Multiple sequence alignment - TraesCS2B01G157800

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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 TraesCS2B01G157800 chr2B 100.000 4484 0 0 1 4484 131587158 131582675 0.000000e+00 8281
1 TraesCS2B01G157800 chr2B 90.401 698 43 10 1068 1762 338730051 338729375 0.000000e+00 896
2 TraesCS2B01G157800 chr2A 93.432 1964 100 22 2536 4484 80618238 80616289 0.000000e+00 2885
3 TraesCS2B01G157800 chr2A 85.944 2611 185 80 3 2508 80620767 80618234 0.000000e+00 2621
4 TraesCS2B01G157800 chr2D 91.603 1965 132 22 2536 4484 80037534 80035587 0.000000e+00 2684
5 TraesCS2B01G157800 chr2D 88.329 2005 133 44 534 2508 80039463 80037530 0.000000e+00 2313
6 TraesCS2B01G157800 chr2D 86.441 295 25 8 237 520 80039738 80039448 4.360000e-80 309
7 TraesCS2B01G157800 chr2D 85.909 220 22 6 3 216 80040014 80039798 4.510000e-55 226
8 TraesCS2B01G157800 chr3B 79.349 2702 368 103 1236 3851 3261566 3258969 0.000000e+00 1724
9 TraesCS2B01G157800 chr3B 90.258 698 46 8 1068 1762 395708411 395707733 0.000000e+00 893
10 TraesCS2B01G157800 chr3B 89.474 171 18 0 1055 1225 3261896 3261726 2.720000e-52 217
11 TraesCS2B01G157800 chr3D 79.855 2482 328 93 1236 3629 2450858 2448461 0.000000e+00 1655
12 TraesCS2B01G157800 chr3D 87.791 172 19 2 1055 1225 2451162 2450992 2.740000e-47 200
13 TraesCS2B01G157800 chrUn 79.735 2413 299 98 1236 3568 270454659 270452357 0.000000e+00 1572
14 TraesCS2B01G157800 chrUn 79.735 2413 299 98 1236 3568 270462923 270460621 0.000000e+00 1572
15 TraesCS2B01G157800 chrUn 79.735 2413 299 98 1236 3568 280683518 280681216 0.000000e+00 1572
16 TraesCS2B01G157800 chrUn 86.628 172 21 2 1055 1225 270454985 270454815 5.920000e-44 189
17 TraesCS2B01G157800 chr3A 78.491 2664 354 117 1237 3816 1621036 1623564 0.000000e+00 1543
18 TraesCS2B01G157800 chr5A 90.923 639 36 8 1068 1703 698851609 698852228 0.000000e+00 839
19 TraesCS2B01G157800 chr5A 90.792 619 35 8 1088 1703 690644679 690644080 0.000000e+00 808


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 TraesCS2B01G157800 chr2B 131582675 131587158 4483 True 8281.0 8281 100.0000 1 4484 1 chr2B.!!$R1 4483
1 TraesCS2B01G157800 chr2B 338729375 338730051 676 True 896.0 896 90.4010 1068 1762 1 chr2B.!!$R2 694
2 TraesCS2B01G157800 chr2A 80616289 80620767 4478 True 2753.0 2885 89.6880 3 4484 2 chr2A.!!$R1 4481
3 TraesCS2B01G157800 chr2D 80035587 80040014 4427 True 1383.0 2684 88.0705 3 4484 4 chr2D.!!$R1 4481
4 TraesCS2B01G157800 chr3B 3258969 3261896 2927 True 970.5 1724 84.4115 1055 3851 2 chr3B.!!$R2 2796
5 TraesCS2B01G157800 chr3B 395707733 395708411 678 True 893.0 893 90.2580 1068 1762 1 chr3B.!!$R1 694
6 TraesCS2B01G157800 chr3D 2448461 2451162 2701 True 927.5 1655 83.8230 1055 3629 2 chr3D.!!$R1 2574
7 TraesCS2B01G157800 chrUn 270460621 270462923 2302 True 1572.0 1572 79.7350 1236 3568 1 chrUn.!!$R1 2332
8 TraesCS2B01G157800 chrUn 280681216 280683518 2302 True 1572.0 1572 79.7350 1236 3568 1 chrUn.!!$R2 2332
9 TraesCS2B01G157800 chrUn 270452357 270454985 2628 True 880.5 1572 83.1815 1055 3568 2 chrUn.!!$R3 2513
10 TraesCS2B01G157800 chr3A 1621036 1623564 2528 False 1543.0 1543 78.4910 1237 3816 1 chr3A.!!$F1 2579
11 TraesCS2B01G157800 chr5A 698851609 698852228 619 False 839.0 839 90.9230 1068 1703 1 chr5A.!!$F1 635
