Multiple sequence alignment - TraesCS7A01G353700

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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 TraesCS7A01G353700 chr7A 100.000 3599 0 0 1 3599 517647309 517643711 0.000000e+00 6647.0
1 TraesCS7A01G353700 chr7A 84.906 636 79 5 1553 2188 733832937 733833555 8.480000e-176 627.0
2 TraesCS7A01G353700 chr7A 83.486 218 25 7 2334 2544 733833579 733833792 3.670000e-45 193.0
3 TraesCS7A01G353700 chr7D 93.622 2587 146 12 1031 3599 478067044 478069629 0.000000e+00 3845.0
4 TraesCS7A01G353700 chr7D 91.151 1051 57 19 2 1042 478065855 478066879 0.000000e+00 1393.0
5 TraesCS7A01G353700 chr7B 90.206 1746 129 13 1269 2987 503147675 503149405 0.000000e+00 2239.0
6 TraesCS7A01G353700 chr7B 91.606 822 47 9 454 1273 503142335 503143136 0.000000e+00 1116.0
7 TraesCS7A01G353700 chr7B 91.608 143 8 3 165 305 503128258 503128398 1.020000e-45 195.0
8 TraesCS7A01G353700 chr7B 88.415 164 13 4 298 461 503137460 503137617 3.670000e-45 193.0
9 TraesCS7A01G353700 chr7B 100.000 35 0 0 461 495 503142309 503142343 8.340000e-07 65.8
10 TraesCS7A01G353700 chr3B 84.566 1082 142 14 1527 2598 727118821 727119887 0.000000e+00 1050.0
11 TraesCS7A01G353700 chr2B 85.600 625 80 6 1692 2308 635171798 635172420 0.000000e+00 647.0
12 TraesCS7A01G353700 chr2B 86.195 297 34 5 2304 2598 635198188 635198479 7.500000e-82 315.0
13 TraesCS7A01G353700 chr6B 84.437 302 42 1 1785 2086 129865578 129865874 3.510000e-75 292.0


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 TraesCS7A01G353700 chr7A 517643711 517647309 3598 True 6647.0 6647 100.0000 1 3599 1 chr7A.!!$R1 3598
1 TraesCS7A01G353700 chr7A 733832937 733833792 855 False 410.0 627 84.1960 1553 2544 2 chr7A.!!$F1 991
2 TraesCS7A01G353700 chr7D 478065855 478069629 3774 False 2619.0 3845 92.3865 2 3599 2 chr7D.!!$F1 3597
3 TraesCS7A01G353700 chr7B 503147675 503149405 1730 False 2239.0 2239 90.2060 1269 2987 1 chr7B.!!$F3 1718
4 TraesCS7A01G353700 chr7B 503142309 503143136 827 False 590.9 1116 95.8030 454 1273 2 chr7B.!!$F4 819
5 TraesCS7A01G353700 chr3B 727118821 727119887 1066 False 1050.0 1050 84.5660 1527 2598 1 chr3B.!!$F1 1071
6 TraesCS7A01G353700 chr2B 635171798 635172420 622 False 647.0 647 85.6000 1692 2308 1 chr2B.!!$F1 616

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
387 396 0.678395 CCGCAGCATCTCCTAGTGAT 59.322 55.0 0.00 0.0 0.0 3.06 F
1060 1247 0.527113 CGTTTGCATTGCCATCTCCA 59.473 50.0 6.12 0.0 0.0 3.86 F
2326 2524 0.120377 TATGGGTTGGGTCAGGAGGT 59.880 55.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 1555 0.319040 CCAGATCGACGATGGCGAAT 60.319 55.0 16.49 0.0 41.52 3.34 R
2513 2718 0.107214 GAAATCAGCGGGATCCACCA 60.107 55.0 15.23 0.0 41.20 4.17 R
3138 3372 0.471211 CTCCTTATCGGCCCTACCCA 60.471 60.0 0.00 0.0 33.26 4.51 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
