Multiple sequence alignment - TraesCS4D01G364500

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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 TraesCS4D01G364500 chr4D 100.000 4029 0 0 1 4029 509341956 509337928 0.000000e+00 7441.0
1 TraesCS4D01G364500 chr4D 85.444 1058 128 15 1982 3027 509283456 509282413 0.000000e+00 1077.0
2 TraesCS4D01G364500 chr4D 83.475 944 90 29 462 1373 509284740 509283831 0.000000e+00 819.0
3 TraesCS4D01G364500 chr4D 84.061 458 56 8 3355 3812 509282229 509281789 3.720000e-115 425.0
4 TraesCS4D01G364500 chr4D 85.987 314 34 7 447 752 509288261 509287950 1.080000e-85 327.0
5 TraesCS4D01G364500 chr4D 86.364 308 24 9 447 752 509355869 509355578 1.810000e-83 320.0
6 TraesCS4D01G364500 chr4D 86.643 277 25 7 448 718 509326371 509326101 3.040000e-76 296.0
7 TraesCS4D01G364500 chr4D 90.000 120 11 1 3911 4029 509281583 509281464 1.940000e-33 154.0
8 TraesCS4D01G364500 chr4D 91.803 61 2 1 1724 1784 509283696 509283639 9.280000e-12 82.4
9 TraesCS4D01G364500 chr4B 96.217 2009 67 7 1908 3908 657516552 657518559 0.000000e+00 3280.0
10 TraesCS4D01G364500 chr4B 89.389 1621 89 32 5 1582 657497402 657498982 0.000000e+00 1964.0
11 TraesCS4D01G364500 chr4B 90.386 1269 56 26 343 1582 657514940 657516171 0.000000e+00 1607.0
12 TraesCS4D01G364500 chr4B 84.826 1061 131 19 1982 3028 657527404 657528448 0.000000e+00 1040.0
13 TraesCS4D01G364500 chr4B 95.911 587 21 2 1908 2491 657499363 657499949 0.000000e+00 948.0
14 TraesCS4D01G364500 chr4B 84.967 459 63 5 3355 3809 657528639 657529095 1.020000e-125 460.0
15 TraesCS4D01G364500 chr4B 84.304 395 46 7 932 1314 657509731 657510121 4.920000e-99 372.0
16 TraesCS4D01G364500 chr4B 94.850 233 8 1 1686 1918 657498981 657499209 1.060000e-95 361.0
17 TraesCS4D01G364500 chr4B 94.850 233 8 1 1686 1918 657516170 657516398 1.060000e-95 361.0
18 TraesCS4D01G364500 chr4B 87.459 303 30 5 5 299 657514453 657514755 3.860000e-90 342.0
19 TraesCS4D01G364500 chr4B 86.977 215 22 2 932 1140 657526418 657526632 1.870000e-58 237.0
20 TraesCS4D01G364500 chr4B 96.000 125 2 3 3905 4027 657518616 657518739 2.460000e-47 200.0
21 TraesCS4D01G364500 chr4B 100.000 33 0 0 1838 1870 657499158 657499190 1.210000e-05 62.1
22 TraesCS4D01G364500 chr4B 100.000 33 0 0 1838 1870 657516347 657516379 1.210000e-05 62.1
23 TraesCS4D01G364500 chr5A 93.267 2109 81 18 1686 3780 698180043 698177982 0.000000e+00 3051.0
24 TraesCS4D01G364500 chr5A 90.465 1248 53 18 355 1582 698181243 698180042 0.000000e+00 1585.0
25 TraesCS4D01G364500 chr5A 84.883 1065 136 19 1982 3032 698163108 698162055 0.000000e+00 1051.0
26 TraesCS4D01G364500 chr5A 83.572 907 95 28 481 1365 698164402 698163528 0.000000e+00 800.0
27 TraesCS4D01G364500 chr5A 85.714 462 61 4 3355 3812 698161872 698161412 2.180000e-132 483.0
28 TraesCS4D01G364500 chr5A 76.768 990 143 50 2621 3580 698144576 698143644 1.310000e-129 473.0
29 TraesCS4D01G364500 chr5A 90.547 201 16 3 5 204 698181955 698181757 3.090000e-66 263.0
30 TraesCS4D01G364500 chr5A 83.062 307 24 13 447 751 698186548 698186268 1.860000e-63 254.0
