Multiple sequence alignment - TraesCS3B01G146700

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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 TraesCS3B01G146700 chr3B 100.000 7081 0 0 1 7081 136492944 136485864 0.000000e+00 13077.0
1 TraesCS3B01G146700 chr3B 98.993 4270 38 5 2813 7081 119083597 119087862 0.000000e+00 7642.0
2 TraesCS3B01G146700 chr3B 79.092 1454 252 40 3599 5014 68403990 68402551 0.000000e+00 953.0
3 TraesCS3B01G146700 chr3B 86.066 244 16 5 711 936 136091719 136091476 5.490000e-61 246.0
4 TraesCS3B01G146700 chr3B 80.564 319 47 12 5897 6205 68401879 68401566 1.540000e-56 231.0
5 TraesCS3B01G146700 chr3A 93.131 2213 139 6 2813 5022 86624030 86626232 0.000000e+00 3232.0
6 TraesCS3B01G146700 chr3A 90.654 1391 108 13 5696 7081 86626618 86627991 0.000000e+00 1829.0
7 TraesCS3B01G146700 chr3A 79.519 1372 235 35 3676 5014 55563409 55562051 0.000000e+00 935.0
8 TraesCS3B01G146700 chr3A 84.167 960 62 35 295 1205 102687060 102686142 0.000000e+00 848.0
9 TraesCS3B01G146700 chr3A 94.359 390 20 2 5268 5655 86626231 86626620 1.310000e-166 597.0
10 TraesCS3B01G146700 chr3A 89.300 243 25 1 6755 6996 75031410 75031652 3.210000e-78 303.0
11 TraesCS3B01G146700 chr3A 73.713 913 165 51 5328 6202 55561938 55561063 3.230000e-73 287.0
12 TraesCS3B01G146700 chr3A 95.882 170 4 1 134 303 102687258 102687092 9.050000e-69 272.0
13 TraesCS3B01G146700 chr3A 76.449 535 95 21 5684 6202 55603334 55602815 1.960000e-65 261.0
14 TraesCS3B01G146700 chr3A 76.449 535 95 21 5684 6202 55605057 55604538 1.960000e-65 261.0
15 TraesCS3B01G146700 chr3A 87.395 238 16 8 712 936 102555015 102554779 1.960000e-65 261.0
16 TraesCS3B01G146700 chr3D 93.186 2216 123 12 2813 5022 73758813 73761006 0.000000e+00 3230.0
17 TraesCS3B01G146700 chr3D 91.493 1822 122 19 5268 7081 73761005 73762801 0.000000e+00 2475.0
18 TraesCS3B01G146700 chr3D 92.314 1236 39 23 1 1205 86358726 86357516 0.000000e+00 1705.0
19 TraesCS3B01G146700 chr3D 78.627 1544 260 51 3517 5014 43781238 43782757 0.000000e+00 959.0
20 TraesCS3B01G146700 chr3D 88.031 259 21 5 5020 5269 17523266 17523009 1.490000e-76 298.0
21 TraesCS3B01G146700 chr3D 86.905 252 33 0 5018 5269 609606585 609606836 4.180000e-72 283.0
22 TraesCS3B01G146700 chr3D 87.008 254 28 3 5022 5270 170773307 170773054 1.500000e-71 281.0
23 TraesCS3B01G146700 chr3D 88.261 230 20 5 712 936 85896777 85896550 1.170000e-67 268.0
24 TraesCS3B01G146700 chr3D 73.997 773 136 40 5328 6067 43782870 43783610 3.280000e-63 254.0
25 TraesCS3B01G146700 chr3D 86.179 246 13 5 712 936 86237292 86237047 5.490000e-61 246.0
26 TraesCS3B01G146700 chr7D 89.275 1613 109 29 1254 2815 210130406 210128807 0.000000e+00 1962.0
27 TraesCS3B01G146700 chr7D 90.054 1297 97 10 1254 2531 208482294 208481011 0.000000e+00 1652.0
28 TraesCS3B01G146700 chr7D 87.603 242 28 2 6755 6995 64691313 64691073 5.410000e-71 279.0
29 TraesCS3B01G146700 chr5A 86.740 1629 127 25 1254 2813 635764911 635766519 0.000000e+00 1729.0
30 TraesCS3B01G146700 chr5A 86.885 244 30 2 6754 6996 479460107 479459865 9.050000e-69 272.0
31 TraesCS3B01G146700 chr2A 88.153 1494 93 30 1387 2814 22604055 22605530 0.000000e+00 1701.0
32 TraesCS3B01G146700 chr2A 88.086 1494 94 30 1387 2814 22636050 22637525 0.000000e+00 1696.0
33 TraesCS3B01G146700 chr2A 87.251 251 32 0 5019 5269 398651764 398652014 3.230000e-73 287.0
34 TraesCS3B01G146700 chr2A 87.251 251 32 0 5019 5269 398690016 398689766 3.230000e-73 287.0
