Multiple sequence alignment - TraesCS3A01G221000

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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 TraesCS3A01G221000 chr3A 100.000 8251 0 0 1 8251 410115598 410107348 0.000000e+00 15237.0
1 TraesCS3A01G221000 chr3A 80.132 906 146 24 1337 2226 419332826 419333713 0.000000e+00 645.0
2 TraesCS3A01G221000 chr3B 97.307 3713 77 9 3003 6710 401808183 401804489 0.000000e+00 6281.0
3 TraesCS3A01G221000 chr3B 96.892 2188 51 9 630 2812 401810357 401808182 0.000000e+00 3648.0
4 TraesCS3A01G221000 chr3B 94.934 908 33 6 7352 8251 401803968 401803066 0.000000e+00 1410.0
5 TraesCS3A01G221000 chr3B 98.102 527 8 1 6768 7294 401804490 401803966 0.000000e+00 917.0
6 TraesCS3A01G221000 chr3B 80.067 898 161 14 1337 2226 406649934 406650821 0.000000e+00 651.0
7 TraesCS3A01G221000 chr3B 86.090 266 17 12 5216 5461 480377207 480376942 1.370000e-67 268.0
8 TraesCS3A01G221000 chr3B 86.008 243 28 5 5221 5458 44856251 44856492 1.060000e-63 255.0
9 TraesCS3A01G221000 chr3B 85.830 247 25 8 5217 5456 45269348 45269591 3.820000e-63 254.0
10 TraesCS3A01G221000 chr3D 94.032 3770 139 28 614 4334 317198418 317202150 0.000000e+00 5637.0
11 TraesCS3A01G221000 chr3D 92.951 2128 78 27 5460 7554 317203597 317205685 0.000000e+00 3033.0
12 TraesCS3A01G221000 chr3D 97.552 858 20 1 4362 5219 317202542 317203398 0.000000e+00 1467.0
13 TraesCS3A01G221000 chr3D 91.991 462 19 6 7567 8021 317205870 317206320 4.200000e-177 632.0
14 TraesCS3A01G221000 chr3D 87.903 248 23 6 5217 5458 26639810 26640056 1.360000e-72 285.0
15 TraesCS3A01G221000 chr4D 80.734 2860 346 107 847 3602 96912130 96909372 0.000000e+00 2039.0
16 TraesCS3A01G221000 chr4D 90.187 856 76 7 4372 5221 96908425 96907572 0.000000e+00 1109.0
17 TraesCS3A01G221000 chr4D 78.811 1581 240 54 5754 7275 96907228 96905684 0.000000e+00 976.0
18 TraesCS3A01G221000 chr4A 82.256 2429 285 88 1259 3596 479412044 479414417 0.000000e+00 1964.0
19 TraesCS3A01G221000 chr4A 90.534 824 70 7 4404 5221 479416367 479417188 0.000000e+00 1083.0
20 TraesCS3A01G221000 chr4A 78.256 1766 267 65 5754 7437 479417532 479419262 0.000000e+00 1026.0
21 TraesCS3A01G221000 chr4A 86.421 869 92 9 4365 5221 497815650 497814796 0.000000e+00 928.0
22 TraesCS3A01G221000 chr4A 81.568 472 66 10 3643 4100 497819216 497818752 3.640000e-98 370.0
23 TraesCS3A01G221000 chr4A 77.650 698 93 40 2929 3602 497819876 497819218 4.710000e-97 366.0
24 TraesCS3A01G221000 chr4A 85.217 115 15 2 3483 3596 479415141 479415254 5.230000e-22 117.0
25 TraesCS3A01G221000 chr4A 85.455 110 14 2 8071 8179 690218473 690218365 6.770000e-21 113.0
26 TraesCS3A01G221000 chr4B 80.141 1702 217 66 1977 3602 138305550 138303894 0.000000e+00 1158.0
27 TraesCS3A01G221000 chr4B 90.290 793 69 7 4435 5221 138302844 138302054 0.000000e+00 1031.0
28 TraesCS3A01G221000 chr4B 80.344 1221 185 35 6083 7275 138301117 138299924 0.000000e+00 874.0
29 TraesCS3A01G221000 chr4B 81.679 1048 123 33 909 1932 138306554 138305552 0.000000e+00 808.0
30 TraesCS3A01G221000 chr4B 84.804 612 80 11 1247 1849 119858920 119859527 3.290000e-168 603.0
31 TraesCS3A01G221000 chr4B 85.632 522 60 10 1841 2352 119866772 119867288 1.220000e-147 534.0
32 TraesCS3A01G221000 chr7B 85.516 863 113 11 4366 5221 665542936 665542079 0.000000e+00 891.0
33 TraesCS3A01G221000 chr7B 74.494 494 96 25 4407 4882 699841618 699841137 3.930000e-43 187.0
34 TraesCS3A01G221000 chr7B 88.372 43 5 0 5861 5903 23255548 23255590 1.500000e-02 52.8
