Multiple sequence alignment - TraesCS2D01G098400

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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 TraesCS2D01G098400 chr2D 100.000 2702 0 0 1 2702 50472225 50474926 0.000000e+00 4990.0
1 TraesCS2D01G098400 chr2D 94.275 524 19 5 2188 2702 451454935 451454414 0.000000e+00 791.0
2 TraesCS2D01G098400 chr2B 87.193 1710 96 46 530 2157 78829702 78831370 0.000000e+00 1831.0
3 TraesCS2D01G098400 chr2B 94.000 350 18 2 56 405 78829289 78829635 6.630000e-146 527.0
4 TraesCS2D01G098400 chr2A 84.997 1713 129 65 542 2175 52132175 52133838 0.000000e+00 1622.0
5 TraesCS2D01G098400 chr2A 90.850 306 18 3 23 323 52131632 52131932 4.190000e-108 401.0
6 TraesCS2D01G098400 chr3D 94.798 519 19 3 2188 2702 6348127 6347613 0.000000e+00 802.0
7 TraesCS2D01G098400 chr4A 89.595 519 21 15 2188 2700 259777837 259777346 1.770000e-176 628.0
8 TraesCS2D01G098400 chr4A 85.897 78 7 4 1503 1578 727804135 727804060 2.230000e-11 80.5
9 TraesCS2D01G098400 chr4A 84.615 78 8 3 1503 1578 727745955 727745880 1.040000e-09 75.0
10 TraesCS2D01G098400 chr4A 83.333 78 9 3 1503 1578 727841788 727841713 4.830000e-08 69.4
11 TraesCS2D01G098400 chr3A 85.824 522 57 13 2188 2702 712658061 712657550 3.060000e-149 538.0
12 TraesCS2D01G098400 chr5A 85.448 536 51 12 2188 2702 631411177 631411706 1.420000e-147 532.0
13 TraesCS2D01G098400 chr5A 91.111 45 4 0 478 522 472108941 472108897 8.080000e-06 62.1
14 TraesCS2D01G098400 chr3B 84.328 536 63 12 2176 2702 769337484 769336961 3.100000e-139 505.0
15 TraesCS2D01G098400 chr3B 90.909 66 5 1 1207 1272 738655572 738655636 1.330000e-13 87.9
16 TraesCS2D01G098400 chr1D 90.024 411 11 15 2304 2702 62337103 62336711 3.100000e-139 505.0
17 TraesCS2D01G098400 chr1D 90.909 44 4 0 478 521 409914490 409914447 2.910000e-05 60.2
18 TraesCS2D01G098400 chr7D 84.659 528 43 15 2188 2702 511659622 511660124 2.420000e-135 492.0
19 TraesCS2D01G098400 chr7D 91.111 45 3 1 478 522 576301042 576300999 2.910000e-05 60.2
20 TraesCS2D01G098400 chr4D 87.912 273 26 4 2349 2620 499878886 499879152 5.620000e-82 315.0
21 TraesCS2D01G098400 chr4D 89.796 49 5 0 478 526 401774656 401774608 2.250000e-06 63.9
22 TraesCS2D01G098400 chr4D 92.683 41 3 0 481 521 419214240 419214280 2.910000e-05 60.2
23 TraesCS2D01G098400 chr1B 92.063 63 5 0 1210 1272 538196074 538196136 3.710000e-14 89.8
24 TraesCS2D01G098400 chr7A 85.714 77 9 2 1503 1578 10017427 10017502 2.230000e-11 80.5
25 TraesCS2D01G098400 chrUn 93.023 43 3 0 486 528 28822839 28822881 2.250000e-06 63.9
26 TraesCS2D01G098400 chrUn 100.000 31 0 0 482 512 88638533 88638563 1.040000e-04 58.4
27 TraesCS2D01G098400 chr5D 91.304 46 3 1 481 525 423269345 423269390 8.080000e-06 62.1
28 TraesCS2D01G098400 chr6D 92.500 40 3 0 482 521 345764567 345764606 1.040000e-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 TraesCS2D01G098400 chr2D 50472225 50474926 2701 False 4990.0 4990 100.0000 1 2702 1 chr2D.!!$F1 2701
1 TraesCS2D01G098400 chr2D 451454414 451454935 521 True 791.0 791 94.2750 2188 2702 1 chr2D.!!$R1 514
2 TraesCS2D01G098400 chr2B 78829289 78831370 2081 False 1179.0 1831 90.5965 56 2157 2 chr2B.!!$F1 2101
3 TraesCS2D01G098400 chr2A 52131632 52133838 2206 False 1011.5 1622 87.9235 23 2175 2 chr2A.!!$F1 2152
4 TraesCS2D01G098400 chr3D 6347613 6348127 514 True 802.0 802 94.7980 2188 2702 1 chr3D.!!$R1 514
5 TraesCS2D01G098400 chr3A 712657550 712658061 511 True 538.0 538 85.8240 2188 2702 1 chr3A.!!$R1 514
