Multiple sequence alignment - TraesCS3A01G052000

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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 TraesCS3A01G052000 chr3A 100.000 2309 0 0 1 2309 27685176 27687484 0.000000e+00 4265.0
1 TraesCS3A01G052000 chr3A 97.910 1483 25 6 75 1554 27686729 27685250 0.000000e+00 2562.0
2 TraesCS3A01G052000 chr2A 98.061 722 11 2 83 802 755356424 755357144 0.000000e+00 1253.0
3 TraesCS3A01G052000 chr2A 97.890 711 12 2 841 1549 755357131 755356422 0.000000e+00 1227.0
4 TraesCS3A01G052000 chr2A 94.966 735 31 6 70 802 377109931 377109201 0.000000e+00 1147.0
5 TraesCS3A01G052000 chr2A 95.352 710 28 5 841 1548 377109214 377109920 0.000000e+00 1123.0
6 TraesCS3A01G052000 chr2A 87.387 222 27 1 2071 2292 628063692 628063912 1.060000e-63 254.0
7 TraesCS3A01G052000 chr2A 89.691 194 19 1 1974 2167 285650665 285650473 1.770000e-61 246.0
8 TraesCS3A01G052000 chr3B 97.103 725 20 1 78 802 782024088 782023365 0.000000e+00 1221.0
9 TraesCS3A01G052000 chr3B 96.910 712 20 2 841 1551 782023378 782024088 0.000000e+00 1192.0
10 TraesCS3A01G052000 chr3B 87.204 422 45 6 1882 2303 446137688 446137276 2.690000e-129 472.0
11 TraesCS3A01G052000 chr3B 85.071 422 51 7 1882 2303 446145095 446144686 9.870000e-114 420.0
12 TraesCS3A01G052000 chr3B 90.541 74 6 1 1 73 446159639 446159566 1.890000e-16 97.1
13 TraesCS3A01G052000 chr2D 95.706 722 29 2 82 802 355483786 355483066 0.000000e+00 1160.0
14 TraesCS3A01G052000 chr2D 95.480 708 30 2 841 1547 355483079 355483785 0.000000e+00 1129.0
15 TraesCS3A01G052000 chr2D 86.585 82 11 0 1 82 578306963 578306882 8.790000e-15 91.6
16 TraesCS3A01G052000 chr5A 94.591 721 36 3 83 802 315537021 315536303 0.000000e+00 1112.0
17 TraesCS3A01G052000 chr5A 94.492 708 36 3 841 1547 315536316 315537021 0.000000e+00 1088.0
18 TraesCS3A01G052000 chr5A 88.041 393 46 1 1898 2290 576265082 576265473 4.490000e-127 464.0
19 TraesCS3A01G052000 chr5D 94.243 608 23 6 79 686 7891868 7892463 0.000000e+00 918.0
20 TraesCS3A01G052000 chr5D 94.234 607 24 5 944 1550 7892463 7891868 0.000000e+00 917.0
21 TraesCS3A01G052000 chr5D 92.951 610 32 5 83 692 7884491 7883893 0.000000e+00 878.0
22 TraesCS3A01G052000 chr5D 92.787 610 33 5 938 1547 7883893 7884491 0.000000e+00 872.0
23 TraesCS3A01G052000 chr5D 87.805 82 10 0 1 82 436206297 436206216 1.890000e-16 97.1
24 TraesCS3A01G052000 chr7D 94.465 542 29 1 83 623 59902862 59902321 0.000000e+00 833.0
25 TraesCS3A01G052000 chr7D 94.150 547 30 2 1007 1551 59902321 59902867 0.000000e+00 832.0
26 TraesCS3A01G052000 chr7D 83.099 213 33 3 2081 2292 520992459 520992669 8.420000e-45 191.0
27 TraesCS3A01G052000 chr2B 86.314 643 63 7 1651 2292 78083512 78082894 0.000000e+00 676.0
28 TraesCS3A01G052000 chr3D 88.698 407 44 2 1886 2292 126233083 126232679 1.590000e-136 496.0
29 TraesCS3A01G052000 chr3D 81.221 213 36 4 2081 2292 23255192 23255401 3.950000e-38 169.0
30 TraesCS3A01G052000 chr3D 90.244 82 8 0 1 82 126233814 126233733 8.720000e-20 108.0
31 TraesCS3A01G052000 chr3D 90.244 82 8 0 1 82 306087857 306087776 8.720000e-20 108.0
32 TraesCS3A01G052000 chr4D 87.260 416 51 2 1882 2297 374604467 374604054 7.470000e-130 473.0
33 TraesCS3A01G052000 chr6D 90.361 166 14 2 1714 1877 427974854 427974689 1.390000e-52 217.0
34 TraesCS3A01G052000 chr7B 82.160 213 35 3 2081 2292 506595695 506595485 1.820000e-41 180.0
35 TraesCS3A01G052000 chr7B 90.667 75 5 2 1 75 506596879 506596807 5.250000e-17 99.0
