Multiple sequence alignment - TraesCS1A01G115500

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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 TraesCS1A01G115500 chr1A 100.000 9877 0 0 1 9877 120001880 120011756 0.000000e+00 18240.0
1 TraesCS1A01G115500 chr1A 97.348 264 7 0 1979 2242 120008870 120009133 5.440000e-122 449.0
2 TraesCS1A01G115500 chr2A 97.354 5292 123 7 1979 7255 82981887 82976598 0.000000e+00 8981.0
3 TraesCS1A01G115500 chr7A 94.119 5169 273 17 1979 7129 649826923 649821768 0.000000e+00 7832.0
4 TraesCS1A01G115500 chrUn 92.807 5005 322 16 1979 6962 92275503 92280490 0.000000e+00 7214.0
5 TraesCS1A01G115500 chr3B 90.393 5236 452 32 1978 7189 763656113 763650905 0.000000e+00 6835.0
6 TraesCS1A01G115500 chr3B 84.493 3147 402 46 4082 7191 25298464 25301561 0.000000e+00 3029.0
7 TraesCS1A01G115500 chr3B 88.562 1495 132 21 5789 7254 772603186 772604670 0.000000e+00 1777.0
8 TraesCS1A01G115500 chr3B 87.132 272 24 9 1979 2243 789351309 789351042 2.090000e-76 298.0
9 TraesCS1A01G115500 chr3B 87.132 272 24 9 1979 2243 789386346 789386079 2.090000e-76 298.0
10 TraesCS1A01G115500 chr4A 89.556 4433 422 22 1979 6390 736455380 736450968 0.000000e+00 5583.0
11 TraesCS1A01G115500 chr4A 82.639 144 20 5 58 197 298243880 298243738 1.350000e-23 122.0
12 TraesCS1A01G115500 chr2B 89.917 4344 398 20 1979 6302 387102651 387098328 0.000000e+00 5559.0
13 TraesCS1A01G115500 chr7B 89.351 3775 356 22 1978 5746 621785022 621788756 0.000000e+00 4702.0
14 TraesCS1A01G115500 chr7B 79.832 119 19 4 80 194 614943667 614943550 2.290000e-11 82.4
15 TraesCS1A01G115500 chr3A 95.925 2675 95 5 1984 4657 708858999 708856338 0.000000e+00 4324.0
16 TraesCS1A01G115500 chr3A 95.717 2615 88 10 4655 7255 708850387 708847783 0.000000e+00 4187.0
17 TraesCS1A01G115500 chr3A 90.189 265 16 5 1979 2242 708848039 708847784 4.420000e-88 337.0
18 TraesCS1A01G115500 chr4D 89.751 3210 284 30 4074 7254 214965208 214968401 0.000000e+00 4063.0
19 TraesCS1A01G115500 chr4D 87.778 270 20 11 1979 2242 214968139 214968401 4.480000e-78 303.0
20 TraesCS1A01G115500 chr3D 89.536 3211 283 25 4072 7254 578172583 578169398 0.000000e+00 4019.0
21 TraesCS1A01G115500 chr3D 80.000 130 19 7 61 185 347446772 347446899 1.370000e-13 89.8
22 TraesCS1A01G115500 chr1D 90.227 2466 149 33 7443 9877 112768585 112770989 0.000000e+00 3134.0
23 TraesCS1A01G115500 chr1D 91.507 1672 61 28 367 1970 112766772 112768430 0.000000e+00 2226.0
24 TraesCS1A01G115500 chr1D 88.952 706 29 24 199 862 112751860 112752558 0.000000e+00 826.0
25 TraesCS1A01G115500 chr1D 87.955 357 34 7 1 350 112766032 112766386 7.140000e-111 412.0
26 TraesCS1A01G115500 chr1D 88.177 203 17 4 1 200 112751589 112751787 1.660000e-57 235.0
27 TraesCS1A01G115500 chr1D 91.964 112 8 1 7294 7404 112768473 112768584 1.330000e-33 156.0
28 TraesCS1A01G115500 chr2D 95.187 1974 87 7 1979 3948 351386802 351384833 0.000000e+00 3112.0
29 TraesCS1A01G115500 chr5B 91.187 2190 188 4 3306 5494 661330939 661328754 0.000000e+00 2970.0
30 TraesCS1A01G115500 chr5B 87.302 63 6 2 82 144 186970622 186970562 4.950000e-08 71.3
