Multiple sequence alignment - TraesCS1B01G032100

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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 TraesCS1B01G032100 chr1B 100.000 4322 0 0 1 4322 15641846 15637525 0.000000e+00 7982.0
1 TraesCS1B01G032100 chr1B 96.008 3357 111 14 973 4322 15519479 15516139 0.000000e+00 5435.0
2 TraesCS1B01G032100 chr1B 93.059 461 11 5 514 974 15519954 15519515 0.000000e+00 654.0
3 TraesCS1B01G032100 chr1B 93.548 372 17 3 606 974 15386240 15386607 8.170000e-152 547.0
4 TraesCS1B01G032100 chr1B 93.548 372 17 3 606 974 15392231 15392598 8.170000e-152 547.0
5 TraesCS1B01G032100 chr1B 93.510 339 16 5 1 333 15523988 15523650 2.320000e-137 499.0
6 TraesCS1B01G032100 chr1B 92.996 257 11 2 197 450 15520218 15519966 6.830000e-98 368.0
7 TraesCS1B01G032100 chr1B 91.176 136 4 1 973 1100 15392634 15392769 1.240000e-40 178.0
8 TraesCS1B01G032100 chr1B 93.878 49 3 0 549 597 15386132 15386180 1.670000e-09 75.0
9 TraesCS1B01G032100 chr1B 93.878 49 3 0 549 597 15392123 15392171 1.670000e-09 75.0
10 TraesCS1B01G032100 chr5D 81.117 1218 224 4 2110 3324 447624694 447623480 0.000000e+00 970.0
11 TraesCS1B01G032100 chr5D 77.923 915 194 7 2231 3141 447706033 447705123 8.110000e-157 564.0
12 TraesCS1B01G032100 chr5D 96.875 32 1 0 1050 1081 447707330 447707299 2.000000e-03 54.7
13 TraesCS1B01G032100 chr5B 77.011 957 213 5 2217 3168 545818886 545819840 3.800000e-150 542.0
14 TraesCS1B01G032100 chr5A 75.591 1057 241 15 2107 3156 565249441 565250487 1.390000e-139 507.0
15 TraesCS1B01G032100 chr4D 76.280 957 211 11 2217 3165 1667189 1668137 3.000000e-136 496.0
16 TraesCS1B01G032100 chr7D 75.242 929 208 17 2253 3168 605165843 605164924 5.170000e-114 422.0
17 TraesCS1B01G032100 chr4A 76.832 764 166 9 2217 2976 603031995 603032751 1.860000e-113 420.0
18 TraesCS1B01G032100 chr6D 76.480 625 127 17 2291 2907 22069049 22068437 5.390000e-84 322.0
19 TraesCS1B01G032100 chr3B 90.476 42 4 0 2879 2920 723460575 723460616 6.040000e-04 56.5
20 TraesCS1B01G032100 chr3B 90.476 42 4 0 2879 2920 723467430 723467471 6.040000e-04 56.5


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 TraesCS1B01G032100 chr1B 15637525 15641846 4321 True 7982.000000 7982 100.000000 1 4322 1 chr1B.!!$R1 4321
1 TraesCS1B01G032100 chr1B 15516139 15523988 7849 True 1739.000000 5435 93.893250 1 4322 4 chr1B.!!$R2 4321
2 TraesCS1B01G032100 chr1B 15392123 15392769 646 False 266.666667 547 92.867333 549 1100 3 chr1B.!!$F2 551
3 TraesCS1B01G032100 chr5D 447623480 447624694 1214 True 970.000000 970 81.117000 2110 3324 1 chr5D.!!$R1 1214
4 TraesCS1B01G032100 chr5D 447705123 447707330 2207 True 309.350000 564 87.399000 1050 3141 2 chr5D.!!$R2 2091
5 TraesCS1B01G032100 chr5B 545818886 545819840 954 False 542.000000 542 77.011000 2217 3168 1 chr5B.!!$F1 951
6 TraesCS1B01G032100 chr5A 565249441 565250487 1046 False 507.000000 507 75.591000 2107 3156 1 chr5A.!!$F1 1049
7 TraesCS1B01G032100 chr4D 1667189 1668137 948 False 496.000000 496 76.280000 2217 3165 1 chr4D.!!$F1 948
