Multiple sequence alignment - TraesCS5A01G075200

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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 TraesCS5A01G075200 chr5A 100.000 4464 0 0 1 4464 89976750 89981213 0.000000e+00 8244.0
1 TraesCS5A01G075200 chr5A 96.147 597 22 1 3869 4464 568332316 568331720 0.000000e+00 974.0
2 TraesCS5A01G075200 chr5A 96.226 53 1 1 3598 3650 43536582 43536633 7.960000e-13 86.1
3 TraesCS5A01G075200 chr5D 92.070 3846 138 58 102 3869 95272658 95276414 0.000000e+00 5258.0
4 TraesCS5A01G075200 chr5B 90.821 3911 151 80 1 3814 102160907 102164706 0.000000e+00 5042.0
5 TraesCS5A01G075200 chr3A 95.710 606 26 0 3859 4464 181138421 181139026 0.000000e+00 976.0
6 TraesCS5A01G075200 chr3A 95.659 599 25 1 3866 4463 742380702 742380104 0.000000e+00 961.0
7 TraesCS5A01G075200 chr3A 95.470 596 27 0 3869 4464 50097565 50098160 0.000000e+00 952.0
8 TraesCS5A01G075200 chr3A 97.872 47 0 1 906 951 23253510 23253556 3.700000e-11 80.5
9 TraesCS5A01G075200 chr4A 95.840 601 24 1 3865 4464 574837147 574836547 0.000000e+00 970.0
10 TraesCS5A01G075200 chr6A 95.380 606 26 2 3858 4461 40587990 40587385 0.000000e+00 963.0
11 TraesCS5A01G075200 chr6A 95.798 595 23 2 3871 4464 515032943 515033536 0.000000e+00 959.0
12 TraesCS5A01G075200 chr6A 78.912 294 55 4 1450 1741 264831350 264831638 4.560000e-45 193.0
13 TraesCS5A01G075200 chr2A 95.050 606 28 2 3861 4464 421223903 421223298 0.000000e+00 952.0
14 TraesCS5A01G075200 chr2A 94.754 610 30 2 3856 4464 535401124 535400516 0.000000e+00 948.0
15 TraesCS5A01G075200 chr2A 80.657 274 48 5 1449 1721 69330578 69330309 1.630000e-49 207.0
16 TraesCS5A01G075200 chr2A 84.043 188 23 5 3151 3336 645826181 645825999 1.650000e-39 174.0
17 TraesCS5A01G075200 chr7B 93.143 175 12 0 1548 1722 332813124 332812950 1.590000e-64 257.0
18 TraesCS5A01G075200 chr7B 87.838 148 7 2 906 1053 332813611 332813475 3.570000e-36 163.0
19 TraesCS5A01G075200 chr6D 79.592 294 53 4 1450 1741 226788095 226787807 2.110000e-48 204.0
20 TraesCS5A01G075200 chr6B 79.252 294 54 4 1450 1741 378960427 378960139 9.790000e-47 198.0
21 TraesCS5A01G075200 chr4D 80.769 260 41 7 1443 1699 173572937 173573190 1.270000e-45 195.0
22 TraesCS5A01G075200 chr4B 80.233 258 42 7 1448 1702 246319270 246319019 7.630000e-43 185.0
23 TraesCS5A01G075200 chr4B 82.632 190 26 5 3151 3338 122712410 122712226 1.290000e-35 161.0
24 TraesCS5A01G075200 chr1A 97.872 47 0 1 906 951 549593184 549593138 3.700000e-11 80.5


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 TraesCS5A01G075200 chr5A 89976750 89981213 4463 False 8244 8244 100.0000 1 4464 1 chr5A.!!$F2 4463
1 TraesCS5A01G075200 chr5A 568331720 568332316 596 True 974 974 96.1470 3869 4464 1 chr5A.!!$R1 595
2 TraesCS5A01G075200 chr5D 95272658 95276414 3756 False 5258 5258 92.0700 102 3869 1 chr5D.!!$F1 3767
3 TraesCS5A01G075200 chr5B 102160907 102164706 3799 False 5042 5042 90.8210 1 3814 1 chr5B.!!$F1 3813
4 TraesCS5A01G075200 chr3A 181138421 181139026 605 False 976 976 95.7100 3859 4464 1 chr3A.!!$F3 605
