Multiple sequence alignment - TraesCS2B01G513900

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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 TraesCS2B01G513900 chr2B 100.000 2273 0 0 1 2273 708864267 708861995 0.000000e+00 4198.0
1 TraesCS2B01G513900 chr2B 89.051 411 44 1 91 500 708871687 708871277 2.010000e-140 508.0
2 TraesCS2B01G513900 chr2B 80.610 557 83 16 788 1335 753952270 753952810 7.560000e-110 407.0
3 TraesCS2B01G513900 chr2B 85.479 365 40 7 981 1335 754001278 754001639 3.570000e-98 368.0
4 TraesCS2B01G513900 chr2B 89.347 291 26 2 987 1275 753974075 753974362 5.970000e-96 361.0
5 TraesCS2B01G513900 chr2B 82.707 399 51 15 1001 1392 708826662 708826275 2.800000e-89 339.0
6 TraesCS2B01G513900 chr2B 88.889 162 8 4 588 744 708870688 708870532 8.290000e-45 191.0
7 TraesCS2B01G513900 chr2B 94.118 51 3 0 531 581 708870789 708870739 6.730000e-11 78.7
8 TraesCS2B01G513900 chr2D 85.843 1109 72 40 531 1616 587112262 587111216 0.000000e+00 1099.0
9 TraesCS2B01G513900 chr2D 83.610 543 71 15 735 1273 617972796 617973324 5.640000e-136 494.0
10 TraesCS2B01G513900 chr2D 83.394 548 61 22 732 1273 617957452 617957975 4.390000e-132 481.0
11 TraesCS2B01G513900 chr2D 89.789 284 26 1 992 1275 617992148 617992428 5.970000e-96 361.0
12 TraesCS2B01G513900 chr2D 89.362 282 30 0 990 1271 617941876 617942157 2.780000e-94 355.0
13 TraesCS2B01G513900 chr2D 90.000 260 24 1 243 500 587113048 587112789 3.620000e-88 335.0
14 TraesCS2B01G513900 chr2D 92.574 202 12 3 46 245 587113409 587113209 1.030000e-73 287.0
15 TraesCS2B01G513900 chr7A 85.275 618 68 16 1677 2273 15613097 15612482 1.150000e-172 616.0
16 TraesCS2B01G513900 chr1D 85.437 618 61 16 1628 2238 421466997 421467592 1.150000e-172 616.0
17 TraesCS2B01G513900 chr1D 83.667 649 75 13 1639 2273 372432230 372431599 1.170000e-162 582.0
18 TraesCS2B01G513900 chr1D 80.539 668 100 19 1626 2273 20872092 20872749 9.440000e-134 486.0
19 TraesCS2B01G513900 chr5D 83.486 654 94 8 1628 2273 331398525 331399172 4.180000e-167 597.0
20 TraesCS2B01G513900 chr5A 80.916 655 100 22 1624 2273 566455263 566455897 5.640000e-136 494.0
21 TraesCS2B01G513900 chr4A 80.699 658 100 14 1628 2273 102861311 102860669 9.440000e-134 486.0
22 TraesCS2B01G513900 chr3A 87.313 402 40 4 1870 2264 507107930 507107533 1.240000e-122 449.0
23 TraesCS2B01G513900 chr2A 82.857 455 70 6 1822 2273 682948436 682948885 3.520000e-108 401.0
24 TraesCS2B01G513900 chr2A 80.657 548 66 21 732 1273 748537617 748538130 2.740000e-104 388.0


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 TraesCS2B01G513900 chr2B 708861995 708864267 2272 True 4198.000000 4198 100.000000 1 2273 1 chr2B.!!$R2 2272
1 TraesCS2B01G513900 chr2B 753952270 753952810 540 False 407.000000 407 80.610000 788 1335 1 chr2B.!!$F1 547
2 TraesCS2B01G513900 chr2B 708870532 708871687 1155 True 259.233333 508 90.686000 91 744 3 chr2B.!!$R3 653
3 TraesCS2B01G513900 chr2D 587111216 587113409 2193 True 573.666667 1099 89.472333 46 1616 3 chr2D.!!$R1 1570
4 TraesCS2B01G513900 chr2D 617972796 617973324 528 False 494.000000 494 83.610000 735 1273 1 chr2D.!!$F3 538
5 TraesCS2B01G513900 chr2D 617957452 617957975 523 False 481.000000 481 83.394000 732 1273 1 chr2D.!!$F2 541
6 TraesCS2B01G513900 chr7A 15612482 15613097 615 True 616.000000 616 85.275000 1677 2273 1 chr7A.!!$R1 596
7 TraesCS2B01G513900 chr1D 421466997 421467592 595 False 616.000000 616 85.437000 1628 2238 1 chr1D.!!$F2 610
