Multiple sequence alignment - TraesCS2A01G543500

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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 TraesCS2A01G543500 chr2A 100.000 3426 0 0 1 3426 753418197 753421622 0.000000e+00 6327.0
1 TraesCS2A01G543500 chr2A 86.432 398 31 8 2924 3316 753412474 753412853 6.840000e-112 414.0
2 TraesCS2A01G543500 chr2A 80.000 555 81 13 1 525 224903247 224903801 1.930000e-102 383.0
3 TraesCS2A01G543500 chr2A 87.736 106 10 2 3135 3240 753409403 753409505 1.670000e-23 121.0
4 TraesCS2A01G543500 chr2B 90.579 2866 172 49 521 3352 763473429 763476230 0.000000e+00 3707.0
5 TraesCS2A01G543500 chr2B 85.102 980 93 23 1898 2864 763331158 763332097 0.000000e+00 952.0
6 TraesCS2A01G543500 chr2B 88.477 486 32 14 2873 3352 763524621 763525088 1.780000e-157 566.0
7 TraesCS2A01G543500 chr2B 78.417 556 88 15 1 525 795795954 795795400 1.970000e-87 333.0
8 TraesCS2A01G543500 chr2B 85.903 227 29 1 1082 1305 39092872 39093098 4.420000e-59 239.0
9 TraesCS2A01G543500 chr2B 87.402 127 12 4 3114 3240 763390129 763390251 3.560000e-30 143.0
10 TraesCS2A01G543500 chr2B 88.393 112 10 3 3129 3240 762834783 762834891 7.710000e-27 132.0
11 TraesCS2A01G543500 chr2B 94.366 71 4 0 3344 3414 518050056 518050126 3.610000e-20 110.0
12 TraesCS2A01G543500 chr2B 100.000 57 0 0 3370 3426 418664249 418664193 4.680000e-19 106.0
13 TraesCS2A01G543500 chr2B 96.610 59 2 0 3368 3426 754984120 754984062 7.820000e-17 99.0
14 TraesCS2A01G543500 chr2D 90.157 1270 91 17 1597 2860 621634830 621636071 0.000000e+00 1622.0
15 TraesCS2A01G543500 chr2D 90.302 1093 54 21 521 1595 621615388 621616446 0.000000e+00 1384.0
16 TraesCS2A01G543500 chr2D 96.258 481 16 2 2873 3352 621667285 621667764 0.000000e+00 787.0
17 TraesCS2A01G543500 chr2D 79.856 556 81 14 1 525 412718386 412718941 8.970000e-101 377.0
18 TraesCS2A01G543500 chr2D 77.338 556 91 17 1 525 404800267 404799716 2.590000e-76 296.0
19 TraesCS2A01G543500 chr3D 81.718 547 78 10 1 525 19291020 19291566 1.460000e-118 436.0
20 TraesCS2A01G543500 chr3D 77.839 546 91 13 10 525 612275590 612275045 9.230000e-81 311.0
21 TraesCS2A01G543500 chr3D 100.000 28 0 0 1932 1959 22303816 22303789 6.000000e-03 52.8
22 TraesCS2A01G543500 chr6D 81.622 555 72 10 1 525 58544781 58545335 1.890000e-117 433.0
23 TraesCS2A01G543500 chr1B 80.104 578 85 20 1849 2405 636738580 636738012 1.480000e-108 403.0
24 TraesCS2A01G543500 chr1B 75.533 797 129 42 736 1509 636739424 636738671 7.090000e-87 331.0
25 TraesCS2A01G543500 chr1B 76.990 578 100 21 940 1509 636727114 636726562 2.000000e-77 300.0
26 TraesCS2A01G543500 chr1B 78.608 388 56 8 1 361 633040373 633040760 7.390000e-57 231.0
27 TraesCS2A01G543500 chr1B 95.312 64 3 0 3351 3414 478590806 478590743 6.050000e-18 102.0
28 TraesCS2A01G543500 chr4A 80.541 555 78 10 1 525 667312346 667312900 1.920000e-107 399.0
29 TraesCS2A01G543500 chr4A 94.737 76 4 0 3351 3426 667379828 667379753 6.010000e-23 119.0
30 TraesCS2A01G543500 chr6A 80.541 555 77 11 1 525 493726765 493726212 6.890000e-107 398.0
31 TraesCS2A01G543500 chr6A 78.611 547 86 13 1 516 617085089 617085635 1.970000e-87 333.0
32 TraesCS2A01G543500 chr6A 82.553 235 35 3 7 236 228630557 228630324 5.800000e-48 202.0
33 TraesCS2A01G543500 chr4B 80.180 555 80 10 1 525 567184937 567184383 4.150000e-104 388.0
34 TraesCS2A01G543500 chr4B 78.198 555 90 12 1 525 178666080 178666633 3.300000e-85 326.0
