Multiple sequence alignment - TraesCS1A01G149600

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 TraesCS1A01G149600 chr1A 100.000 3100 0 0 1 3100 256986339 256983240 0.000000e+00 5725.0
1 TraesCS1A01G149600 chr1B 87.899 1628 96 36 1 1597 296812241 296810684 0.000000e+00 1821.0
2 TraesCS1A01G149600 chr1B 95.122 410 12 3 1725 2126 296810676 296810267 9.370000e-180 640.0
3 TraesCS1A01G149600 chr1B 88.406 138 14 2 1600 1737 294124024 294123889 6.880000e-37 165.0
4 TraesCS1A01G149600 chr1B 89.474 95 4 3 2196 2284 296810025 296809931 7.020000e-22 115.0
5 TraesCS1A01G149600 chr1B 90.541 74 3 3 2125 2198 296810174 296810105 9.150000e-16 95.3
6 TraesCS1A01G149600 chr2A 85.239 1233 83 41 414 1600 759811094 759812273 0.000000e+00 1177.0
7 TraesCS1A01G149600 chr2A 91.777 377 21 5 1741 2116 759812277 759812644 1.650000e-142 516.0
8 TraesCS1A01G149600 chr2A 88.406 138 14 2 1600 1737 115247958 115248093 6.880000e-37 165.0
9 TraesCS1A01G149600 chr2D 90.940 585 38 9 1016 1600 631963295 631962726 0.000000e+00 773.0
10 TraesCS1A01G149600 chr2D 86.006 636 79 8 2330 2961 495874173 495873544 0.000000e+00 673.0
11 TraesCS1A01G149600 chr2D 90.680 397 24 8 1727 2112 631962723 631962329 1.650000e-142 516.0
12 TraesCS1A01G149600 chr2D 82.143 588 65 19 1 576 631972033 631971474 4.680000e-128 468.0
13 TraesCS1A01G149600 chr2D 90.000 310 17 9 574 871 631963728 631963421 3.750000e-104 388.0
14 TraesCS1A01G149600 chr2B 82.366 896 83 43 1 871 775374658 775373813 0.000000e+00 710.0
15 TraesCS1A01G149600 chr2B 83.718 780 93 21 2350 3100 11404264 11403490 0.000000e+00 706.0
16 TraesCS1A01G149600 chr2B 86.927 589 44 10 1016 1600 775373682 775373123 5.640000e-177 630.0
17 TraesCS1A01G149600 chr2B 92.327 391 18 3 1741 2128 775373119 775372738 2.100000e-151 545.0
18 TraesCS1A01G149600 chr2B 95.000 40 2 0 942 981 775373785 775373746 2.580000e-06 63.9
19 TraesCS1A01G149600 chr7D 86.175 651 80 6 2454 3100 518837822 518838466 0.000000e+00 695.0
20 TraesCS1A01G149600 chr7D 88.406 138 14 2 1600 1737 112696645 112696780 6.880000e-37 165.0
21 TraesCS1A01G149600 chr7A 82.939 803 104 17 2326 3100 191698996 191699793 0.000000e+00 693.0
22 TraesCS1A01G149600 chr5D 85.781 640 79 9 2326 2961 27352214 27352845 0.000000e+00 667.0
23 TraesCS1A01G149600 chr5D 90.076 131 12 1 1600 1730 71806159 71806288 5.320000e-38 169.0
24 TraesCS1A01G149600 chr6A 85.344 655 82 11 2326 2974 464505437 464506083 0.000000e+00 665.0
25 TraesCS1A01G149600 chr6A 89.313 131 14 0 1600 1730 117791176 117791046 6.880000e-37 165.0
26 TraesCS1A01G149600 chr5B 84.075 697 99 9 2409 3100 197786492 197787181 0.000000e+00 662.0
27 TraesCS1A01G149600 chr4D 85.647 641 79 11 2326 2961 3273416 3274048 0.000000e+00 662.0
28 TraesCS1A01G149600 chr4D 89.130 138 13 2 1600 1737 203442838 203442703 1.480000e-38 171.0
29 TraesCS1A01G149600 chr1D 86.339 549 64 8 2556 3100 180172340 180172881 3.440000e-164 588.0
30 TraesCS1A01G149600 chr3D 83.654 312 51 0 1034 1345 556028441 556028130 8.410000e-76 294.0
31 TraesCS1A01G149600 chr3D 88.406 138 14 2 1600 1737 338674081 338674216 6.880000e-37 165.0
