Multiple sequence alignment - TraesCS5B01G207600

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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 TraesCS5B01G207600 chr5B 100.000 4694 0 0 1 4694 377202920 377207613 0.000000e+00 8669.0
1 TraesCS5B01G207600 chr5D 93.044 2214 77 40 1918 4067 324759610 324761810 0.000000e+00 3164.0
2 TraesCS5B01G207600 chr5D 96.443 759 15 5 1175 1921 324758831 324759589 0.000000e+00 1242.0
3 TraesCS5B01G207600 chr5D 93.398 621 28 7 562 1176 324758186 324758799 0.000000e+00 907.0
4 TraesCS5B01G207600 chr5D 88.684 433 28 6 4065 4493 324778672 324779087 4.190000e-140 508.0
5 TraesCS5B01G207600 chr5D 93.452 168 9 1 4524 4691 324779536 324779701 1.010000e-61 248.0
6 TraesCS5B01G207600 chr5D 100.000 33 0 0 4484 4516 324779513 324779545 1.410000e-05 62.1
7 TraesCS5B01G207600 chr5A 91.835 1837 93 30 1175 2982 423007961 423009769 0.000000e+00 2508.0
8 TraesCS5B01G207600 chr5A 91.149 1062 43 21 2932 3949 423009752 423010806 0.000000e+00 1393.0
9 TraesCS5B01G207600 chr5A 98.885 538 6 0 1 538 1742800 1742263 0.000000e+00 961.0
10 TraesCS5B01G207600 chr5A 94.884 430 11 4 754 1176 423007504 423007929 0.000000e+00 662.0
11 TraesCS5B01G207600 chr5A 91.409 291 14 5 4316 4595 423029867 423030157 5.700000e-104 388.0
12 TraesCS5B01G207600 chr5A 91.855 221 13 3 4058 4276 423012064 423012281 2.120000e-78 303.0
13 TraesCS5B01G207600 chr5A 86.730 211 19 7 560 765 423007162 423007368 4.730000e-55 226.0
14 TraesCS5B01G207600 chr5A 91.515 165 11 2 4530 4692 423030157 423030320 1.700000e-54 224.0
15 TraesCS5B01G207600 chr2B 99.258 539 4 0 1 539 695407346 695407884 0.000000e+00 974.0
16 TraesCS5B01G207600 chr4A 98.895 543 6 0 1 543 507453278 507452736 0.000000e+00 970.0
17 TraesCS5B01G207600 chr4A 99.074 540 4 1 1 540 32664618 32665156 0.000000e+00 968.0
18 TraesCS5B01G207600 chr3A 99.072 539 4 1 1 539 111575044 111575581 0.000000e+00 966.0
19 TraesCS5B01G207600 chr3A 98.701 539 7 0 1 539 634572453 634572991 0.000000e+00 957.0
20 TraesCS5B01G207600 chr2A 98.887 539 6 0 1 539 514866320 514865782 0.000000e+00 963.0
21 TraesCS5B01G207600 chr2A 98.706 541 7 0 1 541 23441754 23442294 0.000000e+00 961.0
22 TraesCS5B01G207600 chr1A 98.706 541 7 0 1 541 549137642 549138182 0.000000e+00 961.0
23 TraesCS5B01G207600 chr1A 94.595 74 3 1 4450 4522 110160960 110160887 3.840000e-21 113.0
24 TraesCS5B01G207600 chr1D 96.875 64 2 0 4449 4512 107614927 107614864 1.790000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G207600 chr5B 377202920 377207613 4693 False 8669.0 8669 100.000000 1 4694 1 chr5B.!!$F1 4693
1 TraesCS5B01G207600 chr5D 324758186 324761810 3624 False 1771.0 3164 94.295000 562 4067 3 chr5D.!!$F1 3505
2 TraesCS5B01G207600 chr5D 324778672 324779701 1029 False 272.7 508 94.045333 4065 4691 3 chr5D.!!$F2 626
3 TraesCS5B01G207600 chr5A 423007162 423012281 5119 False 1018.4 2508 91.290600 560 4276 5 chr5A.!!$F1 3716
4 TraesCS5B01G207600 chr5A 1742263 1742800 537 True 961.0 961 98.885000 1 538 1 chr5A.!!$R1 537
5 TraesCS5B01G207600 chr2B 695407346 695407884 538 False 974.0 974 99.258000 1 539 1 chr2B.!!$F1 538
6 TraesCS5B01G207600 chr4A 507452736 507453278 542 True 970.0 970 98.895000 1 543 1 chr4A.!!$R1 542
