Multiple sequence alignment - TraesCS7B01G054300

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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 TraesCS7B01G054300 chr7B 100.000 4482 0 0 1 4482 57463737 57459256 0.000000e+00 8277
1 TraesCS7B01G054300 chr7A 94.995 2957 134 7 882 3837 103146518 103143575 0.000000e+00 4628
2 TraesCS7B01G054300 chr7A 93.902 82 3 1 3816 3895 103143550 103143469 6.090000e-24 122
3 TraesCS7B01G054300 chr7D 95.894 2630 105 3 882 3509 101049133 101046505 0.000000e+00 4255
4 TraesCS7B01G054300 chr7D 87.500 1016 73 25 3498 4482 101039664 101038672 0.000000e+00 1123
5 TraesCS7B01G054300 chr7D 87.365 649 60 13 239 877 101049829 101049193 0.000000e+00 725
6 TraesCS7B01G054300 chr7D 83.386 638 82 15 171 798 521890139 521890762 1.810000e-158 569
7 TraesCS7B01G054300 chr7D 92.810 153 11 0 1 153 101049982 101049830 5.840000e-54 222
8 TraesCS7B01G054300 chr5B 83.381 698 88 16 171 858 710169947 710169268 4.920000e-174 621
9 TraesCS7B01G054300 chr3B 83.144 706 89 18 171 858 603825975 603826668 6.370000e-173 617
10 TraesCS7B01G054300 chr3B 82.320 707 95 15 171 858 596242583 596243278 1.800000e-163 586
11 TraesCS7B01G054300 chr2A 84.640 625 75 15 171 783 559827743 559828358 1.780000e-168 603
12 TraesCS7B01G054300 chr2B 84.345 626 76 16 171 784 87333267 87332652 1.070000e-165 593
13 TraesCS7B01G054300 chr1A 85.832 487 59 5 171 655 588667972 588668450 4.000000e-140 508
14 TraesCS7B01G054300 chr1B 80.507 631 92 16 236 858 684732970 684732363 5.290000e-124 455
15 TraesCS7B01G054300 chr1B 89.247 93 8 2 730 821 660475808 660475717 1.020000e-21 115
16 TraesCS7B01G054300 chrUn 77.899 457 85 13 191 641 214697858 214697412 2.050000e-68 270
17 TraesCS7B01G054300 chr5A 74.742 582 105 34 300 850 198241065 198241635 5.840000e-54 222
18 TraesCS7B01G054300 chr5A 88.235 102 7 4 752 850 17677986 17678085 2.830000e-22 117
19 TraesCS7B01G054300 chr2D 88.750 160 17 1 2876 3034 433876979 433877138 1.270000e-45 195


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 TraesCS7B01G054300 chr7B 57459256 57463737 4481 True 8277 8277 100.0000 1 4482 1 chr7B.!!$R1 4481
1 TraesCS7B01G054300 chr7A 103143469 103146518 3049 True 2375 4628 94.4485 882 3895 2 chr7A.!!$R1 3013
2 TraesCS7B01G054300 chr7D 101046505 101049982 3477 True 1734 4255 92.0230 1 3509 3 chr7D.!!$R2 3508
3 TraesCS7B01G054300 chr7D 101038672 101039664 992 True 1123 1123 87.5000 3498 4482 1 chr7D.!!$R1 984
4 TraesCS7B01G054300 chr7D 521890139 521890762 623 False 569 569 83.3860 171 798 1 chr7D.!!$F1 627
5 TraesCS7B01G054300 chr5B 710169268 710169947 679 True 621 621 83.3810 171 858 1 chr5B.!!$R1 687
6 TraesCS7B01G054300 chr3B 603825975 603826668 693 False 617 617 83.1440 171 858 1 chr3B.!!$F2 687
7 TraesCS7B01G054300 chr3B 596242583 596243278 695 False 586 586 82.3200 171 858 1 chr3B.!!$F1 687
8 TraesCS7B01G054300 chr2A 559827743 559828358 615 False 603 603 84.6400 171 783 1 chr2A.!!$F1 612
9 TraesCS7B01G054300 chr2B 87332652 87333267 615 True 593 593 84.3450 171 784 1 chr2B.!!$R1 613
10 TraesCS7B01G054300 chr1B 684732363 684732970 607 True 455 455 80.5070 236 858 1 chr1B.!!$R2 622
11 TraesCS7B01G054300 chr5A 198241065 198241635 570 False 222 222 74.7420 300 850 1 chr5A.!!$F2 550

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
572 580 0.250295 CCCAATGTCACGACACCACT 60.250 55.0 1.15 0.0 45.05 4.00 F
