Multiple sequence alignment - TraesCS4D01G050800

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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 TraesCS4D01G050800 chr4D 100.000 4538 0 0 1 4538 26666651 26671188 0.000000e+00 8381
1 TraesCS4D01G050800 chr4D 85.309 599 70 6 1 582 26529581 26530178 1.810000e-168 603
2 TraesCS4D01G050800 chr4D 94.271 192 11 0 4347 4538 128774996 128774805 1.230000e-75 294
3 TraesCS4D01G050800 chr4A 95.611 2962 86 25 1234 4156 576704004 576701048 0.000000e+00 4710
4 TraesCS4D01G050800 chr4A 93.160 424 22 6 690 1107 576704743 576704321 2.320000e-172 616
5 TraesCS4D01G050800 chr4A 81.280 625 114 3 2442 3064 629859513 629860136 1.880000e-138 503
6 TraesCS4D01G050800 chr4A 93.782 193 12 0 4346 4538 438401268 438401076 1.600000e-74 291
7 TraesCS4D01G050800 chr4A 82.514 183 28 2 4153 4331 576700720 576700538 1.690000e-34 158
8 TraesCS4D01G050800 chr4B 93.369 3137 124 44 1266 4335 39120048 39123167 0.000000e+00 4564
9 TraesCS4D01G050800 chr4B 87.453 534 35 10 503 1010 39119191 39119718 1.820000e-163 586
10 TraesCS4D01G050800 chr4B 86.990 392 32 4 1 380 39118629 39119013 1.510000e-114 424
11 TraesCS4D01G050800 chr4B 96.569 204 6 1 4335 4538 39123467 39123669 2.020000e-88 337
12 TraesCS4D01G050800 chr5D 84.253 616 97 0 2446 3061 388874 388259 6.500000e-168 601
13 TraesCS4D01G050800 chr5D 81.440 625 113 3 2442 3064 538789181 538788558 4.050000e-140 508
14 TraesCS4D01G050800 chr5D 87.186 398 51 0 1797 2194 389377 388980 1.920000e-123 453
15 TraesCS4D01G050800 chr5D 85.464 399 58 0 1796 2194 210375786 210375388 2.530000e-112 416
16 TraesCS4D01G050800 chr5B 80.960 625 116 3 2442 3064 680360033 680359410 4.080000e-135 492
17 TraesCS4D01G050800 chr5B 85.213 399 59 0 1796 2194 223984941 223984543 1.170000e-110 411
18 TraesCS4D01G050800 chr3A 80.161 620 119 4 2447 3064 627253014 627253631 1.150000e-125 460
19 TraesCS4D01G050800 chr5A 87.467 383 48 0 1794 2176 228156 228538 4.170000e-120 442
20 TraesCS4D01G050800 chr5A 84.461 399 62 0 1796 2194 272133045 272132647 1.180000e-105 394
21 TraesCS4D01G050800 chr3D 84.635 397 61 0 1794 2190 484287521 484287917 3.290000e-106 396
22 TraesCS4D01G050800 chr3B 85.117 383 57 0 1796 2178 647078355 647078737 4.260000e-105 392
23 TraesCS4D01G050800 chrUn 93.229 192 13 0 4347 4538 245556886 245557077 2.670000e-72 283
24 TraesCS4D01G050800 chrUn 93.229 192 13 0 4347 4538 272847063 272847254 2.670000e-72 283
25 TraesCS4D01G050800 chrUn 93.229 192 13 0 4347 4538 383463133 383463324 2.670000e-72 283
26 TraesCS4D01G050800 chr7B 93.229 192 13 0 4347 4538 610356555 610356364 2.670000e-72 283
27 TraesCS4D01G050800 chr2B 93.229 192 13 0 4347 4538 77813144 77813335 2.670000e-72 283
28 TraesCS4D01G050800 chr7D 93.158 190 13 0 4347 4536 45288641 45288830 3.460000e-71 279
29 TraesCS4D01G050800 chr2A 83.871 124 15 3 257 380 479830464 479830346 3.710000e-21 113


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 TraesCS4D01G050800 chr4D 26666651 26671188 4537 False 8381.00 8381 100.000000 1 4538 1 chr4D.!!$F2 4537
1 TraesCS4D01G050800 chr4D 26529581 26530178 597 False 603.00 603 85.309000 1 582 1 chr4D.!!$F1 581
2 TraesCS4D01G050800 chr4A 576700538 576704743 4205 True 1828.00 4710 90.428333 690 4331 3 chr4A.!!$R2 3641