31 TraesCS4D01G364500 chr5A 94.681 94 4 1 3911 4003 698177367 698177274 1.170000e-30 145.0
32 TraesCS4D01G364500 chr5A 95.506 89 4 0 3819 3907 698177492 698177580 4.200000e-30 143.0
33 TraesCS4D01G364500 chr5A 98.667 75 1 0 3777 3851 698177726 698177652 2.530000e-27 134.0
34 TraesCS4D01G364500 chrUn 96.129 1421 49 5 2493 3908 343816555 343817974 0.000000e+00 2314.0
35 TraesCS4D01G364500 chrUn 84.304 395 46 7 932 1314 324637537 324637147 4.920000e-99 372.0
36 TraesCS4D01G364500 chrUn 86.977 215 22 2 932 1140 402488104 402487890 1.870000e-58 237.0
37 TraesCS4D01G364500 chrUn 96.000 125 2 3 3905 4027 343818031 343818154 2.460000e-47 200.0
38 TraesCS4D01G364500 chr1D 100.000 107 0 0 1581 1687 11489778 11489672 8.830000e-47 198.0
39 TraesCS4D01G364500 chr1A 96.639 119 4 0 1581 1699 24363120 24363238 8.830000e-47 198.0
40 TraesCS4D01G364500 chr1A 95.798 119 4 1 1581 1699 387511461 387511344 1.480000e-44 191.0
41 TraesCS4D01G364500 chr6D 98.198 111 2 0 1581 1691 457694097 457693987 1.140000e-45 195.0
42 TraesCS4D01G364500 chr2D 96.552 116 4 0 1581 1696 313224905 313224790 4.110000e-45 193.0
43 TraesCS4D01G364500 chr7B 96.522 115 4 0 1581 1695 380869621 380869735 1.480000e-44 191.0
44 TraesCS4D01G364500 chr7B 94.215 121 7 0 1581 1701 32332365 32332245 6.880000e-43 185.0
45 TraesCS4D01G364500 chr7D 93.701 127 5 3 1566 1689 545096040 545095914 1.910000e-43 187.0
46 TraesCS4D01G364500 chr6A 93.651 126 6 1 1581 1704 157967254 157967129 1.910000e-43 187.0


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 TraesCS4D01G364500 chr4D 509337928 509341956 4028 True 7441.000000 7441 100.0000 1 4029 1 chr4D.!!$R2 4028
1 TraesCS4D01G364500 chr4D 509281464 509288261 6797 True 480.733333 1077 86.7950 447 4029 6 chr4D.!!$R4 3582
2 TraesCS4D01G364500 chr4B 657514453 657518739 4286 False 975.350000 3280 94.1520 5 4027 6 chr4B.!!$F3 4022
3 TraesCS4D01G364500 chr4B 657497402 657499949 2547 False 833.775000 1964 95.0375 5 2491 4 chr4B.!!$F2 2486
4 TraesCS4D01G364500 chr4B 657526418 657529095 2677 False 579.000000 1040 85.5900 932 3809 3 chr4B.!!$F4 2877
5 TraesCS4D01G364500 chr5A 698177274 698181955 4681 True 1035.600000 3051 93.5254 5 4003 5 chr5A.!!$R4 3998
6 TraesCS4D01G364500 chr5A 698161412 698164402 2990 True 778.000000 1051 84.7230 481 3812 3 chr5A.!!$R3 3331
7 TraesCS4D01G364500 chr5A 698143644 698144576 932 True 473.000000 473 76.7680 2621 3580 1 chr5A.!!$R1 959
8 TraesCS4D01G364500 chrUn 343816555 343818154 1599 False 1257.000000 2314 96.0645 2493 4027 2 chrUn.!!$F1 1534

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
837 4742 0.036671 TGCAGTGCATGTGAGAGAGG 60.037 55.0 15.37 0.0 31.71 3.69 F
1328 5251 1.009829 GCAAGAGCCCACATCGTAAG 58.990 55.0 0.00 0.0 33.58 2.34 F
2375 6631 0.734889 CGGACCCAGATCACAATTGC 59.265 55.0 5.05 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 5729 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.30 R
2698 6975 1.457346 GCACCTGAACATCAAGAGGG 58.543 55.0 0.00 0.00 0.00 4.30 R
3865 8490 2.742053 CCCAATGACAAAGGTGACTACG 59.258 50.0 0.00 0.00 42.68 3.51 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
