57.192 36.000 0.00 0.00 0.00 3.01
5798 6267 5.779922 AGCGTTGTATTAGACTGAAGAACA 58.220 37.500 0.00 0.00 0.00 3.18
5812 6281 6.048073 CTGAAGAACAGTCGAATTTTGACA 57.952 37.500 17.14 0.00 41.30 3.58
5813 6282 6.048073 TGAAGAACAGTCGAATTTTGACAG 57.952 37.500 17.14 12.30 38.83 3.51
5814 6283 4.474226 AGAACAGTCGAATTTTGACAGC 57.526 40.909 17.14 5.26 38.83 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.614284 GTGTTGAGCATTTTGAATCAGACG 59.386 41.667 0.00 0.00 0.00 4.18
35 36 3.856638 GCGGTGTTGAGCATTTTGAATCA 60.857 43.478 0.00 0.00 0.00 2.57
76 77 7.786178 TTTATCAATGTGATTAGGACCTTCG 57.214 36.000 0.00 0.00 38.26 3.79
114 115 1.302511 GTGTGCGGGACTTGATGGT 60.303 57.895 0.31 0.00 0.00 3.55
121 122 0.395173 AACAAAAGGTGTGCGGGACT 60.395 50.000 0.31 0.00 40.60 3.85
123 124 0.394488 TCAACAAAAGGTGTGCGGGA 60.394 50.000 0.00 0.00 40.60 5.14
127 128 3.502191 TGTTCTCAACAAAAGGTGTGC 57.498 42.857 0.00 0.00 40.60 4.57
128 129 5.066375 TCTCATGTTCTCAACAAAAGGTGTG 59.934 40.000 0.00 0.00 45.86 3.82
131 132 4.823989 CCTCTCATGTTCTCAACAAAAGGT 59.176 41.667 0.00 0.00 45.86 3.50
158 159 2.803956 CCAAGTTTAGGACTTTCCCCC 58.196 52.381 0.00 0.00 46.34 5.40
163 164 4.164843 TCTGTGCCAAGTTTAGGACTTT 57.835 40.909 0.00 0.00 46.34 2.66
168 174 4.676196 GCAATCATCTGTGCCAAGTTTAGG 60.676 45.833 0.00 0.00 34.58 2.69
214 224 2.111384 ACTGAACGGATAGTGCCAGAT 58.889 47.619 0.00 0.00 37.60 2.90
215 225 1.204704 CACTGAACGGATAGTGCCAGA 59.795 52.381 0.00 0.00 38.01 3.86
217 227 0.249120 CCACTGAACGGATAGTGCCA 59.751 55.000 8.99 0.00 42.21 4.92
221 231 3.066342 CGTGATACCACTGAACGGATAGT 59.934 47.826 0.00 0.00 41.06 2.12
226 236 1.625616 GACGTGATACCACTGAACGG 58.374 55.000 0.00 0.00 41.06 4.44
228 238 1.405121 GGGGACGTGATACCACTGAAC 60.405 57.143 0.00 0.00 41.06 3.18
242 252 0.812811 TCTCGTAGTCGATGGGGACG 60.813 60.000 0.00 0.00 45.21 4.79
255 265 6.328714 ACGAAGTCGCTATAGATATCTCGTA 58.671 40.000 8.95 3.23 44.43 3.43
257 267 5.705813 ACGAAGTCGCTATAGATATCTCG 57.294 43.478 8.95 6.86 44.43 4.04
277 287 5.103000 AGTCGGTAGATCTTGAAATTGACG 58.897 41.667 0.00 0.00 0.00 4.35
278 288 6.697892 CCTAGTCGGTAGATCTTGAAATTGAC 59.302 42.308 0.00 0.51 0.00 3.18
282 292 4.039366 GGCCTAGTCGGTAGATCTTGAAAT 59.961 45.833 0.00 0.00 34.25 2.17
286 296 2.307768 TGGCCTAGTCGGTAGATCTTG 58.692 52.381 3.32 0.00 34.25 3.02
292 302 1.315690 TCGAATGGCCTAGTCGGTAG 58.684 55.000 19.64 0.00 46.08 3.18
297 307 2.973945 ACACTTTCGAATGGCCTAGTC 58.026 47.619 14.74 0.00 0.00 2.59
301 311 2.554032 CAGAAACACTTTCGAATGGCCT 59.446 45.455 14.74 1.24 44.29 5.19
302 312 2.351738 CCAGAAACACTTTCGAATGGCC 60.352 50.000 14.74 0.00 44.29 5.36
446 457 2.786495 CCACCGATCTGGACCCGAG 61.786 68.421 10.05 0.00 42.00 4.63