3 TraesCS4D01G050800 chr4A 629859513 629860136 623 False 503.00 503 81.280000 2442 3064 1 chr4A.!!$F1 622
4 TraesCS4D01G050800 chr4B 39118629 39123669 5040 False 1477.75 4564 91.095250 1 4538 4 chr4B.!!$F1 4537
5 TraesCS4D01G050800 chr5D 388259 389377 1118 True 527.00 601 85.719500 1797 3061 2 chr5D.!!$R3 1264
6 TraesCS4D01G050800 chr5D 538788558 538789181 623 True 508.00 508 81.440000 2442 3064 1 chr5D.!!$R2 622
7 TraesCS4D01G050800 chr5B 680359410 680360033 623 True 492.00 492 80.960000 2442 3064 1 chr5B.!!$R2 622
8 TraesCS4D01G050800 chr3A 627253014 627253631 617 False 460.00 460 80.161000 2447 3064 1 chr3A.!!$F1 617

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
272 287 0.031616 CCTAGGCCTCTCCTCCTTGT 60.032 60.0 9.68 0.00 43.20 3.16 F
453 468 0.174617 CCTTGAGGCCGTTCTCTCTC 59.825 60.0 0.00 0.00 34.98 3.20 F
1135 1237 0.034616 CCCCTTCGCAGATGAGATCC 59.965 60.0 0.00 0.00 35.04 3.36 F
1136 1238 0.319383 CCCTTCGCAGATGAGATCCG 60.319 60.0 0.00 0.00 35.04 4.18 F
1192 1294 0.389556 CCATCAGGCCGATCGATCTG 60.390 60.0 22.43 21.34 29.21 2.90 F
1193 1295 0.600057 CATCAGGCCGATCGATCTGA 59.400 55.0 28.78 28.78 40.04 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1116 1218 0.034616 GGATCTCATCTGCGAAGGGG 59.965 60.000 0.00 0.00 0.00 4.79 R
1491 1809 0.103390 TCCGTCGAAGAAACAGTGCA 59.897 50.000 0.00 0.00 39.69 4.57 R
3115 3463 1.961793 AGCAACACCGTAAGCAAAGA 58.038 45.000 0.00 0.00 0.00 2.52 R
3140 3489 2.416836 CCTTTGCAATCCACATCTGCAG 60.417 50.000 7.63 7.63 46.08 4.41 R
3475 3830 3.498018 TGAGGTGACACATGACAAAATCG 59.502 43.478 8.08 0.00 0.00 3.34 R
3548 3903 5.762825 TGAGCAAGAGAATCCATTTATGC 57.237 39.130 0.00 0.00 33.66 3.14 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
77 78 2.006888 GCGAGCAATGGTGTAAAGCTA 58.993 47.619 0.00 0.00 35.36 3.32
89 90 5.705441 TGGTGTAAAGCTAACCTTCTTCATG 59.295 40.000 8.69 0.00 34.90 3.07
95 96 9.384764 GTAAAGCTAACCTTCTTCATGTTAGAT 57.615 33.333 11.63 3.65 42.47 1.98
96 97 7.856145 AAGCTAACCTTCTTCATGTTAGATG 57.144 36.000 11.63 0.21 42.47 2.90
102 103 8.463930 AACCTTCTTCATGTTAGATGTTTTGA 57.536 30.769 0.00 0.00 0.00 2.69
130 131 1.810151 GGTGCTCTGCCGACATTTTTA 59.190 47.619 0.00 0.00 0.00 1.52
140 144 6.318648 TCTGCCGACATTTTTATTAGATGCTT 59.681 34.615 0.00 0.00 0.00 3.91
162 166 2.224892 TGCCAGCATTGTTGGTAGGTTA 60.225 45.455 19.21 0.00 38.02 2.85
176 180 3.006003 GGTAGGTTATAGTGAGGAGCAGC 59.994 52.174 0.00 0.00 0.00 5.25
190 194 0.323178 AGCAGCCCTTTGTCAGATGG 60.323 55.000 0.00 0.00 0.00 3.51
272 287 0.031616 CCTAGGCCTCTCCTCCTTGT 60.032 60.000 9.68 0.00 43.20 3.16
275 290 0.474660 AGGCCTCTCCTCCTTGTTGT 60.475 55.000 0.00 0.00 43.20 3.32
346 361 4.796408 GAGGCTCCCTCTCTCCAA 57.204 61.111 2.15 0.00 46.41 3.53
357 372 1.742831 CTCTCTCCAACGTCTCCTCAG 59.257 57.143 0.00 0.00 0.00 3.35
408 423 1.794222 CCGTCGGAAACATTGGCTC 59.206 57.895 4.91 0.00 0.00 4.70
425 440 3.396260 GCTCGGCCAACATATTACCTA 57.604 47.619 2.24 0.00 0.00 3.08
426 441 3.735591 GCTCGGCCAACATATTACCTAA 58.264 45.455 2.24 0.00 0.00 2.69
442 457 1.763545 CCTAAGTAGTCCCCTTGAGGC 59.236 57.143 0.00 0.00 0.00 4.70
444 459 1.265454 AAGTAGTCCCCTTGAGGCCG 61.265 60.000 0.00 0.00 0.00 6.13
445 460 1.988406 GTAGTCCCCTTGAGGCCGT 60.988 63.158 0.00 0.00 0.00 5.68
446 461 1.229400 TAGTCCCCTTGAGGCCGTT 60.229 57.895 0.00 0.00 0.00 4.44
447 462 1.262640 TAGTCCCCTTGAGGCCGTTC 61.263 60.000 0.00 0.00 0.00 3.95
