Multiple sequence alignment - TraesCS3D01G425100

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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 TraesCS3D01G425100 chr3D 100.000 5841 0 0 1 5841 537145749 537151589 0.000000e+00 10787.0
1 TraesCS3D01G425100 chr3D 89.426 662 27 8 5223 5841 416197947 416197286 0.000000e+00 795.0
2 TraesCS3D01G425100 chr3D 90.164 610 22 7 5270 5841 3073853 3074462 0.000000e+00 760.0
3 TraesCS3D01G425100 chr3D 91.954 87 5 2 4814 4900 537335536 537335620 2.860000e-23 121.0
4 TraesCS3D01G425100 chr3A 94.527 2613 88 26 2625 5211 672553859 672556442 0.000000e+00 3982.0
5 TraesCS3D01G425100 chr3A 93.539 1331 37 20 1 1317 672551172 672552467 0.000000e+00 1936.0
6 TraesCS3D01G425100 chr3A 89.901 911 67 11 1353 2248 672552465 672553365 0.000000e+00 1149.0
7 TraesCS3D01G425100 chr3A 91.136 361 13 3 2245 2604 672553525 672553867 6.850000e-129 472.0
8 TraesCS3D01G425100 chr3A 83.036 224 33 5 2890 3110 672552965 672553186 1.280000e-46 198.0
9 TraesCS3D01G425100 chr3A 86.301 73 8 2 5415 5485 127863418 127863490 1.750000e-10 78.7
10 TraesCS3D01G425100 chr3B 91.671 2089 127 31 3128 5188 710591241 710593310 0.000000e+00 2850.0
11 TraesCS3D01G425100 chr3B 90.168 2207 124 33 1 2149 710587821 710589992 0.000000e+00 2787.0
12 TraesCS3D01G425100 chr3B 87.970 931 71 19 2172 3072 710590175 710591094 0.000000e+00 1061.0
13 TraesCS3D01G425100 chr5D 90.671 611 16 10 5270 5841 487567518 487566910 0.000000e+00 774.0
14 TraesCS3D01G425100 chr5D 89.853 611 21 8 5270 5841 7472999 7472391 0.000000e+00 747.0
15 TraesCS3D01G425100 chr5D 89.396 613 24 7 5270 5841 178468242 178468854 0.000000e+00 734.0
16 TraesCS3D01G425100 chr5D 97.368 38 1 0 5229 5266 421306477 421306440 1.360000e-06 65.8
17 TraesCS3D01G425100 chr5D 91.304 46 3 1 5222 5266 178468175 178468220 1.760000e-05 62.1
18 TraesCS3D01G425100 chr2D 90.640 609 20 6 5270 5841 648154317 648154925 0.000000e+00 774.0
19 TraesCS3D01G425100 chr2D 90.328 610 21 7 5270 5841 15834745 15834136 0.000000e+00 765.0
20 TraesCS3D01G425100 chr2D 95.455 44 2 0 5223 5266 531927469 531927426 2.920000e-08 71.3
21 TraesCS3D01G425100 chr2D 91.489 47 3 1 5220 5266 648154250 648154295 4.890000e-06 63.9
22 TraesCS3D01G425100 chr1D 90.476 609 21 6 5270 5841 460760652 460760044 0.000000e+00 769.0
23 TraesCS3D01G425100 chr1D 91.489 47 2 2 5221 5266 212693925 212693970 4.890000e-06 63.9
24 TraesCS3D01G425100 chr4D 88.702 655 29 10 5231 5841 352520399 352521052 0.000000e+00 758.0
25 TraesCS3D01G425100 chr4D 87.769 605 26 11 5282 5841 119824329 119824930 0.000000e+00 664.0
26 TraesCS3D01G425100 chr7D 90.164 610 19 9 5270 5841 340263218 340262612 0.000000e+00 756.0
27 TraesCS3D01G425100 chr7D 89.869 612 22 8 5270 5841 77442053 77442664 0.000000e+00 750.0
28 TraesCS3D01G425100 chr7D 86.301 73 9 1 5415 5486 603844573 603844645 1.750000e-10 78.7
29 TraesCS3D01G425100 chr7D 95.238 42 2 0 5230 5271 52710821 52710862 3.780000e-07 67.6
30 TraesCS3D01G425100 chr7D 93.333 45 3 0 5222 5266 340263296 340263252 3.780000e-07 67.6
31 TraesCS3D01G425100 chr7D 93.182 44 2 1 5223 5266 399822816 399822774 4.890000e-06 63.9
32 TraesCS3D01G425100 chrUn 86.364 110 5 5 3247 3356 87872504 87872603 1.720000e-20 111.0
33 TraesCS3D01G425100 chrUn 86.364 110 5 5 3247 3356 473181016 473180917 1.720000e-20 111.0