7 TraesCS5B01G207600 chr4A 32664618 32665156 538 False 968.0 968 99.074000 1 540 1 chr4A.!!$F1 539
8 TraesCS5B01G207600 chr3A 111575044 111575581 537 False 966.0 966 99.072000 1 539 1 chr3A.!!$F1 538
9 TraesCS5B01G207600 chr3A 634572453 634572991 538 False 957.0 957 98.701000 1 539 1 chr3A.!!$F2 538
10 TraesCS5B01G207600 chr2A 514865782 514866320 538 True 963.0 963 98.887000 1 539 1 chr2A.!!$R1 538
11 TraesCS5B01G207600 chr2A 23441754 23442294 540 False 961.0 961 98.706000 1 541 1 chr2A.!!$F1 540
12 TraesCS5B01G207600 chr1A 549137642 549138182 540 False 961.0 961 98.706000 1 541 1 chr1A.!!$F1 540

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
545 547 0.103937 GGAGAGAGCCATCCGTCAAG 59.896 60.0 0.0 0.0 0.0 3.02 F
555 557 0.108615 ATCCGTCAAGCAGTCTTCCG 60.109 55.0 0.0 0.0 0.0 4.30 F
838 991 0.254178 AGATCACTCCCACCACATGC 59.746 55.0 0.0 0.0 0.0 4.06 F
2392 2627 0.325016 AACCCCGGTCGAGAAGGTAT 60.325 55.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 1999 0.739561 GCTACGTACTCCCAGAGTGG 59.260 60.000 7.51 2.4 43.30 4.00 R
2393 2628 1.212751 GCGGTTGGAGTTGGAATGC 59.787 57.895 0.00 0.0 0.00 3.56 R
2615 2857 0.960364 TGCCAACTCGCCATTTCTCC 60.960 55.000 0.00 0.0 0.00 3.71 R
4303 5795 0.036732 ACTTCAGGCGAATGCAAGGA 59.963 50.000 0.00 0.0 45.35 3.36 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
181 182 3.881952 ATCAAGCGCACACAGCCGA 62.882 57.895 11.47 0.00 41.38 5.54
543 545 0.753479 GAGGAGAGAGCCATCCGTCA 60.753 60.000 0.00 0.00 40.73 4.35
544 546 0.324738 AGGAGAGAGCCATCCGTCAA 60.325 55.000 0.00 0.00 40.73 3.18
545 547 0.103937 GGAGAGAGCCATCCGTCAAG 59.896 60.000 0.00 0.00 0.00 3.02
546 548 0.529555 GAGAGAGCCATCCGTCAAGC 60.530 60.000 0.00 0.00 0.00 4.01
547 549 1.219124 GAGAGCCATCCGTCAAGCA 59.781 57.895 0.00 0.00 0.00 3.91
548 550 0.809241 GAGAGCCATCCGTCAAGCAG 60.809 60.000 0.00 0.00 0.00 4.24
549 551 1.078848 GAGCCATCCGTCAAGCAGT 60.079 57.895 0.00 0.00 0.00 4.40
550 552 1.078848 AGCCATCCGTCAAGCAGTC 60.079 57.895 0.00 0.00 0.00 3.51
551 553 1.078848 GCCATCCGTCAAGCAGTCT 60.079 57.895 0.00 0.00 0.00 3.24
552 554 0.674895 GCCATCCGTCAAGCAGTCTT 60.675 55.000 0.00 0.00 0.00 3.01
553 555 1.363744 CCATCCGTCAAGCAGTCTTC 58.636 55.000 0.00 0.00 0.00 2.87
554 556 1.363744 CATCCGTCAAGCAGTCTTCC 58.636 55.000 0.00 0.00 0.00 3.46
555 557 0.108615 ATCCGTCAAGCAGTCTTCCG 60.109 55.000 0.00 0.00 0.00 4.30
556 558 1.006102 CCGTCAAGCAGTCTTCCGT 60.006 57.895 0.00 0.00 0.00 4.69
557 559 1.009389 CCGTCAAGCAGTCTTCCGTC 61.009 60.000 0.00 0.00 0.00 4.79
558 560 1.009389 CGTCAAGCAGTCTTCCGTCC 61.009 60.000 0.00 0.00 0.00 4.79
595 597 7.914427 AGTCCTAGGTGTTACATTCATATCA 57.086 36.000 9.08 0.00 0.00 2.15
597 599 8.370940 AGTCCTAGGTGTTACATTCATATCATG 58.629 37.037 9.08 0.00 0.00 3.07
619 621 5.126779 TGTAATATTTCCGCCATAGTTGCA 58.873 37.500 0.00 0.00 0.00 4.08
680 682 8.661352 TGTCTCGCATCATTTAATAAGAATGA 57.339 30.769 2.43 2.43 44.81 2.57
733 738 4.570772 GGCTCCAACCTCTTTTTCAAAAAC 59.429 41.667 0.00 0.00 0.00 2.43
739 744 8.563732 TCCAACCTCTTTTTCAAAAACAAAAAG 58.436 29.630 10.18 10.18 45.95 2.27
740 745 7.807433 CCAACCTCTTTTTCAAAAACAAAAAGG 59.193 33.333 14.54 6.12 45.20 3.11