62 63 1.875514 CAGTGAGTCACCACCACAATG 59.124 52.381 19.71 5.14 37.76 2.82
118 119 0.107456 CACAACCAGTCTCACCTGCT 59.893 55.000 0.00 0.00 0.00 4.24
130 131 5.717178 AGTCTCACCTGCTATGAAGAACTAA 59.283 40.000 0.00 0.00 0.00 2.24
216 411 0.622665 GAGGATGGGGGATATGCCAG 59.377 60.000 15.93 0.00 38.95 4.85
397 764 1.125093 TTTGGGGCGAAGAGTCCTCA 61.125 55.000 0.00 0.00 46.10 3.86
451 819 4.141413 GCCCATGATATAGTATGGATGCCA 60.141 45.833 15.98 0.00 45.32 4.92
518 898 6.125589 AGTATTGGCATGGTTTCCATTTTT 57.874 33.333 0.00 0.00 42.23 1.94
540 922 1.203087 TGTGTTTCTCCCTCGGACCTA 60.203 52.381 0.00 0.00 0.00 3.08
562 945 4.503741 TGTGTTAGCATCTCCTTTTTGC 57.496 40.909 0.00 0.00 36.63 3.68
837 4742 0.036671 TGCAGTGCATGTGAGAGAGG 60.037 55.000 15.37 0.00 31.71 3.69
925 4832 4.164413 TCTTCTTCCTCGACATCTCTCCTA 59.836 45.833 0.00 0.00 0.00 2.94
949 4856 2.203640 TCCTCCACGCACCAGACT 60.204 61.111 0.00 0.00 0.00 3.24
957 4864 1.079819 CGCACCAGACTACACCAGG 60.080 63.158 0.00 0.00 0.00 4.45
1204 5121 2.034066 ACCACCGCAGAACATGGG 59.966 61.111 0.00 0.00 41.42 4.00
1327 5250 3.153024 GCAAGAGCCCACATCGTAA 57.847 52.632 0.00 0.00 33.58 3.18
1328 5251 1.009829 GCAAGAGCCCACATCGTAAG 58.990 55.000 0.00 0.00 33.58 2.34
1329 5252 1.676014 GCAAGAGCCCACATCGTAAGT 60.676 52.381 0.00 0.00 34.34 2.24
1334 5257 3.631227 AGAGCCCACATCGTAAGTAGTAC 59.369 47.826 0.00 0.00 39.48 2.73
1396 5319 2.307686 TCCACGGCTTCCTCCTTAAAAT 59.692 45.455 0.00 0.00 0.00 1.82
1416 5339 9.777008 TTAAAATTCCCCACCTAATTAATGTCT 57.223 29.630 0.00 0.00 0.00 3.41
1565 5625 9.159254 TCTTTAATTCTCTATGGAGGCATAGAA 57.841 33.333 6.21 0.00 41.84 2.10
1582 5642 9.855021 AGGCATAGAATTTGTGTTTTGTATTAC 57.145 29.630 0.00 0.00 0.00 1.89
1583 5643 9.855021 GGCATAGAATTTGTGTTTTGTATTACT 57.145 29.630 0.00 0.00 0.00 2.24
1587 5647 8.706322 AGAATTTGTGTTTTGTATTACTCCCT 57.294 30.769 0.00 0.00 0.00 4.20
1588 5648 8.793592 AGAATTTGTGTTTTGTATTACTCCCTC 58.206 33.333 0.00 0.00 0.00 4.30
1589 5649 6.887626 TTTGTGTTTTGTATTACTCCCTCC 57.112 37.500 0.00 0.00 0.00 4.30
1590 5650 4.571919 TGTGTTTTGTATTACTCCCTCCG 58.428 43.478 0.00 0.00 0.00 4.63
1591 5651 4.040706 TGTGTTTTGTATTACTCCCTCCGT 59.959 41.667 0.00 0.00 0.00 4.69
1592 5652 4.999311 GTGTTTTGTATTACTCCCTCCGTT 59.001 41.667 0.00 0.00 0.00 4.44
1593 5653 5.121298 GTGTTTTGTATTACTCCCTCCGTTC 59.879 44.000 0.00 0.00 0.00 3.95
1594 5654 3.788333 TTGTATTACTCCCTCCGTTCG 57.212 47.619 0.00 0.00 0.00 3.95
1595 5655 2.026641 TGTATTACTCCCTCCGTTCGG 58.973 52.381 4.74 4.74 0.00 4.30
1596 5656 2.301346 GTATTACTCCCTCCGTTCGGA 58.699 52.381 13.34 13.34 0.00 4.55
1597 5657 1.856629 ATTACTCCCTCCGTTCGGAA 58.143 50.000 14.79 0.04 33.41 4.30
1598 5658 1.856629 TTACTCCCTCCGTTCGGAAT 58.143 50.000 14.79 2.09 33.41 3.01
1599 5659 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
1600 5660 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
1601 5661 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1602 5662 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1603 5663 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
1604 5664 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
1605 5665 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
