Multiple sequence alignment - TraesCS2B01G349500

Loading Multiple Alignment...

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 TraesCS2B01G349500 chr2B 100.000 2354 0 0 1 2354 496119153 496116800 0.000000e+00 4348.0
1 TraesCS2B01G349500 chr2B 94.076 709 41 1 757 1465 496512659 496511952 0.000000e+00 1075.0
2 TraesCS2B01G349500 chr2B 89.774 665 42 9 115 756 30992111 30991450 0.000000e+00 828.0
3 TraesCS2B01G349500 chr2B 87.176 655 62 12 829 1465 496351197 496350547 0.000000e+00 725.0
4 TraesCS2B01G349500 chr2B 88.278 546 34 5 1809 2354 496494944 496494429 5.520000e-176 627.0
5 TraesCS2B01G349500 chr2B 85.808 613 55 12 757 1353 496087982 496087386 2.570000e-174 621.0
6 TraesCS2B01G349500 chr2B 86.949 567 55 11 829 1377 496355511 496354946 9.240000e-174 619.0
7 TraesCS2B01G349500 chr2B 86.596 567 57 11 829 1377 496353354 496352789 2.000000e-170 608.0
8 TraesCS2B01G349500 chr2B 87.168 452 43 6 946 1383 496073456 496073006 1.260000e-137 499.0
9 TraesCS2B01G349500 chr2B 91.290 310 25 2 443 751 794590574 794590882 2.800000e-114 422.0
10 TraesCS2B01G349500 chr2B 85.294 340 20 3 1809 2148 496329909 496329600 8.110000e-85 324.0
11 TraesCS2B01G349500 chr2B 92.135 178 12 1 2179 2354 496329485 496329308 1.400000e-62 250.0
12 TraesCS2B01G349500 chr2B 96.454 141 5 0 1512 1652 496511540 496511400 1.410000e-57 233.0
13 TraesCS2B01G349500 chr2B 80.851 329 31 11 757 1066 496213432 496213117 1.820000e-56 230.0
14 TraesCS2B01G349500 chr2B 87.121 132 12 3 2090 2217 496077698 496077568 6.780000e-31 145.0
15 TraesCS2B01G349500 chr2B 97.468 79 0 2 1542 1619 496330033 496329956 1.470000e-27 134.0
16 TraesCS2B01G349500 chr2B 89.157 83 5 3 1383 1465 496541827 496541749 1.490000e-17 100.0
17 TraesCS2B01G349500 chr2B 91.429 70 1 4 1383 1452 496176269 496176205 8.960000e-15 91.6
18 TraesCS2B01G349500 chr5D 93.170 776 36 2 1 759 419274752 419273977 0.000000e+00 1123.0
19 TraesCS2B01G349500 chr5D 96.903 452 14 0 1 452 490578150 490578601 0.000000e+00 758.0
20 TraesCS2B01G349500 chr5D 88.095 126 8 2 1694 1812 423546725 423546850 2.440000e-30 143.0
21 TraesCS2B01G349500 chr5D 88.430 121 8 4 1694 1812 545787764 545787648 8.770000e-30 141.0
22 TraesCS2B01G349500 chr5D 90.196 51 4 1 1762 1812 544664160 544664209 5.430000e-07 65.8
23 TraesCS2B01G349500 chr3B 92.737 771 36 4 3 756 456959082 456958315 0.000000e+00 1096.0
24 TraesCS2B01G349500 chr3B 90.519 770 52 5 7 757 31859463 31860230 0.000000e+00 998.0
25 TraesCS2B01G349500 chr3B 85.156 128 11 6 1694 1819 416577742 416577621 8.830000e-25 124.0
26 TraesCS2B01G349500 chr3B 92.135 89 6 1 1687 1774 706526719 706526631 8.830000e-25 124.0
27 TraesCS2B01G349500 chr4A 91.990 774 41 3 1 757 642509943 642509174 0.000000e+00 1066.0
28 TraesCS2B01G349500 chr4A 97.872 47 0 1 1775 1820 157318667 157318621 1.940000e-11 80.5
29 TraesCS2B01G349500 chr6B 91.624 776 42 7 1 756 701470454 701469682 0.000000e+00 1051.0
30 TraesCS2B01G349500 chr2A 92.826 697 47 2 757 1453 565256069 565256762 0.000000e+00 1007.0
31 TraesCS2B01G349500 chr2A 84.253 616 65 15 757 1353 565288225 565288827 2.620000e-159 571.0
32 TraesCS2B01G349500 chr2A 90.596 436 29 3 1919 2354 565259083 565259506 3.400000e-158 568.0
33 TraesCS2B01G349500 chr2A 82.317 656 69 20 837 1462 565282905 565283543 2.070000e-145 525.0
34 TraesCS2B01G349500 chr2A 84.503 342 18 7 1809 2144 565270855 565271167 2.940000e-79 305.0