750 755 6.875076 TCAAAAACAAAAAGGGGATAAACGA 58.125 32.000 0.00 0.00 0.00 3.85
773 926 4.019501 AGCTTGATTCACTTGGTCTCTCAT 60.020 41.667 0.00 0.00 0.00 2.90
836 989 2.260639 AGAGATCACTCCCACCACAT 57.739 50.000 0.00 0.00 43.53 3.21
838 991 0.254178 AGATCACTCCCACCACATGC 59.746 55.000 0.00 0.00 0.00 4.06
1389 1580 1.691976 AGGTGCATGCCGTAGCTAATA 59.308 47.619 16.68 0.00 36.18 0.98
1392 1583 1.691976 TGCATGCCGTAGCTAATACCT 59.308 47.619 16.68 0.00 40.80 3.08
1808 1999 2.084681 CGACGGCACCGACAAGTAC 61.085 63.158 17.40 0.00 42.83 2.73
1831 2022 1.028330 TCTGGGAGTACGTAGCACCG 61.028 60.000 0.00 0.00 0.00 4.94
1894 2097 8.374327 TGATTGCAGTCAAATCATCTATACTG 57.626 34.615 9.78 0.00 37.87 2.74
2341 2576 1.964552 CTCCAGGGACATCTTGATGC 58.035 55.000 10.20 4.07 0.00 3.91
2392 2627 0.325016 AACCCCGGTCGAGAAGGTAT 60.325 55.000 0.00 0.00 0.00 2.73
2393 2628 1.041447 ACCCCGGTCGAGAAGGTATG 61.041 60.000 0.00 0.00 0.00 2.39
2416 2654 2.280524 CAACTCCAACCGCCACGA 60.281 61.111 0.00 0.00 0.00 4.35
2422 2660 2.367567 ACTCCAACCGCCACGATATATT 59.632 45.455 0.00 0.00 0.00 1.28
2454 2692 3.181490 CCATGTGAATGTGATGGAAGCTG 60.181 47.826 0.00 0.00 39.29 4.24
2498 2740 1.134965 GTCATGACTCTTGACCCCGAG 60.135 57.143 18.83 0.00 38.00 4.63
2594 2836 6.316640 CCGTGATGGACAGAGGTATATACTAG 59.683 46.154 12.54 3.50 42.00 2.57
2595 2837 6.879993 CGTGATGGACAGAGGTATATACTAGT 59.120 42.308 12.54 0.00 0.00 2.57
2596 2838 8.039538 CGTGATGGACAGAGGTATATACTAGTA 58.960 40.741 12.54 4.77 0.00 1.82
2611 2853 4.250116 ACTAGTATGTGCTATGCAGAGC 57.750 45.455 26.11 26.11 40.08 4.09
2626 2868 0.177604 AGAGCAGAGGAGAAATGGCG 59.822 55.000 0.00 0.00 0.00 5.69
2628 2870 0.177604 AGCAGAGGAGAAATGGCGAG 59.822 55.000 0.00 0.00 0.00 5.03
2632 2874 1.065854 AGAGGAGAAATGGCGAGTTGG 60.066 52.381 0.00 0.00 0.00 3.77
2665 2922 2.452006 GTGTTTTCACCGTCTGTGTG 57.548 50.000 0.00 0.00 45.61 3.82
2666 2923 0.730265 TGTTTTCACCGTCTGTGTGC 59.270 50.000 0.00 0.00 45.61 4.57
2777 3034 6.590234 AGACAGAAAAAGTTTGAGTTGGTT 57.410 33.333 0.00 0.00 0.00 3.67
2778 3035 6.389906 AGACAGAAAAAGTTTGAGTTGGTTG 58.610 36.000 0.00 0.00 0.00 3.77
2779 3036 6.208599 AGACAGAAAAAGTTTGAGTTGGTTGA 59.791 34.615 0.00 0.00 0.00 3.18
2780 3037 6.935167 ACAGAAAAAGTTTGAGTTGGTTGAT 58.065 32.000 0.00 0.00 0.00 2.57
2803 3060 4.652881 TGAGATGTCTCCTACTGATTGCAT 59.347 41.667 7.51 0.00 42.20 3.96
2804 3061 4.958509 AGATGTCTCCTACTGATTGCATG 58.041 43.478 0.00 0.00 0.00 4.06
3103 3398 1.467920 GGTACGTACCTACTGCCACT 58.532 55.000 32.93 0.00 43.10 4.00
3113 3408 4.320456 CTGCCACTGACCGTGCCT 62.320 66.667 0.00 0.00 42.42 4.75
3114 3409 4.314440 TGCCACTGACCGTGCCTC 62.314 66.667 0.00 0.00 42.42 4.70
3115 3410 4.008933 GCCACTGACCGTGCCTCT 62.009 66.667 0.00 0.00 42.42 3.69
3116 3411 2.047844 CCACTGACCGTGCCTCTG 60.048 66.667 0.00 0.00 42.42 3.35
3118 3413 2.203640 ACTGACCGTGCCTCTGGA 60.204 61.111 0.00 0.00 0.00 3.86
3121 3418 0.965866 CTGACCGTGCCTCTGGAGTA 60.966 60.000 0.00 0.00 0.00 2.59
3235 3548 1.142748 CACCGTCTGCCTCAGATCC 59.857 63.158 0.00 0.00 42.73 3.36
3458 3775 1.606668 GGCATCACGAAACTTGTTCCA 59.393 47.619 0.00 0.00 0.00 3.53
3702 4027 0.528684 GAGCCGGCTAGCTGTACTTG 60.529 60.000 32.97 7.54 45.15 3.16
