Multiple sequence alignment - TraesCS6A01G361700

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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 TraesCS6A01G361700 chr6A 100.000 4928 0 0 674 5601 591982986 591987913 0.000000e+00 9101.0
1 TraesCS6A01G361700 chr6A 84.480 1192 162 15 3133 4313 591805293 591804114 0.000000e+00 1155.0
2 TraesCS6A01G361700 chr6A 100.000 333 0 0 1 333 591982313 591982645 2.870000e-172 616.0
3 TraesCS6A01G361700 chr6A 84.314 357 47 3 4312 4666 591804084 591803735 1.930000e-89 340.0
4 TraesCS6A01G361700 chr6A 82.110 218 28 7 674 882 591982416 591982631 5.770000e-40 176.0
5 TraesCS6A01G361700 chr6A 82.110 218 28 7 104 319 591982986 591983194 5.770000e-40 176.0
6 TraesCS6A01G361700 chr6D 93.367 2367 122 10 2602 4960 445262419 445264758 0.000000e+00 3469.0
7 TraesCS6A01G361700 chr6D 92.302 1390 101 5 3219 4607 445308771 445310155 0.000000e+00 1969.0
8 TraesCS6A01G361700 chr6D 95.698 1139 44 3 2602 3736 445184672 445185809 0.000000e+00 1827.0
9 TraesCS6A01G361700 chr6D 93.031 1234 81 4 3731 4960 445191037 445192269 0.000000e+00 1797.0
10 TraesCS6A01G361700 chr6D 85.617 1321 168 11 3090 4393 444461344 444460029 0.000000e+00 1367.0
11 TraesCS6A01G361700 chr6D 88.595 982 78 21 1048 2011 445305048 445306013 0.000000e+00 1162.0
12 TraesCS6A01G361700 chr6D 84.236 1053 112 17 974 2011 445182937 445183950 0.000000e+00 976.0
13 TraesCS6A01G361700 chr6D 93.003 586 37 3 2602 3183 445308187 445308772 0.000000e+00 852.0
14 TraesCS6A01G361700 chr6D 89.023 665 54 16 1048 1701 445261552 445262208 0.000000e+00 806.0
15 TraesCS6A01G361700 chr6D 91.731 520 40 2 3904 4422 445311431 445311948 0.000000e+00 719.0
16 TraesCS6A01G361700 chr6D 90.335 538 36 7 2008 2533 445307061 445307594 0.000000e+00 691.0
17 TraesCS6A01G361700 chr6D 88.828 546 35 11 4416 4957 445334430 445334953 0.000000e+00 647.0
18 TraesCS6A01G361700 chr6D 93.898 295 11 2 6 293 445176713 445177007 6.660000e-119 438.0
19 TraesCS6A01G361700 chr6D 88.618 246 17 5 2297 2533 445184110 445184353 7.100000e-74 289.0
20 TraesCS6A01G361700 chr6D 85.159 283 36 1 4380 4662 444459991 444459715 9.180000e-73 285.0
21 TraesCS6A01G361700 chr6D 89.447 199 19 2 2008 2204 445306040 445306238 3.350000e-62 250.0
22 TraesCS6A01G361700 chr6D 85.022 227 23 8 108 330 445260800 445261019 2.630000e-53 220.0
23 TraesCS6A01G361700 chr6D 88.649 185 12 5 1830 2011 445306848 445307026 3.400000e-52 217.0
24 TraesCS6A01G361700 chr6D 84.722 216 22 7 108 319 445304297 445304505 7.360000e-49 206.0
25 TraesCS6A01G361700 chr6D 84.571 175 16 5 691 856 445176835 445177007 4.490000e-36 163.0
26 TraesCS6A01G361700 chr6D 100.000 56 0 0 278 333 445182846 445182901 2.760000e-18 104.0
27 TraesCS6A01G361700 chr6D 96.364 55 2 0 2535 2589 445184578 445184632 2.150000e-14 91.6
28 TraesCS6A01G361700 chr6B 94.542 2052 106 3 2602 4649 670211988 670214037 0.000000e+00 3164.0
29 TraesCS6A01G361700 chr6B 90.182 2037 181 12 2685 4719 671471965 671469946 0.000000e+00 2636.0
30 TraesCS6A01G361700 chr6B 87.440 1043 95 14 976 2011 670209259 670210272 0.000000e+00 1168.0
