Multiple sequence alignment - TraesCS1D01G167600

Loading Multiple Alignment...

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 TraesCS1D01G167600 chr1D 100.000 3905 0 0 1 3905 239559827 239555923 0.000000e+00 7212.0
1 TraesCS1D01G167600 chr1D 80.508 118 22 1 225 342 351254847 351254731 5.370000e-14 89.8
2 TraesCS1D01G167600 chr1B 92.501 3334 163 47 122 3400 334546509 334549810 0.000000e+00 4691.0
3 TraesCS1D01G167600 chr1B 89.005 191 6 4 3702 3887 334549809 334549989 5.080000e-54 222.0
4 TraesCS1D01G167600 chr1B 81.633 98 14 4 8 103 401279666 401279761 1.160000e-10 78.7
5 TraesCS1D01G167600 chr1B 81.633 98 14 4 8 103 595741733 595741828 1.160000e-10 78.7
6 TraesCS1D01G167600 chr1A 94.608 2207 88 17 1493 3676 303729515 303727317 0.000000e+00 3387.0
7 TraesCS1D01G167600 chr1A 94.841 1260 44 13 218 1457 303730771 303729513 0.000000e+00 1947.0
8 TraesCS1D01G167600 chr1A 90.865 208 9 5 3698 3905 303727320 303727123 1.790000e-68 270.0
9 TraesCS1D01G167600 chr1A 80.508 118 22 1 225 342 452043797 452043681 5.370000e-14 89.8
10 TraesCS1D01G167600 chr6D 89.011 91 10 0 12 102 100540809 100540719 3.190000e-21 113.0
11 TraesCS1D01G167600 chr6D 80.672 119 21 2 225 342 386931333 386931450 1.490000e-14 91.6
12 TraesCS1D01G167600 chr7D 82.308 130 21 2 227 355 63561439 63561567 1.150000e-20 111.0
13 TraesCS1D01G167600 chr7A 83.200 125 17 4 220 342 579808517 579808395 1.150000e-20 111.0
14 TraesCS1D01G167600 chr4D 84.946 93 12 2 18 109 117428327 117428236 4.150000e-15 93.5
15 TraesCS1D01G167600 chr4B 80.159 126 20 5 220 342 22464620 22464743 5.370000e-14 89.8
16 TraesCS1D01G167600 chr4B 86.047 86 9 3 18 103 653937351 653937269 5.370000e-14 89.8
17 TraesCS1D01G167600 chr5D 81.905 105 18 1 239 342 255691182 255691078 1.930000e-13 87.9
18 TraesCS1D01G167600 chr3B 82.474 97 14 3 8 103 440032282 440032188 8.990000e-12 82.4
19 TraesCS1D01G167600 chr6B 81.633 98 14 4 8 103 534584652 534584557 1.160000e-10 78.7
20 TraesCS1D01G167600 chr5B 81.443 97 16 2 8 103 108898454 108898359 1.160000e-10 78.7
21 TraesCS1D01G167600 chr5B 81.443 97 16 2 8 103 648808396 648808491 1.160000e-10 78.7


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 TraesCS1D01G167600 chr1D 239555923 239559827 3904 True 7212.0 7212 100.000 1 3905 1 chr1D.!!$R1 3904
1 TraesCS1D01G167600 chr1B 334546509 334549989 3480 False 2456.5 4691 90.753 122 3887 2 chr1B.!!$F3 3765
2 TraesCS1D01G167600 chr1A 303727123 303730771 3648 True 1868.0 3387 93.438 218 3905 3 chr1A.!!$R2 3687

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
105 106 0.041238 TGGGACAGAGGGAGTAGGTG 59.959 60.0 0.0 0.0 0.0 4.00 F
106 107 0.335361 GGGACAGAGGGAGTAGGTGA 59.665 60.0 0.0 0.0 0.0 4.02 F
739 763 0.468648 CCGACCCTTATCACTTCCCC 59.531 60.0 0.0 0.0 0.0 4.81 F
1483 1511 0.603065 GGGGCAAGGCAAAGTTACAG 59.397 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1731 0.110688 CGCCACGCATATTCCAATCG 60.111 55.000 0.00 0.0 0.00 3.34 R
1824 1887 2.386864 TCACAAGGAGACATGGGGG 58.613 57.895 0.00 0.0 32.04 5.40 R
1971 2037 2.476051 CATATTCCGATGCCGCGC 59.524 61.111 0.00 0.0 0.00 6.86 R
3318 3400 0.179045 GCCACTCCAGTGTGTCAGTT 60.179 55.000 5.99 0.0 44.21 3.16 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
24 25 5.878406 AGCATTGCTCAATACTACTACCT 57.122 39.130 5.03 0.00 30.62 3.08