31 TraesCS1A01G115500 chr6B 86.422 2703 326 19 4082 6758 561656986 561659673 0.000000e+00 2920.0
32 TraesCS1A01G115500 chr1B 95.923 1717 57 5 8001 9717 172380386 172382089 0.000000e+00 2771.0
33 TraesCS1A01G115500 chr1B 93.920 1546 57 7 448 1973 172378180 172379708 0.000000e+00 2300.0
34 TraesCS1A01G115500 chr1B 96.608 678 20 3 7256 7932 172379710 172380385 0.000000e+00 1122.0
35 TraesCS1A01G115500 chr1B 98.131 107 2 0 9771 9877 172387189 172387295 4.710000e-43 187.0
36 TraesCS1A01G115500 chr7D 80.000 120 19 4 81 197 10345416 10345533 6.360000e-12 84.2
37 TraesCS1A01G115500 chr6D 77.703 148 23 8 59 197 260058397 260058543 2.290000e-11 82.4
38 TraesCS1A01G115500 chr5A 81.579 76 14 0 65 140 485581949 485582024 8.280000e-06 63.9


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 TraesCS1A01G115500 chr1A 120001880 120011756 9876 False 9344.500000 18240 98.674000 1 9877 2 chr1A.!!$F1 9876
1 TraesCS1A01G115500 chr2A 82976598 82981887 5289 True 8981.000000 8981 97.354000 1979 7255 1 chr2A.!!$R1 5276
2 TraesCS1A01G115500 chr7A 649821768 649826923 5155 True 7832.000000 7832 94.119000 1979 7129 1 chr7A.!!$R1 5150
3 TraesCS1A01G115500 chrUn 92275503 92280490 4987 False 7214.000000 7214 92.807000 1979 6962 1 chrUn.!!$F1 4983
4 TraesCS1A01G115500 chr3B 763650905 763656113 5208 True 6835.000000 6835 90.393000 1978 7189 1 chr3B.!!$R1 5211
5 TraesCS1A01G115500 chr3B 25298464 25301561 3097 False 3029.000000 3029 84.493000 4082 7191 1 chr3B.!!$F1 3109
6 TraesCS1A01G115500 chr3B 772603186 772604670 1484 False 1777.000000 1777 88.562000 5789 7254 1 chr3B.!!$F2 1465
7 TraesCS1A01G115500 chr4A 736450968 736455380 4412 True 5583.000000 5583 89.556000 1979 6390 1 chr4A.!!$R2 4411
8 TraesCS1A01G115500 chr2B 387098328 387102651 4323 True 5559.000000 5559 89.917000 1979 6302 1 chr2B.!!$R1 4323
9 TraesCS1A01G115500 chr7B 621785022 621788756 3734 False 4702.000000 4702 89.351000 1978 5746 1 chr7B.!!$F1 3768
10 TraesCS1A01G115500 chr3A 708856338 708858999 2661 True 4324.000000 4324 95.925000 1984 4657 1 chr3A.!!$R1 2673
11 TraesCS1A01G115500 chr3A 708847783 708850387 2604 True 2262.000000 4187 92.953000 1979 7255 2 chr3A.!!$R2 5276
12 TraesCS1A01G115500 chr4D 214965208 214968401 3193 False 2183.000000 4063 88.764500 1979 7254 2 chr4D.!!$F1 5275
13 TraesCS1A01G115500 chr3D 578169398 578172583 3185 True 4019.000000 4019 89.536000 4072 7254 1 chr3D.!!$R1 3182
14 TraesCS1A01G115500 chr1D 112766032 112770989 4957 False 1482.000000 3134 90.413250 1 9877 4 chr1D.!!$F2 9876
15 TraesCS1A01G115500 chr1D 112751589 112752558 969 False 530.500000 826 88.564500 1 862 2 chr1D.!!$F1 861
16 TraesCS1A01G115500 chr2D 351384833 351386802 1969 True 3112.000000 3112 95.187000 1979 3948 1 chr2D.!!$R1 1969
17 TraesCS1A01G115500 chr5B 661328754 661330939 2185 True 2970.000000 2970 91.187000 3306 5494 1 chr5B.!!$R2 2188
18 TraesCS1A01G115500 chr6B 561656986 561659673 2687 False 2920.000000 2920 86.422000 4082 6758 1 chr6B.!!$F1 2676
