Multiple sequence alignment - TraesCS1B01G265000

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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 TraesCS1B01G265000 chr1B 100.000 2352 0 0 1828 4179 465935370 465937721 0.000000e+00 4344.0
1 TraesCS1B01G265000 chr1B 100.000 1369 0 0 1 1369 465933543 465934911 0.000000e+00 2529.0
2 TraesCS1B01G265000 chr1B 75.527 1614 321 56 1829 3407 461688852 461690426 0.000000e+00 725.0
3 TraesCS1B01G265000 chr1B 75.280 1606 326 50 1828 3398 462080725 462082294 0.000000e+00 701.0
4 TraesCS1B01G265000 chr1B 75.155 1610 320 53 1829 3407 461796823 461798383 0.000000e+00 684.0
5 TraesCS1B01G265000 chr1B 78.696 690 128 19 1828 2507 462084141 462084821 3.830000e-120 442.0
6 TraesCS1B01G265000 chr1B 78.689 671 103 20 1 638 462381802 462382465 1.080000e-110 411.0
7 TraesCS1B01G265000 chr1B 78.689 671 102 21 1 638 462378399 462379061 3.890000e-110 409.0
8 TraesCS1B01G265000 chr1B 78.241 671 106 20 1 638 462006028 462006691 1.090000e-105 394.0
9 TraesCS1B01G265000 chr1B 78.306 673 102 23 1 638 462094682 462095345 1.090000e-105 394.0
10 TraesCS1B01G265000 chr1B 77.645 671 110 20 1 638 462466303 462466966 5.100000e-99 372.0
11 TraesCS1B01G265000 chr1B 79.085 306 46 9 3106 3397 462436383 462436684 1.190000e-45 195.0
12 TraesCS1B01G265000 chr1B 78.618 304 47 10 3106 3395 461760786 461761085 7.130000e-43 185.0
13 TraesCS1B01G265000 chr1B 78.431 306 48 10 3106 3397 461996707 461997008 2.570000e-42 183.0
14 TraesCS1B01G265000 chr1A 94.986 1416 54 6 1980 3378 444459162 444457747 0.000000e+00 2206.0
15 TraesCS1B01G265000 chr1A 92.369 1389 74 8 1 1369 444460701 444459325 0.000000e+00 1949.0
16 TraesCS1B01G265000 chr1A 87.526 489 43 7 3696 4175 353920234 353919755 2.200000e-152 549.0
17 TraesCS1B01G265000 chr1A 80.412 291 49 7 352 638 370669100 370668814 9.100000e-52 215.0
18 TraesCS1B01G265000 chr1A 93.805 113 7 0 1828 1940 444459268 444459156 2.000000e-38 171.0
19 TraesCS1B01G265000 chr1A 84.302 172 22 4 3539 3708 266883426 266883258 3.340000e-36 163.0
20 TraesCS1B01G265000 chr1D 93.588 1388 68 4 1 1369 344748798 344747413 0.000000e+00 2050.0
21 TraesCS1B01G265000 chr1D 92.291 1388 74 4 1 1369 344708248 344706875 0.000000e+00 1940.0
22 TraesCS1B01G265000 chr1D 93.530 881 40 5 2512 3378 344706092 344705215 0.000000e+00 1295.0
23 TraesCS1B01G265000 chr1D 96.028 705 27 1 1828 2531 344706815 344706111 0.000000e+00 1146.0
24 TraesCS1B01G265000 chr1D 95.745 705 29 1 1828 2531 344747361 344746657 0.000000e+00 1134.0
25 TraesCS1B01G265000 chr1D 77.034 1598 308 45 1828 3397 297735439 297733873 0.000000e+00 863.0
26 TraesCS1B01G265000 chr1D 76.880 1609 308 48 1828 3407 297742285 297740712 0.000000e+00 852.0
27 TraesCS1B01G265000 chr1D 76.769 1597 307 44 1828 3394 297814140 297815702 0.000000e+00 835.0
28 TraesCS1B01G265000 chr1D 91.971 548 29 5 2844 3378 344746366 344745821 0.000000e+00 754.0
29 TraesCS1B01G265000 chr1D 75.590 1610 336 40 1833 3418 297867921 297866345 0.000000e+00 743.0
30 TraesCS1B01G265000 chr1D 76.748 1273 247 31 2144 3399 297709790 297708550 0.000000e+00 665.0
31 TraesCS1B01G265000 chr1D 76.475 1288 250 38 2145 3407 297752445 297751186 0.000000e+00 651.0
32 TraesCS1B01G265000 chr1D 94.834 271 13 1 2512 2781 344746638 344746368 5.000000e-114 422.0
33 TraesCS1B01G265000 chr1D 78.783 674 97 29 3 638 297816185 297816850 1.080000e-110 411.0
34 TraesCS1B01G265000 chr1D 81.164 292 45 8 352 638 297706670 297706384 4.200000e-55 226.0
35 TraesCS1B01G265000 chr1D 92.308 52 3 1 640 690 156930207 156930156 5.800000e-09 73.1
36 TraesCS1B01G265000 chrUn 91.971 548 29 5 2844 3378 375174459 375173914 0.000000e+00 754.0
37 TraesCS1B01G265000 chrUn 91.971 548 29 5 2844 3378 398792753 398793298 0.000000e+00 754.0