35 TraesCS2A01G543500 chr4B 100.000 57 0 0 3370 3426 461850088 461850144 4.680000e-19 106.0
36 TraesCS2A01G543500 chr3B 78.339 554 90 15 1 525 28732400 28732952 7.090000e-87 331.0
37 TraesCS2A01G543500 chr1D 77.607 585 91 25 937 1509 462115575 462115019 5.520000e-83 318.0
38 TraesCS2A01G543500 chr1D 80.676 414 66 8 1100 1509 462093071 462092668 3.320000e-80 309.0
39 TraesCS2A01G543500 chr5B 76.978 556 95 15 1 525 461700919 461700366 1.560000e-73 287.0
40 TraesCS2A01G543500 chr5B 78.218 101 22 0 1858 1958 573408248 573408148 7.940000e-07 65.8
41 TraesCS2A01G543500 chr7B 76.812 552 95 16 1 521 68753884 68754433 2.600000e-71 279.0
42 TraesCS2A01G543500 chr7B 81.100 291 52 3 238 525 538579267 538578977 2.660000e-56 230.0
43 TraesCS2A01G543500 chr7B 90.909 77 5 1 3350 3426 529611898 529611824 6.050000e-18 102.0
44 TraesCS2A01G543500 chr5A 100.000 58 0 0 3369 3426 269823294 269823351 1.300000e-19 108.0
45 TraesCS2A01G543500 chr5D 90.411 73 5 2 3354 3426 541565569 541565499 1.010000e-15 95.3
46 TraesCS2A01G543500 chr5D 78.788 99 21 0 1860 1958 466569797 466569699 2.210000e-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 TraesCS2A01G543500 chr2A 753418197 753421622 3425 False 6327.0 6327 100.0000 1 3426 1 chr2A.!!$F2 3425
1 TraesCS2A01G543500 chr2A 224903247 224903801 554 False 383.0 383 80.0000 1 525 1 chr2A.!!$F1 524
2 TraesCS2A01G543500 chr2A 753409403 753412853 3450 False 267.5 414 87.0840 2924 3316 2 chr2A.!!$F3 392
3 TraesCS2A01G543500 chr2B 763473429 763476230 2801 False 3707.0 3707 90.5790 521 3352 1 chr2B.!!$F6 2831
4 TraesCS2A01G543500 chr2B 763331158 763332097 939 False 952.0 952 85.1020 1898 2864 1 chr2B.!!$F4 966
5 TraesCS2A01G543500 chr2B 795795400 795795954 554 True 333.0 333 78.4170 1 525 1 chr2B.!!$R3 524
6 TraesCS2A01G543500 chr2D 621634830 621636071 1241 False 1622.0 1622 90.1570 1597 2860 1 chr2D.!!$F3 1263
7 TraesCS2A01G543500 chr2D 621615388 621616446 1058 False 1384.0 1384 90.3020 521 1595 1 chr2D.!!$F2 1074
8 TraesCS2A01G543500 chr2D 412718386 412718941 555 False 377.0 377 79.8560 1 525 1 chr2D.!!$F1 524
9 TraesCS2A01G543500 chr2D 404799716 404800267 551 True 296.0 296 77.3380 1 525 1 chr2D.!!$R1 524
10 TraesCS2A01G543500 chr3D 19291020 19291566 546 False 436.0 436 81.7180 1 525 1 chr3D.!!$F1 524
11 TraesCS2A01G543500 chr3D 612275045 612275590 545 True 311.0 311 77.8390 10 525 1 chr3D.!!$R2 515
12 TraesCS2A01G543500 chr6D 58544781 58545335 554 False 433.0 433 81.6220 1 525 1 chr6D.!!$F1 524
13 TraesCS2A01G543500 chr1B 636738012 636739424 1412 True 367.0 403 77.8185 736 2405 2 chr1B.!!$R3 1669
14 TraesCS2A01G543500 chr1B 636726562 636727114 552 True 300.0 300 76.9900 940 1509 1 chr1B.!!$R2 569
15 TraesCS2A01G543500 chr4A 667312346 667312900 554 False 399.0 399 80.5410 1 525 1 chr4A.!!$F1 524
16 TraesCS2A01G543500 chr6A 493726212 493726765 553 True 398.0 398 80.5410 1 525 1 chr6A.!!$R2 524
17 TraesCS2A01G543500 chr6A 617085089 617085635 546 False 333.0 333 78.6110 1 516 1 chr6A.!!$F1 515
18 TraesCS2A01G543500 chr4B 567184383 567184937 554 True 388.0 388 80.1800 1 525 1 chr4B.!!$R1 524
19 TraesCS2A01G543500 chr4B 178666080 178666633 553 False 326.0 326 78.1980 1 525 1 chr4B.!!$F1 524
20 TraesCS2A01G543500 chr3B 28732400 28732952 552 False 331.0 331 78.3390 1 525 1 chr3B.!!$F1 524
