Multiple sequence alignment - TraesCS5D01G305600

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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 TraesCS5D01G305600 chr5D 100.000 4774 0 0 1 4774 400412634 400417407 0.000000e+00 8817
1 TraesCS5D01G305600 chr5D 86.525 141 16 3 25 162 312479459 312479599 8.280000e-33 152
2 TraesCS5D01G305600 chr5B 89.833 3403 267 32 657 4002 480414295 480417675 0.000000e+00 4294
3 TraesCS5D01G305600 chr5B 89.265 1565 128 20 1475 3010 480458190 480459743 0.000000e+00 1923
4 TraesCS5D01G305600 chr5B 89.151 1567 133 23 1473 3010 480438423 480439981 0.000000e+00 1917
5 TraesCS5D01G305600 chr5B 89.158 1568 131 21 1474 3010 480462198 480463757 0.000000e+00 1917
6 TraesCS5D01G305600 chr5B 88.896 1567 132 22 1473 3010 480464213 480465766 0.000000e+00 1892
7 TraesCS5D01G305600 chr5B 88.655 1569 134 23 1473 3010 480436417 480437972 0.000000e+00 1871
8 TraesCS5D01G305600 chr5B 88.353 1554 144 21 1487 3010 480456189 480457735 0.000000e+00 1832
9 TraesCS5D01G305600 chr5B 88.186 1566 143 21 1475 3010 480460199 480461752 0.000000e+00 1829
10 TraesCS5D01G305600 chr5B 88.867 1500 134 17 1539 3010 480452495 480453989 0.000000e+00 1814
11 TraesCS5D01G305600 chr5B 88.332 1217 109 18 1473 2660 480434475 480435687 0.000000e+00 1430
12 TraesCS5D01G305600 chr5B 90.155 711 51 5 2 712 480413606 480414297 0.000000e+00 907
13 TraesCS5D01G305600 chr5A 91.829 2521 161 12 1 2486 506113966 506116476 0.000000e+00 3472
14 TraesCS5D01G305600 chr5A 94.888 1389 59 7 2618 4004 506116538 506117916 0.000000e+00 2161
15 TraesCS5D01G305600 chr5A 85.929 533 61 10 4247 4772 316097411 316096886 1.500000e-154 556
16 TraesCS5D01G305600 chr3A 81.983 1049 144 24 874 1904 705428756 705427735 0.000000e+00 848
17 TraesCS5D01G305600 chr3A 80.777 1056 155 28 874 1906 705419470 705418440 0.000000e+00 782
18 TraesCS5D01G305600 chr3A 80.495 1051 152 25 874 1906 705410392 705409377 0.000000e+00 756
19 TraesCS5D01G305600 chr3A 80.568 916 134 22 874 1774 705425853 705424967 0.000000e+00 665
20 TraesCS5D01G305600 chrUn 81.660 1036 140 26 874 1894 45404612 45403612 0.000000e+00 815
21 TraesCS5D01G305600 chr3B 85.325 770 94 13 4011 4769 564200226 564200987 0.000000e+00 778
22 TraesCS5D01G305600 chr3B 80.703 1052 148 31 874 1907 760510889 760509875 0.000000e+00 767
23 TraesCS5D01G305600 chr3B 83.041 684 96 12 873 1541 760502021 760501343 1.900000e-168 603
24 TraesCS5D01G305600 chr3D 80.732 1038 148 28 874 1889 572897833 572898840 0.000000e+00 761
25 TraesCS5D01G305600 chr3D 79.608 255 37 11 3995 4239 395656211 395656460 8.220000e-38 169
26 TraesCS5D01G305600 chr3D 85.621 153 21 1 11 163 583305389 583305238 4.950000e-35 159
27 TraesCS5D01G305600 chr3D 88.281 128 12 3 6 131 562531591 562531717 2.980000e-32 150
28 TraesCS5D01G305600 chr6D 86.331 556 63 8 4219 4768 316228858 316228310 1.140000e-165 593
29 TraesCS5D01G305600 chr6D 81.988 161 24 5 21 179 101213289 101213132 1.080000e-26 132
30 TraesCS5D01G305600 chr2A 85.122 531 67 10 4247 4769 754347551 754348077 2.530000e-147 532
31 TraesCS5D01G305600 chr2A 84.000 175 24 4 2 173 57219305 57219478 1.060000e-36 165
32 TraesCS5D01G305600 chr7D 84.528 530 66 12 4247 4769 579330228 579329708 1.190000e-140 510