38 TraesCS1B01G265000 chrUn 94.307 404 22 1 1828 2230 375175123 375174720 5.940000e-173 617.0
39 TraesCS1B01G265000 chrUn 94.264 401 23 0 969 1369 375175581 375175181 7.680000e-172 614.0
40 TraesCS1B01G265000 chrUn 94.475 362 19 1 1828 2188 477555953 477556314 1.310000e-154 556.0
41 TraesCS1B01G265000 chrUn 94.694 245 11 2 2538 2781 375174704 375174461 3.050000e-101 379.0
42 TraesCS1B01G265000 chrUn 95.021 241 11 1 2542 2781 398792511 398792751 1.100000e-100 377.0
43 TraesCS1B01G265000 chr2D 85.650 662 65 16 3537 4179 74926681 74926031 0.000000e+00 669.0
44 TraesCS1B01G265000 chr2D 83.733 584 57 16 3539 4098 392499119 392499688 6.190000e-143 518.0
45 TraesCS1B01G265000 chr2D 82.759 174 25 5 3539 3708 276908447 276908275 2.600000e-32 150.0
46 TraesCS1B01G265000 chr2D 89.831 59 3 3 640 696 622243398 622243455 5.800000e-09 73.1
47 TraesCS1B01G265000 chr5A 84.558 667 74 11 3539 4179 299569805 299569142 5.890000e-178 634.0
48 TraesCS1B01G265000 chr7D 89.139 488 42 5 3696 4179 113573020 113573500 7.730000e-167 597.0
49 TraesCS1B01G265000 chr7D 83.008 512 56 15 3698 4179 20626260 20626770 6.420000e-118 435.0
50 TraesCS1B01G265000 chr7D 78.893 578 80 25 3539 4086 509244867 509244302 1.850000e-93 353.0
51 TraesCS1B01G265000 chr5D 83.284 682 67 21 3539 4179 543311066 543311741 6.020000e-163 584.0
52 TraesCS1B01G265000 chr5D 79.009 686 89 24 3537 4179 398204327 398203654 6.460000e-113 418.0
53 TraesCS1B01G265000 chr5D 75.934 723 82 41 3537 4179 260676439 260677149 1.900000e-73 287.0
54 TraesCS1B01G265000 chr5D 84.559 272 24 9 3537 3792 286938209 286938478 1.930000e-63 254.0
55 TraesCS1B01G265000 chr5D 81.868 182 25 5 3537 3716 381780039 381780214 3.370000e-31 147.0
56 TraesCS1B01G265000 chr3D 82.413 688 71 24 3536 4179 273486800 273487481 4.720000e-154 555.0
57 TraesCS1B01G265000 chr7B 82.006 678 83 20 3537 4179 720508664 720507991 1.320000e-149 540.0
58 TraesCS1B01G265000 chr7B 83.333 72 8 4 637 707 366355235 366355303 3.490000e-06 63.9
59 TraesCS1B01G265000 chr6D 82.006 678 81 26 3537 4179 444705859 444705188 4.750000e-149 538.0
60 TraesCS1B01G265000 chr2A 81.711 678 81 28 3539 4176 460226542 460227216 3.700000e-145 525.0
61 TraesCS1B01G265000 chr2A 94.231 52 2 1 640 690 87731410 87731359 1.250000e-10 78.7
62 TraesCS1B01G265000 chr4D 79.612 618 67 26 3537 4099 19205468 19204855 5.070000e-104 388.0
63 TraesCS1B01G265000 chr6B 81.061 396 31 24 3568 3932 641448037 641447655 4.120000e-70 276.0


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 TraesCS1B01G265000 chr1B 465933543 465937721 4178 False 3436.500000 4344 100.000000 1 4179 2 chr1B.!!$F11 4178
1 TraesCS1B01G265000 chr1B 461688852 461690426 1574 False 725.000000 725 75.527000 1829 3407 1 chr1B.!!$F1 1578
2 TraesCS1B01G265000 chr1B 461796823 461798383 1560 False 684.000000 684 75.155000 1829 3407 1 chr1B.!!$F3 1578
3 TraesCS1B01G265000 chr1B 462080725 462084821 4096 False 571.500000 701 76.988000 1828 3398 2 chr1B.!!$F9 1570
4 TraesCS1B01G265000 chr1B 462378399 462382465 4066 False 410.000000 411 78.689000 1 638 2 chr1B.!!$F10 637
5 TraesCS1B01G265000 chr1B 462006028 462006691 663 False 394.000000 394 78.241000 1 638 1 chr1B.!!$F5 637
6 TraesCS1B01G265000 chr1B 462094682 462095345 663 False 394.000000 394 78.306000 1 638 1 chr1B.!!$F6 637
7 TraesCS1B01G265000 chr1B 462466303 462466966 663 False 372.000000 372 77.645000 1 638 1 chr1B.!!$F8 637
8 TraesCS1B01G265000 chr1A 444457747 444460701 2954 True 1442.000000 2206 93.720000 1 3378 3 chr1A.!!$R4 3377
9 TraesCS1B01G265000 chr1D 344705215 344708248 3033 True 1460.333333 1940 93.949667 1 3378 3 chr1D.!!$R7 3377
