Multiple sequence alignment - TraesCS7D01G398900

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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 TraesCS7D01G398900 chr7D 100.000 3757 0 0 1 3757 515222770 515219014 0.000000e+00 6938.0
1 TraesCS7D01G398900 chr7D 99.202 3758 29 1 1 3757 515238976 515235219 0.000000e+00 6772.0
2 TraesCS7D01G398900 chr7D 97.282 1030 19 4 619 1643 514091991 514093016 0.000000e+00 1738.0
3 TraesCS7D01G398900 chr7D 97.409 965 23 1 1948 2910 514093015 514093979 0.000000e+00 1642.0
4 TraesCS7D01G398900 chr7D 95.289 849 34 5 771 1615 513311733 513312579 0.000000e+00 1341.0
5 TraesCS7D01G398900 chr7D 94.340 795 38 3 1970 2757 513312637 513313431 0.000000e+00 1212.0
6 TraesCS7D01G398900 chr7D 94.702 755 32 3 3004 3757 514093978 514094725 0.000000e+00 1166.0
7 TraesCS7D01G398900 chr7D 94.705 491 24 2 3130 3619 568402838 568402349 0.000000e+00 761.0
8 TraesCS7D01G398900 chr7D 94.837 368 14 4 252 616 514090472 514090837 1.510000e-158 569.0
9 TraesCS7D01G398900 chr7D 96.805 313 10 0 1638 1950 617014211 617013899 1.200000e-144 523.0
10 TraesCS7D01G398900 chr7D 78.886 341 28 14 575 872 513310135 513310474 1.380000e-44 191.0
11 TraesCS7D01G398900 chr7D 92.233 103 8 0 3655 3757 568402353 568402251 3.020000e-31 147.0
12 TraesCS7D01G398900 chr7A 92.935 1189 53 16 480 1643 586694210 586693028 0.000000e+00 1701.0
13 TraesCS7D01G398900 chr7A 96.580 965 31 1 1948 2910 587519139 587520103 0.000000e+00 1598.0
14 TraesCS7D01G398900 chr7A 96.491 969 28 3 1948 2910 588739772 588738804 0.000000e+00 1596.0
15 TraesCS7D01G398900 chr7A 93.827 891 37 6 771 1643 588740661 588739771 0.000000e+00 1325.0
16 TraesCS7D01G398900 chr7A 95.802 810 30 1 1948 2757 586693029 586692224 0.000000e+00 1304.0
17 TraesCS7D01G398900 chr7A 96.667 660 22 0 984 1643 587518481 587519140 0.000000e+00 1098.0
18 TraesCS7D01G398900 chr7A 89.217 779 40 23 252 994 588751310 588750540 0.000000e+00 933.0
19 TraesCS7D01G398900 chr7A 96.644 447 13 2 3228 3674 588725072 588724628 0.000000e+00 741.0
20 TraesCS7D01G398900 chr7A 92.039 515 27 13 252 760 587517830 587518336 0.000000e+00 712.0
21 TraesCS7D01G398900 chr7A 91.453 234 19 1 3004 3236 588738805 588738572 1.680000e-83 320.0
22 TraesCS7D01G398900 chr7A 91.064 235 19 2 3004 3236 587520102 587520336 2.180000e-82 316.0
23 TraesCS7D01G398900 chr7A 90.000 240 13 9 241 477 588740848 588740617 2.190000e-77 300.0
24 TraesCS7D01G398900 chr7A 95.050 101 5 0 3657 3757 588724605 588724505 3.880000e-35 159.0
25 TraesCS7D01G398900 chr7B 94.701 1038 27 6 605 1615 544981824 544982860 0.000000e+00 1587.0
26 TraesCS7D01G398900 chr7B 95.360 862 21 3 772 1615 545975504 545974644 0.000000e+00 1352.0
27 TraesCS7D01G398900 chr7B 93.981 864 30 6 771 1615 544880922 544881782 0.000000e+00 1288.0