8 TraesCS1B01G032100 chr7D 605164924 605165843 919 True 422.000000 422 75.242000 2253 3168 1 chr7D.!!$R1 915
9 TraesCS1B01G032100 chr4A 603031995 603032751 756 False 420.000000 420 76.832000 2217 2976 1 chr4A.!!$F1 759
10 TraesCS1B01G032100 chr6D 22068437 22069049 612 True 322.000000 322 76.480000 2291 2907 1 chr6D.!!$R1 616

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
506 4084 0.538584 CTGGCATGCAGTAGGTGAGA 59.461 55.0 21.36 0.00 0.00 3.27 F
1322 5082 0.393077 AGTGACTGGTTCAACCTCGG 59.607 55.0 8.40 0.73 39.58 4.63 F
1986 5873 0.771127 TCAACAACCCTTGGCTAGCT 59.229 50.0 15.72 0.00 34.12 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1465 5225 0.540365 CCTTCCATGGTGCAGTTGGT 60.540 55.0 12.58 0.0 0.00 3.67 R
3184 7161 2.198827 TCATTTCGTCCTGGTTGCAT 57.801 45.0 0.00 0.0 0.00 3.96 R
3929 7906 0.595588 AAATGCGCGTGTCATTTCCA 59.404 45.0 18.97 0.0 39.21 3.53 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
44 45 6.680874 ATACTCACTAACCTACTTGTCTCG 57.319 41.667 0.00 0.00 0.00 4.04
161 164 1.847088 GAAGAAGGATAACCCCTGGCT 59.153 52.381 0.00 0.00 36.49 4.75
179 182 2.362736 GCTTCTGCATCAGGACAATGA 58.637 47.619 0.00 0.00 39.41 2.57
183 186 7.117199 GCTTCTGCATCAGGACAATGAATGT 62.117 44.000 0.00 0.00 41.58 2.71
186 189 4.847198 TGCATCAGGACAATGAATGTAGT 58.153 39.130 0.00 0.00 44.12 2.73
190 193 6.707608 GCATCAGGACAATGAATGTAGTCATA 59.292 38.462 0.00 0.00 44.12 2.15
246 253 7.672738 CCAACATGTAAGTACGTGATTAGTTC 58.327 38.462 15.84 0.00 44.02 3.01
284 291 3.000724 GTCGTGCAAGATAAGCAGACATC 59.999 47.826 5.42 0.00 43.63 3.06
358 3936 3.542648 CGTGGTAGTAGGAGAGATGTGA 58.457 50.000 0.00 0.00 0.00 3.58
373 3951 2.915659 TGAACACGGCCGGTCTCT 60.916 61.111 31.76 9.57 0.00 3.10
374 3952 2.126031 GAACACGGCCGGTCTCTC 60.126 66.667 31.76 14.55 0.00 3.20
375 3953 3.966026 GAACACGGCCGGTCTCTCG 62.966 68.421 31.76 10.63 0.00 4.04
415 3993 9.167311 GATCTCATGTTTAATTAGTCCTTGTGT 57.833 33.333 0.00 0.00 0.00 3.72
450 4028 7.603180 ACTCCTGTTCTATCATGTGCTTATA 57.397 36.000 0.00 0.00 0.00 0.98
451 4029 7.665690 ACTCCTGTTCTATCATGTGCTTATAG 58.334 38.462 0.00 0.00 0.00 1.31
452 4030 6.459066 TCCTGTTCTATCATGTGCTTATAGC 58.541 40.000 0.00 0.00 42.82 2.97
453 4031 6.268617 TCCTGTTCTATCATGTGCTTATAGCT 59.731 38.462 0.00 0.00 42.97 3.32
454 4032 6.933521 CCTGTTCTATCATGTGCTTATAGCTT 59.066 38.462 0.00 0.00 42.97 3.74
455 4033 8.090831 CCTGTTCTATCATGTGCTTATAGCTTA 58.909 37.037 0.00 0.00 42.97 3.09
456 4034 8.818141 TGTTCTATCATGTGCTTATAGCTTAC 57.182 34.615 0.00 0.00 42.97 2.34
457 4035 8.642432 TGTTCTATCATGTGCTTATAGCTTACT 58.358 33.333 0.00 0.00 42.97 2.24
482 4060 9.220767 CTAAATATATTAACCAAGCCTCCAGTC 57.779 37.037 0.00 0.00 0.00 3.51
484 4062 1.742308 TTAACCAAGCCTCCAGTCCT 58.258 50.000 0.00 0.00 0.00 3.85
485 4063 0.984230 TAACCAAGCCTCCAGTCCTG 59.016 55.000 0.00 0.00 0.00 3.86
495 4073 3.138798 CAGTCCTGGCTGGCATGC 61.139 66.667 9.90 9.90 35.26 4.06
496 4074 3.654143 AGTCCTGGCTGGCATGCA 61.654 61.111 21.36 4.79 35.26 3.96
