Multiple sequence alignment - TraesCS7B01G229800

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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 TraesCS7B01G229800 chr7B 100.000 6024 0 0 1 6024 431684495 431690518 0.000000e+00 11125
1 TraesCS7B01G229800 chr7D 92.763 2653 125 32 1 2615 416246928 416249551 0.000000e+00 3773
2 TraesCS7B01G229800 chr7D 91.677 2535 148 37 2733 5234 416249662 416252166 0.000000e+00 3454
3 TraesCS7B01G229800 chr7D 86.553 647 61 20 4599 5234 416252587 416253218 0.000000e+00 689
4 TraesCS7B01G229800 chr7D 86.503 652 58 22 4599 5234 416270684 416271321 0.000000e+00 689
5 TraesCS7B01G229800 chr7D 86.565 655 51 19 4599 5234 416268562 416269198 0.000000e+00 688
6 TraesCS7B01G229800 chr7D 85.021 701 72 17 5339 6011 416272728 416273423 0.000000e+00 682
7 TraesCS7B01G229800 chr7D 85.714 651 64 22 4599 5234 416269626 416270262 0.000000e+00 660
8 TraesCS7B01G229800 chr7D 85.100 651 62 19 4599 5234 416271772 416272402 3.060000e-177 632
9 TraesCS7B01G229800 chr7A 91.006 2724 161 45 2745 5412 478582382 478585077 0.000000e+00 3596
10 TraesCS7B01G229800 chr7A 92.467 1500 79 19 144 1619 478579770 478581259 0.000000e+00 2113
11 TraesCS7B01G229800 chr7A 94.602 1093 54 4 1648 2738 478581258 478582347 0.000000e+00 1687
12 TraesCS7B01G229800 chr7A 85.981 321 25 6 5722 6024 478585322 478585640 5.820000e-85 326
13 TraesCS7B01G229800 chr7A 91.667 144 7 3 5494 5633 478585123 478585265 1.710000e-45 195
14 TraesCS7B01G229800 chr7A 92.929 99 7 0 1 99 478579666 478579764 1.750000e-30 145
15 TraesCS7B01G229800 chr2D 86.747 249 30 3 4477 4723 651315640 651315393 2.140000e-69 274
16 TraesCS7B01G229800 chr2D 90.164 122 12 0 1076 1197 651319397 651319276 6.250000e-35 159
17 TraesCS7B01G229800 chr2B 86.531 245 32 1 4477 4721 780785833 780785590 9.950000e-68 268
18 TraesCS7B01G229800 chr2B 88.525 122 14 0 1076 1197 780789598 780789477 1.350000e-31 148
19 TraesCS7B01G229800 chr2A 86.777 242 31 1 4477 4718 776290366 776290606 9.950000e-68 268
20 TraesCS7B01G229800 chr2A 87.597 129 14 1 1071 1197 776286718 776286846 1.350000e-31 148
21 TraesCS7B01G229800 chr6B 94.872 78 4 0 1931 2008 310218305 310218228 8.200000e-24 122
22 TraesCS7B01G229800 chr1B 94.805 77 4 0 1931 2007 347578977 347578901 2.950000e-23 121


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 TraesCS7B01G229800 chr7B 431684495 431690518 6023 False 11125.000000 11125 100.0000 1 6024 1 chr7B.!!$F1 6023
1 TraesCS7B01G229800 chr7D 416246928 416253218 6290 False 2638.666667 3773 90.3310 1 5234 3 chr7D.!!$F1 5233
2 TraesCS7B01G229800 chr7D 416268562 416273423 4861 False 670.200000 689 85.7806 4599 6011 5 chr7D.!!$F2 1412
3 TraesCS7B01G229800 chr7A 478579666 478585640 5974 False 1343.666667 3596 91.4420 1 6024 6 chr7A.!!$F1 6023
4 TraesCS7B01G229800 chr2D 651315393 651319397 4004 True 216.500000 274 88.4555 1076 4723 2 chr2D.!!$R1 3647
5 TraesCS7B01G229800 chr2B 780785590 780789598 4008 True 208.000000 268 87.5280 1076 4721 2 chr2B.!!$R1 3645
6 TraesCS7B01G229800 chr2A 776286718 776290606 3888 False 208.000000 268 87.1870 1071 4718 2 chr2A.!!$F1 3647

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
776 796 0.108520 TCACGTAAACCGAGATGGCC 60.109 55.0 0.00 0.0 43.94 5.36 F
1310 2046 1.111116 TTCCGTCGGTGAAGGTCTGT 61.111 55.0 11.88 0.0 33.12 3.41 F
2921 4158 0.474854 TTGGGAAGTCCTGGCCTGTA 60.475 55.0 3.32 0.0 36.20 2.74 F
3561 4799 0.108186 CTGTGCGGGATTACAGCTCA 60.108 55.0 0.00 0.0 38.01 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 2371 0.458260 ACCACGGAACAACCAAAAGC 59.542 50.000 0.00 0.00 38.90 3.51 R
