Multiple sequence alignment - TraesCS6D01G351300

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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 TraesCS6D01G351300 chr6D 100.000 2087 0 0 1453 3539 448563894 448565980 0.000000e+00 3855.0
1 TraesCS6D01G351300 chr6D 93.984 2111 95 6 1453 3533 448595380 448597488 0.000000e+00 3166.0
2 TraesCS6D01G351300 chr6D 100.000 1256 0 0 1 1256 448562442 448563697 0.000000e+00 2320.0
3 TraesCS6D01G351300 chr6D 87.746 1322 128 19 1708 3004 448579766 448581078 0.000000e+00 1513.0
4 TraesCS6D01G351300 chr6D 86.545 602 47 12 679 1256 448577638 448578229 1.790000e-177 632.0
5 TraesCS6D01G351300 chr6D 89.938 487 46 2 770 1256 448594853 448595336 3.000000e-175 625.0
6 TraesCS6D01G351300 chr6D 91.701 241 14 5 1 237 448576751 448576989 2.630000e-86 329.0
7 TraesCS6D01G351300 chr6D 87.912 273 33 0 3261 3533 448581076 448581348 4.410000e-84 322.0
8 TraesCS6D01G351300 chr6D 83.069 189 11 10 242 409 448577078 448577266 6.120000e-33 152.0
9 TraesCS6D01G351300 chrUn 85.513 1774 213 24 1715 3460 79404502 79406259 0.000000e+00 1812.0
10 TraesCS6D01G351300 chrUn 85.141 1595 194 23 1891 3460 79378408 79379984 0.000000e+00 1592.0
11 TraesCS6D01G351300 chrUn 88.930 542 55 2 1453 1994 472326568 472326032 0.000000e+00 664.0
12 TraesCS6D01G351300 chrUn 80.170 943 133 22 1872 2793 294343963 294344872 0.000000e+00 656.0
13 TraesCS6D01G351300 chrUn 80.085 944 132 16 1872 2793 79438761 79437852 0.000000e+00 651.0
14 TraesCS6D01G351300 chrUn 88.067 419 45 2 1576 1994 477372277 477372690 3.170000e-135 492.0
15 TraesCS6D01G351300 chrUn 90.654 321 22 4 770 1088 79375729 79376043 1.520000e-113 420.0
16 TraesCS6D01G351300 chrUn 90.654 321 22 4 770 1088 79402351 79402665 1.520000e-113 420.0
17 TraesCS6D01G351300 chrUn 87.500 312 22 10 1 300 79374050 79374356 9.410000e-91 344.0
18 TraesCS6D01G351300 chrUn 87.500 312 22 10 1 300 79400674 79400980 9.410000e-91 344.0
19 TraesCS6D01G351300 chrUn 90.580 138 13 0 3323 3460 79380687 79380824 2.170000e-42 183.0
20 TraesCS6D01G351300 chrUn 90.580 138 13 0 3323 3460 79406964 79407101 2.170000e-42 183.0
21 TraesCS6D01G351300 chrUn 93.750 96 6 0 679 774 79375607 79375702 1.020000e-30 145.0
22 TraesCS6D01G351300 chrUn 93.750 96 6 0 679 774 79402229 79402324 1.020000e-30 145.0
23 TraesCS6D01G351300 chrUn 89.320 103 9 2 314 416 79375144 79375244 1.030000e-25 128.0
24 TraesCS6D01G351300 chrUn 89.320 103 9 2 314 416 79401766 79401866 1.030000e-25 128.0
25 TraesCS6D01G351300 chrUn 92.308 39 3 0 1631 1669 114968211 114968173 4.940000e-04 56.5
26 TraesCS6D01G351300 chr6B 86.079 1451 145 29 1453 2864 679567058 679565626 0.000000e+00 1507.0
27 TraesCS6D01G351300 chr6B 84.979 1438 162 25 1465 2864 679552167 679550746 0.000000e+00 1410.0
28 TraesCS6D01G351300 chr6B 84.049 1072 114 27 2496 3532 679547767 679546718 0.000000e+00 979.0
29 TraesCS6D01G351300 chr6B 85.714 623 65 17 1453 2067 679397918 679398524 1.390000e-178 636.0
30 TraesCS6D01G351300 chr6B 86.799 553 59 7 679 1224 679567649 679567104 3.910000e-169 604.0
31 TraesCS6D01G351300 chr6B 78.579 957 136 36 1872 2793 679583959 679584881 5.130000e-158 568.0
32 TraesCS6D01G351300 chr6B 78.579 957 136 36 1872 2793 679599356 679600278 5.130000e-158 568.0
