Multiple sequence alignment - TraesCS4A01G208600

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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 TraesCS4A01G208600 chr4A 100.000 4341 0 0 1 4341 501958071 501962411 0 8017
1 TraesCS4A01G208600 chr4D 95.523 3440 112 17 864 4272 89419389 89422817 0 5461
2 TraesCS4A01G208600 chr4D 84.156 871 108 15 2 862 89418498 89419348 0 817
3 TraesCS4A01G208600 chr4B 93.150 3416 125 29 880 4272 126319781 126323110 0 4911
4 TraesCS4A01G208600 chr4B 85.190 817 96 12 2 808 126317624 126318425 0 815


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 TraesCS4A01G208600 chr4A 501958071 501962411 4340 False 8017 8017 100.0000 1 4341 1 chr4A.!!$F1 4340
1 TraesCS4A01G208600 chr4D 89418498 89422817 4319 False 3139 5461 89.8395 2 4272 2 chr4D.!!$F1 4270
2 TraesCS4A01G208600 chr4B 126317624 126323110 5486 False 2863 4911 89.1700 2 4272 2 chr4B.!!$F1 4270

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
55 56 0.109342 ACCAAGAGCAACCACTCCAG 59.891 55.0 0.00 0.00 37.39 3.86 F
184 186 0.176680 ATGGTGTCCAGATCAGACGC 59.823 55.0 16.87 16.87 42.68 5.19 F
636 648 0.179111 TGACGATGACGGAGGCATTC 60.179 55.0 0.00 0.00 44.46 2.67 F
869 919 0.323725 TTGAGGGAGCTGATTTGCCC 60.324 55.0 0.00 0.00 41.00 5.36 F
1472 2771 0.394352 GATTCATCCCCAGGTGCGTT 60.394 55.0 0.00 0.00 0.00 4.84 F
1481 2780 0.738389 CCAGGTGCGTTCAACAAGTT 59.262 50.0 0.00 0.00 30.55 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 3030 0.669077 AGTCTAATACAGCTCGGGCG 59.331 55.000 0.00 0.0 44.37 6.13 R
2131 3452 1.411977 TGGAGTGCCAACAAAATGGTG 59.588 47.619 0.00 0.0 42.49 4.17 R
2437 3758 4.758674 CCCATACCATTAATGTGAGAGCAG 59.241 45.833 14.25 0.0 0.00 4.24 R
2721 4043 1.160137 CTGCTCTCAAACTTTCGGGG 58.840 55.000 0.00 0.0 0.00 5.73 R
3133 4455 0.546122 ACCTCTGCTGTGTTGGTTGA 59.454 50.000 0.00 0.0 0.00 3.18 R
3458 4780 0.690192 TCGCTCCCACTCCATTCAAA 59.310 50.000 0.00 0.0 0.00 2.69 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
22 23 2.817844 TGTCGATTGAGAGAAGGTCGAA 59.182 45.455 0.00 0.00 42.13 3.71
48 49 1.239347 GACTTGGACCAAGAGCAACC 58.761 55.000 35.69 15.46 43.42 3.77
55 56 0.109342 ACCAAGAGCAACCACTCCAG 59.891 55.000 0.00 0.00 37.39 3.86
62 63 3.953775 AACCACTCCAGCCCACGG 61.954 66.667 0.00 0.00 0.00 4.94
83 84 1.329906 CGAAGGATGAAGAGTGCATGC 59.670 52.381 11.82 11.82 34.72 4.06
103 104 2.432444 CGGCAACTTCAATTCCCACTA 58.568 47.619 0.00 0.00 0.00 2.74
124 125 0.451783 CGCTATGGAACTTGTTGGCC 59.548 55.000 0.00 0.00 0.00 5.36
137 138 2.609299 TGGCCAACCAGGATCCGA 60.609 61.111 0.61 0.00 42.67 4.55
145 146 2.507452 CAGGATCCGATGCAGGCA 59.493 61.111 5.98 0.00 0.00 4.75
148 149 1.059098 AGGATCCGATGCAGGCATTA 58.941 50.000 8.34 0.00 36.70 1.90
162 163 2.018515 GGCATTATCCCCGTCGAAAAA 58.981 47.619 0.00 0.00 0.00 1.94
165 167 3.119779 GCATTATCCCCGTCGAAAAACAA 60.120 43.478 0.00 0.00 0.00 2.83
166 168 4.439563 GCATTATCCCCGTCGAAAAACAAT 60.440 41.667 0.00 0.00 0.00 2.71
173 175 2.603652 CCGTCGAAAAACAATGGTGTCC 60.604 50.000 0.00 0.00 36.80 4.02
178 180 4.215399 TCGAAAAACAATGGTGTCCAGATC 59.785 41.667 0.00 0.00 36.80 2.75
184 186 0.176680 ATGGTGTCCAGATCAGACGC 59.823 55.000 16.87 16.87 42.68 5.19
187 189 1.977009 TGTCCAGATCAGACGCCGT 60.977 57.895 10.32 0.00 37.04 5.68
