Multiple sequence alignment - TraesCS3D01G406500

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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 TraesCS3D01G406500 chr3D 100.000 4326 0 0 1 4326 520324474 520320149 0.000000e+00 7989.0
1 TraesCS3D01G406500 chr3D 88.128 876 89 10 2066 2932 497865434 497866303 0.000000e+00 1027.0
2 TraesCS3D01G406500 chr3D 78.333 1200 214 31 2146 3326 568088173 568087001 0.000000e+00 734.0
3 TraesCS3D01G406500 chr3D 86.254 662 76 8 2921 3570 497866324 497866982 0.000000e+00 704.0
4 TraesCS3D01G406500 chr3D 82.540 567 56 20 42 584 497863392 497863939 3.940000e-125 459.0
5 TraesCS3D01G406500 chr3D 81.145 594 60 20 699 1265 497864863 497865431 3.090000e-116 429.0
6 TraesCS3D01G406500 chr3D 78.439 269 46 7 3960 4223 497864595 497864856 9.620000e-37 165.0
7 TraesCS3D01G406500 chr3D 80.357 168 24 6 1035 1200 570146635 570146475 7.600000e-23 119.0
8 TraesCS3D01G406500 chr3D 78.325 203 29 9 107 297 543104796 543104597 2.730000e-22 117.0
9 TraesCS3D01G406500 chr3D 100.000 31 0 0 1455 1485 58106101 58106071 1.680000e-04 58.4
10 TraesCS3D01G406500 chr3A 93.254 1853 111 8 1951 3789 655628825 655630677 0.000000e+00 2717.0
11 TraesCS3D01G406500 chr3A 95.740 1432 59 2 1992 3422 655897050 655895620 0.000000e+00 2305.0
12 TraesCS3D01G406500 chr3A 87.604 1557 168 18 2066 3604 636541281 636539732 0.000000e+00 1783.0
13 TraesCS3D01G406500 chr3A 90.097 1343 88 20 3 1330 655900564 655899252 0.000000e+00 1701.0
14 TraesCS3D01G406500 chr3A 87.203 1094 98 22 889 1955 655627712 655628790 0.000000e+00 1206.0
15 TraesCS3D01G406500 chr3A 89.523 754 33 11 42 776 655626959 655627685 0.000000e+00 913.0
16 TraesCS3D01G406500 chr3A 77.670 1236 230 33 2120 3336 702491465 702492673 0.000000e+00 712.0
17 TraesCS3D01G406500 chr3A 84.121 529 52 18 3798 4323 636539481 636538982 2.340000e-132 483.0
18 TraesCS3D01G406500 chr3A 86.636 434 45 6 1531 1955 655898653 655898224 6.550000e-128 468.0
19 TraesCS3D01G406500 chr3A 82.118 576 60 21 42 584 636543416 636542851 1.830000e-123 453.0
20 TraesCS3D01G406500 chr3A 91.018 167 9 2 3629 3789 655895610 655895444 2.030000e-53 220.0
21 TraesCS3D01G406500 chr3A 89.655 87 7 2 3798 3882 655895403 655895317 4.570000e-20 110.0
22 TraesCS3D01G406500 chr3A 84.946 93 9 5 478 567 702954943 702954853 5.960000e-14 89.8
23 TraesCS3D01G406500 chr3B 84.838 1761 191 37 2066 3787 658487160 658488883 0.000000e+00 1703.0
24 TraesCS3D01G406500 chr3B 95.031 966 46 2 1994 2958 684762717 684763681 0.000000e+00 1517.0
25 TraesCS3D01G406500 chr3B 91.091 999 55 13 337 1330 684747418 684748387 0.000000e+00 1321.0
26 TraesCS3D01G406500 chr3B 97.541 488 11 1 2935 3422 684763720 684764206 0.000000e+00 833.0
27 TraesCS3D01G406500 chr3B 80.195 1131 202 18 2120 3241 684770133 684771250 0.000000e+00 828.0
28 TraesCS3D01G406500 chr3B 77.461 1331 242 43 2120 3420 756823928 756822626 0.000000e+00 743.0
29 TraesCS3D01G406500 chr3B 82.047 596 56 18 699 1267 658486588 658487159 1.100000e-125 460.0
30 TraesCS3D01G406500 chr3B 82.456 456 49 19 146 584 658485079 658485520 1.900000e-98 370.0
31 TraesCS3D01G406500 chr3B 89.683 252 21 5 54 302 684746770 684747019 2.510000e-82 316.0
32 TraesCS3D01G406500 chr3B 78.361 476 50 23 3835 4308 658489049 658489473 4.290000e-65 259.0
33 TraesCS3D01G406500 chr3B 90.419 167 9 4 3629 3788 684764216 684764382 3.390000e-51 213.0
