Multiple sequence alignment - TraesCS3A01G007500

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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 TraesCS3A01G007500 chr3A 100.000 2372 0 0 1 2372 7652355 7654726 0.000000e+00 4381
1 TraesCS3A01G007500 chr3A 94.213 743 40 3 1 742 486043300 486044040 0.000000e+00 1131
2 TraesCS3A01G007500 chr3A 85.155 613 64 15 157 746 614224391 614223783 9.380000e-169 603
3 TraesCS3A01G007500 chr3A 85.008 607 66 14 157 741 1873566 1874169 5.640000e-166 593
4 TraesCS3A01G007500 chr3A 83.305 581 68 19 190 747 621604815 621604241 2.100000e-140 508
5 TraesCS3A01G007500 chr3A 82.090 603 76 18 163 742 434789343 434789936 9.860000e-134 486
6 TraesCS3A01G007500 chr3A 87.363 182 17 6 1054 1231 300790558 300790737 1.110000e-48 204
7 TraesCS3A01G007500 chr5A 98.922 742 7 1 1 741 69548322 69549063 0.000000e+00 1325
8 TraesCS3A01G007500 chr5A 82.645 726 81 22 56 741 367067885 367068605 3.370000e-168 601
9 TraesCS3A01G007500 chr5A 86.288 423 55 3 321 741 570231807 570232228 7.730000e-125 457
10 TraesCS3A01G007500 chr5A 89.759 166 14 1 1054 1216 705529328 705529493 2.390000e-50 209
11 TraesCS3A01G007500 chr1A 98.248 742 12 1 1 741 541774160 541773419 0.000000e+00 1297
12 TraesCS3A01G007500 chr7A 93.378 740 40 3 1 739 271158213 271158944 0.000000e+00 1086
13 TraesCS3A01G007500 chr7A 82.621 725 82 21 56 741 598253637 598252918 3.370000e-168 601
14 TraesCS3A01G007500 chr7A 82.507 383 40 16 987 1363 653264598 653264959 6.370000e-81 311
15 TraesCS3A01G007500 chr7A 85.906 149 11 7 1596 1739 310580531 310580674 1.470000e-32 150
16 TraesCS3A01G007500 chr7A 85.906 149 11 7 1596 1739 653265135 653265278 1.470000e-32 150
17 TraesCS3A01G007500 chr3B 82.561 1187 99 44 742 1837 5405815 5406984 0.000000e+00 946
18 TraesCS3A01G007500 chr3B 86.111 648 40 19 806 1410 3310518 3309878 0.000000e+00 652
19 TraesCS3A01G007500 chr3B 78.670 361 37 19 1993 2326 5407021 5407368 1.110000e-48 204
20 TraesCS3A01G007500 chr3B 88.485 165 10 3 1682 1837 3309693 3309529 8.650000e-45 191
21 TraesCS3A01G007500 chr3D 81.196 1154 101 50 742 1837 1318076 1316981 0.000000e+00 822
22 TraesCS3A01G007500 chr2A 82.645 726 83 20 56 742 603684905 603684184 9.380000e-169 603
23 TraesCS3A01G007500 chr7B 83.056 602 75 17 163 741 684578178 684578775 2.700000e-144 521
24 TraesCS3A01G007500 chr1B 82.724 602 77 17 163 741 480373507 480374104 5.850000e-141 510
25 TraesCS3A01G007500 chr5B 80.962 499 49 23 1835 2287 528388562 528389060 1.040000e-93 353
26 TraesCS3A01G007500 chr5B 88.664 247 20 4 1594 1837 528388280 528388521 6.410000e-76 294
27 TraesCS3A01G007500 chr6A 81.748 389 44 15 987 1369 87535133 87534766 1.380000e-77 300
28 TraesCS3A01G007500 chr6A 86.577 149 10 7 1596 1739 87534595 87534452 3.160000e-34 156
29 TraesCS3A01G007500 chr4A 82.500 320 36 12 987 1300 682035510 682035815 1.810000e-66 263
30 TraesCS3A01G007500 chr4A 86.577 149 10 6 1596 1739 101823068 101822925 3.160000e-34 156
