Multiple sequence alignment - TraesCS7A01G302500

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 TraesCS7A01G302500 chr7A 100.000 5433 0 0 1 5433 424321319 424315887 0.000000e+00 10033.0
1 TraesCS7A01G302500 chr7A 84.595 753 95 13 1 739 518552028 518551283 0.000000e+00 728.0
2 TraesCS7A01G302500 chr7A 84.118 743 102 11 9 741 202532668 202533404 0.000000e+00 704.0
3 TraesCS7A01G302500 chr7D 90.684 1696 117 25 6 1685 376564583 376562913 0.000000e+00 2218.0
4 TraesCS7A01G302500 chr7D 87.290 1188 75 22 1684 2834 376562859 376561711 0.000000e+00 1288.0
5 TraesCS7A01G302500 chr7D 88.824 689 46 11 2833 3498 376561617 376560937 0.000000e+00 817.0
6 TraesCS7A01G302500 chr7D 84.966 745 90 17 6 739 125910579 125911312 0.000000e+00 736.0
7 TraesCS7A01G302500 chr7D 87.638 542 34 15 4293 4812 376560292 376559762 2.800000e-167 599.0
8 TraesCS7A01G302500 chr7D 97.000 300 7 2 5125 5423 376559450 376559152 2.260000e-138 503.0
9 TraesCS7A01G302500 chr7D 92.920 339 15 5 3569 3904 376560951 376560619 8.180000e-133 484.0
10 TraesCS7A01G302500 chr7D 92.760 221 5 4 3957 4177 376560620 376560411 5.290000e-80 309.0
11 TraesCS7A01G302500 chr7B 97.904 1145 22 1 1775 2917 371736694 371735550 0.000000e+00 1980.0
12 TraesCS7A01G302500 chr7B 93.770 931 34 5 4198 5105 371734276 371733347 0.000000e+00 1376.0
13 TraesCS7A01G302500 chr7B 91.088 864 30 13 822 1685 371737815 371736999 0.000000e+00 1125.0
14 TraesCS7A01G302500 chr7B 98.257 631 6 2 3569 4198 371734931 371734305 0.000000e+00 1099.0
15 TraesCS7A01G302500 chr7B 97.414 580 10 3 2921 3498 371735493 371734917 0.000000e+00 983.0
16 TraesCS7A01G302500 chr7B 87.362 815 84 14 6 809 371744020 371743214 0.000000e+00 917.0
17 TraesCS7A01G302500 chr7B 97.872 94 2 0 1683 1776 371736948 371736855 4.350000e-36 163.0
18 TraesCS7A01G302500 chr7B 100.000 76 0 0 3494 3569 107167623 107167548 2.040000e-29 141.0
19 TraesCS7A01G302500 chr7B 97.531 81 1 1 3490 3569 331021259 331021339 2.640000e-28 137.0
20 TraesCS7A01G302500 chr1B 85.752 765 93 12 3 757 598845624 598846382 0.000000e+00 795.0
21 TraesCS7A01G302500 chr1B 97.297 37 0 1 4205 4241 642955824 642955859 1.630000e-05 62.1
22 TraesCS7A01G302500 chr2D 84.844 739 95 14 8 737 48208894 48209624 0.000000e+00 728.0
23 TraesCS7A01G302500 chr2D 97.143 35 1 0 4205 4239 574101084 574101118 5.880000e-05 60.2
24 TraesCS7A01G302500 chr6A 84.952 731 91 13 19 739 495455516 495454795 0.000000e+00 723.0
25 TraesCS7A01G302500 chr5A 83.487 757 103 18 19 765 649252896 649252152 0.000000e+00 686.0
26 TraesCS7A01G302500 chrUn 85.106 329 45 2 2914 3241 73441466 73441791 3.140000e-87 333.0
27 TraesCS7A01G302500 chrUn 97.531 81 0 2 3489 3569 220138041 220137963 2.640000e-28 137.0
28 TraesCS7A01G302500 chr6B 84.570 337 47 3 2914 3249 80801036 80801368 4.060000e-86 329.0
29 TraesCS7A01G302500 chr6B 85.799 169 21 1 2914 3082 151884684 151884849 5.590000e-40 176.0
30 TraesCS7A01G302500 chr5B 84.570 337 47 3 2914 3249 535100570 535100238 4.060000e-86 329.0
31 TraesCS7A01G302500 chr5B 84.848 330 44 4 2914 3241 52319185 52319510 1.460000e-85 327.0
32 TraesCS7A01G302500 chr5B 100.000 76 0 0 3494 3569 635092807 635092882 2.040000e-29 141.0
