Multiple sequence alignment - TraesCS2D01G237500

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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 TraesCS2D01G237500 chr2D 100.000 2564 0 0 1 2564 241712971 241715534 0.000000e+00 4735.0
1 TraesCS2D01G237500 chr2D 95.249 842 37 1 751 1589 57194683 57193842 0.000000e+00 1330.0
2 TraesCS2D01G237500 chr2D 96.144 752 23 2 1 750 294446797 294447544 0.000000e+00 1223.0
3 TraesCS2D01G237500 chr2D 87.825 846 92 5 751 1591 190430409 190429570 0.000000e+00 981.0
4 TraesCS2D01G237500 chr3B 95.724 842 32 2 751 1588 477881299 477880458 0.000000e+00 1352.0
5 TraesCS2D01G237500 chr3B 82.946 258 36 5 1682 1937 733561487 733561236 2.570000e-55 226.0
6 TraesCS2D01G237500 chr5D 96.809 752 18 3 1 751 339048995 339048249 0.000000e+00 1251.0
7 TraesCS2D01G237500 chr5D 87.470 830 101 1 751 1577 189272837 189272008 0.000000e+00 953.0
8 TraesCS2D01G237500 chr5D 87.470 830 100 2 751 1577 189461639 189460811 0.000000e+00 953.0
9 TraesCS2D01G237500 chr5D 76.863 255 36 14 1691 1939 530939125 530939362 3.460000e-24 122.0
10 TraesCS2D01G237500 chr7D 96.684 754 19 2 1 750 37269379 37270130 0.000000e+00 1249.0
11 TraesCS2D01G237500 chr7D 96.138 751 27 1 1 751 311701561 311700813 0.000000e+00 1225.0
12 TraesCS2D01G237500 chr7D 80.797 276 40 11 1662 1931 577214379 577214111 1.200000e-48 204.0
13 TraesCS2D01G237500 chr7D 95.122 41 2 0 1938 1978 526978324 526978364 5.920000e-07 65.8
14 TraesCS2D01G237500 chr2A 93.160 848 51 3 751 1595 347209034 347209877 0.000000e+00 1238.0
15 TraesCS2D01G237500 chr2A 92.575 862 56 6 1593 2450 281109579 281108722 0.000000e+00 1230.0
16 TraesCS2D01G237500 chr2A 94.118 119 6 1 2446 2564 280929934 280929817 2.030000e-41 180.0
17 TraesCS2D01G237500 chr3D 96.286 754 19 5 1 750 180199004 180198256 0.000000e+00 1229.0
18 TraesCS2D01G237500 chr3A 96.154 754 24 5 1 753 732354745 732353996 0.000000e+00 1227.0
19 TraesCS2D01G237500 chr3A 87.244 831 103 1 751 1578 691087531 691088361 0.000000e+00 944.0
20 TraesCS2D01G237500 chr6D 96.267 750 22 4 1 750 122910000 122910743 0.000000e+00 1225.0
21 TraesCS2D01G237500 chr6D 82.283 254 39 5 1689 1939 406113103 406112853 5.560000e-52 215.0
22 TraesCS2D01G237500 chr6D 79.348 276 46 8 1662 1932 441535723 441535992 1.570000e-42 183.0
23 TraesCS2D01G237500 chr6D 91.026 78 6 1 1706 1782 406113420 406113343 1.250000e-18 104.0
24 TraesCS2D01G237500 chr1D 96.272 751 21 3 1 748 416545723 416544977 0.000000e+00 1225.0
25 TraesCS2D01G237500 chr1D 96.133 750 24 2 1 750 342713720 342714464 0.000000e+00 1219.0
26 TraesCS2D01G237500 chr1D 82.857 210 31 2 1690 1898 317187190 317186985 1.570000e-42 183.0
27 TraesCS2D01G237500 chr5A 87.470 830 101 2 751 1577 429969670 429968841 0.000000e+00 953.0
28 TraesCS2D01G237500 chr5A 87.349 830 101 2 751 1577 583625677 583626505 0.000000e+00 948.0
29 TraesCS2D01G237500 chr5A 79.565 230 40 5 1681 1908 41881891 41881667 9.500000e-35 158.0
30 TraesCS2D01G237500 chr2B 91.978 536 43 0 1637 2172 320738844 320738309 0.000000e+00 752.0
31 TraesCS2D01G237500 chr2B 89.356 357 32 5 2210 2564 332672680 332673032 6.510000e-121 444.0
32 TraesCS2D01G237500 chr6A 85.398 226 28 4 1689 1912 552585152 552584930 1.980000e-56 230.0
33 TraesCS2D01G237500 chr6A 80.130 307 43 11 1637 1932 590047948 590048247 2.000000e-51 213.0
34 TraesCS2D01G237500 chr6A 80.543 221 33 8 1640 1857 552585369 552585156 7.340000e-36 161.0
35 TraesCS2D01G237500 chr4D 80.449 312 42 13 1637 1938 31648597 31648899 1.190000e-53 220.0