12 TraesCS2B01G157800 chr5A 690644080 690644679 599 True 808.0 808 90.7920 1088 1703 1 chr5A.!!$R1 615

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
491 554 0.108992 ACGTGTGTAGGCACCGTATG 60.109 55.0 10.68 0.0 44.41 2.39 F
864 941 0.180406 ACTCAACTGCACGAAAGGGT 59.820 50.0 0.00 0.0 36.38 4.34 F
1827 2165 0.983378 ACTATGACCTCCCACTGGCC 60.983 60.0 0.00 0.0 0.00 5.36 F
2369 2773 1.577328 AACAGCAACGCGGATCAAGG 61.577 55.0 12.47 0.0 0.00 3.61 F
3039 3463 0.826062 CATGGGGAATGAACAAGGCC 59.174 55.0 0.00 0.0 38.72 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2481 0.541063 TGTACGGCTCAGTCCTGGAA 60.541 55.0 0.00 0.00 0.00 3.53 R
2618 3028 0.836400 ACCATCCTGGACTCGTTGGT 60.836 55.0 12.15 12.15 40.96 3.67 R
2931 3351 0.174617 GAGGCTCTGCACTACTCCAC 59.825 60.0 7.40 0.00 0.00 4.02 R
3333 3774 0.601046 TGTCAAGCAGAGACCAAGCG 60.601 55.0 0.00 0.00 35.15 4.68 R
4424 4897 1.131638 TCCACTCACAGCCTCAGTTT 58.868 50.0 0.00 0.00 0.00 2.66 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
24 25 4.724697 CTGCGGCGCGTGAAACAG 62.725 66.667 28.09 13.19 35.74 3.16
47 48 3.368190 CTCTCCACCCAGCAGCGAG 62.368 68.421 0.00 0.00 0.00 5.03
69 70 1.460305 ATCCCGGTGGAGAGATGGG 60.460 63.158 0.00 0.00 46.08 4.00
70 71 2.972589 ATCCCGGTGGAGAGATGGGG 62.973 65.000 0.00 0.00 46.08 4.96
71 72 3.866582 CCGGTGGAGAGATGGGGC 61.867 72.222 0.00 0.00 0.00 5.80
72 73 3.083349 CGGTGGAGAGATGGGGCA 61.083 66.667 0.00 0.00 0.00 5.36
73 74 2.669133 CGGTGGAGAGATGGGGCAA 61.669 63.158 0.00 0.00 0.00 4.52
82 85 2.039879 AGAGATGGGGCAAGTACGTTTT 59.960 45.455 0.00 0.00 0.00 2.43
83 86 2.817844 GAGATGGGGCAAGTACGTTTTT 59.182 45.455 0.00 0.00 0.00 1.94
84 87 4.004982 GAGATGGGGCAAGTACGTTTTTA 58.995 43.478 0.00 0.00 0.00 1.52
85 88 4.595986 AGATGGGGCAAGTACGTTTTTAT 58.404 39.130 0.00 0.00 0.00 1.40
145 149 0.878523 CTGCCAAAACCGACGACAGA 60.879 55.000 0.00 0.00 0.00 3.41
146 150 1.155424 TGCCAAAACCGACGACAGAC 61.155 55.000 0.00 0.00 0.00 3.51
230 265 4.468689 CCGGGGAGACGAAAGGGC 62.469 72.222 0.00 0.00 35.47 5.19
235 270 1.192428 GGGAGACGAAAGGGCTTAGA 58.808 55.000 0.00 0.00 0.00 2.10
304 355 2.190578 CCTCCATTCCACCGGAGC 59.809 66.667 9.46 0.00 46.37 4.70
345 400 4.035324 CGCACGTTATCTTCTCTTCCTCTA 59.965 45.833 0.00 0.00 0.00 2.43
346 401 5.275494 GCACGTTATCTTCTCTTCCTCTAC 58.725 45.833 0.00 0.00 0.00 2.59
351 406 2.093106 TCTTCTCTTCCTCTACCGTGC 58.907 52.381 0.00 0.00 0.00 5.34
447 508 1.787155 CAGTTCAAGTCCAACGAGTCG 59.213 52.381 11.85 11.85 0.00 4.18
454 515 0.388649 GTCCAACGAGTCGCACATCT 60.389 55.000 13.59 0.00 0.00 2.90
464 525 3.896133 GCACATCTGGCCATGCGG 61.896 66.667 13.02 4.05 0.00 5.69
471 532 4.594854 TGGCCATGCGGGTGTGTT 62.595 61.111 0.00 0.00 39.65 3.32
472 533 2.360600 GGCCATGCGGGTGTGTTA 60.361 61.111 0.00 0.00 39.65 2.41
474 535 3.034370 GCCATGCGGGTGTGTTACG 62.034 63.158 0.00 0.00 39.65 3.18
475 536 1.669760 CCATGCGGGTGTGTTACGT 60.670 57.895 0.00 0.00 0.00 3.57
476 537 1.495509 CATGCGGGTGTGTTACGTG 59.504 57.895 0.00 0.00 0.00 4.49
489 552 1.068610 GTTACGTGTGTAGGCACCGTA 60.069 52.381 0.00 13.26 44.41 4.02
491 554 0.108992 ACGTGTGTAGGCACCGTATG 60.109 55.000 10.68 0.00 44.41 2.39
517 580 3.258622 ACTCTTGTACTCTAGCCACCAAC 59.741 47.826 0.00 0.00 0.00 3.77
518 581 2.565834 TCTTGTACTCTAGCCACCAACC 59.434 50.000 0.00 0.00 0.00 3.77
519 582 1.272807 TGTACTCTAGCCACCAACCC 58.727 55.000 0.00 0.00 0.00 4.11
