Multiple sequence alignment - TraesCS7D01G020500

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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 TraesCS7D01G020500 chr7D 100.000 2522 0 0 1 2522 9034056 9031535 0.000000e+00 4658.0
1 TraesCS7D01G020500 chr7D 91.108 686 54 4 1 680 10339034 10339718 0.000000e+00 922.0
2 TraesCS7D01G020500 chr7D 87.195 820 73 19 992 1800 9398457 9399255 0.000000e+00 904.0
3 TraesCS7D01G020500 chr7D 87.500 736 51 17 704 1420 9001092 9000379 0.000000e+00 811.0
4 TraesCS7D01G020500 chr7D 88.372 387 41 2 2136 2522 145205 144823 1.770000e-126 462.0
5 TraesCS7D01G020500 chr7D 86.880 343 23 5 810 1152 10339841 10340161 5.130000e-97 364.0
6 TraesCS7D01G020500 chr7D 86.425 221 24 4 1211 1428 10851369 10851586 1.170000e-58 237.0
7 TraesCS7D01G020500 chr7D 83.209 268 25 9 1818 2067 145478 145213 7.020000e-56 228.0
8 TraesCS7D01G020500 chr7D 91.954 87 2 1 692 773 10339760 10339846 1.590000e-22 117.0
9 TraesCS7D01G020500 chr7D 81.159 138 17 4 437 567 9004305 9004170 4.440000e-18 102.0
10 TraesCS7D01G020500 chr7D 98.039 51 1 0 630 680 9398161 9398211 3.460000e-14 89.8
11 TraesCS7D01G020500 chr7A 85.701 1070 91 30 728 1780 9319404 9318380 0.000000e+00 1072.0
12 TraesCS7D01G020500 chr7A 87.283 920 73 23 683 1592 652923044 652922159 0.000000e+00 1011.0
13 TraesCS7D01G020500 chr7A 90.577 711 45 5 885 1592 9266258 9265567 0.000000e+00 922.0
14 TraesCS7D01G020500 chr7A 91.124 169 10 2 728 891 9267918 9267750 9.080000e-55 224.0
15 TraesCS7D01G020500 chr7A 85.938 128 14 4 650 774 9288709 9288583 1.570000e-27 134.0
16 TraesCS7D01G020500 chr7A 84.211 133 19 2 1817 1948 239138045 239137914 7.320000e-26 128.0
17 TraesCS7D01G020500 chr7A 86.275 102 4 4 683 774 9319541 9319440 4.440000e-18 102.0
18 TraesCS7D01G020500 chr7A 97.143 35 1 0 644 678 9319606 9319572 2.710000e-05 60.2
19 TraesCS7D01G020500 chr7A 92.500 40 3 0 650 689 652923103 652923064 9.740000e-05 58.4
20 TraesCS7D01G020500 chr2B 88.889 396 37 7 1974 2366 690755214 690754823 4.880000e-132 481.0
21 TraesCS7D01G020500 chr2B 89.375 320 33 1 1 320 747577205 747577523 3.910000e-108 401.0
22 TraesCS7D01G020500 chr2B 89.375 320 33 1 1 320 747605820 747606138 3.910000e-108 401.0
23 TraesCS7D01G020500 chr2B 84.000 150 20 4 1802 1948 156003039 156003187 9.410000e-30 141.0
24 TraesCS7D01G020500 chr5A 87.438 406 44 5 1964 2366 617920524 617920925 6.360000e-126 460.0
25 TraesCS7D01G020500 chr5A 82.550 149 22 4 1805 1950 119063693 119063840 7.320000e-26 128.0
26 TraesCS7D01G020500 chr3B 86.700 406 46 8 1964 2366 758918009 758918409 6.400000e-121 444.0
27 TraesCS7D01G020500 chr1B 90.938 320 29 0 4 323 526618841 526618522 4.980000e-117 431.0
28 TraesCS7D01G020500 chr1B 100.000 28 0 0 1798 1825 84375442 84375469 5.000000e-03 52.8
29 TraesCS7D01G020500 chr1D 85.894 397 47 8 2131 2519 323501843 323502238 5.020000e-112 414.0
30 TraesCS7D01G020500 chr1D 87.372 293 32 5 2131 2421 323119124 323119413 5.200000e-87 331.0
31 TraesCS7D01G020500 chr2D 89.375 320 32 2 1 320 555482375 555482692 3.910000e-108 401.0
32 TraesCS7D01G020500 chr2D 88.957 326 33 3 1 324 424394668 424394992 1.410000e-107 399.0
33 TraesCS7D01G020500 chr2D 88.308 325 36 2 1 324 424307696 424308019 3.040000e-104 388.0
34 TraesCS7D01G020500 chr2D 86.466 133 17 1 1817 1948 105590464 105590332 7.270000e-31 145.0
35 TraesCS7D01G020500 chr2D 85.714 133 18 1 1817 1948 91919892 91920024 3.380000e-29 139.0
36 TraesCS7D01G020500 chr2D 91.781 73 6 0 2135 2207 88260400 88260472 4.440000e-18 102.0
37 TraesCS7D01G020500 chr3D 88.854 323 36 0 1 323 402499615 402499937 5.060000e-107 398.0