36 TraesCS2D01G237500 chr4D 79.233 313 48 11 1637 1938 500845185 500844879 4.330000e-48 202.0
37 TraesCS2D01G237500 chr4D 81.124 249 27 8 1691 1937 446096886 446096656 5.640000e-42 182.0
38 TraesCS2D01G237500 chr6B 82.573 241 30 9 1689 1925 599697088 599697320 4.330000e-48 202.0
39 TraesCS2D01G237500 chr6B 79.848 263 40 9 1662 1919 25048570 25048316 2.030000e-41 180.0
40 TraesCS2D01G237500 chr5B 81.673 251 34 7 1691 1939 689342720 689342480 5.600000e-47 198.0
41 TraesCS2D01G237500 chr5B 100.000 28 0 0 1937 1964 552674919 552674946 5.000000e-03 52.8
42 TraesCS2D01G237500 chr7A 85.714 70 10 0 1937 2006 177319417 177319486 9.840000e-10 75.0
43 TraesCS2D01G237500 chr1B 92.683 41 3 0 1938 1978 490009664 490009624 2.760000e-05 60.2


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 TraesCS2D01G237500 chr2D 241712971 241715534 2563 False 4735 4735 100.000 1 2564 1 chr2D.!!$F1 2563
1 TraesCS2D01G237500 chr2D 57193842 57194683 841 True 1330 1330 95.249 751 1589 1 chr2D.!!$R1 838
2 TraesCS2D01G237500 chr2D 294446797 294447544 747 False 1223 1223 96.144 1 750 1 chr2D.!!$F2 749
3 TraesCS2D01G237500 chr2D 190429570 190430409 839 True 981 981 87.825 751 1591 1 chr2D.!!$R2 840
4 TraesCS2D01G237500 chr3B 477880458 477881299 841 True 1352 1352 95.724 751 1588 1 chr3B.!!$R1 837
5 TraesCS2D01G237500 chr5D 339048249 339048995 746 True 1251 1251 96.809 1 751 1 chr5D.!!$R3 750
6 TraesCS2D01G237500 chr5D 189272008 189272837 829 True 953 953 87.470 751 1577 1 chr5D.!!$R1 826
7 TraesCS2D01G237500 chr5D 189460811 189461639 828 True 953 953 87.470 751 1577 1 chr5D.!!$R2 826
8 TraesCS2D01G237500 chr7D 37269379 37270130 751 False 1249 1249 96.684 1 750 1 chr7D.!!$F1 749
9 TraesCS2D01G237500 chr7D 311700813 311701561 748 True 1225 1225 96.138 1 751 1 chr7D.!!$R1 750
10 TraesCS2D01G237500 chr2A 347209034 347209877 843 False 1238 1238 93.160 751 1595 1 chr2A.!!$F1 844
11 TraesCS2D01G237500 chr2A 281108722 281109579 857 True 1230 1230 92.575 1593 2450 1 chr2A.!!$R2 857
12 TraesCS2D01G237500 chr3D 180198256 180199004 748 True 1229 1229 96.286 1 750 1 chr3D.!!$R1 749
13 TraesCS2D01G237500 chr3A 732353996 732354745 749 True 1227 1227 96.154 1 753 1 chr3A.!!$R1 752
14 TraesCS2D01G237500 chr3A 691087531 691088361 830 False 944 944 87.244 751 1578 1 chr3A.!!$F1 827
15 TraesCS2D01G237500 chr6D 122910000 122910743 743 False 1225 1225 96.267 1 750 1 chr6D.!!$F1 749
16 TraesCS2D01G237500 chr1D 416544977 416545723 746 True 1225 1225 96.272 1 748 1 chr1D.!!$R2 747
17 TraesCS2D01G237500 chr1D 342713720 342714464 744 False 1219 1219 96.133 1 750 1 chr1D.!!$F1 749
18 TraesCS2D01G237500 chr5A 429968841 429969670 829 True 953 953 87.470 751 1577 1 chr5A.!!$R2 826
19 TraesCS2D01G237500 chr5A 583625677 583626505 828 False 948 948 87.349 751 1577 1 chr5A.!!$F1 826
20 TraesCS2D01G237500 chr2B 320738309 320738844 535 True 752 752 91.978 1637 2172 1 chr2B.!!$R1 535

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
449 451 1.973812 GTGGCTTCTTGGGGAGCAC 60.974 63.158 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2103 0.324614 TCACCACTGGTTGCATCGAT 59.675 50.0 0.0 0.0 31.02 3.59 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
60 62 2.301346 CCTCTTGCCTCTCTCTCTCTC 58.699 57.143 0.00 0.00 0.00 3.20
61 63 2.092212 CCTCTTGCCTCTCTCTCTCTCT 60.092 54.545 0.00 0.00 0.00 3.10
103 105 2.679349 GCTTTCTTGCCCGATCTCTCTT 60.679 50.000 0.00 0.00 0.00 2.85
197 199 7.012607 AGGATATTTGATTCCCCCATACTTTG 58.987 38.462 0.00 0.00 32.05 2.77
449 451 1.973812 GTGGCTTCTTGGGGAGCAC 60.974 63.158 0.00 0.00 0.00 4.40