34 TraesCS3D01G425100 chrUn 90.541 74 7 0 5433 5506 211005248 211005175 1.340000e-16 99.0
35 TraesCS3D01G425100 chrUn 98.148 54 0 1 3536 3589 87872599 87872651 6.230000e-15 93.5
36 TraesCS3D01G425100 chrUn 98.148 54 0 1 3536 3589 473180921 473180869 6.230000e-15 93.5
37 TraesCS3D01G425100 chr7A 86.667 75 7 3 5415 5486 102043242 102043316 4.850000e-11 80.5
38 TraesCS3D01G425100 chr4B 88.136 59 7 0 5427 5485 607276570 607276512 2.920000e-08 71.3
39 TraesCS3D01G425100 chr5A 92.857 42 3 0 5221 5262 299125364 299125323 1.760000e-05 62.1


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 TraesCS3D01G425100 chr3D 537145749 537151589 5840 False 10787.000000 10787 100.000000 1 5841 1 chr3D.!!$F2 5840
1 TraesCS3D01G425100 chr3D 416197286 416197947 661 True 795.000000 795 89.426000 5223 5841 1 chr3D.!!$R1 618
2 TraesCS3D01G425100 chr3D 3073853 3074462 609 False 760.000000 760 90.164000 5270 5841 1 chr3D.!!$F1 571
3 TraesCS3D01G425100 chr3A 672551172 672556442 5270 False 1547.400000 3982 90.427800 1 5211 5 chr3A.!!$F2 5210
4 TraesCS3D01G425100 chr3B 710587821 710593310 5489 False 2232.666667 2850 89.936333 1 5188 3 chr3B.!!$F1 5187
5 TraesCS3D01G425100 chr5D 487566910 487567518 608 True 774.000000 774 90.671000 5270 5841 1 chr5D.!!$R3 571
6 TraesCS3D01G425100 chr5D 7472391 7472999 608 True 747.000000 747 89.853000 5270 5841 1 chr5D.!!$R1 571
7 TraesCS3D01G425100 chr5D 178468175 178468854 679 False 398.050000 734 90.350000 5222 5841 2 chr5D.!!$F1 619
8 TraesCS3D01G425100 chr2D 15834136 15834745 609 True 765.000000 765 90.328000 5270 5841 1 chr2D.!!$R1 571
9 TraesCS3D01G425100 chr2D 648154250 648154925 675 False 418.950000 774 91.064500 5220 5841 2 chr2D.!!$F1 621
10 TraesCS3D01G425100 chr1D 460760044 460760652 608 True 769.000000 769 90.476000 5270 5841 1 chr1D.!!$R1 571
11 TraesCS3D01G425100 chr4D 352520399 352521052 653 False 758.000000 758 88.702000 5231 5841 1 chr4D.!!$F2 610
12 TraesCS3D01G425100 chr4D 119824329 119824930 601 False 664.000000 664 87.769000 5282 5841 1 chr4D.!!$F1 559
13 TraesCS3D01G425100 chr7D 77442053 77442664 611 False 750.000000 750 89.869000 5270 5841 1 chr7D.!!$F2 571
14 TraesCS3D01G425100 chr7D 340262612 340263296 684 True 411.800000 756 91.748500 5222 5841 2 chr7D.!!$R2 619

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
682 694 0.741221 CCTAGTGGGCTTCAGAACGC 60.741 60.000 0.0 0.0 0.0 4.84 F
2617 3051 0.037590 TTAGGCCCGCACTGAAATGT 59.962 50.000 0.0 0.0 0.0 2.71 F
2906 3345 0.532115 CCTATGCTGCCAAACCCAAC 59.468 55.000 0.0 0.0 0.0 3.77 F
4497 5043 1.003349 CATTTGCCCCCTTGCATTTCA 59.997 47.619 0.0 0.0 41.7 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2622 3056 0.040351 TCTGCTGTCTCCTAGCACCT 59.960 55.0 0.0 0.0 45.52 4.00 R
4482 5028 0.396060 TGTTTGAAATGCAAGGGGGC 59.604 50.0 0.0 0.0 37.87 5.80 R
4757 5311 0.899717 AGCCAAACACCGATGCCAAT 60.900 50.0 0.0 0.0 0.00 3.16 R
5818 6482 2.664402 AATCAAGCAACTGTCCTGGT 57.336 45.0 0.0 0.0 0.00 4.00 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
426 435 3.292936 GCTGCCTTGCACACTGCT 61.293 61.111 0.00 0.00 45.31 4.24
682 694 0.741221 CCTAGTGGGCTTCAGAACGC 60.741 60.000 0.00 0.00 0.00 4.84
830 844 4.537433 GCCTGGCAGCGTCCTAGG 62.537 72.222 15.17 0.82 0.00 3.02