32 TraesCS1A01G149600 chr3A 82.175 331 59 0 1015 1345 692963121 692962791 5.060000e-73 285.0
33 TraesCS1A01G149600 chr3B 84.058 276 44 0 1015 1290 739029670 739029395 1.830000e-67 267.0
34 TraesCS1A01G149600 chr4A 83.770 191 23 5 2911 3100 739876101 739876284 1.140000e-39 174.0
35 TraesCS1A01G149600 chr4A 86.145 166 16 4 2936 3100 41116561 41116402 4.110000e-39 172.0
36 TraesCS1A01G149600 chr4A 88.406 138 14 2 1600 1737 71453979 71453844 6.880000e-37 165.0
37 TraesCS1A01G149600 chr6B 88.406 138 14 2 1600 1737 119539330 119539195 6.880000e-37 165.0


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 TraesCS1A01G149600 chr1A 256983240 256986339 3099 True 5725.000 5725 100.000 1 3100 1 chr1A.!!$R1 3099
1 TraesCS1A01G149600 chr1B 296809931 296812241 2310 True 667.825 1821 90.759 1 2284 4 chr1B.!!$R2 2283
2 TraesCS1A01G149600 chr2A 759811094 759812644 1550 False 846.500 1177 88.508 414 2116 2 chr2A.!!$F2 1702
3 TraesCS1A01G149600 chr2D 495873544 495874173 629 True 673.000 673 86.006 2330 2961 1 chr2D.!!$R1 631
4 TraesCS1A01G149600 chr2D 631962329 631963728 1399 True 559.000 773 90.540 574 2112 3 chr2D.!!$R3 1538
5 TraesCS1A01G149600 chr2D 631971474 631972033 559 True 468.000 468 82.143 1 576 1 chr2D.!!$R2 575
6 TraesCS1A01G149600 chr2B 11403490 11404264 774 True 706.000 706 83.718 2350 3100 1 chr2B.!!$R1 750
7 TraesCS1A01G149600 chr2B 775372738 775374658 1920 True 487.225 710 89.155 1 2128 4 chr2B.!!$R2 2127
8 TraesCS1A01G149600 chr7D 518837822 518838466 644 False 695.000 695 86.175 2454 3100 1 chr7D.!!$F2 646
9 TraesCS1A01G149600 chr7A 191698996 191699793 797 False 693.000 693 82.939 2326 3100 1 chr7A.!!$F1 774
10 TraesCS1A01G149600 chr5D 27352214 27352845 631 False 667.000 667 85.781 2326 2961 1 chr5D.!!$F1 635
11 TraesCS1A01G149600 chr6A 464505437 464506083 646 False 665.000 665 85.344 2326 2974 1 chr6A.!!$F1 648
12 TraesCS1A01G149600 chr5B 197786492 197787181 689 False 662.000 662 84.075 2409 3100 1 chr5B.!!$F1 691
13 TraesCS1A01G149600 chr4D 3273416 3274048 632 False 662.000 662 85.647 2326 2961 1 chr4D.!!$F1 635
14 TraesCS1A01G149600 chr1D 180172340 180172881 541 False 588.000 588 86.339 2556 3100 1 chr1D.!!$F1 544

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
267 276 0.106708 GAATGGATGTCGGCTAGCCA 59.893 55.0 32.47 17.27 35.37 4.75 F
950 1030 0.811915 GAGCACGTAGAGGAGCTCAA 59.188 55.0 17.19 0.00 45.42 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1370 1501 0.319727 TTGCGTACACGGGATTTCGT 60.320 50.0 3.67 0.0 44.91 3.85 R
2816 3158 0.865769 AACGGTCTGATCGCAAACAC 59.134 50.0 10.74 0.0 0.00 3.32 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
40 41 7.222000 TGGTAAATCGCTCAAAAGGTAAAAT 57.778 32.000 0.00 0.00 0.00 1.82
110 111 3.947910 TTCTCGATTTACCACTCGGTT 57.052 42.857 0.00 0.00 46.31 4.44
111 112 3.947910 TCTCGATTTACCACTCGGTTT 57.052 42.857 0.00 0.00 46.31 3.27
112 113 4.261578 TCTCGATTTACCACTCGGTTTT 57.738 40.909 0.00 0.00 46.31 2.43
116 117 3.060363 CGATTTACCACTCGGTTTTCTCG 59.940 47.826 0.00 0.00 46.31 4.04
