Multiple sequence alignment - TraesCS5D01G045200

Loading Multiple Alignment...

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 TraesCS5D01G045200 chr5D 100.000 4098 0 0 1 4098 44492993 44497090 0.000000e+00 7568.0
1 TraesCS5D01G045200 chr5D 81.316 760 126 14 2103 2854 3766507 3767258 1.630000e-168 603.0
2 TraesCS5D01G045200 chr5D 84.413 571 86 1 1192 1759 3765226 3765796 3.580000e-155 558.0
3 TraesCS5D01G045200 chr5D 85.549 173 23 2 1820 1991 3766293 3766464 3.250000e-41 180.0
4 TraesCS5D01G045200 chr5B 93.123 3839 159 40 1 3763 44226918 44223109 0.000000e+00 5529.0
5 TraesCS5D01G045200 chr5B 93.490 2258 114 17 1165 3393 43925270 43927523 0.000000e+00 3325.0
6 TraesCS5D01G045200 chr5B 94.102 1136 47 11 1 1127 43888307 43889431 0.000000e+00 1709.0
7 TraesCS5D01G045200 chr5B 100.000 28 0 0 3628 3655 409054778 409054751 7.000000e-03 52.8
8 TraesCS5D01G045200 chr5A 94.137 3019 128 21 779 3763 34908605 34911608 0.000000e+00 4549.0
9 TraesCS5D01G045200 chr5A 95.558 788 26 6 1 786 34907674 34908454 0.000000e+00 1253.0
10 TraesCS5D01G045200 chr5A 86.667 240 23 4 3864 4095 34911604 34911842 1.460000e-64 257.0
11 TraesCS5D01G045200 chr5A 96.460 113 4 0 3758 3870 362173235 362173347 1.940000e-43 187.0
12 TraesCS5D01G045200 chr2B 84.444 855 95 20 1167 1984 41865833 41864980 0.000000e+00 808.0
13 TraesCS5D01G045200 chr2B 84.073 766 95 18 2113 2855 41864900 41864139 0.000000e+00 713.0
14 TraesCS5D01G045200 chr2B 82.222 765 108 20 2113 2855 41848003 41847245 5.780000e-178 634.0
15 TraesCS5D01G045200 chr2D 88.380 611 68 1 1156 1763 26560180 26559570 0.000000e+00 732.0
16 TraesCS5D01G045200 chr2D 83.594 768 104 14 2113 2862 26559208 26558445 0.000000e+00 701.0
17 TraesCS5D01G045200 chr2D 100.000 28 0 0 3578 3605 247098478 247098451 7.000000e-03 52.8
18 TraesCS5D01G045200 chr2A 87.765 613 71 2 1155 1764 28809660 28809049 0.000000e+00 713.0
19 TraesCS5D01G045200 chr2A 83.528 771 103 16 2113 2862 28808722 28807955 0.000000e+00 699.0
20 TraesCS5D01G045200 chr2A 92.913 127 6 3 3746 3869 28208327 28208201 9.050000e-42 182.0
21 TraesCS5D01G045200 chrUn 80.731 602 96 11 1176 1758 87285401 87286001 6.250000e-123 451.0
22 TraesCS5D01G045200 chrUn 79.853 546 96 5 2117 2649 87283795 87283251 1.790000e-103 387.0
23 TraesCS5D01G045200 chrUn 100.000 28 0 0 3628 3655 101887456 101887429 7.000000e-03 52.8
24 TraesCS5D01G045200 chr7B 80.565 602 97 13 1176 1758 680269222 680268622 2.910000e-121 446.0
25 TraesCS5D01G045200 chr7A 97.297 111 3 0 3760 3870 133053229 133053339 5.410000e-44 189.0
26 TraesCS5D01G045200 chr4B 97.297 111 3 0 3760 3870 528805630 528805520 5.410000e-44 189.0
27 TraesCS5D01G045200 chr7D 95.000 120 5 1 3750 3869 21093598 21093716 1.940000e-43 187.0
28 TraesCS5D01G045200 chr4A 96.429 112 4 0 3759 3870 593739131 593739020 7.000000e-43 185.0
29 TraesCS5D01G045200 chr4A 93.443 122 7 1 3760 3881 594031546 594031426 3.250000e-41 180.0
30 TraesCS5D01G045200 chr6A 95.614 114 4 1 3756 3869 250834625 250834513 9.050000e-42 182.0
31 TraesCS5D01G045200 chr1D 94.167 120 6 1 3749 3867 247520946 247521065 9.050000e-42 182.0
32 TraesCS5D01G045200 chr3D 96.970 33 1 0 3621 3653 406691208 406691240 5.720000e-04 56.5
33 TraesCS5D01G045200 chr1A 100.000 28 0 0 3628 3655 558299883 558299856 7.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G045200 chr5D 44492993 44497090 4097 False 7568.000000 7568 100.000000 1 4098 1 chr5D.!!$F1 4097
1 TraesCS5D01G045200 chr5D 3765226 3767258 2032 False 447.000000 603 83.759333 1192 2854 3 chr5D.!!$F2 1662
