Multiple sequence alignment - TraesCS5A01G291800

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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 TraesCS5A01G291800 chr5A 100.000 6973 0 0 1 6973 502371102 502378074 0.000000e+00 12877.0
1 TraesCS5A01G291800 chr5A 94.333 300 16 1 6320 6618 502383043 502383342 6.370000e-125 459.0
2 TraesCS5A01G291800 chr5A 86.765 68 8 1 6614 6681 502383359 502383425 2.700000e-09 75.0
3 TraesCS5A01G291800 chr5D 96.234 6903 181 37 117 6973 396801055 396807924 0.000000e+00 11234.0
4 TraesCS5A01G291800 chr5D 93.195 1249 54 8 4092 5333 102025759 102024535 0.000000e+00 1807.0
5 TraesCS5A01G291800 chr5D 92.356 798 42 6 3227 4013 102026546 102025757 0.000000e+00 1118.0
6 TraesCS5A01G291800 chr5D 93.333 300 19 1 6320 6618 396813623 396813922 6.420000e-120 442.0
7 TraesCS5A01G291800 chr5D 88.557 201 22 1 6761 6961 396814202 396814401 6.990000e-60 243.0
8 TraesCS5A01G291800 chr5B 93.969 2968 150 19 57 3015 476796158 476799105 0.000000e+00 4462.0
9 TraesCS5A01G291800 chr5B 94.154 2925 104 23 4098 6973 476800761 476803667 0.000000e+00 4392.0
10 TraesCS5A01G291800 chr5B 95.437 1030 43 3 3011 4038 476799498 476800525 0.000000e+00 1639.0
11 TraesCS5A01G291800 chr5B 85.191 655 68 13 6320 6951 476808196 476808844 0.000000e+00 645.0
12 TraesCS5A01G291800 chr5B 80.888 743 81 30 6262 6964 371745117 371745838 4.790000e-146 529.0
13 TraesCS5A01G291800 chr5B 88.811 143 10 5 6073 6211 371744978 371745118 3.340000e-38 171.0
14 TraesCS5A01G291800 chr5B 93.548 62 4 0 6150 6211 633667639 633667578 7.450000e-15 93.5
15 TraesCS5A01G291800 chr1A 92.112 1255 60 12 4092 5331 16516611 16515381 0.000000e+00 1733.0
16 TraesCS5A01G291800 chr1A 92.607 798 40 6 3227 4013 16517398 16516609 0.000000e+00 1129.0
17 TraesCS5A01G291800 chr1D 93.939 660 31 4 4675 5332 452419556 452420208 0.000000e+00 989.0
18 TraesCS5A01G291800 chr2B 82.776 778 79 22 6222 6964 38894606 38893849 1.640000e-180 643.0
19 TraesCS5A01G291800 chr2B 85.305 558 42 16 6086 6618 697550153 697550695 2.210000e-149 540.0
20 TraesCS5A01G291800 chr2B 87.705 244 25 2 6676 6919 697550797 697551035 5.330000e-71 279.0
21 TraesCS5A01G291800 chr2A 82.413 779 81 22 6201 6941 687055667 687056427 4.590000e-176 628.0
22 TraesCS5A01G291800 chr7A 83.357 697 67 18 6201 6867 725248527 725247850 3.600000e-167 599.0
23 TraesCS5A01G291800 chr7A 90.769 65 6 0 5811 5875 260907727 260907791 3.460000e-13 87.9
24 TraesCS5A01G291800 chrUn 81.467 777 75 25 6222 6951 314310430 314311184 2.180000e-159 573.0
25 TraesCS5A01G291800 chr4A 81.486 740 79 30 6262 6964 675184065 675184783 7.900000e-154 555.0
26 TraesCS5A01G291800 chr4A 84.685 555 42 19 6090 6618 492381719 492381182 1.340000e-141 514.0
27 TraesCS5A01G291800 chr4A 87.336 229 24 2 6691 6919 492381066 492380843 2.500000e-64 257.0
28 TraesCS5A01G291800 chr4A 88.811 143 10 5 6073 6211 675183926 675184066 3.340000e-38 171.0
29 TraesCS5A01G291800 chr4B 94.595 111 6 0 2775 2885 440301952 440301842 9.300000e-39 172.0
30 TraesCS5A01G291800 chr1B 88.811 143 10 5 6073 6211 55001032 55001172 3.340000e-38 171.0
31 TraesCS5A01G291800 chr1B 93.694 111 7 0 2775 2885 14711951 14712061 4.330000e-37 167.0
32 TraesCS5A01G291800 chr1B 88.112 143 11 4 6073 6211 54957737 54957877 1.560000e-36 165.0
33 TraesCS5A01G291800 chr7D 89.231 65 7 0 5811 5875 244773951 244774015 1.610000e-11 82.4
34 TraesCS5A01G291800 chr7B 89.231 65 7 0 5811 5875 220134817 220134881 1.610000e-11 82.4


