Multiple sequence alignment - TraesCS7A01G300200

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 TraesCS7A01G300200 chr7A 100.000 4791 0 0 1 4791 415923496 415918706 0.000000e+00 8848.0
1 TraesCS7A01G300200 chr7A 97.856 2938 30 2 1854 4791 415461478 415458574 0.000000e+00 5046.0
2 TraesCS7A01G300200 chr7A 98.593 1421 19 1 82 1502 415464017 415462598 0.000000e+00 2512.0
3 TraesCS7A01G300200 chr7A 82.389 1130 115 49 3024 4110 6430287 6429199 0.000000e+00 907.0
4 TraesCS7A01G300200 chr7A 86.885 610 68 9 2121 2724 505389411 505390014 0.000000e+00 673.0
5 TraesCS7A01G300200 chr7A 99.176 364 3 0 1494 1857 415461976 415461613 0.000000e+00 656.0
6 TraesCS7A01G300200 chr7A 84.533 653 70 22 3471 4110 305501200 305500566 6.810000e-173 617.0
7 TraesCS7A01G300200 chr7A 86.374 455 59 3 4082 4536 305500626 305500175 1.200000e-135 494.0
8 TraesCS7A01G300200 chr7A 86.848 441 50 6 4088 4526 6429253 6428819 2.000000e-133 486.0
9 TraesCS7A01G300200 chr7A 99.111 225 2 0 4527 4751 701103848 701104072 5.770000e-109 405.0
10 TraesCS7A01G300200 chr7A 98.667 225 3 0 4527 4751 528412038 528412262 2.690000e-107 399.0
11 TraesCS7A01G300200 chr7A 91.045 134 11 1 2889 3022 6430471 6430339 3.810000e-41 180.0
12 TraesCS7A01G300200 chr1A 98.012 1509 25 3 3020 4526 47375244 47373739 0.000000e+00 2615.0
13 TraesCS7A01G300200 chr1A 98.546 1169 16 1 1854 3022 47376461 47375294 0.000000e+00 2063.0
14 TraesCS7A01G300200 chr1A 98.057 1132 20 1 371 1502 47378733 47377604 0.000000e+00 1967.0
15 TraesCS7A01G300200 chr1A 90.334 1138 97 5 369 1502 17306510 17305382 0.000000e+00 1480.0
16 TraesCS7A01G300200 chr1A 98.108 370 7 0 1 370 509620852 509620483 0.000000e+00 645.0
17 TraesCS7A01G300200 chr1A 98.082 365 6 1 1494 1857 47376960 47376596 6.760000e-178 634.0
18 TraesCS7A01G300200 chr1A 98.667 225 3 0 4527 4751 63506002 63505778 2.690000e-107 399.0
19 TraesCS7A01G300200 chr1A 79.920 249 33 10 3678 3923 408333351 408333585 2.970000e-37 167.0
20 TraesCS7A01G300200 chr1A 95.238 63 3 0 3411 3473 408333246 408333308 3.050000e-17 100.0
21 TraesCS7A01G300200 chr1A 83.838 99 14 1 3375 3473 26090253 26090349 5.110000e-15 93.5
22 TraesCS7A01G300200 chr1A 84.946 93 9 5 2911 3003 26090090 26090177 6.600000e-14 89.8
23 TraesCS7A01G300200 chr6A 98.888 1169 13 0 1854 3022 589250526 589249358 0.000000e+00 2087.0
24 TraesCS7A01G300200 chr6A 98.146 971 16 2 3020 3989 589249308 589248339 0.000000e+00 1692.0
25 TraesCS7A01G300200 chr6A 98.201 778 14 0 725 1502 589252444 589251667 0.000000e+00 1360.0
26 TraesCS7A01G300200 chr6A 97.989 547 11 0 3979 4525 589248285 589247739 0.000000e+00 950.0
27 TraesCS7A01G300200 chr6A 81.890 1132 120 50 3023 4110 393916355 393915265 0.000000e+00 876.0
28 TraesCS7A01G300200 chr6A 98.077 364 7 0 1494 1857 589251024 589250661 6.760000e-178 634.0
29 TraesCS7A01G300200 chr6A 85.031 648 66 22 3470 4104 18314067 18314696 8.750000e-177 630.0