33 TraesCS6D01G351300 chr6B 78.229 960 137 35 1872 2793 679615344 679616269 1.860000e-152 549.0
34 TraesCS6D01G351300 chr6B 83.442 459 32 19 770 1224 679397447 679397865 1.540000e-103 387.0
35 TraesCS6D01G351300 chr6B 87.500 312 22 10 1 300 679532938 679533244 9.410000e-91 344.0
36 TraesCS6D01G351300 chr6B 86.943 314 22 11 1 300 679395772 679396080 5.660000e-88 335.0
37 TraesCS6D01G351300 chr6B 87.730 163 20 0 1094 1256 679567201 679567039 1.300000e-44 191.0
38 TraesCS6D01G351300 chr6B 93.750 96 6 0 679 774 679397325 679397420 1.020000e-30 145.0
39 TraesCS6D01G351300 chr6B 89.320 103 9 2 314 416 679534030 679534130 1.030000e-25 128.0
40 TraesCS6D01G351300 chr6B 88.350 103 10 2 314 416 679396862 679396962 4.800000e-24 122.0
41 TraesCS6D01G351300 chr6B 97.143 35 1 0 265 299 679569067 679569033 3.820000e-05 60.2
42 TraesCS6D01G351300 chr6A 85.685 1488 142 36 1453 2897 594652595 594654054 0.000000e+00 1502.0
43 TraesCS6D01G351300 chr6A 92.184 998 70 3 1493 2487 594608877 594609869 0.000000e+00 1404.0
44 TraesCS6D01G351300 chr6A 83.828 606 62 12 679 1255 594651986 594652584 8.640000e-151 544.0
45 TraesCS6D01G351300 chr6A 89.956 229 19 3 12 238 594634819 594635045 3.460000e-75 292.0
46 TraesCS6D01G351300 chr6A 87.342 158 20 0 1099 1256 594652457 594652614 7.800000e-42 182.0
47 TraesCS6D01G351300 chr6A 86.709 158 21 0 1099 1256 594608669 594608826 3.630000e-40 176.0
48 TraesCS6D01G351300 chr6A 85.535 159 21 2 1094 1251 594608727 594608884 7.860000e-37 165.0
49 TraesCS6D01G351300 chr6A 95.238 42 1 1 266 307 594635048 594635088 8.200000e-07 65.8
50 TraesCS6D01G351300 chr4D 77.311 119 25 2 3009 3127 3744759 3744875 6.340000e-08 69.4
51 TraesCS6D01G351300 chr7D 93.023 43 3 0 3009 3051 521585225 521585267 2.950000e-06 63.9
52 TraesCS6D01G351300 chr7A 81.707 82 10 5 2973 3051 601473333 601473412 2.950000e-06 63.9


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 TraesCS6D01G351300 chr6D 448562442 448565980 3538 False 3087.500000 3855 100.000000 1 3539 2 chr6D.!!$F1 3538
1 TraesCS6D01G351300 chr6D 448594853 448597488 2635 False 1895.500000 3166 91.961000 770 3533 2 chr6D.!!$F3 2763
2 TraesCS6D01G351300 chr6D 448576751 448581348 4597 False 589.600000 1513 87.394600 1 3533 5 chr6D.!!$F2 3532
3 TraesCS6D01G351300 chrUn 472326032 472326568 536 True 664.000000 664 88.930000 1453 1994 1 chrUn.!!$R3 541
4 TraesCS6D01G351300 chrUn 294343963 294344872 909 False 656.000000 656 80.170000 1872 2793 1 chrUn.!!$F1 921
5 TraesCS6D01G351300 chrUn 79437852 79438761 909 True 651.000000 651 80.085000 1872 2793 1 chrUn.!!$R1 921
6 TraesCS6D01G351300 chrUn 79400674 79407101 6427 False 505.333333 1812 89.552833 1 3460 6 chrUn.!!$F4 3459
7 TraesCS6D01G351300 chrUn 79374050 79380824 6774 False 468.666667 1592 89.490833 1 3460 6 chrUn.!!$F3 3459
8 TraesCS6D01G351300 chr6B 679546718 679552167 5449 True 1194.500000 1410 84.514000 1465 3532 2 chr6B.!!$R1 2067
9 TraesCS6D01G351300 chr6B 679565626 679569067 3441 True 590.550000 1507 89.437750 265 2864 4 chr6B.!!$R2 2599
10 TraesCS6D01G351300 chr6B 679583959 679584881 922 False 568.000000 568 78.579000 1872 2793 1 chr6B.!!$F1 921
11 TraesCS6D01G351300 chr6B 679599356 679600278 922 False 568.000000 568 78.579000 1872 2793 1 chr6B.!!$F2 921
12 TraesCS6D01G351300 chr6B 679615344 679616269 925 False 549.000000 549 78.229000 1872 2793 1 chr6B.!!$F3 921
