Multiple sequence alignment - TraesCS1A01G380200

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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 TraesCS1A01G380200 chr1A 100.000 2424 0 0 1 2424 551640434 551642857 0.000000e+00 4477.0
1 TraesCS1A01G380200 chr1D 89.633 926 59 18 788 1686 460158913 460159828 0.000000e+00 1144.0
2 TraesCS1A01G380200 chr1D 84.655 782 89 14 3 758 460158137 460158913 0.000000e+00 750.0
3 TraesCS1A01G380200 chr1D 74.763 527 86 24 1786 2303 18379038 18379526 2.460000e-45 193.0
4 TraesCS1A01G380200 chr1D 79.310 145 28 2 380 523 17240798 17240941 1.530000e-17 100.0
5 TraesCS1A01G380200 chr1B 83.528 1196 118 37 3 1150 632164675 632165839 0.000000e+00 1044.0
6 TraesCS1A01G380200 chr1B 91.755 473 27 5 1149 1613 632165999 632166467 0.000000e+00 647.0
7 TraesCS1A01G380200 chr1B 78.378 333 56 14 968 1286 546156608 546156938 4.090000e-48 202.0
8 TraesCS1A01G380200 chr1B 75.245 408 78 20 895 1286 535011694 535012094 3.200000e-39 172.0
9 TraesCS1A01G380200 chr7B 84.112 642 68 21 914 1533 43672564 43673193 7.460000e-165 590.0
10 TraesCS1A01G380200 chr7B 76.541 665 110 32 1785 2424 658235464 658236107 3.010000e-84 322.0
11 TraesCS1A01G380200 chr7B 84.416 77 11 1 353 429 497002531 497002606 9.290000e-10 75.0
12 TraesCS1A01G380200 chr5A 79.500 600 96 19 12 598 681235521 681234936 3.750000e-108 401.0
13 TraesCS1A01G380200 chr5A 78.619 449 74 16 1785 2223 487796313 487796749 6.600000e-71 278.0
14 TraesCS1A01G380200 chr5A 84.496 258 37 1 5 259 219830158 219829901 4.000000e-63 252.0
15 TraesCS1A01G380200 chr3D 78.221 652 106 29 1786 2419 77327288 77326655 3.780000e-103 385.0
16 TraesCS1A01G380200 chr7D 81.556 450 63 18 1785 2223 5042312 5042752 1.070000e-93 353.0
17 TraesCS1A01G380200 chr7D 85.772 246 34 1 3 248 265162597 265162841 2.390000e-65 259.0
18 TraesCS1A01G380200 chr7D 86.301 219 13 7 645 857 91106231 91106438 3.140000e-54 222.0
19 TraesCS1A01G380200 chr2D 77.797 590 103 21 1788 2357 603554224 603553643 2.990000e-89 339.0
20 TraesCS1A01G380200 chr2D 74.627 268 53 10 247 509 46195991 46195734 1.190000e-18 104.0
21 TraesCS1A01G380200 chr7A 77.079 541 100 16 1903 2424 546344474 546345009 8.480000e-75 291.0
22 TraesCS1A01G380200 chr7A 77.104 511 100 16 25 526 198408145 198408647 1.840000e-71 279.0
23 TraesCS1A01G380200 chr2B 80.769 390 55 11 21 406 478186706 478186333 1.100000e-73 287.0
24 TraesCS1A01G380200 chr2B 77.586 174 33 6 2230 2400 682225399 682225229 1.530000e-17 100.0
25 TraesCS1A01G380200 chr2B 85.135 74 8 3 353 425 776418010 776417939 3.340000e-09 73.1
26 TraesCS1A01G380200 chr6A 75.733 614 101 33 1786 2368 608966617 608966021 5.140000e-67 265.0
27 TraesCS1A01G380200 chr6D 86.017 236 33 0 12 247 138417639 138417404 1.110000e-63 254.0
28 TraesCS1A01G380200 chr6D 74.734 657 111 33 1786 2419 461870777 461870153 2.410000e-60 243.0
29 TraesCS1A01G380200 chr6D 73.790 248 56 8 353 596 456648125 456647883 3.320000e-14 89.8
30 TraesCS1A01G380200 chr3A 79.028 391 51 22 1910 2289 724933977 724933607 3.110000e-59 239.0
31 TraesCS1A01G380200 chr3A 78.517 391 53 22 1910 2289 724892874 724892504 6.740000e-56 228.0
32 TraesCS1A01G380200 chr5D 74.281 661 116 30 1788 2424 371057696 371058326 1.870000e-56 230.0
33 TraesCS1A01G380200 chr4B 79.553 313 59 5 17 327 659613595 659613904 4.060000e-53 219.0
34 TraesCS1A01G380200 chr4D 73.964 603 103 32 1786 2366 328551373 328551943 6.840000e-46 195.0