38 TraesCS7D01G020500 chr4A 88.545 323 37 0 1 323 41012094 41012416 2.350000e-105 392.0
39 TraesCS7D01G020500 chr6B 89.908 109 10 1 1841 1948 590785139 590785247 3.380000e-29 139.0
40 TraesCS7D01G020500 chr6B 83.942 137 18 4 1817 1950 511341843 511341708 7.320000e-26 128.0
41 TraesCS7D01G020500 chr4B 85.821 134 15 3 1817 1948 150986954 150987085 3.380000e-29 139.0
42 TraesCS7D01G020500 chrUn 82.581 155 20 6 2171 2318 12121139 12120985 2.040000e-26 130.0
43 TraesCS7D01G020500 chr4D 82.581 155 20 3 2171 2318 215158298 215158452 2.040000e-26 130.0
44 TraesCS7D01G020500 chr6A 82.550 149 22 4 1805 1950 479395696 479395843 7.320000e-26 128.0
45 TraesCS7D01G020500 chr6A 83.929 112 13 2 2190 2299 68525872 68525980 4.440000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G020500 chr7D 9031535 9034056 2521 True 4658.000000 4658 100.000000 1 2522 1 chr7D.!!$R1 2521
1 TraesCS7D01G020500 chr7D 9398161 9399255 1094 False 496.900000 904 92.617000 630 1800 2 chr7D.!!$F2 1170
2 TraesCS7D01G020500 chr7D 10339034 10340161 1127 False 467.666667 922 89.980667 1 1152 3 chr7D.!!$F3 1151
3 TraesCS7D01G020500 chr7D 9000379 9004305 3926 True 456.500000 811 84.329500 437 1420 2 chr7D.!!$R3 983
4 TraesCS7D01G020500 chr7D 144823 145478 655 True 345.000000 462 85.790500 1818 2522 2 chr7D.!!$R2 704
5 TraesCS7D01G020500 chr7A 9265567 9267918 2351 True 573.000000 922 90.850500 728 1592 2 chr7A.!!$R3 864
6 TraesCS7D01G020500 chr7A 652922159 652923103 944 True 534.700000 1011 89.891500 650 1592 2 chr7A.!!$R5 942
7 TraesCS7D01G020500 chr7A 9318380 9319606 1226 True 411.400000 1072 89.706333 644 1780 3 chr7A.!!$R4 1136

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
808 3877 0.032678 AGAGAGCACGTGTCCTTGTG 59.967 55.0 18.38 0.0 39.1 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 6657 0.107654 GTGGCGCTCACCTTATCCTT 60.108 55.0 7.64 0.0 40.39 3.36 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
28 29 7.685849 AGTAGGTAGGATAAACTGCCATTTA 57.314 36.000 3.29 0.00 44.63 1.40
29 30 7.506971 AGTAGGTAGGATAAACTGCCATTTAC 58.493 38.462 3.29 0.00 44.63 2.01
39 40 5.693769 AACTGCCATTTACTTCCTAGCTA 57.306 39.130 0.00 0.00 0.00 3.32
41 42 4.101741 ACTGCCATTTACTTCCTAGCTAGG 59.898 45.833 30.94 30.94 45.02 3.02
66 67 2.849880 ACAATGTTCAGTGTGTGTGC 57.150 45.000 5.12 0.00 0.00 4.57
76 77 1.273606 AGTGTGTGTGCTAAGATCGCT 59.726 47.619 0.00 0.00 0.00 4.93
120 121 1.606668 TCTTTAGCCGTTTGCAACCAG 59.393 47.619 0.00 0.00 44.83 4.00
124 125 1.034838 AGCCGTTTGCAACCAGACAA 61.035 50.000 0.00 0.00 44.83 3.18
152 153 5.176407 TGCTTATTTAACAACAGCAACGT 57.824 34.783 0.00 0.00 37.54 3.99
168 169 1.206578 CGTAGGCAACCAAACAGCG 59.793 57.895 0.00 0.00 37.17 5.18
182 183 0.319900 ACAGCGTGCTGACTAGTTGG 60.320 55.000 27.26 0.00 46.30 3.77
189 190 2.054799 TGCTGACTAGTTGGTTCCCTT 58.945 47.619 0.00 0.00 0.00 3.95
200 201 3.085952 TGGTTCCCTTATGCAGAAAGG 57.914 47.619 19.28 19.28 42.73 3.11
201 202 1.751351 GGTTCCCTTATGCAGAAAGGC 59.249 52.381 20.36 10.25 41.91 4.35
206 207 4.464008 TCCCTTATGCAGAAAGGCTAATG 58.536 43.478 20.36 9.99 41.91 1.90
222 223 3.673323 GCTAATGCAGGCAACCAAACTAC 60.673 47.826 0.00 0.00 39.41 2.73
225 226 1.612950 TGCAGGCAACCAAACTACATG 59.387 47.619 0.00 0.00 37.17 3.21
232 233 4.157656 GGCAACCAAACTACATGCAGATAA 59.842 41.667 0.00 0.00 38.73 1.75
235 236 6.267817 CAACCAAACTACATGCAGATAATGG 58.732 40.000 0.00 5.00 0.00 3.16
247 248 4.142182 TGCAGATAATGGTTTTTAGCCTGC 60.142 41.667 0.00 0.00 39.53 4.85
258 259 0.607620 TTAGCCTGCATTTGCCCAAC 59.392 50.000 0.00 0.00 41.18 3.77
