Multiple sequence alignment - TraesCS7A01G399400

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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 TraesCS7A01G399400 chr7A 100.000 4010 0 0 1 4010 579345842 579341833 0.000000e+00 7406
1 TraesCS7A01G399400 chr7A 86.700 3045 379 12 950 3992 579495599 579498619 0.000000e+00 3356
2 TraesCS7A01G399400 chr7A 84.772 2988 409 32 1058 4007 579598420 579601399 0.000000e+00 2955
3 TraesCS7A01G399400 chr7A 97.222 108 3 0 675 782 586353405 586353298 2.460000e-42 183
4 TraesCS7A01G399400 chr7B 84.221 3156 453 24 857 3978 536989230 536992374 0.000000e+00 3027
5 TraesCS7A01G399400 chr7B 87.415 2360 278 15 1159 3512 537214399 537216745 0.000000e+00 2695
6 TraesCS7A01G399400 chr7B 97.653 1491 34 1 2517 4007 537162858 537164347 0.000000e+00 2558
7 TraesCS7A01G399400 chr7B 86.772 378 50 0 3498 3875 537217898 537218275 4.790000e-114 422
8 TraesCS7A01G399400 chr7B 89.720 214 22 0 958 1171 537210821 537211034 1.420000e-69 274
9 TraesCS7A01G399400 chr7B 94.531 128 5 1 657 782 253202377 253202504 3.160000e-46 196
10 TraesCS7A01G399400 chr7D 89.499 1695 178 0 2312 4006 508881296 508882990 0.000000e+00 2145
11 TraesCS7A01G399400 chr7D 87.739 1362 159 5 958 2315 508832041 508833398 0.000000e+00 1583
12 TraesCS7A01G399400 chr7D 85.084 657 47 19 110 734 176351925 176352562 1.220000e-174 623
13 TraesCS7A01G399400 chr3A 93.814 582 18 5 1 574 523842139 523841568 0.000000e+00 859
14 TraesCS7A01G399400 chr5D 86.257 764 44 24 53 782 178522384 178523120 0.000000e+00 773
15 TraesCS7A01G399400 chr1A 86.344 703 61 23 110 782 1841535 1842232 0.000000e+00 734
16 TraesCS7A01G399400 chr2A 86.182 702 57 24 114 782 578648470 578647776 0.000000e+00 723
17 TraesCS7A01G399400 chr2A 96.842 95 1 2 689 782 25676425 25676518 1.490000e-34 158
18 TraesCS7A01G399400 chr3B 84.825 659 48 20 99 724 16396543 16397182 2.050000e-172 616
19 TraesCS7A01G399400 chr3B 84.524 420 36 15 159 552 534103498 534103914 4.860000e-104 388
20 TraesCS7A01G399400 chr3B 90.741 162 14 1 542 703 534104270 534104430 8.730000e-52 215
21 TraesCS7A01G399400 chr3B 91.743 109 7 1 676 782 772129787 772129895 2.500000e-32 150
22 TraesCS7A01G399400 chr2D 93.636 110 7 0 673 782 563200471 563200580 8.920000e-37 165
23 TraesCS7A01G399400 chr4D 98.876 89 1 0 694 782 47736246 47736334 4.150000e-35 159
24 TraesCS7A01G399400 chr4D 90.000 120 12 0 659 778 302044921 302045040 5.370000e-34 156
25 TraesCS7A01G399400 chr3D 90.179 112 10 1 671 782 610965314 610965204 1.160000e-30 145


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 TraesCS7A01G399400 chr7A 579341833 579345842 4009 True 7406.000000 7406 100.0000 1 4010 1 chr7A.!!$R1 4009
1 TraesCS7A01G399400 chr7A 579495599 579498619 3020 False 3356.000000 3356 86.7000 950 3992 1 chr7A.!!$F1 3042
2 TraesCS7A01G399400 chr7A 579598420 579601399 2979 False 2955.000000 2955 84.7720 1058 4007 1 chr7A.!!$F2 2949
3 TraesCS7A01G399400 chr7B 536989230 536992374 3144 False 3027.000000 3027 84.2210 857 3978 1 chr7B.!!$F2 3121
4 TraesCS7A01G399400 chr7B 537162858 537164347 1489 False 2558.000000 2558 97.6530 2517 4007 1 chr7B.!!$F3 1490
5 TraesCS7A01G399400 chr7B 537210821 537218275 7454 False 1130.333333 2695 87.9690 958 3875 3 chr7B.!!$F4 2917
6 TraesCS7A01G399400 chr7D 508881296 508882990 1694 False 2145.000000 2145 89.4990 2312 4006 1 chr7D.!!$F3 1694
7 TraesCS7A01G399400 chr7D 508832041 508833398 1357 False 1583.000000 1583 87.7390 958 2315 1 chr7D.!!$F2 1357
8 TraesCS7A01G399400 chr7D 176351925 176352562 637 False 623.000000 623 85.0840 110 734 1 chr7D.!!$F1 624
