Multiple sequence alignment - TraesCS3A01G119100

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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 TraesCS3A01G119100 chr3A 100.000 4976 0 0 991 5966 91030170 91025195 0.000000e+00 9190
1 TraesCS3A01G119100 chr3A 100.000 433 0 0 1 433 91031160 91030728 0.000000e+00 800
2 TraesCS3A01G119100 chr3A 78.388 273 42 14 3843 4106 697389358 697389622 1.720000e-35 161
3 TraesCS3A01G119100 chr3A 86.408 103 14 0 4109 4211 569232141 569232243 4.890000e-21 113
4 TraesCS3A01G119100 chr3B 91.437 3632 208 49 991 4583 123478516 123474949 0.000000e+00 4889
5 TraesCS3A01G119100 chr3B 90.792 1325 54 29 4651 5944 123474952 123473665 0.000000e+00 1709
6 TraesCS3A01G119100 chr3B 90.152 396 19 8 56 433 123478978 123478585 1.150000e-136 497
7 TraesCS3A01G119100 chr3D 95.038 2116 66 13 2461 4543 76937294 76935185 0.000000e+00 3290
8 TraesCS3A01G119100 chr3D 93.149 1445 43 19 4541 5966 76935101 76933694 0.000000e+00 2069
9 TraesCS3A01G119100 chr3D 90.852 1421 87 24 991 2381 76938833 76937426 0.000000e+00 1864
10 TraesCS3A01G119100 chr3D 91.205 307 12 3 60 351 76939417 76939111 2.590000e-108 403
11 TraesCS3A01G119100 chr3D 76.277 274 40 19 3843 4106 561454371 561454629 8.120000e-24 122
12 TraesCS3A01G119100 chr3D 85.841 113 15 1 4105 4217 57504476 57504587 1.050000e-22 119
13 TraesCS3A01G119100 chr7D 85.862 580 71 8 2508 3082 369910841 369911414 1.840000e-169 606
14 TraesCS3A01G119100 chr7D 86.335 483 58 7 2581 3062 65531121 65531596 2.460000e-143 520
15 TraesCS3A01G119100 chr1D 87.018 493 58 6 2573 3062 378101946 378102435 8.740000e-153 551
16 TraesCS3A01G119100 chr7A 86.377 345 38 7 2508 2847 410410556 410410896 9.450000e-98 368
17 TraesCS3A01G119100 chr7A 87.037 108 14 0 4105 4212 180659512 180659619 8.120000e-24 122
18 TraesCS3A01G119100 chr5B 89.734 263 24 3 4406 4666 121249500 121249761 3.450000e-87 333
19 TraesCS3A01G119100 chr2B 88.764 267 29 1 4401 4666 673002693 673002427 5.770000e-85 326
20 TraesCS3A01G119100 chr5A 89.015 264 25 3 4406 4666 115095123 115095385 2.070000e-84 324
21 TraesCS3A01G119100 chr4A 88.636 264 30 0 4406 4669 165816545 165816282 7.460000e-84 322
22 TraesCS3A01G119100 chr1A 88.192 271 26 4 4401 4666 434422669 434422938 9.650000e-83 318
23 TraesCS3A01G119100 chr1A 87.629 97 9 1 3725 3821 549045583 549045490 6.320000e-20 110
24 TraesCS3A01G119100 chr2A 88.258 264 31 0 4406 4669 606574489 606574226 3.470000e-82 316
25 TraesCS3A01G119100 chr2D 87.500 272 32 2 4407 4677 623492496 623492226 4.490000e-81 313
26 TraesCS3A01G119100 chr2D 86.607 112 14 1 4104 4215 388818864 388818754 8.120000e-24 122
27 TraesCS3A01G119100 chr5D 85.714 112 15 1 4104 4215 282007011 282007121 3.780000e-22 117
28 TraesCS3A01G119100 chr6B 86.111 108 13 2 4105 4211 57393977 57394083 1.360000e-21 115
29 TraesCS3A01G119100 chr7B 85.455 110 14 1 4104 4211 83912862 83912753 4.890000e-21 113


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 TraesCS3A01G119100 chr3A 91025195 91031160 5965 True 4995.0 9190 100.000000 1 5966 2 chr3A.!!$R1 5965
1 TraesCS3A01G119100 chr3B 123473665 123478978 5313 True 2365.0 4889 90.793667 56 5944 3 chr3B.!!$R1 5888
2 TraesCS3A01G119100 chr3D 76933694 76939417 5723 True 1906.5 3290 92.561000 60 5966 4 chr3D.!!$R1 5906
3 TraesCS3A01G119100 chr7D 369910841 369911414 573 False 606.0 606 85.862000 2508 3082 1 chr7D.!!$F2 574

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
