Multiple sequence alignment - TraesCS4B01G206600

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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 TraesCS4B01G206600 chr4B 100.000 4166 0 0 1 4166 439310977 439315142 0.000000e+00 7694.0
1 TraesCS4B01G206600 chr4D 93.540 3390 128 39 1 3337 355813008 355816359 0.000000e+00 4963.0
2 TraesCS4B01G206600 chr4D 93.981 648 25 7 3410 4046 355853053 355853697 0.000000e+00 968.0
3 TraesCS4B01G206600 chr4D 80.929 409 54 16 17 418 488463638 488463247 6.770000e-78 302.0
4 TraesCS4B01G206600 chr4A 95.370 2484 74 16 846 3307 109433764 109431300 0.000000e+00 3912.0
5 TraesCS4B01G206600 chr4A 90.798 652 36 11 3412 4046 109429996 109429352 0.000000e+00 850.0
6 TraesCS4B01G206600 chr4A 94.141 256 3 5 3059 3307 109431088 109430838 3.040000e-101 379.0
7 TraesCS4B01G206600 chr4A 91.667 48 2 2 3565 3611 739156179 739156225 9.670000e-07 65.8
8 TraesCS4B01G206600 chr5D 81.353 606 81 24 1 596 421372967 421372384 8.160000e-127 464.0
9 TraesCS4B01G206600 chr5D 77.724 615 86 34 3 597 524512650 524512067 3.100000e-86 329.0
10 TraesCS4B01G206600 chr2B 80.800 625 76 31 1 609 785903580 785904176 2.280000e-122 449.0
11 TraesCS4B01G206600 chr5A 79.234 679 99 32 33 699 534939413 534938765 6.400000e-118 435.0
12 TraesCS4B01G206600 chr5A 79.557 406 57 21 17 418 670124852 670125235 2.470000e-67 267.0
13 TraesCS4B01G206600 chr2A 83.579 475 45 13 3575 4041 558535389 558534940 8.330000e-112 414.0
14 TraesCS4B01G206600 chr2A 93.182 44 2 1 839 882 19951266 19951224 3.480000e-06 63.9
15 TraesCS4B01G206600 chr2A 93.182 44 2 1 839 882 19951687 19951645 3.480000e-06 63.9
16 TraesCS4B01G206600 chr2A 93.182 44 2 1 839 882 19952013 19951971 3.480000e-06 63.9
17 TraesCS4B01G206600 chr2A 93.182 44 2 1 839 882 19952436 19952394 3.480000e-06 63.9
18 TraesCS4B01G206600 chr6D 80.789 583 63 34 29 591 301122002 301121449 1.080000e-110 411.0
19 TraesCS4B01G206600 chr6D 88.827 179 12 7 1 175 402890559 402890733 3.260000e-51 213.0
20 TraesCS4B01G206600 chr5B 79.245 636 95 28 9 633 6409009 6409618 3.880000e-110 409.0
21 TraesCS4B01G206600 chr1D 79.931 578 77 26 1 567 257510171 257509622 5.050000e-104 388.0
22 TraesCS4B01G206600 chr1D 80.075 266 28 5 3574 3836 193357807 193357564 1.540000e-39 174.0
23 TraesCS4B01G206600 chr7D 84.559 408 44 7 3651 4041 4410856 4410451 1.820000e-103 387.0
24 TraesCS4B01G206600 chr7D 85.366 123 15 1 3651 3770 4411062 4410940 1.570000e-24 124.0
25 TraesCS4B01G206600 chr7D 97.222 36 0 1 3576 3610 4411106 4411071 4.500000e-05 60.2
26 TraesCS4B01G206600 chr7D 97.143 35 0 1 3576 3609 4410900 4410866 1.620000e-04 58.4
27 TraesCS4B01G206600 chr3B 83.166 398 54 12 212 601 756679784 756679392 6.630000e-93 351.0
28 TraesCS4B01G206600 chr3B 96.970 33 1 0 851 883 126734748 126734716 5.820000e-04 56.5
29 TraesCS4B01G206600 chr3D 75.536 793 119 57 1 768 587312941 587312199 1.870000e-83 320.0
30 TraesCS4B01G206600 chr3D 87.719 171 16 5 1 169 611204394 611204227 1.180000e-45 195.0
31 TraesCS4B01G206600 chr3D 96.970 33 1 0 849 881 81123586 81123554 5.820000e-04 56.5
32 TraesCS4B01G206600 chr6A 82.474 388 45 15 1 383 15790420 15790789 6.720000e-83 318.0
33 TraesCS4B01G206600 chr7B 79.202 476 63 25 124 588 448652467 448652917 8.760000e-77 298.0