483 498 0.389391 GGAGGAAAGGCGATCGATGA 59.611 55.000 21.57 0.00 0.00 2.92
488 503 1.202592 GGAAGAGGAGGAAAGGCGATC 60.203 57.143 0.00 0.00 0.00 3.69
614 644 2.182030 CGAGCCTCGGGTGTCTTC 59.818 66.667 6.13 0.00 36.00 2.87
811 1040 1.143838 CAATCGACAGGGGCGATCA 59.856 57.895 7.51 0.00 46.67 2.92
812 1041 1.595382 CCAATCGACAGGGGCGATC 60.595 63.158 7.51 0.00 46.67 3.69
877 1108 1.162800 GGCTGAGCGATGGGAATCAC 61.163 60.000 0.00 0.00 0.00 3.06
880 1111 2.109799 CGGCTGAGCGATGGGAAT 59.890 61.111 0.00 0.00 0.00 3.01
940 1172 2.909457 AATGATGCGCCGGATTGGGT 62.909 55.000 5.05 0.00 38.63 4.51
947 1179 2.024588 CGGAAAATGATGCGCCGG 59.975 61.111 4.18 0.00 38.40 6.13
967 1199 0.457853 TGTCAGCTACGACGATTGGC 60.458 55.000 0.00 0.00 38.84 4.52
972 1204 2.175078 GCGTGTCAGCTACGACGA 59.825 61.111 11.58 0.00 43.82 4.20
973 1205 2.874780 GGCGTGTCAGCTACGACG 60.875 66.667 11.58 8.70 43.82 5.12
1197 1432 2.685380 CCCTCTTCTCCGGTGGCT 60.685 66.667 0.00 0.00 0.00 4.75
1336 1574 1.361668 AACTTATGCGAGCACGGCAG 61.362 55.000 5.52 0.00 40.15 4.85
1347 1585 1.197721 ACGCACTTGCAGAACTTATGC 59.802 47.619 1.21 1.21 44.11 3.14
1412 1650 1.421268 TCCAGTCAGGACACAAGCAAT 59.579 47.619 1.84 0.00 43.07 3.56
1433 1672 4.685030 GCCCTGCAAATTTTCATCATCCAT 60.685 41.667 0.00 0.00 0.00 3.41
1517 1756 3.859414 GCCTGGAGCTCGGCATCT 61.859 66.667 23.24 0.00 45.59 2.90
1538 1777 1.190984 CCATCAATGAAGCGATCGACG 59.809 52.381 21.57 0.00 45.66 5.12
1640 1879 1.661463 AAGCACCTCTCTCCATGGAA 58.339 50.000 17.00 6.19 0.00 3.53
1691 1930 7.447594 AGAGCTCAAAATTGGAATTGATTTGT 58.552 30.769 17.77 0.00 35.20 2.83
2023 2271 1.302271 AGTTTTCTCCCGGCGGTTC 60.302 57.895 26.32 6.64 0.00 3.62
2058 2306 2.301577 AGTTCTAGCGGCACAGATTC 57.698 50.000 1.45 1.74 0.00 2.52
2091 2339 1.338200 GCACACTACAACCTAGCAGCT 60.338 52.381 0.00 0.00 0.00 4.24
2096 2344 2.301870 TCCAAGGCACACTACAACCTAG 59.698 50.000 0.00 0.00 0.00 3.02
2283 2665 4.525912 AGCAAACAAATGGACCTCATTC 57.474 40.909 0.00 0.00 44.68 2.67
2295 2677 6.509418 AAAGTACTGACTCAAGCAAACAAA 57.491 33.333 0.00 0.00 33.58 2.83
2366 2748 6.662755 TCATGCCTAAGAGTTGAAACCATAT 58.337 36.000 0.00 0.00 0.00 1.78
2715 3098 8.931385 AATTTGAAGCGCAATAATAACAGAAT 57.069 26.923 11.47 0.00 36.15 2.40
2727 3110 2.034053 ACGGAGAAAATTTGAAGCGCAA 59.966 40.909 11.47 0.00 33.88 4.85
2745 3128 6.851222 ACATTGATTAGCTAAATCTGACGG 57.149 37.500 10.85 0.00 43.83 4.79
2998 3385 9.542462 GACTGTATGGCACTAAATTAGAATACA 57.458 33.333 7.06 12.36 0.00 2.29
3039 3426 2.158957 ACCAAAAGCTCAGTCGACAAGA 60.159 45.455 19.50 13.99 0.00 3.02
3143 3530 3.616219 ACGGGCATAATAACTTCTTGCA 58.384 40.909 0.00 0.00 35.04 4.08
3240 3627 5.483937 ACAGAGGGAGTACATTACAACATCA 59.516 40.000 0.00 0.00 0.00 3.07