28 TraesCS7D01G398900 chr7B 95.878 752 31 0 1998 2749 544881877 544882628 0.000000e+00 1218.0
29 TraesCS7D01G398900 chr7B 95.878 752 31 0 1998 2749 545974549 545973798 0.000000e+00 1218.0
30 TraesCS7D01G398900 chr7B 95.479 752 34 0 1998 2749 544982955 544983706 0.000000e+00 1201.0
31 TraesCS7D01G398900 chr7B 94.070 371 16 5 252 620 544966589 544966955 3.280000e-155 558.0
32 TraesCS7D01G398900 chr7B 93.458 107 5 2 2909 3014 217312359 217312254 1.400000e-34 158.0
33 TraesCS7D01G398900 chr2D 93.548 496 29 3 3126 3619 100433590 100434084 0.000000e+00 736.0
34 TraesCS7D01G398900 chr2D 93.137 102 7 0 3655 3756 100434080 100434181 2.340000e-32 150.0
35 TraesCS7D01G398900 chr2D 100.000 30 0 0 2867 2896 22419407 22419436 5.240000e-04 56.5
36 TraesCS7D01G398900 chr2D 100.000 30 0 0 2867 2896 409603292 409603263 5.240000e-04 56.5
37 TraesCS7D01G398900 chr6D 92.926 311 19 2 1639 1949 166773130 166773437 2.060000e-122 449.0
38 TraesCS7D01G398900 chr3D 92.063 315 21 2 1636 1949 479746392 479746703 1.240000e-119 440.0
39 TraesCS7D01G398900 chr3D 94.231 104 6 0 2905 3008 290583919 290583816 3.880000e-35 159.0
40 TraesCS7D01G398900 chr1D 91.883 308 22 1 1642 1949 108335704 108335400 9.640000e-116 427.0
41 TraesCS7D01G398900 chr1D 91.290 310 20 5 1642 1950 236959415 236959112 2.090000e-112 416.0
42 TraesCS7D01G398900 chr1D 89.916 119 12 0 2906 3024 433922672 433922790 1.810000e-33 154.0
43 TraesCS7D01G398900 chr2B 91.586 309 22 2 1642 1950 92098595 92098899 1.250000e-114 424.0
44 TraesCS7D01G398900 chr2B 95.000 100 5 0 2907 3006 575876524 575876623 1.400000e-34 158.0
45 TraesCS7D01G398900 chr1A 90.402 323 26 4 1632 1954 15730346 15730029 1.610000e-113 420.0
46 TraesCS7D01G398900 chr6B 90.536 317 26 2 1635 1950 182454032 182453719 2.090000e-112 416.0
47 TraesCS7D01G398900 chr5B 93.396 106 7 0 2903 3008 685439361 685439256 1.400000e-34 158.0
48 TraesCS7D01G398900 chr5B 92.035 113 6 3 2893 3005 591582607 591582716 5.020000e-34 156.0
49 TraesCS7D01G398900 chr2A 94.175 103 4 2 2904 3005 603084637 603084738 5.020000e-34 156.0
50 TraesCS7D01G398900 chr1B 94.898 98 5 0 2908 3005 48923734 48923637 1.810000e-33 154.0
51 TraesCS7D01G398900 chr5D 94.595 37 1 1 2867 2902 71892769 71892805 5.240000e-04 56.5
52 TraesCS7D01G398900 chr5D 100.000 30 0 0 2867 2896 278311338 278311367 5.240000e-04 56.5
53 TraesCS7D01G398900 chr5A 100.000 30 0 0 2867 2896 620406404 620406433 5.240000e-04 56.5


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 TraesCS7D01G398900 chr7D 515219014 515222770 3756 True 6938.000000 6938 100.00000 1 3757 1 chr7D.!!$R1 3756
1 TraesCS7D01G398900 chr7D 515235219 515238976 3757 True 6772.000000 6772 99.20200 1 3757 1 chr7D.!!$R2 3756
2 TraesCS7D01G398900 chr7D 514090472 514094725 4253 False 1278.750000 1738 96.05750 252 3757 4 chr7D.!!$F2 3505
