Multiple sequence alignment - TraesCS1D01G167900

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 TraesCS1D01G167900 chr1D 100.000 6591 0 0 1 6591 239811725 239805135 0.000000e+00 12172.0
1 TraesCS1D01G167900 chr1A 95.358 4459 148 18 1286 5730 303858004 303853591 0.000000e+00 7033.0
2 TraesCS1D01G167900 chr1A 89.375 1327 89 25 7 1289 303859367 303858049 0.000000e+00 1622.0
3 TraesCS1D01G167900 chr1A 90.150 802 41 14 5825 6589 303853291 303852491 0.000000e+00 1009.0
4 TraesCS1D01G167900 chr1B 94.759 2652 92 19 1968 4596 334245228 334242601 0.000000e+00 4084.0
5 TraesCS1D01G167900 chr1B 95.680 1111 46 2 4629 5738 334242605 334241496 0.000000e+00 1784.0
6 TraesCS1D01G167900 chr1B 86.983 991 58 29 349 1289 334246980 334246011 0.000000e+00 1050.0
7 TraesCS1D01G167900 chr1B 94.245 556 25 2 1289 1844 334245964 334245416 0.000000e+00 843.0
8 TraesCS1D01G167900 chr1B 94.091 220 8 2 6066 6284 334241369 334241154 4.930000e-86 329.0
9 TraesCS1D01G167900 chr1B 93.443 122 6 2 6395 6514 334241144 334241023 5.250000e-41 180.0
10 TraesCS1D01G167900 chr2B 83.955 1583 168 46 2707 4255 476397310 476398840 0.000000e+00 1437.0
11 TraesCS1D01G167900 chr2B 84.879 992 111 16 4633 5594 476399891 476400873 0.000000e+00 965.0
12 TraesCS1D01G167900 chr2B 83.571 420 47 13 836 1245 476394922 476395329 2.240000e-99 374.0
13 TraesCS1D01G167900 chr2B 94.286 35 2 0 773 807 476394876 476394910 3.000000e-03 54.7
14 TraesCS1D01G167900 chr2D 84.870 998 106 18 4633 5594 402307682 402306694 0.000000e+00 965.0
15 TraesCS1D01G167900 chr2D 89.093 761 75 5 3498 4254 402308869 402308113 0.000000e+00 939.0
16 TraesCS1D01G167900 chr2D 81.455 701 82 21 2720 3418 402309644 402308990 1.260000e-146 531.0
17 TraesCS1D01G167900 chr2D 84.615 364 37 10 836 1191 402312284 402311932 1.760000e-90 344.0
18 TraesCS1D01G167900 chr2D 83.601 311 38 7 2253 2554 402311295 402310989 5.030000e-71 279.0
19 TraesCS1D01G167900 chr2D 87.850 214 19 6 4352 4560 402307901 402307690 1.840000e-60 244.0
20 TraesCS1D01G167900 chr2D 91.667 48 4 0 1242 1289 402311867 402311820 4.270000e-07 67.6
21 TraesCS1D01G167900 chr2D 97.143 35 1 0 773 807 402312330 402312296 7.140000e-05 60.2
22 TraesCS1D01G167900 chr2A 88.206 814 81 10 3446 4255 539395558 539394756 0.000000e+00 957.0
23 TraesCS1D01G167900 chr2A 84.438 996 112 19 4633 5594 539394451 539393465 0.000000e+00 941.0
24 TraesCS1D01G167900 chr2A 81.132 583 73 23 2929 3500 539396239 539395683 3.650000e-117 433.0
25 TraesCS1D01G167900 chr2A 84.450 373 46 8 874 1245 539398875 539398514 2.260000e-94 357.0
26 TraesCS1D01G167900 chr2A 81.087 423 53 12 1300 1713 539398371 539397967 4.960000e-81 313.0
27 TraesCS1D01G167900 chr2A 83.803 142 22 1 4419 4560 539394599 539394459 4.150000e-27 134.0
28 TraesCS1D01G167900 chr5A 77.204 794 160 17 4759 5538 641731056 641731842 1.690000e-120 444.0
29 TraesCS1D01G167900 chr5D 76.658 814 172 14 4759 5560 513975432 513976239 1.010000e-117 435.0
30 TraesCS1D01G167900 chr5D 100.000 28 0 0 2056 2083 398249250 398249277 1.200000e-02 52.8
31 TraesCS1D01G167900 chr5B 75.910 797 175 13 4759 5543 644887817 644888608 6.200000e-105 392.0
32 TraesCS1D01G167900 chr5B 76.259 417 55 26 55 462 571884798 571885179 1.460000e-41 182.0
