Multiple sequence alignment - TraesCS1D01G033300

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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 TraesCS1D01G033300 chr1D 100.000 6454 0 0 1 6454 13326364 13319911 0.000000e+00 11919.0
1 TraesCS1D01G033300 chr1D 92.695 3176 216 12 3207 6377 13313858 13310694 0.000000e+00 4566.0
2 TraesCS1D01G033300 chr1D 79.717 1129 196 21 1135 2248 13371097 13369987 0.000000e+00 785.0
3 TraesCS1D01G033300 chr1D 83.765 850 80 35 2374 3197 13314742 13313925 0.000000e+00 752.0
4 TraesCS1D01G033300 chr1D 78.153 1126 211 22 1135 2248 14259870 14258768 0.000000e+00 684.0
5 TraesCS1D01G033300 chr1D 82.048 791 123 8 3696 4481 13368368 13367592 0.000000e+00 656.0
6 TraesCS1D01G033300 chr1D 83.360 619 96 6 3671 4284 14257312 14256696 3.380000e-157 566.0
7 TraesCS1D01G033300 chr1D 83.544 316 47 3 1 312 13484315 13484001 2.280000e-74 291.0
8 TraesCS1D01G033300 chr1D 86.111 216 22 6 907 1114 13371413 13371198 6.510000e-55 226.0
9 TraesCS1D01G033300 chr1D 85.366 205 28 2 4299 4503 14256636 14256434 1.820000e-50 211.0
10 TraesCS1D01G033300 chr1D 86.232 138 19 0 4320 4457 452623314 452623177 4.030000e-32 150.0
11 TraesCS1D01G033300 chr1D 82.069 145 22 4 3461 3605 14257487 14257347 3.160000e-23 121.0
12 TraesCS1D01G033300 chr1D 85.088 114 16 1 3492 3605 13368524 13368412 1.470000e-21 115.0
13 TraesCS1D01G033300 chr1B 94.662 4702 195 14 923 5614 19038871 19043526 0.000000e+00 7241.0
14 TraesCS1D01G033300 chr1B 90.941 3654 247 45 2374 5988 19048468 19052076 0.000000e+00 4837.0
15 TraesCS1D01G033300 chr1B 93.423 821 38 6 1 806 19037393 19038212 0.000000e+00 1203.0
16 TraesCS1D01G033300 chr1B 84.864 1176 147 23 1091 2255 19232436 19231281 0.000000e+00 1157.0
17 TraesCS1D01G033300 chr1B 84.481 799 117 7 3671 4465 19219864 19219069 0.000000e+00 782.0
18 TraesCS1D01G033300 chr1B 92.839 391 27 1 5988 6377 19057489 19057879 3.380000e-157 566.0
19 TraesCS1D01G033300 chr1B 91.304 207 11 3 6176 6378 19043526 19043729 6.370000e-70 276.0
20 TraesCS1D01G033300 chr1B 75.573 262 54 8 3070 3328 588327516 588327262 3.160000e-23 121.0
21 TraesCS1D01G033300 chr1B 87.640 89 10 1 3517 3605 19219986 19219899 1.140000e-17 102.0
22 TraesCS1D01G033300 chr1B 89.041 73 8 0 1559 1631 587807098 587807170 2.480000e-14 91.6
23 TraesCS1D01G033300 chr1B 86.567 67 4 5 6386 6447 19057934 19058000 1.160000e-07 69.4
24 TraesCS1D01G033300 chr1A 94.543 4673 201 22 972 5617 14594046 14589401 0.000000e+00 7167.0
25 TraesCS1D01G033300 chr1A 86.655 1154 139 10 1094 2242 14615550 14614407 0.000000e+00 1264.0
26 TraesCS1D01G033300 chr1A 80.788 1015 152 24 3472 4481 14605475 14604499 0.000000e+00 754.0
27 TraesCS1D01G033300 chr1A 91.960 199 15 1 6179 6377 14589401 14589204 1.770000e-70 278.0
28 TraesCS1D01G033300 chr1A 76.145 415 68 19 4057 4457 532530722 532531119 8.540000e-44 189.0
29 TraesCS1D01G033300 chr1A 82.270 141 22 3 2386 2525 532772214 532772076 1.140000e-22 119.0
