Multiple sequence alignment - TraesCS3D01G090800

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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 TraesCS3D01G090800 chr3D 100.000 3278 0 0 1 3278 46095384 46098661 0.000000e+00 6054.0
1 TraesCS3D01G090800 chr3D 77.778 522 67 28 1604 2117 45972795 45973275 3.220000e-70 276.0
2 TraesCS3D01G090800 chr3B 89.401 1670 99 52 665 2289 71646144 71647780 0.000000e+00 2032.0
3 TraesCS3D01G090800 chr3B 91.753 97 8 0 3 99 675030449 675030353 5.710000e-28 135.0
4 TraesCS3D01G090800 chr3B 86.747 83 11 0 537 619 230689852 230689934 3.480000e-15 93.5
5 TraesCS3D01G090800 chr3B 84.337 83 11 2 537 618 675031082 675031163 2.710000e-11 80.5
6 TraesCS3D01G090800 chr3A 92.372 957 42 12 1151 2079 57770251 57769298 0.000000e+00 1334.0
7 TraesCS3D01G090800 chr3A 91.190 420 34 3 199 618 13791027 13790611 4.750000e-158 568.0
8 TraesCS3D01G090800 chr2B 92.105 874 25 13 2408 3252 69646411 69647269 0.000000e+00 1192.0
9 TraesCS3D01G090800 chr2B 85.061 328 41 6 2635 2955 589214882 589215208 8.770000e-86 327.0
10 TraesCS3D01G090800 chr7D 80.113 1775 205 84 700 2377 556326404 556328127 0.000000e+00 1186.0
11 TraesCS3D01G090800 chr7D 95.164 579 9 3 2408 2967 491293223 491293801 0.000000e+00 896.0
12 TraesCS3D01G090800 chr7D 96.008 476 3 1 2408 2867 162831404 162831879 0.000000e+00 760.0
13 TraesCS3D01G090800 chr7D 96.441 281 6 2 2976 3253 18597271 18596992 8.290000e-126 460.0
14 TraesCS3D01G090800 chr2D 92.111 862 23 15 2409 3252 651111419 651112253 0.000000e+00 1173.0
15 TraesCS3D01G090800 chr2D 88.908 577 42 9 2409 2966 109829702 109830275 0.000000e+00 691.0
16 TraesCS3D01G090800 chr2D 86.271 641 55 18 3 617 502497503 502496870 0.000000e+00 665.0
17 TraesCS3D01G090800 chr2D 80.674 564 86 13 2412 2955 502478637 502479197 1.820000e-112 416.0
18 TraesCS3D01G090800 chr4D 96.354 576 5 1 2408 2967 1179241 1179816 0.000000e+00 933.0
19 TraesCS3D01G090800 chr4D 95.130 575 11 2 2409 2967 96586769 96586196 0.000000e+00 891.0
20 TraesCS3D01G090800 chr4D 96.786 280 4 4 2976 3252 1620709 1620986 2.300000e-126 462.0
21 TraesCS3D01G090800 chr4D 96.786 280 4 4 2976 3252 1627706 1627983 2.300000e-126 462.0
22 TraesCS3D01G090800 chr4D 95.730 281 8 1 2976 3252 437723064 437723344 1.790000e-122 449.0
23 TraesCS3D01G090800 chr4D 80.449 624 84 24 12 617 446984151 446984754 3.000000e-120 442.0
24 TraesCS3D01G090800 chr1D 96.354 576 5 1 2408 2967 433931327 433931902 0.000000e+00 933.0
25 TraesCS3D01G090800 chr1D 95.726 585 9 1 2399 2967 112478485 112479069 0.000000e+00 928.0
26 TraesCS3D01G090800 chr1D 90.806 620 54 3 3 621 432328361 432327744 0.000000e+00 826.0
27 TraesCS3D01G090800 chr1D 90.097 616 58 3 3 617 79081357 79081970 0.000000e+00 797.0
