Multiple sequence alignment - TraesCS3B01G475800

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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 TraesCS3B01G475800 chr3B 100.000 6020 0 0 1 6020 724736622 724742641 0.000000e+00 11117.0
1 TraesCS3B01G475800 chr3B 80.659 2761 350 107 1126 3786 732619327 732616651 0.000000e+00 1971.0
2 TraesCS3B01G475800 chr3B 83.429 525 74 10 3789 4312 732616606 732616094 5.460000e-130 475.0
3 TraesCS3B01G475800 chr3B 84.958 472 55 11 4564 5035 732615723 732615268 1.180000e-126 464.0
4 TraesCS3B01G475800 chr3B 79.412 306 48 11 4765 5064 175096909 175096613 1.020000e-47 202.0
5 TraesCS3B01G475800 chr3B 95.833 48 2 0 5732 5779 21324405 21324452 1.800000e-10 78.7
6 TraesCS3B01G475800 chr3A 94.306 4830 218 32 943 5742 684040775 684045577 0.000000e+00 7343.0
7 TraesCS3B01G475800 chr3A 81.170 2735 362 91 1126 3786 688693498 688690843 0.000000e+00 2056.0
8 TraesCS3B01G475800 chr3A 89.141 792 43 16 2 773 684039468 684040236 0.000000e+00 946.0
9 TraesCS3B01G475800 chr3A 91.294 402 29 4 951 1351 122540187 122540583 1.480000e-150 544.0
10 TraesCS3B01G475800 chr3A 91.111 405 26 6 951 1351 433768343 433767945 1.910000e-149 540.0
11 TraesCS3B01G475800 chr3A 82.659 519 77 10 3789 4306 688690798 688690292 1.190000e-121 448.0
12 TraesCS3B01G475800 chr3A 83.898 472 60 11 4564 5035 688689930 688689475 2.580000e-118 436.0
13 TraesCS3B01G475800 chr3A 91.093 247 9 3 5774 6020 684045572 684045805 7.530000e-84 322.0
14 TraesCS3B01G475800 chr3D 93.150 4394 169 51 1 4346 547297250 547301559 0.000000e+00 6325.0
15 TraesCS3B01G475800 chr3D 81.084 2749 342 100 1126 3786 552003086 552000428 0.000000e+00 2032.0
16 TraesCS3B01G475800 chr3D 93.900 1295 59 13 4453 5742 547301664 547302943 0.000000e+00 1936.0
17 TraesCS3B01G475800 chr3D 82.798 529 78 10 3789 4316 552000383 551999867 1.530000e-125 460.0
18 TraesCS3B01G475800 chr3D 84.110 472 59 10 4564 5035 551999456 551999001 5.540000e-120 442.0
19 TraesCS3B01G475800 chr3D 90.000 250 9 5 5774 6020 547302938 547303174 5.860000e-80 309.0
20 TraesCS3B01G475800 chr7D 91.119 563 44 6 4652 5210 12707764 12707204 0.000000e+00 758.0
21 TraesCS3B01G475800 chr7D 94.527 402 16 4 951 1351 85519670 85520066 3.080000e-172 616.0
22 TraesCS3B01G475800 chr6D 93.532 402 20 4 951 1351 32521951 32521555 1.440000e-165 593.0
23 TraesCS3B01G475800 chr6D 92.786 402 17 7 951 1351 65145476 65145866 6.770000e-159 571.0
24 TraesCS3B01G475800 chrUn 92.040 402 25 6 951 1351 31512450 31512055 5.270000e-155 558.0
25 TraesCS3B01G475800 chr2B 91.791 402 28 3 951 1351 765132716 765132319 6.820000e-154 555.0
26 TraesCS3B01G475800 chr1A 84.170 259 35 3 4546 4804 22935698 22935950 4.660000e-61 246.0
27 TraesCS3B01G475800 chr1A 80.142 282 41 11 4765 5040 244562253 244561981 4.760000e-46 196.0
28 TraesCS3B01G475800 chr2A 83.012 259 38 3 4546 4804 536571028 536570776 4.690000e-56 230.0
29 TraesCS3B01G475800 chr2A 97.727 44 1 0 5736 5779 373090476 373090519 6.470000e-10 76.8
30 TraesCS3B01G475800 chr4B 80.496 282 40 11 4765 5040 489161469 489161741 1.020000e-47 202.0
31 TraesCS3B01G475800 chr4B 77.778 288 42 17 2107 2385 17357155 17357429 2.250000e-34 158.0
32 TraesCS3B01G475800 chr4B 92.308 52 3 1 5728 5779 35768673 35768623 8.370000e-09 73.1
33 TraesCS3B01G475800 chr7B 79.085 306 49 11 4765 5064 665368557 665368261 4.760000e-46 196.0