3241 3628 5.978814 ACAGAGGGAGTACATTACAACATC 58.021 41.667 0.00 0.00 0.00 3.06
3242 3629 7.490657 TTACAGAGGGAGTACATTACAACAT 57.509 36.000 0.00 0.00 0.00 2.71
3243 3630 6.921486 TTACAGAGGGAGTACATTACAACA 57.079 37.500 0.00 0.00 0.00 3.33
3244 3631 7.609056 TCTTTACAGAGGGAGTACATTACAAC 58.391 38.462 0.00 0.00 0.00 3.32
3245 3632 7.786046 TCTTTACAGAGGGAGTACATTACAA 57.214 36.000 0.00 0.00 0.00 2.41
3452 3839 2.539476 CCAACAAACAAAGTCCAGCAC 58.461 47.619 0.00 0.00 0.00 4.40
3467 3854 4.953579 ACTGTTTCTTTTAGGAAGCCAACA 59.046 37.500 0.00 0.00 0.00 3.33
3479 3866 8.682936 AGACATCATACAAGACTGTTTCTTTT 57.317 30.769 0.00 0.00 42.37 2.27
3626 4013 4.278419 ACAGGTGGCAGTTTTCAAGTTATC 59.722 41.667 0.00 0.00 0.00 1.75
3778 4167 2.853731 TGGTAAACAACGCAACCAAG 57.146 45.000 0.00 0.00 39.02 3.61
3786 4175 6.814076 TTTTTGCTGTTATGGTAAACAACG 57.186 33.333 0.00 0.00 38.81 4.10
3972 4363 5.249780 TGCCAACTTCCTGAACCTATTAA 57.750 39.130 0.00 0.00 0.00 1.40
3980 4371 6.883744 AGTTTTATTTTGCCAACTTCCTGAA 58.116 32.000 0.00 0.00 0.00 3.02
4172 4563 7.060383 AGACACATTAGGATCCTATGAAGTG 57.940 40.000 22.30 24.61 0.00 3.16
4260 4656 8.842358 AGATTCATTCCGTAAAAGTACTGAAA 57.158 30.769 0.00 0.00 37.11 2.69
4312 4709 7.606456 TCCTACTTGTTCAGACCATGTTATTTC 59.394 37.037 0.00 0.00 0.00 2.17
4412 4809 5.955959 AGTGGAAAAAGTAAAAGTCTGGGTT 59.044 36.000 0.00 0.00 0.00 4.11
4437 4834 4.320690 CGATGTAACAATTTGCAACTTCCG 59.679 41.667 0.00 0.00 30.42 4.30
4610 5007 2.746279 TTGCTTCCTCAAAACCCTCA 57.254 45.000 0.00 0.00 0.00 3.86
4667 5064 1.823610 ACCCGTTGTTCTAGACTAGCC 59.176 52.381 4.47 0.00 0.00 3.93
4673 5070 3.689347 TGTAGCTACCCGTTGTTCTAGA 58.311 45.455 21.01 0.00 0.00 2.43
4705 5102 5.988310 TGTGCCAAGAATCAAAGATGAAT 57.012 34.783 0.00 0.00 39.49 2.57
4720 5117 2.037053 CCGGAACAACATGTGCCAA 58.963 52.632 8.21 0.00 46.94 4.52
4757 5154 0.165944 CCGAGCGACGCTGAAAAATT 59.834 50.000 29.85 0.00 39.88 1.82
4758 5155 0.949105 ACCGAGCGACGCTGAAAAAT 60.949 50.000 29.85 0.00 39.88 1.82
4828 5225 3.381272 GGCGTTATGGGTACTACACACTA 59.619 47.826 0.00 0.00 32.26 2.74
4840 5237 0.109964 CACAACAACGGCGTTATGGG 60.110 55.000 29.24 25.29 0.00 4.00
4849 5246 2.985809 CCATATTGCAACACAACAACGG 59.014 45.455 0.00 0.00 42.27 4.44
4957 5374 4.026145 CCTTGTTTACATTTGTTTGTGCCG 60.026 41.667 0.00 0.00 0.00 5.69
4969 5386 0.239879 CAACGCGGCCTTGTTTACAT 59.760 50.000 12.47 0.00 0.00 2.29
4970 5387 1.096386 ACAACGCGGCCTTGTTTACA 61.096 50.000 12.47 0.00 0.00 2.41
4992 5409 7.556275 ACAGTGAAGAGAACTCTCCTAGAATAG 59.444 40.741 4.77 0.00 43.88 1.73
5065 5482 1.691196 CCCCTGTTGTTTCAAGCTGA 58.309 50.000 0.00 0.00 0.00 4.26
5068 5485 1.989706 TACCCCCTGTTGTTTCAAGC 58.010 50.000 0.00 0.00 0.00 4.01
5070 5487 2.245287 ACCTTACCCCCTGTTGTTTCAA 59.755 45.455 0.00 0.00 0.00 2.69