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 TraesCS5A01G291800 chr5A 502371102 502378074 6972 False 12877.000000 12877 100.0000 1 6973 1 chr5A.!!$F1 6972
1 TraesCS5A01G291800 chr5D 396801055 396807924 6869 False 11234.000000 11234 96.2340 117 6973 1 chr5D.!!$F1 6856
2 TraesCS5A01G291800 chr5D 102024535 102026546 2011 True 1462.500000 1807 92.7755 3227 5333 2 chr5D.!!$R1 2106
3 TraesCS5A01G291800 chr5D 396813623 396814401 778 False 342.500000 442 90.9450 6320 6961 2 chr5D.!!$F2 641
4 TraesCS5A01G291800 chr5B 476796158 476803667 7509 False 3497.666667 4462 94.5200 57 6973 3 chr5B.!!$F3 6916
5 TraesCS5A01G291800 chr5B 476808196 476808844 648 False 645.000000 645 85.1910 6320 6951 1 chr5B.!!$F1 631
6 TraesCS5A01G291800 chr5B 371744978 371745838 860 False 350.000000 529 84.8495 6073 6964 2 chr5B.!!$F2 891
7 TraesCS5A01G291800 chr1A 16515381 16517398 2017 True 1431.000000 1733 92.3595 3227 5331 2 chr1A.!!$R1 2104
8 TraesCS5A01G291800 chr1D 452419556 452420208 652 False 989.000000 989 93.9390 4675 5332 1 chr1D.!!$F1 657
9 TraesCS5A01G291800 chr2B 38893849 38894606 757 True 643.000000 643 82.7760 6222 6964 1 chr2B.!!$R1 742
10 TraesCS5A01G291800 chr2B 697550153 697551035 882 False 409.500000 540 86.5050 6086 6919 2 chr2B.!!$F1 833
11 TraesCS5A01G291800 chr2A 687055667 687056427 760 False 628.000000 628 82.4130 6201 6941 1 chr2A.!!$F1 740
12 TraesCS5A01G291800 chr7A 725247850 725248527 677 True 599.000000 599 83.3570 6201 6867 1 chr7A.!!$R1 666
13 TraesCS5A01G291800 chrUn 314310430 314311184 754 False 573.000000 573 81.4670 6222 6951 1 chrUn.!!$F1 729
14 TraesCS5A01G291800 chr4A 492380843 492381719 876 True 385.500000 514 86.0105 6090 6919 2 chr4A.!!$R1 829
15 TraesCS5A01G291800 chr4A 675183926 675184783 857 False 363.000000 555 85.1485 6073 6964 2 chr4A.!!$F1 891

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
26 27 0.036022 TCACAATGCCACATCCGACA 59.964 50.000 0.00 0.00 0.00 4.35 F
855 877 0.098200 CTGCTGATGTGCAATGGACG 59.902 55.000 0.00 0.00 42.83 4.79 F
1066 1088 0.819582 CTGTTGGCATGGTTCATCCC 59.180 55.000 0.00 0.00 34.77 3.85 F
1152 1174 1.091771 AGCATGATTGGCGGTTCGAG 61.092 55.000 0.00 0.00 36.08 4.04 F
1222 1244 1.347817 GAAGCCTTCGTGCAGAGTCG 61.348 60.000 0.00 0.00 0.00 4.18 F
1374 1396 2.079170 TTGTGATGGGTTTGCCTCAA 57.921 45.000 0.00 0.00 34.45 3.02 F
1992 2017 2.407090 CACACTGCGTCTCTTGATTCA 58.593 47.619 0.00 0.00 0.00 2.57 F
2472 2497 2.814805 ATTGGGTCCCAGAATCTGTG 57.185 50.000 11.40 0.00 33.81 3.66 F
3649 4082 2.488153 GCTGGAACCAAGGTATGTGAAC 59.512 50.000 0.00 0.00 0.00 3.18 F
4465 5081 1.068333 CCCAAACTTGCATCAAGACGG 60.068 52.381 12.89 9.23 43.42 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 1878 0.035630 GCTGAAGTGTCCATGGAGCT 60.036 55.000 16.81 13.80 0.00 4.09 R
2148 2173 2.316108 ACCGCAACCCTTTTGAGATTT 58.684 42.857 0.00 0.00 0.00 2.17 R
2708 2734 2.486982 CACATTCAGGACAGCCAGAAAG 59.513 50.000 0.00 0.00 42.13 2.62 R
3007 3033 2.671914 GCCCAGTGCAAACATGTACATG 60.672 50.000 29.97 29.97 41.37 3.21 R
3171 3594 3.561313 CCCATGCCCCACCTATTGTATAC 60.561 52.174 0.00 0.00 0.00 1.47 R
3348 3772 2.813754 TCCATTTTCGAAGTGGCAGAAG 59.186 45.455 20.78 3.53 33.01 2.85 R
3649 4082 2.572104 AGGCCTTGTAACAACTCCCTAG 59.428 50.000 0.00 0.00 0.00 3.02 R
3662 4095 2.706190 AGTGAGAAGTTACAGGCCTTGT 59.294 45.455 0.00 7.90 43.96 3.16 R
5088 5709 1.003839 GGTGACATGCCAGGTTCGA 60.004 57.895 0.00 0.00 0.00 3.71 R
6084 6768 1.506309 CTAAGCACAGTGGTTGCGCA 61.506 55.000 25.19 5.66 38.66 6.09 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
19 20 2.728690 GAGCAAATCACAATGCCACA 57.271 45.000 0.00 0.00 43.57 4.17
