Multiple sequence alignment - TraesCS7A01G192500

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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 TraesCS7A01G192500 chr7A 100.000 3695 0 0 1 3695 150421480 150417786 0.000000e+00 6824.0
1 TraesCS7A01G192500 chr7A 87.330 221 21 7 618 835 608439029 608439245 2.850000e-61 246.0
2 TraesCS7A01G192500 chr7A 88.966 145 10 4 3 147 608438778 608438640 1.360000e-39 174.0
3 TraesCS7A01G192500 chr7A 92.174 115 7 2 3581 3695 150412922 150412810 1.060000e-35 161.0
4 TraesCS7A01G192500 chr7B 93.375 1434 61 14 1330 2749 112339146 112337733 0.000000e+00 2091.0
5 TraesCS7A01G192500 chr7B 86.771 446 22 9 897 1332 112339594 112339176 2.600000e-126 462.0
6 TraesCS7A01G192500 chr7B 84.122 296 16 16 3140 3416 112335510 112335227 1.320000e-64 257.0
7 TraesCS7A01G192500 chr7B 85.903 227 19 6 3461 3675 112335126 112334901 2.870000e-56 230.0
8 TraesCS7A01G192500 chr7B 100.000 48 0 0 3422 3469 112335197 112335150 5.080000e-14 89.8
9 TraesCS7A01G192500 chr4B 93.101 1435 63 16 1330 2749 402763722 402762309 0.000000e+00 2069.0
10 TraesCS7A01G192500 chr4B 89.234 418 18 6 892 1309 402764169 402763779 7.130000e-137 497.0
11 TraesCS7A01G192500 chr4B 81.864 590 40 24 3141 3675 402759324 402758747 5.670000e-118 435.0
12 TraesCS7A01G192500 chr7D 96.499 1171 41 0 1590 2760 150604049 150602879 0.000000e+00 1936.0
13 TraesCS7A01G192500 chr7D 87.414 437 29 12 892 1321 150604851 150604434 2.580000e-131 479.0
14 TraesCS7A01G192500 chr7D 81.495 562 45 27 2880 3418 150602667 150602142 1.240000e-109 407.0
15 TraesCS7A01G192500 chr7D 82.963 270 33 10 330 588 633184696 633184429 7.980000e-57 231.0
16 TraesCS7A01G192500 chr7D 84.279 229 34 2 619 846 633185265 633185492 4.800000e-54 222.0
17 TraesCS7A01G192500 chr7D 95.349 86 4 0 3461 3546 150602017 150601932 1.790000e-28 137.0
18 TraesCS7A01G192500 chr7D 97.436 39 1 0 3422 3460 150602120 150602082 2.380000e-07 67.6
19 TraesCS7A01G192500 chr4A 93.757 849 38 2 1 834 258630585 258629737 0.000000e+00 1260.0
20 TraesCS7A01G192500 chr2A 97.000 500 15 0 335 834 138107481 138107980 0.000000e+00 841.0
21 TraesCS7A01G192500 chr2A 96.000 350 14 0 1 350 138103792 138104141 1.490000e-158 569.0
22 TraesCS7A01G192500 chr5A 86.745 596 64 9 1 589 638644309 638643722 0.000000e+00 649.0
23 TraesCS7A01G192500 chr5A 87.500 224 26 2 618 841 594973214 594972993 1.320000e-64 257.0
24 TraesCS7A01G192500 chr5A 86.574 216 27 2 619 834 129253847 129253634 1.720000e-58 237.0
25 TraesCS7A01G192500 chr5A 78.610 374 53 17 230 589 324488722 324488362 4.800000e-54 222.0
26 TraesCS7A01G192500 chr5A 83.740 123 11 3 3573 3695 475652626 475652513 1.400000e-19 108.0
27 TraesCS7A01G192500 chr1D 81.834 578 75 19 3 569 41922898 41923456 3.360000e-125 459.0
28 TraesCS7A01G192500 chr1D 77.154 499 63 32 114 589 403043495 403043025 3.690000e-60 243.0
29 TraesCS7A01G192500 chr1B 81.217 575 78 17 3 568 62287408 62287961 1.580000e-118 436.0
30 TraesCS7A01G192500 chr2D 86.574 216 28 1 619 834 450570565 450570779 1.720000e-58 237.0
31 TraesCS7A01G192500 chr2D 82.963 270 33 10 330 588 450569992 450569725 7.980000e-57 231.0
32 TraesCS7A01G192500 chr2D 85.648 216 30 1 619 834 181209173 181208959 3.710000e-55 226.0
33 TraesCS7A01G192500 chr6A 85.321 218 30 2 618 834 573505864 573506080 1.340000e-54 224.0
34 TraesCS7A01G192500 chr6A 86.408 103 11 2 3573 3675 384087874 384087775 3.900000e-20 110.0
35 TraesCS7A01G192500 chr6A 81.061 132 15 5 3547 3673 315489722 315489596 3.040000e-16 97.1
36 TraesCS7A01G192500 chr1A 94.118 85 5 0 4 88 6920348 6920264 2.990000e-26 130.0
