Multiple sequence alignment - TraesCS2D01G444300

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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 TraesCS2D01G444300 chr2D 100.000 3645 0 0 1 3645 555575425 555579069 0.000000e+00 6732.0
1 TraesCS2D01G444300 chr2D 87.228 2341 155 73 1 2241 555394087 555396383 0.000000e+00 2534.0
2 TraesCS2D01G444300 chr2D 87.121 132 17 0 1352 1483 482790040 482790171 2.270000e-32 150.0
3 TraesCS2D01G444300 chr2D 87.121 132 17 0 1352 1483 636638927 636639058 2.270000e-32 150.0
4 TraesCS2D01G444300 chr2B 90.463 3607 197 65 1 3521 662372022 662375567 0.000000e+00 4619.0
5 TraesCS2D01G444300 chr2B 85.429 2251 165 77 153 2323 661850330 661852497 0.000000e+00 2189.0
6 TraesCS2D01G444300 chr2A 84.964 3465 234 130 36 3363 695149090 695152404 0.000000e+00 3247.0
7 TraesCS2D01G444300 chr6D 91.429 140 8 3 1112 1248 352835515 352835653 4.800000e-44 189.0
8 TraesCS2D01G444300 chr6D 88.462 130 15 0 1358 1487 352835668 352835797 1.350000e-34 158.0
9 TraesCS2D01G444300 chr6D 95.349 86 4 0 1584 1669 352835885 352835970 1.770000e-28 137.0
10 TraesCS2D01G444300 chr6D 92.941 85 4 1 3561 3645 389352727 389352809 4.940000e-24 122.0
11 TraesCS2D01G444300 chr6A 93.023 129 8 1 1120 1248 490301789 490301916 1.730000e-43 187.0
12 TraesCS2D01G444300 chr6A 90.000 130 13 0 1358 1487 490301931 490302060 6.260000e-38 169.0
13 TraesCS2D01G444300 chr6A 96.341 82 3 0 1584 1665 490302141 490302222 6.350000e-28 135.0
14 TraesCS2D01G444300 chr6B 90.909 132 11 1 1120 1251 526101297 526101167 3.740000e-40 176.0
15 TraesCS2D01G444300 chr6B 89.231 130 14 0 1358 1487 526101155 526101026 2.910000e-36 163.0
16 TraesCS2D01G444300 chr6B 95.238 84 4 0 1582 1665 526100917 526100834 2.280000e-27 134.0
17 TraesCS2D01G444300 chr7D 93.023 86 5 1 3560 3645 528085017 528085101 1.370000e-24 124.0
18 TraesCS2D01G444300 chr4D 92.135 89 6 1 3558 3645 319092049 319092137 1.370000e-24 124.0
19 TraesCS2D01G444300 chr3D 93.023 86 5 1 3560 3645 426475487 426475571 1.370000e-24 124.0
20 TraesCS2D01G444300 chr7B 91.954 87 6 1 3559 3645 115234267 115234182 1.780000e-23 121.0
21 TraesCS2D01G444300 chr3B 90.698 86 6 1 3560 3645 308212183 308212266 2.970000e-21 113.0
22 TraesCS2D01G444300 chr3B 84.091 88 12 2 3559 3645 478159557 478159643 2.330000e-12 84.2
23 TraesCS2D01G444300 chr5B 85.057 87 13 0 3559 3645 586456632 586456546 5.010000e-14 89.8
24 TraesCS2D01G444300 chr5A 85.185 81 10 2 3560 3639 536815771 536815850 8.390000e-12 82.4


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 TraesCS2D01G444300 chr2D 555575425 555579069 3644 False 6732 6732 100.000 1 3645 1 chr2D.!!$F3 3644
1 TraesCS2D01G444300 chr2D 555394087 555396383 2296 False 2534 2534 87.228 1 2241 1 chr2D.!!$F2 2240
2 TraesCS2D01G444300 chr2B 662372022 662375567 3545 False 4619 4619 90.463 1 3521 1 chr2B.!!$F2 3520
3 TraesCS2D01G444300 chr2B 661850330 661852497 2167 False 2189 2189 85.429 153 2323 1 chr2B.!!$F1 2170
