Multiple sequence alignment - TraesCS6D01G309000

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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 TraesCS6D01G309000 chr6D 100.000 3484 0 0 995 4478 419746987 419750470 0.000000e+00 6434.0
1 TraesCS6D01G309000 chr6D 86.813 1365 115 38 2303 3642 419657292 419658616 0.000000e+00 1463.0
2 TraesCS6D01G309000 chr6D 100.000 661 0 0 1 661 419745993 419746653 0.000000e+00 1221.0
3 TraesCS6D01G309000 chr6D 82.694 1225 147 41 2301 3498 419484919 419486105 0.000000e+00 1027.0
4 TraesCS6D01G309000 chr6D 82.169 1217 157 40 2299 3473 419614586 419615784 0.000000e+00 990.0
5 TraesCS6D01G309000 chr6D 84.486 954 116 22 2459 3395 419447736 419448674 0.000000e+00 913.0
6 TraesCS6D01G309000 chr6D 84.983 879 95 25 2303 3162 419285944 419286804 0.000000e+00 857.0
7 TraesCS6D01G309000 chr6D 82.514 366 38 12 1633 1991 419484205 419484551 9.420000e-77 298.0
8 TraesCS6D01G309000 chr6D 94.536 183 7 2 995 1176 419482539 419482719 3.410000e-71 279.0
9 TraesCS6D01G309000 chr6D 93.642 173 8 2 995 1164 419614310 419614482 5.750000e-64 255.0
10 TraesCS6D01G309000 chr6D 87.907 215 16 5 1809 2019 419447280 419447488 1.240000e-60 244.0
11 TraesCS6D01G309000 chr6D 90.323 186 17 1 995 1179 419444674 419444859 4.480000e-60 243.0
12 TraesCS6D01G309000 chr6D 84.865 185 18 6 1 175 419653954 419654138 1.280000e-40 178.0
13 TraesCS6D01G309000 chr6D 81.951 205 24 10 1457 1650 419483986 419484188 1.290000e-35 161.0
14 TraesCS6D01G309000 chr6D 87.500 128 7 4 1538 1665 419483311 419483429 6.040000e-29 139.0
15 TraesCS6D01G309000 chr6B 94.535 1720 68 12 2224 3924 632787017 632788729 0.000000e+00 2632.0
16 TraesCS6D01G309000 chr6B 85.816 1403 135 34 2303 3667 632565259 632566635 0.000000e+00 1430.0
17 TraesCS6D01G309000 chr6B 83.912 1181 148 27 2302 3461 632422195 632423354 0.000000e+00 1090.0
18 TraesCS6D01G309000 chr6B 83.632 1173 143 32 2301 3441 632503467 632504622 0.000000e+00 1057.0
19 TraesCS6D01G309000 chr6B 84.084 955 109 31 2233 3162 632242671 632243607 0.000000e+00 881.0
20 TraesCS6D01G309000 chr6B 87.755 490 38 6 1585 2070 632786443 632786914 1.820000e-153 553.0
21 TraesCS6D01G309000 chr6B 83.712 528 36 22 146 632 632785612 632786130 1.900000e-123 453.0
22 TraesCS6D01G309000 chr6B 97.191 178 5 0 995 1172 632786237 632786414 7.280000e-78 302.0
23 TraesCS6D01G309000 chr6B 93.684 190 7 2 995 1179 632419979 632420168 3.410000e-71 279.0
24 TraesCS6D01G309000 chr6B 82.515 326 41 12 1672 1991 632421719 632422034 5.710000e-69 272.0
25 TraesCS6D01G309000 chr6B 87.083 240 19 7 1759 1993 632564937 632565169 1.240000e-65 261.0
26 TraesCS6D01G309000 chr6B 90.323 186 17 1 995 1179 632287275 632287460 4.480000e-60 243.0
27 TraesCS6D01G309000 chr6B 93.333 150 8 2 3 150 632784381 632784530 2.100000e-53 220.0
28 TraesCS6D01G309000 chr6B 87.097 186 14 5 1838 2019 632289905 632290084 7.600000e-48 202.0
29 TraesCS6D01G309000 chr6B 78.455 246 33 9 1421 1665 632420706 632420932 4.670000e-30 143.0
30 TraesCS6D01G309000 chr6B 88.496 113 12 1 336 448 632563707 632563818 7.810000e-28 135.0
31 TraesCS6D01G309000 chr6B 100.000 31 0 0 1286 1316 632420366 632420336 1.740000e-04 58.4
32 TraesCS6D01G309000 chr6A 95.136 1686 52 12 2229 3901 562920105 562921773 0.000000e+00 2632.0
33 TraesCS6D01G309000 chr6A 87.346 1383 105 39 2303 3650 562869208 562870555 0.000000e+00 1520.0
34 TraesCS6D01G309000 chr6A 80.614 1434 163 55 2301 3663 562796722 562798111 0.000000e+00 1002.0
35 TraesCS6D01G309000 chr6A 84.615 1014 130 16 2465 3474 562813642 562814633 0.000000e+00 985.0