37 TraesCS7A01G192500 chr6D 82.069 145 11 10 3558 3695 114763931 114764067 3.900000e-20 110.0
38 TraesCS7A01G192500 chr3B 86.139 101 12 2 3573 3673 663553286 663553384 1.400000e-19 108.0
39 TraesCS7A01G192500 chr3D 83.471 121 11 3 3573 3693 395064228 395064117 1.820000e-18 104.0


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 TraesCS7A01G192500 chr7A 150417786 150421480 3694 True 6824.000000 6824 100.000000 1 3695 1 chr7A.!!$R2 3694
1 TraesCS7A01G192500 chr7B 112334901 112339594 4693 True 625.960000 2091 90.034200 897 3675 5 chr7B.!!$R1 2778
2 TraesCS7A01G192500 chr4B 402758747 402764169 5422 True 1000.333333 2069 88.066333 892 3675 3 chr4B.!!$R1 2783
3 TraesCS7A01G192500 chr7D 150601932 150604851 2919 True 605.320000 1936 91.638600 892 3546 5 chr7D.!!$R2 2654
4 TraesCS7A01G192500 chr4A 258629737 258630585 848 True 1260.000000 1260 93.757000 1 834 1 chr4A.!!$R1 833
5 TraesCS7A01G192500 chr2A 138103792 138107980 4188 False 705.000000 841 96.500000 1 834 2 chr2A.!!$F1 833
6 TraesCS7A01G192500 chr5A 638643722 638644309 587 True 649.000000 649 86.745000 1 589 1 chr5A.!!$R5 588
7 TraesCS7A01G192500 chr1D 41922898 41923456 558 False 459.000000 459 81.834000 3 569 1 chr1D.!!$F1 566
8 TraesCS7A01G192500 chr1B 62287408 62287961 553 False 436.000000 436 81.217000 3 568 1 chr1B.!!$F1 565

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
940 4324 0.034896 TTTCCTCTTGACTCGTGCCC 59.965 55.0 0.0 0.0 0.00 5.36 F
1335 4774 0.033011 TCTCCTAGTGGTCCTCTGGC 60.033 60.0 3.6 0.0 34.23 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 6037 1.110518 GGACGGTCCTCCTCATCTCC 61.111 65.000 19.92 0.0 32.53 3.71 R
3159 9458 1.001706 TCACCGAAGAACACGTCAGAG 60.002 52.381 0.00 0.0 0.00 3.35 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
140 143 7.940137 ACTTACATGTGGAGTGGTAAAACAATA 59.060 33.333 9.11 0.00 0.00 1.90
263 268 1.123861 TGTCACTCTGGCTGGCTCTT 61.124 55.000 2.00 0.00 0.00 2.85
296 301 1.792367 CACAAGATGCGTGTCTTTCGA 59.208 47.619 2.30 0.00 36.33 3.71
306 311 3.057019 CGTGTCTTTCGAAAGGTGATCA 58.943 45.455 31.82 20.79 36.67 2.92
661 4045 7.038154 TGTGCAAAAATTAAGTAAGCTGAGT 57.962 32.000 0.00 0.00 0.00 3.41
692 4076 0.179056 CTAACAGGTGGGGCCATACG 60.179 60.000 4.39 0.00 40.61 3.06
705 4089 0.038526 CCATACGCCCTGATACGTCC 60.039 60.000 0.00 0.00 42.46 4.79
757 4141 4.122776 GCGATGTCAAGTTAGATGACCAT 58.877 43.478 4.40 0.00 45.19 3.55
802 4186 5.518848 AGCATCAAACTGAACATTGAACA 57.481 34.783 0.00 0.00 38.88 3.18
834 4218 6.591750 ATGACTTAGGGTGATATTACCTCG 57.408 41.667 15.69 5.38 40.66 4.63
835 4219 5.452255 TGACTTAGGGTGATATTACCTCGT 58.548 41.667 15.69 8.11 40.66 4.18
836 4220 6.604171 TGACTTAGGGTGATATTACCTCGTA 58.396 40.000 15.69 3.81 40.66 3.43
837 4221 6.713903 TGACTTAGGGTGATATTACCTCGTAG 59.286 42.308 15.69 10.51 40.66 3.51
838 4222 6.845908 ACTTAGGGTGATATTACCTCGTAGA 58.154 40.000 15.69 0.00 40.66 2.59
839 4223 7.293073 ACTTAGGGTGATATTACCTCGTAGAA 58.707 38.462 15.69 2.25 40.66 2.10
840 4224 7.781693 ACTTAGGGTGATATTACCTCGTAGAAA 59.218 37.037 15.69 1.30 40.66 2.52
841 4225 8.537728 TTAGGGTGATATTACCTCGTAGAAAA 57.462 34.615 15.69 0.00 40.66 2.29
842 4226 7.427989 AGGGTGATATTACCTCGTAGAAAAA 57.572 36.000 15.69 0.00 40.66 1.94
843 4227 7.270779 AGGGTGATATTACCTCGTAGAAAAAC 58.729 38.462 15.69 0.00 40.66 2.43
844 4228 7.043565 GGGTGATATTACCTCGTAGAAAAACA 58.956 38.462 15.69 0.00 40.66 2.83
845 4229 7.713942 GGGTGATATTACCTCGTAGAAAAACAT 59.286 37.037 15.69 0.00 40.66 2.71
846 4230 9.106070 GGTGATATTACCTCGTAGAAAAACATT 57.894 33.333 9.39 0.00 37.74 2.71