35 TraesCS1A01G380200 chr6B 74.104 251 50 13 353 596 694447838 694447596 3.320000e-14 89.8
36 TraesCS1A01G380200 chr3B 80.000 110 20 2 353 461 473176123 473176231 2.000000e-11 80.5


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 TraesCS1A01G380200 chr1A 551640434 551642857 2423 False 4477.0 4477 100.0000 1 2424 1 chr1A.!!$F1 2423
1 TraesCS1A01G380200 chr1D 460158137 460159828 1691 False 947.0 1144 87.1440 3 1686 2 chr1D.!!$F3 1683
2 TraesCS1A01G380200 chr1B 632164675 632166467 1792 False 845.5 1044 87.6415 3 1613 2 chr1B.!!$F3 1610
3 TraesCS1A01G380200 chr7B 43672564 43673193 629 False 590.0 590 84.1120 914 1533 1 chr7B.!!$F1 619
4 TraesCS1A01G380200 chr7B 658235464 658236107 643 False 322.0 322 76.5410 1785 2424 1 chr7B.!!$F3 639
5 TraesCS1A01G380200 chr5A 681234936 681235521 585 True 401.0 401 79.5000 12 598 1 chr5A.!!$R2 586
6 TraesCS1A01G380200 chr3D 77326655 77327288 633 True 385.0 385 78.2210 1786 2419 1 chr3D.!!$R1 633
7 TraesCS1A01G380200 chr2D 603553643 603554224 581 True 339.0 339 77.7970 1788 2357 1 chr2D.!!$R2 569
8 TraesCS1A01G380200 chr7A 546344474 546345009 535 False 291.0 291 77.0790 1903 2424 1 chr7A.!!$F2 521
9 TraesCS1A01G380200 chr7A 198408145 198408647 502 False 279.0 279 77.1040 25 526 1 chr7A.!!$F1 501
10 TraesCS1A01G380200 chr6A 608966021 608966617 596 True 265.0 265 75.7330 1786 2368 1 chr6A.!!$R1 582
11 TraesCS1A01G380200 chr6D 461870153 461870777 624 True 243.0 243 74.7340 1786 2419 1 chr6D.!!$R3 633
12 TraesCS1A01G380200 chr5D 371057696 371058326 630 False 230.0 230 74.2810 1788 2424 1 chr5D.!!$F1 636

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
764 855 0.031857 CCTCGCAGATCCTAGCACTG 59.968 60.0 3.72 0.0 33.89 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 2027 0.177373 GGGCGGAGGAAATAGAACGT 59.823 55.0 0.0 0.0 0.0 3.99 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
53 59 1.963855 CGCCACCATGACCACGAAA 60.964 57.895 0.00 0.00 0.00 3.46
65 74 1.589461 CACGAAACCGACACGTCCA 60.589 57.895 0.00 0.00 38.18 4.02
267 317 0.608640 GGAACTGGAGAAGGCGAAGA 59.391 55.000 0.00 0.00 0.00 2.87
290 340 1.223487 GTTCTCGGGGCTTATGGCA 59.777 57.895 4.52 0.00 44.01 4.92
305 355 0.409092 TGGCAGGACATGGGAAACAT 59.591 50.000 0.00 0.00 41.57 2.71
313 363 1.304381 ATGGGAAACATGCGCCAGT 60.304 52.632 4.18 0.00 38.70 4.00
348 411 8.258708 AGTTTAGGTTTATAGTCGAATGAGCTT 58.741 33.333 0.00 0.00 0.00 3.74
432 516 6.538742 CAGACGTGTTTATATGAAATCCACCT 59.461 38.462 0.00 0.00 0.00 4.00
486 571 8.719560 TGTATTGTTACTAAAATGTATGCGGA 57.280 30.769 0.00 0.00 0.00 5.54
509 595 2.990830 GATTAGACGGCGGCCTTCCC 62.991 65.000 20.59 5.64 0.00 3.97
519 605 1.818555 GGCCTTCCCACATTCATGC 59.181 57.895 0.00 0.00 0.00 4.06
526 612 3.891400 CACATTCATGCCCGCGGG 61.891 66.667 40.26 40.26 38.57 6.13
542 628 3.346870 GGCTGGGCCCCTTTATCT 58.653 61.111 22.27 0.00 44.06 1.98
554 641 2.614057 CCCTTTATCTGTGAACGGATGC 59.386 50.000 13.87 0.00 41.72 3.91
556 643 2.665649 TTATCTGTGAACGGATGCGT 57.334 45.000 6.39 6.39 41.72 5.24
560 647 1.354337 CTGTGAACGGATGCGTGAGG 61.354 60.000 14.66 0.00 0.00 3.86
566 653 1.086696 ACGGATGCGTGAGGAAATTG 58.913 50.000 12.84 0.00 32.68 2.32
598 686 3.677976 CGTTAAAGATGCCCTAACCTCGT 60.678 47.826 0.00 0.00 0.00 4.18
605 693 1.740285 CCCTAACCTCGTGGATCCG 59.260 63.158 11.17 0.00 37.04 4.18
650 740 0.179062 AATCTCGCAGATCCCAGCAC 60.179 55.000 3.72 0.00 32.89 4.40