33 TraesCS5D01G305600 chr6B 80.943 530 83 14 4219 4735 30127921 30128445 2.070000e-108 403
34 TraesCS5D01G305600 chr2D 80.952 525 83 12 4219 4735 112552566 112552051 2.680000e-107 399
35 TraesCS5D01G305600 chr4A 78.764 518 83 16 4220 4731 736871936 736871440 5.960000e-84 322
36 TraesCS5D01G305600 chr7B 76.749 529 84 18 4219 4716 619168382 619168902 4.740000e-65 259
37 TraesCS5D01G305600 chr7B 85.315 143 17 3 21 162 69822469 69822330 1.380000e-30 145
38 TraesCS5D01G305600 chr1A 83.851 161 22 4 5 163 308211376 308211218 2.980000e-32 150


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 TraesCS5D01G305600 chr5D 400412634 400417407 4773 False 8817.000000 8817 100.000000 1 4774 1 chr5D.!!$F2 4773
1 TraesCS5D01G305600 chr5B 480413606 480417675 4069 False 2600.500000 4294 89.994000 2 4002 2 chr5B.!!$F1 4000
2 TraesCS5D01G305600 chr5B 480452495 480465766 13271 False 1867.833333 1923 88.787500 1473 3010 6 chr5B.!!$F3 1537
3 TraesCS5D01G305600 chr5B 480434475 480439981 5506 False 1739.333333 1917 88.712667 1473 3010 3 chr5B.!!$F2 1537
4 TraesCS5D01G305600 chr5A 506113966 506117916 3950 False 2816.500000 3472 93.358500 1 4004 2 chr5A.!!$F1 4003
5 TraesCS5D01G305600 chr5A 316096886 316097411 525 True 556.000000 556 85.929000 4247 4772 1 chr5A.!!$R1 525
6 TraesCS5D01G305600 chr3A 705418440 705419470 1030 True 782.000000 782 80.777000 874 1906 1 chr3A.!!$R2 1032
7 TraesCS5D01G305600 chr3A 705424967 705428756 3789 True 756.500000 848 81.275500 874 1904 2 chr3A.!!$R3 1030
8 TraesCS5D01G305600 chr3A 705409377 705410392 1015 True 756.000000 756 80.495000 874 1906 1 chr3A.!!$R1 1032
9 TraesCS5D01G305600 chrUn 45403612 45404612 1000 True 815.000000 815 81.660000 874 1894 1 chrUn.!!$R1 1020
10 TraesCS5D01G305600 chr3B 564200226 564200987 761 False 778.000000 778 85.325000 4011 4769 1 chr3B.!!$F1 758
11 TraesCS5D01G305600 chr3B 760509875 760510889 1014 True 767.000000 767 80.703000 874 1907 1 chr3B.!!$R2 1033
12 TraesCS5D01G305600 chr3B 760501343 760502021 678 True 603.000000 603 83.041000 873 1541 1 chr3B.!!$R1 668
13 TraesCS5D01G305600 chr3D 572897833 572898840 1007 False 761.000000 761 80.732000 874 1889 1 chr3D.!!$F3 1015
14 TraesCS5D01G305600 chr6D 316228310 316228858 548 True 593.000000 593 86.331000 4219 4768 1 chr6D.!!$R2 549
15 TraesCS5D01G305600 chr2A 754347551 754348077 526 False 532.000000 532 85.122000 4247 4769 1 chr2A.!!$F2 522
16 TraesCS5D01G305600 chr7D 579329708 579330228 520 True 510.000000 510 84.528000 4247 4769 1 chr7D.!!$R1 522
17 TraesCS5D01G305600 chr6B 30127921 30128445 524 False 403.000000 403 80.943000 4219 4735 1 chr6B.!!$F1 516
18 TraesCS5D01G305600 chr2D 112552051 112552566 515 True 399.000000 399 80.952000 4219 4735 1 chr2D.!!$R1 516
19 TraesCS5D01G305600 chr7B 619168382 619168902 520 False 259.000000 259 76.749000 4219 4716 1 chr7B.!!$F1 497

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
145 147 0.179004 TTTCTCCCACCGCAACACAT 60.179 50.0 0.00 0.0 0.0 3.21 F
1565 1950 0.037790 GTCTTGCCTCTCGTTCTGCT 60.038 55.0 0.00 0.0 0.0 4.24 F
1633 2026 0.463654 ATGGGCGCACATCAACGTAT 60.464 50.0 22.04 0.0 0.0 3.06 F
2594 16007 1.463553 GGGTGTGTTTTGCTGGGAGG 61.464 60.0 0.00 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 12020 0.035881 TGAGCAAGCTGGGTTCTCAG 59.964 55.0 0.00 0.0 37.79 3.35 R