9 TraesCS7A01G399400 chr3A 523841568 523842139 571 True 859.000000 859 93.8140 1 574 1 chr3A.!!$R1 573
10 TraesCS7A01G399400 chr5D 178522384 178523120 736 False 773.000000 773 86.2570 53 782 1 chr5D.!!$F1 729
11 TraesCS7A01G399400 chr1A 1841535 1842232 697 False 734.000000 734 86.3440 110 782 1 chr1A.!!$F1 672
12 TraesCS7A01G399400 chr2A 578647776 578648470 694 True 723.000000 723 86.1820 114 782 1 chr2A.!!$R1 668
13 TraesCS7A01G399400 chr3B 16396543 16397182 639 False 616.000000 616 84.8250 99 724 1 chr3B.!!$F1 625
14 TraesCS7A01G399400 chr3B 534103498 534104430 932 False 301.500000 388 87.6325 159 703 2 chr3B.!!$F3 544

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
801 1225 0.178068 GCAAGCCCGGATGAAGACTA 59.822 55.0 0.73 0.0 0.0 2.59 F
1328 5129 0.249657 GGCCTTCTCAGACGCATAGG 60.250 60.0 0.00 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 5422 0.601311 GTGTGCACCTCTGTCCTGAC 60.601 60.0 15.69 0.00 0.00 3.51 R
3184 7024 0.397564 TCCCTCGGTTGTACCAAACC 59.602 55.0 5.25 5.25 45.24 3.27 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
35 36 5.148502 TCCTAAATAACACCCCAGCAAAAA 58.851 37.500 0.00 0.00 0.00 1.94
87 88 2.384828 ACCTGACTGAGTGTGTGTGTA 58.615 47.619 0.00 0.00 0.00 2.90
106 107 4.250431 GTGTGGGTGTGCGTGTGC 62.250 66.667 0.00 0.00 43.20 4.57
208 214 7.298122 AGCATACTTTAAATCACGTTCACAAG 58.702 34.615 0.00 0.00 0.00 3.16
247 253 7.724061 ACAAATAAAGTTGACCCATTCTACACT 59.276 33.333 0.00 0.00 32.82 3.55
335 347 3.315470 GCTAAAATCGCTCCCCCTTTTAG 59.685 47.826 8.54 8.54 41.11 1.85
369 407 7.741785 TCGGGGTGATGTAAAATAATGAGTAT 58.258 34.615 0.00 0.00 0.00 2.12
425 463 4.376340 AAATTCGGCTGCTTTAATCCTG 57.624 40.909 0.00 0.00 0.00 3.86
554 974 2.288030 GGCGTACGTAGGTATGAAGCAT 60.288 50.000 17.90 0.00 37.77 3.79
605 1025 4.402155 TCAATGGAGGTATCATTGCCAAAC 59.598 41.667 10.79 0.00 46.45 2.93
629 1049 3.086282 AGCCCTATTTGTTAACGGGTTG 58.914 45.455 14.68 0.47 37.24 3.77
657 1077 3.877508 AGTAATTCGCCAGCCATCTTAAC 59.122 43.478 0.00 0.00 0.00 2.01
665 1085 3.740832 GCCAGCCATCTTAACAACAAAAC 59.259 43.478 0.00 0.00 0.00 2.43
795 1219 6.686484 ATATATATATGCAAGCCCGGATGA 57.314 37.500 0.73 0.00 0.00 2.92
796 1220 3.719268 ATATATGCAAGCCCGGATGAA 57.281 42.857 0.73 0.00 0.00 2.57
797 1221 1.901591 ATATGCAAGCCCGGATGAAG 58.098 50.000 0.73 0.00 0.00 3.02
798 1222 0.836606 TATGCAAGCCCGGATGAAGA 59.163 50.000 0.73 0.00 0.00 2.87
799 1223 0.749454 ATGCAAGCCCGGATGAAGAC 60.749 55.000 0.73 0.00 0.00 3.01
800 1224 1.078143 GCAAGCCCGGATGAAGACT 60.078 57.895 0.73 0.00 0.00 3.24
801 1225 0.178068 GCAAGCCCGGATGAAGACTA 59.822 55.000 0.73 0.00 0.00 2.59
802 1226 1.202698 GCAAGCCCGGATGAAGACTAT 60.203 52.381 0.73 0.00 0.00 2.12
803 1227 2.760374 CAAGCCCGGATGAAGACTATC 58.240 52.381 0.73 0.00 0.00 2.08
804 1228 2.088104 AGCCCGGATGAAGACTATCA 57.912 50.000 0.73 0.00 0.00 2.15
805 1229 2.398588 AGCCCGGATGAAGACTATCAA 58.601 47.619 0.73 0.00 32.06 2.57
806 1230 2.366916 AGCCCGGATGAAGACTATCAAG 59.633 50.000 0.73 0.00 32.06 3.02
807 1231 2.103263 GCCCGGATGAAGACTATCAAGT 59.897 50.000 0.73 0.00 39.21 3.16
808 1232 3.722147 CCCGGATGAAGACTATCAAGTG 58.278 50.000 0.73 0.00 35.56 3.16
809 1233 3.133003 CCCGGATGAAGACTATCAAGTGT 59.867 47.826 0.73 0.00 35.56 3.55
810 1234 4.115516 CCGGATGAAGACTATCAAGTGTG 58.884 47.826 0.00 0.00 35.56 3.82
811 1235 4.142160 CCGGATGAAGACTATCAAGTGTGA 60.142 45.833 0.00 0.00 35.56 3.58
812 1236 4.800993 CGGATGAAGACTATCAAGTGTGAC 59.199 45.833 0.00 0.00 36.31 3.67
813 1237 5.393569 CGGATGAAGACTATCAAGTGTGACT 60.394 44.000 0.00 0.00 36.31 3.41