2 TraesCS5D01G045200 chr5B 44223109 44226918 3809 True 5529.000000 5529 93.123000 1 3763 1 chr5B.!!$R1 3762
3 TraesCS5D01G045200 chr5B 43925270 43927523 2253 False 3325.000000 3325 93.490000 1165 3393 1 chr5B.!!$F2 2228
4 TraesCS5D01G045200 chr5B 43888307 43889431 1124 False 1709.000000 1709 94.102000 1 1127 1 chr5B.!!$F1 1126
5 TraesCS5D01G045200 chr5A 34907674 34911842 4168 False 2019.666667 4549 92.120667 1 4095 3 chr5A.!!$F2 4094
6 TraesCS5D01G045200 chr2B 41864139 41865833 1694 True 760.500000 808 84.258500 1167 2855 2 chr2B.!!$R2 1688
7 TraesCS5D01G045200 chr2B 41847245 41848003 758 True 634.000000 634 82.222000 2113 2855 1 chr2B.!!$R1 742
8 TraesCS5D01G045200 chr2D 26558445 26560180 1735 True 716.500000 732 85.987000 1156 2862 2 chr2D.!!$R2 1706
9 TraesCS5D01G045200 chr2A 28807955 28809660 1705 True 706.000000 713 85.646500 1155 2862 2 chr2A.!!$R2 1707
10 TraesCS5D01G045200 chrUn 87285401 87286001 600 False 451.000000 451 80.731000 1176 1758 1 chrUn.!!$F1 582
11 TraesCS5D01G045200 chrUn 87283251 87283795 544 True 387.000000 387 79.853000 2117 2649 1 chrUn.!!$R1 532
12 TraesCS5D01G045200 chr7B 680268622 680269222 600 True 446.000000 446 80.565000 1176 1758 1 chr7B.!!$R1 582

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
182 187 0.109179 TGGTTTGCATCGCTGATTGC 60.109 50.000 0.00 0.0 38.57 3.56 F
974 1180 0.928229 GTGTAAAGCCGGCATCTACG 59.072 55.000 31.54 0.0 0.00 3.51 F
2303 3009 1.153647 CGCTGGCTACGAATCCACA 60.154 57.895 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1024 1235 1.024046 TTACCTCGCGCATTGCATGT 61.024 50.000 8.75 0.65 46.97 3.21 R
2689 3418 2.091432 TCGTTGACAATTGATGCGTACG 59.909 45.455 13.59 11.84 0.00 3.67 R
3460 4230 2.231478 CGGACACATCTGTAACTGTCCT 59.769 50.000 12.59 0.00 42.45 3.85 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
131 136 8.365399 TGATGATTCGTATTTGTCATTCCTAC 57.635 34.615 0.00 0.00 31.86 3.18
156 161 2.540101 GCGCTTACTGGCTGTAATAGTG 59.460 50.000 15.96 13.00 40.02 2.74
182 187 0.109179 TGGTTTGCATCGCTGATTGC 60.109 50.000 0.00 0.00 38.57 3.56
244 252 3.196901 TCTCTTATGCCGCCTCAAGTTTA 59.803 43.478 0.00 0.00 0.00 2.01
245 253 4.130118 CTCTTATGCCGCCTCAAGTTTAT 58.870 43.478 0.00 0.00 0.00 1.40
258 266 6.146021 GCCTCAAGTTTATTCCACATTGTTTG 59.854 38.462 0.00 0.00 0.00 2.93
268 276 4.129380 TCCACATTGTTTGTCTGAGTCAG 58.871 43.478 14.36 14.36 36.00 3.51
293 301 7.661437 AGTGTTTGCAGATCACAACTCTAAATA 59.339 33.333 16.20 0.00 34.94 1.40
323 332 6.762661 CAGTTTTGAAGATTTTGGACACCAAT 59.237 34.615 4.03 0.00 43.55 3.16
449 458 1.663643 GTGTGTGATTGACGTGTGTGT 59.336 47.619 0.00 0.00 0.00 3.72
490 499 4.630940 GGAGAAGAGTTGAGCTGAAAGATG 59.369 45.833 0.00 0.00 34.07 2.90
491 500 5.477510 GAGAAGAGTTGAGCTGAAAGATGA 58.522 41.667 0.00 0.00 34.07 2.92
492 501 6.052405 AGAAGAGTTGAGCTGAAAGATGAT 57.948 37.500 0.00 0.00 34.07 2.45
974 1180 0.928229 GTGTAAAGCCGGCATCTACG 59.072 55.000 31.54 0.00 0.00 3.51
1086 1301 2.725203 TTTGTTCCCGTCTGCCTCCG 62.725 60.000 0.00 0.00 0.00 4.63
1161 1377 1.476891 CGCTTCTCCAGGTACTAGCAA 59.523 52.381 0.00 0.00 36.02 3.91
1282 1501 4.807039 GCCGACGCGTGGTACCAT 62.807 66.667 20.70 0.53 0.00 3.55
1306 1543 1.674057 CTTCTTCCTCAGGCACGGT 59.326 57.895 0.00 0.00 0.00 4.83
1802 2366 5.221722 TGTGCTTTTCCTCTCTGTCAATAGT 60.222 40.000 0.00 0.00 0.00 2.12
1803 2367 5.121454 GTGCTTTTCCTCTCTGTCAATAGTG 59.879 44.000 0.00 0.00 0.00 2.74
1804 2368 5.012046 TGCTTTTCCTCTCTGTCAATAGTGA 59.988 40.000 0.00 0.00 0.00 3.41
