Multiple sequence alignment - TraesCS3B01G466500

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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 TraesCS3B01G466500 chr3B 100.000 5014 0 0 1 5014 708949606 708954619 0.000000e+00 9260.0
1 TraesCS3B01G466500 chr3B 93.427 715 43 4 3411 4123 709073628 709074340 0.000000e+00 1057.0
2 TraesCS3B01G466500 chr3B 92.727 715 48 4 3411 4123 709267817 709268529 0.000000e+00 1029.0
3 TraesCS3B01G466500 chr3B 94.436 665 26 5 4115 4778 709268559 709269213 0.000000e+00 1013.0
4 TraesCS3B01G466500 chr3B 92.982 684 22 8 4115 4797 709074370 709075028 0.000000e+00 974.0
5 TraesCS3B01G466500 chr3B 86.895 496 48 9 1216 1697 231984100 231983608 1.590000e-149 540.0
6 TraesCS3B01G466500 chr3B 86.299 489 49 9 1224 1697 230929290 230928805 2.680000e-142 516.0
7 TraesCS3B01G466500 chr3B 97.297 222 2 1 4797 5014 709075060 709075281 1.700000e-99 374.0
8 TraesCS3B01G466500 chr3B 86.944 337 20 6 4461 4781 790629958 790630286 1.720000e-94 357.0
9 TraesCS3B01G466500 chr3B 87.097 217 14 6 4803 5014 709269325 709269532 3.020000e-57 233.0
10 TraesCS3B01G466500 chr3B 91.057 123 11 0 1043 1165 231984449 231984327 3.100000e-37 167.0
11 TraesCS3B01G466500 chr3B 94.118 102 6 0 1043 1144 230929692 230929591 6.720000e-34 156.0
12 TraesCS3B01G466500 chr3D 95.736 2439 83 10 1702 4123 536436563 536438997 0.000000e+00 3908.0
13 TraesCS3B01G466500 chr3D 86.320 1769 127 54 1 1701 536434805 536436526 0.000000e+00 1820.0
14 TraesCS3B01G466500 chr3D 92.384 709 49 5 3416 4123 536588296 536589000 0.000000e+00 1005.0
15 TraesCS3B01G466500 chr3D 92.319 703 50 4 3416 4117 536878808 536879507 0.000000e+00 996.0
16 TraesCS3B01G466500 chr3D 92.102 709 51 5 3416 4123 536666650 536667354 0.000000e+00 994.0
17 TraesCS3B01G466500 chr3D 90.288 659 33 10 4115 4762 536439060 536439698 0.000000e+00 833.0
18 TraesCS3B01G466500 chr3D 88.705 664 36 17 4115 4762 536879539 536880179 0.000000e+00 774.0
19 TraesCS3B01G466500 chr3D 88.060 670 35 15 4115 4762 536589026 536589672 0.000000e+00 752.0
20 TraesCS3B01G466500 chr3D 88.281 640 43 12 4164 4781 536787354 536787983 0.000000e+00 737.0
21 TraesCS3B01G466500 chr3D 87.294 669 40 15 4115 4762 536667380 536668024 0.000000e+00 723.0
22 TraesCS3B01G466500 chr3D 92.105 228 16 2 3844 4069 536880034 536880261 2.250000e-83 320.0
23 TraesCS3B01G466500 chr3D 90.987 233 14 4 3844 4069 536667879 536668111 1.750000e-79 307.0
24 TraesCS3B01G466500 chr3D 90.798 163 12 3 1837 1998 415924999 415925159 1.090000e-51 215.0
25 TraesCS3B01G466500 chr3D 84.916 179 21 3 4840 5014 536880594 536880770 5.160000e-40 176.0
26 TraesCS3B01G466500 chr3D 84.358 179 21 5 4840 5014 536440116 536440291 8.630000e-38 169.0
27 TraesCS3B01G466500 chr3D 84.358 179 21 5 4840 5014 536511874 536512049 8.630000e-38 169.0
28 TraesCS3B01G466500 chr3D 83.240 179 23 5 4840 5014 536590090 536590265 1.870000e-34 158.0
29 TraesCS3B01G466500 chr3A 95.650 1839 71 9 2228 4063 672085981 672087813 0.000000e+00 2944.0
30 TraesCS3B01G466500 chr3A 87.365 1757 142 38 3 1701 672083594 672085328 0.000000e+00 1941.0
31 TraesCS3B01G466500 chr3A 93.837 503 27 3 1702 2203 672085369 672085868 0.000000e+00 754.0
32 TraesCS3B01G466500 chr3A 90.856 514 26 10 4170 4671 672088272 672088776 0.000000e+00 669.0