189 191 2.887568 CCAGATCAGACGCCGTGC 60.888 66.667 0.00 0.00 0.00 5.34
230 232 2.445155 GACCTTGTGGCCCCCATT 59.555 61.111 0.00 0.00 35.28 3.16
239 241 2.745308 GGCCCCCATTCCAAATGGC 61.745 63.158 12.32 2.72 37.85 4.40
240 242 1.994507 GCCCCCATTCCAAATGGCA 60.995 57.895 12.32 0.00 38.73 4.92
281 283 1.608283 GCCCCCGCATCAAGTACTATC 60.608 57.143 0.00 0.00 34.03 2.08
289 291 4.707448 CGCATCAAGTACTATCTAGGGGAT 59.293 45.833 0.00 0.00 38.38 3.85
292 294 6.350612 GCATCAAGTACTATCTAGGGGATGAC 60.351 46.154 0.00 0.00 35.98 3.06
333 338 2.190578 GTTGGAGGGCTAGCGCAT 59.809 61.111 30.70 17.18 38.10 4.73
341 346 2.711924 GCTAGCGCATCCAGCAAC 59.288 61.111 11.47 0.00 46.13 4.17
355 360 3.329231 CAACGCTTGCCAAGACGA 58.671 55.556 21.91 0.00 34.02 4.20
356 361 1.082756 CAACGCTTGCCAAGACGAC 60.083 57.895 21.91 0.00 34.02 4.34
357 362 1.522806 AACGCTTGCCAAGACGACA 60.523 52.632 21.91 0.00 34.02 4.35
358 363 1.092921 AACGCTTGCCAAGACGACAA 61.093 50.000 21.91 0.00 34.02 3.18
418 430 1.749334 GCCCTCGACCGATCCAAGAT 61.749 60.000 0.00 0.00 0.00 2.40
442 454 0.759346 AAAGAGACCGACACCAGCTT 59.241 50.000 0.00 0.00 0.00 3.74
470 482 1.374758 CTCCTCCGTGTTGGACTGC 60.375 63.158 0.00 0.00 43.74 4.40
534 546 1.078848 CAAGGTTGAGGAGGAGGCG 60.079 63.158 0.00 0.00 0.00 5.52
587 599 1.078143 CAGCTAGGGTGCCTTCCAC 60.078 63.158 0.00 0.00 43.90 4.02
596 608 1.039856 GTGCCTTCCACAATTGGTGT 58.960 50.000 10.83 0.00 46.44 4.16
610 622 4.524316 ATTGGTGTGACATTGACAATGG 57.476 40.909 27.46 12.85 43.21 3.16
627 639 1.075979 TGGCGACAATGACGATGACG 61.076 55.000 9.52 0.00 41.16 4.35
628 640 1.631072 GCGACAATGACGATGACGG 59.369 57.895 9.52 0.00 44.46 4.79
630 642 1.191944 CGACAATGACGATGACGGAG 58.808 55.000 0.00 0.00 44.46 4.63
633 645 0.460109 CAATGACGATGACGGAGGCA 60.460 55.000 0.00 0.00 44.46 4.75
636 648 0.179111 TGACGATGACGGAGGCATTC 60.179 55.000 0.00 0.00 44.46 2.67
663 675 2.636893 CCTTAGAGGTCATCCCCATGAG 59.363 54.545 0.00 0.00 39.86 2.90
664 676 3.581101 CTTAGAGGTCATCCCCATGAGA 58.419 50.000 0.00 0.00 39.86 3.27
670 682 2.026449 GGTCATCCCCATGAGATCATCC 60.026 54.545 0.00 0.00 39.86 3.51
673 685 2.801282 TCCCCATGAGATCATCCTCA 57.199 50.000 0.00 0.00 46.02 3.86
674 686 2.333069 TCCCCATGAGATCATCCTCAC 58.667 52.381 0.00 0.00 44.93 3.51
675 687 1.001746 CCCCATGAGATCATCCTCACG 59.998 57.143 0.00 0.00 44.93 4.35
676 688 1.966354 CCCATGAGATCATCCTCACGA 59.034 52.381 0.00 0.00 44.93 4.35
677 689 2.029200 CCCATGAGATCATCCTCACGAG 60.029 54.545 0.00 0.00 44.93 4.18
698 710 7.130303 CGAGGTCATCGTCTATTATTCTGTA 57.870 40.000 0.00 0.00 46.62 2.74
699 711 7.753659 CGAGGTCATCGTCTATTATTCTGTAT 58.246 38.462 0.00 0.00 46.62 2.29
860 872 6.869206 TTTTAGTATAGTGTTGAGGGAGCT 57.131 37.500 0.00 0.00 0.00 4.09
862 912 3.982516 AGTATAGTGTTGAGGGAGCTGA 58.017 45.455 0.00 0.00 0.00 4.26
869 919 0.323725 TTGAGGGAGCTGATTTGCCC 60.324 55.000 0.00 0.00 41.00 5.36
879 929 1.407979 CTGATTTGCCCTTGGAGATGC 59.592 52.381 0.00 0.00 0.00 3.91
1452 2751 1.229428 TTTTGCGTTGGAGCTCTCTG 58.771 50.000 14.64 2.62 38.13 3.35
1472 2771 0.394352 GATTCATCCCCAGGTGCGTT 60.394 55.000 0.00 0.00 0.00 4.84
1481 2780 0.738389 CCAGGTGCGTTCAACAAGTT 59.262 50.000 0.00 0.00 30.55 2.66
1699 3018 1.075979 TTGACATCCGCATCGACACG 61.076 55.000 2.06 2.06 0.00 4.49
1711 3030 0.863144 TCGACACGGCAAAAAGTAGC 59.137 50.000 0.00 0.00 0.00 3.58
