Multiple sequence alignment - TraesCS5D01G406400

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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 TraesCS5D01G406400 chr5D 100.000 4138 0 0 1 4138 472231648 472235785 0.000000e+00 7642.0
1 TraesCS5D01G406400 chr5D 87.925 265 32 0 2107 2371 303407552 303407816 3.110000e-81 313.0
2 TraesCS5D01G406400 chr5D 92.754 138 10 0 3992 4129 549703910 549704047 2.520000e-47 200.0
3 TraesCS5D01G406400 chr5D 89.231 130 10 2 3994 4123 362655991 362656116 4.280000e-35 159.0
4 TraesCS5D01G406400 chr5D 91.837 98 8 0 2400 2497 303407817 303407914 2.010000e-28 137.0
5 TraesCS5D01G406400 chr5D 88.158 76 6 2 307 381 476041534 476041607 2.050000e-13 87.9
6 TraesCS5D01G406400 chr5B 93.483 4189 142 45 1 4130 578534340 578538456 0.000000e+00 6102.0
7 TraesCS5D01G406400 chr5B 84.235 869 101 18 1784 2646 44679546 44680384 0.000000e+00 813.0
8 TraesCS5D01G406400 chr5B 91.346 104 8 1 3888 3991 421190413 421190515 1.550000e-29 141.0
9 TraesCS5D01G406400 chr5A 86.804 2334 206 51 1602 3871 591439497 591441792 0.000000e+00 2510.0
10 TraesCS5D01G406400 chr5A 96.303 595 14 3 1 595 591392174 591392760 0.000000e+00 970.0
11 TraesCS5D01G406400 chr5A 89.004 773 59 15 683 1433 591438631 591439399 0.000000e+00 933.0
12 TraesCS5D01G406400 chr5A 88.291 316 26 6 6 310 591437981 591438296 6.540000e-98 368.0
13 TraesCS5D01G406400 chr5A 92.661 218 13 2 377 594 591438301 591438515 1.120000e-80 311.0
14 TraesCS5D01G406400 chr5A 89.623 106 11 0 1836 1941 603998490 603998385 7.220000e-28 135.0
15 TraesCS5D01G406400 chr2B 84.046 1053 125 28 1592 2642 37325667 37324656 0.000000e+00 974.0
16 TraesCS5D01G406400 chr2B 88.889 135 15 0 3994 4128 768127680 768127814 2.560000e-37 167.0
17 TraesCS5D01G406400 chr1B 78.883 895 142 35 1204 2084 533759059 533758198 2.790000e-156 562.0
18 TraesCS5D01G406400 chr1B 78.532 899 142 36 1204 2084 640478827 640477962 1.010000e-150 544.0
19 TraesCS5D01G406400 chr1B 92.929 99 7 0 2504 2602 540097987 540098085 1.200000e-30 145.0
20 TraesCS5D01G406400 chr1B 88.496 113 13 0 3889 4001 616430153 616430265 2.010000e-28 137.0
21 TraesCS5D01G406400 chr6D 88.679 265 30 0 2107 2371 79884311 79884047 1.430000e-84 324.0
22 TraesCS5D01G406400 chr6D 92.157 102 8 0 2400 2501 79884046 79883945 1.200000e-30 145.0
23 TraesCS5D01G406400 chr6D 90.141 71 5 2 308 377 95358 95427 1.580000e-14 91.6
24 TraesCS5D01G406400 chr3D 87.925 265 31 1 2107 2371 19630324 19630587 1.120000e-80 311.0
25 TraesCS5D01G406400 chr3D 87.594 266 32 1 2107 2371 536420291 536420556 1.440000e-79 307.0
26 TraesCS5D01G406400 chr3D 92.857 98 7 0 2400 2497 536420557 536420654 4.310000e-30 143.0
27 TraesCS5D01G406400 chr3D 90.196 102 10 0 2400 2501 19630588 19630689 2.600000e-27 134.0