1125 1167 3.124088 CCTCCCCCTCCTCCTCTT 58.876 66.667 0.00 0.00 0.00 2.85
1317 1359 1.808390 GGTACGCCGCGAGATTTGT 60.808 57.895 21.79 0.00 0.00 2.83
1318 1360 1.343821 GTACGCCGCGAGATTTGTG 59.656 57.895 21.79 0.00 0.00 3.33
1319 1361 2.449525 TACGCCGCGAGATTTGTGC 61.450 57.895 21.79 0.00 0.00 4.57
1325 1367 2.148365 GCGAGATTTGTGCGCTTGC 61.148 57.895 9.73 0.00 46.53 4.01
1332 1374 0.801451 TTTGTGCGCTTGCTTGTGTG 60.801 50.000 9.73 0.00 40.12 3.82
1360 1403 3.153130 TCGGTGAATTTGATTGCTTCCA 58.847 40.909 0.00 0.00 0.00 3.53
1409 1452 8.146053 TGATTATTCCTAGAGAAGTTGGAACA 57.854 34.615 0.00 0.00 40.78 3.18
1441 1484 3.262405 TCCTACCTAACAATTTGGTCGCT 59.738 43.478 0.78 0.00 35.48 4.93
1513 1558 1.618343 AGTTGTGCTTTTATGCCCACC 59.382 47.619 0.00 0.00 0.00 4.61
1521 1566 4.345257 TGCTTTTATGCCCACCAGTTTTTA 59.655 37.500 0.00 0.00 0.00 1.52
1522 1567 4.929211 GCTTTTATGCCCACCAGTTTTTAG 59.071 41.667 0.00 0.00 0.00 1.85
1525 1570 7.598759 TTTTATGCCCACCAGTTTTTAGTTA 57.401 32.000 0.00 0.00 0.00 2.24
1526 1571 7.784470 TTTATGCCCACCAGTTTTTAGTTAT 57.216 32.000 0.00 0.00 0.00 1.89
1527 1572 5.659440 ATGCCCACCAGTTTTTAGTTATG 57.341 39.130 0.00 0.00 0.00 1.90
1536 1582 6.490040 ACCAGTTTTTAGTTATGTCATGTGCT 59.510 34.615 0.00 0.00 0.00 4.40
1552 1598 8.793592 TGTCATGTGCTAGTTAGTTATATCGAT 58.206 33.333 2.16 2.16 0.00 3.59
1641 1688 4.278419 GCTGAACACTGAAGTATTGGGTTT 59.722 41.667 0.00 0.00 0.00 3.27
1644 1691 5.654650 TGAACACTGAAGTATTGGGTTTGTT 59.345 36.000 0.00 0.00 0.00 2.83
1645 1692 5.514274 ACACTGAAGTATTGGGTTTGTTG 57.486 39.130 0.00 0.00 0.00 3.33
1646 1693 4.340950 ACACTGAAGTATTGGGTTTGTTGG 59.659 41.667 0.00 0.00 0.00 3.77
1647 1694 3.320826 ACTGAAGTATTGGGTTTGTTGGC 59.679 43.478 0.00 0.00 0.00 4.52
1648 1695 3.300388 TGAAGTATTGGGTTTGTTGGCA 58.700 40.909 0.00 0.00 0.00 4.92
1649 1696 3.068873 TGAAGTATTGGGTTTGTTGGCAC 59.931 43.478 0.00 0.00 0.00 5.01
1650 1697 1.611491 AGTATTGGGTTTGTTGGCACG 59.389 47.619 0.00 0.00 0.00 5.34
1655 1702 2.088423 TGGGTTTGTTGGCACGATATC 58.912 47.619 0.00 0.00 0.00 1.63
1656 1703 2.088423 GGGTTTGTTGGCACGATATCA 58.912 47.619 3.12 0.00 0.00 2.15
1658 1705 3.489059 GGGTTTGTTGGCACGATATCATG 60.489 47.826 3.12 0.00 0.00 3.07
1670 1717 4.026558 CACGATATCATGAACCACAGAACG 60.027 45.833 0.00 0.00 0.00 3.95
1778 1825 7.451566 ACCTTTAATGGTTAGATGAGTTGCTTT 59.548 33.333 7.21 0.00 36.89 3.51
1797 1844 5.970879 GCTTTTAGCATGCTTGATTTATGC 58.029 37.500 28.02 15.00 45.64 3.14
1833 1880 4.177026 CAGCATGTACAGAACCTGTAGTC 58.823 47.826 0.33 0.00 45.88 2.59
1843 1890 4.688879 CAGAACCTGTAGTCGCATTTGTTA 59.311 41.667 0.00 0.00 0.00 2.41
1907 1961 6.048732 TGGCACAGATTGATTGTAGAACTA 57.951 37.500 0.00 0.00 0.00 2.24
1912 1966 7.201478 GCACAGATTGATTGTAGAACTACAGAC 60.201 40.741 13.20 11.80 45.57 3.51
1926 1980 6.483640 AGAACTACAGACTGGTTGTTTTCATC 59.516 38.462 7.51 0.00 36.97 2.92
2082 2148 0.856641 TGCGTGAGTGAGCGTTTTAC 59.143 50.000 0.00 0.00 35.87 2.01
2197 2423 1.000843 TGCTGAACACTGCAGTATCGT 59.999 47.619 21.20 11.03 35.81 3.73
2209 2435 3.743911 TGCAGTATCGTGTTTGTTGGTAG 59.256 43.478 0.00 0.00 0.00 3.18
2218 2444 4.753107 CGTGTTTGTTGGTAGGATGTTACT 59.247 41.667 0.00 0.00 0.00 2.24
2222 2448 7.227116 GTGTTTGTTGGTAGGATGTTACTAACA 59.773 37.037 9.93 9.93 46.49 2.41
2296 2685 4.953579 AGGTGTTTGGAGTGTGTTAACAAT 59.046 37.500 10.51 0.00 38.27 2.71