260 261 2.262292 CCTGCATTTGCCCAACCG 59.738 61.111 0.00 0.00 41.18 4.44
271 272 2.833227 CCAACCGGGTCCAACAGA 59.167 61.111 6.32 0.00 0.00 3.41
283 284 3.557054 GGTCCAACAGAGACAAGTATGCA 60.557 47.826 0.00 0.00 35.89 3.96
316 317 6.469782 AAAACAGAGATGTGAACCAAACAT 57.530 33.333 0.00 0.00 40.93 2.71
338 339 3.521531 TGCCCTAGGTGAATATTGTGACA 59.478 43.478 8.29 0.00 0.00 3.58
346 347 7.149569 AGGTGAATATTGTGACAGTTGAATG 57.850 36.000 0.00 0.00 0.00 2.67
349 350 8.081633 GGTGAATATTGTGACAGTTGAATGAAA 58.918 33.333 0.00 0.00 0.00 2.69
354 355 6.507958 TTGTGACAGTTGAATGAAACTTCA 57.492 33.333 0.00 0.00 38.34 3.02
359 360 6.767423 TGACAGTTGAATGAAACTTCATGAGA 59.233 34.615 5.72 0.00 46.60 3.27
364 365 8.295288 AGTTGAATGAAACTTCATGAGATTGTC 58.705 33.333 5.72 0.00 46.60 3.18
366 367 6.151648 TGAATGAAACTTCATGAGATTGTCCC 59.848 38.462 5.72 0.00 46.60 4.46
476 479 4.394920 CCCGCAAGTATAAGAACAACACAT 59.605 41.667 0.00 0.00 0.00 3.21
477 480 5.583061 CCCGCAAGTATAAGAACAACACATA 59.417 40.000 0.00 0.00 0.00 2.29
598 3453 4.637977 TGCATTGAGGCGATACACATTTTA 59.362 37.500 0.00 0.00 36.28 1.52
599 3454 5.299028 TGCATTGAGGCGATACACATTTTAT 59.701 36.000 0.00 0.00 36.28 1.40
626 3481 3.508012 AGGTGAGATGTACTGACTGACAC 59.492 47.826 0.00 0.00 33.39 3.67
628 3483 4.081972 GGTGAGATGTACTGACTGACACAT 60.082 45.833 0.00 4.78 33.39 3.21
775 3838 1.302033 GCACAGGTCTCACCACCAG 60.302 63.158 0.00 0.00 41.95 4.00
791 3859 1.289066 CAGCAAACGTCTCGGGAGA 59.711 57.895 0.00 0.00 34.56 3.71
808 3877 0.032678 AGAGAGCACGTGTCCTTGTG 59.967 55.000 18.38 0.00 39.10 3.33
879 3948 5.476599 GGAGCTCACTGATCATCACTATACT 59.523 44.000 17.19 0.00 31.67 2.12
916 5483 2.159014 ACCTTAAATACTGCATCGGCGA 60.159 45.455 13.87 13.87 45.35 5.54
943 5515 4.960866 CCAGCACCAGCACCAGCA 62.961 66.667 0.00 0.00 45.49 4.41
944 5516 3.667282 CAGCACCAGCACCAGCAC 61.667 66.667 0.00 0.00 45.49 4.40
945 5517 4.962836 AGCACCAGCACCAGCACC 62.963 66.667 0.00 0.00 45.49 5.01
947 5519 3.289834 CACCAGCACCAGCACCAC 61.290 66.667 0.00 0.00 45.49 4.16
948 5520 4.586235 ACCAGCACCAGCACCACC 62.586 66.667 0.00 0.00 45.49 4.61
951 5523 4.586235 AGCACCAGCACCACCACC 62.586 66.667 0.00 0.00 45.49 4.61
961 5533 1.268845 GCACCACCACCTAAACAAACG 60.269 52.381 0.00 0.00 0.00 3.60
963 5535 1.314730 CCACCACCTAAACAAACGCT 58.685 50.000 0.00 0.00 0.00 5.07
1137 5724 1.534697 CCTCCTCCTCTACCTCGCT 59.465 63.158 0.00 0.00 0.00 4.93
1154 5741 0.532417 GCTGTCTCCTATGCCTGCAG 60.532 60.000 6.78 6.78 0.00 4.41
1155 5742 1.117994 CTGTCTCCTATGCCTGCAGA 58.882 55.000 17.39 0.00 0.00 4.26
1156 5743 0.826715 TGTCTCCTATGCCTGCAGAC 59.173 55.000 17.39 3.38 0.00 3.51
1157 5744 0.249238 GTCTCCTATGCCTGCAGACG 60.249 60.000 17.39 0.00 0.00 4.18
1158 5745 1.593750 CTCCTATGCCTGCAGACGC 60.594 63.158 17.39 11.96 39.24 5.19
1159 5746 2.590007 CCTATGCCTGCAGACGCC 60.590 66.667 17.39 0.80 37.32 5.68
1160 5747 2.963854 CTATGCCTGCAGACGCCG 60.964 66.667 17.39 0.00 37.32 6.46
1251 5844 4.873129 ATGAGCGACGCGGCGATT 62.873 61.111 42.31 26.40 38.18 3.34
1563 6162 2.362397 GCCAGAGTGATGGATCGACTAA 59.638 50.000 0.00 0.00 43.57 2.24
1594 6200 4.163458 TGACCGGAGAATAGCCATAGTTTT 59.837 41.667 9.46 0.00 0.00 2.43
1595 6201 4.704965 ACCGGAGAATAGCCATAGTTTTC 58.295 43.478 9.46 0.00 0.00 2.29
1596 6202 3.741344 CCGGAGAATAGCCATAGTTTTCG 59.259 47.826 0.00 0.00 0.00 3.46
1597 6203 4.369182 CGGAGAATAGCCATAGTTTTCGT 58.631 43.478 0.00 0.00 0.00 3.85
1598 6204 4.809426 CGGAGAATAGCCATAGTTTTCGTT 59.191 41.667 0.00 0.00 0.00 3.85
1599 6205 5.293569 CGGAGAATAGCCATAGTTTTCGTTT 59.706 40.000 0.00 0.00 0.00 3.60