395 416 0.110486 CCCAATAATCCTCGGTGGGG 59.890 60.0 0.00 0.0 44.5 4.96 F
1429 1476 0.456653 GTCAACGTGCATGAATGGCC 60.457 55.0 14.17 0.0 0.0 5.36 F
3035 3227 0.319555 GTGACTCTGCAACTACGCCA 60.320 55.0 0.00 0.0 0.0 5.69 F
3376 3569 0.251341 ACCTTGACTGAATGGTGCCC 60.251 55.0 0.00 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1593 0.240678 CAAACTACATGGCAGCGCAA 59.759 50.000 11.47 0.0 0.00 4.85 R
3374 3567 1.840635 CCTACCTTCCTTCTCCTTGGG 59.159 57.143 0.00 0.0 0.00 4.12 R
4653 4967 1.137697 ACAAAGGACTCCCTCCGTTT 58.862 50.000 0.00 0.0 45.10 3.60 R
5187 5502 1.215655 GCACGCCATGAGACCGTATC 61.216 60.000 0.00 0.0 33.39 2.24 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
28 29 7.639113 AGAGGAAACACTACATTTTGAAACA 57.361 32.000 0.00 0.00 0.00 2.83
29 30 8.237811 AGAGGAAACACTACATTTTGAAACAT 57.762 30.769 0.00 0.00 0.00 2.71
30 31 9.349713 AGAGGAAACACTACATTTTGAAACATA 57.650 29.630 0.00 0.00 0.00 2.29
31 32 9.612620 GAGGAAACACTACATTTTGAAACATAG 57.387 33.333 0.00 0.00 0.00 2.23
32 33 8.576442 AGGAAACACTACATTTTGAAACATAGG 58.424 33.333 0.00 0.00 0.00 2.57
33 34 8.573035 GGAAACACTACATTTTGAAACATAGGA 58.427 33.333 0.00 0.00 0.00 2.94
34 35 9.959749 GAAACACTACATTTTGAAACATAGGAA 57.040 29.630 0.00 0.00 0.00 3.36
35 36 9.965824 AAACACTACATTTTGAAACATAGGAAG 57.034 29.630 0.00 0.00 0.00 3.46
36 37 8.691661 ACACTACATTTTGAAACATAGGAAGT 57.308 30.769 0.00 0.00 0.00 3.01
37 38 9.787435 ACACTACATTTTGAAACATAGGAAGTA 57.213 29.630 0.00 0.00 0.00 2.24
52 53 9.765795 ACATAGGAAGTATATGCTAGAAACAAC 57.234 33.333 0.00 0.00 34.59 3.32
53 54 9.764363 CATAGGAAGTATATGCTAGAAACAACA 57.236 33.333 0.00 0.00 0.00 3.33
54 55 9.988815 ATAGGAAGTATATGCTAGAAACAACAG 57.011 33.333 0.00 0.00 0.00 3.16
55 56 8.079211 AGGAAGTATATGCTAGAAACAACAGA 57.921 34.615 0.00 0.00 0.00 3.41
56 57 8.540388 AGGAAGTATATGCTAGAAACAACAGAA 58.460 33.333 0.00 0.00 0.00 3.02
57 58 9.162764 GGAAGTATATGCTAGAAACAACAGAAA 57.837 33.333 0.00 0.00 0.00 2.52
90 95 4.643387 GTGAACAGGGCCCACGCT 62.643 66.667 27.56 5.52 40.24 5.07
110 115 1.645704 CGACAGGTGGACGACTCGAT 61.646 60.000 5.20 0.00 0.00 3.59
130 135 0.316204 CGTACCTTCGTCACCAGGTT 59.684 55.000 0.00 0.00 40.85 3.50
213 230 0.784778 GAGAAACGCGGTGAAGTCTG 59.215 55.000 12.47 0.00 0.00 3.51
229 246 2.682136 TGGACCCGGCGAATCTCA 60.682 61.111 9.30 3.14 0.00 3.27
230 247 2.107141 GGACCCGGCGAATCTCAG 59.893 66.667 9.30 0.00 0.00 3.35
278 299 2.092861 TCGTCACAAGAAGGGGAAAACA 60.093 45.455 0.00 0.00 0.00 2.83
294 315 1.463674 AACAATCAAGCCACCGATCC 58.536 50.000 0.00 0.00 0.00 3.36
299 320 1.153289 CAAGCCACCGATCCCTCTG 60.153 63.158 0.00 0.00 0.00 3.35
395 416 0.110486 CCCAATAATCCTCGGTGGGG 59.890 60.000 0.00 0.00 44.50 4.96
402 423 1.497309 ATCCTCGGTGGGGAAAAGCA 61.497 55.000 0.00 0.00 36.37 3.91
414 435 4.626081 AAAGCAGCACCGCGACCT 62.626 61.111 8.23 0.00 36.85 3.85
1257 1278 6.145696 GCCTCGCCAAATGTATAACTAACTAG 59.854 42.308 0.00 0.00 0.00 2.57
1288 1309 5.639082 CCCTTTGTTGCATTTCCATTTACTC 59.361 40.000 0.00 0.00 0.00 2.59
1290 1311 6.418057 TTTGTTGCATTTCCATTTACTCCT 57.582 33.333 0.00 0.00 0.00 3.69
1297 1318 7.350382 TGCATTTCCATTTACTCCTATACCAA 58.650 34.615 0.00 0.00 0.00 3.67
1310 1331 5.018809 TCCTATACCAAACTACCTTCGTGT 58.981 41.667 0.00 0.00 0.00 4.49
1314 1335 2.356695 ACCAAACTACCTTCGTGTTTGC 59.643 45.455 11.01 0.00 45.12 3.68
1368 1415 2.345760 GGAACGCCCGAGGTGTAGA 61.346 63.158 9.17 0.00 46.56 2.59
1374 1421 0.739561 GCCCGAGGTGTAGACTGTAG 59.260 60.000 0.00 0.00 0.00 2.74
1375 1422 1.681166 GCCCGAGGTGTAGACTGTAGA 60.681 57.143 0.00 0.00 0.00 2.59