1729 3048 0.940047 GCGCCCGAGCTGTATTAGAC 60.940 60.000 0.00 0.00 36.60 2.59
1762 3081 3.434940 AAGCTTACATCGGAAAACCCT 57.565 42.857 0.00 0.00 0.00 4.34
1783 3102 2.015587 GATTCCGTGAGTAGGACGAGT 58.984 52.381 0.00 0.00 39.21 4.18
1788 3107 2.223294 CCGTGAGTAGGACGAGTCATTC 60.223 54.545 5.55 0.00 39.21 2.67
1799 3120 3.600388 ACGAGTCATTCCATTCCTGTTC 58.400 45.455 0.00 0.00 0.00 3.18
1801 3122 3.868077 CGAGTCATTCCATTCCTGTTCTC 59.132 47.826 0.00 0.00 0.00 2.87
1805 3126 5.942826 AGTCATTCCATTCCTGTTCTCTTTC 59.057 40.000 0.00 0.00 0.00 2.62
1809 3130 6.639632 TTCCATTCCTGTTCTCTTTCTTTG 57.360 37.500 0.00 0.00 0.00 2.77
1810 3131 5.072741 TCCATTCCTGTTCTCTTTCTTTGG 58.927 41.667 0.00 0.00 0.00 3.28
1845 3166 2.611751 TCATTGTATCGCGTCATTTGGG 59.388 45.455 5.77 0.00 0.00 4.12
1849 3170 3.275143 TGTATCGCGTCATTTGGGAAAT 58.725 40.909 5.77 0.00 0.00 2.17
2036 3357 4.041723 AGCGTGCAAAGTTAAATTGTGTC 58.958 39.130 0.00 0.00 0.00 3.67
2131 3452 2.228059 CTGAGGATGGCATGGTCAATC 58.772 52.381 3.81 0.00 0.00 2.67
2304 3625 6.491745 TGGTGAATGCCTTGTAAGTGAAAATA 59.508 34.615 0.00 0.00 0.00 1.40
2437 3758 4.083110 GCATGTAATATGTGCATCCAGGAC 60.083 45.833 0.00 0.00 38.68 3.85
2497 3818 4.524328 AGTTCAAAGGCAAAATACTCTGGG 59.476 41.667 0.00 0.00 0.00 4.45
2664 3986 6.376299 AGCATTCTTTGATTCTCATGCACTTA 59.624 34.615 4.86 0.00 31.75 2.24
2721 4043 2.429927 GGGCATTAATGGACCCAGC 58.570 57.895 20.51 5.02 42.33 4.85
2735 4057 1.244019 CCCAGCCCCGAAAGTTTGAG 61.244 60.000 0.00 0.00 0.00 3.02
2829 4151 7.656137 ACATCTGAAACTTATTGTGTTCGTACT 59.344 33.333 0.00 0.00 0.00 2.73
3002 4324 1.537202 GTTTCAGAGCACATGGACACC 59.463 52.381 0.00 0.00 0.00 4.16
3019 4341 2.159310 ACACCGAAATTGTGTGTGGTTG 60.159 45.455 7.00 0.00 44.85 3.77
3133 4455 4.284490 TCTGCTTGAGGACTACAGACAATT 59.716 41.667 0.00 0.00 32.65 2.32
3151 4473 1.679139 TTCAACCAACACAGCAGAGG 58.321 50.000 0.00 0.00 0.00 3.69
3191 4513 8.208224 TGTTTCTCTTATTGTCTCTGTAAACCA 58.792 33.333 0.00 0.00 0.00 3.67
3232 4554 9.649167 TTTTAGTAGTTTAGCTGTTCATACCTC 57.351 33.333 0.00 0.00 0.00 3.85
3233 4555 6.852420 AGTAGTTTAGCTGTTCATACCTCA 57.148 37.500 0.00 0.00 0.00 3.86
3249 4571 1.545582 CCTCACCATGCCGTTTGAAAT 59.454 47.619 0.00 0.00 0.00 2.17
3347 4669 0.605319 GGAGAACACATGAACCGGCA 60.605 55.000 0.00 0.00 0.00 5.69
3375 4697 2.292267 CTGGATGGCAATCTGGTGTAC 58.708 52.381 0.00 0.00 32.95 2.90
3391 4713 4.141914 TGGTGTACCATATCGTAACATGCA 60.142 41.667 0.00 0.00 42.01 3.96
3409 4731 1.267732 GCATGCATGTCTAGTTGCGAC 60.268 52.381 26.79 0.00 41.80 5.19
3458 4780 3.474798 TGGAAGGTGAGACTGTATCCT 57.525 47.619 0.00 0.00 0.00 3.24
3474 4796 3.659183 ATCCTTTGAATGGAGTGGGAG 57.341 47.619 5.99 0.00 36.99 4.30
3491 4813 1.346068 GGAGCGATCTAGGGCAAGATT 59.654 52.381 0.00 0.00 36.33 2.40
3492 4814 2.224402 GGAGCGATCTAGGGCAAGATTT 60.224 50.000 0.00 0.00 36.33 2.17
3531 4853 4.801147 TTAAGATCAGATGTTGATGCGC 57.199 40.909 0.00 0.00 46.51 6.09
3533 4855 1.938577 AGATCAGATGTTGATGCGCAC 59.061 47.619 14.90 7.75 46.51 5.34
3536 4858 0.247419 CAGATGTTGATGCGCACGAC 60.247 55.000 14.90 17.03 0.00 4.34
3542 4865 4.148825 GATGCGCACGACTCCCCT 62.149 66.667 14.90 0.00 0.00 4.79
3561 4884 1.564348 CTAATTGGTAGGGCTGGGTGT 59.436 52.381 0.00 0.00 0.00 4.16
3569 4892 0.916358 AGGGCTGGGTGTAGAAGCAT 60.916 55.000 0.00 0.00 38.73 3.79
