Multiple sequence alignment - TraesCS6B01G469300

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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 TraesCS6B01G469300 chr6B 100.000 2198 0 0 1 2198 718254418 718252221 0.000000e+00 4060
1 TraesCS6B01G469300 chr6B 80.561 535 72 20 434 946 718596448 718596972 1.230000e-102 383
2 TraesCS6B01G469300 chr6B 100.000 107 0 0 2060 2166 708819576 708819470 4.790000e-47 198
3 TraesCS6B01G469300 chr6B 94.915 118 5 1 2060 2177 30889076 30889192 1.340000e-42 183
4 TraesCS6B01G469300 chr6A 93.837 1655 65 24 1 1652 616889310 616890930 0.000000e+00 2457
5 TraesCS6B01G469300 chr6A 88.462 416 21 11 1646 2051 616892344 616892742 5.490000e-131 477
6 TraesCS6B01G469300 chr6D 86.261 1412 163 21 434 1844 24935293 24933912 0.000000e+00 1504
7 TraesCS6B01G469300 chr7D 77.007 1283 179 64 169 1360 602288425 602287168 1.430000e-176 628
8 TraesCS6B01G469300 chr7D 74.052 844 175 34 968 1788 566520731 566519909 2.740000e-79 305
9 TraesCS6B01G469300 chr7A 75.524 1528 242 78 164 1600 694046075 694044589 1.430000e-176 628
10 TraesCS6B01G469300 chr7A 84.838 277 34 5 968 1243 674139770 674140039 2.780000e-69 272
11 TraesCS6B01G469300 chrUn 76.090 1330 237 49 512 1787 330578383 330579685 8.620000e-174 619
12 TraesCS6B01G469300 chrUn 76.180 1377 206 70 164 1451 87051094 87052437 4.010000e-172 614
13 TraesCS6B01G469300 chrUn 96.396 111 4 0 2056 2166 36601815 36601705 1.340000e-42 183
14 TraesCS6B01G469300 chrUn 96.396 111 4 0 2056 2166 269192269 269192159 1.340000e-42 183
15 TraesCS6B01G469300 chr7B 75.940 1330 241 46 512 1787 726361951 726363255 5.190000e-171 610
16 TraesCS6B01G469300 chr7B 77.108 830 163 16 637 1451 608476946 608477763 2.570000e-124 455
17 TraesCS6B01G469300 chr7B 80.698 430 75 4 512 934 713512655 713513083 5.850000e-86 327
18 TraesCS6B01G469300 chr7B 72.857 840 185 29 968 1784 620678302 620679121 4.690000e-62 248
19 TraesCS6B01G469300 chr5D 77.578 1057 165 49 449 1451 423533955 423534993 6.810000e-160 573
20 TraesCS6B01G469300 chr5D 88.235 255 30 0 976 1230 497821115 497820861 2.740000e-79 305
21 TraesCS6B01G469300 chr5A 77.113 1053 174 45 449 1451 537123599 537124634 4.130000e-152 547
22 TraesCS6B01G469300 chr1D 77.608 853 151 27 924 1762 458873096 458872270 4.240000e-132 481
23 TraesCS6B01G469300 chr1A 76.622 817 155 23 971 1775 551308154 551307362 3.380000e-113 418
24 TraesCS6B01G469300 chr5B 96.491 114 3 1 2057 2169 684616606 684616493 1.040000e-43 187
25 TraesCS6B01G469300 chr5B 95.536 112 5 0 2060 2171 278886986 278886875 1.730000e-41 180
26 TraesCS6B01G469300 chr4A 94.872 117 6 0 2059 2175 381221326 381221442 1.340000e-42 183
27 TraesCS6B01G469300 chr4A 92.000 125 9 1 2042 2166 593739147 593739024 8.070000e-40 174
28 TraesCS6B01G469300 chr3D 92.742 124 6 2 2049 2169 143958600 143958723 2.240000e-40 176
29 TraesCS6B01G469300 chr1B 76.793 237 42 10 1547 1775 630725396 630725165 1.070000e-23 121


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 TraesCS6B01G469300 chr6B 718252221 718254418 2197 True 4060 4060 100.0000 1 2198 1 chr6B.!!$R2 2197
1 TraesCS6B01G469300 chr6B 718596448 718596972 524 False 383 383 80.5610 434 946 1 chr6B.!!$F2 512
2 TraesCS6B01G469300 chr6A 616889310 616892742 3432 False 1467 2457 91.1495 1 2051 2 chr6A.!!$F1 2050
3 TraesCS6B01G469300 chr6D 24933912 24935293 1381 True 1504 1504 86.2610 434 1844 1 chr6D.!!$R1 1410
4 TraesCS6B01G469300 chr7D 602287168 602288425 1257 True 628 628 77.0070 169 1360 1 chr7D.!!$R2 1191
