Multiple sequence alignment - TraesCS5A01G165400

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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 TraesCS5A01G165400 chr5A 100.000 2739 0 0 1 2739 353987495 353990233 0.000000e+00 5059.0
1 TraesCS5A01G165400 chr5A 94.651 673 28 3 1299 1968 354315314 354314647 0.000000e+00 1037.0
2 TraesCS5A01G165400 chr5A 93.697 476 25 3 744 1215 354315784 354315310 0.000000e+00 708.0
3 TraesCS5A01G165400 chr5A 90.222 225 21 1 500 724 354316252 354316029 2.670000e-75 292.0
4 TraesCS5A01G165400 chr5B 91.956 1442 93 17 1300 2739 300097962 300096542 0.000000e+00 1999.0
5 TraesCS5A01G165400 chr5B 90.939 1225 68 18 1 1194 300099195 300097983 0.000000e+00 1607.0
6 TraesCS5A01G165400 chr5B 93.712 652 38 3 1300 1950 299847680 299848329 0.000000e+00 974.0
7 TraesCS5A01G165400 chr5B 93.913 575 25 5 643 1209 299847105 299847677 0.000000e+00 859.0
8 TraesCS5A01G165400 chr5B 93.750 48 3 0 555 602 299847002 299847049 3.780000e-09 73.1
9 TraesCS5A01G165400 chr5D 92.248 1419 83 20 1327 2739 266325798 266324401 0.000000e+00 1986.0
10 TraesCS5A01G165400 chr5D 92.402 895 31 12 325 1214 266326656 266325794 0.000000e+00 1242.0
11 TraesCS5A01G165400 chr5D 94.619 669 33 2 1299 1965 266086008 266086675 0.000000e+00 1033.0
12 TraesCS5A01G165400 chr5D 93.090 521 28 5 701 1215 266085494 266086012 0.000000e+00 756.0
13 TraesCS5A01G165400 chr5D 87.814 279 28 5 487 761 266085220 266085496 3.400000e-84 322.0
14 TraesCS5A01G165400 chr2A 92.765 387 26 2 1356 1741 30072292 30071907 2.380000e-155 558.0
15 TraesCS5A01G165400 chr2A 92.248 387 28 2 1356 1741 30021208 30020823 5.160000e-152 547.0
16 TraesCS5A01G165400 chr2A 80.060 331 53 12 1 321 768544039 768543712 1.640000e-57 233.0
17 TraesCS5A01G165400 chr2A 88.889 153 17 0 998 1150 30127269 30127117 3.600000e-44 189.0
18 TraesCS5A01G165400 chr2A 87.582 153 19 0 998 1150 30086811 30086659 7.790000e-41 178.0
19 TraesCS5A01G165400 chr2D 92.506 387 27 2 1356 1741 27860337 27859952 1.110000e-153 553.0
20 TraesCS5A01G165400 chr2D 92.248 387 28 2 1356 1741 27853934 27853549 5.160000e-152 547.0
21 TraesCS5A01G165400 chr4A 83.951 324 47 4 1 320 468158126 468157804 3.430000e-79 305.0
22 TraesCS5A01G165400 chr4A 81.388 317 49 10 11 320 719889118 719888805 1.630000e-62 250.0
23 TraesCS5A01G165400 chr4A 80.317 315 56 6 11 320 719787556 719787243 1.640000e-57 233.0
24 TraesCS5A01G165400 chr4A 80.189 318 48 11 11 320 719810336 719810026 9.870000e-55 224.0
25 TraesCS5A01G165400 chr7A 80.882 340 44 10 1 319 113494905 113494566 5.860000e-62 248.0
26 TraesCS5A01G165400 chr7A 85.477 241 27 8 1 235 134981541 134981303 7.580000e-61 244.0
27 TraesCS5A01G165400 chr7D 80.952 315 54 6 11 320 15723791 15724104 7.580000e-61 244.0
28 TraesCS5A01G165400 chr3B 78.614 332 56 11 1 320 363322122 363322450 3.580000e-49 206.0
29 TraesCS5A01G165400 chr2B 88.235 153 18 0 998 1150 44361838 44361686 1.680000e-42 183.0
30 TraesCS5A01G165400 chr2B 82.051 78 14 0 2029 2106 789529721 789529644 1.760000e-07 67.6
31 TraesCS5A01G165400 chr3D 83.333 90 14 1 234 323 58404214 58404126 6.290000e-12 82.4
32 TraesCS5A01G165400 chr1A 100.000 28 0 0 2077 2104 40495554 40495527 5.000000e-03 52.8


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 TraesCS5A01G165400 chr5A 353987495 353990233 2738 False 5059.000000 5059 100.000000 1 2739 1 chr5A.!!$F1 2738