34 TraesCS3D01G406500 chr3B 82.270 141 18 5 1062 1200 756709052 756708917 9.830000e-22 115.0
35 TraesCS3D01G406500 chr3B 82.270 141 18 5 1062 1200 756824184 756824049 9.830000e-22 115.0
36 TraesCS3D01G406500 chr3B 89.655 87 7 2 3798 3882 684764424 684764510 4.570000e-20 110.0
37 TraesCS3D01G406500 chr3B 80.142 141 19 4 1074 1205 684769762 684769902 3.560000e-16 97.1
38 TraesCS3D01G406500 chr3B 80.165 121 14 6 186 297 718892711 718892592 9.970000e-12 82.4
39 TraesCS3D01G406500 chr3B 100.000 29 0 0 42 70 684746775 684746803 2.000000e-03 54.7
40 TraesCS3D01G406500 chrUn 77.446 1206 238 28 2146 3337 250030623 250031808 0.000000e+00 689.0
41 TraesCS3D01G406500 chr5B 82.063 223 28 6 3960 4181 338484587 338484798 3.440000e-41 180.0
42 TraesCS3D01G406500 chr5A 78.894 199 30 6 3996 4193 401314449 401314262 1.630000e-24 124.0
43 TraesCS3D01G406500 chr1D 73.307 251 47 11 58 297 464753205 464752964 1.670000e-09 75.0


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 TraesCS3D01G406500 chr3D 520320149 520324474 4325 True 7989.000000 7989 100.000000 1 4326 1 chr3D.!!$R2 4325
1 TraesCS3D01G406500 chr3D 568087001 568088173 1172 True 734.000000 734 78.333000 2146 3326 1 chr3D.!!$R4 1180
2 TraesCS3D01G406500 chr3D 497863392 497866982 3590 False 556.800000 1027 83.301200 42 4223 5 chr3D.!!$F1 4181
3 TraesCS3D01G406500 chr3A 655626959 655630677 3718 False 1612.000000 2717 89.993333 42 3789 3 chr3A.!!$F2 3747
4 TraesCS3D01G406500 chr3A 655895317 655900564 5247 True 960.800000 2305 90.629200 3 3882 5 chr3A.!!$R3 3879
5 TraesCS3D01G406500 chr3A 636538982 636543416 4434 True 906.333333 1783 84.614333 42 4323 3 chr3A.!!$R2 4281
6 TraesCS3D01G406500 chr3A 702491465 702492673 1208 False 712.000000 712 77.670000 2120 3336 1 chr3A.!!$F1 1216
7 TraesCS3D01G406500 chr3B 658485079 658489473 4394 False 698.000000 1703 81.925500 146 4308 4 chr3B.!!$F1 4162
8 TraesCS3D01G406500 chr3B 684762717 684764510 1793 False 668.250000 1517 93.161500 1994 3882 4 chr3B.!!$F3 1888
9 TraesCS3D01G406500 chr3B 684746770 684748387 1617 False 563.900000 1321 93.591333 42 1330 3 chr3B.!!$F2 1288
10 TraesCS3D01G406500 chr3B 684769762 684771250 1488 False 462.550000 828 80.168500 1074 3241 2 chr3B.!!$F4 2167
11 TraesCS3D01G406500 chr3B 756822626 756824184 1558 True 429.000000 743 79.865500 1062 3420 2 chr3B.!!$R3 2358
12 TraesCS3D01G406500 chrUn 250030623 250031808 1185 False 689.000000 689 77.446000 2146 3337 1 chrUn.!!$F1 1191

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
223 257 0.462225 CGCTCCTCGACTCACCTCTA 60.462 60.0 0.0 0.0 41.67 2.43 F
1539 3513 0.179181 CTGCAAGCCATTGTAGCACG 60.179 55.0 0.0 0.0 41.34 5.34 F
1676 3656 0.900182 GGCCTCTTCCCCCAAAGTTG 60.900 60.0 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 3774 0.175760 GATGGTCGGTCTGCAAGCTA 59.824 55.0 0.00 0.0 0.00 3.32 R
2922 6141 0.110419 CGCACCTTCGATCGCAAAAA 60.110 50.0 11.09 0.0 0.00 1.94 R
3592 6938 0.101759 TTGGTAGGCGATACAGCGAC 59.898 55.0 0.00 0.0 40.32 5.19 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
23 24 3.479866 AAGAGGGAAATGGAAATGCCT 57.520 42.857 0.00 0.00 40.45 4.75
34 35 2.847435 GAAATGCCTGCCCAGCTTGC 62.847 60.000 0.00 0.00 0.00 4.01
223 257 0.462225 CGCTCCTCGACTCACCTCTA 60.462 60.000 0.00 0.00 41.67 2.43
297 339 3.411517 CCCCAATCTCCCCGCAGT 61.412 66.667 0.00 0.00 0.00 4.40