3 TraesCS7D01G398900 chr7D 513310135 513313431 3296 False 914.666667 1341 89.50500 575 2757 3 chr7D.!!$F1 2182
4 TraesCS7D01G398900 chr7D 568402251 568402838 587 True 454.000000 761 93.46900 3130 3757 2 chr7D.!!$R4 627
5 TraesCS7D01G398900 chr7A 586692224 586694210 1986 True 1502.500000 1701 94.36850 480 2757 2 chr7A.!!$R2 2277
6 TraesCS7D01G398900 chr7A 588750540 588751310 770 True 933.000000 933 89.21700 252 994 1 chr7A.!!$R1 742
7 TraesCS7D01G398900 chr7A 587517830 587520336 2506 False 931.000000 1598 94.08750 252 3236 4 chr7A.!!$F1 2984
8 TraesCS7D01G398900 chr7A 588738572 588740848 2276 True 885.250000 1596 92.94275 241 3236 4 chr7A.!!$R4 2995
9 TraesCS7D01G398900 chr7A 588724505 588725072 567 True 450.000000 741 95.84700 3228 3757 2 chr7A.!!$R3 529
10 TraesCS7D01G398900 chr7B 544981824 544983706 1882 False 1394.000000 1587 95.09000 605 2749 2 chr7B.!!$F3 2144
11 TraesCS7D01G398900 chr7B 545973798 545975504 1706 True 1285.000000 1352 95.61900 772 2749 2 chr7B.!!$R2 1977
12 TraesCS7D01G398900 chr7B 544880922 544882628 1706 False 1253.000000 1288 94.92950 771 2749 2 chr7B.!!$F2 1978
13 TraesCS7D01G398900 chr2D 100433590 100434181 591 False 443.000000 736 93.34250 3126 3756 2 chr2D.!!$F2 630

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
559 566 3.978855 ACGCGATGAACCTTTTTAAAAGC 59.021 39.130 15.93 0.02 0.0 3.51 F
2114 4203 2.029964 GGCGTGACCGTCAAGGAA 59.970 61.111 15.08 0.00 45.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 4446 2.752358 CTGGAGCCCTTGAGCACA 59.248 61.111 0.00 0.0 34.23 4.57 R
3035 5219 3.417645 CGCGCTAAAGAAAACTCACAAAC 59.582 43.478 5.56 0.0 0.00 2.93 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
478 485 8.079809 AGTAAAAGTGATCCAAAAATAACCACG 58.920 33.333 0.00 0.00 0.00 4.94
479 486 6.642707 AAAGTGATCCAAAAATAACCACGA 57.357 33.333 0.00 0.00 0.00 4.35
480 487 6.642707 AAGTGATCCAAAAATAACCACGAA 57.357 33.333 0.00 0.00 0.00 3.85
481 488 6.834168 AGTGATCCAAAAATAACCACGAAT 57.166 33.333 0.00 0.00 0.00 3.34
483 490 7.758495 AGTGATCCAAAAATAACCACGAATAC 58.242 34.615 0.00 0.00 0.00 1.89
487 494 6.005198 TCCAAAAATAACCACGAATACCTGT 58.995 36.000 0.00 0.00 0.00 4.00
489 496 6.072397 CCAAAAATAACCACGAATACCTGTGA 60.072 38.462 0.00 0.00 38.36 3.58
490 497 7.364200 CAAAAATAACCACGAATACCTGTGAA 58.636 34.615 0.00 0.00 38.36 3.18
495 502 6.677781 AACCACGAATACCTGTGAATATTG 57.322 37.500 0.00 0.00 38.36 1.90
496 503 5.984725 ACCACGAATACCTGTGAATATTGA 58.015 37.500 0.00 0.00 38.36 2.57
497 504 6.591935 ACCACGAATACCTGTGAATATTGAT 58.408 36.000 0.00 0.00 38.36 2.57
498 505 7.732025 ACCACGAATACCTGTGAATATTGATA 58.268 34.615 0.00 0.00 38.36 2.15
499 506 8.208224 ACCACGAATACCTGTGAATATTGATAA 58.792 33.333 0.00 0.00 38.36 1.75
541 548 8.482437 TTGTATGCACAATATTAAAATACGCG 57.518 30.769 3.53 3.53 39.75 6.01
543 550 8.499967 TGTATGCACAATATTAAAATACGCGAT 58.500 29.630 15.93 0.00 0.00 4.58