2684 16097 0.311165 CTCACACTTCCGACAGACGT 59.689 55.0 0.00 0.0 40.78 4.34 R
2917 16330 0.819259 GCACTTGTTGTGGAGGAGCA 60.819 55.0 0.00 0.0 46.27 4.26 R
4121 19571 0.370273 GTTGCGCGACATCTACCTTG 59.630 55.0 23.02 0.0 0.00 3.61 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
68 70 8.077991 TCATGATTTCACAAAATTGAGAGTGAC 58.922 33.333 0.00 0.00 40.37 3.67
116 118 8.888836 AAATATGATCATGGCCATTGAAGATA 57.111 30.769 17.92 15.64 0.00 1.98
142 144 3.192799 TTTTTCTCCCACCGCAACA 57.807 47.368 0.00 0.00 0.00 3.33
145 147 0.179004 TTTCTCCCACCGCAACACAT 60.179 50.000 0.00 0.00 0.00 3.21
180 182 5.291128 GCTAGTAGTAACAATGCATCGTGTT 59.709 40.000 18.21 18.21 40.88 3.32
181 183 6.183360 GCTAGTAGTAACAATGCATCGTGTTT 60.183 38.462 19.10 7.61 38.80 2.83
190 192 1.945522 CATCGTGTTTCGTTGGGCA 59.054 52.632 0.00 0.00 40.80 5.36
209 211 2.489971 CAGAGGAACACCAAACGCTAA 58.510 47.619 0.00 0.00 0.00 3.09
277 279 9.295825 TGAATGTGTTACTTTGTTGGATTATCT 57.704 29.630 0.00 0.00 0.00 1.98
390 392 8.150945 TCAATTGACAACTCTAGAAGTTTAGCT 58.849 33.333 3.38 0.00 46.26 3.32
407 409 8.700439 AGTTTAGCTAAAGGTTAAAACATCCA 57.300 30.769 19.16 0.00 33.60 3.41
450 452 4.895224 TGGTGCGTTTGTATTTGTTACA 57.105 36.364 0.00 0.00 39.07 2.41
474 476 6.572167 TTCATGACATGCATAGTTCAAACA 57.428 33.333 10.76 0.00 34.82 2.83
511 513 8.998377 TGAAAATTAAAGATGACGTCAATCAGA 58.002 29.630 24.13 7.79 30.46 3.27
582 584 6.756542 ACTGTCCTAATTCACAAAAGCAAAAC 59.243 34.615 0.00 0.00 0.00 2.43
669 671 6.978674 TGGTACATTACTTCCTAGGAGATG 57.021 41.667 12.26 15.87 0.00 2.90
716 769 5.779529 TCTACAACCGGACACCTTATATC 57.220 43.478 9.46 0.00 0.00 1.63
901 954 4.885907 CCACATATATTCATCCCCATCTGC 59.114 45.833 0.00 0.00 0.00 4.26
902 955 5.503002 CACATATATTCATCCCCATCTGCA 58.497 41.667 0.00 0.00 0.00 4.41
909 962 0.915872 ATCCCCATCTGCACACTCCA 60.916 55.000 0.00 0.00 0.00 3.86
1034 1095 0.702902 TCCGAGTCTTACACCTCCCT 59.297 55.000 0.00 0.00 0.00 4.20
1121 1185 1.082679 CGCTCACGAGAGGAGTACGA 61.083 60.000 11.94 0.00 43.93 3.43
1123 1187 1.723220 CTCACGAGAGGAGTACGACA 58.277 55.000 1.41 0.00 38.26 4.35
1233 1297 2.045926 GAGGCGGTGCAGTCCATT 60.046 61.111 0.00 0.00 0.00 3.16
1283 1347 6.806739 GTGCTTATCAATTTGGTACCAACTTC 59.193 38.462 27.08 14.23 35.46 3.01
1297 1364 9.362151 TGGTACCAACTTCAAATTTCTCTAAAT 57.638 29.630 13.60 0.00 36.87 1.40
1371 1442 8.832735 AGAAACAAGATGTAATAGTTTAGGGGA 58.167 33.333 0.00 0.00 33.04 4.81
1463 1537 0.250234 ATGCGCTCTTGCCTTGTCTA 59.750 50.000 9.73 0.00 35.36 2.59
1468 1542 2.704572 GCTCTTGCCTTGTCTATGTGT 58.295 47.619 0.00 0.00 0.00 3.72
1470 1544 2.417933 CTCTTGCCTTGTCTATGTGTGC 59.582 50.000 0.00 0.00 0.00 4.57
1476 1550 3.913573 GTCTATGTGTGCGCCGCG 61.914 66.667 8.83 8.83 0.00 6.46
1562 1947 0.605589 CTGGTCTTGCCTCTCGTTCT 59.394 55.000 0.00 0.00 38.35 3.01
1565 1950 0.037790 GTCTTGCCTCTCGTTCTGCT 60.038 55.000 0.00 0.00 0.00 4.24
1633 2026 0.463654 ATGGGCGCACATCAACGTAT 60.464 50.000 22.04 0.00 0.00 3.06
1693 7939 2.906897 ACAACCACAGCAAGCCCG 60.907 61.111 0.00 0.00 0.00 6.13
1745 9945 4.821805 ACTACAGCATGCAGTACTTTTTGT 59.178 37.500 21.98 14.04 41.92 2.83
1778 9980 5.531287 GTCAAACTGTACTTGTTCATTCCCT 59.469 40.000 0.00 0.00 0.00 4.20