25 26 5.848406 AGCATTGCTCAATACTACTACCTC 58.152 41.667 5.03 0.00 30.62 3.85
26 27 4.991687 GCATTGCTCAATACTACTACCTCC 59.008 45.833 0.16 0.00 0.00 4.30
27 28 5.453339 GCATTGCTCAATACTACTACCTCCA 60.453 44.000 0.16 0.00 0.00 3.86
28 29 6.742644 GCATTGCTCAATACTACTACCTCCAT 60.743 42.308 0.16 0.00 0.00 3.41
29 30 6.406692 TTGCTCAATACTACTACCTCCATC 57.593 41.667 0.00 0.00 0.00 3.51
30 31 5.454966 TGCTCAATACTACTACCTCCATCA 58.545 41.667 0.00 0.00 0.00 3.07
31 32 5.302059 TGCTCAATACTACTACCTCCATCAC 59.698 44.000 0.00 0.00 0.00 3.06
32 33 5.302059 GCTCAATACTACTACCTCCATCACA 59.698 44.000 0.00 0.00 0.00 3.58
33 34 6.515862 GCTCAATACTACTACCTCCATCACAG 60.516 46.154 0.00 0.00 0.00 3.66
34 35 6.669631 TCAATACTACTACCTCCATCACAGA 58.330 40.000 0.00 0.00 0.00 3.41
35 36 7.123383 TCAATACTACTACCTCCATCACAGAA 58.877 38.462 0.00 0.00 0.00 3.02
36 37 7.785028 TCAATACTACTACCTCCATCACAGAAT 59.215 37.037 0.00 0.00 0.00 2.40
37 38 9.078990 CAATACTACTACCTCCATCACAGAATA 57.921 37.037 0.00 0.00 0.00 1.75
38 39 9.830186 AATACTACTACCTCCATCACAGAATAT 57.170 33.333 0.00 0.00 0.00 1.28
41 42 9.303116 ACTACTACCTCCATCACAGAATATAAG 57.697 37.037 0.00 0.00 0.00 1.73
42 43 9.521841 CTACTACCTCCATCACAGAATATAAGA 57.478 37.037 0.00 0.00 0.00 2.10
43 44 8.184304 ACTACCTCCATCACAGAATATAAGAC 57.816 38.462 0.00 0.00 0.00 3.01
44 45 6.090483 ACCTCCATCACAGAATATAAGACG 57.910 41.667 0.00 0.00 0.00 4.18
45 46 5.598830 ACCTCCATCACAGAATATAAGACGT 59.401 40.000 0.00 0.00 0.00 4.34
46 47 6.098409 ACCTCCATCACAGAATATAAGACGTT 59.902 38.462 0.00 0.00 0.00 3.99
47 48 6.986817 CCTCCATCACAGAATATAAGACGTTT 59.013 38.462 0.00 0.00 0.00 3.60
48 49 7.495934 CCTCCATCACAGAATATAAGACGTTTT 59.504 37.037 0.00 0.00 0.00 2.43
49 50 8.786826 TCCATCACAGAATATAAGACGTTTTT 57.213 30.769 0.00 0.00 0.00 1.94
50 51 9.878667 TCCATCACAGAATATAAGACGTTTTTA 57.121 29.630 0.00 0.00 0.00 1.52
51 52 9.916397 CCATCACAGAATATAAGACGTTTTTAC 57.084 33.333 0.00 0.00 0.00 2.01
55 56 9.262472 CACAGAATATAAGACGTTTTTACAAGC 57.738 33.333 0.00 0.00 0.00 4.01
56 57 9.216117 ACAGAATATAAGACGTTTTTACAAGCT 57.784 29.630 0.00 0.00 0.00 3.74
65 66 9.662947 AAGACGTTTTTACAAGCTAATATAGGT 57.337 29.630 0.00 0.00 38.32 3.08
66 67 9.662947 AGACGTTTTTACAAGCTAATATAGGTT 57.337 29.630 0.00 0.00 46.49 3.50
76 77 9.223099 ACAAGCTAATATAGGTTACAAAAACGT 57.777 29.630 1.89 0.00 43.99 3.99
77 78 9.698617 CAAGCTAATATAGGTTACAAAAACGTC 57.301 33.333 1.89 0.00 43.99 4.34
78 79 8.429493 AGCTAATATAGGTTACAAAAACGTCC 57.571 34.615 0.00 0.00 31.36 4.79
79 80 8.262933 AGCTAATATAGGTTACAAAAACGTCCT 58.737 33.333 0.00 0.00 31.36 3.85
80 81 9.533253 GCTAATATAGGTTACAAAAACGTCCTA 57.467 33.333 0.00 0.00 33.10 2.94
88 89 9.333724 AGGTTACAAAAACGTCCTATATTATGG 57.666 33.333 0.00 0.00 0.00 2.74
89 90 8.562052 GGTTACAAAAACGTCCTATATTATGGG 58.438 37.037 0.00 0.00 0.00 4.00
90 91 9.328845 GTTACAAAAACGTCCTATATTATGGGA 57.671 33.333 4.74 4.74 37.61 4.37
104 105 2.499566 TGGGACAGAGGGAGTAGGT 58.500 57.895 0.00 0.00 0.00 3.08
105 106 0.041238 TGGGACAGAGGGAGTAGGTG 59.959 60.000 0.00 0.00 0.00 4.00
106 107 0.335361 GGGACAGAGGGAGTAGGTGA 59.665 60.000 0.00 0.00 0.00 4.02
107 108 1.062810 GGGACAGAGGGAGTAGGTGAT 60.063 57.143 0.00 0.00 0.00 3.06
108 109 2.177233 GGGACAGAGGGAGTAGGTGATA 59.823 54.545 0.00 0.00 0.00 2.15
109 110 3.224269 GGACAGAGGGAGTAGGTGATAC 58.776 54.545 0.00 0.00 34.30 2.24
