Multiple sequence alignment - TraesCS2B01G141200

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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 TraesCS2B01G141200 chr2B 100.000 2947 0 0 1 2947 107782178 107785124 0.000000e+00 5443.0
1 TraesCS2B01G141200 chr2B 83.871 992 114 22 1463 2440 107793870 107794829 0.000000e+00 904.0
2 TraesCS2B01G141200 chr2B 84.733 655 82 12 2294 2944 107578242 107578882 8.910000e-180 640.0
3 TraesCS2B01G141200 chr2B 77.993 827 106 53 767 1555 107576684 107577472 1.610000e-122 449.0
4 TraesCS2B01G141200 chr2B 79.803 406 44 20 1065 1433 107793295 107793699 8.100000e-66 261.0
5 TraesCS2B01G141200 chr2B 87.892 223 18 7 855 1073 107793143 107793360 1.360000e-63 254.0
6 TraesCS2B01G141200 chr2B 80.833 240 28 11 772 998 107531444 107531678 3.900000e-39 172.0
7 TraesCS2B01G141200 chr2B 74.017 458 66 33 974 1409 106962775 106962349 1.420000e-28 137.0
8 TraesCS2B01G141200 chr2D 87.428 2951 253 61 63 2947 71564718 71567616 0.000000e+00 3286.0
9 TraesCS2B01G141200 chr2D 90.351 2249 128 24 759 2947 71578101 71580320 0.000000e+00 2868.0
10 TraesCS2B01G141200 chr2D 81.733 1385 182 38 1585 2947 71470721 71472056 0.000000e+00 1090.0
11 TraesCS2B01G141200 chr2D 83.316 941 114 31 1065 1975 71598882 71599809 0.000000e+00 828.0
12 TraesCS2B01G141200 chr2D 87.562 603 63 9 2347 2947 71410212 71410804 0.000000e+00 688.0
13 TraesCS2B01G141200 chr2D 79.548 929 125 32 1065 1942 70674207 70673293 1.170000e-168 603.0
14 TraesCS2B01G141200 chr2D 88.767 454 35 4 1994 2440 71600086 71600530 2.580000e-150 542.0
15 TraesCS2B01G141200 chr2D 84.504 484 64 7 2465 2947 71600521 71600994 4.450000e-128 468.0
16 TraesCS2B01G141200 chr2D 77.671 833 103 55 767 1556 71469755 71470547 5.840000e-117 431.0
17 TraesCS2B01G141200 chr2D 85.986 421 35 11 2034 2440 70672921 70672511 2.100000e-116 429.0
18 TraesCS2B01G141200 chr2D 81.505 319 36 14 772 1073 71598635 71598947 1.060000e-59 241.0
19 TraesCS2B01G141200 chr2D 74.925 666 82 55 804 1431 71399224 71399842 2.960000e-55 226.0
20 TraesCS2B01G141200 chr2D 74.281 626 78 47 831 1429 71594088 71594657 1.390000e-43 187.0
21 TraesCS2B01G141200 chr2D 89.286 140 12 3 771 907 71391146 71391285 3.900000e-39 172.0
22 TraesCS2B01G141200 chr2A 89.709 2303 136 39 722 2947 70643702 70645980 0.000000e+00 2846.0
23 TraesCS2B01G141200 chr2A 84.285 1419 164 37 1065 2440 70655074 70656476 0.000000e+00 1330.0
24 TraesCS2B01G141200 chr2A 84.144 946 97 25 1518 2440 70156029 70155114 0.000000e+00 867.0
25 TraesCS2B01G141200 chr2A 86.235 603 71 9 2347 2947 70278469 70277877 0.000000e+00 643.0
26 TraesCS2B01G141200 chr2A 81.643 621 102 9 2331 2947 70150760 70150148 3.390000e-139 505.0
27 TraesCS2B01G141200 chr2A 79.380 742 101 31 1585 2317 70234288 70233590 2.660000e-130 475.0
28 TraesCS2B01G141200 chr2A 86.898 374 45 2 2578 2947 70230600 70230227 1.630000e-112 416.0
