Multiple sequence alignment - TraesCS7D01G376400

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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 TraesCS7D01G376400 chr7D 100.000 3952 0 0 1 3952 486631584 486627633 0.000000e+00 7299.0
1 TraesCS7D01G376400 chr7D 82.023 2264 299 71 1079 3291 486576403 486574197 0.000000e+00 1827.0
2 TraesCS7D01G376400 chr7D 73.399 812 164 31 1136 1924 486242820 486242038 5.070000e-64 255.0
3 TraesCS7D01G376400 chr7D 82.286 175 23 7 586 758 392638107 392637939 1.140000e-30 145.0
4 TraesCS7D01G376400 chr7B 95.491 3571 123 24 1 3546 516356700 516353143 0.000000e+00 5668.0
5 TraesCS7D01G376400 chr7B 82.232 2285 281 73 1079 3291 516315907 516313676 0.000000e+00 1855.0
6 TraesCS7D01G376400 chr7B 94.771 306 12 2 3650 3952 516353143 516352839 1.290000e-129 473.0
7 TraesCS7D01G376400 chr7A 92.646 2366 87 27 859 3149 555506736 555504383 0.000000e+00 3325.0
8 TraesCS7D01G376400 chr7A 81.607 2278 283 76 1079 3291 555481151 555478945 0.000000e+00 1760.0
9 TraesCS7D01G376400 chr7A 81.532 2258 296 70 1079 3291 555468454 555466273 0.000000e+00 1748.0
10 TraesCS7D01G376400 chr7A 80.855 2246 298 74 1096 3291 555475727 555473564 0.000000e+00 1644.0
11 TraesCS7D01G376400 chr7A 93.283 789 45 4 8 795 555507997 555507216 0.000000e+00 1157.0
12 TraesCS7D01G376400 chr7A 84.982 273 28 5 3692 3951 555472359 555472087 8.420000e-67 265.0
13 TraesCS7D01G376400 chr7A 85.027 187 15 6 2917 3092 555461942 555461758 1.130000e-40 178.0
14 TraesCS7D01G376400 chr7A 97.778 45 1 0 1008 1052 555468498 555468454 1.180000e-10 78.7
15 TraesCS7D01G376400 chr3A 77.591 357 66 10 336 685 475303102 475303451 1.860000e-48 204.0
16 TraesCS7D01G376400 chr3A 95.918 98 3 1 3546 3643 170889990 170889894 1.470000e-34 158.0
17 TraesCS7D01G376400 chr5D 98.913 92 0 1 3542 3633 184636682 184636592 3.160000e-36 163.0
18 TraesCS7D01G376400 chr5D 95.918 98 3 1 3546 3643 252117401 252117305 1.470000e-34 158.0
19 TraesCS7D01G376400 chr4D 97.872 94 2 0 3542 3635 507164788 507164695 3.160000e-36 163.0
20 TraesCS7D01G376400 chr3B 96.040 101 3 1 3543 3643 492773193 492773292 3.160000e-36 163.0
21 TraesCS7D01G376400 chr3B 95.918 98 3 1 3546 3643 122310320 122310224 1.470000e-34 158.0
22 TraesCS7D01G376400 chr5B 96.000 100 2 2 3542 3641 470992370 470992273 1.140000e-35 161.0
23 TraesCS7D01G376400 chr3D 95.050 101 4 1 3543 3643 137515210 137515111 1.470000e-34 158.0
24 TraesCS7D01G376400 chr6D 92.593 108 7 1 3544 3651 95714147 95714253 1.900000e-33 154.0


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 TraesCS7D01G376400 chr7D 486627633 486631584 3951 True 7299.00 7299 100.0000 1 3952 1 chr7D.!!$R4 3951
1 TraesCS7D01G376400 chr7D 486574197 486576403 2206 True 1827.00 1827 82.0230 1079 3291 1 chr7D.!!$R3 2212
2 TraesCS7D01G376400 chr7D 486242038 486242820 782 True 255.00 255 73.3990 1136 1924 1 chr7D.!!$R2 788
3 TraesCS7D01G376400 chr7B 516352839 516356700 3861 True 3070.50 5668 95.1310 1 3952 2 chr7B.!!$R2 3951
4 TraesCS7D01G376400 chr7B 516313676 516315907 2231 True 1855.00 1855 82.2320 1079 3291 1 chr7B.!!$R1 2212
5 TraesCS7D01G376400 chr7A 555504383 555507997 3614 True 2241.00 3325 92.9645 8 3149 2 chr7A.!!$R3 3141
6 TraesCS7D01G376400 chr7A 555466273 555481151 14878 True 1099.14 1760 85.3508 1008 3951 5 chr7A.!!$R2 2943

