Multiple sequence alignment - TraesCS6A01G215700

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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 TraesCS6A01G215700 chr6A 100.000 2860 0 0 1 2860 397486211 397489070 0.000000e+00 5282.0
1 TraesCS6A01G215700 chr2A 95.982 896 31 4 1 894 15932067 15932959 0.000000e+00 1450.0
2 TraesCS6A01G215700 chr2A 81.886 403 53 12 2071 2455 211333383 211332983 3.550000e-84 322.0
3 TraesCS6A01G215700 chr6D 90.604 596 27 10 891 1463 276124818 276125407 0.000000e+00 763.0
4 TraesCS6A01G215700 chr6D 87.194 695 58 13 2073 2743 276128278 276128965 0.000000e+00 761.0
5 TraesCS6A01G215700 chr6D 85.489 317 19 12 1770 2059 276125810 276126126 3.580000e-79 305.0
6 TraesCS6A01G215700 chr6D 91.795 195 13 2 1578 1772 276125430 276125621 4.700000e-68 268.0
7 TraesCS6A01G215700 chr6D 87.736 106 10 3 1461 1565 427992031 427992134 1.390000e-23 121.0
8 TraesCS6A01G215700 chr6B 89.333 600 39 9 891 1467 438086417 438087014 0.000000e+00 730.0
9 TraesCS6A01G215700 chr6B 88.043 276 32 1 1765 2040 438087469 438087743 2.750000e-85 326.0
10 TraesCS6A01G215700 chr6B 91.096 146 11 1 1627 1772 438087042 438087185 2.250000e-46 196.0
11 TraesCS6A01G215700 chr6B 86.525 141 18 1 2603 2742 438090872 438091012 1.370000e-33 154.0
12 TraesCS6A01G215700 chr3B 93.734 383 20 3 381 759 433698404 433698786 3.200000e-159 571.0
13 TraesCS6A01G215700 chr3B 87.062 371 44 4 57 425 433696092 433696460 1.590000e-112 416.0
14 TraesCS6A01G215700 chr3B 90.000 100 10 0 1469 1568 729387588 729387489 2.310000e-26 130.0
15 TraesCS6A01G215700 chr2D 79.747 395 59 10 2071 2452 195727417 195727031 1.690000e-67 267.0
16 TraesCS6A01G215700 chr3A 90.816 98 9 0 1468 1565 424454774 424454677 6.430000e-27 132.0
17 TraesCS6A01G215700 chr3A 90.000 100 10 0 1466 1565 739275016 739275115 2.310000e-26 130.0
18 TraesCS6A01G215700 chr3A 89.000 100 11 0 1469 1568 242726107 242726206 1.080000e-24 124.0
19 TraesCS6A01G215700 chr1A 91.398 93 8 0 1462 1554 83819956 83819864 8.320000e-26 128.0
20 TraesCS6A01G215700 chr4D 89.109 101 11 0 1466 1566 43284106 43284006 2.990000e-25 126.0
21 TraesCS6A01G215700 chr4D 79.104 201 29 9 2075 2272 85827288 85827098 2.990000e-25 126.0
22 TraesCS6A01G215700 chr2B 89.691 97 10 0 1469 1565 716814486 716814582 1.080000e-24 124.0
23 TraesCS6A01G215700 chrUn 86.916 107 11 3 1464 1569 71293292 71293188 1.800000e-22 117.0
24 TraesCS6A01G215700 chr4A 82.883 111 8 6 2748 2855 120370149 120370047 3.920000e-14 89.8
25 TraesCS6A01G215700 chr3D 95.652 46 2 0 1275 1320 418491118 418491163 1.100000e-09 75.0


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 TraesCS6A01G215700 chr6A 397486211 397489070 2859 False 5282.00 5282 100.00000 1 2860 1 chr6A.!!$F1 2859
1 TraesCS6A01G215700 chr2A 15932067 15932959 892 False 1450.00 1450 95.98200 1 894 1 chr2A.!!$F1 893
2 TraesCS6A01G215700 chr6D 276124818 276128965 4147 False 524.25 763 88.77050 891 2743 4 chr6D.!!$F2 1852
3 TraesCS6A01G215700 chr6B 438086417 438091012 4595 False 351.50 730 88.74925 891 2742 4 chr6B.!!$F1 1851
4 TraesCS6A01G215700 chr3B 433696092 433698786 2694 False 493.50 571 90.39800 57 759 2 chr3B.!!$F1 702

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
778 2773 0.770499 TCATGTGAAAGGCCAGGTGA 59.23 50.0 5.01 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2770 9548 0.108138 CGGAAGCGAAGGTGAGGATT 60.108 55.0 0.0 0.0 39.47 3.01 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