19 TraesCS1A01G115500 chr1B 172378180 172382089 3909 False 2064.333333 2771 95.483667 448 9717 3 chr1B.!!$F2 9269

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
879 1381 0.240145 CCGCTTGATATCCGTCGCTA 59.760 55.000 0.00 0.00 0.00 4.26 F
928 1431 1.121407 AGCCCCTTTTGGTTCTTGGC 61.121 55.000 0.00 0.00 40.72 4.52 F
1449 1958 1.331756 GCAGTGTCAAGGACAGTTGTG 59.668 52.381 4.04 0.16 42.73 3.33 F
2187 2731 0.178068 CTAGGTGCGGCACAGGTATT 59.822 55.000 31.74 13.38 35.86 1.89 F
3450 3997 0.591170 CACCATGGAGAAACGCGTTT 59.409 50.000 35.28 35.28 35.14 3.60 F
4043 4592 0.469917 GATCCCCTCGCCAGATTTCA 59.530 55.000 0.00 0.00 0.00 2.69 F
4058 4607 1.281419 TTTCAAGGCGGATCCACCTA 58.719 50.000 21.84 4.36 34.31 3.08 F
4288 4837 4.175337 CGTGTCCCCCATCCGCAT 62.175 66.667 0.00 0.00 0.00 4.73 F
5409 5980 5.156804 GTGGTTGAGTAGAAACACTTGTG 57.843 43.478 0.00 0.00 39.94 3.33 F
5875 6451 2.358247 ACCATCGGCGGTGTGAAC 60.358 61.111 20.02 0.00 38.07 3.18 F
7611 8219 0.461135 CAGTTGCCAACTTGCCTGTT 59.539 50.000 7.51 0.00 40.46 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 2514 0.882484 TTTCCGCATCTCGCACACAA 60.882 50.000 0.00 0.00 42.60 3.33 R
1976 2515 1.301322 TTTCCGCATCTCGCACACA 60.301 52.632 0.00 0.00 42.60 3.72 R
2803 3350 2.884320 TGCACCTACCTCAGTTCACTA 58.116 47.619 0.00 0.00 0.00 2.74 R
3961 4510 1.068753 CTGCCGCAGAAGATCCGAT 59.931 57.895 15.74 0.00 32.44 4.18 R
4908 5470 1.692411 GCCTTCTTCACACCAAACCT 58.308 50.000 0.00 0.00 0.00 3.50 R
5535 6106 0.669077 ACGATCGTCTAGGACATGCC 59.331 55.000 16.60 0.00 32.09 4.40 R
5671 6243 2.172082 TCTTGATCAAGGATCTGGCCAG 59.828 50.000 30.33 27.87 39.56 4.85 R
5875 6451 3.287867 AGTACCATGGCAAGGATCAAG 57.712 47.619 16.88 0.00 0.00 3.02 R
7055 7657 0.253044 GCACTATCAGGGGTCTTGCA 59.747 55.000 0.00 0.00 0.00 4.08 R
7762 8394 1.001293 TGGCAATAAAACGGCAATGCA 59.999 42.857 7.79 0.00 35.57 3.96 R
8887 9522 1.024579 CCCTTTATGACGCCGCTGTT 61.025 55.000 0.00 0.00 0.00 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
73 74 2.891191 TGCCCCTCCGTTTCTAAATT 57.109 45.000 0.00 0.00 0.00 1.82
78 79 5.047872 TGCCCCTCCGTTTCTAAATTTAAAC 60.048 40.000 6.52 6.52 33.26 2.01
219 298 3.742433 ATTTAGACGGATGGAGAGCAG 57.258 47.619 0.00 0.00 0.00 4.24
233 312 3.127030 GGAGAGCAGGTATTTCCGTTTTG 59.873 47.826 0.00 0.00 41.99 2.44
244 326 5.793030 ATTTCCGTTTTGTTTATGGTGGA 57.207 34.783 0.00 0.00 0.00 4.02
249 331 4.542735 CGTTTTGTTTATGGTGGAAGTCC 58.457 43.478 0.00 0.00 0.00 3.85
261 343 3.943671 TGGAAGTCCACCTCAAGAAAA 57.056 42.857 0.00 0.00 42.01 2.29
262 344 4.453480 TGGAAGTCCACCTCAAGAAAAT 57.547 40.909 0.00 0.00 42.01 1.82
396 852 5.176592 GTTCTTGTGGAGTAGTACCAATCC 58.823 45.833 0.46 0.46 39.22 3.01
438 912 4.530857 CGGCCCGCCCTAGTCTTG 62.531 72.222 0.00 0.00 0.00 3.02
481 955 1.143813 TAGGAGGGAGGGTAGGTACG 58.856 60.000 0.00 0.00 0.00 3.67
713 1196 7.671398 AGGGCATCCGAATCTTTATTTATTGAT 59.329 33.333 0.00 0.00 38.33 2.57
714 1197 7.756722 GGGCATCCGAATCTTTATTTATTGATG 59.243 37.037 0.00 0.00 0.00 3.07
715 1198 8.514594 GGCATCCGAATCTTTATTTATTGATGA 58.485 33.333 0.00 0.00 0.00 2.92
879 1381 0.240145 CCGCTTGATATCCGTCGCTA 59.760 55.000 0.00 0.00 0.00 4.26