34 TraesCS4B01G206600 chr7A 85.603 257 24 4 3798 4041 4201723 4201467 1.490000e-64 257.0
35 TraesCS4B01G206600 chr3A 79.639 388 44 27 1 378 530935205 530934843 3.220000e-61 246.0


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 TraesCS4B01G206600 chr4B 439310977 439315142 4165 False 7694.000000 7694 100.000000 1 4166 1 chr4B.!!$F1 4165
1 TraesCS4B01G206600 chr4D 355813008 355816359 3351 False 4963.000000 4963 93.540000 1 3337 1 chr4D.!!$F1 3336
2 TraesCS4B01G206600 chr4D 355853053 355853697 644 False 968.000000 968 93.981000 3410 4046 1 chr4D.!!$F2 636
3 TraesCS4B01G206600 chr4A 109429352 109433764 4412 True 1713.666667 3912 93.436333 846 4046 3 chr4A.!!$R1 3200
4 TraesCS4B01G206600 chr5D 421372384 421372967 583 True 464.000000 464 81.353000 1 596 1 chr5D.!!$R1 595
5 TraesCS4B01G206600 chr5D 524512067 524512650 583 True 329.000000 329 77.724000 3 597 1 chr5D.!!$R2 594
6 TraesCS4B01G206600 chr2B 785903580 785904176 596 False 449.000000 449 80.800000 1 609 1 chr2B.!!$F1 608
7 TraesCS4B01G206600 chr5A 534938765 534939413 648 True 435.000000 435 79.234000 33 699 1 chr5A.!!$R1 666
8 TraesCS4B01G206600 chr6D 301121449 301122002 553 True 411.000000 411 80.789000 29 591 1 chr6D.!!$R1 562
9 TraesCS4B01G206600 chr5B 6409009 6409618 609 False 409.000000 409 79.245000 9 633 1 chr5B.!!$F1 624
10 TraesCS4B01G206600 chr1D 257509622 257510171 549 True 388.000000 388 79.931000 1 567 1 chr1D.!!$R2 566
11 TraesCS4B01G206600 chr3D 587312199 587312941 742 True 320.000000 320 75.536000 1 768 1 chr3D.!!$R2 767

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
203 221 0.040058 ACTTTGATCATGGGCCAGCA 59.960 50.0 13.78 4.64 0.0 4.41 F
936 1072 0.178975 AACCATTGGCCCACGAGAAA 60.179 50.0 0.00 0.00 0.0 2.52 F
1749 1893 0.536724 TGATTGCCTTCTCTAGCGCA 59.463 50.0 11.47 0.00 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1739 0.249322 AACCCCGCTCGTCGATTATG 60.249 55.000 0.0 0.0 41.67 1.90 R
1881 2026 1.004511 AGTACCACTCTGCCGACTACT 59.995 52.381 0.0 0.0 0.00 2.57 R
3648 5005 0.514255 CAGCAACGATGTGTGACTGG 59.486 55.000 0.0 0.0 33.05 4.00 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
201 219 3.967332 AAAACTTTGATCATGGGCCAG 57.033 42.857 13.78 4.37 0.00 4.85
202 220 1.188863 AACTTTGATCATGGGCCAGC 58.811 50.000 13.78 1.68 0.00 4.85
203 221 0.040058 ACTTTGATCATGGGCCAGCA 59.960 50.000 13.78 4.64 0.00 4.41
204 222 1.342674 ACTTTGATCATGGGCCAGCAT 60.343 47.619 13.78 5.97 0.00 3.79
205 223 1.760613 CTTTGATCATGGGCCAGCATT 59.239 47.619 13.78 0.00 0.00 3.56
206 224 2.752075 TTGATCATGGGCCAGCATTA 57.248 45.000 13.78 0.00 0.00 1.90
207 225 2.752075 TGATCATGGGCCAGCATTAA 57.248 45.000 13.78 0.00 0.00 1.40
210 228 3.968649 TGATCATGGGCCAGCATTAAATT 59.031 39.130 13.78 0.00 0.00 1.82
597 643 8.731275 AGGATTAAAACCAAAAGAAACAAAGG 57.269 30.769 5.15 0.00 0.00 3.11
599 645 9.337396 GGATTAAAACCAAAAGAAACAAAGGAT 57.663 29.630 0.00 0.00 0.00 3.24
644 754 7.850501 ACCGAAGAAACAAATGCAAAAATAAG 58.149 30.769 0.00 0.00 0.00 1.73
814 944 4.703382 CCATAAATGGGCCAGCCA 57.297 55.556 13.78 0.00 44.31 4.75
841 971 1.381327 TAGACCCCTTCGGCCAGAG 60.381 63.158 2.24 0.00 33.26 3.35
899 1029 3.041940 CGCCAACGCTTCCTTCGT 61.042 61.111 0.00 0.00 42.54 3.85
900 1030 2.861006 GCCAACGCTTCCTTCGTC 59.139 61.111 0.00 0.00 39.48 4.20
