Multiple sequence alignment - TraesCS2A01G441100

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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 TraesCS2A01G441100 chr2A 100.000 3423 0 0 1 3423 691217897 691214475 0.000000e+00 6322.0
1 TraesCS2A01G441100 chr2A 88.612 922 68 20 999 1898 691185785 691184879 0.000000e+00 1086.0
2 TraesCS2A01G441100 chr2A 93.175 337 22 1 2088 2424 691184502 691184167 8.530000e-136 494.0
3 TraesCS2A01G441100 chr2A 96.739 92 3 0 3319 3410 455340491 455340400 1.640000e-33 154.0
4 TraesCS2A01G441100 chr2D 90.183 1752 80 25 773 2445 547694225 547695963 0.000000e+00 2198.0
5 TraesCS2A01G441100 chr2D 87.393 936 68 20 999 1904 547760767 547761682 0.000000e+00 1029.0
6 TraesCS2A01G441100 chr2D 89.796 784 53 6 1 770 547693421 547694191 0.000000e+00 979.0
7 TraesCS2A01G441100 chr2D 92.623 366 21 1 2086 2445 547761763 547762128 3.910000e-144 521.0
8 TraesCS2A01G441100 chr2D 84.530 543 37 18 3 534 74862310 74862816 8.530000e-136 494.0
9 TraesCS2A01G441100 chr2D 98.462 65 1 0 523 587 74862862 74862926 7.760000e-22 115.0
10 TraesCS2A01G441100 chr1A 95.282 869 41 0 2455 3323 260842916 260842048 0.000000e+00 1378.0
11 TraesCS2A01G441100 chr1A 94.949 99 5 0 3317 3415 547849083 547849181 4.570000e-34 156.0
12 TraesCS2A01G441100 chr1D 95.167 869 42 0 2455 3323 494487552 494486684 0.000000e+00 1373.0
13 TraesCS2A01G441100 chr4D 94.822 869 45 0 2455 3323 126639361 126638493 0.000000e+00 1356.0
14 TraesCS2A01G441100 chr5A 94.361 869 49 0 2455 3323 634632523 634633391 0.000000e+00 1334.0
15 TraesCS2A01G441100 chr5A 93.671 869 54 1 2455 3323 343042678 343043545 0.000000e+00 1299.0
16 TraesCS2A01G441100 chr3B 94.131 869 51 0 2455 3323 541061630 541062498 0.000000e+00 1323.0
17 TraesCS2A01G441100 chr3B 93.023 43 3 0 2031 2073 822727910 822727868 2.850000e-06 63.9
18 TraesCS2A01G441100 chr4A 94.023 870 51 1 2455 3323 438391662 438390793 0.000000e+00 1317.0
19 TraesCS2A01G441100 chr5D 93.807 872 51 1 2455 3323 63607973 63607102 0.000000e+00 1308.0
20 TraesCS2A01G441100 chr5D 97.778 45 1 0 2028 2072 13999812 13999856 1.020000e-10 78.7
21 TraesCS2A01G441100 chr6B 93.585 873 52 4 2455 3323 28112796 28113668 0.000000e+00 1299.0
22 TraesCS2A01G441100 chr2B 89.544 899 72 12 999 1884 654323795 654324684 0.000000e+00 1120.0
23 TraesCS2A01G441100 chr2B 87.649 1004 68 26 934 1898 654355093 654356079 0.000000e+00 1116.0
24 TraesCS2A01G441100 chr2B 88.515 714 43 9 1 686 653969658 653970360 0.000000e+00 828.0
25 TraesCS2A01G441100 chr2B 88.723 603 32 9 3 587 113612607 113613191 0.000000e+00 704.0
26 TraesCS2A01G441100 chr2B 94.460 361 20 0 2086 2446 654356165 654356525 1.070000e-154 556.0
27 TraesCS2A01G441100 chr2B 93.496 369 22 1 2075 2443 654324892 654325258 6.460000e-152 547.0
28 TraesCS2A01G441100 chr2B 94.949 99 3 2 3319 3415 647539445 647539347 1.640000e-33 154.0
29 TraesCS2A01G441100 chr2B 94.898 98 3 2 3312 3408 751263565 751263661 5.920000e-33 152.0
30 TraesCS2A01G441100 chr2B 93.204 103 6 1 3314 3415 13713112 13713010 2.130000e-32 150.0
31 TraesCS2A01G441100 chr3D 95.918 98 4 0 3318 3415 43315817 43315914 3.540000e-35 159.0
32 TraesCS2A01G441100 chr4B 98.864 88 1 0 3320 3407 429694669 429694756 1.270000e-34 158.0
33 TraesCS2A01G441100 chr7B 95.789 95 4 0 3315 3409 733608801 733608895 1.640000e-33 154.0
34 TraesCS2A01G441100 chr7B 89.362 47 5 0 2027 2073 641142750 641142796 3.690000e-05 60.2