4 TraesCS2D01G444300 chr2A 695149090 695152404 3314 False 3247 3247 84.964 36 3363 1 chr2A.!!$F1 3327

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
147 165 0.032615 TGCAGTTCCCCTGGTTTTGT 60.033 50.0 0.0 0.0 41.81 2.83 F
1937 2158 0.036294 TGGACACCGTCACAAACACA 60.036 50.0 0.0 0.0 33.68 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 2275 1.228063 GCCGTCCATGATGCTCCAT 60.228 57.895 0.0 0.0 0.00 3.41 R
3245 3510 0.038251 TCGACAACGAAGCAGCTCAT 60.038 50.000 0.0 0.0 45.74 2.90 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
51 58 5.469421 CCCATTGAATTAAAAACAAGCAGCA 59.531 36.000 0.00 0.00 0.00 4.41
120 138 0.396435 TTGTGAGGTTGCGATCCAGT 59.604 50.000 0.00 0.00 0.00 4.00
142 160 2.121963 TCCTGCAGTTCCCCTGGT 60.122 61.111 13.81 0.00 41.81 4.00
143 161 1.774217 TCCTGCAGTTCCCCTGGTT 60.774 57.895 13.81 0.00 41.81 3.67
147 165 0.032615 TGCAGTTCCCCTGGTTTTGT 60.033 50.000 0.00 0.00 41.81 2.83
149 167 2.026905 GCAGTTCCCCTGGTTTTGTGA 61.027 52.381 0.00 0.00 41.81 3.58
150 168 2.597455 CAGTTCCCCTGGTTTTGTGAT 58.403 47.619 0.00 0.00 37.54 3.06
151 169 3.761897 CAGTTCCCCTGGTTTTGTGATA 58.238 45.455 0.00 0.00 37.54 2.15
154 186 4.832823 AGTTCCCCTGGTTTTGTGATAAAG 59.167 41.667 0.00 0.00 0.00 1.85
205 238 8.391106 CAAGTCTATCAAATAGTAGGTGCAAAC 58.609 37.037 0.00 0.00 34.47 2.93
206 239 7.852263 AGTCTATCAAATAGTAGGTGCAAACT 58.148 34.615 0.00 0.00 34.47 2.66
207 240 8.978472 AGTCTATCAAATAGTAGGTGCAAACTA 58.022 33.333 7.15 7.15 34.47 2.24
208 241 9.250624 GTCTATCAAATAGTAGGTGCAAACTAG 57.749 37.037 9.79 0.00 32.01 2.57
232 265 6.820656 AGTAAAGCTCTGTTGATTCACCTATG 59.179 38.462 0.00 0.00 0.00 2.23
293 331 4.798387 GCGATAAATTTGGTTCGAAGCAAT 59.202 37.500 35.26 25.45 44.73 3.56
294 333 5.288472 GCGATAAATTTGGTTCGAAGCAATT 59.712 36.000 35.26 29.45 44.73 2.32
458 505 2.024655 AGATCATGAACCATGGGCTGTT 60.025 45.455 18.09 0.00 41.66 3.16
533 582 3.818787 CGTCCGGTCGTGGGGTAG 61.819 72.222 13.16 0.00 0.00 3.18
611 668 2.285368 CCCCACCTCCACCTAGCA 60.285 66.667 0.00 0.00 0.00 3.49
768 853 1.113517 ACTCCGGTGTGCAGTGTAGT 61.114 55.000 8.68 0.00 0.00 2.73
770 855 1.069090 CCGGTGTGCAGTGTAGTGT 59.931 57.895 0.00 0.00 0.00 3.55
773 858 1.000607 CGGTGTGCAGTGTAGTGTAGT 60.001 52.381 0.00 0.00 0.00 2.73
774 859 2.404215 GGTGTGCAGTGTAGTGTAGTG 58.596 52.381 0.00 0.00 0.00 2.74
779 864 2.095415 TGCAGTGTAGTGTAGTGTAGCG 60.095 50.000 0.00 0.00 0.00 4.26
790 875 2.349297 AGTGTAGCGAAGTGTAGTGC 57.651 50.000 0.00 0.00 0.00 4.40
986 1099 1.335132 ATATATACCGGCGGCCCTGG 61.335 60.000 28.71 12.54 0.00 4.45
1099 1255 1.618876 TTTGAAGCGGCCGGATAGGA 61.619 55.000 29.38 0.00 45.00 2.94
1114 1277 2.541709 TAGGAGGGAGGGAGGGAGGT 62.542 65.000 0.00 0.00 0.00 3.85
1214 1377 1.221414 GCCTCATCGCCTACATTCAC 58.779 55.000 0.00 0.00 0.00 3.18
1286 1449 4.664677 CACCCCGGCGATCGATCC 62.665 72.222 21.57 10.69 42.43 3.36
1296 1464 1.517276 GCGATCGATCCAACAGTAACG 59.483 52.381 21.57 5.69 0.00 3.18
1323 1503 8.557864 CATGTTCATGCCAATTTTGTTTAAGAA 58.442 29.630 0.00 0.00 0.00 2.52
1329 1509 8.610896 CATGCCAATTTTGTTTAAGAAAACTCA 58.389 29.630 2.14 0.25 44.44 3.41
