Multiple sequence alignment - TraesCS7A01G517500

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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 TraesCS7A01G517500 chr7A 100.000 2549 0 0 1 2549 701581369 701583917 0.000000e+00 4708.0
1 TraesCS7A01G517500 chr7A 98.734 474 6 0 91 564 238820271 238820744 0.000000e+00 843.0
2 TraesCS7A01G517500 chr7A 97.257 474 10 2 91 564 56559801 56559331 0.000000e+00 800.0
3 TraesCS7A01G517500 chr7A 97.826 92 2 0 1 92 65078386 65078295 2.620000e-35 159.0
4 TraesCS7A01G517500 chr7A 95.876 97 4 0 1 97 533735133 533735229 9.440000e-35 158.0
5 TraesCS7A01G517500 chr6B 99.039 1977 17 2 573 2549 660437743 660435769 0.000000e+00 3544.0
6 TraesCS7A01G517500 chr7B 98.939 1979 20 1 572 2549 552932144 552930166 0.000000e+00 3537.0
7 TraesCS7A01G517500 chr7B 98.890 1982 18 3 568 2548 692881447 692883425 0.000000e+00 3535.0
8 TraesCS7A01G517500 chr7B 98.735 1977 25 0 573 2549 1776631 1774655 0.000000e+00 3513.0
9 TraesCS7A01G517500 chr7B 100.000 90 0 0 1 90 425876445 425876356 1.570000e-37 167.0
10 TraesCS7A01G517500 chr7B 98.889 90 1 0 1 90 425885031 425885120 7.300000e-36 161.0
11 TraesCS7A01G517500 chr6A 98.939 1979 19 2 563 2540 617222880 617220903 0.000000e+00 3537.0
12 TraesCS7A01G517500 chr5A 98.787 1979 23 1 571 2549 459744879 459746856 0.000000e+00 3520.0
13 TraesCS7A01G517500 chr3B 98.640 1986 25 1 564 2549 379294084 379296067 0.000000e+00 3517.0
14 TraesCS7A01G517500 chr3B 92.176 409 25 4 99 501 54075212 54074805 2.850000e-159 571.0
15 TraesCS7A01G517500 chr3B 91.400 407 22 5 99 501 54151457 54151060 1.720000e-151 545.0
16 TraesCS7A01G517500 chr3B 91.379 58 5 0 502 559 54073791 54073734 2.100000e-11 80.5
17 TraesCS7A01G517500 chr3B 91.379 58 5 0 502 559 54150038 54149981 2.100000e-11 80.5
18 TraesCS7A01G517500 chr3B 97.436 39 1 0 529 567 3391406 3391368 1.640000e-07 67.6
19 TraesCS7A01G517500 chr4A 98.737 1980 22 3 561 2540 36562904 36564880 0.000000e+00 3515.0
20 TraesCS7A01G517500 chr4A 98.954 478 4 1 91 568 547985644 547986120 0.000000e+00 854.0
21 TraesCS7A01G517500 chr4A 100.000 91 0 0 1 91 36323420 36323510 4.360000e-38 169.0
22 TraesCS7A01G517500 chr4A 98.889 90 1 0 1 90 590267641 590267730 7.300000e-36 161.0
23 TraesCS7A01G517500 chr1A 98.639 1984 23 4 566 2549 22791523 22793502 0.000000e+00 3511.0
24 TraesCS7A01G517500 chr3A 96.732 306 7 2 91 396 723652233 723651931 8.140000e-140 507.0
25 TraesCS7A01G517500 chr3A 97.191 178 4 1 388 564 723650387 723650210 1.480000e-77 300.0
26 TraesCS7A01G517500 chr2B 89.787 235 20 3 270 501 245695656 245695423 5.330000e-77 298.0
27 TraesCS7A01G517500 chr2B 88.235 204 17 2 270 466 188833633 188833836 1.180000e-58 237.0
28 TraesCS7A01G517500 chr2B 92.727 55 3 1 314 367 18913415 18913361 7.560000e-11 78.7
29 TraesCS7A01G517500 chr5B 97.938 97 1 1 1 97 185041429 185041524 1.570000e-37 167.0
30 TraesCS7A01G517500 chr5B 100.000 90 0 0 1 90 696405515 696405426 1.570000e-37 167.0
31 TraesCS7A01G517500 chr5B 98.876 89 1 0 1 89 696413546 696413634 2.620000e-35 159.0
32 TraesCS7A01G517500 chr5B 95.122 41 2 0 462 502 270671424 270671464 5.890000e-07 65.8