10 TraesCS1B01G265000 chr1D 344745821 344748798 2977 True 1090.000000 2050 94.034500 1 3378 4 chr1D.!!$R8 3377
11 TraesCS1B01G265000 chr1D 297733873 297735439 1566 True 863.000000 863 77.034000 1828 3397 1 chr1D.!!$R2 1569
12 TraesCS1B01G265000 chr1D 297740712 297742285 1573 True 852.000000 852 76.880000 1828 3407 1 chr1D.!!$R3 1579
13 TraesCS1B01G265000 chr1D 297866345 297867921 1576 True 743.000000 743 75.590000 1833 3418 1 chr1D.!!$R5 1585
14 TraesCS1B01G265000 chr1D 297751186 297752445 1259 True 651.000000 651 76.475000 2145 3407 1 chr1D.!!$R4 1262
15 TraesCS1B01G265000 chr1D 297814140 297816850 2710 False 623.000000 835 77.776000 3 3394 2 chr1D.!!$F1 3391
16 TraesCS1B01G265000 chr1D 297706384 297709790 3406 True 445.500000 665 78.956000 352 3399 2 chr1D.!!$R6 3047
17 TraesCS1B01G265000 chrUn 375173914 375175581 1667 True 591.000000 754 93.809000 969 3378 4 chrUn.!!$R1 2409
18 TraesCS1B01G265000 chrUn 398792511 398793298 787 False 565.500000 754 93.496000 2542 3378 2 chrUn.!!$F2 836
19 TraesCS1B01G265000 chr2D 74926031 74926681 650 True 669.000000 669 85.650000 3537 4179 1 chr2D.!!$R1 642
20 TraesCS1B01G265000 chr2D 392499119 392499688 569 False 518.000000 518 83.733000 3539 4098 1 chr2D.!!$F1 559
21 TraesCS1B01G265000 chr5A 299569142 299569805 663 True 634.000000 634 84.558000 3539 4179 1 chr5A.!!$R1 640
22 TraesCS1B01G265000 chr7D 20626260 20626770 510 False 435.000000 435 83.008000 3698 4179 1 chr7D.!!$F1 481
23 TraesCS1B01G265000 chr7D 509244302 509244867 565 True 353.000000 353 78.893000 3539 4086 1 chr7D.!!$R1 547
24 TraesCS1B01G265000 chr5D 543311066 543311741 675 False 584.000000 584 83.284000 3539 4179 1 chr5D.!!$F4 640
25 TraesCS1B01G265000 chr5D 398203654 398204327 673 True 418.000000 418 79.009000 3537 4179 1 chr5D.!!$R1 642
26 TraesCS1B01G265000 chr5D 260676439 260677149 710 False 287.000000 287 75.934000 3537 4179 1 chr5D.!!$F1 642
27 TraesCS1B01G265000 chr3D 273486800 273487481 681 False 555.000000 555 82.413000 3536 4179 1 chr3D.!!$F1 643
28 TraesCS1B01G265000 chr7B 720507991 720508664 673 True 540.000000 540 82.006000 3537 4179 1 chr7B.!!$R1 642
29 TraesCS1B01G265000 chr6D 444705188 444705859 671 True 538.000000 538 82.006000 3537 4179 1 chr6D.!!$R1 642
30 TraesCS1B01G265000 chr2A 460226542 460227216 674 False 525.000000 525 81.711000 3539 4176 1 chr2A.!!$F1 637
31 TraesCS1B01G265000 chr4D 19204855 19205468 613 True 388.000000 388 79.612000 3537 4099 1 chr4D.!!$R1 562

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
942 1016 1.442769 GCTTCGAGTTGAATCTGGCA 58.557 50.0 0.0 0.0 35.63 4.92 F
1948 2075 0.182537 TGTGGTTGTGACCTCCTTGG 59.817 55.0 0.0 0.0 46.66 3.61 F
1971 2098 0.034670 GCTCATGGGCTCTGGTTCTT 60.035 55.0 11.3 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2079 0.034670 AAGAACCAGAGCCCATGAGC 60.035 55.0 0.00 0.0 0.0 4.26 R
3131 3315 0.036875 AACTTTTCCCTCTCGGCCTG 59.963 55.0 0.00 0.0 0.0 4.85 R
3435 3650 0.039074 CCATCATAGTCGCGGACTCC 60.039 60.0 6.13 0.0 42.4 3.85 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
94 96 9.973450 ACAATTATTACTTGTGTATGTTTGCAA 57.027 25.926 0.00 0.00 35.57 4.08
106 108 8.554528 TGTGTATGTTTGCAAAACCAATAAATG 58.445 29.630 14.67 0.00 0.00 2.32
418 448 5.558818 GATGGCTGATGAGATAATTCCACT 58.441 41.667 0.00 0.00 0.00 4.00
420 450 5.858381 TGGCTGATGAGATAATTCCACTAC 58.142 41.667 0.00 0.00 0.00 2.73
435 465 3.119388 TCCACTACTCGGTTATGGTTTCG 60.119 47.826 0.00 0.00 0.00 3.46
465 495 8.792830 TCTTTTCAGTTTCTTCTTCTTCTTCA 57.207 30.769 0.00 0.00 0.00 3.02
592 625 3.554324 TGCGACTAACTTTGTTGACAGAC 59.446 43.478 0.00 0.00 0.00 3.51
608 641 4.876107 TGACAGACTTTTTGAGTTCAGACC 59.124 41.667 0.00 0.00 39.19 3.85
610 643 4.878397 ACAGACTTTTTGAGTTCAGACCAG 59.122 41.667 0.00 0.00 39.19 4.00