13 TraesCS6D01G351300 chr6B 679395772 679398524 2752 False 325.000000 636 87.639800 1 2067 5 chr6B.!!$F4 2066
14 TraesCS6D01G351300 chr6B 679532938 679534130 1192 False 236.000000 344 88.410000 1 416 2 chr6B.!!$F5 415
15 TraesCS6D01G351300 chr6A 594651986 594654054 2068 False 742.666667 1502 85.618333 679 2897 3 chr6A.!!$F3 2218
16 TraesCS6D01G351300 chr6A 594608669 594609869 1200 False 581.666667 1404 88.142667 1094 2487 3 chr6A.!!$F1 1393

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
525 1685 0.031585 TTCAACTCACACCGAGGACG 59.968 55.0 0.00 0.0 46.98 4.79 F
629 1824 0.037877 ATATCCATGGCAGCAGCTCC 59.962 55.0 6.96 0.0 41.70 4.70 F
1593 4355 0.320073 TCGTAAGGGAAGTTGTGCGG 60.320 55.0 0.00 0.0 38.47 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 4340 0.609131 CATCCCGCACAACTTCCCTT 60.609 55.000 0.0 0.0 0.00 3.95 R
1626 4388 1.267261 CAGTCGTGGAAGAAGAGACGT 59.733 52.381 0.0 0.0 36.97 4.34 R
3508 12286 0.104725 CTAGAAGCTGGGGAGGGGAT 60.105 60.000 0.0 0.0 0.00 3.85 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
177 183 3.225104 TCTGCCTCTGCACTTTCAAAAT 58.775 40.909 0.00 0.00 44.23 1.82
178 184 4.397420 TCTGCCTCTGCACTTTCAAAATA 58.603 39.130 0.00 0.00 44.23 1.40
181 187 6.015180 TCTGCCTCTGCACTTTCAAAATAAAT 60.015 34.615 0.00 0.00 44.23 1.40
215 230 4.751600 CACTTCCAAAAATTCTTTCTGCCC 59.248 41.667 0.00 0.00 0.00 5.36
238 336 3.842007 TCCCGTGGAAGAAAACTACAA 57.158 42.857 0.00 0.00 0.00 2.41
239 337 3.469739 TCCCGTGGAAGAAAACTACAAC 58.530 45.455 0.00 0.00 0.00 3.32
240 338 3.135167 TCCCGTGGAAGAAAACTACAACT 59.865 43.478 0.00 0.00 0.00 3.16
243 341 5.049886 CCCGTGGAAGAAAACTACAACTAAC 60.050 44.000 0.00 0.00 0.00 2.34
244 342 5.756833 CCGTGGAAGAAAACTACAACTAACT 59.243 40.000 0.00 0.00 0.00 2.24
247 345 7.201582 CGTGGAAGAAAACTACAACTAACTGTT 60.202 37.037 0.00 0.00 39.92 3.16
248 346 8.121086 GTGGAAGAAAACTACAACTAACTGTTC 58.879 37.037 0.00 0.00 36.63 3.18
300 401 6.346678 GCAGTTTAGCACTACAACTAACTGTC 60.347 42.308 15.43 8.30 34.09 3.51
303 404 4.957684 AGCACTACAACTAACTGTCCTT 57.042 40.909 0.00 0.00 0.00 3.36
304 405 7.528996 TTAGCACTACAACTAACTGTCCTTA 57.471 36.000 0.00 0.00 0.00 2.69
312 430 6.100004 ACAACTAACTGTCCTTACATGATCG 58.900 40.000 0.00 0.00 34.37 3.69
409 1536 2.673114 CGCGCAATACCCAACGTGT 61.673 57.895 8.75 0.00 0.00 4.49
410 1537 1.154301 GCGCAATACCCAACGTGTG 60.154 57.895 0.30 0.00 0.00 3.82
411 1538 1.154301 CGCAATACCCAACGTGTGC 60.154 57.895 0.00 0.00 34.88 4.57
412 1539 1.573829 CGCAATACCCAACGTGTGCT 61.574 55.000 0.00 0.00 35.64 4.40
413 1540 1.444836 GCAATACCCAACGTGTGCTA 58.555 50.000 0.00 0.00 35.19 3.49
414 1541 1.807742 GCAATACCCAACGTGTGCTAA 59.192 47.619 0.00 0.00 35.19 3.09
425 1552 5.109210 CAACGTGTGCTAATAATCCTCTCA 58.891 41.667 0.00 0.00 0.00 3.27
428 1555 5.581085 ACGTGTGCTAATAATCCTCTCAAAC 59.419 40.000 0.00 0.00 0.00 2.93
430 1557 5.581085 GTGTGCTAATAATCCTCTCAAACGT 59.419 40.000 0.00 0.00 0.00 3.99
431 1558 5.580691 TGTGCTAATAATCCTCTCAAACGTG 59.419 40.000 0.00 0.00 0.00 4.49
441 1601 2.802247 CTCTCAAACGTGTGCTCATTCA 59.198 45.455 0.00 0.00 0.00 2.57
445 1605 1.674359 AACGTGTGCTCATTCACCAA 58.326 45.000 0.00 0.00 36.17 3.67
463 1623 0.315568 AATCGAGCTAGTCATCGGCC 59.684 55.000 12.19 0.00 39.38 6.13