862 4246 8.788409 GAAAAACATTCTTTTCTGTCCAGTAG 57.212 34.615 2.35 0.00 40.58 2.57
863 4247 8.519799 AAAAACATTCTTTTCTGTCCAGTAGA 57.480 30.769 0.00 0.00 0.00 2.59
864 4248 8.519799 AAAACATTCTTTTCTGTCCAGTAGAA 57.480 30.769 9.75 9.75 32.64 2.10
865 4249 8.519799 AAACATTCTTTTCTGTCCAGTAGAAA 57.480 30.769 10.73 0.00 41.11 2.52
866 4250 8.519799 AACATTCTTTTCTGTCCAGTAGAAAA 57.480 30.769 11.14 11.14 46.29 2.29
886 4270 5.428184 AAAAACATTTGTGTTCCCAAGGA 57.572 34.783 0.00 0.00 0.00 3.36
887 4271 5.428184 AAAACATTTGTGTTCCCAAGGAA 57.572 34.783 0.00 0.00 39.66 3.36
888 4272 5.428184 AAACATTTGTGTTCCCAAGGAAA 57.572 34.783 0.00 0.00 43.86 3.13
889 4273 4.670896 ACATTTGTGTTCCCAAGGAAAG 57.329 40.909 0.00 0.00 43.86 2.62
890 4274 3.387699 ACATTTGTGTTCCCAAGGAAAGG 59.612 43.478 0.00 0.00 43.86 3.11
923 4307 1.428869 CATCTCCCTCGATCCCCTTT 58.571 55.000 0.00 0.00 0.00 3.11
924 4308 1.346068 CATCTCCCTCGATCCCCTTTC 59.654 57.143 0.00 0.00 0.00 2.62
925 4309 0.398664 TCTCCCTCGATCCCCTTTCC 60.399 60.000 0.00 0.00 0.00 3.13
926 4310 0.399233 CTCCCTCGATCCCCTTTCCT 60.399 60.000 0.00 0.00 0.00 3.36
937 4321 1.338200 CCCCTTTCCTCTTGACTCGTG 60.338 57.143 0.00 0.00 0.00 4.35
938 4322 1.433534 CCTTTCCTCTTGACTCGTGC 58.566 55.000 0.00 0.00 0.00 5.34
939 4323 1.433534 CTTTCCTCTTGACTCGTGCC 58.566 55.000 0.00 0.00 0.00 5.01
940 4324 0.034896 TTTCCTCTTGACTCGTGCCC 59.965 55.000 0.00 0.00 0.00 5.36
941 4325 1.827399 TTCCTCTTGACTCGTGCCCC 61.827 60.000 0.00 0.00 0.00 5.80
986 4370 1.019278 CCCGTGCACGAACATAGCTT 61.019 55.000 39.10 0.00 43.02 3.74
992 4376 0.810031 CACGAACATAGCTTCCCCCG 60.810 60.000 0.00 0.00 0.00 5.73
1037 4421 1.915769 AGAGCCACCACCTCCAGAC 60.916 63.158 0.00 0.00 0.00 3.51
1047 4431 1.376466 CCTCCAGACCACCCACTTG 59.624 63.158 0.00 0.00 0.00 3.16
1078 4462 2.827652 GGAAGCAATTCCTCTCCTACG 58.172 52.381 0.00 0.00 38.09 3.51
1297 4699 1.071228 GGGAAACTCAAGGTACGGTGT 59.929 52.381 0.00 0.00 0.00 4.16
1309 4711 3.328637 AGGTACGGTGTTAGGTTTTCCAT 59.671 43.478 0.00 0.00 43.73 3.41
1321 4728 7.508977 TGTTAGGTTTTCCATTTGATTTCTCCT 59.491 33.333 0.00 0.00 43.73 3.69
1322 4729 9.020731 GTTAGGTTTTCCATTTGATTTCTCCTA 57.979 33.333 0.00 0.00 43.73 2.94
1335 4774 0.033011 TCTCCTAGTGGTCCTCTGGC 60.033 60.000 3.60 0.00 34.23 4.85
1346 4785 0.753262 TCCTCTGGCCGATTTAGCTC 59.247 55.000 0.00 0.00 0.00 4.09
1350 4789 0.179111 CTGGCCGATTTAGCTCGTCA 60.179 55.000 0.00 0.00 36.93 4.35
1366 4805 1.740025 CGTCAATTGAGCTTTCCCTCC 59.260 52.381 8.80 0.00 0.00 4.30
1427 4997 2.341846 TTCTTGCCGTTTTCTGGAGT 57.658 45.000 0.00 0.00 0.00 3.85
1428 4998 2.341846 TCTTGCCGTTTTCTGGAGTT 57.658 45.000 0.00 0.00 0.00 3.01
1429 4999 2.218603 TCTTGCCGTTTTCTGGAGTTC 58.781 47.619 0.00 0.00 0.00 3.01
1474 5044 7.232994 CGCTCTTGATAAGCTCAATAAATAGC 58.767 38.462 0.00 0.00 42.87 2.97
1505 5075 3.130516 TGGTTTTACGGTTGAAATGTGCA 59.869 39.130 0.00 0.00 0.00 4.57
1507 5077 4.208253 GGTTTTACGGTTGAAATGTGCAAG 59.792 41.667 0.00 0.00 0.00 4.01
1509 5079 4.902443 TTACGGTTGAAATGTGCAAGAA 57.098 36.364 0.00 0.00 0.00 2.52
1510 5080 3.791973 ACGGTTGAAATGTGCAAGAAA 57.208 38.095 0.00 0.00 0.00 2.52
1515 5085 2.674954 TGAAATGTGCAAGAAATGGCG 58.325 42.857 0.00 0.00 0.00 5.69
1573 5162 1.737793 GGGAGATTGTTTGGCGTAGTG 59.262 52.381 0.00 0.00 0.00 2.74
1579 5168 3.688694 TTGTTTGGCGTAGTGGATAGT 57.311 42.857 0.00 0.00 0.00 2.12
1580 5169 4.804868 TTGTTTGGCGTAGTGGATAGTA 57.195 40.909 0.00 0.00 0.00 1.82
1581 5170 4.114058 TGTTTGGCGTAGTGGATAGTAC 57.886 45.455 0.00 0.00 0.00 2.73
1582 5171 3.765511 TGTTTGGCGTAGTGGATAGTACT 59.234 43.478 0.00 0.00 31.76 2.73
1583 5172 4.142315 TGTTTGGCGTAGTGGATAGTACTC 60.142 45.833 0.00 0.00 31.76 2.59