1806 2370 6.597280 GCTTTTCCTCTCTGTCAATAGTGAAT 59.403 38.462 0.00 0.00 34.87 2.57
1807 2371 7.766278 GCTTTTCCTCTCTGTCAATAGTGAATA 59.234 37.037 0.00 0.00 34.87 1.75
1808 2372 9.311916 CTTTTCCTCTCTGTCAATAGTGAATAG 57.688 37.037 0.00 0.00 34.87 1.73
2038 2739 4.395959 TGGATCGGGTTACACTATCAAC 57.604 45.455 1.66 0.00 0.00 3.18
2303 3009 1.153647 CGCTGGCTACGAATCCACA 60.154 57.895 0.00 0.00 0.00 4.17
2654 3383 3.758554 ACAGATGGGATGTAAGTTGTTGC 59.241 43.478 0.00 0.00 0.00 4.17
2689 3418 4.337274 TGATCATGGATGCAACTTCATCAC 59.663 41.667 0.00 0.00 43.44 3.06
2887 3646 7.865706 ACTTCAAATCCTATGTAATCACCAC 57.134 36.000 0.00 0.00 0.00 4.16
2945 3706 8.481974 TGTCTTGGCATTTGATTGATTTATTG 57.518 30.769 0.00 0.00 0.00 1.90
2986 3747 5.185454 CAGTTGATCCTAGTTTGCCATACA 58.815 41.667 0.00 0.00 0.00 2.29
3010 3771 4.842531 TGATTGTTTCAGATGGGAGCTA 57.157 40.909 0.00 0.00 0.00 3.32
3043 3804 3.194861 TGCGAAGATCAATTACCTTCCG 58.805 45.455 0.00 0.00 34.40 4.30
3056 3817 4.966787 TTCCGCACCCAAGGCCAC 62.967 66.667 5.01 0.00 0.00 5.01
3107 3868 0.382158 TAGAGCTTGACGGAGATGCG 59.618 55.000 0.00 0.00 0.00 4.73
3224 3989 9.699410 TCCTGGAAATGACATTATCTTTGTAAT 57.301 29.630 0.00 0.00 0.00 1.89
3254 4019 4.518211 TGGGCATGTTGCTTTTAAATTTGG 59.482 37.500 0.00 0.00 44.28 3.28
3258 4023 6.648725 GGCATGTTGCTTTTAAATTTGGACTA 59.351 34.615 0.00 0.00 44.28 2.59
3288 4058 7.015389 GGGACAAGACCATTATAAGCTACTAGT 59.985 40.741 0.00 0.00 0.00 2.57
3326 4096 4.202441 GAGAAGGCCATTTATGAAGCTCA 58.798 43.478 5.01 0.00 0.00 4.26
3411 4181 5.023452 TGACCTTGGAGTCACTATATGTGT 58.977 41.667 0.00 0.00 46.27 3.72
3412 4182 5.105351 TGACCTTGGAGTCACTATATGTGTG 60.105 44.000 0.00 4.82 46.27 3.82
3413 4183 4.122776 CCTTGGAGTCACTATATGTGTGC 58.877 47.826 5.99 2.99 46.27 4.57
3450 4220 0.320421 GCAAGCTCCCGTGTGAAGTA 60.320 55.000 0.00 0.00 0.00 2.24
3457 4227 3.427773 GCTCCCGTGTGAAGTAACTCTAG 60.428 52.174 0.00 0.00 0.00 2.43
3460 4230 5.748402 TCCCGTGTGAAGTAACTCTAGATA 58.252 41.667 0.00 0.00 0.00 1.98
3463 4233 5.821470 CCGTGTGAAGTAACTCTAGATAGGA 59.179 44.000 0.00 0.00 0.00 2.94
3465 4235 6.315642 CGTGTGAAGTAACTCTAGATAGGACA 59.684 42.308 0.00 0.00 0.00 4.02
3467 4237 7.337436 GTGTGAAGTAACTCTAGATAGGACAGT 59.663 40.741 0.00 0.00 0.00 3.55
3606 4377 6.350696 CCCTCCGATCCATATTAATTGTCGTA 60.351 42.308 0.00 0.00 0.00 3.43
3646 4417 6.054941 AGTGTGCGACAATTAATATGGATCA 58.945 36.000 0.00 0.00 0.00 2.92
3657 4428 9.511272 CAATTAATATGGATCAGATGGAGTTGA 57.489 33.333 0.00 0.00 0.00 3.18
3763 4534 7.316640 AGCACCGAGATAATATTCATGTACTC 58.683 38.462 0.00 0.00 0.00 2.59
3764 4535 6.531948 GCACCGAGATAATATTCATGTACTCC 59.468 42.308 0.00 0.00 0.00 3.85
3765 4536 7.036220 CACCGAGATAATATTCATGTACTCCC 58.964 42.308 0.00 0.00 0.00 4.30
3766 4537 6.954684 ACCGAGATAATATTCATGTACTCCCT 59.045 38.462 0.00 0.00 0.00 4.20
3767 4538 7.122948 ACCGAGATAATATTCATGTACTCCCTC 59.877 40.741 0.00 0.00 0.00 4.30
3768 4539 7.416890 CCGAGATAATATTCATGTACTCCCTCC 60.417 44.444 0.00 0.00 0.00 4.30
3769 4540 7.411486 AGATAATATTCATGTACTCCCTCCG 57.589 40.000 0.00 0.00 0.00 4.63
3770 4541 6.954684 AGATAATATTCATGTACTCCCTCCGT 59.045 38.462 0.00 0.00 0.00 4.69
3771 4542 5.888982 AATATTCATGTACTCCCTCCGTT 57.111 39.130 0.00 0.00 0.00 4.44
3772 4543 3.821421 ATTCATGTACTCCCTCCGTTC 57.179 47.619 0.00 0.00 0.00 3.95
3773 4544 2.526888 TCATGTACTCCCTCCGTTCT 57.473 50.000 0.00 0.00 0.00 3.01
3774 4545 2.100197 TCATGTACTCCCTCCGTTCTG 58.900 52.381 0.00 0.00 0.00 3.02
3775 4546 2.100197 CATGTACTCCCTCCGTTCTGA 58.900 52.381 0.00 0.00 0.00 3.27
