Multiple sequence alignment - TraesCS1B01G051400

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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 TraesCS1B01G051400 chr1B 100.000 5931 0 0 1 5931 31371728 31377658 0.000000e+00 10953
1 TraesCS1B01G051400 chr1B 90.674 2166 144 20 2600 4741 58026042 58023911 0.000000e+00 2828
2 TraesCS1B01G051400 chr1B 92.507 1001 39 17 1626 2601 58029760 58028771 0.000000e+00 1400
3 TraesCS1B01G051400 chr1B 96.688 785 17 4 4 782 121891844 121891063 0.000000e+00 1297
4 TraesCS1B01G051400 chr1B 96.433 785 21 4 4 782 14895513 14896296 0.000000e+00 1288
5 TraesCS1B01G051400 chr1B 95.349 387 18 0 5364 5750 121891065 121890679 3.040000e-172 616
6 TraesCS1B01G051400 chr1B 83.915 659 68 10 4738 5364 58024044 58023392 3.960000e-166 595
7 TraesCS1B01G051400 chr1B 94.059 303 17 1 5364 5665 14896294 14896596 5.420000e-125 459
8 TraesCS1B01G051400 chr1B 81.239 549 68 25 781 1316 58030751 58030225 1.540000e-110 411
9 TraesCS1B01G051400 chr1B 94.792 96 5 0 4740 4835 31376335 31376430 3.700000e-32 150
10 TraesCS1B01G051400 chr1B 91.892 74 6 0 1230 1303 58030343 58030270 2.920000e-18 104
11 TraesCS1B01G051400 chr5B 93.161 2442 106 21 2640 5045 707937623 707935207 0.000000e+00 3528
12 TraesCS1B01G051400 chr5B 96.306 785 23 2 4 782 506238721 506237937 0.000000e+00 1284
13 TraesCS1B01G051400 chr5B 95.423 568 26 0 5364 5931 506237939 506237372 0.000000e+00 905
14 TraesCS1B01G051400 chr5B 92.593 324 21 2 5043 5363 707935125 707934802 4.190000e-126 462
15 TraesCS1B01G051400 chr7B 97.366 1822 44 2 781 2601 648176741 648174923 0.000000e+00 3096
16 TraesCS1B01G051400 chr7B 96.588 1788 41 8 3577 5363 648172986 648171218 0.000000e+00 2946
17 TraesCS1B01G051400 chr7B 96.303 568 21 0 5364 5931 743566209 743565642 0.000000e+00 933
18 TraesCS1B01G051400 chr7B 97.764 492 10 1 2600 3091 648173467 648172977 0.000000e+00 846
19 TraesCS1B01G051400 chr7B 81.023 1075 122 45 872 1900 674792808 674793846 0.000000e+00 780
20 TraesCS1B01G051400 chr7B 95.681 301 10 1 84 384 743566748 743566451 1.160000e-131 481
21 TraesCS1B01G051400 chr7B 97.107 242 7 0 5690 5931 474910520 474910761 5.530000e-110 409
22 TraesCS1B01G051400 chr7B 93.464 153 10 0 5561 5713 615405214 615405366 1.660000e-55 228
23 TraesCS1B01G051400 chr7B 96.774 93 3 0 4740 4832 648171956 648171864 7.960000e-34 156
24 TraesCS1B01G051400 chr7B 97.701 87 2 0 4 90 743586955 743586869 3.700000e-32 150
25 TraesCS1B01G051400 chr1A 95.696 1789 45 8 3577 5364 589618723 589616966 0.000000e+00 2848
26 TraesCS1B01G051400 chr1A 97.249 1054 25 2 1549 2601 589621710 589620660 0.000000e+00 1783
27 TraesCS1B01G051400 chr1A 97.561 492 11 1 2600 3091 589619204 589618714 0.000000e+00 841
28 TraesCS1B01G051400 chr1A 96.774 93 3 0 4740 4832 589617692 589617600 7.960000e-34 156
29 TraesCS1B01G051400 chr1A 94.792 96 5 0 4608 4703 589617577 589617482 3.700000e-32 150
30 TraesCS1B01G051400 chr2B 90.791 2161 142 20 2600 4738 20346340 20348465 0.000000e+00 2835
31 TraesCS1B01G051400 chr2B 92.408 1001 40 17 1626 2601 20341405 20342394 0.000000e+00 1395
32 TraesCS1B01G051400 chr2B 96.056 786 23 6 4 782 222487353 222488137 0.000000e+00 1273
33 TraesCS1B01G051400 chr2B 95.406 566 26 0 5364 5929 222488135 222488700 0.000000e+00 902
34 TraesCS1B01G051400 chr2B 84.043 658 66 10 4738 5363 20348335 20348985 1.100000e-166 597
