Multiple sequence alignment - TraesCS1D01G075100

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 TraesCS1D01G075100 chr1D 100.000 4117 0 0 1 4117 56876238 56872122 0.000000e+00 7603.0
1 TraesCS1D01G075100 chr1D 93.342 1517 80 12 1822 3324 56429182 56427673 0.000000e+00 2222.0
2 TraesCS1D01G075100 chr1D 92.662 1540 63 17 405 1909 56610981 56609457 0.000000e+00 2172.0
3 TraesCS1D01G075100 chr1D 95.482 1328 26 5 1969 3290 56609460 56608161 0.000000e+00 2089.0
4 TraesCS1D01G075100 chr1D 88.735 1447 80 33 342 1745 56430701 56429295 0.000000e+00 1692.0
5 TraesCS1D01G075100 chr1D 93.040 977 52 8 2371 3332 56529579 56528604 0.000000e+00 1413.0
6 TraesCS1D01G075100 chr1D 90.076 1048 71 19 967 2006 56530856 56529834 0.000000e+00 1328.0
7 TraesCS1D01G075100 chr1D 86.604 642 49 12 335 965 56531517 56530902 0.000000e+00 675.0
8 TraesCS1D01G075100 chr1D 86.530 438 32 11 378 813 56618430 56618018 1.350000e-124 457.0
9 TraesCS1D01G075100 chr1D 86.645 307 30 5 1448 1750 57200749 57200450 3.070000e-86 329.0
10 TraesCS1D01G075100 chr1D 79.008 524 45 22 1879 2368 57073748 57073256 8.650000e-77 298.0
11 TraesCS1D01G075100 chr1D 87.308 260 28 2 83 337 69475714 69475973 4.030000e-75 292.0
12 TraesCS1D01G075100 chr1D 89.121 239 12 9 2067 2296 56529807 56529574 6.740000e-73 285.0
13 TraesCS1D01G075100 chr1D 84.354 294 35 7 335 622 56612630 56612342 1.130000e-70 278.0
14 TraesCS1D01G075100 chr1D 90.196 204 12 4 1247 1450 57212906 57212711 4.080000e-65 259.0
15 TraesCS1D01G075100 chr1D 80.645 155 29 1 3564 3718 486244329 486244176 7.230000e-23 119.0
16 TraesCS1D01G075100 chr1D 93.939 66 3 1 1 66 56618557 56618493 9.420000e-17 99.0
17 TraesCS1D01G075100 chr1D 90.909 66 2 2 1 66 56430753 56430692 7.330000e-13 86.1
18 TraesCS1D01G075100 chr1D 100.000 34 0 0 380 413 56611034 56611001 3.440000e-06 63.9
19 TraesCS1D01G075100 chr1D 100.000 28 0 0 1 28 56611086 56611059 7.000000e-03 52.8
20 TraesCS1D01G075100 chr1A 91.399 1523 88 12 1822 3332 56370165 56371656 0.000000e+00 2047.0
21 TraesCS1D01G075100 chr1A 94.081 1267 62 9 2068 3324 54459970 54461233 0.000000e+00 1912.0
22 TraesCS1D01G075100 chr1A 93.116 1133 59 12 2067 3185 56338470 56339597 0.000000e+00 1642.0
23 TraesCS1D01G075100 chr1A 91.954 783 49 9 967 1745 54458913 54459685 0.000000e+00 1085.0
24 TraesCS1D01G075100 chr1A 90.818 795 47 14 967 1745 56337367 56338151 0.000000e+00 1040.0
25 TraesCS1D01G075100 chr1A 91.840 674 41 8 299 967 56336659 56337323 0.000000e+00 928.0
26 TraesCS1D01G075100 chr1A 89.564 642 50 7 335 967 54458236 54458869 0.000000e+00 798.0
27 TraesCS1D01G075100 chr1A 90.909 484 36 2 1247 1730 56369545 56370020 0.000000e+00 643.0
28 TraesCS1D01G075100 chr1A 84.501 671 56 20 335 967 56367967 56368627 1.630000e-173 619.0
29 TraesCS1D01G075100 chr1A 88.889 306 28 3 1 303 56326362 56326664 5.030000e-99 372.0
30 TraesCS1D01G075100 chr1A 93.243 222 14 1 1010 1231 56369276 56369496 3.970000e-85 326.0
31 TraesCS1D01G075100 chr1A 90.811 185 17 0 1822 2006 56338260 56338444 8.840000e-62 248.0
32 TraesCS1D01G075100 chr1A 92.199 141 11 0 3184 3324 56340308 56340448 2.510000e-47 200.0
