Multiple sequence alignment - TraesCS7A01G151400

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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 TraesCS7A01G151400 chr7A 100.000 5093 0 0 1 5093 105365089 105359997 0.000000e+00 9406.0
1 TraesCS7A01G151400 chr7A 93.103 87 6 0 2867 2953 202289150 202289236 1.490000e-25 128.0
2 TraesCS7A01G151400 chr7A 93.478 46 3 0 4258 4303 664602642 664602597 9.150000e-08 69.4
3 TraesCS7A01G151400 chr7B 93.685 2882 138 21 10 2868 58792569 58789709 0.000000e+00 4274.0
4 TraesCS7A01G151400 chr7B 91.014 2159 110 39 2953 5047 58789707 58787569 0.000000e+00 2835.0
5 TraesCS7A01G151400 chr7B 92.045 88 7 0 2864 2951 60366476 60366563 1.930000e-24 124.0
6 TraesCS7A01G151400 chr7D 94.802 2116 68 14 2343 4440 101616318 101614227 0.000000e+00 3260.0
7 TraesCS7A01G151400 chr7D 89.967 1525 91 17 115 1619 101618664 101617182 0.000000e+00 1912.0
8 TraesCS7A01G151400 chr7D 91.732 641 19 9 4438 5047 101614138 101613501 0.000000e+00 859.0
9 TraesCS7A01G151400 chr7D 95.745 517 15 4 1838 2350 101616885 101616372 0.000000e+00 826.0
10 TraesCS7A01G151400 chr7D 90.588 255 18 4 1478 1732 101617137 101616889 2.940000e-87 333.0
11 TraesCS7A01G151400 chr5B 95.652 92 3 1 2863 2953 457129114 457129205 4.110000e-31 147.0
12 TraesCS7A01G151400 chr5B 97.647 85 2 0 2867 2951 457129203 457129119 4.110000e-31 147.0
13 TraesCS7A01G151400 chr5B 97.561 41 1 0 4258 4298 473175068 473175108 2.540000e-08 71.3
14 TraesCS7A01G151400 chr2B 93.103 87 6 0 2867 2953 23029138 23029052 1.490000e-25 128.0
15 TraesCS7A01G151400 chr2B 85.714 56 4 4 5040 5093 786863939 786863886 7.120000e-04 56.5
16 TraesCS7A01G151400 chr4B 92.045 88 7 0 2864 2951 59873822 59873735 1.930000e-24 124.0
17 TraesCS7A01G151400 chr1A 91.954 87 7 0 2867 2953 27400025 27400111 6.920000e-24 122.0
18 TraesCS7A01G151400 chr1B 85.321 109 13 3 2843 2951 549520039 549520144 5.390000e-20 110.0
19 TraesCS7A01G151400 chr1B 100.000 28 0 0 4259 4286 310148799 310148772 9.000000e-03 52.8
20 TraesCS7A01G151400 chr4D 97.826 46 1 0 4258 4303 397682339 397682294 4.230000e-11 80.5
21 TraesCS7A01G151400 chr5D 97.561 41 1 0 4258 4298 393455301 393455341 2.540000e-08 71.3
22 TraesCS7A01G151400 chr5A 91.837 49 4 0 5040 5088 688538392 688538344 9.150000e-08 69.4
23 TraesCS7A01G151400 chr6B 100.000 29 0 0 4258 4286 555959183 555959155 3.000000e-03 54.7


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 TraesCS7A01G151400 chr7A 105359997 105365089 5092 True 9406.0 9406 100.0000 1 5093 1 chr7A.!!$R1 5092
1 TraesCS7A01G151400 chr7B 58787569 58792569 5000 True 3554.5 4274 92.3495 10 5047 2 chr7B.!!$R1 5037
2 TraesCS7A01G151400 chr7D 101613501 101618664 5163 True 1438.0 3260 92.5668 115 5047 5 chr7D.!!$R1 4932

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
369 377 0.033405 AGCGACAGGGACCTAGCTTA 60.033 55.000 0.00 0.0 30.40 3.09 F
654 675 0.112412 AATTTCTTGCCCGTCCCTGT 59.888 50.000 0.00 0.0 0.00 4.00 F
667 688 0.482446 TCCCTGTGCACCAATTTCCT 59.518 50.000 15.69 0.0 0.00 3.36 F
1595 1805 0.826715 TGTGGCTCAGATAGGACTGC 59.173 55.000 0.00 0.0 37.75 4.40 F
1652 1862 2.093021 TCCGAATGATGATGAGCCACAA 60.093 45.455 0.00 0.0 0.00 3.33 F
1656 1866 2.118313 TGATGATGAGCCACAACAGG 57.882 50.000 0.00 0.0 34.94 4.00 F
2386 2662 2.877097 TGTGCTCCTCTATTTTGCCA 57.123 45.000 0.00 0.0 0.00 4.92 F