30 TraesCS7A01G300200 chr6A 84.337 664 72 21 3469 4119 407366599 407365955 5.270000e-174 621.0
31 TraesCS7A01G300200 chr6A 86.742 445 58 1 4082 4526 18314642 18315085 1.200000e-135 494.0
32 TraesCS7A01G300200 chr6A 82.158 241 30 8 3684 3923 73883145 73883373 1.360000e-45 195.0
33 TraesCS7A01G300200 chr6A 81.019 216 28 9 3267 3473 73882789 73883000 4.960000e-35 159.0
34 TraesCS7A01G300200 chr3A 91.213 1138 85 6 371 1502 723838464 723839592 0.000000e+00 1533.0
35 TraesCS7A01G300200 chr3A 92.547 644 43 2 1854 2493 723840746 723841388 0.000000e+00 918.0
36 TraesCS7A01G300200 chr3A 94.775 555 28 1 3222 3775 723841721 723842275 0.000000e+00 863.0
37 TraesCS7A01G300200 chr3A 93.578 436 25 1 4094 4526 723842493 723842928 0.000000e+00 647.0
38 TraesCS7A01G300200 chr3A 98.108 370 7 0 1 370 689886379 689886748 0.000000e+00 645.0
39 TraesCS7A01G300200 chr3A 98.108 370 7 0 1 370 689927853 689928222 0.000000e+00 645.0
40 TraesCS7A01G300200 chr3A 98.108 370 7 0 1 370 744833894 744833525 0.000000e+00 645.0
41 TraesCS7A01G300200 chr3A 83.279 616 73 15 370 965 746942391 746942996 1.520000e-149 540.0
42 TraesCS7A01G300200 chr3A 92.877 365 19 3 1494 1857 723840253 723840611 1.530000e-144 523.0
43 TraesCS7A01G300200 chr3A 92.715 302 16 3 3776 4075 723842241 723842538 9.530000e-117 431.0
44 TraesCS7A01G300200 chr3A 98.667 225 3 0 4527 4751 11645237 11645461 2.690000e-107 399.0
45 TraesCS7A01G300200 chr3A 98.667 225 3 0 4527 4751 553405914 553406138 2.690000e-107 399.0
46 TraesCS7A01G300200 chr3A 98.667 225 3 0 4527 4751 608711036 608710812 2.690000e-107 399.0
47 TraesCS7A01G300200 chr3A 98.519 135 2 0 2888 3022 723841533 723841667 6.200000e-59 239.0
48 TraesCS7A01G300200 chr6D 80.157 1532 194 67 3034 4527 1548072 1546613 0.000000e+00 1044.0
49 TraesCS7A01G300200 chr6D 86.086 654 62 20 3469 4110 142928312 142927676 0.000000e+00 676.0
50 TraesCS7A01G300200 chr6D 87.191 445 55 2 4082 4526 142927736 142927294 5.530000e-139 505.0
51 TraesCS7A01G300200 chr6D 82.655 467 48 15 3024 3488 142928765 142928330 2.710000e-102 383.0
52 TraesCS7A01G300200 chr6D 91.045 134 10 2 2889 3022 142928948 142928817 3.810000e-41 180.0
53 TraesCS7A01G300200 chr4A 98.378 370 6 0 1 370 208241860 208242229 0.000000e+00 651.0
54 TraesCS7A01G300200 chr4A 98.378 370 6 0 1 370 519623330 519622961 0.000000e+00 651.0
55 TraesCS7A01G300200 chr4A 98.108 370 7 0 1 370 279998649 279999018 0.000000e+00 645.0
56 TraesCS7A01G300200 chr4A 85.517 580 58 13 2146 2724 178746111 178745557 2.490000e-162 582.0
57 TraesCS7A01G300200 chr4A 98.667 225 3 0 4527 4751 240302817 240303041 2.690000e-107 399.0
58 TraesCS7A01G300200 chr4A 84.615 130 19 1 371 499 520442758 520442629 1.400000e-25 128.0
59 TraesCS7A01G300200 chr5A 98.108 370 7 0 1 370 601584050 601584419 0.000000e+00 645.0
60 TraesCS7A01G300200 chr5A 83.761 585 62 24 2120 2697 517912672 517912114 1.530000e-144 523.0
61 TraesCS7A01G300200 chr2A 84.877 648 69 21 3469 4104 269201045 269201675 1.130000e-175 627.0