3247 4484 3.181466 TGACATATGGATCACTTGGACCG 60.181 47.826 7.80 0.00 0.00 4.79 R
4088 5346 0.248990 AACAACATTGTGCCGCACAG 60.249 50.000 24.48 17.09 45.39 3.66 R
5317 9138 0.603569 CAACGAGAGCCAGTACCAGT 59.396 55.000 0.00 0.00 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 8.070034 AGATATCACTTGCAAATTTTGATGGA 57.930 30.769 13.26 3.25 0.00 3.41
495 505 2.263945 GAAACCAAACCAAACCACACG 58.736 47.619 0.00 0.00 0.00 4.49
543 563 1.803519 GCGACAGGAAGAGCACGAG 60.804 63.158 0.00 0.00 0.00 4.18
610 630 1.446272 CGTCCTCGAAGGCCTTGAC 60.446 63.158 26.25 21.80 39.71 3.18
729 749 1.476235 CGACTTCACGTGACGCAACA 61.476 55.000 19.90 0.76 0.00 3.33
730 750 0.859232 GACTTCACGTGACGCAACAT 59.141 50.000 19.90 0.00 0.00 2.71
769 789 2.610976 CCACCTCATTCACGTAAACCGA 60.611 50.000 0.00 0.00 40.70 4.69
774 794 3.517602 TCATTCACGTAAACCGAGATGG 58.482 45.455 0.00 0.00 46.41 3.51
776 796 0.108520 TCACGTAAACCGAGATGGCC 60.109 55.000 0.00 0.00 43.94 5.36
796 816 2.391389 CGCTTTCCGCCAAGAGGTC 61.391 63.158 0.00 0.00 37.19 3.85
805 825 1.870580 CGCCAAGAGGTCACGTAAACA 60.871 52.381 0.00 0.00 37.19 2.83
806 826 1.798813 GCCAAGAGGTCACGTAAACAG 59.201 52.381 0.00 0.00 37.19 3.16
809 829 2.800544 CAAGAGGTCACGTAAACAGTGG 59.199 50.000 0.00 0.00 39.86 4.00
811 831 2.296471 AGAGGTCACGTAAACAGTGGAG 59.704 50.000 0.00 0.00 39.86 3.86
859 879 1.672356 GTGGCACTGTGGTAGGCAG 60.672 63.158 11.13 0.00 38.56 4.85
860 880 2.747855 GGCACTGTGGTAGGCAGC 60.748 66.667 10.21 0.00 37.47 5.25
1058 1090 1.615424 CCGGGGGAGGAAAAGGAGA 60.615 63.158 0.00 0.00 0.00 3.71
1209 1450 2.041265 AGGTCGCTCCATTCCCCT 59.959 61.111 0.00 0.00 39.02 4.79
1210 1451 1.616628 AGGTCGCTCCATTCCCCTT 60.617 57.895 0.00 0.00 39.02 3.95
1212 1453 1.153147 GTCGCTCCATTCCCCTTCC 60.153 63.158 0.00 0.00 0.00 3.46
1222 1469 4.107961 TCCATTCCCCTTCCTTTTTCTCTT 59.892 41.667 0.00 0.00 0.00 2.85
1276 2012 3.962481 CGACTAGCTGCGATTAATTTTGC 59.038 43.478 0.00 0.00 0.00 3.68
1310 2046 1.111116 TTCCGTCGGTGAAGGTCTGT 61.111 55.000 11.88 0.00 33.12 3.41
1323 2059 2.665165 AGGTCTGTCACATTTGCCAAA 58.335 42.857 0.00 0.00 0.00 3.28
1339 2075 9.472361 CATTTGCCAAATTCTCTCATATTTAGG 57.528 33.333 0.00 0.00 0.00 2.69
1462 2198 7.241042 ACTAACAGTAGAAATAGCTTGTGGA 57.759 36.000 0.00 0.00 0.00 4.02
1471 2207 6.161381 AGAAATAGCTTGTGGAAAATGCAAG 58.839 36.000 0.00 0.00 0.00 4.01
1475 2211 3.054878 GCTTGTGGAAAATGCAAGTGAG 58.945 45.455 0.00 0.00 0.00 3.51
1490 2226 1.160137 GTGAGGTGCTTGTTGCCTAG 58.840 55.000 0.00 0.00 42.00 3.02
1533 2269 1.559682 TGCAATGAACCCCTAGTCTCC 59.440 52.381 0.00 0.00 0.00 3.71
1557 2293 6.894339 CTAACTGTAGGATTTGTGGGTTTT 57.106 37.500 0.00 0.00 0.00 2.43
1619 2358 8.154203 TCCAATTGTAGACACTCATCAAGTAAA 58.846 33.333 4.43 0.00 36.07 2.01
1625 2370 5.798132 AGACACTCATCAAGTAAATGCTGA 58.202 37.500 0.00 0.00 36.07 4.26
1626 2371 5.873712 AGACACTCATCAAGTAAATGCTGAG 59.126 40.000 6.60 6.60 44.90 3.35
1633 2379 5.125100 TCAAGTAAATGCTGAGCTTTTGG 57.875 39.130 23.43 12.74 36.74 3.28
1646 2392 1.535226 GCTTTTGGTTGTTCCGTGGTC 60.535 52.381 0.00 0.00 39.52 4.02
1655 2401 1.156736 GTTCCGTGGTCAATCAGTGG 58.843 55.000 0.00 0.00 0.00 4.00
1678 2424 4.217550 GTGCTTAAAATGGTCTGTTGCCTA 59.782 41.667 0.00 0.00 0.00 3.93
1719 2465 9.165035 ACAATTTATTTATCTTTGCAACCCATG 57.835 29.630 0.00 0.00 0.00 3.66
1810 2556 3.499745 GGGTGATTTTACAGGGTGGAAGT 60.500 47.826 0.00 0.00 0.00 3.01
1845 2591 4.496183 TCGTTTGTTACAAACATTTCGTGC 59.504 37.500 31.55 9.67 41.79 5.34
1848 2594 2.223272 TGTTACAAACATTTCGTGCGCA 60.223 40.909 5.66 5.66 36.25 6.09