20 21 3.241067 GAGCAAATCACAATGCCACAT 57.759 42.857 0.00 0.00 43.57 3.21
21 22 3.184541 GAGCAAATCACAATGCCACATC 58.815 45.455 0.00 0.00 43.57 3.06
22 23 2.093869 AGCAAATCACAATGCCACATCC 60.094 45.455 0.00 0.00 43.57 3.51
23 24 2.532235 CAAATCACAATGCCACATCCG 58.468 47.619 0.00 0.00 0.00 4.18
24 25 2.127271 AATCACAATGCCACATCCGA 57.873 45.000 0.00 0.00 0.00 4.55
25 26 1.382522 ATCACAATGCCACATCCGAC 58.617 50.000 0.00 0.00 0.00 4.79
26 27 0.036022 TCACAATGCCACATCCGACA 59.964 50.000 0.00 0.00 0.00 4.35
27 28 0.880441 CACAATGCCACATCCGACAA 59.120 50.000 0.00 0.00 0.00 3.18
28 29 1.473677 CACAATGCCACATCCGACAAT 59.526 47.619 0.00 0.00 0.00 2.71
29 30 2.094597 CACAATGCCACATCCGACAATT 60.095 45.455 0.00 0.00 0.00 2.32
30 31 2.164219 ACAATGCCACATCCGACAATTC 59.836 45.455 0.00 0.00 0.00 2.17
31 32 2.127271 ATGCCACATCCGACAATTCA 57.873 45.000 0.00 0.00 0.00 2.57
32 33 1.452110 TGCCACATCCGACAATTCAG 58.548 50.000 0.00 0.00 0.00 3.02
33 34 1.003003 TGCCACATCCGACAATTCAGA 59.997 47.619 0.00 0.00 0.00 3.27
34 35 2.083774 GCCACATCCGACAATTCAGAA 58.916 47.619 0.00 0.00 0.00 3.02
35 36 2.684881 GCCACATCCGACAATTCAGAAT 59.315 45.455 0.00 0.00 0.00 2.40
36 37 3.129287 GCCACATCCGACAATTCAGAATT 59.871 43.478 2.20 2.20 0.00 2.17
37 38 4.335315 GCCACATCCGACAATTCAGAATTA 59.665 41.667 8.12 0.00 0.00 1.40
38 39 5.163663 GCCACATCCGACAATTCAGAATTAA 60.164 40.000 8.12 0.00 0.00 1.40
39 40 6.489675 CCACATCCGACAATTCAGAATTAAG 58.510 40.000 8.12 0.23 0.00 1.85
40 41 6.316140 CCACATCCGACAATTCAGAATTAAGA 59.684 38.462 8.12 3.94 0.00 2.10
41 42 7.148255 CCACATCCGACAATTCAGAATTAAGAA 60.148 37.037 8.12 0.00 0.00 2.52
42 43 7.693951 CACATCCGACAATTCAGAATTAAGAAC 59.306 37.037 8.12 0.00 0.00 3.01
43 44 6.737254 TCCGACAATTCAGAATTAAGAACC 57.263 37.500 8.12 0.00 0.00 3.62
44 45 5.350365 TCCGACAATTCAGAATTAAGAACCG 59.650 40.000 8.12 6.08 0.00 4.44
45 46 5.022021 CGACAATTCAGAATTAAGAACCGC 58.978 41.667 8.12 0.00 0.00 5.68
46 47 5.310720 ACAATTCAGAATTAAGAACCGCC 57.689 39.130 8.12 0.00 0.00 6.13
47 48 4.764823 ACAATTCAGAATTAAGAACCGCCA 59.235 37.500 8.12 0.00 0.00 5.69
48 49 5.242838 ACAATTCAGAATTAAGAACCGCCAA 59.757 36.000 8.12 0.00 0.00 4.52
49 50 5.975693 ATTCAGAATTAAGAACCGCCAAA 57.024 34.783 0.00 0.00 0.00 3.28
50 51 5.371115 TTCAGAATTAAGAACCGCCAAAG 57.629 39.130 0.00 0.00 0.00 2.77
51 52 3.190535 TCAGAATTAAGAACCGCCAAAGC 59.809 43.478 0.00 0.00 0.00 3.51
78 79 8.068380 GGGAAAACATCGAGCATTACTAATAAC 58.932 37.037 0.00 0.00 0.00 1.89
83 84 8.732746 ACATCGAGCATTACTAATAACCTTTT 57.267 30.769 0.00 0.00 0.00 2.27
87 88 6.018994 CGAGCATTACTAATAACCTTTTCGCT 60.019 38.462 0.00 0.00 0.00 4.93
89 90 6.018994 AGCATTACTAATAACCTTTTCGCTCG 60.019 38.462 0.00 0.00 0.00 5.03
139 140 5.554350 ACTTTTTCCCCCTCTACAAATAGGA 59.446 40.000 0.00 0.00 34.58 2.94
142 143 4.295905 TCCCCCTCTACAAATAGGATGT 57.704 45.455 0.00 0.00 34.58 3.06
181 183 8.885494 TTTCCATACAGTTGAAATTGGAAAAG 57.115 30.769 11.39 0.00 45.37 2.27
371 382 1.929836 GAGAGCAACCGCACAAGATAG 59.070 52.381 0.00 0.00 42.27 2.08
378 389 2.203209 GCACAAGATAGCCCGGGG 60.203 66.667 25.28 9.31 0.00 5.73
396 407 3.930012 CCGGAGAAGGGGATCGCC 61.930 72.222 20.86 20.86 36.09 5.54
518 529 3.786495 AACCCAATCTGGTTTCCCC 57.214 52.632 0.00 0.00 46.45 4.81
543 554 4.469469 TTCCTGAACCAAAGAAATCCCT 57.531 40.909 0.00 0.00 0.00 4.20
544 555 4.469469 TCCTGAACCAAAGAAATCCCTT 57.531 40.909 0.00 0.00 0.00 3.95
594 605 4.058817 GTCAGTTTCTTGATCTGGTTCGT 58.941 43.478 0.00 0.00 0.00 3.85
595 606 4.511826 GTCAGTTTCTTGATCTGGTTCGTT 59.488 41.667 0.00 0.00 0.00 3.85
