Multiple sequence alignment - TraesCS1D01G048000

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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 TraesCS1D01G048000 chr1D 100.000 2815 0 0 967 3781 28165354 28168168 0.000000e+00 5199.0
1 TraesCS1D01G048000 chr1D 100.000 640 0 0 1 640 28164388 28165027 0.000000e+00 1182.0
2 TraesCS1D01G048000 chr1B 94.397 1410 70 8 1946 3350 45479807 45481212 0.000000e+00 2158.0
3 TraesCS1D01G048000 chr1B 94.397 1410 70 8 1946 3350 45540868 45542273 0.000000e+00 2158.0
4 TraesCS1D01G048000 chr1B 89.252 1070 71 16 2714 3781 45253022 45254049 0.000000e+00 1299.0
5 TraesCS1D01G048000 chr1B 93.974 780 41 6 983 1757 45249234 45250012 0.000000e+00 1175.0
6 TraesCS1D01G048000 chr1B 93.292 641 34 4 1 640 45248241 45248873 0.000000e+00 937.0
7 TraesCS1D01G048000 chr1B 95.863 556 20 1 2029 2584 45252472 45253024 0.000000e+00 896.0
8 TraesCS1D01G048000 chr1B 88.053 452 25 14 1 450 45478243 45478667 3.370000e-140 508.0
9 TraesCS1D01G048000 chr1B 87.935 431 25 13 1 431 45535393 45535796 2.040000e-132 483.0
10 TraesCS1D01G048000 chr1B 87.935 431 25 13 1 431 45620656 45621059 2.040000e-132 483.0
11 TraesCS1D01G048000 chr1B 92.657 286 20 1 3494 3778 45598259 45598544 9.770000e-111 411.0
12 TraesCS1D01G048000 chr1B 90.728 302 22 4 1304 1599 45479507 45479808 7.610000e-107 398.0
13 TraesCS1D01G048000 chr1B 88.312 308 17 10 1738 2034 45250047 45250346 6.010000e-93 351.0
14 TraesCS1D01G048000 chr1B 94.180 189 11 0 452 640 45595767 45595955 4.780000e-74 289.0
15 TraesCS1D01G048000 chr1B 93.600 125 7 1 1476 1599 45540745 45540869 6.450000e-43 185.0
16 TraesCS1D01G048000 chr1B 95.161 62 3 0 2258 2319 44851703 44851764 8.640000e-17 99.0
17 TraesCS1D01G048000 chrUn 94.985 1356 63 4 1997 3350 400487679 400486327 0.000000e+00 2122.0
18 TraesCS1D01G048000 chrUn 81.501 573 91 7 2281 2851 37114274 37113715 1.240000e-124 457.0
19 TraesCS1D01G048000 chrUn 81.579 570 90 7 2281 2848 247033002 247033558 1.240000e-124 457.0
20 TraesCS1D01G048000 chrUn 81.501 573 91 7 2281 2851 300943003 300942444 1.240000e-124 457.0
21 TraesCS1D01G048000 chr3B 80.580 345 61 3 968 1312 825849331 825849669 1.040000e-65 261.0
22 TraesCS1D01G048000 chr3B 79.276 304 59 4 1009 1310 28607902 28607601 3.830000e-50 209.0
23 TraesCS1D01G048000 chr3A 80.656 305 57 2 1009 1312 748339494 748339797 6.310000e-58 235.0
24 TraesCS1D01G048000 chr2D 75.479 261 57 6 3525 3781 492725393 492725136 1.840000e-23 121.0
25 TraesCS1D01G048000 chr6A 85.417 96 14 0 3609 3704 453859432 453859337 2.400000e-17 100.0
26 TraesCS1D01G048000 chr5B 77.401 177 35 5 3530 3704 34907419 34907246 2.400000e-17 100.0
27 TraesCS1D01G048000 chr5D 100.000 40 0 0 3739 3778 453827654 453827615 1.460000e-09 75.0
28 TraesCS1D01G048000 chr7A 85.915 71 7 3 3603 3671 436895901 436895832 5.240000e-09 73.1
29 TraesCS1D01G048000 chr5A 90.476 42 1 2 3527 3565 332327272 332327313 7.000000e-03 52.8


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 TraesCS1D01G048000 chr1D 28164388 28168168 3780 False 3190.500000 5199 100.000000 1 3781 2 chr1D.!!$F1 3780
1 TraesCS1D01G048000 chr1B 45540745 45542273 1528 False 1171.500000 2158 93.998500 1476 3350 2 chr1B.!!$F6 1874