788 821 6.901081 AATAGAAAGACAAAGAAGGGTTGG 57.099 37.500 0.00 0.00 0.00 3.77
817 850 4.099419 GCCAAGAAGGGAAGAAAAGAAACA 59.901 41.667 0.00 0.00 38.09 2.83
818 851 5.395214 GCCAAGAAGGGAAGAAAAGAAACAA 60.395 40.000 0.00 0.00 38.09 2.83
819 852 6.042777 CCAAGAAGGGAAGAAAAGAAACAAC 58.957 40.000 0.00 0.00 0.00 3.32
820 853 6.127338 CCAAGAAGGGAAGAAAAGAAACAACT 60.127 38.462 0.00 0.00 0.00 3.16
942 1016 1.442769 GCTTCGAGTTGAATCTGGCA 58.557 50.000 0.00 0.00 35.63 4.92
1075 1149 3.126858 TCGTGGTGATATTTTTGCTGCTC 59.873 43.478 0.00 0.00 0.00 4.26
1188 1262 2.506472 GGTGGAGAGGATTCGGCC 59.494 66.667 0.00 0.00 0.00 6.13
1262 1336 2.387757 GCTCATCTCCTCCTCAACTCT 58.612 52.381 0.00 0.00 0.00 3.24
1299 1377 0.895100 TCTGCTTTGCGGCCTTGATT 60.895 50.000 0.00 0.00 34.49 2.57
1322 1400 1.069935 GATCTGGTTCTAGCGGGGC 59.930 63.158 0.00 0.00 0.00 5.80
1324 1402 3.399181 CTGGTTCTAGCGGGGCCA 61.399 66.667 4.39 0.00 0.00 5.36
1935 2062 1.227853 GAGACGGCACCTTGTGGTT 60.228 57.895 0.00 0.00 46.05 3.67
1937 2064 1.822186 GACGGCACCTTGTGGTTGT 60.822 57.895 0.00 0.00 46.05 3.32
1938 2065 2.058829 GACGGCACCTTGTGGTTGTG 62.059 60.000 0.00 0.00 46.05 3.33
1939 2066 1.821759 CGGCACCTTGTGGTTGTGA 60.822 57.895 0.00 0.00 46.05 3.58
1940 2067 1.733526 GGCACCTTGTGGTTGTGAC 59.266 57.895 0.00 0.00 46.05 3.67
1941 2068 1.733526 GCACCTTGTGGTTGTGACC 59.266 57.895 0.00 0.00 46.05 4.02
1942 2069 0.751643 GCACCTTGTGGTTGTGACCT 60.752 55.000 0.00 0.00 46.05 3.85
1943 2070 1.308998 CACCTTGTGGTTGTGACCTC 58.691 55.000 0.00 0.00 46.05 3.85
1944 2071 0.182775 ACCTTGTGGTTGTGACCTCC 59.817 55.000 0.00 0.00 46.05 4.30
1945 2072 0.474184 CCTTGTGGTTGTGACCTCCT 59.526 55.000 0.00 0.00 46.66 3.69
1946 2073 1.133792 CCTTGTGGTTGTGACCTCCTT 60.134 52.381 0.00 0.00 46.66 3.36
1947 2074 1.949525 CTTGTGGTTGTGACCTCCTTG 59.050 52.381 0.00 0.00 46.66 3.61
1948 2075 0.182537 TGTGGTTGTGACCTCCTTGG 59.817 55.000 0.00 0.00 46.66 3.61
1949 2076 0.472471 GTGGTTGTGACCTCCTTGGA 59.528 55.000 0.00 0.00 46.66 3.53
1950 2077 0.472471 TGGTTGTGACCTCCTTGGAC 59.528 55.000 0.00 0.00 46.66 4.02
1951 2078 0.765510 GGTTGTGACCTCCTTGGACT 59.234 55.000 0.00 0.00 42.99 3.85
1952 2079 1.543429 GGTTGTGACCTCCTTGGACTG 60.543 57.143 0.00 0.00 42.99 3.51
1953 2080 0.108585 TTGTGACCTCCTTGGACTGC 59.891 55.000 0.00 0.00 39.71 4.40
1954 2081 0.764369 TGTGACCTCCTTGGACTGCT 60.764 55.000 0.00 0.00 39.71 4.24
1955 2082 0.036858 GTGACCTCCTTGGACTGCTC 60.037 60.000 0.00 0.00 39.71 4.26
1956 2083 0.471780 TGACCTCCTTGGACTGCTCA 60.472 55.000 0.00 0.00 39.71 4.26
1957 2084 0.908198 GACCTCCTTGGACTGCTCAT 59.092 55.000 0.00 0.00 39.71 2.90
1958 2085 0.617413 ACCTCCTTGGACTGCTCATG 59.383 55.000 0.00 0.00 39.71 3.07
1959 2086 0.107312 CCTCCTTGGACTGCTCATGG 60.107 60.000 0.00 0.00 38.35 3.66
1960 2087 0.107312 CTCCTTGGACTGCTCATGGG 60.107 60.000 0.00 0.00 32.33 4.00
1961 2088 1.751927 CCTTGGACTGCTCATGGGC 60.752 63.158 11.75 11.75 0.00 5.36
1962 2089 1.302285 CTTGGACTGCTCATGGGCT 59.698 57.895 20.42 0.00 0.00 5.19
1963 2090 0.747283 CTTGGACTGCTCATGGGCTC 60.747 60.000 20.42 8.83 0.00 4.70
1964 2091 1.203441 TTGGACTGCTCATGGGCTCT 61.203 55.000 20.42 2.76 0.00 4.09
1965 2092 1.153208 GGACTGCTCATGGGCTCTG 60.153 63.158 20.42 11.40 0.00 3.35
1966 2093 1.153208 GACTGCTCATGGGCTCTGG 60.153 63.158 20.42 8.82 0.00 3.86
1967 2094 1.908340 GACTGCTCATGGGCTCTGGT 61.908 60.000 20.42 12.01 0.00 4.00
1968 2095 1.302285 CTGCTCATGGGCTCTGGTT 59.698 57.895 20.42 0.00 0.00 3.67
1969 2096 0.747283 CTGCTCATGGGCTCTGGTTC 60.747 60.000 20.42 0.00 0.00 3.62
1970 2097 1.203441 TGCTCATGGGCTCTGGTTCT 61.203 55.000 20.42 0.00 0.00 3.01
1971 2098 0.034670 GCTCATGGGCTCTGGTTCTT 60.035 55.000 11.30 0.00 0.00 2.52
1972 2099 1.615384 GCTCATGGGCTCTGGTTCTTT 60.615 52.381 11.30 0.00 0.00 2.52