33 TraesCS3B01G466500 chr3A 85.350 157 13 6 1376 1530 575152152 575152004 2.420000e-33 154.0
34 TraesCS3B01G466500 chr7B 87.834 337 17 9 4461 4781 500217390 500217718 1.700000e-99 374.0
35 TraesCS3B01G466500 chr7B 84.416 154 9 5 1377 1530 365873815 365873953 2.430000e-28 137.0
36 TraesCS3B01G466500 chr7B 94.805 77 4 0 1930 2006 153179516 153179592 2.450000e-23 121.0
37 TraesCS3B01G466500 chr7B 93.478 46 3 0 1554 1599 69169413 69169368 9.010000e-08 69.4
38 TraesCS3B01G466500 chrUn 89.967 299 13 3 4477 4762 359851617 359851911 2.200000e-98 370.0
39 TraesCS3B01G466500 chrUn 90.000 220 20 2 3416 3635 348740510 348740293 2.950000e-72 283.0
40 TraesCS3B01G466500 chrUn 90.000 220 20 2 3416 3635 364369462 364369245 2.950000e-72 283.0
41 TraesCS3B01G466500 chrUn 84.358 179 21 5 4840 5014 404927185 404927010 8.630000e-38 169.0
42 TraesCS3B01G466500 chrUn 83.799 179 22 5 4840 5014 359852329 359852504 4.020000e-36 163.0
43 TraesCS3B01G466500 chrUn 83.799 179 22 5 4840 5014 466164025 466164200 4.020000e-36 163.0
44 TraesCS3B01G466500 chr5B 88.272 324 14 8 4461 4768 233905312 233904997 2.850000e-97 366.0
45 TraesCS3B01G466500 chr5D 91.018 167 14 1 1840 2006 426994724 426994559 1.820000e-54 224.0
46 TraesCS3B01G466500 chr1A 90.588 170 15 1 1837 2006 75110915 75111083 1.820000e-54 224.0
47 TraesCS3B01G466500 chr2A 89.820 167 16 1 1840 2006 482751674 482751509 3.930000e-51 213.0
48 TraesCS3B01G466500 chr7D 86.452 155 15 3 1376 1530 573300691 573300543 1.120000e-36 165.0
49 TraesCS3B01G466500 chr2B 84.828 145 12 5 1386 1530 73074833 73074699 2.430000e-28 137.0
50 TraesCS3B01G466500 chr2B 96.078 51 1 1 4239 4289 512626564 512626515 1.160000e-11 82.4
51 TraesCS3B01G466500 chr4B 93.506 77 5 0 1930 2006 619173300 619173376 1.140000e-21 115.0
52 TraesCS3B01G466500 chr4B 92.208 77 6 0 1930 2006 9819302 9819378 5.310000e-20 110.0
53 TraesCS3B01G466500 chr4D 80.645 155 16 7 1376 1530 210024100 210024240 1.910000e-19 108.0
54 TraesCS3B01G466500 chr4D 100.000 41 0 0 1554 1594 210024238 210024278 5.380000e-10 76.8
55 TraesCS3B01G466500 chr2D 94.737 38 2 0 1376 1413 524269039 524269076 5.420000e-05 60.2


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 TraesCS3B01G466500 chr3B 708949606 708954619 5013 False 9260.000000 9260 100.000000 1 5014 1 chr3B.!!$F1 5013
1 TraesCS3B01G466500 chr3B 709073628 709075281 1653 False 801.666667 1057 94.568667 3411 5014 3 chr3B.!!$F3 1603
2 TraesCS3B01G466500 chr3B 709267817 709269532 1715 False 758.333333 1029 91.420000 3411 5014 3 chr3B.!!$F4 1603
3 TraesCS3B01G466500 chr3B 231983608 231984449 841 True 353.500000 540 88.976000 1043 1697 2 chr3B.!!$R2 654
4 TraesCS3B01G466500 chr3B 230928805 230929692 887 True 336.000000 516 90.208500 1043 1697 2 chr3B.!!$R1 654
5 TraesCS3B01G466500 chr3D 536434805 536440291 5486 False 1682.500000 3908 89.175500 1 5014 4 chr3D.!!$F4 5013
6 TraesCS3B01G466500 chr3D 536787354 536787983 629 False 737.000000 737 88.281000 4164 4781 1 chr3D.!!$F3 617
7 TraesCS3B01G466500 chr3D 536666650 536668111 1461 False 674.666667 994 90.127667 3416 4762 3 chr3D.!!$F6 1346
8 TraesCS3B01G466500 chr3D 536588296 536590265 1969 False 638.333333 1005 87.894667 3416 5014 3 chr3D.!!$F5 1598
