Multiple sequence alignment - TraesCS6A01G363500

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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 TraesCS6A01G363500 chr6A 100.000 3986 0 0 1 3986 592548355 592552340 0.000000e+00 7361
1 TraesCS6A01G363500 chr6A 85.891 1049 131 14 1319 2358 592477394 592476354 0.000000e+00 1101
2 TraesCS6A01G363500 chr6A 86.512 645 80 5 558 1200 592559252 592559891 0.000000e+00 702
3 TraesCS6A01G363500 chr6A 77.931 290 44 14 2912 3189 592539369 592539650 3.190000e-36 163
4 TraesCS6A01G363500 chr6B 95.325 3380 142 9 1 3379 673610108 673606744 0.000000e+00 5352
5 TraesCS6A01G363500 chr6B 94.715 3387 154 16 1 3379 672893024 672896393 0.000000e+00 5240
6 TraesCS6A01G363500 chr6B 96.310 2385 79 2 1 2384 672943600 672945976 0.000000e+00 3908
7 TraesCS6A01G363500 chr6B 85.640 2319 245 38 13 2284 673688369 673690646 0.000000e+00 2357
8 TraesCS6A01G363500 chr6B 85.406 2316 242 42 13 2277 672628598 672626328 0.000000e+00 2316
9 TraesCS6A01G363500 chr6B 88.375 1686 168 13 1354 3029 673544479 673542812 0.000000e+00 2002
10 TraesCS6A01G363500 chr6B 86.498 1859 183 32 1354 3175 673026053 673027880 0.000000e+00 1980
11 TraesCS6A01G363500 chr6B 85.242 1904 199 51 1321 3196 672884364 672886213 0.000000e+00 1884
12 TraesCS6A01G363500 chr6B 86.935 1217 141 9 1 1202 673545897 673544684 0.000000e+00 1351
13 TraesCS6A01G363500 chr6B 86.551 1041 119 19 1337 2362 673757586 673758620 0.000000e+00 1127
14 TraesCS6A01G363500 chr6B 89.710 758 57 11 2418 3156 672945972 672946727 0.000000e+00 948
15 TraesCS6A01G363500 chr6B 90.998 511 46 0 1 511 673024638 673025148 0.000000e+00 689
16 TraesCS6A01G363500 chr6B 86.757 370 20 9 3438 3779 672947079 672947447 6.250000e-103 385
17 TraesCS6A01G363500 chr6B 86.364 374 19 12 3438 3780 672896411 672896783 2.910000e-101 379
18 TraesCS6A01G363500 chr6B 84.496 387 23 11 3438 3788 673606726 673606341 8.200000e-92 348
19 TraesCS6A01G363500 chr6B 90.498 221 18 3 3160 3379 672946843 672947061 5.040000e-74 289
20 TraesCS6A01G363500 chr6D 95.357 3209 112 17 3 3184 445892473 445895671 0.000000e+00 5066
21 TraesCS6A01G363500 chr6D 85.708 2316 246 44 13 2284 445820859 445818585 0.000000e+00 2364
22 TraesCS6A01G363500 chr6D 87.103 1450 165 17 1376 2823 445839184 445840613 0.000000e+00 1622
23 TraesCS6A01G363500 chr6D 85.138 868 100 17 2172 3029 445911217 445912065 0.000000e+00 861
24 TraesCS6A01G363500 chr6D 83.562 584 55 14 3243 3788 445895663 445896243 3.550000e-140 508
25 TraesCS6A01G363500 chr6D 83.976 337 21 16 3255 3575 445840897 445841216 3.900000e-75 292
26 TraesCS6A01G363500 chr6D 82.736 307 34 13 3450 3739 445855420 445855724 5.110000e-64 255
27 TraesCS6A01G363500 chr6D 81.605 299 32 7 2859 3157 445840621 445840896 4.010000e-55 226
28 TraesCS6A01G363500 chr6D 79.327 208 29 9 2922 3116 445810152 445809946 2.500000e-27 134
29 TraesCS6A01G363500 chr5D 89.055 201 20 2 3787 3986 438374931 438375130 8.550000e-62 248
30 TraesCS6A01G363500 chr5B 86.538 208 20 4 3787 3986 532910862 532911069 5.180000e-54 222
31 TraesCS6A01G363500 chr2D 88.439 173 18 1 3802 3972 640364692 640364864 1.450000e-49 207
32 TraesCS6A01G363500 chr2B 88.824 170 18 1 3788 3956 637099411 637099580 1.450000e-49 207