33 TraesCS1D01G075100 chr1B 90.823 1471 91 19 1876 3332 91881289 91879849 0.000000e+00 1929.0
34 TraesCS1D01G075100 chr1B 91.160 871 52 14 1 865 91883280 91882429 0.000000e+00 1158.0
35 TraesCS1D01G075100 chr1B 92.716 810 39 7 940 1739 91882400 91881601 0.000000e+00 1151.0
36 TraesCS1D01G075100 chr1B 81.633 392 55 7 3742 4117 502216727 502216337 4.000000e-80 309.0
37 TraesCS1D01G075100 chr1B 86.207 261 28 5 83 336 397836181 397836440 4.050000e-70 276.0
38 TraesCS1D01G075100 chr1B 85.385 260 31 4 83 336 374925359 374925617 3.160000e-66 263.0
39 TraesCS1D01G075100 chr1B 79.104 201 39 3 3545 3743 638012418 638012219 7.180000e-28 135.0
40 TraesCS1D01G075100 chr1B 92.188 64 5 0 3336 3399 289309900 289309837 1.580000e-14 91.6
41 TraesCS1D01G075100 chr1B 91.111 45 3 1 877 921 91882435 91882392 4.440000e-05 60.2
42 TraesCS1D01G075100 chr5D 82.561 820 86 35 3328 4117 391789022 391789814 0.000000e+00 669.0
43 TraesCS1D01G075100 chr5D 76.429 420 68 25 3337 3737 438401406 438401813 9.030000e-47 198.0
44 TraesCS1D01G075100 chr5D 76.250 400 62 23 1293 1680 276917812 276918190 9.090000e-42 182.0
45 TraesCS1D01G075100 chr5D 77.612 201 44 1 3543 3743 473489727 473489926 2.010000e-23 121.0
46 TraesCS1D01G075100 chr5D 86.667 75 6 4 1110 1182 315485471 315485399 3.410000e-11 80.5
47 TraesCS1D01G075100 chr5D 90.196 51 1 2 3338 3388 473489487 473489533 3.440000e-06 63.9
48 TraesCS1D01G075100 chr7D 77.794 698 88 39 3344 4008 127344483 127345146 6.500000e-98 368.0
49 TraesCS1D01G075100 chr7D 84.615 65 3 7 3324 3388 631085928 631085871 1.600000e-04 58.4
50 TraesCS1D01G075100 chr2A 87.795 254 25 3 89 336 628728193 628727940 4.030000e-75 292.0
51 TraesCS1D01G075100 chr2A 85.246 61 4 5 3336 3395 79440474 79440418 1.600000e-04 58.4
52 TraesCS1D01G075100 chr3A 86.590 261 28 2 83 336 176136764 176136504 8.710000e-72 281.0
53 TraesCS1D01G075100 chr5B 74.387 816 134 37 3337 4114 533009613 533010391 3.130000e-71 279.0
54 TraesCS1D01G075100 chr5B 86.207 261 28 5 83 336 124716653 124716394 4.050000e-70 276.0
55 TraesCS1D01G075100 chr5B 80.328 183 35 1 3543 3725 575524766 575524947 2.000000e-28 137.0
56 TraesCS1D01G075100 chr5B 86.364 66 7 2 1110 1174 363669744 363669680 2.050000e-08 71.3
57 TraesCS1D01G075100 chr2D 85.441 261 30 5 83 336 644830781 644831040 8.780000e-67 265.0
58 TraesCS1D01G075100 chr5A 77.468 395 60 21 1296 1680 365253857 365254232 4.170000e-50 209.0
59 TraesCS1D01G075100 chr7B 82.028 217 32 7 1457 1668 409711889 409711675 1.180000e-40 178.0
60 TraesCS1D01G075100 chr3B 78.610 187 38 2 3543 3729 739911407 739911591 5.590000e-24 122.0
61 TraesCS1D01G075100 chr3D 77.273 220 40 3 1296 1514 120148561 120148351 2.010000e-23 121.0
62 TraesCS1D01G075100 chrUn 78.313 166 32 4 3564 3727 24683060 24683223 2.020000e-18 104.0
63 TraesCS1D01G075100 chr6D 80.833 120 22 1 3564 3683 116346191 116346309 4.380000e-15 93.5
64 TraesCS1D01G075100 chr6D 88.889 54 4 2 3336 3388 389978170 389978222 9.550000e-07 65.8
65 TraesCS1D01G075100 chr4A 87.302 63 6 2 3333 3395 743960295 743960235 2.050000e-08 71.3
66 TraesCS1D01G075100 chr7A 88.679 53 2 2 3336 3388 554406354 554406402 1.240000e-05 62.1