560 562 2.883574 TGGTTATCTCGTGCCTTTACG 58.116 47.619 0.00 0.00 44.98 3.18
580 582 2.973224 CGTGTGCAAGCTTATTTGTGTC 59.027 45.455 0.00 0.00 0.00 3.67
758 771 9.965902 ACTATATCAATCCTTTCAGTTTCTGTT 57.034 29.630 0.00 0.00 32.61 3.16
799 812 3.352648 TGGGCTAAGTTAGGTTTGCATC 58.647 45.455 11.84 0.00 30.76 3.91
1020 1033 1.227147 GGCGGCTCGTGCTATAACA 60.227 57.895 9.61 0.00 39.59 2.41
1043 1056 5.750067 CAGCAAACTATGTCAAAGCAAACTT 59.250 36.000 0.00 0.00 37.90 2.66
1064 1077 6.494059 ACTTCCCTAAGGCAATCAGTAAAAT 58.506 36.000 0.00 0.00 37.01 1.82
1087 1100 0.761802 GGGATGGCTTAGACCTCCTG 59.238 60.000 9.23 0.00 31.42 3.86
1277 1290 2.619074 GCCTTATCCTTGCACAGAAGGT 60.619 50.000 12.32 0.60 42.89 3.50
1389 1405 8.282592 GCAGTGTTCGATGATTGCTATTTTATA 58.717 33.333 4.90 0.00 0.00 0.98
1484 1501 6.017852 GCTAGGCTAGCGAAATTTTCTGTAAT 60.018 38.462 28.98 0.00 42.62 1.89
1513 1530 3.664320 TGGTTTGAGGAGCCTATGGATA 58.336 45.455 0.00 0.00 0.00 2.59
1614 1631 8.837389 ACTAGACGAAAAGAAAATACAAGCTTT 58.163 29.630 0.00 0.00 32.38 3.51
1732 1751 9.426837 ACAAAAATGTGAAGGATGATTAACATG 57.573 29.630 0.00 0.00 34.95 3.21
1750 1769 2.314323 TGCATGTATGATGTCGCAGT 57.686 45.000 0.00 0.00 0.00 4.40
1893 1912 0.667792 GAACGCTGAGGTGGACACTC 60.668 60.000 2.13 0.00 35.55 3.51
1904 1923 2.221169 GTGGACACTCTGCATGTTGAA 58.779 47.619 0.00 0.00 0.00 2.69
1906 1925 2.104622 TGGACACTCTGCATGTTGAAGA 59.895 45.455 0.00 0.00 29.72 2.87
2050 2069 2.060050 AATGGGTGTTGACCGTTTCA 57.940 45.000 0.00 0.00 44.23 2.69
2064 2083 1.486726 CGTTTCATAGGGAGGGCTCTT 59.513 52.381 0.00 0.00 0.00 2.85
2084 2103 2.751436 GATGGCCAAGGCGCTTCA 60.751 61.111 10.96 0.00 43.06 3.02
2111 2130 1.349026 CAACCAGTGGTGAGAGATGGT 59.651 52.381 17.56 0.00 46.05 3.55
2118 2137 1.591703 GTGAGAGATGGTGACGGCA 59.408 57.895 0.00 0.00 0.00 5.69
2153 2172 1.473434 CCTCGGGAGGTGCAAATAGAC 60.473 57.143 6.56 0.00 43.61 2.59
2154 2173 1.207089 CTCGGGAGGTGCAAATAGACA 59.793 52.381 0.00 0.00 0.00 3.41
2206 2225 2.650116 GGGGCTTCTCTGACGAGCA 61.650 63.158 9.05 0.00 38.14 4.26
2207 2226 1.446966 GGGCTTCTCTGACGAGCAC 60.447 63.158 9.05 2.74 38.14 4.40
2208 2227 1.290324 GGCTTCTCTGACGAGCACA 59.710 57.895 9.05 0.00 38.14 4.57
2224 2243 1.949525 GCACATGAACCAGAAGTGTGT 59.050 47.619 0.00 0.00 41.53 3.72
2242 2261 0.667993 GTCTGAGGCGGATGAGAGAG 59.332 60.000 0.00 0.00 0.00 3.20
2244 2263 1.064389 TCTGAGGCGGATGAGAGAGAA 60.064 52.381 0.00 0.00 0.00 2.87
2245 2264 1.753649 CTGAGGCGGATGAGAGAGAAA 59.246 52.381 0.00 0.00 0.00 2.52
2248 2267 1.480137 AGGCGGATGAGAGAGAAAGTG 59.520 52.381 0.00 0.00 0.00 3.16
2249 2268 1.472376 GGCGGATGAGAGAGAAAGTGG 60.472 57.143 0.00 0.00 0.00 4.00
2298 2317 1.371467 TTGAAGGAGGCTGGATTGGA 58.629 50.000 0.00 0.00 0.00 3.53
2324 2343 9.463902 AACTTATAGAGAGTACTTCAGCAACTA 57.536 33.333 0.00 0.00 0.00 2.24
2333 2352 0.400213 TTCAGCAACTAGGGTGGTGG 59.600 55.000 20.97 8.54 36.92 4.61
2334 2353 1.675641 CAGCAACTAGGGTGGTGGC 60.676 63.158 16.16 0.00 34.10 5.01
2338 2358 1.247567 CAACTAGGGTGGTGGCTTTG 58.752 55.000 0.00 0.00 0.00 2.77
2341 2361 0.673644 CTAGGGTGGTGGCTTTGTCG 60.674 60.000 0.00 0.00 0.00 4.35
2367 2387 5.446143 TCGAGCATTTCTTCCTCTATCTC 57.554 43.478 0.00 0.00 0.00 2.75
2373 2393 5.741673 GCATTTCTTCCTCTATCTCAGTCCC 60.742 48.000 0.00 0.00 0.00 4.46
2383 2403 2.604912 TCTCAGTCCCAGTTCTAGCA 57.395 50.000 0.00 0.00 0.00 3.49
2397 2417 6.261826 CCAGTTCTAGCATTAATTGGAGAAGG 59.738 42.308 0.00 1.03 35.17 3.46
2414 2434 4.162690 GCGGGGAGGCTGTCGATT 62.163 66.667 0.00 0.00 0.00 3.34
2421 2441 0.452184 GAGGCTGTCGATTCGAGTGA 59.548 55.000 9.42 0.00 36.23 3.41
