Multiple sequence alignment - TraesCS4D01G114400

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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 TraesCS4D01G114400 chr4D 100.000 3053 0 0 1 3053 95291390 95288338 0.000000e+00 5638.0
1 TraesCS4D01G114400 chr4B 92.902 2522 104 30 571 3042 134826114 134823618 0.000000e+00 3596.0
2 TraesCS4D01G114400 chr4B 92.045 88 7 0 1 88 134853585 134853498 1.150000e-24 124.0
3 TraesCS4D01G114400 chr4B 95.238 42 2 0 459 500 215410509 215410468 1.960000e-07 67.6
4 TraesCS4D01G114400 chr4A 90.821 1961 92 37 505 2419 484671652 484673570 0.000000e+00 2543.0
5 TraesCS4D01G114400 chr4A 91.738 581 19 14 2431 2998 484673708 484674272 0.000000e+00 780.0
6 TraesCS4D01G114400 chr4A 90.398 427 35 5 1 422 484671213 484671638 9.560000e-155 556.0
7 TraesCS4D01G114400 chr5A 87.379 206 26 0 1527 1732 278299834 278299629 1.410000e-58 237.0
8 TraesCS4D01G114400 chrUn 87.019 208 27 0 1527 1734 67924636 67924843 5.090000e-58 235.0
9 TraesCS4D01G114400 chr6D 77.151 372 63 17 20 377 389705294 389704931 2.400000e-46 196.0
10 TraesCS4D01G114400 chr6D 77.049 366 65 14 20 372 458129738 458130097 3.110000e-45 193.0
11 TraesCS4D01G114400 chr6D 76.819 371 65 16 20 376 82143815 82143452 4.020000e-44 189.0
12 TraesCS4D01G114400 chr1D 77.384 367 60 17 20 371 80658615 80658257 2.400000e-46 196.0
13 TraesCS4D01G114400 chr7D 77.112 367 62 18 20 372 60368592 60368234 3.110000e-45 193.0
14 TraesCS4D01G114400 chr7D 76.190 231 35 15 1532 1752 414087256 414087036 1.500000e-18 104.0
15 TraesCS4D01G114400 chr7D 100.000 35 0 0 465 499 89107697 89107663 7.070000e-07 65.8
16 TraesCS4D01G114400 chr5D 77.112 367 63 16 20 372 120783185 120783544 3.110000e-45 193.0
17 TraesCS4D01G114400 chr3A 75.342 365 67 18 20 372 715578646 715578293 1.470000e-33 154.0
18 TraesCS4D01G114400 chr1B 77.824 239 44 9 122 355 512786741 512786975 4.100000e-29 139.0
19 TraesCS4D01G114400 chr7A 75.758 231 36 15 1532 1752 475962905 475962685 6.970000e-17 99.0
20 TraesCS4D01G114400 chr7A 92.857 42 3 0 454 495 135001573 135001532 9.140000e-06 62.1
21 TraesCS4D01G114400 chr7B 76.442 208 31 13 1554 1752 428483411 428483213 2.510000e-16 97.1
22 TraesCS4D01G114400 chr2B 95.652 46 2 0 454 499 789962904 789962949 1.170000e-09 75.0
23 TraesCS4D01G114400 chr2B 93.478 46 3 0 454 499 607551447 607551402 5.460000e-08 69.4
24 TraesCS4D01G114400 chr5B 91.667 48 4 0 454 501 462561687 462561734 1.960000e-07 67.6
25 TraesCS4D01G114400 chr3B 91.489 47 4 0 454 500 96842469 96842515 7.070000e-07 65.8
26 TraesCS4D01G114400 chr3B 100.000 31 0 0 422 452 722303460 722303490 1.180000e-04 58.4
27 TraesCS4D01G114400 chr1A 89.796 49 3 2 452 499 29151585 29151632 9.140000e-06 62.1
28 TraesCS4D01G114400 chr2D 88.000 50 4 2 452 500 91404320 91404368 1.180000e-04 58.4


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 TraesCS4D01G114400 chr4D 95288338 95291390 3052 True 5638 5638 100.000000 1 3053 1 chr4D.!!$R1 3052
1 TraesCS4D01G114400 chr4B 134823618 134826114 2496 True 3596 3596 92.902000 571 3042 1 chr4B.!!$R1 2471
2 TraesCS4D01G114400 chr4A 484671213 484674272 3059 False 1293 2543 90.985667 1 2998 3 chr4A.!!$F1 2997

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
456 462 0.187361 TTTGGGACTGGGGGACAAAG 59.813 55.0 0.0 0.0 0.0 2.77 F
879 897 0.322997 ACTCTCTACCTCACGCTGCT 60.323 55.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1374 0.396417 CCTCAGACCACTCCTCGGAT 60.396 60.0 0.0 0.0 0.0 4.18 R