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 TraesCS6A01G363500 chr6A 592548355 592552340 3985 False 7361.000000 7361 100.00000 1 3986 1 chr6A.!!$F2 3985
1 TraesCS6A01G363500 chr6A 592476354 592477394 1040 True 1101.000000 1101 85.89100 1319 2358 1 chr6A.!!$R1 1039
2 TraesCS6A01G363500 chr6A 592559252 592559891 639 False 702.000000 702 86.51200 558 1200 1 chr6A.!!$F3 642
3 TraesCS6A01G363500 chr6B 673606341 673610108 3767 True 2850.000000 5352 89.91050 1 3788 2 chr6B.!!$R3 3787
4 TraesCS6A01G363500 chr6B 672893024 672896783 3759 False 2809.500000 5240 90.53950 1 3780 2 chr6B.!!$F4 3779
5 TraesCS6A01G363500 chr6B 673688369 673690646 2277 False 2357.000000 2357 85.64000 13 2284 1 chr6B.!!$F2 2271
6 TraesCS6A01G363500 chr6B 672626328 672628598 2270 True 2316.000000 2316 85.40600 13 2277 1 chr6B.!!$R1 2264
7 TraesCS6A01G363500 chr6B 672884364 672886213 1849 False 1884.000000 1884 85.24200 1321 3196 1 chr6B.!!$F1 1875
8 TraesCS6A01G363500 chr6B 673542812 673545897 3085 True 1676.500000 2002 87.65500 1 3029 2 chr6B.!!$R2 3028
9 TraesCS6A01G363500 chr6B 672943600 672947447 3847 False 1382.500000 3908 90.81875 1 3779 4 chr6B.!!$F5 3778
10 TraesCS6A01G363500 chr6B 673024638 673027880 3242 False 1334.500000 1980 88.74800 1 3175 2 chr6B.!!$F6 3174
11 TraesCS6A01G363500 chr6B 673757586 673758620 1034 False 1127.000000 1127 86.55100 1337 2362 1 chr6B.!!$F3 1025
12 TraesCS6A01G363500 chr6D 445892473 445896243 3770 False 2787.000000 5066 89.45950 3 3788 2 chr6D.!!$F4 3785
13 TraesCS6A01G363500 chr6D 445818585 445820859 2274 True 2364.000000 2364 85.70800 13 2284 1 chr6D.!!$R2 2271
14 TraesCS6A01G363500 chr6D 445911217 445912065 848 False 861.000000 861 85.13800 2172 3029 1 chr6D.!!$F2 857
15 TraesCS6A01G363500 chr6D 445839184 445841216 2032 False 713.333333 1622 84.22800 1376 3575 3 chr6D.!!$F3 2199

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
35 36 0.250727 GTGCAGCCTTGGGAGTACAA 60.251 55.000 0.0 0.0 0.00 2.41 F
1017 1060 1.071857 ACCATGCTGCTCATCATCGAT 59.928 47.619 0.0 0.0 31.79 3.59 F
1469 1644 2.670934 CTTGCCACTCTTGCCGCT 60.671 61.111 0.0 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 1644 1.079197 CGCTGTGTAGGTGATGGCA 60.079 57.895 0.00 0.00 0.00 4.92 R
2018 2214 1.084370 AGAATGCCTTGTAGCGACGC 61.084 55.000 13.03 13.03 34.65 5.19 R
3331 3750 0.957395 CGCACTGGGAAGATTGCACT 60.957 55.000 0.00 0.00 34.49 4.40 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
35 36 0.250727 GTGCAGCCTTGGGAGTACAA 60.251 55.000 0.00 0.00 0.00 2.41
360 361 4.508128 CTCATGGGCGCGTACGGT 62.508 66.667 18.39 0.00 40.57 4.83
414 415 4.927782 TTCGCGGTGCTTGTGGCT 62.928 61.111 6.13 0.00 42.39 4.75
426 427 2.678190 GCTTGTGGCTATCGTCTTCCTT 60.678 50.000 0.00 0.00 38.06 3.36
483 484 3.072184 ACAAGAACTCTGATTCCAGTGCT 59.928 43.478 0.00 0.00 41.16 4.40
718 752 1.762460 ACGATTCCCGCTCCCATCT 60.762 57.895 0.00 0.00 43.32 2.90
894 937 4.590553 TGGGACAGCACTGGGGGA 62.591 66.667 2.21 0.00 34.19 4.81
1017 1060 1.071857 ACCATGCTGCTCATCATCGAT 59.928 47.619 0.00 0.00 31.79 3.59
1352 1492 4.377431 CGTAGCAACACTGTTTCTTCCATC 60.377 45.833 0.00 0.00 0.00 3.51
1469 1644 2.670934 CTTGCCACTCTTGCCGCT 60.671 61.111 0.00 0.00 0.00 5.52