2458 2478 8.857694 TTTCAAATAATTAGTTTCTCTCCGGT 57.142 30.769 0.00 0.00 0.00 5.28
2459 2479 7.843490 TCAAATAATTAGTTTCTCTCCGGTG 57.157 36.000 0.00 0.00 0.00 4.94
2460 2480 7.617225 TCAAATAATTAGTTTCTCTCCGGTGA 58.383 34.615 6.00 6.00 0.00 4.02
2461 2481 8.265055 TCAAATAATTAGTTTCTCTCCGGTGAT 58.735 33.333 6.68 0.00 0.00 3.06
2462 2482 8.893727 CAAATAATTAGTTTCTCTCCGGTGATT 58.106 33.333 6.68 0.00 0.00 2.57
2465 2485 9.712305 ATAATTAGTTTCTCTCCGGTGATTATG 57.288 33.333 6.68 0.00 0.00 1.90
2466 2486 3.798202 AGTTTCTCTCCGGTGATTATGC 58.202 45.455 6.68 0.00 0.00 3.14
2467 2487 2.872858 GTTTCTCTCCGGTGATTATGCC 59.127 50.000 6.68 0.00 0.00 4.40
2468 2488 1.048601 TCTCTCCGGTGATTATGCCC 58.951 55.000 6.68 0.00 0.00 5.36
2469 2489 1.051812 CTCTCCGGTGATTATGCCCT 58.948 55.000 6.68 0.00 0.00 5.19
2470 2490 1.001406 CTCTCCGGTGATTATGCCCTC 59.999 57.143 6.68 0.00 0.00 4.30
2471 2491 0.758734 CTCCGGTGATTATGCCCTCA 59.241 55.000 0.00 0.00 0.00 3.86
2472 2492 0.758734 TCCGGTGATTATGCCCTCAG 59.241 55.000 0.00 0.00 0.00 3.35
2473 2493 0.469917 CCGGTGATTATGCCCTCAGT 59.530 55.000 0.00 0.00 0.00 3.41
2474 2494 1.586422 CGGTGATTATGCCCTCAGTG 58.414 55.000 0.00 0.00 0.00 3.66
2475 2495 1.134401 CGGTGATTATGCCCTCAGTGT 60.134 52.381 0.00 0.00 0.00 3.55
2476 2496 2.292267 GGTGATTATGCCCTCAGTGTG 58.708 52.381 0.00 0.00 0.00 3.82
2477 2497 2.092968 GGTGATTATGCCCTCAGTGTGA 60.093 50.000 0.00 0.00 0.00 3.58
2478 2498 3.434167 GGTGATTATGCCCTCAGTGTGAT 60.434 47.826 0.00 0.00 0.00 3.06
2479 2499 4.202441 GTGATTATGCCCTCAGTGTGATT 58.798 43.478 0.00 0.00 0.00 2.57
2480 2500 5.368145 GTGATTATGCCCTCAGTGTGATTA 58.632 41.667 0.00 0.00 0.00 1.75
2481 2501 5.237344 GTGATTATGCCCTCAGTGTGATTAC 59.763 44.000 0.00 0.00 0.00 1.89
2482 2502 4.835284 TTATGCCCTCAGTGTGATTACA 57.165 40.909 0.00 0.00 0.00 2.41
2483 2503 3.939740 ATGCCCTCAGTGTGATTACAT 57.060 42.857 0.00 0.00 39.39 2.29
2484 2504 3.266510 TGCCCTCAGTGTGATTACATC 57.733 47.619 0.00 0.00 39.39 3.06
2485 2505 2.571202 TGCCCTCAGTGTGATTACATCA 59.429 45.455 0.00 0.00 39.39 3.07
2486 2506 3.008923 TGCCCTCAGTGTGATTACATCAA 59.991 43.478 0.00 0.00 41.69 2.57
2487 2507 3.624861 GCCCTCAGTGTGATTACATCAAG 59.375 47.826 0.00 0.00 41.69 3.02
2488 2508 4.623886 GCCCTCAGTGTGATTACATCAAGA 60.624 45.833 0.00 0.00 41.69 3.02
2489 2509 5.114780 CCCTCAGTGTGATTACATCAAGAG 58.885 45.833 0.00 0.00 41.69 2.85
2490 2510 5.337894 CCCTCAGTGTGATTACATCAAGAGT 60.338 44.000 0.00 0.00 41.69 3.24
2491 2511 6.169094 CCTCAGTGTGATTACATCAAGAGTT 58.831 40.000 0.00 0.00 41.69 3.01
2492 2512 7.323420 CCTCAGTGTGATTACATCAAGAGTTA 58.677 38.462 0.00 0.00 41.69 2.24
2493 2513 7.276658 CCTCAGTGTGATTACATCAAGAGTTAC 59.723 40.741 0.00 0.00 41.69 2.50
2494 2514 7.896811 TCAGTGTGATTACATCAAGAGTTACT 58.103 34.615 0.00 0.00 41.69 2.24
2495 2515 8.029522 TCAGTGTGATTACATCAAGAGTTACTC 58.970 37.037 3.85 3.85 41.69 2.59
2496 2516 7.008719 CAGTGTGATTACATCAAGAGTTACTCG 59.991 40.741 6.73 0.00 41.69 4.18
2497 2517 5.805486 TGTGATTACATCAAGAGTTACTCGC 59.195 40.000 6.73 0.00 41.69 5.03
2498 2518 5.805486 GTGATTACATCAAGAGTTACTCGCA 59.195 40.000 6.73 0.00 41.69 5.10
2499 2519 6.477033 GTGATTACATCAAGAGTTACTCGCAT 59.523 38.462 6.73 0.00 41.69 4.73
2500 2520 7.010552 GTGATTACATCAAGAGTTACTCGCATT 59.989 37.037 6.73 0.00 41.69 3.56
2501 2521 8.194769 TGATTACATCAAGAGTTACTCGCATTA 58.805 33.333 6.73 0.00 36.11 1.90
2502 2522 8.942338 ATTACATCAAGAGTTACTCGCATTAA 57.058 30.769 6.73 2.50 35.36 1.40
2503 2523 8.942338 TTACATCAAGAGTTACTCGCATTAAT 57.058 30.769 6.73 0.00 35.36 1.40
2504 2524 7.849804 ACATCAAGAGTTACTCGCATTAATT 57.150 32.000 6.73 0.00 35.36 1.40
