Multiple sequence alignment - TraesCS4A01G298200

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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 TraesCS4A01G298200 chr4A 100.000 4746 0 0 1 4746 597012077 597016822 0.000000e+00 8765.0
1 TraesCS4A01G298200 chr4A 97.464 552 13 1 1 552 527510595 527511145 0.000000e+00 941.0
2 TraesCS4A01G298200 chr4A 79.592 441 88 2 113 552 714229862 714229423 9.910000e-82 315.0
3 TraesCS4A01G298200 chr4B 91.542 1809 89 28 2342 4125 11657506 11655737 0.000000e+00 2435.0
4 TraesCS4A01G298200 chr4B 86.733 1010 80 23 551 1525 11659672 11658682 0.000000e+00 1074.0
5 TraesCS4A01G298200 chr4B 90.851 776 41 11 3997 4746 11662730 11663501 0.000000e+00 1013.0
6 TraesCS4A01G298200 chr4B 83.485 1096 113 39 3680 4746 11665539 11666595 0.000000e+00 959.0
7 TraesCS4A01G298200 chr4B 87.946 672 52 14 3997 4641 11561165 11560496 0.000000e+00 765.0
8 TraesCS4A01G298200 chr4B 88.545 550 63 0 3 552 458897054 458896505 0.000000e+00 667.0
9 TraesCS4A01G298200 chr4B 87.845 543 37 12 1531 2054 11658379 11657847 1.130000e-170 610.0
10 TraesCS4A01G298200 chr4B 90.182 275 16 3 4465 4729 11655139 11654866 9.780000e-92 348.0
11 TraesCS4A01G298200 chr4B 89.573 211 16 6 2042 2248 11657818 11657610 3.640000e-66 263.0
12 TraesCS4A01G298200 chr4B 91.515 165 14 0 3500 3664 11665330 11665494 1.330000e-55 228.0
13 TraesCS4A01G298200 chr4D 92.386 1668 79 18 2342 3999 6424162 6425791 0.000000e+00 2333.0
14 TraesCS4A01G298200 chr4D 88.619 1731 121 30 553 2246 6422385 6424076 0.000000e+00 2036.0
15 TraesCS4A01G298200 chr4D 86.944 337 32 9 3997 4326 6425840 6426171 7.500000e-98 368.0
16 TraesCS4A01G298200 chr4D 100.000 31 0 0 4357 4387 469886804 469886774 1.840000e-04 58.4
17 TraesCS4A01G298200 chr1D 91.636 550 46 0 1 550 18960006 18959457 0.000000e+00 761.0
18 TraesCS4A01G298200 chr1A 91.486 552 47 0 1 552 534589938 534589387 0.000000e+00 760.0
19 TraesCS4A01G298200 chr1A 84.685 111 14 3 2429 2538 314485748 314485640 1.810000e-19 108.0
20 TraesCS4A01G298200 chr1A 74.138 232 54 4 2895 3123 539756836 539757064 1.820000e-14 91.6
21 TraesCS4A01G298200 chr5D 79.291 1072 196 19 2622 3682 491527753 491528809 0.000000e+00 726.0
22 TraesCS4A01G298200 chr5D 77.179 1021 200 27 2676 3675 45379019 45378011 8.920000e-157 564.0
23 TraesCS4A01G298200 chr5A 79.502 1044 189 18 2622 3654 613700664 613701693 0.000000e+00 719.0
24 TraesCS4A01G298200 chr5A 76.765 1020 203 29 2676 3675 36330907 36331912 1.500000e-149 540.0
25 TraesCS4A01G298200 chr5A 77.656 546 121 1 3 547 603410502 603409957 9.840000e-87 331.0
26 TraesCS4A01G298200 chr5A 97.059 34 1 0 1537 1570 702164697 702164730 1.840000e-04 58.4
27 TraesCS4A01G298200 chr5B 78.794 1061 208 11 2623 3676 606301625 606302675 0.000000e+00 697.0
28 TraesCS4A01G298200 chr3B 88.727 550 62 0 3 552 156615500 156616049 0.000000e+00 673.0
29 TraesCS4A01G298200 chr3B 76.046 1052 196 47 2624 3644 795839880 795840906 3.300000e-136 496.0
30 TraesCS4A01G298200 chr7D 86.703 549 73 0 1 549 19315408 19314860 1.130000e-170 610.0
31 TraesCS4A01G298200 chr3A 76.353 1053 200 44 2624 3650 724515604 724516633 1.960000e-143 520.0
32 TraesCS4A01G298200 chr3A 82.645 121 18 3 2423 2542 577631809 577631691 2.340000e-18 104.0