29 TraesCS2B01G141200 chr2A 77.240 826 99 50 770 1559 70235234 70234462 4.580000e-108 401.0
30 TraesCS2B01G141200 chr2A 82.216 343 31 22 770 1089 70654815 70655150 4.840000e-68 268.0
31 TraesCS2B01G141200 chr2A 85.465 172 22 3 877 1048 70284469 70284301 3.020000e-40 176.0
32 TraesCS2B01G141200 chr2A 81.347 193 17 12 767 942 70193011 70193201 3.960000e-29 139.0
33 TraesCS2B01G141200 chr2A 82.927 123 21 0 1153 1275 70291613 70291491 8.630000e-21 111.0
34 TraesCS2B01G141200 chr5D 82.069 435 69 5 126 555 498464535 498464965 2.160000e-96 363.0
35 TraesCS2B01G141200 chr5D 81.280 422 62 10 144 555 28991991 28992405 2.830000e-85 326.0
36 TraesCS2B01G141200 chr3B 80.846 449 73 7 118 555 184957573 184958019 1.010000e-89 340.0
37 TraesCS2B01G141200 chr3B 74.098 305 46 19 446 736 21383757 21384042 8.700000e-16 95.3
38 TraesCS2B01G141200 chr1D 80.631 444 75 6 118 553 444845197 444844757 1.690000e-87 333.0
39 TraesCS2B01G141200 chr1B 79.618 471 81 9 96 555 679398853 679398387 1.020000e-84 324.0
40 TraesCS2B01G141200 chr1B 84.722 72 6 5 557 625 108320178 108320109 1.900000e-07 67.6
41 TraesCS2B01G141200 chr5B 76.391 665 112 26 93 736 672838858 672839498 1.700000e-82 316.0
42 TraesCS2B01G141200 chr4D 79.070 473 85 10 93 555 425694538 425695006 2.210000e-81 313.0
43 TraesCS2B01G141200 chr4D 79.551 445 79 9 118 555 16665889 16666328 1.030000e-79 307.0
44 TraesCS2B01G141200 chr4B 78.390 472 88 9 93 555 4541795 4541329 7.990000e-76 294.0
45 TraesCS2B01G141200 chr6D 75.000 220 44 10 342 555 9789917 9790131 1.120000e-14 91.6
46 TraesCS2B01G141200 chr6D 97.222 36 1 0 590 625 56892630 56892595 8.820000e-06 62.1
47 TraesCS2B01G141200 chr3A 75.130 193 34 12 557 736 669598267 669598076 8.760000e-11 78.7


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 TraesCS2B01G141200 chr2B 107782178 107785124 2946 False 5443.000000 5443 100.000000 1 2947 1 chr2B.!!$F2 2946
1 TraesCS2B01G141200 chr2B 107576684 107578882 2198 False 544.500000 640 81.363000 767 2944 2 chr2B.!!$F3 2177
2 TraesCS2B01G141200 chr2B 107793143 107794829 1686 False 473.000000 904 83.855333 855 2440 3 chr2B.!!$F4 1585
3 TraesCS2B01G141200 chr2D 71564718 71567616 2898 False 3286.000000 3286 87.428000 63 2947 1 chr2D.!!$F4 2884
4 TraesCS2B01G141200 chr2D 71578101 71580320 2219 False 2868.000000 2868 90.351000 759 2947 1 chr2D.!!$F5 2188
5 TraesCS2B01G141200 chr2D 71469755 71472056 2301 False 760.500000 1090 79.702000 767 2947 2 chr2D.!!$F6 2180
6 TraesCS2B01G141200 chr2D 71410212 71410804 592 False 688.000000 688 87.562000 2347 2947 1 chr2D.!!$F3 600
7 TraesCS2B01G141200 chr2D 70672511 70674207 1696 True 516.000000 603 82.767000 1065 2440 2 chr2D.!!$R1 1375
8 TraesCS2B01G141200 chr2D 71594088 71600994 6906 False 453.200000 828 82.474600 772 2947 5 chr2D.!!$F7 2175
9 TraesCS2B01G141200 chr2D 71399224 71399842 618 False 226.000000 226 74.925000 804 1431 1 chr2D.!!$F2 627
10 TraesCS2B01G141200 chr2A 70643702 70645980 2278 False 2846.000000 2846 89.709000 722 2947 1 chr2A.!!$F2 2225