1347 1531 4.985413 ACTCAACTGATGTGTTGTGTTTG 58.015 39.130 8.61 0.00 46.00 2.93
1367 1555 1.227853 GACAGGTTTGCTCCGGTGT 60.228 57.895 0.00 0.00 36.15 4.16
1516 1708 2.749441 GCCTCTTGCAGCACCCTC 60.749 66.667 0.00 0.00 40.77 4.30
1580 1795 1.271379 ACGATTGCTGTCGGACTTGTA 59.729 47.619 9.88 0.00 45.49 2.41
1784 1999 0.391661 CATCCTCTTCCACCACCACG 60.392 60.000 0.00 0.00 0.00 4.94
1847 2062 0.740737 AACAGAGCAACACCAGCAAC 59.259 50.000 0.00 0.00 0.00 4.17
1931 2152 2.421314 CTGCTGGACACCGTCACA 59.579 61.111 0.00 0.00 33.68 3.58
1937 2158 0.036294 TGGACACCGTCACAAACACA 60.036 50.000 0.00 0.00 33.68 3.72
1948 2169 2.118404 CAAACACACACTGCCCGGT 61.118 57.895 0.00 0.00 0.00 5.28
2054 2275 2.805546 GACATCGTGCCGGAGCTA 59.194 61.111 5.05 0.00 40.80 3.32
2254 2487 1.808512 CGACTACCAGCACCAACAACA 60.809 52.381 0.00 0.00 0.00 3.33
2255 2488 2.294074 GACTACCAGCACCAACAACAA 58.706 47.619 0.00 0.00 0.00 2.83
2256 2489 2.021457 ACTACCAGCACCAACAACAAC 58.979 47.619 0.00 0.00 0.00 3.32
2327 2569 0.679505 TGTCGTGCTACTTCCAAGCT 59.320 50.000 0.00 0.00 40.73 3.74
2397 2639 0.898320 AGTTCTCACAGACATCCCCG 59.102 55.000 0.00 0.00 0.00 5.73
2404 2646 2.687566 AGACATCCCCGTGGGTCC 60.688 66.667 3.83 0.00 44.74 4.46
2437 2683 3.294816 GGTATAAACCGTCCGATCTCC 57.705 52.381 0.00 0.00 35.62 3.71
2455 2701 7.081349 CGATCTCCTAGTATAGAAACAAGCAG 58.919 42.308 0.00 0.00 42.77 4.24
2458 2704 4.401519 TCCTAGTATAGAAACAAGCAGCGT 59.598 41.667 0.00 0.00 42.77 5.07
2467 2713 2.125512 AAGCAGCGTGATCGGACC 60.126 61.111 0.00 0.00 37.56 4.46
2547 2795 1.198408 CAAGAGGAGTACGTACGCACA 59.802 52.381 27.07 0.96 0.00 4.57
2624 2877 3.681897 CACACACAAGAGGAGATGCTTAC 59.318 47.826 0.00 0.00 0.00 2.34
2667 2920 0.596600 ACACACTGCGACTACGTTGG 60.597 55.000 0.00 0.00 41.98 3.77
2670 2923 2.261671 CTGCGACTACGTTGGGCT 59.738 61.111 14.05 0.00 41.98 5.19
2698 2951 0.459411 AAAGTGGTGCAACGCAAACC 60.459 50.000 19.16 0.00 41.47 3.27
2789 3042 1.009675 CACACAACAGCGACCAAGC 60.010 57.895 0.00 0.00 37.41 4.01
2858 3114 5.614887 GCGCTTTATCATCGAAATTCCTACC 60.615 44.000 0.00 0.00 0.00 3.18
2865 3121 2.963432 TCGAAATTCCTACCACGGTTC 58.037 47.619 0.00 0.00 0.00 3.62
2934 3191 1.909700 TGATTTGGTGAAGCCTGTCC 58.090 50.000 0.00 0.00 38.35 4.02
2936 3193 0.482446 ATTTGGTGAAGCCTGTCCCA 59.518 50.000 0.00 0.00 38.35 4.37
2941 3198 1.457346 GTGAAGCCTGTCCCATTCTG 58.543 55.000 0.00 0.00 0.00 3.02
3011 3269 4.725169 GCTCTAGTTTACATTTGCTGTCGC 60.725 45.833 0.00 0.00 39.39 5.19
3063 3321 3.592059 TCATTTGTTAGTAGGGCGTCAC 58.408 45.455 0.00 0.00 0.00 3.67
3090 3348 3.912496 TCATGACATGGAGGTAGGTTG 57.088 47.619 15.37 0.00 0.00 3.77
3193 3452 0.972134 CTCCTGGACTTGAGTGCTCA 59.028 55.000 4.31 0.00 37.28 4.26
3239 3504 6.190954 ACGGCCTATTTGTCTTTGATAAAC 57.809 37.500 0.00 0.00 0.00 2.01
3265 3530 0.939577 TGAGCTGCTTCGTTGTCGAC 60.940 55.000 9.11 9.11 46.03 4.20
3274 3539 4.104143 GTTGTCGACGGGCTATGG 57.896 61.111 11.62 0.00 0.00 2.74
3275 3540 1.520787 GTTGTCGACGGGCTATGGG 60.521 63.158 11.62 0.00 0.00 4.00