31 TraesCS6A01G361700 chr6B 93.740 623 33 3 2602 3220 670211153 670211773 0.000000e+00 929.0
32 TraesCS6A01G361700 chr6B 88.136 590 66 3 3831 4419 668910714 668910128 0.000000e+00 699.0
33 TraesCS6A01G361700 chr6B 86.989 538 55 6 2008 2531 670210307 670210843 4.830000e-165 592.0
34 TraesCS6A01G361700 chr6B 88.562 306 27 6 29 333 670207717 670208015 1.150000e-96 364.0
35 TraesCS6A01G361700 chr6B 79.394 495 75 18 993 1471 668913267 668912784 1.950000e-84 324.0
36 TraesCS6A01G361700 chr6B 91.228 228 12 4 715 938 670209030 670209253 2.540000e-78 303.0
37 TraesCS6A01G361700 chr6B 85.616 146 21 0 4473 4618 668910128 668909983 2.700000e-33 154.0
38 TraesCS6A01G361700 chrUn 88.817 1547 141 7 3414 4958 79232454 79233970 0.000000e+00 1869.0
39 TraesCS6A01G361700 chrUn 88.525 305 33 2 1122 1425 79238426 79238729 8.860000e-98 368.0
40 TraesCS6A01G361700 chrUn 81.742 356 53 10 980 1326 79229373 79229725 2.550000e-73 287.0
41 TraesCS6A01G361700 chr5A 96.006 651 14 2 4961 5601 676328294 676328942 0.000000e+00 1048.0
42 TraesCS6A01G361700 chr5A 95.320 641 21 6 4962 5601 644563565 644562933 0.000000e+00 1009.0
43 TraesCS6A01G361700 chr5A 94.745 647 28 3 4959 5601 103459831 103460475 0.000000e+00 1002.0
44 TraesCS6A01G361700 chr5A 94.237 642 29 5 4962 5601 3460604 3461239 0.000000e+00 974.0
45 TraesCS6A01G361700 chr1A 96.106 642 17 4 4962 5601 581120553 581119918 0.000000e+00 1040.0
46 TraesCS6A01G361700 chr3A 95.008 641 25 5 4962 5601 4188157 4187523 0.000000e+00 1000.0
47 TraesCS6A01G361700 chr3A 94.384 641 29 5 4962 5601 3135155 3134521 0.000000e+00 977.0
48 TraesCS6A01G361700 chr2A 94.246 643 25 5 4962 5601 35702007 35702640 0.000000e+00 972.0
49 TraesCS6A01G361700 chr2A 92.857 126 7 1 4962 5087 560211406 560211283 1.240000e-41 182.0
50 TraesCS6A01G361700 chr4A 94.228 641 27 7 4962 5601 577809594 577810225 0.000000e+00 970.0
51 TraesCS6A01G361700 chr7D 78.466 952 186 16 3489 4434 205738439 205737501 6.210000e-169 604.0


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 TraesCS6A01G361700 chr6A 591982313 591987913 5600 False 3297.666667 9101 94.036667 1 5601 3 chr6A.!!$F2 5600
1 TraesCS6A01G361700 chr6A 591803735 591805293 1558 True 747.500000 1155 84.397000 3133 4666 2 chr6A.!!$R1 1533
2 TraesCS6A01G361700 chr6D 445191037 445192269 1232 False 1797.000000 1797 93.031000 3731 4960 1 chr6D.!!$F1 1229
3 TraesCS6A01G361700 chr6D 445260800 445264758 3958 False 1498.333333 3469 89.137333 108 4960 3 chr6D.!!$F5 4852
4 TraesCS6A01G361700 chr6D 444459715 444461344 1629 True 826.000000 1367 85.388000 3090 4662 2 chr6D.!!$R1 1572
5 TraesCS6A01G361700 chr6D 445304297 445311948 7651 False 758.250000 1969 89.848000 108 4607 8 chr6D.!!$F6 4499
6 TraesCS6A01G361700 chr6D 445182846 445185809 2963 False 657.520000 1827 92.983200 278 3736 5 chr6D.!!$F4 3458
7 TraesCS6A01G361700 chr6D 445334430 445334953 523 False 647.000000 647 88.828000 4416 4957 1 chr6D.!!$F2 541
8 TraesCS6A01G361700 chr6B 671469946 671471965 2019 True 2636.000000 2636 90.182000 2685 4719 1 chr6B.!!$R1 2034