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 TraesCS1D01G075100 chr1D 56872122 56876238 4116 True 7603.000000 7603 100.000000 1 4117 1 chr1D.!!$R1 4116
1 TraesCS1D01G075100 chr1D 56427673 56430753 3080 True 1333.366667 2222 90.995333 1 3324 3 chr1D.!!$R6 3323
2 TraesCS1D01G075100 chr1D 56608161 56612630 4469 True 931.140000 2172 94.499600 1 3290 5 chr1D.!!$R8 3289
3 TraesCS1D01G075100 chr1D 56528604 56531517 2913 True 925.250000 1413 89.710250 335 3332 4 chr1D.!!$R7 2997
4 TraesCS1D01G075100 chr1D 56618018 56618557 539 True 278.000000 457 90.234500 1 813 2 chr1D.!!$R9 812
5 TraesCS1D01G075100 chr1A 54458236 54461233 2997 False 1265.000000 1912 91.866333 335 3324 3 chr1A.!!$F2 2989
6 TraesCS1D01G075100 chr1A 56367967 56371656 3689 False 908.750000 2047 90.013000 335 3332 4 chr1A.!!$F4 2997
7 TraesCS1D01G075100 chr1A 56336659 56340448 3789 False 811.600000 1642 91.756800 299 3324 5 chr1A.!!$F3 3025
8 TraesCS1D01G075100 chr1B 91879849 91883280 3431 True 1074.550000 1929 91.452500 1 3332 4 chr1B.!!$R4 3331
9 TraesCS1D01G075100 chr5D 391789022 391789814 792 False 669.000000 669 82.561000 3328 4117 1 chr5D.!!$F2 789
10 TraesCS1D01G075100 chr7D 127344483 127345146 663 False 368.000000 368 77.794000 3344 4008 1 chr7D.!!$F1 664
11 TraesCS1D01G075100 chr5B 533009613 533010391 778 False 279.000000 279 74.387000 3337 4114 1 chr5B.!!$F1 777

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
177 178 0.172352 CAGAGGGAGCAGACGTTCTC 59.828 60.000 0.00 0.0 0.0 2.87 F
178 179 0.251386 AGAGGGAGCAGACGTTCTCA 60.251 55.000 13.06 0.0 0.0 3.27 F
276 277 0.390603 GGGTAGCGTATGTGTGTGCA 60.391 55.000 0.00 0.0 0.0 4.57 F
916 2546 1.273606 CCATCGACGGGAAGAGCATAT 59.726 52.381 0.00 0.0 0.0 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 4218 0.183492 ACATAGTGCGGCCATCCATT 59.817 50.000 2.24 0.0 0.00 3.16 R
2140 4757 1.001020 TGGCCGATGGAATGCTGTT 60.001 52.632 0.00 0.0 0.00 3.16 R
3011 5657 3.002791 AGAATCGTCGTAGTGGTCGTTA 58.997 45.455 0.00 0.0 0.00 3.18 R
3495 6881 0.038310 GGCTCTGCCCCTTGTTTAGT 59.962 55.000 0.00 0.0 44.06 2.24 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
67 68 6.712276 ACTACTAATCTATTGGCTATTGGGC 58.288 40.000 0.00 0.00 41.27 5.36
125 126 2.908688 TGCTGCTCGCATTTATCCTA 57.091 45.000 0.00 0.00 45.47 2.94
126 127 2.759191 TGCTGCTCGCATTTATCCTAG 58.241 47.619 0.00 0.00 45.47 3.02
135 136 9.066892 TGCTCGCATTTATCCTAGATTTATTTT 57.933 29.630 0.00 0.00 0.00 1.82
152 153 3.347958 TTTTATGATTTCCGGCGATGC 57.652 42.857 9.30 0.00 0.00 3.91
154 155 0.249699 TATGATTTCCGGCGATGCGT 60.250 50.000 9.30 0.00 0.00 5.24
161 162 2.809174 CGGCGATGCGTGTTCAGA 60.809 61.111 0.00 0.00 0.00 3.27
167 168 1.078848 ATGCGTGTTCAGAGGGAGC 60.079 57.895 0.00 0.00 0.00 4.70
172 173 0.389166 GTGTTCAGAGGGAGCAGACG 60.389 60.000 0.00 0.00 37.41 4.18
175 176 0.603569 TTCAGAGGGAGCAGACGTTC 59.396 55.000 0.00 0.00 0.00 3.95
176 177 0.251386 TCAGAGGGAGCAGACGTTCT 60.251 55.000 0.00 0.00 0.00 3.01
177 178 0.172352 CAGAGGGAGCAGACGTTCTC 59.828 60.000 0.00 0.00 0.00 2.87
178 179 0.251386 AGAGGGAGCAGACGTTCTCA 60.251 55.000 13.06 0.00 0.00 3.27