1 TraesCS5A01G165400 chr5A 354314647 354316252 1605 True 679.000000 1037 92.856667 500 1968 3 chr5A.!!$R1 1468
2 TraesCS5A01G165400 chr5B 300096542 300099195 2653 True 1803.000000 1999 91.447500 1 2739 2 chr5B.!!$R1 2738
3 TraesCS5A01G165400 chr5B 299847002 299848329 1327 False 635.366667 974 93.791667 555 1950 3 chr5B.!!$F1 1395
4 TraesCS5A01G165400 chr5D 266324401 266326656 2255 True 1614.000000 1986 92.325000 325 2739 2 chr5D.!!$R1 2414
5 TraesCS5A01G165400 chr5D 266085220 266086675 1455 False 703.666667 1033 91.841000 487 1965 3 chr5D.!!$F1 1478

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
749 1095 0.326048 AGGAGTAGGACCAGCAGCAT 60.326 55.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 2494 0.872881 AAGACAACGTCCAACCGTCG 60.873 55.0 0.0 0.0 40.85 5.12 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
17 18 2.203337 TCACTGGTTGTGCCTGGC 60.203 61.111 12.87 12.87 45.81 4.85
50 51 4.906747 AGAAGGAATTGTTCTGAGAGCT 57.093 40.909 0.00 0.00 32.86 4.09
52 53 4.285517 AGAAGGAATTGTTCTGAGAGCTCA 59.714 41.667 17.77 0.00 32.86 4.26
72 73 3.142174 CAGACTTCTCCAGGGTGAAAAC 58.858 50.000 4.57 2.51 0.00 2.43
80 81 4.601857 TCTCCAGGGTGAAAACCTAAGATT 59.398 41.667 0.00 0.00 36.32 2.40
95 96 4.706476 CCTAAGATTTTGGATCAGGCAACA 59.294 41.667 0.00 0.00 41.41 3.33
98 99 3.896888 AGATTTTGGATCAGGCAACAACA 59.103 39.130 0.00 0.00 41.41 3.33
99 100 3.731652 TTTTGGATCAGGCAACAACAG 57.268 42.857 0.00 0.00 41.41 3.16
120 121 2.053627 CGCTTGTGCATTGTTTCCTTC 58.946 47.619 0.00 0.00 39.64 3.46
124 125 4.737352 GCTTGTGCATTGTTTCCTTCTTGA 60.737 41.667 0.00 0.00 39.41 3.02
127 128 4.202141 TGTGCATTGTTTCCTTCTTGAAGG 60.202 41.667 20.21 20.21 41.35 3.46
151 152 6.146898 GCGTTGCTTTTGAAGACCTTTTATA 58.853 36.000 0.00 0.00 0.00 0.98
175 176 3.378911 TTCGTGTGCTGTATCTTGTGA 57.621 42.857 0.00 0.00 0.00 3.58
182 183 4.826733 TGTGCTGTATCTTGTGATGGTTTT 59.173 37.500 0.00 0.00 34.32 2.43
192 193 1.028130 TGATGGTTTTTGTGCGCTGA 58.972 45.000 9.73 0.00 0.00 4.26
209 210 3.456280 GCTGATGAGAGGAGTTGATCAC 58.544 50.000 0.00 0.00 0.00 3.06
211 212 4.340666 GCTGATGAGAGGAGTTGATCACTA 59.659 45.833 0.00 0.00 35.01 2.74
217 218 3.708631 AGAGGAGTTGATCACTATGGTGG 59.291 47.826 9.56 0.00 43.17 4.61
220 221 3.392616 GGAGTTGATCACTATGGTGGGAT 59.607 47.826 9.56 0.00 43.17 3.85
225 226 5.715439 TGATCACTATGGTGGGATCTTTT 57.285 39.130 9.56 0.00 43.17 2.27
248 259 4.864704 TTTCCTTTGGCTTTGTGTATCC 57.135 40.909 0.00 0.00 0.00 2.59
251 262 3.157087 CCTTTGGCTTTGTGTATCCTGT 58.843 45.455 0.00 0.00 0.00 4.00
279 290 8.201554 GTCTTTGAGACATCTTATATGTGCAA 57.798 34.615 3.33 0.00 44.45 4.08
282 293 7.558161 TTGAGACATCTTATATGTGCAAAGG 57.442 36.000 0.00 0.00 31.52 3.11
304 315 5.241949 AGGCTGAGTGTAATAGGTATCTTCG 59.758 44.000 0.00 0.00 0.00 3.79
305 316 4.918583 GCTGAGTGTAATAGGTATCTTCGC 59.081 45.833 0.00 0.00 0.00 4.70
540 568 1.734117 GAAGCCGTGTTTGCCATGC 60.734 57.895 0.00 0.00 0.00 4.06
548 576 3.119673 CCGTGTTTGCCATGCACTATTAA 60.120 43.478 0.00 0.00 38.71 1.40
557 585 4.154918 GCCATGCACTATTAATCTGGTAGC 59.845 45.833 0.00 0.00 0.00 3.58
748 1094 0.545309 AAGGAGTAGGACCAGCAGCA 60.545 55.000 0.00 0.00 0.00 4.41
749 1095 0.326048 AGGAGTAGGACCAGCAGCAT 60.326 55.000 0.00 0.00 0.00 3.79
788 1143 3.928754 TCTATGGTGCAGAGGATAAGGT 58.071 45.455 0.00 0.00 0.00 3.50
805 1160 0.953471 GGTGCGCAGACATGTGGTTA 60.953 55.000 12.22 0.00 37.41 2.85