3573 4896 2.370189 GGCTGGGTGTAGAAGCATAGAT 59.630 50.000 0.00 0.00 38.73 1.98
3722 5045 3.070018 GCCATCATCTAGTGCATACCAC 58.930 50.000 0.00 0.00 45.01 4.16
3804 5127 8.836268 AATGTTCAATTGTGACAGCATTTTAT 57.164 26.923 17.67 2.35 31.90 1.40
3901 5233 7.821595 AACACTGACGATAATGTTTATTCGA 57.178 32.000 0.00 0.00 31.27 3.71
4087 5419 7.201679 CGAATCTTTTCCTGCTTGTTCATCTAT 60.202 37.037 0.00 0.00 0.00 1.98
4229 5561 3.055094 AGGCAAAGTCATCGACATTACCT 60.055 43.478 0.00 0.00 33.74 3.08
4268 5600 3.058160 CTGGCCTGGCTGTTTCCG 61.058 66.667 19.68 0.00 0.00 4.30
4272 5604 1.285950 GCCTGGCTGTTTCCGTTTC 59.714 57.895 12.43 0.00 0.00 2.78
4273 5605 1.172812 GCCTGGCTGTTTCCGTTTCT 61.173 55.000 12.43 0.00 0.00 2.52
4274 5606 1.318576 CCTGGCTGTTTCCGTTTCTT 58.681 50.000 0.00 0.00 0.00 2.52
4275 5607 1.001378 CCTGGCTGTTTCCGTTTCTTG 60.001 52.381 0.00 0.00 0.00 3.02
4276 5608 0.383949 TGGCTGTTTCCGTTTCTTGC 59.616 50.000 0.00 0.00 0.00 4.01
4277 5609 0.383949 GGCTGTTTCCGTTTCTTGCA 59.616 50.000 0.00 0.00 0.00 4.08
4278 5610 1.600413 GGCTGTTTCCGTTTCTTGCAG 60.600 52.381 0.00 0.00 0.00 4.41
4279 5611 1.600413 GCTGTTTCCGTTTCTTGCAGG 60.600 52.381 0.00 0.00 0.00 4.85
4280 5612 1.001378 CTGTTTCCGTTTCTTGCAGGG 60.001 52.381 0.00 0.00 0.00 4.45
4281 5613 1.314730 GTTTCCGTTTCTTGCAGGGA 58.685 50.000 0.00 0.00 0.00 4.20
4282 5614 1.679153 GTTTCCGTTTCTTGCAGGGAA 59.321 47.619 0.00 0.00 36.59 3.97
4283 5615 1.314730 TTCCGTTTCTTGCAGGGAAC 58.685 50.000 9.92 9.92 34.07 3.62
4284 5616 0.181587 TCCGTTTCTTGCAGGGAACA 59.818 50.000 19.06 0.00 0.00 3.18
4285 5617 1.028905 CCGTTTCTTGCAGGGAACAA 58.971 50.000 19.06 0.00 0.00 2.83
4286 5618 1.269051 CCGTTTCTTGCAGGGAACAAC 60.269 52.381 19.06 8.08 0.00 3.32
4287 5619 1.676006 CGTTTCTTGCAGGGAACAACT 59.324 47.619 19.06 0.00 0.00 3.16
4288 5620 2.099098 CGTTTCTTGCAGGGAACAACTT 59.901 45.455 19.06 0.00 0.00 2.66
4289 5621 3.314080 CGTTTCTTGCAGGGAACAACTTA 59.686 43.478 19.06 0.00 0.00 2.24
4290 5622 4.607955 GTTTCTTGCAGGGAACAACTTAC 58.392 43.478 14.80 1.61 0.00 2.34
4291 5623 3.857157 TCTTGCAGGGAACAACTTACT 57.143 42.857 0.00 0.00 0.00 2.24
4292 5624 4.164843 TCTTGCAGGGAACAACTTACTT 57.835 40.909 0.00 0.00 0.00 2.24
4293 5625 3.882888 TCTTGCAGGGAACAACTTACTTG 59.117 43.478 0.00 0.00 35.77 3.16
4294 5626 3.569194 TGCAGGGAACAACTTACTTGA 57.431 42.857 0.00 0.00 33.59 3.02
4295 5627 4.098914 TGCAGGGAACAACTTACTTGAT 57.901 40.909 0.00 0.00 33.59 2.57
4296 5628 5.235850 TGCAGGGAACAACTTACTTGATA 57.764 39.130 0.00 0.00 33.59 2.15
4297 5629 5.815581 TGCAGGGAACAACTTACTTGATAT 58.184 37.500 0.00 0.00 33.59 1.63
4298 5630 5.647658 TGCAGGGAACAACTTACTTGATATG 59.352 40.000 0.00 0.00 33.59 1.78
4299 5631 5.066505 GCAGGGAACAACTTACTTGATATGG 59.933 44.000 0.00 0.00 33.59 2.74
4300 5632 6.180472 CAGGGAACAACTTACTTGATATGGT 58.820 40.000 0.00 0.00 33.59 3.55
4301 5633 6.659242 CAGGGAACAACTTACTTGATATGGTT 59.341 38.462 0.00 0.00 33.59 3.67
4302 5634 6.659242 AGGGAACAACTTACTTGATATGGTTG 59.341 38.462 0.00 0.00 39.58 3.77
4303 5635 6.433093 GGGAACAACTTACTTGATATGGTTGT 59.567 38.462 0.00 0.00 45.64 3.32
4304 5636 7.305474 GGAACAACTTACTTGATATGGTTGTG 58.695 38.462 9.47 0.00 43.85 3.33
4305 5637 6.254281 ACAACTTACTTGATATGGTTGTGC 57.746 37.500 8.19 0.00 43.28 4.57