28 TraesCS5D01G406400 chr3D 91.304 69 5 1 309 377 224894413 224894346 4.400000e-15 93.5
29 TraesCS5D01G406400 chr1A 81.887 265 28 10 1201 1451 551506568 551506826 5.420000e-49 206.0
30 TraesCS5D01G406400 chr1A 84.821 112 15 2 3889 4000 269092670 269092779 1.220000e-20 111.0
31 TraesCS5D01G406400 chr1A 90.000 80 2 2 309 382 11617140 11617219 9.470000e-17 99.0
32 TraesCS5D01G406400 chr2A 90.370 135 12 1 3994 4128 143844079 143843946 4.250000e-40 176.0
33 TraesCS5D01G406400 chr2A 90.291 103 10 0 2400 2502 42807500 42807602 7.220000e-28 135.0
34 TraesCS5D01G406400 chr2A 89.610 77 6 1 308 382 754467810 754467886 3.400000e-16 97.1
35 TraesCS5D01G406400 chr4D 89.286 140 14 1 3994 4132 50663175 50663036 1.530000e-39 174.0
36 TraesCS5D01G406400 chr7A 90.000 130 12 1 3994 4123 725736863 725736991 2.560000e-37 167.0
37 TraesCS5D01G406400 chr1D 92.174 115 9 0 3888 4002 450341189 450341075 3.310000e-36 163.0
38 TraesCS5D01G406400 chr7B 88.060 134 12 2 3994 4123 714551946 714552079 5.540000e-34 156.0
39 TraesCS5D01G406400 chr7B 90.598 117 9 1 3888 4002 609766142 609766026 1.990000e-33 154.0
40 TraesCS5D01G406400 chr7B 88.496 113 13 0 3890 4002 144741801 144741913 2.010000e-28 137.0
41 TraesCS5D01G406400 chr7B 88.496 113 12 1 3889 4000 714551790 714551902 7.220000e-28 135.0
42 TraesCS5D01G406400 chr2D 86.207 145 17 3 3985 4128 281670621 281670763 1.990000e-33 154.0
43 TraesCS5D01G406400 chr7D 93.243 74 4 1 309 382 18437347 18437275 1.570000e-19 108.0
44 TraesCS5D01G406400 chr7D 91.781 73 2 1 308 380 515468080 515468148 9.470000e-17 99.0
45 TraesCS5D01G406400 chr4B 81.579 114 16 4 3889 4002 35519232 35519124 5.700000e-14 89.8


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 TraesCS5D01G406400 chr5D 472231648 472235785 4137 False 7642.0 7642 100.000 1 4138 1 chr5D.!!$F2 4137
1 TraesCS5D01G406400 chr5B 578534340 578538456 4116 False 6102.0 6102 93.483 1 4130 1 chr5B.!!$F3 4129
2 TraesCS5D01G406400 chr5B 44679546 44680384 838 False 813.0 813 84.235 1784 2646 1 chr5B.!!$F1 862
3 TraesCS5D01G406400 chr5A 591437981 591441792 3811 False 1030.5 2510 89.190 6 3871 4 chr5A.!!$F2 3865
4 TraesCS5D01G406400 chr5A 591392174 591392760 586 False 970.0 970 96.303 1 595 1 chr5A.!!$F1 594
5 TraesCS5D01G406400 chr2B 37324656 37325667 1011 True 974.0 974 84.046 1592 2642 1 chr2B.!!$R1 1050
6 TraesCS5D01G406400 chr1B 533758198 533759059 861 True 562.0 562 78.883 1204 2084 1 chr1B.!!$R1 880
7 TraesCS5D01G406400 chr1B 640477962 640478827 865 True 544.0 544 78.532 1204 2084 1 chr1B.!!$R2 880

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
37 38 0.394352 CATGTTGACTGGGCCCTACC 60.394 60.000 25.70 12.1 37.93 3.18 F
587 623 0.588252 CAATTAATCGAGCCCTGCCG 59.412 55.000 0.00 0.0 0.00 5.69 F
1279 1386 0.683504 TCCGCCTCCTACTCTCCAAC 60.684 60.000 0.00 0.0 0.00 3.77 F