36 TraesCS6D01G309000 chr6A 91.699 518 23 9 995 1501 562918912 562919420 0.000000e+00 701.0
37 TraesCS6D01G309000 chr6A 89.182 379 17 8 1 374 562918098 562918457 6.830000e-123 451.0
38 TraesCS6D01G309000 chr6A 89.256 363 24 6 1759 2110 562919684 562920042 1.480000e-119 440.0
39 TraesCS6D01G309000 chr6A 88.308 325 14 6 358 661 562918483 562918804 7.080000e-98 368.0
40 TraesCS6D01G309000 chr6A 76.936 607 83 26 1421 1991 562795590 562796175 4.380000e-75 292.0
41 TraesCS6D01G309000 chr6A 93.443 183 9 2 995 1176 562794941 562795121 7.380000e-68 268.0
42 TraesCS6D01G309000 chr6A 89.450 218 14 4 1807 2019 562761761 562761974 2.660000e-67 267.0
43 TraesCS6D01G309000 chr6A 91.192 193 14 3 1538 1730 562919427 562919616 4.440000e-65 259.0
44 TraesCS6D01G309000 chr6A 91.398 186 15 1 995 1179 562757724 562757909 2.070000e-63 254.0
45 TraesCS6D01G309000 chr6A 87.838 74 9 0 2156 2229 94067043 94067116 2.220000e-13 87.9
46 TraesCS6D01G309000 chr2D 85.512 566 70 10 3922 4477 637872288 637871725 8.350000e-162 580.0
47 TraesCS6D01G309000 chr2D 81.004 558 78 18 3923 4478 621316841 621317372 6.930000e-113 418.0
48 TraesCS6D01G309000 chr2D 83.824 68 11 0 2145 2212 644846399 644846332 1.040000e-06 65.8
49 TraesCS6D01G309000 chr3D 86.071 560 48 13 3922 4476 10835159 10835693 3.880000e-160 575.0
50 TraesCS6D01G309000 chr3D 84.902 563 78 7 3921 4478 387708386 387707826 3.020000e-156 562.0
51 TraesCS6D01G309000 chr1D 82.765 557 68 14 3924 4478 111052878 111052348 5.240000e-129 472.0
52 TraesCS6D01G309000 chr1D 77.034 553 100 20 3924 4471 462689000 462689530 4.380000e-75 292.0
53 TraesCS6D01G309000 chr1D 91.781 73 4 2 3923 3995 33666165 33666235 2.850000e-17 100.0
54 TraesCS6D01G309000 chr5D 77.996 559 97 17 3925 4478 382095183 382095720 1.200000e-85 327.0
55 TraesCS6D01G309000 chr5D 91.667 48 4 0 2165 2212 275415456 275415503 2.890000e-07 67.6
56 TraesCS6D01G309000 chr3B 81.295 139 17 8 3916 4050 170760287 170760154 2.200000e-18 104.0
57 TraesCS6D01G309000 chr3B 88.732 71 8 0 2143 2213 74812181 74812111 2.220000e-13 87.9
58 TraesCS6D01G309000 chr5A 91.429 70 4 2 3922 3991 423829035 423829102 1.330000e-15 95.3
59 TraesCS6D01G309000 chr5A 90.000 60 6 0 2160 2219 706470809 706470868 1.340000e-10 78.7
60 TraesCS6D01G309000 chr5A 88.525 61 7 0 2145 2205 364359831 364359891 1.730000e-09 75.0
61 TraesCS6D01G309000 chr7D 88.312 77 5 4 3921 3994 478773094 478773169 6.170000e-14 89.8
62 TraesCS6D01G309000 chr7D 95.000 40 2 0 2166 2205 56293801 56293840 3.740000e-06 63.9
63 TraesCS6D01G309000 chr7D 86.275 51 7 0 2142 2192 620738221 620738171 6.260000e-04 56.5
64 TraesCS6D01G309000 chr2A 90.000 50 5 0 2163 2212 770189094 770189045 1.040000e-06 65.8


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 TraesCS6D01G309000 chr6D 419745993 419750470 4477 False 3827.500000 6434 100.000000 1 4478 2 chr6D.!!$F6 4477
1 TraesCS6D01G309000 chr6D 419285944 419286804 860 False 857.000000 857 84.983000 2303 3162 1 chr6D.!!$F1 859
2 TraesCS6D01G309000 chr6D 419653954 419658616 4662 False 820.500000 1463 85.839000 1 3642 2 chr6D.!!$F5 3641
3 TraesCS6D01G309000 chr6D 419614310 419615784 1474 False 622.500000 990 87.905500 995 3473 2 chr6D.!!$F4 2478
4 TraesCS6D01G309000 chr6D 419444674 419448674 4000 False 466.666667 913 87.572000 995 3395 3 chr6D.!!$F2 2400
5 TraesCS6D01G309000 chr6D 419482539 419486105 3566 False 380.800000 1027 85.839000 995 3498 5 chr6D.!!$F3 2503
6 TraesCS6D01G309000 chr6B 632503467 632504622 1155 False 1057.000000 1057 83.632000 2301 3441 1 chr6B.!!$F2 1140
7 TraesCS6D01G309000 chr6B 632242671 632243607 936 False 881.000000 881 84.084000 2233 3162 1 chr6B.!!$F1 929