35 TraesCS1B01G051400 chr2B 95.070 284 13 1 4 287 292869020 292868738 4.220000e-121 446
36 TraesCS1B01G051400 chr2B 81.215 543 67 25 778 1307 20340411 20340931 7.160000e-109 405
37 TraesCS1B01G051400 chr2B 91.026 78 7 0 1230 1307 20340822 20340899 8.130000e-19 106
38 TraesCS1B01G051400 chr4A 89.039 1259 88 18 3505 4741 512420657 512419427 0.000000e+00 1515
39 TraesCS1B01G051400 chr4A 92.607 1001 39 18 1626 2601 742905139 742906129 0.000000e+00 1406
40 TraesCS1B01G051400 chr4A 90.130 1003 42 16 1626 2601 512421647 512420675 0.000000e+00 1251
41 TraesCS1B01G051400 chr4A 88.040 1087 83 16 3674 4738 742906381 742907442 0.000000e+00 1243
42 TraesCS1B01G051400 chr4A 84.370 659 64 10 4738 5364 742907312 742907963 1.410000e-170 610
43 TraesCS1B01G051400 chr4A 81.688 557 63 23 781 1307 742904119 742904666 1.530000e-115 427
44 TraesCS1B01G051400 chr4A 81.216 559 64 26 781 1307 710054413 710054962 4.280000e-111 412
45 TraesCS1B01G051400 chr4A 88.474 321 35 2 5044 5364 512419198 512418880 2.590000e-103 387
46 TraesCS1B01G051400 chr4A 85.552 353 37 6 4738 5083 512419560 512419215 2.030000e-94 357
47 TraesCS1B01G051400 chr4A 89.209 278 30 0 5086 5363 710055837 710056114 1.220000e-91 348
48 TraesCS1B01G051400 chr4A 93.590 78 5 0 1230 1307 742904525 742904602 3.760000e-22 117
49 TraesCS1B01G051400 chr4A 94.444 72 4 0 1230 1301 710054821 710054892 1.750000e-20 111
50 TraesCS1B01G051400 chr3D 83.753 1668 131 59 781 2382 578866837 578865244 0.000000e+00 1450
51 TraesCS1B01G051400 chr3D 89.695 689 46 10 2600 3276 578842926 578842251 0.000000e+00 856
52 TraesCS1B01G051400 chr3D 97.107 242 7 0 5690 5931 588084410 588084651 5.530000e-110 409
53 TraesCS1B01G051400 chr7D 83.021 1655 172 55 776 2382 24315990 24314397 0.000000e+00 1399
54 TraesCS1B01G051400 chr7D 97.934 242 5 0 5690 5931 526510340 526510099 2.560000e-113 420
55 TraesCS1B01G051400 chr2A 92.108 1001 43 18 1626 2601 9827430 9826441 0.000000e+00 1378
56 TraesCS1B01G051400 chr2A 88.154 1089 82 15 3674 4741 9826200 9825138 0.000000e+00 1253
57 TraesCS1B01G051400 chr2A 83.988 662 65 14 4738 5366 9825271 9824618 1.100000e-166 597
58 TraesCS1B01G051400 chr2A 81.690 568 63 25 781 1316 9828453 9827895 9.130000e-118 435
59 TraesCS1B01G051400 chr2A 97.107 242 7 0 5690 5931 28104679 28104438 5.530000e-110 409
60 TraesCS1B01G051400 chr2A 93.590 78 5 0 1230 1307 9828045 9827968 3.760000e-22 117
61 TraesCS1B01G051400 chr3B 95.669 785 28 2 4 782 767809045 767809829 0.000000e+00 1256
62 TraesCS1B01G051400 chr3B 95.287 785 28 7 4 782 185513076 185512295 0.000000e+00 1236
63 TraesCS1B01G051400 chr3B 95.645 574 25 0 5358 5931 767809821 767810394 0.000000e+00 922
64 TraesCS1B01G051400 chr3B 93.464 153 10 0 5561 5713 550393318 550393470 1.660000e-55 228
65 TraesCS1B01G051400 chr6B 95.512 713 26 2 4 710 39014203 39013491 0.000000e+00 1134
66 TraesCS1B01G051400 chr6B 92.830 265 19 0 5532 5796 39013495 39013231 9.320000e-103 385
67 TraesCS1B01G051400 chr6B 85.333 225 29 2 5377 5600 35589361 35589140 4.620000e-56 230
68 TraesCS1B01G051400 chr6A 91.912 408 20 7 384 782 20775292 20774889 5.190000e-155 558
69 TraesCS1B01G051400 chr6A 91.912 408 20 5 384 782 20831698 20831295 5.190000e-155 558
70 TraesCS1B01G051400 chr6A 92.373 236 18 0 5364 5599 20831297 20831062 2.650000e-88 337
