Multiple sequence alignment - TraesCS6D01G377200

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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 TraesCS6D01G377200 chr6D 100.000 7374 0 0 1 7374 459835563 459842936 0.000000e+00 13618.0
1 TraesCS6D01G377200 chr6D 89.062 1152 116 7 5361 6507 459924514 459925660 0.000000e+00 1421.0
2 TraesCS6D01G377200 chr6D 83.650 1107 126 30 2342 3440 459921506 459922565 0.000000e+00 990.0
3 TraesCS6D01G377200 chr6D 86.521 549 52 12 4336 4877 459923572 459924105 1.070000e-162 584.0
4 TraesCS6D01G377200 chr6D 89.577 355 35 2 4976 5329 459924168 459924521 4.060000e-122 449.0
5 TraesCS6D01G377200 chr6D 88.961 308 28 3 3955 4259 459923272 459923576 6.980000e-100 375.0
6 TraesCS6D01G377200 chr6D 82.249 338 40 12 6182 6516 460281549 460281229 2.620000e-69 274.0
7 TraesCS6D01G377200 chr6D 83.539 243 25 9 3681 3912 459923040 459923278 5.800000e-51 213.0
8 TraesCS6D01G377200 chr6A 93.049 6100 270 66 1312 7336 605559971 605565991 0.000000e+00 8774.0
9 TraesCS6D01G377200 chr6A 88.735 1154 115 9 5361 6507 605858741 605859886 0.000000e+00 1397.0
10 TraesCS6D01G377200 chr6A 82.034 1308 78 63 1 1216 605558651 605559893 0.000000e+00 968.0
11 TraesCS6D01G377200 chr6A 82.652 1101 144 27 2342 3441 605850504 605851558 0.000000e+00 931.0
12 TraesCS6D01G377200 chr6A 86.384 448 46 7 4336 4782 605852630 605853063 6.690000e-130 475.0
13 TraesCS6D01G377200 chr6A 89.720 321 31 2 5010 5329 605858429 605858748 6.890000e-110 409.0
14 TraesCS6D01G377200 chr6A 100.000 28 0 0 6734 6761 187907194 187907167 1.300000e-02 52.8
15 TraesCS6D01G377200 chr6B 94.357 5263 219 37 2156 7374 699201417 699206645 0.000000e+00 8002.0
16 TraesCS6D01G377200 chr6B 88.238 2236 113 56 1 2167 699199215 699201369 0.000000e+00 2534.0
17 TraesCS6D01G377200 chr6B 89.704 913 85 4 5385 6294 699606765 699607671 0.000000e+00 1157.0
18 TraesCS6D01G377200 chr6B 83.679 1109 135 21 2342 3441 699538741 699539812 0.000000e+00 1003.0
19 TraesCS6D01G377200 chr6B 84.915 769 78 18 5361 6128 699542110 699542841 0.000000e+00 743.0
20 TraesCS6D01G377200 chr6B 86.157 549 55 11 4336 4877 699605672 699606206 2.310000e-159 573.0
21 TraesCS6D01G377200 chr6B 85.428 549 58 12 4336 4877 699540871 699541404 1.080000e-152 551.0
22 TraesCS6D01G377200 chr6B 89.118 340 34 3 4992 5329 699541779 699542117 3.180000e-113 420.0
23 TraesCS6D01G377200 chr6B 89.068 311 27 4 3955 4262 699605373 699605679 5.400000e-101 379.0
24 TraesCS6D01G377200 chr6B 86.446 332 30 7 6291 6618 699609933 699610253 4.230000e-92 350.0
25 TraesCS6D01G377200 chr6B 88.636 264 15 12 93 342 714721765 714721503 2.580000e-79 307.0
26 TraesCS6D01G377200 chr6B 88.372 258 7 8 328 584 714721476 714721241 9.360000e-74 289.0
27 TraesCS6D01G377200 chr6B 87.113 194 24 1 4992 5185 699606571 699606763 1.250000e-52 219.0
28 TraesCS6D01G377200 chr6B 83.539 243 25 7 3681 3912 699540339 699540577 5.800000e-51 213.0
29 TraesCS6D01G377200 chr6B 91.367 139 7 3 6788 6924 699611175 699611310 1.260000e-42 185.0