30 TraesCS1D01G033300 chr1A 75.191 262 55 8 3070 3328 532629419 532629165 1.470000e-21 115.0
31 TraesCS1D01G033300 chr1A 92.208 77 6 0 6378 6454 14589155 14589079 6.840000e-20 110.0
32 TraesCS1D01G033300 chr3D 96.875 32 0 1 5569 5600 594893935 594893965 1.200000e-02 52.8


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 TraesCS1D01G033300 chr1D 13319911 13326364 6453 True 11919.000000 11919 100.000000 1 6454 1 chr1D.!!$R1 6453
1 TraesCS1D01G033300 chr1D 13310694 13314742 4048 True 2659.000000 4566 88.230000 2374 6377 2 chr1D.!!$R4 4003
2 TraesCS1D01G033300 chr1D 13367592 13371413 3821 True 445.500000 785 83.241000 907 4481 4 chr1D.!!$R5 3574
3 TraesCS1D01G033300 chr1D 14256434 14259870 3436 True 395.500000 684 82.237000 1135 4503 4 chr1D.!!$R6 3368
4 TraesCS1D01G033300 chr1B 19048468 19052076 3608 False 4837.000000 4837 90.941000 2374 5988 1 chr1B.!!$F1 3614
5 TraesCS1D01G033300 chr1B 19037393 19043729 6336 False 2906.666667 7241 93.129667 1 6378 3 chr1B.!!$F3 6377
6 TraesCS1D01G033300 chr1B 19231281 19232436 1155 True 1157.000000 1157 84.864000 1091 2255 1 chr1B.!!$R1 1164
7 TraesCS1D01G033300 chr1B 19219069 19219986 917 True 442.000000 782 86.060500 3517 4465 2 chr1B.!!$R3 948
8 TraesCS1D01G033300 chr1B 19057489 19058000 511 False 317.700000 566 89.703000 5988 6447 2 chr1B.!!$F4 459
9 TraesCS1D01G033300 chr1A 14589079 14594046 4967 True 2518.333333 7167 92.903667 972 6454 3 chr1A.!!$R5 5482
10 TraesCS1D01G033300 chr1A 14614407 14615550 1143 True 1264.000000 1264 86.655000 1094 2242 1 chr1A.!!$R2 1148
11 TraesCS1D01G033300 chr1A 14604499 14605475 976 True 754.000000 754 80.788000 3472 4481 1 chr1A.!!$R1 1009

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
595 610 0.107654 AGATGTTGCGGTTCTAGGGC 60.108 55.000 0.00 0.0 0.00 5.19 F
809 825 0.248289 AACCGGTGATAAGTGGGACG 59.752 55.000 8.52 0.0 0.00 4.79 F
813 829 0.462047 GGTGATAAGTGGGACGCAGG 60.462 60.000 0.00 0.0 44.14 4.85 F
1520 2189 0.991355 TTGGACCAGGACAACAGGGT 60.991 55.000 0.00 0.0 36.05 4.34 F
1656 2325 1.073025 CTACCCACAGGCAACAGCA 59.927 57.895 0.00 0.0 41.41 4.41 F
1761 2433 1.203025 AGGCTATGGTACCCTAGGTCG 60.203 57.143 21.57 0.0 37.09 4.79 F
3545 5235 1.679139 TTGTCTGGCAACCAACTCAG 58.321 50.000 0.00 0.0 30.80 3.35 F
5012 6774 1.598130 GCAGCCAACGACCAAGAGT 60.598 57.895 0.00 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 2355 0.314021 CGTTTATCGCGGCGAAGTTC 60.314 55.000 29.93 17.80 39.99 3.01 R
2165 2846 1.077089 GGAGAACAACTCGTAGGCGC 61.077 60.000 0.00 0.00 45.76 6.53 R
2601 4100 5.478332 GTCTGACTTTTCTTGAATTCCCCAT 59.522 40.000 2.27 0.00 0.00 4.00 R
2926 4469 1.198713 TTGGTCTCAGGATCTCAGCC 58.801 55.000 0.00 0.00 0.00 4.85 R
3555 5245 3.318313 TCTTTTGAGAAGTCCAGAGGGT 58.682 45.455 0.00 0.00 34.93 4.34 R
3897 5603 2.232756 TTGTTGTGTGCTAGCTCGAA 57.767 45.000 17.23 6.62 0.00 3.71 R
5021 6783 1.679311 CAGCACCACTCCCAAGCTA 59.321 57.895 0.00 0.00 33.59 3.32 R