3276 3541 3.379865 TTGTCGACGGGCTATGGGC 62.380 63.158 11.62 0.00 40.90 5.36
3277 3542 3.537874 GTCGACGGGCTATGGGCT 61.538 66.667 0.00 0.00 41.46 5.19
3306 3571 2.932614 CAAATCTCACGTGGTGGAGATC 59.067 50.000 17.00 0.00 33.13 2.75
3321 3586 0.389391 AGATCAATGGTACGCCTCGG 59.611 55.000 0.00 0.00 35.27 4.63
3352 3617 0.457851 CGTCCCTCACCTAAGCTGAG 59.542 60.000 0.00 0.00 35.78 3.35
3363 3628 4.264460 CCTAAGCTGAGGTACATCATCC 57.736 50.000 11.14 5.52 0.00 3.51
3368 3633 2.609459 GCTGAGGTACATCATCCGTTTG 59.391 50.000 11.14 0.00 0.00 2.93
3370 3635 4.697514 CTGAGGTACATCATCCGTTTGAT 58.302 43.478 11.14 0.00 36.79 2.57
3401 3666 3.949754 TGGGAAGAACATCATCAAGCATC 59.050 43.478 0.00 0.00 0.00 3.91
3423 3688 0.598419 GCAGCAGCAACCCTTGTTTC 60.598 55.000 0.00 0.00 41.58 2.78
3456 3721 2.833631 ACCGGAGCGATAAAATAGGG 57.166 50.000 9.46 0.00 0.00 3.53
3480 3746 7.326789 GGGTTATCATTATGTCGCAAATGATTG 59.673 37.037 20.50 0.00 45.90 2.67
3522 3788 8.642935 TTGTCTAATTTTGGTCCATGATAACA 57.357 30.769 0.00 0.00 0.00 2.41
3523 3789 8.821686 TGTCTAATTTTGGTCCATGATAACAT 57.178 30.769 0.00 0.00 37.19 2.71
3524 3790 8.902806 TGTCTAATTTTGGTCCATGATAACATC 58.097 33.333 0.00 0.00 34.15 3.06
3525 3791 9.125026 GTCTAATTTTGGTCCATGATAACATCT 57.875 33.333 0.00 0.00 34.15 2.90
3526 3792 9.123902 TCTAATTTTGGTCCATGATAACATCTG 57.876 33.333 0.00 0.00 34.15 2.90
3527 3793 7.722949 AATTTTGGTCCATGATAACATCTGT 57.277 32.000 0.00 0.00 34.15 3.41
3528 3794 6.513806 TTTTGGTCCATGATAACATCTGTG 57.486 37.500 0.00 0.00 34.15 3.66
3529 3795 4.155063 TGGTCCATGATAACATCTGTGG 57.845 45.455 0.00 5.37 37.21 4.17
3530 3796 2.880890 GGTCCATGATAACATCTGTGGC 59.119 50.000 0.00 0.00 36.42 5.01
3531 3797 3.544684 GTCCATGATAACATCTGTGGCA 58.455 45.455 0.00 0.00 36.42 4.92
3532 3798 4.139786 GTCCATGATAACATCTGTGGCAT 58.860 43.478 0.00 0.00 36.42 4.40
3533 3799 4.023450 GTCCATGATAACATCTGTGGCATG 60.023 45.833 0.00 0.00 36.42 4.06
3534 3800 4.139038 CCATGATAACATCTGTGGCATGA 58.861 43.478 15.83 0.00 35.51 3.07
3535 3801 4.765339 CCATGATAACATCTGTGGCATGAT 59.235 41.667 15.83 0.00 35.51 2.45
3536 3802 5.243060 CCATGATAACATCTGTGGCATGATT 59.757 40.000 15.83 0.00 35.51 2.57
3537 3803 6.239204 CCATGATAACATCTGTGGCATGATTT 60.239 38.462 15.83 0.00 35.51 2.17
3538 3804 6.778834 TGATAACATCTGTGGCATGATTTT 57.221 33.333 0.00 0.41 0.00 1.82
3539 3805 7.172868 TGATAACATCTGTGGCATGATTTTT 57.827 32.000 0.00 6.36 0.00 1.94
3561 3827 8.966069 TTTTTATTTTCCCGGAACAAGATTTT 57.034 26.923 0.73 0.00 0.00 1.82
3562 3828 8.966069 TTTTATTTTCCCGGAACAAGATTTTT 57.034 26.923 0.73 0.00 0.00 1.94
3579 3845 3.702147 TTTTTCCGAGGGTACGCAA 57.298 47.368 12.95 0.00 0.00 4.85
3580 3846 1.964552 TTTTTCCGAGGGTACGCAAA 58.035 45.000 12.95 1.04 0.00 3.68
3581 3847 2.188062 TTTTCCGAGGGTACGCAAAT 57.812 45.000 12.95 0.00 0.00 2.32
3582 3848 2.188062 TTTCCGAGGGTACGCAAATT 57.812 45.000 12.95 0.00 0.00 1.82
3583 3849 1.444836 TTCCGAGGGTACGCAAATTG 58.555 50.000 12.95 0.00 0.00 2.32
3584 3850 1.022451 TCCGAGGGTACGCAAATTGC 61.022 55.000 12.95 8.09 40.69 3.56