71 TraesCS1B01G051400 chr6A 93.013 229 16 0 5371 5599 20814932 20814704 9.520000e-88 335
72 TraesCS1B01G051400 chr5D 97.521 242 6 0 5690 5931 442382339 442382580 1.190000e-111 414


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 TraesCS1B01G051400 chr1B 31371728 31377658 5930 False 5551.500000 10953 97.396000 1 5931 2 chr1B.!!$F2 5930
1 TraesCS1B01G051400 chr1B 58023392 58030751 7359 True 1067.600000 2828 88.045400 781 5364 5 chr1B.!!$R1 4583
2 TraesCS1B01G051400 chr1B 121890679 121891844 1165 True 956.500000 1297 96.018500 4 5750 2 chr1B.!!$R2 5746
3 TraesCS1B01G051400 chr1B 14895513 14896596 1083 False 873.500000 1288 95.246000 4 5665 2 chr1B.!!$F1 5661
4 TraesCS1B01G051400 chr5B 707934802 707937623 2821 True 1995.000000 3528 92.877000 2640 5363 2 chr5B.!!$R2 2723
5 TraesCS1B01G051400 chr5B 506237372 506238721 1349 True 1094.500000 1284 95.864500 4 5931 2 chr5B.!!$R1 5927
6 TraesCS1B01G051400 chr7B 648171218 648176741 5523 True 1761.000000 3096 97.123000 781 5363 4 chr7B.!!$R2 4582
7 TraesCS1B01G051400 chr7B 674792808 674793846 1038 False 780.000000 780 81.023000 872 1900 1 chr7B.!!$F3 1028
8 TraesCS1B01G051400 chr7B 743565642 743566748 1106 True 707.000000 933 95.992000 84 5931 2 chr7B.!!$R3 5847
9 TraesCS1B01G051400 chr1A 589616966 589621710 4744 True 1155.600000 2848 96.414400 1549 5364 5 chr1A.!!$R1 3815
10 TraesCS1B01G051400 chr2B 222487353 222488700 1347 False 1087.500000 1273 95.731000 4 5929 2 chr2B.!!$F2 5925
11 TraesCS1B01G051400 chr2B 20340411 20348985 8574 False 1067.600000 2835 87.896600 778 5363 5 chr2B.!!$F1 4585
12 TraesCS1B01G051400 chr4A 512418880 512421647 2767 True 877.500000 1515 88.298750 1626 5364 4 chr4A.!!$R1 3738
13 TraesCS1B01G051400 chr4A 742904119 742907963 3844 False 760.600000 1406 88.059000 781 5364 5 chr4A.!!$F2 4583
14 TraesCS1B01G051400 chr4A 710054413 710056114 1701 False 290.333333 412 88.289667 781 5363 3 chr4A.!!$F1 4582
15 TraesCS1B01G051400 chr3D 578865244 578866837 1593 True 1450.000000 1450 83.753000 781 2382 1 chr3D.!!$R2 1601
16 TraesCS1B01G051400 chr3D 578842251 578842926 675 True 856.000000 856 89.695000 2600 3276 1 chr3D.!!$R1 676
17 TraesCS1B01G051400 chr7D 24314397 24315990 1593 True 1399.000000 1399 83.021000 776 2382 1 chr7D.!!$R1 1606
18 TraesCS1B01G051400 chr2A 9824618 9828453 3835 True 756.000000 1378 87.906000 781 5366 5 chr2A.!!$R2 4585
19 TraesCS1B01G051400 chr3B 185512295 185513076 781 True 1236.000000 1236 95.287000 4 782 1 chr3B.!!$R1 778
20 TraesCS1B01G051400 chr3B 767809045 767810394 1349 False 1089.000000 1256 95.657000 4 5931 2 chr3B.!!$F2 5927
21 TraesCS1B01G051400 chr6B 39013231 39014203 972 True 759.500000 1134 94.171000 4 5796 2 chr6B.!!$R2 5792
22 TraesCS1B01G051400 chr6A 20831062 20831698 636 True 447.500000 558 92.142500 384 5599 2 chr6A.!!$R3 5215

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
758 776 0.173935 TCGACACCGTGTTGAAGTGT 59.826 50.0 17.75 0.0 46.97 3.55 F
759 777 1.003851 CGACACCGTGTTGAAGTGTT 58.996 50.0 12.98 0.0 44.45 3.32 F
2164 2449 0.832135 AGACCGTGCCTTCTCTTCCA 60.832 55.0 0.00 0.0 0.00 3.53 F
3233 7770 0.543174 AGGAAGAGACGCTTGGACCT 60.543 55.0 0.00 0.0 36.83 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 2144 1.173043 CAAGCTGGGAAATTACGGCA 58.827 50.000 10.11 0.0 41.38 5.69 R