1411 1458 1.064314 AGTCGTAGCCTGAGGAGATGT 60.064 52.381 0.65 0.00 0.00 3.06
1423 1470 1.276138 AGGAGATGTCAACGTGCATGA 59.724 47.619 14.17 0.00 0.00 3.07
1429 1476 0.456653 GTCAACGTGCATGAATGGCC 60.457 55.000 14.17 0.00 0.00 5.36
1437 1484 3.441222 CGTGCATGAATGGCCATGTATAT 59.559 43.478 21.63 1.81 44.25 0.86
1438 1485 4.635324 CGTGCATGAATGGCCATGTATATA 59.365 41.667 21.63 2.17 44.25 0.86
1439 1486 5.220719 CGTGCATGAATGGCCATGTATATAG 60.221 44.000 21.63 7.17 44.25 1.31
1479 1526 3.685272 GCTTGTTTCTTACCTAGTGCTCC 59.315 47.826 0.00 0.00 0.00 4.70
1500 1547 6.128063 GCTCCTATGACATTTGGATTAGATGC 60.128 42.308 9.42 5.98 0.00 3.91
1505 1552 2.961062 ACATTTGGATTAGATGCCTGCC 59.039 45.455 0.00 0.00 0.00 4.85
1515 1562 6.040842 GGATTAGATGCCTGCCATTTTTCTTA 59.959 38.462 0.00 0.00 33.29 2.10
1542 1590 7.324935 TCTTTCAGTGTTTGTGTACTTACTGA 58.675 34.615 0.00 0.00 41.73 3.41
1544 1592 7.908827 TTCAGTGTTTGTGTACTTACTGAAA 57.091 32.000 13.34 0.88 46.20 2.69
1545 1593 8.500753 TTCAGTGTTTGTGTACTTACTGAAAT 57.499 30.769 13.34 0.00 46.20 2.17
1547 1595 8.394877 TCAGTGTTTGTGTACTTACTGAAATTG 58.605 33.333 0.00 0.00 40.85 2.32
1548 1596 7.165812 CAGTGTTTGTGTACTTACTGAAATTGC 59.834 37.037 0.00 0.00 38.16 3.56
1549 1597 6.140108 GTGTTTGTGTACTTACTGAAATTGCG 59.860 38.462 0.00 0.00 0.00 4.85
1550 1598 4.398549 TGTGTACTTACTGAAATTGCGC 57.601 40.909 0.00 0.00 0.00 6.09
1551 1599 4.062293 TGTGTACTTACTGAAATTGCGCT 58.938 39.130 9.73 0.00 0.00 5.92
1552 1600 4.084066 TGTGTACTTACTGAAATTGCGCTG 60.084 41.667 9.73 0.00 0.00 5.18
1553 1601 2.619013 ACTTACTGAAATTGCGCTGC 57.381 45.000 9.73 0.00 0.00 5.25
1554 1602 1.200020 ACTTACTGAAATTGCGCTGCC 59.800 47.619 9.73 0.00 0.00 4.85
1555 1603 1.199789 CTTACTGAAATTGCGCTGCCA 59.800 47.619 9.73 0.00 0.00 4.92
1556 1604 1.462616 TACTGAAATTGCGCTGCCAT 58.537 45.000 9.73 0.00 0.00 4.40
1573 1621 3.382865 TGCCATGTAGTTTGCTTTGTTGA 59.617 39.130 0.00 0.00 0.00 3.18
1578 1626 6.974622 CCATGTAGTTTGCTTTGTTGATATCC 59.025 38.462 0.00 0.00 0.00 2.59
1585 1633 3.214328 GCTTTGTTGATATCCGGATGGT 58.786 45.455 27.55 15.32 36.30 3.55
1590 1640 4.196193 TGTTGATATCCGGATGGTTGTTC 58.804 43.478 27.55 13.29 36.30 3.18
1591 1641 4.080582 TGTTGATATCCGGATGGTTGTTCT 60.081 41.667 27.55 0.00 36.30 3.01
1596 1646 1.586154 CCGGATGGTTGTTCTGCACC 61.586 60.000 0.00 0.00 0.00 5.01
1618 1668 3.126073 TGTTGCGATGATAGCAGTGATC 58.874 45.455 0.00 0.00 46.01 2.92
1619 1669 3.126073 GTTGCGATGATAGCAGTGATCA 58.874 45.455 0.00 0.00 46.01 2.92
1699 1749 6.150140 ACTTGCTAGTAAGATGCTTCTTTTGG 59.850 38.462 25.11 11.32 42.29 3.28
1712 1762 4.159506 GCTTCTTTTGGCCATTACCATGTA 59.840 41.667 6.09 0.00 40.13 2.29
1713 1763 5.650543 CTTCTTTTGGCCATTACCATGTAC 58.349 41.667 6.09 0.00 40.13 2.90
1714 1764 4.929479 TCTTTTGGCCATTACCATGTACT 58.071 39.130 6.09 0.00 40.13 2.73
1715 1765 4.704540 TCTTTTGGCCATTACCATGTACTG 59.295 41.667 6.09 0.00 40.13 2.74
1717 1767 4.308526 TTGGCCATTACCATGTACTGAA 57.691 40.909 6.09 0.00 40.13 3.02
1718 1768 3.884895 TGGCCATTACCATGTACTGAAG 58.115 45.455 0.00 0.00 33.75 3.02
1719 1769 3.521531 TGGCCATTACCATGTACTGAAGA 59.478 43.478 0.00 0.00 33.75 2.87
1721 1771 5.133221 GGCCATTACCATGTACTGAAGAAT 58.867 41.667 0.00 0.00 0.00 2.40
1722 1772 5.009010 GGCCATTACCATGTACTGAAGAATG 59.991 44.000 0.00 0.00 0.00 2.67
1723 1773 5.822519 GCCATTACCATGTACTGAAGAATGA 59.177 40.000 10.17 0.00 0.00 2.57
1724 1774 6.318648 GCCATTACCATGTACTGAAGAATGAA 59.681 38.462 10.17 0.00 0.00 2.57
1725 1775 7.467811 GCCATTACCATGTACTGAAGAATGAAG 60.468 40.741 10.17 0.00 0.00 3.02