33 TraesCS7A01G302500 chr5B 98.734 79 0 1 3491 3569 535081840 535081763 7.340000e-29 139.0
34 TraesCS7A01G302500 chr5B 90.698 43 2 2 4207 4249 541337694 541337654 7.600000e-04 56.5
35 TraesCS7A01G302500 chr2B 86.391 169 20 1 2914 3082 657481833 657481668 1.200000e-41 182.0
36 TraesCS7A01G302500 chr2B 100.000 41 0 0 4197 4237 14834365 14834325 5.840000e-10 76.8
37 TraesCS7A01G302500 chr2B 91.489 47 4 0 3913 3959 731716699 731716745 1.260000e-06 65.8
38 TraesCS7A01G302500 chr2B 89.362 47 5 0 3913 3959 655524106 655524152 5.880000e-05 60.2
39 TraesCS7A01G302500 chr2A 86.391 169 20 1 2914 3082 441104049 441104214 1.200000e-41 182.0
40 TraesCS7A01G302500 chr2A 97.561 41 1 0 4197 4237 410850356 410850396 2.710000e-08 71.3
41 TraesCS7A01G302500 chr6D 100.000 76 0 0 3494 3569 163832509 163832584 2.040000e-29 141.0
42 TraesCS7A01G302500 chr4A 100.000 76 0 0 3494 3569 317089808 317089733 2.040000e-29 141.0
43 TraesCS7A01G302500 chr4A 88.462 52 2 4 4193 4241 468754261 468754211 5.880000e-05 60.2
44 TraesCS7A01G302500 chr4B 93.333 90 5 1 3481 3569 304888097 304888008 1.230000e-26 132.0
45 TraesCS7A01G302500 chr4B 90.196 102 7 3 3501 3599 78017577 78017476 4.420000e-26 130.0
46 TraesCS7A01G302500 chr3B 92.683 41 3 0 4197 4237 548835967 548835927 5.880000e-05 60.2
47 TraesCS7A01G302500 chr3B 87.755 49 4 1 4190 4238 685661455 685661501 7.600000e-04 56.5


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 TraesCS7A01G302500 chr7A 424315887 424321319 5432 True 10033.000000 10033 100.000000 1 5433 1 chr7A.!!$R1 5432
1 TraesCS7A01G302500 chr7A 518551283 518552028 745 True 728.000000 728 84.595000 1 739 1 chr7A.!!$R2 738
2 TraesCS7A01G302500 chr7A 202532668 202533404 736 False 704.000000 704 84.118000 9 741 1 chr7A.!!$F1 732
3 TraesCS7A01G302500 chr7D 376559152 376564583 5431 True 888.285714 2218 91.016571 6 5423 7 chr7D.!!$R1 5417
4 TraesCS7A01G302500 chr7D 125910579 125911312 733 False 736.000000 736 84.966000 6 739 1 chr7D.!!$F1 733
5 TraesCS7A01G302500 chr7B 371733347 371737815 4468 True 1121.000000 1980 96.050833 822 5105 6 chr7B.!!$R3 4283
6 TraesCS7A01G302500 chr7B 371743214 371744020 806 True 917.000000 917 87.362000 6 809 1 chr7B.!!$R2 803
7 TraesCS7A01G302500 chr1B 598845624 598846382 758 False 795.000000 795 85.752000 3 757 1 chr1B.!!$F1 754
8 TraesCS7A01G302500 chr2D 48208894 48209624 730 False 728.000000 728 84.844000 8 737 1 chr2D.!!$F1 729
9 TraesCS7A01G302500 chr6A 495454795 495455516 721 True 723.000000 723 84.952000 19 739 1 chr6A.!!$R1 720
10 TraesCS7A01G302500 chr5A 649252152 649252896 744 True 686.000000 686 83.487000 19 765 1 chr5A.!!$R1 746

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
774 809 0.037734 TGCTCTAGTCCAGTCCGTGA 59.962 55.0 0.00 0.0 0.00 4.35 F
1476 1518 0.462759 GGAGCCAGATGCAGGTACAC 60.463 60.0 0.00 0.0 44.83 2.90 F
1543 1590 0.880278 TTGAGTTGAGAGTGCGTGCC 60.880 55.0 0.00 0.0 0.00 5.01 F
3038 3487 1.879575 TTGGGATCCCCTAGAGTGTG 58.120 55.0 28.58 0.0 45.70 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1679 3.243907 GCCTTAACGCATGAGTAGAGGAT 60.244 47.826 25.32 5.19 31.73 3.24 R
