Multiple sequence alignment - TraesCS3D01G246400

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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 TraesCS3D01G246400 chr3D 100.000 2561 0 0 1 2561 343712730 343710170 0.000000e+00 4730.0
1 TraesCS3D01G246400 chr3D 79.722 360 56 15 1652 2002 27062754 27063105 7.080000e-61 244.0
2 TraesCS3D01G246400 chr3D 76.441 399 59 20 2006 2382 335197261 335197646 1.570000e-42 183.0
3 TraesCS3D01G246400 chr3D 91.954 87 1 3 2475 2561 561050811 561050891 1.610000e-22 117.0
4 TraesCS3D01G246400 chr3D 88.660 97 7 4 2465 2561 428370216 428370124 5.790000e-22 115.0
5 TraesCS3D01G246400 chr3B 90.844 1256 88 15 1265 2497 443702449 443701198 0.000000e+00 1657.0
6 TraesCS3D01G246400 chr3B 96.785 622 15 3 506 1122 443703084 443702463 0.000000e+00 1033.0
7 TraesCS3D01G246400 chr3B 89.497 457 27 7 1 449 443703760 443703317 2.230000e-155 558.0
8 TraesCS3D01G246400 chr3B 79.476 229 40 6 2036 2260 39648631 39648406 3.410000e-34 156.0
9 TraesCS3D01G246400 chr3A 92.376 1128 57 13 1 1120 458920571 458921677 0.000000e+00 1580.0
10 TraesCS3D01G246400 chr3A 94.272 419 19 1 1253 1666 458921681 458922099 9.990000e-179 636.0
11 TraesCS3D01G246400 chr3A 84.396 455 67 3 2008 2458 545451707 545452161 6.500000e-121 444.0
12 TraesCS3D01G246400 chr3A 92.800 125 8 1 347 471 623942323 623942446 2.020000e-41 180.0
13 TraesCS3D01G246400 chr5D 84.719 445 53 7 2008 2448 109580131 109579698 5.060000e-117 431.0
14 TraesCS3D01G246400 chr5D 79.808 416 63 10 2037 2434 550400871 550400459 1.500000e-72 283.0
15 TraesCS3D01G246400 chr5A 82.329 498 61 13 2012 2495 139688447 139687963 8.530000e-110 407.0
16 TraesCS3D01G246400 chr5A 83.478 345 42 11 1663 2002 643037670 643038004 8.900000e-80 307.0
17 TraesCS3D01G246400 chr5A 83.188 345 44 10 1663 2002 643045282 643045617 1.150000e-78 303.0
18 TraesCS3D01G246400 chr5A 84.490 245 36 2 2191 2434 230531749 230531506 9.160000e-60 241.0
19 TraesCS3D01G246400 chr5A 84.783 138 11 5 1123 1250 676322074 676322211 2.070000e-26 130.0
20 TraesCS3D01G246400 chr2D 83.262 466 53 16 2008 2456 517893754 517893297 3.070000e-109 405.0
21 TraesCS3D01G246400 chr2D 78.917 351 64 9 1656 2002 207186069 207186413 1.980000e-56 230.0
22 TraesCS3D01G246400 chr2D 89.655 145 5 1 1120 1254 595164807 595164663 2.620000e-40 176.0
23 TraesCS3D01G246400 chr2D 96.154 78 3 0 2484 2561 590448026 590447949 7.440000e-26 128.0
24 TraesCS3D01G246400 chr1B 89.083 229 19 5 287 509 427650768 427650996 1.940000e-71 279.0
25 TraesCS3D01G246400 chr1B 79.598 348 57 12 1665 2006 521185433 521185094 1.180000e-58 237.0
26 TraesCS3D01G246400 chr1A 77.115 520 83 20 2002 2500 426495851 426496355 4.200000e-68 268.0
27 TraesCS3D01G246400 chr1A 81.143 175 31 2 2005 2178 565467407 565467234 3.440000e-29 139.0
28 TraesCS3D01G246400 chr2A 87.391 230 19 9 287 506 719802562 719802333 3.270000e-64 255.0
29 TraesCS3D01G246400 chr2A 83.688 141 13 1 1120 1250 345885568 345885428 9.620000e-25 124.0
30 TraesCS3D01G246400 chr2A 92.683 82 6 0 2480 2561 358314085 358314004 4.480000e-23 119.0
31 TraesCS3D01G246400 chr7B 79.781 366 56 16 2030 2387 467076006 467076361 1.520000e-62 250.0
32 TraesCS3D01G246400 chr7B 85.034 147 22 0 2032 2178 144657899 144657753 1.590000e-32 150.0
33 TraesCS3D01G246400 chr7D 79.882 338 56 8 1663 1996 288463891 288464220 1.180000e-58 237.0
34 TraesCS3D01G246400 chr7D 92.683 82 3 3 2480 2561 279420536 279420458 5.790000e-22 115.0