2505 2525 7.688372 ACATCAAGAGTTACTCGCATTAATTG 58.312 34.615 6.73 4.57 35.36 2.32
2506 2526 6.662414 TCAAGAGTTACTCGCATTAATTGG 57.338 37.500 6.73 0.00 35.36 3.16
2507 2527 5.584649 TCAAGAGTTACTCGCATTAATTGGG 59.415 40.000 6.73 0.00 39.56 4.12
2508 2528 4.451900 AGAGTTACTCGCATTAATTGGGG 58.548 43.478 6.73 0.00 38.74 4.96
2509 2529 3.551846 AGTTACTCGCATTAATTGGGGG 58.448 45.455 0.00 0.00 44.20 5.40
2510 2530 1.975660 TACTCGCATTAATTGGGGGC 58.024 50.000 0.00 0.00 42.42 5.80
2511 2531 0.033601 ACTCGCATTAATTGGGGGCA 60.034 50.000 0.00 0.00 42.42 5.36
2512 2532 0.670162 CTCGCATTAATTGGGGGCAG 59.330 55.000 0.00 0.00 38.74 4.85
2513 2533 0.257328 TCGCATTAATTGGGGGCAGA 59.743 50.000 0.00 0.00 38.74 4.26
2514 2534 1.133513 TCGCATTAATTGGGGGCAGAT 60.134 47.619 0.00 0.00 38.74 2.90
2515 2535 1.688197 CGCATTAATTGGGGGCAGATT 59.312 47.619 0.00 0.00 34.74 2.40
2516 2536 2.288395 CGCATTAATTGGGGGCAGATTC 60.288 50.000 0.00 0.00 34.74 2.52
2517 2537 2.967887 GCATTAATTGGGGGCAGATTCT 59.032 45.455 0.00 0.00 0.00 2.40
2518 2538 3.243975 GCATTAATTGGGGGCAGATTCTG 60.244 47.826 9.40 9.40 34.12 3.02
2519 2539 3.756082 TTAATTGGGGGCAGATTCTGT 57.244 42.857 14.90 0.00 33.43 3.41
2520 2540 2.629017 AATTGGGGGCAGATTCTGTT 57.371 45.000 14.90 0.00 33.43 3.16
2521 2541 3.756082 AATTGGGGGCAGATTCTGTTA 57.244 42.857 14.90 0.00 33.43 2.41
2522 2542 2.806945 TTGGGGGCAGATTCTGTTAG 57.193 50.000 14.90 0.00 33.43 2.34
2523 2543 0.255890 TGGGGGCAGATTCTGTTAGC 59.744 55.000 14.90 0.55 33.43 3.09
2524 2544 0.815615 GGGGGCAGATTCTGTTAGCG 60.816 60.000 14.90 0.00 33.43 4.26
2525 2545 0.178068 GGGGCAGATTCTGTTAGCGA 59.822 55.000 14.90 0.00 33.43 4.93
2526 2546 1.202698 GGGGCAGATTCTGTTAGCGAT 60.203 52.381 14.90 0.00 33.43 4.58
2527 2547 2.139118 GGGCAGATTCTGTTAGCGATC 58.861 52.381 14.90 0.00 33.43 3.69
2528 2548 2.224161 GGGCAGATTCTGTTAGCGATCT 60.224 50.000 14.90 0.00 33.43 2.75
2529 2549 3.005897 GGGCAGATTCTGTTAGCGATCTA 59.994 47.826 14.90 0.00 33.43 1.98
2530 2550 4.233789 GGCAGATTCTGTTAGCGATCTAG 58.766 47.826 14.90 0.00 33.43 2.43
2531 2551 4.233789 GCAGATTCTGTTAGCGATCTAGG 58.766 47.826 14.90 0.00 33.43 3.02
2532 2552 4.233789 CAGATTCTGTTAGCGATCTAGGC 58.766 47.826 5.46 0.00 0.00 3.93
2533 2553 3.257127 AGATTCTGTTAGCGATCTAGGCC 59.743 47.826 0.00 0.00 0.00 5.19
2534 2554 2.366640 TCTGTTAGCGATCTAGGCCT 57.633 50.000 11.78 11.78 0.00 5.19
2535 2555 2.667470 TCTGTTAGCGATCTAGGCCTT 58.333 47.619 12.58 0.00 0.00 4.35
2536 2556 2.362397 TCTGTTAGCGATCTAGGCCTTG 59.638 50.000 12.58 9.98 0.00 3.61
2537 2557 1.202533 TGTTAGCGATCTAGGCCTTGC 60.203 52.381 12.58 8.11 0.00 4.01
2538 2558 1.069358 GTTAGCGATCTAGGCCTTGCT 59.931 52.381 12.58 15.43 36.16 3.91
2539 2559 0.676184 TAGCGATCTAGGCCTTGCTG 59.324 55.000 12.58 2.99 34.05 4.41
2540 2560 1.596477 GCGATCTAGGCCTTGCTGG 60.596 63.158 12.58 2.51 39.35 4.85
2541 2561 1.070445 CGATCTAGGCCTTGCTGGG 59.930 63.158 12.58 0.00 36.00 4.45
2549 2569 4.447734 CCTTGCTGGGCTTCCAAT 57.552 55.556 0.00 0.00 40.58 3.16
2550 2570 2.674958 CCTTGCTGGGCTTCCAATT 58.325 52.632 0.00 0.00 40.58 2.32
2551 2571 1.851304 CCTTGCTGGGCTTCCAATTA 58.149 50.000 0.00 0.00 40.58 1.40
2552 2572 1.478105 CCTTGCTGGGCTTCCAATTAC 59.522 52.381 0.00 0.00 40.58 1.89
2553 2573 1.478105 CTTGCTGGGCTTCCAATTACC 59.522 52.381 0.00 0.00 40.58 2.85
2554 2574 0.407528 TGCTGGGCTTCCAATTACCA 59.592 50.000 0.00 0.00 40.58 3.25
2555 2575 0.817654 GCTGGGCTTCCAATTACCAC 59.182 55.000 0.00 0.00 40.58 4.16
2556 2576 1.474330 CTGGGCTTCCAATTACCACC 58.526 55.000 0.00 0.00 40.58 4.61