8 TraesCS2B01G513900 chr1D 372431599 372432230 631 True 582.000000 582 83.667000 1639 2273 1 chr1D.!!$R1 634
9 TraesCS2B01G513900 chr1D 20872092 20872749 657 False 486.000000 486 80.539000 1626 2273 1 chr1D.!!$F1 647
10 TraesCS2B01G513900 chr5D 331398525 331399172 647 False 597.000000 597 83.486000 1628 2273 1 chr5D.!!$F1 645
11 TraesCS2B01G513900 chr5A 566455263 566455897 634 False 494.000000 494 80.916000 1624 2273 1 chr5A.!!$F1 649
12 TraesCS2B01G513900 chr4A 102860669 102861311 642 True 486.000000 486 80.699000 1628 2273 1 chr4A.!!$R1 645
13 TraesCS2B01G513900 chr2A 748537617 748538130 513 False 388.000000 388 80.657000 732 1273 1 chr2A.!!$F2 541

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
768 1507 0.178533 TCTGGAAAACCAACGTCCGT 59.821 50.0 0.0 0.0 33.87 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 2376 0.035343 GCCCTAACCAGGAGTTGACC 60.035 60.0 0.0 0.0 45.91 4.02 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
18 19 3.568000 TTGCGGCTGGACACATATT 57.432 47.368 0.00 0.00 0.00 1.28
19 20 1.378531 TTGCGGCTGGACACATATTC 58.621 50.000 0.00 0.00 0.00 1.75
20 21 0.541392 TGCGGCTGGACACATATTCT 59.459 50.000 0.00 0.00 0.00 2.40
21 22 1.221414 GCGGCTGGACACATATTCTC 58.779 55.000 0.00 0.00 0.00 2.87
22 23 1.871080 CGGCTGGACACATATTCTCC 58.129 55.000 0.00 0.00 0.00 3.71
23 24 1.138859 CGGCTGGACACATATTCTCCA 59.861 52.381 0.00 0.00 32.93 3.86
24 25 2.419990 CGGCTGGACACATATTCTCCAA 60.420 50.000 0.00 0.00 33.58 3.53
25 26 3.745480 CGGCTGGACACATATTCTCCAAT 60.745 47.826 0.00 0.00 33.58 3.16
26 27 4.503123 CGGCTGGACACATATTCTCCAATA 60.503 45.833 0.00 0.00 33.58 1.90
27 28 4.757149 GGCTGGACACATATTCTCCAATAC 59.243 45.833 0.00 0.00 33.58 1.89
28 29 5.368145 GCTGGACACATATTCTCCAATACA 58.632 41.667 0.00 0.00 33.58 2.29
29 30 6.000219 GCTGGACACATATTCTCCAATACAT 59.000 40.000 0.00 0.00 33.58 2.29
30 31 6.488006 GCTGGACACATATTCTCCAATACATT 59.512 38.462 0.00 0.00 33.58 2.71
31 32 7.013655 GCTGGACACATATTCTCCAATACATTT 59.986 37.037 0.00 0.00 33.58 2.32
32 33 8.821686 TGGACACATATTCTCCAATACATTTT 57.178 30.769 0.00 0.00 30.81 1.82
33 34 9.253832 TGGACACATATTCTCCAATACATTTTT 57.746 29.630 0.00 0.00 30.81 1.94
34 35 9.736023 GGACACATATTCTCCAATACATTTTTC 57.264 33.333 0.00 0.00 0.00 2.29
35 36 9.736023 GACACATATTCTCCAATACATTTTTCC 57.264 33.333 0.00 0.00 0.00 3.13
36 37 9.253832 ACACATATTCTCCAATACATTTTTCCA 57.746 29.630 0.00 0.00 0.00 3.53
37 38 9.520204 CACATATTCTCCAATACATTTTTCCAC 57.480 33.333 0.00 0.00 0.00 4.02
38 39 9.253832 ACATATTCTCCAATACATTTTTCCACA 57.746 29.630 0.00 0.00 0.00 4.17
43 44 9.487790 TTCTCCAATACATTTTTCCACATTTTC 57.512 29.630 0.00 0.00 0.00 2.29
44 45 8.093927 TCTCCAATACATTTTTCCACATTTTCC 58.906 33.333 0.00 0.00 0.00 3.13
45 46 7.972301 TCCAATACATTTTTCCACATTTTCCT 58.028 30.769 0.00 0.00 0.00 3.36
46 47 8.435982 TCCAATACATTTTTCCACATTTTCCTT 58.564 29.630 0.00 0.00 0.00 3.36
47 48 8.505625 CCAATACATTTTTCCACATTTTCCTTG 58.494 33.333 0.00 0.00 0.00 3.61
48 49 7.671495 ATACATTTTTCCACATTTTCCTTGC 57.329 32.000 0.00 0.00 0.00 4.01
49 50 5.683681 ACATTTTTCCACATTTTCCTTGCT 58.316 33.333 0.00 0.00 0.00 3.91
50 51 5.528320 ACATTTTTCCACATTTTCCTTGCTG 59.472 36.000 0.00 0.00 0.00 4.41
51 52 2.818130 TTCCACATTTTCCTTGCTGC 57.182 45.000 0.00 0.00 0.00 5.25
106 107 0.944311 CACAAAGAGCGTGCGGTACT 60.944 55.000 0.00 0.00 0.00 2.73
141 142 8.854614 ACTCTCTAGTTAAATCAGTGCAAAAT 57.145 30.769 0.00 0.00 29.00 1.82
145 146 7.985476 TCTAGTTAAATCAGTGCAAAATAGGC 58.015 34.615 0.00 0.00 0.00 3.93