141 150 7.753580 CGGTTTTTCCTCTACATAAAAATGGTC 59.246 37.037 0.00 0.00 35.31 4.02
143 152 9.841880 GTTTTTCCTCTACATAAAAATGGTCTC 57.158 33.333 0.00 0.00 35.31 3.36
171 180 5.886715 TTTCAAGTTTCAATCGTGCAATG 57.113 34.783 0.00 0.00 0.00 2.82
178 187 3.557577 TCAATCGTGCAATGAAACAGG 57.442 42.857 0.00 0.00 34.16 4.00
195 204 1.542915 CAGGGCATATGGCTACATTGC 59.457 52.381 26.45 9.87 44.01 3.56
239 248 2.022035 TCTAGATGTGGTTGGGGAGGAT 60.022 50.000 0.00 0.00 0.00 3.24
247 256 1.697291 GGTTGGGGAGGATGAGAGGAT 60.697 57.143 0.00 0.00 0.00 3.24
257 266 4.241151 AGGATGAGAGGATGAATGGATGT 58.759 43.478 0.00 0.00 0.00 3.06
267 276 0.106708 GAATGGATGTCGGCTAGCCA 59.893 55.000 32.47 17.27 35.37 4.75
286 295 1.146263 CGCCTAAACCCTGGCTAGG 59.854 63.158 9.64 9.64 46.42 3.02
329 338 4.660521 TGGTAGCCACACCTCCTT 57.339 55.556 1.86 0.00 39.50 3.36
334 343 3.971702 GCCACACCTCCTTGGGCT 61.972 66.667 0.00 0.00 41.39 5.19
336 345 2.046892 CACACCTCCTTGGGCTCG 60.047 66.667 0.00 0.00 41.11 5.03
410 440 2.044946 GGGGCGTCTGATTTGGCT 60.045 61.111 0.00 0.00 0.00 4.75
484 515 1.611851 AGCTCTGGACCACTGGAGG 60.612 63.158 0.71 0.00 0.00 4.30
485 516 2.985456 CTCTGGACCACTGGAGGC 59.015 66.667 0.71 0.00 0.00 4.70
486 517 2.997315 TCTGGACCACTGGAGGCG 60.997 66.667 0.71 0.00 0.00 5.52
487 518 4.087892 CTGGACCACTGGAGGCGG 62.088 72.222 0.71 0.00 0.00 6.13
488 519 4.954118 TGGACCACTGGAGGCGGT 62.954 66.667 0.71 0.00 35.12 5.68
492 523 4.704833 CCACTGGAGGCGGTGGTG 62.705 72.222 0.00 5.61 45.52 4.17
493 524 3.941188 CACTGGAGGCGGTGGTGT 61.941 66.667 0.00 0.00 0.00 4.16
494 525 3.168528 ACTGGAGGCGGTGGTGTT 61.169 61.111 0.00 0.00 0.00 3.32
495 526 2.113139 CTGGAGGCGGTGGTGTTT 59.887 61.111 0.00 0.00 0.00 2.83
496 527 1.528309 CTGGAGGCGGTGGTGTTTT 60.528 57.895 0.00 0.00 0.00 2.43
756 829 5.220472 CCATGCGTGTAGAATACTGACTTTG 60.220 44.000 4.96 0.00 43.54 2.77
761 834 7.601130 TGCGTGTAGAATACTGACTTTGTAAAT 59.399 33.333 0.00 0.00 43.54 1.40
863 942 6.260271 AGCATTCTTAATTAGCGGAACCTAAC 59.740 38.462 0.00 0.00 30.69 2.34
878 957 1.839994 CCTAACAAGGGCCTGATGAGA 59.160 52.381 6.92 0.00 0.00 3.27
879 958 2.420687 CCTAACAAGGGCCTGATGAGAC 60.421 54.545 6.92 0.00 0.00 3.36
950 1030 0.811915 GAGCACGTAGAGGAGCTCAA 59.188 55.000 17.19 0.00 45.42 3.02
1010 1105 3.154473 CTCGGGGATGGAAGGCGA 61.154 66.667 0.00 0.00 0.00 5.54
1282 1413 3.790437 CGCTGGCCATGGAGAGGT 61.790 66.667 18.40 0.00 0.00 3.85
1296 1427 2.833943 GGAGAGGTACCCGGAAAAAGTA 59.166 50.000 8.74 0.00 0.00 2.24
1370 1501 2.126467 GTACGCGTTCAAACAGGTACA 58.874 47.619 20.78 0.00 37.26 2.90
1432 1563 7.408756 TCCATTTTCTTCCTGACCATTAATG 57.591 36.000 8.58 8.58 0.00 1.90
1437 1568 6.455360 TTCTTCCTGACCATTAATGATTGC 57.545 37.500 17.23 3.85 0.00 3.56
1459 1593 4.325472 GCACGTACGAAACTGTTAGCTATT 59.675 41.667 24.41 0.00 0.00 1.73
1492 1626 3.320256 GGGCCAGATTTCTTCATGGATTC 59.680 47.826 4.39 0.00 34.60 2.52
1605 1743 4.657436 CCTCCTGAGGTATGTTACTCAC 57.343 50.000 4.97 0.00 43.61 3.51
1606 1744 4.282496 CCTCCTGAGGTATGTTACTCACT 58.718 47.826 4.97 0.00 43.61 3.41
1607 1745 4.712337 CCTCCTGAGGTATGTTACTCACTT 59.288 45.833 4.97 0.00 43.61 3.16