448 463 2.203938 TCCCCTTGAGGCCGTTCT 60.204 61.111 0.00 0.00 0.00 3.01
450 465 2.294078 CCCCTTGAGGCCGTTCTCT 61.294 63.158 0.00 0.00 34.98 3.10
452 467 1.261238 CCCTTGAGGCCGTTCTCTCT 61.261 60.000 0.00 0.00 34.98 3.10
453 468 0.174617 CCTTGAGGCCGTTCTCTCTC 59.825 60.000 0.00 0.00 34.98 3.20
454 469 0.174617 CTTGAGGCCGTTCTCTCTCC 59.825 60.000 0.00 0.00 34.98 3.71
455 470 0.251832 TTGAGGCCGTTCTCTCTCCT 60.252 55.000 0.00 0.00 34.98 3.69
456 471 0.681564 TGAGGCCGTTCTCTCTCCTC 60.682 60.000 0.00 0.00 42.67 3.71
481 498 2.965147 CCTTTCTCTCATCCCCTCTCTC 59.035 54.545 0.00 0.00 0.00 3.20
491 508 0.323908 CCCCTCTCTCGTTCCTGACT 60.324 60.000 0.00 0.00 0.00 3.41
505 575 1.891150 CCTGACTTGGAGCATTGCTTT 59.109 47.619 13.35 0.00 39.88 3.51
534 604 4.946478 AGCACTCTGTGTACTCTTTTCT 57.054 40.909 0.00 0.00 35.75 2.52
546 616 9.778741 TGTGTACTCTTTTCTTTCTATCAATGT 57.221 29.630 0.00 0.00 0.00 2.71
630 716 7.637709 TCTATGAAATTGATACGACAATCCG 57.362 36.000 0.00 0.00 39.19 4.18
632 718 3.935828 TGAAATTGATACGACAATCCGCA 59.064 39.130 0.00 0.00 39.19 5.69
634 720 2.951457 TTGATACGACAATCCGCAGA 57.049 45.000 0.00 0.00 0.00 4.26
636 722 1.749063 TGATACGACAATCCGCAGAGT 59.251 47.619 0.00 0.00 0.00 3.24
642 728 3.630769 ACGACAATCCGCAGAGTATTCTA 59.369 43.478 0.00 0.00 30.73 2.10
714 800 3.261580 CAAATGCGGGGAAGAAAATTCC 58.738 45.455 0.00 0.00 37.86 3.01
728 814 7.095060 GGAAGAAAATTCCCAAGAAAAGAATGC 60.095 37.037 0.00 0.00 35.09 3.56
745 832 3.705043 ATGCGGAGAAGAAAATCATGC 57.295 42.857 0.00 0.00 0.00 4.06
782 871 2.105128 CGCGCCACCCAAACAAAA 59.895 55.556 0.00 0.00 0.00 2.44
1032 1131 2.363147 GCCTCCTCCACCGTCTCT 60.363 66.667 0.00 0.00 0.00 3.10
1036 1135 2.997315 CCTCCACCGTCTCTGCCA 60.997 66.667 0.00 0.00 0.00 4.92
1107 1209 0.825840 CGATCCTCACCCTCCTCCTC 60.826 65.000 0.00 0.00 0.00 3.71
1108 1210 0.471022 GATCCTCACCCTCCTCCTCC 60.471 65.000 0.00 0.00 0.00 4.30
1109 1211 0.933791 ATCCTCACCCTCCTCCTCCT 60.934 60.000 0.00 0.00 0.00 3.69
1110 1212 1.075600 CCTCACCCTCCTCCTCCTC 60.076 68.421 0.00 0.00 0.00 3.71
1111 1213 1.075600 CTCACCCTCCTCCTCCTCC 60.076 68.421 0.00 0.00 0.00 4.30
1112 1214 1.547755 TCACCCTCCTCCTCCTCCT 60.548 63.158 0.00 0.00 0.00 3.69
1113 1215 1.075600 CACCCTCCTCCTCCTCCTC 60.076 68.421 0.00 0.00 0.00 3.71
1114 1216 2.329399 ACCCTCCTCCTCCTCCTCC 61.329 68.421 0.00 0.00 0.00 4.30
1115 1217 2.018086 CCCTCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1116 1218 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1117 1219 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1118 1220 2.015726 TCCTCCTCCTCCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
1119 1221 2.612251 CTCCTCCTCCTCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
1120 1222 2.018086 CTCCTCCTCCTCCTCCCCT 61.018 68.421 0.00 0.00 0.00 4.79
1121 1223 1.550374 TCCTCCTCCTCCTCCCCTT 60.550 63.158 0.00 0.00 0.00 3.95
1122 1224 1.074850 CCTCCTCCTCCTCCCCTTC 60.075 68.421 0.00 0.00 0.00 3.46
1123 1225 1.456705 CTCCTCCTCCTCCCCTTCG 60.457 68.421 0.00 0.00 0.00 3.79
1124 1226 3.157949 CCTCCTCCTCCCCTTCGC 61.158 72.222 0.00 0.00 0.00 4.70
1125 1227 2.364317 CTCCTCCTCCCCTTCGCA 60.364 66.667 0.00 0.00 0.00 5.10
1126 1228 2.364317 TCCTCCTCCCCTTCGCAG 60.364 66.667 0.00 0.00 0.00 5.18
1127 1229 2.364317 CCTCCTCCCCTTCGCAGA 60.364 66.667 0.00 0.00 0.00 4.26