111 112 4.104420 GGACAGAGGGAGTAGGTGATACTA 59.896 50.000 0.00 0.00 45.06 1.82
112 113 5.051409 ACAGAGGGAGTAGGTGATACTAC 57.949 47.826 0.00 0.00 45.06 2.73
210 215 8.702163 AAATGTAGACAAACTTTTTGGAACAG 57.298 30.769 3.82 0.00 42.39 3.16
211 216 7.639113 ATGTAGACAAACTTTTTGGAACAGA 57.361 32.000 3.82 0.00 42.39 3.41
213 218 6.882140 TGTAGACAAACTTTTTGGAACAGAGA 59.118 34.615 3.82 0.00 42.39 3.10
214 219 7.556275 TGTAGACAAACTTTTTGGAACAGAGAT 59.444 33.333 3.82 0.00 42.39 2.75
216 221 8.519799 AGACAAACTTTTTGGAACAGAGATAA 57.480 30.769 3.82 0.00 42.39 1.75
272 277 8.657074 TTTTGATAAGGATTACATACGGACTG 57.343 34.615 0.00 0.00 30.46 3.51
289 294 3.364366 GGACTGAAATGAGTGAACAAGCG 60.364 47.826 0.00 0.00 0.00 4.68
320 325 5.168569 ACACGTCTATGTACACCAGATTTG 58.831 41.667 11.17 12.47 0.00 2.32
400 405 7.928103 TGTTTAGAGGAGATCGTTATGTAGAC 58.072 38.462 0.00 0.00 0.00 2.59
450 456 5.587388 AGCATCATATGACCCAAAAACAG 57.413 39.130 7.78 0.00 0.00 3.16
451 457 5.018809 AGCATCATATGACCCAAAAACAGT 58.981 37.500 7.78 0.00 0.00 3.55
457 463 1.328279 GACCCAAAAACAGTCCCAGG 58.672 55.000 0.00 0.00 0.00 4.45
477 483 3.823304 AGGAAATCTTGAACTTGTGCTCC 59.177 43.478 0.00 0.00 0.00 4.70
486 492 2.262423 ACTTGTGCTCCTTTGACTCC 57.738 50.000 0.00 0.00 0.00 3.85
489 495 0.756294 TGTGCTCCTTTGACTCCGAA 59.244 50.000 0.00 0.00 0.00 4.30
490 496 1.347707 TGTGCTCCTTTGACTCCGAAT 59.652 47.619 0.00 0.00 0.00 3.34
491 497 1.734465 GTGCTCCTTTGACTCCGAATG 59.266 52.381 0.00 0.00 0.00 2.67
534 543 1.929836 GAGCACTACTGCACTGCATAC 59.070 52.381 3.64 0.00 46.97 2.39
546 555 1.139058 ACTGCATACGTCCTGGAATCC 59.861 52.381 0.00 0.00 0.00 3.01
562 571 3.443045 CCGGGCAAGATGCACCAC 61.443 66.667 4.57 0.00 45.87 4.16
563 572 2.360350 CGGGCAAGATGCACCACT 60.360 61.111 4.57 0.00 45.87 4.00
564 573 2.693762 CGGGCAAGATGCACCACTG 61.694 63.158 4.57 0.00 45.87 3.66
643 660 5.009210 AGCTAGGTTCTACTAAATCAGAGCG 59.991 44.000 0.00 0.00 30.15 5.03
667 691 1.269988 CCGGATACAGCTCATCCACAG 60.270 57.143 19.37 7.54 41.87 3.66
711 735 2.303175 GGCTACAGTCAAACCAACCAA 58.697 47.619 0.00 0.00 0.00 3.67
715 739 0.738389 CAGTCAAACCAACCAAGCGT 59.262 50.000 0.00 0.00 0.00 5.07
739 763 0.468648 CCGACCCTTATCACTTCCCC 59.531 60.000 0.00 0.00 0.00 4.81
780 804 4.805231 CCACCCGTCATACGCGCA 62.805 66.667 5.73 0.00 40.91 6.09
1471 1499 1.208165 AAGGTCTAGGTGGGGGCAAG 61.208 60.000 0.00 0.00 0.00 4.01
1478 1506 2.524148 GTGGGGGCAAGGCAAAGT 60.524 61.111 0.00 0.00 0.00 2.66
1483 1511 0.603065 GGGGCAAGGCAAAGTTACAG 59.397 55.000 0.00 0.00 0.00 2.74
1485 1513 0.603065 GGCAAGGCAAAGTTACAGGG 59.397 55.000 0.00 0.00 0.00 4.45
1493 1521 3.927163 AAGTTACAGGGCGACGCGG 62.927 63.158 14.61 8.46 0.00 6.46
1508 1536 1.000955 ACGCGGTTCAAGTCAAGATCT 59.999 47.619 12.47 0.00 0.00 2.75
1550 1578 9.527157 TGTGAGGGAAAGATCATAATTTTGTTA 57.473 29.630 0.00 0.00 0.00 2.41
1588 1618 3.557577 TTTTGATGTTGGAGATGTGCG 57.442 42.857 0.00 0.00 0.00 5.34
1608 1638 2.356125 CGATGTTCCTCTCCCCATTGTT 60.356 50.000 0.00 0.00 0.00 2.83
1639 1692 7.855784 AAAAGTTTCAGGAGGAACCATAATT 57.144 32.000 0.00 0.00 42.04 1.40
1677 1730 2.107950 TACGTGGAGAATTTGGCCTG 57.892 50.000 3.32 0.00 0.00 4.85
1678 1731 1.244019 ACGTGGAGAATTTGGCCTGC 61.244 55.000 3.32 0.00 0.00 4.85
1729 1785 6.427547 ACGAGTGGCTAGTAGTATCTGATAAC 59.572 42.308 0.00 0.00 0.00 1.89
1824 1887 1.073216 CCTATGCCGATCGCGACATC 61.073 60.000 12.93 5.04 39.86 3.06