35 TraesCS3B01G146700 chr2A 78.220 427 43 25 2433 2814 720543363 720542942 1.990000e-55 228.0
36 TraesCS3B01G146700 chrUn 88.086 1494 94 30 1387 2814 305811581 305813056 0.000000e+00 1696.0
37 TraesCS3B01G146700 chrUn 81.294 572 98 9 4273 4841 471930996 471931561 8.370000e-124 455.0
38 TraesCS3B01G146700 chr7A 86.118 1628 137 25 1254 2812 46909379 46910986 0.000000e+00 1672.0
39 TraesCS3B01G146700 chr7A 85.846 325 25 10 2090 2395 423554676 423554998 6.850000e-85 326.0
40 TraesCS3B01G146700 chr7A 78.654 431 42 21 2430 2815 423555104 423555529 2.550000e-59 241.0
41 TraesCS3B01G146700 chr7A 88.333 60 4 3 3230 3287 384088162 384088104 1.270000e-07 69.4
42 TraesCS3B01G146700 chr6A 85.530 1472 120 29 1387 2788 52024192 52025640 0.000000e+00 1452.0
43 TraesCS3B01G146700 chr6A 90.947 243 21 1 6754 6995 601961128 601961370 6.850000e-85 326.0
44 TraesCS3B01G146700 chr1A 89.809 471 37 2 1254 1724 496324924 496325383 1.700000e-165 593.0
45 TraesCS3B01G146700 chr1A 87.179 468 49 5 1659 2120 537350107 537349645 8.140000e-144 521.0
46 TraesCS3B01G146700 chr1A 84.862 218 23 9 2392 2607 490890182 490890391 2.000000e-50 211.0
47 TraesCS3B01G146700 chr1A 87.313 134 12 5 728 857 124189786 124189918 1.590000e-31 148.0
48 TraesCS3B01G146700 chr4B 87.298 433 35 8 1982 2395 458075999 458075568 1.790000e-130 477.0
49 TraesCS3B01G146700 chr6B 82.392 602 53 18 2260 2815 696768216 696767622 6.430000e-130 475.0
50 TraesCS3B01G146700 chr6B 87.795 254 25 4 5021 5269 647171861 647172113 6.950000e-75 292.0
51 TraesCS3B01G146700 chr6B 87.649 251 29 1 5021 5269 130963021 130963271 2.500000e-74 291.0
52 TraesCS3B01G146700 chr5B 92.135 267 20 1 1255 1520 516460357 516460091 6.710000e-100 375.0
53 TraesCS3B01G146700 chr5B 91.791 268 20 2 1254 1520 698266832 698266566 8.670000e-99 372.0
54 TraesCS3B01G146700 chr5B 91.418 268 21 2 1254 1520 698264545 698264279 4.040000e-97 366.0
55 TraesCS3B01G146700 chr5B 91.418 268 21 2 1254 1520 698269119 698268853 4.040000e-97 366.0
56 TraesCS3B01G146700 chr5B 88.983 236 23 3 6747 6981 447009725 447009492 8.990000e-74 289.0
57 TraesCS3B01G146700 chr2D 87.066 317 24 6 2095 2395 13810422 13810737 6.800000e-90 342.0
58 TraesCS3B01G146700 chr2D 89.300 243 24 2 6754 6995 620601550 620601791 3.210000e-78 303.0
59 TraesCS3B01G146700 chr2D 75.490 204 42 8 3093 3292 589493948 589494147 7.560000e-15 93.5
60 TraesCS3B01G146700 chr2B 87.645 259 24 5 5021 5273 785033483 785033227 1.930000e-75 294.0
61 TraesCS3B01G146700 chr2B 93.103 58 4 0 3243 3300 782184641 782184584 1.270000e-12 86.1
62 TraesCS3B01G146700 chr4A 81.604 212 29 9 2392 2601 14159527 14159730 4.390000e-37 167.0
63 TraesCS3B01G146700 chr1B 80.531 226 29 12 727 937 174783900 174784125 7.350000e-35 159.0
64 TraesCS3B01G146700 chr1B 74.494 247 48 14 3059 3298 94236442 94236204 7.560000e-15 93.5
65 TraesCS3B01G146700 chr5D 90.323 124 6 3 2694 2811 430533468 430533591 2.640000e-34 158.0
66 TraesCS3B01G146700 chr5D 75.304 247 50 11 3057 3297 391058971 391058730 2.700000e-19 108.0
67 TraesCS3B01G146700 chr1D 80.269 223 30 12 728 937 114083271 114083492 9.510000e-34 156.0
68 TraesCS3B01G146700 chr4D 77.725 211 42 5 3093 3300 76023316 76023524 2.680000e-24 124.0


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 TraesCS3B01G146700 chr3B 136485864 136492944 7080 True 13077.0 13077 100.000000 1 7081 1 chr3B.!!$R2 7080
1 TraesCS3B01G146700 chr3B 119083597 119087862 4265 False 7642.0 7642 98.993000 2813 7081 1 chr3B.!!$F1 4268