2279 2566 2.069273 CACCATGTTCTGTCGAGGTTC 58.931 52.381 0.00 0.0 0.00 3.62 R
3497 8034 0.251634 CAGCTCTCTTCCCTCCCAAC 59.748 60.000 0.00 0.0 0.00 3.77 R
5172 10536 0.616891 GGTTATCCCTGACGGTTGGT 59.383 55.000 0.00 0.0 0.00 3.67 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
38 39 4.950050 ACCTCGAATACATAGCCAGAAAG 58.050 43.478 0.00 0.00 0.00 2.62
110 111 3.118482 GGGTCTACAGGTTTACTTAGCCC 60.118 52.174 0.00 0.00 0.00 5.19
111 112 3.773667 GGTCTACAGGTTTACTTAGCCCT 59.226 47.826 0.00 0.00 0.00 5.19
114 115 3.983044 ACAGGTTTACTTAGCCCTCAG 57.017 47.619 0.00 0.00 0.00 3.35
165 166 4.790718 ACTTAAGAAACACAGGGGTCTT 57.209 40.909 10.09 0.00 34.74 3.01
181 182 3.522553 GGTCTTAGTAGCAGCGTTCAAT 58.477 45.455 0.00 0.00 0.00 2.57
247 248 8.383175 AGGTGGATAAGAAGTTCAAAATGTCTA 58.617 33.333 5.50 0.00 0.00 2.59
747 765 1.256652 CGTGAGTACAATCGACACCG 58.743 55.000 0.00 0.00 37.07 4.94
755 773 1.864711 ACAATCGACACCGTGTTGAAG 59.135 47.619 22.66 19.50 43.41 3.02
756 774 1.864711 CAATCGACACCGTGTTGAAGT 59.135 47.619 22.66 12.63 43.41 3.01
757 775 1.497991 ATCGACACCGTGTTGAAGTG 58.502 50.000 22.66 2.97 43.41 3.16
758 776 0.173935 TCGACACCGTGTTGAAGTGT 59.826 50.000 17.75 0.00 46.97 3.55
759 777 1.003851 CGACACCGTGTTGAAGTGTT 58.996 50.000 12.98 0.00 44.45 3.32
760 778 2.159268 TCGACACCGTGTTGAAGTGTTA 60.159 45.455 17.75 0.00 44.45 2.41
761 779 2.034339 CGACACCGTGTTGAAGTGTTAC 60.034 50.000 12.98 0.00 44.45 2.50
762 780 3.192466 GACACCGTGTTGAAGTGTTACT 58.808 45.455 5.45 0.00 44.45 2.24
763 781 3.192466 ACACCGTGTTGAAGTGTTACTC 58.808 45.455 0.00 0.00 41.86 2.59
764 782 2.542595 CACCGTGTTGAAGTGTTACTCC 59.457 50.000 0.00 0.00 0.00 3.85
765 783 2.140717 CCGTGTTGAAGTGTTACTCCC 58.859 52.381 0.00 0.00 0.00 4.30
766 784 2.224209 CCGTGTTGAAGTGTTACTCCCT 60.224 50.000 0.00 0.00 0.00 4.20
767 785 3.057734 CGTGTTGAAGTGTTACTCCCTC 58.942 50.000 0.00 0.00 0.00 4.30
768 786 3.491964 CGTGTTGAAGTGTTACTCCCTCA 60.492 47.826 0.00 0.00 0.00 3.86
769 787 4.448210 GTGTTGAAGTGTTACTCCCTCAA 58.552 43.478 0.00 0.00 0.00 3.02
770 788 4.879545 GTGTTGAAGTGTTACTCCCTCAAA 59.120 41.667 0.00 0.00 28.01 2.69
771 789 4.879545 TGTTGAAGTGTTACTCCCTCAAAC 59.120 41.667 0.00 0.00 28.01 2.93
772 790 5.123936 GTTGAAGTGTTACTCCCTCAAACT 58.876 41.667 0.00 0.00 28.01 2.66
773 791 4.703897 TGAAGTGTTACTCCCTCAAACTG 58.296 43.478 0.00 0.00 0.00 3.16
774 792 3.771577 AGTGTTACTCCCTCAAACTGG 57.228 47.619 0.00 0.00 0.00 4.00
779 797 4.597507 TGTTACTCCCTCAAACTGGAATCT 59.402 41.667 0.00 0.00 0.00 2.40
875 894 1.207811 GTTTTACTGTAGGCCGGGCTA 59.792 52.381 32.25 32.25 0.00 3.93
1257 1354 2.758327 CCTCCATCGTCCGGTCCA 60.758 66.667 0.00 0.00 0.00 4.02
1554 1704 6.909158 ACCTCCTTTTCCTGGATCTAAGATTA 59.091 38.462 0.00 0.00 32.56 1.75
1695 1934 3.615110 CGTCTGTAGCAACCTCACTGAAT 60.615 47.826 0.00 0.00 0.00 2.57
1771 2015 5.911752 AGGTTGTAGCTTCTATGACATCTG 58.088 41.667 0.00 0.00 0.00 2.90
1772 2016 4.509600 GGTTGTAGCTTCTATGACATCTGC 59.490 45.833 0.00 0.00 0.00 4.26
1773 2017 5.355596 GTTGTAGCTTCTATGACATCTGCT 58.644 41.667 0.00 0.74 0.00 4.24
1873 2144 1.678970 GGCTGCCACCCTTTTCGAT 60.679 57.895 15.17 0.00 0.00 3.59
2151 2424 3.795623 ACTGCACGATTTATAGACCGT 57.204 42.857 0.00 0.00 35.46 4.83
2164 2449 0.832135 AGACCGTGCCTTCTCTTCCA 60.832 55.000 0.00 0.00 0.00 3.53
2197 2482 4.023878 GTGGTAAAATTAAGTGTCCGTGCA 60.024 41.667 0.00 0.00 0.00 4.57
