Multiple sequence alignment - TraesCS1D01G123900

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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 TraesCS1D01G123900 chr1D 100.000 6093 0 0 1 6093 126677278 126671186 0.000000e+00 11252.0
1 TraesCS1D01G123900 chr1D 89.109 101 8 3 255 353 86784727 86784628 8.290000e-24 122.0
2 TraesCS1D01G123900 chr1D 100.000 28 0 0 1483 1510 126675722 126675695 1.100000e-02 52.8
3 TraesCS1D01G123900 chr1D 100.000 28 0 0 1557 1584 126675796 126675769 1.100000e-02 52.8
4 TraesCS1D01G123900 chr1B 95.400 3109 70 16 2347 5431 190885946 190882887 0.000000e+00 4881.0
5 TraesCS1D01G123900 chr1B 94.543 1686 52 15 689 2349 190887698 190886028 0.000000e+00 2567.0
6 TraesCS1D01G123900 chr1B 93.182 352 17 5 1 346 190888892 190888542 1.510000e-140 510.0
7 TraesCS1D01G123900 chr1B 93.532 201 12 1 352 552 190888359 190888160 1.280000e-76 298.0
8 TraesCS1D01G123900 chr1B 100.000 28 0 0 1483 1510 190886817 190886790 1.100000e-02 52.8
9 TraesCS1D01G123900 chr1A 95.123 1907 76 6 1483 3372 141437074 141435168 0.000000e+00 2990.0
10 TraesCS1D01G123900 chr1A 97.087 1442 38 3 3992 5431 141434312 141432873 0.000000e+00 2427.0
11 TraesCS1D01G123900 chr1A 97.616 713 17 0 666 1378 141437821 141437109 0.000000e+00 1223.0
12 TraesCS1D01G123900 chr1A 96.998 633 12 3 3371 4001 141434960 141434333 0.000000e+00 1057.0
13 TraesCS1D01G123900 chr1A 91.243 354 22 5 1 346 141438601 141438249 1.990000e-129 473.0
14 TraesCS1D01G123900 chr1A 92.040 201 13 2 352 552 141438063 141437866 4.650000e-71 279.0
15 TraesCS1D01G123900 chr1A 98.551 69 1 0 1516 1584 141437115 141437047 8.290000e-24 122.0
16 TraesCS1D01G123900 chr1A 96.875 32 1 0 5287 5318 570189447 570189478 3.000000e-03 54.7
17 TraesCS1D01G123900 chr1A 100.000 28 0 0 1483 1510 141437000 141436973 1.100000e-02 52.8
18 TraesCS1D01G123900 chr3B 90.705 667 46 5 5431 6093 802725291 802724637 0.000000e+00 874.0
19 TraesCS1D01G123900 chr3B 82.178 101 16 2 2000 2100 15812550 15812452 1.090000e-12 86.1
20 TraesCS1D01G123900 chr5B 89.309 608 47 6 5498 6093 388295193 388294592 0.000000e+00 747.0
21 TraesCS1D01G123900 chr5B 87.368 95 6 5 6000 6093 710497762 710497673 3.000000e-18 104.0
22 TraesCS1D01G123900 chr5B 75.691 181 24 11 3448 3627 308564645 308564806 8.470000e-09 73.1
23 TraesCS1D01G123900 chrUn 92.211 398 19 3 5704 6089 339245294 339244897 2.480000e-153 553.0
24 TraesCS1D01G123900 chr4A 92.211 398 19 3 5704 6089 669865032 669865429 2.480000e-153 553.0
25 TraesCS1D01G123900 chr4A 92.211 398 19 3 5704 6089 669867344 669867741 2.480000e-153 553.0
26 TraesCS1D01G123900 chr4A 79.469 414 64 13 5692 6087 703578489 703578899 2.160000e-69 274.0
27 TraesCS1D01G123900 chr4A 79.277 415 64 14 5692 6087 703633098 703633509 2.800000e-68 270.0
28 TraesCS1D01G123900 chr4A 79.950 404 52 12 5692 6070 703687143 703687542 2.800000e-68 270.0
