Multiple sequence alignment - TraesCS7B01G126000

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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 TraesCS7B01G126000 chr7B 100.000 8459 0 0 1 8459 149603874 149612332 0.000000e+00 15621.0
1 TraesCS7B01G126000 chr7B 88.889 81 9 0 6386 6466 149610339 149610259 5.400000e-17 100.0
2 TraesCS7B01G126000 chr7A 94.387 7055 252 70 1490 8457 190477989 190470992 0.000000e+00 10702.0
3 TraesCS7B01G126000 chr7A 95.562 1014 31 6 1 1002 690031506 690032517 0.000000e+00 1611.0
4 TraesCS7B01G126000 chr7A 95.639 1009 30 4 1 997 504211552 504210546 0.000000e+00 1607.0
5 TraesCS7B01G126000 chr7A 93.451 397 18 6 1104 1496 190478497 190478105 4.400000e-162 582.0
6 TraesCS7B01G126000 chr7D 96.367 4652 128 20 1795 6419 181600189 181604826 0.000000e+00 7616.0
7 TraesCS7B01G126000 chr7D 95.681 1042 38 4 6445 7479 181604825 181605866 0.000000e+00 1668.0
8 TraesCS7B01G126000 chr7D 92.647 884 46 13 7581 8457 181606163 181607034 0.000000e+00 1254.0
9 TraesCS7B01G126000 chr7D 94.913 806 29 5 997 1800 181599268 181600063 0.000000e+00 1251.0
10 TraesCS7B01G126000 chr7D 86.905 84 7 2 6383 6466 179507123 179507202 3.250000e-14 91.6
11 TraesCS7B01G126000 chr7D 86.047 86 7 1 6386 6466 478904331 478904416 4.210000e-13 87.9
12 TraesCS7B01G126000 chr3B 96.032 1008 26 4 1 997 215312662 215311658 0.000000e+00 1628.0
13 TraesCS7B01G126000 chr3B 87.500 88 6 1 6386 6468 783474169 783474082 6.990000e-16 97.1
14 TraesCS7B01G126000 chr4B 95.738 1009 29 5 1 997 37301646 37300640 0.000000e+00 1613.0
15 TraesCS7B01G126000 chr4B 95.639 1009 29 4 1 997 270873416 270872411 0.000000e+00 1605.0
16 TraesCS7B01G126000 chr4D 95.644 1010 30 4 1 998 469322629 469323636 0.000000e+00 1609.0
17 TraesCS7B01G126000 chr4D 93.069 202 3 1 1 191 461791729 461791930 1.390000e-72 285.0
18 TraesCS7B01G126000 chr5D 95.644 1010 29 5 1 997 274780772 274779765 0.000000e+00 1607.0
19 TraesCS7B01G126000 chr5D 95.540 1009 30 5 1 997 233732823 233733828 0.000000e+00 1600.0
20 TraesCS7B01G126000 chr5D 95.115 1003 35 11 1 998 424077784 424078777 0.000000e+00 1568.0
21 TraesCS7B01G126000 chr5D 84.615 91 9 1 6383 6468 439641753 439641843 1.510000e-12 86.1
22 TraesCS7B01G126000 chr1B 95.540 1009 32 3 1 998 328665681 328666687 0.000000e+00 1602.0
23 TraesCS7B01G126000 chr2D 94.851 1010 38 4 1 998 589195581 589194574 0.000000e+00 1565.0
24 TraesCS7B01G126000 chr2D 85.321 109 13 1 6260 6365 439804206 439804098 8.980000e-20 110.0
25 TraesCS7B01G126000 chr2D 85.849 106 12 1 6260 6362 439832596 439832701 8.980000e-20 110.0
26 TraesCS7B01G126000 chr6B 91.460 1007 74 10 1 998 80379871 80380874 0.000000e+00 1373.0
27 TraesCS7B01G126000 chr4A 83.622 519 58 20 5750 6250 613672259 613672768 5.980000e-126 462.0
28 TraesCS7B01G126000 chr3D 90.698 86 6 1 6385 6468 370110107 370110022 6.940000e-21 113.0
29 TraesCS7B01G126000 chr1D 88.506 87 6 1 6380 6466 66562483 66562565 1.500000e-17 102.0
30 TraesCS7B01G126000 chr1A 88.372 86 5 1 6386 6466 568391202 568391287 1.940000e-16 99.0


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 TraesCS7B01G126000 chr7B 149603874 149612332 8458 False 15621.00 15621 100.000 1 8459 1 chr7B.!!$F1 8458
1 TraesCS7B01G126000 chr7A 190470992 190478497 7505 True 5642.00 10702 93.919 1104 8457 2 chr7A.!!$R2 7353
2 TraesCS7B01G126000 chr7A 690031506 690032517 1011 False 1611.00 1611 95.562 1 1002 1 chr7A.!!$F1 1001
