Multiple sequence alignment - TraesCS7B01G363400

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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 TraesCS7B01G363400 chr7B 100.000 4034 0 0 1 4034 626042014 626046047 0.000000e+00 7450.0
1 TraesCS7B01G363400 chr2A 93.969 2653 122 12 1399 4034 595234601 595237232 0.000000e+00 3978.0
2 TraesCS7B01G363400 chr2A 95.014 2086 98 1 1955 4034 585189915 585192000 0.000000e+00 3271.0
3 TraesCS7B01G363400 chr2A 95.972 422 17 0 988 1409 595233005 595233426 0.000000e+00 686.0
4 TraesCS7B01G363400 chr3D 93.504 1832 89 5 2210 4034 19974455 19976263 0.000000e+00 2697.0
5 TraesCS7B01G363400 chr3D 86.360 1173 153 6 2859 4028 186936687 186937855 0.000000e+00 1273.0
6 TraesCS7B01G363400 chr3D 82.048 1387 225 20 2660 4034 432508472 432509846 0.000000e+00 1160.0
7 TraesCS7B01G363400 chr5A 93.303 1747 110 3 2294 4034 698752015 698753760 0.000000e+00 2571.0
8 TraesCS7B01G363400 chr5A 85.714 84 12 0 1352 1435 138176925 138176842 5.550000e-14 89.8
9 TraesCS7B01G363400 chr2D 94.951 1426 72 0 2609 4034 100425972 100427397 0.000000e+00 2235.0
10 TraesCS7B01G363400 chr2D 97.024 168 5 0 2446 2613 100424140 100424307 2.370000e-72 283.0
11 TraesCS7B01G363400 chr2D 91.667 168 14 0 1006 1173 117238513 117238346 2.420000e-57 233.0
12 TraesCS7B01G363400 chr2D 96.154 52 2 0 241 292 429473325 429473274 7.180000e-13 86.1
13 TraesCS7B01G363400 chr3B 85.593 1180 161 8 2859 4034 773358108 773356934 0.000000e+00 1229.0
14 TraesCS7B01G363400 chr3B 89.571 163 17 0 1011 1173 605284646 605284808 1.470000e-49 207.0
15 TraesCS7B01G363400 chr7A 82.327 1375 229 14 2658 4025 271638715 271640082 0.000000e+00 1181.0
16 TraesCS7B01G363400 chr7A 85.324 695 65 16 291 957 575953754 575953069 0.000000e+00 684.0
17 TraesCS7B01G363400 chr7A 85.159 694 65 8 291 957 575732517 575733199 0.000000e+00 676.0
18 TraesCS7B01G363400 chr7A 83.683 429 44 5 286 689 658889093 658889520 8.180000e-102 381.0
19 TraesCS7B01G363400 chr7A 83.171 410 42 9 286 669 576120882 576120474 2.310000e-92 350.0
20 TraesCS7B01G363400 chr7A 90.909 176 16 0 998 1173 17308939 17309114 1.870000e-58 237.0
21 TraesCS7B01G363400 chr7A 87.879 132 12 2 113 241 576121021 576120891 6.980000e-33 152.0
22 TraesCS7B01G363400 chr7A 86.957 138 14 2 107 241 658888948 658889084 6.980000e-33 152.0
23 TraesCS7B01G363400 chr7A 87.603 121 12 1 124 241 575732385 575732505 1.960000e-28 137.0
24 TraesCS7B01G363400 chr7D 83.808 1229 185 11 2813 4034 140816118 140814897 0.000000e+00 1155.0
25 TraesCS7B01G363400 chr7D 92.275 699 28 2 284 957 569502711 569503408 0.000000e+00 968.0
26 TraesCS7B01G363400 chr7D 92.275 699 27 7 284 957 569553983 569554679 0.000000e+00 966.0
27 TraesCS7B01G363400 chr7D 95.312 256 12 0 284 539 569559296 569559551 1.350000e-109 407.0
28 TraesCS7B01G363400 chr7D 95.312 256 12 0 284 539 569583283 569583538 1.350000e-109 407.0