29 TraesCS1D01G123900 chr4A 100.000 29 0 0 5290 5318 624889018 624888990 3.000000e-03 54.7
30 TraesCS1D01G123900 chr6D 80.418 383 44 12 5705 6063 126625247 126625622 4.680000e-66 263.0
31 TraesCS1D01G123900 chr6D 76.190 168 28 9 3445 3602 160397372 160397207 1.820000e-10 78.7
32 TraesCS1D01G123900 chr7D 92.708 96 4 2 254 346 518053295 518053200 1.070000e-27 135.0
33 TraesCS1D01G123900 chr7D 75.194 129 26 4 38 161 145735702 145735829 8.530000e-04 56.5
34 TraesCS1D01G123900 chr4D 91.579 95 6 2 254 346 497356144 497356050 4.960000e-26 130.0
35 TraesCS1D01G123900 chr3D 78.243 239 24 22 5874 6093 152057885 152057656 1.780000e-25 128.0
36 TraesCS1D01G123900 chr2D 90.000 100 6 3 249 346 130427647 130427744 6.410000e-25 126.0
37 TraesCS1D01G123900 chr2D 83.951 81 12 1 2018 2097 553304598 553304518 6.550000e-10 76.8
38 TraesCS1D01G123900 chr2B 90.000 100 6 3 249 346 183656231 183656328 6.410000e-25 126.0
39 TraesCS1D01G123900 chr2B 83.750 80 13 0 2018 2097 659027865 659027786 6.550000e-10 76.8
40 TraesCS1D01G123900 chr2B 100.000 34 0 0 5284 5317 232794521 232794488 5.100000e-06 63.9
41 TraesCS1D01G123900 chr2B 94.444 36 2 0 3560 3595 490115861 490115826 8.530000e-04 56.5
42 TraesCS1D01G123900 chr2A 90.099 101 5 4 249 346 136337991 136338089 6.410000e-25 126.0
43 TraesCS1D01G123900 chr5D 90.323 93 7 2 255 345 195655861 195655953 2.980000e-23 121.0
44 TraesCS1D01G123900 chr7B 77.674 215 26 12 5894 6093 605129385 605129178 1.800000e-20 111.0
45 TraesCS1D01G123900 chr7A 78.710 155 25 4 3497 3644 621913298 621913145 5.030000e-16 97.1
46 TraesCS1D01G123900 chr6B 80.870 115 10 5 5705 5809 18803793 18803905 5.060000e-11 80.5
47 TraesCS1D01G123900 chr6B 90.698 43 4 0 3560 3602 290590972 290590930 2.370000e-04 58.4
48 TraesCS1D01G123900 chr6B 90.698 43 4 0 3560 3602 290622783 290622741 2.370000e-04 58.4
49 TraesCS1D01G123900 chr5A 97.297 37 1 0 5286 5322 346175076 346175112 5.100000e-06 63.9


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 TraesCS1D01G123900 chr1D 126671186 126677278 6092 True 3785.866667 11252 100.00000 1 6093 3 chr1D.!!$R2 6092
1 TraesCS1D01G123900 chr1B 190882887 190888892 6005 True 1661.760000 4881 95.33140 1 5431 5 chr1B.!!$R1 5430
2 TraesCS1D01G123900 chr1A 141432873 141438601 5728 True 1077.975000 2990 96.08225 1 5431 8 chr1A.!!$R1 5430
3 TraesCS1D01G123900 chr3B 802724637 802725291 654 True 874.000000 874 90.70500 5431 6093 1 chr3B.!!$R2 662
4 TraesCS1D01G123900 chr5B 388294592 388295193 601 True 747.000000 747 89.30900 5498 6093 1 chr5B.!!$R1 595
5 TraesCS1D01G123900 chr4A 669865032 669867741 2709 False 553.000000 553 92.21100 5704 6089 2 chr4A.!!$F4 385

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
207 211 0.451783 CAACACCGCCATTAGCTTCC 59.548 55.000 0.00 0.0 40.39 3.46 F
214 218 0.882484 GCCATTAGCTTCCTCCGAGC 60.882 60.000 0.00 0.0 40.43 5.03 F