1128 1230 1.764054 CCTCCTCCCCTTCGCAGAT 60.764 63.158 0.00 0.00 35.04 2.90
1129 1231 1.445095 CTCCTCCCCTTCGCAGATG 59.555 63.158 0.00 0.00 35.04 2.90
1130 1232 1.001631 TCCTCCCCTTCGCAGATGA 59.998 57.895 0.00 0.00 35.04 2.92
1131 1233 1.045350 TCCTCCCCTTCGCAGATGAG 61.045 60.000 0.00 0.00 35.04 2.90
1132 1234 1.045350 CCTCCCCTTCGCAGATGAGA 61.045 60.000 3.20 0.00 35.04 3.27
1133 1235 1.047002 CTCCCCTTCGCAGATGAGAT 58.953 55.000 0.00 0.00 35.04 2.75
1134 1236 1.000731 CTCCCCTTCGCAGATGAGATC 59.999 57.143 0.00 0.00 35.04 2.75
1135 1237 0.034616 CCCCTTCGCAGATGAGATCC 59.965 60.000 0.00 0.00 35.04 3.36
1136 1238 0.319383 CCCTTCGCAGATGAGATCCG 60.319 60.000 0.00 0.00 35.04 4.18
1137 1239 0.943359 CCTTCGCAGATGAGATCCGC 60.943 60.000 0.00 0.00 35.04 5.54
1138 1240 0.943359 CTTCGCAGATGAGATCCGCC 60.943 60.000 0.00 0.00 35.04 6.13
1139 1241 2.356793 CGCAGATGAGATCCGCCC 60.357 66.667 0.00 0.00 28.84 6.13
1140 1242 2.031768 GCAGATGAGATCCGCCCC 59.968 66.667 0.00 0.00 0.00 5.80
1141 1243 2.341543 CAGATGAGATCCGCCCCG 59.658 66.667 0.00 0.00 0.00 5.73
1142 1244 3.620785 AGATGAGATCCGCCCCGC 61.621 66.667 0.00 0.00 0.00 6.13
1143 1245 3.928779 GATGAGATCCGCCCCGCA 61.929 66.667 0.00 0.00 0.00 5.69
1144 1246 3.244580 ATGAGATCCGCCCCGCAT 61.245 61.111 0.00 0.00 0.00 4.73
1145 1247 2.738213 GATGAGATCCGCCCCGCATT 62.738 60.000 0.00 0.00 0.00 3.56
1146 1248 2.974698 GAGATCCGCCCCGCATTG 60.975 66.667 0.00 0.00 0.00 2.82
1152 1254 4.845580 CGCCCCGCATTGCTCTCT 62.846 66.667 7.12 0.00 0.00 3.10
1153 1255 2.899339 GCCCCGCATTGCTCTCTC 60.899 66.667 7.12 0.00 0.00 3.20
1154 1256 2.203126 CCCCGCATTGCTCTCTCC 60.203 66.667 7.12 0.00 0.00 3.71
1155 1257 2.203126 CCCGCATTGCTCTCTCCC 60.203 66.667 7.12 0.00 0.00 4.30
1156 1258 2.739996 CCCGCATTGCTCTCTCCCT 61.740 63.158 7.12 0.00 0.00 4.20
1157 1259 1.227497 CCGCATTGCTCTCTCCCTC 60.227 63.158 7.12 0.00 0.00 4.30
1158 1260 1.227497 CGCATTGCTCTCTCCCTCC 60.227 63.158 7.12 0.00 0.00 4.30
1159 1261 1.148048 GCATTGCTCTCTCCCTCCC 59.852 63.158 0.16 0.00 0.00 4.30
1160 1262 1.344191 GCATTGCTCTCTCCCTCCCT 61.344 60.000 0.16 0.00 0.00 4.20
1161 1263 0.758123 CATTGCTCTCTCCCTCCCTC 59.242 60.000 0.00 0.00 0.00 4.30
1162 1264 0.399806 ATTGCTCTCTCCCTCCCTCC 60.400 60.000 0.00 0.00 0.00 4.30
1163 1265 2.123033 GCTCTCTCCCTCCCTCCC 60.123 72.222 0.00 0.00 0.00 4.30
1164 1266 2.612251 CTCTCTCCCTCCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
1165 1267 3.036959 TCTCTCCCTCCCTCCCCC 61.037 72.222 0.00 0.00 0.00 5.40
1166 1268 4.548513 CTCTCCCTCCCTCCCCCG 62.549 77.778 0.00 0.00 0.00 5.73
1190 1292 4.586618 CCATCAGGCCGATCGATC 57.413 61.111 18.66 15.68 29.21 3.69
1191 1293 1.970639 CCATCAGGCCGATCGATCT 59.029 57.895 22.43 10.49 29.21 2.75
1192 1294 0.389556 CCATCAGGCCGATCGATCTG 60.390 60.000 22.43 21.34 29.21 2.90
1193 1295 0.600057 CATCAGGCCGATCGATCTGA 59.400 55.000 28.78 28.78 40.04 3.27
1194 1296 1.204231 CATCAGGCCGATCGATCTGAT 59.796 52.381 29.92 29.92 44.79 2.90
1202 1304 1.879480 ATCGATCTGATCTCGCGGG 59.121 57.895 15.16 1.01 36.11 6.13
1203 1305 2.206515 ATCGATCTGATCTCGCGGGC 62.207 60.000 15.16 0.00 36.11 6.13
1204 1306 2.429907 GATCTGATCTCGCGGGCG 60.430 66.667 6.13 6.74 41.35 6.13
1205 1307 4.654412 ATCTGATCTCGCGGGCGC 62.654 66.667 6.13 0.00 39.59 6.53
1254 1546 2.417516 CGGATCTCGCGGAATGGT 59.582 61.111 6.13 0.00 0.00 3.55