11 TraesCS2B01G141200 chr2A 70155114 70156029 915 True 867.000000 867 84.144000 1518 2440 1 chr2A.!!$R2 922
12 TraesCS2B01G141200 chr2A 70654815 70656476 1661 False 799.000000 1330 83.250500 770 2440 2 chr2A.!!$F3 1670
13 TraesCS2B01G141200 chr2A 70277877 70278469 592 True 643.000000 643 86.235000 2347 2947 1 chr2A.!!$R3 600
14 TraesCS2B01G141200 chr2A 70150148 70150760 612 True 505.000000 505 81.643000 2331 2947 1 chr2A.!!$R1 616
15 TraesCS2B01G141200 chr2A 70230227 70235234 5007 True 430.666667 475 81.172667 770 2947 3 chr2A.!!$R6 2177
16 TraesCS2B01G141200 chr5B 672838858 672839498 640 False 316.000000 316 76.391000 93 736 1 chr5B.!!$F1 643

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
28 29 0.033090 TCATCGCCATAGCTCAGCTG 59.967 55.0 10.31 7.63 40.10 4.24 F
631 640 0.093026 CGCGTCTTCGGCTTGTTAAG 59.907 55.0 0.00 0.00 37.56 1.85 F
775 797 0.321564 TTCACCCACTGGCTCGAATG 60.322 55.0 0.00 0.00 33.59 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 5959 0.954452 GCCTAAACAAGTGTGCAGCT 59.046 50.000 0.0 0.0 0.0 4.24 R
1834 6090 1.137594 AGAACCGACCATTTCCCCCA 61.138 55.000 0.0 0.0 0.0 4.96 R
2012 6532 1.227380 CGGCTCACAGATACAGGGC 60.227 63.158 0.0 0.0 0.0 5.19 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
17 18 3.076999 TGCCCTTCTTCATCGCCA 58.923 55.556 0.00 0.00 0.00 5.69
18 19 1.609239 TGCCCTTCTTCATCGCCAT 59.391 52.632 0.00 0.00 0.00 4.40
19 20 0.836606 TGCCCTTCTTCATCGCCATA 59.163 50.000 0.00 0.00 0.00 2.74
20 21 1.202687 TGCCCTTCTTCATCGCCATAG 60.203 52.381 0.00 0.00 0.00 2.23
21 22 1.517242 CCCTTCTTCATCGCCATAGC 58.483 55.000 0.00 0.00 0.00 2.97
22 23 1.071385 CCCTTCTTCATCGCCATAGCT 59.929 52.381 0.00 0.00 36.60 3.32
23 24 2.411904 CCTTCTTCATCGCCATAGCTC 58.588 52.381 0.00 0.00 36.60 4.09
24 25 2.224137 CCTTCTTCATCGCCATAGCTCA 60.224 50.000 0.00 0.00 36.60 4.26
25 26 2.808523 TCTTCATCGCCATAGCTCAG 57.191 50.000 0.00 0.00 36.60 3.35
26 27 1.146637 CTTCATCGCCATAGCTCAGC 58.853 55.000 0.00 0.00 36.60 4.26
27 28 0.755079 TTCATCGCCATAGCTCAGCT 59.245 50.000 3.60 3.60 43.41 4.24
28 29 0.033090 TCATCGCCATAGCTCAGCTG 59.967 55.000 10.31 7.63 40.10 4.24
29 30 0.249784 CATCGCCATAGCTCAGCTGT 60.250 55.000 10.31 0.00 40.10 4.40
30 31 0.249784 ATCGCCATAGCTCAGCTGTG 60.250 55.000 16.28 16.28 45.19 3.66
31 32 1.153489 CGCCATAGCTCAGCTGTGT 60.153 57.895 20.85 4.99 44.35 3.72
32 33 1.426816 CGCCATAGCTCAGCTGTGTG 61.427 60.000 20.85 13.57 44.35 3.82
33 34 0.107993 GCCATAGCTCAGCTGTGTGA 60.108 55.000 20.85 3.95 44.35 3.58
51 52 6.413892 TGTGTGAGCATCCATAGTTATTTCA 58.586 36.000 0.00 0.00 0.00 2.69
52 53 6.883756 TGTGTGAGCATCCATAGTTATTTCAA 59.116 34.615 0.00 0.00 0.00 2.69
53 54 7.557358 TGTGTGAGCATCCATAGTTATTTCAAT 59.443 33.333 0.00 0.00 0.00 2.57
54 55 9.056005 GTGTGAGCATCCATAGTTATTTCAATA 57.944 33.333 0.00 0.00 0.00 1.90
55 56 9.797642 TGTGAGCATCCATAGTTATTTCAATAT 57.202 29.630 0.00 0.00 0.00 1.28