8 TraesCS6D01G309000 chr6B 632784381 632788729 4348 False 832.000000 2632 91.305200 3 3924 5 chr6B.!!$F6 3921
9 TraesCS6D01G309000 chr6B 632563707 632566635 2928 False 608.666667 1430 87.131667 336 3667 3 chr6B.!!$F5 3331
10 TraesCS6D01G309000 chr6B 632419979 632423354 3375 False 446.000000 1090 84.641500 995 3461 4 chr6B.!!$F4 2466
11 TraesCS6D01G309000 chr6B 632287275 632290084 2809 False 222.500000 243 88.710000 995 2019 2 chr6B.!!$F3 1024
12 TraesCS6D01G309000 chr6A 562869208 562870555 1347 False 1520.000000 1520 87.346000 2303 3650 1 chr6A.!!$F3 1347
13 TraesCS6D01G309000 chr6A 562813642 562814633 991 False 985.000000 985 84.615000 2465 3474 1 chr6A.!!$F2 1009
14 TraesCS6D01G309000 chr6A 562918098 562921773 3675 False 808.500000 2632 90.795500 1 3901 6 chr6A.!!$F6 3900
15 TraesCS6D01G309000 chr6A 562794941 562798111 3170 False 520.666667 1002 83.664333 995 3663 3 chr6A.!!$F5 2668
16 TraesCS6D01G309000 chr6A 562757724 562761974 4250 False 260.500000 267 90.424000 995 2019 2 chr6A.!!$F4 1024
17 TraesCS6D01G309000 chr2D 637871725 637872288 563 True 580.000000 580 85.512000 3922 4477 1 chr2D.!!$R1 555
18 TraesCS6D01G309000 chr2D 621316841 621317372 531 False 418.000000 418 81.004000 3923 4478 1 chr2D.!!$F1 555
19 TraesCS6D01G309000 chr3D 10835159 10835693 534 False 575.000000 575 86.071000 3922 4476 1 chr3D.!!$F1 554
20 TraesCS6D01G309000 chr3D 387707826 387708386 560 True 562.000000 562 84.902000 3921 4478 1 chr3D.!!$R1 557
21 TraesCS6D01G309000 chr1D 111052348 111052878 530 True 472.000000 472 82.765000 3924 4478 1 chr1D.!!$R1 554
22 TraesCS6D01G309000 chr1D 462689000 462689530 530 False 292.000000 292 77.034000 3924 4471 1 chr1D.!!$F2 547
23 TraesCS6D01G309000 chr5D 382095183 382095720 537 False 327.000000 327 77.996000 3925 4478 1 chr5D.!!$F2 553

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
315 1529 0.742990 GCCATTGGCTGTACGTGCTA 60.743 55.0 20.66 2.17 46.69 3.49 F
1276 2674 0.465705 GAGGATCATGGGTTCGCTCA 59.534 55.0 0.00 0.00 33.17 4.26 F
1770 5785 0.248377 CCGCCTTTACGTACCTCTCG 60.248 60.0 0.00 0.00 0.00 4.04 F
3264 12580 0.109153 TCAGTGTGATTGGTGCAGCT 59.891 50.0 18.08 0.00 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1365 2853 0.099436 GTGATGACTTGGCCAATCGC 59.901 55.000 20.85 16.27 0.00 4.58 R
3022 12279 0.032130 CGATGCCCTGCACGTAGTAT 59.968 55.000 0.00 0.00 43.04 2.12 R
3432 12778 1.811266 CTCCACGCCGAAGACATGG 60.811 63.158 0.00 0.00 0.00 3.66 R
4301 13719 0.741221 GAGCACAAGTTCCGGGCTAG 60.741 60.000 0.00 0.00 34.44 3.42 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
29 31 4.771590 TCATGCCTTTGTAAGCAGAAAG 57.228 40.909 0.00 0.00 43.38 2.62
30 32 4.397420 TCATGCCTTTGTAAGCAGAAAGA 58.603 39.130 0.00 0.00 43.38 2.52
52 66 9.710900 AAAGAAAAACATGATATTGGTCCTTTC 57.289 29.630 0.00 0.00 0.00 2.62
280 1494 2.747855 CTCAGGTGGCCGGAAAGC 60.748 66.667 5.05 0.72 0.00 3.51
294 1508 2.100197 GGAAAGCTATCCAAACCCACC 58.900 52.381 0.00 0.00 39.42 4.61
315 1529 0.742990 GCCATTGGCTGTACGTGCTA 60.743 55.000 20.66 2.17 46.69 3.49
333 1547 4.419522 GCTACCTGCATTTTCGAAAGAA 57.580 40.909 10.98 0.00 44.86 2.52
390 1668 2.434428 AGAGTTGCTCTCCTTTGCATG 58.566 47.619 0.00 0.00 43.71 4.06
450 1728 2.421739 GAGCACTGGGACACACGT 59.578 61.111 0.00 0.00 0.00 4.49
535 1827 0.880278 CCAGCTACGTGCACAGTGTT 60.880 55.000 18.64 0.44 45.94 3.32
568 1873 2.380932 TCTATATAAGGGAGGCGGGTCA 59.619 50.000 0.00 0.00 0.00 4.02
619 1933 2.715749 TGCCAGAGAGAGAGAGAGAG 57.284 55.000 0.00 0.00 0.00 3.20