35 TraesCS3A01G221000 chr5B 83.504 976 127 23 4261 5221 93459236 93460192 0.000000e+00 880.0
36 TraesCS3A01G221000 chr5B 90.353 539 39 6 4 539 516089374 516089902 0.000000e+00 695.0
37 TraesCS3A01G221000 chr6A 93.878 539 31 2 2 539 454472991 454472454 0.000000e+00 811.0
38 TraesCS3A01G221000 chr6A 88.000 75 9 0 8105 8179 51608010 51607936 1.140000e-13 89.8
39 TraesCS3A01G221000 chr5A 83.591 518 73 9 4374 4881 684629502 684628987 7.490000e-130 475.0
40 TraesCS3A01G221000 chr5A 83.684 380 47 10 1 377 308078632 308078999 2.200000e-90 344.0
41 TraesCS3A01G221000 chr5A 83.846 130 20 1 8050 8179 693495241 693495113 1.120000e-23 122.0
42 TraesCS3A01G221000 chr2B 86.104 367 40 7 4 370 16330629 16330274 1.300000e-102 385.0
43 TraesCS3A01G221000 chr2B 88.000 250 20 8 5219 5461 653963248 653963002 3.770000e-73 287.0
44 TraesCS3A01G221000 chr6D 80.073 547 65 23 1 537 119299574 119300086 4.710000e-97 366.0
45 TraesCS3A01G221000 chr6D 83.727 381 47 10 1 378 409779583 409779215 6.130000e-91 346.0
46 TraesCS3A01G221000 chr6D 85.537 242 13 10 5239 5461 73498270 73498032 4.980000e-57 233.0
47 TraesCS3A01G221000 chrUn 85.830 247 25 8 5217 5456 345547250 345547493 3.820000e-63 254.0
48 TraesCS3A01G221000 chrUn 85.830 247 25 8 5217 5456 362558895 362559138 3.820000e-63 254.0
49 TraesCS3A01G221000 chr5D 84.701 268 17 7 5217 5461 538708183 538708449 6.400000e-61 246.0
50 TraesCS3A01G221000 chr5D 85.586 111 14 1 9 119 541812615 541812507 1.880000e-21 115.0
51 TraesCS3A01G221000 chr6B 84.091 264 12 12 5219 5461 147680294 147680040 2.320000e-55 228.0
52 TraesCS3A01G221000 chr6B 86.239 109 15 0 8071 8179 659568084 659567976 1.450000e-22 119.0
53 TraesCS3A01G221000 chr1A 73.507 653 106 35 5754 6364 23454124 23453497 1.410000e-42 185.0
54 TraesCS3A01G221000 chr7D 74.089 494 98 25 4407 4882 610822383 610821902 8.510000e-40 176.0
55 TraesCS3A01G221000 chr7D 79.426 209 37 5 5827 6033 590656944 590656740 8.630000e-30 143.0
56 TraesCS3A01G221000 chr2D 86.429 140 18 1 4366 4505 427946828 427946966 1.430000e-32 152.0


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 TraesCS3A01G221000 chr3A 410107348 410115598 8250 True 15237.000000 15237 100.000000 1 8251 1 chr3A.!!$R1 8250
1 TraesCS3A01G221000 chr3A 419332826 419333713 887 False 645.000000 645 80.132000 1337 2226 1 chr3A.!!$F1 889
2 TraesCS3A01G221000 chr3B 401803066 401810357 7291 True 3064.000000 6281 96.808750 630 8251 4 chr3B.!!$R2 7621
3 TraesCS3A01G221000 chr3B 406649934 406650821 887 False 651.000000 651 80.067000 1337 2226 1 chr3B.!!$F3 889
4 TraesCS3A01G221000 chr3D 317198418 317206320 7902 False 2692.250000 5637 94.131500 614 8021 4 chr3D.!!$F2 7407
5 TraesCS3A01G221000 chr4D 96905684 96912130 6446 True 1374.666667 2039 83.244000 847 7275 3 chr4D.!!$R1 6428
6 TraesCS3A01G221000 chr4A 479412044 479419262 7218 False 1047.500000 1964 84.065750 1259 7437 4 chr4A.!!$F1 6178
7 TraesCS3A01G221000 chr4A 497814796 497819876 5080 True 554.666667 928 81.879667 2929 5221 3 chr4A.!!$R2 2292
8 TraesCS3A01G221000 chr4B 138299924 138306554 6630 True 967.750000 1158 83.113500 909 7275 4 chr4B.!!$R1 6366
9 TraesCS3A01G221000 chr4B 119858920 119859527 607 False 603.000000 603 84.804000 1247 1849 1 chr4B.!!$F1 602
10 TraesCS3A01G221000 chr4B 119866772 119867288 516 False 534.000000 534 85.632000 1841 2352 1 chr4B.!!$F2 511
11 TraesCS3A01G221000 chr7B 665542079 665542936 857 True 891.000000 891 85.516000 4366 5221 1 chr7B.!!$R1 855
12 TraesCS3A01G221000 chr5B 93459236 93460192 956 False 880.000000 880 83.504000 4261 5221 1 chr5B.!!$F1 960