2550 2826 3.330701 TGCTAAAGGATGTCCATATCCCC 59.669 47.826 1.30 0.0 46.38 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 2028 0.249911 CACTGCTACGGGGAATAGCC 60.250 60.000 1.78 0.00 43.75 3.93 R
1912 2123 0.900182 GAAAACAGGGAGGGGGCAAG 60.900 60.000 0.00 0.00 0.00 4.01 R
1983 2194 1.971481 TCACATGAAGCTTGCTGTGT 58.029 45.000 25.72 14.07 39.89 3.72 R
2936 3215 2.169330 ACGAACTACTCCCTCTGTTCC 58.831 52.381 0.00 0.00 36.43 3.62 R
3435 3736 2.338809 ACTCCAACAAGAGATCCCACA 58.661 47.619 0.00 0.00 37.33 4.17 R
3654 3955 1.321474 TTGAGCTGAGCACCAAAAGG 58.679 50.000 7.39 0.00 0.00 3.11 R
3954 4255 0.447011 AGGTTAGCTCGACGTTCTCG 59.553 55.000 0.00 0.00 44.44 4.04 R
4482 4882 1.639298 GAATCTGGTCCGCTGCACAC 61.639 60.000 0.00 0.00 0.00 3.82 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 3.244422 CCACCCATGTAGTACGGCATATT 60.244 47.826 5.18 0.00 0.00 1.28
34 35 5.989777 AGTACGGCATATTCACAATAAGTCC 59.010 40.000 0.00 0.00 0.00 3.85
41 42 7.013655 GGCATATTCACAATAAGTCCTCACATT 59.986 37.037 0.00 0.00 0.00 2.71
44 45 9.685276 ATATTCACAATAAGTCCTCACATTTCA 57.315 29.630 0.00 0.00 0.00 2.69
47 48 6.599244 TCACAATAAGTCCTCACATTTCATCC 59.401 38.462 0.00 0.00 0.00 3.51
56 57 8.306761 AGTCCTCACATTTCATCCAAATAAAAC 58.693 33.333 0.00 0.00 32.48 2.43
58 59 7.234371 TCCTCACATTTCATCCAAATAAAACCA 59.766 33.333 0.00 0.00 32.48 3.67
59 60 7.331687 CCTCACATTTCATCCAAATAAAACCAC 59.668 37.037 0.00 0.00 32.48 4.16
61 62 7.016072 TCACATTTCATCCAAATAAAACCACCT 59.984 33.333 0.00 0.00 32.48 4.00
63 64 6.739331 TTTCATCCAAATAAAACCACCTGT 57.261 33.333 0.00 0.00 0.00 4.00
64 65 5.720371 TCATCCAAATAAAACCACCTGTG 57.280 39.130 0.00 0.00 0.00 3.66
66 67 5.242838 TCATCCAAATAAAACCACCTGTGAC 59.757 40.000 0.00 0.00 0.00 3.67
93 94 2.265904 GGTGGAAAACCGGAGTGCC 61.266 63.158 9.46 3.33 39.81 5.01
107 108 3.071479 GGAGTGCCGTTGAGTTTGATTA 58.929 45.455 0.00 0.00 0.00 1.75
108 109 3.689649 GGAGTGCCGTTGAGTTTGATTAT 59.310 43.478 0.00 0.00 0.00 1.28
109 110 4.873827 GGAGTGCCGTTGAGTTTGATTATA 59.126 41.667 0.00 0.00 0.00 0.98
112 113 6.608610 AGTGCCGTTGAGTTTGATTATAAAC 58.391 36.000 0.00 0.00 40.08 2.01
134 135 1.061857 CAAGGTTTGTTTTGCAACGCC 59.938 47.619 0.00 0.00 36.72 5.68
150 151 1.148310 CGCCTGTTCACATCTTCGTT 58.852 50.000 0.00 0.00 0.00 3.85
163 164 7.581476 TCACATCTTCGTTTCTGTTTTAATCC 58.419 34.615 0.00 0.00 0.00 3.01
213 214 4.351192 CAAAATCGTAAGGTGCATTAGGC 58.649 43.478 0.00 0.00 40.25 3.93
235 236 0.529378 ACGTAATCTCCCGTTTCGCT 59.471 50.000 0.00 0.00 32.50 4.93
253 255 1.065551 GCTGGATATGTTTTCCACGCC 59.934 52.381 0.00 0.00 38.35 5.68
286 293 4.379243 CCGAGGAACACGCAGGCT 62.379 66.667 0.00 0.00 42.01 4.58
295 302 2.185004 ACACGCAGGCTCAATTAACT 57.815 45.000 0.00 0.00 0.00 2.24
296 303 2.076863 ACACGCAGGCTCAATTAACTC 58.923 47.619 0.00 0.00 0.00 3.01
298 305 1.017387 CGCAGGCTCAATTAACTCCC 58.983 55.000 0.00 0.00 0.00 4.30
301 308 3.681594 CGCAGGCTCAATTAACTCCCTAA 60.682 47.826 0.00 0.00 0.00 2.69
303 310 4.843728 CAGGCTCAATTAACTCCCTAACA 58.156 43.478 0.00 0.00 0.00 2.41
362 370 2.893398 CCTACAGCGACAGGGACC 59.107 66.667 0.00 0.00 0.00 4.46
365 373 1.025812 CTACAGCGACAGGGACCTAG 58.974 60.000 0.00 0.00 0.00 3.02
366 374 1.035932 TACAGCGACAGGGACCTAGC 61.036 60.000 0.00 0.00 0.00 3.42
367 375 2.055042 CAGCGACAGGGACCTAGCT 61.055 63.158 8.67 8.67 33.21 3.32
369 377 0.033405 AGCGACAGGGACCTAGCTTA 60.033 55.000 0.00 0.00 30.40 3.09