823 1178 6.328148 TGTGGTTATTTATCCCGACCTTATCT 59.672 38.462 0.00 0.00 0.00 1.98
908 1263 2.005606 TTGTTGCTCAGGAAGGGCCA 62.006 55.000 6.18 0.00 40.02 5.36
1185 1540 9.349145 GTCTCTGTCTTTCTACTCATTTTCTAC 57.651 37.037 0.00 0.00 0.00 2.59
1196 1555 4.527038 ACTCATTTTCTACCTCACGGAAGA 59.473 41.667 0.00 0.00 0.00 2.87
1209 1568 5.586243 CCTCACGGAAGACAATAACAATCAT 59.414 40.000 0.00 0.00 0.00 2.45
1210 1569 6.761242 CCTCACGGAAGACAATAACAATCATA 59.239 38.462 0.00 0.00 0.00 2.15
1211 1570 7.442364 CCTCACGGAAGACAATAACAATCATAT 59.558 37.037 0.00 0.00 0.00 1.78
1212 1571 8.141835 TCACGGAAGACAATAACAATCATATG 57.858 34.615 0.00 0.00 0.00 1.78
1213 1572 7.768582 TCACGGAAGACAATAACAATCATATGT 59.231 33.333 1.90 0.00 34.24 2.29
1214 1573 7.852454 CACGGAAGACAATAACAATCATATGTG 59.148 37.037 1.90 0.00 32.81 3.21
1215 1574 7.768582 ACGGAAGACAATAACAATCATATGTGA 59.231 33.333 1.90 0.00 39.04 3.58
1216 1575 8.611757 CGGAAGACAATAACAATCATATGTGAA 58.388 33.333 1.90 0.00 38.01 3.18
1217 1576 9.722056 GGAAGACAATAACAATCATATGTGAAC 57.278 33.333 1.90 0.00 38.01 3.18
1228 1587 9.412460 ACAATCATATGTGAACTTTCATATGGT 57.588 29.630 18.58 12.61 46.40 3.55
1229 1588 9.888878 CAATCATATGTGAACTTTCATATGGTC 57.111 33.333 18.58 0.00 46.40 4.02
1230 1589 9.631257 AATCATATGTGAACTTTCATATGGTCA 57.369 29.630 18.58 6.47 46.40 4.02
1231 1590 9.631257 ATCATATGTGAACTTTCATATGGTCAA 57.369 29.630 18.58 6.22 46.40 3.18
1232 1591 9.631257 TCATATGTGAACTTTCATATGGTCAAT 57.369 29.630 18.58 0.00 46.40 2.57
1236 1595 8.628630 TGTGAACTTTCATATGGTCAATTACA 57.371 30.769 2.13 0.00 39.73 2.41
1237 1596 9.241919 TGTGAACTTTCATATGGTCAATTACAT 57.758 29.630 2.13 0.00 39.73 2.29
1257 1616 9.621629 ATTACATACAATAGTTTCAAATCCCGA 57.378 29.630 0.00 0.00 0.00 5.14
1258 1617 7.316544 ACATACAATAGTTTCAAATCCCGAC 57.683 36.000 0.00 0.00 0.00 4.79
1259 1618 4.939509 ACAATAGTTTCAAATCCCGACG 57.060 40.909 0.00 0.00 0.00 5.12
1260 1619 4.320870 ACAATAGTTTCAAATCCCGACGT 58.679 39.130 0.00 0.00 0.00 4.34
1261 1620 4.390909 ACAATAGTTTCAAATCCCGACGTC 59.609 41.667 5.18 5.18 0.00 4.34
1262 1621 2.536761 AGTTTCAAATCCCGACGTCA 57.463 45.000 17.16 0.00 0.00 4.35
1263 1622 2.841215 AGTTTCAAATCCCGACGTCAA 58.159 42.857 17.16 0.05 0.00 3.18
1264 1623 3.408634 AGTTTCAAATCCCGACGTCAAT 58.591 40.909 17.16 2.73 0.00 2.57
1265 1624 3.435671 AGTTTCAAATCCCGACGTCAATC 59.564 43.478 17.16 0.00 0.00 2.67
1266 1625 2.753055 TCAAATCCCGACGTCAATCA 57.247 45.000 17.16 0.00 0.00 2.57
1267 1626 2.616960 TCAAATCCCGACGTCAATCAG 58.383 47.619 17.16 0.00 0.00 2.90
1268 1627 1.062587 CAAATCCCGACGTCAATCAGC 59.937 52.381 17.16 0.00 0.00 4.26
1269 1628 0.249120 AATCCCGACGTCAATCAGCA 59.751 50.000 17.16 0.00 0.00 4.41
1270 1629 0.460284 ATCCCGACGTCAATCAGCAC 60.460 55.000 17.16 0.00 0.00 4.40
1271 1630 1.374125 CCCGACGTCAATCAGCACA 60.374 57.895 17.16 0.00 0.00 4.57
1272 1631 1.626654 CCCGACGTCAATCAGCACAC 61.627 60.000 17.16 0.00 0.00 3.82
1273 1632 0.943835 CCGACGTCAATCAGCACACA 60.944 55.000 17.16 0.00 0.00 3.72
1274 1633 0.858583 CGACGTCAATCAGCACACAA 59.141 50.000 17.16 0.00 0.00 3.33
1275 1634 1.460743 CGACGTCAATCAGCACACAAT 59.539 47.619 17.16 0.00 0.00 2.71
1276 1635 2.096268 CGACGTCAATCAGCACACAATT 60.096 45.455 17.16 0.00 0.00 2.32
1277 1636 3.606846 CGACGTCAATCAGCACACAATTT 60.607 43.478 17.16 0.00 0.00 1.82
1278 1637 4.376920 CGACGTCAATCAGCACACAATTTA 60.377 41.667 17.16 0.00 0.00 1.40