36 TraesCS3A01G052000 chr4B 88.608 79 9 0 1 79 636773217 636773295 1.890000e-16 97.1
37 TraesCS3A01G052000 chr1B 88.608 79 9 0 1 79 4155579 4155657 1.890000e-16 97.1
38 TraesCS3A01G052000 chr1D 89.041 73 8 0 1 73 475249280 475249208 8.790000e-15 91.6


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 TraesCS3A01G052000 chr3A 27685176 27687484 2308 False 4265 4265 100.000 1 2309 1 chr3A.!!$F1 2308
1 TraesCS3A01G052000 chr3A 27685250 27686729 1479 True 2562 2562 97.910 75 1554 1 chr3A.!!$R1 1479
2 TraesCS3A01G052000 chr2A 755356424 755357144 720 False 1253 1253 98.061 83 802 1 chr2A.!!$F3 719
3 TraesCS3A01G052000 chr2A 755356422 755357131 709 True 1227 1227 97.890 841 1549 1 chr2A.!!$R3 708
4 TraesCS3A01G052000 chr2A 377109201 377109931 730 True 1147 1147 94.966 70 802 1 chr2A.!!$R2 732
5 TraesCS3A01G052000 chr2A 377109214 377109920 706 False 1123 1123 95.352 841 1548 1 chr2A.!!$F1 707
6 TraesCS3A01G052000 chr3B 782023365 782024088 723 True 1221 1221 97.103 78 802 1 chr3B.!!$R4 724
7 TraesCS3A01G052000 chr3B 782023378 782024088 710 False 1192 1192 96.910 841 1551 1 chr3B.!!$F1 710
8 TraesCS3A01G052000 chr2D 355483066 355483786 720 True 1160 1160 95.706 82 802 1 chr2D.!!$R1 720
9 TraesCS3A01G052000 chr2D 355483079 355483785 706 False 1129 1129 95.480 841 1547 1 chr2D.!!$F1 706
10 TraesCS3A01G052000 chr5A 315536303 315537021 718 True 1112 1112 94.591 83 802 1 chr5A.!!$R1 719
11 TraesCS3A01G052000 chr5A 315536316 315537021 705 False 1088 1088 94.492 841 1547 1 chr5A.!!$F1 706
12 TraesCS3A01G052000 chr5D 7891868 7892463 595 False 918 918 94.243 79 686 1 chr5D.!!$F2 607
13 TraesCS3A01G052000 chr5D 7891868 7892463 595 True 917 917 94.234 944 1550 1 chr5D.!!$R2 606
14 TraesCS3A01G052000 chr5D 7883893 7884491 598 True 878 878 92.951 83 692 1 chr5D.!!$R1 609
15 TraesCS3A01G052000 chr5D 7883893 7884491 598 False 872 872 92.787 938 1547 1 chr5D.!!$F1 609
16 TraesCS3A01G052000 chr7D 59902321 59902862 541 True 833 833 94.465 83 623 1 chr7D.!!$R1 540
17 TraesCS3A01G052000 chr7D 59902321 59902867 546 False 832 832 94.150 1007 1551 1 chr7D.!!$F1 544
18 TraesCS3A01G052000 chr2B 78082894 78083512 618 True 676 676 86.314 1651 2292 1 chr2B.!!$R1 641
19 TraesCS3A01G052000 chr3D 126232679 126233814 1135 True 302 496 89.471 1 2292 2 chr3D.!!$R2 2291

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
73 74 1.593209 GTCGAACACGTTGAGGGCA 60.593 57.895 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 2315 0.040067 GCTACAAGGTTGTGCAGTGC 60.04 55.0 8.58 8.58 42.31 4.4 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
31 32 6.602009 AGGAGTTAACAACAAAGCTTAACACT 59.398 34.615 8.61 0.00 34.24 3.55
37 38 4.461081 ACAACAAAGCTTAACACTCACCAA 59.539 37.500 0.00 0.00 0.00 3.67
73 74 1.593209 GTCGAACACGTTGAGGGCA 60.593 57.895 0.00 0.00 0.00 5.36
794 888 5.796424 ATCCAAATATGCTCCCAAATGAC 57.204 39.130 0.00 0.00 0.00 3.06
802 896 4.365514 TGCTCCCAAATGACTTCAGTTA 57.634 40.909 0.00 0.00 32.46 2.24
803 897 4.922206 TGCTCCCAAATGACTTCAGTTAT 58.078 39.130 0.00 0.00 32.46 1.89
804 898 4.943705 TGCTCCCAAATGACTTCAGTTATC 59.056 41.667 0.00 0.00 32.46 1.75
805 899 4.943705 GCTCCCAAATGACTTCAGTTATCA 59.056 41.667 0.00 0.00 32.46 2.15
807 901 6.404074 GCTCCCAAATGACTTCAGTTATCAAG 60.404 42.308 0.00 0.00 32.46 3.02
808 902 6.778821 TCCCAAATGACTTCAGTTATCAAGA 58.221 36.000 0.00 0.00 32.46 3.02