9 TraesCS6A01G361700 chr6B 670207717 670214037 6320 False 1086.666667 3164 90.416833 29 4649 6 chr6B.!!$F1 4620
10 TraesCS6A01G361700 chr6B 668909983 668913267 3284 True 392.333333 699 84.382000 993 4618 3 chr6B.!!$R2 3625
11 TraesCS6A01G361700 chrUn 79229373 79233970 4597 False 1078.000000 1869 85.279500 980 4958 2 chrUn.!!$F2 3978
12 TraesCS6A01G361700 chr5A 676328294 676328942 648 False 1048.000000 1048 96.006000 4961 5601 1 chr5A.!!$F3 640
13 TraesCS6A01G361700 chr5A 644562933 644563565 632 True 1009.000000 1009 95.320000 4962 5601 1 chr5A.!!$R1 639
14 TraesCS6A01G361700 chr5A 103459831 103460475 644 False 1002.000000 1002 94.745000 4959 5601 1 chr5A.!!$F2 642
15 TraesCS6A01G361700 chr5A 3460604 3461239 635 False 974.000000 974 94.237000 4962 5601 1 chr5A.!!$F1 639
16 TraesCS6A01G361700 chr1A 581119918 581120553 635 True 1040.000000 1040 96.106000 4962 5601 1 chr1A.!!$R1 639
17 TraesCS6A01G361700 chr3A 4187523 4188157 634 True 1000.000000 1000 95.008000 4962 5601 1 chr3A.!!$R2 639
18 TraesCS6A01G361700 chr3A 3134521 3135155 634 True 977.000000 977 94.384000 4962 5601 1 chr3A.!!$R1 639
19 TraesCS6A01G361700 chr2A 35702007 35702640 633 False 972.000000 972 94.246000 4962 5601 1 chr2A.!!$F1 639
20 TraesCS6A01G361700 chr4A 577809594 577810225 631 False 970.000000 970 94.228000 4962 5601 1 chr4A.!!$F1 639
21 TraesCS6A01G361700 chr7D 205737501 205738439 938 True 604.000000 604 78.466000 3489 4434 1 chr7D.!!$R1 945

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
81 82 1.258982 GATGTTCATGATCGGTCGCAC 59.741 52.381 0.0 0.0 0.00 5.34 F
1320 2352 0.735978 TGCGTATCAACAGCACCTCG 60.736 55.000 0.0 0.0 35.81 4.63 F
1586 2692 0.543277 CAGGCAGCCATACTTGAGGA 59.457 55.000 15.8 0.0 0.00 3.71 F
2483 4824 0.689623 AAGCTCACTCCACCAAGAGG 59.310 55.000 0.0 0.0 38.26 3.69 F
2903 5772 0.836606 TGCAGAAACACACAGGGAGA 59.163 50.000 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 2494 0.250513 AAGAGGATGACTTGGACGCC 59.749 55.000 0.00 0.0 0.00 5.68 R
2463 4804 1.338579 CCTCTTGGTGGAGTGAGCTTC 60.339 57.143 0.00 0.0 0.00 3.86 R
3455 8330 0.036199 TTGCGTGCTATAAACGGGGT 60.036 50.000 9.06 0.0 41.31 4.95 R
4405 9551 3.920231 TTCATCTCCACTTCCCTCATG 57.080 47.619 0.00 0.0 0.00 3.07 R
4607 9755 0.882042 AAGCTGTCAAGGACACTGCG 60.882 55.000 0.00 0.0 38.30 5.18 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
23 24 3.854286 CGTTAAGCACGTTTTCTCACT 57.146 42.857 0.00 0.00 44.49 3.41
24 25 4.191662 CGTTAAGCACGTTTTCTCACTT 57.808 40.909 0.00 0.00 44.49 3.16
25 26 3.960002 CGTTAAGCACGTTTTCTCACTTG 59.040 43.478 0.00 0.00 44.49 3.16
26 27 2.475200 AAGCACGTTTTCTCACTTGC 57.525 45.000 0.00 0.00 41.18 4.01
27 28 1.378531 AGCACGTTTTCTCACTTGCA 58.621 45.000 5.27 0.00 42.84 4.08
56 57 9.319143 CCTTTAGACTAGGACTGATTATGTTTG 57.681 37.037 0.00 0.00 34.56 2.93
67 68 4.980590 TGATTATGTTTGTGCCGATGTTC 58.019 39.130 0.00 0.00 0.00 3.18
81 82 1.258982 GATGTTCATGATCGGTCGCAC 59.741 52.381 0.00 0.00 0.00 5.34
91 92 3.004002 TGATCGGTCGCACGACTTTATAT 59.996 43.478 21.19 8.92 46.64 0.86
116 117 9.740710 ATAACTGGCTAAAATGTCTTACTTTCT 57.259 29.630 0.00 0.00 0.00 2.52
