Multiple sequence alignment - TraesCS7B01G337800

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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 TraesCS7B01G337800 chr7B 100.000 2444 0 0 1 2444 592511284 592513727 0.000000e+00 4514.0
1 TraesCS7B01G337800 chr7B 100.000 59 0 0 2132 2190 592513474 592513532 2.570000e-20 110.0
2 TraesCS7B01G337800 chr7D 88.783 1676 90 37 9 1637 548893599 548895223 0.000000e+00 1964.0
3 TraesCS7B01G337800 chr7D 89.726 146 12 1 2299 2444 548964590 548964732 1.490000e-42 183.0
4 TraesCS7B01G337800 chr7D 94.805 77 4 0 2299 2375 548897444 548897520 1.190000e-23 121.0
5 TraesCS7B01G337800 chr7D 91.803 61 4 1 2299 2358 548897381 548897441 1.560000e-12 84.2
6 TraesCS7B01G337800 chr7A 88.144 1670 108 35 1 1637 634387102 634388714 0.000000e+00 1905.0
7 TraesCS7B01G337800 chr7A 91.571 261 21 1 1634 1893 682182048 682181788 2.310000e-95 359.0
8 TraesCS7B01G337800 chr7A 83.594 256 12 7 2191 2444 634389385 634389612 1.900000e-51 213.0
9 TraesCS7B01G337800 chr7A 90.588 85 5 3 2109 2191 634389362 634389445 2.570000e-20 110.0
10 TraesCS7B01G337800 chr5D 93.077 260 17 1 1635 1893 141427784 141428043 1.770000e-101 379.0
11 TraesCS7B01G337800 chr4D 93.077 260 17 1 1635 1893 78773929 78773670 1.770000e-101 379.0
12 TraesCS7B01G337800 chr3A 92.308 260 19 1 1635 1893 65884306 65884047 3.840000e-98 368.0
13 TraesCS7B01G337800 chr3A 92.829 251 17 1 1632 1881 156231479 156231729 1.790000e-96 363.0
14 TraesCS7B01G337800 chr3A 93.145 248 16 1 1635 1881 156231733 156231980 1.790000e-96 363.0
15 TraesCS7B01G337800 chr3A 91.188 261 21 2 1635 1893 11970548 11970808 1.080000e-93 353.0
16 TraesCS7B01G337800 chr5B 91.954 261 20 1 1634 1893 27825039 27825299 4.970000e-97 364.0
17 TraesCS7B01G337800 chr4A 91.288 264 19 2 1634 1893 576577234 576576971 8.310000e-95 357.0


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 TraesCS7B01G337800 chr7B 592511284 592513727 2443 False 2312.000000 4514 100.000 1 2444 2 chr7B.!!$F1 2443
1 TraesCS7B01G337800 chr7D 548893599 548897520 3921 False 723.066667 1964 91.797 9 2375 3 chr7D.!!$F2 2366
2 TraesCS7B01G337800 chr7A 634387102 634389612 2510 False 742.666667 1905 87.442 1 2444 3 chr7A.!!$F1 2443
3 TraesCS7B01G337800 chr3A 156231479 156231980 501 False 363.000000 363 92.987 1632 1881 2 chr3A.!!$F2 249

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
204 205 0.449388 GCTGTGTTCATAGCAGTGCC 59.551 55.0 12.58 0.0 39.67 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 3865 0.026674 CACAACAGCAGTCACGTGTG 59.973 55.0 16.51 8.7 0.0 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
59 60 4.501571 CCTTTGTAGACATGTATAGCGGCT 60.502 45.833 7.98 7.98 0.00 5.52
60 61 3.643159 TGTAGACATGTATAGCGGCTG 57.357 47.619 13.86 0.00 0.00 4.85
61 62 2.956333 TGTAGACATGTATAGCGGCTGT 59.044 45.455 13.86 8.90 0.00 4.40
81 82 7.060633 CGGCTGTTGTTATCTTTGTAATTTCAC 59.939 37.037 0.00 0.00 0.00 3.18
107 108 2.750237 CTGTGGGGCGTTTAGGGC 60.750 66.667 0.00 0.00 0.00 5.19
119 120 2.501261 GTTTAGGGCGACAGGTTTCTT 58.499 47.619 0.00 0.00 0.00 2.52
120 121 2.467566 TTAGGGCGACAGGTTTCTTC 57.532 50.000 0.00 0.00 0.00 2.87
121 122 1.640917 TAGGGCGACAGGTTTCTTCT 58.359 50.000 0.00 0.00 0.00 2.85
139 140 7.865706 TTCTTCTGACCTGATTTTTATAGGC 57.134 36.000 0.00 0.00 34.93 3.93
203 204 1.159285 TGCTGTGTTCATAGCAGTGC 58.841 50.000 17.59 7.13 44.36 4.40
204 205 0.449388 GCTGTGTTCATAGCAGTGCC 59.551 55.000 12.58 0.00 39.67 5.01
