Multiple sequence alignment - TraesCS6B01G042700

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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 TraesCS6B01G042700 chr6B 100.000 4446 0 0 1 4446 26136182 26140627 0.000000e+00 8211.0
1 TraesCS6B01G042700 chr6B 87.661 3339 283 82 1131 4446 26195970 26199202 0.000000e+00 3764.0
2 TraesCS6B01G042700 chr6B 87.341 2125 177 48 1 2059 26032421 26030323 0.000000e+00 2350.0
3 TraesCS6B01G042700 chr6B 89.119 1112 83 18 2900 4008 26028466 26027390 0.000000e+00 1349.0
4 TraesCS6B01G042700 chr6B 91.514 872 53 13 2087 2949 26030324 26029465 0.000000e+00 1181.0
5 TraesCS6B01G042700 chr6B 82.661 1240 184 15 1131 2357 26200667 26201888 0.000000e+00 1070.0
6 TraesCS6B01G042700 chr6B 82.508 1252 181 21 1131 2365 26022675 26021445 0.000000e+00 1064.0
7 TraesCS6B01G042700 chr6B 81.774 1026 160 18 1346 2359 26148332 26149342 0.000000e+00 833.0
8 TraesCS6B01G042700 chr6B 90.476 420 30 6 3998 4413 26027104 26026691 3.020000e-151 545.0
9 TraesCS6B01G042700 chr6B 95.238 273 9 3 2572 2840 26028987 26028715 3.180000e-116 429.0
10 TraesCS6B01G042700 chr6B 77.363 402 75 13 146 534 32730678 32731076 1.610000e-54 224.0
11 TraesCS6B01G042700 chr6B 82.784 273 16 14 882 1135 26195570 26195830 9.690000e-52 215.0
12 TraesCS6B01G042700 chr6B 80.226 177 21 8 597 763 437845931 437845759 2.170000e-23 121.0
13 TraesCS6B01G042700 chr6D 86.948 2919 244 64 1 2824 14303760 14306636 0.000000e+00 3153.0
14 TraesCS6B01G042700 chr6D 88.833 1200 99 25 1637 2821 14364472 14363293 0.000000e+00 1441.0
15 TraesCS6B01G042700 chr6D 79.862 1157 171 31 1234 2359 14328873 14329998 0.000000e+00 789.0
16 TraesCS6B01G042700 chr6D 89.729 516 41 4 1131 1638 14368279 14367768 0.000000e+00 649.0
17 TraesCS6B01G042700 chr6D 87.805 492 54 5 3958 4446 14307244 14307732 4.990000e-159 571.0
18 TraesCS6B01G042700 chr6D 87.221 493 52 7 3958 4446 14362681 14362196 6.500000e-153 551.0
19 TraesCS6B01G042700 chr6D 83.770 610 47 33 2608 3208 14363293 14362727 8.470000e-147 531.0
20 TraesCS6B01G042700 chr6D 83.607 610 48 31 2608 3208 14306632 14307198 3.940000e-145 525.0
21 TraesCS6B01G042700 chr6D 85.714 273 30 4 1131 1397 14353125 14352856 3.390000e-71 279.0
22 TraesCS6B01G042700 chr6D 77.778 486 82 19 1 463 377335197 377335679 4.380000e-70 276.0
23 TraesCS6B01G042700 chr6A 88.596 1710 132 32 1132 2821 15590617 15592283 0.000000e+00 2019.0
24 TraesCS6B01G042700 chr6A 93.750 64 4 0 2608 2671 15592283 15592346 3.660000e-16 97.1
25 TraesCS6B01G042700 chr1A 88.736 435 41 5 3850 4281 93691656 93692085 3.940000e-145 525.0
26 TraesCS6B01G042700 chr1A 87.266 267 33 1 3546 3811 93691389 93691655 2.010000e-78 303.0
27 TraesCS6B01G042700 chr7D 83.066 437 54 12 166 584 192152803 192152369 3.250000e-101 379.0
28 TraesCS6B01G042700 chr7B 76.106 452 86 8 148 578 124539223 124539673 2.690000e-52 217.0
29 TraesCS6B01G042700 chr7B 89.394 66 6 1 149 213 120232941 120232876 1.020000e-11 82.4
30 TraesCS6B01G042700 chr1B 78.182 330 63 7 259 584 17409628 17409952 7.540000e-48 202.0
31 TraesCS6B01G042700 chr1B 77.879 330 64 7 259 584 17418154 17418478 3.510000e-46 196.0
32 TraesCS6B01G042700 chr1B 77.273 330 66 7 259 584 17470097 17470421 7.590000e-43 185.0
33 TraesCS6B01G042700 chr4A 75.773 388 80 10 1 377 178990979 178990595 2.730000e-42 183.0