39 40 8.577296 TGTATCCTACTTTACATCATCTGCTAC 58.423 37.037 0.00 0.00 0.00 3.58
55 56 3.271729 TGCTACGGCATAAAAATTCGGA 58.728 40.909 0.00 0.00 44.28 4.55
56 57 3.311322 TGCTACGGCATAAAAATTCGGAG 59.689 43.478 0.00 0.00 44.28 4.63
57 58 2.844122 ACGGCATAAAAATTCGGAGC 57.156 45.000 0.00 0.00 0.00 4.70
58 59 1.404035 ACGGCATAAAAATTCGGAGCC 59.596 47.619 0.00 0.00 37.32 4.70
60 61 2.031870 GGCATAAAAATTCGGAGCCCT 58.968 47.619 0.00 0.00 34.71 5.19
61 62 2.223805 GGCATAAAAATTCGGAGCCCTG 60.224 50.000 0.00 0.00 34.71 4.45
62 63 2.687935 GCATAAAAATTCGGAGCCCTGA 59.312 45.455 0.00 0.00 0.00 3.86
64 65 4.672409 CATAAAAATTCGGAGCCCTGAAC 58.328 43.478 0.00 0.00 40.21 3.18
65 66 1.165270 AAAATTCGGAGCCCTGAACG 58.835 50.000 0.00 0.00 40.21 3.95
77 80 1.472480 CCCTGAACGCTACATTTTGGG 59.528 52.381 0.00 0.00 0.00 4.12
93 96 2.480642 TGGGCCCCTAAAACTGTTTT 57.519 45.000 22.27 20.87 36.67 2.43
116 119 4.406456 TGGGTGCCCAATTATACATCATC 58.594 43.478 7.63 0.00 44.12 2.92
122 125 6.262944 GTGCCCAATTATACATCATCTGTTGA 59.737 38.462 0.00 0.00 39.39 3.18
125 128 7.522725 GCCCAATTATACATCATCTGTTGAAGG 60.523 40.741 0.00 0.00 39.39 3.46
127 130 9.559732 CCAATTATACATCATCTGTTGAAGGTA 57.440 33.333 0.00 0.51 39.39 3.08
135 138 8.200792 ACATCATCTGTTGAAGGTACTCTAATC 58.799 37.037 0.00 0.00 38.03 1.75
136 139 6.796426 TCATCTGTTGAAGGTACTCTAATCG 58.204 40.000 0.00 0.00 38.49 3.34
162 165 1.271271 GGCTTGGCCCTCTCATATCTG 60.271 57.143 0.00 0.00 44.06 2.90
166 169 4.444876 GCTTGGCCCTCTCATATCTGTAAA 60.445 45.833 0.00 0.00 0.00 2.01
201 204 7.230849 TGACAAATGATAAGCAATCCAAACT 57.769 32.000 0.00 0.00 33.22 2.66
203 206 8.801299 TGACAAATGATAAGCAATCCAAACTAA 58.199 29.630 0.00 0.00 33.22 2.24
204 207 8.986477 ACAAATGATAAGCAATCCAAACTAAC 57.014 30.769 0.00 0.00 33.22 2.34
248 256 9.872757 CATTTGTAGCTTAGTTAAAAGAAACGA 57.127 29.630 0.00 0.00 34.46 3.85
266 274 7.659186 AGAAACGACACTAACTAACTCATCTT 58.341 34.615 0.00 0.00 0.00 2.40
268 276 5.952033 ACGACACTAACTAACTCATCTTCC 58.048 41.667 0.00 0.00 0.00 3.46
271 279 4.463186 ACACTAACTAACTCATCTTCCGCT 59.537 41.667 0.00 0.00 0.00 5.52
324 333 2.217510 TCTCCGCTAGACTTGGTCTT 57.782 50.000 5.50 0.00 40.28 3.01
373 382 1.745087 ACAAGCAAATCCATACCGCAG 59.255 47.619 0.00 0.00 0.00 5.18
387 396 0.678395 CCGCAGCATCTCCTAGTGAT 59.322 55.000 0.00 0.00 0.00 3.06
388 397 1.604947 CCGCAGCATCTCCTAGTGATG 60.605 57.143 14.86 14.86 42.86 3.07
389 398 1.339291 CGCAGCATCTCCTAGTGATGA 59.661 52.381 20.43 1.64 42.68 2.92
390 399 2.029200 CGCAGCATCTCCTAGTGATGAT 60.029 50.000 20.43 14.42 42.68 2.45
397 406 1.974236 CTCCTAGTGATGATGGGTCCC 59.026 57.143 0.00 0.00 0.00 4.46
445 454 6.422400 GCATTGTCGTCCTTTATTTTGGAAAA 59.578 34.615 0.00 0.00 33.72 2.29
448 457 8.950208 TTGTCGTCCTTTATTTTGGAAAATTT 57.050 26.923 2.79 0.00 39.24 1.82
525 534 2.067414 TGCATTTACTCGTGTACGCA 57.933 45.000 7.29 10.03 39.60 5.24