1743 5332 2.438434 GGCACCATCAAGGACGGG 60.438 66.667 0.00 0.00 41.22 5.28
1986 5575 3.119096 GAGAACAGGTTCCGGCGC 61.119 66.667 0.00 0.00 40.33 6.53
2175 5764 2.047179 GTCGGGCACTGGTTCCTC 60.047 66.667 0.00 0.00 33.92 3.71
2429 6018 0.033405 TACAGGGAGGACGAGAAGGG 60.033 60.000 0.00 0.00 0.00 3.95
2448 6037 1.153549 GCTGGGCTACACGGAGAAG 60.154 63.158 0.00 0.00 0.00 2.85
2459 6048 1.680735 CACGGAGAAGGAGATGAGGAG 59.319 57.143 0.00 0.00 0.00 3.69
2676 6265 0.994995 CGTTCAACGAGATCCTGCTG 59.005 55.000 3.01 0.00 46.05 4.41
2713 6302 2.421314 CGCCAGTCCGCCATGATA 59.579 61.111 0.00 0.00 0.00 2.15
2720 6309 1.683917 AGTCCGCCATGATAGTGAGTC 59.316 52.381 0.00 0.00 0.00 3.36
2743 6332 1.756375 GACATGTCTGATCGTGCGCC 61.756 60.000 18.83 0.00 0.00 6.53
2828 6466 2.941720 GAGAGCATCATTGGTTCCAGTC 59.058 50.000 0.00 0.00 37.82 3.51
2830 6468 2.941720 GAGCATCATTGGTTCCAGTCTC 59.058 50.000 0.00 0.00 32.62 3.36
2831 6469 2.575279 AGCATCATTGGTTCCAGTCTCT 59.425 45.455 0.00 0.00 0.00 3.10
2850 6488 5.009854 CTCTGGAGAGAAGATTTGGAGAC 57.990 47.826 0.00 0.00 44.74 3.36
2864 6502 1.416401 TGGAGACTTTGGAGTGGTGTC 59.584 52.381 0.00 0.00 35.88 3.67
2870 6508 1.338020 CTTTGGAGTGGTGTCCTTTGC 59.662 52.381 0.00 0.00 37.52 3.68
2875 6513 2.027192 GGAGTGGTGTCCTTTGCTATGA 60.027 50.000 0.00 0.00 33.30 2.15
2878 6570 5.028549 AGTGGTGTCCTTTGCTATGATAG 57.971 43.478 0.00 0.00 0.00 2.08
2886 6578 7.011482 GTGTCCTTTGCTATGATAGGTTGTAAG 59.989 40.741 1.11 0.00 0.00 2.34
2906 6598 7.861630 TGTAAGTTTCAGAAACAGATTGCTAC 58.138 34.615 24.85 14.31 43.79 3.58
2907 6599 7.715249 TGTAAGTTTCAGAAACAGATTGCTACT 59.285 33.333 24.85 0.35 43.79 2.57
2908 6600 9.204570 GTAAGTTTCAGAAACAGATTGCTACTA 57.795 33.333 24.85 0.00 43.79 1.82
2978 6672 8.492782 TCTAGGAGTACTATATTATTAGCCGCT 58.507 37.037 0.00 0.00 0.00 5.52
2982 6676 7.701501 GGAGTACTATATTATTAGCCGCTGAAC 59.298 40.741 2.16 0.00 0.00 3.18
2988 6683 2.128771 ATTAGCCGCTGAACCAATGT 57.871 45.000 2.16 0.00 0.00 2.71
3054 6758 2.488153 CAAGAGGAACAATTTCGGGGAC 59.512 50.000 0.00 0.00 31.78 4.46
3079 6783 4.637483 TGTTTCTGAAAGTTCCAAGCAG 57.363 40.909 2.48 0.00 33.76 4.24
3083 6787 3.668447 TCTGAAAGTTCCAAGCAGCTAG 58.332 45.455 0.00 0.00 33.76 3.42
3084 6788 2.154462 TGAAAGTTCCAAGCAGCTAGC 58.846 47.619 6.62 6.62 46.19 3.42
3085 6789 6.556191 TCTGAAAGTTCCAAGCAGCTAGCA 62.556 45.833 18.83 0.00 40.13 3.49
3090 6794 5.138883 AGTTCCAAGCAGCTAGCAGAACT 62.139 47.826 18.83 18.91 46.44 3.01
3094 6798 3.776616 GCAGCTAGCAGAACTGGAT 57.223 52.632 18.83 0.00 44.79 3.41
3097 6801 2.938756 GCAGCTAGCAGAACTGGATGTT 60.939 50.000 18.83 0.00 44.44 2.71
3098 6802 3.341823 CAGCTAGCAGAACTGGATGTTT 58.658 45.455 18.83 0.00 38.37 2.83
3099 6803 3.373439 CAGCTAGCAGAACTGGATGTTTC 59.627 47.826 18.83 0.00 38.37 2.78
3100 6804 3.262915 AGCTAGCAGAACTGGATGTTTCT 59.737 43.478 18.83 0.00 39.30 2.52
3101 6805 3.373439 GCTAGCAGAACTGGATGTTTCTG 59.627 47.826 10.63 6.92 39.30 3.02
3102 6806 3.777106 AGCAGAACTGGATGTTTCTGA 57.223 42.857 14.08 0.00 39.30 3.27
3103 6807 4.090761 AGCAGAACTGGATGTTTCTGAA 57.909 40.909 14.08 0.00 39.30 3.02
3104 6808 4.464008 AGCAGAACTGGATGTTTCTGAAA 58.536 39.130 14.08 0.00 39.30 2.69
3109 6813 6.038603 CAGAACTGGATGTTTCTGAAAGTTCA 59.961 38.462 22.45 11.71 42.74 3.18
3116 6820 6.019559 GGATGTTTCTGAAAGTTCAAAGCAAC 60.020 38.462 2.48 0.00 36.64 4.17
3138 6842 4.213564 CAGCAGAACTGGAAATACTCCT 57.786 45.455 3.99 0.00 45.64 3.69
3159 9458 5.104900 TCCTATTTGGGAGCTGAAGTTCTAC 60.105 44.000 4.17 0.00 36.20 2.59
3175 9474 3.808116 TCTACTCTGACGTGTTCTTCG 57.192 47.619 0.00 0.00 0.00 3.79
3207 9506 4.348656 TCTAGATGCGATACGTTTGTCAC 58.651 43.478 0.00 0.00 0.00 3.67