6 TraesCS2D01G098400 chr5A 631411177 631411706 529 False 532.0 532 85.4480 2188 2702 1 chr5A.!!$F1 514
7 TraesCS2D01G098400 chr3B 769336961 769337484 523 True 505.0 505 84.3280 2176 2702 1 chr3B.!!$R1 526
8 TraesCS2D01G098400 chr7D 511659622 511660124 502 False 492.0 492 84.6590 2188 2702 1 chr7D.!!$F1 514

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
907 1066 0.179145 CGGGACACTTGCGTAGTAGG 60.179 60.0 0.0 0.0 34.56 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 2485 0.612732 AACACCCCAGATACGACCGA 60.613 55.0 0.0 0.0 0.0 4.69 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
26 27 3.616219 AGCGTTTTTATACCTGCATGGA 58.384 40.909 8.91 0.00 39.71 3.41
37 38 8.844865 TTATACCTGCATGGACAGATATAGAT 57.155 34.615 8.91 0.00 40.25 1.98
38 39 5.417754 ACCTGCATGGACAGATATAGATG 57.582 43.478 8.91 0.00 40.25 2.90
77 78 3.317993 GGCCGTGTTCATATGCCTTTATT 59.682 43.478 0.00 0.00 39.05 1.40
109 110 2.313051 TTTCGAACCCGTGCAGGACA 62.313 55.000 8.24 0.00 45.00 4.02
182 188 5.277601 TGCTGTATCTTTTGTAAAGCGAC 57.722 39.130 0.00 0.00 31.86 5.19
185 191 2.894307 ATCTTTTGTAAAGCGACGCC 57.106 45.000 17.79 0.92 0.00 5.68
236 242 5.644644 GCGCCTACTTAAGTTTCTGTACTA 58.355 41.667 14.49 0.00 0.00 1.82
237 243 6.271566 GCGCCTACTTAAGTTTCTGTACTAT 58.728 40.000 14.49 0.00 0.00 2.12
238 244 6.198591 GCGCCTACTTAAGTTTCTGTACTATG 59.801 42.308 14.49 0.00 0.00 2.23
274 280 0.729116 GCGATGACACTGTGAATGGG 59.271 55.000 15.86 1.96 0.00 4.00
301 307 5.462068 GTCCCTTTCTTTGGTTTTCGATTTG 59.538 40.000 0.00 0.00 0.00 2.32
323 329 1.933181 TCTTGTTCACTTGTCGCTGTG 59.067 47.619 0.00 0.00 35.68 3.66
405 411 2.791655 AGTACATCTGTCACCGACTGA 58.208 47.619 6.23 6.23 42.75 3.41
408 414 3.238108 ACATCTGTCACCGACTGAATC 57.762 47.619 7.63 0.00 42.10 2.52
411 420 3.961480 TCTGTCACCGACTGAATCAAT 57.039 42.857 1.72 0.00 37.52 2.57
412 421 3.588955 TCTGTCACCGACTGAATCAATG 58.411 45.455 1.72 0.00 37.52 2.82
413 422 3.006859 TCTGTCACCGACTGAATCAATGT 59.993 43.478 1.72 0.00 37.52 2.71
414 423 3.738982 TGTCACCGACTGAATCAATGTT 58.261 40.909 0.00 0.00 33.15 2.71
415 424 4.888917 TGTCACCGACTGAATCAATGTTA 58.111 39.130 0.00 0.00 33.15 2.41
416 425 5.487433 TGTCACCGACTGAATCAATGTTAT 58.513 37.500 0.00 0.00 33.15 1.89
417 426 5.937540 TGTCACCGACTGAATCAATGTTATT 59.062 36.000 0.00 0.00 33.15 1.40
418 427 6.429692 TGTCACCGACTGAATCAATGTTATTT 59.570 34.615 0.00 0.00 33.15 1.40
419 428 7.040755 TGTCACCGACTGAATCAATGTTATTTT 60.041 33.333 0.00 0.00 33.15 1.82
420 429 8.447833 GTCACCGACTGAATCAATGTTATTTTA 58.552 33.333 0.00 0.00 0.00 1.52
421 430 8.664798 TCACCGACTGAATCAATGTTATTTTAG 58.335 33.333 0.00 0.00 0.00 1.85
422 431 8.664798 CACCGACTGAATCAATGTTATTTTAGA 58.335 33.333 0.00 0.00 0.00 2.10
423 432 9.396022 ACCGACTGAATCAATGTTATTTTAGAT 57.604 29.630 0.00 0.00 0.00 1.98
424 433 9.869844 CCGACTGAATCAATGTTATTTTAGATC 57.130 33.333 0.00 0.00 0.00 2.75
470 479 9.710818 TTAGTTTCTACAATATGTACTCCCTCT 57.289 33.333 0.00 0.00 0.00 3.69
472 481 9.884814 AGTTTCTACAATATGTACTCCCTCTAT 57.115 33.333 0.00 0.00 0.00 1.98
474 483 8.880991 TTCTACAATATGTACTCCCTCTATCC 57.119 38.462 0.00 0.00 0.00 2.59
475 484 7.411808 TCTACAATATGTACTCCCTCTATCCC 58.588 42.308 0.00 0.00 0.00 3.85
476 485 5.977533 ACAATATGTACTCCCTCTATCCCA 58.022 41.667 0.00 0.00 0.00 4.37
477 486 6.575411 ACAATATGTACTCCCTCTATCCCAT 58.425 40.000 0.00 0.00 0.00 4.00
478 487 6.441924 ACAATATGTACTCCCTCTATCCCATG 59.558 42.308 0.00 0.00 0.00 3.66
479 488 3.993658 TGTACTCCCTCTATCCCATGT 57.006 47.619 0.00 0.00 0.00 3.21