30 TraesCS6D01G377200 chr6B 98.649 74 1 0 14 87 714721979 714721906 1.670000e-26 132.0
31 TraesCS6D01G377200 chrUn 81.333 375 41 18 1357 1727 305871860 305872209 2.030000e-70 278.0
32 TraesCS6D01G377200 chr3B 81.333 375 41 18 1357 1727 42064932 42065281 2.030000e-70 278.0
33 TraesCS6D01G377200 chr3B 81.333 375 41 15 1357 1727 42091326 42091675 2.030000e-70 278.0
34 TraesCS6D01G377200 chr3B 100.000 28 0 0 6782 6809 486699108 486699081 1.300000e-02 52.8
35 TraesCS6D01G377200 chr5B 78.325 406 73 10 1765 2162 564463061 564463459 1.590000e-61 248.0
36 TraesCS6D01G377200 chr7D 89.394 66 3 4 6762 6825 136410363 136410300 6.130000e-11 80.5
37 TraesCS6D01G377200 chr4A 94.872 39 1 1 6735 6773 101753425 101753388 7.990000e-05 60.2
38 TraesCS6D01G377200 chr4A 100.000 31 0 0 6735 6765 35352454 35352424 2.870000e-04 58.4
39 TraesCS6D01G377200 chr5D 100.000 29 0 0 6735 6763 76981062 76981034 4.000000e-03 54.7
40 TraesCS6D01G377200 chr5D 100.000 29 0 0 6735 6763 445204809 445204837 4.000000e-03 54.7
41 TraesCS6D01G377200 chr2A 100.000 28 0 0 6737 6764 668239041 668239068 1.300000e-02 52.8
42 TraesCS6D01G377200 chr2A 100.000 28 0 0 6735 6762 767784991 767784964 1.300000e-02 52.8


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 TraesCS6D01G377200 chr6D 459835563 459842936 7373 False 13618.000000 13618 100.000000 1 7374 1 chr6D.!!$F1 7373
1 TraesCS6D01G377200 chr6D 459921506 459925660 4154 False 672.000000 1421 86.885000 2342 6507 6 chr6D.!!$F2 4165
2 TraesCS6D01G377200 chr6A 605558651 605565991 7340 False 4871.000000 8774 87.541500 1 7336 2 chr6A.!!$F1 7335
3 TraesCS6D01G377200 chr6A 605858429 605859886 1457 False 903.000000 1397 89.227500 5010 6507 2 chr6A.!!$F3 1497
4 TraesCS6D01G377200 chr6A 605850504 605853063 2559 False 703.000000 931 84.518000 2342 4782 2 chr6A.!!$F2 2440
5 TraesCS6D01G377200 chr6B 699199215 699206645 7430 False 5268.000000 8002 91.297500 1 7374 2 chr6B.!!$F1 7373
6 TraesCS6D01G377200 chr6B 699538741 699542841 4100 False 586.000000 1003 85.335800 2342 6128 5 chr6B.!!$F2 3786
7 TraesCS6D01G377200 chr6B 699605373 699611310 5937 False 477.166667 1157 88.309167 3955 6924 6 chr6B.!!$F3 2969
8 TraesCS6D01G377200 chr6B 714721241 714721979 738 True 242.666667 307 91.885667 14 584 3 chr6B.!!$R1 570

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
829 1064 0.979665 CCCCTCAGTCTCTGCAAAGA 59.020 55.000 0.0 0.0 0.00 2.52 F
1479 1784 0.250338 GCGGTGGGTTCTCTGTTTCT 60.250 55.000 0.0 0.0 0.00 2.52 F
2024 2341 0.963225 TCCTGTTCGTCGTCATGGAA 59.037 50.000 0.0 0.0 0.00 3.53 F
2577 2967 2.005451 CCTCTACACAGCAACAGCATC 58.995 52.381 0.0 0.0 0.00 3.91 F
3620 4471 0.761323 TTGAGTCCTCACGGGGTCAA 60.761 55.000 0.0 0.0 39.66 3.18 F
4615 5482 8.477419 AAAATTCAAAGGTTCCTGATCAAGTA 57.523 30.769 0.0 0.0 0.00 2.24 F
5732 6918 0.811281 CCAATCGGACCTTTCCTTGC 59.189 55.000 0.0 0.0 40.23 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2412 0.179045 CACCATCTTAGAAGGCGGGG 60.179 60.000 3.12 0.00 0.00 5.73 R
2978 3389 0.700564 AATTTCCCTCTGCTGCCTCA 59.299 50.000 0.00 0.00 0.00 3.86 R