306 349 1.595993 CTCCCCGCAGTTTCTCTCGA 61.596 60.000 0.00 0.00 0.00 4.04
362 778 1.134670 GGATTTCGACTACTGGCTGCT 60.135 52.381 0.00 0.00 0.00 4.24
456 872 1.953686 CTAGTCTGCCTCTACCAGAGC 59.046 57.143 0.00 0.00 40.98 4.09
489 918 1.332195 ACAAGAGAAGCAAAAGGGGC 58.668 50.000 0.00 0.00 0.00 5.80
516 945 3.675482 CTTGACTCGCTCGCTCGCT 62.675 63.158 0.00 0.00 0.00 4.93
776 2234 7.286316 CCCCAGTTGAGCATATAAAAAGAAGAT 59.714 37.037 0.00 0.00 0.00 2.40
791 2249 7.995052 AAAAGAAGATTAATAATTGCCCCCT 57.005 32.000 0.00 0.00 0.00 4.79
792 2250 9.500701 AAAAAGAAGATTAATAATTGCCCCCTA 57.499 29.630 0.00 0.00 0.00 3.53
793 2251 9.674705 AAAAGAAGATTAATAATTGCCCCCTAT 57.325 29.630 0.00 0.00 0.00 2.57
999 2533 3.636153 AAGGTAGAACTGAAGGGCATC 57.364 47.619 0.00 0.00 0.00 3.91
1000 2534 2.551270 AGGTAGAACTGAAGGGCATCA 58.449 47.619 0.00 0.00 0.00 3.07
1001 2535 3.118531 AGGTAGAACTGAAGGGCATCAT 58.881 45.455 0.00 0.00 0.00 2.45
1002 2536 3.118112 AGGTAGAACTGAAGGGCATCATG 60.118 47.826 0.00 0.00 0.00 3.07
1300 2854 2.933906 ACACGGTTGATATTACAAGGCG 59.066 45.455 0.00 0.00 0.00 5.52
1339 2930 0.736053 GACACAAAAAGCACCGTCCA 59.264 50.000 0.00 0.00 0.00 4.02
1351 2942 4.523083 AGCACCGTCCATGTTTTACATAT 58.477 39.130 0.00 0.00 36.53 1.78
1353 2944 5.526111 AGCACCGTCCATGTTTTACATATAC 59.474 40.000 0.00 0.00 36.53 1.47
1355 2946 6.017440 GCACCGTCCATGTTTTACATATACAT 60.017 38.462 0.00 0.00 36.53 2.29
1356 2947 7.171848 GCACCGTCCATGTTTTACATATACATA 59.828 37.037 0.00 0.00 36.53 2.29
1357 2948 8.708742 CACCGTCCATGTTTTACATATACATAG 58.291 37.037 0.00 0.00 36.53 2.23
1358 2949 7.386848 ACCGTCCATGTTTTACATATACATAGC 59.613 37.037 0.00 0.00 36.53 2.97
1359 2950 7.148474 CCGTCCATGTTTTACATATACATAGCC 60.148 40.741 0.00 0.00 36.53 3.93
1360 2951 7.602644 CGTCCATGTTTTACATATACATAGCCT 59.397 37.037 0.00 0.00 36.53 4.58
1361 2952 9.938280 GTCCATGTTTTACATATACATAGCCTA 57.062 33.333 0.00 0.00 36.53 3.93
1404 2995 6.647067 GCATCAAACCCATTAGCTAGTACTAG 59.353 42.308 23.25 23.25 36.29 2.57
1405 2996 7.687103 GCATCAAACCCATTAGCTAGTACTAGT 60.687 40.741 26.76 17.34 35.65 2.57
1406 2997 7.344095 TCAAACCCATTAGCTAGTACTAGTC 57.656 40.000 26.76 19.62 35.65 2.59
1407 2998 6.893554 TCAAACCCATTAGCTAGTACTAGTCA 59.106 38.462 26.76 14.63 35.65 3.41
1448 3041 9.239551 GTAACCATGTTTCCTCCTTTTAAGTAT 57.760 33.333 0.00 0.00 0.00 2.12
1452 3045 9.238368 CCATGTTTCCTCCTTTTAAGTATGTTA 57.762 33.333 0.00 0.00 0.00 2.41
1484 3084 3.778075 TGGCTAAGCAGTATGGGACTAAA 59.222 43.478 0.00 0.00 35.64 1.85
1515 3489 2.480419 GTCACAAGATTCGAACACAGGG 59.520 50.000 0.00 0.00 0.00 4.45
1521 3495 1.827399 ATTCGAACACAGGGACGGCT 61.827 55.000 0.00 0.00 0.00 5.52
1522 3496 2.709125 TTCGAACACAGGGACGGCTG 62.709 60.000 0.00 0.00 0.00 4.85
1523 3497 3.050275 GAACACAGGGACGGCTGC 61.050 66.667 0.00 0.00 0.00 5.25
1526 3500 3.052082 CACAGGGACGGCTGCAAG 61.052 66.667 0.50 0.00 0.00 4.01
1539 3513 0.179181 CTGCAAGCCATTGTAGCACG 60.179 55.000 0.00 0.00 41.34 5.34
1554 3528 4.036977 ACGCTAACAACCACGTGG 57.963 55.556 32.83 32.83 37.37 4.94
1570 3544 6.579666 CCACGTGGGTATATAAGTAGCTAA 57.420 41.667 27.57 0.00 0.00 3.09
1572 3546 7.609056 CCACGTGGGTATATAAGTAGCTAAAT 58.391 38.462 27.57 0.00 0.00 1.40
1592 3572 7.043325 GCTAAATACAGATATACATAGGCACGC 60.043 40.741 0.00 0.00 0.00 5.34
1617 3597 4.156190 CCACGATCTGTATAGCGTCCTATT 59.844 45.833 0.00 0.00 35.85 1.73