31 TraesCS3A01G007500 chr4A 85.714 147 11 7 1596 1737 682036035 682036176 1.900000e-31 147
32 TraesCS3A01G007500 chr4D 88.208 212 16 3 1015 1217 321815852 321815641 6.550000e-61 244
33 TraesCS3A01G007500 chr1D 87.111 225 17 6 1017 1231 46107117 46107339 6.550000e-61 244


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 TraesCS3A01G007500 chr3A 7652355 7654726 2371 False 4381.0 4381 100.0000 1 2372 1 chr3A.!!$F2 2371
1 TraesCS3A01G007500 chr3A 486043300 486044040 740 False 1131.0 1131 94.2130 1 742 1 chr3A.!!$F5 741
2 TraesCS3A01G007500 chr3A 614223783 614224391 608 True 603.0 603 85.1550 157 746 1 chr3A.!!$R1 589
3 TraesCS3A01G007500 chr3A 1873566 1874169 603 False 593.0 593 85.0080 157 741 1 chr3A.!!$F1 584
4 TraesCS3A01G007500 chr3A 621604241 621604815 574 True 508.0 508 83.3050 190 747 1 chr3A.!!$R2 557
5 TraesCS3A01G007500 chr3A 434789343 434789936 593 False 486.0 486 82.0900 163 742 1 chr3A.!!$F4 579
6 TraesCS3A01G007500 chr5A 69548322 69549063 741 False 1325.0 1325 98.9220 1 741 1 chr5A.!!$F1 740
7 TraesCS3A01G007500 chr5A 367067885 367068605 720 False 601.0 601 82.6450 56 741 1 chr5A.!!$F2 685
8 TraesCS3A01G007500 chr1A 541773419 541774160 741 True 1297.0 1297 98.2480 1 741 1 chr1A.!!$R1 740
9 TraesCS3A01G007500 chr7A 271158213 271158944 731 False 1086.0 1086 93.3780 1 739 1 chr7A.!!$F1 738
10 TraesCS3A01G007500 chr7A 598252918 598253637 719 True 601.0 601 82.6210 56 741 1 chr7A.!!$R1 685
11 TraesCS3A01G007500 chr7A 653264598 653265278 680 False 230.5 311 84.2065 987 1739 2 chr7A.!!$F3 752
12 TraesCS3A01G007500 chr3B 5405815 5407368 1553 False 575.0 946 80.6155 742 2326 2 chr3B.!!$F1 1584
13 TraesCS3A01G007500 chr3B 3309529 3310518 989 True 421.5 652 87.2980 806 1837 2 chr3B.!!$R1 1031
14 TraesCS3A01G007500 chr3D 1316981 1318076 1095 True 822.0 822 81.1960 742 1837 1 chr3D.!!$R1 1095
15 TraesCS3A01G007500 chr2A 603684184 603684905 721 True 603.0 603 82.6450 56 742 1 chr2A.!!$R1 686
16 TraesCS3A01G007500 chr7B 684578178 684578775 597 False 521.0 521 83.0560 163 741 1 chr7B.!!$F1 578
17 TraesCS3A01G007500 chr1B 480373507 480374104 597 False 510.0 510 82.7240 163 741 1 chr1B.!!$F1 578
18 TraesCS3A01G007500 chr5B 528388280 528389060 780 False 323.5 353 84.8130 1594 2287 2 chr5B.!!$F1 693
19 TraesCS3A01G007500 chr6A 87534452 87535133 681 True 228.0 300 84.1625 987 1739 2 chr6A.!!$R1 752
20 TraesCS3A01G007500 chr4A 682035510 682036176 666 False 205.0 263 84.1070 987 1737 2 chr4A.!!$F1 750

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
978 1060 0.73315 GCCGAAAAAGAAGATCCCGG 59.267 55.0 0.0 0.0 38.58 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 2607 0.669932 CTGACAGAGGAGCACTGTGC 60.67 60.0 24.59 24.59 46.57 4.57 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
565 605 1.270907 TGGCCGGTTTTTATTGCCAT 58.729 45.000 1.90 0.00 46.57 4.40
760 801 0.808755 AGCTTAATTGGAAACCCGCG 59.191 50.000 0.00 0.00 0.00 6.46