1279 1638 5.034554 ACGTCAATCAGCACACAATTTAG 57.965 39.130 0.00 0.00 0.00 1.85
1280 1639 3.848019 CGTCAATCAGCACACAATTTAGC 59.152 43.478 0.00 0.00 0.00 3.09
1281 1640 4.168760 GTCAATCAGCACACAATTTAGCC 58.831 43.478 0.00 0.00 0.00 3.93
1282 1641 3.119884 TCAATCAGCACACAATTTAGCCG 60.120 43.478 0.00 0.00 0.00 5.52
1283 1642 1.164411 TCAGCACACAATTTAGCCGG 58.836 50.000 0.00 0.00 0.00 6.13
1284 1643 0.456653 CAGCACACAATTTAGCCGGC 60.457 55.000 21.89 21.89 0.00 6.13
1285 1644 0.609131 AGCACACAATTTAGCCGGCT 60.609 50.000 34.85 34.85 0.00 5.52
1286 1645 0.243636 GCACACAATTTAGCCGGCTT 59.756 50.000 37.74 15.21 0.00 4.35
1287 1646 1.732405 GCACACAATTTAGCCGGCTTC 60.732 52.381 37.74 0.41 0.00 3.86
1288 1647 1.812571 CACACAATTTAGCCGGCTTCT 59.187 47.619 37.74 17.05 0.00 2.85
1289 1648 2.084546 ACACAATTTAGCCGGCTTCTC 58.915 47.619 37.74 0.00 0.00 2.87
1290 1649 1.401905 CACAATTTAGCCGGCTTCTCC 59.598 52.381 37.74 0.00 0.00 3.71
1291 1650 1.004277 ACAATTTAGCCGGCTTCTCCA 59.996 47.619 37.74 14.26 34.01 3.86
1292 1651 2.301346 CAATTTAGCCGGCTTCTCCAT 58.699 47.619 37.74 16.41 34.01 3.41
1293 1652 2.262423 ATTTAGCCGGCTTCTCCATC 57.738 50.000 37.74 0.00 34.01 3.51
1294 1653 1.204146 TTTAGCCGGCTTCTCCATCT 58.796 50.000 37.74 9.67 34.01 2.90
1295 1654 0.465705 TTAGCCGGCTTCTCCATCTG 59.534 55.000 37.74 0.00 34.01 2.90
1296 1655 0.397114 TAGCCGGCTTCTCCATCTGA 60.397 55.000 37.74 9.65 34.01 3.27
1297 1656 1.053264 AGCCGGCTTCTCCATCTGAT 61.053 55.000 27.08 0.00 34.01 2.90
1303 1662 3.072944 GGCTTCTCCATCTGATATGTGC 58.927 50.000 0.00 0.00 34.01 4.57
1313 1672 6.015603 TCCATCTGATATGTGCAGAACTAGAG 60.016 42.308 0.00 0.00 44.71 2.43
1546 1905 1.251251 GGTACTACGATGGCCGGTAT 58.749 55.000 1.90 0.00 43.93 2.73
1582 1941 1.078426 GCCTATGTTCGGGTGCACT 60.078 57.895 17.98 0.00 0.00 4.40
2003 2370 4.207165 ACCAATGGAAAATATCTCCACCG 58.793 43.478 6.16 3.90 45.67 4.94
2022 2389 2.277084 CGCCGTGCTTATTACTTCCTT 58.723 47.619 0.00 0.00 0.00 3.36
2024 2391 3.267483 GCCGTGCTTATTACTTCCTTCA 58.733 45.455 0.00 0.00 0.00 3.02
2026 2393 4.024809 GCCGTGCTTATTACTTCCTTCATC 60.025 45.833 0.00 0.00 0.00 2.92
2027 2394 4.511826 CCGTGCTTATTACTTCCTTCATCC 59.488 45.833 0.00 0.00 0.00 3.51
2028 2395 4.511826 CGTGCTTATTACTTCCTTCATCCC 59.488 45.833 0.00 0.00 0.00 3.85
2029 2396 5.437060 GTGCTTATTACTTCCTTCATCCCA 58.563 41.667 0.00 0.00 0.00 4.37
2030 2397 5.885912 GTGCTTATTACTTCCTTCATCCCAA 59.114 40.000 0.00 0.00 0.00 4.12
2039 2406 7.797121 ACTTCCTTCATCCCAAAATAATTGT 57.203 32.000 0.00 0.00 0.00 2.71
2040 2407 7.840931 ACTTCCTTCATCCCAAAATAATTGTC 58.159 34.615 0.00 0.00 0.00 3.18
2041 2408 7.675619 ACTTCCTTCATCCCAAAATAATTGTCT 59.324 33.333 0.00 0.00 0.00 3.41
2042 2409 8.434589 TTCCTTCATCCCAAAATAATTGTCTT 57.565 30.769 0.00 0.00 0.00 3.01
2043 2410 9.540538 TTCCTTCATCCCAAAATAATTGTCTTA 57.459 29.630 0.00 0.00 0.00 2.10
2044 2411 9.540538 TCCTTCATCCCAAAATAATTGTCTTAA 57.459 29.630 0.00 0.00 0.00 1.85
2045 2412 9.586435 CCTTCATCCCAAAATAATTGTCTTAAC 57.414 33.333 0.00 0.00 0.00 2.01
2047 2414 8.893563 TCATCCCAAAATAATTGTCTTAACCT 57.106 30.769 0.00 0.00 0.00 3.50
2048 2415 9.320295 TCATCCCAAAATAATTGTCTTAACCTT 57.680 29.630 0.00 0.00 0.00 3.50
2049 2416 9.369904 CATCCCAAAATAATTGTCTTAACCTTG 57.630 33.333 0.00 0.00 0.00 3.61
2050 2417 7.902087 TCCCAAAATAATTGTCTTAACCTTGG 58.098 34.615 0.00 0.00 0.00 3.61
2051 2418 7.511028 TCCCAAAATAATTGTCTTAACCTTGGT 59.489 33.333 0.00 0.00 0.00 3.67