497 4075 3.138798 GTCCTGGCTGGCATGCAG 61.139 66.667 21.36 15.53 35.26 4.41
498 4076 3.654143 TCCTGGCTGGCATGCAGT 61.654 61.111 21.36 0.00 35.26 4.40
499 4077 2.273123 CCTGGCTGGCATGCAGTA 59.727 61.111 21.36 4.10 34.04 2.74
500 4078 1.822613 CCTGGCTGGCATGCAGTAG 60.823 63.158 21.36 15.00 34.04 2.57
501 4079 1.822613 CTGGCTGGCATGCAGTAGG 60.823 63.158 21.36 5.20 34.04 3.18
502 4080 2.273449 GGCTGGCATGCAGTAGGT 59.727 61.111 21.36 0.00 34.04 3.08
503 4081 2.117156 GGCTGGCATGCAGTAGGTG 61.117 63.158 21.36 1.97 34.04 4.00
504 4082 1.078214 GCTGGCATGCAGTAGGTGA 60.078 57.895 21.36 0.00 0.00 4.02
505 4083 1.094073 GCTGGCATGCAGTAGGTGAG 61.094 60.000 21.36 2.80 0.00 3.51
506 4084 0.538584 CTGGCATGCAGTAGGTGAGA 59.461 55.000 21.36 0.00 0.00 3.27
507 4085 1.140452 CTGGCATGCAGTAGGTGAGAT 59.860 52.381 21.36 0.00 0.00 2.75
508 4086 1.139654 TGGCATGCAGTAGGTGAGATC 59.860 52.381 21.36 0.00 0.00 2.75
509 4087 1.415659 GGCATGCAGTAGGTGAGATCT 59.584 52.381 21.36 0.00 0.00 2.75
510 4088 2.481854 GCATGCAGTAGGTGAGATCTG 58.518 52.381 14.21 0.00 0.00 2.90
511 4089 2.102084 GCATGCAGTAGGTGAGATCTGA 59.898 50.000 14.21 0.00 0.00 3.27
512 4090 3.431346 GCATGCAGTAGGTGAGATCTGAA 60.431 47.826 14.21 0.00 0.00 3.02
513 4091 3.876274 TGCAGTAGGTGAGATCTGAAC 57.124 47.619 0.00 0.00 0.00 3.18
514 4092 3.435275 TGCAGTAGGTGAGATCTGAACT 58.565 45.455 4.76 4.76 0.00 3.01
515 4093 3.194329 TGCAGTAGGTGAGATCTGAACTG 59.806 47.826 10.33 8.87 36.74 3.16
516 4094 3.445450 GCAGTAGGTGAGATCTGAACTGA 59.555 47.826 10.33 0.00 35.93 3.41
517 4095 4.099266 GCAGTAGGTGAGATCTGAACTGAT 59.901 45.833 10.33 0.00 35.93 2.90
518 4096 5.590145 CAGTAGGTGAGATCTGAACTGATG 58.410 45.833 10.33 4.68 35.93 3.07
519 4097 3.540314 AGGTGAGATCTGAACTGATGC 57.460 47.619 0.00 0.00 0.00 3.91
520 4098 2.170187 AGGTGAGATCTGAACTGATGCC 59.830 50.000 0.00 0.00 0.00 4.40
521 4099 2.093288 GGTGAGATCTGAACTGATGCCA 60.093 50.000 0.00 0.00 0.00 4.92
522 4100 3.603532 GTGAGATCTGAACTGATGCCAA 58.396 45.455 0.00 0.00 0.00 4.52
523 4101 4.005650 GTGAGATCTGAACTGATGCCAAA 58.994 43.478 0.00 0.00 0.00 3.28
524 4102 4.005650 TGAGATCTGAACTGATGCCAAAC 58.994 43.478 0.00 0.00 0.00 2.93
525 4103 3.005554 AGATCTGAACTGATGCCAAACG 58.994 45.455 0.00 0.00 0.00 3.60
526 4104 2.254546 TCTGAACTGATGCCAAACGT 57.745 45.000 0.00 0.00 0.00 3.99
532 4110 2.331194 ACTGATGCCAAACGTACGTAC 58.669 47.619 23.12 15.90 0.00 3.67
550 4128 5.799213 ACGTACTGTCTACTTACTGTAGGT 58.201 41.667 7.74 7.74 46.45 3.08
556 4134 4.700692 TGTCTACTTACTGTAGGTCTGCAG 59.299 45.833 7.63 7.63 46.45 4.41
597 4175 4.118410 GCAGTCCATCATCAACTAGTCAG 58.882 47.826 0.00 0.00 0.00 3.51
598 4176 4.382470 GCAGTCCATCATCAACTAGTCAGT 60.382 45.833 0.00 0.00 36.19 3.41
599 4177 5.163509 GCAGTCCATCATCAACTAGTCAGTA 60.164 44.000 0.00 0.00 33.48 2.74
600 4178 6.502652 CAGTCCATCATCAACTAGTCAGTAG 58.497 44.000 0.00 0.00 33.48 2.57
601 4179 6.096141 CAGTCCATCATCAACTAGTCAGTAGT 59.904 42.308 0.00 0.00 44.51 2.73
602 4180 6.320164 AGTCCATCATCAACTAGTCAGTAGTC 59.680 42.308 0.00 0.00 41.50 2.59
603 4181 6.095580 GTCCATCATCAACTAGTCAGTAGTCA 59.904 42.308 0.00 0.00 41.50 3.41
