Multiple sequence alignment - TraesCS6D01G205200

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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 TraesCS6D01G205200 chr6D 100.000 3795 0 0 350 4144 291151953 291148159 0.000000e+00 7009.0
1 TraesCS6D01G205200 chr6D 100.000 86 0 0 1 86 291152302 291152217 4.290000e-35 159.0
2 TraesCS6D01G205200 chr6A 91.843 2219 112 26 350 2544 432510654 432512827 0.000000e+00 3031.0
3 TraesCS6D01G205200 chr6A 97.313 707 18 1 2574 3280 432512826 432513531 0.000000e+00 1199.0
4 TraesCS6D01G205200 chr6A 89.352 432 17 9 3713 4144 432519087 432519489 2.210000e-142 516.0
5 TraesCS6D01G205200 chr6A 96.809 282 8 1 3275 3556 432513609 432513889 1.740000e-128 470.0
6 TraesCS6D01G205200 chr6A 96.512 86 3 0 1 86 432510555 432510640 4.320000e-30 143.0
7 TraesCS6D01G205200 chr6A 96.000 50 2 0 3552 3601 432519041 432519090 9.550000e-12 82.4
8 TraesCS6D01G205200 chr6B 90.913 2212 106 31 350 2511 451924355 451926521 0.000000e+00 2883.0
9 TraesCS6D01G205200 chr6B 94.045 890 29 9 2576 3462 451926542 451927410 0.000000e+00 1328.0
10 TraesCS6D01G205200 chr6B 96.899 129 4 0 3749 3877 451927517 451927645 2.510000e-52 217.0
11 TraesCS6D01G205200 chr6B 83.475 236 10 10 3909 4144 451927645 451927851 4.230000e-45 193.0
12 TraesCS6D01G205200 chr6B 95.556 90 4 0 3512 3601 451927407 451927496 1.200000e-30 145.0
13 TraesCS6D01G205200 chr6B 95.402 87 4 0 2512 2598 135505596 135505682 5.590000e-29 139.0
14 TraesCS6D01G205200 chr6B 95.349 86 4 0 1 86 451924257 451924342 2.010000e-28 137.0
15 TraesCS6D01G205200 chr6B 87.387 111 7 5 2498 2601 13827627 13827517 2.020000e-23 121.0
16 TraesCS6D01G205200 chrUn 95.798 119 5 0 3598 3716 82049597 82049479 4.230000e-45 193.0
17 TraesCS6D01G205200 chrUn 82.946 129 18 4 354 481 57650829 57650954 3.390000e-21 113.0
18 TraesCS6D01G205200 chr5B 95.798 119 5 0 3599 3717 711834148 711834030 4.230000e-45 193.0
19 TraesCS6D01G205200 chr5B 93.651 126 6 2 3599 3723 450504267 450504143 1.970000e-43 187.0
20 TraesCS6D01G205200 chr1D 95.833 120 3 2 3600 3717 298558690 298558571 4.230000e-45 193.0
21 TraesCS6D01G205200 chr1D 92.391 92 7 0 2511 2602 3368845 3368754 9.350000e-27 132.0
22 TraesCS6D01G205200 chr1D 89.024 82 7 2 1 81 228824596 228824676 2.640000e-17 100.0
23 TraesCS6D01G205200 chr1D 77.778 162 28 4 357 512 441294398 441294239 4.410000e-15 93.5
24 TraesCS6D01G205200 chr7B 94.309 123 7 0 3598 3720 573939182 573939304 5.470000e-44 189.0
25 TraesCS6D01G205200 chr7B 94.309 123 7 0 3598 3720 573954821 573954943 5.470000e-44 189.0
26 TraesCS6D01G205200 chr3B 93.600 125 8 0 3592 3716 98078000 98078124 1.970000e-43 187.0
27 TraesCS6D01G205200 chr3B 92.366 131 10 0 3599 3729 792568671 792568541 1.970000e-43 187.0
28 TraesCS6D01G205200 chr3B 86.957 69 7 2 3714 3781 111853498 111853565 4.440000e-10 76.8
29 TraesCS6D01G205200 chr4B 91.111 135 10 2 3583 3716 9944327 9944460 9.150000e-42 182.0
30 TraesCS6D01G205200 chr4B 84.091 132 18 3 405 534 322674899 322675029 1.560000e-24 124.0
31 TraesCS6D01G205200 chr4B 88.350 103 4 4 2504 2600 20800600 20800500 2.620000e-22 117.0
32 TraesCS6D01G205200 chr4B 81.818 132 21 3 405 534 322746567 322746697 1.580000e-19 108.0
33 TraesCS6D01G205200 chr7D 94.186 86 4 1 2511 2596 234073672 234073756 3.360000e-26 130.0
34 TraesCS6D01G205200 chr7D 82.105 95 13 2 419 510 40773046 40773139 1.240000e-10 78.7
35 TraesCS6D01G205200 chr4A 81.287 171 20 6 368 534 342449470 342449632 1.210000e-25 128.0
36 TraesCS6D01G205200 chr4A 81.707 164 21 6 380 538 415862685 415862526 1.210000e-25 128.0
