Multiple sequence alignment - TraesCS7D01G074900

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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 TraesCS7D01G074900 chr7D 100.000 2824 0 0 1 2824 44522208 44519385 0.000000e+00 5216.0
1 TraesCS7D01G074900 chr7D 94.286 105 2 4 2469 2571 44570338 44570236 1.050000e-34 158.0
2 TraesCS7D01G074900 chr7D 89.256 121 9 4 2454 2572 44403391 44403273 6.300000e-32 148.0
3 TraesCS7D01G074900 chr7D 89.256 121 9 4 2454 2572 44571608 44571490 6.300000e-32 148.0
4 TraesCS7D01G074900 chr7D 100.000 32 0 0 2563 2594 44572609 44572640 3.040000e-05 60.2
5 TraesCS7D01G074900 chr7A 89.850 798 52 17 479 1273 46965456 46964685 0.000000e+00 998.0
6 TraesCS7D01G074900 chr7A 92.094 468 27 8 18 479 46966094 46965631 0.000000e+00 651.0
7 TraesCS7D01G074900 chr7A 89.239 381 9 9 2199 2571 46964249 46963893 5.550000e-122 448.0
8 TraesCS7D01G074900 chr7A 86.073 438 21 11 1732 2141 46964677 46964252 4.320000e-118 435.0
9 TraesCS7D01G074900 chr7A 84.880 291 22 10 2555 2824 46963847 46963558 9.970000e-70 274.0
10 TraesCS7D01G074900 chr7A 84.871 271 24 14 2563 2824 46974777 46974515 1.000000e-64 257.0
11 TraesCS7D01G074900 chr7A 96.154 78 1 2 2563 2640 46975030 46974955 2.950000e-25 126.0
12 TraesCS7D01G074900 chr7A 87.805 82 9 1 2563 2644 47052883 47052963 8.330000e-16 95.3
13 TraesCS7D01G074900 chr6D 82.092 1128 137 44 831 1939 6343890 6342809 0.000000e+00 904.0
14 TraesCS7D01G074900 chr6D 84.230 539 68 11 830 1360 6365597 6365068 2.510000e-140 508.0
15 TraesCS7D01G074900 chr6D 91.358 81 7 0 1409 1489 6364970 6364890 8.270000e-21 111.0
16 TraesCS7D01G074900 chr2D 82.331 1081 135 33 873 1939 620311608 620310570 0.000000e+00 887.0
17 TraesCS7D01G074900 chr2D 83.516 91 10 2 506 595 2352048 2352134 2.330000e-11 80.5
18 TraesCS7D01G074900 chr4A 92.358 615 39 3 487 1100 655623049 655622442 0.000000e+00 869.0
19 TraesCS7D01G074900 chr4A 91.824 477 24 11 18 482 655623563 655623090 0.000000e+00 651.0
20 TraesCS7D01G074900 chr4A 82.255 541 47 18 1755 2258 655622391 655621863 3.360000e-114 422.0
21 TraesCS7D01G074900 chr4A 90.991 111 9 1 2456 2565 655621589 655621479 6.300000e-32 148.0
22 TraesCS7D01G074900 chr4A 98.765 81 0 1 2483 2563 656038546 656038467 2.930000e-30 143.0
23 TraesCS7D01G074900 chr4A 90.476 105 9 1 2468 2571 655437294 655437190 1.360000e-28 137.0
24 TraesCS7D01G074900 chr3B 81.170 1094 137 45 873 1936 2417377 2416323 0.000000e+00 815.0
25 TraesCS7D01G074900 chr3B 85.551 789 89 19 873 1644 2507902 2508682 0.000000e+00 802.0
26 TraesCS7D01G074900 chrUn 83.669 845 104 20 822 1651 417298929 417298104 0.000000e+00 765.0
27 TraesCS7D01G074900 chrUn 86.316 475 56 4 822 1289 463822891 463822419 2.510000e-140 508.0
28 TraesCS7D01G074900 chrUn 81.034 174 28 5 302 472 15528868 15529039 1.760000e-27 134.0
29 TraesCS7D01G074900 chrUn 81.034 174 28 5 302 472 212997438 212997609 1.760000e-27 134.0
30 TraesCS7D01G074900 chrUn 81.034 174 28 5 302 472 224609612 224609783 1.760000e-27 134.0
31 TraesCS7D01G074900 chrUn 81.034 174 28 5 302 472 255474769 255474940 1.760000e-27 134.0
32 TraesCS7D01G074900 chrUn 81.287 171 27 5 305 472 265176452 265176284 1.760000e-27 134.0