2052 2419 8.808092 CCCAAAATAATTGTCTTAACCTTGGTA 58.192 33.333 0.00 0.00 0.00 3.25
2108 2475 8.147642 AGACACTTATTTTGAAACAGAGTGAG 57.852 34.615 15.94 0.00 37.17 3.51
2198 2566 1.139498 TGGCTCCCCAGAATGTTGGA 61.139 55.000 0.00 0.00 40.87 3.53
2256 2624 4.910304 ACATAGGACTAAATCTCAGGCCAT 59.090 41.667 5.01 0.00 44.48 4.40
2257 2625 6.084738 ACATAGGACTAAATCTCAGGCCATA 58.915 40.000 5.01 0.00 44.48 2.74
2323 2691 7.489113 GGTGCAAAGATGAAATTATTACAGTGG 59.511 37.037 0.00 0.00 0.00 4.00
2358 2726 8.807667 ATTTTTAGAGTGTGAAGCAAATGAAG 57.192 30.769 0.00 0.00 0.00 3.02
2398 2766 8.053355 AGATCTATCAAAGGAAACCGGTTATTT 58.947 33.333 22.60 18.22 0.00 1.40
2406 2774 9.083080 CAAAGGAAACCGGTTATTTCATTTATC 57.917 33.333 22.62 12.91 44.05 1.75
2414 2782 7.705214 CCGGTTATTTCATTTATCCGGTAAAA 58.295 34.615 0.00 3.70 42.89 1.52
2520 2888 1.070601 GCCAGAAGCCAAACCAAACAT 59.929 47.619 0.00 0.00 34.35 2.71
2576 2944 4.691216 GCCACCTAGAAAACTAGTGAAGTG 59.309 45.833 0.00 0.00 38.88 3.16
2586 2954 9.403583 AGAAAACTAGTGAAGTGGTGAAATTAA 57.596 29.630 0.00 0.00 38.88 1.40
2590 2958 8.779354 ACTAGTGAAGTGGTGAAATTAATCTC 57.221 34.615 0.00 0.00 36.93 2.75
2595 2963 7.604164 GTGAAGTGGTGAAATTAATCTCAGAGA 59.396 37.037 1.54 1.54 0.00 3.10
2598 2966 6.983307 AGTGGTGAAATTAATCTCAGAGATCG 59.017 38.462 13.63 0.00 32.89 3.69
2625 2993 2.446435 TGCTTTTGAGGCCAGGTATTC 58.554 47.619 5.01 0.00 0.00 1.75
2636 3005 3.813724 GGCCAGGTATTCGAGTTTATTCC 59.186 47.826 0.00 0.00 0.00 3.01
2703 3073 4.797912 AAAGAACCCTCCCAATATCTCC 57.202 45.455 0.00 0.00 0.00 3.71
2704 3074 2.707554 AGAACCCTCCCAATATCTCCC 58.292 52.381 0.00 0.00 0.00 4.30
2705 3075 2.021042 AGAACCCTCCCAATATCTCCCA 60.021 50.000 0.00 0.00 0.00 4.37
2706 3076 2.843909 ACCCTCCCAATATCTCCCAT 57.156 50.000 0.00 0.00 0.00 4.00
2707 3077 2.352371 ACCCTCCCAATATCTCCCATG 58.648 52.381 0.00 0.00 0.00 3.66
2733 3103 1.954528 ACGTATCGTGCCCCTATCG 59.045 57.895 0.00 0.00 39.18 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.320073 CAATTGCCAGGCACAACCAG 60.320 55.000 15.89 0.00 43.14 4.00
29 30 4.285517 TGAGCTCTCAGAACAATTCCTTCT 59.714 41.667 16.19 0.00 34.14 2.85
50 51 2.398754 TTCACCCTGGAGAAGTCTGA 57.601 50.000 0.00 0.00 0.00 3.27
52 53 2.106684 GGTTTTCACCCTGGAGAAGTCT 59.893 50.000 0.00 0.00 37.03 3.24
54 55 2.136026 AGGTTTTCACCCTGGAGAAGT 58.864 47.619 0.00 0.00 45.63 3.01
72 73 4.706476 TGTTGCCTGATCCAAAATCTTAGG 59.294 41.667 0.00 0.00 0.00 2.69
80 81 1.340889 GCTGTTGTTGCCTGATCCAAA 59.659 47.619 0.00 0.00 0.00 3.28
95 96 0.102844 AACAATGCACAAGCGCTGTT 59.897 45.000 12.58 6.07 46.23 3.16
98 99 0.318955 GGAAACAATGCACAAGCGCT 60.319 50.000 2.64 2.64 46.23 5.92
99 100 0.318955 AGGAAACAATGCACAAGCGC 60.319 50.000 0.00 0.00 46.23 5.92
120 121 2.490328 TCAAAAGCAACGCCTTCAAG 57.510 45.000 0.00 0.00 0.00 3.02
124 125 1.067060 GGTCTTCAAAAGCAACGCCTT 59.933 47.619 0.00 0.00 0.00 4.35
127 128 2.492019 AAGGTCTTCAAAAGCAACGC 57.508 45.000 0.00 0.00 0.00 4.84
151 152 5.238432 TCACAAGATACAGCACACGAAAAAT 59.762 36.000 0.00 0.00 0.00 1.82
156 157 3.253230 CATCACAAGATACAGCACACGA 58.747 45.455 0.00 0.00 31.88 4.35
171 172 0.743688 AGCGCACAAAAACCATCACA 59.256 45.000 11.47 0.00 0.00 3.58
175 176 1.612950 TCATCAGCGCACAAAAACCAT 59.387 42.857 11.47 0.00 0.00 3.55
182 183 0.108472 CTCCTCTCATCAGCGCACAA 60.108 55.000 11.47 0.00 0.00 3.33
192 193 5.215069 ACCATAGTGATCAACTCCTCTCAT 58.785 41.667 0.00 0.00 40.56 2.90