1644 2190 1.000163 ACTGGCCTATAAGCATCGTCG 60.000 52.381 3.32 0.0 0.00 5.12 F
2385 3017 0.250234 TTCTCCCAGATGCTCGGTTG 59.750 55.000 0.00 0.0 0.00 3.77 F
3700 4559 0.697658 TTCTCCCATGCATGGTGACA 59.302 50.000 37.30 21.9 46.65 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 1926 0.451783 GCCAAACCTTGCCAGATACG 59.548 55.000 0.00 0.0 0.00 3.06 R
1760 2308 1.450312 GCCAGTGGTCGCTATGCTT 60.450 57.895 11.74 0.0 0.00 3.91 R
2591 3224 2.863137 GTTTCGCATTTTTCACTGCCAA 59.137 40.909 0.00 0.0 34.89 4.52 R
4351 5249 1.274167 TGCCACTAACCAGTAACGAGG 59.726 52.381 0.00 0.0 32.21 4.63 R
5426 6327 1.443407 CGCATAGGAGGTCCCACAG 59.557 63.158 0.00 0.0 37.41 3.66 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
207 211 0.451783 CAACACCGCCATTAGCTTCC 59.548 55.000 0.00 0.00 40.39 3.46
214 218 0.882484 GCCATTAGCTTCCTCCGAGC 60.882 60.000 0.00 0.00 40.43 5.03
226 230 3.499737 CCGAGCGATTGTGTGCCC 61.500 66.667 0.00 0.00 0.00 5.36
258 262 1.202521 CGAATCACATCATCACGGGGA 60.203 52.381 0.00 0.00 0.00 4.81
303 311 1.404315 GGTGAGACCGTGAGATCAACC 60.404 57.143 0.00 0.00 0.00 3.77
473 669 9.775854 CATTGATCTCACCTAATGTAAGATCTT 57.224 33.333 13.56 13.56 33.82 2.40
508 704 2.749076 CCACATCATCACCGACAACAAT 59.251 45.455 0.00 0.00 0.00 2.71
552 748 2.492881 TCACCGAATACTACGAAAGGCA 59.507 45.455 0.00 0.00 0.00 4.75
553 749 3.056678 TCACCGAATACTACGAAAGGCAA 60.057 43.478 0.00 0.00 0.00 4.52
555 751 2.284417 CCGAATACTACGAAAGGCAAGC 59.716 50.000 0.00 0.00 0.00 4.01
556 752 3.187700 CGAATACTACGAAAGGCAAGCT 58.812 45.455 0.00 0.00 0.00 3.74
558 754 4.206609 CGAATACTACGAAAGGCAAGCTAC 59.793 45.833 0.00 0.00 0.00 3.58
559 755 5.340439 AATACTACGAAAGGCAAGCTACT 57.660 39.130 0.00 0.00 0.00 2.57
585 825 9.753674 TTTATTTTCTGATGAATTGTACTCCCT 57.246 29.630 0.00 0.00 31.56 4.20
586 826 7.872113 ATTTTCTGATGAATTGTACTCCCTC 57.128 36.000 0.00 0.00 31.56 4.30
588 828 3.384789 TCTGATGAATTGTACTCCCTCCG 59.615 47.826 0.00 0.00 0.00 4.63
589 829 3.104512 TGATGAATTGTACTCCCTCCGT 58.895 45.455 0.00 0.00 0.00 4.69
590 830 3.517901 TGATGAATTGTACTCCCTCCGTT 59.482 43.478 0.00 0.00 0.00 4.44
592 832 3.934068 TGAATTGTACTCCCTCCGTTTC 58.066 45.455 0.00 0.00 0.00 2.78
593 833 3.325425 TGAATTGTACTCCCTCCGTTTCA 59.675 43.478 0.00 0.00 0.00 2.69
594 834 4.202377 TGAATTGTACTCCCTCCGTTTCAA 60.202 41.667 0.00 0.00 0.00 2.69
595 835 3.396260 TTGTACTCCCTCCGTTTCAAG 57.604 47.619 0.00 0.00 0.00 3.02
597 837 3.170717 TGTACTCCCTCCGTTTCAAGAT 58.829 45.455 0.00 0.00 0.00 2.40
598 838 4.346730 TGTACTCCCTCCGTTTCAAGATA 58.653 43.478 0.00 0.00 0.00 1.98
600 840 4.903045 ACTCCCTCCGTTTCAAGATAAA 57.097 40.909 0.00 0.00 0.00 1.40
601 841 5.437191 ACTCCCTCCGTTTCAAGATAAAT 57.563 39.130 0.00 0.00 0.00 1.40
602 842 6.555463 ACTCCCTCCGTTTCAAGATAAATA 57.445 37.500 0.00 0.00 0.00 1.40
604 844 7.399634 ACTCCCTCCGTTTCAAGATAAATAAA 58.600 34.615 0.00 0.00 0.00 1.40