33 TraesCS7D01G074900 chrUn 81.287 171 27 5 305 472 268968567 268968399 1.760000e-27 134.0
34 TraesCS7D01G074900 chr3A 83.550 845 105 22 822 1651 49170 49995 0.000000e+00 760.0
35 TraesCS7D01G074900 chr3A 83.589 847 102 21 822 1651 71672 72498 0.000000e+00 760.0
36 TraesCS7D01G074900 chr3A 91.667 96 8 0 2729 2824 523610023 523610118 1.760000e-27 134.0
37 TraesCS7D01G074900 chr6A 83.313 809 99 27 830 1628 5874083 5873301 0.000000e+00 713.0
38 TraesCS7D01G074900 chr6A 91.379 116 8 2 2457 2571 33524601 33524715 1.050000e-34 158.0
39 TraesCS7D01G074900 chr6A 83.721 172 14 10 2404 2564 33391111 33391279 1.750000e-32 150.0
40 TraesCS7D01G074900 chr1A 100.000 83 0 0 2489 2571 292498618 292498700 1.350000e-33 154.0
41 TraesCS7D01G074900 chr2B 81.034 174 28 5 302 472 8363145 8363316 1.760000e-27 134.0
42 TraesCS7D01G074900 chr2B 94.643 56 1 2 2680 2733 670175822 670175877 5.010000e-13 86.1
43 TraesCS7D01G074900 chr5D 89.583 96 10 0 2729 2824 505211319 505211224 3.820000e-24 122.0
44 TraesCS7D01G074900 chr5D 87.755 98 10 1 2729 2824 385950367 385950270 2.300000e-21 113.0
45 TraesCS7D01G074900 chr5D 93.220 59 1 3 2683 2739 293426945 293427002 1.800000e-12 84.2
46 TraesCS7D01G074900 chr5D 90.741 54 5 0 2771 2824 357000295 357000242 3.900000e-09 73.1
47 TraesCS7D01G074900 chr5B 89.583 96 10 0 2729 2824 338934484 338934389 3.820000e-24 122.0
48 TraesCS7D01G074900 chr5B 94.643 56 1 2 2680 2733 640759299 640759354 5.010000e-13 86.1
49 TraesCS7D01G074900 chr5B 93.333 60 1 3 2681 2738 706458174 706458116 5.010000e-13 86.1
50 TraesCS7D01G074900 chr5B 87.671 73 5 3 2672 2741 13084215 13084286 6.480000e-12 82.4
51 TraesCS7D01G074900 chr5A 89.583 96 10 0 2729 2824 632834129 632834034 3.820000e-24 122.0
52 TraesCS7D01G074900 chr6B 88.542 96 11 0 2729 2824 216348420 216348515 1.780000e-22 117.0
53 TraesCS7D01G074900 chr6B 86.458 96 13 0 2729 2824 46084710 46084615 3.850000e-19 106.0
54 TraesCS7D01G074900 chr6B 94.915 59 1 2 2680 2736 468734765 468734823 1.080000e-14 91.6
55 TraesCS7D01G074900 chr3D 93.220 59 2 2 2681 2737 355882415 355882357 5.010000e-13 86.1
56 TraesCS7D01G074900 chr7B 90.625 64 1 5 2683 2744 516791812 516791752 2.330000e-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 TraesCS7D01G074900 chr7D 44519385 44522208 2823 True 5216.0 5216 100.0000 1 2824 1 chr7D.!!$R2 2823
1 TraesCS7D01G074900 chr7A 46963558 46966094 2536 True 561.2 998 88.4272 18 2824 5 chr7A.!!$R1 2806
2 TraesCS7D01G074900 chr6D 6342809 6343890 1081 True 904.0 904 82.0920 831 1939 1 chr6D.!!$R1 1108
3 TraesCS7D01G074900 chr6D 6364890 6365597 707 True 309.5 508 87.7940 830 1489 2 chr6D.!!$R2 659
4 TraesCS7D01G074900 chr2D 620310570 620311608 1038 True 887.0 887 82.3310 873 1939 1 chr2D.!!$R1 1066
5 TraesCS7D01G074900 chr4A 655621479 655623563 2084 True 522.5 869 89.3570 18 2565 4 chr4A.!!$R3 2547
6 TraesCS7D01G074900 chr3B 2416323 2417377 1054 True 815.0 815 81.1700 873 1936 1 chr3B.!!$R1 1063
7 TraesCS7D01G074900 chr3B 2507902 2508682 780 False 802.0 802 85.5510 873 1644 1 chr3B.!!$F1 771
8 TraesCS7D01G074900 chrUn 417298104 417298929 825 True 765.0 765 83.6690 822 1651 1 chrUn.!!$R3 829
9 TraesCS7D01G074900 chr3A 49170 49995 825 False 760.0 760 83.5500 822 1651 1 chr3A.!!$F1 829