5990 7753 1.005394 GGCTGGACGAACGAAGGAA 60.005 57.895 0.14 0.00 0.00 3.36 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
66 70 6.216801 AGCATCAGACAATATTGCAACAAT 57.783 33.333 15.48 0.00 35.79 2.71
110 114 9.432982 TTTTATATAATGGGGATTGCTTCACTT 57.567 29.630 0.00 0.00 0.00 3.16
116 120 5.296151 TGGGGATTGCTTCACTTATAGAG 57.704 43.478 0.00 0.00 0.00 2.43
182 187 1.899814 TGGAGTTGACTAGTGGCGAAT 59.100 47.619 0.00 0.00 0.00 3.34
198 203 4.093703 TGGCGAATGTGTAAAATTCCGTAG 59.906 41.667 0.00 0.00 37.25 3.51
213 218 1.567504 CGTAGGCCTTATGTTGGACG 58.432 55.000 12.58 8.57 37.76 4.79
283 295 4.844267 ACATTAATGTTATTCTTCCGCGC 58.156 39.130 15.47 0.00 37.90 6.86
305 317 4.345257 GCTCATTAGATGGAACCAGACCTA 59.655 45.833 0.00 0.00 0.00 3.08
383 398 0.391661 CGTGCAGCCATTCTAGTGGT 60.392 55.000 1.66 0.00 41.47 4.16
393 408 1.263356 TTCTAGTGGTGTCCTTCGGG 58.737 55.000 0.00 0.00 0.00 5.14
467 482 1.802553 TAGGGGTGGCTATCCTCAAC 58.197 55.000 0.00 0.00 32.46 3.18
468 483 0.988678 AGGGGTGGCTATCCTCAACC 60.989 60.000 0.00 0.00 39.91 3.77
470 485 0.846693 GGGTGGCTATCCTCAACCAT 59.153 55.000 0.00 0.00 40.33 3.55
497 512 1.879796 CGCCATCATCTTTAGGGGCTC 60.880 57.143 0.00 0.00 39.23 4.70
510 525 1.718757 GGGGCTCATGAACATCGCAC 61.719 60.000 6.27 2.21 0.00 5.34
553 568 1.452651 CAGCGGCATTGGAGGTCAT 60.453 57.895 1.45 0.00 0.00 3.06
569 584 5.304686 AGGTCATAGTGAAGAAACACCAA 57.695 39.130 0.00 0.00 41.12 3.67
575 590 8.237267 GTCATAGTGAAGAAACACCAAAATAGG 58.763 37.037 0.00 0.00 41.12 2.57
584 599 5.391312 AACACCAAAATAGGAGATGTTGC 57.609 39.130 0.00 0.00 0.00 4.17
595 610 0.107654 AGATGTTGCGGTTCTAGGGC 60.108 55.000 0.00 0.00 0.00 5.19
617 632 2.378634 AAAGGGGATGGGAGGAGCG 61.379 63.158 0.00 0.00 0.00 5.03
644 659 0.905337 AAGAGAAGGGTGGGAGGACG 60.905 60.000 0.00 0.00 0.00 4.79
645 660 1.305046 GAGAAGGGTGGGAGGACGA 60.305 63.158 0.00 0.00 0.00 4.20
724 739 3.142174 TGCGTTTACAACCACATGATCA 58.858 40.909 0.00 0.00 0.00 2.92
725 740 3.565902 TGCGTTTACAACCACATGATCAA 59.434 39.130 0.00 0.00 0.00 2.57
742 757 9.941325 ACATGATCAAAGATAATAGGAGCTAAG 57.059 33.333 0.00 0.00 0.00 2.18
751 766 3.778954 ATAGGAGCTAAGGCCATGAAC 57.221 47.619 5.01 0.00 39.73 3.18
758 773 2.616510 GCTAAGGCCATGAACAGTGTCT 60.617 50.000 5.01 0.00 0.00 3.41
793 809 1.233919 TACAACCGCCCGTTTTAACC 58.766 50.000 0.00 0.00 29.93 2.85
806 822 3.125658 CGTTTTAACCGGTGATAAGTGGG 59.874 47.826 8.52 0.00 0.00 4.61
807 823 4.325972 GTTTTAACCGGTGATAAGTGGGA 58.674 43.478 8.52 0.00 0.00 4.37
808 824 3.615224 TTAACCGGTGATAAGTGGGAC 57.385 47.619 8.52 0.00 0.00 4.46
809 825 0.248289 AACCGGTGATAAGTGGGACG 59.752 55.000 8.52 0.00 0.00 4.79
810 826 1.520787 CCGGTGATAAGTGGGACGC 60.521 63.158 0.00 0.00 40.45 5.19
811 827 1.216977 CGGTGATAAGTGGGACGCA 59.783 57.895 0.00 0.00 44.14 5.24
812 828 0.806102 CGGTGATAAGTGGGACGCAG 60.806 60.000 0.00 0.00 44.14 5.18
813 829 0.462047 GGTGATAAGTGGGACGCAGG 60.462 60.000 0.00 0.00 44.14 4.85
814 830 1.090052 GTGATAAGTGGGACGCAGGC 61.090 60.000 0.00 0.00 44.14 4.85