596 607 4.750098 TCAGTTTCTTGATCTGGTTCGTTC 59.250 41.667 0.00 0.00 0.00 3.95
597 608 4.511454 CAGTTTCTTGATCTGGTTCGTTCA 59.489 41.667 0.00 0.00 0.00 3.18
643 654 1.172180 TTCTGCGGCACCCTTTTCTG 61.172 55.000 0.00 0.00 0.00 3.02
647 658 2.041153 CGGCACCCTTTTCTGCTTT 58.959 52.632 0.00 0.00 33.63 3.51
648 659 0.318955 CGGCACCCTTTTCTGCTTTG 60.319 55.000 0.00 0.00 33.63 2.77
649 660 0.752658 GGCACCCTTTTCTGCTTTGT 59.247 50.000 0.00 0.00 33.63 2.83
650 661 1.960689 GGCACCCTTTTCTGCTTTGTA 59.039 47.619 0.00 0.00 33.63 2.41
657 668 5.418840 ACCCTTTTCTGCTTTGTATGTATGG 59.581 40.000 0.00 0.00 0.00 2.74
720 731 6.310197 GTTCATGTGTGATTCTAGTTCTTGC 58.690 40.000 0.00 0.00 33.56 4.01
775 786 2.686915 TCGTTCCTAGTTTCCTCGATCC 59.313 50.000 0.00 0.00 0.00 3.36
800 822 3.549794 GCCATCTTAGATGCCTTCTGTT 58.450 45.455 16.18 0.00 35.79 3.16
839 861 7.116805 AGCTGCAAGATTAATTTTTAACACTGC 59.883 33.333 1.02 0.00 34.07 4.40
855 877 0.098200 CTGCTGATGTGCAATGGACG 59.902 55.000 0.00 0.00 42.83 4.79
897 919 5.871539 TGCTGCATTGCATCATATATTACG 58.128 37.500 12.53 0.00 38.13 3.18
900 922 7.121911 GCTGCATTGCATCATATATTACGTAG 58.878 38.462 12.53 0.00 38.13 3.51
903 925 8.442384 TGCATTGCATCATATATTACGTAGTTG 58.558 33.333 7.38 0.00 36.00 3.16
912 934 9.271828 TCATATATTACGTAGTTGGTAGTTCGA 57.728 33.333 0.00 0.00 37.78 3.71
933 955 5.863935 TCGATGTTGTTTCTGATGTGTAGAG 59.136 40.000 0.00 0.00 0.00 2.43
984 1006 3.483421 TCTGCAGAGATAAATGGCCATG 58.517 45.455 21.63 6.68 0.00 3.66
986 1008 2.175284 TGCAGAGATAAATGGCCATGGA 59.825 45.455 21.63 10.95 0.00 3.41
990 1012 4.518211 CAGAGATAAATGGCCATGGAACTC 59.482 45.833 21.63 22.99 0.00 3.01
1066 1088 0.819582 CTGTTGGCATGGTTCATCCC 59.180 55.000 0.00 0.00 34.77 3.85
1080 1102 1.780309 TCATCCCAGGTTCCTTGTTGT 59.220 47.619 0.00 0.00 0.00 3.32
1128 1150 6.472016 TCATCTCCAATTGTTGCAGTAACTA 58.528 36.000 4.43 0.00 40.05 2.24
1152 1174 1.091771 AGCATGATTGGCGGTTCGAG 61.092 55.000 0.00 0.00 36.08 4.04
1222 1244 1.347817 GAAGCCTTCGTGCAGAGTCG 61.348 60.000 0.00 0.00 0.00 4.18
1298 1320 2.918934 TGAAGGGGTCATTGGAAGATCA 59.081 45.455 0.00 0.00 0.00 2.92
1374 1396 2.079170 TTGTGATGGGTTTGCCTCAA 57.921 45.000 0.00 0.00 34.45 3.02
1542 1564 2.998670 CGATCTGAAGAGAAAAGCTGCA 59.001 45.455 1.02 0.00 0.00 4.41
1552 1574 7.392673 TGAAGAGAAAAGCTGCATTAGATTCTT 59.607 33.333 1.02 4.31 32.95 2.52
1556 1578 8.064336 AGAAAAGCTGCATTAGATTCTTTGAT 57.936 30.769 1.02 0.00 32.95 2.57
1605 1627 4.479993 GCTGTCGATGGGCCTGCT 62.480 66.667 4.53 0.00 0.00 4.24
1630 1652 3.696548 CTCCCAAGGCTTAAAACCTGATC 59.303 47.826 0.00 0.00 37.67 2.92
1646 1668 3.370953 CCTGATCCGAGGAATCCAAGTTT 60.371 47.826 0.61 0.00 34.69 2.66
1853 1878 5.818857 GGGTGTTATCGCCTTTAACTAATGA 59.181 40.000 3.47 0.00 43.20 2.57
1992 2017 2.407090 CACACTGCGTCTCTTGATTCA 58.593 47.619 0.00 0.00 0.00 2.57
2082 2107 8.813643 AGTTTAGCAGTAATATATTCACCGAC 57.186 34.615 0.00 0.00 0.00 4.79
2284 2309 5.221501 GCTCAGAGAGATTTAGCCAGAGAAT 60.222 44.000 0.00 0.00 0.00 2.40
2301 2326 8.996271 GCCAGAGAATTTGAAAATGATTTTCTT 58.004 29.630 25.61 15.09 47.00 2.52
2471 2496 3.833559 AAATTGGGTCCCAGAATCTGT 57.166 42.857 11.40 0.00 33.81 3.41
2472 2497 2.814805 ATTGGGTCCCAGAATCTGTG 57.185 50.000 11.40 0.00 33.81 3.66
2599 2624 4.327680 GTGTGGAAAAGATAAGCAGGTCT 58.672 43.478 0.00 0.00 0.00 3.85
2708 2734 6.509656 TCTTGAAATGCAGAATATTGATGGC 58.490 36.000 0.00 0.00 0.00 4.40
2805 2831 3.334910 TTGATGAGGATAGCTCCCTGA 57.665 47.619 11.88 4.64 43.21 3.86
3007 3033 5.807011 GTTTCTGATGAATTGGTGCATTACC 59.193 40.000 0.00 0.00 39.84 2.85
3081 3504 6.535540 CCCTTGCTAGTATAGTAGTCTCTCA 58.464 44.000 14.70 2.93 41.93 3.27