631 641 2.866156 CGATTGCGATATCAACACCACT 59.134 45.455 3.12 0.00 40.82 4.00
641 651 7.401860 CGATATCAACACCACTAAATTCACTG 58.598 38.462 3.12 0.00 0.00 3.66
645 655 1.468520 CACCACTAAATTCACTGGCCG 59.531 52.381 0.00 0.00 0.00 6.13
646 656 1.073284 ACCACTAAATTCACTGGCCGT 59.927 47.619 0.00 0.00 0.00 5.68
647 657 1.468520 CCACTAAATTCACTGGCCGTG 59.531 52.381 18.07 18.07 45.18 4.94
648 658 2.151202 CACTAAATTCACTGGCCGTGT 58.849 47.619 21.61 10.83 44.16 4.49
649 659 2.095768 CACTAAATTCACTGGCCGTGTG 60.096 50.000 21.61 20.41 44.16 3.82
650 660 2.224426 ACTAAATTCACTGGCCGTGTGA 60.224 45.455 22.44 22.44 44.16 3.58
651 661 1.909700 AAATTCACTGGCCGTGTGAT 58.090 45.000 25.41 17.30 42.95 3.06
652 662 2.779755 AATTCACTGGCCGTGTGATA 57.220 45.000 25.41 18.15 42.95 2.15
653 663 3.281727 AATTCACTGGCCGTGTGATAT 57.718 42.857 25.41 19.16 42.95 1.63
654 664 2.309528 TTCACTGGCCGTGTGATATC 57.690 50.000 25.41 0.00 42.95 1.63
655 665 1.485124 TCACTGGCCGTGTGATATCT 58.515 50.000 22.44 0.00 44.16 1.98
656 666 1.831106 TCACTGGCCGTGTGATATCTT 59.169 47.619 22.44 0.00 44.16 2.40
657 667 3.028130 TCACTGGCCGTGTGATATCTTA 58.972 45.455 22.44 4.17 44.16 2.10
658 668 3.449377 TCACTGGCCGTGTGATATCTTAA 59.551 43.478 22.44 3.55 44.16 1.85
659 669 4.081365 TCACTGGCCGTGTGATATCTTAAA 60.081 41.667 22.44 2.95 44.16 1.52
660 670 4.816385 CACTGGCCGTGTGATATCTTAAAT 59.184 41.667 20.09 0.00 38.84 1.40
661 671 5.296780 CACTGGCCGTGTGATATCTTAAATT 59.703 40.000 20.09 0.00 38.84 1.82
666 676 6.292919 GGCCGTGTGATATCTTAAATTCACTC 60.293 42.308 3.98 0.00 39.33 3.51
669 679 6.475727 CGTGTGATATCTTAAATTCACTCGGT 59.524 38.462 14.82 0.00 45.18 4.69
677 687 6.161381 TCTTAAATTCACTCGGTTCCTGTAC 58.839 40.000 0.00 0.00 0.00 2.90
783 794 8.361873 TCAAATTTGACTAGTTTGACGGCAAAC 61.362 37.037 34.62 34.62 45.95 2.93
872 883 2.015227 AACCAACCGCAACCAAGCAG 62.015 55.000 0.00 0.00 0.00 4.24
886 897 2.094286 CCAAGCAGAGAGTACACTCCTG 60.094 54.545 15.66 16.93 43.88 3.86
918 929 5.560183 CGACAAGTGATTTCGGCTTTACTTT 60.560 40.000 0.00 0.00 0.00 2.66
922 933 6.002062 AGTGATTTCGGCTTTACTTTCAAG 57.998 37.500 0.00 0.00 0.00 3.02
942 953 5.188751 TCAAGGTTCCAATTCCAACAAGTTT 59.811 36.000 0.00 0.00 0.00 2.66
943 954 6.381420 TCAAGGTTCCAATTCCAACAAGTTTA 59.619 34.615 0.00 0.00 0.00 2.01
954 965 9.869757 AATTCCAACAAGTTTATATAAGTTGCC 57.130 29.630 15.08 0.00 36.08 4.52
963 974 5.601583 TTATATAAGTTGCCACGGTCTCA 57.398 39.130 0.00 0.00 0.00 3.27
1060 1247 0.527113 CGTTTGCATTGCCATCTCCA 59.473 50.000 6.12 0.00 0.00 3.86
1101 1288 1.523934 GTTAACACCACCGACTTCGTG 59.476 52.381 0.00 0.00 37.74 4.35
1107 1294 4.681978 ACCGACTTCGTGGGCTGC 62.682 66.667 0.00 0.00 34.74 5.25
1110 1297 2.032681 GACTTCGTGGGCTGCCTT 59.967 61.111 19.68 0.00 0.00 4.35
1264 1451 3.533105 ACGCCACACACGTCAGGA 61.533 61.111 0.00 0.00 40.28 3.86