13 TraesCS3A01G221000 chr5B 516089374 516089902 528 False 695.000000 695 90.353000 4 539 1 chr5B.!!$F2 535
14 TraesCS3A01G221000 chr6A 454472454 454472991 537 True 811.000000 811 93.878000 2 539 1 chr6A.!!$R2 537
15 TraesCS3A01G221000 chr5A 684628987 684629502 515 True 475.000000 475 83.591000 4374 4881 1 chr5A.!!$R1 507
16 TraesCS3A01G221000 chr6D 119299574 119300086 512 False 366.000000 366 80.073000 1 537 1 chr6D.!!$F1 536

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
714 728 0.035317 TGCTCAATCAGTGCCTTCGT 59.965 50.000 0.0 0.00 35.92 3.85 F
905 932 1.222113 CTCCTTCCCCTTCTTCCGC 59.778 63.158 0.0 0.00 0.00 5.54 F
1599 1659 2.557056 CACTTCGAGGCGGAAGGATATA 59.443 50.000 20.3 0.00 46.06 0.86 F
2984 3122 1.195900 TGACGCCGTTTTGCATTCTAC 59.804 47.619 0.0 0.00 0.00 2.59 F
3829 4848 4.040952 ACTCCTAAGCTGATTCAAGTGTGT 59.959 41.667 0.0 0.00 0.00 3.72 F
5427 9446 0.736053 TGTTTGACTTGCACGGGAAC 59.264 50.000 0.0 0.00 0.00 3.62 F
5986 10073 0.246360 TGTGAGCTACCACATGACGG 59.754 55.000 0.0 1.45 41.63 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 2045 1.004745 GACCCCATGCTCAAAGGAGAA 59.995 52.381 0.0 0.0 44.26 2.87 R
2861 2997 4.263016 CGATGCAATACAACATGTGTACG 58.737 43.478 0.0 1.5 45.51 3.67 R
3044 3182 3.457380 ACAAGACATGGATGCTATCAGGT 59.543 43.478 0.0 0.0 0.00 4.00 R
3947 4967 1.278985 TGAATCAGAATCCCACACGCT 59.721 47.619 0.0 0.0 0.00 5.07 R
5445 9464 0.105607 ATCCTACTCCCTCCGTTCCC 60.106 60.000 0.0 0.0 0.00 3.97 R
6698 11059 1.133199 ACAAGGACTTTTCCATGCCCA 60.133 47.619 0.0 0.0 43.37 5.36 R
7901 12532 1.421646 ACAAAGGGGTGAAGTGAGAGG 59.578 52.381 0.0 0.0 0.00 3.69 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
66 67 4.069232 CGGGTCGCAGCTCCTTCA 62.069 66.667 0.00 0.00 0.00 3.02
71 72 2.202851 CGCAGCTCCTTCATCGCT 60.203 61.111 0.00 0.00 0.00 4.93
129 132 0.521867 CTCGCGACGTCGGTTGAATA 60.522 55.000 36.13 10.70 40.23 1.75
295 298 0.111253 CAGCTTTGGTGAGGGTCCTT 59.889 55.000 0.00 0.00 32.22 3.36
343 346 1.225426 GCCATGATGGAGGAGTGCA 59.775 57.895 17.22 0.00 40.96 4.57
346 349 1.064906 CCATGATGGAGGAGTGCAAGT 60.065 52.381 5.27 0.00 40.96 3.16
495 509 0.395862 ATCGTGGAGGATCTCGTGGT 60.396 55.000 0.00 0.00 35.07 4.16
543 557 4.090057 GCGCACCGGCTCTGTTTC 62.090 66.667 0.30 0.00 38.10 2.78
544 558 2.357517 CGCACCGGCTCTGTTTCT 60.358 61.111 0.00 0.00 38.10 2.52
545 559 1.961277 CGCACCGGCTCTGTTTCTT 60.961 57.895 0.00 0.00 38.10 2.52
546 560 0.669318 CGCACCGGCTCTGTTTCTTA 60.669 55.000 0.00 0.00 38.10 2.10
547 561 1.519408 GCACCGGCTCTGTTTCTTAA 58.481 50.000 0.00 0.00 36.96 1.85
548 562 1.877443 GCACCGGCTCTGTTTCTTAAA 59.123 47.619 0.00 0.00 36.96 1.52
549 563 2.292292 GCACCGGCTCTGTTTCTTAAAA 59.708 45.455 0.00 0.00 36.96 1.52
550 564 3.243267 GCACCGGCTCTGTTTCTTAAAAA 60.243 43.478 0.00 0.00 36.96 1.94
576 590 8.891671 AAGTACTCATACTACTAGTAGTCAGC 57.108 38.462 33.47 18.90 44.58 4.26
577 591 8.253867 AGTACTCATACTACTAGTAGTCAGCT 57.746 38.462 33.47 20.39 44.58 4.24
578 592 9.365906 AGTACTCATACTACTAGTAGTCAGCTA 57.634 37.037 33.47 19.34 44.58 3.32
579 593 9.979578 GTACTCATACTACTAGTAGTCAGCTAA 57.020 37.037 33.47 18.68 44.58 3.09
581 595 9.902684 ACTCATACTACTAGTAGTCAGCTAAAA 57.097 33.333 33.47 17.36 44.58 1.52
624 638 5.862678 TTTTGTTTGAGGAAAAGGGTAGG 57.137 39.130 0.00 0.00 0.00 3.18
625 639 4.799715 TTGTTTGAGGAAAAGGGTAGGA 57.200 40.909 0.00 0.00 0.00 2.94
626 640 5.333566 TTGTTTGAGGAAAAGGGTAGGAT 57.666 39.130 0.00 0.00 0.00 3.24
627 641 5.333566 TGTTTGAGGAAAAGGGTAGGATT 57.666 39.130 0.00 0.00 0.00 3.01