37 TraesCS6D01G205200 chr2B 93.103 87 4 2 2511 2597 794694550 794694466 4.350000e-25 126.0
38 TraesCS6D01G205200 chr2B 93.103 87 4 2 2511 2597 794803451 794803367 4.350000e-25 126.0
39 TraesCS6D01G205200 chr2B 84.416 77 8 4 5 79 571200411 571200337 5.750000e-09 73.1
40 TraesCS6D01G205200 chr2D 92.222 90 4 2 2506 2593 294473947 294474035 1.560000e-24 124.0
41 TraesCS6D01G205200 chr2D 89.216 102 3 6 2501 2597 643235814 643235912 2.020000e-23 121.0
42 TraesCS6D01G205200 chr5D 81.429 140 12 11 377 509 545398489 545398357 7.330000e-18 102.0
43 TraesCS6D01G205200 chr1A 89.744 78 3 4 6 81 581248521 581248447 1.230000e-15 95.3
44 TraesCS6D01G205200 chr3A 86.957 69 7 2 3714 3781 78190543 78190610 4.440000e-10 76.8
45 TraesCS6D01G205200 chr3D 86.957 69 6 3 3714 3781 67062930 67062996 1.600000e-09 75.0


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 TraesCS6D01G205200 chr6D 291148159 291152302 4143 True 3584.000000 7009 100.000000 1 4144 2 chr6D.!!$R1 4143
1 TraesCS6D01G205200 chr6A 432510555 432513889 3334 False 1210.750000 3031 95.619250 1 3556 4 chr6A.!!$F1 3555
2 TraesCS6D01G205200 chr6B 451924257 451927851 3594 False 817.166667 2883 92.706167 1 4144 6 chr6B.!!$F2 4143

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
613 619 0.323451 GACAGGCCTTCCGGGATTTT 60.323 55.000 0.00 0.0 37.23 1.82 F
1181 1212 0.173708 GAATCCAGAGGCGTCTTCGT 59.826 55.000 6.10 0.0 39.49 3.85 F
1662 1699 1.153647 CGGAGCTGCGTTATGGTGA 60.154 57.895 20.53 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 1518 0.179029 ACGTGCACCTTTAGTTGCCT 60.179 50.0 12.15 0.0 0.0 4.75 R
2852 2913 3.575805 GTCATCTTCCTCAGGATCCTCT 58.424 50.0 12.69 0.0 0.0 3.69 R
3603 3747 0.107848 AAGTATTTGCGGACGGAGGG 60.108 55.0 0.00 0.0 0.0 4.30 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
72 73 7.064134 ACACACGATGTAACCTATGTTAACATG 59.936 37.037 27.62 16.05 40.88 3.21
389 390 1.673993 TGGCCGGTGTGCAGTATTG 60.674 57.895 1.90 0.00 0.00 1.90
412 413 0.822164 CGGTATCAACGGGGAGAAGT 59.178 55.000 0.00 0.00 0.00 3.01
414 415 1.653151 GTATCAACGGGGAGAAGTGC 58.347 55.000 0.00 0.00 0.00 4.40
468 469 6.664515 TGTTCGATGAACCTCATTAACAAAC 58.335 36.000 7.18 5.51 41.35 2.93
476 482 4.479158 ACCTCATTAACAAACCATGGTGT 58.521 39.130 20.60 10.88 0.00 4.16
478 484 4.379394 CCTCATTAACAAACCATGGTGTCG 60.379 45.833 20.60 12.45 0.00 4.35
520 526 4.948004 TCGGTAGATCGATATGCACCTTAT 59.052 41.667 10.30 0.00 33.92 1.73
538 544 9.338622 GCACCTTATATTAGTTCTAACACCATT 57.661 33.333 0.00 0.00 0.00 3.16
553 559 3.181480 ACACCATTTCTTGTTTCGTTGGG 60.181 43.478 0.00 0.00 0.00 4.12
612 618 1.303282 GACAGGCCTTCCGGGATTT 59.697 57.895 0.00 0.00 37.23 2.17
613 619 0.323451 GACAGGCCTTCCGGGATTTT 60.323 55.000 0.00 0.00 37.23 1.82
616 622 1.956477 CAGGCCTTCCGGGATTTTATG 59.044 52.381 0.00 0.00 37.23 1.90
668 675 3.207778 TCGACTGGATTTCGTGGTTTTT 58.792 40.909 0.00 0.00 37.73 1.94
751 762 7.709947 ACATATAGTGGAACAGATTTTGCATG 58.290 34.615 0.00 0.00 41.80 4.06
822 835 1.405121 GGTAAACACAGGGCGGTCTAG 60.405 57.143 0.00 0.00 0.00 2.43
942 970 3.113745 GCCGGTAGCAGCGTAGTA 58.886 61.111 1.90 0.00 42.97 1.82
943 971 1.008767 GCCGGTAGCAGCGTAGTAG 60.009 63.158 1.90 0.00 42.97 2.57
944 972 1.442526 GCCGGTAGCAGCGTAGTAGA 61.443 60.000 1.90 0.00 42.97 2.59
945 973 0.587285 CCGGTAGCAGCGTAGTAGAG 59.413 60.000 0.00 0.00 37.40 2.43
946 974 1.297664 CGGTAGCAGCGTAGTAGAGT 58.702 55.000 0.00 0.00 33.95 3.24
947 975 2.477825 CGGTAGCAGCGTAGTAGAGTA 58.522 52.381 0.00 0.00 33.95 2.59
975 1003 1.278637 GCAACTCGACCAAACCACG 59.721 57.895 0.00 0.00 0.00 4.94