33 TraesCS7A01G517500 chr3D 95.556 45 1 1 529 573 568279564 568279521 1.270000e-08 71.3
34 TraesCS7A01G517500 chr4B 97.436 39 1 0 529 567 644571953 644571991 1.640000e-07 67.6


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 TraesCS7A01G517500 chr7A 701581369 701583917 2548 False 4708.00 4708 100.0000 1 2549 1 chr7A.!!$F3 2548
1 TraesCS7A01G517500 chr6B 660435769 660437743 1974 True 3544.00 3544 99.0390 573 2549 1 chr6B.!!$R1 1976
2 TraesCS7A01G517500 chr7B 552930166 552932144 1978 True 3537.00 3537 98.9390 572 2549 1 chr7B.!!$R3 1977
3 TraesCS7A01G517500 chr7B 692881447 692883425 1978 False 3535.00 3535 98.8900 568 2548 1 chr7B.!!$F2 1980
4 TraesCS7A01G517500 chr7B 1774655 1776631 1976 True 3513.00 3513 98.7350 573 2549 1 chr7B.!!$R1 1976
5 TraesCS7A01G517500 chr6A 617220903 617222880 1977 True 3537.00 3537 98.9390 563 2540 1 chr6A.!!$R1 1977
6 TraesCS7A01G517500 chr5A 459744879 459746856 1977 False 3520.00 3520 98.7870 571 2549 1 chr5A.!!$F1 1978
7 TraesCS7A01G517500 chr3B 379294084 379296067 1983 False 3517.00 3517 98.6400 564 2549 1 chr3B.!!$F1 1985
8 TraesCS7A01G517500 chr3B 54073734 54075212 1478 True 325.75 571 91.7775 99 559 2 chr3B.!!$R2 460
9 TraesCS7A01G517500 chr3B 54149981 54151457 1476 True 312.75 545 91.3895 99 559 2 chr3B.!!$R3 460
10 TraesCS7A01G517500 chr4A 36562904 36564880 1976 False 3515.00 3515 98.7370 561 2540 1 chr4A.!!$F2 1979
11 TraesCS7A01G517500 chr1A 22791523 22793502 1979 False 3511.00 3511 98.6390 566 2549 1 chr1A.!!$F1 1983
12 TraesCS7A01G517500 chr3A 723650210 723652233 2023 True 403.50 507 96.9615 91 564 2 chr3A.!!$R1 473

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
500 504 0.251297 TGTTGGGGCAGGTGAAGATG 60.251 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 3862 1.669115 CCAAGTGCCACTCTGACCG 60.669 63.158 0.0 0.0 0.0 4.79 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
20 21 2.489971 CCAAACATGGTACTGACACGT 58.510 47.619 0.00 0.00 0.00 4.49
21 22 3.655486 CCAAACATGGTACTGACACGTA 58.345 45.455 0.00 0.00 0.00 3.57
22 23 4.059511 CCAAACATGGTACTGACACGTAA 58.940 43.478 0.00 0.00 0.00 3.18
23 24 4.512198 CCAAACATGGTACTGACACGTAAA 59.488 41.667 0.00 0.00 0.00 2.01
24 25 5.007823 CCAAACATGGTACTGACACGTAAAA 59.992 40.000 0.00 0.00 0.00 1.52
25 26 6.293735 CCAAACATGGTACTGACACGTAAAAT 60.294 38.462 0.00 0.00 0.00 1.82
26 27 6.870971 AACATGGTACTGACACGTAAAATT 57.129 33.333 0.00 0.00 0.00 1.82
27 28 6.870971 ACATGGTACTGACACGTAAAATTT 57.129 33.333 0.00 0.00 0.00 1.82
28 29 7.266922 ACATGGTACTGACACGTAAAATTTT 57.733 32.000 8.75 8.75 0.00 1.82
29 30 7.708998 ACATGGTACTGACACGTAAAATTTTT 58.291 30.769 9.06 0.00 0.00 1.94
30 31 7.858879 ACATGGTACTGACACGTAAAATTTTTC 59.141 33.333 9.06 2.94 0.00 2.29
31 32 7.317842 TGGTACTGACACGTAAAATTTTTCA 57.682 32.000 9.06 5.49 0.00 2.69
32 33 7.759465 TGGTACTGACACGTAAAATTTTTCAA 58.241 30.769 9.06 0.00 0.00 2.69
33 34 8.242053 TGGTACTGACACGTAAAATTTTTCAAA 58.758 29.630 9.06 0.00 0.00 2.69
34 35 9.074443 GGTACTGACACGTAAAATTTTTCAAAA 57.926 29.630 9.06 0.00 0.00 2.44
35 36 9.875660 GTACTGACACGTAAAATTTTTCAAAAC 57.124 29.630 9.06 0.00 0.00 2.43