5 TraesCS5A01G075200 chr3A 742380104 742380702 598 True 961 961 95.6590 3866 4463 1 chr3A.!!$R1 597
6 TraesCS5A01G075200 chr3A 50097565 50098160 595 False 952 952 95.4700 3869 4464 1 chr3A.!!$F2 595
7 TraesCS5A01G075200 chr4A 574836547 574837147 600 True 970 970 95.8400 3865 4464 1 chr4A.!!$R1 599
8 TraesCS5A01G075200 chr6A 40587385 40587990 605 True 963 963 95.3800 3858 4461 1 chr6A.!!$R1 603
9 TraesCS5A01G075200 chr6A 515032943 515033536 593 False 959 959 95.7980 3871 4464 1 chr6A.!!$F2 593
10 TraesCS5A01G075200 chr2A 421223298 421223903 605 True 952 952 95.0500 3861 4464 1 chr2A.!!$R2 603
11 TraesCS5A01G075200 chr2A 535400516 535401124 608 True 948 948 94.7540 3856 4464 1 chr2A.!!$R3 608
12 TraesCS5A01G075200 chr7B 332812950 332813611 661 True 210 257 90.4905 906 1722 2 chr7B.!!$R1 816

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
87 88 0.026285 GCATCAACGTACGCCATCAC 59.974 55.0 16.72 0.0 0.0 3.06 F
251 255 0.040058 TCGCCACCTACACTTCCCTA 59.960 55.0 0.00 0.0 0.0 3.53 F
1250 1296 0.867753 CTGCACCGCTACATCGAGTC 60.868 60.0 0.00 0.0 0.0 3.36 F
1752 1818 0.104304 CCCCAGGTACGCACATACTC 59.896 60.0 0.00 0.0 0.0 2.59 F
1753 1819 0.104304 CCCAGGTACGCACATACTCC 59.896 60.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1815 0.251922 AGGCAATGCAATGTGGGAGT 60.252 50.0 7.79 0.0 0.00 3.85 R
1752 1818 0.322322 ACAAGGCAATGCAATGTGGG 59.678 50.0 13.09 0.0 30.12 4.61 R
3104 3182 0.106769 TGGTGTGGATTGCTGTGTGT 60.107 50.0 0.00 0.0 0.00 3.72 R
3358 3447 0.248175 GCATGCATTTCATCGTGCGA 60.248 50.0 14.21 0.0 44.11 5.10 R
3545 3663 0.304705 AGTTCGCAGCAAACAGTTCG 59.695 50.0 0.00 0.0 0.00 3.95 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
20 21 0.409092 TGCCACCATGTTTCTCCCAT 59.591 50.000 0.00 0.00 0.00 4.00
40 41 5.123344 CCCATACAAACCAGCACTACTTAAC 59.877 44.000 0.00 0.00 0.00 2.01
52 53 7.223582 CCAGCACTACTTAACTAATCATCACTG 59.776 40.741 0.00 0.00 0.00 3.66
53 54 7.761704 CAGCACTACTTAACTAATCATCACTGT 59.238 37.037 0.00 0.00 0.00 3.55
54 55 8.314751 AGCACTACTTAACTAATCATCACTGTT 58.685 33.333 0.00 0.00 0.00 3.16
55 56 9.582431 GCACTACTTAACTAATCATCACTGTTA 57.418 33.333 0.00 0.00 0.00 2.41
74 75 9.378551 CACTGTTAGTAATTAACCTAGCATCAA 57.621 33.333 1.75 0.00 40.80 2.57
75 76 9.379791 ACTGTTAGTAATTAACCTAGCATCAAC 57.620 33.333 1.75 0.00 40.80 3.18
76 77 8.415192 TGTTAGTAATTAACCTAGCATCAACG 57.585 34.615 0.00 0.00 40.80 4.10
77 78 8.036575 TGTTAGTAATTAACCTAGCATCAACGT 58.963 33.333 0.00 0.00 40.80 3.99
78 79 9.520204 GTTAGTAATTAACCTAGCATCAACGTA 57.480 33.333 0.00 0.00 36.45 3.57
87 88 0.026285 GCATCAACGTACGCCATCAC 59.974 55.000 16.72 0.00 0.00 3.06
100 101 2.017049 GCCATCACCACATAACAGGTC 58.983 52.381 0.00 0.00 35.52 3.85
121 125 5.454329 GGTCGTAGGGTGCTAATTAAATCCT 60.454 44.000 5.26 5.26 0.00 3.24
129 133 6.239036 GGGTGCTAATTAAATCCTTTAGCCAG 60.239 42.308 12.83 0.00 44.53 4.85
251 255 0.040058 TCGCCACCTACACTTCCCTA 59.960 55.000 0.00 0.00 0.00 3.53
354 359 4.612264 TGACTTCCCACAGTAACCTTAC 57.388 45.455 0.00 0.00 0.00 2.34
358 369 3.775261 TCCCACAGTAACCTTACAACC 57.225 47.619 0.00 0.00 36.12 3.77