370 378 0.822164 GCGACAGGGACCTAGCTTAA 59.178 55.000 0.00 0.00 0.00 1.85
433 445 1.482593 AGGTCAAACGGCTATCCTCAG 59.517 52.381 0.00 0.00 0.00 3.35
538 552 4.957296 TCTTGTTTTACTCACCAGTCTCC 58.043 43.478 0.00 0.00 33.62 3.71
555 576 2.434884 CGATGTTCGCAGGCCACT 60.435 61.111 5.01 0.00 31.14 4.00
585 606 0.901827 TCTGGCTGCTCAATTCGGTA 59.098 50.000 0.00 0.00 0.00 4.02
644 665 2.671396 CTGCTGCAATCCAATTTCTTGC 59.329 45.455 3.02 8.67 44.25 4.01
647 668 1.067000 TGCAATCCAATTTCTTGCCCG 60.067 47.619 11.72 0.00 43.54 6.13
654 675 0.112412 AATTTCTTGCCCGTCCCTGT 59.888 50.000 0.00 0.00 0.00 4.00
667 688 0.482446 TCCCTGTGCACCAATTTCCT 59.518 50.000 15.69 0.00 0.00 3.36
726 751 3.191371 GGCCTTCGATTTGATGTTCTTGT 59.809 43.478 0.00 0.00 0.00 3.16
1037 1062 1.532316 ACGACTTCCCCGAGGACAA 60.532 57.895 0.00 0.00 43.90 3.18
1419 1444 3.164026 TGCAGGTGAGCAAGCATAG 57.836 52.632 0.00 0.00 42.46 2.23
1453 1478 6.425577 TTTTGGTTACACTTGTGTACTGAC 57.574 37.500 12.51 8.83 0.00 3.51
1470 1495 3.802685 ACTGACGAGCTGTAAACTGAAAC 59.197 43.478 0.00 0.00 0.00 2.78
1475 1500 3.430218 CGAGCTGTAAACTGAAACTCTGG 59.570 47.826 0.00 0.00 0.00 3.86
1476 1501 4.632153 GAGCTGTAAACTGAAACTCTGGA 58.368 43.478 0.00 0.00 0.00 3.86
1500 1710 6.827727 ACTGAATTGTAGACTTGTGGTAGTT 58.172 36.000 0.00 0.00 0.00 2.24
1504 1714 8.402472 TGAATTGTAGACTTGTGGTAGTTTTTG 58.598 33.333 0.00 0.00 0.00 2.44
1506 1716 7.925043 TTGTAGACTTGTGGTAGTTTTTGAA 57.075 32.000 0.00 0.00 0.00 2.69
1595 1805 0.826715 TGTGGCTCAGATAGGACTGC 59.173 55.000 0.00 0.00 37.75 4.40
1619 1829 4.685169 TTTCTTTGCTGCTATGCACTAC 57.315 40.909 0.00 0.00 43.20 2.73
1623 1833 2.589492 GCTGCTATGCACTACGGCG 61.589 63.158 4.80 4.80 33.79 6.46
1652 1862 2.093021 TCCGAATGATGATGAGCCACAA 60.093 45.455 0.00 0.00 0.00 3.33
1656 1866 2.118313 TGATGATGAGCCACAACAGG 57.882 50.000 0.00 0.00 34.94 4.00
1667 1877 4.020543 AGCCACAACAGGAAACAAACTTA 58.979 39.130 0.00 0.00 0.00 2.24
1694 1905 4.949238 TGCCATTGGGATATCCATATTTCG 59.051 41.667 23.27 5.29 46.52 3.46
1817 2028 2.973224 GCGGCATAAGCAAAATACATCG 59.027 45.455 0.00 0.00 44.61 3.84
1847 2058 4.696402 CCCCGTAGCAGTGTTATTTTTACA 59.304 41.667 0.00 0.00 0.00 2.41
1851 2062 4.783764 AGCAGTGTTATTTTTACAGCCC 57.216 40.909 0.00 0.00 0.00 5.19
1983 2194 8.735315 GTGATTGCTATGCTTATAGTCTCTCTA 58.265 37.037 0.00 0.00 0.00 2.43
2013 2224 3.940852 AGCTTCATGTGATGTTCGCATTA 59.059 39.130 0.97 0.00 44.40 1.90
2265 2477 4.333926 GCTCTGTACTTCCCAATCATTGAC 59.666 45.833 0.00 0.00 0.00 3.18
2360 2636 9.416794 CTGGTTATGCATAGAGAATAAGTACAG 57.583 37.037 6.50 0.00 0.00 2.74
2386 2662 2.877097 TGTGCTCCTCTATTTTGCCA 57.123 45.000 0.00 0.00 0.00 4.92
2550 2826 3.330701 TGCTAAAGGATGTCCATATCCCC 59.669 47.826 1.30 0.00 46.38 4.81
2853 3132 8.129211 GGTACACCTTACATCTTTATGCATTTC 58.871 37.037 3.54 0.00 36.50 2.17
2881 3160 6.827251 TGCTATAATATACTCCCTCTGTACCG 59.173 42.308 0.00 0.00 0.00 4.02
2936 3215 5.029014 GCTACTCCAGCGACATATATTACG 58.971 45.833 0.00 4.54 41.37 3.18
3014 3293 6.208644 ACACTACAATTTGCTTGCAGTTAAG 58.791 36.000 0.00 0.00 39.06 1.85
3081 3361 6.988580 TGACATATCTGAAATGACTCCATGTC 59.011 38.462 0.00 0.00 45.54 3.06
3135 3415 9.638239 TTCATAGTTTCCAAGATGTTATTTTGC 57.362 29.630 0.00 0.00 0.00 3.68
3179 3459 9.406828 CATGTTCCATATCTTCAAATTAGCATG 57.593 33.333 0.00 0.00 0.00 4.06