28 TraesCS3D01G090800 chr1D 79.029 577 101 11 2408 2967 416035221 416035794 8.590000e-101 377.0
29 TraesCS3D01G090800 chr2A 95.147 577 10 2 2409 2967 726281206 726280630 0.000000e+00 894.0
30 TraesCS3D01G090800 chr6D 95.567 564 7 5 2408 2959 417512316 417511759 0.000000e+00 887.0
31 TraesCS3D01G090800 chr6D 96.029 277 10 1 2976 3252 453242381 453242656 1.790000e-122 449.0
32 TraesCS3D01G090800 chr6D 95.714 280 7 4 2976 3252 245022522 245022799 2.320000e-121 446.0
33 TraesCS3D01G090800 chr5D 94.957 575 13 1 2409 2967 543328958 543328384 0.000000e+00 887.0
34 TraesCS3D01G090800 chr5D 90.407 615 51 5 3 617 133868037 133868643 0.000000e+00 802.0
35 TraesCS3D01G090800 chr5D 96.071 280 6 4 2976 3252 45655833 45656110 4.990000e-123 451.0
36 TraesCS3D01G090800 chr5D 96.029 277 7 4 2976 3252 495381705 495381977 6.450000e-122 448.0
37 TraesCS3D01G090800 chr5D 95.714 280 7 4 2976 3252 463715666 463715943 2.320000e-121 446.0
38 TraesCS3D01G090800 chrUn 94.378 587 5 2 2409 2967 45895378 45895964 0.000000e+00 876.0
39 TraesCS3D01G090800 chrUn 80.879 387 49 10 3 367 276508508 276508125 6.920000e-72 281.0
40 TraesCS3D01G090800 chr5A 90.323 620 55 4 3 618 111291746 111292364 0.000000e+00 808.0
41 TraesCS3D01G090800 chr6B 96.581 468 9 2 2408 2868 49380053 49380520 0.000000e+00 769.0
42 TraesCS3D01G090800 chr6A 79.472 1213 140 42 1259 2405 74718335 74719504 0.000000e+00 760.0
43 TraesCS3D01G090800 chr6A 79.472 1213 140 42 1259 2405 74730015 74731184 0.000000e+00 760.0
44 TraesCS3D01G090800 chr6A 78.895 1213 147 42 1259 2405 74742090 74743259 0.000000e+00 721.0
45 TraesCS3D01G090800 chr7B 78.832 685 83 35 665 1304 603330282 603329615 3.940000e-109 405.0
46 TraesCS3D01G090800 chr7B 78.686 685 84 35 665 1304 603322526 603323193 1.830000e-107 399.0
47 TraesCS3D01G090800 chr7B 91.736 242 19 1 377 618 566834924 566834684 5.240000e-88 335.0
48 TraesCS3D01G090800 chr7B 80.098 407 33 21 2040 2405 603319889 603319490 3.240000e-65 259.0
49 TraesCS3D01G090800 chr7B 83.951 81 13 0 537 617 566835755 566835835 9.750000e-11 78.7


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 TraesCS3D01G090800 chr3D 46095384 46098661 3277 False 6054 6054 100.000 1 3278 1 chr3D.!!$F2 3277
1 TraesCS3D01G090800 chr3B 71646144 71647780 1636 False 2032 2032 89.401 665 2289 1 chr3B.!!$F1 1624
2 TraesCS3D01G090800 chr3A 57769298 57770251 953 True 1334 1334 92.372 1151 2079 1 chr3A.!!$R2 928
3 TraesCS3D01G090800 chr2B 69646411 69647269 858 False 1192 1192 92.105 2408 3252 1 chr2B.!!$F1 844
4 TraesCS3D01G090800 chr7D 556326404 556328127 1723 False 1186 1186 80.113 700 2377 1 chr7D.!!$F3 1677
5 TraesCS3D01G090800 chr7D 491293223 491293801 578 False 896 896 95.164 2408 2967 1 chr7D.!!$F2 559
