Multiple sequence alignment - TraesCS4B01G317500

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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 TraesCS4B01G317500 chr4B 100.000 2622 0 0 1 2622 607289077 607286456 0.000000e+00 4843.0
1 TraesCS4B01G317500 chr4B 89.759 166 17 0 16 181 607288963 607288798 2.040000e-51 213.0
2 TraesCS4B01G317500 chr4B 89.759 166 17 0 115 280 607289062 607288897 2.040000e-51 213.0
3 TraesCS4B01G317500 chr4B 93.798 129 8 0 20 148 607288926 607288798 7.400000e-46 195.0
4 TraesCS4B01G317500 chr4B 93.798 129 8 0 152 280 607289058 607288930 7.400000e-46 195.0
5 TraesCS4B01G317500 chr4D 87.387 1443 70 35 152 1557 479963234 479961867 0.000000e+00 1554.0
6 TraesCS4B01G317500 chr4D 92.527 1017 33 17 1642 2620 479961866 479960855 0.000000e+00 1417.0
7 TraesCS4B01G317500 chr4D 91.892 148 12 0 1 148 479963253 479963106 9.510000e-50 207.0
8 TraesCS4B01G317500 chr4D 91.667 132 11 0 78 209 479963242 479963111 1.600000e-42 183.0
9 TraesCS4B01G317500 chr4D 94.118 68 4 0 10 77 479963178 479963111 1.280000e-18 104.0
10 TraesCS4B01G317500 chr4A 83.951 648 32 23 1756 2350 686384657 686384029 2.950000e-154 555.0
11 TraesCS4B01G317500 chr4A 92.182 307 24 0 2316 2622 686384029 686383723 4.010000e-118 435.0
12 TraesCS4B01G317500 chr4A 79.727 587 71 34 905 1470 686385704 686385145 5.300000e-102 381.0
13 TraesCS4B01G317500 chr4A 88.710 310 25 8 202 501 641601657 641601966 1.150000e-98 370.0
14 TraesCS4B01G317500 chr4A 83.598 189 13 3 2014 2200 641610154 641610326 7.510000e-36 161.0
15 TraesCS4B01G317500 chr6B 80.678 590 78 19 894 1470 674935334 674935900 2.410000e-115 425.0
16 TraesCS4B01G317500 chr6B 90.000 150 8 4 1868 2014 674936260 674936405 1.240000e-43 187.0
17 TraesCS4B01G317500 chr6B 98.000 50 1 0 2150 2199 674935105 674935154 1.290000e-13 87.9
18 TraesCS4B01G317500 chr6B 91.935 62 5 0 2013 2074 674936490 674936551 1.290000e-13 87.9
19 TraesCS4B01G317500 chr2B 81.781 494 65 12 894 1373 572586369 572586851 8.800000e-105 390.0
20 TraesCS4B01G317500 chr2B 79.626 481 66 19 897 1360 701491107 701490642 1.510000e-82 316.0
21 TraesCS4B01G317500 chr2B 89.147 129 13 1 2006 2133 572585825 572585953 2.700000e-35 159.0
22 TraesCS4B01G317500 chr2B 87.288 118 5 5 2136 2243 572587450 572587567 2.740000e-25 126.0
23 TraesCS4B01G317500 chr5B 79.923 518 72 15 894 1392 441446515 441446011 4.150000e-93 351.0
24 TraesCS4B01G317500 chr5B 80.272 441 56 16 947 1371 448804033 448803608 1.180000e-78 303.0
25 TraesCS4B01G317500 chr5B 82.166 157 12 11 1982 2131 441441886 441441739 1.270000e-23 121.0
26 TraesCS4B01G317500 chr5B 100.000 28 0 0 2175 2202 441446676 441446649 5.000000e-03 52.8
27 TraesCS4B01G317500 chr2D 80.882 476 65 17 897 1361 582495018 582494558 4.150000e-93 351.0
28 TraesCS4B01G317500 chr2D 80.444 450 48 19 932 1362 488229100 488229528 9.120000e-80 307.0
29 TraesCS4B01G317500 chr2D 92.157 51 4 0 2156 2206 582495248 582495198 3.620000e-09 73.1
30 TraesCS4B01G317500 chr5A 79.310 493 59 22 894 1373 474537706 474537244 3.280000e-79 305.0
31 TraesCS4B01G317500 chr5A 92.025 163 10 3 2040 2199 474537999 474537837 2.630000e-55 226.0
32 TraesCS4B01G317500 chr5A 84.579 214 19 7 1996 2202 456492539 456492333 1.590000e-47 200.0