374 385 7.069455 ACCTTACAACCAAATAATAATGGAGGC 59.931 37.037 0.00 0.00 39.12 4.70
487 515 6.553100 ACTTCCCTGAGAATATAAGAGAGGTG 59.447 42.308 0.00 0.00 32.82 4.00
552 580 7.882791 TCTTTAGCATGGTGTGATAGAAAAGAA 59.117 33.333 7.89 0.00 26.56 2.52
553 581 7.994425 TTAGCATGGTGTGATAGAAAAGAAA 57.006 32.000 7.89 0.00 29.08 2.52
578 606 2.867624 ACACAATCACCAGAAGTGCAT 58.132 42.857 0.00 0.00 46.81 3.96
625 653 4.274459 CCATTTTTATCTTCTCCTGGCTCG 59.726 45.833 0.00 0.00 0.00 5.03
688 716 1.378124 CGAGGAGGACGAGGAGGAAC 61.378 65.000 0.00 0.00 0.00 3.62
700 728 3.367910 CGAGGAGGAACAAGAGGAGAAAG 60.368 52.174 0.00 0.00 0.00 2.62
701 729 3.580895 GAGGAGGAACAAGAGGAGAAAGT 59.419 47.826 0.00 0.00 0.00 2.66
702 730 3.580895 AGGAGGAACAAGAGGAGAAAGTC 59.419 47.826 0.00 0.00 0.00 3.01
703 731 3.580895 GGAGGAACAAGAGGAGAAAGTCT 59.419 47.826 0.00 0.00 0.00 3.24
784 818 6.357015 TTTCTATCTTTAGGAGGAGGAGGA 57.643 41.667 0.00 0.00 0.00 3.71
827 861 3.044059 GCATTGCTCGTGCCCTGTC 62.044 63.158 7.05 0.00 38.71 3.51
968 1005 2.783510 TCCCCTCACCTCTTTGTTTCTT 59.216 45.455 0.00 0.00 0.00 2.52
969 1006 2.887152 CCCCTCACCTCTTTGTTTCTTG 59.113 50.000 0.00 0.00 0.00 3.02
970 1007 2.887152 CCCTCACCTCTTTGTTTCTTGG 59.113 50.000 0.00 0.00 0.00 3.61
971 1008 3.555966 CCTCACCTCTTTGTTTCTTGGT 58.444 45.455 0.00 0.00 0.00 3.67
972 1009 3.954258 CCTCACCTCTTTGTTTCTTGGTT 59.046 43.478 0.00 0.00 0.00 3.67
973 1010 4.402474 CCTCACCTCTTTGTTTCTTGGTTT 59.598 41.667 0.00 0.00 0.00 3.27
974 1011 5.105351 CCTCACCTCTTTGTTTCTTGGTTTT 60.105 40.000 0.00 0.00 0.00 2.43
975 1012 5.961272 TCACCTCTTTGTTTCTTGGTTTTC 58.039 37.500 0.00 0.00 0.00 2.29
976 1013 5.714806 TCACCTCTTTGTTTCTTGGTTTTCT 59.285 36.000 0.00 0.00 0.00 2.52
1250 1296 0.867753 CTGCACCGCTACATCGAGTC 60.868 60.000 0.00 0.00 0.00 3.36
1428 1494 1.065199 AGAAAGCTCATCAATGGCGGA 60.065 47.619 0.00 0.00 0.00 5.54
1438 1504 1.271934 TCAATGGCGGATTGTTGTTGG 59.728 47.619 6.90 0.00 42.06 3.77
1742 1808 1.677637 CTTCTCCGAGCCCCAGGTAC 61.678 65.000 0.00 0.00 0.00 3.34
1749 1815 1.682451 GAGCCCCAGGTACGCACATA 61.682 60.000 0.00 0.00 0.00 2.29
1750 1816 1.523032 GCCCCAGGTACGCACATAC 60.523 63.158 0.00 0.00 0.00 2.39
1751 1817 1.968050 GCCCCAGGTACGCACATACT 61.968 60.000 0.00 0.00 0.00 2.12
1752 1818 0.104304 CCCCAGGTACGCACATACTC 59.896 60.000 0.00 0.00 0.00 2.59
1753 1819 0.104304 CCCAGGTACGCACATACTCC 59.896 60.000 0.00 0.00 0.00 3.85
1754 1820 0.104304 CCAGGTACGCACATACTCCC 59.896 60.000 0.00 0.00 0.00 4.30
1755 1821 0.821517 CAGGTACGCACATACTCCCA 59.178 55.000 0.00 0.00 0.00 4.37
1777 1843 4.930405 CACATTGCATTGCCTTGTTATCAA 59.070 37.500 6.12 0.00 0.00 2.57
1778 1844 5.408909 CACATTGCATTGCCTTGTTATCAAA 59.591 36.000 6.12 0.00 32.87 2.69
1779 1845 5.409214 ACATTGCATTGCCTTGTTATCAAAC 59.591 36.000 6.12 0.00 36.07 2.93
1781 1847 5.212532 TGCATTGCCTTGTTATCAAACTT 57.787 34.783 6.12 0.00 36.51 2.66
1783 1849 6.934056 TGCATTGCCTTGTTATCAAACTTAT 58.066 32.000 6.12 0.00 36.51 1.73
1786 1852 7.707893 GCATTGCCTTGTTATCAAACTTATCAT 59.292 33.333 0.00 0.00 36.51 2.45
1787 1853 9.241317 CATTGCCTTGTTATCAAACTTATCATC 57.759 33.333 0.00 0.00 36.51 2.92