3704 4029 1.517832 CCGGCTAGCTGTACTTGCT 59.482 57.895 21.93 15.85 45.23 3.91
3705 4030 2.670635 CGGCTAGCTGTACTTGCTG 58.329 57.895 15.85 12.32 45.23 4.41
3707 4032 1.646189 GGCTAGCTGTACTTGCTGTC 58.354 55.000 15.72 12.27 45.23 3.51
3779 4105 1.621317 TCTGCACGTGAGGTTTGGATA 59.379 47.619 22.23 0.00 0.00 2.59
3788 4114 7.090173 CACGTGAGGTTTGGATATTCATTTTT 58.910 34.615 10.90 0.00 0.00 1.94
3791 4117 8.673711 CGTGAGGTTTGGATATTCATTTTTAGA 58.326 33.333 0.00 0.00 0.00 2.10
3922 4262 0.391661 ACATCGCGTCCTGCTGAAAT 60.392 50.000 5.77 0.00 43.27 2.17
3924 4264 1.009829 ATCGCGTCCTGCTGAAATTC 58.990 50.000 5.77 0.00 43.27 2.17
3925 4265 0.320334 TCGCGTCCTGCTGAAATTCA 60.320 50.000 5.77 0.00 43.27 2.57
3926 4266 0.729116 CGCGTCCTGCTGAAATTCAT 59.271 50.000 0.00 0.00 43.27 2.57
3927 4267 1.267732 CGCGTCCTGCTGAAATTCATC 60.268 52.381 0.00 0.00 43.27 2.92
3928 4268 1.739466 GCGTCCTGCTGAAATTCATCA 59.261 47.619 0.00 0.00 41.73 3.07
3934 4274 4.451629 CTGCTGAAATTCATCAGGCTTT 57.548 40.909 16.55 0.00 45.60 3.51
3935 4275 5.571784 CTGCTGAAATTCATCAGGCTTTA 57.428 39.130 16.55 0.00 45.60 1.85
3949 4289 5.216648 TCAGGCTTTATTAACAAAACGCAC 58.783 37.500 0.00 0.00 0.00 5.34
3952 4292 4.384547 GGCTTTATTAACAAAACGCACAGG 59.615 41.667 0.00 0.00 0.00 4.00
3953 4293 4.143410 GCTTTATTAACAAAACGCACAGGC 60.143 41.667 0.00 0.00 0.00 4.85
3954 4294 4.839668 TTATTAACAAAACGCACAGGCT 57.160 36.364 0.00 0.00 38.10 4.58
3955 4295 5.943706 TTATTAACAAAACGCACAGGCTA 57.056 34.783 0.00 0.00 38.10 3.93
3956 4296 3.612472 TTAACAAAACGCACAGGCTAC 57.388 42.857 0.00 0.00 38.10 3.58
3957 4297 1.384525 AACAAAACGCACAGGCTACA 58.615 45.000 0.00 0.00 38.10 2.74
3958 4298 1.604604 ACAAAACGCACAGGCTACAT 58.395 45.000 0.00 0.00 38.10 2.29
3960 4300 3.343617 ACAAAACGCACAGGCTACATAT 58.656 40.909 0.00 0.00 38.10 1.78
3961 4301 4.509616 ACAAAACGCACAGGCTACATATA 58.490 39.130 0.00 0.00 38.10 0.86
3962 4302 5.123227 ACAAAACGCACAGGCTACATATAT 58.877 37.500 0.00 0.00 38.10 0.86
3963 4303 6.285224 ACAAAACGCACAGGCTACATATATA 58.715 36.000 0.00 0.00 38.10 0.86
3966 4357 4.817517 ACGCACAGGCTACATATATAACC 58.182 43.478 0.00 0.00 38.10 2.85
3986 4377 2.270850 GTGCGTTGGGGGCTCATA 59.729 61.111 0.00 0.00 0.00 2.15
4067 5486 5.390613 CACCGACAATTGTAGATTTTGGAC 58.609 41.667 18.97 0.00 0.00 4.02
4072 5491 5.313712 ACAATTGTAGATTTTGGACGGTCT 58.686 37.500 9.97 0.00 0.00 3.85
4140 5632 2.036604 GAGGGGCGGAGAAGAAATCTAG 59.963 54.545 0.00 0.00 38.96 2.43
4151 5643 3.028094 AGAAATCTAGCCTCCGGTGTA 57.972 47.619 0.00 0.00 0.00 2.90
4153 5645 3.967987 AGAAATCTAGCCTCCGGTGTAAT 59.032 43.478 0.00 0.00 0.00 1.89
4156 5648 0.318784 CTAGCCTCCGGTGTAATCGC 60.319 60.000 0.00 0.00 0.00 4.58
4180 5672 1.308998 AAGGTGGTTCTTCACAAGCG 58.691 50.000 0.00 0.00 39.27 4.68
4302 5794 5.063060 CGCTAAGGAATTGGTTGTGTAGTAC 59.937 44.000 0.00 0.00 0.00 2.73
4303 5795 6.171213 GCTAAGGAATTGGTTGTGTAGTACT 58.829 40.000 0.00 0.00 0.00 2.73
4304 5796 6.313164 GCTAAGGAATTGGTTGTGTAGTACTC 59.687 42.308 0.00 0.00 0.00 2.59
4305 5797 5.161943 AGGAATTGGTTGTGTAGTACTCC 57.838 43.478 0.00 0.00 0.00 3.85
4306 5798 4.844655 AGGAATTGGTTGTGTAGTACTCCT 59.155 41.667 0.00 0.00 0.00 3.69
4307 5799 5.309806 AGGAATTGGTTGTGTAGTACTCCTT 59.690 40.000 0.00 0.00 0.00 3.36