3 TraesCS7B01G126000 chr7A 504210546 504211552 1006 True 1607.00 1607 95.639 1 997 1 chr7A.!!$R1 996
4 TraesCS7B01G126000 chr7D 181599268 181607034 7766 False 2947.25 7616 94.902 997 8457 4 chr7D.!!$F3 7460
5 TraesCS7B01G126000 chr3B 215311658 215312662 1004 True 1628.00 1628 96.032 1 997 1 chr3B.!!$R1 996
6 TraesCS7B01G126000 chr4B 37300640 37301646 1006 True 1613.00 1613 95.738 1 997 1 chr4B.!!$R1 996
7 TraesCS7B01G126000 chr4B 270872411 270873416 1005 True 1605.00 1605 95.639 1 997 1 chr4B.!!$R2 996
8 TraesCS7B01G126000 chr4D 469322629 469323636 1007 False 1609.00 1609 95.644 1 998 1 chr4D.!!$F2 997
9 TraesCS7B01G126000 chr5D 274779765 274780772 1007 True 1607.00 1607 95.644 1 997 1 chr5D.!!$R1 996
10 TraesCS7B01G126000 chr5D 233732823 233733828 1005 False 1600.00 1600 95.540 1 997 1 chr5D.!!$F1 996
11 TraesCS7B01G126000 chr5D 424077784 424078777 993 False 1568.00 1568 95.115 1 998 1 chr5D.!!$F2 997
12 TraesCS7B01G126000 chr1B 328665681 328666687 1006 False 1602.00 1602 95.540 1 998 1 chr1B.!!$F1 997
13 TraesCS7B01G126000 chr2D 589194574 589195581 1007 True 1565.00 1565 94.851 1 998 1 chr2D.!!$R2 997
14 TraesCS7B01G126000 chr6B 80379871 80380874 1003 False 1373.00 1373 91.460 1 998 1 chr6B.!!$F1 997
15 TraesCS7B01G126000 chr4A 613672259 613672768 509 False 462.00 462 83.622 5750 6250 1 chr4A.!!$F1 500

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
614 626 0.462581 TGCCGATGGAGATGCTTGAC 60.463 55.000 0.00 0.0 0.00 3.18 F
1068 1086 0.937304 GAGAACACGTGCAGAGCAAA 59.063 50.000 17.22 0.0 41.47 3.68 F
1751 1900 1.016627 TCAGCTGCATATTTCACCGC 58.983 50.000 9.47 0.0 0.00 5.68 F
3191 3507 0.242017 GTCCAACAGATGCAAGTGCC 59.758 55.000 0.00 0.0 41.18 5.01 F
3446 3762 3.682858 ACCCGTATGATTCTGTTTCAACG 59.317 43.478 0.00 0.0 32.50 4.10 F
4076 4395 0.811616 GCCGTTGCTAGTCATGGGAG 60.812 60.000 0.00 0.0 33.53 4.30 F
4892 5214 0.041833 CTCCTCCACCTCCTCCTGAA 59.958 60.000 0.00 0.0 0.00 3.02 F
4910 5232 0.679505 AACCTGAAGAGCACGCTGTA 59.320 50.000 0.00 0.0 0.00 2.74 F
6291 6630 1.205655 GGAGAAGCCAAGGAAAATGCC 59.794 52.381 0.00 0.0 36.34 4.40 F
6750 7101 1.400759 GCTGAAGCAAAGAAGGAAGCG 60.401 52.381 0.00 0.0 41.59 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1627 1771 0.324091 AGCCTCATTGCCCCTTCTTG 60.324 55.000 0.00 0.00 0.00 3.02 R
2539 2854 1.758592 CCCACGGTTTTCCTCTCCA 59.241 57.895 0.00 0.00 37.95 3.86 R
3702 4021 1.673033 GCTTCCGTAGCTGTCACACAT 60.673 52.381 0.00 0.00 46.77 3.21 R
4073 4392 0.253327 GGGGTCAATGTCCACTCTCC 59.747 60.000 0.00 0.00 0.00 3.71 R
4892 5214 0.898320 ATACAGCGTGCTCTTCAGGT 59.102 50.000 0.00 0.00 33.35 4.00 R
5863 6191 1.271054 ACACTCCCACTTGCATGAGTC 60.271 52.381 6.60 0.00 35.97 3.36 R
6458 6802 1.303282 CCAAAGGCCAGTACTCCCC 59.697 63.158 5.01 0.00 0.00 4.81 R
6570 6918 2.689471 GCATGGTCCACAATCAATGCTA 59.311 45.455 0.00 0.00 0.00 3.49 R
7163 7519 0.318699 TTGCTTCTCAGGACGTGACG 60.319 55.000 2.24 2.24 0.00 4.35 R
7648 8224 0.812549 GCATCATGTCATGTGCACCA 59.187 50.000 23.80 5.05 37.30 4.17 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
197 209 3.796111 AGGGTGAAGATGGAAGAAGAGA 58.204 45.455 0.00 0.00 0.00 3.10
205 217 3.829601 AGATGGAAGAAGAGACGTCAAGT 59.170 43.478 19.50 0.90 0.00 3.16
221 233 4.399618 CGTCAAGTCTAAGGGAGAAGATGA 59.600 45.833 0.00 0.00 35.37 2.92
320 332 2.878406 GAGGTCAAGCTTGCACAAGTTA 59.122 45.455 21.99 0.00 40.45 2.24
498 510 1.409427 GGACTACAAGGAGGACATCGG 59.591 57.143 0.00 0.00 0.00 4.18