520 583 1.203262 TGTACTCTAGCCACCAACCCT 60.203 52.381 0.00 0.00 0.00 4.34
521 584 1.907255 GTACTCTAGCCACCAACCCTT 59.093 52.381 0.00 0.00 0.00 3.95
522 585 1.446016 ACTCTAGCCACCAACCCTTT 58.554 50.000 0.00 0.00 0.00 3.11
523 586 1.073923 ACTCTAGCCACCAACCCTTTG 59.926 52.381 0.00 0.00 0.00 2.77
524 587 1.073923 CTCTAGCCACCAACCCTTTGT 59.926 52.381 0.00 0.00 0.00 2.83
525 588 1.497286 TCTAGCCACCAACCCTTTGTT 59.503 47.619 0.00 0.00 37.80 2.83
526 589 2.091555 TCTAGCCACCAACCCTTTGTTT 60.092 45.455 0.00 0.00 34.00 2.83
527 590 0.829990 AGCCACCAACCCTTTGTTTG 59.170 50.000 0.00 0.00 34.00 2.93
528 591 0.813610 GCCACCAACCCTTTGTTTGC 60.814 55.000 0.00 0.00 34.00 3.68
529 592 0.539051 CCACCAACCCTTTGTTTGCA 59.461 50.000 0.00 0.00 34.00 4.08
530 593 1.473080 CCACCAACCCTTTGTTTGCAG 60.473 52.381 0.00 0.00 34.00 4.41
531 594 0.829990 ACCAACCCTTTGTTTGCAGG 59.170 50.000 0.00 0.00 34.00 4.85
532 595 0.829990 CCAACCCTTTGTTTGCAGGT 59.170 50.000 0.00 0.00 34.00 4.00
533 596 1.202521 CCAACCCTTTGTTTGCAGGTC 60.203 52.381 0.00 0.00 34.00 3.85
534 597 1.756538 CAACCCTTTGTTTGCAGGTCT 59.243 47.619 0.00 0.00 34.00 3.85
535 598 1.692411 ACCCTTTGTTTGCAGGTCTC 58.308 50.000 0.00 0.00 0.00 3.36
536 599 1.215423 ACCCTTTGTTTGCAGGTCTCT 59.785 47.619 0.00 0.00 0.00 3.10
537 600 2.441750 ACCCTTTGTTTGCAGGTCTCTA 59.558 45.455 0.00 0.00 0.00 2.43
538 601 3.077359 CCCTTTGTTTGCAGGTCTCTAG 58.923 50.000 0.00 0.00 0.00 2.43
539 602 2.485814 CCTTTGTTTGCAGGTCTCTAGC 59.514 50.000 0.00 0.00 0.00 3.42
540 603 2.185004 TTGTTTGCAGGTCTCTAGCC 57.815 50.000 0.00 0.00 0.00 3.93
541 604 1.055849 TGTTTGCAGGTCTCTAGCCA 58.944 50.000 0.00 0.00 0.00 4.75
542 605 1.270839 TGTTTGCAGGTCTCTAGCCAC 60.271 52.381 0.00 0.00 0.00 5.01
543 606 0.324943 TTTGCAGGTCTCTAGCCACC 59.675 55.000 2.40 2.40 0.00 4.61
544 607 0.835971 TTGCAGGTCTCTAGCCACCA 60.836 55.000 11.38 0.00 34.80 4.17
545 608 0.835971 TGCAGGTCTCTAGCCACCAA 60.836 55.000 11.38 0.00 34.80 3.67
546 609 0.391793 GCAGGTCTCTAGCCACCAAC 60.392 60.000 11.38 1.17 34.80 3.77
596 661 2.825836 GCTAGCACGGCAGGCATT 60.826 61.111 10.63 0.00 0.00 3.56
597 662 1.523711 GCTAGCACGGCAGGCATTA 60.524 57.895 10.63 0.00 0.00 1.90
607 672 1.406539 GGCAGGCATTATCCAAGTGTG 59.593 52.381 0.00 0.00 0.00 3.82
634 699 1.300971 CCCTGCACACATTCACTCCG 61.301 60.000 0.00 0.00 0.00 4.63
642 707 1.069022 CACATTCACTCCGTTGCCTTG 60.069 52.381 0.00 0.00 0.00 3.61
719 794 3.181497 CCTTGGAGAATGGCATTTACGTG 60.181 47.826 14.93 3.99 0.00 4.49
774 850 2.598632 GGCCACGTCGCATCATAGC 61.599 63.158 7.63 0.00 0.00 2.97
793 869 0.747255 CCGAGACGGTCCATCAGAAT 59.253 55.000 4.14 0.00 42.73 2.40
806 882 4.080919 TCCATCAGAATCGTGACCAAGATT 60.081 41.667 10.16 10.16 41.10 2.40
847 924 1.940613 GTGACAACCTTGCTTCGAACT 59.059 47.619 0.00 0.00 0.00 3.01
848 925 2.032808 GTGACAACCTTGCTTCGAACTC 60.033 50.000 0.00 0.00 0.00 3.01
850 927 2.612212 GACAACCTTGCTTCGAACTCAA 59.388 45.455 0.00 0.75 0.00 3.02
863 940 1.264288 GAACTCAACTGCACGAAAGGG 59.736 52.381 0.00 0.00 37.78 3.95
864 941 0.180406 ACTCAACTGCACGAAAGGGT 59.820 50.000 0.00 0.00 36.38 4.34
865 942 1.308998 CTCAACTGCACGAAAGGGTT 58.691 50.000 0.00 0.00 36.38 4.11
871 948 1.154225 GCACGAAAGGGTTGATGCG 60.154 57.895 0.00 0.00 36.38 4.73
898 975 5.554636 CAGCGAAGACAATCAATCAGTAAC 58.445 41.667 0.00 0.00 0.00 2.50
899 976 5.349817 CAGCGAAGACAATCAATCAGTAACT 59.650 40.000 0.00 0.00 0.00 2.24