29 TraesCS7B01G363400 chr7D 96.266 241 9 0 1 241 569553736 569553976 2.920000e-106 396.0
30 TraesCS7B01G363400 chr7D 94.694 245 12 1 2 245 569502464 569502708 2.940000e-101 379.0
31 TraesCS7B01G363400 chr7D 89.212 241 17 2 1 241 569559058 569559289 3.940000e-75 292.0
32 TraesCS7B01G363400 chr7D 88.333 240 19 2 2 241 569583046 569583276 3.070000e-71 279.0
33 TraesCS7B01G363400 chr7D 89.671 213 13 3 746 957 569559615 569559819 3.090000e-66 263.0
34 TraesCS7B01G363400 chr7D 88.679 212 14 3 746 957 569583610 569583811 2.410000e-62 250.0
35 TraesCS7B01G363400 chr7D 91.667 168 14 0 1006 1173 636672017 636672184 2.420000e-57 233.0
36 TraesCS7B01G363400 chr5D 77.083 576 116 12 1328 1899 13999288 13998725 6.510000e-83 318.0
37 TraesCS7B01G363400 chr6D 91.071 168 15 0 1006 1173 120732745 120732578 1.130000e-55 228.0
38 TraesCS7B01G363400 chr5B 92.523 107 8 0 540 646 506972154 506972260 1.940000e-33 154.0
39 TraesCS7B01G363400 chr5B 83.740 123 20 0 1395 1517 327202204 327202326 2.550000e-22 117.0
40 TraesCS7B01G363400 chr5B 98.077 52 1 0 241 292 455636948 455636999 1.540000e-14 91.6
41 TraesCS7B01G363400 chr5B 96.154 52 2 0 241 292 34145456 34145405 7.180000e-13 86.1
42 TraesCS7B01G363400 chr4A 98.077 52 1 0 241 292 295275346 295275397 1.540000e-14 91.6
43 TraesCS7B01G363400 chr4A 96.154 52 2 0 241 292 708910423 708910372 7.180000e-13 86.1
44 TraesCS7B01G363400 chrUn 100.000 47 0 0 241 287 36546817 36546863 2.000000e-13 87.9
45 TraesCS7B01G363400 chrUn 100.000 47 0 0 241 287 275329308 275329262 2.000000e-13 87.9
46 TraesCS7B01G363400 chrUn 100.000 47 0 0 241 287 393315291 393315245 2.000000e-13 87.9
47 TraesCS7B01G363400 chr2B 96.154 52 2 0 241 292 391111885 391111834 7.180000e-13 86.1


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 TraesCS7B01G363400 chr7B 626042014 626046047 4033 False 7450.000000 7450 100.000000 1 4034 1 chr7B.!!$F1 4033
1 TraesCS7B01G363400 chr2A 585189915 585192000 2085 False 3271.000000 3271 95.014000 1955 4034 1 chr2A.!!$F1 2079
2 TraesCS7B01G363400 chr2A 595233005 595237232 4227 False 2332.000000 3978 94.970500 988 4034 2 chr2A.!!$F2 3046
3 TraesCS7B01G363400 chr3D 19974455 19976263 1808 False 2697.000000 2697 93.504000 2210 4034 1 chr3D.!!$F1 1824
4 TraesCS7B01G363400 chr3D 186936687 186937855 1168 False 1273.000000 1273 86.360000 2859 4028 1 chr3D.!!$F2 1169
5 TraesCS7B01G363400 chr3D 432508472 432509846 1374 False 1160.000000 1160 82.048000 2660 4034 1 chr3D.!!$F3 1374
6 TraesCS7B01G363400 chr5A 698752015 698753760 1745 False 2571.000000 2571 93.303000 2294 4034 1 chr5A.!!$F1 1740
7 TraesCS7B01G363400 chr2D 100424140 100427397 3257 False 1259.000000 2235 95.987500 2446 4034 2 chr2D.!!$F1 1588
8 TraesCS7B01G363400 chr3B 773356934 773358108 1174 True 1229.000000 1229 85.593000 2859 4034 1 chr3B.!!$R1 1175