614 626 0.462581 TGCCGATGGAGATGCTTGAC 60.463 55.000 0.00 0.00 0.00 3.18
735 751 3.703286 ACCATGCATCAATGATTGTCG 57.297 42.857 4.93 0.00 0.00 4.35
771 787 8.006298 TGTTTGGAAGTTGATTATGTTCTTGT 57.994 30.769 0.00 0.00 0.00 3.16
950 968 8.584063 AAGTAACACTTCTCAACCCTTAAAAA 57.416 30.769 0.00 0.00 31.77 1.94
960 978 8.472007 TCTCAACCCTTAAAAATGCTTTAAGA 57.528 30.769 14.89 0.00 41.89 2.10
971 989 8.978874 AAAAATGCTTTAAGAATTTGAGGGTT 57.021 26.923 11.31 0.00 33.80 4.11
998 1016 6.472686 AGGGTTCTACTAGTAATGCTCTTG 57.527 41.667 3.76 0.00 0.00 3.02
1053 1071 3.545911 GCCGAAGCGAAACGAGAA 58.454 55.556 0.00 0.00 0.00 2.87
1067 1085 1.215014 CGAGAACACGTGCAGAGCAA 61.215 55.000 17.22 0.00 41.47 3.91
1068 1086 0.937304 GAGAACACGTGCAGAGCAAA 59.063 50.000 17.22 0.00 41.47 3.68
1069 1087 1.330521 GAGAACACGTGCAGAGCAAAA 59.669 47.619 17.22 0.00 41.47 2.44
1070 1088 1.742831 AGAACACGTGCAGAGCAAAAA 59.257 42.857 17.22 0.00 41.47 1.94
1115 1133 2.284921 CCTCCAGCTCCCTCCACA 60.285 66.667 0.00 0.00 0.00 4.17
1153 1174 2.978018 GCACCGCTTCCCTTTTCGG 61.978 63.158 0.00 0.00 46.61 4.30
1161 1182 2.919387 GCTTCCCTTTTCGGCGTAAAAC 60.919 50.000 12.62 0.67 0.00 2.43
1162 1183 1.964552 TCCCTTTTCGGCGTAAAACA 58.035 45.000 12.62 0.00 0.00 2.83
1163 1184 1.603326 TCCCTTTTCGGCGTAAAACAC 59.397 47.619 12.62 0.00 0.00 3.32
1514 1658 9.745880 TTATATTCTGAACACTCGAAGGTTATC 57.254 33.333 1.73 0.00 0.00 1.75
1515 1659 4.451629 TCTGAACACTCGAAGGTTATCC 57.548 45.455 1.73 0.00 0.00 2.59
1528 1672 3.778265 AGGTTATCCTGTTGCATGGTTT 58.222 40.909 0.00 0.00 43.33 3.27
1551 1695 2.633967 TGATTGTTTGGCTGCCTGAATT 59.366 40.909 21.03 0.11 0.00 2.17
1627 1771 2.478894 CTGGACGTGGTAATTGACACAC 59.521 50.000 12.78 4.92 37.45 3.82
1628 1772 2.158943 TGGACGTGGTAATTGACACACA 60.159 45.455 12.78 7.02 37.45 3.72
1635 1779 4.023193 GTGGTAATTGACACACAAGAAGGG 60.023 45.833 8.83 0.00 42.02 3.95
1679 1826 3.149196 CAAAAGGAGAAGTGGCTTGCTA 58.851 45.455 0.00 0.00 0.00 3.49
1723 1871 6.699204 CCTGTGTGCACTATATAGAGTTTCAG 59.301 42.308 19.41 14.45 0.00 3.02
1725 1873 8.288689 TGTGTGCACTATATAGAGTTTCAGTA 57.711 34.615 19.41 0.00 0.00 2.74
1751 1900 1.016627 TCAGCTGCATATTTCACCGC 58.983 50.000 9.47 0.00 0.00 5.68
1773 1922 5.786574 CGCGTGTTAAACAAGTTATTACTGG 59.213 40.000 0.00 0.00 34.01 4.00
1803 2084 1.860641 TAGGGAATTGCCTGAGTCGA 58.139 50.000 27.34 4.19 36.66 4.20
1826 2107 1.242076 AGAAACATGTCCAGTGCAGC 58.758 50.000 0.00 0.00 0.00 5.25
2134 2431 4.033358 GTGAATCTGTGCATGTACAGCTAC 59.967 45.833 31.96 24.31 45.94 3.58
2137 2434 2.029380 TCTGTGCATGTACAGCTACGTT 60.029 45.455 31.96 0.00 45.94 3.99
2146 2443 3.765511 TGTACAGCTACGTTACATCCCTT 59.234 43.478 0.00 0.00 0.00 3.95
2151 2448 5.172934 CAGCTACGTTACATCCCTTGTTAA 58.827 41.667 0.00 0.00 39.87 2.01
2167 2464 5.517770 CCTTGTTAAATAAATGCTGCTGCTC 59.482 40.000 17.00 0.00 40.48 4.26
2331 2638 5.294552 GGAATCAAGGAAGGATCGTTAACAG 59.705 44.000 6.39 0.00 32.64 3.16
2451 2766 8.608844 AGTATAACTACTGAGCATAAAATGCC 57.391 34.615 8.21 1.62 45.60 4.40
2539 2854 2.168728 GGCGTCTATGAAAGAGGGAGTT 59.831 50.000 0.00 0.00 39.92 3.01
2907 3223 8.786710 TTTATATTGTAGCTCCTAACCTGGTA 57.213 34.615 0.00 0.00 0.00 3.25
3154 3470 3.788227 AGTAGCAACAGATCAACCCAA 57.212 42.857 0.00 0.00 0.00 4.12
3191 3507 0.242017 GTCCAACAGATGCAAGTGCC 59.758 55.000 0.00 0.00 41.18 5.01
3341 3657 8.444783 TCTTGTATATTGTATTGTAAGCCCCAT 58.555 33.333 0.00 0.00 0.00 4.00
3414 3730 9.551734 TCATGATTTGTATTCTGTAGATTGGAG 57.448 33.333 0.00 0.00 0.00 3.86