35 TraesCS2A01G441100 chr1B 92.453 106 4 4 3305 3408 134494618 134494721 7.650000e-32 148.0
36 TraesCS2A01G441100 chr7D 86.111 72 6 4 2031 2100 593247827 593247896 1.320000e-09 75.0


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 TraesCS2A01G441100 chr2A 691214475 691217897 3422 True 6322.0 6322 100.0000 1 3423 1 chr2A.!!$R2 3422
1 TraesCS2A01G441100 chr2A 691184167 691185785 1618 True 790.0 1086 90.8935 999 2424 2 chr2A.!!$R3 1425
2 TraesCS2A01G441100 chr2D 547693421 547695963 2542 False 1588.5 2198 89.9895 1 2445 2 chr2D.!!$F2 2444
3 TraesCS2A01G441100 chr2D 547760767 547762128 1361 False 775.0 1029 90.0080 999 2445 2 chr2D.!!$F3 1446
4 TraesCS2A01G441100 chr2D 74862310 74862926 616 False 304.5 494 91.4960 3 587 2 chr2D.!!$F1 584
5 TraesCS2A01G441100 chr1A 260842048 260842916 868 True 1378.0 1378 95.2820 2455 3323 1 chr1A.!!$R1 868
6 TraesCS2A01G441100 chr1D 494486684 494487552 868 True 1373.0 1373 95.1670 2455 3323 1 chr1D.!!$R1 868
7 TraesCS2A01G441100 chr4D 126638493 126639361 868 True 1356.0 1356 94.8220 2455 3323 1 chr4D.!!$R1 868
8 TraesCS2A01G441100 chr5A 634632523 634633391 868 False 1334.0 1334 94.3610 2455 3323 1 chr5A.!!$F2 868
9 TraesCS2A01G441100 chr5A 343042678 343043545 867 False 1299.0 1299 93.6710 2455 3323 1 chr5A.!!$F1 868
10 TraesCS2A01G441100 chr3B 541061630 541062498 868 False 1323.0 1323 94.1310 2455 3323 1 chr3B.!!$F1 868
11 TraesCS2A01G441100 chr4A 438390793 438391662 869 True 1317.0 1317 94.0230 2455 3323 1 chr4A.!!$R1 868
12 TraesCS2A01G441100 chr5D 63607102 63607973 871 True 1308.0 1308 93.8070 2455 3323 1 chr5D.!!$R1 868
13 TraesCS2A01G441100 chr6B 28112796 28113668 872 False 1299.0 1299 93.5850 2455 3323 1 chr6B.!!$F1 868
14 TraesCS2A01G441100 chr2B 654355093 654356525 1432 False 836.0 1116 91.0545 934 2446 2 chr2B.!!$F5 1512
15 TraesCS2A01G441100 chr2B 654323795 654325258 1463 False 833.5 1120 91.5200 999 2443 2 chr2B.!!$F4 1444
16 TraesCS2A01G441100 chr2B 653969658 653970360 702 False 828.0 828 88.5150 1 686 1 chr2B.!!$F2 685
17 TraesCS2A01G441100 chr2B 113612607 113613191 584 False 704.0 704 88.7230 3 587 1 chr2B.!!$F1 584

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
245 263 0.478072 TGATGGCTGGTTCAGTTGGT 59.522 50.0 0.00 0.0 33.43 3.67 F
1108 1278 0.811616 CTACCTCAAGTCCATGGCGC 60.812 60.0 6.96 0.0 0.00 6.53 F
1801 2010 0.111061 TCCACCAGCTGATGCAGTTT 59.889 50.0 17.39 0.0 42.74 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1901 1.293498 CGGGAGGTCCAACACTGAG 59.707 63.158 0.0 0.0 37.91 3.35 R
2183 2689 1.581447 CTTTCGCTCCTTGGGCAAC 59.419 57.895 0.0 0.0 0.00 4.17 R
3402 3922 0.175989 CTCGCCCCTTTGTCCTACTC 59.824 60.000 0.0 0.0 0.00 2.59 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
71 72 2.743928 GGTGGTTGAGCAGCCTCG 60.744 66.667 4.99 0.00 41.13 4.63
84 85 2.506345 GCCTCGCGCTTAGTTCGTC 61.506 63.158 5.56 0.00 0.00 4.20
152 163 6.195700 TGACTACTAGGCTGGAGAAATTAGT 58.804 40.000 4.33 0.30 0.00 2.24
188 199 6.915843 GGGTAATCAAACAATTTATACAGCGG 59.084 38.462 0.00 0.00 0.00 5.52
245 263 0.478072 TGATGGCTGGTTCAGTTGGT 59.522 50.000 0.00 0.00 33.43 3.67
264 282 6.326323 AGTTGGTGATTTTGGGTTTTAGATGT 59.674 34.615 0.00 0.00 0.00 3.06
277 295 6.263617 GGGTTTTAGATGTACCAAACTGAACA 59.736 38.462 0.00 0.00 33.51 3.18
382 401 6.756299 AATGTGGTTGTTTTCAGCAATTTT 57.244 29.167 0.00 0.00 32.61 1.82
426 445 4.439057 TGATACTTGTGGCGATTACCTTC 58.561 43.478 0.00 0.00 0.00 3.46
