Multiple sequence alignment - TraesCS1D01G015600

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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 TraesCS1D01G015600 chr1D 100.000 4435 0 0 1 4435 7315111 7319545 0.000000e+00 8191.0
1 TraesCS1D01G015600 chr6B 92.635 3693 212 29 6 3661 46844237 46840568 0.000000e+00 5258.0
2 TraesCS1D01G015600 chr6B 89.620 2081 164 34 2 2043 106526848 106528915 0.000000e+00 2599.0
3 TraesCS1D01G015600 chr6B 92.940 1728 106 11 1936 3651 106528759 106530482 0.000000e+00 2501.0
4 TraesCS1D01G015600 chr5B 91.280 3853 249 45 15 3790 29221542 29217700 0.000000e+00 5173.0
5 TraesCS1D01G015600 chr5B 88.424 1624 149 27 155 1763 679760953 679759354 0.000000e+00 1921.0
6 TraesCS1D01G015600 chr5B 83.493 418 32 17 3904 4316 426883143 426883528 5.460000e-94 355.0
7 TraesCS1D01G015600 chr5B 84.106 151 7 3 4302 4435 426883546 426883696 3.600000e-26 130.0
8 TraesCS1D01G015600 chr5B 90.476 63 5 1 4061 4123 708327788 708327849 1.020000e-11 82.4
9 TraesCS1D01G015600 chr2B 92.430 3633 190 31 239 3790 767702045 767705673 0.000000e+00 5107.0
10 TraesCS1D01G015600 chr2B 91.825 526 25 8 107 614 659079911 659080436 0.000000e+00 717.0
11 TraesCS1D01G015600 chr2B 91.034 145 13 0 3814 3958 46943999 46943855 3.500000e-46 196.0
12 TraesCS1D01G015600 chrUn 92.717 2348 136 18 1332 3651 34309386 34311726 0.000000e+00 3356.0
13 TraesCS1D01G015600 chrUn 82.213 506 46 16 3904 4390 88737187 88737667 3.210000e-106 396.0
14 TraesCS1D01G015600 chrUn 86.260 262 20 5 3904 4162 60994083 60994331 2.030000e-68 270.0
15 TraesCS1D01G015600 chrUn 93.578 109 5 1 3814 3920 124913694 124913586 1.280000e-35 161.0
16 TraesCS1D01G015600 chr2D 89.711 2352 164 26 12 2317 544213431 544211112 0.000000e+00 2931.0
17 TraesCS1D01G015600 chr2D 95.780 1019 33 5 2782 3790 544211114 544210096 0.000000e+00 1635.0
18 TraesCS1D01G015600 chr2D 79.783 277 27 19 3827 4094 549101136 549101392 1.640000e-39 174.0
19 TraesCS1D01G015600 chr5A 89.681 2132 167 30 2 2091 509880757 509878637 0.000000e+00 2669.0
20 TraesCS1D01G015600 chr5A 93.472 1777 102 10 1886 3651 509878795 509877022 0.000000e+00 2627.0
21 TraesCS1D01G015600 chr5A 85.432 556 33 15 3903 4434 30504824 30505355 6.530000e-148 534.0
22 TraesCS1D01G015600 chr5A 82.940 551 51 12 3904 4435 298128331 298128857 1.450000e-124 457.0
23 TraesCS1D01G015600 chr7B 89.634 2132 168 30 2 2091 581501410 581499290 0.000000e+00 2663.0
24 TraesCS1D01G015600 chr7B 93.191 1777 107 10 1886 3651 581499448 581497675 0.000000e+00 2599.0
25 TraesCS1D01G015600 chr7B 95.238 1533 57 8 2270 3790 700854695 700853167 0.000000e+00 2412.0
26 TraesCS1D01G015600 chr7B 94.697 132 5 1 3791 3920 333979725 333979856 2.090000e-48 204.0
27 TraesCS1D01G015600 chr4A 96.139 1580 45 6 2221 3790 697819780 697818207 0.000000e+00 2566.0
28 TraesCS1D01G015600 chr7A 92.684 1777 115 11 1886 3651 166602366 166600594 0.000000e+00 2547.0
29 TraesCS1D01G015600 chr7A 91.413 1805 134 14 302 2091 166604006 166602208 0.000000e+00 2455.0