3091 3514 8.330247 AGTATAGTAGTCTCTCACTCTTTTCCA 58.670 37.037 0.00 0.00 36.43 3.53
3144 3567 5.950883 GGTGAAGCCCTGAAGTTTTAATAC 58.049 41.667 0.00 0.00 0.00 1.89
3151 3574 6.602009 AGCCCTGAAGTTTTAATACGCTAATT 59.398 34.615 0.00 0.00 0.00 1.40
3265 3689 5.882557 CACCCTATTGCTAATCTTCACAAGT 59.117 40.000 0.00 0.00 0.00 3.16
3348 3772 5.839621 TGCCTCAAGTATCCGTTTACTATC 58.160 41.667 0.00 0.00 32.16 2.08
3357 3781 4.119442 TCCGTTTACTATCTTCTGCCAC 57.881 45.455 0.00 0.00 0.00 5.01
3649 4082 2.488153 GCTGGAACCAAGGTATGTGAAC 59.512 50.000 0.00 0.00 0.00 3.18
3662 4095 6.021030 AGGTATGTGAACTAGGGAGTTGTTA 58.979 40.000 0.00 0.00 46.23 2.41
3770 4205 6.351286 GCTTGGATTTCTTGTTTCCATATGGT 60.351 38.462 21.28 0.00 39.22 3.55
3884 4319 2.374504 ACTGGGATCCCATATCTGCAAG 59.625 50.000 33.89 20.19 46.15 4.01
4056 4492 1.496429 CATAGGTGAAATGCCCCTCCT 59.504 52.381 0.00 0.00 0.00 3.69
4072 4508 2.506231 CCTCCTCCCTCCCTTTAAGTTC 59.494 54.545 0.00 0.00 0.00 3.01
4078 4514 5.429130 CTCCCTCCCTTTAAGTTCATACAC 58.571 45.833 0.00 0.00 0.00 2.90
4121 4733 3.189285 GTTGTATGCCAATGCCATTCAC 58.811 45.455 0.00 0.00 35.02 3.18
4219 4834 7.064229 AGTAGAATTGTCCCAGGTTTGTTTTA 58.936 34.615 0.00 0.00 0.00 1.52
4248 4863 4.189580 ACTGGTTGCCGCTGTGGT 62.190 61.111 9.31 0.00 41.21 4.16
4352 4967 9.109393 GCAATATACTGATACACTGGAAAAAGA 57.891 33.333 0.00 0.00 0.00 2.52
4417 5032 6.879993 TCGAGTAATGGTGTTTGCCTATTTAA 59.120 34.615 0.00 0.00 0.00 1.52
4465 5081 1.068333 CCCAAACTTGCATCAAGACGG 60.068 52.381 12.89 9.23 43.42 4.79
4933 5553 3.941483 CAGAAAGTCGGACTAATGCCAAT 59.059 43.478 11.71 0.00 0.00 3.16
4934 5554 3.941483 AGAAAGTCGGACTAATGCCAATG 59.059 43.478 11.71 0.00 0.00 2.82
4935 5555 2.332063 AGTCGGACTAATGCCAATGG 57.668 50.000 9.33 0.00 0.00 3.16
5088 5709 0.390492 TCAAGATCGATGCAGCGGAT 59.610 50.000 25.69 16.16 0.00 4.18
5090 5711 0.665670 AAGATCGATGCAGCGGATCG 60.666 55.000 25.69 20.17 43.32 3.69
5105 5726 1.009829 GATCGAACCTGGCATGTCAC 58.990 55.000 0.00 0.00 0.00 3.67
5114 5735 0.405198 TGGCATGTCACCAGAACCAT 59.595 50.000 0.00 0.00 32.06 3.55
5128 5757 4.383118 CCAGAACCATTCAATCGGAGTACT 60.383 45.833 0.00 0.00 0.00 2.73
5130 5759 4.223032 AGAACCATTCAATCGGAGTACTGT 59.777 41.667 0.00 0.00 0.00 3.55
5133 5762 6.235231 ACCATTCAATCGGAGTACTGTTAT 57.765 37.500 0.00 0.00 0.00 1.89
5302 5931 3.740115 TCCTTTCTGCACTAGTGAAACC 58.260 45.455 27.08 9.09 37.80 3.27
5413 6069 5.813717 AGAACCGTAACAAAACTACAAAGC 58.186 37.500 0.00 0.00 0.00 3.51
5455 6111 4.583871 TGGAATTGGCAAAAACAACAAGT 58.416 34.783 3.01 0.00 0.00 3.16
5573 6229 1.312815 GGCCTTGACACATGGATAGC 58.687 55.000 0.00 0.00 31.33 2.97
5607 6263 5.517924 TCCCAAAATTGCTGATTAGGATGA 58.482 37.500 0.00 0.00 0.00 2.92
5608 6264 6.138263 TCCCAAAATTGCTGATTAGGATGAT 58.862 36.000 0.00 0.00 0.00 2.45
5609 6265 7.296856 TCCCAAAATTGCTGATTAGGATGATA 58.703 34.615 0.00 0.00 0.00 2.15
5698 6354 3.513680 TCAATTTGGCACATGCAGATC 57.486 42.857 6.15 0.00 44.36 2.75
5743 6421 3.431912 TGCGGCGTTGCATATCTTATTAG 59.568 43.478 9.37 0.00 40.62 1.73
5841 6520 0.038166 GGGTTGAGCATGACTTCCCA 59.962 55.000 0.00 0.00 35.49 4.37
6084 6768 4.870636 TGGGAAATTGCCATTCTAGTGAT 58.129 39.130 0.88 0.00 30.85 3.06
6087 6771 3.976793 AATTGCCATTCTAGTGATGCG 57.023 42.857 0.00 0.00 0.00 4.73
6108 6794 2.602217 GCAACCACTGTGCTTAGTTTCG 60.602 50.000 1.29 0.00 0.00 3.46
6236 6928 1.745827 GCCCAGCTTAGTAAATCCGCA 60.746 52.381 0.00 0.00 0.00 5.69
6386 7101 5.652452 ACAATTGGCTTGGATCCTAACTAAC 59.348 40.000 14.23 0.00 39.30 2.34
6439 7154 5.949354 CAGGGTTCAAATGTGGGTATTTCTA 59.051 40.000 0.00 0.00 0.00 2.10