1973 2100 2.089980 CTCATGGGCTCTGGTTCTTTG 58.910 52.381 0.00 0.00 0.00 2.77
1974 2101 1.180029 CATGGGCTCTGGTTCTTTGG 58.820 55.000 0.00 0.00 0.00 3.28
1975 2102 0.040204 ATGGGCTCTGGTTCTTTGGG 59.960 55.000 0.00 0.00 0.00 4.12
1976 2103 1.065410 TGGGCTCTGGTTCTTTGGGA 61.065 55.000 0.00 0.00 0.00 4.37
1977 2104 0.322906 GGGCTCTGGTTCTTTGGGAG 60.323 60.000 0.00 0.00 0.00 4.30
1978 2105 0.693049 GGCTCTGGTTCTTTGGGAGA 59.307 55.000 0.00 0.00 0.00 3.71
1979 2106 1.339535 GGCTCTGGTTCTTTGGGAGAG 60.340 57.143 0.00 0.00 35.37 3.20
1980 2107 1.349357 GCTCTGGTTCTTTGGGAGAGT 59.651 52.381 0.00 0.00 35.37 3.24
2014 2141 2.435059 GGTGCTCCTCGGTTCTGC 60.435 66.667 0.00 0.00 0.00 4.26
2048 2175 3.960102 AGTTTTTCTGTGGAGATTGGCAA 59.040 39.130 0.68 0.68 0.00 4.52
2108 2235 1.029681 GGTGGAAAGGTGTGTGGTTC 58.970 55.000 0.00 0.00 0.00 3.62
3103 3287 2.936498 CAAGATTGTTCCGGCGACTATT 59.064 45.455 9.30 0.00 0.00 1.73
3131 3315 0.181350 CTCACTATGGAGGGTTGCCC 59.819 60.000 0.00 0.00 45.90 5.36
3184 3372 5.449588 GGACGTGTTCGGATTCTGATTACTA 60.450 44.000 0.00 0.00 41.85 1.82
3226 3432 6.267928 AGCAACTAGGTACTATGGAAGTATGG 59.732 42.308 0.00 0.00 42.63 2.74
3313 3522 3.626028 ATCCTCGTTTGTTTTGAGTGC 57.374 42.857 0.00 0.00 0.00 4.40
3407 3622 5.047188 GCTTAGGAGCTCACTTGTATCTTC 58.953 45.833 17.19 0.00 45.65 2.87
3412 3627 5.721960 AGGAGCTCACTTGTATCTTCCTAAA 59.278 40.000 17.19 0.00 0.00 1.85
3413 3628 5.813157 GGAGCTCACTTGTATCTTCCTAAAC 59.187 44.000 17.19 0.00 0.00 2.01
3414 3629 5.411781 AGCTCACTTGTATCTTCCTAAACG 58.588 41.667 0.00 0.00 0.00 3.60
3415 3630 5.185249 AGCTCACTTGTATCTTCCTAAACGA 59.815 40.000 0.00 0.00 0.00 3.85
3420 3635 7.386848 TCACTTGTATCTTCCTAAACGAAAAGG 59.613 37.037 0.00 0.00 0.00 3.11
3422 3637 7.172703 ACTTGTATCTTCCTAAACGAAAAGGTG 59.827 37.037 0.00 0.00 34.30 4.00
3427 3642 6.761312 TCTTCCTAAACGAAAAGGTGTGATA 58.239 36.000 0.00 0.00 34.30 2.15
3428 3643 6.872020 TCTTCCTAAACGAAAAGGTGTGATAG 59.128 38.462 0.00 0.00 34.30 2.08
3429 3644 4.933400 TCCTAAACGAAAAGGTGTGATAGC 59.067 41.667 0.00 0.00 34.30 2.97
3430 3645 4.693566 CCTAAACGAAAAGGTGTGATAGCA 59.306 41.667 0.00 0.00 0.00 3.49
3431 3646 4.483476 AAACGAAAAGGTGTGATAGCAC 57.517 40.909 3.61 3.61 45.35 4.40
3437 3652 3.305314 GTGTGATAGCACCCCGGA 58.695 61.111 8.95 0.00 44.51 5.14
3438 3653 1.144057 GTGTGATAGCACCCCGGAG 59.856 63.158 8.95 0.00 44.51 4.63
3440 3655 1.327690 TGTGATAGCACCCCGGAGTC 61.328 60.000 8.95 0.00 44.51 3.36
3441 3656 1.760875 TGATAGCACCCCGGAGTCC 60.761 63.158 0.73 0.00 0.00 3.85
3450 3665 2.331805 CCGGAGTCCGCGACTATG 59.668 66.667 26.60 6.70 46.86 2.23
3453 3668 0.386100 CGGAGTCCGCGACTATGATG 60.386 60.000 20.50 0.00 43.53 3.07
3454 3669 0.039074 GGAGTCCGCGACTATGATGG 60.039 60.000 8.23 0.00 43.53 3.51
3455 3670 0.664767 GAGTCCGCGACTATGATGGC 60.665 60.000 8.23 0.00 43.53 4.40
3456 3671 1.067416 GTCCGCGACTATGATGGCA 59.933 57.895 8.23 0.00 0.00 4.92
3458 3673 1.067846 GTCCGCGACTATGATGGCATA 60.068 52.381 8.23 0.00 35.94 3.14
3459 3674 1.824852 TCCGCGACTATGATGGCATAT 59.175 47.619 8.23 0.00 36.45 1.78
3460 3675 3.020984 TCCGCGACTATGATGGCATATA 58.979 45.455 8.23 0.00 36.45 0.86
3461 3676 3.066760 TCCGCGACTATGATGGCATATAG 59.933 47.826 8.23 10.51 36.45 1.31
3462 3677 3.066760 CCGCGACTATGATGGCATATAGA 59.933 47.826 20.84 5.17 36.45 1.98
3464 3679 5.048713 CCGCGACTATGATGGCATATAGATA 60.049 44.000 20.84 8.45 36.45 1.98
3467 3682 7.114106 CGCGACTATGATGGCATATAGATAAAG 59.886 40.741 20.84 7.36 36.45 1.85
3468 3683 8.138074 GCGACTATGATGGCATATAGATAAAGA 58.862 37.037 20.84 0.00 36.45 2.52
3471 3686 9.775854 ACTATGATGGCATATAGATAAAGATGC 57.224 33.333 20.84 0.00 43.19 3.91
3480 3695 9.189156 GCATATAGATAAAGATGCCCCATAAAA 57.811 33.333 0.00 0.00 39.00 1.52
3503 3718 5.499004 AAAAGTAGGTTGAGCCATCTACA 57.501 39.130 0.00 0.00 40.61 2.74