34 TraesCS3B01G475800 chr5D 85.366 123 5 6 1359 1481 562973358 562973249 1.370000e-21 115.0
35 TraesCS3B01G475800 chr5B 97.778 45 1 0 5735 5779 461566625 461566669 1.800000e-10 78.7
36 TraesCS3B01G475800 chr5B 85.075 67 6 4 5715 5779 445557692 445557756 1.400000e-06 65.8
37 TraesCS3B01G475800 chr6B 97.727 44 1 0 5736 5779 3717459 3717416 6.470000e-10 76.8
38 TraesCS3B01G475800 chr6A 97.727 44 1 0 5736 5779 595647203 595647160 6.470000e-10 76.8
39 TraesCS3B01G475800 chr6A 92.308 52 3 1 5729 5779 35575711 35575762 8.370000e-09 73.1
40 TraesCS3B01G475800 chr1B 95.745 47 2 0 5733 5779 503660289 503660243 6.470000e-10 76.8


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 TraesCS3B01G475800 chr3B 724736622 724742641 6019 False 11117.000000 11117 100.000000 1 6020 1 chr3B.!!$F2 6019
1 TraesCS3B01G475800 chr3B 732615268 732619327 4059 True 970.000000 1971 83.015333 1126 5035 3 chr3B.!!$R2 3909
2 TraesCS3B01G475800 chr3A 684039468 684045805 6337 False 2870.333333 7343 91.513333 2 6020 3 chr3A.!!$F2 6018
3 TraesCS3B01G475800 chr3A 688689475 688693498 4023 True 980.000000 2056 82.575667 1126 5035 3 chr3A.!!$R2 3909
4 TraesCS3B01G475800 chr3D 547297250 547303174 5924 False 2856.666667 6325 92.350000 1 6020 3 chr3D.!!$F1 6019
5 TraesCS3B01G475800 chr3D 551999001 552003086 4085 True 978.000000 2032 82.664000 1126 5035 3 chr3D.!!$R1 3909
6 TraesCS3B01G475800 chr7D 12707204 12707764 560 True 758.000000 758 91.119000 4652 5210 1 chr7D.!!$R1 558

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
338 351 0.106217 GGAGAGGAGAGGAGGTGAGG 60.106 65.000 0.00 0.00 0.00 3.86 F
821 858 0.119358 GCCTACCCCATATCCCCTCT 59.881 60.000 0.00 0.00 0.00 3.69 F
1348 1793 0.110056 CGCGCTGAATTTGCTTGTCT 60.110 50.000 5.56 0.00 0.00 3.41 F
2548 3053 0.249826 GAGGGCTATGAGACAGCTGC 60.250 60.000 15.27 6.85 39.09 5.25 F
3176 3706 1.134560 GAGCCGTCAACTATTCCTCGT 59.865 52.381 0.00 0.00 0.00 4.18 F
4397 5214 0.108424 GCCTCTGTGCGTGAATCTCT 60.108 55.000 0.00 0.00 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 1792 0.580104 AACGAAAAACACCGCGAGAG 59.420 50.0 8.23 0.00 0.00 3.20 R
2706 3227 0.108186 AGAATGAGCCGATGCGAACA 60.108 50.0 0.00 0.00 44.33 3.18 R
3140 3670 0.179045 GCTCATCCCAACGCACCTAT 60.179 55.0 0.00 0.00 0.00 2.57 R
3683 4238 0.034670 AGGTCTGCATGAAGAAGCCC 60.035 55.0 4.49 2.56 0.00 5.19 R
4958 5815 0.248377 GTTTGCGCCATCAGCATCTC 60.248 55.0 4.18 0.00 44.74 2.75 R
5835 6719 0.308068 ATCGATACAGACAGCGACGG 59.692 55.0 0.00 0.00 35.44 4.79 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
81 82 0.109532 TCCTGACAAATCAACGCCCA 59.890 50.000 0.00 0.00 33.30 5.36
129 130 8.930846 TTAGAACACAAGTACTAGGAGTAGTT 57.069 34.615 0.00 1.63 43.17 2.24
176 177 6.477688 CCTTCTCGATTTACTTGCGGTTAATA 59.522 38.462 0.00 0.00 28.85 0.98
199 201 1.745232 TTAAATGGATCGCAACGCCT 58.255 45.000 0.00 0.00 0.00 5.52
201 203 0.676466 AAATGGATCGCAACGCCTGA 60.676 50.000 0.00 0.00 0.00 3.86
210 212 1.666553 CAACGCCTGACGGTAGCAA 60.667 57.895 0.00 0.00 42.45 3.91
211 213 1.374252 AACGCCTGACGGTAGCAAG 60.374 57.895 0.00 0.00 42.60 4.01
234 236 3.185594 TGAAACTGGCGACAATTTACTCG 59.814 43.478 0.00 0.00 40.35 4.18
323 331 9.799106 AAAATAAATGTTTTCAGAGAGAGGAGA 57.201 29.630 0.00 0.00 0.00 3.71
331 344 2.126882 CAGAGAGAGGAGAGGAGAGGA 58.873 57.143 0.00 0.00 0.00 3.71