3776 4547 2.297698 TGTACTCCCTCCGTTCTGAA 57.702 50.000 0.00 0.00 0.00 3.02
3777 4548 2.816411 TGTACTCCCTCCGTTCTGAAT 58.184 47.619 0.00 0.00 0.00 2.57
3778 4549 3.170717 TGTACTCCCTCCGTTCTGAATT 58.829 45.455 0.00 0.00 0.00 2.17
3779 4550 4.346730 TGTACTCCCTCCGTTCTGAATTA 58.653 43.478 0.00 0.00 0.00 1.40
3780 4551 4.960469 TGTACTCCCTCCGTTCTGAATTAT 59.040 41.667 0.00 0.00 0.00 1.28
3781 4552 5.424252 TGTACTCCCTCCGTTCTGAATTATT 59.576 40.000 0.00 0.00 0.00 1.40
3782 4553 5.437191 ACTCCCTCCGTTCTGAATTATTT 57.563 39.130 0.00 0.00 0.00 1.40
3783 4554 5.186198 ACTCCCTCCGTTCTGAATTATTTG 58.814 41.667 0.00 0.00 0.00 2.32
3784 4555 5.174037 TCCCTCCGTTCTGAATTATTTGT 57.826 39.130 0.00 0.00 0.00 2.83
3785 4556 5.183228 TCCCTCCGTTCTGAATTATTTGTC 58.817 41.667 0.00 0.00 0.00 3.18
3786 4557 4.034048 CCCTCCGTTCTGAATTATTTGTCG 59.966 45.833 0.00 0.00 0.00 4.35
3787 4558 4.494199 CCTCCGTTCTGAATTATTTGTCGC 60.494 45.833 0.00 0.00 0.00 5.19
3788 4559 3.997681 TCCGTTCTGAATTATTTGTCGCA 59.002 39.130 0.00 0.00 0.00 5.10
3789 4560 4.092821 TCCGTTCTGAATTATTTGTCGCAG 59.907 41.667 0.00 0.00 0.00 5.18
3790 4561 4.334443 CGTTCTGAATTATTTGTCGCAGG 58.666 43.478 0.00 0.00 0.00 4.85
3791 4562 4.142902 CGTTCTGAATTATTTGTCGCAGGT 60.143 41.667 0.00 0.00 0.00 4.00
3792 4563 5.062934 CGTTCTGAATTATTTGTCGCAGGTA 59.937 40.000 0.00 0.00 0.00 3.08
3793 4564 6.238103 CGTTCTGAATTATTTGTCGCAGGTAT 60.238 38.462 0.00 0.00 0.00 2.73
3794 4565 6.603237 TCTGAATTATTTGTCGCAGGTATG 57.397 37.500 0.00 0.00 0.00 2.39
3795 4566 5.527214 TCTGAATTATTTGTCGCAGGTATGG 59.473 40.000 0.00 0.00 0.00 2.74
3796 4567 5.432645 TGAATTATTTGTCGCAGGTATGGA 58.567 37.500 0.00 0.00 0.00 3.41
3797 4568 6.061441 TGAATTATTTGTCGCAGGTATGGAT 58.939 36.000 0.00 0.00 0.00 3.41
3798 4569 5.947228 ATTATTTGTCGCAGGTATGGATG 57.053 39.130 0.00 0.00 0.00 3.51
3799 4570 2.779755 TTTGTCGCAGGTATGGATGT 57.220 45.000 0.00 0.00 0.00 3.06
3800 4571 3.897141 TTTGTCGCAGGTATGGATGTA 57.103 42.857 0.00 0.00 0.00 2.29
3801 4572 4.415881 TTTGTCGCAGGTATGGATGTAT 57.584 40.909 0.00 0.00 0.00 2.29
3802 4573 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
3803 4574 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
3804 4575 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
3805 4576 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
3806 4577 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
3807 4578 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
3808 4579 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
3809 4580 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
3810 4581 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
3811 4582 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
3812 4583 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
3838 4609 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
3839 4610 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
3840 4611 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
3841 4612 6.596309 TCTAGATACATCCATTTCTGCGAT 57.404 37.500 0.00 0.00 0.00 4.58
3842 4613 6.393171 TCTAGATACATCCATTTCTGCGATG 58.607 40.000 0.00 0.00 36.72 3.84
3843 4614 5.219343 AGATACATCCATTTCTGCGATGA 57.781 39.130 3.44 0.00 35.42 2.92
3844 4615 5.236282 AGATACATCCATTTCTGCGATGAG 58.764 41.667 3.44 0.00 35.42 2.90
3845 4616 3.272574 ACATCCATTTCTGCGATGAGT 57.727 42.857 3.44 0.00 35.42 3.41
3846 4617 4.406648 ACATCCATTTCTGCGATGAGTA 57.593 40.909 3.44 0.00 35.42 2.59