181 182 0.526524 GGGAGCAGACGTTCTCATCG 60.527 60.000 13.06 0.00 0.00 3.84
182 183 0.526524 GGAGCAGACGTTCTCATCGG 60.527 60.000 13.06 0.00 0.00 4.18
218 219 2.739913 CGGTGGCTTCGTAAAATCTCAA 59.260 45.455 0.00 0.00 0.00 3.02
223 224 4.635765 TGGCTTCGTAAAATCTCAAGATGG 59.364 41.667 0.00 0.00 34.49 3.51
228 229 6.844696 TCGTAAAATCTCAAGATGGTATGC 57.155 37.500 0.00 0.00 34.49 3.14
238 239 0.882042 GATGGTATGCCGGCTCAGTG 60.882 60.000 29.70 0.00 37.67 3.66
239 240 1.626356 ATGGTATGCCGGCTCAGTGT 61.626 55.000 29.70 7.06 37.67 3.55
260 261 1.762460 CGGAGGTGCTCATAGGGGT 60.762 63.158 0.00 0.00 31.08 4.95
263 264 0.682292 GAGGTGCTCATAGGGGTAGC 59.318 60.000 0.00 0.00 36.77 3.58
266 267 1.325355 GTGCTCATAGGGGTAGCGTA 58.675 55.000 0.00 0.00 39.14 4.42
273 274 2.148446 TAGGGGTAGCGTATGTGTGT 57.852 50.000 0.00 0.00 0.00 3.72
275 276 1.087771 GGGGTAGCGTATGTGTGTGC 61.088 60.000 0.00 0.00 0.00 4.57
276 277 0.390603 GGGTAGCGTATGTGTGTGCA 60.391 55.000 0.00 0.00 0.00 4.57
280 282 3.245284 GGTAGCGTATGTGTGTGCAATAG 59.755 47.826 0.00 0.00 0.00 1.73
296 298 3.206150 CAATAGGGGTGAGTGTATGCAC 58.794 50.000 5.71 5.71 45.57 4.57
357 362 7.502120 AAATCTATTGGCTATTGCAGTAGTG 57.498 36.000 16.62 0.00 41.91 2.74
513 2135 5.195001 ACTCTTCGATCTCCAAAGATAGC 57.805 43.478 0.00 0.00 42.46 2.97
526 2148 9.685276 TCTCCAAAGATAGCATTCAAATCTTAA 57.315 29.630 0.00 0.00 38.65 1.85
595 2217 9.778741 ATACACCGTAAATACATGATCTCAATT 57.221 29.630 0.00 0.00 0.00 2.32
661 2284 5.648092 CCTTCTCCAATGAAGTTAATTCCGT 59.352 40.000 0.00 0.00 41.17 4.69
707 2332 1.693627 ACGTTTACATTTGGCACCCA 58.306 45.000 0.00 0.00 0.00 4.51
714 2339 2.397597 ACATTTGGCACCCAGTTTCTT 58.602 42.857 0.00 0.00 33.81 2.52
768 2393 6.252967 ACAAATCAATACTCGTTCATGCAA 57.747 33.333 0.00 0.00 0.00 4.08
916 2546 1.273606 CCATCGACGGGAAGAGCATAT 59.726 52.381 0.00 0.00 0.00 1.78
955 2585 3.107104 CTGCACACACAACGCGGTT 62.107 57.895 12.47 0.00 0.00 4.44
1231 3489 4.819761 ACGTCGGCGATGCATGCT 62.820 61.111 27.66 6.18 42.00 3.79
1245 3536 1.399727 GCATGCTTGTGTGGTACGTTC 60.400 52.381 11.37 0.00 0.00 3.95
1368 3659 4.715523 CCCCATGGCGTTCACGGT 62.716 66.667 6.09 0.00 40.23 4.83
1369 3660 3.430862 CCCATGGCGTTCACGGTG 61.431 66.667 6.09 0.56 40.23 4.94
1370 3661 2.358125 CCATGGCGTTCACGGTGA 60.358 61.111 6.76 6.76 40.23 4.02
1371 3662 2.390599 CCATGGCGTTCACGGTGAG 61.391 63.158 11.14 1.97 40.23 3.51
1372 3663 1.667830 CATGGCGTTCACGGTGAGT 60.668 57.895 11.14 0.00 40.23 3.41
1373 3664 1.374252 ATGGCGTTCACGGTGAGTC 60.374 57.895 11.14 3.01 40.23 3.36
1910 4518 2.129555 ATTGGACGGCTTCTGTGGCT 62.130 55.000 0.00 0.00 0.00 4.75
1954 4562 7.531857 TGTGAGGGAATTTATTTAGCAAACA 57.468 32.000 0.00 0.00 0.00 2.83
2132 4749 2.113139 AAGAACCACCGTGGCCTG 59.887 61.111 17.99 0.00 42.67 4.85
2140 4757 1.839747 ACCGTGGCCTGTACCAGAA 60.840 57.895 3.32 0.00 41.46 3.02
3011 5657 2.990479 GTCGGAGGGCCTGACAAT 59.010 61.111 12.95 0.00 37.53 2.71
3292 6658 6.155049 CCAACATGACATTTTATTCCCTTCCT 59.845 38.462 0.00 0.00 0.00 3.36
3359 6728 1.133363 TTGAACGAAAGAGGGGGTGA 58.867 50.000 0.00 0.00 0.00 4.02
3412 6785 2.381911 GCAACATCATCCCAGTCCAAT 58.618 47.619 0.00 0.00 0.00 3.16
3456 6835 5.183140 CCAAAGACCAAAAGGAACGACATAT 59.817 40.000 0.00 0.00 0.00 1.78