628 642 6.457159 TGTTTGAGGAAAAGGGTAGGATTA 57.543 37.500 0.00 0.00 0.00 1.75
714 728 0.035317 TGCTCAATCAGTGCCTTCGT 59.965 50.000 0.00 0.00 35.92 3.85
882 908 1.899437 GCTTCCTCATCCGTGGACCA 61.899 60.000 0.00 0.00 34.53 4.02
905 932 1.222113 CTCCTTCCCCTTCTTCCGC 59.778 63.158 0.00 0.00 0.00 5.54
1076 1113 3.763902 TCTTCTCTTCAGATTTCGCGAG 58.236 45.455 9.59 0.00 0.00 5.03
1125 1167 3.636764 ACTGCCTTTGTTCTCCGATTTTT 59.363 39.130 0.00 0.00 0.00 1.94
1199 1241 3.103911 CCTCGTCGTCACGCAACC 61.104 66.667 0.00 0.00 46.28 3.77
1599 1659 2.557056 CACTTCGAGGCGGAAGGATATA 59.443 50.000 20.30 0.00 46.06 0.86
2249 2330 5.103728 TGCCCAATGTCTCCCATAAAGAATA 60.104 40.000 0.00 0.00 31.97 1.75
2363 2469 6.852420 TCACTAGTAACTAGCCTGAATTGT 57.148 37.500 0.00 0.00 37.57 2.71
2434 2543 4.191544 ACGATCCACGATTCAATTCATGT 58.808 39.130 0.00 0.00 45.77 3.21
2581 2711 6.012508 ACCTCTAATTTTTCCTCATCCACTCA 60.013 38.462 0.00 0.00 0.00 3.41
2634 2768 7.715249 TGAGAATATATTTTTCCCAGTTCTCCG 59.285 37.037 0.00 0.00 39.49 4.63
2730 2864 7.770366 ATCTAATGCAAATATCATGCCTTCA 57.230 32.000 10.07 0.66 43.16 3.02
2809 2943 4.122776 GGCATACGATTATCTGGGCTATG 58.877 47.826 0.00 0.00 0.00 2.23
2837 2973 6.624352 TTCAAGATTGCTACAATATCTGCC 57.376 37.500 0.00 0.00 0.00 4.85
2941 3077 7.116662 TGTTAGATACTAAACGCGATTTGTTGT 59.883 33.333 19.48 10.32 0.00 3.32
2984 3122 1.195900 TGACGCCGTTTTGCATTCTAC 59.804 47.619 0.00 0.00 0.00 2.59
3041 3179 7.621991 CATTAACATCGATCTACCAGTTGTTC 58.378 38.462 0.00 0.00 32.30 3.18
3042 3180 5.407407 AACATCGATCTACCAGTTGTTCT 57.593 39.130 0.00 0.00 0.00 3.01
3043 3181 5.407407 ACATCGATCTACCAGTTGTTCTT 57.593 39.130 0.00 0.00 0.00 2.52
3044 3182 6.525578 ACATCGATCTACCAGTTGTTCTTA 57.474 37.500 0.00 0.00 0.00 2.10
3045 3183 6.331061 ACATCGATCTACCAGTTGTTCTTAC 58.669 40.000 0.00 0.00 0.00 2.34
3567 3736 9.798994 GAAAGTATTTTCTCTATAGTTCGGTCA 57.201 33.333 3.60 0.00 39.27 4.02
3683 4695 8.028938 GTGTAGTTTTGAGATGCATGGTTTTAT 58.971 33.333 2.46 0.00 0.00 1.40
3829 4848 4.040952 ACTCCTAAGCTGATTCAAGTGTGT 59.959 41.667 0.00 0.00 0.00 3.72
4334 7964 2.224892 TGCCAGGTACAAAATGTAGGCA 60.225 45.455 14.40 14.40 44.32 4.75
4345 7975 7.391275 GTACAAAATGTAGGCACCTTTAGGTAA 59.609 37.037 0.14 0.00 38.93 2.85
4385 8379 6.757897 CAGGTTTCCTGCATAAAACTCATA 57.242 37.500 18.22 0.00 45.13 2.15
4390 8384 7.283127 GGTTTCCTGCATAAAACTCATATCAGA 59.717 37.037 18.22 0.00 36.01 3.27
4768 8780 0.973632 TTAGTGCCGAGCTTCAGGAA 59.026 50.000 7.85 0.00 0.00 3.36
4928 8946 9.194716 CACTTGTCGTATTATGTTTGAATTACG 57.805 33.333 0.00 0.00 0.00 3.18
5427 9446 0.736053 TGTTTGACTTGCACGGGAAC 59.264 50.000 0.00 0.00 0.00 3.62
5462 9481 3.951765 GGGAACGGAGGGAGTAGG 58.048 66.667 0.00 0.00 0.00 3.18
5468 9487 2.660670 ACGGAGGGAGTAGGATGTAG 57.339 55.000 0.00 0.00 0.00 2.74
5527 9546 7.759489 TCTGCAAACCTTAACATAGTTCAAT 57.241 32.000 0.00 0.00 0.00 2.57
5700 9741 6.439375 TGTAGGTAGCAAGAGAAAGAATACCA 59.561 38.462 0.00 0.00 34.86 3.25
5847 9926 2.077627 GCGAAAAAGGAGAGGAGGAAC 58.922 52.381 0.00 0.00 0.00 3.62
5905 9984 7.458397 CCAAGGGGCTATATTCTTGTGTTATA 58.542 38.462 0.00 0.00 35.98 0.98
5970 10057 0.798159 CATGTCGTGGTGTGGATGTG 59.202 55.000 0.00 0.00 0.00 3.21
5986 10073 0.246360 TGTGAGCTACCACATGACGG 59.754 55.000 0.00 1.45 41.63 4.79
6114 10464 9.595823 TTATGTGTAGGTTAGCTAAGTTTCATC 57.404 33.333 6.38 0.00 0.00 2.92
6449 10803 7.207383 GCAACCAAACTTCTTACCAGTAAAAT 58.793 34.615 0.00 0.00 0.00 1.82
6536 10892 4.603610 AGGGACCCCTTATGATATTCCTTG 59.396 45.833 7.00 0.00 45.70 3.61