2220 3197 9.388346 GACTATGATTACTTTGAGTATCTCACG 57.612 37.037 0.00 0.00 40.46 4.35
2315 3292 8.946085 TGGTAAGTCTCACATGAATAATTGAAC 58.054 33.333 0.00 0.00 0.00 3.18
2321 3298 9.844790 GTCTCACATGAATAATTGAACATCAAA 57.155 29.630 0.00 0.00 40.12 2.69
2364 3341 2.811431 CCTGCCAATTTGTGAGAACGTA 59.189 45.455 0.00 0.00 0.00 3.57
2369 3346 4.675114 GCCAATTTGTGAGAACGTAAAGTG 59.325 41.667 0.00 0.00 0.00 3.16
2370 3347 5.732247 GCCAATTTGTGAGAACGTAAAGTGT 60.732 40.000 6.09 0.00 0.00 3.55
2373 3350 8.714179 CCAATTTGTGAGAACGTAAAGTGTATA 58.286 33.333 6.09 0.00 0.00 1.47
2376 3353 8.821147 TTTGTGAGAACGTAAAGTGTATATGT 57.179 30.769 0.00 0.00 0.00 2.29
2601 3590 5.765677 TCGGTCCATTTATCTGTTTCACAAA 59.234 36.000 0.00 0.00 0.00 2.83
2632 3621 3.887621 TTCCTGAGTTCCTATCCAACG 57.112 47.619 0.00 0.00 0.00 4.10
2674 3663 8.763601 AGTTAAAGCATACTTCTCTTCTATGGT 58.236 33.333 0.00 0.00 34.05 3.55
2675 3664 8.821894 GTTAAAGCATACTTCTCTTCTATGGTG 58.178 37.037 0.00 0.00 34.05 4.17
2738 3728 7.450074 TCTTTCAATAAGGAAACACTAGCAGA 58.550 34.615 0.00 0.00 33.48 4.26
2742 3732 2.440539 AGGAAACACTAGCAGACACG 57.559 50.000 0.00 0.00 0.00 4.49
2752 3770 1.229428 AGCAGACACGTTGTGATTGG 58.771 50.000 3.61 0.00 36.96 3.16
2786 3808 9.906660 TGGTTACATTAGATTCAATTTGACAAC 57.093 29.630 0.00 0.00 0.00 3.32
2912 4149 3.620488 TGTTGCAGATATTGGGAAGTCC 58.380 45.455 0.00 0.00 0.00 3.85
2921 4158 0.474854 TTGGGAAGTCCTGGCCTGTA 60.475 55.000 3.32 0.00 36.20 2.74
2927 4164 4.386424 GGGAAGTCCTGGCCTGTATTAATT 60.386 45.833 3.32 0.00 35.95 1.40
3009 4246 2.042741 TTGCTGGGATGCCATGGG 60.043 61.111 15.13 0.00 0.00 4.00
3050 4287 4.835284 TGCCCTTGTAATATCAGTCACA 57.165 40.909 0.00 0.00 0.00 3.58
3101 4338 7.903145 TGCTCTACCTGACTTCTAAACAATAA 58.097 34.615 0.00 0.00 0.00 1.40
3102 4339 8.035394 TGCTCTACCTGACTTCTAAACAATAAG 58.965 37.037 0.00 0.00 0.00 1.73
3148 4385 4.127566 GGCAAAGTGGCATCATGTTATT 57.872 40.909 0.00 0.00 43.14 1.40
3163 4400 9.507280 CATCATGTTATTTTTATCAGGACACAC 57.493 33.333 0.00 0.00 0.00 3.82
3175 4412 4.960938 TCAGGACACACCATCTTATATGC 58.039 43.478 0.00 0.00 42.04 3.14
3244 4481 4.947388 GGCAATGATCCCTTAACTGTTGTA 59.053 41.667 2.69 0.00 0.00 2.41
3247 4484 7.196331 GCAATGATCCCTTAACTGTTGTAATC 58.804 38.462 2.69 0.77 0.00 1.75
3533 4771 0.179032 TCACATGCACACCGTTTCCT 60.179 50.000 0.00 0.00 0.00 3.36
3561 4799 0.108186 CTGTGCGGGATTACAGCTCA 60.108 55.000 0.00 0.00 38.01 4.26
3690 4936 2.224843 TGGTGAAGTCCATGCACTCATT 60.225 45.455 0.00 0.00 33.25 2.57
3747 4993 7.148340 GCTATCATCTATATGTTCTGGTTTGCC 60.148 40.741 0.00 0.00 34.50 4.52
3783 5029 2.827800 TCAGCTCTGGTCAAGTTCTG 57.172 50.000 0.00 0.00 0.00 3.02
3894 5140 1.063038 ACCCCTCATATTGGCATTGCA 60.063 47.619 11.39 0.00 0.00 4.08
3930 5176 1.169661 TTGGCTGTTACTGGGCAACG 61.170 55.000 11.75 0.00 41.76 4.10
3936 5182 1.683917 TGTTACTGGGCAACGCAATTT 59.316 42.857 0.00 0.00 37.60 1.82
4024 5270 0.685097 ATCGGTAAGCACCACACACT 59.315 50.000 0.00 0.00 46.14 3.55
4078 5336 9.856162 TTTAACATTAGAAGGTACTGTTTTCCT 57.144 29.630 0.48 0.00 40.86 3.36
4088 5346 2.490991 ACTGTTTTCCTTACGGCTGAC 58.509 47.619 0.00 0.00 0.00 3.51
4305 5565 1.821753 CTCGGGAAGACAGTGTCATCT 59.178 52.381 24.73 9.00 34.60 2.90
4430 5690 1.382522 ACAACTGTCTTGTGTGGCTG 58.617 50.000 0.00 0.00 0.00 4.85
4434 5694 1.065491 ACTGTCTTGTGTGGCTGTGAA 60.065 47.619 0.00 0.00 0.00 3.18
4435 5695 2.016318 CTGTCTTGTGTGGCTGTGAAA 58.984 47.619 0.00 0.00 0.00 2.69
4450 5710 2.177173 GTGAAAAGAATTGCGCCGATC 58.823 47.619 4.18 0.00 0.00 3.69
4452 5712 0.098728 AAAAGAATTGCGCCGATCCG 59.901 50.000 4.18 0.00 0.00 4.18
4461 5721 1.641677 CGCCGATCCGAATTGGTTC 59.358 57.895 0.00 0.00 38.56 3.62