928 1431 1.121407 AGCCCCTTTTGGTTCTTGGC 61.121 55.000 0.00 0.00 40.72 4.52
1116 1619 4.767255 CCTGCGGCTCCCTGTGAC 62.767 72.222 0.00 0.00 0.00 3.67
1270 1779 4.772687 GAAACCCCCGAGACCCGC 62.773 72.222 0.00 0.00 36.84 6.13
1392 1901 6.607198 GGATCAAGATTAAGGTTGGGAATTCA 59.393 38.462 7.93 0.00 0.00 2.57
1449 1958 1.331756 GCAGTGTCAAGGACAGTTGTG 59.668 52.381 4.04 0.16 42.73 3.33
1521 2030 3.587797 TCATCTACGGAGGTGTTTGAC 57.412 47.619 8.02 0.00 35.11 3.18
1653 2162 3.571401 CCCTGTTTTCTTGATTCTGCACT 59.429 43.478 0.00 0.00 0.00 4.40
1677 2189 5.993748 TGGTTCCCTTGTTTTGGATATTC 57.006 39.130 0.00 0.00 0.00 1.75
2011 2550 0.462789 AAACGTCTTGACCTCGGTGT 59.537 50.000 0.00 0.00 0.00 4.16
2141 2685 7.604657 AGAGTAGGTTACAGGAGATATTTGG 57.395 40.000 0.00 0.00 0.00 3.28
2187 2731 0.178068 CTAGGTGCGGCACAGGTATT 59.822 55.000 31.74 13.38 35.86 1.89
2225 2769 1.871039 GGTGCACAATGTAACGTGACT 59.129 47.619 20.43 0.00 35.02 3.41
2737 3284 5.662674 ACTTACAAGTGTAGAGGATGACC 57.337 43.478 0.00 0.00 37.98 4.02
2803 3350 3.926616 ACAATACGTTTAGCAGCAGTCT 58.073 40.909 0.00 0.00 0.00 3.24
3231 3778 8.840833 TGAGTACAAATATGTATGTGTTGTGT 57.159 30.769 1.42 0.00 43.60 3.72
3450 3997 0.591170 CACCATGGAGAAACGCGTTT 59.409 50.000 35.28 35.28 35.14 3.60
3608 4155 5.099042 ACCAATCTAGCTTTGTACCGATT 57.901 39.130 0.00 0.00 0.00 3.34
3628 4176 5.237344 CGATTAATGGTTCCATCTGACTTCC 59.763 44.000 4.72 0.00 0.00 3.46
3777 4325 8.582437 TCATCATTCAAAGCTTCTTCAAGATTT 58.418 29.630 0.00 0.00 46.83 2.17
3912 4461 2.082231 CCTGATGTTTCTGCCACAGAG 58.918 52.381 0.00 0.00 41.75 3.35
3961 4510 2.900273 CCGCCGAATCCTCCTGAA 59.100 61.111 0.00 0.00 0.00 3.02
4043 4592 0.469917 GATCCCCTCGCCAGATTTCA 59.530 55.000 0.00 0.00 0.00 2.69
4058 4607 1.281419 TTTCAAGGCGGATCCACCTA 58.719 50.000 21.84 4.36 34.31 3.08
4288 4837 4.175337 CGTGTCCCCCATCCGCAT 62.175 66.667 0.00 0.00 0.00 4.73
5229 5791 5.370814 CGATCAAATTTTCGTTCGACAAGA 58.629 37.500 4.46 0.00 0.00 3.02
5409 5980 5.156804 GTGGTTGAGTAGAAACACTTGTG 57.843 43.478 0.00 0.00 39.94 3.33
5535 6106 6.129352 GCAAGCGTTCAACTAAAGAAAATGAG 60.129 38.462 0.00 0.00 0.00 2.90
5875 6451 2.358247 ACCATCGGCGGTGTGAAC 60.358 61.111 20.02 0.00 38.07 3.18
6703 7300 2.784984 TCCTCCCGGACCCAGATT 59.215 61.111 0.73 0.00 33.30 2.40
7055 7657 1.221635 TGCATGTTATAGGCAGGGGT 58.778 50.000 0.00 0.00 41.85 4.95
7062 7664 0.837272 TATAGGCAGGGGTGCAAGAC 59.163 55.000 0.00 0.00 36.33 3.01
7072 7674 0.912486 GGTGCAAGACCCCTGATAGT 59.088 55.000 0.00 0.00 39.10 2.12
7208 7815 2.511818 CACAGGTATAGGTGCGGGA 58.488 57.895 0.00 0.00 0.00 5.14
7266 7874 6.100404 TGTGTTTAACAGGTCGTATTAGGT 57.900 37.500 0.00 0.00 33.78 3.08
7292 7900 5.105554 TCACTGAGAAGTCCAAGAGCTTATC 60.106 44.000 0.00 0.00 34.59 1.75
7564 8172 8.538039 GTTTATATAACAAGGAGTCGTTGTAGC 58.462 37.037 26.60 11.78 40.76 3.58
7611 8219 0.461135 CAGTTGCCAACTTGCCTGTT 59.539 50.000 7.51 0.00 40.46 3.16
7744 8376 5.255397 TCCAGTTTCCACAGACCATAATT 57.745 39.130 0.00 0.00 0.00 1.40
7752 8384 9.561069 GTTTCCACAGACCATAATTCATATACT 57.439 33.333 0.00 0.00 0.00 2.12