478 1638 2.279517 GCCTGTCGTCCGGCATAG 60.280 66.667 10.00 0.00 45.59 2.23
515 1675 1.462670 GCAGCTAGCTGTTCAACTCAC 59.537 52.381 37.91 19.22 45.24 3.51
516 1676 2.759191 CAGCTAGCTGTTCAACTCACA 58.241 47.619 32.46 0.00 39.10 3.58
517 1677 2.478134 CAGCTAGCTGTTCAACTCACAC 59.522 50.000 32.46 0.00 39.10 3.82
518 1678 1.801178 GCTAGCTGTTCAACTCACACC 59.199 52.381 7.70 0.00 0.00 4.16
519 1679 2.061773 CTAGCTGTTCAACTCACACCG 58.938 52.381 0.00 0.00 0.00 4.94
523 1683 1.068588 CTGTTCAACTCACACCGAGGA 59.931 52.381 0.00 0.00 46.98 3.71
524 1684 1.202486 TGTTCAACTCACACCGAGGAC 60.202 52.381 0.00 0.00 46.98 3.85
525 1685 0.031585 TTCAACTCACACCGAGGACG 59.968 55.000 0.00 0.00 46.98 4.79
543 1703 2.783135 ACGGAATGTCAACTGCTTGAT 58.217 42.857 0.00 0.00 38.69 2.57
553 1713 0.103937 ACTGCTTGATCGAGCTAGCC 59.896 55.000 30.52 14.87 43.11 3.93
563 1723 1.131883 TCGAGCTAGCCGTTAACTGTC 59.868 52.381 20.20 5.38 0.00 3.51
564 1724 1.546834 GAGCTAGCCGTTAACTGTCG 58.453 55.000 12.13 0.00 0.00 4.35
589 1775 0.881118 TTGAGCTTTGACATTCCGGC 59.119 50.000 0.00 0.00 0.00 6.13
594 1780 2.527547 CTTTGACATTCCGGCCGTGC 62.528 60.000 26.12 12.28 0.00 5.34
602 1788 2.992607 TTCCGGCCGTGCGTTAGTTT 62.993 55.000 26.12 0.00 0.00 2.66
603 1789 2.172419 CGGCCGTGCGTTAGTTTG 59.828 61.111 19.50 0.00 0.00 2.93
604 1790 2.127003 GGCCGTGCGTTAGTTTGC 60.127 61.111 0.00 0.00 0.00 3.68
605 1791 2.634777 GCCGTGCGTTAGTTTGCA 59.365 55.556 0.00 0.00 39.13 4.08
606 1792 1.440353 GCCGTGCGTTAGTTTGCAG 60.440 57.895 0.00 0.00 42.68 4.41
607 1793 1.440353 CCGTGCGTTAGTTTGCAGC 60.440 57.895 0.00 0.00 42.68 5.25
608 1794 1.440353 CGTGCGTTAGTTTGCAGCC 60.440 57.895 0.00 0.00 42.68 4.85
609 1795 1.081442 GTGCGTTAGTTTGCAGCCC 60.081 57.895 0.00 0.00 42.68 5.19
610 1796 1.527148 TGCGTTAGTTTGCAGCCCA 60.527 52.632 0.00 0.00 35.90 5.36
626 1821 2.264124 CCATATCCATGGCAGCAGC 58.736 57.895 6.96 0.00 45.29 5.25
629 1824 0.037877 ATATCCATGGCAGCAGCTCC 59.962 55.000 6.96 0.00 41.70 4.70
635 1830 3.402681 GGCAGCAGCTCCCCACTA 61.403 66.667 0.00 0.00 41.70 2.74
636 1831 2.124942 GCAGCAGCTCCCCACTAC 60.125 66.667 0.00 0.00 37.91 2.73
639 1834 1.079256 AGCAGCTCCCCACTACTCA 59.921 57.895 0.00 0.00 0.00 3.41
640 1835 1.219393 GCAGCTCCCCACTACTCAC 59.781 63.158 0.00 0.00 0.00 3.51
641 1836 1.901085 CAGCTCCCCACTACTCACC 59.099 63.158 0.00 0.00 0.00 4.02
642 1837 1.682684 AGCTCCCCACTACTCACCG 60.683 63.158 0.00 0.00 0.00 4.94
643 1838 2.893398 CTCCCCACTACTCACCGC 59.107 66.667 0.00 0.00 0.00 5.68
646 1841 2.125512 CCCACTACTCACCGCTGC 60.126 66.667 0.00 0.00 0.00 5.25
647 1842 2.650116 CCCACTACTCACCGCTGCT 61.650 63.158 0.00 0.00 0.00 4.24
649 1844 1.153745 CACTACTCACCGCTGCTCC 60.154 63.158 0.00 0.00 0.00 4.70
650 1845 1.606601 ACTACTCACCGCTGCTCCA 60.607 57.895 0.00 0.00 0.00 3.86
651 1846 1.185618 ACTACTCACCGCTGCTCCAA 61.186 55.000 0.00 0.00 0.00 3.53
652 1847 0.459237 CTACTCACCGCTGCTCCAAG 60.459 60.000 0.00 0.00 0.00 3.61
656 1879 3.616721 ACCGCTGCTCCAAGTCGT 61.617 61.111 0.00 0.00 0.00 4.34
657 1880 3.114616 CCGCTGCTCCAAGTCGTG 61.115 66.667 0.00 0.00 0.00 4.35
665 1888 1.270358 GCTCCAAGTCGTGAGTTTCCT 60.270 52.381 0.00 0.00 0.00 3.36
673 1896 3.833070 AGTCGTGAGTTTCCTATTCACCT 59.167 43.478 0.00 0.00 38.34 4.00
674 1897 4.082136 AGTCGTGAGTTTCCTATTCACCTC 60.082 45.833 0.00 0.00 38.34 3.85