3549 4400 0.179150 CGTCCACTGAGCTAGCACTC 60.179 60.000 18.83 7.30 37.19 3.51 R
4222 5088 1.094785 GTGGAAACCGTATGCTGCAT 58.905 50.000 20.18 20.18 0.00 3.96 R
4703 5570 2.808543 GCCTTTGAACAGACGAGTCATT 59.191 45.455 5.99 0.00 0.00 2.57 R
5984 7173 2.035632 TGGTTGTTGGTTGATGGGAAC 58.964 47.619 0.00 0.00 0.00 3.62 R
7241 11554 1.804151 TCCGCACACAACAAGAATAGC 59.196 47.619 0.00 0.00 0.00 2.97 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
156 292 4.183865 CGGCACTTGATGATCTCAGTTAA 58.816 43.478 0.00 0.00 34.68 2.01
189 332 1.317613 TTCTTGGACTGCGCATTGTT 58.682 45.000 12.24 0.00 0.00 2.83
203 346 4.789481 GCGCATTGTTGAAAGTCTGAAAGA 60.789 41.667 0.30 0.00 43.69 2.52
292 435 2.795175 TCGTTCTCTTCAGTGGTGTC 57.205 50.000 0.00 0.00 0.00 3.67
410 602 3.427098 GCGGTTTATTTGCTTGTACTCCC 60.427 47.826 0.00 0.00 0.00 4.30
415 607 1.053424 TTTGCTTGTACTCCCTCCGT 58.947 50.000 0.00 0.00 0.00 4.69
418 610 1.418637 TGCTTGTACTCCCTCCGTTTT 59.581 47.619 0.00 0.00 0.00 2.43
439 631 2.995258 TGTAATTAAGCGACGTGGTTCC 59.005 45.455 0.00 0.00 39.46 3.62
476 673 9.453325 TGAACTAAAAACCACGTCATTTATTTC 57.547 29.630 0.00 0.89 32.26 2.17
478 675 7.942990 ACTAAAAACCACGTCATTTATTTCCA 58.057 30.769 0.00 0.00 0.00 3.53
481 678 7.471657 AAAACCACGTCATTTATTTCCAAAC 57.528 32.000 0.00 0.00 0.00 2.93
482 679 4.789784 ACCACGTCATTTATTTCCAAACG 58.210 39.130 0.00 0.00 35.00 3.60
483 680 4.162812 CCACGTCATTTATTTCCAAACGG 58.837 43.478 0.00 0.00 33.26 4.44
484 681 4.083217 CCACGTCATTTATTTCCAAACGGA 60.083 41.667 0.00 0.00 33.26 4.69
485 682 5.086058 CACGTCATTTATTTCCAAACGGAG 58.914 41.667 0.00 0.00 32.88 4.63
486 683 4.155280 ACGTCATTTATTTCCAAACGGAGG 59.845 41.667 0.00 0.00 32.88 4.30
487 684 4.438200 CGTCATTTATTTCCAAACGGAGGG 60.438 45.833 0.00 0.00 32.88 4.30
488 685 4.703093 GTCATTTATTTCCAAACGGAGGGA 59.297 41.667 0.00 0.00 32.88 4.20
489 686 5.359860 GTCATTTATTTCCAAACGGAGGGAT 59.640 40.000 0.00 0.00 32.88 3.85
490 687 5.955355 TCATTTATTTCCAAACGGAGGGATT 59.045 36.000 0.00 0.00 32.88 3.01
491 688 6.439058 TCATTTATTTCCAAACGGAGGGATTT 59.561 34.615 0.00 0.00 32.88 2.17
492 689 5.907866 TTATTTCCAAACGGAGGGATTTC 57.092 39.130 0.00 0.00 32.88 2.17
493 690 2.209690 TTCCAAACGGAGGGATTTCC 57.790 50.000 0.00 0.00 32.88 3.13
494 691 1.068948 TCCAAACGGAGGGATTTCCA 58.931 50.000 0.00 0.00 37.05 3.53
495 692 1.425831 TCCAAACGGAGGGATTTCCAA 59.574 47.619 0.00 0.00 37.05 3.53
496 693 2.158445 TCCAAACGGAGGGATTTCCAAA 60.158 45.455 0.00 0.00 37.05 3.28
537 734 7.568199 AAGTTAAAGAAGAAAGCTGCAAGTA 57.432 32.000 1.02 0.00 35.30 2.24
540 737 7.499232 AGTTAAAGAAGAAAGCTGCAAGTAGAA 59.501 33.333 1.02 0.00 35.30 2.10
541 738 6.890979 AAAGAAGAAAGCTGCAAGTAGAAT 57.109 33.333 1.02 0.00 35.30 2.40
542 739 7.986085 AAAGAAGAAAGCTGCAAGTAGAATA 57.014 32.000 1.02 0.00 35.30 1.75
612 820 2.342354 CGCAAAAATCCGATTTGTCAGC 59.658 45.455 7.13 8.12 39.42 4.26
816 1051 1.492764 GTTCCCGAATCTACCCCTCA 58.507 55.000 0.00 0.00 0.00 3.86
817 1052 1.413077 GTTCCCGAATCTACCCCTCAG 59.587 57.143 0.00 0.00 0.00 3.35
824 1059 2.080654 ATCTACCCCTCAGTCTCTGC 57.919 55.000 0.00 0.00 0.00 4.26