815 831 1.523938 GATAAGTGGGACGCAGGCC 60.524 63.158 0.00 0.00 44.14 5.19
816 832 2.942648 GATAAGTGGGACGCAGGCCC 62.943 65.000 12.08 12.08 46.22 5.80
822 1390 4.408821 GGACGCAGGCCCACATGA 62.409 66.667 0.00 0.00 0.00 3.07
824 1392 3.315142 GACGCAGGCCCACATGAGA 62.315 63.158 0.00 0.00 0.00 3.27
825 1393 2.046023 CGCAGGCCCACATGAGAA 60.046 61.111 0.00 0.00 0.00 2.87
830 1398 2.022195 CAGGCCCACATGAGAATTCAG 58.978 52.381 8.44 0.00 36.61 3.02
835 1403 2.422519 CCCACATGAGAATTCAGAGGGG 60.423 54.545 8.44 6.85 38.21 4.79
839 1407 3.784763 ACATGAGAATTCAGAGGGGTGAT 59.215 43.478 8.44 0.00 36.61 3.06
841 1409 4.934797 TGAGAATTCAGAGGGGTGATTT 57.065 40.909 8.44 0.00 0.00 2.17
845 1413 7.413446 TGAGAATTCAGAGGGGTGATTTTATT 58.587 34.615 8.44 0.00 0.00 1.40
846 1414 8.556589 TGAGAATTCAGAGGGGTGATTTTATTA 58.443 33.333 8.44 0.00 0.00 0.98
848 1416 8.560903 AGAATTCAGAGGGGTGATTTTATTAGT 58.439 33.333 8.44 0.00 0.00 2.24
852 1420 8.618240 TCAGAGGGGTGATTTTATTAGTTAGA 57.382 34.615 0.00 0.00 0.00 2.10
853 1421 9.053472 TCAGAGGGGTGATTTTATTAGTTAGAA 57.947 33.333 0.00 0.00 0.00 2.10
854 1422 9.681062 CAGAGGGGTGATTTTATTAGTTAGAAA 57.319 33.333 0.00 0.00 0.00 2.52
855 1423 9.907229 AGAGGGGTGATTTTATTAGTTAGAAAG 57.093 33.333 0.00 0.00 0.00 2.62
856 1424 9.121658 GAGGGGTGATTTTATTAGTTAGAAAGG 57.878 37.037 0.00 0.00 0.00 3.11
857 1425 8.842764 AGGGGTGATTTTATTAGTTAGAAAGGA 58.157 33.333 0.00 0.00 0.00 3.36
858 1426 9.470399 GGGGTGATTTTATTAGTTAGAAAGGAA 57.530 33.333 0.00 0.00 0.00 3.36
887 1461 6.436944 CGTACAGAACGTAAACACATTACA 57.563 37.500 0.00 0.00 46.72 2.41
896 1470 7.816945 ACGTAAACACATTACATAGGTGTAC 57.183 36.000 0.00 0.00 44.40 2.90
931 1509 4.717280 AGTAGGCATGTAGTTTCCTTAGCT 59.283 41.667 0.00 0.00 0.00 3.32
1113 1781 5.590530 TCTGTTATTGGCTTCTCTCTCTC 57.409 43.478 0.00 0.00 0.00 3.20
1130 1798 2.809119 CTCTCAATCATGCTGCCTCATC 59.191 50.000 0.00 0.00 0.00 2.92
1131 1799 2.171870 TCTCAATCATGCTGCCTCATCA 59.828 45.455 0.00 0.00 0.00 3.07
1198 1867 1.003646 ACAGGGAGAGGAGAGCTACA 58.996 55.000 0.00 0.00 0.00 2.74
1329 1998 2.930562 AGCCTGCGGAGTTTCCCT 60.931 61.111 2.36 0.00 31.13 4.20
1488 2157 1.671054 CTGGACGGCGGTGAACATT 60.671 57.895 13.24 0.00 0.00 2.71
1520 2189 0.991355 TTGGACCAGGACAACAGGGT 60.991 55.000 0.00 0.00 36.05 4.34
1653 2322 1.374947 GCTCTACCCACAGGCAACA 59.625 57.895 0.00 0.00 41.41 3.33
1656 2325 1.073025 CTACCCACAGGCAACAGCA 59.927 57.895 0.00 0.00 41.41 4.41
1737 2409 2.573462 CAGGTTCCCCGATGATCCATAT 59.427 50.000 0.00 0.00 35.12 1.78
1761 2433 1.203025 AGGCTATGGTACCCTAGGTCG 60.203 57.143 21.57 0.00 37.09 4.79
1818 2490 2.202570 GTGGACGACGTCGATGGG 60.203 66.667 41.52 15.30 43.02 4.00
2101 2782 5.644636 GTCTACAATAAATTCACCAACCCGA 59.355 40.000 0.00 0.00 0.00 5.14
2165 2846 3.285215 GCTGCCGCCCATCATCAG 61.285 66.667 0.00 0.00 0.00 2.90
2601 4100 5.912149 AATCAAGATGGCATTCCCTAGTA 57.088 39.130 0.00 0.00 0.00 1.82
2625 4124 4.827284 TGGGGAATTCAAGAAAAGTCAGAC 59.173 41.667 7.93 0.00 0.00 3.51