604 4182 6.836007 TCCATCATCAACTAGTCAGTAGTCAT 59.164 38.462 0.00 0.00 41.50 3.06
605 4183 7.343057 TCCATCATCAACTAGTCAGTAGTCATT 59.657 37.037 0.00 0.00 41.50 2.57
606 4184 8.633561 CCATCATCAACTAGTCAGTAGTCATTA 58.366 37.037 0.00 0.00 41.50 1.90
607 4185 9.676195 CATCATCAACTAGTCAGTAGTCATTAG 57.324 37.037 0.00 0.00 41.50 1.73
608 4186 8.809468 TCATCAACTAGTCAGTAGTCATTAGT 57.191 34.615 0.00 0.00 41.50 2.24
609 4187 8.894731 TCATCAACTAGTCAGTAGTCATTAGTC 58.105 37.037 0.00 0.00 41.50 2.59
610 4188 8.678199 CATCAACTAGTCAGTAGTCATTAGTCA 58.322 37.037 0.00 0.00 41.50 3.41
818 4461 2.613506 GCGGGACCAGGTTTCAACG 61.614 63.158 0.00 0.00 0.00 4.10
1270 5006 3.364441 GCAGCGCCACCATCAACA 61.364 61.111 2.29 0.00 0.00 3.33
1287 5047 3.002791 CAACAACGATGTGCCAGTCTAT 58.997 45.455 0.00 0.00 40.46 1.98
1316 5076 3.769739 AGCACATAGTGACTGGTTCAA 57.230 42.857 0.00 0.00 35.39 2.69
1319 5079 3.807209 GCACATAGTGACTGGTTCAACCT 60.807 47.826 8.40 0.00 35.84 3.50
1322 5082 0.393077 AGTGACTGGTTCAACCTCGG 59.607 55.000 8.40 0.73 39.58 4.63
1323 5083 1.070786 TGACTGGTTCAACCTCGGC 59.929 57.895 8.40 1.45 39.58 5.54
1465 5225 4.077184 CCCCGGTCAGCGCTAACA 62.077 66.667 13.86 0.00 0.00 2.41
1468 5228 2.048597 CGGTCAGCGCTAACACCA 60.049 61.111 24.52 0.00 0.00 4.17
1513 5306 0.881796 TCTCTACTGGTGTCACTGCG 59.118 55.000 2.35 0.00 0.00 5.18
1592 5385 6.543735 AGCCCCTACCTTCATGAATAAATAC 58.456 40.000 8.96 0.00 0.00 1.89
1593 5386 5.411669 GCCCCTACCTTCATGAATAAATACG 59.588 44.000 8.96 0.00 0.00 3.06
1597 5390 8.582437 CCCTACCTTCATGAATAAATACGTAGA 58.418 37.037 8.96 0.00 0.00 2.59
1642 5435 6.036953 TCACTTTGTTGTTTTCATTTCATGCC 59.963 34.615 0.00 0.00 0.00 4.40
1763 5650 2.159421 GCAGACATCAATGAGTGCTTGG 60.159 50.000 11.54 0.00 37.20 3.61
1831 5718 4.202284 GGATATTTTGATTGTGGCTGCCAT 60.202 41.667 26.22 9.13 35.28 4.40
1875 5762 4.811969 ACGTACCTTATGGATGTGTCAA 57.188 40.909 0.81 0.00 37.04 3.18
1884 5771 6.423604 CCTTATGGATGTGTCAAAACCAAAAC 59.576 38.462 0.00 0.00 34.28 2.43
1919 5806 3.446873 GGACACCCATATGCAAAATGACA 59.553 43.478 12.66 0.00 0.00 3.58
1924 5811 6.594937 ACACCCATATGCAAAATGACATTTTC 59.405 34.615 20.73 15.88 40.27 2.29
1935 5822 3.973206 TGACATTTTCCGCCTCTCTTA 57.027 42.857 0.00 0.00 0.00 2.10
1948 5835 6.315642 TCCGCCTCTCTTAGTATATATTGTCG 59.684 42.308 0.00 0.00 0.00 4.35
1985 5872 1.168714 CTCAACAACCCTTGGCTAGC 58.831 55.000 6.04 6.04 34.12 3.42
1986 5873 0.771127 TCAACAACCCTTGGCTAGCT 59.229 50.000 15.72 0.00 34.12 3.32
1988 5875 2.027192 TCAACAACCCTTGGCTAGCTAG 60.027 50.000 16.84 16.84 34.12 3.42
1989 5876 1.952621 ACAACCCTTGGCTAGCTAGA 58.047 50.000 25.15 0.90 34.12 2.43
1990 5877 2.482494 ACAACCCTTGGCTAGCTAGAT 58.518 47.619 25.15 0.00 34.12 1.98
1991 5878 2.436173 ACAACCCTTGGCTAGCTAGATC 59.564 50.000 25.15 15.11 34.12 2.75
1992 5879 2.703007 CAACCCTTGGCTAGCTAGATCT 59.297 50.000 25.15 0.00 0.00 2.75
1993 5880 3.053359 ACCCTTGGCTAGCTAGATCTT 57.947 47.619 25.15 0.00 0.00 2.40
1994 5881 3.388913 ACCCTTGGCTAGCTAGATCTTT 58.611 45.455 25.15 0.00 0.00 2.52