4308 5800 5.411669 GGAATTGGTTGTGTAGTACTCCTTG 59.588 44.000 0.00 0.00 0.00 3.61
4309 5801 3.396260 TGGTTGTGTAGTACTCCTTGC 57.604 47.619 0.00 0.00 0.00 4.01
4310 5802 2.701423 TGGTTGTGTAGTACTCCTTGCA 59.299 45.455 0.00 0.00 0.00 4.08
4311 5803 3.326588 TGGTTGTGTAGTACTCCTTGCAT 59.673 43.478 0.00 0.00 0.00 3.96
4312 5804 4.202419 TGGTTGTGTAGTACTCCTTGCATT 60.202 41.667 0.00 0.00 0.00 3.56
4313 5805 4.392138 GGTTGTGTAGTACTCCTTGCATTC 59.608 45.833 0.00 0.00 0.00 2.67
4314 5806 3.845178 TGTGTAGTACTCCTTGCATTCG 58.155 45.455 0.00 0.00 0.00 3.34
4338 5830 4.202264 CCTGAAGTTGAGTACAGTTCACCT 60.202 45.833 0.00 0.00 31.84 4.00
4353 5845 1.962807 TCACCTTGTTCCTGGCAAATG 59.037 47.619 0.00 0.00 0.00 2.32
4358 5850 1.164411 TGTTCCTGGCAAATGTAGCG 58.836 50.000 0.00 0.00 0.00 4.26
4437 5933 1.136565 ATTTCGCGGAAATGGCACG 59.863 52.632 2.72 0.00 40.24 5.34
4440 5936 4.160635 CGCGGAAATGGCACGTCC 62.161 66.667 0.00 8.00 0.00 4.79
4442 5938 2.332654 GCGGAAATGGCACGTCCTT 61.333 57.895 14.50 0.00 35.26 3.36
4458 5954 4.196193 CGTCCTTGCCTGTAATAATTCCA 58.804 43.478 0.00 0.00 0.00 3.53
4478 5974 3.120923 CCAAAGATGCATCAAAACGTTGC 60.121 43.478 27.81 0.97 40.21 4.17
4479 5975 1.967762 AGATGCATCAAAACGTTGCG 58.032 45.000 27.81 0.00 42.29 4.85
4480 5976 0.984109 GATGCATCAAAACGTTGCGG 59.016 50.000 21.92 0.00 42.29 5.69
4516 6447 9.490379 CATTCGCCTCCTAAATAAAATACTAGT 57.510 33.333 0.00 0.00 0.00 2.57
4517 6448 9.708092 ATTCGCCTCCTAAATAAAATACTAGTC 57.292 33.333 0.00 0.00 0.00 2.59
4518 6449 7.664758 TCGCCTCCTAAATAAAATACTAGTCC 58.335 38.462 0.00 0.00 0.00 3.85
4519 6450 6.872547 CGCCTCCTAAATAAAATACTAGTCCC 59.127 42.308 0.00 0.00 0.00 4.46
4520 6451 7.166851 GCCTCCTAAATAAAATACTAGTCCCC 58.833 42.308 0.00 0.00 0.00 4.81
4521 6452 7.017353 GCCTCCTAAATAAAATACTAGTCCCCT 59.983 40.741 0.00 0.00 0.00 4.79
4522 6453 9.611491 CCTCCTAAATAAAATACTAGTCCCCTA 57.389 37.037 0.00 0.00 0.00 3.53
4586 6517 8.793592 GGATACTACATATTTGGAAACCAATCC 58.206 37.037 4.03 1.34 43.55 3.01
4691 6622 5.942826 ACAAAGATTTGATTCACCCTCTCTC 59.057 40.000 12.07 0.00 40.55 3.20
4692 6623 4.769345 AGATTTGATTCACCCTCTCTCC 57.231 45.455 0.00 0.00 0.00 3.71
4693 6624 4.107072 AGATTTGATTCACCCTCTCTCCA 58.893 43.478 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 161 2.948323 CTGTGTGCGCTTGATGCA 59.052 55.556 9.73 0.00 43.06 3.96
543 545 1.001406 CTTCTGGACGGAAGACTGCTT 59.999 52.381 14.26 0.00 43.70 3.91
544 546 0.605589 CTTCTGGACGGAAGACTGCT 59.394 55.000 14.26 0.00 43.70 4.24
545 547 0.318762 ACTTCTGGACGGAAGACTGC 59.681 55.000 23.67 0.00 43.70 4.40
546 548 1.401670 CGACTTCTGGACGGAAGACTG 60.402 57.143 23.67 12.07 43.70 3.51
547 549 0.882474 CGACTTCTGGACGGAAGACT 59.118 55.000 23.67 5.91 43.70 3.24
548 550 0.879765 TCGACTTCTGGACGGAAGAC 59.120 55.000 23.67 17.41 43.70 3.01
549 551 0.879765 GTCGACTTCTGGACGGAAGA 59.120 55.000 23.67 3.08 43.70 2.87
550 552 0.596577 TGTCGACTTCTGGACGGAAG 59.403 55.000 17.92 17.10 45.68 3.46
551 553 1.254026 ATGTCGACTTCTGGACGGAA 58.746 50.000 17.92 0.00 35.95 4.30
552 554 2.014857 CTATGTCGACTTCTGGACGGA 58.985 52.381 17.92 0.00 35.95 4.69
553 555 1.743958 ACTATGTCGACTTCTGGACGG 59.256 52.381 17.92 0.00 35.95 4.79