1206 2562 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1207 2563 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1208 2564 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1209 2565 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1210 2566 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
1211 2567 4.646945 TCTCTCTCTCTCTCTCTCTCTCAC 59.353 50.000 0.00 0.00 0.00 3.51
1212 2568 4.352893 TCTCTCTCTCTCTCTCTCTCACA 58.647 47.826 0.00 0.00 0.00 3.58
1213 2569 4.160439 TCTCTCTCTCTCTCTCTCTCACAC 59.840 50.000 0.00 0.00 0.00 3.82
1276 2674 0.465705 GAGGATCATGGGTTCGCTCA 59.534 55.000 0.00 0.00 33.17 4.26
1324 2765 2.342650 ATGCATGTCACCGTTGCCC 61.343 57.895 0.00 0.00 35.51 5.36
1326 2767 2.560119 GCATGTCACCGTTGCCCAA 61.560 57.895 0.00 0.00 0.00 4.12
1327 2768 1.285641 CATGTCACCGTTGCCCAAC 59.714 57.895 1.12 1.12 37.92 3.77
1365 2853 3.491342 TCCGGTAGAGGATCAAGATGAG 58.509 50.000 0.00 0.00 37.82 2.90
1374 2962 1.534595 GATCAAGATGAGCGATTGGCC 59.465 52.381 0.00 0.00 45.17 5.36
1405 3008 6.327154 TCACACGTACAATAGGACATGTAAG 58.673 40.000 0.00 0.00 37.47 2.34
1498 3490 5.884232 AGTTAGTTCGAAAAACTTTGGAGGT 59.116 36.000 17.21 0.00 29.25 3.85
1500 3492 3.380320 AGTTCGAAAAACTTTGGAGGTGG 59.620 43.478 0.00 0.00 0.00 4.61
1503 4246 1.691976 GAAAAACTTTGGAGGTGGGGG 59.308 52.381 0.00 0.00 0.00 5.40
1529 4272 4.536765 AGGGACAACTGAACAAACAGATT 58.463 39.130 0.00 0.00 40.63 2.40
1531 4274 4.044426 GGACAACTGAACAAACAGATTGC 58.956 43.478 0.00 0.00 43.13 3.56
1532 4275 3.694734 ACAACTGAACAAACAGATTGCG 58.305 40.909 0.00 0.00 43.13 4.85
1536 4286 2.912967 CTGAACAAACAGATTGCGATGC 59.087 45.455 0.00 0.00 43.13 3.91
1590 4346 2.411290 CAAACGTGCACCACCACC 59.589 61.111 12.15 0.00 32.10 4.61
1602 4360 1.497278 CACCACCATCGAGCAAACG 59.503 57.895 0.00 0.00 0.00 3.60
1701 5299 6.371825 GTGGATCCTAAACCAGAAAAGTACTG 59.628 42.308 14.23 0.00 36.82 2.74
1703 5301 6.371825 GGATCCTAAACCAGAAAAGTACTGTG 59.628 42.308 3.84 0.00 34.04 3.66
1713 5315 4.394300 AGAAAAGTACTGTGCATGCATCTC 59.606 41.667 25.64 11.96 0.00 2.75
1770 5785 0.248377 CCGCCTTTACGTACCTCTCG 60.248 60.000 0.00 0.00 0.00 4.04
2001 10932 1.421268 GCATGGGACCCATATGTCAGA 59.579 52.381 26.09 0.00 43.15 3.27
2024 10957 0.527565 AAGCATGCACCGTTGATTCC 59.472 50.000 21.98 0.00 0.00 3.01
2063 11103 6.443792 TGGAAAAGAACGCCTAAAGATTTTC 58.556 36.000 0.00 0.00 35.48 2.29
2103 11152 6.721321 TCATAAACTTGGTCGAACTTTTCAC 58.279 36.000 0.33 0.00 0.00 3.18
2106 11155 3.349022 ACTTGGTCGAACTTTTCACCAA 58.651 40.909 0.33 15.79 42.75 3.67
2110 11159 2.540973 GGTCGAACTTTTCACCAACTGC 60.541 50.000 0.00 0.00 33.70 4.40
2114 11163 3.502211 CGAACTTTTCACCAACTGCCTAT 59.498 43.478 0.00 0.00 0.00 2.57
2146 11220 3.821033 ACTGAGGGAGTGCAATTTTGTAC 59.179 43.478 3.66 3.66 42.99 2.90
2155 11229 5.338614 GTGCAATTTTGTACTACGTCTGT 57.661 39.130 0.00 0.00 40.10 3.41
2156 11230 6.456447 GTGCAATTTTGTACTACGTCTGTA 57.544 37.500 0.00 0.00 40.10 2.74
2157 11231 6.294363 GTGCAATTTTGTACTACGTCTGTAC 58.706 40.000 18.90 18.90 40.10 2.90
2158 11232 5.406175 TGCAATTTTGTACTACGTCTGTACC 59.594 40.000 21.31 10.15 39.42 3.34
2159 11233 5.406175 GCAATTTTGTACTACGTCTGTACCA 59.594 40.000 21.31 12.69 39.42 3.25
2160 11234 6.073657 GCAATTTTGTACTACGTCTGTACCAA 60.074 38.462 21.31 16.43 39.42 3.67
2161 11235 7.518689 GCAATTTTGTACTACGTCTGTACCAAA 60.519 37.037 21.57 21.57 38.74 3.28
2162 11236 8.336806 CAATTTTGTACTACGTCTGTACCAAAA 58.663 33.333 22.39 22.96 38.28 2.44
2163 11237 8.611654 ATTTTGTACTACGTCTGTACCAAAAT 57.388 30.769 24.51 24.51 38.28 1.82
2164 11238 7.410800 TTTGTACTACGTCTGTACCAAAATG 57.589 36.000 21.31 0.00 39.42 2.32
2166 11240 7.213216 TGTACTACGTCTGTACCAAAATGTA 57.787 36.000 21.31 5.30 39.42 2.29