21 TraesCS2A01G543500 chr1D 462115019 462115575 556 True 318.0 318 77.6070 937 1509 1 chr1D.!!$R2 572
22 TraesCS2A01G543500 chr5B 461700366 461700919 553 True 287.0 287 76.9780 1 525 1 chr5B.!!$R1 524
23 TraesCS2A01G543500 chr7B 68753884 68754433 549 False 279.0 279 76.8120 1 521 1 chr7B.!!$F1 520

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
889 981 0.179045 ATAGCCACTAAGCCAAGCCG 60.179 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 2572 0.816825 ACGCATGCCTGATGGACATC 60.817 55.0 13.15 5.37 38.29 3.06 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
55 56 8.637196 TTCACAGTAGACTCTATATACCATGG 57.363 38.462 11.19 11.19 0.00 3.66
70 72 1.135315 CCATGGACTCACGCATTTTGG 60.135 52.381 5.56 0.00 0.00 3.28
76 78 2.550606 GACTCACGCATTTTGGGTTACA 59.449 45.455 0.00 0.00 40.90 2.41
81 83 2.035321 ACGCATTTTGGGTTACAAGTGG 59.965 45.455 0.00 0.00 40.90 4.00
82 84 2.035321 CGCATTTTGGGTTACAAGTGGT 59.965 45.455 0.00 0.00 40.82 4.16
117 119 8.485392 AGAAATTTTGGAGGTCAAAGATTTCAA 58.515 29.630 18.47 0.00 45.00 2.69
159 162 4.210331 GTGGTATCTTCGTAGGGGAGTTA 58.790 47.826 0.00 0.00 0.00 2.24
176 179 5.652452 GGGAGTTATGCTAACCAAAGACAAT 59.348 40.000 0.00 0.00 0.00 2.71
186 189 3.149196 ACCAAAGACAATCTTGCACGAT 58.851 40.909 0.00 0.00 36.71 3.73
188 191 3.058016 CCAAAGACAATCTTGCACGATGT 60.058 43.478 6.44 7.15 36.71 3.06
192 195 4.314961 AGACAATCTTGCACGATGTAACA 58.685 39.130 6.44 0.00 0.00 2.41
193 196 4.937620 AGACAATCTTGCACGATGTAACAT 59.062 37.500 6.44 0.00 0.00 2.71
225 234 4.520111 AGTATTGCTTTTGTGCTCATGACA 59.480 37.500 0.00 0.00 0.00 3.58
236 245 6.426980 TGTGCTCATGACAAGATAATCAAC 57.573 37.500 0.00 0.00 0.00 3.18
248 286 5.940192 AGATAATCAACTTTGCGTGTTCA 57.060 34.783 0.00 0.00 0.00 3.18
272 310 5.819991 ACATGGTCAGTCATCCAAATAGTT 58.180 37.500 0.00 0.00 37.27 2.24
332 370 2.838813 TGGTCATTGGTTGGTCGGTATA 59.161 45.455 0.00 0.00 0.00 1.47
350 388 8.885722 GTCGGTATACCAAATAGATTCAAAACA 58.114 33.333 21.76 0.00 35.14 2.83
366 406 3.560636 AAACACTAATATGGGCGAGCT 57.439 42.857 0.00 0.00 0.00 4.09
466 507 2.166741 TTTTGTTGAACGCACTCACG 57.833 45.000 0.00 0.00 39.50 4.35
497 538 4.771577 TGGTCTATACTACAACAACCGGAA 59.228 41.667 9.46 0.00 0.00 4.30
545 586 6.887002 TGTGTTGGTAAATCCTGCATATTGTA 59.113 34.615 0.00 0.00 37.07 2.41
588 632 3.209410 CTGACTGAAAGCCTGAAACACT 58.791 45.455 0.00 0.00 37.60 3.55
613 657 5.286082 GCTAAGTTGAAATTTGGTATGCGTG 59.714 40.000 0.00 0.00 0.00 5.34
621 665 0.533978 TTGGTATGCGTGCACTGTGT 60.534 50.000 16.19 0.71 0.00 3.72
704 748 3.083349 TGTCCGGCCCTCATCAGG 61.083 66.667 0.00 0.00 39.98 3.86
721 765 2.335712 GGTAGTGTGCAGGGCAAGC 61.336 63.158 0.00 0.00 41.47 4.01
793 856 2.084546 GCTACAAGTAAGGCACCAAGG 58.915 52.381 0.00 0.00 0.00 3.61
883 975 4.363034 GCCGATAGCCACTAAGCC 57.637 61.111 0.00 0.00 34.35 4.35
884 976 1.445942 GCCGATAGCCACTAAGCCA 59.554 57.895 0.00 0.00 34.35 4.75
885 977 0.179056 GCCGATAGCCACTAAGCCAA 60.179 55.000 0.00 0.00 34.35 4.52
886 978 1.871080 CCGATAGCCACTAAGCCAAG 58.129 55.000 0.00 0.00 0.00 3.61
888 980 1.598882 GATAGCCACTAAGCCAAGCC 58.401 55.000 0.00 0.00 0.00 4.35
889 981 0.179045 ATAGCCACTAAGCCAAGCCG 60.179 55.000 0.00 0.00 0.00 5.52
890 982 1.261938 TAGCCACTAAGCCAAGCCGA 61.262 55.000 0.00 0.00 0.00 5.54
892 984 1.003839 CCACTAAGCCAAGCCGACA 60.004 57.895 0.00 0.00 0.00 4.35
893 985 1.021390 CCACTAAGCCAAGCCGACAG 61.021 60.000 0.00 0.00 0.00 3.51