1608 1746 5.163499 CCTCCTGAGGTATGTTACTCACTTC 60.163 48.000 4.97 0.00 43.61 3.01
1609 1747 4.398358 TCCTGAGGTATGTTACTCACTTCG 59.602 45.833 0.00 0.00 38.71 3.79
1610 1748 4.158025 CCTGAGGTATGTTACTCACTTCGT 59.842 45.833 0.00 0.00 38.71 3.85
1611 1749 5.306532 TGAGGTATGTTACTCACTTCGTC 57.693 43.478 0.00 0.00 38.71 4.20
1612 1750 5.008331 TGAGGTATGTTACTCACTTCGTCT 58.992 41.667 0.00 0.00 38.71 4.18
1613 1751 5.123502 TGAGGTATGTTACTCACTTCGTCTC 59.876 44.000 0.00 0.00 38.71 3.36
1614 1752 5.008331 AGGTATGTTACTCACTTCGTCTCA 58.992 41.667 0.00 0.00 0.00 3.27
1615 1753 5.475909 AGGTATGTTACTCACTTCGTCTCAA 59.524 40.000 0.00 0.00 0.00 3.02
1616 1754 6.015688 AGGTATGTTACTCACTTCGTCTCAAA 60.016 38.462 0.00 0.00 0.00 2.69
1617 1755 6.643770 GGTATGTTACTCACTTCGTCTCAAAA 59.356 38.462 0.00 0.00 0.00 2.44
1618 1756 7.331193 GGTATGTTACTCACTTCGTCTCAAAAT 59.669 37.037 0.00 0.00 0.00 1.82
1619 1757 7.730364 ATGTTACTCACTTCGTCTCAAAATT 57.270 32.000 0.00 0.00 0.00 1.82
1620 1758 7.173863 TGTTACTCACTTCGTCTCAAAATTC 57.826 36.000 0.00 0.00 0.00 2.17
1621 1759 6.984474 TGTTACTCACTTCGTCTCAAAATTCT 59.016 34.615 0.00 0.00 0.00 2.40
1622 1760 7.494625 TGTTACTCACTTCGTCTCAAAATTCTT 59.505 33.333 0.00 0.00 0.00 2.52
1623 1761 6.292389 ACTCACTTCGTCTCAAAATTCTTG 57.708 37.500 0.00 0.00 0.00 3.02
1624 1762 5.817816 ACTCACTTCGTCTCAAAATTCTTGT 59.182 36.000 0.00 0.00 0.00 3.16
1625 1763 6.018669 ACTCACTTCGTCTCAAAATTCTTGTC 60.019 38.462 0.00 0.00 0.00 3.18
1626 1764 6.049149 TCACTTCGTCTCAAAATTCTTGTCT 58.951 36.000 0.00 0.00 0.00 3.41
1627 1765 6.538742 TCACTTCGTCTCAAAATTCTTGTCTT 59.461 34.615 0.00 0.00 0.00 3.01
1628 1766 7.709182 TCACTTCGTCTCAAAATTCTTGTCTTA 59.291 33.333 0.00 0.00 0.00 2.10
1629 1767 8.335356 CACTTCGTCTCAAAATTCTTGTCTTAA 58.665 33.333 0.00 0.00 0.00 1.85
1630 1768 8.889717 ACTTCGTCTCAAAATTCTTGTCTTAAA 58.110 29.630 0.00 0.00 0.00 1.52
1631 1769 9.884465 CTTCGTCTCAAAATTCTTGTCTTAAAT 57.116 29.630 0.00 0.00 0.00 1.40
1677 1815 9.952030 TCTAATACCAAAACATGACTTGATACA 57.048 29.630 0.00 0.00 0.00 2.29
1680 1818 6.515272 ACCAAAACATGACTTGATACATCC 57.485 37.500 0.00 0.00 0.00 3.51
1681 1819 6.009589 ACCAAAACATGACTTGATACATCCA 58.990 36.000 0.00 0.00 0.00 3.41
1682 1820 6.664816 ACCAAAACATGACTTGATACATCCAT 59.335 34.615 0.00 0.00 0.00 3.41
1683 1821 7.833682 ACCAAAACATGACTTGATACATCCATA 59.166 33.333 0.00 0.00 0.00 2.74
1684 1822 8.853126 CCAAAACATGACTTGATACATCCATAT 58.147 33.333 0.00 0.00 0.00 1.78
1717 1855 8.848474 AATCTAAGACAATAATATTGGGACGG 57.152 34.615 16.36 5.02 0.00 4.79
1718 1856 7.606135 TCTAAGACAATAATATTGGGACGGA 57.394 36.000 16.36 6.94 0.00 4.69
1719 1857 7.667557 TCTAAGACAATAATATTGGGACGGAG 58.332 38.462 16.36 6.71 0.00 4.63
1720 1858 5.228945 AGACAATAATATTGGGACGGAGG 57.771 43.478 16.36 0.00 0.00 4.30
1721 1859 4.905456 AGACAATAATATTGGGACGGAGGA 59.095 41.667 16.36 0.00 0.00 3.71
1722 1860 5.368523 AGACAATAATATTGGGACGGAGGAA 59.631 40.000 16.36 0.00 0.00 3.36
1723 1861 5.621193 ACAATAATATTGGGACGGAGGAAG 58.379 41.667 16.36 0.00 0.00 3.46