9 TraesCS7B01G363400 chr7A 271638715 271640082 1367 False 1181.000000 1181 82.327000 2658 4025 1 chr7A.!!$F2 1367
10 TraesCS7B01G363400 chr7A 575953069 575953754 685 True 684.000000 684 85.324000 291 957 1 chr7A.!!$R1 666
11 TraesCS7B01G363400 chr7A 575732385 575733199 814 False 406.500000 676 86.381000 124 957 2 chr7A.!!$F3 833
12 TraesCS7B01G363400 chr7A 658888948 658889520 572 False 266.500000 381 85.320000 107 689 2 chr7A.!!$F4 582
13 TraesCS7B01G363400 chr7A 576120474 576121021 547 True 251.000000 350 85.525000 113 669 2 chr7A.!!$R2 556
14 TraesCS7B01G363400 chr7D 140814897 140816118 1221 True 1155.000000 1155 83.808000 2813 4034 1 chr7D.!!$R1 1221
15 TraesCS7B01G363400 chr7D 569553736 569554679 943 False 681.000000 966 94.270500 1 957 2 chr7D.!!$F3 956
16 TraesCS7B01G363400 chr7D 569502464 569503408 944 False 673.500000 968 93.484500 2 957 2 chr7D.!!$F2 955
17 TraesCS7B01G363400 chr7D 569559058 569559819 761 False 320.666667 407 91.398333 1 957 3 chr7D.!!$F4 956
18 TraesCS7B01G363400 chr7D 569583046 569583811 765 False 312.000000 407 90.774667 2 957 3 chr7D.!!$F5 955
19 TraesCS7B01G363400 chr5D 13998725 13999288 563 True 318.000000 318 77.083000 1328 1899 1 chr5D.!!$R1 571

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
92 93 0.034756 TCGCAGCAAGCTGGTTTCTA 59.965 50.0 22.2 0.0 43.77 2.10 F
263 267 0.179054 CCCTAGCCGCCTTCCTTAAC 60.179 60.0 0.0 0.0 0.00 2.01 F
1253 1284 0.179081 AAATCGTCTAGGGCTTCGGC 60.179 55.0 0.0 0.0 40.88 5.54 F
2745 5659 0.033601 ACCTCTCTGATGGCGTCTCT 60.034 55.0 8.4 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1247 1278 0.320946 TTTTGGTAGACCCGCCGAAG 60.321 55.000 0.0 0.0 35.15 3.79 R
2079 3306 0.673644 AGACACGCACATAGTTGCCC 60.674 55.000 0.0 0.0 39.53 5.36 R
2843 5757 0.468226 TGAAACCACAAGCTCGTCCT 59.532 50.000 0.0 0.0 0.00 3.85 R
4003 6940 1.074926 ATCCTGTCCATCGCCTCCT 60.075 57.895 0.0 0.0 0.00 3.69 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
92 93 0.034756 TCGCAGCAAGCTGGTTTCTA 59.965 50.000 22.20 0.00 43.77 2.10
241 245 1.432270 CGGAAAAGAGGGAGCGATGC 61.432 60.000 0.00 0.00 0.00 3.91
242 246 1.432270 GGAAAAGAGGGAGCGATGCG 61.432 60.000 0.00 0.00 0.00 4.73
244 248 4.537433 AAGAGGGAGCGATGCGGC 62.537 66.667 0.00 0.00 0.00 6.53
249 253 4.671569 GGAGCGATGCGGCCCTAG 62.672 72.222 0.00 0.00 0.00 3.02
260 264 3.798511 GCCCTAGCCGCCTTCCTT 61.799 66.667 0.00 0.00 0.00 3.36
261 265 2.440817 GCCCTAGCCGCCTTCCTTA 61.441 63.158 0.00 0.00 0.00 2.69
262 266 1.979619 GCCCTAGCCGCCTTCCTTAA 61.980 60.000 0.00 0.00 0.00 1.85
263 267 0.179054 CCCTAGCCGCCTTCCTTAAC 60.179 60.000 0.00 0.00 0.00 2.01
264 268 0.539986 CCTAGCCGCCTTCCTTAACA 59.460 55.000 0.00 0.00 0.00 2.41
265 269 1.065709 CCTAGCCGCCTTCCTTAACAA 60.066 52.381 0.00 0.00 0.00 2.83
266 270 2.280628 CTAGCCGCCTTCCTTAACAAG 58.719 52.381 0.00 0.00 0.00 3.16