2873 3125 0.244721 CGATCAGTCACAGCCTCACA 59.755 55.0 0.0 0.0 0.0 3.58 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
27 28 2.031120 CCCTTTCTTGTTTGCAGGTCA 58.969 47.619 0.00 0.00 0.00 4.02
32 33 4.370364 TTCTTGTTTGCAGGTCACTTTC 57.630 40.909 0.00 0.00 0.00 2.62
41 42 1.790623 CAGGTCACTTTCCGTTGTACG 59.209 52.381 0.00 0.00 42.11 3.67
73 74 5.452078 TGTATGTGATCTACGATGCATCA 57.548 39.130 25.70 7.21 0.00 3.07
88 89 5.504010 CGATGCATCAAACATAGTACCAACC 60.504 44.000 25.70 0.00 0.00 3.77
99 100 2.774687 AGTACCAACCGTTGCTTAAGG 58.225 47.619 5.68 0.00 0.00 2.69
106 107 1.169661 CCGTTGCTTAAGGTGGTGCA 61.170 55.000 4.29 0.00 0.00 4.57
111 112 1.002659 TGCTTAAGGTGGTGCATACGT 59.997 47.619 4.29 0.00 0.00 3.57
115 116 1.234821 AAGGTGGTGCATACGTGTTG 58.765 50.000 0.00 0.00 0.00 3.33
118 119 1.302913 TGGTGCATACGTGTTGGGG 60.303 57.895 0.00 0.00 0.00 4.96
145 149 2.825457 GCCAGGGAGGTTTTTACCCAAT 60.825 50.000 0.00 0.00 45.43 3.16
152 156 8.421002 CAGGGAGGTTTTTACCCAATATTAATG 58.579 37.037 0.00 0.00 45.43 1.90
157 161 8.777089 AGGTTTTTACCCAATATTAATGGCAAT 58.223 29.630 0.00 0.00 36.58 3.56
179 183 3.634397 TGATCTTCAGATTGGTCCACC 57.366 47.619 0.00 0.00 34.37 4.61
185 189 1.550524 TCAGATTGGTCCACCTTCTCG 59.449 52.381 0.00 0.00 36.82 4.04
187 191 1.276421 AGATTGGTCCACCTTCTCGTG 59.724 52.381 0.00 0.00 36.82 4.35
191 195 0.319641 GGTCCACCTTCTCGTGTGAC 60.320 60.000 0.00 0.00 35.21 3.67
205 209 5.121925 TCTCGTGTGACATAGACTTAGTGTC 59.878 44.000 0.00 7.85 45.67 3.67
234 238 1.630369 AGGACTTCACTGCTGCCATTA 59.370 47.619 0.00 0.00 0.00 1.90
240 244 0.659427 CACTGCTGCCATTATGTCGG 59.341 55.000 0.00 0.00 0.00 4.79
246 250 3.323691 TGCTGCCATTATGTCGGTATACT 59.676 43.478 2.25 0.00 0.00 2.12
283 287 2.222027 ACTTGTTTCTGTAGGCTGTGC 58.778 47.619 0.00 0.00 0.00 4.57
305 311 1.190833 AGCTATCCAGAGGCCGGATG 61.191 60.000 18.18 9.04 43.29 3.51
326 332 4.048504 TGTCGCTTCATATGTATGTTCCG 58.951 43.478 1.90 0.00 35.26 4.30
357 363 8.667987 TGCTACATTTTGAGTTAATAAAAGCG 57.332 30.769 0.00 0.00 0.00 4.68
360 366 9.274065 CTACATTTTGAGTTAATAAAAGCGTCC 57.726 33.333 0.00 0.00 0.00 4.79
376 382 3.632145 AGCGTCCTTTGTTGAAAAGATGT 59.368 39.130 0.00 0.00 0.00 3.06
382 388 7.463544 GTCCTTTGTTGAAAAGATGTTTTTGG 58.536 34.615 1.67 0.00 35.94 3.28
440 446 9.683069 AAATGCTAAGTTGAGACACTTATTTTG 57.317 29.630 0.00 0.00 38.34 2.44
441 447 7.202016 TGCTAAGTTGAGACACTTATTTTGG 57.798 36.000 0.00 0.00 38.34 3.28
442 448 6.206634 TGCTAAGTTGAGACACTTATTTTGGG 59.793 38.462 0.00 0.00 38.34 4.12
443 449 6.430000 GCTAAGTTGAGACACTTATTTTGGGA 59.570 38.462 0.00 0.00 38.34 4.37
444 450 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
445 451 5.941788 AGTTGAGACACTTATTTTGGGACT 58.058 37.500 0.00 0.00 0.00 3.85
446 452 5.765182 AGTTGAGACACTTATTTTGGGACTG 59.235 40.000 0.00 0.00 0.00 3.51
447 453 4.651778 TGAGACACTTATTTTGGGACTGG 58.348 43.478 0.00 0.00 0.00 4.00
448 454 4.010349 GAGACACTTATTTTGGGACTGGG 58.990 47.826 0.00 0.00 0.00 4.45
449 455 3.089284 GACACTTATTTTGGGACTGGGG 58.911 50.000 0.00 0.00 0.00 4.96
450 456 2.225267 ACACTTATTTTGGGACTGGGGG 60.225 50.000 0.00 0.00 0.00 5.40
451 457 2.042433 CACTTATTTTGGGACTGGGGGA 59.958 50.000 0.00 0.00 0.00 4.81
452 458 2.042569 ACTTATTTTGGGACTGGGGGAC 59.957 50.000 0.00 0.00 0.00 4.46
453 459 1.761711 TATTTTGGGACTGGGGGACA 58.238 50.000 0.00 0.00 0.00 4.02
454 460 0.863956 ATTTTGGGACTGGGGGACAA 59.136 50.000 0.00 0.00 0.00 3.18