5 TraesCS6B01G469300 chr7D 566519909 566520731 822 True 305 305 74.0520 968 1788 1 chr7D.!!$R1 820
6 TraesCS6B01G469300 chr7A 694044589 694046075 1486 True 628 628 75.5240 164 1600 1 chr7A.!!$R1 1436
7 TraesCS6B01G469300 chrUn 330578383 330579685 1302 False 619 619 76.0900 512 1787 1 chrUn.!!$F2 1275
8 TraesCS6B01G469300 chrUn 87051094 87052437 1343 False 614 614 76.1800 164 1451 1 chrUn.!!$F1 1287
9 TraesCS6B01G469300 chr7B 726361951 726363255 1304 False 610 610 75.9400 512 1787 1 chr7B.!!$F4 1275
10 TraesCS6B01G469300 chr7B 608476946 608477763 817 False 455 455 77.1080 637 1451 1 chr7B.!!$F1 814
11 TraesCS6B01G469300 chr7B 620678302 620679121 819 False 248 248 72.8570 968 1784 1 chr7B.!!$F2 816
12 TraesCS6B01G469300 chr5D 423533955 423534993 1038 False 573 573 77.5780 449 1451 1 chr5D.!!$F1 1002
13 TraesCS6B01G469300 chr5A 537123599 537124634 1035 False 547 547 77.1130 449 1451 1 chr5A.!!$F1 1002
14 TraesCS6B01G469300 chr1D 458872270 458873096 826 True 481 481 77.6080 924 1762 1 chr1D.!!$R1 838
15 TraesCS6B01G469300 chr1A 551307362 551308154 792 True 418 418 76.6220 971 1775 1 chr1A.!!$R1 804

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
184 186 1.545428 GGAGAACATCAAGCACCCACA 60.545 52.381 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 3560 1.019673 CCTGGAGCATGTTTGGATCG 58.98 55.0 0.0 0.0 0.0 3.69 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
76 78 9.462174 CTAAATTGACAACATCTGTGCTAAAAA 57.538 29.630 0.00 0.00 38.84 1.94
153 155 3.118811 TGGACTTTGCAAAACCTTTGGAG 60.119 43.478 25.22 10.76 0.00 3.86
161 163 3.570125 GCAAAACCTTTGGAGCTCTAACT 59.430 43.478 12.63 0.00 0.00 2.24
162 164 4.557496 GCAAAACCTTTGGAGCTCTAACTG 60.557 45.833 12.63 8.92 0.00 3.16
184 186 1.545428 GGAGAACATCAAGCACCCACA 60.545 52.381 0.00 0.00 0.00 4.17
280 283 5.402054 TCCCCTAAATGCAGGTTCATAAT 57.598 39.130 0.00 0.00 33.44 1.28
284 287 6.127083 CCCCTAAATGCAGGTTCATAATTTGT 60.127 38.462 0.00 0.00 33.44 2.83
315 318 9.229784 CTGAAAACATCAACATTGCATATCTAC 57.770 33.333 0.00 0.00 37.67 2.59
320 323 9.836864 AACATCAACATTGCATATCTACTAGAA 57.163 29.630 0.00 0.00 0.00 2.10
351 355 1.962807 CATGACAGGGAAGGCACAAAA 59.037 47.619 0.00 0.00 0.00 2.44
354 358 1.963515 GACAGGGAAGGCACAAAACAT 59.036 47.619 0.00 0.00 0.00 2.71
363 367 7.839200 AGGGAAGGCACAAAACATTAATATACT 59.161 33.333 0.00 0.00 0.00 2.12
427 431 7.545965 CGACTAGATAGGAAACTTGAACAATGT 59.454 37.037 0.00 0.00 43.67 2.71
497 552 9.851686 TTGCATTTTCTGATCCAGTATATAAGT 57.148 29.630 0.00 0.00 32.61 2.24
546 611 4.924625 ACACACAGACTACCATCTCTAGT 58.075 43.478 0.00 0.00 0.00 2.57
710 789 2.975489 CCCAGCCACTAGACTCCATTAT 59.025 50.000 0.00 0.00 0.00 1.28
949 1031 3.740115 TCCTCTTCTTGTCCTTTTTCCG 58.260 45.455 0.00 0.00 0.00 4.30
1247 1362 4.680237 TGGGAGCACCTTGTCGCG 62.680 66.667 0.00 0.00 41.11 5.87
1428 1567 2.051334 TGTACACTGGCTTGTGCTTT 57.949 45.000 10.25 0.00 41.30 3.51
1473 1612 2.164219 ACACACCTTTGCTTTCACAGTG 59.836 45.455 0.00 0.00 0.00 3.66
1491 1630 4.532126 ACAGTGTTCTGGTAATCCTCATCA 59.468 41.667 0.00 0.00 45.14 3.07
1607 1752 1.207593 CGAAAGCACGGGAGCAAAG 59.792 57.895 0.00 0.00 36.85 2.77
1686 3252 1.097547 GGTAGCCGTAGTCCGTGCTA 61.098 60.000 0.00 0.00 36.13 3.49
1795 3364 2.653726 CCCATCGGAAATCACCATTGA 58.346 47.619 0.00 0.00 35.73 2.57
1844 3413 4.492570 CGATACGATCAAGGCAGAACAAAC 60.493 45.833 0.00 0.00 0.00 2.93
1846 3415 3.149196 ACGATCAAGGCAGAACAAACAT 58.851 40.909 0.00 0.00 0.00 2.71