2348 2737 4.826733 TGTATGGAACTTGCTTGATTGTGT 59.173 37.500 0.00 0.00 0.00 3.72
2349 2738 3.713858 TGGAACTTGCTTGATTGTGTG 57.286 42.857 0.00 0.00 0.00 3.82
2498 2888 9.529823 TGGTAATGGTGGTGTTTGTATATTTAA 57.470 29.630 0.00 0.00 0.00 1.52
2581 2984 5.682943 TTTTGAAGTCGTATTTCCTGTGG 57.317 39.130 0.00 0.00 0.00 4.17
2605 3039 1.964448 AAAAAGTGCGCTTAGGCCC 59.036 52.632 13.93 0.00 33.95 5.80
2606 3040 1.862602 AAAAAGTGCGCTTAGGCCCG 61.863 55.000 13.93 0.00 33.95 6.13
2612 3046 4.451150 CGCTTAGGCCCGCACTGA 62.451 66.667 0.00 0.00 34.44 3.41
2613 3047 2.046314 GCTTAGGCCCGCACTGAA 60.046 61.111 0.00 0.00 0.00 3.02
2614 3048 1.674322 GCTTAGGCCCGCACTGAAA 60.674 57.895 0.00 0.00 0.00 2.69
2615 3049 1.032114 GCTTAGGCCCGCACTGAAAT 61.032 55.000 0.00 0.00 0.00 2.17
2616 3050 0.734889 CTTAGGCCCGCACTGAAATG 59.265 55.000 0.00 0.00 0.00 2.32
2617 3051 0.037590 TTAGGCCCGCACTGAAATGT 59.962 50.000 0.00 0.00 0.00 2.71
2618 3052 0.676466 TAGGCCCGCACTGAAATGTG 60.676 55.000 0.00 0.00 40.62 3.21
2627 3061 1.470098 CACTGAAATGTGCCTAGGTGC 59.530 52.381 11.31 4.18 0.00 5.01
2628 3062 1.352352 ACTGAAATGTGCCTAGGTGCT 59.648 47.619 11.31 0.00 0.00 4.40
2629 3063 2.571653 ACTGAAATGTGCCTAGGTGCTA 59.428 45.455 11.31 0.00 0.00 3.49
2630 3064 3.201290 CTGAAATGTGCCTAGGTGCTAG 58.799 50.000 11.31 0.00 34.16 3.42
2730 3164 3.250040 CACTGTTAGTGCCTAGCGTTTTT 59.750 43.478 0.00 0.00 39.62 1.94
2906 3345 0.532115 CCTATGCTGCCAAACCCAAC 59.468 55.000 0.00 0.00 0.00 3.77
2917 3356 2.364002 CCAAACCCAACGACCTTTCAAT 59.636 45.455 0.00 0.00 0.00 2.57
3052 3499 4.822036 TTACGTGCATGCTTGTTTAGTT 57.178 36.364 20.33 0.00 0.00 2.24
3109 3609 7.144722 TGCATACAATTATATAGCTTGTGCC 57.855 36.000 16.92 9.35 40.80 5.01
3110 3610 6.150976 TGCATACAATTATATAGCTTGTGCCC 59.849 38.462 16.92 9.13 40.80 5.36
3112 3612 4.714632 ACAATTATATAGCTTGTGCCCGT 58.285 39.130 10.38 0.00 40.80 5.28
3124 3662 1.944024 TGTGCCCGTCTTACTGTTTTG 59.056 47.619 0.00 0.00 0.00 2.44
3152 3690 2.765689 TGATTGGGGTCAAAAGTGGT 57.234 45.000 0.00 0.00 36.36 4.16
3426 3964 2.574824 CCATGGGCCTGAGATCATATGA 59.425 50.000 8.10 8.10 0.00 2.15
3430 3968 5.329191 TGGGCCTGAGATCATATGATTTT 57.671 39.130 19.11 10.92 34.37 1.82
3431 3969 5.708544 TGGGCCTGAGATCATATGATTTTT 58.291 37.500 19.11 8.55 34.37 1.94
3432 3970 6.851318 TGGGCCTGAGATCATATGATTTTTA 58.149 36.000 19.11 7.39 34.37 1.52
3433 3971 7.296856 TGGGCCTGAGATCATATGATTTTTAA 58.703 34.615 19.11 3.91 34.37 1.52
3436 3974 7.020010 GCCTGAGATCATATGATTTTTAAGCG 58.980 38.462 19.11 8.34 34.37 4.68
3437 3975 7.020010 CCTGAGATCATATGATTTTTAAGCGC 58.980 38.462 19.11 0.00 34.37 5.92
3438 3976 6.902341 TGAGATCATATGATTTTTAAGCGCC 58.098 36.000 19.11 3.01 34.37 6.53
3443 3981 9.229784 GATCATATGATTTTTAAGCGCCATATG 57.770 33.333 19.11 22.40 42.12 1.78
3447 3985 3.857549 TTTTTAAGCGCCATATGCACA 57.142 38.095 2.29 0.00 41.33 4.57
3448 3986 4.383850 TTTTTAAGCGCCATATGCACAT 57.616 36.364 2.29 0.00 41.33 3.21
3499 4037 7.686938 CGGTTTCTGTTAATAAGTTTCTAAGCG 59.313 37.037 0.00 0.00 0.00 4.68
3513 4051 3.024547 TCTAAGCGTATTCAGCTGGAGT 58.975 45.455 15.13 2.70 45.31 3.85
3530 4068 3.628942 TGGAGTTTGAGATATGTGCATGC 59.371 43.478 11.82 11.82 0.00 4.06
3771 4309 3.398967 ACAACACCCCATGCCTATGATAT 59.601 43.478 0.00 0.00 36.36 1.63
3916 4454 6.313905 ACTCTGAACCTTTTATTCGTAGCATG 59.686 38.462 0.00 0.00 0.00 4.06