1596 1708 0.451783 GGCCTACATTGCTGTTTCGG 59.548 55.000 0.00 0.0 36.79 4.30 F
2502 2649 3.072330 TCAGCTGGTTCAGGTATGTTTCA 59.928 43.478 15.13 0.0 40.40 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1576 0.255890 CAGGATTCGACATTGGGGGT 59.744 55.000 0.00 0.0 0.00 4.95 R
1472 1584 0.610174 AAGCAGAGCAGGATTCGACA 59.390 50.000 0.00 0.0 0.00 4.35 R
2502 2649 6.923670 TGGAATTACCTCTACCATAGACTCT 58.076 40.000 0.00 0.0 39.86 3.24 R
2538 2685 7.174080 GCTCCAGTTATCTAGATCCATTTTTCC 59.826 40.741 8.95 0.0 0.00 3.13 R
3949 4148 0.456221 TGTTTCCGCTTCCGCAAAAA 59.544 45.000 0.00 0.0 35.30 1.94 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
37 38 0.394352 CATGTTGACTGGGCCCTACC 60.394 60.000 25.70 12.10 37.93 3.18
317 331 3.764972 CTCTTTTCGGTTCTACTCCCTCT 59.235 47.826 0.00 0.00 0.00 3.69
350 364 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
584 620 4.876107 ACTTGTACAATTAATCGAGCCCTG 59.124 41.667 9.13 0.00 0.00 4.45
587 623 0.588252 CAATTAATCGAGCCCTGCCG 59.412 55.000 0.00 0.00 0.00 5.69
633 703 7.753309 TGTATGTATGTTTAGGCTTTGTTGT 57.247 32.000 0.00 0.00 0.00 3.32
634 704 8.172352 TGTATGTATGTTTAGGCTTTGTTGTT 57.828 30.769 0.00 0.00 0.00 2.83
635 705 8.079203 TGTATGTATGTTTAGGCTTTGTTGTTG 58.921 33.333 0.00 0.00 0.00 3.33
663 733 2.017049 ACATAGGCGACCATCTTTTGC 58.983 47.619 0.00 0.00 0.00 3.68
664 734 1.334869 CATAGGCGACCATCTTTTGCC 59.665 52.381 0.00 0.00 43.22 4.52
671 741 2.684881 CGACCATCTTTTGCCTGCTATT 59.315 45.455 0.00 0.00 0.00 1.73
675 745 4.340381 ACCATCTTTTGCCTGCTATTCATC 59.660 41.667 0.00 0.00 0.00 2.92
676 746 4.583489 CCATCTTTTGCCTGCTATTCATCT 59.417 41.667 0.00 0.00 0.00 2.90
821 908 6.456181 CGCTGTATTTTCCTTTTCTGCTAGAG 60.456 42.308 0.00 0.00 0.00 2.43
822 909 6.183360 GCTGTATTTTCCTTTTCTGCTAGAGG 60.183 42.308 0.00 0.00 0.00 3.69
838 938 4.688413 GCTAGAGGCTGCATATGTTAGAAC 59.312 45.833 4.29 1.42 38.06 3.01
840 940 5.365021 AGAGGCTGCATATGTTAGAACTT 57.635 39.130 4.29 0.00 0.00 2.66
841 941 6.485830 AGAGGCTGCATATGTTAGAACTTA 57.514 37.500 4.29 0.00 0.00 2.24
845 945 6.989169 AGGCTGCATATGTTAGAACTTAGAAG 59.011 38.462 4.29 0.00 0.00 2.85
846 946 6.763610 GGCTGCATATGTTAGAACTTAGAAGT 59.236 38.462 4.29 0.00 42.04 3.01
847 947 7.926555 GGCTGCATATGTTAGAACTTAGAAGTA 59.073 37.037 4.29 0.00 38.57 2.24
848 948 8.973378 GCTGCATATGTTAGAACTTAGAAGTAG 58.027 37.037 4.29 0.00 38.57 2.57
849 949 9.469807 CTGCATATGTTAGAACTTAGAAGTAGG 57.530 37.037 4.29 0.00 38.57 3.18
850 950 9.197306 TGCATATGTTAGAACTTAGAAGTAGGA 57.803 33.333 4.29 0.00 38.57 2.94
851 951 9.465985 GCATATGTTAGAACTTAGAAGTAGGAC 57.534 37.037 4.29 0.00 38.57 3.85
859 959 7.668492 AGAACTTAGAAGTAGGACACGAAAAT 58.332 34.615 0.00 0.00 38.57 1.82
860 960 7.813627 AGAACTTAGAAGTAGGACACGAAAATC 59.186 37.037 0.00 0.00 38.57 2.17