894 986 0.320771 CACTAAGCCAAGCCGACAGT 60.321 55.000 0.00 0.00 0.00 3.55
895 987 0.320771 ACTAAGCCAAGCCGACAGTG 60.321 55.000 0.00 0.00 0.00 3.66
896 988 1.639298 CTAAGCCAAGCCGACAGTGC 61.639 60.000 0.00 0.00 0.00 4.40
928 1020 1.669760 CCCGCGCTCCACTTGTAAA 60.670 57.895 5.56 0.00 0.00 2.01
948 1040 5.840940 AAATCTCGCACTATATAAACGCC 57.159 39.130 0.00 0.00 0.00 5.68
989 1092 5.610398 TCAAGCAGAAGTTTGTGTAGATCA 58.390 37.500 0.00 0.00 37.27 2.92
1176 1279 2.879462 CGTTCGTACCTGAGCGCC 60.879 66.667 2.29 0.00 35.86 6.53
1179 1282 3.332493 TTCGTACCTGAGCGCCGAC 62.332 63.158 2.29 0.00 0.00 4.79
1305 1408 3.807368 CTCACCGGGGAGGAGTTT 58.193 61.111 27.05 0.00 45.00 2.66
1400 1506 2.888863 CCTCTGGTCGTCTGGCTC 59.111 66.667 0.00 0.00 0.00 4.70
1402 1508 1.510383 CTCTGGTCGTCTGGCTCTG 59.490 63.158 0.00 0.00 0.00 3.35
1403 1509 2.125753 CTGGTCGTCTGGCTCTGC 60.126 66.667 0.00 0.00 0.00 4.26
1554 1663 0.328258 GACCCTGGTAAGTGCCACAT 59.672 55.000 0.00 0.00 34.36 3.21
1561 1671 1.613437 GGTAAGTGCCACATGCTTTGT 59.387 47.619 0.00 0.00 42.00 2.83
1573 1683 5.920273 CCACATGCTTTGTACGAAGAAATTT 59.080 36.000 24.46 8.86 36.57 1.82
1634 1744 8.811017 TCAAGGATGGCAACTTTATTTATGAAA 58.189 29.630 5.22 0.00 37.61 2.69
1676 1791 9.973450 TTTGGATGATAAATTTCAGTTTTTCGA 57.027 25.926 0.00 0.00 0.00 3.71
1678 1793 9.973450 TGGATGATAAATTTCAGTTTTTCGAAA 57.027 25.926 6.47 6.47 35.70 3.46
1681 1796 9.981114 ATGATAAATTTCAGTTTTTCGAAAGGT 57.019 25.926 10.98 0.00 34.78 3.50
1682 1797 9.810545 TGATAAATTTCAGTTTTTCGAAAGGTT 57.189 25.926 10.98 0.00 34.78 3.50
1740 1858 3.857665 GTCAGAGCGATGTTATTTCGTGA 59.142 43.478 0.00 0.00 38.81 4.35
1794 1912 6.238211 GGAATCTCATCCATTTCAACTACGTG 60.238 42.308 0.00 0.00 39.42 4.49
2140 2283 0.811281 CCAAGAACGAATTGGCCCTC 59.189 55.000 0.00 0.00 40.74 4.30
2429 2572 2.279741 CTTACCCGACCATGTGATGTG 58.720 52.381 0.00 0.00 0.00 3.21
2431 2574 0.911769 ACCCGACCATGTGATGTGAT 59.088 50.000 0.00 0.00 0.00 3.06
2432 2575 1.302366 CCCGACCATGTGATGTGATG 58.698 55.000 0.00 0.00 0.00 3.07
2433 2576 1.407299 CCCGACCATGTGATGTGATGT 60.407 52.381 0.00 0.00 0.00 3.06
2434 2577 1.935873 CCGACCATGTGATGTGATGTC 59.064 52.381 0.00 0.00 0.00 3.06
2435 2578 1.935873 CGACCATGTGATGTGATGTCC 59.064 52.381 0.00 0.00 0.00 4.02
2436 2579 2.677613 CGACCATGTGATGTGATGTCCA 60.678 50.000 0.00 0.00 0.00 4.02
2437 2580 3.548770 GACCATGTGATGTGATGTCCAT 58.451 45.455 0.00 0.00 0.00 3.41
2438 2581 3.548770 ACCATGTGATGTGATGTCCATC 58.451 45.455 0.22 0.22 39.32 3.51
2440 2583 3.564225 CCATGTGATGTGATGTCCATCAG 59.436 47.826 10.13 0.00 46.80 2.90
2441 2584 3.271055 TGTGATGTGATGTCCATCAGG 57.729 47.619 10.13 0.00 46.80 3.86
2442 2585 1.945394 GTGATGTGATGTCCATCAGGC 59.055 52.381 10.13 1.20 46.80 4.85
2444 2587 3.997223 GTGATGTGATGTCCATCAGGCAT 60.997 47.826 10.13 10.73 46.80 4.40
2445 2588 6.042365 GTGATGTGATGTCCATCAGGCATG 62.042 50.000 14.53 0.00 46.80 4.06
2446 2589 3.105187 TGATGTCCATCAGGCATGC 57.895 52.632 9.90 9.90 42.42 4.06
2447 2590 0.816421 TGATGTCCATCAGGCATGCG 60.816 55.000 12.44 0.00 42.42 4.73
2448 2591 0.816825 GATGTCCATCAGGCATGCGT 60.817 55.000 12.44 9.84 37.74 5.24
2491 2634 0.460284 TAAGTAAGCTCGCAGGCAGC 60.460 55.000 7.36 7.36 40.87 5.25
2539 2683 0.110688 CGTGCATTTGTGACGTCCTG 60.111 55.000 14.12 4.13 0.00 3.86
2550 2694 0.525668 GACGTCCTGCCTATGTCGTG 60.526 60.000 3.51 0.00 0.00 4.35
2556 2700 3.006967 GTCCTGCCTATGTCGTGGATTAT 59.993 47.826 0.00 0.00 0.00 1.28