977 1005 2.241880 AACTCGACCAAACCACGCG 61.242 57.895 3.53 3.53 0.00 6.01
978 1006 2.355363 CTCGACCAAACCACGCGA 60.355 61.111 15.93 0.00 0.00 5.87
979 1007 1.952133 CTCGACCAAACCACGCGAA 60.952 57.895 15.93 0.00 0.00 4.70
1181 1212 0.173708 GAATCCAGAGGCGTCTTCGT 59.826 55.000 6.10 0.00 39.49 3.85
1411 1442 5.910614 AGTTTACTACACCCGGATTATGAC 58.089 41.667 0.73 0.00 0.00 3.06
1422 1453 4.746611 CCCGGATTATGACGTTTTAGGTAC 59.253 45.833 0.73 0.00 0.00 3.34
1424 1455 6.239008 CCCGGATTATGACGTTTTAGGTACTA 60.239 42.308 0.73 0.00 41.75 1.82
1487 1518 5.200483 ACCTGAGTTCTTTTGATTGGACAA 58.800 37.500 0.00 0.00 0.00 3.18
1564 1601 6.318913 AGTATAGTGGCATCCTAGTCTCATT 58.681 40.000 0.00 0.00 0.00 2.57
1596 1633 6.674760 GCGTATTTTAGAAGTGTTAGCTTGGG 60.675 42.308 0.00 0.00 0.00 4.12
1612 1649 9.623000 GTTAGCTTGGGGTTCTATTTAAAGATA 57.377 33.333 0.00 0.00 0.00 1.98
1662 1699 1.153647 CGGAGCTGCGTTATGGTGA 60.154 57.895 20.53 0.00 0.00 4.02
1792 1831 9.102757 CTCTTGCACTGAAACAATATGTATAGT 57.897 33.333 0.00 0.00 0.00 2.12
1822 1861 4.277672 GGTAAGACACTTTGAAGGTTTCCC 59.722 45.833 0.00 0.00 0.00 3.97
1842 1881 2.093447 CCCCTAGGTTAGAGTTGTGCAG 60.093 54.545 8.29 0.00 0.00 4.41
1858 1897 1.202758 TGCAGACCGAGGTTCAAATGT 60.203 47.619 0.00 0.00 0.00 2.71
1886 1925 3.628032 TCGTCCCAAAATAAATATGCGCA 59.372 39.130 14.96 14.96 0.00 6.09
1933 1972 9.790389 AGTCGTGTTTGTATTTAAAACAATCAA 57.210 25.926 18.22 8.18 46.11 2.57
1961 2000 7.011382 AGTAGATATTTAGGGATCAGACGGTT 58.989 38.462 0.00 0.00 0.00 4.44
2298 2351 2.813754 CCATTCCGTGACTGTTGAATGT 59.186 45.455 15.55 0.00 41.44 2.71
2544 2602 7.439056 CCCCGTAAAGAAATATAAGAGCGTTTA 59.561 37.037 0.00 0.00 0.00 2.01
2545 2603 8.485591 CCCGTAAAGAAATATAAGAGCGTTTAG 58.514 37.037 0.00 0.00 0.00 1.85
2546 2604 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
2559 2617 7.811117 AGAGCGTTTAGATCACTAGTTATCT 57.189 36.000 20.50 20.50 37.82 1.98
2560 2618 8.905660 AGAGCGTTTAGATCACTAGTTATCTA 57.094 34.615 18.73 18.73 37.82 1.98
2561 2619 9.339850 AGAGCGTTTAGATCACTAGTTATCTAA 57.660 33.333 25.56 25.56 40.96 2.10
2562 2620 9.947669 GAGCGTTTAGATCACTAGTTATCTAAA 57.052 33.333 30.85 30.85 45.59 1.85
2567 2625 9.947669 TTTAGATCACTAGTTATCTAAACGCTC 57.052 33.333 30.85 7.25 44.14 5.03
2568 2626 7.811117 AGATCACTAGTTATCTAAACGCTCT 57.189 36.000 16.35 0.00 30.65 4.09
2569 2627 8.228035 AGATCACTAGTTATCTAAACGCTCTT 57.772 34.615 16.35 0.00 30.65 2.85
2570 2628 9.339850 AGATCACTAGTTATCTAAACGCTCTTA 57.660 33.333 16.35 0.00 30.65 2.10
2647 2708 3.088532 TCTTTTGTGTTGGCACTGAAGT 58.911 40.909 0.00 0.00 45.44 3.01
2981 3042 7.121315 GGGTTTGAGCTATTCAGAAATGTTAGT 59.879 37.037 0.00 0.00 37.07 2.24
3136 3197 6.040247 CCTATACGACACAATAAGCTGTTGA 58.960 40.000 16.47 0.00 0.00 3.18
3156 3217 8.669946 TGTTGAATGTTCAGTAGTTATGTTCA 57.330 30.769 0.00 0.00 38.61 3.18
3173 3234 6.550938 ATGTTCACTGATCTGATACTCCAA 57.449 37.500 6.60 0.00 0.00 3.53
3260 3321 8.784043 AGTTAGAATGACACATTGGTTAAACTC 58.216 33.333 1.64 0.00 0.00 3.01
3311 3455 9.626045 AAATTATTTGAAGTTCTAGCTTTTCCG 57.374 29.630 4.17 0.00 0.00 4.30
3328 3472 9.059260 AGCTTTTCCGTAAGTCAAATTTAGTTA 57.941 29.630 0.00 0.00 0.00 2.24
3376 3520 5.525745 TCTCTGTTTGTGTTCTTAAATCGCA 59.474 36.000 0.00 0.00 0.00 5.10
3390 3534 4.395959 AAATCGCAAATTGGATGATGCT 57.604 36.364 0.00 0.00 36.67 3.79
3426 3570 9.683069 AAGTATGAACACATCTCATTTTCAAAC 57.317 29.630 0.00 0.00 35.21 2.93
3502 3646 9.489084 CAATGATATTTTTATAGACTCGGTCCA 57.511 33.333 1.06 0.00 32.18 4.02
3568 3712 5.887214 ATTTGAAACTAAGGCCCTGTTTT 57.113 34.783 16.16 5.06 34.55 2.43