267 271 0.960861 AGCCGCCTTCCTTAACAAGC 60.961 55.000 0.00 0.00 0.00 4.01
268 272 1.934220 GCCGCCTTCCTTAACAAGCC 61.934 60.000 0.00 0.00 0.00 4.35
269 273 1.313091 CCGCCTTCCTTAACAAGCCC 61.313 60.000 0.00 0.00 0.00 5.19
270 274 0.322546 CGCCTTCCTTAACAAGCCCT 60.323 55.000 0.00 0.00 0.00 5.19
271 275 1.464734 GCCTTCCTTAACAAGCCCTC 58.535 55.000 0.00 0.00 0.00 4.30
272 276 1.739067 CCTTCCTTAACAAGCCCTCG 58.261 55.000 0.00 0.00 0.00 4.63
273 277 1.278127 CCTTCCTTAACAAGCCCTCGA 59.722 52.381 0.00 0.00 0.00 4.04
274 278 2.622436 CTTCCTTAACAAGCCCTCGAG 58.378 52.381 5.13 5.13 0.00 4.04
275 279 0.249398 TCCTTAACAAGCCCTCGAGC 59.751 55.000 6.99 0.00 0.00 5.03
276 280 0.744771 CCTTAACAAGCCCTCGAGCC 60.745 60.000 6.99 0.00 0.00 4.70
277 281 0.250513 CTTAACAAGCCCTCGAGCCT 59.749 55.000 6.99 2.15 0.00 4.58
278 282 0.249398 TTAACAAGCCCTCGAGCCTC 59.751 55.000 6.99 0.00 0.00 4.70
279 283 1.614241 TAACAAGCCCTCGAGCCTCC 61.614 60.000 6.99 0.00 0.00 4.30
280 284 3.080121 CAAGCCCTCGAGCCTCCT 61.080 66.667 6.99 0.00 0.00 3.69
281 285 2.284995 AAGCCCTCGAGCCTCCTT 60.285 61.111 6.99 3.25 0.00 3.36
282 286 1.920835 AAGCCCTCGAGCCTCCTTT 60.921 57.895 6.99 0.00 0.00 3.11
300 304 1.159285 TTGCGCAACCTGATTCTGAG 58.841 50.000 21.02 0.00 0.00 3.35
333 337 2.856988 GGAGGTGGTGGGTGGGAA 60.857 66.667 0.00 0.00 0.00 3.97
398 402 1.602323 ACAATTTCCCGCTTGCCGA 60.602 52.632 0.00 0.00 40.02 5.54
455 459 1.545428 GCCACCTCAACTGATTGTCCA 60.545 52.381 0.00 0.00 37.11 4.02
696 725 1.631405 TGAATCCAAACAGCCCCTTG 58.369 50.000 0.00 0.00 0.00 3.61
748 777 6.385649 AATCTTTTTCGTTCAACTGCCTAA 57.614 33.333 0.00 0.00 0.00 2.69
969 1000 3.329743 CATGATCATGTTCGGCAAGTC 57.670 47.619 24.87 0.00 34.23 3.01
970 1001 2.768253 TGATCATGTTCGGCAAGTCT 57.232 45.000 0.00 0.00 0.00 3.24
971 1002 2.349590 TGATCATGTTCGGCAAGTCTG 58.650 47.619 0.00 0.00 0.00 3.51
972 1003 2.028203 TGATCATGTTCGGCAAGTCTGA 60.028 45.455 0.00 0.00 0.00 3.27
973 1004 2.542020 TCATGTTCGGCAAGTCTGAA 57.458 45.000 0.00 0.00 37.72 3.02
979 1010 2.325583 TCGGCAAGTCTGAACTTTGT 57.674 45.000 0.00 0.00 43.28 2.83
980 1011 2.639065 TCGGCAAGTCTGAACTTTGTT 58.361 42.857 0.00 0.00 43.28 2.83
981 1012 2.354510 TCGGCAAGTCTGAACTTTGTTG 59.645 45.455 0.00 0.00 43.28 3.33
982 1013 2.541588 CGGCAAGTCTGAACTTTGTTGG 60.542 50.000 0.00 0.00 43.28 3.77
983 1014 2.463876 GCAAGTCTGAACTTTGTTGGC 58.536 47.619 0.00 0.00 43.28 4.52
984 1015 2.099756 GCAAGTCTGAACTTTGTTGGCT 59.900 45.455 0.00 0.00 43.28 4.75
985 1016 3.793465 GCAAGTCTGAACTTTGTTGGCTC 60.793 47.826 0.00 0.00 43.28 4.70
986 1017 2.576615 AGTCTGAACTTTGTTGGCTCC 58.423 47.619 0.00 0.00 28.74 4.70
1016 1047 2.997899 GCATGCAGTTAGGCGATCT 58.002 52.632 14.21 0.00 36.28 2.75
1074 1105 2.348998 CCCTCTGTGTGTGGCCTC 59.651 66.667 3.32 0.00 0.00 4.70
1075 1106 2.219875 CCCTCTGTGTGTGGCCTCT 61.220 63.158 3.32 0.00 0.00 3.69