6668 11029 4.816786 GCCATTTGCAAACAATGTTCTT 57.183 36.364 15.41 0.00 40.77 2.52
6695 11056 7.041098 CCTGAACTTTCTGTAGCATACTTGTTT 60.041 37.037 0.00 0.00 43.54 2.83
6698 11059 7.986085 ACTTTCTGTAGCATACTTGTTTGAT 57.014 32.000 0.00 0.00 43.54 2.57
6801 11168 8.349983 AGGTGTGTTTTACATCATTTCTAACAC 58.650 33.333 0.00 0.00 43.10 3.32
6969 11363 7.081526 AGCTGTTATTGCTCTGTTTATCTTG 57.918 36.000 0.00 0.00 35.67 3.02
7319 11731 8.642935 TGTTATTTTCCTCATGAATGTTGGTA 57.357 30.769 0.00 0.00 31.67 3.25
7321 11733 9.921637 GTTATTTTCCTCATGAATGTTGGTAAA 57.078 29.630 0.00 1.22 32.24 2.01
7322 11734 9.921637 TTATTTTCCTCATGAATGTTGGTAAAC 57.078 29.630 0.00 0.00 36.78 2.01
7324 11736 4.647611 TCCTCATGAATGTTGGTAAACGT 58.352 39.130 0.00 0.00 39.30 3.99
7327 11739 6.711194 TCCTCATGAATGTTGGTAAACGTTTA 59.289 34.615 16.59 16.59 43.91 2.01
7328 11740 7.021196 CCTCATGAATGTTGGTAAACGTTTAG 58.979 38.462 20.66 5.92 43.91 1.85
7329 11741 7.308348 CCTCATGAATGTTGGTAAACGTTTAGT 60.308 37.037 20.66 0.00 43.91 2.24
7330 11742 7.932335 TCATGAATGTTGGTAAACGTTTAGTT 58.068 30.769 20.66 9.09 43.91 2.24
7331 11743 7.858382 TCATGAATGTTGGTAAACGTTTAGTTG 59.142 33.333 20.66 6.99 43.91 3.16
7332 11744 7.086230 TGAATGTTGGTAAACGTTTAGTTGT 57.914 32.000 20.66 3.51 43.91 3.32
7333 11745 7.188157 TGAATGTTGGTAAACGTTTAGTTGTC 58.812 34.615 20.66 8.79 43.91 3.18
7334 11746 6.930667 ATGTTGGTAAACGTTTAGTTGTCT 57.069 33.333 20.66 3.06 43.37 3.41
7335 11747 8.436046 AATGTTGGTAAACGTTTAGTTGTCTA 57.564 30.769 20.66 4.45 41.72 2.59
7352 11764 7.699878 AGTTGTCTAGGTTTCCTTGGATTATT 58.300 34.615 0.00 0.00 34.61 1.40
7356 11768 6.261158 GTCTAGGTTTCCTTGGATTATTCAGC 59.739 42.308 0.00 0.00 34.61 4.26
7437 11855 6.128526 GGATAATCTATTTCGTGCCAAGCTAC 60.129 42.308 0.00 0.00 0.00 3.58
7541 11983 2.358939 CAAGAATGGCTTGCTGGAAC 57.641 50.000 0.00 0.00 46.67 3.62
7630 12247 2.676342 GTGTTTATCCCAGGCTTGTACG 59.324 50.000 0.00 0.00 0.00 3.67
7645 12262 7.381678 CAGGCTTGTACGTATTTCTAGGATTAC 59.618 40.741 0.00 0.00 0.00 1.89
7730 12351 2.533318 GTTGAGAGCAACCCTGTCG 58.467 57.895 0.00 0.00 46.80 4.35
7805 12426 5.692928 TGTACAGGAGGAAGGAGACTATAC 58.307 45.833 0.00 0.00 42.68 1.47
7806 12427 5.432390 TGTACAGGAGGAAGGAGACTATACT 59.568 44.000 0.00 0.00 42.68 2.12
7807 12428 6.618610 TGTACAGGAGGAAGGAGACTATACTA 59.381 42.308 0.00 0.00 42.68 1.82
7808 12429 5.944135 ACAGGAGGAAGGAGACTATACTAC 58.056 45.833 0.00 0.00 42.68 2.73
7809 12430 5.673113 ACAGGAGGAAGGAGACTATACTACT 59.327 44.000 0.00 0.00 42.68 2.57
7810 12431 6.183361 ACAGGAGGAAGGAGACTATACTACTC 60.183 46.154 0.00 0.00 42.68 2.59
7811 12432 6.043938 CAGGAGGAAGGAGACTATACTACTCT 59.956 46.154 0.00 0.00 42.68 3.24
7812 12433 6.043938 AGGAGGAAGGAGACTATACTACTCTG 59.956 46.154 0.00 0.00 42.68 3.35
7813 12434 5.627135 AGGAAGGAGACTATACTACTCTGC 58.373 45.833 0.00 0.00 42.68 4.26
7814 12435 4.453136 GGAAGGAGACTATACTACTCTGCG 59.547 50.000 0.00 0.00 42.68 5.18
7833 12464 1.691215 GCAGCTCAGCTCAGCGTAAC 61.691 60.000 3.13 0.00 44.82 2.50
7901 12532 4.171416 GCTGCTAGGCGCTTGCAC 62.171 66.667 7.64 6.94 37.31 4.57
8004 12635 5.927281 ATTTGCAAATAGCTCTTGGTCAT 57.073 34.783 22.95 0.00 45.94 3.06
8061 12694 7.763985 CCCAATGATAACACCCTACAAAAATTC 59.236 37.037 0.00 0.00 0.00 2.17
8087 12720 5.977171 TGTCAATGGATTAAATACGACGG 57.023 39.130 0.00 0.00 0.00 4.79
8088 12721 5.662456 TGTCAATGGATTAAATACGACGGA 58.338 37.500 0.00 0.00 0.00 4.69
8108 12741 3.000322 GGAACGTCTATGCAGTTCGATTG 60.000 47.826 9.01 0.00 43.57 2.67
8224 12857 1.612950 TGGATGCACGCAAATGAAACT 59.387 42.857 0.00 0.00 0.00 2.66