3585 3851 1.302383 CCGAGGGTACGCAAATTGCA 61.302 55.000 18.65 0.00 45.36 4.08
3586 3852 0.732571 CGAGGGTACGCAAATTGCAT 59.267 50.000 18.65 5.08 45.36 3.96
3587 3853 1.937223 CGAGGGTACGCAAATTGCATA 59.063 47.619 18.65 3.89 45.36 3.14
3588 3854 2.286184 CGAGGGTACGCAAATTGCATAC 60.286 50.000 18.65 16.68 45.36 2.39
3594 3860 3.354089 ACGCAAATTGCATACCATAGC 57.646 42.857 18.65 0.00 45.36 2.97
3595 3861 2.951642 ACGCAAATTGCATACCATAGCT 59.048 40.909 18.65 0.00 45.36 3.32
3596 3862 3.381272 ACGCAAATTGCATACCATAGCTT 59.619 39.130 18.65 0.00 45.36 3.74
3597 3863 4.142182 ACGCAAATTGCATACCATAGCTTT 60.142 37.500 18.65 0.00 45.36 3.51
3598 3864 5.067153 ACGCAAATTGCATACCATAGCTTTA 59.933 36.000 18.65 0.00 45.36 1.85
3599 3865 6.151691 CGCAAATTGCATACCATAGCTTTAT 58.848 36.000 18.65 0.00 45.36 1.40
3600 3866 7.040755 ACGCAAATTGCATACCATAGCTTTATA 60.041 33.333 18.65 0.00 45.36 0.98
3601 3867 7.482743 CGCAAATTGCATACCATAGCTTTATAG 59.517 37.037 18.65 0.00 45.36 1.31
3602 3868 8.514594 GCAAATTGCATACCATAGCTTTATAGA 58.485 33.333 13.73 0.00 44.26 1.98
3607 3873 9.494271 TTGCATACCATAGCTTTATAGAAGAAG 57.506 33.333 0.00 0.00 0.00 2.85
3608 3874 8.870116 TGCATACCATAGCTTTATAGAAGAAGA 58.130 33.333 0.00 0.00 0.00 2.87
3609 3875 9.364989 GCATACCATAGCTTTATAGAAGAAGAG 57.635 37.037 0.00 0.00 0.00 2.85
3626 3892 9.660180 AGAAGAAGAGAAAATTAGTACATGACC 57.340 33.333 0.00 0.00 0.00 4.02
3627 3893 8.794335 AAGAAGAGAAAATTAGTACATGACCC 57.206 34.615 0.00 0.00 0.00 4.46
3628 3894 7.339482 AGAAGAGAAAATTAGTACATGACCCC 58.661 38.462 0.00 0.00 0.00 4.95
3629 3895 6.893020 AGAGAAAATTAGTACATGACCCCT 57.107 37.500 0.00 0.00 0.00 4.79
3630 3896 7.989947 AGAGAAAATTAGTACATGACCCCTA 57.010 36.000 0.00 0.00 0.00 3.53
3631 3897 7.793036 AGAGAAAATTAGTACATGACCCCTAC 58.207 38.462 0.00 0.00 0.00 3.18
3632 3898 6.896883 AGAAAATTAGTACATGACCCCTACC 58.103 40.000 0.00 0.00 0.00 3.18
3633 3899 6.445786 AGAAAATTAGTACATGACCCCTACCA 59.554 38.462 0.00 0.00 0.00 3.25
3634 3900 5.625568 AATTAGTACATGACCCCTACCAC 57.374 43.478 0.00 0.00 0.00 4.16
3635 3901 2.942604 AGTACATGACCCCTACCACT 57.057 50.000 0.00 0.00 0.00 4.00
3636 3902 2.748388 AGTACATGACCCCTACCACTC 58.252 52.381 0.00 0.00 0.00 3.51
3637 3903 1.407979 GTACATGACCCCTACCACTCG 59.592 57.143 0.00 0.00 0.00 4.18
3638 3904 1.144057 CATGACCCCTACCACTCGC 59.856 63.158 0.00 0.00 0.00 5.03
3639 3905 1.001760 ATGACCCCTACCACTCGCT 59.998 57.895 0.00 0.00 0.00 4.93
3640 3906 1.330655 ATGACCCCTACCACTCGCTG 61.331 60.000 0.00 0.00 0.00 5.18
3641 3907 1.982938 GACCCCTACCACTCGCTGT 60.983 63.158 0.00 0.00 0.00 4.40
3642 3908 2.227089 GACCCCTACCACTCGCTGTG 62.227 65.000 2.10 2.10 45.80 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 138 2.288025 GGGGAACTGCAGGACGGTA 61.288 63.158 19.93 0.00 36.64 4.02
187 220 9.431887 CTTTACTAGTTTGCACCTACTATTTGA 57.568 33.333 0.00 0.00 0.00 2.69
188 221 8.175716 GCTTTACTAGTTTGCACCTACTATTTG 58.824 37.037 0.00 0.00 0.00 2.32
193 226 5.246429 AGAGCTTTACTAGTTTGCACCTACT 59.754 40.000 0.00 0.00 0.00 2.57