480 489 3.845860 TGTACTCCCTCTATCCCATGTC 58.154 50.000 0.00 0.00 0.00 3.06
481 490 3.206639 TGTACTCCCTCTATCCCATGTCA 59.793 47.826 0.00 0.00 0.00 3.58
482 491 2.969628 ACTCCCTCTATCCCATGTCAG 58.030 52.381 0.00 0.00 0.00 3.51
483 492 1.622811 CTCCCTCTATCCCATGTCAGC 59.377 57.143 0.00 0.00 0.00 4.26
484 493 1.221523 TCCCTCTATCCCATGTCAGCT 59.778 52.381 0.00 0.00 0.00 4.24
485 494 2.053244 CCCTCTATCCCATGTCAGCTT 58.947 52.381 0.00 0.00 0.00 3.74
486 495 2.224475 CCCTCTATCCCATGTCAGCTTG 60.224 54.545 0.00 0.00 0.00 4.01
487 496 2.702478 CCTCTATCCCATGTCAGCTTGA 59.298 50.000 0.00 0.00 0.00 3.02
488 497 3.135348 CCTCTATCCCATGTCAGCTTGAA 59.865 47.826 0.00 0.00 0.00 2.69
489 498 4.384537 CCTCTATCCCATGTCAGCTTGAAA 60.385 45.833 0.00 0.00 0.00 2.69
490 499 5.178096 TCTATCCCATGTCAGCTTGAAAA 57.822 39.130 0.00 0.00 0.00 2.29
491 500 5.569355 TCTATCCCATGTCAGCTTGAAAAA 58.431 37.500 0.00 0.00 0.00 1.94
492 501 4.525912 ATCCCATGTCAGCTTGAAAAAC 57.474 40.909 0.00 0.00 0.00 2.43
493 502 2.293122 TCCCATGTCAGCTTGAAAAACG 59.707 45.455 0.00 0.00 0.00 3.60
494 503 2.034558 CCCATGTCAGCTTGAAAAACGT 59.965 45.455 0.00 0.00 0.00 3.99
495 504 3.490761 CCCATGTCAGCTTGAAAAACGTT 60.491 43.478 0.00 0.00 0.00 3.99
496 505 3.730715 CCATGTCAGCTTGAAAAACGTTC 59.269 43.478 0.00 0.00 0.00 3.95
497 506 4.498009 CCATGTCAGCTTGAAAAACGTTCT 60.498 41.667 0.00 0.00 0.00 3.01
498 507 4.695217 TGTCAGCTTGAAAAACGTTCTT 57.305 36.364 0.00 0.00 0.00 2.52
499 508 5.804692 TGTCAGCTTGAAAAACGTTCTTA 57.195 34.783 0.00 0.00 0.00 2.10
500 509 6.371809 TGTCAGCTTGAAAAACGTTCTTAT 57.628 33.333 0.00 0.00 0.00 1.73
501 510 7.485418 TGTCAGCTTGAAAAACGTTCTTATA 57.515 32.000 0.00 0.00 0.00 0.98
502 511 8.094798 TGTCAGCTTGAAAAACGTTCTTATAT 57.905 30.769 0.00 0.00 0.00 0.86
503 512 8.564574 TGTCAGCTTGAAAAACGTTCTTATATT 58.435 29.630 0.00 0.00 0.00 1.28
512 521 9.845305 GAAAAACGTTCTTATATTATGAGACGG 57.155 33.333 0.00 8.31 0.00 4.79
513 522 7.404139 AAACGTTCTTATATTATGAGACGGC 57.596 36.000 0.00 0.00 0.00 5.68
514 523 6.328641 ACGTTCTTATATTATGAGACGGCT 57.671 37.500 0.00 0.00 0.00 5.52
515 524 6.150318 ACGTTCTTATATTATGAGACGGCTG 58.850 40.000 0.00 0.00 0.00 4.85
516 525 5.573282 CGTTCTTATATTATGAGACGGCTGG 59.427 44.000 0.00 0.00 0.00 4.85
517 526 6.569801 CGTTCTTATATTATGAGACGGCTGGA 60.570 42.308 0.00 0.00 0.00 3.86
563 586 7.946776 CCTATCATCCCTTATTCTTGGTCAATT 59.053 37.037 0.00 0.00 0.00 2.32
601 624 4.101898 TGGTTACTGTACACATGGACTTGT 59.898 41.667 0.00 0.00 0.00 3.16
619 761 4.035208 ACTTGTCTGGCTGTAAACTTTTCG 59.965 41.667 0.00 0.00 0.00 3.46
696 842 3.689347 TGCTTGGACTGCATTTACATCT 58.311 40.909 0.00 0.00 35.31 2.90
700 846 3.419943 TGGACTGCATTTACATCTTGCA 58.580 40.909 0.00 0.00 43.63 4.08
778 924 6.841443 CAGCTTCACTGTTCTGGATAATAG 57.159 41.667 0.00 0.00 41.86 1.73
779 925 6.344500 CAGCTTCACTGTTCTGGATAATAGT 58.656 40.000 0.00 0.00 41.86 2.12
821 980 6.434028 CCATCACCACAAGGAAAAGATCTAAA 59.566 38.462 0.00 0.00 38.69 1.85
822 981 7.039784 CCATCACCACAAGGAAAAGATCTAAAA 60.040 37.037 0.00 0.00 38.69 1.52
823 982 7.889873 TCACCACAAGGAAAAGATCTAAAAA 57.110 32.000 0.00 0.00 38.69 1.94
848 1007 2.024414 GACAGGTGGTTCTGCAGTTTT 58.976 47.619 14.67 0.00 38.26 2.43
873 1032 6.544928 AAAGGAAAAATGGTCTTGTGAACT 57.455 33.333 0.00 0.00 0.00 3.01
874 1033 7.654022 AAAGGAAAAATGGTCTTGTGAACTA 57.346 32.000 0.00 0.00 0.00 2.24
877 1036 7.514721 AGGAAAAATGGTCTTGTGAACTAGTA 58.485 34.615 0.00 0.00 0.00 1.82
882 1041 2.093606 GGTCTTGTGAACTAGTAGGGGC 60.094 54.545 0.00 0.00 0.00 5.80