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
34 35 0.251165 GTGGGCATGTGGTAGGTTGT 60.251 55.0 0.00 0.00 0.00 3.32 F
451 453 0.388520 CTCGTCGCAGGTCATGACAA 60.389 55.0 26.47 4.31 32.91 3.18 F
1612 2083 0.251354 AGTGCTTGATCGATGCCTGT 59.749 50.0 0.54 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1612 2083 0.909623 GAAGGGATTCCAGAACGGGA 59.090 55.000 4.80 0.00 34.83 5.14 R
2189 2720 2.803492 GCTGGCCAGTATCTTAACCTCG 60.803 54.545 32.81 4.47 0.00 4.63 R
3537 16794 0.030369 CGGAGGGAGTACATACGCAC 59.970 60.000 0.00 0.00 0.00 5.34 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
22 23 1.136329 AGACTGGACCTTGTGGGCAT 61.136 55.000 0.00 0.00 45.45 4.40
34 35 0.251165 GTGGGCATGTGGTAGGTTGT 60.251 55.000 0.00 0.00 0.00 3.32
122 124 2.456577 AGTTTTGCATGACCCCATACC 58.543 47.619 0.00 0.00 0.00 2.73
132 134 4.733077 TGACCCCATACCTTTTTCAAGA 57.267 40.909 0.00 0.00 30.57 3.02
164 166 4.514401 CCTCTTAATAGTGTGGTTGTCCC 58.486 47.826 0.00 0.00 0.00 4.46
165 167 4.181578 CTCTTAATAGTGTGGTTGTCCCG 58.818 47.826 0.00 0.00 35.15 5.14
239 241 4.864247 CCTTTTCTTTTGAAGTGTGTGTGG 59.136 41.667 0.00 0.00 39.88 4.17
241 243 2.374184 TCTTTTGAAGTGTGTGTGGGG 58.626 47.619 0.00 0.00 0.00 4.96
242 244 2.025793 TCTTTTGAAGTGTGTGTGGGGA 60.026 45.455 0.00 0.00 0.00 4.81
243 245 2.051334 TTTGAAGTGTGTGTGGGGAG 57.949 50.000 0.00 0.00 0.00 4.30
314 316 8.303156 CAATGACACACCAAAATACCATTTAGA 58.697 33.333 0.00 0.00 0.00 2.10
387 389 3.540314 TTGGTGTGCTTCAAAAATGCT 57.460 38.095 0.00 0.00 0.00 3.79
434 436 5.605534 TGAGTATTTGAAGCCTCATAGCTC 58.394 41.667 0.00 0.00 44.11 4.09
437 439 2.586258 TTGAAGCCTCATAGCTCGTC 57.414 50.000 0.00 0.00 44.11 4.20
451 453 0.388520 CTCGTCGCAGGTCATGACAA 60.389 55.000 26.47 4.31 32.91 3.18
481 483 6.714356 TGTTAACTTGGACAACATGATCATCA 59.286 34.615 4.86 0.00 0.00 3.07
532 534 1.548081 TGCAATTGTCTCATGGTGGG 58.452 50.000 7.40 0.00 0.00 4.61
552 555 1.577421 CCGAAACGTCGCCCAAATT 59.423 52.632 0.00 0.00 46.28 1.82
615 618 2.945008 CAAGAAGCTCACAACCAACTGA 59.055 45.455 0.00 0.00 0.00 3.41
674 678 8.143193 TCATAGCATTTGATTCTTGTGTGTTTT 58.857 29.630 0.00 0.00 0.00 2.43
736 740 3.840890 TGTTGCGTTTGAGTTTCAGTT 57.159 38.095 0.00 0.00 0.00 3.16
743 747 4.733405 GCGTTTGAGTTTCAGTTGTTAAGG 59.267 41.667 0.00 0.00 0.00 2.69
822 835 5.734031 AAATTTTAGGGGGTGAGCTAGAT 57.266 39.130 0.00 0.00 0.00 1.98
933 1371 3.048600 TGGTAATGGGATCTGAAGGAGG 58.951 50.000 0.00 0.00 0.00 4.30
981 1419 1.318158 AATCGCTCCGGGTAGAACGT 61.318 55.000 0.00 0.00 0.00 3.99
1605 2076 1.066858 GGAACTGGAGTGCTTGATCGA 60.067 52.381 0.00 0.00 0.00 3.59
1612 2083 0.251354 AGTGCTTGATCGATGCCTGT 59.749 50.000 0.54 0.00 0.00 4.00
2026 2542 5.614324 AACTTATTCCATCCACATCGAGA 57.386 39.130 0.00 0.00 0.00 4.04
2189 2720 1.947456 GTGAATTTGGGTATCTCCGGC 59.053 52.381 0.00 0.00 37.00 6.13
2649 3199 3.257393 CACAGGTATCTCTGCAGTGTTC 58.743 50.000 14.67 6.37 38.26 3.18
2687 3237 2.032550 CAGGCATTCATTACCGCTTGAG 59.967 50.000 0.00 0.00 33.68 3.02
2789 3340 7.503566 TGATCCATACCTTTTGAGGATTCATTC 59.496 37.037 0.00 0.00 39.10 2.67
2835 16057 5.070001 TGTTTAGTTTCTTGTAGGCATGCT 58.930 37.500 18.92 6.26 0.00 3.79
2836 16058 6.234920 TGTTTAGTTTCTTGTAGGCATGCTA 58.765 36.000 18.92 5.20 0.00 3.49
2837 16059 6.148811 TGTTTAGTTTCTTGTAGGCATGCTAC 59.851 38.462 18.92 17.09 0.00 3.58