3374 3675 3.937814 ACTTATCTTTGACGCATGACCA 58.062 40.909 0.00 0.00 0.00 4.02
3381 3682 6.266168 TCTTTGACGCATGACCAAAATAAT 57.734 33.333 0.00 0.00 30.56 1.28
3383 3684 7.995289 TCTTTGACGCATGACCAAAATAATAT 58.005 30.769 0.00 0.00 30.56 1.28
3384 3685 9.114952 TCTTTGACGCATGACCAAAATAATATA 57.885 29.630 0.00 0.00 30.56 0.86
3435 3736 4.157840 GGGTTTATCTTCGCAATTGGTTCT 59.842 41.667 7.72 0.00 0.00 3.01
3813 4114 6.208599 TCACAAGAACAGAGTTCAAAAACCTT 59.791 34.615 11.92 0.00 35.92 3.50
3954 4255 1.139734 TGCTGAGGCTCGACGAATC 59.860 57.895 10.42 0.00 39.59 2.52
3984 4285 2.031930 CGAGCTAACCTCTCTTACCGTC 59.968 54.545 0.00 0.00 38.49 4.79
4000 4301 1.464429 CGTCGACAAGAATCCGAGCG 61.464 60.000 17.16 0.00 32.65 5.03
4151 4454 9.334947 ACAGACATATAGTTGAAAAGGATCATG 57.665 33.333 0.00 0.00 0.00 3.07
4183 4486 7.949428 CACATTGTGTTGTTTTTAGTTGTTCAC 59.051 33.333 8.69 0.00 0.00 3.18
4184 4487 7.653713 ACATTGTGTTGTTTTTAGTTGTTCACA 59.346 29.630 0.00 0.00 0.00 3.58
4242 4546 5.690409 GCAAATCATCAAATGCCAGATAGTG 59.310 40.000 0.00 0.00 32.73 2.74
4256 4560 5.803967 GCCAGATAGTGCTTTGAAATTTGAG 59.196 40.000 0.00 0.00 0.00 3.02
4281 4585 3.260884 TCCCTCCGATCCATATTACTTGC 59.739 47.826 0.00 0.00 0.00 4.01
4285 4589 2.612972 CCGATCCATATTACTTGCCGCT 60.613 50.000 0.00 0.00 0.00 5.52
4295 4599 1.439679 ACTTGCCGCTGCTTTAGTAC 58.560 50.000 0.70 0.00 38.71 2.73
4301 4605 2.225727 GCCGCTGCTTTAGTACAACTTT 59.774 45.455 0.00 0.00 33.53 2.66
4335 4639 9.832445 TCTTTTAAACTCTCACTGTGTTATCTT 57.168 29.630 7.79 0.85 32.77 2.40
4336 4640 9.869844 CTTTTAAACTCTCACTGTGTTATCTTG 57.130 33.333 7.79 0.00 32.77 3.02
4337 4641 9.607988 TTTTAAACTCTCACTGTGTTATCTTGA 57.392 29.630 7.79 0.00 32.77 3.02
4340 4644 6.019779 ACTCTCACTGTGTTATCTTGACTC 57.980 41.667 7.79 0.00 0.00 3.36
4341 4645 5.536538 ACTCTCACTGTGTTATCTTGACTCA 59.463 40.000 7.79 0.00 0.00 3.41
4432 4741 0.886490 CTGGCCAGTTCACACCTCAC 60.886 60.000 25.53 0.00 0.00 3.51
4605 5006 5.765176 TGATTTCATTCTTGACAGCAACAG 58.235 37.500 0.00 0.00 25.77 3.16
4649 5050 1.440618 TTAGAGTGACCCCTTTGGCA 58.559 50.000 0.00 0.00 37.83 4.92
4699 5119 0.037326 TCACAATCTCACGAGGTGGC 60.037 55.000 0.00 0.00 33.87 5.01
4706 5126 2.582052 TCTCACGAGGTGGCAAAATTT 58.418 42.857 0.00 0.00 33.87 1.82
4812 5258 0.036952 TCTCAAAGGGAGCTTGCGAG 60.037 55.000 0.00 0.00 43.70 5.03
4813 5259 1.003355 TCAAAGGGAGCTTGCGAGG 60.003 57.895 2.37 0.00 0.00 4.63
4834 5280 2.289694 GGGCGTGCTCTTATGGATATGT 60.290 50.000 0.00 0.00 0.00 2.29
4880 5326 5.409643 GGTGACCATATTTCATGAGTTCG 57.590 43.478 0.00 0.00 0.00 3.95
4951 5398 1.197721 CCTCACCAATGCAAGAACGAC 59.802 52.381 0.00 0.00 0.00 4.34
4994 5441 6.933514 AATAGGTTGGTTTTCAATGACCAT 57.066 33.333 0.00 0.00 44.83 3.55
5062 5509 8.992835 TTAGAGAAAACTATACTTTTCGTCCC 57.007 34.615 10.21 4.45 42.59 4.46
5063 5510 7.242322 AGAGAAAACTATACTTTTCGTCCCT 57.758 36.000 10.21 5.93 42.59 4.20
5064 5511 7.321908 AGAGAAAACTATACTTTTCGTCCCTC 58.678 38.462 10.21 0.00 42.59 4.30
5065 5512 7.001099 AGAAAACTATACTTTTCGTCCCTCA 57.999 36.000 10.21 0.00 42.59 3.86
5066 5513 7.447594 AGAAAACTATACTTTTCGTCCCTCAA 58.552 34.615 10.21 0.00 42.59 3.02
5067 5514 8.101419 AGAAAACTATACTTTTCGTCCCTCAAT 58.899 33.333 10.21 0.00 42.59 2.57
5068 5515 8.631480 AAAACTATACTTTTCGTCCCTCAATT 57.369 30.769 0.00 0.00 0.00 2.32
5069 5516 7.845066 AACTATACTTTTCGTCCCTCAATTC 57.155 36.000 0.00 0.00 0.00 2.17