1724 1862 5.132144 ACAATAATATTGGGACGGAGGAAGT 59.868 40.000 16.36 0.00 0.00 3.01
1725 1863 6.328148 ACAATAATATTGGGACGGAGGAAGTA 59.672 38.462 16.36 0.00 0.00 2.24
1868 2021 1.997606 CGGTTCCTAAATGACGACACC 59.002 52.381 0.00 0.00 0.00 4.16
1953 2106 4.719369 ACGACGAGTGGAAGCCGC 62.719 66.667 0.00 0.00 0.00 6.53
2024 2177 1.307097 GATTGCAGGGAGCTGATCAC 58.693 55.000 0.00 0.00 45.94 3.06
2091 2247 2.625790 GTGATTGCCAACAAGTACCCAA 59.374 45.455 0.00 0.00 39.69 4.12
2116 2272 3.084786 GCTGAGTTGGTTAGATGGCTTT 58.915 45.455 0.00 0.00 0.00 3.51
2118 2274 4.095036 GCTGAGTTGGTTAGATGGCTTTAC 59.905 45.833 0.00 0.00 0.00 2.01
2138 2388 1.375523 GGAAGCGACAATCACGGGT 60.376 57.895 0.00 0.00 0.00 5.28
2146 2396 0.252197 ACAATCACGGGTCTAAGGCC 59.748 55.000 0.00 0.00 0.00 5.19
2150 2400 2.687566 ACGGGTCTAAGGCCTGGG 60.688 66.667 5.69 1.66 36.71 4.45
2162 2412 4.743018 CCTGGGCTAGGTTGTTGG 57.257 61.111 9.06 0.00 42.00 3.77
2163 2413 1.767692 CCTGGGCTAGGTTGTTGGT 59.232 57.895 9.06 0.00 42.00 3.67
2164 2414 0.112412 CCTGGGCTAGGTTGTTGGTT 59.888 55.000 9.06 0.00 42.00 3.67
2204 2536 1.235724 GCCGCAGTGTAAGGTTTTCT 58.764 50.000 0.00 0.00 0.00 2.52
2205 2537 1.197036 GCCGCAGTGTAAGGTTTTCTC 59.803 52.381 0.00 0.00 0.00 2.87
2207 2539 3.863400 GCCGCAGTGTAAGGTTTTCTCTA 60.863 47.826 0.00 0.00 0.00 2.43
2264 2602 4.089065 GTCAATTTGTTTCTTCATCGCAGC 59.911 41.667 0.00 0.00 0.00 5.25
2277 2615 1.640428 TCGCAGCAAGTCGAAATAGG 58.360 50.000 0.00 0.00 0.00 2.57
2284 2622 5.119898 GCAGCAAGTCGAAATAGGATCATAG 59.880 44.000 0.00 0.00 0.00 2.23
2285 2623 5.636965 CAGCAAGTCGAAATAGGATCATAGG 59.363 44.000 0.00 0.00 0.00 2.57
2286 2624 5.540337 AGCAAGTCGAAATAGGATCATAGGA 59.460 40.000 0.00 0.00 0.00 2.94
2287 2625 5.866633 GCAAGTCGAAATAGGATCATAGGAG 59.133 44.000 0.00 0.00 0.00 3.69
2288 2626 5.652994 AGTCGAAATAGGATCATAGGAGC 57.347 43.478 0.00 0.00 0.00 4.70
2293 2631 2.665603 GGATCATAGGAGCCCCGC 59.334 66.667 0.00 0.00 43.99 6.13
2294 2632 1.915769 GGATCATAGGAGCCCCGCT 60.916 63.158 0.00 0.00 43.99 5.52
2317 2655 4.890306 GCCTCTCTCCCCCTCCCC 62.890 77.778 0.00 0.00 0.00 4.81
2318 2656 4.179599 CCTCTCTCCCCCTCCCCC 62.180 77.778 0.00 0.00 0.00 5.40
2319 2657 4.548513 CTCTCTCCCCCTCCCCCG 62.549 77.778 0.00 0.00 0.00 5.73
2321 2659 4.862823 CTCTCCCCCTCCCCCGTC 62.863 77.778 0.00 0.00 0.00 4.79
2515 2853 4.147449 CCCTGGATCTCGCGTGCA 62.147 66.667 5.77 0.00 0.00 4.57
2517 2855 2.182791 CTGGATCTCGCGTGCAGT 59.817 61.111 5.77 0.00 31.31 4.40
2544 2882 4.521062 GCAGCGCTCCCGTCTCAT 62.521 66.667 7.13 0.00 36.67 2.90
2577 2916 3.160047 CGGCCTCCTGCTGGATCT 61.160 66.667 13.33 0.00 43.04 2.75
2758 3097 0.674895 GTGGACTCCCAGTGTCATGC 60.675 60.000 0.00 0.00 44.55 4.06
2786 3125 2.045926 GTGGCTTGGCGGATCTGT 60.046 61.111 2.89 0.00 0.00 3.41
2828 3170 1.739929 ATCGGCGTGTTTGCGATCA 60.740 52.632 6.85 0.00 35.06 2.92
2884 3226 0.529378 GGTCGCTACTCCCTTCGAAA 59.471 55.000 0.00 0.00 32.49 3.46
2902 3244 2.032681 GGTTGGCCTTCTCGCAGT 59.967 61.111 3.32 0.00 0.00 4.40
2934 3276 4.394078 CGTCTCGCGTCCGGTGAA 62.394 66.667 5.77 0.00 34.08 3.18
3053 3426 1.179174 CGCAGGAGGGTCGATGGATA 61.179 60.000 0.00 0.00 0.00 2.59