3595 3739 5.865085 TGAGTGTAAAATTAGTGTGCTCCT 58.135 37.500 0.00 0.00 0.00 3.69
3597 3741 5.865085 AGTGTAAAATTAGTGTGCTCCTCA 58.135 37.500 0.00 0.00 0.00 3.86
3598 3742 5.934625 AGTGTAAAATTAGTGTGCTCCTCAG 59.065 40.000 0.00 0.00 0.00 3.35
3599 3743 5.701290 GTGTAAAATTAGTGTGCTCCTCAGT 59.299 40.000 0.00 0.00 0.00 3.41
3600 3744 6.872020 GTGTAAAATTAGTGTGCTCCTCAGTA 59.128 38.462 0.00 0.00 0.00 2.74
3601 3745 6.872020 TGTAAAATTAGTGTGCTCCTCAGTAC 59.128 38.462 0.00 0.00 35.86 2.73
3602 3746 5.746990 AAATTAGTGTGCTCCTCAGTACT 57.253 39.130 0.00 0.00 36.27 2.73
3603 3747 4.993029 ATTAGTGTGCTCCTCAGTACTC 57.007 45.455 0.00 0.00 36.27 2.59
3604 3748 1.551452 AGTGTGCTCCTCAGTACTCC 58.449 55.000 0.00 0.00 36.27 3.85
3605 3749 0.533032 GTGTGCTCCTCAGTACTCCC 59.467 60.000 0.00 0.00 36.27 4.30
3606 3750 0.409876 TGTGCTCCTCAGTACTCCCT 59.590 55.000 0.00 0.00 36.27 4.20
3607 3751 1.107945 GTGCTCCTCAGTACTCCCTC 58.892 60.000 0.00 0.00 32.68 4.30
3608 3752 0.033011 TGCTCCTCAGTACTCCCTCC 60.033 60.000 0.00 0.00 0.00 4.30
3609 3753 1.104577 GCTCCTCAGTACTCCCTCCG 61.105 65.000 0.00 0.00 0.00 4.63
3610 3754 0.256464 CTCCTCAGTACTCCCTCCGT 59.744 60.000 0.00 0.00 0.00 4.69
3611 3755 0.255318 TCCTCAGTACTCCCTCCGTC 59.745 60.000 0.00 0.00 0.00 4.79
3612 3756 0.752376 CCTCAGTACTCCCTCCGTCC 60.752 65.000 0.00 0.00 0.00 4.79
3613 3757 1.077930 TCAGTACTCCCTCCGTCCG 60.078 63.158 0.00 0.00 0.00 4.79
3614 3758 2.439883 AGTACTCCCTCCGTCCGC 60.440 66.667 0.00 0.00 0.00 5.54
3615 3759 2.753043 GTACTCCCTCCGTCCGCA 60.753 66.667 0.00 0.00 0.00 5.69
3616 3760 2.036098 TACTCCCTCCGTCCGCAA 59.964 61.111 0.00 0.00 0.00 4.85
3617 3761 1.607178 TACTCCCTCCGTCCGCAAA 60.607 57.895 0.00 0.00 0.00 3.68
3618 3762 0.974010 TACTCCCTCCGTCCGCAAAT 60.974 55.000 0.00 0.00 0.00 2.32
3619 3763 0.974010 ACTCCCTCCGTCCGCAAATA 60.974 55.000 0.00 0.00 0.00 1.40
3620 3764 0.529992 CTCCCTCCGTCCGCAAATAC 60.530 60.000 0.00 0.00 0.00 1.89
3621 3765 0.974010 TCCCTCCGTCCGCAAATACT 60.974 55.000 0.00 0.00 0.00 2.12
3622 3766 0.107848 CCCTCCGTCCGCAAATACTT 60.108 55.000 0.00 0.00 0.00 2.24
3623 3767 1.006832 CCTCCGTCCGCAAATACTTG 58.993 55.000 0.00 0.00 35.49 3.16
3624 3768 1.674817 CCTCCGTCCGCAAATACTTGT 60.675 52.381 0.00 0.00 34.79 3.16
3625 3769 1.659098 CTCCGTCCGCAAATACTTGTC 59.341 52.381 0.00 0.00 34.79 3.18
3626 3770 1.001068 TCCGTCCGCAAATACTTGTCA 59.999 47.619 0.00 0.00 34.79 3.58
3627 3771 2.006888 CCGTCCGCAAATACTTGTCAT 58.993 47.619 0.00 0.00 34.79 3.06
3628 3772 2.030457 CCGTCCGCAAATACTTGTCATC 59.970 50.000 0.00 0.00 34.79 2.92
3629 3773 2.670905 CGTCCGCAAATACTTGTCATCA 59.329 45.455 0.00 0.00 34.79 3.07
3630 3774 3.124466 CGTCCGCAAATACTTGTCATCAA 59.876 43.478 0.00 0.00 34.79 2.57
3631 3775 4.377943 CGTCCGCAAATACTTGTCATCAAA 60.378 41.667 0.00 0.00 34.79 2.69
3632 3776 5.457140 GTCCGCAAATACTTGTCATCAAAA 58.543 37.500 0.00 0.00 34.79 2.44
3633 3777 6.092748 GTCCGCAAATACTTGTCATCAAAAT 58.907 36.000 0.00 0.00 34.79 1.82
3634 3778 6.033831 GTCCGCAAATACTTGTCATCAAAATG 59.966 38.462 0.00 0.00 34.79 2.32
3635 3779 6.072230 TCCGCAAATACTTGTCATCAAAATGA 60.072 34.615 0.00 0.00 34.91 2.57
3636 3780 6.585702 CCGCAAATACTTGTCATCAAAATGAA 59.414 34.615 0.00 0.00 43.42 2.57
3637 3781 7.276218 CCGCAAATACTTGTCATCAAAATGAAT 59.724 33.333 0.00 0.00 43.42 2.57
3638 3782 8.105742 CGCAAATACTTGTCATCAAAATGAATG 58.894 33.333 0.00 0.00 43.42 2.67
3639 3783 9.142515 GCAAATACTTGTCATCAAAATGAATGA 57.857 29.630 0.00 0.00 43.42 2.57
3645 3789 8.995220 ACTTGTCATCAAAATGAATGAAAATGG 58.005 29.630 0.00 0.00 43.42 3.16