1600 6206 6.509677 CGGAGAATAGCCATAGTTTTCGTTTC 60.510 42.308 0.00 0.00 0.00 2.78
1601 6207 6.539103 GGAGAATAGCCATAGTTTTCGTTTCT 59.461 38.462 0.00 0.00 0.00 2.52
1602 6208 7.308782 AGAATAGCCATAGTTTTCGTTTCTG 57.691 36.000 0.00 0.00 0.00 3.02
1603 6209 7.103641 AGAATAGCCATAGTTTTCGTTTCTGA 58.896 34.615 0.00 0.00 0.00 3.27
1604 6210 7.770897 AGAATAGCCATAGTTTTCGTTTCTGAT 59.229 33.333 0.00 0.00 0.00 2.90
1605 6211 5.551760 AGCCATAGTTTTCGTTTCTGATG 57.448 39.130 0.00 0.00 0.00 3.07
1606 6212 5.245531 AGCCATAGTTTTCGTTTCTGATGA 58.754 37.500 0.00 0.00 0.00 2.92
1607 6213 5.352569 AGCCATAGTTTTCGTTTCTGATGAG 59.647 40.000 0.00 0.00 0.00 2.90
1608 6214 5.351465 GCCATAGTTTTCGTTTCTGATGAGA 59.649 40.000 0.00 0.00 0.00 3.27
1609 6215 6.037610 GCCATAGTTTTCGTTTCTGATGAGAT 59.962 38.462 0.00 0.00 0.00 2.75
1610 6216 7.414540 GCCATAGTTTTCGTTTCTGATGAGATT 60.415 37.037 0.00 0.00 0.00 2.40
1611 6217 9.098355 CCATAGTTTTCGTTTCTGATGAGATTA 57.902 33.333 0.00 0.00 0.00 1.75
1613 6219 7.066374 AGTTTTCGTTTCTGATGAGATTAGC 57.934 36.000 0.00 0.00 0.00 3.09
1614 6220 6.092807 AGTTTTCGTTTCTGATGAGATTAGCC 59.907 38.462 0.00 0.00 0.00 3.93
1615 6221 3.706698 TCGTTTCTGATGAGATTAGCCG 58.293 45.455 0.00 0.00 0.00 5.52
1616 6222 3.130516 TCGTTTCTGATGAGATTAGCCGT 59.869 43.478 0.00 0.00 0.00 5.68
1617 6223 4.337274 TCGTTTCTGATGAGATTAGCCGTA 59.663 41.667 0.00 0.00 0.00 4.02
1618 6224 4.677378 CGTTTCTGATGAGATTAGCCGTAG 59.323 45.833 0.00 0.00 0.00 3.51
1619 6225 5.593010 GTTTCTGATGAGATTAGCCGTAGT 58.407 41.667 0.00 0.00 0.00 2.73
1629 6235 2.162338 TAGCCGTAGTGTGGTGTGGC 62.162 60.000 0.00 0.00 42.76 5.01
1673 6279 4.091509 GTGTACAGGAGTATTTGCGAAGTG 59.908 45.833 0.00 0.00 31.84 3.16
1674 6311 2.699954 ACAGGAGTATTTGCGAAGTGG 58.300 47.619 0.00 0.00 0.00 4.00
1676 6313 3.244422 ACAGGAGTATTTGCGAAGTGGAA 60.244 43.478 0.00 0.00 0.00 3.53
1828 6465 5.180271 TCTTTACCCACTAATAAAGCACGG 58.820 41.667 0.00 0.00 37.99 4.94
1832 6469 5.362105 ACCCACTAATAAAGCACGGATTA 57.638 39.130 0.00 0.00 0.00 1.75
1834 6471 5.820947 ACCCACTAATAAAGCACGGATTAAG 59.179 40.000 0.00 0.00 0.00 1.85
1835 6472 5.277828 CCCACTAATAAAGCACGGATTAAGC 60.278 44.000 0.00 0.00 0.00 3.09
1851 6488 4.446413 GCCGGTCGGGTTCATCGT 62.446 66.667 11.60 0.00 38.44 3.73
1854 6491 2.884207 GGTCGGGTTCATCGTCGC 60.884 66.667 0.00 0.00 0.00 5.19
1867 6504 1.154543 CGTCGCGCCCTTTTTACAC 60.155 57.895 0.00 0.00 0.00 2.90
1869 6506 0.308376 GTCGCGCCCTTTTTACACAA 59.692 50.000 0.00 0.00 0.00 3.33
1887 6524 4.401202 ACACAAAGGTCCTGTGGTTTTTAG 59.599 41.667 13.94 0.00 46.89 1.85
1901 6538 4.833938 TGGTTTTTAGGAATTAAACCCGCT 59.166 37.500 14.42 0.00 46.49 5.52
1919 6556 4.451900 CCGCTGTCCCTATTTTAGTGAAT 58.548 43.478 0.00 0.00 0.00 2.57
1970 6628 7.787623 AAAATCCTCAGTTTCATTTCTCCAT 57.212 32.000 0.00 0.00 0.00 3.41
1972 6630 4.012374 TCCTCAGTTTCATTTCTCCATGC 58.988 43.478 0.00 0.00 0.00 4.06
1980 6638 0.753111 ATTTCTCCATGCCCGCTTCC 60.753 55.000 0.00 0.00 0.00 3.46
2068 6726 3.955101 CGAGGAGCGCCGGAGTAG 61.955 72.222 5.05 0.00 39.96 2.57
2069 6727 2.516460 GAGGAGCGCCGGAGTAGA 60.516 66.667 5.05 0.00 39.96 2.59
2070 6728 2.044252 AGGAGCGCCGGAGTAGAA 60.044 61.111 5.05 0.00 39.96 2.10
2072 6730 2.413765 GAGCGCCGGAGTAGAAGG 59.586 66.667 5.05 0.00 0.00 3.46
2073 6731 2.044252 AGCGCCGGAGTAGAAGGA 60.044 61.111 5.05 0.00 0.00 3.36
2074 6732 2.065906 GAGCGCCGGAGTAGAAGGAG 62.066 65.000 5.05 0.00 0.00 3.69
2075 6733 2.413765 CGCCGGAGTAGAAGGAGC 59.586 66.667 5.05 0.00 0.00 4.70
2076 6734 2.413765 GCCGGAGTAGAAGGAGCG 59.586 66.667 5.05 0.00 0.00 5.03
2077 6735 2.413765 CCGGAGTAGAAGGAGCGC 59.586 66.667 0.00 0.00 0.00 5.92
