Multiple sequence alignment - TraesCS2B01G373100

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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 TraesCS2B01G373100 chr2B 100.000 6123 0 0 1 6123 531713700 531719822 0.000000e+00 11308.0
1 TraesCS2B01G373100 chr2D 95.648 4251 141 26 557 4786 451455022 451459249 0.000000e+00 6785.0
2 TraesCS2B01G373100 chr2D 93.215 1297 63 12 4850 6123 451459248 451460542 0.000000e+00 1884.0
3 TraesCS2B01G373100 chr2D 89.873 79 2 2 4785 4858 376701261 376701184 5.050000e-16 97.1
4 TraesCS2B01G373100 chr2A 94.436 2678 110 23 560 3225 597853154 597850504 0.000000e+00 4084.0
5 TraesCS2B01G373100 chr2A 94.887 1193 52 7 3505 4691 597850035 597848846 0.000000e+00 1857.0
6 TraesCS2B01G373100 chr2A 89.430 1211 95 21 4942 6123 597847137 597845931 0.000000e+00 1496.0
7 TraesCS2B01G373100 chr2A 96.853 286 9 0 3223 3508 597850423 597850138 4.290000e-131 479.0
8 TraesCS2B01G373100 chr2A 90.654 107 4 5 4650 4750 597848855 597848749 2.980000e-28 137.0
9 TraesCS2B01G373100 chr2A 90.789 76 3 2 4782 4854 90424877 90424951 1.400000e-16 99.0
10 TraesCS2B01G373100 chr2A 84.158 101 10 5 4762 4859 771521407 771521504 6.530000e-15 93.5
11 TraesCS2B01G373100 chr4D 91.549 568 32 9 1 557 427034656 427034094 0.000000e+00 769.0
12 TraesCS2B01G373100 chr3A 89.876 563 32 15 4 556 440609765 440610312 0.000000e+00 701.0
13 TraesCS2B01G373100 chr3A 94.030 67 3 1 4785 4851 621834341 621834406 3.910000e-17 100.0
14 TraesCS2B01G373100 chr5B 90.093 535 45 7 24 553 263551092 263551623 0.000000e+00 688.0
15 TraesCS2B01G373100 chr5B 86.847 555 61 9 1 549 36378099 36377551 1.460000e-170 610.0
16 TraesCS2B01G373100 chr3B 88.351 558 56 8 2 555 151575012 151574460 0.000000e+00 662.0
17 TraesCS2B01G373100 chr7A 87.522 561 50 8 1 556 664235200 664234655 1.120000e-176 630.0
18 TraesCS2B01G373100 chr7A 91.346 104 9 0 5042 5145 40256687 40256790 6.400000e-30 143.0
19 TraesCS2B01G373100 chr7D 86.988 561 55 13 4 557 110603170 110602621 3.140000e-172 616.0
20 TraesCS2B01G373100 chr7D 91.346 104 7 1 5042 5145 40343906 40344007 2.300000e-29 141.0
21 TraesCS2B01G373100 chr7D 81.034 174 30 3 5242 5413 40344010 40344182 1.070000e-27 135.0
22 TraesCS2B01G373100 chr7B 91.150 452 32 6 2 451 710152520 710152965 1.890000e-169 606.0
23 TraesCS2B01G373100 chr7B 88.608 79 5 3 4778 4856 296330896 296330822 6.530000e-15 93.5
24 TraesCS2B01G373100 chr1A 88.987 454 37 11 110 556 572242023 572242470 3.230000e-152 549.0
25 TraesCS2B01G373100 chr5D 87.742 155 17 1 2853 3007 139954118 139954270 4.880000e-41 180.0
26 TraesCS2B01G373100 chr5D 95.652 69 3 0 4783 4851 41140037 41139969 1.800000e-20 111.0
27 TraesCS2B01G373100 chr5D 90.667 75 4 3 4784 4858 39033247 39033176 5.050000e-16 97.1
28 TraesCS2B01G373100 chr5A 95.522 67 2 1 4785 4851 422040358 422040423 8.390000e-19 106.0
29 TraesCS2B01G373100 chr5A 94.118 68 3 1 4785 4851 624782050 624782117 1.090000e-17 102.0


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 TraesCS2B01G373100 chr2B 531713700 531719822 6122 False 11308.0 11308 100.0000 1 6123 1 chr2B.!!$F1 6122
1 TraesCS2B01G373100 chr2D 451455022 451460542 5520 False 4334.5 6785 94.4315 557 6123 2 chr2D.!!$F1 5566
2 TraesCS2B01G373100 chr2A 597845931 597853154 7223 True 1610.6 4084 93.2520 560 6123 5 chr2A.!!$R1 5563