3646 3790 9.210329 CTTGTCATCAAAATGAATGAAAATGGA 57.790 29.630 0.00 0.00 43.42 3.41
3647 3791 9.727859 TTGTCATCAAAATGAATGAAAATGGAT 57.272 25.926 0.00 0.00 43.42 3.41
3648 3792 9.157104 TGTCATCAAAATGAATGAAAATGGATG 57.843 29.630 0.00 0.00 43.42 3.51
3649 3793 9.158233 GTCATCAAAATGAATGAAAATGGATGT 57.842 29.630 0.00 0.00 43.42 3.06
3659 3803 9.685276 TGAATGAAAATGGATGTATCTACAACT 57.315 29.630 0.00 0.00 39.99 3.16
3708 3852 8.945481 TTTAATGATAAGTATTTTCGGACGGA 57.055 30.769 0.00 0.00 0.00 4.69
3709 3853 8.583810 TTAATGATAAGTATTTTCGGACGGAG 57.416 34.615 0.00 0.00 0.00 4.63
3710 3854 4.940463 TGATAAGTATTTTCGGACGGAGG 58.060 43.478 0.00 0.00 0.00 4.30
3711 3855 2.685850 AAGTATTTTCGGACGGAGGG 57.314 50.000 0.00 0.00 0.00 4.30
3743 3887 6.796705 ACTCAAGTTTGAACTAAATACCGG 57.203 37.500 0.00 0.00 38.57 5.28
3744 3888 5.704053 ACTCAAGTTTGAACTAAATACCGGG 59.296 40.000 6.32 0.00 38.57 5.73
3745 3889 4.456566 TCAAGTTTGAACTAAATACCGGGC 59.543 41.667 6.32 0.00 38.57 6.13
3746 3890 4.023726 AGTTTGAACTAAATACCGGGCA 57.976 40.909 6.32 0.00 37.52 5.36
3747 3891 4.007659 AGTTTGAACTAAATACCGGGCAG 58.992 43.478 6.32 0.00 37.52 4.85
3748 3892 2.032680 TGAACTAAATACCGGGCAGC 57.967 50.000 6.32 0.00 0.00 5.25
3749 3893 1.279558 TGAACTAAATACCGGGCAGCA 59.720 47.619 6.32 0.00 0.00 4.41
3750 3894 1.669265 GAACTAAATACCGGGCAGCAC 59.331 52.381 6.32 0.00 0.00 4.40
3751 3895 0.461339 ACTAAATACCGGGCAGCACG 60.461 55.000 11.11 11.11 0.00 5.34
3805 3949 6.332630 CAAAGAGGGTAATATTTTGCACCAG 58.667 40.000 7.30 0.00 32.42 4.00
3877 4021 3.119352 GCATTTTGGAGCCTGGTTTCTAG 60.119 47.826 0.00 0.00 0.00 2.43
3878 4022 3.876309 TTTTGGAGCCTGGTTTCTAGT 57.124 42.857 0.00 0.00 0.00 2.57
3879 4023 2.859165 TTGGAGCCTGGTTTCTAGTG 57.141 50.000 0.00 0.00 0.00 2.74
3881 4025 1.902508 TGGAGCCTGGTTTCTAGTGAG 59.097 52.381 0.00 0.00 0.00 3.51
3882 4026 2.180276 GGAGCCTGGTTTCTAGTGAGA 58.820 52.381 0.00 0.00 0.00 3.27
3883 4027 2.093921 GGAGCCTGGTTTCTAGTGAGAC 60.094 54.545 0.00 0.00 0.00 3.36
3884 4028 2.563179 GAGCCTGGTTTCTAGTGAGACA 59.437 50.000 0.00 0.00 0.00 3.41
3886 4030 3.584848 AGCCTGGTTTCTAGTGAGACAAT 59.415 43.478 0.00 0.00 0.00 2.71
3887 4031 4.777896 AGCCTGGTTTCTAGTGAGACAATA 59.222 41.667 0.00 0.00 0.00 1.90
3889 4033 6.611642 AGCCTGGTTTCTAGTGAGACAATATA 59.388 38.462 0.00 0.00 0.00 0.86
3891 4035 7.934120 GCCTGGTTTCTAGTGAGACAATATATT 59.066 37.037 0.00 0.00 0.00 1.28
3892 4036 9.838339 CCTGGTTTCTAGTGAGACAATATATTT 57.162 33.333 0.00 0.00 0.00 1.40
3997 4141 5.690097 GCTGTGGACCCTATATTTTGGATGA 60.690 44.000 0.00 0.00 0.00 2.92
4022 4167 2.492088 GGGGGCTGAAATCTTGTTGTAC 59.508 50.000 0.00 0.00 0.00 2.90
4037 4182 9.778741 ATCTTGTTGTACTCTATTTCAGACAAA 57.221 29.630 0.00 0.00 0.00 2.83
4038 4183 9.778741 TCTTGTTGTACTCTATTTCAGACAAAT 57.221 29.630 0.00 0.00 0.00 2.32
4041 4186 9.990360 TGTTGTACTCTATTTCAGACAAATACA 57.010 29.630 0.00 0.00 0.00 2.29
4047 4192 9.507329 ACTCTATTTCAGACAAATACATGTTGT 57.493 29.630 2.30 1.69 41.84 3.32
4052 4197 8.902540 TTTCAGACAAATACATGTTGTACTCT 57.097 30.769 2.30 0.00 39.29 3.24
4053 4198 9.990360 TTTCAGACAAATACATGTTGTACTCTA 57.010 29.630 2.30 0.00 39.29 2.43
4084 4229 0.108992 TACGGCGATGTGAACAGACC 60.109 55.000 16.62 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
389 390 2.895372 CCCCGTTGATACCGCTGC 60.895 66.667 0.00 0.00 0.00 5.25
390 391 1.227263 CTCCCCGTTGATACCGCTG 60.227 63.158 0.00 0.00 0.00 5.18
414 415 0.838122 CCCTAGGGCCTGACTATGGG 60.838 65.000 16.90 13.43 0.00 4.00
468 469 1.197492 CAATCACACACGACACCATGG 59.803 52.381 11.19 11.19 0.00 3.66
476 482 3.925379 AGTATCAAGCAATCACACACGA 58.075 40.909 0.00 0.00 0.00 4.35