1274 1566 2.798009 CGCCGCCCCTGTATTTTG 59.202 61.111 0.00 0.00 0.00 2.44
1295 1588 1.246649 TGTTGTTCATTCATGCCGCT 58.753 45.000 0.00 0.00 0.00 5.52
1406 1703 7.201530 CCATGGTCTCTCTGTTTCGTTATTAAC 60.202 40.741 2.57 0.00 0.00 2.01
1476 1794 9.433153 GAATTGATTGATAGTCTCATCATGCTA 57.567 33.333 0.00 0.00 34.95 3.49
1480 1798 8.518702 TGATTGATAGTCTCATCATGCTACTAC 58.481 37.037 2.10 0.00 34.95 2.73
1481 1799 8.648698 ATTGATAGTCTCATCATGCTACTACT 57.351 34.615 2.10 0.00 34.95 2.57
1483 1801 8.785329 TGATAGTCTCATCATGCTACTACTAG 57.215 38.462 2.10 0.00 29.93 2.57
1484 1802 8.598041 TGATAGTCTCATCATGCTACTACTAGA 58.402 37.037 0.00 0.00 29.93 2.43
1486 1804 9.973661 ATAGTCTCATCATGCTACTACTAGAAT 57.026 33.333 0.00 0.00 0.00 2.40
1587 1910 3.731717 GCGTAGATTCTCCTTTGATCGAC 59.268 47.826 0.00 0.00 0.00 4.20
1618 1945 4.023279 TGTGCAATAACTGTAGCTTTGTGG 60.023 41.667 0.00 0.00 0.00 4.17
1710 2038 2.238898 GGTATGGTCAAGGTAAGCCACT 59.761 50.000 0.00 0.00 37.19 4.00
1743 2071 2.095059 GCGTCTTGCATCTTTGGTTCAT 60.095 45.455 0.00 0.00 45.45 2.57
1762 2090 1.067295 TGGAAATGCCACTGTCCTCT 58.933 50.000 0.00 0.00 43.33 3.69
1956 2284 4.559862 CTTGACTCTCAAGTACCCCATT 57.440 45.455 4.13 0.00 46.50 3.16
2305 2637 3.185594 TCTCAAATCGTTTTGTGGTAGCG 59.814 43.478 16.38 0.00 42.37 4.26
3072 3420 4.258543 CCTTCCAGCAGGTAAATAAACGA 58.741 43.478 0.00 0.00 35.89 3.85
3126 3475 6.820470 TGGATTTTTGTTTCTTTGCTTACG 57.180 33.333 0.00 0.00 0.00 3.18
3140 3489 1.753956 CTTACGGTGTTGCTTGTTGC 58.246 50.000 0.00 0.00 43.25 4.17
3475 3830 0.392060 AGAAATACGGGCGGTGTTCC 60.392 55.000 8.08 0.00 0.00 3.62
3548 3903 3.245518 TGATCCTACATGGTGTTGTCG 57.754 47.619 0.00 0.00 37.07 4.35
3552 3907 2.498078 TCCTACATGGTGTTGTCGCATA 59.502 45.455 0.00 0.00 37.07 3.14
3678 4034 1.379710 TGTGTGTGTGGCCTTTGCT 60.380 52.632 3.32 0.00 37.74 3.91
3691 4048 2.599659 CCTTTGCTCAATCGGCTTTTC 58.400 47.619 0.00 0.00 0.00 2.29
3692 4049 2.030007 CCTTTGCTCAATCGGCTTTTCA 60.030 45.455 0.00 0.00 0.00 2.69
3747 4105 4.927049 TGATCTGATGCCTTCCTTTCTTT 58.073 39.130 0.00 0.00 0.00 2.52
3771 4130 2.793585 CGATGTGCTGGAATGTTCATGC 60.794 50.000 0.00 0.00 0.00 4.06
3809 4169 2.278401 GCTTTAGCAGCGCATGGC 60.278 61.111 11.47 10.74 39.29 4.40
3828 4190 2.287009 GGCTACATGATTACGCTTTGCC 60.287 50.000 0.00 0.00 0.00 4.52
3867 4237 7.308589 CGACATTCCTGTAAAAAGTGGAATCTT 60.309 37.037 0.00 0.00 44.59 2.40
3868 4238 7.886338 ACATTCCTGTAAAAAGTGGAATCTTC 58.114 34.615 0.00 0.00 44.59 2.87
4091 4465 1.815003 GGCCTGACAAATCCTCAGTTG 59.185 52.381 0.00 0.00 34.42 3.16
4135 4517 4.095483 TGGTCGTACCGAGATAGAAAGTTC 59.905 45.833 0.00 0.00 42.58 3.01
4136 4518 4.095483 GGTCGTACCGAGATAGAAAGTTCA 59.905 45.833 0.00 0.00 36.23 3.18
4137 4519 5.264712 GTCGTACCGAGATAGAAAGTTCAG 58.735 45.833 0.00 0.00 36.23 3.02
4138 4520 5.064452 GTCGTACCGAGATAGAAAGTTCAGA 59.936 44.000 0.00 0.00 36.23 3.27
4202 4917 7.179516 TGTGGGTGTTAATGAGATACTCTAACA 59.820 37.037 0.00 0.00 32.55 2.41
4285 5007 2.540931 GTGTTTCTGGCAAGCAAATGTG 59.459 45.455 0.00 0.00 0.00 3.21
4306 5028 5.923114 TGTGAGCTAGATGAAATAGAATCGC 59.077 40.000 0.00 0.00 0.00 4.58
4312 5034 6.253298 GCTAGATGAAATAGAATCGCAGCTAG 59.747 42.308 0.00 0.00 44.18 3.42
4495 5517 4.116238 GAGAAATTCTTGTCTAGAGCGGG 58.884 47.826 0.00 0.00 33.51 6.13
4496 5518 2.990066 AATTCTTGTCTAGAGCGGGG 57.010 50.000 0.00 0.00 33.51 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.257561 CTCAATGACGGCTCGCGG 61.258 66.667 6.13 0.00 0.00 6.46