538 623 1.394917 CAGTACTGCATCGACAAAGCC 59.605 52.381 10.54 0.00 0.00 4.35
629 733 1.379710 TCCGCACCAATTGGGATGG 60.380 57.895 27.89 23.21 40.70 3.51
725 829 3.511146 CACATGCCAGTAGGAATTTGGTT 59.489 43.478 0.00 0.00 36.89 3.67
729 833 6.096846 ACATGCCAGTAGGAATTTGGTTAATC 59.903 38.462 0.00 0.00 36.89 1.75
737 841 4.099419 AGGAATTTGGTTAATCGCCATTCC 59.901 41.667 12.43 12.43 41.80 3.01
753 857 5.584649 CGCCATTCCACTAGAAGAAACATAA 59.415 40.000 0.00 0.00 38.07 1.90
758 862 7.907214 TTCCACTAGAAGAAACATAAGAAGC 57.093 36.000 0.00 0.00 0.00 3.86
770 874 7.437862 AGAAACATAAGAAGCTCGATGAAGATC 59.562 37.037 0.00 0.00 0.00 2.75
771 875 6.154203 ACATAAGAAGCTCGATGAAGATCA 57.846 37.500 0.00 0.00 0.00 2.92
789 924 5.191426 AGATCATGGACTCCTTTGTTGATG 58.809 41.667 0.00 0.00 0.00 3.07
830 965 1.123077 CCTCAGTTCGATCCCCATCA 58.877 55.000 0.00 0.00 0.00 3.07
831 966 1.696336 CCTCAGTTCGATCCCCATCAT 59.304 52.381 0.00 0.00 0.00 2.45
832 967 2.289320 CCTCAGTTCGATCCCCATCATC 60.289 54.545 0.00 0.00 0.00 2.92
847 982 3.005791 CCATCATCGGGGGCTTTATTTTC 59.994 47.826 0.00 0.00 0.00 2.29
852 987 1.754803 CGGGGGCTTTATTTTCCTTCC 59.245 52.381 0.00 0.00 0.00 3.46
916 1073 1.134189 GGTAAACTCGGGGGAAGATGG 60.134 57.143 0.00 0.00 0.00 3.51
921 1078 2.031163 CGGGGGAAGATGGATCGC 59.969 66.667 0.00 0.00 0.00 4.58
955 1112 6.404712 AATCGTTCGGATCTGTTAGTTTTC 57.595 37.500 0.42 0.00 33.02 2.29
1002 1172 4.650754 AACACTAGCGGAGTAGGTAATG 57.349 45.455 0.00 0.00 35.64 1.90
1011 1181 3.243569 CGGAGTAGGTAATGGCAGAAGAG 60.244 52.174 0.00 0.00 0.00 2.85
1108 1278 0.811616 CTACCTCAAGTCCATGGCGC 60.812 60.000 6.96 0.00 0.00 6.53
1360 1548 3.744719 TGTCCCGCCTTCTCGTCG 61.745 66.667 0.00 0.00 0.00 5.12
1692 1901 2.359850 TTCCCGCATGTCAGGTGC 60.360 61.111 0.00 0.00 39.18 5.01
1695 1904 2.046988 CCGCATGTCAGGTGCTCA 60.047 61.111 0.00 0.00 40.37 4.26
1726 1935 0.951558 CCCGCATGTTATACAAGGCC 59.048 55.000 0.00 0.00 31.42 5.19
1801 2010 0.111061 TCCACCAGCTGATGCAGTTT 59.889 50.000 17.39 0.00 42.74 2.66
1817 2026 4.954442 GCAGTTTTGCTTAAGGTACTACG 58.046 43.478 4.29 0.00 46.95 3.51
1818 2027 4.450080 GCAGTTTTGCTTAAGGTACTACGT 59.550 41.667 4.29 0.00 46.95 3.57
1819 2028 5.634859 GCAGTTTTGCTTAAGGTACTACGTA 59.365 40.000 4.29 0.00 46.95 3.57
1820 2029 6.312180 GCAGTTTTGCTTAAGGTACTACGTAT 59.688 38.462 4.29 0.00 46.95 3.06
1821 2030 7.489113 GCAGTTTTGCTTAAGGTACTACGTATA 59.511 37.037 4.29 0.00 46.95 1.47
1898 2119 6.457663 CGTTCGCATTTATACCAATTCCTCAA 60.458 38.462 0.00 0.00 0.00 3.02
1980 2485 6.532302 TGAGCGCTTAACAAGAATATAAACGA 59.468 34.615 13.26 0.00 0.00 3.85
2062 2568 9.899661 AATAGTTTAGATTGCTTACCACATGTA 57.100 29.630 0.00 0.00 0.00 2.29
2064 2570 8.438676 AGTTTAGATTGCTTACCACATGTATC 57.561 34.615 0.00 0.00 0.00 2.24
2067 2573 5.744171 AGATTGCTTACCACATGTATCACA 58.256 37.500 0.00 0.00 0.00 3.58
2090 2596 8.580720 CACATGGTTAGAGTAGTGCTATCTTAT 58.419 37.037 0.00 0.00 0.00 1.73
2116 2622 8.231692 TGATAGTTTTTGACTTGTTGGATTGA 57.768 30.769 0.00 0.00 39.86 2.57
2144 2650 1.014564 GCTACACAACTGGAGCGACC 61.015 60.000 0.00 0.00 44.74 4.79
2173 2679 5.132502 TGTGTGAAGATCCTGACAAAATGT 58.867 37.500 0.00 0.00 0.00 2.71
2175 2681 6.770303 TGTGTGAAGATCCTGACAAAATGTAA 59.230 34.615 0.00 0.00 0.00 2.41
2183 2689 3.119849 CCTGACAAAATGTAAAGAGGCCG 60.120 47.826 0.00 0.00 0.00 6.13
2290 2802 4.213694 GCTCAAGTCTTGATGGATATGCAG 59.786 45.833 15.60 1.79 39.30 4.41
2305 2817 5.183331 GGATATGCAGATGATGATGCTGTTT 59.817 40.000 0.00 0.00 42.98 2.83