4470 5730 4.360951 TCCGAATTGGTTCCTTAACACT 57.639 40.909 0.00 0.00 37.34 3.55
4479 5739 4.196971 GGTTCCTTAACACTGTGAACTGT 58.803 43.478 15.86 0.00 37.34 3.55
4508 5891 1.766625 TTGCGGTTACGGGGAAAGGA 61.767 55.000 0.00 0.00 41.36 3.36
4526 5909 1.453155 GATTCTGCAAAGCCTCCGAA 58.547 50.000 0.00 0.00 0.00 4.30
4568 5951 0.108377 ACAACATACTGCGCATCGGA 60.108 50.000 12.24 0.00 0.00 4.55
4577 5960 0.676466 TGCGCATCGGAAAGGTGAAT 60.676 50.000 5.66 0.00 30.86 2.57
4586 5969 2.676750 CGGAAAGGTGAATGTCATCGGA 60.677 50.000 0.00 0.00 31.44 4.55
4633 7074 4.363990 CGTGAGCCTGTCCAGCGT 62.364 66.667 0.00 0.00 34.64 5.07
4697 7138 4.158579 TCTGCTCACAACAAGATATCGTCT 59.841 41.667 0.00 0.00 39.43 4.18
4736 7177 6.656632 CTGGTAAGCAAGTGATATCCTCTA 57.343 41.667 0.00 0.00 0.00 2.43
4737 7178 7.055667 CTGGTAAGCAAGTGATATCCTCTAA 57.944 40.000 0.00 0.00 0.00 2.10
4747 7188 6.157211 AGTGATATCCTCTAAAAATACGGCG 58.843 40.000 4.80 4.80 0.00 6.46
4748 7189 6.015688 AGTGATATCCTCTAAAAATACGGCGA 60.016 38.462 16.62 0.00 0.00 5.54
4761 7209 0.680280 ACGGCGACACTCACCTATCT 60.680 55.000 16.62 0.00 0.00 1.98
4795 7243 7.751732 TGCATGCATAACTGAACTTAACTTAG 58.248 34.615 18.46 0.00 0.00 2.18
4828 7289 6.385843 TGACATATGTGTACATTTTGGTTGC 58.614 36.000 14.43 0.00 39.09 4.17
4861 7322 3.687102 CTCGGGTACGTGGTGGCA 61.687 66.667 0.00 0.00 41.85 4.92
4886 7347 2.185310 CTTCTTCGGGGTGGTGGAGG 62.185 65.000 0.00 0.00 0.00 4.30
5025 7486 3.136123 CACGCAGGGCCCTTGATG 61.136 66.667 26.10 16.81 0.00 3.07
5055 7517 3.504863 CTTTGGGCATTGATCGACTTTG 58.495 45.455 0.00 0.00 0.00 2.77
5117 7579 7.956420 TGGCTTTGACCATAATAATACTACG 57.044 36.000 0.00 0.00 33.75 3.51
5119 7581 7.439955 TGGCTTTGACCATAATAATACTACGTG 59.560 37.037 0.00 0.00 33.75 4.49
5199 7670 1.608283 GGACCGTGGAAAAGACCTCTG 60.608 57.143 0.00 0.00 0.00 3.35
5203 8765 2.338500 CGTGGAAAAGACCTCTGCTAC 58.662 52.381 0.00 0.00 0.00 3.58
5210 8772 5.394224 AAAAGACCTCTGCTACTAGTGTC 57.606 43.478 5.39 2.32 0.00 3.67
5277 9056 0.405198 TGGTGGATGTTGCTCCATGT 59.595 50.000 0.00 0.00 46.67 3.21
5283 9062 2.012673 GATGTTGCTCCATGTCTGACC 58.987 52.381 5.17 0.00 0.00 4.02
5301 9122 5.365605 TCTGACCGTTCAACCTATATCCATT 59.634 40.000 0.00 0.00 0.00 3.16
5321 9142 7.696981 TCCATTCTAGGTATAGGTAGTACTGG 58.303 42.308 5.39 0.00 0.00 4.00
5322 9143 7.296628 TCCATTCTAGGTATAGGTAGTACTGGT 59.703 40.741 5.39 0.00 0.00 4.00
5323 9144 8.609483 CCATTCTAGGTATAGGTAGTACTGGTA 58.391 40.741 5.39 0.00 0.00 3.25
5324 9145 9.447157 CATTCTAGGTATAGGTAGTACTGGTAC 57.553 40.741 5.39 2.97 36.35 3.34
5326 9147 8.200024 TCTAGGTATAGGTAGTACTGGTACTG 57.800 42.308 19.83 2.98 45.25 2.74
5327 9148 6.198237 AGGTATAGGTAGTACTGGTACTGG 57.802 45.833 19.83 0.00 45.25 4.00
5328 9149 4.764308 GGTATAGGTAGTACTGGTACTGGC 59.236 50.000 19.83 13.33 45.25 4.85
5329 9150 4.810584 ATAGGTAGTACTGGTACTGGCT 57.189 45.455 19.83 0.80 45.25 4.75
5330 9151 3.015675 AGGTAGTACTGGTACTGGCTC 57.984 52.381 19.83 9.71 45.25 4.70
5331 9152 2.581709 AGGTAGTACTGGTACTGGCTCT 59.418 50.000 19.83 10.62 45.25 4.09
5332 9153 2.950975 GGTAGTACTGGTACTGGCTCTC 59.049 54.545 19.83 6.59 45.25 3.20
5333 9154 1.752683 AGTACTGGTACTGGCTCTCG 58.247 55.000 11.97 0.00 44.11 4.04
5334 9155 1.004511 AGTACTGGTACTGGCTCTCGT 59.995 52.381 11.97 0.00 44.11 4.18
5335 9156 1.817447 GTACTGGTACTGGCTCTCGTT 59.183 52.381 3.89 0.00 33.45 3.85
5336 9157 0.603569 ACTGGTACTGGCTCTCGTTG 59.396 55.000 0.00 0.00 0.00 4.10
5337 9158 0.603569 CTGGTACTGGCTCTCGTTGT 59.396 55.000 0.00 0.00 0.00 3.32
5347 9168 4.693283 TGGCTCTCGTTGTTATAATGGAG 58.307 43.478 0.00 0.00 0.00 3.86