2789 4293 8.730680 TCCTCAATTCTCACATTTTTAGTAAGC 58.269 33.333 0.00 0.00 0.00 3.09
2910 4427 8.469200 TCTCATTATTTTGTGATGGGATGTTTC 58.531 33.333 0.00 0.00 29.04 2.78
2926 4469 6.813152 GGGATGTTTCAGGTCATAACATTTTG 59.187 38.462 0.00 0.00 41.24 2.44
3087 4676 4.953579 TGCTTTTTGTAGAAACCTGTCCTT 59.046 37.500 0.00 0.00 0.00 3.36
3156 4748 4.381718 GGCTCTCCAATACTTGTACGTTCT 60.382 45.833 0.00 0.00 0.00 3.01
3329 4991 4.431416 TTGACAGTCATGTAAGTTGGGT 57.569 40.909 3.45 0.00 40.68 4.51
3375 5057 7.107639 AGCAACCACACTTATTTACAAACTT 57.892 32.000 0.00 0.00 0.00 2.66
3378 5060 6.399639 ACCACACTTATTTACAAACTTGGG 57.600 37.500 0.00 0.00 0.00 4.12
3489 5179 8.114290 CGAATTGCTTTGAGTTATTATGTACGT 58.886 33.333 0.00 0.00 0.00 3.57
3490 5180 9.210426 GAATTGCTTTGAGTTATTATGTACGTG 57.790 33.333 0.00 0.00 0.00 4.49
3545 5235 1.679139 TTGTCTGGCAACCAACTCAG 58.321 50.000 0.00 0.00 30.80 3.35
4484 6245 5.930569 ACTAACTACGGCTAACAAAAAGGAG 59.069 40.000 0.00 0.00 0.00 3.69
4684 6445 4.847198 TCAAATCCAGAGCAGCTTATTGA 58.153 39.130 0.00 0.00 0.00 2.57
5012 6774 1.598130 GCAGCCAACGACCAAGAGT 60.598 57.895 0.00 0.00 0.00 3.24
5021 6783 1.884579 ACGACCAAGAGTGACGTGTAT 59.115 47.619 0.00 0.00 36.66 2.29
5027 6789 3.859961 CCAAGAGTGACGTGTATAGCTTG 59.140 47.826 0.00 0.00 33.26 4.01
5180 6942 5.323382 TGCAGGGTGGTTATGATATCAAT 57.677 39.130 9.99 1.44 0.00 2.57
5330 7092 4.935495 CACACCGGTGGCAGCAGT 62.935 66.667 36.47 12.80 41.45 4.40
5355 7117 6.484977 TGGCGATGATAATTACAATGCTTACA 59.515 34.615 0.00 0.00 0.00 2.41
5454 7216 3.712881 GCCCGACAGCACGTTGAC 61.713 66.667 0.00 0.00 0.00 3.18
5533 7296 7.837863 TGTAGTTATTTCTCTCTCGTTTCCAT 58.162 34.615 0.00 0.00 0.00 3.41
5715 7478 4.223953 AGAAAGAAGGGCCGATAGATGTA 58.776 43.478 0.00 0.00 39.76 2.29
5716 7479 4.654262 AGAAAGAAGGGCCGATAGATGTAA 59.346 41.667 0.00 0.00 39.76 2.41
5772 7535 2.710220 TGCATGTTAGCTGCAACAAG 57.290 45.000 17.15 14.72 46.06 3.16
5813 7576 2.894387 GCCAGAGCAGCCTAAGCG 60.894 66.667 0.00 0.00 46.67 4.68
5829 7592 8.056638 AGCCTAAGCGTCTGTAGTACAACTAC 62.057 46.154 4.21 9.74 46.53 2.73
6035 7798 9.586435 AAAAGAAAACTAACTTGATTGGAACTG 57.414 29.630 0.00 0.00 0.00 3.16
6104 7867 2.735762 GCTCGTCCTTGGTGAGTGTATC 60.736 54.545 11.20 0.00 32.32 2.24
6112 7875 1.964933 TGGTGAGTGTATCGTGGTTGA 59.035 47.619 0.00 0.00 0.00 3.18
6137 7901 5.244402 TGGTTCATCACATTGCAAGAATCTT 59.756 36.000 4.94 0.00 0.00 2.40
6153 7917 7.167136 GCAAGAATCTTCAGTCAAACTTTCTTG 59.833 37.037 18.25 18.25 45.72 3.02
6235 8003 1.310933 CCATGAGCAGAACCTGGCAC 61.311 60.000 0.00 0.00 31.21 5.01
6271 8039 1.001974 CATCACCGTCACTTCTCCCAA 59.998 52.381 0.00 0.00 0.00 4.12
6280 8048 0.694771 ACTTCTCCCAAGATGCAGCA 59.305 50.000 4.07 0.00 31.45 4.41
6298 8066 4.736759 GCAGCATCCAATGGATCTGAAAAG 60.737 45.833 29.11 14.34 40.98 2.27
6306 8075 8.648698 TCCAATGGATCTGAAAAGAAATTGTA 57.351 30.769 0.00 0.00 0.00 2.41
6381 8198 4.730657 CTGCTTCCAACTCAGCAATTAAG 58.269 43.478 0.00 0.00 45.36 1.85