1915 1981 3.555547 GTGGTTCAGAAATTGCGCTTTTT 59.444 39.130 9.73 8.49 0.00 1.94
1971 2037 9.533253 AACTTTTTGTTAAGGATCTTTGATGTG 57.467 29.630 0.00 0.00 37.07 3.21
1974 2040 3.126858 TGTTAAGGATCTTTGATGTGCGC 59.873 43.478 0.00 0.00 0.00 6.09
1995 2061 1.739067 GCATCGGAATATGCCTACCC 58.261 55.000 0.00 0.00 45.31 3.69
2018 2084 6.294286 CCCTTTTGTTTTTGGCGTTAGATCTA 60.294 38.462 0.00 0.00 0.00 1.98
2049 2115 9.755122 ATTTTTCTTGCCCTCTACTAATAAACT 57.245 29.630 0.00 0.00 0.00 2.66
2053 2119 8.548880 TCTTGCCCTCTACTAATAAACTATGT 57.451 34.615 0.00 0.00 0.00 2.29
2054 2120 9.650714 TCTTGCCCTCTACTAATAAACTATGTA 57.349 33.333 0.00 0.00 0.00 2.29
2096 2162 1.738365 GCTGATGCGTGTGACTGATCT 60.738 52.381 0.00 0.00 0.00 2.75
2142 2208 2.202797 GAGATCTTGAGCGGCGCA 60.203 61.111 35.02 13.72 0.00 6.09
2343 2409 4.719369 GACTTCCTGTCGGCGCGT 62.719 66.667 8.43 0.00 35.81 6.01
2670 2736 2.285083 CTCTCTTCCTCGTCGTCAGAT 58.715 52.381 0.00 0.00 0.00 2.90
2754 2820 4.626081 GAGCCCGTGGTGTGCAGT 62.626 66.667 0.00 0.00 0.00 4.40
2862 2928 4.570663 CTCGCCGGGATCGTCACC 62.571 72.222 2.18 0.00 33.95 4.02
2877 2943 1.519455 CACCTTCGCCGACATCCTC 60.519 63.158 0.00 0.00 0.00 3.71
2886 2952 0.324943 CCGACATCCTCAGGGTGTTT 59.675 55.000 12.14 0.00 30.85 2.83
3074 3142 2.034053 TGAAACATGTTCCCGTTTGCTC 59.966 45.455 12.39 2.90 35.53 4.26
3079 3147 1.021202 TGTTCCCGTTTGCTCTGTTG 58.979 50.000 0.00 0.00 0.00 3.33
3081 3149 1.002792 GTTCCCGTTTGCTCTGTTGTC 60.003 52.381 0.00 0.00 0.00 3.18
3085 3153 2.099098 CCCGTTTGCTCTGTTGTCTTTT 59.901 45.455 0.00 0.00 0.00 2.27
3086 3154 3.428862 CCCGTTTGCTCTGTTGTCTTTTT 60.429 43.478 0.00 0.00 0.00 1.94
3118 3186 3.839051 GGTGCTGAACCTGAAGATTTC 57.161 47.619 0.00 0.00 46.55 2.17
3188 3266 3.319137 TGCTGTTTCTAAGCTGACGAT 57.681 42.857 0.00 0.00 41.42 3.73
3318 3400 5.661056 ACTCCGATAAACTGAACATCTGA 57.339 39.130 0.00 0.00 0.00 3.27
3354 3437 5.468540 AGTGGCATCTATTTACTGCGATA 57.531 39.130 0.00 0.00 36.76 2.92
3432 3515 1.738099 GTGCCGTGACCTACAGCTG 60.738 63.158 13.48 13.48 0.00 4.24
3466 3549 2.264455 AGCCTCAGAGATGGAAGTGTT 58.736 47.619 0.00 0.00 0.00 3.32
3474 3557 6.814043 TCAGAGATGGAAGTGTTGATAGATG 58.186 40.000 0.00 0.00 0.00 2.90
3578 3661 1.202855 AGTCTCATTGTGCTTGTGGCT 60.203 47.619 0.00 0.00 42.39 4.75
3590 3673 2.935201 GCTTGTGGCTACTGAATCTCTG 59.065 50.000 0.64 0.00 38.06 3.35
3664 3747 1.067060 TGTCGGATAACTCTGGCGATG 59.933 52.381 0.00 0.00 34.96 3.84
3668 3751 2.748605 GGATAACTCTGGCGATGACAG 58.251 52.381 0.00 0.00 40.64 3.51
3672 3755 1.217511 CTCTGGCGATGACAGCAGT 59.782 57.895 0.00 0.00 38.81 4.40
3673 3756 0.457443 CTCTGGCGATGACAGCAGTA 59.543 55.000 0.00 0.00 38.81 2.74
3674 3757 0.457443 TCTGGCGATGACAGCAGTAG 59.543 55.000 0.00 0.00 38.81 2.57
3675 3758 0.457443 CTGGCGATGACAGCAGTAGA 59.543 55.000 0.00 0.00 29.34 2.59
3676 3759 0.173481 TGGCGATGACAGCAGTAGAC 59.827 55.000 0.00 0.00 36.08 2.59
3677 3760 0.528684 GGCGATGACAGCAGTAGACC 60.529 60.000 0.00 0.00 36.08 3.85
3678 3761 0.867753 GCGATGACAGCAGTAGACCG 60.868 60.000 0.00 0.00 34.19 4.79
3679 3762 0.248661 CGATGACAGCAGTAGACCGG 60.249 60.000 0.00 0.00 0.00 5.28
3680 3763 0.818296 GATGACAGCAGTAGACCGGT 59.182 55.000 6.92 6.92 0.00 5.28
3681 3764 0.532573 ATGACAGCAGTAGACCGGTG 59.467 55.000 14.63 0.00 36.70 4.94
3682 3765 0.826256 TGACAGCAGTAGACCGGTGT 60.826 55.000 14.63 12.06 45.91 4.16
