Multiple sequence alignment - TraesCS5A01G250300

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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 TraesCS5A01G250300 chr5A 100.000 5666 0 0 1 5666 465990390 465996055 0.000000e+00 10464.0
1 TraesCS5A01G250300 chr5A 86.576 1773 147 43 2874 4623 466037521 466035817 0.000000e+00 1871.0
2 TraesCS5A01G250300 chr5A 90.604 1043 80 12 1700 2731 466038558 466037523 0.000000e+00 1367.0
3 TraesCS5A01G250300 chr5A 88.560 743 65 15 775 1507 466039740 466039008 0.000000e+00 883.0
4 TraesCS5A01G250300 chr5A 83.714 350 32 16 1265 1596 466038899 466038557 1.980000e-79 307.0
5 TraesCS5A01G250300 chr5A 97.273 110 3 0 1592 1701 306879012 306879121 2.700000e-43 187.0
6 TraesCS5A01G250300 chr5A 90.299 134 11 2 1590 1722 32138142 32138010 2.100000e-39 174.0
7 TraesCS5A01G250300 chr5B 94.780 4004 147 28 1701 5666 430670621 430674600 0.000000e+00 6180.0
8 TraesCS5A01G250300 chr5B 88.616 1669 112 33 2874 4523 430751307 430749698 0.000000e+00 1958.0
9 TraesCS5A01G250300 chr5B 89.549 1043 82 12 1700 2731 430752335 430751309 0.000000e+00 1297.0
10 TraesCS5A01G250300 chr5B 89.614 1011 64 15 602 1588 430669579 430670572 0.000000e+00 1247.0
11 TraesCS5A01G250300 chr5B 86.245 807 50 32 748 1507 430753231 430752439 0.000000e+00 819.0
12 TraesCS5A01G250300 chr5B 82.400 250 32 10 2 243 215076978 215077223 2.070000e-49 207.0
13 TraesCS5A01G250300 chr5D 93.117 2499 128 27 1700 4183 364666074 364668543 0.000000e+00 3622.0
14 TraesCS5A01G250300 chr5D 95.041 1472 45 13 4210 5666 364668531 364669989 0.000000e+00 2289.0
15 TraesCS5A01G250300 chr5D 90.508 1043 80 12 1700 2731 364765778 364764744 0.000000e+00 1360.0
16 TraesCS5A01G250300 chr5D 87.257 1028 89 21 3513 4529 364764027 364763031 0.000000e+00 1134.0
17 TraesCS5A01G250300 chr5D 90.498 863 50 13 757 1596 364665222 364666075 0.000000e+00 1110.0
18 TraesCS5A01G250300 chr5D 85.537 968 78 28 670 1596 364766723 364765777 0.000000e+00 955.0
19 TraesCS5A01G250300 chr5D 89.680 562 46 7 2874 3426 364764742 364764184 0.000000e+00 706.0
20 TraesCS5A01G250300 chr5D 88.807 545 53 5 3758 4295 30615835 30615292 0.000000e+00 662.0
21 TraesCS5A01G250300 chr5D 82.378 471 63 15 4363 4825 30613885 30613427 5.320000e-105 392.0
22 TraesCS5A01G250300 chr5D 82.297 418 53 16 2204 2604 30673524 30673111 5.440000e-90 342.0
23 TraesCS5A01G250300 chr5D 94.118 85 5 0 602 686 364665138 364665222 4.610000e-26 130.0
24 TraesCS5A01G250300 chr2A 91.722 604 34 8 1 600 261662707 261663298 0.000000e+00 824.0
25 TraesCS5A01G250300 chr3A 89.106 615 42 9 1 600 640525018 640525622 0.000000e+00 741.0
26 TraesCS5A01G250300 chr3A 85.915 568 38 11 13 542 41093283 41093846 8.240000e-158 568.0
27 TraesCS5A01G250300 chr3A 85.827 254 26 9 1 250 640524855 640525102 1.570000e-65 261.0
28 TraesCS5A01G250300 chr3A 85.433 254 28 6 1 248 41093250 41093500 7.280000e-64 255.0
29 TraesCS5A01G250300 chr3A 94.355 124 7 0 477 600 41093849 41093972 2.080000e-44 191.0
30 TraesCS5A01G250300 chr3A 96.429 112 4 0 1590 1701 673617346 673617457 9.690000e-43 185.0
31 TraesCS5A01G250300 chr3A 94.167 120 6 1 1583 1702 550641828 550641946 1.250000e-41 182.0
32 TraesCS5A01G250300 chr3A 90.909 44 4 0 632 675 26202927 26202884 6.130000e-05 60.2
33 TraesCS5A01G250300 chr3D 81.677 644 70 29 1 612 481718287 481717660 5.100000e-135 492.0
34 TraesCS5A01G250300 chr1A 93.805 226 3 3 728 951 439339879 439339663 4.230000e-86 329.0
35 TraesCS5A01G250300 chr7B 83.077 260 34 8 2 255 716229198 716229453 1.590000e-55 228.0