544 551 7.780253 ATGCACAATATTAAAATACGCGATG 57.220 32.000 15.93 0.00 0.00 3.84
545 552 6.949449 TGCACAATATTAAAATACGCGATGA 58.051 32.000 15.93 0.00 0.00 2.92
546 553 7.410485 TGCACAATATTAAAATACGCGATGAA 58.590 30.769 15.93 0.00 0.00 2.57
547 554 7.374754 TGCACAATATTAAAATACGCGATGAAC 59.625 33.333 15.93 0.00 0.00 3.18
548 555 7.149192 GCACAATATTAAAATACGCGATGAACC 60.149 37.037 15.93 0.00 0.00 3.62
549 556 8.067784 CACAATATTAAAATACGCGATGAACCT 58.932 33.333 15.93 0.00 0.00 3.50
551 558 9.445786 CAATATTAAAATACGCGATGAACCTTT 57.554 29.630 15.93 4.81 0.00 3.11
555 562 9.843334 ATTAAAATACGCGATGAACCTTTTTAA 57.157 25.926 15.93 15.16 34.03 1.52
556 563 9.674824 TTAAAATACGCGATGAACCTTTTTAAA 57.325 25.926 15.93 0.00 29.37 1.52
557 564 8.576936 AAAATACGCGATGAACCTTTTTAAAA 57.423 26.923 15.93 0.00 0.00 1.52
558 565 7.790861 AATACGCGATGAACCTTTTTAAAAG 57.209 32.000 15.93 10.23 0.00 2.27
559 566 3.978855 ACGCGATGAACCTTTTTAAAAGC 59.021 39.130 15.93 0.02 0.00 3.51
561 568 4.143618 CGCGATGAACCTTTTTAAAAGCAC 60.144 41.667 11.59 6.02 0.00 4.40
562 569 4.742659 GCGATGAACCTTTTTAAAAGCACA 59.257 37.500 11.59 10.64 0.00 4.57
563 570 5.233263 GCGATGAACCTTTTTAAAAGCACAA 59.767 36.000 11.59 0.00 0.00 3.33
564 571 6.636443 CGATGAACCTTTTTAAAAGCACAAC 58.364 36.000 11.59 8.62 0.00 3.32
565 572 6.254589 CGATGAACCTTTTTAAAAGCACAACA 59.745 34.615 11.59 7.43 0.00 3.33
566 573 6.959671 TGAACCTTTTTAAAAGCACAACAG 57.040 33.333 11.59 0.00 0.00 3.16
567 574 5.350091 TGAACCTTTTTAAAAGCACAACAGC 59.650 36.000 11.59 0.00 0.00 4.40
568 575 4.826556 ACCTTTTTAAAAGCACAACAGCA 58.173 34.783 11.59 0.00 36.85 4.41
569 576 5.241662 ACCTTTTTAAAAGCACAACAGCAA 58.758 33.333 11.59 0.00 36.85 3.91
571 578 6.205658 ACCTTTTTAAAAGCACAACAGCAAAA 59.794 30.769 11.59 0.00 36.85 2.44
572 579 7.080724 CCTTTTTAAAAGCACAACAGCAAAAA 58.919 30.769 11.59 0.00 36.85 1.94
574 581 9.766277 CTTTTTAAAAGCACAACAGCAAAAATA 57.234 25.926 4.42 0.00 36.85 1.40
577 584 9.713740 TTTAAAAGCACAACAGCAAAAATATTG 57.286 25.926 0.00 0.00 36.85 1.90
578 585 6.923928 AAAGCACAACAGCAAAAATATTGT 57.076 29.167 0.00 0.00 36.85 2.71
1702 3778 9.990360 CAAATTACAGGTACCAAGGTAAAATTT 57.010 29.630 20.60 16.77 31.86 1.82
2114 4203 2.029964 GGCGTGACCGTCAAGGAA 59.970 61.111 15.08 0.00 45.00 3.36
2357 4446 2.755650 GACATCACCGTCAAGAACTGT 58.244 47.619 0.00 0.00 35.88 3.55
2768 4857 2.096496 CGCGGCATGATTTCTTTTCTCT 59.904 45.455 0.00 0.00 0.00 3.10
2911 5000 8.759481 TGAGAATTAGTCATCTCACATCTACT 57.241 34.615 1.55 0.00 45.27 2.57
2912 5001 8.845227 TGAGAATTAGTCATCTCACATCTACTC 58.155 37.037 1.55 0.00 45.27 2.59
2913 5002 8.177119 AGAATTAGTCATCTCACATCTACTCC 57.823 38.462 0.00 0.00 0.00 3.85
2914 5003 6.909550 ATTAGTCATCTCACATCTACTCCC 57.090 41.667 0.00 0.00 0.00 4.30
2915 5004 4.534647 AGTCATCTCACATCTACTCCCT 57.465 45.455 0.00 0.00 0.00 4.20