676 1899 3.679083 CGTGAGTTTCCTATTCACCTCCC 60.679 52.174 0.00 0.00 38.34 4.30
697 1987 3.134458 CTCTTCAATAATCACCCTCGCC 58.866 50.000 0.00 0.00 0.00 5.54
732 2025 6.568869 CAATAGCAAAACATTCCCGGATTAA 58.431 36.000 0.73 0.00 0.00 1.40
811 2155 0.392863 AGCTGTATCGCCATTGTGCA 60.393 50.000 0.00 0.00 0.00 4.57
875 2219 1.293924 CACGATTGTCATCCAGAGCC 58.706 55.000 0.00 0.00 0.00 4.70
877 2221 0.467384 CGATTGTCATCCAGAGCCCT 59.533 55.000 0.00 0.00 0.00 5.19
1005 2351 2.586079 CTAGCGACCACCATGGCG 60.586 66.667 13.04 8.51 42.67 5.69
1009 2355 2.264480 CGACCACCATGGCGAAGA 59.736 61.111 13.04 0.00 42.67 2.87
1077 2423 4.715523 TGCCAAGCAGGGTACGGC 62.716 66.667 0.00 0.00 43.28 5.68
1131 2477 1.228769 TAGTCCTCCGCCGCCATAT 60.229 57.895 0.00 0.00 0.00 1.78
1141 2487 1.550130 GCCGCCATATACCCCTAGCA 61.550 60.000 0.00 0.00 0.00 3.49
1146 2492 1.628846 CCATATACCCCTAGCACACCC 59.371 57.143 0.00 0.00 0.00 4.61
1176 2522 4.994756 CCCACCCCTGCAACACCC 62.995 72.222 0.00 0.00 0.00 4.61
1578 4340 2.277692 CGCGCGGAAGACATCGTA 60.278 61.111 24.84 0.00 0.00 3.43
1593 4355 0.320073 TCGTAAGGGAAGTTGTGCGG 60.320 55.000 0.00 0.00 38.47 5.69
1626 4388 2.562738 CGGTATCATGGCTGGACTCATA 59.437 50.000 0.00 0.00 0.00 2.15
1737 5864 4.081917 TGAAATGTACGTAGGCTGATGTGA 60.082 41.667 0.00 0.00 0.00 3.58
2112 6612 1.302285 CAAGGGGCTGACTGCTGAT 59.698 57.895 4.20 0.00 42.39 2.90
2319 6834 3.207778 CCCTAACAAGGTCGACAACAAA 58.792 45.455 18.91 0.00 0.00 2.83
2331 6846 6.423001 AGGTCGACAACAAATACTACAAGAAC 59.577 38.462 18.91 0.00 0.00 3.01
2378 6893 2.667536 GGATGCCGCGCTCATGAT 60.668 61.111 15.23 0.00 0.00 2.45
2472 6987 1.152756 AATGGTAAGGATGGGCGCC 60.153 57.895 21.18 21.18 0.00 6.53
2537 10426 1.548973 GGCGTCGTCAACTCACACTG 61.549 60.000 0.00 0.00 0.00 3.66
2706 10623 4.023021 GCATTGTGGCATTTTGGTTTTCAT 60.023 37.500 0.00 0.00 0.00 2.57
2812 10730 3.273434 TGCTGTGCTCAAATATGTCTCC 58.727 45.455 0.00 0.00 0.00 3.71
2825 10743 0.601057 TGTCTCCGTTGCATCGAAGA 59.399 50.000 18.44 10.49 45.75 2.87
2905 10823 6.494893 TCAAATTCAGAATTGGTAAGACGG 57.505 37.500 9.24 0.00 0.00 4.79
3053 10979 1.825474 AGAGGTGGGTAACGATCACTG 59.175 52.381 0.00 0.00 37.60 3.66
3059 10985 2.365941 TGGGTAACGATCACTGTCACAA 59.634 45.455 0.00 0.00 37.60 3.33
3072 10998 3.722147 CTGTCACAACAGCTAGAACACT 58.278 45.455 0.00 0.00 46.01 3.55
3119 11045 3.637030 GCGCCGATTTCCGTAGCC 61.637 66.667 0.00 0.00 36.31 3.93
3145 11072 1.498264 TACTTATACCCCTTGCCGCA 58.502 50.000 0.00 0.00 0.00 5.69
3213 11140 2.289882 GCCTCTGAGGTATGCATGCATA 60.290 50.000 31.75 31.75 37.80 3.14
3245 11172 4.130118 GGGTATAGCATCACTTTGTGAGG 58.870 47.826 7.83 7.83 46.04 3.86
3252 11179 1.159713 TCACTTTGTGAGGCAGCACG 61.160 55.000 0.00 0.00 41.63 5.34
3255 11182 1.572085 CTTTGTGAGGCAGCACGGAG 61.572 60.000 0.00 3.34 41.63 4.63
3259 11186 2.435059 GAGGCAGCACGGAGAACC 60.435 66.667 0.00 0.00 0.00 3.62
3270 11197 2.842320 GGAGAACCGCCAAGAGAAC 58.158 57.895 0.00 0.00 0.00 3.01
3290 11217 3.017442 ACTAGAGAGTACAAGATGCGCA 58.983 45.455 14.96 14.96 32.65 6.09
3305 11232 2.166829 TGCGCATTGGGAAACACTTAT 58.833 42.857 5.66 0.00 0.00 1.73
3372 11300 4.675510 CGCATAATTGGCTGAACATTCTT 58.324 39.130 2.98 0.00 0.00 2.52
3389 11317 6.245408 ACATTCTTGAATTTACAGCCACCTA 58.755 36.000 0.00 0.00 0.00 3.08
3390 11318 6.891908 ACATTCTTGAATTTACAGCCACCTAT 59.108 34.615 0.00 0.00 0.00 2.57