1876 14084 7.459795 TGATGCAACCATAAGAATGTACAAA 57.540 32.000 0.00 0.00 0.00 2.83
1877 14085 8.065473 TGATGCAACCATAAGAATGTACAAAT 57.935 30.769 0.00 0.00 0.00 2.32
1935 14144 7.611213 AAAGTTATCCGTTGGTTTCATCTAG 57.389 36.000 0.00 0.00 0.00 2.43
1950 14159 7.600752 GGTTTCATCTAGCTATGAACTATGGTC 59.399 40.741 10.77 0.00 43.69 4.02
1954 14182 3.760580 AGCTATGAACTATGGTCTGGC 57.239 47.619 0.00 0.00 0.00 4.85
2179 14410 2.943033 GGGTTGGGATCTAAACACATCG 59.057 50.000 11.48 0.00 29.82 3.84
2261 14493 2.338620 TGAAGGCGACGTCACTGG 59.661 61.111 17.16 0.00 44.08 4.00
2276 14508 4.074970 GTCACTGGGAACAACAATGATCT 58.925 43.478 0.00 0.00 42.06 2.75
2279 14511 4.074970 ACTGGGAACAACAATGATCTGAC 58.925 43.478 0.00 0.00 42.06 3.51
2294 14526 5.418676 TGATCTGACGAATGATTTACTGCA 58.581 37.500 0.00 0.00 0.00 4.41
2303 14535 7.250569 ACGAATGATTTACTGCAACCAATTAG 58.749 34.615 0.00 0.00 0.00 1.73
2310 14542 4.237349 ACTGCAACCAATTAGGAAAACG 57.763 40.909 0.00 0.00 41.22 3.60
2486 15871 9.458727 AATGTGATATGGACATTCAGATTATCC 57.541 33.333 13.07 0.00 39.34 2.59
2488 15873 8.663167 TGTGATATGGACATTCAGATTATCCTT 58.337 33.333 0.00 0.00 0.00 3.36
2536 15948 8.136165 ACATCTAAACATAGTCGAAGTGATACC 58.864 37.037 0.00 0.00 0.00 2.73
2557 15970 8.863872 ATACCCACATGTAGGATTTTTATAGC 57.136 34.615 17.82 0.00 0.00 2.97
2594 16007 1.463553 GGGTGTGTTTTGCTGGGAGG 61.464 60.000 0.00 0.00 0.00 4.30
2684 16097 4.180817 CGCCACACTTTCTGACATACATA 58.819 43.478 0.00 0.00 0.00 2.29
2824 16237 7.049799 TGGCAATAATGGAAAAGTATAAGGC 57.950 36.000 0.00 0.00 0.00 4.35
2851 16264 5.221185 CCAGCTCAAATATGATGGAAGTTGG 60.221 44.000 0.00 0.00 37.75 3.77
2917 16330 2.158234 AGAGGAAGACACTGAAGGAGGT 60.158 50.000 0.00 0.00 0.00 3.85
2918 16331 1.974236 AGGAAGACACTGAAGGAGGTG 59.026 52.381 0.00 0.00 39.13 4.00
3022 18444 4.579340 CACTTATCAATGCAGGAGCTCAAT 59.421 41.667 17.19 0.00 42.74 2.57
3249 18671 3.764237 TTCAATCCCTATAGTTCCCGC 57.236 47.619 0.00 0.00 0.00 6.13
3422 18870 3.613737 CGATGATTGCCAAATGTTTGTCC 59.386 43.478 4.92 0.00 36.45 4.02
3616 19066 3.489059 GGAATGTTCCATGCCAATGTACG 60.489 47.826 6.91 0.00 46.76 3.67
3741 19191 0.799393 GAAGGCAGCGGAAGAAGAAC 59.201 55.000 0.00 0.00 0.00 3.01
3746 19196 1.069636 GCAGCGGAAGAAGAACAACAG 60.070 52.381 0.00 0.00 0.00 3.16
3817 19267 2.112297 GTCCGGAACCACCAGCAA 59.888 61.111 5.23 0.00 38.90 3.91
3839 19289 4.952262 TCATTGCACATTGTCTAAGCTC 57.048 40.909 0.00 0.00 0.00 4.09
3905 19355 8.153221 TGTGGATTCTTACTAGGGTAATTTCA 57.847 34.615 0.00 0.00 37.30 2.69
3915 19365 5.944007 ACTAGGGTAATTTCATGTTGTGGAC 59.056 40.000 0.00 0.00 0.00 4.02
3969 19419 4.709397 TCCTCTGGTTGTGAACAATTTTGT 59.291 37.500 0.00 0.00 44.72 2.83
3973 19423 4.169508 TGGTTGTGAACAATTTTGTGACG 58.830 39.130 0.00 0.00 41.31 4.35
4015 19465 5.693104 TCGATTTAAATATGGGTCACGCTAC 59.307 40.000 0.00 0.00 0.00 3.58
4028 19478 2.126580 GCTACGCGTCAACCGACT 60.127 61.111 18.63 0.00 40.23 4.18
4032 19482 0.179181 TACGCGTCAACCGACTGATC 60.179 55.000 18.63 0.00 40.23 2.92
4035 19485 1.429463 GCGTCAACCGACTGATCTTT 58.571 50.000 0.00 0.00 40.23 2.52
4037 19487 2.223377 GCGTCAACCGACTGATCTTTTT 59.777 45.455 0.00 0.00 40.23 1.94
4041 19491 6.423862 CGTCAACCGACTGATCTTTTTAAAA 58.576 36.000 0.00 0.00 40.23 1.52