2557 2577 0.040499 TGGGCTTCCAATTACCACCC 59.960 55.000 0.00 0.00 37.67 4.61
2558 2578 0.040499 GGGCTTCCAATTACCACCCA 59.960 55.000 0.00 0.00 35.84 4.51
2559 2579 1.474330 GGCTTCCAATTACCACCCAG 58.526 55.000 0.00 0.00 0.00 4.45
2560 2580 0.817654 GCTTCCAATTACCACCCAGC 59.182 55.000 0.00 0.00 0.00 4.85
2561 2581 1.474330 CTTCCAATTACCACCCAGCC 58.526 55.000 0.00 0.00 0.00 4.85
2562 2582 0.040499 TTCCAATTACCACCCAGCCC 59.960 55.000 0.00 0.00 0.00 5.19
2563 2583 1.143329 TCCAATTACCACCCAGCCCA 61.143 55.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 21 1.394532 AGGTGGGAGGTAGGAGAAGA 58.605 55.000 0.00 0.00 0.00 2.87
60 62 4.276926 GCTTTAATGGCAGTAATGGAGGAG 59.723 45.833 18.28 9.28 0.00 3.69
61 63 4.079787 AGCTTTAATGGCAGTAATGGAGGA 60.080 41.667 18.28 0.00 0.00 3.71
103 105 1.145571 ACAAGTTTGGGTGGCTAGGA 58.854 50.000 0.00 0.00 0.00 2.94
197 199 5.977129 CCAAGAGTAACAAAATCCACACAAC 59.023 40.000 0.00 0.00 0.00 3.32
321 323 1.692411 ACAAACAAGGTTGAGGCTCC 58.308 50.000 12.86 0.00 32.59 4.70
449 451 1.302033 GAGTGGTGTGGAGGCACAG 60.302 63.158 0.00 0.00 40.89 3.66
560 562 3.963665 TGACACAAATAAGCTTGCACAC 58.036 40.909 9.86 0.00 0.00 3.82
580 582 2.756760 ACACAAGCAAGCAAGGGATATG 59.243 45.455 0.00 0.00 0.00 1.78
740 753 7.645058 TTCTGAAACAGAAACTGAAAGGATT 57.355 32.000 11.06 0.00 45.84 3.01
758 771 1.416401 AGACCTGTTTCGCCTTCTGAA 59.584 47.619 0.00 0.00 0.00 3.02
799 812 4.409570 GCACAAGCTGTATTGATCACTTG 58.590 43.478 15.99 15.99 40.19 3.16
868 881 8.199449 GCCCAATTCAAATATTTCTTGATCTCA 58.801 33.333 12.81 0.00 32.98 3.27
1020 1033 5.520376 AGTTTGCTTTGACATAGTTTGCT 57.480 34.783 0.00 0.00 0.00 3.91
1043 1056 6.410388 CCCTATTTTACTGATTGCCTTAGGGA 60.410 42.308 0.00 0.00 44.01 4.20
1064 1077 0.949582 AGGTCTAAGCCATCCCCCTA 59.050 55.000 0.00 0.00 0.00 3.53
1087 1100 4.944048 ACATTTAGCTTCACAAAACCCAC 58.056 39.130 0.00 0.00 0.00 4.61
1162 1175 4.021102 TGAACCTTCCTTTGTCATCTCC 57.979 45.455 0.00 0.00 0.00 3.71
1277 1290 2.240160 ACAATAAGGCGATTACACCCCA 59.760 45.455 0.00 0.00 0.00 4.96
1389 1405 9.886132 AACCTCGTAATAGTAAATTCACAAGAT 57.114 29.630 0.00 0.00 0.00 2.40
1484 1501 2.025321 GGCTCCTCAAACCAATCCCTAA 60.025 50.000 0.00 0.00 0.00 2.69
1513 1530 7.383687 TCGTCAGTAAGGAAAGATACAATGTT 58.616 34.615 0.00 0.00 0.00 2.71
1732 1751 3.680642 AAACTGCGACATCATACATGC 57.319 42.857 0.00 0.00 0.00 4.06
1817 1836 7.220683 CCATTAAACCATGCATTTTAAGTCTCG 59.779 37.037 17.09 7.23 32.21 4.04
1893 1912 4.524316 TCCCAATTTCTTCAACATGCAG 57.476 40.909 0.00 0.00 0.00 4.41
2032 2051 2.286365 ATGAAACGGTCAACACCCAT 57.714 45.000 0.00 0.00 40.50 4.00
2049 2068 1.070445 CGCAAGAGCCCTCCCTATG 59.930 63.158 0.00 0.00 43.02 2.23
2050 2069 1.075226 TCGCAAGAGCCCTCCCTAT 60.075 57.895 0.00 0.00 45.01 2.57
2084 2103 0.324614 TCACCACTGGTTGCATCGAT 59.675 50.000 0.00 0.00 31.02 3.59
2197 2216 1.073964 CTGGTTCATGTGCTCGTCAG 58.926 55.000 0.00 0.00 0.00 3.51
2201 2220 1.462283 CACTTCTGGTTCATGTGCTCG 59.538 52.381 0.00 0.00 0.00 5.03
2206 2225 3.134623 TCAGACACACTTCTGGTTCATGT 59.865 43.478 0.46 0.00 42.95 3.21
2207 2226 3.732212 TCAGACACACTTCTGGTTCATG 58.268 45.455 0.46 0.00 42.95 3.07
2208 2227 3.244353 CCTCAGACACACTTCTGGTTCAT 60.244 47.826 0.46 0.00 42.95 2.57
2224 2243 0.548510 TCTCTCTCATCCGCCTCAGA 59.451 55.000 0.00 0.00 0.00 3.27
2242 2261 1.372087 CCATGAGCTCCGCCACTTTC 61.372 60.000 12.15 0.00 0.00 2.62
2244 2263 2.270205 CCATGAGCTCCGCCACTT 59.730 61.111 12.15 0.00 0.00 3.16
2245 2264 3.790437 CCCATGAGCTCCGCCACT 61.790 66.667 12.15 0.00 0.00 4.00
2248 2267 2.281345 CATCCCATGAGCTCCGCC 60.281 66.667 12.15 0.00 0.00 6.13