35 TraesCS3D01G246400 chr5B 79.710 345 57 11 1664 2003 229822821 229823157 1.180000e-58 237.0
36 TraesCS3D01G246400 chr5B 79.480 346 60 10 1662 2003 72464221 72464559 4.260000e-58 235.0
37 TraesCS3D01G246400 chrUn 90.062 161 14 2 287 445 111203433 111203273 9.290000e-50 207.0
38 TraesCS3D01G246400 chr4B 81.731 208 30 6 2008 2210 398793830 398794034 1.580000e-37 167.0
39 TraesCS3D01G246400 chr4B 86.111 144 10 1 1120 1253 494694799 494694656 2.050000e-31 147.0
40 TraesCS3D01G246400 chr6A 87.234 141 8 1 1120 1250 11882895 11882755 4.410000e-33 152.0
41 TraesCS3D01G246400 chr6A 81.818 132 15 9 2434 2561 242208106 242207980 4.510000e-18 102.0
42 TraesCS3D01G246400 chr2B 78.926 242 32 14 2004 2230 785095220 785095457 2.050000e-31 147.0
43 TraesCS3D01G246400 chr1D 85.816 141 10 1 1120 1250 313569908 313570048 9.550000e-30 141.0
44 TraesCS3D01G246400 chr1D 92.771 83 2 4 2480 2561 295865186 295865265 1.610000e-22 117.0
45 TraesCS3D01G246400 chr6D 92.771 83 2 4 2480 2561 15304012 15303933 1.610000e-22 117.0
46 TraesCS3D01G246400 chr6D 92.771 83 2 4 2480 2561 403131439 403131360 1.610000e-22 117.0
47 TraesCS3D01G246400 chr4A 80.986 142 10 8 1123 1250 472946823 472946685 2.100000e-16 97.1
48 TraesCS3D01G246400 chr4A 85.965 57 6 2 238 294 688994784 688994730 2.750000e-05 60.2


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 TraesCS3D01G246400 chr3D 343710170 343712730 2560 True 4730.000000 4730 100.000000 1 2561 1 chr3D.!!$R1 2560
1 TraesCS3D01G246400 chr3B 443701198 443703760 2562 True 1082.666667 1657 92.375333 1 2497 3 chr3B.!!$R2 2496
2 TraesCS3D01G246400 chr3A 458920571 458922099 1528 False 1108.000000 1580 93.324000 1 1666 2 chr3A.!!$F3 1665
3 TraesCS3D01G246400 chr1A 426495851 426496355 504 False 268.000000 268 77.115000 2002 2500 1 chr1A.!!$F1 498

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
940 1146 0.798776 GAGTGAGCCACCAAATCACG 59.201 55.0 2.18 0.0 46.25 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 2770 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.0 15.81 0.0 43.2 4.57 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 3.793492 GCCTTTGCTCGCAATCTATTTTC 59.207 43.478 5.03 0.00 35.70 2.29
94 99 6.583427 ACGACTAAAACAAAAAGTTGGTTGAC 59.417 34.615 6.56 0.00 44.07 3.18
105 110 4.654091 AGTTGGTTGACAAATTGACAGG 57.346 40.909 0.00 0.00 41.58 4.00
255 264 6.805713 ACAGGGCAATTTATTACAGCAATAC 58.194 36.000 0.00 0.00 0.00 1.89
257 266 7.777910 ACAGGGCAATTTATTACAGCAATACTA 59.222 33.333 0.00 0.00 0.00 1.82
325 338 3.162666 TGTATGACCCGTGAAAGACTCT 58.837 45.455 0.00 0.00 0.00 3.24
618 820 1.068921 GCTAGTAGCTGGCCTGCTC 59.931 63.158 37.00 26.84 42.97 4.26
862 1068 2.683933 AAGTCCGGTCAGCGGGAT 60.684 61.111 16.90 0.69 44.32 3.85
870 1076 1.112113 GGTCAGCGGGATAGACTTCA 58.888 55.000 0.00 0.00 32.98 3.02
876 1082 1.476891 GCGGGATAGACTTCAGACACA 59.523 52.381 0.00 0.00 0.00 3.72
887 1093 4.494484 ACTTCAGACACAAAAACAAAGCC 58.506 39.130 0.00 0.00 0.00 4.35
940 1146 0.798776 GAGTGAGCCACCAAATCACG 59.201 55.000 2.18 0.00 46.25 4.35
951 1157 1.872952 CCAAATCACGCAGTTCTGTCA 59.127 47.619 1.78 0.00 41.61 3.58
1122 1328 0.249120 TGGGCGGTGAGTATTCAGTG 59.751 55.000 0.00 0.00 32.98 3.66
1123 1329 1.090052 GGGCGGTGAGTATTCAGTGC 61.090 60.000 3.75 3.75 35.15 4.40
1124 1330 1.090052 GGCGGTGAGTATTCAGTGCC 61.090 60.000 12.92 12.92 43.48 5.01
1125 1331 0.108138 GCGGTGAGTATTCAGTGCCT 60.108 55.000 1.42 0.00 32.98 4.75