8232 12865 4.864247 GCACGCAAATGAAACTTTCCATAT 59.136 37.500 0.00 0.00 0.00 1.78
8246 12879 6.795399 ACTTTCCATATGCTTATTGAAACCG 58.205 36.000 12.27 8.35 30.48 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 0.254178 AGATGCTGGAACCAAGCGAT 59.746 50.000 0.00 0.00 0.00 4.58
71 72 2.040145 TGATGTGAGATGCTGGAACCAA 59.960 45.455 0.00 0.00 0.00 3.67
121 124 2.413634 CCGGCGTGAAACTTATTCAACC 60.414 50.000 6.01 0.00 31.75 3.77
129 132 2.282180 ATGGCCGGCGTGAAACTT 60.282 55.556 22.54 0.00 31.75 2.66
226 229 2.449464 CATCCCTGCTCCATTTGTTGA 58.551 47.619 0.00 0.00 0.00 3.18
295 298 1.760875 CTAGCTCCGCCCACCCTAA 60.761 63.158 0.00 0.00 0.00 2.69
331 334 2.624838 CAAACAACTTGCACTCCTCCAT 59.375 45.455 0.00 0.00 0.00 3.41
332 335 2.023673 CAAACAACTTGCACTCCTCCA 58.976 47.619 0.00 0.00 0.00 3.86
343 346 1.507141 CGCTCTCCCGCAAACAACTT 61.507 55.000 0.00 0.00 0.00 2.66
550 564 9.328845 GCTGACTACTAGTAGTATGAGTACTTT 57.671 37.037 30.80 8.07 45.63 2.66
551 565 8.707449 AGCTGACTACTAGTAGTATGAGTACTT 58.293 37.037 30.80 8.56 45.63 2.24
552 566 8.253867 AGCTGACTACTAGTAGTATGAGTACT 57.746 38.462 30.80 18.97 45.63 2.73
553 567 9.979578 TTAGCTGACTACTAGTAGTATGAGTAC 57.020 37.037 30.80 18.66 45.63 2.73
555 569 9.902684 TTTTAGCTGACTACTAGTAGTATGAGT 57.097 33.333 30.80 18.33 45.63 3.41
601 615 5.958987 TCCTACCCTTTTCCTCAAACAAAAA 59.041 36.000 0.00 0.00 0.00 1.94
602 616 5.520751 TCCTACCCTTTTCCTCAAACAAAA 58.479 37.500 0.00 0.00 0.00 2.44
603 617 5.132043 TCCTACCCTTTTCCTCAAACAAA 57.868 39.130 0.00 0.00 0.00 2.83
604 618 4.799715 TCCTACCCTTTTCCTCAAACAA 57.200 40.909 0.00 0.00 0.00 2.83
605 619 5.333566 AATCCTACCCTTTTCCTCAAACA 57.666 39.130 0.00 0.00 0.00 2.83
606 620 8.272889 ACTATAATCCTACCCTTTTCCTCAAAC 58.727 37.037 0.00 0.00 0.00 2.93
607 621 8.272173 CACTATAATCCTACCCTTTTCCTCAAA 58.728 37.037 0.00 0.00 0.00 2.69
608 622 7.637301 GCACTATAATCCTACCCTTTTCCTCAA 60.637 40.741 0.00 0.00 0.00 3.02
609 623 6.183361 GCACTATAATCCTACCCTTTTCCTCA 60.183 42.308 0.00 0.00 0.00 3.86
610 624 6.231951 GCACTATAATCCTACCCTTTTCCTC 58.768 44.000 0.00 0.00 0.00 3.71
611 625 5.221661 CGCACTATAATCCTACCCTTTTCCT 60.222 44.000 0.00 0.00 0.00 3.36
612 626 4.995487 CGCACTATAATCCTACCCTTTTCC 59.005 45.833 0.00 0.00 0.00 3.13
613 627 4.451435 GCGCACTATAATCCTACCCTTTTC 59.549 45.833 0.30 0.00 0.00 2.29
614 628 4.102681 AGCGCACTATAATCCTACCCTTTT 59.897 41.667 11.47 0.00 0.00 2.27
615 629 3.646637 AGCGCACTATAATCCTACCCTTT 59.353 43.478 11.47 0.00 0.00 3.11
616 630 3.240302 AGCGCACTATAATCCTACCCTT 58.760 45.455 11.47 0.00 0.00 3.95
617 631 2.890814 AGCGCACTATAATCCTACCCT 58.109 47.619 11.47 0.00 0.00 4.34
618 632 4.796038 TTAGCGCACTATAATCCTACCC 57.204 45.455 11.47 0.00 0.00 3.69
619 633 7.318141 TGTTATTAGCGCACTATAATCCTACC 58.682 38.462 11.47 0.00 0.00 3.18
620 634 8.808529 CATGTTATTAGCGCACTATAATCCTAC 58.191 37.037 11.47 5.34 0.00 3.18
621 635 8.528643 ACATGTTATTAGCGCACTATAATCCTA 58.471 33.333 11.47 0.00 0.00 2.94
622 636 7.386851 ACATGTTATTAGCGCACTATAATCCT 58.613 34.615 11.47 0.00 0.00 3.24
623 637 7.462856 CGACATGTTATTAGCGCACTATAATCC 60.463 40.741 11.47 0.49 0.00 3.01
624 638 7.272731 TCGACATGTTATTAGCGCACTATAATC 59.727 37.037 11.47 4.23 0.00 1.75
625 639 7.061905 GTCGACATGTTATTAGCGCACTATAAT 59.938 37.037 11.47 7.54 0.00 1.28
626 640 6.361481 GTCGACATGTTATTAGCGCACTATAA 59.639 38.462 11.47 7.46 0.00 0.98
627 641 5.854866 GTCGACATGTTATTAGCGCACTATA 59.145 40.000 11.47 0.61 0.00 1.31
628 642 4.680110 GTCGACATGTTATTAGCGCACTAT 59.320 41.667 11.47 1.72 0.00 2.12
667 681 4.821589 CCTCGGCGTTCTGCTCCC 62.822 72.222 6.85 0.00 45.43 4.30