140 141 3.877508 GGAGTTCCACATAATTTCCCTCG 59.122 47.826 0.00 0.00 35.64 4.63
161 162 5.305585 TCGGGGAAAATCAATCATAGCTAC 58.694 41.667 0.00 0.00 0.00 3.58
179 180 4.697352 AGCTACATCATGCGTTTTTCTTCT 59.303 37.500 0.00 0.00 0.00 2.85
183 184 3.988379 TCATGCGTTTTTCTTCTTGCT 57.012 38.095 0.00 0.00 0.00 3.91
184 185 4.305989 TCATGCGTTTTTCTTCTTGCTT 57.694 36.364 0.00 0.00 0.00 3.91
190 191 3.803778 CGTTTTTCTTCTTGCTTGCCAAT 59.196 39.130 0.00 0.00 31.91 3.16
255 260 1.461127 GCTCTTGCAACGGACTAACAG 59.539 52.381 0.00 0.00 39.41 3.16
256 261 2.755650 CTCTTGCAACGGACTAACAGT 58.244 47.619 0.00 0.00 0.00 3.55
257 262 3.859627 GCTCTTGCAACGGACTAACAGTA 60.860 47.826 0.00 0.00 39.41 2.74
258 263 4.304110 CTCTTGCAACGGACTAACAGTAA 58.696 43.478 0.00 0.00 0.00 2.24
259 264 4.053295 TCTTGCAACGGACTAACAGTAAC 58.947 43.478 0.00 0.00 0.00 2.50
260 265 3.455990 TGCAACGGACTAACAGTAACA 57.544 42.857 0.00 0.00 0.00 2.41
268 273 7.224522 ACGGACTAACAGTAACACTAAATCT 57.775 36.000 0.00 0.00 0.00 2.40
695 701 2.561419 TGTCCTACTTTCAGGGAGTTCG 59.439 50.000 0.00 0.00 36.26 3.95
697 703 2.824341 TCCTACTTTCAGGGAGTTCGAC 59.176 50.000 0.00 0.00 36.26 4.20
725 1719 5.371115 TTCCCTCGTGAAAAATCAATCAC 57.629 39.130 0.00 0.00 41.95 3.06
748 1742 7.542534 ACGGTTATATCGTGCATTTTTCTTA 57.457 32.000 0.00 0.00 39.55 2.10
847 1848 1.859080 CTAACTCCGGCGTGCTAAATC 59.141 52.381 6.01 0.00 0.00 2.17
942 1952 6.101881 TCTCTCTCTCTCTCTCTCTCTCTCTA 59.898 46.154 0.00 0.00 0.00 2.43
944 1954 7.990055 TCTCTCTCTCTCTCTCTCTCTCTATA 58.010 42.308 0.00 0.00 0.00 1.31
945 1955 8.619281 TCTCTCTCTCTCTCTCTCTCTCTATAT 58.381 40.741 0.00 0.00 0.00 0.86
946 1956 9.913310 CTCTCTCTCTCTCTCTCTCTCTATATA 57.087 40.741 0.00 0.00 0.00 0.86
1018 2028 2.410322 AATGAGTGCCTGGCCGTTGA 62.410 55.000 17.53 0.00 0.00 3.18
1242 2274 4.815973 TCCTACAGCCCGCCCCAT 62.816 66.667 0.00 0.00 0.00 4.00
1320 2352 0.735978 TGCGTATCAACAGCACCTCG 60.736 55.000 0.00 0.00 35.81 4.63
1413 2454 1.303091 GCGACGGGCCATACTTTGTT 61.303 55.000 4.39 0.00 34.80 2.83
1449 2490 3.825014 AGAACAACTTAGTAGCACTCGGA 59.175 43.478 0.00 0.00 0.00 4.55
1538 2582 2.224523 CGGGCACAGGTTACATGGATAT 60.225 50.000 1.27 0.00 0.00 1.63
1540 2584 3.181445 GGGCACAGGTTACATGGATATGA 60.181 47.826 1.27 0.00 37.73 2.15
1541 2585 4.067896 GGCACAGGTTACATGGATATGAG 58.932 47.826 1.27 0.00 37.73 2.90
1581 2687 3.089838 TGCCAGGCAGCCATACTT 58.910 55.556 11.22 0.00 33.32 2.24
1586 2692 0.543277 CAGGCAGCCATACTTGAGGA 59.457 55.000 15.80 0.00 0.00 3.71
1630 2742 1.096386 TCAACGGGTTGGTTTCGGTG 61.096 55.000 11.31 0.00 42.24 4.94
1642 2754 6.426025 GGTTGGTTTCGGTGATTATAGATACC 59.574 42.308 0.00 0.00 35.98 2.73
1812 2927 2.880268 CAGTGATCACAGTTTCTGCCAA 59.120 45.455 27.02 0.00 34.37 4.52
1826 2941 2.092646 TCTGCCAAAACTACACCACAGT 60.093 45.455 0.00 0.00 0.00 3.55
1860 2975 6.890293 AGGTCTTCTTTATGGTTATGAGGAC 58.110 40.000 0.00 0.00 34.45 3.85
1861 2976 5.753921 GGTCTTCTTTATGGTTATGAGGACG 59.246 44.000 0.00 0.00 35.51 4.79
1877 2998 0.824109 GACGATGGTGATCCTGGTGA 59.176 55.000 0.00 0.00 34.23 4.02