3057 3430 1.062428 AGGAGGGTCGATGGATACCAA 60.062 52.381 0.00 0.00 36.95 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 8.709386 TTCGAGAAATTTTGTTTGAATTGGAA 57.291 26.923 0.00 0.00 0.00 3.53
110 111 8.680039 TTTTATGTAGAGGAAAAACCGAGAAA 57.320 30.769 0.00 0.00 44.74 2.52
111 112 8.680039 TTTTTATGTAGAGGAAAAACCGAGAA 57.320 30.769 0.00 0.00 44.74 2.87
112 113 8.726988 CATTTTTATGTAGAGGAAAAACCGAGA 58.273 33.333 0.00 0.00 44.74 4.04
116 117 8.803235 AGACCATTTTTATGTAGAGGAAAAACC 58.197 33.333 0.00 0.00 35.51 3.27
141 150 7.059945 GCACGATTGAAACTTGAAAATGTAGAG 59.940 37.037 0.00 0.00 0.00 2.43
143 152 6.636447 TGCACGATTGAAACTTGAAAATGTAG 59.364 34.615 0.00 0.00 0.00 2.74
171 180 2.930950 TGTAGCCATATGCCCTGTTTC 58.069 47.619 0.00 0.00 42.71 2.78
178 187 4.202141 TGAAAAGCAATGTAGCCATATGCC 60.202 41.667 0.00 0.00 42.71 4.40
219 228 1.879575 TCCTCCCCAACCACATCTAG 58.120 55.000 0.00 0.00 0.00 2.43
239 248 2.366590 CCGACATCCATTCATCCTCTCA 59.633 50.000 0.00 0.00 0.00 3.27
247 256 0.106708 GGCTAGCCGACATCCATTCA 59.893 55.000 20.16 0.00 0.00 2.57
293 302 2.646930 CACTTGGCTAGCCATGAATGA 58.353 47.619 41.18 25.17 46.64 2.57
320 329 2.203788 TCGAGCCCAAGGAGGTGT 60.204 61.111 0.00 0.00 34.66 4.16
329 338 3.068691 CGGTTCTCCTCGAGCCCA 61.069 66.667 6.99 0.00 39.67 5.36
372 382 1.077716 CCTCCAAACCCCGGCTAAG 60.078 63.158 0.00 0.00 0.00 2.18
863 942 0.747283 GCTGTCTCATCAGGCCCTTG 60.747 60.000 0.00 0.00 36.12 3.61
878 957 2.048023 CAATCCATGTGGCGGCTGT 61.048 57.895 11.43 0.00 34.44 4.40
879 958 1.597797 AACAATCCATGTGGCGGCTG 61.598 55.000 11.43 0.00 42.99 4.85
934 1013 5.463724 GGAATAATTTGAGCTCCTCTACGTG 59.536 44.000 12.15 0.00 0.00 4.49
950 1030 6.375455 AGCGTGTGAAAATCAGAGGAATAATT 59.625 34.615 1.95 0.00 28.44 1.40
1296 1427 3.927163 GACGAACACGGCCACGGAT 62.927 63.158 2.24 0.00 46.48 4.18
1370 1501 0.319727 TTGCGTACACGGGATTTCGT 60.320 50.000 3.67 0.00 44.91 3.85
1432 1563 3.515071 AACAGTTTCGTACGTGCAATC 57.485 42.857 16.05 1.85 0.00 2.67
1437 1568 5.720433 GCAATAGCTAACAGTTTCGTACGTG 60.720 44.000 16.05 8.62 37.91 4.49
1459 1593 1.803453 ATCTGGCCCTTTCCCTTGCA 61.803 55.000 0.00 0.00 0.00 4.08
1605 1743 9.884465 ATTTAAGACAAGAATTTTGAGACGAAG 57.116 29.630 0.00 0.00 0.00 3.79
1651 1789 9.952030 TGTATCAAGTCATGTTTTGGTATTAGA 57.048 29.630 10.53 0.00 0.00 2.10
1654 1792 8.686334 GGATGTATCAAGTCATGTTTTGGTATT 58.314 33.333 10.53 2.99 0.00 1.89
1655 1793 7.833682 TGGATGTATCAAGTCATGTTTTGGTAT 59.166 33.333 10.53 3.28 0.00 2.73
1656 1794 7.171653 TGGATGTATCAAGTCATGTTTTGGTA 58.828 34.615 10.53 6.50 0.00 3.25
1657 1795 6.009589 TGGATGTATCAAGTCATGTTTTGGT 58.990 36.000 10.53 7.28 0.00 3.67
1658 1796 6.513806 TGGATGTATCAAGTCATGTTTTGG 57.486 37.500 10.53 0.00 0.00 3.28
1691 1829 9.284968 CCGTCCCAATATTATTGTCTTAGATTT 57.715 33.333 13.87 0.00 0.00 2.17
1692 1830 8.656806 TCCGTCCCAATATTATTGTCTTAGATT 58.343 33.333 13.87 0.00 0.00 2.40
1693 1831 8.202461 TCCGTCCCAATATTATTGTCTTAGAT 57.798 34.615 13.87 0.00 0.00 1.98
1694 1832 7.256190 CCTCCGTCCCAATATTATTGTCTTAGA 60.256 40.741 13.87 5.87 0.00 2.10