3973 4513 6.701145 TTGCCTTTCTGTAACATTTGTGTA 57.299 33.333 0.00 0.00 0.00 2.90
4128 4668 5.105392 TGCTTATTACATTTTCTGCCCTTGG 60.105 40.000 0.00 0.00 0.00 3.61
4287 4829 8.277490 TGTACTAGTCAATCCAGTAGTGTTAG 57.723 38.462 0.00 0.00 34.81 2.34
4374 4917 5.964958 ACCCTTCACACATTTGTCTTATG 57.035 39.130 0.00 0.00 31.66 1.90
4382 4925 3.068590 CACATTTGTCTTATGCCCATCCC 59.931 47.826 0.00 0.00 0.00 3.85
4393 4936 1.389609 GCCCATCCCATTGCTGTCAG 61.390 60.000 0.00 0.00 0.00 3.51
4497 5043 1.003349 CATTTGCCCCCTTGCATTTCA 59.997 47.619 0.00 0.00 41.70 2.69
4504 5050 3.140623 CCCCCTTGCATTTCAAACAAAG 58.859 45.455 0.00 0.00 33.65 2.77
4515 5061 5.715434 TTTCAAACAAAGTACATAGCCCC 57.285 39.130 0.00 0.00 0.00 5.80
4516 5062 4.650972 TCAAACAAAGTACATAGCCCCT 57.349 40.909 0.00 0.00 0.00 4.79
4542 5094 3.208594 TCCATTGATGTGCTACATGCTC 58.791 45.455 6.52 0.00 39.27 4.26
4589 5143 8.651588 CATATGACCTCGAGTATATTTTCTTGC 58.348 37.037 12.31 0.00 0.00 4.01
4590 5144 5.357257 TGACCTCGAGTATATTTTCTTGCC 58.643 41.667 12.31 0.00 0.00 4.52
4612 5166 4.038402 CCCATACATCTGGCCTTGATTTTC 59.962 45.833 3.32 0.00 34.77 2.29
4651 5205 7.505923 ACATGCCACATATACTCTACTCTGTTA 59.494 37.037 0.00 0.00 0.00 2.41
4694 5248 6.934056 AGAATATATTGTGGTTTGCAGCAAA 58.066 32.000 16.93 16.93 30.33 3.68
4757 5311 2.130193 CTGGATGGGGGATTCTTCTCA 58.870 52.381 0.00 0.00 0.00 3.27
5027 5584 6.169557 TGGATATGCTTCCTTACGTTATGT 57.830 37.500 0.00 0.00 36.68 2.29
5118 5691 4.711846 TGAGTACTGATGTGCTGATACCTT 59.288 41.667 0.00 0.00 39.21 3.50
5190 5764 3.563808 ACGTGCTCATCTCATACTCTCTC 59.436 47.826 0.00 0.00 0.00 3.20
5201 5775 3.445450 TCATACTCTCTCTTGGTGTCTGC 59.555 47.826 0.00 0.00 0.00 4.26
5207 5781 0.250640 CTCTTGGTGTCTGCTTGGCT 60.251 55.000 0.00 0.00 0.00 4.75
5211 5785 1.032014 TGGTGTCTGCTTGGCTTTTC 58.968 50.000 0.00 0.00 0.00 2.29
5212 5786 1.322442 GGTGTCTGCTTGGCTTTTCT 58.678 50.000 0.00 0.00 0.00 2.52
5213 5787 1.683385 GGTGTCTGCTTGGCTTTTCTT 59.317 47.619 0.00 0.00 0.00 2.52
5214 5788 2.287849 GGTGTCTGCTTGGCTTTTCTTC 60.288 50.000 0.00 0.00 0.00 2.87
5215 5789 2.620585 GTGTCTGCTTGGCTTTTCTTCT 59.379 45.455 0.00 0.00 0.00 2.85
5216 5790 2.620115 TGTCTGCTTGGCTTTTCTTCTG 59.380 45.455 0.00 0.00 0.00 3.02
5217 5791 2.030451 GTCTGCTTGGCTTTTCTTCTGG 60.030 50.000 0.00 0.00 0.00 3.86
5218 5792 0.675633 TGCTTGGCTTTTCTTCTGGC 59.324 50.000 0.00 0.00 0.00 4.85
5219 5793 0.675633 GCTTGGCTTTTCTTCTGGCA 59.324 50.000 0.00 0.00 34.48 4.92
5220 5794 1.274447 GCTTGGCTTTTCTTCTGGCAT 59.726 47.619 0.00 0.00 36.21 4.40
5266 5840 2.974698 AGCTGCGCTCGTTTGCTT 60.975 55.556 9.73 0.00 30.62 3.91
5268 5842 2.633657 CTGCGCTCGTTTGCTTGT 59.366 55.556 9.73 0.00 0.00 3.16
5375 5989 7.658167 TGACACACTCTTTATTCCGTTTCATTA 59.342 33.333 0.00 0.00 0.00 1.90
5716 6374 9.606631 AGTTGCTTGGTTTTGTTATTGAAATTA 57.393 25.926 0.00 0.00 0.00 1.40
5835 6499 3.569194 TTTACCAGGACAGTTGCTTGA 57.431 42.857 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
426 435 3.093057 GAGCCAAGAAGACCAGAGTAGA 58.907 50.000 0.00 0.00 0.00 2.59
585 595 2.355108 GGTGCATGTTTCAGAGGAGCTA 60.355 50.000 0.00 0.00 0.00 3.32
690 702 4.379243 CCCAGCTCGGCAGTTCGT 62.379 66.667 0.00 0.00 0.00 3.85
710 724 2.902423 AAAAGCATATCCCGCGGCCA 62.902 55.000 22.85 8.89 0.00 5.36
830 844 3.202706 GGGGATCGCACCGCTTTC 61.203 66.667 12.32 0.00 39.35 2.62