1788 1854 7.936496 TGCCTTGTTATCAAACTTATCATCA 57.064 32.000 0.00 0.00 36.51 3.07
1789 1855 8.523915 TGCCTTGTTATCAAACTTATCATCAT 57.476 30.769 0.00 0.00 36.51 2.45
1790 1856 8.623903 TGCCTTGTTATCAAACTTATCATCATC 58.376 33.333 0.00 0.00 36.51 2.92
1791 1857 8.623903 GCCTTGTTATCAAACTTATCATCATCA 58.376 33.333 0.00 0.00 36.51 3.07
1807 1873 5.763204 TCATCATCAATCATCCATCACACTG 59.237 40.000 0.00 0.00 0.00 3.66
1808 1874 4.457466 TCATCAATCATCCATCACACTGG 58.543 43.478 0.00 0.00 37.66 4.00
1811 1877 2.343484 ATCATCCATCACACTGGCTG 57.657 50.000 0.00 0.00 36.16 4.85
1812 1878 1.278537 TCATCCATCACACTGGCTGA 58.721 50.000 0.00 0.00 38.71 4.26
1813 1879 1.065926 TCATCCATCACACTGGCTGAC 60.066 52.381 0.00 0.00 36.71 3.51
1814 1880 1.065636 CATCCATCACACTGGCTGACT 60.066 52.381 0.00 0.00 34.95 3.41
1815 1881 0.322648 TCCATCACACTGGCTGACTG 59.677 55.000 0.00 0.00 36.16 3.51
1816 1882 0.322648 CCATCACACTGGCTGACTGA 59.677 55.000 0.00 0.00 0.00 3.41
1817 1883 1.065636 CCATCACACTGGCTGACTGAT 60.066 52.381 0.00 1.01 0.00 2.90
1818 1884 2.617276 CCATCACACTGGCTGACTGATT 60.617 50.000 0.00 0.00 0.00 2.57
1819 1885 2.462456 TCACACTGGCTGACTGATTC 57.538 50.000 0.00 0.00 0.00 2.52
1827 1893 4.100035 ACTGGCTGACTGATTCGATTGATA 59.900 41.667 0.00 0.00 0.00 2.15
1841 1907 6.075762 TCGATTGATAAATTTGGATGCTGG 57.924 37.500 0.00 0.00 0.00 4.85
2006 2072 2.432628 GTGTTCTCCACCTCGCCG 60.433 66.667 0.00 0.00 38.18 6.46
2366 2432 4.544689 CTCTCAGTCGAGCCCGCG 62.545 72.222 0.00 0.00 39.30 6.46
2447 2513 4.400961 GAGCCGTCAAGCCTGCCT 62.401 66.667 0.00 0.00 0.00 4.75
2617 2683 4.475135 GTCGCTCCCCCTGGAAGC 62.475 72.222 0.00 0.15 41.17 3.86
2771 2849 1.309499 CCGACAACCTCGCTCTCTCT 61.309 60.000 0.00 0.00 41.46 3.10
2834 2912 3.984732 AAGAAGCCCAGGGTGCCC 61.985 66.667 7.55 0.00 0.00 5.36
3011 3089 1.519455 GGCGTTCACCTCATCCGAG 60.519 63.158 0.00 0.00 39.16 4.63
3085 3163 1.123077 AGCAAGGTCAGTCACACTCA 58.877 50.000 0.00 0.00 0.00 3.41
3104 3182 3.551846 TCACACGCTCATCATCCTACTA 58.448 45.455 0.00 0.00 0.00 1.82
3115 3193 5.129320 TCATCATCCTACTACACACAGCAAT 59.871 40.000 0.00 0.00 0.00 3.56
3133 3211 5.183713 CAGCAATCCACACCAAAATCTCTTA 59.816 40.000 0.00 0.00 0.00 2.10
3141 3219 7.021196 CCACACCAAAATCTCTTATACAAACG 58.979 38.462 0.00 0.00 0.00 3.60
3142 3220 7.021196 CACACCAAAATCTCTTATACAAACGG 58.979 38.462 0.00 0.00 0.00 4.44
3357 3446 0.320374 TCGATCAACCACCTCACACC 59.680 55.000 0.00 0.00 0.00 4.16
3358 3447 0.321671 CGATCAACCACCTCACACCT 59.678 55.000 0.00 0.00 0.00 4.00
3359 3448 1.673033 CGATCAACCACCTCACACCTC 60.673 57.143 0.00 0.00 0.00 3.85
3361 3450 1.961277 CAACCACCTCACACCTCGC 60.961 63.158 0.00 0.00 0.00 5.03
3363 3452 2.357517 CCACCTCACACCTCGCAC 60.358 66.667 0.00 0.00 0.00 5.34
3364 3453 2.734723 CACCTCACACCTCGCACG 60.735 66.667 0.00 0.00 0.00 5.34
3365 3454 2.910479 ACCTCACACCTCGCACGA 60.910 61.111 0.00 0.00 0.00 4.35
3366 3455 2.276116 ACCTCACACCTCGCACGAT 61.276 57.895 0.00 0.00 0.00 3.73
3367 3456 1.807165 CCTCACACCTCGCACGATG 60.807 63.158 0.00 0.00 0.00 3.84
3368 3457 1.212751 CTCACACCTCGCACGATGA 59.787 57.895 2.30 0.00 0.00 2.92