829 1064 0.979665 CCCCTCAGTCTCTGCAAAGA 59.020 55.000 0.00 0.00 0.00 2.52
904 1139 1.081175 GCTGGAAAAAGTGGCGAGC 60.081 57.895 0.00 0.00 0.00 5.03
939 1177 3.535962 CAGCCGAGCTCTCCCCTC 61.536 72.222 12.85 0.00 36.40 4.30
940 1178 4.851214 AGCCGAGCTCTCCCCTCC 62.851 72.222 12.85 0.00 30.62 4.30
942 1180 4.150454 CCGAGCTCTCCCCTCCCT 62.150 72.222 12.85 0.00 0.00 4.20
1199 1479 2.123409 CACCCTGTTTGTTGGTGGG 58.877 57.895 0.00 0.00 44.64 4.61
1252 1550 0.918983 ATTTCGCTCCAGGGGAATCA 59.081 50.000 0.00 0.00 44.41 2.57
1265 1563 2.024414 GGGAATCAGTTTCGAATGGGG 58.976 52.381 0.00 0.00 34.98 4.96
1279 1577 3.359523 GGGGTTCGGTTCGTTGGC 61.360 66.667 0.00 0.00 0.00 4.52
1303 1601 2.974698 GGCGCCGATTCTGGATGG 60.975 66.667 12.58 0.00 0.00 3.51
1316 1614 1.493022 CTGGATGGGGTTTCGGGATTA 59.507 52.381 0.00 0.00 0.00 1.75
1352 1651 1.678970 GGGGTTCGCTGATGGCTTT 60.679 57.895 0.00 0.00 39.13 3.51
1448 1748 3.966218 CGTTTCAGTTCGATTTTGTCCAC 59.034 43.478 0.00 0.00 0.00 4.02
1452 1752 1.531149 AGTTCGATTTTGTCCACTGCG 59.469 47.619 0.00 0.00 0.00 5.18
1478 1783 0.534203 TGCGGTGGGTTCTCTGTTTC 60.534 55.000 0.00 0.00 0.00 2.78
1479 1784 0.250338 GCGGTGGGTTCTCTGTTTCT 60.250 55.000 0.00 0.00 0.00 2.52
1480 1785 1.512926 CGGTGGGTTCTCTGTTTCTG 58.487 55.000 0.00 0.00 0.00 3.02
1481 1786 1.202651 CGGTGGGTTCTCTGTTTCTGT 60.203 52.381 0.00 0.00 0.00 3.41
1482 1787 2.745152 CGGTGGGTTCTCTGTTTCTGTT 60.745 50.000 0.00 0.00 0.00 3.16
1483 1788 3.288092 GGTGGGTTCTCTGTTTCTGTTT 58.712 45.455 0.00 0.00 0.00 2.83
1531 1837 1.620589 ATGGATGGGGGAGTGCTGT 60.621 57.895 0.00 0.00 0.00 4.40
1585 1896 1.531602 GAATAGGTGGGCATGGGGC 60.532 63.158 0.00 0.00 43.74 5.80
1613 1924 5.249420 AGTTAGCATCTTCTCCTTCCAAAC 58.751 41.667 0.00 0.00 0.00 2.93
1623 1934 5.693769 TCTCCTTCCAAACGATATTCCTT 57.306 39.130 0.00 0.00 0.00 3.36
1687 2000 2.093306 TGATTGGTCTGCGACGAAAT 57.907 45.000 0.00 8.31 34.32 2.17
1797 2110 1.004560 CTCGAGCAGAGGTTTGGCA 60.005 57.895 0.00 0.00 43.20 4.92
1969 2282 3.125316 CGCTGATAAAGACCTGTTGAACC 59.875 47.826 0.00 0.00 0.00 3.62
1987 2300 5.793817 TGAACCGATATGATCATGTAAGGG 58.206 41.667 18.72 14.87 0.00 3.95
1992 2305 5.394663 CCGATATGATCATGTAAGGGACCTC 60.395 48.000 18.72 0.00 0.00 3.85
2021 2338 2.663602 CTCTTTCCTGTTCGTCGTCATG 59.336 50.000 0.00 0.00 0.00 3.07
2024 2341 0.963225 TCCTGTTCGTCGTCATGGAA 59.037 50.000 0.00 0.00 0.00 3.53
2027 2344 2.094258 CCTGTTCGTCGTCATGGAATTG 59.906 50.000 0.00 0.00 0.00 2.32
2039 2356 6.072008 TCGTCATGGAATTGTTGATGTTTGAT 60.072 34.615 0.00 0.00 0.00 2.57
2040 2357 6.034150 CGTCATGGAATTGTTGATGTTTGATG 59.966 38.462 0.00 0.00 0.00 3.07
2041 2358 6.869913 GTCATGGAATTGTTGATGTTTGATGT 59.130 34.615 0.00 0.00 0.00 3.06
2053 2370 9.760660 GTTGATGTTTGATGTTGTTATCTCTAC 57.239 33.333 0.00 0.00 0.00 2.59
2084 2408 2.029649 TGTTAGTTCTGCCGGTACTGAC 60.030 50.000 1.90 9.34 0.00 3.51
2088 2412 2.067013 GTTCTGCCGGTACTGACTTTC 58.933 52.381 1.90 0.00 0.00 2.62
2173 2557 4.623932 ACCGGTACAATATGATGCAGAT 57.376 40.909 4.49 0.00 0.00 2.90