3683 3766 0.388649 GACAGCAGTAGACCGGTGTG 60.389 60.000 14.63 5.00 43.46 3.82
3684 3767 1.113517 ACAGCAGTAGACCGGTGTGT 61.114 55.000 14.63 0.00 41.96 3.72
3685 3768 0.667487 CAGCAGTAGACCGGTGTGTG 60.667 60.000 14.63 11.97 0.00 3.82
3686 3769 1.113517 AGCAGTAGACCGGTGTGTGT 61.114 55.000 14.63 0.00 0.00 3.72
3687 3770 0.944311 GCAGTAGACCGGTGTGTGTG 60.944 60.000 14.63 8.72 0.00 3.82
3688 3771 0.671796 CAGTAGACCGGTGTGTGTGA 59.328 55.000 14.63 0.00 0.00 3.58
3689 3772 1.272490 CAGTAGACCGGTGTGTGTGAT 59.728 52.381 14.63 0.00 0.00 3.06
3690 3773 2.490509 CAGTAGACCGGTGTGTGTGATA 59.509 50.000 14.63 0.00 0.00 2.15
3691 3774 2.753452 AGTAGACCGGTGTGTGTGATAG 59.247 50.000 14.63 0.00 0.00 2.08
3692 3775 0.895530 AGACCGGTGTGTGTGATAGG 59.104 55.000 14.63 0.00 0.00 2.57
3693 3776 0.108329 GACCGGTGTGTGTGATAGGG 60.108 60.000 14.63 0.00 0.00 3.53
3694 3777 1.220749 CCGGTGTGTGTGATAGGGG 59.779 63.158 0.00 0.00 0.00 4.79
3695 3778 1.449601 CGGTGTGTGTGATAGGGGC 60.450 63.158 0.00 0.00 0.00 5.80
3696 3779 1.077716 GGTGTGTGTGATAGGGGCC 60.078 63.158 0.00 0.00 0.00 5.80
3821 3909 1.001760 GAGGCTCTACCCAGTCCCA 59.998 63.158 7.40 0.00 40.58 4.37
3822 3910 1.002274 AGGCTCTACCCAGTCCCAG 59.998 63.158 0.00 0.00 40.58 4.45
3823 3911 1.001760 GGCTCTACCCAGTCCCAGA 59.998 63.158 0.00 0.00 0.00 3.86
3824 3912 1.331399 GGCTCTACCCAGTCCCAGAC 61.331 65.000 0.00 0.00 0.00 3.51
3825 3913 0.324830 GCTCTACCCAGTCCCAGACT 60.325 60.000 0.00 0.00 44.44 3.24
3826 3914 1.770294 CTCTACCCAGTCCCAGACTC 58.230 60.000 0.00 0.00 41.37 3.36
3827 3915 0.335361 TCTACCCAGTCCCAGACTCC 59.665 60.000 0.00 0.00 41.37 3.85
3828 3916 0.688087 CTACCCAGTCCCAGACTCCC 60.688 65.000 0.00 0.00 41.37 4.30
3850 3938 1.876156 GTGCTTCACCTGTTCCTTCTG 59.124 52.381 0.00 0.00 0.00 3.02
3856 3944 3.305720 TCACCTGTTCCTTCTGTACTGT 58.694 45.455 0.00 0.00 0.00 3.55
3857 3945 4.476297 TCACCTGTTCCTTCTGTACTGTA 58.524 43.478 0.00 0.00 0.00 2.74
3888 3976 1.839424 AAGGATTTGGCCTGCACTAC 58.161 50.000 3.32 0.00 38.58 2.73
3893 3981 3.567579 TTGGCCTGCACTACCCAGC 62.568 63.158 3.32 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.310113 GGAGGTAGTAGTATTGAGCAATGCTAT 60.310 40.741 19.17 1.06 44.01 2.97
1 2 6.015350 GGAGGTAGTAGTATTGAGCAATGCTA 60.015 42.308 8.12 14.37 42.40 3.49
2 3 5.221541 GGAGGTAGTAGTATTGAGCAATGCT 60.222 44.000 7.79 7.79 44.15 3.79
3 4 4.991687 GGAGGTAGTAGTATTGAGCAATGC 59.008 45.833 0.00 0.00 34.26 3.56
4 5 6.161855 TGGAGGTAGTAGTATTGAGCAATG 57.838 41.667 5.99 0.00 32.50 2.82
5 6 6.554982 TGATGGAGGTAGTAGTATTGAGCAAT 59.445 38.462 0.97 0.97 34.93 3.56
6 7 5.897250 TGATGGAGGTAGTAGTATTGAGCAA 59.103 40.000 0.00 0.00 0.00 3.91
7 8 5.302059 GTGATGGAGGTAGTAGTATTGAGCA 59.698 44.000 0.00 0.00 0.00 4.26
8 9 5.302059 TGTGATGGAGGTAGTAGTATTGAGC 59.698 44.000 0.00 0.00 0.00 4.26
9 10 6.773200 TCTGTGATGGAGGTAGTAGTATTGAG 59.227 42.308 0.00 0.00 0.00 3.02
10 11 6.669631 TCTGTGATGGAGGTAGTAGTATTGA 58.330 40.000 0.00 0.00 0.00 2.57
11 12 6.961360 TCTGTGATGGAGGTAGTAGTATTG 57.039 41.667 0.00 0.00 0.00 1.90
12 13 9.830186 ATATTCTGTGATGGAGGTAGTAGTATT 57.170 33.333 0.00 0.00 0.00 1.89
15 16 9.303116 CTTATATTCTGTGATGGAGGTAGTAGT 57.697 37.037 0.00 0.00 0.00 2.73
16 17 9.521841 TCTTATATTCTGTGATGGAGGTAGTAG 57.478 37.037 0.00 0.00 0.00 2.57
17 18 9.298250 GTCTTATATTCTGTGATGGAGGTAGTA 57.702 37.037 0.00 0.00 0.00 1.82