3208 9507 3.232213 AGATGCGATACGTTTGTCACT 57.768 42.857 0.00 0.00 0.00 3.41
3209 9508 4.365899 AGATGCGATACGTTTGTCACTA 57.634 40.909 0.00 0.00 0.00 2.74
3210 9509 4.103357 AGATGCGATACGTTTGTCACTAC 58.897 43.478 0.00 0.00 0.00 2.73
3211 9510 3.285816 TGCGATACGTTTGTCACTACA 57.714 42.857 0.00 0.00 0.00 2.74
3212 9511 3.640592 TGCGATACGTTTGTCACTACAA 58.359 40.909 0.00 0.00 43.85 2.41
3213 9512 3.426191 TGCGATACGTTTGTCACTACAAC 59.574 43.478 0.00 0.00 45.18 3.32
3214 9513 3.671928 GCGATACGTTTGTCACTACAACT 59.328 43.478 0.00 0.00 45.18 3.16
3219 9518 5.961395 ACGTTTGTCACTACAACTACAAG 57.039 39.130 0.00 0.00 45.18 3.16
3244 9543 0.321387 TCCTCTACTGCTGTCGTCGT 60.321 55.000 0.00 0.00 0.00 4.34
3345 9645 2.627863 TTGCCAACATATTCGTGTGC 57.372 45.000 0.00 0.00 31.49 4.57
3348 9648 2.556189 TGCCAACATATTCGTGTGCTTT 59.444 40.909 0.00 0.00 31.49 3.51
3349 9649 3.753797 TGCCAACATATTCGTGTGCTTTA 59.246 39.130 0.00 0.00 31.49 1.85
3350 9650 4.397730 TGCCAACATATTCGTGTGCTTTAT 59.602 37.500 0.00 0.00 31.49 1.40
3351 9651 5.105957 TGCCAACATATTCGTGTGCTTTATT 60.106 36.000 0.00 0.00 31.49 1.40
3352 9652 5.455525 GCCAACATATTCGTGTGCTTTATTC 59.544 40.000 0.00 0.00 31.49 1.75
3354 9654 6.247903 CAACATATTCGTGTGCTTTATTCGT 58.752 36.000 0.00 0.00 31.49 3.85
3524 9932 3.596066 TTCGGCCTGCAGTCAGCTC 62.596 63.158 13.81 2.85 45.94 4.09
3553 9961 9.708222 GTCATACACTTTGCATTAATTAGTCTG 57.292 33.333 0.00 0.00 0.00 3.51
3554 9962 8.397906 TCATACACTTTGCATTAATTAGTCTGC 58.602 33.333 8.86 8.86 35.21 4.26
3557 9965 6.370442 ACACTTTGCATTAATTAGTCTGCGTA 59.630 34.615 10.36 0.00 37.44 4.42
3591 10001 9.793259 ATTTGTCCAAAGTTATCTCTACTTTCA 57.207 29.630 0.00 0.00 42.32 2.69
3593 10003 8.777865 TGTCCAAAGTTATCTCTACTTTCATG 57.222 34.615 0.00 0.00 42.32 3.07
3594 10004 8.593679 TGTCCAAAGTTATCTCTACTTTCATGA 58.406 33.333 0.00 0.00 42.32 3.07
3595 10005 8.874816 GTCCAAAGTTATCTCTACTTTCATGAC 58.125 37.037 0.00 0.00 42.32 3.06
3597 10007 8.660373 CCAAAGTTATCTCTACTTTCATGACAC 58.340 37.037 0.00 0.00 42.32 3.67
3598 10008 9.429359 CAAAGTTATCTCTACTTTCATGACACT 57.571 33.333 0.00 0.00 42.32 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.426504 ACATGACTTCTCATCCTGCTTAAG 58.573 41.667 0.00 0.00 34.65 1.85
67 68 8.500753 AAAACTTGTAAGTACTGTGTTGATGA 57.499 30.769 0.00 0.00 38.57 2.92
112 115 7.455058 TGTTTTACCACTCCACATGTAAGTAT 58.545 34.615 11.55 7.06 0.00 2.12
146 149 6.367983 ACCATCCTGATGTGCAATTAGTATT 58.632 36.000 6.40 0.00 37.11 1.89
263 268 3.193267 GCATCTTGTGGATACTGCCAAAA 59.807 43.478 0.00 0.00 40.20 2.44
661 4045 0.396435 CCTGTTAGTGAGTGGTGGCA 59.604 55.000 0.00 0.00 0.00 4.92
692 4076 2.585247 GTGCGGACGTATCAGGGC 60.585 66.667 0.00 0.00 0.00 5.19
705 4089 0.787908 GGTCACAAAATACGCGTGCG 60.788 55.000 24.59 13.39 46.03 5.34
784 4168 6.266168 ACTTGTGTTCAATGTTCAGTTTGA 57.734 33.333 0.00 0.00 32.82 2.69
802 4186 6.875972 ATCACCCTAAGTCATAGAACTTGT 57.124 37.500 0.00 0.00 39.74 3.16
819 4203 7.043565 TGTTTTTCTACGAGGTAATATCACCC 58.956 38.462 0.00 0.00 39.62 4.61
834 4218 8.406297 ACTGGACAGAAAAGAATGTTTTTCTAC 58.594 33.333 13.89 11.61 0.00 2.59
835 4219 8.519799 ACTGGACAGAAAAGAATGTTTTTCTA 57.480 30.769 13.89 2.80 0.00 2.10
836 4220 7.410120 ACTGGACAGAAAAGAATGTTTTTCT 57.590 32.000 6.29 10.21 0.00 2.52
837 4221 8.621286 TCTACTGGACAGAAAAGAATGTTTTTC 58.379 33.333 6.29 6.76 0.00 2.29
838 4222 8.519799 TCTACTGGACAGAAAAGAATGTTTTT 57.480 30.769 6.29 0.00 0.00 1.94
839 4223 8.519799 TTCTACTGGACAGAAAAGAATGTTTT 57.480 30.769 6.29 0.00 0.00 2.43
840 4224 8.519799 TTTCTACTGGACAGAAAAGAATGTTT 57.480 30.769 6.29 0.00 38.68 2.83