62 TraesCS7A01G300200 chr2A 99.111 225 2 0 4527 4751 119637503 119637727 5.770000e-109 405.0
63 TraesCS7A01G300200 chr2A 82.443 262 36 6 1239 1497 541819817 541819563 2.240000e-53 220.0
64 TraesCS7A01G300200 chr5B 85.838 579 56 13 2146 2724 649922869 649922317 4.130000e-165 592.0
65 TraesCS7A01G300200 chr5B 85.391 575 59 12 2150 2724 35684769 35684220 1.500000e-159 573.0
66 TraesCS7A01G300200 chr4B 87.719 513 55 6 370 875 41007214 41007725 4.130000e-165 592.0
67 TraesCS7A01G300200 chrUn 85.789 577 57 13 2148 2724 89270455 89271006 5.340000e-164 588.0
68 TraesCS7A01G300200 chr6B 84.656 567 70 11 3470 4026 265325141 265324582 2.520000e-152 549.0
69 TraesCS7A01G300200 chr6B 80.838 167 31 1 371 536 565747960 565748126 3.890000e-26 130.0
70 TraesCS7A01G300200 chr2D 81.779 697 72 34 3837 4526 319684579 319685227 2.540000e-147 532.0
71 TraesCS7A01G300200 chr2D 77.902 448 54 23 3675 4107 131302579 131302996 2.230000e-58 237.0
72 TraesCS7A01G300200 chr2D 94.737 57 3 0 3411 3467 131302477 131302533 6.600000e-14 89.8
73 TraesCS7A01G300200 chr7D 86.441 413 48 6 3469 3875 632225108 632224698 3.400000e-121 446.0
74 TraesCS7A01G300200 chr7D 91.111 135 10 2 2888 3022 632225866 632225734 1.060000e-41 182.0
75 TraesCS7A01G300200 chr7D 88.281 128 13 2 3024 3149 632225682 632225555 8.300000e-33 152.0
76 TraesCS7A01G300200 chr1B 76.327 452 59 26 3483 3923 126992448 126992862 1.050000e-46 198.0
77 TraesCS7A01G300200 chr7B 91.111 135 11 1 2888 3022 2232346 2232213 1.060000e-41 182.0
78 TraesCS7A01G300200 chr7B 93.651 63 4 0 3411 3473 54264358 54264420 1.420000e-15 95.3
79 TraesCS7A01G300200 chr5D 80.769 208 32 8 1291 1494 426053921 426053718 6.420000e-34 156.0
80 TraesCS7A01G300200 chr4D 84.733 131 17 3 371 499 143450635 143450764 1.400000e-25 128.0
81 TraesCS7A01G300200 chr3B 91.304 46 2 2 4052 4095 757238346 757238391 1.440000e-05 62.1


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 TraesCS7A01G300200 chr7A 415918706 415923496 4790 True 8848.000000 8848 100.000000 1 4791 1 chr7A.!!$R1 4790
1 TraesCS7A01G300200 chr7A 415458574 415464017 5443 True 2738.000000 5046 98.541667 82 4791 3 chr7A.!!$R4 4709
2 TraesCS7A01G300200 chr7A 505389411 505390014 603 False 673.000000 673 86.885000 2121 2724 1 chr7A.!!$F1 603
3 TraesCS7A01G300200 chr7A 305500175 305501200 1025 True 555.500000 617 85.453500 3471 4536 2 chr7A.!!$R3 1065
4 TraesCS7A01G300200 chr7A 6428819 6430471 1652 True 524.333333 907 86.760667 2889 4526 3 chr7A.!!$R2 1637
5 TraesCS7A01G300200 chr1A 47373739 47378733 4994 True 1819.750000 2615 98.174250 371 4526 4 chr1A.!!$R4 4155
6 TraesCS7A01G300200 chr1A 17305382 17306510 1128 True 1480.000000 1480 90.334000 369 1502 1 chr1A.!!$R1 1133
7 TraesCS7A01G300200 chr6A 589247739 589252444 4705 True 1344.600000 2087 98.260200 725 4525 5 chr6A.!!$R3 3800
8 TraesCS7A01G300200 chr6A 393915265 393916355 1090 True 876.000000 876 81.890000 3023 4110 1 chr6A.!!$R1 1087