2349 2861 6.259550 ACTCAACTGGCAAAAGATATTCAC 57.740 37.500 0.00 0.00 0.00 3.18
2350 2862 5.183904 ACTCAACTGGCAAAAGATATTCACC 59.816 40.000 0.00 0.00 0.00 4.02
2382 2894 9.461312 AGGATTTAGTCATTACAAAATACAGCA 57.539 29.630 0.00 0.00 0.00 4.41
2404 2916 2.705658 TGTCCTAGGAATGCGATCCATT 59.294 45.455 14.65 8.59 46.57 3.16
2424 2936 5.491982 CATTATCCAACTCTACCCATAGCC 58.508 45.833 0.00 0.00 0.00 3.93
2736 3251 8.774546 ATCACCTCTAGATTATCTGAGTTGAA 57.225 34.615 17.82 8.46 32.11 2.69
2752 3267 4.202441 AGTTGAAGATTAGGCGATTGCAT 58.798 39.130 7.38 1.37 45.35 3.96
2765 3280 4.675161 TGCATCCCGCCCTTTGCA 62.675 61.111 0.00 0.00 42.41 4.08
2776 3291 1.468914 GCCCTTTGCACTAGTGTTAGC 59.531 52.381 23.44 13.93 40.77 3.09
2908 3423 1.555075 GTACCCTTCAGCATGTCCTGA 59.445 52.381 0.00 0.00 39.94 3.86
2992 3508 1.808411 TCATGGACGCCTTTGAAGAC 58.192 50.000 0.00 0.00 0.00 3.01
2995 3511 0.599204 TGGACGCCTTTGAAGACGAC 60.599 55.000 6.46 0.32 35.38 4.34
3035 3551 1.988107 TGAGGGCTATGATCCCCATTC 59.012 52.381 7.44 0.00 45.03 2.67
3054 3570 6.072618 CCCATTCATATCTGAGTTGCATTCTC 60.073 42.308 11.08 11.08 31.68 2.87
3056 3572 7.012989 CCATTCATATCTGAGTTGCATTCTCAA 59.987 37.037 18.28 12.03 40.68 3.02
3087 3603 5.049405 CCTTGTGCACTAATTTTCGTCTCTT 60.049 40.000 19.41 0.00 0.00 2.85
3195 3711 5.881923 AAAAGGTATTCCAGTATCGCCTA 57.118 39.130 0.00 0.00 35.89 3.93
3280 3796 6.869206 ACCTCCTTTGCTTTAGTACATAGA 57.131 37.500 0.00 0.00 0.00 1.98
3323 3843 5.360144 TCTTCTACACCCTGATAGCAAGTAC 59.640 44.000 0.00 0.00 0.00 2.73
3324 3844 4.868268 TCTACACCCTGATAGCAAGTACT 58.132 43.478 0.00 0.00 0.00 2.73
3325 3845 4.888239 TCTACACCCTGATAGCAAGTACTC 59.112 45.833 0.00 0.00 0.00 2.59
3326 3846 2.766828 ACACCCTGATAGCAAGTACTCC 59.233 50.000 0.00 0.00 0.00 3.85
3327 3847 2.103263 CACCCTGATAGCAAGTACTCCC 59.897 54.545 0.00 0.00 0.00 4.30
3328 3848 2.022918 ACCCTGATAGCAAGTACTCCCT 60.023 50.000 0.00 0.00 0.00 4.20
3329 3849 2.630580 CCCTGATAGCAAGTACTCCCTC 59.369 54.545 0.00 0.00 0.00 4.30
3330 3850 2.630580 CCTGATAGCAAGTACTCCCTCC 59.369 54.545 0.00 0.00 0.00 4.30
3331 3851 2.294791 CTGATAGCAAGTACTCCCTCCG 59.705 54.545 0.00 0.00 0.00 4.63
3332 3852 2.308690 GATAGCAAGTACTCCCTCCGT 58.691 52.381 0.00 0.00 0.00 4.69
3333 3853 2.226962 TAGCAAGTACTCCCTCCGTT 57.773 50.000 0.00 0.00 0.00 4.44
3334 3854 0.896226 AGCAAGTACTCCCTCCGTTC 59.104 55.000 0.00 0.00 0.00 3.95
3335 3855 0.108281 GCAAGTACTCCCTCCGTTCC 60.108 60.000 0.00 0.00 0.00 3.62
3336 3856 1.263356 CAAGTACTCCCTCCGTTCCA 58.737 55.000 0.00 0.00 0.00 3.53
3337 3857 1.621814 CAAGTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
3338 3858 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
3339 3859 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
3340 3860 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
3341 3861 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
3342 3862 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3343 3863 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
3344 3864 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3345 3865 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
3346 3866 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
3347 3867 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
3348 3868 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
3349 3869 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