2167 11241 7.656412 TGTACTACGTCTGTACCAAAATGTAA 58.344 34.615 21.31 4.78 39.42 2.41
2168 11242 7.809331 TGTACTACGTCTGTACCAAAATGTAAG 59.191 37.037 21.31 0.15 39.42 2.34
2170 11244 7.609056 ACTACGTCTGTACCAAAATGTAAGAT 58.391 34.615 0.00 0.00 0.00 2.40
2173 11247 6.708949 ACGTCTGTACCAAAATGTAAGATGTT 59.291 34.615 0.00 0.00 31.53 2.71
2174 11248 7.227910 ACGTCTGTACCAAAATGTAAGATGTTT 59.772 33.333 0.00 0.00 31.53 2.83
2175 11249 8.073768 CGTCTGTACCAAAATGTAAGATGTTTT 58.926 33.333 0.00 0.00 0.00 2.43
2176 11250 9.744468 GTCTGTACCAAAATGTAAGATGTTTTT 57.256 29.630 0.00 0.00 0.00 1.94
2177 11251 9.743057 TCTGTACCAAAATGTAAGATGTTTTTG 57.257 29.630 0.00 0.00 38.28 2.44
2178 11252 8.359060 TGTACCAAAATGTAAGATGTTTTTGC 57.641 30.769 0.00 0.00 37.60 3.68
2181 11276 7.047271 ACCAAAATGTAAGATGTTTTTGCAGT 58.953 30.769 0.00 0.00 37.60 4.40
2183 11278 8.397148 CCAAAATGTAAGATGTTTTTGCAGTTT 58.603 29.630 0.00 0.00 38.37 2.66
2205 11300 8.440048 GTTTAAATTAAACAGCAAAAACGTCG 57.560 30.769 20.12 0.00 45.54 5.12
2206 11301 7.737525 TTAAATTAAACAGCAAAAACGTCGT 57.262 28.000 0.00 0.00 0.00 4.34
2207 11302 8.832487 TTAAATTAAACAGCAAAAACGTCGTA 57.168 26.923 0.00 0.00 0.00 3.43
2208 11303 7.917720 AAATTAAACAGCAAAAACGTCGTAT 57.082 28.000 0.00 0.00 0.00 3.06
2211 11306 9.615295 AATTAAACAGCAAAAACGTCGTATATT 57.385 25.926 0.00 0.00 0.00 1.28
2212 11307 8.644264 TTAAACAGCAAAAACGTCGTATATTC 57.356 30.769 0.00 0.00 0.00 1.75
2213 11308 6.476243 AACAGCAAAAACGTCGTATATTCT 57.524 33.333 0.00 0.00 0.00 2.40
2214 11309 5.854157 ACAGCAAAAACGTCGTATATTCTG 58.146 37.500 0.00 6.80 0.00 3.02
2215 11310 5.163893 ACAGCAAAAACGTCGTATATTCTGG 60.164 40.000 16.05 1.64 0.00 3.86
2217 11312 6.035220 CAGCAAAAACGTCGTATATTCTGGTA 59.965 38.462 0.00 0.00 0.00 3.25
2219 11314 6.397243 CAAAAACGTCGTATATTCTGGTACG 58.603 40.000 0.00 0.00 43.61 3.67
2220 11315 3.885484 ACGTCGTATATTCTGGTACGG 57.115 47.619 0.00 0.00 42.76 4.02
2221 11316 2.549754 ACGTCGTATATTCTGGTACGGG 59.450 50.000 0.00 1.61 42.76 5.28
2223 11318 3.120408 CGTCGTATATTCTGGTACGGGAG 60.120 52.174 5.28 0.00 42.76 4.30
2225 11320 4.997395 GTCGTATATTCTGGTACGGGAGTA 59.003 45.833 5.28 0.00 46.17 2.59
2314 11507 1.552799 ATCGTCATGTGCAGGGGACA 61.553 55.000 10.92 0.00 0.00 4.02
2452 11680 8.348507 ACTCTTTCTTGATTTCAAACTGATGTC 58.651 33.333 0.00 0.00 35.15 3.06
2454 11682 6.618287 TTCTTGATTTCAAACTGATGTCGT 57.382 33.333 0.00 0.00 35.15 4.34
3264 12580 0.109153 TCAGTGTGATTGGTGCAGCT 59.891 50.000 18.08 0.00 0.00 4.24
3601 12963 3.694072 TGTATGGAGGCGAATTTTTCCTG 59.306 43.478 0.00 0.00 0.00 3.86
3657 13025 4.711399 ACGATCCAATCATGTCATGTGAT 58.289 39.130 12.54 10.15 37.91 3.06
3784 13152 6.621596 GCTTAACTGGTGCTTCAACTGATTAG 60.622 42.308 0.00 0.00 0.00 1.73
3854 13222 5.241728 GGAAAGAGTCCAAATGTGCTTTAGT 59.758 40.000 0.00 0.00 46.97 2.24
3870 13238 5.070446 TGCTTTAGTCTTTGAGAGAAGGACA 59.930 40.000 0.00 0.00 35.79 4.02
3902 13270 2.774439 ACACACTTCGCATTTCCAAC 57.226 45.000 0.00 0.00 0.00 3.77
3910 13278 4.694037 ACTTCGCATTTCCAACCTACTAAC 59.306 41.667 0.00 0.00 0.00 2.34
3912 13280 5.664294 TCGCATTTCCAACCTACTAACTA 57.336 39.130 0.00 0.00 0.00 2.24
3970 13338 5.738225 CGCGTCCGGCTTTAAATTAATAAAA 59.262 36.000 0.00 0.00 40.44 1.52
4008 13382 4.109050 CACAAGGTTTAAACAACGCACAT 58.891 39.130 19.57 0.00 0.00 3.21
4011 13385 5.066764 ACAAGGTTTAAACAACGCACATACT 59.933 36.000 19.57 1.15 0.00 2.12
4021 13395 2.688507 ACGCACATACTCAAGAACCAG 58.311 47.619 0.00 0.00 0.00 4.00
4023 13397 2.668457 CGCACATACTCAAGAACCAGAC 59.332 50.000 0.00 0.00 0.00 3.51
4054 13428 2.667199 ACACCGGCCACGCTTAAC 60.667 61.111 0.00 0.00 39.22 2.01