5070 5517 6.346896 ACTATACTTTTCGTCCCTCAATTCC 58.653 40.000 0.00 0.00 0.00 3.01
5071 5518 3.790089 ACTTTTCGTCCCTCAATTCCT 57.210 42.857 0.00 0.00 0.00 3.36
5072 5519 3.676093 ACTTTTCGTCCCTCAATTCCTC 58.324 45.455 0.00 0.00 0.00 3.71
5073 5520 2.380084 TTTCGTCCCTCAATTCCTCG 57.620 50.000 0.00 0.00 0.00 4.63
5074 5521 1.263356 TTCGTCCCTCAATTCCTCGT 58.737 50.000 0.00 0.00 0.00 4.18
5075 5522 0.530744 TCGTCCCTCAATTCCTCGTG 59.469 55.000 0.00 0.00 0.00 4.35
5076 5523 0.530744 CGTCCCTCAATTCCTCGTGA 59.469 55.000 0.00 0.00 0.00 4.35
5077 5524 1.067142 CGTCCCTCAATTCCTCGTGAA 60.067 52.381 0.00 0.00 37.38 3.18
5078 5525 2.622436 GTCCCTCAATTCCTCGTGAAG 58.378 52.381 0.00 0.00 36.14 3.02
5079 5526 2.028020 GTCCCTCAATTCCTCGTGAAGT 60.028 50.000 0.00 0.00 36.14 3.01
5080 5527 2.233922 TCCCTCAATTCCTCGTGAAGTC 59.766 50.000 0.00 0.00 36.14 3.01
5081 5528 2.234908 CCCTCAATTCCTCGTGAAGTCT 59.765 50.000 0.00 0.00 36.14 3.24
5082 5529 3.447586 CCCTCAATTCCTCGTGAAGTCTA 59.552 47.826 0.00 0.00 36.14 2.59
5083 5530 4.440802 CCCTCAATTCCTCGTGAAGTCTAG 60.441 50.000 0.00 0.00 36.14 2.43
5084 5531 4.399618 CCTCAATTCCTCGTGAAGTCTAGA 59.600 45.833 0.00 0.00 36.14 2.43
5085 5532 5.068460 CCTCAATTCCTCGTGAAGTCTAGAT 59.932 44.000 0.00 0.00 36.14 1.98
5086 5533 6.406400 CCTCAATTCCTCGTGAAGTCTAGATT 60.406 42.308 0.00 0.00 36.14 2.40
5087 5534 6.936279 TCAATTCCTCGTGAAGTCTAGATTT 58.064 36.000 0.00 0.00 36.14 2.17
5088 5535 8.063200 TCAATTCCTCGTGAAGTCTAGATTTA 57.937 34.615 0.00 0.00 36.14 1.40
5089 5536 8.191446 TCAATTCCTCGTGAAGTCTAGATTTAG 58.809 37.037 0.00 0.00 36.14 1.85
5090 5537 7.648039 ATTCCTCGTGAAGTCTAGATTTAGT 57.352 36.000 0.00 0.00 36.14 2.24
5091 5538 6.680874 TCCTCGTGAAGTCTAGATTTAGTC 57.319 41.667 0.00 0.00 0.00 2.59
5092 5539 5.589452 TCCTCGTGAAGTCTAGATTTAGTCC 59.411 44.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.468226 ATGCCGTACTACATGGGTGG 59.532 55.000 0.00 0.00 33.38 4.61
1 2 3.678056 ATATGCCGTACTACATGGGTG 57.322 47.619 0.00 0.00 33.38 4.61
2 3 3.644265 TGAATATGCCGTACTACATGGGT 59.356 43.478 0.00 0.00 33.38 4.51
3 4 3.994392 GTGAATATGCCGTACTACATGGG 59.006 47.826 0.00 0.00 33.38 4.00
4 5 4.627058 TGTGAATATGCCGTACTACATGG 58.373 43.478 0.00 0.00 36.25 3.66
5 6 6.785488 ATTGTGAATATGCCGTACTACATG 57.215 37.500 7.52 0.00 0.00 3.21
6 7 8.148351 ACTTATTGTGAATATGCCGTACTACAT 58.852 33.333 3.39 3.39 0.00 2.29
7 8 7.494211 ACTTATTGTGAATATGCCGTACTACA 58.506 34.615 0.00 0.00 0.00 2.74
8 9 7.115947 GGACTTATTGTGAATATGCCGTACTAC 59.884 40.741 0.00 0.00 0.00 2.73
9 10 7.014905 AGGACTTATTGTGAATATGCCGTACTA 59.985 37.037 0.00 0.00 0.00 1.82
10 11 5.989777 GGACTTATTGTGAATATGCCGTACT 59.010 40.000 0.00 0.00 0.00 2.73
11 12 5.989777 AGGACTTATTGTGAATATGCCGTAC 59.010 40.000 0.00 0.00 0.00 3.67
12 13 6.169557 AGGACTTATTGTGAATATGCCGTA 57.830 37.500 0.00 0.00 0.00 4.02
13 14 5.036117 AGGACTTATTGTGAATATGCCGT 57.964 39.130 0.00 0.00 0.00 5.68
14 15 5.050091 GTGAGGACTTATTGTGAATATGCCG 60.050 44.000 0.00 0.00 0.00 5.69
22 23 6.599244 GGATGAAATGTGAGGACTTATTGTGA 59.401 38.462 0.00 0.00 0.00 3.58
34 35 7.331687 GGTGGTTTTATTTGGATGAAATGTGAG 59.668 37.037 0.00 0.00 35.74 3.51
41 42 5.835819 TCACAGGTGGTTTTATTTGGATGAA 59.164 36.000 0.00 0.00 0.00 2.57
44 45 4.217550 CGTCACAGGTGGTTTTATTTGGAT 59.782 41.667 0.00 0.00 0.00 3.41
47 48 4.822036 TCGTCACAGGTGGTTTTATTTG 57.178 40.909 0.00 0.00 0.00 2.32