916 993 3.123943 CTCAGCAGGAGCCTAGCTA 57.876 57.895 11.36 0.00 39.88 3.32
931 1008 2.718731 CTACGAGGGCTCAGCTCG 59.281 66.667 6.75 6.75 44.96 5.03
1038 1147 2.037251 ACTGTTGCTGGTGGTAGTACTG 59.963 50.000 5.39 0.00 0.00 2.74
1044 1153 1.217244 GGTGGTAGTACTGGCGGTG 59.783 63.158 9.79 0.00 0.00 4.94
1046 1155 2.186125 GGTAGTACTGGCGGTGGC 59.814 66.667 9.79 1.79 38.90 5.01
1047 1156 2.356780 GGTAGTACTGGCGGTGGCT 61.357 63.158 9.79 9.72 39.81 4.75
1048 1157 1.141234 GTAGTACTGGCGGTGGCTC 59.859 63.158 9.79 0.00 39.81 4.70
1050 1159 2.791613 TAGTACTGGCGGTGGCTCCA 62.792 60.000 9.79 0.00 39.81 3.86
1394 1680 3.006247 GCTTGACAGAGGTCTTCATTCC 58.994 50.000 0.00 0.00 44.61 3.01
1492 1778 7.404980 GGTCCAGGATTTTCCCAGGTATATATA 59.595 40.741 0.00 0.00 37.19 0.86
1493 1779 9.004231 GTCCAGGATTTTCCCAGGTATATATAT 57.996 37.037 0.00 0.00 37.19 0.86
1601 1900 6.159988 AGTAGTTTCTGATGTAGAGTTGTGC 58.840 40.000 0.00 0.00 36.61 4.57
1604 1903 6.701340 AGTTTCTGATGTAGAGTTGTGCATA 58.299 36.000 0.00 0.00 36.61 3.14
1648 1947 2.715763 AGGTGAACCAGGAAGGAGTA 57.284 50.000 1.62 0.00 41.22 2.59
1716 2032 1.422531 ATTTTCTGCACCTGGGCAAA 58.577 45.000 10.39 4.04 44.40 3.68
1796 2134 3.010584 GGATTAGGCATCACCCCATATGT 59.989 47.826 1.24 0.00 40.58 2.29
1827 2165 0.983378 ACTATGACCTCCCACTGGCC 60.983 60.000 0.00 0.00 0.00 5.36
1885 2231 6.246420 AGATTGTGTAAGCATTTCAGACAC 57.754 37.500 0.00 0.00 40.62 3.67
1887 2233 3.146066 TGTGTAAGCATTTCAGACACCC 58.854 45.455 0.00 0.00 39.71 4.61
1934 2288 6.676237 TTAAGCATGTCTTTTGATGCGATA 57.324 33.333 7.53 0.00 44.08 2.92
1941 2314 6.122850 TGTCTTTTGATGCGATATCCTTTG 57.877 37.500 0.00 0.00 0.00 2.77
2037 2410 2.154798 CTTCAACGAGCCGAGGGTCA 62.155 60.000 19.67 0.00 42.17 4.02
2066 2439 2.777114 TCTGGGCTATGACAATGGCTTA 59.223 45.455 0.00 0.00 40.04 3.09
2157 2530 3.313526 GCACAATATCATCCTTTCGCACT 59.686 43.478 0.00 0.00 0.00 4.40
2369 2773 1.577328 AACAGCAACGCGGATCAAGG 61.577 55.000 12.47 0.00 0.00 3.61
2428 2832 5.458948 TGGTAAGACCCTGAAACCATTTCAT 60.459 40.000 4.55 0.00 41.46 2.57
2508 2915 3.630312 TGTCACTAACTTTGTTTGGAGGC 59.370 43.478 0.00 0.00 0.00 4.70
2510 2917 4.278419 GTCACTAACTTTGTTTGGAGGCAT 59.722 41.667 0.00 0.00 0.00 4.40
2514 2921 1.761784 ACTTTGTTTGGAGGCATGCAA 59.238 42.857 21.36 0.00 34.60 4.08
2521 2928 1.927487 TGGAGGCATGCAAACTGAAT 58.073 45.000 21.36 0.00 0.00 2.57
2522 2929 3.084536 TGGAGGCATGCAAACTGAATA 57.915 42.857 21.36 0.00 0.00 1.75
2524 2931 4.790937 TGGAGGCATGCAAACTGAATATA 58.209 39.130 21.36 0.00 0.00 0.86
2528 2935 7.670979 TGGAGGCATGCAAACTGAATATATATT 59.329 33.333 21.36 7.72 0.00 1.28
2618 3028 2.221299 AGGTTGCCGGGCTTCAGTA 61.221 57.895 21.46 0.00 0.00 2.74
2621 3031 2.521451 TTGCCGGGCTTCAGTACCA 61.521 57.895 21.46 0.00 0.00 3.25
2698 3108 5.046591 CACTTCTTACTACATGAAGGACCCA 60.047 44.000 0.00 0.00 40.87 4.51
2793 3206 3.340814 TCACTCCAAATCCTTCTGCTC 57.659 47.619 0.00 0.00 0.00 4.26
2798 3216 4.414846 ACTCCAAATCCTTCTGCTCCATAT 59.585 41.667 0.00 0.00 0.00 1.78
2799 3217 5.103771 ACTCCAAATCCTTCTGCTCCATATT 60.104 40.000 0.00 0.00 0.00 1.28
2899 3319 8.809066 TGTAAGTGCAGTTCTAGGTTTATCTTA 58.191 33.333 10.78 0.00 0.00 2.10
2904 3324 9.595823 GTGCAGTTCTAGGTTTATCTTATGTAA 57.404 33.333 0.00 0.00 0.00 2.41
2931 3351 4.686554 GGGTATACTGTAGTACTCCGTACG 59.313 50.000 8.69 8.69 43.05 3.67
3039 3463 0.826062 CATGGGGAATGAACAAGGCC 59.174 55.000 0.00 0.00 38.72 5.19