3 TraesCS2B01G373100 chr4D 427034094 427034656 562 True 769.0 769 91.5490 1 557 1 chr4D.!!$R1 556
4 TraesCS2B01G373100 chr3A 440609765 440610312 547 False 701.0 701 89.8760 4 556 1 chr3A.!!$F1 552
5 TraesCS2B01G373100 chr5B 263551092 263551623 531 False 688.0 688 90.0930 24 553 1 chr5B.!!$F1 529
6 TraesCS2B01G373100 chr5B 36377551 36378099 548 True 610.0 610 86.8470 1 549 1 chr5B.!!$R1 548
7 TraesCS2B01G373100 chr3B 151574460 151575012 552 True 662.0 662 88.3510 2 555 1 chr3B.!!$R1 553
8 TraesCS2B01G373100 chr7A 664234655 664235200 545 True 630.0 630 87.5220 1 556 1 chr7A.!!$R1 555
9 TraesCS2B01G373100 chr7D 110602621 110603170 549 True 616.0 616 86.9880 4 557 1 chr7D.!!$R1 553

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
718 754 1.447945 GCCTCAGCTTGTTCTTCTCC 58.552 55.000 0.00 0.0 35.50 3.71 F
1137 1173 0.458669 TCCGGGAGCTCGTGATTTAC 59.541 55.000 7.83 0.0 0.00 2.01 F
1140 1176 0.539986 GGGAGCTCGTGATTTACCCA 59.460 55.000 7.83 0.0 36.27 4.51 F
1850 1890 0.676466 CCCGCATTGTTGGTCAGCTA 60.676 55.000 0.00 0.0 0.00 3.32 F
2088 2130 1.673665 GGATGCCATCGATCCAGCC 60.674 63.158 12.50 12.5 39.49 4.85 F
2326 2371 2.360165 GGATGCCTGCATAAAACTGAGG 59.640 50.000 4.30 0.0 36.70 3.86 F
3954 4191 2.972713 TGCCACAGTAGGAGAAAGACTT 59.027 45.455 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2130 0.035458 AACGTCCTGGCCTTCTCAAG 59.965 55.000 3.32 0.00 0.00 3.02 R
2326 2371 1.242076 ATCAAGCAGTGGCAAGTGAC 58.758 50.000 0.00 0.00 44.61 3.67 R
2418 2463 6.414408 AGACTTCAAGCAAATTCGTCATAG 57.586 37.500 0.00 0.00 0.00 2.23 R
3841 4078 1.153309 TAGCATCTCGACGGACGGA 60.153 57.895 0.00 0.00 42.82 4.69 R
3954 4191 7.719193 TCCATTTCAGTCAACAAAGTTGATAGA 59.281 33.333 14.77 12.55 0.00 1.98 R
4186 4423 0.249238 GTGCATGCTAGAGAGGGACG 60.249 60.000 20.33 0.00 0.00 4.79 R
5549 7332 0.880278 CGGCATAATCACCCCGACAG 60.880 60.000 0.00 0.00 43.20 3.51 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
59 60 8.661352 AACCTGAAAAACTATTGAAAACATGG 57.339 30.769 0.00 0.00 0.00 3.66
64 65 9.311916 TGAAAAACTATTGAAAACATGGACAAG 57.688 29.630 0.00 0.00 0.00 3.16
66 67 9.883142 AAAAACTATTGAAAACATGGACAAGAA 57.117 25.926 0.00 0.00 0.00 2.52
81 82 8.838365 CATGGACAAGAATTTGAAATTCCAAAA 58.162 29.630 22.94 8.38 38.48 2.44
82 83 8.207521 TGGACAAGAATTTGAAATTCCAAAAC 57.792 30.769 22.94 13.54 39.20 2.43
83 84 7.826252 TGGACAAGAATTTGAAATTCCAAAACA 59.174 29.630 22.94 15.48 39.20 2.83
530 562 2.026301 CGAAGCCCCGACGAGATC 59.974 66.667 0.00 0.00 0.00 2.75
534 566 3.607661 GCCCCGACGAGATCCTCC 61.608 72.222 0.00 0.00 0.00 4.30
678 711 2.224159 GCCCTTCACCCTCCTCACA 61.224 63.158 0.00 0.00 0.00 3.58
718 754 1.447945 GCCTCAGCTTGTTCTTCTCC 58.552 55.000 0.00 0.00 35.50 3.71
727 763 2.035442 GTTCTTCTCCGTGGCAGCC 61.035 63.158 3.66 3.66 0.00 4.85
771 807 4.974438 AGGAACCTCCCCACGGCA 62.974 66.667 0.00 0.00 37.19 5.69
857 893 2.760385 GGCGTCCTAGGGCTCACT 60.760 66.667 12.53 0.00 0.00 3.41
880 916 1.553248 GGTTTATCCCTGGTTTTGGCC 59.447 52.381 0.00 0.00 0.00 5.36
883 919 1.502527 TATCCCTGGTTTTGGCCCGT 61.503 55.000 0.00 0.00 0.00 5.28
948 984 4.980805 TCCCGCCTGCACGACAAC 62.981 66.667 0.00 0.00 34.06 3.32
1113 1149 0.610785 GGAACCGAATGGCCCTTCAA 60.611 55.000 19.27 0.00 39.70 2.69
1137 1173 0.458669 TCCGGGAGCTCGTGATTTAC 59.541 55.000 7.83 0.00 0.00 2.01
1140 1176 0.539986 GGGAGCTCGTGATTTACCCA 59.460 55.000 7.83 0.00 36.27 4.51