225 226 5.365314 AGGATACACAAAGCCAAAGGAAAAA 59.635 36.000 0.00 0.00 41.41 1.94
237 248 7.819415 TCTCAAAGACATACAGGATACACAAAG 59.181 37.037 0.00 0.00 41.41 2.77
239 250 7.097192 GTCTCAAAGACATACAGGATACACAA 58.903 38.462 2.28 0.00 44.45 3.33
270 281 3.077484 ACACTCAGCCTTTGCACATAT 57.923 42.857 0.00 0.00 41.13 1.78
273 284 2.340210 TTACACTCAGCCTTTGCACA 57.660 45.000 0.00 0.00 41.13 4.57
279 290 6.239064 CGAAGATACCTATTACACTCAGCCTT 60.239 42.308 0.00 0.00 0.00 4.35
282 293 4.918583 GCGAAGATACCTATTACACTCAGC 59.081 45.833 0.00 0.00 0.00 4.26
328 339 8.262227 TCCCACGTAGAATTATATTTCACTGTT 58.738 33.333 9.42 0.00 0.00 3.16
332 343 6.704493 TGCTCCCACGTAGAATTATATTTCAC 59.296 38.462 9.42 5.50 0.00 3.18
338 349 6.041637 ACTTGATGCTCCCACGTAGAATTATA 59.958 38.462 0.00 0.00 0.00 0.98
394 421 3.605634 TGGTCACCATTTGTAATCTCCG 58.394 45.455 0.00 0.00 0.00 4.63
557 585 0.949105 GGGCATCCGCATTAGGTACG 60.949 60.000 0.00 0.00 41.24 3.67
681 751 5.835113 TTGCATTATTCTCTAGGTTTGCC 57.165 39.130 0.00 0.00 0.00 4.52
756 1111 0.937304 CACCATAGAATCAACGGCCG 59.063 55.000 26.86 26.86 0.00 6.13
788 1143 1.819928 AATAACCACATGTCTGCGCA 58.180 45.000 10.98 10.98 0.00 6.09
908 1263 3.146847 GCAGCGGCTTATATAACCCTTT 58.853 45.455 0.00 0.00 36.96 3.11
1210 1569 9.241919 TGTAATTGACCATATGAAAGTTCACAT 57.758 29.630 3.65 0.00 40.49 3.21
1211 1570 8.628630 TGTAATTGACCATATGAAAGTTCACA 57.371 30.769 3.65 0.00 40.49 3.58
1231 1590 9.621629 TCGGGATTTGAAACTATTGTATGTAAT 57.378 29.630 0.00 0.00 0.00 1.89
1232 1591 8.885722 GTCGGGATTTGAAACTATTGTATGTAA 58.114 33.333 0.00 0.00 0.00 2.41
1233 1592 7.223193 CGTCGGGATTTGAAACTATTGTATGTA 59.777 37.037 0.00 0.00 0.00 2.29
1234 1593 6.036735 CGTCGGGATTTGAAACTATTGTATGT 59.963 38.462 0.00 0.00 0.00 2.29
1235 1594 6.036735 ACGTCGGGATTTGAAACTATTGTATG 59.963 38.462 0.00 0.00 0.00 2.39
1236 1595 6.110707 ACGTCGGGATTTGAAACTATTGTAT 58.889 36.000 0.00 0.00 0.00 2.29
1237 1596 5.481105 ACGTCGGGATTTGAAACTATTGTA 58.519 37.500 0.00 0.00 0.00 2.41
1238 1597 4.320870 ACGTCGGGATTTGAAACTATTGT 58.679 39.130 0.00 0.00 0.00 2.71
1239 1598 4.390603 TGACGTCGGGATTTGAAACTATTG 59.609 41.667 11.62 0.00 0.00 1.90
1240 1599 4.571919 TGACGTCGGGATTTGAAACTATT 58.428 39.130 11.62 0.00 0.00 1.73
1241 1600 4.196626 TGACGTCGGGATTTGAAACTAT 57.803 40.909 11.62 0.00 0.00 2.12
1242 1601 3.663995 TGACGTCGGGATTTGAAACTA 57.336 42.857 11.62 0.00 0.00 2.24
1243 1602 2.536761 TGACGTCGGGATTTGAAACT 57.463 45.000 11.62 0.00 0.00 2.66
1244 1603 3.187637 TGATTGACGTCGGGATTTGAAAC 59.812 43.478 11.62 0.00 0.00 2.78
1245 1604 3.403968 TGATTGACGTCGGGATTTGAAA 58.596 40.909 11.62 0.00 0.00 2.69
1246 1605 3.000041 CTGATTGACGTCGGGATTTGAA 59.000 45.455 11.62 0.00 0.00 2.69
1247 1606 2.616960 CTGATTGACGTCGGGATTTGA 58.383 47.619 11.62 0.00 0.00 2.69
1248 1607 1.062587 GCTGATTGACGTCGGGATTTG 59.937 52.381 11.62 0.00 0.00 2.32
1249 1608 1.338674 TGCTGATTGACGTCGGGATTT 60.339 47.619 11.62 0.00 0.00 2.17
1250 1609 0.249120 TGCTGATTGACGTCGGGATT 59.751 50.000 11.62 0.00 0.00 3.01
1251 1610 0.460284 GTGCTGATTGACGTCGGGAT 60.460 55.000 11.62 4.82 0.00 3.85
1252 1611 1.080093 GTGCTGATTGACGTCGGGA 60.080 57.895 11.62 0.00 0.00 5.14
1253 1612 1.374125 TGTGCTGATTGACGTCGGG 60.374 57.895 11.62 0.15 0.00 5.14
1254 1613 0.943835 TGTGTGCTGATTGACGTCGG 60.944 55.000 11.62 0.00 0.00 4.79
1255 1614 0.858583 TTGTGTGCTGATTGACGTCG 59.141 50.000 11.62 0.00 0.00 5.12