2261 2645 3.670523 GCTTAGTAGTTGCTTTGCTTTGC 59.329 43.478 0.00 0.00 0.00 3.68
2265 2649 4.389374 AGTAGTTGCTTTGCTTTGCTAGA 58.611 39.130 0.00 0.00 0.00 2.43
2278 2662 5.859557 GCTTTGCTAGAAGCTTGTAGTAAC 58.140 41.667 26.49 16.20 46.55 2.50
2577 2967 2.005451 CCTCTACACAGCAACAGCATC 58.995 52.381 0.00 0.00 0.00 3.91
2660 3050 7.043125 GCAACAGAGAAAGAACAAAAGGAAATC 60.043 37.037 0.00 0.00 0.00 2.17
2896 3286 3.645212 TCTCATCAAGGCCCAGAAGATAG 59.355 47.826 0.00 0.00 0.00 2.08
2978 3389 8.987890 CGTGTTAAAAGGAAAATTGATTTGGAT 58.012 29.630 0.00 0.00 0.00 3.41
3299 3713 6.017400 TGAAGTTCAGATTGAATGGAAAGC 57.983 37.500 0.08 0.00 38.79 3.51
3339 3756 4.762289 ACCCAACTGTAATGATCTCCTC 57.238 45.455 0.00 0.00 0.00 3.71
3566 4417 3.363787 TGAGTGCTAGCTCAGTGGA 57.636 52.632 17.23 0.00 40.23 4.02
3620 4471 0.761323 TTGAGTCCTCACGGGGTCAA 60.761 55.000 0.00 0.00 39.66 3.18
4222 5088 9.787532 GTAGTTCATGCATGCTAAAATCTAAAA 57.212 29.630 22.25 3.43 0.00 1.52
4615 5482 8.477419 AAAATTCAAAGGTTCCTGATCAAGTA 57.523 30.769 0.00 0.00 0.00 2.24
4827 5695 5.189180 GTCAAGAATTTCTATGCCTCACCT 58.811 41.667 0.00 0.00 0.00 4.00
5419 6605 4.576463 GTTGGCACATATTCCTACAGAAGG 59.424 45.833 0.00 0.00 43.19 3.46
5732 6918 0.811281 CCAATCGGACCTTTCCTTGC 59.189 55.000 0.00 0.00 40.23 4.01
5867 7056 1.223211 GGCTTCCCTGGAGCTTCTC 59.777 63.158 7.26 0.00 0.00 2.87
6061 7250 0.400594 AGACCGGTAAAAGCTGGCTT 59.599 50.000 7.34 1.60 38.45 4.35
6072 7261 1.449778 GCTGGCTTAACCCGGAGAC 60.450 63.158 0.73 0.00 37.83 3.36
6289 7481 2.270434 TGGATCTAAACCAGAGGGCT 57.730 50.000 0.00 0.00 36.48 5.19
6432 9898 2.964464 TGTTAGTCCCTTCCGTTGTGTA 59.036 45.455 0.00 0.00 0.00 2.90
6559 10048 7.984617 TGATAGATTGATGGTCAATGAACGTAA 59.015 33.333 9.70 0.00 46.20 3.18
6716 10231 4.826556 AGTTTGCTAGAGAGTGGATTGAC 58.173 43.478 0.00 0.00 0.00 3.18
6782 11035 9.000486 AGTATTTTTCTAAGAGTACACCAAAGC 58.000 33.333 0.00 0.00 0.00 3.51
6938 11220 1.134551 GCAAACCACCAACACCAACAT 60.135 47.619 0.00 0.00 0.00 2.71
6952 11234 0.809385 CAACATCTGCTTGCCTCCAG 59.191 55.000 0.00 0.00 0.00 3.86
6955 11237 3.355957 ATCTGCTTGCCTCCAGCCC 62.356 63.158 0.00 0.00 42.71 5.19
6963 11245 4.351054 CCTCCAGCCCGCAACCTT 62.351 66.667 0.00 0.00 0.00 3.50
7000 11282 2.092212 AGATAGCCCCATTGGTGTTCTG 60.092 50.000 1.20 0.00 36.04 3.02
7011 11293 5.295292 CCATTGGTGTTCTGTGATGATCTAC 59.705 44.000 0.00 0.00 0.00 2.59
7014 11296 3.452627 GGTGTTCTGTGATGATCTACCCT 59.547 47.826 0.00 0.00 0.00 4.34
7028 11311 3.578978 TCTACCCTATTGAATACCCGCA 58.421 45.455 0.00 0.00 0.00 5.69
7118 11404 2.224793 CCGAAAGTTCCTCCTTTCCCTT 60.225 50.000 7.79 0.00 44.81 3.95
7256 11569 4.288626 TCCCCTTAGCTATTCTTGTTGTGT 59.711 41.667 0.00 0.00 0.00 3.72
7291 11604 5.411361 TGTCAAGAATGTTCCTATTTGTCGG 59.589 40.000 0.00 0.00 0.00 4.79
7355 11668 7.985184 AGATGCTTGATATGTCATTTTTGCATT 59.015 29.630 13.73 6.44 37.51 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 308 0.592637 TCAACAATGCGCAGTCCAAG 59.407 50.000 18.32 3.40 0.00 3.61
175 311 1.001378 ACTTTCAACAATGCGCAGTCC 60.001 47.619 18.32 0.00 0.00 3.85