33 TraesCS1D01G167900 chr4D 87.456 287 35 1 6008 6293 46622157 46621871 4.930000e-86 329.0
34 TraesCS1D01G167900 chr4B 86.986 292 37 1 6003 6293 68119381 68119090 1.770000e-85 327.0
35 TraesCS1D01G167900 chr4A 87.108 287 36 1 6008 6293 533461604 533461318 2.290000e-84 324.0
36 TraesCS1D01G167900 chr4A 86.411 287 38 1 6008 6293 552256371 552256657 4.960000e-81 313.0
37 TraesCS1D01G167900 chr6A 77.778 414 54 22 56 462 59504797 59504415 3.090000e-53 220.0
38 TraesCS1D01G167900 chr3B 91.489 47 2 2 639 684 430523531 430523576 5.520000e-06 63.9
39 TraesCS1D01G167900 chr7A 97.143 35 1 0 637 671 618675140 618675174 7.140000e-05 60.2


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 TraesCS1D01G167900 chr1D 239805135 239811725 6590 True 12172.000000 12172 100.000000 1 6591 1 chr1D.!!$R1 6590
1 TraesCS1D01G167900 chr1A 303852491 303859367 6876 True 3221.333333 7033 91.627667 7 6589 3 chr1A.!!$R1 6582
2 TraesCS1D01G167900 chr1B 334241023 334246980 5957 True 1378.333333 4084 93.200167 349 6514 6 chr1B.!!$R1 6165
3 TraesCS1D01G167900 chr2B 476394876 476400873 5997 False 707.675000 1437 86.672750 773 5594 4 chr2B.!!$F1 4821
4 TraesCS1D01G167900 chr2D 402306694 402312330 5636 True 428.725000 965 87.536750 773 5594 8 chr2D.!!$R1 4821
5 TraesCS1D01G167900 chr2A 539393465 539398875 5410 True 522.500000 957 83.852667 874 5594 6 chr2A.!!$R1 4720
6 TraesCS1D01G167900 chr5A 641731056 641731842 786 False 444.000000 444 77.204000 4759 5538 1 chr5A.!!$F1 779
7 TraesCS1D01G167900 chr5D 513975432 513976239 807 False 435.000000 435 76.658000 4759 5560 1 chr5D.!!$F2 801
8 TraesCS1D01G167900 chr5B 644887817 644888608 791 False 392.000000 392 75.910000 4759 5543 1 chr5B.!!$F2 784

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
114 115 0.108019 ACAGTGGGAAAGACCGGTTC 59.892 55.000 9.42 1.37 40.11 3.62 F
1212 1281 0.392863 TTCATGGTGATGGCTGGACG 60.393 55.000 0.00 0.00 0.00 4.79 F
1919 2252 0.244721 CCTGCCACCAAAGCTAAAGC 59.755 55.000 0.00 0.00 42.49 3.51 F
1961 2294 1.066303 TGCGCAACGTTCCAAGAAAAT 59.934 42.857 8.16 0.00 0.00 1.82 F
2204 2545 1.293498 CTACCGGCTTGCTCACACT 59.707 57.895 0.00 0.00 0.00 3.55 F
3489 5330 1.072648 CGTGGTGGGGAACTTTCCTTA 59.927 52.381 7.93 0.00 46.72 2.69 F
5317 8123 0.761187 AGCACCGCACCATGATCTAT 59.239 50.000 0.00 0.00 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 1565 0.671251 TTTTGGCCCAACATCGACAC 59.329 50.000 0.00 0.00 0.00 3.67 R
2204 2545 1.002624 CCTTTGGCCCGCTAGTTCA 60.003 57.895 0.00 0.00 0.00 3.18 R
2773 4336 4.017407 TCATACTAGGTGGGTCTTCAGTCT 60.017 45.833 0.00 0.00 0.00 3.24 R
3024 4656 4.130118 ACAGTTTGAGATCTCCAACACAC 58.870 43.478 30.68 14.01 37.60 3.82 R
3568 5410 4.202336 GCCAGATTGATGAGGATGAGAGAA 60.202 45.833 0.00 0.00 0.00 2.87 R
5413 8219 1.003851 ATCCGTTGGCGATGTTTACG 58.996 50.000 0.00 0.00 41.33 3.18 R
6474 9521 1.613437 CGGATGCAAAGGGAACAAGTT 59.387 47.619 0.00 0.00 0.00 2.66 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
50 51 1.771255 GAAGGGTGATAGCAGGGTCAT 59.229 52.381 0.00 0.00 0.00 3.06
59 60 0.835941 AGCAGGGTCATCATGAGGAC 59.164 55.000 28.01 28.01 41.00 3.85
63 64 3.012518 CAGGGTCATCATGAGGACAAAC 58.987 50.000 33.97 24.68 43.26 2.93
73 74 0.329596 GAGGACAAACAGGGAGGCAT 59.670 55.000 0.00 0.00 0.00 4.40