30 TraesCS1D01G015600 chr3B 89.318 2022 161 34 2 1976 464196191 464198204 0.000000e+00 2486.0
31 TraesCS1D01G015600 chr3B 90.390 1769 136 20 1886 3637 506491239 506492990 0.000000e+00 2294.0
32 TraesCS1D01G015600 chr3B 90.083 1452 123 13 2 1443 506480450 506481890 0.000000e+00 1864.0
33 TraesCS1D01G015600 chr3B 93.939 132 6 1 3791 3920 9145947 9145816 9.730000e-47 198.0
34 TraesCS1D01G015600 chr7D 92.881 604 29 12 24 614 106582842 106582240 0.000000e+00 865.0
35 TraesCS1D01G015600 chr7D 85.817 557 34 16 3904 4432 270726488 270727027 2.330000e-152 549.0
36 TraesCS1D01G015600 chr7D 84.211 266 27 11 3791 4045 412409929 412410190 1.230000e-60 244.0
37 TraesCS1D01G015600 chr7D 82.784 273 27 14 3790 4045 412430210 412430479 4.460000e-55 226.0
38 TraesCS1D01G015600 chr4B 90.205 633 42 7 2 614 108900171 108900803 0.000000e+00 808.0
39 TraesCS1D01G015600 chr4B 89.320 206 10 2 3904 4109 668876932 668877125 9.530000e-62 248.0
40 TraesCS1D01G015600 chr4B 84.462 251 23 5 3904 4154 362688517 362688751 2.670000e-57 233.0
41 TraesCS1D01G015600 chr4B 81.919 271 33 5 4180 4435 362762078 362762347 9.660000e-52 215.0
42 TraesCS1D01G015600 chr3A 84.810 553 41 13 3904 4433 691740459 691739927 2.370000e-142 516.0
43 TraesCS1D01G015600 chr1B 84.211 437 35 19 3904 4331 647541455 647541866 1.160000e-105 394.0
44 TraesCS1D01G015600 chr1B 85.859 297 25 6 3904 4200 647588292 647588571 2.590000e-77 300.0
45 TraesCS1D01G015600 chr1B 93.939 132 6 1 3791 3920 42283301 42283432 9.730000e-47 198.0
46 TraesCS1D01G015600 chr1B 80.625 160 16 11 4180 4331 647531157 647531309 4.690000e-20 110.0
47 TraesCS1D01G015600 chr3D 86.728 324 22 4 3904 4219 612166935 612166625 1.530000e-89 340.0
48 TraesCS1D01G015600 chr3D 84.167 240 20 7 4212 4435 612166214 612165977 2.690000e-52 217.0


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 TraesCS1D01G015600 chr1D 7315111 7319545 4434 False 8191.0 8191 100.0000 1 4435 1 chr1D.!!$F1 4434
1 TraesCS1D01G015600 chr6B 46840568 46844237 3669 True 5258.0 5258 92.6350 6 3661 1 chr6B.!!$R1 3655
2 TraesCS1D01G015600 chr6B 106526848 106530482 3634 False 2550.0 2599 91.2800 2 3651 2 chr6B.!!$F1 3649
3 TraesCS1D01G015600 chr5B 29217700 29221542 3842 True 5173.0 5173 91.2800 15 3790 1 chr5B.!!$R1 3775
4 TraesCS1D01G015600 chr5B 679759354 679760953 1599 True 1921.0 1921 88.4240 155 1763 1 chr5B.!!$R2 1608
5 TraesCS1D01G015600 chr5B 426883143 426883696 553 False 242.5 355 83.7995 3904 4435 2 chr5B.!!$F2 531
6 TraesCS1D01G015600 chr2B 767702045 767705673 3628 False 5107.0 5107 92.4300 239 3790 1 chr2B.!!$F2 3551
7 TraesCS1D01G015600 chr2B 659079911 659080436 525 False 717.0 717 91.8250 107 614 1 chr2B.!!$F1 507
8 TraesCS1D01G015600 chrUn 34309386 34311726 2340 False 3356.0 3356 92.7170 1332 3651 1 chrUn.!!$F1 2319
9 TraesCS1D01G015600 chr2D 544210096 544213431 3335 True 2283.0 2931 92.7455 12 3790 2 chr2D.!!$R1 3778
10 TraesCS1D01G015600 chr5A 509877022 509880757 3735 True 2648.0 2669 91.5765 2 3651 2 chr5A.!!$R1 3649