455 461 0.637195 TTTTGGGACTGGGGGACAAA 59.363 50.000 0.00 0.00 0.00 2.83
456 462 0.187361 TTTGGGACTGGGGGACAAAG 59.813 55.000 0.00 0.00 0.00 2.77
457 463 0.996762 TTGGGACTGGGGGACAAAGT 60.997 55.000 0.00 0.00 0.00 2.66
458 464 0.996762 TGGGACTGGGGGACAAAGTT 60.997 55.000 0.00 0.00 0.00 2.66
459 465 1.069775 GGGACTGGGGGACAAAGTTA 58.930 55.000 0.00 0.00 0.00 2.24
460 466 1.004394 GGGACTGGGGGACAAAGTTAG 59.996 57.143 0.00 0.00 0.00 2.34
461 467 1.703513 GGACTGGGGGACAAAGTTAGT 59.296 52.381 0.00 0.00 0.00 2.24
462 468 2.908351 GGACTGGGGGACAAAGTTAGTA 59.092 50.000 0.00 0.00 0.00 1.82
463 469 3.328637 GGACTGGGGGACAAAGTTAGTAA 59.671 47.826 0.00 0.00 0.00 2.24
464 470 4.202493 GGACTGGGGGACAAAGTTAGTAAA 60.202 45.833 0.00 0.00 0.00 2.01
465 471 5.379187 GACTGGGGGACAAAGTTAGTAAAA 58.621 41.667 0.00 0.00 0.00 1.52
466 472 5.768752 ACTGGGGGACAAAGTTAGTAAAAA 58.231 37.500 0.00 0.00 0.00 1.94
467 473 5.831525 ACTGGGGGACAAAGTTAGTAAAAAG 59.168 40.000 0.00 0.00 0.00 2.27
468 474 5.768752 TGGGGGACAAAGTTAGTAAAAAGT 58.231 37.500 0.00 0.00 0.00 2.66
469 475 6.196434 TGGGGGACAAAGTTAGTAAAAAGTT 58.804 36.000 0.00 0.00 0.00 2.66
470 476 6.097129 TGGGGGACAAAGTTAGTAAAAAGTTG 59.903 38.462 0.00 0.00 0.00 3.16
471 477 6.321945 GGGGGACAAAGTTAGTAAAAAGTTGA 59.678 38.462 0.00 0.00 0.00 3.18
472 478 7.423199 GGGGACAAAGTTAGTAAAAAGTTGAG 58.577 38.462 0.00 0.00 0.00 3.02
473 479 7.283807 GGGGACAAAGTTAGTAAAAAGTTGAGA 59.716 37.037 0.00 0.00 0.00 3.27
474 480 8.127327 GGGACAAAGTTAGTAAAAAGTTGAGAC 58.873 37.037 0.00 0.00 0.00 3.36
475 481 8.671028 GGACAAAGTTAGTAAAAAGTTGAGACA 58.329 33.333 0.00 0.00 0.00 3.41
476 482 9.486857 GACAAAGTTAGTAAAAAGTTGAGACAC 57.513 33.333 0.00 0.00 0.00 3.67
477 483 9.227777 ACAAAGTTAGTAAAAAGTTGAGACACT 57.772 29.630 0.00 0.00 0.00 3.55
493 499 9.535878 GTTGAGACACTTATTTTAGGATAGAGG 57.464 37.037 0.00 0.00 0.00 3.69
494 500 8.251383 TGAGACACTTATTTTAGGATAGAGGG 57.749 38.462 0.00 0.00 0.00 4.30
495 501 8.065627 TGAGACACTTATTTTAGGATAGAGGGA 58.934 37.037 0.00 0.00 0.00 4.20
496 502 8.485578 AGACACTTATTTTAGGATAGAGGGAG 57.514 38.462 0.00 0.00 0.00 4.30
497 503 8.068733 AGACACTTATTTTAGGATAGAGGGAGT 58.931 37.037 0.00 0.00 0.00 3.85
498 504 9.364653 GACACTTATTTTAGGATAGAGGGAGTA 57.635 37.037 0.00 0.00 0.00 2.59
499 505 9.900112 ACACTTATTTTAGGATAGAGGGAGTAT 57.100 33.333 0.00 0.00 0.00 2.12
514 520 3.385111 GGGAGTATGATCGAAACAGTCCT 59.615 47.826 14.93 6.63 0.00 3.85
515 521 4.583489 GGGAGTATGATCGAAACAGTCCTA 59.417 45.833 14.93 0.00 0.00 2.94
526 532 6.796426 TCGAAACAGTCCTATAGTCTTGATG 58.204 40.000 0.00 0.00 0.00 3.07
529 535 4.884961 ACAGTCCTATAGTCTTGATGGGT 58.115 43.478 0.00 0.00 0.00 4.51
590 596 3.874392 ATTCCTCAATTCAAAAGGCCG 57.126 42.857 0.00 0.00 0.00 6.13
591 597 0.887933 TCCTCAATTCAAAAGGCCGC 59.112 50.000 0.00 0.00 0.00 6.53
596 603 2.061028 CAATTCAAAAGGCCGCAGAAC 58.939 47.619 0.00 0.00 0.00 3.01
600 607 1.754226 TCAAAAGGCCGCAGAACTTTT 59.246 42.857 0.00 0.00 41.34 2.27
614 621 9.203421 CCGCAGAACTTTTAAAAATAAATTCCT 57.797 29.630 1.66 0.00 0.00 3.36
665 672 5.738783 GCGTAACCACCGGTAGGATAAATAA 60.739 44.000 24.32 0.73 41.02 1.40
667 674 6.760770 CGTAACCACCGGTAGGATAAATAAAA 59.239 38.462 24.32 0.00 41.02 1.52
668 675 7.442062 CGTAACCACCGGTAGGATAAATAAAAT 59.558 37.037 24.32 1.17 41.02 1.82
669 676 9.777297 GTAACCACCGGTAGGATAAATAAAATA 57.223 33.333 24.32 0.00 41.02 1.40