3369 3458 0.388520 CTCACACCTCGCACGATGAA 60.389 55.000 2.30 0.00 0.00 2.57
3370 3459 0.032815 TCACACCTCGCACGATGAAA 59.967 50.000 2.30 0.00 0.00 2.69
3371 3460 1.078709 CACACCTCGCACGATGAAAT 58.921 50.000 2.30 0.00 0.00 2.17
3372 3461 1.078709 ACACCTCGCACGATGAAATG 58.921 50.000 2.30 0.00 0.00 2.32
3380 3470 1.835121 CACGATGAAATGCATGCCTG 58.165 50.000 16.68 0.00 37.34 4.85
3432 3522 3.935315 TGCTGACCTCATTCTTCTTCTG 58.065 45.455 0.00 0.00 0.00 3.02
3447 3543 4.771114 TCTTCTGGACAGGAAACAAGAA 57.229 40.909 0.00 0.00 0.00 2.52
3473 3569 0.732196 GCAGCACTGAGACTGAGACG 60.732 60.000 10.57 0.00 35.90 4.18
3474 3570 0.877743 CAGCACTGAGACTGAGACGA 59.122 55.000 0.00 0.00 35.90 4.20
3475 3571 1.135717 CAGCACTGAGACTGAGACGAG 60.136 57.143 0.00 0.00 35.90 4.18
3476 3572 1.160989 GCACTGAGACTGAGACGAGA 58.839 55.000 0.00 0.00 0.00 4.04
3477 3573 1.130373 GCACTGAGACTGAGACGAGAG 59.870 57.143 0.00 0.00 0.00 3.20
3478 3574 2.694213 CACTGAGACTGAGACGAGAGA 58.306 52.381 0.00 0.00 0.00 3.10
3479 3575 2.672874 CACTGAGACTGAGACGAGAGAG 59.327 54.545 0.00 0.00 0.00 3.20
3480 3576 2.565391 ACTGAGACTGAGACGAGAGAGA 59.435 50.000 0.00 0.00 0.00 3.10
3481 3577 3.190079 CTGAGACTGAGACGAGAGAGAG 58.810 54.545 0.00 0.00 0.00 3.20
3539 3657 2.746279 TTTTCCCCTTGACTCTTGCA 57.254 45.000 0.00 0.00 0.00 4.08
3545 3663 1.471684 CCCTTGACTCTTGCAGCAATC 59.528 52.381 8.67 4.18 0.00 2.67
3563 3681 0.303493 TCGAACTGTTTGCTGCGAAC 59.697 50.000 22.85 22.85 0.00 3.95
3575 3693 2.288334 TGCTGCGAACTTCCTACGTTTA 60.288 45.455 0.00 0.00 0.00 2.01
3578 3696 4.695200 CTGCGAACTTCCTACGTTTAAAC 58.305 43.478 8.35 8.35 0.00 2.01
3579 3697 4.370917 TGCGAACTTCCTACGTTTAAACT 58.629 39.130 16.01 6.22 0.00 2.66
3638 3757 4.774124 AGCAAGATTGTATAGAGCTGCAA 58.226 39.130 1.02 0.00 0.00 4.08
3697 3816 0.117140 TGTCACCTCCCATCTCCTGT 59.883 55.000 0.00 0.00 0.00 4.00
3698 3817 0.539051 GTCACCTCCCATCTCCTGTG 59.461 60.000 0.00 0.00 0.00 3.66
3701 3820 1.352352 CACCTCCCATCTCCTGTGTTT 59.648 52.381 0.00 0.00 0.00 2.83
3732 3861 1.003839 CTCAGCCGGTTGTGCCTTA 60.004 57.895 18.51 0.00 34.25 2.69
3747 3876 5.515106 TGTGCCTTACTAATGCCCTTTTAT 58.485 37.500 0.00 0.00 0.00 1.40
3748 3877 6.664714 TGTGCCTTACTAATGCCCTTTTATA 58.335 36.000 0.00 0.00 0.00 0.98
3778 3909 6.877611 TGAAAAGAAGAAGAATAAACGCCT 57.122 33.333 0.00 0.00 0.00 5.52
3842 3992 2.685897 TGTTGTTGGTAAGGCAGAACAC 59.314 45.455 0.00 0.00 0.00 3.32
3843 3993 1.588674 TGTTGGTAAGGCAGAACACG 58.411 50.000 0.00 0.00 0.00 4.49
3954 4104 1.001624 CATGAGCGCACGAATCTTGA 58.998 50.000 11.47 0.00 0.00 3.02
4137 4287 0.328258 ATCTTGCCTACACGCCCTTT 59.672 50.000 0.00 0.00 0.00 3.11
4184 4334 1.206610 TGCCATGTGTTTTTGCACTGT 59.793 42.857 0.00 0.00 39.89 3.55
4208 4358 1.073199 GCAACTGCCCCTAGTGTGT 59.927 57.895 0.00 0.00 34.31 3.72
4432 4583 6.458210 CAACTCTTCCTTTTTACATGGCAAT 58.542 36.000 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.024414 GTATGGGAGAAACATGGTGGC 58.976 52.381 0.00 0.00 0.00 5.01
5 6 4.086457 GGTTTGTATGGGAGAAACATGGT 58.914 43.478 0.00 0.00 41.90 3.55
20 21 8.369424 TGATTAGTTAAGTAGTGCTGGTTTGTA 58.631 33.333 0.00 0.00 0.00 2.41