3463 3932 0.032130 ATGCTACGGTCGCTGTATGG 59.968 55.000 6.21 0.00 0.00 2.74 R
3507 3978 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96 R
4798 5353 1.089920 CTTGTACCAGGCATGCTGTC 58.910 55.000 18.92 0.18 0.00 3.51 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
52 54 4.049186 GAGCTTATTTTCGGACGCTATGA 58.951 43.478 0.00 0.00 0.00 2.15
59 62 4.335082 TTTCGGACGCTATGACATTTTG 57.665 40.909 0.00 0.00 0.00 2.44
138 141 0.456221 AGTTGGTCGTATCTGCGGAG 59.544 55.000 0.00 0.00 0.00 4.63
139 142 0.172803 GTTGGTCGTATCTGCGGAGT 59.827 55.000 3.10 0.00 0.00 3.85
140 143 0.172578 TTGGTCGTATCTGCGGAGTG 59.827 55.000 3.10 0.00 0.00 3.51
147 150 2.476686 CGTATCTGCGGAGTGTTCGTAA 60.477 50.000 3.10 0.00 0.00 3.18
160 175 0.040646 TTCGTAAGCAGGAGGAGGGA 59.959 55.000 0.00 0.00 37.18 4.20
250 267 1.459209 CTCATTCAACAACGCAGCGTA 59.541 47.619 23.30 4.23 39.99 4.42
401 419 6.808829 TCTTGCTCAACTTGTTGATTGATTT 58.191 32.000 15.35 0.00 34.43 2.17
475 495 1.338484 CCACATCACAGAGGGACAGTG 60.338 57.143 0.00 0.00 37.35 3.66
522 546 1.478510 CTGAAGGAGGAGTATGCGTGT 59.521 52.381 0.00 0.00 0.00 4.49
721 747 1.404035 GGGTTGAAATGTATGCGGGTC 59.596 52.381 0.00 0.00 0.00 4.46
741 767 2.452813 CGTTGGATGACGGCCTTCG 61.453 63.158 4.57 0.00 45.88 3.79
746 772 1.691976 TGGATGACGGCCTTCGATATT 59.308 47.619 4.57 0.00 42.43 1.28
757 783 2.030457 CCTTCGATATTTGTGTCCGTGC 59.970 50.000 0.00 0.00 0.00 5.34
766 792 0.538746 TGTGTCCGTGCTCTAGTCCA 60.539 55.000 0.00 0.00 0.00 4.02
768 794 0.251209 TGTCCGTGCTCTAGTCCAGT 60.251 55.000 0.00 0.00 0.00 4.00
769 795 0.452585 GTCCGTGCTCTAGTCCAGTC 59.547 60.000 0.00 0.00 0.00 3.51
771 797 1.429825 CGTGCTCTAGTCCAGTCCG 59.570 63.158 0.00 0.00 0.00 4.79
774 809 0.037734 TGCTCTAGTCCAGTCCGTGA 59.962 55.000 0.00 0.00 0.00 4.35
811 846 2.892425 GCCGTCGGAGATGCCTTG 60.892 66.667 17.49 0.00 43.31 3.61
812 847 2.892425 CCGTCGGAGATGCCTTGC 60.892 66.667 4.91 0.00 43.31 4.01
813 848 2.125552 CGTCGGAGATGCCTTGCA 60.126 61.111 0.00 0.00 44.86 4.08
869 905 3.122948 ACAAACGGTTCGATCGATGAAAG 59.877 43.478 20.18 11.23 0.00 2.62
897 933 2.126031 GAGGCTCACCGGTTCGTC 60.126 66.667 2.97 4.72 42.76 4.20
961 997 2.733218 CGCGTCTCGTCAGCCAAA 60.733 61.111 0.00 0.00 0.00 3.28
962 998 2.720758 CGCGTCTCGTCAGCCAAAG 61.721 63.158 0.00 0.00 0.00 2.77
963 999 3.016474 GCGTCTCGTCAGCCAAAGC 62.016 63.158 0.00 0.00 40.32 3.51
1186 1228 4.154347 GCCTGTGCTCCTCCTCCG 62.154 72.222 0.00 0.00 33.53 4.63
1188 1230 4.504916 CTGTGCTCCTCCTCCGCG 62.505 72.222 0.00 0.00 0.00 6.46
1337 1379 1.923909 CCCTCCCCCTTTCCGTTCT 60.924 63.158 0.00 0.00 0.00 3.01
1476 1518 0.462759 GGAGCCAGATGCAGGTACAC 60.463 60.000 0.00 0.00 44.83 2.90
1543 1590 0.880278 TTGAGTTGAGAGTGCGTGCC 60.880 55.000 0.00 0.00 0.00 5.01
1653 1700 4.592485 ATCCTCTACTCATGCGTTAAGG 57.408 45.455 8.99 8.99 0.00 2.69
1761 1863 4.551702 TGCATGTGTATACCACTGTCTT 57.448 40.909 0.00 0.00 44.81 3.01
1762 1864 4.252878 TGCATGTGTATACCACTGTCTTG 58.747 43.478 0.00 0.00 44.81 3.02
1983 2249 4.275936 ACTGTATGTGAGCCAAGTGTTTTC 59.724 41.667 0.00 0.00 0.00 2.29
2126 2421 2.066262 CCAAACGTAGAGTGCGTGAAT 58.934 47.619 0.00 0.00 42.10 2.57