36 37 8.751302 ACTGACACGTAAAATTTTTCAAAACT 57.249 26.923 9.06 0.00 0.00 2.66
37 38 8.643752 ACTGACACGTAAAATTTTTCAAAACTG 58.356 29.630 9.06 4.32 0.00 3.16
38 39 7.954447 TGACACGTAAAATTTTTCAAAACTGG 58.046 30.769 9.06 0.00 0.00 4.00
39 40 7.599245 TGACACGTAAAATTTTTCAAAACTGGT 59.401 29.630 9.06 2.04 0.00 4.00
40 41 8.983307 ACACGTAAAATTTTTCAAAACTGGTA 57.017 26.923 9.06 0.00 0.00 3.25
41 42 8.862074 ACACGTAAAATTTTTCAAAACTGGTAC 58.138 29.630 9.06 0.00 0.00 3.34
42 43 8.322428 CACGTAAAATTTTTCAAAACTGGTACC 58.678 33.333 9.06 4.43 0.00 3.34
43 44 8.033626 ACGTAAAATTTTTCAAAACTGGTACCA 58.966 29.630 15.39 15.39 0.00 3.25
44 45 8.870879 CGTAAAATTTTTCAAAACTGGTACCAA 58.129 29.630 17.11 0.00 0.00 3.67
48 49 7.707774 ATTTTTCAAAACTGGTACCAATTCG 57.292 32.000 17.11 7.56 0.00 3.34
49 50 3.907894 TCAAAACTGGTACCAATTCGC 57.092 42.857 17.11 0.00 0.00 4.70
50 51 2.554893 TCAAAACTGGTACCAATTCGCC 59.445 45.455 17.11 0.00 0.00 5.54
51 52 2.279935 AAACTGGTACCAATTCGCCA 57.720 45.000 17.11 0.00 0.00 5.69
52 53 1.530323 AACTGGTACCAATTCGCCAC 58.470 50.000 17.11 0.00 0.00 5.01
53 54 0.322187 ACTGGTACCAATTCGCCACC 60.322 55.000 17.11 0.00 0.00 4.61
54 55 0.322098 CTGGTACCAATTCGCCACCA 60.322 55.000 17.11 0.00 37.68 4.17
55 56 0.606944 TGGTACCAATTCGCCACCAC 60.607 55.000 13.60 0.00 34.40 4.16
56 57 1.641123 GGTACCAATTCGCCACCACG 61.641 60.000 7.15 0.00 0.00 4.94
57 58 1.376166 TACCAATTCGCCACCACGG 60.376 57.895 0.00 0.00 38.11 4.94
66 67 3.381136 CCACCACGGCCCCAATTG 61.381 66.667 0.00 0.00 0.00 2.32
67 68 2.600173 CACCACGGCCCCAATTGT 60.600 61.111 4.43 0.00 0.00 2.71
68 69 2.600173 ACCACGGCCCCAATTGTG 60.600 61.111 4.43 0.00 0.00 3.33
69 70 3.381136 CCACGGCCCCAATTGTGG 61.381 66.667 10.37 10.37 45.17 4.17
70 71 2.600173 CACGGCCCCAATTGTGGT 60.600 61.111 8.84 0.00 44.30 4.16
71 72 1.303724 CACGGCCCCAATTGTGGTA 60.304 57.895 8.84 0.00 44.30 3.25
72 73 1.303806 ACGGCCCCAATTGTGGTAC 60.304 57.895 8.84 1.73 44.30 3.34
73 74 1.001393 CGGCCCCAATTGTGGTACT 60.001 57.895 8.84 0.00 44.30 2.73
74 75 0.253610 CGGCCCCAATTGTGGTACTA 59.746 55.000 8.84 0.00 44.30 1.82
75 76 1.133915 CGGCCCCAATTGTGGTACTAT 60.134 52.381 8.84 0.00 44.30 2.12
76 77 2.583143 GGCCCCAATTGTGGTACTATC 58.417 52.381 8.84 0.00 44.30 2.08
77 78 2.218603 GCCCCAATTGTGGTACTATCG 58.781 52.381 8.84 0.00 44.30 2.92
78 79 2.420967 GCCCCAATTGTGGTACTATCGT 60.421 50.000 8.84 0.00 44.30 3.73
79 80 3.202906 CCCCAATTGTGGTACTATCGTG 58.797 50.000 4.43 0.00 44.30 4.35
80 81 3.370103 CCCCAATTGTGGTACTATCGTGT 60.370 47.826 4.43 0.00 44.30 4.49
81 82 4.141892 CCCCAATTGTGGTACTATCGTGTA 60.142 45.833 4.43 0.00 44.30 2.90
82 83 5.421277 CCCAATTGTGGTACTATCGTGTAA 58.579 41.667 4.43 0.00 44.30 2.41
83 84 6.053005 CCCAATTGTGGTACTATCGTGTAAT 58.947 40.000 4.43 0.00 44.30 1.89
84 85 6.540914 CCCAATTGTGGTACTATCGTGTAATT 59.459 38.462 4.43 0.00 44.30 1.40
85 86 7.711772 CCCAATTGTGGTACTATCGTGTAATTA 59.288 37.037 4.43 0.00 44.30 1.40
86 87 9.100554 CCAATTGTGGTACTATCGTGTAATTAA 57.899 33.333 4.43 0.00 40.42 1.40
87 88 9.910511 CAATTGTGGTACTATCGTGTAATTAAC 57.089 33.333 0.00 0.00 0.00 2.01