2 TraesCS1D01G048000 chr1B 45478243 45481212 2969 False 1021.333333 2158 91.059333 1 3350 3 chr1B.!!$F5 3349
3 TraesCS1D01G048000 chr1B 45248241 45254049 5808 False 931.600000 1299 92.138600 1 3781 5 chr1B.!!$F4 3780
4 TraesCS1D01G048000 chr1B 45595767 45598544 2777 False 350.000000 411 93.418500 452 3778 2 chr1B.!!$F7 3326
5 TraesCS1D01G048000 chrUn 400486327 400487679 1352 True 2122.000000 2122 94.985000 1997 3350 1 chrUn.!!$R3 1353
6 TraesCS1D01G048000 chrUn 37113715 37114274 559 True 457.000000 457 81.501000 2281 2851 1 chrUn.!!$R1 570
7 TraesCS1D01G048000 chrUn 247033002 247033558 556 False 457.000000 457 81.579000 2281 2848 1 chrUn.!!$F1 567
8 TraesCS1D01G048000 chrUn 300942444 300943003 559 True 457.000000 457 81.501000 2281 2851 1 chrUn.!!$R2 570

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
498 502 0.110373 CGCGCAAAAGTCTACCCAAC 60.110 55.0 8.75 0.0 0.0 3.77 F
1296 1318 0.102481 TCGCGCTTCTCAATACCCTC 59.898 55.0 5.56 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1321 1343 0.461961 GCCTCAACGAGCTCCTATGT 59.538 55.0 8.47 0.0 0.0 2.29 R
2899 5125 0.177373 CTACCTCCCGCCCTAACAAC 59.823 60.0 0.00 0.0 0.0 3.32 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
50 51 9.144085 GTTCTAGTAAATTTACGCAATCAATCG 57.856 33.333 19.92 0.31 38.65 3.34
227 228 5.695851 AGCTCAGATAAAACAAACTGTGG 57.304 39.130 0.00 0.00 0.00 4.17
296 297 6.092259 ACGCAATTAAACCAGAACTAAGCTAG 59.908 38.462 0.00 0.00 0.00 3.42
297 298 6.312918 CGCAATTAAACCAGAACTAAGCTAGA 59.687 38.462 0.00 0.00 0.00 2.43
298 299 7.465173 GCAATTAAACCAGAACTAAGCTAGAC 58.535 38.462 0.00 0.00 0.00 2.59
306 307 8.172352 ACCAGAACTAAGCTAGACATATACTG 57.828 38.462 0.00 0.00 0.00 2.74
308 309 9.286170 CCAGAACTAAGCTAGACATATACTGTA 57.714 37.037 0.00 0.00 38.54 2.74
339 340 5.047943 ACAGAACTACAACGAGTAAGCTCAT 60.048 40.000 0.00 0.00 41.71 2.90
363 364 3.648339 AAACAAATTGCAGCGACATCT 57.352 38.095 0.00 0.00 0.00 2.90
377 379 7.356641 CAGCGACATCTACTGCATTATTATT 57.643 36.000 0.00 0.00 0.00 1.40
378 380 7.451429 CAGCGACATCTACTGCATTATTATTC 58.549 38.462 0.00 0.00 0.00 1.75
498 502 0.110373 CGCGCAAAAGTCTACCCAAC 60.110 55.000 8.75 0.00 0.00 3.77
564 568 2.644299 CTGGCCATGATTAGGGTCCATA 59.356 50.000 5.51 0.00 34.84 2.74
565 569 3.059853 TGGCCATGATTAGGGTCCATAA 58.940 45.455 0.00 0.00 31.91 1.90
566 570 3.662148 TGGCCATGATTAGGGTCCATAAT 59.338 43.478 8.52 8.52 31.91 1.28
567 571 4.855018 TGGCCATGATTAGGGTCCATAATA 59.145 41.667 8.75 0.00 31.91 0.98
568 572 5.495802 TGGCCATGATTAGGGTCCATAATAT 59.504 40.000 8.75 1.71 31.91 1.28
569 573 5.829924 GGCCATGATTAGGGTCCATAATATG 59.170 44.000 8.75 11.69 0.00 1.78
610 614 7.264373 AGATTAAAAATTCCCTAGCATGACG 57.736 36.000 0.00 0.00 0.00 4.35
1003 1025 4.964897 AGACAGAGAGAGAGAGAGAGATGA 59.035 45.833 0.00 0.00 0.00 2.92
1019 1041 2.045926 GACAAGCATGGAGGGCGT 60.046 61.111 0.00 0.00 36.08 5.68
1028 1050 1.561769 ATGGAGGGCGTGGTGATCAA 61.562 55.000 0.00 0.00 0.00 2.57
1054 1076 1.347707 GGACTGTGGAGGTCAATGACA 59.652 52.381 15.86 0.00 35.61 3.58
1058 1080 3.055530 ACTGTGGAGGTCAATGACATCTC 60.056 47.826 24.28 16.89 42.11 2.75
1119 1141 2.490991 GGGACTGTGTTGTTCCTACAC 58.509 52.381 0.00 0.00 44.73 2.90
1122 1144 2.234300 CTGTGTTGTTCCTACACGGT 57.766 50.000 8.87 0.00 46.85 4.83