36 TraesCS5A01G250300 chr7B 97.143 35 1 0 566 600 191685470 191685504 6.130000e-05 60.2
37 TraesCS5A01G250300 chr7D 83.077 260 32 11 1 254 619119511 619119764 5.710000e-55 226.0
38 TraesCS5A01G250300 chr4A 82.558 258 32 13 1 254 484549713 484549465 1.240000e-51 215.0
39 TraesCS5A01G250300 chr4A 96.429 112 4 0 1593 1704 416231393 416231504 9.690000e-43 185.0
40 TraesCS5A01G250300 chr4A 92.683 123 9 0 1594 1716 366478633 366478511 1.620000e-40 178.0
41 TraesCS5A01G250300 chr4B 98.148 108 2 0 1594 1701 579456707 579456814 7.490000e-44 189.0
42 TraesCS5A01G250300 chr4B 100.000 34 0 0 3246 3279 666785483 666785450 4.740000e-06 63.9
43 TraesCS5A01G250300 chr6D 96.429 112 4 0 1593 1704 468640891 468641002 9.690000e-43 185.0
44 TraesCS5A01G250300 chr1B 95.614 114 5 0 1590 1703 687254054 687253941 3.490000e-42 183.0
45 TraesCS5A01G250300 chr1B 97.143 35 1 0 567 601 428105492 428105526 6.130000e-05 60.2
46 TraesCS5A01G250300 chr6A 97.143 35 1 0 635 669 494361375 494361341 6.130000e-05 60.2
47 TraesCS5A01G250300 chr6B 97.059 34 1 0 567 600 550364972 550365005 2.200000e-04 58.4


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 TraesCS5A01G250300 chr5A 465990390 465996055 5665 False 10464.00 10464 100.000000 1 5666 1 chr5A.!!$F2 5665
1 TraesCS5A01G250300 chr5A 466035817 466039740 3923 True 1107.00 1871 87.363500 775 4623 4 chr5A.!!$R2 3848
2 TraesCS5A01G250300 chr5B 430669579 430674600 5021 False 3713.50 6180 92.197000 602 5666 2 chr5B.!!$F2 5064
3 TraesCS5A01G250300 chr5B 430749698 430753231 3533 True 1358.00 1958 88.136667 748 4523 3 chr5B.!!$R1 3775
4 TraesCS5A01G250300 chr5D 364665138 364669989 4851 False 1787.75 3622 93.193500 602 5666 4 chr5D.!!$F1 5064
5 TraesCS5A01G250300 chr5D 364763031 364766723 3692 True 1038.75 1360 88.245500 670 4529 4 chr5D.!!$R3 3859
6 TraesCS5A01G250300 chr5D 30613427 30615835 2408 True 527.00 662 85.592500 3758 4825 2 chr5D.!!$R2 1067
7 TraesCS5A01G250300 chr2A 261662707 261663298 591 False 824.00 824 91.722000 1 600 1 chr2A.!!$F1 599
8 TraesCS5A01G250300 chr3A 640524855 640525622 767 False 501.00 741 87.466500 1 600 2 chr3A.!!$F4 599
9 TraesCS5A01G250300 chr3A 41093250 41093972 722 False 338.00 568 88.567667 1 600 3 chr3A.!!$F3 599
10 TraesCS5A01G250300 chr3D 481717660 481718287 627 True 492.00 492 81.677000 1 612 1 chr3D.!!$R1 611

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
961 1329 0.103390 TCTCCAACGCGTTCAGTTCA 59.897 50.000 23.92 2.49 0.00 3.18 F
1633 2441 0.179084 ACTTGTCGCGGGTATGGATG 60.179 55.000 6.13 0.00 0.00 3.51 F
3279 4125 0.842030 AGTCAAGAGCCATGGGTCCA 60.842 55.000 34.70 19.59 42.97 4.02 F
3959 4905 2.546778 TGTCAACGTTCAGTTCCTCAC 58.453 47.619 0.00 0.00 42.02 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2909 3734 2.110967 CGCCTGATGCAGAGGTTGG 61.111 63.158 14.50 2.31 41.33 3.77 R
3472 4415 1.836166 ACCATGACCATGACTCCTCAG 59.164 52.381 11.28 0.00 41.20 3.35 R
4657 7015 1.760613 AGCATGCTTCCCATTTGGATG 59.239 47.619 16.30 0.00 44.66 3.51 R
5180 7547 2.028839 CAGGATTCAGGTGCATTGCAAA 60.029 45.455 13.94 4.33 41.47 3.68 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
52 196 5.241506 AGCCGATGAACTCTTTTCAAAATCA 59.758 36.000 0.00 0.00 31.55 2.57
97 262 7.077050 TGAACCTTTTTCCCAAATTGATGAT 57.923 32.000 0.00 0.00 0.00 2.45
98 263 7.516452 TGAACCTTTTTCCCAAATTGATGATT 58.484 30.769 0.00 0.00 0.00 2.57
400 634 5.622041 TCTTAAAGTTTTCGCGTTGTTATGC 59.378 36.000 5.77 0.00 0.00 3.14
477 713 4.753877 CGGCGCGAGTTCGACTCA 62.754 66.667 12.10 0.00 45.30 3.41
479 715 1.063649 GGCGCGAGTTCGACTCATA 59.936 57.895 12.10 0.00 45.30 2.15