10 TraesCS7D01G074900 chr3A 71672 72498 826 False 760.0 760 83.5890 822 1651 1 chr3A.!!$F2 829
11 TraesCS7D01G074900 chr6A 5873301 5874083 782 True 713.0 713 83.3130 830 1628 1 chr6A.!!$R1 798

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
921 1122 1.314534 TGAATGCCATCAAGGGTGCG 61.315 55.0 0.0 0.0 38.09 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 2197 0.031043 TGTCGACGGTGGTGTACTTG 59.969 55.0 11.62 0.0 0.0 3.16 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
50 51 3.127589 GTTTTTATTTTGGCTGTGGCGT 58.872 40.909 0.00 0.00 39.81 5.68
183 185 8.864087 TCATATCATGCTTACTCTACTGTCAAT 58.136 33.333 0.00 0.00 0.00 2.57
184 186 8.923683 CATATCATGCTTACTCTACTGTCAATG 58.076 37.037 0.00 0.00 0.00 2.82
186 188 3.861840 TGCTTACTCTACTGTCAATGGC 58.138 45.455 0.00 0.00 0.00 4.40
201 205 8.368668 ACTGTCAATGGCTACTAACTTATATCC 58.631 37.037 0.00 0.00 0.00 2.59
205 209 6.912951 ATGGCTACTAACTTATATCCGTGT 57.087 37.500 0.00 0.00 0.00 4.49
236 240 8.894768 AGAGGTGAAGTGAAATATACTATTGC 57.105 34.615 0.00 0.00 0.00 3.56
237 241 8.709308 AGAGGTGAAGTGAAATATACTATTGCT 58.291 33.333 0.00 0.00 0.00 3.91
238 242 8.668510 AGGTGAAGTGAAATATACTATTGCTG 57.331 34.615 0.00 0.00 0.00 4.41
240 244 7.499232 GGTGAAGTGAAATATACTATTGCTGGT 59.501 37.037 0.00 0.00 0.00 4.00
252 265 4.773149 ACTATTGCTGGTCCTACTATAGGC 59.227 45.833 4.43 0.00 45.82 3.93
264 277 7.452189 GGTCCTACTATAGGCAAGACTTCTTAT 59.548 40.741 4.43 0.00 45.82 1.73
343 357 6.840780 ATTTAACTGAGGTGCTTAATGCTT 57.159 33.333 0.00 0.00 43.37 3.91
350 364 6.261826 ACTGAGGTGCTTAATGCTTCATTATC 59.738 38.462 0.73 0.00 43.37 1.75
501 696 6.157994 TCCTCTACTGTTAATTGCTTATGGGT 59.842 38.462 0.00 0.00 0.00 4.51
522 717 7.134162 TGGGTATATAGGGTCTTTGTAGTGAA 58.866 38.462 0.00 0.00 0.00 3.18
523 718 7.624478 TGGGTATATAGGGTCTTTGTAGTGAAA 59.376 37.037 0.00 0.00 0.00 2.69
524 719 8.657712 GGGTATATAGGGTCTTTGTAGTGAAAT 58.342 37.037 0.00 0.00 0.00 2.17
525 720 9.708092 GGTATATAGGGTCTTTGTAGTGAAATC 57.292 37.037 0.00 0.00 0.00 2.17
576 771 5.657474 TGTACATAAGGCTTCTTACCTTCG 58.343 41.667 1.30 0.00 44.35 3.79
598 793 8.682128 TTCGAATTAGCATTTGAAATTGTACC 57.318 30.769 0.00 0.00 39.11 3.34
670 865 7.173218 TGAAAGAATACATGTGACTCAAGTTCC 59.827 37.037 9.11 0.00 0.00 3.62
801 996 5.233050 GCTGGAAAAAGAAAAAGAGTCTTGC 59.767 40.000 6.06 0.00 35.50 4.01
921 1122 1.314534 TGAATGCCATCAAGGGTGCG 61.315 55.000 0.00 0.00 38.09 5.34
990 1193 4.637534 CGAGAATTGTCATGGGAATGAAGT 59.362 41.667 3.24 0.00 31.60 3.01
1027 1234 7.933577 TGTCATCAAGGTCAGATTATATCAACC 59.066 37.037 0.00 0.00 37.53 3.77
1070 1281 1.663074 GGCTGCGGATCGATCACTC 60.663 63.158 25.93 14.29 0.00 3.51
1117 1335 2.354704 CCATCCGAGTTTGGCTCTAACA 60.355 50.000 0.00 0.00 41.98 2.41
1171 1389 4.201812 CCACATTGTATGCTGGTAAAGTCG 60.202 45.833 0.00 0.00 31.28 4.18
1205 1423 0.111832 ATCGAGGCGGAGGGTATACA 59.888 55.000 5.01 0.00 0.00 2.29
1211 1429 3.961408 GAGGCGGAGGGTATACATCATAT 59.039 47.826 5.01 0.00 0.00 1.78
1244 1462 3.419759 CGGGTTCGCCGAAACCTG 61.420 66.667 29.42 19.46 46.38 4.00
1313 1531 2.755655 CCGACAAGATCACTGTCCTAGT 59.244 50.000 17.59 0.00 41.36 2.57
1329 1547 3.068732 TCCTAGTCGATGGAGATGCAAAG 59.931 47.826 0.00 0.00 0.00 2.77
1340 1561 2.819608 GAGATGCAAAGGGTAAAGCACA 59.180 45.455 0.00 0.00 40.14 4.57