1215 1237 2.109181 GACCTCCGTGGCTATGGC 59.891 66.667 2.82 0.00 40.22 4.40
1276 1298 1.265905 TCCATATCGTCGGTGACATCG 59.734 52.381 0.39 0.39 32.09 3.84
1296 1318 0.102481 TCGCGCTTCTCAATACCCTC 59.898 55.000 5.56 0.00 0.00 4.30
1318 1340 3.026694 GGGCTTGCAAAGGTATGATTCT 58.973 45.455 0.00 0.00 46.35 2.40
1321 1343 4.640201 GGCTTGCAAAGGTATGATTCTGTA 59.360 41.667 0.00 0.00 46.35 2.74
1355 1377 2.049627 GAGGCCGGCCATTCTGATCT 62.050 60.000 45.13 23.42 38.92 2.75
1364 1386 4.241681 GGCCATTCTGATCTATCGAAGAC 58.758 47.826 0.00 0.00 42.51 3.01
1365 1387 4.021544 GGCCATTCTGATCTATCGAAGACT 60.022 45.833 0.00 0.00 42.51 3.24
1366 1388 4.922692 GCCATTCTGATCTATCGAAGACTG 59.077 45.833 0.00 0.00 42.51 3.51
1413 1437 6.926272 TGTGGTTCATAGCCAAAATTTAACAC 59.074 34.615 0.00 0.00 37.81 3.32
1417 1441 7.116233 GGTTCATAGCCAAAATTTAACACACTG 59.884 37.037 0.00 0.00 0.00 3.66
1431 1455 4.737855 ACACACTGTACTGAGTCAACTT 57.262 40.909 6.77 0.00 0.00 2.66
1521 1549 6.385033 AGTCCTTAAGTGTATGTACGTGTTC 58.615 40.000 0.00 0.00 0.00 3.18
1597 1625 6.371809 ACTTTTGTCGATCAAACTTGCTAA 57.628 33.333 11.15 0.00 44.39 3.09
1622 1650 2.543777 AGTGTGGCAAACGTAGACAT 57.456 45.000 1.33 0.00 0.00 3.06
1636 1664 4.330074 ACGTAGACATGCTAATCTTTGTGC 59.670 41.667 0.00 0.00 0.00 4.57
1639 1667 3.693085 AGACATGCTAATCTTTGTGCTGG 59.307 43.478 0.00 0.00 0.00 4.85
1660 1688 3.007635 GCGGTCCTTTTGCACTTAGTAT 58.992 45.455 0.00 0.00 0.00 2.12
1664 1692 6.183360 GCGGTCCTTTTGCACTTAGTATTAAT 60.183 38.462 0.00 0.00 0.00 1.40
1766 1850 9.588096 AGTGGGAAAGTTCTTTTAATGATAAGT 57.412 29.630 0.00 0.00 0.00 2.24
1818 1902 0.740737 ATAAAGATGCAAGTGGCCGC 59.259 50.000 8.71 8.71 43.89 6.53
1820 1904 1.181098 AAAGATGCAAGTGGCCGCTT 61.181 50.000 26.01 26.01 43.89 4.68
1861 1945 5.136105 GGATAATGGCTGGAGATCACTTTT 58.864 41.667 0.00 0.00 0.00 2.27
1862 1946 5.595952 GGATAATGGCTGGAGATCACTTTTT 59.404 40.000 0.00 0.00 0.00 1.94
1893 1977 4.472833 AGAAAGGCTGGAGATCACTTATGT 59.527 41.667 0.00 0.00 0.00 2.29
1898 1982 5.053145 GGCTGGAGATCACTTATGTTGTAG 58.947 45.833 0.00 0.00 0.00 2.74
1901 1985 7.437748 GCTGGAGATCACTTATGTTGTAGTAT 58.562 38.462 0.00 0.00 0.00 2.12
1902 1986 7.383572 GCTGGAGATCACTTATGTTGTAGTATG 59.616 40.741 0.00 0.00 0.00 2.39
1904 1988 8.977412 TGGAGATCACTTATGTTGTAGTATGAA 58.023 33.333 0.00 0.00 0.00 2.57
1905 1989 9.817809 GGAGATCACTTATGTTGTAGTATGAAA 57.182 33.333 0.00 0.00 0.00 2.69
1907 1991 9.601217 AGATCACTTATGTTGTAGTATGAAACC 57.399 33.333 0.00 0.00 0.00 3.27
1922 2012 5.743636 ATGAAACCATTAGTGTGCCAAAT 57.256 34.783 0.00 0.00 0.00 2.32
1932 2022 2.028748 AGTGTGCCAAATGATCAAAGCC 60.029 45.455 0.00 0.00 0.00 4.35
1934 2024 2.633967 TGTGCCAAATGATCAAAGCCTT 59.366 40.909 0.00 0.00 0.00 4.35
1937 2027 3.579586 TGCCAAATGATCAAAGCCTTCTT 59.420 39.130 0.00 0.00 0.00 2.52
1938 2028 4.179298 GCCAAATGATCAAAGCCTTCTTC 58.821 43.478 0.00 0.00 0.00 2.87
1939 2029 4.322198 GCCAAATGATCAAAGCCTTCTTCA 60.322 41.667 0.00 0.00 0.00 3.02
1944 2039 8.780249 CAAATGATCAAAGCCTTCTTCAAAAAT 58.220 29.630 0.00 0.00 0.00 1.82
1975 2070 5.580691 TCAATGCCTTTGTATCGAACTAGTG 59.419 40.000 0.00 0.00 36.65 2.74
1977 2072 5.648178 TGCCTTTGTATCGAACTAGTGTA 57.352 39.130 0.00 0.00 0.00 2.90