33 TraesCS4B01G317500 chr6A 88.942 208 19 4 1868 2074 593354534 593354738 1.200000e-63 254.0
34 TraesCS4B01G317500 chr5D 86.449 214 15 7 1996 2202 371441355 371441149 3.400000e-54 222.0
35 TraesCS4B01G317500 chr6D 89.167 120 7 4 1959 2074 446490610 446490727 7.560000e-31 145.0


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 TraesCS4B01G317500 chr4B 607286456 607289077 2621 True 1131.80 4843 93.422800 1 2622 5 chr4B.!!$R1 2621
1 TraesCS4B01G317500 chr4D 479960855 479963253 2398 True 693.00 1554 91.518200 1 2620 5 chr4D.!!$R1 2619
2 TraesCS4B01G317500 chr4A 686383723 686385704 1981 True 457.00 555 85.286667 905 2622 3 chr4A.!!$R1 1717
3 TraesCS4B01G317500 chr2B 572585825 572587567 1742 False 225.00 390 86.072000 894 2243 3 chr2B.!!$F1 1349
4 TraesCS4B01G317500 chr5B 441446011 441446676 665 True 201.90 351 89.961500 894 2202 2 chr5B.!!$R3 1308
5 TraesCS4B01G317500 chr2D 582494558 582495248 690 True 212.05 351 86.519500 897 2206 2 chr2D.!!$R1 1309
6 TraesCS4B01G317500 chr5A 474537244 474537999 755 True 265.50 305 85.667500 894 2199 2 chr5A.!!$R2 1305

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
694 712 0.031994 CCCTTTCCGTTTGCACTTGG 59.968 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2398 3015 0.319211 CCGTACGAGTGCTTGGTTGA 60.319 55.0 18.76 0.0 0.0 3.18 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
92 93 1.071567 GCCTTGAGCGTCGTGTACTC 61.072 60.000 0.00 0.00 0.00 2.59
93 94 0.456312 CCTTGAGCGTCGTGTACTCC 60.456 60.000 0.00 0.00 0.00 3.85
94 95 0.456312 CTTGAGCGTCGTGTACTCCC 60.456 60.000 0.00 0.00 0.00 4.30
95 96 1.870055 TTGAGCGTCGTGTACTCCCC 61.870 60.000 0.00 0.00 0.00 4.81
96 97 3.392595 GAGCGTCGTGTACTCCCCG 62.393 68.421 0.00 0.00 0.00 5.73
97 98 4.487412 GCGTCGTGTACTCCCCGG 62.487 72.222 0.00 0.00 0.00 5.73
99 100 4.139234 GTCGTGTACTCCCCGGCC 62.139 72.222 0.00 0.00 0.00 6.13
121 122 4.309950 GGGCCTTGGTCGTCGTGT 62.310 66.667 0.84 0.00 0.00 4.49
122 123 2.652530 GGCCTTGGTCGTCGTGTA 59.347 61.111 0.00 0.00 0.00 2.90
123 124 1.735559 GGCCTTGGTCGTCGTGTAC 60.736 63.158 0.00 0.00 0.00 2.90
126 127 0.453950 CCTTGGTCGTCGTGTACTCG 60.454 60.000 10.97 10.97 0.00 4.18
127 128 1.063951 CTTGGTCGTCGTGTACTCGC 61.064 60.000 12.30 7.00 0.00 5.03
128 129 2.202401 GGTCGTCGTGTACTCGCC 60.202 66.667 12.30 0.00 0.00 5.54
129 130 2.572647 GTCGTCGTGTACTCGCCG 60.573 66.667 13.81 13.81 33.62 6.46
130 131 3.792047 TCGTCGTGTACTCGCCGG 61.792 66.667 18.73 0.00 33.18 6.13
155 156 2.047274 GGCCTTGCTCGCAGTGTA 60.047 61.111 0.00 0.00 0.00 2.90
156 157 2.391389 GGCCTTGCTCGCAGTGTAC 61.391 63.158 0.00 0.00 0.00 2.90
220 221 4.681978 GGGCCTTGAGCGTCGTGT 62.682 66.667 0.84 0.00 45.17 4.49
221 222 2.260434 GGCCTTGAGCGTCGTGTA 59.740 61.111 0.00 0.00 45.17 2.90
222 223 2.092882 GGCCTTGAGCGTCGTGTAC 61.093 63.158 0.00 0.00 45.17 2.90
223 224 1.080705 GCCTTGAGCGTCGTGTACT 60.081 57.895 0.00 0.00 0.00 2.73
224 225 1.071567 GCCTTGAGCGTCGTGTACTC 61.072 60.000 0.00 0.00 0.00 2.59
226 227 1.328439 CTTGAGCGTCGTGTACTCAC 58.672 55.000 0.47 0.00 40.03 3.51
227 228 0.039798 TTGAGCGTCGTGTACTCACC 60.040 55.000 0.47 0.00 40.03 4.02
228 229 1.511464 GAGCGTCGTGTACTCACCG 60.511 63.158 0.00 0.00 41.09 4.94
229 230 2.503375 GCGTCGTGTACTCACCGG 60.503 66.667 0.00 0.00 41.09 5.28
230 231 2.503375 CGTCGTGTACTCACCGGC 60.503 66.667 0.00 0.00 41.09 6.13