814 1238 6.402222 GGATGAAGACTATCAAGTGTGACTT 58.598 40.000 0.00 0.00 39.39 3.01
815 1239 6.876257 GGATGAAGACTATCAAGTGTGACTTT 59.124 38.462 0.00 0.00 36.03 2.66
816 1240 7.148507 GGATGAAGACTATCAAGTGTGACTTTG 60.149 40.741 0.00 0.00 36.03 2.77
817 1241 6.816136 TGAAGACTATCAAGTGTGACTTTGA 58.184 36.000 5.77 5.77 36.03 2.69
818 1242 7.272244 TGAAGACTATCAAGTGTGACTTTGAA 58.728 34.615 7.07 0.00 36.03 2.69
819 1243 7.768582 TGAAGACTATCAAGTGTGACTTTGAAA 59.231 33.333 7.07 0.00 36.03 2.69
820 1244 7.721286 AGACTATCAAGTGTGACTTTGAAAG 57.279 36.000 2.89 2.89 36.03 2.62
821 1245 7.500992 AGACTATCAAGTGTGACTTTGAAAGA 58.499 34.615 12.53 0.00 36.03 2.52
822 1246 8.153550 AGACTATCAAGTGTGACTTTGAAAGAT 58.846 33.333 12.53 0.00 36.03 2.40
823 1247 8.316640 ACTATCAAGTGTGACTTTGAAAGATC 57.683 34.615 12.53 6.29 36.03 2.75
824 1248 7.933577 ACTATCAAGTGTGACTTTGAAAGATCA 59.066 33.333 12.53 8.75 36.03 2.92
825 1249 6.363577 TCAAGTGTGACTTTGAAAGATCAC 57.636 37.500 22.27 22.27 36.03 3.06
826 1250 5.296780 TCAAGTGTGACTTTGAAAGATCACC 59.703 40.000 24.23 18.80 36.03 4.02
827 1251 4.780815 AGTGTGACTTTGAAAGATCACCA 58.219 39.130 24.23 15.82 38.06 4.17
828 1252 4.818546 AGTGTGACTTTGAAAGATCACCAG 59.181 41.667 24.23 0.00 38.06 4.00
829 1253 4.576463 GTGTGACTTTGAAAGATCACCAGT 59.424 41.667 24.23 1.16 38.06 4.00
830 1254 5.066505 GTGTGACTTTGAAAGATCACCAGTT 59.933 40.000 24.23 0.11 38.06 3.16
831 1255 5.066375 TGTGACTTTGAAAGATCACCAGTTG 59.934 40.000 24.23 0.00 38.06 3.16
832 1256 5.296780 GTGACTTTGAAAGATCACCAGTTGA 59.703 40.000 20.20 0.00 39.11 3.18
834 1258 6.547141 TGACTTTGAAAGATCACCAGTTGATT 59.453 34.615 12.53 0.00 45.67 2.57
835 1259 7.068593 TGACTTTGAAAGATCACCAGTTGATTT 59.931 33.333 12.53 0.00 45.67 2.17
836 1260 8.463930 ACTTTGAAAGATCACCAGTTGATTTA 57.536 30.769 12.53 0.00 45.67 1.40
837 1261 9.082313 ACTTTGAAAGATCACCAGTTGATTTAT 57.918 29.630 12.53 0.00 45.67 1.40
840 1264 9.739276 TTGAAAGATCACCAGTTGATTTATACT 57.261 29.630 0.00 0.00 45.67 2.12
876 1300 5.187186 TGGTCTACAACTTACTTGATCCTCC 59.813 44.000 0.00 0.00 33.59 4.30
878 1302 5.014858 TCTACAACTTACTTGATCCTCCGT 58.985 41.667 0.00 0.00 33.59 4.69
881 1305 2.973945 ACTTACTTGATCCTCCGTTGC 58.026 47.619 0.00 0.00 0.00 4.17
883 1307 3.244422 ACTTACTTGATCCTCCGTTGCAA 60.244 43.478 0.00 0.00 0.00 4.08
884 1308 1.813513 ACTTGATCCTCCGTTGCAAG 58.186 50.000 0.00 0.00 41.15 4.01
887 1311 0.250684 TGATCCTCCGTTGCAAGCAA 60.251 50.000 0.00 2.89 0.00 3.91
897 1321 3.374745 CGTTGCAAGCAAGTTTCTGAAT 58.625 40.909 7.88 0.00 36.52 2.57
900 1324 5.630680 CGTTGCAAGCAAGTTTCTGAATATT 59.369 36.000 7.88 0.00 36.52 1.28
902 1326 6.330004 TGCAAGCAAGTTTCTGAATATTCA 57.670 33.333 17.07 17.07 35.57 2.57
918 1342 8.887036 TGAATATTCAGTAGTTGTGCGATATT 57.113 30.769 14.23 0.00 32.50 1.28
922 1346 9.982651 ATATTCAGTAGTTGTGCGATATTTAGT 57.017 29.630 0.00 0.00 0.00 2.24
923 1347 8.718102 ATTCAGTAGTTGTGCGATATTTAGTT 57.282 30.769 0.00 0.00 0.00 2.24
924 1348 7.520119 TCAGTAGTTGTGCGATATTTAGTTG 57.480 36.000 0.00 0.00 0.00 3.16
926 1350 8.245491 TCAGTAGTTGTGCGATATTTAGTTGTA 58.755 33.333 0.00 0.00 0.00 2.41
927 1351 9.031360 CAGTAGTTGTGCGATATTTAGTTGTAT 57.969 33.333 0.00 0.00 0.00 2.29
928 1352 9.031360 AGTAGTTGTGCGATATTTAGTTGTATG 57.969 33.333 0.00 0.00 0.00 2.39
931 1355 8.175069 AGTTGTGCGATATTTAGTTGTATGTTG 58.825 33.333 0.00 0.00 0.00 3.33
932 1356 6.482835 TGTGCGATATTTAGTTGTATGTTGC 58.517 36.000 0.00 0.00 0.00 4.17
933 1357 6.092807 TGTGCGATATTTAGTTGTATGTTGCA 59.907 34.615 0.00 0.00 32.10 4.08
934 1358 6.964370 GTGCGATATTTAGTTGTATGTTGCAA 59.036 34.615 0.00 0.00 35.09 4.08