2285 2572 6.262496 GGGTATAAGCCAAATTACAGAACCTC 59.738 42.308 0.00 0.00 35.40 3.85
2341 2628 5.740513 GCTGATGGATCTGTCCCTTTAGTAC 60.741 48.000 0.00 0.00 44.41 2.73
2342 2629 5.277250 TGATGGATCTGTCCCTTTAGTACA 58.723 41.667 0.00 0.00 44.41 2.90
2343 2630 5.905331 TGATGGATCTGTCCCTTTAGTACAT 59.095 40.000 0.00 0.00 44.41 2.29
2529 2823 0.995728 GTCTTTCTGCTGTAGCTCGC 59.004 55.000 5.38 0.00 42.66 5.03
2580 2874 4.558178 TGTCCATTGCACATTTTGATGAC 58.442 39.130 0.00 0.00 0.00 3.06
2643 7168 7.331089 AGGAAGAGTTTTGGGTAAGTAGAAT 57.669 36.000 0.00 0.00 0.00 2.40
2747 7284 3.382546 AGAACTTGTTTGAGCTGCATGTT 59.617 39.130 1.02 0.00 34.61 2.71
3031 7568 6.721208 ACATCAAAGGAATACAAGACCAACAT 59.279 34.615 0.00 0.00 0.00 2.71
3063 7600 3.439293 CGAGAAGCTCGCTTGAAATCTA 58.561 45.455 9.15 0.00 46.75 1.98
3076 7613 6.348050 CGCTTGAAATCTAAGGATATTGCTCC 60.348 42.308 0.00 0.00 35.37 4.70
3081 7618 7.285401 TGAAATCTAAGGATATTGCTCCAAACC 59.715 37.037 0.00 0.00 37.81 3.27
3133 7670 6.621812 GCACAACAATATTTGGTATGTCGTGA 60.622 38.462 0.44 0.00 34.12 4.35
3136 7673 9.168451 ACAACAATATTTGGTATGTCGTGATTA 57.832 29.630 0.00 0.00 34.12 1.75
3154 7691 8.122330 TCGTGATTATTGTATGATTTGCTTCAC 58.878 33.333 0.00 0.00 0.00 3.18
3168 7705 8.898761 TGATTTGCTTCACACTTAGTTTTTCTA 58.101 29.630 0.00 0.00 0.00 2.10
3192 7729 4.649088 ACATGATGATGCCATGACTTTG 57.351 40.909 0.00 0.00 42.89 2.77
3196 7733 3.129813 TGATGATGCCATGACTTTGCTTC 59.870 43.478 0.00 0.00 32.09 3.86
3198 7735 2.892215 TGATGCCATGACTTTGCTTCAA 59.108 40.909 0.00 0.00 36.58 2.69
3202 7739 5.465532 TGCCATGACTTTGCTTCAATTTA 57.534 34.783 0.00 0.00 0.00 1.40
3204 7741 5.870433 TGCCATGACTTTGCTTCAATTTATG 59.130 36.000 0.00 0.00 0.00 1.90
3205 7742 5.870978 GCCATGACTTTGCTTCAATTTATGT 59.129 36.000 0.00 0.00 0.00 2.29
3212 7749 8.177119 ACTTTGCTTCAATTTATGTGGTCTTA 57.823 30.769 0.00 0.00 0.00 2.10
3224 7761 5.776173 ATGTGGTCTTATAGGAAGAGACG 57.224 43.478 0.00 0.00 40.47 4.18
3233 7770 0.543174 AGGAAGAGACGCTTGGACCT 60.543 55.000 0.00 0.00 36.83 3.85
3245 7782 1.827399 TTGGACCTGAGAAGGCGACC 61.827 60.000 0.00 0.00 0.00 4.79
3299 7836 5.181748 GGAATGAAGAATGTGAGTAGCAGT 58.818 41.667 0.00 0.00 0.00 4.40
3347 7884 1.820519 GGTGCAATCATGAGCCAGAAA 59.179 47.619 0.09 0.00 0.00 2.52
3360 7897 1.802508 GCCAGAAAGCACAAAAACGCT 60.803 47.619 0.00 0.00 41.20 5.07
3372 7909 5.387342 GCACAAAAACGCTTTGTATGTCATC 60.387 40.000 13.96 0.00 40.30 2.92
3388 7925 5.276461 TGTCATCGTTTCTACTGCCATAT 57.724 39.130 0.00 0.00 0.00 1.78
3398 7935 7.148573 CGTTTCTACTGCCATATTGCTTATAGG 60.149 40.741 0.00 0.00 0.00 2.57
3403 7940 7.660030 ACTGCCATATTGCTTATAGGTTTTT 57.340 32.000 0.00 0.00 0.00 1.94
3405 7942 9.196139 ACTGCCATATTGCTTATAGGTTTTTAA 57.804 29.630 0.00 0.00 0.00 1.52
3408 7945 9.678941 GCCATATTGCTTATAGGTTTTTAAGAC 57.321 33.333 0.00 0.00 0.00 3.01
3476 8013 3.750130 CAGGATGACTATACTGCATTGGC 59.250 47.826 0.00 0.00 38.38 4.52
3477 8014 3.649981 AGGATGACTATACTGCATTGGCT 59.350 43.478 0.00 0.00 41.91 4.75
3497 8034 7.531857 TGGCTAAAGAGAAGTATCCAGATAG 57.468 40.000 0.00 0.00 0.00 2.08
3514 8051 1.867363 TAGTTGGGAGGGAAGAGAGC 58.133 55.000 0.00 0.00 0.00 4.09
3564 8101 1.451927 TGGCATTCCTCATGGTCGC 60.452 57.895 0.00 0.00 32.81 5.19
3629 8661 6.830873 ATCAGCAGCTAGAAAAAGAAATGT 57.169 33.333 0.00 0.00 0.00 2.71
3778 8810 9.171877 TCATAACTGTATGTACAAATTCATGCA 57.828 29.630 0.00 0.00 38.63 3.96