841 4225 8.519799 TTTTCTACTGGACAGAAAAGAATGTT 57.480 30.769 6.29 0.00 43.56 2.71
842 4226 8.519799 TTTTTCTACTGGACAGAAAAGAATGT 57.480 30.769 6.29 0.00 46.87 2.71
868 4252 3.387699 CCTTTCCTTGGGAACACAAATGT 59.612 43.478 0.00 0.00 41.87 2.71
869 4253 3.640967 TCCTTTCCTTGGGAACACAAATG 59.359 43.478 0.00 0.00 41.87 2.32
870 4254 3.922375 TCCTTTCCTTGGGAACACAAAT 58.078 40.909 0.00 0.00 41.87 2.32
871 4255 3.390175 TCCTTTCCTTGGGAACACAAA 57.610 42.857 0.00 0.00 41.87 2.83
872 4256 3.295973 CTTCCTTTCCTTGGGAACACAA 58.704 45.455 0.00 0.00 41.87 3.33
873 4257 2.424234 CCTTCCTTTCCTTGGGAACACA 60.424 50.000 0.00 0.00 41.87 3.72
874 4258 2.158519 TCCTTCCTTTCCTTGGGAACAC 60.159 50.000 0.00 0.00 41.87 3.32
875 4259 2.140224 TCCTTCCTTTCCTTGGGAACA 58.860 47.619 0.00 0.00 41.87 3.18
876 4260 2.971901 TCCTTCCTTTCCTTGGGAAC 57.028 50.000 0.00 0.00 41.87 3.62
877 4261 2.110011 CCTTCCTTCCTTTCCTTGGGAA 59.890 50.000 0.00 0.00 40.27 3.97
878 4262 1.710809 CCTTCCTTCCTTTCCTTGGGA 59.289 52.381 0.00 0.00 0.00 4.37
879 4263 1.710809 TCCTTCCTTCCTTTCCTTGGG 59.289 52.381 0.00 0.00 0.00 4.12
880 4264 3.746792 ATCCTTCCTTCCTTTCCTTGG 57.253 47.619 0.00 0.00 0.00 3.61
881 4265 4.019858 GGAATCCTTCCTTCCTTTCCTTG 58.980 47.826 0.00 0.00 46.57 3.61
882 4266 4.323569 GGAATCCTTCCTTCCTTTCCTT 57.676 45.455 0.00 0.00 46.57 3.36
905 4289 1.723288 GAAAGGGGATCGAGGGAGAT 58.277 55.000 0.00 0.00 0.00 2.75
923 4307 2.283529 GGGGCACGAGTCAAGAGGA 61.284 63.158 0.00 0.00 0.00 3.71
924 4308 2.266055 GGGGCACGAGTCAAGAGG 59.734 66.667 0.00 0.00 0.00 3.69
965 4349 1.813753 CTATGTTCGTGCACGGGGG 60.814 63.158 36.41 17.68 40.29 5.40
1037 4421 2.358737 GGAGCGACAAGTGGGTGG 60.359 66.667 0.00 0.00 0.00 4.61
1047 4431 2.543067 ATTGCTTCCTGGGGAGCGAC 62.543 60.000 11.77 0.00 31.21 5.19
1078 4462 1.829096 GGAGGAGGGCGTAGAGGAC 60.829 68.421 0.00 0.00 0.00 3.85
1297 4699 9.243105 CTAGGAGAAATCAAATGGAAAACCTAA 57.757 33.333 0.00 0.00 0.00 2.69
1309 4711 5.046304 CAGAGGACCACTAGGAGAAATCAAA 60.046 44.000 0.00 0.00 38.69 2.69
1321 4728 0.325296 AATCGGCCAGAGGACCACTA 60.325 55.000 2.24 0.00 0.00 2.74
1322 4729 1.201429 AAATCGGCCAGAGGACCACT 61.201 55.000 2.24 0.00 0.00 4.00
1335 4774 4.443850 CTCAATTGACGAGCTAAATCGG 57.556 45.455 3.38 0.00 46.91 4.18
1346 4785 1.740025 GGAGGGAAAGCTCAATTGACG 59.260 52.381 3.38 2.41 0.00 4.35
1350 4789 1.844687 GCTGGAGGGAAAGCTCAATT 58.155 50.000 0.00 0.00 36.47 2.32
1427 4997 9.257651 GAGCGCCTTTTATAAATACTTCTAGAA 57.742 33.333 2.29 4.81 0.00 2.10
1428 4998 8.639761 AGAGCGCCTTTTATAAATACTTCTAGA 58.360 33.333 2.29 0.00 0.00 2.43
1429 4999 8.819643 AGAGCGCCTTTTATAAATACTTCTAG 57.180 34.615 2.29 0.00 0.00 2.43
1474 5044 1.504446 CGTAAAACCACCATGGCCG 59.496 57.895 13.04 4.10 42.67 6.13
1505 5075 3.900941 GTGAAATCACACGCCATTTCTT 58.099 40.909 8.63 0.00 45.75 2.52
1537 5107 0.544120 TCCCAGGAACCCAAAATGCC 60.544 55.000 0.00 0.00 0.00 4.40
1579 5168 7.970102 ACAAGGAAACATTTAGTACTGGAGTA 58.030 34.615 5.39 0.00 0.00 2.59
1580 5169 6.838382 ACAAGGAAACATTTAGTACTGGAGT 58.162 36.000 5.39 0.00 0.00 3.85
1581 5170 6.090898 CGACAAGGAAACATTTAGTACTGGAG 59.909 42.308 5.39 0.00 0.00 3.86
1582 5171 5.929992 CGACAAGGAAACATTTAGTACTGGA 59.070 40.000 5.39 0.00 0.00 3.86
1583 5172 5.699458 ACGACAAGGAAACATTTAGTACTGG 59.301 40.000 5.39 0.00 0.00 4.00
1600 5189 2.280524 TCGGGCCAACACGACAAG 60.281 61.111 4.39 0.00 33.69 3.16
1966 5555 1.376037 GCCGGAACCTGTTCTCCTG 60.376 63.158 5.05 0.00 39.45 3.86
1986 5575 3.003173 TGCTCCCGGAAGACCCAG 61.003 66.667 0.73 0.00 34.14 4.45
2175 5764 3.151710 TGGTAGACGCCGGGGATG 61.152 66.667 27.23 0.00 0.00 3.51