7801 8433 0.403271 ATGCACCTGCCAAAGTCTCT 59.597 50.000 0.00 0.00 41.18 3.10
7886 8521 4.389374 ACTTCAATCATGTCTTCACCGTT 58.611 39.130 0.00 0.00 0.00 4.44
7965 8600 6.320672 AGCTGCAGATCATTAGCATTAGTTTT 59.679 34.615 20.43 0.00 38.59 2.43
7966 8601 6.976925 GCTGCAGATCATTAGCATTAGTTTTT 59.023 34.615 20.43 0.00 37.68 1.94
7992 8627 6.207025 TGCCGCTTTTCTGTACCTTTATTTAA 59.793 34.615 0.00 0.00 0.00 1.52
8226 8861 1.561643 CTCCTTCACTAGTGGCAGGA 58.438 55.000 28.97 28.97 37.80 3.86
8657 9292 0.807496 GCACTGCCACATTTCCTCTC 59.193 55.000 0.00 0.00 0.00 3.20
8868 9503 7.632462 GCAAGAAGATACTGATTGAGGAAGAGA 60.632 40.741 0.00 0.00 0.00 3.10
8917 9552 3.133362 CGTCATAAAGGGGTAGTGGCTTA 59.867 47.826 0.00 0.00 0.00 3.09
8939 9574 8.598075 GCTTAAATTTTGTTTGCTGATCCTATG 58.402 33.333 0.00 0.00 0.00 2.23
8981 9616 1.769465 GGTCCTTCCTCCCAAGATACC 59.231 57.143 0.00 0.00 0.00 2.73
8984 9619 2.317900 TCCTTCCTCCCAAGATACCAGA 59.682 50.000 0.00 0.00 0.00 3.86
9087 9724 8.225603 TGCTACAAGATTTCAAACTCTTTCTT 57.774 30.769 0.00 0.00 29.34 2.52
9194 9831 2.714808 AGGAAGTCTTTGTTAGGGGGT 58.285 47.619 0.00 0.00 0.00 4.95
9195 9832 3.878086 AGGAAGTCTTTGTTAGGGGGTA 58.122 45.455 0.00 0.00 0.00 3.69
9242 9879 6.828273 TCCGGAGACATCAAATTTTACATGAT 59.172 34.615 0.00 0.00 34.22 2.45
9245 9882 8.183536 CGGAGACATCAAATTTTACATGATTGA 58.816 33.333 0.00 0.86 31.65 2.57
9296 9933 9.357652 CATGGTGTTATAGACTTTTGATTTTGG 57.642 33.333 0.00 0.00 0.00 3.28
9364 10002 1.819288 TCGTAGCAAGTCTTCCAGAGG 59.181 52.381 0.00 0.00 0.00 3.69
9506 10144 6.206243 AGGTTCACATTGATCAAGAACTGAAG 59.794 38.462 25.82 13.96 37.67 3.02
9507 10145 6.376978 GTTCACATTGATCAAGAACTGAAGG 58.623 40.000 22.42 9.86 37.67 3.46
9527 10165 2.964464 GGCATCTTCATCCTCTCTCTCA 59.036 50.000 0.00 0.00 0.00 3.27
9531 10169 2.038659 CTTCATCCTCTCTCTCACCCC 58.961 57.143 0.00 0.00 0.00 4.95
9588 10226 3.751518 ACAAAACCCATCCTGTCTACAC 58.248 45.455 0.00 0.00 0.00 2.90
9638 10276 1.079987 TCTTCTGCTGCCTCCTCCT 59.920 57.895 0.00 0.00 0.00 3.69
9670 10308 4.458989 GTGGCCATCAACTCATCAAACTTA 59.541 41.667 9.72 0.00 0.00 2.24
9707 10345 4.337763 CACTATCTCAATCTGCGCAAAAC 58.662 43.478 13.05 0.00 0.00 2.43
9708 10346 4.002982 ACTATCTCAATCTGCGCAAAACA 58.997 39.130 13.05 0.00 0.00 2.83
9719 10357 3.435566 TGCGCAAAACATTCAACGTAAA 58.564 36.364 8.16 0.00 0.00 2.01
9720 10358 4.045104 TGCGCAAAACATTCAACGTAAAT 58.955 34.783 8.16 0.00 0.00 1.40
9721 10359 5.212934 TGCGCAAAACATTCAACGTAAATA 58.787 33.333 8.16 0.00 0.00 1.40
9722 10360 5.859114 TGCGCAAAACATTCAACGTAAATAT 59.141 32.000 8.16 0.00 0.00 1.28
9723 10361 6.363626 TGCGCAAAACATTCAACGTAAATATT 59.636 30.769 8.16 0.00 0.00 1.28
9724 10362 6.887247 GCGCAAAACATTCAACGTAAATATTC 59.113 34.615 0.30 0.00 0.00 1.75
9725 10363 7.380320 CGCAAAACATTCAACGTAAATATTCC 58.620 34.615 0.00 0.00 0.00 3.01
9726 10364 7.462200 CGCAAAACATTCAACGTAAATATTCCC 60.462 37.037 0.00 0.00 0.00 3.97
9727 10365 7.201487 GCAAAACATTCAACGTAAATATTCCCC 60.201 37.037 0.00 0.00 0.00 4.81
9728 10366 5.744666 ACATTCAACGTAAATATTCCCCG 57.255 39.130 0.00 0.00 0.00 5.73