9 TraesCS3B01G466500 chr3D 536878808 536880770 1962 False 566.500000 996 89.511250 3416 5014 4 chr3D.!!$F7 1598
10 TraesCS3B01G466500 chr3A 672083594 672088776 5182 False 1577.000000 2944 91.927000 3 4671 4 chr3A.!!$F1 4668
11 TraesCS3B01G466500 chrUn 359851617 359852504 887 False 266.500000 370 86.883000 4477 5014 2 chrUn.!!$F2 537

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
302 315 0.109723 CCCACTCCGGAACCAAAAGA 59.890 55.000 5.23 0.0 36.56 2.52 F
562 609 0.249868 CTTGGACCGCACTGACAGAA 60.250 55.000 10.08 0.0 0.00 3.02 F
639 687 0.537188 CGCAGACTCCAGTACCCAAT 59.463 55.000 0.00 0.0 0.00 3.16 F
1685 2001 0.884514 TTGAGACGTCTCTGCTCTGG 59.115 55.000 37.63 0.0 43.25 3.86 F
2658 3109 0.823356 TGCAAGGCTTGGGTGAGAAC 60.823 55.000 27.25 9.5 0.00 3.01 F
2934 3386 1.458445 CTGCGAGATATGGTGAATGCG 59.542 52.381 0.00 0.0 0.00 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 1958 0.387202 AGCCGAGACGATCCATTCTG 59.613 55.000 0.00 0.00 0.00 3.02 R
2281 2732 0.877071 AAGCACGACCAAAGATGCAG 59.123 50.000 0.00 0.00 40.63 4.41 R
2542 2993 1.465777 CAAGTGACATGCGATGCAAGA 59.534 47.619 0.61 0.00 43.62 3.02 R
3341 3793 3.132824 GGGGCAAGTCCATTTAATTCCAG 59.867 47.826 0.00 0.00 36.21 3.86 R
3893 4346 0.911525 ATCCTCACCACCAGTCTGGG 60.912 60.000 23.06 11.51 43.37 4.45 R
4781 5635 0.108585 TGGCAAGTCCTTCCTGTGAC 59.891 55.000 0.00 0.00 35.26 3.67 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
67 77 5.880054 ACAAGAAGGATTAATCGGTGTTG 57.120 39.130 17.96 17.96 0.00 3.33
121 132 7.618117 TGTTTTCCTAGTCATGAGTATCTACCA 59.382 37.037 10.70 2.23 34.92 3.25
141 152 8.081633 TCTACCACATTTTTGCTTATCAAGTTG 58.918 33.333 0.00 0.00 35.84 3.16
294 307 1.136828 CCATATTCCCCACTCCGGAA 58.863 55.000 5.23 0.00 43.43 4.30
297 310 0.252789 TATTCCCCACTCCGGAACCA 60.253 55.000 5.23 0.00 42.11 3.67
300 313 1.151908 CCCCACTCCGGAACCAAAA 59.848 57.895 5.23 0.00 36.56 2.44
301 314 0.893727 CCCCACTCCGGAACCAAAAG 60.894 60.000 5.23 0.00 36.56 2.27
302 315 0.109723 CCCACTCCGGAACCAAAAGA 59.890 55.000 5.23 0.00 36.56 2.52
303 316 1.477923 CCCACTCCGGAACCAAAAGAA 60.478 52.381 5.23 0.00 36.56 2.52
304 317 2.303175 CCACTCCGGAACCAAAAGAAA 58.697 47.619 5.23 0.00 36.56 2.52
311 324 5.838529 TCCGGAACCAAAAGAAATTTCTTC 58.161 37.500 28.87 17.47 46.22 2.87
312 325 5.596772 TCCGGAACCAAAAGAAATTTCTTCT 59.403 36.000 28.87 16.49 46.22 2.85
315 328 8.736244 CCGGAACCAAAAGAAATTTCTTCTATA 58.264 33.333 28.87 0.00 46.22 1.31
367 403 8.668510 TCTTCTACATGAGAATTAGCAAATCC 57.331 34.615 0.00 0.00 43.39 3.01
368 404 7.439356 TCTTCTACATGAGAATTAGCAAATCCG 59.561 37.037 0.00 0.00 43.39 4.18
402 449 6.426646 CCATTTAGCTATGGGACTTCTACT 57.573 41.667 7.54 0.00 41.18 2.57
412 459 4.944177 TGGGACTTCTACTAGGCTTTAGT 58.056 43.478 0.00 0.00 0.00 2.24
416 463 6.550481 GGGACTTCTACTAGGCTTTAGTACAT 59.450 42.308 0.00 0.00 0.00 2.29
457 504 7.655328 GTGAGGACACAATTGAGATCTTATAGG 59.345 40.741 13.59 0.00 45.32 2.57
513 560 1.880027 GTCAACGGAGCCAAAATCACT 59.120 47.619 0.00 0.00 0.00 3.41
516 563 2.554032 CAACGGAGCCAAAATCACTCTT 59.446 45.455 0.00 0.00 0.00 2.85
517 564 2.427506 ACGGAGCCAAAATCACTCTTC 58.572 47.619 0.00 0.00 0.00 2.87
519 566 3.260884 ACGGAGCCAAAATCACTCTTCTA 59.739 43.478 0.00 0.00 0.00 2.10