809 903 7.405292 TCCCAAATGACTTCAGTTATCAAGAT 58.595 34.615 0.00 0.00 32.46 2.40
811 905 9.177608 CCCAAATGACTTCAGTTATCAAGATAA 57.822 33.333 0.00 0.00 32.46 1.75
817 911 9.645059 TGACTTCAGTTATCAAGATAAAGAGTG 57.355 33.333 4.21 5.92 35.30 3.51
821 915 9.996554 TTCAGTTATCAAGATAAAGAGTGTTCA 57.003 29.630 4.21 0.00 35.30 3.18
824 918 8.887717 AGTTATCAAGATAAAGAGTGTTCATGC 58.112 33.333 4.21 0.00 35.30 4.06
825 919 8.887717 GTTATCAAGATAAAGAGTGTTCATGCT 58.112 33.333 4.21 0.00 35.30 3.79
828 922 8.654230 TCAAGATAAAGAGTGTTCATGCTATC 57.346 34.615 0.00 0.00 0.00 2.08
829 923 8.260114 TCAAGATAAAGAGTGTTCATGCTATCA 58.740 33.333 0.00 0.00 0.00 2.15
830 924 8.549548 CAAGATAAAGAGTGTTCATGCTATCAG 58.450 37.037 0.00 0.00 0.00 2.90
831 925 8.016301 AGATAAAGAGTGTTCATGCTATCAGA 57.984 34.615 0.00 0.00 0.00 3.27
832 926 8.649591 AGATAAAGAGTGTTCATGCTATCAGAT 58.350 33.333 0.00 0.00 0.00 2.90
835 929 8.604640 AAAGAGTGTTCATGCTATCAGATATG 57.395 34.615 0.00 0.00 0.00 1.78
837 931 5.243981 AGTGTTCATGCTATCAGATATGCC 58.756 41.667 8.53 0.00 0.00 4.40
838 932 4.394300 GTGTTCATGCTATCAGATATGCCC 59.606 45.833 8.53 0.00 0.00 5.36
839 933 3.920231 TCATGCTATCAGATATGCCCC 57.080 47.619 8.53 0.00 0.00 5.80
1380 2098 8.293699 TGTAGCTTCTATGATACTTGAGTTCA 57.706 34.615 0.00 0.00 30.97 3.18
1550 2273 4.722700 TTGAGCCGGCCCTGCTTC 62.723 66.667 26.15 13.99 39.69 3.86
1560 2283 2.764128 CCTGCTTCCGGCCTCCTA 60.764 66.667 0.00 0.00 40.92 2.94
1561 2284 2.501610 CTGCTTCCGGCCTCCTAC 59.498 66.667 0.00 0.00 40.92 3.18
1562 2285 2.284331 TGCTTCCGGCCTCCTACA 60.284 61.111 0.00 0.00 40.92 2.74
1563 2286 1.689233 TGCTTCCGGCCTCCTACAT 60.689 57.895 0.00 0.00 40.92 2.29
1564 2287 1.227674 GCTTCCGGCCTCCTACATG 60.228 63.158 0.00 0.00 34.27 3.21
1565 2288 1.447643 CTTCCGGCCTCCTACATGG 59.552 63.158 0.00 0.00 37.10 3.66
1566 2289 1.002403 TTCCGGCCTCCTACATGGA 59.998 57.895 0.00 0.00 43.86 3.41
1567 2290 0.399949 TTCCGGCCTCCTACATGGAT 60.400 55.000 0.00 0.00 45.16 3.41
1568 2291 0.832135 TCCGGCCTCCTACATGGATC 60.832 60.000 0.00 0.00 45.16 3.36
1569 2292 0.833834 CCGGCCTCCTACATGGATCT 60.834 60.000 0.00 0.00 45.16 2.75
1570 2293 0.319728 CGGCCTCCTACATGGATCTG 59.680 60.000 0.00 0.00 45.16 2.90
1571 2294 0.689623 GGCCTCCTACATGGATCTGG 59.310 60.000 0.00 0.00 45.16 3.86
1572 2295 0.689623 GCCTCCTACATGGATCTGGG 59.310 60.000 0.00 0.00 45.16 4.45
1573 2296 1.356124 CCTCCTACATGGATCTGGGG 58.644 60.000 0.00 0.00 45.16 4.96
1574 2297 0.689623 CTCCTACATGGATCTGGGGC 59.310 60.000 0.00 0.00 45.16 5.80
1575 2298 1.121407 TCCTACATGGATCTGGGGCG 61.121 60.000 0.00 0.00 40.56 6.13
1576 2299 1.302033 CTACATGGATCTGGGGCGC 60.302 63.158 0.00 0.00 0.00 6.53
1577 2300 2.043604 CTACATGGATCTGGGGCGCA 62.044 60.000 10.83 3.57 0.00 6.09
1578 2301 2.324014 TACATGGATCTGGGGCGCAC 62.324 60.000 10.83 4.83 0.00 5.34
1579 2302 3.092511 ATGGATCTGGGGCGCACT 61.093 61.111 10.74 0.00 0.00 4.40
1580 2303 3.411114 ATGGATCTGGGGCGCACTG 62.411 63.158 10.74 5.69 0.00 3.66
1590 2313 4.962122 GCGCACTGCACAACGTGG 62.962 66.667 0.30 0.00 45.45 4.94
1591 2314 4.312231 CGCACTGCACAACGTGGG 62.312 66.667 6.50 6.50 37.66 4.61
1592 2315 3.964875 GCACTGCACAACGTGGGG 61.965 66.667 6.02 0.00 33.64 4.96
1593 2316 3.964875 CACTGCACAACGTGGGGC 61.965 66.667 11.24 11.24 33.64 5.80
1594 2317 4.497984 ACTGCACAACGTGGGGCA 62.498 61.111 20.93 20.93 33.64 5.36
1595 2318 3.964875 CTGCACAACGTGGGGCAC 61.965 66.667 18.01 0.00 33.64 5.01
1596 2319 4.497984 TGCACAACGTGGGGCACT 62.498 61.111 18.01 0.00 33.64 4.40