600 919 2.735237 GCCGATTAGGAGGTCCCG 59.265 66.667 0.00 0.00 45.00 5.14
731 1050 4.995058 TTCGGCCTTCCCCACCCT 62.995 66.667 0.00 0.00 0.00 4.34
960 1328 1.214367 TTCTCCAACGCGTTCAGTTC 58.786 50.000 23.92 0.00 0.00 3.01
961 1329 0.103390 TCTCCAACGCGTTCAGTTCA 59.897 50.000 23.92 2.49 0.00 3.18
962 1330 0.508641 CTCCAACGCGTTCAGTTCAG 59.491 55.000 23.92 8.97 0.00 3.02
963 1331 0.179094 TCCAACGCGTTCAGTTCAGT 60.179 50.000 23.92 0.00 0.00 3.41
964 1332 0.655733 CCAACGCGTTCAGTTCAGTT 59.344 50.000 23.92 0.00 0.00 3.16
1002 1373 2.436824 GCGGACTTTCCAGGAGGC 60.437 66.667 0.00 0.00 35.91 4.70
1027 1401 2.945984 CGTTCGGCTGTGCATTGT 59.054 55.556 0.00 0.00 0.00 2.71
1041 1415 2.933495 CATTGTGGAACCATGCTCAG 57.067 50.000 0.00 0.00 32.96 3.35
1042 1416 2.165167 CATTGTGGAACCATGCTCAGT 58.835 47.619 0.00 0.00 32.96 3.41
1101 1475 3.308530 GGTGAGTCGATTTTGCCTTTTG 58.691 45.455 0.00 0.00 0.00 2.44
1145 1528 4.680237 TGCACAACGGGAGGAGCG 62.680 66.667 0.00 0.00 0.00 5.03
1158 1541 0.674895 AGGAGCGCACCATTCAGTTC 60.675 55.000 26.04 1.76 0.00 3.01
1233 1617 8.478877 TCTAGAGAACAAGAAGGATACCATTTC 58.521 37.037 0.00 0.00 37.17 2.17
1336 2086 6.610075 AACCCATGCTGAAATTTTGACTAT 57.390 33.333 0.00 0.00 0.00 2.12
1367 2117 8.038862 AGTAACATGGTGAATGAGGATAGAAT 57.961 34.615 0.00 0.00 38.72 2.40
1371 2121 4.129380 TGGTGAATGAGGATAGAATTGCG 58.871 43.478 0.00 0.00 0.00 4.85
1405 2155 1.000607 GTAACGAGTGTCTGTCAGCCA 60.001 52.381 0.00 0.00 0.00 4.75
1413 2163 0.388649 GTCTGTCAGCCATTCGACGT 60.389 55.000 0.00 0.00 34.78 4.34
1507 2257 4.273005 TCGAGACACAAGCTTTGTTTTC 57.727 40.909 13.21 12.58 43.23 2.29
1588 2341 4.917415 AGCGCAGATTATTTTGAACACAAC 59.083 37.500 11.47 0.00 0.00 3.32
1594 2402 9.793252 GCAGATTATTTTGAACACAACTGATAT 57.207 29.630 0.00 0.00 0.00 1.63
1600 2408 7.681939 TTTTGAACACAACTGATATACTCCC 57.318 36.000 0.00 0.00 0.00 4.30
1601 2409 6.620877 TTGAACACAACTGATATACTCCCT 57.379 37.500 0.00 0.00 0.00 4.20
1602 2410 6.222038 TGAACACAACTGATATACTCCCTC 57.778 41.667 0.00 0.00 0.00 4.30
1603 2411 5.128827 TGAACACAACTGATATACTCCCTCC 59.871 44.000 0.00 0.00 0.00 4.30
1604 2412 3.637229 ACACAACTGATATACTCCCTCCG 59.363 47.826 0.00 0.00 0.00 4.63
1605 2413 3.637229 CACAACTGATATACTCCCTCCGT 59.363 47.826 0.00 0.00 0.00 4.69
1606 2414 4.099573 CACAACTGATATACTCCCTCCGTT 59.900 45.833 0.00 0.00 0.00 4.44
1607 2415 4.341520 ACAACTGATATACTCCCTCCGTTC 59.658 45.833 0.00 0.00 0.00 3.95
1608 2416 3.498334 ACTGATATACTCCCTCCGTTCC 58.502 50.000 0.00 0.00 0.00 3.62
1609 2417 2.488545 CTGATATACTCCCTCCGTTCCG 59.511 54.545 0.00 0.00 0.00 4.30
1610 2418 2.107031 TGATATACTCCCTCCGTTCCGA 59.893 50.000 0.00 0.00 0.00 4.55
1611 2419 2.734755 TATACTCCCTCCGTTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
1612 2420 2.083628 ATACTCCCTCCGTTCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
1613 2421 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
1614 2422 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
1615 2423 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1616 2424 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
1617 2425 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
1618 2426 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1619 2427 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1620 2428 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1621 2429 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
1622 2430 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
1623 2431 1.266211 CGTTCCGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 35.93 5.87