1695 1833 6.874134 CCTCCGTCCCAATATTATTGTCTTAG 59.126 42.308 13.87 5.27 0.00 2.18
1696 1834 6.555738 TCCTCCGTCCCAATATTATTGTCTTA 59.444 38.462 13.87 0.00 0.00 2.10
1697 1835 5.368523 TCCTCCGTCCCAATATTATTGTCTT 59.631 40.000 13.87 0.00 0.00 3.01
1698 1836 4.905456 TCCTCCGTCCCAATATTATTGTCT 59.095 41.667 13.87 0.00 0.00 3.41
1699 1837 5.223449 TCCTCCGTCCCAATATTATTGTC 57.777 43.478 13.87 5.10 0.00 3.18
1700 1838 5.132144 ACTTCCTCCGTCCCAATATTATTGT 59.868 40.000 13.87 0.00 0.00 2.71
1701 1839 5.621193 ACTTCCTCCGTCCCAATATTATTG 58.379 41.667 9.09 9.09 0.00 1.90
1702 1840 5.906772 ACTTCCTCCGTCCCAATATTATT 57.093 39.130 0.00 0.00 0.00 1.40
1703 1841 6.082707 AGTACTTCCTCCGTCCCAATATTAT 58.917 40.000 0.00 0.00 0.00 1.28
1704 1842 5.461327 AGTACTTCCTCCGTCCCAATATTA 58.539 41.667 0.00 0.00 0.00 0.98
1705 1843 4.296056 AGTACTTCCTCCGTCCCAATATT 58.704 43.478 0.00 0.00 0.00 1.28
1706 1844 3.924922 AGTACTTCCTCCGTCCCAATAT 58.075 45.455 0.00 0.00 0.00 1.28
1707 1845 3.393426 AGTACTTCCTCCGTCCCAATA 57.607 47.619 0.00 0.00 0.00 1.90
1708 1846 2.249309 AGTACTTCCTCCGTCCCAAT 57.751 50.000 0.00 0.00 0.00 3.16
1709 1847 2.019807 AAGTACTTCCTCCGTCCCAA 57.980 50.000 1.12 0.00 0.00 4.12
1710 1848 2.019807 AAAGTACTTCCTCCGTCCCA 57.980 50.000 8.95 0.00 0.00 4.37
1711 1849 2.827921 TGTAAAGTACTTCCTCCGTCCC 59.172 50.000 8.95 0.00 0.00 4.46
1712 1850 3.509184 ACTGTAAAGTACTTCCTCCGTCC 59.491 47.826 8.95 0.00 0.00 4.79
1713 1851 4.483311 CACTGTAAAGTACTTCCTCCGTC 58.517 47.826 8.95 0.00 0.00 4.79
1714 1852 3.257624 CCACTGTAAAGTACTTCCTCCGT 59.742 47.826 8.95 2.78 0.00 4.69
1715 1853 3.846360 CCACTGTAAAGTACTTCCTCCG 58.154 50.000 8.95 2.19 0.00 4.63
1716 1854 3.597255 GCCACTGTAAAGTACTTCCTCC 58.403 50.000 8.95 0.00 0.00 4.30
1717 1855 3.597255 GGCCACTGTAAAGTACTTCCTC 58.403 50.000 8.95 3.41 0.00 3.71
1718 1856 2.028385 CGGCCACTGTAAAGTACTTCCT 60.028 50.000 8.95 0.00 0.00 3.36
1719 1857 2.289257 ACGGCCACTGTAAAGTACTTCC 60.289 50.000 8.95 3.49 0.00 3.46
1720 1858 3.036075 ACGGCCACTGTAAAGTACTTC 57.964 47.619 8.95 0.00 0.00 3.01
1721 1859 3.480505 AACGGCCACTGTAAAGTACTT 57.519 42.857 2.24 1.12 0.00 2.24
1722 1860 3.135994 CAAACGGCCACTGTAAAGTACT 58.864 45.455 2.24 0.00 0.00 2.73
1723 1861 2.874086 ACAAACGGCCACTGTAAAGTAC 59.126 45.455 2.24 0.00 0.00 2.73
1724 1862 3.196939 ACAAACGGCCACTGTAAAGTA 57.803 42.857 2.24 0.00 0.00 2.24
1725 1863 2.047002 ACAAACGGCCACTGTAAAGT 57.953 45.000 2.24 0.00 0.00 2.66
1957 2110 3.285215 CCATGAGCCGCTGCATCC 61.285 66.667 0.00 0.00 41.13 3.51
1970 2123 2.438434 GGGTTCCACGAGGCCATG 60.438 66.667 5.01 0.00 33.74 3.66
2024 2177 2.159476 CGACTTTGAGAACATGGGCATG 60.159 50.000 0.00 0.00 44.15 4.06
2091 2247 3.620966 GCCATCTAACCAACTCAGCTTCT 60.621 47.826 0.00 0.00 0.00 2.85
2116 2272 1.403647 CCGTGATTGTCGCTTCCAGTA 60.404 52.381 0.00 0.00 0.00 2.74
2118 2274 1.361668 CCCGTGATTGTCGCTTCCAG 61.362 60.000 0.00 0.00 0.00 3.86
2138 2388 4.728780 CCTAGCCCAGGCCTTAGA 57.271 61.111 0.00 0.00 43.17 2.10
2146 2396 1.247567 CAACCAACAACCTAGCCCAG 58.752 55.000 0.00 0.00 0.00 4.45
2150 2400 3.003378 GTGAGAACAACCAACAACCTAGC 59.997 47.826 0.00 0.00 0.00 3.42