1152 1188 2.994186 TTTACCCATTCCTCTACGCC 57.006 50.000 0.00 0.00 0.00 5.68
1207 1243 1.552792 CTCCTGTCCCCTTCTCTTCAC 59.447 57.143 0.00 0.00 0.00 3.18
1235 1271 2.346803 CAATTTCATCGTCTGACGGGT 58.653 47.619 27.69 15.36 42.81 5.28
1249 1285 3.469739 TGACGGGTCTTCTTTAACCAAC 58.530 45.455 0.00 0.00 37.28 3.77
1255 1291 4.885325 GGGTCTTCTTTAACCAACTTGTGA 59.115 41.667 0.00 0.00 37.28 3.58
1280 1316 2.405805 TGCTGTGTGTGCTTGCGTT 61.406 52.632 0.00 0.00 0.00 4.84
1385 1422 2.869233 ACAAATGTTGACCAGTGTGC 57.131 45.000 0.00 0.00 0.00 4.57
1410 1447 8.518702 GCTTCTTAGGATTGATTCTTGTTCTTT 58.481 33.333 0.00 0.00 0.00 2.52
1537 1574 9.817809 TTAGTCTTAATCTGCCAAATAGTACTG 57.182 33.333 5.39 0.00 0.00 2.74
1588 1628 6.585416 TCATCATTAAGTGCTCTAATCTGCA 58.415 36.000 0.00 0.00 36.79 4.41
1687 1727 1.404181 GCATACTCTCAGGCGTCACAA 60.404 52.381 0.00 0.00 0.00 3.33
1850 1890 0.676466 CCCGCATTGTTGGTCAGCTA 60.676 55.000 0.00 0.00 0.00 3.32
1889 1929 7.661127 TGGAAATAAGAAATCGTCGAAGAAA 57.339 32.000 4.85 0.00 39.69 2.52
1913 1953 1.937223 CCTCACGTAGTTGTTGTTGCA 59.063 47.619 0.00 0.00 41.61 4.08
1953 1993 1.737793 CGCCAGTTGGAGGATTGTAAC 59.262 52.381 1.45 0.00 37.39 2.50
2044 2086 9.261180 CATGAGAAGTAGTTCTACTGAAACAAA 57.739 33.333 12.87 0.00 43.50 2.83
2088 2130 1.673665 GGATGCCATCGATCCAGCC 60.674 63.158 12.50 12.50 39.49 4.85
2326 2371 2.360165 GGATGCCTGCATAAAACTGAGG 59.640 50.000 4.30 0.00 36.70 3.86
2418 2463 5.039333 GCATTGTCTGAATCCATTAACTGC 58.961 41.667 0.00 0.00 0.00 4.40
2773 2818 8.458843 GTGAGATATGTTTTGCTTTAGGCTTTA 58.541 33.333 0.00 0.00 42.39 1.85
2784 2829 9.781633 TTTGCTTTAGGCTTTATTATATACGGA 57.218 29.630 0.00 0.00 42.39 4.69
2785 2830 9.953565 TTGCTTTAGGCTTTATTATATACGGAT 57.046 29.630 0.00 0.00 42.39 4.18
2786 2831 9.595823 TGCTTTAGGCTTTATTATATACGGATC 57.404 33.333 0.00 0.00 42.39 3.36
2787 2832 9.043079 GCTTTAGGCTTTATTATATACGGATCC 57.957 37.037 0.00 0.00 38.06 3.36
2788 2833 9.543783 CTTTAGGCTTTATTATATACGGATCCC 57.456 37.037 6.06 0.00 0.00 3.85
2789 2834 8.849543 TTAGGCTTTATTATATACGGATCCCT 57.150 34.615 6.06 0.00 0.00 4.20
2790 2835 7.125792 AGGCTTTATTATATACGGATCCCTG 57.874 40.000 6.06 0.00 0.00 4.45
3200 3247 9.669353 GTATGACATCAAGCTGGTTTATTAATG 57.331 33.333 0.00 0.00 0.00 1.90
3201 3248 6.563422 TGACATCAAGCTGGTTTATTAATGC 58.437 36.000 0.00 0.00 0.00 3.56
3213 3260 7.414436 TGGTTTATTAATGCGAGTATTTGCTC 58.586 34.615 0.00 0.00 34.60 4.26
3316 3446 6.114187 TCTGTTCAAGATGTACACCTCATT 57.886 37.500 0.00 0.00 0.00 2.57
3495 3625 4.747009 GCCCCTAAAAGGTATGAGATCCAC 60.747 50.000 0.00 0.00 31.93 4.02
3505 3635 5.067936 AGGTATGAGATCCACGTGTCTTAAG 59.932 44.000 15.65 0.00 0.00 1.85
3509 3639 6.132791 TGAGATCCACGTGTCTTAAGTATC 57.867 41.667 15.65 4.44 0.00 2.24
3625 3862 8.442632 TTCTATCCTTTTGCAACTATCTGATG 57.557 34.615 0.00 0.00 0.00 3.07
3652 3889 3.828921 ACTTGCATCTGATATGGTGCAT 58.171 40.909 3.23 0.00 45.80 3.96
3760 3997 8.519799 TCTTAGAAACTGTTCCTGAATTTTGT 57.480 30.769 0.00 0.00 33.92 2.83
3954 4191 2.972713 TGCCACAGTAGGAGAAAGACTT 59.027 45.455 0.00 0.00 0.00 3.01
4061 4298 6.043854 ACTGAATCCCTACTTCTCTTTGTC 57.956 41.667 0.00 0.00 0.00 3.18
4062 4299 5.782845 ACTGAATCCCTACTTCTCTTTGTCT 59.217 40.000 0.00 0.00 0.00 3.41
4077 4314 8.779354 TCTCTTTGTCTTAAAAGGCTATCTTC 57.221 34.615 0.00 0.00 37.67 2.87