52 53 8.416485 ACGTTGATGCTAGGTTAATTACTAAC 57.584 34.615 0.00 0.00 39.45 2.34
53 54 9.520204 GTACGTTGATGCTAGGTTAATTACTAA 57.480 33.333 0.00 0.00 0.00 2.24
54 55 7.857389 CGTACGTTGATGCTAGGTTAATTACTA 59.143 37.037 7.22 0.00 0.00 1.82
55 56 6.694411 CGTACGTTGATGCTAGGTTAATTACT 59.306 38.462 7.22 0.00 0.00 2.24
58 59 4.269363 GCGTACGTTGATGCTAGGTTAATT 59.731 41.667 17.90 0.00 0.00 1.40
74 75 0.818938 TATGTGGTGATGGCGTACGT 59.181 50.000 17.90 0.00 0.00 3.57
75 76 1.591158 GTTATGTGGTGATGGCGTACG 59.409 52.381 11.84 11.84 0.00 3.67
76 77 2.607635 CTGTTATGTGGTGATGGCGTAC 59.392 50.000 0.00 0.00 0.00 3.67
77 78 2.419436 CCTGTTATGTGGTGATGGCGTA 60.419 50.000 0.00 0.00 0.00 4.42
78 79 1.678728 CCTGTTATGTGGTGATGGCGT 60.679 52.381 0.00 0.00 0.00 5.68
87 88 1.829222 ACCCTACGACCTGTTATGTGG 59.171 52.381 0.00 0.00 0.00 4.17
100 101 6.937436 AAAGGATTTAATTAGCACCCTACG 57.063 37.500 0.00 0.00 35.86 3.51
121 125 7.479352 TCAAAATTGAATCATCCTGGCTAAA 57.521 32.000 0.00 0.00 33.55 1.85
129 133 3.549070 GTGCGCTCAAAATTGAATCATCC 59.451 43.478 9.73 0.00 36.64 3.51
251 255 3.878699 TCATGTGATTGCATTATGTCGCT 59.121 39.130 0.00 0.00 0.00 4.93
354 359 6.219417 TGTGCCTCCATTATTATTTGGTTG 57.781 37.500 0.00 0.00 34.48 3.77
407 418 7.235606 AGCCTGGTGTCTTACATACATGTATAT 59.764 37.037 17.86 10.02 42.32 0.86
415 426 3.939066 ACAAGCCTGGTGTCTTACATAC 58.061 45.455 0.00 0.00 0.00 2.39
416 427 4.634012 AACAAGCCTGGTGTCTTACATA 57.366 40.909 0.00 0.00 0.00 2.29
428 445 2.787994 ACTGATCCAGAAACAAGCCTG 58.212 47.619 0.45 0.00 35.18 4.85
487 515 1.534729 CTCCCTGGTTAAGTGCAACC 58.465 55.000 0.00 0.00 46.90 3.77
546 574 7.610865 TCTGGTGATTGTGTTTTCTTTCTTTT 58.389 30.769 0.00 0.00 0.00 2.27
578 606 1.916181 GGGACATGGAGAGGGAGAAAA 59.084 52.381 0.00 0.00 0.00 2.29
625 653 0.748005 TAATTCCTTGCGCTGGCCTC 60.748 55.000 9.73 0.00 38.85 4.70
688 716 1.349026 TGGGCAGACTTTCTCCTCTTG 59.651 52.381 0.00 0.00 0.00 3.02
827 861 1.101049 GTCTCCTCTGCCTCCTCTCG 61.101 65.000 0.00 0.00 0.00 4.04
968 1005 2.610374 CGTCGACCAAGAAAGAAAACCA 59.390 45.455 10.58 0.00 0.00 3.67
969 1006 2.032290 CCGTCGACCAAGAAAGAAAACC 60.032 50.000 10.58 0.00 0.00 3.27
970 1007 2.601504 GCCGTCGACCAAGAAAGAAAAC 60.602 50.000 10.58 0.00 0.00 2.43
971 1008 1.600485 GCCGTCGACCAAGAAAGAAAA 59.400 47.619 10.58 0.00 0.00 2.29
972 1009 1.223187 GCCGTCGACCAAGAAAGAAA 58.777 50.000 10.58 0.00 0.00 2.52
973 1010 0.105224 TGCCGTCGACCAAGAAAGAA 59.895 50.000 10.58 0.00 0.00 2.52
974 1011 0.599204 GTGCCGTCGACCAAGAAAGA 60.599 55.000 10.58 0.00 0.00 2.52
975 1012 1.860078 GTGCCGTCGACCAAGAAAG 59.140 57.895 10.58 0.00 0.00 2.62
976 1013 1.952133 CGTGCCGTCGACCAAGAAA 60.952 57.895 10.58 0.00 0.00 2.52
1114 1157 1.050988 ACAGGCCTGCTCCATATCGT 61.051 55.000 33.06 5.96 0.00 3.73
1139 1182 1.078214 CCAAGATCAAGCGCCTCCA 60.078 57.895 2.29 0.00 0.00 3.86
1371 1437 2.356818 ATTGCCGCGAGAGGAGCTAC 62.357 60.000 8.23 0.00 0.00 3.58
1428 1494 1.118838 CACCCACCACCAACAACAAT 58.881 50.000 0.00 0.00 0.00 2.71
1438 1504 2.436646 CCGATCTGCACCCACCAC 60.437 66.667 0.00 0.00 0.00 4.16
1742 1808 0.378257 GCAATGTGGGAGTATGTGCG 59.622 55.000 0.00 0.00 0.00 5.34