33 TraesCS4A01G298200 chr3D 75.642 1051 212 39 2624 3649 593236137 593237168 2.570000e-132 483.0
34 TraesCS4A01G298200 chr3D 84.615 104 14 2 2437 2540 610408850 610408951 8.400000e-18 102.0
35 TraesCS4A01G298200 chr3D 84.112 107 15 2 2437 2543 615396770 615396666 8.400000e-18 102.0
36 TraesCS4A01G298200 chr7B 85.185 108 13 3 2432 2538 523736804 523736909 1.810000e-19 108.0
37 TraesCS4A01G298200 chr6D 85.577 104 13 2 2441 2544 72031150 72031251 1.810000e-19 108.0
38 TraesCS4A01G298200 chr6D 85.185 108 13 3 2426 2531 430014839 430014733 1.810000e-19 108.0
39 TraesCS4A01G298200 chrUn 84.762 105 14 2 2437 2541 94303652 94303550 2.340000e-18 104.0
40 TraesCS4A01G298200 chr1B 71.591 440 108 13 2895 3327 603294698 603295127 2.340000e-18 104.0
41 TraesCS4A01G298200 chr1B 96.970 33 1 0 1537 1569 572305657 572305625 6.630000e-04 56.5
42 TraesCS4A01G298200 chr2A 95.745 47 2 0 2622 2668 114488433 114488387 5.090000e-10 76.8


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 TraesCS4A01G298200 chr4A 597012077 597016822 4745 False 8765.000000 8765 100.000000 1 4746 1 chr4A.!!$F2 4745
1 TraesCS4A01G298200 chr4A 527510595 527511145 550 False 941.000000 941 97.464000 1 552 1 chr4A.!!$F1 551
2 TraesCS4A01G298200 chr4B 11654866 11659672 4806 True 946.000000 2435 89.175000 551 4729 5 chr4B.!!$R3 4178
3 TraesCS4A01G298200 chr4B 11560496 11561165 669 True 765.000000 765 87.946000 3997 4641 1 chr4B.!!$R1 644
4 TraesCS4A01G298200 chr4B 11662730 11666595 3865 False 733.333333 1013 88.617000 3500 4746 3 chr4B.!!$F1 1246
5 TraesCS4A01G298200 chr4B 458896505 458897054 549 True 667.000000 667 88.545000 3 552 1 chr4B.!!$R2 549
6 TraesCS4A01G298200 chr4D 6422385 6426171 3786 False 1579.000000 2333 89.316333 553 4326 3 chr4D.!!$F1 3773
7 TraesCS4A01G298200 chr1D 18959457 18960006 549 True 761.000000 761 91.636000 1 550 1 chr1D.!!$R1 549
8 TraesCS4A01G298200 chr1A 534589387 534589938 551 True 760.000000 760 91.486000 1 552 1 chr1A.!!$R2 551
9 TraesCS4A01G298200 chr5D 491527753 491528809 1056 False 726.000000 726 79.291000 2622 3682 1 chr5D.!!$F1 1060
10 TraesCS4A01G298200 chr5D 45378011 45379019 1008 True 564.000000 564 77.179000 2676 3675 1 chr5D.!!$R1 999
11 TraesCS4A01G298200 chr5A 613700664 613701693 1029 False 719.000000 719 79.502000 2622 3654 1 chr5A.!!$F2 1032
12 TraesCS4A01G298200 chr5A 36330907 36331912 1005 False 540.000000 540 76.765000 2676 3675 1 chr5A.!!$F1 999
13 TraesCS4A01G298200 chr5A 603409957 603410502 545 True 331.000000 331 77.656000 3 547 1 chr5A.!!$R1 544
14 TraesCS4A01G298200 chr5B 606301625 606302675 1050 False 697.000000 697 78.794000 2623 3676 1 chr5B.!!$F1 1053
15 TraesCS4A01G298200 chr3B 156615500 156616049 549 False 673.000000 673 88.727000 3 552 1 chr3B.!!$F1 549
16 TraesCS4A01G298200 chr3B 795839880 795840906 1026 False 496.000000 496 76.046000 2624 3644 1 chr3B.!!$F2 1020
17 TraesCS4A01G298200 chr7D 19314860 19315408 548 True 610.000000 610 86.703000 1 549 1 chr7D.!!$R1 548
18 TraesCS4A01G298200 chr3A 724515604 724516633 1029 False 520.000000 520 76.353000 2624 3650 1 chr3A.!!$F1 1026