4090 13465 2.443324 GGCAAGGCCCCAACCTAA 59.557 61.111 0.00 0.00 44.06 2.69
4092 13467 1.228737 GCAAGGCCCCAACCTAACA 60.229 57.895 0.00 0.00 39.93 2.41
4093 13468 1.250840 GCAAGGCCCCAACCTAACAG 61.251 60.000 0.00 0.00 39.93 3.16
4105 13480 4.278170 CCAACCTAACAGCTGAATGAACAA 59.722 41.667 23.35 0.00 0.00 2.83
4107 13482 4.460263 ACCTAACAGCTGAATGAACAACA 58.540 39.130 23.35 0.00 0.00 3.33
4243 13660 1.269448 AGTTCGGCATCGCATTGTTTT 59.731 42.857 0.00 0.00 36.13 2.43
4256 13673 1.835494 TTGTTTTCCCAACGGTGTCA 58.165 45.000 0.00 0.00 0.00 3.58
4300 13718 5.995282 ACATTTGAAAACTACATCAGTCGGA 59.005 36.000 0.00 0.00 36.04 4.55
4301 13719 5.917541 TTTGAAAACTACATCAGTCGGAC 57.082 39.130 0.00 0.00 36.04 4.79
4307 13725 1.609555 CTACATCAGTCGGACTAGCCC 59.390 57.143 10.87 0.00 0.00 5.19
4338 13756 5.534278 TGTGCTCCATAGTCATTTTGTTTCA 59.466 36.000 0.00 0.00 0.00 2.69
4437 13855 1.227823 CCGTCAACAACTCAGCCCA 60.228 57.895 0.00 0.00 0.00 5.36
4457 13875 3.002656 CCACGATCTCGGATTCCAATTTG 59.997 47.826 3.09 0.00 44.95 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 22 8.370182 ACCAATATCATGTTTTTCTTTCTGCTT 58.630 29.630 0.00 0.00 0.00 3.91
29 31 7.761249 CCAGAAAGGACCAATATCATGTTTTTC 59.239 37.037 0.00 0.00 41.22 2.29
30 32 7.454380 TCCAGAAAGGACCAATATCATGTTTTT 59.546 33.333 0.00 0.00 43.07 1.94
52 66 5.892160 TGCAAATCAAGAGATTCTTCCAG 57.108 39.130 0.00 0.00 43.52 3.86
193 1305 0.543749 CACTTTGCCCCTAGCTAGCT 59.456 55.000 23.12 23.12 44.23 3.32
194 1306 0.541863 TCACTTTGCCCCTAGCTAGC 59.458 55.000 15.74 6.62 44.23 3.42
280 1494 1.453197 GGCGGGTGGGTTTGGATAG 60.453 63.158 0.00 0.00 0.00 2.08
347 1561 4.416513 TCTCTCTCTCTCTCATCCCATCTT 59.583 45.833 0.00 0.00 0.00 2.40
348 1562 3.982730 TCTCTCTCTCTCTCATCCCATCT 59.017 47.826 0.00 0.00 0.00 2.90
388 1666 6.068498 TCCCAGTTTAATATTCCACTTCCCAT 60.068 38.462 0.00 0.00 0.00 4.00
390 1668 5.762279 TCCCAGTTTAATATTCCACTTCCC 58.238 41.667 0.00 0.00 0.00 3.97
433 1711 0.666577 GTACGTGTGTCCCAGTGCTC 60.667 60.000 0.00 0.00 0.00 4.26
471 1753 1.285280 TGGGTGGATCCGAGTCATTT 58.715 50.000 7.39 0.00 37.00 2.32
472 1754 1.141657 CATGGGTGGATCCGAGTCATT 59.858 52.381 7.39 0.00 37.00 2.57
535 1827 3.128764 CCTTATATAGACGCGCTCCATCA 59.871 47.826 5.73 0.00 0.00 3.07
568 1873 0.036388 AATCGATGAGGCAACACCGT 60.036 50.000 0.00 0.00 46.52 4.83
619 1933 2.356135 AGTCTTCGCTCTCACTCTCTC 58.644 52.381 0.00 0.00 0.00 3.20
1122 2463 1.823976 GAAGTAGAGGGCGAAGGGG 59.176 63.158 0.00 0.00 0.00 4.79
1206 2562 1.001406 TGTGTGTGTGTGTGTGTGAGA 59.999 47.619 0.00 0.00 0.00 3.27
1207 2563 1.128507 GTGTGTGTGTGTGTGTGTGAG 59.871 52.381 0.00 0.00 0.00 3.51
1208 2564 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
1209 2565 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1210 2566 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1211 2567 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1212 2568 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
1213 2569 1.128507 GTCTGTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1290 2688 0.179189 GCATGCTCGGTTACACTTGC 60.179 55.000 11.37 0.00 0.00 4.01
1291 2689 1.155889 TGCATGCTCGGTTACACTTG 58.844 50.000 20.33 0.00 0.00 3.16
1324 2765 4.154195 CGGATGTTTGTCCTAGGAAAGTTG 59.846 45.833 14.65 0.00 36.07 3.16
1326 2767 3.307480 CCGGATGTTTGTCCTAGGAAAGT 60.307 47.826 14.65 0.00 36.07 2.66
1327 2768 3.270877 CCGGATGTTTGTCCTAGGAAAG 58.729 50.000 14.65 0.00 36.07 2.62
1363 2851 0.659957 GATGACTTGGCCAATCGCTC 59.340 55.000 20.85 14.29 37.74 5.03
1365 2853 0.099436 GTGATGACTTGGCCAATCGC 59.901 55.000 20.85 16.27 0.00 4.58
1374 2962 5.288712 GTCCTATTGTACGTGTGATGACTTG 59.711 44.000 0.00 0.00 0.00 3.16