1606 5666 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
1607 5667 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
1608 5668 3.319755 TCCGTTCGGAATTACTTGTCAC 58.680 45.455 11.66 0.00 0.00 3.67
1609 5669 2.091588 CCGTTCGGAATTACTTGTCACG 59.908 50.000 5.19 0.00 0.00 4.35
1610 5670 2.091588 CGTTCGGAATTACTTGTCACGG 59.908 50.000 0.00 0.00 0.00 4.94
1611 5671 3.319755 GTTCGGAATTACTTGTCACGGA 58.680 45.455 0.00 0.00 0.00 4.69
1612 5672 3.663995 TCGGAATTACTTGTCACGGAA 57.336 42.857 0.00 0.00 0.00 4.30
1613 5673 3.992643 TCGGAATTACTTGTCACGGAAA 58.007 40.909 0.00 0.00 0.00 3.13
1614 5674 4.571919 TCGGAATTACTTGTCACGGAAAT 58.428 39.130 0.00 0.00 0.00 2.17
1615 5675 4.390603 TCGGAATTACTTGTCACGGAAATG 59.609 41.667 0.00 0.00 0.00 2.32
1616 5676 4.436852 CGGAATTACTTGTCACGGAAATGG 60.437 45.833 0.00 0.00 0.00 3.16
1617 5677 4.698304 GGAATTACTTGTCACGGAAATGGA 59.302 41.667 0.00 0.00 0.00 3.41
1618 5678 5.357032 GGAATTACTTGTCACGGAAATGGAT 59.643 40.000 0.00 0.00 0.00 3.41
1619 5679 5.818136 ATTACTTGTCACGGAAATGGATG 57.182 39.130 0.00 0.00 0.00 3.51
1620 5680 3.140325 ACTTGTCACGGAAATGGATGT 57.860 42.857 0.00 0.00 0.00 3.06
1621 5681 4.280436 ACTTGTCACGGAAATGGATGTA 57.720 40.909 0.00 0.00 0.00 2.29
1622 5682 4.843728 ACTTGTCACGGAAATGGATGTAT 58.156 39.130 0.00 0.00 0.00 2.29
1623 5683 4.876107 ACTTGTCACGGAAATGGATGTATC 59.124 41.667 0.00 0.00 0.00 2.24
1624 5684 4.753516 TGTCACGGAAATGGATGTATCT 57.246 40.909 0.00 0.00 0.00 1.98
1625 5685 5.862678 TGTCACGGAAATGGATGTATCTA 57.137 39.130 0.00 0.00 0.00 1.98
1626 5686 5.842907 TGTCACGGAAATGGATGTATCTAG 58.157 41.667 0.00 0.00 0.00 2.43
1627 5687 5.596772 TGTCACGGAAATGGATGTATCTAGA 59.403 40.000 0.00 0.00 0.00 2.43
1628 5688 5.921408 GTCACGGAAATGGATGTATCTAGAC 59.079 44.000 0.00 0.00 0.00 2.59
1629 5689 5.596772 TCACGGAAATGGATGTATCTAGACA 59.403 40.000 0.00 0.00 0.00 3.41
1630 5690 6.267699 TCACGGAAATGGATGTATCTAGACAT 59.732 38.462 0.00 0.00 42.82 3.06
1631 5691 7.450323 TCACGGAAATGGATGTATCTAGACATA 59.550 37.037 0.00 0.00 40.18 2.29
1632 5692 8.253810 CACGGAAATGGATGTATCTAGACATAT 58.746 37.037 0.00 0.00 40.18 1.78
1633 5693 8.816894 ACGGAAATGGATGTATCTAGACATATT 58.183 33.333 0.00 0.00 40.18 1.28
1634 5694 9.658799 CGGAAATGGATGTATCTAGACATATTT 57.341 33.333 0.00 0.31 40.18 1.40
1658 5718 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
1659 5719 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
1660 5720 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
1661 5721 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
1662 5722 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
1663 5723 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
1664 5724 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
1665 5725 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
1666 5726 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
1667 5727 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
1668 5728 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
1669 5729 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
1670 5730 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