901 1031 1.668151 GCCAACGCTTCCTTCGTCT 60.668 57.895 0.00 0.00 39.48 4.18
922 1057 3.710209 AGCAGCTCTGAACTAAACCAT 57.290 42.857 0.29 0.00 0.00 3.55
936 1072 0.178975 AACCATTGGCCCACGAGAAA 60.179 50.000 0.00 0.00 0.00 2.52
943 1079 1.671379 GCCCACGAGAAAGACCCAC 60.671 63.158 0.00 0.00 0.00 4.61
1006 1149 4.947147 GCAGACCCGCACCACCAA 62.947 66.667 0.00 0.00 0.00 3.67
1007 1150 2.978010 CAGACCCGCACCACCAAC 60.978 66.667 0.00 0.00 0.00 3.77
1008 1151 4.265056 AGACCCGCACCACCAACC 62.265 66.667 0.00 0.00 0.00 3.77
1015 1158 1.901464 GCACCACCAACCCGTTCAT 60.901 57.895 0.00 0.00 0.00 2.57
1094 1238 2.831770 CGGAGGCCATGGCTATGT 59.168 61.111 34.70 17.83 38.98 2.29
1096 1240 1.839191 GGAGGCCATGGCTATGTCA 59.161 57.895 34.70 0.00 38.98 3.58
1198 1342 3.402628 TTTTAGGCTCTGTCACTGACC 57.597 47.619 6.72 0.00 0.00 4.02
1264 1408 1.069022 CACCTCAACACCATCAAAGCG 60.069 52.381 0.00 0.00 0.00 4.68
1267 1411 2.086869 CTCAACACCATCAAAGCGGAT 58.913 47.619 0.00 0.00 0.00 4.18
1324 1468 4.070716 CTCAACCTCTTGATCCATATGCC 58.929 47.826 0.00 0.00 35.78 4.40
1335 1479 1.760029 TCCATATGCCTGTGCGAGTAA 59.240 47.619 0.00 0.00 41.78 2.24
1442 1586 1.272480 ACTACATGGTCCAAAAGGGCC 60.272 52.381 0.00 0.00 36.21 5.80
1512 1656 5.523916 TGCTCTATCTTTTTCTTACGATGGC 59.476 40.000 0.00 0.00 0.00 4.40
1518 1662 6.817765 TCTTTTTCTTACGATGGCTGATTT 57.182 33.333 0.00 0.00 0.00 2.17
1535 1679 9.688091 TGGCTGATTTATTTGTAATAGTGGTTA 57.312 29.630 0.00 0.00 0.00 2.85
1544 1688 7.429636 TTTGTAATAGTGGTTACTGACTTGC 57.570 36.000 0.00 0.00 37.78 4.01
1545 1689 6.354794 TGTAATAGTGGTTACTGACTTGCT 57.645 37.500 0.00 0.00 37.78 3.91
1586 1730 3.485877 GCTTGTATGAAACGGCTGTCATC 60.486 47.826 0.00 1.13 36.00 2.92
1595 1739 3.444703 ACGGCTGTCATCTAGAACATC 57.555 47.619 0.00 0.00 0.00 3.06
1669 1813 1.860484 GCCAGCTTGCTCAAGTCACC 61.860 60.000 1.78 0.00 40.45 4.02
1679 1823 2.654863 CTCAAGTCACCCAACAAGGTT 58.345 47.619 0.00 0.00 38.39 3.50
1681 1825 1.111277 AAGTCACCCAACAAGGTTGC 58.889 50.000 3.63 0.00 38.39 4.17
1699 1843 5.900123 AGGTTGCTCCTTTCTCTATAAGCTA 59.100 40.000 0.00 0.00 45.67 3.32
1713 1857 9.008965 TCTCTATAAGCTAAAATGCAACACAAA 57.991 29.630 0.00 0.00 34.99 2.83
1749 1893 0.536724 TGATTGCCTTCTCTAGCGCA 59.463 50.000 11.47 0.00 0.00 6.09
1849 1993 2.702270 AAGCCCATTTTGAAGACCCT 57.298 45.000 0.00 0.00 0.00 4.34
1852 1996 2.158325 AGCCCATTTTGAAGACCCTCAA 60.158 45.455 0.00 0.00 33.48 3.02
1881 2026 4.693566 GTGAACATGTTCGATTTCCCAGTA 59.306 41.667 28.55 8.17 42.28 2.74
2024 2169 4.070009 GGGTTTCAACGGTATTGTCTTCT 58.930 43.478 0.00 0.00 0.00 2.85
2256 2401 5.451103 GCGGAGATATCTATATTGCAGCTCA 60.451 44.000 4.89 0.00 0.00 4.26
2412 2557 7.994425 TTGTATACCTTGATGTGACAATTGT 57.006 32.000 11.78 11.78 0.00 2.71
2743 2890 7.201830 GCCAGAGTAAGTGTCTTGTATATCTGA 60.202 40.741 0.00 0.00 33.89 3.27
2813 2960 2.673893 GCTTTCCGGCCAAATTAACCAG 60.674 50.000 2.24 0.00 0.00 4.00
3004 3151 4.908601 TTCAAGGAAGCAGTCAAGGATA 57.091 40.909 0.00 0.00 0.00 2.59
3102 3711 4.164413 GGTTGAAGGGGATAGTAGCTCTTT 59.836 45.833 0.00 0.00 0.00 2.52
3103 3712 5.361427 GTTGAAGGGGATAGTAGCTCTTTC 58.639 45.833 3.31 3.31 0.00 2.62
3255 3871 7.535139 AGGTTTGTATGTCACCATAATTTTCG 58.465 34.615 0.00 0.00 35.37 3.46
3258 3874 4.336993 TGTATGTCACCATAATTTTCGGCC 59.663 41.667 0.00 0.00 35.37 6.13