1219 1250 1.487231 CGTCGCAAGGAAACTCACG 59.513 57.895 0.00 0.00 42.68 4.35
1224 1255 2.540931 TCGCAAGGAAACTCACGTAAAC 59.459 45.455 0.00 0.00 42.68 2.01
1247 1278 4.308265 GACTCCATAAAATCGTCTAGGGC 58.692 47.826 0.00 0.00 0.00 5.19
1253 1284 0.179081 AAATCGTCTAGGGCTTCGGC 60.179 55.000 0.00 0.00 40.88 5.54
1307 1338 3.304911 TCGGAGTCTTGAGATCTCCAT 57.695 47.619 20.03 1.33 45.51 3.41
1309 1340 4.026744 TCGGAGTCTTGAGATCTCCATTT 58.973 43.478 20.03 2.13 45.51 2.32
1315 1346 0.530650 TGAGATCTCCATTTCGCCGC 60.531 55.000 20.03 0.00 0.00 6.53
1334 1365 1.372997 CGCCCGCTAATATGTCGCT 60.373 57.895 0.00 0.00 0.00 4.93
1365 1396 0.321122 AGTCAGGAAAGAAGCCGCTG 60.321 55.000 0.00 0.00 0.00 5.18
1450 2666 1.453379 CCGAAGCCTACCTCCGAGA 60.453 63.158 0.00 0.00 0.00 4.04
1524 2740 2.342279 CAGTTGAAGACGGCGGGA 59.658 61.111 13.24 0.00 0.00 5.14
1641 2868 1.684450 GAAGGAGAGGATTCCGAGGAC 59.316 57.143 0.00 0.00 42.29 3.85
1653 2880 2.026879 GAGGACGATGCCGAGCTC 59.973 66.667 2.73 2.73 39.50 4.09
1764 2991 4.469945 CCATCCCCTAGTACTCTGTTTGAA 59.530 45.833 0.00 0.00 0.00 2.69
1842 3069 7.414098 GGTGATAACAAATATCTCGTGCACTTT 60.414 37.037 16.19 4.43 40.96 2.66
1845 3072 4.072131 ACAAATATCTCGTGCACTTTGGT 58.928 39.130 23.00 10.46 0.00 3.67
1854 3081 2.644992 CACTTTGGTTGCGAGGCC 59.355 61.111 0.00 0.00 0.00 5.19
1968 3195 4.899502 ACTACAAGTTGGACAAGATGAGG 58.100 43.478 7.96 0.00 0.00 3.86
1986 3213 1.890979 GATCTGGGTGCGCATCCTG 60.891 63.158 37.76 35.72 31.21 3.86
2070 3297 1.327303 TTTTGCAAATGGAGCTCGGT 58.673 45.000 13.65 0.00 0.00 4.69
2079 3306 1.137825 GGAGCTCGGTGAGAAGACG 59.862 63.158 7.83 0.00 0.00 4.18
2088 3315 1.207329 GGTGAGAAGACGGGCAACTAT 59.793 52.381 0.00 0.00 0.00 2.12
2098 3325 0.673644 GGGCAACTATGTGCGTGTCT 60.674 55.000 0.00 0.00 45.91 3.41
2277 3515 4.766272 CGGAAGGTGAGAGGAGGA 57.234 61.111 0.00 0.00 0.00 3.71
2337 3576 4.697756 CCACGCCGCTTTGGGAGA 62.698 66.667 0.73 0.00 38.63 3.71
2418 3657 1.228583 AGAGAGCACAGGGTCGTCA 60.229 57.895 0.00 0.00 46.06 4.35
2496 3741 0.542333 ATGCAGCAGATCACAGCTCT 59.458 50.000 0.00 0.00 36.76 4.09
2704 5618 2.530177 CGCTGCGTAATCTTTCTCAGA 58.470 47.619 14.93 0.00 35.33 3.27
2745 5659 0.033601 ACCTCTCTGATGGCGTCTCT 60.034 55.000 8.40 0.00 0.00 3.10
2789 5703 0.671781 GGTGATCAAGTCGCTGCTGT 60.672 55.000 0.00 0.00 37.50 4.40
2843 5757 7.654520 GGTGATTTATGCTAATACGTCCAGTAA 59.345 37.037 0.00 0.00 39.04 2.24
2937 5851 0.327259 ATGGCGATGGGATGATGGAG 59.673 55.000 0.00 0.00 0.00 3.86
3046 5960 6.498303 TCAGGAGCAATGAATATCCTAAGCTA 59.502 38.462 0.00 0.00 40.23 3.32
3059 5973 0.460311 TAAGCTAGAACTGCCGAGGC 59.540 55.000 7.26 7.26 42.35 4.70
3145 6060 5.437060 TGTTTTTCTTTGTGAGACTAGGCT 58.563 37.500 0.00 0.00 33.02 4.58
3151 6066 4.459685 TCTTTGTGAGACTAGGCTGTCTAC 59.540 45.833 0.42 14.42 46.11 2.59
3193 6108 0.803117 GCTCGGTTGGGTTTAAGAGC 59.197 55.000 0.00 0.00 43.11 4.09