1766 1941 4.724036 GCGAACAACTCCATTTACGTCATC 60.724 45.833 0.00 0.00 0.00 2.92
2018 2214 2.612221 GGTCCTCTTGTACAACTTCCCG 60.612 54.545 3.59 0.00 0.00 5.14
2321 2517 3.446570 AATTCAGCAGCTGCCGCC 61.447 61.111 34.39 8.12 43.38 6.13
2341 2537 2.379567 CCCCATCCATATCCCATGAACA 59.620 50.000 0.00 0.00 0.00 3.18
2342 2538 3.562826 CCCCATCCATATCCCATGAACAG 60.563 52.174 0.00 0.00 0.00 3.16
2343 2539 3.562826 CCCATCCATATCCCATGAACAGG 60.563 52.174 0.00 0.00 0.00 4.00
2432 2658 0.107703 TGCTAGGAATCTTGGTGGCG 60.108 55.000 0.00 0.00 0.00 5.69
2828 3057 5.084818 TGTCAATATGGTCTGATCGTTGT 57.915 39.130 0.00 0.00 0.00 3.32
2984 3234 5.199982 TGGATAAACCTGCTTCCCAATTA 57.800 39.130 0.00 0.00 39.86 1.40
3031 3283 2.903784 TCACTAGGCAGGTGTGTGTATT 59.096 45.455 9.10 0.00 36.25 1.89
3197 3615 4.092968 GCCTGAAGTACTTGTTAATCCACG 59.907 45.833 14.14 0.00 0.00 4.94
3202 3620 6.938030 TGAAGTACTTGTTAATCCACGGATTT 59.062 34.615 14.14 0.61 41.55 2.17
3238 3656 7.283354 GGTGATTCTTTCCGATCCTATTTTTCT 59.717 37.037 0.00 0.00 0.00 2.52
3241 3659 7.787725 TTCTTTCCGATCCTATTTTTCTAGC 57.212 36.000 0.00 0.00 0.00 3.42
3247 3665 5.233988 CGATCCTATTTTTCTAGCCCTGAG 58.766 45.833 0.00 0.00 0.00 3.35
3261 3679 2.838736 CCCTGAGGTATTGTCCAATCG 58.161 52.381 0.00 0.00 32.50 3.34
3267 3685 6.868864 CCTGAGGTATTGTCCAATCGTAATAG 59.131 42.308 0.00 0.00 32.50 1.73
3349 3768 0.524862 CAGTGCAATCTTCCCAGTGC 59.475 55.000 0.00 0.00 37.51 4.40
3355 3774 1.244019 AATCTTCCCAGTGCGGCAAC 61.244 55.000 3.23 0.00 0.00 4.17
3445 3879 3.186001 CGCCGTTAGTCGATAGTAGATGT 59.814 47.826 0.00 0.00 42.86 3.06
3610 4050 0.742281 GCTCCTTGCGATCTTCTGCA 60.742 55.000 0.00 0.00 39.81 4.41
3613 4053 1.699656 CCTTGCGATCTTCTGCACGG 61.700 60.000 2.29 2.29 42.94 4.94
3620 4060 1.274703 ATCTTCTGCACGGGGGACAT 61.275 55.000 0.00 0.00 0.00 3.06
3633 4073 0.675522 GGGACATCGGAAAGCGGAAA 60.676 55.000 0.00 0.00 0.00 3.13
3692 4160 1.068250 CGATTCCCGGAGAGAAGGC 59.932 63.158 0.73 0.00 33.91 4.35
3762 4242 4.859798 GTGACATTCAAAAACAAACCGTGA 59.140 37.500 0.00 0.00 0.00 4.35
3774 4254 3.111939 CCGTGAAAACCGGCAACA 58.888 55.556 0.00 0.00 38.85 3.33
3780 4260 2.093537 GAAAACCGGCAACATGGGCA 62.094 55.000 0.00 0.00 0.00 5.36
3781 4261 2.376228 AAAACCGGCAACATGGGCAC 62.376 55.000 0.00 2.96 0.00 5.01
3788 4268 0.596082 GCAACATGGGCACGTAGTTT 59.404 50.000 6.74 0.00 41.61 2.66
3789 4269 1.000717 GCAACATGGGCACGTAGTTTT 60.001 47.619 6.74 0.00 41.61 2.43
3790 4270 2.544903 GCAACATGGGCACGTAGTTTTT 60.545 45.455 6.74 0.00 41.61 1.94
3811 4291 6.811253 TTTTTAGCAACGACCATCATAACT 57.189 33.333 0.00 0.00 0.00 2.24
3812 4292 7.908827 TTTTTAGCAACGACCATCATAACTA 57.091 32.000 0.00 0.00 0.00 2.24
3813 4293 7.534085 TTTTAGCAACGACCATCATAACTAG 57.466 36.000 0.00 0.00 0.00 2.57
3814 4294 3.458189 AGCAACGACCATCATAACTAGC 58.542 45.455 0.00 0.00 0.00 3.42
3815 4295 3.133003 AGCAACGACCATCATAACTAGCT 59.867 43.478 0.00 0.00 0.00 3.32
3816 4296 3.871594 GCAACGACCATCATAACTAGCTT 59.128 43.478 0.00 0.00 0.00 3.74
3817 4297 4.332819 GCAACGACCATCATAACTAGCTTT 59.667 41.667 0.00 0.00 0.00 3.51
3818 4298 5.522460 GCAACGACCATCATAACTAGCTTTA 59.478 40.000 0.00 0.00 0.00 1.85
3819 4299 6.202954 GCAACGACCATCATAACTAGCTTTAT 59.797 38.462 0.00 0.00 0.00 1.40