3259 3875 3.080300 TGTCACCATAATTTTCGGCCT 57.920 42.857 0.00 0.00 0.00 5.19
3318 3934 6.567602 AACTTCTCTGCATATTACTCCCTT 57.432 37.500 0.00 0.00 0.00 3.95
3329 3945 6.743208 GCATATTACTCCCTTCGTCCCAAATA 60.743 42.308 0.00 0.00 0.00 1.40
3331 3947 3.629142 ACTCCCTTCGTCCCAAATAAG 57.371 47.619 0.00 0.00 0.00 1.73
3332 3948 2.289565 CTCCCTTCGTCCCAAATAAGC 58.710 52.381 0.00 0.00 0.00 3.09
3333 3949 1.014352 CCCTTCGTCCCAAATAAGCG 58.986 55.000 0.00 0.00 0.00 4.68
3334 3950 1.406341 CCCTTCGTCCCAAATAAGCGA 60.406 52.381 0.00 0.00 0.00 4.93
3335 3951 1.664151 CCTTCGTCCCAAATAAGCGAC 59.336 52.381 0.00 0.00 0.00 5.19
3337 3953 2.004583 TCGTCCCAAATAAGCGACTG 57.995 50.000 0.00 0.00 0.00 3.51
3338 3954 1.546923 TCGTCCCAAATAAGCGACTGA 59.453 47.619 0.00 0.00 0.00 3.41
3339 3955 2.028839 TCGTCCCAAATAAGCGACTGAA 60.029 45.455 0.00 0.00 0.00 3.02
3340 3956 2.348666 CGTCCCAAATAAGCGACTGAAG 59.651 50.000 0.00 0.00 0.00 3.02
3342 3958 4.501071 GTCCCAAATAAGCGACTGAAGTA 58.499 43.478 0.00 0.00 0.00 2.24
3343 3959 4.329256 GTCCCAAATAAGCGACTGAAGTAC 59.671 45.833 0.00 0.00 0.00 2.73
3348 4511 7.305474 CCAAATAAGCGACTGAAGTACAAAAT 58.695 34.615 0.00 0.00 0.00 1.82
3349 4512 7.807907 CCAAATAAGCGACTGAAGTACAAAATT 59.192 33.333 0.00 0.00 0.00 1.82
3351 4514 7.667043 ATAAGCGACTGAAGTACAAAATTGA 57.333 32.000 0.00 0.00 0.00 2.57
3384 4547 8.777865 ATTTAAAGTTACTTAGACCGTAACCC 57.222 34.615 0.00 0.00 44.76 4.11
3385 4548 5.806654 AAAGTTACTTAGACCGTAACCCA 57.193 39.130 0.00 0.00 44.76 4.51
3386 4549 6.364568 AAAGTTACTTAGACCGTAACCCAT 57.635 37.500 0.00 0.00 44.76 4.00
3387 4550 6.364568 AAGTTACTTAGACCGTAACCCATT 57.635 37.500 0.00 0.00 44.76 3.16
3388 4551 7.480760 AAGTTACTTAGACCGTAACCCATTA 57.519 36.000 0.00 0.00 44.76 1.90
3389 4552 7.666063 AGTTACTTAGACCGTAACCCATTAT 57.334 36.000 8.86 0.00 44.76 1.28
3390 4553 8.082672 AGTTACTTAGACCGTAACCCATTATT 57.917 34.615 8.86 0.00 44.76 1.40
3392 4555 6.549433 ACTTAGACCGTAACCCATTATTGA 57.451 37.500 0.00 0.00 0.00 2.57
3393 4556 6.579865 ACTTAGACCGTAACCCATTATTGAG 58.420 40.000 0.00 0.00 0.00 3.02
3394 4557 6.155737 ACTTAGACCGTAACCCATTATTGAGT 59.844 38.462 0.00 0.00 0.00 3.41
3395 4558 5.019785 AGACCGTAACCCATTATTGAGTC 57.980 43.478 0.00 0.00 0.00 3.36
3398 4561 4.715297 ACCGTAACCCATTATTGAGTCTCT 59.285 41.667 0.65 0.00 0.00 3.10
3399 4562 5.050490 CCGTAACCCATTATTGAGTCTCTG 58.950 45.833 0.65 0.00 0.00 3.35
3400 4563 5.163447 CCGTAACCCATTATTGAGTCTCTGA 60.163 44.000 0.65 0.00 0.00 3.27
3402 4565 5.762179 AACCCATTATTGAGTCTCTGACA 57.238 39.130 0.65 0.00 34.60 3.58
3403 4566 5.762179 ACCCATTATTGAGTCTCTGACAA 57.238 39.130 0.65 0.00 34.60 3.18
3404 4567 6.319048 ACCCATTATTGAGTCTCTGACAAT 57.681 37.500 0.65 0.00 37.82 2.71
3405 4568 6.118170 ACCCATTATTGAGTCTCTGACAATG 58.882 40.000 0.65 5.91 36.06 2.82
3408 4571 6.482641 CCATTATTGAGTCTCTGACAATGGAG 59.517 42.308 20.19 0.00 40.45 3.86
3540 4895 8.271458 TGCCTAGAGACATGGAATATAACAAAA 58.729 33.333 0.00 0.00 0.00 2.44
3636 4993 2.821366 CCGCTTCGGCTGCTTGAT 60.821 61.111 0.00 0.00 41.17 2.57
3648 5005 3.113745 CTTGATGCATGTCCCCGC 58.886 61.111 2.46 0.00 0.00 6.13
3649 5006 2.440065 TTGATGCATGTCCCCGCC 60.440 61.111 2.46 0.00 0.00 6.13
3668 5025 1.220529 CAGTCACACATCGTTGCTGT 58.779 50.000 0.00 0.00 0.00 4.40
3691 5048 1.735376 TTATCTCCTCAGGCGTCCGC 61.735 60.000 2.45 2.45 41.06 5.54