56 57 1.495584 CGTGGTTTCGTCACAGGTGG 61.496 60.000 0.00 0.00 35.03 4.61
58 59 1.227438 CCGTGGTTTCGTCACAGGT 60.227 57.895 0.00 0.00 35.03 4.00
59 60 1.227438 ACCGTGGTTTCGTCACAGG 60.227 57.895 0.00 0.00 35.03 4.00
61 62 1.521906 CCACCGTGGTTTCGTCACA 60.522 57.895 9.64 0.00 35.03 3.58
63 64 0.107800 TTTCCACCGTGGTTTCGTCA 60.108 50.000 17.32 0.00 39.03 4.35
64 65 1.015868 TTTTCCACCGTGGTTTCGTC 58.984 50.000 17.32 0.00 39.03 4.20
66 67 0.029700 GGTTTTCCACCGTGGTTTCG 59.970 55.000 17.32 0.00 39.03 3.46
88 89 6.205853 TGTTTATAATCAAACTCAACGGCACT 59.794 34.615 0.00 0.00 38.85 4.40
93 94 8.073768 ACCTTGTGTTTATAATCAAACTCAACG 58.926 33.333 10.47 9.73 42.43 4.10
107 108 6.401581 CGTTGCAAAACAAACCTTGTGTTTAT 60.402 34.615 0.00 0.00 45.97 1.40
108 109 5.107453 CGTTGCAAAACAAACCTTGTGTTTA 60.107 36.000 0.00 0.00 45.97 2.01
112 113 2.473704 GCGTTGCAAAACAAACCTTGTG 60.474 45.455 0.00 0.00 44.59 3.33
134 135 5.409643 AACAGAAACGAAGATGTGAACAG 57.590 39.130 0.00 0.00 0.00 3.16
150 151 5.055265 TGGTGGACAGGATTAAAACAGAA 57.945 39.130 0.00 0.00 0.00 3.02
163 164 2.025981 TGGATGAGGAATTGGTGGACAG 60.026 50.000 0.00 0.00 0.00 3.51
213 214 0.643820 GAAACGGGAGATTACGTGCG 59.356 55.000 0.00 0.00 43.31 5.34
219 220 1.187974 TCCAGCGAAACGGGAGATTA 58.812 50.000 0.00 0.00 37.77 1.75
235 236 1.283613 AGGGCGTGGAAAACATATCCA 59.716 47.619 0.00 0.00 44.58 3.41
253 255 2.022762 GGTTTTGCGCGCGATAGG 59.977 61.111 37.18 3.91 0.00 2.57
274 281 2.484264 AGTTAATTGAGCCTGCGTGTTC 59.516 45.455 0.00 0.00 0.00 3.18
286 293 5.414454 GTGTGCATGTTAGGGAGTTAATTGA 59.586 40.000 0.00 0.00 0.00 2.57
295 302 0.037590 GTGGGTGTGCATGTTAGGGA 59.962 55.000 0.00 0.00 0.00 4.20
296 303 0.038166 AGTGGGTGTGCATGTTAGGG 59.962 55.000 0.00 0.00 0.00 3.53
298 305 0.523072 GCAGTGGGTGTGCATGTTAG 59.477 55.000 0.00 0.00 40.86 2.34
301 308 2.598394 GGCAGTGGGTGTGCATGT 60.598 61.111 0.00 0.00 43.12 3.21
303 310 1.904865 CTTGGCAGTGGGTGTGCAT 60.905 57.895 0.00 0.00 43.12 3.96
336 343 4.473520 CGCTGTAGGGTGGGGCAG 62.474 72.222 0.00 0.00 0.00 4.85
339 346 3.000819 TGTCGCTGTAGGGTGGGG 61.001 66.667 0.00 0.00 0.00 4.96
346 353 1.025812 CTAGGTCCCTGTCGCTGTAG 58.974 60.000 0.00 0.00 0.00 2.74
538 552 1.148157 CTAGTGGCCTGCGAACATCG 61.148 60.000 3.32 0.00 43.89 3.84
591 612 4.869297 CCAATTGCTTTCACACAACAAAGA 59.131 37.500 0.00 0.00 32.20 2.52
592 613 4.494526 GCCAATTGCTTTCACACAACAAAG 60.495 41.667 0.00 0.00 36.87 2.77
593 614 3.373439 GCCAATTGCTTTCACACAACAAA 59.627 39.130 0.00 0.00 36.87 2.83
594 615 2.935201 GCCAATTGCTTTCACACAACAA 59.065 40.909 0.00 0.00 36.87 2.83
595 616 2.548875 GCCAATTGCTTTCACACAACA 58.451 42.857 0.00 0.00 36.87 3.33
596 617 1.866601 GGCCAATTGCTTTCACACAAC 59.133 47.619 0.00 0.00 40.92 3.32
597 618 1.483827 TGGCCAATTGCTTTCACACAA 59.516 42.857 0.61 0.00 40.92 3.33
598 619 1.117994 TGGCCAATTGCTTTCACACA 58.882 45.000 0.61 0.00 40.92 3.72
599 620 1.501169 GTGGCCAATTGCTTTCACAC 58.499 50.000 7.24 0.00 40.92 3.82
600 621 0.392336 GGTGGCCAATTGCTTTCACA 59.608 50.000 7.24 0.00 40.92 3.58
644 665 3.567579 ATTGGTGCACAGGGACGGG 62.568 63.158 20.43 0.00 36.00 5.28
647 668 0.603065 GGAAATTGGTGCACAGGGAC 59.397 55.000 20.43 0.52 34.10 4.46
654 675 4.815308 CACAAAAATGAGGAAATTGGTGCA 59.185 37.500 0.00 0.00 0.00 4.57
667 688 2.627699 GGAGGGACAAGCACAAAAATGA 59.372 45.455 0.00 0.00 0.00 2.57
697 718 1.450312 AAATCGAAGGCCGCCTGAG 60.450 57.895 14.19 10.39 38.37 3.35