1126 1332 1.645034 CGGTGAGTATTCAGTGCCTG 58.355 55.000 0.00 0.00 32.98 4.85
1127 1333 1.066858 CGGTGAGTATTCAGTGCCTGT 60.067 52.381 0.00 0.00 32.98 4.00
1128 1334 2.612972 CGGTGAGTATTCAGTGCCTGTT 60.613 50.000 0.00 0.00 32.98 3.16
1129 1335 3.003480 GGTGAGTATTCAGTGCCTGTTC 58.997 50.000 0.00 0.00 32.98 3.18
1130 1336 2.668457 GTGAGTATTCAGTGCCTGTTCG 59.332 50.000 0.00 0.00 32.98 3.95
1131 1337 2.271800 GAGTATTCAGTGCCTGTTCGG 58.728 52.381 2.68 0.00 32.61 4.30
1132 1338 1.623811 AGTATTCAGTGCCTGTTCGGT 59.376 47.619 2.68 0.00 32.61 4.69
1133 1339 2.829720 AGTATTCAGTGCCTGTTCGGTA 59.170 45.455 2.68 0.00 32.61 4.02
1138 1344 3.908737 GTGCCTGTTCGGTACTTCT 57.091 52.632 0.00 0.00 44.19 2.85
1139 1345 1.711206 GTGCCTGTTCGGTACTTCTC 58.289 55.000 0.00 0.00 44.19 2.87
1140 1346 0.606604 TGCCTGTTCGGTACTTCTCC 59.393 55.000 0.00 0.00 34.25 3.71
1141 1347 0.108281 GCCTGTTCGGTACTTCTCCC 60.108 60.000 0.00 0.00 34.25 4.30
1142 1348 1.263356 CCTGTTCGGTACTTCTCCCA 58.737 55.000 0.00 0.00 0.00 4.37
1143 1349 1.831736 CCTGTTCGGTACTTCTCCCAT 59.168 52.381 0.00 0.00 0.00 4.00
1144 1350 2.236395 CCTGTTCGGTACTTCTCCCATT 59.764 50.000 0.00 0.00 0.00 3.16
1145 1351 3.307480 CCTGTTCGGTACTTCTCCCATTT 60.307 47.826 0.00 0.00 0.00 2.32
1146 1352 3.933332 CTGTTCGGTACTTCTCCCATTTC 59.067 47.826 0.00 0.00 0.00 2.17
1147 1353 3.325425 TGTTCGGTACTTCTCCCATTTCA 59.675 43.478 0.00 0.00 0.00 2.69
1148 1354 4.202377 TGTTCGGTACTTCTCCCATTTCAA 60.202 41.667 0.00 0.00 0.00 2.69
1149 1355 4.627284 TCGGTACTTCTCCCATTTCAAA 57.373 40.909 0.00 0.00 0.00 2.69
1150 1356 4.975631 TCGGTACTTCTCCCATTTCAAAA 58.024 39.130 0.00 0.00 0.00 2.44
1151 1357 4.758165 TCGGTACTTCTCCCATTTCAAAAC 59.242 41.667 0.00 0.00 0.00 2.43
1152 1358 4.760204 CGGTACTTCTCCCATTTCAAAACT 59.240 41.667 0.00 0.00 0.00 2.66
1153 1359 5.106673 CGGTACTTCTCCCATTTCAAAACTC 60.107 44.000 0.00 0.00 0.00 3.01
1154 1360 5.183331 GGTACTTCTCCCATTTCAAAACTCC 59.817 44.000 0.00 0.00 0.00 3.85
1155 1361 4.803452 ACTTCTCCCATTTCAAAACTCCA 58.197 39.130 0.00 0.00 0.00 3.86
1156 1362 4.584743 ACTTCTCCCATTTCAAAACTCCAC 59.415 41.667 0.00 0.00 0.00 4.02
1157 1363 4.453480 TCTCCCATTTCAAAACTCCACT 57.547 40.909 0.00 0.00 0.00 4.00
1158 1364 4.398319 TCTCCCATTTCAAAACTCCACTC 58.602 43.478 0.00 0.00 0.00 3.51
1159 1365 3.496331 TCCCATTTCAAAACTCCACTCC 58.504 45.455 0.00 0.00 0.00 3.85
1160 1366 2.228822 CCCATTTCAAAACTCCACTCCG 59.771 50.000 0.00 0.00 0.00 4.63
1161 1367 2.884639 CCATTTCAAAACTCCACTCCGT 59.115 45.455 0.00 0.00 0.00 4.69
1162 1368 3.304659 CCATTTCAAAACTCCACTCCGTG 60.305 47.826 0.00 0.00 0.00 4.94
1163 1369 1.305201 TTCAAAACTCCACTCCGTGC 58.695 50.000 0.00 0.00 31.34 5.34
1164 1370 0.878523 TCAAAACTCCACTCCGTGCG 60.879 55.000 0.00 0.00 31.34 5.34
1165 1371 0.878523 CAAAACTCCACTCCGTGCGA 60.879 55.000 0.00 0.00 31.34 5.10
1166 1372 0.600255 AAAACTCCACTCCGTGCGAG 60.600 55.000 9.44 9.44 44.95 5.03
1167 1373 2.436087 AAACTCCACTCCGTGCGAGG 62.436 60.000 13.28 0.00 43.57 4.63
1168 1374 3.062466 CTCCACTCCGTGCGAGGA 61.062 66.667 0.00 0.00 43.57 3.71
1179 1385 3.386237 GCGAGGAGCTGGGTCTGT 61.386 66.667 0.00 0.00 44.04 3.41
1180 1386 2.575993 CGAGGAGCTGGGTCTGTG 59.424 66.667 0.00 0.00 0.00 3.66
1181 1387 2.267324 GAGGAGCTGGGTCTGTGC 59.733 66.667 0.00 0.00 0.00 4.57
1182 1388 3.655810 GAGGAGCTGGGTCTGTGCG 62.656 68.421 0.00 0.00 0.00 5.34
1183 1389 3.695606 GGAGCTGGGTCTGTGCGA 61.696 66.667 0.00 0.00 0.00 5.10
1184 1390 2.581354 GAGCTGGGTCTGTGCGAT 59.419 61.111 0.00 0.00 0.00 4.58