4186 4423 1.192146 TGGTACCCACCTGTCTCTGC 61.192 60.000 10.07 0.00 45.98 4.26
4448 4685 1.202348 GCCAGTTCAATACACAAGGCC 59.798 52.381 0.00 0.00 34.94 5.19
4451 4688 3.091545 CAGTTCAATACACAAGGCCCAT 58.908 45.455 0.00 0.00 0.00 4.00
4615 4854 8.076178 GTGTTACACAAGCATTTTAGATCAGTT 58.924 33.333 10.96 0.00 34.08 3.16
4750 5032 6.525578 TCTCTACAACCGTCTAAACATGAT 57.474 37.500 0.00 0.00 0.00 2.45
4759 6539 3.356290 GTCTAAACATGATGGCCTTGGT 58.644 45.455 3.32 0.00 0.00 3.67
4790 6571 8.506168 TGACAAACTGATAATGAAATACTCCC 57.494 34.615 0.00 0.00 0.00 4.30
4791 6572 8.328758 TGACAAACTGATAATGAAATACTCCCT 58.671 33.333 0.00 0.00 0.00 4.20
4792 6573 8.738645 ACAAACTGATAATGAAATACTCCCTC 57.261 34.615 0.00 0.00 0.00 4.30
4793 6574 8.552296 ACAAACTGATAATGAAATACTCCCTCT 58.448 33.333 0.00 0.00 0.00 3.69
4812 6593 9.796120 CTCCCTCTATAAAGAAATATAAGAGCG 57.204 37.037 0.00 0.00 0.00 5.03
4813 6594 9.310449 TCCCTCTATAAAGAAATATAAGAGCGT 57.690 33.333 0.00 0.00 0.00 5.07
4814 6595 9.930693 CCCTCTATAAAGAAATATAAGAGCGTT 57.069 33.333 0.00 0.00 0.00 4.84
4832 6613 8.172352 AGAGCGTTTAGATCACTATCTTATGT 57.828 34.615 0.00 0.00 39.55 2.29
4833 6614 8.634444 AGAGCGTTTAGATCACTATCTTATGTT 58.366 33.333 0.00 0.00 39.55 2.71
4834 6615 9.250624 GAGCGTTTAGATCACTATCTTATGTTT 57.749 33.333 0.00 0.00 39.55 2.83
4835 6616 9.250624 AGCGTTTAGATCACTATCTTATGTTTC 57.749 33.333 0.00 0.00 39.55 2.78
4836 6617 9.250624 GCGTTTAGATCACTATCTTATGTTTCT 57.749 33.333 0.00 0.00 39.55 2.52
4842 6623 9.751542 AGATCACTATCTTATGTTTCTTTACGG 57.248 33.333 0.00 0.00 39.55 4.02
4843 6624 9.745880 GATCACTATCTTATGTTTCTTTACGGA 57.254 33.333 0.00 0.00 0.00 4.69
4844 6625 9.751542 ATCACTATCTTATGTTTCTTTACGGAG 57.248 33.333 0.00 0.00 0.00 4.63
4845 6626 8.195436 TCACTATCTTATGTTTCTTTACGGAGG 58.805 37.037 0.00 0.00 0.00 4.30
4846 6627 7.438459 CACTATCTTATGTTTCTTTACGGAGGG 59.562 40.741 0.00 0.00 0.00 4.30
4937 6718 2.805845 GTGCATTGAATCATCAGCACC 58.194 47.619 18.21 6.49 45.20 5.01
4952 6733 0.251354 GCACCAGGAGAGCAGAATGA 59.749 55.000 0.00 0.00 39.69 2.57
5185 6967 4.287067 AGCTTTTCCTGTAGGAGATCAACA 59.713 41.667 0.26 0.00 46.36 3.33
5188 6970 5.407407 TTTCCTGTAGGAGATCAACAGAC 57.593 43.478 15.16 3.22 46.36 3.51
5220 7002 4.039092 GCAGGGGAGGCAAGCTCA 62.039 66.667 0.00 0.00 0.00 4.26
5230 7012 3.084786 GAGGCAAGCTCAATAAACCAGT 58.915 45.455 0.00 0.00 0.00 4.00
5253 7035 5.698545 GTGATCTATCTTTGCAGGGTGATAC 59.301 44.000 0.00 0.00 0.00 2.24
5290 7072 5.353678 GTCTAGCAAGAATGTCTGCAATCTT 59.646 40.000 0.00 0.00 43.47 2.40
5294 7076 4.778534 AAGAATGTCTGCAATCTTGTGG 57.221 40.909 0.00 0.00 41.72 4.17
5349 7131 1.731720 AAGGAGAAGAGCGCATGTTC 58.268 50.000 11.47 9.31 0.00 3.18
5359 7141 1.135112 AGCGCATGTTCGACAGTGATA 60.135 47.619 11.47 0.00 0.00 2.15
5365 7147 5.061684 CGCATGTTCGACAGTGATAAGTTTA 59.938 40.000 0.00 0.00 0.00 2.01
5385 7167 0.179171 CAAGGCATGAGAAAGCTGCG 60.179 55.000 0.00 0.00 36.76 5.18
5388 7170 1.062206 GCATGAGAAAGCTGCGAGC 59.938 57.895 0.00 0.47 42.84 5.03
5549 7332 2.355209 CCCTGGCACTCTTCTTTACTCC 60.355 54.545 0.00 0.00 0.00 3.85
5638 7421 1.527034 TTGCCTGTGCTGATTCAGTC 58.473 50.000 14.90 8.08 38.71 3.51
5787 7570 4.516698 TGCAACAGAGATGTTCTTTCTTCC 59.483 41.667 0.00 0.00 32.41 3.46
5934 7721 1.902508 TGATCACCTCCTGAACCTGAC 59.097 52.381 0.00 0.00 30.60 3.51
5947 7734 5.755375 CCTGAACCTGACATATGTACATGAC 59.245 44.000 18.81 5.36 0.00 3.06