691 705 1.676635 GGCACTGATTGAGCAGGCA 60.677 57.895 1.02 0.00 40.20 4.75
714 728 1.376683 CGAAAGGCCGAATGGGTGA 60.377 57.895 0.00 0.00 38.44 4.02
787 801 4.514577 CGCTGTAGACGGGCAGGG 62.515 72.222 0.00 0.00 38.85 4.45
882 908 2.270858 GAAGAAGGGGAAGGAGGAGTT 58.729 52.381 0.00 0.00 0.00 3.01
905 932 3.386543 GGATCAGTCCAATGTCCCG 57.613 57.895 0.00 0.00 44.42 5.14
1018 1045 0.108992 GGCATGACGTACCGTTCAGA 60.109 55.000 0.00 0.00 41.37 3.27
1076 1113 2.617274 GCTGCCGTGTTCCTTGGTC 61.617 63.158 0.00 0.00 0.00 4.02
1125 1167 3.369471 CCTCTTTCCTTGCGAATCCTACA 60.369 47.826 0.00 0.00 0.00 2.74
1199 1241 2.588314 GCATCTGAGCCTGCTCCG 60.588 66.667 16.06 10.20 42.09 4.63
1599 1659 2.750350 CTCCCAGTCCCGTTTGCT 59.250 61.111 0.00 0.00 0.00 3.91
1975 2045 1.004745 GACCCCATGCTCAAAGGAGAA 59.995 52.381 0.00 0.00 44.26 2.87
2249 2330 6.800890 AGGACCCATAAAACTAACTTCCATT 58.199 36.000 0.00 0.00 0.00 3.16
2568 2698 6.070021 ACAAGATAAACATGAGTGGATGAGGA 60.070 38.462 0.00 0.00 0.00 3.71
2634 2768 6.099341 CCCACATTTAAAGTTACTTGATGGC 58.901 40.000 15.61 0.00 0.00 4.40
2860 2996 4.587306 GATGCAATACAACATGTGTACGG 58.413 43.478 0.00 2.21 45.51 4.02
2861 2997 4.263016 CGATGCAATACAACATGTGTACG 58.737 43.478 0.00 1.50 45.51 3.67
2941 3077 9.766277 GTCATTGTTGCAAAAGTAAATTCAAAA 57.234 25.926 0.00 0.00 0.00 2.44
3041 3179 5.480642 AGACATGGATGCTATCAGGTAAG 57.519 43.478 0.00 0.00 0.00 2.34
3042 3180 5.130975 ACAAGACATGGATGCTATCAGGTAA 59.869 40.000 0.00 0.00 0.00 2.85
3043 3181 4.655649 ACAAGACATGGATGCTATCAGGTA 59.344 41.667 0.00 0.00 0.00 3.08
3044 3182 3.457380 ACAAGACATGGATGCTATCAGGT 59.543 43.478 0.00 0.00 0.00 4.00
3045 3183 4.082665 ACAAGACATGGATGCTATCAGG 57.917 45.455 0.00 0.00 0.00 3.86
3342 3507 5.916883 CAGATTATTTTGATGGATGGCGTTC 59.083 40.000 0.00 0.00 0.00 3.95
3829 4848 2.564771 CTCGCAAATAATCAGAGCCCA 58.435 47.619 0.00 0.00 0.00 5.36
3947 4967 1.278985 TGAATCAGAATCCCACACGCT 59.721 47.619 0.00 0.00 0.00 5.07
4220 7845 3.435327 TCTGCATTGTATTGTTGTCCGAC 59.565 43.478 0.00 0.00 0.00 4.79
4385 8379 7.004555 TCTGTATAAACCACAACAGTCTGAT 57.995 36.000 6.91 0.00 40.18 2.90
4390 8384 8.458573 TTTCATTCTGTATAAACCACAACAGT 57.541 30.769 0.00 0.00 40.18 3.55
4768 8780 7.070198 TCCATTGCATCCATTTCATCATACTTT 59.930 33.333 0.00 0.00 0.00 2.66
4928 8946 5.698089 TGTATGCAATAGATAGCTCTGCAAC 59.302 40.000 18.27 16.58 42.71 4.17
5263 9282 1.021968 AAACAGGCACTCGTTTGACC 58.978 50.000 0.00 0.00 37.92 4.02
5349 9368 6.817184 ACAACGTCTGCAATACCTAATAGAT 58.183 36.000 0.00 0.00 0.00 1.98
5427 9446 5.407387 CGTTCCCGAATATAAGGTGTATTGG 59.593 44.000 0.00 0.00 35.63 3.16
5445 9464 0.105607 ATCCTACTCCCTCCGTTCCC 60.106 60.000 0.00 0.00 0.00 3.97
5462 9481 5.511234 AATTGATTGCTCAAGGCTACATC 57.489 39.130 0.00 0.00 44.32 3.06
5468 9487 3.916761 TGTGAAATTGATTGCTCAAGGC 58.083 40.909 0.00 0.00 44.32 4.35
5551 9570 6.072199 AGGTATCTCCAAATTTCAGCTCTT 57.928 37.500 0.00 0.00 39.02 2.85
5664 9705 7.342026 TCTCTTGCTACCTACAGTTGATAATGA 59.658 37.037 0.00 0.00 0.00 2.57
5700 9741 5.509498 ACTCCACAATGCTTGTATTATGGT 58.491 37.500 8.22 0.00 43.23 3.55
5722 9763 7.781548 TTATTTGGAGCCTTAACTCGATAAC 57.218 36.000 0.00 0.00 37.57 1.89
5847 9926 3.967332 AATGGCTGATTGTTTCTTGGG 57.033 42.857 0.00 0.00 0.00 4.12
5970 10057 2.094762 AAACCGTCATGTGGTAGCTC 57.905 50.000 11.84 0.00 39.29 4.09
6114 10464 5.253330 TCCCCAAGCTACAAAATCAAGTAG 58.747 41.667 0.00 0.00 40.45 2.57
6192 10542 2.893489 GTTTTGCCCTCAGGAACTCAAT 59.107 45.455 0.00 0.00 34.60 2.57