4306 5638 6.003950 ACAACTTACTTGATATGGTTGTGCT 58.996 36.000 8.19 0.00 43.28 4.40
4307 5639 6.490040 ACAACTTACTTGATATGGTTGTGCTT 59.510 34.615 8.19 0.00 43.28 3.91
4308 5640 6.743575 ACTTACTTGATATGGTTGTGCTTC 57.256 37.500 0.00 0.00 0.00 3.86
4309 5641 5.648092 ACTTACTTGATATGGTTGTGCTTCC 59.352 40.000 0.00 0.00 0.00 3.46
4310 5642 4.032960 ACTTGATATGGTTGTGCTTCCA 57.967 40.909 0.00 0.00 38.14 3.53
4311 5643 4.603131 ACTTGATATGGTTGTGCTTCCAT 58.397 39.130 0.00 0.00 45.10 3.41
4312 5644 5.018809 ACTTGATATGGTTGTGCTTCCATT 58.981 37.500 2.05 0.00 43.22 3.16
4313 5645 5.481473 ACTTGATATGGTTGTGCTTCCATTT 59.519 36.000 2.05 0.00 43.22 2.32
4314 5646 5.327616 TGATATGGTTGTGCTTCCATTTG 57.672 39.130 2.05 0.00 43.22 2.32
4315 5647 2.460757 ATGGTTGTGCTTCCATTTGC 57.539 45.000 0.00 0.00 41.02 3.68
4316 5648 1.117994 TGGTTGTGCTTCCATTTGCA 58.882 45.000 0.00 0.00 36.79 4.08
4317 5649 1.483827 TGGTTGTGCTTCCATTTGCAA 59.516 42.857 0.00 0.00 41.10 4.08
4318 5650 2.137523 GGTTGTGCTTCCATTTGCAAG 58.862 47.619 0.00 0.00 41.10 4.01
4319 5651 2.224018 GGTTGTGCTTCCATTTGCAAGA 60.224 45.455 0.00 0.00 41.10 3.02
4320 5652 3.054878 GTTGTGCTTCCATTTGCAAGAG 58.945 45.455 0.00 0.00 41.10 2.85
4321 5653 2.585330 TGTGCTTCCATTTGCAAGAGA 58.415 42.857 0.00 0.00 41.10 3.10
4322 5654 2.957680 TGTGCTTCCATTTGCAAGAGAA 59.042 40.909 0.00 3.61 41.10 2.87
4323 5655 3.243501 TGTGCTTCCATTTGCAAGAGAAC 60.244 43.478 0.00 0.18 41.10 3.01
4324 5656 3.005155 GTGCTTCCATTTGCAAGAGAACT 59.995 43.478 0.00 0.00 41.10 3.01
4325 5657 3.638160 TGCTTCCATTTGCAAGAGAACTT 59.362 39.130 0.00 0.00 36.15 2.66
4336 5668 3.778954 AAGAGAACTTGACCCTTCTGG 57.221 47.619 0.00 0.00 36.03 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.017442 TCGACCTTCTCTCAATCGACAT 58.983 45.455 0.00 0.00 36.92 3.06
5 6 2.093973 TGGCTTCGACCTTCTCTCAATC 60.094 50.000 0.00 0.00 0.00 2.67
10 11 0.610687 CCTTGGCTTCGACCTTCTCT 59.389 55.000 0.00 0.00 0.00 3.10
55 56 3.969250 TTCATCCTTCGCCGTGGGC 62.969 63.158 0.00 0.00 46.75 5.36
62 63 1.329906 CATGCACTCTTCATCCTTCGC 59.670 52.381 0.00 0.00 0.00 4.70
83 84 1.247567 AGTGGGAATTGAAGTTGCCG 58.752 50.000 0.00 0.00 41.97 5.69
91 92 2.224281 CCATAGCGCTAGTGGGAATTGA 60.224 50.000 25.84 4.62 0.00 2.57
103 104 1.453155 CCAACAAGTTCCATAGCGCT 58.547 50.000 17.26 17.26 0.00 5.92
124 125 0.816825 CCTGCATCGGATCCTGGTTG 60.817 60.000 10.75 1.92 0.00 3.77
135 136 1.300971 CGGGGATAATGCCTGCATCG 61.301 60.000 4.89 0.00 35.31 3.84
137 138 0.250901 GACGGGGATAATGCCTGCAT 60.251 55.000 0.00 0.00 37.83 3.96
145 146 4.097286 CCATTGTTTTTCGACGGGGATAAT 59.903 41.667 0.00 0.00 0.00 1.28
148 149 1.816224 CCATTGTTTTTCGACGGGGAT 59.184 47.619 0.00 0.00 0.00 3.85
162 163 2.354103 CGTCTGATCTGGACACCATTGT 60.354 50.000 15.72 0.00 39.32 2.71
165 167 0.176680 GCGTCTGATCTGGACACCAT 59.823 55.000 15.72 0.00 33.73 3.55
166 168 1.591703 GCGTCTGATCTGGACACCA 59.408 57.895 15.72 0.00 33.73 4.17
173 175 2.887568 GGCACGGCGTCTGATCTG 60.888 66.667 10.85 0.00 0.00 2.90
226 228 0.982704 TTGGGTGCCATTTGGAATGG 59.017 50.000 13.96 13.96 41.99 3.16
227 229 1.338960 GGTTGGGTGCCATTTGGAATG 60.339 52.381 0.00 0.00 37.39 2.67
228 230 0.983467 GGTTGGGTGCCATTTGGAAT 59.017 50.000 0.00 0.00 37.39 3.01
230 232 1.535202 GGGTTGGGTGCCATTTGGA 60.535 57.895 0.00 0.00 37.39 3.53