1847 3416 3.058016 ACGATCAAGGCAGAACAAACATG 60.058 43.478 0.00 0.00 0.00 3.21
1848 3417 2.798976 TCAAGGCAGAACAAACATGC 57.201 45.000 0.00 0.00 39.25 4.06
1849 3418 2.030371 TCAAGGCAGAACAAACATGCA 58.970 42.857 0.00 0.00 41.78 3.96
1850 3419 2.129607 CAAGGCAGAACAAACATGCAC 58.870 47.619 0.00 0.00 41.78 4.57
1851 3420 1.401761 AGGCAGAACAAACATGCACA 58.598 45.000 0.00 0.00 41.78 4.57
1852 3421 1.755959 AGGCAGAACAAACATGCACAA 59.244 42.857 0.00 0.00 41.78 3.33
1853 3422 2.366266 AGGCAGAACAAACATGCACAAT 59.634 40.909 0.00 0.00 41.78 2.71
1854 3423 3.132925 GGCAGAACAAACATGCACAATT 58.867 40.909 0.00 0.00 41.78 2.32
1855 3424 3.560896 GGCAGAACAAACATGCACAATTT 59.439 39.130 0.00 0.00 41.78 1.82
1856 3425 4.520078 GCAGAACAAACATGCACAATTTG 58.480 39.130 14.47 14.47 39.75 2.32
1866 3435 1.729284 GCACAATTTGCCCCAAGATG 58.271 50.000 0.00 0.00 46.63 2.90
1867 3436 1.275856 GCACAATTTGCCCCAAGATGA 59.724 47.619 0.00 0.00 46.63 2.92
1868 3437 2.675889 GCACAATTTGCCCCAAGATGAG 60.676 50.000 0.00 0.00 46.63 2.90
1869 3438 2.827322 CACAATTTGCCCCAAGATGAGA 59.173 45.455 0.00 0.00 0.00 3.27
1875 3444 6.872585 ATTTGCCCCAAGATGAGAAAATAA 57.127 33.333 0.00 0.00 0.00 1.40
2006 3578 0.379669 GCGATCCAAACATGCTCCAG 59.620 55.000 0.00 0.00 0.00 3.86
2051 3629 1.203300 TGAGTGTCTCCCCCAAGATGA 60.203 52.381 0.00 0.00 0.00 2.92
2052 3630 1.484240 GAGTGTCTCCCCCAAGATGAG 59.516 57.143 0.00 0.00 0.00 2.90
2053 3631 1.203364 AGTGTCTCCCCCAAGATGAGT 60.203 52.381 0.00 0.00 0.00 3.41
2054 3632 1.065854 GTGTCTCCCCCAAGATGAGTG 60.066 57.143 0.00 0.00 0.00 3.51
2055 3633 0.543749 GTCTCCCCCAAGATGAGTGG 59.456 60.000 0.00 0.00 35.77 4.00
2056 3634 0.119155 TCTCCCCCAAGATGAGTGGT 59.881 55.000 0.00 0.00 34.01 4.16
2057 3635 1.364678 TCTCCCCCAAGATGAGTGGTA 59.635 52.381 0.00 0.00 34.01 3.25
2058 3636 2.022035 TCTCCCCCAAGATGAGTGGTAT 60.022 50.000 0.00 0.00 34.01 2.73
2059 3637 2.780010 CTCCCCCAAGATGAGTGGTATT 59.220 50.000 0.00 0.00 34.01 1.89
2060 3638 3.973973 CTCCCCCAAGATGAGTGGTATTA 59.026 47.826 0.00 0.00 34.01 0.98
2061 3639 3.714798 TCCCCCAAGATGAGTGGTATTAC 59.285 47.826 0.00 0.00 34.01 1.89
2062 3640 3.716872 CCCCCAAGATGAGTGGTATTACT 59.283 47.826 0.00 0.00 34.01 2.24
2063 3641 4.202367 CCCCCAAGATGAGTGGTATTACTC 60.202 50.000 0.00 0.00 45.71 2.59
2064 3642 4.202367 CCCCAAGATGAGTGGTATTACTCC 60.202 50.000 0.00 0.00 45.07 3.85
2065 3643 4.202367 CCCAAGATGAGTGGTATTACTCCC 60.202 50.000 0.00 0.00 45.07 4.30
2066 3644 4.656112 CCAAGATGAGTGGTATTACTCCCT 59.344 45.833 0.00 0.00 45.07 4.20
2067 3645 5.221541 CCAAGATGAGTGGTATTACTCCCTC 60.222 48.000 0.00 0.00 45.07 4.30
2068 3646 4.484912 AGATGAGTGGTATTACTCCCTCC 58.515 47.826 0.00 0.00 45.07 4.30
2069 3647 2.662866 TGAGTGGTATTACTCCCTCCG 58.337 52.381 0.00 0.00 45.07 4.63
2070 3648 2.024655 TGAGTGGTATTACTCCCTCCGT 60.025 50.000 0.00 0.00 45.07 4.69
2071 3649 3.029570 GAGTGGTATTACTCCCTCCGTT 58.970 50.000 0.00 0.00 40.92 4.44
2072 3650 3.029570 AGTGGTATTACTCCCTCCGTTC 58.970 50.000 0.00 0.00 0.00 3.95
2073 3651 2.102084 GTGGTATTACTCCCTCCGTTCC 59.898 54.545 0.00 0.00 0.00 3.62
2074 3652 1.339291 GGTATTACTCCCTCCGTTCCG 59.661 57.143 0.00 0.00 0.00 4.30
2075 3653 2.301346 GTATTACTCCCTCCGTTCCGA 58.699 52.381 0.00 0.00 0.00 4.55
2076 3654 1.856629 ATTACTCCCTCCGTTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
2077 3655 1.856629 TTACTCCCTCCGTTCCGAAT 58.143 50.000 0.00 0.00 0.00 3.34
2078 3656 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