1256 1615 3.542712 AATTGTGTGCTGATTGACGTC 57.457 42.857 9.11 9.11 0.00 4.34
1257 1616 3.988379 AAATTGTGTGCTGATTGACGT 57.012 38.095 0.00 0.00 0.00 4.34
1258 1617 3.848019 GCTAAATTGTGTGCTGATTGACG 59.152 43.478 0.00 0.00 0.00 4.35
1259 1618 4.168760 GGCTAAATTGTGTGCTGATTGAC 58.831 43.478 0.00 0.00 0.00 3.18
1260 1619 3.119884 CGGCTAAATTGTGTGCTGATTGA 60.120 43.478 0.00 0.00 34.02 2.57
1261 1620 3.173599 CGGCTAAATTGTGTGCTGATTG 58.826 45.455 0.00 0.00 34.02 2.67
1262 1621 2.164219 CCGGCTAAATTGTGTGCTGATT 59.836 45.455 0.00 0.00 34.02 2.57
1263 1622 1.745087 CCGGCTAAATTGTGTGCTGAT 59.255 47.619 0.00 0.00 34.02 2.90
1264 1623 1.164411 CCGGCTAAATTGTGTGCTGA 58.836 50.000 0.00 0.00 34.02 4.26
1265 1624 0.456653 GCCGGCTAAATTGTGTGCTG 60.457 55.000 22.15 0.00 0.00 4.41
1266 1625 0.609131 AGCCGGCTAAATTGTGTGCT 60.609 50.000 31.86 0.00 0.00 4.40
1267 1626 0.243636 AAGCCGGCTAAATTGTGTGC 59.756 50.000 33.07 0.00 0.00 4.57
1268 1627 1.812571 AGAAGCCGGCTAAATTGTGTG 59.187 47.619 33.07 0.00 0.00 3.82
1269 1628 2.084546 GAGAAGCCGGCTAAATTGTGT 58.915 47.619 33.07 11.88 0.00 3.72
1270 1629 1.401905 GGAGAAGCCGGCTAAATTGTG 59.598 52.381 33.07 0.00 0.00 3.33
1271 1630 1.004277 TGGAGAAGCCGGCTAAATTGT 59.996 47.619 33.07 13.77 40.66 2.71
1272 1631 1.750193 TGGAGAAGCCGGCTAAATTG 58.250 50.000 33.07 0.00 40.66 2.32
1273 1632 2.173569 AGATGGAGAAGCCGGCTAAATT 59.826 45.455 33.07 15.20 40.66 1.82
1274 1633 1.771255 AGATGGAGAAGCCGGCTAAAT 59.229 47.619 33.07 19.11 40.66 1.40
1275 1634 1.134401 CAGATGGAGAAGCCGGCTAAA 60.134 52.381 33.07 14.18 40.66 1.85
1276 1635 0.465705 CAGATGGAGAAGCCGGCTAA 59.534 55.000 33.07 13.80 40.66 3.09
1277 1636 0.397114 TCAGATGGAGAAGCCGGCTA 60.397 55.000 33.07 15.07 40.66 3.93
1278 1637 1.053264 ATCAGATGGAGAAGCCGGCT 61.053 55.000 27.08 27.08 40.66 5.52
1279 1638 0.681733 TATCAGATGGAGAAGCCGGC 59.318 55.000 21.89 21.89 40.66 6.13
1280 1639 2.301296 ACATATCAGATGGAGAAGCCGG 59.699 50.000 0.00 0.00 40.66 6.13
1281 1640 3.324117 CACATATCAGATGGAGAAGCCG 58.676 50.000 0.00 0.00 40.66 5.52
1282 1641 3.072944 GCACATATCAGATGGAGAAGCC 58.927 50.000 0.00 0.00 37.10 4.35
1283 1642 3.736720 TGCACATATCAGATGGAGAAGC 58.263 45.455 0.00 0.00 0.00 3.86
1284 1643 5.211174 TCTGCACATATCAGATGGAGAAG 57.789 43.478 0.00 0.00 37.80 2.85
1285 1644 5.129980 AGTTCTGCACATATCAGATGGAGAA 59.870 40.000 3.65 3.65 45.14 2.87
1286 1645 4.652881 AGTTCTGCACATATCAGATGGAGA 59.347 41.667 0.00 0.00 39.96 3.71
1287 1646 4.958509 AGTTCTGCACATATCAGATGGAG 58.041 43.478 0.00 0.00 39.96 3.86
1288 1647 5.835280 TCTAGTTCTGCACATATCAGATGGA 59.165 40.000 0.00 0.00 39.96 3.41
1289 1648 6.094193 TCTAGTTCTGCACATATCAGATGG 57.906 41.667 0.00 0.00 39.96 3.51
1290 1649 6.747125 ACTCTAGTTCTGCACATATCAGATG 58.253 40.000 0.00 0.00 39.96 2.90
1291 1650 6.975196 ACTCTAGTTCTGCACATATCAGAT 57.025 37.500 0.00 0.00 39.96 2.90
1292 1651 6.782082 AACTCTAGTTCTGCACATATCAGA 57.218 37.500 0.00 0.00 38.67 3.27
1293 1652 9.838975 CTATAACTCTAGTTCTGCACATATCAG 57.161 37.037 0.00 0.00 39.31 2.90
1294 1653 9.355916 ACTATAACTCTAGTTCTGCACATATCA 57.644 33.333 0.00 0.00 39.31 2.15
1295 1654 9.834628 GACTATAACTCTAGTTCTGCACATATC 57.165 37.037 0.00 0.00 39.31 1.63
1296 1655 9.581289 AGACTATAACTCTAGTTCTGCACATAT 57.419 33.333 0.00 0.00 39.31 1.78
1297 1656 8.841300 CAGACTATAACTCTAGTTCTGCACATA 58.159 37.037 0.00 0.00 39.31 2.29