3820 4300 7.254795 GCAACGACCATCATAACTAGCTTTATT 60.255 37.037 0.00 0.00 0.00 1.40
3821 4301 9.256477 CAACGACCATCATAACTAGCTTTATTA 57.744 33.333 0.00 0.00 0.00 0.98
3822 4302 9.998106 AACGACCATCATAACTAGCTTTATTAT 57.002 29.630 0.00 0.00 0.00 1.28
3823 4303 9.424319 ACGACCATCATAACTAGCTTTATTATG 57.576 33.333 13.95 13.95 37.55 1.90
3824 4304 9.639601 CGACCATCATAACTAGCTTTATTATGA 57.360 33.333 20.42 20.42 44.95 2.15
3860 4340 8.945481 AATATATCATCTATGAGCTTGCTGAC 57.055 34.615 0.00 0.00 40.64 3.51
3861 4341 3.465742 TCATCTATGAGCTTGCTGACC 57.534 47.619 0.00 0.00 32.11 4.02
3862 4342 2.767960 TCATCTATGAGCTTGCTGACCA 59.232 45.455 0.00 0.00 32.11 4.02
3863 4343 3.198417 TCATCTATGAGCTTGCTGACCAA 59.802 43.478 0.00 0.00 32.11 3.67
3864 4344 3.701205 TCTATGAGCTTGCTGACCAAA 57.299 42.857 0.00 0.00 31.94 3.28
3865 4345 4.019792 TCTATGAGCTTGCTGACCAAAA 57.980 40.909 0.00 0.00 31.94 2.44
3866 4346 4.592942 TCTATGAGCTTGCTGACCAAAAT 58.407 39.130 0.00 0.00 31.94 1.82
3867 4347 3.587797 ATGAGCTTGCTGACCAAAATG 57.412 42.857 0.00 0.00 31.94 2.32
3868 4348 2.309613 TGAGCTTGCTGACCAAAATGT 58.690 42.857 0.00 0.00 31.94 2.71
3869 4349 2.294233 TGAGCTTGCTGACCAAAATGTC 59.706 45.455 0.00 0.00 35.77 3.06
3870 4350 2.294233 GAGCTTGCTGACCAAAATGTCA 59.706 45.455 0.00 0.00 42.75 3.58
3877 4357 3.159213 TGACCAAAATGTCAGATGGCT 57.841 42.857 2.16 0.00 40.22 4.75
3878 4358 3.084039 TGACCAAAATGTCAGATGGCTC 58.916 45.455 2.16 1.40 40.22 4.70
3879 4359 2.086869 ACCAAAATGTCAGATGGCTCG 58.913 47.619 2.16 0.00 36.37 5.03
3880 4360 2.086869 CCAAAATGTCAGATGGCTCGT 58.913 47.619 0.00 0.00 0.00 4.18
3881 4361 2.159476 CCAAAATGTCAGATGGCTCGTG 60.159 50.000 0.00 0.00 0.00 4.35
3882 4362 1.089920 AAATGTCAGATGGCTCGTGC 58.910 50.000 0.00 0.00 38.76 5.34
3883 4363 0.036105 AATGTCAGATGGCTCGTGCA 60.036 50.000 12.07 0.00 41.91 4.57
3884 4364 0.036105 ATGTCAGATGGCTCGTGCAA 60.036 50.000 12.07 0.00 41.91 4.08
3885 4365 0.950555 TGTCAGATGGCTCGTGCAAC 60.951 55.000 12.07 2.07 41.91 4.17
3886 4366 1.375908 TCAGATGGCTCGTGCAACC 60.376 57.895 12.07 0.00 41.91 3.77
3887 4367 1.672030 CAGATGGCTCGTGCAACCA 60.672 57.895 12.07 0.47 41.91 3.67
3888 4368 1.073025 AGATGGCTCGTGCAACCAA 59.927 52.632 12.07 0.00 41.91 3.67
3889 4369 0.537143 AGATGGCTCGTGCAACCAAA 60.537 50.000 12.07 0.00 41.91 3.28
3890 4370 0.313672 GATGGCTCGTGCAACCAAAA 59.686 50.000 12.07 0.00 41.91 2.44
3891 4371 0.749649 ATGGCTCGTGCAACCAAAAA 59.250 45.000 12.07 0.00 41.91 1.94
3892 4372 0.102120 TGGCTCGTGCAACCAAAAAG 59.898 50.000 12.07 0.00 41.91 2.27
3893 4373 0.383949 GGCTCGTGCAACCAAAAAGA 59.616 50.000 12.07 0.00 41.91 2.52
3894 4374 1.202359 GGCTCGTGCAACCAAAAAGAA 60.202 47.619 12.07 0.00 41.91 2.52
3895 4375 2.119457 GCTCGTGCAACCAAAAAGAAG 58.881 47.619 4.26 0.00 39.41 2.85
3896 4376 2.223479 GCTCGTGCAACCAAAAAGAAGA 60.223 45.455 4.26 0.00 39.41 2.87
3897 4377 3.621794 CTCGTGCAACCAAAAAGAAGAG 58.378 45.455 0.00 0.00 0.00 2.85
3898 4378 3.275143 TCGTGCAACCAAAAAGAAGAGA 58.725 40.909 0.00 0.00 0.00 3.10
3899 4379 3.882888 TCGTGCAACCAAAAAGAAGAGAT 59.117 39.130 0.00 0.00 0.00 2.75
3900 4380 4.024048 TCGTGCAACCAAAAAGAAGAGATC 60.024 41.667 0.00 0.00 0.00 2.75
3901 4381 4.023707 CGTGCAACCAAAAAGAAGAGATCT 60.024 41.667 0.00 0.00 41.32 2.75