116 117 3.676093 AGAAAAGACCTTAGCCTTTCCG 58.324 45.455 0.00 0.00 32.01 4.30
132 133 2.745100 CGTCTCCTCCCGTCGACA 60.745 66.667 17.16 0.00 0.00 4.35
156 157 2.765807 CTGGTCCGGCCCATCTCT 60.766 66.667 3.78 0.00 36.04 3.10
161 162 1.075301 TCCGGCCCATCTCTGATGA 60.075 57.895 8.91 0.00 0.00 2.92
241 242 5.221130 CCGTTCTCGTTCTTATTAGATCCC 58.779 45.833 0.00 0.00 35.01 3.85
308 309 4.225267 AGGAATAATGTCTCCCACGTTCTT 59.775 41.667 0.00 0.00 35.68 2.52
327 329 1.327303 TTCTTGTCCCAATGGTGTGC 58.673 50.000 0.00 0.00 0.00 4.57
332 334 1.032114 GTCCCAATGGTGTGCCTAGC 61.032 60.000 0.00 0.00 35.27 3.42
347 356 2.990674 CTAGCATCGTCGCGTGGAGG 62.991 65.000 5.77 7.75 36.85 4.30
356 365 2.920645 CGCGTGGAGGTGTGTCTCT 61.921 63.158 0.00 0.00 34.39 3.10
367 376 3.117851 AGGTGTGTCTCTATCGGATCTCA 60.118 47.826 0.00 0.00 0.00 3.27
375 384 3.497332 TCTATCGGATCTCACGGGATTT 58.503 45.455 0.00 0.00 0.00 2.17
383 392 0.321298 CTCACGGGATTTGGTCGGTT 60.321 55.000 0.00 0.00 0.00 4.44
384 393 0.975135 TCACGGGATTTGGTCGGTTA 59.025 50.000 0.00 0.00 0.00 2.85
419 428 0.613260 CTGTTTGGATCCGGTCTCCA 59.387 55.000 20.19 20.19 41.03 3.86
428 437 0.815734 TCCGGTCTCCATTCGTCTTC 59.184 55.000 0.00 0.00 0.00 2.87
444 453 6.841443 TCGTCTTCGTTTGGTTGTTTATAA 57.159 33.333 0.00 0.00 38.33 0.98
473 482 5.821516 TCCTTCTGATCTACGACTTTCTC 57.178 43.478 0.00 0.00 0.00 2.87
474 483 5.502079 TCCTTCTGATCTACGACTTTCTCT 58.498 41.667 0.00 0.00 0.00 3.10
489 498 1.399714 TCTCTATCGGCGATGGTTGT 58.600 50.000 31.08 8.24 0.00 3.32
491 500 2.953648 TCTCTATCGGCGATGGTTGTTA 59.046 45.455 31.08 11.62 0.00 2.41
494 503 2.396590 ATCGGCGATGGTTGTTACTT 57.603 45.000 23.36 0.00 0.00 2.24
498 507 1.402325 GGCGATGGTTGTTACTTTGGC 60.402 52.381 0.00 0.00 0.00 4.52
501 510 0.601057 ATGGTTGTTACTTTGGCGCC 59.399 50.000 22.73 22.73 0.00 6.53
514 523 2.742116 GGCGCCTTGGTCCTATGGA 61.742 63.158 22.15 0.00 0.00 3.41
525 534 2.028930 GGTCCTATGGAGCCTTATCACG 60.029 54.545 4.60 0.00 43.62 4.35
538 547 1.671979 TATCACGACGACTTCCCGAT 58.328 50.000 0.00 0.00 0.00 4.18
564 573 8.461249 TGTCTACTACAACAAGAACTTCTACT 57.539 34.615 0.00 0.00 34.29 2.57
565 574 9.565090 TGTCTACTACAACAAGAACTTCTACTA 57.435 33.333 0.00 0.00 34.29 1.82
566 575 9.824534 GTCTACTACAACAAGAACTTCTACTAC 57.175 37.037 0.00 0.00 0.00 2.73
567 576 9.565090 TCTACTACAACAAGAACTTCTACTACA 57.435 33.333 0.00 0.00 0.00 2.74
572 581 8.197988 ACAACAAGAACTTCTACTACAACAAG 57.802 34.615 0.00 0.00 0.00 3.16
573 582 6.846325 ACAAGAACTTCTACTACAACAAGC 57.154 37.500 0.00 0.00 0.00 4.01
583 592 2.218603 CTACAACAAGCTTTGTCCGGT 58.781 47.619 7.05 6.62 44.59 5.28
585 594 1.822371 ACAACAAGCTTTGTCCGGTTT 59.178 42.857 0.00 0.00 44.59 3.27
593 602 2.413837 CTTTGTCCGGTTTCGATGAGT 58.586 47.619 0.00 0.00 39.00 3.41
608 617 0.251608 TGAGTGAGGGGTGATGACGA 60.252 55.000 0.00 0.00 0.00 4.20
629 638 2.377310 GCGCGTCTTCGGCTTGTTA 61.377 57.895 8.43 0.00 37.56 2.41
631 640 0.093026 CGCGTCTTCGGCTTGTTAAG 59.907 55.000 0.00 0.00 37.56 1.85