554 556 2.223294 GGACTATGTCGACTTCTGGACG 60.223 54.545 17.92 0.00 35.95 4.79
555 557 3.018149 AGGACTATGTCGACTTCTGGAC 58.982 50.000 17.92 4.21 32.65 4.02
556 558 3.367646 AGGACTATGTCGACTTCTGGA 57.632 47.619 17.92 0.00 32.65 3.86
557 559 3.566322 CCTAGGACTATGTCGACTTCTGG 59.434 52.174 17.92 2.14 32.65 3.86
558 560 4.035792 CACCTAGGACTATGTCGACTTCTG 59.964 50.000 17.98 9.55 32.65 3.02
595 597 5.767665 TGCAACTATGGCGGAAATATTACAT 59.232 36.000 0.00 0.00 0.00 2.29
597 599 5.682943 TGCAACTATGGCGGAAATATTAC 57.317 39.130 0.00 0.00 0.00 1.89
607 609 6.813649 AGTATATAACAGATGCAACTATGGCG 59.186 38.462 0.00 0.00 0.00 5.69
609 611 8.314021 TGGAGTATATAACAGATGCAACTATGG 58.686 37.037 0.00 0.00 0.00 2.74
675 677 5.050644 TCAATTGATGCACACAGTCATTC 57.949 39.130 3.38 0.00 0.00 2.67
728 733 5.756347 GCTCGTTTATCCCCTTTTTGTTTTT 59.244 36.000 0.00 0.00 0.00 1.94
733 738 4.217550 TCAAGCTCGTTTATCCCCTTTTTG 59.782 41.667 0.00 0.00 0.00 2.44
739 744 3.312697 GTGAATCAAGCTCGTTTATCCCC 59.687 47.826 0.00 0.00 0.00 4.81
740 745 4.192317 AGTGAATCAAGCTCGTTTATCCC 58.808 43.478 0.00 0.00 0.00 3.85
750 755 3.326006 TGAGAGACCAAGTGAATCAAGCT 59.674 43.478 0.00 0.00 0.00 3.74
773 926 6.839134 TGGGCTATCACATTTAGAGTAGAGAA 59.161 38.462 0.00 0.00 0.00 2.87
836 989 2.426738 GTTGCACTGCCCAATTATAGCA 59.573 45.455 0.00 0.00 34.79 3.49
838 991 4.717233 TTGTTGCACTGCCCAATTATAG 57.283 40.909 0.00 0.00 0.00 1.31
918 1072 3.103911 CGACGTCGTGCCTGGTTC 61.104 66.667 29.08 0.00 34.11 3.62
1389 1580 2.300437 CCTTCCTTGTCGAGAGAAAGGT 59.700 50.000 13.09 0.00 45.01 3.50
1392 1583 2.037251 CCACCTTCCTTGTCGAGAGAAA 59.963 50.000 0.00 0.00 45.01 2.52
1808 1999 0.739561 GCTACGTACTCCCAGAGTGG 59.260 60.000 7.51 2.40 43.30 4.00
1831 2022 1.683943 TGATTGCTAGGATTGCTGCC 58.316 50.000 0.00 0.00 0.00 4.85
1894 2097 7.215085 ACCTTATTCGTTTGATAGGGATGTAC 58.785 38.462 0.00 0.00 0.00 2.90
1956 2183 3.056322 GCCTCAACATTTGCTCCTTGAAT 60.056 43.478 0.00 0.00 0.00 2.57
2392 2627 1.523154 GCGGTTGGAGTTGGAATGCA 61.523 55.000 0.00 0.00 0.00 3.96
2393 2628 1.212751 GCGGTTGGAGTTGGAATGC 59.787 57.895 0.00 0.00 0.00 3.56
2416 2654 5.387788 TCACATGGCTGCCAAGAAATATAT 58.612 37.500 28.63 5.33 36.95 0.86
2422 2660 1.546923 CATTCACATGGCTGCCAAGAA 59.453 47.619 28.63 27.09 36.95 2.52
2430 2668 2.812836 TCCATCACATTCACATGGCT 57.187 45.000 0.00 0.00 37.57 4.75
2454 2692 6.906659 CCTGCAGGTGAATCATATACATTTC 58.093 40.000 25.53 0.00 0.00 2.17
2611 2853 2.005451 CAACTCGCCATTTCTCCTCTG 58.995 52.381 0.00 0.00 0.00 3.35
2615 2857 0.960364 TGCCAACTCGCCATTTCTCC 60.960 55.000 0.00 0.00 0.00 3.71
2628 2870 2.358898 ACACAGAAATGTGAGTGCCAAC 59.641 45.455 14.85 0.00 42.02 3.77
2632 2874 4.500477 GTGAAAACACAGAAATGTGAGTGC 59.500 41.667 14.85 2.04 42.02 4.40
2639 2881 4.201910 ACAGACGGTGAAAACACAGAAATG 60.202 41.667 7.39 5.58 0.00 2.32
2642 2884 2.980568 ACAGACGGTGAAAACACAGAA 58.019 42.857 7.39 0.00 0.00 3.02
2665 2922 4.778143 ATGGAACCGTCTGCCCGC 62.778 66.667 0.00 0.00 0.00 6.13
2666 2923 2.511600 GATGGAACCGTCTGCCCG 60.512 66.667 5.88 0.00 0.00 6.13
2764 3021 5.380043 ACATCTCATCAACCAACTCAAACT 58.620 37.500 0.00 0.00 0.00 2.66
2777 3034 5.221402 GCAATCAGTAGGAGACATCTCATCA 60.221 44.000 10.95 0.00 44.60 3.07