478 484 3.062639 CCGAGTATCAAGCAATCACACAC 59.937 47.826 0.00 0.00 33.17 3.82
538 544 0.741915 GCACCCCAACGAAACAAGAA 59.258 50.000 0.00 0.00 0.00 2.52
539 545 0.106918 AGCACCCCAACGAAACAAGA 60.107 50.000 0.00 0.00 0.00 3.02
553 559 1.731720 CTCCACTAGAGCAAAGCACC 58.268 55.000 0.00 0.00 35.31 5.01
612 618 3.688235 CACCGGAAACCTAAACCCATAA 58.312 45.455 9.46 0.00 0.00 1.90
613 619 2.618559 GCACCGGAAACCTAAACCCATA 60.619 50.000 9.46 0.00 0.00 2.74
616 622 0.537828 TGCACCGGAAACCTAAACCC 60.538 55.000 9.46 0.00 0.00 4.11
668 675 8.568794 CATCGATAAGGACATGTAGAAACTCTA 58.431 37.037 0.00 0.00 0.00 2.43
702 709 6.662865 AGACCAGTATATTGTCATCTCCTG 57.337 41.667 0.00 0.00 0.00 3.86
703 710 7.298374 TGTAGACCAGTATATTGTCATCTCCT 58.702 38.462 0.00 0.00 0.00 3.69
718 729 6.432581 TCTGTTCCACTATATGTAGACCAGT 58.567 40.000 3.17 0.00 0.00 4.00
802 815 0.609662 TAGACCGCCCTGTGTTTACC 59.390 55.000 0.00 0.00 0.00 2.85
822 835 4.325741 GCATGGCCAAAAACAAAACAAAAC 59.674 37.500 10.96 0.00 0.00 2.43
939 967 1.165284 GCGGCGCCTACTACTCTACT 61.165 60.000 26.68 0.00 0.00 2.57
940 968 1.282265 GCGGCGCCTACTACTCTAC 59.718 63.158 26.68 0.00 0.00 2.59
941 969 0.749091 TTGCGGCGCCTACTACTCTA 60.749 55.000 30.82 2.71 0.00 2.43
942 970 2.050350 TTGCGGCGCCTACTACTCT 61.050 57.895 30.82 0.00 0.00 3.24
943 971 1.877165 GTTGCGGCGCCTACTACTC 60.877 63.158 30.82 6.68 0.00 2.59
944 972 2.183555 GTTGCGGCGCCTACTACT 59.816 61.111 30.82 0.00 0.00 2.57
945 973 1.877165 GAGTTGCGGCGCCTACTAC 60.877 63.158 30.82 21.75 0.00 2.73
946 974 2.493030 GAGTTGCGGCGCCTACTA 59.507 61.111 30.82 10.75 0.00 1.82
947 975 4.796231 CGAGTTGCGGCGCCTACT 62.796 66.667 28.87 28.87 36.03 2.57
1242 1273 4.377760 TTCTCCTCGTCGGGGGCT 62.378 66.667 12.24 0.00 32.36 5.19
1378 1409 6.427547 CCGGGTGTAGTAAACTAAAATGACAA 59.572 38.462 0.00 0.00 0.00 3.18
1379 1410 5.933463 CCGGGTGTAGTAAACTAAAATGACA 59.067 40.000 0.00 0.00 0.00 3.58
1390 1421 4.402155 ACGTCATAATCCGGGTGTAGTAAA 59.598 41.667 0.00 0.00 0.00 2.01
1411 1442 6.860080 TCATCCACTCTTAGTACCTAAAACG 58.140 40.000 0.00 0.00 0.00 3.60
1422 1453 7.353414 TCCTACTGATTTCATCCACTCTTAG 57.647 40.000 0.00 0.00 0.00 2.18
1424 1455 6.627087 TTCCTACTGATTTCATCCACTCTT 57.373 37.500 0.00 0.00 0.00 2.85
1487 1518 0.179029 ACGTGCACCTTTAGTTGCCT 60.179 50.000 12.15 0.00 0.00 4.75
1495 1526 2.333014 CACAAACAAACGTGCACCTTT 58.667 42.857 12.15 9.71 0.00 3.11
1496 1527 1.989430 CACAAACAAACGTGCACCTT 58.011 45.000 12.15 2.80 0.00 3.50
1564 1601 6.854496 ACACTTCTAAAATACGCAAGAACA 57.146 33.333 0.00 0.00 43.62 3.18
1676 1713 3.181397 CGCTCCTAAAATGCAACAATGG 58.819 45.455 0.00 0.00 0.00 3.16
1792 1831 5.995282 CCTTCAAAGTGTCTTACCATACACA 59.005 40.000 8.18 0.00 46.71 3.72
1822 1861 2.832129 TCTGCACAACTCTAACCTAGGG 59.168 50.000 14.81 0.00 0.00 3.53
1842 1881 4.561735 TTTTGACATTTGAACCTCGGTC 57.438 40.909 0.00 0.00 0.00 4.79
1858 1897 7.433719 CGCATATTTATTTTGGGACGATTTTGA 59.566 33.333 0.00 0.00 0.00 2.69
1886 1925 4.008330 CTCAAGACAAGCATTCAGTGGAT 58.992 43.478 0.00 0.00 0.00 3.41
1933 1972 7.039644 CCGTCTGATCCCTAAATATCTACTGTT 60.040 40.741 0.00 0.00 0.00 3.16
2298 2351 5.164620 TGTCTCAAAATATGCAGGAGTCA 57.835 39.130 0.00 0.00 0.00 3.41
2544 2602 7.811117 AGAGCGTTTAGATAACTAGTGATCT 57.189 36.000 23.66 23.66 36.40 2.75
2560 2618 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
2561 2619 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
2562 2620 7.147707 ACCCTCTGTAAAGAAATATAAGAGCGT 60.148 37.037 0.00 0.00 0.00 5.07
2563 2621 7.169982 CACCCTCTGTAAAGAAATATAAGAGCG 59.830 40.741 0.00 0.00 0.00 5.03