34 TraesCS6B01G042700 chr1D 76.471 221 31 12 150 351 415127024 415127242 2.830000e-17 100.0
35 TraesCS6B01G042700 chr7A 87.500 72 6 3 146 216 80202593 80202662 3.690000e-11 80.5
36 TraesCS6B01G042700 chr3B 76.687 163 26 11 62 213 588855684 588855523 3.690000e-11 80.5
37 TraesCS6B01G042700 chr2D 87.500 72 6 3 146 216 313803734 313803665 3.690000e-11 80.5
38 TraesCS6B01G042700 chr5B 84.146 82 10 2 687 766 16611359 16611439 4.770000e-10 76.8
39 TraesCS6B01G042700 chr5B 84.146 82 10 2 687 766 16643735 16643815 4.770000e-10 76.8
40 TraesCS6B01G042700 chr5B 88.525 61 7 0 706 766 16667926 16667986 1.720000e-09 75.0
41 TraesCS6B01G042700 chr5B 82.927 82 11 2 687 766 16529188 16529268 2.220000e-08 71.3
42 TraesCS6B01G042700 chr5B 82.927 82 11 2 687 766 16572788 16572868 2.220000e-08 71.3
43 TraesCS6B01G042700 chr5A 80.851 94 15 3 671 763 645492904 645492995 2.220000e-08 71.3


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 TraesCS6B01G042700 chr6B 26136182 26140627 4445 False 8211.000000 8211 100.000000 1 4446 1 chr6B.!!$F1 4445
1 TraesCS6B01G042700 chr6B 26195570 26201888 6318 False 1683.000000 3764 84.368667 882 4446 3 chr6B.!!$F4 3564
2 TraesCS6B01G042700 chr6B 26026691 26032421 5730 True 1170.800000 2350 90.737600 1 4413 5 chr6B.!!$R3 4412
3 TraesCS6B01G042700 chr6B 26021445 26022675 1230 True 1064.000000 1064 82.508000 1131 2365 1 chr6B.!!$R1 1234
4 TraesCS6B01G042700 chr6B 26148332 26149342 1010 False 833.000000 833 81.774000 1346 2359 1 chr6B.!!$F2 1013
5 TraesCS6B01G042700 chr6D 14303760 14307732 3972 False 1416.333333 3153 86.120000 1 4446 3 chr6D.!!$F3 4445
6 TraesCS6B01G042700 chr6D 14362196 14368279 6083 True 793.000000 1441 87.388250 1131 4446 4 chr6D.!!$R2 3315
7 TraesCS6B01G042700 chr6D 14328873 14329998 1125 False 789.000000 789 79.862000 1234 2359 1 chr6D.!!$F1 1125
8 TraesCS6B01G042700 chr6A 15590617 15592346 1729 False 1058.050000 2019 91.173000 1132 2821 2 chr6A.!!$F1 1689
9 TraesCS6B01G042700 chr1A 93691389 93692085 696 False 414.000000 525 88.001000 3546 4281 2 chr1A.!!$F1 735

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
105 106 0.245266 TCGTTGGTTCGCTGATGCTA 59.755 50.0 0.00 0.00 36.97 3.49 F
511 523 0.250989 TTTAGGGCACTTGGGTTCCG 60.251 55.0 0.00 0.00 29.38 4.30 F
1045 1126 0.386858 TGAGCTTCAGACGTACGTGC 60.387 55.0 28.16 21.73 0.00 5.34 F
1946 5520 0.248539 GACCTACGCTACAGCTTCCG 60.249 60.0 0.00 0.00 39.32 4.30 F
2001 5584 0.038526 GTGTCTGGTTCGATGACGGT 60.039 55.0 0.00 0.00 40.21 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1087 1168 0.549469 GGTTCCCCCATCGTTGGTAT 59.451 55.000 11.51 0.0 41.91 2.73 R
1920 5494 0.608856 TGTAGCGTAGGTCCCAACGA 60.609 55.000 16.44 0.0 41.55 3.85 R
1974 5557 1.524863 CGAACCAGACACTCCTCGGT 61.525 60.000 0.00 0.0 0.00 4.69 R
2912 7639 1.683917 ACCAATACCAAGCGCAAACAA 59.316 42.857 11.47 0.0 0.00 2.83 R
3954 8707 2.892784 AGGCTCGTCAAGGTATTAGC 57.107 50.000 0.00 0.0 0.00 3.09 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
27 28 1.932604 GCGCTGGGATCTTACTCATCG 60.933 57.143 0.00 0.00 33.81 3.84
37 38 4.232188 TCTTACTCATCGACCTACCACT 57.768 45.455 0.00 0.00 0.00 4.00
59 60 1.078759 CAGAGCCACGTTCGGACATC 61.079 60.000 0.00 0.00 0.00 3.06
69 70 4.647615 CGGACATCGGCCGGCTAG 62.648 72.222 28.56 20.78 44.87 3.42
96 97 1.594293 ACAGTGGCTCGTTGGTTCG 60.594 57.895 0.00 0.00 0.00 3.95
98 99 2.665185 GTGGCTCGTTGGTTCGCT 60.665 61.111 0.00 0.00 0.00 4.93