807 823 4.894784 AGTAGATAAATACGGGCACATGG 58.105 43.478 0.00 0.00 0.00 3.66
879 897 0.322997 ACTCTCTACCTCACGCTGCT 60.323 55.000 0.00 0.00 0.00 4.24
960 986 1.337071 AGCTCGTCTTCAGTTCGTTCA 59.663 47.619 0.00 0.00 0.00 3.18
974 1001 2.380941 TCGTTCATCTCCGGTAATCCA 58.619 47.619 0.00 0.00 0.00 3.41
979 1006 2.963101 TCATCTCCGGTAATCCATTCGT 59.037 45.455 0.00 0.00 0.00 3.85
982 1009 2.124903 CTCCGGTAATCCATTCGTTCG 58.875 52.381 0.00 0.00 0.00 3.95
988 1015 0.725117 AATCCATTCGTTCGAACCGC 59.275 50.000 22.07 0.00 0.00 5.68
1341 1374 2.895682 TTTCTCGACGACGACCGCA 61.896 57.895 5.75 0.00 43.81 5.69
1344 1377 4.170062 TCGACGACGACCGCATCC 62.170 66.667 5.75 0.00 43.81 3.51
1443 1476 0.321564 CGTCCAACTCCATCTTGGCA 60.322 55.000 0.00 0.00 38.50 4.92
1641 1677 4.760047 GGCTGGGAAGCGCTCGAA 62.760 66.667 12.06 0.00 35.24 3.71
1976 2019 4.020617 CCTGCAGGGCAAGGACGA 62.021 66.667 26.14 0.00 38.41 4.20
1977 2020 2.435586 CTGCAGGGCAAGGACGAG 60.436 66.667 5.57 0.00 38.41 4.18
1978 2021 3.965539 CTGCAGGGCAAGGACGAGG 62.966 68.421 5.57 0.00 38.41 4.63
1979 2022 3.706373 GCAGGGCAAGGACGAGGA 61.706 66.667 0.00 0.00 0.00 3.71
1980 2023 2.581354 CAGGGCAAGGACGAGGAG 59.419 66.667 0.00 0.00 0.00 3.69
1981 2024 2.685380 AGGGCAAGGACGAGGAGG 60.685 66.667 0.00 0.00 0.00 4.30
1982 2025 2.683933 GGGCAAGGACGAGGAGGA 60.684 66.667 0.00 0.00 0.00 3.71
1983 2026 2.726351 GGGCAAGGACGAGGAGGAG 61.726 68.421 0.00 0.00 0.00 3.69
1984 2027 2.726351 GGCAAGGACGAGGAGGAGG 61.726 68.421 0.00 0.00 0.00 4.30
1989 2032 1.152839 GGACGAGGAGGAGGAGGAG 60.153 68.421 0.00 0.00 0.00 3.69
2055 2119 0.891373 TGAGGAGTGCACACTAGCTC 59.109 55.000 21.04 14.69 42.66 4.09
2070 2134 5.543020 ACACTAGCTCCTTGGTTAGTTAACT 59.457 40.000 13.68 13.68 36.47 2.24
2257 2347 5.772825 TGTTCACCTCTCCTTCAATTTTG 57.227 39.130 0.00 0.00 0.00 2.44
2265 2355 7.383300 CACCTCTCCTTCAATTTTGAAAATGTC 59.617 37.037 3.62 0.00 45.61 3.06
2277 2367 4.777140 TGAAAATGTCGATGATAGCACG 57.223 40.909 0.00 0.00 0.00 5.34
2306 2396 6.790285 ACGGAGTATTTACAAACATTTCGT 57.210 33.333 0.00 0.00 41.94 3.85
2328 2420 1.817099 CATCGTTGGAGCCTGGAGC 60.817 63.158 0.00 0.00 44.25 4.70
2344 2443 1.700955 GAGCAGGGATCCAATGCATT 58.299 50.000 31.47 18.70 42.45 3.56
2347 2446 1.202486 GCAGGGATCCAATGCATTGTG 60.202 52.381 31.87 23.98 39.75 3.33
2350 2449 2.109774 GGGATCCAATGCATTGTGGAA 58.890 47.619 31.87 17.78 46.78 3.53
2351 2450 2.159057 GGGATCCAATGCATTGTGGAAC 60.159 50.000 31.87 23.56 46.78 3.62
2352 2451 2.159057 GGATCCAATGCATTGTGGAACC 60.159 50.000 31.87 27.41 46.78 3.62
2354 2453 2.538222 TCCAATGCATTGTGGAACCAT 58.462 42.857 31.87 0.00 41.02 3.55
2355 2454 2.234168 TCCAATGCATTGTGGAACCATG 59.766 45.455 31.87 16.75 42.43 3.66
2367 2466 2.102578 GGAACCATGCATTGTAGGCTT 58.897 47.619 3.50 0.00 0.00 4.35
2371 2470 1.952296 CCATGCATTGTAGGCTTCTCC 59.048 52.381 0.00 0.00 0.00 3.71
2489 2720 0.725117 CCGCTGGTTAACGTGAATCC 59.275 55.000 0.00 0.00 0.00 3.01
2660 2891 3.127533 GCACGCTTGGCAGTAGGG 61.128 66.667 2.06 2.06 0.00 3.53
2669 2900 0.546747 TGGCAGTAGGGCTAACCACT 60.547 55.000 0.00 0.00 43.89 4.00
2673 2904 2.101082 GCAGTAGGGCTAACCACTACTC 59.899 54.545 2.43 0.00 42.99 2.59
2721 2958 4.435877 CGAAGTACGTCTACCTAATTTCGC 59.564 45.833 7.22 0.00 37.22 4.70
2843 3087 2.571757 GTCGATGACAGGTCGCCA 59.428 61.111 0.00 0.00 38.88 5.69
2869 3121 0.037697 GTGGTGGTAGCGTGTGATGA 60.038 55.000 0.00 0.00 0.00 2.92
2870 3122 0.246360 TGGTGGTAGCGTGTGATGAG 59.754 55.000 0.00 0.00 0.00 2.90