3416 3732 7.861629 TGATTTGTATTCTGTAGATTGGAGGT 58.138 34.615 0.00 0.00 0.00 3.85
3438 3754 5.408604 GGTATTAAGCACCCGTATGATTCTG 59.591 44.000 0.00 0.00 29.40 3.02
3445 3761 4.671766 GCACCCGTATGATTCTGTTTCAAC 60.672 45.833 0.00 0.00 0.00 3.18
3446 3762 3.682858 ACCCGTATGATTCTGTTTCAACG 59.317 43.478 0.00 0.00 32.50 4.10
3500 3816 6.763355 TCAGATTAAGAAGTTTGAGCTCAGT 58.237 36.000 17.43 2.87 0.00 3.41
3524 3840 6.772770 TCGTCTTACGATGAAATTTGTTCA 57.227 33.333 0.00 0.00 46.73 3.18
3546 3865 8.680903 GTTCACTTTCAGGTTATTCATGATCAT 58.319 33.333 1.18 1.18 36.72 2.45
3673 3992 8.514594 CAGAAAATGTTGCTGAGGAATTTACTA 58.485 33.333 0.00 0.00 0.00 1.82
3702 4021 3.822735 CTGAGCCAACTCTGGAAAATGAA 59.177 43.478 0.00 0.00 46.92 2.57
3714 4033 3.890756 TGGAAAATGAATGTGTGACAGCT 59.109 39.130 0.00 0.00 0.00 4.24
3801 4120 6.708054 AGGCTATAATGCATGAACAGAGTAAC 59.292 38.462 0.00 0.00 34.04 2.50
3927 4246 5.751128 GCCTACTCATATGGGGTACTCTGTA 60.751 48.000 7.68 0.00 0.00 2.74
3981 4300 5.991933 ATGTCGAAGCATATCCTAGTGAT 57.008 39.130 0.00 0.00 37.49 3.06
4076 4395 0.811616 GCCGTTGCTAGTCATGGGAG 60.812 60.000 0.00 0.00 33.53 4.30
4320 4639 8.617290 TGAGATACGAATAGCAGACTGTAATA 57.383 34.615 3.99 0.00 0.00 0.98
4553 4872 1.068741 CTGGGAATAGGTACTGGCGAC 59.931 57.143 0.00 0.00 41.52 5.19
4588 4907 5.705609 GTTGAGGAACCATGTACAACATT 57.294 39.130 0.00 0.00 36.53 2.71
4814 5136 4.103785 CCACAGGATAATGACATTCCTCCT 59.896 45.833 19.50 19.50 37.80 3.69
4817 5139 4.596643 CAGGATAATGACATTCCTCCTCCT 59.403 45.833 21.26 15.02 37.80 3.69
4892 5214 0.041833 CTCCTCCACCTCCTCCTGAA 59.958 60.000 0.00 0.00 0.00 3.02
4903 5225 0.979665 CCTCCTGAACCTGAAGAGCA 59.020 55.000 0.00 0.00 0.00 4.26
4910 5232 0.679505 AACCTGAAGAGCACGCTGTA 59.320 50.000 0.00 0.00 0.00 2.74
5177 5499 4.761235 TTATAGCTATCCTTCCGTCACG 57.239 45.455 10.16 0.00 0.00 4.35
5304 5626 7.489113 CCCTTGTTGCAAATAGTAATGTGAATC 59.511 37.037 0.00 0.00 0.00 2.52
5368 5690 3.849911 CGTCTTTGAGCCAATCAGTAGA 58.150 45.455 0.00 0.00 39.68 2.59
5449 5771 5.811100 GCACCACTAATCAGACTAAAGGTAC 59.189 44.000 0.00 0.00 0.00 3.34
5493 5815 9.422681 AGGACACTTCATCTTACTAGCTTATAA 57.577 33.333 0.00 0.00 0.00 0.98
5589 5911 8.637099 TCATCACTGAGATCTAATAAGAAGGTG 58.363 37.037 0.00 0.00 34.73 4.00
5687 6012 1.694169 CTACCATCCACTGCCCCCT 60.694 63.158 0.00 0.00 0.00 4.79
5735 6060 8.791675 TGAAGAAATTTAACACACTGCATGATA 58.208 29.630 0.00 0.00 0.00 2.15
5830 6156 4.892934 ACTGTTCTTGGCCAGTTTATTTCA 59.107 37.500 5.11 0.00 38.76 2.69
6291 6630 1.205655 GGAGAAGCCAAGGAAAATGCC 59.794 52.381 0.00 0.00 36.34 4.40
6339 6678 6.069673 ACTGGTATTGTTCCTTCACCATATGA 60.070 38.462 3.65 0.00 38.54 2.15
6340 6679 6.910191 TGGTATTGTTCCTTCACCATATGAT 58.090 36.000 3.65 0.00 37.11 2.45
6458 6802 4.093408 CAGCGACAATTAATATGGATCGGG 59.907 45.833 0.00 0.00 0.00 5.14
6517 6861 9.224267 TCTCAAATTTATCCTTTCTGAGTCTTG 57.776 33.333 0.00 0.00 0.00 3.02
6570 6918 7.786030 TGCTTATAGACTTGAACTCTTGCTAT 58.214 34.615 0.00 0.00 0.00 2.97
6591 6942 1.479323 AGCATTGATTGTGGACCATGC 59.521 47.619 0.00 1.04 0.00 4.06
6615 6966 8.902806 TGCCATTTCTAGGATTACAAATGTTAG 58.097 33.333 9.96 0.00 35.37 2.34
6622 6973 4.949856 AGGATTACAAATGTTAGGCACCTG 59.050 41.667 0.00 0.00 0.00 4.00
6636 6987 5.488262 AGGCACCTGCATTTAATCTTTTT 57.512 34.783 0.00 0.00 44.36 1.94
6671 7022 6.833041 TGGGATTGTTCTAGTTTGTAACTCA 58.167 36.000 0.00 0.00 41.77 3.41