3460 6839 7.125792 AGACCAAAAGGAACGACATATATCT 57.874 36.000 0.00 0.00 0.00 1.98
3508 6894 7.667557 AGATAAAAGAAAACTAAACAAGGGGC 58.332 34.615 0.00 0.00 0.00 5.80
3509 6895 5.685520 AAAAGAAAACTAAACAAGGGGCA 57.314 34.783 0.00 0.00 0.00 5.36
3510 6896 4.937201 AAGAAAACTAAACAAGGGGCAG 57.063 40.909 0.00 0.00 0.00 4.85
3513 6899 1.911057 AACTAAACAAGGGGCAGAGC 58.089 50.000 0.00 0.00 0.00 4.09
3525 6911 1.181098 GGCAGAGCCCTGAAAGCAAA 61.181 55.000 0.00 0.00 44.06 3.68
3526 6912 0.038801 GCAGAGCCCTGAAAGCAAAC 60.039 55.000 0.00 0.00 43.02 2.93
3527 6913 1.613836 CAGAGCCCTGAAAGCAAACT 58.386 50.000 0.00 0.00 43.02 2.66
3551 6948 3.329542 GATCAGTTCCCCAGCCGCA 62.330 63.158 0.00 0.00 0.00 5.69
3577 6974 3.797353 GGCCTCCATCCCTGCGAA 61.797 66.667 0.00 0.00 0.00 4.70
3637 7034 2.197577 GCTCCGAGCATCAGTAGTTTC 58.802 52.381 15.78 0.00 41.89 2.78
3639 7036 3.066900 GCTCCGAGCATCAGTAGTTTCTA 59.933 47.826 15.78 0.00 41.89 2.10
3642 7039 6.222038 TCCGAGCATCAGTAGTTTCTATTT 57.778 37.500 0.00 0.00 33.17 1.40
3645 7042 6.535150 CCGAGCATCAGTAGTTTCTATTTTGA 59.465 38.462 0.00 0.00 33.17 2.69
3730 7128 5.786264 ATGGGATCATGAATCTTCTTTGC 57.214 39.130 0.00 0.00 34.56 3.68
3731 7129 4.863548 TGGGATCATGAATCTTCTTTGCT 58.136 39.130 0.00 0.00 34.56 3.91
3732 7130 4.885907 TGGGATCATGAATCTTCTTTGCTC 59.114 41.667 0.00 0.00 34.56 4.26
3733 7131 5.131784 GGGATCATGAATCTTCTTTGCTCT 58.868 41.667 0.00 0.00 34.56 4.09
3734 7132 6.126681 TGGGATCATGAATCTTCTTTGCTCTA 60.127 38.462 0.00 0.00 34.56 2.43
3735 7133 6.769822 GGGATCATGAATCTTCTTTGCTCTAA 59.230 38.462 0.00 0.00 34.56 2.10
3736 7134 7.284034 GGGATCATGAATCTTCTTTGCTCTAAA 59.716 37.037 0.00 0.00 34.56 1.85
3737 7135 8.680903 GGATCATGAATCTTCTTTGCTCTAAAA 58.319 33.333 0.00 0.00 34.56 1.52
3739 7137 9.852091 ATCATGAATCTTCTTTGCTCTAAAAAC 57.148 29.630 0.00 0.00 0.00 2.43
3740 7138 8.849168 TCATGAATCTTCTTTGCTCTAAAAACA 58.151 29.630 0.00 0.00 0.00 2.83
3741 7139 9.467258 CATGAATCTTCTTTGCTCTAAAAACAA 57.533 29.630 0.00 0.00 0.00 2.83
3743 7141 9.467258 TGAATCTTCTTTGCTCTAAAAACAATG 57.533 29.630 0.00 0.00 0.00 2.82
3744 7142 9.683069 GAATCTTCTTTGCTCTAAAAACAATGA 57.317 29.630 0.00 0.00 0.00 2.57
3747 7145 9.683069 TCTTCTTTGCTCTAAAAACAATGAATC 57.317 29.630 0.00 0.00 37.06 2.52
3748 7146 9.688592 CTTCTTTGCTCTAAAAACAATGAATCT 57.311 29.630 0.00 0.00 37.06 2.40
3750 7148 9.683069 TCTTTGCTCTAAAAACAATGAATCTTC 57.317 29.630 0.00 0.00 0.00 2.87
3768 7166 9.683069 TGAATCTTCTTTGCTCTAAAAACAATC 57.317 29.630 0.00 0.00 0.00 2.67
3824 7222 3.372025 GCAGAAATCCCAACCAGGACTAT 60.372 47.826 0.00 0.00 39.24 2.12
3825 7223 4.202441 CAGAAATCCCAACCAGGACTATG 58.798 47.826 0.00 0.00 39.24 2.23
3841 7252 7.363431 CAGGACTATGTTCTTTTCAGGTTTTC 58.637 38.462 0.00 0.00 0.00 2.29
3859 7270 7.277098 CAGGTTTTCATCCAAATATTCAAGCAG 59.723 37.037 0.00 0.00 0.00 4.24
3885 7300 6.423905 TCACTTGAATTCGAGTTGTTCTAAGG 59.576 38.462 23.36 10.69 38.50 2.69
3896 7311 4.035208 AGTTGTTCTAAGGTCAAAAGCACG 59.965 41.667 0.00 0.00 0.00 5.34
3899 7314 5.117584 TGTTCTAAGGTCAAAAGCACGTTA 58.882 37.500 0.00 0.00 0.00 3.18
3902 7317 6.870971 TCTAAGGTCAAAAGCACGTTAAAT 57.129 33.333 0.00 0.00 0.00 1.40