232 233 3.740397 TCGTGTACTCACCGGCCG 61.740 66.667 21.04 21.04 41.09 6.13
251 252 4.681978 GTGGGCCTTGCTCGTCGT 62.682 66.667 4.53 0.00 0.00 4.34
252 253 4.680237 TGGGCCTTGCTCGTCGTG 62.680 66.667 4.53 0.00 0.00 4.35
253 254 4.681978 GGGCCTTGCTCGTCGTGT 62.682 66.667 0.84 0.00 0.00 4.49
254 255 2.260434 GGCCTTGCTCGTCGTGTA 59.740 61.111 0.00 0.00 0.00 2.90
255 256 2.092882 GGCCTTGCTCGTCGTGTAC 61.093 63.158 0.00 0.00 0.00 2.90
256 257 1.080705 GCCTTGCTCGTCGTGTACT 60.081 57.895 0.00 0.00 0.00 2.73
257 258 1.071567 GCCTTGCTCGTCGTGTACTC 61.072 60.000 0.00 0.00 0.00 2.59
259 260 1.396543 CTTGCTCGTCGTGTACTCGC 61.397 60.000 12.30 7.00 0.00 5.03
260 261 2.576317 GCTCGTCGTGTACTCGCC 60.576 66.667 12.30 0.00 0.00 5.54
262 263 3.713615 CTCGTCGTGTACTCGCCGG 62.714 68.421 18.73 0.00 33.18 6.13
264 265 4.409218 GTCGTGTACTCGCCGGCA 62.409 66.667 28.98 12.94 0.00 5.69
265 266 4.111016 TCGTGTACTCGCCGGCAG 62.111 66.667 28.98 23.74 0.00 4.85
417 418 3.160047 AGCATGGCCTCCTCCTCG 61.160 66.667 3.32 0.00 0.00 4.63
474 475 1.450312 CGCTCCCTTGGTGTCCATC 60.450 63.158 0.00 0.00 31.53 3.51
515 517 4.187694 GGCTTGGTAGAGAGATCAAAGTG 58.812 47.826 0.00 0.00 0.00 3.16
516 518 4.187694 GCTTGGTAGAGAGATCAAAGTGG 58.812 47.826 0.00 0.00 0.00 4.00
517 519 3.895232 TGGTAGAGAGATCAAAGTGGC 57.105 47.619 0.00 0.00 0.00 5.01
519 521 2.501723 GGTAGAGAGATCAAAGTGGCCA 59.498 50.000 0.00 0.00 0.00 5.36
522 524 4.104383 AGAGAGATCAAAGTGGCCAAAA 57.896 40.909 7.24 0.00 0.00 2.44
523 525 4.473444 AGAGAGATCAAAGTGGCCAAAAA 58.527 39.130 7.24 0.00 0.00 1.94
545 547 3.477210 AAAGGATGCTAGGGAATCGAC 57.523 47.619 0.00 0.00 0.00 4.20
555 557 1.064611 AGGGAATCGACCGAGAAGAGA 60.065 52.381 0.00 0.00 0.00 3.10
558 560 2.359531 GGAATCGACCGAGAAGAGATGT 59.640 50.000 0.00 0.00 0.00 3.06
565 567 4.614764 CGACCGAGAAGAGATGTGGATATG 60.615 50.000 0.00 0.00 0.00 1.78
613 629 3.443588 GCAGGGGCGTTTTCTTGT 58.556 55.556 0.00 0.00 0.00 3.16
614 630 1.285950 GCAGGGGCGTTTTCTTGTC 59.714 57.895 0.00 0.00 0.00 3.18
618 635 1.574702 GGGGCGTTTTCTTGTCGAGG 61.575 60.000 0.00 0.00 0.00 4.63
626 643 3.753294 TTTCTTGTCGAGGAGAAAGCT 57.247 42.857 15.49 0.00 37.06 3.74
660 677 1.677552 GGGACAAGGAAGAAGCGGA 59.322 57.895 0.00 0.00 0.00 5.54
680 698 1.893919 GAGGACGAGCAGCTCCCTTT 61.894 60.000 18.45 3.24 0.00 3.11
694 712 0.031994 CCCTTTCCGTTTGCACTTGG 59.968 55.000 0.00 0.00 0.00 3.61
698 716 2.570415 TTCCGTTTGCACTTGGGATA 57.430 45.000 0.00 0.00 0.00 2.59
703 722 4.080807 TCCGTTTGCACTTGGGATAAGATA 60.081 41.667 0.00 0.00 0.00 1.98
712 731 7.663081 TGCACTTGGGATAAGATAATCTTCATC 59.337 37.037 0.00 0.00 37.89 2.92
739 761 7.640240 CGATCAGAAAAGAAAAGAGTTCGTTTT 59.360 33.333 0.00 0.80 32.01 2.43
742 764 9.550811 TCAGAAAAGAAAAGAGTTCGTTTTTAC 57.449 29.630 2.38 0.00 32.01 2.01
743 765 9.556030 CAGAAAAGAAAAGAGTTCGTTTTTACT 57.444 29.630 2.38 0.00 32.01 2.24
749 771 9.597170 AGAAAAGAGTTCGTTTTTACTACTTCT 57.403 29.630 0.00 0.00 0.00 2.85
750 772 9.634300 GAAAAGAGTTCGTTTTTACTACTTCTG 57.366 33.333 0.00 0.00 0.00 3.02
751 773 8.937634 AAAGAGTTCGTTTTTACTACTTCTGA 57.062 30.769 0.00 0.00 0.00 3.27
752 774 9.543783 AAAGAGTTCGTTTTTACTACTTCTGAT 57.456 29.630 0.00 0.00 0.00 2.90
753 775 8.745464 AGAGTTCGTTTTTACTACTTCTGATC 57.255 34.615 0.00 0.00 0.00 2.92