2079 3657 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2080 3658 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2081 3659 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2082 3660 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2083 3661 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2084 3662 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2085 3663 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2086 3664 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
2087 3665 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
2088 3666 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
2089 3667 2.347452 CGTTCCGAATTACTTGTCGCAT 59.653 45.455 0.00 0.00 35.93 4.73
2090 3668 3.670203 GTTCCGAATTACTTGTCGCATG 58.330 45.455 0.00 0.00 35.93 4.06
2091 3669 2.967362 TCCGAATTACTTGTCGCATGT 58.033 42.857 0.00 4.39 35.93 3.21
2092 3670 4.112716 TCCGAATTACTTGTCGCATGTA 57.887 40.909 0.00 2.87 35.93 2.29
2093 3671 4.689071 TCCGAATTACTTGTCGCATGTAT 58.311 39.130 0.00 0.00 35.93 2.29
2094 3672 4.506288 TCCGAATTACTTGTCGCATGTATG 59.494 41.667 0.00 0.00 35.93 2.39
2095 3673 4.318760 CCGAATTACTTGTCGCATGTATGG 60.319 45.833 0.00 4.42 35.93 2.74
2096 3674 4.506288 CGAATTACTTGTCGCATGTATGGA 59.494 41.667 0.00 0.00 0.00 3.41
2097 3675 5.177511 CGAATTACTTGTCGCATGTATGGAT 59.822 40.000 0.00 0.00 0.00 3.41
2098 3676 5.929697 ATTACTTGTCGCATGTATGGATG 57.070 39.130 0.00 0.00 0.00 3.51
2099 3677 3.266510 ACTTGTCGCATGTATGGATGT 57.733 42.857 0.00 0.00 0.00 3.06
2100 3678 4.400529 ACTTGTCGCATGTATGGATGTA 57.599 40.909 0.00 0.00 0.00 2.29
2101 3679 4.960938 ACTTGTCGCATGTATGGATGTAT 58.039 39.130 0.00 0.00 0.00 2.29
2102 3680 5.368145 ACTTGTCGCATGTATGGATGTATT 58.632 37.500 0.00 0.00 0.00 1.89
2103 3681 5.822519 ACTTGTCGCATGTATGGATGTATTT 59.177 36.000 0.00 0.00 0.00 1.40
2104 3682 6.989759 ACTTGTCGCATGTATGGATGTATTTA 59.010 34.615 0.00 0.00 0.00 1.40
2105 3683 7.171508 ACTTGTCGCATGTATGGATGTATTTAG 59.828 37.037 0.00 0.00 0.00 1.85
2106 3684 6.754193 TGTCGCATGTATGGATGTATTTAGA 58.246 36.000 0.00 0.00 0.00 2.10
2107 3685 7.386059 TGTCGCATGTATGGATGTATTTAGAT 58.614 34.615 0.00 0.00 0.00 1.98
2108 3686 7.331687 TGTCGCATGTATGGATGTATTTAGATG 59.668 37.037 0.00 0.00 0.00 2.90
2109 3687 7.331934 GTCGCATGTATGGATGTATTTAGATGT 59.668 37.037 0.00 0.00 0.00 3.06
2110 3688 8.527810 TCGCATGTATGGATGTATTTAGATGTA 58.472 33.333 0.00 0.00 0.00 2.29
2111 3689 9.317936 CGCATGTATGGATGTATTTAGATGTAT 57.682 33.333 0.00 0.00 0.00 2.29
2141 3719 9.632807 AATTCTAGATACATCTATTTCAGCGAC 57.367 33.333 0.00 0.00 38.60 5.19
2142 3720 6.832804 TCTAGATACATCTATTTCAGCGACG 58.167 40.000 0.00 0.00 38.60 5.12
2143 3721 5.690997 AGATACATCTATTTCAGCGACGA 57.309 39.130 0.00 0.00 34.85 4.20
2144 3722 5.694816 AGATACATCTATTTCAGCGACGAG 58.305 41.667 0.00 0.00 34.85 4.18
2145 3723 3.784701 ACATCTATTTCAGCGACGAGT 57.215 42.857 0.00 0.00 0.00 4.18
2146 3724 4.895224 ACATCTATTTCAGCGACGAGTA 57.105 40.909 0.00 0.00 0.00 2.59
2147 3725 5.244785 ACATCTATTTCAGCGACGAGTAA 57.755 39.130 0.00 0.00 0.00 2.24
2148 3726 5.833082 ACATCTATTTCAGCGACGAGTAAT 58.167 37.500 0.00 0.00 0.00 1.89
2149 3727 6.273825 ACATCTATTTCAGCGACGAGTAATT 58.726 36.000 0.00 0.00 0.00 1.40
2150 3728 6.757010 ACATCTATTTCAGCGACGAGTAATTT 59.243 34.615 0.00 0.00 0.00 1.82
2151 3729 6.569228 TCTATTTCAGCGACGAGTAATTTG 57.431 37.500 0.00 0.00 0.00 2.32
2152 3730 4.600012 ATTTCAGCGACGAGTAATTTGG 57.400 40.909 0.00 0.00 0.00 3.28
2153 3731 3.306917 TTCAGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