239 241 0.036875 GACTTCAGAGGGGTTGGGTG 59.963 60.000 0.00 0.00 0.00 4.61
240 242 1.481056 CGACTTCAGAGGGGTTGGGT 61.481 60.000 0.00 0.00 0.00 4.51
281 283 2.682594 TCATGACCTGTCATCCCCTAG 58.317 52.381 9.76 0.00 46.57 3.02
289 291 4.084011 TGACATGTTTCATGACCTGTCA 57.916 40.909 16.51 16.51 46.08 3.58
292 294 4.267536 AGGATGACATGTTTCATGACCTG 58.732 43.478 15.25 0.00 36.30 4.00
341 346 1.082756 GTTGTCGTCTTGGCAAGCG 60.083 57.895 26.82 26.82 0.00 4.68
345 350 2.970324 GGCGTTGTCGTCTTGGCA 60.970 61.111 0.00 0.00 38.74 4.92
354 359 1.626654 CGAGGATGTGTGGCGTTGTC 61.627 60.000 0.00 0.00 0.00 3.18
355 360 1.667830 CGAGGATGTGTGGCGTTGT 60.668 57.895 0.00 0.00 0.00 3.32
356 361 3.027170 GCGAGGATGTGTGGCGTTG 62.027 63.158 0.00 0.00 0.00 4.10
357 362 2.742372 GCGAGGATGTGTGGCGTT 60.742 61.111 0.00 0.00 0.00 4.84
358 363 3.529341 TTGCGAGGATGTGTGGCGT 62.529 57.895 0.00 0.00 0.00 5.68
418 430 0.391597 GGTGTCGGTCTCTTTGGTGA 59.608 55.000 0.00 0.00 0.00 4.02
470 482 3.379240 CATAACTCATGCTCTGACTCGG 58.621 50.000 0.00 0.00 0.00 4.63
502 514 1.708341 ACCTTGCATTGACTTGCCTT 58.292 45.000 0.00 0.00 42.06 4.35
507 519 3.152341 CTCCTCAACCTTGCATTGACTT 58.848 45.455 0.00 0.00 32.67 3.01
534 546 1.812922 CTCACGGCACATCAGCTCC 60.813 63.158 0.00 0.00 34.17 4.70
538 550 2.733671 CGCACTCACGGCACATCAG 61.734 63.158 0.00 0.00 0.00 2.90
541 553 2.738521 GACGCACTCACGGCACAT 60.739 61.111 0.00 0.00 42.03 3.21
574 586 3.056213 CAATTGTGGAAGGCACCCT 57.944 52.632 0.00 0.00 33.87 4.34
587 599 4.687018 CCATTGTCAATGTCACACCAATTG 59.313 41.667 21.32 0.00 37.18 2.32
596 608 1.889545 TGTCGCCATTGTCAATGTCA 58.110 45.000 21.32 12.89 37.18 3.58
603 615 1.075542 TCGTCATTGTCGCCATTGTC 58.924 50.000 0.00 0.00 0.00 3.18
610 622 0.800683 TCCGTCATCGTCATTGTCGC 60.801 55.000 0.00 0.00 35.01 5.19
615 627 0.465705 ATGCCTCCGTCATCGTCATT 59.534 50.000 0.00 0.00 35.01 2.57
616 628 0.465705 AATGCCTCCGTCATCGTCAT 59.534 50.000 0.00 0.00 35.01 3.06
633 645 0.831307 GACCTCTAAGGCCACCGAAT 59.169 55.000 5.01 0.00 39.63 3.34
636 648 0.105039 GATGACCTCTAAGGCCACCG 59.895 60.000 5.01 0.00 39.63 4.94
676 688 9.742144 ACTATACAGAATAATAGACGATGACCT 57.258 33.333 0.00 0.00 31.44 3.85
713 725 5.221165 GCACCAGCTTCAAACTAAACCTAAA 60.221 40.000 0.00 0.00 37.91 1.85
723 735 0.874390 TCATCGCACCAGCTTCAAAC 59.126 50.000 0.00 0.00 39.10 2.93
840 852 5.125367 TCAGCTCCCTCAACACTATACTA 57.875 43.478 0.00 0.00 0.00 1.82
841 853 3.982516 TCAGCTCCCTCAACACTATACT 58.017 45.455 0.00 0.00 0.00 2.12
847 859 1.200948 GCAAATCAGCTCCCTCAACAC 59.799 52.381 0.00 0.00 0.00 3.32
852 864 1.611965 AGGGCAAATCAGCTCCCTC 59.388 57.895 2.54 0.00 45.63 4.30
858 870 1.407979 CATCTCCAAGGGCAAATCAGC 59.592 52.381 0.00 0.00 0.00 4.26
859 871 1.407979 GCATCTCCAAGGGCAAATCAG 59.592 52.381 0.00 0.00 0.00 2.90
860 872 1.477553 GCATCTCCAAGGGCAAATCA 58.522 50.000 0.00 0.00 0.00 2.57
862 912 0.688749 GGGCATCTCCAAGGGCAAAT 60.689 55.000 0.00 0.00 36.21 2.32
869 919 1.626356 TTCTCGGGGGCATCTCCAAG 61.626 60.000 0.00 0.00 36.21 3.61
879 929 0.897863 TTTTGTGCCATTCTCGGGGG 60.898 55.000 0.00 0.00 0.00 5.40
968 2267 2.281208 TTGGTGACCCCGAAAGCG 60.281 61.111 0.00 0.00 35.15 4.68
969 2268 2.626780 GCTTGGTGACCCCGAAAGC 61.627 63.158 8.40 8.40 35.71 3.51
1452 2751 1.526917 CGCACCTGGGGATGAATCC 60.527 63.158 0.00 0.26 46.41 3.01