3101 3527 3.135994 TCCTTTCTGAAAACGGTACTGC 58.864 45.455 0.23 0.00 0.00 4.40
3111 3537 2.656560 ACGGTACTGCTGATCTCAAC 57.343 50.000 0.23 0.00 0.00 3.18
3122 3548 5.414360 TGCTGATCTCAACTGATAACTGTC 58.586 41.667 0.00 0.00 0.00 3.51
3176 3608 4.116961 CGTTCTCAACTAACAAGGACACA 58.883 43.478 0.00 0.00 0.00 3.72
3188 3620 4.813027 ACAAGGACACAAATGATCAATGC 58.187 39.130 0.00 0.00 0.00 3.56
3264 3705 1.593006 CACGACACAATAAGGATCCGC 59.407 52.381 5.98 0.00 0.00 5.54
3333 3774 0.036671 CCCGAGTGGTTGGGTACTTC 60.037 60.000 0.00 0.00 42.29 3.01
3465 3906 2.158449 GTGGTTCAAGAACATGCTCTCG 59.842 50.000 14.25 0.00 42.85 4.04
3501 3944 2.905415 AGGATTGCAAACAGGATCCA 57.095 45.000 15.82 0.00 40.39 3.41
3520 3971 3.394274 TCCAGGAGGATCAGTTGTTTCAA 59.606 43.478 0.00 0.00 39.61 2.69
3525 3976 5.893824 AGGAGGATCAGTTGTTTCAACTTTT 59.106 36.000 11.68 3.75 36.25 2.27
3570 4022 7.169982 GTGTATGTTTATCATAGCACCTCAGAC 59.830 40.741 0.00 0.00 39.36 3.51
3635 4096 7.985752 GCTTTGCCCGTCCTTATATATAATACT 59.014 37.037 5.64 0.00 0.00 2.12
3774 4239 7.809331 TCAAATGAGACAATTTCAACAGCATAC 59.191 33.333 0.00 0.00 0.00 2.39
3781 4246 4.724074 ATTTCAACAGCATACCACATGG 57.276 40.909 0.00 0.00 42.17 3.66
3805 4270 2.842496 TCACAGAGGAAAGCCAGATGAT 59.158 45.455 0.00 0.00 36.29 2.45
3806 4271 4.033009 TCACAGAGGAAAGCCAGATGATA 58.967 43.478 0.00 0.00 36.29 2.15
3812 4277 6.771749 CAGAGGAAAGCCAGATGATAAATTCT 59.228 38.462 0.00 0.00 36.29 2.40
3823 4292 6.971184 CAGATGATAAATTCTCTGCAAACCAC 59.029 38.462 0.00 0.00 0.00 4.16
3830 4299 0.673644 CTCTGCAAACCACTACCCCG 60.674 60.000 0.00 0.00 0.00 5.73
3848 4317 6.248569 ACCCCGAAACTGAACTCATTATAT 57.751 37.500 0.00 0.00 0.00 0.86
3887 4356 8.877864 ATTCCAACAGTACCAATTATTTCTCA 57.122 30.769 0.00 0.00 0.00 3.27
3898 4367 5.457799 CCAATTATTTCTCATGCTTCTTGCG 59.542 40.000 0.00 0.00 46.63 4.85
3977 4446 9.539825 CTGCCATCTATATGACTATCCATTTAC 57.460 37.037 0.00 0.00 34.84 2.01
4040 4509 8.102716 GCTATTGCGAACACGTAAATATCTATC 58.897 37.037 0.00 0.00 35.61 2.08
4050 4519 9.406113 ACACGTAAATATCTATCCCTATCCTAC 57.594 37.037 0.00 0.00 0.00 3.18
4153 4622 4.838986 AGCTAACTTGACCTTTCCAGTAGA 59.161 41.667 0.00 0.00 27.65 2.59
4154 4623 5.485708 AGCTAACTTGACCTTTCCAGTAGAT 59.514 40.000 0.00 0.00 27.65 1.98
4228 4698 3.638160 ACTTCAGCCTGCAATCTGAAAAA 59.362 39.130 22.69 8.72 45.36 1.94
4230 4700 4.877378 TCAGCCTGCAATCTGAAAAATT 57.123 36.364 13.35 0.00 36.50 1.82
4276 4748 4.291249 AGAAGCCTGGGAATTGGTAAGTAA 59.709 41.667 0.00 0.00 0.00 2.24
4281 4753 5.589050 GCCTGGGAATTGGTAAGTAAAGTAG 59.411 44.000 0.00 0.00 0.00 2.57
4368 4841 3.257393 AGTTGATCGTCAGACATCAAGC 58.743 45.455 20.09 16.24 39.22 4.01
4385 4858 1.219646 AGCTTGCCACAAAATTTGCG 58.780 45.000 5.52 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.517316 AGATTTCTGTTTCACGCGCC 59.483 50.000 5.73 0.00 0.00 6.53
23 24 1.558756 CTGCTGGGTGGAGAGATTTCT 59.441 52.381 0.00 0.00 36.08 2.52
24 25 2.016096 GCTGCTGGGTGGAGAGATTTC 61.016 57.143 0.00 0.00 36.08 2.17
47 48 1.690219 ATCTCTCCACCGGGATGCAC 61.690 60.000 6.32 0.00 43.91 4.57
69 70 3.432933 TCGTGGATAAAAACGTACTTGCC 59.567 43.478 0.00 0.00 40.61 4.52
70 71 4.634991 CTCGTGGATAAAAACGTACTTGC 58.365 43.478 0.00 0.00 40.61 4.01
71 72 4.634991 GCTCGTGGATAAAAACGTACTTG 58.365 43.478 0.00 0.00 40.61 3.16
72 73 3.365820 CGCTCGTGGATAAAAACGTACTT 59.634 43.478 0.00 0.00 40.61 2.24