1995 5882 3.783082 ACCCTTGGCTAGCTAGATCTTTT 59.217 43.478 25.15 0.00 0.00 2.27
1996 5883 4.228438 ACCCTTGGCTAGCTAGATCTTTTT 59.772 41.667 25.15 0.04 0.00 1.94
2075 5962 6.094742 TGCGCATACTCTATTTTCCATTGAAA 59.905 34.615 5.66 0.00 38.69 2.69
2246 6207 5.179368 AGAAGTTCTTCAATCAAAATCGCGA 59.821 36.000 13.09 13.09 0.00 5.87
2247 6208 5.551760 AGTTCTTCAATCAAAATCGCGAT 57.448 34.783 17.62 17.62 0.00 4.58
2379 6341 2.189521 GGTGGAGGCCATGGTACG 59.810 66.667 14.67 0.00 35.28 3.67
2928 6905 7.598118 GGAGTACTTCTTGTTGAGTTACTTACC 59.402 40.741 0.00 0.00 29.52 2.85
3017 6994 6.959361 TGCTTGAACAAGACAATCTAGTTTC 58.041 36.000 17.19 0.00 40.79 2.78
3126 7103 2.043664 AGAGGAGAGACCAACCATGAGA 59.956 50.000 0.00 0.00 42.04 3.27
3134 7111 1.202927 ACCAACCATGAGACAAGTGGG 60.203 52.381 0.00 0.00 37.33 4.61
3184 7161 2.832838 AGGATCACGCCCCATATGATA 58.167 47.619 3.65 0.00 33.21 2.15
3194 7171 3.359033 CCCCATATGATATGCAACCAGG 58.641 50.000 3.65 2.16 0.00 4.45
3273 7250 1.866015 TGGGGGATGTGAGTAGACAG 58.134 55.000 0.00 0.00 0.00 3.51
3342 7319 8.394877 CGTTAAGTTGGTTGATATTTGAGCATA 58.605 33.333 0.00 0.00 0.00 3.14
3447 7424 7.555087 TGTGTTTTCTTTGACTTTTGATCCAT 58.445 30.769 0.00 0.00 0.00 3.41
3470 7447 5.610398 TGTCTTGAATGTGGCGATATGTAT 58.390 37.500 0.00 0.00 0.00 2.29
3511 7488 4.092771 TCACACTCATAACTAGTGACGC 57.907 45.455 10.02 0.00 45.89 5.19
3556 7533 1.757118 TCCTCCTGCCTTACAATCTCG 59.243 52.381 0.00 0.00 0.00 4.04
3586 7563 1.822371 TGACTGGCTATTCTACACGCA 59.178 47.619 0.00 0.00 0.00 5.24
3681 7658 6.611381 TCTTACTGCAGCAATTCATAACAAC 58.389 36.000 15.27 0.00 0.00 3.32
3689 7666 7.083858 GCAGCAATTCATAACAACTTTAGACA 58.916 34.615 0.00 0.00 0.00 3.41
3858 7835 3.943381 TCTAAAGCCTGCACAGATTCATG 59.057 43.478 0.00 0.00 0.00 3.07
3885 7862 3.469899 TGTCTACATTGCAATGCGTTC 57.530 42.857 33.94 22.81 40.04 3.95
3924 7901 1.019278 AGCCGGAGTACATTGTTGCG 61.019 55.000 5.05 0.00 0.00 4.85
3972 7949 4.164843 ACTGTTGAAGCCAAGACCTTTA 57.835 40.909 0.00 0.00 32.06 1.85
3973 7950 4.137543 ACTGTTGAAGCCAAGACCTTTAG 58.862 43.478 0.00 0.00 32.06 1.85
4084 8061 0.035152 TGCCAGCATTGATCGAGGTT 60.035 50.000 0.00 0.00 0.00 3.50
4096 8073 3.058293 TGATCGAGGTTGCACACATTTTC 60.058 43.478 0.00 0.00 0.00 2.29
4202 8179 3.345508 AAGGATTTTCTCCCCGTGTAC 57.654 47.619 0.00 0.00 46.27 2.90
4203 8180 2.547990 AGGATTTTCTCCCCGTGTACT 58.452 47.619 0.00 0.00 46.27 2.73
4245 8222 8.757164 AGCTGTTTAACAACTTAAATATTGCC 57.243 30.769 0.00 0.00 34.93 4.52
4272 8249 6.472486 CCGACGTATACTATTCCATGCTTATG 59.528 42.308 0.56 0.00 0.00 1.90
4307 8284 8.539770 AATCAAAAAGCAGATCGATCGTATAT 57.460 30.769 19.33 0.52 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 9.023962 TGATTATATGTTCAGGCAAGTCTTTTT 57.976 29.630 0.00 0.00 0.00 1.94
87 88 7.512130 TCATGATTATATGTTCAGGCAAGTCT 58.488 34.615 0.00 0.00 0.00 3.24
140 142 1.847088 GCCAGGGGTTATCCTTCTTCT 59.153 52.381 0.00 0.00 34.31 2.85
161 164 4.338012 ACATTCATTGTCCTGATGCAGAA 58.662 39.130 0.00 0.00 30.89 3.02
201 207 4.009675 TGGCACACTCTGGATTTTACATC 58.990 43.478 0.00 0.00 0.00 3.06