1349 1570 1.877443 GGGTAAAGCACACATCGTGTT 59.123 47.619 0.00 0.00 45.08 3.32
1361 1588 1.509644 ATCGTGTTGCTGCCACTGTG 61.510 55.000 5.42 0.00 0.00 3.66
1362 1589 2.179547 CGTGTTGCTGCCACTGTGA 61.180 57.895 9.86 0.00 0.00 3.58
1363 1590 1.650912 GTGTTGCTGCCACTGTGAG 59.349 57.895 9.86 0.39 0.00 3.51
1364 1591 1.097547 GTGTTGCTGCCACTGTGAGT 61.098 55.000 9.86 0.00 0.00 3.41
1367 1594 1.532868 GTTGCTGCCACTGTGAGTAAG 59.467 52.381 9.86 2.35 0.00 2.34
1369 1596 1.140852 TGCTGCCACTGTGAGTAAGTT 59.859 47.619 9.86 0.00 0.00 2.66
1370 1597 1.801178 GCTGCCACTGTGAGTAAGTTC 59.199 52.381 9.86 0.00 0.00 3.01
1371 1598 2.061773 CTGCCACTGTGAGTAAGTTCG 58.938 52.381 9.86 0.00 0.00 3.95
1372 1599 0.790814 GCCACTGTGAGTAAGTTCGC 59.209 55.000 9.86 0.00 0.00 4.70
1373 1600 1.872237 GCCACTGTGAGTAAGTTCGCA 60.872 52.381 9.86 0.00 36.28 5.10
1374 1601 2.479837 CCACTGTGAGTAAGTTCGCAA 58.520 47.619 9.86 0.00 37.16 4.85
1417 1713 7.274447 TGATCTGTAATCTGTATTGATGCACA 58.726 34.615 0.00 0.00 0.00 4.57
1489 1785 2.995574 ACGACCCGAGAACCCTGG 60.996 66.667 0.00 0.00 0.00 4.45
1524 1820 2.749044 AGGCTGCTGGCGAACATG 60.749 61.111 11.49 0.00 44.18 3.21
1563 1859 1.153289 CGCCATGTGGGAGAGGAAG 60.153 63.158 0.54 0.00 39.08 3.46
1564 1860 1.617018 CGCCATGTGGGAGAGGAAGA 61.617 60.000 0.54 0.00 39.08 2.87
1586 1885 0.537188 GGCAGGACTTTCCAGATCGA 59.463 55.000 0.00 0.00 39.61 3.59
1590 1889 0.173708 GGACTTTCCAGATCGAGCGT 59.826 55.000 0.00 0.00 36.28 5.07
1591 1890 1.272781 GACTTTCCAGATCGAGCGTG 58.727 55.000 0.00 0.00 0.00 5.34
1623 1922 4.701765 CGGATCTCCTCAAGTTGATCAAT 58.298 43.478 12.12 0.00 37.60 2.57
1639 1939 4.347876 TGATCAATGGTAGGAGGGTACATG 59.652 45.833 0.00 0.00 0.00 3.21
1657 1967 2.182842 GCATCATCGTGCACCTCCC 61.183 63.158 12.15 0.00 44.43 4.30
1658 1968 1.884464 CATCATCGTGCACCTCCCG 60.884 63.158 12.15 0.00 0.00 5.14
1660 1970 4.838152 CATCGTGCACCTCCCGGG 62.838 72.222 16.85 16.85 41.89 5.73
1689 1999 2.050918 TGGTGGTCTTGTGTACATGGA 58.949 47.619 0.00 0.00 0.00 3.41
1690 2000 2.038426 TGGTGGTCTTGTGTACATGGAG 59.962 50.000 0.00 0.00 0.00 3.86
1692 2002 1.003118 TGGTCTTGTGTACATGGAGCC 59.997 52.381 16.38 10.36 0.00 4.70
1725 2035 4.142271 CCTCTGACCTCTCTTGACATGTAC 60.142 50.000 0.00 0.00 0.00 2.90
1800 2124 3.691342 TCTTGGTGAGGGGCGACG 61.691 66.667 0.00 0.00 0.00 5.12
1801 2125 4.003788 CTTGGTGAGGGGCGACGT 62.004 66.667 0.00 0.00 0.00 4.34
1802 2126 2.601067 TTGGTGAGGGGCGACGTA 60.601 61.111 0.00 0.00 0.00 3.57
1803 2127 2.830704 CTTGGTGAGGGGCGACGTAC 62.831 65.000 0.00 0.00 0.00 3.67
1813 2137 2.674084 GCGACGTACCAAGCCAACC 61.674 63.158 0.00 0.00 0.00 3.77
1859 2183 3.391382 GGCCACCGAGCTGTACCT 61.391 66.667 0.00 0.00 0.00 3.08
1860 2184 2.184579 GCCACCGAGCTGTACCTC 59.815 66.667 0.00 0.00 0.00 3.85
1892 2216 0.031043 CAAGTACACCACCGTCGACA 59.969 55.000 17.16 0.00 0.00 4.35
1902 2237 1.136147 CCGTCGACAAGTACCTCGG 59.864 63.158 17.16 3.46 0.00 4.63
1928 2263 1.072331 TCCTCTGACAGTTCTTTGGCC 59.928 52.381 0.00 0.00 0.00 5.36
1970 2323 2.189257 ACGCAGTTGCACACCAGA 59.811 55.556 4.84 0.00 37.78 3.86
2036 2389 9.167311 AGTTATACCTGATTGCTTACTTTTCAG 57.833 33.333 0.00 0.00 34.86 3.02
2062 2415 6.347696 AGAGACTGATCTTGGCTTGAATAAG 58.652 40.000 0.00 0.00 34.34 1.73