2916 5005 4.469657 AGTCATCTCACATCTACTCCCTC 58.530 47.826 0.00 0.00 0.00 4.30
2917 5006 3.572255 GTCATCTCACATCTACTCCCTCC 59.428 52.174 0.00 0.00 0.00 4.30
2918 5007 2.350057 TCTCACATCTACTCCCTCCG 57.650 55.000 0.00 0.00 0.00 4.63
2919 5008 1.564818 TCTCACATCTACTCCCTCCGT 59.435 52.381 0.00 0.00 0.00 4.69
2920 5009 2.025226 TCTCACATCTACTCCCTCCGTT 60.025 50.000 0.00 0.00 0.00 4.44
2921 5010 2.359531 CTCACATCTACTCCCTCCGTTC 59.640 54.545 0.00 0.00 0.00 3.95
2922 5011 1.409427 CACATCTACTCCCTCCGTTCC 59.591 57.143 0.00 0.00 0.00 3.62
2923 5012 1.006758 ACATCTACTCCCTCCGTTCCA 59.993 52.381 0.00 0.00 0.00 3.53
2924 5013 2.320781 CATCTACTCCCTCCGTTCCAT 58.679 52.381 0.00 0.00 0.00 3.41
2925 5014 3.117246 ACATCTACTCCCTCCGTTCCATA 60.117 47.826 0.00 0.00 0.00 2.74
2926 5015 3.675348 TCTACTCCCTCCGTTCCATAA 57.325 47.619 0.00 0.00 0.00 1.90
2927 5016 4.194678 TCTACTCCCTCCGTTCCATAAT 57.805 45.455 0.00 0.00 0.00 1.28
2928 5017 5.329191 TCTACTCCCTCCGTTCCATAATA 57.671 43.478 0.00 0.00 0.00 0.98
2929 5018 5.322754 TCTACTCCCTCCGTTCCATAATAG 58.677 45.833 0.00 0.00 0.00 1.73
2930 5019 4.194678 ACTCCCTCCGTTCCATAATAGA 57.805 45.455 0.00 0.00 0.00 1.98
2931 5020 4.753186 ACTCCCTCCGTTCCATAATAGAT 58.247 43.478 0.00 0.00 0.00 1.98
2932 5021 4.528596 ACTCCCTCCGTTCCATAATAGATG 59.471 45.833 0.00 0.00 0.00 2.90
2933 5022 4.747583 TCCCTCCGTTCCATAATAGATGA 58.252 43.478 0.00 0.00 0.00 2.92
2934 5023 4.527038 TCCCTCCGTTCCATAATAGATGAC 59.473 45.833 0.00 0.00 0.00 3.06
2935 5024 4.528596 CCCTCCGTTCCATAATAGATGACT 59.471 45.833 0.00 0.00 0.00 3.41
2936 5025 5.336849 CCCTCCGTTCCATAATAGATGACTC 60.337 48.000 0.00 0.00 0.00 3.36
2937 5026 5.243954 CCTCCGTTCCATAATAGATGACTCA 59.756 44.000 0.00 0.00 0.00 3.41
2938 5027 6.239317 CCTCCGTTCCATAATAGATGACTCAA 60.239 42.308 0.00 0.00 0.00 3.02
2939 5028 6.513180 TCCGTTCCATAATAGATGACTCAAC 58.487 40.000 0.00 0.00 0.00 3.18
2940 5029 6.323996 TCCGTTCCATAATAGATGACTCAACT 59.676 38.462 0.00 0.00 0.00 3.16
2941 5030 6.986817 CCGTTCCATAATAGATGACTCAACTT 59.013 38.462 0.00 0.00 0.00 2.66
2942 5031 7.495934 CCGTTCCATAATAGATGACTCAACTTT 59.504 37.037 0.00 0.00 0.00 2.66
2943 5032 9.529325 CGTTCCATAATAGATGACTCAACTTTA 57.471 33.333 0.00 0.00 0.00 1.85
2979 5068 8.756486 AATACAAAGTTAGTACAAAGTTGGGT 57.244 30.769 0.00 0.00 0.00 4.51
2980 5069 6.688637 ACAAAGTTAGTACAAAGTTGGGTC 57.311 37.500 0.00 0.00 0.00 4.46
2981 5070 6.181908 ACAAAGTTAGTACAAAGTTGGGTCA 58.818 36.000 0.00 0.00 0.00 4.02
2982 5071 6.831868 ACAAAGTTAGTACAAAGTTGGGTCAT 59.168 34.615 0.00 0.00 0.00 3.06
2983 5072 7.340999 ACAAAGTTAGTACAAAGTTGGGTCATT 59.659 33.333 0.00 0.00 0.00 2.57
2984 5073 7.891498 AAGTTAGTACAAAGTTGGGTCATTT 57.109 32.000 0.00 0.00 0.00 2.32
2985 5074 8.983702 AAGTTAGTACAAAGTTGGGTCATTTA 57.016 30.769 0.00 0.00 0.00 1.40
2986 5075 9.582648 AAGTTAGTACAAAGTTGGGTCATTTAT 57.417 29.630 0.00 0.00 0.00 1.40