80 81 0.622665 AACAGGGAGGCATTGAGAGG 59.377 55.000 0.00 0.00 0.00 3.69
87 88 0.255318 AGGCATTGAGAGGAGGCAAG 59.745 55.000 0.00 0.00 0.00 4.01
88 89 0.750911 GGCATTGAGAGGAGGCAAGG 60.751 60.000 0.00 0.00 0.00 3.61
109 110 1.671379 GGCGACAGTGGGAAAGACC 60.671 63.158 0.00 0.00 38.08 3.85
114 115 0.108019 ACAGTGGGAAAGACCGGTTC 59.892 55.000 9.42 1.37 40.11 3.62
119 120 2.322830 GGAAAGACCGGTTCGTGGC 61.323 63.158 9.42 0.00 0.00 5.01
128 129 1.069513 CCGGTTCGTGGCCAGAATATA 59.930 52.381 5.11 0.00 0.00 0.86
129 130 2.404215 CGGTTCGTGGCCAGAATATAG 58.596 52.381 5.11 2.26 0.00 1.31
131 132 3.391049 GGTTCGTGGCCAGAATATAGAC 58.609 50.000 5.11 0.00 0.00 2.59
142 143 4.045104 CAGAATATAGACGTGACAGTGGC 58.955 47.826 0.00 0.00 0.00 5.01
143 144 3.699538 AGAATATAGACGTGACAGTGGCA 59.300 43.478 0.00 0.00 0.00 4.92
160 161 1.952296 GGCATCATCACATCCTCCAAC 59.048 52.381 0.00 0.00 0.00 3.77
186 187 4.724279 AGAAAAGGGAAAGAAGTGGCTA 57.276 40.909 0.00 0.00 0.00 3.93
188 189 3.441500 AAAGGGAAAGAAGTGGCTAGG 57.558 47.619 0.00 0.00 0.00 3.02
194 195 1.059913 AAGAAGTGGCTAGGTGTGCT 58.940 50.000 0.00 0.00 0.00 4.40
206 207 1.001406 AGGTGTGCTCCGAAAAGAGAG 59.999 52.381 0.00 0.00 35.82 3.20
223 224 9.294030 GAAAAGAGAGGTGCATTGTTATTATTG 57.706 33.333 0.00 0.00 0.00 1.90
229 230 7.331687 AGAGGTGCATTGTTATTATTGTTTTGC 59.668 33.333 0.00 0.00 0.00 3.68
232 233 7.095271 GGTGCATTGTTATTATTGTTTTGCAGT 60.095 33.333 0.00 0.00 38.15 4.40
254 255 8.961092 GCAGTATGTCTATATTTGCAATTTGTG 58.039 33.333 0.00 0.00 39.31 3.33
260 261 8.458052 TGTCTATATTTGCAATTTGTGTAGTGG 58.542 33.333 0.00 0.00 0.00 4.00
266 267 5.781210 TGCAATTTGTGTAGTGGAATCAA 57.219 34.783 0.00 0.00 0.00 2.57
267 268 6.343716 TGCAATTTGTGTAGTGGAATCAAT 57.656 33.333 0.00 0.00 0.00 2.57
274 275 7.433708 TTGTGTAGTGGAATCAATTGTGTAG 57.566 36.000 5.13 0.00 0.00 2.74
278 279 6.816640 TGTAGTGGAATCAATTGTGTAGTAGC 59.183 38.462 5.13 0.00 0.00 3.58
285 286 4.002982 TCAATTGTGTAGTAGCCAAGCAG 58.997 43.478 5.13 0.00 0.00 4.24
287 288 1.348064 TGTGTAGTAGCCAAGCAGGT 58.652 50.000 0.00 0.00 40.61 4.00
288 289 1.697432 TGTGTAGTAGCCAAGCAGGTT 59.303 47.619 0.00 0.00 40.61 3.50
486 508 1.022735 GGCTTGACTGGCATGAGATG 58.977 55.000 0.00 0.00 0.00 2.90
494 520 4.593033 GCATGAGATGGCCCATGT 57.407 55.556 17.65 0.00 41.49 3.21
501 527 3.979911 TGAGATGGCCCATGTTTGTAAT 58.020 40.909 0.00 0.00 0.00 1.89
504 530 5.954752 TGAGATGGCCCATGTTTGTAATTTA 59.045 36.000 0.00 0.00 0.00 1.40
505 531 6.610830 TGAGATGGCCCATGTTTGTAATTTAT 59.389 34.615 0.00 0.00 0.00 1.40
506 532 6.819284 AGATGGCCCATGTTTGTAATTTATG 58.181 36.000 0.00 0.00 0.00 1.90
507 533 4.764172 TGGCCCATGTTTGTAATTTATGC 58.236 39.130 0.00 0.00 0.00 3.14
508 534 4.223700 TGGCCCATGTTTGTAATTTATGCA 59.776 37.500 0.00 0.00 0.00 3.96
509 535 5.181748 GGCCCATGTTTGTAATTTATGCAA 58.818 37.500 0.00 0.00 0.00 4.08
510 536 5.821995 GGCCCATGTTTGTAATTTATGCAAT 59.178 36.000 0.00 0.00 33.42 3.56
511 537 6.989169 GGCCCATGTTTGTAATTTATGCAATA 59.011 34.615 0.00 0.00 33.42 1.90
512 538 7.661027 GGCCCATGTTTGTAATTTATGCAATAT 59.339 33.333 0.00 0.00 33.42 1.28
543 579 2.178474 GCACATGCTGGTGAATTACG 57.822 50.000 11.70 0.00 41.32 3.18
554 590 6.646653 TGCTGGTGAATTACGATGATATCTTC 59.353 38.462 3.98 6.41 0.00 2.87