868 968 1.401018 GGACACGAAAATCCGCTTTGG 60.401 52.381 0.00 0.00 40.09 3.28
884 984 1.577468 TTGGCATGGCGAATACGTAG 58.423 50.000 15.27 0.00 41.98 3.51
941 1041 5.285651 GTCAGAATCGATAAGGTTCAGAGG 58.714 45.833 0.00 0.00 42.37 3.69
1274 1381 2.604152 CCCTCCGCCTCCTACTCT 59.396 66.667 0.00 0.00 0.00 3.24
1279 1386 0.683504 TCCGCCTCCTACTCTCCAAC 60.684 60.000 0.00 0.00 0.00 3.77
1280 1387 1.677637 CCGCCTCCTACTCTCCAACC 61.678 65.000 0.00 0.00 0.00 3.77
1281 1388 0.684805 CGCCTCCTACTCTCCAACCT 60.685 60.000 0.00 0.00 0.00 3.50
1282 1389 1.574263 GCCTCCTACTCTCCAACCTT 58.426 55.000 0.00 0.00 0.00 3.50
1322 1434 6.073440 TCCGTACTTTGCTTAAACATTGTCTC 60.073 38.462 0.00 0.00 0.00 3.36
1438 1550 1.941812 CAATCGTAATGCTCCCGGC 59.058 57.895 0.00 0.00 42.22 6.13
1439 1551 1.227853 AATCGTAATGCTCCCGGCC 60.228 57.895 0.00 0.00 40.92 6.13
1441 1553 1.768684 ATCGTAATGCTCCCGGCCAT 61.769 55.000 2.24 0.00 40.92 4.40
1452 1564 1.003118 TCCCGGCCATACTGATATTGC 59.997 52.381 2.24 0.00 0.00 3.56
1458 1570 5.178061 CGGCCATACTGATATTGCTATTGA 58.822 41.667 2.24 0.00 31.53 2.57
1468 1580 7.831193 ACTGATATTGCTATTGATATTCACCCC 59.169 37.037 0.00 0.00 0.00 4.95
1470 1582 4.805140 TTGCTATTGATATTCACCCCCA 57.195 40.909 0.00 0.00 0.00 4.96
1471 1583 4.805140 TGCTATTGATATTCACCCCCAA 57.195 40.909 0.00 0.00 0.00 4.12
1472 1584 5.337956 TGCTATTGATATTCACCCCCAAT 57.662 39.130 0.00 0.00 0.00 3.16
1473 1585 5.078949 TGCTATTGATATTCACCCCCAATG 58.921 41.667 0.00 0.00 0.00 2.82
1474 1586 5.079643 GCTATTGATATTCACCCCCAATGT 58.920 41.667 0.00 0.00 0.00 2.71
1475 1587 5.183904 GCTATTGATATTCACCCCCAATGTC 59.816 44.000 0.00 0.00 0.00 3.06
1476 1588 3.207265 TGATATTCACCCCCAATGTCG 57.793 47.619 0.00 0.00 0.00 4.35
1477 1589 2.774809 TGATATTCACCCCCAATGTCGA 59.225 45.455 0.00 0.00 0.00 4.20
1480 1592 2.122783 TTCACCCCCAATGTCGAATC 57.877 50.000 0.00 0.00 0.00 2.52
1490 1602 0.829333 ATGTCGAATCCTGCTCTGCT 59.171 50.000 0.00 0.00 0.00 4.24
1491 1603 0.610174 TGTCGAATCCTGCTCTGCTT 59.390 50.000 0.00 0.00 0.00 3.91
1492 1604 1.002430 TGTCGAATCCTGCTCTGCTTT 59.998 47.619 0.00 0.00 0.00 3.51
1493 1605 2.233676 TGTCGAATCCTGCTCTGCTTTA 59.766 45.455 0.00 0.00 0.00 1.85
1494 1606 2.863137 GTCGAATCCTGCTCTGCTTTAG 59.137 50.000 0.00 0.00 0.00 1.85
1495 1607 2.497675 TCGAATCCTGCTCTGCTTTAGT 59.502 45.455 0.00 0.00 0.00 2.24
1496 1608 3.055819 TCGAATCCTGCTCTGCTTTAGTT 60.056 43.478 0.00 0.00 0.00 2.24
1497 1609 3.308323 CGAATCCTGCTCTGCTTTAGTTC 59.692 47.826 0.00 0.00 0.00 3.01
1498 1610 2.770164 TCCTGCTCTGCTTTAGTTCC 57.230 50.000 0.00 0.00 0.00 3.62
1499 1611 1.279271 TCCTGCTCTGCTTTAGTTCCC 59.721 52.381 0.00 0.00 0.00 3.97
1500 1612 1.003580 CCTGCTCTGCTTTAGTTCCCA 59.996 52.381 0.00 0.00 0.00 4.37
1501 1613 2.356535 CCTGCTCTGCTTTAGTTCCCAT 60.357 50.000 0.00 0.00 0.00 4.00