6385 8202 4.640771 TCCAACTCAGCAATTAAGTCCT 57.359 40.909 0.00 0.00 0.00 3.85
6397 8214 3.857157 TTAAGTCCTGGCAAGAACACT 57.143 42.857 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 76 8.217799 CCCCATTATATAAAAGTCAGGAGAACA 58.782 37.037 0.00 0.00 0.00 3.18
76 80 9.236006 CAATCCCCATTATATAAAAGTCAGGAG 57.764 37.037 0.00 0.00 0.00 3.69
182 187 3.706600 AGGCCTACGGAATTTTACACA 57.293 42.857 1.29 0.00 0.00 3.72
198 203 2.870411 GACATACGTCCAACATAAGGCC 59.130 50.000 0.00 0.00 36.02 5.19
199 204 3.308866 GTGACATACGTCCAACATAAGGC 59.691 47.826 0.00 0.00 41.85 4.35
283 295 6.485830 TTAGGTCTGGTTCCATCTAATGAG 57.514 41.667 0.00 0.00 0.00 2.90
331 346 4.041938 AGGCAAAACCATTCAATCCACAAT 59.958 37.500 0.00 0.00 43.14 2.71
334 349 3.683365 AGGCAAAACCATTCAATCCAC 57.317 42.857 0.00 0.00 43.14 4.02
393 408 1.344763 CTCCTAATGACGACCATCCCC 59.655 57.143 0.00 0.00 33.53 4.81
402 417 0.179111 TGGCGCTTCTCCTAATGACG 60.179 55.000 7.64 0.00 0.00 4.35
407 422 1.897133 TGTAGTTGGCGCTTCTCCTAA 59.103 47.619 7.64 0.00 0.00 2.69
467 482 0.877071 GATGATGGCGGCAACTATGG 59.123 55.000 18.31 0.00 0.00 2.74
468 483 1.888215 AGATGATGGCGGCAACTATG 58.112 50.000 18.31 0.00 0.00 2.23
470 485 2.418368 AAAGATGATGGCGGCAACTA 57.582 45.000 18.31 5.61 0.00 2.24
497 512 1.062002 GTTACCCGTGCGATGTTCATG 59.938 52.381 0.00 0.00 0.00 3.07
510 525 3.242739 GCAAATGAGCACATAGTTACCCG 60.243 47.826 0.00 0.00 35.50 5.28
553 568 7.741785 TCTCCTATTTTGGTGTTTCTTCACTA 58.258 34.615 0.00 0.00 38.28 2.74
569 584 4.222124 AGAACCGCAACATCTCCTATTT 57.778 40.909 0.00 0.00 0.00 1.40
575 590 1.941325 CCCTAGAACCGCAACATCTC 58.059 55.000 0.00 0.00 0.00 2.75
584 599 1.165270 CCTTTGTTGCCCTAGAACCG 58.835 55.000 0.00 0.00 0.00 4.44
595 610 0.704076 TCCTCCCATCCCCTTTGTTG 59.296 55.000 0.00 0.00 0.00 3.33
617 632 2.092699 CCCACCCTTCTCTTCTCCATTC 60.093 54.545 0.00 0.00 0.00 2.67
644 659 5.693814 CACATCTTTGCCTACTTCTTTGTC 58.306 41.667 0.00 0.00 0.00 3.18
645 660 4.022849 GCACATCTTTGCCTACTTCTTTGT 60.023 41.667 0.00 0.00 36.42 2.83
724 739 6.273260 TCATGGCCTTAGCTCCTATTATCTTT 59.727 38.462 3.32 0.00 39.73 2.52
725 740 5.787494 TCATGGCCTTAGCTCCTATTATCTT 59.213 40.000 3.32 0.00 39.73 2.40
742 757 2.622436 GTAGAGACACTGTTCATGGCC 58.378 52.381 0.00 0.00 0.00 5.36
774 789 1.233919 GGTTAAAACGGGCGGTTGTA 58.766 50.000 11.40 7.46 39.30 2.41
793 809 0.806102 CTGCGTCCCACTTATCACCG 60.806 60.000 0.00 0.00 0.00 4.94
806 822 2.803155 TTCTCATGTGGGCCTGCGTC 62.803 60.000 4.53 0.00 0.00 5.19
807 823 2.202236 ATTCTCATGTGGGCCTGCGT 62.202 55.000 4.53 0.00 0.00 5.24
808 824 1.033746 AATTCTCATGTGGGCCTGCG 61.034 55.000 4.53 0.00 0.00 5.18
809 825 0.743097 GAATTCTCATGTGGGCCTGC 59.257 55.000 4.53 0.00 0.00 4.85
810 826 2.022195 CTGAATTCTCATGTGGGCCTG 58.978 52.381 4.53 0.00 0.00 4.85
811 827 1.918262 TCTGAATTCTCATGTGGGCCT 59.082 47.619 4.53 0.00 0.00 5.19
812 828 2.295885 CTCTGAATTCTCATGTGGGCC 58.704 52.381 7.05 0.00 0.00 5.80