88 89 9.880157 AATTGTGGTACTATCGTGTAATTAACT 57.120 29.630 0.00 0.00 0.00 2.24
89 90 8.915871 TTGTGGTACTATCGTGTAATTAACTC 57.084 34.615 0.00 0.00 0.00 3.01
142 143 5.106712 TGCGTATGATCAAACCTTCAAACTC 60.107 40.000 0.00 0.00 0.00 3.01
289 293 1.021202 TTCTCAAAGGTGTGTTGCCG 58.979 50.000 0.00 0.00 0.00 5.69
324 328 5.011533 AGACTAGATGTTCTGCTCTTGTGTT 59.988 40.000 0.00 0.00 29.57 3.32
342 346 5.587289 TGTGTTTGAACAATCTTAGTTGGC 58.413 37.500 0.00 0.00 41.21 4.52
396 400 7.912778 AACCTGCCCATGTTGTATATAAAAT 57.087 32.000 0.00 0.00 0.00 1.82
398 402 9.600432 AACCTGCCCATGTTGTATATAAAATAT 57.400 29.630 0.00 0.00 0.00 1.28
453 457 8.523523 TTTTTGTCAAAATACATCAGCTCATG 57.476 30.769 11.44 0.00 0.00 3.07
454 458 5.823209 TGTCAAAATACATCAGCTCATGG 57.177 39.130 1.59 0.00 0.00 3.66
455 459 5.255687 TGTCAAAATACATCAGCTCATGGT 58.744 37.500 1.59 0.00 0.00 3.55
456 460 5.355071 TGTCAAAATACATCAGCTCATGGTC 59.645 40.000 1.59 0.00 0.00 4.02
457 461 5.355071 GTCAAAATACATCAGCTCATGGTCA 59.645 40.000 1.59 0.00 0.00 4.02
458 462 5.355071 TCAAAATACATCAGCTCATGGTCAC 59.645 40.000 1.59 0.00 0.00 3.67
459 463 4.767578 AATACATCAGCTCATGGTCACT 57.232 40.909 1.59 0.00 0.00 3.41
460 464 2.398252 ACATCAGCTCATGGTCACTG 57.602 50.000 1.59 0.00 0.00 3.66
461 465 1.904537 ACATCAGCTCATGGTCACTGA 59.095 47.619 1.59 9.31 42.89 3.41
462 466 2.303890 ACATCAGCTCATGGTCACTGAA 59.696 45.455 1.59 0.00 42.08 3.02
463 467 3.054582 ACATCAGCTCATGGTCACTGAAT 60.055 43.478 1.59 2.58 42.08 2.57
464 468 4.162888 ACATCAGCTCATGGTCACTGAATA 59.837 41.667 1.59 0.00 42.08 1.75
465 469 4.824479 TCAGCTCATGGTCACTGAATAA 57.176 40.909 0.00 0.00 36.27 1.40
466 470 5.164620 TCAGCTCATGGTCACTGAATAAA 57.835 39.130 0.00 0.00 36.27 1.40
467 471 4.937620 TCAGCTCATGGTCACTGAATAAAC 59.062 41.667 0.00 0.00 36.27 2.01
468 472 4.940046 CAGCTCATGGTCACTGAATAAACT 59.060 41.667 0.00 0.00 31.67 2.66
469 473 4.940046 AGCTCATGGTCACTGAATAAACTG 59.060 41.667 0.00 0.00 0.00 3.16
470 474 4.937620 GCTCATGGTCACTGAATAAACTGA 59.062 41.667 0.00 0.00 0.00 3.41
471 475 5.587844 GCTCATGGTCACTGAATAAACTGAT 59.412 40.000 0.00 0.00 0.00 2.90
472 476 6.457934 GCTCATGGTCACTGAATAAACTGATG 60.458 42.308 0.00 0.00 0.00 3.07
473 477 6.475504 TCATGGTCACTGAATAAACTGATGT 58.524 36.000 0.00 0.00 0.00 3.06
474 478 6.942005 TCATGGTCACTGAATAAACTGATGTT 59.058 34.615 0.00 0.00 38.16 2.71
475 479 6.558771 TGGTCACTGAATAAACTGATGTTG 57.441 37.500 0.00 0.00 36.39 3.33
476 480 6.295249 TGGTCACTGAATAAACTGATGTTGA 58.705 36.000 0.00 0.00 36.39 3.18
477 481 6.204688 TGGTCACTGAATAAACTGATGTTGAC 59.795 38.462 0.00 0.00 36.39 3.18
478 482 6.428159 GGTCACTGAATAAACTGATGTTGACT 59.572 38.462 0.00 0.00 36.39 3.41
479 483 7.602644 GGTCACTGAATAAACTGATGTTGACTA 59.397 37.037 0.00 0.00 36.39 2.59
480 484 9.155975 GTCACTGAATAAACTGATGTTGACTAT 57.844 33.333 0.00 0.00 36.39 2.12
481 485 9.725019 TCACTGAATAAACTGATGTTGACTATT 57.275 29.630 0.00 0.00 36.39 1.73
482 486 9.764870 CACTGAATAAACTGATGTTGACTATTG 57.235 33.333 0.00 0.00 36.39 1.90
483 487 9.507329 ACTGAATAAACTGATGTTGACTATTGT 57.493 29.630 0.00 0.00 36.39 2.71
486 490 9.559958 GAATAAACTGATGTTGACTATTGTTGG 57.440 33.333 0.00 0.00 36.39 3.77