1333 1692 4.763279 TGCAAATCAGATTGACAGTCATGT 59.237 37.500 3.45 0.00 44.31 3.21
1334 1693 5.305139 TGCAAATCAGATTGACAGTCATG 57.695 39.130 3.45 0.00 31.84 3.07
1336 1695 3.754850 CCTGCAAATCAGATTGACAGTCA 59.245 43.478 18.09 0.00 45.72 3.41
1337 1696 3.755378 ACCTGCAAATCAGATTGACAGTC 59.245 43.478 18.09 0.00 45.72 3.51
1339 1698 3.504906 ACACCTGCAAATCAGATTGACAG 59.495 43.478 14.75 14.75 45.72 3.51
1546 1905 0.961019 GCAGCTTCCACATTGTCCAA 59.039 50.000 0.00 0.00 0.00 3.53
1582 1941 1.005037 GATCACCTGTGTGGCGTCA 60.005 57.895 0.00 0.00 42.98 4.35
2003 2370 3.267483 TGAAGGAAGTAATAAGCACGGC 58.733 45.455 0.00 0.00 0.00 5.68
2022 2389 8.893563 AGGTTAAGACAATTATTTTGGGATGA 57.106 30.769 0.00 0.00 0.00 2.92
2024 2391 8.539544 CCAAGGTTAAGACAATTATTTTGGGAT 58.460 33.333 0.00 0.00 0.00 3.85
2026 2393 7.676004 ACCAAGGTTAAGACAATTATTTTGGG 58.324 34.615 0.00 0.00 36.53 4.12
2081 2448 9.607988 TCACTCTGTTTCAAAATAAGTGTCTTA 57.392 29.630 6.83 0.00 35.37 2.10
2082 2449 8.506168 TCACTCTGTTTCAAAATAAGTGTCTT 57.494 30.769 6.83 0.00 35.37 3.01
2083 2450 7.770897 ACTCACTCTGTTTCAAAATAAGTGTCT 59.229 33.333 6.83 0.00 35.37 3.41
2084 2451 7.920738 ACTCACTCTGTTTCAAAATAAGTGTC 58.079 34.615 6.83 0.00 35.37 3.67
2085 2452 7.865706 ACTCACTCTGTTTCAAAATAAGTGT 57.134 32.000 6.83 3.93 35.37 3.55
2086 2453 9.046296 AGTACTCACTCTGTTTCAAAATAAGTG 57.954 33.333 0.00 0.00 35.20 3.16
2087 2454 9.614792 AAGTACTCACTCTGTTTCAAAATAAGT 57.385 29.630 0.00 0.00 32.29 2.24
2105 2472 8.177663 CCGTCGACTACTAATAAAAAGTACTCA 58.822 37.037 14.70 0.00 0.00 3.41
2108 2475 8.578769 CAACCGTCGACTACTAATAAAAAGTAC 58.421 37.037 14.70 0.00 0.00 2.73
2126 2494 0.872881 AAGACAACGTCCAACCGTCG 60.873 55.000 0.00 0.00 40.85 5.12
2232 2600 4.721776 TGGCCTGAGATTTAGTCCTATGTT 59.278 41.667 3.32 0.00 0.00 2.71
2297 2665 7.489113 CCACTGTAATAATTTCATCTTTGCACC 59.511 37.037 0.00 0.00 0.00 5.01
2344 2712 8.746751 GTTTTTCTCTAACTTCATTTGCTTCAC 58.253 33.333 0.00 0.00 0.00 3.18
2406 2774 9.813446 ACACTTCTATTATAGACTTTTTACCGG 57.187 33.333 0.00 0.00 33.84 5.28
2438 2806 8.232913 ACACAACAAGAGTATACAAACCATTT 57.767 30.769 5.50 0.00 0.00 2.32
2520 2888 4.314740 AAAGCACATTTAGCGGTTTTGA 57.685 36.364 0.00 0.00 37.01 2.69
2576 2944 7.778470 AACGATCTCTGAGATTAATTTCACC 57.222 36.000 20.40 4.68 34.53 4.02
2586 2954 4.573900 AGCAACAAAACGATCTCTGAGAT 58.426 39.130 19.63 19.63 37.73 2.75
2590 2958 5.273170 TCAAAAGCAACAAAACGATCTCTG 58.727 37.500 0.00 0.00 0.00 3.35
2595 2963 3.123050 GCCTCAAAAGCAACAAAACGAT 58.877 40.909 0.00 0.00 0.00 3.73
2598 2966 2.609002 CTGGCCTCAAAAGCAACAAAAC 59.391 45.455 3.32 0.00 0.00 2.43
2625 2993 6.113411 ACTATCAACTTGGGGAATAAACTCG 58.887 40.000 0.00 0.00 0.00 4.18
2636 3005 7.827236 TGGTGACTAAATAACTATCAACTTGGG 59.173 37.037 0.00 0.00 0.00 4.12
2656 3025 3.963129 TCATACCCAAGGAATTGGTGAC 58.037 45.455 6.29 0.00 40.46 3.67
2657 3026 4.666412 TTCATACCCAAGGAATTGGTGA 57.334 40.909 6.29 1.30 40.46 4.02
2683 3053 3.056832 GGGAGATATTGGGAGGGTTCTT 58.943 50.000 0.00 0.00 0.00 2.52
2703 3073 1.844771 CGATACGTGGGCATGCATGG 61.845 60.000 27.34 13.04 0.00 3.66
2704 3074 1.159713 ACGATACGTGGGCATGCATG 61.160 55.000 22.70 22.70 39.18 4.06
2705 3075 1.146041 ACGATACGTGGGCATGCAT 59.854 52.632 21.36 2.33 39.18 3.96
2706 3076 2.581895 ACGATACGTGGGCATGCA 59.418 55.556 21.36 0.00 39.18 3.96


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

AutoCloner maintained by Alex Coulton.