1671 5731 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
1672 5732 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
1673 5733 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
1674 5734 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
1675 5735 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
1676 5736 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
1677 5737 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
1678 5738 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
1679 5739 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
1680 5740 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
1681 5741 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
1682 5742 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
1683 5743 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
1684 5744 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
1685 5745 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
1686 5746 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
1693 5753 2.947652 CGAACGGAGGGAGTAGTTGATA 59.052 50.000 0.00 0.00 0.00 2.15
1694 5754 3.379372 CGAACGGAGGGAGTAGTTGATAA 59.621 47.826 0.00 0.00 0.00 1.75
1714 5774 8.050778 TGATAAAGAATTGTATGGGTTGTCAC 57.949 34.615 0.00 0.00 0.00 3.67
1715 5775 7.888021 TGATAAAGAATTGTATGGGTTGTCACT 59.112 33.333 0.00 0.00 0.00 3.41
1716 5776 6.575162 AAAGAATTGTATGGGTTGTCACTC 57.425 37.500 0.00 0.00 0.00 3.51
1717 5777 5.241403 AGAATTGTATGGGTTGTCACTCA 57.759 39.130 0.00 0.00 37.98 3.41
1791 5851 7.992608 ACAAGGTAATCAGTCATACATGCATAA 59.007 33.333 0.00 0.00 0.00 1.90
1853 5913 0.825010 CACAGCTGGGGCAAGACTTT 60.825 55.000 19.93 0.00 41.70 2.66
1857 5917 2.424956 CAGCTGGGGCAAGACTTTAATC 59.575 50.000 5.57 0.00 41.70 1.75
2237 6491 3.118408 TGATCGAGATCGGGTCCAAAAAT 60.118 43.478 8.37 0.00 40.63 1.82
2253 6507 7.042119 GGTCCAAAAATGAACAAAACCATACAG 60.042 37.037 0.00 0.00 0.00 2.74
2318 6572 7.328737 TCAGGAAATTGCCTACTTAGTTACTC 58.671 38.462 4.05 0.00 36.22 2.59
2375 6631 0.734889 CGGACCCAGATCACAATTGC 59.265 55.000 5.05 0.00 0.00 3.56
2379 6635 2.681848 GACCCAGATCACAATTGCTGAG 59.318 50.000 5.05 0.00 0.00 3.35
2457 6723 8.009409 CACGCATGTACATAATACACCTAATTG 58.991 37.037 8.32 0.00 0.00 2.32
2574 6849 6.942576 AGAATAGTTACAATCAAGTGCACCTT 59.057 34.615 14.63 4.39 0.00 3.50
2780 7065 6.430616 TGAAGCAATCATGACTATTGACACAA 59.569 34.615 10.95 0.00 36.61 3.33
3010 7301 6.295349 CGCCCTATGATCCTAGTAAACTTCAT 60.295 42.308 4.57 1.79 0.00 2.57
3013 7304 8.875168 CCCTATGATCCTAGTAAACTTCATCTT 58.125 37.037 4.57 0.00 0.00 2.40
3083 7374 9.479549 ACATATTTACTTTTGATTGATCCACCT 57.520 29.630 0.00 0.00 0.00 4.00
3125 7419 8.314143 TCAAAGTAAAATAAGTCGGTTAGTGG 57.686 34.615 0.00 0.00 0.00 4.00
3381 7683 6.932400 TGTAACCAGTTGAATTAAGTCATCGT 59.068 34.615 6.42 0.00 0.00 3.73
3410 7713 8.398665 ACTCAAAATTAAATACGGATGAGCTTC 58.601 33.333 0.00 0.00 37.22 3.86
3691 8004 2.514205 AGTTGCATGGAAAACTGTGC 57.486 45.000 0.00 0.00 35.34 4.57
3809 8389 6.909550 AGTGATCCTTCATCTATGAGGTAC 57.090 41.667 1.96 0.00 38.19 3.34
3865 8490 2.741517 TGTGTATGTGTGTGTGCATAGC 59.258 45.455 0.00 0.00 0.00 2.97