4075 9107 7.174772 ACACTGTGTTGCATATGAGATTGTTTA 59.825 33.333 7.80 0.00 0.00 2.01
4120 9154 3.402058 GATGTTTGCATCTGTGAGCTC 57.598 47.619 6.82 6.82 45.97 4.09
4179 9215 7.116233 CCCAATTTCCGTATAAATAATGCTTGC 59.884 37.037 0.00 0.00 0.00 4.01
4306 9356 6.879458 GGTTATGTTGTCTCCACTTGTTATCT 59.121 38.462 0.00 0.00 0.00 1.98
4377 9432 5.165961 TGGTTACTTCTTGATTCAGGGAG 57.834 43.478 2.62 2.62 0.00 4.30
4691 9772 2.504175 TGGATGGTACCTTTGTAGCCTC 59.496 50.000 14.36 0.00 43.30 4.70
4696 9777 2.757314 GGTACCTTTGTAGCCTCGTAGT 59.243 50.000 4.06 0.00 39.10 2.73
4701 9782 4.465305 ACCTTTGTAGCCTCGTAGTGTAAT 59.535 41.667 0.00 0.00 0.00 1.89
4709 9790 5.488341 AGCCTCGTAGTGTAATTTGTTGAT 58.512 37.500 0.00 0.00 0.00 2.57
4870 10073 7.157347 GGAACTGATGATGCTATATGAAGTCA 58.843 38.462 0.00 0.00 0.00 3.41
4871 10074 7.823310 GGAACTGATGATGCTATATGAAGTCAT 59.177 37.037 0.00 0.00 40.22 3.06
5009 10219 0.036732 ATGTGACAGTGACGGCCAAT 59.963 50.000 2.24 0.00 0.00 3.16
5093 10457 4.684724 ACAGGTATAAGTCCTTCCTGACA 58.315 43.478 16.10 0.00 45.76 3.58
5133 10497 6.761714 GTGGACGACAGGAATATGTATTTTCT 59.238 38.462 0.00 0.00 32.25 2.52
5172 10536 2.543445 CGCAACATTTCTTTCCTGTGCA 60.543 45.455 0.00 0.00 0.00 4.57
5209 10573 6.093633 GGATAACCGACAGCATTAATATTCCC 59.906 42.308 0.00 0.00 0.00 3.97
5366 10732 4.139786 AGTCACGTTTCTGGTAGTGTCTA 58.860 43.478 0.00 0.00 32.88 2.59
5448 10814 2.558359 CCTCCCTGTTGAACCAATGAAC 59.442 50.000 0.00 0.00 0.00 3.18
5488 10854 7.322664 CAGTAAAATTCTCTTCTCTCTCTGCT 58.677 38.462 0.00 0.00 0.00 4.24
5500 10866 1.136695 CTCTCTGCTACTGGCTGGAAG 59.863 57.143 0.00 0.00 42.39 3.46
5521 10887 2.027100 GTCCCTCCACTGTTTTCCCTAG 60.027 54.545 0.00 0.00 0.00 3.02
5524 10890 2.427506 CTCCACTGTTTTCCCTAGTGC 58.572 52.381 0.00 0.00 40.26 4.40
5563 10929 3.112580 GTGTTAAATGCACGCACAAACT 58.887 40.909 0.00 0.00 0.00 2.66
5568 10934 2.051345 GCACGCACAAACTTCCCG 60.051 61.111 0.00 0.00 0.00 5.14
5574 10940 1.377229 CACAAACTTCCCGGGCCTA 59.623 57.895 18.49 2.08 0.00 3.93
5602 10968 2.398588 CTCCCTCCACAATGGCTAGTA 58.601 52.381 0.00 0.00 37.47 1.82
5652 11018 3.269178 TGCATGACGAAATGATGCAGTA 58.731 40.909 0.00 0.00 45.76 2.74
5773 11139 8.814038 ATAATGCTAACCATGAAGTCTTCTTT 57.186 30.769 13.67 4.79 33.49 2.52
5909 11275 9.790389 AGTAAAGATTGTGAACTCTATTAGACG 57.210 33.333 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.787725 ATTCGAGGTTTCCAACTTGTATATC 57.212 36.000 0.00 0.00 0.00 1.63
1 2 8.262227 TGTATTCGAGGTTTCCAACTTGTATAT 58.738 33.333 0.00 0.00 0.00 0.86
2 3 7.613585 TGTATTCGAGGTTTCCAACTTGTATA 58.386 34.615 0.00 0.00 0.00 1.47
20 21 6.146837 CCAATCTCTTTCTGGCTATGTATTCG 59.853 42.308 0.00 0.00 0.00 3.34
114 115 9.445878 AAATCTGTTAAACTAGCTAGGTAAACC 57.554 33.333 24.35 11.33 0.00 3.27
141 142 6.449830 AGACCCCTGTGTTTCTTAAGTTAT 57.550 37.500 1.63 0.00 0.00 1.89
165 166 3.861113 CGGTTTATTGAACGCTGCTACTA 59.139 43.478 0.00 0.00 39.22 1.82
181 182 3.993081 CCAAATGCAAAGCAATCGGTTTA 59.007 39.130 0.00 0.00 43.62 2.01
247 248 2.435437 AGGCAGAACAACCATGCTTTTT 59.565 40.909 0.00 0.00 39.88 1.94
747 765 4.067972 TGAGGGAGTAACACTTCAACAC 57.932 45.455 0.00 0.00 29.26 3.32
755 773 3.764237 TCCAGTTTGAGGGAGTAACAC 57.236 47.619 0.00 0.00 0.00 3.32
756 774 4.597507 AGATTCCAGTTTGAGGGAGTAACA 59.402 41.667 0.00 0.00 34.02 2.41
757 775 5.046231 AGAGATTCCAGTTTGAGGGAGTAAC 60.046 44.000 0.00 0.00 34.02 2.50