2 TraesCS3B01G146700 chr3B 68401566 68403990 2424 True 592.0 953 79.828000 3599 6205 2 chr3B.!!$R3 2606
3 TraesCS3B01G146700 chr3A 86624030 86627991 3961 False 1886.0 3232 92.714667 2813 7081 3 chr3A.!!$F2 4268
4 TraesCS3B01G146700 chr3A 55561063 55563409 2346 True 611.0 935 76.616000 3676 6202 2 chr3A.!!$R2 2526
5 TraesCS3B01G146700 chr3A 102686142 102687258 1116 True 560.0 848 90.024500 134 1205 2 chr3A.!!$R4 1071
6 TraesCS3B01G146700 chr3A 55602815 55605057 2242 True 261.0 261 76.449000 5684 6202 2 chr3A.!!$R3 518
7 TraesCS3B01G146700 chr3D 73758813 73762801 3988 False 2852.5 3230 92.339500 2813 7081 2 chr3D.!!$F3 4268
8 TraesCS3B01G146700 chr3D 86357516 86358726 1210 True 1705.0 1705 92.314000 1 1205 1 chr3D.!!$R4 1204
9 TraesCS3B01G146700 chr3D 43781238 43783610 2372 False 606.5 959 76.312000 3517 6067 2 chr3D.!!$F2 2550
10 TraesCS3B01G146700 chr7D 210128807 210130406 1599 True 1962.0 1962 89.275000 1254 2815 1 chr7D.!!$R3 1561
11 TraesCS3B01G146700 chr7D 208481011 208482294 1283 True 1652.0 1652 90.054000 1254 2531 1 chr7D.!!$R2 1277
12 TraesCS3B01G146700 chr5A 635764911 635766519 1608 False 1729.0 1729 86.740000 1254 2813 1 chr5A.!!$F1 1559
13 TraesCS3B01G146700 chr2A 22604055 22605530 1475 False 1701.0 1701 88.153000 1387 2814 1 chr2A.!!$F1 1427
14 TraesCS3B01G146700 chr2A 22636050 22637525 1475 False 1696.0 1696 88.086000 1387 2814 1 chr2A.!!$F2 1427
15 TraesCS3B01G146700 chrUn 305811581 305813056 1475 False 1696.0 1696 88.086000 1387 2814 1 chrUn.!!$F1 1427
16 TraesCS3B01G146700 chrUn 471930996 471931561 565 False 455.0 455 81.294000 4273 4841 1 chrUn.!!$F2 568
17 TraesCS3B01G146700 chr7A 46909379 46910986 1607 False 1672.0 1672 86.118000 1254 2812 1 chr7A.!!$F1 1558
18 TraesCS3B01G146700 chr7A 423554676 423555529 853 False 283.5 326 82.250000 2090 2815 2 chr7A.!!$F2 725
19 TraesCS3B01G146700 chr6A 52024192 52025640 1448 False 1452.0 1452 85.530000 1387 2788 1 chr6A.!!$F1 1401
20 TraesCS3B01G146700 chr6B 696767622 696768216 594 True 475.0 475 82.392000 2260 2815 1 chr6B.!!$R1 555
21 TraesCS3B01G146700 chr5B 698264279 698269119 4840 True 368.0 372 91.542333 1254 1520 3 chr5B.!!$R3 266

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
284 285 0.250209 AGGTCTCGCCATGCATCATC 60.250 55.000 0.00 0.0 40.61 2.92 F
1056 1150 0.172803 TTAGCGAGGAAGCGAGGAAC 59.827 55.000 0.00 0.0 43.00 3.62 F
1208 1303 0.322546 GGGCTCCTTCGGTTGAATGT 60.323 55.000 0.00 0.0 32.61 2.71 F
2292 2455 0.034670 GCTTCCCAGATCTGCAAGGT 60.035 55.000 23.84 0.0 0.00 3.50 F
2632 5284 1.270041 GGAGTTGGAGGAGATCGATGC 60.270 57.143 0.54 0.0 0.00 3.91 F
4094 6823 2.302157 ACTTGGCTTGGACTACCACTAC 59.698 50.000 0.00 0.0 46.80 2.73 F
4731 7471 6.430451 AGTCTACAATGCGTTCTTTTTCTTG 58.570 36.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 1331 0.253044 CCCCGATGACATGTGGACTT 59.747 55.000 1.15 0.00 0.00 3.01 R
2292 2455 0.179004 ACGGGGAATGAGTGTTGCAA 60.179 50.000 0.00 0.00 0.00 4.08 R
2524 5136 0.535335 AAATTCGAGGTGCCGCTCTA 59.465 50.000 0.00 0.00 0.00 2.43 R
4094 6823 1.683917 AGTTCCCCGATCTCATTCTCG 59.316 52.381 0.00 0.00 34.73 4.04 R
4379 7111 3.554731 CCTCATATGCGCTGCACTATATG 59.445 47.826 9.73 12.49 43.04 1.78 R
5014 7755 2.124277 AAACGGAGGGAGTAATTGGC 57.876 50.000 0.00 0.00 0.00 4.52 R
7029 12212 6.299141 TGGAACAGAAGCTTGAAATTCTACT 58.701 36.000 2.10 0.00 34.04 2.57 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
43 44 3.902150 TCAAATCAGATCGCTACGGATC 58.098 45.455 0.00 0.00 42.52 3.36
44 45 2.620779 AATCAGATCGCTACGGATCG 57.379 50.000 0.00 0.00 45.90 3.69