633 642 2.331194 GCGTCTTCGGCTTGTTAAGTA 58.669 47.619 0.00 0.00 37.56 2.24
634 643 2.928116 GCGTCTTCGGCTTGTTAAGTAT 59.072 45.455 0.00 0.00 37.56 2.12
636 645 4.492085 GCGTCTTCGGCTTGTTAAGTATTC 60.492 45.833 0.00 0.00 37.56 1.75
637 646 4.032558 CGTCTTCGGCTTGTTAAGTATTCC 59.967 45.833 0.00 0.00 0.00 3.01
640 649 5.642063 TCTTCGGCTTGTTAAGTATTCCTTG 59.358 40.000 0.00 0.00 34.46 3.61
654 670 7.752713 TAAGTATTCCTTGGTAGGTGGTCTACA 60.753 40.741 5.67 0.00 40.93 2.74
679 695 8.499162 CAGATCTGATCGTTATTTTCATTACCC 58.501 37.037 18.34 0.00 0.00 3.69
705 725 9.959749 CTTAGCTTTGTACTACCAAAATTGAAA 57.040 29.630 0.00 0.00 34.15 2.69
763 785 5.582665 GCAACAAAGTTTAACATTTCACCCA 59.417 36.000 0.00 0.00 0.00 4.51
764 786 6.456315 GCAACAAAGTTTAACATTTCACCCAC 60.456 38.462 0.00 0.00 0.00 4.61
775 797 0.321564 TTCACCCACTGGCTCGAATG 60.322 55.000 0.00 0.00 33.59 2.67
823 4619 0.765519 ACAACCCGAACCCCACTAGT 60.766 55.000 0.00 0.00 0.00 2.57
853 4655 2.450609 TAGAACAGAACCCGCAAGAC 57.549 50.000 0.00 0.00 43.02 3.01
897 4703 1.123928 CCCCTGTTCCTCGCTAATCT 58.876 55.000 0.00 0.00 0.00 2.40
918 4726 1.203174 CCATTTCCCACAAACCCCTCT 60.203 52.381 0.00 0.00 0.00 3.69
919 4727 2.042433 CCATTTCCCACAAACCCCTCTA 59.958 50.000 0.00 0.00 0.00 2.43
923 4731 0.845102 CCCACAAACCCCTCTACCCT 60.845 60.000 0.00 0.00 0.00 4.34
1166 5076 4.099170 CTTCGTCCTCCGCGTCGT 62.099 66.667 4.92 0.00 36.19 4.34
1198 5108 3.447025 ATCTACCTGGGCTTCGCGC 62.447 63.158 0.00 0.00 41.94 6.86
1432 5407 4.082787 CGTGCAAATTAACTCCCTGTGATT 60.083 41.667 0.00 0.00 0.00 2.57
1441 5416 9.547279 AATTAACTCCCTGTGATTTTTAATCCT 57.453 29.630 0.00 0.00 0.00 3.24
1534 5604 8.533657 TGGTCTAATTAATTTCGTAGTTCAGGA 58.466 33.333 5.91 0.00 0.00 3.86
1556 5626 5.184864 GGATGTCCTGATGATGAGTAGTAGG 59.815 48.000 0.00 0.00 0.00 3.18
1559 5641 4.764823 GTCCTGATGATGAGTAGTAGGAGG 59.235 50.000 0.00 0.00 33.85 4.30
1562 5644 4.991776 TGATGATGAGTAGTAGGAGGAGG 58.008 47.826 0.00 0.00 0.00 4.30
1570 5808 4.237018 AGTAGTAGGAGGAGGAGGAGTAG 58.763 52.174 0.00 0.00 0.00 2.57
1573 5811 3.460712 AGTAGGAGGAGGAGGAGTAGTTC 59.539 52.174 0.00 0.00 0.00 3.01
1606 5853 5.042593 GTGTTCATCACTTCATTTGCAACA 58.957 37.500 0.00 0.00 43.13 3.33
1617 5864 5.735285 TCATTTGCAACATACCATTTCCA 57.265 34.783 0.00 0.00 0.00 3.53
1638 5888 9.883142 TTTCCAAACCATTCCATATTTAATGTC 57.117 29.630 6.20 0.00 32.34 3.06
1643 5893 8.780616 AACCATTCCATATTTAATGTCCATCA 57.219 30.769 6.20 0.00 32.34 3.07
1694 5950 1.741401 CGCCTTCGGAGCAATCACA 60.741 57.895 0.00 0.00 0.00 3.58
1695 5951 1.699656 CGCCTTCGGAGCAATCACAG 61.700 60.000 0.00 0.00 0.00 3.66
1703 5959 0.615331 GAGCAATCACAGGGGAGTCA 59.385 55.000 0.00 0.00 0.00 3.41
1834 6090 5.047448 CACATGTGAAGGGATCGATATCTCT 60.047 44.000 21.64 0.00 45.39 3.10
1987 6252 5.339008 TCGCAGTTCTGTTGAGGTATATT 57.661 39.130 1.78 0.00 0.00 1.28
2012 6532 0.319405 CTCCCCCTTTTGCTTTGCTG 59.681 55.000 0.00 0.00 0.00 4.41