2154 3732 3.306917 TCAGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
2155 3733 2.991190 TCAGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
2156 3734 1.990563 AGCGACGAGTAATTTGGAACG 59.009 47.619 0.00 0.00 0.00 3.95
2157 3735 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
2158 3736 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
2159 3737 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2160 3738 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2161 3739 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2162 3740 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2163 3741 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2164 3742 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2165 3743 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
2166 3744 3.629142 AATTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
2167 3745 2.019807 TTTGGAACGGAGGGAGTAGT 57.980 50.000 0.00 0.00 0.00 2.73
2168 3746 2.905415 TTGGAACGGAGGGAGTAGTA 57.095 50.000 0.00 0.00 0.00 1.82
2169 3747 2.431954 TGGAACGGAGGGAGTAGTAG 57.568 55.000 0.00 0.00 0.00 2.57
2170 3748 1.918262 TGGAACGGAGGGAGTAGTAGA 59.082 52.381 0.00 0.00 0.00 2.59
2171 3749 2.296792 GGAACGGAGGGAGTAGTAGAC 58.703 57.143 0.00 0.00 0.00 2.59
2172 3750 2.356535 GGAACGGAGGGAGTAGTAGACA 60.357 54.545 0.00 0.00 0.00 3.41
2173 3751 3.350833 GAACGGAGGGAGTAGTAGACAA 58.649 50.000 0.00 0.00 0.00 3.18
2174 3752 3.446442 ACGGAGGGAGTAGTAGACAAA 57.554 47.619 0.00 0.00 0.00 2.83
2175 3753 3.087781 ACGGAGGGAGTAGTAGACAAAC 58.912 50.000 0.00 0.00 0.00 2.93
2176 3754 3.087031 CGGAGGGAGTAGTAGACAAACA 58.913 50.000 0.00 0.00 0.00 2.83
2177 3755 3.128938 CGGAGGGAGTAGTAGACAAACAG 59.871 52.174 0.00 0.00 0.00 3.16
2178 3756 3.119065 GGAGGGAGTAGTAGACAAACAGC 60.119 52.174 0.00 0.00 0.00 4.40
2179 3757 3.764972 GAGGGAGTAGTAGACAAACAGCT 59.235 47.826 0.00 0.00 0.00 4.24
2180 3758 3.764972 AGGGAGTAGTAGACAAACAGCTC 59.235 47.826 0.00 0.00 0.00 4.09
2181 3759 3.510360 GGGAGTAGTAGACAAACAGCTCA 59.490 47.826 0.00 0.00 0.00 4.26
2182 3760 4.160626 GGGAGTAGTAGACAAACAGCTCAT 59.839 45.833 0.00 0.00 0.00 2.90
2183 3761 5.360144 GGGAGTAGTAGACAAACAGCTCATA 59.640 44.000 0.00 0.00 0.00 2.15
2184 3762 6.041069 GGGAGTAGTAGACAAACAGCTCATAT 59.959 42.308 0.00 0.00 0.00 1.78
2185 3763 6.920758 GGAGTAGTAGACAAACAGCTCATATG 59.079 42.308 0.00 0.00 0.00 1.78
2186 3764 7.201830 GGAGTAGTAGACAAACAGCTCATATGA 60.202 40.741 5.07 5.07 0.00 2.15
2187 3765 8.067751 AGTAGTAGACAAACAGCTCATATGAA 57.932 34.615 6.90 0.00 0.00 2.57
2188 3766 7.976734 AGTAGTAGACAAACAGCTCATATGAAC 59.023 37.037 6.90 2.04 0.00 3.18
2189 3767 6.701340 AGTAGACAAACAGCTCATATGAACA 58.299 36.000 6.90 0.00 0.00 3.18
2190 3768 7.161404 AGTAGACAAACAGCTCATATGAACAA 58.839 34.615 6.90 0.00 0.00 2.83
2191 3769 7.826252 AGTAGACAAACAGCTCATATGAACAAT 59.174 33.333 6.90 0.00 0.00 2.71
2192 3770 9.098355 GTAGACAAACAGCTCATATGAACAATA 57.902 33.333 6.90 0.00 0.00 1.90
2193 3771 8.206325 AGACAAACAGCTCATATGAACAATAG 57.794 34.615 6.90 0.00 0.00 1.73
2194 3772 7.281774 AGACAAACAGCTCATATGAACAATAGG 59.718 37.037 6.90 0.00 0.00 2.57
2195 3773 6.183360 ACAAACAGCTCATATGAACAATAGGC 60.183 38.462 6.90 4.88 0.00 3.93
2196 3774 5.301835 ACAGCTCATATGAACAATAGGCT 57.698 39.130 6.90 7.17 0.00 4.58
2197 3775 5.688807 ACAGCTCATATGAACAATAGGCTT 58.311 37.500 6.90 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.804396 TTGAGTGCACAATTGGGCCG 61.804 55.000 29.13 6.17 45.73 6.13