2778 3035 5.221402 TGCAATCAGTAGGAGACATCTCATC 60.221 44.000 10.95 1.16 44.60 2.92
2779 3036 4.652881 TGCAATCAGTAGGAGACATCTCAT 59.347 41.667 10.95 6.27 44.60 2.90
2780 3037 4.026052 TGCAATCAGTAGGAGACATCTCA 58.974 43.478 10.95 0.00 44.60 3.27
2803 3060 4.697514 GCTGCTCTCAACCTATACATTCA 58.302 43.478 0.00 0.00 0.00 2.57
2804 3061 3.738282 CGCTGCTCTCAACCTATACATTC 59.262 47.826 0.00 0.00 0.00 2.67
2846 3108 3.573538 AGAACCTCTGGATCATCGAGATG 59.426 47.826 0.00 6.74 37.00 2.90
3093 3388 4.578913 CACGGTCAGTGGCAGTAG 57.421 61.111 0.00 0.00 46.77 2.57
3103 3398 1.076014 TACTCCAGAGGCACGGTCA 59.924 57.895 0.00 0.00 0.00 4.02
3235 3548 1.432514 CGTGATGAACCACTCACCAG 58.567 55.000 0.00 0.00 38.83 4.00
3302 3619 0.383231 AGCATACGTACGTACCAGCC 59.617 55.000 28.99 15.22 33.01 4.85
3458 3775 1.698506 TCAAACCAAACCGGCTGAAT 58.301 45.000 0.00 0.00 39.03 2.57
3702 4027 4.141482 TGGGAATGGGATTTACTAGACAGC 60.141 45.833 0.00 0.00 0.00 4.40
3704 4029 5.431731 ACATGGGAATGGGATTTACTAGACA 59.568 40.000 0.00 0.00 0.00 3.41
3705 4030 5.765182 CACATGGGAATGGGATTTACTAGAC 59.235 44.000 0.00 0.00 0.00 2.59
3707 4032 5.940617 TCACATGGGAATGGGATTTACTAG 58.059 41.667 0.00 0.00 0.00 2.57
3779 4105 9.712305 CCTCGGTGTATCTATCTAAAAATGAAT 57.288 33.333 0.00 0.00 0.00 2.57
3788 4114 6.000219 GTGTTACCCTCGGTGTATCTATCTA 59.000 44.000 0.00 0.00 36.19 1.98
3791 4117 3.567164 CGTGTTACCCTCGGTGTATCTAT 59.433 47.826 0.00 0.00 36.19 1.98
3922 4262 6.584563 GCGTTTTGTTAATAAAGCCTGATGAA 59.415 34.615 6.07 0.00 0.00 2.57
3924 4264 5.861251 TGCGTTTTGTTAATAAAGCCTGATG 59.139 36.000 6.07 0.00 0.00 3.07
3925 4265 5.861787 GTGCGTTTTGTTAATAAAGCCTGAT 59.138 36.000 6.07 0.00 0.00 2.90
3926 4266 5.216648 GTGCGTTTTGTTAATAAAGCCTGA 58.783 37.500 6.07 0.00 0.00 3.86
3927 4267 4.979197 TGTGCGTTTTGTTAATAAAGCCTG 59.021 37.500 6.07 0.00 0.00 4.85
3928 4268 5.189659 TGTGCGTTTTGTTAATAAAGCCT 57.810 34.783 6.07 0.00 0.00 4.58
3929 4269 4.384547 CCTGTGCGTTTTGTTAATAAAGCC 59.615 41.667 6.07 1.26 0.00 4.35
3931 4271 5.219633 AGCCTGTGCGTTTTGTTAATAAAG 58.780 37.500 0.00 0.00 44.33 1.85
3932 4272 5.189659 AGCCTGTGCGTTTTGTTAATAAA 57.810 34.783 0.00 0.00 44.33 1.40
3934 4274 4.755629 TGTAGCCTGTGCGTTTTGTTAATA 59.244 37.500 0.00 0.00 44.33 0.98
3935 4275 3.566322 TGTAGCCTGTGCGTTTTGTTAAT 59.434 39.130 0.00 0.00 44.33 1.40
3949 4289 5.178797 GCACCAGGTTATATATGTAGCCTG 58.821 45.833 25.93 25.93 46.60 4.85
3952 4292 4.817517 ACGCACCAGGTTATATATGTAGC 58.182 43.478 0.00 0.00 0.00 3.58
3953 4293 5.637810 CCAACGCACCAGGTTATATATGTAG 59.362 44.000 0.00 0.00 0.00 2.74
3954 4294 5.511716 CCCAACGCACCAGGTTATATATGTA 60.512 44.000 0.00 0.00 0.00 2.29
3955 4295 4.385825 CCAACGCACCAGGTTATATATGT 58.614 43.478 0.00 0.00 0.00 2.29
3956 4296 3.751175 CCCAACGCACCAGGTTATATATG 59.249 47.826 0.00 0.00 0.00 1.78
3957 4297 3.244770 CCCCAACGCACCAGGTTATATAT 60.245 47.826 0.00 0.00 0.00 0.86
3958 4298 2.105134 CCCCAACGCACCAGGTTATATA 59.895 50.000 0.00 0.00 0.00 0.86
3960 4300 0.253610 CCCCAACGCACCAGGTTATA 59.746 55.000 0.00 0.00 0.00 0.98
3961 4301 1.001393 CCCCAACGCACCAGGTTAT 60.001 57.895 0.00 0.00 0.00 1.89
3962 4302 2.432563 CCCCAACGCACCAGGTTA 59.567 61.111 0.00 0.00 0.00 2.85
3963 4303 4.596585 CCCCCAACGCACCAGGTT 62.597 66.667 0.00 0.00 0.00 3.50