205 211 3.826524 TGTTGGCACACTCTGGATTTTA 58.173 40.909 0.00 0.00 39.29 1.52
358 3936 4.052229 CGAGAGACCGGCCGTGTT 62.052 66.667 26.12 7.77 0.00 3.32
373 3951 2.776659 ATCGAGTGTGGACGATCGA 58.223 52.632 24.34 8.13 44.14 3.59
427 4005 6.589523 GCTATAAGCACATGATAGAACAGGAG 59.410 42.308 0.00 0.00 41.89 3.69
455 4033 8.724310 ACTGGAGGCTTGGTTAATATATTTAGT 58.276 33.333 2.68 0.00 0.00 2.24
456 4034 9.220767 GACTGGAGGCTTGGTTAATATATTTAG 57.779 37.037 2.68 0.00 0.00 1.85
457 4035 8.161425 GGACTGGAGGCTTGGTTAATATATTTA 58.839 37.037 2.68 0.00 0.00 1.40
458 4036 7.004691 GGACTGGAGGCTTGGTTAATATATTT 58.995 38.462 2.68 0.00 0.00 1.40
459 4037 6.332901 AGGACTGGAGGCTTGGTTAATATATT 59.667 38.462 2.97 2.97 0.00 1.28
460 4038 5.852250 AGGACTGGAGGCTTGGTTAATATAT 59.148 40.000 0.00 0.00 0.00 0.86
461 4039 5.071788 CAGGACTGGAGGCTTGGTTAATATA 59.928 44.000 0.00 0.00 0.00 0.86
462 4040 4.047883 AGGACTGGAGGCTTGGTTAATAT 58.952 43.478 0.00 0.00 0.00 1.28
463 4041 3.199946 CAGGACTGGAGGCTTGGTTAATA 59.800 47.826 0.00 0.00 0.00 0.98
464 4042 2.025887 CAGGACTGGAGGCTTGGTTAAT 60.026 50.000 0.00 0.00 0.00 1.40
465 4043 1.351017 CAGGACTGGAGGCTTGGTTAA 59.649 52.381 0.00 0.00 0.00 2.01
478 4056 3.138798 GCATGCCAGCCAGGACTG 61.139 66.667 6.36 0.00 41.22 3.51
479 4057 3.640257 CTGCATGCCAGCCAGGACT 62.640 63.158 16.68 0.00 41.22 3.85
480 4058 2.541547 TACTGCATGCCAGCCAGGAC 62.542 60.000 16.68 0.00 45.78 3.85
482 4060 1.822613 CTACTGCATGCCAGCCAGG 60.823 63.158 16.68 0.00 45.78 4.45
484 4062 2.273123 CCTACTGCATGCCAGCCA 59.727 61.111 16.68 3.93 45.78 4.75
485 4063 2.117156 CACCTACTGCATGCCAGCC 61.117 63.158 16.68 0.00 45.78 4.85
486 4064 1.078214 TCACCTACTGCATGCCAGC 60.078 57.895 16.68 0.00 45.78 4.85
488 4066 1.139654 GATCTCACCTACTGCATGCCA 59.860 52.381 16.68 2.21 0.00 4.92
489 4067 1.415659 AGATCTCACCTACTGCATGCC 59.584 52.381 16.68 0.00 0.00 4.40
490 4068 2.102084 TCAGATCTCACCTACTGCATGC 59.898 50.000 11.82 11.82 0.00 4.06
491 4069 4.118410 GTTCAGATCTCACCTACTGCATG 58.882 47.826 0.00 0.00 0.00 4.06
492 4070 4.029520 AGTTCAGATCTCACCTACTGCAT 58.970 43.478 0.00 0.00 0.00 3.96
493 4071 3.194329 CAGTTCAGATCTCACCTACTGCA 59.806 47.826 0.00 0.00 0.00 4.41
494 4072 3.445450 TCAGTTCAGATCTCACCTACTGC 59.555 47.826 0.00 0.00 33.40 4.40
495 4073 5.590145 CATCAGTTCAGATCTCACCTACTG 58.410 45.833 0.00 2.85 34.38 2.74
496 4074 4.099266 GCATCAGTTCAGATCTCACCTACT 59.901 45.833 0.00 0.00 0.00 2.57
497 4075 4.367450 GCATCAGTTCAGATCTCACCTAC 58.633 47.826 0.00 0.00 0.00 3.18
498 4076 3.386078 GGCATCAGTTCAGATCTCACCTA 59.614 47.826 0.00 0.00 0.00 3.08
499 4077 2.170187 GGCATCAGTTCAGATCTCACCT 59.830 50.000 0.00 0.00 0.00 4.00
500 4078 2.093288 TGGCATCAGTTCAGATCTCACC 60.093 50.000 0.00 0.00 0.00 4.02
501 4079 3.257469 TGGCATCAGTTCAGATCTCAC 57.743 47.619 0.00 0.00 0.00 3.51
502 4080 3.986996 TTGGCATCAGTTCAGATCTCA 57.013 42.857 0.00 0.00 0.00 3.27
503 4081 3.063180 CGTTTGGCATCAGTTCAGATCTC 59.937 47.826 0.00 0.00 0.00 2.75
504 4082 3.005554 CGTTTGGCATCAGTTCAGATCT 58.994 45.455 0.00 0.00 0.00 2.75