11 TraesCS1D01G015600 chr5A 30504824 30505355 531 False 534.0 534 85.4320 3903 4434 1 chr5A.!!$F1 531
12 TraesCS1D01G015600 chr5A 298128331 298128857 526 False 457.0 457 82.9400 3904 4435 1 chr5A.!!$F2 531
13 TraesCS1D01G015600 chr7B 581497675 581501410 3735 True 2631.0 2663 91.4125 2 3651 2 chr7B.!!$R2 3649
14 TraesCS1D01G015600 chr7B 700853167 700854695 1528 True 2412.0 2412 95.2380 2270 3790 1 chr7B.!!$R1 1520
15 TraesCS1D01G015600 chr4A 697818207 697819780 1573 True 2566.0 2566 96.1390 2221 3790 1 chr4A.!!$R1 1569
16 TraesCS1D01G015600 chr7A 166600594 166604006 3412 True 2501.0 2547 92.0485 302 3651 2 chr7A.!!$R1 3349
17 TraesCS1D01G015600 chr3B 464196191 464198204 2013 False 2486.0 2486 89.3180 2 1976 1 chr3B.!!$F1 1974
18 TraesCS1D01G015600 chr3B 506491239 506492990 1751 False 2294.0 2294 90.3900 1886 3637 1 chr3B.!!$F3 1751
19 TraesCS1D01G015600 chr3B 506480450 506481890 1440 False 1864.0 1864 90.0830 2 1443 1 chr3B.!!$F2 1441
20 TraesCS1D01G015600 chr7D 106582240 106582842 602 True 865.0 865 92.8810 24 614 1 chr7D.!!$R1 590
21 TraesCS1D01G015600 chr7D 270726488 270727027 539 False 549.0 549 85.8170 3904 4432 1 chr7D.!!$F1 528
22 TraesCS1D01G015600 chr4B 108900171 108900803 632 False 808.0 808 90.2050 2 614 1 chr4B.!!$F1 612
23 TraesCS1D01G015600 chr3A 691739927 691740459 532 True 516.0 516 84.8100 3904 4433 1 chr3A.!!$R1 529
24 TraesCS1D01G015600 chr3D 612165977 612166935 958 True 278.5 340 85.4475 3904 4435 2 chr3D.!!$R1 531

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
948 1046 0.250038 CTGCCGAATGGACCGATGAT 60.250 55.000 0.00 0.0 37.49 2.45 F
1437 1591 1.360551 CCGCATCTGGTCTACCTCG 59.639 63.158 0.02 0.0 36.82 4.63 F
2871 3199 0.467804 GAGAAGGACATGCCCTCCTC 59.532 60.000 0.00 0.0 37.13 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 2676 3.554934 AGATCAAAGAACACACTTGCCA 58.445 40.909 0.00 0.0 0.0 4.92 R
3050 3379 2.887152 GGTGCACCTCTTTGAAAGTCAT 59.113 45.455 29.12 0.0 0.0 3.06 R
4276 5092 0.243907 CTCCGGATATGCGTACCAGG 59.756 60.000 15.77 0.0 0.0 4.45 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
76 78 1.002900 CTTCGCAAAAAGCAGAACCGA 60.003 47.619 0.00 0.00 46.13 4.69
353 425 0.962356 CATCTGCCGCCACTTCCTTT 60.962 55.000 0.00 0.00 0.00 3.11
418 490 3.664025 CTGGCCGCAAGATCCACGA 62.664 63.158 0.00 0.00 43.02 4.35
432 504 0.600255 CCACGACAGAGAAGCCGTTT 60.600 55.000 0.00 0.00 32.50 3.60
528 613 5.827797 TGTAGCCCCAATTTCTTGTGATATC 59.172 40.000 0.00 0.00 0.00 1.63
695 782 9.617523 CACATAATTATATACTGATGGATGCCA 57.382 33.333 0.00 0.00 38.19 4.92
700 787 7.848223 TTATATACTGATGGATGCCAATTCG 57.152 36.000 0.00 0.00 36.95 3.34
753 840 6.204688 TGTTTGTGAGATGGTAGTGATTGTTC 59.795 38.462 0.00 0.00 0.00 3.18
948 1046 0.250038 CTGCCGAATGGACCGATGAT 60.250 55.000 0.00 0.00 37.49 2.45
1039 1165 3.884693 GACACCCAATGCATATGATGACA 59.115 43.478 6.97 0.00 0.00 3.58
1046 1172 5.336451 CCAATGCATATGATGACATGGGAAG 60.336 44.000 6.97 0.00 38.80 3.46
1168 1294 3.462678 GCGAGACTGGAGGGGTCC 61.463 72.222 0.00 0.00 34.56 4.46