6 TraesCS3D01G090800 chr2D 651111419 651112253 834 False 1173 1173 92.111 2409 3252 1 chr2D.!!$F3 843
7 TraesCS3D01G090800 chr2D 109829702 109830275 573 False 691 691 88.908 2409 2966 1 chr2D.!!$F1 557
8 TraesCS3D01G090800 chr2D 502496870 502497503 633 True 665 665 86.271 3 617 1 chr2D.!!$R1 614
9 TraesCS3D01G090800 chr2D 502478637 502479197 560 False 416 416 80.674 2412 2955 1 chr2D.!!$F2 543
10 TraesCS3D01G090800 chr4D 1179241 1179816 575 False 933 933 96.354 2408 2967 1 chr4D.!!$F1 559
11 TraesCS3D01G090800 chr4D 96586196 96586769 573 True 891 891 95.130 2409 2967 1 chr4D.!!$R1 558
12 TraesCS3D01G090800 chr4D 446984151 446984754 603 False 442 442 80.449 12 617 1 chr4D.!!$F5 605
13 TraesCS3D01G090800 chr1D 433931327 433931902 575 False 933 933 96.354 2408 2967 1 chr1D.!!$F4 559
14 TraesCS3D01G090800 chr1D 112478485 112479069 584 False 928 928 95.726 2399 2967 1 chr1D.!!$F2 568
15 TraesCS3D01G090800 chr1D 432327744 432328361 617 True 826 826 90.806 3 621 1 chr1D.!!$R1 618
16 TraesCS3D01G090800 chr1D 79081357 79081970 613 False 797 797 90.097 3 617 1 chr1D.!!$F1 614
17 TraesCS3D01G090800 chr1D 416035221 416035794 573 False 377 377 79.029 2408 2967 1 chr1D.!!$F3 559
18 TraesCS3D01G090800 chr2A 726280630 726281206 576 True 894 894 95.147 2409 2967 1 chr2A.!!$R1 558
19 TraesCS3D01G090800 chr6D 417511759 417512316 557 True 887 887 95.567 2408 2959 1 chr6D.!!$R1 551
20 TraesCS3D01G090800 chr5D 543328384 543328958 574 True 887 887 94.957 2409 2967 1 chr5D.!!$R1 558
21 TraesCS3D01G090800 chr5D 133868037 133868643 606 False 802 802 90.407 3 617 1 chr5D.!!$F2 614
22 TraesCS3D01G090800 chrUn 45895378 45895964 586 False 876 876 94.378 2409 2967 1 chrUn.!!$F1 558
23 TraesCS3D01G090800 chr5A 111291746 111292364 618 False 808 808 90.323 3 618 1 chr5A.!!$F1 615
24 TraesCS3D01G090800 chr6A 74718335 74719504 1169 False 760 760 79.472 1259 2405 1 chr6A.!!$F1 1146
25 TraesCS3D01G090800 chr6A 74730015 74731184 1169 False 760 760 79.472 1259 2405 1 chr6A.!!$F2 1146
26 TraesCS3D01G090800 chr6A 74742090 74743259 1169 False 721 721 78.895 1259 2405 1 chr6A.!!$F3 1146
27 TraesCS3D01G090800 chr7B 603329615 603330282 667 True 405 405 78.832 665 1304 1 chr7B.!!$R3 639
28 TraesCS3D01G090800 chr7B 603322526 603323193 667 False 399 399 78.686 665 1304 1 chr7B.!!$F2 639

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
264 290 0.460311 CCTAATGGCGTCCTTCGTCT 59.540 55.0 0.0 0.0 45.15 4.18 F
1488 1655 0.253327 GGATCAGGAAGGTGGTGGTC 59.747 60.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1552 1731 0.038744 AATCTGGCACCTTGACCTGG 59.961 55.0 0.0 0.0 0.0 4.45 R
2971 3296 0.533491 CGTGAATGGTCCTCCGGTAA 59.467 55.0 0.0 0.0 36.3 2.85 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
34 35 1.792949 GTTCGTGCTTGTACAGGACTG 59.207 52.381 9.51 0.00 41.70 3.51