2564 2622 7.988028 ACACCCTCTGTAAAGAAATATAAGAGC 59.012 37.037 0.00 0.00 0.00 4.09
2620 2681 3.843999 GTGCCAACACAAAAGAAGAACA 58.156 40.909 0.00 0.00 46.61 3.18
2647 2708 5.221621 TGTGTGATAAGACAGTGACCATCAA 60.222 40.000 0.00 0.00 0.00 2.57
2852 2913 3.575805 GTCATCTTCCTCAGGATCCTCT 58.424 50.000 12.69 0.00 0.00 3.69
2981 3042 4.344102 AGAGCCTATATAAGCCGACACAAA 59.656 41.667 0.00 0.00 0.00 2.83
3156 3217 4.408270 AGCACATTGGAGTATCAGATCAGT 59.592 41.667 0.00 0.00 36.25 3.41
3173 3234 5.125900 TGCTTATAATGCACTTTCAGCACAT 59.874 36.000 7.45 0.00 45.95 3.21
3232 3293 8.564574 GTTTAACCAATGTGTCATTCTAACTGA 58.435 33.333 0.00 0.00 0.00 3.41
3260 3321 7.416817 TGAAATGGAGTATATCAAAATGCACG 58.583 34.615 0.00 0.00 0.00 5.34
3328 3472 5.719085 AGATACTGACCTTTCTCACATCTGT 59.281 40.000 0.00 0.00 0.00 3.41
3502 3646 8.635765 TGTCCTAAATCAAACATTCTTAAGCT 57.364 30.769 0.00 0.00 0.00 3.74
3568 3712 7.094805 GGAGCACACTAATTTTACACTCAATCA 60.095 37.037 0.00 0.00 0.00 2.57
3588 3732 1.107945 GAGGGAGTACTGAGGAGCAC 58.892 60.000 0.00 0.00 0.00 4.40
3595 3739 1.077930 CGGACGGAGGGAGTACTGA 60.078 63.158 0.00 0.00 0.00 3.41
3597 3741 2.439883 GCGGACGGAGGGAGTACT 60.440 66.667 0.00 0.00 0.00 2.73
3598 3742 1.880819 TTTGCGGACGGAGGGAGTAC 61.881 60.000 0.00 0.00 0.00 2.73
3599 3743 0.974010 ATTTGCGGACGGAGGGAGTA 60.974 55.000 0.00 0.00 0.00 2.59
3600 3744 0.974010 TATTTGCGGACGGAGGGAGT 60.974 55.000 0.00 0.00 0.00 3.85
3601 3745 0.529992 GTATTTGCGGACGGAGGGAG 60.530 60.000 0.00 0.00 0.00 4.30
3602 3746 0.974010 AGTATTTGCGGACGGAGGGA 60.974 55.000 0.00 0.00 0.00 4.20
3603 3747 0.107848 AAGTATTTGCGGACGGAGGG 60.108 55.000 0.00 0.00 0.00 4.30
3604 3748 1.006832 CAAGTATTTGCGGACGGAGG 58.993 55.000 0.00 0.00 0.00 4.30
3605 3749 1.659098 GACAAGTATTTGCGGACGGAG 59.341 52.381 0.00 0.00 37.85 4.63
3606 3750 1.001068 TGACAAGTATTTGCGGACGGA 59.999 47.619 0.00 0.00 37.85 4.69
3607 3751 1.434555 TGACAAGTATTTGCGGACGG 58.565 50.000 0.00 0.00 37.85 4.79
3608 3752 2.670905 TGATGACAAGTATTTGCGGACG 59.329 45.455 0.00 0.00 37.85 4.79
3609 3753 4.678509 TTGATGACAAGTATTTGCGGAC 57.321 40.909 0.00 0.00 37.85 4.79
3610 3754 5.697473 TTTTGATGACAAGTATTTGCGGA 57.303 34.783 0.00 0.00 37.85 5.54
3611 3755 6.092092 TCATTTTGATGACAAGTATTTGCGG 58.908 36.000 0.00 0.00 37.85 5.69
3612 3756 7.565450 TTCATTTTGATGACAAGTATTTGCG 57.435 32.000 0.00 0.00 37.85 4.85
3613 3757 9.142515 TCATTCATTTTGATGACAAGTATTTGC 57.857 29.630 0.00 0.00 37.85 3.68
3619 3763 8.995220 CCATTTTCATTCATTTTGATGACAAGT 58.005 29.630 0.00 0.00 37.32 3.16
3620 3764 9.210329 TCCATTTTCATTCATTTTGATGACAAG 57.790 29.630 0.00 0.00 37.32 3.16
3621 3765 9.727859 ATCCATTTTCATTCATTTTGATGACAA 57.272 25.926 0.00 0.00 0.00 3.18
3622 3766 9.157104 CATCCATTTTCATTCATTTTGATGACA 57.843 29.630 0.00 0.00 0.00 3.58
3623 3767 9.158233 ACATCCATTTTCATTCATTTTGATGAC 57.842 29.630 0.00 0.00 32.39 3.06
3633 3777 9.685276 AGTTGTAGATACATCCATTTTCATTCA 57.315 29.630 0.00 0.00 35.89 2.57
3682 3826 9.381033 TCCGTCCGAAAATACTTATCATTAAAA 57.619 29.630 0.00 0.00 0.00 1.52
3683 3827 8.945481 TCCGTCCGAAAATACTTATCATTAAA 57.055 30.769 0.00 0.00 0.00 1.52
3684 3828 7.654520 CCTCCGTCCGAAAATACTTATCATTAA 59.345 37.037 0.00 0.00 0.00 1.40
3685 3829 7.149973 CCTCCGTCCGAAAATACTTATCATTA 58.850 38.462 0.00 0.00 0.00 1.90
3686 3830 5.989777 CCTCCGTCCGAAAATACTTATCATT 59.010 40.000 0.00 0.00 0.00 2.57
3687 3831 5.510861 CCCTCCGTCCGAAAATACTTATCAT 60.511 44.000 0.00 0.00 0.00 2.45
3688 3832 4.202182 CCCTCCGTCCGAAAATACTTATCA 60.202 45.833 0.00 0.00 0.00 2.15