726 751 2.995466 CAAGAAATTCAGCGCTTGGA 57.005 45.000 7.50 0.00 35.34 3.53
899 924 2.673341 ACTGCCTCTCGACGAGCA 60.673 61.111 20.11 14.35 38.49 4.26
900 925 2.202544 CACTGCCTCTCGACGAGC 60.203 66.667 20.11 10.22 38.49 5.03
1037 1062 4.066139 GCACATTGGCCTCCCCCT 62.066 66.667 3.32 0.00 0.00 4.79
1414 1439 3.066380 CCAAAAGCCCAAAACACTATGC 58.934 45.455 0.00 0.00 0.00 3.14
1419 1444 3.619483 GTGTAACCAAAAGCCCAAAACAC 59.381 43.478 0.00 0.00 0.00 3.32
1453 1478 3.430218 CCAGAGTTTCAGTTTACAGCTCG 59.570 47.826 0.00 0.00 0.00 5.03
1470 1495 5.636965 CACAAGTCTACAATTCAGTCCAGAG 59.363 44.000 0.00 0.00 0.00 3.35
1475 1500 6.456501 ACTACCACAAGTCTACAATTCAGTC 58.543 40.000 0.00 0.00 0.00 3.51
1476 1501 6.420913 ACTACCACAAGTCTACAATTCAGT 57.579 37.500 0.00 0.00 0.00 3.41
1500 1710 3.196469 TCACCAGCACCAAATGTTCAAAA 59.804 39.130 0.00 0.00 0.00 2.44
1504 1714 2.362077 ACTTCACCAGCACCAAATGTTC 59.638 45.455 0.00 0.00 0.00 3.18
1506 1716 2.071778 ACTTCACCAGCACCAAATGT 57.928 45.000 0.00 0.00 0.00 2.71
1595 1805 3.513680 TGCATAGCAGCAAAGAAATGG 57.486 42.857 0.00 0.00 42.46 3.16
1619 1829 2.029288 ATTCGGATGCATAGCGCCG 61.029 57.895 16.30 16.30 45.61 6.46
1694 1905 9.823098 CTATATGCAATTCAGTTATTCAGAAGC 57.177 33.333 0.00 0.00 0.00 3.86
1748 1959 3.010200 ACAGCTCCATTGATTCCTTCC 57.990 47.619 0.00 0.00 0.00 3.46
1817 2028 0.249911 CACTGCTACGGGGAATAGCC 60.250 60.000 1.78 0.00 43.75 3.93
1847 2058 7.406104 AGTTACATTTAATCAAGAGAAGGGCT 58.594 34.615 0.00 0.00 0.00 5.19
1877 2088 8.058847 AGAAAATCCATAGCCTGTTACCAAATA 58.941 33.333 0.00 0.00 0.00 1.40
1912 2123 0.900182 GAAAACAGGGAGGGGGCAAG 60.900 60.000 0.00 0.00 0.00 4.01
1983 2194 1.971481 TCACATGAAGCTTGCTGTGT 58.029 45.000 25.72 14.07 39.89 3.72
2013 2224 2.024655 ACTCCCAGACATCAATGCCAAT 60.025 45.455 0.00 0.00 0.00 3.16
2493 2769 7.501225 GCTAAAATTACCAAGGCAGAAGGTATA 59.499 37.037 0.00 0.00 37.70 1.47
2853 3132 7.710676 ACAGAGGGAGTATATTATAGCACAG 57.289 40.000 0.00 0.00 0.00 3.66
2881 3160 4.430908 GCTACCCCAGCGACATATATTAC 58.569 47.826 0.00 0.00 41.37 1.89
2936 3215 2.169330 ACGAACTACTCCCTCTGTTCC 58.831 52.381 0.00 0.00 36.43 3.62
3035 3314 5.125578 GTCAAGTACAGATGAATTTTCCCCC 59.874 44.000 0.00 0.00 0.00 5.40
3081 3361 9.442047 AGTCTATAACATGAAGTGAAAAGGAAG 57.558 33.333 0.00 0.00 0.00 3.46
3135 3415 8.739039 TGGAACATGTTGAAAAGATATTGTAGG 58.261 33.333 17.58 0.00 0.00 3.18
3399 3700 5.472301 AGATAAACCCAATGAATCCCTGT 57.528 39.130 0.00 0.00 0.00 4.00
3435 3736 2.338809 ACTCCAACAAGAGATCCCACA 58.661 47.619 0.00 0.00 37.33 4.17
3627 3928 2.424601 CCACTTGATGCGGTTGATCATT 59.575 45.455 0.00 0.00 29.96 2.57
3654 3955 1.321474 TTGAGCTGAGCACCAAAAGG 58.679 50.000 7.39 0.00 0.00 3.11
3813 4114 1.523711 GATCAAGATCGCGGCCCAA 60.524 57.895 6.13 0.00 0.00 4.12
3954 4255 0.447011 AGGTTAGCTCGACGTTCTCG 59.553 55.000 0.00 0.00 44.44 4.04
3984 4285 2.517450 GGCGCTCGGATTCTTGTCG 61.517 63.158 7.64 0.00 0.00 4.35
4183 4486 9.356433 TGTAAAATGAATGAATACAACAGCATG 57.644 29.630 0.00 0.00 46.00 4.06
4242 4546 4.082517 GGAGGGAGTCTCAAATTTCAAAGC 60.083 45.833 1.47 0.00 44.19 3.51
4256 4560 4.345854 AGTAATATGGATCGGAGGGAGTC 58.654 47.826 0.00 0.00 0.00 3.36
4281 4585 4.689345 ACTAAAGTTGTACTAAAGCAGCGG 59.311 41.667 0.00 0.00 0.00 5.52
4285 4589 9.609346 AGAAGAAACTAAAGTTGTACTAAAGCA 57.391 29.630 0.00 0.00 38.44 3.91
4301 4605 9.886132 ACAGTGAGAGTTTAAAAGAAGAAACTA 57.114 29.630 0.00 0.00 44.04 2.24