47 48 3.043999 GCACCGCCTACCATCCCTT 62.044 63.158 0.00 0.00 0.00 3.95
92 93 4.778143 GCCAGGAACGACGGCCAT 62.778 66.667 2.24 0.00 40.07 4.40
176 178 0.809636 GGCGGTTGCAGCAAAAACTT 60.810 50.000 10.11 0.00 45.35 2.66
251 2195 6.755461 ATCTCATTAGTCGTAGCAAAATCG 57.245 37.500 0.00 0.00 0.00 3.34
300 2244 3.645975 CGTCGCGGGTTGCAACTT 61.646 61.111 27.64 0.00 46.97 2.66
330 2274 6.616017 TGAACGCATGTAGCAAATTTAATCA 58.384 32.000 0.00 0.00 46.13 2.57
354 2298 2.571206 GTGGAAGCAAAAATCGACGAC 58.429 47.619 0.00 0.00 0.00 4.34
370 2314 1.004292 ACGACAGTTGTAGCAAAACGC 60.004 47.619 0.00 0.00 42.91 4.84
459 2452 3.438781 GCATCTAAACATCACGGTTCCAA 59.561 43.478 0.00 0.00 0.00 3.53
661 2655 4.413851 GGAGAGAGGAGGGGAATAAAACAT 59.586 45.833 0.00 0.00 0.00 2.71
712 2707 5.986501 TGTAGAGAAAGAGAAAGGAGGAC 57.013 43.478 0.00 0.00 0.00 3.85
778 2773 0.770499 TCATGTGAAAGGCCAGGTGA 59.230 50.000 5.01 0.00 0.00 4.02
898 2893 5.224135 CGGAAAACGTTTCCCATAAAACAT 58.776 37.500 17.03 0.00 38.73 2.71
901 2896 6.587226 GGAAAACGTTTCCCATAAAACATACC 59.413 38.462 11.92 0.00 38.73 2.73
920 2918 1.034838 CCGACTCCCTCTGGTCTGAG 61.035 65.000 0.00 0.00 0.00 3.35
960 2961 1.981495 CAGTCCTTCCCTCCAACTTCT 59.019 52.381 0.00 0.00 0.00 2.85
1160 3176 4.514577 CGGTGCGCCCTCGATCTT 62.515 66.667 11.56 0.00 38.10 2.40
1174 3190 4.099266 CCTCGATCTTTCTCATCTTCCTGT 59.901 45.833 0.00 0.00 0.00 4.00
1179 3195 7.502561 TCGATCTTTCTCATCTTCCTGTATACA 59.497 37.037 5.25 5.25 0.00 2.29
1181 3197 9.421806 GATCTTTCTCATCTTCCTGTATACATG 57.578 37.037 5.91 3.74 0.00 3.21
1205 3238 3.248630 TTGGCTAACAAGCGTGCGC 62.249 57.895 8.67 8.67 42.33 6.09
1329 3362 2.383527 CGCCGCAACTCTCTTGTCC 61.384 63.158 0.00 0.00 0.00 4.02
1347 3380 0.318784 CCTTCGTCTACGCCTATGGC 60.319 60.000 0.00 0.00 46.75 4.40
1358 3391 1.941812 CCTATGGCCATTTCGTCGC 59.058 57.895 26.37 0.00 0.00 5.19
1449 3482 2.515926 TGGACTCTGCGCTAATGATC 57.484 50.000 9.73 0.00 0.00 2.92
1463 3496 0.464036 ATGATCACGGTGCGGTGTAT 59.536 50.000 2.51 0.00 39.00 2.29
1466 3499 1.335810 GATCACGGTGCGGTGTATCTA 59.664 52.381 2.51 0.00 39.00 1.98
1467 3500 0.736636 TCACGGTGCGGTGTATCTAG 59.263 55.000 2.51 0.00 39.00 2.43
1468 3501 0.454600 CACGGTGCGGTGTATCTAGT 59.545 55.000 0.00 0.00 33.24 2.57
1469 3502 1.672363 CACGGTGCGGTGTATCTAGTA 59.328 52.381 0.00 0.00 33.24 1.82
1471 3504 1.945394 CGGTGCGGTGTATCTAGTACT 59.055 52.381 0.00 0.00 34.27 2.73
1472 3505 2.032204 CGGTGCGGTGTATCTAGTACTC 60.032 54.545 0.00 0.00 34.27 2.59
1473 3506 2.292845 GGTGCGGTGTATCTAGTACTCC 59.707 54.545 0.00 10.86 41.46 3.85
1474 3507 2.292845 GTGCGGTGTATCTAGTACTCCC 59.707 54.545 0.00 8.51 41.72 4.30
1475 3508 2.174210 TGCGGTGTATCTAGTACTCCCT 59.826 50.000 0.00 0.00 41.72 4.20
1476 3509 2.813172 GCGGTGTATCTAGTACTCCCTC 59.187 54.545 0.00 0.00 41.72 4.30
1477 3510 3.410508 CGGTGTATCTAGTACTCCCTCC 58.589 54.545 0.00 0.00 41.72 4.30
1478 3511 3.410508 GGTGTATCTAGTACTCCCTCCG 58.589 54.545 0.00 0.00 39.82 4.63
1479 3512 3.181446 GGTGTATCTAGTACTCCCTCCGT 60.181 52.174 0.00 0.00 39.82 4.69
1480 3513 4.064388 GTGTATCTAGTACTCCCTCCGTC 58.936 52.174 0.00 0.00 34.27 4.79
1481 3514 3.972638 TGTATCTAGTACTCCCTCCGTCT 59.027 47.826 0.00 0.00 34.27 4.18
1482 3515 3.775261 ATCTAGTACTCCCTCCGTCTC 57.225 52.381 0.00 0.00 0.00 3.36