35 TraesCS2B01G349500 chr2A 91.781 219 12 2 1483 1695 565270640 565270858 1.370000e-77 300.0
36 TraesCS2B01G349500 chr2A 85.268 224 27 4 1998 2217 565314495 565314716 2.350000e-55 226.0
37 TraesCS2B01G349500 chr2A 90.984 122 8 1 2234 2352 565271712 565271833 6.730000e-36 161.0
38 TraesCS2B01G349500 chr2A 95.294 85 3 1 1691 1774 389221174 389221090 1.470000e-27 134.0
39 TraesCS2B01G349500 chr2A 95.918 49 1 1 1775 1822 12169683 12169731 6.970000e-11 78.7
40 TraesCS2B01G349500 chrUn 90.629 779 42 6 1 751 3682533 3681758 0.000000e+00 1005.0
41 TraesCS2B01G349500 chrUn 96.018 452 18 0 1 452 468798904 468799355 0.000000e+00 736.0
42 TraesCS2B01G349500 chr7B 88.950 733 50 10 52 756 107381809 107382538 0.000000e+00 876.0
43 TraesCS2B01G349500 chr7D 92.896 549 22 2 1 532 9258198 9257650 0.000000e+00 782.0
44 TraesCS2B01G349500 chr7D 95.575 452 19 1 1 452 491654197 491653747 0.000000e+00 723.0
45 TraesCS2B01G349500 chr7D 90.196 51 4 1 1762 1812 6818738 6818787 5.430000e-07 65.8
46 TraesCS2B01G349500 chr7D 90.196 51 4 1 1762 1812 612887003 612887052 5.430000e-07 65.8
47 TraesCS2B01G349500 chr6D 96.288 458 15 2 1 457 457495546 457495090 0.000000e+00 750.0
48 TraesCS2B01G349500 chr6D 96.239 452 17 0 1 452 320014250 320013799 0.000000e+00 741.0
49 TraesCS2B01G349500 chr6D 88.136 59 7 0 1775 1833 130273366 130273308 1.170000e-08 71.3
50 TraesCS2B01G349500 chr6D 88.136 59 7 0 1775 1833 366999136 366999078 1.170000e-08 71.3
51 TraesCS2B01G349500 chr3D 95.354 452 21 0 1 452 484297213 484297664 0.000000e+00 719.0
52 TraesCS2B01G349500 chr3D 95.181 83 3 1 1693 1774 412074487 412074569 1.900000e-26 130.0
53 TraesCS2B01G349500 chr3D 89.831 59 2 4 1770 1825 549376429 549376372 3.250000e-09 73.1
54 TraesCS2B01G349500 chr2D 90.433 439 31 6 1919 2354 423308888 423308458 3.400000e-158 568.0
55 TraesCS2B01G349500 chr2D 83.048 643 52 24 814 1420 423292542 423291921 4.450000e-147 531.0
56 TraesCS2B01G349500 chr2D 89.549 421 29 7 949 1363 423288191 423287780 9.640000e-144 520.0
57 TraesCS2B01G349500 chr2D 85.127 511 42 12 814 1298 423347836 423347334 2.100000e-135 492.0
58 TraesCS2B01G349500 chr2D 91.589 214 10 2 1486 1695 423309148 423308939 2.960000e-74 289.0
59 TraesCS2B01G349500 chr2D 83.333 324 34 9 2034 2354 423291422 423291116 4.950000e-72 281.0
60 TraesCS2B01G349500 chr2D 86.857 175 16 5 1515 1686 423347153 423346983 3.090000e-44 189.0
61 TraesCS2B01G349500 chr2D 91.139 79 7 0 1541 1619 423291765 423291687 8.900000e-20 108.0
62 TraesCS2B01G349500 chr2D 93.478 46 1 1 1809 1852 423308942 423308897 1.510000e-07 67.6
63 TraesCS2B01G349500 chr2D 90.196 51 4 1 1762 1812 72820030 72820079 5.430000e-07 65.8
64 TraesCS2B01G349500 chr1B 95.294 85 3 1 1691 1774 522838624 522838708 1.470000e-27 134.0
65 TraesCS2B01G349500 chr1B 89.796 49 5 0 1765 1813 677128229 677128181 1.950000e-06 63.9
66 TraesCS2B01G349500 chr1A 92.391 92 3 3 1694 1784 480758913 480758825 6.830000e-26 128.0
67 TraesCS2B01G349500 chr7A 92.222 90 5 2 1686 1774 454289143 454289231 2.460000e-25 126.0
68 TraesCS2B01G349500 chr4B 92.593 54 3 1 1775 1827 97895010 97895063 2.510000e-10 76.8


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 TraesCS2B01G349500 chr2B 496116800 496119153 2353 True 4348.000000 4348 100.000000 1 2354 1 chr2B.!!$R5 2353
1 TraesCS2B01G349500 chr2B 30991450 30992111 661 True 828.000000 828 89.774000 115 756 1 chr2B.!!$R1 641