3075 16332 3.712187 GTCAGAGTATACTGAGCTTGGC 58.288 50.000 10.90 0.00 45.67 4.52
3145 16402 2.027929 CCCCATGTTTGTGCATCATGTT 60.028 45.455 16.64 0.00 37.73 2.71
3213 16470 7.256296 GGCTGGTAAAAGCATATGGGATAAATT 60.256 37.037 4.56 0.00 45.43 1.82
3223 16480 6.968904 GCATATGGGATAAATTGCTTATGACG 59.031 38.462 4.56 0.00 29.89 4.35
3229 16486 5.473504 GGATAAATTGCTTATGACGGTGGAT 59.526 40.000 0.00 0.00 29.89 3.41
3230 16487 6.016276 GGATAAATTGCTTATGACGGTGGATT 60.016 38.462 0.00 0.00 29.89 3.01
3275 16532 6.881065 AGATGTAGCAGATTAGTTGAGCAAAA 59.119 34.615 0.00 0.00 0.00 2.44
3345 16602 1.022735 ACTCTATGTCGGTACCGCTG 58.977 55.000 29.64 15.76 39.59 5.18
3377 16634 2.867109 ATTGGTCAGTTGGAGTGGAG 57.133 50.000 0.00 0.00 0.00 3.86
3389 16646 1.210722 GGAGTGGAGGAAATCTGGTCC 59.789 57.143 0.00 0.00 35.17 4.46
3485 16742 4.094294 CAGCTTGATTTTGATTTGGCATGG 59.906 41.667 0.00 0.00 0.00 3.66
3498 16755 1.672356 GCATGGTCTGTCACGCCTT 60.672 57.895 0.00 0.00 0.00 4.35
3527 16784 5.861251 TGTTACTTCAGTTTTTGCAACAGTG 59.139 36.000 0.00 2.23 0.00 3.66
3533 16790 3.088532 AGTTTTTGCAACAGTGGACTCA 58.911 40.909 0.00 0.00 0.00 3.41
3535 16792 3.502191 TTTTGCAACAGTGGACTCAAC 57.498 42.857 0.00 0.00 0.00 3.18
3537 16794 1.667236 TGCAACAGTGGACTCAACAG 58.333 50.000 0.00 0.00 0.00 3.16
3538 16795 1.065491 TGCAACAGTGGACTCAACAGT 60.065 47.619 0.00 0.00 34.57 3.55
3540 16797 1.331756 CAACAGTGGACTCAACAGTGC 59.668 52.381 0.00 0.00 41.77 4.40
3543 16800 1.037493 AGTGGACTCAACAGTGCGTA 58.963 50.000 0.00 0.00 43.86 4.42
3545 16802 1.726791 GTGGACTCAACAGTGCGTATG 59.273 52.381 0.00 0.00 43.86 2.39
3547 16804 2.559231 TGGACTCAACAGTGCGTATGTA 59.441 45.455 0.00 0.00 43.86 2.29
3548 16805 2.921754 GGACTCAACAGTGCGTATGTAC 59.078 50.000 0.00 0.00 30.37 2.90
3549 16806 3.367087 GGACTCAACAGTGCGTATGTACT 60.367 47.826 0.00 0.00 42.21 2.73
3550 16807 3.834610 ACTCAACAGTGCGTATGTACTC 58.165 45.455 2.29 0.00 39.18 2.59
3551 16808 3.179830 CTCAACAGTGCGTATGTACTCC 58.820 50.000 2.29 0.00 39.18 3.85
3552 16809 2.094390 TCAACAGTGCGTATGTACTCCC 60.094 50.000 2.29 0.00 39.18 4.30
3553 16810 1.848652 ACAGTGCGTATGTACTCCCT 58.151 50.000 2.29 0.00 39.18 4.20
3554 16811 1.749634 ACAGTGCGTATGTACTCCCTC 59.250 52.381 2.29 0.00 39.18 4.30
3555 16812 1.067212 CAGTGCGTATGTACTCCCTCC 59.933 57.143 2.29 0.00 39.18 4.30
3556 16813 0.030369 GTGCGTATGTACTCCCTCCG 59.970 60.000 0.00 0.00 0.00 4.63
3557 16814 0.394762 TGCGTATGTACTCCCTCCGT 60.395 55.000 0.00 0.00 0.00 4.69
3558 16815 0.743097 GCGTATGTACTCCCTCCGTT 59.257 55.000 0.00 0.00 0.00 4.44
3559 16816 1.268948 GCGTATGTACTCCCTCCGTTC 60.269 57.143 0.00 0.00 0.00 3.95
3560 16817 1.336125 CGTATGTACTCCCTCCGTTCC 59.664 57.143 0.00 0.00 0.00 3.62
3561 16818 2.381911 GTATGTACTCCCTCCGTTCCA 58.618 52.381 0.00 0.00 0.00 3.53
3562 16819 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
3563 16820 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
3564 16821 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
3565 16822 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
3566 16823 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
3567 16824 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3568 16825 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3569 16826 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