670 760 5.493735 GCACTGATGCGTATACTCTTTTTC 58.506 41.667 0.56 0.00 43.33 2.29
671 761 5.292101 GCACTGATGCGTATACTCTTTTTCT 59.708 40.000 0.56 0.00 43.33 2.52
673 763 7.176075 CACTGATGCGTATACTCTTTTTCTTG 58.824 38.462 0.56 0.00 0.00 3.02
674 764 6.874134 ACTGATGCGTATACTCTTTTTCTTGT 59.126 34.615 0.56 0.00 0.00 3.16
675 765 7.063544 ACTGATGCGTATACTCTTTTTCTTGTC 59.936 37.037 0.56 0.00 0.00 3.18
764 855 0.031857 CCTCGCAGATCCTAGCACTG 59.968 60.000 3.72 0.00 33.89 3.66
770 861 2.102084 GCAGATCCTAGCACTGATGTGA 59.898 50.000 9.65 0.00 46.55 3.58
780 871 7.016563 TCCTAGCACTGATGTGAATATTATGGT 59.983 37.037 0.00 0.00 46.55 3.55
796 887 2.282701 TGGTTACTAATCACCGCGTC 57.717 50.000 4.92 0.00 35.60 5.19
824 915 4.039852 TGGTGATTATACGCATTCCTAGCA 59.960 41.667 0.00 0.00 0.00 3.49
827 918 5.696724 GTGATTATACGCATTCCTAGCAAGT 59.303 40.000 0.00 0.00 0.00 3.16
828 919 5.926542 TGATTATACGCATTCCTAGCAAGTC 59.073 40.000 0.00 0.00 0.00 3.01
829 920 5.531122 TTATACGCATTCCTAGCAAGTCT 57.469 39.130 0.00 0.00 0.00 3.24
830 921 2.301577 ACGCATTCCTAGCAAGTCTC 57.698 50.000 0.00 0.00 0.00 3.36
831 922 1.203928 CGCATTCCTAGCAAGTCTCG 58.796 55.000 0.00 0.00 0.00 4.04
832 923 1.469940 CGCATTCCTAGCAAGTCTCGT 60.470 52.381 0.00 0.00 0.00 4.18
833 924 2.197577 GCATTCCTAGCAAGTCTCGTC 58.802 52.381 0.00 0.00 0.00 4.20
869 960 4.830826 CATATGTGTCATGCAGATGCTT 57.169 40.909 6.35 0.00 42.66 3.91
870 961 4.537015 CATATGTGTCATGCAGATGCTTG 58.463 43.478 13.01 13.01 44.56 4.01
871 962 0.524414 TGTGTCATGCAGATGCTTGC 59.476 50.000 14.08 10.47 43.38 4.01
902 993 6.129393 GGAACGTGATCATCGACAATTAATG 58.871 40.000 19.74 0.00 0.00 1.90
982 1096 8.705594 CCCTTCTAAAACTACCTCATAATCTCA 58.294 37.037 0.00 0.00 0.00 3.27
1074 1193 8.786826 TTCTTATGGTTGGACAATGTAAGTAG 57.213 34.615 0.00 0.00 0.00 2.57
1085 1204 8.758829 TGGACAATGTAAGTAGACATCACTATT 58.241 33.333 0.00 0.00 39.16 1.73
1228 1512 1.326213 CGCTGGTCTCCTCACCTGAT 61.326 60.000 1.02 0.00 37.53 2.90
1335 1619 2.433838 CTGCGTCACTCTGCCAGG 60.434 66.667 0.00 0.00 0.00 4.45
1372 1656 7.244886 TGATTCCTATGAAGAGTGTCAAAGA 57.755 36.000 0.00 0.00 33.05 2.52
1404 1691 0.108585 ATACCGCAGCCCATACTTGG 59.891 55.000 0.00 0.00 43.23 3.61
1419 1706 1.373590 CTTGGAAATACGGGTGGGCG 61.374 60.000 0.00 0.00 0.00 6.13
1437 1724 4.221262 TGGGCGTTAACAGAATACACTACT 59.779 41.667 6.39 0.00 0.00 2.57
1438 1725 4.565564 GGGCGTTAACAGAATACACTACTG 59.434 45.833 6.39 0.00 37.62 2.74
1439 1726 4.565564 GGCGTTAACAGAATACACTACTGG 59.434 45.833 6.39 0.00 36.17 4.00
1490 1794 9.438291 CTACCTTTTCATGAGTTTATTATTGCG 57.562 33.333 0.00 0.00 0.00 4.85
1518 1822 6.391227 AAAAAGTGAGTTGAAATCCGATGT 57.609 33.333 0.00 0.00 0.00 3.06
1528 1832 1.972872 AATCCGATGTGGCCAATCTC 58.027 50.000 7.24 3.37 37.80 2.75
1562 1866 7.855409 TCTTATTTATTGAAATGATTCGTGCCG 59.145 33.333 0.00 0.00 38.46 5.69
1572 1876 4.680237 TCGTGCCGCCAGTTGAGG 62.680 66.667 0.00 0.00 0.00 3.86
1645 1950 6.753107 AAAACTCAACCGGTCAATATTAGG 57.247 37.500 8.04 0.00 0.00 2.69
1653 1958 6.997239 ACCGGTCAATATTAGGAGAAAAAC 57.003 37.500 0.00 0.00 0.00 2.43
1654 1959 6.478129 ACCGGTCAATATTAGGAGAAAAACA 58.522 36.000 0.00 0.00 0.00 2.83
1656 1961 7.449086 ACCGGTCAATATTAGGAGAAAAACAAA 59.551 33.333 0.00 0.00 0.00 2.83
1666 1971 6.396829 AGGAGAAAAACAAAGTCCATTGAG 57.603 37.500 0.00 0.00 34.38 3.02
1686 1991 5.014858 TGAGTTCACGACTTACCTCCTAAT 58.985 41.667 0.00 0.00 39.19 1.73
1687 1992 5.479375 TGAGTTCACGACTTACCTCCTAATT 59.521 40.000 0.00 0.00 39.19 1.40