762 803 1.731098 GCTTAATTGGAAACCCGCGTG 60.731 52.381 4.92 0.00 0.00 5.34
816 857 1.802715 CGTTGTAATCCGGTCGCGT 60.803 57.895 5.77 0.00 0.00 6.01
863 907 0.945813 GTCACGTCTCTATCTCCCCG 59.054 60.000 0.00 0.00 0.00 5.73
911 972 4.681978 AGCCGCAGTCCACGAACC 62.682 66.667 0.00 0.00 0.00 3.62
978 1060 0.733150 GCCGAAAAAGAAGATCCCGG 59.267 55.000 0.00 0.00 38.58 5.73
1047 1139 2.263540 GTCGCGGCCCTTTGTCTA 59.736 61.111 6.13 0.00 0.00 2.59
1060 1158 1.252215 TTGTCTATGGTGGTCGGCGA 61.252 55.000 4.99 4.99 0.00 5.54
1364 1468 2.034687 TGCTTTCCTGCTGCTCCC 59.965 61.111 0.00 0.00 0.00 4.30
1373 1477 1.667154 CTGCTGCTCCCGCACTAGTA 61.667 60.000 0.00 0.00 42.25 1.82
1381 1485 1.565759 TCCCGCACTAGTAACCCTCTA 59.434 52.381 0.00 0.00 0.00 2.43
1389 1506 5.632118 CACTAGTAACCCTCTATCTGGCTA 58.368 45.833 0.00 0.00 0.00 3.93
1413 1530 2.771943 TCATCCACCCCTGTAGATTGAC 59.228 50.000 0.00 0.00 0.00 3.18
1420 1537 2.170607 CCCCTGTAGATTGACGGATGTT 59.829 50.000 0.00 0.00 0.00 2.71
1423 1540 3.865745 CCTGTAGATTGACGGATGTTGTC 59.134 47.826 0.00 0.00 36.88 3.18
1424 1541 4.382040 CCTGTAGATTGACGGATGTTGTCT 60.382 45.833 0.00 0.00 37.26 3.41
1425 1542 4.494484 TGTAGATTGACGGATGTTGTCTG 58.506 43.478 0.00 0.00 37.26 3.51
1426 1543 3.961480 AGATTGACGGATGTTGTCTGA 57.039 42.857 0.00 0.00 37.26 3.27
1427 1544 4.271696 AGATTGACGGATGTTGTCTGAA 57.728 40.909 0.00 0.00 37.26 3.02
1428 1545 4.836825 AGATTGACGGATGTTGTCTGAAT 58.163 39.130 0.00 0.00 37.26 2.57
1429 1546 5.977635 AGATTGACGGATGTTGTCTGAATA 58.022 37.500 0.00 0.00 37.26 1.75
1430 1547 5.812642 AGATTGACGGATGTTGTCTGAATAC 59.187 40.000 0.00 0.00 37.26 1.89
1431 1548 4.801330 TGACGGATGTTGTCTGAATACT 57.199 40.909 0.00 0.00 37.26 2.12
1434 1551 4.495422 ACGGATGTTGTCTGAATACTGAC 58.505 43.478 0.00 0.00 42.57 3.51
1436 1553 3.865745 GGATGTTGTCTGAATACTGACGG 59.134 47.826 0.00 0.00 44.27 4.79
1438 1555 2.299013 TGTTGTCTGAATACTGACGGCT 59.701 45.455 0.00 0.00 44.27 5.52
1439 1556 2.654749 TGTCTGAATACTGACGGCTG 57.345 50.000 0.00 0.00 44.27 4.85
1441 1558 1.134965 GTCTGAATACTGACGGCTGCT 60.135 52.381 0.00 0.00 35.84 4.24
1443 1560 0.608130 TGAATACTGACGGCTGCTGT 59.392 50.000 15.10 15.10 0.00 4.40
1445 1562 1.021390 AATACTGACGGCTGCTGTGC 61.021 55.000 20.51 11.04 0.00 4.57
1448 1565 3.871248 CTGACGGCTGCTGTGCTGA 62.871 63.158 20.51 0.00 41.56 4.26
1494 1633 9.660180 GTAATTCTAGGTCTTGAGTTCAATTCT 57.340 33.333 0.00 0.00 35.02 2.40
1513 1672 7.557719 TCAATTCTAAAGGCAATCTAAGAAGGG 59.442 37.037 0.00 0.00 33.72 3.95
1551 1712 4.320788 CCTTTCTGCATCCTGTTCTTGTTC 60.321 45.833 0.00 0.00 0.00 3.18
1555 1716 2.087646 GCATCCTGTTCTTGTTCCTCC 58.912 52.381 0.00 0.00 0.00 4.30
1556 1717 2.716217 CATCCTGTTCTTGTTCCTCCC 58.284 52.381 0.00 0.00 0.00 4.30
1567 1729 5.208121 TCTTGTTCCTCCCTTGATTTGTTT 58.792 37.500 0.00 0.00 0.00 2.83
1580 1742 3.640498 TGATTTGTTTGTTCATGGAGGCA 59.360 39.130 0.00 0.00 0.00 4.75
1592 1754 6.599244 TGTTCATGGAGGCAATAACTTCTAAG 59.401 38.462 0.00 0.00 0.00 2.18