776 813 0.257039 GAGGAACCACATCCATGGCT 59.743 55.0 6.96 0.0 44.33 4.75 F
2249 2343 0.895100 TCCAGAAAATGCAGGCGCTT 60.895 50.0 7.64 0.0 39.64 4.68 F
3140 3234 0.253044 ACACGGAGGCAGCATTGTAT 59.747 50.0 0.00 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1943 0.814457 GTATGCAACCAAATCCGGCA 59.186 50.000 0.00 0.00 39.03 5.69 R
2655 2749 1.278127 ACCTGGAGTGAACCCGTAATG 59.722 52.381 0.00 0.00 0.00 1.90 R
3173 3267 0.179045 ACTTCTCGCTGTGCACCTTT 60.179 50.000 15.69 0.00 0.00 3.11 R
4449 4620 0.590195 GCCTCCATCGCATGCTAAAG 59.410 55.000 17.13 5.85 0.00 1.85 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
56 57 2.587522 GGATACCTGAAAATGCCCTCC 58.412 52.381 0.00 0.00 0.00 4.30
119 120 7.224362 CACTTGAAATGAGATCTAGAAATCGCT 59.776 37.037 0.00 0.00 0.00 4.93
136 137 3.963733 CTGAAGAAGCATCACCCCA 57.036 52.632 0.00 0.00 0.00 4.96
147 148 2.445427 CATCACCCCATGCAGTACAAA 58.555 47.619 0.00 0.00 0.00 2.83
153 154 1.612950 CCCATGCAGTACAAACTTGCA 59.387 47.619 8.92 8.92 41.07 4.08
154 155 2.035704 CCCATGCAGTACAAACTTGCAA 59.964 45.455 10.35 0.00 40.58 4.08
155 156 3.306225 CCCATGCAGTACAAACTTGCAAT 60.306 43.478 10.35 0.00 40.58 3.56
156 157 3.922240 CCATGCAGTACAAACTTGCAATC 59.078 43.478 10.35 0.00 40.58 2.67
157 158 4.321452 CCATGCAGTACAAACTTGCAATCT 60.321 41.667 10.35 0.00 40.58 2.40
158 159 5.106197 CCATGCAGTACAAACTTGCAATCTA 60.106 40.000 10.35 0.00 40.58 1.98
159 160 6.405065 CCATGCAGTACAAACTTGCAATCTAT 60.405 38.462 10.35 0.00 40.58 1.98
160 161 6.182039 TGCAGTACAAACTTGCAATCTATC 57.818 37.500 0.00 0.00 37.05 2.08
161 162 5.704978 TGCAGTACAAACTTGCAATCTATCA 59.295 36.000 0.00 0.00 37.05 2.15
162 163 6.375174 TGCAGTACAAACTTGCAATCTATCAT 59.625 34.615 0.00 0.00 37.05 2.45
163 164 6.909357 GCAGTACAAACTTGCAATCTATCATC 59.091 38.462 0.00 0.00 31.97 2.92
164 165 7.414429 GCAGTACAAACTTGCAATCTATCATCA 60.414 37.037 0.00 0.00 31.97 3.07
165 166 7.907045 CAGTACAAACTTGCAATCTATCATCAC 59.093 37.037 0.00 0.00 31.97 3.06
166 167 6.199937 ACAAACTTGCAATCTATCATCACC 57.800 37.500 0.00 0.00 0.00 4.02
167 168 5.711506 ACAAACTTGCAATCTATCATCACCA 59.288 36.000 0.00 0.00 0.00 4.17
168 169 6.209192 ACAAACTTGCAATCTATCATCACCAA 59.791 34.615 0.00 0.00 0.00 3.67
169 170 6.839124 AACTTGCAATCTATCATCACCAAA 57.161 33.333 0.00 0.00 0.00 3.28
200 202 2.430332 GGGACACATGAGGAGAAGAGAG 59.570 54.545 0.00 0.00 0.00 3.20
230 234 6.509418 AAAATGACACACACTTACAACACT 57.491 33.333 0.00 0.00 0.00 3.55
233 237 4.765273 TGACACACACTTACAACACTCAT 58.235 39.130 0.00 0.00 0.00 2.90
286 290 3.480470 ACAATACAACAAGAGCACTGCT 58.520 40.909 2.22 2.22 43.88 4.24
294 298 5.007724 ACAACAAGAGCACTGCTAAAGTAAC 59.992 40.000 2.71 0.00 39.88 2.50
295 299 3.741344 ACAAGAGCACTGCTAAAGTAACG 59.259 43.478 2.71 0.00 39.88 3.18
296 300 3.936372 AGAGCACTGCTAAAGTAACGA 57.064 42.857 2.71 0.00 39.88 3.85
297 301 4.252971 AGAGCACTGCTAAAGTAACGAA 57.747 40.909 2.71 0.00 39.88 3.85
298 302 4.822026 AGAGCACTGCTAAAGTAACGAAT 58.178 39.130 2.71 0.00 39.88 3.34
299 303 5.238583 AGAGCACTGCTAAAGTAACGAATT 58.761 37.500 2.71 0.00 39.88 2.17
300 304 6.395629 AGAGCACTGCTAAAGTAACGAATTA 58.604 36.000 2.71 0.00 39.88 1.40
301 305 7.042335 AGAGCACTGCTAAAGTAACGAATTAT 58.958 34.615 2.71 0.00 39.88 1.28
302 306 7.549488 AGAGCACTGCTAAAGTAACGAATTATT 59.451 33.333 2.71 0.00 39.88 1.40
388 393 2.205074 GCATCCGAGAGTACACAATGG 58.795 52.381 0.00 0.00 0.00 3.16
400 405 3.049674 CAATGGCGCGACACCACT 61.050 61.111 21.63 0.00 40.82 4.00