9 TraesCS7A01G300200 chr6A 407365955 407366599 644 True 621.000000 621 84.337000 3469 4119 1 chr6A.!!$R2 650
10 TraesCS7A01G300200 chr6A 18314067 18315085 1018 False 562.000000 630 85.886500 3470 4526 2 chr6A.!!$F1 1056
11 TraesCS7A01G300200 chr3A 723838464 723842928 4464 False 736.285714 1533 93.746286 371 4526 7 chr3A.!!$F6 4155
12 TraesCS7A01G300200 chr3A 746942391 746942996 605 False 540.000000 540 83.279000 370 965 1 chr3A.!!$F5 595
13 TraesCS7A01G300200 chr6D 1546613 1548072 1459 True 1044.000000 1044 80.157000 3034 4527 1 chr6D.!!$R1 1493
14 TraesCS7A01G300200 chr6D 142927294 142928948 1654 True 436.000000 676 86.744250 2889 4526 4 chr6D.!!$R2 1637
15 TraesCS7A01G300200 chr4A 178745557 178746111 554 True 582.000000 582 85.517000 2146 2724 1 chr4A.!!$R1 578
16 TraesCS7A01G300200 chr5A 517912114 517912672 558 True 523.000000 523 83.761000 2120 2697 1 chr5A.!!$R1 577
17 TraesCS7A01G300200 chr2A 269201045 269201675 630 False 627.000000 627 84.877000 3469 4104 1 chr2A.!!$F2 635
18 TraesCS7A01G300200 chr5B 649922317 649922869 552 True 592.000000 592 85.838000 2146 2724 1 chr5B.!!$R2 578
19 TraesCS7A01G300200 chr5B 35684220 35684769 549 True 573.000000 573 85.391000 2150 2724 1 chr5B.!!$R1 574
20 TraesCS7A01G300200 chr4B 41007214 41007725 511 False 592.000000 592 87.719000 370 875 1 chr4B.!!$F1 505
21 TraesCS7A01G300200 chrUn 89270455 89271006 551 False 588.000000 588 85.789000 2148 2724 1 chrUn.!!$F1 576
22 TraesCS7A01G300200 chr6B 265324582 265325141 559 True 549.000000 549 84.656000 3470 4026 1 chr6B.!!$R1 556
23 TraesCS7A01G300200 chr2D 319684579 319685227 648 False 532.000000 532 81.779000 3837 4526 1 chr2D.!!$F1 689
24 TraesCS7A01G300200 chr7D 632224698 632225866 1168 True 260.000000 446 88.611000 2888 3875 3 chr7D.!!$R1 987

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
330 331 0.252284 AGGTTCTGGTGATCCCGTCT 60.252 55.000 0.0 0.0 33.59 4.18 F
968 1025 0.905357 CAGACCCCACGGAGAAATCT 59.095 55.000 0.0 0.0 0.00 2.40 F
1040 1097 2.832778 TTGCTGCTTGGCTCCTCCA 61.833 57.895 0.0 0.0 44.85 3.86 F
2325 3196 4.409247 AGTCTTCAGTCCACCTGTTTAGTT 59.591 41.667 0.0 0.0 42.19 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 2357 6.115446 TCACTTCCAATATGACACATCCTTC 58.885 40.000 0.00 0.00 0.00 3.46 R
3362 4440 7.817962 GCACTGAGTTAAACTCTACAAATAGGA 59.182 37.037 0.00 0.00 45.27 2.94 R
3561 4723 4.852134 TCACTGCAAGCAATGTTACATT 57.148 36.364 4.56 4.56 37.60 2.71 R
4591 5886 0.955919 GGACAAGAAGACAAGGGGCG 60.956 60.000 0.00 0.00 0.00 6.13 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
29 30 6.648879 TGTCATATATCGACAATCACTCCA 57.351 37.500 12.65 0.0 40.34 3.86
30 31 7.049799 TGTCATATATCGACAATCACTCCAA 57.950 36.000 12.65 0.0 40.34 3.53
31 32 6.923508 TGTCATATATCGACAATCACTCCAAC 59.076 38.462 12.65 0.0 40.34 3.77
32 33 6.923508 GTCATATATCGACAATCACTCCAACA 59.076 38.462 0.00 0.0 33.43 3.33