1597 2320 3.964875 GCACAACGTGGGGCACTG 61.965 66.667 13.69 0.00 33.64 3.66
1598 2321 3.964875 CACAACGTGGGGCACTGC 61.965 66.667 0.00 0.00 31.34 4.40
1599 2322 4.497984 ACAACGTGGGGCACTGCA 62.498 61.111 2.82 0.00 31.34 4.41
1600 2323 3.964875 CAACGTGGGGCACTGCAC 61.965 66.667 2.82 0.00 31.34 4.57
1601 2324 4.497984 AACGTGGGGCACTGCACA 62.498 61.111 5.44 0.00 30.93 4.57
1602 2325 4.497984 ACGTGGGGCACTGCACAA 62.498 61.111 5.44 0.00 30.93 3.33
1603 2326 3.964875 CGTGGGGCACTGCACAAC 61.965 66.667 5.44 2.65 31.50 3.32
1604 2327 3.605664 GTGGGGCACTGCACAACC 61.606 66.667 5.44 1.23 27.77 3.77
1605 2328 3.819652 TGGGGCACTGCACAACCT 61.820 61.111 5.44 0.00 30.93 3.50
1606 2329 2.521708 GGGGCACTGCACAACCTT 60.522 61.111 5.44 0.00 30.93 3.50
1607 2330 2.730094 GGGCACTGCACAACCTTG 59.270 61.111 2.82 0.00 0.00 3.61
1608 2331 2.127232 GGGCACTGCACAACCTTGT 61.127 57.895 2.82 0.00 43.36 3.16
1609 2332 0.821711 GGGCACTGCACAACCTTGTA 60.822 55.000 2.82 0.00 39.91 2.41
1610 2333 0.593128 GGCACTGCACAACCTTGTAG 59.407 55.000 2.82 0.00 39.91 2.74
1611 2334 0.040067 GCACTGCACAACCTTGTAGC 60.040 55.000 0.00 0.00 39.91 3.58
1612 2335 0.235665 CACTGCACAACCTTGTAGCG 59.764 55.000 0.00 0.00 39.91 4.26
1613 2336 0.179056 ACTGCACAACCTTGTAGCGT 60.179 50.000 0.00 0.00 39.91 5.07
1614 2337 1.069513 ACTGCACAACCTTGTAGCGTA 59.930 47.619 0.00 0.00 39.91 4.42
1615 2338 1.726791 CTGCACAACCTTGTAGCGTAG 59.273 52.381 0.00 0.00 39.91 3.51
1616 2339 1.076332 GCACAACCTTGTAGCGTAGG 58.924 55.000 0.00 0.00 39.91 3.18
1617 2340 1.076332 CACAACCTTGTAGCGTAGGC 58.924 55.000 0.00 0.00 39.91 3.93
1618 2341 0.389426 ACAACCTTGTAGCGTAGGCG 60.389 55.000 1.05 0.00 40.16 5.52
1619 2342 0.389426 CAACCTTGTAGCGTAGGCGT 60.389 55.000 1.05 0.00 46.35 5.68
1620 2343 0.389426 AACCTTGTAGCGTAGGCGTG 60.389 55.000 1.05 0.00 46.35 5.34
1621 2344 1.518572 CCTTGTAGCGTAGGCGTGG 60.519 63.158 1.05 0.00 46.35 4.94
1622 2345 1.509463 CTTGTAGCGTAGGCGTGGA 59.491 57.895 1.05 0.00 46.35 4.02
1623 2346 0.525668 CTTGTAGCGTAGGCGTGGAG 60.526 60.000 1.05 0.00 46.35 3.86
1624 2347 2.278661 GTAGCGTAGGCGTGGAGC 60.279 66.667 1.05 0.00 46.35 4.70
1635 2358 4.643387 GTGGAGCAACGGGGCACT 62.643 66.667 3.39 0.00 35.83 4.40
1636 2359 4.641645 TGGAGCAACGGGGCACTG 62.642 66.667 0.00 0.00 35.83 3.66
1641 2364 3.215568 CAACGGGGCACTGCACAA 61.216 61.111 5.44 0.00 30.93 3.33
1642 2365 3.216292 AACGGGGCACTGCACAAC 61.216 61.111 5.44 0.00 30.93 3.32
1643 2366 4.497984 ACGGGGCACTGCACAACA 62.498 61.111 5.44 0.00 30.93 3.33
1644 2367 2.985282 CGGGGCACTGCACAACAT 60.985 61.111 5.44 0.00 30.93 2.71
1645 2368 2.652530 GGGGCACTGCACAACATG 59.347 61.111 5.44 0.00 30.93 3.21
1646 2369 1.902918 GGGGCACTGCACAACATGA 60.903 57.895 5.44 0.00 30.93 3.07
1647 2370 1.582968 GGGCACTGCACAACATGAG 59.417 57.895 0.00 0.00 0.00 2.90
1648 2371 1.582968 GGCACTGCACAACATGAGG 59.417 57.895 0.00 0.00 0.00 3.86
1649 2372 1.080974 GCACTGCACAACATGAGGC 60.081 57.895 0.00 0.00 0.00 4.70
1681 2404 1.424493 CGTCTCCATTGCGCTCTTCC 61.424 60.000 9.73 0.00 0.00 3.46
1682 2405 1.092345 GTCTCCATTGCGCTCTTCCC 61.092 60.000 9.73 0.00 0.00 3.97
1702 2425 4.776322 TGGCGCCCAAGGATGACG 62.776 66.667 26.77 0.00 0.00 4.35
1724 2447 4.569023 CCGTGCGCCGATAGCTCA 62.569 66.667 17.96 0.00 40.39 4.26
1772 2495 4.704833 TGCCCGAACAGCTCCAGC 62.705 66.667 0.00 0.00 42.49 4.85
1781 2504 2.601666 AGCTCCAGCCAGTCGACA 60.602 61.111 19.50 0.00 43.38 4.35