205 238 6.402222 AGGTGAATCAACAGAGCTTTACTAG 58.598 40.000 0.00 0.00 0.00 2.57
206 239 6.360370 AGGTGAATCAACAGAGCTTTACTA 57.640 37.500 0.00 0.00 0.00 1.82
207 240 5.234466 AGGTGAATCAACAGAGCTTTACT 57.766 39.130 0.00 0.00 0.00 2.24
208 241 6.037610 CCATAGGTGAATCAACAGAGCTTTAC 59.962 42.308 0.00 0.00 0.00 2.01
232 265 1.856265 CGCACTGTTTGGAAGCTCCC 61.856 60.000 0.00 0.00 35.03 4.30
293 331 5.335348 GGAACAGTAAGCAAATAAAGCGGAA 60.335 40.000 0.00 0.00 37.01 4.30
294 333 4.155280 GGAACAGTAAGCAAATAAAGCGGA 59.845 41.667 0.00 0.00 37.01 5.54
418 464 0.461548 TGGCAATGGCGAAAAACACA 59.538 45.000 1.51 0.00 42.47 3.72
419 465 1.139163 CTGGCAATGGCGAAAAACAC 58.861 50.000 1.51 0.00 42.47 3.32
768 853 3.365666 GCACTACACTTCGCTACACTACA 60.366 47.826 0.00 0.00 0.00 2.74
770 855 3.079578 AGCACTACACTTCGCTACACTA 58.920 45.455 0.00 0.00 31.60 2.74
773 858 1.883926 TCAGCACTACACTTCGCTACA 59.116 47.619 0.00 0.00 32.29 2.74
774 859 2.251893 GTCAGCACTACACTTCGCTAC 58.748 52.381 0.00 0.00 32.29 3.58
779 864 2.802816 CCACTTGTCAGCACTACACTTC 59.197 50.000 0.00 0.00 0.00 3.01
790 875 4.722700 CCCGGCCCCACTTGTCAG 62.723 72.222 0.00 0.00 0.00 3.51
986 1099 2.672996 ATGCAACCGGGACACTGC 60.673 61.111 6.32 7.10 35.32 4.40
1099 1255 4.423209 GCACCTCCCTCCCTCCCT 62.423 72.222 0.00 0.00 0.00 4.20
1114 1277 4.440829 GGCCTTTCCCCATCGGCA 62.441 66.667 0.00 0.00 44.23 5.69
1244 1407 1.549203 CATTACCTGCTTGCTTGGGT 58.451 50.000 9.18 9.28 36.02 4.51
1271 1434 3.923864 TTGGATCGATCGCCGGGG 61.924 66.667 18.81 13.31 39.14 5.73
1276 1439 1.517276 CGTTACTGTTGGATCGATCGC 59.483 52.381 18.81 12.27 0.00 4.58
1329 1509 3.130340 GTCCCAAACACAACACATCAGTT 59.870 43.478 0.00 0.00 0.00 3.16
1347 1531 2.359975 CCGGAGCAAACCTGTCCC 60.360 66.667 0.00 0.00 0.00 4.46
1516 1708 6.741992 TTACACATGTATGGAGCTTTCTTG 57.258 37.500 0.00 0.00 0.00 3.02
1580 1795 1.407437 GCGATCTTGGACCACCTGAAT 60.407 52.381 0.00 0.00 37.04 2.57
1784 1999 2.012948 GGTGGTCGTCGTCGTTGTC 61.013 63.158 1.33 0.00 38.33 3.18
1829 2044 1.439353 CGTTGCTGGTGTTGCTCTGT 61.439 55.000 0.00 0.00 0.00 3.41
1847 2062 2.160417 GTCCAGCTCAAATTCCAACTCG 59.840 50.000 0.00 0.00 0.00 4.18
1931 2152 1.822186 GACCGGGCAGTGTGTGTTT 60.822 57.895 0.00 0.00 0.00 2.83
1937 2158 2.982130 GAGATGACCGGGCAGTGT 59.018 61.111 18.96 1.18 0.00 3.55
2054 2275 1.228063 GCCGTCCATGATGCTCCAT 60.228 57.895 0.00 0.00 0.00 3.41
2397 2639 1.202463 CGAGTGATCTCATGGACCCAC 60.202 57.143 0.00 2.34 40.44 4.61
2437 2683 5.340803 TCACGCTGCTTGTTTCTATACTAG 58.659 41.667 6.01 0.00 0.00 2.57
2458 2704 1.982395 AGTCTTGGCGGTCCGATCA 60.982 57.895 17.49 9.64 34.14 2.92
2467 2713 2.159240 TGTACTAGCATCAGTCTTGGCG 60.159 50.000 0.00 0.00 0.00 5.69
2522 2770 1.134560 GTACGTACTCCTCTTGCAGGG 59.865 57.143 18.47 0.00 43.67 4.45
2530 2778 2.352651 TGTATGTGCGTACGTACTCCTC 59.647 50.000 31.45 20.36 45.42 3.71
2547 2795 2.038557 AGTCTTCGTGCTGGGTTTGTAT 59.961 45.455 0.00 0.00 0.00 2.29
2624 2877 8.283992 TGTACAACGTGTATGGAAAAGTTATTG 58.716 33.333 0.00 0.00 35.05 1.90