2 TraesCS2B01G349500 chr2B 496511400 496512659 1259 True 654.000000 1075 95.265000 757 1652 2 chr2B.!!$R12 895
3 TraesCS2B01G349500 chr2B 496350547 496355511 4964 True 650.666667 725 86.907000 829 1465 3 chr2B.!!$R11 636
4 TraesCS2B01G349500 chr2B 496494429 496494944 515 True 627.000000 627 88.278000 1809 2354 1 chr2B.!!$R8 545
5 TraesCS2B01G349500 chr2B 496087386 496087982 596 True 621.000000 621 85.808000 757 1353 1 chr2B.!!$R4 596
6 TraesCS2B01G349500 chr2B 496329308 496330033 725 True 236.000000 324 91.632333 1542 2354 3 chr2B.!!$R10 812
7 TraesCS2B01G349500 chr5D 419273977 419274752 775 True 1123.000000 1123 93.170000 1 759 1 chr5D.!!$R1 758
8 TraesCS2B01G349500 chr3B 456958315 456959082 767 True 1096.000000 1096 92.737000 3 756 1 chr3B.!!$R2 753
9 TraesCS2B01G349500 chr3B 31859463 31860230 767 False 998.000000 998 90.519000 7 757 1 chr3B.!!$F1 750
10 TraesCS2B01G349500 chr4A 642509174 642509943 769 True 1066.000000 1066 91.990000 1 757 1 chr4A.!!$R2 756
11 TraesCS2B01G349500 chr6B 701469682 701470454 772 True 1051.000000 1051 91.624000 1 756 1 chr6B.!!$R1 755
12 TraesCS2B01G349500 chr2A 565256069 565259506 3437 False 787.500000 1007 91.711000 757 2354 2 chr2A.!!$F5 1597
13 TraesCS2B01G349500 chr2A 565288225 565288827 602 False 571.000000 571 84.253000 757 1353 1 chr2A.!!$F3 596
14 TraesCS2B01G349500 chr2A 565282905 565283543 638 False 525.000000 525 82.317000 837 1462 1 chr2A.!!$F2 625
15 TraesCS2B01G349500 chr2A 565270640 565271833 1193 False 255.333333 305 89.089333 1483 2352 3 chr2A.!!$F6 869
16 TraesCS2B01G349500 chrUn 3681758 3682533 775 True 1005.000000 1005 90.629000 1 751 1 chrUn.!!$R1 750
17 TraesCS2B01G349500 chr7B 107381809 107382538 729 False 876.000000 876 88.950000 52 756 1 chr7B.!!$F1 704
18 TraesCS2B01G349500 chr7D 9257650 9258198 548 True 782.000000 782 92.896000 1 532 1 chr7D.!!$R1 531
19 TraesCS2B01G349500 chr2D 423287780 423292542 4762 True 360.000000 531 86.767250 814 2354 4 chr2D.!!$R1 1540
20 TraesCS2B01G349500 chr2D 423346983 423347836 853 True 340.500000 492 85.992000 814 1686 2 chr2D.!!$R3 872
21 TraesCS2B01G349500 chr2D 423308458 423309148 690 True 308.200000 568 91.833333 1486 2354 3 chr2D.!!$R2 868

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
732 782 0.179119 GACCGTTGATACGTCCAGGG 60.179 60.0 0.0 0.0 46.2 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 9144 0.532862 CCAGTCTGGTTGTCGTGCTT 60.533 55.0 11.09 0.0 31.35 3.91 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
562 611 3.483869 GCCCGCCCTTCTCCTCAT 61.484 66.667 0.00 0.00 0.00 2.90
662 712 1.337354 CGCCGCCCCAAACTAAATTTT 60.337 47.619 0.00 0.00 0.00 1.82
663 713 2.773487 GCCGCCCCAAACTAAATTTTT 58.227 42.857 0.00 0.00 0.00 1.94
723 773 6.879276 ATCTTCTAATCTCGACCGTTGATA 57.121 37.500 0.00 0.00 0.00 2.15
724 774 6.057627 TCTTCTAATCTCGACCGTTGATAC 57.942 41.667 0.00 0.00 0.00 2.24
732 782 0.179119 GACCGTTGATACGTCCAGGG 60.179 60.000 0.00 0.00 46.20 4.45
752 802 1.338484 GGGGGTTGTACCGAAGAAGAC 60.338 57.143 0.00 0.00 39.83 3.01
783 833 0.669318 TCGCCTCGAACACCAACATC 60.669 55.000 0.00 0.00 31.06 3.06
793 843 1.097547 CACCAACATCTCCCCATCGC 61.098 60.000 0.00 0.00 0.00 4.58
867 917 5.431179 GGTGAGGAACCCTATTCAGTTTA 57.569 43.478 0.00 0.00 44.02 2.01
1027 5427 0.673644 CGACAAGAGCCGGTCCAAAT 60.674 55.000 1.90 0.00 0.00 2.32