3847 4618 4.769688 ACATCCATTTCTGCGATGAGTAA 58.230 39.130 3.44 0.00 35.42 2.24
3848 4619 5.371526 ACATCCATTTCTGCGATGAGTAAT 58.628 37.500 3.44 0.00 35.42 1.89
3849 4620 5.824624 ACATCCATTTCTGCGATGAGTAATT 59.175 36.000 3.44 0.00 35.42 1.40
3850 4621 6.319658 ACATCCATTTCTGCGATGAGTAATTT 59.680 34.615 3.44 0.00 35.42 1.82
3851 4622 6.122850 TCCATTTCTGCGATGAGTAATTTG 57.877 37.500 0.00 0.00 0.00 2.32
3852 4623 5.879777 TCCATTTCTGCGATGAGTAATTTGA 59.120 36.000 0.00 0.00 0.00 2.69
3853 4624 6.374053 TCCATTTCTGCGATGAGTAATTTGAA 59.626 34.615 0.00 0.00 0.00 2.69
3854 4625 7.028962 CCATTTCTGCGATGAGTAATTTGAAA 58.971 34.615 0.00 0.00 0.00 2.69
3855 4626 7.008628 CCATTTCTGCGATGAGTAATTTGAAAC 59.991 37.037 0.00 0.00 0.00 2.78
3856 4627 5.203358 TCTGCGATGAGTAATTTGAAACG 57.797 39.130 0.00 0.00 0.00 3.60
3857 4628 4.092821 TCTGCGATGAGTAATTTGAAACGG 59.907 41.667 0.00 0.00 0.00 4.44
3858 4629 3.997681 TGCGATGAGTAATTTGAAACGGA 59.002 39.130 0.00 0.00 0.00 4.69
3859 4630 4.092821 TGCGATGAGTAATTTGAAACGGAG 59.907 41.667 0.00 0.00 0.00 4.63
3860 4631 4.494199 GCGATGAGTAATTTGAAACGGAGG 60.494 45.833 0.00 0.00 0.00 4.30
3861 4632 4.034048 CGATGAGTAATTTGAAACGGAGGG 59.966 45.833 0.00 0.00 0.00 4.30
3862 4633 4.627284 TGAGTAATTTGAAACGGAGGGA 57.373 40.909 0.00 0.00 0.00 4.20
3863 4634 4.575885 TGAGTAATTTGAAACGGAGGGAG 58.424 43.478 0.00 0.00 0.00 4.30
3864 4635 4.041198 TGAGTAATTTGAAACGGAGGGAGT 59.959 41.667 0.00 0.00 0.00 3.85
3865 4636 5.246656 TGAGTAATTTGAAACGGAGGGAGTA 59.753 40.000 0.00 0.00 0.00 2.59
3866 4637 5.485620 AGTAATTTGAAACGGAGGGAGTAC 58.514 41.667 0.00 0.00 0.00 2.73
3867 4638 4.635699 AATTTGAAACGGAGGGAGTACT 57.364 40.909 0.00 0.00 0.00 2.73
3943 4714 6.820656 GTGGCTGAATATATGTTCATAGAGGG 59.179 42.308 14.42 4.38 37.47 4.30
3960 4731 8.455682 TCATAGAGGGTTTAAAACTAAAATGCG 58.544 33.333 2.72 0.00 0.00 4.73
3963 4734 8.570068 AGAGGGTTTAAAACTAAAATGCGATA 57.430 30.769 2.72 0.00 0.00 2.92
3964 4735 9.016438 AGAGGGTTTAAAACTAAAATGCGATAA 57.984 29.630 2.72 0.00 0.00 1.75
3965 4736 9.628746 GAGGGTTTAAAACTAAAATGCGATAAA 57.371 29.630 2.72 0.00 0.00 1.40
3981 4759 4.566759 GCGATAAAAGGAAAGGGAAAATGC 59.433 41.667 0.00 0.00 0.00 3.56
3987 4765 7.984422 AAAAGGAAAGGGAAAATGCAATAAG 57.016 32.000 0.00 0.00 0.00 1.73
3995 4773 6.881570 AGGGAAAATGCAATAAGAGGAAATG 58.118 36.000 0.00 0.00 0.00 2.32
4095 4873 8.446599 AGAACAATAGGAAGAACGAAAAGAAA 57.553 30.769 0.00 0.00 0.00 2.52
4096 4874 8.343366 AGAACAATAGGAAGAACGAAAAGAAAC 58.657 33.333 0.00 0.00 0.00 2.78
4097 4875 7.562454 ACAATAGGAAGAACGAAAAGAAACA 57.438 32.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 187 0.390860 ATGCGTCCTAGCTGGCTTAG 59.609 55.000 0.00 0.00 38.13 2.18
244 252 5.132502 TGACTCAGACAAACAATGTGGAAT 58.867 37.500 0.00 0.00 44.12 3.01
245 253 4.522114 TGACTCAGACAAACAATGTGGAA 58.478 39.130 0.00 0.00 44.12 3.53
258 266 2.826428 TCTGCAAACACTGACTCAGAC 58.174 47.619 13.25 0.00 35.18 3.51
268 276 5.673337 TTAGAGTTGTGATCTGCAAACAC 57.327 39.130 9.61 9.61 35.45 3.32
293 301 7.492344 GTGTCCAAAATCTTCAAAACTGTCAAT 59.508 33.333 0.00 0.00 0.00 2.57
315 324 6.238484 GCTGGTGATCTACAAATATTGGTGTC 60.238 42.308 5.69 2.52 34.12 3.67
323 332 5.826208 TCGAGTAGCTGGTGATCTACAAATA 59.174 40.000 0.00 0.00 38.05 1.40
449 458 9.231297 CTCTTCTCCCATCATAAACAGTTAAAA 57.769 33.333 0.00 0.00 0.00 1.52
490 499 4.023365 GGTTTCTGCATTAGCCTCATCATC 60.023 45.833 0.00 0.00 41.13 2.92
491 500 3.887716 GGTTTCTGCATTAGCCTCATCAT 59.112 43.478 0.00 0.00 41.13 2.45
492 501 3.282021 GGTTTCTGCATTAGCCTCATCA 58.718 45.455 0.00 0.00 41.13 3.07