883 1042 2.093606 GTCTTGTGAACTAGTAGGGGCC 60.094 54.545 0.00 0.00 0.00 5.80
884 1043 0.899720 TTGTGAACTAGTAGGGGCCG 59.100 55.000 0.00 0.00 0.00 6.13
885 1044 0.974010 TGTGAACTAGTAGGGGCCGG 60.974 60.000 0.00 0.00 0.00 6.13
886 1045 1.382146 TGAACTAGTAGGGGCCGGG 60.382 63.158 2.18 0.00 0.00 5.73
904 1063 2.654877 CCGGGACACTTGCGTAGT 59.345 61.111 0.00 0.00 37.68 2.73
907 1066 0.179145 CGGGACACTTGCGTAGTAGG 60.179 60.000 0.00 0.00 34.56 3.18
923 1082 5.515626 CGTAGTAGGAGTAGTTGCATTGAAC 59.484 44.000 0.00 0.00 0.00 3.18
925 1084 2.699954 AGGAGTAGTTGCATTGAACCG 58.300 47.619 0.00 0.00 0.00 4.44
1026 1185 3.512516 GCCCGGAGTGAATGCTGC 61.513 66.667 0.73 0.00 0.00 5.25
1040 1199 3.036084 CTGCCGTCGTGTCACACC 61.036 66.667 1.24 0.00 0.00 4.16
1041 1200 4.934942 TGCCGTCGTGTCACACCG 62.935 66.667 1.24 0.53 0.00 4.94
1042 1201 4.634133 GCCGTCGTGTCACACCGA 62.634 66.667 8.03 3.58 0.00 4.69
1043 1202 2.257371 CCGTCGTGTCACACCGAT 59.743 61.111 8.03 0.00 0.00 4.18
1044 1203 1.800315 CCGTCGTGTCACACCGATC 60.800 63.158 8.03 1.82 0.00 3.69
1045 1204 2.144069 CGTCGTGTCACACCGATCG 61.144 63.158 8.51 8.51 0.00 3.69
1046 1205 2.126618 TCGTGTCACACCGATCGC 60.127 61.111 10.32 0.00 0.00 4.58
1047 1206 3.179265 CGTGTCACACCGATCGCC 61.179 66.667 10.32 0.00 0.00 5.54
1074 1233 1.739929 AAATCGACGCGCCATGTCA 60.740 52.632 5.73 2.66 36.11 3.58
1108 1291 1.633561 CACCTGCATATATCGCGAGG 58.366 55.000 16.66 10.24 35.26 4.63
1111 1294 1.404717 CCTGCATATATCGCGAGGCTT 60.405 52.381 16.66 0.00 0.00 4.35
1202 1397 1.136110 GCCGAGAAGGGAAGAGAAGAG 59.864 57.143 0.00 0.00 41.48 2.85
1205 1400 1.136110 GAGAAGGGAAGAGAAGAGCGG 59.864 57.143 0.00 0.00 0.00 5.52
1263 1458 4.394712 GTGCTCCCTCCCGTGGTG 62.395 72.222 0.00 0.00 0.00 4.17
1272 1467 4.954970 CCCGTGGTGGTGCTGCTT 62.955 66.667 0.00 0.00 35.15 3.91
1276 1471 1.526917 GTGGTGGTGCTGCTTGTCT 60.527 57.895 0.00 0.00 0.00 3.41
1278 1473 1.968540 GGTGGTGCTGCTTGTCTCC 60.969 63.158 0.00 0.00 0.00 3.71
1726 1938 4.033776 CCCGTGACCCATGCCAGT 62.034 66.667 0.00 0.00 0.00 4.00
1727 1939 2.747460 CCGTGACCCATGCCAGTG 60.747 66.667 0.00 0.00 0.00 3.66
1729 1941 3.064324 GTGACCCATGCCAGTGCC 61.064 66.667 0.00 0.00 36.33 5.01
1736 1956 3.329889 ATGCCAGTGCCCGAGGAA 61.330 61.111 0.00 0.00 36.33 3.36
1749 1969 0.247974 CGAGGAACTGTACGGCGTAG 60.248 60.000 21.64 14.40 41.55 3.51
1832 2069 6.016443 TCCCGACGGTTTTGTATATTGTTTTT 60.016 34.615 13.94 0.00 0.00 1.94
1833 2070 7.173907 TCCCGACGGTTTTGTATATTGTTTTTA 59.826 33.333 13.94 0.00 0.00 1.52
1860 2105 1.409427 AGATCGTCCGTTCATTCCTCC 59.591 52.381 1.17 0.00 0.00 4.30
1862 2107 1.263356 TCGTCCGTTCATTCCTCCTT 58.737 50.000 0.00 0.00 0.00 3.36
1864 2109 2.038033 TCGTCCGTTCATTCCTCCTTTT 59.962 45.455 0.00 0.00 0.00 2.27
1869 2114 5.704053 GTCCGTTCATTCCTCCTTTTCTTTA 59.296 40.000 0.00 0.00 0.00 1.85
1874 2119 7.755373 CGTTCATTCCTCCTTTTCTTTATTTCC 59.245 37.037 0.00 0.00 0.00 3.13
1882 2127 8.210946 CCTCCTTTTCTTTATTTCCTTTTTGGT 58.789 33.333 0.00 0.00 37.07 3.67
1914 2166 3.749064 GCACGAGAGAGCGGTGGA 61.749 66.667 0.00 0.00 38.08 4.02
1955 2207 4.679654 GGTTTTCTCGCAGTTTGTTAATGG 59.320 41.667 0.00 0.00 0.00 3.16
1956 2208 3.552604 TTCTCGCAGTTTGTTAATGGC 57.447 42.857 0.00 0.00 0.00 4.40
1957 2209 1.463056 TCTCGCAGTTTGTTAATGGCG 59.537 47.619 0.00 0.00 45.24 5.69
1958 2210 0.109964 TCGCAGTTTGTTAATGGCGC 60.110 50.000 0.00 0.00 43.72 6.53
1959 2211 1.395068 CGCAGTTTGTTAATGGCGCG 61.395 55.000 0.00 0.00 37.96 6.86
1960 2212 0.386731 GCAGTTTGTTAATGGCGCGT 60.387 50.000 8.43 0.00 0.00 6.01