32 33 1.810030 GGCGGACGACCTCAATGAC 60.810 63.158 1.72 0.00 0.00 3.06
58 59 3.181510 GGTTAGCTTTACACCATTGCTCG 60.182 47.826 0.00 0.00 35.47 5.03
77 78 8.463930 TCAAAACATCTAACATGAAGAAGGTT 57.536 30.769 0.00 8.24 0.00 3.50
89 90 3.131046 CCCATGGCCTCAAAACATCTAAC 59.869 47.826 6.09 0.00 0.00 2.34
95 96 1.470996 GCACCCATGGCCTCAAAACA 61.471 55.000 6.09 0.00 0.00 2.83
96 97 1.187567 AGCACCCATGGCCTCAAAAC 61.188 55.000 6.09 0.00 0.00 2.43
102 103 4.437587 GCAGAGCACCCATGGCCT 62.438 66.667 6.09 1.41 0.00 5.19
140 144 1.255882 CCTACCAACAATGCTGGCAA 58.744 50.000 2.04 0.00 37.48 4.52
162 166 1.211457 CAAAGGGCTGCTCCTCACTAT 59.789 52.381 9.63 0.00 35.80 2.12
176 180 1.002134 ACGGCCATCTGACAAAGGG 60.002 57.895 2.24 0.00 0.00 3.95
272 287 2.855514 GCCAGGCGCCAAGAAACAA 61.856 57.895 31.54 0.00 0.00 2.83
275 290 2.203480 AAGCCAGGCGCCAAGAAA 60.203 55.556 31.54 0.00 38.78 2.52
346 361 0.323816 TGATGAGGCTGAGGAGACGT 60.324 55.000 0.00 0.00 29.20 4.34
389 404 2.178273 GCCAATGTTTCCGACGGC 59.822 61.111 9.66 0.00 0.00 5.68
392 407 1.794222 CCGAGCCAATGTTTCCGAC 59.206 57.895 0.00 0.00 0.00 4.79
393 408 2.038269 GCCGAGCCAATGTTTCCGA 61.038 57.895 0.00 0.00 0.00 4.55
408 423 5.850614 ACTACTTAGGTAATATGTTGGCCG 58.149 41.667 0.00 0.00 0.00 6.13
425 440 1.265454 CGGCCTCAAGGGGACTACTT 61.265 60.000 0.00 0.00 42.68 2.24
426 441 1.686110 CGGCCTCAAGGGGACTACT 60.686 63.158 0.00 0.00 42.68 2.57
442 457 1.758906 GGGGGAGGAGAGAGAACGG 60.759 68.421 0.00 0.00 0.00 4.44
467 484 1.036707 GGAACGAGAGAGGGGATGAG 58.963 60.000 0.00 0.00 0.00 2.90
481 498 1.466167 CAATGCTCCAAGTCAGGAACG 59.534 52.381 0.00 0.00 37.20 3.95
505 575 1.526686 CACAGAGTGCTTGGTGCCA 60.527 57.895 0.00 0.00 42.00 4.92
512 582 5.283457 AGAAAAGAGTACACAGAGTGCTT 57.717 39.130 0.00 0.00 43.67 3.91
513 583 4.946478 AGAAAAGAGTACACAGAGTGCT 57.054 40.909 0.00 0.00 46.49 4.40
515 585 9.134734 GATAGAAAGAAAAGAGTACACAGAGTG 57.865 37.037 0.00 0.00 39.75 3.51
534 604 7.121020 TGCTTGTGCATCTTACATTGATAGAAA 59.879 33.333 0.00 0.00 45.31 2.52
605 691 7.148573 GCGGATTGTCGTATCAATTTCATAGAT 60.149 37.037 0.00 0.00 38.03 1.98
656 742 3.085533 TGTGGGGAACGAATTGGTTATG 58.914 45.455 5.77 0.00 0.00 1.90
660 746 2.074729 TTTGTGGGGAACGAATTGGT 57.925 45.000 0.00 0.00 0.00 3.67
714 800 3.753272 TCTTCTCCGCATTCTTTTCTTGG 59.247 43.478 0.00 0.00 0.00 3.61
718 804 6.381801 TGATTTTCTTCTCCGCATTCTTTTC 58.618 36.000 0.00 0.00 0.00 2.29
728 814 2.223433 GCCAGCATGATTTTCTTCTCCG 60.223 50.000 0.00 0.00 39.69 4.63
768 855 1.003108 CGTTGTTTTGTTTGGGTGGC 58.997 50.000 0.00 0.00 0.00 5.01
777 864 0.100503 GCTGGCACTCGTTGTTTTGT 59.899 50.000 0.00 0.00 0.00 2.83
1078 1180 0.101939 GTGAGGATCGTTACCGGGAC 59.898 60.000 6.32 2.82 38.61 4.46
1089 1191 0.471022 GGAGGAGGAGGGTGAGGATC 60.471 65.000 0.00 0.00 0.00 3.36
1093 1195 1.075600 GGAGGAGGAGGAGGGTGAG 60.076 68.421 0.00 0.00 0.00 3.51
1094 1196 1.547755 AGGAGGAGGAGGAGGGTGA 60.548 63.158 0.00 0.00 0.00 4.02
1095 1197 1.075600 GAGGAGGAGGAGGAGGGTG 60.076 68.421 0.00 0.00 0.00 4.61
1096 1198 2.329399 GGAGGAGGAGGAGGAGGGT 61.329 68.421 0.00 0.00 0.00 4.34
1097 1199 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
1100 1202 2.015726 GGGAGGAGGAGGAGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