159 161 6.419413 TGCAAAATAGGCAAAACTTTACTTCG 59.581 34.615 0.00 0.00 38.54 3.79
184 186 4.321230 CCACTTAGGCCACTTCATTGAAAC 60.321 45.833 5.01 0.00 0.00 2.78
257 422 9.119418 TCTTTCTGTTCTACATGTCAAAAATCA 57.881 29.630 0.00 0.00 0.00 2.57
338 506 8.597662 AACAATTTTTCTTCATGTTGATGGAG 57.402 30.769 0.00 0.00 36.60 3.86
363 531 8.552296 AGACTATCTATTTTGGTCCATCAACTT 58.448 33.333 0.00 0.00 0.00 2.66
367 535 6.454795 TCTATTTTGGTCCATCAACTTTTGC 58.545 36.000 0.00 0.00 0.00 3.68
373 541 2.802247 GTCCATCAACTTTTGCCAAAGC 59.198 45.455 10.05 0.00 43.03 3.51
380 548 4.704057 TCAACTTTTGCCAAAGCCAAAAAT 59.296 33.333 10.05 0.00 43.03 1.82
387 555 6.949352 TTGCCAAAGCCAAAAATTCAAATA 57.051 29.167 0.00 0.00 38.69 1.40
474 642 3.243401 GGTTTTAATAATGAGGCGGCAGG 60.243 47.826 13.08 0.00 0.00 4.85
500 668 2.076863 CCTACAACTTAGCTGCCACAC 58.923 52.381 0.00 0.00 0.00 3.82
504 941 2.139917 CAACTTAGCTGCCACACGTTA 58.860 47.619 0.00 0.00 0.00 3.18
578 1267 3.958147 TCTTGATACACGCTATCTTCCCA 59.042 43.478 3.17 0.00 0.00 4.37
664 1397 2.724839 CGGCGAGCAAGTAAAATGACAC 60.725 50.000 0.00 0.00 0.00 3.67
703 1441 1.065273 CGGGACCGACAACGATAGG 59.935 63.158 4.40 0.00 42.83 2.57
718 1456 1.733360 GATAGGTGCGGCGTAAACAAA 59.267 47.619 9.37 0.00 0.00 2.83
720 1458 1.096386 AGGTGCGGCGTAAACAAACA 61.096 50.000 9.37 0.00 0.00 2.83
721 1459 0.248539 GGTGCGGCGTAAACAAACAA 60.249 50.000 9.37 0.00 0.00 2.83
722 1460 1.117234 GTGCGGCGTAAACAAACAAG 58.883 50.000 9.37 0.00 0.00 3.16
723 1461 0.733729 TGCGGCGTAAACAAACAAGT 59.266 45.000 9.37 0.00 0.00 3.16
749 1487 4.629779 CGGAAAGCACCCGGTATT 57.370 55.556 0.00 0.00 43.05 1.89
768 1507 0.178533 TCTGGAAAACCAACGTCCGT 59.821 50.000 0.00 0.00 33.87 4.69
811 1551 1.338136 CCCAGCCTCCGTCCTGTATT 61.338 60.000 0.00 0.00 0.00 1.89
819 1559 3.197116 CCTCCGTCCTGTATTTAACCACT 59.803 47.826 0.00 0.00 0.00 4.00
842 1584 0.621082 CCCACCTCCTTTCTTCCTCC 59.379 60.000 0.00 0.00 0.00 4.30
851 1593 3.084786 CCTTTCTTCCTCCCATCAACAC 58.915 50.000 0.00 0.00 0.00 3.32
854 1596 3.140325 TCTTCCTCCCATCAACACAAC 57.860 47.619 0.00 0.00 0.00 3.32
880 1622 4.082408 CACAAGCATCAATCATCCAACAGT 60.082 41.667 0.00 0.00 0.00 3.55
896 1640 7.815840 TCCAACAGTTCAGTTCATTCATAAA 57.184 32.000 0.00 0.00 0.00 1.40
897 1641 8.408043 TCCAACAGTTCAGTTCATTCATAAAT 57.592 30.769 0.00 0.00 0.00 1.40
973 1731 0.817654 CGGATCAGTCAGCAGTACCA 59.182 55.000 0.00 0.00 0.00 3.25
977 1735 3.133721 GGATCAGTCAGCAGTACCATCTT 59.866 47.826 0.00 0.00 0.00 2.40
996 1758 1.550327 TCACCAACGCAGAGAGAGAT 58.450 50.000 0.00 0.00 0.00 2.75
1324 2093 1.675483 TGTGTTTGCTGCAGTAACCAG 59.325 47.619 17.39 0.00 0.00 4.00
1382 2152 4.790765 ATACCACGACGATGATGATGAT 57.209 40.909 0.00 0.00 0.00 2.45
1383 2153 2.747436 ACCACGACGATGATGATGATG 58.253 47.619 0.00 0.00 0.00 3.07
1384 2154 2.362077 ACCACGACGATGATGATGATGA 59.638 45.455 0.00 0.00 0.00 2.92
1388 2158 5.049886 CCACGACGATGATGATGATGAAAAT 60.050 40.000 0.00 0.00 0.00 1.82
1401 2171 7.888424 TGATGATGAAAATTTCTGTCACATGT 58.112 30.769 13.52 0.00 31.41 3.21
1415 2185 7.402054 TCTGTCACATGTGTTTATATTCCCTT 58.598 34.615 24.63 0.00 0.00 3.95
1418 2188 7.888021 TGTCACATGTGTTTATATTCCCTTCTT 59.112 33.333 24.63 0.00 0.00 2.52
1419 2189 8.184192 GTCACATGTGTTTATATTCCCTTCTTG 58.816 37.037 24.63 0.00 0.00 3.02
1421 2191 8.184192 CACATGTGTTTATATTCCCTTCTTGTC 58.816 37.037 18.03 0.00 0.00 3.18
1423 2193 9.613428 CATGTGTTTATATTCCCTTCTTGTCTA 57.387 33.333 0.00 0.00 0.00 2.59
1434 2204 8.704849 TTCCCTTCTTGTCTATTTGATTTTGA 57.295 30.769 0.00 0.00 0.00 2.69