1961 2213 1.326576 CAGTTTGTTAATGGCGCGTG 58.673 50.000 8.43 0.00 0.00 5.34
1962 2214 0.386731 AGTTTGTTAATGGCGCGTGC 60.387 50.000 13.78 13.78 41.71 5.34
2104 2382 2.696566 TCGCTCACGAGATCTCTCC 58.303 57.895 20.26 3.54 45.12 3.71
2107 2385 0.028770 GCTCACGAGATCTCTCCGTG 59.971 60.000 22.70 22.70 42.80 4.94
2185 2463 4.346129 GCTTTATTTTCTGGCGACTGATG 58.654 43.478 0.00 0.00 38.17 3.07
2186 2464 4.731773 GCTTTATTTTCTGGCGACTGATGG 60.732 45.833 0.00 0.00 38.17 3.51
2214 2492 3.595758 AACGGTTCGGTCGGTCGT 61.596 61.111 0.00 0.00 35.48 4.34
2223 2501 1.755783 GGTCGGTCGTATCTGGGGT 60.756 63.158 0.00 0.00 0.00 4.95
2358 2643 2.888464 AAGCATCAGCAGCTCGCCAT 62.888 55.000 0.00 0.00 42.53 4.40
2564 2869 1.130561 GGACGCTGGTTGTAGCATTTC 59.869 52.381 0.00 0.00 43.87 2.17
2672 3004 8.765488 TCCAGCAAAAATATCATAAATGAGGA 57.235 30.769 0.00 0.00 40.64 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.315482 TCCATGCAGGTATAAAAACGCTATATA 58.685 33.333 0.00 0.00 39.02 0.86
1 2 7.119262 GTCCATGCAGGTATAAAAACGCTATAT 59.881 37.037 0.00 0.00 39.02 0.86
2 3 6.425721 GTCCATGCAGGTATAAAAACGCTATA 59.574 38.462 0.00 0.00 39.02 1.31
3 4 5.238650 GTCCATGCAGGTATAAAAACGCTAT 59.761 40.000 0.00 0.00 39.02 2.97
4 5 4.573201 GTCCATGCAGGTATAAAAACGCTA 59.427 41.667 0.00 0.00 39.02 4.26
5 6 3.377172 GTCCATGCAGGTATAAAAACGCT 59.623 43.478 0.00 0.00 39.02 5.07
6 7 3.127895 TGTCCATGCAGGTATAAAAACGC 59.872 43.478 0.00 0.00 39.02 4.84
7 8 4.634004 TCTGTCCATGCAGGTATAAAAACG 59.366 41.667 0.00 0.00 39.02 3.60
8 9 6.699575 ATCTGTCCATGCAGGTATAAAAAC 57.300 37.500 0.00 0.00 39.02 2.43
9 10 9.725019 CTATATCTGTCCATGCAGGTATAAAAA 57.275 33.333 11.95 0.00 41.66 1.94
10 11 9.100197 TCTATATCTGTCCATGCAGGTATAAAA 57.900 33.333 11.95 4.33 41.66 1.52
11 12 8.664669 TCTATATCTGTCCATGCAGGTATAAA 57.335 34.615 11.95 0.81 41.66 1.40
12 13 8.699130 CATCTATATCTGTCCATGCAGGTATAA 58.301 37.037 11.95 6.47 41.66 0.98
13 14 7.841222 ACATCTATATCTGTCCATGCAGGTATA 59.159 37.037 10.91 10.91 40.04 1.47
14 15 6.671340 ACATCTATATCTGTCCATGCAGGTAT 59.329 38.462 10.01 10.01 43.13 2.73
15 16 6.019108 ACATCTATATCTGTCCATGCAGGTA 58.981 40.000 0.00 0.00 36.62 3.08
16 17 4.842948 ACATCTATATCTGTCCATGCAGGT 59.157 41.667 0.00 0.00 39.02 4.00
17 18 5.176592 CACATCTATATCTGTCCATGCAGG 58.823 45.833 0.00 0.00 37.12 4.85
18 19 5.176592 CCACATCTATATCTGTCCATGCAG 58.823 45.833 0.00 0.00 37.81 4.41
19 20 4.564199 GCCACATCTATATCTGTCCATGCA 60.564 45.833 0.00 0.00 0.00 3.96
20 21 3.937706 GCCACATCTATATCTGTCCATGC 59.062 47.826 0.00 0.00 0.00 4.06
21 22 4.224594 AGGCCACATCTATATCTGTCCATG 59.775 45.833 5.01 0.00 0.00 3.66
26 27 2.028658 CGCAGGCCACATCTATATCTGT 60.029 50.000 5.01 0.00 0.00 3.41
139 140 4.436718 GCAAACTTCGGTTGCAAAACAAAT 60.437 37.500 11.40 0.00 40.82 2.32
182 188 1.968017 ACAGGTTGTGATGCAGGCG 60.968 57.895 0.00 0.00 0.00 5.52
236 242 2.876550 CGCCACATCACAGATTCATCAT 59.123 45.455 0.00 0.00 0.00 2.45
237 243 2.093553 TCGCCACATCACAGATTCATCA 60.094 45.455 0.00 0.00 0.00 3.07
238 244 2.554142 TCGCCACATCACAGATTCATC 58.446 47.619 0.00 0.00 0.00 2.92
274 280 3.547413 CGAAAACCAAAGAAAGGGACGAC 60.547 47.826 0.00 0.00 0.00 4.34
288 294 5.802956 GTGAACAAGAACAAATCGAAAACCA 59.197 36.000 0.00 0.00 0.00 3.67
301 307 2.351726 ACAGCGACAAGTGAACAAGAAC 59.648 45.455 0.00 0.00 0.00 3.01
414 423 9.747898 TGCTACCAAAGGAAAAGATCTAAAATA 57.252 29.630 0.00 0.00 0.00 1.40
415 424 8.650143 TGCTACCAAAGGAAAAGATCTAAAAT 57.350 30.769 0.00 0.00 0.00 1.82