332 345 2.105477 CAGAGAGAGGAGAGGAGAGGAG 59.895 59.091 0.00 0.00 0.00 3.69
333 346 1.421646 GAGAGAGGAGAGGAGAGGAGG 59.578 61.905 0.00 0.00 0.00 4.30
334 347 1.222567 GAGAGGAGAGGAGAGGAGGT 58.777 60.000 0.00 0.00 0.00 3.85
335 348 0.926293 AGAGGAGAGGAGAGGAGGTG 59.074 60.000 0.00 0.00 0.00 4.00
336 349 0.923358 GAGGAGAGGAGAGGAGGTGA 59.077 60.000 0.00 0.00 0.00 4.02
337 350 0.926293 AGGAGAGGAGAGGAGGTGAG 59.074 60.000 0.00 0.00 0.00 3.51
338 351 0.106217 GGAGAGGAGAGGAGGTGAGG 60.106 65.000 0.00 0.00 0.00 3.86
745 782 0.179113 CTCTCTCTCCTCCGCTTTGC 60.179 60.000 0.00 0.00 0.00 3.68
821 858 0.119358 GCCTACCCCATATCCCCTCT 59.881 60.000 0.00 0.00 0.00 3.69
826 872 1.158705 CCCATATCCCCTCTCCCGT 59.841 63.158 0.00 0.00 0.00 5.28
855 901 3.897505 CACAAAACATTTCCTTCCCCTCT 59.102 43.478 0.00 0.00 0.00 3.69
884 930 2.439701 TGCCGCTCCGCTACTACT 60.440 61.111 0.00 0.00 0.00 2.57
885 931 1.153107 TGCCGCTCCGCTACTACTA 60.153 57.895 0.00 0.00 0.00 1.82
886 932 1.282265 GCCGCTCCGCTACTACTAC 59.718 63.158 0.00 0.00 0.00 2.73
887 933 1.165284 GCCGCTCCGCTACTACTACT 61.165 60.000 0.00 0.00 0.00 2.57
888 934 0.867086 CCGCTCCGCTACTACTACTC 59.133 60.000 0.00 0.00 0.00 2.59
889 935 0.867086 CGCTCCGCTACTACTACTCC 59.133 60.000 0.00 0.00 0.00 3.85
890 936 1.540797 CGCTCCGCTACTACTACTCCT 60.541 57.143 0.00 0.00 0.00 3.69
891 937 2.145536 GCTCCGCTACTACTACTCCTC 58.854 57.143 0.00 0.00 0.00 3.71
892 938 2.224354 GCTCCGCTACTACTACTCCTCT 60.224 54.545 0.00 0.00 0.00 3.69
893 939 3.656559 CTCCGCTACTACTACTCCTCTC 58.343 54.545 0.00 0.00 0.00 3.20
894 940 3.307506 TCCGCTACTACTACTCCTCTCT 58.692 50.000 0.00 0.00 0.00 3.10
895 941 3.321682 TCCGCTACTACTACTCCTCTCTC 59.678 52.174 0.00 0.00 0.00 3.20
896 942 3.555586 CCGCTACTACTACTCCTCTCTCC 60.556 56.522 0.00 0.00 0.00 3.71
930 976 2.378634 CCTCCATCTCCCACCCCAC 61.379 68.421 0.00 0.00 0.00 4.61
933 979 2.286425 CATCTCCCACCCCACCCT 60.286 66.667 0.00 0.00 0.00 4.34
934 980 2.042930 ATCTCCCACCCCACCCTC 59.957 66.667 0.00 0.00 0.00 4.30
935 981 4.715130 TCTCCCACCCCACCCTCG 62.715 72.222 0.00 0.00 0.00 4.63
1124 1542 0.535553 TTTACCGGCGCTGGTTTTCT 60.536 50.000 43.53 22.78 43.56 2.52
1347 1792 1.668253 GCGCGCTGAATTTGCTTGTC 61.668 55.000 26.67 0.00 0.00 3.18
1348 1793 0.110056 CGCGCTGAATTTGCTTGTCT 60.110 50.000 5.56 0.00 0.00 3.41
1350 1795 1.198637 GCGCTGAATTTGCTTGTCTCT 59.801 47.619 0.00 0.00 0.00 3.10
1352 1797 2.473540 CGCTGAATTTGCTTGTCTCTCG 60.474 50.000 3.52 0.00 0.00 4.04
1353 1798 2.727298 GCTGAATTTGCTTGTCTCTCGC 60.727 50.000 0.00 0.00 0.00 5.03
1356 1801 0.320771 ATTTGCTTGTCTCTCGCGGT 60.321 50.000 6.13 0.00 0.00 5.68
1529 1979 2.124487 CAATTCCGCCCCGCCTTA 60.124 61.111 0.00 0.00 0.00 2.69
1592 2042 1.618343 TCGGTCAGCTGATTTGTCTGA 59.382 47.619 21.47 13.89 34.78 3.27
1601 2056 4.461781 AGCTGATTTGTCTGAGGGATTTTG 59.538 41.667 0.00 0.00 0.00 2.44
1602 2057 4.741342 CTGATTTGTCTGAGGGATTTTGC 58.259 43.478 0.00 0.00 0.00 3.68
1944 2416 3.841255 TGGTATGTGTCCATTCTACACCA 59.159 43.478 4.09 0.00 45.33 4.17
2236 2723 1.079405 ACGCCCCAACACATCTACG 60.079 57.895 0.00 0.00 0.00 3.51
2441 2930 2.033801 CAGGTCTGTTGCTGTTTCCTTG 59.966 50.000 0.00 0.00 0.00 3.61
2442 2931 2.092429 AGGTCTGTTGCTGTTTCCTTGA 60.092 45.455 0.00 0.00 0.00 3.02
2457 2947 4.508551 TCCTTGATCACCAGCATAACAT 57.491 40.909 0.00 0.00 0.00 2.71
2483 2988 2.863132 ACCCGGTGCTAAATGTGTTA 57.137 45.000 0.00 0.00 0.00 2.41