1981 2078 7.919091 TGCCTTTGTATCGAACTAGTGTATTAG 59.081 37.037 0.00 0.00 0.00 1.73
2042 2139 3.447586 GTGATGAGCCTTAGTACCACTGA 59.552 47.826 0.00 0.00 0.00 3.41
2135 4360 2.259204 GCGTGGTACGTGTGCCTA 59.741 61.111 8.60 0.00 44.73 3.93
2621 4846 1.538687 CGTACCACTTCGAGGGGGTT 61.539 60.000 27.95 11.26 45.32 4.11
2623 4848 1.252904 TACCACTTCGAGGGGGTTCG 61.253 60.000 27.95 0.00 45.32 3.95
2642 4867 2.504519 GAGTACATCCACGGGGGC 59.495 66.667 2.42 0.00 36.21 5.80
2769 4994 4.926238 ACGACTTCATCATCAAGTTCTCAC 59.074 41.667 0.00 0.00 34.10 3.51
2848 5073 4.403015 TGATCTTGCGTGTGTATGTTTG 57.597 40.909 0.00 0.00 0.00 2.93
2865 5090 6.906157 ATGTTTGTTCTTGGATCATCTGTT 57.094 33.333 0.00 0.00 0.00 3.16
2874 5099 5.964477 TCTTGGATCATCTGTTTACCTACCT 59.036 40.000 0.00 0.00 0.00 3.08
2886 5112 5.046159 TGTTTACCTACCTGTTCCGATTGAT 60.046 40.000 0.00 0.00 0.00 2.57
2899 5125 9.603298 CTGTTCCGATTGATAAATGTTGATATG 57.397 33.333 0.00 0.00 0.00 1.78
2910 5136 5.499139 AATGTTGATATGTTGTTAGGGCG 57.501 39.130 0.00 0.00 0.00 6.13
2934 5160 2.658489 AGGTAGGGTTTACCAGAGAGGA 59.342 50.000 6.18 0.00 43.89 3.71
2946 5172 8.697292 GTTTACCAGAGAGGAGATGTACTTTAT 58.303 37.037 0.00 0.00 41.22 1.40
3069 7598 2.223340 GCGATTCATCCATGTTGTCACC 60.223 50.000 0.00 0.00 0.00 4.02
3090 7619 0.250295 CTCCTCTTTGCCACCGTCAA 60.250 55.000 0.00 0.00 0.00 3.18
3150 7679 2.490991 CGGTGAGCATGATCATCACAT 58.509 47.619 23.08 4.66 44.08 3.21
3155 7684 4.334481 GTGAGCATGATCATCACATGTCAA 59.666 41.667 17.94 0.00 44.52 3.18
3194 7723 6.204688 ACGAGTCTGTTGCTTCATCAAATTTA 59.795 34.615 0.00 0.00 0.00 1.40
3207 7736 6.626302 TCATCAAATTTAAATTCCACGGACC 58.374 36.000 13.68 0.00 0.00 4.46
3209 7738 4.833380 TCAAATTTAAATTCCACGGACCCA 59.167 37.500 13.68 0.00 0.00 4.51
3211 7740 5.337578 AATTTAAATTCCACGGACCCATG 57.662 39.130 7.64 0.00 0.00 3.66
3254 7783 5.414360 TGTCTCTTCTACACTCAATGCATC 58.586 41.667 0.00 0.00 0.00 3.91
3294 7823 1.062428 CCCCTAGTCTATGACCCACCA 60.062 57.143 0.00 0.00 32.18 4.17
3295 7824 2.427889 CCCCTAGTCTATGACCCACCAT 60.428 54.545 0.00 0.00 32.18 3.55
3296 7825 2.634940 CCCTAGTCTATGACCCACCATG 59.365 54.545 0.00 0.00 32.18 3.66
3297 7826 3.309296 CCTAGTCTATGACCCACCATGT 58.691 50.000 0.00 0.00 32.18 3.21
3298 7827 3.322254 CCTAGTCTATGACCCACCATGTC 59.678 52.174 0.00 0.00 32.18 3.06
3299 7828 1.757118 AGTCTATGACCCACCATGTCG 59.243 52.381 0.00 0.00 35.46 4.35
3300 7829 1.480954 GTCTATGACCCACCATGTCGT 59.519 52.381 0.00 0.00 35.46 4.34
3301 7830 1.754803 TCTATGACCCACCATGTCGTC 59.245 52.381 0.00 0.00 35.46 4.20
3302 7831 0.458260 TATGACCCACCATGTCGTCG 59.542 55.000 0.00 0.00 35.46 5.12
3303 7832 1.541310 ATGACCCACCATGTCGTCGT 61.541 55.000 0.00 0.00 35.46 4.34
3304 7833 1.005394 GACCCACCATGTCGTCGTT 60.005 57.895 0.00 0.00 0.00 3.85
3350 7879 9.565213 CTTACCTACACTACACATACTTGTAAC 57.435 37.037 0.00 0.00 33.76 2.50
3351 7880 6.615088 ACCTACACTACACATACTTGTAACG 58.385 40.000 0.00 0.00 33.76 3.18
3352 7881 5.514204 CCTACACTACACATACTTGTAACGC 59.486 44.000 0.00 0.00 33.76 4.84
3353 7882 3.916172 ACACTACACATACTTGTAACGCG 59.084 43.478 3.53 3.53 33.76 6.01
3354 7883 3.916172 CACTACACATACTTGTAACGCGT 59.084 43.478 5.58 5.58 33.76 6.01
3355 7884 4.029861 CACTACACATACTTGTAACGCGTC 59.970 45.833 14.44 0.25 33.76 5.19