537 584 7.119846 ACTCTTCTATATTTTCTTGTGGTGCAC 59.880 37.037 8.80 8.80 34.56 4.57
539 586 3.848272 ATATTTTCTTGTGGTGCACCG 57.152 42.857 30.07 16.33 39.43 4.94
540 587 1.398692 ATTTTCTTGTGGTGCACCGT 58.601 45.000 30.07 5.21 39.43 4.83
544 591 1.523711 CTTGTGGTGCACCGTGACT 60.524 57.895 30.07 0.00 39.43 3.41
553 600 3.542676 ACCGTGACTTGGACCGCA 61.543 61.111 0.00 0.00 0.00 5.69
561 608 1.367471 CTTGGACCGCACTGACAGA 59.633 57.895 10.08 0.00 0.00 3.41
562 609 0.249868 CTTGGACCGCACTGACAGAA 60.250 55.000 10.08 0.00 0.00 3.02
569 616 2.549754 ACCGCACTGACAGAATGAAAAG 59.450 45.455 10.08 0.00 39.69 2.27
570 617 2.095567 CCGCACTGACAGAATGAAAAGG 60.096 50.000 10.08 0.00 39.69 3.11
571 618 2.807967 CGCACTGACAGAATGAAAAGGA 59.192 45.455 10.08 0.00 39.69 3.36
575 622 3.817647 ACTGACAGAATGAAAAGGACAGC 59.182 43.478 10.08 0.00 39.69 4.40
576 623 4.070716 CTGACAGAATGAAAAGGACAGCT 58.929 43.478 0.00 0.00 39.69 4.24
580 627 6.205464 TGACAGAATGAAAAGGACAGCTTAAG 59.795 38.462 0.00 0.00 39.69 1.85
590 637 5.061920 AGGACAGCTTAAGAAACTACGAG 57.938 43.478 6.67 0.00 0.00 4.18
591 638 4.523558 AGGACAGCTTAAGAAACTACGAGT 59.476 41.667 6.67 0.00 0.00 4.18
592 639 5.010820 AGGACAGCTTAAGAAACTACGAGTT 59.989 40.000 6.67 0.00 40.80 3.01
612 660 6.178239 AGTTTATAAGAACAACGCATGTCC 57.822 37.500 0.00 0.00 42.99 4.02
614 662 5.539582 TTATAAGAACAACGCATGTCCAC 57.460 39.130 0.00 0.00 42.99 4.02
617 665 2.413837 AGAACAACGCATGTCCACTAC 58.586 47.619 0.00 0.00 42.99 2.73
624 672 1.002366 GCATGTCCACTACTTCGCAG 58.998 55.000 0.00 0.00 0.00 5.18
628 676 1.540267 TGTCCACTACTTCGCAGACTC 59.460 52.381 0.00 0.00 34.32 3.36
639 687 0.537188 CGCAGACTCCAGTACCCAAT 59.463 55.000 0.00 0.00 0.00 3.16
698 749 4.031201 CAGCGGTAACAAATAATTTTGCCG 59.969 41.667 10.78 10.78 45.01 5.69
699 750 3.304826 GCGGTAACAAATAATTTTGCCGG 59.695 43.478 15.20 0.00 45.01 6.13
713 764 6.959639 ATTTTGCCGGTCATTACTATGAAT 57.040 33.333 1.90 0.00 42.23 2.57
719 770 6.071560 TGCCGGTCATTACTATGAATACTAGG 60.072 42.308 1.90 0.00 42.23 3.02
765 820 6.347696 TCAAGCAATGTTTCCACTTTGAAAT 58.652 32.000 5.43 0.00 39.40 2.17
849 909 6.507023 AGTCAATGTGCTCAAAAAGGTAAAG 58.493 36.000 0.00 0.00 0.00 1.85
851 911 4.935352 ATGTGCTCAAAAAGGTAAAGCA 57.065 36.364 0.00 0.00 40.45 3.91
876 938 7.612065 AGTAAATTTAAAACCCCTTGAAGCT 57.388 32.000 0.00 0.00 0.00 3.74
894 956 2.173569 AGCTCAACCATATTCCCCACTC 59.826 50.000 0.00 0.00 0.00 3.51
895 957 2.838736 CTCAACCATATTCCCCACTCG 58.161 52.381 0.00 0.00 0.00 4.18
955 1017 1.577328 AACCAAAGAGCCATCGTGCG 61.577 55.000 0.00 0.00 36.02 5.34
956 1018 2.034879 CCAAAGAGCCATCGTGCGT 61.035 57.895 0.00 0.00 36.02 5.24
957 1019 1.133253 CAAAGAGCCATCGTGCGTG 59.867 57.895 0.00 0.00 36.02 5.34
958 1020 2.680913 AAAGAGCCATCGTGCGTGC 61.681 57.895 0.00 0.00 36.02 5.34
999 1061 1.339929 GGCTGGGTTGGTTAGTTGTTG 59.660 52.381 0.00 0.00 0.00 3.33
1625 1941 1.597742 TCTCACTGCTTTTGCTGGTC 58.402 50.000 0.00 0.00 46.73 4.02
1642 1958 4.767255 CGCTCTGTCCTGTGGCCC 62.767 72.222 0.00 0.00 0.00 5.80
1685 2001 0.884514 TTGAGACGTCTCTGCTCTGG 59.115 55.000 37.63 0.00 43.25 3.86
1743 2100 5.983720 ACTGTACTGCTACAAAACACACTAG 59.016 40.000 0.00 0.00 32.24 2.57
1765 2122 3.782046 ACGGACGAAAGATCACAATAGG 58.218 45.455 0.00 0.00 0.00 2.57