3868 8493 2.378445 ATGTGTGTGTGCATAGCGTA 57.622 45.000 0.00 0.00 0.00 4.42
3892 8682 5.193728 AGTCACCTTTGTCATTGGGGTATAT 59.806 40.000 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.308047 TCCGATCGGATTTGGCATTG 58.692 50.000 32.59 2.86 39.76 2.82
1 2 3.798794 TCCGATCGGATTTGGCATT 57.201 47.368 32.59 0.00 39.76 3.56
38 39 1.956170 GGTGGTGACTCACTGTGCG 60.956 63.158 9.08 0.00 37.75 5.34
118 119 4.708177 GGGAGCATGCTTAGTTCTTCATA 58.292 43.478 23.61 0.00 0.00 2.15
130 131 4.039092 AGCAACCGGGAGCATGCT 62.039 61.111 22.92 22.92 42.74 3.79
327 527 3.711059 CTCCAGAGGTGCCCATGCC 62.711 68.421 0.00 0.00 36.33 4.40
328 528 2.124403 CTCCAGAGGTGCCCATGC 60.124 66.667 0.00 0.00 38.26 4.06
369 736 0.178987 TTCGCCCCAAAGCTTAACCA 60.179 50.000 0.00 0.00 0.00 3.67
380 747 2.119611 TGAGGACTCTTCGCCCCA 59.880 61.111 0.56 0.00 0.00 4.96
385 752 1.889829 AGAACCAGTGAGGACTCTTCG 59.110 52.381 0.56 0.00 41.22 3.79
397 764 8.747538 AACTAAACTGTAAAATGAGAACCAGT 57.252 30.769 0.00 0.00 34.82 4.00
518 898 1.202722 GGTCCGAGGGAGAAACACAAA 60.203 52.381 0.00 0.00 29.39 2.83
527 907 1.486211 AACACATAGGTCCGAGGGAG 58.514 55.000 0.00 0.00 29.39 4.30
540 922 5.064441 GCAAAAAGGAGATGCTAACACAT 57.936 39.130 0.00 0.00 37.12 3.21
837 4742 4.522971 GCTAGGGCTGTACTGTGC 57.477 61.111 1.46 0.05 35.22 4.57
1092 5006 1.664965 GAAGAACTGGTGCTCGCGT 60.665 57.895 5.77 0.00 0.00 6.01
1204 5121 3.319755 CTGTTTCATGAAATGGTGTGGC 58.680 45.455 23.05 8.87 46.73 5.01
1334 5257 9.593134 AGAGATGAAACAATTAAGCAGTACTAG 57.407 33.333 0.00 0.00 0.00 2.57
1396 5319 7.947782 AGATAGACATTAATTAGGTGGGGAA 57.052 36.000 5.32 0.00 0.00 3.97
1565 5625 6.150474 CGGAGGGAGTAATACAAAACACAAAT 59.850 38.462 0.00 0.00 0.00 2.32
1582 5642 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
1583 5643 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
1584 5644 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
1585 5645 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
1586 5646 3.367025 GTGACAAGTAATTCCGAACGGAG 59.633 47.826 15.34 5.60 46.06 4.63
1587 5647 3.319755 GTGACAAGTAATTCCGAACGGA 58.680 45.455 12.04 12.04 43.52 4.69
1588 5648 2.091588 CGTGACAAGTAATTCCGAACGG 59.908 50.000 6.94 6.94 0.00 4.44
1589 5649 2.091588 CCGTGACAAGTAATTCCGAACG 59.908 50.000 0.00 0.00 0.00 3.95
1590 5650 3.319755 TCCGTGACAAGTAATTCCGAAC 58.680 45.455 0.00 0.00 0.00 3.95
1591 5651 3.663995 TCCGTGACAAGTAATTCCGAA 57.336 42.857 0.00 0.00 0.00 4.30
1592 5652 3.663995 TTCCGTGACAAGTAATTCCGA 57.336 42.857 0.00 0.00 0.00 4.55
1593 5653 4.436852 CCATTTCCGTGACAAGTAATTCCG 60.437 45.833 0.00 0.00 0.00 4.30
1594 5654 4.698304 TCCATTTCCGTGACAAGTAATTCC 59.302 41.667 0.00 0.00 0.00 3.01
1595 5655 5.873179 TCCATTTCCGTGACAAGTAATTC 57.127 39.130 0.00 0.00 0.00 2.17
1596 5656 5.710099 ACATCCATTTCCGTGACAAGTAATT 59.290 36.000 0.00 0.00 0.00 1.40
1597 5657 5.253330 ACATCCATTTCCGTGACAAGTAAT 58.747 37.500 0.00 0.00 0.00 1.89
1598 5658 4.647611 ACATCCATTTCCGTGACAAGTAA 58.352 39.130 0.00 0.00 0.00 2.24
1599 5659 4.280436 ACATCCATTTCCGTGACAAGTA 57.720 40.909 0.00 0.00 0.00 2.24
1600 5660 3.140325 ACATCCATTTCCGTGACAAGT 57.860 42.857 0.00 0.00 0.00 3.16