205 206 1.812235 CTGTGTTCATAGCAGTGCCA 58.188 50.000 12.58 0.00 0.00 4.92
206 207 2.153645 CTGTGTTCATAGCAGTGCCAA 58.846 47.619 12.58 0.00 0.00 4.52
207 208 1.879380 TGTGTTCATAGCAGTGCCAAC 59.121 47.619 12.58 10.33 0.00 3.77
208 209 2.154462 GTGTTCATAGCAGTGCCAACT 58.846 47.619 12.58 0.00 36.98 3.16
216 217 3.289834 AGTGCCAACTGCCAAGCG 61.290 61.111 0.00 0.00 40.16 4.68
236 237 3.314553 CGTCCTGTAATCGAACTGTTGT 58.685 45.455 0.00 0.00 0.00 3.32
237 238 3.739300 CGTCCTGTAATCGAACTGTTGTT 59.261 43.478 0.00 0.00 39.42 2.83
238 239 4.376008 CGTCCTGTAATCGAACTGTTGTTG 60.376 45.833 0.00 0.00 36.39 3.33
263 264 1.008538 GCTTGTTTGGTCCAGTGCG 60.009 57.895 0.00 0.00 0.00 5.34
270 271 4.309950 GGTCCAGTGCGTCGGGTT 62.310 66.667 0.00 0.00 33.18 4.11
294 295 3.683581 GCGAATCTGTTGCCAAGAC 57.316 52.632 0.00 0.00 0.00 3.01
317 339 1.743958 GCTACTGTGTAGAGCCGAAGA 59.256 52.381 8.71 0.00 0.00 2.87
318 340 2.163815 GCTACTGTGTAGAGCCGAAGAA 59.836 50.000 8.71 0.00 0.00 2.52
322 344 1.544691 TGTGTAGAGCCGAAGAAGGTC 59.455 52.381 0.00 0.00 0.00 3.85
344 366 3.058708 CACACGACAAATCTGTGCTGAAT 60.059 43.478 0.00 0.00 35.30 2.57
345 367 4.152223 CACACGACAAATCTGTGCTGAATA 59.848 41.667 0.00 0.00 35.30 1.75
349 371 4.627035 CGACAAATCTGTGCTGAATACTCA 59.373 41.667 0.00 0.00 35.30 3.41
373 395 3.504906 GGCAACTAAGTACAAAAGGGGTC 59.495 47.826 0.00 0.00 0.00 4.46
412 434 4.208047 CGAAGTGACGATCATTTCATCCTC 59.792 45.833 16.94 0.00 41.42 3.71
451 473 6.309436 CAACTGCAGATGTGTTGTAGTTATG 58.691 40.000 23.35 0.00 45.54 1.90
469 491 2.064434 TGGAACACCATTGTTGAGCA 57.936 45.000 0.00 0.00 46.43 4.26
470 492 2.596346 TGGAACACCATTGTTGAGCAT 58.404 42.857 0.00 0.00 46.43 3.79
471 493 2.557924 TGGAACACCATTGTTGAGCATC 59.442 45.455 0.00 0.00 46.43 3.91
472 494 2.557924 GGAACACCATTGTTGAGCATCA 59.442 45.455 0.00 0.00 46.43 3.07
473 495 6.566704 ATGGAACACCATTGTTGAGCATCAT 61.567 40.000 0.00 0.00 45.94 2.45
474 496 8.515528 ATGGAACACCATTGTTGAGCATCATG 62.516 42.308 0.00 0.00 45.94 3.07
507 529 1.078848 CTGGAACTCCAAGCTCCCG 60.079 63.158 0.00 0.00 46.97 5.14
528 550 4.455877 CCGAGCTGGACCAATAAATTATCC 59.544 45.833 0.00 0.00 42.00 2.59
554 576 6.705825 GTGAGGTTACTTTGAATTGGCAATTT 59.294 34.615 25.02 12.34 0.00 1.82
555 577 7.226523 GTGAGGTTACTTTGAATTGGCAATTTT 59.773 33.333 25.02 6.34 0.00 1.82
556 578 7.772757 TGAGGTTACTTTGAATTGGCAATTTTT 59.227 29.630 25.02 5.55 0.00 1.94
624 646 5.336690 GGATGCAGGCAAAGTCTCAAATTAA 60.337 40.000 0.00 0.00 0.00 1.40
720 742 1.596752 ACGTGTCGGCAGCAAATCA 60.597 52.632 0.00 0.00 0.00 2.57
744 766 1.021390 CGCCGACCTGAAGCATCTTT 61.021 55.000 0.00 0.00 0.00 2.52
746 768 1.089920 CCGACCTGAAGCATCTTTGG 58.910 55.000 0.00 0.00 0.00 3.28
747 769 1.611673 CCGACCTGAAGCATCTTTGGT 60.612 52.381 2.52 2.52 34.30 3.67
748 770 1.734465 CGACCTGAAGCATCTTTGGTC 59.266 52.381 14.65 14.65 37.57 4.02
749 771 1.734465 GACCTGAAGCATCTTTGGTCG 59.266 52.381 11.35 0.00 34.31 4.79
915 953 0.813821 GCAGCCTCATCTTCCCAAAC 59.186 55.000 0.00 0.00 0.00 2.93
974 1012 3.648982 CAAAGCGCACACAGCCGA 61.649 61.111 11.47 0.00 41.38 5.54
987 1025 4.443266 GCCGAAGCTCGAGCACCT 62.443 66.667 36.87 21.81 43.74 4.00
991 1029 0.524392 CGAAGCTCGAGCACCTACTG 60.524 60.000 36.87 16.20 43.74 2.74
992 1030 0.528470 GAAGCTCGAGCACCTACTGT 59.472 55.000 36.87 12.98 45.16 3.55
1012 1050 2.364973 TAGACATGCAGGCCGGGA 60.365 61.111 2.18 0.91 0.00 5.14