1878 2999 1.414181 GACGATGGTGATCCTGGTGAT 59.586 52.381 0.00 0.00 36.01 3.06
1959 3088 5.643777 CCATGGCTGCTATGGTAATAGTAAC 59.356 44.000 30.32 0.00 40.15 2.50
2056 3261 7.122353 AGCTAGATAGAGTGTTTTCCGAGTAAA 59.878 37.037 0.00 0.00 0.00 2.01
2061 3266 8.699283 ATAGAGTGTTTTCCGAGTAAACATAC 57.301 34.615 11.11 9.07 44.52 2.39
2097 3314 2.481185 GCCCAAGCACAAAAATGTGATG 59.519 45.455 12.80 9.83 42.02 3.07
2099 3316 2.481185 CCAAGCACAAAAATGTGATGGC 59.519 45.455 12.80 0.00 42.02 4.40
2109 3326 7.546316 CACAAAAATGTGATGGCATAATGAAGA 59.454 33.333 0.00 0.00 42.02 2.87
2114 3331 8.645814 AATGTGATGGCATAATGAAGATACAT 57.354 30.769 0.00 0.00 0.00 2.29
2117 3334 7.173735 TGTGATGGCATAATGAAGATACATGTC 59.826 37.037 0.00 0.00 0.00 3.06
2118 3335 7.173735 GTGATGGCATAATGAAGATACATGTCA 59.826 37.037 0.00 0.00 35.85 3.58
2160 4475 5.968387 AAGTCGCCGTAAAGAAAGATATG 57.032 39.130 0.00 0.00 0.00 1.78
2168 4483 6.680378 GCCGTAAAGAAAGATATGTGGCAAAT 60.680 38.462 0.00 0.00 38.60 2.32
2369 4698 7.971004 ATGAGTACAATATGCGTATACATCG 57.029 36.000 3.32 0.00 0.00 3.84
2463 4804 7.714377 ACAAATCATCAAAGCCACTAGATCTAG 59.286 37.037 25.26 25.26 39.04 2.43
2483 4824 0.689623 AAGCTCACTCCACCAAGAGG 59.310 55.000 0.00 0.00 38.26 3.69
2533 4874 2.061773 CATGCAGTATGTAGTAGCCGC 58.938 52.381 0.00 0.00 39.31 6.53
2589 5427 9.988350 CCACAATTATCAGTTTAGTTATGACAC 57.012 33.333 0.00 0.00 0.00 3.67
2716 5583 3.434319 CTTGCGCGGCATTGACCT 61.434 61.111 8.83 0.00 38.76 3.85
2898 5767 2.129607 GGCAATTGCAGAAACACACAG 58.870 47.619 30.32 0.00 44.36 3.66
2903 5772 0.836606 TGCAGAAACACACAGGGAGA 59.163 50.000 0.00 0.00 0.00 3.71
3225 6944 2.390599 CCGGTGTCAAGATGGTGCG 61.391 63.158 0.00 0.00 0.00 5.34
3358 7108 5.709966 AGAATTCAGTTGCCCGAAATTAAC 58.290 37.500 8.44 0.00 0.00 2.01
3359 7109 5.242838 AGAATTCAGTTGCCCGAAATTAACA 59.757 36.000 8.44 0.00 0.00 2.41
3455 8330 4.757657 TCATTTTACTTTTAGTGCTCGCCA 59.242 37.500 0.00 0.00 0.00 5.69
3793 8671 7.016072 TCCCAAATCAACCATAGAAATGTTGTT 59.984 33.333 0.00 0.00 31.57 2.83
4111 9159 1.626654 CTACAGCCGTGCAAGGAACG 61.627 60.000 23.82 11.50 40.70 3.95
4248 9310 1.007038 GTAGTGGTGGCAACGACGA 60.007 57.895 0.00 0.00 39.77 4.20
4405 9551 2.798364 GGGAGAAGAGCGGCCTACC 61.798 68.421 0.00 0.00 0.00 3.18
4607 9755 4.264460 AGTTATCCTCGATGATCTTGCC 57.736 45.455 6.46 0.00 0.00 4.52
4623 9771 2.320587 GCCGCAGTGTCCTTGACAG 61.321 63.158 0.00 0.00 43.57 3.51
4626 9774 0.882042 CGCAGTGTCCTTGACAGCTT 60.882 55.000 0.00 0.00 43.57 3.74
4733 9885 7.530861 CGTGTGCTTCTTTCTTTGTATTCTAAC 59.469 37.037 0.00 0.00 0.00 2.34
4801 9953 9.778741 CTCCAACCTCTTACTAATGCATATTTA 57.221 33.333 0.00 0.00 0.00 1.40
4802 9954 9.778741 TCCAACCTCTTACTAATGCATATTTAG 57.221 33.333 0.00 1.34 0.00 1.85
4803 9955 9.561069 CCAACCTCTTACTAATGCATATTTAGT 57.439 33.333 14.03 14.03 0.00 2.24
4806 9958 9.547753 ACCTCTTACTAATGCATATTTAGTGTG 57.452 33.333 17.57 11.51 0.00 3.82
4807 9959 8.499162 CCTCTTACTAATGCATATTTAGTGTGC 58.501 37.037 17.57 0.00 44.39 4.57
4808 9960 8.072238 TCTTACTAATGCATATTTAGTGTGCG 57.928 34.615 17.57 6.70 46.81 5.34