414 419 2.428187 CACTTGTGCCGTGGGGTA 59.572 61.111 0.00 0.00 34.97 3.69
424 429 2.093075 TGCCGTGGGGTATAATCGAAAA 60.093 45.455 0.00 0.00 34.97 2.29
454 461 1.497991 CAAAGACGACACCACGACAT 58.502 50.000 0.00 0.00 37.03 3.06
484 491 3.967715 GACAAGGTCGAAGGGCAC 58.032 61.111 0.00 0.00 0.00 5.01
555 563 2.202987 CGCATCTGAGACTGCCCC 60.203 66.667 9.98 0.00 34.89 5.80
560 568 1.064906 CATCTGAGACTGCCCCAATGT 60.065 52.381 0.00 0.00 0.00 2.71
572 580 0.250295 CCCAATGTCACGACACCACT 60.250 55.000 1.15 0.00 45.05 4.00
596 604 1.134487 CGTGCGGCACAATCGAAAT 59.866 52.632 30.23 0.00 33.40 2.17
604 612 1.399599 GCACAATCGAAATGTCACGCA 60.400 47.619 4.40 0.00 0.00 5.24
655 664 3.762288 GCCATCGGTATAGTCACATAGGA 59.238 47.826 0.00 0.00 0.00 2.94
660 669 3.887110 CGGTATAGTCACATAGGACACCA 59.113 47.826 0.00 0.00 40.29 4.17
665 674 1.809619 CACATAGGACACCACCGCG 60.810 63.158 0.00 0.00 34.73 6.46
666 675 2.890474 CATAGGACACCACCGCGC 60.890 66.667 0.00 0.00 34.73 6.86
689 711 0.533032 GTAGAGACACCCTGAGCACC 59.467 60.000 0.00 0.00 0.00 5.01
695 717 1.601759 CACCCTGAGCACCAACCAG 60.602 63.158 0.00 0.00 0.00 4.00
776 813 0.257039 GAGGAACCACATCCATGGCT 59.743 55.000 6.96 0.00 44.33 4.75
869 908 2.485479 GGCTCTTCCACTCTTTGACACA 60.485 50.000 0.00 0.00 34.01 3.72
870 909 2.545946 GCTCTTCCACTCTTTGACACAC 59.454 50.000 0.00 0.00 0.00 3.82
875 914 5.710099 TCTTCCACTCTTTGACACACTTTTT 59.290 36.000 0.00 0.00 0.00 1.94
876 915 5.309323 TCCACTCTTTGACACACTTTTTG 57.691 39.130 0.00 0.00 0.00 2.44
878 917 5.095490 CCACTCTTTGACACACTTTTTGAC 58.905 41.667 0.00 0.00 0.00 3.18
880 919 5.569059 CACTCTTTGACACACTTTTTGACAC 59.431 40.000 0.00 0.00 0.00 3.67
887 980 5.048846 ACACACTTTTTGACACCTAGGAT 57.951 39.130 17.98 2.27 0.00 3.24
900 993 7.168219 TGACACCTAGGATAAATATGCCATTC 58.832 38.462 17.98 0.00 0.00 2.67
907 1000 6.180472 AGGATAAATATGCCATTCCGTTAGG 58.820 40.000 0.00 0.00 39.46 2.69
925 1018 5.331235 CGTTAGGAAATTGAAACGTTTGCAC 60.331 40.000 20.10 4.66 39.73 4.57
964 1057 3.664486 CGATCGAACGGCTACATTTCTAG 59.336 47.826 10.26 0.00 0.00 2.43
965 1058 2.805845 TCGAACGGCTACATTTCTAGC 58.194 47.619 0.00 0.00 38.80 3.42
966 1059 2.426024 TCGAACGGCTACATTTCTAGCT 59.574 45.455 0.00 0.00 39.39 3.32
976 1070 6.071896 GGCTACATTTCTAGCTTCAAAAACCT 60.072 38.462 0.00 0.00 39.39 3.50
1278 1372 4.452733 CCAGTCCCGACCGCTTCC 62.453 72.222 0.00 0.00 0.00 3.46
1336 1430 1.758906 CCGACCTCCTCTTCCCCTC 60.759 68.421 0.00 0.00 0.00 4.30
1391 1485 1.075425 CGCTCAACTCTTCCAGCTCG 61.075 60.000 0.00 0.00 0.00 5.03
1601 1695 4.056125 CTCGCCGTGCTGTCCAGA 62.056 66.667 0.00 0.00 0.00 3.86
1646 1740 1.348008 GGATGGTCAGGGCAGGATCA 61.348 60.000 0.00 0.00 0.00 2.92
1668 1762 2.668889 AGCCTGACTCGACGACGT 60.669 61.111 0.00 0.00 40.69 4.34
1736 1830 1.648467 GAAGGTGCGTCCATGCCTTC 61.648 60.000 10.56 10.56 46.57 3.46
1808 1902 1.377202 ACTGTATGCCAAGTGCGGG 60.377 57.895 0.00 0.00 45.60 6.13
1813 1907 2.813226 TATGCCAAGTGCGGGGACAC 62.813 60.000 0.00 0.00 45.60 3.67
1849 1943 2.039084 GTCTCTTTGACAGGATGGTGGT 59.961 50.000 0.00 0.00 44.73 4.16
1912 2006 2.430332 CGGTTAATGGCATGGTTGGATT 59.570 45.455 0.00 0.00 0.00 3.01
2000 2094 2.927856 ATCCCGGTGCACAGTCCA 60.928 61.111 20.43 0.48 0.00 4.02
2249 2343 0.895100 TCCAGAAAATGCAGGCGCTT 60.895 50.000 7.64 0.00 39.64 4.68
2381 2475 6.655003 ACCTCGAACTCAATGTTTATGTCATT 59.345 34.615 0.00 0.00 39.30 2.57
2655 2749 1.473434 CCTTCCGGTCAATGACTAGCC 60.473 57.143 13.53 0.00 32.47 3.93