2264 5853 3.423154 GCACGGCCTCCTTGAACG 61.423 66.667 0.00 0.00 0.00 3.95
2325 5914 3.414700 GTGACCGCGACCAGCTTG 61.415 66.667 8.23 0.00 45.59 4.01
2429 6018 2.579684 CTTCTCCGTGTAGCCCAGCC 62.580 65.000 0.00 0.00 0.00 4.85
2448 6037 1.110518 GGACGGTCCTCCTCATCTCC 61.111 65.000 19.92 0.00 32.53 3.71
2649 6238 1.681825 TCTCGTTGAACGTGTCGATG 58.318 50.000 17.86 0.00 43.14 3.84
2713 6302 1.815613 CAGACATGTCTCCGACTCACT 59.184 52.381 25.58 0.00 37.98 3.41
2720 6309 1.832600 CACGATCAGACATGTCTCCG 58.167 55.000 25.58 26.35 37.98 4.63
2743 6332 7.301054 AGCAAAAGAATCATTAACTGAACTCG 58.699 34.615 0.00 0.00 37.44 4.18
2750 6339 5.163854 CCGACGAGCAAAAGAATCATTAACT 60.164 40.000 0.00 0.00 0.00 2.24
2828 6466 4.711355 AGTCTCCAAATCTTCTCTCCAGAG 59.289 45.833 0.00 0.00 43.36 3.35
2830 6468 5.419239 AAGTCTCCAAATCTTCTCTCCAG 57.581 43.478 0.00 0.00 0.00 3.86
2831 6469 5.513788 CCAAAGTCTCCAAATCTTCTCTCCA 60.514 44.000 0.00 0.00 0.00 3.86
2837 6475 4.457257 CCACTCCAAAGTCTCCAAATCTTC 59.543 45.833 0.00 0.00 31.71 2.87
2838 6476 4.141158 ACCACTCCAAAGTCTCCAAATCTT 60.141 41.667 0.00 0.00 31.71 2.40
2840 6478 3.503748 CACCACTCCAAAGTCTCCAAATC 59.496 47.826 0.00 0.00 31.71 2.17
2841 6479 3.117512 ACACCACTCCAAAGTCTCCAAAT 60.118 43.478 0.00 0.00 31.71 2.32
2842 6480 2.241176 ACACCACTCCAAAGTCTCCAAA 59.759 45.455 0.00 0.00 31.71 3.28
2843 6481 1.843851 ACACCACTCCAAAGTCTCCAA 59.156 47.619 0.00 0.00 31.71 3.53
2844 6482 1.416401 GACACCACTCCAAAGTCTCCA 59.584 52.381 0.00 0.00 31.71 3.86
2845 6483 1.270893 GGACACCACTCCAAAGTCTCC 60.271 57.143 0.00 0.00 31.71 3.71
2846 6484 1.694696 AGGACACCACTCCAAAGTCTC 59.305 52.381 0.00 0.00 31.71 3.36
2847 6485 1.807814 AGGACACCACTCCAAAGTCT 58.192 50.000 0.00 0.00 31.71 3.24
2848 6486 2.618709 CAAAGGACACCACTCCAAAGTC 59.381 50.000 0.00 0.00 31.71 3.01
2849 6487 2.654863 CAAAGGACACCACTCCAAAGT 58.345 47.619 0.00 0.00 35.60 2.66
2850 6488 1.338020 GCAAAGGACACCACTCCAAAG 59.662 52.381 0.00 0.00 31.94 2.77
2864 6502 7.865706 AACTTACAACCTATCATAGCAAAGG 57.134 36.000 0.00 0.00 35.14 3.11
2875 6513 9.574516 AATCTGTTTCTGAAACTTACAACCTAT 57.425 29.630 27.75 9.88 41.90 2.57
2878 6570 6.417930 GCAATCTGTTTCTGAAACTTACAACC 59.582 38.462 27.75 11.63 41.90 3.77
2886 6578 7.659652 ACTAGTAGCAATCTGTTTCTGAAAC 57.340 36.000 22.94 22.94 41.73 2.78
2906 6598 5.473504 AGCAAAACACAACCCTGATAACTAG 59.526 40.000 0.00 0.00 0.00 2.57
2907 6599 5.381757 AGCAAAACACAACCCTGATAACTA 58.618 37.500 0.00 0.00 0.00 2.24
2908 6600 4.215109 AGCAAAACACAACCCTGATAACT 58.785 39.130 0.00 0.00 0.00 2.24
2951 6643 9.287373 GCGGCTAATAATATAGTACTCCTAGAT 57.713 37.037 0.00 0.00 0.00 1.98
2954 6646 8.270030 TCAGCGGCTAATAATATAGTACTCCTA 58.730 37.037 0.26 0.00 0.00 2.94
2955 6647 7.117397 TCAGCGGCTAATAATATAGTACTCCT 58.883 38.462 0.26 0.00 0.00 3.69
2956 6648 7.330900 TCAGCGGCTAATAATATAGTACTCC 57.669 40.000 0.26 0.00 0.00 3.85
2957 6649 7.701501 GGTTCAGCGGCTAATAATATAGTACTC 59.298 40.741 0.26 0.00 0.00 2.59
2958 6650 7.177921 TGGTTCAGCGGCTAATAATATAGTACT 59.822 37.037 0.26 0.00 0.00 2.73
2959 6651 7.318141 TGGTTCAGCGGCTAATAATATAGTAC 58.682 38.462 0.26 0.00 0.00 2.73
2960 6652 7.470935 TGGTTCAGCGGCTAATAATATAGTA 57.529 36.000 0.26 0.00 0.00 1.82
2961 6653 6.354794 TGGTTCAGCGGCTAATAATATAGT 57.645 37.500 0.26 0.00 0.00 2.12
2962 6654 7.334421 ACATTGGTTCAGCGGCTAATAATATAG 59.666 37.037 0.26 0.00 0.00 1.31
2963 6655 7.165485 ACATTGGTTCAGCGGCTAATAATATA 58.835 34.615 0.26 0.00 0.00 0.86
2964 6656 6.003950 ACATTGGTTCAGCGGCTAATAATAT 58.996 36.000 0.26 0.00 0.00 1.28
2965 6657 5.373222 ACATTGGTTCAGCGGCTAATAATA 58.627 37.500 0.26 0.00 0.00 0.98
2966 6658 4.207165 ACATTGGTTCAGCGGCTAATAAT 58.793 39.130 0.26 0.00 0.00 1.28