2078 6736 2.413765 CGGAGTAGAAGGAGCGCC 59.586 66.667 2.29 0.00 0.00 6.53
2079 6737 2.415608 CGGAGTAGAAGGAGCGCCA 61.416 63.158 9.88 0.00 36.29 5.69
2080 6738 1.439644 GGAGTAGAAGGAGCGCCAG 59.560 63.158 9.88 0.00 36.29 4.85
2081 6739 1.439644 GAGTAGAAGGAGCGCCAGG 59.560 63.158 9.88 0.00 36.29 4.45
2082 6740 2.022240 GAGTAGAAGGAGCGCCAGGG 62.022 65.000 9.88 0.00 36.29 4.45
2083 6741 2.764128 TAGAAGGAGCGCCAGGGG 60.764 66.667 9.88 0.00 36.29 4.79
2101 6759 4.961511 GTGTGTGTCGCGGCAGGA 62.962 66.667 16.68 0.00 0.00 3.86
2102 6760 4.662961 TGTGTGTCGCGGCAGGAG 62.663 66.667 16.68 0.00 0.00 3.69
2103 6761 4.664677 GTGTGTCGCGGCAGGAGT 62.665 66.667 16.68 0.00 0.00 3.85
2104 6762 4.662961 TGTGTCGCGGCAGGAGTG 62.663 66.667 16.68 0.00 0.00 3.51
2124 6782 4.529219 CACGGCGGCTCATGGCTA 62.529 66.667 13.24 0.00 41.46 3.93
2125 6783 4.530857 ACGGCGGCTCATGGCTAC 62.531 66.667 13.24 0.09 41.46 3.58
2126 6784 4.529219 CGGCGGCTCATGGCTACA 62.529 66.667 7.61 0.00 41.46 2.74
2127 6785 2.590007 GGCGGCTCATGGCTACAG 60.590 66.667 0.00 0.00 41.46 2.74
2128 6786 3.275338 GCGGCTCATGGCTACAGC 61.275 66.667 6.20 0.94 41.46 4.40
2140 6798 2.820619 CTACAGCCGCGACGCTCTA 61.821 63.158 19.02 0.00 36.82 2.43
2150 6808 1.360820 CGACGCTCTACAGTCTGAGA 58.639 55.000 6.91 4.52 35.38 3.27
2198 6856 2.668550 GGAACACTCCACGGTGGC 60.669 66.667 22.42 6.97 41.96 5.01
2230 6888 3.279183 CTCTGACGAACGGAGGCT 58.721 61.111 12.73 0.00 45.42 4.58
2251 6909 1.801309 GCGGCGATAGGAGAAGCTCT 61.801 60.000 12.98 0.00 0.00 4.09
2253 6911 1.036707 GGCGATAGGAGAAGCTCTGT 58.963 55.000 0.00 0.00 0.00 3.41
2331 6989 4.170062 CTGCGCGTTGCTGGATGG 62.170 66.667 8.43 0.00 46.63 3.51
2338 6996 2.361483 TTGCTGGATGGTGCGCAT 60.361 55.556 15.91 0.00 31.77 4.73
2342 7000 1.746239 CTGGATGGTGCGCATGTGA 60.746 57.895 15.91 0.00 0.00 3.58
2344 7002 1.746615 GGATGGTGCGCATGTGACT 60.747 57.895 15.91 0.00 0.00 3.41
2345 7003 1.426621 GATGGTGCGCATGTGACTG 59.573 57.895 15.91 0.00 0.00 3.51
2346 7004 1.300971 GATGGTGCGCATGTGACTGT 61.301 55.000 15.91 0.00 0.00 3.55
2354 7012 1.873486 CGCATGTGACTGTGACCTTCA 60.873 52.381 0.00 0.00 0.00 3.02
2357 7015 1.496060 TGTGACTGTGACCTTCACCT 58.504 50.000 10.15 0.00 46.40 4.00
2371 7029 2.128507 CACCTACCGGCCTCCTCTC 61.129 68.421 0.00 0.00 0.00 3.20
2412 7070 0.179111 TCGCACCAAGGCTAGATTCG 60.179 55.000 0.00 0.00 0.00 3.34
2413 7071 1.766143 CGCACCAAGGCTAGATTCGC 61.766 60.000 0.00 0.00 0.00 4.70
2435 7093 1.302033 CTGCGTCCAACTCAGCCTT 60.302 57.895 0.00 0.00 0.00 4.35
2442 7100 1.676967 CAACTCAGCCTTCCCCTGC 60.677 63.158 0.00 0.00 0.00 4.85
2481 7139 0.033796 CAACCTCATCCCCATGCAGT 60.034 55.000 0.00 0.00 0.00 4.40
2484 7142 0.033796 CCTCATCCCCATGCAGTTGT 60.034 55.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.685849 AATGGCAGTTTATCCTACCTACTAA 57.314 36.000 0.00 0.00 0.00 2.24
15 16 6.062258 AGCTAGGAAGTAAATGGCAGTTTA 57.938 37.500 5.17 1.96 0.00 2.01
18 19 4.101741 CCTAGCTAGGAAGTAAATGGCAGT 59.898 45.833 32.79 0.00 46.63 4.40
39 40 4.462483 ACACACTGAACATTGTTTTGTCCT 59.538 37.500 3.08 0.00 0.00 3.85
41 42 5.060816 CACACACACTGAACATTGTTTTGTC 59.939 40.000 3.08 0.00 0.00 3.18
76 77 3.377485 GTGATCACCACTTCTCGCTACTA 59.623 47.826 15.31 0.00 42.44 1.82
90 91 2.906354 ACGGCTAAAGATGTGATCACC 58.094 47.619 22.85 8.64 0.00 4.02
120 121 6.469595 TGTTGTTAAATAAGCAACACGTTGTC 59.530 34.615 11.33 4.41 44.82 3.18
124 125 4.973663 GCTGTTGTTAAATAAGCAACACGT 59.026 37.500 5.39 0.00 44.82 4.49
148 149 0.666374 GCTGTTTGGTTGCCTACGTT 59.334 50.000 0.00 0.00 0.00 3.99
151 152 0.040425 CACGCTGTTTGGTTGCCTAC 60.040 55.000 0.00 0.00 0.00 3.18