3350 3870 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
3351 3871 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
3352 3872 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
3353 3873 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
3354 3874 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
3355 3875 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
3356 3876 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
3357 3877 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
3358 3878 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
3359 3879 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
3360 3880 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
3383 3903 8.983702 ACTAATTTTAGTACAAAGTTGGGTCA 57.016 30.769 1.15 0.00 41.92 4.02
3384 3904 9.582648 ACTAATTTTAGTACAAAGTTGGGTCAT 57.417 29.630 1.15 0.00 41.92 3.06
3386 3906 8.706322 AATTTTAGTACAAAGTTGGGTCATCT 57.294 30.769 0.00 0.00 0.00 2.90
3387 3907 9.802039 AATTTTAGTACAAAGTTGGGTCATCTA 57.198 29.630 0.00 0.00 0.00 1.98
3388 3908 9.975218 ATTTTAGTACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 0.00 1.98
3389 3909 9.802039 TTTTAGTACAAAGTTGGGTCATCTATT 57.198 29.630 0.00 0.00 0.00 1.73
3390 3910 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
3391 3911 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
3392 3912 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
3393 3913 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
3394 3914 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
3395 3915 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
3396 3916 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
3397 3917 5.640147 AGTTGGGTCATCTATTTTGGAACA 58.360 37.500 0.00 0.00 0.00 3.18
3398 3918 5.711976 AGTTGGGTCATCTATTTTGGAACAG 59.288 40.000 0.00 0.00 42.39 3.16
3399 3919 5.512942 TGGGTCATCTATTTTGGAACAGA 57.487 39.130 0.00 0.00 42.39 3.41
3400 3920 5.500234 TGGGTCATCTATTTTGGAACAGAG 58.500 41.667 0.00 0.00 42.39 3.35
3401 3921 4.884164 GGGTCATCTATTTTGGAACAGAGG 59.116 45.833 0.00 0.00 42.39 3.69
3402 3922 4.884164 GGTCATCTATTTTGGAACAGAGGG 59.116 45.833 0.00 0.00 42.39 4.30
3403 3923 5.339200 GGTCATCTATTTTGGAACAGAGGGA 60.339 44.000 0.00 0.00 42.39 4.20
3404 3924 5.819901 GTCATCTATTTTGGAACAGAGGGAG 59.180 44.000 0.00 0.00 42.39 4.30
3405 3925 5.488919 TCATCTATTTTGGAACAGAGGGAGT 59.511 40.000 0.00 0.00 42.39 3.85
3406 3926 6.672218 TCATCTATTTTGGAACAGAGGGAGTA 59.328 38.462 0.00 0.00 42.39 2.59
3407 3927 6.546428 TCTATTTTGGAACAGAGGGAGTAG 57.454 41.667 0.00 0.00 42.39 2.57
3408 3928 4.576330 ATTTTGGAACAGAGGGAGTAGG 57.424 45.455 0.00 0.00 42.39 3.18
3409 3929 3.269592 TTTGGAACAGAGGGAGTAGGA 57.730 47.619 0.00 0.00 42.39 2.94
3410 3930 2.233305 TGGAACAGAGGGAGTAGGAC 57.767 55.000 0.00 0.00 0.00 3.85
3411 3931 1.431633 TGGAACAGAGGGAGTAGGACA 59.568 52.381 0.00 0.00 0.00 4.02
3412 3932 2.158219 TGGAACAGAGGGAGTAGGACAA 60.158 50.000 0.00 0.00 0.00 3.18
3413 3933 2.904434 GGAACAGAGGGAGTAGGACAAA 59.096 50.000 0.00 0.00 0.00 2.83
3414 3934 3.055747 GGAACAGAGGGAGTAGGACAAAG 60.056 52.174 0.00 0.00 0.00 2.77
3415 3935 2.541466 ACAGAGGGAGTAGGACAAAGG 58.459 52.381 0.00 0.00 0.00 3.11
3416 3936 1.834263 CAGAGGGAGTAGGACAAAGGG 59.166 57.143 0.00 0.00 0.00 3.95
3417 3937 1.205055 GAGGGAGTAGGACAAAGGGG 58.795 60.000 0.00 0.00 0.00 4.79
3418 3938 0.914902 AGGGAGTAGGACAAAGGGGC 60.915 60.000 0.00 0.00 0.00 5.80
3419 3939 1.221021 GGAGTAGGACAAAGGGGCG 59.779 63.158 0.00 0.00 0.00 6.13