2530 3035 1.414919 AGCTTCGTGTTGGTGTTAGGA 59.585 47.619 0.00 0.00 0.00 2.94
2548 3053 0.249826 GAGGGCTATGAGACAGCTGC 60.250 60.000 15.27 6.85 39.09 5.25
2676 3190 7.328737 ACAAACCTAGGTATGAACATGTCTAC 58.671 38.462 16.67 1.79 0.00 2.59
2689 3203 4.621991 ACATGTCTACGGCAATCATACTC 58.378 43.478 0.00 0.00 0.00 2.59
2864 3385 2.496899 TCAGGATGAGGTTTGAAGGC 57.503 50.000 0.00 0.00 42.56 4.35
2919 3445 6.999272 TGTTGTATTTGCTTTCCCTACAAGTA 59.001 34.615 0.00 0.00 34.11 2.24
2934 3460 6.205853 CCCTACAAGTATAGTTTTGTGTGCAA 59.794 38.462 0.00 0.00 37.98 4.08
2952 3478 2.438434 GATCCCCCAACAGCACCG 60.438 66.667 0.00 0.00 0.00 4.94
2981 3508 8.868522 AGATCATTTCTAATCTGTTGTTTCCA 57.131 30.769 0.00 0.00 31.09 3.53
3111 3641 7.339721 TGTTATTTTGTACAACTTGAAGGGTGA 59.660 33.333 8.07 0.00 0.00 4.02
3129 3659 4.019174 GGTGACATGTTCATGGAGGATTT 58.981 43.478 15.71 0.00 36.32 2.17
3140 3670 5.879763 TCATGGAGGATTTCTTCTGAAACA 58.120 37.500 0.00 0.00 43.90 2.83
3173 3703 2.103263 GGATGAGCCGTCAACTATTCCT 59.897 50.000 0.00 0.00 35.88 3.36
3176 3706 1.134560 GAGCCGTCAACTATTCCTCGT 59.865 52.381 0.00 0.00 0.00 4.18
3302 3832 6.313411 CAGTTTCTCCTGAATCATCTGTTCTC 59.687 42.308 0.00 0.00 34.23 2.87
3683 4238 4.381292 GCTCAATCTTTTGGTGATTCCCAG 60.381 45.833 0.00 0.00 35.49 4.45
4041 4644 5.941647 GGGTTTAAAGTTGATACTACCAGCA 59.058 40.000 0.00 0.00 32.96 4.41
4065 4668 3.054065 CCCTTCTAACCATTTGAGCTCCT 60.054 47.826 12.15 0.00 0.00 3.69
4115 4718 2.114056 CAAATTCAAGCATCCGCATCG 58.886 47.619 0.00 0.00 42.27 3.84
4125 4728 2.536928 GCATCCGCATCGTTAACTCAAC 60.537 50.000 3.71 0.00 38.36 3.18
4134 4737 3.920446 TCGTTAACTCAACTGCAGCATA 58.080 40.909 15.27 0.00 34.77 3.14
4193 4796 3.173151 TGCTGGGACTACTGAGAATGAA 58.827 45.455 0.00 0.00 0.00 2.57
4283 4886 3.568007 GGAGTTGCACAAAGGTATTGTCA 59.432 43.478 0.00 0.00 0.00 3.58
4382 5013 6.088824 CACTTTGTCATAAATCTGTTGCCTC 58.911 40.000 0.00 0.00 0.00 4.70
4394 5211 0.166814 GTTGCCTCTGTGCGTGAATC 59.833 55.000 0.00 0.00 0.00 2.52
4396 5213 0.390340 TGCCTCTGTGCGTGAATCTC 60.390 55.000 0.00 0.00 0.00 2.75
4397 5214 0.108424 GCCTCTGTGCGTGAATCTCT 60.108 55.000 0.00 0.00 0.00 3.10
4400 5217 2.414481 CCTCTGTGCGTGAATCTCTTTG 59.586 50.000 0.00 0.00 0.00 2.77
4401 5218 3.062763 CTCTGTGCGTGAATCTCTTTGT 58.937 45.455 0.00 0.00 0.00 2.83
4403 5220 4.627058 TCTGTGCGTGAATCTCTTTGTTA 58.373 39.130 0.00 0.00 0.00 2.41
4412 5231 8.653338 GCGTGAATCTCTTTGTTACTTATGTTA 58.347 33.333 0.00 0.00 0.00 2.41
4538 5393 4.231718 TCTTGCGTTATTTGTTTGGTCC 57.768 40.909 0.00 0.00 0.00 4.46
4582 5437 1.270252 CCCATGGTTTTGCAGGTTCAC 60.270 52.381 11.73 0.00 0.00 3.18
4672 5527 7.358655 AGCTGAGCTAGACAGGATGTTTGAG 62.359 48.000 4.49 0.00 44.93 3.02
4788 5643 5.655090 GGGAGTAAGCCCTCTATCTATCTTC 59.345 48.000 0.00 0.00 45.12 2.87
4806 5663 2.073117 TCGTGCTTGCTTTGATACGA 57.927 45.000 0.00 0.00 38.10 3.43
4887 5744 3.426695 GCAACATAGTGCGCAAGATCTTT 60.427 43.478 14.00 0.00 43.02 2.52
4947 5804 1.710244 TCATCTGCCCCAAGAAAGGAA 59.290 47.619 0.00 0.00 0.00 3.36
4958 5815 3.823304 CCAAGAAAGGAAGAAGGTTCTGG 59.177 47.826 0.00 0.00 37.65 3.86
4959 5816 4.446311 CCAAGAAAGGAAGAAGGTTCTGGA 60.446 45.833 0.00 0.00 37.65 3.86
5020 5877 6.201044 CACGTCAAGCCATTTAGATAACTAGG 59.799 42.308 0.00 0.00 0.00 3.02
5061 5918 5.187621 TCCCGAATCCTTTCTATTGGTTT 57.812 39.130 0.00 0.00 0.00 3.27