2978 6672 4.706476 GGAAGATGATTGGACATTGGTTCA 59.294 41.667 0.00 0.00 0.00 3.18
2982 6676 3.887716 GAGGGAAGATGATTGGACATTGG 59.112 47.826 0.00 0.00 0.00 3.16
2988 6683 3.263170 TGAAACGAGGGAAGATGATTGGA 59.737 43.478 0.00 0.00 0.00 3.53
3054 6758 5.218139 GCTTGGAACTTTCAGAAACATCAG 58.782 41.667 0.00 0.00 0.00 2.90
3079 6783 3.373439 CAGAAACATCCAGTTCTGCTAGC 59.627 47.826 8.10 8.10 40.26 3.42
3083 6787 4.276926 ACTTTCAGAAACATCCAGTTCTGC 59.723 41.667 8.24 0.00 40.26 4.26
3084 6788 6.038603 TGAACTTTCAGAAACATCCAGTTCTG 59.961 38.462 17.94 7.01 39.49 3.02
3085 6789 6.122277 TGAACTTTCAGAAACATCCAGTTCT 58.878 36.000 17.94 0.00 39.49 3.01
3087 6791 6.773976 TTGAACTTTCAGAAACATCCAGTT 57.226 33.333 0.00 0.00 39.34 3.16
3090 6794 5.126869 TGCTTTGAACTTTCAGAAACATCCA 59.873 36.000 0.00 0.00 38.61 3.41
3091 6795 5.591099 TGCTTTGAACTTTCAGAAACATCC 58.409 37.500 0.00 0.00 38.61 3.51
3093 6797 5.812127 GGTTGCTTTGAACTTTCAGAAACAT 59.188 36.000 0.00 0.00 38.61 2.71
3094 6798 5.167845 GGTTGCTTTGAACTTTCAGAAACA 58.832 37.500 0.00 0.00 38.61 2.83
3097 6801 4.677779 GCTGGTTGCTTTGAACTTTCAGAA 60.678 41.667 0.00 0.00 37.31 3.02
3098 6802 3.181487 GCTGGTTGCTTTGAACTTTCAGA 60.181 43.478 0.00 0.00 37.31 3.27
3099 6803 3.118542 GCTGGTTGCTTTGAACTTTCAG 58.881 45.455 0.00 0.00 37.31 3.02
3100 6804 2.495270 TGCTGGTTGCTTTGAACTTTCA 59.505 40.909 0.00 0.00 43.37 2.69
3101 6805 3.118542 CTGCTGGTTGCTTTGAACTTTC 58.881 45.455 0.00 0.00 43.37 2.62
3102 6806 2.760092 TCTGCTGGTTGCTTTGAACTTT 59.240 40.909 0.00 0.00 43.37 2.66
3103 6807 2.378038 TCTGCTGGTTGCTTTGAACTT 58.622 42.857 0.00 0.00 43.37 2.66
3104 6808 2.057137 TCTGCTGGTTGCTTTGAACT 57.943 45.000 0.00 0.00 43.37 3.01
3136 6840 4.227864 AGAACTTCAGCTCCCAAATAGG 57.772 45.455 0.00 0.00 37.03 2.57
3137 6841 5.983540 AGTAGAACTTCAGCTCCCAAATAG 58.016 41.667 0.00 0.00 0.00 1.73
3138 6842 5.721960 AGAGTAGAACTTCAGCTCCCAAATA 59.278 40.000 8.24 0.00 0.00 1.40
3148 9447 4.491234 ACACGTCAGAGTAGAACTTCAG 57.509 45.455 0.00 0.00 0.00 3.02
3159 9458 1.001706 TCACCGAAGAACACGTCAGAG 60.002 52.381 0.00 0.00 0.00 3.35
3175 9474 5.795939 CGTATCGCATCTAGATTTACTCACC 59.204 44.000 1.33 0.00 0.00 4.02
3207 9506 3.442076 AGGACCCCTCTTGTAGTTGTAG 58.558 50.000 0.00 0.00 0.00 2.74
3208 9507 3.438183 GAGGACCCCTCTTGTAGTTGTA 58.562 50.000 5.78 0.00 46.41 2.41
3209 9508 2.258109 GAGGACCCCTCTTGTAGTTGT 58.742 52.381 5.78 0.00 46.41 3.32
3244 9543 2.857575 TAGAGAGCGCCACCGACGTA 62.858 60.000 2.29 0.00 36.29 3.57
3262 9561 1.399440 GTCCACACGTATCTGCGACTA 59.601 52.381 0.00 0.00 35.59 2.59
3285 9584 4.827087 CAGATGCCTCGCCGCAGT 62.827 66.667 2.72 0.00 43.26 4.40
3286 9585 3.804153 ATCAGATGCCTCGCCGCAG 62.804 63.158 2.72 0.00 43.26 5.18
3287 9586 3.797225 GATCAGATGCCTCGCCGCA 62.797 63.158 0.00 0.00 44.35 5.69
3288 9587 2.985512 AAGATCAGATGCCTCGCCGC 62.986 60.000 0.00 0.00 0.00 6.53
3332 9632 5.579119 TGACGAATAAAGCACACGAATATGT 59.421 36.000 0.00 0.00 0.00 2.29
3345 9645 2.223340 GCAGGCCACATGACGAATAAAG 60.223 50.000 5.01 0.00 0.00 1.85
3348 9648 0.463654 GGCAGGCCACATGACGAATA 60.464 55.000 5.01 0.00 35.81 1.75
3349 9649 1.750399 GGCAGGCCACATGACGAAT 60.750 57.895 5.01 0.00 35.81 3.34
3350 9650 2.359850 GGCAGGCCACATGACGAA 60.360 61.111 5.01 0.00 35.81 3.85
3418 9738 4.320202 GCAAAAGTCAAAAGCGGTCAGATA 60.320 41.667 0.00 0.00 0.00 1.98
3419 9739 3.550842 GCAAAAGTCAAAAGCGGTCAGAT 60.551 43.478 0.00 0.00 0.00 2.90
3565 9975 9.793259 TGAAAGTAGAGATAACTTTGGACAAAT 57.207 29.630 5.98 0.00 44.94 2.32


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

AutoCloner maintained by Alex Coulton.