1483 3516 2.475155 TCTAGTACTCCCTCCGTCTCA 58.525 52.381 0.00 0.00 0.00 3.27
1484 3517 2.842496 TCTAGTACTCCCTCCGTCTCAA 59.158 50.000 0.00 0.00 0.00 3.02
1485 3518 2.599408 AGTACTCCCTCCGTCTCAAA 57.401 50.000 0.00 0.00 0.00 2.69
1486 3519 3.103080 AGTACTCCCTCCGTCTCAAAT 57.897 47.619 0.00 0.00 0.00 2.32
1487 3520 3.442076 AGTACTCCCTCCGTCTCAAATT 58.558 45.455 0.00 0.00 0.00 1.82
1488 3521 4.607239 AGTACTCCCTCCGTCTCAAATTA 58.393 43.478 0.00 0.00 0.00 1.40
1489 3522 5.021458 AGTACTCCCTCCGTCTCAAATTAA 58.979 41.667 0.00 0.00 0.00 1.40
1490 3523 4.473477 ACTCCCTCCGTCTCAAATTAAG 57.527 45.455 0.00 0.00 0.00 1.85
1491 3524 3.838903 ACTCCCTCCGTCTCAAATTAAGT 59.161 43.478 0.00 0.00 0.00 2.24
1492 3525 4.184629 CTCCCTCCGTCTCAAATTAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
1493 3526 3.835978 TCCCTCCGTCTCAAATTAAGTGA 59.164 43.478 0.00 0.00 0.00 3.41
1494 3527 3.933332 CCCTCCGTCTCAAATTAAGTGAC 59.067 47.826 4.01 4.01 0.00 3.67
1495 3528 4.322801 CCCTCCGTCTCAAATTAAGTGACT 60.323 45.833 9.77 0.00 0.00 3.41
1496 3529 4.865365 CCTCCGTCTCAAATTAAGTGACTC 59.135 45.833 9.77 0.00 0.00 3.36
1497 3530 5.462530 TCCGTCTCAAATTAAGTGACTCA 57.537 39.130 9.77 0.00 0.00 3.41
1498 3531 5.849510 TCCGTCTCAAATTAAGTGACTCAA 58.150 37.500 9.77 0.00 0.00 3.02
1499 3532 6.464222 TCCGTCTCAAATTAAGTGACTCAAT 58.536 36.000 9.77 0.00 0.00 2.57
1500 3533 6.934645 TCCGTCTCAAATTAAGTGACTCAATT 59.065 34.615 0.00 0.00 0.00 2.32
1501 3534 7.444183 TCCGTCTCAAATTAAGTGACTCAATTT 59.556 33.333 0.60 0.60 33.31 1.82
1502 3535 8.076178 CCGTCTCAAATTAAGTGACTCAATTTT 58.924 33.333 3.73 0.00 31.27 1.82
1555 3588 9.370126 CAAAGTTGAGTCACTTATTTTAGAACG 57.630 33.333 0.00 0.00 35.87 3.95
1556 3589 7.653767 AGTTGAGTCACTTATTTTAGAACGG 57.346 36.000 0.00 0.00 0.00 4.44
1557 3590 7.439381 AGTTGAGTCACTTATTTTAGAACGGA 58.561 34.615 0.00 0.00 0.00 4.69
1558 3591 7.929785 AGTTGAGTCACTTATTTTAGAACGGAA 59.070 33.333 0.00 0.00 0.00 4.30
1559 3592 7.884816 TGAGTCACTTATTTTAGAACGGAAG 57.115 36.000 0.00 0.00 0.00 3.46
1560 3593 6.872020 TGAGTCACTTATTTTAGAACGGAAGG 59.128 38.462 0.00 0.00 0.00 3.46
1561 3594 7.001099 AGTCACTTATTTTAGAACGGAAGGA 57.999 36.000 0.00 0.00 0.00 3.36
1562 3595 7.097834 AGTCACTTATTTTAGAACGGAAGGAG 58.902 38.462 0.00 0.00 0.00 3.69
1576 3609 5.950023 ACGGAAGGAGTAGATAGATACCAA 58.050 41.667 0.00 0.00 0.00 3.67
1579 3612 8.168725 ACGGAAGGAGTAGATAGATACCAATAA 58.831 37.037 0.00 0.00 0.00 1.40
1605 3643 2.832838 TGCAGTGAAATCCTCCTCCTA 58.167 47.619 0.00 0.00 0.00 2.94
1606 3644 3.181329 TGCAGTGAAATCCTCCTCCTAA 58.819 45.455 0.00 0.00 0.00 2.69
1625 3663 5.012046 TCCTAAAGATGACTTGCTCAGAACA 59.988 40.000 0.00 0.00 36.39 3.18
1626 3664 5.879223 CCTAAAGATGACTTGCTCAGAACAT 59.121 40.000 0.00 0.00 36.39 2.71
1802 4138 2.548707 GCTTGCAGTCCCATCGATCATA 60.549 50.000 0.00 0.00 0.00 2.15
1809 4145 1.204704 TCCCATCGATCATATGGACGC 59.795 52.381 20.66 0.00 45.77 5.19
1847 4183 0.525668 CTCTTGGCTACCGTGCTACG 60.526 60.000 2.27 2.27 42.11 3.51
1906 4270 2.833338 CAATTGATGGGGCCTTCAGAAA 59.167 45.455 0.84 1.31 32.87 2.52
1919 4283 4.800249 GCCTTCAGAAATTGCCAATGAACA 60.800 41.667 0.00 0.00 0.00 3.18
1941 4305 6.624423 ACAGAATAAATTTCGCTGCAAATCT 58.376 32.000 12.23 0.00 0.00 2.40
1942 4306 6.529125 ACAGAATAAATTTCGCTGCAAATCTG 59.471 34.615 12.23 15.44 0.00 2.90
1943 4307 6.529125 CAGAATAAATTTCGCTGCAAATCTGT 59.471 34.615 0.00 0.00 0.00 3.41