2407 2707 3.308438 AGATTGTTGGAAATGCACTGC 57.692 42.857 0.00 0.00 0.00 4.40
2426 2726 3.694734 TGCGCTTATTTTAGCATTGCTC 58.305 40.909 15.81 0.00 41.28 4.26
2679 2979 8.957466 GGTCCATAGCAAGAAAACTTAAGTTAT 58.043 33.333 20.83 7.90 37.25 1.89
2699 2999 8.243289 AGTTATTTGCATGTAATTTTCAGCAC 57.757 30.769 0.00 0.00 0.00 4.40
2807 3107 8.628882 ACGAAACCTTCTTTTTAGTTTCATTG 57.371 30.769 13.14 2.22 45.28 2.82
2891 3286 8.804204 ACCTTGTATGGACTTATGTAGCTATAC 58.196 37.037 0.00 0.00 31.43 1.47
2917 3312 6.698008 TCTGCATTTAGGATTACCAACATG 57.302 37.500 0.00 0.00 38.94 3.21
2959 3407 8.712103 GTTTCATAGGTAGGTCTAGGGTTAAAT 58.288 37.037 0.00 0.00 0.00 1.40
2960 3408 9.956558 TTTCATAGGTAGGTCTAGGGTTAAATA 57.043 33.333 0.00 0.00 0.00 1.40
2961 3409 9.956558 TTCATAGGTAGGTCTAGGGTTAAATAA 57.043 33.333 0.00 0.00 0.00 1.40
3038 3487 1.879575 TTGGGATCCCCTAGAGTGTG 58.120 55.000 28.58 0.00 45.70 3.82
3053 3502 6.265649 CCTAGAGTGTGTAGCATACCAGTATT 59.734 42.308 0.00 0.00 42.12 1.89
3353 3822 6.502136 AGCTAGTAAGATTTTGGTTTGCTC 57.498 37.500 0.00 0.00 0.00 4.26
3402 3871 7.496529 TTCAGCTTATGTTTGCCATAGTATC 57.503 36.000 0.00 0.00 37.34 2.24
3508 3979 6.901081 ATGTTTTCTATATAAAGGGCAGCC 57.099 37.500 1.26 1.26 0.00 4.85
3509 3980 5.137551 TGTTTTCTATATAAAGGGCAGCCC 58.862 41.667 24.90 24.90 45.90 5.19
3520 3991 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
3521 3992 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
3522 3993 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
3523 3994 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
3524 3995 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
3525 3996 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
3526 3997 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
3527 3998 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
3528 3999 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
3530 4001 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3531 4002 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3532 4003 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3533 4004 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3536 4007 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
3548 4019 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
3549 4020 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
3550 4021 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
3551 4022 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
3552 4023 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
3553 4024 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
3554 4025 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
3555 4026 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
3556 4027 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
3557 4028 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
3558 4029 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
3559 4030 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
3560 4031 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
3561 4032 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
3562 4033 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