33 34 7.600375 GTCATATATCGACAATCACTCCAACAT 59.400 37.037 0.00 0.0 33.43 2.71
34 35 7.599998 TCATATATCGACAATCACTCCAACATG 59.400 37.037 0.00 0.0 0.00 3.21
35 36 3.401033 TCGACAATCACTCCAACATGT 57.599 42.857 0.00 0.0 0.00 3.21
36 37 3.325870 TCGACAATCACTCCAACATGTC 58.674 45.455 0.00 0.0 35.13 3.06
37 38 3.729526 GACAATCACTCCAACATGTCG 57.270 47.619 0.00 0.0 0.00 4.35
38 39 3.067106 GACAATCACTCCAACATGTCGT 58.933 45.455 0.00 0.0 0.00 4.34
39 40 3.476552 ACAATCACTCCAACATGTCGTT 58.523 40.909 0.00 0.0 38.83 3.85
40 41 3.498397 ACAATCACTCCAACATGTCGTTC 59.502 43.478 0.00 0.0 34.86 3.95
41 42 2.163818 TCACTCCAACATGTCGTTCC 57.836 50.000 0.00 0.0 34.86 3.62
42 43 1.414550 TCACTCCAACATGTCGTTCCA 59.585 47.619 0.00 0.0 34.86 3.53
43 44 2.038426 TCACTCCAACATGTCGTTCCAT 59.962 45.455 0.00 0.0 34.86 3.41
44 45 2.416547 CACTCCAACATGTCGTTCCATC 59.583 50.000 0.00 0.0 34.86 3.51
45 46 2.009774 CTCCAACATGTCGTTCCATCC 58.990 52.381 0.00 0.0 34.86 3.51
46 47 1.349357 TCCAACATGTCGTTCCATCCA 59.651 47.619 0.00 0.0 34.86 3.41
47 48 2.026356 TCCAACATGTCGTTCCATCCAT 60.026 45.455 0.00 0.0 34.86 3.41
48 49 2.355756 CCAACATGTCGTTCCATCCATC 59.644 50.000 0.00 0.0 34.86 3.51
49 50 2.332063 ACATGTCGTTCCATCCATCC 57.668 50.000 0.00 0.0 0.00 3.51
50 51 1.559219 ACATGTCGTTCCATCCATCCA 59.441 47.619 0.00 0.0 0.00 3.41
51 52 2.026356 ACATGTCGTTCCATCCATCCAA 60.026 45.455 0.00 0.0 0.00 3.53
52 53 2.401583 TGTCGTTCCATCCATCCAAG 57.598 50.000 0.00 0.0 0.00 3.61
53 54 1.628340 TGTCGTTCCATCCATCCAAGT 59.372 47.619 0.00 0.0 0.00 3.16
54 55 2.280628 GTCGTTCCATCCATCCAAGTC 58.719 52.381 0.00 0.0 0.00 3.01
55 56 1.905894 TCGTTCCATCCATCCAAGTCA 59.094 47.619 0.00 0.0 0.00 3.41
56 57 2.093500 TCGTTCCATCCATCCAAGTCAG 60.093 50.000 0.00 0.0 0.00 3.51
57 58 2.648059 GTTCCATCCATCCAAGTCAGG 58.352 52.381 0.00 0.0 0.00 3.86
58 59 1.216064 TCCATCCATCCAAGTCAGGG 58.784 55.000 0.00 0.0 0.00 4.45
59 60 1.216064 CCATCCATCCAAGTCAGGGA 58.784 55.000 0.00 0.0 39.14 4.20
60 61 1.142465 CCATCCATCCAAGTCAGGGAG 59.858 57.143 0.00 0.0 37.96 4.30
61 62 2.121948 CATCCATCCAAGTCAGGGAGA 58.878 52.381 0.00 0.0 37.96 3.71
62 63 2.575921 TCCATCCAAGTCAGGGAGAT 57.424 50.000 0.00 0.0 37.96 2.75
63 64 3.706389 TCCATCCAAGTCAGGGAGATA 57.294 47.619 0.00 0.0 37.96 1.98
64 65 3.581101 TCCATCCAAGTCAGGGAGATAG 58.419 50.000 0.00 0.0 37.96 2.08
65 66 3.051803 TCCATCCAAGTCAGGGAGATAGT 60.052 47.826 0.00 0.0 37.96 2.12
66 67 3.323403 CCATCCAAGTCAGGGAGATAGTC 59.677 52.174 0.00 0.0 37.96 2.59
67 68 3.033659 TCCAAGTCAGGGAGATAGTCC 57.966 52.381 0.00 0.0 46.10 3.85
68 69 2.587777 TCCAAGTCAGGGAGATAGTCCT 59.412 50.000 0.00 0.0 46.06 3.85
69 70 3.012959 TCCAAGTCAGGGAGATAGTCCTT 59.987 47.826 0.00 0.0 46.06 3.36
75 76 3.413105 AGGGAGATAGTCCTTGAGCTT 57.587 47.619 0.00 0.0 46.06 3.74
76 77 4.544564 AGGGAGATAGTCCTTGAGCTTA 57.455 45.455 0.00 0.0 46.06 3.09
77 78 4.479158 AGGGAGATAGTCCTTGAGCTTAG 58.521 47.826 0.00 0.0 46.06 2.18
78 79 4.078863 AGGGAGATAGTCCTTGAGCTTAGT 60.079 45.833 0.00 0.0 46.06 2.24