3401 11329 4.547671 ACAGCCACCTATACTCTACACAT 58.452 43.478 0.00 0.00 0.00 3.21
3460 12238 1.270550 AGCTGCTATTGCCAACAACAC 59.729 47.619 0.00 0.00 38.99 3.32
3497 12275 6.427853 GGTCAATTCTTTTGGCAGCTTTAAAT 59.572 34.615 0.00 0.00 0.00 1.40
3508 12286 6.940739 TGGCAGCTTTAAATAAAATAAGCCA 58.059 32.000 0.00 0.00 42.98 4.75
3526 12304 0.400525 CATCCCCTCCCCAGCTTCTA 60.401 60.000 0.00 0.00 0.00 2.10
3533 12311 1.218196 CTCCCCAGCTTCTAGGGTCTA 59.782 57.143 6.13 0.00 43.89 2.59
3534 12312 1.649633 TCCCCAGCTTCTAGGGTCTAA 59.350 52.381 6.13 0.00 43.89 2.10
3535 12313 1.763545 CCCCAGCTTCTAGGGTCTAAC 59.236 57.143 6.13 0.00 43.89 2.34
3536 12314 1.409427 CCCAGCTTCTAGGGTCTAACG 59.591 57.143 0.00 0.00 40.34 3.18
3537 12315 2.100989 CCAGCTTCTAGGGTCTAACGT 58.899 52.381 0.00 0.00 0.00 3.99
3538 12316 2.159226 CCAGCTTCTAGGGTCTAACGTG 60.159 54.545 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 106 3.188048 ACTTACTGACGTACTCCTTCGTG 59.812 47.826 0.00 0.00 40.39 4.35
197 203 4.318332 GAAGGGGCAGAAAGAATTTTTGG 58.682 43.478 0.00 0.00 40.22 3.28
238 336 8.209584 TCTGTATCCTATCGTAGAACAGTTAGT 58.790 37.037 0.00 0.00 43.58 2.24
239 337 8.497554 GTCTGTATCCTATCGTAGAACAGTTAG 58.502 40.741 0.00 0.00 43.58 2.34
240 338 7.989170 TGTCTGTATCCTATCGTAGAACAGTTA 59.011 37.037 0.00 0.00 43.58 2.24
243 341 6.260271 TGTGTCTGTATCCTATCGTAGAACAG 59.740 42.308 0.00 0.00 43.58 3.16
244 342 6.037940 GTGTGTCTGTATCCTATCGTAGAACA 59.962 42.308 0.00 0.00 43.58 3.18
247 345 5.061853 GGTGTGTCTGTATCCTATCGTAGA 58.938 45.833 0.00 0.00 45.75 2.59
248 346 4.820173 TGGTGTGTCTGTATCCTATCGTAG 59.180 45.833 0.00 0.00 0.00 3.51
300 401 4.033358 GCAGTCAACTTCGATCATGTAAGG 59.967 45.833 0.00 0.00 0.00 2.69
303 404 3.056179 TGGCAGTCAACTTCGATCATGTA 60.056 43.478 0.00 0.00 0.00 2.29
304 405 2.289631 TGGCAGTCAACTTCGATCATGT 60.290 45.455 0.00 0.00 0.00 3.21
312 430 4.276926 ACTCTGAAAATGGCAGTCAACTTC 59.723 41.667 0.00 0.00 34.98 3.01
380 1503 0.109179 TATTGCGCGGTTCGTGTAGT 60.109 50.000 8.83 0.00 39.70 2.73
389 1512 3.122323 CGTTGGGTATTGCGCGGT 61.122 61.111 8.83 0.00 0.00 5.68
409 1536 5.580691 CACACGTTTGAGAGGATTATTAGCA 59.419 40.000 0.00 0.00 0.00 3.49
410 1537 5.502544 GCACACGTTTGAGAGGATTATTAGC 60.503 44.000 5.75 0.00 0.00 3.09
411 1538 5.812642 AGCACACGTTTGAGAGGATTATTAG 59.187 40.000 5.75 0.00 0.00 1.73
412 1539 5.730550 AGCACACGTTTGAGAGGATTATTA 58.269 37.500 5.75 0.00 0.00 0.98
413 1540 4.579869 AGCACACGTTTGAGAGGATTATT 58.420 39.130 5.75 0.00 0.00 1.40
414 1541 4.184629 GAGCACACGTTTGAGAGGATTAT 58.815 43.478 5.75 0.00 0.00 1.28
425 1552 1.674359 TGGTGAATGAGCACACGTTT 58.326 45.000 0.00 0.00 40.52 3.60
428 1555 1.201954 CGATTGGTGAATGAGCACACG 60.202 52.381 0.00 0.00 40.52 4.49
430 1557 2.349590 CTCGATTGGTGAATGAGCACA 58.650 47.619 0.00 0.00 40.52 4.57
441 1601 1.338337 CCGATGACTAGCTCGATTGGT 59.662 52.381 10.52 0.00 37.05 3.67
445 1605 0.538516 AGGCCGATGACTAGCTCGAT 60.539 55.000 10.52 0.00 37.05 3.59
463 1623 1.226974 CCACTATGCCGGACGACAG 60.227 63.158 5.05 0.00 0.00 3.51
474 1634 0.882042 GCTCCGGTGCATCCACTATG 60.882 60.000 23.09 0.00 41.75 2.23
478 1638 2.821366 CTGCTCCGGTGCATCCAC 60.821 66.667 29.68 0.59 42.48 4.02
506 1666 0.031585 CGTCCTCGGTGTGAGTTGAA 59.968 55.000 0.00 0.00 43.64 2.69
507 1667 1.658114 CGTCCTCGGTGTGAGTTGA 59.342 57.895 0.00 0.00 43.64 3.18