2871 3123 1.084370 GGTGGTAGCGTGTGATGAGC 61.084 60.000 0.00 0.00 0.00 4.26
2872 3124 1.084370 GTGGTAGCGTGTGATGAGCC 61.084 60.000 0.00 0.00 0.00 4.70
2873 3125 1.257750 TGGTAGCGTGTGATGAGCCT 61.258 55.000 0.00 0.00 0.00 4.58
2874 3126 0.807667 GGTAGCGTGTGATGAGCCTG 60.808 60.000 0.00 0.00 0.00 4.85
2875 3127 0.108615 GTAGCGTGTGATGAGCCTGT 60.109 55.000 0.00 0.00 0.00 4.00
2876 3128 0.108662 TAGCGTGTGATGAGCCTGTG 60.109 55.000 0.00 0.00 0.00 3.66
2877 3129 1.374631 GCGTGTGATGAGCCTGTGA 60.375 57.895 0.00 0.00 0.00 3.58
2878 3130 1.357258 GCGTGTGATGAGCCTGTGAG 61.357 60.000 0.00 0.00 0.00 3.51
2879 3131 0.738762 CGTGTGATGAGCCTGTGAGG 60.739 60.000 0.00 0.00 38.80 3.86
2925 3177 1.573829 GGCGAGTTTGAATGCGGTCA 61.574 55.000 0.00 0.00 0.00 4.02
2929 3181 2.476185 CGAGTTTGAATGCGGTCAATCC 60.476 50.000 3.01 0.00 37.36 3.01
2991 3243 6.072230 GCTTTCCTCCTCAAGATATAAATGGC 60.072 42.308 0.00 0.00 0.00 4.40
2993 3245 3.686726 CCTCCTCAAGATATAAATGGCGC 59.313 47.826 0.00 0.00 0.00 6.53
3016 3268 5.221342 GCACTGGCAGTACTAGTATTCTGAT 60.221 44.000 21.59 4.04 38.17 2.90
3042 3294 0.108804 GATCTCAAAGTGCGTCCGGA 60.109 55.000 0.00 0.00 0.00 5.14
3043 3295 0.389948 ATCTCAAAGTGCGTCCGGAC 60.390 55.000 25.28 25.28 36.69 4.79
3044 3296 1.300620 CTCAAAGTGCGTCCGGACA 60.301 57.895 32.80 13.27 38.98 4.02
3045 3297 1.284982 CTCAAAGTGCGTCCGGACAG 61.285 60.000 32.80 24.88 38.98 3.51
3046 3298 1.300620 CAAAGTGCGTCCGGACAGA 60.301 57.895 32.80 16.54 38.98 3.41
3047 3299 0.670546 CAAAGTGCGTCCGGACAGAT 60.671 55.000 32.80 13.60 38.98 2.90
3048 3300 0.670546 AAAGTGCGTCCGGACAGATG 60.671 55.000 32.80 18.15 38.98 2.90
3049 3301 3.188786 GTGCGTCCGGACAGATGC 61.189 66.667 32.80 26.53 46.86 3.91
3051 3303 4.796231 GCGTCCGGACAGATGCGT 62.796 66.667 32.80 0.00 38.90 5.24
3052 3304 2.880879 CGTCCGGACAGATGCGTG 60.881 66.667 32.80 11.27 38.12 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.031120 TGACCTGCAAACAAGAAAGGG 58.969 47.619 0.00 0.00 31.98 3.95
8 9 2.689983 AGTGACCTGCAAACAAGAAAGG 59.310 45.455 0.00 0.00 0.00 3.11
27 28 0.105408 AGGTGCGTACAACGGAAAGT 59.895 50.000 5.86 0.00 45.07 2.66
32 33 1.458064 CAAAGTAGGTGCGTACAACGG 59.542 52.381 5.86 0.00 42.82 4.44
41 42 5.459107 CGTAGATCACATACAAAGTAGGTGC 59.541 44.000 14.90 4.81 0.00 5.01
73 74 3.746940 AGCAACGGTTGGTACTATGTTT 58.253 40.909 22.73 0.00 40.04 2.83
88 89 0.881118 ATGCACCACCTTAAGCAACG 59.119 50.000 0.00 0.00 40.76 4.10
99 100 1.582610 CCCCAACACGTATGCACCAC 61.583 60.000 0.00 0.00 0.00 4.16
122 123 0.113580 GGTAAAAACCTCCCTGGCCA 59.886 55.000 4.71 4.71 40.22 5.36
125 126 2.687003 TTGGGTAAAAACCTCCCTGG 57.313 50.000 0.00 0.00 41.58 4.45
128 132 7.688328 GCCATTAATATTGGGTAAAAACCTCCC 60.688 40.741 0.00 0.00 41.41 4.30
152 156 5.182760 GGACCAATCTGAAGATCATATTGCC 59.817 44.000 11.04 6.30 38.71 4.52
157 161 4.971282 AGGTGGACCAATCTGAAGATCATA 59.029 41.667 0.00 0.00 38.89 2.15
166 170 1.276421 ACGAGAAGGTGGACCAATCTG 59.724 52.381 9.74 6.03 35.47 2.90
179 183 6.024664 CACTAAGTCTATGTCACACGAGAAG 58.975 44.000 0.00 0.00 0.00 2.85
191 195 8.126502 TCCTATGGGACAGACACTAAGTCTATG 61.127 44.444 0.00 0.00 45.53 2.23
218 222 2.031314 CGACATAATGGCAGCAGTGAAG 59.969 50.000 0.00 0.00 0.00 3.02
224 228 2.928801 ATACCGACATAATGGCAGCA 57.071 45.000 0.00 0.00 0.00 4.41
283 287 1.581954 CGGCCTCTGGATAGCTACG 59.418 63.158 0.00 0.00 0.00 3.51
292 298 4.899239 GCGACATCCGGCCTCTGG 62.899 72.222 0.00 0.00 39.04 3.86