1688 1993 5.963594 AGTTCACGACTTACCTCCTAATTC 58.036 41.667 0.00 0.00 33.92 2.17
1689 1994 5.479375 AGTTCACGACTTACCTCCTAATTCA 59.521 40.000 0.00 0.00 33.92 2.57
1690 1995 6.154706 AGTTCACGACTTACCTCCTAATTCAT 59.845 38.462 0.00 0.00 33.92 2.57
1691 1996 6.540438 TCACGACTTACCTCCTAATTCATT 57.460 37.500 0.00 0.00 0.00 2.57
1692 1997 6.942976 TCACGACTTACCTCCTAATTCATTT 58.057 36.000 0.00 0.00 0.00 2.32
1693 1998 8.070034 TCACGACTTACCTCCTAATTCATTTA 57.930 34.615 0.00 0.00 0.00 1.40
1694 1999 8.195436 TCACGACTTACCTCCTAATTCATTTAG 58.805 37.037 0.00 0.00 37.61 1.85
1695 2000 8.195436 CACGACTTACCTCCTAATTCATTTAGA 58.805 37.037 0.00 0.00 39.86 2.10
1696 2001 8.755977 ACGACTTACCTCCTAATTCATTTAGAA 58.244 33.333 0.00 0.00 39.86 2.10
1697 2002 9.250624 CGACTTACCTCCTAATTCATTTAGAAG 57.749 37.037 0.00 0.00 39.86 2.85
1698 2003 9.549078 GACTTACCTCCTAATTCATTTAGAAGG 57.451 37.037 0.00 0.00 45.54 3.46
1699 2004 7.993758 ACTTACCTCCTAATTCATTTAGAAGGC 59.006 37.037 0.00 0.00 44.28 4.35
1700 2005 5.696030 ACCTCCTAATTCATTTAGAAGGCC 58.304 41.667 0.00 0.00 44.28 5.19
1701 2006 5.193728 ACCTCCTAATTCATTTAGAAGGCCA 59.806 40.000 5.01 0.00 44.28 5.36
1702 2007 6.126068 ACCTCCTAATTCATTTAGAAGGCCAT 60.126 38.462 5.01 0.00 44.28 4.40
1703 2008 7.073725 ACCTCCTAATTCATTTAGAAGGCCATA 59.926 37.037 5.01 0.00 44.28 2.74
1704 2009 7.944554 CCTCCTAATTCATTTAGAAGGCCATAA 59.055 37.037 5.01 0.00 35.85 1.90
1705 2010 8.691661 TCCTAATTCATTTAGAAGGCCATAAC 57.308 34.615 5.01 0.00 39.86 1.89
1706 2011 7.444183 TCCTAATTCATTTAGAAGGCCATAACG 59.556 37.037 5.01 0.00 39.86 3.18
1707 2012 7.444183 CCTAATTCATTTAGAAGGCCATAACGA 59.556 37.037 5.01 0.00 39.86 3.85
1708 2013 6.867662 ATTCATTTAGAAGGCCATAACGAG 57.132 37.500 5.01 0.00 40.15 4.18
1709 2014 5.353394 TCATTTAGAAGGCCATAACGAGT 57.647 39.130 5.01 0.00 0.00 4.18
1710 2015 5.741011 TCATTTAGAAGGCCATAACGAGTT 58.259 37.500 5.01 0.00 0.00 3.01
1711 2016 6.880484 TCATTTAGAAGGCCATAACGAGTTA 58.120 36.000 5.01 0.00 0.00 2.24
1712 2017 7.506114 TCATTTAGAAGGCCATAACGAGTTAT 58.494 34.615 5.01 2.87 36.27 1.89
1713 2018 8.644216 TCATTTAGAAGGCCATAACGAGTTATA 58.356 33.333 5.01 0.00 34.27 0.98
1714 2019 9.436957 CATTTAGAAGGCCATAACGAGTTATAT 57.563 33.333 5.01 0.00 34.27 0.86
1718 2023 7.556844 AGAAGGCCATAACGAGTTATATATGG 58.443 38.462 5.01 9.04 44.93 2.74
1719 2024 7.399191 AGAAGGCCATAACGAGTTATATATGGA 59.601 37.037 15.75 0.00 44.93 3.41
1720 2025 7.490657 AGGCCATAACGAGTTATATATGGAA 57.509 36.000 15.75 0.00 44.93 3.53
1721 2026 7.913789 AGGCCATAACGAGTTATATATGGAAA 58.086 34.615 15.75 0.00 44.93 3.13
1722 2027 8.380099 AGGCCATAACGAGTTATATATGGAAAA 58.620 33.333 15.75 0.00 44.93 2.29
1723 2028 8.448615 GGCCATAACGAGTTATATATGGAAAAC 58.551 37.037 15.75 0.00 44.93 2.43
1724 2029 8.166706 GCCATAACGAGTTATATATGGAAAACG 58.833 37.037 15.75 0.00 44.93 3.60
1725 2030 9.199982 CCATAACGAGTTATATATGGAAAACGT 57.800 33.333 8.02 0.00 44.93 3.99
1728 2033 8.937634 AACGAGTTATATATGGAAAACGTTCT 57.062 30.769 0.00 0.00 35.88 3.01
1739 2044 3.999769 GAAAACGTTCTATTTCCTCCGC 58.000 45.455 0.00 0.00 30.98 5.54
1740 2045 2.019948 AACGTTCTATTTCCTCCGCC 57.980 50.000 0.00 0.00 0.00 6.13
1741 2046 0.177373 ACGTTCTATTTCCTCCGCCC 59.823 55.000 0.00 0.00 0.00 6.13
1742 2047 0.464452 CGTTCTATTTCCTCCGCCCT 59.536 55.000 0.00 0.00 0.00 5.19
1743 2048 1.134491 CGTTCTATTTCCTCCGCCCTT 60.134 52.381 0.00 0.00 0.00 3.95
1744 2049 2.562635 GTTCTATTTCCTCCGCCCTTC 58.437 52.381 0.00 0.00 0.00 3.46