5952 7739 6.270815 ACCTGACATATGTACATGACGTTAC 58.729 40.000 18.81 4.36 0.00 2.50
5962 7750 3.550950 CATGACGTTACATGGTTTGCA 57.449 42.857 8.91 0.00 42.45 4.08
5963 7751 4.095410 CATGACGTTACATGGTTTGCAT 57.905 40.909 8.91 0.00 42.45 3.96
5965 7753 2.486203 TGACGTTACATGGTTTGCATCC 59.514 45.455 0.00 0.00 0.00 3.51
5966 7754 2.747446 GACGTTACATGGTTTGCATCCT 59.253 45.455 0.00 0.00 0.00 3.24
5975 7770 5.481473 ACATGGTTTGCATCCTAAATCTGTT 59.519 36.000 0.00 0.00 0.00 3.16
5988 7783 8.806429 TCCTAAATCTGTTCAATTTGCATCTA 57.194 30.769 0.00 0.00 0.00 1.98
5990 7785 8.461222 CCTAAATCTGTTCAATTTGCATCTACA 58.539 33.333 0.00 0.00 0.00 2.74
5995 7790 7.022979 TCTGTTCAATTTGCATCTACATTTCG 58.977 34.615 0.00 0.00 0.00 3.46
5997 7792 7.537715 TGTTCAATTTGCATCTACATTTCGAT 58.462 30.769 0.00 0.00 0.00 3.59
6006 7801 6.801377 TGCATCTACATTTCGATTGTCAAAAC 59.199 34.615 4.92 0.00 0.00 2.43
6008 7803 5.379003 TCTACATTTCGATTGTCAAAACGC 58.621 37.500 4.92 0.00 32.14 4.84
6020 7815 1.002251 TCAAAACGCGGATTGGTTGTC 60.002 47.619 21.03 0.00 0.00 3.18
6029 7824 2.360801 CGGATTGGTTGTCAAGTGGTTT 59.639 45.455 0.00 0.00 38.95 3.27
6031 7826 4.555906 CGGATTGGTTGTCAAGTGGTTTAC 60.556 45.833 0.00 0.00 38.95 2.01
6032 7827 4.339814 GGATTGGTTGTCAAGTGGTTTACA 59.660 41.667 0.00 0.00 38.95 2.41
6033 7828 4.974368 TTGGTTGTCAAGTGGTTTACAG 57.026 40.909 0.00 0.00 0.00 2.74
6035 7830 3.942748 TGGTTGTCAAGTGGTTTACAGTC 59.057 43.478 0.00 0.00 30.66 3.51
6037 7832 4.035208 GGTTGTCAAGTGGTTTACAGTCTG 59.965 45.833 0.00 0.00 30.66 3.51
6039 7834 5.092554 TGTCAAGTGGTTTACAGTCTGAA 57.907 39.130 6.91 0.00 30.66 3.02
6043 7838 5.105106 TCAAGTGGTTTACAGTCTGAACAGA 60.105 40.000 6.91 0.00 34.56 3.41
6069 7876 6.580416 CGACATACAGATTACAGCTATCAGTG 59.420 42.308 3.88 0.00 0.00 3.66
6072 7879 8.646004 ACATACAGATTACAGCTATCAGTGAAT 58.354 33.333 0.00 0.00 0.00 2.57
6094 7901 5.947228 TTTACAGTCTGCATTTCTTCAGG 57.053 39.130 0.00 0.00 0.00 3.86
6113 7920 5.211201 TCAGGAAGTCATGGATCTGACATA 58.789 41.667 15.28 0.00 46.45 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 9.695526 TCAAATTCTTGTCCATGTTTTCAATAG 57.304 29.630 0.00 0.00 33.94 1.73
526 555 0.757188 ATTGACGCTCGGGAGGATCT 60.757 55.000 0.00 0.00 33.73 2.75
530 562 1.107538 TCCTATTGACGCTCGGGAGG 61.108 60.000 0.00 0.00 0.00 4.30
534 566 0.673985 TGGATCCTATTGACGCTCGG 59.326 55.000 14.23 0.00 0.00 4.63
678 711 0.397816 CACGGGAGAGGAGGAAGGAT 60.398 60.000 0.00 0.00 0.00 3.24
704 739 0.603975 GCCACGGAGAAGAACAAGCT 60.604 55.000 0.00 0.00 0.00 3.74
710 745 2.347490 GGCTGCCACGGAGAAGAA 59.653 61.111 15.17 0.00 0.00 2.52
727 763 4.093952 CTCGCCTTTGCCGCTGTG 62.094 66.667 0.00 0.00 0.00 3.66
754 790 4.974438 TGCCGTGGGGAGGTTCCT 62.974 66.667 0.00 0.00 36.57 3.36
758 794 3.322466 CTCTTGCCGTGGGGAGGT 61.322 66.667 0.00 0.00 34.06 3.85
870 906 1.302993 GAGCTACGGGCCAAAACCA 60.303 57.895 4.39 0.00 43.05 3.67
883 919 1.152138 TAGGGAATCGCCGGAGCTA 59.848 57.895 5.05 0.00 37.63 3.32
950 986 1.884075 CGTGGGGGATGTCAAGTCGA 61.884 60.000 0.00 0.00 0.00 4.20
993 1029 0.179094 TTACCTCGCCCATTACGCTG 60.179 55.000 0.00 0.00 0.00 5.18
1137 1173 2.421739 CGGGCGTAGAGGAATGGG 59.578 66.667 0.00 0.00 0.00 4.00
1140 1176 2.762459 TGGCGGGCGTAGAGGAAT 60.762 61.111 0.00 0.00 0.00 3.01
1235 1271 6.601332 AGGATCACAAGTTGGTTAAAGAAGA 58.399 36.000 7.96 0.00 0.00 2.87