2705 2799 1.180029 GCACTTGCATGGTGGATCTT 58.820 50.000 17.91 0.00 41.59 2.40
2708 2802 3.087031 CACTTGCATGGTGGATCTTCTT 58.913 45.455 11.14 0.00 0.00 2.52
3086 3180 3.940221 TCTACTCGTACTTGGAGAAGCTC 59.060 47.826 3.60 0.00 35.49 4.09
3140 3234 0.253044 ACACGGAGGCAGCATTGTAT 59.747 50.000 0.00 0.00 0.00 2.29
3173 3267 4.820775 AGGAAGAGAAGGAGCATATGGTA 58.179 43.478 7.54 0.00 0.00 3.25
3176 3270 5.994668 GGAAGAGAAGGAGCATATGGTAAAG 59.005 44.000 7.54 0.00 0.00 1.85
3192 3286 0.179045 AAAGGTGCACAGCGAGAAGT 60.179 50.000 20.43 0.00 0.00 3.01
3215 3309 1.334869 GCCATCGCCTTTGGATTACTG 59.665 52.381 0.00 0.00 36.26 2.74
3221 3315 5.092554 TCGCCTTTGGATTACTGAATACA 57.907 39.130 0.00 0.00 33.80 2.29
3266 3360 1.507140 TCAAGAACCTGAGGGTGTGT 58.493 50.000 2.38 0.00 46.67 3.72
3275 3369 0.398522 TGAGGGTGTGTCTGGACTGT 60.399 55.000 2.38 0.00 0.00 3.55
3296 3390 5.919755 TGTCATAACGCCACCAAGATTATA 58.080 37.500 0.00 0.00 0.00 0.98
3338 3432 0.687920 TTGTGGTTAGGGATGCGTCA 59.312 50.000 8.47 0.00 0.00 4.35
3391 3485 3.197766 TCCTGTGGTGATTACTGGTGATC 59.802 47.826 0.00 0.00 38.07 2.92
3437 3531 9.393249 CTCTTAACAGATGATTAGTCGATTCTC 57.607 37.037 0.00 0.00 0.00 2.87
3438 3532 8.903820 TCTTAACAGATGATTAGTCGATTCTCA 58.096 33.333 0.00 0.00 0.00 3.27
3493 3587 9.178758 CTGAGCTAAAATAATTTGTAACCCTCT 57.821 33.333 0.00 0.00 0.00 3.69
3501 3595 1.847798 TTGTAACCCTCTGGCGCCAT 61.848 55.000 32.87 17.19 33.59 4.40
3550 3646 3.609853 TGACTCATAACCAGCACATTCC 58.390 45.455 0.00 0.00 0.00 3.01
3551 3647 2.945668 GACTCATAACCAGCACATTCCC 59.054 50.000 0.00 0.00 0.00 3.97
3624 3720 6.092122 TCTCTCGCCAGTATACAACAATTTTG 59.908 38.462 5.50 0.00 0.00 2.44
3648 3744 1.736681 GCTCATGGAGAAGCACAACTC 59.263 52.381 0.00 0.00 0.00 3.01
3659 3755 2.704572 AGCACAACTCCTTCAGCATAC 58.295 47.619 0.00 0.00 0.00 2.39
3664 3760 4.067896 ACAACTCCTTCAGCATACAGTTG 58.932 43.478 7.84 7.84 44.11 3.16
3677 3773 4.608445 GCATACAGTTGAAGTCGTTCACAC 60.608 45.833 0.00 0.00 42.60 3.82
3692 3788 4.083855 CGTTCACACAAACATAGTGCTGAT 60.084 41.667 0.00 0.00 40.59 2.90
3693 3789 5.149273 GTTCACACAAACATAGTGCTGATG 58.851 41.667 0.00 0.00 40.59 3.07
3716 3812 5.600898 TGATAGAACCCTTGTAATGGATCGA 59.399 40.000 0.00 0.00 31.60 3.59
3722 3818 7.832187 AGAACCCTTGTAATGGATCGAAAATTA 59.168 33.333 0.00 0.00 31.60 1.40
3738 3834 9.814899 ATCGAAAATTATAATGTTTGATTGCCA 57.185 25.926 19.54 1.64 34.47 4.92
3739 3835 9.645059 TCGAAAATTATAATGTTTGATTGCCAA 57.355 25.926 12.61 0.00 0.00 4.52
3898 4042 9.468532 TCATTACTTCACAATAGATTCTCGATG 57.531 33.333 0.00 0.00 0.00 3.84
3900 4044 6.227298 ACTTCACAATAGATTCTCGATGGT 57.773 37.500 0.00 0.00 0.00 3.55
3901 4045 6.045318 ACTTCACAATAGATTCTCGATGGTG 58.955 40.000 0.00 0.00 35.53 4.17
3902 4046 5.598416 TCACAATAGATTCTCGATGGTGT 57.402 39.130 4.57 0.00 35.66 4.16
3905 4057 4.572389 ACAATAGATTCTCGATGGTGTTGC 59.428 41.667 0.00 0.00 0.00 4.17
3907 4059 2.898705 AGATTCTCGATGGTGTTGCTC 58.101 47.619 0.00 0.00 0.00 4.26
3916 4068 1.155889 TGGTGTTGCTCGCTGTAATG 58.844 50.000 0.00 0.00 0.00 1.90
3921 4073 2.223144 TGTTGCTCGCTGTAATGACAAC 59.777 45.455 0.00 0.00 34.35 3.32
3927 4079 1.136363 CGCTGTAATGACAACGTGGTG 60.136 52.381 0.00 0.00 39.71 4.17
3940 4092 1.555075 ACGTGGTGTCTGCTAATGGAT 59.445 47.619 0.00 0.00 0.00 3.41
3941 4093 2.027192 ACGTGGTGTCTGCTAATGGATT 60.027 45.455 0.00 0.00 0.00 3.01
3942 4094 2.352651 CGTGGTGTCTGCTAATGGATTG 59.647 50.000 0.00 0.00 0.00 2.67
3943 4095 2.684881 GTGGTGTCTGCTAATGGATTGG 59.315 50.000 0.00 0.00 0.00 3.16