5077 5934 3.734463 TGGTTTAAGCTGATGTCGTTCA 58.266 40.909 0.00 0.00 0.00 3.18
5158 6016 7.342799 AGCATGGTCACAGGATATTATTGTTTT 59.657 33.333 0.00 0.00 0.00 2.43
5267 6130 0.034059 GGCATGAGGTGAGGTATCGG 59.966 60.000 0.00 0.00 0.00 4.18
5343 6206 6.826668 TGAAGTAACTCCTGATGTCTTTTGA 58.173 36.000 0.00 0.00 0.00 2.69
5397 6260 0.467804 CAACCCAACCCAACCCTTTG 59.532 55.000 0.00 0.00 0.00 2.77
5437 6302 6.901300 TGCTAGGTAATGTAGAGAGAGAGAA 58.099 40.000 0.00 0.00 0.00 2.87
5438 6303 6.995686 TGCTAGGTAATGTAGAGAGAGAGAAG 59.004 42.308 0.00 0.00 0.00 2.85
5439 6304 7.147461 TGCTAGGTAATGTAGAGAGAGAGAAGA 60.147 40.741 0.00 0.00 0.00 2.87
5524 6396 4.278419 AGGGCCAAGATTTATTATTGTCGC 59.722 41.667 6.18 0.00 0.00 5.19
5573 6446 1.765904 CTTAGCCCTCCCTCCTCTTTC 59.234 57.143 0.00 0.00 0.00 2.62
5633 6512 4.453339 GCTAGCTAGCGTTAGTAAGTACG 58.547 47.826 28.89 0.00 39.82 3.67
5634 6513 4.025313 GCTAGCTAGCGTTAGTAAGTACGT 60.025 45.833 28.89 0.00 39.82 3.57
5635 6514 5.175856 GCTAGCTAGCGTTAGTAAGTACGTA 59.824 44.000 28.89 0.00 39.82 3.57
5736 6620 8.818141 ATATGTACGTCTGATCCTGTTTAATG 57.182 34.615 0.00 0.00 0.00 1.90
5737 6621 6.032956 TGTACGTCTGATCCTGTTTAATGT 57.967 37.500 0.00 0.00 0.00 2.71
5738 6622 7.160547 TGTACGTCTGATCCTGTTTAATGTA 57.839 36.000 0.00 0.00 0.00 2.29
5739 6623 7.031372 TGTACGTCTGATCCTGTTTAATGTAC 58.969 38.462 0.00 0.00 0.00 2.90
5740 6624 6.282199 ACGTCTGATCCTGTTTAATGTACT 57.718 37.500 0.00 0.00 0.00 2.73
5741 6625 7.400599 ACGTCTGATCCTGTTTAATGTACTA 57.599 36.000 0.00 0.00 0.00 1.82
5742 6626 7.256286 ACGTCTGATCCTGTTTAATGTACTAC 58.744 38.462 0.00 0.00 0.00 2.73
5743 6627 6.696148 CGTCTGATCCTGTTTAATGTACTACC 59.304 42.308 0.00 0.00 0.00 3.18
5744 6628 7.416438 CGTCTGATCCTGTTTAATGTACTACCT 60.416 40.741 0.00 0.00 0.00 3.08
5745 6629 7.921745 GTCTGATCCTGTTTAATGTACTACCTC 59.078 40.741 0.00 0.00 0.00 3.85
5746 6630 7.069578 TCTGATCCTGTTTAATGTACTACCTCC 59.930 40.741 0.00 0.00 0.00 4.30
5747 6631 5.587388 TCCTGTTTAATGTACTACCTCCG 57.413 43.478 0.00 0.00 0.00 4.63
5748 6632 5.018809 TCCTGTTTAATGTACTACCTCCGT 58.981 41.667 0.00 0.00 0.00 4.69
5749 6633 5.126061 TCCTGTTTAATGTACTACCTCCGTC 59.874 44.000 0.00 0.00 0.00 4.79
5750 6634 5.126707 CCTGTTTAATGTACTACCTCCGTCT 59.873 44.000 0.00 0.00 0.00 4.18
5751 6635 6.319658 CCTGTTTAATGTACTACCTCCGTCTA 59.680 42.308 0.00 0.00 0.00 2.59
5752 6636 7.325660 TGTTTAATGTACTACCTCCGTCTAG 57.674 40.000 0.00 0.00 0.00 2.43
5753 6637 6.319658 TGTTTAATGTACTACCTCCGTCTAGG 59.680 42.308 0.00 0.00 42.82 3.02
5763 6647 4.571372 CCTCCGTCTAGGTGAATAAGTC 57.429 50.000 0.00 0.00 41.99 3.01
5764 6648 3.952323 CCTCCGTCTAGGTGAATAAGTCA 59.048 47.826 0.00 0.00 41.99 3.41
5765 6649 4.585162 CCTCCGTCTAGGTGAATAAGTCAT 59.415 45.833 0.00 0.00 38.90 3.06
5766 6650 5.069251 CCTCCGTCTAGGTGAATAAGTCATT 59.931 44.000 0.00 0.00 38.90 2.57
5767 6651 6.145338 TCCGTCTAGGTGAATAAGTCATTC 57.855 41.667 0.00 0.00 40.27 2.67
5768 6652 5.655090 TCCGTCTAGGTGAATAAGTCATTCA 59.345 40.000 0.00 0.00 43.86 2.57
5849 6733 3.755628 GGCCCGTCGCTGTCTGTA 61.756 66.667 0.00 0.00 37.74 2.74
5897 6781 4.974468 CACCGTATGTGCAATCGC 57.026 55.556 0.00 0.00 38.34 4.58
5909 6793 0.179105 GCAATCGCAATGCAATCCCA 60.179 50.000 5.91 0.00 43.29 4.37
5969 6856 4.898320 TGATTTATCAGTCGGATGGATGG 58.102 43.478 0.00 0.00 36.72 3.51