1028 5428 1.534729 GACAAGAGCCGGTCCAAATT 58.465 50.000 1.90 0.00 0.00 1.82
1034 5434 2.505819 AGAGCCGGTCCAAATTACTGAT 59.494 45.455 1.90 0.00 0.00 2.90
1081 5481 2.123939 CCATGGGCATAACCGGCA 60.124 61.111 2.85 0.00 40.62 5.69
1166 5566 2.357517 CAAGAAGCTCGGCCACGT 60.358 61.111 2.24 0.00 41.85 4.49
1181 5581 1.745087 CCACGTCCAAATCATCAAGGG 59.255 52.381 0.00 0.00 0.00 3.95
1226 5626 3.379452 AGAAGAAGAAGGATGACCCGAT 58.621 45.455 0.00 0.00 40.87 4.18
1329 5741 1.334160 TGGTAGTCTGCGAGGAACAA 58.666 50.000 0.00 0.00 0.00 2.83
1335 5747 1.301401 CTGCGAGGAACAACCCGAA 60.301 57.895 0.00 0.00 40.05 4.30
1357 5769 2.203070 GCCGGACCATGTAGCTGG 60.203 66.667 5.05 0.00 42.35 4.85
1492 8176 6.093771 TGAATCTCAGTTCTCGTAGTTCCTAC 59.906 42.308 0.00 0.00 33.99 3.18
1626 8385 3.515502 GTCCTCCAATCATATGATCGGGA 59.484 47.826 25.82 25.82 36.31 5.14
1662 8432 3.193395 TCCATATATAAGCCCGGTCCA 57.807 47.619 0.00 0.00 0.00 4.02
1691 8461 5.798132 ACTGAATAAGATCTGCACAGTCAA 58.202 37.500 14.83 0.00 32.84 3.18
1693 8463 5.798132 TGAATAAGATCTGCACAGTCAAGT 58.202 37.500 0.00 0.00 0.00 3.16
1694 8464 6.935167 TGAATAAGATCTGCACAGTCAAGTA 58.065 36.000 0.00 0.00 0.00 2.24
1695 8465 6.813649 TGAATAAGATCTGCACAGTCAAGTAC 59.186 38.462 0.00 0.00 0.00 2.73
1696 8466 4.881019 AAGATCTGCACAGTCAAGTACT 57.119 40.909 0.00 0.00 39.81 2.73
1697 8467 4.448537 AGATCTGCACAGTCAAGTACTC 57.551 45.455 0.00 0.00 35.76 2.59
1698 8468 3.194542 AGATCTGCACAGTCAAGTACTCC 59.805 47.826 0.00 0.00 35.76 3.85
1699 8469 1.618837 TCTGCACAGTCAAGTACTCCC 59.381 52.381 0.00 0.00 35.76 4.30
1700 8470 1.620819 CTGCACAGTCAAGTACTCCCT 59.379 52.381 0.00 0.00 35.76 4.20
1701 8471 1.618837 TGCACAGTCAAGTACTCCCTC 59.381 52.381 0.00 0.00 35.76 4.30
1702 8472 1.066787 GCACAGTCAAGTACTCCCTCC 60.067 57.143 0.00 0.00 35.76 4.30
1703 8473 1.202582 CACAGTCAAGTACTCCCTCCG 59.797 57.143 0.00 0.00 35.76 4.63
1704 8474 1.203025 ACAGTCAAGTACTCCCTCCGT 60.203 52.381 0.00 0.00 35.76 4.69
1705 8475 1.893801 CAGTCAAGTACTCCCTCCGTT 59.106 52.381 0.00 0.00 35.76 4.44
1706 8476 2.299297 CAGTCAAGTACTCCCTCCGTTT 59.701 50.000 0.00 0.00 35.76 3.60
1707 8477 2.561858 AGTCAAGTACTCCCTCCGTTTC 59.438 50.000 0.00 0.00 30.33 2.78
1708 8478 2.561858 GTCAAGTACTCCCTCCGTTTCT 59.438 50.000 0.00 0.00 0.00 2.52
1709 8479 3.760684 GTCAAGTACTCCCTCCGTTTCTA 59.239 47.826 0.00 0.00 0.00 2.10
1710 8480 4.219288 GTCAAGTACTCCCTCCGTTTCTAA 59.781 45.833 0.00 0.00 0.00 2.10
1711 8481 4.834496 TCAAGTACTCCCTCCGTTTCTAAA 59.166 41.667 0.00 0.00 0.00 1.85
1712 8482 5.482878 TCAAGTACTCCCTCCGTTTCTAAAT 59.517 40.000 0.00 0.00 0.00 1.40
1713 8483 6.664816 TCAAGTACTCCCTCCGTTTCTAAATA 59.335 38.462 0.00 0.00 0.00 1.40
1714 8484 7.343833 TCAAGTACTCCCTCCGTTTCTAAATAT 59.656 37.037 0.00 0.00 0.00 1.28
1715 8485 8.636213 CAAGTACTCCCTCCGTTTCTAAATATA 58.364 37.037 0.00 0.00 0.00 0.86
1716 8486 8.773033 AGTACTCCCTCCGTTTCTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
1717 8487 8.858094 AGTACTCCCTCCGTTTCTAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
1718 8488 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
1719 8489 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
1720 8490 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
1721 8491 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
1722 8492 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