4809 9961 7.923878 TCTTACTAATGCATATTTAGTGTGCGA 59.076 33.333 17.57 8.33 46.81 5.10
4889 10042 9.241317 CATGTCAAATACTTGGATATCAAAAGC 57.759 33.333 14.26 0.00 34.56 3.51
4898 10052 5.659440 TGGATATCAAAAGCTTTGGTTCC 57.341 39.130 13.54 16.71 0.00 3.62
5013 10167 0.603975 GATCAGCCCATTAGTCCCGC 60.604 60.000 0.00 0.00 0.00 6.13
5303 11363 4.323792 CCCCAGTGCTCTATTTTTCTCTGA 60.324 45.833 0.00 0.00 0.00 3.27
5322 11382 3.474570 CGAGGGGGAGAGGGCTTG 61.475 72.222 0.00 0.00 0.00 4.01
5323 11383 3.093172 GAGGGGGAGAGGGCTTGG 61.093 72.222 0.00 0.00 0.00 3.61
5336 11396 0.250727 GGCTTGGTGTGGTGCTCTAA 60.251 55.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.350772 GGGATGCAAGTGAGAAAACGTG 60.351 50.000 0.00 0.00 33.33 4.49
11 12 1.880027 GGGATGCAAGTGAGAAAACGT 59.120 47.619 0.00 0.00 0.00 3.99
12 13 2.154462 AGGGATGCAAGTGAGAAAACG 58.846 47.619 0.00 0.00 0.00 3.60
13 14 4.590850 AAAGGGATGCAAGTGAGAAAAC 57.409 40.909 0.00 0.00 0.00 2.43
14 15 5.473504 GTCTAAAGGGATGCAAGTGAGAAAA 59.526 40.000 0.00 0.00 0.00 2.29
15 16 5.003804 GTCTAAAGGGATGCAAGTGAGAAA 58.996 41.667 0.00 0.00 0.00 2.52
16 17 4.287067 AGTCTAAAGGGATGCAAGTGAGAA 59.713 41.667 0.00 0.00 0.00 2.87
17 18 3.840666 AGTCTAAAGGGATGCAAGTGAGA 59.159 43.478 0.00 0.00 0.00 3.27
18 19 4.213564 AGTCTAAAGGGATGCAAGTGAG 57.786 45.455 0.00 0.00 0.00 3.51
19 20 4.162320 CCTAGTCTAAAGGGATGCAAGTGA 59.838 45.833 0.00 0.00 0.00 3.41
20 21 4.162320 TCCTAGTCTAAAGGGATGCAAGTG 59.838 45.833 0.00 0.00 34.66 3.16
21 22 4.162509 GTCCTAGTCTAAAGGGATGCAAGT 59.837 45.833 0.00 0.00 34.66 3.16
22 23 4.407296 AGTCCTAGTCTAAAGGGATGCAAG 59.593 45.833 0.00 0.00 34.66 4.01
23 24 4.162320 CAGTCCTAGTCTAAAGGGATGCAA 59.838 45.833 0.00 0.00 34.66 4.08
24 25 3.706594 CAGTCCTAGTCTAAAGGGATGCA 59.293 47.826 0.00 0.00 34.66 3.96
25 26 3.961408 TCAGTCCTAGTCTAAAGGGATGC 59.039 47.826 0.00 0.00 34.66 3.91
26 27 6.739331 AATCAGTCCTAGTCTAAAGGGATG 57.261 41.667 0.00 0.00 34.66 3.51
27 28 8.013667 ACATAATCAGTCCTAGTCTAAAGGGAT 58.986 37.037 0.00 0.00 34.66 3.85
67 68 0.802222 AAGTCGTGCGACCGATCATG 60.802 55.000 19.35 0.00 45.59 3.07
75 76 4.085210 GCCAGTTATATAAAGTCGTGCGAC 60.085 45.833 15.92 15.92 44.86 5.19
91 92 8.999431 CAGAAAGTAAGACATTTTAGCCAGTTA 58.001 33.333 0.00 0.00 0.00 2.24
116 117 3.596046 AGGGAAATTATGTGGAACTCCCA 59.404 43.478 8.42 0.00 43.04 4.37
140 141 6.716628 TGATGTAGCTATGATTGATTTTCCCC 59.283 38.462 0.00 0.00 0.00 4.81
156 157 4.697352 AGAAGAAAAACGCATGATGTAGCT 59.303 37.500 0.00 0.00 0.00 3.32
161 162 4.232221 AGCAAGAAGAAAAACGCATGATG 58.768 39.130 0.00 0.00 0.00 3.07
179 180 6.922957 CACTTTTTAGTTAGATTGGCAAGCAA 59.077 34.615 18.69 7.21 0.00 3.91
183 184 7.575414 TGACACTTTTTAGTTAGATTGGCAA 57.425 32.000 0.68 0.68 0.00 4.52
184 185 7.665559 AGATGACACTTTTTAGTTAGATTGGCA 59.334 33.333 0.00 0.00 0.00 4.92
247 252 6.034683 CGCCAGATTTAGTGTTACTGTTAGTC 59.965 42.308 0.00 0.00 0.00 2.59
255 260 6.558909 ACTACTACGCCAGATTTAGTGTTAC 58.441 40.000 0.00 0.00 0.00 2.50
256 261 6.764308 ACTACTACGCCAGATTTAGTGTTA 57.236 37.500 0.00 0.00 0.00 2.41
257 262 5.656213 ACTACTACGCCAGATTTAGTGTT 57.344 39.130 0.00 0.00 0.00 3.32