974 1180 3.684788 ACGTTGTGTGATTATTCTGGCTC 59.315 43.478 0.00 0.00 0.00 4.70
1022 1233 2.466982 CCTCGCGCATTGCATGTCT 61.467 57.895 8.75 0.00 46.97 3.41
1024 1235 1.024046 TTACCTCGCGCATTGCATGT 61.024 50.000 8.75 0.65 46.97 3.21
1086 1301 2.384203 GGCTGATCCGTTACTGTGC 58.616 57.895 0.00 0.00 0.00 4.57
1161 1377 2.224606 CCACTGCTATCGCCATTGATT 58.775 47.619 0.00 0.00 34.43 2.57
1281 1500 1.222936 CTGAGGAAGAAGGCGGCAT 59.777 57.895 13.08 0.00 0.00 4.40
1282 1501 2.665000 CTGAGGAAGAAGGCGGCA 59.335 61.111 13.08 0.00 0.00 5.69
1802 2366 6.602803 TGCAATTTAAGGAGCATCACTATTCA 59.397 34.615 0.00 0.00 36.25 2.57
1803 2367 6.914757 GTGCAATTTAAGGAGCATCACTATTC 59.085 38.462 0.00 0.00 39.43 1.75
1804 2368 6.377996 TGTGCAATTTAAGGAGCATCACTATT 59.622 34.615 0.00 0.00 39.43 1.73
1806 2370 5.252547 TGTGCAATTTAAGGAGCATCACTA 58.747 37.500 0.00 0.00 39.43 2.74
1807 2371 4.081406 TGTGCAATTTAAGGAGCATCACT 58.919 39.130 0.00 0.00 39.43 3.41
1808 2372 4.418392 CTGTGCAATTTAAGGAGCATCAC 58.582 43.478 0.00 0.00 39.43 3.06
1997 2690 6.993786 TCCATTTACTGCATCGTATGAAAA 57.006 33.333 0.00 0.00 0.00 2.29
1998 2691 6.073819 CGATCCATTTACTGCATCGTATGAAA 60.074 38.462 0.00 0.00 33.29 2.69
2006 2699 2.851195 ACCCGATCCATTTACTGCATC 58.149 47.619 0.00 0.00 0.00 3.91
2012 2705 6.518493 TGATAGTGTAACCCGATCCATTTAC 58.482 40.000 0.00 0.00 37.80 2.01
2038 2739 6.016777 AGCAAACAAATTACCTTGACTCTCTG 60.017 38.462 0.00 0.00 0.00 3.35
2303 3009 2.827190 CACATGATGGCGCTGGCT 60.827 61.111 7.64 0.00 39.81 4.75
2654 3383 6.039382 TGCATCCATGATCAATGAGAGAAAAG 59.961 38.462 9.57 0.00 38.72 2.27
2689 3418 2.091432 TCGTTGACAATTGATGCGTACG 59.909 45.455 13.59 11.84 0.00 3.67
2885 3644 8.343366 CAAATGAATTCTACTGATCTCATGGTG 58.657 37.037 7.05 0.00 29.69 4.17
2887 3646 7.228906 AGCAAATGAATTCTACTGATCTCATGG 59.771 37.037 7.05 0.00 29.69 3.66
2921 3681 8.483307 ACAATAAATCAATCAAATGCCAAGAC 57.517 30.769 0.00 0.00 0.00 3.01
2965 3726 6.509418 TTTGTATGGCAAACTAGGATCAAC 57.491 37.500 0.00 0.00 41.68 3.18
2986 3747 5.021458 AGCTCCCATCTGAAACAATCATTT 58.979 37.500 0.00 0.00 37.44 2.32
3010 3771 4.711399 TGATCTTCGCATCAGGATTCAAT 58.289 39.130 0.00 0.00 0.00 2.57
3043 3804 4.284550 TCCAGTGGCCTTGGGTGC 62.285 66.667 21.89 0.00 36.34 5.01
3098 3859 2.900122 AAACATTGAACGCATCTCCG 57.100 45.000 0.00 0.00 0.00 4.63
3229 3994 6.294620 CCAAATTTAAAAGCAACATGCCCATT 60.295 34.615 0.00 0.00 46.52 3.16
3239 4004 7.070074 TCCCTTGTAGTCCAAATTTAAAAGCAA 59.930 33.333 0.00 0.00 31.20 3.91
3254 4019 3.983044 ATGGTCTTGTCCCTTGTAGTC 57.017 47.619 0.00 0.00 0.00 2.59
3258 4023 5.044846 AGCTTATAATGGTCTTGTCCCTTGT 60.045 40.000 0.00 0.00 0.00 3.16
3326 4096 5.047802 CCATTCAACCAAATGTACTCAAGCT 60.048 40.000 0.00 0.00 35.31 3.74
3411 4181 3.244526 TGCCTATCTTTGACTTGTGAGCA 60.245 43.478 0.00 0.00 0.00 4.26
3412 4182 3.338249 TGCCTATCTTTGACTTGTGAGC 58.662 45.455 0.00 0.00 0.00 4.26
3413 4183 4.142730 GCTTGCCTATCTTTGACTTGTGAG 60.143 45.833 0.00 0.00 0.00 3.51
3450 4220 8.056400 ACATCTGTAACTGTCCTATCTAGAGTT 58.944 37.037 0.00 0.00 0.00 3.01
3457 4227 5.593010 GGACACATCTGTAACTGTCCTATC 58.407 45.833 8.19 0.00 41.67 2.08
3460 4230 2.231478 CGGACACATCTGTAACTGTCCT 59.769 50.000 12.59 0.00 42.45 3.85
3463 4233 3.509967 TGATCGGACACATCTGTAACTGT 59.490 43.478 0.00 0.00 32.47 3.55
3465 4235 4.801330 TTGATCGGACACATCTGTAACT 57.199 40.909 0.00 0.00 32.47 2.24
3467 4237 6.215495 TGTATTGATCGGACACATCTGTAA 57.785 37.500 0.00 0.00 32.47 2.41
3579 4350 4.849810 ACAATTAATATGGATCGGAGGGGA 59.150 41.667 0.00 0.00 0.00 4.81