754 776 7.813627 AGAGTTCGTTTTTACTACTTCTGATCC 59.186 37.037 0.00 0.00 0.00 3.36
755 777 6.585322 AGTTCGTTTTTACTACTTCTGATCCG 59.415 38.462 0.00 0.00 0.00 4.18
756 778 6.258230 TCGTTTTTACTACTTCTGATCCGA 57.742 37.500 0.00 0.00 0.00 4.55
757 779 6.680810 TCGTTTTTACTACTTCTGATCCGAA 58.319 36.000 0.00 0.00 0.00 4.30
758 780 6.583806 TCGTTTTTACTACTTCTGATCCGAAC 59.416 38.462 0.00 0.00 0.00 3.95
759 781 6.585322 CGTTTTTACTACTTCTGATCCGAACT 59.415 38.462 0.00 0.00 0.00 3.01
760 782 7.201333 CGTTTTTACTACTTCTGATCCGAACTC 60.201 40.741 0.00 0.00 0.00 3.01
761 783 5.831702 TTACTACTTCTGATCCGAACTCC 57.168 43.478 0.00 0.00 0.00 3.85
762 784 3.698289 ACTACTTCTGATCCGAACTCCA 58.302 45.455 0.00 0.00 0.00 3.86
763 785 4.087182 ACTACTTCTGATCCGAACTCCAA 58.913 43.478 0.00 0.00 0.00 3.53
764 786 4.527038 ACTACTTCTGATCCGAACTCCAAA 59.473 41.667 0.00 0.00 0.00 3.28
765 787 3.931578 ACTTCTGATCCGAACTCCAAAG 58.068 45.455 0.00 0.00 0.00 2.77
766 788 3.325135 ACTTCTGATCCGAACTCCAAAGT 59.675 43.478 0.00 0.00 37.32 2.66
767 789 3.319137 TCTGATCCGAACTCCAAAGTG 57.681 47.619 0.00 0.00 35.36 3.16
768 790 2.632996 TCTGATCCGAACTCCAAAGTGT 59.367 45.455 0.00 0.00 35.36 3.55
785 807 2.035576 AGTGTTACTTCCTCGTGTGGTC 59.964 50.000 0.00 0.00 0.00 4.02
808 830 9.353999 GGTCAATTTGTGTTCTTATCCAATTAC 57.646 33.333 0.00 0.00 0.00 1.89
856 878 3.306433 GGGACGCTCTCTTTCTCTTTCTT 60.306 47.826 0.00 0.00 0.00 2.52
857 879 4.311606 GGACGCTCTCTTTCTCTTTCTTT 58.688 43.478 0.00 0.00 0.00 2.52
858 880 4.387559 GGACGCTCTCTTTCTCTTTCTTTC 59.612 45.833 0.00 0.00 0.00 2.62
859 881 4.311606 ACGCTCTCTTTCTCTTTCTTTCC 58.688 43.478 0.00 0.00 0.00 3.13
860 882 4.202264 ACGCTCTCTTTCTCTTTCTTTCCA 60.202 41.667 0.00 0.00 0.00 3.53
861 883 4.752101 CGCTCTCTTTCTCTTTCTTTCCAA 59.248 41.667 0.00 0.00 0.00 3.53
862 884 5.107143 CGCTCTCTTTCTCTTTCTTTCCAAG 60.107 44.000 0.00 0.00 0.00 3.61
863 885 5.762711 GCTCTCTTTCTCTTTCTTTCCAAGT 59.237 40.000 0.00 0.00 0.00 3.16
864 886 6.262049 GCTCTCTTTCTCTTTCTTTCCAAGTT 59.738 38.462 0.00 0.00 0.00 2.66
865 887 7.519809 GCTCTCTTTCTCTTTCTTTCCAAGTTC 60.520 40.741 0.00 0.00 0.00 3.01
866 888 7.569240 TCTCTTTCTCTTTCTTTCCAAGTTCT 58.431 34.615 0.00 0.00 0.00 3.01
867 889 8.049721 TCTCTTTCTCTTTCTTTCCAAGTTCTT 58.950 33.333 0.00 0.00 0.00 2.52
868 890 8.581253 TCTTTCTCTTTCTTTCCAAGTTCTTT 57.419 30.769 0.00 0.00 0.00 2.52
869 891 8.678199 TCTTTCTCTTTCTTTCCAAGTTCTTTC 58.322 33.333 0.00 0.00 0.00 2.62
870 892 6.944234 TCTCTTTCTTTCCAAGTTCTTTCC 57.056 37.500 0.00 0.00 0.00 3.13
933 958 0.951040 GCTTCCTCCACAAGACACGG 60.951 60.000 0.00 0.00 0.00 4.94
995 1030 0.527385 CCACCAAAGCAACACAACCG 60.527 55.000 0.00 0.00 0.00 4.44
998 1033 0.249405 CCAAAGCAACACAACCGCAT 60.249 50.000 0.00 0.00 0.00 4.73
1068 1113 1.137872 CTTTCGGGACCTGATGGAGAG 59.862 57.143 3.15 0.00 37.04 3.20
1276 1366 1.571773 CCGACCCCATCCCCTTCTTT 61.572 60.000 0.00 0.00 0.00 2.52
1339 1435 0.514255 CGTCCGTCGAGTCACACTAA 59.486 55.000 0.00 0.00 42.86 2.24
1343 1439 2.159612 TCCGTCGAGTCACACTAAATCG 60.160 50.000 0.00 0.00 34.80 3.34
1347 1443 2.481568 TCGAGTCACACTAAATCGTCGT 59.518 45.455 0.00 0.00 35.05 4.34
1349 1445 2.839026 GAGTCACACTAAATCGTCGTCG 59.161 50.000 0.00 0.00 38.55 5.12
1387 1495 7.631933 AGATGGCCTATCGTTACTACTACTAT 58.368 38.462 3.32 0.00 40.86 2.12