1772 2129 7.254795 GGACGAAAGATCACAATAGGTTAATGG 60.255 40.741 0.00 0.00 0.00 3.16
1818 2177 3.686016 TCAAAGATAAACACCCAGGCTC 58.314 45.455 0.00 0.00 0.00 4.70
1928 2287 2.103263 AGGCCGCTATCTCCTTTACTTG 59.897 50.000 0.00 0.00 0.00 3.16
2109 2472 4.622740 GGAACTGAATCAAAATTGCGGAAG 59.377 41.667 0.00 0.00 0.00 3.46
2111 2474 3.056607 ACTGAATCAAAATTGCGGAAGGG 60.057 43.478 0.00 0.00 0.00 3.95
2113 2476 3.193267 TGAATCAAAATTGCGGAAGGGAG 59.807 43.478 0.00 0.00 0.00 4.30
2135 2498 4.081420 AGTGCTGAGGTAACCTATTGTCTG 60.081 45.833 0.00 0.00 31.76 3.51
2150 2513 3.819564 TGTCTGCTACACTTGACAGTT 57.180 42.857 0.00 0.00 34.94 3.16
2193 2556 7.596749 TCTTGTAAGAAATTCTCGATTGGAC 57.403 36.000 0.00 0.00 30.73 4.02
2219 2590 4.142004 GGTGTGTCTATACATTTCGAGGGT 60.142 45.833 0.00 0.00 38.08 4.34
2242 2693 9.715121 GGGTTAATCGATATTACTTATTGTGGA 57.285 33.333 0.00 0.00 0.00 4.02
2281 2732 6.983307 AGCAGACTTGATACACATAATGTCTC 59.017 38.462 0.00 0.00 42.09 3.36
2291 2742 6.432607 ACACATAATGTCTCTGCATCTTTG 57.567 37.500 0.00 0.00 36.54 2.77
2302 2753 2.679837 CTGCATCTTTGGTCGTGCTTAT 59.320 45.455 0.00 0.00 38.37 1.73
2305 2756 3.126858 GCATCTTTGGTCGTGCTTATCAA 59.873 43.478 0.00 0.00 34.85 2.57
2324 2775 6.780457 ATCAACCACTGCAAATTTATAGCT 57.220 33.333 0.00 0.00 0.00 3.32
2325 2776 7.880160 ATCAACCACTGCAAATTTATAGCTA 57.120 32.000 0.00 0.00 0.00 3.32
2415 2866 2.289820 CGATGACAATGAGGCTGGATTG 59.710 50.000 12.26 12.26 35.95 2.67
2470 2921 1.453745 ACTGCACGGCCCATTATGG 60.454 57.895 3.85 3.85 37.25 2.74
2658 3109 0.823356 TGCAAGGCTTGGGTGAGAAC 60.823 55.000 27.25 9.50 0.00 3.01
2934 3386 1.458445 CTGCGAGATATGGTGAATGCG 59.542 52.381 0.00 0.00 0.00 4.73
2944 3396 1.872952 TGGTGAATGCGTCTGTTCTTG 59.127 47.619 0.00 0.00 0.00 3.02
3326 3778 5.359194 TTCTCTGTCATTCATACCCTTCC 57.641 43.478 0.00 0.00 0.00 3.46
3327 3779 4.624913 TCTCTGTCATTCATACCCTTCCT 58.375 43.478 0.00 0.00 0.00 3.36
3391 3843 6.043411 CCATACTAGTTCCTTCTAAGTGTGC 58.957 44.000 0.00 0.00 0.00 4.57
3860 4313 2.094234 GCACAAAATCCCCGCAGTTAAT 60.094 45.455 0.00 0.00 0.00 1.40
3885 4338 2.625790 GCGATTCACAGGAGTAGGAGAT 59.374 50.000 0.00 0.00 0.00 2.75
3893 4346 7.171630 TCACAGGAGTAGGAGATTAAAAGTC 57.828 40.000 0.00 0.00 0.00 3.01
3973 4427 3.058016 CCGGCATCATTCATATGGTTCAC 60.058 47.826 2.13 0.00 32.40 3.18
4038 4493 4.826274 TCCAGGAAGATGTTCTAACAGG 57.174 45.455 2.24 0.00 43.04 4.00
4078 4533 4.684703 CCTTTTCGTTGATCTTACGACACT 59.315 41.667 18.75 0.00 46.50 3.55
4123 4579 5.687730 GGTCATGATATAGTGAGAACGTGTG 59.312 44.000 0.00 0.00 0.00 3.82
4124 4580 5.174035 GTCATGATATAGTGAGAACGTGTGC 59.826 44.000 0.00 0.00 0.00 4.57
4125 4581 4.712122 TGATATAGTGAGAACGTGTGCA 57.288 40.909 0.00 0.00 0.00 4.57
4127 4583 5.660460 TGATATAGTGAGAACGTGTGCATT 58.340 37.500 0.00 0.00 0.00 3.56
4128 4584 6.801575 TGATATAGTGAGAACGTGTGCATTA 58.198 36.000 0.00 0.00 0.00 1.90
4130 4586 3.660501 AGTGAGAACGTGTGCATTAGA 57.339 42.857 0.00 0.00 0.00 2.10
4158 4685 6.734137 CACACTTACAAACATGTGTACCAAT 58.266 36.000 0.00 0.00 41.04 3.16
4326 5145 4.702247 TTGATACGTTCGTTCTGTGTTG 57.298 40.909 2.62 0.00 0.00 3.33
4327 5146 3.708890 TGATACGTTCGTTCTGTGTTGT 58.291 40.909 2.62 0.00 0.00 3.32
4328 5147 4.114073 TGATACGTTCGTTCTGTGTTGTT 58.886 39.130 2.62 0.00 0.00 2.83
4416 5235 4.591924 AGTAGTGGTAGCACAGTAGGTTTT 59.408 41.667 25.75 5.46 0.00 2.43