45 46 1.809684 ATCAGATCGCTACGGATCGA 58.190 50.000 0.00 0.00 45.90 3.59
56 57 1.818850 ACGGATCGACGATAAACACG 58.181 50.000 10.97 12.41 37.61 4.49
63 64 1.317611 CGACGATAAACACGCACTGAG 59.682 52.381 0.00 0.00 0.00 3.35
64 65 2.592194 GACGATAAACACGCACTGAGA 58.408 47.619 0.00 0.00 0.00 3.27
81 82 3.706594 CTGAGACTGGGATTACTGGCTTA 59.293 47.826 0.00 0.00 0.00 3.09
130 131 3.791928 CGAGTCGCCGATGGAGTCG 62.792 68.421 0.00 11.27 46.82 4.18
191 192 0.254178 CCTGAACCCCTGATGGACAG 59.746 60.000 0.00 0.00 45.36 3.51
272 273 3.226347 GACGAATTTTTGCAAGGTCTCG 58.774 45.455 16.59 16.59 0.00 4.04
284 285 0.250209 AGGTCTCGCCATGCATCATC 60.250 55.000 0.00 0.00 40.61 2.92
285 286 0.533531 GGTCTCGCCATGCATCATCA 60.534 55.000 0.00 0.00 37.17 3.07
286 287 1.520494 GTCTCGCCATGCATCATCAT 58.480 50.000 0.00 0.00 0.00 2.45
287 288 1.878088 GTCTCGCCATGCATCATCATT 59.122 47.619 0.00 0.00 0.00 2.57
288 289 1.877443 TCTCGCCATGCATCATCATTG 59.123 47.619 0.00 0.00 0.00 2.82
290 291 1.605232 TCGCCATGCATCATCATTGAC 59.395 47.619 0.00 0.00 33.85 3.18
292 293 2.809696 CGCCATGCATCATCATTGACTA 59.190 45.455 0.00 0.00 33.85 2.59
293 294 3.120304 CGCCATGCATCATCATTGACTAG 60.120 47.826 0.00 0.00 33.85 2.57
301 339 5.604565 CATCATCATTGACTAGTGCCAGTA 58.395 41.667 0.00 0.00 33.85 2.74
333 371 4.842531 TGATGATGGTAGCAGGAAGAAA 57.157 40.909 0.00 0.00 0.00 2.52
345 383 3.428589 GCAGGAAGAAATTGTGAGCATCC 60.429 47.826 0.00 0.00 0.00 3.51
407 445 3.258872 TGGCGGTACATACCATACCATAC 59.741 47.826 8.76 0.00 46.80 2.39
410 448 4.155826 GCGGTACATACCATACCATACGTA 59.844 45.833 8.76 0.00 46.80 3.57
424 462 1.182667 TACGTACATCCTGCAGCAGT 58.817 50.000 21.26 8.63 0.00 4.40
791 837 1.993956 CTCTCCGTCTCCATCATCCT 58.006 55.000 0.00 0.00 0.00 3.24
1056 1150 0.172803 TTAGCGAGGAAGCGAGGAAC 59.827 55.000 0.00 0.00 43.00 3.62
1063 1157 1.590147 GAAGCGAGGAACGGAAGGA 59.410 57.895 0.00 0.00 42.83 3.36
1084 1179 3.795638 GCGGGGCGAGTTTAAGAG 58.204 61.111 0.00 0.00 0.00 2.85
1090 1185 0.442699 GGCGAGTTTAAGAGTTGGCG 59.557 55.000 0.00 0.00 0.00 5.69
1199 1294 2.026301 GTCGATCGGGCTCCTTCG 59.974 66.667 16.41 0.00 0.00 3.79
1205 1300 1.550130 ATCGGGCTCCTTCGGTTGAA 61.550 55.000 0.00 0.00 0.00 2.69
1206 1301 1.078426 CGGGCTCCTTCGGTTGAAT 60.078 57.895 0.00 0.00 32.61 2.57
1207 1302 1.369091 CGGGCTCCTTCGGTTGAATG 61.369 60.000 0.00 0.00 32.61 2.67
1208 1303 0.322546 GGGCTCCTTCGGTTGAATGT 60.323 55.000 0.00 0.00 32.61 2.71
1209 1304 1.087501 GGCTCCTTCGGTTGAATGTC 58.912 55.000 0.00 0.00 32.61 3.06
1210 1305 1.339151 GGCTCCTTCGGTTGAATGTCT 60.339 52.381 0.00 0.00 32.61 3.41
1211 1306 2.003301 GCTCCTTCGGTTGAATGTCTC 58.997 52.381 0.00 0.00 32.61 3.36
1212 1307 2.354203 GCTCCTTCGGTTGAATGTCTCT 60.354 50.000 0.00 0.00 32.61 3.10
1213 1308 3.257393 CTCCTTCGGTTGAATGTCTCTG 58.743 50.000 0.00 0.00 32.61 3.35
1214 1309 2.632996 TCCTTCGGTTGAATGTCTCTGT 59.367 45.455 0.00 0.00 32.61 3.41
1215 1310 3.830178 TCCTTCGGTTGAATGTCTCTGTA 59.170 43.478 0.00 0.00 32.61 2.74
1216 1311 4.282449 TCCTTCGGTTGAATGTCTCTGTAA 59.718 41.667 0.00 0.00 32.61 2.41
1217 1312 4.994852 CCTTCGGTTGAATGTCTCTGTAAA 59.005 41.667 0.00 0.00 32.61 2.01
1218 1313 5.643777 CCTTCGGTTGAATGTCTCTGTAAAT 59.356 40.000 0.00 0.00 32.61 1.40
1219 1314 6.816640 CCTTCGGTTGAATGTCTCTGTAAATA 59.183 38.462 0.00 0.00 32.61 1.40
1220 1315 7.333423 CCTTCGGTTGAATGTCTCTGTAAATAA 59.667 37.037 0.00 0.00 32.61 1.40
1221 1316 7.591006 TCGGTTGAATGTCTCTGTAAATAAC 57.409 36.000 0.00 0.00 0.00 1.89