605 845 7.886446 ACTCCCTCCGTTTCAAGATAAATAAAA 59.114 33.333 0.00 0.00 0.00 1.52
606 846 8.638629 TCCCTCCGTTTCAAGATAAATAAAAA 57.361 30.769 0.00 0.00 0.00 1.94
607 847 9.250246 TCCCTCCGTTTCAAGATAAATAAAAAT 57.750 29.630 0.00 0.00 0.00 1.82
608 848 9.869757 CCCTCCGTTTCAAGATAAATAAAAATT 57.130 29.630 0.00 0.00 0.00 1.82
638 878 9.983804 CATCTATTTTAAAACGGAAGAAGTACC 57.016 33.333 1.97 0.00 0.00 3.34
639 879 9.955102 ATCTATTTTAAAACGGAAGAAGTACCT 57.045 29.630 1.97 0.00 0.00 3.08
640 880 9.783081 TCTATTTTAAAACGGAAGAAGTACCTT 57.217 29.630 1.97 0.00 0.00 3.50
644 884 8.454570 TTTAAAACGGAAGAAGTACCTTTCAT 57.545 30.769 0.00 0.00 0.00 2.57
647 887 6.600882 AACGGAAGAAGTACCTTTCATCTA 57.399 37.500 0.00 0.00 0.00 1.98
649 889 7.184067 ACGGAAGAAGTACCTTTCATCTATT 57.816 36.000 0.00 0.00 0.00 1.73
650 890 7.621796 ACGGAAGAAGTACCTTTCATCTATTT 58.378 34.615 0.00 0.00 0.00 1.40
652 892 8.391106 CGGAAGAAGTACCTTTCATCTATTTTG 58.609 37.037 0.00 0.00 0.00 2.44
653 893 9.449719 GGAAGAAGTACCTTTCATCTATTTTGA 57.550 33.333 0.00 0.00 0.00 2.69
657 897 9.543018 GAAGTACCTTTCATCTATTTTGAAACG 57.457 33.333 0.00 0.00 37.97 3.60
658 898 8.040716 AGTACCTTTCATCTATTTTGAAACGG 57.959 34.615 0.00 0.00 37.97 4.44
659 899 7.881232 AGTACCTTTCATCTATTTTGAAACGGA 59.119 33.333 15.28 1.11 37.97 4.69
660 900 7.145932 ACCTTTCATCTATTTTGAAACGGAG 57.854 36.000 15.28 1.18 37.97 4.63
661 901 6.151144 ACCTTTCATCTATTTTGAAACGGAGG 59.849 38.462 15.28 9.43 37.97 4.30
662 902 6.404734 CCTTTCATCTATTTTGAAACGGAGGG 60.405 42.308 0.00 0.00 37.97 4.30
664 904 5.183228 TCATCTATTTTGAAACGGAGGGAC 58.817 41.667 0.00 0.00 0.00 4.46
665 905 6.521770 TTCATCTATTTTGAAACGGAGGGACT 60.522 38.462 0.00 0.00 33.20 3.85
760 1283 2.282462 CACCTCACCACCAAGCCC 60.282 66.667 0.00 0.00 0.00 5.19
1189 1713 5.822278 TCTAGTTTCGTATGCTTGAGCTAG 58.178 41.667 4.44 0.00 42.66 3.42
1197 1721 3.641434 ATGCTTGAGCTAGTTGGATGT 57.359 42.857 4.44 0.00 42.66 3.06
1410 1934 6.745159 ATATACTACACAGCTCGTATCTGG 57.255 41.667 0.00 0.00 35.94 3.86
1468 1992 8.582437 TCTGCAAATACACCTAGTATACATACC 58.418 37.037 5.50 0.00 42.56 2.73
1631 2177 1.722034 ATACATGATCCGACTGGCCT 58.278 50.000 3.32 0.00 34.14 5.19
1644 2190 1.000163 ACTGGCCTATAAGCATCGTCG 60.000 52.381 3.32 0.00 0.00 5.12
1729 2277 4.836125 ACAATTGTGGAGTTGTGATCAC 57.164 40.909 19.27 19.27 37.19 3.06
1760 2308 1.148048 TAGGCACACAACAGCAGCA 59.852 52.632 0.00 0.00 0.00 4.41
1800 2348 1.972660 GCCGGTGAGTTGGGCTAGAT 61.973 60.000 1.90 0.00 43.52 1.98
1868 2416 0.874607 GCGAGGGCAAGTACGTATGG 60.875 60.000 0.00 0.00 39.62 2.74
1969 2517 9.065798 TGGTTAGTATTAGTTTTTGGTTGTACC 57.934 33.333 0.00 0.00 39.22 3.34
1984 2532 4.037089 GGTTGTACCTTCCGAACACAAAAT 59.963 41.667 0.00 0.00 34.73 1.82
2065 2613 5.659440 TCTCCTTCATAAATTTTGCCACC 57.341 39.130 0.00 0.00 0.00 4.61
2185 2733 3.388497 TGAGCAGGAGGTCATGACT 57.612 52.632 24.50 11.25 46.52 3.41
2225 2773 1.067295 ACTGAGCCCTGAATTGGTGA 58.933 50.000 0.00 0.00 0.00 4.02