3932 4412 9.882996 ACAATTATTATGATTCGCTAACACATG 57.117 29.630 0.00 0.00 0.00 3.21
3935 4415 5.657470 TTATGATTCGCTAACACATGAGC 57.343 39.130 0.00 0.00 35.24 4.26
3936 4416 3.251479 TGATTCGCTAACACATGAGCT 57.749 42.857 0.00 0.00 36.50 4.09
3937 4417 2.931969 TGATTCGCTAACACATGAGCTG 59.068 45.455 0.00 0.00 36.50 4.24
3938 4418 1.078709 TTCGCTAACACATGAGCTGC 58.921 50.000 0.00 0.00 36.50 5.25
3939 4419 0.247460 TCGCTAACACATGAGCTGCT 59.753 50.000 0.00 0.00 36.50 4.24
3940 4420 1.081892 CGCTAACACATGAGCTGCTT 58.918 50.000 2.53 0.00 36.50 3.91
3941 4421 1.201998 CGCTAACACATGAGCTGCTTG 60.202 52.381 2.53 1.02 36.50 4.01
3942 4422 2.079158 GCTAACACATGAGCTGCTTGA 58.921 47.619 2.53 0.00 35.73 3.02
3943 4423 2.681848 GCTAACACATGAGCTGCTTGAT 59.318 45.455 2.53 0.00 35.73 2.57
3944 4424 3.128242 GCTAACACATGAGCTGCTTGATT 59.872 43.478 2.53 2.69 35.73 2.57
3945 4425 4.333649 GCTAACACATGAGCTGCTTGATTA 59.666 41.667 2.53 3.67 35.73 1.75
3946 4426 4.959596 AACACATGAGCTGCTTGATTAG 57.040 40.909 2.53 0.00 0.00 1.73
3958 4438 4.210832 GCTTGATTAGCGGACCAATAAC 57.789 45.455 0.00 0.00 40.71 1.89
3959 4439 3.625764 GCTTGATTAGCGGACCAATAACA 59.374 43.478 0.00 0.00 40.71 2.41
3960 4440 4.095782 GCTTGATTAGCGGACCAATAACAA 59.904 41.667 0.00 0.00 40.71 2.83
3961 4441 5.221048 GCTTGATTAGCGGACCAATAACAAT 60.221 40.000 0.00 0.00 40.71 2.71
3962 4442 5.749596 TGATTAGCGGACCAATAACAATG 57.250 39.130 0.00 0.00 0.00 2.82
3963 4443 5.189928 TGATTAGCGGACCAATAACAATGT 58.810 37.500 0.00 0.00 0.00 2.71
3964 4444 5.650266 TGATTAGCGGACCAATAACAATGTT 59.350 36.000 3.43 3.43 0.00 2.71
3965 4445 5.968528 TTAGCGGACCAATAACAATGTTT 57.031 34.783 3.17 0.00 0.00 2.83
3966 4446 7.337184 TGATTAGCGGACCAATAACAATGTTTA 59.663 33.333 3.17 0.00 0.00 2.01
3967 4447 7.633193 TTAGCGGACCAATAACAATGTTTAT 57.367 32.000 3.17 0.00 0.00 1.40
3968 4448 8.734218 TTAGCGGACCAATAACAATGTTTATA 57.266 30.769 3.17 0.00 0.00 0.98
3969 4449 7.259290 AGCGGACCAATAACAATGTTTATAG 57.741 36.000 3.17 0.00 0.00 1.31
3970 4450 7.051623 AGCGGACCAATAACAATGTTTATAGA 58.948 34.615 3.17 0.00 0.00 1.98
3971 4451 7.012044 AGCGGACCAATAACAATGTTTATAGAC 59.988 37.037 3.17 0.00 0.00 2.59
3972 4452 7.342194 CGGACCAATAACAATGTTTATAGACG 58.658 38.462 3.17 0.00 0.00 4.18
3973 4453 7.223193 CGGACCAATAACAATGTTTATAGACGA 59.777 37.037 3.17 0.00 0.00 4.20
3974 4454 8.333186 GGACCAATAACAATGTTTATAGACGAC 58.667 37.037 3.17 0.00 0.00 4.34
3975 4455 8.205131 ACCAATAACAATGTTTATAGACGACC 57.795 34.615 3.17 0.00 0.00 4.79
3976 4456 7.825270 ACCAATAACAATGTTTATAGACGACCA 59.175 33.333 3.17 0.00 0.00 4.02
3977 4457 8.836413 CCAATAACAATGTTTATAGACGACCAT 58.164 33.333 3.17 0.00 0.00 3.55
3980 4460 6.920569 ACAATGTTTATAGACGACCATTCC 57.079 37.500 0.00 0.00 0.00 3.01
3981 4461 6.650120 ACAATGTTTATAGACGACCATTCCT 58.350 36.000 0.00 0.00 0.00 3.36
3982 4462 7.788026 ACAATGTTTATAGACGACCATTCCTA 58.212 34.615 0.00 0.00 0.00 2.94
3983 4463 8.429641 ACAATGTTTATAGACGACCATTCCTAT 58.570 33.333 0.00 0.00 0.00 2.57
3984 4464 9.923143 CAATGTTTATAGACGACCATTCCTATA 57.077 33.333 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
414 415 4.885907 ACGAGGATGTAAAGGAAGACGATA 59.114 41.667 0.00 0.00 0.00 2.92
426 427 5.462530 TCAACTTGAGAACGAGGATGTAA 57.537 39.130 0.00 0.00 32.13 2.41