604 641 8.608844 ATTGATTCATAGTATTCCCTTCGTTC 57.391 34.615 0.00 0.00 0.00 3.95
606 643 4.579454 TCATAGTATTCCCTTCGTTCCG 57.421 45.455 0.00 0.00 0.00 4.30
619 662 7.922837 TCCCTTCGTTCCGAAATAAATAATTC 58.077 34.615 0.47 0.00 45.23 2.17
622 665 7.376072 CCTTCGTTCCGAAATAAATAATTCAGC 59.624 37.037 0.47 0.00 45.23 4.26
714 760 7.390718 AGGGCATTCAAGTAGTAACAGTAAAAG 59.609 37.037 0.00 0.00 0.00 2.27
769 815 2.906897 CACCTTGCCGCTTGTGGT 60.907 61.111 2.01 0.00 0.00 4.16
770 816 2.594592 ACCTTGCCGCTTGTGGTC 60.595 61.111 2.01 0.00 0.00 4.02
771 817 2.281761 CCTTGCCGCTTGTGGTCT 60.282 61.111 2.01 0.00 0.00 3.85
775 821 2.435059 GCCGCTTGTGGTCTCTCC 60.435 66.667 2.01 0.00 0.00 3.71
1055 1116 0.621571 CCTCTCACCCCATCCTCCAA 60.622 60.000 0.00 0.00 0.00 3.53
1107 1168 1.423921 TCTTCTTCCTCCGGGCTTTTT 59.576 47.619 0.00 0.00 0.00 1.94
1196 1257 2.828095 CCGCGGCCATGGAATTCA 60.828 61.111 18.40 0.00 0.00 2.57
1212 1281 0.392863 TTCATGGTGATGGCTGGACG 60.393 55.000 0.00 0.00 0.00 4.79
1343 1522 1.227853 ACTGAAAGGTGGGCGTGTC 60.228 57.895 0.00 0.00 39.30 3.67
1375 1554 6.395426 TTCAGATTCATGGATTGGTAATGC 57.605 37.500 0.00 0.00 0.00 3.56
1386 1565 1.674359 TGGTAATGCGGGTATTGCAG 58.326 50.000 0.00 0.00 46.98 4.41
1394 1573 0.930310 CGGGTATTGCAGTGTCGATG 59.070 55.000 0.00 0.00 0.00 3.84
1773 1973 0.392461 TAAACCATCGGCCTCTGCAC 60.392 55.000 0.00 0.00 40.13 4.57
1827 2035 8.506140 AATTAATGATAATGCCGAACAAATCG 57.494 30.769 0.00 0.00 40.16 3.34
1876 2209 0.321564 CGAGGCCATCCACAAAGACA 60.322 55.000 5.01 0.00 33.74 3.41
1903 2236 1.593265 GCAGCATCCCCAAAACCTG 59.407 57.895 0.00 0.00 0.00 4.00
1919 2252 0.244721 CCTGCCACCAAAGCTAAAGC 59.755 55.000 0.00 0.00 42.49 3.51
1961 2294 1.066303 TGCGCAACGTTCCAAGAAAAT 59.934 42.857 8.16 0.00 0.00 1.82
2085 2425 2.988493 TCAACAAGGTAACGATGTACGC 59.012 45.455 0.00 0.00 46.94 4.42
2204 2545 1.293498 CTACCGGCTTGCTCACACT 59.707 57.895 0.00 0.00 0.00 3.55
2386 2735 3.943381 CAGTTGCAAGAATCTCATGGCTA 59.057 43.478 0.00 0.00 0.00 3.93
2436 2786 7.442364 CCTCAAGAAAGTTGTGATCTTAGTTCA 59.558 37.037 0.00 0.00 32.38 3.18
2489 2844 5.953183 TCATGTTCATTTCAGGTTGCATAC 58.047 37.500 0.00 0.00 0.00 2.39
2532 2887 3.008813 AGCATATTAGCTCACATGGGAGG 59.991 47.826 26.06 8.81 42.18 4.30
2609 4075 2.009051 TGTTGATTAGCCAGCACATCG 58.991 47.619 0.00 0.00 0.00 3.84
2675 4142 6.035542 CGACTAGAGGCTTCTTCTTCATTTTC 59.964 42.308 2.68 0.00 34.79 2.29
2773 4336 7.281098 TCACCGCTAATATTACCCAATTAACA 58.719 34.615 0.00 0.00 0.00 2.41
2842 4413 5.473504 ACAACTACTTCAGCTATTTTGGTGG 59.526 40.000 0.00 0.00 36.25 4.61
3024 4656 4.852134 TTTCATGACAAACTGGTCCATG 57.148 40.909 0.00 0.00 36.97 3.66
3365 4999 7.294584 TGAAAGGAAGATTACCAAAAGAGGAA 58.705 34.615 0.00 0.00 0.00 3.36
3424 5058 8.965172 GGTGTAATAGTGTATACTTTCATCACG 58.035 37.037 4.17 0.00 38.36 4.35
3489 5330 1.072648 CGTGGTGGGGAACTTTCCTTA 59.927 52.381 7.93 0.00 46.72 2.69
3565 5407 8.601546 AGAGTGAAGAAGATATTTGGTTTCTCT 58.398 33.333 0.00 0.00 0.00 3.10
3568 5410 8.787852 GTGAAGAAGATATTTGGTTTCTCTGTT 58.212 33.333 0.00 0.00 0.00 3.16
3724 5566 7.320399 TGAACTTTCTTAAGTCGATAGCATCA 58.680 34.615 1.63 1.41 43.74 3.07
4296 6387 6.347859 AGTCTAAAGAACACCCTTACAGAG 57.652 41.667 0.00 0.00 0.00 3.35