1185 1391 1.078848 GAGCTGGGTCTGTGCGATT 60.079 57.895 0.00 0.00 0.00 3.34
1186 1392 1.364626 GAGCTGGGTCTGTGCGATTG 61.365 60.000 0.00 0.00 0.00 2.67
1187 1393 3.044059 GCTGGGTCTGTGCGATTGC 62.044 63.158 0.00 0.00 43.20 3.56
1204 1410 4.708968 CGCTATCGCTCCCTCCGC 62.709 72.222 0.00 0.00 0.00 5.54
1205 1411 3.299190 GCTATCGCTCCCTCCGCT 61.299 66.667 0.00 0.00 0.00 5.52
1206 1412 2.958576 CTATCGCTCCCTCCGCTC 59.041 66.667 0.00 0.00 0.00 5.03
1207 1413 2.597805 TATCGCTCCCTCCGCTCC 60.598 66.667 0.00 0.00 0.00 4.70
1212 1418 2.904866 CTCCCTCCGCTCCGAGAG 60.905 72.222 0.00 0.00 30.97 3.20
1213 1419 3.707640 CTCCCTCCGCTCCGAGAGT 62.708 68.421 0.00 0.00 30.97 3.24
1214 1420 2.756283 CCCTCCGCTCCGAGAGTT 60.756 66.667 0.00 0.00 30.97 3.01
1215 1421 2.492090 CCTCCGCTCCGAGAGTTG 59.508 66.667 0.00 0.00 30.97 3.16
1216 1422 2.202676 CTCCGCTCCGAGAGTTGC 60.203 66.667 0.00 0.00 30.97 4.17
1217 1423 2.989253 TCCGCTCCGAGAGTTGCA 60.989 61.111 0.00 0.00 31.39 4.08
1218 1424 2.507992 CCGCTCCGAGAGTTGCAG 60.508 66.667 0.00 0.00 31.39 4.41
1219 1425 3.184683 CGCTCCGAGAGTTGCAGC 61.185 66.667 0.00 0.00 31.39 5.25
1220 1426 2.264166 GCTCCGAGAGTTGCAGCT 59.736 61.111 1.30 1.30 31.39 4.24
1221 1427 2.099431 GCTCCGAGAGTTGCAGCTG 61.099 63.158 8.19 10.11 31.39 4.24
1222 1428 1.291588 CTCCGAGAGTTGCAGCTGT 59.708 57.895 16.64 3.02 0.00 4.40
1223 1429 1.005748 TCCGAGAGTTGCAGCTGTG 60.006 57.895 16.64 0.00 0.00 3.66
1224 1430 2.031516 CCGAGAGTTGCAGCTGTGG 61.032 63.158 16.64 5.11 0.00 4.17
1225 1431 1.005748 CGAGAGTTGCAGCTGTGGA 60.006 57.895 16.64 0.00 0.00 4.02
1226 1432 1.013005 CGAGAGTTGCAGCTGTGGAG 61.013 60.000 16.64 0.00 0.00 3.86
1227 1433 1.297456 GAGAGTTGCAGCTGTGGAGC 61.297 60.000 16.64 0.00 46.64 4.70
1235 1441 3.695606 GCTGTGGAGCGGAGTGGA 61.696 66.667 0.00 0.00 34.87 4.02
1236 1442 3.023949 GCTGTGGAGCGGAGTGGAT 62.024 63.158 0.00 0.00 34.87 3.41
1237 1443 1.142748 CTGTGGAGCGGAGTGGATC 59.857 63.158 0.00 0.00 0.00 3.36
1238 1444 2.303549 CTGTGGAGCGGAGTGGATCC 62.304 65.000 4.20 4.20 45.64 3.36
1245 1451 2.818132 GGAGTGGATCCGAGCAGG 59.182 66.667 7.39 0.00 38.67 4.85
1246 1452 2.801631 GGAGTGGATCCGAGCAGGG 61.802 68.421 7.39 0.00 38.67 4.45
1247 1453 3.453070 GAGTGGATCCGAGCAGGGC 62.453 68.421 7.39 0.00 41.52 5.19
1248 1454 3.474570 GTGGATCCGAGCAGGGCT 61.475 66.667 7.39 0.00 43.88 5.19
1249 1455 2.688666 TGGATCCGAGCAGGGCTT 60.689 61.111 7.39 0.00 39.88 4.35
1250 1456 2.110006 GGATCCGAGCAGGGCTTC 59.890 66.667 0.00 0.00 39.88 3.86
1251 1457 2.735772 GGATCCGAGCAGGGCTTCA 61.736 63.158 0.00 0.00 39.88 3.02
1256 1462 1.517257 CGAGCAGGGCTTCAGTACG 60.517 63.158 0.00 0.00 39.88 3.67
1328 1534 0.965439 TGTTTGTGTATTGCAGGGGC 59.035 50.000 0.00 0.00 41.68 5.80
1371 1577 0.321210 ACACCATGACGGCGAATCAA 60.321 50.000 16.62 0.00 39.03 2.57
1416 1622 0.874175 CGGCGAGCGATGGAAATGTA 60.874 55.000 0.00 0.00 0.00 2.29
1736 1950 8.984891 TTTCACAATATAAGGTGCATTTCTTG 57.015 30.769 9.28 6.34 35.04 3.02
1753 1967 7.327032 GCATTTCTTGTAACTCCTCAACATTTC 59.673 37.037 0.00 0.00 0.00 2.17
1754 1968 6.539649 TTCTTGTAACTCCTCAACATTTCG 57.460 37.500 0.00 0.00 0.00 3.46
1758 1972 6.687081 TGTAACTCCTCAACATTTCGTTTT 57.313 33.333 0.00 0.00 34.86 2.43
1768 1982 4.483476 ACATTTCGTTTTTAGCGCTCTT 57.517 36.364 16.34 0.00 0.00 2.85
1771 1985 4.539509 TTTCGTTTTTAGCGCTCTTGAA 57.460 36.364 16.34 8.27 0.00 2.69
1843 2058 4.895224 AAAAAGGAAAGTGTCTCGGTTC 57.105 40.909 0.00 0.00 0.00 3.62
1851 2066 1.344438 AGTGTCTCGGTTCTGATTGCA 59.656 47.619 0.00 0.00 0.00 4.08