3912 7327 6.481954 AAAGCACGTTAAATTAGACTCCAG 57.518 37.500 0.00 0.00 0.00 3.86
3924 7339 8.789767 AAATTAGACTCCAGATCAATCTAGGA 57.210 34.615 0.00 9.41 34.85 2.94
3928 7343 4.293494 ACTCCAGATCAATCTAGGAGCAA 58.707 43.478 23.81 4.35 45.63 3.91
3942 7357 6.970484 TCTAGGAGCAAAACAATCAAAGAAC 58.030 36.000 0.00 0.00 0.00 3.01
3957 7372 6.432607 TCAAAGAACAGATGATCAATGCTC 57.567 37.500 0.00 3.08 0.00 4.26
3989 7404 6.013725 TGTCCACAGTATACACATTCCTTTCT 60.014 38.462 5.50 0.00 0.00 2.52
3992 7407 6.352222 CCACAGTATACACATTCCTTTCTCCT 60.352 42.308 5.50 0.00 0.00 3.69
4000 7416 5.222213 ACACATTCCTTTCTCCTTTCCATCT 60.222 40.000 0.00 0.00 0.00 2.90
4035 7451 7.530426 AGATTGTCTTTGGTTAGAATGCTTT 57.470 32.000 0.00 0.00 0.00 3.51
4064 7480 5.048224 AGCAATCAACCAGAAGAACATCTTG 60.048 40.000 0.00 0.00 36.73 3.02
4091 7507 2.027837 GGCTGGCACTTTGATTTTCCAT 60.028 45.455 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 7.504924 TCGCCGGAAATCATAAAATAAATCT 57.495 32.000 5.05 0.00 0.00 2.40
126 127 7.201350 GCATCGCCGGAAATCATAAAATAAATC 60.201 37.037 5.05 0.00 0.00 2.17
135 136 0.249699 ACGCATCGCCGGAAATCATA 60.250 50.000 5.05 0.00 0.00 2.15
137 138 2.125310 ACGCATCGCCGGAAATCA 60.125 55.556 5.05 0.00 0.00 2.57
152 153 0.389166 GTCTGCTCCCTCTGAACACG 60.389 60.000 0.00 0.00 0.00 4.49
154 155 0.827925 ACGTCTGCTCCCTCTGAACA 60.828 55.000 0.00 0.00 0.00 3.18
161 162 0.820871 GATGAGAACGTCTGCTCCCT 59.179 55.000 9.61 0.00 0.00 4.20
167 168 1.828832 GTAGCCGATGAGAACGTCTG 58.171 55.000 0.00 0.00 0.00 3.51
172 173 0.595310 GCCTCGTAGCCGATGAGAAC 60.595 60.000 6.96 0.00 43.06 3.01
175 176 2.050895 CGCCTCGTAGCCGATGAG 60.051 66.667 0.00 0.00 43.27 2.90
176 177 4.266070 GCGCCTCGTAGCCGATGA 62.266 66.667 0.00 0.00 43.27 2.92
182 183 4.625781 CCGTAGGCGCCTCGTAGC 62.626 72.222 36.73 17.61 46.14 3.58
202 203 5.803020 ACCATCTTGAGATTTTACGAAGC 57.197 39.130 0.00 0.00 31.21 3.86
218 219 1.050988 ACTGAGCCGGCATACCATCT 61.051 55.000 31.54 4.27 34.57 2.90
223 224 0.528684 GAGACACTGAGCCGGCATAC 60.529 60.000 31.54 19.58 0.00 2.39
228 229 3.057547 CTCCGAGACACTGAGCCGG 62.058 68.421 0.00 0.00 41.36 6.13
238 239 0.671251 CCTATGAGCACCTCCGAGAC 59.329 60.000 0.00 0.00 0.00 3.36
239 240 0.468214 CCCTATGAGCACCTCCGAGA 60.468 60.000 0.00 0.00 0.00 4.04
260 261 3.453424 CCTATTGCACACACATACGCTA 58.547 45.455 0.00 0.00 0.00 4.26
263 264 1.939934 CCCCTATTGCACACACATACG 59.060 52.381 0.00 0.00 0.00 3.06
266 267 1.354031 TCACCCCTATTGCACACACAT 59.646 47.619 0.00 0.00 0.00 3.21
273 274 2.421388 GCATACACTCACCCCTATTGCA 60.421 50.000 0.00 0.00 0.00 4.08
275 276 3.206150 GTGCATACACTCACCCCTATTG 58.794 50.000 0.00 0.00 43.85 1.90
276 277 2.158957 CGTGCATACACTCACCCCTATT 60.159 50.000 0.00 0.00 45.10 1.73
280 282 0.321298 AACGTGCATACACTCACCCC 60.321 55.000 0.00 0.00 45.10 4.95
296 298 3.551890 AGACACAAGCGCTCATATAAACG 59.448 43.478 12.06 0.00 0.00 3.60
350 355 7.554118 ACAATATGAGATGGGTTTTCACTACTG 59.446 37.037 0.00 0.00 0.00 2.74
357 362 5.841957 AGCACAATATGAGATGGGTTTTC 57.158 39.130 0.00 0.00 0.00 2.29
661 2284 5.943349 TCCCCGTATCTGAACTTATTTGA 57.057 39.130 0.00 0.00 0.00 2.69