3505 3720 5.700402 AAGTAGGTTGAGCCATCTACATT 57.300 39.130 0.00 0.00 40.61 2.71
3506 3721 5.028549 AGTAGGTTGAGCCATCTACATTG 57.971 43.478 0.00 0.00 40.61 2.82
3507 3722 4.716784 AGTAGGTTGAGCCATCTACATTGA 59.283 41.667 0.00 0.00 40.61 2.57
3509 3724 5.121380 AGGTTGAGCCATCTACATTGATT 57.879 39.130 0.00 0.00 40.61 2.57
3511 3726 5.954150 AGGTTGAGCCATCTACATTGATTTT 59.046 36.000 0.00 0.00 40.61 1.82
3512 3727 6.438425 AGGTTGAGCCATCTACATTGATTTTT 59.562 34.615 0.00 0.00 40.61 1.94
3533 3748 4.468095 TTTTCTTCTCAACGCAAGCTAC 57.532 40.909 0.00 0.00 45.62 3.58
3534 3749 2.080286 TCTTCTCAACGCAAGCTACC 57.920 50.000 0.00 0.00 45.62 3.18
3585 3801 2.396157 GGGCTCGAAAAATCGCCGT 61.396 57.895 5.17 0.00 43.38 5.68
3591 3807 1.017177 CGAAAAATCGCCGTCTGGGA 61.017 55.000 0.00 0.00 40.60 4.37
3706 4029 4.002906 AGACATTCAGTAAACTTCGGCA 57.997 40.909 0.00 0.00 0.00 5.69
3958 6393 1.757405 GCAGTGATCTCCTCTAGGGCT 60.757 57.143 0.00 0.00 35.41 5.19
3964 6693 0.560193 TCTCCTCTAGGGCTCAGCAT 59.440 55.000 0.00 0.00 35.41 3.79
4111 6900 1.587054 CTCTTCGGCTTGACGAGGT 59.413 57.895 7.82 0.00 44.47 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 96 4.906747 ACATGGCCACATTTATTGGTTT 57.093 36.364 8.16 0.00 36.40 3.27
106 108 5.423610 AGAGATATGACCTATACATGGCCAC 59.576 44.000 8.16 0.00 0.00 5.01
175 177 7.481642 TGAGACGATTGAGTAGTAGGAAAATC 58.518 38.462 0.00 0.00 0.00 2.17
394 424 4.391216 GTGGAATTATCTCATCAGCCATCG 59.609 45.833 0.00 0.00 0.00 3.84
418 448 2.231964 AGCACGAAACCATAACCGAGTA 59.768 45.455 0.00 0.00 0.00 2.59
420 450 1.722011 AGCACGAAACCATAACCGAG 58.278 50.000 0.00 0.00 0.00 4.63
435 465 6.790282 AGAAGAAGAAACTGAAAAGAAGCAC 58.210 36.000 0.00 0.00 0.00 4.40
592 625 6.284459 AGTAGTCTGGTCTGAACTCAAAAAG 58.716 40.000 0.00 0.00 0.00 2.27
608 641 3.868077 GCAATCCACTAGCAAGTAGTCTG 59.132 47.826 0.00 0.00 40.27 3.51
610 643 3.118592 AGGCAATCCACTAGCAAGTAGTC 60.119 47.826 0.00 0.00 40.27 2.59
645 678 9.334947 GGATTTTTACCCTACTGTTTATAGTCC 57.665 37.037 0.00 0.00 32.19 3.85
669 702 9.643735 TTTTAGTTTATAAAAGTTGGAGTGGGA 57.356 29.630 0.00 0.00 0.00 4.37
767 800 4.414182 TCCCAACCCTTCTTTGTCTTTCTA 59.586 41.667 0.00 0.00 0.00 2.10
775 808 2.760650 GGCTTATCCCAACCCTTCTTTG 59.239 50.000 0.00 0.00 0.00 2.77
788 821 3.933861 TCTTCCCTTCTTGGCTTATCC 57.066 47.619 0.00 0.00 0.00 2.59
856 893 8.748412 TGGCTGCTTTGTTTTATGTAATCTATT 58.252 29.630 0.00 0.00 0.00 1.73
872 909 1.102809 TGTGAGGTGTGGCTGCTTTG 61.103 55.000 0.00 0.00 0.00 2.77
942 1016 0.544595 ACCCTAGTCGCCCTTGAGTT 60.545 55.000 0.00 0.00 0.00 3.01
987 1061 2.801631 CGACATGGGAGGGAGAGGC 61.802 68.421 0.00 0.00 0.00 4.70
1062 1136 1.816224 GGGAACGGAGCAGCAAAAATA 59.184 47.619 0.00 0.00 0.00 1.40
1262 1336 0.544120 GACAAGGCCAATGGGGGAAA 60.544 55.000 5.01 0.00 37.04 3.13
1299 1377 1.207089 CCGCTAGAACCAGATCCAACA 59.793 52.381 0.00 0.00 0.00 3.33
1322 1400 1.330655 ATCGAGCCTACACCACCTGG 61.331 60.000 0.00 0.00 42.17 4.45
1324 1402 0.824759 GAATCGAGCCTACACCACCT 59.175 55.000 0.00 0.00 0.00 4.00
1935 2062 0.764369 AGCAGTCCAAGGAGGTCACA 60.764 55.000 0.00 0.00 39.02 3.58
1937 2064 0.471780 TGAGCAGTCCAAGGAGGTCA 60.472 55.000 6.25 6.25 39.02 4.02
1938 2065 0.908198 ATGAGCAGTCCAAGGAGGTC 59.092 55.000 0.00 0.00 39.02 3.85
1939 2066 0.617413 CATGAGCAGTCCAAGGAGGT 59.383 55.000 0.00 0.00 39.02 3.85
1940 2067 0.107312 CCATGAGCAGTCCAAGGAGG 60.107 60.000 0.00 0.00 39.47 4.30
1941 2068 0.107312 CCCATGAGCAGTCCAAGGAG 60.107 60.000 0.00 0.00 0.00 3.69
1942 2069 1.993653 CCCATGAGCAGTCCAAGGA 59.006 57.895 0.00 0.00 0.00 3.36
1943 2070 1.751927 GCCCATGAGCAGTCCAAGG 60.752 63.158 0.00 0.00 0.00 3.61
1944 2071 0.747283 GAGCCCATGAGCAGTCCAAG 60.747 60.000 0.76 0.00 34.23 3.61