3563 4034 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
3564 4035 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
3565 4036 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
3566 4037 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
3577 4048 5.784578 ACCACTTTGGGTCTTATGTTTTC 57.215 39.130 0.00 0.00 43.37 2.29
3578 4049 5.454966 ACCACTTTGGGTCTTATGTTTTCT 58.545 37.500 0.00 0.00 43.37 2.52
3579 4050 6.607019 ACCACTTTGGGTCTTATGTTTTCTA 58.393 36.000 0.00 0.00 43.37 2.10
3580 4051 7.238710 ACCACTTTGGGTCTTATGTTTTCTAT 58.761 34.615 0.00 0.00 43.37 1.98
3581 4052 8.387813 ACCACTTTGGGTCTTATGTTTTCTATA 58.612 33.333 0.00 0.00 43.37 1.31
3582 4053 9.408648 CCACTTTGGGTCTTATGTTTTCTATAT 57.591 33.333 0.00 0.00 32.67 0.86
3879 4352 4.870123 CTATCAGCATGGTAGCTCTCTT 57.130 45.455 0.00 0.00 43.80 2.85
4078 4551 4.450082 TGATGTGTCGTAGTATTGCAGT 57.550 40.909 0.00 0.00 0.00 4.40
4189 4662 1.450642 GATTTACTCCCTCCGCCCC 59.549 63.158 0.00 0.00 0.00 5.80
4209 4711 4.539870 CCCATCATATAGCTTGCAAAACG 58.460 43.478 0.00 0.00 0.00 3.60
4237 4739 0.561184 TCATGGGACGGAGGGAGTAT 59.439 55.000 0.00 0.00 0.00 2.12
4253 4755 7.012421 GGAGGGAGTATTTTACTTTGTGCATAG 59.988 40.741 0.00 0.00 39.59 2.23
4339 4874 5.107182 CGCATCATCCTTCTCATGTGTTATC 60.107 44.000 0.00 0.00 0.00 1.75
4643 5195 4.082354 CAGATCATCTATCGCCACATCAGA 60.082 45.833 0.00 0.00 39.79 3.27
4715 5267 3.198068 ACTAATACAATCACGCAGCAGG 58.802 45.455 0.00 0.00 0.00 4.85
4738 5290 4.679639 GCGTATCACCATGGTCTTGAGTTA 60.680 45.833 16.53 0.00 0.00 2.24
4798 5353 0.321671 TGTTTCTTCTGGAGGAGGCG 59.678 55.000 0.00 0.00 0.00 5.52
4844 5403 3.250280 CAGATGGCATATGCTCTCACAAC 59.750 47.826 26.12 13.92 41.70 3.32
4848 5407 1.600957 GCATATGCTCTCACAACGCAT 59.399 47.619 20.64 0.00 45.45 4.73
4849 5408 2.601504 GCATATGCTCTCACAACGCATG 60.602 50.000 20.64 0.00 43.56 4.06
4850 5409 2.385013 TATGCTCTCACAACGCATGT 57.615 45.000 6.26 0.00 43.56 3.21
4851 5410 1.527034 ATGCTCTCACAACGCATGTT 58.473 45.000 0.00 0.00 42.30 2.71
4897 5456 2.625639 AGATCTTCCAGAAGTGGGTGT 58.374 47.619 7.26 0.00 45.11 4.16
4905 5464 6.214615 TCTTCCAGAAGTGGGTGTATCAATTA 59.785 38.462 7.26 0.00 45.11 1.40
4937 5496 7.548427 CCATGTATGATGTACCAAAATTTTGCA 59.452 33.333 22.90 16.38 36.86 4.08
4964 5523 9.511144 TCGTTTTTCTTCTTTTAGGAAATTGAC 57.489 29.630 0.00 0.00 0.00 3.18
5029 5588 1.618837 TCACTAACCACTCAGCTGGTC 59.381 52.381 15.13 0.00 44.32 4.02
5120 5734 8.198109 TCCTCTGTTGTAGAAATGTAATCTAGC 58.802 37.037 0.00 0.00 34.32 3.42
5123 5737 9.944376 TCTGTTGTAGAAATGTAATCTAGCTTT 57.056 29.630 0.00 0.00 30.84 3.51
5157 5781 4.141855 GCTTGTAGACTTAAAAGCGCAA 57.858 40.909 11.47 0.00 39.62 4.85
5256 5880 5.129815 TGGTAGTAGAGTTTCAACCAACACT 59.870 40.000 0.00 0.00 34.20 3.55
5277 5901 7.382898 ACACTGAAGACTCCTCTTTATCTTTC 58.617 38.462 0.00 0.00 36.82 2.62
5296 5920 2.111384 TCCTTACCCAGCTGATGAGAC 58.889 52.381 17.39 0.00 0.00 3.36
5303 5927 2.512515 GCTGATGAGACGGTGGGC 60.513 66.667 0.00 0.00 0.00 5.36
5416 6040 7.147897 ACGATCTATGATAACCACTCTTGTCAA 60.148 37.037 0.00 0.00 0.00 3.18
5420 6044 6.992063 ATGATAACCACTCTTGTCAATGAC 57.008 37.500 6.41 6.41 0.00 3.06