707 2332 5.181433 GGAGATTTTGCGACCTTAAGAAACT 59.819 40.000 3.36 0.00 0.00 2.66
714 2339 3.007506 TGTGAGGAGATTTTGCGACCTTA 59.992 43.478 0.00 0.00 0.00 2.69
768 2393 4.803098 ATCCTAGAATAATTACGCGCCT 57.197 40.909 5.73 0.00 0.00 5.52
908 2538 4.704057 TGATCAGCGAGTATGATATGCTCT 59.296 41.667 0.00 0.00 39.49 4.09
916 2546 2.359214 GTGGAGTGATCAGCGAGTATGA 59.641 50.000 0.00 0.00 0.00 2.15
1198 3446 2.745037 GTGCTTACCCCGTGGTCA 59.255 61.111 0.00 0.00 43.06 4.02
1245 3536 0.931702 TGCACGAACCAAACACGTAG 59.068 50.000 0.00 0.00 38.47 3.51
1368 3659 1.293179 CAGCATGGTCACCGACTCA 59.707 57.895 0.00 0.00 32.47 3.41
1369 3660 0.737715 GACAGCATGGTCACCGACTC 60.738 60.000 0.00 0.00 43.62 3.36
1370 3661 1.293498 GACAGCATGGTCACCGACT 59.707 57.895 0.00 0.00 43.62 4.18
1371 3662 2.094659 CGACAGCATGGTCACCGAC 61.095 63.158 0.00 0.00 43.62 4.79
1372 3663 2.261361 CGACAGCATGGTCACCGA 59.739 61.111 0.00 0.00 43.62 4.69
1373 3664 2.048222 ACGACAGCATGGTCACCG 60.048 61.111 0.00 1.38 43.62 4.94
1708 4019 1.092921 ACCTGTTTCGCGTGCTTCAA 61.093 50.000 5.77 0.00 0.00 2.69
1802 4218 0.183492 ACATAGTGCGGCCATCCATT 59.817 50.000 2.24 0.00 0.00 3.16
1944 4552 8.081633 CACCACTCTATGAAATTGTTTGCTAAA 58.918 33.333 0.00 0.00 0.00 1.85
1954 4562 8.938883 ACTATATGACCACCACTCTATGAAATT 58.061 33.333 0.00 0.00 0.00 1.82
2132 4749 3.063997 CGATGGAATGCTGTTTCTGGTAC 59.936 47.826 0.00 0.00 0.00 3.34
2140 4757 1.001020 TGGCCGATGGAATGCTGTT 60.001 52.632 0.00 0.00 0.00 3.16
3011 5657 3.002791 AGAATCGTCGTAGTGGTCGTTA 58.997 45.455 0.00 0.00 0.00 3.18
3122 5768 4.823442 TGCACATCTCTTGACTGAAAACAT 59.177 37.500 0.00 0.00 0.00 2.71
3359 6728 4.682778 TCGTTAATGAAATCGGAGGGAT 57.317 40.909 0.00 0.00 36.78 3.85
3438 6811 8.262227 TGTAAGATATATGTCGTTCCTTTTGGT 58.738 33.333 0.00 0.00 41.38 3.67
3439 6812 8.657074 TGTAAGATATATGTCGTTCCTTTTGG 57.343 34.615 0.00 0.00 42.21 3.28
3488 6874 4.959839 TCTGCCCCTTGTTTAGTTTTCTTT 59.040 37.500 0.00 0.00 0.00 2.52
3490 6876 4.145052 CTCTGCCCCTTGTTTAGTTTTCT 58.855 43.478 0.00 0.00 0.00 2.52
3491 6877 3.305403 GCTCTGCCCCTTGTTTAGTTTTC 60.305 47.826 0.00 0.00 0.00 2.29
3495 6881 0.038310 GGCTCTGCCCCTTGTTTAGT 59.962 55.000 0.00 0.00 44.06 2.24
3496 6882 2.873797 GGCTCTGCCCCTTGTTTAG 58.126 57.895 0.00 0.00 44.06 1.85
3508 6894 1.268899 CAGTTTGCTTTCAGGGCTCTG 59.731 52.381 7.48 7.48 42.21 3.35
3509 6895 1.143684 TCAGTTTGCTTTCAGGGCTCT 59.856 47.619 0.00 0.00 0.00 4.09
3510 6896 1.609208 TCAGTTTGCTTTCAGGGCTC 58.391 50.000 0.00 0.00 0.00 4.70
3513 6899 3.480470 TCTCTTCAGTTTGCTTTCAGGG 58.520 45.455 0.00 0.00 0.00 4.45
3515 6901 5.929278 CTGATCTCTTCAGTTTGCTTTCAG 58.071 41.667 0.00 0.00 45.79 3.02
3516 6902 5.936686 CTGATCTCTTCAGTTTGCTTTCA 57.063 39.130 0.00 0.00 45.79 2.69
3527 6913 1.556911 GCTGGGGAACTGATCTCTTCA 59.443 52.381 0.00 0.00 0.00 3.02
3551 6948 2.285969 ATGGAGGCCCTGAGTGCT 60.286 61.111 0.00 0.00 0.00 4.40
3560 6957 3.764160 CTTCGCAGGGATGGAGGCC 62.764 68.421 0.00 0.00 0.00 5.19
3577 6974 4.878397 GTGGCAAGTGAGATATACAAAGCT 59.122 41.667 0.00 0.00 0.00 3.74
3580 6977 4.523083 GGGTGGCAAGTGAGATATACAAA 58.477 43.478 0.00 0.00 0.00 2.83
3658 7056 9.962809 ATTGGATTGATGAATGGTTTATTTTGT 57.037 25.926 0.00 0.00 0.00 2.83