1961 4325 9.459276 CAAATCTGTTTTTGTTTACTTTTGTCG 57.541 29.630 0.00 0.00 32.99 4.35
1969 4333 6.477669 TTGTTTACTTTTGTCGTGTGTACA 57.522 33.333 0.00 0.00 0.00 2.90
1972 4336 5.705813 TTACTTTTGTCGTGTGTACACTG 57.294 39.130 25.60 17.90 44.34 3.66
2044 4408 4.970662 TGATCTCTTGTTATGCCTTTGC 57.029 40.909 0.00 0.00 38.26 3.68
2046 4410 3.153369 TCTCTTGTTATGCCTTTGCCA 57.847 42.857 0.00 0.00 36.33 4.92
2062 4426 5.122396 CCTTTGCCACTCTACTTTATGTGTC 59.878 44.000 0.00 0.00 0.00 3.67
2064 4428 5.420725 TGCCACTCTACTTTATGTGTCAT 57.579 39.130 0.00 0.00 0.00 3.06
2065 4429 5.178061 TGCCACTCTACTTTATGTGTCATG 58.822 41.667 0.00 0.00 0.00 3.07
2067 4431 5.874810 GCCACTCTACTTTATGTGTCATGAA 59.125 40.000 0.00 0.00 0.00 2.57
2068 4432 6.540189 GCCACTCTACTTTATGTGTCATGAAT 59.460 38.462 0.00 0.00 0.00 2.57
2069 4433 7.710907 GCCACTCTACTTTATGTGTCATGAATA 59.289 37.037 0.00 0.00 0.00 1.75
2071 4435 9.254133 CACTCTACTTTATGTGTCATGAATAGG 57.746 37.037 0.00 0.00 0.00 2.57
2085 6650 7.015682 TGTCATGAATAGGAATAGGAACTCTCC 59.984 40.741 0.00 0.00 41.75 3.71
2119 6686 9.914834 TGCACCCTATATGAATAGTAAAGTTTT 57.085 29.630 0.00 0.00 34.36 2.43
2161 6734 8.672823 AGTAATCTAAAAATTCGGGGTATCAC 57.327 34.615 0.00 0.00 0.00 3.06
2180 6753 3.587061 TCACACCTGGTCAACCATTCTAT 59.413 43.478 1.58 0.00 46.46 1.98
2182 6755 4.396166 CACACCTGGTCAACCATTCTATTC 59.604 45.833 1.58 0.00 46.46 1.75
2189 6762 5.249622 TGGTCAACCATTCTATTCCTGTGTA 59.750 40.000 0.00 0.00 42.01 2.90
2195 6768 7.923414 ACCATTCTATTCCTGTGTAAAGTTC 57.077 36.000 0.00 0.00 0.00 3.01
2216 6789 5.351948 TCCGTGAAGAAATGACATCCATA 57.648 39.130 0.00 0.00 34.45 2.74
2220 6793 6.201044 CCGTGAAGAAATGACATCCATAGTAC 59.799 42.308 0.00 0.00 34.45 2.73
2233 6806 7.341805 ACATCCATAGTACTCTCAGCAAAAAT 58.658 34.615 0.00 0.00 0.00 1.82
2325 6901 9.370126 GTGAATATCACGGATTTAATTTCTTCG 57.630 33.333 0.00 0.00 37.67 3.79
2328 6904 3.062909 TCACGGATTTAATTTCTTCGCGG 59.937 43.478 6.13 0.00 0.00 6.46
2339 6915 0.592637 TCTTCGCGGAACTTCGTACA 59.407 50.000 6.13 0.00 0.00 2.90
2363 6939 4.039973 TGAGTAGAATGAACGACCAGGTTT 59.960 41.667 0.00 0.00 0.00 3.27
2452 7456 2.224161 ACCGAGAGCTCCTATGCATTTC 60.224 50.000 10.93 0.00 34.99 2.17
2654 9432 2.459555 ATCTTGATCGCCCCCAAATT 57.540 45.000 0.00 0.00 0.00 1.82
2660 9438 0.034477 ATCGCCCCCAAATTCGAAGT 60.034 50.000 3.35 0.00 34.50 3.01
2661 9439 0.250989 TCGCCCCCAAATTCGAAGTT 60.251 50.000 4.77 4.77 0.00 2.66
2677 9455 5.877031 TCGAAGTTAGACTACAAATCCGAG 58.123 41.667 0.00 0.00 0.00 4.63
2688 9466 8.246180 AGACTACAAATCCGAGTATAAAAACGA 58.754 33.333 0.00 0.00 0.00 3.85
2695 9473 5.410067 TCCGAGTATAAAAACGAAACGGAT 58.590 37.500 0.00 0.00 41.32 4.18
2697 9475 4.953814 CGAGTATAAAAACGAAACGGATGC 59.046 41.667 0.00 0.00 0.00 3.91
2709 9487 1.153369 CGGATGCATCACTTCGGGT 60.153 57.895 27.25 0.00 0.00 5.28
2734 9512 6.919721 TCATTCGGTTTGGAGGAATTAAAAG 58.080 36.000 0.00 0.00 0.00 2.27
2765 9543 9.590451 AAACAATGCATGATATCAGTTTTTAGG 57.410 29.630 11.78 0.00 0.00 2.69
2766 9544 8.297470 ACAATGCATGATATCAGTTTTTAGGT 57.703 30.769 11.78 0.44 0.00 3.08
2767 9545 8.752187 ACAATGCATGATATCAGTTTTTAGGTT 58.248 29.630 11.78 0.00 0.00 3.50
2768 9546 9.590451 CAATGCATGATATCAGTTTTTAGGTTT 57.410 29.630 11.78 0.00 0.00 3.27
2779 9557 8.173542 TCAGTTTTTAGGTTTTAATCCTCACC 57.826 34.615 0.00 0.00 36.60 4.02
2780 9558 8.002459 TCAGTTTTTAGGTTTTAATCCTCACCT 58.998 33.333 0.00 0.00 42.55 4.00