18 19 7.040340 CGTCTTATATTCTGTGATGGAGGTAGT 60.040 40.741 0.00 0.00 0.00 2.73
19 20 7.040340 ACGTCTTATATTCTGTGATGGAGGTAG 60.040 40.741 0.00 0.00 0.00 3.18
20 21 6.776116 ACGTCTTATATTCTGTGATGGAGGTA 59.224 38.462 0.00 0.00 0.00 3.08
21 22 5.598830 ACGTCTTATATTCTGTGATGGAGGT 59.401 40.000 0.00 0.00 0.00 3.85
22 23 6.090483 ACGTCTTATATTCTGTGATGGAGG 57.910 41.667 0.00 0.00 0.00 4.30
23 24 8.425577 AAAACGTCTTATATTCTGTGATGGAG 57.574 34.615 0.00 0.00 0.00 3.86
24 25 8.786826 AAAAACGTCTTATATTCTGTGATGGA 57.213 30.769 0.00 0.00 0.00 3.41
25 26 9.916397 GTAAAAACGTCTTATATTCTGTGATGG 57.084 33.333 0.00 0.00 0.00 3.51
29 30 9.262472 GCTTGTAAAAACGTCTTATATTCTGTG 57.738 33.333 0.00 0.00 0.00 3.66
30 31 9.216117 AGCTTGTAAAAACGTCTTATATTCTGT 57.784 29.630 0.00 0.00 0.00 3.41
39 40 9.662947 ACCTATATTAGCTTGTAAAAACGTCTT 57.337 29.630 0.00 0.00 0.00 3.01
40 41 9.662947 AACCTATATTAGCTTGTAAAAACGTCT 57.337 29.630 0.00 0.00 0.00 4.18
50 51 9.223099 ACGTTTTTGTAACCTATATTAGCTTGT 57.777 29.630 0.00 0.00 0.00 3.16
51 52 9.698617 GACGTTTTTGTAACCTATATTAGCTTG 57.301 33.333 0.00 0.00 0.00 4.01
52 53 8.886719 GGACGTTTTTGTAACCTATATTAGCTT 58.113 33.333 0.00 0.00 0.00 3.74
53 54 8.262933 AGGACGTTTTTGTAACCTATATTAGCT 58.737 33.333 0.00 0.00 0.00 3.32
54 55 8.429493 AGGACGTTTTTGTAACCTATATTAGC 57.571 34.615 0.00 0.00 0.00 3.09
62 63 9.333724 CCATAATATAGGACGTTTTTGTAACCT 57.666 33.333 0.00 0.00 0.00 3.50
63 64 8.562052 CCCATAATATAGGACGTTTTTGTAACC 58.438 37.037 0.00 0.00 0.00 2.85
64 65 9.328845 TCCCATAATATAGGACGTTTTTGTAAC 57.671 33.333 0.00 0.00 0.00 2.50
65 66 9.328845 GTCCCATAATATAGGACGTTTTTGTAA 57.671 33.333 2.27 0.00 40.65 2.41
66 67 8.891671 GTCCCATAATATAGGACGTTTTTGTA 57.108 34.615 2.27 0.00 40.65 2.41
67 68 7.797038 GTCCCATAATATAGGACGTTTTTGT 57.203 36.000 2.27 0.00 40.65 2.83
76 77 5.318889 ACTCCCTCTGTCCCATAATATAGGA 59.681 44.000 0.00 0.00 0.00 2.94
77 78 5.594777 ACTCCCTCTGTCCCATAATATAGG 58.405 45.833 0.00 0.00 0.00 2.57
78 79 6.836527 CCTACTCCCTCTGTCCCATAATATAG 59.163 46.154 0.00 0.00 0.00 1.31
79 80 6.279682 ACCTACTCCCTCTGTCCCATAATATA 59.720 42.308 0.00 0.00 0.00 0.86
80 81 5.078006 ACCTACTCCCTCTGTCCCATAATAT 59.922 44.000 0.00 0.00 0.00 1.28
81 82 4.422592 ACCTACTCCCTCTGTCCCATAATA 59.577 45.833 0.00 0.00 0.00 0.98
82 83 3.210074 ACCTACTCCCTCTGTCCCATAAT 59.790 47.826 0.00 0.00 0.00 1.28
83 84 2.590611 ACCTACTCCCTCTGTCCCATAA 59.409 50.000 0.00 0.00 0.00 1.90
84 85 2.091278 CACCTACTCCCTCTGTCCCATA 60.091 54.545 0.00 0.00 0.00 2.74
85 86 1.019650 ACCTACTCCCTCTGTCCCAT 58.980 55.000 0.00 0.00 0.00 4.00
86 87 0.041238 CACCTACTCCCTCTGTCCCA 59.959 60.000 0.00 0.00 0.00 4.37
87 88 0.335361 TCACCTACTCCCTCTGTCCC 59.665 60.000 0.00 0.00 0.00 4.46
88 89 2.463047 ATCACCTACTCCCTCTGTCC 57.537 55.000 0.00 0.00 0.00 4.02
89 90 4.173290 AGTATCACCTACTCCCTCTGTC 57.827 50.000 0.00 0.00 35.73 3.51
90 91 4.727841 AGTAGTATCACCTACTCCCTCTGT 59.272 45.833 0.00 0.00 43.17 3.41
91 92 5.313280 AGTAGTATCACCTACTCCCTCTG 57.687 47.826 0.00 0.00 43.17 3.35
99 100 4.396522 ACGGATGGAGTAGTATCACCTAC 58.603 47.826 0.00 0.00 38.05 3.18
100 101 4.506271 GGACGGATGGAGTAGTATCACCTA 60.506 50.000 0.00 0.00 0.00 3.08
101 102 3.488363 GACGGATGGAGTAGTATCACCT 58.512 50.000 0.00 0.00 0.00 4.00
102 103 2.557490 GGACGGATGGAGTAGTATCACC 59.443 54.545 0.00 0.00 0.00 4.02