1500 3492 1.205460 TTCAGTTGTCCCTAGCCCCC 61.205 60.000 0.00 0.00 0.00 5.40
1503 4246 2.552743 GTTTGTTCAGTTGTCCCTAGCC 59.447 50.000 0.00 0.00 0.00 3.93
1529 4272 1.009078 CGATCTTCCTTTGCATCGCA 58.991 50.000 0.00 0.00 36.47 5.10
1531 4274 0.940126 CCCGATCTTCCTTTGCATCG 59.060 55.000 0.00 0.00 38.28 3.84
1532 4275 2.332063 TCCCGATCTTCCTTTGCATC 57.668 50.000 0.00 0.00 0.00 3.91
1536 4286 6.919721 TGTTAATTTTCCCGATCTTCCTTTG 58.080 36.000 0.00 0.00 0.00 2.77
1590 4346 1.507713 CGTGTGCGTTTGCTCGATG 60.508 57.895 0.00 0.00 43.34 3.84
1602 4360 1.461237 CCGAACGAATTGTACGTGTGC 60.461 52.381 0.00 0.00 43.16 4.57
1687 5285 2.554032 GCATGCACAGTACTTTTCTGGT 59.446 45.455 14.21 0.00 37.25 4.00
1701 5299 6.534436 AGAATAAGATATCGAGATGCATGCAC 59.466 38.462 25.37 16.77 0.00 4.57
1703 5301 8.815141 ATAGAATAAGATATCGAGATGCATGC 57.185 34.615 11.82 11.82 0.00 4.06
1713 5315 7.220300 GCCGGTACACAATAGAATAAGATATCG 59.780 40.741 1.90 0.00 0.00 2.92
1730 5332 3.391049 GGAAGATATCTTGCCGGTACAC 58.609 50.000 22.61 4.75 38.21 2.90
1770 5785 7.720442 TCCATATATAGTAGATGCTGCATGAC 58.280 38.462 21.53 16.81 0.00 3.06
1810 9363 4.814771 TCTGCTAATTGATGCACTCTGATG 59.185 41.667 0.00 0.00 35.20 3.07
1863 10767 1.002087 GCCGGTTAGCTAGCCACATAT 59.998 52.381 24.40 0.00 0.00 1.78
1987 10906 3.181451 TGCTTCCATCTGACATATGGGTC 60.181 47.826 17.32 9.02 43.52 4.46
1993 10924 3.208594 GTGCATGCTTCCATCTGACATA 58.791 45.455 20.33 0.00 0.00 2.29
2001 10932 0.608856 TCAACGGTGCATGCTTCCAT 60.609 50.000 20.33 7.25 0.00 3.41
2103 11152 2.562298 TGCTTGGAAAATAGGCAGTTGG 59.438 45.455 0.00 0.00 0.00 3.77
2106 11155 2.821969 CAGTGCTTGGAAAATAGGCAGT 59.178 45.455 0.00 0.00 37.08 4.40
2110 11159 3.019564 CCCTCAGTGCTTGGAAAATAGG 58.980 50.000 0.00 0.00 0.00 2.57
2114 11163 1.494721 ACTCCCTCAGTGCTTGGAAAA 59.505 47.619 0.00 0.00 32.26 2.29
2146 11220 7.544566 ACATCTTACATTTTGGTACAGACGTAG 59.455 37.037 0.00 0.00 42.39 3.51
2147 11221 7.380536 ACATCTTACATTTTGGTACAGACGTA 58.619 34.615 0.00 0.00 42.39 3.57
2149 11223 6.721571 ACATCTTACATTTTGGTACAGACG 57.278 37.500 0.00 0.00 42.39 4.18
2152 11226 8.487176 GCAAAAACATCTTACATTTTGGTACAG 58.513 33.333 10.66 0.00 42.39 2.74
2155 11229 8.200792 ACTGCAAAAACATCTTACATTTTGGTA 58.799 29.630 10.66 0.00 41.02 3.25
2156 11230 7.047271 ACTGCAAAAACATCTTACATTTTGGT 58.953 30.769 10.66 0.81 41.02 3.67
2157 11231 7.481275 ACTGCAAAAACATCTTACATTTTGG 57.519 32.000 10.66 0.00 41.02 3.28
2178 11252 9.403869 GACGTTTTTGCTGTTTAATTTAAACTG 57.596 29.630 24.86 24.30 46.20 3.16
2181 11276 8.170999 ACGACGTTTTTGCTGTTTAATTTAAA 57.829 26.923 0.00 0.00 0.00 1.52
2192 11287 5.163893 ACCAGAATATACGACGTTTTTGCTG 60.164 40.000 5.50 7.81 0.00 4.41
2195 11290 6.397243 CGTACCAGAATATACGACGTTTTTG 58.603 40.000 5.50 0.00 45.51 2.44
2198 11293 4.498009 CCCGTACCAGAATATACGACGTTT 60.498 45.833 5.50 0.00 45.51 3.60
2199 11294 3.003689 CCCGTACCAGAATATACGACGTT 59.996 47.826 5.50 0.00 45.51 3.99
2200 11295 2.549754 CCCGTACCAGAATATACGACGT 59.450 50.000 5.52 5.52 45.51 4.34
2201 11296 2.807967 TCCCGTACCAGAATATACGACG 59.192 50.000 5.42 0.00 45.51 5.12
2202 11297 3.817647 ACTCCCGTACCAGAATATACGAC 59.182 47.826 5.42 0.00 45.51 4.34
2203 11298 4.090761 ACTCCCGTACCAGAATATACGA 57.909 45.455 5.42 0.00 45.51 3.43
2205 11300 7.118971 CACTACTACTCCCGTACCAGAATATAC 59.881 44.444 0.00 0.00 0.00 1.47
2206 11301 7.164122 CACTACTACTCCCGTACCAGAATATA 58.836 42.308 0.00 0.00 0.00 0.86
2207 11302 6.002704 CACTACTACTCCCGTACCAGAATAT 58.997 44.000 0.00 0.00 0.00 1.28
2208 11303 5.104360 ACACTACTACTCCCGTACCAGAATA 60.104 44.000 0.00 0.00 0.00 1.75
2211 11306 2.573462 ACACTACTACTCCCGTACCAGA 59.427 50.000 0.00 0.00 0.00 3.86