1352 1492 3.209410 AGTTCAGTTCAGTTTGCAGAGG 58.791 45.455 0.00 0.00 0.00 3.69
1421 1596 2.817396 GAGCGAGCCTTGTCCAGC 60.817 66.667 0.00 0.00 0.00 4.85
1469 1644 1.079197 CGCTGTGTAGGTGATGGCA 60.079 57.895 0.00 0.00 0.00 4.92
1855 2033 4.836825 CCTCTTCTCCAGCAACTGATTTA 58.163 43.478 0.00 0.00 32.44 1.40
2018 2214 1.084370 AGAATGCCTTGTAGCGACGC 61.084 55.000 13.03 13.03 34.65 5.19
2321 2517 3.562826 CCTGTTCATGGGATATGGATGGG 60.563 52.174 0.00 0.00 0.00 4.00
2341 2537 3.843619 CCTTTCTTCTTCTTCCTCCTCCT 59.156 47.826 0.00 0.00 0.00 3.69
2342 2538 3.841255 TCCTTTCTTCTTCTTCCTCCTCC 59.159 47.826 0.00 0.00 0.00 4.30
2343 2539 5.247337 TCTTCCTTTCTTCTTCTTCCTCCTC 59.753 44.000 0.00 0.00 0.00 3.71
2984 3234 2.366266 ACAAACAATGTTGGCATGCTCT 59.634 40.909 18.92 0.00 40.06 4.09
3031 3283 4.508551 ACCTTGCATAATCAGTGGATCA 57.491 40.909 0.00 0.00 31.88 2.92
3184 3602 4.804108 TGCAAAATCCGTGGATTAACAAG 58.196 39.130 14.25 4.88 43.26 3.16
3197 3615 6.645790 AGAATCACCTATCATGCAAAATCC 57.354 37.500 0.00 0.00 0.00 3.01
3202 3620 4.576053 CGGAAAGAATCACCTATCATGCAA 59.424 41.667 0.00 0.00 0.00 4.08
3238 3656 2.561209 TGGACAATACCTCAGGGCTA 57.439 50.000 0.00 0.00 35.63 3.93
3241 3659 2.170607 ACGATTGGACAATACCTCAGGG 59.829 50.000 0.00 0.00 38.88 4.45
3261 3679 8.731605 TCTCGGTCAGTGATTATCATCTATTAC 58.268 37.037 0.00 0.00 0.00 1.89
3267 3685 4.321601 CCCTCTCGGTCAGTGATTATCATC 60.322 50.000 0.00 0.00 0.00 2.92
3331 3750 0.957395 CGCACTGGGAAGATTGCACT 60.957 55.000 0.00 0.00 34.49 4.40
3333 3752 1.675310 CCGCACTGGGAAGATTGCA 60.675 57.895 0.00 0.00 34.49 4.08
3355 3774 2.031516 CCTGCAGCTGTTCGGTGAG 61.032 63.158 16.64 0.49 43.75 3.51
3419 3842 3.812166 TATCGACTAACGGCGGCGC 62.812 63.158 32.57 26.17 42.82 6.53
3420 3843 1.724929 CTATCGACTAACGGCGGCG 60.725 63.158 31.06 31.06 42.82 6.46
3445 3879 1.133761 AGCCTCTGATCCTAGCGTACA 60.134 52.381 0.00 0.00 0.00 2.90
3610 4050 2.987125 CTTTCCGATGTCCCCCGT 59.013 61.111 0.00 0.00 0.00 5.28
3613 4053 2.513897 CCGCTTTCCGATGTCCCC 60.514 66.667 0.00 0.00 40.02 4.81
3620 4060 1.671054 CTGGCTTTCCGCTTTCCGA 60.671 57.895 0.00 0.00 40.02 4.55
3670 4138 3.528370 CTCTCCGGGAATCGCCGT 61.528 66.667 0.00 0.00 37.63 5.68
3698 4166 4.069232 CGCGAGCCAGAACCAGGA 62.069 66.667 0.00 0.00 0.00 3.86
3723 4203 2.499693 TGTCACTGTCCACTCAAGACAA 59.500 45.455 0.00 0.00 43.36 3.18
3762 4242 2.136878 TGCCCATGTTGCCGGTTTT 61.137 52.632 1.90 0.00 0.00 2.43
3788 4268 6.811253 AGTTATGATGGTCGTTGCTAAAAA 57.189 33.333 0.00 0.00 0.00 1.94
3789 4269 6.036735 GCTAGTTATGATGGTCGTTGCTAAAA 59.963 38.462 0.00 0.00 0.00 1.52
3790 4270 5.522460 GCTAGTTATGATGGTCGTTGCTAAA 59.478 40.000 0.00 0.00 0.00 1.85
3791 4271 5.047847 GCTAGTTATGATGGTCGTTGCTAA 58.952 41.667 0.00 0.00 0.00 3.09
3792 4272 4.341235 AGCTAGTTATGATGGTCGTTGCTA 59.659 41.667 0.00 0.00 0.00 3.49
3793 4273 3.133003 AGCTAGTTATGATGGTCGTTGCT 59.867 43.478 0.00 0.00 0.00 3.91
3794 4274 3.458189 AGCTAGTTATGATGGTCGTTGC 58.542 45.455 0.00 0.00 0.00 4.17
3795 4275 7.715265 ATAAAGCTAGTTATGATGGTCGTTG 57.285 36.000 0.00 0.00 0.00 4.10
3796 4276 9.998106 ATAATAAAGCTAGTTATGATGGTCGTT 57.002 29.630 0.00 0.00 0.00 3.85
3797 4277 9.424319 CATAATAAAGCTAGTTATGATGGTCGT 57.576 33.333 15.34 0.00 37.79 4.34