1472 2771 4.261322 GCTGAGATTTCTGCAACTTGTTGA 60.261 41.667 16.57 2.46 44.82 3.18
1570 2888 5.416083 TGGTATGTCACGAGGTTTCTTATG 58.584 41.667 0.00 0.00 0.00 1.90
1672 2991 2.851263 TGCGGATGTCAAGGTTAGTT 57.149 45.000 0.00 0.00 0.00 2.24
1699 3018 2.178273 CGGGCGCTACTTTTTGCC 59.822 61.111 7.64 0.00 46.82 4.52
1700 3019 1.134694 CTCGGGCGCTACTTTTTGC 59.865 57.895 7.64 0.00 0.00 3.68
1711 3030 0.669077 AGTCTAATACAGCTCGGGCG 59.331 55.000 0.00 0.00 44.37 6.13
1726 3045 9.771534 GATGTAAGCTTATTGGAGAAATAGTCT 57.228 33.333 9.88 0.00 40.25 3.24
1729 3048 7.872993 TCCGATGTAAGCTTATTGGAGAAATAG 59.127 37.037 9.88 0.00 33.01 1.73
1762 3081 2.014857 CTCGTCCTACTCACGGAATCA 58.985 52.381 0.00 0.00 37.85 2.57
1783 3102 6.131972 AGAAAGAGAACAGGAATGGAATGA 57.868 37.500 0.00 0.00 0.00 2.57
1788 3107 4.219288 CCCAAAGAAAGAGAACAGGAATGG 59.781 45.833 0.00 0.00 0.00 3.16
2036 3357 6.258230 TGCTCAAAAACATGAGGATTACTG 57.742 37.500 0.00 0.00 45.60 2.74
2131 3452 1.411977 TGGAGTGCCAACAAAATGGTG 59.588 47.619 0.00 0.00 42.49 4.17
2331 3652 6.012858 ACCACTATCAAAAGGTACATCAAGGA 60.013 38.462 0.00 0.00 31.32 3.36
2387 3708 5.005875 GTGCTAAAGAAATCTAAGGACGCTC 59.994 44.000 2.95 0.00 0.00 5.03
2437 3758 4.758674 CCCATACCATTAATGTGAGAGCAG 59.241 45.833 14.25 0.00 0.00 4.24
2689 4011 3.070115 TGCCCAAGCATGAAACCAT 57.930 47.368 0.00 0.00 46.52 3.55
2721 4043 1.160137 CTGCTCTCAAACTTTCGGGG 58.840 55.000 0.00 0.00 0.00 5.73
2868 4190 5.233988 GGCTCTGATTGCCTAATAGTACAG 58.766 45.833 0.00 0.00 46.38 2.74
2924 4246 3.436015 CACTCATCTTGCTCAACTCCAAG 59.564 47.826 0.00 0.00 39.74 3.61
3002 4324 1.486439 GCCAACCACACACAATTTCG 58.514 50.000 0.00 0.00 0.00 3.46
3019 4341 4.109050 TGAAAAATCACTGAAACAACGCC 58.891 39.130 0.00 0.00 0.00 5.68
3075 4397 1.135689 CGTTGCATAAAGACCACTGCC 60.136 52.381 0.00 0.00 33.70 4.85
3133 4455 0.546122 ACCTCTGCTGTGTTGGTTGA 59.454 50.000 0.00 0.00 0.00 3.18
3191 4513 8.919777 AACTACTAAAAGACTAAAACCATGCT 57.080 30.769 0.00 0.00 0.00 3.79
3232 4554 3.925913 CCTAAATTTCAAACGGCATGGTG 59.074 43.478 0.00 0.00 0.00 4.17
3233 4555 3.616317 GCCTAAATTTCAAACGGCATGGT 60.616 43.478 0.00 0.00 37.48 3.55
3249 4571 1.136828 ACCTCCGCCATATGCCTAAA 58.863 50.000 0.00 0.00 36.24 1.85
3347 4669 1.968493 GATTGCCATCCAGCATTCCAT 59.032 47.619 0.00 0.00 43.64 3.41
3375 4697 4.408694 CATGCATGCATGTTACGATATGG 58.591 43.478 40.30 19.14 46.20 2.74
3391 4713 1.135112 TCGTCGCAACTAGACATGCAT 60.135 47.619 16.14 0.00 42.68 3.96
3398 4720 2.486592 TCACATCTTCGTCGCAACTAGA 59.513 45.455 0.00 0.00 0.00 2.43
3409 4731 3.850273 GCTGCTCATTTTTCACATCTTCG 59.150 43.478 0.00 0.00 0.00 3.79
3458 4780 0.690192 TCGCTCCCACTCCATTCAAA 59.310 50.000 0.00 0.00 0.00 2.69
3474 4796 2.565841 ACAAATCTTGCCCTAGATCGC 58.434 47.619 0.00 0.00 33.81 4.58
3531 4853 2.102588 CCTACCAATTAGGGGAGTCGTG 59.897 54.545 0.00 0.00 43.71 4.35
3542 4865 1.676248 ACACCCAGCCCTACCAATTA 58.324 50.000 0.00 0.00 0.00 1.40
3561 4884 4.240888 GCTTGCGATCATCTATGCTTCTA 58.759 43.478 0.00 0.00 0.00 2.10
3613 4936 7.615403 TGCATGTCTATATAGAGGATTTGGTC 58.385 38.462 12.87 0.00 32.01 4.02
3722 5045 8.720909 TGTCATTATTAACATCAACACGTTTG 57.279 30.769 0.00 0.00 0.00 2.93
3804 5127 6.488683 ACTGGTGCTTTGCAAGTAGTATAAAA 59.511 34.615 0.00 0.00 41.47 1.52
3901 5233 0.531532 CAAGGCGGAATGCTCTCGAT 60.532 55.000 0.00 0.00 45.43 3.59