3356 7885 2.331194 ACACATACTTGTAACGCGTCC 58.669 47.619 14.44 7.13 33.76 4.79
3357 7886 1.657094 CACATACTTGTAACGCGTCCC 59.343 52.381 14.44 6.70 33.76 4.46
3358 7887 1.273048 ACATACTTGTAACGCGTCCCA 59.727 47.619 14.44 9.78 33.16 4.37
3359 7888 2.288948 ACATACTTGTAACGCGTCCCAA 60.289 45.455 14.44 17.24 33.16 4.12
3360 7889 2.747396 TACTTGTAACGCGTCCCAAT 57.253 45.000 14.44 10.69 0.00 3.16
3361 7890 1.435577 ACTTGTAACGCGTCCCAATC 58.564 50.000 14.44 0.13 0.00 2.67
3362 7891 1.270412 ACTTGTAACGCGTCCCAATCA 60.270 47.619 14.44 3.01 0.00 2.57
3363 7892 1.127951 CTTGTAACGCGTCCCAATCAC 59.872 52.381 14.44 2.83 0.00 3.06
3364 7893 0.319083 TGTAACGCGTCCCAATCACT 59.681 50.000 14.44 0.00 0.00 3.41
3365 7894 1.545136 TGTAACGCGTCCCAATCACTA 59.455 47.619 14.44 0.00 0.00 2.74
3366 7895 2.190981 GTAACGCGTCCCAATCACTAG 58.809 52.381 14.44 0.00 0.00 2.57
3367 7896 0.606604 AACGCGTCCCAATCACTAGT 59.393 50.000 14.44 0.00 0.00 2.57
3368 7897 1.466856 ACGCGTCCCAATCACTAGTA 58.533 50.000 5.58 0.00 0.00 1.82
3369 7898 1.133790 ACGCGTCCCAATCACTAGTAC 59.866 52.381 5.58 0.00 0.00 2.73
3370 7899 1.404391 CGCGTCCCAATCACTAGTACT 59.596 52.381 0.00 0.00 0.00 2.73
3371 7900 2.159282 CGCGTCCCAATCACTAGTACTT 60.159 50.000 0.00 0.00 0.00 2.24
3372 7901 3.187700 GCGTCCCAATCACTAGTACTTG 58.812 50.000 0.00 0.59 0.00 3.16
3373 7902 3.368116 GCGTCCCAATCACTAGTACTTGT 60.368 47.826 0.00 1.41 0.00 3.16
3374 7903 4.142315 GCGTCCCAATCACTAGTACTTGTA 60.142 45.833 9.68 0.28 0.00 2.41
3375 7904 5.579718 CGTCCCAATCACTAGTACTTGTAG 58.420 45.833 9.68 0.00 0.00 2.74
3408 7937 1.278985 TCGCCACCATCTCACTTGAAT 59.721 47.619 0.00 0.00 0.00 2.57
3438 7967 7.484641 GTGCGTTCATACATGATACATTGTTTT 59.515 33.333 0.00 0.00 36.56 2.43
3441 7970 9.553418 CGTTCATACATGATACATTGTTTTCAA 57.447 29.630 0.00 0.00 39.26 2.69
3456 7985 5.036090 TGTTTTCAATATAGCATTGCAGCG 58.964 37.500 11.91 0.00 40.15 5.18
3487 8016 4.576463 AGCATTGGTTTGAGATATTCGACC 59.424 41.667 0.00 0.00 35.99 4.79
3488 8017 4.335315 GCATTGGTTTGAGATATTCGACCA 59.665 41.667 0.00 0.00 40.67 4.02
3554 8084 2.157738 CTCCAAAGCTGACCCTCAAAG 58.842 52.381 0.00 0.00 0.00 2.77
3633 8163 2.270850 GGCTATCCAACCGTGCCA 59.729 61.111 0.00 0.00 42.79 4.92
3673 8203 4.495844 GGATTTCAACAATCCGGACGATTC 60.496 45.833 6.12 0.00 39.28 2.52
3704 8234 7.955324 CGAACACGACATAATTCAACATAGTTT 59.045 33.333 0.00 0.00 0.00 2.66
3705 8235 8.948853 AACACGACATAATTCAACATAGTTTG 57.051 30.769 0.00 0.00 0.00 2.93
3730 8260 7.819415 TGGATAGAAAATAGCATAAGTCATCCG 59.181 37.037 0.00 0.00 31.67 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 6.512253 GCCGTTTATAGTAAATTACCAGCCAC 60.512 42.308 0.00 0.00 0.00 5.01
227 228 6.018262 TGCACTAATAATACAATGGAAGTCGC 60.018 38.462 0.00 0.00 0.00 5.19
306 307 8.739649 ACTCGTTGTAGTTCTGTTTTCTATAC 57.260 34.615 0.00 0.00 0.00 1.47
308 309 9.408069 CTTACTCGTTGTAGTTCTGTTTTCTAT 57.592 33.333 0.00 0.00 32.08 1.98
339 340 6.851609 AGATGTCGCTGCAATTTGTTTTATA 58.148 32.000 0.00 0.00 0.00 0.98
390 392 8.659491 GTGGTTCATATATGTACATGTATGCAG 58.341 37.037 32.16 18.68 40.50 4.41
479 483 0.110373 GTTGGGTAGACTTTTGCGCG 60.110 55.000 0.00 0.00 0.00 6.86
537 541 4.729868 ACCCTAATCATGGCCAGTTTATC 58.270 43.478 13.05 0.00 0.00 1.75
543 547 0.846015 TGGACCCTAATCATGGCCAG 59.154 55.000 13.05 3.43 0.00 4.85