79 80 4.038642 GGGAGATAGTCCTTGAGCTTAGTG 59.961 50.000 0.00 0.0 46.06 2.74
80 81 4.890581 GGAGATAGTCCTTGAGCTTAGTGA 59.109 45.833 0.00 0.0 42.99 3.41
81 82 5.361285 GGAGATAGTCCTTGAGCTTAGTGAA 59.639 44.000 0.00 0.0 42.99 3.18
82 83 6.127310 GGAGATAGTCCTTGAGCTTAGTGAAA 60.127 42.308 0.00 0.0 42.99 2.69
83 84 6.872920 AGATAGTCCTTGAGCTTAGTGAAAG 58.127 40.000 0.00 0.0 38.32 2.62
84 85 4.278975 AGTCCTTGAGCTTAGTGAAAGG 57.721 45.455 0.00 0.0 39.02 3.11
171 172 3.939592 CCGTAGAACATCCCTCTTTTTCC 59.060 47.826 0.00 0.0 0.00 3.13
178 179 2.781681 TCCCTCTTTTTCCGATGACC 57.218 50.000 0.00 0.0 0.00 4.02
330 331 0.252284 AGGTTCTGGTGATCCCGTCT 60.252 55.000 0.00 0.0 33.59 4.18
443 444 4.288626 TGGGTTAAGGACAAACTATCTGCT 59.711 41.667 0.00 0.0 0.00 4.24
965 1022 1.460689 ACCAGACCCCACGGAGAAA 60.461 57.895 0.00 0.0 0.00 2.52
968 1025 0.905357 CAGACCCCACGGAGAAATCT 59.095 55.000 0.00 0.0 0.00 2.40
1040 1097 2.832778 TTGCTGCTTGGCTCCTCCA 61.833 57.895 0.00 0.0 44.85 3.86
1631 2357 6.336842 ACTCCTCTTGAAATTGAATTGTGG 57.663 37.500 0.00 0.0 0.00 4.17
2325 3196 4.409247 AGTCTTCAGTCCACCTGTTTAGTT 59.591 41.667 0.00 0.0 42.19 2.24
3104 4052 6.416631 AGCTAAGATGCATGAGATACAGAA 57.583 37.500 2.46 0.0 34.99 3.02
3561 4723 8.806429 TCAAACAATTCCTGCTTGATCTAATA 57.194 30.769 0.00 0.0 35.64 0.98
4134 5422 5.368145 AGACATGTTACTTTGAGTGAAGCA 58.632 37.500 0.00 0.0 0.00 3.91
4204 5499 9.247861 GAATGAATATTACATTAGGGATGCCTT 57.752 33.333 12.53 0.0 39.47 4.35
4365 5660 0.831711 ACGGGCAAGGGCAAAGAAAT 60.832 50.000 0.00 0.0 43.71 2.17
4611 5906 0.609406 GCCCCTTGTCTTCTTGTCCC 60.609 60.000 0.00 0.0 0.00 4.46
4700 5995 9.313118 GTGTAATCCTTTTTGTGAATGTTCTTT 57.687 29.630 0.00 0.0 0.00 2.52
4773 6068 6.760291 AGTAGTCTTGAGTTTGTTAGGAAGG 58.240 40.000 0.00 0.0 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.648879 TGGAGTGATTGTCGATATATGACA 57.351 37.500 11.58 11.58 44.17 3.58
7 8 6.923508 TGTTGGAGTGATTGTCGATATATGAC 59.076 38.462 0.00 0.00 36.88 3.06
8 9 7.049799 TGTTGGAGTGATTGTCGATATATGA 57.950 36.000 0.00 0.00 0.00 2.15
9 10 7.386025 ACATGTTGGAGTGATTGTCGATATATG 59.614 37.037 0.00 0.00 0.00 1.78
10 11 7.445121 ACATGTTGGAGTGATTGTCGATATAT 58.555 34.615 0.00 0.00 0.00 0.86
11 12 6.816136 ACATGTTGGAGTGATTGTCGATATA 58.184 36.000 0.00 0.00 0.00 0.86
12 13 5.674525 ACATGTTGGAGTGATTGTCGATAT 58.325 37.500 0.00 0.00 0.00 1.63
13 14 5.084818 ACATGTTGGAGTGATTGTCGATA 57.915 39.130 0.00 0.00 0.00 2.92
14 15 3.935203 GACATGTTGGAGTGATTGTCGAT 59.065 43.478 0.00 0.00 0.00 3.59
15 16 3.325870 GACATGTTGGAGTGATTGTCGA 58.674 45.455 0.00 0.00 0.00 4.20
16 17 2.092681 CGACATGTTGGAGTGATTGTCG 59.907 50.000 5.04 8.59 46.70 4.35
17 18 3.067106 ACGACATGTTGGAGTGATTGTC 58.933 45.455 17.50 0.00 0.00 3.18
18 19 3.126001 ACGACATGTTGGAGTGATTGT 57.874 42.857 17.50 0.00 0.00 2.71
19 20 3.120199 GGAACGACATGTTGGAGTGATTG 60.120 47.826 17.50 0.00 42.09 2.67
20 21 3.074412 GGAACGACATGTTGGAGTGATT 58.926 45.455 17.50 1.19 42.09 2.57