1624 2432 1.060122 GTTCCGAATTACTTGTCGCGG 59.940 52.381 6.13 0.00 40.06 6.46
1625 2433 0.458889 TCCGAATTACTTGTCGCGGG 60.459 55.000 6.13 0.00 39.24 6.13
1626 2434 0.738412 CCGAATTACTTGTCGCGGGT 60.738 55.000 6.13 3.16 35.93 5.28
1627 2435 1.469595 CCGAATTACTTGTCGCGGGTA 60.470 52.381 6.13 2.12 35.93 3.69
1628 2436 2.466846 CGAATTACTTGTCGCGGGTAT 58.533 47.619 6.13 0.00 0.00 2.73
1629 2437 2.217847 CGAATTACTTGTCGCGGGTATG 59.782 50.000 6.13 0.00 0.00 2.39
1630 2438 2.234300 ATTACTTGTCGCGGGTATGG 57.766 50.000 6.13 0.00 0.00 2.74
1631 2439 1.184431 TTACTTGTCGCGGGTATGGA 58.816 50.000 6.13 0.00 0.00 3.41
1632 2440 1.405872 TACTTGTCGCGGGTATGGAT 58.594 50.000 6.13 0.00 0.00 3.41
1633 2441 0.179084 ACTTGTCGCGGGTATGGATG 60.179 55.000 6.13 0.00 0.00 3.51
1634 2442 0.179084 CTTGTCGCGGGTATGGATGT 60.179 55.000 6.13 0.00 0.00 3.06
1635 2443 1.067974 CTTGTCGCGGGTATGGATGTA 59.932 52.381 6.13 0.00 0.00 2.29
1636 2444 1.334160 TGTCGCGGGTATGGATGTAT 58.666 50.000 6.13 0.00 0.00 2.29
1637 2445 1.271379 TGTCGCGGGTATGGATGTATC 59.729 52.381 6.13 0.00 0.00 2.24
1638 2446 1.544691 GTCGCGGGTATGGATGTATCT 59.455 52.381 6.13 0.00 0.00 1.98
1639 2447 2.751259 GTCGCGGGTATGGATGTATCTA 59.249 50.000 6.13 0.00 0.00 1.98
1640 2448 3.014623 TCGCGGGTATGGATGTATCTAG 58.985 50.000 6.13 0.00 0.00 2.43
1641 2449 3.014623 CGCGGGTATGGATGTATCTAGA 58.985 50.000 0.00 0.00 0.00 2.43
1642 2450 3.632604 CGCGGGTATGGATGTATCTAGAT 59.367 47.826 10.73 10.73 0.00 1.98
1643 2451 4.498177 CGCGGGTATGGATGTATCTAGATG 60.498 50.000 15.79 0.00 0.00 2.90
1644 2452 4.402793 GCGGGTATGGATGTATCTAGATGT 59.597 45.833 15.79 1.25 0.00 3.06
1645 2453 5.593095 GCGGGTATGGATGTATCTAGATGTA 59.407 44.000 15.79 4.44 0.00 2.29
1646 2454 6.265649 GCGGGTATGGATGTATCTAGATGTAT 59.734 42.308 15.79 9.11 0.00 2.29
1647 2455 7.201920 GCGGGTATGGATGTATCTAGATGTATT 60.202 40.741 15.79 0.00 0.00 1.89
1648 2456 8.696374 CGGGTATGGATGTATCTAGATGTATTT 58.304 37.037 15.79 0.00 0.00 1.40
1673 2481 6.814506 AGTTATAGATGCATCCATTTCTGC 57.185 37.500 23.06 6.53 38.87 4.26
1674 2482 5.410746 AGTTATAGATGCATCCATTTCTGCG 59.589 40.000 23.06 0.00 41.32 5.18
1675 2483 2.336945 AGATGCATCCATTTCTGCGA 57.663 45.000 23.06 0.00 41.32 5.10
1676 2484 1.945394 AGATGCATCCATTTCTGCGAC 59.055 47.619 23.06 0.00 41.32 5.19
1677 2485 1.672363 GATGCATCCATTTCTGCGACA 59.328 47.619 16.23 0.00 41.32 4.35
1678 2486 1.532523 TGCATCCATTTCTGCGACAA 58.467 45.000 0.00 0.00 41.32 3.18
1679 2487 1.469703 TGCATCCATTTCTGCGACAAG 59.530 47.619 0.00 0.00 41.32 3.16
1680 2488 1.470098 GCATCCATTTCTGCGACAAGT 59.530 47.619 0.00 0.00 0.00 3.16
1681 2489 2.677836 GCATCCATTTCTGCGACAAGTA 59.322 45.455 0.00 0.00 0.00 2.24
1682 2490 3.126858 GCATCCATTTCTGCGACAAGTAA 59.873 43.478 0.00 0.00 0.00 2.24
1683 2491 4.201950 GCATCCATTTCTGCGACAAGTAAT 60.202 41.667 0.00 0.00 0.00 1.89
1684 2492 5.677091 GCATCCATTTCTGCGACAAGTAATT 60.677 40.000 0.00 0.00 0.00 1.40
1685 2493 5.957842 TCCATTTCTGCGACAAGTAATTT 57.042 34.783 0.00 0.00 0.00 1.82
1686 2494 5.698832 TCCATTTCTGCGACAAGTAATTTG 58.301 37.500 0.00 0.00 42.68 2.32
1687 2495 4.858692 CCATTTCTGCGACAAGTAATTTGG 59.141 41.667 0.00 0.00 41.25 3.28
1688 2496 5.335583 CCATTTCTGCGACAAGTAATTTGGA 60.336 40.000 0.00 0.00 41.25 3.53
1689 2497 5.759506 TTTCTGCGACAAGTAATTTGGAA 57.240 34.783 0.00 0.00 41.25 3.53
1690 2498 4.742438 TCTGCGACAAGTAATTTGGAAC 57.258 40.909 0.00 0.00 41.25 3.62
1691 2499 3.185594 TCTGCGACAAGTAATTTGGAACG 59.814 43.478 0.00 0.00 41.25 3.95
1692 2500 2.224549 TGCGACAAGTAATTTGGAACGG 59.775 45.455 0.00 0.00 41.25 4.44
1693 2501 2.481185 GCGACAAGTAATTTGGAACGGA 59.519 45.455 0.00 0.00 41.25 4.69