19 TraesCS4A01G298200 chr3D 593236137 593237168 1031 False 483.000000 483 75.642000 2624 3649 1 chr3D.!!$F1 1025

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
560 561 0.250727 ATGGGGACGACTTTGGTGTG 60.251 55.0 0.00 0.0 0.0 3.82 F
860 893 0.456142 GGAGCCAAAATCCGCGTTTC 60.456 55.0 4.92 0.0 0.0 2.78 F
2476 2937 0.322546 GAGGCCGGGTGTTTCTTGAT 60.323 55.0 2.18 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2455 2916 0.323629 CAAGAAACACCCGGCCTCTA 59.676 55.0 0.00 0.00 0.00 2.43 R
2851 3330 1.550327 TGAGGAACTGCACGATCTCT 58.450 50.0 0.00 0.00 41.55 3.10 R
3965 4505 0.161658 GACAACGACGTGCACATGAG 59.838 55.0 18.64 7.33 0.00 2.90 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
560 561 0.250727 ATGGGGACGACTTTGGTGTG 60.251 55.000 0.00 0.00 0.00 3.82
579 582 2.537625 GTGAGTGTCGCTGATCTATTGC 59.462 50.000 0.00 0.00 0.00 3.56
686 700 3.494045 TCGTCATCACAGATCACTCAC 57.506 47.619 0.00 0.00 0.00 3.51
687 701 2.819608 TCGTCATCACAGATCACTCACA 59.180 45.455 0.00 0.00 0.00 3.58
688 702 3.119708 TCGTCATCACAGATCACTCACAG 60.120 47.826 0.00 0.00 0.00 3.66
844 877 2.363795 TACGTCCCCCAGCTGGAG 60.364 66.667 34.91 22.25 37.39 3.86
859 892 1.175983 TGGAGCCAAAATCCGCGTTT 61.176 50.000 4.92 0.00 39.91 3.60
860 893 0.456142 GGAGCCAAAATCCGCGTTTC 60.456 55.000 4.92 0.00 0.00 2.78
869 902 0.999406 ATCCGCGTTTCATTCGTGAG 59.001 50.000 4.92 0.00 40.55 3.51
879 912 4.527509 TTCATTCGTGAGCTCTTCTTCT 57.472 40.909 16.19 0.00 0.00 2.85
881 914 4.489810 TCATTCGTGAGCTCTTCTTCTTC 58.510 43.478 16.19 0.00 0.00 2.87
882 915 3.305398 TTCGTGAGCTCTTCTTCTTCC 57.695 47.619 16.19 0.00 0.00 3.46
886 931 1.546476 TGAGCTCTTCTTCTTCCGTCC 59.454 52.381 16.19 0.00 0.00 4.79
902 947 1.098712 GTCCGTGTGTGGCCTCAAAA 61.099 55.000 9.53 0.00 0.00 2.44
903 948 0.817634 TCCGTGTGTGGCCTCAAAAG 60.818 55.000 9.53 6.50 0.00 2.27
904 949 1.008538 CGTGTGTGGCCTCAAAAGC 60.009 57.895 9.53 0.00 0.00 3.51
907 952 1.953686 GTGTGTGGCCTCAAAAGCTTA 59.046 47.619 9.53 0.00 0.00 3.09
909 954 2.360801 TGTGTGGCCTCAAAAGCTTAAC 59.639 45.455 9.53 0.00 0.00 2.01
912 957 1.133325 TGGCCTCAAAAGCTTAACCCA 60.133 47.619 3.32 0.00 0.00 4.51
913 958 1.546029 GGCCTCAAAAGCTTAACCCAG 59.454 52.381 0.00 0.00 0.00 4.45
973 1021 4.947147 TGCGTGGCCCGAAAGCTT 62.947 61.111 16.53 0.00 39.56 3.74
974 1022 2.744709 GCGTGGCCCGAAAGCTTA 60.745 61.111 16.53 0.00 39.56 3.09
976 1024 2.750888 CGTGGCCCGAAAGCTTAGC 61.751 63.158 0.00 0.00 39.56 3.09
977 1025 1.377333 GTGGCCCGAAAGCTTAGCT 60.377 57.895 0.00 0.00 42.56 3.32
1005 1056 0.745486 CTGGTGCTTCGATCATGGCA 60.745 55.000 0.00 0.00 0.00 4.92
1381 1438 7.294245 TCCTTAATCCATGATGATCCTCTTCTT 59.706 37.037 0.00 0.00 0.00 2.52
1411 1468 2.747436 TCGATTCAGAATCTCGCATGG 58.253 47.619 19.05 4.07 35.73 3.66
1438 1495 5.942236 TCTCTGCTTATTCTGTTTTCATGCT 59.058 36.000 0.00 0.00 0.00 3.79
1460 1517 3.402110 TGTTCATCGATGCTTCTGTTGT 58.598 40.909 20.81 0.00 0.00 3.32
1462 1519 3.317603 TCATCGATGCTTCTGTTGTCA 57.682 42.857 20.81 0.00 0.00 3.58
1463 1520 3.865446 TCATCGATGCTTCTGTTGTCAT 58.135 40.909 20.81 0.00 0.00 3.06
1464 1521 3.867493 TCATCGATGCTTCTGTTGTCATC 59.133 43.478 20.81 0.00 33.79 2.92
1465 1522 3.317603 TCGATGCTTCTGTTGTCATCA 57.682 42.857 0.00 0.00 36.13 3.07
1466 1523 3.663025 TCGATGCTTCTGTTGTCATCAA 58.337 40.909 0.00 0.00 36.13 2.57