1650 3630 1.006922 GCAAGAACAGCCTGGTTGC 60.007 57.895 10.72 11.39 37.00 4.17
1652 3632 1.152963 AAGAACAGCCTGGTTGCGT 60.153 52.632 10.72 0.00 36.02 5.24
1657 3637 2.972505 AGCCTGGTTGCGTGTTCG 60.973 61.111 0.00 0.00 40.37 3.95
1664 3644 2.110213 TTGCGTGTTCGGCCTCTT 59.890 55.556 0.00 0.00 37.56 2.85
1672 3652 2.157452 TTCGGCCTCTTCCCCCAAA 61.157 57.895 0.00 0.00 0.00 3.28
1676 3656 0.900182 GGCCTCTTCCCCCAAAGTTG 60.900 60.000 0.00 0.00 0.00 3.16
1740 3721 1.538512 TCATGCAAGCTGACTGAAAGC 59.461 47.619 0.00 0.00 37.60 3.51
1747 3728 1.664649 CTGACTGAAAGCCGCGTCA 60.665 57.895 4.92 0.33 37.60 4.35
1786 3770 1.583986 TTGCACCAGCCGCAAATAC 59.416 52.632 0.00 0.00 45.91 1.89
1813 3797 1.191489 TTGCAGACCGACCATCCTGA 61.191 55.000 0.00 0.00 0.00 3.86
1908 3892 2.201732 GCGTTTATGAGAATCGCCTCA 58.798 47.619 4.10 0.00 46.02 3.86
1921 3906 2.977914 TCGCCTCAAAATCTCTTCCAG 58.022 47.619 0.00 0.00 0.00 3.86
1997 5120 2.081462 CCGAAACGCCTCCTTAAACAT 58.919 47.619 0.00 0.00 0.00 2.71
2022 5145 7.206687 TGATTTTGAGGCGTTTAGAAAAATGT 58.793 30.769 0.00 0.00 34.61 2.71
2142 5352 8.506168 TGGATTTTCTGAATAAGTACATGTCC 57.494 34.615 0.00 0.00 0.00 4.02
2217 5429 2.431454 TGAATTATGCAGCAACACCGA 58.569 42.857 0.00 0.00 0.00 4.69
2395 5607 2.135933 CCTGAGAACGACTTCAACACC 58.864 52.381 0.00 0.00 0.00 4.16
2599 5814 5.064452 CCTGTTGCATTACTCATTGACTCTC 59.936 44.000 0.00 0.00 0.00 3.20
2635 5850 5.707066 ATCTTTACAGGCTCCAGAAGATT 57.293 39.130 6.26 0.00 31.74 2.40
2828 6045 4.348168 AGGGAGGCGTTCTGATATAATTGT 59.652 41.667 0.00 0.00 0.00 2.71
2901 6120 5.310409 TGGTCTCAGAGGTCATTTCTTTT 57.690 39.130 0.00 0.00 0.00 2.27
2922 6141 8.362639 TCTTTTCTTTCTTTTCTAGCATGCATT 58.637 29.630 21.98 1.90 0.00 3.56
3117 6430 0.757188 CGGGAGCATGACCCTAGAGT 60.757 60.000 20.79 0.00 44.72 3.24
3167 6481 1.197721 GCATATTCGCGGGATTTCTGG 59.802 52.381 6.13 0.00 0.00 3.86
3236 6550 0.669318 TGAATTCGTGAGGACCGTGC 60.669 55.000 0.04 0.00 0.00 5.34
3338 6658 4.373156 AAGGCATGATTATCAGGTACCC 57.627 45.455 8.74 1.78 29.72 3.69
3527 6871 1.134098 CATGGGTGATTCGTAAGGGCT 60.134 52.381 0.00 0.00 38.47 5.19
3548 6892 0.612744 AAGAGAAGCACTGGAGCCTC 59.387 55.000 0.00 0.00 34.23 4.70
3570 6914 3.736483 ACAGTTCGCAAGCTGTGG 58.264 55.556 0.00 0.00 43.45 4.17
3592 6938 1.812571 CCAAAAACCCGAGAGTGATGG 59.187 52.381 0.00 0.00 0.00 3.51
3596 6942 2.105128 CCCGAGAGTGATGGTCGC 59.895 66.667 0.00 0.00 32.25 5.19
3789 7188 9.513906 TTATCTGATAATGTGGTTGACTTTGAA 57.486 29.630 6.01 0.00 0.00 2.69
3790 7189 7.439157 TCTGATAATGTGGTTGACTTTGAAG 57.561 36.000 0.00 0.00 0.00 3.02
3791 7190 7.223584 TCTGATAATGTGGTTGACTTTGAAGA 58.776 34.615 0.00 0.00 0.00 2.87
3792 7191 7.719193 TCTGATAATGTGGTTGACTTTGAAGAA 59.281 33.333 0.00 0.00 0.00 2.52
3793 7192 7.648142 TGATAATGTGGTTGACTTTGAAGAAC 58.352 34.615 0.00 0.00 0.00 3.01
3795 7194 4.695217 TGTGGTTGACTTTGAAGAACAC 57.305 40.909 0.00 0.00 0.00 3.32
3796 7195 4.075682 TGTGGTTGACTTTGAAGAACACA 58.924 39.130 0.00 0.00 0.00 3.72
3888 7406 2.380941 ACCCATTAATGGCGGTTTACC 58.619 47.619 26.53 0.00 46.70 2.85
3889 7407 1.684450 CCCATTAATGGCGGTTTACCC 59.316 52.381 26.53 0.00 46.70 3.69
3902 7420 1.145571 TTTACCCAACTGCCAGACCT 58.854 50.000 0.00 0.00 0.00 3.85
3903 7421 2.032965 TTACCCAACTGCCAGACCTA 57.967 50.000 0.00 0.00 0.00 3.08
3904 7422 1.568504 TACCCAACTGCCAGACCTAG 58.431 55.000 0.00 0.00 0.00 3.02
3905 7423 1.201429 ACCCAACTGCCAGACCTAGG 61.201 60.000 7.41 7.41 0.00 3.02