4320 6411 3.009723 AGAGACCTTTGTGTGTTGTGTG 58.990 45.455 0.00 0.00 0.00 3.82
4496 7252 4.830600 TGTTTCATTACTTTGTCCCTTCCC 59.169 41.667 0.00 0.00 0.00 3.97
4745 7520 1.269958 CCAGGTCACATCTGTCCAGA 58.730 55.000 0.00 0.00 42.37 3.86
4805 7580 3.788227 TGGGTAGCAATGAAGAGTGTT 57.212 42.857 0.00 0.00 0.00 3.32
5221 8027 0.899019 TTGCCTACGCCATCACACTA 59.101 50.000 0.00 0.00 0.00 2.74
5272 8078 1.892209 CTACTTCGGCAAACAACCCT 58.108 50.000 0.00 0.00 0.00 4.34
5317 8123 0.761187 AGCACCGCACCATGATCTAT 59.239 50.000 0.00 0.00 0.00 1.98
5494 8300 3.069158 CCATGATGATCCTTCCTTTTGGC 59.931 47.826 0.00 0.00 40.12 4.52
5506 8312 2.642311 TCCTTTTGGCATCTGTGTCCTA 59.358 45.455 0.00 0.00 40.12 2.94
5561 8367 3.072330 TGACAGAGACAATGCCAAGGTAA 59.928 43.478 0.00 0.00 0.00 2.85
5654 8460 8.939201 TTCAAGCTTATTTGTGAATGTTTTGA 57.061 26.923 0.00 0.00 0.00 2.69
5666 8472 9.814899 TTGTGAATGTTTTGATTGTAAATCAGT 57.185 25.926 3.15 0.00 0.00 3.41
5760 8747 5.704888 ACTGTCTTCATCTTACTGAACTCG 58.295 41.667 0.00 0.00 31.98 4.18
5775 8762 6.787225 ACTGAACTCGATAACTATCAGTGAC 58.213 40.000 5.51 0.00 44.10 3.67
5809 8796 4.776435 TCTCTTCATATTGATGTGGGCA 57.224 40.909 0.00 0.00 34.41 5.36
5814 8801 6.131264 TCTTCATATTGATGTGGGCATTTCT 58.869 36.000 0.00 0.00 35.07 2.52
5817 8832 6.604171 TCATATTGATGTGGGCATTTCTACT 58.396 36.000 0.00 0.00 35.07 2.57
5820 8835 4.142609 TGATGTGGGCATTTCTACTCTC 57.857 45.455 0.00 0.00 35.07 3.20
5823 8838 4.207891 TGTGGGCATTTCTACTCTCTTC 57.792 45.455 0.00 0.00 0.00 2.87
5849 8864 9.746711 CTAATCACGCTATCAATATAAAAGCAC 57.253 33.333 0.00 0.00 32.69 4.40
5855 8870 8.433126 ACGCTATCAATATAAAAGCACGATTAC 58.567 33.333 0.00 0.00 32.69 1.89
5856 8871 7.627193 CGCTATCAATATAAAAGCACGATTACG 59.373 37.037 0.00 0.00 45.75 3.18
5930 8945 6.034150 GCATTTAAACGTTATAACTGCCAACC 59.966 38.462 21.21 6.74 34.62 3.77
5936 8951 3.749088 CGTTATAACTGCCAACCTTGACA 59.251 43.478 13.56 0.00 0.00 3.58
5984 8999 1.270358 ACAGGAGTTTCAGCTCGAACC 60.270 52.381 5.36 2.02 36.41 3.62
6006 9021 0.528017 CTGGAGAAGCGTAGTGAGCA 59.472 55.000 0.00 0.00 37.01 4.26
6007 9022 0.243907 TGGAGAAGCGTAGTGAGCAC 59.756 55.000 0.00 0.00 37.01 4.40
6017 9044 2.688446 CGTAGTGAGCACTTCCCTGATA 59.312 50.000 8.60 0.00 42.54 2.15
6029 9056 8.099537 AGCACTTCCCTGATATAAGACATAATG 58.900 37.037 0.00 0.00 0.00 1.90
6031 9058 9.650539 CACTTCCCTGATATAAGACATAATGAG 57.349 37.037 0.00 0.00 0.00 2.90
6035 9062 6.157645 CCCTGATATAAGACATAATGAGGCCT 59.842 42.308 3.86 3.86 0.00 5.19
6038 9065 8.206126 TGATATAAGACATAATGAGGCCTTGA 57.794 34.615 6.77 0.00 0.00 3.02
6053 9080 3.412386 GCCTTGAAGGTGTGTGACTATT 58.588 45.455 13.58 0.00 37.80 1.73
6236 9264 2.038295 CCTGAATCCCTAGATGTGGAGC 59.962 54.545 0.00 0.00 33.27 4.70
6379 9418 7.660208 AGTCTTAATGGTGAAAACGACAGTAAT 59.340 33.333 0.00 0.00 0.00 1.89
6380 9419 8.928733 GTCTTAATGGTGAAAACGACAGTAATA 58.071 33.333 0.00 0.00 0.00 0.98
6381 9420 9.661563 TCTTAATGGTGAAAACGACAGTAATAT 57.338 29.630 0.00 0.00 0.00 1.28
6386 9425 8.604640 TGGTGAAAACGACAGTAATATAAACA 57.395 30.769 0.00 0.00 0.00 2.83
6387 9426 8.714179 TGGTGAAAACGACAGTAATATAAACAG 58.286 33.333 0.00 0.00 0.00 3.16
6474 9521 7.037586 AGGTAAATCTTCCCAGATACTTCAACA 60.038 37.037 0.00 0.00 39.00 3.33
6479 9526 5.997746 TCTTCCCAGATACTTCAACAACTTG 59.002 40.000 0.00 0.00 0.00 3.16