1608 1774 4.545823 TCTAAGTTTTCGTTGCAACTGG 57.454 40.909 26.09 12.63 33.38 4.00
1642 1813 6.979817 GCTCTGCCAGATCTGATATAATACAG 59.020 42.308 24.62 15.48 35.72 2.74
1643 1814 6.871844 TCTGCCAGATCTGATATAATACAGC 58.128 40.000 24.62 14.25 34.57 4.40
1664 1836 6.156256 ACAGCATAGAGTACTACCAATTTGGA 59.844 38.462 22.19 5.08 40.96 3.53
1665 1837 7.147479 ACAGCATAGAGTACTACCAATTTGGAT 60.147 37.037 22.19 8.80 40.96 3.41
1666 1838 7.386299 CAGCATAGAGTACTACCAATTTGGATC 59.614 40.741 22.19 9.22 40.96 3.36
1667 1839 7.291182 AGCATAGAGTACTACCAATTTGGATCT 59.709 37.037 22.19 14.77 40.96 2.75
1668 1840 7.386299 GCATAGAGTACTACCAATTTGGATCTG 59.614 40.741 22.19 10.41 40.96 2.90
1669 1841 6.875972 AGAGTACTACCAATTTGGATCTGT 57.124 37.500 22.19 14.89 40.96 3.41
1670 1842 6.644347 AGAGTACTACCAATTTGGATCTGTG 58.356 40.000 22.19 7.31 40.96 3.66
1671 1843 6.213600 AGAGTACTACCAATTTGGATCTGTGT 59.786 38.462 22.19 11.94 40.96 3.72
1672 1844 7.399191 AGAGTACTACCAATTTGGATCTGTGTA 59.601 37.037 22.19 11.11 40.96 2.90
1759 1940 7.439356 TCTTGAGAATATTATTGACTCTTGGCG 59.561 37.037 0.00 0.00 0.00 5.69
1775 1956 3.716006 CGGCACTGTTGGACGCTG 61.716 66.667 0.00 0.00 0.00 5.18
1846 2073 1.103398 AGCACAAGCCGCTCAACTTT 61.103 50.000 0.00 0.00 43.56 2.66
1858 2085 3.004734 CGCTCAACTTTGATTGGTCCTTT 59.995 43.478 0.00 0.00 36.46 3.11
1870 2097 8.737168 TTGATTGGTCCTTTTATCTGTGATAG 57.263 34.615 0.00 0.00 0.00 2.08
1899 2126 3.190118 CAGTCCTTGCAAAGTTCATCTCC 59.810 47.826 0.00 0.00 44.25 3.71
1935 2163 5.687770 AAAATCCCGGCAAAAGAAAAATG 57.312 34.783 0.00 0.00 0.00 2.32
1937 2165 1.346068 TCCCGGCAAAAGAAAAATGGG 59.654 47.619 0.00 0.00 36.72 4.00
1973 2207 6.038603 GCAAATCCATTATTCTCACAGCACTA 59.961 38.462 0.00 0.00 0.00 2.74
1975 2209 5.675684 TCCATTATTCTCACAGCACTACA 57.324 39.130 0.00 0.00 0.00 2.74
1977 2211 7.360113 TCCATTATTCTCACAGCACTACATA 57.640 36.000 0.00 0.00 0.00 2.29
1978 2212 7.436933 TCCATTATTCTCACAGCACTACATAG 58.563 38.462 0.00 0.00 0.00 2.23
1980 2214 7.383572 CCATTATTCTCACAGCACTACATAGTC 59.616 40.741 0.00 0.00 33.46 2.59
1981 2215 7.646548 TTATTCTCACAGCACTACATAGTCT 57.353 36.000 0.00 0.00 33.46 3.24
1982 2216 8.747538 TTATTCTCACAGCACTACATAGTCTA 57.252 34.615 0.00 0.00 33.46 2.59
1988 2233 8.465273 TCACAGCACTACATAGTCTACATTAT 57.535 34.615 0.00 0.00 33.46 1.28
1989 2234 8.568794 TCACAGCACTACATAGTCTACATTATC 58.431 37.037 0.00 0.00 33.46 1.75
2000 2245 9.096160 CATAGTCTACATTATCCATCATTCAGC 57.904 37.037 0.00 0.00 0.00 4.26
2083 2337 5.810095 ACTGAACCTACGGTTACTAGTAGT 58.190 41.667 8.14 8.14 46.95 2.73
2119 2373 1.792118 GCACCACCGGTTCAGTTTCC 61.792 60.000 2.97 0.00 31.02 3.13
2120 2374 1.149854 ACCACCGGTTCAGTTTCCC 59.850 57.895 2.97 0.00 27.29 3.97
2123 2377 0.666374 CACCGGTTCAGTTTCCCAAC 59.334 55.000 2.97 0.00 0.00 3.77
2127 2381 2.166664 CCGGTTCAGTTTCCCAACAAAA 59.833 45.455 0.00 0.00 35.05 2.44
2130 2384 4.570930 GGTTCAGTTTCCCAACAAAAACA 58.429 39.130 0.00 0.00 37.74 2.83
2131 2385 4.390603 GGTTCAGTTTCCCAACAAAAACAC 59.609 41.667 0.00 0.00 37.74 3.32