935 1359 6.964370 TGCGATATTTAGTTGTATGTTGCAAC 59.036 34.615 22.83 22.83 44.57 4.17
947 1371 3.222173 TGTTGCAACTGGTTATCCACT 57.778 42.857 28.61 0.00 39.03 4.00
948 1372 3.146066 TGTTGCAACTGGTTATCCACTC 58.854 45.455 28.61 0.00 39.03 3.51
949 1373 3.181445 TGTTGCAACTGGTTATCCACTCT 60.181 43.478 28.61 0.00 39.03 3.24
950 1374 4.041075 TGTTGCAACTGGTTATCCACTCTA 59.959 41.667 28.61 1.09 39.03 2.43
953 1377 5.914033 TGCAACTGGTTATCCACTCTATAC 58.086 41.667 0.00 0.00 39.03 1.47
954 1378 5.661312 TGCAACTGGTTATCCACTCTATACT 59.339 40.000 0.00 0.00 39.03 2.12
955 1379 6.837048 TGCAACTGGTTATCCACTCTATACTA 59.163 38.462 0.00 0.00 39.03 1.82
956 1380 7.146648 GCAACTGGTTATCCACTCTATACTAC 58.853 42.308 0.00 0.00 39.03 2.73
1008 1432 7.121315 GGAATATTCCTTGATTACATGGCTACC 59.879 40.741 24.74 0.00 44.11 3.18
1179 4980 1.002430 CTCCTTGTAGTTGGAGCAGCA 59.998 52.381 0.00 0.00 42.62 4.41
1202 5003 2.479566 AGGCAACATGTAGTGGACAG 57.520 50.000 0.00 0.00 42.79 3.51
1219 5020 8.723942 AGTGGACAGAAATCAGATATTGTTAC 57.276 34.615 0.00 0.00 0.00 2.50
1227 5028 6.615264 AATCAGATATTGTTACTGCAGCAG 57.385 37.500 21.54 21.54 37.52 4.24
1260 5061 4.505808 CAGTCTCTGATGCAGAAGATGTT 58.494 43.478 1.85 0.00 40.18 2.71
1276 5077 7.754027 CAGAAGATGTTTTGGATGAGTTTGATC 59.246 37.037 0.00 0.00 0.00 2.92
1298 5099 9.466497 TGATCATATGCTTTTAAAAGAGAAGGT 57.534 29.630 28.11 11.51 38.28 3.50
1328 5129 0.249657 GGCCTTCTCAGACGCATAGG 60.250 60.000 0.00 0.00 0.00 2.57
1341 5142 1.686052 CGCATAGGCTCCTCTTCTCTT 59.314 52.381 0.00 0.00 38.10 2.85
1345 5146 4.740334 GCATAGGCTCCTCTTCTCTTTCTG 60.740 50.000 0.00 0.00 36.96 3.02
1357 5158 3.650139 TCTCTTTCTGTTGGTAAGCGTC 58.350 45.455 0.00 0.00 0.00 5.19
1365 5166 1.529865 GTTGGTAAGCGTCTGGTCAAC 59.470 52.381 0.00 0.00 0.00 3.18
1413 5214 3.222603 GAAGGTCCTCAAAAGCTTGGAA 58.777 45.455 0.00 0.00 34.77 3.53
1416 5217 2.297315 GGTCCTCAAAAGCTTGGAAAGG 59.703 50.000 0.00 5.42 46.35 3.11
1423 5224 4.827284 TCAAAAGCTTGGAAAGGGTTAGAG 59.173 41.667 0.00 0.00 46.35 2.43
1434 5235 2.260822 AGGGTTAGAGCTTCTGCAGAA 58.739 47.619 26.87 26.87 42.74 3.02
1436 5237 2.744741 GGGTTAGAGCTTCTGCAGAAAC 59.255 50.000 28.16 24.00 42.74 2.78
1453 5254 1.508632 AACGTTTGTCCGAGTGATGG 58.491 50.000 0.00 0.00 0.00 3.51
1459 5260 1.026182 TGTCCGAGTGATGGCATTGC 61.026 55.000 0.00 0.00 0.00 3.56
1462 5263 1.721664 CCGAGTGATGGCATTGCAGG 61.722 60.000 11.39 0.00 0.00 4.85
1466 5267 1.305465 TGATGGCATTGCAGGGCTT 60.305 52.632 11.39 8.43 0.00 4.35
1483 5284 1.743394 GCTTTAACCCCATTCAGTCCG 59.257 52.381 0.00 0.00 0.00 4.79
1485 5286 3.620472 GCTTTAACCCCATTCAGTCCGTA 60.620 47.826 0.00 0.00 0.00 4.02
1499 5300 1.001633 GTCCGTACAATGTGTCCCAGT 59.998 52.381 0.00 0.00 0.00 4.00
1579 5380 4.385405 AGCTCGTGGGTCAGCTGC 62.385 66.667 9.47 4.04 44.58 5.25
1594 5395 5.470368 GTCAGCTGCTGTATAAATCCGATA 58.530 41.667 27.24 2.21 32.61 2.92
1601 5402 8.076178 GCTGCTGTATAAATCCGATAAATGTTT 58.924 33.333 0.00 0.00 0.00 2.83
1602 5403 9.385902 CTGCTGTATAAATCCGATAAATGTTTG 57.614 33.333 0.00 0.00 0.00 2.93
1604 5405 9.382244 GCTGTATAAATCCGATAAATGTTTGTC 57.618 33.333 0.00 0.00 0.00 3.18
1610 5411 7.524294 AATCCGATAAATGTTTGTCAAATGC 57.476 32.000 0.40 0.00 0.00 3.56
1612 5413 6.686630 TCCGATAAATGTTTGTCAAATGCTT 58.313 32.000 0.40 0.00 0.00 3.91
1614 5415 8.465999 TCCGATAAATGTTTGTCAAATGCTTAT 58.534 29.630 0.40 5.18 0.00 1.73
1619 5420 8.524870 AAATGTTTGTCAAATGCTTATCAGTC 57.475 30.769 0.40 0.00 0.00 3.51
1621 5422 4.944962 TTGTCAAATGCTTATCAGTCGG 57.055 40.909 0.00 0.00 0.00 4.79