70 74 1.017177 TACGCATGTGTCTTTCGGCC 61.017 55.000 16.65 0.00 0.00 6.13
81 85 2.095718 GTCTTTCGGCCACACTTCAATC 60.096 50.000 2.24 0.00 0.00 2.67
86 90 1.457346 GGCCACACTTCAATCCTCAG 58.543 55.000 0.00 0.00 0.00 3.35
99 103 1.746470 TCCTCAGTCGATGCTCGTTA 58.254 50.000 0.00 0.00 41.35 3.18
121 141 2.783135 TCAGAAGAAGTTCATGTGGCC 58.217 47.619 5.50 0.00 34.82 5.36
205 231 1.115930 ACCCTCTGAGACACAGCGTT 61.116 55.000 6.17 0.00 45.38 4.84
217 243 1.092921 ACAGCGTTGACGAAGCCAAA 61.093 50.000 6.16 0.00 43.02 3.28
240 266 1.648467 GATGTTGAGCTTGGTCCGGC 61.648 60.000 0.00 0.00 0.00 6.13
264 290 0.460311 CCTAATGGCGTCCTTCGTCT 59.540 55.000 0.00 0.00 45.15 4.18
318 344 2.771762 GGGCTCCTGGCTCCTCAT 60.772 66.667 4.47 0.00 41.46 2.90
439 507 2.290641 TGGCTATGATGTTTTGACCCGT 60.291 45.455 0.00 0.00 0.00 5.28
456 525 2.412870 CCGTGTAACATGAGACAAGCA 58.587 47.619 0.00 0.00 35.74 3.91
520 590 2.242965 TGTGAGGGTTAGGATAGACCGA 59.757 50.000 0.00 0.00 44.74 4.69
524 594 4.140994 TGAGGGTTAGGATAGACCGAGATT 60.141 45.833 0.00 0.00 44.74 2.40
535 606 2.836262 GACCGAGATTAGAGAGGTCGA 58.164 52.381 0.00 0.00 41.38 4.20
566 637 4.655963 CTTCAGGGATTTGAAGGTGAAGA 58.344 43.478 7.66 0.00 46.55 2.87
618 689 6.940298 CAGGGTTTATTTTAGACTTCACTCCA 59.060 38.462 0.00 0.00 0.00 3.86
620 691 8.170730 AGGGTTTATTTTAGACTTCACTCCATT 58.829 33.333 0.00 0.00 0.00 3.16
621 692 9.457436 GGGTTTATTTTAGACTTCACTCCATTA 57.543 33.333 0.00 0.00 0.00 1.90
626 697 7.938140 TTTTAGACTTCACTCCATTATTGGG 57.062 36.000 3.86 0.00 43.81 4.12
627 698 6.636454 TTAGACTTCACTCCATTATTGGGT 57.364 37.500 3.86 0.00 43.81 4.51
628 699 4.848357 AGACTTCACTCCATTATTGGGTG 58.152 43.478 14.31 14.31 43.81 4.61
629 700 3.947834 GACTTCACTCCATTATTGGGTGG 59.052 47.826 17.71 10.16 43.81 4.61
630 701 2.435372 TCACTCCATTATTGGGTGGC 57.565 50.000 17.71 0.00 43.81 5.01
631 702 1.024271 CACTCCATTATTGGGTGGCG 58.976 55.000 13.32 0.00 43.81 5.69
632 703 0.916086 ACTCCATTATTGGGTGGCGA 59.084 50.000 3.86 0.00 43.81 5.54
633 704 1.494721 ACTCCATTATTGGGTGGCGAT 59.505 47.619 3.86 0.00 43.81 4.58
634 705 2.708861 ACTCCATTATTGGGTGGCGATA 59.291 45.455 3.86 0.00 43.81 2.92
635 706 3.074412 CTCCATTATTGGGTGGCGATAC 58.926 50.000 3.86 0.00 43.81 2.24
636 707 2.439880 TCCATTATTGGGTGGCGATACA 59.560 45.455 3.86 0.00 43.81 2.29
637 708 2.552315 CCATTATTGGGTGGCGATACAC 59.448 50.000 0.00 0.00 39.56 2.90
638 709 1.942677 TTATTGGGTGGCGATACACG 58.057 50.000 0.00 0.00 42.23 4.49
663 734 2.806929 CTCCTCTCGAGCTGGCAG 59.193 66.667 10.94 10.94 0.00 4.85
687 758 1.446792 CCTCTCTCAACACGCGCAT 60.447 57.895 5.73 0.00 0.00 4.73
717 790 1.740025 CCGTTCTTCCCTTTGATGCTC 59.260 52.381 0.00 0.00 0.00 4.26
719 792 3.077359 CGTTCTTCCCTTTGATGCTCTT 58.923 45.455 0.00 0.00 0.00 2.85