3944 4096 2.575735 TGGTGTCTGCTAATGGATTGGA 59.424 45.455 0.00 0.00 0.00 3.53
3948 4100 4.033009 TGTCTGCTAATGGATTGGAGAGA 58.967 43.478 0.00 0.00 0.00 3.10
3950 4102 3.070734 TCTGCTAATGGATTGGAGAGAGC 59.929 47.826 0.00 0.00 0.00 4.09
3951 4103 2.773661 TGCTAATGGATTGGAGAGAGCA 59.226 45.455 0.00 0.00 36.39 4.26
3953 4105 3.181456 GCTAATGGATTGGAGAGAGCACT 60.181 47.826 0.00 0.00 0.00 4.40
3992 4144 2.029838 AAAGTTATCGAGGGCAGCTG 57.970 50.000 10.11 10.11 0.00 4.24
4062 4214 0.671781 AGGTTTGCTGCTGAGCTACG 60.672 55.000 5.83 0.00 46.39 3.51
4088 4240 3.009363 TCTTGGTCATGGCAGAATCTTCA 59.991 43.478 0.00 0.00 0.00 3.02
4131 4289 4.692625 CCAGATTTCGAGACATGTGTTCTT 59.307 41.667 1.15 0.00 0.00 2.52
4214 4378 4.611310 TCGTGTTGAATAGAGAGTACCG 57.389 45.455 0.00 0.00 0.00 4.02
4225 4389 3.973425 AGAGAGTACCGGTAGGCTTAAA 58.027 45.455 16.41 0.00 42.76 1.52
4226 4390 4.544683 AGAGAGTACCGGTAGGCTTAAAT 58.455 43.478 16.41 0.00 42.76 1.40
4227 4391 4.341520 AGAGAGTACCGGTAGGCTTAAATG 59.658 45.833 16.41 0.00 42.76 2.32
4267 4431 8.800332 AGTAATACGAAGAAAGGACTGTTAAGA 58.200 33.333 0.00 0.00 0.00 2.10
4283 4451 8.600449 ACTGTTAAGAAGAGTGATGAAGAAAG 57.400 34.615 0.00 0.00 33.21 2.62
4284 4452 8.424918 ACTGTTAAGAAGAGTGATGAAGAAAGA 58.575 33.333 0.00 0.00 33.21 2.52
4298 4466 9.070179 TGATGAAGAAAGAAGATTCATGACAAA 57.930 29.630 0.00 0.00 42.25 2.83
4301 4469 8.347771 TGAAGAAAGAAGATTCATGACAAACAG 58.652 33.333 0.00 0.00 0.00 3.16
4353 4523 9.217278 AGATAATTAACTTATGAGCTGCATGAG 57.783 33.333 1.02 12.96 43.99 2.90
4358 4528 6.770746 AACTTATGAGCTGCATGAGAATTT 57.229 33.333 18.26 6.03 41.73 1.82
4362 4532 7.226325 ACTTATGAGCTGCATGAGAATTTAGTC 59.774 37.037 18.26 0.00 41.73 2.59
4364 4534 3.201290 AGCTGCATGAGAATTTAGTCCG 58.799 45.455 1.02 0.00 0.00 4.79
4405 4576 2.256461 CTTTGGCCGCTTGCAGTC 59.744 61.111 0.00 0.00 43.89 3.51
4406 4577 2.518112 TTTGGCCGCTTGCAGTCA 60.518 55.556 0.00 0.00 43.89 3.41
4407 4578 2.467946 CTTTGGCCGCTTGCAGTCAG 62.468 60.000 0.00 0.00 43.89 3.51
4409 4580 4.704833 GGCCGCTTGCAGTCAGGA 62.705 66.667 0.00 0.00 43.89 3.86
4410 4581 3.426568 GCCGCTTGCAGTCAGGAC 61.427 66.667 4.14 0.00 40.77 3.85
4411 4582 2.345244 CCGCTTGCAGTCAGGACT 59.655 61.111 0.00 0.00 43.61 3.85
4425 4596 1.070445 CAGGACTCAGGATCCAGATGC 59.930 57.143 15.82 6.20 38.86 3.91
4426 4597 1.062275 AGGACTCAGGATCCAGATGCT 60.062 52.381 15.82 9.27 40.25 3.79
4437 4608 7.123397 TCAGGATCCAGATGCTATTCAGTATAC 59.877 40.741 15.82 0.00 37.39 1.47
4439 4610 7.622878 AGGATCCAGATGCTATTCAGTATACAT 59.377 37.037 15.82 0.00 37.74 2.29
4449 4620 6.369065 GCTATTCAGTATACATAACCAGGCAC 59.631 42.308 5.50 0.00 0.00 5.01
4454 4625 7.497595 TCAGTATACATAACCAGGCACTTTAG 58.502 38.462 5.50 0.00 34.60 1.85
4461 4632 1.026182 CCAGGCACTTTAGCATGCGA 61.026 55.000 13.01 3.59 44.30 5.10
4477 4648 0.109132 GCGATGGAGGCAAACAAAGG 60.109 55.000 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.640952 CATTTTCAGGTATCCCTTTCCTTTATA 57.359 33.333 0.00 0.00 39.89 0.98
31 32 3.384789 GGGCATTTTCAGGTATCCCTTTC 59.615 47.826 0.00 0.00 39.89 2.62
33 34 2.587307 AGGGCATTTTCAGGTATCCCTT 59.413 45.455 0.00 0.00 39.89 3.95
36 37 2.175715 AGGAGGGCATTTTCAGGTATCC 59.824 50.000 0.00 0.00 0.00 2.59
39 40 2.274542 TGAGGAGGGCATTTTCAGGTA 58.725 47.619 0.00 0.00 0.00 3.08
45 46 2.250924 CTGGTTTGAGGAGGGCATTTT 58.749 47.619 0.00 0.00 0.00 1.82
56 57 6.744112 TGTGTTATTTAAAGCCTGGTTTGAG 58.256 36.000 0.00 0.00 0.00 3.02