860 874 6.285990 ACTAGTAGTTGTTGTTGTTGTAGGG 58.714 40.000 0.00 0.00 0.00 3.53
861 875 7.042254 GGAACTAGTAGTTGTTGTTGTTGTAGG 60.042 40.741 20.21 0.00 38.80 3.18
862 876 7.042254 GGGAACTAGTAGTTGTTGTTGTTGTAG 60.042 40.741 20.21 0.00 38.80 2.74
864 878 5.587443 GGGAACTAGTAGTTGTTGTTGTTGT 59.413 40.000 20.21 0.00 38.80 3.32
865 879 5.008316 GGGGAACTAGTAGTTGTTGTTGTTG 59.992 44.000 20.21 0.00 38.80 3.33
866 880 5.128205 GGGGAACTAGTAGTTGTTGTTGTT 58.872 41.667 20.21 0.00 38.80 2.83
1317 1359 0.950836 AATACACACAAGCAAGCGCA 59.049 45.000 11.47 0.00 42.27 6.09
1318 1360 1.197721 AGAATACACACAAGCAAGCGC 59.802 47.619 0.00 0.00 38.99 5.92
1319 1361 3.482786 GAAGAATACACACAAGCAAGCG 58.517 45.455 0.00 0.00 0.00 4.68
1325 1367 5.862924 ATTCACCGAAGAATACACACAAG 57.137 39.130 1.17 0.00 36.51 3.16
1332 1374 6.555315 AGCAATCAAATTCACCGAAGAATAC 58.445 36.000 3.28 0.00 37.24 1.89
1360 1403 3.197766 TCGAAGCCACTAAATCTCCACAT 59.802 43.478 0.00 0.00 0.00 3.21
1441 1484 4.142071 TGTTAGCAAACACAATGAAAGGCA 60.142 37.500 0.00 0.00 40.69 4.75
1513 1558 8.721478 ACTAGCACATGACATAACTAAAAACTG 58.279 33.333 0.00 0.00 0.00 3.16
1525 1570 8.793592 TCGATATAACTAACTAGCACATGACAT 58.206 33.333 0.00 0.00 0.00 3.06
1526 1571 8.161699 TCGATATAACTAACTAGCACATGACA 57.838 34.615 0.00 0.00 0.00 3.58
1527 1572 9.066939 CATCGATATAACTAACTAGCACATGAC 57.933 37.037 0.00 0.00 0.00 3.06
1594 1641 6.060136 CACACCAACATCCATAATGATCTCT 58.940 40.000 0.00 0.00 38.83 3.10
1629 1676 2.035321 CGTGCCAACAAACCCAATACTT 59.965 45.455 0.00 0.00 0.00 2.24
1641 1688 2.942376 GGTTCATGATATCGTGCCAACA 59.058 45.455 21.77 5.77 33.05 3.33
1644 1691 2.093235 TGTGGTTCATGATATCGTGCCA 60.093 45.455 18.51 17.23 33.05 4.92
1645 1692 2.545526 CTGTGGTTCATGATATCGTGCC 59.454 50.000 18.51 15.12 33.05 5.01
1646 1693 3.457234 TCTGTGGTTCATGATATCGTGC 58.543 45.455 18.51 6.97 33.05 5.34
1647 1694 4.026558 CGTTCTGTGGTTCATGATATCGTG 60.027 45.833 17.42 17.42 0.00 4.35
1648 1695 4.112634 CGTTCTGTGGTTCATGATATCGT 58.887 43.478 0.00 0.00 0.00 3.73
1649 1696 4.359706 TCGTTCTGTGGTTCATGATATCG 58.640 43.478 0.00 0.00 0.00 2.92
1650 1697 5.580691 TGTTCGTTCTGTGGTTCATGATATC 59.419 40.000 0.00 0.00 0.00 1.63
1655 1702 4.488126 AATGTTCGTTCTGTGGTTCATG 57.512 40.909 0.00 0.00 0.00 3.07
1656 1703 6.817765 ATTAATGTTCGTTCTGTGGTTCAT 57.182 33.333 0.00 0.00 0.00 2.57
1658 1705 7.095355 ACTGTATTAATGTTCGTTCTGTGGTTC 60.095 37.037 0.00 0.00 0.00 3.62
1670 1717 7.611213 AGCACTACCAACTGTATTAATGTTC 57.389 36.000 0.00 0.00 0.00 3.18
1778 1825 4.497842 CCACGCATAAATCAAGCATGCTAA 60.498 41.667 23.00 13.11 42.28 3.09
1794 1841 0.673437 CTGGGAACAAAACCACGCAT 59.327 50.000 0.00 0.00 42.06 4.73
1797 1844 0.673437 ATGCTGGGAACAAAACCACG 59.327 50.000 0.00 0.00 42.06 4.94
1833 1880 5.574055 GGCATTCCATCATATAACAAATGCG 59.426 40.000 10.07 0.00 45.13 4.73
1843 1890 3.568443 TGTGCTTGGCATTCCATCATAT 58.432 40.909 0.00 0.00 43.05 1.78
1907 1961 5.930135 AGTAGATGAAAACAACCAGTCTGT 58.070 37.500 0.00 0.00 0.00 3.41
1912 1966 6.428159 AGCAAGTAGTAGATGAAAACAACCAG 59.572 38.462 0.00 0.00 0.00 4.00
2082 2148 5.125739 TGGTATAAATAAAAACTGGTGGCCG 59.874 40.000 0.00 0.00 0.00 6.13
2195 2421 4.753107 AGTAACATCCTACCAACAAACACG 59.247 41.667 0.00 0.00 0.00 4.49
2197 2423 7.281098 TGTTAGTAACATCCTACCAACAAACA 58.719 34.615 11.75 0.00 32.70 2.83