104 105 1.005037 TCGTTGGTTCGCTGATGCT 60.005 52.632 0.00 0.00 36.97 3.79
105 106 0.245266 TCGTTGGTTCGCTGATGCTA 59.755 50.000 0.00 0.00 36.97 3.49
128 129 6.141847 AGTCATCAAGTGTGATCACTCCCC 62.142 50.000 25.55 11.42 41.32 4.81
153 154 3.420397 GGTCTTGTACCGAGCACTC 57.580 57.895 6.59 0.00 38.88 3.51
163 170 1.084370 CCGAGCACTCCGAAACATCC 61.084 60.000 0.00 0.00 0.00 3.51
194 202 5.222631 GTGTTCTTCAAATGCGAAAAGGAT 58.777 37.500 0.00 0.00 0.00 3.24
195 203 6.378582 GTGTTCTTCAAATGCGAAAAGGATA 58.621 36.000 0.00 0.00 0.00 2.59
225 234 2.415697 ATTTTGCGGTTGTTCTTCGG 57.584 45.000 0.00 0.00 0.00 4.30
277 286 9.657419 AAAATTATAGGAAGGATGCAAGTTTTG 57.343 29.630 0.00 0.00 0.00 2.44
278 287 6.773976 TTATAGGAAGGATGCAAGTTTTGG 57.226 37.500 0.00 0.00 0.00 3.28
283 292 5.543790 AGGAAGGATGCAAGTTTTGGTATTT 59.456 36.000 0.00 0.00 0.00 1.40
288 297 5.994668 GGATGCAAGTTTTGGTATTTGGAAA 59.005 36.000 0.00 0.00 0.00 3.13
318 327 9.900710 AATACATCGATCTATTGTTAGAGACAC 57.099 33.333 5.26 0.00 37.86 3.67
334 343 5.798132 AGAGACACATTTGCTAGATGTTCA 58.202 37.500 0.00 0.00 35.64 3.18
336 345 6.883217 AGAGACACATTTGCTAGATGTTCATT 59.117 34.615 0.00 0.00 35.64 2.57
354 365 6.646653 TGTTCATTCACTACTTGCTAGAGTTG 59.353 38.462 1.04 0.00 0.00 3.16
372 383 2.818432 GTTGAGACTAGAGACGACCCAA 59.182 50.000 0.00 0.00 0.00 4.12
386 397 2.095263 CGACCCAATGTCCAATTGTGTC 60.095 50.000 4.43 4.27 41.18 3.67
436 447 6.877611 ACTCAAGAAGCCGATAAAGAAAAA 57.122 33.333 0.00 0.00 0.00 1.94
437 448 7.454260 ACTCAAGAAGCCGATAAAGAAAAAT 57.546 32.000 0.00 0.00 0.00 1.82
440 452 9.495754 CTCAAGAAGCCGATAAAGAAAAATAAG 57.504 33.333 0.00 0.00 0.00 1.73
450 462 8.190784 CGATAAAGAAAAATAAGAATGTGGGCT 58.809 33.333 0.00 0.00 0.00 5.19
492 504 7.806180 AGTATTAAATGAACTAGTGGGAGCAT 58.194 34.615 0.00 0.00 0.00 3.79
506 518 1.106285 GAGCATTTAGGGCACTTGGG 58.894 55.000 0.00 0.00 0.00 4.12
509 521 1.204704 GCATTTAGGGCACTTGGGTTC 59.795 52.381 0.00 0.00 0.00 3.62
510 522 1.824852 CATTTAGGGCACTTGGGTTCC 59.175 52.381 0.00 0.00 0.00 3.62
511 523 0.250989 TTTAGGGCACTTGGGTTCCG 60.251 55.000 0.00 0.00 29.38 4.30
523 535 1.271163 TGGGTTCCGATTGAAGTGTCC 60.271 52.381 0.00 0.00 32.37 4.02
578 590 4.695455 TCCTTTAGCGAAGAATTGGTGAAG 59.305 41.667 4.67 0.00 37.57 3.02
589 624 7.744715 CGAAGAATTGGTGAAGTGTGTTAATAC 59.255 37.037 0.00 0.00 0.00 1.89
593 628 7.994425 ATTGGTGAAGTGTGTTAATACATGA 57.006 32.000 8.38 0.00 36.50 3.07
614 649 3.344515 AGAGAAGTTTATTTCGGTGGCC 58.655 45.455 0.00 0.00 32.33 5.36
632 667 6.541969 GGTGGCCGAAAATTAAATGAATTTG 58.458 36.000 0.00 0.00 45.21 2.32
633 668 6.370166 GGTGGCCGAAAATTAAATGAATTTGA 59.630 34.615 0.00 0.00 45.21 2.69
634 669 7.233689 GTGGCCGAAAATTAAATGAATTTGAC 58.766 34.615 0.00 0.00 45.21 3.18
635 670 6.931281 TGGCCGAAAATTAAATGAATTTGACA 59.069 30.769 0.00 0.00 45.21 3.58
636 671 7.442364 TGGCCGAAAATTAAATGAATTTGACAA 59.558 29.630 0.00 0.00 45.21 3.18
637 672 8.286097 GGCCGAAAATTAAATGAATTTGACAAA 58.714 29.630 2.48 2.48 45.21 2.83
638 673 9.657121 GCCGAAAATTAAATGAATTTGACAAAA 57.343 25.926 4.41 0.00 45.21 2.44
725 760 4.673534 AAAGTTTACTCGGCCATTTACG 57.326 40.909 2.24 0.00 0.00 3.18
734 769 1.531149 CGGCCATTTACGCCTCTATTG 59.469 52.381 2.24 0.00 44.73 1.90
743 778 2.474112 ACGCCTCTATTGTTTAGGGGA 58.526 47.619 11.13 0.00 43.98 4.81
748 783 3.557264 CCTCTATTGTTTAGGGGATCGGC 60.557 52.174 0.00 0.00 37.37 5.54