1502 1614 3.350833 CTGCTCTGCTTTAGTTCCCATT 58.649 45.455 0.00 0.00 0.00 3.16
1503 1615 3.347216 TGCTCTGCTTTAGTTCCCATTC 58.653 45.455 0.00 0.00 0.00 2.67
1504 1616 3.009473 TGCTCTGCTTTAGTTCCCATTCT 59.991 43.478 0.00 0.00 0.00 2.40
1505 1617 4.013050 GCTCTGCTTTAGTTCCCATTCTT 58.987 43.478 0.00 0.00 0.00 2.52
1515 1627 8.754991 TTTAGTTCCCATTCTTTTCAGTTACA 57.245 30.769 0.00 0.00 0.00 2.41
1516 1628 8.934023 TTAGTTCCCATTCTTTTCAGTTACAT 57.066 30.769 0.00 0.00 0.00 2.29
1529 1641 4.894784 TCAGTTACATTGTTCACTCCTCC 58.105 43.478 0.00 0.00 0.00 4.30
1530 1642 4.003648 CAGTTACATTGTTCACTCCTCCC 58.996 47.826 0.00 0.00 0.00 4.30
1539 1651 3.117322 TGTTCACTCCTCCCCATTTTCAA 60.117 43.478 0.00 0.00 0.00 2.69
1541 1653 5.222233 TGTTCACTCCTCCCCATTTTCAATA 60.222 40.000 0.00 0.00 0.00 1.90
1542 1654 4.855340 TCACTCCTCCCCATTTTCAATAC 58.145 43.478 0.00 0.00 0.00 1.89
1544 1656 4.399303 CACTCCTCCCCATTTTCAATACAC 59.601 45.833 0.00 0.00 0.00 2.90
1546 1658 4.599041 TCCTCCCCATTTTCAATACACTG 58.401 43.478 0.00 0.00 0.00 3.66
1549 1661 5.480073 CCTCCCCATTTTCAATACACTGAAA 59.520 40.000 0.00 0.00 42.21 2.69
1578 1690 9.947669 CTAAGCTTATTTCTTCAATCAATCTGG 57.052 33.333 6.64 0.00 0.00 3.86
1581 1693 6.183360 GCTTATTTCTTCAATCAATCTGGCCT 60.183 38.462 3.32 0.00 0.00 5.19
1582 1694 7.013655 GCTTATTTCTTCAATCAATCTGGCCTA 59.986 37.037 3.32 0.00 0.00 3.93
1584 1696 4.842531 TCTTCAATCAATCTGGCCTACA 57.157 40.909 3.32 0.00 0.00 2.74
1585 1697 5.378230 TCTTCAATCAATCTGGCCTACAT 57.622 39.130 3.32 0.00 0.00 2.29
1589 1701 3.589951 ATCAATCTGGCCTACATTGCT 57.410 42.857 3.32 0.00 0.00 3.91
1590 1702 2.646930 TCAATCTGGCCTACATTGCTG 58.353 47.619 3.32 0.00 0.00 4.41
1592 1704 2.756760 CAATCTGGCCTACATTGCTGTT 59.243 45.455 3.32 0.00 36.79 3.16
1594 1706 2.436417 TCTGGCCTACATTGCTGTTTC 58.564 47.619 3.32 0.00 36.79 2.78
1595 1707 1.131126 CTGGCCTACATTGCTGTTTCG 59.869 52.381 3.32 0.00 36.79 3.46
1596 1708 0.451783 GGCCTACATTGCTGTTTCGG 59.548 55.000 0.00 0.00 36.79 4.30
1992 2128 6.394640 TCCCCCAGGTAACAATATTAGGATTT 59.605 38.462 0.00 0.00 41.41 2.17
2007 2143 6.971726 TTAGGATTTCACTATCTTAGGCGA 57.028 37.500 0.00 0.00 0.00 5.54
2049 2189 9.664332 GTCCTCATAGTAAGATTACCGTATCTA 57.336 37.037 0.00 0.00 33.81 1.98
2502 2649 3.072330 TCAGCTGGTTCAGGTATGTTTCA 59.928 43.478 15.13 0.00 40.40 2.69
2538 2685 9.191995 GTAGAGGTAATTCCAACAAATGTTTTG 57.808 33.333 0.00 0.00 35.83 2.44
2562 2709 8.101309 TGGAAAAATGGATCTAGATAACTGGA 57.899 34.615 4.89 0.00 37.97 3.86
3521 3690 4.465632 AATGAACGTGATGGTAGTAGCA 57.534 40.909 4.19 4.19 0.00 3.49
3907 4106 1.187974 TAGGGATGAAAACGGAGCGA 58.812 50.000 0.00 0.00 0.00 4.93
3912 4111 2.031508 GGATGAAAACGGAGCGAAAACA 60.032 45.455 0.00 0.00 0.00 2.83
3934 4133 4.393062 CAGACGAAATTGAGTGCTACCATT 59.607 41.667 0.00 0.00 0.00 3.16