5412 9233 3.763360 CTGGTGTAAAGCAATGGAATGGA 59.237 43.478 0.00 0.00 0.00 3.41
5490 9316 5.642491 ACTAAGAAAACGTATTTCCTGCTCC 59.358 40.000 15.14 0.00 0.00 4.70
5496 9322 1.291132 GTATTTCCTGCTCCTGTCGC 58.709 55.000 0.00 0.00 0.00 5.19
5536 9362 1.617850 TCCTAAGAAAACGTGCCGGTA 59.382 47.619 1.90 0.00 0.00 4.02
5550 9376 1.135344 GCCGGTAGTCAACAGAGACTC 60.135 57.143 1.90 0.00 45.35 3.36
5551 9377 2.160205 CCGGTAGTCAACAGAGACTCA 58.840 52.381 5.02 0.00 45.35 3.41
5633 9462 3.455910 CTGGTGGGTTTAGATGGATGAGA 59.544 47.826 0.00 0.00 0.00 3.27
5670 9536 2.897326 TGGAGTGGAGACGAGAATGAAA 59.103 45.455 0.00 0.00 0.00 2.69
5671 9537 3.323691 TGGAGTGGAGACGAGAATGAAAA 59.676 43.478 0.00 0.00 0.00 2.29
5672 9538 4.020218 TGGAGTGGAGACGAGAATGAAAAT 60.020 41.667 0.00 0.00 0.00 1.82
5673 9539 4.331168 GGAGTGGAGACGAGAATGAAAATG 59.669 45.833 0.00 0.00 0.00 2.32
5674 9540 5.152623 AGTGGAGACGAGAATGAAAATGA 57.847 39.130 0.00 0.00 0.00 2.57
5675 9541 5.551233 AGTGGAGACGAGAATGAAAATGAA 58.449 37.500 0.00 0.00 0.00 2.57
5692 9558 1.152963 AACTCACAGCCACCACCAC 60.153 57.895 0.00 0.00 0.00 4.16
5710 9576 6.555360 ACCACCACCAACTCCAATTTATTTAA 59.445 34.615 0.00 0.00 0.00 1.52
5711 9577 7.236640 ACCACCACCAACTCCAATTTATTTAAT 59.763 33.333 0.00 0.00 0.00 1.40
5712 9578 8.100164 CCACCACCAACTCCAATTTATTTAATT 58.900 33.333 0.00 0.00 36.90 1.40
5746 9639 3.766151 GACGGTCGTCTAATGATTCACA 58.234 45.455 15.25 0.00 41.57 3.58
5751 9644 5.051441 CGGTCGTCTAATGATTCACATGAAG 60.051 44.000 0.00 0.00 39.39 3.02
5765 9658 8.809468 ATTCACATGAAGTCTACTCTACACTA 57.191 34.615 0.00 0.00 37.48 2.74
5766 9659 7.851387 TCACATGAAGTCTACTCTACACTAG 57.149 40.000 0.00 0.00 0.00 2.57
5823 9716 0.394216 TGTCGGCCATCTGAAATGGG 60.394 55.000 2.24 0.00 39.53 4.00
5831 9724 2.767394 CCATCTGAAATGGGAATTGCCA 59.233 45.455 21.95 21.95 38.95 4.92
5945 9850 0.179108 CGCCTCCTAAAAGGTCTCCG 60.179 60.000 0.00 0.00 38.79 4.63
5981 9886 1.066858 TCATTTCCTGTCACTCTCCGC 60.067 52.381 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 7.121168 TGCAAGTGATATCTTTGGTTTCTTAGG 59.879 37.037 16.86 0.00 0.00 2.69
142 143 5.945784 TGCAGCTGTAGGAAAACAATAGAAT 59.054 36.000 16.64 0.00 0.00 2.40
520 540 0.108472 TGCTCTTCCTGTCGCATCTG 60.108 55.000 0.00 0.00 0.00 2.90
529 549 0.967887 TCCTCCTCGTGCTCTTCCTG 60.968 60.000 0.00 0.00 0.00 3.86
543 563 0.615850 CAGGTCACTTCCCTTCCTCC 59.384 60.000 0.00 0.00 0.00 4.30
747 767 2.610976 CGGTTTACGTGAATGAGGTGGA 60.611 50.000 0.00 0.00 37.93 4.02
769 789 4.489771 CGGAAAGCGGGGCCATCT 62.490 66.667 4.39 0.00 0.00 2.90
790 810 2.296471 CTCCACTGTTTACGTGACCTCT 59.704 50.000 0.00 0.00 34.35 3.69
796 816 1.415374 CGGACTCCACTGTTTACGTG 58.585 55.000 0.00 0.00 0.00 4.49
805 825 1.179814 ACTCGAAAGCGGACTCCACT 61.180 55.000 0.00 0.00 38.28 4.00
806 826 0.319641 AACTCGAAAGCGGACTCCAC 60.320 55.000 0.00 0.00 38.28 4.02
809 829 1.782181 GCAACTCGAAAGCGGACTC 59.218 57.895 0.00 0.00 38.28 3.36
1222 1469 4.157656 AGCGGCAGAAAAATAGTAAATGCA 59.842 37.500 1.45 0.00 33.94 3.96
1310 2046 5.988310 ATGAGAGAATTTGGCAAATGTGA 57.012 34.783 24.96 6.39 0.00 3.58
1339 2075 4.779993 ACCCATCCTTGGAAGATCTAAC 57.220 45.455 0.00 0.00 46.92 2.34
1349 2085 1.417890 CTAGGCTGTACCCATCCTTGG 59.582 57.143 0.00 0.00 38.21 3.61
1462 2198 2.431782 ACAAGCACCTCACTTGCATTTT 59.568 40.909 3.52 0.00 46.81 1.82
1533 2269 4.569719 ACCCACAAATCCTACAGTTAGG 57.430 45.455 0.00 0.00 46.03 2.69
1548 2284 3.041946 ACCTTATTTGGCAAAACCCACA 58.958 40.909 17.70 0.00 37.83 4.17
1619 2358 2.036346 GGAACAACCAAAAGCTCAGCAT 59.964 45.455 0.00 0.00 38.79 3.79
1625 2370 0.744281 CCACGGAACAACCAAAAGCT 59.256 50.000 0.00 0.00 38.90 3.74