3998 5330 2.373169 ACAAGCAAGAAGAGACCCATCA 59.627 45.455 0.00 0.00 0.00 3.07
4087 5419 3.608796 TCTGATGGTGAAATTCATGCGA 58.391 40.909 0.00 0.00 0.00 5.10
4155 5487 3.198635 GGTGATCCTCATCCAGAAACTGA 59.801 47.826 0.00 0.00 32.44 3.41
4187 5519 0.322008 GGGAAGAGCTTGGTCCTGTG 60.322 60.000 10.17 0.00 0.00 3.66
4229 5561 0.968405 GCAAGGGCAATGAAGACCAA 59.032 50.000 0.00 0.00 40.05 3.67
4261 5593 1.028905 CCCTGCAAGAAACGGAAACA 58.971 50.000 0.00 0.00 34.07 2.83
4268 5600 3.801114 AAGTTGTTCCCTGCAAGAAAC 57.199 42.857 0.61 0.00 34.07 2.78
4272 5604 3.882888 TCAAGTAAGTTGTTCCCTGCAAG 59.117 43.478 0.00 0.00 37.43 4.01
4273 5605 3.892284 TCAAGTAAGTTGTTCCCTGCAA 58.108 40.909 0.00 0.00 37.43 4.08
4274 5606 3.569194 TCAAGTAAGTTGTTCCCTGCA 57.431 42.857 0.00 0.00 37.43 4.41
4275 5607 5.066505 CCATATCAAGTAAGTTGTTCCCTGC 59.933 44.000 0.00 0.00 37.43 4.85
4276 5608 6.180472 ACCATATCAAGTAAGTTGTTCCCTG 58.820 40.000 0.00 0.00 37.43 4.45
4277 5609 6.388619 ACCATATCAAGTAAGTTGTTCCCT 57.611 37.500 0.00 0.00 37.43 4.20
4278 5610 6.433093 ACAACCATATCAAGTAAGTTGTTCCC 59.567 38.462 0.00 0.00 39.15 3.97
4279 5611 7.305474 CACAACCATATCAAGTAAGTTGTTCC 58.695 38.462 3.74 0.00 39.70 3.62
4280 5612 6.801862 GCACAACCATATCAAGTAAGTTGTTC 59.198 38.462 3.74 0.00 39.70 3.18
4281 5613 6.490040 AGCACAACCATATCAAGTAAGTTGTT 59.510 34.615 3.74 0.00 39.70 2.83
4282 5614 6.003950 AGCACAACCATATCAAGTAAGTTGT 58.996 36.000 0.00 0.00 41.10 3.32
4283 5615 6.500684 AGCACAACCATATCAAGTAAGTTG 57.499 37.500 0.00 0.00 36.99 3.16
4284 5616 6.151144 GGAAGCACAACCATATCAAGTAAGTT 59.849 38.462 0.00 0.00 0.00 2.66
4285 5617 5.648092 GGAAGCACAACCATATCAAGTAAGT 59.352 40.000 0.00 0.00 0.00 2.24
4286 5618 5.647658 TGGAAGCACAACCATATCAAGTAAG 59.352 40.000 0.00 0.00 0.00 2.34
4287 5619 5.565509 TGGAAGCACAACCATATCAAGTAA 58.434 37.500 0.00 0.00 0.00 2.24
4288 5620 5.172687 TGGAAGCACAACCATATCAAGTA 57.827 39.130 0.00 0.00 0.00 2.24
4289 5621 4.032960 TGGAAGCACAACCATATCAAGT 57.967 40.909 0.00 0.00 0.00 3.16
4290 5622 5.587388 AATGGAAGCACAACCATATCAAG 57.413 39.130 0.00 0.00 44.79 3.02
4291 5623 5.722263 CAAATGGAAGCACAACCATATCAA 58.278 37.500 0.00 0.00 44.79 2.57
4292 5624 4.381825 GCAAATGGAAGCACAACCATATCA 60.382 41.667 0.00 0.00 44.79 2.15
4293 5625 4.114794 GCAAATGGAAGCACAACCATATC 58.885 43.478 0.00 0.00 44.79 1.63
4294 5626 3.514706 TGCAAATGGAAGCACAACCATAT 59.485 39.130 0.00 0.00 44.79 1.78
4295 5627 2.896044 TGCAAATGGAAGCACAACCATA 59.104 40.909 0.00 0.00 44.79 2.74
4297 5629 1.117994 TGCAAATGGAAGCACAACCA 58.882 45.000 0.00 0.00 40.57 3.67
4298 5630 2.137523 CTTGCAAATGGAAGCACAACC 58.862 47.619 0.00 0.00 41.05 3.77
4299 5631 3.054878 CTCTTGCAAATGGAAGCACAAC 58.945 45.455 9.52 0.00 42.29 3.32
4300 5632 2.957680 TCTCTTGCAAATGGAAGCACAA 59.042 40.909 9.52 0.00 42.29 3.33
4301 5633 2.585330 TCTCTTGCAAATGGAAGCACA 58.415 42.857 9.52 0.00 42.29 4.57
4302 5634 3.005155 AGTTCTCTTGCAAATGGAAGCAC 59.995 43.478 9.52 6.58 42.29 4.40
4303 5635 3.225104 AGTTCTCTTGCAAATGGAAGCA 58.775 40.909 9.52 0.00 42.29 3.91
4304 5636 3.930634 AGTTCTCTTGCAAATGGAAGC 57.069 42.857 9.52 0.00 42.29 3.86
4316 5648 3.778954 CCAGAAGGGTCAAGTTCTCTT 57.221 47.619 0.00 0.00 30.31 2.85


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

AutoCloner maintained by Alex Coulton.