176 312 2.031682 AGACTTTCAACAATGCGCAGTC 60.032 45.455 18.32 14.15 31.70 3.51
177 313 1.949525 AGACTTTCAACAATGCGCAGT 59.050 42.857 18.32 11.60 0.00 4.40
178 314 2.031769 TCAGACTTTCAACAATGCGCAG 60.032 45.455 18.32 5.51 0.00 5.18
189 332 5.296780 AGCGACATTTTCTTTCAGACTTTCA 59.703 36.000 0.00 0.00 0.00 2.69
203 346 5.200368 ACTTGAATCCAAAGCGACATTTT 57.800 34.783 0.00 0.00 0.00 1.82
292 435 5.163854 GCAGCATATACCTAGGTTAAATGCG 60.164 44.000 30.31 26.84 39.27 4.73
410 602 4.143263 ACGTCGCTTAATTACAAAACGGAG 60.143 41.667 11.83 0.00 33.48 4.63
415 607 5.421212 AACCACGTCGCTTAATTACAAAA 57.579 34.783 0.00 0.00 0.00 2.44
418 610 2.995258 GGAACCACGTCGCTTAATTACA 59.005 45.455 0.00 0.00 0.00 2.41
476 673 1.917872 TTGGAAATCCCTCCGTTTGG 58.082 50.000 0.00 0.00 38.44 3.28
478 675 1.883926 CGTTTGGAAATCCCTCCGTTT 59.116 47.619 0.00 0.00 38.44 3.60
481 678 0.035820 TCCGTTTGGAAATCCCTCCG 60.036 55.000 0.00 0.00 42.85 4.63
482 679 1.682087 CCTCCGTTTGGAAATCCCTCC 60.682 57.143 0.00 0.00 45.87 4.30
483 680 1.682087 CCCTCCGTTTGGAAATCCCTC 60.682 57.143 0.00 0.00 45.87 4.30
484 681 0.331616 CCCTCCGTTTGGAAATCCCT 59.668 55.000 0.00 0.00 45.87 4.20
485 682 0.330267 TCCCTCCGTTTGGAAATCCC 59.670 55.000 0.00 0.00 45.87 3.85
486 683 1.004394 ACTCCCTCCGTTTGGAAATCC 59.996 52.381 0.00 0.00 45.87 3.01
487 684 2.491675 ACTCCCTCCGTTTGGAAATC 57.508 50.000 0.00 0.00 45.87 2.17
488 685 2.355818 GCTACTCCCTCCGTTTGGAAAT 60.356 50.000 0.00 0.00 45.87 2.17
489 686 1.002773 GCTACTCCCTCCGTTTGGAAA 59.997 52.381 0.00 0.00 45.87 3.13
490 687 0.611714 GCTACTCCCTCCGTTTGGAA 59.388 55.000 0.00 0.00 45.87 3.53
491 688 0.543410 TGCTACTCCCTCCGTTTGGA 60.543 55.000 0.00 0.00 43.88 3.53
492 689 0.391263 GTGCTACTCCCTCCGTTTGG 60.391 60.000 0.00 0.00 0.00 3.28
493 690 0.320374 TGTGCTACTCCCTCCGTTTG 59.680 55.000 0.00 0.00 0.00 2.93
494 691 1.053424 TTGTGCTACTCCCTCCGTTT 58.947 50.000 0.00 0.00 0.00 3.60
495 692 1.002087 CTTTGTGCTACTCCCTCCGTT 59.998 52.381 0.00 0.00 0.00 4.44
496 693 0.608640 CTTTGTGCTACTCCCTCCGT 59.391 55.000 0.00 0.00 0.00 4.69
537 734 5.170748 CGGTGGGTTTTTACGTAGTATTCT 58.829 41.667 0.00 0.00 45.21 2.40
540 737 3.860641 CCGGTGGGTTTTTACGTAGTAT 58.139 45.455 0.00 0.00 45.21 2.12
541 738 3.311486 CCGGTGGGTTTTTACGTAGTA 57.689 47.619 0.00 0.00 45.11 1.82
569 773 6.647067 TGCGTGGAAAGGTTAAATAAAATTGG 59.353 34.615 0.00 0.00 0.00 3.16
612 820 0.764890 TGTGGGTCTCAGGGTCAAAG 59.235 55.000 0.00 0.00 0.00 2.77
816 1051 0.036022 GCAGGGTCTTTGCAGAGACT 59.964 55.000 29.95 13.94 44.32 3.24
817 1052 0.957888 GGCAGGGTCTTTGCAGAGAC 60.958 60.000 25.30 25.30 43.28 3.36
900 1135 1.564622 CCGCCGTATTCATTGCTCG 59.435 57.895 0.00 0.00 0.00 5.03
904 1139 2.631428 CGCCCGCCGTATTCATTG 59.369 61.111 0.00 0.00 0.00 2.82
933 1171 4.772231 CGGTTCCGAGGGAGGGGA 62.772 72.222 5.19 0.00 31.21 4.81
937 1175 0.535335 TCAATTCGGTTCCGAGGGAG 59.465 55.000 13.56 6.43 39.68 4.30
938 1176 0.978151 TTCAATTCGGTTCCGAGGGA 59.022 50.000 13.56 9.94 39.68 4.20
939 1177 2.038387 ATTCAATTCGGTTCCGAGGG 57.962 50.000 13.56 7.98 39.68 4.30