2144 2516 0.599558 TTGCTTGCTTCTGATGCACC 59.400 50.000 16.67 11.63 40.40 5.01
2145 2517 0.537828 TGCTTGCTTCTGATGCACCA 60.538 50.000 16.67 13.72 40.40 4.17
2179 2554 2.884012 TGGTGGTGTGTTGCTATCTTTG 59.116 45.455 0.00 0.00 0.00 2.77
2183 2558 2.351738 GGTGTGTTGCTATCTTTGTGGC 60.352 50.000 0.00 0.00 0.00 5.01
2188 2563 0.676466 TGCTATCTTTGTGGCACCCG 60.676 55.000 16.26 3.32 0.00 5.28
2191 2566 0.981183 TATCTTTGTGGCACCCGACT 59.019 50.000 16.26 0.00 0.00 4.18
2197 2572 1.340088 TGTGGCACCCGACTAACTAA 58.660 50.000 16.26 0.00 0.00 2.24
2316 2757 8.896744 TCTTAATCAATAAGAATTCTGTGGCAG 58.103 33.333 9.17 0.00 45.47 4.85
2318 2759 6.690194 ATCAATAAGAATTCTGTGGCAGAC 57.310 37.500 9.17 0.00 40.46 3.51
2319 2760 4.943705 TCAATAAGAATTCTGTGGCAGACC 59.056 41.667 9.17 0.00 40.46 3.85
2320 2761 1.813513 AAGAATTCTGTGGCAGACCG 58.186 50.000 9.17 0.00 40.46 4.79
2321 2762 0.976641 AGAATTCTGTGGCAGACCGA 59.023 50.000 7.30 0.00 40.46 4.69
2322 2763 1.347707 AGAATTCTGTGGCAGACCGAA 59.652 47.619 7.30 0.00 40.46 4.30
2323 2764 2.026822 AGAATTCTGTGGCAGACCGAAT 60.027 45.455 7.30 0.00 40.46 3.34
2324 2765 1.742761 ATTCTGTGGCAGACCGAATG 58.257 50.000 0.00 0.00 40.46 2.67
2325 2766 0.684535 TTCTGTGGCAGACCGAATGA 59.315 50.000 0.00 0.00 40.46 2.57
2326 2767 0.684535 TCTGTGGCAGACCGAATGAA 59.315 50.000 0.00 0.00 35.39 2.57
2327 2768 1.071542 TCTGTGGCAGACCGAATGAAA 59.928 47.619 0.00 0.00 35.39 2.69
2328 2769 1.197721 CTGTGGCAGACCGAATGAAAC 59.802 52.381 0.00 0.00 39.70 2.78
2329 2770 1.234821 GTGGCAGACCGAATGAAACA 58.765 50.000 0.00 0.00 39.70 2.83
2330 2771 1.197721 GTGGCAGACCGAATGAAACAG 59.802 52.381 0.00 0.00 39.70 3.16
2331 2772 0.169009 GGCAGACCGAATGAAACAGC 59.831 55.000 0.00 0.00 0.00 4.40
2332 2773 0.874390 GCAGACCGAATGAAACAGCA 59.126 50.000 0.00 0.00 0.00 4.41
2333 2774 1.266718 GCAGACCGAATGAAACAGCAA 59.733 47.619 0.00 0.00 0.00 3.91
2334 2775 2.287547 GCAGACCGAATGAAACAGCAAA 60.288 45.455 0.00 0.00 0.00 3.68
2335 2776 3.795150 GCAGACCGAATGAAACAGCAAAA 60.795 43.478 0.00 0.00 0.00 2.44
2336 2777 4.358851 CAGACCGAATGAAACAGCAAAAA 58.641 39.130 0.00 0.00 0.00 1.94
2426 2887 1.043816 TTGCTTGGCCCAAAATCGAA 58.956 45.000 0.00 0.00 0.00 3.71
2433 2902 1.471501 GGCCCAAAATCGAATCTTGGC 60.472 52.381 14.84 12.27 38.64 4.52
2451 2920 2.215196 GGCACGTTGAGAAGGTGTTTA 58.785 47.619 10.01 0.00 46.10 2.01
2453 2922 3.065648 GGCACGTTGAGAAGGTGTTTAAA 59.934 43.478 10.01 0.00 46.10 1.52
2623 3154 5.073144 ACAATCCCTCTAGACACAAAAGGAA 59.927 40.000 0.00 0.00 0.00 3.36
2638 3169 8.611757 ACACAAAAGGAAAAATAAGAAACATGC 58.388 29.630 0.00 0.00 0.00 4.06
2639 3170 8.610896 CACAAAAGGAAAAATAAGAAACATGCA 58.389 29.630 0.00 0.00 0.00 3.96
2658 3189 3.193903 TGCATACATTCTGTGCTGCAAAT 59.806 39.130 2.77 0.00 42.89 2.32
2659 3190 3.795101 GCATACATTCTGTGCTGCAAATC 59.205 43.478 2.77 0.00 38.99 2.17
2661 3192 1.881973 ACATTCTGTGCTGCAAATCGT 59.118 42.857 2.77 0.06 0.00 3.73
2664 3195 3.536158 TTCTGTGCTGCAAATCGTAAC 57.464 42.857 2.77 0.00 0.00 2.50
2689 3237 7.078851 CGGTGCAATCTACTACTAGTTCATAG 58.921 42.308 0.00 1.09 37.53 2.23
2691 3239 7.863375 GGTGCAATCTACTACTAGTTCATAGTG 59.137 40.741 0.00 0.00 44.69 2.74
2730 3280 7.954620 ACTTATATTTAGGAACGGAGGGAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