2221 6808 4.580167 TGGTCATTGCCTATTAGCATTCAC 59.420 41.667 0.00 0.00 43.64 3.18
2264 6851 5.000591 TCGATCTTAAATTGTGCAAGGTGA 58.999 37.500 0.00 0.00 0.00 4.02
2317 6908 3.496884 TGCCTTTGTTACGAAGTGATGAC 59.503 43.478 11.01 0.00 45.73 3.06
2423 7214 2.270923 TGTATCATTGCAGCGAGTGAC 58.729 47.619 0.00 0.00 0.00 3.67
2448 7239 6.867799 TTATAACATTGTTTGCATGCTTCG 57.132 33.333 20.33 2.96 0.00 3.79
2596 9929 5.163834 GCATTTGGCAATTATGACTTTGTGG 60.164 40.000 14.49 0.00 43.97 4.17
2599 9932 3.253230 GGCAATTATGACTTTGTGGCAC 58.747 45.455 11.55 11.55 35.90 5.01
2736 10072 6.424207 GCTATGCCCACTACATTTTAGTAGAC 59.576 42.308 8.01 0.00 43.24 2.59
2772 10108 1.004277 GTCCGCTGTTCTGTGACTCG 61.004 60.000 0.00 0.00 0.00 4.18
2794 10135 9.492973 ACTCGGTTTAGTGCTTTTATACTTTAA 57.507 29.630 0.00 0.00 0.00 1.52
2917 10262 4.363999 AGACGTCTCTTTGAGAACAGTTG 58.636 43.478 13.58 0.00 40.59 3.16
2930 10275 9.942850 TTTGAGAACAGTTGATATCTGATGTTA 57.057 29.630 15.35 0.00 36.81 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.836606 TATGGCGATGAAGAAGGGCA 59.163 50.000 0.00 0.00 39.37 5.36
2 3 1.071385 AGCTATGGCGATGAAGAAGGG 59.929 52.381 0.00 0.00 44.37 3.95
3 4 2.224137 TGAGCTATGGCGATGAAGAAGG 60.224 50.000 0.00 0.00 44.37 3.46
4 5 3.058450 CTGAGCTATGGCGATGAAGAAG 58.942 50.000 0.00 0.00 44.37 2.85
5 6 2.804572 GCTGAGCTATGGCGATGAAGAA 60.805 50.000 0.00 0.00 44.37 2.52
6 7 1.269988 GCTGAGCTATGGCGATGAAGA 60.270 52.381 0.00 0.00 44.37 2.87
7 8 1.146637 GCTGAGCTATGGCGATGAAG 58.853 55.000 0.00 0.00 44.37 3.02
8 9 0.755079 AGCTGAGCTATGGCGATGAA 59.245 50.000 4.49 0.00 44.37 2.57
9 10 0.033090 CAGCTGAGCTATGGCGATGA 59.967 55.000 8.42 0.00 44.37 2.92
10 11 0.249784 ACAGCTGAGCTATGGCGATG 60.250 55.000 23.35 0.00 44.37 3.84
11 12 0.249784 CACAGCTGAGCTATGGCGAT 60.250 55.000 23.35 0.00 44.37 4.58
12 13 1.142531 CACAGCTGAGCTATGGCGA 59.857 57.895 23.35 0.00 44.37 5.54
13 14 1.153489 ACACAGCTGAGCTATGGCG 60.153 57.895 23.35 2.19 37.40 5.69
14 15 0.107993 TCACACAGCTGAGCTATGGC 60.108 55.000 23.35 0.00 37.40 4.40
15 16 1.937278 CTCACACAGCTGAGCTATGG 58.063 55.000 23.35 6.29 37.40 2.74
26 27 6.539826 TGAAATAACTATGGATGCTCACACAG 59.460 38.462 0.00 0.00 0.00 3.66
27 28 6.413892 TGAAATAACTATGGATGCTCACACA 58.586 36.000 0.00 0.00 0.00 3.72
28 29 6.925610 TGAAATAACTATGGATGCTCACAC 57.074 37.500 0.00 0.00 0.00 3.82
29 30 9.797642 ATATTGAAATAACTATGGATGCTCACA 57.202 29.630 0.00 0.00 0.00 3.58
56 57 9.082313 TCTTTCAAAAGAAATAAGATTGGAGCT 57.918 29.630 2.74 0.00 41.75 4.09
88 89 3.305403 GGCTAAGGTCTTTTCTTGTTGCC 60.305 47.826 0.00 0.00 33.32 4.52
116 117 2.698763 GGTGTCGACGGGAGGAGAC 61.699 68.421 11.62 0.19 39.62 3.36
161 162 2.169810 ACCTCCATGGCCCAAAGGT 61.170 57.895 14.84 14.84 40.22 3.50
216 217 5.221204 GGATCTAATAAGAACGAGAACGGGT 60.221 44.000 0.00 0.00 37.42 5.28
308 309 2.095769 GGCACACCATTGGGACAAGAA 61.096 52.381 7.78 0.00 39.10 2.52
327 329 2.655364 CCACGCGACGATGCTAGG 60.655 66.667 15.93 0.00 0.00 3.02