1694 2502 3.424433 GCGACAAGTAATTTGGAACGGAG 60.424 47.826 0.00 0.00 41.25 4.63
1695 2503 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
1696 2504 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
1697 2505 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
1698 2506 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
1741 2549 4.023291 TCTTTTGAAAAAGGACAGCCTGT 58.977 39.130 13.99 0.00 46.28 4.00
1751 2559 3.500343 AGGACAGCCTGTATTTTTGCTT 58.500 40.909 0.00 0.00 44.90 3.91
1752 2560 3.256631 AGGACAGCCTGTATTTTTGCTTG 59.743 43.478 0.00 0.00 44.90 4.01
1759 2567 5.361857 AGCCTGTATTTTTGCTTGCAGATAT 59.638 36.000 0.00 0.00 0.00 1.63
1810 2619 6.652481 AGTTTCAAGTCACTCAGATGTTATGG 59.348 38.462 0.00 0.00 0.00 2.74
1879 2688 6.575162 AAGTGCCATACTACTTCTTTTTGG 57.425 37.500 0.00 0.00 39.18 3.28
2024 2834 2.134789 AATCTGAACATGCCACCTCC 57.865 50.000 0.00 0.00 0.00 4.30
2225 3035 3.388024 TCCTTGACAGAGCACAGTTACTT 59.612 43.478 0.00 0.00 0.00 2.24
2283 3093 8.735692 TGCTGTAAGATATCATGAAACATGAA 57.264 30.769 16.42 8.22 34.07 2.57
2284 3094 9.346005 TGCTGTAAGATATCATGAAACATGAAT 57.654 29.630 16.42 11.67 34.07 2.57
2429 3241 4.260170 GACGGAGGTACTTCTGAAGTCTA 58.740 47.826 25.12 7.60 41.55 2.59
2430 3242 4.660168 ACGGAGGTACTTCTGAAGTCTAA 58.340 43.478 25.12 6.86 41.55 2.10
2431 3243 4.701171 ACGGAGGTACTTCTGAAGTCTAAG 59.299 45.833 25.12 15.62 41.55 2.18
2443 3255 6.336566 TCTGAAGTCTAAGTCTTCATGCATC 58.663 40.000 11.81 0.00 46.30 3.91
2539 3356 3.253432 GCCATTCTTTTCGTCTGGTCTTT 59.747 43.478 0.00 0.00 0.00 2.52
2774 3597 7.630242 ATCATTGTATTAAGTGGACAACAGG 57.370 36.000 0.00 0.00 35.99 4.00
2781 3604 3.297134 AAGTGGACAACAGGACATTGT 57.703 42.857 0.00 0.00 42.95 2.71
2819 3642 9.393512 TGAATTGAAAAACATTCAGGTTTCATT 57.606 25.926 0.00 0.00 39.93 2.57
2821 3644 8.735692 ATTGAAAAACATTCAGGTTTCATTGT 57.264 26.923 0.00 0.00 39.93 2.71
2909 3734 3.142174 GAGCTCCATACCAATAAGCACC 58.858 50.000 0.87 0.00 35.42 5.01
2945 3770 1.004927 GCGTCGTATCTTGATGGTTGC 60.005 52.381 0.00 0.00 0.00 4.17
2950 3775 3.447229 TCGTATCTTGATGGTTGCTCTCA 59.553 43.478 0.00 0.00 0.00 3.27
3135 3974 5.569823 GGAAATAACTTGCGCGTTTTCATTA 59.430 36.000 8.43 0.00 0.00 1.90
3279 4125 0.842030 AGTCAAGAGCCATGGGTCCA 60.842 55.000 34.70 19.59 42.97 4.02
3386 4232 8.224389 TGCACAAGTACATGCTATATTTGATT 57.776 30.769 15.21 0.00 42.55 2.57
3467 4410 5.105756 GGCCATGTTACTTAGTCAGCAATTT 60.106 40.000 0.00 0.00 0.00 1.82
3472 4415 7.129109 TGTTACTTAGTCAGCAATTTAGCAC 57.871 36.000 0.00 0.00 36.85 4.40
3477 4420 3.341823 AGTCAGCAATTTAGCACTGAGG 58.658 45.455 0.00 0.00 39.69 3.86
3531 4474 5.418676 ACACTTTGTGAATTGACCCTTTTG 58.581 37.500 4.61 0.00 36.96 2.44
3547 4490 5.712917 ACCCTTTTGTTTAACAAGTGACTCA 59.287 36.000 10.51 0.00 39.53 3.41
3668 4612 4.999311 AGCTGCCATTTCCTTTTTGAATTC 59.001 37.500 0.00 0.00 0.00 2.17
3959 4905 2.546778 TGTCAACGTTCAGTTCCTCAC 58.453 47.619 0.00 0.00 42.02 3.51
4107 5058 4.208746 TCCATTTTTCGTTTGTAGGTGGT 58.791 39.130 0.00 0.00 0.00 4.16
4221 5175 3.274288 GCCAAGAACGATTCTCCATCTT 58.726 45.455 0.00 0.00 39.61 2.40
4562 6891 9.303116 TCTTTTAAAAATAACCTGTCCTGCATA 57.697 29.630 1.66 0.00 0.00 3.14
4814 7176 2.290260 CCCTGATTTACCTGTGCACTGA 60.290 50.000 23.75 5.35 0.00 3.41
5114 7481 0.251297 CACTGGTCCATGCCTTTCCA 60.251 55.000 0.00 0.00 0.00 3.53
5169 7536 3.570975 ACTTGATTTGATGACAGCTTGCA 59.429 39.130 0.00 0.00 0.00 4.08
5204 7571 2.028748 GCAATGCACCTGAATCCTGTTT 60.029 45.455 0.00 0.00 0.00 2.83
5276 7643 9.950680 ATAATTTTCATATTAACTCTTGGCACG 57.049 29.630 0.00 0.00 0.00 5.34