73 74 2.919229 CGCTCGTGGATAAAAACGTACT 59.081 45.455 0.00 0.00 40.61 2.73
82 85 1.138036 CACCGACGCTCGTGGATAA 59.862 57.895 14.48 0.00 38.40 1.75
83 86 2.795973 CACCGACGCTCGTGGATA 59.204 61.111 14.48 0.00 38.40 2.59
84 87 4.796231 GCACCGACGCTCGTGGAT 62.796 66.667 14.48 0.00 38.40 3.41
220 255 1.137282 CTCCCTCTAAGCCCTTTCGTC 59.863 57.143 0.00 0.00 0.00 4.20
289 340 2.682136 TCGCTCCGGTGGAATGGA 60.682 61.111 0.00 0.00 0.00 3.41
386 441 2.090210 TGTGGGAGATAAGATGGGGCTA 60.090 50.000 0.00 0.00 0.00 3.93
387 442 1.345422 TGTGGGAGATAAGATGGGGCT 60.345 52.381 0.00 0.00 0.00 5.19
388 443 1.140312 TGTGGGAGATAAGATGGGGC 58.860 55.000 0.00 0.00 0.00 5.80
447 508 3.896133 CCGCATGGCCAGATGTGC 61.896 66.667 17.43 17.43 33.29 4.57
454 515 3.197579 TAACACACCCGCATGGCCA 62.198 57.895 8.56 8.56 37.83 5.36
464 525 1.142474 GCCTACACACGTAACACACC 58.858 55.000 0.00 0.00 0.00 4.16
517 580 1.986882 AGAGACCTGCAAACAAAGGG 58.013 50.000 0.00 0.00 37.94 3.95
518 581 2.485814 GCTAGAGACCTGCAAACAAAGG 59.514 50.000 0.00 0.00 39.65 3.11
519 582 2.485814 GGCTAGAGACCTGCAAACAAAG 59.514 50.000 0.00 0.00 0.00 2.77
520 583 2.158682 TGGCTAGAGACCTGCAAACAAA 60.159 45.455 0.00 0.00 0.00 2.83
521 584 1.419762 TGGCTAGAGACCTGCAAACAA 59.580 47.619 0.00 0.00 0.00 2.83
522 585 1.055849 TGGCTAGAGACCTGCAAACA 58.944 50.000 0.00 0.00 0.00 2.83
523 586 1.443802 GTGGCTAGAGACCTGCAAAC 58.556 55.000 0.00 0.00 0.00 2.93
524 587 0.324943 GGTGGCTAGAGACCTGCAAA 59.675 55.000 0.00 0.00 0.00 3.68
525 588 0.835971 TGGTGGCTAGAGACCTGCAA 60.836 55.000 10.92 0.00 32.98 4.08
526 589 0.835971 TTGGTGGCTAGAGACCTGCA 60.836 55.000 10.92 0.00 32.98 4.41
527 590 0.391793 GTTGGTGGCTAGAGACCTGC 60.392 60.000 10.92 2.26 32.98 4.85
528 591 0.250513 GGTTGGTGGCTAGAGACCTG 59.749 60.000 10.92 0.00 32.98 4.00
529 592 0.910088 GGGTTGGTGGCTAGAGACCT 60.910 60.000 10.92 0.00 32.98 3.85
530 593 1.198759 TGGGTTGGTGGCTAGAGACC 61.199 60.000 0.00 0.00 0.00 3.85
531 594 0.250513 CTGGGTTGGTGGCTAGAGAC 59.749 60.000 0.00 0.00 0.00 3.36
532 595 1.553690 GCTGGGTTGGTGGCTAGAGA 61.554 60.000 0.00 0.00 0.00 3.10
533 596 1.078143 GCTGGGTTGGTGGCTAGAG 60.078 63.158 0.00 0.00 0.00 2.43
534 597 1.538876 AGCTGGGTTGGTGGCTAGA 60.539 57.895 0.00 0.00 32.94 2.43
535 598 1.377725 CAGCTGGGTTGGTGGCTAG 60.378 63.158 5.57 0.00 33.43 3.42
536 599 1.422977 TTCAGCTGGGTTGGTGGCTA 61.423 55.000 15.13 0.00 36.25 3.93
537 600 2.766925 TTCAGCTGGGTTGGTGGCT 61.767 57.895 15.13 0.00 36.25 4.75
538 601 2.203480 TTCAGCTGGGTTGGTGGC 60.203 61.111 15.13 0.00 36.25 5.01
539 602 1.903404 GGTTCAGCTGGGTTGGTGG 60.903 63.158 15.13 0.00 36.25 4.61
540 603 1.152777 TGGTTCAGCTGGGTTGGTG 60.153 57.895 15.13 0.00 36.85 4.17
541 604 1.151450 CTGGTTCAGCTGGGTTGGT 59.849 57.895 15.13 0.00 0.00 3.67
542 605 1.604593 CCTGGTTCAGCTGGGTTGG 60.605 63.158 15.13 6.59 0.00 3.77
543 606 0.607489 CTCCTGGTTCAGCTGGGTTG 60.607 60.000 15.13 0.92 0.00 3.77
544 607 1.062488 ACTCCTGGTTCAGCTGGGTT 61.062 55.000 15.13 0.00 0.00 4.11
545 608 0.178903 TACTCCTGGTTCAGCTGGGT 60.179 55.000 15.13 0.00 0.00 4.51
546 609 0.984230 TTACTCCTGGTTCAGCTGGG 59.016 55.000 15.13 6.75 0.00 4.45
634 699 1.308998 AGCATATACGGCAAGGCAAC 58.691 50.000 1.52 0.00 0.00 4.17
642 707 1.002468 CAAGGTGCAAGCATATACGGC 60.002 52.381 0.00 0.00 36.26 5.68
719 794 2.500098 TCCAGGTGTTACTATCAGTGGC 59.500 50.000 0.00 0.00 0.00 5.01