2781 9559 8.638873 CAGTTTTTAGGTTTTAATCCTCACCTT 58.361 33.333 0.00 0.00 40.32 3.50
2782 9560 8.857098 AGTTTTTAGGTTTTAATCCTCACCTTC 58.143 33.333 0.00 0.00 40.32 3.46
2783 9561 7.443259 TTTTAGGTTTTAATCCTCACCTTCG 57.557 36.000 0.00 0.00 40.32 3.79
2784 9562 3.344515 AGGTTTTAATCCTCACCTTCGC 58.655 45.455 0.00 0.00 36.09 4.70
2785 9563 3.009143 AGGTTTTAATCCTCACCTTCGCT 59.991 43.478 0.00 0.00 36.09 4.93
2786 9564 3.756963 GGTTTTAATCCTCACCTTCGCTT 59.243 43.478 0.00 0.00 0.00 4.68
2787 9565 4.142665 GGTTTTAATCCTCACCTTCGCTTC 60.143 45.833 0.00 0.00 0.00 3.86
2788 9566 2.981859 TAATCCTCACCTTCGCTTCC 57.018 50.000 0.00 0.00 0.00 3.46
2789 9567 0.108138 AATCCTCACCTTCGCTTCCG 60.108 55.000 0.00 0.00 0.00 4.30
2790 9568 1.258445 ATCCTCACCTTCGCTTCCGT 61.258 55.000 0.00 0.00 35.54 4.69
2791 9569 1.446272 CCTCACCTTCGCTTCCGTC 60.446 63.158 0.00 0.00 35.54 4.79
2792 9570 1.801913 CTCACCTTCGCTTCCGTCG 60.802 63.158 0.00 0.00 35.54 5.12
2793 9571 2.049433 CACCTTCGCTTCCGTCGT 60.049 61.111 0.00 0.00 35.54 4.34
2794 9572 2.087009 CACCTTCGCTTCCGTCGTC 61.087 63.158 0.00 0.00 35.54 4.20
2795 9573 2.257371 CCTTCGCTTCCGTCGTCA 59.743 61.111 0.00 0.00 35.54 4.35
2796 9574 2.087009 CCTTCGCTTCCGTCGTCAC 61.087 63.158 0.00 0.00 35.54 3.67
2797 9575 2.049802 TTCGCTTCCGTCGTCACC 60.050 61.111 0.00 0.00 35.54 4.02
2798 9576 3.884581 TTCGCTTCCGTCGTCACCG 62.885 63.158 0.00 0.00 35.54 4.94
2822 9600 4.680237 CCGCCGTGTGCTTCCTCA 62.680 66.667 0.00 0.00 38.05 3.86
2823 9601 3.414700 CGCCGTGTGCTTCCTCAC 61.415 66.667 0.00 0.00 38.05 3.51
2827 9605 2.661866 GTGTGCTTCCTCACGCGT 60.662 61.111 5.58 5.58 39.73 6.01
2828 9606 2.355837 TGTGCTTCCTCACGCGTC 60.356 61.111 9.86 0.00 39.73 5.19
2829 9607 2.355837 GTGCTTCCTCACGCGTCA 60.356 61.111 9.86 0.00 0.00 4.35
2830 9608 2.355837 TGCTTCCTCACGCGTCAC 60.356 61.111 9.86 0.00 0.00 3.67
2831 9609 3.112709 GCTTCCTCACGCGTCACC 61.113 66.667 9.86 0.00 0.00 4.02
2832 9610 2.805353 CTTCCTCACGCGTCACCG 60.805 66.667 9.86 0.00 37.07 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.954868 GACCATAGCGCGTCCACG 60.955 66.667 8.43 0.00 43.27 4.94
25 26 1.682451 GGATGGTAGGCGGTGCACTA 61.682 60.000 17.98 0.00 0.00 2.74
47 48 2.809174 CGACGAGCGTCAATGGCA 60.809 61.111 21.09 0.00 44.77 4.92
79 80 4.446413 ACCGATGGCCGTCGTTCC 62.446 66.667 37.85 8.52 39.89 3.62
176 178 1.067060 GACCGATGACGATGGTGATGA 59.933 52.381 0.00 0.00 42.66 2.92
224 226 9.774742 GATTTTGCTACGACTAATGAGATTTTT 57.225 29.630 0.00 0.00 0.00 1.94
225 227 8.116753 CGATTTTGCTACGACTAATGAGATTTT 58.883 33.333 0.00 0.00 0.00 1.82
235 2179 2.419673 TCGTCCGATTTTGCTACGACTA 59.580 45.455 0.00 0.00 37.63 2.59
251 2195 2.054140 TTTTGCTGCAACCGTCGTCC 62.054 55.000 15.72 0.00 0.00 4.79
330 2274 3.611530 CGTCGATTTTTGCTTCCACCAAT 60.612 43.478 0.00 0.00 0.00 3.16
354 2298 0.306533 ACGGCGTTTTGCTACAACTG 59.693 50.000 6.77 0.00 45.43 3.16
459 2452 1.068281 TGCAACATGGCGTTCAAATGT 59.932 42.857 0.00 0.00 34.86 2.71
627 2621 3.364549 CTCCTCTCTCCACATGTCTCTT 58.635 50.000 0.00 0.00 0.00 2.85
712 2707 4.275936 TCTTTCTTCTCCTTTGCCTTTTCG 59.724 41.667 0.00 0.00 0.00 3.46
778 2773 1.801309 CGTTTTTGTGCGGGGTCCAT 61.801 55.000 0.00 0.00 0.00 3.41
787 2782 1.668628 CCTGGCCATACGTTTTTGTGC 60.669 52.381 5.51 0.00 0.00 4.57
877 2872 6.587226 GGGTATGTTTTATGGGAAACGTTTTC 59.413 38.462 15.89 13.44 41.32 2.29
901 2896 1.000771 TCAGACCAGAGGGAGTCGG 60.001 63.158 0.00 0.00 38.08 4.79