2744 3294 5.650703 GGAGGGAGTATATCACTAAGCTCTC 59.349 48.000 0.00 0.00 43.76 3.20
2755 3305 5.586877 TCACTAAGCTCTCTAGGGGTAAAA 58.413 41.667 0.00 0.00 0.00 1.52
2760 3310 1.769465 CTCTCTAGGGGTAAAAGGCCC 59.231 57.143 0.00 0.00 45.35 5.80
2768 3318 3.612795 GGGTAAAAGGCCCCTCAATAT 57.387 47.619 0.00 0.00 40.26 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.818121 TTTCGTCCCGGTGCAGTGG 62.818 63.158 0.00 0.00 0.00 4.00
2 3 2.280524 TTTCGTCCCGGTGCAGTG 60.281 61.111 0.00 0.00 0.00 3.66
3 4 2.030562 CTTTCGTCCCGGTGCAGT 59.969 61.111 0.00 0.00 0.00 4.40
5 6 3.936203 AGCTTTCGTCCCGGTGCA 61.936 61.111 0.00 0.00 0.00 4.57
6 7 3.423154 CAGCTTTCGTCCCGGTGC 61.423 66.667 0.00 0.00 0.00 5.01
7 8 2.501223 TAGCAGCTTTCGTCCCGGTG 62.501 60.000 0.00 0.00 0.00 4.94
8 9 1.614241 ATAGCAGCTTTCGTCCCGGT 61.614 55.000 0.00 0.00 0.00 5.28
9 10 0.462047 AATAGCAGCTTTCGTCCCGG 60.462 55.000 0.00 0.00 0.00 5.73
10 11 0.652592 CAATAGCAGCTTTCGTCCCG 59.347 55.000 0.00 0.00 0.00 5.14
11 12 1.739067 ACAATAGCAGCTTTCGTCCC 58.261 50.000 0.00 0.00 0.00 4.46
12 13 3.831715 AAACAATAGCAGCTTTCGTCC 57.168 42.857 0.00 0.00 0.00 4.79
13 14 7.796958 AATAAAAACAATAGCAGCTTTCGTC 57.203 32.000 0.00 0.00 0.00 4.20
14 15 8.487176 CAAAATAAAAACAATAGCAGCTTTCGT 58.513 29.630 0.00 0.00 0.00 3.85
15 16 7.951565 CCAAAATAAAAACAATAGCAGCTTTCG 59.048 33.333 0.00 0.00 0.00 3.46
16 17 7.746034 GCCAAAATAAAAACAATAGCAGCTTTC 59.254 33.333 0.00 0.00 0.00 2.62
20 21 6.147656 ACAGCCAAAATAAAAACAATAGCAGC 59.852 34.615 0.00 0.00 0.00 5.25
183 185 6.720112 AACACGGATATAAGTTAGTAGCCA 57.280 37.500 0.00 0.00 0.00 4.75
184 186 9.136952 CATAAACACGGATATAAGTTAGTAGCC 57.863 37.037 0.00 0.00 0.00 3.93
201 205 4.556233 TCACTTCACCTCTCATAAACACG 58.444 43.478 0.00 0.00 0.00 4.49
237 241 7.586779 TAAGAAGTCTTGCCTATAGTAGGACCA 60.587 40.741 7.20 0.00 41.57 4.02
238 242 6.776603 TAAGAAGTCTTGCCTATAGTAGGACC 59.223 42.308 7.20 0.00 41.57 4.46
240 244 8.449625 AGATAAGAAGTCTTGCCTATAGTAGGA 58.550 37.037 7.20 0.00 41.57 2.94
343 357 3.296854 ACAGGTAGCAGGACGATAATGA 58.703 45.455 0.00 0.00 0.00 2.57
350 364 1.132643 GTACAGACAGGTAGCAGGACG 59.867 57.143 0.00 0.00 0.00 4.79
441 457 9.549078 TTGTAAATTCCATTTAACTTGGGAAAC 57.451 29.630 0.00 0.00 42.26 2.78
522 717 7.173907 CAGCGGTCTCCAATAAATAGATTGATT 59.826 37.037 0.00 0.00 38.83 2.57
523 718 6.652481 CAGCGGTCTCCAATAAATAGATTGAT 59.348 38.462 0.00 0.00 38.83 2.57
524 719 5.991606 CAGCGGTCTCCAATAAATAGATTGA 59.008 40.000 0.00 0.00 38.83 2.57
525 720 5.180117 CCAGCGGTCTCCAATAAATAGATTG 59.820 44.000 0.00 0.00 36.70 2.67
544 739 1.806623 GCCTTATGTACAGGACCAGCG 60.807 57.143 0.33 0.00 32.41 5.18
576 771 8.372521 CAACGGTACAATTTCAAATGCTAATTC 58.627 33.333 0.00 0.00 0.00 2.17
598 793 6.257849 ACCACTTGTATCAATATACAGCAACG 59.742 38.462 0.00 0.00 46.58 4.10
663 858 3.482722 CAGTGCTGCATTAGGAACTTG 57.517 47.619 5.27 0.00 41.75 3.16
684 879 3.067180 ACAACTGGTTTGCAGAATGACAG 59.933 43.478 0.00 0.00 39.01 3.51
787 982 1.604278 ACGGCTGCAAGACTCTTTTTC 59.396 47.619 0.50 0.00 42.99 2.29
819 1014 6.826231 TCCACACACAGAAAACTATCAAAAGA 59.174 34.615 0.00 0.00 0.00 2.52
921 1122 0.596083 CAGCCGAGATCACGACATCC 60.596 60.000 14.43 0.00 35.09 3.51
971 1174 4.646492 GCCTACTTCATTCCCATGACAATT 59.354 41.667 0.00 0.00 39.28 2.32