1629 5430 1.476891 GCTTATCAGTCGGTCAGGACA 59.523 52.381 1.41 0.00 39.42 4.02
1749 5550 4.583073 AGAATGTGGGTTAGTGTTTCCAAC 59.417 41.667 0.00 0.00 0.00 3.77
1763 5564 6.934083 AGTGTTTCCAACAACTTTGACAAAAT 59.066 30.769 1.62 0.00 44.16 1.82
1768 5569 9.712305 TTTCCAACAACTTTGACAAAATTAGAA 57.288 25.926 1.62 0.00 0.00 2.10
1797 5600 6.656693 CCAAAGAGATCATATCATACCCAACC 59.343 42.308 0.00 0.00 0.00 3.77
1801 5604 7.126061 AGAGATCATATCATACCCAACCGATA 58.874 38.462 0.00 0.00 0.00 2.92
1819 5622 5.052481 CCGATAGTGAGAATGCTGAATTGA 58.948 41.667 0.00 0.00 0.00 2.57
1848 5651 7.448748 TTTTAATTTCAGTAAGCTCCAGGAC 57.551 36.000 0.00 0.00 0.00 3.85
1856 5659 3.444388 AGTAAGCTCCAGGACGAACTTAG 59.556 47.826 0.00 0.00 0.00 2.18
1959 5763 8.550710 ACAAACAAATGTGGATGGAAATAATG 57.449 30.769 0.00 0.00 30.82 1.90
1997 5828 2.171003 GTTTACAAGGCCAGGAAGCAT 58.829 47.619 5.01 0.00 0.00 3.79
2079 5910 5.179452 TCATTTTAGAAGGTCTGGGAAGG 57.821 43.478 0.00 0.00 0.00 3.46
2094 5925 3.053693 TGGGAAGGGATGATAGTTGGTTG 60.054 47.826 0.00 0.00 0.00 3.77
2097 5928 4.141482 GGAAGGGATGATAGTTGGTTGCTA 60.141 45.833 0.00 0.00 0.00 3.49
2160 5991 2.079925 CCAGAGTTGAAGCAGTTAGGC 58.920 52.381 0.00 0.00 0.00 3.93
2209 6040 2.838202 TCACCTCTAGCCCTAAAGGTTG 59.162 50.000 0.00 0.00 40.13 3.77
2217 6048 1.203013 GCCCTAAAGGTTGTTGGAGGT 60.203 52.381 0.00 0.00 38.26 3.85
2267 6098 4.006319 GAGTGGGAGGATGTTCTTCAAAG 58.994 47.826 0.00 0.00 0.00 2.77
2292 6123 8.102047 AGAGATGTCCTCAATCCAAATGATATC 58.898 37.037 0.00 0.00 44.40 1.63
2298 6129 7.718753 GTCCTCAATCCAAATGATATCTTGACT 59.281 37.037 3.98 0.00 31.83 3.41
2394 6225 6.753107 AAGGGTTACCGTATTGATTCAAAG 57.247 37.500 2.68 0.00 43.47 2.77
2567 6398 6.210796 ACGTTATGCATGATTCATTGAATGG 58.789 36.000 16.41 7.16 31.89 3.16
2568 6399 6.183360 ACGTTATGCATGATTCATTGAATGGT 60.183 34.615 16.41 2.39 31.89 3.55
2610 6441 1.342374 GGGGAATGCTTCAGGGTTGAT 60.342 52.381 0.00 0.00 32.27 2.57
2619 6459 0.994247 TCAGGGTTGATCATGGCAGT 59.006 50.000 0.00 0.00 0.00 4.40
2702 6542 4.777366 TCTTGTGAACTATGATGGTCTCCA 59.223 41.667 0.00 0.00 38.19 3.86
2901 6741 1.677518 CGCACTTATTACCCACTGCCA 60.678 52.381 0.00 0.00 0.00 4.92
2950 6790 7.728148 TCTACAGTCCTTGTTTGTGTTGTATA 58.272 34.615 0.00 0.00 41.29 1.47
2999 6839 2.719798 CTCAAACAAGTGGAAACAGCG 58.280 47.619 0.00 0.00 44.46 5.18
3008 6848 4.701956 AGTGGAAACAGCGGAAATATTG 57.298 40.909 0.00 0.00 44.46 1.90
3486 7326 6.035758 GGCTGAGAAGATTGAAATTGATTTGC 59.964 38.462 0.00 0.00 0.00 3.68
3629 8636 3.883669 CTGGATTCCCTTCTCTGGAAAG 58.116 50.000 0.00 0.00 44.64 2.62
4007 9014 5.918426 TTTGGCATTGATGAGCAGAATAA 57.082 34.783 0.00 0.00 0.00 1.40
4008 9015 6.474140 TTTGGCATTGATGAGCAGAATAAT 57.526 33.333 0.00 0.00 0.00 1.28
4009 9016 6.474140 TTGGCATTGATGAGCAGAATAATT 57.526 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 4.460683 ACACGCACACCCACACGT 62.461 61.111 0.00 0.00 39.78 4.49
106 107 4.918060 CACACGCACACGCACACG 62.918 66.667 0.00 0.00 45.53 4.49
425 463 3.013921 TCATGGCGTTCCTTTTATGGAC 58.986 45.455 0.00 0.00 35.58 4.02
605 1025 4.457466 ACCCGTTAACAAATAGGGCTATG 58.543 43.478 13.66 0.00 45.75 2.23
629 1049 0.733150 GCTGGCGAATTACTGGGTTC 59.267 55.000 0.00 0.00 0.00 3.62
657 1077 5.559427 TGGATCGTATCATGGTTTTGTTG 57.441 39.130 0.00 0.00 0.00 3.33
665 1085 1.148310 GCCGTTGGATCGTATCATGG 58.852 55.000 0.00 0.00 0.00 3.66
778 1202 1.421268 TCTTCATCCGGGCTTGCATAT 59.579 47.619 0.00 0.00 0.00 1.78
779 1203 0.836606 TCTTCATCCGGGCTTGCATA 59.163 50.000 0.00 0.00 0.00 3.14
780 1204 0.749454 GTCTTCATCCGGGCTTGCAT 60.749 55.000 0.00 0.00 0.00 3.96
781 1205 1.377202 GTCTTCATCCGGGCTTGCA 60.377 57.895 0.00 0.00 0.00 4.08