721 794 2.977914 TCTTCCCTTTGATGCTCTTCG 58.022 47.619 0.00 0.00 0.00 3.79
739 812 3.655481 CACCGAAACCAGAGTGCC 58.345 61.111 0.00 0.00 0.00 5.01
743 816 2.317609 CGAAACCAGAGTGCCCGTG 61.318 63.158 0.00 0.00 0.00 4.94
780 862 4.325119 CACCAAAATGGCAAAATCCATCA 58.675 39.130 0.00 0.00 45.64 3.07
781 863 4.944930 CACCAAAATGGCAAAATCCATCAT 59.055 37.500 0.00 0.00 45.64 2.45
782 864 5.065474 CACCAAAATGGCAAAATCCATCATC 59.935 40.000 0.00 0.00 45.64 2.92
851 938 2.650116 GCCGTCTCTCTTCAGGCCA 61.650 63.158 5.01 0.00 41.81 5.36
854 941 1.587043 CGTCTCTCTTCAGGCCACGA 61.587 60.000 5.01 0.00 0.00 4.35
871 958 1.817099 GATCCCGCACTTGCTCCAG 60.817 63.158 0.00 0.00 39.32 3.86
917 1024 1.585006 GTCTCGGAAAGCGACCTGA 59.415 57.895 0.00 0.00 0.00 3.86
956 1082 4.816984 GCCGAGGTCGAGGGGAGA 62.817 72.222 0.00 0.00 43.02 3.71
960 1086 1.038130 CGAGGTCGAGGGGAGATTGT 61.038 60.000 0.00 0.00 43.02 2.71
989 1115 0.463833 CCGCTCCCGCTTAGGAAATT 60.464 55.000 0.00 0.00 45.00 1.82
1084 1214 2.417516 GGCTGCTCCGAATCGCTA 59.582 61.111 0.00 0.00 0.00 4.26
1161 1291 2.364317 CTCTCCCGCCTTCCCTCA 60.364 66.667 0.00 0.00 0.00 3.86
1272 1414 4.332543 ACCTTCCTCGCCCTCCCA 62.333 66.667 0.00 0.00 0.00 4.37
1331 1473 2.176247 ATCCTCTTACGTGTCCCCAT 57.824 50.000 0.00 0.00 0.00 4.00
1365 1507 1.227853 GTTCTTCCTGGTGCACCGT 60.228 57.895 30.07 0.00 39.43 4.83
1383 1525 2.202810 GACGGCAGCTGCTACCTC 60.203 66.667 35.82 20.82 41.70 3.85
1406 1560 0.910088 AACCCTTCTTCCGGGGAGAG 60.910 60.000 4.93 0.00 46.40 3.20
1488 1655 0.253327 GGATCAGGAAGGTGGTGGTC 59.747 60.000 0.00 0.00 0.00 4.02
1544 1723 1.471676 GGTCACGATCTTTCCTCGCAT 60.472 52.381 0.00 0.00 39.71 4.73
1855 2061 1.135053 GCTCCGTCTTCTACCTTGTCC 60.135 57.143 0.00 0.00 0.00 4.02
1925 2131 4.394712 CGTGGTCTGGGAGGGTGC 62.395 72.222 0.00 0.00 0.00 5.01
1995 2201 2.365105 GGGGTGGACCTGATCGGA 60.365 66.667 2.08 0.00 40.03 4.55
2080 2286 1.674764 CTCTCAGTCGCTCCCTGCAT 61.675 60.000 0.00 0.00 43.06 3.96
2099 2305 1.001764 CAGCCCAATGTGGAGCTCA 60.002 57.895 17.19 0.00 40.46 4.26
2212 2444 1.745489 GACGGGACAATGGAGCCAC 60.745 63.158 0.00 0.00 0.00 5.01
2280 2515 0.913934 TCCCTGCCCATGCTTGAGTA 60.914 55.000 0.22 0.00 38.71 2.59
2306 2541 8.331931 ACATATATCTGTCCTCCTTGGTTTAA 57.668 34.615 0.00 0.00 37.07 1.52
2311 2546 2.224354 TGTCCTCCTTGGTTTAACCGTC 60.224 50.000 9.77 0.00 42.58 4.79
2312 2547 2.048601 TCCTCCTTGGTTTAACCGTCA 58.951 47.619 9.77 0.00 42.58 4.35
2314 2549 3.117963 TCCTCCTTGGTTTAACCGTCAAA 60.118 43.478 9.77 0.00 42.58 2.69
2315 2550 3.252458 CCTCCTTGGTTTAACCGTCAAAG 59.748 47.826 9.77 7.23 42.58 2.77
2318 2553 4.948621 TCCTTGGTTTAACCGTCAAAGAAA 59.051 37.500 9.77 0.00 42.58 2.52
2355 2609 6.479990 TCTGATTTGAGTATGCCAGTTAATCG 59.520 38.462 0.00 0.00 0.00 3.34
2398 2653 2.418368 AAAAGCTATGCCCGTGATGA 57.582 45.000 0.00 0.00 0.00 2.92