3664 7062 9.029368 TGTGTAATTGGATTGATGAATGGTTTA 57.971 29.630 0.00 0.00 0.00 2.01
3666 7064 7.479352 TGTGTAATTGGATTGATGAATGGTT 57.521 32.000 0.00 0.00 0.00 3.67
3686 7084 7.554118 CCCATGACTTTTATCAGACTTATGTGT 59.446 37.037 0.00 0.00 30.46 3.72
3725 7123 9.688592 AGAAGATTCATTGTTTTTAGAGCAAAG 57.311 29.630 0.00 0.00 0.00 2.77
3728 7126 9.467258 CAAAGAAGATTCATTGTTTTTAGAGCA 57.533 29.630 3.07 0.00 32.82 4.26
3729 7127 8.430828 GCAAAGAAGATTCATTGTTTTTAGAGC 58.569 33.333 11.01 0.00 37.96 4.09
3730 7128 9.688592 AGCAAAGAAGATTCATTGTTTTTAGAG 57.311 29.630 11.01 0.00 37.96 2.43
3731 7129 9.683069 GAGCAAAGAAGATTCATTGTTTTTAGA 57.317 29.630 11.01 0.00 37.96 2.10
3732 7130 9.688592 AGAGCAAAGAAGATTCATTGTTTTTAG 57.311 29.630 11.01 0.00 37.96 1.85
3738 7136 9.468532 GTTTTTAGAGCAAAGAAGATTCATTGT 57.531 29.630 11.01 0.79 37.96 2.71
3739 7137 9.467258 TGTTTTTAGAGCAAAGAAGATTCATTG 57.533 29.630 6.25 6.25 38.51 2.82
3742 7140 9.683069 GATTGTTTTTAGAGCAAAGAAGATTCA 57.317 29.630 0.00 0.00 0.00 2.57
3743 7141 9.905171 AGATTGTTTTTAGAGCAAAGAAGATTC 57.095 29.630 0.00 0.00 0.00 2.52
3744 7142 9.905171 GAGATTGTTTTTAGAGCAAAGAAGATT 57.095 29.630 0.00 0.00 0.00 2.40
3745 7143 9.071276 TGAGATTGTTTTTAGAGCAAAGAAGAT 57.929 29.630 0.00 0.00 0.00 2.40
3746 7144 8.450578 TGAGATTGTTTTTAGAGCAAAGAAGA 57.549 30.769 0.00 0.00 0.00 2.87
3747 7145 9.688592 AATGAGATTGTTTTTAGAGCAAAGAAG 57.311 29.630 0.00 0.00 0.00 2.85
3749 7147 9.683069 GAAATGAGATTGTTTTTAGAGCAAAGA 57.317 29.630 0.00 0.00 0.00 2.52
3750 7148 9.688592 AGAAATGAGATTGTTTTTAGAGCAAAG 57.311 29.630 0.00 0.00 0.00 2.77
3783 7181 7.875316 TTCTGCGATATTCTAGTCTATTTGC 57.125 36.000 0.00 0.00 0.00 3.68
3788 7186 6.719829 TGGGATTTCTGCGATATTCTAGTCTA 59.280 38.462 0.00 0.00 0.00 2.59
3793 7191 5.163248 TGGTTGGGATTTCTGCGATATTCTA 60.163 40.000 0.00 0.00 0.00 2.10
3824 7222 6.537453 TTGGATGAAAACCTGAAAAGAACA 57.463 33.333 0.00 0.00 0.00 3.18
3825 7223 9.710900 ATATTTGGATGAAAACCTGAAAAGAAC 57.289 29.630 0.00 0.00 0.00 3.01
3841 7252 6.446781 AGTGACTGCTTGAATATTTGGATG 57.553 37.500 0.00 0.00 0.00 3.51
3859 7270 5.659048 AGAACAACTCGAATTCAAGTGAC 57.341 39.130 0.00 0.00 0.00 3.67
3871 7282 4.272504 TGCTTTTGACCTTAGAACAACTCG 59.727 41.667 0.00 0.00 0.00 4.18
3885 7300 6.795593 GGAGTCTAATTTAACGTGCTTTTGAC 59.204 38.462 0.00 0.00 0.00 3.18
3899 7314 8.789767 TCCTAGATTGATCTGGAGTCTAATTT 57.210 34.615 5.99 0.00 37.57 1.82
3902 7317 5.772672 GCTCCTAGATTGATCTGGAGTCTAA 59.227 44.000 24.36 0.96 44.73 2.10
3912 7327 7.325660 TGATTGTTTTGCTCCTAGATTGATC 57.674 36.000 0.00 0.00 0.00 2.92
3923 7338 6.919662 TCATCTGTTCTTTGATTGTTTTGCTC 59.080 34.615 0.00 0.00 0.00 4.26
3924 7339 6.808829 TCATCTGTTCTTTGATTGTTTTGCT 58.191 32.000 0.00 0.00 0.00 3.91
3928 7343 9.419297 CATTGATCATCTGTTCTTTGATTGTTT 57.581 29.630 0.00 0.00 30.48 2.83
3957 7372 5.965922 TGTGTATACTGTGGACAAGATGAG 58.034 41.667 4.17 0.00 0.00 2.90
4035 7451 3.738982 TCTTCTGGTTGATTGCTCGAAA 58.261 40.909 0.00 0.00 0.00 3.46
4045 7461 6.119240 AGATCAAGATGTTCTTCTGGTTGA 57.881 37.500 0.00 0.00 33.78 3.18
4064 7480 1.538047 TCAAAGTGCCAGCCAAGATC 58.462 50.000 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.