1329 1516 1.146930 CAGCGGTGGCCATGACTAT 59.853 57.895 9.72 0.00 41.24 2.12
1375 1562 4.776322 CGGCTCACCCATTCGCCA 62.776 66.667 0.00 0.00 42.59 5.69
1383 1570 1.300931 CCCATTCGCCATCGTCGAT 60.301 57.895 0.75 0.75 35.75 3.59
1419 1606 3.958822 GATCCGCGTTGACGTCCGT 62.959 63.158 14.12 0.00 42.22 4.69
1579 1766 1.522569 GGCCTGATGCTACGGAAGT 59.477 57.895 0.00 0.00 42.46 3.01
1819 2006 0.471780 TCTCCTCACCAAGTGGCAGA 60.472 55.000 0.00 0.00 39.32 4.26
2323 2521 0.550914 GCATATGGGTTGGGTCAGGA 59.449 55.000 4.56 0.00 0.00 3.86
2326 2524 0.120377 TATGGGTTGGGTCAGGAGGT 59.880 55.000 0.00 0.00 0.00 3.85
2327 2525 1.208165 ATGGGTTGGGTCAGGAGGTC 61.208 60.000 0.00 0.00 0.00 3.85
2524 2729 2.965716 GAAGGCCATGGTGGATCCCG 62.966 65.000 14.67 0.00 40.96 5.14
2556 2761 0.391661 GGAACGAGCAGAGCATTCCA 60.392 55.000 12.13 0.00 37.31 3.53
2564 2769 2.016096 GCAGAGCATTCCACCTCTTCC 61.016 57.143 0.00 0.00 36.33 3.46
2601 2806 1.334599 GGCACGACGCAGAATTGAAAA 60.335 47.619 0.00 0.00 45.17 2.29
2645 2850 6.873997 TGTCTTGAAGAAGTTACTTGACTCA 58.126 36.000 0.93 0.00 0.00 3.41
2652 2857 7.709613 TGAAGAAGTTACTTGACTCAAAGTACC 59.290 37.037 0.93 0.00 41.25 3.34
2666 2871 6.883217 ACTCAAAGTACCGAAGTCTAGATGTA 59.117 38.462 0.00 0.00 0.00 2.29
2734 2942 5.278266 CCTCAAAATTAGAAACCGCTTGTGA 60.278 40.000 0.00 0.00 0.00 3.58
2737 2945 5.705609 AAATTAGAAACCGCTTGTGATGT 57.294 34.783 0.00 0.00 0.00 3.06
2763 2971 4.663636 GTTTCCAACGACTATCACAAGG 57.336 45.455 0.00 0.00 0.00 3.61
2770 2978 1.291132 GACTATCACAAGGCCGCTTC 58.709 55.000 0.00 0.00 0.00 3.86
2775 2984 2.264005 TCACAAGGCCGCTTCTAAAA 57.736 45.000 0.00 0.00 0.00 1.52
2885 3118 1.353609 GCATTTGCGGCCATGTTGAC 61.354 55.000 2.24 0.00 0.00 3.18
2893 3126 0.328258 GGCCATGTTGACTGTACCCT 59.672 55.000 0.00 0.00 0.00 4.34
2933 3167 1.608590 AGTGTTGGTTTCCTGATTGCG 59.391 47.619 0.00 0.00 0.00 4.85
2952 3186 2.360165 GCGAAGATGCAAAATCATCCCT 59.640 45.455 0.00 0.00 42.84 4.20
2963 3197 2.596904 ATCATCCCTCGTTGTAACCG 57.403 50.000 0.00 0.00 0.00 4.44
2988 3222 1.639722 TCAGAATCGTCTCCACCCAA 58.360 50.000 0.00 0.00 28.78 4.12
2992 3226 2.571653 AGAATCGTCTCCACCCAAATCA 59.428 45.455 0.00 0.00 0.00 2.57
2994 3228 2.940994 TCGTCTCCACCCAAATCAAA 57.059 45.000 0.00 0.00 0.00 2.69
2996 3230 3.146066 TCGTCTCCACCCAAATCAAAAG 58.854 45.455 0.00 0.00 0.00 2.27
3008 3242 6.779539 ACCCAAATCAAAAGAGTCTTTCTCAT 59.220 34.615 18.28 8.07 44.98 2.90
3013 3247 9.741647 AAATCAAAAGAGTCTTTCTCATGAAAC 57.258 29.630 18.28 0.00 44.98 2.78
3018 3252 7.588143 AAGAGTCTTTCTCATGAAACATACG 57.412 36.000 0.00 0.00 44.98 3.06
3025 3259 4.258543 TCTCATGAAACATACGGAAACCC 58.741 43.478 0.00 0.00 0.00 4.11
3026 3260 4.006989 CTCATGAAACATACGGAAACCCA 58.993 43.478 0.00 0.00 0.00 4.51
3027 3261 3.754323 TCATGAAACATACGGAAACCCAC 59.246 43.478 0.00 0.00 0.00 4.61
3029 3263 3.142951 TGAAACATACGGAAACCCACTG 58.857 45.455 0.00 0.00 0.00 3.66