5081 5498 2.107726 AGACAAGTTTCACCTTACCCCC 59.892 50.000 0.00 0.00 0.00 5.40
5135 5552 8.881743 GTGTGTTATTGTTAATATACAACGGGA 58.118 33.333 0.00 0.00 40.53 5.14
5148 5565 7.159322 ACCAGTTTTGTGTGTGTTATTGTTA 57.841 32.000 0.00 0.00 0.00 2.41
5163 5580 3.420893 TGGCCAGATTCTACCAGTTTTG 58.579 45.455 0.00 0.00 0.00 2.44
5165 5582 4.322057 AATGGCCAGATTCTACCAGTTT 57.678 40.909 13.05 0.00 35.20 2.66
5171 5588 2.565841 AGCGAAATGGCCAGATTCTAC 58.434 47.619 24.00 17.99 0.00 2.59
5229 5646 9.217278 CTTTAGAGATTCCTGATTATGACCATG 57.783 37.037 0.00 0.00 0.00 3.66
5251 5668 8.514330 TTTTCCTTCTTGCTGACTTTACTTTA 57.486 30.769 0.00 0.00 0.00 1.85
5255 5672 8.648557 AAATTTTTCCTTCTTGCTGACTTTAC 57.351 30.769 0.00 0.00 0.00 2.01
5280 5697 6.071334 ACAAGATACGAATTCAAGACCTGAGA 60.071 38.462 6.22 0.00 34.81 3.27
5333 5750 0.827368 GCAAGACCTGGCTAGCTAGT 59.173 55.000 24.56 14.71 0.00 2.57
5380 5800 6.675026 AGCACGTTTTCCTACTTTTTATTCC 58.325 36.000 0.00 0.00 0.00 3.01
5408 5833 2.154462 ACTCAAACGAAATGGCCAGAG 58.846 47.619 13.05 12.19 0.00 3.35
5510 5940 2.945008 TCAACACTCAGTTTCTTGCTGG 59.055 45.455 0.00 0.00 38.74 4.85
5613 6072 7.241628 AGGTCTCCAAAAAGAAGATTAACCAT 58.758 34.615 0.00 0.00 0.00 3.55
5659 6118 6.038603 ACATGCATAAATAGTACAACCTGCTG 59.961 38.462 0.00 0.81 0.00 4.41
5660 6119 6.122277 ACATGCATAAATAGTACAACCTGCT 58.878 36.000 0.00 0.00 0.00 4.24
5661 6120 6.377327 ACATGCATAAATAGTACAACCTGC 57.623 37.500 0.00 0.00 0.00 4.85
5682 6141 7.011295 CACAGTCAATACACATGCACATATACA 59.989 37.037 0.00 0.00 0.00 2.29
5683 6142 7.011389 ACACAGTCAATACACATGCACATATAC 59.989 37.037 0.00 0.00 0.00 1.47
5733 6202 4.502259 GGAGATGCATTAGTTCGGTCAGAT 60.502 45.833 0.00 0.00 0.00 2.90
5750 6219 5.947228 TTAAGCACTTTGTTCTGGAGATG 57.053 39.130 0.00 0.00 0.00 2.90
5771 6240 8.870879 GTTCTTCAGTCTAATACAACGCTAATT 58.129 33.333 0.00 0.00 0.00 1.40
5772 6241 8.033038 TGTTCTTCAGTCTAATACAACGCTAAT 58.967 33.333 0.00 0.00 0.00 1.73
5773 6242 7.372714 TGTTCTTCAGTCTAATACAACGCTAA 58.627 34.615 0.00 0.00 0.00 3.09
5774 6243 6.916440 TGTTCTTCAGTCTAATACAACGCTA 58.084 36.000 0.00 0.00 0.00 4.26
5775 6244 5.779922 TGTTCTTCAGTCTAATACAACGCT 58.220 37.500 0.00 0.00 0.00 5.07
5776 6245 6.083925 CTGTTCTTCAGTCTAATACAACGC 57.916 41.667 0.00 0.00 39.17 4.84
5790 6259 5.504010 GCTGTCAAAATTCGACTGTTCTTCA 60.504 40.000 13.08 0.00 35.46 3.02
5791 6260 4.906437 GCTGTCAAAATTCGACTGTTCTTC 59.094 41.667 13.08 0.00 35.46 2.87
5792 6261 4.848757 GCTGTCAAAATTCGACTGTTCTT 58.151 39.130 13.08 0.00 35.46 2.52
5793 6262 4.474226 GCTGTCAAAATTCGACTGTTCT 57.526 40.909 13.08 0.00 35.46 3.01


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

AutoCloner maintained by Alex Coulton.