6482 9529 5.763204 TCCCAGATACTTCAACAACTTGTTC 59.237 40.000 4.06 0.00 38.77 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.056660 TCACCACCTCCCTTCTTGTC 58.943 55.000 0.00 0.00 0.00 3.18
1 2 0.765510 GTCACCACCTCCCTTCTTGT 59.234 55.000 0.00 0.00 0.00 3.16
2 3 0.764890 TGTCACCACCTCCCTTCTTG 59.235 55.000 0.00 0.00 0.00 3.02
3 4 1.059913 CTGTCACCACCTCCCTTCTT 58.940 55.000 0.00 0.00 0.00 2.52
4 5 0.838122 CCTGTCACCACCTCCCTTCT 60.838 60.000 0.00 0.00 0.00 2.85
5 6 0.836400 TCCTGTCACCACCTCCCTTC 60.836 60.000 0.00 0.00 0.00 3.46
50 51 1.630369 CCTCCCTGTTTGTCCTCATGA 59.370 52.381 0.00 0.00 0.00 3.07
59 60 2.089980 CTCTCAATGCCTCCCTGTTTG 58.910 52.381 0.00 0.00 0.00 2.93
63 64 0.469070 CTCCTCTCAATGCCTCCCTG 59.531 60.000 0.00 0.00 0.00 4.45
73 74 1.925455 CCCCCTTGCCTCCTCTCAA 60.925 63.158 0.00 0.00 0.00 3.02
88 89 3.920093 CTTTCCCACTGTCGCCCCC 62.920 68.421 0.00 0.00 0.00 5.40
96 97 0.949105 CGAACCGGTCTTTCCCACTG 60.949 60.000 8.04 0.00 0.00 3.66
104 105 3.530910 CTGGCCACGAACCGGTCTT 62.531 63.158 8.04 0.00 0.00 3.01
109 110 2.035449 TCTATATTCTGGCCACGAACCG 59.965 50.000 16.66 0.73 0.00 4.44
114 115 2.034179 TCACGTCTATATTCTGGCCACG 59.966 50.000 0.00 2.58 0.00 4.94
119 120 4.611943 CCACTGTCACGTCTATATTCTGG 58.388 47.826 0.00 0.00 0.00 3.86
128 129 0.610174 ATGATGCCACTGTCACGTCT 59.390 50.000 0.00 0.00 0.00 4.18
129 130 1.002366 GATGATGCCACTGTCACGTC 58.998 55.000 0.00 0.00 0.00 4.34
131 132 0.723414 GTGATGATGCCACTGTCACG 59.277 55.000 0.00 0.00 31.15 4.35
142 143 4.267536 ACAAGTTGGAGGATGTGATGATG 58.732 43.478 7.96 0.00 0.00 3.07
143 144 4.581309 ACAAGTTGGAGGATGTGATGAT 57.419 40.909 7.96 0.00 0.00 2.45
160 161 5.278512 GCCACTTCTTTCCCTTTTCTACAAG 60.279 44.000 0.00 0.00 0.00 3.16
186 187 1.001406 CTCTCTTTTCGGAGCACACCT 59.999 52.381 0.00 0.00 33.70 4.00
188 189 1.270358 ACCTCTCTTTTCGGAGCACAC 60.270 52.381 0.00 0.00 33.70 3.82
194 195 2.224523 ACAATGCACCTCTCTTTTCGGA 60.225 45.455 0.00 0.00 0.00 4.55
206 207 7.095271 ACTGCAAAACAATAATAACAATGCACC 60.095 33.333 0.00 0.00 36.46 5.01
223 224 8.909708 TTGCAAATATAGACATACTGCAAAAC 57.090 30.769 0.00 0.00 41.39 2.43
236 237 8.800370 TCCACTACACAAATTGCAAATATAGA 57.200 30.769 1.71 0.00 0.00 1.98
239 240 8.530311 TGATTCCACTACACAAATTGCAAATAT 58.470 29.630 1.71 0.00 0.00 1.28
254 255 6.258068 GGCTACTACACAATTGATTCCACTAC 59.742 42.308 13.59 0.00 0.00 2.73
260 261 5.123820 TGCTTGGCTACTACACAATTGATTC 59.876 40.000 13.59 0.00 0.00 2.52
266 267 2.305927 ACCTGCTTGGCTACTACACAAT 59.694 45.455 0.00 0.00 40.22 2.71
267 268 1.697432 ACCTGCTTGGCTACTACACAA 59.303 47.619 0.00 0.00 40.22 3.33
423 424 8.484008 GCACACATAAATTCACGTTAAAAATGT 58.516 29.630 0.00 0.00 0.00 2.71
426 437 7.987268 TGCACACATAAATTCACGTTAAAAA 57.013 28.000 0.00 0.00 0.00 1.94
431 442 7.312154 ACATAATGCACACATAAATTCACGTT 58.688 30.769 0.00 0.00 34.62 3.99
486 508 4.764172 TGCATAAATTACAAACATGGGCC 58.236 39.130 0.00 0.00 0.00 5.80
505 531 8.461222 GCATGTGCTTAGGAATATAATATTGCA 58.539 33.333 0.00 0.00 38.21 4.08
506 532 8.847444 GCATGTGCTTAGGAATATAATATTGC 57.153 34.615 0.00 0.00 38.21 3.56
714 760 3.354089 TGCTTTCTTGCACTACTTTGC 57.646 42.857 0.00 0.00 43.31 3.68
733 779 3.548014 GGTGGTGAACAGATTTTGTCGTG 60.548 47.826 0.00 0.00 39.73 4.35