2249 2268 2.824546 TCATCCCATGAGCTCCGC 59.175 61.111 12.15 0.00 33.59 5.54
2289 2308 8.472007 AGTACTCTCTATAAGTTCCAATCCAG 57.528 38.462 0.00 0.00 0.00 3.86
2298 2317 8.356000 AGTTGCTGAAGTACTCTCTATAAGTT 57.644 34.615 0.00 0.00 0.00 2.66
2324 2343 2.113139 CGACAAAGCCACCACCCT 59.887 61.111 0.00 0.00 0.00 4.34
2333 2352 1.071605 ATGCTCGAAGACGACAAAGC 58.928 50.000 0.00 0.00 43.81 3.51
2334 2353 3.430218 AGAAATGCTCGAAGACGACAAAG 59.570 43.478 0.00 0.00 43.81 2.77
2338 2358 2.345942 GGAAGAAATGCTCGAAGACGAC 59.654 50.000 0.00 0.00 43.81 4.34
2367 2387 5.297776 CCAATTAATGCTAGAACTGGGACTG 59.702 44.000 0.00 0.00 0.00 3.51
2373 2393 6.238593 GCCTTCTCCAATTAATGCTAGAACTG 60.239 42.308 0.00 0.00 30.71 3.16
2383 2403 1.850345 TCCCCGCCTTCTCCAATTAAT 59.150 47.619 0.00 0.00 0.00 1.40
2397 2417 4.162690 AATCGACAGCCTCCCCGC 62.163 66.667 0.00 0.00 0.00 6.13
2406 2426 5.553396 CGAATCAATTCACTCGAATCGACAG 60.553 44.000 0.00 0.00 41.12 3.51
2414 2434 6.720012 TGAAATTCGAATCAATTCACTCGA 57.280 33.333 16.18 0.00 38.47 4.04
2444 2464 4.202223 GGCATAATCACCGGAGAGAAACTA 60.202 45.833 9.46 0.00 0.00 2.24
2450 2470 1.001406 GAGGGCATAATCACCGGAGAG 59.999 57.143 9.46 0.00 0.00 3.20
2451 2471 1.048601 GAGGGCATAATCACCGGAGA 58.951 55.000 9.46 6.11 0.00 3.71
2452 2472 0.758734 TGAGGGCATAATCACCGGAG 59.241 55.000 9.46 0.00 0.00 4.63
2453 2473 0.758734 CTGAGGGCATAATCACCGGA 59.241 55.000 9.46 0.00 0.00 5.14
2454 2474 0.469917 ACTGAGGGCATAATCACCGG 59.530 55.000 0.00 0.00 0.00 5.28
2455 2475 1.134401 ACACTGAGGGCATAATCACCG 60.134 52.381 0.00 0.00 0.00 4.94
2456 2476 2.092968 TCACACTGAGGGCATAATCACC 60.093 50.000 0.00 0.00 0.00 4.02
2457 2477 3.266510 TCACACTGAGGGCATAATCAC 57.733 47.619 0.00 0.00 0.00 3.06
2458 2478 4.508551 AATCACACTGAGGGCATAATCA 57.491 40.909 0.00 0.00 0.00 2.57
2459 2479 5.368145 TGTAATCACACTGAGGGCATAATC 58.632 41.667 0.00 0.00 0.00 1.75
2460 2480 5.372343 TGTAATCACACTGAGGGCATAAT 57.628 39.130 0.00 0.00 0.00 1.28
2461 2481 4.835284 TGTAATCACACTGAGGGCATAA 57.165 40.909 0.00 0.00 0.00 1.90
2462 2482 4.960938 GATGTAATCACACTGAGGGCATA 58.039 43.478 0.00 0.00 44.70 3.14
2463 2483 3.813443 GATGTAATCACACTGAGGGCAT 58.187 45.455 0.00 0.00 44.70 4.40
2464 2484 3.266510 GATGTAATCACACTGAGGGCA 57.733 47.619 0.00 0.00 44.70 5.36
2476 2496 7.470289 AATGCGAGTAACTCTTGATGTAATC 57.530 36.000 0.00 0.00 45.83 1.75
2477 2497 8.942338 TTAATGCGAGTAACTCTTGATGTAAT 57.058 30.769 0.00 0.00 0.00 1.89
2478 2498 8.942338 ATTAATGCGAGTAACTCTTGATGTAA 57.058 30.769 0.00 0.00 0.00 2.41
2479 2499 8.817100 CAATTAATGCGAGTAACTCTTGATGTA 58.183 33.333 0.00 0.00 0.00 2.29
2480 2500 7.201644 CCAATTAATGCGAGTAACTCTTGATGT 60.202 37.037 0.00 0.00 0.00 3.06
2481 2501 7.128331 CCAATTAATGCGAGTAACTCTTGATG 58.872 38.462 0.00 0.00 0.00 3.07
2482 2502 6.260936 CCCAATTAATGCGAGTAACTCTTGAT 59.739 38.462 0.00 0.00 0.00 2.57
2483 2503 5.584649 CCCAATTAATGCGAGTAACTCTTGA 59.415 40.000 0.00 0.00 0.00 3.02
2484 2504 5.220854 CCCCAATTAATGCGAGTAACTCTTG 60.221 44.000 0.00 0.00 0.00 3.02
2485 2505 4.881850 CCCCAATTAATGCGAGTAACTCTT 59.118 41.667 0.00 0.00 0.00 2.85
2486 2506 4.451900 CCCCAATTAATGCGAGTAACTCT 58.548 43.478 0.00 0.00 0.00 3.24
2487 2507 3.564225 CCCCCAATTAATGCGAGTAACTC 59.436 47.826 0.00 0.00 0.00 3.01
2488 2508 3.551846 CCCCCAATTAATGCGAGTAACT 58.448 45.455 0.00 0.00 0.00 2.24
2489 2509 2.034179 GCCCCCAATTAATGCGAGTAAC 59.966 50.000 0.00 0.00 0.00 2.50
2490 2510 2.303175 GCCCCCAATTAATGCGAGTAA 58.697 47.619 0.00 0.00 0.00 2.24
2491 2511 1.213182 TGCCCCCAATTAATGCGAGTA 59.787 47.619 0.00 0.00 0.00 2.59