940 1178 2.097466 CCAATTCAATTCGGTTCCGAGG 59.903 50.000 13.56 5.89 39.68 4.63
941 1179 3.006940 TCCAATTCAATTCGGTTCCGAG 58.993 45.455 13.56 3.65 39.68 4.63
942 1180 3.006940 CTCCAATTCAATTCGGTTCCGA 58.993 45.455 10.00 10.00 36.63 4.55
984 1222 1.078708 CCCCTCGCTCGCCTTTTTA 60.079 57.895 0.00 0.00 0.00 1.52
1160 1434 3.741476 GAAACCAGCAGGCGCCAG 61.741 66.667 31.54 23.68 39.83 4.85
1199 1479 2.037367 GCCCCTCCCTTTTCCACC 59.963 66.667 0.00 0.00 0.00 4.61
1265 1563 1.785951 GCTAGCCAACGAACCGAAC 59.214 57.895 2.29 0.00 0.00 3.95
1303 1601 1.093496 CGCCAGTAATCCCGAAACCC 61.093 60.000 0.00 0.00 0.00 4.11
1352 1651 0.934496 CAGAAACAACTCGAACGCCA 59.066 50.000 0.00 0.00 0.00 5.69
1448 1748 1.591594 CCACCGCATAGTACCGCAG 60.592 63.158 0.00 0.00 0.00 5.18
1452 1752 0.828677 AGAACCCACCGCATAGTACC 59.171 55.000 0.00 0.00 0.00 3.34
1478 1783 1.557832 TCGATTCCCCCACCTAAACAG 59.442 52.381 0.00 0.00 0.00 3.16
1479 1784 1.659022 TCGATTCCCCCACCTAAACA 58.341 50.000 0.00 0.00 0.00 2.83
1480 1785 3.211865 GAATCGATTCCCCCACCTAAAC 58.788 50.000 24.74 0.00 0.00 2.01
1481 1786 3.570912 GAATCGATTCCCCCACCTAAA 57.429 47.619 24.74 0.00 0.00 1.85
1506 1811 1.715931 ACTCCCCCATCCATCAAACAA 59.284 47.619 0.00 0.00 0.00 2.83
1531 1837 7.446769 TCCATCAGTAACAAGTAAAGCTAACA 58.553 34.615 0.00 0.00 0.00 2.41
1585 1896 6.547880 TGGAAGGAGAAGATGCTAACTACTAG 59.452 42.308 0.00 0.00 0.00 2.57
1623 1934 3.328931 GCCTCAATCCATCCTCTCCATAA 59.671 47.826 0.00 0.00 0.00 1.90
1687 2000 1.916874 TGGTGGAAATGTAATCCGGGA 59.083 47.619 0.00 0.00 39.98 5.14
1745 2058 9.017669 GCATAGCAGAAGAAAATGTTATTTCAG 57.982 33.333 2.99 0.00 40.89 3.02
1797 2110 2.202623 GCGCTCATCTCGAACCGT 60.203 61.111 0.00 0.00 0.00 4.83
1892 2205 0.391263 CCCACCGCTAGAAACAGGAC 60.391 60.000 0.00 0.00 0.00 3.85
1969 2282 5.655488 GAGGTCCCTTACATGATCATATCG 58.345 45.833 8.15 0.00 0.00 2.92
1987 2300 3.086282 AGGAAAGAGAGAACTCGAGGTC 58.914 50.000 23.21 23.21 46.64 3.85
1992 2305 3.238441 CGAACAGGAAAGAGAGAACTCG 58.762 50.000 0.00 0.00 46.64 4.18
2021 2338 7.481275 AACAACATCAAACATCAACAATTCC 57.519 32.000 0.00 0.00 0.00 3.01
2024 2341 9.630098 GAGATAACAACATCAAACATCAACAAT 57.370 29.630 0.00 0.00 0.00 2.71
2027 2344 9.760660 GTAGAGATAACAACATCAAACATCAAC 57.239 33.333 0.00 0.00 0.00 3.18
2039 2356 6.530019 TCAGATGCAGTAGAGATAACAACA 57.470 37.500 0.00 0.00 0.00 3.33
2040 2357 6.983307 ACATCAGATGCAGTAGAGATAACAAC 59.017 38.462 10.59 0.00 0.00 3.32
2041 2358 7.117285 ACATCAGATGCAGTAGAGATAACAA 57.883 36.000 10.59 0.00 0.00 2.83
2053 2370 3.311871 GGCAGAACTAACATCAGATGCAG 59.688 47.826 10.59 10.23 34.17 4.41
2084 2408 2.565841 CATCTTAGAAGGCGGGGAAAG 58.434 52.381 0.00 0.00 0.00 2.62
2088 2412 0.179045 CACCATCTTAGAAGGCGGGG 60.179 60.000 3.12 0.00 0.00 5.73
2173 2557 4.855340 CCAAACCAAAAGGAGGAGCTATA 58.145 43.478 0.00 0.00 0.00 1.31
2222 2606 6.927294 ACTAAGCATTTATCTTACAGGCAC 57.073 37.500 0.00 0.00 0.00 5.01
2225 2609 8.552034 GCAACTACTAAGCATTTATCTTACAGG 58.448 37.037 0.00 0.00 0.00 4.00
2261 2645 7.542824 GGTTCAGAAGTTACTACAAGCTTCTAG 59.457 40.741 7.17 7.17 43.81 2.43