1870 2085 9.890629 TGATTGCATGTATCTCTTACTACTTTT 57.109 29.630 10.13 0.00 0.00 2.27
1976 2191 4.408694 GTCACCGTGCCAAAATTATACAC 58.591 43.478 0.00 0.00 0.00 2.90
1977 2192 4.072839 TCACCGTGCCAAAATTATACACA 58.927 39.130 0.00 0.00 0.00 3.72
2112 2327 2.825532 ACCCATTCCCAAAATGTCTTCG 59.174 45.455 0.00 0.00 0.00 3.79
2117 2332 1.804151 TCCCAAAATGTCTTCGCTTCG 59.196 47.619 0.00 0.00 0.00 3.79
2152 2367 2.552591 CCATTTCTGGCCCAAATTTGCA 60.553 45.455 12.92 4.87 35.23 4.08
2258 2486 3.866910 GTCTTTATTAATGACGACCGCCA 59.133 43.478 5.77 0.00 0.00 5.69
2260 2488 5.007332 GTCTTTATTAATGACGACCGCCAAT 59.993 40.000 5.77 0.00 0.00 3.16
2472 2708 4.436998 CCTTCGCCGGCGTCTTCT 62.437 66.667 44.16 0.00 40.74 2.85
2497 2733 1.744368 CCTCAGCTGCGCATCAACT 60.744 57.895 12.24 3.19 0.00 3.16
2498 2734 1.424240 CTCAGCTGCGCATCAACTG 59.576 57.895 12.24 16.39 39.60 3.16
2499 2735 1.296755 CTCAGCTGCGCATCAACTGT 61.297 55.000 12.24 0.00 39.34 3.55
2500 2736 0.886043 TCAGCTGCGCATCAACTGTT 60.886 50.000 12.24 0.00 39.34 3.16
2501 2737 0.728129 CAGCTGCGCATCAACTGTTG 60.728 55.000 12.24 14.24 34.90 3.33
2502 2738 1.443194 GCTGCGCATCAACTGTTGG 60.443 57.895 19.55 6.56 0.00 3.77
2503 2739 1.210931 CTGCGCATCAACTGTTGGG 59.789 57.895 19.55 13.30 0.00 4.12
2504 2740 2.203972 CTGCGCATCAACTGTTGGGG 62.204 60.000 19.55 13.50 0.00 4.96
2505 2741 1.971167 GCGCATCAACTGTTGGGGA 60.971 57.895 19.55 1.84 0.00 4.81
2506 2742 1.523154 GCGCATCAACTGTTGGGGAA 61.523 55.000 19.55 1.48 0.00 3.97
2507 2743 0.240945 CGCATCAACTGTTGGGGAAC 59.759 55.000 19.55 5.52 0.00 3.62
2508 2744 0.240945 GCATCAACTGTTGGGGAACG 59.759 55.000 19.55 4.53 0.00 3.95
2509 2745 1.604604 CATCAACTGTTGGGGAACGT 58.395 50.000 19.55 0.00 0.00 3.99
2510 2746 2.773487 CATCAACTGTTGGGGAACGTA 58.227 47.619 19.55 0.00 0.00 3.57
2511 2747 2.536761 TCAACTGTTGGGGAACGTAG 57.463 50.000 19.55 0.00 0.00 3.51
2513 2749 2.964464 TCAACTGTTGGGGAACGTAGTA 59.036 45.455 19.55 0.00 45.00 1.82
2514 2750 3.387374 TCAACTGTTGGGGAACGTAGTAA 59.613 43.478 19.55 0.00 45.00 2.24
2515 2751 4.040706 TCAACTGTTGGGGAACGTAGTAAT 59.959 41.667 19.55 0.00 45.00 1.89
2516 2752 4.628963 ACTGTTGGGGAACGTAGTAATT 57.371 40.909 0.00 0.00 45.00 1.40
2517 2753 4.976864 ACTGTTGGGGAACGTAGTAATTT 58.023 39.130 0.00 0.00 45.00 1.82
2518 2754 4.999311 ACTGTTGGGGAACGTAGTAATTTC 59.001 41.667 0.00 0.00 45.00 2.17
2519 2755 4.970711 TGTTGGGGAACGTAGTAATTTCA 58.029 39.130 0.00 0.00 45.00 2.69
2520 2756 5.374921 TGTTGGGGAACGTAGTAATTTCAA 58.625 37.500 0.00 0.00 45.00 2.69
2521 2757 5.826737 TGTTGGGGAACGTAGTAATTTCAAA 59.173 36.000 0.00 0.00 45.00 2.69
2522 2758 6.320672 TGTTGGGGAACGTAGTAATTTCAAAA 59.679 34.615 0.00 0.00 45.00 2.44
2523 2759 6.956202 TGGGGAACGTAGTAATTTCAAAAA 57.044 33.333 0.00 0.00 45.00 1.94
2541 2777 0.515564 AAAACATCCTACGCACACGC 59.484 50.000 0.00 0.00 45.53 5.34
2542 2778 0.601576 AAACATCCTACGCACACGCA 60.602 50.000 0.00 0.00 45.53 5.24
2543 2779 0.601576 AACATCCTACGCACACGCAA 60.602 50.000 0.00 0.00 45.53 4.85
2544 2780 1.014044 ACATCCTACGCACACGCAAG 61.014 55.000 0.00 0.00 45.53 4.01
2545 2781 0.735978 CATCCTACGCACACGCAAGA 60.736 55.000 0.00 0.00 45.53 3.02
2546 2782 0.175760 ATCCTACGCACACGCAAGAT 59.824 50.000 0.00 0.00 45.53 2.40
2547 2783 0.457853 TCCTACGCACACGCAAGATC 60.458 55.000 0.00 0.00 45.53 2.75
2548 2784 0.735978 CCTACGCACACGCAAGATCA 60.736 55.000 0.00 0.00 45.53 2.92
2549 2785 1.280982 CTACGCACACGCAAGATCAT 58.719 50.000 0.00 0.00 45.53 2.45