487 491 5.964958 AACTGATGTTGACTATTGTTGGG 57.035 39.130 0.00 0.00 34.71 4.12
488 492 4.335416 ACTGATGTTGACTATTGTTGGGG 58.665 43.478 0.00 0.00 0.00 4.96
489 493 3.088532 TGATGTTGACTATTGTTGGGGC 58.911 45.455 0.00 0.00 0.00 5.80
490 494 2.666272 TGTTGACTATTGTTGGGGCA 57.334 45.000 0.00 0.00 0.00 5.36
491 495 2.513753 TGTTGACTATTGTTGGGGCAG 58.486 47.619 0.00 0.00 0.00 4.85
492 496 1.818674 GTTGACTATTGTTGGGGCAGG 59.181 52.381 0.00 0.00 0.00 4.85
493 497 1.072266 TGACTATTGTTGGGGCAGGT 58.928 50.000 0.00 0.00 0.00 4.00
494 498 1.271871 TGACTATTGTTGGGGCAGGTG 60.272 52.381 0.00 0.00 0.00 4.00
495 499 1.004277 GACTATTGTTGGGGCAGGTGA 59.996 52.381 0.00 0.00 0.00 4.02
496 500 1.427368 ACTATTGTTGGGGCAGGTGAA 59.573 47.619 0.00 0.00 0.00 3.18
497 501 2.094675 CTATTGTTGGGGCAGGTGAAG 58.905 52.381 0.00 0.00 0.00 3.02
498 502 0.482446 ATTGTTGGGGCAGGTGAAGA 59.518 50.000 0.00 0.00 0.00 2.87
499 503 0.482446 TTGTTGGGGCAGGTGAAGAT 59.518 50.000 0.00 0.00 0.00 2.40
500 504 0.251297 TGTTGGGGCAGGTGAAGATG 60.251 55.000 0.00 0.00 0.00 2.90
501 505 1.304381 TTGGGGCAGGTGAAGATGC 60.304 57.895 0.00 0.00 41.80 3.91
502 506 2.079088 TTGGGGCAGGTGAAGATGCA 62.079 55.000 0.00 0.00 44.37 3.96
503 507 1.304381 GGGGCAGGTGAAGATGCAA 60.304 57.895 0.00 0.00 44.37 4.08
504 508 0.899717 GGGGCAGGTGAAGATGCAAA 60.900 55.000 0.00 0.00 44.37 3.68
505 509 1.188863 GGGCAGGTGAAGATGCAAAT 58.811 50.000 0.00 0.00 44.37 2.32
506 510 2.378038 GGGCAGGTGAAGATGCAAATA 58.622 47.619 0.00 0.00 44.37 1.40
507 511 2.961062 GGGCAGGTGAAGATGCAAATAT 59.039 45.455 0.00 0.00 44.37 1.28
508 512 3.005155 GGGCAGGTGAAGATGCAAATATC 59.995 47.826 0.00 0.00 44.37 1.63
509 513 3.887716 GGCAGGTGAAGATGCAAATATCT 59.112 43.478 0.00 0.00 44.37 1.98
511 515 5.163478 GGCAGGTGAAGATGCAAATATCTTT 60.163 40.000 1.99 0.00 45.00 2.52
512 516 6.335777 GCAGGTGAAGATGCAAATATCTTTT 58.664 36.000 1.99 0.00 45.00 2.27
513 517 6.474751 GCAGGTGAAGATGCAAATATCTTTTC 59.525 38.462 1.99 0.00 45.00 2.29
514 518 7.541162 CAGGTGAAGATGCAAATATCTTTTCA 58.459 34.615 1.99 0.00 45.00 2.69
515 519 7.487189 CAGGTGAAGATGCAAATATCTTTTCAC 59.513 37.037 9.49 9.49 45.00 3.18
516 520 7.177216 AGGTGAAGATGCAAATATCTTTTCACA 59.823 33.333 16.38 3.33 45.00 3.58
517 521 7.977853 GGTGAAGATGCAAATATCTTTTCACAT 59.022 33.333 16.38 0.00 45.00 3.21
525 529 9.667989 TGCAAATATCTTTTCACATAATGATCG 57.332 29.630 0.00 0.00 37.11 3.69
526 530 9.669353 GCAAATATCTTTTCACATAATGATCGT 57.331 29.630 0.00 0.00 37.11 3.73
532 536 8.115491 TCTTTTCACATAATGATCGTAAGTCG 57.885 34.615 0.00 0.00 37.11 4.18
540 544 2.097160 TCGTAAGTCGAGACGCGC 59.903 61.111 5.73 0.00 44.01 6.86
541 545 3.295462 CGTAAGTCGAGACGCGCG 61.295 66.667 30.96 30.96 42.86 6.86
542 546 2.202272 GTAAGTCGAGACGCGCGT 60.202 61.111 38.52 38.52 40.61 6.01
543 547 1.795177 GTAAGTCGAGACGCGCGTT 60.795 57.895 38.03 25.58 40.61 4.84
544 548 1.794785 TAAGTCGAGACGCGCGTTG 60.795 57.895 38.03 27.76 40.61 4.10
563 567 1.359848 GCACGTGCATGCTTACTAGT 58.640 50.000 34.52 0.00 42.62 2.57
564 568 2.536365 GCACGTGCATGCTTACTAGTA 58.464 47.619 34.52 0.00 42.62 1.82
565 569 3.123804 GCACGTGCATGCTTACTAGTAT 58.876 45.455 34.52 0.00 42.62 2.12