2209 2435 6.704493 TGTCTGTTCTGTTGTTAGTAACATCC 59.296 38.462 16.26 10.60 41.79 3.51
2218 2444 6.345298 TGTCTCAATGTCTGTTCTGTTGTTA 58.655 36.000 0.00 0.00 0.00 2.41
2222 2448 5.028549 ACTGTCTCAATGTCTGTTCTGTT 57.971 39.130 0.00 0.00 0.00 3.16
2296 2685 9.748708 CATTCATCTTAAAGAAGGTCAAACAAA 57.251 29.630 0.00 0.00 33.09 2.83
2348 2737 1.786937 ACATGCTGGGAACAAAACCA 58.213 45.000 0.00 0.00 42.06 3.67
2349 2738 3.368323 CCATACATGCTGGGAACAAAACC 60.368 47.826 6.96 0.00 42.06 3.27
2392 2781 5.759059 AGAACACCACACATTCCATCATAT 58.241 37.500 0.00 0.00 0.00 1.78
2498 2888 6.071320 GGACCCATAAATCTGCCTCTTATTT 58.929 40.000 0.00 0.00 0.00 1.40
2504 2894 3.217626 CTTGGACCCATAAATCTGCCTC 58.782 50.000 0.00 0.00 0.00 4.70
2564 2967 5.733620 TTACTCCACAGGAAATACGACTT 57.266 39.130 0.00 0.00 0.00 3.01
2595 3029 3.950794 TTCAGTGCGGGCCTAAGCG 62.951 63.158 0.84 0.00 41.24 4.68
2599 3033 0.676466 CACATTTCAGTGCGGGCCTA 60.676 55.000 0.84 0.00 32.04 3.93
2600 3034 1.973281 CACATTTCAGTGCGGGCCT 60.973 57.895 0.84 0.00 32.04 5.19
2607 3041 1.470098 GCACCTAGGCACATTTCAGTG 59.530 52.381 9.30 0.00 42.37 3.66
2608 3042 1.352352 AGCACCTAGGCACATTTCAGT 59.648 47.619 9.30 0.00 35.83 3.41
2609 3043 2.119801 AGCACCTAGGCACATTTCAG 57.880 50.000 9.30 0.00 35.83 3.02
2610 3044 2.092968 CCTAGCACCTAGGCACATTTCA 60.093 50.000 9.30 0.00 45.64 2.69
2611 3045 2.565841 CCTAGCACCTAGGCACATTTC 58.434 52.381 9.30 0.00 45.64 2.17
2612 3046 2.717639 CCTAGCACCTAGGCACATTT 57.282 50.000 9.30 0.00 45.64 2.32
2620 3054 1.680735 CTGCTGTCTCCTAGCACCTAG 59.319 57.143 0.00 0.00 45.52 3.02
2621 3055 1.285078 TCTGCTGTCTCCTAGCACCTA 59.715 52.381 0.00 0.00 45.52 3.08
2622 3056 0.040351 TCTGCTGTCTCCTAGCACCT 59.960 55.000 0.00 0.00 45.52 4.00
2623 3057 0.898320 TTCTGCTGTCTCCTAGCACC 59.102 55.000 0.00 0.00 45.52 5.01
2624 3058 1.734047 CGTTCTGCTGTCTCCTAGCAC 60.734 57.143 0.00 0.00 45.52 4.40
2626 3060 0.804156 GCGTTCTGCTGTCTCCTAGC 60.804 60.000 0.00 0.00 41.73 3.42
2627 3061 0.179124 GGCGTTCTGCTGTCTCCTAG 60.179 60.000 0.00 0.00 45.43 3.02
2628 3062 0.612174 AGGCGTTCTGCTGTCTCCTA 60.612 55.000 0.00 0.00 45.43 2.94
2629 3063 0.612174 TAGGCGTTCTGCTGTCTCCT 60.612 55.000 0.00 0.00 45.43 3.69
2630 3064 0.179124 CTAGGCGTTCTGCTGTCTCC 60.179 60.000 0.00 0.00 45.43 3.71
2631 3065 0.804156 GCTAGGCGTTCTGCTGTCTC 60.804 60.000 0.00 0.00 45.43 3.36
2632 3066 1.216710 GCTAGGCGTTCTGCTGTCT 59.783 57.895 0.00 0.00 45.43 3.41
2673 3107 1.813786 CTAGCGCCTATCTCACCTACC 59.186 57.143 2.29 0.00 0.00 3.18
2730 3164 1.606668 GCTTCGTTGAACACCATGGAA 59.393 47.619 21.47 0.00 0.00 3.53
2734 3168 2.020720 TGTTGCTTCGTTGAACACCAT 58.979 42.857 0.00 0.00 0.00 3.55
2809 3244 5.786311 ACATGTGGTGAATTCTTGAAATGG 58.214 37.500 7.05 0.00 0.00 3.16
2906 3345 5.991606 TCTGCCAGATTATATTGAAAGGTCG 59.008 40.000 0.00 0.00 0.00 4.79
2943 3382 7.992180 ACATGAAAACAATCAAACTGAAGTC 57.008 32.000 0.00 0.00 32.06 3.01
2993 3432 4.826733 TGAATTTGGAACACAGTGCTATGT 59.173 37.500 0.00 0.00 39.29 2.29
3109 3609 5.479716 AAACTCACAAAACAGTAAGACGG 57.520 39.130 0.00 0.00 0.00 4.79
3110 3610 7.847487 TCATAAACTCACAAAACAGTAAGACG 58.153 34.615 0.00 0.00 0.00 4.18
3124 3662 5.975693 TTTGACCCCAATCATAAACTCAC 57.024 39.130 0.00 0.00 31.46 3.51
3152 3690 7.716799 AATAAAACCAGATCAGCCAAATACA 57.283 32.000 0.00 0.00 0.00 2.29
3436 3974 4.096231 TGTGTGAAACTATGTGCATATGGC 59.904 41.667 6.16 0.00 40.04 4.40