1445 1483 2.579201 CGGGCAGTACCAGTGAGG 59.421 66.667 0.00 0.00 42.05 3.86
1446 1484 1.982395 CGGGCAGTACCAGTGAGGA 60.982 63.158 0.00 0.00 42.05 3.71
1454 1495 2.015587 GTACCAGTGAGGACGTAGGAG 58.984 57.143 0.00 0.00 41.22 3.69
1455 1496 0.966370 ACCAGTGAGGACGTAGGAGC 60.966 60.000 0.00 0.00 41.22 4.70
1469 1510 1.153168 GGAGCACGGCCATGTATGT 60.153 57.895 2.24 0.00 0.00 2.29
1470 1511 0.105964 GGAGCACGGCCATGTATGTA 59.894 55.000 2.24 0.00 0.00 2.29
1475 1516 1.227999 ACGGCCATGTATGTATGCGC 61.228 55.000 2.24 0.00 0.00 6.09
1485 1534 1.773410 ATGTATGCGCGCGTATGTAA 58.227 45.000 37.78 24.54 0.00 2.41
1538 1590 4.623167 CAGAGCAATAATTATCTCCCGACG 59.377 45.833 9.47 0.00 0.00 5.12
1539 1591 4.523173 AGAGCAATAATTATCTCCCGACGA 59.477 41.667 9.47 0.00 0.00 4.20
1540 1592 5.186021 AGAGCAATAATTATCTCCCGACGAT 59.814 40.000 9.47 0.00 0.00 3.73
1541 1593 5.411781 AGCAATAATTATCTCCCGACGATC 58.588 41.667 0.00 0.00 0.00 3.69
1542 1594 5.047306 AGCAATAATTATCTCCCGACGATCA 60.047 40.000 0.00 0.00 0.00 2.92
1560 1612 7.167468 CGACGATCATGACAAACTATGTTGATA 59.833 37.037 0.00 0.00 44.12 2.15
1581 1633 1.615107 GACCGCTTTTCACGACCTCG 61.615 60.000 0.00 0.00 46.33 4.63
1614 1668 3.312421 CCCCGAAAATGCTACTACACATG 59.688 47.826 0.00 0.00 0.00 3.21
1625 1681 6.285829 GCTACTACACATGCGGGTAGCTAA 62.286 50.000 22.35 9.80 46.56 3.09
1632 1688 3.364277 GCGGGTAGCTAAGAACCAG 57.636 57.895 5.76 2.67 44.04 4.00
1644 1700 0.324460 AGAACCAGGTACTCCCTCCG 60.324 60.000 0.00 0.00 43.86 4.63
1769 1826 3.871006 CAGTAGATGCGGCATGACTTAAA 59.129 43.478 21.98 0.00 0.00 1.52
1776 1833 4.233789 TGCGGCATGACTTAAATTTTCAC 58.766 39.130 0.00 0.00 0.00 3.18
1781 1838 7.462724 GCGGCATGACTTAAATTTTCACATTAC 60.463 37.037 0.00 0.00 0.00 1.89
1884 1941 8.378172 TCTTATATGCAGAATAAAAAGGACCG 57.622 34.615 0.00 0.00 0.00 4.79
1885 1942 7.444183 TCTTATATGCAGAATAAAAAGGACCGG 59.556 37.037 0.00 0.00 0.00 5.28
1886 1943 3.426787 TGCAGAATAAAAAGGACCGGA 57.573 42.857 9.46 0.00 0.00 5.14
1887 1944 3.343617 TGCAGAATAAAAAGGACCGGAG 58.656 45.455 9.46 0.00 0.00 4.63
1915 1972 2.287427 CGTAGGTGTAGCATTACTCCCG 60.287 54.545 1.70 0.00 42.03 5.14
1932 1989 1.108776 CCGAGACGAATTCCTACCCA 58.891 55.000 0.00 0.00 0.00 4.51
1938 1995 1.141053 ACGAATTCCTACCCATGCCTC 59.859 52.381 0.00 0.00 0.00 4.70
1954 2011 4.361971 TCCGGAGACCACTCGCCT 62.362 66.667 0.00 0.00 43.44 5.52
1958 2023 2.283529 GGAGACCACTCGCCTGGAA 61.284 63.158 0.00 0.00 43.44 3.53
1968 2033 1.879380 CTCGCCTGGAAAATTCACACA 59.121 47.619 0.00 0.00 0.00 3.72
1975 2040 3.715495 TGGAAAATTCACACATGTGCAC 58.285 40.909 25.68 10.75 45.25 4.57
1991 2056 4.850859 GTGCACGCACATAACTTACATA 57.149 40.909 17.03 0.00 45.53 2.29
1992 2057 4.574759 GTGCACGCACATAACTTACATAC 58.425 43.478 17.03 0.00 45.53 2.39
1993 2058 3.619483 TGCACGCACATAACTTACATACC 59.381 43.478 0.00 0.00 0.00 2.73
1994 2059 3.869246 GCACGCACATAACTTACATACCT 59.131 43.478 0.00 0.00 0.00 3.08
1996 2061 5.521010 GCACGCACATAACTTACATACCTTA 59.479 40.000 0.00 0.00 0.00 2.69
1997 2062 6.292168 GCACGCACATAACTTACATACCTTAG 60.292 42.308 0.00 0.00 0.00 2.18
1998 2063 5.751990 ACGCACATAACTTACATACCTTAGC 59.248 40.000 0.00 0.00 0.00 3.09
2003 3853 3.175109 ACTTACATACCTTAGCGTGGC 57.825 47.619 0.00 0.00 0.00 5.01
2013 3863 2.536761 TTAGCGTGGCTAAGTGTTGT 57.463 45.000 6.00 0.00 44.75 3.32
2015 3865 1.082104 GCGTGGCTAAGTGTTGTGC 60.082 57.895 0.00 0.00 0.00 4.57
2016 3866 1.781025 GCGTGGCTAAGTGTTGTGCA 61.781 55.000 0.00 0.00 0.00 4.57