765 800 1.723288 GGCTAGAGATGCCCTAACCT 58.277 55.000 0.00 0.00 44.32 3.50
768 803 2.036604 GCTAGAGATGCCCTAACCTCAC 59.963 54.545 0.00 0.00 0.00 3.51
784 819 3.194755 ACCTCACGTGTACTGATGCATTA 59.805 43.478 16.51 0.00 0.00 1.90
786 821 4.811024 CCTCACGTGTACTGATGCATTATT 59.189 41.667 16.51 0.00 0.00 1.40
787 822 5.277011 CCTCACGTGTACTGATGCATTATTG 60.277 44.000 16.51 0.00 0.00 1.90
830 873 9.998106 AACTATGATGATAATACTTGTGTACCC 57.002 33.333 0.00 0.00 0.00 3.69
845 895 6.129414 TGTGTACCCCATAGTTTGTTGTAT 57.871 37.500 0.00 0.00 0.00 2.29
848 898 7.607223 TGTGTACCCCATAGTTTGTTGTATAAC 59.393 37.037 0.00 0.00 37.32 1.89
875 925 7.633361 TTTTTCTGTCAGAATACTACGTGTC 57.367 36.000 15.95 0.00 33.67 3.67
890 940 2.073816 CGTGTCCCATGTAGTTTGTCC 58.926 52.381 0.00 0.00 0.00 4.02
895 945 2.028476 TCCCATGTAGTTTGTCCAGACG 60.028 50.000 0.00 0.00 0.00 4.18
1028 1109 3.092301 TGTTGTTCCATTGTGGTTGTGA 58.908 40.909 0.00 0.00 39.03 3.58
1045 1126 0.386858 TGAGCTTCAGACGTACGTGC 60.387 55.000 28.16 21.73 0.00 5.34
1047 1128 1.080705 GCTTCAGACGTACGTGCCT 60.081 57.895 28.16 15.00 0.00 4.75
1048 1129 1.071567 GCTTCAGACGTACGTGCCTC 61.072 60.000 28.16 11.42 0.00 4.70
1087 1168 3.706698 CAGCAAAACCGATCTCGATCTA 58.293 45.455 0.22 0.00 43.02 1.98
1157 1398 2.125350 GGAGGCCTTGCTCGTCAG 60.125 66.667 6.77 0.00 0.00 3.51
1284 1525 1.210478 AGCCTATCCAACGTCTGCAAT 59.790 47.619 0.00 0.00 0.00 3.56
1531 1789 3.156334 GCGTGTGCACCTTAGACG 58.844 61.111 19.01 19.01 42.15 4.18
1532 1790 2.380410 GCGTGTGCACCTTAGACGG 61.380 63.158 22.93 9.28 42.15 4.79
1533 1791 2.380410 CGTGTGCACCTTAGACGGC 61.380 63.158 15.69 0.00 32.01 5.68
1534 1792 2.048597 TGTGCACCTTAGACGGCG 60.049 61.111 15.69 4.80 0.00 6.46
1535 1793 3.488090 GTGCACCTTAGACGGCGC 61.488 66.667 6.90 0.00 32.80 6.53
1536 1794 3.691342 TGCACCTTAGACGGCGCT 61.691 61.111 6.90 8.04 33.35 5.92
1537 1795 3.188786 GCACCTTAGACGGCGCTG 61.189 66.667 16.39 16.39 0.00 5.18
1538 1796 3.188786 CACCTTAGACGGCGCTGC 61.189 66.667 18.15 9.47 0.00 5.25
1539 1797 3.691342 ACCTTAGACGGCGCTGCA 61.691 61.111 18.15 0.00 0.00 4.41
1878 5452 2.492088 CTGGGTACTCATGTCTTCGTCA 59.508 50.000 0.00 0.00 0.00 4.35
1887 5461 3.303135 TCTTCGTCACCGCCTGCT 61.303 61.111 0.00 0.00 0.00 4.24
1920 5494 1.080434 GCTCGAGAGCGACAACCTT 60.080 57.895 18.75 0.00 45.29 3.50
1946 5520 0.248539 GACCTACGCTACAGCTTCCG 60.249 60.000 0.00 0.00 39.32 4.30
1974 5557 6.480763 TGATGGCAACTACTATTTCTTCCAA 58.519 36.000 0.00 0.00 37.61 3.53
2001 5584 0.038526 GTGTCTGGTTCGATGACGGT 60.039 55.000 0.00 0.00 40.21 4.83
2160 5743 2.435938 TGGAACATCTTCGCGGGC 60.436 61.111 6.13 0.00 0.00 6.13
2223 5806 3.998672 TCCTGTTGGGACGGCGAC 61.999 66.667 16.62 7.58 39.58 5.19
2272 5863 4.022935 CCTTGTTGCTTGCACTAGAATGAA 60.023 41.667 0.00 0.00 0.00 2.57
2278 5869 5.434408 TGCTTGCACTAGAATGAATCAGAT 58.566 37.500 0.00 0.00 0.00 2.90
2279 5870 5.296035 TGCTTGCACTAGAATGAATCAGATG 59.704 40.000 0.00 0.00 0.00 2.90
2388 6029 0.935898 GCAGGATCGAACTCAGCATG 59.064 55.000 0.00 0.00 37.54 4.06
2398 6039 2.865119 ACTCAGCATGTTCATGGTCA 57.135 45.000 13.45 1.79 37.40 4.02
2748 7247 4.440758 ACTTTTTGTCGCAAATCACATTCG 59.559 37.500 5.97 0.00 0.00 3.34
2768 7267 9.010029 ACATTCGTACTTTCAAAGTATCCAATT 57.990 29.630 13.18 0.00 45.05 2.32
2860 7587 3.056107 ACAACTGAGCGGCTAGTGATAAA 60.056 43.478 0.60 0.00 0.00 1.40