4042 19492 6.573725 CGTCAACCGACTGATCTTTTTAAAAG 59.426 38.462 10.89 10.89 40.23 2.27
4043 19493 7.517734 CGTCAACCGACTGATCTTTTTAAAAGA 60.518 37.037 20.42 20.42 40.23 2.52
4044 19494 7.586664 GTCAACCGACTGATCTTTTTAAAAGAC 59.413 37.037 20.54 14.82 39.22 3.01
4045 19495 6.555812 ACCGACTGATCTTTTTAAAAGACC 57.444 37.500 20.54 13.07 0.00 3.85
4049 19499 4.217767 ACTGATCTTTTTAAAAGACCCGCC 59.782 41.667 20.54 9.47 0.00 6.13
4098 19548 4.081697 TGAATAGCCGTGTGATCTCTCAAA 60.082 41.667 0.00 0.00 31.85 2.69
4099 19549 4.679373 ATAGCCGTGTGATCTCTCAAAT 57.321 40.909 0.00 0.00 31.85 2.32
4100 19550 2.625737 AGCCGTGTGATCTCTCAAATG 58.374 47.619 0.00 0.00 31.85 2.32
4101 19551 2.234661 AGCCGTGTGATCTCTCAAATGA 59.765 45.455 0.00 0.00 31.85 2.57
4103 19553 3.193263 CCGTGTGATCTCTCAAATGAGG 58.807 50.000 10.37 2.24 42.30 3.86
4104 19554 3.368843 CCGTGTGATCTCTCAAATGAGGT 60.369 47.826 10.37 0.00 42.30 3.85
4105 19555 3.615937 CGTGTGATCTCTCAAATGAGGTG 59.384 47.826 10.37 4.68 42.30 4.00
4106 19556 4.573900 GTGTGATCTCTCAAATGAGGTGT 58.426 43.478 10.37 0.00 42.30 4.16
4107 19557 4.391216 GTGTGATCTCTCAAATGAGGTGTG 59.609 45.833 10.37 0.32 42.30 3.82
4108 19558 4.040829 TGTGATCTCTCAAATGAGGTGTGT 59.959 41.667 10.37 0.00 42.30 3.72
4109 19559 4.629200 GTGATCTCTCAAATGAGGTGTGTC 59.371 45.833 10.37 7.59 42.30 3.67
4110 19560 3.685139 TCTCTCAAATGAGGTGTGTCC 57.315 47.619 10.37 0.00 42.30 4.02
4111 19561 2.972021 TCTCTCAAATGAGGTGTGTCCA 59.028 45.455 10.37 0.00 42.30 4.02
4121 19571 1.956477 AGGTGTGTCCAGAATTGCAAC 59.044 47.619 0.00 0.00 39.02 4.17
4125 19575 2.361757 TGTGTCCAGAATTGCAACAAGG 59.638 45.455 0.00 1.63 0.00 3.61
4133 19583 5.392380 CCAGAATTGCAACAAGGTAGATGTC 60.392 44.000 0.00 0.00 0.00 3.06
4137 19587 0.370273 CAACAAGGTAGATGTCGCGC 59.630 55.000 0.00 0.00 0.00 6.86
4138 19588 0.037697 AACAAGGTAGATGTCGCGCA 60.038 50.000 8.75 2.86 0.00 6.09
4171 19626 3.340814 ACAATTGTTGCAAAACCACCA 57.659 38.095 4.92 0.00 0.00 4.17
4172 19627 3.269178 ACAATTGTTGCAAAACCACCAG 58.731 40.909 4.92 0.00 0.00 4.00
4176 19631 0.459489 GTTGCAAAACCACCAGAGCA 59.541 50.000 0.00 0.00 0.00 4.26
4185 19640 4.701956 AACCACCAGAGCATTATTTTCG 57.298 40.909 0.00 0.00 0.00 3.46
4186 19641 2.423538 ACCACCAGAGCATTATTTTCGC 59.576 45.455 0.00 0.00 0.00 4.70
4194 19649 5.457799 CAGAGCATTATTTTCGCCAGAATTG 59.542 40.000 0.00 0.00 36.09 2.32
4228 19683 4.619336 GTCTTCAACGTTTTTGCAACAAGA 59.381 37.500 0.00 0.00 0.00 3.02
4231 19686 7.167468 GTCTTCAACGTTTTTGCAACAAGATAT 59.833 33.333 0.00 0.00 0.00 1.63
4260 19721 4.290155 CGTAACTTGCTCTGCAACAATTT 58.710 39.130 0.45 0.00 43.99 1.82
4349 19833 6.048073 GCAAAATAGATATGTTGCGTGAGA 57.952 37.500 11.05 0.00 44.29 3.27
4355 19839 5.536554 AGATATGTTGCGTGAGAACTTTG 57.463 39.130 0.00 0.00 0.00 2.77
4433 19925 1.247567 AAATGTTGTTGCGGGAGGAG 58.752 50.000 0.00 0.00 0.00 3.69
4453 19947 6.182627 AGGAGTTCTGCAACATGAATAATGA 58.817 36.000 0.00 0.00 38.72 2.57
4501 20480 3.314913 TGATGTCGTTTGCTGTGTGAATT 59.685 39.130 0.00 0.00 0.00 2.17
4542 20533 2.370281 TGATGTTGCGAGAGGACTTC 57.630 50.000 0.00 0.00 0.00 3.01
4574 20565 5.399013 AGCCATTGTTGCGAAAAGTATAAC 58.601 37.500 0.00 0.00 0.00 1.89
4580 20573 7.452630 TTGTTGCGAAAAGTATAACAAAACC 57.547 32.000 0.00 0.00 38.03 3.27