1222 1317 6.592607 TCGGTTGAATGTCTCTGTAAATAACC 59.407 38.462 0.00 0.00 0.00 2.85
1223 1318 6.370442 CGGTTGAATGTCTCTGTAAATAACCA 59.630 38.462 0.00 0.00 34.92 3.67
1224 1319 7.094975 CGGTTGAATGTCTCTGTAAATAACCAA 60.095 37.037 0.00 0.00 34.92 3.67
1225 1320 8.573035 GGTTGAATGTCTCTGTAAATAACCAAA 58.427 33.333 0.00 0.00 35.23 3.28
1226 1321 9.394477 GTTGAATGTCTCTGTAAATAACCAAAC 57.606 33.333 0.00 0.00 0.00 2.93
1227 1322 8.684386 TGAATGTCTCTGTAAATAACCAAACA 57.316 30.769 0.00 0.00 0.00 2.83
1228 1323 9.295825 TGAATGTCTCTGTAAATAACCAAACAT 57.704 29.630 0.00 0.00 0.00 2.71
1244 1339 7.589958 ACCAAACATTAATGTAAAGTCCACA 57.410 32.000 21.07 0.00 40.80 4.17
1245 1340 8.189119 ACCAAACATTAATGTAAAGTCCACAT 57.811 30.769 21.07 0.00 40.80 3.21
1246 1341 8.087750 ACCAAACATTAATGTAAAGTCCACATG 58.912 33.333 21.07 7.78 40.80 3.21
1247 1342 8.087750 CCAAACATTAATGTAAAGTCCACATGT 58.912 33.333 21.07 0.00 40.80 3.21
1248 1343 9.128107 CAAACATTAATGTAAAGTCCACATGTC 57.872 33.333 21.07 0.00 40.80 3.06
1249 1344 7.994425 ACATTAATGTAAAGTCCACATGTCA 57.006 32.000 19.51 0.00 39.68 3.58
1250 1345 8.579850 ACATTAATGTAAAGTCCACATGTCAT 57.420 30.769 19.51 0.00 39.68 3.06
1251 1346 8.677300 ACATTAATGTAAAGTCCACATGTCATC 58.323 33.333 19.51 0.00 39.68 2.92
1252 1347 5.801350 AATGTAAAGTCCACATGTCATCG 57.199 39.130 0.00 0.00 36.74 3.84
1301 1396 0.672401 GGGCGAGACGACAAAATGGA 60.672 55.000 0.00 0.00 36.10 3.41
1362 1458 9.982291 GTATTTCGAAAGCAATTCAGTACATAA 57.018 29.630 16.80 0.00 37.96 1.90
1373 1469 9.869844 GCAATTCAGTACATAACATAGATTGAC 57.130 33.333 0.00 0.00 0.00 3.18
1435 1531 5.153950 AGTTCTACAAAGGATCGCTCTTT 57.846 39.130 0.00 0.00 35.09 2.52
1510 1607 5.049129 GTCAAAGCTGATAGCAACTTGAAGT 60.049 40.000 0.00 0.00 45.56 3.01
1529 1626 7.800155 TGAAGTGTTTGTGTTATCATGAGAA 57.200 32.000 0.09 0.00 0.00 2.87
1530 1627 8.394971 TGAAGTGTTTGTGTTATCATGAGAAT 57.605 30.769 5.98 0.00 0.00 2.40
1531 1628 9.500785 TGAAGTGTTTGTGTTATCATGAGAATA 57.499 29.630 5.98 0.07 0.00 1.75
1534 1631 9.671279 AGTGTTTGTGTTATCATGAGAATATGA 57.329 29.630 5.98 0.00 41.00 2.15
1535 1632 9.926751 GTGTTTGTGTTATCATGAGAATATGAG 57.073 33.333 5.98 0.00 40.16 2.90
1536 1633 9.889128 TGTTTGTGTTATCATGAGAATATGAGA 57.111 29.630 5.98 0.00 40.16 3.27
1639 1736 3.133141 AGTCTCCAAAGCTTCCTGAAC 57.867 47.619 0.00 0.00 0.00 3.18
1666 1763 5.803237 TGATCAGATCTGTGCATCAGTAT 57.197 39.130 21.92 5.10 43.97 2.12
1667 1764 6.170846 TGATCAGATCTGTGCATCAGTATT 57.829 37.500 21.92 3.74 43.97 1.89
1668 1765 6.589135 TGATCAGATCTGTGCATCAGTATTT 58.411 36.000 21.92 2.92 43.97 1.40
1783 1880 7.013274 CCAATAACTCCAACTTTGAGAAACTGA 59.987 37.037 0.00 0.00 0.00 3.41
1869 1967 4.865365 GGAAAAGAGTCTATGTCTCCAACG 59.135 45.833 0.00 0.00 32.93 4.10
1878 1976 2.417339 TGTCTCCAACGAACTCGAAG 57.583 50.000 6.05 0.00 43.02 3.79
1933 2031 7.356089 TCCGGTATAGTCATTTGTCATAGTT 57.644 36.000 0.00 0.00 0.00 2.24
1985 2083 6.970043 TCAACATAACTTTGAGAAACCGTTTG 59.030 34.615 0.00 0.00 0.00 2.93
2009 2107 4.378774 ACAAATTTAGCACAGCATTTGCA 58.621 34.783 5.20 0.00 42.83 4.08
2044 2145 8.992835 ATCATTCAATAAAAGTCTTTTGAGCC 57.007 30.769 18.89 0.00 34.19 4.70
2055 2156 5.066593 AGTCTTTTGAGCCAAGTAAGAAGG 58.933 41.667 0.00 0.00 26.96 3.46
2248 2411 6.656270 CCAAAGCACCTGAATATGAGCATATA 59.344 38.462 3.59 0.00 33.86 0.86
2249 2412 7.361542 CCAAAGCACCTGAATATGAGCATATAC 60.362 40.741 3.59 0.00 33.86 1.47
2292 2455 0.034670 GCTTCCCAGATCTGCAAGGT 60.035 55.000 23.84 0.00 0.00 3.50
2346 2510 3.102204 CCCTGGATCCAATGAAGCTTTT 58.898 45.455 17.00 0.00 0.00 2.27