3223 6138 2.816204 TTCGATTGTGTGGGTCGTAA 57.184 45.000 0.00 0.00 36.77 3.18
3347 6283 3.832237 CTGGCGGCTCACCTGTGTT 62.832 63.158 11.43 0.00 0.00 3.32
3615 6551 1.033202 ACGGGCAAACGTCAAGGTTT 61.033 50.000 0.00 0.00 45.08 3.27
3660 6596 2.673775 TGCTTGGAGGGATGTTTTCA 57.326 45.000 0.00 0.00 0.00 2.69
3683 6619 1.134907 CATGCAAGGGTGGAGCATTTC 60.135 52.381 0.00 0.00 45.98 2.17
3704 6640 2.590007 GCGCCAAGCTCCGATCAT 60.590 61.111 0.00 0.00 44.04 2.45
3791 6728 0.971386 ACGAGGTTATGTGGGAACGT 59.029 50.000 0.00 0.00 0.00 3.99
3863 6800 7.283127 GGCTCTATGTTGAATCTTGGTGATTTA 59.717 37.037 0.00 0.00 44.70 1.40
4003 6940 6.888105 TGAATGCAGATAGAAAGGACATACA 58.112 36.000 0.00 0.00 0.00 2.29
4012 6949 1.794714 AAGGACATACAGGAGGCGAT 58.205 50.000 0.00 0.00 0.00 4.58
4013 6950 1.043816 AGGACATACAGGAGGCGATG 58.956 55.000 0.00 0.00 0.00 3.84
4028 6965 1.739035 GCGATGGACAGGATGAACGAA 60.739 52.381 0.00 0.00 39.69 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.597854 CTCTTCCACAGCAACGGCA 60.598 57.895 0.00 0.00 44.61 5.69
130 131 4.139786 CCCATAATTGGTGAGTGATGAGG 58.860 47.826 0.00 0.00 41.91 3.86
190 194 1.750778 CACGCCTCCAAAGCCATTAAT 59.249 47.619 0.00 0.00 0.00 1.40
192 196 0.679640 CCACGCCTCCAAAGCCATTA 60.680 55.000 0.00 0.00 0.00 1.90
244 248 0.179054 GTTAAGGAAGGCGGCTAGGG 60.179 60.000 13.71 0.00 0.00 3.53
246 250 2.280628 CTTGTTAAGGAAGGCGGCTAG 58.719 52.381 13.71 0.00 0.00 3.42
247 251 1.677820 GCTTGTTAAGGAAGGCGGCTA 60.678 52.381 13.71 0.00 0.00 3.93
248 252 0.960861 GCTTGTTAAGGAAGGCGGCT 60.961 55.000 5.25 5.25 0.00 5.52
249 253 1.506718 GCTTGTTAAGGAAGGCGGC 59.493 57.895 0.00 0.00 0.00 6.53
250 254 1.313091 GGGCTTGTTAAGGAAGGCGG 61.313 60.000 12.19 0.00 44.78 6.13
251 255 0.322546 AGGGCTTGTTAAGGAAGGCG 60.323 55.000 12.19 0.00 44.78 5.52
252 256 1.464734 GAGGGCTTGTTAAGGAAGGC 58.535 55.000 10.73 10.73 43.49 4.35
253 257 1.278127 TCGAGGGCTTGTTAAGGAAGG 59.722 52.381 0.00 0.00 0.00 3.46
254 258 2.622436 CTCGAGGGCTTGTTAAGGAAG 58.378 52.381 3.91 0.00 0.00 3.46
255 259 1.338769 GCTCGAGGGCTTGTTAAGGAA 60.339 52.381 15.58 0.00 0.00 3.36
256 260 0.249398 GCTCGAGGGCTTGTTAAGGA 59.751 55.000 15.58 0.00 0.00 3.36
257 261 0.744771 GGCTCGAGGGCTTGTTAAGG 60.745 60.000 15.58 0.00 37.53 2.69
258 262 2.768834 GGCTCGAGGGCTTGTTAAG 58.231 57.895 15.58 0.00 37.53 1.85
266 270 2.124942 CAAAGGAGGCTCGAGGGC 60.125 66.667 15.58 7.43 41.20 5.19
267 271 2.124942 GCAAAGGAGGCTCGAGGG 60.125 66.667 15.58 0.00 0.00 4.30
268 272 2.510238 CGCAAAGGAGGCTCGAGG 60.510 66.667 15.58 0.00 0.00 4.63
269 273 3.191539 GCGCAAAGGAGGCTCGAG 61.192 66.667 8.45 8.45 0.00 4.04
270 274 3.529341 TTGCGCAAAGGAGGCTCGA 62.529 57.895 22.78 0.00 0.00 4.04
271 275 3.049674 TTGCGCAAAGGAGGCTCG 61.050 61.111 22.78 0.00 0.00 5.03
272 276 2.563427 GTTGCGCAAAGGAGGCTC 59.437 61.111 26.87 5.78 0.00 4.70
273 277 2.985847 GGTTGCGCAAAGGAGGCT 60.986 61.111 26.87 0.00 0.00 4.58