2561 2705 4.703093 TGCCTATGTCGTGGATTATATCGA 59.297 41.667 0.00 0.00 0.00 3.59
2565 2709 4.761235 TGTCGTGGATTATATCGAGACC 57.239 45.455 0.00 0.00 33.09 3.85
2566 2710 3.187842 TGTCGTGGATTATATCGAGACCG 59.812 47.826 0.00 0.00 33.09 4.79
2567 2711 2.161012 TCGTGGATTATATCGAGACCGC 59.839 50.000 0.00 0.00 35.37 5.68
2568 2712 2.161808 CGTGGATTATATCGAGACCGCT 59.838 50.000 0.00 0.00 35.37 5.52
2572 2716 6.238293 CGTGGATTATATCGAGACCGCTATTA 60.238 42.308 0.00 0.00 35.37 0.98
2575 2719 7.040617 TGGATTATATCGAGACCGCTATTATCC 60.041 40.741 14.49 14.49 44.63 2.59
2580 2725 3.190744 TCGAGACCGCTATTATCCATGTC 59.809 47.826 0.00 0.00 35.37 3.06
2583 2728 4.077108 AGACCGCTATTATCCATGTCGTA 58.923 43.478 0.00 0.00 0.00 3.43
2786 2947 5.794687 GCATGCCAATAACGTGCTATATA 57.205 39.130 6.36 0.00 44.79 0.86
2950 3111 4.481930 TTGGAAAGTCACAAGCAATACG 57.518 40.909 0.00 0.00 0.00 3.06
2982 3143 7.551262 TGAATAATCTTGCGTGGTACAAATACT 59.449 33.333 0.00 0.00 44.16 2.12
3010 3171 7.980099 AGAAGAAAAATGATGAAATGCCATCTC 59.020 33.333 0.00 0.00 42.49 2.75
3123 3284 4.528596 AGGATTATCACTCCAATCTACGGG 59.471 45.833 0.00 0.00 35.08 5.28
3279 3449 6.817765 TTTAGGAGTTCATGTGGAAACATC 57.182 37.500 0.00 0.00 46.14 3.06
3352 3522 7.095774 CCCGTGCTTAATATTAGTGTGATGTAC 60.096 40.741 0.00 0.00 0.00 2.90
3353 3523 7.652105 CCGTGCTTAATATTAGTGTGATGTACT 59.348 37.037 0.00 0.00 0.00 2.73
3354 3524 8.691727 CGTGCTTAATATTAGTGTGATGTACTC 58.308 37.037 0.00 0.00 0.00 2.59
3355 3525 8.979574 GTGCTTAATATTAGTGTGATGTACTCC 58.020 37.037 0.00 0.00 0.00 3.85
3356 3526 8.148351 TGCTTAATATTAGTGTGATGTACTCCC 58.852 37.037 0.00 0.00 0.00 4.30
3357 3527 8.368668 GCTTAATATTAGTGTGATGTACTCCCT 58.631 37.037 0.00 0.00 0.00 4.20
3358 3528 9.915629 CTTAATATTAGTGTGATGTACTCCCTC 57.084 37.037 0.00 0.00 0.00 4.30
3359 3529 6.919775 ATATTAGTGTGATGTACTCCCTCC 57.080 41.667 0.00 0.00 0.00 4.30
3360 3530 1.475403 AGTGTGATGTACTCCCTCCG 58.525 55.000 0.00 0.00 0.00 4.63
3361 3531 1.183549 GTGTGATGTACTCCCTCCGT 58.816 55.000 0.00 0.00 0.00 4.69
3362 3532 1.549170 GTGTGATGTACTCCCTCCGTT 59.451 52.381 0.00 0.00 0.00 4.44
3363 3533 1.822990 TGTGATGTACTCCCTCCGTTC 59.177 52.381 0.00 0.00 0.00 3.95
3364 3534 2.100989 GTGATGTACTCCCTCCGTTCT 58.899 52.381 0.00 0.00 0.00 3.01
3365 3535 2.496470 GTGATGTACTCCCTCCGTTCTT 59.504 50.000 0.00 0.00 0.00 2.52
3366 3536 3.698040 GTGATGTACTCCCTCCGTTCTTA 59.302 47.826 0.00 0.00 0.00 2.10
3367 3537 4.159135 GTGATGTACTCCCTCCGTTCTTAA 59.841 45.833 0.00 0.00 0.00 1.85
3368 3538 4.773674 TGATGTACTCCCTCCGTTCTTAAA 59.226 41.667 0.00 0.00 0.00 1.52
3369 3539 5.424252 TGATGTACTCCCTCCGTTCTTAAAT 59.576 40.000 0.00 0.00 0.00 1.40
3370 3540 6.608405 TGATGTACTCCCTCCGTTCTTAAATA 59.392 38.462 0.00 0.00 0.00 1.40
3371 3541 6.212888 TGTACTCCCTCCGTTCTTAAATAC 57.787 41.667 0.00 0.00 0.00 1.89
3372 3542 5.954150 TGTACTCCCTCCGTTCTTAAATACT 59.046 40.000 0.00 0.00 0.00 2.12
3373 3543 5.595257 ACTCCCTCCGTTCTTAAATACTC 57.405 43.478 0.00 0.00 0.00 2.59
3374 3544 4.405036 ACTCCCTCCGTTCTTAAATACTCC 59.595 45.833 0.00 0.00 0.00 3.85
3375 3545 3.708121 TCCCTCCGTTCTTAAATACTCCC 59.292 47.826 0.00 0.00 0.00 4.30
3376 3546 3.710165 CCCTCCGTTCTTAAATACTCCCT 59.290 47.826 0.00 0.00 0.00 4.20
3377 3547 4.202233 CCCTCCGTTCTTAAATACTCCCTC 60.202 50.000 0.00 0.00 0.00 4.30
3378 3548 4.202233 CCTCCGTTCTTAAATACTCCCTCC 60.202 50.000 0.00 0.00 0.00 4.30