2024 3874 4.662859 GTGTTGTGCACACGTGAC 57.337 55.556 25.01 15.77 46.51 3.67
2025 3875 2.086510 GTGTTGTGCACACGTGACT 58.913 52.632 25.01 0.00 46.51 3.41
2026 3876 0.247655 GTGTTGTGCACACGTGACTG 60.248 55.000 25.01 12.47 46.51 3.51
2027 3877 1.297598 GTTGTGCACACGTGACTGC 60.298 57.895 25.01 22.51 0.00 4.40
2028 3878 1.449423 TTGTGCACACGTGACTGCT 60.449 52.632 25.66 1.34 34.29 4.24
2029 3879 1.704387 TTGTGCACACGTGACTGCTG 61.704 55.000 25.66 14.16 34.29 4.41
2030 3880 2.173669 GTGCACACGTGACTGCTGT 61.174 57.895 25.66 0.00 34.29 4.40
2031 3881 1.449423 TGCACACGTGACTGCTGTT 60.449 52.632 25.66 0.00 34.29 3.16
2032 3882 1.010797 GCACACGTGACTGCTGTTG 60.011 57.895 25.01 8.43 0.00 3.33
2033 3883 1.705337 GCACACGTGACTGCTGTTGT 61.705 55.000 25.01 0.00 0.00 3.32
2034 3884 0.026674 CACACGTGACTGCTGTTGTG 59.973 55.000 25.01 17.15 33.42 3.33
2082 3996 3.044305 GCCTGGACACGTGACTGC 61.044 66.667 25.01 15.93 0.00 4.40
2095 4009 1.293963 TGACTGCAGATGCTTCACGC 61.294 55.000 23.35 4.91 42.66 5.34
2097 4011 2.747460 TGCAGATGCTTCACGCCC 60.747 61.111 6.35 0.00 42.66 6.13
2100 4014 2.125512 AGATGCTTCACGCCCGAC 60.126 61.111 2.07 0.00 38.05 4.79
2151 4261 4.037923 GCCACACACCCCTATATGAAAATG 59.962 45.833 0.00 0.00 0.00 2.32
2152 4262 5.445069 CCACACACCCCTATATGAAAATGA 58.555 41.667 0.00 0.00 0.00 2.57
2198 4315 7.851387 TTTCAAAAATTCTAAAACACACCCC 57.149 32.000 0.00 0.00 0.00 4.95
2199 4316 6.800072 TCAAAAATTCTAAAACACACCCCT 57.200 33.333 0.00 0.00 0.00 4.79
2200 4317 7.899648 TCAAAAATTCTAAAACACACCCCTA 57.100 32.000 0.00 0.00 0.00 3.53
2201 4318 8.485578 TCAAAAATTCTAAAACACACCCCTAT 57.514 30.769 0.00 0.00 0.00 2.57
2202 4319 9.589461 TCAAAAATTCTAAAACACACCCCTATA 57.411 29.630 0.00 0.00 0.00 1.31
2205 4322 9.762381 AAAATTCTAAAACACACCCCTATATGA 57.238 29.630 0.00 0.00 0.00 2.15
2206 4323 9.762381 AAATTCTAAAACACACCCCTATATGAA 57.238 29.630 0.00 0.00 0.00 2.57
2207 4324 9.762381 AATTCTAAAACACACCCCTATATGAAA 57.238 29.630 0.00 0.00 0.00 2.69
2208 4325 9.762381 ATTCTAAAACACACCCCTATATGAAAA 57.238 29.630 0.00 0.00 0.00 2.29
2209 4326 9.762381 TTCTAAAACACACCCCTATATGAAAAT 57.238 29.630 0.00 0.00 0.00 1.82
2210 4327 9.184523 TCTAAAACACACCCCTATATGAAAATG 57.815 33.333 0.00 0.00 0.00 2.32
2211 4328 9.184523 CTAAAACACACCCCTATATGAAAATGA 57.815 33.333 0.00 0.00 0.00 2.57
2212 4329 7.404671 AAACACACCCCTATATGAAAATGAC 57.595 36.000 0.00 0.00 0.00 3.06
2213 4330 6.073447 ACACACCCCTATATGAAAATGACA 57.927 37.500 0.00 0.00 0.00 3.58
2214 4331 6.672593 ACACACCCCTATATGAAAATGACAT 58.327 36.000 0.00 0.00 0.00 3.06
2215 4332 7.125391 ACACACCCCTATATGAAAATGACATT 58.875 34.615 0.00 0.00 0.00 2.71
2216 4333 7.619302 ACACACCCCTATATGAAAATGACATTT 59.381 33.333 7.62 7.62 0.00 2.32
2287 4467 4.757019 TGTGTACCACAGTTACCTTCAA 57.243 40.909 0.00 0.00 39.62 2.69
2288 4468 5.298989 TGTGTACCACAGTTACCTTCAAT 57.701 39.130 0.00 0.00 39.62 2.57
2289 4469 5.060506 TGTGTACCACAGTTACCTTCAATG 58.939 41.667 0.00 0.00 39.62 2.82
2290 4470 5.163290 TGTGTACCACAGTTACCTTCAATGA 60.163 40.000 0.00 0.00 39.62 2.57
2291 4471 5.938125 GTGTACCACAGTTACCTTCAATGAT 59.062 40.000 0.00 0.00 34.08 2.45
2292 4472 6.092259 GTGTACCACAGTTACCTTCAATGATC 59.908 42.308 0.00 0.00 34.08 2.92
2293 4473 5.241403 ACCACAGTTACCTTCAATGATCA 57.759 39.130 0.00 0.00 0.00 2.92
2294 4474 5.819991 ACCACAGTTACCTTCAATGATCAT 58.180 37.500 1.18 1.18 0.00 2.45
2295 4475 6.248433 ACCACAGTTACCTTCAATGATCATT 58.752 36.000 15.36 15.36 0.00 2.57