119 120 1.956636 GCATGGGGTGATGCTTCTTCA 60.957 52.381 0.00 0.00 44.57 3.02
136 137 6.375174 TGATAGATTGCAAGTTTGTACTGCAT 59.625 34.615 4.94 0.00 37.85 3.96
147 148 6.839124 TTTTGGTGATGATAGATTGCAAGT 57.161 33.333 4.94 0.00 0.00 3.16
168 169 4.344104 CTCATGTGTCCCCCTGTATTTTT 58.656 43.478 0.00 0.00 0.00 1.94
169 170 3.309121 CCTCATGTGTCCCCCTGTATTTT 60.309 47.826 0.00 0.00 0.00 1.82
182 184 5.083122 TCTTTCTCTCTTCTCCTCATGTGT 58.917 41.667 0.00 0.00 0.00 3.72
211 213 4.195225 TGAGTGTTGTAAGTGTGTGTCA 57.805 40.909 0.00 0.00 0.00 3.58
220 224 5.046591 TCTCCCCTGTTATGAGTGTTGTAAG 60.047 44.000 0.00 0.00 0.00 2.34
221 225 4.841813 TCTCCCCTGTTATGAGTGTTGTAA 59.158 41.667 0.00 0.00 0.00 2.41
230 234 5.538433 CCTTTTTGTTTCTCCCCTGTTATGA 59.462 40.000 0.00 0.00 0.00 2.15
233 237 4.079096 TCCCTTTTTGTTTCTCCCCTGTTA 60.079 41.667 0.00 0.00 0.00 2.41
286 290 7.361889 TGGCGTTCAATAATTCGTTACTTTA 57.638 32.000 0.00 0.00 0.00 1.85
294 298 2.788786 GCCAATGGCGTTCAATAATTCG 59.211 45.455 9.14 0.00 39.62 3.34
319 323 2.435059 GTCCTGGCTTGGTCTCGC 60.435 66.667 0.00 0.00 0.00 5.03
400 405 1.473610 CGATTATACCCCACGGCACAA 60.474 52.381 0.00 0.00 0.00 3.33
414 419 4.242475 TGCTCGTGTGTCTTTTCGATTAT 58.758 39.130 0.00 0.00 0.00 1.28
424 429 0.384309 TCGTCTTTGCTCGTGTGTCT 59.616 50.000 0.00 0.00 0.00 3.41
484 491 0.899720 TGGTTTGGTCTACTAGGCGG 59.100 55.000 0.00 0.00 0.00 6.13
555 563 1.939934 ACAAGTGGTGTCGTGACATTG 59.060 47.619 5.91 8.88 43.97 2.82
582 590 1.786575 CGTGACATTTCGATTGTGCCG 60.787 52.381 6.28 4.90 0.00 5.69
596 604 2.243957 CGTCTTGGCTTGCGTGACA 61.244 57.895 10.11 0.00 0.00 3.58
604 612 0.178068 ATATGGCGTCGTCTTGGCTT 59.822 50.000 0.00 0.00 0.00 4.35
660 669 3.507009 GTCTCTACCTCGCGCGGT 61.507 66.667 31.69 25.78 41.10 5.68
665 674 0.680280 TCAGGGTGTCTCTACCTCGC 60.680 60.000 0.00 0.00 40.66 5.03
666 675 1.384525 CTCAGGGTGTCTCTACCTCG 58.615 60.000 0.00 0.00 40.66 4.63
668 677 0.409876 TGCTCAGGGTGTCTCTACCT 59.590 55.000 0.00 0.00 40.66 3.08
669 678 0.533032 GTGCTCAGGGTGTCTCTACC 59.467 60.000 0.00 0.00 40.10 3.18
670 679 0.533032 GGTGCTCAGGGTGTCTCTAC 59.467 60.000 0.00 0.00 0.00 2.59
671 680 0.114364 TGGTGCTCAGGGTGTCTCTA 59.886 55.000 0.00 0.00 0.00 2.43
689 711 2.672714 TCGTCGATGTTCTTCTGGTTG 58.327 47.619 4.21 0.00 0.00 3.77
695 717 2.841329 CTCGTCTTCGTCGATGTTCTTC 59.159 50.000 4.21 0.00 36.73 2.87
830 869 1.993956 CCCCCTTGTCATGTTGTCAA 58.006 50.000 0.00 0.00 0.00 3.18
839 878 1.463214 TGGAAGAGCCCCCTTGTCA 60.463 57.895 0.00 0.00 34.97 3.58
869 908 8.903820 GCATATTTATCCTAGGTGTCAAAAAGT 58.096 33.333 9.08 0.00 0.00 2.66
870 909 8.352942 GGCATATTTATCCTAGGTGTCAAAAAG 58.647 37.037 9.08 0.00 0.00 2.27
875 914 6.702449 ATGGCATATTTATCCTAGGTGTCA 57.298 37.500 9.08 5.83 0.00 3.58
876 915 6.599638 GGAATGGCATATTTATCCTAGGTGTC 59.400 42.308 9.08 0.00 0.00 3.67
878 917 5.586243 CGGAATGGCATATTTATCCTAGGTG 59.414 44.000 9.08 0.00 0.00 4.00
880 919 5.745227 ACGGAATGGCATATTTATCCTAGG 58.255 41.667 0.82 0.82 0.00 3.02
900 993 4.147479 GCAAACGTTTCAATTTCCTAACGG 59.853 41.667 11.37 0.00 45.41 4.44
964 1057 5.465390 GGGTTTGTTATGAGGTTTTTGAAGC 59.535 40.000 0.00 0.00 0.00 3.86
965 1058 5.989168 GGGGTTTGTTATGAGGTTTTTGAAG 59.011 40.000 0.00 0.00 0.00 3.02
966 1059 5.452077 CGGGGTTTGTTATGAGGTTTTTGAA 60.452 40.000 0.00 0.00 0.00 2.69
976 1070 0.609681 GTGGCCGGGGTTTGTTATGA 60.610 55.000 2.18 0.00 0.00 2.15
1265 1359 3.755628 CGAAGGAAGCGGTCGGGA 61.756 66.667 0.00 0.00 0.00 5.14