4067 5486 1.221021 GGGCTCCAAACCTAGACCG 59.779 63.158 0.00 0.00 29.20 4.79
4072 5491 3.087065 GCCTGGGCTCCAAACCTA 58.913 61.111 4.12 0.00 38.26 3.08
4151 5643 1.002773 AGAACCACCTTAACGGCGATT 59.997 47.619 16.62 6.95 35.61 3.34
4153 5645 0.393820 AAGAACCACCTTAACGGCGA 59.606 50.000 16.62 0.00 35.61 5.54
4156 5648 2.841215 TGTGAAGAACCACCTTAACGG 58.159 47.619 0.00 0.00 36.26 4.44
4158 5650 3.303791 CGCTTGTGAAGAACCACCTTAAC 60.304 47.826 0.00 0.00 36.26 2.01
4276 5768 3.074412 ACACAACCAATTCCTTAGCGAG 58.926 45.455 0.00 0.00 0.00 5.03
4279 5771 6.171213 AGTACTACACAACCAATTCCTTAGC 58.829 40.000 0.00 0.00 0.00 3.09
4281 5773 6.499350 AGGAGTACTACACAACCAATTCCTTA 59.501 38.462 8.10 0.00 0.00 2.69
4282 5774 5.309806 AGGAGTACTACACAACCAATTCCTT 59.690 40.000 8.10 0.00 0.00 3.36
4283 5775 4.844655 AGGAGTACTACACAACCAATTCCT 59.155 41.667 8.10 0.00 0.00 3.36
4302 5794 0.731417 CTTCAGGCGAATGCAAGGAG 59.269 55.000 0.00 0.00 45.35 3.69
4303 5795 0.036732 ACTTCAGGCGAATGCAAGGA 59.963 50.000 0.00 0.00 45.35 3.36
4304 5796 0.883833 AACTTCAGGCGAATGCAAGG 59.116 50.000 0.00 0.00 45.35 3.61
4305 5797 1.536766 TCAACTTCAGGCGAATGCAAG 59.463 47.619 0.00 0.00 45.35 4.01
4306 5798 1.536766 CTCAACTTCAGGCGAATGCAA 59.463 47.619 0.00 0.00 45.35 4.08
4307 5799 1.159285 CTCAACTTCAGGCGAATGCA 58.841 50.000 0.00 0.00 45.35 3.96
4308 5800 1.160137 ACTCAACTTCAGGCGAATGC 58.840 50.000 0.00 0.00 41.71 3.56
4309 5801 3.325870 TGTACTCAACTTCAGGCGAATG 58.674 45.455 0.00 0.00 0.00 2.67
4310 5802 3.006967 ACTGTACTCAACTTCAGGCGAAT 59.993 43.478 0.00 0.00 32.92 3.34
4311 5803 2.364324 ACTGTACTCAACTTCAGGCGAA 59.636 45.455 0.00 0.00 32.92 4.70
4312 5804 1.961394 ACTGTACTCAACTTCAGGCGA 59.039 47.619 0.00 0.00 32.92 5.54
4313 5805 2.440539 ACTGTACTCAACTTCAGGCG 57.559 50.000 0.00 0.00 32.92 5.52
4314 5806 3.495001 GTGAACTGTACTCAACTTCAGGC 59.505 47.826 0.00 0.00 32.92 4.85
4338 5830 1.539388 CGCTACATTTGCCAGGAACAA 59.461 47.619 0.00 0.00 0.00 2.83
4353 5845 1.250476 CGCAATTTTCACAGCGCTAC 58.750 50.000 10.99 0.00 43.80 3.58
4358 5850 1.269517 TGGGTTCGCAATTTTCACAGC 60.270 47.619 0.00 0.00 0.00 4.40
4396 5892 4.574828 TGCAGTAGTTGTGTTTCTTCCTTC 59.425 41.667 0.00 0.00 0.00 3.46
4437 5933 6.377146 TCTTTGGAATTATTACAGGCAAGGAC 59.623 38.462 1.61 0.00 0.00 3.85
4440 5936 6.698766 GCATCTTTGGAATTATTACAGGCAAG 59.301 38.462 0.00 0.00 0.00 4.01
4442 5938 5.655974 TGCATCTTTGGAATTATTACAGGCA 59.344 36.000 0.00 0.00 0.00 4.75
4458 5954 2.725723 CGCAACGTTTTGATGCATCTTT 59.274 40.909 26.32 8.04 45.93 2.52
4478 5974 0.248621 GGCGAATGCAAGGAAATCCG 60.249 55.000 0.00 0.00 45.35 4.18
4479 5975 1.066152 GAGGCGAATGCAAGGAAATCC 59.934 52.381 0.00 0.00 45.35 3.01
4480 5976 1.066152 GGAGGCGAATGCAAGGAAATC 59.934 52.381 0.00 0.00 45.35 2.17
4553 6484 8.798975 TTCCAAATATGTAGTATCCTCTTCCT 57.201 34.615 0.00 0.00 0.00 3.36
4554 6485 9.274206 GTTTCCAAATATGTAGTATCCTCTTCC 57.726 37.037 0.00 0.00 0.00 3.46
4650 6581 6.662865 TCTTTGTCATTAAAATGCCTTCCA 57.337 33.333 0.00 0.00 36.36 3.53
4667 6598 5.885465 AGAGAGGGTGAATCAAATCTTTGT 58.115 37.500 2.82 0.00 39.18 2.83
4672 6603 4.494091 TGGAGAGAGGGTGAATCAAATC 57.506 45.455 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.