1429 1537 4.224370 GGATCACTAGTTGGTTGGGTCTTA 59.776 45.833 0.00 0.00 0.00 2.10
1484 1594 8.038351 TCGTCATTATGTTCAAGTCTGGATTAA 58.962 33.333 0.00 0.00 0.00 1.40
1485 1595 8.664798 CGTCATTATGTTCAAGTCTGGATTAAA 58.335 33.333 0.00 0.00 0.00 1.52
1516 1626 8.739972 AGGAACTGTATATTGTGGATTTTTGAC 58.260 33.333 0.00 0.00 37.18 3.18
1601 2030 5.874810 CACTTTGTATTCCCTTCTCGATTCA 59.125 40.000 0.00 0.00 0.00 2.57
1608 2037 9.109393 TGTATTCCCTTCTCGATTCAAATAAAG 57.891 33.333 0.00 0.00 0.00 1.85
1669 2157 9.547753 GAATTCCTAAGATGTGCACTTTATCTA 57.452 33.333 19.41 3.25 31.30 1.98
1677 2167 8.743085 AGATGTGCACTTTATCTATCAAACAT 57.257 30.769 19.41 0.00 29.82 2.71
1702 2192 6.490566 TTTCGCTGGTTTTCTAATCCTAAC 57.509 37.500 0.00 0.00 0.00 2.34
1730 2223 3.836562 AGGGTTAAACAGGACGTATGTCT 59.163 43.478 14.61 0.00 44.83 3.41
1738 2231 3.769844 ACAGGACGTATGTCTCTCCAATT 59.230 43.478 14.61 0.00 44.83 2.32
1745 2247 6.507900 ACGTATGTCTCTCCAATTCTATGTG 58.492 40.000 0.00 0.00 0.00 3.21
1793 2297 0.389948 ATCCAACGCCTCGACTGTTC 60.390 55.000 0.00 0.00 0.00 3.18
1804 2308 2.971915 CTCGACTGTTCAACGAGTGTAC 59.028 50.000 0.00 0.00 45.23 2.90
1812 2316 5.802064 TGTTCAACGAGTGTACAAATCAAC 58.198 37.500 0.00 0.88 34.88 3.18
1830 2358 5.135508 TCAACGTTTGTTTCCCAGAAAAA 57.864 34.783 0.00 0.00 35.72 1.94
1924 2465 9.424319 TGTGAAGATCCTATCGCTAATAATTTC 57.576 33.333 0.00 0.00 0.00 2.17
1925 2466 9.424319 GTGAAGATCCTATCGCTAATAATTTCA 57.576 33.333 0.00 0.00 0.00 2.69
1940 2481 7.454260 AATAATTTCAACAACCTCAGGAGAC 57.546 36.000 0.00 0.00 0.00 3.36
1941 2482 2.930826 TTCAACAACCTCAGGAGACC 57.069 50.000 0.00 0.00 0.00 3.85
2105 2652 3.895232 ACATACATGACTGGACTGACC 57.105 47.619 0.00 0.00 39.54 4.02
2367 2984 0.251209 TCCTGTGCCGACTGTAGTCT 60.251 55.000 10.05 0.00 42.66 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.511464 GTACACGACGCTCAGGACG 60.511 63.158 0.00 0.00 0.00 4.79
70 71 4.379243 CACGACGCTCAAGGCCCT 62.379 66.667 0.00 0.00 37.74 5.19
104 105 2.934570 TACACGACGACCAAGGCCC 61.935 63.158 0.00 0.00 0.00 5.80
106 107 0.731855 GAGTACACGACGACCAAGGC 60.732 60.000 0.00 0.00 0.00 4.35
107 108 0.453950 CGAGTACACGACGACCAAGG 60.454 60.000 6.90 0.00 35.09 3.61
108 109 1.063951 GCGAGTACACGACGACCAAG 61.064 60.000 17.12 0.00 35.09 3.61
109 110 1.081906 GCGAGTACACGACGACCAA 60.082 57.895 17.12 0.00 35.09 3.67
110 111 2.557805 GCGAGTACACGACGACCA 59.442 61.111 17.12 0.00 35.09 4.02
137 138 3.605749 TACACTGCGAGCAAGGCCC 62.606 63.158 0.00 0.00 0.00 5.80
138 139 2.047274 TACACTGCGAGCAAGGCC 60.047 61.111 0.00 0.00 0.00 5.19
139 140 1.355066 GAGTACACTGCGAGCAAGGC 61.355 60.000 0.00 0.00 0.00 4.35
142 143 1.733041 GCGAGTACACTGCGAGCAA 60.733 57.895 0.00 0.00 0.00 3.91
143 144 2.126463 GCGAGTACACTGCGAGCA 60.126 61.111 0.00 0.00 0.00 4.26
144 145 2.881352 GGCGAGTACACTGCGAGC 60.881 66.667 0.00 0.00 0.00 5.03
146 147 4.111016 CCGGCGAGTACACTGCGA 62.111 66.667 9.30 0.00 0.00 5.10
203 204 3.291101 TACACGACGCTCAAGGCCC 62.291 63.158 0.00 0.00 37.74 5.80
204 205 2.092882 GTACACGACGCTCAAGGCC 61.093 63.158 0.00 0.00 37.74 5.19
205 206 1.071567 GAGTACACGACGCTCAAGGC 61.072 60.000 0.00 0.00 37.64 4.35
206 207 0.240145 TGAGTACACGACGCTCAAGG 59.760 55.000 0.00 0.00 36.46 3.61
207 208 1.328439 GTGAGTACACGACGCTCAAG 58.672 55.000 4.75 0.00 40.40 3.02