1726 1776 7.554118 CCATTACCATGTACTGAAGAATGAAGT 59.446 37.037 10.17 0.00 0.00 3.01
1727 1777 8.950210 CATTACCATGTACTGAAGAATGAAGTT 58.050 33.333 0.00 0.00 0.00 2.66
1729 1779 9.653287 TTACCATGTACTGAAGAATGAAGTTAG 57.347 33.333 0.00 0.00 0.00 2.34
1731 1781 8.543774 ACCATGTACTGAAGAATGAAGTTAGAT 58.456 33.333 0.00 0.00 0.00 1.98
1752 1802 7.230849 AGATAGAGAATAGCAGTCTCAATGG 57.769 40.000 13.44 0.00 43.39 3.16
1919 1970 7.982761 ACTAGTATGTATGCCTGTACTACTC 57.017 40.000 0.00 0.00 0.00 2.59
1935 1986 4.718961 ACTACTCATTCTGTTGCCACTTT 58.281 39.130 0.00 0.00 0.00 2.66
2071 2122 8.435931 AAATGTAGATAGATGTATGCCTACCA 57.564 34.615 6.38 0.00 0.00 3.25
2084 2135 0.527565 CCTACCACTGCCAAATGTGC 59.472 55.000 0.00 0.00 33.26 4.57
2135 2186 7.246311 CACCTTCTTTGTATTCATAAGCACTG 58.754 38.462 0.00 0.00 0.00 3.66
2390 2449 7.621428 ATTGAACTATGAAGTGTTGATCTGG 57.379 36.000 0.00 0.00 35.62 3.86
2400 2459 2.744202 GTGTTGATCTGGTAAGGTGCTG 59.256 50.000 0.00 0.00 0.00 4.41
2420 2479 5.712446 TGCTGACTTGAGATCTAGTTACACT 59.288 40.000 0.00 0.00 32.36 3.55
2424 2483 9.602568 CTGACTTGAGATCTAGTTACACTAGTA 57.397 37.037 10.12 0.00 46.31 1.82
2452 2511 3.535280 TGTCAACACTTGCTCTGTGTA 57.465 42.857 9.56 0.00 46.46 2.90
2492 2657 4.944962 TGGATCGTTGCTGATTTTACAG 57.055 40.909 0.00 0.00 40.43 2.74
2848 3017 8.621532 TGGATAGTGTCTTCATTATAAATGGC 57.378 34.615 0.12 0.00 28.89 4.40
2849 3018 8.217111 TGGATAGTGTCTTCATTATAAATGGCA 58.783 33.333 0.00 0.00 28.89 4.92
2885 3077 5.178096 TCTCCCTGAATGTGCAGAATTTA 57.822 39.130 0.00 0.00 38.14 1.40
2918 3110 3.904136 AACAGAAGGCAAATGTTCTCG 57.096 42.857 0.00 0.00 31.72 4.04
2991 3183 2.060383 CCCAGAGAGGCATCCGACA 61.060 63.158 0.00 0.00 35.39 4.35
3035 3227 0.319555 GTGACTCTGCAACTACGCCA 60.320 55.000 0.00 0.00 0.00 5.69
3182 3374 2.884639 ACGCTTGGTGCTTCTTATTGTT 59.115 40.909 0.00 0.00 40.11 2.83
3230 3423 8.573885 TGACACTCCTAATAAATGGTATAGACG 58.426 37.037 0.00 0.00 0.00 4.18
3286 3479 6.856895 AGAGCCAGTAGTATTTTGAAATTGC 58.143 36.000 0.00 0.00 0.00 3.56
3290 3483 6.572314 GCCAGTAGTATTTTGAAATTGCACCT 60.572 38.462 0.00 0.00 0.00 4.00
3374 3567 1.541588 GGAACCTTGACTGAATGGTGC 59.458 52.381 0.00 0.00 32.53 5.01
3376 3569 0.251341 ACCTTGACTGAATGGTGCCC 60.251 55.000 0.00 0.00 0.00 5.36
3482 3679 6.183361 TGCAATACTCCAAGGCTCATATAACT 60.183 38.462 0.00 0.00 0.00 2.24
3488 3685 4.716784 TCCAAGGCTCATATAACTGTCTGT 59.283 41.667 0.00 0.00 0.00 3.41
3509 3706 9.836076 GTCTGTTAAACAATGGAATACTAAACC 57.164 33.333 0.00 0.00 0.00 3.27
3535 3732 7.875316 ACAAATATATACACGCAGATCTGAC 57.125 36.000 27.04 15.81 0.00 3.51
3551 3751 6.019479 CAGATCTGACCTTAACGAACTAATGC 60.019 42.308 18.34 0.00 0.00 3.56
3599 3821 7.638683 CGTTACTGTTGCTTAACCATATAAAGC 59.361 37.037 0.00 0.00 44.63 3.51
3600 3822 8.674607 GTTACTGTTGCTTAACCATATAAAGCT 58.325 33.333 7.68 0.00 44.66 3.74
3601 3823 7.321745 ACTGTTGCTTAACCATATAAAGCTC 57.678 36.000 7.68 2.64 44.66 4.09
3602 3824 7.112779 ACTGTTGCTTAACCATATAAAGCTCT 58.887 34.615 7.68 0.00 44.66 4.09
3603 3825 7.066284 ACTGTTGCTTAACCATATAAAGCTCTG 59.934 37.037 7.68 7.31 44.66 3.35
3604 3826 6.183360 TGTTGCTTAACCATATAAAGCTCTGC 60.183 38.462 7.68 0.00 44.66 4.26
3605 3827 5.436175 TGCTTAACCATATAAAGCTCTGCA 58.564 37.500 7.68 0.00 44.66 4.41
3606 3828 5.885352 TGCTTAACCATATAAAGCTCTGCAA 59.115 36.000 7.68 0.00 44.66 4.08
3607 3829 6.038603 TGCTTAACCATATAAAGCTCTGCAAG 59.961 38.462 7.68 0.00 44.66 4.01
3608 3830 6.038714 GCTTAACCATATAAAGCTCTGCAAGT 59.961 38.462 0.00 0.00 41.85 3.16