152 153 1.791103 GCACGCTGTTTGGTTGCCTA 61.791 55.000 0.00 0.00 0.00 3.93
182 183 2.728007 AGCCTTTCTGCATAAGGGAAC 58.272 47.619 22.37 10.87 42.01 3.62
189 190 3.216800 CCTGCATTAGCCTTTCTGCATA 58.783 45.455 0.00 0.00 43.12 3.14
200 201 1.273327 AGTTTGGTTGCCTGCATTAGC 59.727 47.619 0.00 0.00 42.57 3.09
201 202 3.505680 TGTAGTTTGGTTGCCTGCATTAG 59.494 43.478 0.00 0.00 0.00 1.73
206 207 1.669795 GCATGTAGTTTGGTTGCCTGC 60.670 52.381 0.00 0.00 0.00 4.85
222 223 5.981315 CAGGCTAAAAACCATTATCTGCATG 59.019 40.000 0.00 0.00 0.00 4.06
225 226 4.142182 TGCAGGCTAAAAACCATTATCTGC 60.142 41.667 0.00 0.00 39.60 4.26
232 233 3.337358 GCAAATGCAGGCTAAAAACCAT 58.663 40.909 0.00 0.00 41.59 3.55
235 236 2.076100 GGGCAAATGCAGGCTAAAAAC 58.924 47.619 7.80 0.00 44.36 2.43
242 243 2.046988 GGTTGGGCAAATGCAGGC 60.047 61.111 7.80 0.00 44.36 4.85
258 259 0.320771 CTTGTCTCTGTTGGACCCGG 60.321 60.000 0.00 0.00 33.22 5.73
260 261 3.600388 CATACTTGTCTCTGTTGGACCC 58.400 50.000 0.00 0.00 33.22 4.46
263 264 4.350368 TTGCATACTTGTCTCTGTTGGA 57.650 40.909 0.00 0.00 0.00 3.53
283 284 5.774690 TCACATCTCTGTTTTAGGGCATTTT 59.225 36.000 0.00 0.00 31.62 1.82
316 317 3.521531 TGTCACAATATTCACCTAGGGCA 59.478 43.478 14.81 0.00 0.00 5.36
338 339 8.174733 ACAATCTCATGAAGTTTCATTCAACT 57.825 30.769 4.66 0.00 45.13 3.16
375 376 2.351244 ACGCAGTGCAGCTAGGCTA 61.351 57.895 16.83 0.00 42.51 3.93
598 3453 6.836007 TCAGTCAGTACATCTCACCTCAATAT 59.164 38.462 0.00 0.00 0.00 1.28
599 3454 6.095580 GTCAGTCAGTACATCTCACCTCAATA 59.904 42.308 0.00 0.00 0.00 1.90
626 3481 2.666190 CCCGGCCGTGATGCTATG 60.666 66.667 26.12 4.67 0.00 2.23
628 3483 3.845259 GACCCGGCCGTGATGCTA 61.845 66.667 26.12 0.00 0.00 3.49
697 3661 5.073311 TCAAGTGTTACTCCTACAGCATC 57.927 43.478 0.00 0.00 0.00 3.91
699 3667 4.526650 TGATCAAGTGTTACTCCTACAGCA 59.473 41.667 0.00 0.00 0.00 4.41
701 3669 6.634805 ACATGATCAAGTGTTACTCCTACAG 58.365 40.000 2.13 0.00 0.00 2.74
775 3838 0.456995 CTCTCTCCCGAGACGTTTGC 60.457 60.000 0.00 0.00 41.26 3.68
791 3859 4.758692 CACAAGGACACGTGCTCT 57.241 55.556 17.22 10.55 0.00 4.09
808 3877 3.003689 CCCGATCAAGATATTTGTGGTGC 59.996 47.826 0.00 0.00 0.00 5.01
810 3879 4.444876 CCTCCCGATCAAGATATTTGTGGT 60.445 45.833 0.00 0.00 0.00 4.16
823 3892 2.058001 ATCACGTGCCTCCCGATCA 61.058 57.895 11.67 0.00 0.00 2.92
879 3948 4.418401 GTGGCGGCCGTACGTACA 62.418 66.667 28.70 13.31 35.98 2.90
943 5515 1.026584 GCGTTTGTTTAGGTGGTGGT 58.973 50.000 0.00 0.00 0.00 4.16
944 5516 1.001815 CAGCGTTTGTTTAGGTGGTGG 60.002 52.381 0.00 0.00 0.00 4.61
945 5517 1.944024 TCAGCGTTTGTTTAGGTGGTG 59.056 47.619 0.00 0.00 34.52 4.17
946 5518 2.335316 TCAGCGTTTGTTTAGGTGGT 57.665 45.000 0.00 0.00 34.52 4.16
947 5519 2.161609 GGATCAGCGTTTGTTTAGGTGG 59.838 50.000 0.00 0.00 34.52 4.61
948 5520 2.811431 TGGATCAGCGTTTGTTTAGGTG 59.189 45.455 0.00 0.00 35.00 4.00
951 5523 4.070581 CTGTGGATCAGCGTTTGTTTAG 57.929 45.455 0.00 0.00 37.36 1.85
963 5535 1.215382 CGTCGGAAGCTGTGGATCA 59.785 57.895 0.00 0.00 0.00 2.92
1137 5724 3.305181 TCTGCAGGCATAGGAGACA 57.695 52.632 15.13 0.00 0.00 3.41
1594 6200 3.130516 ACGGCTAATCTCATCAGAAACGA 59.869 43.478 0.00 0.00 30.24 3.85
1595 6201 3.448686 ACGGCTAATCTCATCAGAAACG 58.551 45.455 0.00 0.00 30.24 3.60
1596 6202 5.460419 CACTACGGCTAATCTCATCAGAAAC 59.540 44.000 0.00 0.00 30.24 2.78
1597 6203 5.127194 ACACTACGGCTAATCTCATCAGAAA 59.873 40.000 0.00 0.00 30.24 2.52
1598 6204 4.645136 ACACTACGGCTAATCTCATCAGAA 59.355 41.667 0.00 0.00 30.24 3.02
1599 6205 4.036852 CACACTACGGCTAATCTCATCAGA 59.963 45.833 0.00 0.00 0.00 3.27
1600 6206 4.294232 CACACTACGGCTAATCTCATCAG 58.706 47.826 0.00 0.00 0.00 2.90