2230 2778 2.686915 GAGCCCTGAATTGGTGATTCTG 59.313 50.000 1.09 0.71 43.74 3.02
2258 2806 4.512484 TGATTGTTGTGAGTTGTGAGACA 58.488 39.130 0.00 0.00 0.00 3.41
2308 2856 3.089784 CGCCAATTCGAAGGGACG 58.910 61.111 19.68 17.23 0.00 4.79
2385 3017 0.250234 TTCTCCCAGATGCTCGGTTG 59.750 55.000 0.00 0.00 0.00 3.77
2429 3061 1.639635 GGTCCATGGGAGGCTGATGT 61.640 60.000 13.02 0.00 29.39 3.06
2443 3075 2.739932 GCTGATGTCCGCTTACACTGAT 60.740 50.000 0.00 0.00 30.75 2.90
2543 3175 4.044426 GTGCAATATTCTGGAATTTCGCC 58.956 43.478 1.01 0.00 32.50 5.54
2591 3224 6.301169 AGCTAGTACAGTTCAATAGCCTTT 57.699 37.500 0.00 0.00 39.72 3.11
2615 3248 3.121778 GGCAGTGAAAAATGCGAAACATC 59.878 43.478 0.00 0.00 43.49 3.06
2724 3363 8.854614 ATGTCAGTTTTAATAACTTCTGCTCT 57.145 30.769 0.00 0.00 0.00 4.09
2820 3459 5.811399 TTGAGGTATTATCTTTTGTGCCG 57.189 39.130 0.00 0.00 0.00 5.69
2855 3494 4.528596 ACCTACTACAGACTCATTGCAACT 59.471 41.667 0.00 0.00 0.00 3.16
3039 3678 7.041098 ACACTATGACTGTCTTTGCTTAAAAGG 60.041 37.037 9.51 0.00 44.69 3.11
3123 3762 6.828785 AGTTTGACACCAATTAGTTCTCTTGT 59.171 34.615 0.00 0.00 31.46 3.16
3180 3829 2.338577 TTTTGTTGGTTTGCCCCATG 57.661 45.000 0.00 0.00 33.60 3.66
3343 3992 4.437682 ACTGGATGAACTTTTCACTGGA 57.562 40.909 0.00 0.00 43.48 3.86
3487 4345 1.434696 CTGCGGGGATTGATTGCAC 59.565 57.895 0.00 0.00 0.00 4.57
3696 4555 1.560505 GGTTTTCTCCCATGCATGGT 58.439 50.000 37.30 0.00 46.65 3.55
3697 4556 1.205417 GGTTTTCTCCCATGCATGGTG 59.795 52.381 37.30 29.47 46.65 4.17
3698 4557 2.170166 GTTTTCTCCCATGCATGGTGA 58.830 47.619 37.30 30.92 46.65 4.02
3699 4558 1.838112 TTTCTCCCATGCATGGTGAC 58.162 50.000 37.30 0.00 46.65 3.67
3700 4559 0.697658 TTCTCCCATGCATGGTGACA 59.302 50.000 37.30 21.90 46.65 3.58
3739 4603 8.150945 TGCATATTGAGAGAAATAGGTTAGGAC 58.849 37.037 0.00 0.00 0.00 3.85
3943 4809 4.404185 AGACCCAGGCCTTCTTTATTTT 57.596 40.909 0.00 0.00 0.00 1.82
4053 4949 5.559770 TGATCCTGCTTTGAGATTGTACAA 58.440 37.500 11.41 11.41 0.00 2.41
4166 5062 6.875726 CCTTCTGATGATGTAAGTCTTGTCAA 59.124 38.462 0.00 0.00 0.00 3.18
4167 5063 7.551974 CCTTCTGATGATGTAAGTCTTGTCAAT 59.448 37.037 0.00 0.00 0.00 2.57
4351 5249 5.163530 TGTGGATGATGATATTTGGTGCAAC 60.164 40.000 0.00 0.00 0.00 4.17
4381 5279 2.301870 TGGTTAGTGGCACTCCTACTTG 59.698 50.000 25.80 0.00 0.00 3.16
4408 5306 9.737427 TTACGTGTTACAAACAAATGAATCAAT 57.263 25.926 0.00 0.00 44.16 2.57
4746 5644 0.833287 GCTCTCCAATACTGCCTGGA 59.167 55.000 0.00 0.00 39.47 3.86
4856 5754 6.271391 CCTATGTGGGTGTATCCTTATGGTTA 59.729 42.308 0.00 0.00 36.25 2.85
4955 5856 2.738846 CCAGTGATATATGCTCGTTGGC 59.261 50.000 0.00 0.00 0.00 4.52
5147 6048 5.105797 GCATGAACAGGTTAACATGGATTCA 60.106 40.000 22.90 21.92 39.96 2.57
5241 6142 5.348724 CGAATAACTACAGATGTGCACTTGT 59.651 40.000 19.41 19.98 0.00 3.16
5284 6185 5.048852 AGCTGCATGTCTTCTCTTTCTTTTC 60.049 40.000 1.02 0.00 0.00 2.29