3609 3831 7.226720 GCTTAACCATATAAAGCTCTGCAAGTA 59.773 37.037 0.00 0.00 41.85 2.24
3610 3832 9.277783 CTTAACCATATAAAGCTCTGCAAGTAT 57.722 33.333 0.00 0.00 33.76 2.12
3611 3833 9.627123 TTAACCATATAAAGCTCTGCAAGTATT 57.373 29.630 0.00 0.00 33.76 1.89
4019 4243 7.739444 TCACACCCTAGAGAATCCCATTATAAT 59.261 37.037 0.00 0.00 33.66 1.28
4113 4339 4.171044 AGAAGGATACATGGTACTCCCTCT 59.829 45.833 0.00 0.00 41.41 3.69
4146 4372 3.684788 AGTTGTCGCTGAAATGGATGTAC 59.315 43.478 0.00 0.00 0.00 2.90
4153 4379 4.441495 CGCTGAAATGGATGTACCTAGACA 60.441 45.833 0.00 0.00 39.86 3.41
4177 4403 6.897259 TGTTTTAGTGTTAGATACATCCGC 57.103 37.500 0.00 0.00 39.39 5.54
4214 4440 8.982471 TTAATATGGATTGGAGGGAGTATGTA 57.018 34.615 0.00 0.00 0.00 2.29
4305 4532 2.325661 TCTGGTCCCTGATCTGTTGA 57.674 50.000 0.00 0.00 0.00 3.18
4476 4705 7.262048 GTCAAACCTCATAAACTTTGACCAAA 58.738 34.615 9.86 0.00 43.35 3.28
4606 4920 8.846211 TGGTTTTCTCTATAAACTTGGTCAAAG 58.154 33.333 0.00 0.00 42.07 2.77
4628 4942 7.954788 AAGTTTGCAAAGTTTAACAAGTCAA 57.045 28.000 23.54 0.00 0.00 3.18
4666 4980 4.138487 ACATTATGAAACGGAGGGAGTC 57.862 45.455 0.00 0.00 0.00 3.36
4784 5098 7.094762 GGTTAAGAGTCTTCCCTTAAATGTGTG 60.095 40.741 9.12 0.00 36.83 3.82
4788 5102 4.072131 GTCTTCCCTTAAATGTGTGCTCA 58.928 43.478 0.00 0.00 0.00 4.26
5073 5387 4.019950 TGGGATGATGATGATGATAAGCGT 60.020 41.667 0.00 0.00 0.00 5.07
5216 5531 1.070821 CATGGCGTGCGGTGATATAG 58.929 55.000 0.00 0.00 0.00 1.31
5217 5532 0.037326 ATGGCGTGCGGTGATATAGG 60.037 55.000 0.00 0.00 0.00 2.57
5277 5600 0.616111 AATCCTCTGTCGGTCCTGCT 60.616 55.000 0.00 0.00 0.00 4.24
5287 5610 1.968540 GGTCCTGCTCTTTTGCGCT 60.969 57.895 9.73 0.00 35.36 5.92
5320 5643 0.179000 ATTCCGGCTCTCCATGTGTC 59.821 55.000 0.00 0.00 0.00 3.67
5362 5685 1.266989 CGTCCTTTTGGCTCAGAAACC 59.733 52.381 0.00 0.00 40.12 3.27
5457 5796 2.224450 CCCTTTCCACTTTCCAGTACGT 60.224 50.000 0.00 0.00 0.00 3.57
5488 5830 0.108615 CGAAGAGAACGGTGGCAGAT 60.109 55.000 0.00 0.00 0.00 2.90
5559 5901 1.285023 ACGGAGTACACGTGCAGAC 59.715 57.895 17.22 11.54 43.78 3.51
5603 5945 2.109181 GACGTAGGCAGGCATCCC 59.891 66.667 0.00 0.00 0.00 3.85
5663 6005 1.169661 ATAGACCTCAGCTCGCTCGG 61.170 60.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.740123 TGTTTCAAAATGTAGTGTTTCCTCTA 57.260 30.769 0.00 0.00 0.00 2.43
4 5 7.639113 TGTTTCAAAATGTAGTGTTTCCTCT 57.361 32.000 0.00 0.00 0.00 3.69
6 7 8.576442 CCTATGTTTCAAAATGTAGTGTTTCCT 58.424 33.333 0.00 0.00 0.00 3.36
7 8 8.573035 TCCTATGTTTCAAAATGTAGTGTTTCC 58.427 33.333 0.00 0.00 0.00 3.13
8 9 9.959749 TTCCTATGTTTCAAAATGTAGTGTTTC 57.040 29.630 0.00 0.00 0.00 2.78
9 10 9.965824 CTTCCTATGTTTCAAAATGTAGTGTTT 57.034 29.630 0.00 0.00 0.00 2.83
10 11 9.131791 ACTTCCTATGTTTCAAAATGTAGTGTT 57.868 29.630 0.00 0.00 0.00 3.32
11 12 8.691661 ACTTCCTATGTTTCAAAATGTAGTGT 57.308 30.769 0.00 0.00 0.00 3.55
26 27 9.765795 GTTGTTTCTAGCATATACTTCCTATGT 57.234 33.333 0.00 0.00 0.00 2.29
27 28 9.764363 TGTTGTTTCTAGCATATACTTCCTATG 57.236 33.333 0.00 0.00 0.00 2.23
28 29 9.988815 CTGTTGTTTCTAGCATATACTTCCTAT 57.011 33.333 0.00 0.00 0.00 2.57
29 30 9.197306 TCTGTTGTTTCTAGCATATACTTCCTA 57.803 33.333 0.00 0.00 0.00 2.94
30 31 8.079211 TCTGTTGTTTCTAGCATATACTTCCT 57.921 34.615 0.00 0.00 0.00 3.36
31 32 8.718102 TTCTGTTGTTTCTAGCATATACTTCC 57.282 34.615 0.00 0.00 0.00 3.46
56 57 9.927668 CCCTGTTCACTATTTCATTGTTTATTT 57.072 29.630 0.00 0.00 0.00 1.40
57 58 8.034804 GCCCTGTTCACTATTTCATTGTTTATT 58.965 33.333 0.00 0.00 0.00 1.40