610 614 4.850680 TGTAGATTGGGTGGTTGTAATCC 58.149 43.478 0.00 0.00 31.56 3.01
966 970 3.699538 TCTCTGTCTTAGTGTGTGTGTGT 59.300 43.478 0.00 0.00 0.00 3.72
967 971 4.036852 TCTCTCTGTCTTAGTGTGTGTGTG 59.963 45.833 0.00 0.00 0.00 3.82
968 972 4.207955 TCTCTCTGTCTTAGTGTGTGTGT 58.792 43.478 0.00 0.00 0.00 3.72
969 973 4.517075 TCTCTCTCTGTCTTAGTGTGTGTG 59.483 45.833 0.00 0.00 0.00 3.82
970 974 4.720046 TCTCTCTCTGTCTTAGTGTGTGT 58.280 43.478 0.00 0.00 0.00 3.72
971 975 5.000591 TCTCTCTCTCTGTCTTAGTGTGTG 58.999 45.833 0.00 0.00 0.00 3.82
972 976 5.012664 TCTCTCTCTCTCTGTCTTAGTGTGT 59.987 44.000 0.00 0.00 0.00 3.72
973 977 5.487433 TCTCTCTCTCTCTGTCTTAGTGTG 58.513 45.833 0.00 0.00 0.00 3.82
974 978 5.483937 TCTCTCTCTCTCTCTGTCTTAGTGT 59.516 44.000 0.00 0.00 0.00 3.55
975 979 5.977635 TCTCTCTCTCTCTCTGTCTTAGTG 58.022 45.833 0.00 0.00 0.00 2.74
976 980 5.958380 TCTCTCTCTCTCTCTCTGTCTTAGT 59.042 44.000 0.00 0.00 0.00 2.24
977 981 6.471233 TCTCTCTCTCTCTCTCTGTCTTAG 57.529 45.833 0.00 0.00 0.00 2.18
978 982 6.611236 TCATCTCTCTCTCTCTCTCTGTCTTA 59.389 42.308 0.00 0.00 0.00 2.10
979 983 5.426509 TCATCTCTCTCTCTCTCTCTGTCTT 59.573 44.000 0.00 0.00 0.00 3.01
980 984 4.964897 TCATCTCTCTCTCTCTCTCTGTCT 59.035 45.833 0.00 0.00 0.00 3.41
981 985 5.053145 GTCATCTCTCTCTCTCTCTCTGTC 58.947 50.000 0.00 0.00 0.00 3.51
1003 1025 2.360350 CACGCCCTCCATGCTTGT 60.360 61.111 0.00 0.00 0.00 3.16
1028 1050 3.314331 CCTCCACAGTCCGGTGCT 61.314 66.667 0.00 0.00 37.46 4.40
1054 1076 2.583319 CGCCACGTGCATCGAGAT 60.583 61.111 10.91 0.00 42.86 2.75
1104 1126 2.695127 AACCGTGTAGGAACAACACA 57.305 45.000 7.10 0.00 46.05 3.72
1122 1144 1.483415 GTGTACCATAGCTCCGGGAAA 59.517 52.381 0.00 0.00 0.00 3.13
1276 1298 0.179108 AGGGTATTGAGAAGCGCGAC 60.179 55.000 12.10 0.04 0.00 5.19
1296 1318 1.392589 ATCATACCTTTGCAAGCCCG 58.607 50.000 0.00 0.00 0.00 6.13
1318 1340 2.688446 CCTCAACGAGCTCCTATGTACA 59.312 50.000 8.47 0.00 0.00 2.90
1321 1343 0.461961 GCCTCAACGAGCTCCTATGT 59.538 55.000 8.47 0.00 0.00 2.29
1374 1398 2.495155 ACCACACAAGCATGCTGATA 57.505 45.000 23.48 0.00 0.00 2.15
1413 1437 4.989168 GGGTTAAGTTGACTCAGTACAGTG 59.011 45.833 0.00 0.00 0.00 3.66
1417 1441 4.392138 GCATGGGTTAAGTTGACTCAGTAC 59.608 45.833 6.50 0.00 29.67 2.73
1597 1625 6.167685 TGTCTACGTTTGCCACACTATAATT 58.832 36.000 0.00 0.00 0.00 1.40
1622 1650 0.804364 CGCCAGCACAAAGATTAGCA 59.196 50.000 0.00 0.00 0.00 3.49
1636 1664 1.455383 AAGTGCAAAAGGACCGCCAG 61.455 55.000 0.00 0.00 36.29 4.85
1639 1667 1.235724 ACTAAGTGCAAAAGGACCGC 58.764 50.000 0.00 0.00 0.00 5.68
1708 1738 7.499321 AAACAAAACTGATACCGATGTAACA 57.501 32.000 0.00 0.00 0.00 2.41
1714 1744 5.470777 TCCGAAAAACAAAACTGATACCGAT 59.529 36.000 0.00 0.00 0.00 4.18
1717 1747 7.749126 CACTATCCGAAAAACAAAACTGATACC 59.251 37.037 0.00 0.00 0.00 2.73
1723 1753 5.134661 TCCCACTATCCGAAAAACAAAACT 58.865 37.500 0.00 0.00 0.00 2.66
1764 1848 8.621532 TGCAGAAATCTTAAGTGTAAATGACT 57.378 30.769 1.63 0.00 0.00 3.41
1766 1850 8.846943 TCTGCAGAAATCTTAAGTGTAAATGA 57.153 30.769 15.67 0.00 0.00 2.57
1779 1863 9.896645 TCTTTATCACTAAATCTGCAGAAATCT 57.103 29.630 22.50 7.92 0.00 2.40
1785 1869 7.255491 TGCATCTTTATCACTAAATCTGCAG 57.745 36.000 7.63 7.63 38.21 4.41