982 1185 1.334869 CATTGCCGGCCTACTTCATTC 59.665 52.381 26.77 0.00 0.00 2.67
990 1193 0.254462 TTGATGACATTGCCGGCCTA 59.746 50.000 26.77 13.06 0.00 3.93
1027 1234 4.511454 TCGTTCCATCAACAAAGAAGACAG 59.489 41.667 0.00 0.00 34.20 3.51
1070 1281 1.863454 GCCTCTGTGCATCAACTATCG 59.137 52.381 0.00 0.00 0.00 2.92
1114 1332 1.338769 GGTGTGAACCCGCTCTATGTT 60.339 52.381 0.00 0.00 0.00 2.71
1117 1335 1.515954 CGGTGTGAACCCGCTCTAT 59.484 57.895 0.00 0.00 38.85 1.98
1205 1423 5.814188 CCGTTGCAGCAGACATATATATGAT 59.186 40.000 26.05 13.01 37.15 2.45
1211 1429 1.484653 ACCCGTTGCAGCAGACATATA 59.515 47.619 0.24 0.00 0.00 0.86
1244 1462 2.985512 ATCGCCGATGCTCAGAAGGC 62.986 60.000 0.00 0.00 44.00 4.35
1282 1500 0.323542 ATCTTGTCGGACGGAGGACT 60.324 55.000 3.34 0.00 34.31 3.85
1313 1531 0.911769 ACCCTTTGCATCTCCATCGA 59.088 50.000 0.00 0.00 0.00 3.59
1340 1561 1.227943 AGTGGCAGCAACACGATGT 60.228 52.632 1.78 0.00 43.41 3.06
1349 1570 0.758734 ACTTACTCACAGTGGCAGCA 59.241 50.000 0.00 0.00 0.00 4.41
1371 1598 0.521242 CGCAGGATGTAACGCTTTGC 60.521 55.000 0.00 0.00 39.31 3.68
1372 1599 3.586039 CGCAGGATGTAACGCTTTG 57.414 52.632 0.00 0.00 39.31 2.77
1391 1683 7.440255 TGTGCATCAATACAGATTACAGATCAG 59.560 37.037 0.00 0.00 0.00 2.90
1417 1713 2.118404 CCACCACAAACACCGCTGT 61.118 57.895 0.00 0.00 0.00 4.40
1476 1772 1.192146 TCTTGTCCAGGGTTCTCGGG 61.192 60.000 0.00 0.00 0.00 5.14
1500 1796 1.886313 CGCCAGCAGCCTCATGTAG 60.886 63.158 0.00 0.00 38.78 2.74
1511 1807 1.965930 GACACCATGTTCGCCAGCA 60.966 57.895 0.00 0.00 0.00 4.41
1514 1810 2.033448 GGGACACCATGTTCGCCA 59.967 61.111 0.00 0.00 36.50 5.69
1548 1844 0.176680 CCGTCTTCCTCTCCCACATG 59.823 60.000 0.00 0.00 0.00 3.21
1563 1859 1.376037 CTGGAAAGTCCTGCCCGTC 60.376 63.158 0.00 0.00 37.46 4.79
1564 1860 1.201429 ATCTGGAAAGTCCTGCCCGT 61.201 55.000 0.00 0.00 37.46 5.28
1623 1922 2.047061 GATGCATGTACCCTCCTACCA 58.953 52.381 2.46 0.00 0.00 3.25
1639 1939 2.182842 GGGAGGTGCACGATGATGC 61.183 63.158 11.45 0.00 46.32 3.91
1653 1962 1.227943 CCATATGTGTGCCCGGGAG 60.228 63.158 29.31 0.00 0.00 4.30
1657 1967 1.077787 ACCACCATATGTGTGCCCG 60.078 57.895 15.13 7.65 43.85 6.13
1658 1968 0.255890 AGACCACCATATGTGTGCCC 59.744 55.000 15.13 10.31 43.85 5.36
1660 1970 2.162208 CACAAGACCACCATATGTGTGC 59.838 50.000 15.13 6.41 43.85 4.57
1664 1974 4.901197 TGTACACAAGACCACCATATGT 57.099 40.909 1.24 0.00 0.00 2.29
1665 1975 4.576053 CCATGTACACAAGACCACCATATG 59.424 45.833 0.00 0.00 0.00 1.78
1674 1984 2.076863 GTGGCTCCATGTACACAAGAC 58.923 52.381 0.00 0.00 34.16 3.01
1675 1985 1.696884 TGTGGCTCCATGTACACAAGA 59.303 47.619 0.00 0.00 40.50 3.02
1677 1987 1.881925 GCTGTGGCTCCATGTACACAA 60.882 52.381 0.00 0.00 42.55 3.33
1678 1988 0.321564 GCTGTGGCTCCATGTACACA 60.322 55.000 0.00 8.18 41.11 3.72
1679 1989 2.471255 GCTGTGGCTCCATGTACAC 58.529 57.895 0.00 0.00 35.22 2.90
1690 2000 3.054503 CAGAGGTGCAGCTGTGGC 61.055 66.667 29.75 13.83 39.06 5.01
1692 2002 1.670406 GGTCAGAGGTGCAGCTGTG 60.670 63.158 31.06 31.06 33.90 3.66
1725 2035 1.355563 CCGCTTCTGCATGCATGAG 59.644 57.895 30.64 21.35 39.64 2.90
1800 2124 0.034337 TGTCGAGGTTGGCTTGGTAC 59.966 55.000 0.00 0.00 0.00 3.34
1801 2125 0.981183 ATGTCGAGGTTGGCTTGGTA 59.019 50.000 0.00 0.00 0.00 3.25