2296 4476 6.721208 ACCACAGTTACCTTCAATGATCATTT 59.279 34.615 18.41 6.51 0.00 2.32
2297 4477 7.233348 ACCACAGTTACCTTCAATGATCATTTT 59.767 33.333 18.41 0.00 0.00 1.82
2298 4478 8.090214 CCACAGTTACCTTCAATGATCATTTTT 58.910 33.333 18.41 0.00 0.00 1.94
2329 4518 8.849168 TGATCATTTTTGGTAGTATAATGCTGG 58.151 33.333 0.00 0.00 0.00 4.85
2330 4519 8.995027 ATCATTTTTGGTAGTATAATGCTGGA 57.005 30.769 0.00 0.00 0.00 3.86
2331 4520 8.815565 TCATTTTTGGTAGTATAATGCTGGAA 57.184 30.769 0.00 0.00 0.00 3.53
2332 4521 8.682710 TCATTTTTGGTAGTATAATGCTGGAAC 58.317 33.333 0.00 0.00 0.00 3.62
2333 4522 7.399245 TTTTTGGTAGTATAATGCTGGAACC 57.601 36.000 0.00 0.00 0.00 3.62
2334 4523 5.702065 TTGGTAGTATAATGCTGGAACCA 57.298 39.130 0.00 0.00 34.09 3.67
2335 4524 5.031066 TGGTAGTATAATGCTGGAACCAC 57.969 43.478 0.00 0.00 31.06 4.16
2366 4555 9.904198 TGATAATTCCAACAGTTATCTGATTGA 57.096 29.630 7.81 0.00 43.76 2.57
2371 4560 8.812513 TTCCAACAGTTATCTGATTGATTCAT 57.187 30.769 7.81 0.00 43.76 2.57
2395 4584 8.688184 CATACTATTAATGGTTGTACTTCGACG 58.312 37.037 9.95 0.00 0.00 5.12
2401 4590 3.061322 TGGTTGTACTTCGACGAATTGG 58.939 45.455 11.30 2.14 0.00 3.16
2407 4596 2.413837 ACTTCGACGAATTGGGAACAG 58.586 47.619 11.30 0.00 44.54 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 8.409371 TGCAGTGAAATTACAAAGATAACAACA 58.591 29.630 0.00 0.00 0.00 3.33
60 61 8.795786 TGCAGTGAAATTACAAAGATAACAAC 57.204 30.769 0.00 0.00 0.00 3.32
61 62 9.409312 CATGCAGTGAAATTACAAAGATAACAA 57.591 29.630 0.00 0.00 0.00 2.83
81 82 3.138798 GCCCCACAGCTCATGCAG 61.139 66.667 0.00 0.00 42.74 4.41
107 108 2.821991 AGGTCAGAAGAAACCTGTCG 57.178 50.000 0.00 0.00 44.26 4.35
119 120 6.313519 ACAGCCTATAAAAATCAGGTCAGA 57.686 37.500 0.00 0.00 0.00 3.27
120 121 7.275920 AGTACAGCCTATAAAAATCAGGTCAG 58.724 38.462 0.00 0.00 0.00 3.51
121 122 7.195374 AGTACAGCCTATAAAAATCAGGTCA 57.805 36.000 0.00 0.00 0.00 4.02
139 140 1.174783 AGGTGGTGCTACGAGTACAG 58.825 55.000 0.00 0.00 32.12 2.74
202 203 4.043200 GGACGCTTGGCAGTTGGC 62.043 66.667 0.00 0.00 43.74 4.52
203 204 2.281761 AGGACGCTTGGCAGTTGG 60.282 61.111 0.00 0.00 0.00 3.77
204 205 0.602638 TACAGGACGCTTGGCAGTTG 60.603 55.000 0.00 0.00 0.00 3.16
205 206 0.107831 TTACAGGACGCTTGGCAGTT 59.892 50.000 0.00 0.00 0.00 3.16
206 207 0.324943 ATTACAGGACGCTTGGCAGT 59.675 50.000 0.00 0.00 0.00 4.40
207 208 1.009829 GATTACAGGACGCTTGGCAG 58.990 55.000 0.00 0.00 0.00 4.85
208 209 0.739462 CGATTACAGGACGCTTGGCA 60.739 55.000 0.00 0.00 0.00 4.92
216 217 4.084013 CCAACAACAGTTCGATTACAGGAC 60.084 45.833 0.00 0.00 0.00 3.85
236 237 0.396974 ACCAAACAAGCCTCAGCCAA 60.397 50.000 0.00 0.00 41.25 4.52
237 238 0.823356 GACCAAACAAGCCTCAGCCA 60.823 55.000 0.00 0.00 41.25 4.75
238 239 1.527433 GGACCAAACAAGCCTCAGCC 61.527 60.000 0.00 0.00 41.25 4.85
263 264 1.366854 GATTCGCCCTTCAACCCGAC 61.367 60.000 0.00 0.00 0.00 4.79
270 271 0.960364 GGCAACAGATTCGCCCTTCA 60.960 55.000 0.00 0.00 40.07 3.02
294 295 1.472878 TCGGCTCTACACAGTAGCTTG 59.527 52.381 0.00 0.00 36.48 4.01
317 339 2.872245 CACAGATTTGTCGTGTGACCTT 59.128 45.455 0.00 0.00 43.58 3.50
318 340 2.483876 CACAGATTTGTCGTGTGACCT 58.516 47.619 0.00 0.00 43.58 3.85
322 344 1.866601 TCAGCACAGATTTGTCGTGTG 59.133 47.619 0.00 0.00 43.70 3.82
344 366 6.708949 CCTTTTGTACTTAGTTGCCTTGAGTA 59.291 38.462 0.00 0.00 0.00 2.59
345 367 5.531287 CCTTTTGTACTTAGTTGCCTTGAGT 59.469 40.000 0.00 0.00 0.00 3.41
349 371 4.149598 CCCCTTTTGTACTTAGTTGCCTT 58.850 43.478 0.00 0.00 0.00 4.35