2550 2786 0.998669 TACGCACACGCAAGATCATG 59.001 50.000 0.00 0.00 45.53 3.07
2551 2787 1.061411 CGCACACGCAAGATCATGG 59.939 57.895 0.00 0.00 43.62 3.66
2552 2788 1.638388 CGCACACGCAAGATCATGGT 61.638 55.000 0.00 0.00 43.62 3.55
2553 2789 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
2554 2790 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
2555 2791 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
2556 2792 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
2557 2793 1.019673 ACGCAAGATCATGGTGATGC 58.980 50.000 0.00 3.06 37.20 3.91
2558 2794 1.018910 CGCAAGATCATGGTGATGCA 58.981 50.000 11.83 0.00 37.20 3.96
2559 2795 1.607148 CGCAAGATCATGGTGATGCAT 59.393 47.619 0.00 0.00 37.20 3.96
2560 2796 2.809696 CGCAAGATCATGGTGATGCATA 59.190 45.455 0.00 0.00 37.20 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 89 4.277476 TCCTGTCAATTTGTCAACCAACT 58.723 39.130 0.00 0.00 31.20 3.16
307 319 2.530701 AGAGAGTCTTTCACGGGTCAT 58.469 47.619 0.00 0.00 0.00 3.06
313 326 5.718649 TTCAACAAAGAGAGTCTTTCACG 57.281 39.130 0.00 0.00 42.60 4.35
325 338 6.537453 TGGGAACAGAATTTTCAACAAAGA 57.463 33.333 0.00 0.00 35.01 2.52
519 721 1.702401 TGTATTTGTGGTCAGCTCCCA 59.298 47.619 0.00 0.00 0.00 4.37
691 894 1.609320 GGCTGTTGAGGAAGTCTGTCC 60.609 57.143 0.00 0.00 38.03 4.02
862 1068 6.404293 GGCTTTGTTTTTGTGTCTGAAGTCTA 60.404 38.462 0.00 0.00 0.00 2.59
870 1076 1.203523 TGCGGCTTTGTTTTTGTGTCT 59.796 42.857 0.00 0.00 0.00 3.41
876 1082 2.323968 ATTGGTGCGGCTTTGTTTTT 57.676 40.000 0.00 0.00 0.00 1.94
887 1093 3.508840 GAGGCGGGAATTGGTGCG 61.509 66.667 0.00 0.00 0.00 5.34
940 1146 3.084579 CCGCGATGACAGAACTGC 58.915 61.111 8.23 0.00 0.00 4.40
1122 1328 0.108281 GGGAGAAGTACCGAACAGGC 60.108 60.000 0.00 0.00 46.52 4.85
1124 1330 3.611766 AATGGGAGAAGTACCGAACAG 57.388 47.619 0.00 0.00 0.00 3.16
1125 1331 3.325425 TGAAATGGGAGAAGTACCGAACA 59.675 43.478 0.00 0.00 0.00 3.18
1126 1332 3.934068 TGAAATGGGAGAAGTACCGAAC 58.066 45.455 0.00 0.00 0.00 3.95
1127 1333 4.627284 TTGAAATGGGAGAAGTACCGAA 57.373 40.909 0.00 0.00 0.00 4.30
1128 1334 4.627284 TTTGAAATGGGAGAAGTACCGA 57.373 40.909 0.00 0.00 0.00 4.69
1129 1335 4.760204 AGTTTTGAAATGGGAGAAGTACCG 59.240 41.667 0.00 0.00 0.00 4.02
1130 1336 5.183331 GGAGTTTTGAAATGGGAGAAGTACC 59.817 44.000 0.00 0.00 0.00 3.34
1131 1337 5.768164 TGGAGTTTTGAAATGGGAGAAGTAC 59.232 40.000 0.00 0.00 0.00 2.73
1132 1338 5.768164 GTGGAGTTTTGAAATGGGAGAAGTA 59.232 40.000 0.00 0.00 0.00 2.24
1133 1339 4.584743 GTGGAGTTTTGAAATGGGAGAAGT 59.415 41.667 0.00 0.00 0.00 3.01
1134 1340 4.829492 AGTGGAGTTTTGAAATGGGAGAAG 59.171 41.667 0.00 0.00 0.00 2.85
1135 1341 4.803452 AGTGGAGTTTTGAAATGGGAGAA 58.197 39.130 0.00 0.00 0.00 2.87
1136 1342 4.398319 GAGTGGAGTTTTGAAATGGGAGA 58.602 43.478 0.00 0.00 0.00 3.71
1137 1343 3.507622 GGAGTGGAGTTTTGAAATGGGAG 59.492 47.826 0.00 0.00 0.00 4.30
1138 1344 3.496331 GGAGTGGAGTTTTGAAATGGGA 58.504 45.455 0.00 0.00 0.00 4.37
1139 1345 2.228822 CGGAGTGGAGTTTTGAAATGGG 59.771 50.000 0.00 0.00 0.00 4.00
1140 1346 2.884639 ACGGAGTGGAGTTTTGAAATGG 59.115 45.455 0.00 0.00 42.51 3.16
1159 1365 4.803426 GACCCAGCTCCTCGCACG 62.803 72.222 0.00 0.00 42.61 5.34
1160 1366 3.386237 AGACCCAGCTCCTCGCAC 61.386 66.667 0.00 0.00 42.61 5.34
1161 1367 3.385384 CAGACCCAGCTCCTCGCA 61.385 66.667 0.00 0.00 42.61 5.10
1162 1368 3.386237 ACAGACCCAGCTCCTCGC 61.386 66.667 0.00 0.00 39.57 5.03
1163 1369 2.575993 CACAGACCCAGCTCCTCG 59.424 66.667 0.00 0.00 0.00 4.63