566 570 4.295870 GCACGTGCATGCTTACTAGTATA 58.704 43.478 34.52 0.00 42.62 1.47
624 628 1.342174 CATGTGCTCAGTTTTGCCCTT 59.658 47.619 0.00 0.00 0.00 3.95
1170 1668 3.545703 CAGCGAGAATGGGGTAAGAATT 58.454 45.455 0.00 0.00 0.00 2.17
2415 3862 4.764679 TGTTGCACTACCACATGATTTC 57.235 40.909 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.660629 TTTACGTGTCAGTACCATGTTTG 57.339 39.130 0.00 0.00 34.13 2.93
5 6 7.858382 TGAAAAATTTTACGTGTCAGTACCATG 59.142 33.333 3.34 0.00 0.00 3.66
8 9 8.617761 TTTGAAAAATTTTACGTGTCAGTACC 57.382 30.769 3.34 0.00 0.00 3.34
9 10 9.875660 GTTTTGAAAAATTTTACGTGTCAGTAC 57.124 29.630 3.34 3.02 0.00 2.73
11 12 8.643752 CAGTTTTGAAAAATTTTACGTGTCAGT 58.356 29.630 3.34 0.00 0.00 3.41
12 13 8.107564 CCAGTTTTGAAAAATTTTACGTGTCAG 58.892 33.333 3.34 0.00 0.00 3.51
13 14 7.599245 ACCAGTTTTGAAAAATTTTACGTGTCA 59.401 29.630 3.34 1.01 0.00 3.58
14 15 7.955502 ACCAGTTTTGAAAAATTTTACGTGTC 58.044 30.769 3.34 0.00 0.00 3.67
15 16 7.892778 ACCAGTTTTGAAAAATTTTACGTGT 57.107 28.000 3.34 0.00 0.00 4.49
16 17 8.322428 GGTACCAGTTTTGAAAAATTTTACGTG 58.678 33.333 7.15 0.00 0.00 4.49
17 18 8.033626 TGGTACCAGTTTTGAAAAATTTTACGT 58.966 29.630 11.60 0.00 0.00 3.57
18 19 8.408743 TGGTACCAGTTTTGAAAAATTTTACG 57.591 30.769 11.60 0.00 0.00 3.18
22 23 8.608317 CGAATTGGTACCAGTTTTGAAAAATTT 58.392 29.630 22.16 0.00 0.00 1.82
23 24 7.254624 GCGAATTGGTACCAGTTTTGAAAAATT 60.255 33.333 22.16 11.71 0.00 1.82
24 25 6.201997 GCGAATTGGTACCAGTTTTGAAAAAT 59.798 34.615 22.16 3.47 0.00 1.82
25 26 5.520649 GCGAATTGGTACCAGTTTTGAAAAA 59.479 36.000 22.16 1.01 0.00 1.94
26 27 5.044558 GCGAATTGGTACCAGTTTTGAAAA 58.955 37.500 22.16 1.77 0.00 2.29
27 28 4.500035 GGCGAATTGGTACCAGTTTTGAAA 60.500 41.667 22.16 2.53 0.00 2.69
28 29 3.004944 GGCGAATTGGTACCAGTTTTGAA 59.995 43.478 22.16 3.31 0.00 2.69
29 30 2.554893 GGCGAATTGGTACCAGTTTTGA 59.445 45.455 22.16 4.07 0.00 2.69
30 31 2.294791 TGGCGAATTGGTACCAGTTTTG 59.705 45.455 22.16 19.20 0.00 2.44
31 32 2.295070 GTGGCGAATTGGTACCAGTTTT 59.705 45.455 22.16 13.98 31.46 2.43
32 33 1.883926 GTGGCGAATTGGTACCAGTTT 59.116 47.619 22.16 16.33 31.46 2.66
33 34 1.530323 GTGGCGAATTGGTACCAGTT 58.470 50.000 21.53 21.53 31.46 3.16
34 35 0.322187 GGTGGCGAATTGGTACCAGT 60.322 55.000 15.65 9.80 31.46 4.00
35 36 0.322098 TGGTGGCGAATTGGTACCAG 60.322 55.000 15.65 4.48 36.56 4.00
36 37 0.606944 GTGGTGGCGAATTGGTACCA 60.607 55.000 11.60 11.60 38.98 3.25
37 38 1.641123 CGTGGTGGCGAATTGGTACC 61.641 60.000 4.43 4.43 0.00 3.34
38 39 1.641123 CCGTGGTGGCGAATTGGTAC 61.641 60.000 0.00 0.00 0.00 3.34
39 40 1.376166 CCGTGGTGGCGAATTGGTA 60.376 57.895 0.00 0.00 0.00 3.25
40 41 2.671619 CCGTGGTGGCGAATTGGT 60.672 61.111 0.00 0.00 0.00 3.67
49 50 3.381136 CAATTGGGGCCGTGGTGG 61.381 66.667 0.00 0.00 42.50 4.61
50 51 2.600173 ACAATTGGGGCCGTGGTG 60.600 61.111 10.83 0.00 0.00 4.17
51 52 2.600173 CACAATTGGGGCCGTGGT 60.600 61.111 10.83 0.00 0.00 4.16
52 53 3.381136 CCACAATTGGGGCCGTGG 61.381 66.667 15.25 12.29 42.72 4.94
142 143 9.683069 GCTTTGTTTATGATATGGAACCTAATG 57.317 33.333 0.00 0.00 0.00 1.90