5421 6045 5.863965 TGATAACCACTCTTGTCAATGACA 58.136 37.500 12.63 12.63 41.09 3.58
5422 6046 6.475504 TGATAACCACTCTTGTCAATGACAT 58.524 36.000 17.48 0.00 42.40 3.06
5423 6047 6.595326 TGATAACCACTCTTGTCAATGACATC 59.405 38.462 17.48 7.98 42.40 3.06
5424 6048 4.630644 ACCACTCTTGTCAATGACATCT 57.369 40.909 17.48 0.00 42.40 2.90
5425 6049 4.321718 ACCACTCTTGTCAATGACATCTG 58.678 43.478 17.48 11.75 42.40 2.90
5426 6050 4.202398 ACCACTCTTGTCAATGACATCTGT 60.202 41.667 17.48 12.34 42.40 3.41
5427 6051 4.153655 CCACTCTTGTCAATGACATCTGTG 59.846 45.833 17.48 21.25 42.40 3.66
5428 6052 4.992951 CACTCTTGTCAATGACATCTGTGA 59.007 41.667 24.65 15.05 42.40 3.58
5429 6053 5.467735 CACTCTTGTCAATGACATCTGTGAA 59.532 40.000 24.65 8.69 42.40 3.18
5430 6054 5.699915 ACTCTTGTCAATGACATCTGTGAAG 59.300 40.000 17.48 9.54 42.40 3.02
5431 6055 5.857268 TCTTGTCAATGACATCTGTGAAGA 58.143 37.500 17.48 11.72 42.40 2.87
5432 6056 6.470278 TCTTGTCAATGACATCTGTGAAGAT 58.530 36.000 17.48 0.00 42.40 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 6.543831 GCCATCCTTCATACTCTACAAAATGT 59.456 38.462 0.00 0.00 0.00 2.71
59 62 3.612955 GCTCGCCATCCTTCATACTCTAC 60.613 52.174 0.00 0.00 0.00 2.59
138 141 1.404315 CCTCCTCCTGCTTACGAACAC 60.404 57.143 0.00 0.00 0.00 3.32
139 142 0.895530 CCTCCTCCTGCTTACGAACA 59.104 55.000 0.00 0.00 0.00 3.18
140 143 0.175989 CCCTCCTCCTGCTTACGAAC 59.824 60.000 0.00 0.00 0.00 3.95
147 150 4.814041 GGCCTCCCTCCTCCTGCT 62.814 72.222 0.00 0.00 0.00 4.24
192 207 1.444119 ATGTGCTTTCGTGCGTGGTT 61.444 50.000 0.00 0.00 35.36 3.67
218 233 6.129035 CGTTGTTGAATGAGTACATGTCGTAA 60.129 38.462 0.00 0.00 36.79 3.18
250 267 2.287427 CCAGCGATACGATAACGACCTT 60.287 50.000 0.00 0.00 42.66 3.50
285 302 6.993786 TGTTACAAAACTTGATGACACTGA 57.006 33.333 0.00 0.00 36.51 3.41
362 379 6.639632 TGAGCAAGAGAAAGCAAAACTTAT 57.360 33.333 0.00 0.00 37.75 1.73
401 419 4.334203 GTGTACACCAACATTGAGTGAACA 59.666 41.667 15.42 5.16 35.09 3.18
475 495 7.997107 TCATCCAATAGTGTGTACGTAAATC 57.003 36.000 0.00 0.00 0.00 2.17
522 546 4.748277 TCATCAACAGATCATGCTCTCA 57.252 40.909 0.00 0.00 0.00 3.27
548 572 7.231467 ACTAGATTAACTGGTTGTCCAACATT 58.769 34.615 11.89 5.85 43.81 2.71
721 747 1.635663 GAAGGCCGTCATCCAACGTG 61.636 60.000 14.36 0.00 41.01 4.49
741 767 4.683832 ACTAGAGCACGGACACAAATATC 58.316 43.478 0.00 0.00 0.00 1.63
746 772 0.601558 GGACTAGAGCACGGACACAA 59.398 55.000 0.00 0.00 0.00 3.33
757 783 1.746220 CCTTCACGGACTGGACTAGAG 59.254 57.143 0.00 0.00 33.16 2.43
766 792 3.790089 AAATTTCCTCCTTCACGGACT 57.210 42.857 0.00 0.00 36.69 3.85
768 794 3.592059 CGTAAATTTCCTCCTTCACGGA 58.408 45.455 0.00 0.00 40.30 4.69
769 795 2.676342 CCGTAAATTTCCTCCTTCACGG 59.324 50.000 9.71 9.71 41.32 4.94
771 797 3.682696 ACCCGTAAATTTCCTCCTTCAC 58.317 45.455 0.00 0.00 0.00 3.18
774 809 2.938314 GCGACCCGTAAATTTCCTCCTT 60.938 50.000 0.00 0.00 0.00 3.36
809 844 5.581874 CACAGTGAGATATGTACACATGCAA 59.418 40.000 0.00 0.00 37.15 4.08
811 846 5.351458 TCACAGTGAGATATGTACACATGC 58.649 41.667 0.00 0.00 37.15 4.06
812 847 9.533253 TTAATCACAGTGAGATATGTACACATG 57.467 33.333 9.64 0.00 37.15 3.21