518 1678 1.350193 CAGTTGACATTCCGTCCTCG 58.650 55.000 0.00 0.00 44.71 4.63
519 1679 1.079503 GCAGTTGACATTCCGTCCTC 58.920 55.000 0.00 0.00 44.71 3.71
521 1681 1.197721 CAAGCAGTTGACATTCCGTCC 59.802 52.381 0.00 0.00 44.71 4.79
523 1683 2.254546 TCAAGCAGTTGACATTCCGT 57.745 45.000 0.00 0.00 37.79 4.69
524 1684 2.222886 CGATCAAGCAGTTGACATTCCG 60.223 50.000 0.00 0.00 45.58 4.30
525 1685 3.002791 TCGATCAAGCAGTTGACATTCC 58.997 45.455 0.00 0.00 45.58 3.01
526 1686 3.484886 GCTCGATCAAGCAGTTGACATTC 60.485 47.826 0.00 0.00 45.58 2.67
527 1687 2.417933 GCTCGATCAAGCAGTTGACATT 59.582 45.455 0.00 0.00 45.58 2.71
528 1688 2.005451 GCTCGATCAAGCAGTTGACAT 58.995 47.619 0.00 0.00 45.58 3.06
543 1703 1.131883 GACAGTTAACGGCTAGCTCGA 59.868 52.381 25.67 7.52 0.00 4.04
553 1713 2.118683 TCAACGAACCGACAGTTAACG 58.881 47.619 0.00 0.00 39.40 3.18
563 1723 0.934496 TGTCAAAGCTCAACGAACCG 59.066 50.000 0.00 0.00 0.00 4.44
564 1724 3.555518 GAATGTCAAAGCTCAACGAACC 58.444 45.455 0.00 0.00 0.00 3.62
589 1775 1.440353 GCTGCAAACTAACGCACGG 60.440 57.895 0.00 0.00 33.75 4.94
594 1780 2.290641 GGATATGGGCTGCAAACTAACG 59.709 50.000 0.50 0.00 0.00 3.18
609 1795 1.166129 GAGCTGCTGCCATGGATATG 58.834 55.000 18.40 2.49 40.80 1.78
610 1796 0.037877 GGAGCTGCTGCCATGGATAT 59.962 55.000 18.40 0.00 40.80 1.63
619 1814 2.124942 GTAGTGGGGAGCTGCTGC 60.125 66.667 13.20 13.20 40.05 5.25
626 1821 1.682684 AGCGGTGAGTAGTGGGGAG 60.683 63.158 0.00 0.00 0.00 4.30
629 1824 2.125512 GCAGCGGTGAGTAGTGGG 60.126 66.667 20.69 0.00 0.00 4.61
635 1830 2.345244 CTTGGAGCAGCGGTGAGT 59.655 61.111 20.69 3.86 0.00 3.41
636 1831 1.739562 GACTTGGAGCAGCGGTGAG 60.740 63.158 20.69 8.81 0.00 3.51
639 1834 3.616721 ACGACTTGGAGCAGCGGT 61.617 61.111 0.00 0.00 0.00 5.68
640 1835 3.114616 CACGACTTGGAGCAGCGG 61.115 66.667 0.00 0.00 0.00 5.52
641 1836 2.049156 TCACGACTTGGAGCAGCG 60.049 61.111 0.00 0.00 0.00 5.18
642 1837 0.601311 AACTCACGACTTGGAGCAGC 60.601 55.000 0.00 0.00 34.48 5.25
643 1838 1.795286 GAAACTCACGACTTGGAGCAG 59.205 52.381 0.00 0.00 34.48 4.24
646 1841 2.821991 AGGAAACTCACGACTTGGAG 57.178 50.000 0.00 0.00 32.90 3.86
647 1842 4.282449 TGAATAGGAAACTCACGACTTGGA 59.718 41.667 0.00 0.00 43.67 3.53
649 1844 4.389077 GGTGAATAGGAAACTCACGACTTG 59.611 45.833 0.00 0.00 43.67 3.16
650 1845 4.283722 AGGTGAATAGGAAACTCACGACTT 59.716 41.667 0.00 0.00 43.67 3.01
651 1846 3.833070 AGGTGAATAGGAAACTCACGACT 59.167 43.478 0.00 0.00 43.67 4.18
652 1847 4.174762 GAGGTGAATAGGAAACTCACGAC 58.825 47.826 0.00 0.00 43.67 4.34
656 1879 3.775316 GAGGGAGGTGAATAGGAAACTCA 59.225 47.826 0.00 0.00 43.67 3.41
657 1880 4.034410 AGAGGGAGGTGAATAGGAAACTC 58.966 47.826 0.00 0.00 43.67 3.01
665 1888 7.420214 GGTGATTATTGAAGAGGGAGGTGAATA 60.420 40.741 0.00 0.00 0.00 1.75
673 1896 3.388024 CGAGGGTGATTATTGAAGAGGGA 59.612 47.826 0.00 0.00 0.00 4.20
674 1897 3.733337 CGAGGGTGATTATTGAAGAGGG 58.267 50.000 0.00 0.00 0.00 4.30
676 1899 3.134458 GGCGAGGGTGATTATTGAAGAG 58.866 50.000 0.00 0.00 0.00 2.85
697 1987 2.744461 TGCTATTGCACCGTGTACG 58.256 52.632 0.00 0.00 45.31 3.67
811 2155 4.324991 GGGAAGCGAACGTGGGGT 62.325 66.667 0.00 0.00 0.00 4.95
875 2219 1.925455 TCCAAAGGGGAGAGCCAGG 60.925 63.158 0.00 0.00 42.15 4.45
1024 2370 3.329301 GAGCAGCGCGATGAGAGC 61.329 66.667 30.90 13.11 46.45 4.09