3580 4351 5.179452 ACAATTAATATGGATCGGAGGGG 57.821 43.478 0.00 0.00 0.00 4.79
3606 4377 7.171848 TGTCGCACACTTATTACAACTTTGTAT 59.828 33.333 2.71 0.00 42.66 2.29
3619 4390 8.621532 ATCCATATTAATTGTCGCACACTTAT 57.378 30.769 0.00 0.00 0.00 1.73
3746 4517 7.171630 ACGGAGGGAGTACATGAATATTATC 57.828 40.000 0.00 0.00 0.00 1.75
3763 4534 4.034048 CGACAAATAATTCAGAACGGAGGG 59.966 45.833 0.00 0.00 0.00 4.30
3764 4535 4.494199 GCGACAAATAATTCAGAACGGAGG 60.494 45.833 0.00 0.00 0.00 4.30
3765 4536 4.092821 TGCGACAAATAATTCAGAACGGAG 59.907 41.667 0.00 0.00 0.00 4.63
3766 4537 3.997681 TGCGACAAATAATTCAGAACGGA 59.002 39.130 0.00 0.00 0.00 4.69
3767 4538 4.334443 CTGCGACAAATAATTCAGAACGG 58.666 43.478 0.00 0.00 0.00 4.44
3768 4539 4.142902 ACCTGCGACAAATAATTCAGAACG 60.143 41.667 0.00 0.00 0.00 3.95
3769 4540 5.296813 ACCTGCGACAAATAATTCAGAAC 57.703 39.130 0.00 0.00 0.00 3.01
3770 4541 6.038161 CCATACCTGCGACAAATAATTCAGAA 59.962 38.462 0.00 0.00 0.00 3.02
3771 4542 5.527214 CCATACCTGCGACAAATAATTCAGA 59.473 40.000 0.00 0.00 0.00 3.27
3772 4543 5.527214 TCCATACCTGCGACAAATAATTCAG 59.473 40.000 0.00 0.00 0.00 3.02
3773 4544 5.432645 TCCATACCTGCGACAAATAATTCA 58.567 37.500 0.00 0.00 0.00 2.57
3774 4545 6.017109 ACATCCATACCTGCGACAAATAATTC 60.017 38.462 0.00 0.00 0.00 2.17
3775 4546 5.827797 ACATCCATACCTGCGACAAATAATT 59.172 36.000 0.00 0.00 0.00 1.40
3776 4547 5.376625 ACATCCATACCTGCGACAAATAAT 58.623 37.500 0.00 0.00 0.00 1.28
3777 4548 4.776349 ACATCCATACCTGCGACAAATAA 58.224 39.130 0.00 0.00 0.00 1.40
3778 4549 4.415881 ACATCCATACCTGCGACAAATA 57.584 40.909 0.00 0.00 0.00 1.40
3779 4550 3.281727 ACATCCATACCTGCGACAAAT 57.718 42.857 0.00 0.00 0.00 2.32
3780 4551 2.779755 ACATCCATACCTGCGACAAA 57.220 45.000 0.00 0.00 0.00 2.83
3781 4552 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
3782 4553 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
3783 4554 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
3784 4555 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
3785 4556 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
3786 4557 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
3812 4583 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
3813 4584 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
3814 4585 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
3815 4586 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
3816 4587 6.216569 TCGCAGAAATGGATGTATCTAGAAC 58.783 40.000 0.00 0.00 0.00 3.01
3817 4588 6.405278 TCGCAGAAATGGATGTATCTAGAA 57.595 37.500 0.00 0.00 0.00 2.10
3818 4589 6.209391 TCATCGCAGAAATGGATGTATCTAGA 59.791 38.462 0.00 0.00 43.58 2.43
3819 4590 6.393171 TCATCGCAGAAATGGATGTATCTAG 58.607 40.000 0.80 0.00 43.58 2.43
3820 4591 6.015095 ACTCATCGCAGAAATGGATGTATCTA 60.015 38.462 0.80 0.00 43.58 1.98
3821 4592 5.219343 TCATCGCAGAAATGGATGTATCT 57.781 39.130 0.80 0.00 43.58 1.98
3822 4593 4.993584 ACTCATCGCAGAAATGGATGTATC 59.006 41.667 0.80 0.00 43.58 2.24
3823 4594 4.965814 ACTCATCGCAGAAATGGATGTAT 58.034 39.130 0.80 0.00 43.58 2.29
3824 4595 4.406648 ACTCATCGCAGAAATGGATGTA 57.593 40.909 0.80 0.00 43.58 2.29
3825 4596 3.272574 ACTCATCGCAGAAATGGATGT 57.727 42.857 0.80 0.00 43.58 3.06
3826 4597 5.936686 ATTACTCATCGCAGAAATGGATG 57.063 39.130 0.00 0.00 43.58 3.51
3827 4598 6.543465 TCAAATTACTCATCGCAGAAATGGAT 59.457 34.615 0.00 0.00 43.58 3.41
3828 4599 5.879777 TCAAATTACTCATCGCAGAAATGGA 59.120 36.000 0.00 0.00 43.58 3.41
3829 4600 6.122850 TCAAATTACTCATCGCAGAAATGG 57.877 37.500 0.00 0.00 43.58 3.16