4590 20585 6.134535 AGTATAACAAAACCATCCTGACCA 57.865 37.500 0.00 0.00 0.00 4.02
4626 20621 0.682855 CGAGAAGGGAGTCTGGAGCT 60.683 60.000 0.00 0.00 0.00 4.09
4633 20628 1.449246 GAGTCTGGAGCTGCGCAAT 60.449 57.895 13.05 2.16 0.00 3.56
4650 20645 2.684927 GCAATTAGGCTGATGGTGACCT 60.685 50.000 2.11 0.00 36.27 3.85
4731 20810 7.740805 AGATGGAGAATACATAAGGAAAGGAC 58.259 38.462 0.00 0.00 0.00 3.85
4762 20848 0.460284 GACACGTGCTGGACATAGGG 60.460 60.000 17.22 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 70 2.558378 CTGCATCACCCAGATACACTG 58.442 52.381 0.00 0.00 45.36 3.66
133 135 2.625823 GGACCCATGTGTTGCGGTG 61.626 63.158 0.00 0.00 31.41 4.94
134 136 2.282180 GGACCCATGTGTTGCGGT 60.282 61.111 0.00 0.00 33.23 5.68
135 137 1.178534 AAAGGACCCATGTGTTGCGG 61.179 55.000 0.00 0.00 0.00 5.69
136 138 0.673437 AAAAGGACCCATGTGTTGCG 59.327 50.000 0.00 0.00 0.00 4.85
142 144 3.587506 ACTACTAGCAAAAGGACCCATGT 59.412 43.478 0.00 0.00 0.00 3.21
145 147 4.594062 TGTTACTACTAGCAAAAGGACCCA 59.406 41.667 0.00 0.00 0.00 4.51
180 182 0.534203 GTGTTCCTCTGCCCAACGAA 60.534 55.000 0.00 0.00 0.00 3.85
181 183 1.070786 GTGTTCCTCTGCCCAACGA 59.929 57.895 0.00 0.00 0.00 3.85
190 192 2.490991 GTTAGCGTTTGGTGTTCCTCT 58.509 47.619 0.00 0.00 34.23 3.69
277 279 7.555087 ACTCAAAACTCAATTGTGGAATTTCA 58.445 30.769 11.89 0.00 28.65 2.69
284 286 6.966435 AAACAACTCAAAACTCAATTGTGG 57.034 33.333 11.89 6.13 30.99 4.17
390 392 8.646900 AGAAATTGCTGGATGTTTTAACCTTTA 58.353 29.630 0.00 0.00 0.00 1.85
400 402 8.729805 TTTTGTTAAAGAAATTGCTGGATGTT 57.270 26.923 0.00 0.00 0.00 2.71
407 409 7.065683 CACCAACCTTTTGTTAAAGAAATTGCT 59.934 33.333 0.00 0.00 42.78 3.91
450 452 7.121611 TCTGTTTGAACTATGCATGTCATGAAT 59.878 33.333 17.24 14.10 36.63 2.57
511 513 7.924541 TCCTACCCTAGAAAATTACATGTGTT 58.075 34.615 9.11 0.11 0.00 3.32
582 584 9.543018 GTCATAGACGAATTTGGAAAGTTAAAG 57.457 33.333 0.00 0.00 0.00 1.85
669 671 5.474189 AGCTCTAAGGGTCGACATAACTATC 59.526 44.000 18.91 0.51 0.00 2.08
716 769 1.242076 CCTCCAGAAGTTTGGCACAG 58.758 55.000 0.00 0.00 42.39 3.66
749 802 2.625314 TGACAATTTTGCATCCGGACAA 59.375 40.909 6.12 4.49 0.00 3.18
827 880 4.514577 CGGCGGGCGAGTCTTGAT 62.515 66.667 20.10 0.00 0.00 2.57
901 954 2.867109 AGGGTTTCATCTGGAGTGTG 57.133 50.000 0.00 0.00 0.00 3.82
902 955 2.237392 GCTAGGGTTTCATCTGGAGTGT 59.763 50.000 0.00 0.00 0.00 3.55
909 962 0.107654 GTGCGGCTAGGGTTTCATCT 60.108 55.000 0.00 0.00 0.00 2.90
963 1024 1.593469 GATCGCCGGAAGTAAGCTTTC 59.407 52.381 5.05 0.00 34.61 2.62
1034 1095 2.281484 GCTCCCGGCAGTCAACAA 60.281 61.111 0.00 0.00 41.35 2.83
1297 1364 1.343681 ACGCATCCCCCTAACCTTCTA 60.344 52.381 0.00 0.00 0.00 2.10
1371 1442 3.473113 AGGCAACCCACCATCTTTAAT 57.527 42.857 0.00 0.00 37.17 1.40
1470 1544 4.876081 GCAAGATCAAGCGCGGCG 62.876 66.667 19.62 19.62 0.00 6.46
1476 1550 4.510038 TTCTTTTGAGGCAAGATCAAGC 57.490 40.909 0.00 0.00 37.91 4.01
1562 1947 3.474486 TTGCGCCTTCTCCACAGCA 62.474 57.895 4.18 0.00 0.00 4.41
1565 1950 1.891919 GTGTTGCGCCTTCTCCACA 60.892 57.895 4.18 0.00 0.00 4.17
1633 2026 2.669229 TGTACCGACGCCGAGACA 60.669 61.111 0.00 0.00 38.22 3.41
1658 2051 3.117491 TGTCTACCGTATCCCTAGACG 57.883 52.381 0.00 0.00 39.45 4.18
1693 7939 1.719780 CGAGCACACGAACTAAGGAAC 59.280 52.381 0.00 0.00 35.09 3.62