3420 3940 1.262640 GGAGTAGGACAAAGGGGCGA 61.263 60.000 0.00 0.00 0.00 5.54
3421 3941 0.175989 GAGTAGGACAAAGGGGCGAG 59.824 60.000 0.00 0.00 0.00 5.03
3422 3942 1.221021 GTAGGACAAAGGGGCGAGG 59.779 63.158 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 0.453950 TCAGTCGACGAACTAAGCGC 60.454 55.000 10.46 0.00 0.00 5.92
152 163 5.309638 TGTTTGATTACCCTCGTGAATTCA 58.690 37.500 3.38 3.38 0.00 2.57
222 240 2.624838 CAACTGAACCAGCCATCACTTT 59.375 45.455 0.00 0.00 34.37 2.66
245 263 7.841282 TTGGTACATCTAAAACCCAAAATCA 57.159 32.000 0.00 0.00 39.30 2.57
264 282 4.502171 CATGCACATGTTCAGTTTGGTA 57.498 40.909 4.16 0.00 34.23 3.25
277 295 1.464608 GTCGCACAAGTACATGCACAT 59.535 47.619 14.68 0.00 42.17 3.21
382 401 5.593909 TCAAAATCCAAGTTCAAAGCAGAGA 59.406 36.000 0.00 0.00 0.00 3.10
426 445 3.599730 GGAAGCAATCCCAGAAAAAGG 57.400 47.619 0.00 0.00 43.00 3.11
489 512 2.539953 CGTGCCGCTTCTTGTGTAAAAA 60.540 45.455 0.00 0.00 0.00 1.94
490 513 1.003331 CGTGCCGCTTCTTGTGTAAAA 60.003 47.619 0.00 0.00 0.00 1.52
492 515 0.249531 TCGTGCCGCTTCTTGTGTAA 60.250 50.000 0.00 0.00 0.00 2.41
493 516 0.249531 TTCGTGCCGCTTCTTGTGTA 60.250 50.000 0.00 0.00 0.00 2.90
504 532 1.012486 GTACTGGGTTCTTCGTGCCG 61.012 60.000 0.00 0.00 0.00 5.69
538 623 0.667184 GAAAAATGCACTGCCCCACG 60.667 55.000 0.00 0.00 0.00 4.94
644 748 2.086094 CATGGTGTGCATAAGCTGTGA 58.914 47.619 3.69 0.00 42.74 3.58
713 817 5.300792 GGAATGGCGATTAACCAAATTCCTA 59.699 40.000 7.58 0.00 40.75 2.94
725 829 5.607939 TTCTTCTAGTGGAATGGCGATTA 57.392 39.130 0.00 0.00 33.01 1.75
729 833 3.334691 TGTTTCTTCTAGTGGAATGGCG 58.665 45.455 0.00 0.00 33.01 5.69
737 841 7.030165 TCGAGCTTCTTATGTTTCTTCTAGTG 58.970 38.462 0.00 0.00 0.00 2.74
753 857 3.640498 TCCATGATCTTCATCGAGCTTCT 59.360 43.478 0.00 0.00 34.28 2.85
758 862 3.573538 AGGAGTCCATGATCTTCATCGAG 59.426 47.826 12.86 0.00 34.28 4.04
770 874 5.191426 AGATCATCAACAAAGGAGTCCATG 58.809 41.667 12.86 12.45 0.00 3.66
771 875 5.191323 AGAGATCATCAACAAAGGAGTCCAT 59.809 40.000 12.86 0.00 0.00 3.41
789 924 2.359531 CCTACGGACCAAGTCAGAGATC 59.640 54.545 1.86 0.00 33.68 2.75
830 965 3.296854 GAAGGAAAATAAAGCCCCCGAT 58.703 45.455 0.00 0.00 0.00 4.18
831 966 2.622190 GGAAGGAAAATAAAGCCCCCGA 60.622 50.000 0.00 0.00 0.00 5.14
832 967 1.754803 GGAAGGAAAATAAAGCCCCCG 59.245 52.381 0.00 0.00 0.00 5.73
847 982 4.521062 CGCTGGAGCCGAGGAAGG 62.521 72.222 0.00 0.00 37.91 3.46
852 987 2.027314 CTGATCGCTGGAGCCGAG 59.973 66.667 0.00 0.00 37.91 4.63
955 1112 7.439157 TCATCTTTGAGTTTGAGTAATGGTG 57.561 36.000 0.00 0.00 0.00 4.17
1002 1172 1.153389 GGCTCTGCTCTCTTCTGCC 60.153 63.158 0.00 0.00 0.00 4.85
1108 1278 4.081030 CTTCACCGCGCTGTGCAG 62.081 66.667 25.04 20.45 46.97 4.41
1131 1301 2.833582 TGGAGAGCGTCGGGGATC 60.834 66.667 0.00 0.00 0.00 3.36
1501 1710 2.045045 CATGTCATGGCCGGTGGT 60.045 61.111 1.90 0.00 0.00 4.16
1563 1772 1.299468 GACGAGCTCCGCCATGTAG 60.299 63.158 8.47 0.00 43.32 2.74
1692 1901 1.293498 CGGGAGGTCCAACACTGAG 59.707 63.158 0.00 0.00 37.91 3.35
1695 1904 2.224159 ATGCGGGAGGTCCAACACT 61.224 57.895 0.00 0.00 37.91 3.55
1737 1946 2.551459 AGCAAACTCAACTGACTCATGC 59.449 45.455 0.00 0.00 0.00 4.06
1746 1955 2.555547 GCCGGCAGCAAACTCAACT 61.556 57.895 24.80 0.00 42.97 3.16
1863 2080 2.295253 AATGCGAACGGGAAGTAGAG 57.705 50.000 0.00 0.00 0.00 2.43
1910 2131 3.250762 TGTCGTGCCTTTCATTCTTTGAG 59.749 43.478 0.00 0.00 35.27 3.02