1626 2371 0.458260 ACCACGGAACAACCAAAAGC 59.542 50.000 0.00 0.00 38.90 3.51
1633 2379 2.032030 CACTGATTGACCACGGAACAAC 60.032 50.000 0.00 0.00 0.00 3.32
1646 2392 5.047802 AGACCATTTTAAGCACCACTGATTG 60.048 40.000 0.00 0.00 0.00 2.67
1655 2401 3.005791 AGGCAACAGACCATTTTAAGCAC 59.994 43.478 0.00 0.00 41.41 4.40
1678 2424 2.610438 ATTGTGAAGGAGGGCAATGT 57.390 45.000 0.00 0.00 31.29 2.71
1719 2465 5.448360 GCAACAAATCTCTGCATCTCCTTAC 60.448 44.000 0.00 0.00 36.09 2.34
1810 2556 6.825284 TGTAACAAACGACGTTCTATTCAA 57.175 33.333 14.58 0.00 0.00 2.69
1845 2591 4.484236 TCCAAAAATAATGAACAGCTGCG 58.516 39.130 15.27 0.00 0.00 5.18
2373 3350 7.229306 TGACAGAAAGAGAACAAATTAGCACAT 59.771 33.333 0.00 0.00 0.00 3.21
2375 3352 6.853362 GTGACAGAAAGAGAACAAATTAGCAC 59.147 38.462 0.00 0.00 0.00 4.40
2376 3353 6.767902 AGTGACAGAAAGAGAACAAATTAGCA 59.232 34.615 0.00 0.00 0.00 3.49
2554 3543 4.258702 AGTGCAAGTAGTACCAAGACAG 57.741 45.455 0.00 0.00 32.67 3.51
2623 3612 3.526931 ATGGACAGACACGTTGGATAG 57.473 47.619 0.00 0.00 0.00 2.08
2631 3620 7.865889 TGCTTTAACTATATATGGACAGACACG 59.134 37.037 2.68 0.00 0.00 4.49
2632 3621 9.712305 ATGCTTTAACTATATATGGACAGACAC 57.288 33.333 2.68 0.00 0.00 3.67
2674 3663 7.860373 GTGTAACTTGCAGTGAAATAATGTTCA 59.140 33.333 0.00 0.00 35.14 3.18
2675 3664 7.860373 TGTGTAACTTGCAGTGAAATAATGTTC 59.140 33.333 0.00 0.00 38.04 3.18
2715 3705 6.995686 TGTCTGCTAGTGTTTCCTTATTGAAA 59.004 34.615 0.00 0.00 32.02 2.69
2716 3706 6.426937 GTGTCTGCTAGTGTTTCCTTATTGAA 59.573 38.462 0.00 0.00 0.00 2.69
2720 3710 4.021368 ACGTGTCTGCTAGTGTTTCCTTAT 60.021 41.667 0.00 0.00 0.00 1.73
2738 3728 5.180492 CCAAGTAATACCAATCACAACGTGT 59.820 40.000 0.00 0.00 34.79 4.49
2742 3732 8.101654 TGTAACCAAGTAATACCAATCACAAC 57.898 34.615 0.00 0.00 0.00 3.32
2807 3829 8.559536 GCAAAGCATGTACATAGCTCTAAAATA 58.440 33.333 23.84 0.00 37.70 1.40
2808 3830 7.284034 AGCAAAGCATGTACATAGCTCTAAAAT 59.716 33.333 23.84 11.29 37.70 1.82
2809 3831 6.599244 AGCAAAGCATGTACATAGCTCTAAAA 59.401 34.615 23.84 0.00 37.70 1.52
2812 3834 5.282055 AGCAAAGCATGTACATAGCTCTA 57.718 39.130 23.84 0.00 37.70 2.43
2829 3851 8.892723 CCAAGAATCTACATATACACAAGCAAA 58.107 33.333 0.00 0.00 0.00 3.68
2912 4149 5.410067 CCACAAACAATTAATACAGGCCAG 58.590 41.667 5.01 0.00 0.00 4.85
2948 4185 7.012799 GCTAACCAGATCAAAGATAGGAAAAGG 59.987 40.741 0.00 0.00 0.00 3.11
3009 4246 4.333926 GGCATTGAAGAGGATCACTGTTAC 59.666 45.833 0.00 0.00 37.82 2.50
3138 4375 8.686334 GGTGTGTCCTGATAAAAATAACATGAT 58.314 33.333 0.00 0.00 0.00 2.45
3148 4385 9.559732 CATATAAGATGGTGTGTCCTGATAAAA 57.440 33.333 0.00 0.00 37.07 1.52
3193 4430 5.822519 CCAGCCAGCTGAGTACATAAAATAA 59.177 40.000 21.01 0.00 46.30 1.40
3244 4481 4.103153 ACATATGGATCACTTGGACCGATT 59.897 41.667 7.80 0.00 0.00 3.34
3247 4484 3.181466 TGACATATGGATCACTTGGACCG 60.181 47.826 7.80 0.00 0.00 4.79
3533 4771 0.394216 ATCCCGCACAGCTTATTGCA 60.394 50.000 11.30 0.00 45.94 4.08
3690 4936 4.464008 AGTATGGTACGACCGGAAAGATA 58.536 43.478 9.46 0.00 42.58 1.98
3747 4993 2.222596 GCTGAAAAGATACAGTGTCGCG 60.223 50.000 0.00 0.00 36.62 5.87
3783 5029 3.682858 ACTCTGCATTGCAATCATTTTGC 59.317 39.130 9.53 11.25 45.11 3.68
3894 5140 3.711190 AGCCAAACAGGTGGAAAAGAATT 59.289 39.130 0.00 0.00 41.65 2.17
3930 5176 3.184541 AGAGCATGCGATGAAAAATTGC 58.815 40.909 13.01 0.00 0.00 3.56
3936 5182 1.660607 GTCGAAGAGCATGCGATGAAA 59.339 47.619 13.01 0.00 36.95 2.69
4024 5270 7.253905 AGAGTTATTTGCCAGTCTAAGGTTA 57.746 36.000 0.00 0.00 0.00 2.85
4078 5336 2.048597 CCGCACAGTCAGCCGTAA 60.049 61.111 0.00 0.00 0.00 3.18