3060 3294 2.783828 AGAGAAGATGCGGACATACG 57.216 50.000 0.00 0.00 36.35 3.06
3061 3295 2.298610 AGAGAAGATGCGGACATACGA 58.701 47.619 0.00 0.00 36.35 3.43
3067 3301 0.385751 ATGCGGACATACGAGTGGAG 59.614 55.000 0.00 0.00 33.67 3.86
3090 3324 6.258160 AGAAACAATGTATATGCGACAAAGC 58.742 36.000 0.00 0.00 37.71 3.51
3091 3325 4.195744 ACAATGTATATGCGACAAAGCG 57.804 40.909 0.00 0.00 40.67 4.68
3115 3349 3.270877 GAATAAGCAAAAGCCTCGAGGA 58.729 45.455 35.69 11.11 37.39 3.71
3123 3357 4.132999 GCCTCGAGGATGAAAGGC 57.867 61.111 35.69 14.25 46.76 4.35
3138 3372 1.740285 AGGCGTGTCGTCTTCTTGT 59.260 52.632 0.00 0.00 39.37 3.16
3149 3383 1.078426 CTTCTTGTGGGTAGGGCCG 60.078 63.158 0.00 0.00 38.44 6.13
3188 3422 7.293073 AGTTGAGAAATCACATATTAGGGCAT 58.707 34.615 0.00 0.00 0.00 4.40
3218 3452 2.286025 GCGTACCCAAAATCGGACATAC 59.714 50.000 0.00 0.00 0.00 2.39
3221 3455 5.535333 CGTACCCAAAATCGGACATACTAT 58.465 41.667 0.00 0.00 0.00 2.12
3226 3460 5.987347 CCCAAAATCGGACATACTATACGTT 59.013 40.000 0.00 0.00 0.00 3.99
3235 3469 4.913376 ACATACTATACGTTCACGGACAC 58.087 43.478 4.07 0.00 44.95 3.67
3241 3475 4.913335 ATACGTTCACGGACACAGATAT 57.087 40.909 4.07 0.00 44.95 1.63
3251 3485 1.957177 GACACAGATATGAGAGCGGGA 59.043 52.381 0.00 0.00 0.00 5.14
3255 3489 2.560542 ACAGATATGAGAGCGGGACATC 59.439 50.000 0.00 0.00 0.00 3.06
3262 3496 2.933287 AGCGGGACATCCAACCCA 60.933 61.111 0.00 0.00 45.83 4.51
3265 3499 1.906105 GCGGGACATCCAACCCACTA 61.906 60.000 0.00 0.00 45.83 2.74
3266 3500 0.107848 CGGGACATCCAACCCACTAC 60.108 60.000 0.00 0.00 45.83 2.73
3274 3508 1.564818 TCCAACCCACTACACCAAACA 59.435 47.619 0.00 0.00 0.00 2.83
3286 3520 6.098409 CACTACACCAAACATCTACCCTATCT 59.902 42.308 0.00 0.00 0.00 1.98
3309 3543 3.554324 GCCCCTGTTTTCGTTTTCTTTTC 59.446 43.478 0.00 0.00 0.00 2.29
3310 3544 3.794564 CCCCTGTTTTCGTTTTCTTTTCG 59.205 43.478 0.00 0.00 0.00 3.46
3311 3545 3.242016 CCCTGTTTTCGTTTTCTTTTCGC 59.758 43.478 0.00 0.00 0.00 4.70
3312 3546 3.062124 CCTGTTTTCGTTTTCTTTTCGCG 60.062 43.478 0.00 0.00 0.00 5.87
3331 3570 4.983538 TCGCGTCACTCAAAATAAGTACAA 59.016 37.500 5.77 0.00 0.00 2.41
3447 3694 6.746104 TCAAACATAAATTCAACTTGCACG 57.254 33.333 0.00 0.00 0.00 5.34
3452 3699 6.908825 ACATAAATTCAACTTGCACGTATGT 58.091 32.000 0.00 0.00 0.00 2.29
3454 3701 7.865385 ACATAAATTCAACTTGCACGTATGTTT 59.135 29.630 0.00 0.00 0.00 2.83
3459 3706 4.025229 TCAACTTGCACGTATGTTTGAGTC 60.025 41.667 0.00 0.00 0.00 3.36
3465 3712 3.512680 CACGTATGTTTGAGTCCTCTCC 58.487 50.000 0.00 0.00 39.75 3.71
3466 3713 3.056821 CACGTATGTTTGAGTCCTCTCCA 60.057 47.826 0.00 0.00 39.75 3.86
3470 3717 6.070995 ACGTATGTTTGAGTCCTCTCCATTAA 60.071 38.462 0.00 0.00 39.75 1.40
3474 3721 6.778821 TGTTTGAGTCCTCTCCATTAAATGA 58.221 36.000 0.00 0.00 39.75 2.57
3506 3753 4.202243 GCTCAACCAGATCATTCTAGAGCT 60.202 45.833 14.70 0.00 38.02 4.09