920 2918 2.756760 TGGAATGATCAAAGCTTGAGGC 59.243 45.455 0.00 0.00 43.98 4.70
1066 3067 3.745803 GAAGACGAGGCGGACGGT 61.746 66.667 0.00 0.00 34.93 4.83
1121 3122 1.370064 GTGTTGGAGTAGGTGCCGT 59.630 57.895 0.00 0.00 0.00 5.68
1159 3175 8.144478 GCTACATGTATACAGGAAGATGAGAAA 58.856 37.037 23.38 0.00 0.00 2.52
1160 3176 7.255977 GGCTACATGTATACAGGAAGATGAGAA 60.256 40.741 23.38 1.63 0.00 2.87
1205 3238 2.023771 ACATCAGTCACTGCACGCG 61.024 57.895 3.53 3.53 0.00 6.01
1206 3239 1.494628 CACATCAGTCACTGCACGC 59.505 57.895 0.00 0.00 0.00 5.34
1347 3380 1.143969 GGTACTCCGCGACGAAATGG 61.144 60.000 8.23 0.00 0.00 3.16
1449 3482 0.454600 ACTAGATACACCGCACCGTG 59.545 55.000 0.00 0.00 39.75 4.94
1463 3496 2.475155 TGAGACGGAGGGAGTACTAGA 58.525 52.381 0.00 0.00 0.00 2.43
1466 3499 2.599408 TTTGAGACGGAGGGAGTACT 57.401 50.000 0.00 0.00 0.00 2.73
1467 3500 3.889520 AATTTGAGACGGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
1468 3501 5.021458 ACTTAATTTGAGACGGAGGGAGTA 58.979 41.667 0.00 0.00 0.00 2.59
1469 3502 3.838903 ACTTAATTTGAGACGGAGGGAGT 59.161 43.478 0.00 0.00 0.00 3.85
1471 3504 3.835978 TCACTTAATTTGAGACGGAGGGA 59.164 43.478 0.00 0.00 0.00 4.20
1472 3505 3.933332 GTCACTTAATTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
1473 3506 4.822026 AGTCACTTAATTTGAGACGGAGG 58.178 43.478 0.00 0.00 34.56 4.30
1474 3507 5.470368 TGAGTCACTTAATTTGAGACGGAG 58.530 41.667 0.00 0.00 34.56 4.63
1475 3508 5.462530 TGAGTCACTTAATTTGAGACGGA 57.537 39.130 0.00 0.00 34.56 4.69
1476 3509 6.727824 ATTGAGTCACTTAATTTGAGACGG 57.272 37.500 0.00 0.00 34.56 4.79
1529 3562 9.370126 CGTTCTAAAATAAGTGACTCAACTTTG 57.630 33.333 0.00 0.00 40.77 2.77
1530 3563 8.557029 CCGTTCTAAAATAAGTGACTCAACTTT 58.443 33.333 0.00 0.00 40.77 2.66
1531 3564 7.929785 TCCGTTCTAAAATAAGTGACTCAACTT 59.070 33.333 0.00 0.00 42.89 2.66
1532 3565 7.439381 TCCGTTCTAAAATAAGTGACTCAACT 58.561 34.615 0.00 0.00 0.00 3.16
1533 3566 7.647907 TCCGTTCTAAAATAAGTGACTCAAC 57.352 36.000 0.00 0.00 0.00 3.18
1534 3567 7.386848 CCTTCCGTTCTAAAATAAGTGACTCAA 59.613 37.037 0.00 0.00 0.00 3.02
1535 3568 6.872020 CCTTCCGTTCTAAAATAAGTGACTCA 59.128 38.462 0.00 0.00 0.00 3.41
1536 3569 7.095270 TCCTTCCGTTCTAAAATAAGTGACTC 58.905 38.462 0.00 0.00 0.00 3.36
1537 3570 7.001099 TCCTTCCGTTCTAAAATAAGTGACT 57.999 36.000 0.00 0.00 0.00 3.41
1538 3571 6.872547 ACTCCTTCCGTTCTAAAATAAGTGAC 59.127 38.462 0.00 0.00 0.00 3.67
1539 3572 7.001099 ACTCCTTCCGTTCTAAAATAAGTGA 57.999 36.000 0.00 0.00 0.00 3.41
1540 3573 8.248945 TCTACTCCTTCCGTTCTAAAATAAGTG 58.751 37.037 0.00 0.00 0.00 3.16
1541 3574 8.358582 TCTACTCCTTCCGTTCTAAAATAAGT 57.641 34.615 0.00 0.00 0.00 2.24
1544 3577 9.857656 TCTATCTACTCCTTCCGTTCTAAAATA 57.142 33.333 0.00 0.00 0.00 1.40
1545 3578 8.763984 TCTATCTACTCCTTCCGTTCTAAAAT 57.236 34.615 0.00 0.00 0.00 1.82
1546 3579 8.763984 ATCTATCTACTCCTTCCGTTCTAAAA 57.236 34.615 0.00 0.00 0.00 1.52
1547 3580 9.282569 GTATCTATCTACTCCTTCCGTTCTAAA 57.717 37.037 0.00 0.00 0.00 1.85
1548 3581 7.882271 GGTATCTATCTACTCCTTCCGTTCTAA 59.118 40.741 0.00 0.00 0.00 2.10
1549 3582 7.016957 TGGTATCTATCTACTCCTTCCGTTCTA 59.983 40.741 0.00 0.00 0.00 2.10
1550 3583 6.183361 TGGTATCTATCTACTCCTTCCGTTCT 60.183 42.308 0.00 0.00 0.00 3.01
1551 3584 6.002704 TGGTATCTATCTACTCCTTCCGTTC 58.997 44.000 0.00 0.00 0.00 3.95
1552 3585 5.950023 TGGTATCTATCTACTCCTTCCGTT 58.050 41.667 0.00 0.00 0.00 4.44