1487 1544 9.738832 CATCAACTCATCATGTTATAATTGCAA 57.261 29.630 0.00 0.00 0.00 4.08
1513 1627 8.411991 TTTTAATTACTCCCTCCGTTTCAAAT 57.588 30.769 0.00 0.00 0.00 2.32
1549 1903 7.108841 ACTTTGTACAGAGTTCAGACACTTA 57.891 36.000 13.05 0.00 0.00 2.24
1560 1914 7.599245 AGAGTTCAGACACTTATTTTAAGACGG 59.401 37.037 1.47 0.00 0.00 4.79
1563 1917 7.223260 TCAGACACTTATTTTAAGACGGAGA 57.777 36.000 1.47 0.00 0.00 3.71
1564 1918 7.663827 TCAGACACTTATTTTAAGACGGAGAA 58.336 34.615 1.47 0.00 0.00 2.87
1584 1938 8.543774 CGGAGAAAGTATTTGATAGTGATGTTC 58.456 37.037 0.00 0.00 39.27 3.18
1737 2095 2.508526 TCCTCTTCCAAAAGCTTGAGC 58.491 47.619 0.00 0.00 42.49 4.26
1772 2130 4.754618 GGCCCAAAACCTTTATCTTGTTTG 59.245 41.667 0.00 0.00 32.85 2.93
1910 2276 2.983791 GCAACCTTGGCATGGCAT 59.016 55.556 23.96 5.26 0.00 4.40
1911 2277 1.448893 GCAACCTTGGCATGGCATG 60.449 57.895 23.96 23.72 0.00 4.06
1922 2288 2.417339 CATGGCATGCATCAGCTTAC 57.583 50.000 21.36 0.00 42.74 2.34
1948 2318 6.537301 TGCAACATAAAGCTACCTACACATAC 59.463 38.462 0.00 0.00 0.00 2.39
1987 2357 2.360350 CCTGCCCAGTTGATGCGT 60.360 61.111 0.00 0.00 0.00 5.24
2033 2406 7.335422 ACTTATCTGCTAACTTGTTCTTGGATG 59.665 37.037 0.00 0.00 0.00 3.51
2039 2412 6.097554 TGCTAACTTGTTCTTGGATGGAAAAA 59.902 34.615 0.00 0.00 0.00 1.94
2120 2540 0.611200 AACCCACGTGGATCGATCAA 59.389 50.000 36.07 13.56 42.86 2.57
2147 2567 5.049405 CACTGAATTCTTGTCGCCTAAAAGT 60.049 40.000 7.05 0.00 0.00 2.66
2179 2602 2.559998 TATTGCTAAAAAGCAGCGCC 57.440 45.000 2.29 0.00 46.21 6.53
2243 2666 3.653836 ACCCACCAAGTCCTTAACACATA 59.346 43.478 0.00 0.00 0.00 2.29
2245 2668 5.222254 ACCCACCAAGTCCTTAACACATATT 60.222 40.000 0.00 0.00 0.00 1.28
2246 2669 5.357032 CCCACCAAGTCCTTAACACATATTC 59.643 44.000 0.00 0.00 0.00 1.75
2247 2670 6.180472 CCACCAAGTCCTTAACACATATTCT 58.820 40.000 0.00 0.00 0.00 2.40
2248 2671 6.316390 CCACCAAGTCCTTAACACATATTCTC 59.684 42.308 0.00 0.00 0.00 2.87
2249 2672 6.878923 CACCAAGTCCTTAACACATATTCTCA 59.121 38.462 0.00 0.00 0.00 3.27
2250 2673 7.390440 CACCAAGTCCTTAACACATATTCTCAA 59.610 37.037 0.00 0.00 0.00 3.02
2251 2674 7.942341 ACCAAGTCCTTAACACATATTCTCAAA 59.058 33.333 0.00 0.00 0.00 2.69
2252 2675 8.792633 CCAAGTCCTTAACACATATTCTCAAAA 58.207 33.333 0.00 0.00 0.00 2.44
2305 2728 1.066908 CGACATGGGCACAAACTGTTT 59.933 47.619 0.00 0.00 0.00 2.83
2306 2729 2.742774 GACATGGGCACAAACTGTTTC 58.257 47.619 2.13 0.00 0.00 2.78
2319 2744 5.235401 ACAAACTGTTTCGTGCAAAGTTTTT 59.765 32.000 2.13 0.00 0.00 1.94
2320 2745 5.509605 AACTGTTTCGTGCAAAGTTTTTC 57.490 34.783 0.00 0.00 0.00 2.29
2322 2747 4.985409 ACTGTTTCGTGCAAAGTTTTTCAA 59.015 33.333 0.00 0.00 0.00 2.69
2329 2754 4.490799 CGTGCAAAGTTTTTCAAGAACTGC 60.491 41.667 0.00 0.00 37.41 4.40
2344 2769 5.702349 AGAACTGCTTTCTTTCTTCCATG 57.298 39.130 0.00 0.00 42.37 3.66
2346 2771 3.225104 ACTGCTTTCTTTCTTCCATGCA 58.775 40.909 0.00 0.00 0.00 3.96
2347 2772 3.638160 ACTGCTTTCTTTCTTCCATGCAA 59.362 39.130 0.00 0.00 0.00 4.08
2348 2773 4.282703 ACTGCTTTCTTTCTTCCATGCAAT 59.717 37.500 0.00 0.00 0.00 3.56
2406 2867 2.879462 GGTGAACTAGCCGTCGCG 60.879 66.667 0.00 0.00 41.18 5.87
2412 2873 1.859427 AACTAGCCGTCGCGACTGAA 61.859 55.000 33.94 19.08 41.18 3.02