1278 1372 2.815647 GAGGAGGGCGTTGCGAAG 60.816 66.667 0.00 0.00 0.00 3.79
1336 1430 1.306226 AAGGAGAAGGAGTCGGGGG 60.306 63.158 0.00 0.00 0.00 5.40
1401 1495 2.103340 GGCGGAGAGAGAAGCGAC 59.897 66.667 0.00 0.00 0.00 5.19
1599 1693 1.840650 CCTCCATGGCCTCCGATCT 60.841 63.158 6.96 0.00 0.00 2.75
1646 1740 4.427661 GTCGAGTCAGGCTGCGCT 62.428 66.667 10.34 10.38 0.00 5.92
1668 1762 2.264480 CGGCAGGACGGATGACAA 59.736 61.111 0.00 0.00 0.00 3.18
1736 1830 1.447317 CCAATCCGCATTTCTCCCCG 61.447 60.000 0.00 0.00 0.00 5.73
1808 1902 3.036084 CGTGCACACTCCGTGTCC 61.036 66.667 18.64 0.00 43.92 4.02
1813 1907 3.097728 GACGTCGTGCACACTCCG 61.098 66.667 18.64 14.37 0.00 4.63
1849 1943 0.814457 GTATGCAACCAAATCCGGCA 59.186 50.000 0.00 0.00 39.03 5.69
1877 1971 4.202264 CCATTAACCGAGTAGCCTGAGATT 60.202 45.833 0.00 0.00 0.00 2.40
1912 2006 1.270625 CCTTAAACAGCTCCACCGACA 60.271 52.381 0.00 0.00 0.00 4.35
2000 2094 2.017049 GTAAGCTGTTCATGCCCGAAT 58.983 47.619 0.00 0.00 0.00 3.34
2249 2343 0.814457 GCGGATTTGGTGGCACATTA 59.186 50.000 20.82 3.51 44.52 1.90
2381 2475 2.385013 ACATGTCAATGAGCGCTGTA 57.615 45.000 18.48 3.36 37.24 2.74
2655 2749 1.278127 ACCTGGAGTGAACCCGTAATG 59.722 52.381 0.00 0.00 0.00 1.90
3035 3129 4.386951 TGTGGGTGGGCACGATCG 62.387 66.667 14.88 14.88 0.00 3.69
3086 3180 4.334759 CCAGCCTCAATCATCTTTGTAGTG 59.665 45.833 0.00 0.00 0.00 2.74
3140 3234 0.323957 TCTCTTCCTCCTCGACGTCA 59.676 55.000 17.16 1.87 0.00 4.35
3173 3267 0.179045 ACTTCTCGCTGTGCACCTTT 60.179 50.000 15.69 0.00 0.00 3.11
3176 3270 1.571460 CAACTTCTCGCTGTGCACC 59.429 57.895 15.69 0.00 0.00 5.01
3212 3306 3.248024 TGTCCCAGGTTCTGTATTCAGT 58.752 45.455 0.00 0.00 41.91 3.41
3215 3309 3.769844 TCTCTGTCCCAGGTTCTGTATTC 59.230 47.826 0.00 0.00 31.51 1.75
3221 3315 2.465813 CTGATCTCTGTCCCAGGTTCT 58.534 52.381 0.00 0.00 31.51 3.01
3257 3351 0.318762 GACAGTCCAGACACACCCTC 59.681 60.000 0.00 0.00 0.00 4.30
3266 3360 1.067142 GTGGCGTTATGACAGTCCAGA 60.067 52.381 0.00 0.00 34.99 3.86
3275 3369 6.170506 GGATATAATCTTGGTGGCGTTATGA 58.829 40.000 0.00 0.00 0.00 2.15
3296 3390 1.599047 CCTCTGCGTCACCTTGGAT 59.401 57.895 0.00 0.00 0.00 3.41
3362 3456 2.363306 AATCACCACAGGAGCAAACA 57.637 45.000 0.00 0.00 0.00 2.83
3391 3485 2.092538 AGATCAGAGCAAATCCCAGTGG 60.093 50.000 0.63 0.63 0.00 4.00
3493 3587 1.068753 CCACACAAAAATGGCGCCA 59.931 52.632 34.80 34.80 0.00 5.69
3501 3595 3.096092 ACTTTCTCCAGCCACACAAAAA 58.904 40.909 0.00 0.00 0.00 1.94
3542 3638 2.094026 GGAACTGAAATGGGGAATGTGC 60.094 50.000 0.00 0.00 0.00 4.57
3550 3646 3.230134 TCTTGTTGGGAACTGAAATGGG 58.770 45.455 0.00 0.00 0.00 4.00
3551 3647 3.305608 GCTCTTGTTGGGAACTGAAATGG 60.306 47.826 0.00 0.00 0.00 3.16
3596 3692 3.762288 TGTTGTATACTGGCGAGAGAGTT 59.238 43.478 1.44 0.00 0.00 3.01
3624 3720 1.077930 TGCTTCTCCATGAGCTGGC 60.078 57.895 0.00 0.41 45.52 4.85
3659 3755 4.088648 GTTTGTGTGAACGACTTCAACTG 58.911 43.478 0.00 0.00 38.17 3.16
3664 3760 5.432157 CACTATGTTTGTGTGAACGACTTC 58.568 41.667 0.00 0.00 33.95 3.01
3677 3773 6.017605 GGGTTCTATCATCAGCACTATGTTTG 60.018 42.308 0.00 0.00 0.00 2.93
3692 3788 5.600898 TCGATCCATTACAAGGGTTCTATCA 59.399 40.000 3.14 0.00 0.00 2.15
3693 3789 6.097915 TCGATCCATTACAAGGGTTCTATC 57.902 41.667 3.14 0.00 0.00 2.08
3722 3818 6.913873 GCAATCTTGGCAATCAAACATTAT 57.086 33.333 0.00 0.00 34.56 1.28
3856 4000 9.137459 TGAAGTAATGATTTGTTACCAGGAAAA 57.863 29.630 0.00 0.00 33.55 2.29