2212 11307 2.996631 ACACTACTACTCCCGTACCAG 58.003 52.381 0.00 0.00 0.00 4.00
2213 11308 3.244875 TGAACACTACTACTCCCGTACCA 60.245 47.826 0.00 0.00 0.00 3.25
2214 11309 3.347216 TGAACACTACTACTCCCGTACC 58.653 50.000 0.00 0.00 0.00 3.34
2215 11310 5.573337 AATGAACACTACTACTCCCGTAC 57.427 43.478 0.00 0.00 0.00 3.67
2217 11312 5.011329 TGAAAATGAACACTACTACTCCCGT 59.989 40.000 0.00 0.00 0.00 5.28
2219 11314 6.228258 TGTGAAAATGAACACTACTACTCCC 58.772 40.000 0.00 0.00 37.81 4.30
2220 11315 7.907214 ATGTGAAAATGAACACTACTACTCC 57.093 36.000 0.00 0.00 37.81 3.85
2221 11316 8.596380 GCTATGTGAAAATGAACACTACTACTC 58.404 37.037 0.00 0.00 37.81 2.59
2223 11318 8.480643 AGCTATGTGAAAATGAACACTACTAC 57.519 34.615 0.00 0.00 37.81 2.73
2314 11507 3.350833 GTGATTGTCATCTTTGGCCTCT 58.649 45.455 3.32 0.00 0.00 3.69
2452 11680 1.073199 AGGCCTGAGAAACCCAACG 59.927 57.895 3.11 0.00 0.00 4.10
2454 11682 0.178992 CACAGGCCTGAGAAACCCAA 60.179 55.000 39.19 0.00 0.00 4.12
2533 11787 1.890894 CGGGAGGATGTTGACGAGT 59.109 57.895 0.00 0.00 0.00 4.18
2611 11865 1.751927 GATCTTGGCCTGGCTGTGG 60.752 63.158 19.68 6.87 0.00 4.17
3022 12279 0.032130 CGATGCCCTGCACGTAGTAT 59.968 55.000 0.00 0.00 43.04 2.12
3264 12580 4.298626 AGTAGAGGCCTCCAACAATGATA 58.701 43.478 29.54 8.80 0.00 2.15
3432 12778 1.811266 CTCCACGCCGAAGACATGG 60.811 63.158 0.00 0.00 0.00 3.66
3514 12868 2.159503 AGACGGATCGATGATCGTATGC 60.160 50.000 15.06 10.85 39.72 3.14
3601 12963 3.505293 AGCTGACCAGAAGAAGAAAATGC 59.495 43.478 0.47 0.00 0.00 3.56
3657 13025 3.625313 CACTCGCTGATCTTCTCTCACTA 59.375 47.826 0.00 0.00 0.00 2.74
3784 13152 7.708998 ACTAGCTAGTCACAACTAAAGATAGC 58.291 38.462 20.95 0.00 35.13 2.97
3831 13199 6.205658 AGACTAAAGCACATTTGGACTCTTTC 59.794 38.462 0.00 0.00 30.83 2.62
3854 13222 4.624843 GCCATGATGTCCTTCTCTCAAAGA 60.625 45.833 0.00 0.00 0.00 2.52
3870 13238 1.552578 AGTGTGTTGCATGCCATGAT 58.447 45.000 16.68 0.00 0.00 2.45
3970 13338 1.672356 GTGATGCTGCCTTCGTGGT 60.672 57.895 0.00 0.00 38.35 4.16
4008 13382 4.659111 TGAAACGTCTGGTTCTTGAGTA 57.341 40.909 0.00 0.00 38.08 2.59
4011 13385 3.601435 TGTTGAAACGTCTGGTTCTTGA 58.399 40.909 0.00 0.00 38.08 3.02
4021 13395 0.028902 GTGTGGCCTGTTGAAACGTC 59.971 55.000 3.32 0.00 0.00 4.34
4023 13397 1.358759 GGTGTGGCCTGTTGAAACG 59.641 57.895 3.32 0.00 0.00 3.60
4050 13424 6.001460 CCCTCTGAACTATGGTTTGTGTTAA 58.999 40.000 0.00 0.00 35.58 2.01
4054 13428 2.749621 GCCCTCTGAACTATGGTTTGTG 59.250 50.000 0.00 0.00 35.58 3.33
4090 13465 4.202050 GGAGTTTGTTGTTCATTCAGCTGT 60.202 41.667 14.67 0.00 0.00 4.40
4092 13467 3.319122 GGGAGTTTGTTGTTCATTCAGCT 59.681 43.478 0.00 0.00 0.00 4.24
4093 13468 3.319122 AGGGAGTTTGTTGTTCATTCAGC 59.681 43.478 0.00 0.00 0.00 4.26
4105 13480 2.638363 GGTCTGTTAGGAGGGAGTTTGT 59.362 50.000 0.00 0.00 0.00 2.83
4107 13482 2.267192 GGGTCTGTTAGGAGGGAGTTT 58.733 52.381 0.00 0.00 0.00 2.66
4183 13597 1.216064 AGATTGCCAGCAGTATCCCA 58.784 50.000 1.59 0.00 0.00 4.37
4243 13660 0.762418 AGATGTTGACACCGTTGGGA 59.238 50.000 0.00 0.00 36.97 4.37
4273 13691 6.792250 CGACTGATGTAGTTTTCAAATGTCAC 59.208 38.462 0.00 0.00 40.53 3.67
4287 13705 1.609555 GGGCTAGTCCGACTGATGTAG 59.390 57.143 11.52 1.24 34.94 2.74
4288 13706 1.688772 GGGCTAGTCCGACTGATGTA 58.311 55.000 11.52 0.00 34.94 2.29
4300 13718 1.003718 GCACAAGTTCCGGGCTAGT 60.004 57.895 0.00 0.00 0.00 2.57
4301 13719 0.741221 GAGCACAAGTTCCGGGCTAG 60.741 60.000 0.00 0.00 34.44 3.42
4437 13855 3.206150 CCAAATTGGAATCCGAGATCGT 58.794 45.455 6.04 0.00 40.96 3.73


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

AutoCloner maintained by Alex Coulton.