9729 10367 4.577283 ACATTCAACGTAAATATTCCCCGG 59.423 41.667 0.00 0.00 0.00 5.73
9730 10368 3.196939 TCAACGTAAATATTCCCCGGG 57.803 47.619 15.80 15.80 0.00 5.73
9731 10369 2.158784 TCAACGTAAATATTCCCCGGGG 60.159 50.000 35.80 35.80 0.00 5.73
9732 10370 1.805180 ACGTAAATATTCCCCGGGGA 58.195 50.000 39.67 39.67 43.52 4.81
9785 10423 8.677300 TCTGAATGATATCCTGCTAAAAACAAC 58.323 33.333 0.00 0.00 0.00 3.32
9803 10441 9.850628 AAAAACAACATTCTGATGATATGACAG 57.149 29.630 0.00 0.00 36.73 3.51
9808 10446 9.485206 CAACATTCTGATGATATGACAGTATGA 57.515 33.333 17.87 0.00 39.78 2.15
9871 10509 6.156775 TCATCTCATCCTTGATTTCCACAGTA 59.843 38.462 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.891191 ATTTAGAAACGGAGGGGCAA 57.109 45.000 0.00 0.00 0.00 4.52
55 56 5.404946 GTTTAAATTTAGAAACGGAGGGGC 58.595 41.667 0.00 0.00 0.00 5.80
142 144 5.709164 GGACTACCTACGGAGCAAATAGATA 59.291 44.000 0.00 0.00 0.00 1.98
219 298 5.865013 CCACCATAAACAAAACGGAAATACC 59.135 40.000 0.00 0.00 0.00 2.73
244 326 8.923270 TCATTTTTATTTTCTTGAGGTGGACTT 58.077 29.630 0.00 0.00 0.00 3.01
249 331 7.441017 TGGGTCATTTTTATTTTCTTGAGGTG 58.559 34.615 0.00 0.00 0.00 4.00
261 343 5.893824 GTGAATCCTCCTGGGTCATTTTTAT 59.106 40.000 0.00 0.00 32.89 1.40
262 344 5.261216 GTGAATCCTCCTGGGTCATTTTTA 58.739 41.667 0.00 0.00 32.89 1.52
396 852 0.749454 GGCTCAGCCCAGTAATGGTG 60.749 60.000 3.37 0.70 44.06 4.17
438 912 0.533032 CTTCTCCCGTTCCTCCACTC 59.467 60.000 0.00 0.00 0.00 3.51
481 955 1.071567 CTTTTCCCTCTCGCGACGTC 61.072 60.000 3.71 5.18 0.00 4.34
604 1087 3.493440 GCCGCGTTACTTTCCCGG 61.493 66.667 4.92 0.00 41.72 5.73
610 1093 1.782044 TTTAACTCGCCGCGTTACTT 58.218 45.000 13.39 2.85 0.00 2.24
713 1196 3.218453 TGGGAGAGAAAAACGCAATTCA 58.782 40.909 0.00 0.00 0.00 2.57
714 1197 3.915437 TGGGAGAGAAAAACGCAATTC 57.085 42.857 0.00 0.00 0.00 2.17
715 1198 3.383185 TGTTGGGAGAGAAAAACGCAATT 59.617 39.130 0.00 0.00 38.35 2.32
858 1360 2.022129 CGACGGATATCAAGCGGGC 61.022 63.158 4.83 0.00 0.00 6.13
879 1381 2.102578 CCCAAAGGAATGAAAGCCGAT 58.897 47.619 0.00 0.00 33.47 4.18
914 1417 2.543653 CCTCAACGCCAAGAACCAAAAG 60.544 50.000 0.00 0.00 0.00 2.27
928 1431 4.148825 CTCCGGCCCTCCTCAACG 62.149 72.222 0.00 0.00 0.00 4.10
1116 1619 1.888215 ATCCACCATTGCTATCTGCG 58.112 50.000 0.00 0.00 46.63 5.18
1243 1752 2.822701 GGGGTTTCCCGACGATGC 60.823 66.667 0.00 0.00 46.66 3.91
1262 1771 1.467713 CGTACTTTCTGAGCGGGTCTC 60.468 57.143 8.82 0.00 42.23 3.36
1270 1779 2.729882 CCGGTGAAACGTACTTTCTGAG 59.270 50.000 14.65 8.39 39.36 3.35
1271 1780 2.361757 TCCGGTGAAACGTACTTTCTGA 59.638 45.455 0.00 7.18 39.36 3.27
1392 1901 1.554160 CTGATGAGCCTCTTGAGGTGT 59.446 52.381 16.95 6.04 0.00 4.16
1428 1937 1.210478 ACAACTGTCCTTGACACTGCT 59.790 47.619 0.00 0.00 37.67 4.24
1619 2128 0.974010 AAACAGGGCAGCCATGGATG 60.974 55.000 29.13 25.84 39.88 3.51
1695 2207 5.480422 TCTCCTGCTAGTACATCACAAAAGA 59.520 40.000 0.00 0.00 0.00 2.52
1696 2208 5.578727 GTCTCCTGCTAGTACATCACAAAAG 59.421 44.000 0.00 0.00 0.00 2.27
1778 2296 4.875536 TGTATGTGAGTTGGTATGTGCATC 59.124 41.667 0.00 0.00 0.00 3.91