3570 16827 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3571 16828 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
3572 16829 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
3573 16830 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
3574 16831 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
3575 16832 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
3576 16833 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
3577 16834 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
3578 16835 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
3579 16836 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
3580 16837 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
3581 16838 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
3582 16839 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
3583 16840 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
3584 16841 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
3585 16842 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
3586 16843 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
3587 16844 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
3588 16845 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
3589 16846 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
3590 16847 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
3591 16848 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
3592 16849 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
3593 16850 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
3594 16851 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
3608 16865 7.922505 TCAAATTTGAACTAAAACCATGACG 57.077 32.000 18.45 0.00 33.55 4.35
3609 16866 7.708051 TCAAATTTGAACTAAAACCATGACGA 58.292 30.769 18.45 0.00 33.55 4.20
3610 16867 7.860373 TCAAATTTGAACTAAAACCATGACGAG 59.140 33.333 18.45 0.00 33.55 4.18
3611 16868 6.877611 ATTTGAACTAAAACCATGACGAGT 57.122 33.333 0.00 0.00 0.00 4.18
3612 16869 7.972832 ATTTGAACTAAAACCATGACGAGTA 57.027 32.000 0.00 0.00 0.00 2.59
3613 16870 7.789273 TTTGAACTAAAACCATGACGAGTAA 57.211 32.000 0.00 0.00 0.00 2.24
3614 16871 7.972832 TTGAACTAAAACCATGACGAGTAAT 57.027 32.000 0.00 0.00 0.00 1.89
3615 16872 7.972832 TGAACTAAAACCATGACGAGTAATT 57.027 32.000 0.00 0.00 0.00 1.40
3616 16873 8.385898 TGAACTAAAACCATGACGAGTAATTT 57.614 30.769 0.00 0.00 0.00 1.82
3617 16874 8.286800 TGAACTAAAACCATGACGAGTAATTTG 58.713 33.333 0.00 0.00 0.00 2.32
3618 16875 7.141100 ACTAAAACCATGACGAGTAATTTGG 57.859 36.000 0.00 0.00 0.00 3.28
3619 16876 6.938030 ACTAAAACCATGACGAGTAATTTGGA 59.062 34.615 0.00 0.00 0.00 3.53
3620 16877 6.642707 AAAACCATGACGAGTAATTTGGAA 57.357 33.333 0.00 0.00 0.00 3.53
3621 16878 5.622770 AACCATGACGAGTAATTTGGAAC 57.377 39.130 0.00 0.00 0.00 3.62
3622 16879 3.682858 ACCATGACGAGTAATTTGGAACG 59.317 43.478 0.00 0.00 0.00 3.95
3623 16880 3.063452 CCATGACGAGTAATTTGGAACGG 59.937 47.826 0.00 0.00 0.00 4.44
3624 16881 3.663995 TGACGAGTAATTTGGAACGGA 57.336 42.857 0.00 0.00 0.00 4.69
3625 16882 3.581755 TGACGAGTAATTTGGAACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
3626 16883 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3627 16884 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3628 16885 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