1910 2634 3.744719 CGGTGAGGGCGAGTTCGA 61.745 66.667 5.60 0.00 43.02 3.71
1911 2635 2.893398 GGTGAGGGCGAGTTCGAT 59.107 61.111 5.60 0.00 43.02 3.59
1912 2636 1.519455 GGTGAGGGCGAGTTCGATG 60.519 63.158 5.60 0.00 43.02 3.84
1913 2637 1.519455 GTGAGGGCGAGTTCGATGG 60.519 63.158 5.60 0.00 43.02 3.51
1914 2638 1.680989 TGAGGGCGAGTTCGATGGA 60.681 57.895 5.60 0.00 43.02 3.41
1915 2639 1.066587 GAGGGCGAGTTCGATGGAG 59.933 63.158 5.60 0.00 43.02 3.86
1916 2640 2.107141 GGGCGAGTTCGATGGAGG 59.893 66.667 5.60 0.00 43.02 4.30
1917 2641 2.722201 GGGCGAGTTCGATGGAGGT 61.722 63.158 5.60 0.00 43.02 3.85
1918 2642 1.227002 GGCGAGTTCGATGGAGGTC 60.227 63.158 5.60 0.00 43.02 3.85
1919 2643 1.227002 GCGAGTTCGATGGAGGTCC 60.227 63.158 5.60 0.00 43.02 4.46
1920 2644 1.064296 CGAGTTCGATGGAGGTCCG 59.936 63.158 0.00 0.00 43.02 4.79
1992 2716 4.493747 GCGGCGAGCGAAGTAGGT 62.494 66.667 12.98 0.00 35.41 3.08
1993 2717 2.579787 CGGCGAGCGAAGTAGGTG 60.580 66.667 0.00 0.00 0.00 4.00
1994 2718 2.882876 GGCGAGCGAAGTAGGTGA 59.117 61.111 0.00 0.00 0.00 4.02
1995 2719 1.226717 GGCGAGCGAAGTAGGTGAG 60.227 63.158 0.00 0.00 0.00 3.51
1996 2720 1.654954 GGCGAGCGAAGTAGGTGAGA 61.655 60.000 0.00 0.00 0.00 3.27
1997 2721 0.248296 GCGAGCGAAGTAGGTGAGAG 60.248 60.000 0.00 0.00 0.00 3.20
1998 2722 1.088306 CGAGCGAAGTAGGTGAGAGT 58.912 55.000 0.00 0.00 0.00 3.24
1999 2723 1.202087 CGAGCGAAGTAGGTGAGAGTG 60.202 57.143 0.00 0.00 0.00 3.51
2000 2724 1.813786 GAGCGAAGTAGGTGAGAGTGT 59.186 52.381 0.00 0.00 0.00 3.55
2026 2750 2.025510 TGAGATGAGGTGCTCAGAGAGA 60.026 50.000 0.00 0.00 44.08 3.10
2037 2761 2.102925 GCTCAGAGAGAAGAGGGATTGG 59.897 54.545 0.00 0.00 32.54 3.16
2042 2766 2.437651 GAGAGAAGAGGGATTGGGGAAG 59.562 54.545 0.00 0.00 0.00 3.46
2062 2786 6.082707 GGAAGGTTAGGGAGGTGATTATCTA 58.917 44.000 0.00 0.00 0.00 1.98
2079 2803 2.204237 TCTATAAGCACGTACGAGCGA 58.796 47.619 27.60 21.09 36.83 4.93
2149 2873 0.633733 CTGTCGATTCGGACGTTTCG 59.366 55.000 6.18 6.00 39.83 3.46
2158 2882 1.006571 GGACGTTTCGAGTGAGCCA 60.007 57.895 0.00 0.00 0.00 4.75
2162 2886 2.035442 GTTTCGAGTGAGCCAGGCC 61.035 63.158 8.22 0.00 0.00 5.19
2191 2915 3.007635 GCCTTTAAGAACCGTGCTATGT 58.992 45.455 0.00 0.00 0.00 2.29
2194 2918 4.809426 CCTTTAAGAACCGTGCTATGTAGG 59.191 45.833 0.00 0.00 0.00 3.18
2202 2926 1.379527 GTGCTATGTAGGCCCAACAC 58.620 55.000 10.56 4.49 0.00 3.32
2221 2945 3.694072 ACACTATATGCGTGCAACCAAAT 59.306 39.130 0.00 0.00 35.84 2.32
2224 2948 5.007626 CACTATATGCGTGCAACCAAATAGT 59.992 40.000 0.00 5.26 0.00 2.12
2241 2965 6.350445 CCAAATAGTCCACCTCCAAAAAGATG 60.350 42.308 0.00 0.00 0.00 2.90
2247 2971 2.232941 CACCTCCAAAAAGATGCTGCAT 59.767 45.455 16.20 16.20 0.00 3.96
2252 2976 0.523072 AAAAAGATGCTGCATCGCGT 59.477 45.000 30.53 19.88 44.67 6.01
2255 2979 3.945434 GATGCTGCATCGCGTGGG 61.945 66.667 25.09 0.00 31.01 4.61
2276 3000 3.512516 GGTTGGGCTCGATGCAGC 61.513 66.667 8.71 0.00 45.15 5.25
2292 3016 2.909965 GCCAACCAAACTCGCCCA 60.910 61.111 0.00 0.00 0.00 5.36
2293 3017 2.494530 GCCAACCAAACTCGCCCAA 61.495 57.895 0.00 0.00 0.00 4.12
2294 3018 2.022240 GCCAACCAAACTCGCCCAAA 62.022 55.000 0.00 0.00 0.00 3.28
2295 3019 0.031994 CCAACCAAACTCGCCCAAAG 59.968 55.000 0.00 0.00 0.00 2.77
2296 3020 0.744281 CAACCAAACTCGCCCAAAGT 59.256 50.000 0.00 0.00 0.00 2.66
2297 3021 0.744281 AACCAAACTCGCCCAAAGTG 59.256 50.000 0.00 0.00 0.00 3.16
2298 3022 0.395173 ACCAAACTCGCCCAAAGTGT 60.395 50.000 0.00 0.00 0.00 3.55