1749 1815 0.251922 AGGCAATGCAATGTGGGAGT 60.252 50.000 7.79 0.00 0.00 3.85
1750 1816 0.899720 AAGGCAATGCAATGTGGGAG 59.100 50.000 7.79 0.00 0.00 4.30
1751 1817 0.609151 CAAGGCAATGCAATGTGGGA 59.391 50.000 7.79 0.00 0.00 4.37
1752 1818 0.322322 ACAAGGCAATGCAATGTGGG 59.678 50.000 13.09 0.00 30.12 4.61
1753 1819 2.172851 AACAAGGCAATGCAATGTGG 57.827 45.000 14.28 0.00 31.32 4.17
1754 1820 4.496360 TGATAACAAGGCAATGCAATGTG 58.504 39.130 14.28 5.70 31.32 3.21
1755 1821 4.804868 TGATAACAAGGCAATGCAATGT 57.195 36.364 7.79 8.46 31.99 2.71
1777 1843 9.011095 GTGATGGATGATTGATGATGATAAGTT 57.989 33.333 0.00 0.00 0.00 2.66
1778 1844 8.161425 TGTGATGGATGATTGATGATGATAAGT 58.839 33.333 0.00 0.00 0.00 2.24
1779 1845 8.451748 GTGTGATGGATGATTGATGATGATAAG 58.548 37.037 0.00 0.00 0.00 1.73
1781 1847 7.606456 CAGTGTGATGGATGATTGATGATGATA 59.394 37.037 0.00 0.00 0.00 2.15
1783 1849 5.763204 CAGTGTGATGGATGATTGATGATGA 59.237 40.000 0.00 0.00 0.00 2.92
1786 1852 4.457466 CCAGTGTGATGGATGATTGATGA 58.543 43.478 0.00 0.00 43.57 2.92
1787 1853 3.004419 GCCAGTGTGATGGATGATTGATG 59.996 47.826 0.00 0.00 43.57 3.07
1788 1854 3.117625 AGCCAGTGTGATGGATGATTGAT 60.118 43.478 0.00 0.00 43.57 2.57
1789 1855 2.240414 AGCCAGTGTGATGGATGATTGA 59.760 45.455 0.00 0.00 43.57 2.57
1790 1856 2.651455 AGCCAGTGTGATGGATGATTG 58.349 47.619 0.00 0.00 43.57 2.67
1807 1873 5.991328 TTTATCAATCGAATCAGTCAGCC 57.009 39.130 0.00 0.00 0.00 4.85
1808 1874 7.377928 CCAAATTTATCAATCGAATCAGTCAGC 59.622 37.037 0.00 0.00 0.00 4.26
1811 1877 9.390795 CATCCAAATTTATCAATCGAATCAGTC 57.609 33.333 0.00 0.00 0.00 3.51
1812 1878 7.864379 GCATCCAAATTTATCAATCGAATCAGT 59.136 33.333 0.00 0.00 0.00 3.41
1813 1879 8.080417 AGCATCCAAATTTATCAATCGAATCAG 58.920 33.333 0.00 0.00 0.00 2.90
1814 1880 7.863877 CAGCATCCAAATTTATCAATCGAATCA 59.136 33.333 0.00 0.00 0.00 2.57
1815 1881 7.327761 CCAGCATCCAAATTTATCAATCGAATC 59.672 37.037 0.00 0.00 0.00 2.52
1816 1882 7.149973 CCAGCATCCAAATTTATCAATCGAAT 58.850 34.615 0.00 0.00 0.00 3.34
1817 1883 6.506147 CCAGCATCCAAATTTATCAATCGAA 58.494 36.000 0.00 0.00 0.00 3.71
1818 1884 5.507817 GCCAGCATCCAAATTTATCAATCGA 60.508 40.000 0.00 0.00 0.00 3.59
1819 1885 4.682860 GCCAGCATCCAAATTTATCAATCG 59.317 41.667 0.00 0.00 0.00 3.34
1827 1893 1.218854 GCCGCCAGCATCCAAATTT 59.781 52.632 0.00 0.00 42.97 1.82
1841 1907 0.740868 TGTAGCACTTGATCTGCCGC 60.741 55.000 2.04 0.00 35.01 6.53
2447 2513 1.281353 CTTGTTTGGCGCGCACTTA 59.719 52.632 34.42 13.13 0.00 2.24
2537 2603 2.437359 ATGCTCTTGTGCGCCCTC 60.437 61.111 4.18 0.00 35.36 4.30
2757 2835 3.293702 GCCAGAGAGAGCGAGGTT 58.706 61.111 0.00 0.00 0.00 3.50
2804 2882 1.603455 CTTCTTGGCCCAGGCGAAA 60.603 57.895 7.55 1.82 43.06 3.46
3085 3163 3.066900 GTGTAGTAGGATGATGAGCGTGT 59.933 47.826 0.00 0.00 0.00 4.49
3104 3182 0.106769 TGGTGTGGATTGCTGTGTGT 60.107 50.000 0.00 0.00 0.00 3.72
3115 3193 7.094975 CGTTTGTATAAGAGATTTTGGTGTGGA 60.095 37.037 0.00 0.00 0.00 4.02
3133 3211 8.287439 TGATCAAAATAACCATCCGTTTGTAT 57.713 30.769 0.00 0.00 35.79 2.29
3141 3219 6.294397 GCTCCAGATGATCAAAATAACCATCC 60.294 42.308 0.00 0.00 35.48 3.51