2420 2881 1.582502 CGTCGCGACTGAAAACTATCC 59.417 52.381 33.94 6.07 0.00 2.59
2439 2900 3.728845 TCCTCTGTTAGTGTTGCTTGTC 58.271 45.455 0.00 0.00 0.00 3.18
2469 2930 1.827399 CTGTGTAGAGGCCGGGTGTT 61.827 60.000 2.18 0.00 0.00 3.32
2470 2931 1.373812 GTGTAGAGGCCGGGTGTTT 59.626 57.895 2.18 0.00 0.00 2.83
2471 2932 0.672711 GTGTAGAGGCCGGGTGTTTC 60.673 60.000 2.18 0.00 0.00 2.78
2472 2933 0.834687 TGTAGAGGCCGGGTGTTTCT 60.835 55.000 2.18 0.00 0.00 2.52
2473 2934 0.323957 GTAGAGGCCGGGTGTTTCTT 59.676 55.000 2.18 0.00 0.00 2.52
2474 2935 0.323629 TAGAGGCCGGGTGTTTCTTG 59.676 55.000 2.18 0.00 0.00 3.02
2475 2936 1.072505 GAGGCCGGGTGTTTCTTGA 59.927 57.895 2.18 0.00 0.00 3.02
2476 2937 0.322546 GAGGCCGGGTGTTTCTTGAT 60.323 55.000 2.18 0.00 0.00 2.57
2477 2938 0.322546 AGGCCGGGTGTTTCTTGATC 60.323 55.000 2.18 0.00 0.00 2.92
2478 2939 0.608035 GGCCGGGTGTTTCTTGATCA 60.608 55.000 2.18 0.00 0.00 2.92
2479 2940 1.463674 GCCGGGTGTTTCTTGATCAT 58.536 50.000 2.18 0.00 0.00 2.45
2480 2941 1.133025 GCCGGGTGTTTCTTGATCATG 59.867 52.381 2.18 0.00 0.00 3.07
2481 2942 2.436417 CCGGGTGTTTCTTGATCATGT 58.564 47.619 8.33 0.00 0.00 3.21
2482 2943 2.819608 CCGGGTGTTTCTTGATCATGTT 59.180 45.455 8.33 0.00 0.00 2.71
2483 2944 3.255642 CCGGGTGTTTCTTGATCATGTTT 59.744 43.478 8.33 0.00 0.00 2.83
2484 2945 4.261994 CCGGGTGTTTCTTGATCATGTTTT 60.262 41.667 8.33 0.00 0.00 2.43
2485 2946 4.681025 CGGGTGTTTCTTGATCATGTTTTG 59.319 41.667 8.33 0.00 0.00 2.44
2486 2947 5.600696 GGGTGTTTCTTGATCATGTTTTGT 58.399 37.500 8.33 0.00 0.00 2.83
2487 2948 6.514212 CGGGTGTTTCTTGATCATGTTTTGTA 60.514 38.462 8.33 0.00 0.00 2.41
2488 2949 7.378181 GGGTGTTTCTTGATCATGTTTTGTAT 58.622 34.615 8.33 0.00 0.00 2.29
2502 2977 4.881273 TGTTTTGTATCCGCTTGATGCTAT 59.119 37.500 3.59 0.00 37.04 2.97
2851 3330 0.397675 AGATCTCCGGCCTCATGACA 60.398 55.000 0.00 0.00 0.00 3.58
3256 3738 3.425578 CGAGGACGTCAAGAGCATT 57.574 52.632 18.91 0.00 34.56 3.56
3694 4217 2.101770 CGGCCGACGGTACTCTTC 59.898 66.667 24.07 0.00 39.42 2.87
3791 4315 3.487209 GCGGTGCTAGTTAGTAGTGACTC 60.487 52.174 0.00 0.00 37.10 3.36
3801 4325 5.352016 AGTTAGTAGTGACTCGAGCAGTTAG 59.648 44.000 13.61 0.00 37.10 2.34
3825 4356 4.733077 ACAGGAAGGAGCTAGCTAGATA 57.267 45.455 25.15 0.00 0.00 1.98
3837 4368 7.255660 GGAGCTAGCTAGATATTACACACTTGT 60.256 40.741 25.15 0.00 40.02 3.16
3899 4439 9.397280 ACGCTACTGTAGTATATATGATCACAT 57.603 33.333 15.71 0.00 40.16 3.21
3933 4473 4.475747 ACCTCGGATTCCAAGGGTTTATTA 59.524 41.667 14.33 0.00 34.31 0.98
3934 4474 5.063880 CCTCGGATTCCAAGGGTTTATTAG 58.936 45.833 1.23 0.00 0.00 1.73
3935 4475 5.163237 CCTCGGATTCCAAGGGTTTATTAGA 60.163 44.000 1.23 0.00 0.00 2.10
3936 4476 6.465894 CCTCGGATTCCAAGGGTTTATTAGAT 60.466 42.308 1.23 0.00 0.00 1.98
3937 4477 6.296026 TCGGATTCCAAGGGTTTATTAGATG 58.704 40.000 3.09 0.00 0.00 2.90
3938 4478 6.062095 CGGATTCCAAGGGTTTATTAGATGT 58.938 40.000 3.09 0.00 0.00 3.06
3939 4479 7.071447 TCGGATTCCAAGGGTTTATTAGATGTA 59.929 37.037 3.09 0.00 0.00 2.29
3940 4480 7.883311 CGGATTCCAAGGGTTTATTAGATGTAT 59.117 37.037 3.09 0.00 0.00 2.29
3943 4483 9.740710 ATTCCAAGGGTTTATTAGATGTATAGC 57.259 33.333 0.00 0.00 0.00 2.97
3962 4502 4.219264 AGCTAGCAAGAAAGATTGAGCT 57.781 40.909 18.83 0.00 36.23 4.09