3379 3549 3.382546 TCCGTTCTTAAATACTCCCTCCG 59.617 47.826 0.00 0.00 0.00 4.63
3380 3550 3.131755 CCGTTCTTAAATACTCCCTCCGT 59.868 47.826 0.00 0.00 0.00 4.69
3381 3551 4.382362 CCGTTCTTAAATACTCCCTCCGTT 60.382 45.833 0.00 0.00 0.00 4.44
3382 3552 4.802563 CGTTCTTAAATACTCCCTCCGTTC 59.197 45.833 0.00 0.00 0.00 3.95
3383 3553 5.114780 GTTCTTAAATACTCCCTCCGTTCC 58.885 45.833 0.00 0.00 0.00 3.62
3384 3554 4.617593 TCTTAAATACTCCCTCCGTTCCT 58.382 43.478 0.00 0.00 0.00 3.36
3385 3555 5.769835 TCTTAAATACTCCCTCCGTTCCTA 58.230 41.667 0.00 0.00 0.00 2.94
3386 3556 6.197168 TCTTAAATACTCCCTCCGTTCCTAA 58.803 40.000 0.00 0.00 0.00 2.69
3387 3557 6.669154 TCTTAAATACTCCCTCCGTTCCTAAA 59.331 38.462 0.00 0.00 0.00 1.85
3388 3558 5.970501 AAATACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
3389 3559 4.957684 ATACTCCCTCCGTTCCTAAATG 57.042 45.455 0.00 0.00 0.00 2.32
3390 3560 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
3391 3561 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
3392 3562 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
3393 3563 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
3394 3564 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
3395 3565 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
3396 3566 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
3397 3567 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
3398 3568 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
3399 3569 6.092259 CCTCCGTTCCTAAATGTAAGTCTTTG 59.908 42.308 0.00 0.00 0.00 2.77
3400 3570 6.527423 TCCGTTCCTAAATGTAAGTCTTTGT 58.473 36.000 0.00 0.00 0.00 2.83
3401 3571 7.669427 TCCGTTCCTAAATGTAAGTCTTTGTA 58.331 34.615 0.00 0.00 0.00 2.41
3402 3572 7.816031 TCCGTTCCTAAATGTAAGTCTTTGTAG 59.184 37.037 0.00 0.00 0.00 2.74
3403 3573 7.816031 CCGTTCCTAAATGTAAGTCTTTGTAGA 59.184 37.037 0.00 0.00 0.00 2.59
3404 3574 9.367444 CGTTCCTAAATGTAAGTCTTTGTAGAT 57.633 33.333 0.00 0.00 31.86 1.98
3418 3588 8.865090 AGTCTTTGTAGATATTCCACTAGATGG 58.135 37.037 0.00 0.43 40.44 3.51
3419 3589 8.861086 GTCTTTGTAGATATTCCACTAGATGGA 58.139 37.037 9.25 9.25 43.64 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 2.550606 TGTAACCCAAAATGCGTGAGTC 59.449 45.455 0.00 0.00 0.00 3.36
159 162 4.523943 TGCAAGATTGTCTTTGGTTAGCAT 59.476 37.500 0.00 0.00 33.78 3.79
176 179 7.317390 TCTTACTTATGTTACATCGTGCAAGA 58.683 34.615 4.40 4.40 0.00 3.02
192 195 9.014297 AGCACAAAAGCAATACTTCTTACTTAT 57.986 29.630 0.00 0.00 37.75 1.73
193 196 8.391075 AGCACAAAAGCAATACTTCTTACTTA 57.609 30.769 0.00 0.00 37.75 2.24
225 234 6.312399 TGAACACGCAAAGTTGATTATCTT 57.688 33.333 0.00 0.00 0.00 2.40
236 245 2.223456 TGACCATGTTGAACACGCAAAG 60.223 45.455 0.00 0.00 0.00 2.77
248 286 5.819991 ACTATTTGGATGACTGACCATGTT 58.180 37.500 0.00 0.00 36.02 2.71
272 310 7.121463 ACACTTGTTGGCGGATATAAATTTGTA 59.879 33.333 0.00 0.00 0.00 2.41
290 328 5.417580 ACCAAATATATCGGCAACACTTGTT 59.582 36.000 1.82 0.00 39.12 2.83
303 341 6.293955 CCGACCAACCAATGACCAAATATATC 60.294 42.308 0.00 0.00 0.00 1.63
341 379 5.221048 GCTCGCCCATATTAGTGTTTTGAAT 60.221 40.000 0.00 0.00 0.00 2.57
350 388 3.600388 GCATAAGCTCGCCCATATTAGT 58.400 45.455 0.00 0.00 37.91 2.24
366 406 6.312918 GTCGAAGTGATCAAAGTAAGGCATAA 59.687 38.462 0.00 0.00 0.00 1.90
466 507 5.063438 TGTTGTAGTATAGACCACGTACGAC 59.937 44.000 24.41 6.82 0.00 4.34
497 538 1.406180 GCCTTTAACAACGGTTGGTGT 59.594 47.619 21.14 9.94 37.88 4.16