332 334 2.880879 CACCTCCACGCGACGATG 60.881 66.667 15.93 7.02 0.00 3.84
347 356 3.303461 CGTGAGATCCGATAGAGACACAC 60.303 52.174 0.00 0.00 39.76 3.82
356 365 2.299013 CCAAATCCCGTGAGATCCGATA 59.701 50.000 0.00 0.00 0.00 2.92
367 376 1.407712 CCATAACCGACCAAATCCCGT 60.408 52.381 0.00 0.00 0.00 5.28
375 384 0.533491 CCGAAGACCATAACCGACCA 59.467 55.000 0.00 0.00 0.00 4.02
383 392 2.747177 ACAGATCCACCGAAGACCATA 58.253 47.619 0.00 0.00 0.00 2.74
384 393 1.573108 ACAGATCCACCGAAGACCAT 58.427 50.000 0.00 0.00 0.00 3.55
419 428 4.625972 AAACAACCAAACGAAGACGAAT 57.374 36.364 0.00 0.00 42.66 3.34
428 437 8.079809 AGGATCAAACTTATAAACAACCAAACG 58.920 33.333 0.00 0.00 0.00 3.60
473 482 3.093717 AGTAACAACCATCGCCGATAG 57.906 47.619 0.00 0.00 0.00 2.08
474 483 3.530265 AAGTAACAACCATCGCCGATA 57.470 42.857 0.00 0.00 0.00 2.92
489 498 0.891904 GGACCAAGGCGCCAAAGTAA 60.892 55.000 31.54 0.00 0.00 2.24
491 500 1.774894 TAGGACCAAGGCGCCAAAGT 61.775 55.000 31.54 22.03 0.00 2.66
494 503 1.077787 CATAGGACCAAGGCGCCAA 60.078 57.895 31.54 3.10 0.00 4.52
498 507 1.227674 GCTCCATAGGACCAAGGCG 60.228 63.158 0.00 0.00 0.00 5.52
501 510 3.648067 TGATAAGGCTCCATAGGACCAAG 59.352 47.826 0.00 0.00 0.00 3.61
514 523 1.134560 GGAAGTCGTCGTGATAAGGCT 59.865 52.381 0.00 0.00 0.00 4.58
521 530 0.109458 CAATCGGGAAGTCGTCGTGA 60.109 55.000 0.00 0.00 0.00 4.35
525 534 2.422832 AGTAGACAATCGGGAAGTCGTC 59.577 50.000 0.00 0.00 37.36 4.20
538 547 8.910944 AGTAGAAGTTCTTGTTGTAGTAGACAA 58.089 33.333 11.40 0.00 46.03 3.18
554 563 7.247929 ACAAAGCTTGTTGTAGTAGAAGTTC 57.752 36.000 0.00 0.00 42.22 3.01
556 565 5.758784 GGACAAAGCTTGTTGTAGTAGAAGT 59.241 40.000 0.00 0.00 45.52 3.01
558 567 4.748102 CGGACAAAGCTTGTTGTAGTAGAA 59.252 41.667 0.00 0.00 45.52 2.10
560 569 3.432252 CCGGACAAAGCTTGTTGTAGTAG 59.568 47.826 0.00 0.00 45.52 2.57
563 572 2.218603 ACCGGACAAAGCTTGTTGTAG 58.781 47.619 9.46 0.00 45.52 2.74
564 573 2.335316 ACCGGACAAAGCTTGTTGTA 57.665 45.000 9.46 0.00 45.52 2.41
565 574 1.470051 AACCGGACAAAGCTTGTTGT 58.530 45.000 9.46 0.47 45.52 3.32
566 575 2.459934 GAAACCGGACAAAGCTTGTTG 58.540 47.619 9.46 0.00 45.52 3.33
567 576 1.064952 CGAAACCGGACAAAGCTTGTT 59.935 47.619 9.46 0.00 45.52 2.83
572 581 1.128692 CTCATCGAAACCGGACAAAGC 59.871 52.381 9.46 0.00 0.00 3.51
573 582 2.157668 CACTCATCGAAACCGGACAAAG 59.842 50.000 9.46 0.00 0.00 2.77
583 592 1.639722 TCACCCCTCACTCATCGAAA 58.360 50.000 0.00 0.00 0.00 3.46
585 594 1.114627 CATCACCCCTCACTCATCGA 58.885 55.000 0.00 0.00 0.00 3.59
593 602 2.348104 CCGTCGTCATCACCCCTCA 61.348 63.158 0.00 0.00 0.00 3.86
637 646 4.098654 CAGATCTGTAGACCACCTACCAAG 59.901 50.000 14.95 0.00 45.60 3.61
640 649 3.899726 TCAGATCTGTAGACCACCTACC 58.100 50.000 21.92 0.00 45.60 3.18
654 670 8.432805 AGGGTAATGAAAATAACGATCAGATCT 58.567 33.333 8.82 0.00 0.00 2.75
656 672 8.980481 AAGGGTAATGAAAATAACGATCAGAT 57.020 30.769 0.00 0.00 0.00 2.90
661 677 8.747538 AAGCTAAGGGTAATGAAAATAACGAT 57.252 30.769 0.00 0.00 0.00 3.73