373 395 4.344668 CGTCAGAGTACAGACGCG 57.655 61.111 18.08 3.53 45.50 6.01
451 473 2.557924 TGATGCTCAACAATGGTGTTCC 59.442 45.455 0.00 0.00 45.00 3.62
471 493 1.201647 CAGGTTTCAAGCCTCAGCATG 59.798 52.381 0.00 0.00 43.56 4.06
472 494 1.542492 CAGGTTTCAAGCCTCAGCAT 58.458 50.000 0.00 0.00 43.56 3.79
473 495 0.538057 CCAGGTTTCAAGCCTCAGCA 60.538 55.000 0.00 0.00 43.56 4.41
474 496 0.250901 TCCAGGTTTCAAGCCTCAGC 60.251 55.000 0.00 0.00 40.32 4.26
475 497 1.882623 GTTCCAGGTTTCAAGCCTCAG 59.117 52.381 0.00 0.00 33.31 3.35
476 498 1.494721 AGTTCCAGGTTTCAAGCCTCA 59.505 47.619 0.00 0.00 33.31 3.86
477 499 2.155279 GAGTTCCAGGTTTCAAGCCTC 58.845 52.381 0.00 0.00 33.31 4.70
478 500 1.202940 GGAGTTCCAGGTTTCAAGCCT 60.203 52.381 0.00 0.00 36.66 4.58
479 501 1.248486 GGAGTTCCAGGTTTCAAGCC 58.752 55.000 0.00 0.00 35.64 4.35
480 502 1.981256 TGGAGTTCCAGGTTTCAAGC 58.019 50.000 0.00 0.00 42.01 4.01
507 529 5.049405 CACGGATAATTTATTGGTCCAGCTC 60.049 44.000 0.00 0.00 0.00 4.09
528 550 3.252215 TGCCAATTCAAAGTAACCTCACG 59.748 43.478 0.00 0.00 0.00 4.35
579 601 4.124970 CCATGTCACTGACGATCAATGAT 58.875 43.478 0.00 0.00 34.99 2.45
584 606 2.739609 GCATCCATGTCACTGACGATCA 60.740 50.000 4.71 0.00 34.95 2.92
624 646 0.676782 CCCCGAGCATTTTCGAGGTT 60.677 55.000 0.00 0.00 43.03 3.50
654 676 2.431454 CAGGAAAGAGGCTTCTTCACC 58.569 52.381 19.71 19.71 42.80 4.02
716 738 1.153369 CAGGTCGGCGATGGTGATT 60.153 57.895 14.79 0.00 0.00 2.57
720 742 2.579201 CTTCAGGTCGGCGATGGT 59.421 61.111 14.79 0.00 0.00 3.55
786 819 2.804828 CTTTCTCCTGGGCGGTCCAC 62.805 65.000 0.00 0.00 41.46 4.02
787 820 2.528127 TTTCTCCTGGGCGGTCCA 60.528 61.111 0.00 0.00 44.79 4.02
788 821 1.838073 TTCTTTCTCCTGGGCGGTCC 61.838 60.000 0.00 0.00 0.00 4.46
789 822 0.036306 TTTCTTTCTCCTGGGCGGTC 59.964 55.000 0.00 0.00 0.00 4.79
790 823 0.036875 CTTTCTTTCTCCTGGGCGGT 59.963 55.000 0.00 0.00 0.00 5.68
791 824 0.324943 TCTTTCTTTCTCCTGGGCGG 59.675 55.000 0.00 0.00 0.00 6.13
792 825 1.677217 CCTCTTTCTTTCTCCTGGGCG 60.677 57.143 0.00 0.00 0.00 6.13
793 826 1.630878 TCCTCTTTCTTTCTCCTGGGC 59.369 52.381 0.00 0.00 0.00 5.36
794 827 3.680490 GTTCCTCTTTCTTTCTCCTGGG 58.320 50.000 0.00 0.00 0.00 4.45
795 828 3.330267 CGTTCCTCTTTCTTTCTCCTGG 58.670 50.000 0.00 0.00 0.00 4.45
915 953 3.577848 TCATTCAATTCAACTGGTTGGGG 59.422 43.478 12.65 2.22 40.78 4.96
972 1010 0.524392 CAGTAGGTGCTCGAGCTTCG 60.524 60.000 35.27 14.55 42.66 3.79
974 1012 1.473278 GTACAGTAGGTGCTCGAGCTT 59.527 52.381 35.27 23.11 42.66 3.74
985 1023 3.243569 GCCTGCATGTCTAGTACAGTAGG 60.244 52.174 15.38 15.38 42.70 3.18
987 1025 2.693591 GGCCTGCATGTCTAGTACAGTA 59.306 50.000 0.00 0.00 42.70 2.74
991 1029 0.249489 CCGGCCTGCATGTCTAGTAC 60.249 60.000 0.00 0.00 0.00 2.73
992 1030 1.399744 CCCGGCCTGCATGTCTAGTA 61.400 60.000 0.00 0.00 0.00 1.82
1075 1113 4.162690 GGCCCGCGTCTTCTCCAT 62.163 66.667 4.92 0.00 0.00 3.41
1250 1288 3.379445 CCTGCGACGGGTGGTACT 61.379 66.667 0.00 0.00 0.00 2.73
1445 1483 3.077519 ATGGCCGTGCTCCTACGTC 62.078 63.158 0.00 0.00 42.24 4.34
1446 1484 3.075005 ATGGCCGTGCTCCTACGT 61.075 61.111 0.00 0.00 42.24 3.57
1454 1495 0.238289 GCATACATACATGGCCGTGC 59.762 55.000 25.30 4.23 0.00 5.34
1455 1496 0.512518 CGCATACATACATGGCCGTG 59.487 55.000 23.83 23.83 0.00 4.94
1469 1510 1.270110 CGGTTACATACGCGCGCATA 61.270 55.000 32.58 22.65 0.00 3.14
1470 1511 2.582265 CGGTTACATACGCGCGCAT 61.582 57.895 32.58 21.80 0.00 4.73