769 815 2.617538 ACGGGAGGGAGGGAGAGA 60.618 66.667 0.00 0.00 0.00 3.10
770 816 2.443016 CACGGGAGGGAGGGAGAG 60.443 72.222 0.00 0.00 32.31 3.20
771 817 3.273654 ACACGGGAGGGAGGGAGA 61.274 66.667 0.00 0.00 36.77 3.71
1055 1116 2.160721 ATGGATAGGTCACCTCGTGT 57.839 50.000 0.00 0.00 34.61 4.49
1107 1168 1.492319 CGTCACAAGAACCGGCGAAA 61.492 55.000 9.30 0.00 0.00 3.46
1196 1257 1.524002 CTCGTCCAGCCATCACCAT 59.476 57.895 0.00 0.00 0.00 3.55
1343 1522 3.557185 TCCATGAATCTGAAATCGAAGCG 59.443 43.478 0.00 0.00 0.00 4.68
1375 1554 0.930310 CATCGACACTGCAATACCCG 59.070 55.000 0.00 0.00 0.00 5.28
1386 1565 0.671251 TTTTGGCCCAACATCGACAC 59.329 50.000 0.00 0.00 0.00 3.67
1407 1586 4.418973 ACAGTGATGATTCTGCAGCTAT 57.581 40.909 9.47 4.73 35.37 2.97
1773 1973 5.801350 ATACAGTTGTGTGAATCAATCGG 57.199 39.130 0.00 0.00 37.52 4.18
1848 2181 2.429610 GTGGATGGCCTCGAGTACTTTA 59.570 50.000 12.31 0.00 34.31 1.85
1853 2186 1.207089 CTTTGTGGATGGCCTCGAGTA 59.793 52.381 12.31 0.00 34.31 2.59
1903 2236 0.811281 ATCGCTTTAGCTTTGGTGGC 59.189 50.000 0.00 0.00 39.32 5.01
1919 2252 6.251589 CGCACTTTGCCTCTACTAATATATCG 59.748 42.308 0.00 0.00 41.12 2.92
1930 2263 1.565156 CGTTGCGCACTTTGCCTCTA 61.565 55.000 11.12 0.00 41.12 2.43
1931 2264 2.896801 CGTTGCGCACTTTGCCTCT 61.897 57.895 11.12 0.00 41.12 3.69
1932 2265 2.427410 CGTTGCGCACTTTGCCTC 60.427 61.111 11.12 0.00 41.12 4.70
1961 2294 0.951558 GCGGTTCCTTCTTGAAAGCA 59.048 50.000 0.00 0.00 33.21 3.91
2085 2425 3.971453 ATCAGGCAGCGTCGACGTG 62.971 63.158 35.48 29.93 42.22 4.49
2168 2509 1.066918 GTGTGGTGGACGACGAGTT 59.933 57.895 0.00 0.00 0.00 3.01
2204 2545 1.002624 CCTTTGGCCCGCTAGTTCA 60.003 57.895 0.00 0.00 0.00 3.18
2386 2735 4.415881 TGCAACACCTTCGTATGGATAT 57.584 40.909 0.00 0.00 0.00 1.63
2489 2844 4.636206 GCTAATCCCTTGACACTAACCAAG 59.364 45.833 0.00 0.00 39.43 3.61
2532 2887 6.609616 TGATAATGGGGTTAATGGGAAAGAAC 59.390 38.462 0.00 0.00 0.00 3.01
2609 4075 8.814235 CAAATCATGATTTTCTAGCAAATGACC 58.186 33.333 27.30 0.00 38.84 4.02
2773 4336 4.017407 TCATACTAGGTGGGTCTTCAGTCT 60.017 45.833 0.00 0.00 0.00 3.24
2842 4413 7.332926 TGATCAAGCAATCTGTTCTAACTCTTC 59.667 37.037 0.00 0.00 0.00 2.87
2903 4475 7.820386 TGCTGCTCAATATTCATTGTTCAATTT 59.180 29.630 0.00 0.00 41.96 1.82
2974 4606 4.657504 TGGTTTGATCTGGCTCTAGATGAT 59.342 41.667 0.31 0.00 37.53 2.45
3024 4656 4.130118 ACAGTTTGAGATCTCCAACACAC 58.870 43.478 30.68 14.01 37.60 3.82
3424 5058 4.579454 TCTATTACACTCATGCCGGTAC 57.421 45.455 1.90 0.00 0.00 3.34
3489 5330 7.336679 TGTTTATGCTGTAGAATGCAACTATGT 59.663 33.333 0.00 0.00 42.74 2.29
3565 5407 6.346896 CAGATTGATGAGGATGAGAGAAACA 58.653 40.000 0.00 0.00 0.00 2.83
3568 5410 4.202336 GCCAGATTGATGAGGATGAGAGAA 60.202 45.833 0.00 0.00 0.00 2.87
4296 6387 3.557595 CACAACACACAAAGGTCTCTCTC 59.442 47.826 0.00 0.00 0.00 3.20
4320 6411 7.625817 GCATCTATATGATCACCAAATCACTGC 60.626 40.741 0.00 0.00 38.43 4.40
4539 7297 7.166473 GTCACATTTCAAGTTAACAAGCTTCAG 59.834 37.037 8.61 0.00 0.00 3.02
4713 7488 1.978580 TGACCTGGGAAAAGAGGAGAC 59.021 52.381 0.00 0.00 33.16 3.36
4714 7489 1.978580 GTGACCTGGGAAAAGAGGAGA 59.021 52.381 0.00 0.00 33.16 3.71
4753 7528 3.146066 CAGATAGAGGTCGGAGGAAGAG 58.854 54.545 0.00 0.00 0.00 2.85