5334 6235 6.596309 TGTCGCTCAAATGGATCTAGATAT 57.404 37.500 4.89 0.00 0.00 1.63
5426 6327 1.794701 ACGCATGATCATGTCGTATGC 59.205 47.619 35.27 23.29 43.80 3.14
5447 6348 4.301027 GGGACCTCCTATGCGCCG 62.301 72.222 4.18 0.00 35.95 6.46
5449 6350 4.971125 GACCTCCTATGCGCCGCC 62.971 72.222 6.63 0.00 0.00 6.13
5569 6471 4.747529 GAAGTTACCCCCGCGCGT 62.748 66.667 29.95 12.94 0.00 6.01
5605 6507 2.210116 ACGTCTGTTTGCTACACAAGG 58.790 47.619 0.00 0.00 40.06 3.61
5647 6549 2.871637 GCGGCTGCATATGTCCAATAGA 60.872 50.000 14.08 0.00 42.15 1.98
5657 6559 4.607293 ATGTCCAATAGAGCATCGCTAA 57.393 40.909 0.00 0.00 39.88 3.09
5658 6560 4.607293 TGTCCAATAGAGCATCGCTAAT 57.393 40.909 0.00 0.00 39.88 1.73
5672 6574 8.438676 AGCATCGCTAATGTATTTAAGAACTT 57.561 30.769 0.00 0.00 36.99 2.66
5673 6575 9.542462 AGCATCGCTAATGTATTTAAGAACTTA 57.458 29.630 0.00 0.00 36.99 2.24
5886 9116 6.594937 AGGTGTTTCGACAAAAGTGTACTTTA 59.405 34.615 10.15 0.00 44.69 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.125367 TGGGTTGACTAGTAGATCTGCTA 57.875 43.478 18.18 18.18 0.00 3.49
107 109 1.452833 GTACTCGTAGCCCCCGACT 60.453 63.158 0.00 0.00 0.00 4.18
207 211 2.456119 GGCACACAATCGCTCGGAG 61.456 63.158 0.00 0.00 0.00 4.63
214 218 1.926511 GCTGAAGGGGCACACAATCG 61.927 60.000 0.00 0.00 0.00 3.34
226 230 1.805539 TGATTCGCGACGCTGAAGG 60.806 57.895 23.68 8.79 0.00 3.46
258 262 8.420222 CCTAATGTGAGATCTCATACAAGTCTT 58.580 37.037 27.51 16.50 42.18 3.01
290 294 1.904287 TTTTGGGGTTGATCTCACGG 58.096 50.000 0.00 0.00 0.00 4.94
349 358 9.508642 TTGATGGTTCAACCTTAAAAAGTTTTT 57.491 25.926 17.26 17.26 39.58 1.94
473 669 1.906574 GATGTGGGGGAGACTTGTGTA 59.093 52.381 0.00 0.00 0.00 2.90
508 704 1.739035 GCAGCGCTGGTGAACTATGTA 60.739 52.381 36.47 0.00 32.22 2.29
559 755 9.753674 AGGGAGTACAATTCATCAGAAAATAAA 57.246 29.630 0.00 0.00 37.29 1.40
581 821 8.638629 TTTTTATTTATCTTGAAACGGAGGGA 57.361 30.769 0.00 0.00 0.00 4.20
582 822 9.869757 AATTTTTATTTATCTTGAAACGGAGGG 57.130 29.630 0.00 0.00 0.00 4.30
612 852 9.983804 GGTACTTCTTCCGTTTTAAAATAGATG 57.016 33.333 3.52 6.78 0.00 2.90
613 853 9.955102 AGGTACTTCTTCCGTTTTAAAATAGAT 57.045 29.630 3.52 0.00 27.25 1.98
633 873 7.881232 TCCGTTTCAAAATAGATGAAAGGTACT 59.119 33.333 15.96 0.00 44.81 2.73
635 875 7.335924 CCTCCGTTTCAAAATAGATGAAAGGTA 59.664 37.037 15.96 4.64 44.81 3.08
636 876 6.151144 CCTCCGTTTCAAAATAGATGAAAGGT 59.849 38.462 15.96 0.00 44.81 3.50
637 877 6.404734 CCCTCCGTTTCAAAATAGATGAAAGG 60.405 42.308 12.31 12.31 44.81 3.11
638 878 6.374333 TCCCTCCGTTTCAAAATAGATGAAAG 59.626 38.462 2.20 0.00 44.81 2.62
639 879 6.150474 GTCCCTCCGTTTCAAAATAGATGAAA 59.850 38.462 0.00 0.00 42.73 2.69
640 880 5.646360 GTCCCTCCGTTTCAAAATAGATGAA 59.354 40.000 0.00 0.00 35.11 2.57
641 881 5.045869 AGTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
642 882 5.186198 AGTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