1553 3586 5.579753 TGGTATCTATCTACTCCTTCCGT 57.420 43.478 0.00 0.00 0.00 4.69
1554 3587 8.460428 GTTATTGGTATCTATCTACTCCTTCCG 58.540 40.741 0.00 0.00 0.00 4.30
1555 3588 9.536510 AGTTATTGGTATCTATCTACTCCTTCC 57.463 37.037 0.00 0.00 0.00 3.46
1557 3590 9.315363 CCAGTTATTGGTATCTATCTACTCCTT 57.685 37.037 0.00 0.00 42.41 3.36
1558 3591 8.887264 CCAGTTATTGGTATCTATCTACTCCT 57.113 38.462 0.00 0.00 42.41 3.69
1586 3619 3.914426 TTAGGAGGAGGATTTCACTGC 57.086 47.619 0.00 0.00 0.00 4.40
1589 3622 6.052360 GTCATCTTTAGGAGGAGGATTTCAC 58.948 44.000 0.00 0.00 35.31 3.18
1591 3624 6.493189 AGTCATCTTTAGGAGGAGGATTTC 57.507 41.667 0.00 0.00 35.31 2.17
1605 3643 8.263640 AGTATATGTTCTGAGCAAGTCATCTTT 58.736 33.333 0.00 0.00 33.51 2.52
1606 3644 7.790027 AGTATATGTTCTGAGCAAGTCATCTT 58.210 34.615 0.00 0.00 33.51 2.40
1772 3810 2.093288 TGGGACTGCAAGCATAAGAGAG 60.093 50.000 0.00 0.00 37.60 3.20
1809 4145 3.772025 AGAGTGTTCCTCCAATGGACTAG 59.228 47.826 0.00 0.00 41.47 2.57
1847 4183 1.129437 GAACAAGCTCATGACCGCTTC 59.871 52.381 16.89 5.55 44.06 3.86
1906 4270 7.201548 GCGAAATTTATTCTGTTCATTGGCAAT 60.202 33.333 6.96 6.96 0.00 3.56
1919 4283 6.624423 ACAGATTTGCAGCGAAATTTATTCT 58.376 32.000 0.00 0.00 0.00 2.40
1941 4305 6.696148 ACACACGACAAAAGTAAACAAAAACA 59.304 30.769 0.00 0.00 0.00 2.83
1942 4306 7.096183 ACACACGACAAAAGTAAACAAAAAC 57.904 32.000 0.00 0.00 0.00 2.43
1943 4307 7.859377 TGTACACACGACAAAAGTAAACAAAAA 59.141 29.630 0.00 0.00 0.00 1.94
1961 4325 7.045416 TGGATGGAATAATACAGTGTACACAC 58.955 38.462 27.06 4.51 46.77 3.82
2044 4408 9.254133 CTATTCATGACACATAAAGTAGAGTGG 57.746 37.037 0.00 0.00 36.35 4.00
2046 4410 9.201989 TCCTATTCATGACACATAAAGTAGAGT 57.798 33.333 0.00 0.00 0.00 3.24
2062 4426 6.393990 CGGAGAGTTCCTATTCCTATTCATG 58.606 44.000 0.00 0.00 41.67 3.07
2064 4428 4.281182 GCGGAGAGTTCCTATTCCTATTCA 59.719 45.833 0.00 0.00 41.67 2.57
2065 4429 4.525100 AGCGGAGAGTTCCTATTCCTATTC 59.475 45.833 0.00 0.00 41.67 1.75
2067 4431 3.829601 CAGCGGAGAGTTCCTATTCCTAT 59.170 47.826 0.00 0.00 41.67 2.57
2068 4432 3.223435 CAGCGGAGAGTTCCTATTCCTA 58.777 50.000 0.00 0.00 41.67 2.94
2069 4433 2.035632 CAGCGGAGAGTTCCTATTCCT 58.964 52.381 0.00 0.00 41.67 3.36
2071 4435 1.539280 GGCAGCGGAGAGTTCCTATTC 60.539 57.143 0.00 0.00 41.67 1.75
2137 6704 8.340443 GTGTGATACCCCGAATTTTTAGATTAC 58.660 37.037 0.00 0.00 0.00 1.89
2138 6705 7.499895 GGTGTGATACCCCGAATTTTTAGATTA 59.500 37.037 0.00 0.00 44.15 1.75
2170 6743 7.393515 GGAACTTTACACAGGAATAGAATGGTT 59.606 37.037 0.00 0.00 0.00 3.67
2180 6753 3.823281 TCACGGAACTTTACACAGGAA 57.177 42.857 0.00 0.00 0.00 3.36
2182 6755 3.724374 TCTTCACGGAACTTTACACAGG 58.276 45.455 0.00 0.00 0.00 4.00
2189 6762 5.048713 GGATGTCATTTCTTCACGGAACTTT 60.049 40.000 0.00 0.00 0.00 2.66
2195 6768 5.118990 ACTATGGATGTCATTTCTTCACGG 58.881 41.667 0.00 0.00 37.30 4.94
2216 6789 6.942532 TTTGTCATTTTTGCTGAGAGTACT 57.057 33.333 0.00 0.00 0.00 2.73
2314 6890 3.742369 ACGAAGTTCCGCGAAGAAATTAA 59.258 39.130 8.23 0.00 37.78 1.40
2325 6901 1.992170 ACTCATGTACGAAGTTCCGC 58.008 50.000 0.00 0.00 37.78 5.54
2328 6904 7.253354 CGTTCATTCTACTCATGTACGAAGTTC 60.253 40.741 6.29 0.00 43.95 3.01
2339 6915 3.769844 ACCTGGTCGTTCATTCTACTCAT 59.230 43.478 0.00 0.00 0.00 2.90
2433 7437 2.411904 GGAAATGCATAGGAGCTCTCG 58.588 52.381 14.64 0.80 34.99 4.04
2452 7456 9.268268 TGACTATAAAGTAATAAATGAAGGCGG 57.732 33.333 0.00 0.00 35.56 6.13