4514 5335 9.255029 ACACTTTTATCATGGGCTACTAATTTT 57.745 29.630 0.00 0.00 0.00 1.82
4529 5350 8.669243 GCTACTAATTTTTAGCTTGTCATGTCT 58.331 33.333 0.00 0.00 38.16 3.41
4781 5635 3.434319 GTGCGCCATGACACTGGG 61.434 66.667 4.18 0.00 36.75 4.45
4795 5649 2.765352 CTGGGTCACAGGAAGGACT 58.235 57.895 0.00 0.00 43.70 3.85
4796 5650 1.059913 CTGGGTCACAGGAAGGACTT 58.940 55.000 0.00 0.00 43.70 3.01
4883 6147 9.884636 TTCGATTTCTATTTGGAATTCAGACTA 57.115 29.630 7.93 0.00 0.00 2.59
4982 6247 7.328404 TGCATATATATCCAGAGGGTCAAAA 57.672 36.000 0.00 0.00 34.93 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.249911 GAGCCCGCGAAATGGTAGAT 60.250 55.000 8.23 0.00 0.00 1.98
67 77 2.224784 ACAACCGAATTTGTTACCGCTC 59.775 45.455 0.00 0.00 36.22 5.03
121 132 6.282930 AGCACAACTTGATAAGCAAAAATGT 58.717 32.000 0.00 0.00 35.74 2.71
157 168 4.514066 CCTTACCACACCTCAAAGTACAAC 59.486 45.833 0.00 0.00 0.00 3.32
158 169 4.445162 CCCTTACCACACCTCAAAGTACAA 60.445 45.833 0.00 0.00 0.00 2.41
270 283 0.472471 GAGTGGGGAATATGGCCGAA 59.528 55.000 0.00 0.00 0.00 4.30
367 403 9.840427 CCCATAGCTAAATGGTTTTATATTTCG 57.160 33.333 13.38 0.00 44.29 3.46
386 422 3.502356 AGCCTAGTAGAAGTCCCATAGC 58.498 50.000 0.00 0.00 0.00 2.97
390 437 4.944177 ACTAAAGCCTAGTAGAAGTCCCA 58.056 43.478 0.00 0.00 0.00 4.37
416 463 9.562408 TTGTGTCCTCACTTTTATATTTACACA 57.438 29.630 0.00 0.00 44.14 3.72
489 536 4.023536 GTGATTTTGGCTCCGTTGACTTAA 60.024 41.667 0.00 0.00 0.00 1.85
496 543 2.568623 AGAGTGATTTTGGCTCCGTT 57.431 45.000 0.00 0.00 0.00 4.44
499 546 8.457238 AAATATAGAAGAGTGATTTTGGCTCC 57.543 34.615 0.00 0.00 0.00 4.70
513 560 6.374333 GGTGCACCACAAGAAAATATAGAAGA 59.626 38.462 31.23 0.00 35.86 2.87
516 563 4.634004 CGGTGCACCACAAGAAAATATAGA 59.366 41.667 34.16 0.00 35.86 1.98
517 564 4.394920 ACGGTGCACCACAAGAAAATATAG 59.605 41.667 34.16 15.42 35.86 1.31
519 566 3.057596 CACGGTGCACCACAAGAAAATAT 60.058 43.478 34.16 0.00 35.86 1.28
528 575 1.817520 CAAGTCACGGTGCACCACA 60.818 57.895 34.16 15.20 35.86 4.17
537 584 3.041940 GTGCGGTCCAAGTCACGG 61.042 66.667 0.00 0.00 0.00 4.94
539 586 1.069090 TCAGTGCGGTCCAAGTCAC 59.931 57.895 0.00 0.00 0.00 3.67
540 587 1.069090 GTCAGTGCGGTCCAAGTCA 59.931 57.895 0.00 0.00 0.00 3.41
544 591 0.396435 ATTCTGTCAGTGCGGTCCAA 59.604 50.000 0.00 0.00 0.00 3.53
553 600 3.817647 GCTGTCCTTTTCATTCTGTCAGT 59.182 43.478 0.00 0.00 0.00 3.41
561 608 7.588497 AGTTTCTTAAGCTGTCCTTTTCATT 57.412 32.000 0.00 0.00 34.95 2.57
562 609 7.095187 CGTAGTTTCTTAAGCTGTCCTTTTCAT 60.095 37.037 0.00 0.00 34.95 2.57
569 616 4.807443 ACTCGTAGTTTCTTAAGCTGTCC 58.193 43.478 0.00 0.00 0.00 4.02
570 617 6.766452 AAACTCGTAGTTTCTTAAGCTGTC 57.234 37.500 0.00 0.00 44.47 3.51
571 618 9.918630 TTATAAACTCGTAGTTTCTTAAGCTGT 57.081 29.630 13.76 0.00 44.47 4.40
580 627 7.681650 GCGTTGTTCTTATAAACTCGTAGTTTC 59.318 37.037 13.76 2.85 44.47 2.78
590 637 5.793457 GTGGACATGCGTTGTTCTTATAAAC 59.207 40.000 0.00 0.00 39.18 2.01
591 638 5.703592 AGTGGACATGCGTTGTTCTTATAAA 59.296 36.000 0.00 0.00 39.18 1.40
592 639 5.242434 AGTGGACATGCGTTGTTCTTATAA 58.758 37.500 0.00 0.00 39.18 0.98
593 640 4.827692 AGTGGACATGCGTTGTTCTTATA 58.172 39.130 0.00 0.00 39.18 0.98
605 653 1.002366 CTGCGAAGTAGTGGACATGC 58.998 55.000 0.00 0.00 34.87 4.06