3906 7424 1.604378 CCAACTGCCAGACCTAGGG 59.396 63.158 14.81 0.00 0.00 3.53
3946 7464 1.967319 TCAGAGGCAGTTGACCAAAC 58.033 50.000 0.00 0.00 39.24 2.93
3995 7513 8.045176 AGCACTCCAGTTTATTGTTCTTATTC 57.955 34.615 0.00 0.00 0.00 1.75
4030 7548 6.189677 TGGTGCTTGTGTTAATGCTAATAC 57.810 37.500 0.00 0.00 31.59 1.89
4041 7559 9.680315 GTGTTAATGCTAATACTGTACTAGGAG 57.320 37.037 5.57 0.00 0.00 3.69
4042 7560 9.417561 TGTTAATGCTAATACTGTACTAGGAGT 57.582 33.333 5.57 4.53 0.00 3.85
4046 7564 9.863650 AATGCTAATACTGTACTAGGAGTAGAA 57.136 33.333 13.03 5.95 39.73 2.10
4071 7591 9.777575 AAATTACAGTAAAAATGTATGTACCGC 57.222 29.630 0.00 0.00 33.36 5.68
4076 7596 7.966204 ACAGTAAAAATGTATGTACCGCAAATC 59.034 33.333 0.00 0.00 0.00 2.17
4089 7609 5.099042 ACCGCAAATCCAGTTAGTATCTT 57.901 39.130 0.00 0.00 0.00 2.40
4094 7614 7.441157 CCGCAAATCCAGTTAGTATCTTATTCA 59.559 37.037 0.00 0.00 0.00 2.57
4112 7632 4.356405 TTCAATGCTCAACTGGAAGAGA 57.644 40.909 0.00 0.00 37.43 3.10
4182 7702 7.068839 ACAAATATCCTCTGTAGTAGTGACAGG 59.931 40.741 3.15 0.00 43.76 4.00
4184 7704 3.952931 TCCTCTGTAGTAGTGACAGGTC 58.047 50.000 3.15 0.00 43.76 3.85
4187 7707 3.332919 TCTGTAGTAGTGACAGGTCGTC 58.667 50.000 3.15 0.00 43.76 4.20
4215 7735 3.534357 TCCCAATTTGACCCTTTAGCA 57.466 42.857 0.00 0.00 0.00 3.49
4222 7742 7.035612 CCAATTTGACCCTTTAGCATTTCTAC 58.964 38.462 0.00 0.00 0.00 2.59
4239 7759 0.184933 TACTTGCTGGCCCAAACAGT 59.815 50.000 0.00 0.00 38.22 3.55
4276 7796 5.587443 CAGATTGAGAAGCACATTGACCATA 59.413 40.000 0.00 0.00 0.00 2.74
4300 7820 1.685421 GCCCCCAATAAGCAGCCAA 60.685 57.895 0.00 0.00 0.00 4.52
4312 7832 0.961019 GCAGCCAAAACAGTCATCCA 59.039 50.000 0.00 0.00 0.00 3.41
4315 7835 1.547372 AGCCAAAACAGTCATCCATGC 59.453 47.619 0.00 0.00 0.00 4.06
4317 7837 2.028748 GCCAAAACAGTCATCCATGCTT 60.029 45.455 0.00 0.00 0.00 3.91
4318 7838 3.581755 CCAAAACAGTCATCCATGCTTG 58.418 45.455 0.00 0.00 0.00 4.01
4319 7839 3.256383 CCAAAACAGTCATCCATGCTTGA 59.744 43.478 0.22 0.00 0.00 3.02
4320 7840 4.482386 CAAAACAGTCATCCATGCTTGAG 58.518 43.478 0.22 0.00 0.00 3.02
4321 7841 1.747709 ACAGTCATCCATGCTTGAGC 58.252 50.000 0.22 0.00 42.50 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.598807 AGGCATTTCCATTTCCCTCTTTTT 59.401 37.500 0.00 0.00 37.29 1.94
1 2 4.019950 CAGGCATTTCCATTTCCCTCTTTT 60.020 41.667 0.00 0.00 37.29 2.27
8 9 0.178767 GGGCAGGCATTTCCATTTCC 59.821 55.000 0.00 0.00 37.29 3.13
15 16 1.217244 CAAGCTGGGCAGGCATTTC 59.783 57.895 0.00 0.00 0.00 2.17
16 17 2.951101 GCAAGCTGGGCAGGCATTT 61.951 57.895 5.80 0.00 31.89 2.32
23 24 2.979676 CAGTTCGCAAGCTGGGCA 60.980 61.111 10.80 0.00 37.18 5.36
34 35 3.103911 GCCGTCGTGTCCAGTTCG 61.104 66.667 0.00 0.00 0.00 3.95
92 123 0.041238 AACATCCCCGACTCTCTCCA 59.959 55.000 0.00 0.00 0.00 3.86
174 205 2.331805 CGCCGTCATCGTAGAGGG 59.668 66.667 12.16 12.16 43.63 4.30
234 268 2.817396 GAGGAGGCGCTTGAGCAC 60.817 66.667 7.64 0.00 42.21 4.40
235 269 4.441695 CGAGGAGGCGCTTGAGCA 62.442 66.667 7.64 0.00 42.21 4.26
236 270 4.443266 ACGAGGAGGCGCTTGAGC 62.443 66.667 7.64 0.00 37.78 4.26
237 271 2.202676 GACGAGGAGGCGCTTGAG 60.203 66.667 7.64 0.00 33.86 3.02
321 364 2.631418 GTCAGGATCGACGACAAGAA 57.369 50.000 0.00 0.00 0.00 2.52
349 755 1.023513 CCTGCAAGCAGCCAGTAGTC 61.024 60.000 16.33 0.00 44.83 2.59
350 756 1.002868 CCTGCAAGCAGCCAGTAGT 60.003 57.895 16.33 0.00 44.83 2.73