3512 3759 4.946445 CAGATCATTCTAGAGCTGCTCAA 58.054 43.478 29.49 16.58 43.95 3.02
3534 3781 2.540101 GAGTTCCTCAATGCCGAATACG 59.460 50.000 0.00 0.00 39.43 3.06
3536 3783 2.218953 TCCTCAATGCCGAATACGTC 57.781 50.000 0.00 0.00 37.88 4.34
3556 3803 5.971202 ACGTCGATGCATTTGGATAAAATTC 59.029 36.000 4.06 0.00 36.28 2.17
3558 3805 7.011950 ACGTCGATGCATTTGGATAAAATTCTA 59.988 33.333 4.06 0.00 36.28 2.10
3569 3816 7.715265 TGGATAAAATTCTAGAACATCGCTC 57.285 36.000 7.48 1.26 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.603180 AGCAGATGATGTAAAGTAGGATACA 57.397 36.000 0.00 0.00 46.26 2.29
39 40 1.269051 GGGCTCCGAATTTTTATGCCG 60.269 52.381 0.00 0.00 39.73 5.69
43 44 3.377172 CGTTCAGGGCTCCGAATTTTTAT 59.623 43.478 0.00 0.00 0.00 1.40
52 53 2.202756 GTAGCGTTCAGGGCTCCG 60.203 66.667 0.00 0.00 41.80 4.63
53 54 0.107654 AATGTAGCGTTCAGGGCTCC 60.108 55.000 0.00 0.00 41.80 4.70
55 56 1.812571 CAAAATGTAGCGTTCAGGGCT 59.187 47.619 0.00 0.00 44.35 5.19
56 57 1.135402 CCAAAATGTAGCGTTCAGGGC 60.135 52.381 0.00 0.00 0.00 5.19
57 58 1.472480 CCCAAAATGTAGCGTTCAGGG 59.528 52.381 0.00 0.00 0.00 4.45
58 59 1.135402 GCCCAAAATGTAGCGTTCAGG 60.135 52.381 0.00 0.00 0.00 3.86
60 61 0.885196 GGCCCAAAATGTAGCGTTCA 59.115 50.000 0.00 0.00 0.00 3.18
61 62 0.172578 GGGCCCAAAATGTAGCGTTC 59.827 55.000 19.95 0.00 0.00 3.95
62 63 1.254975 GGGGCCCAAAATGTAGCGTT 61.255 55.000 26.86 0.00 0.00 4.84
64 65 0.106918 TAGGGGCCCAAAATGTAGCG 60.107 55.000 27.72 0.00 0.00 4.26
65 66 2.153034 TTAGGGGCCCAAAATGTAGC 57.847 50.000 27.72 1.71 0.00 3.58
77 80 2.436542 ACCCAAAAACAGTTTTAGGGGC 59.563 45.455 30.83 0.00 44.78 5.80
106 109 8.768501 AGAGTACCTTCAACAGATGATGTATA 57.231 34.615 0.00 0.00 43.00 1.47
107 110 7.667575 AGAGTACCTTCAACAGATGATGTAT 57.332 36.000 0.00 0.00 43.00 2.29
108 111 8.589701 TTAGAGTACCTTCAACAGATGATGTA 57.410 34.615 0.00 0.00 43.00 2.29
116 119 5.357314 TCTCCGATTAGAGTACCTTCAACAG 59.643 44.000 0.00 0.00 35.28 3.16
122 125 3.212685 CCGTCTCCGATTAGAGTACCTT 58.787 50.000 0.00 0.00 35.28 3.50
125 128 2.220313 AGCCGTCTCCGATTAGAGTAC 58.780 52.381 0.00 0.00 35.28 2.73
127 130 1.405821 CAAGCCGTCTCCGATTAGAGT 59.594 52.381 0.00 0.00 35.28 3.24
248 256 4.463186 AGCGGAAGATGAGTTAGTTAGTGT 59.537 41.667 0.00 0.00 0.00 3.55
266 274 5.790593 AGAGTGATGTTTTACTTAAGCGGA 58.209 37.500 1.29 0.00 0.00 5.54
268 276 6.237861 GGCTAGAGTGATGTTTTACTTAAGCG 60.238 42.308 1.29 0.00 36.57 4.68
271 279 7.389607 GGTTGGCTAGAGTGATGTTTTACTTAA 59.610 37.037 0.00 0.00 0.00 1.85
373 382 2.636893 ACCCATCATCACTAGGAGATGC 59.363 50.000 17.79 0.00 41.98 3.91
387 396 4.408821 GTGCGCAGGGACCCATCA 62.409 66.667 12.22 1.44 0.00 3.07
448 457 6.770785 GGCATGTCCATACAAAGTCCTAAATA 59.229 38.462 0.00 0.00 39.58 1.40
449 458 5.594317 GGCATGTCCATACAAAGTCCTAAAT 59.406 40.000 0.00 0.00 39.58 1.40
452 461 3.521531 TGGCATGTCCATACAAAGTCCTA 59.478 43.478 4.93 0.00 40.72 2.94