1974 2513 1.565156 TTCCGCATCTCGCACACAAC 61.565 55.000 0.00 0.00 42.60 3.32
1975 2514 0.882484 TTTCCGCATCTCGCACACAA 60.882 50.000 0.00 0.00 42.60 3.33
1976 2515 1.301322 TTTCCGCATCTCGCACACA 60.301 52.632 0.00 0.00 42.60 3.72
2011 2550 1.302431 CATGCAACACGTCCCCTCA 60.302 57.895 0.00 0.00 0.00 3.86
2187 2731 3.691342 CGAAGGAGTCCCGCACCA 61.691 66.667 5.25 0.00 37.58 4.17
2737 3284 5.865552 CCAATGTTGGTCTGAATTTTAGCAG 59.134 40.000 3.58 0.00 43.43 4.24
2803 3350 2.884320 TGCACCTACCTCAGTTCACTA 58.116 47.619 0.00 0.00 0.00 2.74
3231 3778 8.057536 ACACCTCACTGTTTATTTACAACAAA 57.942 30.769 0.00 0.00 33.74 2.83
3405 3952 5.306937 TCTGGAAGAAGAGGTGTACATGAAA 59.693 40.000 0.00 0.00 42.31 2.69
3608 4155 5.032846 AGAGGAAGTCAGATGGAACCATTA 58.967 41.667 7.79 0.00 36.70 1.90
3628 4176 5.123027 GCAAGTGGGTCTTTAGAATCAAGAG 59.877 44.000 0.00 0.00 33.63 2.85
3777 4325 2.384433 TGAACCCGGTGAACCCCAA 61.384 57.895 0.00 0.00 0.00 4.12
3912 4461 1.078143 AGCTTCTGCCGTGGGATTC 60.078 57.895 0.00 0.00 40.80 2.52
3961 4510 1.068753 CTGCCGCAGAAGATCCGAT 59.931 57.895 15.74 0.00 32.44 4.18
4411 4960 4.256180 GCCGCCCTTGGGATCGAT 62.256 66.667 10.36 0.00 0.00 3.59
4908 5470 1.692411 GCCTTCTTCACACCAAACCT 58.308 50.000 0.00 0.00 0.00 3.50
5054 5616 1.893137 AGCACCGTCACATAGTTGAGA 59.107 47.619 0.00 0.00 0.00 3.27
5409 5980 5.360714 TCATCAATTGCCTTATCCTGTTTCC 59.639 40.000 0.00 0.00 0.00 3.13
5535 6106 0.669077 ACGATCGTCTAGGACATGCC 59.331 55.000 16.60 0.00 32.09 4.40
5671 6243 2.172082 TCTTGATCAAGGATCTGGCCAG 59.828 50.000 30.33 27.87 39.56 4.85
5875 6451 3.287867 AGTACCATGGCAAGGATCAAG 57.712 47.619 16.88 0.00 0.00 3.02
6703 7300 2.531685 CCCAACCCTCTCCACCCA 60.532 66.667 0.00 0.00 0.00 4.51
7055 7657 0.253044 GCACTATCAGGGGTCTTGCA 59.747 55.000 0.00 0.00 0.00 4.08
7062 7664 4.321718 CATCTTGTATGCACTATCAGGGG 58.678 47.826 0.00 0.00 0.00 4.79
7072 7674 8.210265 TGTAATATCTCAACCATCTTGTATGCA 58.790 33.333 0.00 0.00 0.00 3.96
7266 7874 4.348486 AGCTCTTGGACTTCTCAGTGATA 58.652 43.478 0.00 0.00 31.22 2.15
7292 7900 7.672983 ATATATGTTCGGGTAAATTCAGCTG 57.327 36.000 7.63 7.63 0.00 4.24
7422 8030 6.716628 TGGTATCACAAAAGCTCTTCTGAAAT 59.283 34.615 0.00 0.00 0.00 2.17
7564 8172 8.550376 CAAAATCAACTGTTTTCATTGGGTAAG 58.450 33.333 0.00 0.00 0.00 2.34
7611 8219 1.821753 GTAGACCAGCTTGAGCAGAGA 59.178 52.381 5.70 0.00 45.16 3.10
7744 8376 8.405531 GGCAATGCAAAGTTTCTTAGTATATGA 58.594 33.333 7.79 0.00 0.00 2.15
7752 8384 4.314740 AACGGCAATGCAAAGTTTCTTA 57.685 36.364 7.79 0.00 0.00 2.10
7762 8394 1.001293 TGGCAATAAAACGGCAATGCA 59.999 42.857 7.79 0.00 35.57 3.96
7880 8515 3.935203 AGATTGATTAGACTGCAACGGTG 59.065 43.478 0.00 0.00 0.00 4.94
7886 8521 7.692460 AAATGAACAGATTGATTAGACTGCA 57.308 32.000 0.00 0.00 34.25 4.41
7935 8570 2.801679 GCTAATGATCTGCAGCTCAGTC 59.198 50.000 22.24 7.29 43.32 3.51
7965 8600 1.975660 AGGTACAGAAAAGCGGCAAA 58.024 45.000 1.45 0.00 0.00 3.68
7966 8601 1.975660 AAGGTACAGAAAAGCGGCAA 58.024 45.000 1.45 0.00 0.00 4.52
7967 8602 1.975660 AAAGGTACAGAAAAGCGGCA 58.024 45.000 1.45 0.00 0.00 5.69
7992 8627 6.605119 AGGGTAAATAGCATTAGCATCAAGT 58.395 36.000 7.94 0.00 45.49 3.16