3629 16886 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
3630 16887 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
3631 16888 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
3632 16889 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
3633 16890 1.719529 TTTGGAACGGAGGGAGTACA 58.280 50.000 0.00 0.00 0.00 2.90
3634 16891 1.946984 TTGGAACGGAGGGAGTACAT 58.053 50.000 0.00 0.00 0.00 2.29
3635 16892 1.481871 TGGAACGGAGGGAGTACATC 58.518 55.000 0.00 0.00 0.00 3.06
3636 16893 1.006758 TGGAACGGAGGGAGTACATCT 59.993 52.381 0.00 0.00 0.00 2.90
3637 16894 2.242965 TGGAACGGAGGGAGTACATCTA 59.757 50.000 0.00 0.00 0.00 1.98
3638 16895 3.117246 TGGAACGGAGGGAGTACATCTAT 60.117 47.826 0.00 0.00 0.00 1.98
3639 16896 4.105217 TGGAACGGAGGGAGTACATCTATA 59.895 45.833 0.00 0.00 0.00 1.31
3640 16897 5.075493 GGAACGGAGGGAGTACATCTATAA 58.925 45.833 0.00 0.00 0.00 0.98
3641 16898 5.715753 GGAACGGAGGGAGTACATCTATAAT 59.284 44.000 0.00 0.00 0.00 1.28
3642 16899 6.350277 GGAACGGAGGGAGTACATCTATAATG 60.350 46.154 0.00 0.00 0.00 1.90
3643 16900 4.463186 ACGGAGGGAGTACATCTATAATGC 59.537 45.833 0.00 0.00 0.00 3.56
3644 16901 4.462834 CGGAGGGAGTACATCTATAATGCA 59.537 45.833 0.00 0.00 0.00 3.96
3645 16902 5.393569 CGGAGGGAGTACATCTATAATGCAG 60.394 48.000 0.00 0.00 0.00 4.41
3646 16903 5.413309 AGGGAGTACATCTATAATGCAGC 57.587 43.478 0.00 0.00 0.00 5.25
3647 16904 4.223923 AGGGAGTACATCTATAATGCAGCC 59.776 45.833 0.00 0.00 0.00 4.85
3648 16905 4.177026 GGAGTACATCTATAATGCAGCCG 58.823 47.826 0.00 0.00 0.00 5.52
3659 16916 3.393089 AATGCAGCCGGAATAGACTAG 57.607 47.619 5.05 0.00 0.00 2.57
3662 16919 2.500098 TGCAGCCGGAATAGACTAGTTT 59.500 45.455 5.05 0.00 0.00 2.66
3727 16987 2.592102 ATGCACAATCTGGGAACTGT 57.408 45.000 0.00 0.00 0.00 3.55
3766 17026 2.094417 GCTCTTCCTGAAAAATCGACGG 59.906 50.000 0.00 0.00 0.00 4.79
3809 17069 2.218953 TTCGTTCTGTGAGAAAGCGT 57.781 45.000 0.00 0.00 35.75 5.07
3819 17079 3.223423 TGAGAAAGCGTCTGATCTCAC 57.777 47.619 15.24 0.00 42.36 3.51
3831 17091 4.759693 GTCTGATCTCACTATCGATGACCT 59.240 45.833 8.54 0.00 0.00 3.85
3909 17169 9.733556 TTTTGGAATCATTAGCTGTTCTACTTA 57.266 29.630 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.962356 CATGCCCACAAGGTCCAGTC 60.962 60.000 0.00 0.00 38.26 3.51
22 23 1.003118 GCTCATGGACAACCTACCACA 59.997 52.381 0.00 0.00 39.06 4.17
34 35 1.067295 ACTTCCCAAGTGCTCATGGA 58.933 50.000 11.45 0.00 41.01 3.41
122 124 2.552743 GGGGTCGAGGTTCTTGAAAAAG 59.447 50.000 0.00 0.00 0.00 2.27
132 134 3.705072 CACTATTAAGAGGGGTCGAGGTT 59.295 47.826 1.59 0.00 0.00 3.50
164 166 4.387256 TGTTTTGGTTTCTTTTGAGTTGCG 59.613 37.500 0.00 0.00 0.00 4.85
165 167 5.854431 TGTTTTGGTTTCTTTTGAGTTGC 57.146 34.783 0.00 0.00 0.00 4.17
167 169 8.445275 AGTTTTGTTTTGGTTTCTTTTGAGTT 57.555 26.923 0.00 0.00 0.00 3.01
254 256 7.016153 AGGTTTTATATGGAGACTGTTGACA 57.984 36.000 0.00 0.00 0.00 3.58
314 316 8.611654 ATTCTTGCTGAAAGTGCATTTAATTT 57.388 26.923 0.00 0.00 40.34 1.82
387 389 3.631686 CAGGGTCATGGATAATCGCAAAA 59.368 43.478 0.00 0.00 0.00 2.44
434 436 0.943835 TGTTGTCATGACCTGCGACG 60.944 55.000 22.85 0.00 32.17 5.12
451 453 5.592282 TCATGTTGTCCAAGTTAACACATGT 59.408 36.000 22.22 0.00 37.17 3.21
481 483 1.204941 CGGGTCATCTCTTTCGTCCTT 59.795 52.381 0.00 0.00 0.00 3.36