21 22 2.038426 TGGAACGACATGTTGGAGTGAT 59.962 45.455 17.50 0.00 42.09 3.06
22 23 1.414550 TGGAACGACATGTTGGAGTGA 59.585 47.619 17.50 0.00 42.09 3.41
23 24 1.877637 TGGAACGACATGTTGGAGTG 58.122 50.000 17.50 0.00 42.09 3.51
24 25 2.615493 GGATGGAACGACATGTTGGAGT 60.615 50.000 17.50 4.89 42.09 3.85
25 26 2.009774 GGATGGAACGACATGTTGGAG 58.990 52.381 17.50 4.27 42.09 3.86
26 27 1.349357 TGGATGGAACGACATGTTGGA 59.651 47.619 17.50 0.00 42.09 3.53
27 28 1.819928 TGGATGGAACGACATGTTGG 58.180 50.000 17.50 7.14 42.09 3.77
28 29 2.355756 GGATGGATGGAACGACATGTTG 59.644 50.000 11.78 11.78 42.09 3.33
29 30 2.026356 TGGATGGATGGAACGACATGTT 60.026 45.455 0.00 0.00 45.61 2.71
30 31 1.559219 TGGATGGATGGAACGACATGT 59.441 47.619 0.00 0.00 0.00 3.21
31 32 2.330440 TGGATGGATGGAACGACATG 57.670 50.000 0.00 0.00 0.00 3.21
32 33 2.239654 ACTTGGATGGATGGAACGACAT 59.760 45.455 0.00 0.00 0.00 3.06
33 34 1.628340 ACTTGGATGGATGGAACGACA 59.372 47.619 0.00 0.00 0.00 4.35
34 35 2.280628 GACTTGGATGGATGGAACGAC 58.719 52.381 0.00 0.00 0.00 4.34
35 36 1.905894 TGACTTGGATGGATGGAACGA 59.094 47.619 0.00 0.00 0.00 3.85
36 37 2.283298 CTGACTTGGATGGATGGAACG 58.717 52.381 0.00 0.00 0.00 3.95
37 38 2.648059 CCTGACTTGGATGGATGGAAC 58.352 52.381 0.00 0.00 0.00 3.62
38 39 1.565759 CCCTGACTTGGATGGATGGAA 59.434 52.381 0.00 0.00 0.00 3.53
39 40 1.216064 CCCTGACTTGGATGGATGGA 58.784 55.000 0.00 0.00 0.00 3.41
40 41 1.142465 CTCCCTGACTTGGATGGATGG 59.858 57.143 0.00 0.00 0.00 3.51
41 42 2.121948 TCTCCCTGACTTGGATGGATG 58.878 52.381 0.00 0.00 0.00 3.51
42 43 2.575921 TCTCCCTGACTTGGATGGAT 57.424 50.000 0.00 0.00 0.00 3.41
43 44 2.575921 ATCTCCCTGACTTGGATGGA 57.424 50.000 0.00 0.00 0.00 3.41
44 45 3.312890 ACTATCTCCCTGACTTGGATGG 58.687 50.000 0.00 0.00 0.00 3.51
45 46 3.323403 GGACTATCTCCCTGACTTGGATG 59.677 52.174 0.00 0.00 31.83 3.51
46 47 3.208692 AGGACTATCTCCCTGACTTGGAT 59.791 47.826 0.00 0.00 40.53 3.41
47 48 2.587777 AGGACTATCTCCCTGACTTGGA 59.412 50.000 0.00 0.00 40.53 3.53
48 49 3.039252 AGGACTATCTCCCTGACTTGG 57.961 52.381 0.00 0.00 40.53 3.61
49 50 4.026744 TCAAGGACTATCTCCCTGACTTG 58.973 47.826 0.00 0.00 40.53 3.16
50 51 4.285863 CTCAAGGACTATCTCCCTGACTT 58.714 47.826 0.00 0.00 40.53 3.01
51 52 3.909732 CTCAAGGACTATCTCCCTGACT 58.090 50.000 0.00 0.00 40.53 3.41
52 53 2.364002 GCTCAAGGACTATCTCCCTGAC 59.636 54.545 0.00 0.00 40.53 3.51
53 54 2.246067 AGCTCAAGGACTATCTCCCTGA 59.754 50.000 0.00 0.00 40.53 3.86
54 55 2.676748 AGCTCAAGGACTATCTCCCTG 58.323 52.381 0.00 0.00 40.53 4.45
55 56 3.413105 AAGCTCAAGGACTATCTCCCT 57.587 47.619 0.00 0.00 40.53 4.20
56 57 4.038642 CACTAAGCTCAAGGACTATCTCCC 59.961 50.000 0.00 0.00 40.53 4.30
57 58 4.890581 TCACTAAGCTCAAGGACTATCTCC 59.109 45.833 0.00 0.00 39.81 3.71
58 59 6.458232 TTCACTAAGCTCAAGGACTATCTC 57.542 41.667 0.00 0.00 0.00 2.75
59 60 6.127196 CCTTTCACTAAGCTCAAGGACTATCT 60.127 42.308 0.00 0.00 36.84 1.98
60 61 6.045955 CCTTTCACTAAGCTCAAGGACTATC 58.954 44.000 0.00 0.00 36.84 2.08