3938 4137 5.920273 ACGAAATTGAGTGCTACCATTTTTG 59.080 36.000 0.00 0.00 0.00 2.44
3939 4138 5.920273 CGAAATTGAGTGCTACCATTTTTGT 59.080 36.000 0.00 0.00 0.00 2.83
3940 4139 6.420604 CGAAATTGAGTGCTACCATTTTTGTT 59.579 34.615 0.00 0.00 0.00 2.83
3941 4140 7.042791 CGAAATTGAGTGCTACCATTTTTGTTT 60.043 33.333 0.00 0.00 0.00 2.83
3942 4141 8.504812 AAATTGAGTGCTACCATTTTTGTTTT 57.495 26.923 0.00 0.00 0.00 2.43
3943 4142 7.713764 ATTGAGTGCTACCATTTTTGTTTTC 57.286 32.000 0.00 0.00 0.00 2.29
3944 4143 6.214191 TGAGTGCTACCATTTTTGTTTTCA 57.786 33.333 0.00 0.00 0.00 2.69
3945 4144 6.815089 TGAGTGCTACCATTTTTGTTTTCAT 58.185 32.000 0.00 0.00 0.00 2.57
3946 4145 7.946207 TGAGTGCTACCATTTTTGTTTTCATA 58.054 30.769 0.00 0.00 0.00 2.15
3947 4146 8.584157 TGAGTGCTACCATTTTTGTTTTCATAT 58.416 29.630 0.00 0.00 0.00 1.78
3948 4147 9.423061 GAGTGCTACCATTTTTGTTTTCATATT 57.577 29.630 0.00 0.00 0.00 1.28
3949 4148 9.777297 AGTGCTACCATTTTTGTTTTCATATTT 57.223 25.926 0.00 0.00 0.00 1.40
3990 4189 7.948034 ACAAATATAGAAACCCCGAAAATGA 57.052 32.000 0.00 0.00 0.00 2.57
4098 4297 7.902920 ATGAATTGGTTACATGGCTAGAAAT 57.097 32.000 0.00 0.00 0.00 2.17
4099 4298 8.995027 ATGAATTGGTTACATGGCTAGAAATA 57.005 30.769 0.00 0.00 0.00 1.40
4135 4334 7.592938 TGTCAGCAACTTAACATAAAATCAGG 58.407 34.615 0.00 0.00 0.00 3.86
4136 4335 7.446931 TGTCAGCAACTTAACATAAAATCAGGA 59.553 33.333 0.00 0.00 0.00 3.86
4137 4336 7.965107 GTCAGCAACTTAACATAAAATCAGGAG 59.035 37.037 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
317 331 3.061322 CCACGACGAGTAATTTGGAACA 58.939 45.455 0.00 0.00 0.00 3.18
350 364 3.260632 CCCTCCGTTCCAAATTTCCAAAT 59.739 43.478 0.00 0.00 0.00 2.32
584 620 1.722011 ACACAACATACTACAGCGGC 58.278 50.000 0.00 0.00 0.00 6.53
587 623 6.262601 ACAACAAAACACAACATACTACAGC 58.737 36.000 0.00 0.00 0.00 4.40
633 703 3.055747 TGGTCGCCTATGTAATGTGACAA 60.056 43.478 0.00 0.00 40.39 3.18
634 704 2.498078 TGGTCGCCTATGTAATGTGACA 59.502 45.455 0.00 0.00 40.39 3.58
635 705 3.173668 TGGTCGCCTATGTAATGTGAC 57.826 47.619 0.00 0.00 38.47 3.67
663 733 3.307550 CCAGGATCCAGATGAATAGCAGG 60.308 52.174 15.82 0.00 0.00 4.85
664 734 3.327172 ACCAGGATCCAGATGAATAGCAG 59.673 47.826 15.82 0.00 0.00 4.24
671 741 0.543277 GCACACCAGGATCCAGATGA 59.457 55.000 15.82 0.00 0.00 2.92
675 745 0.679002 CAAGGCACACCAGGATCCAG 60.679 60.000 15.82 5.70 39.06 3.86
676 746 1.379916 CAAGGCACACCAGGATCCA 59.620 57.895 15.82 0.00 39.06 3.41
761 843 2.838736 TCAAGCTCAACTCCACACTTC 58.161 47.619 0.00 0.00 0.00 3.01
768 850 1.339438 TGCAGGATCAAGCTCAACTCC 60.339 52.381 9.60 0.00 0.00 3.85
821 908 6.763610 ACTTCTAAGTTCTAACATATGCAGCC 59.236 38.462 1.58 0.00 35.21 4.85
822 909 7.778470 ACTTCTAAGTTCTAACATATGCAGC 57.222 36.000 1.58 0.00 35.21 5.25
838 938 5.515626 CGGATTTTCGTGTCCTACTTCTAAG 59.484 44.000 0.00 0.00 32.19 2.18