644 884 4.903045 AGTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
647 887 3.073356 TGGTAGTCCCTCCGTTTCAAAAT 59.927 43.478 0.00 0.00 0.00 1.82
649 889 2.048601 TGGTAGTCCCTCCGTTTCAAA 58.951 47.619 0.00 0.00 0.00 2.69
650 890 1.719529 TGGTAGTCCCTCCGTTTCAA 58.280 50.000 0.00 0.00 0.00 2.69
652 892 1.829222 TGATGGTAGTCCCTCCGTTTC 59.171 52.381 0.00 0.00 0.00 2.78
653 893 1.946984 TGATGGTAGTCCCTCCGTTT 58.053 50.000 0.00 0.00 0.00 3.60
654 894 1.762957 CATGATGGTAGTCCCTCCGTT 59.237 52.381 0.00 0.00 0.00 4.44
655 895 1.414158 CATGATGGTAGTCCCTCCGT 58.586 55.000 0.00 0.00 0.00 4.69
657 897 1.694696 GTCCATGATGGTAGTCCCTCC 59.305 57.143 11.87 0.00 39.03 4.30
658 898 1.694696 GGTCCATGATGGTAGTCCCTC 59.305 57.143 11.87 0.00 39.03 4.30
659 899 1.807814 GGTCCATGATGGTAGTCCCT 58.192 55.000 11.87 0.00 39.03 4.20
660 900 0.393077 CGGTCCATGATGGTAGTCCC 59.607 60.000 11.87 4.40 39.03 4.46
661 901 0.393077 CCGGTCCATGATGGTAGTCC 59.607 60.000 11.87 9.06 39.03 3.85
662 902 0.249911 GCCGGTCCATGATGGTAGTC 60.250 60.000 11.87 1.28 39.03 2.59
664 904 1.071471 GGCCGGTCCATGATGGTAG 59.929 63.158 11.87 4.16 39.03 3.18
665 905 1.690985 TGGCCGGTCCATGATGGTA 60.691 57.895 11.87 0.00 40.72 3.25
1189 1713 0.877071 CCAGCACAGTCACATCCAAC 59.123 55.000 0.00 0.00 0.00 3.77
1197 1721 1.036481 TTGCAAAGCCAGCACAGTCA 61.036 50.000 0.00 0.00 42.54 3.41
1389 1913 3.253677 GCCAGATACGAGCTGTGTAGTAT 59.746 47.826 0.00 0.00 33.06 2.12
1390 1914 2.617308 GCCAGATACGAGCTGTGTAGTA 59.383 50.000 0.00 0.00 0.00 1.82
1402 1926 0.451783 GCCAAACCTTGCCAGATACG 59.548 55.000 0.00 0.00 0.00 3.06
1425 1949 4.992688 TGCAGAAAAATTTAGGTATGGCG 58.007 39.130 0.00 0.00 0.00 5.69
1461 1985 9.426837 GACAAAGTTTACATGTACTGGTATGTA 57.573 33.333 4.68 0.00 38.41 2.29
1468 1992 6.293407 CCCAGTGACAAAGTTTACATGTACTG 60.293 42.308 4.68 7.98 33.46 2.74
1644 2190 8.856490 TTTTTAGAGAACAGATTGAGCAAAAC 57.144 30.769 0.00 0.00 0.00 2.43
1760 2308 1.450312 GCCAGTGGTCGCTATGCTT 60.450 57.895 11.74 0.00 0.00 3.91
1800 2348 4.160439 CCAGTAGTTCTCACATCCTTGCTA 59.840 45.833 0.00 0.00 0.00 3.49
1969 2517 8.889717 AGGTATGTATTATTTTGTGTTCGGAAG 58.110 33.333 0.00 0.00 0.00 3.46
1971 2519 9.537192 CTAGGTATGTATTATTTTGTGTTCGGA 57.463 33.333 0.00 0.00 0.00 4.55
2065 2613 5.748630 GCGAAGGCAAGAATAATTTTTAGGG 59.251 40.000 0.00 0.00 39.62 3.53
2183 2731 7.337942 CAGTTATCCTGAAATAGAAAAGGCAGT 59.662 37.037 0.00 0.00 44.49 4.40
2185 2733 7.630242 CAGTTATCCTGAAATAGAAAAGGCA 57.370 36.000 0.00 0.00 44.49 4.75
2225 2773 5.011329 ACTCACAACAATCAATTGGCAGAAT 59.989 36.000 5.42 0.00 41.96 2.40
2230 2778 4.209703 CACAACTCACAACAATCAATTGGC 59.790 41.667 5.42 0.00 41.96 4.52
2258 2806 1.033574 CTACGGCCTAGCTGCTTACT 58.966 55.000 7.79 0.00 38.71 2.24
2308 2856 7.170658 TGAAACAACAAGCTTATAAACCAATGC 59.829 33.333 0.00 0.00 0.00 3.56
2409 3041 1.308128 ATCAGCCTCCCATGGACCA 60.308 57.895 15.22 0.00 0.00 4.02