58 59 7.363793 GGCCCTGTTCACTATTTCATTGTTTAT 60.364 37.037 0.00 0.00 0.00 1.40
90 95 2.322830 CGAGTCGTCCACCTGTCGA 61.323 63.158 3.82 0.00 0.00 4.20
110 115 0.538057 ACCTGGTGACGAAGGTACGA 60.538 55.000 6.79 0.00 45.15 3.43
213 230 2.107141 CTGAGATTCGCCGGGTCC 59.893 66.667 2.18 0.00 0.00 4.46
229 246 2.241176 AGACGAAGGGAGAGATGAGTCT 59.759 50.000 0.00 0.00 37.42 3.24
230 247 2.616842 GAGACGAAGGGAGAGATGAGTC 59.383 54.545 0.00 0.00 0.00 3.36
278 299 0.181350 GAGGGATCGGTGGCTTGATT 59.819 55.000 0.00 0.00 0.00 2.57
294 315 1.676967 GCTGGAAACTGGGCAGAGG 60.677 63.158 0.00 0.00 0.00 3.69
299 320 0.678048 AATCGAGCTGGAAACTGGGC 60.678 55.000 1.37 0.00 0.00 5.36
377 398 1.136828 TCCCCACCGAGGATTATTGG 58.863 55.000 0.00 0.00 41.22 3.16
378 399 3.290948 TTTCCCCACCGAGGATTATTG 57.709 47.619 0.00 0.00 41.22 1.90
395 416 2.127232 GTCGCGGTGCTGCTTTTC 60.127 61.111 6.13 0.00 0.00 2.29
414 435 2.595095 GGGATTGATGGCGGGTGA 59.405 61.111 0.00 0.00 0.00 4.02
415 436 2.519302 GGGGATTGATGGCGGGTG 60.519 66.667 0.00 0.00 0.00 4.61
1270 1291 7.284489 TGGTATAGGAGTAAATGGAAATGCAAC 59.716 37.037 0.00 0.00 0.00 4.17
1271 1292 7.350382 TGGTATAGGAGTAAATGGAAATGCAA 58.650 34.615 0.00 0.00 0.00 4.08
1272 1293 6.905736 TGGTATAGGAGTAAATGGAAATGCA 58.094 36.000 0.00 0.00 0.00 3.96
1273 1294 7.817418 TTGGTATAGGAGTAAATGGAAATGC 57.183 36.000 0.00 0.00 0.00 3.56
1288 1309 5.334724 ACACGAAGGTAGTTTGGTATAGG 57.665 43.478 0.00 0.00 0.00 2.57
1297 1318 1.944032 ACGCAAACACGAAGGTAGTT 58.056 45.000 0.00 0.00 36.70 2.24
1310 1331 2.909965 GAGGGGGCACAACGCAAA 60.910 61.111 0.00 0.00 45.17 3.68
1330 1376 1.177401 GAGATCCCAACCAAACAGCC 58.823 55.000 0.00 0.00 0.00 4.85
1337 1383 1.594833 CGTTCCGAGATCCCAACCA 59.405 57.895 0.00 0.00 0.00 3.67
1355 1401 0.739561 CTACAGTCTACACCTCGGGC 59.260 60.000 0.00 0.00 0.00 6.13
1359 1405 3.611970 TGAGCTCTACAGTCTACACCTC 58.388 50.000 16.19 0.00 0.00 3.85
1362 1408 3.701241 GCATGAGCTCTACAGTCTACAC 58.299 50.000 16.19 0.00 37.91 2.90
1391 1438 1.064314 ACATCTCCTCAGGCTACGACT 60.064 52.381 0.00 0.00 0.00 4.18
1392 1439 1.335496 GACATCTCCTCAGGCTACGAC 59.665 57.143 0.00 0.00 0.00 4.34
1411 1458 0.892814 TGGCCATTCATGCACGTTGA 60.893 50.000 0.00 0.00 0.00 3.18
1437 1484 7.207383 ACAAGCATGCTTCGTACAATATACTA 58.793 34.615 29.81 0.00 33.42 1.82
1438 1485 6.049149 ACAAGCATGCTTCGTACAATATACT 58.951 36.000 29.81 0.96 33.42 2.12
1439 1486 6.287107 ACAAGCATGCTTCGTACAATATAC 57.713 37.500 29.81 0.00 33.42 1.47
1479 1526 6.349115 GCAGGCATCTAATCCAAATGTCATAG 60.349 42.308 0.00 0.00 0.00 2.23
1500 1547 7.330208 CACTGAAAGATTAAGAAAAATGGCAGG 59.670 37.037 0.00 0.00 37.43 4.85
1515 1562 8.612619 CAGTAAGTACACAAACACTGAAAGATT 58.387 33.333 0.00 0.00 36.37 2.40
1542 1590 1.176527 ACTACATGGCAGCGCAATTT 58.823 45.000 11.47 0.00 0.00 1.82
1544 1592 1.135315 CAAACTACATGGCAGCGCAAT 60.135 47.619 11.47 0.00 0.00 3.56
1545 1593 0.240678 CAAACTACATGGCAGCGCAA 59.759 50.000 11.47 0.00 0.00 4.85
1547 1595 1.514873 GCAAACTACATGGCAGCGC 60.515 57.895 0.00 0.00 0.00 5.92
1548 1596 0.523072 AAGCAAACTACATGGCAGCG 59.477 50.000 0.00 0.00 0.00 5.18
1549 1597 2.288395 ACAAAGCAAACTACATGGCAGC 60.288 45.455 0.00 0.00 0.00 5.25
1550 1598 3.648339 ACAAAGCAAACTACATGGCAG 57.352 42.857 0.00 0.00 0.00 4.85
1551 1599 3.382865 TCAACAAAGCAAACTACATGGCA 59.617 39.130 0.00 0.00 0.00 4.92
1552 1600 3.976169 TCAACAAAGCAAACTACATGGC 58.024 40.909 0.00 0.00 0.00 4.40
1553 1601 6.974622 GGATATCAACAAAGCAAACTACATGG 59.025 38.462 4.83 0.00 0.00 3.66