274 278 2.985847 AGGTTGCGCAAAGGAGGC 60.986 61.111 26.87 11.21 0.00 4.70
275 279 0.962356 ATCAGGTTGCGCAAAGGAGG 60.962 55.000 26.87 12.86 0.00 4.30
276 280 0.883833 AATCAGGTTGCGCAAAGGAG 59.116 50.000 26.87 15.02 0.00 3.69
277 281 0.881118 GAATCAGGTTGCGCAAAGGA 59.119 50.000 26.87 21.61 0.00 3.36
278 282 0.883833 AGAATCAGGTTGCGCAAAGG 59.116 50.000 26.87 16.93 0.00 3.11
279 283 1.536766 TCAGAATCAGGTTGCGCAAAG 59.463 47.619 26.87 17.62 0.00 2.77
280 284 1.536766 CTCAGAATCAGGTTGCGCAAA 59.463 47.619 26.87 9.95 0.00 3.68
281 285 1.159285 CTCAGAATCAGGTTGCGCAA 58.841 50.000 21.02 21.02 0.00 4.85
282 286 1.300971 GCTCAGAATCAGGTTGCGCA 61.301 55.000 5.66 5.66 0.00 6.09
300 304 2.974698 CCCGCTGAATCCATCCGC 60.975 66.667 0.00 0.00 35.16 5.54
333 337 3.386402 TCTTGGGTTCAAAATTTTCGGCT 59.614 39.130 0.00 0.00 31.77 5.52
677 706 1.631405 CAAGGGGCTGTTTGGATTCA 58.369 50.000 0.00 0.00 0.00 2.57
696 725 2.285773 CCTTTTGGGGCAGAAGGGC 61.286 63.158 0.00 0.00 40.62 5.19
748 777 9.900710 TTAGATAAACACAAAATATGTTGCGTT 57.099 25.926 6.25 6.25 41.46 4.84
949 980 2.941064 AGACTTGCCGAACATGATCATG 59.059 45.455 29.95 29.95 44.15 3.07
957 988 2.325583 AAGTTCAGACTTGCCGAACA 57.674 45.000 0.00 0.00 44.27 3.18
958 989 2.354821 ACAAAGTTCAGACTTGCCGAAC 59.645 45.455 0.00 0.00 45.18 3.95
959 990 2.639065 ACAAAGTTCAGACTTGCCGAA 58.361 42.857 0.00 0.00 45.18 4.30
960 991 2.325583 ACAAAGTTCAGACTTGCCGA 57.674 45.000 0.00 0.00 45.18 5.54
961 992 2.541588 CCAACAAAGTTCAGACTTGCCG 60.542 50.000 0.00 0.00 45.18 5.69
962 993 2.799562 GCCAACAAAGTTCAGACTTGCC 60.800 50.000 0.00 0.00 45.18 4.52
963 994 2.099756 AGCCAACAAAGTTCAGACTTGC 59.900 45.455 0.00 0.00 45.18 4.01
964 995 3.243201 GGAGCCAACAAAGTTCAGACTTG 60.243 47.826 0.00 0.00 45.18 3.16
966 997 2.576615 GGAGCCAACAAAGTTCAGACT 58.423 47.619 0.00 0.00 37.87 3.24
967 998 1.264288 CGGAGCCAACAAAGTTCAGAC 59.736 52.381 0.00 0.00 0.00 3.51
968 999 1.593196 CGGAGCCAACAAAGTTCAGA 58.407 50.000 0.00 0.00 0.00 3.27
1060 1091 0.681733 GAAGAGAGGCCACACACAGA 59.318 55.000 5.01 0.00 0.00 3.41
1074 1105 2.815647 GGCTTGGACGCGGAAGAG 60.816 66.667 12.47 4.13 0.00 2.85
1075 1106 4.388499 GGGCTTGGACGCGGAAGA 62.388 66.667 12.47 0.00 0.00 2.87
1167 1198 1.298713 CGATCTTGACTCGGAGGCG 60.299 63.158 10.23 0.00 32.58 5.52
1219 1250 6.882458 AGACGATTTTATGGAGTCGTTTAC 57.118 37.500 0.66 0.00 46.07 2.01
1224 1255 4.547532 CCCTAGACGATTTTATGGAGTCG 58.452 47.826 0.00 0.00 39.78 4.18
1247 1278 0.320946 TTTTGGTAGACCCGCCGAAG 60.321 55.000 0.00 0.00 35.15 3.79
1253 1284 1.528161 GTTGTCGTTTTGGTAGACCCG 59.472 52.381 0.00 0.00 35.15 5.28
1295 1326 1.939974 CGGCGAAATGGAGATCTCAA 58.060 50.000 23.85 14.13 0.00 3.02
1315 1346 2.380410 GCGACATATTAGCGGGCGG 61.380 63.158 0.00 0.00 0.00 6.13
1497 2713 4.261801 CCGTCTTCAACTGGTTCCATATT 58.738 43.478 0.00 0.00 0.00 1.28