2861 7588 3.166489 ACTGAGCGGCTAGTGATAAAC 57.834 47.619 0.60 0.00 0.00 2.01
2873 7600 8.700644 CGGCTAGTGATAAACTGATAATTACAC 58.299 37.037 0.00 0.00 40.26 2.90
2898 7625 8.956426 ACCTTACACAAAGACACCATATTAATG 58.044 33.333 0.00 0.00 37.38 1.90
2919 7646 5.058149 TGGTGATCATGTGTATTGTTTGC 57.942 39.130 0.00 0.00 0.00 3.68
2930 7662 4.323336 GTGTATTGTTTGCGCTTGGTATTG 59.677 41.667 9.73 0.00 0.00 1.90
2935 7667 4.262617 TGTTTGCGCTTGGTATTGGTATA 58.737 39.130 9.73 0.00 0.00 1.47
2946 7678 8.774586 GCTTGGTATTGGTATAAGAACACATAG 58.225 37.037 0.00 0.00 0.00 2.23
2979 7711 9.766754 ACAGATCTCCATAGTTATATCTGATGT 57.233 33.333 15.03 0.00 41.73 3.06
3012 7752 6.827586 ACACTAGGCAAAATTTCCGATTAA 57.172 33.333 0.00 0.00 0.00 1.40
3018 7758 5.893824 AGGCAAAATTTCCGATTAAGATCCT 59.106 36.000 0.00 0.00 0.00 3.24
3019 7759 7.060421 AGGCAAAATTTCCGATTAAGATCCTA 58.940 34.615 0.00 0.00 0.00 2.94
3053 7801 8.893727 AGCTAGTTTTTATGCGATTTTAGATGT 58.106 29.630 0.00 0.00 0.00 3.06
3124 7874 6.545666 CACATGACAAATGCCCTAAGGTTATA 59.454 38.462 0.00 0.00 34.57 0.98
3262 8013 7.257722 ACAACAAATTGACTTTGACAGGTAAG 58.742 34.615 0.00 0.00 45.96 2.34
3266 8017 8.962679 ACAAATTGACTTTGACAGGTAAGTAAA 58.037 29.630 0.00 0.00 45.96 2.01
3342 8093 4.882427 TCACGATTTTAAACACCCTGTCAA 59.118 37.500 0.00 0.00 0.00 3.18
3527 8278 6.924913 TTGTAAATCAAATGTGAATCCCCA 57.075 33.333 0.00 0.00 37.30 4.96
3530 8281 7.739825 TGTAAATCAAATGTGAATCCCCAAAA 58.260 30.769 0.00 0.00 37.30 2.44
3631 8383 7.572523 AATTATGTGGTTCAGGTGATGTATG 57.427 36.000 0.00 0.00 0.00 2.39
3656 8408 8.516234 TGTATGGTATTGATTTGGTGTTTGTAC 58.484 33.333 0.00 0.00 0.00 2.90
3666 8418 6.621316 TTTGGTGTTTGTACGTGTTGATAT 57.379 33.333 0.00 0.00 0.00 1.63
3674 8426 9.425577 TGTTTGTACGTGTTGATATATTTCTCA 57.574 29.630 0.00 0.00 0.00 3.27
3746 8498 9.642343 ATTTAATTTTCCAAGGAGGGAGTATAC 57.358 33.333 0.00 0.00 38.42 1.47
3837 8589 7.424803 TCATGGTAAAAGATTCAACACACTTG 58.575 34.615 0.00 0.00 0.00 3.16
3873 8625 3.563808 AGATGTTGTACGCAAGAAAGCAA 59.436 39.130 0.00 0.00 43.62 3.91
3909 8662 7.596995 CACCGCTTTTAATTTAGTTGATCCAAA 59.403 33.333 0.00 0.00 0.00 3.28
3910 8663 8.311109 ACCGCTTTTAATTTAGTTGATCCAAAT 58.689 29.630 0.00 0.00 0.00 2.32
3935 8688 9.740710 ATAGTACTAAAAAGGCACAAGAAAGAT 57.259 29.630 6.70 0.00 0.00 2.40
3954 8707 9.460019 AGAAAGATATGAAAGGAAAGGAGAAAG 57.540 33.333 0.00 0.00 0.00 2.62
3975 8730 3.318557 AGCTAATACCTTGACGAGCCTAC 59.681 47.826 0.00 0.00 0.00 3.18
3995 8750 6.872020 GCCTACGTAGCTCCATTTTTATATGA 59.128 38.462 17.41 0.00 0.00 2.15
4030 9084 8.905850 CAATATACCTAATTATGCATGCCATCA 58.094 33.333 16.68 0.00 35.34 3.07
4036 9090 7.284716 ACCTAATTATGCATGCCATCATCTATG 59.715 37.037 16.68 0.00 35.34 2.23
4037 9091 4.976224 TTATGCATGCCATCATCTATGC 57.024 40.909 16.68 0.00 44.56 3.14
4174 9233 7.208064 ACTACAAGGGGAAGCATATTTTCTA 57.792 36.000 0.00 0.00 0.00 2.10
4192 9251 8.928270 ATTTTCTACTAGGTTAGTTGACGATG 57.072 34.615 0.00 0.00 39.58 3.84
4234 9293 8.739972 GTTATTGGATATTGCACTATTAAGGGG 58.260 37.037 0.00 0.00 0.00 4.79
4235 9294 5.922960 TGGATATTGCACTATTAAGGGGT 57.077 39.130 0.00 0.00 0.00 4.95
4244 9303 4.576463 GCACTATTAAGGGGTCATGTGAAG 59.424 45.833 0.00 0.00 0.00 3.02
4323 9382 6.463995 AACTTTGTACATGAAAAAGGAGCA 57.536 33.333 17.52 0.00 35.64 4.26
4351 9410 0.248215 GCATCTTTCCAACGCCATCG 60.248 55.000 0.00 0.00 42.43 3.84
4372 9432 3.484649 CGTATTCACCCGTTTCGATACAG 59.515 47.826 6.81 0.00 0.00 2.74