3142 3220 6.489361 AGCTCCAGATGATCAAAATAACCATC 59.511 38.462 0.00 0.00 35.21 3.51
3178 3261 4.039124 GCTTCTGAAACCAGGAAAAATGGA 59.961 41.667 0.00 0.00 40.51 3.41
3179 3262 4.202243 TGCTTCTGAAACCAGGAAAAATGG 60.202 41.667 0.00 0.00 43.87 3.16
3257 3346 3.432588 AGGAGCTCGTCGACGTGG 61.433 66.667 34.40 27.34 40.80 4.94
3259 3348 4.104417 GCAGGAGCTCGTCGACGT 62.104 66.667 34.40 18.37 40.80 4.34
3344 3433 2.426023 GCGAGGTGTGAGGTGGTT 59.574 61.111 0.00 0.00 0.00 3.67
3357 3446 1.738432 CATGCATTTCATCGTGCGAG 58.262 50.000 0.00 0.00 44.11 5.03
3358 3447 0.248175 GCATGCATTTCATCGTGCGA 60.248 50.000 14.21 0.00 44.11 5.10
3359 3448 1.204228 GGCATGCATTTCATCGTGCG 61.204 55.000 21.36 0.00 43.96 5.34
3361 3450 1.835121 CAGGCATGCATTTCATCGTG 58.165 50.000 21.36 0.00 31.79 4.35
3380 3470 3.558033 TCAGGGGAATTAATTAACCCGC 58.442 45.455 24.27 18.28 42.90 6.13
3385 3475 4.403113 GGCGGTTTCAGGGGAATTAATTAA 59.597 41.667 0.00 0.00 31.93 1.40
3432 3522 2.155279 GCTCCTTCTTGTTTCCTGTCC 58.845 52.381 0.00 0.00 0.00 4.02
3447 3543 1.912264 TCTCAGTGCTGCTGCTCCT 60.912 57.895 17.00 9.51 44.66 3.69
3473 3569 3.062585 GCATGTGTGCCTCTCTCTC 57.937 57.895 0.00 0.00 45.76 3.20
3523 3641 1.376466 GCTGCAAGAGTCAAGGGGA 59.624 57.895 0.00 0.00 34.07 4.81
3545 3663 0.304705 AGTTCGCAGCAAACAGTTCG 59.695 50.000 0.00 0.00 0.00 3.95
3563 3681 6.796705 ACCATTCAGTTTAAACGTAGGAAG 57.203 37.500 12.54 7.42 0.00 3.46
3575 3693 5.245751 TGAATGCATGGTAACCATTCAGTTT 59.754 36.000 16.84 1.82 45.69 2.66
3578 3696 4.987408 TGAATGCATGGTAACCATTCAG 57.013 40.909 16.84 0.00 45.69 3.02
3697 3816 3.084039 CTGAGCTAGCCATGGAAAAACA 58.916 45.455 18.40 6.84 0.00 2.83
3698 3817 3.772060 CTGAGCTAGCCATGGAAAAAC 57.228 47.619 18.40 0.00 0.00 2.43
3760 3891 4.154918 CAGCAAGGCGTTTATTCTTCTTCT 59.845 41.667 0.00 0.00 0.00 2.85
3763 3894 3.674997 TCAGCAAGGCGTTTATTCTTCT 58.325 40.909 0.00 0.00 0.00 2.85
3764 3895 4.346129 CATCAGCAAGGCGTTTATTCTTC 58.654 43.478 0.00 0.00 0.00 2.87
3767 3898 2.454055 GCATCAGCAAGGCGTTTATTC 58.546 47.619 0.00 0.00 41.58 1.75
3770 3901 0.322456 AGGCATCAGCAAGGCGTTTA 60.322 50.000 0.00 0.00 44.61 2.01
3772 3903 2.034687 AGGCATCAGCAAGGCGTT 59.965 55.556 0.00 0.00 44.61 4.84
3778 3909 1.187974 CAATTCCCAGGCATCAGCAA 58.812 50.000 0.00 0.00 44.61 3.91
3814 3945 2.610232 GCCTTACCAACAACAGCAATGG 60.610 50.000 0.00 0.00 38.91 3.16
3842 3992 3.877508 AGAAAAGGGAAAACAGAGTCACG 59.122 43.478 0.00 0.00 0.00 4.35
3843 3993 5.836821 AAGAAAAGGGAAAACAGAGTCAC 57.163 39.130 0.00 0.00 0.00 3.67
3887 4037 1.226018 GATGCAAACGCCTACACGC 60.226 57.895 0.00 0.00 36.19 5.34
3929 4079 3.853330 CGTGCGCTCATGAACGGG 61.853 66.667 19.29 7.56 32.55 5.28
4016 4166 1.821759 CCTGTGTGGTGAAACGGCA 60.822 57.895 0.00 0.00 38.12 5.69
4126 4276 0.611714 GGAGAGGAAAAGGGCGTGTA 59.388 55.000 0.00 0.00 0.00 2.90
4137 4287 1.779061 GCTTGGGTGTGGGAGAGGAA 61.779 60.000 0.00 0.00 0.00 3.36
4208 4358 5.799827 AAGTTGCCACCTGCTTATAAAAA 57.200 34.783 0.00 0.00 42.00 1.94


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

AutoCloner maintained by Alex Coulton.