505 4083 2.744202 ACGTTTGGCATCAGTTCAGATC 59.256 45.455 0.00 0.00 0.00 2.75
506 4084 2.783135 ACGTTTGGCATCAGTTCAGAT 58.217 42.857 0.00 0.00 0.00 2.90
507 4085 2.254546 ACGTTTGGCATCAGTTCAGA 57.745 45.000 0.00 0.00 0.00 3.27
508 4086 2.159841 CGTACGTTTGGCATCAGTTCAG 60.160 50.000 7.22 0.00 0.00 3.02
509 4087 1.795872 CGTACGTTTGGCATCAGTTCA 59.204 47.619 7.22 0.00 0.00 3.18
510 4088 1.796459 ACGTACGTTTGGCATCAGTTC 59.204 47.619 16.72 0.00 0.00 3.01
511 4089 1.873698 ACGTACGTTTGGCATCAGTT 58.126 45.000 16.72 0.00 0.00 3.16
512 4090 2.029649 AGTACGTACGTTTGGCATCAGT 60.030 45.455 27.92 5.60 0.00 3.41
513 4091 2.344441 CAGTACGTACGTTTGGCATCAG 59.656 50.000 27.92 3.13 0.00 2.90
514 4092 2.288334 ACAGTACGTACGTTTGGCATCA 60.288 45.455 27.92 2.14 0.00 3.07
515 4093 2.331194 ACAGTACGTACGTTTGGCATC 58.669 47.619 27.92 8.52 0.00 3.91
516 4094 2.029649 AGACAGTACGTACGTTTGGCAT 60.030 45.455 28.83 17.04 0.00 4.40
517 4095 1.337703 AGACAGTACGTACGTTTGGCA 59.662 47.619 28.83 11.54 0.00 4.92
518 4096 2.056094 AGACAGTACGTACGTTTGGC 57.944 50.000 27.92 25.15 0.00 4.52
519 4097 4.410492 AGTAGACAGTACGTACGTTTGG 57.590 45.455 27.92 17.45 0.00 3.28
520 4098 6.517714 CAGTAAGTAGACAGTACGTACGTTTG 59.482 42.308 27.92 24.89 37.43 2.93
521 4099 6.202954 ACAGTAAGTAGACAGTACGTACGTTT 59.797 38.462 27.92 13.40 37.43 3.60
522 4100 5.696724 ACAGTAAGTAGACAGTACGTACGTT 59.303 40.000 27.92 8.35 37.43 3.99
523 4101 5.230942 ACAGTAAGTAGACAGTACGTACGT 58.769 41.667 25.98 25.98 37.43 3.57
524 4102 5.769967 ACAGTAAGTAGACAGTACGTACG 57.230 43.478 19.49 15.01 37.43 3.67
567 4145 1.404391 GATGATGGACTGCTTGGCTTG 59.596 52.381 0.00 0.00 0.00 4.01
597 4175 3.194861 TGCGCCATTGACTAATGACTAC 58.805 45.455 4.18 0.00 45.21 2.73
598 4176 3.132111 TCTGCGCCATTGACTAATGACTA 59.868 43.478 4.18 0.00 45.21 2.59
599 4177 2.093500 TCTGCGCCATTGACTAATGACT 60.093 45.455 4.18 0.00 45.21 3.41
600 4178 2.279741 TCTGCGCCATTGACTAATGAC 58.720 47.619 4.18 0.00 45.21 3.06
601 4179 2.689553 TCTGCGCCATTGACTAATGA 57.310 45.000 4.18 0.00 45.21 2.57
602 4180 3.120408 GCTATCTGCGCCATTGACTAATG 60.120 47.826 4.18 0.00 42.66 1.90
603 4181 3.070018 GCTATCTGCGCCATTGACTAAT 58.930 45.455 4.18 0.00 0.00 1.73
604 4182 2.483876 GCTATCTGCGCCATTGACTAA 58.516 47.619 4.18 0.00 0.00 2.24
605 4183 1.270305 GGCTATCTGCGCCATTGACTA 60.270 52.381 4.18 0.00 46.77 2.59
606 4184 0.533755 GGCTATCTGCGCCATTGACT 60.534 55.000 4.18 0.00 46.77 3.41
607 4185 1.944778 GGCTATCTGCGCCATTGAC 59.055 57.895 4.18 0.00 46.77 3.18
608 4186 4.462394 GGCTATCTGCGCCATTGA 57.538 55.556 4.18 0.00 46.77 2.57
658 4301 0.173481 TCGTGATCAGTACTGCTGCC 59.827 55.000 18.45 7.25 44.66 4.85
818 4461 1.522806 TGGTGTTGTCGCAGGTGAC 60.523 57.895 6.05 6.05 39.37 3.67
1152 4843 0.179134 CGTTGTCGACATCCTCCTCC 60.179 60.000 20.80 0.00 39.71 4.30
1154 4845 2.957060 TCGTTGTCGACATCCTCCT 58.043 52.632 20.80 0.00 41.35 3.69
1270 5006 2.621338 CACATAGACTGGCACATCGTT 58.379 47.619 0.00 0.00 38.20 3.85
1322 5082 1.815421 ATCAGAACGATGGCCACGC 60.815 57.895 22.27 11.67 31.20 5.34