1169 1295 2.037367 CGAGACTGGAGGGGTCCA 59.963 66.667 0.00 0.00 38.25 4.02
1240 1369 4.691216 AGGCGAAAGTTGTAAGTTCTCATC 59.309 41.667 0.00 0.00 0.00 2.92
1241 1370 4.451096 GGCGAAAGTTGTAAGTTCTCATCA 59.549 41.667 0.00 0.00 0.00 3.07
1302 1433 9.757227 ATGCTTTATGTACTAATGTCTCTCTTC 57.243 33.333 0.00 0.00 0.00 2.87
1388 1542 3.119602 CCTGTGCATCTTGTTTGAGGATG 60.120 47.826 0.00 0.00 39.59 3.51
1437 1591 1.360551 CCGCATCTGGTCTACCTCG 59.639 63.158 0.02 0.00 36.82 4.63
1500 1654 4.989279 AAATCACCGATCTTGATTTGGG 57.011 40.909 22.12 4.84 46.93 4.12
1502 1656 1.912731 TCACCGATCTTGATTTGGGGA 59.087 47.619 4.39 4.39 0.00 4.81
1508 1662 4.022589 CCGATCTTGATTTGGGGAATGATG 60.023 45.833 0.00 0.00 0.00 3.07
1597 1751 4.127907 AGAAGAACAAGAAACCGAAGACC 58.872 43.478 0.00 0.00 0.00 3.85
1644 1798 8.608844 ATTAGAAAGATTAGTTCTATTGCCCG 57.391 34.615 0.00 0.00 37.41 6.13
1646 1800 3.127425 AGATTAGTTCTATTGCCCGGC 57.873 47.619 1.04 1.04 30.96 6.13
1741 1895 1.599071 CGTGATTGTGGCGCAATAGAT 59.401 47.619 24.89 5.24 46.90 1.98
1759 1913 4.160642 AGATGGCACTGATGAGCATTTA 57.839 40.909 0.00 0.00 0.00 1.40
1982 2187 2.098293 GCCTATGTTGGCGAACCTG 58.902 57.895 9.25 0.00 43.74 4.00
2000 2301 5.339008 ACCTGTTATTATCTTGTGCTCGA 57.661 39.130 0.00 0.00 0.00 4.04
2048 2372 9.141400 GGTGAATCTATTATTATCTTGTCGGTC 57.859 37.037 0.00 0.00 0.00 4.79
2126 2450 4.605640 TTGATATGGCAGATGTCATCGA 57.394 40.909 2.64 0.00 39.96 3.59
2155 2479 8.855110 AGTGATAGTGAGGATGACAATAGTTAG 58.145 37.037 0.00 0.00 0.00 2.34
2324 2648 1.557099 AGAGACTATTGCCACACCGA 58.443 50.000 0.00 0.00 0.00 4.69
2352 2676 6.715280 AGACCTACACAATGTTGAGAATGAT 58.285 36.000 0.00 0.00 0.00 2.45
2481 2805 6.669154 ACATTGGGAGGTTGTGAATCAAATAT 59.331 34.615 0.00 0.00 37.81 1.28
2799 3127 5.234972 TCGATATGCACTTCACTTATGCTTG 59.765 40.000 0.00 0.00 40.13 4.01
2807 3135 5.183713 CACTTCACTTATGCTTGAATTGGGA 59.816 40.000 0.00 0.00 31.88 4.37
2832 3160 5.126067 ACCTGGTTCTATGCATGATACAAC 58.874 41.667 10.16 4.67 0.00 3.32
2871 3199 0.467804 GAGAAGGACATGCCCTCCTC 59.532 60.000 0.00 0.00 37.13 3.71
2986 3315 9.169592 TCAATTTAGGCAAGTATTACCTTGTAC 57.830 33.333 0.00 0.00 39.33 2.90
2990 3319 6.062258 AGGCAAGTATTACCTTGTACATGT 57.938 37.500 2.69 2.69 39.33 3.21
3024 3353 6.707440 AATAGAGATGGATATCTAGCACCG 57.293 41.667 7.11 0.00 43.63 4.94
3039 3368 1.603678 GCACCGTACAAAGGAGAACGA 60.604 52.381 0.00 0.00 37.53 3.85
3046 3375 5.983720 CCGTACAAAGGAGAACGATATCATT 59.016 40.000 3.12 0.00 37.53 2.57
3050 3379 6.414732 ACAAAGGAGAACGATATCATTTCCA 58.585 36.000 14.13 0.00 29.17 3.53
3153 3482 3.395941 AGAGAACCTTTGGAGTGTGGAAT 59.604 43.478 0.00 0.00 0.00 3.01
3247 3583 1.676014 GCACAACTATGTTCGCCTCCT 60.676 52.381 0.00 0.00 37.82 3.69
3310 3646 3.951037 CCGGATTATGTTCCAACAATCCA 59.049 43.478 17.58 0.00 42.47 3.41
3311 3647 4.584325 CCGGATTATGTTCCAACAATCCAT 59.416 41.667 17.58 1.71 42.47 3.41
3559 3914 9.191479 TGGTTCTTTATCTAAACTTGGTGAAAA 57.809 29.630 0.00 0.00 0.00 2.29
3668 4027 5.388371 GCCAAAATCGCAGAAAAATACACAC 60.388 40.000 0.00 0.00 43.58 3.82