3830 4601 7.253092 CGTTTCAAATTACTCATCGCAGAAATG 60.253 37.037 0.00 0.00 43.58 2.32
3831 4602 6.742718 CGTTTCAAATTACTCATCGCAGAAAT 59.257 34.615 0.00 0.00 43.58 2.17
3832 4603 6.077197 CGTTTCAAATTACTCATCGCAGAAA 58.923 36.000 0.00 0.00 43.58 2.52
3833 4604 5.390461 CCGTTTCAAATTACTCATCGCAGAA 60.390 40.000 0.00 0.00 43.58 3.02
3834 4605 4.092821 CCGTTTCAAATTACTCATCGCAGA 59.907 41.667 0.00 0.00 45.75 4.26
3835 4606 4.092821 TCCGTTTCAAATTACTCATCGCAG 59.907 41.667 0.00 0.00 0.00 5.18
3836 4607 3.997681 TCCGTTTCAAATTACTCATCGCA 59.002 39.130 0.00 0.00 0.00 5.10
3837 4608 4.494199 CCTCCGTTTCAAATTACTCATCGC 60.494 45.833 0.00 0.00 0.00 4.58
3838 4609 4.034048 CCCTCCGTTTCAAATTACTCATCG 59.966 45.833 0.00 0.00 0.00 3.84
3839 4610 5.183228 TCCCTCCGTTTCAAATTACTCATC 58.817 41.667 0.00 0.00 0.00 2.92
3840 4611 5.174037 TCCCTCCGTTTCAAATTACTCAT 57.826 39.130 0.00 0.00 0.00 2.90
3841 4612 4.041198 ACTCCCTCCGTTTCAAATTACTCA 59.959 41.667 0.00 0.00 0.00 3.41
3842 4613 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
3843 4614 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
3844 4615 5.485620 AGTACTCCCTCCGTTTCAAATTAC 58.514 41.667 0.00 0.00 0.00 1.89
3845 4616 5.750352 AGTACTCCCTCCGTTTCAAATTA 57.250 39.130 0.00 0.00 0.00 1.40
3846 4617 4.635699 AGTACTCCCTCCGTTTCAAATT 57.364 40.909 0.00 0.00 0.00 1.82
3847 4618 4.635699 AAGTACTCCCTCCGTTTCAAAT 57.364 40.909 0.00 0.00 0.00 2.32
3848 4619 4.426736 AAAGTACTCCCTCCGTTTCAAA 57.573 40.909 0.00 0.00 0.00 2.69
3849 4620 5.549742 TTAAAGTACTCCCTCCGTTTCAA 57.450 39.130 0.00 0.00 0.00 2.69
3850 4621 5.549742 TTTAAAGTACTCCCTCCGTTTCA 57.450 39.130 0.00 0.00 0.00 2.69
3851 4622 8.728337 ATATTTTAAAGTACTCCCTCCGTTTC 57.272 34.615 0.00 0.00 0.00 2.78
3852 4623 9.170734 GAATATTTTAAAGTACTCCCTCCGTTT 57.829 33.333 0.00 0.00 0.00 3.60
3853 4624 8.323567 TGAATATTTTAAAGTACTCCCTCCGTT 58.676 33.333 0.00 0.00 0.00 4.44
3854 4625 7.854337 TGAATATTTTAAAGTACTCCCTCCGT 58.146 34.615 0.00 0.00 0.00 4.69
3855 4626 8.904099 ATGAATATTTTAAAGTACTCCCTCCG 57.096 34.615 0.00 0.00 0.00 4.63
3900 4671 6.208402 TCAGCCACTTATGCAAGATTTTGTAA 59.792 34.615 0.00 0.00 36.65 2.41
3907 4678 7.886970 ACATATATTCAGCCACTTATGCAAGAT 59.113 33.333 0.00 0.00 35.60 2.40
3910 4681 7.501892 TGAACATATATTCAGCCACTTATGCAA 59.498 33.333 0.00 0.00 33.62 4.08
3951 4722 7.095695 TCCCTTTCCTTTTATCGCATTTTAG 57.904 36.000 0.00 0.00 0.00 1.85
3952 4723 7.469537 TTCCCTTTCCTTTTATCGCATTTTA 57.530 32.000 0.00 0.00 0.00 1.52
3953 4724 5.993748 TCCCTTTCCTTTTATCGCATTTT 57.006 34.783 0.00 0.00 0.00 1.82
3954 4725 5.993748 TTCCCTTTCCTTTTATCGCATTT 57.006 34.783 0.00 0.00 0.00 2.32
3955 4726 5.993748 TTTCCCTTTCCTTTTATCGCATT 57.006 34.783 0.00 0.00 0.00 3.56
3956 4727 5.993748 TTTTCCCTTTCCTTTTATCGCAT 57.006 34.783 0.00 0.00 0.00 4.73
3957 4728 5.719173 CATTTTCCCTTTCCTTTTATCGCA 58.281 37.500 0.00 0.00 0.00 5.10
3958 4729 4.566759 GCATTTTCCCTTTCCTTTTATCGC 59.433 41.667 0.00 0.00 0.00 4.58
3960 4731 9.665719 TTATTGCATTTTCCCTTTCCTTTTATC 57.334 29.630 0.00 0.00 0.00 1.75
3963 4734 7.744733 TCTTATTGCATTTTCCCTTTCCTTTT 58.255 30.769 0.00 0.00 0.00 2.27
3964 4735 7.315066 TCTTATTGCATTTTCCCTTTCCTTT 57.685 32.000 0.00 0.00 0.00 3.11
3965 4736 6.070596 CCTCTTATTGCATTTTCCCTTTCCTT 60.071 38.462 0.00 0.00 0.00 3.36
3987 4765 9.803315 AGTTTTTGTTCTTACTTTCATTTCCTC 57.197 29.630 0.00 0.00 0.00 3.71
4071 4849 8.126700 TGTTTCTTTTCGTTCTTCCTATTGTTC 58.873 33.333 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.