3754 5114 5.335976 GCCAATTACTTGTTTCTTAGCAGCT 60.336 40.000 0.00 0.00 0.00 4.24
3816 5176 2.281070 ACTCAGCCACGCAACAGG 60.281 61.111 0.00 0.00 0.00 4.00
3838 5198 4.957684 CGCATGATCTCCGCCGCT 62.958 66.667 0.00 0.00 0.00 5.52
4056 5426 0.694771 AAAAACTACTCCCCCGTCCC 59.305 55.000 0.00 0.00 0.00 4.46
4057 5427 0.474273 AAAACTACTCCCCCGTCCCA 60.474 55.000 0.00 0.00 0.00 4.37
4058 5428 0.253020 AAACTACTCCCCCGTCCCAT 60.253 55.000 0.00 0.00 0.00 4.00
4059 5429 0.638292 AACTACTCCCCCGTCCCATA 59.362 55.000 0.00 0.00 0.00 2.74
4060 5430 0.638292 ACTACTCCCCCGTCCCATAA 59.362 55.000 0.00 0.00 0.00 1.90
4061 5431 1.222298 ACTACTCCCCCGTCCCATAAT 59.778 52.381 0.00 0.00 0.00 1.28
4062 5432 1.623811 CTACTCCCCCGTCCCATAATG 59.376 57.143 0.00 0.00 0.00 1.90
4063 5433 0.327191 ACTCCCCCGTCCCATAATGT 60.327 55.000 0.00 0.00 0.00 2.71
4064 5434 1.061967 ACTCCCCCGTCCCATAATGTA 60.062 52.381 0.00 0.00 0.00 2.29
4065 5435 2.051692 CTCCCCCGTCCCATAATGTAA 58.948 52.381 0.00 0.00 0.00 2.41
4066 5436 2.038557 CTCCCCCGTCCCATAATGTAAG 59.961 54.545 0.00 0.00 0.00 2.34
4067 5437 2.051692 CCCCCGTCCCATAATGTAAGA 58.948 52.381 0.00 0.00 0.00 2.10
4068 5438 2.224450 CCCCCGTCCCATAATGTAAGAC 60.224 54.545 0.00 0.00 0.00 3.01
4070 5440 2.101917 CCCGTCCCATAATGTAAGACGT 59.898 50.000 9.63 0.00 46.62 4.34
4071 5441 3.431207 CCCGTCCCATAATGTAAGACGTT 60.431 47.826 9.63 0.00 46.62 3.99
4072 5442 4.186159 CCGTCCCATAATGTAAGACGTTT 58.814 43.478 9.63 0.00 46.62 3.60
4073 5443 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
4074 5444 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
4130 5500 8.535690 AGTATAAAGTTGACTCTTACAAGCAC 57.464 34.615 0.00 0.00 0.00 4.40
4131 5501 8.148351 AGTATAAAGTTGACTCTTACAAGCACA 58.852 33.333 0.00 0.00 0.00 4.57
4132 5502 7.986085 ATAAAGTTGACTCTTACAAGCACAT 57.014 32.000 0.00 0.00 0.00 3.21
4133 5503 6.699575 AAAGTTGACTCTTACAAGCACATT 57.300 33.333 0.00 0.00 0.00 2.71
4134 5504 5.679734 AGTTGACTCTTACAAGCACATTG 57.320 39.130 0.00 0.00 45.01 2.82
4135 5505 5.368145 AGTTGACTCTTACAAGCACATTGA 58.632 37.500 0.00 0.00 41.83 2.57
4136 5506 5.822519 AGTTGACTCTTACAAGCACATTGAA 59.177 36.000 0.00 0.00 41.83 2.69
4137 5507 6.318648 AGTTGACTCTTACAAGCACATTGAAA 59.681 34.615 0.00 0.00 41.83 2.69
4138 5508 6.060028 TGACTCTTACAAGCACATTGAAAC 57.940 37.500 0.00 0.00 41.83 2.78
4139 5509 5.095691 ACTCTTACAAGCACATTGAAACG 57.904 39.130 0.00 0.00 41.83 3.60
4140 5510 3.884169 TCTTACAAGCACATTGAAACGC 58.116 40.909 0.00 0.00 41.83 4.84
4141 5511 3.313803 TCTTACAAGCACATTGAAACGCA 59.686 39.130 0.00 0.00 41.83 5.24
4142 5512 2.575694 ACAAGCACATTGAAACGCAA 57.424 40.000 0.00 0.00 41.83 4.85
4143 5513 2.886081 ACAAGCACATTGAAACGCAAA 58.114 38.095 0.00 0.00 41.83 3.68
4144 5514 2.602660 ACAAGCACATTGAAACGCAAAC 59.397 40.909 0.00 0.00 41.83 2.93
4145 5515 2.575694 AGCACATTGAAACGCAAACA 57.424 40.000 0.00 0.00 40.48 2.83
4146 5516 2.886081 AGCACATTGAAACGCAAACAA 58.114 38.095 0.00 0.00 40.48 2.83
4147 5517 3.257393 AGCACATTGAAACGCAAACAAA 58.743 36.364 0.00 0.00 40.48 2.83
4148 5518 3.681897 AGCACATTGAAACGCAAACAAAA 59.318 34.783 0.00 0.00 40.48 2.44
4149 5519 4.153117 AGCACATTGAAACGCAAACAAAAA 59.847 33.333 0.00 0.00 40.48 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
568 614 9.898152 TTGTTTCTTTTGGTTTTAATCCTCAAT 57.102 25.926 0.00 0.00 0.00 2.57