3698 4061 2.205022 AGCAGCTTTGTAATCTGGCA 57.795 45.000 0.00 0.00 0.00 4.92
3761 4126 2.123982 CCATCAAGCAGCTCCCCC 60.124 66.667 0.00 0.00 0.00 5.40
3795 4160 3.987404 CCTTCCTGGGCTTGTTCG 58.013 61.111 0.00 0.00 0.00 3.95
3796 4161 1.374947 CCTTCCTGGGCTTGTTCGA 59.625 57.895 0.00 0.00 0.00 3.71
3797 4162 0.955919 CCTTCCTGGGCTTGTTCGAC 60.956 60.000 0.00 0.00 0.00 4.20
3798 4163 1.291877 CTTCCTGGGCTTGTTCGACG 61.292 60.000 0.00 0.00 0.00 5.12
3799 4164 1.750341 TTCCTGGGCTTGTTCGACGA 61.750 55.000 0.00 0.00 0.00 4.20
3800 4165 1.738099 CCTGGGCTTGTTCGACGAG 60.738 63.158 0.00 0.00 32.67 4.18
3801 4166 1.289066 CTGGGCTTGTTCGACGAGA 59.711 57.895 0.00 0.00 31.05 4.04
3802 4167 0.108615 CTGGGCTTGTTCGACGAGAT 60.109 55.000 0.00 0.00 31.05 2.75
3803 4168 0.320374 TGGGCTTGTTCGACGAGATT 59.680 50.000 0.00 0.00 31.05 2.40
3804 4169 1.270625 TGGGCTTGTTCGACGAGATTT 60.271 47.619 0.00 0.00 31.05 2.17
3805 4170 1.804748 GGGCTTGTTCGACGAGATTTT 59.195 47.619 0.00 0.00 31.05 1.82
3806 4171 2.412847 GGGCTTGTTCGACGAGATTTTG 60.413 50.000 0.00 0.00 31.05 2.44
3807 4172 2.412847 GGCTTGTTCGACGAGATTTTGG 60.413 50.000 0.00 0.00 31.05 3.28
3808 4173 2.478894 GCTTGTTCGACGAGATTTTGGA 59.521 45.455 0.00 0.00 31.05 3.53
3809 4174 3.664537 GCTTGTTCGACGAGATTTTGGAC 60.665 47.826 0.00 0.00 31.05 4.02
3810 4175 3.380479 TGTTCGACGAGATTTTGGACT 57.620 42.857 0.00 0.00 0.00 3.85
3811 4176 4.508461 TGTTCGACGAGATTTTGGACTA 57.492 40.909 0.00 0.00 0.00 2.59
3812 4177 4.232221 TGTTCGACGAGATTTTGGACTAC 58.768 43.478 0.00 0.00 0.00 2.73
3813 4178 4.232221 GTTCGACGAGATTTTGGACTACA 58.768 43.478 0.00 0.00 0.00 2.74
3814 4179 4.713824 TCGACGAGATTTTGGACTACAT 57.286 40.909 0.00 0.00 0.00 2.29
3815 4180 5.068234 TCGACGAGATTTTGGACTACATT 57.932 39.130 0.00 0.00 0.00 2.71
3816 4181 5.475719 TCGACGAGATTTTGGACTACATTT 58.524 37.500 0.00 0.00 0.00 2.32
3817 4182 5.929992 TCGACGAGATTTTGGACTACATTTT 59.070 36.000 0.00 0.00 0.00 1.82
3818 4183 6.015504 CGACGAGATTTTGGACTACATTTTG 58.984 40.000 0.00 0.00 0.00 2.44
3819 4184 6.347402 CGACGAGATTTTGGACTACATTTTGT 60.347 38.462 0.00 0.00 0.00 2.83
3820 4185 7.148705 CGACGAGATTTTGGACTACATTTTGTA 60.149 37.037 0.00 0.00 0.00 2.41
3821 4186 8.561738 ACGAGATTTTGGACTACATTTTGTAT 57.438 30.769 0.00 0.00 31.66 2.29
3822 4187 8.450964 ACGAGATTTTGGACTACATTTTGTATG 58.549 33.333 0.00 0.00 31.66 2.39
3823 4188 8.664798 CGAGATTTTGGACTACATTTTGTATGA 58.335 33.333 0.00 0.00 31.66 2.15
3855 4220 9.691362 AAAAGTTGTGTGATGATAATTTGTACC 57.309 29.630 0.00 0.00 0.00 3.34
3856 4221 7.994425 AGTTGTGTGATGATAATTTGTACCA 57.006 32.000 0.00 0.00 0.00 3.25
3857 4222 8.402798 AGTTGTGTGATGATAATTTGTACCAA 57.597 30.769 0.00 0.00 0.00 3.67
3858 4223 8.855110 AGTTGTGTGATGATAATTTGTACCAAA 58.145 29.630 0.00 0.00 0.00 3.28
3859 4224 9.469807 GTTGTGTGATGATAATTTGTACCAAAA 57.530 29.630 0.00 0.00 0.00 2.44
3896 4261 3.467374 CTCATAACTTGAGGAGGAGCC 57.533 52.381 0.00 0.00 46.89 4.70
3940 4305 0.182299 TGCCCACGGATATTGCATGA 59.818 50.000 0.00 0.00 0.00 3.07
3944 4309 1.875514 CCACGGATATTGCATGAGTGG 59.124 52.381 0.00 8.96 41.09 4.00