1107 1209 3.157949 GCGAAGGGGAGGAGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
1108 1210 2.364317 TGCGAAGGGGAGGAGGAG 60.364 66.667 0.00 0.00 0.00 3.69
1109 1211 2.243774 ATCTGCGAAGGGGAGGAGGA 62.244 60.000 0.00 0.00 34.34 3.71
1110 1212 1.764054 ATCTGCGAAGGGGAGGAGG 60.764 63.158 0.00 0.00 34.34 4.30
1111 1213 1.045350 TCATCTGCGAAGGGGAGGAG 61.045 60.000 0.00 0.00 34.34 3.69
1112 1214 1.001631 TCATCTGCGAAGGGGAGGA 59.998 57.895 0.00 0.00 34.34 3.71
1113 1215 1.045350 TCTCATCTGCGAAGGGGAGG 61.045 60.000 11.01 0.00 34.34 4.30
1114 1216 1.000731 GATCTCATCTGCGAAGGGGAG 59.999 57.143 6.03 6.03 34.99 4.30
1115 1217 1.043816 GATCTCATCTGCGAAGGGGA 58.956 55.000 0.00 0.00 0.00 4.81
1116 1218 0.034616 GGATCTCATCTGCGAAGGGG 59.965 60.000 0.00 0.00 0.00 4.79
1117 1219 0.319383 CGGATCTCATCTGCGAAGGG 60.319 60.000 0.00 0.00 0.00 3.95
1118 1220 3.191903 CGGATCTCATCTGCGAAGG 57.808 57.895 0.00 0.00 0.00 3.46
1124 1226 2.341543 CGGGGCGGATCTCATCTG 59.658 66.667 0.00 0.00 38.71 2.90
1125 1227 3.620785 GCGGGGCGGATCTCATCT 61.621 66.667 0.00 0.00 0.00 2.90
1126 1228 2.738213 AATGCGGGGCGGATCTCATC 62.738 60.000 0.00 0.00 36.82 2.92
1127 1229 2.822637 AATGCGGGGCGGATCTCAT 61.823 57.895 0.00 0.00 36.82 2.90
1128 1230 3.479203 AATGCGGGGCGGATCTCA 61.479 61.111 0.00 0.00 36.82 3.27
1129 1231 2.974698 CAATGCGGGGCGGATCTC 60.975 66.667 0.00 0.00 36.82 2.75
1135 1237 4.845580 AGAGAGCAATGCGGGGCG 62.846 66.667 0.00 0.00 34.54 6.13
1136 1238 2.899339 GAGAGAGCAATGCGGGGC 60.899 66.667 0.00 0.00 0.00 5.80
1137 1239 2.203126 GGAGAGAGCAATGCGGGG 60.203 66.667 0.00 0.00 0.00 5.73
1138 1240 2.203126 GGGAGAGAGCAATGCGGG 60.203 66.667 0.00 0.00 0.00 6.13
1139 1241 1.227497 GAGGGAGAGAGCAATGCGG 60.227 63.158 0.00 0.00 0.00 5.69
1140 1242 1.227497 GGAGGGAGAGAGCAATGCG 60.227 63.158 0.00 0.00 0.00 4.73
1141 1243 1.148048 GGGAGGGAGAGAGCAATGC 59.852 63.158 0.00 0.00 0.00 3.56
1142 1244 0.758123 GAGGGAGGGAGAGAGCAATG 59.242 60.000 0.00 0.00 0.00 2.82
1143 1245 0.399806 GGAGGGAGGGAGAGAGCAAT 60.400 60.000 0.00 0.00 0.00 3.56
1144 1246 1.002274 GGAGGGAGGGAGAGAGCAA 59.998 63.158 0.00 0.00 0.00 3.91
1145 1247 2.693017 GGAGGGAGGGAGAGAGCA 59.307 66.667 0.00 0.00 0.00 4.26
1146 1248 2.123033 GGGAGGGAGGGAGAGAGC 60.123 72.222 0.00 0.00 0.00 4.09
1147 1249 2.612251 GGGGAGGGAGGGAGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
1148 1250 3.036959 GGGGGAGGGAGGGAGAGA 61.037 72.222 0.00 0.00 0.00 3.10
1149 1251 4.548513 CGGGGGAGGGAGGGAGAG 62.549 77.778 0.00 0.00 0.00 3.20
1173 1275 0.389556 CAGATCGATCGGCCTGATGG 60.390 60.000 23.80 12.47 37.47 3.51
1174 1276 0.600057 TCAGATCGATCGGCCTGATG 59.400 55.000 25.51 10.80 37.47 3.07
1175 1277 1.476085 GATCAGATCGATCGGCCTGAT 59.524 52.381 32.88 32.88 45.77 2.90
1176 1278 0.884514 GATCAGATCGATCGGCCTGA 59.115 55.000 28.78 28.78 41.24 3.86
1177 1279 3.415237 GATCAGATCGATCGGCCTG 57.585 57.895 19.25 22.81 41.24 4.85
1184 1286 1.879480 CCCGCGAGATCAGATCGAT 59.121 57.895 8.23 0.00 42.76 3.59
1185 1287 2.909209 GCCCGCGAGATCAGATCGA 61.909 63.158 8.23 0.00 42.76 3.59
1186 1288 2.429907 GCCCGCGAGATCAGATCG 60.430 66.667 8.23 0.00 43.00 3.69
1187 1289 2.429907 CGCCCGCGAGATCAGATC 60.430 66.667 8.23 1.64 42.83 2.75
1188 1290 4.654412 GCGCCCGCGAGATCAGAT 62.654 66.667 14.24 0.00 42.83 2.90
1254 1546 2.260088 AAAATACAGGGGCGGCGCTA 62.260 55.000 32.30 16.17 0.00 4.26