1980 2485 5.130350 TCTTTTCTTTTTGTCGGATCCACT 58.870 37.500 13.41 0.00 0.00 4.00
2034 2539 8.892723 CATGTGGTAAGCAATCTAAACTATTCA 58.107 33.333 0.00 0.00 0.00 2.57
2035 2540 8.893727 ACATGTGGTAAGCAATCTAAACTATTC 58.106 33.333 0.00 0.00 0.00 1.75
2039 2545 8.046708 TGATACATGTGGTAAGCAATCTAAACT 58.953 33.333 9.11 0.00 35.14 2.66
2044 2550 5.744171 TGTGATACATGTGGTAAGCAATCT 58.256 37.500 9.11 0.00 35.14 2.40
2062 2568 6.780031 AGATAGCACTACTCTAACCATGTGAT 59.220 38.462 0.00 0.00 0.00 3.06
2064 2570 6.398234 AGATAGCACTACTCTAACCATGTG 57.602 41.667 0.00 0.00 0.00 3.21
2067 2573 9.368416 TCAATAAGATAGCACTACTCTAACCAT 57.632 33.333 0.00 0.00 0.00 3.55
2090 2596 8.690884 TCAATCCAACAAGTCAAAAACTATCAA 58.309 29.630 0.00 0.00 37.17 2.57
2183 2689 1.581447 CTTTCGCTCCTTGGGCAAC 59.419 57.895 0.00 0.00 0.00 4.17
2290 2802 5.684550 TGCTCATAAACAGCATCATCATC 57.315 39.130 0.00 0.00 42.09 2.92
2305 2817 3.953712 TCCTCACGTTCTTTGCTCATA 57.046 42.857 0.00 0.00 0.00 2.15
2349 2861 5.116180 TGTAATGACTAAATCCTGCTTCGG 58.884 41.667 0.00 0.00 0.00 4.30
2350 2862 6.662414 TTGTAATGACTAAATCCTGCTTCG 57.338 37.500 0.00 0.00 0.00 3.79
2382 2894 2.329267 TGGATCGCATTCCTAGGACAT 58.671 47.619 12.22 5.81 36.68 3.06
2404 2916 4.487282 AGGCTATGGGTAGAGTTGGATA 57.513 45.455 0.00 0.00 0.00 2.59
2593 3105 8.270744 AGATTCAAACATTGTAATAGAGAGGCT 58.729 33.333 0.00 0.00 0.00 4.58
2639 3151 2.299013 TCAATGACTGCTTCCACTACGT 59.701 45.455 0.00 0.00 0.00 3.57
2765 3280 5.010282 CCTCAAATTTGGGCTAACACTAGT 58.990 41.667 17.90 0.00 0.00 2.57
2776 3291 2.833943 AGCTTTAGCCCTCAAATTTGGG 59.166 45.455 17.90 14.78 46.00 4.12
2908 3423 3.820467 TCAATGTTGACGCCTCTTTTGAT 59.180 39.130 0.00 0.00 31.01 2.57
2992 3508 6.521477 TCACATACAATTTTGTAAATGCGTCG 59.479 34.615 7.20 0.00 45.74 5.12
2995 3511 6.253298 CCCTCACATACAATTTTGTAAATGCG 59.747 38.462 7.20 4.48 45.74 4.73
3035 3551 7.704271 ACAATTGAGAATGCAACTCAGATATG 58.296 34.615 20.51 18.85 0.00 1.78
3054 3570 7.481275 AAATTAGTGCACAAGGAAACAATTG 57.519 32.000 21.04 3.24 0.00 2.32
3056 3572 6.420604 CGAAAATTAGTGCACAAGGAAACAAT 59.579 34.615 21.04 2.36 0.00 2.71
3087 3603 3.653164 TCAGCTTGGTATCTATGGTGGA 58.347 45.455 0.00 0.00 0.00 4.02
3195 3711 0.904649 TGAGGTTGATCGTGCTGGAT 59.095 50.000 0.00 0.00 0.00 3.41
3241 3757 1.210722 GAGGTTTGGAAGAGGCTAGGG 59.789 57.143 0.00 0.00 0.00 3.53
3285 3801 2.533266 AGAAGACACGAAGCACATGT 57.467 45.000 0.00 0.00 0.00 3.21
3314 3834 2.097825 GAACGGAGGGAGTACTTGCTA 58.902 52.381 0.00 0.00 0.00 3.49
3323 3843 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
3324 3844 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
3325 3845 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
3326 3846 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
3327 3847 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
3328 3848 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
3329 3849 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
3330 3850 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
3331 3851 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
3332 3852 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
3333 3853 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
3334 3854 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
3358 3878 8.983702 TGACCCAACTTTGTACTAAAATTAGT 57.016 30.769 10.43 10.43 45.39 2.24
3360 3880 9.802039 AGATGACCCAACTTTGTACTAAAATTA 57.198 29.630 0.00 0.00 0.00 1.40