612 660 1.542030 ACTGGAGTCTGCGAAGTAGTG 59.458 52.381 0.00 0.00 42.21 2.74
614 662 2.097791 GGTACTGGAGTCTGCGAAGTAG 59.902 54.545 0.00 0.00 43.21 2.57
617 665 0.173708 GGGTACTGGAGTCTGCGAAG 59.826 60.000 0.00 0.00 0.00 3.79
624 672 5.310451 TGTGTTAAATTGGGTACTGGAGTC 58.690 41.667 0.00 0.00 0.00 3.36
628 676 4.079253 AGCTGTGTTAAATTGGGTACTGG 58.921 43.478 0.00 0.00 0.00 4.00
659 710 3.144506 CCGCTGAATGCCTGATAAATCT 58.855 45.455 0.00 0.00 38.78 2.40
668 719 1.904287 TTTGTTACCGCTGAATGCCT 58.096 45.000 0.00 0.00 38.78 4.75
698 749 8.639761 ACACACCTAGTATTCATAGTAATGACC 58.360 37.037 0.00 0.00 41.87 4.02
699 750 9.680315 GACACACCTAGTATTCATAGTAATGAC 57.320 37.037 0.00 0.00 41.87 3.06
713 764 9.787435 AAACAAAAATGATAGACACACCTAGTA 57.213 29.630 0.00 0.00 0.00 1.82
719 770 9.173939 CTTGAGAAACAAAAATGATAGACACAC 57.826 33.333 0.00 0.00 38.08 3.82
727 778 8.441312 AACATTGCTTGAGAAACAAAAATGAT 57.559 26.923 16.85 8.40 40.82 2.45
765 820 3.509575 GTGCCCATGAGTTATCACCAAAA 59.490 43.478 0.00 0.00 38.57 2.44
833 893 6.458232 TTACTTGCTTTACCTTTTTGAGCA 57.542 33.333 0.00 0.00 41.19 4.26
834 894 7.946655 ATTTACTTGCTTTACCTTTTTGAGC 57.053 32.000 0.00 0.00 0.00 4.26
849 909 7.307751 GCTTCAAGGGGTTTTAAATTTACTTGC 60.308 37.037 14.56 4.96 35.35 4.01
851 911 8.029782 AGCTTCAAGGGGTTTTAAATTTACTT 57.970 30.769 0.00 0.00 0.00 2.24
876 938 1.488812 CCGAGTGGGGAATATGGTTGA 59.511 52.381 0.00 0.00 0.00 3.18
900 962 4.490606 TATGGGGGCAGCTCCGGA 62.491 66.667 4.81 2.93 34.94 5.14
955 1017 1.433837 CGGGGCGTTGTAATAGGCAC 61.434 60.000 0.00 0.00 0.00 5.01
956 1018 1.153329 CGGGGCGTTGTAATAGGCA 60.153 57.895 0.00 0.00 0.00 4.75
957 1019 1.144496 TCGGGGCGTTGTAATAGGC 59.856 57.895 0.00 0.00 0.00 3.93
958 1020 0.872881 CGTCGGGGCGTTGTAATAGG 60.873 60.000 0.00 0.00 0.00 2.57
1595 1911 0.878086 GCAGTGAGATAAGGGAGCGC 60.878 60.000 0.00 0.00 0.00 5.92
1625 1941 4.767255 GGGCCACAGGACAGAGCG 62.767 72.222 4.39 0.00 27.52 5.03
1642 1958 0.387202 AGCCGAGACGATCCATTCTG 59.613 55.000 0.00 0.00 0.00 3.02
1685 2001 2.132740 TTGGAGCACAAAACGCAATC 57.867 45.000 0.00 0.00 35.79 2.67
1743 2100 3.797256 CCTATTGTGATCTTTCGTCCGTC 59.203 47.826 0.00 0.00 0.00 4.79
1765 2122 5.705609 ACAGTGTTCAATGGACCATTAAC 57.294 39.130 19.41 20.42 32.35 2.01
1772 2129 5.874810 TGAGCTTATACAGTGTTCAATGGAC 59.125 40.000 0.00 0.00 0.00 4.02
1818 2177 2.097629 CAGCCATGAGAGCAATGTTCAG 59.902 50.000 0.00 0.00 0.00 3.02
1860 2219 2.352960 GACCACTGCTGCTAAATAGTGC 59.647 50.000 10.56 0.00 39.27 4.40
2009 2370 2.945668 CAAACCAGCCAGATAGCTTACC 59.054 50.000 0.00 0.00 42.61 2.85
2109 2472 1.861982 TAGGTTACCTCAGCACTCCC 58.138 55.000 7.39 0.00 34.61 4.30
2111 2474 4.160626 AGACAATAGGTTACCTCAGCACTC 59.839 45.833 7.39 0.00 34.61 3.51
2113 2476 4.184629 CAGACAATAGGTTACCTCAGCAC 58.815 47.826 7.39 0.00 34.61 4.40
2135 2498 5.207768 CAAACATGAACTGTCAAGTGTAGC 58.792 41.667 0.00 0.00 35.89 3.58
2150 2513 7.523293 ACAAGATCAAACCATACAAACATGA 57.477 32.000 0.00 0.00 0.00 3.07
2193 2556 5.463392 CCTCGAAATGTATAGACACACCATG 59.537 44.000 0.00 0.00 38.76 3.66
2213 2584 9.635520 ACAATAAGTAATATCGATTAACCCTCG 57.364 33.333 1.71 0.00 37.47 4.63
2242 2693 2.774234 AGTCTGCTTGTGGCCATACTAT 59.226 45.455 9.72 0.00 40.92 2.12