1601 5661 5.118990 AGATACATCCATTTCCGTGACAAG 58.881 41.667 0.00 0.00 0.00 3.16
1602 5662 5.097742 AGATACATCCATTTCCGTGACAA 57.902 39.130 0.00 0.00 0.00 3.18
1603 5663 4.753516 AGATACATCCATTTCCGTGACA 57.246 40.909 0.00 0.00 0.00 3.58
1604 5664 5.921408 GTCTAGATACATCCATTTCCGTGAC 59.079 44.000 0.00 0.00 0.00 3.67
1605 5665 5.596772 TGTCTAGATACATCCATTTCCGTGA 59.403 40.000 0.00 0.00 0.00 4.35
1606 5666 5.842907 TGTCTAGATACATCCATTTCCGTG 58.157 41.667 0.00 0.00 0.00 4.94
1607 5667 6.672266 ATGTCTAGATACATCCATTTCCGT 57.328 37.500 0.00 0.00 35.08 4.69
1608 5668 9.658799 AAATATGTCTAGATACATCCATTTCCG 57.341 33.333 0.00 0.00 40.52 4.30
1632 5692 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
1633 5693 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
1634 5694 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
1635 5695 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
1636 5696 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
1637 5697 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
1638 5698 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
1639 5699 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
1640 5700 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
1641 5701 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
1642 5702 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
1643 5703 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
1644 5704 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
1645 5705 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
1646 5706 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
1647 5707 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
1648 5708 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
1649 5709 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
1650 5710 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
1651 5711 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
1652 5712 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
1653 5713 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
1654 5714 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
1655 5715 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
1656 5716 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
1657 5717 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
1658 5718 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
1659 5719 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
1660 5720 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
1661 5721 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
1662 5722 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
1663 5723 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
1664 5724 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1665 5725 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1666 5726 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
1667 5727 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
1668 5728 1.341778 ACTACTCCCTCCGTTCGGAAT 60.342 52.381 14.79 2.09 33.41 3.01
1669 5729 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