1745 2050 2.170817 GTTCTATTTCCTCCGCCCTTCT 59.829 50.000 0.00 0.00 0.00 2.85
1746 2051 2.040178 TCTATTTCCTCCGCCCTTCTC 58.960 52.381 0.00 0.00 0.00 2.87
1747 2052 1.762957 CTATTTCCTCCGCCCTTCTCA 59.237 52.381 0.00 0.00 0.00 3.27
1748 2053 0.253327 ATTTCCTCCGCCCTTCTCAC 59.747 55.000 0.00 0.00 0.00 3.51
1749 2054 0.836400 TTTCCTCCGCCCTTCTCACT 60.836 55.000 0.00 0.00 0.00 3.41
1750 2055 1.544825 TTCCTCCGCCCTTCTCACTG 61.545 60.000 0.00 0.00 0.00 3.66
1751 2056 1.984570 CCTCCGCCCTTCTCACTGA 60.985 63.158 0.00 0.00 0.00 3.41
1752 2057 1.333636 CCTCCGCCCTTCTCACTGAT 61.334 60.000 0.00 0.00 0.00 2.90
1753 2058 0.179089 CTCCGCCCTTCTCACTGATG 60.179 60.000 0.00 0.00 0.00 3.07
1754 2059 0.614697 TCCGCCCTTCTCACTGATGA 60.615 55.000 0.00 0.00 0.00 2.92
1775 2080 6.882610 TGAGATACATCCATTATTTGGTGC 57.117 37.500 0.00 0.00 46.52 5.01
1776 2081 6.363882 TGAGATACATCCATTATTTGGTGCA 58.636 36.000 0.00 0.00 46.52 4.57
1777 2082 7.005902 TGAGATACATCCATTATTTGGTGCAT 58.994 34.615 0.00 0.00 46.52 3.96
1778 2083 8.162746 TGAGATACATCCATTATTTGGTGCATA 58.837 33.333 0.00 0.00 46.52 3.14
1779 2084 8.571461 AGATACATCCATTATTTGGTGCATAG 57.429 34.615 0.00 0.00 46.52 2.23
1780 2085 7.613022 AGATACATCCATTATTTGGTGCATAGG 59.387 37.037 0.00 0.00 46.52 2.57
1781 2086 5.457686 ACATCCATTATTTGGTGCATAGGT 58.542 37.500 0.00 0.00 46.52 3.08
1782 2087 5.898972 ACATCCATTATTTGGTGCATAGGTT 59.101 36.000 0.00 0.00 46.52 3.50
1783 2088 5.850557 TCCATTATTTGGTGCATAGGTTG 57.149 39.130 0.00 0.00 46.52 3.77
1799 2104 3.812262 AGGTTGTACTAGCAAAACGGTT 58.188 40.909 9.12 0.00 0.00 4.44
1805 2110 0.110373 CTAGCAAAACGGTTCGTGCC 60.110 55.000 19.85 7.79 39.99 5.01
1816 2121 0.600782 GTTCGTGCCTTACAACGGGA 60.601 55.000 0.00 0.00 0.00 5.14
1823 2128 3.254903 GTGCCTTACAACGGGAGAAAAAT 59.745 43.478 0.00 0.00 0.00 1.82
1825 2130 5.124936 GTGCCTTACAACGGGAGAAAAATAT 59.875 40.000 0.00 0.00 0.00 1.28
1829 2134 9.227777 GCCTTACAACGGGAGAAAAATATATAT 57.772 33.333 0.00 0.00 0.00 0.86
1861 2168 7.946219 TCTCTGATGGCCATTATCATATTTTGT 59.054 33.333 21.84 0.00 34.33 2.83
1871 2178 9.188588 CCATTATCATATTTTGTTGCATCACTC 57.811 33.333 0.00 0.00 0.00 3.51
1896 2206 8.251026 TCAGATACATTACTCTCATTTTCGTGT 58.749 33.333 0.00 0.00 0.00 4.49
1960 2273 1.455786 CGTGACCATATCGGAAATCGC 59.544 52.381 0.00 0.00 38.63 4.58
1972 2285 2.272700 CGGAAATCGCGAACATTTTTCG 59.727 45.455 15.24 16.03 44.06 3.46
1980 2293 4.786068 TCGCGAACATTTTTCGAATTCATC 59.214 37.500 6.20 0.00 43.97 2.92
2111 2448 7.873739 AAAACATTTTTCTTGAATAGGCGAG 57.126 32.000 0.00 0.00 0.00 5.03
2173 2514 5.067153 TGGAACAACTTTTGACATTCACGAT 59.933 36.000 0.00 0.00 31.92 3.73
2235 2592 8.752005 TCATTTTCTAAATTCCCGAGAATCAT 57.248 30.769 0.00 0.00 42.03 2.45
2311 2670 7.665080 AATTCGCGAACATTTTCTAAATAGC 57.335 32.000 26.00 0.00 0.00 2.97
2318 2679 7.305418 GCGAACATTTTCTAAATAGCCGATTTG 60.305 37.037 4.78 0.00 38.27 2.32
2334 2695 8.411318 AGCCGATTTGTTTTCATTTCATTATC 57.589 30.769 0.00 0.00 0.00 1.75
2406 2769 8.806177 ATTTACCGGACATTTGTTTTTAGAAC 57.194 30.769 9.46 0.00 0.00 3.01
2419 2782 7.518731 TGTTTTTAGAACTGTGCACATTTTC 57.481 32.000 22.00 23.37 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.733960 TGTCCTCGCCGTCGTCTG 61.734 66.667 0.00 0.00 36.96 3.51
1 2 3.735029 GTGTCCTCGCCGTCGTCT 61.735 66.667 0.00 0.00 36.96 4.18
113 122 0.322975 GCCTTCTTGAGACCAGAGCA 59.677 55.000 0.00 0.00 0.00 4.26
181 190 2.831333 CCAAGCGACTAATCAGCTGAT 58.169 47.619 23.75 23.75 41.53 2.90