2399 2654 2.418368 AAAGCTATGCCCGTGATGAA 57.582 45.000 0.00 0.00 0.00 2.57
2400 2655 1.959042 AAGCTATGCCCGTGATGAAG 58.041 50.000 0.00 0.00 0.00 3.02
2401 2656 1.123077 AGCTATGCCCGTGATGAAGA 58.877 50.000 0.00 0.00 0.00 2.87
2402 2657 1.486310 AGCTATGCCCGTGATGAAGAA 59.514 47.619 0.00 0.00 0.00 2.52
2403 2658 1.599542 GCTATGCCCGTGATGAAGAAC 59.400 52.381 0.00 0.00 0.00 3.01
2404 2659 2.905075 CTATGCCCGTGATGAAGAACA 58.095 47.619 0.00 0.00 0.00 3.18
2405 2660 2.425143 ATGCCCGTGATGAAGAACAT 57.575 45.000 0.00 0.00 42.47 2.71
2406 2661 2.198827 TGCCCGTGATGAAGAACATT 57.801 45.000 0.00 0.00 39.56 2.71
2967 3292 5.335430 CGACTCGGTTTCTAATTCGTATACG 59.665 44.000 19.23 19.23 41.45 3.06
2968 3293 9.556618 CCGACTCGGTTTCTAATTCGTATACGA 62.557 44.444 23.54 23.54 43.76 3.43
3252 3588 4.519350 GGCCTAGCCCATTAATTCTAACAC 59.481 45.833 0.00 0.00 44.06 3.32
3253 3589 5.130350 GCCTAGCCCATTAATTCTAACACA 58.870 41.667 0.00 0.00 0.00 3.72
3254 3590 5.770162 GCCTAGCCCATTAATTCTAACACAT 59.230 40.000 0.00 0.00 0.00 3.21
3255 3591 6.265422 GCCTAGCCCATTAATTCTAACACATT 59.735 38.462 0.00 0.00 0.00 2.71
3256 3592 7.201911 GCCTAGCCCATTAATTCTAACACATTT 60.202 37.037 0.00 0.00 0.00 2.32
3257 3593 9.349713 CCTAGCCCATTAATTCTAACACATTTA 57.650 33.333 0.00 0.00 0.00 1.40
3260 3596 9.646522 AGCCCATTAATTCTAACACATTTATCT 57.353 29.630 0.00 0.00 0.00 1.98
3261 3597 9.683069 GCCCATTAATTCTAACACATTTATCTG 57.317 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.486982 GCACGAACTAGTACCTGAGTGA 59.513 50.000 0.00 0.00 0.00 3.41
1 2 2.488545 AGCACGAACTAGTACCTGAGTG 59.511 50.000 0.00 2.22 0.00 3.51
7 8 4.164294 CTGTACAAGCACGAACTAGTACC 58.836 47.826 0.00 0.00 32.92 3.34
34 35 1.867233 CGTACATGGCTGGCTTGATAC 59.133 52.381 21.26 16.84 0.00 2.24
70 74 3.303881 TCGACTGAGGATTGAAGTGTG 57.696 47.619 0.00 0.00 0.00 3.82
99 103 3.760684 GGCCACATGAACTTCTTCTGATT 59.239 43.478 0.00 0.00 0.00 2.57
205 231 1.347707 ACATCTCCTTTGGCTTCGTCA 59.652 47.619 0.00 0.00 0.00 4.35
217 243 1.280421 GGACCAAGCTCAACATCTCCT 59.720 52.381 0.00 0.00 0.00 3.69
240 266 0.393077 AAGGACGCCATTAGGGATCG 59.607 55.000 0.00 0.00 40.01 3.69
264 290 3.320626 CAGAGCTGTTCGTCATCAAGAA 58.679 45.455 0.00 0.00 0.00 2.52
347 388 1.162698 GCCATACGATGAGCATGCAT 58.837 50.000 21.98 5.15 0.00 3.96
351 392 0.107268 TGCTGCCATACGATGAGCAT 59.893 50.000 0.00 0.00 35.84 3.79
358 399 2.125147 GTGCCTGCTGCCATACGA 60.125 61.111 0.00 0.00 40.16 3.43
380 421 0.822532 CCTGATTGGAGATGCAGCCC 60.823 60.000 0.00 0.00 38.35 5.19
439 507 5.008613 GGAAACTTGCTTGTCTCATGTTACA 59.991 40.000 0.00 0.00 33.35 2.41
456 525 2.039879 AGCACAATCCTACCGGAAACTT 59.960 45.455 9.46 0.00 44.02 2.66
520 590 3.494749 CGGTACCTCGACCTCTCTAATCT 60.495 52.174 10.90 0.00 37.34 2.40