2385 2549 7.617723 ACACAAGAGTATGAACTAGGAAGAGAT 59.382 37.037 0.00 0.00 35.56 2.75
2449 2773 4.994852 TCAATTCCTCAAACGTCTACTTGG 59.005 41.667 0.00 0.00 0.00 3.61
2500 5112 2.270434 TGGGGAAGAGAATAGCACCT 57.730 50.000 0.00 0.00 0.00 4.00
2576 5188 3.041940 CGGCGGCGTTGTTCTCTT 61.042 61.111 24.74 0.00 0.00 2.85
2582 5194 2.343101 CGGCGTTGTTCTCTTGGATTA 58.657 47.619 0.00 0.00 0.00 1.75
2608 5230 2.840203 TTTGGGGAGGAGGCGAGGAT 62.840 60.000 0.00 0.00 0.00 3.24
2632 5284 1.270041 GGAGTTGGAGGAGATCGATGC 60.270 57.143 0.54 0.00 0.00 3.91
2747 5439 4.510167 ACACGTATACTACTACCTGGGT 57.490 45.455 0.00 0.00 0.00 4.51
3086 5780 4.261801 CCCCGTCCATATTTATTAGGCAG 58.738 47.826 0.00 0.00 0.00 4.85
3392 6086 4.493872 CCAACAAACAAATGCTGGAAAACG 60.494 41.667 0.00 0.00 38.56 3.60
3393 6087 3.855858 ACAAACAAATGCTGGAAAACGT 58.144 36.364 0.00 0.00 0.00 3.99
3672 6378 4.351192 AGTTGCACACGAATTTGAAGTTC 58.649 39.130 0.00 0.00 0.00 3.01
4094 6823 2.302157 ACTTGGCTTGGACTACCACTAC 59.698 50.000 0.00 0.00 46.80 2.73
4731 7471 6.430451 AGTCTACAATGCGTTCTTTTTCTTG 58.570 36.000 0.00 0.00 0.00 3.02
4911 7652 8.737175 CCCGTATTATAGCTACAAAGATCACTA 58.263 37.037 0.00 0.00 0.00 2.74
5014 7755 3.200165 AGGTTAAATCCTCCTTCCCTTCG 59.800 47.826 0.00 0.00 31.32 3.79
5030 7771 0.177141 TTCGCCAATTACTCCCTCCG 59.823 55.000 0.00 0.00 0.00 4.63
5258 7999 9.946165 AAGCTAATATGCGGACTAAATAAAAAC 57.054 29.630 0.00 0.00 38.13 2.43
7029 12212 4.753516 TTCCACTGAACTCTTTGACTCA 57.246 40.909 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.317611 CTCAGTGCGTGTTTATCGTCG 59.682 52.381 0.00 0.00 0.00 5.12
44 45 2.341760 GTCTCAGTGCGTGTTTATCGTC 59.658 50.000 0.00 0.00 0.00 4.20
45 46 2.030185 AGTCTCAGTGCGTGTTTATCGT 60.030 45.455 0.00 0.00 0.00 3.73
56 57 2.419297 CCAGTAATCCCAGTCTCAGTGC 60.419 54.545 0.00 0.00 0.00 4.40
63 64 4.965200 AGATAAGCCAGTAATCCCAGTC 57.035 45.455 0.00 0.00 0.00 3.51
64 65 4.475016 ACAAGATAAGCCAGTAATCCCAGT 59.525 41.667 0.00 0.00 0.00 4.00
81 82 1.927527 AGGCCAGGGAGCACAAGAT 60.928 57.895 5.01 0.00 0.00 2.40
111 112 3.471244 GACTCCATCGGCGACTCGG 62.471 68.421 13.76 13.87 0.00 4.63
112 113 2.024871 GACTCCATCGGCGACTCG 59.975 66.667 13.76 3.42 0.00 4.18
126 127 1.529865 CGATGATTCATGCATGCGACT 59.470 47.619 22.25 5.86 0.00 4.18
130 131 0.728129 CCGCGATGATTCATGCATGC 60.728 55.000 22.25 11.82 0.00 4.06
191 192 2.416893 GGCGGAAAATGAGTCAAGTCTC 59.583 50.000 0.00 0.00 35.28 3.36
272 273 3.819337 ACTAGTCAATGATGATGCATGGC 59.181 43.478 2.46 0.00 38.01 4.40
284 285 4.456280 TCTGTACTGGCACTAGTCAATG 57.544 45.455 0.00 0.00 32.19 2.82
285 286 5.483685 TTTCTGTACTGGCACTAGTCAAT 57.516 39.130 0.00 0.00 32.19 2.57
286 287 4.948341 TTTCTGTACTGGCACTAGTCAA 57.052 40.909 0.00 0.00 32.19 3.18
287 288 4.380550 CGATTTCTGTACTGGCACTAGTCA 60.381 45.833 0.00 0.00 32.19 3.41
288 289 4.106197 CGATTTCTGTACTGGCACTAGTC 58.894 47.826 0.00 0.00 32.19 2.59
290 291 4.111375 ACGATTTCTGTACTGGCACTAG 57.889 45.455 0.00 0.00 0.00 2.57
292 293 3.067106 CAACGATTTCTGTACTGGCACT 58.933 45.455 0.00 0.00 0.00 4.40
293 294 3.064207 TCAACGATTTCTGTACTGGCAC 58.936 45.455 0.00 0.00 0.00 5.01
301 339 4.572389 GCTACCATCATCAACGATTTCTGT 59.428 41.667 0.00 0.00 0.00 3.41
333 371 3.867600 GCATAGATCCGGATGCTCACAAT 60.868 47.826 24.82 6.40 44.15 2.71
345 383 5.052481 TCTGTTCAATGAAGCATAGATCCG 58.948 41.667 0.00 0.00 0.00 4.18
407 445 2.515926 ATACTGCTGCAGGATGTACG 57.484 50.000 31.00 7.14 33.16 3.67
410 448 9.745018 AATAATAATAATACTGCTGCAGGATGT 57.255 29.630 27.11 18.38 34.89 3.06