4000 4365 9.487790 CTGTTGGCTAAAAGAAATTTTAATGGA 57.512 29.630 0.00 0.00 32.27 3.41
4048 4426 9.892130 AACTGTATATTAAGCTAGCTCAAGTTT 57.108 29.630 19.65 3.31 0.00 2.66
4049 4427 9.892130 ACTGTATATTAAGCTAGCTCAAGTTTT 57.108 29.630 19.65 2.48 0.00 2.43
4056 4434 9.672673 ATTAAGCTAGCTCAAGTTTTCTATGAA 57.327 29.630 19.65 0.00 0.00 2.57
4057 4435 6.976636 AGCTAGCTCAAGTTTTCTATGAAC 57.023 37.500 12.68 0.00 0.00 3.18
4132 4529 4.457496 CACGGAGCAGCCCATCGT 62.457 66.667 0.00 0.00 34.19 3.73
4158 4555 2.125512 GAGCGCACCGGTTGATCT 60.126 61.111 11.47 0.00 37.83 2.75
4168 4565 3.260475 CCGGTTGATCTGGTGATTACA 57.740 47.619 0.00 0.00 37.78 2.41
4256 5071 9.616634 AATATGTTCCATTGTACGTACGTATAG 57.383 33.333 29.05 18.34 32.82 1.31
4275 5091 2.125310 TGAATACGTGCCCGCCTG 60.125 61.111 0.00 0.00 37.70 4.85
4276 5092 3.573491 GAATACGTGCCCGCCTGC 61.573 66.667 0.00 0.00 37.70 4.85
4290 5107 0.951040 GCCTGCCTGGTACGCATATC 60.951 60.000 0.00 0.00 38.35 1.63
4291 5108 0.320771 CCTGCCTGGTACGCATATCC 60.321 60.000 0.00 0.00 35.25 2.59
4292 5109 0.667487 CTGCCTGGTACGCATATCCG 60.667 60.000 0.00 0.00 35.25 4.18
4349 5212 2.915349 ACAAAGATCATGCATCGAGCT 58.085 42.857 10.00 10.00 45.94 4.09
4404 5273 6.144080 CAGCTAGGTACGTATCAAGTAATTGC 59.856 42.308 8.86 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.638133 CACTGCTGAATCCTCGTCTG 58.362 55.000 0.00 0.00 0.00 3.51
73 75 3.058501 ACCGTAATTTTGAGCAACTTCGG 60.059 43.478 0.00 0.00 40.00 4.30
76 78 3.317993 AGCACCGTAATTTTGAGCAACTT 59.682 39.130 0.00 0.00 0.00 2.66
179 212 3.071206 GCAGAGGAGGAGCGTGGA 61.071 66.667 0.00 0.00 0.00 4.02
248 313 2.355946 ATGCGTAGATCCGAGGCAT 58.644 52.632 15.88 15.88 42.08 4.40
249 314 1.660355 GATGCGTAGATCCGAGGCA 59.340 57.895 13.19 13.19 41.48 4.75
250 315 1.442857 CGATGCGTAGATCCGAGGC 60.443 63.158 3.56 3.56 0.00 4.70
418 490 1.375326 GGGGAAACGGCTTCTCTGT 59.625 57.895 0.12 0.00 34.59 3.41
432 504 3.811702 CTCACCTTGAGCTGGGGA 58.188 61.111 0.00 0.00 37.72 4.81
528 613 3.441496 AAAGGTGCACACATCAGTTTG 57.559 42.857 20.43 0.00 0.00 2.93
695 782 6.432936 CAGCATGAATATGTAGCAACGAATT 58.567 36.000 0.00 0.00 39.69 2.17
700 787 4.825546 AGCAGCATGAATATGTAGCAAC 57.174 40.909 0.00 0.00 39.69 4.17
753 840 8.827832 ATAATCATGTGTCCAAATATATGGGG 57.172 34.615 0.00 1.18 41.05 4.96
1039 1165 2.312741 TCAGCAAGAATTCCCTTCCCAT 59.687 45.455 0.65 0.00 34.11 4.00
1046 1172 2.751806 CCAGTTCTCAGCAAGAATTCCC 59.248 50.000 0.65 0.00 45.57 3.97
1166 1292 4.640201 CAGTGTTTTTCTCAAAGTCCTGGA 59.360 41.667 0.00 0.00 0.00 3.86
1168 1294 5.123820 TCACAGTGTTTTTCTCAAAGTCCTG 59.876 40.000 0.00 0.00 0.00 3.86
1169 1295 5.253330 TCACAGTGTTTTTCTCAAAGTCCT 58.747 37.500 0.00 0.00 0.00 3.85
1210 1339 2.882927 ACAACTTTCGCCTTTTTCCC 57.117 45.000 0.00 0.00 0.00 3.97
1273 1402 9.534565 GAGAGACATTAGTACATAAAGCATGAA 57.465 33.333 0.00 0.00 38.10 2.57
1302 1433 2.639839 CCTGGGAGGTCCTATTGTATGG 59.360 54.545 0.00 0.00 36.20 2.74
1365 1519 2.106338 TCCTCAAACAAGATGCACAGGA 59.894 45.455 0.00 0.00 0.00 3.86
1437 1591 0.815615 CAATGCCGAACTAGAGGGGC 60.816 60.000 13.36 13.36 45.76 5.80