208 209 0.039798 GGTGAGTACACGACGCTCAA 60.040 55.000 4.75 0.00 46.77 3.02
209 210 1.577922 GGTGAGTACACGACGCTCA 59.422 57.895 0.00 0.00 46.77 4.26
211 212 2.559840 CGGTGAGTACACGACGCT 59.440 61.111 0.00 0.00 46.77 5.07
212 213 2.503375 CCGGTGAGTACACGACGC 60.503 66.667 0.00 0.00 46.77 5.19
213 214 2.503375 GCCGGTGAGTACACGACG 60.503 66.667 1.90 0.00 46.77 5.12
214 215 2.126189 GGCCGGTGAGTACACGAC 60.126 66.667 1.90 0.00 46.77 4.34
234 235 4.681978 ACGACGAGCAAGGCCCAC 62.682 66.667 0.00 0.00 0.00 4.61
235 236 4.680237 CACGACGAGCAAGGCCCA 62.680 66.667 0.00 0.00 0.00 5.36
236 237 3.291101 TACACGACGAGCAAGGCCC 62.291 63.158 0.00 0.00 0.00 5.80
237 238 2.092882 GTACACGACGAGCAAGGCC 61.093 63.158 0.00 0.00 0.00 5.19
238 239 1.071567 GAGTACACGACGAGCAAGGC 61.072 60.000 0.00 0.00 0.00 4.35
239 240 0.793478 CGAGTACACGACGAGCAAGG 60.793 60.000 6.90 0.00 35.09 3.61
240 241 1.396543 GCGAGTACACGACGAGCAAG 61.397 60.000 17.12 0.00 36.01 4.01
241 242 1.441515 GCGAGTACACGACGAGCAA 60.442 57.895 17.12 0.00 36.01 3.91
243 244 2.576317 GGCGAGTACACGACGAGC 60.576 66.667 17.12 0.00 35.47 5.03
247 248 4.409218 TGCCGGCGAGTACACGAC 62.409 66.667 23.90 13.03 38.00 4.34
268 269 4.479993 CCTCAAGAGCCAGGCCCG 62.480 72.222 8.22 0.00 0.00 6.13
462 463 1.354337 CGAGTGCGATGGACACCAAG 61.354 60.000 0.00 0.00 40.82 3.61
523 525 4.200092 GTCGATTCCCTAGCATCCTTTTT 58.800 43.478 0.00 0.00 0.00 1.94
525 527 2.104963 GGTCGATTCCCTAGCATCCTTT 59.895 50.000 0.00 0.00 0.00 3.11
526 528 1.694696 GGTCGATTCCCTAGCATCCTT 59.305 52.381 0.00 0.00 0.00 3.36
528 530 0.038159 CGGTCGATTCCCTAGCATCC 60.038 60.000 0.00 0.00 0.00 3.51
529 531 0.959553 TCGGTCGATTCCCTAGCATC 59.040 55.000 0.00 0.00 0.00 3.91
545 547 3.616076 GCCATATCCACATCTCTTCTCGG 60.616 52.174 0.00 0.00 0.00 4.63
555 557 0.887836 CGCAGCAGCCATATCCACAT 60.888 55.000 0.00 0.00 37.52 3.21
558 560 2.111669 CCGCAGCAGCCATATCCA 59.888 61.111 0.00 0.00 37.52 3.41
660 677 2.757917 GGGAGCTGCTCGTCCTCT 60.758 66.667 22.25 0.00 32.90 3.69
680 698 2.039216 TCTTATCCCAAGTGCAAACGGA 59.961 45.455 0.00 0.00 0.00 4.69
694 712 8.690884 TCTGATCGGATGAAGATTATCTTATCC 58.309 37.037 20.81 20.81 36.73 2.59
698 716 9.270640 CTTTTCTGATCGGATGAAGATTATCTT 57.729 33.333 17.26 7.23 39.87 2.40
703 722 7.928307 TTTCTTTTCTGATCGGATGAAGATT 57.072 32.000 21.97 0.00 0.00 2.40
712 731 5.177696 ACGAACTCTTTTCTTTTCTGATCGG 59.822 40.000 0.00 0.00 0.00 4.18
739 761 5.258841 TGGAGTTCGGATCAGAAGTAGTAA 58.741 41.667 14.82 0.68 34.24 2.24
742 764 4.720649 TTGGAGTTCGGATCAGAAGTAG 57.279 45.455 14.82 0.00 34.24 2.57
743 765 4.527038 ACTTTGGAGTTCGGATCAGAAGTA 59.473 41.667 14.82 0.00 34.24 2.24
744 766 3.325135 ACTTTGGAGTTCGGATCAGAAGT 59.675 43.478 14.77 14.77 36.57 3.01
745 767 3.681897 CACTTTGGAGTTCGGATCAGAAG 59.318 47.826 8.65 0.00 32.54 2.85
746 768 3.071023 ACACTTTGGAGTTCGGATCAGAA 59.929 43.478 4.00 4.00 32.54 3.02
747 769 2.632996 ACACTTTGGAGTTCGGATCAGA 59.367 45.455 0.00 0.00 32.54 3.27
748 770 3.045601 ACACTTTGGAGTTCGGATCAG 57.954 47.619 0.00 0.00 32.54 2.90
749 771 3.485463 AACACTTTGGAGTTCGGATCA 57.515 42.857 0.00 0.00 32.54 2.92
750 772 4.566987 AGTAACACTTTGGAGTTCGGATC 58.433 43.478 0.00 0.00 32.54 3.36
751 773 4.618920 AGTAACACTTTGGAGTTCGGAT 57.381 40.909 0.00 0.00 32.54 4.18
752 774 4.374399 GAAGTAACACTTTGGAGTTCGGA 58.626 43.478 0.00 0.00 38.80 4.55