305 311 3.120991 GCGGAACATACATATGAAGCGAC 60.121 47.826 10.38 0.00 37.15 5.19
326 332 9.787532 TTATTAACTCAAAATGTAGCATCAAGC 57.212 29.630 0.00 0.00 46.19 4.01
357 363 7.333174 TCCAAAAACATCTTTTCAACAAAGGAC 59.667 33.333 0.00 0.00 30.89 3.85
422 428 5.765182 CAGTCCCAAAATAAGTGTCTCAACT 59.235 40.000 0.00 0.00 0.00 3.16
424 430 5.070001 CCAGTCCCAAAATAAGTGTCTCAA 58.930 41.667 0.00 0.00 0.00 3.02
426 432 4.010349 CCCAGTCCCAAAATAAGTGTCTC 58.990 47.826 0.00 0.00 0.00 3.36
427 433 3.245264 CCCCAGTCCCAAAATAAGTGTCT 60.245 47.826 0.00 0.00 0.00 3.41
430 436 2.042433 TCCCCCAGTCCCAAAATAAGTG 59.958 50.000 0.00 0.00 0.00 3.16
431 437 2.042569 GTCCCCCAGTCCCAAAATAAGT 59.957 50.000 0.00 0.00 0.00 2.24
432 438 2.042433 TGTCCCCCAGTCCCAAAATAAG 59.958 50.000 0.00 0.00 0.00 1.73
435 441 0.863956 TTGTCCCCCAGTCCCAAAAT 59.136 50.000 0.00 0.00 0.00 1.82
436 442 0.637195 TTTGTCCCCCAGTCCCAAAA 59.363 50.000 0.00 0.00 0.00 2.44
437 443 0.187361 CTTTGTCCCCCAGTCCCAAA 59.813 55.000 0.00 0.00 0.00 3.28
438 444 0.996762 ACTTTGTCCCCCAGTCCCAA 60.997 55.000 0.00 0.00 0.00 4.12
439 445 0.996762 AACTTTGTCCCCCAGTCCCA 60.997 55.000 0.00 0.00 0.00 4.37
440 446 1.004394 CTAACTTTGTCCCCCAGTCCC 59.996 57.143 0.00 0.00 0.00 4.46
441 447 1.703513 ACTAACTTTGTCCCCCAGTCC 59.296 52.381 0.00 0.00 0.00 3.85
442 448 4.628963 TTACTAACTTTGTCCCCCAGTC 57.371 45.455 0.00 0.00 0.00 3.51
443 449 5.391577 TTTTACTAACTTTGTCCCCCAGT 57.608 39.130 0.00 0.00 0.00 4.00
444 450 5.831525 ACTTTTTACTAACTTTGTCCCCCAG 59.168 40.000 0.00 0.00 0.00 4.45
445 451 5.768752 ACTTTTTACTAACTTTGTCCCCCA 58.231 37.500 0.00 0.00 0.00 4.96
446 452 6.321945 TCAACTTTTTACTAACTTTGTCCCCC 59.678 38.462 0.00 0.00 0.00 5.40
447 453 7.283807 TCTCAACTTTTTACTAACTTTGTCCCC 59.716 37.037 0.00 0.00 0.00 4.81
448 454 8.127327 GTCTCAACTTTTTACTAACTTTGTCCC 58.873 37.037 0.00 0.00 0.00 4.46
449 455 8.671028 TGTCTCAACTTTTTACTAACTTTGTCC 58.329 33.333 0.00 0.00 0.00 4.02
450 456 9.486857 GTGTCTCAACTTTTTACTAACTTTGTC 57.513 33.333 0.00 0.00 0.00 3.18
451 457 9.227777 AGTGTCTCAACTTTTTACTAACTTTGT 57.772 29.630 0.00 0.00 0.00 2.83
467 473 9.535878 CCTCTATCCTAAAATAAGTGTCTCAAC 57.464 37.037 0.00 0.00 0.00 3.18
468 474 8.705594 CCCTCTATCCTAAAATAAGTGTCTCAA 58.294 37.037 0.00 0.00 0.00 3.02
469 475 8.065627 TCCCTCTATCCTAAAATAAGTGTCTCA 58.934 37.037 0.00 0.00 0.00 3.27
470 476 8.480133 TCCCTCTATCCTAAAATAAGTGTCTC 57.520 38.462 0.00 0.00 0.00 3.36
471 477 8.068733 ACTCCCTCTATCCTAAAATAAGTGTCT 58.931 37.037 0.00 0.00 0.00 3.41
472 478 8.252624 ACTCCCTCTATCCTAAAATAAGTGTC 57.747 38.462 0.00 0.00 0.00 3.67
473 479 9.900112 ATACTCCCTCTATCCTAAAATAAGTGT 57.100 33.333 0.00 0.00 0.00 3.55
478 484 9.409918 CGATCATACTCCCTCTATCCTAAAATA 57.590 37.037 0.00 0.00 0.00 1.40
479 485 8.116669 TCGATCATACTCCCTCTATCCTAAAAT 58.883 37.037 0.00 0.00 0.00 1.82
480 486 7.467650 TCGATCATACTCCCTCTATCCTAAAA 58.532 38.462 0.00 0.00 0.00 1.52
481 487 7.029053 TCGATCATACTCCCTCTATCCTAAA 57.971 40.000 0.00 0.00 0.00 1.85
482 488 6.638021 TCGATCATACTCCCTCTATCCTAA 57.362 41.667 0.00 0.00 0.00 2.69
483 489 6.638021 TTCGATCATACTCCCTCTATCCTA 57.362 41.667 0.00 0.00 0.00 2.94
484 490 5.522315 TTCGATCATACTCCCTCTATCCT 57.478 43.478 0.00 0.00 0.00 3.24
485 491 5.477291 TGTTTCGATCATACTCCCTCTATCC 59.523 44.000 0.00 0.00 0.00 2.59
486 492 6.207810 ACTGTTTCGATCATACTCCCTCTATC 59.792 42.308 0.00 0.00 0.00 2.08
487 493 6.071984 ACTGTTTCGATCATACTCCCTCTAT 58.928 40.000 0.00 0.00 0.00 1.98