1249 1285 2.031420 CACACAGCACAAGGATCACAAG 60.031 50.000 0.00 0.00 0.00 3.16
1255 1291 0.179009 AGCACACACAGCACAAGGAT 60.179 50.000 0.00 0.00 0.00 3.24
1280 1316 1.792757 AATCCTCTGGGCCACTGCAA 61.793 55.000 0.00 0.00 40.13 4.08
1410 1447 2.297701 GAACCAGGCTTGTCTGACAAA 58.702 47.619 22.25 8.26 37.69 2.83
1533 1570 8.394877 CAAATACACACTGAGAAACAAACAGTA 58.605 33.333 0.00 0.00 41.93 2.74
1535 1572 6.692681 CCAAATACACACTGAGAAACAAACAG 59.307 38.462 0.00 0.00 37.62 3.16
1537 1574 5.977129 CCCAAATACACACTGAGAAACAAAC 59.023 40.000 0.00 0.00 0.00 2.93
1588 1628 6.093404 CACAGAATACGTACTGTCAAGACAT 58.907 40.000 14.12 0.00 44.07 3.06
1669 1709 1.478510 CCTTGTGACGCCTGAGAGTAT 59.521 52.381 0.00 0.00 0.00 2.12
1850 1890 8.324191 TCTTATTTCCATCCATCAGAGTTAGT 57.676 34.615 0.00 0.00 0.00 2.24
1889 1929 3.814005 ACAACAACTACGTGAGGAAGT 57.186 42.857 0.00 0.00 33.57 3.01
1913 1953 4.694037 GGCGTTTCTAACCTGTTAGTTGAT 59.306 41.667 14.82 0.00 42.29 2.57
1953 1993 1.734707 GCATGGCAGTTAAAGCAGCAG 60.735 52.381 0.00 0.00 0.00 4.24
2044 2086 6.550108 ACCCTACACATTACGAGACAAGATAT 59.450 38.462 0.00 0.00 0.00 1.63
2088 2130 0.035458 AACGTCCTGGCCTTCTCAAG 59.965 55.000 3.32 0.00 0.00 3.02
2326 2371 1.242076 ATCAAGCAGTGGCAAGTGAC 58.758 50.000 0.00 0.00 44.61 3.67
2418 2463 6.414408 AGACTTCAAGCAAATTCGTCATAG 57.586 37.500 0.00 0.00 0.00 2.23
2489 2534 9.643693 AGCGATAATTTGAAGATCAACATTTTT 57.356 25.926 0.00 0.00 35.89 1.94
2778 2823 9.877222 TGTATTATATGATACAGGGATCCGTAT 57.123 33.333 14.54 9.22 37.53 3.06
2779 2824 9.703677 TTGTATTATATGATACAGGGATCCGTA 57.296 33.333 17.01 4.24 41.89 4.02
2780 2825 8.603898 TTGTATTATATGATACAGGGATCCGT 57.396 34.615 17.01 2.61 41.89 4.69
2781 2826 9.314321 GTTTGTATTATATGATACAGGGATCCG 57.686 37.037 17.01 0.00 41.89 4.18
3157 3203 9.750125 GATGTCATACACTCATACAAAGTGATA 57.250 33.333 10.04 0.53 45.64 2.15
3165 3212 6.044682 CAGCTTGATGTCATACACTCATACA 58.955 40.000 0.00 0.00 0.00 2.29
3213 3260 8.325997 GGATAGCAAACATACTACAACTAAACG 58.674 37.037 0.00 0.00 0.00 3.60
3316 3446 9.753674 AATATTTCAAAACCTAGATGACCTTCA 57.246 29.630 0.00 0.00 0.00 3.02
3495 3625 8.857216 AGTTTTATGTTCGATACTTAAGACACG 58.143 33.333 10.09 10.88 35.58 4.49
3625 3862 6.493116 CACCATATCAGATGCAAGTTTCTTC 58.507 40.000 0.00 0.00 0.00 2.87
3760 3997 3.835978 TCTCGGTTCTGGTCCTGATAAAA 59.164 43.478 0.00 0.00 0.00 1.52
3841 4078 1.153309 TAGCATCTCGACGGACGGA 60.153 57.895 0.00 0.00 42.82 4.69
3954 4191 7.719193 TCCATTTCAGTCAACAAAGTTGATAGA 59.281 33.333 14.77 12.55 0.00 1.98
4186 4423 0.249238 GTGCATGCTAGAGAGGGACG 60.249 60.000 20.33 0.00 0.00 4.79
4448 4685 0.878523 TTATCGCGGCCTCGAAATGG 60.879 55.000 23.35 0.00 42.15 3.16
4451 4688 1.227147 CCTTATCGCGGCCTCGAAA 60.227 57.895 23.35 15.61 42.15 3.46
4565 4804 4.900635 ACTTGAACAAAAGCTCAATCGT 57.099 36.364 0.00 0.00 31.40 3.73
4567 4806 5.172053 CACGAACTTGAACAAAAGCTCAATC 59.828 40.000 0.00 0.00 31.40 2.67
4615 4854 3.625764 GTGATTGCGTTATCCAAGGCTTA 59.374 43.478 0.00 0.00 44.13 3.09
4686 4968 3.745975 CACAACCAGAGTCGCTTGAATTA 59.254 43.478 4.95 0.00 0.00 1.40
4750 5032 5.184864 CAGTTTGTCAATATAACCAAGGCCA 59.815 40.000 5.01 0.00 0.00 5.36
4787 6568 9.310449 ACGCTCTTATATTTCTTTATAGAGGGA 57.690 33.333 16.73 0.00 37.30 4.20
4788 6569 9.930693 AACGCTCTTATATTTCTTTATAGAGGG 57.069 33.333 0.00 0.00 38.95 4.30