1435 2205 8.884124 TCCCTTCTTGTCTATTTGATTTTGAT 57.116 30.769 0.00 0.00 0.00 2.57
1436 2206 8.742777 TCCCTTCTTGTCTATTTGATTTTGATG 58.257 33.333 0.00 0.00 0.00 3.07
1437 2207 8.742777 CCCTTCTTGTCTATTTGATTTTGATGA 58.257 33.333 0.00 0.00 0.00 2.92
1438 2208 9.565213 CCTTCTTGTCTATTTGATTTTGATGAC 57.435 33.333 0.00 0.00 0.00 3.06
1439 2209 9.565213 CTTCTTGTCTATTTGATTTTGATGACC 57.435 33.333 0.00 0.00 0.00 4.02
1440 2210 7.751732 TCTTGTCTATTTGATTTTGATGACCG 58.248 34.615 0.00 0.00 0.00 4.79
1441 2211 5.879237 TGTCTATTTGATTTTGATGACCGC 58.121 37.500 0.00 0.00 0.00 5.68
1444 2214 2.892373 TTGATTTTGATGACCGCGAC 57.108 45.000 8.23 1.20 0.00 5.19
1446 2216 0.996462 GATTTTGATGACCGCGACGA 59.004 50.000 8.23 0.00 0.00 4.20
1452 2222 1.209275 GATGACCGCGACGAGGAATG 61.209 60.000 25.04 0.00 0.00 2.67
1453 2223 1.945354 ATGACCGCGACGAGGAATGT 61.945 55.000 25.04 0.71 0.00 2.71
1456 2226 2.180769 CGCGACGAGGAATGTGGA 59.819 61.111 0.00 0.00 0.00 4.02
1460 2230 0.388134 CGACGAGGAATGTGGACGTT 60.388 55.000 0.00 0.00 37.32 3.99
1471 2241 3.428746 TGTGGACGTTTCAATTGGTTG 57.571 42.857 5.42 0.00 36.65 3.77
1475 2245 2.480416 GGACGTTTCAATTGGTTGTGCA 60.480 45.455 5.42 0.00 36.69 4.57
1481 2251 1.962100 TCAATTGGTTGTGCATGCAGA 59.038 42.857 23.41 18.82 36.69 4.26
1482 2252 2.063266 CAATTGGTTGTGCATGCAGAC 58.937 47.619 23.41 21.61 0.00 3.51
1484 2254 1.401761 TTGGTTGTGCATGCAGACTT 58.598 45.000 23.41 0.00 0.00 3.01
1486 2256 0.953727 GGTTGTGCATGCAGACTTGA 59.046 50.000 23.41 0.82 0.00 3.02
1488 2258 2.749076 GGTTGTGCATGCAGACTTGATA 59.251 45.455 23.41 0.00 0.00 2.15
1495 2265 5.181433 GTGCATGCAGACTTGATATGATCAT 59.819 40.000 23.41 13.81 39.39 2.45
1500 2270 3.683340 CAGACTTGATATGATCATGGCCG 59.317 47.826 18.72 5.53 41.91 6.13
1506 2276 0.686789 TATGATCATGGCCGGTCTGG 59.313 55.000 18.72 0.00 42.50 3.86
1516 2291 1.141053 GGCCGGTCTGGTCTGAAATAT 59.859 52.381 1.90 0.00 40.15 1.28
1536 2311 0.723981 GAATGTCTTCGCTCTGCACC 59.276 55.000 0.00 0.00 0.00 5.01
1550 2325 2.032634 GCACCTTGCCGAATCGACA 61.033 57.895 3.36 0.00 37.42 4.35
1551 2326 1.369091 GCACCTTGCCGAATCGACAT 61.369 55.000 3.36 0.00 37.42 3.06
1555 2330 1.528586 CCTTGCCGAATCGACATGATC 59.471 52.381 3.36 0.00 35.84 2.92
1567 2342 6.759497 ATCGACATGATCAATCCTCGTATA 57.241 37.500 0.00 0.00 28.49 1.47
1570 2345 6.151144 TCGACATGATCAATCCTCGTATATGT 59.849 38.462 0.00 0.00 0.00 2.29
1573 2348 8.354711 ACATGATCAATCCTCGTATATGTACT 57.645 34.615 0.00 0.00 0.00 2.73
1577 2352 8.856103 TGATCAATCCTCGTATATGTACTGAAA 58.144 33.333 0.00 0.00 0.00 2.69
1579 2354 7.145985 TCAATCCTCGTATATGTACTGAAAGC 58.854 38.462 0.00 0.00 37.60 3.51
1582 2357 3.635331 TCGTATATGTACTGAAAGCGGC 58.365 45.455 0.00 0.00 37.60 6.53
1583 2358 3.067040 TCGTATATGTACTGAAAGCGGCA 59.933 43.478 1.45 0.00 37.60 5.69
1584 2359 3.987868 CGTATATGTACTGAAAGCGGCAT 59.012 43.478 1.45 0.00 37.60 4.40
1585 2360 4.090066 CGTATATGTACTGAAAGCGGCATC 59.910 45.833 1.45 0.29 37.60 3.91
1586 2361 2.698855 ATGTACTGAAAGCGGCATCT 57.301 45.000 1.45 0.00 37.60 2.90
1587 2362 2.010145 TGTACTGAAAGCGGCATCTC 57.990 50.000 1.45 0.00 37.60 2.75
1591 2368 0.095935 CTGAAAGCGGCATCTCGTTG 59.904 55.000 1.45 0.00 0.00 4.10
1599 2376 1.267532 CGGCATCTCGTTGATTTTCCG 60.268 52.381 0.00 0.00 35.35 4.30
1616 2393 0.249398 CCGGTCAACTCCTGGTTAGG 59.751 60.000 0.00 0.00 46.06 2.69
1617 2394 0.249398 CGGTCAACTCCTGGTTAGGG 59.751 60.000 0.00 0.00 44.70 3.53
1618 2395 0.035343 GGTCAACTCCTGGTTAGGGC 60.035 60.000 0.00 0.00 44.70 5.19