6800 7702 5.011227 TGGTTACCTTTTGTTTCAATAGGCC 59.989 40.000 15.23 0.00 0.00 5.19
6919 7831 8.696410 TTTGAAACAACAAGGTAAATCAAGAC 57.304 30.769 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.728690 TGTGGCATTGTGATTTGCTC 57.271 45.000 0.00 0.00 38.88 4.26
2 3 2.273557 GGATGTGGCATTGTGATTTGC 58.726 47.619 0.00 0.00 38.14 3.68
6 7 1.339920 TGTCGGATGTGGCATTGTGAT 60.340 47.619 0.00 0.00 0.00 3.06
7 8 0.036022 TGTCGGATGTGGCATTGTGA 59.964 50.000 0.00 0.00 0.00 3.58
8 9 0.880441 TTGTCGGATGTGGCATTGTG 59.120 50.000 0.00 0.00 0.00 3.33
9 10 1.838112 ATTGTCGGATGTGGCATTGT 58.162 45.000 0.00 0.00 0.00 2.71
10 11 2.164017 TGAATTGTCGGATGTGGCATTG 59.836 45.455 0.00 0.00 0.00 2.82
11 12 2.424601 CTGAATTGTCGGATGTGGCATT 59.575 45.455 0.00 0.00 30.94 3.56
12 13 2.019249 CTGAATTGTCGGATGTGGCAT 58.981 47.619 0.00 0.00 30.94 4.40
13 14 1.003003 TCTGAATTGTCGGATGTGGCA 59.997 47.619 0.00 0.00 34.02 4.92
14 15 1.737838 TCTGAATTGTCGGATGTGGC 58.262 50.000 0.00 0.00 34.02 5.01
15 16 4.970662 AATTCTGAATTGTCGGATGTGG 57.029 40.909 14.47 0.00 38.98 4.17
16 17 7.307493 TCTTAATTCTGAATTGTCGGATGTG 57.693 36.000 22.47 5.34 38.98 3.21
17 18 7.148239 GGTTCTTAATTCTGAATTGTCGGATGT 60.148 37.037 22.47 0.00 38.98 3.06
18 19 7.189512 GGTTCTTAATTCTGAATTGTCGGATG 58.810 38.462 22.47 7.40 38.98 3.51
19 20 6.037172 CGGTTCTTAATTCTGAATTGTCGGAT 59.963 38.462 22.47 0.41 38.98 4.18
20 21 5.350365 CGGTTCTTAATTCTGAATTGTCGGA 59.650 40.000 22.47 12.91 37.38 4.55
21 22 5.560148 CGGTTCTTAATTCTGAATTGTCGG 58.440 41.667 22.47 11.22 32.38 4.79
22 23 5.022021 GCGGTTCTTAATTCTGAATTGTCG 58.978 41.667 22.47 16.45 32.38 4.35
23 24 5.106317 TGGCGGTTCTTAATTCTGAATTGTC 60.106 40.000 22.47 8.50 32.38 3.18
24 25 4.764823 TGGCGGTTCTTAATTCTGAATTGT 59.235 37.500 22.47 3.15 32.38 2.71
25 26 5.309323 TGGCGGTTCTTAATTCTGAATTG 57.691 39.130 22.47 9.43 32.38 2.32
26 27 5.975693 TTGGCGGTTCTTAATTCTGAATT 57.024 34.783 18.64 18.64 34.90 2.17
27 28 5.622233 GCTTTGGCGGTTCTTAATTCTGAAT 60.622 40.000 0.00 0.00 0.00 2.57
28 29 4.320935 GCTTTGGCGGTTCTTAATTCTGAA 60.321 41.667 0.00 0.00 0.00 3.02
29 30 3.190535 GCTTTGGCGGTTCTTAATTCTGA 59.809 43.478 0.00 0.00 0.00 3.27
30 31 3.501950 GCTTTGGCGGTTCTTAATTCTG 58.498 45.455 0.00 0.00 0.00 3.02
31 32 3.850122 GCTTTGGCGGTTCTTAATTCT 57.150 42.857 0.00 0.00 0.00 2.40
44 45 0.732538 CGATGTTTTCCCGCTTTGGC 60.733 55.000 0.00 0.00 35.87 4.52
45 46 0.878416 TCGATGTTTTCCCGCTTTGG 59.122 50.000 0.00 0.00 37.55 3.28
46 47 1.729149 GCTCGATGTTTTCCCGCTTTG 60.729 52.381 0.00 0.00 0.00 2.77
47 48 0.521735 GCTCGATGTTTTCCCGCTTT 59.478 50.000 0.00 0.00 0.00 3.51
48 49 0.605319 TGCTCGATGTTTTCCCGCTT 60.605 50.000 0.00 0.00 0.00 4.68
49 50 0.392998 ATGCTCGATGTTTTCCCGCT 60.393 50.000 0.00 0.00 0.00 5.52
50 51 0.451783 AATGCTCGATGTTTTCCCGC 59.548 50.000 0.00 0.00 0.00 6.13
51 52 2.936498 AGTAATGCTCGATGTTTTCCCG 59.064 45.455 0.00 0.00 0.00 5.14
52 53 6.619801 ATTAGTAATGCTCGATGTTTTCCC 57.380 37.500 0.00 0.00 0.00 3.97
53 54 8.068380 GGTTATTAGTAATGCTCGATGTTTTCC 58.932 37.037 5.61 0.00 0.00 3.13
54 55 8.827677 AGGTTATTAGTAATGCTCGATGTTTTC 58.172 33.333 5.61 0.00 0.00 2.29
55 56 8.732746 AGGTTATTAGTAATGCTCGATGTTTT 57.267 30.769 5.61 0.00 0.00 2.43
78 79 5.286082 CCAAATCAAATTACGAGCGAAAAGG 59.714 40.000 0.00 0.00 0.00 3.11
83 84 3.749088 ACACCAAATCAAATTACGAGCGA 59.251 39.130 0.00 0.00 0.00 4.93
87 88 5.446143 AGCAACACCAAATCAAATTACGA 57.554 34.783 0.00 0.00 0.00 3.43
113 114 7.054751 CCTATTTGTAGAGGGGGAAAAAGTAG 58.945 42.308 0.00 0.00 0.00 2.57
116 117 6.074698 TCCTATTTGTAGAGGGGGAAAAAG 57.925 41.667 0.00 0.00 33.39 2.27