1164 1370 2.267324 GCACAGACCCAGCTCCTC 59.733 66.667 0.00 0.00 0.00 3.71
1165 1371 3.699894 CGCACAGACCCAGCTCCT 61.700 66.667 0.00 0.00 0.00 3.69
1166 1372 2.527951 AATCGCACAGACCCAGCTCC 62.528 60.000 0.00 0.00 0.00 4.70
1167 1373 1.078848 AATCGCACAGACCCAGCTC 60.079 57.895 0.00 0.00 0.00 4.09
1168 1374 1.376424 CAATCGCACAGACCCAGCT 60.376 57.895 0.00 0.00 0.00 4.24
1169 1375 3.044059 GCAATCGCACAGACCCAGC 62.044 63.158 0.00 0.00 38.36 4.85
1170 1376 2.743752 CGCAATCGCACAGACCCAG 61.744 63.158 0.00 0.00 38.40 4.45
1171 1377 2.741985 CGCAATCGCACAGACCCA 60.742 61.111 0.00 0.00 38.40 4.51
1189 1395 2.631580 GGAGCGGAGGGAGCGATAG 61.632 68.421 0.00 0.00 40.04 2.08
1190 1396 2.597805 GGAGCGGAGGGAGCGATA 60.598 66.667 0.00 0.00 40.04 2.92
1195 1401 2.904866 CTCTCGGAGCGGAGGGAG 60.905 72.222 0.00 0.00 36.60 4.30
1196 1402 3.283812 AACTCTCGGAGCGGAGGGA 62.284 63.158 11.33 0.00 36.60 4.20
1197 1403 2.756283 AACTCTCGGAGCGGAGGG 60.756 66.667 0.00 3.67 40.49 4.30
1198 1404 2.492090 CAACTCTCGGAGCGGAGG 59.508 66.667 0.00 0.32 34.74 4.30
1199 1405 2.202676 GCAACTCTCGGAGCGGAG 60.203 66.667 0.00 0.00 32.04 4.63
1200 1406 2.989253 TGCAACTCTCGGAGCGGA 60.989 61.111 0.00 0.00 32.04 5.54
1201 1407 2.507992 CTGCAACTCTCGGAGCGG 60.508 66.667 0.00 0.00 32.04 5.52
1202 1408 3.184683 GCTGCAACTCTCGGAGCG 61.185 66.667 0.00 0.00 38.10 5.03
1204 1410 1.013005 CACAGCTGCAACTCTCGGAG 61.013 60.000 15.27 0.00 35.52 4.63
1205 1411 1.005748 CACAGCTGCAACTCTCGGA 60.006 57.895 15.27 0.00 0.00 4.55
1206 1412 2.031516 CCACAGCTGCAACTCTCGG 61.032 63.158 15.27 0.00 0.00 4.63
1207 1413 1.005748 TCCACAGCTGCAACTCTCG 60.006 57.895 15.27 0.00 0.00 4.04
1208 1414 1.297456 GCTCCACAGCTGCAACTCTC 61.297 60.000 15.27 0.00 43.09 3.20
1209 1415 1.302351 GCTCCACAGCTGCAACTCT 60.302 57.895 15.27 0.00 43.09 3.24
1210 1416 2.675056 CGCTCCACAGCTGCAACTC 61.675 63.158 15.27 0.00 44.40 3.01
1211 1417 2.667536 CGCTCCACAGCTGCAACT 60.668 61.111 15.27 0.00 44.40 3.16
1212 1418 3.730761 CCGCTCCACAGCTGCAAC 61.731 66.667 15.27 0.00 44.40 4.17
1213 1419 3.889134 CTCCGCTCCACAGCTGCAA 62.889 63.158 15.27 0.00 44.40 4.08
1214 1420 4.383861 CTCCGCTCCACAGCTGCA 62.384 66.667 15.27 0.00 44.40 4.41
1215 1421 4.385405 ACTCCGCTCCACAGCTGC 62.385 66.667 15.27 0.00 44.40 5.25
1216 1422 2.433838 CACTCCGCTCCACAGCTG 60.434 66.667 13.48 13.48 44.40 4.24
1217 1423 3.699894 CCACTCCGCTCCACAGCT 61.700 66.667 0.00 0.00 44.40 4.24
1218 1424 2.914777 GATCCACTCCGCTCCACAGC 62.915 65.000 0.00 0.00 42.96 4.40
1219 1425 1.142748 GATCCACTCCGCTCCACAG 59.857 63.158 0.00 0.00 0.00 3.66
1220 1426 2.359169 GGATCCACTCCGCTCCACA 61.359 63.158 6.95 0.00 33.29 4.17
1221 1427 2.501610 GGATCCACTCCGCTCCAC 59.498 66.667 6.95 0.00 33.29 4.02
1228 1434 2.801631 CCCTGCTCGGATCCACTCC 61.802 68.421 13.41 0.00 41.07 3.85
1229 1435 2.818132 CCCTGCTCGGATCCACTC 59.182 66.667 13.41 0.00 33.16 3.51
1230 1436 3.474570 GCCCTGCTCGGATCCACT 61.475 66.667 13.41 0.00 33.16 4.00
1231 1437 2.932130 GAAGCCCTGCTCGGATCCAC 62.932 65.000 13.41 0.58 38.25 4.02
1232 1438 2.688666 AAGCCCTGCTCGGATCCA 60.689 61.111 13.41 0.00 38.25 3.41
1233 1439 2.110006 GAAGCCCTGCTCGGATCC 59.890 66.667 0.00 0.00 38.25 3.36
1234 1440 1.227497 CTGAAGCCCTGCTCGGATC 60.227 63.158 0.00 0.00 38.25 3.36
1235 1441 0.687757 TACTGAAGCCCTGCTCGGAT 60.688 55.000 0.00 0.00 38.25 4.18
1236 1442 1.304962 TACTGAAGCCCTGCTCGGA 60.305 57.895 0.00 0.00 38.25 4.55
1237 1443 1.153549 GTACTGAAGCCCTGCTCGG 60.154 63.158 0.00 0.00 38.25 4.63