416 425 7.724061 ACTGCTACCAAAGGAAAAGATCTAAAA 59.276 33.333 0.00 0.00 0.00 1.52
417 426 7.231467 ACTGCTACCAAAGGAAAAGATCTAAA 58.769 34.615 0.00 0.00 0.00 1.85
418 427 6.779860 ACTGCTACCAAAGGAAAAGATCTAA 58.220 36.000 0.00 0.00 0.00 2.10
419 428 6.374417 ACTGCTACCAAAGGAAAAGATCTA 57.626 37.500 0.00 0.00 0.00 1.98
420 429 5.248380 ACTGCTACCAAAGGAAAAGATCT 57.752 39.130 0.00 0.00 0.00 2.75
421 430 5.966742 AACTGCTACCAAAGGAAAAGATC 57.033 39.130 0.00 0.00 0.00 2.75
422 431 6.731292 AAAACTGCTACCAAAGGAAAAGAT 57.269 33.333 0.00 0.00 0.00 2.40
423 432 6.831868 ACTAAAACTGCTACCAAAGGAAAAGA 59.168 34.615 0.00 0.00 0.00 2.52
424 433 7.039313 ACTAAAACTGCTACCAAAGGAAAAG 57.961 36.000 0.00 0.00 0.00 2.27
425 434 7.412853 AACTAAAACTGCTACCAAAGGAAAA 57.587 32.000 0.00 0.00 0.00 2.29
426 435 7.340999 AGAAACTAAAACTGCTACCAAAGGAAA 59.659 33.333 0.00 0.00 0.00 3.13
427 436 6.831868 AGAAACTAAAACTGCTACCAAAGGAA 59.168 34.615 0.00 0.00 0.00 3.36
428 437 6.362248 AGAAACTAAAACTGCTACCAAAGGA 58.638 36.000 0.00 0.00 0.00 3.36
429 438 6.635030 AGAAACTAAAACTGCTACCAAAGG 57.365 37.500 0.00 0.00 0.00 3.11
463 472 1.622811 GCTGACATGGGATAGAGGGAG 59.377 57.143 0.00 0.00 0.00 4.30
464 473 1.221523 AGCTGACATGGGATAGAGGGA 59.778 52.381 0.00 0.00 0.00 4.20
465 474 1.727062 AGCTGACATGGGATAGAGGG 58.273 55.000 0.00 0.00 0.00 4.30
466 475 2.702478 TCAAGCTGACATGGGATAGAGG 59.298 50.000 0.00 0.00 0.00 3.69
467 476 4.412796 TTCAAGCTGACATGGGATAGAG 57.587 45.455 0.00 0.00 0.00 2.43
468 477 4.842531 TTTCAAGCTGACATGGGATAGA 57.157 40.909 0.00 0.00 0.00 1.98
469 478 5.644644 GTTTTTCAAGCTGACATGGGATAG 58.355 41.667 0.00 0.00 0.00 2.08
470 479 4.155826 CGTTTTTCAAGCTGACATGGGATA 59.844 41.667 0.00 0.00 0.00 2.59
471 480 3.057315 CGTTTTTCAAGCTGACATGGGAT 60.057 43.478 0.00 0.00 0.00 3.85
472 481 2.293122 CGTTTTTCAAGCTGACATGGGA 59.707 45.455 0.00 0.00 0.00 4.37
473 482 2.034558 ACGTTTTTCAAGCTGACATGGG 59.965 45.455 0.00 0.00 0.00 4.00
474 483 3.354089 ACGTTTTTCAAGCTGACATGG 57.646 42.857 0.00 0.00 0.00 3.66
475 484 4.601019 AGAACGTTTTTCAAGCTGACATG 58.399 39.130 0.46 0.00 0.00 3.21
476 485 4.900635 AGAACGTTTTTCAAGCTGACAT 57.099 36.364 0.46 0.00 0.00 3.06
477 486 4.695217 AAGAACGTTTTTCAAGCTGACA 57.305 36.364 0.46 0.00 0.00 3.58
478 487 8.950403 AATATAAGAACGTTTTTCAAGCTGAC 57.050 30.769 7.42 0.00 0.00 3.51
486 495 9.845305 CCGTCTCATAATATAAGAACGTTTTTC 57.155 33.333 7.42 0.00 0.00 2.29
487 496 8.333186 GCCGTCTCATAATATAAGAACGTTTTT 58.667 33.333 9.22 9.22 0.00 1.94
488 497 7.709613 AGCCGTCTCATAATATAAGAACGTTTT 59.290 33.333 0.46 0.00 0.00 2.43
489 498 7.169308 CAGCCGTCTCATAATATAAGAACGTTT 59.831 37.037 0.46 0.00 0.00 3.60
490 499 6.641314 CAGCCGTCTCATAATATAAGAACGTT 59.359 38.462 0.00 0.00 0.00 3.99
491 500 6.150318 CAGCCGTCTCATAATATAAGAACGT 58.850 40.000 0.00 0.00 0.00 3.99
492 501 5.573282 CCAGCCGTCTCATAATATAAGAACG 59.427 44.000 0.00 0.00 0.00 3.95
493 502 6.688578 TCCAGCCGTCTCATAATATAAGAAC 58.311 40.000 0.00 0.00 0.00 3.01
494 503 6.493802 ACTCCAGCCGTCTCATAATATAAGAA 59.506 38.462 0.00 0.00 0.00 2.52
495 504 6.010850 ACTCCAGCCGTCTCATAATATAAGA 58.989 40.000 0.00 0.00 0.00 2.10
496 505 6.274157 ACTCCAGCCGTCTCATAATATAAG 57.726 41.667 0.00 0.00 0.00 1.73
497 506 7.173032 TCTACTCCAGCCGTCTCATAATATAA 58.827 38.462 0.00 0.00 0.00 0.98
498 507 6.718294 TCTACTCCAGCCGTCTCATAATATA 58.282 40.000 0.00 0.00 0.00 0.86
499 508 5.571285 TCTACTCCAGCCGTCTCATAATAT 58.429 41.667 0.00 0.00 0.00 1.28
500 509 4.981812 TCTACTCCAGCCGTCTCATAATA 58.018 43.478 0.00 0.00 0.00 0.98