258 263 6.764308 TTACTACTACGCCAGATTTAGTGT 57.236 37.500 0.00 0.00 0.00 3.55
259 264 7.919091 TGATTTACTACTACGCCAGATTTAGTG 59.081 37.037 0.00 0.00 0.00 2.74
260 265 8.004087 TGATTTACTACTACGCCAGATTTAGT 57.996 34.615 0.00 0.00 0.00 2.24
268 273 4.665212 CGAACTGATTTACTACTACGCCA 58.335 43.478 0.00 0.00 0.00 5.69
695 701 7.535139 TGATTTTTCACGAGGGAAATTATGTC 58.465 34.615 0.99 0.00 36.71 3.06
697 703 8.931385 ATTGATTTTTCACGAGGGAAATTATG 57.069 30.769 0.99 0.00 36.71 1.90
725 1719 8.891928 CATTAAGAAAAATGCACGATATAACCG 58.108 33.333 0.00 0.00 30.59 4.44
748 1742 1.377987 TTAGCTTTCGGCCCGCATT 60.378 52.632 0.00 0.00 43.05 3.56
847 1848 4.504132 GCTGGGTCTAGCGAACTG 57.496 61.111 0.00 0.00 33.46 3.16
907 1915 5.610132 AGAGAGAGAGAGAGAGAGATGGATT 59.390 44.000 0.00 0.00 0.00 3.01
908 1916 5.161135 AGAGAGAGAGAGAGAGAGATGGAT 58.839 45.833 0.00 0.00 0.00 3.41
909 1917 4.560739 AGAGAGAGAGAGAGAGAGATGGA 58.439 47.826 0.00 0.00 0.00 3.41
910 1918 4.592351 AGAGAGAGAGAGAGAGAGAGATGG 59.408 50.000 0.00 0.00 0.00 3.51
911 1919 5.539574 AGAGAGAGAGAGAGAGAGAGAGATG 59.460 48.000 0.00 0.00 0.00 2.90
972 1982 9.744468 GTTTGTTTTTCCTCAACAACTACATAT 57.256 29.630 0.00 0.00 42.48 1.78
1029 2039 2.099062 GCGGCAGAGAACATTGCG 59.901 61.111 0.00 0.00 41.17 4.85
1242 2274 3.132139 CCGTCGCCGAGGAAGAGA 61.132 66.667 8.59 0.00 35.63 3.10
1266 2298 3.681473 TCGATGTCGAGCACCTGT 58.319 55.556 0.21 0.00 44.22 4.00
1316 2348 3.380004 GTCATAGAGGATATCCAGCGAGG 59.620 52.174 23.81 12.62 38.89 4.63
1320 2352 3.759086 TGTCGTCATAGAGGATATCCAGC 59.241 47.826 23.81 14.61 38.89 4.85
1394 2435 1.303091 AACAAAGTATGGCCCGTCGC 61.303 55.000 0.00 0.00 0.00 5.19
1449 2490 1.815421 GATGACTTGGACGCCGCAT 60.815 57.895 0.00 0.00 0.00 4.73
1453 2494 0.250513 AAGAGGATGACTTGGACGCC 59.749 55.000 0.00 0.00 0.00 5.68
1454 2495 1.363744 CAAGAGGATGACTTGGACGC 58.636 55.000 0.00 0.00 40.39 5.19
1477 2518 1.334869 GCTGACAAGGGTGTTGTTCTG 59.665 52.381 0.00 0.00 38.41 3.02
1581 2687 1.734137 GTAGGAAGCGCGATCCTCA 59.266 57.895 32.27 19.61 44.01 3.86
1642 2754 5.703978 TCCACAATTAACACATTGACCTG 57.296 39.130 0.48 0.00 37.55 4.00
1702 2817 2.501881 GGCTGTGTACGCGTTATTTTG 58.498 47.619 20.78 5.23 0.00 2.44
1703 2818 1.465777 GGGCTGTGTACGCGTTATTTT 59.534 47.619 20.78 0.00 0.00 1.82
1704 2819 1.081094 GGGCTGTGTACGCGTTATTT 58.919 50.000 20.78 0.00 0.00 1.40
1726 2841 2.202236 ATCGCCCAGGTCAGCATTGT 62.202 55.000 0.00 0.00 0.00 2.71
1826 2941 8.477419 ACCATAAAGAAGACCTTGATCAAAAA 57.523 30.769 9.88 0.00 34.79 1.94
1959 3088 8.807667 AAAGAAAGAAATATTTGAGCAGTGTG 57.192 30.769 5.17 0.00 0.00 3.82
2001 3167 7.642586 GTGCGGTGGCTAAATAAAGTAAATTAG 59.357 37.037 0.00 0.00 40.82 1.73
2004 3172 5.163591 GGTGCGGTGGCTAAATAAAGTAAAT 60.164 40.000 0.00 0.00 40.82 1.40
2056 3261 3.510719 GCAATGTGCCATTTTCGTATGT 58.489 40.909 0.00 0.00 37.42 2.29
2080 3286 3.472283 TGCCATCACATTTTTGTGCTT 57.528 38.095 1.27 0.00 39.49 3.91
2097 3314 5.704515 AGCTGACATGTATCTTCATTATGCC 59.295 40.000 0.00 0.00 0.00 4.40
2099 3316 6.932960 TGGAGCTGACATGTATCTTCATTATG 59.067 38.462 0.00 0.00 0.00 1.90