2429 3061 1.804151 GCAAACATCAGTGTAAGCGGA 59.196 47.619 0.00 0.00 37.67 5.54
2443 3075 1.028905 GTGGCCAACTACAGCAAACA 58.971 50.000 7.24 0.00 0.00 2.83
2526 3158 4.073293 AGACGGCGAAATTCCAGAATAT 57.927 40.909 16.62 0.00 0.00 1.28
2591 3224 2.863137 GTTTCGCATTTTTCACTGCCAA 59.137 40.909 0.00 0.00 34.89 4.52
2724 3363 5.889853 ACGTATACCTTCTCCACTTGTATGA 59.110 40.000 0.00 0.00 0.00 2.15
2820 3459 5.642491 GTCTGTAGTAGGTTCCCAACAAATC 59.358 44.000 0.00 0.00 0.00 2.17
2902 3541 4.647611 ACACGGATACTTTCAACCATTGA 58.352 39.130 0.00 0.00 38.04 2.57
2912 3551 4.517832 GGAAACTTCCAACACGGATACTTT 59.482 41.667 3.50 0.00 45.80 2.66
3696 4555 3.431673 TGCACCCATCTTAACATGTCA 57.568 42.857 0.00 0.00 0.00 3.58
3697 4556 6.262944 TCAATATGCACCCATCTTAACATGTC 59.737 38.462 0.00 0.00 32.85 3.06
3698 4557 6.128486 TCAATATGCACCCATCTTAACATGT 58.872 36.000 0.00 0.00 32.85 3.21
3699 4558 6.487668 TCTCAATATGCACCCATCTTAACATG 59.512 38.462 0.00 0.00 32.85 3.21
3700 4559 6.604171 TCTCAATATGCACCCATCTTAACAT 58.396 36.000 0.00 0.00 32.85 2.71
3739 4603 2.096565 CCACTGCGATAATGATTCAGCG 60.097 50.000 0.00 0.00 0.00 5.18
3797 4663 2.817258 CCTCAATTTTTCCGTACTGCCA 59.183 45.455 0.00 0.00 0.00 4.92
3943 4809 7.496346 ACTCTTGAACACATAGGGATAAGAA 57.504 36.000 0.00 0.00 0.00 2.52
4053 4949 5.184864 TGCGTGGTCCAAAATTGAAGATTAT 59.815 36.000 0.00 0.00 0.00 1.28
4351 5249 1.274167 TGCCACTAACCAGTAACGAGG 59.726 52.381 0.00 0.00 32.21 4.63
4381 5279 8.549777 TGATTCATTTGTTTGTAACACGTAAC 57.450 30.769 0.00 0.00 41.97 2.50
4617 5515 1.620819 CTAGGGCAGTTCTGTGACACT 59.379 52.381 7.20 0.00 0.00 3.55
4746 5644 3.260632 GTCCAACCATAATGCCCAAAAGT 59.739 43.478 0.00 0.00 0.00 2.66
4922 5823 8.609483 AGCATATATCACTGGGAATGAAGTAAT 58.391 33.333 0.00 0.00 0.00 1.89
4955 5856 2.415090 GCAAGTGCAGCATGTTAAGGAG 60.415 50.000 0.00 0.00 41.59 3.69
5147 6048 3.262915 AGAGCTGCCACAGAGTTTAGATT 59.737 43.478 0.00 0.00 32.44 2.40
5241 6142 3.952323 AGCTCTACTTCGCAGGTACAATA 59.048 43.478 0.00 0.00 0.00 1.90
5334 6235 8.124823 CCGTACTACTTGTCGTTCAAATAGATA 58.875 37.037 14.40 5.16 37.87 1.98
5358 6259 2.016393 TTGCTACAGCCTCCGATCCG 62.016 60.000 0.00 0.00 41.18 4.18
5426 6327 1.443407 CGCATAGGAGGTCCCACAG 59.557 63.158 0.00 0.00 37.41 3.66
5449 6350 1.538276 CTCGCTATTTGCCGCAAAAG 58.462 50.000 21.80 18.87 36.90 2.27
5521 6423 3.370978 CGATTTTTACCGCTGAGACACAT 59.629 43.478 0.00 0.00 0.00 3.21
5569 6471 4.047059 GTCGCGGGTTCGAGTCCA 62.047 66.667 6.13 0.00 39.34 4.02
5571 6473 4.395583 ACGTCGCGGGTTCGAGTC 62.396 66.667 20.66 0.00 39.34 3.36
5573 6475 4.099170 AGACGTCGCGGGTTCGAG 62.099 66.667 20.66 4.50 39.34 4.04
5580 6482 1.731613 TAGCAAACAGACGTCGCGG 60.732 57.895 10.46 6.64 0.00 6.46
5647 6549 8.438676 AAGTTCTTAAATACATTAGCGATGCT 57.561 30.769 0.00 0.00 43.41 3.79
5892 9122 7.062839 TGGCGCATTTTCAAAATATAACACTTC 59.937 33.333 10.83 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.