2134 2394 3.857093 CAGTTTCCCAACAAAAACACGAG 59.143 43.478 0.00 0.00 37.74 4.18
2185 2445 3.772387 TGCCAAATACCACCATCAAAGA 58.228 40.909 0.00 0.00 0.00 2.52
2193 2470 8.359642 CAAATACCACCATCAAAGAAAGAAAGA 58.640 33.333 0.00 0.00 0.00 2.52
2203 2480 9.242477 CATCAAAGAAAGAAAGAAAGAAACCTC 57.758 33.333 0.00 0.00 0.00 3.85
2229 2507 2.815211 GCGGCATCACTGAAGCGA 60.815 61.111 0.00 0.00 0.00 4.93
2263 2546 4.264083 ACCAAATCTCTCACCATCACCAAT 60.264 41.667 0.00 0.00 0.00 3.16
2269 2552 5.573219 TCTCTCACCATCACCAATGAATTT 58.427 37.500 0.00 0.00 38.69 1.82
2288 2571 3.988976 TTACCAGCAGAAGATGAAGCT 57.011 42.857 0.00 0.00 37.95 3.74
2302 2585 1.985159 TGAAGCTGATTACTGTGGGGT 59.015 47.619 0.00 0.00 0.00 4.95
2311 2594 5.697067 TGATTACTGTGGGGTTTTACACTT 58.303 37.500 0.00 0.00 38.39 3.16
2312 2595 6.130569 TGATTACTGTGGGGTTTTACACTTT 58.869 36.000 0.00 0.00 38.39 2.66
2314 2597 2.429250 ACTGTGGGGTTTTACACTTTGC 59.571 45.455 0.00 0.00 38.39 3.68
2316 2599 2.428890 TGTGGGGTTTTACACTTTGCAG 59.571 45.455 0.00 0.00 38.39 4.41
2319 2602 3.633065 TGGGGTTTTACACTTTGCAGTAC 59.367 43.478 0.00 0.00 0.00 2.73
2320 2603 3.887110 GGGGTTTTACACTTTGCAGTACT 59.113 43.478 0.00 0.00 0.00 2.73
2321 2604 5.065235 GGGGTTTTACACTTTGCAGTACTA 58.935 41.667 0.00 0.00 0.00 1.82
2322 2605 5.049198 GGGGTTTTACACTTTGCAGTACTAC 60.049 44.000 0.00 0.00 0.00 2.73
2323 2606 5.761726 GGGTTTTACACTTTGCAGTACTACT 59.238 40.000 0.00 0.00 0.00 2.57
2333 2616 2.732412 CAGTACTACTGCACAGTGCT 57.268 50.000 25.83 9.77 45.31 4.40
2334 2617 2.600731 CAGTACTACTGCACAGTGCTC 58.399 52.381 25.83 7.97 45.31 4.26
2335 2618 1.546476 AGTACTACTGCACAGTGCTCC 59.454 52.381 25.83 6.35 45.31 4.70
2336 2619 1.546476 GTACTACTGCACAGTGCTCCT 59.454 52.381 25.83 10.70 45.31 3.69
2337 2620 0.605589 ACTACTGCACAGTGCTCCTC 59.394 55.000 25.83 0.00 45.31 3.71
2338 2621 0.894141 CTACTGCACAGTGCTCCTCT 59.106 55.000 25.83 6.65 45.31 3.69
2339 2622 0.605083 TACTGCACAGTGCTCCTCTG 59.395 55.000 25.83 11.25 45.31 3.35
2340 2623 1.370437 CTGCACAGTGCTCCTCTGT 59.630 57.895 25.83 0.00 45.31 3.41
2341 2624 0.669932 CTGCACAGTGCTCCTCTGTC 60.670 60.000 25.83 0.00 45.31 3.51
2342 2625 1.368950 GCACAGTGCTCCTCTGTCA 59.631 57.895 18.92 0.00 43.14 3.58
2343 2626 0.669932 GCACAGTGCTCCTCTGTCAG 60.670 60.000 18.92 0.00 43.14 3.51
2344 2627 0.964700 CACAGTGCTCCTCTGTCAGA 59.035 55.000 1.78 1.78 43.14 3.27
2345 2628 1.342496 CACAGTGCTCCTCTGTCAGAA 59.658 52.381 3.67 0.00 43.14 3.02
2346 2629 2.042464 ACAGTGCTCCTCTGTCAGAAA 58.958 47.619 3.67 0.00 41.52 2.52
2347 2630 2.435805 ACAGTGCTCCTCTGTCAGAAAA 59.564 45.455 3.67 0.00 41.52 2.29
2348 2631 3.118261 ACAGTGCTCCTCTGTCAGAAAAA 60.118 43.478 3.67 0.00 41.52 1.94
2349 2632 3.249559 CAGTGCTCCTCTGTCAGAAAAAC 59.750 47.826 3.67 0.00 0.00 2.43
2350 2633 2.550180 GTGCTCCTCTGTCAGAAAAACC 59.450 50.000 3.67 0.00 0.00 3.27
2351 2634 2.172505 TGCTCCTCTGTCAGAAAAACCA 59.827 45.455 3.67 0.00 0.00 3.67