1554 1602 6.688385 CGGATATCAACAAAGCAAACTACATG 59.312 38.462 4.83 0.00 0.00 3.21
1555 1603 6.183360 CCGGATATCAACAAAGCAAACTACAT 60.183 38.462 0.00 0.00 0.00 2.29
1556 1604 5.123186 CCGGATATCAACAAAGCAAACTACA 59.877 40.000 0.00 0.00 0.00 2.74
1573 1621 2.172505 TGCAGAACAACCATCCGGATAT 59.827 45.455 18.63 5.48 35.59 1.63
1578 1626 0.606401 AGGTGCAGAACAACCATCCG 60.606 55.000 0.00 0.00 36.21 4.18
1596 1646 2.543641 TCACTGCTATCATCGCAACAG 58.456 47.619 0.00 0.00 36.88 3.16
1618 1668 2.602878 GCACAAAATGAGGCAGATGTG 58.397 47.619 0.00 0.00 40.72 3.21
1619 1669 1.547372 GGCACAAAATGAGGCAGATGT 59.453 47.619 0.00 0.00 33.95 3.06
1699 1749 5.822519 TCATTCTTCAGTACATGGTAATGGC 59.177 40.000 0.00 0.00 38.19 4.40
1721 1771 8.988546 AGACTGCTATTCTCTATCTAACTTCA 57.011 34.615 0.00 0.00 0.00 3.02
1722 1772 9.062524 TGAGACTGCTATTCTCTATCTAACTTC 57.937 37.037 10.05 0.00 40.30 3.01
1723 1773 8.988546 TGAGACTGCTATTCTCTATCTAACTT 57.011 34.615 10.05 0.00 40.30 2.66
1724 1774 8.988546 TTGAGACTGCTATTCTCTATCTAACT 57.011 34.615 10.05 0.00 40.30 2.24
1725 1775 9.624697 CATTGAGACTGCTATTCTCTATCTAAC 57.375 37.037 10.05 0.00 40.30 2.34
1726 1776 8.801299 CCATTGAGACTGCTATTCTCTATCTAA 58.199 37.037 10.05 0.00 40.30 2.10
1727 1777 7.395772 CCCATTGAGACTGCTATTCTCTATCTA 59.604 40.741 10.05 0.00 40.30 1.98
1729 1779 6.210385 TCCCATTGAGACTGCTATTCTCTATC 59.790 42.308 10.05 0.00 40.30 2.08
1731 1781 5.458595 TCCCATTGAGACTGCTATTCTCTA 58.541 41.667 10.05 4.56 40.30 2.43
1733 1783 4.679373 TCCCATTGAGACTGCTATTCTC 57.321 45.455 3.61 3.61 40.10 2.87
1734 1784 5.643421 AATCCCATTGAGACTGCTATTCT 57.357 39.130 0.00 0.00 0.00 2.40
1735 1785 9.107177 CATATAATCCCATTGAGACTGCTATTC 57.893 37.037 0.00 0.00 0.00 1.75
1736 1786 7.555554 GCATATAATCCCATTGAGACTGCTATT 59.444 37.037 0.00 0.00 0.00 1.73
1737 1787 7.052873 GCATATAATCCCATTGAGACTGCTAT 58.947 38.462 0.00 0.00 0.00 2.97
1738 1788 6.013466 TGCATATAATCCCATTGAGACTGCTA 60.013 38.462 0.00 0.00 0.00 3.49
1739 1789 5.221986 TGCATATAATCCCATTGAGACTGCT 60.222 40.000 0.00 0.00 0.00 4.24
1740 1790 5.005740 TGCATATAATCCCATTGAGACTGC 58.994 41.667 0.00 0.00 0.00 4.40
1752 1802 4.495349 GCACATCGCTGATGCATATAATCC 60.495 45.833 15.41 0.00 43.15 3.01
1839 1889 0.465287 TCACTGCACAGCACTTGAGA 59.535 50.000 0.00 0.00 33.79 3.27
1907 1958 3.619038 GCAACAGAATGAGTAGTACAGGC 59.381 47.826 2.52 0.00 39.69 4.85
1935 1986 1.257743 AGCGGAGACAAGCACTCTAA 58.742 50.000 0.00 0.00 35.10 2.10
2071 2122 2.102757 TGTTCAATGCACATTTGGCAGT 59.897 40.909 0.00 0.00 45.68 4.40
2156 2208 0.623723 GGTGGGAGGCCAAACTGATA 59.376 55.000 5.01 0.00 0.00 2.15
2157 2209 1.142688 AGGTGGGAGGCCAAACTGAT 61.143 55.000 5.01 0.00 0.00 2.90
2159 2211 0.404040 TTAGGTGGGAGGCCAAACTG 59.596 55.000 5.01 0.00 0.00 3.16
2389 2448 3.196685 AGATCTCAAGTCAGCACCTTACC 59.803 47.826 0.00 0.00 0.00 2.85
2390 2449 4.464069 AGATCTCAAGTCAGCACCTTAC 57.536 45.455 0.00 0.00 0.00 2.34
2420 2479 7.165485 AGCAAGTGTTGACATAATTGGTACTA 58.835 34.615 8.58 0.00 30.93 1.82
2424 2483 5.048504 CAGAGCAAGTGTTGACATAATTGGT 60.049 40.000 9.56 9.56 33.38 3.67
2492 2657 3.574284 TGCCACTGTAAACAATCATGC 57.426 42.857 0.00 0.00 0.00 4.06
2856 3048 2.821969 GCACATTCAGGGAGAAACACAT 59.178 45.455 0.00 0.00 40.22 3.21
2885 3077 3.321968 GCCTTCTGTTTTCATGGACCTTT 59.678 43.478 0.00 0.00 0.00 3.11
2918 3110 2.915738 CATCTTTTGCAGCTGAGGAC 57.084 50.000 20.43 0.00 0.00 3.85
3035 3227 4.406456 TGCAATGGTACCTCTGAAACAAT 58.594 39.130 14.36 0.00 0.00 2.71
3230 3423 5.730289 GCAGGGAATTGTTTTGCAAAACTTC 60.730 40.000 39.89 34.74 46.37 3.01