797 927 0.106066 TCTGGCTGGCCCATTTATGG 60.106 55.000 9.28 1.59 44.33 2.74
800 930 2.513738 AGTAATCTGGCTGGCCCATTTA 59.486 45.455 9.28 1.86 44.33 1.40
810 940 2.022918 AGGGGTCTACAGTAATCTGGCT 60.023 50.000 0.47 0.00 45.14 4.75
841 971 0.524862 TAAGCGAGACCGACAGTTCC 59.475 55.000 0.00 0.00 38.22 3.62
891 1021 1.474478 CAGAGCTGCTAGACGAAGGAA 59.526 52.381 0.15 0.00 0.00 3.36
892 1022 1.098869 CAGAGCTGCTAGACGAAGGA 58.901 55.000 0.15 0.00 0.00 3.36
899 1029 3.832490 TGGTTTAGTTCAGAGCTGCTAGA 59.168 43.478 0.15 0.45 0.00 2.43
900 1030 4.193826 TGGTTTAGTTCAGAGCTGCTAG 57.806 45.455 0.15 0.00 0.00 3.42
901 1031 4.826274 ATGGTTTAGTTCAGAGCTGCTA 57.174 40.909 0.15 0.00 0.00 3.49
922 1057 1.072505 GGTCTTTCTCGTGGGCCAA 59.927 57.895 8.40 0.00 0.00 4.52
960 1096 1.229464 AGGAGAGCTGCAGAACCCT 60.229 57.895 20.43 14.23 0.00 4.34
961 1097 1.078567 CAGGAGAGCTGCAGAACCC 60.079 63.158 20.43 12.08 0.00 4.11
962 1098 1.078567 CCAGGAGAGCTGCAGAACC 60.079 63.158 20.43 13.75 0.00 3.62
964 1100 1.881903 CGACCAGGAGAGCTGCAGAA 61.882 60.000 20.43 0.00 0.00 3.02
1041 1184 2.358615 TGCTCGCGGAAATGTGCT 60.359 55.556 6.13 0.00 0.00 4.40
1090 1234 3.096092 GGTGGATTTGGCCTTTGACATA 58.904 45.455 3.32 0.00 0.00 2.29
1094 1238 1.531739 GCGGTGGATTTGGCCTTTGA 61.532 55.000 3.32 0.00 0.00 2.69
1096 1240 2.282783 GGCGGTGGATTTGGCCTTT 61.283 57.895 3.32 0.00 42.29 3.11
1167 1311 1.139058 GAGCCTAAAATCGGAGGAGCA 59.861 52.381 0.00 0.00 34.46 4.26
1264 1408 2.054453 GCACCTTCCCTTGGCATCC 61.054 63.158 0.00 0.00 0.00 3.51
1324 1468 4.928661 ATTTTAGCTGTTACTCGCACAG 57.071 40.909 0.00 0.00 43.99 3.66
1335 1479 7.962441 ACAAGGAAATTTGGTATTTTAGCTGT 58.038 30.769 0.00 0.00 32.32 4.40
1442 1586 1.742768 GGACGATGAGGTAGGGCAG 59.257 63.158 0.00 0.00 0.00 4.85
1506 1650 8.017373 CCACTATTACAAATAAATCAGCCATCG 58.983 37.037 0.00 0.00 0.00 3.84
1518 1662 9.158233 GCAAGTCAGTAACCACTATTACAAATA 57.842 33.333 0.00 0.00 37.49 1.40
1535 1679 4.960938 TCAGAACATAACAGCAAGTCAGT 58.039 39.130 0.00 0.00 0.00 3.41
1538 1682 6.486253 TTCATCAGAACATAACAGCAAGTC 57.514 37.500 0.00 0.00 0.00 3.01
1539 1683 7.310664 CAATTCATCAGAACATAACAGCAAGT 58.689 34.615 0.00 0.00 36.39 3.16
1540 1684 6.252869 GCAATTCATCAGAACATAACAGCAAG 59.747 38.462 0.00 0.00 36.39 4.01
1541 1685 6.071784 AGCAATTCATCAGAACATAACAGCAA 60.072 34.615 0.00 0.00 36.39 3.91
1542 1686 5.416639 AGCAATTCATCAGAACATAACAGCA 59.583 36.000 0.00 0.00 36.39 4.41
1543 1687 5.888105 AGCAATTCATCAGAACATAACAGC 58.112 37.500 0.00 0.00 36.39 4.40
1544 1688 7.310664 ACAAGCAATTCATCAGAACATAACAG 58.689 34.615 0.00 0.00 36.39 3.16
1545 1689 7.218228 ACAAGCAATTCATCAGAACATAACA 57.782 32.000 0.00 0.00 36.39 2.41
1586 1730 4.551509 CGCTCGTCGATTATGATGTTCTAG 59.448 45.833 0.00 0.00 41.67 2.43
1595 1739 0.249322 AACCCCGCTCGTCGATTATG 60.249 55.000 0.00 0.00 41.67 1.90
1679 1823 7.227512 GCATTTTAGCTTATAGAGAAAGGAGCA 59.772 37.037 0.00 0.00 32.78 4.26
1681 1825 8.668510 TGCATTTTAGCTTATAGAGAAAGGAG 57.331 34.615 0.00 0.00 34.99 3.69
1749 1893 4.766373 TGCACAAGACAACAATATCACCAT 59.234 37.500 0.00 0.00 0.00 3.55
1881 2026 1.004511 AGTACCACTCTGCCGACTACT 59.995 52.381 0.00 0.00 0.00 2.57
2256 2401 6.066690 CCCCAATGAATCTATGAAGACACAT 58.933 40.000 0.00 0.00 33.57 3.21
2552 2699 9.528018 CAAAATTAGAAGGTGCAGTTAGAAAAA 57.472 29.630 0.00 0.00 0.00 1.94