1723 8493 9.043079 CCCTCCGTTTCTAAATATAAGTCTTTC 57.957 37.037 0.00 0.00 0.00 2.62
1724 8494 9.819267 CCTCCGTTTCTAAATATAAGTCTTTCT 57.181 33.333 0.00 0.00 0.00 2.52
1739 8509 9.883142 ATAAGTCTTTCTAGAGATTCCAACAAG 57.117 33.333 0.00 0.00 0.00 3.16
1740 8510 7.309770 AGTCTTTCTAGAGATTCCAACAAGT 57.690 36.000 0.00 0.00 0.00 3.16
1741 8511 7.158021 AGTCTTTCTAGAGATTCCAACAAGTG 58.842 38.462 0.00 0.00 0.00 3.16
1742 8512 7.015682 AGTCTTTCTAGAGATTCCAACAAGTGA 59.984 37.037 0.00 0.00 0.00 3.41
1743 8513 7.117092 GTCTTTCTAGAGATTCCAACAAGTGAC 59.883 40.741 0.00 0.00 0.00 3.67
1744 8514 6.672266 TTCTAGAGATTCCAACAAGTGACT 57.328 37.500 0.00 0.00 0.00 3.41
1745 8515 7.776618 TTCTAGAGATTCCAACAAGTGACTA 57.223 36.000 0.00 0.00 0.00 2.59
1746 8516 7.159322 TCTAGAGATTCCAACAAGTGACTAC 57.841 40.000 0.00 0.00 0.00 2.73
1747 8517 5.808366 AGAGATTCCAACAAGTGACTACA 57.192 39.130 0.00 0.00 0.00 2.74
1748 8518 6.365970 AGAGATTCCAACAAGTGACTACAT 57.634 37.500 0.00 0.00 0.00 2.29
1749 8519 7.482169 AGAGATTCCAACAAGTGACTACATA 57.518 36.000 0.00 0.00 0.00 2.29
1750 8520 7.324178 AGAGATTCCAACAAGTGACTACATAC 58.676 38.462 0.00 0.00 0.00 2.39
1751 8521 7.004555 AGATTCCAACAAGTGACTACATACA 57.995 36.000 0.00 0.00 0.00 2.29
1752 8522 7.450074 AGATTCCAACAAGTGACTACATACAA 58.550 34.615 0.00 0.00 0.00 2.41
1753 8523 7.936847 AGATTCCAACAAGTGACTACATACAAA 59.063 33.333 0.00 0.00 0.00 2.83
1754 8524 7.867305 TTCCAACAAGTGACTACATACAAAA 57.133 32.000 0.00 0.00 0.00 2.44
1755 8525 7.867305 TCCAACAAGTGACTACATACAAAAA 57.133 32.000 0.00 0.00 0.00 1.94
1779 8549 8.627208 AAAAATGAGTGAATCTACACATGTCT 57.373 30.769 0.00 0.00 42.45 3.41
1780 8550 9.725019 AAAAATGAGTGAATCTACACATGTCTA 57.275 29.630 0.00 0.00 42.45 2.59
1781 8551 9.725019 AAAATGAGTGAATCTACACATGTCTAA 57.275 29.630 0.00 0.00 42.45 2.10
1782 8552 9.725019 AAATGAGTGAATCTACACATGTCTAAA 57.275 29.630 0.00 0.00 42.45 1.85
1783 8553 9.725019 AATGAGTGAATCTACACATGTCTAAAA 57.275 29.630 0.00 0.00 42.45 1.52
1784 8554 9.725019 ATGAGTGAATCTACACATGTCTAAAAA 57.275 29.630 0.00 0.00 42.45 1.94
1785 8555 9.208022 TGAGTGAATCTACACATGTCTAAAAAG 57.792 33.333 0.00 0.00 42.45 2.27
1786 8556 9.424319 GAGTGAATCTACACATGTCTAAAAAGA 57.576 33.333 0.00 0.00 42.45 2.52
1787 8557 9.209175 AGTGAATCTACACATGTCTAAAAAGAC 57.791 33.333 0.00 0.00 42.45 3.01
1788 8558 9.209175 GTGAATCTACACATGTCTAAAAAGACT 57.791 33.333 0.00 0.00 40.11 3.24
1789 8559 9.778741 TGAATCTACACATGTCTAAAAAGACTT 57.221 29.630 0.00 0.00 39.41 3.01
1806 8576 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
1807 8577 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
1813 8583 8.731591 TTATATTTAGGAACGGAGGGAGTATT 57.268 34.615 0.00 0.00 0.00 1.89
1907 8728 5.885465 ACATCAGGAGAAGGTCTGATTTTT 58.115 37.500 3.40 0.00 45.32 1.94
1951 8772 7.596749 TTCTTCGTCTTCTTACATTCCATTC 57.403 36.000 0.00 0.00 0.00 2.67
1963 8784 4.428570 ACATTCCATTCCATTTGGTTCCT 58.571 39.130 0.00 0.00 35.64 3.36
2036 8857 3.253061 TGGGCCGGGTCAATGACA 61.253 61.111 15.86 0.00 33.68 3.58
2043 8864 2.420129 GCCGGGTCAATGACAAGAGTAT 60.420 50.000 15.86 0.00 33.68 2.12
2062 8883 5.408356 AGTATAGTAACCAAACTGCTGACG 58.592 41.667 0.00 0.00 0.00 4.35
2085 8906 7.186804 ACGAGAAGTTTGTGACAATAACAAAG 58.813 34.615 0.00 0.00 45.49 2.77
2124 8951 1.065418 CAGGTTGTCTACATCCCCACC 60.065 57.143 6.59 0.53 36.59 4.61
2164 9138 1.185315 GTATTGGCCACCAACTGCAT 58.815 50.000 3.88 0.00 46.95 3.96