4387 9447 4.688879 TCGATACAGCGTTTGAAAATGAGT 59.311 37.500 0.00 0.31 0.00 3.41
4432 9492 9.712305 TTTGAAAACAAACAAATACCTTCTTCA 57.288 25.926 0.00 0.00 32.26 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.288518 GGTCGATGAGTAAGATCCCAGC 60.289 54.545 0.00 0.00 0.00 4.85
12 13 3.506844 GGTAGGTCGATGAGTAAGATCCC 59.493 52.174 0.00 0.00 0.00 3.85
27 28 1.219393 GCTCTGCCAGTGGTAGGTC 59.781 63.158 25.06 14.10 36.09 3.85
78 79 1.594293 CGAACCAACGAGCCACTGT 60.594 57.895 0.00 0.00 35.09 3.55
82 83 2.449031 ATCAGCGAACCAACGAGCCA 62.449 55.000 0.00 0.00 35.09 4.75
138 139 0.242825 TTCGGAGTGCTCGGTACAAG 59.757 55.000 0.00 0.00 0.00 3.16
145 146 1.084370 GGGATGTTTCGGAGTGCTCG 61.084 60.000 0.00 0.00 0.00 5.03
153 154 4.141144 CCATCCGGGATGTTTCGG 57.859 61.111 29.93 14.73 46.89 4.30
163 170 1.904287 TTTGAAGAACACCCATCCGG 58.096 50.000 0.00 0.00 37.81 5.14
194 202 2.502538 ACCGCAAAATAGCACTACCCTA 59.497 45.455 0.00 0.00 0.00 3.53
195 203 1.280998 ACCGCAAAATAGCACTACCCT 59.719 47.619 0.00 0.00 0.00 4.34
225 234 1.737793 AGTCCCAAATTGCGACGAATC 59.262 47.619 0.00 0.00 0.00 2.52
249 258 7.352079 ACTTGCATCCTTCCTATAATTTTGG 57.648 36.000 0.00 0.00 0.00 3.28
257 266 4.677182 ACCAAAACTTGCATCCTTCCTAT 58.323 39.130 0.00 0.00 0.00 2.57
277 286 9.665264 GATCGATGTATTCTTTTTCCAAATACC 57.335 33.333 0.54 0.00 35.81 2.73
283 292 9.613428 ACAATAGATCGATGTATTCTTTTTCCA 57.387 29.630 21.38 0.00 0.00 3.53
310 319 6.935167 TGAACATCTAGCAAATGTGTCTCTA 58.065 36.000 0.00 0.00 37.42 2.43
316 325 6.849502 AGTGAATGAACATCTAGCAAATGTG 58.150 36.000 0.00 0.00 37.42 3.21
318 327 8.206325 AGTAGTGAATGAACATCTAGCAAATG 57.794 34.615 0.00 0.00 0.00 2.32
334 343 6.435904 AGTCTCAACTCTAGCAAGTAGTGAAT 59.564 38.462 0.00 0.00 0.00 2.57
336 345 5.317808 AGTCTCAACTCTAGCAAGTAGTGA 58.682 41.667 0.00 0.00 0.00 3.41
354 365 3.018149 ACATTGGGTCGTCTCTAGTCTC 58.982 50.000 0.00 0.00 0.00 3.36
372 383 2.038426 TCACCTCGACACAATTGGACAT 59.962 45.455 10.83 0.00 0.00 3.06
386 397 2.726760 CACTTCGTTCTTCTTCACCTCG 59.273 50.000 0.00 0.00 0.00 4.63
436 447 7.761981 ATATCTCCATAGCCCACATTCTTAT 57.238 36.000 0.00 0.00 0.00 1.73
437 448 8.122481 TCTATATCTCCATAGCCCACATTCTTA 58.878 37.037 0.00 0.00 0.00 2.10
440 452 6.609212 TCTCTATATCTCCATAGCCCACATTC 59.391 42.308 0.00 0.00 0.00 2.67
485 497 1.106285 CAAGTGCCCTAAATGCTCCC 58.894 55.000 0.00 0.00 0.00 4.30
492 504 0.250989 CGGAACCCAAGTGCCCTAAA 60.251 55.000 0.00 0.00 38.74 1.85
506 518 4.766404 AATTGGACACTTCAATCGGAAC 57.234 40.909 0.00 0.00 34.15 3.62
509 521 5.772521 AGAAAAATTGGACACTTCAATCGG 58.227 37.500 0.00 0.00 34.15 4.18
510 522 8.970691 ATAAGAAAAATTGGACACTTCAATCG 57.029 30.769 0.00 0.00 34.15 3.34
552 564 2.683362 CCAATTCTTCGCTAAAGGACCC 59.317 50.000 0.00 0.00 35.54 4.46
589 624 5.447818 GCCACCGAAATAAACTTCTCTCATG 60.448 44.000 0.00 0.00 0.00 3.07
593 628 3.344515 GGCCACCGAAATAAACTTCTCT 58.655 45.455 0.00 0.00 0.00 3.10
644 679 9.832445 GTTTCTAGTTGATCCCATACATTTAGA 57.168 33.333 0.00 0.00 0.00 2.10
645 680 8.765219 CGTTTCTAGTTGATCCCATACATTTAG 58.235 37.037 0.00 0.00 0.00 1.85
646 681 8.479689 TCGTTTCTAGTTGATCCCATACATTTA 58.520 33.333 0.00 0.00 0.00 1.40
647 682 7.280205 GTCGTTTCTAGTTGATCCCATACATTT 59.720 37.037 0.00 0.00 0.00 2.32
648 683 6.761714 GTCGTTTCTAGTTGATCCCATACATT 59.238 38.462 0.00 0.00 0.00 2.71
649 684 6.281405 GTCGTTTCTAGTTGATCCCATACAT 58.719 40.000 0.00 0.00 0.00 2.29