3963 4503 4.190772 AGCTAGCAAGAAAGATTGAGCTC 58.809 43.478 18.83 6.82 36.26 4.09
3964 4504 3.937706 GCTAGCAAGAAAGATTGAGCTCA 59.062 43.478 13.74 13.74 31.00 4.26
3965 4505 4.201802 GCTAGCAAGAAAGATTGAGCTCAC 60.202 45.833 18.03 6.00 31.00 3.51
3966 4506 4.018484 AGCAAGAAAGATTGAGCTCACT 57.982 40.909 18.03 11.94 31.55 3.41
3967 4507 4.002316 AGCAAGAAAGATTGAGCTCACTC 58.998 43.478 22.82 22.82 43.76 3.51
4024 4625 0.033503 TGAGGGCGAGTCTATCACCA 60.034 55.000 0.00 0.00 31.10 4.17
4193 5182 1.266124 GCGTTTTGCGGTGTACAAGC 61.266 55.000 15.34 15.34 41.69 4.01
4236 5226 2.664424 CGCCGGTTATGTTTGTCAAGTG 60.664 50.000 1.90 0.00 0.00 3.16
4292 5282 6.776116 TGAGTAGTCCTCATATGGTTTATCGT 59.224 38.462 2.13 0.00 45.34 3.73
4358 5352 9.833917 TTGTATATGGTTTATGTTCCGTCAATA 57.166 29.630 0.00 0.00 0.00 1.90
4434 5432 6.715344 TCATACATGTTTTAACACTCGACC 57.285 37.500 2.30 0.00 42.51 4.79
4461 5459 5.010282 ACTTGGTTAAGCCTAATTCCACTG 58.990 41.667 1.51 0.00 37.43 3.66
4481 5480 4.343526 ACTGAGAACTAGCCACATCCTATG 59.656 45.833 0.00 0.00 0.00 2.23
4483 5482 3.041211 AGAACTAGCCACATCCTATGCA 58.959 45.455 0.00 0.00 0.00 3.96
4505 5504 4.664150 AAAATCGTTGTGGGATGTTTGT 57.336 36.364 0.00 0.00 0.00 2.83
4603 5602 5.088739 CGATACACTTTCATGTTGCTTTCC 58.911 41.667 0.00 0.00 33.85 3.13
4608 5607 3.385755 ACTTTCATGTTGCTTTCCTTGCT 59.614 39.130 0.00 0.00 0.00 3.91
4641 5650 0.511653 GAACGAACGTTTCCAGAGCC 59.488 55.000 13.56 0.00 38.60 4.70
4651 5660 4.172512 CCAGAGCCCGCTCATGCT 62.173 66.667 18.44 0.00 44.99 3.79
4721 5740 4.180946 CGACAGCTAGCCGCGAGT 62.181 66.667 12.13 2.44 45.59 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
560 561 2.537625 GTGCAATAGATCAGCGACACTC 59.462 50.000 0.00 0.00 0.00 3.51
844 877 1.653609 GAATGAAACGCGGATTTTGGC 59.346 47.619 12.47 0.00 0.00 4.52
859 892 4.489810 GAAGAAGAAGAGCTCACGAATGA 58.510 43.478 17.77 0.00 0.00 2.57
860 893 3.616379 GGAAGAAGAAGAGCTCACGAATG 59.384 47.826 17.77 0.00 0.00 2.67
869 902 0.244178 ACGGACGGAAGAAGAAGAGC 59.756 55.000 0.00 0.00 0.00 4.09
879 912 4.612412 GGCCACACACGGACGGAA 62.612 66.667 0.00 0.00 0.00 4.30
882 915 3.800685 TTGAGGCCACACACGGACG 62.801 63.158 5.01 0.00 40.05 4.79
886 931 1.008538 GCTTTTGAGGCCACACACG 60.009 57.895 5.01 0.00 0.00 4.49
917 962 3.144120 GAACGATCGGAGCAAGCGC 62.144 63.158 20.98 0.00 38.99 5.92
918 963 2.849966 CGAACGATCGGAGCAAGCG 61.850 63.158 20.98 7.92 45.32 4.68
976 1024 2.192608 GAAGCACCAGAGCGGCAAAG 62.193 60.000 1.45 0.00 39.03 2.77
977 1025 2.203337 AAGCACCAGAGCGGCAAA 60.203 55.556 1.45 0.00 39.03 3.68
978 1026 2.669569 GAAGCACCAGAGCGGCAA 60.670 61.111 1.45 0.00 39.03 4.52
980 1028 4.742201 TCGAAGCACCAGAGCGGC 62.742 66.667 0.00 0.00 39.03 6.53
1133 1187 1.035932 GCCATTGTCCTGCAGCATCT 61.036 55.000 8.66 0.00 0.00 2.90
1207 1261 4.933064 GACCTCGATGCCGGAGCG 62.933 72.222 5.05 5.26 44.31 5.03
1381 1438 6.537453 AGATTCTGAATCGAAGAGGAAGAA 57.463 37.500 21.15 0.00 43.63 2.52
1411 1468 4.697352 TGAAAACAGAATAAGCAGAGAGGC 59.303 41.667 0.00 0.00 0.00 4.70
1438 1495 3.814842 ACAACAGAAGCATCGATGAACAA 59.185 39.130 29.20 0.00 0.00 2.83
1460 1517 9.122779 TGCAATTATAACATGATGAGTTGATGA 57.877 29.630 0.00 0.00 0.00 2.92