679 695 9.959749 TTTCAATTTTGGTAGTACAAAGCTAAG 57.040 29.630 2.06 0.00 40.97 2.18
763 785 3.329889 TGCCCCATTCGAGCCAGT 61.330 61.111 0.00 0.00 0.00 4.00
764 786 2.825836 GTGCCCCATTCGAGCCAG 60.826 66.667 0.00 0.00 0.00 4.85
775 797 1.095807 GCGGAAATAGTGAGTGCCCC 61.096 60.000 0.00 0.00 0.00 5.80
805 4584 0.321298 CACTAGTGGGGTTCGGGTTG 60.321 60.000 15.49 0.00 0.00 3.77
823 4619 4.403734 GGTTCTGTTCTAACCCATTTCCA 58.596 43.478 0.00 0.00 40.49 3.53
897 4703 0.863956 AGGGGTTTGTGGGAAATGGA 59.136 50.000 0.00 0.00 0.00 3.41
1050 4900 3.781770 GACGATCTGCTCCGGCTGG 62.782 68.421 4.71 4.71 39.59 4.85
1051 4901 2.279120 GACGATCTGCTCCGGCTG 60.279 66.667 0.00 0.00 39.59 4.85
1052 4902 3.893763 CGACGATCTGCTCCGGCT 61.894 66.667 0.00 0.00 39.59 5.52
1141 5027 2.683933 GAGGACGAAGGGGAGGCA 60.684 66.667 0.00 0.00 0.00 4.75
1173 5083 4.399764 CCCAGGTAGATGAGGGCA 57.600 61.111 0.00 0.00 33.91 5.36
1198 5108 1.959899 GCAGACACGATCCACGCAAG 61.960 60.000 0.00 0.00 46.94 4.01
1328 5259 4.742201 CGCACAGTAGCAGGGCGT 62.742 66.667 1.12 0.00 42.51 5.68
1432 5407 6.318648 ACAGCTGCAATTCGATAGGATTAAAA 59.681 34.615 15.27 0.00 44.27 1.52
1441 5416 5.230182 CCTATGTACAGCTGCAATTCGATA 58.770 41.667 15.27 0.28 0.00 2.92
1534 5604 5.958321 TCCTACTACTCATCATCAGGACAT 58.042 41.667 0.00 0.00 0.00 3.06
1556 5626 4.773149 TGAAAAGAACTACTCCTCCTCCTC 59.227 45.833 0.00 0.00 0.00 3.71
1559 5641 6.937465 ACAAATGAAAAGAACTACTCCTCCTC 59.063 38.462 0.00 0.00 0.00 3.71
1562 5644 7.497925 ACACAAATGAAAAGAACTACTCCTC 57.502 36.000 0.00 0.00 0.00 3.71
1606 5853 8.565780 AATATGGAATGGTTTGGAAATGGTAT 57.434 30.769 0.00 0.00 0.00 2.73
1617 5864 9.211410 TGATGGACATTAAATATGGAATGGTTT 57.789 29.630 12.24 0.00 37.37 3.27
1643 5893 6.581712 ACAGCAATTTCAACAAAACCATACT 58.418 32.000 0.00 0.00 0.00 2.12
1694 5950 2.527624 TGTGCAGCTGACTCCCCT 60.528 61.111 20.43 0.00 0.00 4.79
1695 5951 2.359230 GTGTGCAGCTGACTCCCC 60.359 66.667 20.43 0.00 0.00 4.81
1703 5959 0.954452 GCCTAAACAAGTGTGCAGCT 59.046 50.000 0.00 0.00 0.00 4.24
1834 6090 1.137594 AGAACCGACCATTTCCCCCA 61.138 55.000 0.00 0.00 0.00 4.96
1987 6252 4.349365 CAAAGCAAAAGGGGGAGGTATAA 58.651 43.478 0.00 0.00 0.00 0.98
2012 6532 1.227380 CGGCTCACAGATACAGGGC 60.227 63.158 0.00 0.00 0.00 5.19
2221 6808 4.273235 TCGATGTCAATCCCAATTTCATCG 59.727 41.667 18.68 18.68 45.74 3.84
2264 6851 5.590259 AGAAGTGTAGAACTGCAACAATTGT 59.410 36.000 4.92 4.92 39.81 2.71
2423 7214 7.220491 TCGAAGCATGCAAACAATGTTATAATG 59.780 33.333 21.98 4.95 0.00 1.90
2599 9932 4.505191 TCTTTTTACCAGAGTCACGAAACG 59.495 41.667 0.00 0.00 0.00 3.60
2736 10072 1.606224 GGACAAAGGCACAATGGCAAG 60.606 52.381 5.10 0.00 46.46 4.01
2798 10140 7.972832 ACATGATCAAACCGTTTACTTTCTA 57.027 32.000 0.00 0.00 0.00 2.10
2856 10201 5.522824 GCATAGCACCACCTTAAAGTACTAC 59.477 44.000 0.00 0.00 0.00 2.73
2917 10262 9.755804 TGACATGAACTTCTAACATCAGATATC 57.244 33.333 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.