351 757 1.002868 ACCTGCAAGCAGCCAGTAG 60.003 57.895 16.33 4.56 44.83 2.57
362 778 1.021202 CGTTCTTTGACCACCTGCAA 58.979 50.000 0.00 0.00 0.00 4.08
456 872 0.742990 TCTTGTTAGCAATCCGGCGG 60.743 55.000 22.51 22.51 39.27 6.13
489 918 1.743252 GCGAGTCAAGCTTCCAGGG 60.743 63.158 0.00 0.00 0.00 4.45
584 1013 6.422701 CGCCAATTATGATACTCTTAAACCGA 59.577 38.462 0.00 0.00 0.00 4.69
776 2234 9.984590 GGAAGTTATATAGGGGGCAATTATTAA 57.015 33.333 0.00 0.00 0.00 1.40
778 2236 7.893833 GTGGAAGTTATATAGGGGGCAATTATT 59.106 37.037 0.00 0.00 0.00 1.40
779 2237 7.241888 AGTGGAAGTTATATAGGGGGCAATTAT 59.758 37.037 0.00 0.00 0.00 1.28
780 2238 6.564927 AGTGGAAGTTATATAGGGGGCAATTA 59.435 38.462 0.00 0.00 0.00 1.40
781 2239 5.375655 AGTGGAAGTTATATAGGGGGCAATT 59.624 40.000 0.00 0.00 0.00 2.32
782 2240 4.920129 AGTGGAAGTTATATAGGGGGCAAT 59.080 41.667 0.00 0.00 0.00 3.56
783 2241 4.312487 AGTGGAAGTTATATAGGGGGCAA 58.688 43.478 0.00 0.00 0.00 4.52
784 2242 3.908103 GAGTGGAAGTTATATAGGGGGCA 59.092 47.826 0.00 0.00 0.00 5.36
785 2243 4.020128 CAGAGTGGAAGTTATATAGGGGGC 60.020 50.000 0.00 0.00 0.00 5.80
786 2244 4.020128 GCAGAGTGGAAGTTATATAGGGGG 60.020 50.000 0.00 0.00 0.00 5.40
787 2245 4.593206 TGCAGAGTGGAAGTTATATAGGGG 59.407 45.833 0.00 0.00 0.00 4.79
788 2246 5.808366 TGCAGAGTGGAAGTTATATAGGG 57.192 43.478 0.00 0.00 0.00 3.53
789 2247 5.698545 GCTTGCAGAGTGGAAGTTATATAGG 59.301 44.000 9.53 0.00 45.89 2.57
790 2248 6.283694 TGCTTGCAGAGTGGAAGTTATATAG 58.716 40.000 9.53 0.00 45.89 1.31
791 2249 6.233905 TGCTTGCAGAGTGGAAGTTATATA 57.766 37.500 9.53 0.00 45.89 0.86
792 2250 5.102953 TGCTTGCAGAGTGGAAGTTATAT 57.897 39.130 9.53 0.00 45.89 0.86
793 2251 4.551702 TGCTTGCAGAGTGGAAGTTATA 57.448 40.909 9.53 0.00 45.89 0.98
794 2252 3.423539 TGCTTGCAGAGTGGAAGTTAT 57.576 42.857 9.53 0.00 45.89 1.89
795 2253 2.928801 TGCTTGCAGAGTGGAAGTTA 57.071 45.000 9.53 0.00 45.89 2.24
910 2372 5.241728 GCTAACAGGAAGGTTGAATGAAAGT 59.758 40.000 0.00 0.00 32.29 2.66
999 2533 2.158652 AGGAAGGAGATGGTGATGCATG 60.159 50.000 2.46 0.00 0.00 4.06
1000 2534 2.133520 AGGAAGGAGATGGTGATGCAT 58.866 47.619 0.00 0.00 0.00 3.96
1001 2535 1.588239 AGGAAGGAGATGGTGATGCA 58.412 50.000 0.00 0.00 0.00 3.96
1002 2536 3.471680 GTTAGGAAGGAGATGGTGATGC 58.528 50.000 0.00 0.00 0.00 3.91
1300 2854 4.876107 TGTCTTTTGGAGGCGATTTAGATC 59.124 41.667 0.00 0.00 30.55 2.75
1313 2867 3.674682 CGGTGCTTTTTGTGTCTTTTGGA 60.675 43.478 0.00 0.00 0.00 3.53
1363 2954 9.181061 GGGTTTGATGCTTAGGTTAACTAATAA 57.819 33.333 5.42 2.54 40.71 1.40
1364 2955 8.330247 TGGGTTTGATGCTTAGGTTAACTAATA 58.670 33.333 5.42 0.00 40.71 0.98
1365 2956 7.179269 TGGGTTTGATGCTTAGGTTAACTAAT 58.821 34.615 5.42 0.00 40.71 1.73
1366 2957 6.544650 TGGGTTTGATGCTTAGGTTAACTAA 58.455 36.000 5.42 2.05 39.31 2.24
1367 2958 6.129414 TGGGTTTGATGCTTAGGTTAACTA 57.871 37.500 5.42 0.00 0.00 2.24
1368 2959 4.993028 TGGGTTTGATGCTTAGGTTAACT 58.007 39.130 5.42 0.00 0.00 2.24
1369 2960 5.914898 ATGGGTTTGATGCTTAGGTTAAC 57.085 39.130 0.00 0.00 0.00 2.01
1381 2972 7.563924 TGACTAGTACTAGCTAATGGGTTTGAT 59.436 37.037 26.54 4.90 36.66 2.57
1383 2974 7.108841 TGACTAGTACTAGCTAATGGGTTTG 57.891 40.000 26.54 3.00 36.66 2.93
1448 3041 5.967088 TGCTTAGCCAACAAAAGTTTAACA 58.033 33.333 0.29 0.00 0.00 2.41
1452 3045 4.736126 ACTGCTTAGCCAACAAAAGTTT 57.264 36.364 0.29 0.00 0.00 2.66
1457 3050 3.088532 CCCATACTGCTTAGCCAACAAA 58.911 45.455 0.29 0.00 0.00 2.83