4806 6587 8.634444 ACATAAGATAGTGATCTAAACGCTCTT 58.366 33.333 0.00 1.56 41.87 2.85
4807 6588 8.172352 ACATAAGATAGTGATCTAAACGCTCT 57.828 34.615 0.00 0.00 41.87 4.09
4808 6589 8.804688 AACATAAGATAGTGATCTAAACGCTC 57.195 34.615 0.00 0.00 41.87 5.03
4809 6590 9.250624 GAAACATAAGATAGTGATCTAAACGCT 57.749 33.333 0.00 0.00 41.87 5.07
4810 6591 9.250624 AGAAACATAAGATAGTGATCTAAACGC 57.749 33.333 0.00 0.00 41.87 4.84
4816 6597 9.751542 CCGTAAAGAAACATAAGATAGTGATCT 57.248 33.333 0.00 0.00 44.79 2.75
4817 6598 9.745880 TCCGTAAAGAAACATAAGATAGTGATC 57.254 33.333 0.00 0.00 0.00 2.92
4818 6599 9.751542 CTCCGTAAAGAAACATAAGATAGTGAT 57.248 33.333 0.00 0.00 0.00 3.06
4819 6600 8.195436 CCTCCGTAAAGAAACATAAGATAGTGA 58.805 37.037 0.00 0.00 0.00 3.41
4820 6601 7.438459 CCCTCCGTAAAGAAACATAAGATAGTG 59.562 40.741 0.00 0.00 0.00 2.74
4821 6602 7.343833 TCCCTCCGTAAAGAAACATAAGATAGT 59.656 37.037 0.00 0.00 0.00 2.12
4822 6603 7.723324 TCCCTCCGTAAAGAAACATAAGATAG 58.277 38.462 0.00 0.00 0.00 2.08
4823 6604 7.343833 ACTCCCTCCGTAAAGAAACATAAGATA 59.656 37.037 0.00 0.00 0.00 1.98
4824 6605 6.156429 ACTCCCTCCGTAAAGAAACATAAGAT 59.844 38.462 0.00 0.00 0.00 2.40
4825 6606 5.482878 ACTCCCTCCGTAAAGAAACATAAGA 59.517 40.000 0.00 0.00 0.00 2.10
4826 6607 5.731591 ACTCCCTCCGTAAAGAAACATAAG 58.268 41.667 0.00 0.00 0.00 1.73
4827 6608 5.750352 ACTCCCTCCGTAAAGAAACATAA 57.250 39.130 0.00 0.00 0.00 1.90
4828 6609 5.163478 GCTACTCCCTCCGTAAAGAAACATA 60.163 44.000 0.00 0.00 0.00 2.29
4829 6610 4.382793 GCTACTCCCTCCGTAAAGAAACAT 60.383 45.833 0.00 0.00 0.00 2.71
4830 6611 3.056322 GCTACTCCCTCCGTAAAGAAACA 60.056 47.826 0.00 0.00 0.00 2.83
4831 6612 3.195182 AGCTACTCCCTCCGTAAAGAAAC 59.805 47.826 0.00 0.00 0.00 2.78
4832 6613 3.438183 AGCTACTCCCTCCGTAAAGAAA 58.562 45.455 0.00 0.00 0.00 2.52
4833 6614 3.097342 AGCTACTCCCTCCGTAAAGAA 57.903 47.619 0.00 0.00 0.00 2.52
4834 6615 2.758979 CAAGCTACTCCCTCCGTAAAGA 59.241 50.000 0.00 0.00 0.00 2.52
4835 6616 2.496470 ACAAGCTACTCCCTCCGTAAAG 59.504 50.000 0.00 0.00 0.00 1.85
4836 6617 2.532843 ACAAGCTACTCCCTCCGTAAA 58.467 47.619 0.00 0.00 0.00 2.01
4837 6618 2.226962 ACAAGCTACTCCCTCCGTAA 57.773 50.000 0.00 0.00 0.00 3.18
4838 6619 2.226962 AACAAGCTACTCCCTCCGTA 57.773 50.000 0.00 0.00 0.00 4.02
4839 6620 1.823610 GTAACAAGCTACTCCCTCCGT 59.176 52.381 0.00 0.00 0.00 4.69
4840 6621 1.822990 TGTAACAAGCTACTCCCTCCG 59.177 52.381 0.00 0.00 0.00 4.63
4841 6622 3.097614 TCTGTAACAAGCTACTCCCTCC 58.902 50.000 0.00 0.00 0.00 4.30
4842 6623 4.803098 TTCTGTAACAAGCTACTCCCTC 57.197 45.455 0.00 0.00 0.00 4.30
4843 6624 5.763876 AATTCTGTAACAAGCTACTCCCT 57.236 39.130 0.00 0.00 0.00 4.20
4844 6625 6.313164 GTGTAATTCTGTAACAAGCTACTCCC 59.687 42.308 0.00 0.00 0.00 4.30
4845 6626 7.097834 AGTGTAATTCTGTAACAAGCTACTCC 58.902 38.462 0.00 0.00 0.00 3.85
4846 6627 9.804758 ATAGTGTAATTCTGTAACAAGCTACTC 57.195 33.333 0.00 0.00 0.00 2.59
4901 6682 5.769662 TCAATGCACATAAAGTTCCTGTTCT 59.230 36.000 0.00 0.00 0.00 3.01
4937 6718 4.686191 AATAGGTCATTCTGCTCTCCTG 57.314 45.455 0.00 0.00 0.00 3.86
4952 6733 8.308931 TGTCGAATACTTGACACTTAAATAGGT 58.691 33.333 0.00 0.00 40.02 3.08
5203 6985 2.850828 ATTGAGCTTGCCTCCCCTGC 62.851 60.000 0.00 0.00 39.98 4.85
5220 7002 7.284034 CCTGCAAAGATAGATCACTGGTTTATT 59.716 37.037 0.00 0.00 0.00 1.40
5230 7012 5.221722 GGTATCACCCTGCAAAGATAGATCA 60.222 44.000 0.00 0.00 30.04 2.92