2170 9144 1.408683 GGCCACCAACTGCATAGATCA 60.409 52.381 0.00 0.00 0.00 2.92
2177 9235 2.931969 CAACTGCATAGATCAAGCACGA 59.068 45.455 0.00 0.00 34.13 4.35
2277 9645 6.309980 TGCACCGATATTTAAGTTTTTGCATG 59.690 34.615 0.00 0.00 31.59 4.06
2282 9652 8.372521 CCGATATTTAAGTTTTTGCATGTGAAC 58.627 33.333 0.00 0.00 0.00 3.18
2283 9653 8.910666 CGATATTTAAGTTTTTGCATGTGAACA 58.089 29.630 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 2.665603 GAGGAGCTCGCCCACTTT 59.334 61.111 7.83 0.00 0.00 2.66
339 351 3.129287 CCTTTGACAGCTCGGCATTAATT 59.871 43.478 0.00 0.00 0.00 1.40
554 603 2.049767 TGTACGCCGCATGAGGAGA 61.050 57.895 24.96 6.73 35.00 3.71
636 686 4.266543 TTTGGGGCGGCGTACCAA 62.267 61.111 25.77 25.77 42.16 3.67
662 712 4.348020 AAGTGAGTAGGGGTAGGATGAA 57.652 45.455 0.00 0.00 0.00 2.57
663 713 5.459241 GGATAAGTGAGTAGGGGTAGGATGA 60.459 48.000 0.00 0.00 0.00 2.92
732 782 0.978907 TCTTCTTCGGTACAACCCCC 59.021 55.000 0.00 0.00 33.75 5.40
752 802 1.226717 GAGGCGAGGCTAGAACACG 60.227 63.158 0.00 0.00 0.00 4.49
783 833 4.598894 CAGGAGCGCGATGGGGAG 62.599 72.222 12.10 0.00 0.00 4.30
1081 5481 4.335647 CAGCTGGTCCCTGGCGTT 62.336 66.667 5.57 0.00 0.00 4.84
1166 5566 1.570501 CCTCCCCCTTGATGATTTGGA 59.429 52.381 0.00 0.00 0.00 3.53
1181 5581 1.604915 GGCTTCTTCACCTCCTCCC 59.395 63.158 0.00 0.00 0.00 4.30
1252 5658 4.183686 GTAGTAGCACGGCGGCGA 62.184 66.667 38.93 13.16 39.27 5.54
1329 5741 2.281276 GTCCGGCAGTTTTCGGGT 60.281 61.111 0.00 0.00 45.69 5.28
1335 5747 0.676782 GCTACATGGTCCGGCAGTTT 60.677 55.000 0.00 0.00 0.00 2.66
1357 5769 2.476854 GCACGTCAAAATGGATCTCTGC 60.477 50.000 0.00 0.00 0.00 4.26
1454 5896 5.625150 ACTGAGATTCATATAACCAAGGGC 58.375 41.667 0.00 0.00 0.00 5.19
1456 5898 7.383572 CGAGAACTGAGATTCATATAACCAAGG 59.616 40.741 0.00 0.00 0.00 3.61
1492 8176 6.360909 TGTCCTATTTGACGCACATGTAGTG 61.361 44.000 10.40 8.63 40.90 2.74
1510 8239 7.042950 GTCTATCTATCTATCGTGCTGTCCTA 58.957 42.308 0.00 0.00 0.00 2.94
1662 8432 8.263640 ACTGTGCAGATCTTATTCAGTTCTTAT 58.736 33.333 6.17 0.00 30.15 1.73
1691 8461 8.773033 TTATATTTAGAAACGGAGGGAGTACT 57.227 34.615 0.00 0.00 0.00 2.73
1693 8463 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
1694 8464 7.564292 AGACTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
1695 8465 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
1696 8466 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
1697 8467 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
1698 8468 9.819267 AGAAAGACTTATATTTAGAAACGGAGG 57.181 33.333 0.00 0.00 0.00 4.30
1713 8483 9.883142 CTTGTTGGAATCTCTAGAAAGACTTAT 57.117 33.333 0.00 0.00 0.00 1.73
1714 8484 8.871125 ACTTGTTGGAATCTCTAGAAAGACTTA 58.129 33.333 0.00 0.00 0.00 2.24
1715 8485 7.659390 CACTTGTTGGAATCTCTAGAAAGACTT 59.341 37.037 0.00 0.00 0.00 3.01
1716 8486 7.015682 TCACTTGTTGGAATCTCTAGAAAGACT 59.984 37.037 0.00 0.00 0.00 3.24
1717 8487 7.117092 GTCACTTGTTGGAATCTCTAGAAAGAC 59.883 40.741 0.00 0.00 0.00 3.01
1718 8488 7.015682 AGTCACTTGTTGGAATCTCTAGAAAGA 59.984 37.037 0.00 0.00 0.00 2.52
1719 8489 7.158021 AGTCACTTGTTGGAATCTCTAGAAAG 58.842 38.462 0.00 0.00 0.00 2.62
1720 8490 7.067496 AGTCACTTGTTGGAATCTCTAGAAA 57.933 36.000 0.00 0.00 0.00 2.52
1721 8491 6.672266 AGTCACTTGTTGGAATCTCTAGAA 57.328 37.500 0.00 0.00 0.00 2.10
1722 8492 6.719829 TGTAGTCACTTGTTGGAATCTCTAGA 59.280 38.462 0.00 0.00 0.00 2.43
1723 8493 6.925211 TGTAGTCACTTGTTGGAATCTCTAG 58.075 40.000 0.00 0.00 0.00 2.43