3689 3833 4.038402 TCCCTCCGTCCGAAAATACTTATC 59.962 45.833 0.00 0.00 0.00 1.75
3690 3834 3.962718 TCCCTCCGTCCGAAAATACTTAT 59.037 43.478 0.00 0.00 0.00 1.73
3691 3835 3.364549 TCCCTCCGTCCGAAAATACTTA 58.635 45.455 0.00 0.00 0.00 2.24
3692 3836 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
3693 3837 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
3694 3838 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
3695 3839 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
3696 3840 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
3697 3841 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
3698 3842 1.856629 AATACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
3699 3843 1.856629 AAATACTCCCTCCGTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
3700 3844 2.689983 GTTAAATACTCCCTCCGTCCGA 59.310 50.000 0.00 0.00 0.00 4.55
3701 3845 2.692041 AGTTAAATACTCCCTCCGTCCG 59.308 50.000 0.00 0.00 28.23 4.79
3702 3846 4.319139 GAGTTAAATACTCCCTCCGTCC 57.681 50.000 0.00 0.00 46.30 4.79
3709 3853 9.498176 TAGTTCAAACTTGAGTTAAATACTCCC 57.502 33.333 0.00 0.00 44.65 4.30
3741 3885 4.320928 TTTTTCGCGTGCTGCCCG 62.321 61.111 5.77 0.00 42.08 6.13
3762 3906 1.643286 TGGCCCTGTTTGGATTGGATA 59.357 47.619 0.00 0.00 38.35 2.59
3805 3949 0.103937 AGAGGCTATTGTCTCAGCGC 59.896 55.000 11.34 0.00 46.70 5.92
3854 3998 1.344114 GAAACCAGGCTCCAAAATGCA 59.656 47.619 0.00 0.00 0.00 3.96
3946 4090 9.750125 CACTATAATCAAGTAATAGCTGTGTCA 57.250 33.333 0.00 0.00 0.00 3.58
4038 4183 9.990360 TTTGTCTGAAATAGAGTACAACATGTA 57.010 29.630 0.00 0.00 35.70 2.29
4039 4184 8.902540 TTTGTCTGAAATAGAGTACAACATGT 57.097 30.769 0.00 0.00 35.70 3.21
4042 4187 9.135843 CGTATTTGTCTGAAATAGAGTACAACA 57.864 33.333 0.00 0.00 35.70 3.33
4043 4188 8.592998 CCGTATTTGTCTGAAATAGAGTACAAC 58.407 37.037 0.00 0.00 35.70 3.32
4044 4189 7.277098 GCCGTATTTGTCTGAAATAGAGTACAA 59.723 37.037 0.00 0.00 35.70 2.41
4045 4190 6.755141 GCCGTATTTGTCTGAAATAGAGTACA 59.245 38.462 0.00 0.00 35.70 2.90
4046 4191 6.074994 CGCCGTATTTGTCTGAAATAGAGTAC 60.075 42.308 0.00 0.00 35.70 2.73
4047 4192 5.975344 CGCCGTATTTGTCTGAAATAGAGTA 59.025 40.000 0.00 0.00 35.70 2.59
4048 4193 4.804139 CGCCGTATTTGTCTGAAATAGAGT 59.196 41.667 0.00 0.00 35.70 3.24
4049 4194 5.041287 TCGCCGTATTTGTCTGAAATAGAG 58.959 41.667 0.00 0.00 35.70 2.43
4050 4195 5.001237 TCGCCGTATTTGTCTGAAATAGA 57.999 39.130 0.00 0.00 0.00 1.98
4051 4196 5.234329 ACATCGCCGTATTTGTCTGAAATAG 59.766 40.000 0.00 0.00 0.00 1.73
4052 4197 5.006261 CACATCGCCGTATTTGTCTGAAATA 59.994 40.000 0.00 0.00 0.00 1.40
4053 4198 3.938963 ACATCGCCGTATTTGTCTGAAAT 59.061 39.130 0.00 0.00 0.00 2.17
4054 4199 3.124466 CACATCGCCGTATTTGTCTGAAA 59.876 43.478 0.00 0.00 0.00 2.69
4055 4200 2.670905 CACATCGCCGTATTTGTCTGAA 59.329 45.455 0.00 0.00 0.00 3.02
4056 4201 2.094442 TCACATCGCCGTATTTGTCTGA 60.094 45.455 0.00 0.00 0.00 3.27
4057 4202 2.267426 TCACATCGCCGTATTTGTCTG 58.733 47.619 0.00 0.00 0.00 3.51
4058 4203 2.665649 TCACATCGCCGTATTTGTCT 57.334 45.000 0.00 0.00 0.00 3.41
4059 4204 2.413796 TGTTCACATCGCCGTATTTGTC 59.586 45.455 0.00 0.00 0.00 3.18
4060 4205 2.415168 CTGTTCACATCGCCGTATTTGT 59.585 45.455 0.00 0.00 0.00 2.83
4061 4206 2.670905 TCTGTTCACATCGCCGTATTTG 59.329 45.455 0.00 0.00 0.00 2.32
4062 4207 2.671396 GTCTGTTCACATCGCCGTATTT 59.329 45.455 0.00 0.00 0.00 1.40
4063 4208 2.268298 GTCTGTTCACATCGCCGTATT 58.732 47.619 0.00 0.00 0.00 1.89
4084 4229 3.308053 CAGCATCTCTGTACCATCGTTTG 59.692 47.826 0.00 0.00 38.02 2.93


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

AutoCloner maintained by Alex Coulton.