552 555 2.601240 TGGTGAAATGCTTGGATCCA 57.399 45.000 11.44 11.44 0.00 3.41
615 618 4.450419 CGTTGCTCAACAAGATCTCTCTTT 59.550 41.667 12.54 0.00 39.78 2.52
981 1419 1.856873 AATGGGGACTGGCCTGGAA 60.857 57.895 14.82 0.00 36.66 3.53
1577 2048 4.452733 CTCCAGTTCCCGGTCGCC 62.453 72.222 0.00 0.00 0.00 5.54
1605 2076 1.488705 TTCCAGAACGGGACAGGCAT 61.489 55.000 0.00 0.00 36.46 4.40
1612 2083 0.909623 GAAGGGATTCCAGAACGGGA 59.090 55.000 4.80 0.00 34.83 5.14
2189 2720 2.803492 GCTGGCCAGTATCTTAACCTCG 60.803 54.545 32.81 4.47 0.00 4.63
2675 3225 1.137872 CTGCTCTCCTCAAGCGGTAAT 59.862 52.381 0.00 0.00 42.83 1.89
2687 3237 1.886777 GCAAGATCGGCTGCTCTCC 60.887 63.158 0.00 0.00 0.00 3.71
2789 3340 4.665281 CAAGATCTTGCAGAGAACAGTG 57.335 45.455 21.96 0.00 38.06 3.66
2836 16058 9.209175 GTAGTTGAAAAACTCAGACATATCAGT 57.791 33.333 0.00 0.00 34.81 3.41
2837 16059 8.660373 GGTAGTTGAAAAACTCAGACATATCAG 58.340 37.037 0.00 0.00 34.81 2.90
3075 16332 1.454976 CCATCCTGATCCTGGCCAG 59.545 63.158 26.87 26.87 0.00 4.85
3102 16359 5.109903 GGACACAAGCAGAAGAACGTATAT 58.890 41.667 0.00 0.00 0.00 0.86
3103 16360 4.491676 GGACACAAGCAGAAGAACGTATA 58.508 43.478 0.00 0.00 0.00 1.47
3145 16402 8.511604 TCCCATTTTTCTTGCAAATAAACAAA 57.488 26.923 0.00 0.00 0.00 2.83
3164 16421 1.910671 AGCAATGTGCCATTTCCCATT 59.089 42.857 0.00 0.00 46.52 3.16
3316 16573 4.495422 ACCGACATAGAGTAAGCAAACAG 58.505 43.478 0.00 0.00 0.00 3.16
3345 16602 1.291132 GACCAATAGCTTCAGTCGGC 58.709 55.000 0.00 0.00 0.00 5.54
3445 16702 3.412386 AGCTGTAAGTGGCCTTTTGTAG 58.588 45.455 3.32 3.00 35.30 2.74
3503 16760 5.861251 CACTGTTGCAAAAACTGAAGTAACA 59.139 36.000 0.00 0.00 0.00 2.41
3517 16774 2.016318 CTGTTGAGTCCACTGTTGCAA 58.984 47.619 0.00 0.00 0.00 4.08
3520 16777 1.331756 GCACTGTTGAGTCCACTGTTG 59.668 52.381 4.39 3.04 0.00 3.33
3527 16784 2.080286 ACATACGCACTGTTGAGTCC 57.920 50.000 0.00 0.00 37.00 3.85
3533 16790 2.165845 GAGGGAGTACATACGCACTGTT 59.834 50.000 1.98 0.00 39.89 3.16
3535 16792 1.067212 GGAGGGAGTACATACGCACTG 59.933 57.143 1.98 0.00 39.89 3.66
3537 16794 0.030369 CGGAGGGAGTACATACGCAC 59.970 60.000 0.00 0.00 0.00 5.34
3538 16795 0.394762 ACGGAGGGAGTACATACGCA 60.395 55.000 0.00 0.00 0.00 5.24
3540 16797 1.336125 GGAACGGAGGGAGTACATACG 59.664 57.143 0.00 0.00 0.00 3.06
3543 16800 1.946984 TTGGAACGGAGGGAGTACAT 58.053 50.000 0.00 0.00 0.00 2.29
3545 16802 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
3547 16804 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
3548 16805 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
3549 16806 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
3550 16807 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3551 16808 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3552 16809 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
3553 16810 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
3554 16811 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
3555 16812 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
3556 16813 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
3557 16814 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
3558 16815 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
3559 16816 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