1619 2396 0.690762 GTCAACTCCTGGTTAGGGCA 59.309 55.000 0.00 0.00 44.70 5.36
1620 2397 1.073284 GTCAACTCCTGGTTAGGGCAA 59.927 52.381 0.00 0.00 44.70 4.52
1621 2398 1.073284 TCAACTCCTGGTTAGGGCAAC 59.927 52.381 0.00 0.00 44.70 4.17
1622 2399 1.073923 CAACTCCTGGTTAGGGCAACT 59.926 52.381 0.00 0.00 44.70 3.16
1673 2450 9.162764 TGTTTTATTTCTCTAATCAGCACCTAC 57.837 33.333 0.00 0.00 0.00 3.18
1710 2487 8.801882 TCCACCATAAGGAAGTAACATTTTAG 57.198 34.615 0.00 0.00 38.69 1.85
1721 2509 5.351405 AGTAACATTTTAGTCCTCTCCCCT 58.649 41.667 0.00 0.00 0.00 4.79
1725 2513 4.589374 ACATTTTAGTCCTCTCCCCTATCG 59.411 45.833 0.00 0.00 0.00 2.92
1733 2521 2.365941 CCTCTCCCCTATCGTTTCCTTC 59.634 54.545 0.00 0.00 0.00 3.46
1776 2564 3.362851 GAGTAAAAGCCACGCCGCG 62.363 63.158 12.14 12.14 0.00 6.46
1794 2593 2.041922 CCCTCTCGTCATCCCCCA 60.042 66.667 0.00 0.00 0.00 4.96
1797 2596 2.758327 TCTCGTCATCCCCCACGG 60.758 66.667 0.00 0.00 36.64 4.94
1895 2712 2.920912 ACGTCCAGCCCTTTCGGA 60.921 61.111 0.00 0.00 0.00 4.55
2000 2821 1.366111 TTTTCTATCAGCCGCCGCAC 61.366 55.000 0.00 0.00 37.52 5.34
2166 2991 1.595929 TGAACCGAGCCGTTTGGAC 60.596 57.895 0.00 0.00 37.49 4.02
2169 2994 2.742372 CCGAGCCGTTTGGACTGG 60.742 66.667 0.00 0.00 37.49 4.00
2187 3012 2.817258 CTGGACCAAGCCGTTTGAATTA 59.183 45.455 0.00 0.00 39.21 1.40
2217 3042 2.505819 GAGGTTGAGGGAGATGGCTTTA 59.494 50.000 0.00 0.00 0.00 1.85
2235 3060 4.037446 GCTTTAGAGGACTCGTCATCATCT 59.963 45.833 13.34 6.55 42.31 2.90
2264 3089 4.331168 GGAAGAAGACGATGATGACTTTGG 59.669 45.833 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.138859 TGGAGAATATGTGTCCAGCCG 59.861 52.381 0.00 0.00 35.36 5.52
4 5 3.281727 TTGGAGAATATGTGTCCAGCC 57.718 47.619 2.20 0.00 41.42 4.85
5 6 5.368145 TGTATTGGAGAATATGTGTCCAGC 58.632 41.667 2.20 0.00 41.42 4.85
6 7 8.455903 AAATGTATTGGAGAATATGTGTCCAG 57.544 34.615 2.20 0.00 41.42 3.86
8 9 9.736023 GAAAAATGTATTGGAGAATATGTGTCC 57.264 33.333 0.00 0.00 0.00 4.02
9 10 9.736023 GGAAAAATGTATTGGAGAATATGTGTC 57.264 33.333 0.00 0.00 0.00 3.67
10 11 9.253832 TGGAAAAATGTATTGGAGAATATGTGT 57.746 29.630 0.00 0.00 0.00 3.72
11 12 9.520204 GTGGAAAAATGTATTGGAGAATATGTG 57.480 33.333 0.00 0.00 0.00 3.21
12 13 9.253832 TGTGGAAAAATGTATTGGAGAATATGT 57.746 29.630 0.00 0.00 0.00 2.29
17 18 9.487790 GAAAATGTGGAAAAATGTATTGGAGAA 57.512 29.630 0.00 0.00 0.00 2.87
18 19 8.093927 GGAAAATGTGGAAAAATGTATTGGAGA 58.906 33.333 0.00 0.00 0.00 3.71
19 20 8.096414 AGGAAAATGTGGAAAAATGTATTGGAG 58.904 33.333 0.00 0.00 0.00 3.86
20 21 7.972301 AGGAAAATGTGGAAAAATGTATTGGA 58.028 30.769 0.00 0.00 0.00 3.53
21 22 8.505625 CAAGGAAAATGTGGAAAAATGTATTGG 58.494 33.333 0.00 0.00 0.00 3.16
22 23 8.016801 GCAAGGAAAATGTGGAAAAATGTATTG 58.983 33.333 0.00 0.00 0.00 1.90
23 24 7.938490 AGCAAGGAAAATGTGGAAAAATGTATT 59.062 29.630 0.00 0.00 0.00 1.89
24 25 7.388500 CAGCAAGGAAAATGTGGAAAAATGTAT 59.612 33.333 0.00 0.00 0.00 2.29
25 26 6.705381 CAGCAAGGAAAATGTGGAAAAATGTA 59.295 34.615 0.00 0.00 0.00 2.29
26 27 5.528320 CAGCAAGGAAAATGTGGAAAAATGT 59.472 36.000 0.00 0.00 0.00 2.71
27 28 5.561339 GCAGCAAGGAAAATGTGGAAAAATG 60.561 40.000 0.00 0.00 0.00 2.32
28 29 4.516321 GCAGCAAGGAAAATGTGGAAAAAT 59.484 37.500 0.00 0.00 0.00 1.82
29 30 3.876320 GCAGCAAGGAAAATGTGGAAAAA 59.124 39.130 0.00 0.00 0.00 1.94
30 31 3.465871 GCAGCAAGGAAAATGTGGAAAA 58.534 40.909 0.00 0.00 0.00 2.29
31 32 2.224257 GGCAGCAAGGAAAATGTGGAAA 60.224 45.455 0.00 0.00 0.00 3.13
32 33 1.344114 GGCAGCAAGGAAAATGTGGAA 59.656 47.619 0.00 0.00 0.00 3.53