76 78 8.543774 AGATGACTTTCATTCTGGTGTAGTATT 58.456 33.333 0.00 0.00 37.20 1.89
78 80 7.397476 AGAGATGACTTTCATTCTGGTGTAGTA 59.603 37.037 0.00 0.00 37.20 1.82
79 81 6.212388 AGAGATGACTTTCATTCTGGTGTAGT 59.788 38.462 0.00 0.00 37.20 2.73
80 82 6.638610 AGAGATGACTTTCATTCTGGTGTAG 58.361 40.000 0.00 0.00 37.20 2.74
153 155 4.727507 TGATGTTCTCCTCAGTTAGAGC 57.272 45.455 0.00 0.00 43.31 4.09
161 163 1.003580 GGGTGCTTGATGTTCTCCTCA 59.996 52.381 0.00 0.00 0.00 3.86
162 164 1.003580 TGGGTGCTTGATGTTCTCCTC 59.996 52.381 0.00 0.00 0.00 3.71
184 186 4.650972 TTAAGTACCCAGCAACCTTCAT 57.349 40.909 0.00 0.00 0.00 2.57
280 283 8.871862 CAATGTTGATGTTTTCAGAAAGACAAA 58.128 29.630 12.17 4.36 35.27 2.83
284 287 6.571605 TGCAATGTTGATGTTTTCAGAAAGA 58.428 32.000 0.00 0.00 35.27 2.52
315 318 8.210946 TCCCTGTCATGTATAACCATTTTCTAG 58.789 37.037 0.00 0.00 0.00 2.43
320 323 6.129179 CCTTCCCTGTCATGTATAACCATTT 58.871 40.000 0.00 0.00 0.00 2.32
323 327 3.118038 GCCTTCCCTGTCATGTATAACCA 60.118 47.826 0.00 0.00 0.00 3.67
351 355 8.965819 TGCATTTGTTGTCCAGTATATTAATGT 58.034 29.630 0.00 0.00 0.00 2.71
354 358 8.341892 TGTGCATTTGTTGTCCAGTATATTAA 57.658 30.769 0.00 0.00 0.00 1.40
363 367 5.781210 TTTATCTGTGCATTTGTTGTCCA 57.219 34.783 0.00 0.00 0.00 4.02
546 611 6.069994 TGCTCTTATGCATATTTGGAATCCA 58.930 36.000 7.36 0.00 38.12 3.41
710 789 0.249953 TCCCTCGCGTTTGCTAACAA 60.250 50.000 5.77 0.00 39.65 2.83
1247 1362 2.696707 ACCAATGATGATGATGCCAACC 59.303 45.455 0.00 0.00 0.00 3.77
1428 1567 3.138304 CAGTTTCATCGACCAGGTTGAA 58.862 45.455 14.03 7.35 29.05 2.69
1473 1612 8.908786 TTGATAATGATGAGGATTACCAGAAC 57.091 34.615 0.00 0.00 38.94 3.01
1491 1630 6.647229 TCTGCATGTCTCAGTTCTTGATAAT 58.353 36.000 0.00 0.00 34.68 1.28
1686 3252 2.048503 GCCTACGCCGTTGACACT 60.049 61.111 0.00 0.00 0.00 3.55
1705 3271 3.036429 GCGACCTGAGCCCTTCCAT 62.036 63.158 0.00 0.00 0.00 3.41
1805 3374 4.504097 TCGTATCGTCTCTTGCATGAATTG 59.496 41.667 0.00 0.00 0.00 2.32
1814 3383 3.046390 GCCTTGATCGTATCGTCTCTTG 58.954 50.000 0.00 0.00 0.00 3.02
1848 3417 2.827322 TCTCATCTTGGGGCAAATTGTG 59.173 45.455 0.00 0.00 0.00 3.33
1849 3418 3.173953 TCTCATCTTGGGGCAAATTGT 57.826 42.857 0.00 0.00 0.00 2.71
1850 3419 4.540359 TTTCTCATCTTGGGGCAAATTG 57.460 40.909 0.00 0.00 0.00 2.32
1851 3420 5.767277 ATTTTCTCATCTTGGGGCAAATT 57.233 34.783 0.00 0.00 0.00 1.82
1852 3421 6.872585 TTATTTTCTCATCTTGGGGCAAAT 57.127 33.333 0.00 0.00 0.00 2.32
1853 3422 6.872585 ATTATTTTCTCATCTTGGGGCAAA 57.127 33.333 0.00 0.00 0.00 3.68
1854 3423 6.213195 ACAATTATTTTCTCATCTTGGGGCAA 59.787 34.615 0.00 0.00 0.00 4.52
1855 3424 5.721000 ACAATTATTTTCTCATCTTGGGGCA 59.279 36.000 0.00 0.00 0.00 5.36
1856 3425 6.044682 CACAATTATTTTCTCATCTTGGGGC 58.955 40.000 0.00 0.00 0.00 5.80
1857 3426 6.044682 GCACAATTATTTTCTCATCTTGGGG 58.955 40.000 0.00 0.00 0.00 4.96
1858 3427 6.755141 CAGCACAATTATTTTCTCATCTTGGG 59.245 38.462 0.00 0.00 0.00 4.12
1859 3428 6.255020 GCAGCACAATTATTTTCTCATCTTGG 59.745 38.462 0.00 0.00 0.00 3.61
1860 3429 7.033791 AGCAGCACAATTATTTTCTCATCTTG 58.966 34.615 0.00 0.00 0.00 3.02
1861 3430 7.166691 AGCAGCACAATTATTTTCTCATCTT 57.833 32.000 0.00 0.00 0.00 2.40
1862 3431 6.770746 AGCAGCACAATTATTTTCTCATCT 57.229 33.333 0.00 0.00 0.00 2.90
1863 3432 9.525409 AATTAGCAGCACAATTATTTTCTCATC 57.475 29.630 0.00 0.00 0.00 2.92
1864 3433 9.525409 GAATTAGCAGCACAATTATTTTCTCAT 57.475 29.630 0.00 0.00 0.00 2.90
1865 3434 8.522003 TGAATTAGCAGCACAATTATTTTCTCA 58.478 29.630 0.00 0.00 0.00 3.27
1866 3435 8.915871 TGAATTAGCAGCACAATTATTTTCTC 57.084 30.769 0.00 0.00 0.00 2.87