3897 4041 1.155889 CATTACAGCGAGCAACACCA 58.844 50.000 0.00 0.00 0.00 4.17
3898 4042 1.128692 GTCATTACAGCGAGCAACACC 59.871 52.381 0.00 0.00 0.00 4.16
3900 4044 2.162319 TGTCATTACAGCGAGCAACA 57.838 45.000 0.00 0.00 0.00 3.33
3901 4045 2.839474 GTTGTCATTACAGCGAGCAAC 58.161 47.619 0.00 0.00 36.83 4.17
3916 4068 1.860676 TTAGCAGACACCACGTTGTC 58.139 50.000 11.62 11.62 45.45 3.18
3921 4073 2.315925 ATCCATTAGCAGACACCACG 57.684 50.000 0.00 0.00 0.00 4.94
3927 4079 4.630111 CTCTCTCCAATCCATTAGCAGAC 58.370 47.826 0.00 0.00 0.00 3.51
3992 4144 5.314923 TCATTCAGCATCTTAGGCAAAAC 57.685 39.130 0.00 0.00 0.00 2.43
3999 4151 4.634883 ACTGCAGTTCATTCAGCATCTTAG 59.365 41.667 15.25 0.00 36.28 2.18
4062 4214 2.359850 TGCCATGACCAAGACGGC 60.360 61.111 0.00 0.00 43.28 5.68
4088 4240 2.838360 TGGCACACACTGGCTGAT 59.162 55.556 0.00 0.00 45.96 2.90
4200 4364 3.753815 AGCCTACCGGTACTCTCTATTC 58.246 50.000 11.16 0.00 0.00 1.75
4206 4370 4.099113 GTCATTTAAGCCTACCGGTACTCT 59.901 45.833 11.16 7.64 0.00 3.24
4207 4371 4.366586 GTCATTTAAGCCTACCGGTACTC 58.633 47.826 11.16 5.20 0.00 2.59
4214 4378 4.781934 AGACATGGTCATTTAAGCCTACC 58.218 43.478 0.00 0.00 34.60 3.18
4225 4389 7.327975 TCGTATTACTTTCAAGACATGGTCAT 58.672 34.615 0.00 0.00 34.60 3.06
4226 4390 6.693466 TCGTATTACTTTCAAGACATGGTCA 58.307 36.000 0.00 0.00 34.60 4.02
4227 4391 7.544566 TCTTCGTATTACTTTCAAGACATGGTC 59.455 37.037 0.00 0.00 0.00 4.02
4267 4431 8.948145 CATGAATCTTCTTTCTTCATCACTCTT 58.052 33.333 0.00 0.00 37.48 2.85
4283 4451 6.566197 AGTTCCTGTTTGTCATGAATCTTC 57.434 37.500 0.00 0.00 34.33 2.87
4284 4452 8.517878 CAATAGTTCCTGTTTGTCATGAATCTT 58.482 33.333 0.00 0.00 34.33 2.40
4298 4466 6.711277 TCATAAGCTTGACAATAGTTCCTGT 58.289 36.000 9.86 0.00 0.00 4.00
4301 4469 6.818644 TGTCTCATAAGCTTGACAATAGTTCC 59.181 38.462 9.86 0.00 36.64 3.62
4344 4514 2.939103 ACGGACTAAATTCTCATGCAGC 59.061 45.455 0.00 0.00 0.00 5.25
4353 4523 5.485620 AGGTAGGAACAACGGACTAAATTC 58.514 41.667 0.00 0.00 0.00 2.17
4358 4528 3.019564 GCTAGGTAGGAACAACGGACTA 58.980 50.000 0.00 0.00 0.00 2.59
4362 4532 1.136500 GGAGCTAGGTAGGAACAACGG 59.864 57.143 0.00 0.00 0.00 4.44
4364 4534 3.097614 TGAGGAGCTAGGTAGGAACAAC 58.902 50.000 0.00 0.00 0.00 3.32
4405 4576 1.070445 GCATCTGGATCCTGAGTCCTG 59.930 57.143 23.74 18.04 36.68 3.86
4406 4577 1.062275 AGCATCTGGATCCTGAGTCCT 60.062 52.381 23.74 16.55 36.68 3.85
4407 4578 1.422531 AGCATCTGGATCCTGAGTCC 58.577 55.000 23.74 14.90 36.26 3.85
4408 4579 4.282957 TGAATAGCATCTGGATCCTGAGTC 59.717 45.833 23.74 17.48 0.00 3.36
4409 4580 4.229639 TGAATAGCATCTGGATCCTGAGT 58.770 43.478 23.74 14.41 0.00 3.41
4410 4581 4.283978 ACTGAATAGCATCTGGATCCTGAG 59.716 45.833 23.74 16.85 0.00 3.35
4411 4582 4.229639 ACTGAATAGCATCTGGATCCTGA 58.770 43.478 22.12 22.12 0.00 3.86
4425 4596 7.671302 AGTGCCTGGTTATGTATACTGAATAG 58.329 38.462 4.17 2.27 0.00 1.73
4426 4597 7.612065 AGTGCCTGGTTATGTATACTGAATA 57.388 36.000 4.17 0.00 0.00 1.75
4437 4608 3.489738 GCATGCTAAAGTGCCTGGTTATG 60.490 47.826 11.37 0.00 35.35 1.90
4439 4610 2.091541 GCATGCTAAAGTGCCTGGTTA 58.908 47.619 11.37 0.00 35.35 2.85
4449 4620 0.590195 GCCTCCATCGCATGCTAAAG 59.410 55.000 17.13 5.85 0.00 1.85
4454 4625 1.226773 GTTTGCCTCCATCGCATGC 60.227 57.895 7.91 7.91 35.83 4.06
4461 4632 2.962859 AGAACCTTTGTTTGCCTCCAT 58.037 42.857 0.00 0.00 33.97 3.41


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

AutoCloner maintained by Alex Coulton.