758 776 5.094387 AGAGATTCCAGTTTGAGGGAGTAA 58.906 41.667 0.00 0.00 34.02 2.24
759 777 4.689062 AGAGATTCCAGTTTGAGGGAGTA 58.311 43.478 0.00 0.00 34.02 2.59
760 778 3.525862 AGAGATTCCAGTTTGAGGGAGT 58.474 45.455 0.00 0.00 34.02 3.85
761 779 4.141824 GGTAGAGATTCCAGTTTGAGGGAG 60.142 50.000 0.00 0.00 34.02 4.30
762 780 3.775316 GGTAGAGATTCCAGTTTGAGGGA 59.225 47.826 0.00 0.00 0.00 4.20
763 781 3.519510 TGGTAGAGATTCCAGTTTGAGGG 59.480 47.826 0.00 0.00 0.00 4.30
764 782 4.764172 CTGGTAGAGATTCCAGTTTGAGG 58.236 47.826 3.38 0.00 44.19 3.86
772 790 2.034685 CGCGATTCTGGTAGAGATTCCA 59.965 50.000 0.00 0.00 30.27 3.53
773 791 2.293677 TCGCGATTCTGGTAGAGATTCC 59.706 50.000 3.71 0.00 30.27 3.01
774 792 3.003897 AGTCGCGATTCTGGTAGAGATTC 59.996 47.826 14.06 0.00 0.00 2.52
779 797 3.276857 ACTTAGTCGCGATTCTGGTAGA 58.723 45.455 14.06 0.00 0.00 2.59
875 894 1.539827 GTGCAAAAACCTGTCGGCTAT 59.460 47.619 0.00 0.00 0.00 2.97
1242 1339 3.072468 GGTGGACCGGACGATGGA 61.072 66.667 9.46 0.00 0.00 3.41
1449 1598 1.739562 CAGCCAGAGGTGAAGACGC 60.740 63.158 0.00 0.00 44.53 5.19
1554 1704 4.633565 GCTACACAAGAAATAGAGCAAGCT 59.366 41.667 0.00 0.00 0.00 3.74
1695 1934 6.037786 ACAGAAGCTACAACATGTTAGCTA 57.962 37.500 27.87 11.38 44.21 3.32
1873 2144 1.173043 CAAGCTGGGAAATTACGGCA 58.827 50.000 10.11 0.00 41.38 5.69
1952 2224 7.856894 GCAGCACAAATAACAATTCACAAAAAT 59.143 29.630 0.00 0.00 0.00 1.82
2151 2424 2.470990 TCAGCTATGGAAGAGAAGGCA 58.529 47.619 0.00 0.00 0.00 4.75
2164 2449 7.888546 ACACTTAATTTTACCACCTTCAGCTAT 59.111 33.333 0.00 0.00 0.00 2.97
2279 2566 2.069273 CACCATGTTCTGTCGAGGTTC 58.931 52.381 0.00 0.00 0.00 3.62
2285 2572 2.732412 ACTCTCACCATGTTCTGTCG 57.268 50.000 0.00 0.00 0.00 4.35
2341 2628 4.711399 TCATTACAGCCCTCTTGATGATG 58.289 43.478 0.00 0.00 0.00 3.07
2342 2629 5.378230 TTCATTACAGCCCTCTTGATGAT 57.622 39.130 0.00 0.00 0.00 2.45
2343 2630 4.842531 TTCATTACAGCCCTCTTGATGA 57.157 40.909 0.00 0.00 0.00 2.92
2529 2823 4.707030 TTGTGATTTCATAGCCAGCAAG 57.293 40.909 0.00 0.00 0.00 4.01
2580 2874 6.980397 GGCTGTCATGGATTATTTTTAAGGTG 59.020 38.462 0.00 0.00 0.00 4.00
2747 7284 3.092301 ACTGTCATCTTCCTCGTCATCA 58.908 45.455 0.00 0.00 0.00 3.07
3031 7568 2.038975 CTTCTCGTCCCCTCCCCA 59.961 66.667 0.00 0.00 0.00 4.96
3063 7600 3.545703 CTCGGTTTGGAGCAATATCCTT 58.454 45.455 0.00 0.00 40.29 3.36
3076 7613 1.738099 CGTGAGCCTCCTCGGTTTG 60.738 63.158 0.00 0.00 41.13 2.93
3081 7618 1.878656 AAAGGTCGTGAGCCTCCTCG 61.879 60.000 0.00 0.00 41.13 4.63
3136 7673 8.340618 ACTAAGTGTGAAGCAAATCATACAAT 57.659 30.769 13.60 7.01 42.06 2.71
3142 7679 7.771183 AGAAAAACTAAGTGTGAAGCAAATCA 58.229 30.769 0.00 0.00 0.00 2.57
3168 7705 6.737622 GCAAAGTCATGGCATCATCATGTAAT 60.738 38.462 0.00 0.00 41.79 1.89
3177 7714 2.516906 TGAAGCAAAGTCATGGCATCA 58.483 42.857 0.00 0.00 33.45 3.07
3178 7715 3.581024 TTGAAGCAAAGTCATGGCATC 57.419 42.857 0.00 0.00 0.00 3.91
3192 7729 8.677148 TCCTATAAGACCACATAAATTGAAGC 57.323 34.615 0.00 0.00 0.00 3.86
3198 7735 8.361139 CGTCTCTTCCTATAAGACCACATAAAT 58.639 37.037 0.00 0.00 36.84 1.40
3202 7739 4.038162 GCGTCTCTTCCTATAAGACCACAT 59.962 45.833 0.00 0.00 36.84 3.21
3204 7741 3.633065 AGCGTCTCTTCCTATAAGACCAC 59.367 47.826 0.00 0.00 36.84 4.16
3205 7742 3.899726 AGCGTCTCTTCCTATAAGACCA 58.100 45.455 0.00 0.00 36.84 4.02