1795 1879 3.019564 GGCCACTTGCATCTTTATCACT 58.980 45.455 0.00 0.00 43.89 3.41
1838 1922 4.363991 AAGTGATCTCCAGCCATTATCC 57.636 45.455 0.00 0.00 0.00 2.59
1870 1954 4.472833 ACATAAGTGATCTCCAGCCTTTCT 59.527 41.667 0.00 0.00 0.00 2.52
1893 1977 6.373216 GGCACACTAATGGTTTCATACTACAA 59.627 38.462 0.00 0.00 32.44 2.41
1898 1982 5.637006 TTGGCACACTAATGGTTTCATAC 57.363 39.130 0.00 0.00 39.29 2.39
1901 1985 4.586421 TCATTTGGCACACTAATGGTTTCA 59.414 37.500 9.16 0.00 40.97 2.69
1902 1986 5.132897 TCATTTGGCACACTAATGGTTTC 57.867 39.130 9.16 0.00 40.97 2.78
1904 1988 4.771577 TGATCATTTGGCACACTAATGGTT 59.228 37.500 9.16 0.00 40.97 3.67
1905 1989 4.343231 TGATCATTTGGCACACTAATGGT 58.657 39.130 9.16 2.90 40.97 3.55
1906 1990 4.987408 TGATCATTTGGCACACTAATGG 57.013 40.909 9.16 0.00 40.97 3.16
1907 1991 5.290158 GCTTTGATCATTTGGCACACTAATG 59.710 40.000 0.00 3.72 41.64 1.90
1922 2012 9.260002 GTTTATTTTTGAAGAAGGCTTTGATCA 57.740 29.630 0.00 3.85 33.61 2.92
1932 2022 8.375465 GGCATTGATCGTTTATTTTTGAAGAAG 58.625 33.333 0.00 0.00 0.00 2.85
1934 2024 7.601856 AGGCATTGATCGTTTATTTTTGAAGA 58.398 30.769 0.00 0.00 0.00 2.87
1937 2027 7.655328 ACAAAGGCATTGATCGTTTATTTTTGA 59.345 29.630 9.74 0.00 41.85 2.69
1938 2028 7.795859 ACAAAGGCATTGATCGTTTATTTTTG 58.204 30.769 9.74 0.00 41.85 2.44
1939 2029 7.961325 ACAAAGGCATTGATCGTTTATTTTT 57.039 28.000 9.74 0.00 41.85 1.94
1944 2039 5.813157 TCGATACAAAGGCATTGATCGTTTA 59.187 36.000 23.16 11.53 42.74 2.01
1975 2070 6.405619 GGACTGGAGACACCACTAACTAATAC 60.406 46.154 0.00 0.00 44.64 1.89
1977 2072 4.466726 GGACTGGAGACACCACTAACTAAT 59.533 45.833 0.00 0.00 44.64 1.73
1981 2078 1.968493 TGGACTGGAGACACCACTAAC 59.032 52.381 0.00 0.00 44.64 2.34
2042 2139 7.921786 TTCAAATTTCTCCGTATGAAGACAT 57.078 32.000 0.00 0.00 40.16 3.06
2162 4387 2.280797 GCGAGGCTGGTGTTGACA 60.281 61.111 0.00 0.00 0.00 3.58
2384 4609 1.234821 TGTTGTCGTGCATTTCCTCC 58.765 50.000 0.00 0.00 0.00 4.30
2621 4846 1.755395 CCCGTGGATGTACTCCCGA 60.755 63.158 16.24 0.00 44.23 5.14
2623 4848 2.440817 CCCCCGTGGATGTACTCCC 61.441 68.421 8.36 3.66 44.23 4.30
2642 4867 1.374252 CACGTCCTCCTTGAACCCG 60.374 63.158 0.00 0.00 0.00 5.28
2705 4930 2.372890 TGCCCTCTCCAGCTGGATG 61.373 63.158 35.11 27.54 44.46 3.51
2769 4994 3.459598 TGAATCCCATCTTAGGTTGGAGG 59.540 47.826 3.57 0.00 35.01 4.30
2848 5073 6.539103 GGTAGGTAAACAGATGATCCAAGAAC 59.461 42.308 0.00 0.00 0.00 3.01
2865 5090 6.795144 TTATCAATCGGAACAGGTAGGTAA 57.205 37.500 0.00 0.00 0.00 2.85
2874 5099 9.119418 ACATATCAACATTTATCAATCGGAACA 57.881 29.630 0.00 0.00 0.00 3.18
2886 5112 6.038825 CCGCCCTAACAACATATCAACATTTA 59.961 38.462 0.00 0.00 0.00 1.40
2899 5125 0.177373 CTACCTCCCGCCCTAACAAC 59.823 60.000 0.00 0.00 0.00 3.32
2910 5136 2.117051 CTCTGGTAAACCCTACCTCCC 58.883 57.143 2.81 0.00 38.39 4.30
3069 7598 0.390472 GACGGTGGCAAAGAGGAGAG 60.390 60.000 0.00 0.00 0.00 3.20
3140 7669 3.752747 TGGTGTGTTGACATGTGATGATC 59.247 43.478 1.15 0.00 33.63 2.92
3150 7679 2.160615 CGTGAAAAGTGGTGTGTTGACA 59.839 45.455 0.00 0.00 0.00 3.58
3155 7684 2.093658 AGACTCGTGAAAAGTGGTGTGT 60.094 45.455 0.00 0.00 0.00 3.72
3194 7723 2.025416 TCATCATGGGTCCGTGGAATTT 60.025 45.455 9.12 0.00 33.99 1.82
3207 7736 1.364901 GCGCCCCAAATCATCATGG 59.635 57.895 0.00 0.00 36.42 3.66