8390 9025 4.223700 ACACCTCTCTGCACAATTAGATGA 59.776 41.667 0.00 0.00 0.00 2.92
8884 9519 1.463056 CTTTATGACGCCGCTGTTGAA 59.537 47.619 0.00 0.00 0.00 2.69
8887 9522 1.024579 CCCTTTATGACGCCGCTGTT 61.025 55.000 0.00 0.00 0.00 3.16
8917 9552 7.767198 CCATCATAGGATCAGCAAACAAAATTT 59.233 33.333 0.00 0.00 0.00 1.82
8963 9598 2.317900 TCTGGTATCTTGGGAGGAAGGA 59.682 50.000 0.00 0.00 0.00 3.36
8981 9616 2.126463 TCGCGAAACCGAGCTCTG 60.126 61.111 6.20 8.03 32.74 3.35
9087 9724 1.276421 GTCAGGGCAAGCTGAGACTAA 59.724 52.381 0.00 0.00 0.00 2.24
9173 9810 3.878086 ACCCCCTAACAAAGACTTCCTA 58.122 45.455 0.00 0.00 0.00 2.94
9176 9813 7.133133 TCATATACCCCCTAACAAAGACTTC 57.867 40.000 0.00 0.00 0.00 3.01
9194 9831 9.104965 CGGAGTTAATTTCACTGGTTTCATATA 57.895 33.333 0.00 0.00 0.00 0.86
9195 9832 7.067008 CCGGAGTTAATTTCACTGGTTTCATAT 59.933 37.037 0.00 0.00 0.00 1.78
9273 9910 7.328493 GCACCAAAATCAAAAGTCTATAACACC 59.672 37.037 0.00 0.00 0.00 4.16
9281 9918 4.162131 AGTTGGCACCAAAATCAAAAGTCT 59.838 37.500 3.10 0.00 37.70 3.24
9364 10002 5.391416 GCAAGAGCTGAGAATTTAAGTGTCC 60.391 44.000 0.00 0.00 37.91 4.02
9506 10144 2.964464 TGAGAGAGAGGATGAAGATGCC 59.036 50.000 0.00 0.00 0.00 4.40
9507 10145 3.243839 GGTGAGAGAGAGGATGAAGATGC 60.244 52.174 0.00 0.00 0.00 3.91
9570 10208 2.253610 TCGTGTAGACAGGATGGGTTT 58.746 47.619 1.04 0.00 43.62 3.27
9588 10226 3.799420 GCAGACCTAGAAATTGCTAGTCG 59.201 47.826 17.70 7.32 36.88 4.18
9638 10276 4.783621 GATGGCCACAGCTGCGGA 62.784 66.667 25.00 4.67 39.73 5.54
9646 10284 2.557924 GTTTGATGAGTTGATGGCCACA 59.442 45.455 8.16 5.62 0.00 4.17
9670 10308 1.667154 TAGTGCTGCGGAAGAGCGAT 61.667 55.000 0.00 0.00 40.67 4.58
9707 10345 4.023536 CCCGGGGAATATTTACGTTGAATG 60.024 45.833 14.71 0.00 0.00 2.67
9708 10346 4.139038 CCCGGGGAATATTTACGTTGAAT 58.861 43.478 14.71 0.00 0.00 2.57
9723 10361 1.688811 CAACATTCTTCCCCGGGGA 59.311 57.895 39.67 39.67 43.52 4.81
9724 10362 1.379843 CCAACATTCTTCCCCGGGG 60.380 63.158 35.80 35.80 0.00 5.73
9725 10363 1.379843 CCCAACATTCTTCCCCGGG 60.380 63.158 15.80 15.80 0.00 5.73
9726 10364 1.379843 CCCCAACATTCTTCCCCGG 60.380 63.158 0.00 0.00 0.00 5.73
9727 10365 0.621609 TACCCCAACATTCTTCCCCG 59.378 55.000 0.00 0.00 0.00 5.73
9728 10366 2.911552 TTACCCCAACATTCTTCCCC 57.088 50.000 0.00 0.00 0.00 4.81
9729 10367 4.836175 TCTTTTTACCCCAACATTCTTCCC 59.164 41.667 0.00 0.00 0.00 3.97
9730 10368 6.183360 TGTTCTTTTTACCCCAACATTCTTCC 60.183 38.462 0.00 0.00 0.00 3.46
9731 10369 6.811954 TGTTCTTTTTACCCCAACATTCTTC 58.188 36.000 0.00 0.00 0.00 2.87
9732 10370 6.800072 TGTTCTTTTTACCCCAACATTCTT 57.200 33.333 0.00 0.00 0.00 2.52
9733 10371 6.800072 TTGTTCTTTTTACCCCAACATTCT 57.200 33.333 0.00 0.00 0.00 2.40
9734 10372 9.366216 GATATTGTTCTTTTTACCCCAACATTC 57.634 33.333 0.00 0.00 0.00 2.67
9735 10373 9.100197 AGATATTGTTCTTTTTACCCCAACATT 57.900 29.630 0.00 0.00 0.00 2.71
9803 10441 6.064717 AGGCCAAGGTCAGAATAATTCATAC 58.935 40.000 5.01 0.00 0.00 2.39
9808 10446 5.046376 CCAAAAGGCCAAGGTCAGAATAATT 60.046 40.000 5.01 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.