4088 5346 0.248990 AACAACATTGTGCCGCACAG 60.249 50.000 24.48 17.09 45.39 3.66
4215 5475 4.448210 CTTTAAGTATACACCGCACCCAT 58.552 43.478 5.50 0.00 0.00 4.00
4285 5545 1.821753 AGATGACACTGTCTTCCCGAG 59.178 52.381 17.39 0.00 37.41 4.63
4287 5547 2.029020 TGAAGATGACACTGTCTTCCCG 60.029 50.000 17.39 0.00 46.13 5.14
4305 5565 1.612462 CCCAAGCAGCAGTGAGATGAA 60.612 52.381 0.00 0.00 35.00 2.57
4430 5690 2.177173 GATCGGCGCAATTCTTTTCAC 58.823 47.619 10.83 0.00 0.00 3.18
4434 5694 0.742990 TCGGATCGGCGCAATTCTTT 60.743 50.000 10.83 0.00 0.00 2.52
4435 5695 0.742990 TTCGGATCGGCGCAATTCTT 60.743 50.000 10.83 0.00 0.00 2.52
4450 5710 3.818773 ACAGTGTTAAGGAACCAATTCGG 59.181 43.478 0.00 0.00 42.50 4.30
4452 5712 6.039382 AGTTCACAGTGTTAAGGAACCAATTC 59.961 38.462 16.46 0.00 38.83 2.17
4461 5721 3.945285 ACCAACAGTTCACAGTGTTAAGG 59.055 43.478 0.00 0.00 43.59 2.69
4470 5730 2.346766 ATCTGCACCAACAGTTCACA 57.653 45.000 0.00 0.00 38.84 3.58
4479 5739 0.878416 GTAACCGCAATCTGCACCAA 59.122 50.000 0.00 0.00 45.36 3.67
4508 5891 1.168714 GTTCGGAGGCTTTGCAGAAT 58.831 50.000 0.00 0.00 0.00 2.40
4568 5951 3.600388 GTCTCCGATGACATTCACCTTT 58.400 45.455 0.00 0.00 36.97 3.11
4577 5960 0.738975 GGATCACGTCTCCGATGACA 59.261 55.000 0.00 0.00 36.82 3.58
4586 5969 1.410365 CCCAGGTAGAGGATCACGTCT 60.410 57.143 0.00 0.00 42.65 4.18
4725 7166 6.154445 GTCGCCGTATTTTTAGAGGATATCA 58.846 40.000 4.83 0.00 0.00 2.15
4727 7168 5.924825 GTGTCGCCGTATTTTTAGAGGATAT 59.075 40.000 0.00 0.00 0.00 1.63
4729 7170 4.117685 GTGTCGCCGTATTTTTAGAGGAT 58.882 43.478 0.00 0.00 0.00 3.24
4734 7175 3.061697 GGTGAGTGTCGCCGTATTTTTAG 59.938 47.826 0.00 0.00 37.29 1.85
4736 7177 1.802365 GGTGAGTGTCGCCGTATTTTT 59.198 47.619 0.00 0.00 37.29 1.94
4737 7178 1.435577 GGTGAGTGTCGCCGTATTTT 58.564 50.000 0.00 0.00 37.29 1.82
4747 7188 4.783055 TCTAGGACAGATAGGTGAGTGTC 58.217 47.826 0.00 0.00 38.89 3.67
4748 7189 4.864483 TCTAGGACAGATAGGTGAGTGT 57.136 45.455 0.00 0.00 0.00 3.55
4761 7209 4.101430 TCAGTTATGCATGCATCTAGGACA 59.899 41.667 35.35 14.61 37.82 4.02
4795 7243 0.870393 CACATATGTCATGCCGGAGC 59.130 55.000 5.05 0.00 40.48 4.70
4846 7307 4.302509 TGTGCCACCACGTACCCG 62.303 66.667 0.00 0.00 45.04 5.28
4861 7322 1.674057 CACCCCGAAGAAGAGCTGT 59.326 57.895 0.00 0.00 0.00 4.40
5017 7478 3.196254 CCAAAGGTTTGATCCATCAAGGG 59.804 47.826 3.95 0.00 46.34 3.95
5025 7486 2.566724 TCAATGCCCAAAGGTTTGATCC 59.433 45.455 3.95 0.00 40.55 3.36
5055 7517 3.029570 CCTCTGGTAACCCTACACTACC 58.970 54.545 0.00 0.00 36.42 3.18
5199 7670 6.043411 AGGAAATTTCATCGACACTAGTAGC 58.957 40.000 19.49 0.00 0.00 3.58
5203 8765 7.017645 CACAAAGGAAATTTCATCGACACTAG 58.982 38.462 19.49 5.26 0.00 2.57
5210 8772 5.104374 CCCATCACAAAGGAAATTTCATCG 58.896 41.667 19.49 10.04 0.00 3.84
5277 9056 4.283337 TGGATATAGGTTGAACGGTCAGA 58.717 43.478 2.09 0.00 34.49 3.27
5283 9062 6.994221 ACCTAGAATGGATATAGGTTGAACG 58.006 40.000 0.00 0.00 45.57 3.95
5301 9122 7.236432 CCAGTACCAGTACTACCTATACCTAGA 59.764 44.444 10.04 0.00 43.98 2.43
5316 9137 1.816835 CAACGAGAGCCAGTACCAGTA 59.183 52.381 0.00 0.00 0.00 2.74
5317 9138 0.603569 CAACGAGAGCCAGTACCAGT 59.396 55.000 0.00 0.00 0.00 4.00
5318 9139 0.603569 ACAACGAGAGCCAGTACCAG 59.396 55.000 0.00 0.00 0.00 4.00
5319 9140 1.045407 AACAACGAGAGCCAGTACCA 58.955 50.000 0.00 0.00 0.00 3.25
5320 9141 3.521947 ATAACAACGAGAGCCAGTACC 57.478 47.619 0.00 0.00 0.00 3.34
5321 9142 5.462398 CCATTATAACAACGAGAGCCAGTAC 59.538 44.000 0.00 0.00 0.00 2.73
5322 9143 5.361571 TCCATTATAACAACGAGAGCCAGTA 59.638 40.000 0.00 0.00 0.00 2.74
5323 9144 4.161565 TCCATTATAACAACGAGAGCCAGT 59.838 41.667 0.00 0.00 0.00 4.00