5335 7703 4.335594 ACTCTGCACACTTTTGTTTAGGAC 59.664 41.667 0.00 0.00 31.66 3.85
5487 7864 1.926510 TGCGTGTGAGATCATTTAGCG 59.073 47.619 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 196 8.711457 GGTTCATCGATTTTGAAAATGTTCATT 58.289 29.630 8.03 0.00 43.29 2.57
477 713 6.141685 GTCTCGCGAAAAACACACAAAAATAT 59.858 34.615 11.33 0.00 0.00 1.28
479 715 4.264380 GTCTCGCGAAAAACACACAAAAAT 59.736 37.500 11.33 0.00 0.00 1.82
721 1040 2.204090 GGACTGGAGGGTGGGGAA 60.204 66.667 0.00 0.00 0.00 3.97
960 1328 2.863153 CGAGCCCGCAAGAAACTG 59.137 61.111 0.00 0.00 43.02 3.16
987 1355 1.219393 CGAGCCTCCTGGAAAGTCC 59.781 63.158 0.00 0.00 36.96 3.85
991 1359 4.082523 CGCCGAGCCTCCTGGAAA 62.083 66.667 0.00 0.00 34.57 3.13
1020 1392 0.889994 GAGCATGGTTCCACAATGCA 59.110 50.000 16.76 0.00 40.41 3.96
1027 1401 0.764271 TGACACTGAGCATGGTTCCA 59.236 50.000 0.00 0.00 0.00 3.53
1041 1415 0.531974 TGCAGGTTCGGACTTGACAC 60.532 55.000 10.68 0.00 35.02 3.67
1042 1416 0.179234 TTGCAGGTTCGGACTTGACA 59.821 50.000 10.68 4.61 35.02 3.58
1101 1475 1.470098 ACATTGCCGCTTTCAGACATC 59.530 47.619 0.00 0.00 0.00 3.06
1158 1541 5.046376 AGGCAAATTTGGAGGAAAACCATAG 60.046 40.000 19.47 0.00 37.26 2.23
1226 1609 2.496899 AGGCATGAAGTCGAAATGGT 57.503 45.000 0.00 0.00 0.00 3.55
1233 1617 0.877649 AGCGCATAGGCATGAAGTCG 60.878 55.000 11.47 0.00 41.24 4.18
1336 2086 5.104941 CCTCATTCACCATGTTACTCCTACA 60.105 44.000 0.00 0.00 34.06 2.74
1367 2117 4.593157 GTTACAACTGACATCAAACGCAA 58.407 39.130 0.00 0.00 0.00 4.85
1371 2121 5.006358 ACACTCGTTACAACTGACATCAAAC 59.994 40.000 0.00 0.00 0.00 2.93
1405 2155 3.199677 TCAAGACAAAACCACGTCGAAT 58.800 40.909 0.00 0.00 37.23 3.34
1413 2163 1.339610 CGGCCATTCAAGACAAAACCA 59.660 47.619 2.24 0.00 0.00 3.67
1524 2276 6.347969 GGGAAACAATTTACCACGTTACTCTC 60.348 42.308 0.00 0.00 43.54 3.20
1534 2286 7.841282 TTATTGTCAGGGAAACAATTTACCA 57.159 32.000 5.37 0.00 46.69 3.25
1604 2412 1.060122 CCGCGACAAGTAATTCGGAAC 59.940 52.381 8.23 0.00 39.23 3.62
1605 2413 1.352114 CCGCGACAAGTAATTCGGAA 58.648 50.000 8.23 0.00 39.23 4.30
1606 2414 0.458889 CCCGCGACAAGTAATTCGGA 60.459 55.000 8.23 0.00 39.23 4.55
1607 2415 0.738412 ACCCGCGACAAGTAATTCGG 60.738 55.000 8.23 0.00 35.73 4.30
1608 2416 1.912001 TACCCGCGACAAGTAATTCG 58.088 50.000 8.23 0.00 38.31 3.34
1609 2417 2.542595 CCATACCCGCGACAAGTAATTC 59.457 50.000 8.23 0.00 0.00 2.17
1610 2418 2.168936 TCCATACCCGCGACAAGTAATT 59.831 45.455 8.23 0.00 0.00 1.40
1611 2419 1.758280 TCCATACCCGCGACAAGTAAT 59.242 47.619 8.23 0.00 0.00 1.89
1612 2420 1.184431 TCCATACCCGCGACAAGTAA 58.816 50.000 8.23 0.00 0.00 2.24
1613 2421 1.067974 CATCCATACCCGCGACAAGTA 59.932 52.381 8.23 4.04 0.00 2.24
1614 2422 0.179084 CATCCATACCCGCGACAAGT 60.179 55.000 8.23 1.45 0.00 3.16
1615 2423 0.179084 ACATCCATACCCGCGACAAG 60.179 55.000 8.23 0.00 0.00 3.16
1616 2424 1.112950 TACATCCATACCCGCGACAA 58.887 50.000 8.23 0.00 0.00 3.18
1617 2425 1.271379 GATACATCCATACCCGCGACA 59.729 52.381 8.23 0.00 0.00 4.35
1618 2426 1.544691 AGATACATCCATACCCGCGAC 59.455 52.381 8.23 0.00 0.00 5.19
1619 2427 1.919240 AGATACATCCATACCCGCGA 58.081 50.000 8.23 0.00 0.00 5.87
1620 2428 3.014623 TCTAGATACATCCATACCCGCG 58.985 50.000 0.00 0.00 0.00 6.46
1621 2429 4.402793 ACATCTAGATACATCCATACCCGC 59.597 45.833 4.54 0.00 0.00 6.13
1622 2430 7.825331 ATACATCTAGATACATCCATACCCG 57.175 40.000 4.54 0.00 0.00 5.28
1647 2455 8.786898 GCAGAAATGGATGCATCTATAACTAAA 58.213 33.333 23.98 1.92 42.11 1.85
1648 2456 7.118245 CGCAGAAATGGATGCATCTATAACTAA 59.882 37.037 23.98 2.87 42.68 2.24
1649 2457 6.591448 CGCAGAAATGGATGCATCTATAACTA 59.409 38.462 23.98 0.00 42.68 2.24