103 104 2.557490 GGGACGGATGGAGTAGTATCAC 59.443 54.545 0.00 0.00 0.00 3.06
104 105 2.176148 TGGGACGGATGGAGTAGTATCA 59.824 50.000 0.00 0.00 0.00 2.15
105 106 2.872732 TGGGACGGATGGAGTAGTATC 58.127 52.381 0.00 0.00 0.00 2.24
106 107 3.323774 TTGGGACGGATGGAGTAGTAT 57.676 47.619 0.00 0.00 0.00 2.12
107 108 2.832643 TTGGGACGGATGGAGTAGTA 57.167 50.000 0.00 0.00 0.00 1.82
108 109 1.946984 TTTGGGACGGATGGAGTAGT 58.053 50.000 0.00 0.00 0.00 2.73
109 110 3.343941 TTTTTGGGACGGATGGAGTAG 57.656 47.619 0.00 0.00 0.00 2.57
131 132 7.334844 TGTCTCGATAACACATCTAAGACAT 57.665 36.000 11.90 0.00 35.51 3.06
150 151 9.962783 ACGAATGTACCTACTAAAATATGTCTC 57.037 33.333 0.00 0.00 0.00 3.36
251 256 8.926710 CATTTCAGTCCGTATGTAATCCTTATC 58.073 37.037 0.00 0.00 0.00 1.75
259 264 6.275494 TCACTCATTTCAGTCCGTATGTAA 57.725 37.500 0.00 0.00 0.00 2.41
272 277 2.481952 AGAGCGCTTGTTCACTCATTTC 59.518 45.455 13.26 0.00 0.00 2.17
289 294 5.287992 GGTGTACATAGACGTGTTTTAGAGC 59.712 44.000 0.00 0.00 33.62 4.09
400 405 5.178797 ACAGTATCTTTGGTTCAGATTCGG 58.821 41.667 0.00 0.00 32.94 4.30
450 456 4.022849 CACAAGTTCAAGATTTCCTGGGAC 60.023 45.833 0.00 0.00 0.00 4.46
451 457 4.144297 CACAAGTTCAAGATTTCCTGGGA 58.856 43.478 0.00 0.00 0.00 4.37
457 463 5.444663 AAGGAGCACAAGTTCAAGATTTC 57.555 39.130 0.00 0.00 0.00 2.17
534 543 3.323758 TTGCCCGGATTCCAGGACG 62.324 63.158 9.29 0.00 0.00 4.79
546 555 2.360350 AGTGGTGCATCTTGCCCG 60.360 61.111 0.00 0.00 44.23 6.13
562 571 3.189618 TCCAGAAGATATGCAGTGCAG 57.810 47.619 24.20 6.85 43.65 4.41
563 572 3.632643 TTCCAGAAGATATGCAGTGCA 57.367 42.857 22.22 22.22 44.86 4.57
564 573 4.132336 TGATTCCAGAAGATATGCAGTGC 58.868 43.478 8.58 8.58 0.00 4.40
650 674 2.609427 TGCTGTGGATGAGCTGTATC 57.391 50.000 0.00 0.00 37.35 2.24
667 691 0.808125 TTTATGCGGTGGTGTCATGC 59.192 50.000 0.00 0.00 0.00 4.06
711 735 2.941563 ATAAGGGTCGGGGCTACGCT 62.942 60.000 0.00 0.00 41.41 5.07
715 739 0.263765 AGTGATAAGGGTCGGGGCTA 59.736 55.000 0.00 0.00 0.00 3.93
719 743 0.468648 GGGAAGTGATAAGGGTCGGG 59.531 60.000 0.00 0.00 0.00 5.14
862 886 2.173569 CGAGAGGGGGATCTGGATTTTT 59.826 50.000 0.00 0.00 0.00 1.94
1471 1499 1.873863 GTCGCCCTGTAACTTTGCC 59.126 57.895 0.00 0.00 0.00 4.52
1478 1506 3.919973 GAACCGCGTCGCCCTGTAA 62.920 63.158 12.44 0.00 0.00 2.41
1485 1513 2.480426 CTTGACTTGAACCGCGTCGC 62.480 60.000 7.29 7.29 0.00 5.19
1584 1614 1.153349 GGGGAGAGGAACATCGCAC 60.153 63.158 0.00 0.00 0.00 5.34
1588 1618 3.019564 CAACAATGGGGAGAGGAACATC 58.980 50.000 0.00 0.00 0.00 3.06
1677 1730 0.385974 GCCACGCATATTCCAATCGC 60.386 55.000 0.00 0.00 0.00 4.58
1678 1731 0.110688 CGCCACGCATATTCCAATCG 60.111 55.000 0.00 0.00 0.00 3.34
1824 1887 2.386864 TCACAAGGAGACATGGGGG 58.613 57.895 0.00 0.00 32.04 5.40
1953 2019 3.685058 GCGCACATCAAAGATCCTTAAC 58.315 45.455 0.30 0.00 0.00 2.01
1971 2037 2.476051 CATATTCCGATGCCGCGC 59.524 61.111 0.00 0.00 0.00 6.86
1990 2056 3.446310 ACGCCAAAAACAAAAGGGTAG 57.554 42.857 0.00 0.00 0.00 3.18
1995 2061 8.073768 TCTTAGATCTAACGCCAAAAACAAAAG 58.926 33.333 11.24 0.00 0.00 2.27
2084 2150 2.740981 CTGCAGGAAAGATCAGTCACAC 59.259 50.000 5.57 0.00 0.00 3.82
2096 2162 2.575532 CTTCCAAGACACTGCAGGAAA 58.424 47.619 19.93 0.00 37.86 3.13
2862 2928 1.227089 CCTGAGGATGTCGGCGAAG 60.227 63.158 12.92 2.87 0.00 3.79
2877 2943 0.307760 GCTGTTCACGAAACACCCTG 59.692 55.000 4.42 0.00 42.95 4.45