2670 2923 1.036481 TGCACCACTTTGCTGCTTCA 61.036 50.000 0.00 0.00 43.41 3.02
2698 2951 2.021457 ACCTTGACCCGTTTTTGACTG 58.979 47.619 0.00 0.00 0.00 3.51
2915 3171 1.547675 GGGACAGGCTTCACCAAATCA 60.548 52.381 0.00 0.00 43.14 2.57
2934 3191 1.202336 GCGAATGGGAAAGCAGAATGG 60.202 52.381 0.00 0.00 35.86 3.16
2936 3193 1.747355 CAGCGAATGGGAAAGCAGAAT 59.253 47.619 0.00 0.00 0.00 2.40
2941 3198 1.308069 TGAGCAGCGAATGGGAAAGC 61.308 55.000 0.00 0.00 0.00 3.51
3011 3269 1.739562 GCCTGCTCACTCAAGGACG 60.740 63.158 0.00 0.00 0.00 4.79
3035 3293 7.051623 ACGCCCTACTAACAAATGAATCAATA 58.948 34.615 0.00 0.00 0.00 1.90
3063 3321 0.947660 CTCCATGTCATGATCCGCGG 60.948 60.000 22.12 22.12 0.00 6.46
3090 3348 2.108362 CCGGATCCCGTGTTAGGC 59.892 66.667 6.06 0.00 46.80 3.93
3193 3452 5.013258 AGTGGTACTCTAGTTTCTTCCCT 57.987 43.478 0.00 0.00 0.00 4.20
3239 3504 4.060900 ACAACGAAGCAGCTCATATATGG 58.939 43.478 12.78 5.05 0.00 2.74
3245 3510 0.038251 TCGACAACGAAGCAGCTCAT 60.038 50.000 0.00 0.00 45.74 2.90
3247 3512 4.245054 TCGACAACGAAGCAGCTC 57.755 55.556 0.00 0.00 45.74 4.09
3265 3530 2.045926 GCCATAGCCCATAGCCCG 60.046 66.667 0.00 0.00 45.47 6.13
3268 3533 0.401738 TTGGAGCCATAGCCCATAGC 59.598 55.000 0.00 0.00 38.58 2.97
3271 3536 1.785208 AGATTTGGAGCCATAGCCCAT 59.215 47.619 0.00 0.00 38.58 4.00
3272 3537 1.143684 GAGATTTGGAGCCATAGCCCA 59.856 52.381 0.00 0.00 41.25 5.36
3273 3538 1.143684 TGAGATTTGGAGCCATAGCCC 59.856 52.381 0.00 0.00 41.25 5.19
3274 3539 2.225467 GTGAGATTTGGAGCCATAGCC 58.775 52.381 0.00 0.00 41.25 3.93
3275 3540 1.869767 CGTGAGATTTGGAGCCATAGC 59.130 52.381 0.00 0.00 40.32 2.97
3276 3541 2.868583 CACGTGAGATTTGGAGCCATAG 59.131 50.000 10.90 0.00 0.00 2.23
3277 3542 2.419990 CCACGTGAGATTTGGAGCCATA 60.420 50.000 19.30 0.00 31.39 2.74
3306 3571 0.390603 TTCACCGAGGCGTACCATTG 60.391 55.000 0.00 0.00 39.06 2.82
3321 3586 1.202486 TGAGGGACGCGGAATATTCAC 60.202 52.381 17.07 7.60 0.00 3.18
3363 3628 6.494893 TCTTCCCAGAATAAACATCAAACG 57.505 37.500 0.00 0.00 0.00 3.60
3368 3633 7.630242 TGATGTTCTTCCCAGAATAAACATC 57.370 36.000 22.95 22.95 41.26 3.06
3370 3635 7.174413 TGATGATGTTCTTCCCAGAATAAACA 58.826 34.615 7.47 7.47 41.26 2.83
3371 3636 7.630242 TGATGATGTTCTTCCCAGAATAAAC 57.370 36.000 0.00 0.00 41.26 2.01
3375 3640 4.643784 GCTTGATGATGTTCTTCCCAGAAT 59.356 41.667 0.00 0.00 41.26 2.40
3378 3643 3.349927 TGCTTGATGATGTTCTTCCCAG 58.650 45.455 0.00 0.00 0.00 4.45
3379 3644 3.438216 TGCTTGATGATGTTCTTCCCA 57.562 42.857 0.00 0.00 0.00 4.37
3380 3645 3.003068 CGATGCTTGATGATGTTCTTCCC 59.997 47.826 0.00 0.00 0.00 3.97
3381 3646 3.547613 GCGATGCTTGATGATGTTCTTCC 60.548 47.826 0.00 0.00 0.00 3.46
3419 3684 2.199236 GGTATCGGTGGATGACGAAAC 58.801 52.381 0.00 0.00 42.88 2.78
3423 3688 4.628160 CGGTATCGGTGGATGACG 57.372 61.111 0.00 0.00 34.00 4.35
3447 3712 9.562408 TTGCGACATAATGATAACCCTATTTTA 57.438 29.630 0.00 0.00 0.00 1.52
3456 3721 8.786937 ACAATCATTTGCGACATAATGATAAC 57.213 30.769 18.31 0.00 45.79 1.89
3508 3774 3.685265 GCCACAGATGTTATCATGGACCA 60.685 47.826 13.30 0.00 39.09 4.02