5974 6861 3.510459 ATCAGTCGGATGGATGGATACA 58.490 45.455 0.00 0.00 43.71 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 9.069082 CAGCATATACAACTACTCCTAGTACTT 57.931 37.037 0.00 0.00 32.46 2.24
134 135 9.950496 ATCGAGAAGGATATAAATTAACAGCAT 57.050 29.630 0.00 0.00 0.00 3.79
176 177 4.518970 AGGCGTTGCGATCCATTTAATTAT 59.481 37.500 0.00 0.00 0.00 1.28
184 185 1.815421 GTCAGGCGTTGCGATCCAT 60.815 57.895 0.00 0.00 0.00 3.41
199 201 2.479837 CAGTTTCACTTGCTACCGTCA 58.520 47.619 0.00 0.00 0.00 4.35
201 203 1.878953 CCAGTTTCACTTGCTACCGT 58.121 50.000 0.00 0.00 0.00 4.83
204 206 1.194772 GTCGCCAGTTTCACTTGCTAC 59.805 52.381 0.00 0.00 35.00 3.58
210 212 4.134563 AGTAAATTGTCGCCAGTTTCACT 58.865 39.130 0.00 0.00 33.23 3.41
211 213 4.464112 GAGTAAATTGTCGCCAGTTTCAC 58.536 43.478 0.00 0.00 33.23 3.18
223 225 4.857588 CGTAGAGTGAAGCGAGTAAATTGT 59.142 41.667 0.00 0.00 0.00 2.71
224 226 5.093457 TCGTAGAGTGAAGCGAGTAAATTG 58.907 41.667 0.00 0.00 0.00 2.32
234 236 2.342910 TCGGTTTCGTAGAGTGAAGC 57.657 50.000 0.00 0.00 38.43 3.86
239 241 1.665161 CGTGCTTCGGTTTCGTAGAGT 60.665 52.381 0.00 0.00 36.14 3.24
294 302 9.415544 CCTCTCTCTGAAAACATTTATTTTTGG 57.584 33.333 0.00 0.00 31.90 3.28
306 314 4.340617 TCTCCTCTCCTCTCTCTGAAAAC 58.659 47.826 0.00 0.00 0.00 2.43
311 319 2.105477 CTCCTCTCCTCTCCTCTCTCTG 59.895 59.091 0.00 0.00 0.00 3.35
323 331 2.366570 GCCCTCACCTCCTCTCCT 59.633 66.667 0.00 0.00 0.00 3.69
655 676 4.379243 AAGCCGAGCCGACTGTGG 62.379 66.667 0.00 0.00 0.00 4.17
721 752 0.107410 GCGGAGGAGAGAGAGAGACA 60.107 60.000 0.00 0.00 0.00 3.41
745 782 2.101209 GAAACACACTCACCCACGCG 62.101 60.000 3.53 3.53 0.00 6.01
821 858 1.770927 TTTTGTGGGGAGGACGGGA 60.771 57.895 0.00 0.00 0.00 5.14
826 872 2.178984 AGGAAATGTTTTGTGGGGAGGA 59.821 45.455 0.00 0.00 0.00 3.71
855 901 0.818296 GAGCGGCAGTAGAAAGAGGA 59.182 55.000 1.45 0.00 0.00 3.71
884 930 1.502690 AGCGAGAGGAGAGAGGAGTA 58.497 55.000 0.00 0.00 0.00 2.59
885 931 0.623723 AAGCGAGAGGAGAGAGGAGT 59.376 55.000 0.00 0.00 0.00 3.85
886 932 1.308998 GAAGCGAGAGGAGAGAGGAG 58.691 60.000 0.00 0.00 0.00 3.69
887 933 0.106918 GGAAGCGAGAGGAGAGAGGA 60.107 60.000 0.00 0.00 0.00 3.71
888 934 1.106944 GGGAAGCGAGAGGAGAGAGG 61.107 65.000 0.00 0.00 0.00 3.69
889 935 1.106944 GGGGAAGCGAGAGGAGAGAG 61.107 65.000 0.00 0.00 0.00 3.20
890 936 1.076632 GGGGAAGCGAGAGGAGAGA 60.077 63.158 0.00 0.00 0.00 3.10
891 937 0.686112 AAGGGGAAGCGAGAGGAGAG 60.686 60.000 0.00 0.00 0.00 3.20
892 938 0.252284 AAAGGGGAAGCGAGAGGAGA 60.252 55.000 0.00 0.00 0.00 3.71
893 939 0.176910 GAAAGGGGAAGCGAGAGGAG 59.823 60.000 0.00 0.00 0.00 3.69
894 940 1.265454 GGAAAGGGGAAGCGAGAGGA 61.265 60.000 0.00 0.00 0.00 3.71
895 941 1.222113 GGAAAGGGGAAGCGAGAGG 59.778 63.158 0.00 0.00 0.00 3.69
896 942 0.176910 GAGGAAAGGGGAAGCGAGAG 59.823 60.000 0.00 0.00 0.00 3.20
1077 1483 3.159298 CCAACGAGGTGGAGGATTG 57.841 57.895 0.00 0.00 41.65 2.67
1347 1792 0.580104 AACGAAAAACACCGCGAGAG 59.420 50.000 8.23 0.00 0.00 3.20
1348 1793 1.008329 AAACGAAAAACACCGCGAGA 58.992 45.000 8.23 0.00 0.00 4.04
1350 1795 1.531470 GGAAAACGAAAAACACCGCGA 60.531 47.619 8.23 0.00 0.00 5.87
1352 1797 1.849829 CTGGAAAACGAAAAACACCGC 59.150 47.619 0.00 0.00 0.00 5.68
1353 1798 2.159352 ACCTGGAAAACGAAAAACACCG 60.159 45.455 0.00 0.00 0.00 4.94
1356 1801 3.090037 TCCACCTGGAAAACGAAAAACA 58.910 40.909 0.00 0.00 42.18 2.83
1529 1979 6.766467 ACGAACAAGTAGAAGACAATTTTCCT 59.234 34.615 0.00 0.00 0.00 3.36