1323 5083 2.009108 CATCAGAACGATGGCCACG 58.991 57.895 21.20 21.20 46.73 4.94
1345 5105 4.607025 GGGCCCGGGTTTGTCCAA 62.607 66.667 24.63 0.00 38.11 3.53
1465 5225 0.540365 CCTTCCATGGTGCAGTTGGT 60.540 55.000 12.58 0.00 0.00 3.67
1468 5228 1.607467 GGCCTTCCATGGTGCAGTT 60.607 57.895 12.58 0.00 0.00 3.16
1513 5306 1.987807 TTGCCCTCATAGCCAGGCTC 61.988 60.000 20.38 1.45 45.94 4.70
1739 5533 1.400846 GCACTCATTGATGTCTGCAGG 59.599 52.381 15.13 0.00 34.03 4.85
1831 5718 3.008594 TGGCGTTTCCTTCAAATCCTCTA 59.991 43.478 0.00 0.00 35.26 2.43
1875 5762 2.820787 TCACCTGTGTTCGTTTTGGTTT 59.179 40.909 0.00 0.00 0.00 3.27
1884 5771 2.900528 GTGTCCTCACCTGTGTTCG 58.099 57.895 0.00 0.00 38.51 3.95
1919 5806 9.877178 CAATATATACTAAGAGAGGCGGAAAAT 57.123 33.333 0.00 0.00 0.00 1.82
1924 5811 6.093771 ACGACAATATATACTAAGAGAGGCGG 59.906 42.308 0.00 0.00 0.00 6.13
2246 6207 3.875727 CACTAGCTGCTGCAATAACTGAT 59.124 43.478 18.42 0.00 42.74 2.90
2247 6208 3.264947 CACTAGCTGCTGCAATAACTGA 58.735 45.455 18.42 0.00 42.74 3.41
2379 6341 7.288158 AGGTCTGATAGTATTCCTTTGTAGACC 59.712 40.741 0.00 0.00 46.65 3.85
2928 6905 5.757320 CCTATACTTGACTGGCATCTTTCTG 59.243 44.000 0.00 0.00 0.00 3.02
3017 6994 4.527509 ACAATCTGCGGATCTAGTATGG 57.472 45.455 8.88 0.00 0.00 2.74
3126 7103 3.628646 GAGCGCCATCCCCACTTGT 62.629 63.158 2.29 0.00 0.00 3.16
3134 7111 2.586357 GACCTTCGAGCGCCATCC 60.586 66.667 2.29 0.00 0.00 3.51
3184 7161 2.198827 TCATTTCGTCCTGGTTGCAT 57.801 45.000 0.00 0.00 0.00 3.96
3194 7171 8.851960 TGTAGTATAACTGTCATCATTTCGTC 57.148 34.615 0.00 0.00 0.00 4.20
3273 7250 3.259625 AGAACTCCTCTTCTTGGCTGTAC 59.740 47.826 0.00 0.00 0.00 2.90
3409 7386 9.107177 TCAAAGAAAACACAATGCACATATTTT 57.893 25.926 0.00 0.00 0.00 1.82
3447 7424 3.872696 ACATATCGCCACATTCAAGACA 58.127 40.909 0.00 0.00 0.00 3.41
3470 7447 7.606073 AGTGTGATACAACTAATGCACATTACA 59.394 33.333 0.00 0.00 38.35 2.41
3511 7488 6.690530 TGAAGAAAATTTTGTAGATGGCTGG 58.309 36.000 8.47 0.00 0.00 4.85
3556 7533 5.729510 AGAATAGCCAGTCACTCTTTTCTC 58.270 41.667 0.00 0.00 0.00 2.87
3689 7666 9.030452 TCCTACAAATAAAACCATTGCTGTAAT 57.970 29.630 0.00 0.00 0.00 1.89
3858 7835 4.736793 GCATTGCAATGTAGACATACTTGC 59.263 41.667 33.67 17.18 41.42 4.01
3885 7862 3.119352 GCTTCATAAACAGAGGGCAAAGG 60.119 47.826 0.00 0.00 0.00 3.11
3924 7901 1.882198 CGCGTGTCATTTCCATTGTC 58.118 50.000 0.00 0.00 0.00 3.18
3929 7906 0.595588 AAATGCGCGTGTCATTTCCA 59.404 45.000 18.97 0.00 39.21 3.53
3930 7907 1.259316 GAAATGCGCGTGTCATTTCC 58.741 50.000 28.80 19.16 46.92 3.13
4084 8061 3.002451 GCAAAAGCATGAAAATGTGTGCA 59.998 39.130 0.00 0.00 39.94 4.57
4096 8073 3.536956 AGATTCCCATGCAAAAGCATG 57.463 42.857 20.32 20.32 44.93 4.06
4107 8084 2.026262 AGTAACGTGCCAAGATTCCCAT 60.026 45.455 0.00 0.00 0.00 4.00
4135 8112 1.982958 TCCTTTGTAGGTGGTTCCCTC 59.017 52.381 0.00 0.00 42.60 4.30
4245 8222 3.918591 GCATGGAATAGTATACGTCGGTG 59.081 47.826 0.00 1.54 0.00 4.94
4272 8249 6.530019 TCTGCTTTTTGATTTATCCTTCCC 57.470 37.500 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.