214 223 1.490490 TGGGAACTGAAGTTGTCTGCT 59.510 47.619 0.00 0.00 38.56 4.24
267 317 2.158755 CCATAAGCCCCGAGAACTGAAT 60.159 50.000 0.00 0.00 0.00 2.57
305 355 2.401583 ACTAAATGATCACTGGCGCA 57.598 45.000 10.83 0.00 0.00 6.09
348 411 7.441890 TTGGACATATTTCAACTAAAAGCGA 57.558 32.000 0.00 0.00 0.00 4.93
406 490 6.537301 GGTGGATTTCATATAAACACGTCTGA 59.463 38.462 0.00 0.00 0.00 3.27
408 492 6.538742 CAGGTGGATTTCATATAAACACGTCT 59.461 38.462 0.00 0.00 0.00 4.18
432 516 3.489398 CCGGACAAAATTCGTTCAAACCA 60.489 43.478 0.00 0.00 0.00 3.67
486 571 1.267121 AGGCCGCCGTCTAATCATAT 58.733 50.000 3.05 0.00 0.00 1.78
509 595 3.891400 CCCGCGGGCATGAATGTG 61.891 66.667 34.96 3.26 0.00 3.21
526 612 0.753111 CACAGATAAAGGGGCCCAGC 60.753 60.000 27.72 6.99 0.00 4.85
531 617 1.065709 TCCGTTCACAGATAAAGGGGC 60.066 52.381 0.00 0.00 32.56 5.80
554 641 0.391927 TACCCGCCAATTTCCTCACG 60.392 55.000 0.00 0.00 0.00 4.35
556 643 0.393808 GCTACCCGCCAATTTCCTCA 60.394 55.000 0.00 0.00 0.00 3.86
580 667 1.065418 CCACGAGGTTAGGGCATCTTT 60.065 52.381 0.00 0.00 0.00 2.52
650 740 7.295952 ACAAGAAAAAGAGTATACGCATCAG 57.704 36.000 9.39 2.45 0.00 2.90
664 754 3.877508 AGTGTTCCCTCGACAAGAAAAAG 59.122 43.478 0.00 0.00 0.00 2.27
668 758 2.036387 TCAGTGTTCCCTCGACAAGAA 58.964 47.619 0.00 0.00 0.00 2.52
670 760 2.341257 CATCAGTGTTCCCTCGACAAG 58.659 52.381 0.00 0.00 0.00 3.16
671 761 1.608025 GCATCAGTGTTCCCTCGACAA 60.608 52.381 0.00 0.00 0.00 3.18
673 763 1.078759 CGCATCAGTGTTCCCTCGAC 61.079 60.000 0.00 0.00 0.00 4.20
674 764 1.215382 CGCATCAGTGTTCCCTCGA 59.785 57.895 0.00 0.00 0.00 4.04
675 765 0.172578 TACGCATCAGTGTTCCCTCG 59.827 55.000 0.00 0.00 39.61 4.63
770 861 7.156673 ACGCGGTGATTAGTAACCATAATATT 58.843 34.615 12.47 0.00 36.14 1.28
780 871 4.500205 CCATAAGGACGCGGTGATTAGTAA 60.500 45.833 12.47 0.00 36.89 2.24
796 887 6.173339 AGGAATGCGTATAATCACCATAAGG 58.827 40.000 0.00 0.00 42.21 2.69
824 915 0.592148 GTGTGAGACGGACGAGACTT 59.408 55.000 0.00 0.00 0.00 3.01
827 918 3.250986 CGTGTGAGACGGACGAGA 58.749 61.111 0.00 0.00 44.85 4.04
862 953 3.059884 CGTTCCATATACGCAAGCATCT 58.940 45.455 0.00 0.00 45.62 2.90
863 954 2.800544 ACGTTCCATATACGCAAGCATC 59.199 45.455 0.00 0.00 42.49 3.91
864 955 2.543848 CACGTTCCATATACGCAAGCAT 59.456 45.455 0.00 0.00 42.49 3.79
866 957 2.198406 TCACGTTCCATATACGCAAGC 58.802 47.619 0.00 0.00 42.49 4.01
867 958 4.048504 TGATCACGTTCCATATACGCAAG 58.951 43.478 0.00 0.00 42.49 4.01
868 959 4.048241 TGATCACGTTCCATATACGCAA 57.952 40.909 0.00 0.00 42.49 4.85
869 960 3.719173 TGATCACGTTCCATATACGCA 57.281 42.857 0.00 0.00 42.49 5.24
870 961 3.300853 CGATGATCACGTTCCATATACGC 59.699 47.826 0.00 0.00 42.49 4.42
871 962 4.553815 GTCGATGATCACGTTCCATATACG 59.446 45.833 14.43 0.00 44.20 3.06
902 993 8.753133 TGCCTCAGTATATATATAGGCATATGC 58.247 37.037 26.67 19.79 44.91 3.14
957 1069 9.535878 GTGAGATTATGAGGTAGTTTTAGAAGG 57.464 37.037 0.00 0.00 0.00 3.46
982 1096 4.659111 TCATATTCCACGAACCGTATGT 57.341 40.909 0.00 0.00 38.32 2.29
1037 1153 3.099141 ACCATAAGAAGGCACCCAATTG 58.901 45.455 0.00 0.00 0.00 2.32
1038 1154 3.473113 ACCATAAGAAGGCACCCAATT 57.527 42.857 0.00 0.00 0.00 2.32
1228 1512 6.959639 AATTTCAAGGTAAGTTTGCTCTCA 57.040 33.333 0.00 0.00 0.00 3.27
1335 1619 8.931837 CTTCATAGGAATCATAACACGGTACGC 61.932 44.444 0.00 0.00 44.77 4.42
1372 1656 2.687935 CTGCGGTATACTTGGGCAATTT 59.312 45.455 2.25 0.00 32.59 1.82