1592 2042 2.362889 CCGCCTGGCAAAATCCCT 60.363 61.111 20.29 0.00 0.00 4.20
1659 2115 3.482722 TTCACGGTAGAGCTTACTTCG 57.517 47.619 0.00 0.00 0.00 3.79
1944 2416 0.767375 AAGCCCCATACGCATGATCT 59.233 50.000 0.00 0.00 33.67 2.75
2236 2723 9.661187 CTCACAATTTATAGACAGATTTGATGC 57.339 33.333 0.00 0.00 0.00 3.91
2399 2888 0.746659 GGAAAATGAAGGCATCCCCG 59.253 55.000 0.00 0.00 39.21 5.73
2441 2930 7.196331 GGTTAAGAAATGTTATGCTGGTGATC 58.804 38.462 0.00 0.00 0.00 2.92
2442 2931 6.096846 GGGTTAAGAAATGTTATGCTGGTGAT 59.903 38.462 0.00 0.00 0.00 3.06
2457 2947 4.216687 CACATTTAGCACCGGGTTAAGAAA 59.783 41.667 6.32 0.00 0.00 2.52
2530 3035 1.694133 GGCAGCTGTCTCATAGCCCT 61.694 60.000 16.64 0.00 42.07 5.19
2548 3053 0.535102 ACTGAAGAAGGCACGTTGGG 60.535 55.000 0.00 0.00 0.00 4.12
2676 3190 9.809096 ATTACATATAGAAGAGTATGATTGCCG 57.191 33.333 0.00 0.00 33.56 5.69
2703 3224 1.382522 ATGAGCCGATGCGAACAAAT 58.617 45.000 0.00 0.00 44.33 2.32
2704 3225 1.130373 GAATGAGCCGATGCGAACAAA 59.870 47.619 0.00 0.00 44.33 2.83
2705 3226 0.726827 GAATGAGCCGATGCGAACAA 59.273 50.000 0.00 0.00 44.33 2.83
2706 3227 0.108186 AGAATGAGCCGATGCGAACA 60.108 50.000 0.00 0.00 44.33 3.18
2864 3385 1.447489 CTGCTCTGGTGCCTCTTCG 60.447 63.158 0.00 0.00 0.00 3.79
2889 3410 8.861086 TGTAGGGAAAGCAAATACAACAAATAA 58.139 29.630 0.00 0.00 0.00 1.40
2890 3411 8.410673 TGTAGGGAAAGCAAATACAACAAATA 57.589 30.769 0.00 0.00 0.00 1.40
2891 3412 7.296628 TGTAGGGAAAGCAAATACAACAAAT 57.703 32.000 0.00 0.00 0.00 2.32
2892 3413 6.716934 TGTAGGGAAAGCAAATACAACAAA 57.283 33.333 0.00 0.00 0.00 2.83
2893 3414 6.322712 ACTTGTAGGGAAAGCAAATACAACAA 59.677 34.615 0.00 0.00 33.89 2.83
2919 3445 3.763897 GGGGATCTTGCACACAAAACTAT 59.236 43.478 0.00 0.00 34.74 2.12
2934 3460 2.971598 CGGTGCTGTTGGGGGATCT 61.972 63.158 0.00 0.00 0.00 2.75
2981 3508 7.253905 AGTACCAGTAAACCTACATGACAAT 57.746 36.000 0.00 0.00 0.00 2.71
3107 3637 2.787473 TCCTCCATGAACATGTCACC 57.213 50.000 12.74 0.00 39.72 4.02
3111 3641 5.651139 CAGAAGAAATCCTCCATGAACATGT 59.349 40.000 12.74 0.00 37.11 3.21
3129 3659 3.678056 ACGCACCTATGTTTCAGAAGA 57.322 42.857 0.00 0.00 0.00 2.87
3140 3670 0.179045 GCTCATCCCAACGCACCTAT 60.179 55.000 0.00 0.00 0.00 2.57
3173 3703 3.042682 AGGAGAGACTCTATCTGGACGA 58.957 50.000 4.57 0.00 38.00 4.20
3176 3706 3.788708 TCCAAGGAGAGACTCTATCTGGA 59.211 47.826 18.49 18.49 38.00 3.86
3364 3895 5.988310 TTCAAGAGCATCACATTTGGAAT 57.012 34.783 0.00 0.00 37.82 3.01
3377 3908 1.000060 GGCAGCAACATTTCAAGAGCA 60.000 47.619 0.00 0.00 0.00 4.26
3683 4238 0.034670 AGGTCTGCATGAAGAAGCCC 60.035 55.000 4.49 2.56 0.00 5.19
3987 4590 1.268079 GAAACCACTGCCTTCTCTTGC 59.732 52.381 0.00 0.00 0.00 4.01
4041 4644 2.649816 AGCTCAAATGGTTAGAAGGGGT 59.350 45.455 0.00 0.00 0.00 4.95
4065 4668 0.322366 TCGTGGATTGCAGCCATTGA 60.322 50.000 12.77 11.09 37.81 2.57
4099 4702 2.017138 TAACGATGCGGATGCTTGAA 57.983 45.000 0.00 0.00 43.34 2.69
4115 4718 4.213270 TGTGTATGCTGCAGTTGAGTTAAC 59.787 41.667 16.64 0.00 39.65 2.01
4134 4737 3.002791 CAGGAATACAATCAGCGTGTGT 58.997 45.455 0.00 0.00 0.00 3.72
4193 4796 2.631545 AGGAGCTTGCTGAATGCTTTTT 59.368 40.909 0.00 0.00 43.37 1.94
4283 4886 5.664294 TGGCATGAACATAAAGAAAGCAT 57.336 34.783 0.00 0.00 0.00 3.79
4382 5013 3.885484 AACAAAGAGATTCACGCACAG 57.115 42.857 0.00 0.00 0.00 3.66