1945 2072 1.203441 AGAGCCCATGAGCAGTCCAA 61.203 55.000 0.76 0.00 34.23 3.53
1946 2073 1.614525 AGAGCCCATGAGCAGTCCA 60.615 57.895 0.76 0.00 34.23 4.02
1947 2074 1.153208 CAGAGCCCATGAGCAGTCC 60.153 63.158 0.76 0.00 34.23 3.85
1948 2075 1.153208 CCAGAGCCCATGAGCAGTC 60.153 63.158 0.76 0.00 34.23 3.51
1949 2076 1.495579 AACCAGAGCCCATGAGCAGT 61.496 55.000 0.76 0.00 34.23 4.40
1950 2077 0.747283 GAACCAGAGCCCATGAGCAG 60.747 60.000 0.76 0.00 34.23 4.24
1951 2078 1.203441 AGAACCAGAGCCCATGAGCA 61.203 55.000 0.76 0.00 34.23 4.26
1952 2079 0.034670 AAGAACCAGAGCCCATGAGC 60.035 55.000 0.00 0.00 0.00 4.26
1953 2080 2.089980 CAAAGAACCAGAGCCCATGAG 58.910 52.381 0.00 0.00 0.00 2.90
1954 2081 1.272092 CCAAAGAACCAGAGCCCATGA 60.272 52.381 0.00 0.00 0.00 3.07
1955 2082 1.180029 CCAAAGAACCAGAGCCCATG 58.820 55.000 0.00 0.00 0.00 3.66
1956 2083 0.040204 CCCAAAGAACCAGAGCCCAT 59.960 55.000 0.00 0.00 0.00 4.00
1957 2084 1.065410 TCCCAAAGAACCAGAGCCCA 61.065 55.000 0.00 0.00 0.00 5.36
1958 2085 0.322906 CTCCCAAAGAACCAGAGCCC 60.323 60.000 0.00 0.00 0.00 5.19
1959 2086 0.693049 TCTCCCAAAGAACCAGAGCC 59.307 55.000 0.00 0.00 0.00 4.70
1960 2087 1.349357 ACTCTCCCAAAGAACCAGAGC 59.651 52.381 0.00 0.00 35.01 4.09
1961 2088 3.181450 ACAACTCTCCCAAAGAACCAGAG 60.181 47.826 0.00 0.00 37.27 3.35
1962 2089 2.777692 ACAACTCTCCCAAAGAACCAGA 59.222 45.455 0.00 0.00 32.23 3.86
1963 2090 2.880890 CACAACTCTCCCAAAGAACCAG 59.119 50.000 0.00 0.00 32.23 4.00
1964 2091 2.507886 TCACAACTCTCCCAAAGAACCA 59.492 45.455 0.00 0.00 32.23 3.67
1965 2092 3.208747 TCACAACTCTCCCAAAGAACC 57.791 47.619 0.00 0.00 32.23 3.62
1966 2093 4.023707 CACATCACAACTCTCCCAAAGAAC 60.024 45.833 0.00 0.00 32.23 3.01
1967 2094 4.136796 CACATCACAACTCTCCCAAAGAA 58.863 43.478 0.00 0.00 32.23 2.52
1968 2095 3.496692 CCACATCACAACTCTCCCAAAGA 60.497 47.826 0.00 0.00 0.00 2.52
1969 2096 2.816087 CCACATCACAACTCTCCCAAAG 59.184 50.000 0.00 0.00 0.00 2.77
1970 2097 2.174639 ACCACATCACAACTCTCCCAAA 59.825 45.455 0.00 0.00 0.00 3.28
1971 2098 1.774254 ACCACATCACAACTCTCCCAA 59.226 47.619 0.00 0.00 0.00 4.12
1972 2099 1.434188 ACCACATCACAACTCTCCCA 58.566 50.000 0.00 0.00 0.00 4.37
1973 2100 2.154462 CAACCACATCACAACTCTCCC 58.846 52.381 0.00 0.00 0.00 4.30
1974 2101 2.154462 CCAACCACATCACAACTCTCC 58.846 52.381 0.00 0.00 0.00 3.71
1975 2102 2.549754 CACCAACCACATCACAACTCTC 59.450 50.000 0.00 0.00 0.00 3.20
1976 2103 2.575532 CACCAACCACATCACAACTCT 58.424 47.619 0.00 0.00 0.00 3.24
1977 2104 1.608590 CCACCAACCACATCACAACTC 59.391 52.381 0.00 0.00 0.00 3.01
1978 2105 1.691196 CCACCAACCACATCACAACT 58.309 50.000 0.00 0.00 0.00 3.16
1979 2106 0.673437 CCCACCAACCACATCACAAC 59.327 55.000 0.00 0.00 0.00 3.32
1980 2107 0.260230 ACCCACCAACCACATCACAA 59.740 50.000 0.00 0.00 0.00 3.33
2014 2141 6.311935 TCCACAGAAAAACTAATATTCGGACG 59.688 38.462 0.00 0.00 0.00 4.79
2022 2149 6.945435 TGCCAATCTCCACAGAAAAACTAATA 59.055 34.615 0.00 0.00 30.24 0.98
2048 2175 1.098050 GAATCGGCACTTGCTGGAAT 58.902 50.000 10.15 0.00 46.99 3.01
2135 2262 1.369321 CTATCCCCTTCTGCCTCGC 59.631 63.158 0.00 0.00 0.00 5.03
2598 2773 4.780815 TGGTTGTATCAGGCAAGATAAGG 58.219 43.478 1.88 0.00 32.64 2.69
2599 2774 5.882557 AGTTGGTTGTATCAGGCAAGATAAG 59.117 40.000 1.88 0.00 32.64 1.73
2602 2778 4.307032 AGTTGGTTGTATCAGGCAAGAT 57.693 40.909 0.00 0.00 0.00 2.40
2918 3102 2.117156 GCATGATCACCAGCCGCTT 61.117 57.895 0.00 0.00 0.00 4.68
3103 3287 2.424091 CCTCCATAGTGAGCTCTCTCCA 60.424 54.545 21.00 6.17 38.58 3.86
3131 3315 0.036875 AACTTTTCCCTCTCGGCCTG 59.963 55.000 0.00 0.00 0.00 4.85
3184 3372 1.797211 GCTGCCGCTCGGATAGTAGT 61.797 60.000 13.11 0.00 37.50 2.73
3226 3432 4.507710 TGACACAGAGGCATCATAAAGTC 58.492 43.478 0.00 2.07 0.00 3.01
3313 3522 6.986817 AGAACATGAGAGTGATTAATAACCCG 59.013 38.462 0.00 0.00 0.00 5.28