1601 6207 3.068165 CCACACTACGGCTAATCTCATCA 59.932 47.826 0.00 0.00 0.00 3.07
1602 6208 3.068307 ACCACACTACGGCTAATCTCATC 59.932 47.826 0.00 0.00 0.00 2.92
1603 6209 3.031736 ACCACACTACGGCTAATCTCAT 58.968 45.455 0.00 0.00 0.00 2.90
1604 6210 2.165641 CACCACACTACGGCTAATCTCA 59.834 50.000 0.00 0.00 0.00 3.27
1605 6211 2.165845 ACACCACACTACGGCTAATCTC 59.834 50.000 0.00 0.00 0.00 2.75
1606 6212 2.094182 CACACCACACTACGGCTAATCT 60.094 50.000 0.00 0.00 0.00 2.40
1607 6213 2.268298 CACACCACACTACGGCTAATC 58.732 52.381 0.00 0.00 0.00 1.75
1608 6214 1.066430 CCACACCACACTACGGCTAAT 60.066 52.381 0.00 0.00 0.00 1.73
1609 6215 0.319083 CCACACCACACTACGGCTAA 59.681 55.000 0.00 0.00 0.00 3.09
1610 6216 1.969085 CCACACCACACTACGGCTA 59.031 57.895 0.00 0.00 0.00 3.93
1611 6217 2.741092 CCACACCACACTACGGCT 59.259 61.111 0.00 0.00 0.00 5.52
1612 6218 3.047877 GCCACACCACACTACGGC 61.048 66.667 0.00 0.00 0.00 5.68
1613 6219 2.358247 GGCCACACCACACTACGG 60.358 66.667 0.00 0.00 38.86 4.02
1614 6220 2.423874 TGGCCACACCACACTACG 59.576 61.111 0.00 0.00 46.36 3.51
1673 6279 3.947834 AGCCAGTAATACAAGCACATTCC 59.052 43.478 7.29 0.00 0.00 3.01
1674 6311 4.035675 GGAGCCAGTAATACAAGCACATTC 59.964 45.833 7.29 0.00 0.00 2.67
1676 6313 3.545703 GGAGCCAGTAATACAAGCACAT 58.454 45.455 7.29 0.00 0.00 3.21
1801 6438 8.885722 CGTGCTTTATTAGTGGGTAAAGATAAA 58.114 33.333 8.58 0.00 39.24 1.40
1802 6439 7.496591 CCGTGCTTTATTAGTGGGTAAAGATAA 59.503 37.037 8.58 0.00 39.24 1.75
1803 6440 6.987992 CCGTGCTTTATTAGTGGGTAAAGATA 59.012 38.462 8.58 0.00 39.24 1.98
1804 6441 5.820947 CCGTGCTTTATTAGTGGGTAAAGAT 59.179 40.000 8.58 0.00 39.24 2.40
1805 6442 5.046448 TCCGTGCTTTATTAGTGGGTAAAGA 60.046 40.000 8.58 0.00 39.24 2.52
1806 6443 5.180271 TCCGTGCTTTATTAGTGGGTAAAG 58.820 41.667 0.00 0.00 39.66 1.85
1807 6444 5.163281 TCCGTGCTTTATTAGTGGGTAAA 57.837 39.130 0.00 0.00 0.00 2.01
1808 6445 4.822685 TCCGTGCTTTATTAGTGGGTAA 57.177 40.909 0.00 0.00 0.00 2.85
1809 6446 5.362105 AATCCGTGCTTTATTAGTGGGTA 57.638 39.130 0.00 0.00 0.00 3.69
1810 6447 3.926058 ATCCGTGCTTTATTAGTGGGT 57.074 42.857 0.00 0.00 0.00 4.51
1811 6448 5.277828 GCTTAATCCGTGCTTTATTAGTGGG 60.278 44.000 0.00 0.00 0.00 4.61
1812 6449 5.277828 GGCTTAATCCGTGCTTTATTAGTGG 60.278 44.000 0.00 0.00 0.00 4.00
1813 6450 5.558273 CGGCTTAATCCGTGCTTTATTAGTG 60.558 44.000 9.59 0.00 44.18 2.74
1814 6451 4.510340 CGGCTTAATCCGTGCTTTATTAGT 59.490 41.667 9.59 0.00 44.18 2.24
1815 6452 5.018695 CGGCTTAATCCGTGCTTTATTAG 57.981 43.478 9.59 0.00 44.18 1.73
1828 6465 0.108041 TGAACCCGACCGGCTTAATC 60.108 55.000 0.00 0.00 33.26 1.75
1832 6469 2.267961 GATGAACCCGACCGGCTT 59.732 61.111 0.00 0.00 33.26 4.35
1834 6471 4.446413 ACGATGAACCCGACCGGC 62.446 66.667 0.00 0.00 33.26 6.13
1835 6472 2.202703 GACGATGAACCCGACCGG 60.203 66.667 0.00 0.00 37.81 5.28
1837 6474 2.884207 GCGACGATGAACCCGACC 60.884 66.667 0.00 0.00 0.00 4.79
1848 6485 1.300775 TGTAAAAAGGGCGCGACGA 60.301 52.632 12.10 0.00 0.00 4.20
1851 6488 1.002251 CTTTGTGTAAAAAGGGCGCGA 60.002 47.619 12.10 0.00 34.19 5.87
1867 6504 4.211920 TCCTAAAAACCACAGGACCTTTG 58.788 43.478 0.18 0.18 33.48 2.77
1869 6506 4.529716 TTCCTAAAAACCACAGGACCTT 57.470 40.909 0.00 0.00 38.19 3.50
1887 6524 1.100510 GGGACAGCGGGTTTAATTCC 58.899 55.000 0.00 0.00 0.00 3.01
1901 6538 9.581289 TTTTTCAGATTCACTAAAATAGGGACA 57.419 29.630 0.00 0.00 38.09 4.02
1952 6589 3.129988 GGGCATGGAGAAATGAAACTGAG 59.870 47.826 0.00 0.00 0.00 3.35
1953 6590 3.091545 GGGCATGGAGAAATGAAACTGA 58.908 45.455 0.00 0.00 0.00 3.41
1965 6623 1.379044 AAAGGAAGCGGGCATGGAG 60.379 57.895 0.00 0.00 0.00 3.86