2987 5076 9.582648 AGTTAGTACAAAGTTGGGTCATTTATT 57.417 29.630 0.00 0.00 0.00 1.40
2994 5083 9.758651 ACAAAGTTGGGTCATTTATTTTAGAAC 57.241 29.630 0.00 0.00 0.00 3.01
2995 5084 8.911662 CAAAGTTGGGTCATTTATTTTAGAACG 58.088 33.333 0.00 0.00 0.00 3.95
2996 5085 7.153217 AGTTGGGTCATTTATTTTAGAACGG 57.847 36.000 0.00 0.00 0.00 4.44
2997 5086 6.943718 AGTTGGGTCATTTATTTTAGAACGGA 59.056 34.615 0.00 0.00 0.00 4.69
2998 5087 6.995511 TGGGTCATTTATTTTAGAACGGAG 57.004 37.500 0.00 0.00 0.00 4.63
2999 5088 5.883673 TGGGTCATTTATTTTAGAACGGAGG 59.116 40.000 0.00 0.00 0.00 4.30
3000 5089 5.298527 GGGTCATTTATTTTAGAACGGAGGG 59.701 44.000 0.00 0.00 0.00 4.30
3001 5090 6.117488 GGTCATTTATTTTAGAACGGAGGGA 58.883 40.000 0.00 0.00 0.00 4.20
3002 5091 6.260271 GGTCATTTATTTTAGAACGGAGGGAG 59.740 42.308 0.00 0.00 0.00 4.30
3008 5192 8.593945 TTATTTTAGAACGGAGGGAGTAACTA 57.406 34.615 0.00 0.00 0.00 2.24
3362 5549 1.961394 GCATTCATGGTGATGGAGCAT 59.039 47.619 0.00 0.00 43.85 3.79
3513 5700 3.805971 AGTACAGTGCAGTTAAAACGACC 59.194 43.478 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
518 525 8.775884 CATCGCGTATTTTAATATTGTGCATAC 58.224 33.333 5.77 0.00 0.00 2.39
520 527 7.580600 TCATCGCGTATTTTAATATTGTGCAT 58.419 30.769 5.77 0.00 0.00 3.96
521 528 6.949449 TCATCGCGTATTTTAATATTGTGCA 58.051 32.000 5.77 0.00 0.00 4.57
522 529 7.149192 GGTTCATCGCGTATTTTAATATTGTGC 60.149 37.037 5.77 0.00 0.00 4.57
523 530 8.067784 AGGTTCATCGCGTATTTTAATATTGTG 58.932 33.333 5.77 0.00 0.00 3.33
524 531 8.149973 AGGTTCATCGCGTATTTTAATATTGT 57.850 30.769 5.77 0.00 0.00 2.71
525 532 9.445786 AAAGGTTCATCGCGTATTTTAATATTG 57.554 29.630 5.77 0.00 0.00 1.90
529 536 9.843334 TTAAAAAGGTTCATCGCGTATTTTAAT 57.157 25.926 5.77 0.00 30.44 1.40
530 537 9.674824 TTTAAAAAGGTTCATCGCGTATTTTAA 57.325 25.926 5.77 10.32 32.36 1.52
531 538 9.674824 TTTTAAAAAGGTTCATCGCGTATTTTA 57.325 25.926 5.77 5.28 0.00 1.52
532 539 8.576936 TTTTAAAAAGGTTCATCGCGTATTTT 57.423 26.923 5.77 6.16 0.00 1.82
533 540 7.148869 GCTTTTAAAAAGGTTCATCGCGTATTT 60.149 33.333 5.77 0.00 0.00 1.40
534 541 6.307077 GCTTTTAAAAAGGTTCATCGCGTATT 59.693 34.615 5.77 0.00 0.00 1.89
535 542 5.798434 GCTTTTAAAAAGGTTCATCGCGTAT 59.202 36.000 5.77 0.00 0.00 3.06
537 544 3.978855 GCTTTTAAAAAGGTTCATCGCGT 59.021 39.130 5.77 0.00 0.00 6.01
538 545 3.978217 TGCTTTTAAAAAGGTTCATCGCG 59.022 39.130 0.00 0.00 0.00 5.87
539 546 4.742659 TGTGCTTTTAAAAAGGTTCATCGC 59.257 37.500 1.66 0.00 0.00 4.58
540 547 6.254589 TGTTGTGCTTTTAAAAAGGTTCATCG 59.745 34.615 1.66 0.00 0.00 3.84
541 548 7.532682 TGTTGTGCTTTTAAAAAGGTTCATC 57.467 32.000 1.66 3.20 0.00 2.92
543 550 5.350091 GCTGTTGTGCTTTTAAAAAGGTTCA 59.650 36.000 1.66 0.58 0.00 3.18
544 551 5.350091 TGCTGTTGTGCTTTTAAAAAGGTTC 59.650 36.000 1.66 0.00 0.00 3.62
545 552 5.241662 TGCTGTTGTGCTTTTAAAAAGGTT 58.758 33.333 1.66 0.00 0.00 3.50