2886 2952 0.598419 CTCACTGCAGCTGTTCACGA 60.598 55.000 15.27 5.29 0.00 4.35
2991 3057 1.134220 ACAGGAAACGAACAAGGCAGA 60.134 47.619 0.00 0.00 0.00 4.26
3056 3123 1.608590 CAGAGCAAACGGGAACATGTT 59.391 47.619 11.78 11.78 0.00 2.71
3086 3154 1.189752 TCAGCACCACCAAGCAAAAA 58.810 45.000 0.00 0.00 0.00 1.94
3087 3155 1.134848 GTTCAGCACCACCAAGCAAAA 60.135 47.619 0.00 0.00 0.00 2.44
3102 3170 5.884792 AGCATAAGGAAATCTTCAGGTTCAG 59.115 40.000 0.00 0.00 36.93 3.02
3188 3266 9.866655 AATAAAAATGGATGGCTAATCTCTACA 57.133 29.630 0.93 0.00 35.43 2.74
3318 3400 0.179045 GCCACTCCAGTGTGTCAGTT 60.179 55.000 5.99 0.00 44.21 3.16
3354 3437 6.814954 ACATCACTTGTGGGATATTCTAGT 57.185 37.500 0.64 0.00 37.11 2.57
3466 3549 3.570540 CCACTCCTGTCCTCATCTATCA 58.429 50.000 0.00 0.00 0.00 2.15
3474 3557 0.326264 AACATGCCACTCCTGTCCTC 59.674 55.000 0.00 0.00 0.00 3.71
3534 3617 6.658849 TGCCAGGTTTAACATCTGTACATAT 58.341 36.000 0.00 0.00 0.00 1.78
3578 3661 7.065085 GCAAAGCATAACTTCAGAGATTCAGTA 59.935 37.037 0.00 0.00 37.75 2.74
3590 3673 4.418392 CATGGACAGCAAAGCATAACTTC 58.582 43.478 0.00 0.00 37.75 3.01
3664 3747 0.388649 CACACCGGTCTACTGCTGTC 60.389 60.000 2.59 0.00 0.00 3.51
3668 3751 0.944311 CACACACACCGGTCTACTGC 60.944 60.000 2.59 0.00 0.00 4.40
3672 3755 2.097036 CCTATCACACACACCGGTCTA 58.903 52.381 2.59 0.00 0.00 2.59
3673 3756 0.895530 CCTATCACACACACCGGTCT 59.104 55.000 2.59 0.00 0.00 3.85
3674 3757 0.108329 CCCTATCACACACACCGGTC 60.108 60.000 2.59 0.00 0.00 4.79
3675 3758 1.550130 CCCCTATCACACACACCGGT 61.550 60.000 0.00 0.00 0.00 5.28
3676 3759 1.220749 CCCCTATCACACACACCGG 59.779 63.158 0.00 0.00 0.00 5.28
3677 3760 1.449601 GCCCCTATCACACACACCG 60.450 63.158 0.00 0.00 0.00 4.94
3678 3761 1.077716 GGCCCCTATCACACACACC 60.078 63.158 0.00 0.00 0.00 4.16
3679 3762 1.139058 CTAGGCCCCTATCACACACAC 59.861 57.143 0.00 0.00 0.00 3.82
3680 3763 1.007842 TCTAGGCCCCTATCACACACA 59.992 52.381 0.00 0.00 0.00 3.72
3681 3764 1.689273 CTCTAGGCCCCTATCACACAC 59.311 57.143 0.00 0.00 0.00 3.82
3682 3765 1.413082 CCTCTAGGCCCCTATCACACA 60.413 57.143 0.00 0.00 0.00 3.72
3683 3766 1.343069 CCTCTAGGCCCCTATCACAC 58.657 60.000 0.00 0.00 0.00 3.82
3684 3767 0.191064 CCCTCTAGGCCCCTATCACA 59.809 60.000 0.00 0.00 0.00 3.58
3685 3768 3.074788 CCCTCTAGGCCCCTATCAC 57.925 63.158 0.00 0.00 0.00 3.06
3695 3778 1.208293 GAGGAACACTTGCCCTCTAGG 59.792 57.143 9.76 0.00 42.36 3.02
3696 3779 2.682155 GAGGAACACTTGCCCTCTAG 57.318 55.000 9.76 0.00 42.36 2.43
3752 3840 5.463724 CGTTTATCTCCTCTCAAGGTTATGC 59.536 44.000 0.00 0.00 43.82 3.14
3821 3909 0.472734 AGGTGAAGCACTGGGAGTCT 60.473 55.000 0.00 0.00 34.40 3.24
3822 3910 0.321122 CAGGTGAAGCACTGGGAGTC 60.321 60.000 0.00 0.00 34.40 3.36
3823 3911 1.056700 ACAGGTGAAGCACTGGGAGT 61.057 55.000 0.00 0.00 34.40 3.85
3824 3912 0.109342 AACAGGTGAAGCACTGGGAG 59.891 55.000 0.00 0.00 34.40 4.30
3825 3913 0.108585 GAACAGGTGAAGCACTGGGA 59.891 55.000 0.00 0.00 34.40 4.37
3826 3914 0.890996 GGAACAGGTGAAGCACTGGG 60.891 60.000 0.00 0.00 34.40 4.45
3827 3915 0.109342 AGGAACAGGTGAAGCACTGG 59.891 55.000 0.00 0.00 34.40 4.00
3828 3916 1.876156 GAAGGAACAGGTGAAGCACTG 59.124 52.381 0.00 0.00 34.40 3.66
3850 3938 8.904099 AATCCTTTTGGCTACATATACAGTAC 57.096 34.615 0.00 0.00 40.12 2.73


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

AutoCloner maintained by Alex Coulton.