3798 4278 9.639601 TCATAATAAAGCTAGTTATGATGGTCG 57.360 33.333 17.54 0.00 38.94 4.79
3834 4314 9.381033 GTCAGCAAGCTCATAGATGATATATTT 57.619 33.333 0.00 0.00 36.02 1.40
3835 4315 7.986320 GGTCAGCAAGCTCATAGATGATATATT 59.014 37.037 0.00 0.00 36.02 1.28
3836 4316 7.125356 TGGTCAGCAAGCTCATAGATGATATAT 59.875 37.037 0.00 0.00 36.02 0.86
3837 4317 6.438425 TGGTCAGCAAGCTCATAGATGATATA 59.562 38.462 0.00 0.00 36.02 0.86
3838 4318 5.247792 TGGTCAGCAAGCTCATAGATGATAT 59.752 40.000 0.00 0.00 36.02 1.63
3839 4319 4.590222 TGGTCAGCAAGCTCATAGATGATA 59.410 41.667 0.00 0.00 36.02 2.15
3840 4320 3.390311 TGGTCAGCAAGCTCATAGATGAT 59.610 43.478 0.00 0.00 36.02 2.45
3841 4321 2.767960 TGGTCAGCAAGCTCATAGATGA 59.232 45.455 0.00 0.00 35.16 2.92
3842 4322 3.189618 TGGTCAGCAAGCTCATAGATG 57.810 47.619 0.00 0.00 0.00 2.90
3843 4323 3.920231 TTGGTCAGCAAGCTCATAGAT 57.080 42.857 0.00 0.00 0.00 1.98
3844 4324 3.701205 TTTGGTCAGCAAGCTCATAGA 57.299 42.857 0.00 0.00 0.00 1.98
3845 4325 4.157289 ACATTTTGGTCAGCAAGCTCATAG 59.843 41.667 0.00 0.00 0.00 2.23
3846 4326 4.081406 ACATTTTGGTCAGCAAGCTCATA 58.919 39.130 0.00 0.00 0.00 2.15
3847 4327 2.895404 ACATTTTGGTCAGCAAGCTCAT 59.105 40.909 0.00 0.00 0.00 2.90
3848 4328 2.294233 GACATTTTGGTCAGCAAGCTCA 59.706 45.455 0.00 0.00 37.73 4.26
3849 4329 2.294233 TGACATTTTGGTCAGCAAGCTC 59.706 45.455 0.00 0.00 42.56 4.09
3850 4330 2.309613 TGACATTTTGGTCAGCAAGCT 58.690 42.857 0.00 0.00 42.56 3.74
3851 4331 2.798976 TGACATTTTGGTCAGCAAGC 57.201 45.000 0.00 0.00 42.56 4.01
3857 4337 3.084039 GAGCCATCTGACATTTTGGTCA 58.916 45.455 0.00 0.00 45.06 4.02
3858 4338 2.096496 CGAGCCATCTGACATTTTGGTC 59.904 50.000 0.00 0.00 38.29 4.02
3859 4339 2.086869 CGAGCCATCTGACATTTTGGT 58.913 47.619 0.00 0.00 0.00 3.67
3860 4340 2.086869 ACGAGCCATCTGACATTTTGG 58.913 47.619 0.00 0.00 0.00 3.28
3861 4341 2.730090 GCACGAGCCATCTGACATTTTG 60.730 50.000 0.00 0.00 33.58 2.44
3862 4342 1.470098 GCACGAGCCATCTGACATTTT 59.530 47.619 0.00 0.00 33.58 1.82
3863 4343 1.089920 GCACGAGCCATCTGACATTT 58.910 50.000 0.00 0.00 33.58 2.32
3864 4344 0.036105 TGCACGAGCCATCTGACATT 60.036 50.000 1.39 0.00 41.13 2.71
3865 4345 0.036105 TTGCACGAGCCATCTGACAT 60.036 50.000 1.39 0.00 41.13 3.06
3866 4346 0.950555 GTTGCACGAGCCATCTGACA 60.951 55.000 1.39 0.00 41.13 3.58
3867 4347 1.639298 GGTTGCACGAGCCATCTGAC 61.639 60.000 1.39 0.00 41.13 3.51
3868 4348 1.375908 GGTTGCACGAGCCATCTGA 60.376 57.895 1.39 0.00 41.13 3.27
3869 4349 1.236616 TTGGTTGCACGAGCCATCTG 61.237 55.000 1.39 0.00 41.13 2.90
3870 4350 0.537143 TTTGGTTGCACGAGCCATCT 60.537 50.000 1.39 0.00 41.13 2.90
3871 4351 0.313672 TTTTGGTTGCACGAGCCATC 59.686 50.000 1.39 0.00 41.13 3.51
3872 4352 0.749649 TTTTTGGTTGCACGAGCCAT 59.250 45.000 1.39 0.00 41.13 4.40
3873 4353 0.102120 CTTTTTGGTTGCACGAGCCA 59.898 50.000 1.39 0.00 41.13 4.75
3874 4354 0.383949 TCTTTTTGGTTGCACGAGCC 59.616 50.000 1.39 0.00 41.13 4.70
3875 4355 2.119457 CTTCTTTTTGGTTGCACGAGC 58.881 47.619 0.00 0.00 42.57 5.03
3876 4356 3.312421 TCTCTTCTTTTTGGTTGCACGAG 59.688 43.478 0.00 0.00 0.00 4.18
3877 4357 3.275143 TCTCTTCTTTTTGGTTGCACGA 58.725 40.909 0.00 0.00 0.00 4.35
3878 4358 3.691049 TCTCTTCTTTTTGGTTGCACG 57.309 42.857 0.00 0.00 0.00 5.34