1867 3436 8.526147 ACTGAATTAGCAGCACAATTATTTTCT 58.474 29.630 0.00 0.00 39.51 2.52
1868 3437 8.693542 ACTGAATTAGCAGCACAATTATTTTC 57.306 30.769 0.00 0.00 39.51 2.29
1869 3438 7.485913 CGACTGAATTAGCAGCACAATTATTTT 59.514 33.333 0.00 0.00 39.51 1.82
1875 3444 2.096496 GCGACTGAATTAGCAGCACAAT 59.904 45.455 0.00 0.00 39.51 2.71
1932 3504 5.007385 AGATTTGAGCTCATGCAAATTCC 57.993 39.130 19.04 3.61 42.81 3.01
1986 3558 1.031571 TGGAGCATGTTTGGATCGCC 61.032 55.000 0.00 0.00 0.00 5.54
1988 3560 1.019673 CCTGGAGCATGTTTGGATCG 58.980 55.000 0.00 0.00 0.00 3.69
2006 3578 3.543680 TCTGTAGCCTAAGCAACATCC 57.456 47.619 0.00 0.00 43.56 3.51
2051 3629 2.842645 ACGGAGGGAGTAATACCACT 57.157 50.000 0.00 0.00 0.00 4.00
2052 3630 2.102084 GGAACGGAGGGAGTAATACCAC 59.898 54.545 0.00 0.00 0.00 4.16
2053 3631 2.391678 GGAACGGAGGGAGTAATACCA 58.608 52.381 0.00 0.00 0.00 3.25
2069 3647 3.124636 ACATGCGACAAGTAATTCGGAAC 59.875 43.478 0.00 0.00 39.13 3.62
2070 3648 3.331150 ACATGCGACAAGTAATTCGGAA 58.669 40.909 0.00 0.00 39.13 4.30
2071 3649 2.967362 ACATGCGACAAGTAATTCGGA 58.033 42.857 0.00 0.00 40.02 4.55
2072 3650 4.318760 CCATACATGCGACAAGTAATTCGG 60.319 45.833 0.00 0.00 35.73 4.30
2073 3651 4.506288 TCCATACATGCGACAAGTAATTCG 59.494 41.667 0.00 0.00 38.31 3.34
2074 3652 5.984233 TCCATACATGCGACAAGTAATTC 57.016 39.130 0.00 0.00 0.00 2.17
2075 3653 5.822519 ACATCCATACATGCGACAAGTAATT 59.177 36.000 0.00 0.00 0.00 1.40
2076 3654 5.368145 ACATCCATACATGCGACAAGTAAT 58.632 37.500 0.00 0.00 0.00 1.89
2077 3655 4.765273 ACATCCATACATGCGACAAGTAA 58.235 39.130 0.00 0.00 0.00 2.24
2078 3656 4.400529 ACATCCATACATGCGACAAGTA 57.599 40.909 0.00 0.00 0.00 2.24
2079 3657 3.266510 ACATCCATACATGCGACAAGT 57.733 42.857 0.00 0.00 0.00 3.16
2080 3658 5.929697 AATACATCCATACATGCGACAAG 57.070 39.130 0.00 0.00 0.00 3.16
2081 3659 7.213678 TCTAAATACATCCATACATGCGACAA 58.786 34.615 0.00 0.00 0.00 3.18
2082 3660 6.754193 TCTAAATACATCCATACATGCGACA 58.246 36.000 0.00 0.00 0.00 4.35
2083 3661 7.331934 ACATCTAAATACATCCATACATGCGAC 59.668 37.037 0.00 0.00 0.00 5.19
2084 3662 7.386059 ACATCTAAATACATCCATACATGCGA 58.614 34.615 0.00 0.00 0.00 5.10
2085 3663 7.601073 ACATCTAAATACATCCATACATGCG 57.399 36.000 0.00 0.00 0.00 4.73
2115 3693 9.632807 GTCGCTGAAATAGATGTATCTAGAATT 57.367 33.333 0.00 3.41 42.20 2.17
2116 3694 7.965655 CGTCGCTGAAATAGATGTATCTAGAAT 59.034 37.037 0.00 0.00 42.20 2.40
2117 3695 7.172703 TCGTCGCTGAAATAGATGTATCTAGAA 59.827 37.037 0.00 0.00 42.20 2.10
2118 3696 6.649557 TCGTCGCTGAAATAGATGTATCTAGA 59.350 38.462 7.57 0.00 42.20 2.43
2119 3697 6.832804 TCGTCGCTGAAATAGATGTATCTAG 58.167 40.000 7.57 0.00 42.20 2.43
2120 3698 6.427242 ACTCGTCGCTGAAATAGATGTATCTA 59.573 38.462 4.22 4.22 43.00 1.98
2121 3699 5.239744 ACTCGTCGCTGAAATAGATGTATCT 59.760 40.000 0.00 0.00 40.86 1.98
2122 3700 5.453648 ACTCGTCGCTGAAATAGATGTATC 58.546 41.667 0.00 0.00 0.00 2.24
2123 3701 5.440234 ACTCGTCGCTGAAATAGATGTAT 57.560 39.130 0.00 0.00 0.00 2.29
2124 3702 4.895224 ACTCGTCGCTGAAATAGATGTA 57.105 40.909 0.00 0.00 0.00 2.29
2125 3703 3.784701 ACTCGTCGCTGAAATAGATGT 57.215 42.857 0.00 0.00 0.00 3.06
2126 3704 6.755461 AATTACTCGTCGCTGAAATAGATG 57.245 37.500 0.00 0.00 0.00 2.90
2127 3705 6.201044 CCAAATTACTCGTCGCTGAAATAGAT 59.799 38.462 0.00 0.00 0.00 1.98
2128 3706 5.518847 CCAAATTACTCGTCGCTGAAATAGA 59.481 40.000 0.00 0.00 0.00 1.98
2129 3707 5.518847 TCCAAATTACTCGTCGCTGAAATAG 59.481 40.000 0.00 0.00 0.00 1.73