440 478 4.900635 ACCAAGAATGTTGTTGTGAGAC 57.099 40.909 2.56 0.00 30.21 3.36
443 481 3.194329 TGCAACCAAGAATGTTGTTGTGA 59.806 39.130 5.19 0.00 43.86 3.58
444 482 3.519579 TGCAACCAAGAATGTTGTTGTG 58.480 40.909 5.19 0.00 43.86 3.33
445 483 3.430651 CCTGCAACCAAGAATGTTGTTGT 60.431 43.478 5.19 0.00 43.86 3.32
446 484 3.125316 CCTGCAACCAAGAATGTTGTTG 58.875 45.455 5.19 0.00 43.86 3.33
447 485 2.765699 ACCTGCAACCAAGAATGTTGTT 59.234 40.909 5.19 0.00 43.86 2.83
466 504 3.740115 ACATCAGTCCTGTAACAACACC 58.260 45.455 0.00 0.00 0.00 4.16
683 729 2.582436 GCACCAAGCCGTAGCCTA 59.418 61.111 0.00 0.00 41.25 3.93
1047 1141 1.292541 GTTCCTTCCGTTCCTCGCT 59.707 57.895 0.00 0.00 38.35 4.93
1199 1294 7.681939 TGGTTATTTACAGAGACATTCAACC 57.318 36.000 0.00 0.00 33.83 3.77
1218 1313 9.132923 TGTGGACTTTACATTAATGTTTGGTTA 57.867 29.630 25.31 4.42 41.97 2.85
1219 1314 8.012957 TGTGGACTTTACATTAATGTTTGGTT 57.987 30.769 25.31 7.62 41.97 3.67
1220 1315 7.589958 TGTGGACTTTACATTAATGTTTGGT 57.410 32.000 25.31 19.24 41.97 3.67
1221 1316 8.087750 ACATGTGGACTTTACATTAATGTTTGG 58.912 33.333 25.31 16.62 41.97 3.28
1222 1317 9.128107 GACATGTGGACTTTACATTAATGTTTG 57.872 33.333 25.31 16.99 41.97 2.93
1223 1318 8.855110 TGACATGTGGACTTTACATTAATGTTT 58.145 29.630 25.31 8.62 41.97 2.83
1224 1319 8.402798 TGACATGTGGACTTTACATTAATGTT 57.597 30.769 25.31 8.29 41.97 2.71
1225 1320 7.994425 TGACATGTGGACTTTACATTAATGT 57.006 32.000 23.80 23.80 44.48 2.71
1226 1321 7.852454 CGATGACATGTGGACTTTACATTAATG 59.148 37.037 14.01 14.01 36.67 1.90
1227 1322 7.012327 CCGATGACATGTGGACTTTACATTAAT 59.988 37.037 1.15 0.00 36.67 1.40
1228 1323 6.315144 CCGATGACATGTGGACTTTACATTAA 59.685 38.462 1.15 0.00 36.67 1.40
1229 1324 5.815222 CCGATGACATGTGGACTTTACATTA 59.185 40.000 1.15 0.00 36.67 1.90
1230 1325 4.635765 CCGATGACATGTGGACTTTACATT 59.364 41.667 1.15 0.00 36.67 2.71
1231 1326 4.191544 CCGATGACATGTGGACTTTACAT 58.808 43.478 1.15 0.00 39.23 2.29
1232 1327 3.595173 CCGATGACATGTGGACTTTACA 58.405 45.455 1.15 0.00 0.00 2.41
1233 1328 2.936498 CCCGATGACATGTGGACTTTAC 59.064 50.000 1.15 0.00 0.00 2.01
1234 1329 2.093181 CCCCGATGACATGTGGACTTTA 60.093 50.000 1.15 0.00 0.00 1.85
1235 1330 1.340017 CCCCGATGACATGTGGACTTT 60.340 52.381 1.15 0.00 0.00 2.66
1236 1331 0.253044 CCCCGATGACATGTGGACTT 59.747 55.000 1.15 0.00 0.00 3.01
1237 1332 1.907739 CCCCGATGACATGTGGACT 59.092 57.895 1.15 0.00 0.00 3.85
1238 1333 1.819632 GCCCCGATGACATGTGGAC 60.820 63.158 1.15 0.00 0.00 4.02
1239 1334 2.589540 GCCCCGATGACATGTGGA 59.410 61.111 1.15 0.00 0.00 4.02
1240 1335 2.516930 GGCCCCGATGACATGTGG 60.517 66.667 1.15 0.00 0.00 4.17
1241 1336 2.896854 CGGCCCCGATGACATGTG 60.897 66.667 1.15 0.00 42.83 3.21
1242 1337 4.175337 CCGGCCCCGATGACATGT 62.175 66.667 8.54 0.00 42.83 3.21
1243 1338 4.175337 ACCGGCCCCGATGACATG 62.175 66.667 8.54 0.00 42.83 3.21
1244 1339 3.861797 GACCGGCCCCGATGACAT 61.862 66.667 8.54 0.00 42.83 3.06
1247 1342 3.759910 TATGGACCGGCCCCGATGA 62.760 63.158 3.55 0.00 42.83 2.92
1248 1343 3.238497 TATGGACCGGCCCCGATG 61.238 66.667 3.55 0.00 42.83 3.84
1249 1344 3.239253 GTATGGACCGGCCCCGAT 61.239 66.667 3.55 0.00 42.83 4.18
1250 1345 2.659946 TATGTATGGACCGGCCCCGA 62.660 60.000 3.55 0.00 42.83 5.14
1251 1346 1.550130 ATATGTATGGACCGGCCCCG 61.550 60.000 3.55 0.00 39.44 5.73
1252 1347 0.696501 AATATGTATGGACCGGCCCC 59.303 55.000 3.55 5.29 34.97 5.80
1301 1396 8.144862 TGAATTTTTATTTGTCCATAAGGGCT 57.855 30.769 0.00 0.00 41.31 5.19
1362 1458 6.123651 AGTTCTCTAGACCGTCAATCTATGT 58.876 40.000 0.40 0.00 0.00 2.29