61 62 5.627968 GCCTTTCACTAAGCTCAAGGACTAT 60.628 44.000 0.29 0.00 36.84 2.12
62 63 4.322801 GCCTTTCACTAAGCTCAAGGACTA 60.323 45.833 0.29 0.00 36.84 2.59
63 64 3.558109 GCCTTTCACTAAGCTCAAGGACT 60.558 47.826 0.29 0.00 36.84 3.85
64 65 2.744741 GCCTTTCACTAAGCTCAAGGAC 59.255 50.000 0.29 0.00 36.84 3.85
65 66 2.639839 AGCCTTTCACTAAGCTCAAGGA 59.360 45.455 0.29 0.00 36.84 3.36
66 67 3.064900 AGCCTTTCACTAAGCTCAAGG 57.935 47.619 0.00 0.00 37.63 3.61
67 68 4.067896 TGAAGCCTTTCACTAAGCTCAAG 58.932 43.478 0.00 0.00 38.37 3.02
68 69 4.085357 TGAAGCCTTTCACTAAGCTCAA 57.915 40.909 0.00 0.00 38.37 3.02
69 70 3.769739 TGAAGCCTTTCACTAAGCTCA 57.230 42.857 0.00 0.00 38.37 4.26
70 71 4.006319 ACATGAAGCCTTTCACTAAGCTC 58.994 43.478 0.00 0.00 45.54 4.09
71 72 4.006319 GACATGAAGCCTTTCACTAAGCT 58.994 43.478 0.00 0.00 45.54 3.74
72 73 3.181516 CGACATGAAGCCTTTCACTAAGC 60.182 47.826 0.00 0.00 45.54 3.09
73 74 4.245660 TCGACATGAAGCCTTTCACTAAG 58.754 43.478 0.00 0.00 45.54 2.18
74 75 4.021456 TCTCGACATGAAGCCTTTCACTAA 60.021 41.667 0.00 0.00 45.54 2.24
75 76 3.509967 TCTCGACATGAAGCCTTTCACTA 59.490 43.478 0.00 0.00 45.54 2.74
76 77 2.300152 TCTCGACATGAAGCCTTTCACT 59.700 45.455 0.00 0.00 45.54 3.41
77 78 2.413453 GTCTCGACATGAAGCCTTTCAC 59.587 50.000 0.00 0.00 45.54 3.18
78 79 2.688507 GTCTCGACATGAAGCCTTTCA 58.311 47.619 0.00 0.00 46.67 2.69
79 80 1.656095 CGTCTCGACATGAAGCCTTTC 59.344 52.381 0.00 0.00 0.00 2.62
80 81 1.714794 CGTCTCGACATGAAGCCTTT 58.285 50.000 0.00 0.00 0.00 3.11
81 82 0.737715 GCGTCTCGACATGAAGCCTT 60.738 55.000 0.00 0.00 33.90 4.35
82 83 1.153745 GCGTCTCGACATGAAGCCT 60.154 57.895 0.00 0.00 33.90 4.58
83 84 1.153745 AGCGTCTCGACATGAAGCC 60.154 57.895 0.00 0.00 39.17 4.35
84 85 0.456824 TCAGCGTCTCGACATGAAGC 60.457 55.000 0.00 3.43 38.77 3.86
171 172 3.740631 TCATCATGAAGGAGGTCATCG 57.259 47.619 0.00 0.00 36.04 3.84
178 179 3.293337 TGCCCAAATCATCATGAAGGAG 58.707 45.455 0.00 0.00 0.00 3.69
247 248 4.287067 TGGGCAAAGGACATAGGAGATATC 59.713 45.833 0.00 0.00 0.00 1.63
330 331 1.055849 ACACCACATGCTGGAGTACA 58.944 50.000 17.76 0.00 41.72 2.90
443 444 0.742505 CGGCAGTAACGACATCCCTA 59.257 55.000 0.00 0.00 0.00 3.53
965 1022 1.138568 CCAATGGAGGAGGCTCAGAT 58.861 55.000 17.69 0.82 0.00 2.90
968 1025 3.001514 GCCAATGGAGGAGGCTCA 58.998 61.111 17.69 0.00 44.92 4.26
1040 1097 2.627737 GCGACGACCCTGAGACAGT 61.628 63.158 0.00 0.00 0.00 3.55
1083 1140 4.610714 GGAGGGCCGCGGAGAATC 62.611 72.222 33.48 19.72 0.00 2.52
1631 2357 6.115446 TCACTTCCAATATGACACATCCTTC 58.885 40.000 0.00 0.00 0.00 3.46
3362 4440 7.817962 GCACTGAGTTAAACTCTACAAATAGGA 59.182 37.037 0.00 0.00 45.27 2.94
3561 4723 4.852134 TCACTGCAAGCAATGTTACATT 57.148 36.364 4.56 4.56 37.60 2.71
4591 5886 0.955919 GGACAAGAAGACAAGGGGCG 60.956 60.000 0.00 0.00 0.00 6.13
4611 5906 1.986413 CAAGGGGTGGAGAGGTCAG 59.014 63.158 0.00 0.00 0.00 3.51
4700 5995 2.351447 CGCTCTTTACTTGGACTCGTCA 60.351 50.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.