2130 3708 5.412640 TCCAAATTACTCGTCGCTGAAATA 58.587 37.500 0.00 0.00 0.00 1.40
2131 3709 4.250464 TCCAAATTACTCGTCGCTGAAAT 58.750 39.130 0.00 0.00 0.00 2.17
2132 3710 3.655486 TCCAAATTACTCGTCGCTGAAA 58.345 40.909 0.00 0.00 0.00 2.69
2133 3711 3.306917 TCCAAATTACTCGTCGCTGAA 57.693 42.857 0.00 0.00 0.00 3.02
2134 3712 2.991190 GTTCCAAATTACTCGTCGCTGA 59.009 45.455 0.00 0.00 0.00 4.26
2135 3713 2.222508 CGTTCCAAATTACTCGTCGCTG 60.223 50.000 0.00 0.00 0.00 5.18
2136 3714 1.990563 CGTTCCAAATTACTCGTCGCT 59.009 47.619 0.00 0.00 0.00 4.93
2137 3715 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
2138 3716 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2139 3717 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2140 3718 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2141 3719 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2142 3720 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2143 3721 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2144 3722 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2145 3723 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
2146 3724 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
2147 3725 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
2148 3726 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2149 3727 2.309755 TCTACTACTCCCTCCGTTCCAA 59.690 50.000 0.00 0.00 0.00 3.53
2150 3728 1.918262 TCTACTACTCCCTCCGTTCCA 59.082 52.381 0.00 0.00 0.00 3.53
2151 3729 2.296792 GTCTACTACTCCCTCCGTTCC 58.703 57.143 0.00 0.00 0.00 3.62
2152 3730 2.996631 TGTCTACTACTCCCTCCGTTC 58.003 52.381 0.00 0.00 0.00 3.95
2153 3731 3.446442 TTGTCTACTACTCCCTCCGTT 57.554 47.619 0.00 0.00 0.00 4.44
2154 3732 3.087781 GTTTGTCTACTACTCCCTCCGT 58.912 50.000 0.00 0.00 0.00 4.69
2155 3733 3.087031 TGTTTGTCTACTACTCCCTCCG 58.913 50.000 0.00 0.00 0.00 4.63
2156 3734 3.119065 GCTGTTTGTCTACTACTCCCTCC 60.119 52.174 0.00 0.00 0.00 4.30
2157 3735 3.764972 AGCTGTTTGTCTACTACTCCCTC 59.235 47.826 0.00 0.00 0.00 4.30
2158 3736 3.764972 GAGCTGTTTGTCTACTACTCCCT 59.235 47.826 0.00 0.00 0.00 4.20
2159 3737 3.510360 TGAGCTGTTTGTCTACTACTCCC 59.490 47.826 0.00 0.00 0.00 4.30
2160 3738 4.785511 TGAGCTGTTTGTCTACTACTCC 57.214 45.455 0.00 0.00 0.00 3.85
2161 3739 7.708051 TCATATGAGCTGTTTGTCTACTACTC 58.292 38.462 0.00 0.00 0.00 2.59
2162 3740 7.646548 TCATATGAGCTGTTTGTCTACTACT 57.353 36.000 0.00 0.00 0.00 2.57
2163 3741 7.759886 TGTTCATATGAGCTGTTTGTCTACTAC 59.240 37.037 18.83 4.06 0.00 2.73
2164 3742 7.836842 TGTTCATATGAGCTGTTTGTCTACTA 58.163 34.615 18.83 0.00 0.00 1.82
2165 3743 6.701340 TGTTCATATGAGCTGTTTGTCTACT 58.299 36.000 18.83 0.00 0.00 2.57
2166 3744 6.968131 TGTTCATATGAGCTGTTTGTCTAC 57.032 37.500 18.83 5.21 0.00 2.59
2167 3745 9.317936 CTATTGTTCATATGAGCTGTTTGTCTA 57.682 33.333 18.83 0.00 0.00 2.59
2168 3746 7.281774 CCTATTGTTCATATGAGCTGTTTGTCT 59.718 37.037 18.83 0.48 0.00 3.41
2169 3747 7.412853 CCTATTGTTCATATGAGCTGTTTGTC 58.587 38.462 18.83 0.00 0.00 3.18
2170 3748 6.183360 GCCTATTGTTCATATGAGCTGTTTGT 60.183 38.462 18.83 3.59 0.00 2.83
2171 3749 6.039047 AGCCTATTGTTCATATGAGCTGTTTG 59.961 38.462 18.83 7.57 0.00 2.93
2172 3750 6.125029 AGCCTATTGTTCATATGAGCTGTTT 58.875 36.000 18.83 5.55 0.00 2.83
2173 3751 5.688807 AGCCTATTGTTCATATGAGCTGTT 58.311 37.500 18.83 7.63 0.00 3.16
2174 3752 5.301835 AGCCTATTGTTCATATGAGCTGT 57.698 39.130 18.83 10.66 0.00 4.40


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

AutoCloner maintained by Alex Coulton.