4805 7580 9.676861 ATGATCTGAAATGTCTTCACTTTCATA 57.323 29.630 0.00 0.00 38.01 2.15
5213 8019 5.846164 TGATACCCATGAGGAATAGTGTGAT 59.154 40.000 7.17 0.00 39.89 3.06
5221 8027 3.982730 TGATGGTGATACCCATGAGGAAT 59.017 43.478 7.17 0.00 45.31 3.01
5272 8078 1.027357 GGACTACCTCCGCGAACATA 58.973 55.000 8.23 0.00 0.00 2.29
5413 8219 1.003851 ATCCGTTGGCGATGTTTACG 58.996 50.000 0.00 0.00 41.33 3.18
5494 8300 4.502259 GGGCTGTAGAATAGGACACAGATG 60.502 50.000 4.83 0.00 40.67 2.90
5506 8312 4.042934 ACAAGGTACAAAGGGCTGTAGAAT 59.957 41.667 0.00 0.00 32.49 2.40
5561 8367 1.912043 CTCCTGGTCCTTGAATCTGGT 59.088 52.381 0.00 0.00 0.00 4.00
5608 8414 9.605275 CTTGAATCCTTATCAGAAACATCACTA 57.395 33.333 0.00 0.00 0.00 2.74
5666 8472 7.175467 CCCTGATAGCATATATTGTCTTTTGCA 59.825 37.037 0.00 0.00 32.66 4.08
5748 8735 8.613482 TCACTGATAGTTATCGAGTTCAGTAAG 58.387 37.037 11.70 4.83 41.22 2.34
5775 8762 7.821359 TCAATATGAAGAGAAGGAAAGTGTGAG 59.179 37.037 0.00 0.00 0.00 3.51
5781 8768 7.013083 CCCACATCAATATGAAGAGAAGGAAAG 59.987 40.741 0.00 0.00 36.54 2.62
5789 8776 6.264744 AGAAATGCCCACATCAATATGAAGAG 59.735 38.462 0.00 0.00 34.62 2.85
5809 8796 7.341445 AGCGTGATTAGAAGAGAGTAGAAAT 57.659 36.000 0.00 0.00 0.00 2.17
5814 8801 7.803279 TTGATAGCGTGATTAGAAGAGAGTA 57.197 36.000 0.00 0.00 0.00 2.59
5823 8838 9.746711 GTGCTTTTATATTGATAGCGTGATTAG 57.253 33.333 0.00 0.00 34.65 1.73
5843 8858 4.893424 ATATTTGGCGTAATCGTGCTTT 57.107 36.364 0.00 0.00 39.49 3.51
5849 8864 5.996219 TCCATTGAATATTTGGCGTAATCG 58.004 37.500 0.42 0.00 40.37 3.34
5855 8870 7.710475 ACCTTTTAATCCATTGAATATTTGGCG 59.290 33.333 0.42 0.00 0.00 5.69
5856 8871 8.962884 ACCTTTTAATCCATTGAATATTTGGC 57.037 30.769 0.42 0.00 0.00 4.52
5942 8957 5.147162 GTGCTGCTGTATGTTTTACTGTTC 58.853 41.667 0.00 0.00 0.00 3.18
5960 8975 1.155042 GAGCTGAAACTCCTGTGCTG 58.845 55.000 0.00 0.00 0.00 4.41
5984 8999 1.403679 CTCACTACGCTTCTCCAGGAG 59.596 57.143 10.70 10.70 0.00 3.69
6006 9021 8.820831 CCTCATTATGTCTTATATCAGGGAAGT 58.179 37.037 0.00 0.00 0.00 3.01
6007 9022 7.768120 GCCTCATTATGTCTTATATCAGGGAAG 59.232 40.741 0.00 0.00 0.00 3.46
6017 9044 6.126361 ACCTTCAAGGCCTCATTATGTCTTAT 60.126 38.462 5.23 0.00 39.63 1.73
6029 9056 0.108585 TCACACACCTTCAAGGCCTC 59.891 55.000 5.23 0.00 39.63 4.70
6031 9058 0.179018 AGTCACACACCTTCAAGGCC 60.179 55.000 2.20 0.00 39.63 5.19
6035 9062 7.124298 AGCTAGATAATAGTCACACACCTTCAA 59.876 37.037 0.00 0.00 0.00 2.69
6038 9065 6.607600 TGAGCTAGATAATAGTCACACACCTT 59.392 38.462 0.00 0.00 0.00 3.50
6144 9172 8.695284 GTGTTCGCAATACATTCTCTATTAGAG 58.305 37.037 13.60 13.60 43.64 2.43
6236 9264 5.530171 AGCCTGCAAATACAGACATAGAATG 59.470 40.000 0.00 0.00 40.25 2.67
6354 9382 5.668558 ACTGTCGTTTTCACCATTAAGAC 57.331 39.130 0.00 0.00 0.00 3.01
6385 9424 7.295201 GCGTCTCTCAGTTATCTACTTATCTG 58.705 42.308 0.00 0.00 33.85 2.90
6386 9425 6.428771 GGCGTCTCTCAGTTATCTACTTATCT 59.571 42.308 0.00 0.00 33.85 1.98
6387 9426 6.205076 TGGCGTCTCTCAGTTATCTACTTATC 59.795 42.308 0.00 0.00 33.85 1.75
6392 9438 3.628487 ACTGGCGTCTCTCAGTTATCTAC 59.372 47.826 0.00 0.00 40.91 2.59
6393 9439 3.628032 CACTGGCGTCTCTCAGTTATCTA 59.372 47.826 0.00 0.00 41.71 1.98
6474 9521 1.613437 CGGATGCAAAGGGAACAAGTT 59.387 47.619 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.