747 823 1.153647 CGACGTGGCCTTGATGCTA 60.154 57.895 3.32 0.00 0.00 3.49
793 869 3.599343 CATCTTGGAATCTTGGTCACGA 58.401 45.455 0.00 0.00 0.00 4.35
806 882 0.179048 ATCGCAATCCGCATCTTGGA 60.179 50.000 0.00 0.00 42.60 3.53
847 924 1.021202 CAACCCTTTCGTGCAGTTGA 58.979 50.000 6.85 0.00 40.12 3.18
848 925 1.021202 TCAACCCTTTCGTGCAGTTG 58.979 50.000 6.43 6.43 39.28 3.16
850 927 1.238439 CATCAACCCTTTCGTGCAGT 58.762 50.000 0.00 0.00 0.00 4.40
863 940 2.839324 CTTCGCTGCACCGCATCAAC 62.839 60.000 0.00 0.00 38.13 3.18
864 941 2.667874 TTCGCTGCACCGCATCAA 60.668 55.556 0.00 0.00 38.13 2.57
865 942 3.120385 CTTCGCTGCACCGCATCA 61.120 61.111 0.00 0.00 38.13 3.07
871 948 0.874390 TTGATTGTCTTCGCTGCACC 59.126 50.000 0.00 0.00 0.00 5.01
898 975 0.673437 GTAGCTAGGCTCCTGCTGAG 59.327 60.000 16.39 0.00 44.47 3.35
899 976 1.103987 CGTAGCTAGGCTCCTGCTGA 61.104 60.000 16.39 2.59 40.44 4.26
912 989 2.043450 AGCTGAGCCCTCGTAGCT 60.043 61.111 0.00 4.76 45.23 3.32
913 990 2.415426 GAGCTGAGCCCTCGTAGC 59.585 66.667 0.00 0.00 36.45 3.58
914 991 2.718731 CGAGCTGAGCCCTCGTAG 59.281 66.667 0.00 0.00 45.17 3.51
958 1056 2.125269 GGAATGACGGGGACACGG 60.125 66.667 0.00 0.00 38.39 4.94
1394 1680 1.135139 CATCCTCCTACACACACCTCG 59.865 57.143 0.00 0.00 0.00 4.63
1492 1778 5.675684 TCAGGACACACACACACATATAT 57.324 39.130 0.00 0.00 0.00 0.86
1493 1779 5.395214 GGATCAGGACACACACACACATATA 60.395 44.000 0.00 0.00 0.00 0.86
1494 1780 4.507710 GATCAGGACACACACACACATAT 58.492 43.478 0.00 0.00 0.00 1.78
1495 1781 3.306710 GGATCAGGACACACACACACATA 60.307 47.826 0.00 0.00 0.00 2.29
1496 1782 2.550855 GGATCAGGACACACACACACAT 60.551 50.000 0.00 0.00 0.00 3.21
1497 1783 1.202639 GGATCAGGACACACACACACA 60.203 52.381 0.00 0.00 0.00 3.72
1498 1784 1.512926 GGATCAGGACACACACACAC 58.487 55.000 0.00 0.00 0.00 3.82
1501 1787 0.976641 GAGGGATCAGGACACACACA 59.023 55.000 0.00 0.00 0.00 3.72
1504 1790 0.827368 GAGGAGGGATCAGGACACAC 59.173 60.000 0.00 0.00 0.00 3.82
1509 1795 0.719015 AGTTGGAGGAGGGATCAGGA 59.281 55.000 0.00 0.00 0.00 3.86
1565 1864 5.003804 TCAGAAACTACTTTTGATCCAGGC 58.996 41.667 0.00 0.00 0.00 4.85
1601 1900 8.796475 CCCAGTCCCATCTACAATTTTATTATG 58.204 37.037 0.00 0.00 0.00 1.90
1604 1903 6.980577 TCCCAGTCCCATCTACAATTTTATT 58.019 36.000 0.00 0.00 0.00 1.40
1648 1947 5.756918 TCTATGAGCCTGTTGTAGTAGTCT 58.243 41.667 0.00 0.00 0.00 3.24
1716 2032 0.990374 ACCCTGATGCTGAGAGCTTT 59.010 50.000 0.00 0.00 42.97 3.51
1796 2134 5.206587 GGAGGTCATAGTGGTAGAGGTTTA 58.793 45.833 0.00 0.00 0.00 2.01
1827 2165 1.967066 CCTAGGTACTGCTGATGGAGG 59.033 57.143 0.00 0.00 41.52 4.30
1885 2231 2.504367 ACTCTGAAATGTGGAAACGGG 58.496 47.619 0.00 0.00 0.00 5.28
1887 2233 4.811555 TCAACTCTGAAATGTGGAAACG 57.188 40.909 0.00 0.00 0.00 3.60
1941 2314 0.800683 GCAAACGCGCCCCTTTTATC 60.801 55.000 5.73 0.00 0.00 1.75
2108 2481 0.541063 TGTACGGCTCAGTCCTGGAA 60.541 55.000 0.00 0.00 0.00 3.53
2203 2576 8.296713 GCATTCAAGTGAAAAATGACTTAGGTA 58.703 33.333 0.00 0.00 37.61 3.08
2204 2577 7.147976 GCATTCAAGTGAAAAATGACTTAGGT 58.852 34.615 0.00 0.00 37.61 3.08
2205 2578 6.587608 GGCATTCAAGTGAAAAATGACTTAGG 59.412 38.462 0.00 0.00 35.86 2.69
2206 2579 6.587608 GGGCATTCAAGTGAAAAATGACTTAG 59.412 38.462 0.00 0.00 38.28 2.18
2207 2580 6.041409 TGGGCATTCAAGTGAAAAATGACTTA 59.959 34.615 0.00 0.00 38.28 2.24
2253 2636 2.851195 ACACAGTTCACATTCACTCCC 58.149 47.619 0.00 0.00 0.00 4.30