33 34 0.968405 GGCAGCAAGGAAAATGTGGA 59.032 50.000 0.00 0.00 0.00 4.02
34 35 0.680618 TGGCAGCAAGGAAAATGTGG 59.319 50.000 0.00 0.00 0.00 4.17
35 36 1.606224 GGTGGCAGCAAGGAAAATGTG 60.606 52.381 12.58 0.00 0.00 3.21
36 37 0.681175 GGTGGCAGCAAGGAAAATGT 59.319 50.000 12.58 0.00 0.00 2.71
37 38 0.037046 GGGTGGCAGCAAGGAAAATG 60.037 55.000 19.48 0.00 0.00 2.32
38 39 0.471591 TGGGTGGCAGCAAGGAAAAT 60.472 50.000 19.48 0.00 0.00 1.82
39 40 0.471591 ATGGGTGGCAGCAAGGAAAA 60.472 50.000 19.48 0.00 0.00 2.29
40 41 0.407528 TATGGGTGGCAGCAAGGAAA 59.592 50.000 19.48 0.00 0.00 3.13
41 42 0.323360 GTATGGGTGGCAGCAAGGAA 60.323 55.000 19.48 0.00 0.00 3.36
42 43 1.207488 AGTATGGGTGGCAGCAAGGA 61.207 55.000 19.48 0.00 0.00 3.36
43 44 0.323725 AAGTATGGGTGGCAGCAAGG 60.324 55.000 19.48 0.00 0.00 3.61
44 45 2.418368 TAAGTATGGGTGGCAGCAAG 57.582 50.000 19.48 0.00 0.00 4.01
45 46 2.653726 CATAAGTATGGGTGGCAGCAA 58.346 47.619 19.48 7.83 0.00 3.91
46 47 2.346766 CATAAGTATGGGTGGCAGCA 57.653 50.000 19.48 5.16 0.00 4.41
69 70 4.725790 TGTGGTGACAGTGAGATCATAG 57.274 45.455 0.00 0.00 44.46 2.23
106 107 5.801531 TTAACTAGAGAGTTCTTGCCACA 57.198 39.130 0.00 0.00 42.50 4.17
145 146 3.982576 AGTGGGCGAAGTAAAGTTTTG 57.017 42.857 0.00 0.00 0.00 2.44
317 485 7.771927 AGTCTCCATCAACATGAAGAAAAAT 57.228 32.000 0.00 0.00 30.57 1.82
333 501 7.293299 TGATGGACCAAAATAGATAGTCTCCAT 59.707 37.037 0.00 0.00 36.00 3.41
338 506 8.738645 AAGTTGATGGACCAAAATAGATAGTC 57.261 34.615 0.00 0.00 0.00 2.59
367 535 9.657419 ATCTAGTATTTGAATTTTTGGCTTTGG 57.343 29.630 0.00 0.00 0.00 3.28
387 555 9.574516 ACCTTGATAGACAAAAACAAATCTAGT 57.425 29.630 0.00 0.00 38.08 2.57
443 611 8.230486 CGCCTCATTATTAAAACCTCATACATC 58.770 37.037 0.00 0.00 0.00 3.06
449 617 3.630312 GCCGCCTCATTATTAAAACCTCA 59.370 43.478 0.00 0.00 0.00 3.86
474 642 2.076863 CAGCTAAGTTGTAGGTGTGCC 58.923 52.381 4.74 0.00 38.02 5.01
530 967 8.036273 TCCACCGAGTAGAAACAAATTTTATC 57.964 34.615 0.00 0.00 0.00 1.75
541 1230 5.655090 TGTATCAAGATCCACCGAGTAGAAA 59.345 40.000 0.00 0.00 0.00 2.52
578 1267 3.561143 AGCCGACAGAGATAAGACTGAT 58.439 45.455 0.00 0.00 37.54 2.90
654 1387 1.072489 TGCCCACCTCGTGTCATTTTA 59.928 47.619 0.00 0.00 0.00 1.52
682 1420 1.936436 TATCGTTGTCGGTCCCGGTG 61.936 60.000 5.80 0.00 40.25 4.94
683 1421 1.660560 CTATCGTTGTCGGTCCCGGT 61.661 60.000 5.80 0.00 40.25 5.28
684 1422 1.065273 CTATCGTTGTCGGTCCCGG 59.935 63.158 5.80 0.00 40.25 5.73
685 1423 1.065273 CCTATCGTTGTCGGTCCCG 59.935 63.158 0.00 0.00 41.35 5.14
686 1424 0.179119 CACCTATCGTTGTCGGTCCC 60.179 60.000 0.00 0.00 37.69 4.46
687 1425 0.804933 GCACCTATCGTTGTCGGTCC 60.805 60.000 0.00 0.00 37.69 4.46
688 1426 1.138047 CGCACCTATCGTTGTCGGTC 61.138 60.000 0.00 0.00 37.69 4.79
689 1427 1.153901 CGCACCTATCGTTGTCGGT 60.154 57.895 0.00 0.00 37.69 4.69
690 1428 1.876714 CCGCACCTATCGTTGTCGG 60.877 63.158 0.00 0.00 37.69 4.79
703 1441 1.117234 CTTGTTTGTTTACGCCGCAC 58.883 50.000 0.00 0.00 0.00 5.34
718 1456 2.876550 GCTTTCCGGTCACTTTACTTGT 59.123 45.455 0.00 0.00 0.00 3.16
720 1458 2.876550 GTGCTTTCCGGTCACTTTACTT 59.123 45.455 0.00 0.00 0.00 2.24
721 1459 2.490991 GTGCTTTCCGGTCACTTTACT 58.509 47.619 0.00 0.00 0.00 2.24
722 1460 1.534163 GGTGCTTTCCGGTCACTTTAC 59.466 52.381 0.00 0.00 0.00 2.01
723 1461 1.543871 GGGTGCTTTCCGGTCACTTTA 60.544 52.381 0.00 0.00 0.00 1.85
768 1507 0.817634 CCGGAGCAAAACAGTGGTCA 60.818 55.000 0.00 0.00 45.76 4.02
811 1551 0.971386 GAGGTGGGACGAGTGGTTAA 59.029 55.000 0.00 0.00 0.00 2.01