2352 2635 3.214328 GCTCCTCTGTCAGAAAAACCAA 58.786 45.455 3.67 0.00 0.00 3.67
2353 2636 3.632145 GCTCCTCTGTCAGAAAAACCAAA 59.368 43.478 3.67 0.00 0.00 3.28
2354 2637 4.097892 GCTCCTCTGTCAGAAAAACCAAAA 59.902 41.667 3.67 0.00 0.00 2.44
2355 2638 5.734503 GCTCCTCTGTCAGAAAAACCAAAAG 60.735 44.000 3.67 0.00 0.00 2.27
2356 2639 5.261216 TCCTCTGTCAGAAAAACCAAAAGT 58.739 37.500 3.67 0.00 0.00 2.66
2357 2640 6.419791 TCCTCTGTCAGAAAAACCAAAAGTA 58.580 36.000 3.67 0.00 0.00 2.24
2358 2641 6.317893 TCCTCTGTCAGAAAAACCAAAAGTAC 59.682 38.462 3.67 0.00 0.00 2.73
2359 2642 6.318900 CCTCTGTCAGAAAAACCAAAAGTACT 59.681 38.462 3.67 0.00 0.00 2.73
2360 2643 7.497909 CCTCTGTCAGAAAAACCAAAAGTACTA 59.502 37.037 3.67 0.00 0.00 1.82
2361 2644 8.795842 TCTGTCAGAAAAACCAAAAGTACTAA 57.204 30.769 0.00 0.00 0.00 2.24
2362 2645 9.403583 TCTGTCAGAAAAACCAAAAGTACTAAT 57.596 29.630 0.00 0.00 0.00 1.73
2364 2647 9.796120 TGTCAGAAAAACCAAAAGTACTAATTG 57.204 29.630 12.26 12.26 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
565 605 3.751175 GGTCTTGCTTGTAAGTGCACATA 59.249 43.478 21.04 8.97 39.05 2.29
760 801 4.729856 CGACGGGTTCGGGGTCAC 62.730 72.222 0.00 0.00 44.60 3.67
768 809 3.406559 GCCATTAGCGACGGGTTC 58.593 61.111 0.00 0.00 0.00 3.62
799 840 0.094046 CAACGCGACCGGATTACAAC 59.906 55.000 15.93 0.00 39.22 3.32
800 841 1.015085 CCAACGCGACCGGATTACAA 61.015 55.000 15.93 0.00 39.22 2.41
801 842 1.446445 CCAACGCGACCGGATTACA 60.446 57.895 15.93 0.00 39.22 2.41
863 907 2.558378 GTCCCGATTGGTTAAGTAGCC 58.442 52.381 0.00 0.00 34.77 3.93
950 1023 0.250553 TCTTTTTCGGCGGTGGTGAT 60.251 50.000 7.21 0.00 0.00 3.06
990 1082 2.107141 GACGGCATCCTTCCTCGG 59.893 66.667 0.00 0.00 0.00 4.63
1039 1131 1.369625 GCCGACCACCATAGACAAAG 58.630 55.000 0.00 0.00 0.00 2.77
1041 1133 1.216977 CGCCGACCACCATAGACAA 59.783 57.895 0.00 0.00 0.00 3.18
1044 1136 3.203442 GTCGCCGACCACCATAGA 58.797 61.111 5.81 0.00 0.00 1.98
1296 1400 2.427753 GGATTCCTAGCGGGGCTG 59.572 66.667 0.00 0.00 40.10 4.85
1364 1468 3.253677 CCAGATAGAGGGTTACTAGTGCG 59.746 52.174 5.39 0.00 0.00 5.34
1373 1477 2.091055 TGAGCTAGCCAGATAGAGGGTT 60.091 50.000 12.13 0.00 38.04 4.11
1389 1506 0.339859 TCTACAGGGGTGGATGAGCT 59.660 55.000 0.00 0.00 28.51 4.09
1413 1530 3.547868 CGTCAGTATTCAGACAACATCCG 59.452 47.826 0.00 0.00 34.48 4.18
1420 1537 1.404181 GCAGCCGTCAGTATTCAGACA 60.404 52.381 0.00 0.00 34.48 3.41
1423 1540 1.284657 CAGCAGCCGTCAGTATTCAG 58.715 55.000 0.00 0.00 0.00 3.02
1424 1541 0.608130 ACAGCAGCCGTCAGTATTCA 59.392 50.000 0.00 0.00 0.00 2.57
1425 1542 1.002366 CACAGCAGCCGTCAGTATTC 58.998 55.000 0.00 0.00 0.00 1.75
1426 1543 1.021390 GCACAGCAGCCGTCAGTATT 61.021 55.000 0.00 0.00 0.00 1.89
1427 1544 1.448540 GCACAGCAGCCGTCAGTAT 60.449 57.895 0.00 0.00 0.00 2.12
1428 1545 2.048222 GCACAGCAGCCGTCAGTA 60.048 61.111 0.00 0.00 0.00 2.74
1429 1546 3.933722 AGCACAGCAGCCGTCAGT 61.934 61.111 0.00 0.00 34.23 3.41
1430 1547 3.420606 CAGCACAGCAGCCGTCAG 61.421 66.667 0.00 0.00 34.23 3.51