813 829 2.295885 CCTCTGAATTCTCATGTGGGC 58.704 52.381 7.05 0.00 0.00 5.36
814 830 2.422519 CCCCTCTGAATTCTCATGTGGG 60.423 54.545 7.05 12.39 35.47 4.61
815 831 2.240667 ACCCCTCTGAATTCTCATGTGG 59.759 50.000 7.05 3.35 0.00 4.17
816 832 3.054875 TCACCCCTCTGAATTCTCATGTG 60.055 47.826 7.05 6.97 0.00 3.21
817 833 3.184628 TCACCCCTCTGAATTCTCATGT 58.815 45.455 7.05 0.00 0.00 3.21
818 834 3.920231 TCACCCCTCTGAATTCTCATG 57.080 47.619 7.05 0.00 0.00 3.07
819 835 5.463051 AAATCACCCCTCTGAATTCTCAT 57.537 39.130 7.05 0.00 0.00 2.90
822 1390 8.560903 ACTAATAAAATCACCCCTCTGAATTCT 58.439 33.333 7.05 0.00 0.00 2.40
825 1393 9.853177 CTAACTAATAAAATCACCCCTCTGAAT 57.147 33.333 0.00 0.00 0.00 2.57
830 1398 9.121658 CCTTTCTAACTAATAAAATCACCCCTC 57.878 37.037 0.00 0.00 0.00 4.30
845 1413 9.066892 TCTGTACGTAAACTTCCTTTCTAACTA 57.933 33.333 0.00 0.00 0.00 2.24
846 1414 7.945134 TCTGTACGTAAACTTCCTTTCTAACT 58.055 34.615 0.00 0.00 0.00 2.24
848 1416 7.379529 CGTTCTGTACGTAAACTTCCTTTCTAA 59.620 37.037 0.00 0.00 45.14 2.10
850 1418 5.689068 CGTTCTGTACGTAAACTTCCTTTCT 59.311 40.000 0.00 0.00 45.14 2.52
852 1420 5.895216 CGTTCTGTACGTAAACTTCCTTT 57.105 39.130 0.00 0.00 45.14 3.11
866 1434 8.306038 ACCTATGTAATGTGTTTACGTTCTGTA 58.694 33.333 0.00 0.00 42.68 2.74
867 1435 7.117236 CACCTATGTAATGTGTTTACGTTCTGT 59.883 37.037 0.00 0.00 42.68 3.41
868 1436 7.117236 ACACCTATGTAATGTGTTTACGTTCTG 59.883 37.037 0.00 0.00 42.68 3.02
896 1470 5.329035 ACATGCCTACTAAGCAAAAATGG 57.671 39.130 0.00 0.00 44.83 3.16
944 1522 4.027050 GCTAACGAAGAAGCGTAATGGTAC 60.027 45.833 0.00 0.00 44.86 3.34
960 1538 0.954938 TGCATGCAAGCTGCTAACGA 60.955 50.000 20.30 0.00 45.31 3.85
1045 1625 1.227263 GTGCGCGACCATGGAGTAT 60.227 57.895 21.47 0.00 0.00 2.12
1113 1781 2.425668 TGTTGATGAGGCAGCATGATTG 59.574 45.455 0.00 0.00 39.69 2.67
1198 1867 0.522180 AGCTTTGTCTCGTCGTCGAT 59.478 50.000 5.00 0.00 45.21 3.59
1329 1998 2.965147 GCAGTTGCGAACGCCATCA 61.965 57.895 16.27 0.00 41.09 3.07
1488 2157 1.152922 GTCCAACCCCCACAACGAA 60.153 57.895 0.00 0.00 0.00 3.85
1520 2189 3.822192 CGATCGCCTCCACCGTCA 61.822 66.667 0.26 0.00 0.00 4.35
1686 2355 0.314021 CGTTTATCGCGGCGAAGTTC 60.314 55.000 29.93 17.80 39.99 3.01
1818 2490 3.119096 GGCGCCTCAAACTCGTCC 61.119 66.667 22.15 0.00 0.00 4.79
2101 2782 1.153489 CGATGTAGCTGCTGTGGCT 60.153 57.895 13.43 0.00 43.02 4.75
2165 2846 1.077089 GGAGAACAACTCGTAGGCGC 61.077 60.000 0.00 0.00 45.76 6.53
2500 3192 6.699575 AATAACTTACATGCTTGTGATCCC 57.300 37.500 15.08 0.00 36.53 3.85
2601 4100 5.478332 GTCTGACTTTTCTTGAATTCCCCAT 59.522 40.000 2.27 0.00 0.00 4.00
2910 4427 4.701651 TCTCAGCCAAAATGTTATGACCTG 59.298 41.667 0.00 0.00 0.00 4.00
2926 4469 1.198713 TTGGTCTCAGGATCTCAGCC 58.801 55.000 0.00 0.00 0.00 4.85
2980 4523 4.529769 TCTCTGACCACACTCATCTTTGAT 59.470 41.667 0.00 0.00 0.00 2.57
3016 4560 6.952773 TTTCCATGGTTGTATACATAAGGC 57.047 37.500 12.58 0.00 0.00 4.35
3156 4748 4.934356 AGGCCAAATAAATCCAGAACTCA 58.066 39.130 5.01 0.00 0.00 3.41