453 462 2.308570 TGGCATGTCCATACAAAGTCCT 59.691 45.455 4.93 0.00 40.72 3.85
497 506 6.735678 ACACGAGTAAATGCATTCATGTAA 57.264 33.333 13.38 0.00 32.23 2.41
594 604 4.911610 CGCAATCGAAAACTGAATTTGAGT 59.088 37.500 0.00 0.00 38.10 3.41
625 635 1.468520 CGGCCAGTGAATTTAGTGGTG 59.531 52.381 21.56 12.90 42.12 4.17
641 651 5.527582 AGTGAATTTAAGATATCACACGGCC 59.472 40.000 5.32 0.00 43.53 6.13
645 655 7.772332 ACCGAGTGAATTTAAGATATCACAC 57.228 36.000 5.32 0.00 43.53 3.82
646 656 7.494625 GGAACCGAGTGAATTTAAGATATCACA 59.505 37.037 5.32 0.00 43.53 3.58
647 657 7.711339 AGGAACCGAGTGAATTTAAGATATCAC 59.289 37.037 5.32 0.00 41.88 3.06
648 658 7.710907 CAGGAACCGAGTGAATTTAAGATATCA 59.289 37.037 5.32 0.00 0.00 2.15
649 659 7.711339 ACAGGAACCGAGTGAATTTAAGATATC 59.289 37.037 0.00 0.00 0.00 1.63
650 660 7.565680 ACAGGAACCGAGTGAATTTAAGATAT 58.434 34.615 0.00 0.00 0.00 1.63
651 661 6.942976 ACAGGAACCGAGTGAATTTAAGATA 58.057 36.000 0.00 0.00 0.00 1.98
652 662 5.805728 ACAGGAACCGAGTGAATTTAAGAT 58.194 37.500 0.00 0.00 0.00 2.40
653 663 5.223449 ACAGGAACCGAGTGAATTTAAGA 57.777 39.130 0.00 0.00 0.00 2.10
654 664 6.164176 AGTACAGGAACCGAGTGAATTTAAG 58.836 40.000 0.00 0.00 0.00 1.85
655 665 6.105397 AGTACAGGAACCGAGTGAATTTAA 57.895 37.500 0.00 0.00 0.00 1.52
656 666 5.733620 AGTACAGGAACCGAGTGAATTTA 57.266 39.130 0.00 0.00 0.00 1.40
657 667 4.618920 AGTACAGGAACCGAGTGAATTT 57.381 40.909 0.00 0.00 0.00 1.82
658 668 4.618920 AAGTACAGGAACCGAGTGAATT 57.381 40.909 0.00 0.00 0.00 2.17
659 669 4.618920 AAAGTACAGGAACCGAGTGAAT 57.381 40.909 0.00 0.00 0.00 2.57
660 670 4.411256 AAAAGTACAGGAACCGAGTGAA 57.589 40.909 0.00 0.00 0.00 3.18
661 671 5.733620 ATAAAAGTACAGGAACCGAGTGA 57.266 39.130 0.00 0.00 0.00 3.41
666 676 7.919621 CCTAGACTAATAAAAGTACAGGAACCG 59.080 40.741 0.00 0.00 34.56 4.44
669 679 7.417116 CGCCCTAGACTAATAAAAGTACAGGAA 60.417 40.741 0.00 0.00 34.56 3.36
677 687 4.039366 AGAGCCGCCCTAGACTAATAAAAG 59.961 45.833 0.00 0.00 0.00 2.27
783 794 1.167851 ATGGTCGCACAACAAGGATG 58.832 50.000 0.00 0.00 0.00 3.51
872 883 1.551452 ACCAGCAGGAGTGTACTCTC 58.449 55.000 15.15 15.15 42.48 3.20
886 897 0.593128 AATCACTTGTCGCAACCAGC 59.407 50.000 0.00 0.00 40.87 4.85
918 929 4.285863 ACTTGTTGGAATTGGAACCTTGA 58.714 39.130 0.00 0.00 0.00 3.02
942 953 4.038763 CCTGAGACCGTGGCAACTTATATA 59.961 45.833 0.00 0.00 37.61 0.86
943 954 3.181465 CCTGAGACCGTGGCAACTTATAT 60.181 47.826 0.00 0.00 37.61 0.86
954 965 1.214062 GAGTCAGCCTGAGACCGTG 59.786 63.158 0.00 0.00 36.68 4.94
1107 1294 2.203549 GAGGAAGGTGGAGGGCAAGG 62.204 65.000 0.00 0.00 0.00 3.61
1110 1297 2.610859 GGAGGAAGGTGGAGGGCA 60.611 66.667 0.00 0.00 0.00 5.36
1329 1516 2.279073 CGGTAGGAGAGCCCCTCA 59.721 66.667 6.13 0.00 43.76 3.86
1364 1551 2.028125 ATCGACGATGGCGAATGGGT 62.028 55.000 10.09 0.00 41.52 4.51