546 553 4.826556 TGCTGTTGTGCTTTTAAAAAGGT 58.173 34.783 1.66 0.00 0.00 3.50
547 554 5.793026 TTGCTGTTGTGCTTTTAAAAAGG 57.207 34.783 1.66 0.00 0.00 3.11
548 555 8.672214 ATTTTTGCTGTTGTGCTTTTAAAAAG 57.328 26.923 1.66 0.00 32.08 2.27
551 558 9.713740 CAATATTTTTGCTGTTGTGCTTTTAAA 57.286 25.926 0.00 0.00 0.00 1.52
553 560 8.430801 ACAATATTTTTGCTGTTGTGCTTTTA 57.569 26.923 0.00 0.00 32.30 1.52
554 561 7.319142 ACAATATTTTTGCTGTTGTGCTTTT 57.681 28.000 0.00 0.00 32.30 2.27
555 562 6.018016 GGACAATATTTTTGCTGTTGTGCTTT 60.018 34.615 0.00 0.00 37.88 3.51
556 563 5.466393 GGACAATATTTTTGCTGTTGTGCTT 59.534 36.000 0.00 0.00 37.88 3.91
557 564 4.990426 GGACAATATTTTTGCTGTTGTGCT 59.010 37.500 0.00 0.00 37.88 4.40
558 565 4.990426 AGGACAATATTTTTGCTGTTGTGC 59.010 37.500 0.00 0.00 40.14 4.57
559 566 7.481275 AAAGGACAATATTTTTGCTGTTGTG 57.519 32.000 0.00 0.00 33.55 3.33
1021 3047 2.411904 CAGGAGCAACAAGACTCTCAC 58.588 52.381 0.00 0.00 33.29 3.51
1702 3778 6.528537 AGTTGGCTTGTCAATTATGCATTA 57.471 33.333 3.54 0.00 0.00 1.90
2114 4203 4.681978 GGCGCGGTCACCTTCACT 62.682 66.667 8.83 0.00 0.00 3.41
2357 4446 2.752358 CTGGAGCCCTTGAGCACA 59.248 61.111 0.00 0.00 34.23 4.57
2546 4635 4.405196 TGTTTTTGAACGAAACGTCCTTC 58.595 39.130 0.00 0.00 39.99 3.46
2768 4857 3.936453 GCACTTGGTACATCCGAAATACA 59.064 43.478 0.00 0.00 39.30 2.29
2908 4997 5.329191 TCTATTATGGAACGGAGGGAGTA 57.671 43.478 0.00 0.00 0.00 2.59
2909 4998 4.194678 TCTATTATGGAACGGAGGGAGT 57.805 45.455 0.00 0.00 0.00 3.85
2910 4999 4.772624 TCATCTATTATGGAACGGAGGGAG 59.227 45.833 0.00 0.00 0.00 4.30
2911 5000 4.527038 GTCATCTATTATGGAACGGAGGGA 59.473 45.833 0.00 0.00 0.00 4.20
2912 5001 4.528596 AGTCATCTATTATGGAACGGAGGG 59.471 45.833 0.00 0.00 0.00 4.30
2913 5002 5.243954 TGAGTCATCTATTATGGAACGGAGG 59.756 44.000 0.00 0.00 0.00 4.30
2914 5003 6.332735 TGAGTCATCTATTATGGAACGGAG 57.667 41.667 0.00 0.00 0.00 4.63
2915 5004 6.323996 AGTTGAGTCATCTATTATGGAACGGA 59.676 38.462 1.70 0.00 0.00 4.69
2916 5005 6.516718 AGTTGAGTCATCTATTATGGAACGG 58.483 40.000 1.70 0.00 0.00 4.44
2917 5006 8.425577 AAAGTTGAGTCATCTATTATGGAACG 57.574 34.615 4.14 0.00 0.00 3.95
2953 5042 9.850198 ACCCAACTTTGTACTAACTTTGTATTA 57.150 29.630 0.00 0.00 0.00 0.98
2954 5043 8.756486 ACCCAACTTTGTACTAACTTTGTATT 57.244 30.769 0.00 0.00 0.00 1.89
2955 5044 7.994334 TGACCCAACTTTGTACTAACTTTGTAT 59.006 33.333 0.00 0.00 0.00 2.29
2956 5045 7.337167 TGACCCAACTTTGTACTAACTTTGTA 58.663 34.615 0.00 0.00 0.00 2.41
2957 5046 6.181908 TGACCCAACTTTGTACTAACTTTGT 58.818 36.000 0.00 0.00 0.00 2.83
2958 5047 6.687081 TGACCCAACTTTGTACTAACTTTG 57.313 37.500 0.00 0.00 0.00 2.77
2959 5048 7.891498 AATGACCCAACTTTGTACTAACTTT 57.109 32.000 0.00 0.00 0.00 2.66
2960 5049 7.891498 AAATGACCCAACTTTGTACTAACTT 57.109 32.000 0.00 0.00 0.00 2.66