3879 4359 5.444663 AGATCTCTTCTTTTTGGTTGCAC 57.555 39.130 0.00 0.00 0.00 4.57
3880 4360 7.765695 ATAAGATCTCTTCTTTTTGGTTGCA 57.234 32.000 0.00 0.00 42.15 4.08
3881 4361 9.561270 GTAATAAGATCTCTTCTTTTTGGTTGC 57.439 33.333 0.00 0.00 42.15 4.17
3906 4386 9.882996 CATGTGTTAGCGAATCATAATAATTGT 57.117 29.630 0.00 0.00 0.00 2.71
3909 4389 8.446273 GCTCATGTGTTAGCGAATCATAATAAT 58.554 33.333 0.00 0.00 0.00 1.28
3910 4390 7.657354 AGCTCATGTGTTAGCGAATCATAATAA 59.343 33.333 0.00 0.00 43.63 1.40
3911 4391 7.116805 CAGCTCATGTGTTAGCGAATCATAATA 59.883 37.037 0.00 0.00 43.63 0.98
3912 4392 5.994054 AGCTCATGTGTTAGCGAATCATAAT 59.006 36.000 0.00 0.00 43.63 1.28
3913 4393 5.234972 CAGCTCATGTGTTAGCGAATCATAA 59.765 40.000 0.00 0.00 43.63 1.90
3914 4394 4.746611 CAGCTCATGTGTTAGCGAATCATA 59.253 41.667 0.00 0.00 43.63 2.15
3915 4395 3.558829 CAGCTCATGTGTTAGCGAATCAT 59.441 43.478 0.00 0.00 43.63 2.45
3916 4396 2.931969 CAGCTCATGTGTTAGCGAATCA 59.068 45.455 0.00 0.00 43.63 2.57
3917 4397 2.286067 GCAGCTCATGTGTTAGCGAATC 60.286 50.000 0.00 0.00 43.63 2.52
3918 4398 1.667724 GCAGCTCATGTGTTAGCGAAT 59.332 47.619 0.00 0.00 43.63 3.34
3919 4399 1.078709 GCAGCTCATGTGTTAGCGAA 58.921 50.000 0.00 0.00 43.63 4.70
3920 4400 0.247460 AGCAGCTCATGTGTTAGCGA 59.753 50.000 0.00 0.00 43.63 4.93
3921 4401 1.081892 AAGCAGCTCATGTGTTAGCG 58.918 50.000 0.00 0.00 43.63 4.26
3922 4402 2.079158 TCAAGCAGCTCATGTGTTAGC 58.921 47.619 0.00 0.00 39.08 3.09
3923 4403 4.959596 AATCAAGCAGCTCATGTGTTAG 57.040 40.909 0.00 0.00 0.00 2.34
3925 4405 4.959596 CTAATCAAGCAGCTCATGTGTT 57.040 40.909 0.00 0.00 0.00 3.32
3938 4418 5.811399 TTGTTATTGGTCCGCTAATCAAG 57.189 39.130 0.00 0.00 0.00 3.02
3939 4419 5.650266 ACATTGTTATTGGTCCGCTAATCAA 59.350 36.000 0.00 0.00 0.00 2.57
3940 4420 5.189928 ACATTGTTATTGGTCCGCTAATCA 58.810 37.500 0.00 0.00 0.00 2.57
3941 4421 5.751243 ACATTGTTATTGGTCCGCTAATC 57.249 39.130 0.00 0.00 0.00 1.75
3942 4422 6.524101 AAACATTGTTATTGGTCCGCTAAT 57.476 33.333 1.76 0.00 0.00 1.73
3943 4423 5.968528 AAACATTGTTATTGGTCCGCTAA 57.031 34.783 1.76 0.00 0.00 3.09
3944 4424 8.205512 TCTATAAACATTGTTATTGGTCCGCTA 58.794 33.333 1.76 0.00 0.00 4.26
3945 4425 7.012044 GTCTATAAACATTGTTATTGGTCCGCT 59.988 37.037 1.76 0.00 0.00 5.52
3946 4426 7.130269 GTCTATAAACATTGTTATTGGTCCGC 58.870 38.462 1.76 0.00 0.00 5.54
3947 4427 7.223193 TCGTCTATAAACATTGTTATTGGTCCG 59.777 37.037 1.76 1.53 0.00 4.79
3948 4428 8.333186 GTCGTCTATAAACATTGTTATTGGTCC 58.667 37.037 1.76 0.00 0.00 4.46
3949 4429 8.333186 GGTCGTCTATAAACATTGTTATTGGTC 58.667 37.037 1.76 0.00 0.00 4.02
3950 4430 7.825270 TGGTCGTCTATAAACATTGTTATTGGT 59.175 33.333 1.76 0.00 0.00 3.67
3951 4431 8.203937 TGGTCGTCTATAAACATTGTTATTGG 57.796 34.615 1.76 0.00 0.00 3.16
3954 4434 9.052759 GGAATGGTCGTCTATAAACATTGTTAT 57.947 33.333 1.76 0.51 0.00 1.89
3955 4435 8.262227 AGGAATGGTCGTCTATAAACATTGTTA 58.738 33.333 1.76 0.00 0.00 2.41
3956 4436 7.110155 AGGAATGGTCGTCTATAAACATTGTT 58.890 34.615 0.00 0.00 0.00 2.83
3957 4437 6.650120 AGGAATGGTCGTCTATAAACATTGT 58.350 36.000 0.00 0.00 0.00 2.71
3958 4438 8.833231 ATAGGAATGGTCGTCTATAAACATTG 57.167 34.615 0.00 0.00 0.00 2.82


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

AutoCloner maintained by Alex Coulton.