588 632 5.048364 ACGCATACCAAATTTCAACTTAGCA 60.048 36.000 0.00 0.00 0.00 3.49
613 657 4.789095 TTTTCGTCTTCTAACACAGTGC 57.211 40.909 0.00 0.00 0.00 4.40
621 665 7.780008 TTCTGTCAACATTTTCGTCTTCTAA 57.220 32.000 0.00 0.00 0.00 2.10
698 742 0.745845 GCCCTGCACACTACCTGATG 60.746 60.000 0.00 0.00 0.00 3.07
704 748 2.335712 GGCTTGCCCTGCACACTAC 61.336 63.158 0.00 0.00 38.71 2.73
721 765 0.750182 ACACGAGTTGGTTGGGTTGG 60.750 55.000 0.00 0.00 0.00 3.77
727 771 0.029300 CTTGGCACACGAGTTGGTTG 59.971 55.000 0.00 0.00 39.29 3.77
761 824 0.169672 CTTGTAGCAGTGCACCATGC 59.830 55.000 20.26 20.26 45.29 4.06
871 963 1.220749 CGGCTTGGCTTAGTGGCTA 59.779 57.895 0.00 0.00 42.34 3.93
876 968 0.320771 CACTGTCGGCTTGGCTTAGT 60.321 55.000 0.00 0.00 0.00 2.24
882 974 1.448540 CTAGGCACTGTCGGCTTGG 60.449 63.158 10.48 0.00 42.62 3.61
883 975 0.459237 CTCTAGGCACTGTCGGCTTG 60.459 60.000 10.48 9.21 42.62 4.01
884 976 0.612174 TCTCTAGGCACTGTCGGCTT 60.612 55.000 10.48 0.00 42.62 4.35
885 977 1.000771 TCTCTAGGCACTGTCGGCT 60.001 57.895 10.18 10.18 45.09 5.52
886 978 1.139947 GTCTCTAGGCACTGTCGGC 59.860 63.158 0.00 0.00 41.52 5.54
888 980 1.800655 GCATGTCTCTAGGCACTGTCG 60.801 57.143 0.00 0.00 41.52 4.35
889 981 1.480137 AGCATGTCTCTAGGCACTGTC 59.520 52.381 0.00 0.00 41.52 3.51
890 982 1.480137 GAGCATGTCTCTAGGCACTGT 59.520 52.381 9.16 0.00 36.55 3.55
892 984 1.118838 GGAGCATGTCTCTAGGCACT 58.881 55.000 14.20 0.00 41.60 4.40
893 985 0.105778 GGGAGCATGTCTCTAGGCAC 59.894 60.000 14.20 0.00 41.60 5.01
894 986 1.395045 CGGGAGCATGTCTCTAGGCA 61.395 60.000 14.20 0.00 41.60 4.75
895 987 1.365633 CGGGAGCATGTCTCTAGGC 59.634 63.158 14.20 0.00 41.60 3.93
928 1020 3.672511 CGGGCGTTTATATAGTGCGAGAT 60.673 47.826 0.00 0.00 0.00 2.75
948 1040 1.002366 GAGCATGCAAGTGTAGACGG 58.998 55.000 21.98 0.00 0.00 4.79
989 1092 4.363999 GGAGAAAGACATGTCGATCGATT 58.636 43.478 22.50 9.42 34.09 3.34
1003 1106 2.272146 GCCGCCATGGGAGAAAGA 59.728 61.111 15.13 0.00 38.63 2.52
1305 1408 1.138036 CGACGCATACCTTCCGACA 59.862 57.895 0.00 0.00 0.00 4.35
1446 1555 2.045926 CCTTTGGCCCTCCAGTCG 60.046 66.667 0.00 0.00 44.53 4.18
1554 1663 4.742659 GGCAAAATTTCTTCGTACAAAGCA 59.257 37.500 0.00 0.00 0.00 3.91
1561 1671 3.187637 CGTCAGGGCAAAATTTCTTCGTA 59.812 43.478 0.00 0.00 0.00 3.43
1590 1700 7.333528 TCCTTGAATAACTAAACATGCCATC 57.666 36.000 0.00 0.00 0.00 3.51
1591 1701 7.201938 CCATCCTTGAATAACTAAACATGCCAT 60.202 37.037 0.00 0.00 0.00 4.40
1592 1702 6.096705 CCATCCTTGAATAACTAAACATGCCA 59.903 38.462 0.00 0.00 0.00 4.92
1610 1720 8.592809 TGTTTCATAAATAAAGTTGCCATCCTT 58.407 29.630 0.00 0.00 0.00 3.36
1709 1824 2.228103 ACATCGCTCTGACGTTTCTACA 59.772 45.455 0.00 0.00 0.00 2.74
1710 1825 2.864968 ACATCGCTCTGACGTTTCTAC 58.135 47.619 0.00 0.00 0.00 2.59
1712 1827 2.440539 AACATCGCTCTGACGTTTCT 57.559 45.000 0.00 0.00 25.90 2.52
1740 1858 8.798859 AAACAAGCTCTAATGATAAGTGTCAT 57.201 30.769 0.00 0.00 40.44 3.06
1794 1912 5.672421 TTAGTTAAAGGAGGCCAGTACTC 57.328 43.478 5.01 0.00 0.00 2.59
1841 1972 0.961857 CAGCTAACTGCATGCACCCA 60.962 55.000 18.46 3.10 45.94 4.51
2429 2572 0.816825 ACGCATGCCTGATGGACATC 60.817 55.000 13.15 5.37 38.29 3.06
2431 2574 1.746239 CACGCATGCCTGATGGACA 60.746 57.895 13.15 0.00 34.57 4.02
2432 2575 3.104766 CACGCATGCCTGATGGAC 58.895 61.111 13.15 0.00 34.57 4.02
2433 2576 2.825387 GCACGCATGCCTGATGGA 60.825 61.111 19.22 0.00 46.97 3.41