1503 3477 2.029964 GCCGTCCCTGTGTTCGAA 59.970 61.111 0.00 0.00 0.00 3.71
1521 3495 1.875262 CGTGCTACAATGGCTTGCA 59.125 52.632 0.00 0.00 35.69 4.08
1522 3496 1.514873 GCGTGCTACAATGGCTTGC 60.515 57.895 0.00 0.00 35.69 4.01
1523 3497 1.368641 TAGCGTGCTACAATGGCTTG 58.631 50.000 0.00 0.00 38.39 4.01
1526 3500 1.083489 TGTTAGCGTGCTACAATGGC 58.917 50.000 0.05 0.00 0.00 4.40
1527 3501 2.159572 GGTTGTTAGCGTGCTACAATGG 60.160 50.000 15.06 0.00 0.00 3.16
1570 3544 5.395324 GGGCGTGCCTATGTATATCTGTATT 60.395 44.000 11.25 0.00 36.10 1.89
1572 3546 3.446161 GGGCGTGCCTATGTATATCTGTA 59.554 47.826 11.25 0.00 36.10 2.74
1592 3572 0.959553 ACGCTATACAGATCGTGGGG 59.040 55.000 1.23 3.16 33.59 4.96
1617 3597 1.771073 CTTGCCTTCGTGTTGTGCGA 61.771 55.000 0.00 0.00 36.51 5.10
1650 3630 2.434359 GGGAAGAGGCCGAACACG 60.434 66.667 0.00 0.00 0.00 4.49
1652 3632 3.327404 GGGGGAAGAGGCCGAACA 61.327 66.667 0.00 0.00 0.00 3.18
1657 3637 0.900182 CAACTTTGGGGGAAGAGGCC 60.900 60.000 0.00 0.00 0.00 5.19
1677 3657 1.092348 GTGTCGCTGTTTAATCCCCC 58.908 55.000 0.00 0.00 0.00 5.40
1678 3658 1.092348 GGTGTCGCTGTTTAATCCCC 58.908 55.000 0.00 0.00 0.00 4.81
1689 3669 2.119655 CGGCCTACTAGGTGTCGCT 61.120 63.158 0.00 0.00 37.80 4.93
1789 3773 0.613260 ATGGTCGGTCTGCAAGCTAA 59.387 50.000 0.00 0.00 0.00 3.09
1790 3774 0.175760 GATGGTCGGTCTGCAAGCTA 59.824 55.000 0.00 0.00 0.00 3.32
1825 3809 2.508887 GCGCTGTGCTCAGAGGAG 60.509 66.667 19.61 8.02 43.76 3.69
1826 3810 4.074526 GGCGCTGTGCTCAGAGGA 62.075 66.667 19.61 0.00 43.76 3.71
1853 3837 1.079503 GGCGTTTCTCAGAAATCGCT 58.920 50.000 29.36 0.00 43.42 4.93
1855 3839 1.798223 TGTGGCGTTTCTCAGAAATCG 59.202 47.619 2.39 9.95 0.00 3.34
1908 3892 4.734266 AGCCTGAAACTGGAAGAGATTTT 58.266 39.130 0.00 0.00 37.43 1.82
1997 5120 7.206687 ACATTTTTCTAAACGCCTCAAAATCA 58.793 30.769 0.00 0.00 0.00 2.57
2217 5429 1.774217 TTCCTGGGCTCCAAGGTGT 60.774 57.895 9.13 0.00 30.80 4.16
2395 5607 0.888619 TGACTAGGCTCTTCACCACG 59.111 55.000 0.00 0.00 0.00 4.94
2599 5814 7.121315 AGCCTGTAAAGATAAGGTTTTGCTTAG 59.879 37.037 0.00 0.00 33.34 2.18
2635 5850 5.579047 TGCTGGGATGAGATTCCTTTTTAA 58.421 37.500 0.00 0.00 35.97 1.52
2828 6045 3.116939 TGGAAGGAAAGGGAATTTGGTGA 60.117 43.478 0.00 0.00 0.00 4.02
2922 6141 0.110419 CGCACCTTCGATCGCAAAAA 60.110 50.000 11.09 0.00 0.00 1.94
3117 6430 6.266323 GTGCTGAGAGTCTTGTTTATATCGA 58.734 40.000 0.00 0.00 0.00 3.59
3167 6481 1.534729 ACCGGCTCAAACAAAGATCC 58.465 50.000 0.00 0.00 0.00 3.36
3236 6550 1.402259 CTCTAGGATATACCGCCGCTG 59.598 57.143 0.00 0.00 44.74 5.18
3262 6582 3.726517 GCGCGCTCCTCTTGCAAA 61.727 61.111 26.67 0.00 0.00 3.68
3493 6830 0.819259 CCCATGGCCATGTTCCGTAG 60.819 60.000 37.30 22.91 37.11 3.51
3506 6843 1.967319 CCCTTACGAATCACCCATGG 58.033 55.000 4.14 4.14 0.00 3.66
3527 6871 0.322975 GGCTCCAGTGCTTCTCTTCA 59.677 55.000 0.00 0.00 0.00 3.02
3548 6892 2.253452 GCTTGCGAACTGTGCTGG 59.747 61.111 0.00 0.00 0.00 4.85
3570 6914 0.536460 TCACTCTCGGGTTTTTGGCC 60.536 55.000 0.00 0.00 0.00 5.36
3592 6938 0.101759 TTGGTAGGCGATACAGCGAC 59.898 55.000 0.00 0.00 40.32 5.19
3627 7017 6.094048 GCCATGTTGAGAGATACAAAGCTAAA 59.906 38.462 0.00 0.00 0.00 1.85
3743 7141 9.238368 CAGATAAGGGGAAAATACAAACACTTA 57.762 33.333 0.00 0.00 0.00 2.24
3789 7188 8.784043 GTTCTTCAAACTACCATATTGTGTTCT 58.216 33.333 0.00 0.00 0.00 3.01