6750 7101 1.400759 GCTGAAGCAAAGAAGGAAGCG 60.401 52.381 0.00 0.00 41.59 4.68
6912 7266 5.809001 AGCTAAAACATCCAGACTGAATGA 58.191 37.500 8.87 0.00 0.00 2.57
7125 7480 9.220767 GATTAGTTGAAGATGGTCTAGTTTTGT 57.779 33.333 0.00 0.00 0.00 2.83
7163 7519 0.663568 CCTCGATCGATACGTTGCCC 60.664 60.000 19.78 0.00 0.00 5.36
7186 7566 1.289066 CGTCCTGAGAAGCAACCGA 59.711 57.895 0.00 0.00 0.00 4.69
7227 7607 6.547880 TGGTTTTGAGGCTGTATTGTTTCTTA 59.452 34.615 0.00 0.00 0.00 2.10
7325 7705 6.312426 ACTTGAGATCGAATTACTGAAGCAAG 59.688 38.462 0.00 0.00 35.33 4.01
7357 7737 3.801114 AGTTGCTGACCAAGGAAAAAC 57.199 42.857 0.00 0.00 38.05 2.43
7456 7836 9.211485 TCAATTTTAGGTTGTGCTAACTACTAC 57.789 33.333 4.78 0.00 33.23 2.73
7565 8108 1.340017 GCCCTCAGACACCATTTGCTA 60.340 52.381 0.00 0.00 0.00 3.49
7576 8119 5.460646 ACACCATTTGCTAGATTTCGTTTG 58.539 37.500 0.00 0.00 0.00 2.93
7578 8121 3.859386 CCATTTGCTAGATTTCGTTTGCC 59.141 43.478 0.00 0.00 0.00 4.52
7579 8122 3.569250 TTTGCTAGATTTCGTTTGCCC 57.431 42.857 0.00 0.00 0.00 5.36
7604 8180 2.307049 CAATTGACGTCCGCAAGTTTC 58.693 47.619 14.12 0.00 0.00 2.78
7606 8182 0.806884 TTGACGTCCGCAAGTTTCGT 60.807 50.000 14.12 0.00 38.30 3.85
7611 8187 1.511147 CGTCCGCAAGTTTCGTTTTTG 59.489 47.619 0.00 0.00 0.00 2.44
7612 8188 2.521996 GTCCGCAAGTTTCGTTTTTGT 58.478 42.857 0.00 0.00 0.00 2.83
7614 8190 3.365520 GTCCGCAAGTTTCGTTTTTGTTT 59.634 39.130 0.00 0.00 0.00 2.83
7615 8191 3.988517 TCCGCAAGTTTCGTTTTTGTTTT 59.011 34.783 0.00 0.00 0.00 2.43
7616 8192 4.078346 CCGCAAGTTTCGTTTTTGTTTTG 58.922 39.130 0.00 0.00 0.00 2.44
7617 8193 4.143305 CCGCAAGTTTCGTTTTTGTTTTGA 60.143 37.500 0.00 0.00 0.00 2.69
7618 8194 4.774054 CGCAAGTTTCGTTTTTGTTTTGAC 59.226 37.500 0.00 0.00 0.00 3.18
7619 8195 5.387958 CGCAAGTTTCGTTTTTGTTTTGACT 60.388 36.000 0.00 0.00 0.00 3.41
7620 8196 6.183359 CGCAAGTTTCGTTTTTGTTTTGACTA 60.183 34.615 0.00 0.00 0.00 2.59
7621 8197 7.164204 GCAAGTTTCGTTTTTGTTTTGACTAG 58.836 34.615 0.00 0.00 0.00 2.57
7648 8224 2.852075 TGGGTGTTTCGGGGCTCT 60.852 61.111 0.00 0.00 0.00 4.09
7711 8287 7.658525 AAAGCAATGGTGTCATCCAAATATA 57.341 32.000 0.00 0.00 41.09 0.86
7865 8441 9.533831 ACTTCAATAAATTGACCAATAGGAAGT 57.466 29.630 4.89 14.43 45.63 3.01
7926 8503 7.121020 TGAACTGTCTGCATAGCAAATCAAATA 59.879 33.333 0.00 0.00 38.41 1.40
7960 8537 5.182001 CAGACATCACAGGGTTTAGGAAAAG 59.818 44.000 0.00 0.00 0.00 2.27
7973 8550 7.620491 GGGTTTAGGAAAAGGTTTATCCCATAA 59.380 37.037 0.00 0.00 36.75 1.90
7983 8560 5.014228 AGGTTTATCCCATAATACAGAGCCC 59.986 44.000 0.00 0.00 36.75 5.19
8003 8580 2.354821 CCCTTATGGCGCTTTACAAGTC 59.645 50.000 7.64 0.00 0.00 3.01
8004 8581 2.354821 CCTTATGGCGCTTTACAAGTCC 59.645 50.000 7.64 0.00 0.00 3.85
8025 8602 1.959085 CAGCCAGGTTTGCGACAAT 59.041 52.632 0.00 0.00 0.00 2.71
8051 8628 4.215349 GCTCTTTCAGCCGCTGAT 57.785 55.556 23.48 0.00 43.17 2.90
8053 8630 1.023513 GCTCTTTCAGCCGCTGATGT 61.024 55.000 23.48 0.00 43.17 3.06
8190 8767 2.092429 AGCCCCACAACACCTACATATG 60.092 50.000 0.00 0.00 0.00 1.78
8196 8773 4.035558 CCACAACACCTACATATGTCATGC 59.964 45.833 12.68 0.00 0.00 4.06
8237 8814 5.588246 TCACAAGACAAGAAACATAACAGCA 59.412 36.000 0.00 0.00 0.00 4.41
8238 8815 6.262944 TCACAAGACAAGAAACATAACAGCAT 59.737 34.615 0.00 0.00 0.00 3.79
8251 8828 8.647143 AACATAACAGCATACATTATTTTGGC 57.353 30.769 0.00 0.00 0.00 4.52
8278 8855 8.492673 AGAATATGAACTCGCACAAGAAATAA 57.507 30.769 0.00 0.00 0.00 1.40
8306 8883 5.305644 GGCTGGATCTATCTACAAAGAGGAA 59.694 44.000 0.00 0.00 34.49 3.36