2445 2588 3.539107 GTACGTAGGTGCGCACGC 61.539 66.667 32.35 24.53 41.80 5.34
2446 2589 3.235437 CGTACGTAGGTGCGCACG 61.235 66.667 32.35 23.78 44.85 5.34
2539 2683 5.066117 TCTCGATATAATCCACGACATAGGC 59.934 44.000 0.00 0.00 0.00 3.93
2550 2694 7.040617 TGGATAATAGCGGTCTCGATATAATCC 60.041 40.741 0.00 0.00 45.67 3.01
2556 2700 4.948004 ACATGGATAATAGCGGTCTCGATA 59.052 41.667 0.00 0.00 41.62 2.92
2561 2705 2.891580 ACGACATGGATAATAGCGGTCT 59.108 45.455 0.00 0.00 0.00 3.85
2565 2709 5.161358 ACACATACGACATGGATAATAGCG 58.839 41.667 0.00 0.00 0.00 4.26
2566 2710 7.507672 GTACACATACGACATGGATAATAGC 57.492 40.000 0.00 0.00 0.00 2.97
2583 2728 9.642327 TGATAGTTTATTGTTACACGTACACAT 57.358 29.630 0.00 0.00 0.00 3.21
2922 3083 3.243068 GCTTGTGACTTTCCAATCGTTGT 60.243 43.478 0.00 0.00 0.00 3.32
2950 3111 4.094887 ACCACGCAAGATTATTCATGTGTC 59.905 41.667 6.18 0.00 41.06 3.67
2982 3143 6.995364 TGGCATTTCATCATTTTTCTTCTCA 58.005 32.000 0.00 0.00 0.00 3.27
3010 3171 1.873591 CTGGAGGGAAACAAAGACACG 59.126 52.381 0.00 0.00 0.00 4.49
3096 3257 5.378230 AGATTGGAGTGATAATCCTTGCA 57.622 39.130 0.00 0.00 37.74 4.08
3123 3284 0.944386 TCGACTGAAGGCAAAACTGC 59.056 50.000 0.00 0.00 0.00 4.40
3306 3476 6.596497 CACGGGTAACATTTCTACCACTAAAT 59.404 38.462 1.73 0.00 40.64 1.40
3352 3522 4.202233 GGGAGTATTTAAGAACGGAGGGAG 60.202 50.000 0.00 0.00 0.00 4.30
3353 3523 3.708121 GGGAGTATTTAAGAACGGAGGGA 59.292 47.826 0.00 0.00 0.00 4.20
3354 3524 3.710165 AGGGAGTATTTAAGAACGGAGGG 59.290 47.826 0.00 0.00 0.00 4.30
3355 3525 4.202233 GGAGGGAGTATTTAAGAACGGAGG 60.202 50.000 0.00 0.00 0.00 4.30
3356 3526 4.499357 CGGAGGGAGTATTTAAGAACGGAG 60.499 50.000 0.00 0.00 0.00 4.63
3357 3527 3.382546 CGGAGGGAGTATTTAAGAACGGA 59.617 47.826 0.00 0.00 0.00 4.69
3358 3528 3.131755 ACGGAGGGAGTATTTAAGAACGG 59.868 47.826 0.00 0.00 0.00 4.44
3359 3529 4.382345 ACGGAGGGAGTATTTAAGAACG 57.618 45.455 0.00 0.00 0.00 3.95
3360 3530 5.105023 AGGAACGGAGGGAGTATTTAAGAAC 60.105 44.000 0.00 0.00 0.00 3.01
3361 3531 5.028131 AGGAACGGAGGGAGTATTTAAGAA 58.972 41.667 0.00 0.00 0.00 2.52
3362 3532 4.617593 AGGAACGGAGGGAGTATTTAAGA 58.382 43.478 0.00 0.00 0.00 2.10
3363 3533 6.475596 TTAGGAACGGAGGGAGTATTTAAG 57.524 41.667 0.00 0.00 0.00 1.85
3364 3534 6.872585 TTTAGGAACGGAGGGAGTATTTAA 57.127 37.500 0.00 0.00 0.00 1.52
3365 3535 6.384886 ACATTTAGGAACGGAGGGAGTATTTA 59.615 38.462 0.00 0.00 0.00 1.40
3366 3536 5.191124 ACATTTAGGAACGGAGGGAGTATTT 59.809 40.000 0.00 0.00 0.00 1.40
3367 3537 4.720273 ACATTTAGGAACGGAGGGAGTATT 59.280 41.667 0.00 0.00 0.00 1.89
3368 3538 4.296056 ACATTTAGGAACGGAGGGAGTAT 58.704 43.478 0.00 0.00 0.00 2.12
3369 3539 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
3370 3540 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
3371 3541 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
3372 3542 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
3373 3543 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
3374 3544 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
3375 3545 6.649557 ACAAAGACTTACATTTAGGAACGGAG 59.350 38.462 0.00 0.00 0.00 4.63
3376 3546 6.527423 ACAAAGACTTACATTTAGGAACGGA 58.473 36.000 0.00 0.00 0.00 4.69
3377 3547 6.796705 ACAAAGACTTACATTTAGGAACGG 57.203 37.500 0.00 0.00 0.00 4.44
3378 3548 8.752766 TCTACAAAGACTTACATTTAGGAACG 57.247 34.615 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.