840 940 4.676196 GCGGATTTTCGTGTCCTACTTCTA 60.676 45.833 0.00 0.00 32.19 2.10
841 941 3.846360 CGGATTTTCGTGTCCTACTTCT 58.154 45.455 0.00 0.00 32.19 2.85
845 945 2.005971 AGCGGATTTTCGTGTCCTAC 57.994 50.000 0.00 0.00 32.19 3.18
846 946 2.739913 CAAAGCGGATTTTCGTGTCCTA 59.260 45.455 0.00 0.00 32.19 2.94
847 947 1.535462 CAAAGCGGATTTTCGTGTCCT 59.465 47.619 0.00 0.00 32.19 3.85
848 948 1.401018 CCAAAGCGGATTTTCGTGTCC 60.401 52.381 0.00 0.00 36.56 4.02
849 949 1.963747 CCAAAGCGGATTTTCGTGTC 58.036 50.000 0.00 0.00 36.56 3.67
850 950 0.039527 GCCAAAGCGGATTTTCGTGT 60.040 50.000 0.00 0.00 36.56 4.49
851 951 0.039617 TGCCAAAGCGGATTTTCGTG 60.040 50.000 0.00 0.00 44.31 4.35
852 952 0.887933 ATGCCAAAGCGGATTTTCGT 59.112 45.000 0.00 0.00 44.31 3.85
853 953 1.270971 CATGCCAAAGCGGATTTTCG 58.729 50.000 0.00 0.00 44.31 3.46
868 968 2.034001 GTCAACTACGTATTCGCCATGC 60.034 50.000 0.00 0.00 41.18 4.06
890 990 1.463444 GTTGGTGGAGACGTATTGCAC 59.537 52.381 13.55 13.55 36.31 4.57
1266 1371 2.113777 AGGGAAAGGTTGGAGAGTAGGA 59.886 50.000 0.00 0.00 0.00 2.94
1268 1375 2.907042 ACAGGGAAAGGTTGGAGAGTAG 59.093 50.000 0.00 0.00 0.00 2.57
1271 1378 2.959465 AACAGGGAAAGGTTGGAGAG 57.041 50.000 0.00 0.00 0.00 3.20
1274 1381 1.477923 CGGAAACAGGGAAAGGTTGGA 60.478 52.381 0.00 0.00 0.00 3.53
1322 1434 0.860203 CGCATCGAATTGCTGCACAG 60.860 55.000 0.00 0.00 39.69 3.66
1441 1553 9.890629 GGGTGAATATCAATAGCAATATCAGTA 57.109 33.333 0.00 0.00 0.00 2.74
1452 1564 5.412594 CGACATTGGGGGTGAATATCAATAG 59.587 44.000 0.00 0.00 0.00 1.73
1458 1570 3.943671 TTCGACATTGGGGGTGAATAT 57.056 42.857 0.00 0.00 0.00 1.28
1464 1576 0.255890 CAGGATTCGACATTGGGGGT 59.744 55.000 0.00 0.00 0.00 4.95
1468 1580 1.938577 CAGAGCAGGATTCGACATTGG 59.061 52.381 0.00 0.00 0.00 3.16
1470 1582 1.209019 AGCAGAGCAGGATTCGACATT 59.791 47.619 0.00 0.00 0.00 2.71
1471 1583 0.829333 AGCAGAGCAGGATTCGACAT 59.171 50.000 0.00 0.00 0.00 3.06
1472 1584 0.610174 AAGCAGAGCAGGATTCGACA 59.390 50.000 0.00 0.00 0.00 4.35
1473 1585 1.731720 AAAGCAGAGCAGGATTCGAC 58.268 50.000 0.00 0.00 0.00 4.20
1474 1586 2.497675 ACTAAAGCAGAGCAGGATTCGA 59.502 45.455 0.00 0.00 0.00 3.71
1475 1587 2.898705 ACTAAAGCAGAGCAGGATTCG 58.101 47.619 0.00 0.00 0.00 3.34
1476 1588 3.625313 GGAACTAAAGCAGAGCAGGATTC 59.375 47.826 0.00 0.00 0.00 2.52
1477 1589 3.615155 GGAACTAAAGCAGAGCAGGATT 58.385 45.455 0.00 0.00 0.00 3.01
1480 1592 1.003580 TGGGAACTAAAGCAGAGCAGG 59.996 52.381 0.00 0.00 0.00 4.85
1490 1602 8.754991 TGTAACTGAAAAGAATGGGAACTAAA 57.245 30.769 0.00 0.00 0.00 1.85
1491 1603 8.934023 ATGTAACTGAAAAGAATGGGAACTAA 57.066 30.769 0.00 0.00 0.00 2.24
1492 1604 8.792633 CAATGTAACTGAAAAGAATGGGAACTA 58.207 33.333 0.00 0.00 0.00 2.24
1493 1605 7.287696 ACAATGTAACTGAAAAGAATGGGAACT 59.712 33.333 0.00 0.00 0.00 3.01