8323 8900 5.312079 AGAGGAAAAGAAGGATGTGTTCAG 58.688 41.667 0.00 0.00 0.00 3.02
8337 8914 1.488812 TGTTCAGTTGGCTACCACAGT 59.511 47.619 0.00 0.00 30.78 3.55
8354 8931 2.440253 ACAGTTGGCCACACCTAAGTTA 59.560 45.455 3.88 0.00 40.22 2.24
8410 8987 6.149474 AGTCTTGGTAAAAGCATATGTGTGAC 59.851 38.462 4.29 0.00 0.00 3.67
8435 9012 7.122650 ACATGTGGATTATGTTAGGAACCAAAG 59.877 37.037 0.00 0.00 35.32 2.77
8436 9013 6.548321 TGTGGATTATGTTAGGAACCAAAGT 58.452 36.000 0.00 0.00 0.00 2.66
8439 9023 6.657541 TGGATTATGTTAGGAACCAAAGTCAC 59.342 38.462 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 209 3.764218 TCTTCTCCCTTAGACTTGACGT 58.236 45.455 0.00 0.00 32.51 4.34
205 217 4.425772 TGTGGTTCATCTTCTCCCTTAGA 58.574 43.478 0.00 0.00 0.00 2.10
221 233 3.087031 CTCTTGCCTTCATCATGTGGTT 58.913 45.455 0.00 0.00 0.00 3.67
320 332 1.405105 TGCTTCTTCACGCTTTGCTTT 59.595 42.857 0.00 0.00 0.00 3.51
498 510 2.360801 CGGAACATCCTCTTCCTCTCTC 59.639 54.545 0.00 0.00 35.86 3.20
529 541 4.082136 GGAGTGTCACCTCGAAAAGTAGAT 60.082 45.833 0.00 0.00 31.98 1.98
735 751 6.391537 TCAACTTCCAAACAAACTACCAAAC 58.608 36.000 0.00 0.00 0.00 2.93
929 947 6.098266 AGCATTTTTAAGGGTTGAGAAGTGTT 59.902 34.615 0.00 0.00 0.00 3.32
950 968 9.710900 CTTAAAACCCTCAAATTCTTAAAGCAT 57.289 29.630 0.00 0.00 0.00 3.79
960 978 7.302948 AGTAGAACCCTTAAAACCCTCAAATT 58.697 34.615 0.00 0.00 0.00 1.82
971 989 8.605325 AGAGCATTACTAGTAGAACCCTTAAA 57.395 34.615 3.59 0.00 0.00 1.52
974 992 6.127026 CCAAGAGCATTACTAGTAGAACCCTT 60.127 42.308 3.59 3.49 0.00 3.95
1050 1068 1.378531 TTTTGCTCTGCACGTGTTCT 58.621 45.000 18.38 0.00 38.71 3.01
1115 1133 1.337118 GAATCAGGAGGAGAGGCGAT 58.663 55.000 0.00 0.00 0.00 4.58
1153 1174 2.670210 CGTCGGGGGTGTTTTACGC 61.670 63.158 0.00 0.00 41.21 4.42
1181 1202 4.776308 TGTCTTCTTCTAGGGTTAGGGTTC 59.224 45.833 0.00 0.00 0.00 3.62
1514 1658 3.061322 CAATCACAAACCATGCAACAGG 58.939 45.455 0.00 0.00 0.00 4.00
1515 1659 3.719924 ACAATCACAAACCATGCAACAG 58.280 40.909 0.00 0.00 0.00 3.16
1528 1672 0.675083 CAGGCAGCCAAACAATCACA 59.325 50.000 15.80 0.00 0.00 3.58
1551 1695 5.715439 ATCCACTTAATCAGGATGGACAA 57.285 39.130 0.00 0.00 42.12 3.18
1627 1771 0.324091 AGCCTCATTGCCCCTTCTTG 60.324 55.000 0.00 0.00 0.00 3.02
1628 1772 1.298953 TAGCCTCATTGCCCCTTCTT 58.701 50.000 0.00 0.00 0.00 2.52
1635 1779 5.168569 GTTTTAGGTTTTAGCCTCATTGCC 58.831 41.667 0.00 0.00 39.94 4.52
1691 1838 8.301252 TCTATATAGTGCACACAGGTTTAAGA 57.699 34.615 21.04 6.84 0.00 2.10
1698 1845 6.573434 TGAAACTCTATATAGTGCACACAGG 58.427 40.000 21.04 4.01 0.00 4.00
1723 1871 6.909357 GTGAAATATGCAGCTGAAAGTGATAC 59.091 38.462 20.43 3.84 35.30 2.24
1725 1873 5.163581 GGTGAAATATGCAGCTGAAAGTGAT 60.164 40.000 20.43 0.00 35.30 3.06
1751 1900 8.336806 TGAACCAGTAATAACTTGTTTAACACG 58.663 33.333 0.00 0.00 40.61 4.49
1773 1922 4.043435 AGGCAATTCCCTATATCCCTGAAC 59.957 45.833 0.00 0.00 32.11 3.18
1803 2084 2.158623 TGCACTGGACATGTTTCTTCCT 60.159 45.455 0.00 0.00 0.00 3.36
1930 2225 3.901844 ACTAGTAGTTTTGGTGGCTCTCA 59.098 43.478 0.00 0.00 0.00 3.27
1935 2230 6.877322 TGATCTTTACTAGTAGTTTTGGTGGC 59.123 38.462 8.40 0.00 0.00 5.01
1963 2258 4.374399 AGCTTCAAACTCCAAAAATGCAG 58.626 39.130 0.00 0.00 0.00 4.41
2134 2431 8.188139 AGCATTTATTTAACAAGGGATGTAACG 58.812 33.333 0.00 0.00 42.99 3.18
2137 2434 7.341769 AGCAGCATTTATTTAACAAGGGATGTA 59.658 33.333 0.00 0.00 42.99 2.29
2146 2443 5.641783 TGAGCAGCAGCATTTATTTAACA 57.358 34.783 3.17 0.00 45.49 2.41