819 1559 0.974383 GAAGAAAGGAGGTGGGACGA 59.026 55.000 0.00 0.00 0.00 4.20
842 1584 3.314913 TGCTTGTGTAGTTGTGTTGATGG 59.685 43.478 0.00 0.00 0.00 3.51
851 1593 5.124297 TGGATGATTGATGCTTGTGTAGTTG 59.876 40.000 0.00 0.00 0.00 3.16
854 1596 5.124297 TGTTGGATGATTGATGCTTGTGTAG 59.876 40.000 0.00 0.00 0.00 2.74
880 1622 8.461222 CCTTGTGCTATTTATGAATGAACTGAA 58.539 33.333 0.00 0.00 0.00 3.02
896 1640 0.328258 GGGTGTGGACCTTGTGCTAT 59.672 55.000 0.00 0.00 42.66 2.97
897 1641 0.766674 AGGGTGTGGACCTTGTGCTA 60.767 55.000 0.00 0.00 42.66 3.49
973 1731 1.895798 TCTCTCTGCGTTGGTGAAGAT 59.104 47.619 0.00 0.00 0.00 2.40
977 1735 1.550327 ATCTCTCTCTGCGTTGGTGA 58.450 50.000 0.00 0.00 0.00 4.02
996 1758 4.927782 GCCGCACCCGCCATGATA 62.928 66.667 0.00 0.00 33.11 2.15
1157 1922 2.669569 GAAGCTGCTTCGTGCCCA 60.670 61.111 24.86 0.00 42.00 5.36
1324 2093 1.755783 CCAGCTGATTTCCAGGCCC 60.756 63.158 17.39 0.00 43.13 5.80
1348 2117 4.088071 CGTCGTGGTATATTACAATCGCAG 59.912 45.833 0.00 0.00 0.00 5.18
1349 2118 3.976306 CGTCGTGGTATATTACAATCGCA 59.024 43.478 0.00 0.00 0.00 5.10
1388 2158 7.888021 AGGGAATATAAACACATGTGACAGAAA 59.112 33.333 31.94 12.55 0.00 2.52
1410 2180 8.742777 CATCAAAATCAAATAGACAAGAAGGGA 58.257 33.333 0.00 0.00 0.00 4.20
1411 2181 8.742777 TCATCAAAATCAAATAGACAAGAAGGG 58.257 33.333 0.00 0.00 0.00 3.95
1415 2185 7.626240 GCGGTCATCAAAATCAAATAGACAAGA 60.626 37.037 0.00 0.00 0.00 3.02
1418 2188 5.447144 CGCGGTCATCAAAATCAAATAGACA 60.447 40.000 0.00 0.00 0.00 3.41
1419 2189 4.963953 CGCGGTCATCAAAATCAAATAGAC 59.036 41.667 0.00 0.00 0.00 2.59
1421 2191 4.963953 GTCGCGGTCATCAAAATCAAATAG 59.036 41.667 6.13 0.00 0.00 1.73
1423 2193 3.727673 CGTCGCGGTCATCAAAATCAAAT 60.728 43.478 6.13 0.00 0.00 2.32
1424 2194 2.412195 CGTCGCGGTCATCAAAATCAAA 60.412 45.455 6.13 0.00 0.00 2.69
1425 2195 1.127766 CGTCGCGGTCATCAAAATCAA 59.872 47.619 6.13 0.00 0.00 2.57
1426 2196 0.718904 CGTCGCGGTCATCAAAATCA 59.281 50.000 6.13 0.00 0.00 2.57
1427 2197 0.996462 TCGTCGCGGTCATCAAAATC 59.004 50.000 6.13 0.00 0.00 2.17
1428 2198 0.999406 CTCGTCGCGGTCATCAAAAT 59.001 50.000 6.13 0.00 0.00 1.82
1429 2199 1.011968 CCTCGTCGCGGTCATCAAAA 61.012 55.000 6.13 0.00 0.00 2.44
1430 2200 1.445410 CCTCGTCGCGGTCATCAAA 60.445 57.895 6.13 0.00 0.00 2.69
1431 2201 1.868987 TTCCTCGTCGCGGTCATCAA 61.869 55.000 6.13 0.00 0.00 2.57
1432 2202 1.663379 ATTCCTCGTCGCGGTCATCA 61.663 55.000 6.13 0.00 0.00 3.07
1433 2203 1.065928 ATTCCTCGTCGCGGTCATC 59.934 57.895 6.13 0.00 0.00 2.92
1434 2204 1.226974 CATTCCTCGTCGCGGTCAT 60.227 57.895 6.13 0.00 0.00 3.06
1435 2205 2.180769 CATTCCTCGTCGCGGTCA 59.819 61.111 6.13 0.00 0.00 4.02
1436 2206 2.158959 CACATTCCTCGTCGCGGTC 61.159 63.158 6.13 0.00 0.00 4.79
1437 2207 2.126071 CACATTCCTCGTCGCGGT 60.126 61.111 6.13 0.00 0.00 5.68
1438 2208 2.885644 CCACATTCCTCGTCGCGG 60.886 66.667 6.13 0.00 0.00 6.46
1439 2209 2.158959 GTCCACATTCCTCGTCGCG 61.159 63.158 0.00 0.00 0.00 5.87
1440 2210 2.158959 CGTCCACATTCCTCGTCGC 61.159 63.158 0.00 0.00 0.00 5.19
1441 2211 0.388134 AACGTCCACATTCCTCGTCG 60.388 55.000 0.00 0.00 33.67 5.12
1444 2214 1.790755 TGAAACGTCCACATTCCTCG 58.209 50.000 0.00 0.00 0.00 4.63
1446 2216 3.255642 CCAATTGAAACGTCCACATTCCT 59.744 43.478 7.12 0.00 0.00 3.36
1452 2222 3.112580 CACAACCAATTGAAACGTCCAC 58.887 45.455 7.12 0.00 39.30 4.02
1453 2223 2.480416 GCACAACCAATTGAAACGTCCA 60.480 45.455 7.12 0.00 39.30 4.02
1456 2226 2.949451 TGCACAACCAATTGAAACGT 57.051 40.000 7.12 0.00 39.30 3.99