1650 2458 5.410746 CGCAGAAATGGATGCATCTATAACT 59.589 40.000 23.98 20.95 42.68 2.24
1651 2459 5.409520 TCGCAGAAATGGATGCATCTATAAC 59.590 40.000 23.98 19.37 42.68 1.89
1652 2460 5.409520 GTCGCAGAAATGGATGCATCTATAA 59.590 40.000 23.98 9.69 42.68 0.98
1653 2461 4.931601 GTCGCAGAAATGGATGCATCTATA 59.068 41.667 23.98 12.61 42.68 1.31
1654 2462 3.750130 GTCGCAGAAATGGATGCATCTAT 59.250 43.478 25.28 22.14 42.68 1.98
1655 2463 3.133691 GTCGCAGAAATGGATGCATCTA 58.866 45.455 25.28 20.79 42.68 1.98
1656 2464 1.945394 GTCGCAGAAATGGATGCATCT 59.055 47.619 25.28 6.25 42.68 2.90
1657 2465 1.672363 TGTCGCAGAAATGGATGCATC 59.328 47.619 18.81 18.81 42.68 3.91
1658 2466 1.753930 TGTCGCAGAAATGGATGCAT 58.246 45.000 0.00 0.00 42.68 3.96
1659 2467 1.469703 CTTGTCGCAGAAATGGATGCA 59.530 47.619 0.00 0.00 42.68 3.96
1660 2468 1.470098 ACTTGTCGCAGAAATGGATGC 59.530 47.619 0.00 0.00 39.69 3.91
1661 2469 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
1662 2470 6.324819 CAAATTACTTGTCGCAGAAATGGAT 58.675 36.000 0.00 0.00 39.69 3.41
1663 2471 5.335583 CCAAATTACTTGTCGCAGAAATGGA 60.336 40.000 0.00 0.00 39.69 3.41
1664 2472 4.858692 CCAAATTACTTGTCGCAGAAATGG 59.141 41.667 0.00 0.00 39.69 3.16
1665 2473 5.698832 TCCAAATTACTTGTCGCAGAAATG 58.301 37.500 0.00 0.00 39.69 2.32
1666 2474 5.957842 TCCAAATTACTTGTCGCAGAAAT 57.042 34.783 0.00 0.00 39.69 2.17
1667 2475 5.516090 GTTCCAAATTACTTGTCGCAGAAA 58.484 37.500 0.00 0.00 39.69 2.52
1668 2476 4.319190 CGTTCCAAATTACTTGTCGCAGAA 60.319 41.667 0.00 0.00 39.69 3.02
1669 2477 3.185594 CGTTCCAAATTACTTGTCGCAGA 59.814 43.478 0.00 0.00 32.65 4.26
1670 2478 3.479006 CGTTCCAAATTACTTGTCGCAG 58.521 45.455 0.00 0.00 32.65 5.18
1671 2479 2.224549 CCGTTCCAAATTACTTGTCGCA 59.775 45.455 0.00 0.00 32.65 5.10
1672 2480 2.481185 TCCGTTCCAAATTACTTGTCGC 59.519 45.455 0.00 0.00 32.65 5.19
1673 2481 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
1674 2482 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
1675 2483 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
1676 2484 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
1677 2485 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
1678 2486 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
1679 2487 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
1680 2488 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
1681 2489 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
1682 2490 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
1683 2491 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1684 2492 1.621814 CAACTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
1685 2493 1.263356 CAACTACTCCCTCCGTTCCA 58.737 55.000 0.00 0.00 0.00 3.53
1686 2494 1.067071 CACAACTACTCCCTCCGTTCC 60.067 57.143 0.00 0.00 0.00 3.62
1687 2495 1.891150 TCACAACTACTCCCTCCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
1688 2496 2.005370 TCACAACTACTCCCTCCGTT 57.995 50.000 0.00 0.00 0.00 4.44
1689 2497 1.893801 CTTCACAACTACTCCCTCCGT 59.106 52.381 0.00 0.00 0.00 4.69
1690 2498 1.893801 ACTTCACAACTACTCCCTCCG 59.106 52.381 0.00 0.00 0.00 4.63
1691 2499 3.323979 TCAACTTCACAACTACTCCCTCC 59.676 47.826 0.00 0.00 0.00 4.30
1692 2500 4.602340 TCAACTTCACAACTACTCCCTC 57.398 45.455 0.00 0.00 0.00 4.30
1693 2501 5.308237 AGATTCAACTTCACAACTACTCCCT 59.692 40.000 0.00 0.00 0.00 4.20
1694 2502 5.552178 AGATTCAACTTCACAACTACTCCC 58.448 41.667 0.00 0.00 0.00 4.30
1695 2503 8.254508 AGATAGATTCAACTTCACAACTACTCC 58.745 37.037 0.00 0.00 0.00 3.85
1696 2504 9.646427 AAGATAGATTCAACTTCACAACTACTC 57.354 33.333 0.00 0.00 0.00 2.59