1802 2126 0.110486 AATGTCGAGGTTGGCTTGGT 59.890 50.000 0.00 0.00 0.00 3.67
1803 2127 0.523072 CAATGTCGAGGTTGGCTTGG 59.477 55.000 0.00 0.00 0.00 3.61
1861 2185 4.424566 TACTTGTCGACGGCGGCC 62.425 66.667 15.22 9.54 42.58 6.13
1862 2186 3.177249 GTACTTGTCGACGGCGGC 61.177 66.667 9.21 9.21 43.78 6.53
1863 2187 2.084681 GTGTACTTGTCGACGGCGG 61.085 63.158 12.58 0.00 38.28 6.13
1864 2188 2.084681 GGTGTACTTGTCGACGGCG 61.085 63.158 2.87 2.87 39.35 6.46
1865 2189 1.007038 TGGTGTACTTGTCGACGGC 60.007 57.895 11.62 0.00 0.00 5.68
1869 2193 0.311790 GACGGTGGTGTACTTGTCGA 59.688 55.000 0.00 0.00 0.00 4.20
1872 2196 0.031178 GTCGACGGTGGTGTACTTGT 59.969 55.000 0.00 0.00 0.00 3.16
1873 2197 0.031043 TGTCGACGGTGGTGTACTTG 59.969 55.000 11.62 0.00 0.00 3.16
1892 2216 3.459063 GAGGCGGCCGAGGTACTT 61.459 66.667 33.48 6.70 41.55 2.24
1902 2237 2.844072 GAACTGTCAGAGGAGGCGGC 62.844 65.000 6.91 0.00 0.00 6.53
1940 2275 4.408821 TGCGTTAGGGGCTGCCAG 62.409 66.667 22.05 5.18 0.00 4.85
1970 2323 3.749226 CAAGGCCAGAGACTTCTTCTTT 58.251 45.455 5.01 0.00 33.22 2.52
2036 2389 2.499289 TCAAGCCAAGATCAGTCTCTCC 59.501 50.000 0.00 0.00 32.15 3.71
2038 2391 4.840716 ATTCAAGCCAAGATCAGTCTCT 57.159 40.909 0.00 0.00 32.15 3.10
2062 2415 2.926420 AAACGAAATGCCCCACCGC 61.926 57.895 0.00 0.00 0.00 5.68
2064 2417 1.291906 CCAAACGAAATGCCCCACC 59.708 57.895 0.00 0.00 0.00 4.61
2144 2516 1.688197 ACCACCAGCCATTGTTTCTTG 59.312 47.619 0.00 0.00 0.00 3.02
2145 2517 1.688197 CACCACCAGCCATTGTTTCTT 59.312 47.619 0.00 0.00 0.00 2.52
2179 2554 2.676342 CAATTAGTTAGTCGGGTGCCAC 59.324 50.000 0.00 0.00 0.00 5.01
2183 2558 6.548441 TTTTCACAATTAGTTAGTCGGGTG 57.452 37.500 0.00 0.00 0.00 4.61
2191 2566 9.474920 CTCCAAATTGCTTTTCACAATTAGTTA 57.525 29.630 2.45 0.00 44.76 2.24
2197 2572 5.987347 CAGTCTCCAAATTGCTTTTCACAAT 59.013 36.000 0.00 0.00 39.38 2.71
2416 2877 2.095263 ACGTGCCAAGATTCGATTTTGG 60.095 45.455 15.11 15.11 43.31 3.28
2426 2887 1.072331 ACCTTCTCAACGTGCCAAGAT 59.928 47.619 0.00 0.00 0.00 2.40
2433 2902 5.728351 TCTTTAAACACCTTCTCAACGTG 57.272 39.130 0.00 0.00 0.00 4.49
2474 2943 6.102615 AGCTACATCCCCTTGTTGGATAATTA 59.897 38.462 0.00 0.00 40.68 1.40
2647 3178 0.515127 CCGTTACGATTTGCAGCACA 59.485 50.000 6.24 0.00 0.00 4.57
2658 3189 3.691118 AGTAGTAGATTGCACCGTTACGA 59.309 43.478 6.24 0.00 0.00 3.43
2659 3190 4.025015 AGTAGTAGATTGCACCGTTACG 57.975 45.455 0.00 0.00 0.00 3.18
2661 3192 6.375174 TGAACTAGTAGTAGATTGCACCGTTA 59.625 38.462 11.68 0.00 0.00 3.18
2664 3195 5.244785 TGAACTAGTAGTAGATTGCACCG 57.755 43.478 11.68 0.00 0.00 4.94
2702 3250 5.541484 TCCCTCCGTTCCTAAATATAAGTCC 59.459 44.000 0.00 0.00 0.00 3.85
2719 3269 4.337145 AGCTTAGTGATATACTCCCTCCG 58.663 47.826 0.00 0.00 40.89 4.63
2730 3280 6.526056 TTACCCCTAGAGAGCTTAGTGATA 57.474 41.667 0.00 0.00 0.00 2.15
2762 3312 7.194112 TCAGTTGGACACCTCAATATATTGA 57.806 36.000 23.46 23.46 43.94 2.57
2767 3317 7.161773 CAATTTCAGTTGGACACCTCAATAT 57.838 36.000 0.00 0.00 0.00 1.28
2768 3318 6.573664 CAATTTCAGTTGGACACCTCAATA 57.426 37.500 0.00 0.00 0.00 1.90
2795 3346 3.773418 TGACTTGGTCAAAATCGGGTA 57.227 42.857 0.00 0.00 39.78 3.69


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

AutoCloner maintained by Alex Coulton.