2492 2512 0.033601 TGCCCCCAATTAATGCGAGT 60.034 50.000 0.00 0.00 0.00 4.18
2493 2513 0.670162 CTGCCCCCAATTAATGCGAG 59.330 55.000 0.00 0.00 0.00 5.03
2494 2514 0.257328 TCTGCCCCCAATTAATGCGA 59.743 50.000 0.00 0.00 0.00 5.10
2495 2515 1.331214 ATCTGCCCCCAATTAATGCG 58.669 50.000 0.00 0.00 0.00 4.73
2496 2516 2.967887 AGAATCTGCCCCCAATTAATGC 59.032 45.455 0.00 0.00 0.00 3.56
2497 2517 3.962718 ACAGAATCTGCCCCCAATTAATG 59.037 43.478 10.62 0.00 34.37 1.90
2498 2518 4.270317 ACAGAATCTGCCCCCAATTAAT 57.730 40.909 10.62 0.00 34.37 1.40
2499 2519 3.756082 ACAGAATCTGCCCCCAATTAA 57.244 42.857 10.62 0.00 34.37 1.40
2500 2520 3.756082 AACAGAATCTGCCCCCAATTA 57.244 42.857 10.62 0.00 34.37 1.40
2501 2521 2.629017 AACAGAATCTGCCCCCAATT 57.371 45.000 10.62 0.00 34.37 2.32
2502 2522 2.687914 GCTAACAGAATCTGCCCCCAAT 60.688 50.000 10.62 0.00 34.37 3.16
2503 2523 1.340991 GCTAACAGAATCTGCCCCCAA 60.341 52.381 10.62 0.00 34.37 4.12
2504 2524 0.255890 GCTAACAGAATCTGCCCCCA 59.744 55.000 10.62 0.00 34.37 4.96
2505 2525 0.815615 CGCTAACAGAATCTGCCCCC 60.816 60.000 10.62 0.00 34.37 5.40
2506 2526 0.178068 TCGCTAACAGAATCTGCCCC 59.822 55.000 10.62 0.00 34.37 5.80
2507 2527 2.139118 GATCGCTAACAGAATCTGCCC 58.861 52.381 10.62 0.00 34.37 5.36
2508 2528 3.104843 AGATCGCTAACAGAATCTGCC 57.895 47.619 10.62 0.00 34.37 4.85
2509 2529 4.233789 CCTAGATCGCTAACAGAATCTGC 58.766 47.826 10.62 0.00 34.37 4.26
2510 2530 4.233789 GCCTAGATCGCTAACAGAATCTG 58.766 47.826 8.98 8.98 37.52 2.90
2511 2531 3.257127 GGCCTAGATCGCTAACAGAATCT 59.743 47.826 0.00 0.00 0.00 2.40
2512 2532 3.257127 AGGCCTAGATCGCTAACAGAATC 59.743 47.826 1.29 0.00 0.00 2.52
2513 2533 3.235200 AGGCCTAGATCGCTAACAGAAT 58.765 45.455 1.29 0.00 0.00 2.40
2514 2534 2.667470 AGGCCTAGATCGCTAACAGAA 58.333 47.619 1.29 0.00 0.00 3.02
2515 2535 2.362397 CAAGGCCTAGATCGCTAACAGA 59.638 50.000 5.16 0.00 0.00 3.41
2516 2536 2.748605 CAAGGCCTAGATCGCTAACAG 58.251 52.381 5.16 0.00 0.00 3.16
2517 2537 1.202533 GCAAGGCCTAGATCGCTAACA 60.203 52.381 5.16 0.00 0.00 2.41
2518 2538 1.069358 AGCAAGGCCTAGATCGCTAAC 59.931 52.381 5.16 0.00 0.00 2.34
2519 2539 1.069204 CAGCAAGGCCTAGATCGCTAA 59.931 52.381 5.16 0.00 0.00 3.09
2520 2540 0.676184 CAGCAAGGCCTAGATCGCTA 59.324 55.000 5.16 0.00 0.00 4.26
2521 2541 1.445095 CAGCAAGGCCTAGATCGCT 59.555 57.895 5.16 6.71 0.00 4.93
2522 2542 1.596477 CCAGCAAGGCCTAGATCGC 60.596 63.158 5.16 4.10 0.00 4.58
2523 2543 1.070445 CCCAGCAAGGCCTAGATCG 59.930 63.158 5.16 0.00 35.39 3.69
2532 2552 1.478105 GTAATTGGAAGCCCAGCAAGG 59.522 52.381 0.00 0.00 44.60 3.61
2533 2553 1.478105 GGTAATTGGAAGCCCAGCAAG 59.522 52.381 0.00 0.00 44.60 4.01
2534 2554 1.203112 TGGTAATTGGAAGCCCAGCAA 60.203 47.619 0.00 0.00 44.60 3.91
2535 2555 0.407528 TGGTAATTGGAAGCCCAGCA 59.592 50.000 0.00 0.00 44.60 4.41
2536 2556 0.817654 GTGGTAATTGGAAGCCCAGC 59.182 55.000 0.00 0.00 44.60 4.85
2537 2557 1.474330 GGTGGTAATTGGAAGCCCAG 58.526 55.000 0.00 0.00 44.60 4.45
2538 2558 0.040499 GGGTGGTAATTGGAAGCCCA 59.960 55.000 0.00 0.00 41.64 5.36
2539 2559 0.040499 TGGGTGGTAATTGGAAGCCC 59.960 55.000 0.00 0.00 35.37 5.19
2540 2560 1.474330 CTGGGTGGTAATTGGAAGCC 58.526 55.000 0.00 0.00 0.00 4.35
2541 2561 0.817654 GCTGGGTGGTAATTGGAAGC 59.182 55.000 0.00 0.00 0.00 3.86
2542 2562 1.474330 GGCTGGGTGGTAATTGGAAG 58.526 55.000 0.00 0.00 0.00 3.46
2543 2563 0.040499 GGGCTGGGTGGTAATTGGAA 59.960 55.000 0.00 0.00 0.00 3.53
2544 2564 1.143329 TGGGCTGGGTGGTAATTGGA 61.143 55.000 0.00 0.00 0.00 3.53
2545 2565 1.386155 TGGGCTGGGTGGTAATTGG 59.614 57.895 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.