753 775 3.497262 GGAAGTAACACTTTGGAGTTCGG 59.503 47.826 0.00 0.00 38.80 4.30
754 776 4.377897 AGGAAGTAACACTTTGGAGTTCG 58.622 43.478 0.00 0.00 38.80 3.95
755 777 4.448060 CGAGGAAGTAACACTTTGGAGTTC 59.552 45.833 0.00 0.00 38.80 3.01
756 778 4.141779 ACGAGGAAGTAACACTTTGGAGTT 60.142 41.667 0.00 0.00 38.80 3.01
757 779 3.387050 ACGAGGAAGTAACACTTTGGAGT 59.613 43.478 0.00 0.00 38.80 3.85
758 780 3.741344 CACGAGGAAGTAACACTTTGGAG 59.259 47.826 0.00 0.00 38.80 3.86
759 781 3.133362 ACACGAGGAAGTAACACTTTGGA 59.867 43.478 0.00 0.00 38.80 3.53
760 782 3.247648 CACACGAGGAAGTAACACTTTGG 59.752 47.826 0.00 0.00 38.80 3.28
761 783 3.247648 CCACACGAGGAAGTAACACTTTG 59.752 47.826 0.00 0.00 38.80 2.77
762 784 3.118519 ACCACACGAGGAAGTAACACTTT 60.119 43.478 0.00 0.00 38.80 2.66
763 785 2.433239 ACCACACGAGGAAGTAACACTT 59.567 45.455 0.00 0.00 41.95 3.16
764 786 2.035576 GACCACACGAGGAAGTAACACT 59.964 50.000 0.00 0.00 0.00 3.55
765 787 2.223876 TGACCACACGAGGAAGTAACAC 60.224 50.000 0.00 0.00 0.00 3.32
766 788 2.033372 TGACCACACGAGGAAGTAACA 58.967 47.619 0.00 0.00 0.00 2.41
767 789 2.806608 TGACCACACGAGGAAGTAAC 57.193 50.000 0.00 0.00 0.00 2.50
768 790 4.345859 AATTGACCACACGAGGAAGTAA 57.654 40.909 0.00 0.00 0.00 2.24
808 830 6.485830 TGTGAACCTCCTCTTGGATAATAG 57.514 41.667 0.00 0.00 42.29 1.73
812 834 3.056107 CGTTGTGAACCTCCTCTTGGATA 60.056 47.826 0.00 0.00 42.29 2.59
813 835 2.289694 CGTTGTGAACCTCCTCTTGGAT 60.290 50.000 0.00 0.00 42.29 3.41
814 836 1.070134 CGTTGTGAACCTCCTCTTGGA 59.930 52.381 0.00 0.00 40.69 3.53
815 837 1.512926 CGTTGTGAACCTCCTCTTGG 58.487 55.000 0.00 0.00 0.00 3.61
816 838 1.512926 CCGTTGTGAACCTCCTCTTG 58.487 55.000 0.00 0.00 0.00 3.02
821 843 1.666872 CGTCCCGTTGTGAACCTCC 60.667 63.158 0.00 0.00 0.00 4.30
828 850 0.600255 AAAGAGAGCGTCCCGTTGTG 60.600 55.000 0.00 0.00 0.00 3.33
856 878 3.206639 AGGGGAAAGGAAAGAACTTGGAA 59.793 43.478 0.00 0.00 0.00 3.53
857 879 2.789399 AGGGGAAAGGAAAGAACTTGGA 59.211 45.455 0.00 0.00 0.00 3.53
858 880 3.244887 AGGGGAAAGGAAAGAACTTGG 57.755 47.619 0.00 0.00 0.00 3.61
859 881 4.986783 AGTAGGGGAAAGGAAAGAACTTG 58.013 43.478 0.00 0.00 0.00 3.16
860 882 4.043059 GGAGTAGGGGAAAGGAAAGAACTT 59.957 45.833 0.00 0.00 0.00 2.66
861 883 3.587951 GGAGTAGGGGAAAGGAAAGAACT 59.412 47.826 0.00 0.00 0.00 3.01
862 884 3.329814 TGGAGTAGGGGAAAGGAAAGAAC 59.670 47.826 0.00 0.00 0.00 3.01
863 885 3.604787 TGGAGTAGGGGAAAGGAAAGAA 58.395 45.455 0.00 0.00 0.00 2.52
864 886 3.285290 TGGAGTAGGGGAAAGGAAAGA 57.715 47.619 0.00 0.00 0.00 2.52
865 887 3.330998 ACTTGGAGTAGGGGAAAGGAAAG 59.669 47.826 0.00 0.00 0.00 2.62
866 888 3.329814 GACTTGGAGTAGGGGAAAGGAAA 59.670 47.826 0.00 0.00 0.00 3.13
867 889 2.910977 GACTTGGAGTAGGGGAAAGGAA 59.089 50.000 0.00 0.00 0.00 3.36
868 890 2.547990 GACTTGGAGTAGGGGAAAGGA 58.452 52.381 0.00 0.00 0.00 3.36
869 891 1.560146 GGACTTGGAGTAGGGGAAAGG 59.440 57.143 0.00 0.00 0.00 3.11
870 892 2.266279 TGGACTTGGAGTAGGGGAAAG 58.734 52.381 0.00 0.00 0.00 2.62
923 945 3.637273 GGGGAGGCCGTGTCTTGT 61.637 66.667 0.00 0.00 0.00 3.16
933 958 2.237392 CCTACTTATATGCAGGGGAGGC 59.763 54.545 0.00 0.00 0.00 4.70
966 994 3.886550 CTTTGGTGGGCAGGGGGTC 62.887 68.421 0.00 0.00 0.00 4.46
967 995 3.914713 CTTTGGTGGGCAGGGGGT 61.915 66.667 0.00 0.00 0.00 4.95