3209 7738 1.076118 TGGCGCCCCAAATCATCAT 60.076 52.632 26.77 0.00 38.46 2.45
3211 7740 2.785425 GGTGGCGCCCCAAATCATC 61.785 63.158 26.77 0.00 44.33 2.92
3254 7783 2.359531 GGAAGGAGTGTGAGGACGATAG 59.640 54.545 0.00 0.00 46.19 2.08
3294 7823 1.259507 CGGTGACAAAAACGACGACAT 59.740 47.619 0.00 0.00 0.00 3.06
3295 7824 0.646381 CGGTGACAAAAACGACGACA 59.354 50.000 0.00 0.00 0.00 4.35
3296 7825 0.042794 CCGGTGACAAAAACGACGAC 60.043 55.000 0.00 0.00 0.00 4.34
3297 7826 0.459934 ACCGGTGACAAAAACGACGA 60.460 50.000 6.12 0.00 0.00 4.20
3298 7827 0.315544 CACCGGTGACAAAAACGACG 60.316 55.000 31.31 0.00 0.00 5.12
3299 7828 0.028374 CCACCGGTGACAAAAACGAC 59.972 55.000 36.07 0.00 0.00 4.34
3300 7829 0.392729 ACCACCGGTGACAAAAACGA 60.393 50.000 36.07 0.00 32.98 3.85
3301 7830 1.262151 CTACCACCGGTGACAAAAACG 59.738 52.381 36.07 18.20 36.19 3.60
3302 7831 1.002142 GCTACCACCGGTGACAAAAAC 60.002 52.381 36.07 13.88 36.19 2.43
3303 7832 1.310904 GCTACCACCGGTGACAAAAA 58.689 50.000 36.07 12.48 36.19 1.94
3304 7833 0.535553 GGCTACCACCGGTGACAAAA 60.536 55.000 36.07 14.22 36.19 2.44
3350 7879 1.404391 AGTACTAGTGATTGGGACGCG 59.596 52.381 3.53 3.53 0.00 6.01
3351 7880 3.187700 CAAGTACTAGTGATTGGGACGC 58.812 50.000 5.39 0.00 0.00 5.19
3352 7881 4.451629 ACAAGTACTAGTGATTGGGACG 57.548 45.455 19.88 0.00 0.00 4.79
3353 7882 6.152323 TCACTACAAGTACTAGTGATTGGGAC 59.848 42.308 18.80 4.65 43.34 4.46
3354 7883 6.250711 TCACTACAAGTACTAGTGATTGGGA 58.749 40.000 18.80 11.93 43.34 4.37
3355 7884 6.525578 TCACTACAAGTACTAGTGATTGGG 57.474 41.667 18.80 15.43 43.34 4.12
3361 7890 5.394224 CCCACCATCACTACAAGTACTAGTG 60.394 48.000 15.38 15.38 41.71 2.74
3362 7891 4.710375 CCCACCATCACTACAAGTACTAGT 59.290 45.833 0.00 0.00 0.00 2.57
3363 7892 4.441634 GCCCACCATCACTACAAGTACTAG 60.442 50.000 0.00 0.00 0.00 2.57
3364 7893 3.449737 GCCCACCATCACTACAAGTACTA 59.550 47.826 0.00 0.00 0.00 1.82
3365 7894 2.236395 GCCCACCATCACTACAAGTACT 59.764 50.000 0.00 0.00 0.00 2.73
3366 7895 2.027561 TGCCCACCATCACTACAAGTAC 60.028 50.000 0.00 0.00 0.00 2.73
3367 7896 2.261729 TGCCCACCATCACTACAAGTA 58.738 47.619 0.00 0.00 0.00 2.24
3368 7897 1.064003 TGCCCACCATCACTACAAGT 58.936 50.000 0.00 0.00 0.00 3.16
3369 7898 2.425143 ATGCCCACCATCACTACAAG 57.575 50.000 0.00 0.00 0.00 3.16
3438 7967 2.549329 CACCGCTGCAATGCTATATTGA 59.451 45.455 6.82 0.00 0.00 2.57
3441 7970 1.527034 CCACCGCTGCAATGCTATAT 58.473 50.000 6.82 0.00 0.00 0.86
3467 7996 4.570772 CGTGGTCGAATATCTCAAACCAAT 59.429 41.667 0.00 0.00 39.83 3.16
3507 8036 2.490328 AAGCAACCAACATGAACACG 57.510 45.000 0.00 0.00 0.00 4.49
3554 8084 1.583054 GGGACGGATACAATGTCTGC 58.417 55.000 0.00 0.00 33.21 4.26
3593 8123 4.980903 CCGCATAATTGCCCGCGC 62.981 66.667 0.00 0.00 46.57 6.86
3602 8132 0.324943 ATAGCCGGCTTCCGCATAAT 59.675 50.000 37.74 16.94 46.86 1.28
3633 8163 6.987386 TGAAATCCGGTTTGAAATGTATGTT 58.013 32.000 0.00 0.00 0.00 2.71
3704 8234 7.819415 CGGATGACTTATGCTATTTTCTATCCA 59.181 37.037 0.00 0.00 31.78 3.41
3705 8235 7.819900 ACGGATGACTTATGCTATTTTCTATCC 59.180 37.037 0.00 0.00 0.00 2.59
3756 8286 5.507077 TCGTTGAATTTGAACTACTGTTGC 58.493 37.500 0.00 0.00 36.39 4.17


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

AutoCloner maintained by Alex Coulton.