1670 5730 0.038744 AACTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
1671 5731 0.172803 CAACTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30
1672 5732 1.171308 TCAACTACTCCCTCCGTTCG 58.829 55.000 0.00 0.00 0.00 3.95
1673 5733 4.996788 TTATCAACTACTCCCTCCGTTC 57.003 45.455 0.00 0.00 0.00 3.95
1674 5734 5.021458 TCTTTATCAACTACTCCCTCCGTT 58.979 41.667 0.00 0.00 0.00 4.44
1675 5735 4.607239 TCTTTATCAACTACTCCCTCCGT 58.393 43.478 0.00 0.00 0.00 4.69
1676 5736 5.593679 TTCTTTATCAACTACTCCCTCCG 57.406 43.478 0.00 0.00 0.00 4.63
1677 5737 7.339482 ACAATTCTTTATCAACTACTCCCTCC 58.661 38.462 0.00 0.00 0.00 4.30
1679 5739 9.838339 CATACAATTCTTTATCAACTACTCCCT 57.162 33.333 0.00 0.00 0.00 4.20
1680 5740 9.057089 CCATACAATTCTTTATCAACTACTCCC 57.943 37.037 0.00 0.00 0.00 4.30
1681 5741 9.057089 CCCATACAATTCTTTATCAACTACTCC 57.943 37.037 0.00 0.00 0.00 3.85
1682 5742 9.614792 ACCCATACAATTCTTTATCAACTACTC 57.385 33.333 0.00 0.00 0.00 2.59
1683 5743 9.975218 AACCCATACAATTCTTTATCAACTACT 57.025 29.630 0.00 0.00 0.00 2.57
1685 5745 9.747898 ACAACCCATACAATTCTTTATCAACTA 57.252 29.630 0.00 0.00 0.00 2.24
1686 5746 8.650143 ACAACCCATACAATTCTTTATCAACT 57.350 30.769 0.00 0.00 0.00 3.16
1693 5753 6.068010 TGAGTGACAACCCATACAATTCTTT 58.932 36.000 0.00 0.00 0.00 2.52
1694 5754 5.630121 TGAGTGACAACCCATACAATTCTT 58.370 37.500 0.00 0.00 0.00 2.52
1791 5851 8.550376 GTTATTGCACACAAGTCAAATTTTCAT 58.450 29.630 0.00 0.00 39.69 2.57
2112 6366 3.817647 AGACTTGCAAAACTAGCTCAAGG 59.182 43.478 12.18 0.00 38.64 3.61
2253 6507 7.890515 ACAAGGATCTTCTTTTCTTTCCATTC 58.109 34.615 0.00 0.00 0.00 2.67
2265 6519 8.568794 GCAAACTAACTAAACAAGGATCTTCTT 58.431 33.333 0.00 0.00 0.00 2.52
2318 6572 4.736793 GCCATGTTCAAAAGATTGATAGCG 59.263 41.667 0.00 0.00 44.70 4.26
2375 6631 9.678941 GATTTTTAAAAGGTGTAACTTCCTCAG 57.321 33.333 0.14 0.00 36.74 3.35
2457 6723 8.343974 TCAATTGGTCTACGAATATACGTTTC 57.656 34.615 5.42 0.00 44.14 2.78
2698 6975 1.457346 GCACCTGAACATCAAGAGGG 58.543 55.000 0.00 0.00 0.00 4.30
2780 7065 1.616921 CAGGCCCCACCATCATCTT 59.383 57.895 0.00 0.00 43.14 2.40
3069 7360 3.084039 GCTTCACAGGTGGATCAATCAA 58.916 45.455 0.00 0.00 0.00 2.57
3083 7374 4.398988 ACTTTGATGAACAACTGCTTCACA 59.601 37.500 0.00 0.00 38.29 3.58
3125 7419 4.516698 ACATAATGGCTCCAATCGATCAAC 59.483 41.667 0.00 0.00 0.00 3.18
3238 7534 9.606631 AAAGTAGCTATCCTCTTGAAATTACAG 57.393 33.333 0.00 0.00 0.00 2.74
3381 7683 7.254319 GCTCATCCGTATTTAATTTTGAGTCGA 60.254 37.037 0.00 0.00 33.57 4.20
3563 7876 8.677300 CACAGCTTTTTAATATACATGTGGTCT 58.323 33.333 9.11 0.00 33.60 3.85
3564 7877 7.432252 GCACAGCTTTTTAATATACATGTGGTC 59.568 37.037 9.11 0.00 36.81 4.02
3691 8004 7.226128 ACAGCTGTAATGATGTCTTGATATGTG 59.774 37.037 20.16 0.00 30.00 3.21
3809 8389 9.205916 CAAACGATGGACAAACTAATTAATACG 57.794 33.333 0.00 0.00 0.00 3.06
3865 8490 2.742053 CCCAATGACAAAGGTGACTACG 59.258 50.000 0.00 0.00 42.68 3.51
3892 8682 5.070446 AGACATTCGTATCCCAAGCTTCATA 59.930 40.000 0.00 0.00 0.00 2.15
3997 8850 6.340522 TCTAATCACTTTCATCGAGCATTGA 58.659 36.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.