1724 8494 6.911250 TGTAGTCACTTGTTGGAATCTCTA 57.089 37.500 0.00 0.00 0.00 2.43
1725 8495 5.808366 TGTAGTCACTTGTTGGAATCTCT 57.192 39.130 0.00 0.00 0.00 3.10
1726 8496 7.097192 TGTATGTAGTCACTTGTTGGAATCTC 58.903 38.462 0.00 0.00 0.00 2.75
1727 8497 7.004555 TGTATGTAGTCACTTGTTGGAATCT 57.995 36.000 0.00 0.00 0.00 2.40
1728 8498 7.667043 TTGTATGTAGTCACTTGTTGGAATC 57.333 36.000 0.00 0.00 0.00 2.52
1729 8499 8.458573 TTTTGTATGTAGTCACTTGTTGGAAT 57.541 30.769 0.00 0.00 0.00 3.01
1730 8500 7.867305 TTTTGTATGTAGTCACTTGTTGGAA 57.133 32.000 0.00 0.00 0.00 3.53
1731 8501 7.867305 TTTTTGTATGTAGTCACTTGTTGGA 57.133 32.000 0.00 0.00 0.00 3.53
1754 8524 8.627208 AGACATGTGTAGATTCACTCATTTTT 57.373 30.769 1.15 0.00 38.90 1.94
1755 8525 9.725019 TTAGACATGTGTAGATTCACTCATTTT 57.275 29.630 1.15 0.00 38.90 1.82
1756 8526 9.725019 TTTAGACATGTGTAGATTCACTCATTT 57.275 29.630 1.15 0.00 38.90 2.32
1757 8527 9.725019 TTTTAGACATGTGTAGATTCACTCATT 57.275 29.630 1.15 0.00 38.90 2.57
1758 8528 9.725019 TTTTTAGACATGTGTAGATTCACTCAT 57.275 29.630 1.15 0.00 38.90 2.90
1759 8529 9.208022 CTTTTTAGACATGTGTAGATTCACTCA 57.792 33.333 1.15 0.00 38.90 3.41
1760 8530 9.424319 TCTTTTTAGACATGTGTAGATTCACTC 57.576 33.333 1.15 0.00 38.90 3.51
1761 8531 9.209175 GTCTTTTTAGACATGTGTAGATTCACT 57.791 33.333 1.15 0.00 37.65 3.41
1762 8532 9.209175 AGTCTTTTTAGACATGTGTAGATTCAC 57.791 33.333 1.15 0.00 41.02 3.18
1763 8533 9.778741 AAGTCTTTTTAGACATGTGTAGATTCA 57.221 29.630 1.15 0.00 41.02 2.57
1780 8550 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
1781 8551 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
1782 8552 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1783 8553 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1784 8554 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1785 8555 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1786 8556 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1787 8557 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1788 8558 8.591072 CAATACTCCCTCCGTTCCTAAATATAA 58.409 37.037 0.00 0.00 0.00 0.98
1789 8559 7.731688 ACAATACTCCCTCCGTTCCTAAATATA 59.268 37.037 0.00 0.00 0.00 0.86
1790 8560 6.557633 ACAATACTCCCTCCGTTCCTAAATAT 59.442 38.462 0.00 0.00 0.00 1.28
1791 8561 5.901276 ACAATACTCCCTCCGTTCCTAAATA 59.099 40.000 0.00 0.00 0.00 1.40
1792 8562 4.720273 ACAATACTCCCTCCGTTCCTAAAT 59.280 41.667 0.00 0.00 0.00 1.40
1793 8563 4.098894 ACAATACTCCCTCCGTTCCTAAA 58.901 43.478 0.00 0.00 0.00 1.85
1794 8564 3.716431 ACAATACTCCCTCCGTTCCTAA 58.284 45.455 0.00 0.00 0.00 2.69
1795 8565 3.393426 ACAATACTCCCTCCGTTCCTA 57.607 47.619 0.00 0.00 0.00 2.94
1796 8566 2.249309 ACAATACTCCCTCCGTTCCT 57.751 50.000 0.00 0.00 0.00 3.36
1797 8567 4.476628 TTAACAATACTCCCTCCGTTCC 57.523 45.455 0.00 0.00 0.00 3.62
1798 8568 4.874396 CCTTTAACAATACTCCCTCCGTTC 59.126 45.833 0.00 0.00 0.00 3.95
1799 8569 4.287845 ACCTTTAACAATACTCCCTCCGTT 59.712 41.667 0.00 0.00 0.00 4.44
1800 8570 3.842436 ACCTTTAACAATACTCCCTCCGT 59.158 43.478 0.00 0.00 0.00 4.69
1801 8571 4.482952 ACCTTTAACAATACTCCCTCCG 57.517 45.455 0.00 0.00 0.00 4.63
1802 8572 6.008331 ACAAACCTTTAACAATACTCCCTCC 58.992 40.000 0.00 0.00 0.00 4.30
1803 8573 8.803397 ATACAAACCTTTAACAATACTCCCTC 57.197 34.615 0.00 0.00 0.00 4.30
1804 8574 9.239551 GAATACAAACCTTTAACAATACTCCCT 57.760 33.333 0.00 0.00 0.00 4.20