1077 2423 2.847715 GGGACCGGGGTGGGATAG 60.848 72.222 6.32 0.00 44.64 2.08
1101 2447 2.184579 GGACTAGGTGTGCTCGGC 59.815 66.667 0.00 0.00 33.97 5.54
1131 2477 0.616679 GACTGGGTGTGCTAGGGGTA 60.617 60.000 0.00 0.00 0.00 3.69
1141 2487 4.954118 TGGCGGAGGACTGGGTGT 62.954 66.667 0.00 0.00 0.00 4.16
1146 2492 4.394712 GTGGGTGGCGGAGGACTG 62.395 72.222 0.00 0.00 0.00 3.51
1176 2522 3.087253 TATGGCGGTGGGGGACTG 61.087 66.667 0.00 0.00 0.00 3.51
1578 4340 0.609131 CATCCCGCACAACTTCCCTT 60.609 55.000 0.00 0.00 0.00 3.95
1593 4355 2.203153 ATACCGGCGTTGGCATCC 60.203 61.111 6.01 0.00 42.47 3.51
1626 4388 1.267261 CAGTCGTGGAAGAAGAGACGT 59.733 52.381 0.00 0.00 36.97 4.34
1737 5864 8.644374 ACAAATAAACCATTATACACCACACT 57.356 30.769 0.00 0.00 31.44 3.55
2112 6612 2.174360 CCAGAGAGTGTGACCATCTCA 58.826 52.381 14.18 0.00 41.58 3.27
2319 6834 4.081862 TGGCTAAGCACGTTCTTGTAGTAT 60.082 41.667 10.86 0.00 0.00 2.12
2331 6846 2.094659 CACCTCGTGGCTAAGCACG 61.095 63.158 2.76 6.86 45.09 5.34
2378 6893 2.635714 CTGCACTTGTATCATCTGCCA 58.364 47.619 0.00 0.00 0.00 4.92
2472 6987 2.854777 GAGATTGGTCTTGACGTCGATG 59.145 50.000 11.62 2.26 33.97 3.84
2706 10623 5.843019 ACAACTTCCATAAGAGGAAAGGA 57.157 39.130 0.00 0.00 46.44 3.36
2812 10730 6.193410 CACAATAATTCTTCTTCGATGCAACG 59.807 38.462 10.48 10.48 0.00 4.10
2825 10743 9.630098 CATTAAGTTGAGCACACAATAATTCTT 57.370 29.630 0.00 0.00 32.36 2.52
2901 10819 4.787999 GTGATCGACACCTCCGTC 57.212 61.111 6.82 0.00 43.05 4.79
2968 10892 1.747206 GCGCAGTATGTTCCCCTTCAT 60.747 52.381 0.30 0.00 39.31 2.57
3053 10979 3.669122 CGTAGTGTTCTAGCTGTTGTGAC 59.331 47.826 0.00 0.00 0.00 3.67
3059 10985 3.069079 TCTCCGTAGTGTTCTAGCTGT 57.931 47.619 0.00 0.00 0.00 4.40
3072 10998 6.533723 CACTAACAATTTGCACTATCTCCGTA 59.466 38.462 0.00 0.00 0.00 4.02
3119 11045 5.557866 GGCAAGGGGTATAAGTATAACCTG 58.442 45.833 11.38 5.22 43.93 4.00
3145 11072 3.930035 AGGATAGTCCGGAGAAATCCTT 58.070 45.455 26.05 15.73 42.75 3.36
3148 11075 3.568853 TCGAAGGATAGTCCGGAGAAATC 59.431 47.826 3.06 8.28 42.75 2.17
3192 11119 0.179037 TGCATGCATACCTCAGAGGC 60.179 55.000 18.46 2.78 39.63 4.70
3252 11179 0.321996 AGTTCTCTTGGCGGTTCTCC 59.678 55.000 0.00 0.00 0.00 3.71
3255 11182 2.492484 TCTCTAGTTCTCTTGGCGGTTC 59.508 50.000 0.00 0.00 0.00 3.62
3259 11186 3.690139 TGTACTCTCTAGTTCTCTTGGCG 59.310 47.826 0.00 0.00 37.15 5.69
3270 11197 3.699779 TGCGCATCTTGTACTCTCTAG 57.300 47.619 5.66 0.00 0.00 2.43
3290 11217 4.325344 CCTCCTCCATAAGTGTTTCCCAAT 60.325 45.833 0.00 0.00 0.00 3.16
3305 11232 2.364317 CGCCTTCTCCCTCCTCCA 60.364 66.667 0.00 0.00 0.00 3.86
3351 11279 5.653507 TCAAGAATGTTCAGCCAATTATGC 58.346 37.500 0.00 0.00 0.00 3.14
3372 11300 6.808321 AGAGTATAGGTGGCTGTAAATTCA 57.192 37.500 0.00 0.00 0.00 2.57
3379 11307 3.977312 TGTGTAGAGTATAGGTGGCTGT 58.023 45.455 0.00 0.00 0.00 4.40
3389 11317 3.118261 CCACCCTGCAATGTGTAGAGTAT 60.118 47.826 12.70 0.00 31.36 2.12
3390 11318 2.236146 CCACCCTGCAATGTGTAGAGTA 59.764 50.000 12.70 0.00 31.36 2.59
3401 11329 1.065410 TTCCTTCTCCCACCCTGCAA 61.065 55.000 0.00 0.00 0.00 4.08
3460 12238 4.939052 AGAATTGACCCCTAGTGTATCG 57.061 45.455 0.00 0.00 0.00 2.92
3497 12275 2.449345 GGGGAGGGGATGGCTTATTTTA 59.551 50.000 0.00 0.00 0.00 1.52
3508 12286 0.104725 CTAGAAGCTGGGGAGGGGAT 60.105 60.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.