1475 1516 0.918619 CTGAACCGGTTACATACGCG 59.081 55.000 22.33 3.53 0.00 6.01
1485 1534 1.640917 ACTGATACACCTGAACCGGT 58.359 50.000 0.00 0.00 37.93 5.28
1539 1591 9.113838 GGTCTTATCAACATAGTTTGTCATGAT 57.886 33.333 0.00 6.27 38.64 2.45
1540 1592 7.277760 CGGTCTTATCAACATAGTTTGTCATGA 59.722 37.037 0.00 0.00 37.68 3.07
1541 1593 7.401860 CGGTCTTATCAACATAGTTTGTCATG 58.598 38.462 0.00 0.00 37.68 3.07
1542 1594 6.037172 GCGGTCTTATCAACATAGTTTGTCAT 59.963 38.462 0.00 0.00 37.68 3.06
1560 1612 0.106149 AGGTCGTGAAAAGCGGTCTT 59.894 50.000 0.00 0.00 0.00 3.01
1581 1633 1.565067 TTTTCGGGGAGAGAGGGTAC 58.435 55.000 0.00 0.00 0.00 3.34
1614 1668 0.179081 CCTGGTTCTTAGCTACCCGC 60.179 60.000 0.00 0.00 39.57 6.13
1644 1700 7.781548 TCTTATATGCGAACTAAAAAGGACC 57.218 36.000 0.00 0.00 0.00 4.46
1736 1793 5.764686 TGCCGCATCTACTGATATTGATTTT 59.235 36.000 0.00 0.00 0.00 1.82
1743 1800 3.513119 AGTCATGCCGCATCTACTGATAT 59.487 43.478 14.39 0.00 0.00 1.63
1872 1929 2.238898 CACTCCCTCCGGTCCTTTTTAT 59.761 50.000 0.00 0.00 0.00 1.40
1881 1938 2.754658 CTACGCACTCCCTCCGGT 60.755 66.667 0.00 0.00 0.00 5.28
1882 1939 3.528370 CCTACGCACTCCCTCCGG 61.528 72.222 0.00 0.00 0.00 5.14
1883 1940 2.754658 ACCTACGCACTCCCTCCG 60.755 66.667 0.00 0.00 0.00 4.63
1884 1941 0.682209 TACACCTACGCACTCCCTCC 60.682 60.000 0.00 0.00 0.00 4.30
1885 1942 0.739561 CTACACCTACGCACTCCCTC 59.260 60.000 0.00 0.00 0.00 4.30
1886 1943 1.321074 GCTACACCTACGCACTCCCT 61.321 60.000 0.00 0.00 0.00 4.20
1887 1944 1.141234 GCTACACCTACGCACTCCC 59.859 63.158 0.00 0.00 0.00 4.30
1888 1945 0.460311 ATGCTACACCTACGCACTCC 59.540 55.000 0.00 0.00 36.37 3.85
1889 1946 2.295253 AATGCTACACCTACGCACTC 57.705 50.000 0.00 0.00 36.37 3.51
1890 1947 2.758979 AGTAATGCTACACCTACGCACT 59.241 45.455 0.00 0.00 36.37 4.40
1891 1948 3.114065 GAGTAATGCTACACCTACGCAC 58.886 50.000 0.00 0.00 36.37 5.34
1892 1949 2.100252 GGAGTAATGCTACACCTACGCA 59.900 50.000 0.00 0.00 36.23 5.24
1893 1950 2.545322 GGGAGTAATGCTACACCTACGC 60.545 54.545 0.77 0.00 38.47 4.42
1915 1972 2.484889 GCATGGGTAGGAATTCGTCTC 58.515 52.381 3.47 0.00 0.00 3.36
1938 1995 4.135153 CAGGCGAGTGGTCTCCGG 62.135 72.222 0.00 0.00 37.40 5.14
1975 2040 5.107989 CGCTAAGGTATGTAAGTTATGTGCG 60.108 44.000 0.00 0.00 0.00 5.34
1994 2059 2.139917 CACAACACTTAGCCACGCTAA 58.860 47.619 5.99 5.99 46.97 3.09
1996 2061 1.507141 GCACAACACTTAGCCACGCT 61.507 55.000 0.00 0.00 43.41 5.07
1997 2062 1.082104 GCACAACACTTAGCCACGC 60.082 57.895 0.00 0.00 0.00 5.34
1998 2063 0.041312 GTGCACAACACTTAGCCACG 60.041 55.000 13.17 0.00 46.41 4.94
2010 3860 1.449423 AGCAGTCACGTGTGCACAA 60.449 52.632 26.83 2.20 42.47 3.33
2013 3863 1.449423 AACAGCAGTCACGTGTGCA 60.449 52.632 26.83 2.65 42.47 4.57
2015 3865 0.026674 CACAACAGCAGTCACGTGTG 59.973 55.000 16.51 8.70 0.00 3.82
2016 3866 1.705337 GCACAACAGCAGTCACGTGT 61.705 55.000 16.51 0.00 0.00 4.49
2017 3867 1.010797 GCACAACAGCAGTCACGTG 60.011 57.895 9.94 9.94 0.00 4.49
2018 3868 1.449423 TGCACAACAGCAGTCACGT 60.449 52.632 0.00 0.00 40.11 4.49
2019 3869 1.010797 GTGCACAACAGCAGTCACG 60.011 57.895 13.17 0.00 46.69 4.35
2020 3870 0.248215 GTGTGCACAACAGCAGTCAC 60.248 55.000 23.59 0.42 46.69 3.67
2021 3871 1.704387 CGTGTGCACAACAGCAGTCA 61.704 55.000 23.59 0.00 46.69 3.41
2022 3872 1.010797 CGTGTGCACAACAGCAGTC 60.011 57.895 23.59 5.36 46.69 3.51
2023 3873 1.745115 ACGTGTGCACAACAGCAGT 60.745 52.632 23.59 11.77 46.69 4.40