5324 9145 4.693283 TCCATTATAACAACGAGAGCCAG 58.307 43.478 0.00 0.00 0.00 4.85
5325 9146 4.442893 CCTCCATTATAACAACGAGAGCCA 60.443 45.833 0.00 0.00 0.00 4.75
5326 9147 4.058817 CCTCCATTATAACAACGAGAGCC 58.941 47.826 0.00 0.00 0.00 4.70
5327 9148 4.694339 ACCTCCATTATAACAACGAGAGC 58.306 43.478 0.00 0.00 0.00 4.09
5328 9149 6.150396 AGACCTCCATTATAACAACGAGAG 57.850 41.667 0.00 0.00 0.00 3.20
5329 9150 6.238953 GCTAGACCTCCATTATAACAACGAGA 60.239 42.308 0.00 0.00 0.00 4.04
5330 9151 5.921408 GCTAGACCTCCATTATAACAACGAG 59.079 44.000 0.00 0.00 0.00 4.18
5331 9152 5.361571 TGCTAGACCTCCATTATAACAACGA 59.638 40.000 0.00 0.00 0.00 3.85
5332 9153 5.597806 TGCTAGACCTCCATTATAACAACG 58.402 41.667 0.00 0.00 0.00 4.10
5333 9154 7.715249 TCATTGCTAGACCTCCATTATAACAAC 59.285 37.037 0.00 0.00 0.00 3.32
5334 9155 7.801104 TCATTGCTAGACCTCCATTATAACAA 58.199 34.615 0.00 0.00 0.00 2.83
5335 9156 7.373617 TCATTGCTAGACCTCCATTATAACA 57.626 36.000 0.00 0.00 0.00 2.41
5336 9157 8.097038 TCATCATTGCTAGACCTCCATTATAAC 58.903 37.037 0.00 0.00 0.00 1.89
5337 9158 8.206126 TCATCATTGCTAGACCTCCATTATAA 57.794 34.615 0.00 0.00 0.00 0.98
5347 9168 2.289002 CGCCTTTCATCATTGCTAGACC 59.711 50.000 0.00 0.00 0.00 3.85
5425 9246 5.969402 TGGTTTCCAATCCCATTCCATTTAT 59.031 36.000 0.00 0.00 0.00 1.40
5426 9247 5.345418 TGGTTTCCAATCCCATTCCATTTA 58.655 37.500 0.00 0.00 0.00 1.40
5430 9251 3.266477 TTGGTTTCCAATCCCATTCCA 57.734 42.857 0.00 0.00 38.75 3.53
5490 9316 2.202797 ATAGCAGCCACGCGACAG 60.203 61.111 15.93 0.92 36.85 3.51
5496 9322 3.187227 GGATTATTCACATAGCAGCCACG 59.813 47.826 0.00 0.00 0.00 4.94
5551 9377 9.621629 TCGGGTAATCTCACAATATTTTATTGT 57.378 29.630 7.00 7.00 42.38 2.71
5606 9435 0.909623 ATCTAAACCCACCAGACCCG 59.090 55.000 0.00 0.00 0.00 5.28
5633 9462 3.137913 CACTCCAATCTCCCTCATCCATT 59.862 47.826 0.00 0.00 0.00 3.16
5670 9536 1.609208 GTGGTGGCTGTGAGTTCATT 58.391 50.000 0.00 0.00 0.00 2.57
5671 9537 0.250901 GGTGGTGGCTGTGAGTTCAT 60.251 55.000 0.00 0.00 0.00 2.57
5672 9538 1.148273 GGTGGTGGCTGTGAGTTCA 59.852 57.895 0.00 0.00 0.00 3.18
5673 9539 1.148273 TGGTGGTGGCTGTGAGTTC 59.852 57.895 0.00 0.00 0.00 3.01
5674 9540 1.152963 GTGGTGGTGGCTGTGAGTT 60.153 57.895 0.00 0.00 0.00 3.01
5675 9541 2.510906 GTGGTGGTGGCTGTGAGT 59.489 61.111 0.00 0.00 0.00 3.41
5710 9576 5.899299 ACGACCGTCTACTGCTTTATAAAT 58.101 37.500 0.00 0.00 0.00 1.40
5711 9577 5.314923 ACGACCGTCTACTGCTTTATAAA 57.685 39.130 0.00 0.00 0.00 1.40
5712 9578 4.913376 GACGACCGTCTACTGCTTTATAA 58.087 43.478 14.52 0.00 41.57 0.98
5714 9580 3.417690 GACGACCGTCTACTGCTTTAT 57.582 47.619 14.52 0.00 41.57 1.40
5725 9591 3.766151 TGTGAATCATTAGACGACCGTC 58.234 45.455 14.03 14.03 44.86 4.79
5726 9592 3.861276 TGTGAATCATTAGACGACCGT 57.139 42.857 0.00 0.00 0.00 4.83
5730 9596 6.867550 AGACTTCATGTGAATCATTAGACGA 58.132 36.000 0.00 0.00 34.09 4.20
5765 9658 6.317140 CCTGCACACACATGTAGATAATTTCT 59.683 38.462 0.00 0.00 36.72 2.52
5766 9659 6.094048 ACCTGCACACACATGTAGATAATTTC 59.906 38.462 0.00 0.00 36.72 2.17
5831 9724 3.702555 GCGCGACGTTGACAAGCT 61.703 61.111 12.10 0.00 0.00 3.74
5903 9808 0.323302 TGTATGAACGGAGGCAGCAA 59.677 50.000 0.00 0.00 0.00 3.91
5945 9850 4.562552 GGAAATGATGCCTAGCTAGGACTC 60.563 50.000 38.74 30.67 46.63 3.36
5981 9886 2.005960 CTCTTCCACTACGGCCGAGG 62.006 65.000 35.90 25.82 31.02 4.63
5990 9899 8.001875 ACTCTAATATGAAGCTCTCTTCCACTA 58.998 37.037 0.00 0.00 46.28 2.74
5991 9900 6.838612 ACTCTAATATGAAGCTCTCTTCCACT 59.161 38.462 0.00 0.00 46.28 4.00


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

AutoCloner maintained by Alex Coulton.