2299 2606 5.786121 TCCTTCCTTGATTCCATCTCTTT 57.214 39.130 0.00 0.00 0.00 2.52
2300 2607 5.454471 CGATCCTTCCTTGATTCCATCTCTT 60.454 44.000 0.00 0.00 0.00 2.85
2301 2608 4.040217 CGATCCTTCCTTGATTCCATCTCT 59.960 45.833 0.00 0.00 0.00 3.10
2302 2609 4.202305 ACGATCCTTCCTTGATTCCATCTC 60.202 45.833 0.00 0.00 0.00 2.75
2451 2766 7.282585 TCAAGGTCTATTGGATATTTGGAGTG 58.717 38.462 0.00 0.00 0.00 3.51
2521 2836 4.712337 TCTCCAACTCCCTCTTTCATAGAC 59.288 45.833 0.00 0.00 0.00 2.59
2539 2854 1.758592 CCCACGGTTTTCCTCTCCA 59.241 57.895 0.00 0.00 37.95 3.86
2907 3223 3.494223 GGCGGCCCAGCAATAATTAAAAT 60.494 43.478 8.12 0.00 39.27 1.82
3154 3470 2.576648 GGACTCCCCTTAGTTTCACCAT 59.423 50.000 0.00 0.00 0.00 3.55
3414 3730 5.408604 CAGAATCATACGGGTGCTTAATACC 59.591 44.000 1.38 1.38 37.48 2.73
3416 3732 6.169557 ACAGAATCATACGGGTGCTTAATA 57.830 37.500 0.00 0.00 0.00 0.98
3438 3754 9.031360 TGCAAGATAAGATACTATCGTTGAAAC 57.969 33.333 0.00 0.00 34.11 2.78
3445 3761 8.726068 TCTTCTCTGCAAGATAAGATACTATCG 58.274 37.037 8.75 0.00 46.99 2.92
3524 3840 7.067859 CACCATGATCATGAATAACCTGAAAGT 59.932 37.037 32.71 16.15 41.20 2.66
3546 3865 3.118555 CGTTATCCCCAGTTACATCACCA 60.119 47.826 0.00 0.00 0.00 4.17
3702 4021 1.673033 GCTTCCGTAGCTGTCACACAT 60.673 52.381 0.00 0.00 46.77 3.21
3927 4246 1.350351 AGGACATGTGCTTGAGCTTCT 59.650 47.619 14.93 0.00 42.66 2.85
3981 4300 1.680735 GTGCCATTTCCAACAGACACA 59.319 47.619 0.00 0.00 0.00 3.72
4073 4392 0.253327 GGGGTCAATGTCCACTCTCC 59.747 60.000 0.00 0.00 0.00 3.71
4076 4395 1.826385 CAAGGGGTCAATGTCCACTC 58.174 55.000 1.02 0.00 37.79 3.51
4320 4639 1.783979 AGATCCATACGAGGAGAGGGT 59.216 52.381 0.00 0.00 41.90 4.34
4588 4907 5.070446 ACACCTTGTGAGTTCTGAACAGATA 59.930 40.000 21.50 4.07 35.72 1.98
4814 5136 1.074090 TTCTGGTGGTGGTGGAGGA 60.074 57.895 0.00 0.00 0.00 3.71
4817 5139 1.127567 CCTCTTCTGGTGGTGGTGGA 61.128 60.000 0.00 0.00 0.00 4.02
4892 5214 0.898320 ATACAGCGTGCTCTTCAGGT 59.102 50.000 0.00 0.00 33.35 4.00
4903 5225 3.691118 AGCATGAACAAATGATACAGCGT 59.309 39.130 0.00 0.00 0.00 5.07
5177 5499 1.661341 CTACTTCAGTGGCAGCCATC 58.339 55.000 19.75 11.63 35.28 3.51
5304 5626 4.808414 TCACTTTATCAGACTCCACAGG 57.192 45.455 0.00 0.00 0.00 4.00
5464 5786 5.482175 AGCTAGTAAGATGAAGTGTCCTTGT 59.518 40.000 0.00 0.00 0.00 3.16
5493 5815 8.389603 CAGTGCAAATGTCAAAACTAAAACAAT 58.610 29.630 0.00 0.00 0.00 2.71
5589 5911 3.983044 ACCTTATCCACCAGACTTGAC 57.017 47.619 0.00 0.00 0.00 3.18
5687 6012 5.247337 TCATTAATGTCAGGACACCACACTA 59.753 40.000 14.97 0.00 45.05 2.74
5735 6060 5.902613 ACACACAATTAGCAGTAATGCAT 57.097 34.783 18.53 5.20 37.25 3.96
5830 6156 4.383661 TGGACGACCTATATTGTGCACAAT 60.384 41.667 38.78 38.78 41.89 2.71
5863 6191 1.271054 ACACTCCCACTTGCATGAGTC 60.271 52.381 6.60 0.00 35.97 3.36
6291 6630 2.437651 ACCACCAAGGGGAACAAAATTG 59.562 45.455 0.00 0.00 43.89 2.32
6434 6778 4.093408 CCGATCCATATTAATTGTCGCTGG 59.907 45.833 0.00 0.00 0.00 4.85
6458 6802 1.303282 CCAAAGGCCAGTACTCCCC 59.697 63.158 5.01 0.00 0.00 4.81
6473 6817 7.537596 TTTGAGAAAGAGGAAAATATGCCAA 57.462 32.000 0.00 0.00 0.00 4.52
6570 6918 2.689471 GCATGGTCCACAATCAATGCTA 59.311 45.455 0.00 0.00 0.00 3.49
6591 6942 8.352942 GCCTAACATTTGTAATCCTAGAAATGG 58.647 37.037 15.19 3.54 46.03 3.16
6651 7002 7.715249 TGAGCTTGAGTTACAAACTAGAACAAT 59.285 33.333 0.00 0.00 43.03 2.71
6671 7022 6.240894 TGATGAAGATTACCAAGTTGAGCTT 58.759 36.000 3.87 0.00 38.08 3.74