2299 3023 0.744281 CCAAACTCGCCCAAAGTGTT 59.256 50.000 0.00 0.00 0.00 3.32
2300 3024 1.136110 CCAAACTCGCCCAAAGTGTTT 59.864 47.619 0.00 0.00 36.23 2.83
2301 3025 2.459934 CAAACTCGCCCAAAGTGTTTC 58.540 47.619 0.00 0.00 34.40 2.78
2302 3026 2.052782 AACTCGCCCAAAGTGTTTCT 57.947 45.000 0.00 0.00 0.00 2.52
2303 3027 2.052782 ACTCGCCCAAAGTGTTTCTT 57.947 45.000 0.00 0.00 38.10 2.52
2304 3028 2.375146 ACTCGCCCAAAGTGTTTCTTT 58.625 42.857 0.00 0.00 45.96 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.138125 TCGACGAAATAAGGTACCAAACT 57.862 39.130 15.94 0.00 0.00 2.66
802 896 9.270640 GATAGCATGAACACTCTTTATCTTGAT 57.729 33.333 0.00 0.00 0.00 2.57
803 897 8.260114 TGATAGCATGAACACTCTTTATCTTGA 58.740 33.333 0.00 0.00 0.00 3.02
804 898 8.429493 TGATAGCATGAACACTCTTTATCTTG 57.571 34.615 0.00 0.00 0.00 3.02
805 899 8.481314 TCTGATAGCATGAACACTCTTTATCTT 58.519 33.333 0.00 0.00 0.00 2.40
807 901 8.830201 ATCTGATAGCATGAACACTCTTTATC 57.170 34.615 0.00 0.00 0.00 1.75
809 903 9.702494 CATATCTGATAGCATGAACACTCTTTA 57.298 33.333 0.00 0.00 0.00 1.85
811 905 6.649973 GCATATCTGATAGCATGAACACTCTT 59.350 38.462 0.00 0.00 0.00 2.85
813 907 5.350914 GGCATATCTGATAGCATGAACACTC 59.649 44.000 15.82 0.00 0.00 3.51
814 908 5.243981 GGCATATCTGATAGCATGAACACT 58.756 41.667 15.82 0.00 0.00 3.55
815 909 4.394300 GGGCATATCTGATAGCATGAACAC 59.606 45.833 15.82 0.00 0.00 3.32
817 911 3.944015 GGGGCATATCTGATAGCATGAAC 59.056 47.826 15.82 4.53 0.00 3.18
819 913 3.199289 CAGGGGCATATCTGATAGCATGA 59.801 47.826 15.82 0.00 33.11 3.07
820 914 3.542648 CAGGGGCATATCTGATAGCATG 58.457 50.000 15.82 7.60 33.11 4.06
821 915 2.508716 CCAGGGGCATATCTGATAGCAT 59.491 50.000 15.82 0.00 33.11 3.79
823 917 1.211457 CCCAGGGGCATATCTGATAGC 59.789 57.143 0.00 6.96 33.11 2.97
824 918 2.770802 CTCCCAGGGGCATATCTGATAG 59.229 54.545 5.33 0.00 33.11 2.08
825 919 2.837947 CTCCCAGGGGCATATCTGATA 58.162 52.381 5.33 0.00 33.11 2.15
826 920 1.666365 CTCCCAGGGGCATATCTGAT 58.334 55.000 5.33 0.00 33.11 2.90
827 921 1.130054 GCTCCCAGGGGCATATCTGA 61.130 60.000 5.33 0.00 33.11 3.27
828 922 1.377994 GCTCCCAGGGGCATATCTG 59.622 63.158 5.33 0.00 34.68 2.90
829 923 0.477202 ATGCTCCCAGGGGCATATCT 60.477 55.000 22.62 0.00 45.74 1.98
830 924 1.289160 TATGCTCCCAGGGGCATATC 58.711 55.000 24.38 5.46 45.74 1.63
831 925 3.519173 TATGCTCCCAGGGGCATAT 57.481 52.632 24.38 8.44 45.74 1.78
834 928 0.106066 CAAATATGCTCCCAGGGGCA 60.106 55.000 14.89 14.89 42.80 5.36
835 929 0.829182 CCAAATATGCTCCCAGGGGC 60.829 60.000 5.33 8.91 34.68 5.80
837 931 2.986534 ATCCAAATATGCTCCCAGGG 57.013 50.000 0.00 0.00 0.00 4.45
838 932 4.109877 AGAATCCAAATATGCTCCCAGG 57.890 45.455 0.00 0.00 0.00 4.45
839 933 4.891756 ACAAGAATCCAAATATGCTCCCAG 59.108 41.667 0.00 0.00 0.00 4.45
1557 2280 1.372683 CGCCCCAGATCCATGTAGG 59.627 63.158 0.00 0.00 39.47 3.18
1558 2281 1.302033 GCGCCCCAGATCCATGTAG 60.302 63.158 0.00 0.00 0.00 2.74
1559 2282 2.069430 TGCGCCCCAGATCCATGTA 61.069 57.895 4.18 0.00 0.00 2.29
1560 2283 3.410628 TGCGCCCCAGATCCATGT 61.411 61.111 4.18 0.00 0.00 3.21
1561 2284 2.903855 GTGCGCCCCAGATCCATG 60.904 66.667 4.18 0.00 0.00 3.66
1562 2285 3.092511 AGTGCGCCCCAGATCCAT 61.093 61.111 4.18 0.00 0.00 3.41
1563 2286 4.100084 CAGTGCGCCCCAGATCCA 62.100 66.667 4.18 0.00 0.00 3.41
1565 2288 4.783621 TGCAGTGCGCCCCAGATC 62.784 66.667 11.20 0.00 41.33 2.75
1572 2295 4.962122 CACGTTGTGCAGTGCGCC 62.962 66.667 25.10 11.70 41.33 6.53
1573 2296 4.962122 CCACGTTGTGCAGTGCGC 62.962 66.667 21.77 21.77 42.89 6.09