782 1206 0.178068 TAGTCTTCATCCGGGCTTGC 59.822 55.000 0.00 0.00 0.00 4.01
783 1207 2.103094 TGATAGTCTTCATCCGGGCTTG 59.897 50.000 0.00 0.00 0.00 4.01
784 1208 2.398588 TGATAGTCTTCATCCGGGCTT 58.601 47.619 0.00 0.00 0.00 4.35
785 1209 2.088104 TGATAGTCTTCATCCGGGCT 57.912 50.000 0.00 0.00 0.00 5.19
786 1210 2.103263 ACTTGATAGTCTTCATCCGGGC 59.897 50.000 0.00 0.00 0.00 6.13
787 1211 3.133003 ACACTTGATAGTCTTCATCCGGG 59.867 47.826 0.00 0.00 30.26 5.73
788 1212 4.115516 CACACTTGATAGTCTTCATCCGG 58.884 47.826 0.00 0.00 30.26 5.14
789 1213 4.800993 GTCACACTTGATAGTCTTCATCCG 59.199 45.833 0.00 0.00 33.11 4.18
790 1214 5.971763 AGTCACACTTGATAGTCTTCATCC 58.028 41.667 0.00 0.00 33.11 3.51
791 1215 7.600375 TCAAAGTCACACTTGATAGTCTTCATC 59.400 37.037 0.00 0.00 38.66 2.92
792 1216 7.445121 TCAAAGTCACACTTGATAGTCTTCAT 58.555 34.615 0.00 0.00 38.66 2.57
793 1217 6.816136 TCAAAGTCACACTTGATAGTCTTCA 58.184 36.000 0.00 0.00 38.66 3.02
794 1218 7.715265 TTCAAAGTCACACTTGATAGTCTTC 57.285 36.000 0.00 0.00 38.66 2.87
795 1219 7.987458 TCTTTCAAAGTCACACTTGATAGTCTT 59.013 33.333 0.00 0.00 38.66 3.01
796 1220 7.500992 TCTTTCAAAGTCACACTTGATAGTCT 58.499 34.615 0.00 0.00 38.66 3.24
797 1221 7.715265 TCTTTCAAAGTCACACTTGATAGTC 57.285 36.000 0.00 0.00 38.66 2.59
798 1222 7.933577 TGATCTTTCAAAGTCACACTTGATAGT 59.066 33.333 0.00 0.00 38.66 2.12
799 1223 8.226448 GTGATCTTTCAAAGTCACACTTGATAG 58.774 37.037 19.61 4.63 38.66 2.08
800 1224 7.173218 GGTGATCTTTCAAAGTCACACTTGATA 59.827 37.037 23.07 0.00 38.66 2.15
801 1225 6.016777 GGTGATCTTTCAAAGTCACACTTGAT 60.017 38.462 23.07 0.50 38.66 2.57
802 1226 5.296780 GGTGATCTTTCAAAGTCACACTTGA 59.703 40.000 23.07 0.00 38.66 3.02
803 1227 5.066375 TGGTGATCTTTCAAAGTCACACTTG 59.934 40.000 23.07 0.00 38.66 3.16
804 1228 5.192927 TGGTGATCTTTCAAAGTCACACTT 58.807 37.500 23.07 0.00 40.80 3.16
805 1229 4.780815 TGGTGATCTTTCAAAGTCACACT 58.219 39.130 23.07 0.00 39.31 3.55
806 1230 4.576463 ACTGGTGATCTTTCAAAGTCACAC 59.424 41.667 23.07 17.89 39.31 3.82
807 1231 4.780815 ACTGGTGATCTTTCAAAGTCACA 58.219 39.130 23.07 14.06 39.31 3.58
808 1232 5.296780 TCAACTGGTGATCTTTCAAAGTCAC 59.703 40.000 17.70 17.70 38.09 3.67
809 1233 5.436175 TCAACTGGTGATCTTTCAAAGTCA 58.564 37.500 0.00 0.00 32.56 3.41
810 1234 6.566197 ATCAACTGGTGATCTTTCAAAGTC 57.434 37.500 1.47 0.00 44.01 3.01
811 1235 6.966534 AATCAACTGGTGATCTTTCAAAGT 57.033 33.333 8.93 0.00 46.80 2.66
814 1238 9.739276 AGTATAAATCAACTGGTGATCTTTCAA 57.261 29.630 8.93 0.00 46.80 2.69
849 1273 6.042781 AGGATCAAGTAAGTTGTAGACCACAA 59.957 38.462 0.00 0.00 44.97 3.33
850 1274 5.542635 AGGATCAAGTAAGTTGTAGACCACA 59.457 40.000 0.00 0.00 37.43 4.17
851 1275 6.038997 AGGATCAAGTAAGTTGTAGACCAC 57.961 41.667 0.00 0.00 37.43 4.16
852 1276 5.187186 GGAGGATCAAGTAAGTTGTAGACCA 59.813 44.000 0.00 0.00 37.43 4.02
853 1277 5.662456 GGAGGATCAAGTAAGTTGTAGACC 58.338 45.833 0.00 0.00 37.43 3.85
854 1278 5.105837 ACGGAGGATCAAGTAAGTTGTAGAC 60.106 44.000 0.00 0.00 37.43 2.59
855 1279 5.014858 ACGGAGGATCAAGTAAGTTGTAGA 58.985 41.667 0.00 0.00 37.43 2.59
856 1280 5.326200 ACGGAGGATCAAGTAAGTTGTAG 57.674 43.478 0.00 0.00 37.43 2.74
857 1281 5.475719 CAACGGAGGATCAAGTAAGTTGTA 58.524 41.667 0.00 0.00 37.43 2.41
858 1282 4.315803 CAACGGAGGATCAAGTAAGTTGT 58.684 43.478 0.00 0.00 37.43 3.32
868 1292 0.250684 TTGCTTGCAACGGAGGATCA 60.251 50.000 3.70 0.00 36.25 2.92
876 1300 2.473530 TCAGAAACTTGCTTGCAACG 57.526 45.000 3.70 4.02 0.00 4.10
878 1302 6.747125 TGAATATTCAGAAACTTGCTTGCAA 58.253 32.000 14.23 7.83 32.50 4.08