1431 1548 3.244281 ATCAGCACAGCAGCCGTCA 62.244 57.895 0.00 0.00 34.23 4.35
1434 1551 2.745100 ACATCAGCACAGCAGCCG 60.745 61.111 0.00 0.00 34.23 5.52
1436 1553 0.672711 TCAGACATCAGCACAGCAGC 60.673 55.000 0.00 0.00 0.00 5.25
1438 1555 2.027469 AGATTCAGACATCAGCACAGCA 60.027 45.455 0.00 0.00 0.00 4.41
1439 1556 2.630158 AGATTCAGACATCAGCACAGC 58.370 47.619 0.00 0.00 0.00 4.40
1441 1558 7.294017 TCATATAGATTCAGACATCAGCACA 57.706 36.000 0.00 0.00 0.00 4.57
1443 1560 8.373220 ACATTCATATAGATTCAGACATCAGCA 58.627 33.333 0.00 0.00 0.00 4.41
1485 1624 9.780413 CTTCTTAGATTGCCTTTAGAATTGAAC 57.220 33.333 0.00 0.00 0.00 3.18
1494 1633 5.222254 ACCAACCCTTCTTAGATTGCCTTTA 60.222 40.000 0.00 0.00 0.00 1.85
1495 1634 4.089361 CCAACCCTTCTTAGATTGCCTTT 58.911 43.478 0.00 0.00 0.00 3.11
1513 1672 1.961394 GAAAGGAGGAACCCAACCAAC 59.039 52.381 0.00 0.00 40.05 3.77
1551 1712 4.935352 TGAACAAACAAATCAAGGGAGG 57.065 40.909 0.00 0.00 0.00 4.30
1555 1716 5.232463 CCTCCATGAACAAACAAATCAAGG 58.768 41.667 0.00 0.00 34.18 3.61
1556 1717 4.687483 GCCTCCATGAACAAACAAATCAAG 59.313 41.667 0.00 0.00 0.00 3.02
1567 1729 4.922206 AGAAGTTATTGCCTCCATGAACA 58.078 39.130 0.00 0.00 0.00 3.18
1592 1754 1.786579 GCATCCAGTTGCAACGAAAAC 59.213 47.619 23.21 9.49 42.31 2.43
1638 1809 7.343574 TCCAAATTGGTAGTACTCTATGCTGTA 59.656 37.037 12.28 0.00 39.03 2.74
1642 1813 7.386299 CAGATCCAAATTGGTAGTACTCTATGC 59.614 40.741 12.28 0.00 39.03 3.14
1643 1814 8.424918 ACAGATCCAAATTGGTAGTACTCTATG 58.575 37.037 12.28 1.36 39.03 2.23
1658 1830 8.000709 ACCAATCATACATACACAGATCCAAAT 58.999 33.333 0.00 0.00 0.00 2.32
1661 1833 6.290605 CACCAATCATACATACACAGATCCA 58.709 40.000 0.00 0.00 0.00 3.41
1664 1836 5.933617 AGCACCAATCATACATACACAGAT 58.066 37.500 0.00 0.00 0.00 2.90
1665 1837 5.357742 AGCACCAATCATACATACACAGA 57.642 39.130 0.00 0.00 0.00 3.41
1666 1838 6.441093 AAAGCACCAATCATACATACACAG 57.559 37.500 0.00 0.00 0.00 3.66
1667 1839 7.772757 TCATAAAGCACCAATCATACATACACA 59.227 33.333 0.00 0.00 0.00 3.72
1668 1840 8.153479 TCATAAAGCACCAATCATACATACAC 57.847 34.615 0.00 0.00 0.00 2.90
1669 1841 8.210265 TCTCATAAAGCACCAATCATACATACA 58.790 33.333 0.00 0.00 0.00 2.29
1670 1842 8.607441 TCTCATAAAGCACCAATCATACATAC 57.393 34.615 0.00 0.00 0.00 2.39
1671 1843 9.223099 CATCTCATAAAGCACCAATCATACATA 57.777 33.333 0.00 0.00 0.00 2.29
1672 1844 7.722728 ACATCTCATAAAGCACCAATCATACAT 59.277 33.333 0.00 0.00 0.00 2.29
1749 1927 1.598130 AACAGTGCCGCCAAGAGTC 60.598 57.895 0.00 0.00 0.00 3.36
1759 1940 2.725203 TACCAGCGTCCAACAGTGCC 62.725 60.000 0.00 0.00 0.00 5.01
1772 1953 2.093447 AGCACTACAAGATGGTACCAGC 60.093 50.000 22.75 22.75 0.00 4.85
1775 1956 3.056107 TGACAGCACTACAAGATGGTACC 60.056 47.826 4.43 4.43 0.00 3.34
1846 2073 7.987458 GTCTATCACAGATAAAAGGACCAATCA 59.013 37.037 0.00 0.00 35.17 2.57
1880 2107 2.038426 TCGGAGATGAACTTTGCAAGGA 59.962 45.455 16.36 0.00 0.00 3.36
1914 2141 4.071423 CCATTTTTCTTTTGCCGGGATTT 58.929 39.130 2.18 0.00 0.00 2.17