1574 2297 4.312231 CCCACGTTGTGCAGTGCG 62.312 66.667 11.20 0.00 37.07 5.34
1575 2298 3.964875 CCCCACGTTGTGCAGTGC 61.965 66.667 8.58 8.58 37.07 4.40
1576 2299 3.964875 GCCCCACGTTGTGCAGTG 61.965 66.667 0.00 0.00 38.05 3.66
1577 2300 4.497984 TGCCCCACGTTGTGCAGT 62.498 61.111 0.00 0.00 31.34 4.40
1578 2301 3.964875 GTGCCCCACGTTGTGCAG 61.965 66.667 0.00 0.00 33.80 4.41
1579 2302 4.497984 AGTGCCCCACGTTGTGCA 62.498 61.111 0.00 0.00 39.64 4.57
1580 2303 3.964875 CAGTGCCCCACGTTGTGC 61.965 66.667 0.00 0.00 39.64 4.57
1581 2304 3.964875 GCAGTGCCCCACGTTGTG 61.965 66.667 2.85 0.00 39.64 3.33
1582 2305 4.497984 TGCAGTGCCCCACGTTGT 62.498 61.111 13.72 0.00 39.64 3.32
1583 2306 3.964875 GTGCAGTGCCCCACGTTG 61.965 66.667 13.72 0.00 39.64 4.10
1584 2307 4.497984 TGTGCAGTGCCCCACGTT 62.498 61.111 13.72 0.00 39.64 3.99
1585 2308 4.497984 TTGTGCAGTGCCCCACGT 62.498 61.111 13.72 0.00 39.64 4.49
1586 2309 3.964875 GTTGTGCAGTGCCCCACG 61.965 66.667 13.72 0.00 39.64 4.94
1587 2310 3.605664 GGTTGTGCAGTGCCCCAC 61.606 66.667 13.72 2.50 34.10 4.61
1588 2311 3.372422 AAGGTTGTGCAGTGCCCCA 62.372 57.895 13.72 6.57 0.00 4.96
1589 2312 2.521708 AAGGTTGTGCAGTGCCCC 60.522 61.111 13.72 7.36 0.00 5.80
1590 2313 0.821711 TACAAGGTTGTGCAGTGCCC 60.822 55.000 13.72 6.32 42.31 5.36
1591 2314 0.593128 CTACAAGGTTGTGCAGTGCC 59.407 55.000 13.72 4.57 42.31 5.01
1592 2315 0.040067 GCTACAAGGTTGTGCAGTGC 60.040 55.000 8.58 8.58 42.31 4.40
1593 2316 0.235665 CGCTACAAGGTTGTGCAGTG 59.764 55.000 5.59 0.00 42.31 3.66
1594 2317 0.179056 ACGCTACAAGGTTGTGCAGT 60.179 50.000 5.59 7.08 42.31 4.40
1595 2318 1.726791 CTACGCTACAAGGTTGTGCAG 59.273 52.381 5.59 0.00 42.31 4.41
1596 2319 1.606994 CCTACGCTACAAGGTTGTGCA 60.607 52.381 5.59 0.00 42.31 4.57
1597 2320 1.076332 CCTACGCTACAAGGTTGTGC 58.924 55.000 5.59 6.45 42.31 4.57
1598 2321 1.076332 GCCTACGCTACAAGGTTGTG 58.924 55.000 5.59 0.00 42.31 3.33
1599 2322 0.389426 CGCCTACGCTACAAGGTTGT 60.389 55.000 0.24 0.24 44.86 3.32
1600 2323 0.389426 ACGCCTACGCTACAAGGTTG 60.389 55.000 0.00 0.00 45.53 3.77
1601 2324 0.389426 CACGCCTACGCTACAAGGTT 60.389 55.000 0.00 0.00 45.53 3.50
1602 2325 1.214589 CACGCCTACGCTACAAGGT 59.785 57.895 0.00 0.00 45.53 3.50
1603 2326 1.518572 CCACGCCTACGCTACAAGG 60.519 63.158 0.00 0.00 45.53 3.61
1604 2327 0.525668 CTCCACGCCTACGCTACAAG 60.526 60.000 0.00 0.00 45.53 3.16
1605 2328 1.509463 CTCCACGCCTACGCTACAA 59.491 57.895 0.00 0.00 45.53 2.41
1606 2329 3.060020 GCTCCACGCCTACGCTACA 62.060 63.158 0.00 0.00 45.53 2.74
1607 2330 2.278661 GCTCCACGCCTACGCTAC 60.279 66.667 0.00 0.00 45.53 3.58
1608 2331 2.344981 TTGCTCCACGCCTACGCTA 61.345 57.895 0.00 0.00 45.53 4.26
1609 2332 3.691342 TTGCTCCACGCCTACGCT 61.691 61.111 0.00 0.00 45.53 5.07
1610 2333 3.488090 GTTGCTCCACGCCTACGC 61.488 66.667 0.00 0.00 45.53 4.42
1612 2335 2.813908 CCGTTGCTCCACGCCTAC 60.814 66.667 0.00 0.00 38.93 3.18
1613 2336 4.077184 CCCGTTGCTCCACGCCTA 62.077 66.667 0.00 0.00 38.93 3.93
1618 2341 4.643387 AGTGCCCCGTTGCTCCAC 62.643 66.667 0.00 0.00 0.00 4.02
1619 2342 4.641645 CAGTGCCCCGTTGCTCCA 62.642 66.667 0.00 0.00 0.00 3.86
1624 2347 3.215568 TTGTGCAGTGCCCCGTTG 61.216 61.111 13.72 0.00 0.00 4.10
1625 2348 3.216292 GTTGTGCAGTGCCCCGTT 61.216 61.111 13.72 0.00 0.00 4.44
1626 2349 3.790416 ATGTTGTGCAGTGCCCCGT 62.790 57.895 13.72 0.00 0.00 5.28
1627 2350 2.985282 ATGTTGTGCAGTGCCCCG 60.985 61.111 13.72 0.00 0.00 5.73