897 1321 9.811995 AACTAAATATCGCACAACTACTGAATA 57.188 29.630 0.00 0.00 0.00 1.75
900 1324 7.094631 ACAACTAAATATCGCACAACTACTGA 58.905 34.615 0.00 0.00 0.00 3.41
902 1326 9.031360 CATACAACTAAATATCGCACAACTACT 57.969 33.333 0.00 0.00 0.00 2.57
906 1330 7.044966 GCAACATACAACTAAATATCGCACAAC 60.045 37.037 0.00 0.00 0.00 3.32
921 1345 5.048364 TGGATAACCAGTTGCAACATACAAC 60.048 40.000 30.11 15.08 46.18 3.32
922 1346 5.073428 TGGATAACCAGTTGCAACATACAA 58.927 37.500 30.11 13.50 41.77 2.41
923 1347 4.657013 TGGATAACCAGTTGCAACATACA 58.343 39.130 30.11 18.29 41.77 2.29
924 1348 4.700213 AGTGGATAACCAGTTGCAACATAC 59.300 41.667 30.11 15.97 46.54 2.39
926 1350 3.766545 AGTGGATAACCAGTTGCAACAT 58.233 40.909 30.11 15.12 46.54 2.71
927 1351 3.222173 AGTGGATAACCAGTTGCAACA 57.778 42.857 30.11 10.66 46.54 3.33
955 1379 8.625651 TGTACAACATAGCAGTTAAATGTTTGT 58.374 29.630 4.65 8.79 40.83 2.83
956 1380 9.117145 CTGTACAACATAGCAGTTAAATGTTTG 57.883 33.333 4.65 3.08 40.83 2.93
1008 1432 2.677199 ACAACACTGACTGCTGATACG 58.323 47.619 0.00 0.00 0.00 3.06
1179 4980 3.181445 TGTCCACTACATGTTGCCTTTCT 60.181 43.478 2.30 0.00 31.43 2.52
1202 5003 7.011763 TCTGCTGCAGTAACAATATCTGATTTC 59.988 37.037 27.24 0.00 32.61 2.17
1219 5020 1.743394 TGCATCTTTCATCTGCTGCAG 59.257 47.619 23.31 23.31 34.92 4.41
1227 5028 4.024725 GCATCAGAGACTGCATCTTTCATC 60.025 45.833 0.00 0.00 38.00 2.92
1260 5061 7.649533 AAGCATATGATCAAACTCATCCAAA 57.350 32.000 6.97 0.00 37.13 3.28
1276 5077 9.565213 CTCAACCTTCTCTTTTAAAAGCATATG 57.435 33.333 20.93 12.24 35.99 1.78
1298 5099 2.624838 CTGAGAAGGCCTTTTTGCTCAA 59.375 45.455 26.17 15.20 32.65 3.02
1328 5129 3.244387 ACCAACAGAAAGAGAAGAGGAGC 60.244 47.826 0.00 0.00 0.00 4.70
1341 5142 1.414919 ACCAGACGCTTACCAACAGAA 59.585 47.619 0.00 0.00 0.00 3.02
1345 5146 1.529865 GTTGACCAGACGCTTACCAAC 59.470 52.381 0.00 0.00 0.00 3.77
1374 5175 3.568538 CTTCCGCAAATTTGACCTGAAG 58.431 45.455 22.31 19.13 0.00 3.02
1413 5214 2.260822 TCTGCAGAAGCTCTAACCCTT 58.739 47.619 15.67 0.00 42.74 3.95
1416 5217 2.413453 CGTTTCTGCAGAAGCTCTAACC 59.587 50.000 32.01 13.54 42.74 2.85
1423 5224 2.376032 GACAAACGTTTCTGCAGAAGC 58.624 47.619 27.81 27.81 42.57 3.86
1434 5235 1.508632 CCATCACTCGGACAAACGTT 58.491 50.000 0.00 0.00 34.94 3.99
1436 5237 0.948623 TGCCATCACTCGGACAAACG 60.949 55.000 0.00 0.00 0.00 3.60
1453 5254 0.108186 GGGTTAAAGCCCTGCAATGC 60.108 55.000 0.00 0.00 45.22 3.56
1462 5263 2.100197 GGACTGAATGGGGTTAAAGCC 58.900 52.381 0.00 0.00 34.31 4.35
1466 5267 2.905085 TGTACGGACTGAATGGGGTTAA 59.095 45.455 0.00 0.00 0.00 2.01
1483 5284 4.694037 GGTTCTTACTGGGACACATTGTAC 59.306 45.833 0.00 0.00 0.00 2.90
1485 5286 3.137544 TGGTTCTTACTGGGACACATTGT 59.862 43.478 0.00 0.00 0.00 2.71
1499 5300 4.662278 CAAAAGGGATCCAGTGGTTCTTA 58.338 43.478 15.23 0.00 0.00 2.10
1594 5395 7.326789 CGACTGATAAGCATTTGACAAACATTT 59.673 33.333 1.94 0.90 0.00 2.32
1601 5402 3.932710 GACCGACTGATAAGCATTTGACA 59.067 43.478 0.00 0.00 0.00 3.58
1602 5403 3.932710 TGACCGACTGATAAGCATTTGAC 59.067 43.478 0.00 0.00 0.00 3.18
1604 5405 3.310774 CCTGACCGACTGATAAGCATTTG 59.689 47.826 0.00 0.00 0.00 2.32
1608 5409 1.476891 GTCCTGACCGACTGATAAGCA 59.523 52.381 0.00 0.00 0.00 3.91
1610 5411 3.017442 TCTGTCCTGACCGACTGATAAG 58.983 50.000 0.00 0.00 36.25 1.73
1612 5413 2.644676 CTCTGTCCTGACCGACTGATA 58.355 52.381 0.00 0.00 39.21 2.15
1614 5415 0.609406 CCTCTGTCCTGACCGACTGA 60.609 60.000 0.00 0.00 38.10 3.41
1617 5418 1.587054 CACCTCTGTCCTGACCGAC 59.413 63.158 0.00 0.00 0.00 4.79
1618 5419 2.276116 GCACCTCTGTCCTGACCGA 61.276 63.158 0.00 0.00 0.00 4.69