3374 3567 1.840635 CCTACCTTCCTTCTCCTTGGG 59.159 57.143 0.00 0.00 0.00 4.12
3376 3569 4.910458 TTTCCTACCTTCCTTCTCCTTG 57.090 45.455 0.00 0.00 0.00 3.61
3509 3706 8.217115 GTCAGATCTGCGTGTATATATTTGTTG 58.783 37.037 18.36 0.00 0.00 3.33
3524 3721 2.561733 TCGTTAAGGTCAGATCTGCG 57.438 50.000 18.36 13.30 0.00 5.18
3535 3732 5.712217 TCGATTGCATTAGTTCGTTAAGG 57.288 39.130 0.00 0.00 33.52 2.69
3551 3751 4.259970 CGCAAGAGTAGTCCAATTCGATTG 60.260 45.833 0.00 0.00 43.02 2.67
3617 3839 2.844122 AAACCAAACTCGTGAAGCAC 57.156 45.000 0.00 0.00 0.00 4.40
3618 3840 2.750166 TCAAAACCAAACTCGTGAAGCA 59.250 40.909 0.00 0.00 0.00 3.91
3619 3841 3.414549 TCAAAACCAAACTCGTGAAGC 57.585 42.857 0.00 0.00 0.00 3.86
3903 4125 8.204836 TCTAAGATTGCCTACTCCTGAAAATAC 58.795 37.037 0.00 0.00 0.00 1.89
3918 4140 4.246458 ACGACTCAAAGTCTAAGATTGCC 58.754 43.478 5.63 0.00 42.92 4.52
4113 4339 5.529581 TCAGCGACAACTAATATGGATCA 57.470 39.130 0.00 0.00 0.00 2.92
4153 4379 7.272978 AGCGGATGTATCTAACACTAAAACAT 58.727 34.615 0.00 0.00 42.09 2.71
4177 4403 6.312487 CAATCCATATTAATCAGCGCTCAAG 58.688 40.000 7.13 0.00 0.00 3.02
4185 4411 7.025520 ACTCCCTCCAATCCATATTAATCAG 57.974 40.000 0.00 0.00 0.00 2.90
4186 4412 8.551440 CATACTCCCTCCAATCCATATTAATCA 58.449 37.037 0.00 0.00 0.00 2.57
4214 4440 2.484264 GAGAAGCGCCTACACAAACATT 59.516 45.455 2.29 0.00 0.00 2.71
4305 4532 8.816894 TGCCTAGCTAGCTTAATAATACTTGAT 58.183 33.333 24.88 0.00 0.00 2.57
4390 4619 3.763897 GGGAGTATTGGCACAGAAAACAT 59.236 43.478 0.00 0.00 42.39 2.71
4391 4620 3.153919 GGGAGTATTGGCACAGAAAACA 58.846 45.455 0.00 0.00 42.39 2.83
4606 4920 8.995419 TTTTTGACTTGTTAAACTTTGCAAAC 57.005 26.923 8.05 0.00 0.00 2.93
4644 4958 4.100498 GGACTCCCTCCGTTTCATAATGTA 59.900 45.833 0.00 0.00 0.00 2.29
4653 4967 1.137697 ACAAAGGACTCCCTCCGTTT 58.862 50.000 0.00 0.00 45.10 3.60
4666 4980 9.793252 CTGAGATAATTTTACCATGAACAAAGG 57.207 33.333 0.00 0.00 0.00 3.11
4754 5068 6.713731 TTAAGGGAAGACTCTTAACCCAAT 57.286 37.500 15.05 8.06 42.11 3.16
4784 5098 2.483106 CTGCCATACATAGCACATGAGC 59.517 50.000 7.07 7.07 34.68 4.26
4788 5102 3.999001 CGATTCTGCCATACATAGCACAT 59.001 43.478 0.00 0.00 34.68 3.21
5187 5502 1.215655 GCACGCCATGAGACCGTATC 61.216 60.000 0.00 0.00 33.39 2.24
5192 5507 4.760047 ACCGCACGCCATGAGACC 62.760 66.667 0.00 0.00 0.00 3.85
5216 5531 4.742438 TTTCAGCAAAGATTACACGACC 57.258 40.909 0.00 0.00 0.00 4.79
5217 5532 6.142817 ACATTTTCAGCAAAGATTACACGAC 58.857 36.000 0.00 0.00 0.00 4.34
5277 5600 1.615883 AGAGACAGAGAGCGCAAAAGA 59.384 47.619 11.47 0.00 0.00 2.52
5287 5610 2.952978 GCCGGAATTAGAGAGACAGAGA 59.047 50.000 5.05 0.00 0.00 3.10
5362 5685 6.310224 ACATCGTTTGAACCAAAACAGAAAAG 59.690 34.615 0.00 0.00 39.53 2.27
5417 5755 2.664436 GGTTCGAAACAGGACGCGG 61.664 63.158 12.47 0.00 0.00 6.46
5457 5796 2.599281 TCTTCGACTGGCACCGGA 60.599 61.111 9.46 0.00 0.00 5.14
5488 5830 1.455402 TGCTGCTGCTGTTGGGAAA 60.455 52.632 17.00 0.00 40.48 3.13
5595 5937 4.082523 CCGTGTCGTGGGATGCCT 62.083 66.667 4.35 0.00 0.00 4.75
5639 5981 0.589223 CGAGCTGAGGTCTATCCGTC 59.411 60.000 10.18 0.00 41.99 4.79
5663 6005 0.301987 GCTTATCTTTCCGCAGCGAC 59.698 55.000 18.75 0.00 0.00 5.19
5722 6072 3.423154 CCGTTTCTGGTCTGCGCC 61.423 66.667 4.18 0.00 0.00 6.53
5777 6132 4.808364 GCTCTGTTGCTGGTTTATAGAGAG 59.192 45.833 0.00 0.00 33.76 3.20
5778 6133 4.222810 TGCTCTGTTGCTGGTTTATAGAGA 59.777 41.667 0.00 0.00 33.76 3.10


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

AutoCloner maintained by Alex Coulton.