1628 2351 1.870055 CTCATGTTGTGCAGTGCCCC 61.870 60.000 13.72 3.61 0.00 5.80
1629 2352 1.582968 CTCATGTTGTGCAGTGCCC 59.417 57.895 13.72 0.28 0.00 5.36
1630 2353 1.582968 CCTCATGTTGTGCAGTGCC 59.417 57.895 13.72 4.57 0.00 5.01
1631 2354 1.080974 GCCTCATGTTGTGCAGTGC 60.081 57.895 8.58 8.58 0.00 4.40
1632 2355 1.208358 CGCCTCATGTTGTGCAGTG 59.792 57.895 0.00 0.00 0.00 3.66
1633 2356 1.968017 CCGCCTCATGTTGTGCAGT 60.968 57.895 0.00 0.00 0.00 4.40
1634 2357 2.872557 CCGCCTCATGTTGTGCAG 59.127 61.111 0.00 0.00 0.00 4.41
1635 2358 3.364441 GCCGCCTCATGTTGTGCA 61.364 61.111 0.00 0.00 0.00 4.57
1636 2359 4.465512 CGCCGCCTCATGTTGTGC 62.466 66.667 0.00 0.00 0.00 4.57
1637 2360 3.803082 CCGCCGCCTCATGTTGTG 61.803 66.667 0.00 0.00 0.00 3.33
1638 2361 4.329545 ACCGCCGCCTCATGTTGT 62.330 61.111 0.00 0.00 0.00 3.32
1639 2362 3.803082 CACCGCCGCCTCATGTTG 61.803 66.667 0.00 0.00 0.00 3.33
1663 2386 1.092345 GGGAAGAGCGCAATGGAGAC 61.092 60.000 11.47 0.00 0.00 3.36
1702 2425 4.501714 TATCGGCGCACGGACCAC 62.502 66.667 10.83 0.00 44.45 4.16
1877 2601 3.884350 CGGATTCGTCCGCCTCGA 61.884 66.667 3.73 0.00 46.76 4.04
1888 2612 2.107141 CTCGCCCTCACCGGATTC 59.893 66.667 9.46 0.00 33.16 2.52
1889 2613 2.240162 GAACTCGCCCTCACCGGATT 62.240 60.000 9.46 0.00 33.16 3.01
1896 2620 1.667154 CTCCATCGAACTCGCCCTCA 61.667 60.000 0.00 0.00 39.60 3.86
1910 2634 3.550431 CCATCGCCGGACCTCCAT 61.550 66.667 5.05 0.00 35.14 3.41
1913 2637 4.222847 GTCCCATCGCCGGACCTC 62.223 72.222 5.05 0.00 43.48 3.85
1995 2719 1.824230 ACCTCATCTCAGAGCACACTC 59.176 52.381 0.00 0.00 43.82 3.51
1996 2720 1.549620 CACCTCATCTCAGAGCACACT 59.450 52.381 0.00 0.00 34.26 3.55
1997 2721 2.006056 GCACCTCATCTCAGAGCACAC 61.006 57.143 0.00 0.00 34.26 3.82
1998 2722 0.248565 GCACCTCATCTCAGAGCACA 59.751 55.000 0.00 0.00 34.26 4.57
1999 2723 0.536260 AGCACCTCATCTCAGAGCAC 59.464 55.000 0.00 0.00 34.26 4.40
2000 2724 0.822811 GAGCACCTCATCTCAGAGCA 59.177 55.000 0.00 0.00 34.26 4.26
2005 2729 2.025510 TCTCTCTGAGCACCTCATCTCA 60.026 50.000 0.00 0.00 39.92 3.27
2013 2737 0.823460 CCCTCTTCTCTCTGAGCACC 59.177 60.000 0.00 0.00 0.00 5.01
2026 2750 1.773541 AACCTTCCCCAATCCCTCTT 58.226 50.000 0.00 0.00 0.00 2.85
2037 2761 1.894699 ATCACCTCCCTAACCTTCCC 58.105 55.000 0.00 0.00 0.00 3.97
2042 2766 7.180408 TGCTTATAGATAATCACCTCCCTAACC 59.820 40.741 0.00 0.00 0.00 2.85
2062 2786 1.823828 CTTCGCTCGTACGTGCTTAT 58.176 50.000 31.84 0.00 33.07 1.73
2112 2836 1.968540 GTTTCTTGCGAGCCTGGCT 60.969 57.895 23.64 23.64 43.88 4.75
2121 2845 1.201812 CCGAATCGACAGTTTCTTGCG 60.202 52.381 3.36 0.00 0.00 4.85
2133 2857 0.518636 ACTCGAAACGTCCGAATCGA 59.481 50.000 3.36 16.05 41.53 3.59
2134 2858 0.633733 CACTCGAAACGTCCGAATCG 59.366 55.000 12.85 0.00 35.48 3.34
2149 2873 1.676967 CTTTGGGCCTGGCTCACTC 60.677 63.158 23.44 1.32 39.49 3.51
2162 2886 2.030274 CGGTTCTTAAAGGCACCTTTGG 60.030 50.000 22.18 15.03 44.84 3.28
2172 2896 4.270325 GCCTACATAGCACGGTTCTTAAAG 59.730 45.833 0.00 0.00 0.00 1.85
2191 2915 2.043992 ACGCATATAGTGTTGGGCCTA 58.956 47.619 4.53 0.00 37.83 3.93
2194 2918 0.307760 GCACGCATATAGTGTTGGGC 59.692 55.000 10.86 0.00 39.40 5.36
2202 2926 5.334105 GGACTATTTGGTTGCACGCATATAG 60.334 44.000 0.00 0.00 0.00 1.31
2221 2945 3.330701 AGCATCTTTTTGGAGGTGGACTA 59.669 43.478 0.00 0.00 0.00 2.59
2224 2948 2.517959 CAGCATCTTTTTGGAGGTGGA 58.482 47.619 0.00 0.00 0.00 4.02
2276 3000 0.031994 CTTTGGGCGAGTTTGGTTGG 59.968 55.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.