3361 3881 8.706322 AGATGACCCAACTTTGTACTAAAATT 57.294 30.769 0.00 0.00 0.00 1.82
3362 3882 9.975218 ATAGATGACCCAACTTTGTACTAAAAT 57.025 29.630 0.00 0.00 0.00 1.82
3363 3883 9.802039 AATAGATGACCCAACTTTGTACTAAAA 57.198 29.630 0.00 0.00 0.00 1.52
3364 3884 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
3365 3885 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
3366 3886 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
3367 3887 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
3368 3888 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
3369 3889 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
3370 3890 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
3371 3891 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
3372 3892 6.553100 TGTTCCAAAATAGATGACCCAACTTT 59.447 34.615 0.00 0.00 0.00 2.66
3373 3893 6.074648 TGTTCCAAAATAGATGACCCAACTT 58.925 36.000 0.00 0.00 0.00 2.66
3374 3894 5.640147 TGTTCCAAAATAGATGACCCAACT 58.360 37.500 0.00 0.00 0.00 3.16
3375 3895 5.710099 TCTGTTCCAAAATAGATGACCCAAC 59.290 40.000 0.00 0.00 28.72 3.77
3376 3896 5.886609 TCTGTTCCAAAATAGATGACCCAA 58.113 37.500 0.00 0.00 28.72 4.12
3377 3897 5.500234 CTCTGTTCCAAAATAGATGACCCA 58.500 41.667 0.00 0.00 32.88 4.51
3378 3898 4.884164 CCTCTGTTCCAAAATAGATGACCC 59.116 45.833 0.00 0.00 32.88 4.46
3379 3899 4.884164 CCCTCTGTTCCAAAATAGATGACC 59.116 45.833 0.00 0.00 32.88 4.02
3380 3900 5.745227 TCCCTCTGTTCCAAAATAGATGAC 58.255 41.667 0.00 0.00 32.88 3.06
3381 3901 5.488919 ACTCCCTCTGTTCCAAAATAGATGA 59.511 40.000 0.00 0.00 32.88 2.92
3382 3902 5.749462 ACTCCCTCTGTTCCAAAATAGATG 58.251 41.667 0.00 0.00 32.88 2.90
3383 3903 6.100424 CCTACTCCCTCTGTTCCAAAATAGAT 59.900 42.308 0.00 0.00 32.88 1.98
3384 3904 5.425539 CCTACTCCCTCTGTTCCAAAATAGA 59.574 44.000 0.00 0.00 32.42 1.98
3385 3905 5.425539 TCCTACTCCCTCTGTTCCAAAATAG 59.574 44.000 0.00 0.00 0.00 1.73
3386 3906 5.189145 GTCCTACTCCCTCTGTTCCAAAATA 59.811 44.000 0.00 0.00 0.00 1.40
3387 3907 4.019231 GTCCTACTCCCTCTGTTCCAAAAT 60.019 45.833 0.00 0.00 0.00 1.82
3388 3908 3.326880 GTCCTACTCCCTCTGTTCCAAAA 59.673 47.826 0.00 0.00 0.00 2.44
3389 3909 2.904434 GTCCTACTCCCTCTGTTCCAAA 59.096 50.000 0.00 0.00 0.00 3.28
3390 3910 2.158219 TGTCCTACTCCCTCTGTTCCAA 60.158 50.000 0.00 0.00 0.00 3.53
3391 3911 1.431633 TGTCCTACTCCCTCTGTTCCA 59.568 52.381 0.00 0.00 0.00 3.53
3392 3912 2.233305 TGTCCTACTCCCTCTGTTCC 57.767 55.000 0.00 0.00 0.00 3.62
3393 3913 3.055747 CCTTTGTCCTACTCCCTCTGTTC 60.056 52.174 0.00 0.00 0.00 3.18
3394 3914 2.907042 CCTTTGTCCTACTCCCTCTGTT 59.093 50.000 0.00 0.00 0.00 3.16
3395 3915 2.541466 CCTTTGTCCTACTCCCTCTGT 58.459 52.381 0.00 0.00 0.00 3.41
3396 3916 1.834263 CCCTTTGTCCTACTCCCTCTG 59.166 57.143 0.00 0.00 0.00 3.35
3397 3917 1.273896 CCCCTTTGTCCTACTCCCTCT 60.274 57.143 0.00 0.00 0.00 3.69
3398 3918 1.205055 CCCCTTTGTCCTACTCCCTC 58.795 60.000 0.00 0.00 0.00 4.30
3399 3919 0.914902 GCCCCTTTGTCCTACTCCCT 60.915 60.000 0.00 0.00 0.00 4.20
3400 3920 1.608154 GCCCCTTTGTCCTACTCCC 59.392 63.158 0.00 0.00 0.00 4.30
3401 3921 1.221021 CGCCCCTTTGTCCTACTCC 59.779 63.158 0.00 0.00 0.00 3.85
3402 3922 0.175989 CTCGCCCCTTTGTCCTACTC 59.824 60.000 0.00 0.00 0.00 2.59
3403 3923 1.265454 CCTCGCCCCTTTGTCCTACT 61.265 60.000 0.00 0.00 0.00 2.57
3404 3924 1.221021 CCTCGCCCCTTTGTCCTAC 59.779 63.158 0.00 0.00 0.00 3.18
3405 3925 3.721868 CCTCGCCCCTTTGTCCTA 58.278 61.111 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.