1261 1553 3.744238 ACAACAACAAAATACAGGGGC 57.256 42.857 0.00 0.00 0.00 5.80
1274 1566 1.720852 GCGGCATGAATGAACAACAAC 59.279 47.619 0.00 0.00 0.00 3.32
1295 1588 1.123077 AGCAGATCTACATTCCCGCA 58.877 50.000 0.00 0.00 0.00 5.69
1379 1672 1.338200 ACGAAACAGAGAGACCATGGC 60.338 52.381 13.04 4.70 0.00 4.40
1384 1677 6.867293 ACAGTTAATAACGAAACAGAGAGACC 59.133 38.462 0.00 0.00 36.23 3.85
1385 1678 7.870588 ACAGTTAATAACGAAACAGAGAGAC 57.129 36.000 0.00 0.00 36.23 3.36
1406 1703 7.972277 TCCGCAACTTAATACTACTAAGAACAG 59.028 37.037 0.00 0.00 31.91 3.16
1491 1809 0.103390 TCCGTCGAAGAAACAGTGCA 59.897 50.000 0.00 0.00 39.69 4.57
1587 1910 2.866156 ACAGTTATTGCACATCGATCGG 59.134 45.455 16.41 2.12 0.00 4.18
1618 1945 3.611766 TCTACCTACAGCAAAAGCTCC 57.388 47.619 0.00 0.00 0.00 4.70
1710 2038 1.005037 AAGACGCTCGTGGAATGCA 60.005 52.632 0.00 0.00 0.00 3.96
1743 2071 1.067295 AGAGGACAGTGGCATTTCCA 58.933 50.000 12.78 0.00 44.18 3.53
1755 2083 6.932400 ACGAATGTTATGTTACAAAGAGGACA 59.068 34.615 0.00 0.00 0.00 4.02
1758 2086 6.148811 ACCACGAATGTTATGTTACAAAGAGG 59.851 38.462 0.00 0.00 0.00 3.69
1762 2090 5.531659 ACCACCACGAATGTTATGTTACAAA 59.468 36.000 0.00 0.00 0.00 2.83
2305 2637 5.334414 CCAGATGTCACAGAACAAAACTAGC 60.334 44.000 0.00 0.00 31.81 3.42
3072 3420 3.534554 TGAATGAAGTACGATGCTGCAT 58.465 40.909 16.20 16.20 33.82 3.96
3111 3459 3.732471 GCAACACCGTAAGCAAAGAAACA 60.732 43.478 0.00 0.00 0.00 2.83
3115 3463 1.961793 AGCAACACCGTAAGCAAAGA 58.038 45.000 0.00 0.00 0.00 2.52
3140 3489 2.416836 CCTTTGCAATCCACATCTGCAG 60.417 50.000 7.63 7.63 46.08 4.41
3475 3830 3.498018 TGAGGTGACACATGACAAAATCG 59.502 43.478 8.08 0.00 0.00 3.34
3548 3903 5.762825 TGAGCAAGAGAATCCATTTATGC 57.237 39.130 0.00 0.00 33.66 3.14
3552 3907 7.039223 ACAAGAAATGAGCAAGAGAATCCATTT 60.039 33.333 0.00 0.00 37.06 2.32
3678 4034 1.265635 CACCGTTGAAAAGCCGATTGA 59.734 47.619 0.00 0.00 0.00 2.57
3691 4048 0.874390 CATCACAGAACCCACCGTTG 59.126 55.000 0.00 0.00 33.74 4.10
3692 4049 0.762418 TCATCACAGAACCCACCGTT 59.238 50.000 0.00 0.00 37.41 4.44
3747 4105 2.076100 GAACATTCCAGCACATCGACA 58.924 47.619 0.00 0.00 0.00 4.35
3771 4130 4.643784 AGCCTGAGCAATAGAATTCTTTGG 59.356 41.667 14.36 4.49 43.56 3.28
3809 4169 5.050490 ACTAGGCAAAGCGTAATCATGTAG 58.950 41.667 0.00 0.00 0.00 2.74
3841 4211 5.682943 TTCCACTTTTTACAGGAATGTCG 57.317 39.130 0.00 0.00 35.35 4.35
3867 4237 4.963318 TCTTGCTGGAAGAAAAGAGAGA 57.037 40.909 9.29 0.00 37.78 3.10
3868 4238 4.142643 GCATCTTGCTGGAAGAAAAGAGAG 60.143 45.833 15.62 2.21 44.11 3.20
3953 4327 5.887598 CCAACCTGTGAGATTCCAAATATCA 59.112 40.000 0.00 0.00 0.00 2.15
4117 4499 8.530269 TTTTTCTGAACTTTCTATCTCGGTAC 57.470 34.615 0.00 0.00 0.00 3.34
4170 4885 8.548877 AGTATCTCATTAACACCCACAAGTATT 58.451 33.333 0.00 0.00 0.00 1.89
4285 5007 5.062058 GCTGCGATTCTATTTCATCTAGCTC 59.938 44.000 0.00 0.00 30.56 4.09
4344 5366 3.065648 GCTTCGCCCCGAATTTGTAAATA 59.934 43.478 0.18 0.00 44.85 1.40
4359 5381 9.071164 AAGATATCTTTCATTGAAGGCTTCGCC 62.071 40.741 21.42 0.00 40.37 5.54
4360 5382 3.772060 ATCTTTCATTGAAGGCTTCGC 57.228 42.857 21.42 0.65 0.00 4.70
4495 5517 3.948473 GGCTTTAATCAAGACCTCCTTCC 59.052 47.826 0.00 0.00 33.74 3.46
4496 5518 3.623510 CGGCTTTAATCAAGACCTCCTTC 59.376 47.826 0.00 0.00 37.18 3.46


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

AutoCloner maintained by Alex Coulton.