2743 2890 6.434028 ACACTTATCCTACATTGCACATTGTT 59.566 34.615 3.75 0.00 0.00 2.83
2813 2960 5.047235 ACAGTACTGTGACAATAAGAGGACC 60.047 44.000 27.41 0.00 43.11 4.46
3004 3151 1.741706 CATGCGGCAGAAGTCTTCAAT 59.258 47.619 14.97 0.00 0.00 2.57
3102 3711 1.214175 TGTGCCCTTTGGTTTGAGAGA 59.786 47.619 0.00 0.00 0.00 3.10
3103 3712 1.691196 TGTGCCCTTTGGTTTGAGAG 58.309 50.000 0.00 0.00 0.00 3.20
3160 3771 8.557029 CCATCTACAAAAACGGAGGTTATATTC 58.443 37.037 0.00 0.00 34.62 1.75
3161 3772 8.050930 ACCATCTACAAAAACGGAGGTTATATT 58.949 33.333 0.00 0.00 34.62 1.28
3163 3774 6.949715 ACCATCTACAAAAACGGAGGTTATA 58.050 36.000 0.00 0.00 34.62 0.98
3164 3775 5.812286 ACCATCTACAAAAACGGAGGTTAT 58.188 37.500 0.00 0.00 34.62 1.89
3165 3776 5.231702 ACCATCTACAAAAACGGAGGTTA 57.768 39.130 0.00 0.00 34.62 2.85
3166 3777 4.094830 ACCATCTACAAAAACGGAGGTT 57.905 40.909 0.00 0.00 38.22 3.50
3168 3779 4.794169 CAAACCATCTACAAAAACGGAGG 58.206 43.478 0.00 0.00 0.00 4.30
3171 3782 3.971150 TGCAAACCATCTACAAAAACGG 58.029 40.909 0.00 0.00 0.00 4.44
3255 3871 3.697619 AAGTACTACCAAACAGAGGCC 57.302 47.619 0.00 0.00 0.00 5.19
3329 3945 5.527582 ACTCAATTTTGTACTTCAGTCGCTT 59.472 36.000 0.00 0.00 0.00 4.68
3331 3947 5.050363 TGACTCAATTTTGTACTTCAGTCGC 60.050 40.000 0.00 0.00 31.19 5.19
3332 3948 6.201044 AGTGACTCAATTTTGTACTTCAGTCG 59.799 38.462 0.00 0.00 31.19 4.18
3333 3949 7.484035 AGTGACTCAATTTTGTACTTCAGTC 57.516 36.000 0.00 0.00 0.00 3.51
3334 3950 7.865706 AAGTGACTCAATTTTGTACTTCAGT 57.134 32.000 0.00 0.00 0.00 3.41
3367 4530 8.076910 TCAATAATGGGTTACGGTCTAAGTAA 57.923 34.615 0.00 0.00 0.00 2.24
3368 4531 7.342799 ACTCAATAATGGGTTACGGTCTAAGTA 59.657 37.037 0.00 0.00 36.68 2.24
3369 4532 6.155737 ACTCAATAATGGGTTACGGTCTAAGT 59.844 38.462 0.00 0.00 36.68 2.24
3370 4533 6.579865 ACTCAATAATGGGTTACGGTCTAAG 58.420 40.000 0.00 0.00 36.68 2.18
3371 4534 6.381994 AGACTCAATAATGGGTTACGGTCTAA 59.618 38.462 0.00 0.00 41.50 2.10
3372 4535 5.895534 AGACTCAATAATGGGTTACGGTCTA 59.104 40.000 0.00 0.00 41.50 2.59
3373 4536 4.715297 AGACTCAATAATGGGTTACGGTCT 59.285 41.667 0.00 0.00 41.50 3.85
3376 4539 5.050490 CAGAGACTCAATAATGGGTTACGG 58.950 45.833 5.02 0.00 41.50 4.02
3377 4540 5.749109 GTCAGAGACTCAATAATGGGTTACG 59.251 44.000 5.02 0.00 41.50 3.18
3378 4541 6.640518 TGTCAGAGACTCAATAATGGGTTAC 58.359 40.000 5.02 0.00 41.50 2.50
3379 4542 6.867519 TGTCAGAGACTCAATAATGGGTTA 57.132 37.500 5.02 0.00 41.50 2.85
3380 4543 5.762179 TGTCAGAGACTCAATAATGGGTT 57.238 39.130 5.02 0.00 41.50 4.11
3383 4546 6.351711 TCCATTGTCAGAGACTCAATAATGG 58.648 40.000 24.99 24.99 39.91 3.16
3384 4547 7.046652 ACTCCATTGTCAGAGACTCAATAATG 58.953 38.462 5.02 11.51 34.13 1.90
3385 4548 7.192852 ACTCCATTGTCAGAGACTCAATAAT 57.807 36.000 5.02 0.15 34.13 1.28
3386 4549 6.611613 ACTCCATTGTCAGAGACTCAATAA 57.388 37.500 5.02 0.00 34.13 1.40
3387 4550 7.718334 TTACTCCATTGTCAGAGACTCAATA 57.282 36.000 5.02 0.00 34.13 1.90
3388 4551 6.611613 TTACTCCATTGTCAGAGACTCAAT 57.388 37.500 5.02 0.00 34.13 2.57
3389 4552 6.419484 TTTACTCCATTGTCAGAGACTCAA 57.581 37.500 5.02 0.00 34.13 3.02
3390 4553 6.419484 TTTTACTCCATTGTCAGAGACTCA 57.581 37.500 5.02 0.00 34.13 3.41
3481 4835 6.041523 GGTCCTTAACTATCTTCTGAGATGCT 59.958 42.308 0.00 0.00 42.55 3.79