3560 16817 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
3561 16818 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
3562 16819 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
3563 16820 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
3564 16821 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
3565 16822 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
3566 16823 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
3567 16824 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
3568 16825 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
3569 16826 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
3570 16827 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
3583 16840 8.191446 TCGTCATGGTTTTAGTTCAAATTTGAA 58.809 29.630 26.01 26.01 44.31 2.69
3584 16841 7.708051 TCGTCATGGTTTTAGTTCAAATTTGA 58.292 30.769 16.91 16.91 34.92 2.69
3585 16842 7.647715 ACTCGTCATGGTTTTAGTTCAAATTTG 59.352 33.333 12.15 12.15 0.00 2.32
3586 16843 7.712797 ACTCGTCATGGTTTTAGTTCAAATTT 58.287 30.769 0.00 0.00 0.00 1.82
3587 16844 7.272037 ACTCGTCATGGTTTTAGTTCAAATT 57.728 32.000 0.00 0.00 0.00 1.82
3588 16845 6.877611 ACTCGTCATGGTTTTAGTTCAAAT 57.122 33.333 0.00 0.00 0.00 2.32
3589 16846 7.789273 TTACTCGTCATGGTTTTAGTTCAAA 57.211 32.000 0.00 0.00 0.00 2.69
3590 16847 7.972832 ATTACTCGTCATGGTTTTAGTTCAA 57.027 32.000 0.00 0.00 0.00 2.69
3591 16848 7.972832 AATTACTCGTCATGGTTTTAGTTCA 57.027 32.000 0.00 0.00 0.00 3.18
3592 16849 7.749126 CCAAATTACTCGTCATGGTTTTAGTTC 59.251 37.037 0.00 0.00 0.00 3.01
3593 16850 7.446013 TCCAAATTACTCGTCATGGTTTTAGTT 59.554 33.333 0.00 0.00 0.00 2.24
3594 16851 6.938030 TCCAAATTACTCGTCATGGTTTTAGT 59.062 34.615 0.00 0.00 0.00 2.24
3595 16852 7.372451 TCCAAATTACTCGTCATGGTTTTAG 57.628 36.000 0.00 0.00 0.00 1.85
3596 16853 7.571613 CGTTCCAAATTACTCGTCATGGTTTTA 60.572 37.037 0.00 0.00 0.00 1.52
3597 16854 6.443792 GTTCCAAATTACTCGTCATGGTTTT 58.556 36.000 0.00 0.00 0.00 2.43
3598 16855 5.334569 CGTTCCAAATTACTCGTCATGGTTT 60.335 40.000 0.00 0.00 0.00 3.27
3599 16856 4.153475 CGTTCCAAATTACTCGTCATGGTT 59.847 41.667 0.00 0.00 0.00 3.67
3600 16857 3.682858 CGTTCCAAATTACTCGTCATGGT 59.317 43.478 0.00 0.00 0.00 3.55
3601 16858 3.063452 CCGTTCCAAATTACTCGTCATGG 59.937 47.826 0.00 0.00 0.00 3.66
3602 16859 3.930229 TCCGTTCCAAATTACTCGTCATG 59.070 43.478 0.00 0.00 0.00 3.07
3603 16860 4.181578 CTCCGTTCCAAATTACTCGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
3604 16861 3.581755 CTCCGTTCCAAATTACTCGTCA 58.418 45.455 0.00 0.00 0.00 4.35
3605 16862 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
3606 16863 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
3607 16864 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3608 16865 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
3609 16866 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3610 16867 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3611 16868 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
3612 16869 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
3613 16870 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
3614 16871 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
3615 16872 1.829222 GATGTACTCCCTCCGTTCCAA 59.171 52.381 0.00 0.00 0.00 3.53