1745 9945 5.048364 ACAAGTACAGTTTGACACAGCAAAA 60.048 36.000 0.00 0.00 39.26 2.44
1811 12013 4.389374 CAAGCTGGGTTCTCAGAGTTTTA 58.611 43.478 3.66 0.00 36.93 1.52
1818 12020 0.035881 TGAGCAAGCTGGGTTCTCAG 59.964 55.000 0.00 0.00 37.79 3.35
1935 14144 2.035961 TCGCCAGACCATAGTTCATAGC 59.964 50.000 0.00 0.00 0.00 2.97
1954 14182 5.048991 ACAAGTTAAAGTGGCTATTTGGTCG 60.049 40.000 0.00 0.00 0.00 4.79
2093 14324 6.519382 CATCCTTCAGTACAGCATCAATAGA 58.481 40.000 0.00 0.00 0.00 1.98
2103 14334 3.340814 AACCAGCATCCTTCAGTACAG 57.659 47.619 0.00 0.00 0.00 2.74
2179 14410 9.614792 ATCAATAACCAATAGTAGGAAAGACAC 57.385 33.333 0.00 0.00 0.00 3.67
2261 14493 5.122239 TCATTCGTCAGATCATTGTTGTTCC 59.878 40.000 0.00 0.00 0.00 3.62
2276 14508 4.068599 TGGTTGCAGTAAATCATTCGTCA 58.931 39.130 0.00 0.00 0.00 4.35
2279 14511 6.692681 CCTAATTGGTTGCAGTAAATCATTCG 59.307 38.462 0.00 0.00 0.00 3.34
2294 14526 1.542472 CCCGCGTTTTCCTAATTGGTT 59.458 47.619 4.92 0.00 37.07 3.67
2303 14535 4.823790 ACAATATTATCCCGCGTTTTCC 57.176 40.909 4.92 0.00 0.00 3.13
2310 14542 7.324178 AGAGAAGACATACAATATTATCCCGC 58.676 38.462 0.00 0.00 0.00 6.13
2354 14586 9.986833 GAACAAAACACAAGAAAAATAAGCATT 57.013 25.926 0.00 0.00 0.00 3.56
2536 15948 8.686334 ACAAAGCTATAAAAATCCTACATGTGG 58.314 33.333 9.11 5.17 0.00 4.17
2557 15970 2.211806 CCCACAATGTTTGCCACAAAG 58.788 47.619 0.00 0.00 39.50 2.77
2594 16007 5.185056 ACACAATACTTTGGGAAAGGTATGC 59.815 40.000 0.00 0.00 42.82 3.14
2684 16097 0.311165 CTCACACTTCCGACAGACGT 59.689 55.000 0.00 0.00 40.78 4.34
2824 16237 5.359009 ACTTCCATCATATTTGAGCTGGTTG 59.641 40.000 0.00 3.84 34.77 3.77
2851 16264 3.084039 TCTCCACAACAAGATGGATTGC 58.916 45.455 0.00 0.00 44.06 3.56
2917 16330 0.819259 GCACTTGTTGTGGAGGAGCA 60.819 55.000 0.00 0.00 46.27 4.26
2918 16331 1.518903 GGCACTTGTTGTGGAGGAGC 61.519 60.000 0.00 0.00 46.27 4.70
3022 18444 6.939622 ACACTTGATGTCATAACAGATCTCA 58.060 36.000 0.00 0.00 36.54 3.27
3050 18472 4.102681 AGGTAATACTGTGTATCTTGGGGC 59.897 45.833 0.00 0.00 0.00 5.80
3422 18870 4.135306 TCTCATAGAGCCTACAAGGTACG 58.865 47.826 0.00 0.00 37.80 3.67
3616 19066 4.461081 TGTCATAACCAGGGCATGTAAAAC 59.539 41.667 0.00 0.00 0.00 2.43
3741 19191 3.837213 ATTTGCGTCATCTTCCTGTTG 57.163 42.857 0.00 0.00 0.00 3.33
3746 19196 5.992217 ACTAGGAATATTTGCGTCATCTTCC 59.008 40.000 0.00 0.00 0.00 3.46
3789 19239 1.406539 GGTTCCGGACGTCTGCTAATA 59.593 52.381 19.31 0.00 0.00 0.98
3791 19241 1.180456 TGGTTCCGGACGTCTGCTAA 61.180 55.000 19.31 12.04 0.00 3.09
3817 19267 5.191426 AGAGCTTAGACAATGTGCAATGAT 58.809 37.500 0.00 0.00 0.00 2.45
3839 19289 3.057174 ACACGAGCTCTCAGAGGTAAAAG 60.057 47.826 6.31 1.68 40.67 2.27
3905 19355 3.763897 GCCCTGATAAAAGTCCACAACAT 59.236 43.478 0.00 0.00 0.00 2.71
3935 19385 2.185004 ACCAGAGGAAATCCACAACG 57.815 50.000 1.67 0.00 38.89 4.10
3969 19419 5.107645 CGATAATTTGTGTTCACTCACGTCA 60.108 40.000 4.59 0.00 40.74 4.35
3973 19423 9.820229 TTAAATCGATAATTTGTGTTCACTCAC 57.180 29.630 0.00 0.00 38.08 3.51
4019 19469 7.255001 GGTCTTTTAAAAAGATCAGTCGGTTGA 60.255 37.037 1.66 0.00 0.00 3.18
4022 19472 5.472478 GGGTCTTTTAAAAAGATCAGTCGGT 59.528 40.000 0.00 0.00 0.00 4.69
4026 19476 4.217767 GGCGGGTCTTTTAAAAAGATCAGT 59.782 41.667 0.00 0.00 0.00 3.41