1500 1654 2.352960 GGTTGCTCTTCGACATCATTCC 59.647 50.000 0.00 0.00 0.00 3.01
1502 1656 3.340814 AGGTTGCTCTTCGACATCATT 57.659 42.857 0.00 0.00 0.00 2.57
1508 1662 1.000955 TGGAGAAGGTTGCTCTTCGAC 59.999 52.381 8.56 7.00 45.60 4.20
1597 1751 0.167470 CCTCTTGCATCACTTGTGCG 59.833 55.000 0.00 0.00 45.37 5.34
1644 1798 0.951558 AAACGATGTGTGTGAAGGCC 59.048 50.000 0.00 0.00 0.00 5.19
1646 1800 3.961477 TTGAAACGATGTGTGTGAAGG 57.039 42.857 0.00 0.00 0.00 3.46
1741 1895 4.678574 GCAATTAAATGCTCATCAGTGCCA 60.679 41.667 8.29 0.00 43.06 4.92
2000 2301 8.976353 TCACCAACATAGGCATAAATATTGTTT 58.024 29.630 0.00 0.00 0.00 2.83
2126 2450 9.373450 ACTATTGTCATCCTCACTATCACTATT 57.627 33.333 0.00 0.00 0.00 1.73
2155 2479 6.313658 GCATAACCAAATTCCTCATTGTTTCC 59.686 38.462 0.00 0.00 0.00 3.13
2324 2648 5.080337 TCTCAACATTGTGTAGGTCTCTCT 58.920 41.667 0.00 0.00 0.00 3.10
2352 2676 3.554934 AGATCAAAGAACACACTTGCCA 58.445 40.909 0.00 0.00 0.00 4.92
2481 2805 7.022055 TGTTTGAAGCGATTTTGAGTTCTTA 57.978 32.000 0.00 0.00 0.00 2.10
2799 3127 4.142160 GCATAGAACCAGGTTTCCCAATTC 60.142 45.833 6.21 0.00 0.00 2.17
2807 3135 5.754782 TGTATCATGCATAGAACCAGGTTT 58.245 37.500 6.21 0.00 0.00 3.27
2832 3160 6.682423 TCTCAATTGCATGGTATAACACAG 57.318 37.500 0.00 0.00 0.00 3.66
2986 3315 6.183360 CCATCTCTATTAGGATACCCGACATG 60.183 46.154 0.00 0.00 37.58 3.21
2990 3319 5.791303 TCCATCTCTATTAGGATACCCGA 57.209 43.478 0.00 0.00 37.58 5.14
3024 3353 7.494625 TGGAAATGATATCGTTCTCCTTTGTAC 59.505 37.037 24.17 8.01 0.00 2.90
3039 3368 8.910944 CCTCTTTGAAAGTCATGGAAATGATAT 58.089 33.333 4.68 0.00 32.61 1.63
3046 3375 3.569701 GCACCTCTTTGAAAGTCATGGAA 59.430 43.478 4.68 0.00 0.00 3.53
3050 3379 2.887152 GGTGCACCTCTTTGAAAGTCAT 59.113 45.455 29.12 0.00 0.00 3.06
3153 3482 4.202441 GGCATCTTGAGGAGAATTTGCTA 58.798 43.478 0.00 0.00 37.80 3.49
3247 3583 8.408043 AACAAAGTGGATATCATCTTTGTCAA 57.592 30.769 32.64 0.00 45.50 3.18
3416 3766 4.072131 GACTTCACCAACCAAGAGCAATA 58.928 43.478 0.00 0.00 0.00 1.90
3698 4061 2.040278 TGGGCTGAAAAGAGTACTGCAT 59.960 45.455 0.00 0.00 0.00 3.96
3761 4126 0.622665 AGGGAGTCTGAAGCCCATTG 59.377 55.000 15.92 0.00 44.55 2.82
3790 4155 3.380479 AGTCCAAAATCTCGTCGAACA 57.620 42.857 0.00 0.00 0.00 3.18
3791 4156 4.232221 TGTAGTCCAAAATCTCGTCGAAC 58.768 43.478 0.00 0.00 0.00 3.95
3792 4157 4.508461 TGTAGTCCAAAATCTCGTCGAA 57.492 40.909 0.00 0.00 0.00 3.71
3793 4158 4.713824 ATGTAGTCCAAAATCTCGTCGA 57.286 40.909 0.00 0.00 0.00 4.20
3794 4159 5.779806 AAATGTAGTCCAAAATCTCGTCG 57.220 39.130 0.00 0.00 0.00 5.12
3795 4160 6.899114 ACAAAATGTAGTCCAAAATCTCGTC 58.101 36.000 0.00 0.00 0.00 4.20
3796 4161 6.877611 ACAAAATGTAGTCCAAAATCTCGT 57.122 33.333 0.00 0.00 0.00 4.18
3797 4162 8.664798 TCATACAAAATGTAGTCCAAAATCTCG 58.335 33.333 0.00 0.00 36.14 4.04
3829 4194 9.691362 GGTACAAATTATCATCACACAACTTTT 57.309 29.630 0.00 0.00 0.00 2.27
3830 4195 8.855110 TGGTACAAATTATCATCACACAACTTT 58.145 29.630 0.00 0.00 31.92 2.66
3831 4196 8.402798 TGGTACAAATTATCATCACACAACTT 57.597 30.769 0.00 0.00 31.92 2.66