2428 2832 7.233348 ACTTCTGAAGCAAAATTTTATCCTGGA 59.767 33.333 17.00 0.00 0.00 3.86
2522 2929 8.763601 GTCAAGGAACCTGCTAGGATAATATAT 58.236 37.037 8.91 0.00 37.67 0.86
2524 2931 6.013293 GGTCAAGGAACCTGCTAGGATAATAT 60.013 42.308 8.91 0.00 37.67 1.28
2528 2935 3.039011 GGTCAAGGAACCTGCTAGGATA 58.961 50.000 8.91 0.00 37.67 2.59
2534 2944 1.142688 ATGGGGTCAAGGAACCTGCT 61.143 55.000 0.00 0.00 39.79 4.24
2618 3028 0.836400 ACCATCCTGGACTCGTTGGT 60.836 55.000 12.15 12.15 40.96 3.67
2621 3031 1.348064 TTCACCATCCTGGACTCGTT 58.652 50.000 0.00 0.00 40.96 3.85
2698 3108 2.971598 CGTCAGGTTCCATGCCCCT 61.972 63.158 0.00 0.00 0.00 4.79
2793 3206 7.937942 AGGATCTGAGAATGTGAAGAAATATGG 59.062 37.037 0.00 0.00 0.00 2.74
2798 3216 6.364568 TGAGGATCTGAGAATGTGAAGAAA 57.635 37.500 0.00 0.00 34.92 2.52
2799 3217 6.155737 TCATGAGGATCTGAGAATGTGAAGAA 59.844 38.462 0.00 0.00 34.92 2.52
2904 3324 7.025520 ACGGAGTACTACAGTATACCCATAT 57.974 40.000 5.80 0.00 41.94 1.78
2931 3351 0.174617 GAGGCTCTGCACTACTCCAC 59.825 60.000 7.40 0.00 0.00 4.02
2989 3413 1.192146 AGCCAGTCGGAGTTTGCCTA 61.192 55.000 1.54 0.00 0.00 3.93
3039 3463 8.765219 CCATATCTTTCTTTAACATAGGTCACG 58.235 37.037 0.00 0.00 0.00 4.35
3101 3527 7.099266 AGAGACAGTTATCAGTTGAGATCAG 57.901 40.000 0.00 0.00 0.00 2.90
3188 3620 5.163269 TGGTCCATTCCTGTCAGATCATAAG 60.163 44.000 0.00 0.00 0.00 1.73
3264 3705 6.073657 GCTCGGTTATGTAGTCTCTGTAGTAG 60.074 46.154 0.00 0.00 0.00 2.57
3333 3774 0.601046 TGTCAAGCAGAGACCAAGCG 60.601 55.000 0.00 0.00 35.15 4.68
3395 3836 6.471233 TCAGAGTATTGAAGTCCACATAGG 57.529 41.667 0.00 0.00 39.47 2.57
3465 3906 3.306472 TCCTAGCTCCTCTTCTTCTCC 57.694 52.381 0.00 0.00 0.00 3.71
3501 3944 4.713792 AGTTGAAACAACTGATCCTCCT 57.286 40.909 14.90 0.00 0.00 3.69
3635 4096 4.406456 ACATGTCTTTGCTTCCCATTGTA 58.594 39.130 0.00 0.00 0.00 2.41
3636 4097 3.233507 ACATGTCTTTGCTTCCCATTGT 58.766 40.909 0.00 0.00 0.00 2.71
3637 4098 3.508793 AGACATGTCTTTGCTTCCCATTG 59.491 43.478 22.89 0.00 36.31 2.82
3774 4239 1.077930 CCTCTGTGAGGCCATGTGG 60.078 63.158 5.01 0.00 43.29 4.17
3805 4270 5.007682 GGGTAGTGGTTTGCAGAGAATTTA 58.992 41.667 0.00 0.00 0.00 1.40
3806 4271 3.826729 GGGTAGTGGTTTGCAGAGAATTT 59.173 43.478 0.00 0.00 0.00 1.82
3812 4277 1.122632 TCGGGGTAGTGGTTTGCAGA 61.123 55.000 0.00 0.00 0.00 4.26
3823 4292 3.611766 ATGAGTTCAGTTTCGGGGTAG 57.388 47.619 0.00 0.00 0.00 3.18
3963 4432 8.561536 TGGATAGAAAGGTAAATGGATAGTCA 57.438 34.615 0.00 0.00 0.00 3.41
3977 4446 5.124617 GGTGAAAAGCTCTTGGATAGAAAGG 59.875 44.000 0.00 0.00 30.91 3.11
4040 4509 5.639506 CGCAGATAACAAATGTAGGATAGGG 59.360 44.000 0.00 0.00 0.00 3.53
4050 4519 1.949525 CCTCCCCGCAGATAACAAATG 59.050 52.381 0.00 0.00 0.00 2.32
4153 4622 8.432805 GCAAGGAGTTGGCACCTATATATATAT 58.567 37.037 10.10 10.10 34.53 0.86
4154 4623 7.623677 AGCAAGGAGTTGGCACCTATATATATA 59.376 37.037 2.49 2.49 34.53 0.86
4276 4748 3.356529 AACTTAGCTGCATGCCTACTT 57.643 42.857 16.68 1.83 44.23 2.24
4281 4753 3.274288 ACTTCTAACTTAGCTGCATGCC 58.726 45.455 16.68 0.00 44.23 4.40
4340 4813 5.147330 TGTCTGACGATCAACTTGGTAAT 57.853 39.130 2.98 0.00 0.00 1.89
4341 4814 4.594123 TGTCTGACGATCAACTTGGTAA 57.406 40.909 2.98 0.00 0.00 2.85
4385 4858 3.450817 CCATTAATTGAACCCTGAACCCC 59.549 47.826 0.00 0.00 0.00 4.95
4424 4897 1.131638 TCCACTCACAGCCTCAGTTT 58.868 50.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.