152 153 6.496565 TCCAATTTCAACTGTATGGAAACCAT 59.503 34.615 8.35 8.35 46.99 3.55
181 183 9.766277 TTTGCGCCAAATTGAAAATAATATTTC 57.234 25.926 4.18 0.00 39.28 2.17
223 233 0.611896 CGGCCCATTCCTTTTCACCT 60.612 55.000 0.00 0.00 0.00 4.00
258 268 4.922103 GCTTAAATAGATTCCTACCGTCCG 59.078 45.833 0.00 0.00 0.00 4.79
293 304 2.415983 TTGGGTTCTTCTCTCTCCCA 57.584 50.000 0.00 0.00 45.20 4.37
355 366 1.429423 GGCTATCTTGTGCGGTTGC 59.571 57.895 0.00 0.00 43.20 4.17
378 389 4.610714 GCGATCCCCTTCTCCGGC 62.611 72.222 0.00 0.00 0.00 6.13
518 529 5.511373 GGGATTTCTTTGGTTCAGGAAAAGG 60.511 44.000 0.00 0.00 32.84 3.11
643 654 7.439056 CCAAAAATCCATCCATACATACAAAGC 59.561 37.037 0.00 0.00 0.00 3.51
647 658 6.549364 GGACCAAAAATCCATCCATACATACA 59.451 38.462 0.00 0.00 36.15 2.29
648 659 6.293955 CGGACCAAAAATCCATCCATACATAC 60.294 42.308 0.00 0.00 35.83 2.39
649 660 5.767665 CGGACCAAAAATCCATCCATACATA 59.232 40.000 0.00 0.00 35.83 2.29
650 661 4.584325 CGGACCAAAAATCCATCCATACAT 59.416 41.667 0.00 0.00 35.83 2.29
657 668 3.951680 ACCATACGGACCAAAAATCCATC 59.048 43.478 0.00 0.00 35.83 3.51
720 731 0.873312 CCACATCGATGACCAGAGCG 60.873 60.000 31.33 2.03 0.00 5.03
775 786 3.223661 GGCATCTAAGATGGCCTCG 57.776 57.895 3.32 0.00 43.09 4.63
785 796 1.354031 TGGGCAACAGAAGGCATCTAA 59.646 47.619 0.00 0.00 36.32 2.10
800 822 3.117926 TCTTGCAGCTAAATCTATGGGCA 60.118 43.478 0.00 0.00 0.00 5.36
839 861 1.167851 AACCGTCCATTGCACATCAG 58.832 50.000 0.00 0.00 0.00 2.90
855 877 5.852755 GCAGCAAAATCAGCAAATAAAAACC 59.147 36.000 0.00 0.00 0.00 3.27
897 919 6.423001 AGAAACAACATCGAACTACCAACTAC 59.577 38.462 0.00 0.00 0.00 2.73
900 922 5.235616 TCAGAAACAACATCGAACTACCAAC 59.764 40.000 0.00 0.00 0.00 3.77
903 925 5.408604 ACATCAGAAACAACATCGAACTACC 59.591 40.000 0.00 0.00 0.00 3.18
911 933 5.163814 GCCTCTACACATCAGAAACAACATC 60.164 44.000 0.00 0.00 0.00 3.06
912 934 4.697352 GCCTCTACACATCAGAAACAACAT 59.303 41.667 0.00 0.00 0.00 2.71
933 955 2.099756 GGCATTGTCCATTTACAGAGCC 59.900 50.000 0.00 0.00 41.08 4.70
984 1006 3.119849 CCACATTGTCGAATTGGAGTTCC 60.120 47.826 0.00 0.00 0.00 3.62
986 1008 3.253188 CACCACATTGTCGAATTGGAGTT 59.747 43.478 6.14 0.00 0.00 3.01
990 1012 2.551887 TGTCACCACATTGTCGAATTGG 59.448 45.455 0.00 0.00 0.00 3.16
1039 1061 2.440409 ACCATGCCAACAGTTCAGATC 58.560 47.619 0.00 0.00 0.00 2.75
1040 1062 2.592102 ACCATGCCAACAGTTCAGAT 57.408 45.000 0.00 0.00 0.00 2.90
1066 1088 4.423732 CTGAACAAACAACAAGGAACCTG 58.576 43.478 0.00 0.00 0.00 4.00
1080 1102 3.315191 GCACAGTTTAGAGCCTGAACAAA 59.685 43.478 10.82 0.00 33.30 2.83
1128 1150 0.322816 ACCGCCAATCATGCTCTTGT 60.323 50.000 0.00 0.00 0.00 3.16
1152 1174 1.022735 CAGCAGTGAAGATGCCATCC 58.977 55.000 0.00 0.00 44.97 3.51
1245 1267 4.572985 TCAATCTCCAAAACTGTTGCAG 57.427 40.909 0.00 0.00 37.52 4.41
1298 1320 5.323371 TGCTCCTAAAATGCGCTAATTTT 57.677 34.783 18.75 18.75 41.45 1.82
1374 1396 3.054065 CCTCCTCCTTAATTGCAGGAACT 60.054 47.826 9.01 0.00 40.09 3.01
1410 1432 6.254522 AGGAGGACTAACTACACATGTACTT 58.745 40.000 0.00 0.00 0.00 2.24
1552 1574 8.162085 TCCAAAATTTCCATCAAATCCAATCAA 58.838 29.630 0.00 0.00 33.16 2.57
1556 1578 5.939296 GCTCCAAAATTTCCATCAAATCCAA 59.061 36.000 0.00 0.00 33.16 3.53
1605 1627 1.627864 GTTTTAAGCCTTGGGAGCCA 58.372 50.000 0.00 0.00 0.00 4.75
1618 1640 4.226394 TGGATTCCTCGGATCAGGTTTTAA 59.774 41.667 3.95 0.00 34.76 1.52
1630 1652 5.428253 TGATCTAAAACTTGGATTCCTCGG 58.572 41.667 3.95 0.00 30.39 4.63
1646 1668 3.133901 TCGCAACTTAGGGCATGATCTAA 59.866 43.478 0.00 2.51 0.00 2.10