4028 19478 3.189702 CGGCGGGTCTTTTAAAAAGATCA 59.810 43.478 0.00 0.00 0.00 2.92
4032 19482 1.667756 GGCGGCGGGTCTTTTAAAAAG 60.668 52.381 9.78 0.00 0.00 2.27
4035 19485 0.956902 GAGGCGGCGGGTCTTTTAAA 60.957 55.000 9.78 0.00 0.00 1.52
4037 19487 2.266689 GAGGCGGCGGGTCTTTTA 59.733 61.111 9.78 0.00 0.00 1.52
4075 19525 3.023832 TGAGAGATCACACGGCTATTCA 58.976 45.455 0.00 0.00 0.00 2.57
4098 19548 2.224843 TGCAATTCTGGACACACCTCAT 60.225 45.455 0.00 0.00 39.86 2.90
4099 19549 1.142667 TGCAATTCTGGACACACCTCA 59.857 47.619 0.00 0.00 39.86 3.86
4100 19550 1.896220 TGCAATTCTGGACACACCTC 58.104 50.000 0.00 0.00 39.86 3.85
4101 19551 1.956477 GTTGCAATTCTGGACACACCT 59.044 47.619 0.59 0.00 39.86 4.00
4103 19553 3.374745 CTTGTTGCAATTCTGGACACAC 58.625 45.455 0.59 0.00 0.00 3.82
4104 19554 2.361757 CCTTGTTGCAATTCTGGACACA 59.638 45.455 0.59 0.00 0.00 3.72
4105 19555 2.362077 ACCTTGTTGCAATTCTGGACAC 59.638 45.455 0.59 0.00 0.00 3.67
4106 19556 2.665165 ACCTTGTTGCAATTCTGGACA 58.335 42.857 0.59 0.00 0.00 4.02
4107 19557 4.072131 TCTACCTTGTTGCAATTCTGGAC 58.928 43.478 0.59 0.00 0.00 4.02
4108 19558 4.365514 TCTACCTTGTTGCAATTCTGGA 57.634 40.909 0.59 0.00 0.00 3.86
4109 19559 4.460382 ACATCTACCTTGTTGCAATTCTGG 59.540 41.667 0.59 5.82 0.00 3.86
4110 19560 5.633830 ACATCTACCTTGTTGCAATTCTG 57.366 39.130 0.59 0.00 0.00 3.02
4111 19561 4.393062 CGACATCTACCTTGTTGCAATTCT 59.607 41.667 0.59 0.00 0.00 2.40
4121 19571 0.370273 GTTGCGCGACATCTACCTTG 59.630 55.000 23.02 0.00 0.00 3.61
4125 19575 1.910880 CGAGTTGCGCGACATCTAC 59.089 57.895 28.83 13.17 0.00 2.59
4137 19587 2.233355 CAATTGTTGTAGCGCGAGTTG 58.767 47.619 12.10 0.00 0.00 3.16
4138 19588 1.871039 ACAATTGTTGTAGCGCGAGTT 59.129 42.857 12.10 0.00 43.27 3.01
4158 19613 1.412079 ATGCTCTGGTGGTTTTGCAA 58.588 45.000 0.00 0.00 34.07 4.08
4161 19616 5.345741 CGAAAATAATGCTCTGGTGGTTTTG 59.654 40.000 0.00 0.00 0.00 2.44
4171 19626 5.126061 ACAATTCTGGCGAAAATAATGCTCT 59.874 36.000 0.00 0.00 31.91 4.09
4172 19627 5.343249 ACAATTCTGGCGAAAATAATGCTC 58.657 37.500 0.00 0.00 31.91 4.26
4185 19640 8.825745 TGAAGACAAAATAAAAACAATTCTGGC 58.174 29.630 0.00 0.00 0.00 4.85
4228 19683 5.050091 GCAGAGCAAGTTACGCAACATATAT 60.050 40.000 0.56 0.00 37.10 0.86
4231 19686 2.415168 GCAGAGCAAGTTACGCAACATA 59.585 45.455 0.56 0.00 37.10 2.29
4260 19721 1.819288 TCGGTGGTTTTGCAACAAAGA 59.181 42.857 0.00 0.00 34.15 2.52
4330 19802 7.201644 CCAAAGTTCTCACGCAACATATCTATT 60.202 37.037 0.00 0.00 0.00 1.73
4345 19829 3.295093 TCCATTGTTGCCAAAGTTCTCA 58.705 40.909 0.00 0.00 33.44 3.27
4349 19833 5.806654 ATACTTCCATTGTTGCCAAAGTT 57.193 34.783 0.00 0.00 33.44 2.66
4355 19839 2.529151 CGCAATACTTCCATTGTTGCC 58.471 47.619 0.00 0.00 41.43 4.52
4410 19902 2.752354 CCTCCCGCAACAACATTTATGA 59.248 45.455 0.00 0.00 0.00 2.15
4574 20565 2.226437 CGTTCTGGTCAGGATGGTTTTG 59.774 50.000 0.00 0.00 36.16 2.44
4580 20573 0.526211 TCGTCGTTCTGGTCAGGATG 59.474 55.000 0.00 0.00 37.54 3.51
4590 20585 2.257676 GCCCTTCGTCGTCGTTCT 59.742 61.111 1.33 0.00 38.33 3.01
4626 20621 0.394216 ACCATCAGCCTAATTGCGCA 60.394 50.000 5.66 5.66 36.02 6.09
4633 20628 1.833630 CTCAGGTCACCATCAGCCTAA 59.166 52.381 0.00 0.00 0.00 2.69
4731 20810 2.093973 AGCACGTGTCCTTATCCTCTTG 60.094 50.000 18.38 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.