2574 7592 9.875691 GGAGTAACATAGATCATAACATGCATA 57.124 33.333 0.00 0.00 0.00 3.14
2654 9432 5.413833 ACTCGGATTTGTAGTCTAACTTCGA 59.586 40.000 0.00 0.00 0.00 3.71
2661 9439 9.507280 CGTTTTTATACTCGGATTTGTAGTCTA 57.493 33.333 0.00 0.00 0.00 2.59
2677 9455 6.193959 GTGATGCATCCGTTTCGTTTTTATAC 59.806 38.462 23.67 5.65 0.00 1.47
2683 9461 2.151202 AGTGATGCATCCGTTTCGTTT 58.849 42.857 23.67 0.00 0.00 3.60
2688 9466 1.086696 CCGAAGTGATGCATCCGTTT 58.913 50.000 23.67 14.50 0.00 3.60
2695 9473 2.083774 GAATGAACCCGAAGTGATGCA 58.916 47.619 0.00 0.00 0.00 3.96
2697 9475 1.665679 CCGAATGAACCCGAAGTGATG 59.334 52.381 0.00 0.00 0.00 3.07
2709 9487 6.902771 TTTAATTCCTCCAAACCGAATGAA 57.097 33.333 0.00 0.00 0.00 2.57
2753 9531 8.803235 GGTGAGGATTAAAACCTAAAAACTGAT 58.197 33.333 4.84 0.00 37.93 2.90
2754 9532 8.002459 AGGTGAGGATTAAAACCTAAAAACTGA 58.998 33.333 4.84 0.00 41.28 3.41
2755 9533 8.178313 AGGTGAGGATTAAAACCTAAAAACTG 57.822 34.615 4.84 0.00 41.28 3.16
2756 9534 8.777578 AAGGTGAGGATTAAAACCTAAAAACT 57.222 30.769 4.84 0.98 42.25 2.66
2757 9535 7.806487 CGAAGGTGAGGATTAAAACCTAAAAAC 59.194 37.037 4.84 2.92 42.25 2.43
2758 9536 7.522562 GCGAAGGTGAGGATTAAAACCTAAAAA 60.523 37.037 4.84 0.00 42.25 1.94
2759 9537 6.072342 GCGAAGGTGAGGATTAAAACCTAAAA 60.072 38.462 4.84 0.00 42.25 1.52
2760 9538 5.413523 GCGAAGGTGAGGATTAAAACCTAAA 59.586 40.000 4.84 0.00 42.25 1.85
2761 9539 4.939439 GCGAAGGTGAGGATTAAAACCTAA 59.061 41.667 4.84 0.00 42.25 2.69
2762 9540 4.224370 AGCGAAGGTGAGGATTAAAACCTA 59.776 41.667 4.84 0.00 42.25 3.08
2763 9541 3.009143 AGCGAAGGTGAGGATTAAAACCT 59.991 43.478 4.56 4.56 45.01 3.50
2764 9542 3.344515 AGCGAAGGTGAGGATTAAAACC 58.655 45.455 0.00 0.00 36.17 3.27
2765 9543 4.142665 GGAAGCGAAGGTGAGGATTAAAAC 60.143 45.833 0.00 0.00 39.47 2.43
2766 9544 4.007659 GGAAGCGAAGGTGAGGATTAAAA 58.992 43.478 0.00 0.00 39.47 1.52
2767 9545 3.606687 GGAAGCGAAGGTGAGGATTAAA 58.393 45.455 0.00 0.00 39.47 1.52
2768 9546 2.418197 CGGAAGCGAAGGTGAGGATTAA 60.418 50.000 0.00 0.00 39.47 1.40
2769 9547 1.136305 CGGAAGCGAAGGTGAGGATTA 59.864 52.381 0.00 0.00 39.47 1.75
2770 9548 0.108138 CGGAAGCGAAGGTGAGGATT 60.108 55.000 0.00 0.00 39.47 3.01
2771 9549 1.258445 ACGGAAGCGAAGGTGAGGAT 61.258 55.000 0.00 0.00 39.47 3.24
2772 9550 1.874345 GACGGAAGCGAAGGTGAGGA 61.874 60.000 0.00 0.00 39.47 3.71
2773 9551 1.446272 GACGGAAGCGAAGGTGAGG 60.446 63.158 0.00 0.00 39.47 3.86
2774 9552 1.801913 CGACGGAAGCGAAGGTGAG 60.802 63.158 0.00 0.00 39.47 3.51
2775 9553 2.257371 CGACGGAAGCGAAGGTGA 59.743 61.111 0.00 0.00 39.47 4.02
2776 9554 2.049433 ACGACGGAAGCGAAGGTG 60.049 61.111 0.00 0.00 39.47 4.00
2777 9555 2.257676 GACGACGGAAGCGAAGGT 59.742 61.111 0.00 0.00 44.60 3.50
2778 9556 2.087009 GTGACGACGGAAGCGAAGG 61.087 63.158 0.00 0.00 35.27 3.46
2779 9557 2.087009 GGTGACGACGGAAGCGAAG 61.087 63.158 0.00 0.00 35.27 3.79
2780 9558 2.049802 GGTGACGACGGAAGCGAA 60.050 61.111 0.00 0.00 35.27 4.70
2810 9588 2.658707 GACGCGTGAGGAAGCACAC 61.659 63.158 20.70 0.00 38.69 3.82
2811 9589 2.355837 GACGCGTGAGGAAGCACA 60.356 61.111 20.70 0.00 38.69 4.57
2812 9590 2.355837 TGACGCGTGAGGAAGCAC 60.356 61.111 20.70 0.00 35.46 4.40
2813 9591 2.355837 GTGACGCGTGAGGAAGCA 60.356 61.111 20.70 2.69 0.00 3.91
2814 9592 3.112709 GGTGACGCGTGAGGAAGC 61.113 66.667 20.70 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.