5281 7063 5.176223 GTGTCAAATTTCCACAAGATTGCAG 59.824 40.000 11.02 0.00 0.00 4.41
5290 7072 4.281435 AGCATGATGTGTCAAATTTCCACA 59.719 37.500 17.84 17.84 42.70 4.17
5341 7123 2.923655 ACTTATCACTGTCGAACATGCG 59.076 45.455 0.00 0.00 0.00 4.73
5349 7131 4.688879 TGCCTTGTAAACTTATCACTGTCG 59.311 41.667 0.00 0.00 0.00 4.35
5359 7141 4.829492 AGCTTTCTCATGCCTTGTAAACTT 59.171 37.500 0.00 0.00 0.00 2.66
5365 7147 0.886563 GCAGCTTTCTCATGCCTTGT 59.113 50.000 0.00 0.00 33.81 3.16
5388 7170 1.439679 GTACGTCTCCAAGCCCTTTG 58.560 55.000 0.00 0.00 36.50 2.77
5549 7332 0.880278 CGGCATAATCACCCCGACAG 60.880 60.000 0.00 0.00 43.20 3.51
5638 7421 3.508744 AGCAATTTGCCGGACAATAAG 57.491 42.857 17.51 3.31 46.52 1.73
5787 7570 9.884299 CATAAATGCAATATGTTTTGTGTTACG 57.116 29.630 12.44 0.00 0.00 3.18
5834 7617 6.464222 CAAGGTAAGTTACAGTCTCATTCCA 58.536 40.000 14.81 0.00 0.00 3.53
5840 7623 5.135508 TCTGCAAGGTAAGTTACAGTCTC 57.864 43.478 14.81 0.00 0.00 3.36
5934 7721 7.477144 AACCATGTAACGTCATGTACATATG 57.523 36.000 8.32 6.06 42.29 1.78
5947 7734 4.955925 TTAGGATGCAAACCATGTAACG 57.044 40.909 14.25 0.00 33.29 3.18
5952 7739 5.587388 ACAGATTTAGGATGCAAACCATG 57.413 39.130 14.25 0.00 33.29 3.66
5959 7747 6.101332 GCAAATTGAACAGATTTAGGATGCA 58.899 36.000 0.00 0.00 0.00 3.96
5960 7748 6.101332 TGCAAATTGAACAGATTTAGGATGC 58.899 36.000 0.00 0.00 0.00 3.91
5961 7749 8.195436 AGATGCAAATTGAACAGATTTAGGATG 58.805 33.333 0.00 0.00 0.00 3.51
5962 7750 8.302515 AGATGCAAATTGAACAGATTTAGGAT 57.697 30.769 0.00 0.00 0.00 3.24
5963 7751 7.707624 AGATGCAAATTGAACAGATTTAGGA 57.292 32.000 0.00 0.00 0.00 2.94
5975 7770 7.537715 ACAATCGAAATGTAGATGCAAATTGA 58.462 30.769 5.50 0.00 0.00 2.57
5988 7783 2.970609 CGCGTTTTGACAATCGAAATGT 59.029 40.909 14.49 6.90 38.45 2.71
5990 7785 2.224549 TCCGCGTTTTGACAATCGAAAT 59.775 40.909 4.92 0.00 32.83 2.17
5995 7790 2.250188 CCAATCCGCGTTTTGACAATC 58.750 47.619 16.97 0.00 0.00 2.67
5997 7792 1.025812 ACCAATCCGCGTTTTGACAA 58.974 45.000 16.97 0.00 0.00 3.18
6006 7801 0.110238 CACTTGACAACCAATCCGCG 60.110 55.000 0.00 0.00 33.68 6.46
6008 7803 1.604604 ACCACTTGACAACCAATCCG 58.395 50.000 0.00 0.00 33.68 4.18
6020 7815 5.006746 GTCTGTTCAGACTGTAAACCACTTG 59.993 44.000 21.22 0.00 36.01 3.16
6029 7824 4.758165 TGTATGTCGTCTGTTCAGACTGTA 59.242 41.667 24.21 13.69 36.71 2.74
6031 7826 4.083271 TCTGTATGTCGTCTGTTCAGACTG 60.083 45.833 24.21 18.72 36.71 3.51
6032 7827 4.072839 TCTGTATGTCGTCTGTTCAGACT 58.927 43.478 24.21 12.41 36.71 3.24
6033 7828 4.421033 TCTGTATGTCGTCTGTTCAGAC 57.579 45.455 19.32 19.32 35.59 3.51
6035 7830 6.322491 TGTAATCTGTATGTCGTCTGTTCAG 58.678 40.000 0.00 0.00 0.00 3.02
6037 7832 5.230306 GCTGTAATCTGTATGTCGTCTGTTC 59.770 44.000 0.00 0.00 0.00 3.18
6039 7834 4.399618 AGCTGTAATCTGTATGTCGTCTGT 59.600 41.667 0.00 0.00 0.00 3.41
6043 7838 6.263392 ACTGATAGCTGTAATCTGTATGTCGT 59.737 38.462 0.00 0.00 34.81 4.34
6044 7839 6.580416 CACTGATAGCTGTAATCTGTATGTCG 59.420 42.308 0.00 0.00 34.81 4.35
6045 7840 7.652727 TCACTGATAGCTGTAATCTGTATGTC 58.347 38.462 0.00 0.00 34.81 3.06
6069 7876 7.025963 CCTGAAGAAATGCAGACTGTAAATTC 58.974 38.462 3.99 8.93 34.06 2.17
6072 7879 5.620206 TCCTGAAGAAATGCAGACTGTAAA 58.380 37.500 3.99 0.00 34.06 2.01


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

AutoCloner maintained by Alex Coulton.