501 510 3.833732 TCTACTCCAGCCGTCTCATAAT 58.166 45.455 0.00 0.00 0.00 1.28
502 511 3.292492 TCTACTCCAGCCGTCTCATAA 57.708 47.619 0.00 0.00 0.00 1.90
503 512 3.149981 CATCTACTCCAGCCGTCTCATA 58.850 50.000 0.00 0.00 0.00 2.15
504 513 1.959985 CATCTACTCCAGCCGTCTCAT 59.040 52.381 0.00 0.00 0.00 2.90
505 514 1.064685 TCATCTACTCCAGCCGTCTCA 60.065 52.381 0.00 0.00 0.00 3.27
506 515 1.681538 TCATCTACTCCAGCCGTCTC 58.318 55.000 0.00 0.00 0.00 3.36
507 516 2.373335 ATCATCTACTCCAGCCGTCT 57.627 50.000 0.00 0.00 0.00 4.18
508 517 4.021894 ACATTATCATCTACTCCAGCCGTC 60.022 45.833 0.00 0.00 0.00 4.79
509 518 3.898123 ACATTATCATCTACTCCAGCCGT 59.102 43.478 0.00 0.00 0.00 5.68
510 519 4.240888 CACATTATCATCTACTCCAGCCG 58.759 47.826 0.00 0.00 0.00 5.52
511 520 4.993584 CACACATTATCATCTACTCCAGCC 59.006 45.833 0.00 0.00 0.00 4.85
512 521 5.605534 ACACACATTATCATCTACTCCAGC 58.394 41.667 0.00 0.00 0.00 4.85
513 522 7.014711 AGGTACACACATTATCATCTACTCCAG 59.985 40.741 0.00 0.00 0.00 3.86
514 523 6.839134 AGGTACACACATTATCATCTACTCCA 59.161 38.462 0.00 0.00 0.00 3.86
515 524 7.291411 AGGTACACACATTATCATCTACTCC 57.709 40.000 0.00 0.00 0.00 3.85
517 526 9.588096 TGATAGGTACACACATTATCATCTACT 57.412 33.333 0.00 0.00 32.38 2.57
563 586 3.949113 AGTAACCAGGCGAACAAGAAAAA 59.051 39.130 0.00 0.00 0.00 1.94
619 761 4.165779 CTGGGCAATAAATCGTGACAAAC 58.834 43.478 0.00 0.00 0.00 2.93
700 846 4.218417 GTGTGGTACCTCTCAATTGCAAAT 59.782 41.667 14.36 0.00 0.00 2.32
777 923 5.770162 TGATGGATGATACACAGATCGTACT 59.230 40.000 0.00 0.00 0.00 2.73
778 924 5.859114 GTGATGGATGATACACAGATCGTAC 59.141 44.000 0.00 0.00 34.05 3.67
779 925 5.048013 GGTGATGGATGATACACAGATCGTA 60.048 44.000 0.00 0.00 35.33 3.43
821 980 4.469657 TGCAGAACCACCTGTCTTATTTT 58.530 39.130 0.00 0.00 36.57 1.82
822 981 4.074970 CTGCAGAACCACCTGTCTTATTT 58.925 43.478 8.42 0.00 36.57 1.40
823 982 3.073062 ACTGCAGAACCACCTGTCTTATT 59.927 43.478 23.35 0.00 36.57 1.40
824 983 2.639839 ACTGCAGAACCACCTGTCTTAT 59.360 45.455 23.35 0.00 36.57 1.73
825 984 2.047061 ACTGCAGAACCACCTGTCTTA 58.953 47.619 23.35 0.00 36.57 2.10
826 985 0.839946 ACTGCAGAACCACCTGTCTT 59.160 50.000 23.35 0.00 36.57 3.01
827 986 0.839946 AACTGCAGAACCACCTGTCT 59.160 50.000 23.35 0.00 36.57 3.41
828 987 1.680338 AAACTGCAGAACCACCTGTC 58.320 50.000 23.35 0.00 36.57 3.51
829 988 2.143876 AAAACTGCAGAACCACCTGT 57.856 45.000 23.35 0.00 36.57 4.00
830 989 4.647424 TTTAAAACTGCAGAACCACCTG 57.353 40.909 23.35 0.00 37.23 4.00
831 990 4.099419 CCTTTTAAAACTGCAGAACCACCT 59.901 41.667 23.35 0.00 0.00 4.00
832 991 4.098807 TCCTTTTAAAACTGCAGAACCACC 59.901 41.667 23.35 0.00 0.00 4.61
833 992 5.257082 TCCTTTTAAAACTGCAGAACCAC 57.743 39.130 23.35 0.00 0.00 4.16
834 993 5.923733 TTCCTTTTAAAACTGCAGAACCA 57.076 34.783 23.35 0.00 0.00 3.67
835 994 7.603963 TTTTTCCTTTTAAAACTGCAGAACC 57.396 32.000 23.35 0.00 0.00 3.62
836 995 8.122330 CCATTTTTCCTTTTAAAACTGCAGAAC 58.878 33.333 23.35 0.00 31.32 3.01
837 996 7.826744 ACCATTTTTCCTTTTAAAACTGCAGAA 59.173 29.630 23.35 0.04 31.32 3.02
838 997 7.334858 ACCATTTTTCCTTTTAAAACTGCAGA 58.665 30.769 23.35 0.00 31.32 4.26
839 998 7.495606 AGACCATTTTTCCTTTTAAAACTGCAG 59.504 33.333 13.48 13.48 31.32 4.41
840 999 7.334858 AGACCATTTTTCCTTTTAAAACTGCA 58.665 30.769 0.00 0.00 31.32 4.41
841 1000 7.786178 AGACCATTTTTCCTTTTAAAACTGC 57.214 32.000 0.00 0.00 31.32 4.40
848 1007 8.073467 AGTTCACAAGACCATTTTTCCTTTTA 57.927 30.769 0.00 0.00 0.00 1.52
900 1059 5.811100 GGTTCAATGCAACTACTCCTACTAC 59.189 44.000 0.00 0.00 0.00 2.73