233 234 5.994668 GGGGCAGAAACAAAACATTAAATCA 59.005 36.000 0.00 0.00 0.00 2.57
289 293 2.097791 ACATCTAGTCTTCGCCTTCGAC 59.902 50.000 0.00 0.00 45.43 4.20
324 328 3.888323 TGCTGCCAACTAAGATTGTTCAA 59.112 39.130 0.00 0.00 0.00 2.69
428 432 7.599621 CCATGAGCTGATGTATTTTGACAAAAA 59.400 33.333 16.85 1.90 39.53 1.94
429 433 7.092079 CCATGAGCTGATGTATTTTGACAAAA 58.908 34.615 15.39 15.39 31.83 2.44
433 437 5.355071 TGACCATGAGCTGATGTATTTTGAC 59.645 40.000 12.38 0.00 0.00 3.18
435 439 5.356190 AGTGACCATGAGCTGATGTATTTTG 59.644 40.000 12.38 0.00 0.00 2.44
437 441 4.880120 CAGTGACCATGAGCTGATGTATTT 59.120 41.667 12.38 0.00 0.00 1.40
439 443 3.708121 TCAGTGACCATGAGCTGATGTAT 59.292 43.478 12.38 0.00 33.62 2.29
440 444 3.099141 TCAGTGACCATGAGCTGATGTA 58.901 45.455 12.38 0.00 33.62 2.29
441 445 1.904537 TCAGTGACCATGAGCTGATGT 59.095 47.619 12.38 0.36 33.62 3.06
442 446 2.685850 TCAGTGACCATGAGCTGATG 57.314 50.000 6.14 6.14 33.62 3.07
443 447 3.928005 ATTCAGTGACCATGAGCTGAT 57.072 42.857 0.00 0.00 37.74 2.90
444 448 4.824479 TTATTCAGTGACCATGAGCTGA 57.176 40.909 0.00 0.00 36.35 4.26
445 449 4.940046 AGTTTATTCAGTGACCATGAGCTG 59.060 41.667 0.00 0.00 0.00 4.24
446 450 4.940046 CAGTTTATTCAGTGACCATGAGCT 59.060 41.667 0.00 0.00 0.00 4.09
447 451 4.937620 TCAGTTTATTCAGTGACCATGAGC 59.062 41.667 0.00 0.00 0.00 4.26
448 452 6.596888 ACATCAGTTTATTCAGTGACCATGAG 59.403 38.462 0.00 0.00 0.00 2.90
449 453 6.475504 ACATCAGTTTATTCAGTGACCATGA 58.524 36.000 0.00 0.00 0.00 3.07
450 454 6.748333 ACATCAGTTTATTCAGTGACCATG 57.252 37.500 0.00 0.00 0.00 3.66
451 455 6.942005 TCAACATCAGTTTATTCAGTGACCAT 59.058 34.615 0.00 0.00 35.28 3.55
452 456 6.204688 GTCAACATCAGTTTATTCAGTGACCA 59.795 38.462 0.00 0.00 35.28 4.02
453 457 6.428159 AGTCAACATCAGTTTATTCAGTGACC 59.572 38.462 0.00 0.00 35.28 4.02
454 458 7.426929 AGTCAACATCAGTTTATTCAGTGAC 57.573 36.000 0.00 0.00 35.28 3.67
455 459 9.725019 AATAGTCAACATCAGTTTATTCAGTGA 57.275 29.630 0.00 0.00 35.28 3.41
456 460 9.764870 CAATAGTCAACATCAGTTTATTCAGTG 57.235 33.333 0.00 0.00 35.28 3.66
457 461 9.507329 ACAATAGTCAACATCAGTTTATTCAGT 57.493 29.630 0.00 0.00 35.28 3.41
460 464 9.559958 CCAACAATAGTCAACATCAGTTTATTC 57.440 33.333 0.00 0.00 35.28 1.75
461 465 8.522830 CCCAACAATAGTCAACATCAGTTTATT 58.477 33.333 0.00 0.00 35.28 1.40
462 466 7.122650 CCCCAACAATAGTCAACATCAGTTTAT 59.877 37.037 0.00 0.00 35.28 1.40
463 467 6.432783 CCCCAACAATAGTCAACATCAGTTTA 59.567 38.462 0.00 0.00 35.28 2.01
464 468 5.243730 CCCCAACAATAGTCAACATCAGTTT 59.756 40.000 0.00 0.00 35.28 2.66
465 469 4.766891 CCCCAACAATAGTCAACATCAGTT 59.233 41.667 0.00 0.00 38.88 3.16
466 470 4.335416 CCCCAACAATAGTCAACATCAGT 58.665 43.478 0.00 0.00 0.00 3.41
467 471 3.129287 GCCCCAACAATAGTCAACATCAG 59.871 47.826 0.00 0.00 0.00 2.90
468 472 3.088532 GCCCCAACAATAGTCAACATCA 58.911 45.455 0.00 0.00 0.00 3.07
469 473 3.088532 TGCCCCAACAATAGTCAACATC 58.911 45.455 0.00 0.00 0.00 3.06
470 474 3.091545 CTGCCCCAACAATAGTCAACAT 58.908 45.455 0.00 0.00 0.00 2.71
471 475 2.513753 CTGCCCCAACAATAGTCAACA 58.486 47.619 0.00 0.00 0.00 3.33
472 476 1.818674 CCTGCCCCAACAATAGTCAAC 59.181 52.381 0.00 0.00 0.00 3.18