3437 3975 5.123661 TGTGTGTGAAACTATGTGCATATGG 59.876 40.000 6.16 5.67 38.04 2.74
3438 3976 6.180771 TGTGTGTGAAACTATGTGCATATG 57.819 37.500 6.16 0.00 38.04 1.78
3443 3981 3.300009 GCTTGTGTGTGAAACTATGTGC 58.700 45.455 0.00 0.00 38.04 4.57
3447 3985 4.067896 CAGAGGCTTGTGTGTGAAACTAT 58.932 43.478 0.00 0.00 38.04 2.12
3448 3986 3.133901 TCAGAGGCTTGTGTGTGAAACTA 59.866 43.478 0.00 0.00 38.04 2.24
3499 4037 6.989169 ACATATCTCAAACTCCAGCTGAATAC 59.011 38.462 17.39 0.00 0.00 1.89
3513 4051 5.416639 ACAAGAAGCATGCACATATCTCAAA 59.583 36.000 21.98 0.00 0.00 2.69
3530 4068 4.761739 TCATTTGCTGGTTCCTACAAGAAG 59.238 41.667 0.00 0.00 0.00 2.85
3839 4377 5.104067 ACAGGGTAGTTAGGGGATTCAAATC 60.104 44.000 0.00 0.00 34.66 2.17
3973 4513 1.136329 AGGTGCCTGAGGGTGATTGT 61.136 55.000 0.00 0.00 34.45 2.71
4128 4668 7.010339 AGAAATAGGGACTCCTTACATATGC 57.990 40.000 1.58 0.00 41.56 3.14
4287 4829 8.887717 ACTGAAACAATATATCTTCACTCTTGC 58.112 33.333 0.00 0.00 0.00 4.01
4374 4917 1.380246 TGACAGCAATGGGATGGGC 60.380 57.895 0.00 0.00 37.17 5.36
4382 4925 8.559536 TCTTTACTAAAAGAACTGACAGCAATG 58.440 33.333 1.25 0.00 46.32 2.82
4482 5028 0.396060 TGTTTGAAATGCAAGGGGGC 59.604 50.000 0.00 0.00 37.87 5.80
4497 5043 6.740944 AAAAAGGGGCTATGTACTTTGTTT 57.259 33.333 0.00 0.00 33.79 2.83
4589 5143 2.965671 ATCAAGGCCAGATGTATGGG 57.034 50.000 5.01 0.00 40.97 4.00
4590 5144 4.261322 CGAAAATCAAGGCCAGATGTATGG 60.261 45.833 5.01 0.00 43.72 2.74
4651 5205 5.483685 TTCTCATGTTAGGTACAGCAAGT 57.516 39.130 0.00 0.00 40.83 3.16
4694 5248 7.976175 GTCATTGTTCTTCTTCTTTTTCCTTGT 59.024 33.333 0.00 0.00 0.00 3.16
4757 5311 0.899717 AGCCAAACACCGATGCCAAT 60.900 50.000 0.00 0.00 0.00 3.16
4888 5445 7.924412 TCCATATAACTTTGCTAAGTCCTAACG 59.076 37.037 13.94 2.18 43.74 3.18
4905 5462 7.013369 GGAAACACCATTTCCTCTCCATATAAC 59.987 40.741 10.54 0.00 43.45 1.89
4906 5463 7.060421 GGAAACACCATTTCCTCTCCATATAA 58.940 38.462 10.54 0.00 43.45 0.98
4908 5465 5.044179 TGGAAACACCATTTCCTCTCCATAT 60.044 40.000 17.07 0.00 46.16 1.78
4947 5504 2.351253 CCGCATGTCGAAAAATTCCACA 60.351 45.455 10.48 0.00 41.67 4.17
5027 5584 0.973632 TCCCGCTAACAAGAGAAGCA 59.026 50.000 0.00 0.00 35.98 3.91
5050 5607 0.698238 AAGGCCATAACCACAGCAGA 59.302 50.000 5.01 0.00 0.00 4.26
5051 5608 1.549203 AAAGGCCATAACCACAGCAG 58.451 50.000 5.01 0.00 0.00 4.24
5111 5673 6.112058 AGAATGCTCACAGAAAGAAGGTATC 58.888 40.000 0.00 0.00 0.00 2.24
5118 5691 6.455360 ACAAAAAGAATGCTCACAGAAAGA 57.545 33.333 0.00 0.00 0.00 2.52
5190 5764 1.035139 AAAGCCAAGCAGACACCAAG 58.965 50.000 0.00 0.00 0.00 3.61
5201 5775 3.672767 AATGCCAGAAGAAAAGCCAAG 57.327 42.857 0.00 0.00 0.00 3.61
5262 5836 2.327343 GCATCTGACGGCACAAGCA 61.327 57.895 0.00 0.00 44.61 3.91
5266 5840 1.810853 CATCGCATCTGACGGCACA 60.811 57.895 0.00 0.00 0.00 4.57
5268 5842 0.673437 TATCATCGCATCTGACGGCA 59.327 50.000 0.00 0.00 0.00 5.69
5312 5916 9.525409 GCACGTTAGTATCTCTTCCTAATTAAA 57.475 33.333 0.00 0.00 0.00 1.52
5313 5917 8.689061 TGCACGTTAGTATCTCTTCCTAATTAA 58.311 33.333 0.00 0.00 0.00 1.40
5385 6003 4.090354 CGACGCTCGGTTGAAAAGTTATAA 59.910 41.667 0.00 0.00 36.00 0.98
5489 6119 8.962884 ATGTTTAAAAGGATCAAAGTTGCTTT 57.037 26.923 0.00 0.00 33.58 3.51
5818 6482 2.664402 AATCAAGCAACTGTCCTGGT 57.336 45.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.