650 685 5.394883 GGTCGTTTCTAGTTGATCCCATACA 60.395 44.000 0.00 0.00 0.00 2.29
651 686 5.048507 GGTCGTTTCTAGTTGATCCCATAC 58.951 45.833 0.00 0.00 0.00 2.39
652 687 4.712829 TGGTCGTTTCTAGTTGATCCCATA 59.287 41.667 0.00 0.00 0.00 2.74
653 688 3.517901 TGGTCGTTTCTAGTTGATCCCAT 59.482 43.478 0.00 0.00 0.00 4.00
654 689 2.901192 TGGTCGTTTCTAGTTGATCCCA 59.099 45.455 0.00 0.00 0.00 4.37
661 696 8.949177 TCTTTTAAGTTTTGGTCGTTTCTAGTT 58.051 29.630 0.00 0.00 0.00 2.24
697 732 4.312443 TGGCCGAGTAAACTTTACTGAAG 58.688 43.478 17.26 9.24 41.32 3.02
699 734 4.546829 ATGGCCGAGTAAACTTTACTGA 57.453 40.909 17.26 0.00 0.00 3.41
725 760 3.557264 CCGATCCCCTAAACAATAGAGGC 60.557 52.174 0.00 0.00 0.00 4.70
734 769 2.595238 TCTCTAGCCGATCCCCTAAAC 58.405 52.381 0.00 0.00 0.00 2.01
748 783 2.294791 CGTGAGGTTAGGGCATCTCTAG 59.705 54.545 0.00 0.00 0.00 2.43
765 800 4.570369 CCAATAATGCATCAGTACACGTGA 59.430 41.667 25.01 2.68 0.00 4.35
768 803 3.561310 AGCCAATAATGCATCAGTACACG 59.439 43.478 0.00 0.00 0.00 4.49
784 819 9.071276 CATAGTTCCTGTGAATAATAAGCCAAT 57.929 33.333 0.00 0.00 31.98 3.16
786 821 7.801104 TCATAGTTCCTGTGAATAATAAGCCA 58.199 34.615 0.00 0.00 29.08 4.75
787 822 8.725148 CATCATAGTTCCTGTGAATAATAAGCC 58.275 37.037 0.00 0.00 35.41 4.35
816 853 6.786122 ACAAACTATGGGGTACACAAGTATT 58.214 36.000 0.00 0.00 30.67 1.89
855 905 3.693085 GGGACACGTAGTATTCTGACAGA 59.307 47.826 0.00 0.00 41.61 3.41
857 907 3.423749 TGGGACACGTAGTATTCTGACA 58.576 45.455 0.00 0.00 41.61 3.58
873 923 3.335579 GTCTGGACAAACTACATGGGAC 58.664 50.000 0.00 0.00 0.00 4.46
875 925 2.346803 CGTCTGGACAAACTACATGGG 58.653 52.381 0.00 0.00 0.00 4.00
890 940 1.154016 CTACTGCACGTCCCGTCTG 60.154 63.158 0.00 0.00 38.32 3.51
895 945 2.380084 TCAAATCTACTGCACGTCCC 57.620 50.000 0.00 0.00 0.00 4.46
904 954 5.187967 AGTCGGACAAGGAATCAAATCTACT 59.812 40.000 11.27 0.00 0.00 2.57
1028 1109 1.080705 GGCACGTACGTCTGAAGCT 60.081 57.895 19.94 0.00 0.00 3.74
1087 1168 0.549469 GGTTCCCCCATCGTTGGTAT 59.451 55.000 11.51 0.00 41.91 2.73
1887 5461 3.226429 GAGCTGCTGGTCGTGGTGA 62.226 63.158 7.01 0.00 0.00 4.02
1920 5494 0.608856 TGTAGCGTAGGTCCCAACGA 60.609 55.000 16.44 0.00 41.55 3.85
1974 5557 1.524863 CGAACCAGACACTCCTCGGT 61.525 60.000 0.00 0.00 0.00 4.69
2001 5584 2.232208 CCTGTAGCACAGTGTCATCTCA 59.768 50.000 13.06 0.00 44.50 3.27
2160 5743 3.527775 GAGCAGGCTGGGGCGATAG 62.528 68.421 17.64 0.00 39.81 2.08
2223 5806 4.151798 GCTCGAATTTTTGTCTTTCCTCG 58.848 43.478 0.00 0.00 0.00 4.63
2272 5863 4.218635 GCATGATGCTTCCATTCATCTGAT 59.781 41.667 10.72 0.00 40.96 2.90
2278 5869 4.321675 GCATATGCATGATGCTTCCATTCA 60.322 41.667 22.84 0.00 45.31 2.57
2279 5870 4.174009 GCATATGCATGATGCTTCCATTC 58.826 43.478 22.84 0.00 45.31 2.67
2388 6029 8.438676 AAGCTATAAGTAATGTGACCATGAAC 57.561 34.615 0.00 0.00 0.00 3.18
2423 6064 3.504520 GGAATCTTACCCGCAAAAGAACA 59.495 43.478 0.00 0.00 35.47 3.18
2424 6065 3.756963 AGGAATCTTACCCGCAAAAGAAC 59.243 43.478 0.00 0.00 35.47 3.01
2582 6226 6.267928 ACAGAGGTCTACACAACTAACTGAAT 59.732 38.462 0.00 0.00 0.00 2.57
2802 7305 7.435068 TTTCCAAGGACTCGATTTCTTTAAG 57.565 36.000 0.00 0.00 0.00 1.85
2860 7587 9.216117 GTCTTTGTGTAAGGTGTAATTATCAGT 57.784 33.333 0.00 0.00 34.46 3.41
2861 7588 9.214957 TGTCTTTGTGTAAGGTGTAATTATCAG 57.785 33.333 0.00 0.00 34.46 2.90
2873 7600 8.405531 CCATTAATATGGTGTCTTTGTGTAAGG 58.594 37.037 0.00 0.00 45.34 2.69