1404 1691 1.398041 GTTAACGCCCACCCGTATTTC 59.602 52.381 0.00 0.00 41.16 2.17
1437 1724 7.857456 ACCAATCAACACACTATCTTATACCA 58.143 34.615 0.00 0.00 0.00 3.25
1438 1725 9.257651 GTACCAATCAACACACTATCTTATACC 57.742 37.037 0.00 0.00 0.00 2.73
1562 1866 1.680338 AAACTCACACCTCAACTGGC 58.320 50.000 0.00 0.00 0.00 4.85
1634 1939 9.841880 GGACTTTGTTTTTCTCCTAATATTGAC 57.158 33.333 0.00 0.00 0.00 3.18
1645 1950 7.220875 GTGAACTCAATGGACTTTGTTTTTCTC 59.779 37.037 0.00 0.00 0.00 2.87
1653 1958 3.809832 AGTCGTGAACTCAATGGACTTTG 59.190 43.478 4.41 0.00 32.71 2.77
1654 1959 4.073293 AGTCGTGAACTCAATGGACTTT 57.927 40.909 4.41 0.00 32.71 2.66
1656 1961 3.753294 AAGTCGTGAACTCAATGGACT 57.247 42.857 4.41 4.41 37.17 3.85
1666 1971 5.717119 TGAATTAGGAGGTAAGTCGTGAAC 58.283 41.667 0.00 0.00 38.35 3.18
1686 1991 5.741011 ACTCGTTATGGCCTTCTAAATGAA 58.259 37.500 3.32 0.00 0.00 2.57
1687 1992 5.353394 ACTCGTTATGGCCTTCTAAATGA 57.647 39.130 3.32 0.00 0.00 2.57
1688 1993 7.730364 ATAACTCGTTATGGCCTTCTAAATG 57.270 36.000 3.32 0.00 34.71 2.32
1692 1997 8.692710 CCATATATAACTCGTTATGGCCTTCTA 58.307 37.037 3.32 0.00 35.91 2.10
1693 1998 7.399191 TCCATATATAACTCGTTATGGCCTTCT 59.601 37.037 3.32 0.00 40.50 2.85
1694 1999 7.553334 TCCATATATAACTCGTTATGGCCTTC 58.447 38.462 3.32 0.00 40.50 3.46
1695 2000 7.490657 TCCATATATAACTCGTTATGGCCTT 57.509 36.000 3.32 0.00 40.50 4.35
1696 2001 7.490657 TTCCATATATAACTCGTTATGGCCT 57.509 36.000 3.32 0.00 40.50 5.19
1697 2002 8.448615 GTTTTCCATATATAACTCGTTATGGCC 58.551 37.037 11.51 0.00 40.50 5.36
1698 2003 8.166706 CGTTTTCCATATATAACTCGTTATGGC 58.833 37.037 11.51 0.00 40.50 4.40
1699 2004 9.199982 ACGTTTTCCATATATAACTCGTTATGG 57.800 33.333 11.51 7.52 41.55 2.74
1703 2008 8.937634 AGAACGTTTTCCATATATAACTCGTT 57.062 30.769 0.46 0.00 39.73 3.85
1718 2023 3.181513 GGCGGAGGAAATAGAACGTTTTC 60.182 47.826 0.46 1.70 0.00 2.29
1719 2024 2.745821 GGCGGAGGAAATAGAACGTTTT 59.254 45.455 0.46 0.00 0.00 2.43
1720 2025 2.353323 GGCGGAGGAAATAGAACGTTT 58.647 47.619 0.46 0.00 0.00 3.60
1721 2026 1.406477 GGGCGGAGGAAATAGAACGTT 60.406 52.381 0.00 0.00 0.00 3.99
1722 2027 0.177373 GGGCGGAGGAAATAGAACGT 59.823 55.000 0.00 0.00 0.00 3.99
1723 2028 0.464452 AGGGCGGAGGAAATAGAACG 59.536 55.000 0.00 0.00 0.00 3.95
1724 2029 2.170817 AGAAGGGCGGAGGAAATAGAAC 59.829 50.000 0.00 0.00 0.00 3.01
1725 2030 2.434702 GAGAAGGGCGGAGGAAATAGAA 59.565 50.000 0.00 0.00 0.00 2.10
1726 2031 2.040178 GAGAAGGGCGGAGGAAATAGA 58.960 52.381 0.00 0.00 0.00 1.98
1727 2032 1.762957 TGAGAAGGGCGGAGGAAATAG 59.237 52.381 0.00 0.00 0.00 1.73
1728 2033 1.485066 GTGAGAAGGGCGGAGGAAATA 59.515 52.381 0.00 0.00 0.00 1.40
1729 2034 0.253327 GTGAGAAGGGCGGAGGAAAT 59.747 55.000 0.00 0.00 0.00 2.17
1730 2035 0.836400 AGTGAGAAGGGCGGAGGAAA 60.836 55.000 0.00 0.00 0.00 3.13
1731 2036 1.229209 AGTGAGAAGGGCGGAGGAA 60.229 57.895 0.00 0.00 0.00 3.36
1732 2037 1.984570 CAGTGAGAAGGGCGGAGGA 60.985 63.158 0.00 0.00 0.00 3.71
1733 2038 1.333636 ATCAGTGAGAAGGGCGGAGG 61.334 60.000 0.00 0.00 0.00 4.30
1734 2039 0.179089 CATCAGTGAGAAGGGCGGAG 60.179 60.000 0.00 0.00 0.00 4.63
1735 2040 0.614697 TCATCAGTGAGAAGGGCGGA 60.615 55.000 0.00 0.00 0.00 5.54
1736 2041 1.900351 TCATCAGTGAGAAGGGCGG 59.100 57.895 0.00 0.00 0.00 6.13
1763 2068 7.333528 AGTACAACCTATGCACCAAATAATG 57.666 36.000 0.00 0.00 0.00 1.90
1764 2069 7.228706 GCTAGTACAACCTATGCACCAAATAAT 59.771 37.037 0.00 0.00 0.00 1.28
1765 2070 6.540914 GCTAGTACAACCTATGCACCAAATAA 59.459 38.462 0.00 0.00 0.00 1.40