3616 16873 1.006758 AGATGTACTCCCTCCGTTCCA 59.993 52.381 0.00 0.00 0.00 3.53
3617 16874 1.777941 AGATGTACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
3618 16875 6.622549 CATTATAGATGTACTCCCTCCGTTC 58.377 44.000 0.00 0.00 0.00 3.95
3619 16876 5.047235 GCATTATAGATGTACTCCCTCCGTT 60.047 44.000 0.00 0.00 0.00 4.44
3620 16877 4.463186 GCATTATAGATGTACTCCCTCCGT 59.537 45.833 0.00 0.00 0.00 4.69
3621 16878 4.462834 TGCATTATAGATGTACTCCCTCCG 59.537 45.833 0.00 0.00 0.00 4.63
3622 16879 5.625656 GCTGCATTATAGATGTACTCCCTCC 60.626 48.000 0.00 0.00 0.00 4.30
3623 16880 5.415221 GCTGCATTATAGATGTACTCCCTC 58.585 45.833 0.00 0.00 0.00 4.30
3624 16881 4.223923 GGCTGCATTATAGATGTACTCCCT 59.776 45.833 0.50 0.00 0.00 4.20
3625 16882 4.508662 GGCTGCATTATAGATGTACTCCC 58.491 47.826 0.50 0.00 0.00 4.30
3626 16883 4.177026 CGGCTGCATTATAGATGTACTCC 58.823 47.826 0.50 0.00 0.00 3.85
3627 16884 4.082190 TCCGGCTGCATTATAGATGTACTC 60.082 45.833 0.50 0.00 0.00 2.59
3628 16885 3.832490 TCCGGCTGCATTATAGATGTACT 59.168 43.478 0.50 0.00 0.00 2.73
3629 16886 4.188247 TCCGGCTGCATTATAGATGTAC 57.812 45.455 0.50 0.00 0.00 2.90
3630 16887 4.882842 TTCCGGCTGCATTATAGATGTA 57.117 40.909 0.50 0.00 0.00 2.29
3631 16888 3.769739 TTCCGGCTGCATTATAGATGT 57.230 42.857 0.50 0.00 0.00 3.06
3632 16889 5.521735 GTCTATTCCGGCTGCATTATAGATG 59.478 44.000 0.50 0.00 30.11 2.90
3633 16890 5.423610 AGTCTATTCCGGCTGCATTATAGAT 59.576 40.000 0.50 0.00 30.11 1.98
3634 16891 4.772624 AGTCTATTCCGGCTGCATTATAGA 59.227 41.667 0.50 5.58 0.00 1.98
3635 16892 5.078411 AGTCTATTCCGGCTGCATTATAG 57.922 43.478 0.50 3.34 0.00 1.31
3636 16893 5.715279 ACTAGTCTATTCCGGCTGCATTATA 59.285 40.000 0.50 0.00 0.00 0.98
3637 16894 4.528596 ACTAGTCTATTCCGGCTGCATTAT 59.471 41.667 0.50 0.00 0.00 1.28
3638 16895 3.895656 ACTAGTCTATTCCGGCTGCATTA 59.104 43.478 0.50 0.00 0.00 1.90
3639 16896 2.700897 ACTAGTCTATTCCGGCTGCATT 59.299 45.455 0.50 0.00 0.00 3.56
3640 16897 2.320781 ACTAGTCTATTCCGGCTGCAT 58.679 47.619 0.50 0.00 0.00 3.96
3641 16898 1.776662 ACTAGTCTATTCCGGCTGCA 58.223 50.000 0.50 0.00 0.00 4.41
3642 16899 2.892784 AACTAGTCTATTCCGGCTGC 57.107 50.000 0.00 0.00 0.00 5.25
3643 16900 4.504858 ACAAAACTAGTCTATTCCGGCTG 58.495 43.478 0.00 0.00 0.00 4.85
3644 16901 4.820894 ACAAAACTAGTCTATTCCGGCT 57.179 40.909 0.00 0.00 0.00 5.52
3645 16902 4.331992 GGAACAAAACTAGTCTATTCCGGC 59.668 45.833 0.00 0.00 0.00 6.13
3646 16903 5.484715 TGGAACAAAACTAGTCTATTCCGG 58.515 41.667 16.97 0.00 37.53 5.14
3690 16950 8.972458 TTGTGCATATTTAGGCTGAGTAATTA 57.028 30.769 0.00 0.00 33.54 1.40
3727 16987 6.423905 GGAAGAGCGTATTATTTACAGATGCA 59.576 38.462 0.00 0.00 0.00 3.96
3766 17026 8.519492 AAACATTTGCAACAGAATACACATAC 57.481 30.769 0.00 0.00 0.00 2.39
3809 17069 4.979335 AGGTCATCGATAGTGAGATCAGA 58.021 43.478 0.00 0.00 37.40 3.27
3886 17146 9.383519 CTTTAAGTAGAACAGCTAATGATTCCA 57.616 33.333 0.00 0.00 0.00 3.53
3887 17147 9.601217 TCTTTAAGTAGAACAGCTAATGATTCC 57.399 33.333 0.00 0.00 0.00 3.01
3892 17152 7.559845 GCGATCTTTAAGTAGAACAGCTAATG 58.440 38.462 0.00 0.00 0.00 1.90
3896 17156 4.106197 CGCGATCTTTAAGTAGAACAGCT 58.894 43.478 0.00 0.00 0.00 4.24
3909 17169 2.094762 ACCTAAACAGCGCGATCTTT 57.905 45.000 12.10 6.56 0.00 2.52


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

AutoCloner maintained by Alex Coulton.