524 594 1.489481 TCGGTACCTCGACCTCTCTA 58.511 55.000 10.90 0.00 37.34 2.43
535 606 2.236395 CAAATCCCTGAAGTCGGTACCT 59.764 50.000 10.90 0.00 0.00 3.08
544 615 8.445987 TGAATCTTCACCTTCAAATCCCTGAAG 61.446 40.741 6.40 6.40 40.90 3.02
564 635 3.757270 AGGGATCGACGTAGATGAATCT 58.243 45.455 16.28 5.13 40.86 2.40
566 637 4.395625 TGTAGGGATCGACGTAGATGAAT 58.604 43.478 16.28 3.94 0.00 2.57
618 689 2.489971 CGTGTATCGCCACCCAATAAT 58.510 47.619 0.00 0.00 31.47 1.28
620 691 3.671262 CGTGTATCGCCACCCAATA 57.329 52.632 0.00 0.00 31.47 1.90
621 692 4.532490 CGTGTATCGCCACCCAAT 57.468 55.556 0.00 0.00 31.47 3.16
646 717 2.806929 CTGCCAGCTCGAGAGGAG 59.193 66.667 23.68 14.56 46.06 3.69
647 718 3.456365 GCTGCCAGCTCGAGAGGA 61.456 66.667 23.68 9.50 38.45 3.71
648 719 4.869440 CGCTGCCAGCTCGAGAGG 62.869 72.222 18.75 17.87 39.60 3.69
649 720 4.869440 CCGCTGCCAGCTCGAGAG 62.869 72.222 18.75 7.53 39.60 3.20
661 732 3.393970 TTGAGAGAGGGCCCGCTG 61.394 66.667 34.82 0.00 0.00 5.18
662 733 3.394836 GTTGAGAGAGGGCCCGCT 61.395 66.667 30.18 30.18 0.00 5.52
663 734 3.706373 TGTTGAGAGAGGGCCCGC 61.706 66.667 19.43 19.43 0.00 6.13
667 738 2.811317 CGCGTGTTGAGAGAGGGC 60.811 66.667 0.00 0.00 0.00 5.19
687 758 1.595929 GAAGAACGGTGGGCGTTCA 60.596 57.895 8.10 0.00 45.53 3.18
717 790 0.600255 ACTCTGGTTTCGGTGCGAAG 60.600 55.000 0.00 0.00 46.43 3.79
719 792 1.300620 CACTCTGGTTTCGGTGCGA 60.301 57.895 0.00 0.00 0.00 5.10
721 794 2.946762 GCACTCTGGTTTCGGTGC 59.053 61.111 0.00 0.00 45.93 5.01
739 812 2.032528 TGAGAGGGCTTTGCACGG 59.967 61.111 0.00 0.00 36.86 4.94
743 816 1.973812 GGTGGTGAGAGGGCTTTGC 60.974 63.158 0.00 0.00 0.00 3.68
780 862 2.444895 GGGACGAGCTCAGGGGAT 60.445 66.667 15.40 0.00 0.00 3.85
843 930 4.467084 GCGGGATCGTGGCCTGAA 62.467 66.667 3.32 0.00 38.89 3.02
980 1106 1.067706 TCACCGTCGCGAATTTCCTAA 60.068 47.619 12.06 0.00 0.00 2.69
989 1115 4.829518 CGAGCATCACCGTCGCGA 62.830 66.667 3.71 3.71 33.17 5.87
1074 1204 3.706140 GCTGGTGTAGCGATTCGG 58.294 61.111 8.34 0.00 43.63 4.30
1135 1265 3.760035 GCGGGAGAGCACGAGGAA 61.760 66.667 0.00 0.00 45.89 3.36
1309 1451 2.027561 TGGGGACACGTAAGAGGATTTG 60.028 50.000 0.00 0.00 43.62 2.32
1365 1507 2.997315 AGGTAGCAGCTGCCGTCA 60.997 61.111 34.39 15.09 41.15 4.35
1383 1525 1.375523 CCCGGAAGAAGGGTTCGTG 60.376 63.158 0.73 0.00 43.89 4.35
1406 1560 2.352422 TGATGTGCAGAGGGGTGC 59.648 61.111 0.00 0.00 44.27 5.01
1548 1727 3.050275 GCACCTTGACCTGGCGAC 61.050 66.667 0.00 0.00 0.00 5.19
1549 1728 4.329545 GGCACCTTGACCTGGCGA 62.330 66.667 0.00 0.00 0.00 5.54
1552 1731 0.038744 AATCTGGCACCTTGACCTGG 59.961 55.000 0.00 0.00 0.00 4.45
1554 1733 0.773644 ACAATCTGGCACCTTGACCT 59.226 50.000 10.37 0.00 0.00 3.85
1555 1734 0.883833 CACAATCTGGCACCTTGACC 59.116 55.000 10.37 0.00 0.00 4.02