1917 2145 1.346068 CCCATTTTTCTTTTGCCGGGA 59.654 47.619 2.18 0.00 34.10 5.14
1919 2147 2.829741 TCCCATTTTTCTTTTGCCGG 57.170 45.000 0.00 0.00 0.00 6.13
1922 2150 5.176774 CCGTAGTTTCCCATTTTTCTTTTGC 59.823 40.000 0.00 0.00 0.00 3.68
1935 2163 2.014857 GGATTTGCTCCGTAGTTTCCC 58.985 52.381 0.00 0.00 33.29 3.97
1968 2202 8.523658 TGATGGATAATGTAGACTATGTAGTGC 58.476 37.037 0.00 0.00 36.50 4.40
1975 2209 9.044646 AGCTGAATGATGGATAATGTAGACTAT 57.955 33.333 0.00 0.00 0.00 2.12
1977 2211 7.313740 AGCTGAATGATGGATAATGTAGACT 57.686 36.000 0.00 0.00 0.00 3.24
1982 2216 9.445878 CAGTTATAGCTGAATGATGGATAATGT 57.554 33.333 10.88 0.00 38.70 2.71
2039 2289 7.796838 TCAGTATTGATTTTCGACTTCAGTTG 58.203 34.615 0.00 0.00 0.00 3.16
2048 2298 6.880822 CGTAGGTTCAGTATTGATTTTCGA 57.119 37.500 0.00 0.00 32.27 3.71
2083 2337 2.159099 GGTGCGATCTGATTCACAGGTA 60.159 50.000 18.85 0.00 45.76 3.08
2119 2373 4.800993 TGCATTAACTCGTGTTTTTGTTGG 59.199 37.500 8.32 0.00 37.59 3.77
2120 2374 5.554324 GCTGCATTAACTCGTGTTTTTGTTG 60.554 40.000 8.32 5.59 37.59 3.33
2123 2377 4.290155 AGCTGCATTAACTCGTGTTTTTG 58.710 39.130 8.32 7.80 37.59 2.44
2127 2381 4.188247 TCTAGCTGCATTAACTCGTGTT 57.812 40.909 8.09 8.09 39.98 3.32
2130 2384 5.419542 TCATTTCTAGCTGCATTAACTCGT 58.580 37.500 1.02 0.00 0.00 4.18
2131 2385 5.973651 TCATTTCTAGCTGCATTAACTCG 57.026 39.130 1.02 0.00 0.00 4.18
2134 2394 8.383318 TCCTATTCATTTCTAGCTGCATTAAC 57.617 34.615 1.02 0.00 0.00 2.01
2185 2445 5.437946 ACGGAGAGGTTTCTTTCTTTCTTT 58.562 37.500 0.00 0.00 32.53 2.52
2193 2470 1.954382 GCCAAACGGAGAGGTTTCTTT 59.046 47.619 0.00 0.00 38.01 2.52
2229 2507 2.108952 AGAGATTTGGTTGAGGCCTTGT 59.891 45.455 6.77 0.00 0.00 3.16
2263 2546 5.124457 GCTTCATCTTCTGCTGGTAAATTCA 59.876 40.000 0.00 0.00 0.00 2.57
2269 2552 3.257469 CAGCTTCATCTTCTGCTGGTA 57.743 47.619 5.98 0.00 46.24 3.25
2288 2571 5.313280 AGTGTAAAACCCCACAGTAATCA 57.687 39.130 0.00 0.00 33.99 2.57
2324 2607 0.669932 CTGACAGAGGAGCACTGTGC 60.670 60.000 24.59 24.59 46.57 4.57
2325 2608 0.964700 TCTGACAGAGGAGCACTGTG 59.035 55.000 0.00 2.76 46.57 3.66
2327 2610 2.827800 TTTCTGACAGAGGAGCACTG 57.172 50.000 5.10 0.00 40.68 3.66
2328 2611 3.471680 GTTTTTCTGACAGAGGAGCACT 58.528 45.455 5.10 0.00 0.00 4.40
2329 2612 2.550180 GGTTTTTCTGACAGAGGAGCAC 59.450 50.000 5.10 0.34 0.00 4.40
2330 2613 2.172505 TGGTTTTTCTGACAGAGGAGCA 59.827 45.455 5.10 8.56 0.00 4.26
2331 2614 2.851195 TGGTTTTTCTGACAGAGGAGC 58.149 47.619 5.10 6.22 0.00 4.70
2332 2615 5.358160 ACTTTTGGTTTTTCTGACAGAGGAG 59.642 40.000 5.10 0.00 0.00 3.69
2333 2616 5.261216 ACTTTTGGTTTTTCTGACAGAGGA 58.739 37.500 5.10 0.00 0.00 3.71
2334 2617 5.582689 ACTTTTGGTTTTTCTGACAGAGG 57.417 39.130 5.10 0.00 0.00 3.69
2335 2618 7.321745 AGTACTTTTGGTTTTTCTGACAGAG 57.678 36.000 5.10 0.00 0.00 3.35
2336 2619 8.795842 TTAGTACTTTTGGTTTTTCTGACAGA 57.204 30.769 0.00 0.00 0.00 3.41
2338 2621 9.796120 CAATTAGTACTTTTGGTTTTTCTGACA 57.204 29.630 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.