2160 4475 7.432350 TTTTCCACAATTATTGATTTGCCAC 57.568 32.000 12.28 0.00 0.00 5.01
2358 4687 1.463444 GCAAATCCCCGATGTATACGC 59.537 52.381 0.00 0.00 0.00 4.42
2369 4698 4.336713 GTGACTGAGAAATAGCAAATCCCC 59.663 45.833 0.00 0.00 0.00 4.81
2404 4734 8.651588 GTGAGCGAGGAAACATATCTATTAATG 58.348 37.037 0.00 0.00 0.00 1.90
2421 4753 5.109210 TGATTTGTATTACTGTGAGCGAGG 58.891 41.667 0.00 0.00 0.00 4.63
2463 4804 1.338579 CCTCTTGGTGGAGTGAGCTTC 60.339 57.143 0.00 0.00 0.00 3.86
2533 4874 7.439655 GGATAAGTCCACTTAGAATACAAGCTG 59.560 40.741 5.46 0.00 44.42 4.24
2680 5547 2.417719 AGCTGTCGTGGAATTGAAGAC 58.582 47.619 0.00 0.00 0.00 3.01
2716 5583 6.369615 GGTCGGCTAAGAAACAACTATTTACA 59.630 38.462 0.00 0.00 0.00 2.41
2834 5703 9.860898 CTGGATAATCACATTCGTTGATATCTA 57.139 33.333 3.98 0.00 0.00 1.98
2898 5767 3.817647 GGCACTGACAATCATATTCTCCC 59.182 47.826 0.00 0.00 0.00 4.30
2903 5772 3.461085 AGGAGGGCACTGACAATCATATT 59.539 43.478 0.00 0.00 0.00 1.28
3270 6992 6.524101 TCATTACCTGTAAATGGCCTTTTC 57.476 37.500 19.12 11.80 0.00 2.29
3358 7108 9.916397 GGTATCATAGACGAAAATACAAAGTTG 57.084 33.333 0.00 0.00 0.00 3.16
3359 7109 9.661563 TGGTATCATAGACGAAAATACAAAGTT 57.338 29.630 0.00 0.00 0.00 2.66
3455 8330 0.036199 TTGCGTGCTATAAACGGGGT 60.036 50.000 9.06 0.00 41.31 4.95
3793 8671 5.972935 TCAAGACAACATCCGATTAGCTTA 58.027 37.500 0.00 0.00 0.00 3.09
4111 9159 4.161102 ACATGGGGTCTAAGTAGCCTATC 58.839 47.826 0.00 0.00 36.21 2.08
4248 9310 7.259290 ACAAAATGTGAAACGAGACTAACAT 57.741 32.000 0.00 0.00 42.39 2.71
4405 9551 3.920231 TTCATCTCCACTTCCCTCATG 57.080 47.619 0.00 0.00 0.00 3.07
4607 9755 0.882042 AAGCTGTCAAGGACACTGCG 60.882 55.000 0.00 0.00 38.30 5.18
4623 9771 3.865224 CAAAGGTGCAAAACATCAAGC 57.135 42.857 0.00 0.00 0.00 4.01
4757 9909 2.037902 GGAGATTCCAGTAGCTAAGGGC 59.962 54.545 12.26 4.50 36.28 5.19
4801 9953 4.499019 CCAAAACTAAAACCATCGCACACT 60.499 41.667 0.00 0.00 0.00 3.55
4802 9954 3.733727 CCAAAACTAAAACCATCGCACAC 59.266 43.478 0.00 0.00 0.00 3.82
4803 9955 3.381908 ACCAAAACTAAAACCATCGCACA 59.618 39.130 0.00 0.00 0.00 4.57
4804 9956 3.972403 ACCAAAACTAAAACCATCGCAC 58.028 40.909 0.00 0.00 0.00 5.34
4805 9957 4.657436 AACCAAAACTAAAACCATCGCA 57.343 36.364 0.00 0.00 0.00 5.10
4806 9958 5.044558 TGAAACCAAAACTAAAACCATCGC 58.955 37.500 0.00 0.00 0.00 4.58
4807 9959 6.699642 ACATGAAACCAAAACTAAAACCATCG 59.300 34.615 0.00 0.00 0.00 3.84
4808 9960 7.708752 TGACATGAAACCAAAACTAAAACCATC 59.291 33.333 0.00 0.00 0.00 3.51
4809 9961 7.560368 TGACATGAAACCAAAACTAAAACCAT 58.440 30.769 0.00 0.00 0.00 3.55
4886 10039 2.755952 ACTTCCTGGAACCAAAGCTT 57.244 45.000 4.68 0.00 0.00 3.74
4889 10042 6.840780 ATGATTTACTTCCTGGAACCAAAG 57.159 37.500 4.68 0.00 0.00 2.77
5013 10167 2.362242 TCCCGGTTCTGGACTGAAG 58.638 57.895 0.00 0.00 36.72 3.02
5114 11171 1.074072 CCGGTTCATCCCACCAACA 59.926 57.895 0.00 0.00 33.36 3.33
5170 11227 1.527380 GTTCAAGCCACCAACCGGA 60.527 57.895 9.46 0.00 35.59 5.14
5322 11382 1.797025 GTGAGTTAGAGCACCACACC 58.203 55.000 0.00 0.00 0.00 4.16
5336 11396 1.644509 TGTGTGCATAGGAGGTGAGT 58.355 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.