3540 4895 5.692928 AGATCCTTGCAGCTTCATAGAATT 58.307 37.500 0.00 0.00 0.00 2.17
3636 4993 4.408821 GACTGGCGGGGACATGCA 62.409 66.667 0.00 0.00 32.78 3.96
3648 5005 0.514255 CAGCAACGATGTGTGACTGG 59.486 55.000 0.00 0.00 33.05 4.00
3649 5006 1.220529 ACAGCAACGATGTGTGACTG 58.779 50.000 0.00 0.00 39.21 3.51
3668 5025 2.584236 GACGCCTGAGGAGATAAGGTA 58.416 52.381 9.85 0.00 33.34 3.08
3691 5048 3.057876 CGACGAGATAGATTTCCTGGAGG 60.058 52.174 0.00 0.00 0.00 4.30
3754 5114 3.451178 CGGGAGGGAGAAAGTGAAGATTA 59.549 47.826 0.00 0.00 0.00 1.75
3816 5176 3.993234 CGGAGATCATGCGCGCAC 61.993 66.667 39.05 24.03 35.37 5.34
3825 5185 3.531207 CTGGAGCGGCGGAGATCA 61.531 66.667 9.78 0.00 0.00 2.92
4042 5412 1.623811 CATTATGGGACGGGGGAGTAG 59.376 57.143 0.00 0.00 0.00 2.57
4043 5413 1.061967 ACATTATGGGACGGGGGAGTA 60.062 52.381 0.00 0.00 0.00 2.59
4044 5414 0.327191 ACATTATGGGACGGGGGAGT 60.327 55.000 0.00 0.00 0.00 3.85
4045 5415 1.724545 TACATTATGGGACGGGGGAG 58.275 55.000 0.00 0.00 0.00 4.30
4046 5416 2.051692 CTTACATTATGGGACGGGGGA 58.948 52.381 0.00 0.00 0.00 4.81
4047 5417 2.051692 TCTTACATTATGGGACGGGGG 58.948 52.381 0.00 0.00 0.00 5.40
4048 5418 2.547218 CGTCTTACATTATGGGACGGGG 60.547 54.545 20.50 3.61 43.69 5.73
4049 5419 2.750948 CGTCTTACATTATGGGACGGG 58.249 52.381 20.50 4.10 43.69 5.28
4104 5474 9.635520 GTGCTTGTAAGAGTCAACTTTATACTA 57.364 33.333 0.00 0.00 0.00 1.82
4105 5475 8.148351 TGTGCTTGTAAGAGTCAACTTTATACT 58.852 33.333 0.00 0.00 0.00 2.12
4106 5476 8.306680 TGTGCTTGTAAGAGTCAACTTTATAC 57.693 34.615 0.00 0.00 0.00 1.47
4107 5477 9.502091 AATGTGCTTGTAAGAGTCAACTTTATA 57.498 29.630 0.00 0.00 0.00 0.98
4108 5478 7.986085 ATGTGCTTGTAAGAGTCAACTTTAT 57.014 32.000 0.00 0.00 0.00 1.40
4109 5479 7.497579 TCAATGTGCTTGTAAGAGTCAACTTTA 59.502 33.333 0.00 0.00 36.20 1.85
4110 5480 6.318648 TCAATGTGCTTGTAAGAGTCAACTTT 59.681 34.615 0.00 0.00 36.20 2.66
4111 5481 5.822519 TCAATGTGCTTGTAAGAGTCAACTT 59.177 36.000 0.00 0.00 36.20 2.66
4112 5482 5.368145 TCAATGTGCTTGTAAGAGTCAACT 58.632 37.500 0.00 0.00 36.20 3.16
4113 5483 5.673337 TCAATGTGCTTGTAAGAGTCAAC 57.327 39.130 0.00 0.00 36.20 3.18
4114 5484 6.494842 GTTTCAATGTGCTTGTAAGAGTCAA 58.505 36.000 0.00 0.00 36.20 3.18
4115 5485 5.277297 CGTTTCAATGTGCTTGTAAGAGTCA 60.277 40.000 0.00 0.00 36.20 3.41
4116 5486 5.140177 CGTTTCAATGTGCTTGTAAGAGTC 58.860 41.667 0.00 0.00 36.20 3.36
4117 5487 4.554723 GCGTTTCAATGTGCTTGTAAGAGT 60.555 41.667 0.00 0.00 36.20 3.24
4118 5488 3.908382 GCGTTTCAATGTGCTTGTAAGAG 59.092 43.478 0.00 0.00 36.20 2.85
4119 5489 3.313803 TGCGTTTCAATGTGCTTGTAAGA 59.686 39.130 0.00 0.00 36.20 2.10
4120 5490 3.626977 TGCGTTTCAATGTGCTTGTAAG 58.373 40.909 0.00 0.00 36.20 2.34
4121 5491 3.699779 TGCGTTTCAATGTGCTTGTAA 57.300 38.095 0.00 0.00 36.20 2.41
4122 5492 3.699779 TTGCGTTTCAATGTGCTTGTA 57.300 38.095 0.00 0.00 36.20 2.41
4123 5493 2.575694 TTGCGTTTCAATGTGCTTGT 57.424 40.000 0.00 0.00 36.20 3.16
4124 5494 2.602211 TGTTTGCGTTTCAATGTGCTTG 59.398 40.909 0.00 0.00 34.12 4.01
4125 5495 2.886081 TGTTTGCGTTTCAATGTGCTT 58.114 38.095 0.00 0.00 34.12 3.91
4126 5496 2.575694 TGTTTGCGTTTCAATGTGCT 57.424 40.000 0.00 0.00 34.12 4.40
4127 5497 3.648179 TTTGTTTGCGTTTCAATGTGC 57.352 38.095 0.00 0.00 34.12 4.57


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

AutoCloner maintained by Alex Coulton.