2961 5050 9.582648 AATAAATGACCCAACTTTGTACTAACT 57.417 29.630 0.00 0.00 0.00 2.24
2968 5057 9.758651 GTTCTAAAATAAATGACCCAACTTTGT 57.241 29.630 0.00 0.00 0.00 2.83
2969 5058 8.911662 CGTTCTAAAATAAATGACCCAACTTTG 58.088 33.333 0.00 0.00 0.00 2.77
2970 5059 8.085909 CCGTTCTAAAATAAATGACCCAACTTT 58.914 33.333 0.00 0.00 0.00 2.66
2971 5060 7.449086 TCCGTTCTAAAATAAATGACCCAACTT 59.551 33.333 0.00 0.00 0.00 2.66
2972 5061 6.943718 TCCGTTCTAAAATAAATGACCCAACT 59.056 34.615 0.00 0.00 0.00 3.16
2973 5062 7.148355 TCCGTTCTAAAATAAATGACCCAAC 57.852 36.000 0.00 0.00 0.00 3.77
2974 5063 6.376018 CCTCCGTTCTAAAATAAATGACCCAA 59.624 38.462 0.00 0.00 0.00 4.12
2975 5064 5.883673 CCTCCGTTCTAAAATAAATGACCCA 59.116 40.000 0.00 0.00 0.00 4.51
2976 5065 5.298527 CCCTCCGTTCTAAAATAAATGACCC 59.701 44.000 0.00 0.00 0.00 4.46
2977 5066 6.117488 TCCCTCCGTTCTAAAATAAATGACC 58.883 40.000 0.00 0.00 0.00 4.02
2978 5067 6.822170 ACTCCCTCCGTTCTAAAATAAATGAC 59.178 38.462 0.00 0.00 0.00 3.06
2979 5068 6.954232 ACTCCCTCCGTTCTAAAATAAATGA 58.046 36.000 0.00 0.00 0.00 2.57
2980 5069 8.610035 GTTACTCCCTCCGTTCTAAAATAAATG 58.390 37.037 0.00 0.00 0.00 2.32
2981 5070 8.546322 AGTTACTCCCTCCGTTCTAAAATAAAT 58.454 33.333 0.00 0.00 0.00 1.40
2982 5071 7.910584 AGTTACTCCCTCCGTTCTAAAATAAA 58.089 34.615 0.00 0.00 0.00 1.40
2983 5072 7.486407 AGTTACTCCCTCCGTTCTAAAATAA 57.514 36.000 0.00 0.00 0.00 1.40
2984 5073 7.836183 AGTAGTTACTCCCTCCGTTCTAAAATA 59.164 37.037 0.00 0.00 0.00 1.40
2985 5074 6.666980 AGTAGTTACTCCCTCCGTTCTAAAAT 59.333 38.462 0.00 0.00 0.00 1.82
2986 5075 6.012745 AGTAGTTACTCCCTCCGTTCTAAAA 58.987 40.000 0.00 0.00 0.00 1.52
2987 5076 5.574188 AGTAGTTACTCCCTCCGTTCTAAA 58.426 41.667 0.00 0.00 0.00 1.85
2988 5077 5.184892 AGTAGTTACTCCCTCCGTTCTAA 57.815 43.478 0.00 0.00 0.00 2.10
2989 5078 4.851639 AGTAGTTACTCCCTCCGTTCTA 57.148 45.455 0.00 0.00 0.00 2.10
2990 5079 3.735720 AGTAGTTACTCCCTCCGTTCT 57.264 47.619 0.00 0.00 0.00 3.01
2991 5080 5.009510 GGATTAGTAGTTACTCCCTCCGTTC 59.990 48.000 0.00 0.00 37.73 3.95
2992 5081 4.892345 GGATTAGTAGTTACTCCCTCCGTT 59.108 45.833 0.00 0.00 37.73 4.44
2993 5082 4.167697 AGGATTAGTAGTTACTCCCTCCGT 59.832 45.833 0.00 0.00 37.73 4.69
2994 5083 4.727677 AGGATTAGTAGTTACTCCCTCCG 58.272 47.826 0.00 0.00 37.73 4.63
2995 5084 7.125356 TCAAAAGGATTAGTAGTTACTCCCTCC 59.875 40.741 0.00 1.81 37.73 4.30
2996 5085 8.075761 TCAAAAGGATTAGTAGTTACTCCCTC 57.924 38.462 0.00 0.00 37.73 4.30
2997 5086 8.625467 ATCAAAAGGATTAGTAGTTACTCCCT 57.375 34.615 0.00 0.00 37.73 4.20
2998 5087 9.761504 GTATCAAAAGGATTAGTAGTTACTCCC 57.238 37.037 0.00 0.00 37.44 4.30
3035 5219 3.417645 CGCGCTAAAGAAAACTCACAAAC 59.582 43.478 5.56 0.00 0.00 2.93
3362 5549 5.584649 CAGTGAGTTTTCAGTCCTTGTAACA 59.415 40.000 0.00 0.00 34.74 2.41


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

AutoCloner maintained by Alex Coulton.