488 494 5.446860 ACTGTTTCGATCATACTCCCTCTA 58.553 41.667 0.00 0.00 0.00 2.43
489 495 4.282496 ACTGTTTCGATCATACTCCCTCT 58.718 43.478 0.00 0.00 0.00 3.69
490 496 4.500035 GGACTGTTTCGATCATACTCCCTC 60.500 50.000 0.00 0.00 0.00 4.30
491 497 3.385111 GGACTGTTTCGATCATACTCCCT 59.615 47.826 0.00 0.00 0.00 4.20
492 498 3.385111 AGGACTGTTTCGATCATACTCCC 59.615 47.826 0.00 0.00 0.00 4.30
493 499 4.657436 AGGACTGTTTCGATCATACTCC 57.343 45.455 0.00 0.00 0.00 3.85
494 500 8.101654 ACTATAGGACTGTTTCGATCATACTC 57.898 38.462 4.43 0.00 0.00 2.59
495 501 7.940137 AGACTATAGGACTGTTTCGATCATACT 59.060 37.037 4.43 0.00 0.00 2.12
496 502 8.101654 AGACTATAGGACTGTTTCGATCATAC 57.898 38.462 4.43 0.00 0.00 2.39
497 503 8.568794 CAAGACTATAGGACTGTTTCGATCATA 58.431 37.037 4.43 0.00 0.00 2.15
498 504 7.285629 TCAAGACTATAGGACTGTTTCGATCAT 59.714 37.037 4.43 0.00 0.00 2.45
499 505 6.602009 TCAAGACTATAGGACTGTTTCGATCA 59.398 38.462 4.43 0.00 0.00 2.92
500 506 7.028926 TCAAGACTATAGGACTGTTTCGATC 57.971 40.000 4.43 0.00 0.00 3.69
501 507 7.429633 CATCAAGACTATAGGACTGTTTCGAT 58.570 38.462 4.43 0.58 0.00 3.59
502 508 6.183360 CCATCAAGACTATAGGACTGTTTCGA 60.183 42.308 4.43 0.00 0.00 3.71
503 509 5.980116 CCATCAAGACTATAGGACTGTTTCG 59.020 44.000 4.43 0.00 0.00 3.46
540 546 9.011095 GTAGGAGTTCATAGGCTTTTAGTTTTT 57.989 33.333 0.00 0.00 0.00 1.94
556 562 5.477607 TTGAGGAATTTCGTAGGAGTTCA 57.522 39.130 11.99 0.00 0.00 3.18
614 621 3.765511 CAGCTCTTCCCAATTTGGAATGA 59.234 43.478 17.24 9.82 43.29 2.57
665 672 5.120830 CGTGTCAGCTAGCTTCAGTTTATTT 59.879 40.000 16.46 0.00 0.00 1.40
667 674 4.177026 CGTGTCAGCTAGCTTCAGTTTAT 58.823 43.478 16.46 0.00 0.00 1.40
668 675 3.575630 CGTGTCAGCTAGCTTCAGTTTA 58.424 45.455 16.46 0.00 0.00 2.01
669 676 2.408050 CGTGTCAGCTAGCTTCAGTTT 58.592 47.619 16.46 0.00 0.00 2.66
746 760 4.379499 CGTAGAGTTGTAGAGTGTGATGCA 60.379 45.833 0.00 0.00 0.00 3.96
879 897 0.913924 GGTAATGGAGGGAAACGGGA 59.086 55.000 0.00 0.00 0.00 5.14
945 965 2.917971 CGGAGATGAACGAACTGAAGAC 59.082 50.000 0.00 0.00 0.00 3.01
960 986 3.552273 CGAACGAATGGATTACCGGAGAT 60.552 47.826 9.46 0.02 39.42 2.75
974 1001 2.377310 CCACGCGGTTCGAACGAAT 61.377 57.895 21.34 4.80 41.67 3.34
979 1006 4.238654 AACCCCACGCGGTTCGAA 62.239 61.111 12.47 0.00 42.71 3.71
988 1015 2.362375 CCCCATTGGAACCCCACG 60.362 66.667 3.62 0.00 43.41 4.94
1046 1073 4.856607 GAGAAGGCTCGTCGGCGG 62.857 72.222 10.62 0.65 44.22 6.13
1341 1374 0.396417 CCTCAGACCACTCCTCGGAT 60.396 60.000 0.00 0.00 0.00 4.18
1344 1377 2.888863 GCCTCAGACCACTCCTCG 59.111 66.667 0.00 0.00 0.00 4.63
1641 1677 0.966370 GGTACCACACGAGGAGCTCT 60.966 60.000 14.64 0.00 0.00 4.09
1824 1867 4.697756 GTGCTGGTGCTGGCGGTA 62.698 66.667 0.00 0.00 40.48 4.02
1970 2013 1.619975 TCCTCCTCCTCCTCGTCCT 60.620 63.158 0.00 0.00 0.00 3.85
1971 2014 1.152839 CTCCTCCTCCTCCTCGTCC 60.153 68.421 0.00 0.00 0.00 4.79
1972 2015 1.152839 CCTCCTCCTCCTCCTCGTC 60.153 68.421 0.00 0.00 0.00 4.20
1973 2016 1.619975 TCCTCCTCCTCCTCCTCGT 60.620 63.158 0.00 0.00 0.00 4.18
1974 2017 1.150536 CTCCTCCTCCTCCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
1975 2018 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1976 2019 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1977 2020 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1978 2021 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1979 2022 1.087725 TCCTCCTCCTCCTCCTCCT 59.912 63.158 0.00 0.00 0.00 3.69