2268 2719 5.356190 CCAAAGATGCAGAGACATTATGTGT 59.644 40.000 1.24 0.00 45.83 3.72
2276 2727 1.344438 ACGACCAAAGATGCAGAGACA 59.656 47.619 0.00 0.00 0.00 3.41
2281 2732 0.877071 AAGCACGACCAAAGATGCAG 59.123 50.000 0.00 0.00 40.63 4.41
2302 2753 6.183360 GCTAGCTATAAATTTGCAGTGGTTGA 60.183 38.462 7.70 0.00 0.00 3.18
2305 2756 5.192927 TGCTAGCTATAAATTTGCAGTGGT 58.807 37.500 17.23 0.00 0.00 4.16
2324 2775 2.806434 ACCAATGTTGCCTGATTGCTA 58.194 42.857 0.00 0.00 0.00 3.49
2325 2776 1.636148 ACCAATGTTGCCTGATTGCT 58.364 45.000 0.00 0.00 0.00 3.91
2362 2813 7.197017 AGCACTTAGTTACTCTGTTATCATCG 58.803 38.462 0.00 0.00 0.00 3.84
2415 2866 6.870965 AGAGATACTGAACACAGAAACATGTC 59.129 38.462 0.00 0.00 35.80 3.06
2470 2921 5.228665 GGAGCGTATTTACTTAGGATCACC 58.771 45.833 0.00 0.00 0.00 4.02
2539 2990 2.751259 AGTGACATGCGATGCAAGAAAT 59.249 40.909 0.61 0.00 43.62 2.17
2542 2993 1.465777 CAAGTGACATGCGATGCAAGA 59.534 47.619 0.61 0.00 43.62 3.02
2613 3064 8.704668 AGGATTTTCCACAGTTAAGAAAAACAT 58.295 29.630 6.89 1.48 41.39 2.71
2658 3109 7.935338 ATAGACAGCTTTTTGTGTGATTTTG 57.065 32.000 0.00 0.00 0.00 2.44
2874 3326 3.196939 TGATGCATCGGAATCACATGA 57.803 42.857 21.34 0.00 33.96 3.07
2944 3396 6.590677 GTGTATCTCCCAAAGTCTGAAACTAC 59.409 42.308 0.00 0.00 37.17 2.73
3341 3793 3.132824 GGGGCAAGTCCATTTAATTCCAG 59.867 47.826 0.00 0.00 36.21 3.86
3391 3843 4.444056 CGAAACCATAAACAAAAGCCACTG 59.556 41.667 0.00 0.00 0.00 3.66
3885 4338 2.781174 ACCACCAGTCTGGGACTTTTAA 59.219 45.455 23.06 0.00 41.37 1.52
3893 4346 0.911525 ATCCTCACCACCAGTCTGGG 60.912 60.000 23.06 11.51 43.37 4.45
3941 4394 2.513666 GATGCCGGTTCGCCATCA 60.514 61.111 12.50 0.00 37.00 3.07
4030 4485 5.768317 GCAAAAATGTTAGTGCCTGTTAGA 58.232 37.500 0.00 0.00 0.00 2.10
4038 4493 3.401033 AAGGGGCAAAAATGTTAGTGC 57.599 42.857 0.00 0.00 36.24 4.40
4123 4579 7.979115 TGTTTGTAAGTGTGTTTTCTAATGC 57.021 32.000 0.00 0.00 0.00 3.56
4124 4580 9.515020 ACATGTTTGTAAGTGTGTTTTCTAATG 57.485 29.630 0.00 0.00 33.16 1.90
4125 4581 9.515020 CACATGTTTGTAAGTGTGTTTTCTAAT 57.485 29.630 0.00 0.00 37.70 1.73
4158 4685 6.413892 TGAATACATTGCAACATCCAGTCTA 58.586 36.000 0.00 0.00 0.00 2.59
4197 5004 6.435292 AAAGGGCTCAAGAAGTAGTAAGAA 57.565 37.500 0.00 0.00 0.00 2.52
4250 5069 7.041372 TGAGTGGTTAGCTATCTCAAAAACAAC 60.041 37.037 12.64 4.31 33.18 3.32
4316 5135 3.938963 TCTCACAGGAAACAACACAGAAC 59.061 43.478 0.00 0.00 0.00 3.01
4326 5145 3.190118 CCAGAGCATTTCTCACAGGAAAC 59.810 47.826 0.00 0.00 44.35 2.78
4327 5146 3.415212 CCAGAGCATTTCTCACAGGAAA 58.585 45.455 0.00 0.00 44.35 3.13
4328 5147 2.290514 CCCAGAGCATTTCTCACAGGAA 60.291 50.000 0.00 0.00 44.35 3.36
4416 5235 5.721480 TCTTACATCCTGATTCACTTCCTGA 59.279 40.000 0.00 0.00 0.00 3.86
4514 5335 3.324846 ACAGGACAGACATGACAAGCTAA 59.675 43.478 0.00 0.00 34.19 3.09
4529 5350 2.694628 AGAAATTGCTGCAAACAGGACA 59.305 40.909 20.06 0.00 44.82 4.02
4781 5635 0.108585 TGGCAAGTCCTTCCTGTGAC 59.891 55.000 0.00 0.00 35.26 3.67
4784 5638 2.683211 ATTTGGCAAGTCCTTCCTGT 57.317 45.000 0.00 0.00 35.26 4.00
4785 5639 5.665916 ATAAATTTGGCAAGTCCTTCCTG 57.334 39.130 0.00 0.00 35.26 3.86
4883 6147 3.257393 CATCTTGCAGACGAGCTTTAGT 58.743 45.455 0.00 0.00 34.99 2.24
4982 6247 7.609918 GCACCCCAACCAAATCTTAAATTAAAT 59.390 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.