814 849 9.366216 GTTTAATCACAGTGAGATATGTACACA 57.634 33.333 9.64 0.00 37.05 3.72
815 850 8.818057 GGTTTAATCACAGTGAGATATGTACAC 58.182 37.037 9.64 0.00 35.15 2.90
869 905 1.019805 GTGAGCCTCCCAGTTTACGC 61.020 60.000 0.00 0.00 0.00 4.42
897 933 3.554129 GGTTTTCAAAATCGGACCCAAGG 60.554 47.826 0.00 0.00 0.00 3.61
963 999 2.559840 CAGCACTCAAGCGGCAAG 59.440 61.111 1.45 0.00 40.15 4.01
964 1000 2.979676 CCAGCACTCAAGCGGCAA 60.980 61.111 1.45 0.00 40.15 4.52
1318 1360 2.939353 AACGGAAAGGGGGAGGGG 60.939 66.667 0.00 0.00 0.00 4.79
1337 1379 1.069973 CGAACAGCAGCGAATTTGTGA 60.070 47.619 0.00 0.00 0.00 3.58
1374 1416 1.804151 GCAGGATAAACAAGCACACGA 59.196 47.619 0.00 0.00 0.00 4.35
1476 1518 1.167781 TGTGTCATGTGTGCTGCCTG 61.168 55.000 0.00 0.00 0.00 4.85
1543 1590 2.774126 CGTCACGCATGCACTGAG 59.226 61.111 19.57 2.94 0.00 3.35
1627 1674 4.974368 ACGCATGAGTAGAGGATATAGC 57.026 45.455 0.00 0.00 0.00 2.97
1630 1677 5.336849 GCCTTAACGCATGAGTAGAGGATAT 60.337 44.000 25.32 3.94 31.73 1.63
1632 1679 3.243907 GCCTTAACGCATGAGTAGAGGAT 60.244 47.826 25.32 5.19 31.73 3.24
1983 2249 7.609532 AGTGGAAGACAAGAAAATCCAGATTAG 59.390 37.037 0.00 0.00 40.65 1.73
2231 2526 6.530120 TGTAAAATCAGGCTTTCAGTACAGA 58.470 36.000 0.00 0.00 0.00 3.41
2407 2707 6.204359 AGATTGAGCAATGCTAAAATAAGCG 58.796 36.000 8.12 0.00 45.85 4.68
2426 2726 4.818546 ACGAATATCCCTGCAAGAAGATTG 59.181 41.667 0.00 0.00 34.07 2.67
2679 2979 4.615949 ACGTGCTGAAAATTACATGCAAA 58.384 34.783 0.00 0.00 32.10 3.68
2697 2997 4.679197 CCACAAAATATGTTGTCCAACGTG 59.321 41.667 8.38 9.23 41.46 4.49
2699 2999 4.865776 ACCACAAAATATGTTGTCCAACG 58.134 39.130 8.38 0.00 41.46 4.10
2891 3286 7.156876 TGTTGGTAATCCTAAATGCAGAAAG 57.843 36.000 0.00 0.00 34.23 2.62
3038 3487 6.163135 AGTCCTTGAATACTGGTATGCTAC 57.837 41.667 1.07 0.00 0.00 3.58
3053 3502 6.665992 ACAAGACTACACATTAGTCCTTGA 57.334 37.500 19.37 0.00 43.61 3.02
3402 3871 6.697892 GGAATCTTGTATGAAACTACGAGAGG 59.302 42.308 7.15 0.00 42.59 3.69
3463 3932 0.032130 ATGCTACGGTCGCTGTATGG 59.968 55.000 6.21 0.00 0.00 2.74
3502 3973 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
3503 3974 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
3504 3975 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
3505 3976 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
3506 3977 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
3507 3978 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
3508 3979 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
3509 3980 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
3510 3981 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
3531 4002 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
3532 4003 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
3533 4004 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
3534 4005 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
3535 4006 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
3536 4007 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
3537 4008 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
3538 4009 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