904 1063 3.857052 CGGTTCAATGCAACTACTCCTA 58.143 45.455 0.00 0.00 0.00 2.94
907 1066 1.804151 TGCGGTTCAATGCAACTACTC 59.196 47.619 0.00 0.00 38.34 2.59
925 1084 1.518133 AGAGCTCGCGTGATCTTGC 60.518 57.895 21.86 8.67 26.91 4.01
1026 1185 1.800315 GATCGGTGTGACACGACGG 60.800 63.158 17.87 12.89 42.39 4.79
1040 1199 0.810031 ATTTGACTTCGGGGCGATCG 60.810 55.000 11.69 11.69 35.23 3.69
1041 1200 0.938008 GATTTGACTTCGGGGCGATC 59.062 55.000 0.00 0.00 35.23 3.69
1042 1201 0.810031 CGATTTGACTTCGGGGCGAT 60.810 55.000 0.00 0.00 35.23 4.58
1043 1202 1.447140 CGATTTGACTTCGGGGCGA 60.447 57.895 0.00 0.00 33.05 5.54
1044 1203 1.447140 TCGATTTGACTTCGGGGCG 60.447 57.895 0.00 0.00 37.22 6.13
1045 1204 1.693083 CGTCGATTTGACTTCGGGGC 61.693 60.000 2.63 0.00 45.87 5.80
1046 1205 1.693083 GCGTCGATTTGACTTCGGGG 61.693 60.000 0.00 0.00 45.87 5.73
1047 1206 1.708027 GCGTCGATTTGACTTCGGG 59.292 57.895 0.00 0.00 45.87 5.14
1090 1249 0.108615 GCCTCGCGATATATGCAGGT 60.109 55.000 10.36 0.00 34.88 4.00
1091 1250 0.174389 AGCCTCGCGATATATGCAGG 59.826 55.000 10.36 5.73 35.26 4.85
1094 1277 1.002366 CCAAGCCTCGCGATATATGC 58.998 55.000 10.36 7.94 0.00 3.14
1172 1362 2.720758 CTTCTCGGCTGTTCACGCG 61.721 63.158 3.53 3.53 0.00 6.01
1188 1378 1.599576 GCCGCTCTTCTCTTCCCTT 59.400 57.895 0.00 0.00 0.00 3.95
1262 1457 2.031012 CGGAGACAAGCAGCACCA 59.969 61.111 0.00 0.00 0.00 4.17
1263 1458 2.031163 ACGGAGACAAGCAGCACC 59.969 61.111 0.00 0.00 0.00 5.01
1265 1460 2.031012 CCACGGAGACAAGCAGCA 59.969 61.111 0.00 0.00 0.00 4.41
1610 1805 2.520741 GCTCCTCCTCCTCCTCGG 60.521 72.222 0.00 0.00 0.00 4.63
1611 1806 1.827789 CAGCTCCTCCTCCTCCTCG 60.828 68.421 0.00 0.00 0.00 4.63
1678 1873 2.511600 CGACCAGAACCATCCGCC 60.512 66.667 0.00 0.00 0.00 6.13
1725 1937 1.445582 CGTACAGTTCCTCGGGCAC 60.446 63.158 0.00 0.00 0.00 5.01
1726 1938 2.642254 CCGTACAGTTCCTCGGGCA 61.642 63.158 0.00 0.00 39.41 5.36
1727 1939 2.183555 CCGTACAGTTCCTCGGGC 59.816 66.667 0.00 0.00 39.41 6.13
1729 1941 1.647545 TACGCCGTACAGTTCCTCGG 61.648 60.000 0.00 0.00 44.86 4.63
1736 1956 2.401766 CGTCCCTACGCCGTACAGT 61.402 63.158 0.00 0.00 43.12 3.55
1771 1995 2.740826 GTACGTGCATGCCGGTGT 60.741 61.111 25.35 16.49 0.00 4.16
1780 2016 4.673298 CAGGCCACCGTACGTGCA 62.673 66.667 15.21 0.00 41.53 4.57
1812 2048 7.534918 GCTCGTAAAAACAATATACAAAACCGT 59.465 33.333 0.00 0.00 0.00 4.83
1860 2105 9.986833 CACAACCAAAAAGGAAATAAAGAAAAG 57.013 29.630 0.00 0.00 41.22 2.27
1862 2107 8.103935 ACCACAACCAAAAAGGAAATAAAGAAA 58.896 29.630 0.00 0.00 41.22 2.52
1864 2109 7.189079 ACCACAACCAAAAAGGAAATAAAGA 57.811 32.000 0.00 0.00 41.22 2.52
1869 2114 4.081365 ACGAACCACAACCAAAAAGGAAAT 60.081 37.500 0.00 0.00 41.22 2.17
1874 2119 3.224884 ACACGAACCACAACCAAAAAG 57.775 42.857 0.00 0.00 0.00 2.27
1882 2127 2.299562 GTGCGTACACGAACCACAA 58.700 52.632 5.84 0.00 41.94 3.33
1914 2166 2.412591 ACCAGCTAAGCTCCATACCAT 58.587 47.619 0.00 0.00 36.40 3.55
1971 2227 4.137872 AACCTGCCATGCATGCGC 62.138 61.111 24.69 24.69 38.13 6.09
2033 2289 1.641677 GCAAGCGAGAACAACGTGT 59.358 52.632 0.00 0.00 0.00 4.49
2207 2485 0.612732 AACACCCCAGATACGACCGA 60.613 55.000 0.00 0.00 0.00 4.69
2214 2492 5.836024 AAGACAAACTAACACCCCAGATA 57.164 39.130 0.00 0.00 0.00 1.98
2223 2501 7.397892 TGATGGACAAAAAGACAAACTAACA 57.602 32.000 0.00 0.00 0.00 2.41
2537 2842 1.045407 ACAACCAGCGTCCTACAGAA 58.955 50.000 0.00 0.00 0.00 3.02
2564 2869 3.989817 GGAGCTGCAAACAATACCAAAAG 59.010 43.478 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.