1766 2071 6.053005 GCTAGTACAACCTATGCACCAAATA 58.947 40.000 0.00 0.00 0.00 1.40
1767 2072 4.881850 GCTAGTACAACCTATGCACCAAAT 59.118 41.667 0.00 0.00 0.00 2.32
1768 2073 4.258543 GCTAGTACAACCTATGCACCAAA 58.741 43.478 0.00 0.00 0.00 3.28
1769 2074 3.262151 TGCTAGTACAACCTATGCACCAA 59.738 43.478 0.00 0.00 0.00 3.67
1770 2075 2.835156 TGCTAGTACAACCTATGCACCA 59.165 45.455 0.00 0.00 0.00 4.17
1771 2076 3.536956 TGCTAGTACAACCTATGCACC 57.463 47.619 0.00 0.00 0.00 5.01
1772 2077 5.628134 GTTTTGCTAGTACAACCTATGCAC 58.372 41.667 0.00 0.00 0.00 4.57
1773 2078 4.390603 CGTTTTGCTAGTACAACCTATGCA 59.609 41.667 4.54 0.00 0.00 3.96
1774 2079 4.201783 CCGTTTTGCTAGTACAACCTATGC 60.202 45.833 4.54 0.00 0.00 3.14
1775 2080 4.933400 ACCGTTTTGCTAGTACAACCTATG 59.067 41.667 4.54 0.00 0.00 2.23
1776 2081 5.156608 ACCGTTTTGCTAGTACAACCTAT 57.843 39.130 4.54 0.00 0.00 2.57
1777 2082 4.605640 ACCGTTTTGCTAGTACAACCTA 57.394 40.909 4.54 0.00 0.00 3.08
1778 2083 3.480505 ACCGTTTTGCTAGTACAACCT 57.519 42.857 4.54 0.00 0.00 3.50
1779 2084 3.363280 CGAACCGTTTTGCTAGTACAACC 60.363 47.826 4.54 0.00 0.00 3.77
1780 2085 3.245990 ACGAACCGTTTTGCTAGTACAAC 59.754 43.478 0.00 0.21 36.35 3.32
1781 2086 3.245754 CACGAACCGTTTTGCTAGTACAA 59.754 43.478 0.00 0.00 38.32 2.41
1782 2087 2.796031 CACGAACCGTTTTGCTAGTACA 59.204 45.455 0.00 0.00 38.32 2.90
1783 2088 2.410646 GCACGAACCGTTTTGCTAGTAC 60.411 50.000 10.23 0.00 38.32 2.73
1799 2104 1.180456 TCTCCCGTTGTAAGGCACGA 61.180 55.000 0.00 0.00 0.00 4.35
1829 2134 7.797121 TGATAATGGCCATCAGAGACTATAA 57.203 36.000 21.08 1.23 0.00 0.98
1830 2135 7.984859 ATGATAATGGCCATCAGAGACTATA 57.015 36.000 21.08 4.42 35.93 1.31
1834 2141 7.934855 AAATATGATAATGGCCATCAGAGAC 57.065 36.000 21.08 8.35 35.93 3.36
1839 2146 6.930164 GCAACAAAATATGATAATGGCCATCA 59.070 34.615 21.08 14.91 36.86 3.07
1840 2147 6.930164 TGCAACAAAATATGATAATGGCCATC 59.070 34.615 21.08 8.50 0.00 3.51
1849 2156 8.735692 TCTGAGTGATGCAACAAAATATGATA 57.264 30.769 0.00 0.00 0.00 2.15
1871 2178 8.412608 ACACGAAAATGAGAGTAATGTATCTG 57.587 34.615 0.00 0.00 0.00 2.90
1934 2247 4.987408 TTCCGATATGGTCACGAGTTTA 57.013 40.909 0.00 0.00 39.52 2.01
1945 2258 2.131972 TGTTCGCGATTTCCGATATGG 58.868 47.619 10.88 0.00 41.76 2.74
1952 2265 3.484683 TCGAAAAATGTTCGCGATTTCC 58.515 40.909 20.49 3.35 41.30 3.13
1960 2273 7.319227 TGTTGATGAATTCGAAAAATGTTCG 57.681 32.000 0.00 0.00 42.74 3.95
2140 2477 5.872070 GTCAAAAGTTGTTCCACAATTTCCA 59.128 36.000 0.00 0.00 40.59 3.53
2142 2479 6.959671 TGTCAAAAGTTGTTCCACAATTTC 57.040 33.333 0.00 0.00 40.59 2.17
2145 2482 6.534793 GTGAATGTCAAAAGTTGTTCCACAAT 59.465 34.615 0.00 0.00 40.59 2.71
2147 2484 5.406649 GTGAATGTCAAAAGTTGTTCCACA 58.593 37.500 0.00 0.00 0.00 4.17
2204 2552 7.775093 TCTCGGGAATTTAGAAAATGATCATGT 59.225 33.333 9.46 0.00 0.00 3.21
2247 2604 6.867662 ATTCAAAAACTCTTCGTGACTGAT 57.132 33.333 0.00 0.00 0.00 2.90
2249 2606 7.740519 AAAATTCAAAAACTCTTCGTGACTG 57.259 32.000 0.00 0.00 0.00 3.51
2286 2644 7.220108 GGCTATTTAGAAAATGTTCGCGAATTT 59.780 33.333 26.23 20.66 38.90 1.82
2303 2662 9.352784 TGAAATGAAAACAAATCGGCTATTTAG 57.647 29.630 0.00 0.00 35.54 1.85
2305 2664 8.776376 ATGAAATGAAAACAAATCGGCTATTT 57.224 26.923 0.00 0.00 38.36 1.40
2309 2668 8.034215 TGATAATGAAATGAAAACAAATCGGCT 58.966 29.630 0.00 0.00 0.00 5.52
2389 2752 6.529829 TGTGCACAGTTCTAAAAACAAATGTC 59.470 34.615 17.42 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.