1970 6628 2.034066 CTGGAAAGGAAGCGGGCA 59.966 61.111 0.00 0.00 0.00 5.36
1972 6630 2.751837 GGCTGGAAAGGAAGCGGG 60.752 66.667 0.00 0.00 40.46 6.13
1995 6653 1.134670 GCGCTCACCTTATCCTTCTGT 60.135 52.381 0.00 0.00 0.00 3.41
1999 6657 0.107654 GTGGCGCTCACCTTATCCTT 60.108 55.000 7.64 0.00 40.39 3.36
2064 6722 2.060980 CCCTGGCGCTCCTTCTACT 61.061 63.158 7.64 0.00 0.00 2.57
2084 6742 4.961511 TCCTGCCGCGACACACAC 62.962 66.667 8.23 0.00 0.00 3.82
2085 6743 4.662961 CTCCTGCCGCGACACACA 62.663 66.667 8.23 0.00 0.00 3.72
2086 6744 4.664677 ACTCCTGCCGCGACACAC 62.665 66.667 8.23 0.00 0.00 3.82
2087 6745 4.662961 CACTCCTGCCGCGACACA 62.663 66.667 8.23 1.24 0.00 3.72
2107 6765 4.529219 TAGCCATGAGCCGCCGTG 62.529 66.667 0.00 0.00 45.47 4.94
2108 6766 4.530857 GTAGCCATGAGCCGCCGT 62.531 66.667 0.00 0.00 45.47 5.68
2109 6767 4.529219 TGTAGCCATGAGCCGCCG 62.529 66.667 0.00 0.00 45.47 6.46
2110 6768 2.590007 CTGTAGCCATGAGCCGCC 60.590 66.667 0.00 0.00 45.47 6.13
2111 6769 3.275338 GCTGTAGCCATGAGCCGC 61.275 66.667 0.00 0.00 45.47 6.53
2122 6780 2.820619 TAGAGCGTCGCGGCTGTAG 61.821 63.158 20.89 0.00 44.93 2.74
2123 6781 2.820922 TAGAGCGTCGCGGCTGTA 60.821 61.111 20.89 11.91 44.93 2.74
2124 6782 4.477975 GTAGAGCGTCGCGGCTGT 62.478 66.667 20.89 12.94 44.93 4.40
2125 6783 4.476410 TGTAGAGCGTCGCGGCTG 62.476 66.667 20.89 6.39 44.93 4.85
2127 6785 4.477975 ACTGTAGAGCGTCGCGGC 62.478 66.667 12.30 1.93 0.00 6.53
2128 6786 2.277373 GACTGTAGAGCGTCGCGG 60.277 66.667 12.30 0.00 0.00 6.46
2129 6787 1.581402 CAGACTGTAGAGCGTCGCG 60.581 63.158 12.30 0.00 35.38 5.87
2130 6788 0.247894 CTCAGACTGTAGAGCGTCGC 60.248 60.000 9.80 9.80 35.38 5.19
2131 6789 1.061421 GTCTCAGACTGTAGAGCGTCG 59.939 57.143 0.00 0.00 35.38 5.12
2132 6790 1.061421 CGTCTCAGACTGTAGAGCGTC 59.939 57.143 2.61 0.00 31.55 5.19
2133 6791 1.080298 CGTCTCAGACTGTAGAGCGT 58.920 55.000 2.61 0.00 31.55 5.07
2134 6792 0.247894 GCGTCTCAGACTGTAGAGCG 60.248 60.000 2.61 15.30 35.79 5.03
2140 6798 2.336478 CCTCCGCGTCTCAGACTGT 61.336 63.158 4.92 0.00 0.00 3.55
2150 6808 3.382832 CCTTCCACTCCTCCGCGT 61.383 66.667 4.92 0.00 0.00 6.01
2180 6838 2.032071 CCACCGTGGAGTGTTCCC 59.968 66.667 12.68 0.00 43.33 3.97
2183 6841 4.619227 CCGCCACCGTGGAGTGTT 62.619 66.667 22.37 0.00 42.83 3.32
2209 6867 4.415332 TCCGTTCGTCAGAGCCGC 62.415 66.667 0.00 0.00 0.00 6.53
2210 6868 2.202492 CTCCGTTCGTCAGAGCCG 60.202 66.667 0.00 0.00 0.00 5.52
2216 6874 2.882876 GCTAGCCTCCGTTCGTCA 59.117 61.111 2.29 0.00 0.00 4.35
2230 6888 0.537600 AGCTTCTCCTATCGCCGCTA 60.538 55.000 0.00 0.00 0.00 4.26
2318 6976 4.465512 CGCACCATCCAGCAACGC 62.466 66.667 0.00 0.00 0.00 4.84
2322 6980 3.135457 CATGCGCACCATCCAGCA 61.135 61.111 14.90 0.00 44.13 4.41
2331 6989 1.205064 GTCACAGTCACATGCGCAC 59.795 57.895 14.90 0.00 0.00 5.34
2345 7003 1.079336 GCCGGTAGGTGAAGGTCAC 60.079 63.158 1.90 0.00 46.23 3.67
2346 7004 2.288025 GGCCGGTAGGTGAAGGTCA 61.288 63.158 1.90 0.00 40.50 4.02
2354 7012 2.279408 GAGAGGAGGCCGGTAGGT 59.721 66.667 1.90 0.00 40.50 3.08
2357 7015 2.050350 CAACGAGAGGAGGCCGGTA 61.050 63.158 1.90 0.00 0.00 4.02
2398 7056 2.589492 CGCGCGAATCTAGCCTTGG 61.589 63.158 28.94 0.00 0.00 3.61
2402 7060 3.696426 CAGCGCGCGAATCTAGCC 61.696 66.667 37.18 13.39 0.00 3.93
2424 7082 1.676967 GCAGGGGAAGGCTGAGTTG 60.677 63.158 0.00 0.00 0.00 3.16
2426 7084 3.710722 CGCAGGGGAAGGCTGAGT 61.711 66.667 0.00 0.00 0.00 3.41
2452 7110 1.306141 ATGAGGTTGGGAGAGGCGA 60.306 57.895 0.00 0.00 0.00 5.54
2463 7121 0.706433 AACTGCATGGGGATGAGGTT 59.294 50.000 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.