1589 2816 1.764854 GGGCCTTCCTCATACCGGA 60.765 63.158 9.46 0.00 0.00 5.14
1594 2821 1.459539 CCTCCGGGCCTTCCTCATA 60.460 63.158 0.84 0.00 0.00 2.15
1641 2868 4.193334 TCCACGAGCTCGGCATCG 62.193 66.667 36.93 19.95 44.95 3.84
1653 2880 1.213013 CTCCAAGTCGACCTCCACG 59.787 63.158 13.01 0.00 0.00 4.94
1692 2919 1.539869 AGTCCATGGGTGCTCCTGT 60.540 57.895 13.02 0.00 36.20 4.00
1764 2991 4.613437 ACCTCCAACCATCTGCAATATTT 58.387 39.130 0.00 0.00 0.00 1.40
1842 3069 4.015406 ATGTCGGCCTCGCAACCA 62.015 61.111 0.00 0.00 36.13 3.67
1845 3072 2.434185 GACATGTCGGCCTCGCAA 60.434 61.111 10.69 0.00 36.13 4.85
1854 3081 2.175530 GTAGGACACGAGACATGTCG 57.824 55.000 19.85 12.52 46.19 4.35
1968 3195 1.890979 CAGGATGCGCACCCAGATC 60.891 63.158 26.19 11.08 0.00 2.75
1986 3213 2.496942 CCAGTTCATGGGCACATCC 58.503 57.895 0.00 0.00 46.36 3.51
2070 3297 1.899814 ACATAGTTGCCCGTCTTCTCA 59.100 47.619 0.00 0.00 0.00 3.27
2079 3306 0.673644 AGACACGCACATAGTTGCCC 60.674 55.000 0.00 0.00 39.53 5.36
2088 3315 4.927782 GCCACCCAGACACGCACA 62.928 66.667 0.00 0.00 0.00 4.57
2277 3515 2.370189 GCTATACTTGCCAGATGGAGGT 59.630 50.000 2.18 0.47 37.39 3.85
2337 3576 1.810412 GCTTTCACTGTTCCGGACTGT 60.810 52.381 1.83 7.20 40.59 3.55
2496 3741 0.893270 CATCAACGGCAGGGTTTCCA 60.893 55.000 0.00 0.00 34.83 3.53
2595 3840 0.796312 GTACCTGAACATGCACGTGG 59.204 55.000 18.88 2.89 0.00 4.94
2704 5618 5.338365 GTCTACGTCGTCCATATTCACTTT 58.662 41.667 0.00 0.00 0.00 2.66
2760 5674 4.783621 TGATCACCAGCAGCGGCC 62.784 66.667 4.82 0.00 42.56 6.13
2789 5703 3.107975 TAGCCTCCTCCCCGCCTA 61.108 66.667 0.00 0.00 0.00 3.93
2843 5757 0.468226 TGAAACCACAAGCTCGTCCT 59.532 50.000 0.00 0.00 0.00 3.85
2937 5851 2.436646 CCGTCCACCATGTCCTGC 60.437 66.667 0.00 0.00 0.00 4.85
3145 6060 7.977853 GGTACCTCTTCATTTTATTCGTAGACA 59.022 37.037 4.06 0.00 34.32 3.41
3151 6066 5.501897 GCACGGTACCTCTTCATTTTATTCG 60.502 44.000 10.90 0.00 0.00 3.34
3182 6097 4.790765 AGCATCAAAAGCTCTTAAACCC 57.209 40.909 0.00 0.00 38.01 4.11
3193 6108 4.383649 CCACACAATCGAAAGCATCAAAAG 59.616 41.667 0.00 0.00 0.00 2.27
3223 6138 4.019174 CCAATACAAAGCAAGACCTCCAT 58.981 43.478 0.00 0.00 0.00 3.41
3347 6283 1.226859 CGTTCGAGGCTCGCCATAA 60.227 57.895 31.01 17.59 40.21 1.90
3615 6551 1.821759 CCACAACACGGTCAAGGCA 60.822 57.895 0.00 0.00 0.00 4.75
3704 6640 1.075601 ACTTGAGGAGGATGGCCAAA 58.924 50.000 10.96 0.00 36.29 3.28
3791 6728 2.874245 TCAGGGAGGGAGGGGTCA 60.874 66.667 0.00 0.00 0.00 4.02
3861 6798 7.914427 TCATATTTCCTAGTCCAGAAGCTAA 57.086 36.000 0.00 0.00 0.00 3.09
3863 6800 6.556495 TCATCATATTTCCTAGTCCAGAAGCT 59.444 38.462 0.00 0.00 0.00 3.74
4003 6940 1.074926 ATCCTGTCCATCGCCTCCT 60.075 57.895 0.00 0.00 0.00 3.69
4012 6949 1.608025 GCAGTTCGTTCATCCTGTCCA 60.608 52.381 0.00 0.00 0.00 4.02
4013 6950 1.079503 GCAGTTCGTTCATCCTGTCC 58.920 55.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.