1557 1736 0.111061 AGCACAATCTGGCACCTTGA 59.889 50.000 10.37 0.00 0.00 3.02
1559 1738 0.896940 CCAGCACAATCTGGCACCTT 60.897 55.000 0.00 0.00 46.11 3.50
1626 1808 3.869912 GCTCACCTTGGAAGAGTGCAATA 60.870 47.826 12.56 0.00 34.22 1.90
1671 1853 4.040952 AGTTCAGAGCCACTCTTGTTATGT 59.959 41.667 0.00 0.00 38.99 2.29
1672 1854 4.391216 CAGTTCAGAGCCACTCTTGTTATG 59.609 45.833 0.00 0.00 38.99 1.90
1674 1856 3.803715 GCAGTTCAGAGCCACTCTTGTTA 60.804 47.826 0.00 0.00 38.99 2.41
1819 2025 4.778143 GCGCCAGGTTCGGTCCAT 62.778 66.667 0.00 0.00 0.00 3.41
2080 2286 1.300963 GAGCTCCACATTGGGCTGA 59.699 57.895 0.87 0.00 41.79 4.26
2197 2429 1.379044 CCAGTGGCTCCATTGTCCC 60.379 63.158 9.99 0.00 32.72 4.46
2212 2444 2.202492 CGGTTCGCTCGTCTCCAG 60.202 66.667 0.00 0.00 0.00 3.86
2236 2468 2.045340 GGTGGGTTCCCATGGACG 60.045 66.667 15.22 0.00 38.49 4.79
2280 2515 6.831664 AACCAAGGAGGACAGATATATGTT 57.168 37.500 4.16 0.00 41.22 2.71
2355 2609 2.742589 CTCCTCGTTTTACAAGGGAAGC 59.257 50.000 0.00 0.00 0.00 3.86
2387 2642 2.198827 AATGTTCTTCATCACGGGCA 57.801 45.000 0.00 0.00 35.48 5.36
2389 2644 4.503741 ACAAAATGTTCTTCATCACGGG 57.496 40.909 0.00 0.00 35.48 5.28
2390 2645 4.681025 CCAACAAAATGTTCTTCATCACGG 59.319 41.667 0.00 0.00 38.77 4.94
2391 2646 5.518812 TCCAACAAAATGTTCTTCATCACG 58.481 37.500 0.00 0.00 38.77 4.35
2392 2647 7.951530 ATTCCAACAAAATGTTCTTCATCAC 57.048 32.000 0.00 0.00 38.77 3.06
2397 2652 9.087424 GCCTAATATTCCAACAAAATGTTCTTC 57.913 33.333 0.00 0.00 38.77 2.87
2398 2653 8.592809 TGCCTAATATTCCAACAAAATGTTCTT 58.407 29.630 0.00 0.00 38.77 2.52
2399 2654 8.133024 TGCCTAATATTCCAACAAAATGTTCT 57.867 30.769 0.00 0.00 38.77 3.01
2400 2655 8.770438 TTGCCTAATATTCCAACAAAATGTTC 57.230 30.769 0.00 0.00 38.77 3.18
2401 2656 8.374743 ACTTGCCTAATATTCCAACAAAATGTT 58.625 29.630 0.00 0.00 42.08 2.71
2402 2657 7.906327 ACTTGCCTAATATTCCAACAAAATGT 58.094 30.769 0.00 0.00 0.00 2.71
2403 2658 8.776376 AACTTGCCTAATATTCCAACAAAATG 57.224 30.769 0.00 0.00 0.00 2.32
2404 2659 8.592809 TGAACTTGCCTAATATTCCAACAAAAT 58.407 29.630 0.00 0.00 0.00 1.82
2405 2660 7.957002 TGAACTTGCCTAATATTCCAACAAAA 58.043 30.769 0.00 0.00 0.00 2.44
2406 2661 7.531857 TGAACTTGCCTAATATTCCAACAAA 57.468 32.000 0.00 0.00 0.00 2.83
2967 3292 2.235402 TGAATGGTCCTCCGGTAAGTTC 59.765 50.000 0.00 0.00 36.30 3.01
2968 3293 2.027469 GTGAATGGTCCTCCGGTAAGTT 60.027 50.000 0.00 0.00 36.30 2.66
2971 3296 0.533491 CGTGAATGGTCCTCCGGTAA 59.467 55.000 0.00 0.00 36.30 2.85
2972 3297 1.952102 GCGTGAATGGTCCTCCGGTA 61.952 60.000 0.00 0.00 36.30 4.02
2973 3298 2.978824 CGTGAATGGTCCTCCGGT 59.021 61.111 0.00 0.00 36.30 5.28
2974 3299 2.511600 GCGTGAATGGTCCTCCGG 60.512 66.667 0.00 0.00 36.30 5.14
2978 3303 2.108514 CATGCGCGTGAATGGTCCT 61.109 57.895 25.38 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.