2898 7625 4.097714 CGCAAACAATACACATGATCACC 58.902 43.478 0.00 0.00 0.00 4.02
2912 7639 1.683917 ACCAATACCAAGCGCAAACAA 59.316 42.857 11.47 0.00 0.00 2.83
2919 7646 5.583061 TGTGTTCTTATACCAATACCAAGCG 59.417 40.000 0.00 0.00 0.00 4.68
3228 7979 8.997323 TCAAAGTCAATTTGTTGTTTTGTTGAT 58.003 25.926 0.00 0.00 46.96 2.57
3242 7993 9.185680 AGTTTACTTACCTGTCAAAGTCAATTT 57.814 29.630 0.00 0.00 37.19 1.82
3384 8135 8.770438 AAACAACTTAAAACATTGCTCTGAAA 57.230 26.923 0.00 0.00 0.00 2.69
3502 8253 7.555087 TGGGGATTCACATTTGATTTACAATC 58.445 34.615 0.00 0.00 38.36 2.67
3507 8258 8.824783 AGATTTTGGGGATTCACATTTGATTTA 58.175 29.630 0.00 0.00 0.00 1.40
3515 8266 8.260114 GTCATAAAAGATTTTGGGGATTCACAT 58.740 33.333 0.82 0.00 0.00 3.21
3527 8278 7.174946 AGACCGTGTCATGTCATAAAAGATTTT 59.825 33.333 0.00 0.00 34.60 1.82
3530 8281 5.734720 AGACCGTGTCATGTCATAAAAGAT 58.265 37.500 0.00 0.00 34.60 2.40
3590 8342 8.939929 CCACATAATTATTTCTATGCGAGACAT 58.060 33.333 0.00 0.00 43.18 3.06
3593 8345 8.902540 AACCACATAATTATTTCTATGCGAGA 57.097 30.769 0.00 0.00 0.00 4.04
3613 8365 4.816385 CCATACATACATCACCTGAACCAC 59.184 45.833 0.00 0.00 0.00 4.16
3631 8383 7.694784 CGTACAAACACCAAATCAATACCATAC 59.305 37.037 0.00 0.00 0.00 2.39
3716 8468 8.156820 ACTCCCTCCTTGGAAAATTAAATTTTG 58.843 33.333 0.00 0.00 42.15 2.44
3730 8482 3.375699 ACACAGTATACTCCCTCCTTGG 58.624 50.000 1.26 0.00 0.00 3.61
3837 8589 4.134563 ACAACATCTGGTCCAAAGTACAC 58.865 43.478 0.00 0.00 0.00 2.90
3909 8662 9.740710 ATCTTTCTTGTGCCTTTTTAGTACTAT 57.259 29.630 2.79 0.00 0.00 2.12
3912 8665 9.774742 CATATCTTTCTTGTGCCTTTTTAGTAC 57.225 33.333 0.00 0.00 0.00 2.73
3913 8666 9.733556 TCATATCTTTCTTGTGCCTTTTTAGTA 57.266 29.630 0.00 0.00 0.00 1.82
3914 8667 8.635765 TCATATCTTTCTTGTGCCTTTTTAGT 57.364 30.769 0.00 0.00 0.00 2.24
3915 8668 9.912634 TTTCATATCTTTCTTGTGCCTTTTTAG 57.087 29.630 0.00 0.00 0.00 1.85
3916 8669 9.912634 CTTTCATATCTTTCTTGTGCCTTTTTA 57.087 29.630 0.00 0.00 0.00 1.52
3935 8688 9.614792 GTATTAGCTTTCTCCTTTCCTTTCATA 57.385 33.333 0.00 0.00 0.00 2.15
3954 8707 2.892784 AGGCTCGTCAAGGTATTAGC 57.107 50.000 0.00 0.00 0.00 3.09
3975 8730 9.639601 TCTATGTCATATAAAAATGGAGCTACG 57.360 33.333 0.00 0.00 0.00 3.51
4030 9084 5.940192 TCAAGTGTTTTCAACGCATAGAT 57.060 34.783 3.20 0.00 44.15 1.98
4056 9110 8.716674 ATATGCTGAGGAATCAACCATAAATT 57.283 30.769 0.00 0.00 0.00 1.82
4075 9129 9.948964 TGTGCTCATGTTATTCTAATATATGCT 57.051 29.630 0.00 0.00 0.00 3.79
4094 9152 4.463539 AGGTGATGCAATATTTTGTGCTCA 59.536 37.500 0.00 0.00 41.48 4.26
4133 9191 7.760340 CCCTTGTAGTTCATTCTACTTCAGTAC 59.240 40.741 0.00 0.00 40.39 2.73
4174 9233 5.948162 TCCTTACATCGTCAACTAACCTAGT 59.052 40.000 0.00 0.00 41.73 2.57
4230 9289 1.004044 CTCTTGCTTCACATGACCCCT 59.996 52.381 0.00 0.00 0.00 4.79
4234 9293 1.527034 TGCCTCTTGCTTCACATGAC 58.473 50.000 0.00 0.00 42.00 3.06
4235 9294 2.275134 TTGCCTCTTGCTTCACATGA 57.725 45.000 0.00 0.00 42.00 3.07
4244 9303 3.721035 ACAACATCTTTTTGCCTCTTGC 58.279 40.909 0.00 0.00 41.77 4.01
4351 9410 3.244579 GCTGTATCGAAACGGGTGAATAC 59.755 47.826 0.00 0.00 0.00 1.89
4418 9478 5.478332 AGAGCCCTTTTGAAGAAGGTATTTG 59.522 40.000 3.26 0.00 43.84 2.32
4423 9483 3.602205 AAGAGCCCTTTTGAAGAAGGT 57.398 42.857 3.26 0.00 43.84 3.50


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

AutoCloner maintained by Alex Coulton.