3539 4010 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
3540 4011 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
3541 4012 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
3542 4013 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
3543 4014 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
3544 4015 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
3545 4016 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
3546 4017 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
3547 4018 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
3548 4019 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
3549 4020 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
3550 4021 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
3555 4026 5.454966 AGAAAACATAAGACCCAAAGTGGT 58.545 37.500 0.00 0.00 42.79 4.16
3556 4027 7.703058 ATAGAAAACATAAGACCCAAAGTGG 57.297 36.000 0.00 0.00 37.25 4.00
3876 4349 5.721480 TGAGAGAGAGAGAGAGAGAGAAAGA 59.279 44.000 0.00 0.00 0.00 2.52
3877 4350 5.982356 TGAGAGAGAGAGAGAGAGAGAAAG 58.018 45.833 0.00 0.00 0.00 2.62
3878 4351 6.566079 ATGAGAGAGAGAGAGAGAGAGAAA 57.434 41.667 0.00 0.00 0.00 2.52
3879 4352 6.239036 CGTATGAGAGAGAGAGAGAGAGAGAA 60.239 46.154 0.00 0.00 0.00 2.87
4189 4662 6.895898 AGATCGTTTTGCAAGCTATATGATG 58.104 36.000 0.00 0.00 0.00 3.07
4209 4711 4.100189 CCCTCCGTCCCATGATATAAGATC 59.900 50.000 0.00 0.00 0.00 2.75
4219 4721 1.424638 AATACTCCCTCCGTCCCATG 58.575 55.000 0.00 0.00 0.00 3.66
4253 4755 9.922305 GAAACAGCTGAACAAATACAGATATAC 57.078 33.333 23.35 0.00 36.38 1.47
4313 4848 1.140452 ACATGAGAAGGATGATGCGCT 59.860 47.619 9.73 0.00 0.00 5.92
4662 5214 1.476891 GACTCCATTGACTCAGGCGTA 59.523 52.381 0.00 0.00 0.00 4.42
4715 5267 2.205074 CTCAAGACCATGGTGATACGC 58.795 52.381 25.52 6.49 0.00 4.42
4738 5290 5.566429 GCGACAGAGATATGATGAGTCCATT 60.566 44.000 0.00 0.00 32.09 3.16
4798 5353 1.089920 CTTGTACCAGGCATGCTGTC 58.910 55.000 18.92 0.18 0.00 3.51
4844 5403 2.034675 GCAAACAAACTGTCAACATGCG 60.035 45.455 0.00 0.00 0.00 4.73
4848 5407 1.813178 TCGGCAAACAAACTGTCAACA 59.187 42.857 0.00 0.00 0.00 3.33
4849 5408 2.553079 TCGGCAAACAAACTGTCAAC 57.447 45.000 0.00 0.00 0.00 3.18
4850 5409 3.443037 CAATCGGCAAACAAACTGTCAA 58.557 40.909 0.00 0.00 0.00 3.18
4851 5410 2.797792 GCAATCGGCAAACAAACTGTCA 60.798 45.455 0.00 0.00 43.97 3.58
4897 5456 6.353404 TCATACATGGGCGACTAATTGATA 57.647 37.500 0.00 0.00 0.00 2.15
4905 5464 2.037251 GGTACATCATACATGGGCGACT 59.963 50.000 0.00 0.00 0.00 4.18
5029 5588 6.377327 AAGTTACTCAACTGAACATTGGTG 57.623 37.500 0.00 0.00 44.41 4.17
5058 5617 3.890147 ACACTTAGTCCTTCAGTTCGAGT 59.110 43.478 0.00 0.00 0.00 4.18
5062 5621 4.338379 ACCACACTTAGTCCTTCAGTTC 57.662 45.455 0.00 0.00 0.00 3.01
5179 5803 0.530744 TTCCGGAGATTCCACAGTCG 59.469 55.000 3.34 0.00 35.91 4.18
5185 5809 1.339631 ACGCAAATTCCGGAGATTCCA 60.340 47.619 3.34 0.00 35.91 3.53
5256 5880 7.560796 AAGGAAAGATAAAGAGGAGTCTTCA 57.439 36.000 4.93 0.00 42.59 3.02
5277 5901 1.202463 CGTCTCATCAGCTGGGTAAGG 60.202 57.143 15.13 0.00 0.00 2.69
5296 5920 0.322456 TTCTCCTTCAATGCCCACCG 60.322 55.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.