4412 5231 9.211410 AGTATCCTGCTATATCTTGCTCATAAT 57.789 33.333 0.00 0.00 0.00 1.28
4427 5246 5.902681 GTGTGAACACATAGTATCCTGCTA 58.097 41.667 10.78 0.00 45.75 3.49
4475 5314 5.067413 CAGGATAGTGCAATTGAATTCAGCT 59.933 40.000 10.34 3.76 0.00 4.24
4538 5393 6.700520 GGGAGTATCATAAAAGTTAGTGGTCG 59.299 42.308 0.00 0.00 36.25 4.79
4551 5406 4.892934 GCAAAACCATGGGGAGTATCATAA 59.107 41.667 18.09 0.00 36.25 1.90
4672 5527 5.239306 TGAAGACATCAGTTCACCATCAAAC 59.761 40.000 0.00 0.00 33.04 2.93
4788 5643 2.495939 GTTCGTATCAAAGCAAGCACG 58.504 47.619 0.00 0.00 0.00 5.34
4806 5663 1.263217 GAAGCGGATTTGTGTGACGTT 59.737 47.619 0.00 0.00 0.00 3.99
4887 5744 3.373877 GGACCTCCTCCTTGGTGTAGATA 60.374 52.174 0.00 0.00 36.59 1.98
4947 5804 2.544721 TCAGCATCTCCAGAACCTTCT 58.455 47.619 0.00 0.00 38.25 2.85
4958 5815 0.248377 GTTTGCGCCATCAGCATCTC 60.248 55.000 4.18 0.00 44.74 2.75
4959 5816 1.805254 GTTTGCGCCATCAGCATCT 59.195 52.632 4.18 0.00 44.74 2.90
5020 5877 2.280628 GAGGCACACATACCTAGTTGC 58.719 52.381 0.00 0.00 36.05 4.17
5061 5918 2.736721 GCACTTGAACGACATCAGCTTA 59.263 45.455 0.00 0.00 0.00 3.09
5077 5934 6.006449 AGGTCAAGTAGAATTTGATGCACTT 58.994 36.000 0.00 0.00 36.96 3.16
5158 6016 5.352293 GGTGATGCGAATCATATCATAGCAA 59.648 40.000 9.89 0.00 36.69 3.91
5267 6130 1.376037 CAGGACAAAGCTCCCCGTC 60.376 63.158 0.00 0.00 0.00 4.79
5407 6270 8.998277 TCTCTCTACATTACCTAGCAAGTAAT 57.002 34.615 1.47 1.47 40.26 1.89
5632 6511 7.781548 AAATAATACAGGGTACTTGCTTACG 57.218 36.000 0.00 0.00 0.00 3.18
5634 6513 9.617523 GGTTAAATAATACAGGGTACTTGCTTA 57.382 33.333 0.00 0.00 0.00 3.09
5635 6514 7.281549 CGGTTAAATAATACAGGGTACTTGCTT 59.718 37.037 0.00 0.00 0.00 3.91
5742 6626 3.952323 TGACTTATTCACCTAGACGGAGG 59.048 47.826 0.00 0.00 42.89 4.30
5743 6627 5.776173 ATGACTTATTCACCTAGACGGAG 57.224 43.478 0.00 0.00 36.92 4.63
5744 6628 6.145338 GAATGACTTATTCACCTAGACGGA 57.855 41.667 0.00 0.00 43.79 4.69
5759 6643 9.745880 CCATTAATAGTACTACGTGAATGACTT 57.254 33.333 19.60 6.45 0.00 3.01
5760 6644 7.866393 GCCATTAATAGTACTACGTGAATGACT 59.134 37.037 19.60 0.00 0.00 3.41
5761 6645 7.866393 AGCCATTAATAGTACTACGTGAATGAC 59.134 37.037 19.60 13.21 0.00 3.06
5762 6646 7.948357 AGCCATTAATAGTACTACGTGAATGA 58.052 34.615 19.60 0.00 0.00 2.57
5763 6647 9.856488 ATAGCCATTAATAGTACTACGTGAATG 57.144 33.333 4.31 11.52 0.00 2.67
5766 6650 9.948964 TCTATAGCCATTAATAGTACTACGTGA 57.051 33.333 4.31 0.00 0.00 4.35
5768 6652 9.956640 ACTCTATAGCCATTAATAGTACTACGT 57.043 33.333 4.31 0.00 0.00 3.57
5772 6656 9.809395 TCACACTCTATAGCCATTAATAGTACT 57.191 33.333 0.00 0.00 0.00 2.73
5835 6719 0.308068 ATCGATACAGACAGCGACGG 59.692 55.000 0.00 0.00 35.44 4.79
5849 6733 2.917751 ATGCGTCCCGGGATCGAT 60.918 61.111 34.74 24.93 39.00 3.59
5895 6779 1.514657 CGTGTGGGATTGCATTGCG 60.515 57.895 3.84 0.00 0.00 4.85
5896 6780 1.806758 GCGTGTGGGATTGCATTGC 60.807 57.895 0.46 0.46 0.00 3.56
5897 6781 0.733566 GTGCGTGTGGGATTGCATTG 60.734 55.000 0.00 0.00 39.85 2.82
5898 6782 1.586028 GTGCGTGTGGGATTGCATT 59.414 52.632 0.00 0.00 39.85 3.56
5899 6783 2.689785 CGTGCGTGTGGGATTGCAT 61.690 57.895 0.00 0.00 39.85 3.96
5900 6784 3.353029 CGTGCGTGTGGGATTGCA 61.353 61.111 0.00 0.00 34.44 4.08
5909 6793 1.831389 GATCAGTTGTGCGTGCGTGT 61.831 55.000 0.00 0.00 0.00 4.49
5969 6856 2.743938 CACTGCTCCGTGGTATGTATC 58.256 52.381 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.