1494 1606 7.433680 ACAATGTAACTGAAAAGAATGGGAAC 58.566 34.615 0.00 0.00 0.00 3.62
1495 1607 7.595819 ACAATGTAACTGAAAAGAATGGGAA 57.404 32.000 0.00 0.00 0.00 3.97
1496 1608 7.286546 TGAACAATGTAACTGAAAAGAATGGGA 59.713 33.333 0.00 0.00 0.00 4.37
1497 1609 7.382218 GTGAACAATGTAACTGAAAAGAATGGG 59.618 37.037 0.00 0.00 0.00 4.00
1498 1610 8.137437 AGTGAACAATGTAACTGAAAAGAATGG 58.863 33.333 1.44 0.00 0.00 3.16
1499 1611 9.173939 GAGTGAACAATGTAACTGAAAAGAATG 57.826 33.333 6.40 0.00 0.00 2.67
1500 1612 8.352942 GGAGTGAACAATGTAACTGAAAAGAAT 58.647 33.333 6.40 0.00 0.00 2.40
1501 1613 7.556275 AGGAGTGAACAATGTAACTGAAAAGAA 59.444 33.333 6.40 0.00 0.00 2.52
1502 1614 7.054124 AGGAGTGAACAATGTAACTGAAAAGA 58.946 34.615 6.40 0.00 0.00 2.52
1503 1615 7.264373 AGGAGTGAACAATGTAACTGAAAAG 57.736 36.000 6.40 0.00 0.00 2.27
1504 1616 6.262273 GGAGGAGTGAACAATGTAACTGAAAA 59.738 38.462 6.40 0.00 0.00 2.29
1505 1617 5.763204 GGAGGAGTGAACAATGTAACTGAAA 59.237 40.000 6.40 0.00 0.00 2.69
1515 1627 3.833559 AAATGGGGAGGAGTGAACAAT 57.166 42.857 0.00 0.00 0.00 2.71
1516 1628 3.117322 TGAAAATGGGGAGGAGTGAACAA 60.117 43.478 0.00 0.00 0.00 2.83
1566 1678 3.633525 GCAATGTAGGCCAGATTGATTGA 59.366 43.478 21.28 0.00 39.67 2.57
1570 1682 2.025981 ACAGCAATGTAGGCCAGATTGA 60.026 45.455 21.28 0.00 39.67 2.57
1573 1685 2.814805 AACAGCAATGTAGGCCAGAT 57.185 45.000 5.01 0.00 0.00 2.90
1575 1687 1.131126 CGAAACAGCAATGTAGGCCAG 59.869 52.381 5.01 0.00 0.00 4.85
1578 1690 1.448985 TCCGAAACAGCAATGTAGGC 58.551 50.000 0.00 0.00 0.00 3.93
1581 1693 3.627395 AGGATCCGAAACAGCAATGTA 57.373 42.857 5.98 0.00 0.00 2.29
1582 1694 2.496899 AGGATCCGAAACAGCAATGT 57.503 45.000 5.98 0.00 0.00 2.71
1584 1696 3.744660 GGATAGGATCCGAAACAGCAAT 58.255 45.455 5.98 0.00 40.13 3.56
1585 1697 3.194005 GGATAGGATCCGAAACAGCAA 57.806 47.619 5.98 0.00 40.13 3.91
1596 1708 2.977808 TCAGGGTCCAAGGATAGGATC 58.022 52.381 0.00 0.00 37.52 3.36
1992 2128 4.022242 GCAGGTAATCGCCTAAGATAGTGA 60.022 45.833 0.00 0.00 37.04 3.41
2007 2143 5.830799 TGAGGACATCATATGCAGGTAAT 57.169 39.130 0.00 0.00 31.12 1.89
2502 2649 6.923670 TGGAATTACCTCTACCATAGACTCT 58.076 40.000 0.00 0.00 39.86 3.24
2538 2685 7.174080 GCTCCAGTTATCTAGATCCATTTTTCC 59.826 40.741 8.95 0.00 0.00 3.13
3521 3690 9.665264 GATTTTGAAACAAAGATAGAAGAACGT 57.335 29.630 0.00 0.00 0.00 3.99
3907 4106 4.900635 AGCACTCAATTTCGTCTGTTTT 57.099 36.364 0.00 0.00 0.00 2.43
3912 4111 3.678056 TGGTAGCACTCAATTTCGTCT 57.322 42.857 0.00 0.00 0.00 4.18
3949 4148 0.456221 TGTTTCCGCTTCCGCAAAAA 59.544 45.000 0.00 0.00 35.30 1.94
3956 4155 6.263344 GGTTTCTATATTTGTTTCCGCTTCC 58.737 40.000 0.00 0.00 0.00 3.46
3963 4162 9.083080 CATTTTCGGGGTTTCTATATTTGTTTC 57.917 33.333 0.00 0.00 0.00 2.78
3990 4189 3.181448 ACACCCACTTATGTTTCCGTCTT 60.181 43.478 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.