6271 10623 8.972127 AGCAAGTCTAGAGTACATAGAAATCAA 58.028 33.333 0.00 0.00 31.27 2.57
6449 10803 1.301401 GTGTACCGAGTGGCAAGCA 60.301 57.895 0.00 0.00 39.70 3.91
6668 11029 6.166279 CAAGTATGCTACAGAAAGTTCAGGA 58.834 40.000 0.00 0.00 0.00 3.86
6695 11056 1.358787 AGGACTTTTCCATGCCCATCA 59.641 47.619 0.00 0.00 45.72 3.07
6698 11059 1.133199 ACAAGGACTTTTCCATGCCCA 60.133 47.619 0.00 0.00 43.37 5.36
6735 11096 3.821841 GCACCACTGCACAAAACTATAC 58.178 45.455 0.00 0.00 43.62 1.47
6801 11168 6.279227 TGGTGAACAAAAACAATTTATGCG 57.721 33.333 0.00 0.00 0.00 4.73
6969 11363 7.992754 ATATTCTCCTCCATTCTAAACATGC 57.007 36.000 0.00 0.00 0.00 4.06
7019 11413 1.681793 TCCTCGCGGAGAATTTCCTAG 59.318 52.381 6.13 0.00 44.41 3.02
7319 11731 6.351711 AGGAAACCTAGACAACTAAACGTTT 58.648 36.000 18.90 18.90 28.62 3.60
7321 11733 5.541953 AGGAAACCTAGACAACTAAACGT 57.458 39.130 0.00 0.00 28.47 3.99
7322 11734 5.178809 CCAAGGAAACCTAGACAACTAAACG 59.821 44.000 0.00 0.00 31.13 3.60
7324 11736 6.503560 TCCAAGGAAACCTAGACAACTAAA 57.496 37.500 0.00 0.00 31.13 1.85
7327 11739 5.584551 AATCCAAGGAAACCTAGACAACT 57.415 39.130 0.00 0.00 31.13 3.16
7328 11740 7.610305 TGAATAATCCAAGGAAACCTAGACAAC 59.390 37.037 0.00 0.00 31.13 3.32
7329 11741 7.695055 TGAATAATCCAAGGAAACCTAGACAA 58.305 34.615 0.00 0.00 31.13 3.18
7330 11742 7.265599 TGAATAATCCAAGGAAACCTAGACA 57.734 36.000 0.00 0.00 31.13 3.41
7331 11743 6.261158 GCTGAATAATCCAAGGAAACCTAGAC 59.739 42.308 0.00 0.00 31.13 2.59
7332 11744 6.158695 AGCTGAATAATCCAAGGAAACCTAGA 59.841 38.462 0.00 0.00 31.13 2.43
7333 11745 6.360618 AGCTGAATAATCCAAGGAAACCTAG 58.639 40.000 0.00 0.00 31.13 3.02
7334 11746 6.327386 AGCTGAATAATCCAAGGAAACCTA 57.673 37.500 0.00 0.00 31.13 3.08
7335 11747 5.198602 AGCTGAATAATCCAAGGAAACCT 57.801 39.130 0.00 0.00 33.87 3.50
7352 11764 2.224499 TGTCAATGCTACACCAAGCTGA 60.224 45.455 0.00 0.00 43.19 4.26
7356 11768 5.337554 CATTCATGTCAATGCTACACCAAG 58.662 41.667 0.00 0.00 33.47 3.61
7437 11855 2.787723 GCCGTTCATTCATACAAGCACG 60.788 50.000 0.00 0.00 0.00 5.34
7443 11861 5.847111 ACTAGTAGCCGTTCATTCATACA 57.153 39.130 0.00 0.00 0.00 2.29
7541 11983 7.164122 AGTACACAATATCAGGATAAGCATGG 58.836 38.462 0.00 0.00 0.00 3.66
7615 12232 3.454812 AGAAATACGTACAAGCCTGGGAT 59.545 43.478 0.00 0.00 0.00 3.85
7630 12247 7.861872 GGACTCTCAACGTAATCCTAGAAATAC 59.138 40.741 0.00 0.00 0.00 1.89
7645 12262 5.088739 GCAACAAATATTGGACTCTCAACG 58.911 41.667 0.00 0.00 34.12 4.10
7762 12383 3.896888 ACATGAAACAGGCAGGATTTTGA 59.103 39.130 0.00 0.00 0.00 2.69
7805 12426 1.877617 GCTGAGCTGCGCAGAGTAG 60.878 63.158 40.21 29.92 33.20 2.57
7806 12427 2.182791 GCTGAGCTGCGCAGAGTA 59.817 61.111 40.21 22.37 33.20 2.59
7807 12428 3.646023 GAGCTGAGCTGCGCAGAGT 62.646 63.158 40.21 26.04 39.88 3.24
7808 12429 2.886604 GAGCTGAGCTGCGCAGAG 60.887 66.667 40.21 28.07 39.88 3.35
7809 12430 3.688159 TGAGCTGAGCTGCGCAGA 61.688 61.111 40.21 19.26 39.88 4.26
7814 12435 1.446792 TTACGCTGAGCTGAGCTGC 60.447 57.895 23.02 9.51 39.88 5.25
7833 12464 1.808945 GATCTTGGCAGGTGAACACTG 59.191 52.381 4.96 0.00 38.95 3.66
7901 12532 1.421646 ACAAAGGGGTGAAGTGAGAGG 59.578 52.381 0.00 0.00 0.00 3.69
8061 12694 7.375808 CCGTCGTATTTAATCCATTGACAATTG 59.624 37.037 3.24 3.24 0.00 2.32
8087 12720 3.857665 TCAATCGAACTGCATAGACGTTC 59.142 43.478 5.86 5.86 35.04 3.95
8088 12721 3.845178 TCAATCGAACTGCATAGACGTT 58.155 40.909 0.00 0.00 0.00 3.99
8224 12857 5.888724 TCCGGTTTCAATAAGCATATGGAAA 59.111 36.000 7.30 7.30 38.54 3.13


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

AutoCloner maintained by Alex Coulton.