2155 2405 3.427503 CCTGTGTGAGAACAACCAACAAC 60.428 47.826 0.00 0.00 0.00 3.32
2157 2407 2.290641 ACCTGTGTGAGAACAACCAACA 60.291 45.455 0.00 0.00 0.00 3.33
2158 2408 2.354821 GACCTGTGTGAGAACAACCAAC 59.645 50.000 0.00 0.00 0.00 3.77
2160 2410 1.557371 TGACCTGTGTGAGAACAACCA 59.443 47.619 0.00 0.00 0.00 3.67
2161 2411 1.940613 GTGACCTGTGTGAGAACAACC 59.059 52.381 0.00 0.00 0.00 3.77
2162 2412 1.593006 CGTGACCTGTGTGAGAACAAC 59.407 52.381 0.00 0.00 0.00 3.32
2163 2413 1.478916 TCGTGACCTGTGTGAGAACAA 59.521 47.619 0.00 0.00 0.00 2.83
2164 2414 1.107945 TCGTGACCTGTGTGAGAACA 58.892 50.000 0.00 0.00 0.00 3.18
2204 2536 2.760092 GCTCCCCAACATTTTGCATAGA 59.240 45.455 0.00 0.00 0.00 1.98
2205 2537 2.762327 AGCTCCCCAACATTTTGCATAG 59.238 45.455 0.00 0.00 0.00 2.23
2207 2539 1.276989 CAGCTCCCCAACATTTTGCAT 59.723 47.619 0.00 0.00 0.00 3.96
2264 2602 5.866633 GCTCCTATGATCCTATTTCGACTTG 59.133 44.000 0.00 0.00 0.00 3.16
2277 2615 3.798758 AGCGGGGCTCCTATGATC 58.201 61.111 0.00 0.00 30.62 2.92
2300 2638 4.890306 GGGGAGGGGGAGAGAGGC 62.890 77.778 0.00 0.00 0.00 4.70
2301 2639 4.179599 GGGGGAGGGGGAGAGAGG 62.180 77.778 0.00 0.00 0.00 3.69
2302 2640 4.548513 CGGGGGAGGGGGAGAGAG 62.549 77.778 0.00 0.00 0.00 3.20
2304 2642 4.862823 GACGGGGGAGGGGGAGAG 62.863 77.778 0.00 0.00 0.00 3.20
2367 2705 3.803162 GCAGGGAGGGAGAAGGCC 61.803 72.222 0.00 0.00 0.00 5.19
2368 2706 2.690510 AGCAGGGAGGGAGAAGGC 60.691 66.667 0.00 0.00 0.00 4.35
2372 2710 2.363018 CACGAGCAGGGAGGGAGA 60.363 66.667 0.00 0.00 0.00 3.71
2373 2711 3.465403 CCACGAGCAGGGAGGGAG 61.465 72.222 0.00 0.00 0.00 4.30
2635 2974 3.390521 CCTAGCACCGGAGCCACA 61.391 66.667 20.91 5.27 34.23 4.17
2637 2976 2.759973 CTCCTAGCACCGGAGCCA 60.760 66.667 20.91 5.96 41.39 4.75
2713 3052 2.662596 GACCTCCACATGTCGCCA 59.337 61.111 0.00 0.00 0.00 5.69
2758 3097 1.586028 CAAGCCACCATGAAACCGG 59.414 57.895 0.00 0.00 0.00 5.28
2816 3158 0.865769 AACGGTCTGATCGCAAACAC 59.134 50.000 10.74 0.00 0.00 3.32
2820 3162 1.011968 CCGAAACGGTCTGATCGCAA 61.012 55.000 10.74 0.00 42.73 4.85
2893 3235 2.415491 CGATGGACTACAACTGCGAGAA 60.415 50.000 0.00 0.00 0.00 2.87
2895 3237 1.550065 CGATGGACTACAACTGCGAG 58.450 55.000 0.00 0.00 0.00 5.03
2898 3240 1.281899 GAGCGATGGACTACAACTGC 58.718 55.000 0.00 0.00 0.00 4.40
2902 3244 1.400846 GAGACGAGCGATGGACTACAA 59.599 52.381 0.00 0.00 0.00 2.41
2926 3268 2.747686 GGTCCTGCTTTCACCGGA 59.252 61.111 9.46 0.00 0.00 5.14
2933 3275 2.262915 CGAGCTCGGTCCTGCTTT 59.737 61.111 28.40 0.00 39.91 3.51
2934 3276 2.992114 ACGAGCTCGGTCCTGCTT 60.992 61.111 36.93 13.33 44.95 3.91
2970 3312 4.818314 GGGGGATGAGGTCAGTCT 57.182 61.111 0.00 0.00 0.00 3.24
2994 3366 2.125512 GGTCCTGCAGCACCGTAG 60.126 66.667 12.00 0.00 0.00 3.51
3034 3406 1.179174 TATCCATCGACCCTCCTGCG 61.179 60.000 0.00 0.00 0.00 5.18
3053 3426 1.635817 ATAGGTCGGCCAGCATTGGT 61.636 55.000 9.71 0.00 46.80 3.67
3057 3430 1.149174 CCAATAGGTCGGCCAGCAT 59.851 57.895 9.71 0.00 37.19 3.79


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

AutoCloner maintained by Alex Coulton.