3399 3614 6.425721 CACACCTTTTCGTTTAGGAAGATACA 59.574 38.462 0.00 0.00 35.45 2.29
3401 3616 6.761312 TCACACCTTTTCGTTTAGGAAGATA 58.239 36.000 0.00 0.00 35.45 1.98
3407 3622 4.693566 TGCTATCACACCTTTTCGTTTAGG 59.306 41.667 0.00 0.00 37.56 2.69
3420 3635 1.144057 CTCCGGGGTGCTATCACAC 59.856 63.158 0.00 0.00 45.77 3.82
3422 3637 1.442148 GACTCCGGGGTGCTATCAC 59.558 63.158 14.62 0.00 42.40 3.06
3435 3650 0.039074 CCATCATAGTCGCGGACTCC 60.039 60.000 6.13 0.00 42.40 3.85
3436 3651 0.664767 GCCATCATAGTCGCGGACTC 60.665 60.000 6.13 0.00 42.40 3.36
3437 3652 1.364171 GCCATCATAGTCGCGGACT 59.636 57.895 6.13 11.31 45.54 3.85
3438 3653 0.319900 ATGCCATCATAGTCGCGGAC 60.320 55.000 6.13 3.09 0.00 4.79
3440 3655 2.299993 ATATGCCATCATAGTCGCGG 57.700 50.000 6.13 0.00 38.46 6.46
3441 3656 4.292977 TCTATATGCCATCATAGTCGCG 57.707 45.455 0.00 0.00 38.46 5.87
3442 3657 8.138074 TCTTTATCTATATGCCATCATAGTCGC 58.862 37.037 0.00 0.00 38.46 5.19
3445 3660 9.775854 GCATCTTTATCTATATGCCATCATAGT 57.224 33.333 0.00 0.00 38.46 2.12
3454 3669 8.752005 TTTATGGGGCATCTTTATCTATATGC 57.248 34.615 0.00 0.00 43.13 3.14
3480 3695 5.876357 TGTAGATGGCTCAACCTACTTTTT 58.124 37.500 0.00 0.00 40.22 1.94
3481 3696 5.499004 TGTAGATGGCTCAACCTACTTTT 57.501 39.130 0.00 0.00 40.22 2.27
3482 3697 5.700402 ATGTAGATGGCTCAACCTACTTT 57.300 39.130 0.00 0.00 40.22 2.66
3484 3699 4.716784 TCAATGTAGATGGCTCAACCTACT 59.283 41.667 0.00 0.00 40.22 2.57
3485 3700 5.023533 TCAATGTAGATGGCTCAACCTAC 57.976 43.478 0.00 0.00 40.22 3.18
3486 3701 5.894298 ATCAATGTAGATGGCTCAACCTA 57.106 39.130 0.00 0.00 40.22 3.08
3487 3702 4.785346 ATCAATGTAGATGGCTCAACCT 57.215 40.909 0.00 0.00 40.22 3.50
3488 3703 5.841957 AAATCAATGTAGATGGCTCAACC 57.158 39.130 0.00 0.00 39.84 3.77
3511 3726 4.261031 GGTAGCTTGCGTTGAGAAGAAAAA 60.261 41.667 0.00 0.00 0.00 1.94
3512 3727 3.250040 GGTAGCTTGCGTTGAGAAGAAAA 59.750 43.478 0.00 0.00 0.00 2.29
3513 3728 2.806244 GGTAGCTTGCGTTGAGAAGAAA 59.194 45.455 0.00 0.00 0.00 2.52
3515 3730 1.343142 TGGTAGCTTGCGTTGAGAAGA 59.657 47.619 0.00 0.00 0.00 2.87
3516 3731 1.795768 TGGTAGCTTGCGTTGAGAAG 58.204 50.000 0.00 0.00 0.00 2.85
3517 3732 2.472695 ATGGTAGCTTGCGTTGAGAA 57.527 45.000 0.00 0.00 0.00 2.87
3518 3733 2.472695 AATGGTAGCTTGCGTTGAGA 57.527 45.000 0.00 0.00 0.00 3.27
3519 3734 3.521560 TCTAATGGTAGCTTGCGTTGAG 58.478 45.455 0.00 0.00 0.00 3.02
3520 3735 3.521560 CTCTAATGGTAGCTTGCGTTGA 58.478 45.455 0.00 0.00 0.00 3.18
3521 3736 2.030946 GCTCTAATGGTAGCTTGCGTTG 59.969 50.000 0.00 0.00 35.80 4.10
3523 3738 1.207089 TGCTCTAATGGTAGCTTGCGT 59.793 47.619 0.00 0.00 39.53 5.24
3524 3739 1.939974 TGCTCTAATGGTAGCTTGCG 58.060 50.000 0.00 0.00 39.53 4.85
3526 3741 4.202295 TGGAGATGCTCTAATGGTAGCTTG 60.202 45.833 0.00 0.00 39.53 4.01
3527 3742 3.969976 TGGAGATGCTCTAATGGTAGCTT 59.030 43.478 0.00 0.00 39.53 3.74
3529 3744 3.864160 GCTGGAGATGCTCTAATGGTAGC 60.864 52.174 0.00 0.00 39.25 3.58
3530 3745 3.306641 GGCTGGAGATGCTCTAATGGTAG 60.307 52.174 0.00 0.00 0.00 3.18
3531 3746 2.634940 GGCTGGAGATGCTCTAATGGTA 59.365 50.000 0.00 0.00 0.00 3.25
3532 3747 1.419387 GGCTGGAGATGCTCTAATGGT 59.581 52.381 0.00 0.00 0.00 3.55
3533 3748 1.607509 CGGCTGGAGATGCTCTAATGG 60.608 57.143 0.00 0.00 0.00 3.16
3534 3749 1.069823 ACGGCTGGAGATGCTCTAATG 59.930 52.381 0.00 0.00 0.00 1.90
3591 3807 0.878961 GATTTTATCGCCGGGTCGCT 60.879 55.000 2.18 0.00 0.00 4.93
3617 3834 4.460683 TGGAAACCCGATCGGCCG 62.461 66.667 29.12 22.12 33.26 6.13
3688 3990 4.749245 AGTTGCCGAAGTTTACTGAATG 57.251 40.909 0.00 0.00 0.00 2.67
3942 6377 1.480312 GCTGAGCCCTAGAGGAGATCA 60.480 57.143 0.00 1.39 38.24 2.92
4111 6900 4.465446 CTCCTCGGCTCCTCCCCA 62.465 72.222 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.