3212 7749 1.757699 GGTCCAAGCGTCTCTTCCTAT 59.242 52.381 0.00 0.00 31.27 2.57
3224 7761 1.743252 CGCCTTCTCAGGTCCAAGC 60.743 63.158 0.00 0.00 43.18 4.01
3245 7782 5.905480 TTGCAGTATATGTATTCAGCGTG 57.095 39.130 0.00 0.00 0.00 5.34
3299 7836 1.079956 GATTGCGCCATTGTTGCCA 60.080 52.632 4.18 0.00 0.00 4.92
3311 7848 2.121786 GCACCATTGCTAATGATTGCG 58.878 47.619 9.56 0.00 46.17 4.85
3347 7884 4.040445 ACATACAAAGCGTTTTTGTGCT 57.960 36.364 22.19 11.76 44.97 4.40
3360 7897 5.350365 GGCAGTAGAAACGATGACATACAAA 59.650 40.000 0.00 0.00 0.00 2.83
3372 7909 4.882671 AAGCAATATGGCAGTAGAAACG 57.117 40.909 4.54 0.00 35.83 3.60
3403 7940 9.426837 ACAACATGCTAGTAAATTAACGTCTTA 57.573 29.630 0.00 0.00 0.00 2.10
3405 7942 7.601130 TCACAACATGCTAGTAAATTAACGTCT 59.399 33.333 0.00 0.00 0.00 4.18
3408 7945 8.012809 TGTTCACAACATGCTAGTAAATTAACG 58.987 33.333 0.00 0.00 36.25 3.18
3436 7973 9.956720 GTCATCCTGACAATCAAAAATTATAGG 57.043 33.333 2.48 0.00 46.22 2.57
3454 7991 3.750130 GCCAATGCAGTATAGTCATCCTG 59.250 47.826 0.00 0.00 37.47 3.86
3469 8006 5.126067 TGGATACTTCTCTTTAGCCAATGC 58.874 41.667 0.00 0.00 30.78 3.56
3476 8013 8.364142 CCCAACTATCTGGATACTTCTCTTTAG 58.636 40.741 0.00 0.00 38.96 1.85
3477 8014 8.065627 TCCCAACTATCTGGATACTTCTCTTTA 58.934 37.037 0.00 0.00 38.96 1.85
3497 8034 0.251634 CAGCTCTCTTCCCTCCCAAC 59.748 60.000 0.00 0.00 0.00 3.77
3514 8051 1.877576 TACAGCAGCTCACCGTCCAG 61.878 60.000 0.00 0.00 0.00 3.86
3564 8101 0.880278 CCCCATCGCCTATTGACACG 60.880 60.000 0.00 0.00 0.00 4.49
3629 8661 2.160219 GTGAGCGAAATTGATGCACTGA 59.840 45.455 0.00 0.00 0.00 3.41
3778 8810 6.182627 TGAGATCCATTGCTTTAGAATGTGT 58.817 36.000 0.00 0.00 0.00 3.72
4120 9154 7.704472 AGCTAAAGAATCTTGTGAGAATAGACG 59.296 37.037 0.00 0.00 35.07 4.18
4179 9215 3.565764 TCAGATGGACCTTAAGCATGG 57.434 47.619 0.00 0.00 0.00 3.66
4277 9327 5.067283 ACAAGTGGAGACAACATAACCAAAC 59.933 40.000 0.00 0.00 46.06 2.93
4377 9432 3.002759 GCCGGCTTGAGATGAGTTATTTC 59.997 47.826 22.15 0.00 0.00 2.17
4994 10204 2.690778 GCCATTGGCCGTCACTGTC 61.691 63.158 17.28 0.00 44.06 3.51
5009 10219 0.955428 GCGTTCATTCCTGTGAGCCA 60.955 55.000 0.00 0.00 0.00 4.75
5042 10253 6.278363 TCAGCCGACAGGAAAATTATACTAC 58.722 40.000 0.00 0.00 41.02 2.73
5093 10457 1.694696 GTCCACCTGTCAGGAAAGACT 59.305 52.381 26.18 0.00 37.67 3.24
5133 10497 2.288666 GCGTCAGATTTATGCTTCCCA 58.711 47.619 0.00 0.00 0.00 4.37
5172 10536 0.616891 GGTTATCCCTGACGGTTGGT 59.383 55.000 0.00 0.00 0.00 3.67
5340 10706 4.340381 ACACTACCAGAAACGTGACTAAGT 59.660 41.667 0.00 0.00 0.00 2.24
5366 10732 1.840635 GCTATTTCACCCTGGACCTCT 59.159 52.381 0.00 0.00 0.00 3.69
5488 10854 0.617820 GGAGGGACTTCCAGCCAGTA 60.618 60.000 0.00 0.00 41.55 2.74
5500 10866 0.771755 AGGGAAAACAGTGGAGGGAC 59.228 55.000 0.00 0.00 0.00 4.46
5563 10929 2.689771 GGAAGGTAGGCCCGGGAA 60.690 66.667 29.31 5.38 38.74 3.97
5568 10934 2.773053 GGAGGGGAAGGTAGGCCC 60.773 72.222 0.00 0.00 43.91 5.80
5574 10940 2.125225 GTGGAGGGAGGGGAAGGT 59.875 66.667 0.00 0.00 0.00 3.50
5602 10968 5.703592 TGTTTGTTCTTATATGTGCCTTCGT 59.296 36.000 0.00 0.00 0.00 3.85
5633 10999 5.919272 ATCTACTGCATCATTTCGTCATG 57.081 39.130 0.00 0.00 0.00 3.07
5652 11018 5.046950 GGACAAGTGAGGAGTTCTGTAATCT 60.047 44.000 0.00 0.00 0.00 2.40
5773 11139 9.513906 TGTTTTCATCACTCCTTTGTTATATGA 57.486 29.630 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.