6750 7101 4.026145 GCTGCACGAATAGATTCAGTCTTC 60.026 45.833 0.00 0.00 38.42 2.87
6912 7266 8.523915 TGTATTTATTGGAAACTGAGATGCAT 57.476 30.769 0.00 0.00 0.00 3.96
7125 7480 4.660168 GAGGTACGGGGATATCTACAGAA 58.340 47.826 2.05 0.00 0.00 3.02
7163 7519 0.318699 TTGCTTCTCAGGACGTGACG 60.319 55.000 2.24 2.24 0.00 4.35
7186 7566 7.255942 CCTCAAAACCAAGGTAACATCAGAAAT 60.256 37.037 0.00 0.00 41.41 2.17
7227 7607 8.915057 CACTATGATCTTCCAGTGGAAAATAT 57.085 34.615 24.59 17.50 41.54 1.28
7241 7621 3.208692 ACTCTCCTCCCCACTATGATCTT 59.791 47.826 0.00 0.00 0.00 2.40
7325 7705 6.452494 TGGTCAGCAACTAACTAGTAGATC 57.548 41.667 3.59 0.00 34.99 2.75
7357 7737 0.591170 CCACCACTTAACAAGGCACG 59.409 55.000 0.00 0.00 0.00 5.34
7533 8075 4.023963 GTGTCTGAGGGCACTTTTAAGTTC 60.024 45.833 0.00 0.00 37.08 3.01
7543 8086 0.883833 CAAATGGTGTCTGAGGGCAC 59.116 55.000 0.00 0.00 35.07 5.01
7578 8121 1.501741 CGGACGTCAATTGCCTTGG 59.498 57.895 18.91 0.00 35.43 3.61
7579 8122 1.154225 GCGGACGTCAATTGCCTTG 60.154 57.895 18.91 0.00 36.09 3.61
7604 8180 8.953990 CCATAAAGTCTAGTCAAAACAAAAACG 58.046 33.333 0.00 0.00 0.00 3.60
7606 8182 9.796120 CACCATAAAGTCTAGTCAAAACAAAAA 57.204 29.630 0.00 0.00 0.00 1.94
7611 8187 6.002082 ACCCACCATAAAGTCTAGTCAAAAC 58.998 40.000 0.00 0.00 0.00 2.43
7612 8188 6.001460 CACCCACCATAAAGTCTAGTCAAAA 58.999 40.000 0.00 0.00 0.00 2.44
7614 8190 4.595781 ACACCCACCATAAAGTCTAGTCAA 59.404 41.667 0.00 0.00 0.00 3.18
7615 8191 4.164981 ACACCCACCATAAAGTCTAGTCA 58.835 43.478 0.00 0.00 0.00 3.41
7616 8192 4.820894 ACACCCACCATAAAGTCTAGTC 57.179 45.455 0.00 0.00 0.00 2.59
7617 8193 5.557866 GAAACACCCACCATAAAGTCTAGT 58.442 41.667 0.00 0.00 0.00 2.57
7618 8194 4.630069 CGAAACACCCACCATAAAGTCTAG 59.370 45.833 0.00 0.00 0.00 2.43
7619 8195 4.563993 CCGAAACACCCACCATAAAGTCTA 60.564 45.833 0.00 0.00 0.00 2.59
7620 8196 3.408634 CGAAACACCCACCATAAAGTCT 58.591 45.455 0.00 0.00 0.00 3.24
7621 8197 2.486592 CCGAAACACCCACCATAAAGTC 59.513 50.000 0.00 0.00 0.00 3.01
7648 8224 0.812549 GCATCATGTCATGTGCACCA 59.187 50.000 23.80 5.05 37.30 4.17
7711 8287 8.506168 TCTGTTCTACTTTCTTTTGTGATTGT 57.494 30.769 0.00 0.00 0.00 2.71
7800 8376 5.049543 GGAGCTGATATTCTTGCATCTGAAC 60.050 44.000 0.00 0.00 0.00 3.18
7850 8426 7.286546 TGATGTTTCAAACTTCCTATTGGTCAA 59.713 33.333 12.38 0.00 35.38 3.18
7865 8441 3.306225 GCATGGAAGCCTGATGTTTCAAA 60.306 43.478 0.00 0.00 0.00 2.69
7891 8467 1.881973 GCAGACAGTTCAAAGCATCCA 59.118 47.619 0.00 0.00 0.00 3.41
7926 8503 3.560025 CCTGTGATGTCTGGCCTTAGTTT 60.560 47.826 3.32 0.00 0.00 2.66
7960 8537 5.254115 GGGCTCTGTATTATGGGATAAACC 58.746 45.833 0.00 0.00 38.08 3.27
8046 8623 1.403679 AGACAGCGAGACTACATCAGC 59.596 52.381 0.00 0.00 34.55 4.26
8051 8628 2.783609 ACCTAGACAGCGAGACTACA 57.216 50.000 0.00 0.00 0.00 2.74
8053 8630 3.055312 TCTGAACCTAGACAGCGAGACTA 60.055 47.826 0.00 0.00 34.57 2.59
8190 8767 3.360249 ACACTCTTTTTGCTGCATGAC 57.640 42.857 1.84 0.00 0.00 3.06
8196 8773 6.634436 GTCTTGTGATAACACTCTTTTTGCTG 59.366 38.462 4.65 0.00 46.07 4.41
8251 8828 5.784750 TCTTGTGCGAGTTCATATTCTTG 57.215 39.130 0.00 0.00 0.00 3.02
8278 8855 6.139671 TCTTTGTAGATAGATCCAGCCTTCT 58.860 40.000 0.00 0.00 0.00 2.85
8306 8883 3.319122 GCCAACTGAACACATCCTTCTTT 59.681 43.478 0.00 0.00 0.00 2.52
8337 8914 2.882229 GCCATAACTTAGGTGTGGCCAA 60.882 50.000 24.74 0.00 44.89 4.52
8410 8987 7.122650 ACTTTGGTTCCTAACATAATCCACATG 59.877 37.037 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.