1373 1469 7.879160 ACTATTAGGATGTAGTTCTCTAGACCG 59.121 40.741 0.00 0.00 0.00 4.79
1435 1531 3.586470 TTGTCTCTTTGTGGCCCTTAA 57.414 42.857 0.00 0.00 0.00 1.85
1442 1538 3.063180 GCGAGATGATTGTCTCTTTGTGG 59.937 47.826 2.83 0.00 41.95 4.17
1510 1607 9.889128 TCTCATATTCTCATGATAACACAAACA 57.111 29.630 0.00 0.00 34.50 2.83
1619 1716 2.439507 TGTTCAGGAAGCTTTGGAGACT 59.560 45.455 0.00 0.00 0.00 3.24
1639 1736 4.997395 TGATGCACAGATCTGATCATCATG 59.003 41.667 34.12 22.46 41.99 3.07
1667 1764 9.612066 AGAAAGCAAAGTTGGATGAAATAAAAA 57.388 25.926 0.00 0.00 0.00 1.94
1668 1765 9.260002 GAGAAAGCAAAGTTGGATGAAATAAAA 57.740 29.630 0.00 0.00 0.00 1.52
1706 1803 5.381174 TGAAAGATTGAATGGTCTTGCTG 57.619 39.130 0.00 0.00 35.03 4.41
1744 1841 8.581578 GTTGGAGTTATTGGGAAACTATTTCAA 58.418 33.333 3.87 0.00 41.43 2.69
1746 1843 8.349568 AGTTGGAGTTATTGGGAAACTATTTC 57.650 34.615 0.00 0.00 37.31 2.17
1766 1863 5.731686 GCTGAACTCAGTTTCTCAAAGTTGG 60.732 44.000 8.46 0.00 45.45 3.77
1845 1943 4.720649 TGGAGACATAGACTCTTTTCCG 57.279 45.455 0.00 0.00 35.10 4.30
1869 1967 4.295051 GTGCTATGGAGATCTTCGAGTTC 58.705 47.826 0.00 0.00 0.00 3.01
1911 2009 9.524106 TTACAACTATGACAAATGACTATACCG 57.476 33.333 0.00 0.00 0.00 4.02
1933 2031 6.968263 AGATGATCTCTTCTCGGAATTACA 57.032 37.500 0.00 0.00 0.00 2.41
1985 2083 5.404968 TGCAAATGCTGTGCTAAATTTGTAC 59.595 36.000 6.97 1.88 42.69 2.90
2044 2145 9.383519 TCAGAAGTATATTTGCCTTCTTACTTG 57.616 33.333 0.00 0.00 42.18 3.16
2224 2387 4.913335 ATGCTCATATTCAGGTGCTTTG 57.087 40.909 0.00 0.00 0.00 2.77
2248 2411 4.761739 ACATCAACAATTCGACATCAAGGT 59.238 37.500 0.00 0.00 0.00 3.50
2249 2412 5.300969 ACATCAACAATTCGACATCAAGG 57.699 39.130 0.00 0.00 0.00 3.61
2292 2455 0.179004 ACGGGGAATGAGTGTTGCAA 60.179 50.000 0.00 0.00 0.00 4.08
2346 2510 4.980573 ACTCTTGTGTTGGCCTGTTATTA 58.019 39.130 3.32 0.00 0.00 0.98
2385 2549 1.829222 GGTACGTCTCCCTCCAATTCA 59.171 52.381 0.00 0.00 0.00 2.57
2449 2773 0.605319 TGCATCCTCAACGTTCCCAC 60.605 55.000 0.00 0.00 0.00 4.61
2524 5136 0.535335 AAATTCGAGGTGCCGCTCTA 59.465 50.000 0.00 0.00 0.00 2.43
2525 5137 1.021390 CAAATTCGAGGTGCCGCTCT 61.021 55.000 0.00 0.00 0.00 4.09
2576 5188 4.793520 TCCTCCCCAAAATTCTCTAATCCA 59.206 41.667 0.00 0.00 0.00 3.41
2582 5194 1.286257 GCCTCCTCCCCAAAATTCTCT 59.714 52.381 0.00 0.00 0.00 3.10
2591 5205 2.400461 TATCCTCGCCTCCTCCCCA 61.400 63.158 0.00 0.00 0.00 4.96
2608 5230 2.241430 TCGATCTCCTCCAACTCCAGTA 59.759 50.000 0.00 0.00 0.00 2.74
2616 5238 1.043116 ACCGCATCGATCTCCTCCAA 61.043 55.000 0.00 0.00 0.00 3.53
3086 5780 4.525912 ACTTGGGCTCAAAATGTGAATC 57.474 40.909 0.00 0.00 35.22 2.52
3232 5926 5.418840 GGGCCAAATTTTGACTCTAGATTCA 59.581 40.000 8.62 8.62 0.00 2.57
3392 6086 4.361451 AGCATCGAAACAAATCATGGAC 57.639 40.909 0.00 0.00 0.00 4.02
3393 6087 5.506151 GCATAGCATCGAAACAAATCATGGA 60.506 40.000 0.00 0.00 0.00 3.41
3470 6165 9.023967 CCGCCAAAAATAATAATTCTTTCAGAG 57.976 33.333 0.00 0.00 0.00 3.35
3672 6378 4.805192 GGCAGTTGCATGGTATTACAAATG 59.195 41.667 6.43 0.00 44.36 2.32
4094 6823 1.683917 AGTTCCCCGATCTCATTCTCG 59.316 52.381 0.00 0.00 34.73 4.04
4379 7111 3.554731 CCTCATATGCGCTGCACTATATG 59.445 47.826 9.73 12.49 43.04 1.78
4462 7194 5.067273 TGGTGATTCCAAATGTTCTAACGT 58.933 37.500 0.00 0.00 44.12 3.99
5014 7755 2.124277 AAACGGAGGGAGTAATTGGC 57.876 50.000 0.00 0.00 0.00 4.52
7029 12212 6.299141 TGGAACAGAAGCTTGAAATTCTACT 58.701 36.000 2.10 0.00 34.04 2.57


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

AutoCloner maintained by Alex Coulton.