1487 1544 8.411991 TTTGAAACGGAGGGAGTAATTAAAAT 57.588 30.769 0.00 0.00 0.00 1.82
1504 1561 8.523464 CAAAGTTGAGACACTTAATTTGAAACG 58.477 33.333 0.00 0.00 35.87 3.60
1513 1627 7.553334 ACTCTGTACAAAGTTGAGACACTTAA 58.447 34.615 14.14 0.00 35.87 1.85
1778 2136 2.715749 TAGGCATCCACTGTGAATGG 57.284 50.000 9.11 0.00 38.71 3.16
1791 2149 6.515512 ACCTATGGTGAGTATTTTAGGCAT 57.484 37.500 0.00 0.00 32.98 4.40
1907 2273 0.736636 TGCAGTAAGCTGATGCATGC 59.263 50.000 11.82 11.82 44.56 4.06
1911 2277 4.621068 TTATGTTGCAGTAAGCTGATGC 57.379 40.909 10.31 10.31 45.28 3.91
1920 2286 6.103997 GTGTAGGTAGCTTTATGTTGCAGTA 58.896 40.000 0.00 0.00 0.00 2.74
1922 2288 4.935205 TGTGTAGGTAGCTTTATGTTGCAG 59.065 41.667 0.00 0.00 0.00 4.41
1987 2357 4.894784 AGTGCCGAAAGTTAGATTCTTCA 58.105 39.130 0.00 0.00 0.00 3.02
2065 2480 7.750458 GCATGACAGATCGTTTTCAGAAATTTA 59.250 33.333 0.00 0.00 0.00 1.40
2120 2540 1.523758 GCGACAAGAATTCAGTGGGT 58.476 50.000 8.44 0.00 0.00 4.51
2164 2584 0.733909 CAAGGGCGCTGCTTTTTAGC 60.734 55.000 7.64 0.00 37.80 3.09
2176 2599 2.353889 CACTGAAATCAGATCAAGGGCG 59.646 50.000 16.93 0.00 46.59 6.13
2179 2602 2.686915 GGCCACTGAAATCAGATCAAGG 59.313 50.000 16.93 10.55 46.59 3.61
2286 2709 2.742774 GAAACAGTTTGTGCCCATGTC 58.257 47.619 2.34 0.00 0.00 3.06
2305 2728 4.856487 CAGTTCTTGAAAAACTTTGCACGA 59.144 37.500 0.00 0.00 34.79 4.35
2306 2729 4.490799 GCAGTTCTTGAAAAACTTTGCACG 60.491 41.667 0.00 0.00 34.79 5.34
2346 2771 2.990740 TACAGGGACAGGGCAAAATT 57.009 45.000 0.00 0.00 0.00 1.82
2347 2772 2.311542 TGATACAGGGACAGGGCAAAAT 59.688 45.455 0.00 0.00 0.00 1.82
2348 2773 1.707989 TGATACAGGGACAGGGCAAAA 59.292 47.619 0.00 0.00 0.00 2.44
2406 2867 7.379750 ACACTAACAGAGGATAGTTTTCAGTC 58.620 38.462 0.00 0.00 31.00 3.51
2412 2873 6.115448 AGCAACACTAACAGAGGATAGTTT 57.885 37.500 0.00 0.00 31.00 2.66
2420 2881 3.059325 GCAGACAAGCAACACTAACAGAG 60.059 47.826 0.00 0.00 0.00 3.35
2452 2913 0.672711 GAAACACCCGGCCTCTACAC 60.673 60.000 0.00 0.00 0.00 2.90
2455 2916 0.323629 CAAGAAACACCCGGCCTCTA 59.676 55.000 0.00 0.00 0.00 2.43
2469 2930 5.647658 AGCGGATACAAAACATGATCAAGAA 59.352 36.000 4.68 0.00 0.00 2.52
2470 2931 5.185454 AGCGGATACAAAACATGATCAAGA 58.815 37.500 4.68 0.00 0.00 3.02
2471 2932 5.490139 AGCGGATACAAAACATGATCAAG 57.510 39.130 0.00 0.00 0.00 3.02
2472 2933 5.414144 TCAAGCGGATACAAAACATGATCAA 59.586 36.000 0.00 0.00 0.00 2.57
2473 2934 4.940654 TCAAGCGGATACAAAACATGATCA 59.059 37.500 0.00 0.00 0.00 2.92
2474 2935 5.484173 TCAAGCGGATACAAAACATGATC 57.516 39.130 0.00 0.00 0.00 2.92
2475 2936 5.734220 GCATCAAGCGGATACAAAACATGAT 60.734 40.000 0.00 0.00 33.95 2.45
2476 2937 4.438608 GCATCAAGCGGATACAAAACATGA 60.439 41.667 0.00 0.00 33.95 3.07
2477 2938 3.792956 GCATCAAGCGGATACAAAACATG 59.207 43.478 0.00 0.00 33.95 3.21
2478 2939 4.032703 GCATCAAGCGGATACAAAACAT 57.967 40.909 0.00 0.00 33.95 2.71
2479 2940 3.485947 GCATCAAGCGGATACAAAACA 57.514 42.857 0.00 0.00 33.95 2.83
2851 3330 1.550327 TGAGGAACTGCACGATCTCT 58.450 50.000 0.00 0.00 41.55 3.10
2977 3459 1.666553 GATGTTGCCGTCGACCACA 60.667 57.895 10.58 8.37 0.00 4.17
3254 3736 1.341531 CTCGAAGTAGCCCGGATCAAT 59.658 52.381 0.73 0.00 0.00 2.57
3256 3738 1.735376 GCTCGAAGTAGCCCGGATCA 61.735 60.000 0.73 0.00 36.45 2.92