975 1003 0.179086 GGTTGTGTTGCTTTGGTGGG 60.179 55.000 0.00 0.00 0.00 4.61
995 1030 3.313750 GACGATGTCGCTGGATGC 58.686 61.111 1.77 0.00 44.43 3.91
1028 1069 1.131315 GCTGAGATCGAAAACTTGCCC 59.869 52.381 0.00 0.00 0.00 5.36
1030 1071 3.820777 AAGCTGAGATCGAAAACTTGC 57.179 42.857 0.00 0.00 0.00 4.01
1068 1113 4.785453 CCACCGGAGCCTCCTTGC 62.785 72.222 9.46 0.00 33.30 4.01
1101 1146 3.358076 GACTCCTTCTCCGGCACCG 62.358 68.421 1.02 1.02 39.44 4.94
1102 1147 2.579738 GACTCCTTCTCCGGCACC 59.420 66.667 0.00 0.00 0.00 5.01
1103 1148 2.182030 CGACTCCTTCTCCGGCAC 59.818 66.667 0.00 0.00 0.00 5.01
1163 1253 1.301293 GGTCCTTGGCCTTCTCCAG 59.699 63.158 3.32 0.00 37.44 3.86
1333 1429 1.195448 ACGACGACGACGATTTAGTGT 59.805 47.619 25.15 0.00 42.66 3.55
1347 1443 0.919300 CATCTAGACGACGACGACGA 59.081 55.000 25.15 3.20 42.66 4.20
1349 1445 0.316032 GCCATCTAGACGACGACGAC 60.316 60.000 15.32 8.08 42.66 4.34
1387 1495 9.604569 AGTGATCCTCATAGAGTAGTAGTAGTA 57.395 37.037 0.00 0.00 0.00 1.82
1412 1520 8.631480 ACTAAAAATAAGACCCAACCAACTAG 57.369 34.615 0.00 0.00 0.00 2.57
1450 1559 6.472486 ACTTGAACATAATGACGACGATACAG 59.528 38.462 0.00 0.00 0.00 2.74
1484 1594 7.016153 TCCACAATATACAGTTCCTCAAGTT 57.984 36.000 0.00 0.00 0.00 2.66
1485 1595 6.620877 TCCACAATATACAGTTCCTCAAGT 57.379 37.500 0.00 0.00 0.00 3.16
1523 1633 8.869897 TGTTCGACATAATCACTTGACTAATTC 58.130 33.333 0.00 0.00 0.00 2.17
1585 1994 8.581253 AACTTTATTTGAATCGAGAAGGGAAT 57.419 30.769 0.00 0.00 0.00 3.01
1608 2037 7.010023 CAGACGCTCTAAAAACAATCTGTAAC 58.990 38.462 0.00 0.00 0.00 2.50
1618 2048 3.863041 AGGATCCAGACGCTCTAAAAAC 58.137 45.455 15.82 0.00 0.00 2.43
1622 2052 4.470602 TCATAAGGATCCAGACGCTCTAA 58.529 43.478 15.82 0.00 0.00 2.10
1628 2058 5.220710 AGGAATTCATAAGGATCCAGACG 57.779 43.478 15.82 0.00 32.47 4.18
1629 2059 7.967908 TCTTAGGAATTCATAAGGATCCAGAC 58.032 38.462 29.67 1.13 39.78 3.51
1669 2157 6.924111 AGAAAACCAGCGAAATATGTTTGAT 58.076 32.000 0.00 0.00 0.00 2.57
1675 2163 7.264373 AGGATTAGAAAACCAGCGAAATATG 57.736 36.000 0.00 0.00 0.00 1.78
1677 2167 7.010738 CGTTAGGATTAGAAAACCAGCGAAATA 59.989 37.037 0.00 0.00 0.00 1.40
1702 2192 2.285977 GTCCTGTTTAACCCTATGGCG 58.714 52.381 0.00 0.00 33.59 5.69
1730 2223 7.918076 AGGACTAAAACACATAGAATTGGAGA 58.082 34.615 0.00 0.00 0.00 3.71
1738 2231 6.614694 TGCCTTAGGACTAAAACACATAGA 57.385 37.500 0.69 0.00 0.00 1.98
1745 2247 4.519350 ACTGCTTTGCCTTAGGACTAAAAC 59.481 41.667 0.69 0.00 0.00 2.43
1793 2297 4.446857 ACGTTGATTTGTACACTCGTTG 57.553 40.909 0.00 0.00 0.00 4.10
1804 2308 4.677584 TCTGGGAAACAAACGTTGATTTG 58.322 39.130 13.16 5.58 43.81 2.32
1830 2358 3.874392 GCAATTGCAGGTCTACCATTT 57.126 42.857 25.36 0.00 41.59 2.32
1924 2465 2.638480 TTGGTCTCCTGAGGTTGTTG 57.362 50.000 0.00 0.00 0.00 3.33
1925 2466 3.662759 TTTTGGTCTCCTGAGGTTGTT 57.337 42.857 0.00 0.00 0.00 2.83
1951 2492 1.193874 CTGGTTCGTTCGTTTGCTACC 59.806 52.381 0.00 0.00 0.00 3.18
1953 2494 2.512485 TCTGGTTCGTTCGTTTGCTA 57.488 45.000 0.00 0.00 0.00 3.49
2105 2652 2.819608 TGGCCCTTCATTCTTTTTCTCG 59.180 45.455 0.00 0.00 0.00 4.04
2395 3012 1.798813 GTACGAGTGCTTGGTTGAAGG 59.201 52.381 0.00 0.00 31.56 3.46
2398 3015 0.319211 CCGTACGAGTGCTTGGTTGA 60.319 55.000 18.76 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.