3329 4991 9.908747 TTGCTAATTAGTTAGGGCTAATTGTTA 57.091 29.630 13.91 4.79 45.69 2.41
3375 5057 5.415389 GCATATGTGTCATATATTGTGCCCA 59.585 40.000 4.29 0.00 0.00 5.36
3459 5141 4.965119 ATAACTCAAAGCAATTCGGTCC 57.035 40.909 0.00 0.00 0.00 4.46
3555 5245 3.318313 TCTTTTGAGAAGTCCAGAGGGT 58.682 45.455 0.00 0.00 34.93 4.34
3897 5603 2.232756 TTGTTGTGTGCTAGCTCGAA 57.767 45.000 17.23 6.62 0.00 3.71
4327 6088 4.887071 TGATGAATCCGGGTTAAAATCTGG 59.113 41.667 0.00 0.00 36.87 3.86
4555 6316 9.474920 CAAATACAATAACAACATGTTTGTCCT 57.525 29.630 14.47 3.68 41.45 3.85
4660 6421 2.875094 AAGCTGCTCTGGATTTGAGT 57.125 45.000 1.00 0.00 34.30 3.41
4684 6445 5.316158 AGGCCATAACTATTGAAGAGCAT 57.684 39.130 5.01 0.00 0.00 3.79
5012 6774 2.165641 CACTCCCAAGCTATACACGTCA 59.834 50.000 0.00 0.00 0.00 4.35
5021 6783 1.679311 CAGCACCACTCCCAAGCTA 59.321 57.895 0.00 0.00 33.59 3.32
5027 6789 3.618780 CTCCAGCAGCACCACTCCC 62.619 68.421 0.00 0.00 0.00 4.30
5141 6903 4.673298 ATTCGCGCGTCCACCACA 62.673 61.111 30.98 4.20 0.00 4.17
5180 6942 4.947147 GCCACCTTCCACACGCCA 62.947 66.667 0.00 0.00 0.00 5.69
5330 7092 6.484977 TGTAAGCATTGTAATTATCATCGCCA 59.515 34.615 0.00 0.00 0.00 5.69
5336 7098 8.826710 GCACTAGTGTAAGCATTGTAATTATCA 58.173 33.333 23.44 0.00 0.00 2.15
5355 7117 2.657237 GGTGGACTGCGCACTAGT 59.343 61.111 5.66 2.22 0.00 2.57
5636 7399 9.265901 CGATTCATCATAAATTACACTCCTTCT 57.734 33.333 0.00 0.00 0.00 2.85
5690 7453 5.308237 ACATCTATCGGCCCTTCTTTCTATT 59.692 40.000 0.00 0.00 0.00 1.73
5715 7478 0.528470 GAGGTACGCTGCTCTGACTT 59.472 55.000 0.00 0.00 0.00 3.01
5716 7479 0.322997 AGAGGTACGCTGCTCTGACT 60.323 55.000 0.00 0.00 36.88 3.41
5772 7535 5.448225 CGAACATATATGGAAGGCATGATGC 60.448 44.000 16.96 9.33 44.08 3.91
5779 7542 2.744202 CTGGCGAACATATATGGAAGGC 59.256 50.000 16.96 17.07 0.00 4.35
5858 7621 9.059260 TCTACCTACAGCGTTTTATTTTCTTTT 57.941 29.630 0.00 0.00 0.00 2.27
5990 7753 1.005394 GGCTGGACGAACGAAGGAA 60.005 57.895 0.14 0.00 0.00 3.36
6035 7798 2.380084 TAGCATTTCCGTGGTCTGAC 57.620 50.000 0.00 0.00 0.00 3.51
6112 7875 5.421056 AGATTCTTGCAATGTGATGAACCAT 59.579 36.000 0.00 0.00 0.00 3.55
6122 7886 6.040166 AGTTTGACTGAAGATTCTTGCAATGT 59.960 34.615 3.03 0.00 0.00 2.71
6137 7901 7.921786 TCTCTTTTCAAGAAAGTTTGACTGA 57.078 32.000 0.00 0.00 36.84 3.41
6153 7917 8.433893 GTCGTTTTACCTTACTCATCTCTTTTC 58.566 37.037 0.00 0.00 0.00 2.29
6235 8003 3.123621 GGTGATGACTGTTGAAGCTAACG 59.876 47.826 0.00 0.00 33.28 3.18
6271 8039 2.108425 AGATCCATTGGATGCTGCATCT 59.892 45.455 33.94 17.94 43.27 2.90
6280 8048 8.142485 ACAATTTCTTTTCAGATCCATTGGAT 57.858 30.769 18.23 18.23 46.28 3.41
6306 8075 6.016024 TGTCTGCTTCATTTGCTTTCTAACAT 60.016 34.615 0.00 0.00 0.00 2.71
6381 8198 1.070758 TCAGAGTGTTCTTGCCAGGAC 59.929 52.381 0.00 0.00 0.00 3.85
6385 8202 1.762370 TCAGTCAGAGTGTTCTTGCCA 59.238 47.619 5.11 0.00 0.00 4.92
6397 8214 5.665916 TGTTGAGAGCATAATCAGTCAGA 57.334 39.130 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.