4315 4619 6.821388 AGTCAAGATAACACAGTGAGAGTTT 58.179 36.000 7.81 0.00 33.05 2.66
4432 4741 7.549615 TTGAGAGCTCAAATCATGTAGATTG 57.450 36.000 17.77 0.00 46.09 2.67
4482 4882 1.639298 GAATCTGGTCCGCTGCACAC 61.639 60.000 0.00 0.00 0.00 3.82
4579 4980 5.225899 TGCTGTCAAGAATGAAATCATCG 57.774 39.130 0.00 0.00 37.30 3.84
4649 5050 2.632996 TCCCAATTCGTCTTGTGTCTCT 59.367 45.455 0.00 0.00 0.00 3.10
4755 5176 1.404181 CGATCTCCCTTCGAGCAACAA 60.404 52.381 0.00 0.00 38.88 2.83
4812 5258 0.685097 TATCCATAAGAGCACGCCCC 59.315 55.000 0.00 0.00 0.00 5.80
4813 5259 2.289694 ACATATCCATAAGAGCACGCCC 60.290 50.000 0.00 0.00 0.00 6.13
4834 5280 6.485984 CCCAAATTTCATGAAAAATGGTCACA 59.514 34.615 32.39 11.45 37.90 3.58
4938 5385 5.351465 ACATAGATTTCGTCGTTCTTGCATT 59.649 36.000 0.00 0.00 0.00 3.56
4951 5398 6.818644 CCTATTATGGTGGGACATAGATTTCG 59.181 42.308 0.00 0.00 44.52 3.46
4994 5441 5.152934 ACTTGAACCACCTCCTAAGAGTAA 58.847 41.667 0.00 0.00 38.58 2.24
5036 5483 9.428097 GGGACGAAAAGTATAGTTTTCTCTAAA 57.572 33.333 29.79 0.00 42.09 1.85
5039 5486 7.039223 TGAGGGACGAAAAGTATAGTTTTCTCT 60.039 37.037 29.79 23.23 42.09 3.10
5040 5487 7.095270 TGAGGGACGAAAAGTATAGTTTTCTC 58.905 38.462 29.79 25.43 42.09 2.87
5041 5488 7.001099 TGAGGGACGAAAAGTATAGTTTTCT 57.999 36.000 29.79 21.45 42.09 2.52
5042 5489 7.662604 TTGAGGGACGAAAAGTATAGTTTTC 57.337 36.000 26.07 26.07 41.24 2.29
5043 5490 8.631480 AATTGAGGGACGAAAAGTATAGTTTT 57.369 30.769 16.46 16.46 32.18 2.43
5045 5492 6.822170 GGAATTGAGGGACGAAAAGTATAGTT 59.178 38.462 0.00 0.00 0.00 2.24
5047 5494 6.583562 AGGAATTGAGGGACGAAAAGTATAG 58.416 40.000 0.00 0.00 0.00 1.31
5048 5495 6.555463 AGGAATTGAGGGACGAAAAGTATA 57.445 37.500 0.00 0.00 0.00 1.47
5050 5497 4.619863 CGAGGAATTGAGGGACGAAAAGTA 60.620 45.833 0.00 0.00 0.00 2.24
5051 5498 3.676093 GAGGAATTGAGGGACGAAAAGT 58.324 45.455 0.00 0.00 0.00 2.66
5052 5499 2.673368 CGAGGAATTGAGGGACGAAAAG 59.327 50.000 0.00 0.00 0.00 2.27
5053 5500 2.038033 ACGAGGAATTGAGGGACGAAAA 59.962 45.455 0.00 0.00 0.00 2.29
5054 5501 1.621814 ACGAGGAATTGAGGGACGAAA 59.378 47.619 0.00 0.00 0.00 3.46
5055 5502 1.067142 CACGAGGAATTGAGGGACGAA 60.067 52.381 0.00 0.00 0.00 3.85
5056 5503 0.530744 CACGAGGAATTGAGGGACGA 59.469 55.000 0.00 0.00 0.00 4.20
5057 5504 0.530744 TCACGAGGAATTGAGGGACG 59.469 55.000 0.00 0.00 0.00 4.79
5058 5505 2.028020 ACTTCACGAGGAATTGAGGGAC 60.028 50.000 0.00 0.00 34.32 4.46
5059 5506 2.233922 GACTTCACGAGGAATTGAGGGA 59.766 50.000 0.00 0.00 34.32 4.20
5060 5507 2.234908 AGACTTCACGAGGAATTGAGGG 59.765 50.000 0.00 0.00 34.32 4.30
5061 5508 3.601443 AGACTTCACGAGGAATTGAGG 57.399 47.619 0.00 0.00 34.32 3.86
5062 5509 5.568685 TCTAGACTTCACGAGGAATTGAG 57.431 43.478 0.00 0.00 34.32 3.02
5063 5510 6.531503 AATCTAGACTTCACGAGGAATTGA 57.468 37.500 0.00 0.00 34.32 2.57
5064 5511 7.976734 ACTAAATCTAGACTTCACGAGGAATTG 59.023 37.037 0.00 0.00 34.32 2.32
5065 5512 8.068892 ACTAAATCTAGACTTCACGAGGAATT 57.931 34.615 0.00 0.00 34.32 2.17
5066 5513 7.201839 GGACTAAATCTAGACTTCACGAGGAAT 60.202 40.741 0.00 0.00 34.32 3.01
5067 5514 6.095160 GGACTAAATCTAGACTTCACGAGGAA 59.905 42.308 0.00 0.00 0.00 3.36
5068 5515 5.589452 GGACTAAATCTAGACTTCACGAGGA 59.411 44.000 0.00 0.00 0.00 3.71
5069 5516 5.823353 GGACTAAATCTAGACTTCACGAGG 58.177 45.833 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.