1853 1878 0.035630 GCTGAAGTGTCCATGGAGCT 60.036 55.000 16.81 13.80 0.00 4.09
1992 2017 4.019174 CTGGCCAAGTAGGTGATTCAAAT 58.981 43.478 7.01 0.00 40.61 2.32
2082 2107 2.335712 GCCCTCAAGCAAAGGACCG 61.336 63.158 0.93 0.00 35.83 4.79
2148 2173 2.316108 ACCGCAACCCTTTTGAGATTT 58.684 42.857 0.00 0.00 0.00 2.17
2301 2326 8.690203 TTGATATTTCTGTTTCCTTCAAGTCA 57.310 30.769 0.00 0.00 0.00 3.41
2329 2354 3.061295 CCATGTTCAGAACGATCTTCACG 59.939 47.826 8.80 0.00 32.03 4.35
2338 2363 2.809446 TCTATCGCCATGTTCAGAACG 58.191 47.619 8.80 0.00 0.00 3.95
2599 2624 5.526111 GGAAAGTAGTAAAAGACACACTGCA 59.474 40.000 0.00 0.00 0.00 4.41
2684 2710 6.322969 AGCCATCAATATTCTGCATTTCAAGA 59.677 34.615 0.00 0.00 0.00 3.02
2708 2734 2.486982 CACATTCAGGACAGCCAGAAAG 59.513 50.000 0.00 0.00 42.13 2.62
2805 2831 6.363626 GCAAGATCAATCGACGAATAGTACAT 59.636 38.462 0.00 0.00 0.00 2.29
3007 3033 2.671914 GCCCAGTGCAAACATGTACATG 60.672 50.000 29.97 29.97 41.37 3.21
3081 3504 9.574516 AGTCAAGTGTTATATTTGGAAAAGAGT 57.425 29.630 0.00 0.00 0.00 3.24
3091 3514 8.806146 AGGCAAAATGAGTCAAGTGTTATATTT 58.194 29.630 0.00 0.00 0.00 1.40
3171 3594 3.561313 CCCATGCCCCACCTATTGTATAC 60.561 52.174 0.00 0.00 0.00 1.47
3348 3772 2.813754 TCCATTTTCGAAGTGGCAGAAG 59.186 45.455 20.78 3.53 33.01 2.85
3649 4082 2.572104 AGGCCTTGTAACAACTCCCTAG 59.428 50.000 0.00 0.00 0.00 3.02
3662 4095 2.706190 AGTGAGAAGTTACAGGCCTTGT 59.294 45.455 0.00 7.90 43.96 3.16
4056 4492 4.081309 CGTGTATGAACTTAAAGGGAGGGA 60.081 45.833 0.00 0.00 0.00 4.20
4248 4863 4.072839 CGATCAGTATACTGGCCTAGTCA 58.927 47.826 28.33 10.48 43.91 3.41
4417 5032 4.729868 AGGCGAATAATTATGAGCCCTTT 58.270 39.130 27.43 15.11 45.16 3.11
4776 5396 1.136695 CCTGTTCACAGCCTGCAAAAA 59.863 47.619 1.01 0.00 42.47 1.94
4933 5553 2.136298 TTTGACAGAAGCAACCACCA 57.864 45.000 0.00 0.00 0.00 4.17
4934 5554 4.072131 TCTATTTGACAGAAGCAACCACC 58.928 43.478 0.00 0.00 0.00 4.61
4935 5555 5.035784 GTCTATTTGACAGAAGCAACCAC 57.964 43.478 0.00 0.00 44.73 4.16
5088 5709 1.003839 GGTGACATGCCAGGTTCGA 60.004 57.895 0.00 0.00 0.00 3.71
5090 5711 4.819783 TGGTGACATGCCAGGTTC 57.180 55.556 0.00 0.00 33.40 3.62
5105 5726 2.991250 ACTCCGATTGAATGGTTCTGG 58.009 47.619 0.00 0.00 0.00 3.86
5114 5735 5.220989 CCTCGATAACAGTACTCCGATTGAA 60.221 44.000 0.00 0.00 0.00 2.69
5128 5757 1.676529 CGCCTCTCTTCCTCGATAACA 59.323 52.381 0.00 0.00 0.00 2.41
5130 5759 2.343484 TCGCCTCTCTTCCTCGATAA 57.657 50.000 0.00 0.00 0.00 1.75
5133 5762 1.475403 AAATCGCCTCTCTTCCTCGA 58.525 50.000 0.00 0.00 0.00 4.04
5413 6069 4.631813 TCCAATTTTGTTCGGTTTGTTTGG 59.368 37.500 0.00 0.00 33.92 3.28
5529 6185 4.982701 GGCTGCCACTGCACCCTT 62.983 66.667 15.17 0.00 44.23 3.95
5573 6229 7.549839 TCAGCAATTTTGGGAAATCTAGAATG 58.450 34.615 0.00 0.00 34.44 2.67
5608 6264 9.787532 GCAACAGCAAAATCTCAGTATTTTATA 57.212 29.630 0.00 0.00 37.03 0.98
5609 6265 8.526147 AGCAACAGCAAAATCTCAGTATTTTAT 58.474 29.630 0.00 0.00 37.03 1.40
5759 6437 8.571336 CAGATGTAACTTCAAGACAGGAAAATT 58.429 33.333 0.00 0.00 0.00 1.82
5841 6520 2.166664 GTCGAAGTACTTGGGATCAGCT 59.833 50.000 14.14 0.00 0.00 4.24
6084 6768 1.506309 CTAAGCACAGTGGTTGCGCA 61.506 55.000 25.19 5.66 38.66 6.09
6087 6771 2.602217 CGAAACTAAGCACAGTGGTTGC 60.602 50.000 25.19 8.06 38.66 4.17
6386 7101 5.207110 AGATGATCACTTCCAGATTACCG 57.793 43.478 0.00 0.00 0.00 4.02
6439 7154 1.681166 GGCAGCTCATGGTTCTGATGT 60.681 52.381 11.97 0.00 0.00 3.06
6800 7702 4.416516 AGGTTTTACTTCATCTTTGGGGG 58.583 43.478 0.00 0.00 0.00 5.40
6919 7831 5.875910 TGCTTTGCCCATAAGAAATCAATTG 59.124 36.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.