1980 2023 1.231928 GTCCTCCTCCTCCTCCTCC 59.768 68.421 0.00 0.00 0.00 4.30
1981 2024 1.231928 GGTCCTCCTCCTCCTCCTC 59.768 68.421 0.00 0.00 0.00 3.71
1982 2025 1.230819 AGGTCCTCCTCCTCCTCCT 60.231 63.158 0.00 0.00 40.58 3.69
1983 2026 3.446050 AGGTCCTCCTCCTCCTCC 58.554 66.667 0.00 0.00 40.58 4.30
2055 2119 5.523438 TTTTGCCAGTTAACTAACCAAGG 57.477 39.130 8.04 5.43 36.88 3.61
2070 2134 4.438065 CGAATAACCGATGACATTTTGCCA 60.438 41.667 0.00 0.00 0.00 4.92
2112 2187 1.312371 GCTAATCAAACAGGGCCGCA 61.312 55.000 0.00 0.00 0.00 5.69
2257 2347 5.175673 TGATCGTGCTATCATCGACATTTTC 59.824 40.000 0.00 0.00 36.46 2.29
2265 2355 3.101546 CCGTATGATCGTGCTATCATCG 58.898 50.000 11.43 13.20 43.81 3.84
2273 2363 5.217393 TGTAAATACTCCGTATGATCGTGC 58.783 41.667 0.00 0.00 0.00 5.34
2328 2420 1.411246 CCACAATGCATTGGATCCCTG 59.589 52.381 35.85 25.06 41.96 4.45
2329 2421 1.288633 TCCACAATGCATTGGATCCCT 59.711 47.619 35.85 16.62 41.96 4.20
2344 2443 2.445427 CCTACAATGCATGGTTCCACA 58.555 47.619 13.06 0.00 0.00 4.17
2347 2446 1.767759 AGCCTACAATGCATGGTTCC 58.232 50.000 13.06 1.27 0.00 3.62
2349 2448 3.019564 GAGAAGCCTACAATGCATGGTT 58.980 45.455 13.06 5.00 0.00 3.67
2350 2449 2.648059 GAGAAGCCTACAATGCATGGT 58.352 47.619 12.36 12.36 0.00 3.55
2351 2450 1.952296 GGAGAAGCCTACAATGCATGG 59.048 52.381 0.00 0.00 0.00 3.66
2352 2451 2.646930 TGGAGAAGCCTACAATGCATG 58.353 47.619 0.00 0.00 37.63 4.06
2354 2453 2.819608 GTTTGGAGAAGCCTACAATGCA 59.180 45.455 0.00 0.00 42.49 3.96
2355 2454 2.819608 TGTTTGGAGAAGCCTACAATGC 59.180 45.455 0.00 0.00 42.49 3.56
2356 2455 3.441572 CCTGTTTGGAGAAGCCTACAATG 59.558 47.826 0.00 0.00 42.49 2.82
2371 2470 4.336889 TCAGTGGAAGTACTCCTGTTTG 57.663 45.455 0.00 0.00 45.64 2.93
2422 2644 5.561532 CGCAGTAATTGATGGATGGATGAAC 60.562 44.000 0.00 0.00 0.00 3.18
2660 2891 4.034975 CACGTAGTAGGAGTAGTGGTTAGC 59.965 50.000 0.00 0.00 41.61 3.09
2669 2900 3.943381 CACATCACCACGTAGTAGGAGTA 59.057 47.826 0.00 0.00 41.61 2.59
2673 2904 4.386867 AATCACATCACCACGTAGTAGG 57.613 45.455 0.00 0.00 41.61 3.18
2708 2945 5.289675 CACAGAGAACAGCGAAATTAGGTAG 59.710 44.000 0.00 0.00 0.00 3.18
2843 3087 1.359117 CGCTACCACCACGATCGAT 59.641 57.895 24.34 0.00 0.00 3.59
2871 3123 0.612229 ATCAGTCACAGCCTCACAGG 59.388 55.000 0.00 0.00 38.80 4.00
2872 3124 1.735038 CGATCAGTCACAGCCTCACAG 60.735 57.143 0.00 0.00 0.00 3.66
2873 3125 0.244721 CGATCAGTCACAGCCTCACA 59.755 55.000 0.00 0.00 0.00 3.58
2874 3126 1.080995 GCGATCAGTCACAGCCTCAC 61.081 60.000 0.00 0.00 0.00 3.51
2875 3127 1.216444 GCGATCAGTCACAGCCTCA 59.784 57.895 0.00 0.00 0.00 3.86
2876 3128 1.080995 GTGCGATCAGTCACAGCCTC 61.081 60.000 0.00 0.00 33.63 4.70
2877 3129 1.079543 GTGCGATCAGTCACAGCCT 60.080 57.895 0.00 0.00 33.63 4.58
2878 3130 1.079543 AGTGCGATCAGTCACAGCC 60.080 57.895 10.95 0.00 35.76 4.85
2879 3131 1.357258 CCAGTGCGATCAGTCACAGC 61.357 60.000 10.95 0.00 35.76 4.40
2880 3132 0.738762 CCCAGTGCGATCAGTCACAG 60.739 60.000 10.95 4.55 35.76 3.66
2881 3133 1.293179 CCCAGTGCGATCAGTCACA 59.707 57.895 10.95 0.00 35.76 3.58
2882 3134 2.103042 GCCCAGTGCGATCAGTCAC 61.103 63.158 0.00 0.00 0.00 3.67
2883 3135 2.265739 GCCCAGTGCGATCAGTCA 59.734 61.111 0.00 0.00 0.00 3.41
2991 3243 3.066900 AGAATACTAGTACTGCCAGTGCG 59.933 47.826 7.83 0.00 41.78 5.34
2993 3245 5.836821 TCAGAATACTAGTACTGCCAGTG 57.163 43.478 7.83 0.00 0.00 3.66
3016 3268 1.338105 CGCACTTTGAGATCCTGACCA 60.338 52.381 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.