1723 2531 6.478512 AAAATACAGGCTGTCCTTTTTCAA 57.521 33.333 25.80 3.01 41.93 2.69
1741 2549 7.140705 CGGAATGATATCTGCAAGCAAAAATA 58.859 34.615 3.98 0.00 0.00 1.40
1751 2559 4.021981 CAGACCTACGGAATGATATCTGCA 60.022 45.833 3.98 0.00 0.00 4.41
1752 2560 4.021894 ACAGACCTACGGAATGATATCTGC 60.022 45.833 3.98 0.00 36.60 4.26
1759 2567 1.204704 CAGCACAGACCTACGGAATGA 59.795 52.381 0.00 0.00 0.00 2.57
1879 2688 7.988028 AGTAAAGTTATATGCCACTTCTTCTCC 59.012 37.037 0.00 0.00 31.79 3.71
2024 2834 7.999679 TGGCAAAGAAAATAGTAGATGGAATG 58.000 34.615 0.00 0.00 0.00 2.67
2253 3063 8.959548 TGTTTCATGATATCTTACAGCAACAAT 58.040 29.630 3.98 0.00 0.00 2.71
2288 3098 2.357327 GCACATGAGAATGCAAAGCA 57.643 45.000 0.00 0.00 44.86 3.91
2370 3182 4.523083 AGAAGTATTTGGCCTTAATGCGA 58.477 39.130 3.32 0.00 0.00 5.10
2429 3241 8.404000 GTGAATCTATTTGATGCATGAAGACTT 58.596 33.333 2.46 0.00 42.34 3.01
2430 3242 7.013083 GGTGAATCTATTTGATGCATGAAGACT 59.987 37.037 2.46 0.00 42.34 3.24
2431 3243 7.013083 AGGTGAATCTATTTGATGCATGAAGAC 59.987 37.037 2.46 0.00 42.34 3.01
2539 3356 3.382865 TGTGAACAAATGGCAACTGCTAA 59.617 39.130 1.06 0.00 41.70 3.09
2662 3483 8.037758 GCAGATAGCAACTAATATGTAGGATGT 58.962 37.037 0.00 0.00 44.79 3.06
2760 3582 4.133820 CACAATGTCCTGTTGTCCACTTA 58.866 43.478 0.00 0.00 37.69 2.24
2774 3597 8.503196 TCAATTCAACATGTACTACACAATGTC 58.497 33.333 0.00 0.00 41.55 3.06
2869 3692 4.344865 GACCCCAAGGCTTGCGGA 62.345 66.667 32.02 0.00 36.11 5.54
2885 3710 3.711190 TGCTTATTGGTATGGAGCTCTGA 59.289 43.478 14.64 0.55 34.56 3.27
2909 3734 2.110967 CGCCTGATGCAGAGGTTGG 61.111 63.158 14.50 2.31 41.33 3.77
2990 3822 5.491982 CTGCCTCTACATACTTGGAAGTTT 58.508 41.667 0.00 0.00 40.37 2.66
2991 3823 4.080863 CCTGCCTCTACATACTTGGAAGTT 60.081 45.833 0.00 0.00 40.37 2.66
3135 3974 7.228108 CAGTTATTGATATCTGGCTGACATGTT 59.772 37.037 0.00 0.00 0.00 2.71
3217 4063 9.310716 GGTTACTGGTAGTAAGTTAGCTAATTG 57.689 37.037 9.88 0.00 40.95 2.32
3386 4232 4.072131 GGAGTGACAAACTAGGCATGAAA 58.928 43.478 0.00 0.00 40.07 2.69
3467 4410 2.103373 GACCATGACTCCTCAGTGCTA 58.897 52.381 0.00 0.00 30.63 3.49
3472 4415 1.836166 ACCATGACCATGACTCCTCAG 59.164 52.381 11.28 0.00 41.20 3.35
3477 4420 5.489792 ACCATATACCATGACCATGACTC 57.510 43.478 11.28 0.00 41.20 3.36
3531 4474 7.915397 ACATGTTGATTGAGTCACTTGTTAAAC 59.085 33.333 0.00 0.00 36.32 2.01
3668 4612 7.598759 AGTGGACACTAGTAAAGTATATGGG 57.401 40.000 2.58 0.00 40.43 4.00
3913 4859 5.944007 GGTCTAATAGCAAAAAGAAGGGACA 59.056 40.000 0.00 0.00 0.00 4.02
3959 4905 8.585018 AGATTTTTCCTATTAACACAACAAGGG 58.415 33.333 0.00 0.00 0.00 3.95
4107 5058 2.244251 CGCGTACGAACTTGTACATGA 58.756 47.619 21.65 0.00 43.89 3.07
4270 5224 4.278170 TCTTGCCAGGTGTTAGATTGTTTG 59.722 41.667 0.00 0.00 0.00 2.93
4554 6883 2.099141 GCATCGCCTAATATGCAGGA 57.901 50.000 7.65 0.00 46.19 3.86
4562 6891 6.233434 TGAAATGAATCTAGCATCGCCTAAT 58.767 36.000 0.00 0.00 0.00 1.73
4611 6943 2.937591 AGTGCAATCATTGTTCGCAAG 58.062 42.857 0.00 0.00 40.85 4.01
4657 7015 1.760613 AGCATGCTTCCCATTTGGATG 59.239 47.619 16.30 0.00 44.66 3.51
5114 7481 4.065423 CGTGAGCGTGTGAATACAAAAT 57.935 40.909 0.00 0.00 38.82 1.82
5180 7547 2.028839 CAGGATTCAGGTGCATTGCAAA 60.029 45.455 13.94 4.33 41.47 3.68
5266 7633 5.545658 AATTTGTATGTACGTGCCAAGAG 57.454 39.130 0.00 0.00 0.00 2.85
5335 7703 6.252441 CAGTAGCAAGTCTCGAAGATACAAAG 59.748 42.308 0.00 0.00 35.99 2.77
5549 7927 7.011016 CCTTGTTTTAACTTCAGCGGAAAAATT 59.989 33.333 0.00 0.00 31.35 1.82


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

AutoCloner maintained by Alex Coulton.