1238 1444 1.517257 CGTACTGAAGCCCTGCTCG 60.517 63.158 0.00 0.00 38.25 5.03
1239 1445 1.811679 GCGTACTGAAGCCCTGCTC 60.812 63.158 0.00 0.00 38.25 4.26
1240 1446 2.266055 GCGTACTGAAGCCCTGCT 59.734 61.111 0.00 0.00 42.56 4.24
1246 1452 1.497722 GCTGTTGGCGTACTGAAGC 59.502 57.895 0.00 0.00 0.00 3.86
1261 1467 0.680618 TCAAACCAATTGGCCAGCTG 59.319 50.000 24.79 6.78 39.62 4.24
1273 1479 3.181503 GCTAGTCGATCGTACTCAAACCA 60.182 47.826 15.94 1.09 0.00 3.67
1318 1524 1.077716 GTAACTCCGCCCCTGCAAT 60.078 57.895 0.00 0.00 37.32 3.56
1611 1822 9.494271 CAGGACATTAAATATAGTACACAGCAT 57.506 33.333 0.00 0.00 0.00 3.79
1720 1934 6.485171 AGGAGTTACAAGAAATGCACCTTAT 58.515 36.000 0.00 0.00 0.00 1.73
1725 1939 5.008613 TGTTGAGGAGTTACAAGAAATGCAC 59.991 40.000 0.00 0.00 0.00 4.57
1736 1950 7.322938 GCTAAAAACGAAATGTTGAGGAGTTAC 59.677 37.037 0.00 0.00 40.84 2.50
1776 1990 6.122277 TGCAATCGGGAAGAGATATTTTTCT 58.878 36.000 0.00 0.00 0.00 2.52
1788 2002 4.818546 AGAGAAATACATGCAATCGGGAAG 59.181 41.667 0.00 0.00 0.00 3.46
1790 2004 4.422073 AGAGAAATACATGCAATCGGGA 57.578 40.909 0.00 0.00 0.00 5.14
1832 2047 1.795768 TGCAATCAGAACCGAGACAC 58.204 50.000 0.00 0.00 0.00 3.67
1843 2058 9.539825 AAAGTAGTAAGAGATACATGCAATCAG 57.460 33.333 10.38 0.00 36.94 2.90
1976 2191 9.813826 ATACTCCCTCCATTCCTTTATTTAATG 57.186 33.333 0.00 0.00 0.00 1.90
1977 2192 9.813826 CATACTCCCTCCATTCCTTTATTTAAT 57.186 33.333 0.00 0.00 0.00 1.40
1995 2210 4.443621 GGAGTTGCTCTTAACATACTCCC 58.556 47.826 0.00 0.00 43.65 4.30
2056 2271 3.343421 ACTTTTGTCCGCGGCGAC 61.343 61.111 25.92 15.89 0.00 5.19
2122 2337 3.864686 CAGAAATGGGTCCGCGCG 61.865 66.667 25.67 25.67 0.00 6.86
2137 2352 0.672401 CAGCTGCAAATTTGGGCCAG 60.672 55.000 19.47 17.38 0.00 4.85
2138 2353 1.120184 TCAGCTGCAAATTTGGGCCA 61.120 50.000 19.47 0.00 0.00 5.36
2152 2367 3.490759 CGCCGACGCATTTCAGCT 61.491 61.111 0.00 0.00 34.03 4.24
2212 2440 4.410400 GGTAGTTGGGCGGCTGCT 62.410 66.667 18.85 7.30 42.25 4.24
2387 2616 2.325583 TGGCGATGGCTAGGTTTTAG 57.674 50.000 0.00 0.00 39.81 1.85
2466 2702 3.708220 CTGAGGCCGGCGAGAAGAC 62.708 68.421 22.54 4.09 0.00 3.01
2497 2733 4.970711 TGAAATTACTACGTTCCCCAACA 58.029 39.130 0.00 0.00 32.14 3.33
2498 2734 5.945466 TTGAAATTACTACGTTCCCCAAC 57.055 39.130 0.00 0.00 0.00 3.77
2499 2735 6.956202 TTTTGAAATTACTACGTTCCCCAA 57.044 33.333 0.00 0.00 0.00 4.12
2500 2736 6.956202 TTTTTGAAATTACTACGTTCCCCA 57.044 33.333 0.00 0.00 0.00 4.96
2521 2757 1.069500 GCGTGTGCGTAGGATGTTTTT 60.069 47.619 0.00 0.00 40.81 1.94
2522 2758 0.515564 GCGTGTGCGTAGGATGTTTT 59.484 50.000 0.00 0.00 40.81 2.43
2523 2759 2.159181 GCGTGTGCGTAGGATGTTT 58.841 52.632 0.00 0.00 40.81 2.83
2524 2760 3.870606 GCGTGTGCGTAGGATGTT 58.129 55.556 0.00 0.00 40.81 2.71
2525 2761 4.613358 ATCTTGCGTGTGCGTAGGATGT 62.613 50.000 2.53 0.00 44.66 3.06
2526 2762 2.068942 ATCTTGCGTGTGCGTAGGATG 61.069 52.381 2.53 0.00 44.66 3.51
2534 2770 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
2535 2771 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
2536 2772 2.011947 CATCACCATGATCTTGCGTGT 58.988 47.619 19.89 6.63 34.28 4.49
2537 2773 1.268386 GCATCACCATGATCTTGCGTG 60.268 52.381 17.02 17.02 34.28 5.34
2538 2774 1.019673 GCATCACCATGATCTTGCGT 58.980 50.000 3.07 0.87 34.28 5.24
2539 2775 1.018910 TGCATCACCATGATCTTGCG 58.981 50.000 3.07 0.30 34.28 4.85


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

AutoCloner maintained by Alex Coulton.