3832 4197 7.994425 TGGTACAAATTATCATCACACAACT 57.006 32.000 0.00 0.00 31.92 3.16
3877 4242 3.121929 AGGCTCCTCCTCAAGTTATGA 57.878 47.619 0.00 0.00 43.20 2.15
3878 4243 4.590647 TCATAGGCTCCTCCTCAAGTTATG 59.409 45.833 0.00 0.00 43.20 1.90
3879 4244 4.820775 TCATAGGCTCCTCCTCAAGTTAT 58.179 43.478 0.00 0.00 43.20 1.89
3880 4245 4.265856 TCATAGGCTCCTCCTCAAGTTA 57.734 45.455 0.00 0.00 43.20 2.24
3881 4246 3.121929 TCATAGGCTCCTCCTCAAGTT 57.878 47.619 0.00 0.00 43.20 2.66
3882 4247 2.856760 TCATAGGCTCCTCCTCAAGT 57.143 50.000 0.00 0.00 43.20 3.16
3883 4248 4.703379 AATTCATAGGCTCCTCCTCAAG 57.297 45.455 0.00 0.00 43.20 3.02
3884 4249 4.228210 ACAAATTCATAGGCTCCTCCTCAA 59.772 41.667 0.00 0.00 43.20 3.02
3885 4250 3.782523 ACAAATTCATAGGCTCCTCCTCA 59.217 43.478 0.00 0.00 43.20 3.86
3886 4251 4.133078 CACAAATTCATAGGCTCCTCCTC 58.867 47.826 0.00 0.00 43.20 3.71
3888 4253 3.629398 CACACAAATTCATAGGCTCCTCC 59.371 47.826 0.00 0.00 0.00 4.30
3889 4254 3.629398 CCACACAAATTCATAGGCTCCTC 59.371 47.826 0.00 0.00 0.00 3.71
3890 4255 3.266772 TCCACACAAATTCATAGGCTCCT 59.733 43.478 0.00 0.00 0.00 3.69
3891 4256 3.620488 TCCACACAAATTCATAGGCTCC 58.380 45.455 0.00 0.00 0.00 4.70
3892 4257 3.065925 GCTCCACACAAATTCATAGGCTC 59.934 47.826 0.00 0.00 0.00 4.70
3893 4258 3.019564 GCTCCACACAAATTCATAGGCT 58.980 45.455 0.00 0.00 0.00 4.58
3894 4259 2.754552 TGCTCCACACAAATTCATAGGC 59.245 45.455 0.00 0.00 0.00 3.93
3895 4260 4.142315 CCTTGCTCCACACAAATTCATAGG 60.142 45.833 0.00 0.00 0.00 2.57
3896 4261 4.701651 TCCTTGCTCCACACAAATTCATAG 59.298 41.667 0.00 0.00 0.00 2.23
3897 4262 4.661222 TCCTTGCTCCACACAAATTCATA 58.339 39.130 0.00 0.00 0.00 2.15
3898 4263 3.499338 TCCTTGCTCCACACAAATTCAT 58.501 40.909 0.00 0.00 0.00 2.57
3899 4264 2.886523 CTCCTTGCTCCACACAAATTCA 59.113 45.455 0.00 0.00 0.00 2.57
3900 4265 2.887152 ACTCCTTGCTCCACACAAATTC 59.113 45.455 0.00 0.00 0.00 2.17
3901 4266 2.624838 CACTCCTTGCTCCACACAAATT 59.375 45.455 0.00 0.00 0.00 1.82
3940 4305 2.027073 CGTGCACGTGTATGCCACT 61.027 57.895 30.50 0.00 45.50 4.00
4000 4365 2.116827 TCAATTAACCGGCCATTCGT 57.883 45.000 0.00 0.00 0.00 3.85
4057 4435 1.593209 AGTTGCACCCACGTACACG 60.593 57.895 0.00 0.00 46.33 4.49
4158 4555 3.949132 TGCAATGCTAGTGTAATCACCA 58.051 40.909 6.82 0.00 44.83 4.17
4233 5048 5.916883 GCTATACGTACGTACAATGGAACAT 59.083 40.000 28.99 13.39 36.83 2.71
4237 5052 4.815846 TCAGCTATACGTACGTACAATGGA 59.184 41.667 28.99 20.01 33.01 3.41
4256 5071 3.573491 GGCGGGCACGTATTCAGC 61.573 66.667 11.45 0.00 43.45 4.26
4275 5091 1.374252 CCGGATATGCGTACCAGGC 60.374 63.158 15.77 0.00 0.00 4.85
4276 5092 0.243907 CTCCGGATATGCGTACCAGG 59.756 60.000 15.77 0.00 0.00 4.45
4316 5168 7.332182 TGCATGATCTTTGTACGTATAAACACA 59.668 33.333 12.80 12.54 0.00 3.72
4349 5212 4.020617 CGGGCCTGGAGTGCTTCA 62.021 66.667 2.57 0.00 0.00 3.02
4404 5273 2.941720 GACAAGCCTGCAGATAAAGGAG 59.058 50.000 17.39 0.00 35.40 3.69


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

AutoCloner maintained by Alex Coulton.