3790 7189 8.564574 TGTTCTTCAAACTACCATATTGTGTTC 58.435 33.333 0.00 0.00 0.00 3.18
3791 7190 8.349983 GTGTTCTTCAAACTACCATATTGTGTT 58.650 33.333 0.00 0.00 0.00 3.32
3792 7191 7.500892 TGTGTTCTTCAAACTACCATATTGTGT 59.499 33.333 0.00 0.00 0.00 3.72
3793 7192 7.870826 TGTGTTCTTCAAACTACCATATTGTG 58.129 34.615 0.00 0.00 0.00 3.33
3822 7254 5.244189 TGTTCTGTACTAGTGAGGAGTCT 57.756 43.478 5.39 0.00 0.00 3.24
3888 7406 1.604378 CCCTAGGTCTGGCAGTTGG 59.396 63.158 15.27 5.77 0.00 3.77
3889 7407 1.201429 ACCCCTAGGTCTGGCAGTTG 61.201 60.000 15.27 0.00 46.45 3.16
3902 7420 2.585900 ACTGACCTATCACTGACCCCTA 59.414 50.000 0.00 0.00 0.00 3.53
3903 7421 1.362932 ACTGACCTATCACTGACCCCT 59.637 52.381 0.00 0.00 0.00 4.79
3904 7422 1.757699 GACTGACCTATCACTGACCCC 59.242 57.143 0.00 0.00 0.00 4.95
3905 7423 1.757699 GGACTGACCTATCACTGACCC 59.242 57.143 0.00 0.00 35.41 4.46
3906 7424 2.457598 TGGACTGACCTATCACTGACC 58.542 52.381 0.00 0.00 39.86 4.02
3946 7464 7.558161 TCACATATTGTCCTATTTCAAGCAG 57.442 36.000 0.00 0.00 0.00 4.24
3947 7465 6.038603 GCTCACATATTGTCCTATTTCAAGCA 59.961 38.462 0.00 0.00 0.00 3.91
3948 7466 6.038603 TGCTCACATATTGTCCTATTTCAAGC 59.961 38.462 0.00 0.00 0.00 4.01
3949 7467 7.281774 AGTGCTCACATATTGTCCTATTTCAAG 59.718 37.037 2.63 0.00 0.00 3.02
3950 7468 7.112122 AGTGCTCACATATTGTCCTATTTCAA 58.888 34.615 2.63 0.00 0.00 2.69
3951 7469 6.653020 AGTGCTCACATATTGTCCTATTTCA 58.347 36.000 2.63 0.00 0.00 2.69
3952 7470 6.203723 GGAGTGCTCACATATTGTCCTATTTC 59.796 42.308 2.63 0.00 0.00 2.17
3953 7471 6.058183 GGAGTGCTCACATATTGTCCTATTT 58.942 40.000 2.63 0.00 0.00 1.40
3954 7472 5.130975 TGGAGTGCTCACATATTGTCCTATT 59.869 40.000 2.63 0.00 0.00 1.73
3955 7473 4.655649 TGGAGTGCTCACATATTGTCCTAT 59.344 41.667 2.63 0.00 0.00 2.57
3956 7474 4.030216 TGGAGTGCTCACATATTGTCCTA 58.970 43.478 2.63 0.00 0.00 2.94
4045 7563 9.777575 GCGGTACATACATTTTTACTGTAATTT 57.222 29.630 0.37 0.00 33.12 1.82
4046 7564 8.948145 TGCGGTACATACATTTTTACTGTAATT 58.052 29.630 0.37 0.00 33.12 1.40
4061 7581 5.114081 ACTAACTGGATTTGCGGTACATAC 58.886 41.667 0.00 0.00 0.00 2.39
4065 7585 5.598769 AGATACTAACTGGATTTGCGGTAC 58.401 41.667 0.00 0.00 0.00 3.34
4076 7596 8.893219 TGAGCATTGAATAAGATACTAACTGG 57.107 34.615 0.00 0.00 0.00 4.00
4089 7609 5.877012 GTCTCTTCCAGTTGAGCATTGAATA 59.123 40.000 0.00 0.00 0.00 1.75
4094 7614 3.777106 TGTCTCTTCCAGTTGAGCATT 57.223 42.857 0.00 0.00 0.00 3.56
4139 7659 7.283127 GGATATTTGTTTAGACCAGCAGAATCA 59.717 37.037 0.00 0.00 0.00 2.57
4143 7663 6.156949 AGAGGATATTTGTTTAGACCAGCAGA 59.843 38.462 0.00 0.00 0.00 4.26
4182 7702 6.458342 GGTCAAATTGGGATAAGAATGACGAC 60.458 42.308 0.00 0.00 37.42 4.34
4184 7704 5.221048 GGGTCAAATTGGGATAAGAATGACG 60.221 44.000 0.00 0.00 37.42 4.35
4187 7707 6.796785 AAGGGTCAAATTGGGATAAGAATG 57.203 37.500 0.00 0.00 0.00 2.67
4188 7708 7.069950 GCTAAAGGGTCAAATTGGGATAAGAAT 59.930 37.037 0.00 0.00 0.00 2.40
4215 7735 2.562738 GTTTGGGCCAGCAAGTAGAAAT 59.437 45.455 6.23 0.00 0.00 2.17
4222 7742 0.883833 CTACTGTTTGGGCCAGCAAG 59.116 55.000 6.23 8.10 33.09 4.01
4239 7759 7.093771 TGCTTCTCAATCTGTTATCTGTCACTA 60.094 37.037 0.00 0.00 0.00 2.74
4276 7796 2.634453 GCTGCTTATTGGGGGCAATAAT 59.366 45.455 0.00 0.00 36.70 1.28
4300 7820 2.490903 GCTCAAGCATGGATGACTGTTT 59.509 45.455 0.00 0.00 41.59 2.83


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

AutoCloner maintained by Alex Coulton.