1805 8575 9.239551 AGAATACAAACCTTTAACAATACTCCC 57.760 33.333 0.00 0.00 0.00 4.30
1907 8728 5.650283 AGAAAATCAGACCATACCCCAAAA 58.350 37.500 0.00 0.00 0.00 2.44
1908 8729 5.269554 AGAAAATCAGACCATACCCCAAA 57.730 39.130 0.00 0.00 0.00 3.28
1909 8730 4.946160 AGAAAATCAGACCATACCCCAA 57.054 40.909 0.00 0.00 0.00 4.12
1910 8731 4.625324 CGAAGAAAATCAGACCATACCCCA 60.625 45.833 0.00 0.00 0.00 4.96
1911 8732 3.877508 CGAAGAAAATCAGACCATACCCC 59.122 47.826 0.00 0.00 0.00 4.95
1912 8733 4.514401 ACGAAGAAAATCAGACCATACCC 58.486 43.478 0.00 0.00 0.00 3.69
1913 8734 5.420409 AGACGAAGAAAATCAGACCATACC 58.580 41.667 0.00 0.00 0.00 2.73
1914 8735 6.814146 AGAAGACGAAGAAAATCAGACCATAC 59.186 38.462 0.00 0.00 0.00 2.39
1915 8736 6.936279 AGAAGACGAAGAAAATCAGACCATA 58.064 36.000 0.00 0.00 0.00 2.74
1916 8737 5.799213 AGAAGACGAAGAAAATCAGACCAT 58.201 37.500 0.00 0.00 0.00 3.55
1917 8738 5.215252 AGAAGACGAAGAAAATCAGACCA 57.785 39.130 0.00 0.00 0.00 4.02
1918 8739 6.645415 TGTAAGAAGACGAAGAAAATCAGACC 59.355 38.462 0.00 0.00 0.00 3.85
1919 8740 7.639162 TGTAAGAAGACGAAGAAAATCAGAC 57.361 36.000 0.00 0.00 0.00 3.51
1920 8741 8.833231 AATGTAAGAAGACGAAGAAAATCAGA 57.167 30.769 0.00 0.00 0.00 3.27
1921 8742 8.171840 GGAATGTAAGAAGACGAAGAAAATCAG 58.828 37.037 0.00 0.00 0.00 2.90
1922 8743 7.659799 TGGAATGTAAGAAGACGAAGAAAATCA 59.340 33.333 0.00 0.00 0.00 2.57
1923 8744 8.029642 TGGAATGTAAGAAGACGAAGAAAATC 57.970 34.615 0.00 0.00 0.00 2.17
1924 8745 7.979444 TGGAATGTAAGAAGACGAAGAAAAT 57.021 32.000 0.00 0.00 0.00 1.82
1925 8746 7.979444 ATGGAATGTAAGAAGACGAAGAAAA 57.021 32.000 0.00 0.00 0.00 2.29
1926 8747 7.119262 GGAATGGAATGTAAGAAGACGAAGAAA 59.881 37.037 0.00 0.00 0.00 2.52
1927 8748 6.594159 GGAATGGAATGTAAGAAGACGAAGAA 59.406 38.462 0.00 0.00 0.00 2.52
1928 8749 6.106673 GGAATGGAATGTAAGAAGACGAAGA 58.893 40.000 0.00 0.00 0.00 2.87
1963 8784 2.356382 AGAAAATCGTGCGTTTGGTTCA 59.644 40.909 0.00 0.00 0.00 3.18
1990 8811 7.338703 CCCACTGACTGATGTAGTAACTAGTAA 59.661 40.741 0.00 0.00 40.53 2.24
1991 8812 6.827251 CCCACTGACTGATGTAGTAACTAGTA 59.173 42.308 0.00 0.00 40.53 1.82
1992 8813 5.652891 CCCACTGACTGATGTAGTAACTAGT 59.347 44.000 0.00 0.00 40.53 2.57
1993 8814 5.067936 CCCCACTGACTGATGTAGTAACTAG 59.932 48.000 0.00 0.00 40.53 2.57
1994 8815 4.954202 CCCCACTGACTGATGTAGTAACTA 59.046 45.833 0.00 0.00 40.53 2.24
1995 8816 3.769844 CCCCACTGACTGATGTAGTAACT 59.230 47.826 0.00 0.00 40.53 2.24
1996 8817 3.118738 CCCCCACTGACTGATGTAGTAAC 60.119 52.174 0.00 0.00 40.53 2.50
2036 8857 7.097834 GTCAGCAGTTTGGTTACTATACTCTT 58.902 38.462 0.00 0.00 0.00 2.85
2043 8864 3.570975 TCTCGTCAGCAGTTTGGTTACTA 59.429 43.478 0.00 0.00 0.00 1.82
2062 8883 7.480810 ACCTTTGTTATTGTCACAAACTTCTC 58.519 34.615 0.00 0.00 38.84 2.87
2085 8906 4.020485 ACCTGATACCAACAGTCTTGTACC 60.020 45.833 0.00 0.00 36.23 3.34
2164 9138 2.560981 TCTGGTTGTCGTGCTTGATCTA 59.439 45.455 0.00 0.00 0.00 1.98
2170 9144 0.532862 CCAGTCTGGTTGTCGTGCTT 60.533 55.000 11.09 0.00 31.35 3.91
2199 9257 7.510675 TCATTAGAACAGTTCCTAAATCCCT 57.489 36.000 9.85 0.00 0.00 4.20
2277 9645 3.839293 ACTCTACAGAGCGAATGTTCAC 58.161 45.455 6.15 0.00 45.79 3.18
2282 9652 5.228220 CGAAGTTTACTCTACAGAGCGAATG 59.772 44.000 6.15 0.00 45.79 2.67
2283 9653 5.123502 TCGAAGTTTACTCTACAGAGCGAAT 59.876 40.000 6.15 0.00 45.79 3.34


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

AutoCloner maintained by Alex Coulton.