1619 5420 2.262915 GCACCTCTGTCCTGACCG 59.737 66.667 0.00 0.00 0.00 4.79
1621 5422 0.601311 GTGTGCACCTCTGTCCTGAC 60.601 60.000 15.69 0.00 0.00 3.51
1629 5430 2.106511 ACCAACAATAGTGTGCACCTCT 59.893 45.455 15.69 14.90 38.27 3.69
1665 5466 2.099405 AGCTGAGCCAGAGTAGTCTTC 58.901 52.381 0.00 0.00 32.44 2.87
1708 5509 5.180117 ACATTCTCACGTCAAAAGAATCCAG 59.820 40.000 8.34 3.17 37.59 3.86
1768 5569 9.116080 TGGGTATGATATGATCTCTTTGGTAAT 57.884 33.333 0.00 0.00 0.00 1.89
1772 5573 6.656693 GGTTGGGTATGATATGATCTCTTTGG 59.343 42.308 0.00 0.00 0.00 3.28
1786 5589 3.905968 TCTCACTATCGGTTGGGTATGA 58.094 45.455 0.00 0.00 0.00 2.15
1792 5595 2.868583 CAGCATTCTCACTATCGGTTGG 59.131 50.000 0.00 0.00 0.00 3.77
1797 5600 5.752472 AGTCAATTCAGCATTCTCACTATCG 59.248 40.000 0.00 0.00 0.00 2.92
1801 5604 7.934855 AATTAGTCAATTCAGCATTCTCACT 57.065 32.000 0.00 0.00 27.60 3.41
1836 5639 3.693807 TCTAAGTTCGTCCTGGAGCTTA 58.306 45.455 0.00 3.57 38.28 3.09
1838 5641 2.217510 TCTAAGTTCGTCCTGGAGCT 57.782 50.000 0.00 0.00 0.00 4.09
1848 5651 4.358494 ACGAAGTCTCCATCTAAGTTCG 57.642 45.455 9.33 9.33 46.22 3.95
1856 5659 3.516615 CTCTTGGAACGAAGTCTCCATC 58.483 50.000 0.00 0.00 45.00 3.51
1977 5781 1.616159 TGCTTCCTGGCCTTGTAAAC 58.384 50.000 3.32 0.00 0.00 2.01
1979 5783 1.354031 TCATGCTTCCTGGCCTTGTAA 59.646 47.619 3.32 0.00 0.00 2.41
1997 5828 3.322541 TGTTCGGGTTGTCACTAGAATCA 59.677 43.478 0.00 0.00 0.00 2.57
2079 5910 5.471456 CCTGAATAGCAACCAACTATCATCC 59.529 44.000 0.00 0.00 30.00 3.51
2094 5925 1.233019 ATGCACATCGCCTGAATAGC 58.767 50.000 0.00 0.00 41.33 2.97
2097 5928 1.135527 CCAAATGCACATCGCCTGAAT 59.864 47.619 0.00 0.00 41.33 2.57
2199 6030 3.502123 TGACCTCCAACAACCTTTAGG 57.498 47.619 0.00 0.00 42.17 2.69
2209 6040 9.366216 GTATTTTCCATTTAAATGACCTCCAAC 57.634 33.333 26.32 13.27 38.70 3.77
2217 6048 9.585099 GCATCACTGTATTTTCCATTTAAATGA 57.415 29.630 26.32 11.82 38.70 2.57
2267 6098 8.102047 AGATATCATTTGGATTGAGGACATCTC 58.898 37.037 5.32 0.00 38.92 2.75
2310 6141 4.023536 TGTTCCGGCAAACTTTCATAACTC 60.024 41.667 0.00 0.00 0.00 3.01
2394 6225 5.046448 AGCTATCCACATCCAGATCAATCTC 60.046 44.000 0.00 0.00 34.22 2.75
2456 6287 4.078395 AGCCCCTTCCAATATCTTCCAAAT 60.078 41.667 0.00 0.00 0.00 2.32
2457 6288 3.272020 AGCCCCTTCCAATATCTTCCAAA 59.728 43.478 0.00 0.00 0.00 3.28
2560 6391 2.542020 TGAAGTGCGAGACCATTCAA 57.458 45.000 0.00 0.00 0.00 2.69
2567 6398 2.143122 TGGAAACATGAAGTGCGAGAC 58.857 47.619 0.00 0.00 33.40 3.36
2568 6399 2.542020 TGGAAACATGAAGTGCGAGA 57.458 45.000 0.00 0.00 33.40 4.04
2610 6441 1.379916 CTCCCCAACACTGCCATGA 59.620 57.895 0.00 0.00 0.00 3.07
2702 6542 7.928167 TCAGAATCATAAATGTACGCAATCTCT 59.072 33.333 0.00 0.00 0.00 3.10
2901 6741 5.624159 TGATTGAGTCTGGAGATTGTTGTT 58.376 37.500 0.00 0.00 0.00 2.83
2999 6839 5.755849 TCACTTCCCTCCTTCAATATTTCC 58.244 41.667 0.00 0.00 0.00 3.13
3008 6848 3.579151 AGTAGTGTTCACTTCCCTCCTTC 59.421 47.826 10.74 0.00 0.00 3.46
3184 7024 0.397564 TCCCTCGGTTGTACCAAACC 59.602 55.000 5.25 5.25 45.24 3.27
3197 7037 4.576463 CCCTAATTTTGTTCAGATCCCTCG 59.424 45.833 0.00 0.00 0.00 4.63
3259 7099 2.129555 GACTTTGCAGCCTCCTCCCA 62.130 60.000 0.00 0.00 0.00 4.37
3486 7326 6.127591 CCTCCCATCTATTACAATCTCGTAGG 60.128 46.154 0.00 0.00 0.00 3.18
3544 8551 1.352156 CGCCGCACTTCAAGAGTACC 61.352 60.000 0.00 0.00 36.65 3.34
3594 8601 3.703052 GGAATCCAGCATGACCAAAGAAT 59.297 43.478 0.00 0.00 39.69 2.40
3629 8636 1.666189 GTAGGCGTTCCAGAAGCAATC 59.334 52.381 0.00 0.00 33.74 2.67


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

AutoCloner maintained by Alex Coulton.