2024 3874 1.297819 CACGTGTGCACAACAGCAG 60.298 57.895 23.59 11.14 46.69 4.24
2025 3875 1.743252 TCACGTGTGCACAACAGCA 60.743 52.632 23.59 1.54 40.26 4.41
2026 3876 1.297598 GTCACGTGTGCACAACAGC 60.298 57.895 23.59 8.22 40.26 4.40
2027 3877 0.026674 CAGTCACGTGTGCACAACAG 59.973 55.000 23.59 17.97 40.26 3.16
2028 3878 1.976478 GCAGTCACGTGTGCACAACA 61.976 55.000 23.59 2.35 39.62 3.33
2029 3879 1.297598 GCAGTCACGTGTGCACAAC 60.298 57.895 23.59 16.27 39.62 3.32
2030 3880 1.704387 CTGCAGTCACGTGTGCACAA 61.704 55.000 24.89 2.20 44.70 3.33
2031 3881 2.125350 TGCAGTCACGTGTGCACA 60.125 55.556 24.89 17.42 44.70 4.57
2032 3882 1.224069 ATCTGCAGTCACGTGTGCAC 61.224 55.000 24.89 10.75 44.70 4.57
2034 3884 1.494628 CATCTGCAGTCACGTGTGC 59.505 57.895 20.76 20.76 40.29 4.57
2069 3919 1.630244 GCATCTGCAGTCACGTGTCC 61.630 60.000 16.51 7.65 41.59 4.02
2070 3920 0.668706 AGCATCTGCAGTCACGTGTC 60.669 55.000 16.51 10.42 45.16 3.67
2095 4009 3.098555 GCATTAGGCAACGTCGGG 58.901 61.111 0.00 0.00 43.97 5.14
2104 4018 2.954318 ACATGAGTCCAATGCATTAGGC 59.046 45.455 12.53 6.47 45.13 3.93
2105 4019 3.949754 ACACATGAGTCCAATGCATTAGG 59.050 43.478 12.53 15.39 0.00 2.69
2107 4021 3.129113 GCACACATGAGTCCAATGCATTA 59.871 43.478 12.53 0.00 0.00 1.90
2184 4301 9.184523 CATTTTCATATAGGGGTGTGTTTTAGA 57.815 33.333 0.00 0.00 0.00 2.10
2185 4302 9.184523 TCATTTTCATATAGGGGTGTGTTTTAG 57.815 33.333 0.00 0.00 0.00 1.85
2186 4303 8.962679 GTCATTTTCATATAGGGGTGTGTTTTA 58.037 33.333 0.00 0.00 0.00 1.52
2187 4304 7.453126 TGTCATTTTCATATAGGGGTGTGTTTT 59.547 33.333 0.00 0.00 0.00 2.43
2188 4305 6.951198 TGTCATTTTCATATAGGGGTGTGTTT 59.049 34.615 0.00 0.00 0.00 2.83
2189 4306 6.489603 TGTCATTTTCATATAGGGGTGTGTT 58.510 36.000 0.00 0.00 0.00 3.32
2190 4307 6.073447 TGTCATTTTCATATAGGGGTGTGT 57.927 37.500 0.00 0.00 0.00 3.72
2191 4308 7.587037 AATGTCATTTTCATATAGGGGTGTG 57.413 36.000 0.00 0.00 0.00 3.82
2192 4309 8.608185 AAAATGTCATTTTCATATAGGGGTGT 57.392 30.769 16.26 0.00 37.96 4.16
2244 4361 9.927668 ACACAGTTTGATATCCCAAAAATTTAG 57.072 29.630 0.00 0.00 37.72 1.85
2327 4516 3.434453 GGAATTATCATCCCGTGGTTCCA 60.434 47.826 0.00 0.00 35.22 3.53
2328 4517 3.146847 GGAATTATCATCCCGTGGTTCC 58.853 50.000 0.00 0.00 0.00 3.62
2329 4518 3.815809 TGGAATTATCATCCCGTGGTTC 58.184 45.455 0.00 0.00 36.04 3.62
2330 4519 3.943671 TGGAATTATCATCCCGTGGTT 57.056 42.857 0.00 0.00 36.04 3.67
2331 4520 3.053991 TGTTGGAATTATCATCCCGTGGT 60.054 43.478 0.00 0.00 36.04 4.16
2332 4521 3.550820 TGTTGGAATTATCATCCCGTGG 58.449 45.455 0.00 0.00 36.04 4.94
2333 4522 4.199310 ACTGTTGGAATTATCATCCCGTG 58.801 43.478 0.00 0.00 36.04 4.94
2334 4523 4.503714 ACTGTTGGAATTATCATCCCGT 57.496 40.909 0.00 0.00 36.04 5.28
2335 4524 6.936900 AGATAACTGTTGGAATTATCATCCCG 59.063 38.462 2.69 0.00 37.64 5.14
2371 4560 7.984391 TCGTCGAAGTACAACCATTAATAGTA 58.016 34.615 0.00 0.00 0.00 1.82
2376 4565 6.128499 CCAATTCGTCGAAGTACAACCATTAA 60.128 38.462 13.88 0.00 0.00 1.40
2377 4566 5.349270 CCAATTCGTCGAAGTACAACCATTA 59.651 40.000 13.88 0.00 0.00 1.90
2378 4567 4.153475 CCAATTCGTCGAAGTACAACCATT 59.847 41.667 13.88 0.00 0.00 3.16
2393 4582 0.476771 ACCCACTGTTCCCAATTCGT 59.523 50.000 0.00 0.00 0.00 3.85
2395 4584 3.963129 TCATACCCACTGTTCCCAATTC 58.037 45.455 0.00 0.00 0.00 2.17
2401 4590 2.467566 ACGTTCATACCCACTGTTCC 57.532 50.000 0.00 0.00 0.00 3.62
2407 4596 4.493545 CGAGCATTAAACGTTCATACCCAC 60.494 45.833 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.