3711 4234 1.074775 ATGGCCGCAAGAACCAAGA 59.925 52.632 0.00 0.00 44.69 3.02
3801 4325 1.408969 AGCTAGCTCCTTCCTGTAGC 58.591 55.000 12.68 0.00 37.05 3.58
3899 4439 2.545550 ATCCGAGGTCCATGGGGTCA 62.546 60.000 13.02 0.00 34.93 4.02
3902 4442 1.451936 GAATCCGAGGTCCATGGGG 59.548 63.158 13.02 4.60 0.00 4.96
3933 4473 8.646004 TCAATCTTTCTTGCTAGCTATACATCT 58.354 33.333 17.23 0.00 0.00 2.90
3934 4474 8.824159 TCAATCTTTCTTGCTAGCTATACATC 57.176 34.615 17.23 0.00 0.00 3.06
3935 4475 7.387397 GCTCAATCTTTCTTGCTAGCTATACAT 59.613 37.037 17.23 0.00 0.00 2.29
3936 4476 6.703607 GCTCAATCTTTCTTGCTAGCTATACA 59.296 38.462 17.23 0.00 0.00 2.29
3937 4477 6.928492 AGCTCAATCTTTCTTGCTAGCTATAC 59.072 38.462 17.23 0.00 35.64 1.47
3938 4478 7.060383 AGCTCAATCTTTCTTGCTAGCTATA 57.940 36.000 17.23 0.00 35.64 1.31
3939 4479 5.927819 AGCTCAATCTTTCTTGCTAGCTAT 58.072 37.500 17.23 0.00 35.64 2.97
3940 4480 5.105187 TGAGCTCAATCTTTCTTGCTAGCTA 60.105 40.000 15.67 7.59 36.80 3.32
3941 4481 4.190772 GAGCTCAATCTTTCTTGCTAGCT 58.809 43.478 17.23 0.00 38.38 3.32
3942 4482 3.937706 TGAGCTCAATCTTTCTTGCTAGC 59.062 43.478 15.67 8.10 0.00 3.42
3943 4483 5.177326 AGTGAGCTCAATCTTTCTTGCTAG 58.823 41.667 20.19 0.00 0.00 3.42
3964 4504 0.529773 ACAACGACGTGCACATGAGT 60.530 50.000 18.64 6.20 0.00 3.41
3965 4505 0.161658 GACAACGACGTGCACATGAG 59.838 55.000 18.64 7.33 0.00 2.90
3966 4506 0.249280 AGACAACGACGTGCACATGA 60.249 50.000 18.64 0.00 0.00 3.07
3967 4507 0.161658 GAGACAACGACGTGCACATG 59.838 55.000 18.64 8.04 0.00 3.21
3968 4508 0.944311 GGAGACAACGACGTGCACAT 60.944 55.000 18.64 0.00 0.00 3.21
3969 4509 1.590525 GGAGACAACGACGTGCACA 60.591 57.895 18.64 0.00 0.00 4.57
3970 4510 2.308039 GGGAGACAACGACGTGCAC 61.308 63.158 6.82 6.82 0.00 4.57
3971 4511 2.023414 AAGGGAGACAACGACGTGCA 62.023 55.000 0.00 0.00 0.00 4.57
3972 4512 1.300697 AAGGGAGACAACGACGTGC 60.301 57.895 0.00 0.00 0.00 5.34
4184 4811 3.623060 CCACATAGTCCATGCTTGTACAC 59.377 47.826 0.00 0.00 38.29 2.90
4193 5182 1.665679 GCAACGACCACATAGTCCATG 59.334 52.381 0.00 0.00 40.78 3.66
4236 5226 2.396590 AACCCATGACCACACGATAC 57.603 50.000 0.00 0.00 0.00 2.24
4326 5316 9.100554 CGGAACATAAACCATATACAAACTACA 57.899 33.333 0.00 0.00 0.00 2.74
4332 5322 8.740123 ATTGACGGAACATAAACCATATACAA 57.260 30.769 0.00 0.00 0.00 2.41
4407 5405 8.492748 GTCGAGTGTTAAAACATGTATGAAAGA 58.507 33.333 0.00 0.00 41.59 2.52
4423 5421 1.538512 CCAAGTCTCGGTCGAGTGTTA 59.461 52.381 18.18 0.00 42.49 2.41
4434 5432 4.571176 GGAATTAGGCTTAACCAAGTCTCG 59.429 45.833 0.00 0.00 43.33 4.04
4461 5459 3.070159 TGCATAGGATGTGGCTAGTTCTC 59.930 47.826 0.00 0.00 0.00 2.87
4481 5480 3.025287 ACATCCCACAACGATTTTTGC 57.975 42.857 0.00 0.00 0.00 3.68
4483 5482 5.017294 ACAAACATCCCACAACGATTTTT 57.983 34.783 0.00 0.00 0.00 1.94
4505 5504 2.166459 CCTCTTCGAGACATAGTGCCAA 59.834 50.000 0.00 0.00 0.00 4.52
4542 5541 1.142097 GGAAGAGACCAGCTACGCC 59.858 63.158 0.00 0.00 0.00 5.68
4632 5641 2.586245 CATGAGCGGGCTCTGGAA 59.414 61.111 20.27 1.76 43.12 3.53
4651 5660 3.874383 AGCTGCTCTACTCCTAGATCA 57.126 47.619 0.00 0.00 0.00 2.92
4721 5740 2.601240 TGTTGCATTTGGATCCCTCA 57.399 45.000 9.90 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.