1460 2230 2.364647 TCTGCATGCACAACCAATTGAA 59.635 40.909 18.46 0.00 39.30 2.69
1471 2241 4.514066 TGATCATATCAAGTCTGCATGCAC 59.486 41.667 18.46 8.42 36.11 4.57
1475 2245 4.700692 GCCATGATCATATCAAGTCTGCAT 59.299 41.667 8.15 0.00 43.50 3.96
1481 2251 2.373169 ACCGGCCATGATCATATCAAGT 59.627 45.455 8.15 1.07 43.50 3.16
1482 2252 3.005554 GACCGGCCATGATCATATCAAG 58.994 50.000 8.15 0.43 43.50 3.02
1484 2254 2.027837 CAGACCGGCCATGATCATATCA 60.028 50.000 8.15 0.00 44.55 2.15
1486 2256 1.280133 CCAGACCGGCCATGATCATAT 59.720 52.381 8.15 0.00 0.00 1.78
1488 2258 1.348008 ACCAGACCGGCCATGATCAT 61.348 55.000 0.00 1.18 39.03 2.45
1495 2265 1.488705 ATTTCAGACCAGACCGGCCA 61.489 55.000 0.00 0.00 39.03 5.36
1500 2270 6.352516 AGACATTCATATTTCAGACCAGACC 58.647 40.000 0.00 0.00 0.00 3.85
1506 2276 6.478344 AGAGCGAAGACATTCATATTTCAGAC 59.522 38.462 0.00 0.00 34.94 3.51
1516 2291 1.432514 GTGCAGAGCGAAGACATTCA 58.567 50.000 0.00 0.00 34.94 2.57
1536 2311 2.204237 TGATCATGTCGATTCGGCAAG 58.796 47.619 18.18 13.58 46.66 4.01
1550 2325 8.581253 TCAGTACATATACGAGGATTGATCAT 57.419 34.615 0.00 0.00 36.33 2.45
1551 2326 7.996098 TCAGTACATATACGAGGATTGATCA 57.004 36.000 0.00 0.00 36.33 2.92
1555 2330 6.088217 CGCTTTCAGTACATATACGAGGATTG 59.912 42.308 0.00 0.00 36.33 2.67
1567 2342 2.555199 GAGATGCCGCTTTCAGTACAT 58.445 47.619 0.00 0.00 0.00 2.29
1570 2345 0.530744 ACGAGATGCCGCTTTCAGTA 59.469 50.000 0.00 0.00 0.00 2.74
1573 2348 0.320334 TCAACGAGATGCCGCTTTCA 60.320 50.000 0.00 0.00 0.00 2.69
1577 2352 1.398390 GAAAATCAACGAGATGCCGCT 59.602 47.619 0.00 0.00 36.96 5.52
1579 2354 1.267532 CGGAAAATCAACGAGATGCCG 60.268 52.381 12.89 12.89 39.05 5.69
1582 2357 3.000041 TGACCGGAAAATCAACGAGATG 59.000 45.455 9.46 0.00 36.96 2.90
1583 2358 3.328382 TGACCGGAAAATCAACGAGAT 57.672 42.857 9.46 0.00 39.09 2.75
1584 2359 2.803956 GTTGACCGGAAAATCAACGAGA 59.196 45.455 16.96 0.00 43.72 4.04
1585 2360 3.183237 GTTGACCGGAAAATCAACGAG 57.817 47.619 16.96 0.00 43.72 4.18
1591 2368 2.084546 CCAGGAGTTGACCGGAAAATC 58.915 52.381 9.46 11.04 34.73 2.17
1599 2376 0.035343 GCCCTAACCAGGAGTTGACC 60.035 60.000 0.00 0.00 45.91 4.02
1616 2393 5.799827 ATACTCCTCTAATCAGAGTTGCC 57.200 43.478 0.00 0.00 46.01 4.52
1617 2394 9.771534 ATTTTATACTCCTCTAATCAGAGTTGC 57.228 33.333 0.00 0.00 46.01 4.17
1665 2442 0.263765 TAAGGGATCGGGTAGGTGCT 59.736 55.000 0.00 0.00 0.00 4.40
1673 2450 1.362224 ATGGTGGATAAGGGATCGGG 58.638 55.000 0.00 0.00 35.12 5.14
1703 2480 4.589374 ACGATAGGGGAGAGGACTAAAATG 59.411 45.833 0.00 0.00 43.77 2.32
1710 2487 1.687660 GGAAACGATAGGGGAGAGGAC 59.312 57.143 0.00 0.00 43.77 3.85
1721 2509 6.400568 ACGGAGTAAATTGAAGGAAACGATA 58.599 36.000 0.00 0.00 41.94 2.92
1776 2564 3.551407 GGGGGATGACGAGAGGGC 61.551 72.222 0.00 0.00 0.00 5.19
1867 2678 1.301401 CTGGACGTCGGGCAGAAAA 60.301 57.895 13.21 0.00 0.00 2.29
1936 2757 4.675510 GATGAATCAACAACAATGGCGAT 58.324 39.130 0.00 0.00 0.00 4.58
2000 2821 0.238289 GGTGTGCAATCAACGTGAGG 59.762 55.000 0.00 0.00 0.00 3.86
2099 2923 2.797792 GCCAATTCGTCAAACACTTGCA 60.798 45.455 0.00 0.00 32.14 4.08
2166 2991 1.247567 ATTCAAACGGCTTGGTCCAG 58.752 50.000 0.00 0.00 35.56 3.86
2169 2994 6.260050 TCATCTATAATTCAAACGGCTTGGTC 59.740 38.462 0.33 0.00 35.56 4.02
2187 3012 5.149584 TCTCCCTCAACCTCTTCATCTAT 57.850 43.478 0.00 0.00 0.00 1.98
2217 3042 3.289407 TCAGATGATGACGAGTCCTCT 57.711 47.619 9.31 1.16 31.12 3.69
2235 3060 4.706962 TCATCATCGTCTTCTTCCTCTTCA 59.293 41.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.