473 477 1.427368 ACCTGCCCCAACAATAGTCAA 59.573 47.619 0.00 0.00 0.00 3.18
474 478 1.072266 ACCTGCCCCAACAATAGTCA 58.928 50.000 0.00 0.00 0.00 3.41
475 479 1.004277 TCACCTGCCCCAACAATAGTC 59.996 52.381 0.00 0.00 0.00 2.59
476 480 1.072266 TCACCTGCCCCAACAATAGT 58.928 50.000 0.00 0.00 0.00 2.12
477 481 2.094675 CTTCACCTGCCCCAACAATAG 58.905 52.381 0.00 0.00 0.00 1.73
478 482 1.707989 TCTTCACCTGCCCCAACAATA 59.292 47.619 0.00 0.00 0.00 1.90
479 483 0.482446 TCTTCACCTGCCCCAACAAT 59.518 50.000 0.00 0.00 0.00 2.71
480 484 0.482446 ATCTTCACCTGCCCCAACAA 59.518 50.000 0.00 0.00 0.00 2.83
481 485 0.251297 CATCTTCACCTGCCCCAACA 60.251 55.000 0.00 0.00 0.00 3.33
482 486 1.598701 GCATCTTCACCTGCCCCAAC 61.599 60.000 0.00 0.00 32.15 3.77
483 487 1.304381 GCATCTTCACCTGCCCCAA 60.304 57.895 0.00 0.00 32.15 4.12
484 488 2.079088 TTGCATCTTCACCTGCCCCA 62.079 55.000 0.00 0.00 37.59 4.96
485 489 0.899717 TTTGCATCTTCACCTGCCCC 60.900 55.000 0.00 0.00 37.59 5.80
486 490 1.188863 ATTTGCATCTTCACCTGCCC 58.811 50.000 0.00 0.00 37.59 5.36
487 491 3.887716 AGATATTTGCATCTTCACCTGCC 59.112 43.478 0.00 0.00 37.59 4.85
488 492 5.511234 AAGATATTTGCATCTTCACCTGC 57.489 39.130 0.00 0.00 40.47 4.85
489 493 7.487189 GTGAAAAGATATTTGCATCTTCACCTG 59.513 37.037 0.00 0.00 43.01 4.00
490 494 7.177216 TGTGAAAAGATATTTGCATCTTCACCT 59.823 33.333 13.49 0.00 43.01 4.00
491 495 7.315142 TGTGAAAAGATATTTGCATCTTCACC 58.685 34.615 13.49 3.71 43.01 4.02
492 496 8.922058 ATGTGAAAAGATATTTGCATCTTCAC 57.078 30.769 10.80 10.80 43.01 3.18
499 503 9.667989 CGATCATTATGTGAAAAGATATTTGCA 57.332 29.630 0.00 0.00 40.97 4.08
500 504 9.669353 ACGATCATTATGTGAAAAGATATTTGC 57.331 29.630 0.00 0.00 40.97 3.68
506 510 8.755941 CGACTTACGATCATTATGTGAAAAGAT 58.244 33.333 0.00 0.00 45.77 2.40
507 511 7.971722 TCGACTTACGATCATTATGTGAAAAGA 59.028 33.333 0.00 0.00 46.45 2.52
508 512 8.115491 TCGACTTACGATCATTATGTGAAAAG 57.885 34.615 0.00 0.00 46.45 2.27
524 528 3.295462 CGCGCGTCTCGACTTACG 61.295 66.667 24.19 5.98 41.67 3.18
525 529 1.795177 AACGCGCGTCTCGACTTAC 60.795 57.895 37.77 0.00 41.67 2.34
526 530 1.794785 CAACGCGCGTCTCGACTTA 60.795 57.895 37.77 0.00 41.67 2.24
527 531 3.097728 CAACGCGCGTCTCGACTT 61.098 61.111 37.77 16.50 41.67 3.01
544 548 1.359848 ACTAGTAAGCATGCACGTGC 58.640 50.000 33.11 33.11 45.38 5.34
545 549 8.689251 ATATTATACTAGTAAGCATGCACGTG 57.311 34.615 21.98 12.28 0.00 4.49
547 551 9.452065 CCTATATTATACTAGTAAGCATGCACG 57.548 37.037 21.98 3.52 0.00 5.34
548 552 9.751542 CCCTATATTATACTAGTAAGCATGCAC 57.248 37.037 21.98 10.48 0.00 4.57
549 553 9.488762 ACCCTATATTATACTAGTAAGCATGCA 57.511 33.333 21.98 0.00 0.00 3.96
566 570 9.321532 GGGCAAAAGGATAATTAACCCTATATT 57.678 33.333 8.09 3.65 31.84 1.28
624 628 3.251479 ACTGAGCACAATTCGCATCTA 57.749 42.857 0.00 0.00 0.00 1.98
890 1388 0.962855 CCGTGCTCTCTCTCTCACCA 60.963 60.000 0.00 0.00 0.00 4.17
893 1391 2.402572 CGCCGTGCTCTCTCTCTCA 61.403 63.158 0.00 0.00 0.00 3.27
1901 3154 8.785329 TTCAATTAGCTTCCACAAAAAGTTTT 57.215 26.923 0.00 0.00 0.00 2.43
2415 3862 1.669115 CCAAGTGCCACTCTGACCG 60.669 63.158 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.