3536 3802 8.966069 AAAATCTTGTTCCGGGAAAATAAAAA 57.034 26.923 11.82 0.00 0.00 1.94
3537 3803 8.966069 AAAAATCTTGTTCCGGGAAAATAAAA 57.034 26.923 11.82 1.07 0.00 1.52
3561 3827 1.964552 TTTGCGTACCCTCGGAAAAA 58.035 45.000 3.64 0.00 44.93 1.94
3562 3828 3.702147 TTTGCGTACCCTCGGAAAA 57.298 47.368 3.64 0.00 44.93 2.29
3564 3830 1.444836 CAATTTGCGTACCCTCGGAA 58.555 50.000 0.00 0.00 39.14 4.30
3565 3831 1.022451 GCAATTTGCGTACCCTCGGA 61.022 55.000 5.49 0.00 31.71 4.55
3566 3832 1.427819 GCAATTTGCGTACCCTCGG 59.572 57.895 5.49 0.00 31.71 4.63
3576 3842 8.514594 TCTATAAAGCTATGGTATGCAATTTGC 58.485 33.333 14.49 14.49 45.29 3.68
3581 3847 9.494271 CTTCTTCTATAAAGCTATGGTATGCAA 57.506 33.333 0.00 0.00 0.00 4.08
3582 3848 8.870116 TCTTCTTCTATAAAGCTATGGTATGCA 58.130 33.333 0.00 0.00 0.00 3.96
3583 3849 9.364989 CTCTTCTTCTATAAAGCTATGGTATGC 57.635 37.037 0.00 0.00 0.00 3.14
3600 3866 9.660180 GGTCATGTACTAATTTTCTCTTCTTCT 57.340 33.333 0.00 0.00 0.00 2.85
3601 3867 8.884726 GGGTCATGTACTAATTTTCTCTTCTTC 58.115 37.037 0.00 0.00 0.00 2.87
3602 3868 7.829706 GGGGTCATGTACTAATTTTCTCTTCTT 59.170 37.037 0.00 0.00 0.00 2.52
3603 3869 7.182930 AGGGGTCATGTACTAATTTTCTCTTCT 59.817 37.037 0.00 0.00 0.00 2.85
3604 3870 7.339482 AGGGGTCATGTACTAATTTTCTCTTC 58.661 38.462 0.00 0.00 0.00 2.87
3605 3871 7.272144 AGGGGTCATGTACTAATTTTCTCTT 57.728 36.000 0.00 0.00 0.00 2.85
3606 3872 6.893020 AGGGGTCATGTACTAATTTTCTCT 57.107 37.500 0.00 0.00 0.00 3.10
3607 3873 6.990939 GGTAGGGGTCATGTACTAATTTTCTC 59.009 42.308 0.00 0.00 0.00 2.87
3608 3874 6.445786 TGGTAGGGGTCATGTACTAATTTTCT 59.554 38.462 0.00 0.00 0.00 2.52
3609 3875 6.541278 GTGGTAGGGGTCATGTACTAATTTTC 59.459 42.308 0.00 0.00 0.00 2.29
3610 3876 6.216868 AGTGGTAGGGGTCATGTACTAATTTT 59.783 38.462 0.00 0.00 0.00 1.82
3611 3877 5.729718 AGTGGTAGGGGTCATGTACTAATTT 59.270 40.000 0.00 0.00 0.00 1.82
3612 3878 5.286221 AGTGGTAGGGGTCATGTACTAATT 58.714 41.667 0.00 0.00 0.00 1.40
3613 3879 4.892198 AGTGGTAGGGGTCATGTACTAAT 58.108 43.478 0.00 0.00 0.00 1.73
3614 3880 4.284178 GAGTGGTAGGGGTCATGTACTAA 58.716 47.826 0.00 0.00 0.00 2.24
3615 3881 3.686405 CGAGTGGTAGGGGTCATGTACTA 60.686 52.174 0.00 0.00 0.00 1.82
3616 3882 2.748388 GAGTGGTAGGGGTCATGTACT 58.252 52.381 0.00 0.00 0.00 2.73
3617 3883 1.407979 CGAGTGGTAGGGGTCATGTAC 59.592 57.143 0.00 0.00 0.00 2.90
3618 3884 1.771565 CGAGTGGTAGGGGTCATGTA 58.228 55.000 0.00 0.00 0.00 2.29
3619 3885 1.614241 GCGAGTGGTAGGGGTCATGT 61.614 60.000 0.00 0.00 0.00 3.21
3620 3886 1.144057 GCGAGTGGTAGGGGTCATG 59.856 63.158 0.00 0.00 0.00 3.07
3621 3887 1.001760 AGCGAGTGGTAGGGGTCAT 59.998 57.895 0.00 0.00 0.00 3.06
3622 3888 1.982395 CAGCGAGTGGTAGGGGTCA 60.982 63.158 0.00 0.00 0.00 4.02
3623 3889 1.982938 ACAGCGAGTGGTAGGGGTC 60.983 63.158 0.00 0.00 0.00 4.46
3624 3890 2.119832 ACAGCGAGTGGTAGGGGT 59.880 61.111 0.00 0.00 0.00 4.95
3625 3891 2.579201 CACAGCGAGTGGTAGGGG 59.421 66.667 4.63 0.00 44.69 4.79


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

AutoCloner maintained by Alex Coulton.