2265 2649 5.925509 TGGTTCAGAAGTTACTACAAGCTT 58.074 37.500 0.00 0.00 0.00 3.74
2302 2686 1.493022 CCACCCCCTTCGATTTCCATA 59.507 52.381 0.00 0.00 0.00 2.74
2486 2873 9.209175 GAAGGTAGACAATCAACATATGGATAC 57.791 37.037 7.80 0.00 0.00 2.24
2660 3050 0.737019 GCAATGGTTCGCACAATGGG 60.737 55.000 0.00 0.00 0.00 4.00
2896 3286 8.467598 TGTTCTTACATTGACTAGGTCTGATAC 58.532 37.037 0.00 0.00 33.15 2.24
2978 3389 0.700564 AATTTCCCTCTGCTGCCTCA 59.299 50.000 0.00 0.00 0.00 3.86
3415 3832 5.537300 ATCAGCATAAACGAGGTACAGAT 57.463 39.130 0.00 0.00 0.00 2.90
3549 4400 0.179150 CGTCCACTGAGCTAGCACTC 60.179 60.000 18.83 7.30 37.19 3.51
3566 4417 2.702592 TTCAACAACCTGAACTCCGT 57.297 45.000 0.00 0.00 30.31 4.69
4222 5088 1.094785 GTGGAAACCGTATGCTGCAT 58.905 50.000 20.18 20.18 0.00 3.96
4615 5482 3.296854 GGTTTTGTTTTCCTCCTGGACT 58.703 45.455 0.00 0.00 43.06 3.85
4635 5502 7.387673 GGTTGAACTTCCCAAAATTAAATCTGG 59.612 37.037 0.00 0.00 0.00 3.86
4703 5570 2.808543 GCCTTTGAACAGACGAGTCATT 59.191 45.455 5.99 0.00 0.00 2.57
4827 5695 7.624549 ACTGACTGAAAATAATCCTCTAAGCA 58.375 34.615 0.00 0.00 0.00 3.91
5164 6350 9.315363 TCATAAAAATTTGGGTACAAGGTATGT 57.685 29.630 0.00 0.00 46.36 2.29
5335 6521 8.141909 CCTCCATGAAATAACTTATCGTGACTA 58.858 37.037 0.00 0.00 32.98 2.59
5732 6918 3.767230 CTGAAGGTGCACGTCGCG 61.767 66.667 13.21 0.00 46.97 5.87
5984 7173 2.035632 TGGTTGTTGGTTGATGGGAAC 58.964 47.619 0.00 0.00 0.00 3.62
6061 7250 2.334946 CGACCACGTCTCCGGGTTA 61.335 63.158 0.00 0.00 37.63 2.85
6531 10020 7.500227 ACGTTCATTGACCATCAATCTATCAAT 59.500 33.333 1.02 0.00 43.03 2.57
6533 10022 6.348498 ACGTTCATTGACCATCAATCTATCA 58.652 36.000 1.02 0.00 43.03 2.15
6534 10023 6.851222 ACGTTCATTGACCATCAATCTATC 57.149 37.500 1.02 0.00 43.03 2.08
6535 10024 8.908786 ATTACGTTCATTGACCATCAATCTAT 57.091 30.769 0.00 0.00 43.03 1.98
6536 10025 9.825109 TTATTACGTTCATTGACCATCAATCTA 57.175 29.630 0.00 0.00 43.03 1.98
6537 10026 8.731275 TTATTACGTTCATTGACCATCAATCT 57.269 30.769 0.00 0.00 43.03 2.40
6559 10048 8.449423 TTGGGGATGTAGATAGCTTGTATTAT 57.551 34.615 0.00 0.00 0.00 1.28
6716 10231 8.788325 ATATAAGACACACATCCATGATCATG 57.212 34.615 25.97 25.97 38.51 3.07
6821 11102 4.820897 TGTTCGCATTTGTGATAGACTCT 58.179 39.130 0.00 0.00 34.19 3.24
6938 11220 4.039092 GGGCTGGAGGCAAGCAGA 62.039 66.667 8.75 0.00 42.69 4.26
6963 11245 5.453339 GGGCTATCTACTCATGTGTTAAGCA 60.453 44.000 5.63 0.00 0.00 3.91
7000 11282 7.331791 GGGTATTCAATAGGGTAGATCATCAC 58.668 42.308 0.00 0.00 0.00 3.06
7011 11293 2.631160 TGTGCGGGTATTCAATAGGG 57.369 50.000 0.00 0.00 0.00 3.53
7014 11296 3.980646 GCAATGTGCGGGTATTCAATA 57.019 42.857 0.00 0.00 31.71 1.90
7028 11311 3.574614 GTCCGTTAAAGCAATGCAATGT 58.425 40.909 8.35 0.00 0.00 2.71
7199 11511 2.285368 TCAACCCCCTCGATGGCT 60.285 61.111 0.39 0.00 0.00 4.75
7241 11554 1.804151 TCCGCACACAACAAGAATAGC 59.196 47.619 0.00 0.00 0.00 2.97
7256 11569 2.032528 CTTGACAGGCCTTCCGCA 59.967 61.111 0.00 0.00 40.31 5.69
7291 11604 3.434310 CCAGATAAAGCCCCTTCCTCTTC 60.434 52.174 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.