1368 1555 0.319040 CCAGATCGACGATGGCGAAT 60.319 55.000 16.49 0.00 41.52 3.34
1375 1562 4.630785 CGCCGCCAGATCGACGAT 62.631 66.667 10.78 10.78 37.52 3.73
1410 1597 2.683859 CGACCTGCTACGGACGTCA 61.684 63.158 18.91 0.00 37.43 4.35
2138 2326 1.984570 TCCTCCAGGAACCAGCTCG 60.985 63.158 0.00 0.00 42.18 5.03
2239 2429 3.188786 CAGGTTGTAGAGCGCGCC 61.189 66.667 30.33 19.60 0.00 6.53
2323 2521 3.461773 CATCTCCCGGTGCGACCT 61.462 66.667 0.00 0.00 35.66 3.85
2326 2524 3.147595 CTCCATCTCCCGGTGCGA 61.148 66.667 0.00 0.00 0.00 5.10
2327 2525 4.899239 GCTCCATCTCCCGGTGCG 62.899 72.222 0.00 0.00 33.73 5.34
2513 2718 0.107214 GAAATCAGCGGGATCCACCA 60.107 55.000 15.23 0.00 41.20 4.17
2556 2761 1.916181 CCACCTGGTAATGGAAGAGGT 59.084 52.381 0.00 0.00 38.34 3.85
2601 2806 9.971922 CAAGACAAGAGAAAAATTAACATTCCT 57.028 29.630 0.00 0.00 0.00 3.36
2672 2877 7.090953 TCCACGACAAGTTTGAATTTTACTT 57.909 32.000 0.00 0.00 32.60 2.24
2676 2883 5.748152 CACATCCACGACAAGTTTGAATTTT 59.252 36.000 0.00 0.00 0.00 1.82
2763 2971 0.672711 AGTCGGGTTTTAGAAGCGGC 60.673 55.000 0.00 0.00 34.67 6.53
2770 2978 5.796350 ATCGATGAAAAGTCGGGTTTTAG 57.204 39.130 0.00 0.00 39.45 1.85
2775 2984 3.782046 CAGTATCGATGAAAAGTCGGGT 58.218 45.455 8.54 0.00 39.45 5.28
2858 3091 1.028905 GGCCGCAAATGCCTAATACA 58.971 50.000 0.00 0.00 45.70 2.29
2885 3118 3.401033 TGTTGATCACACAGGGTACAG 57.599 47.619 0.00 0.00 0.00 2.74
2893 3126 4.996758 CACTCATAGGTTGTTGATCACACA 59.003 41.667 0.00 0.49 33.98 3.72
2933 3167 3.629398 ACGAGGGATGATTTTGCATCTTC 59.371 43.478 0.00 0.00 43.25 2.87
2952 3186 2.756207 TCTGATCATCCGGTTACAACGA 59.244 45.455 0.00 0.00 0.00 3.85
2963 3197 3.553922 GGTGGAGACGATTCTGATCATCC 60.554 52.174 0.00 0.00 33.13 3.51
2988 3222 8.906867 TGTTTCATGAGAAAGACTCTTTTGATT 58.093 29.630 5.49 0.00 43.95 2.57
2992 3226 8.499162 CGTATGTTTCATGAGAAAGACTCTTTT 58.501 33.333 5.49 0.00 43.95 2.27
2994 3228 6.591834 CCGTATGTTTCATGAGAAAGACTCTT 59.408 38.462 0.00 0.00 43.95 2.85
2996 3230 6.100004 TCCGTATGTTTCATGAGAAAGACTC 58.900 40.000 0.00 0.00 43.95 3.36
3008 3242 3.142951 CAGTGGGTTTCCGTATGTTTCA 58.857 45.455 0.00 0.00 35.24 2.69
3013 3247 0.802494 GCACAGTGGGTTTCCGTATG 59.198 55.000 1.84 0.00 35.24 2.39
3018 3252 2.027192 TCTCATAGCACAGTGGGTTTCC 60.027 50.000 1.84 0.00 0.00 3.13
3025 3259 5.718146 TCTTCTCTTTCTCATAGCACAGTG 58.282 41.667 0.00 0.00 0.00 3.66
3026 3260 5.991933 TCTTCTCTTTCTCATAGCACAGT 57.008 39.130 0.00 0.00 0.00 3.55
3027 3261 5.234757 GCATCTTCTCTTTCTCATAGCACAG 59.765 44.000 0.00 0.00 0.00 3.66
3029 3263 4.208873 CGCATCTTCTCTTTCTCATAGCAC 59.791 45.833 0.00 0.00 0.00 4.40
3060 3294 5.753438 TCGCATATACATTGTTTCTCCACTC 59.247 40.000 0.00 0.00 0.00 3.51
3061 3295 5.523916 GTCGCATATACATTGTTTCTCCACT 59.476 40.000 0.00 0.00 0.00 4.00
3067 3301 5.169561 CGCTTTGTCGCATATACATTGTTTC 59.830 40.000 0.00 0.00 0.00 2.78
3090 3324 2.476185 CGAGGCTTTTGCTTATTCACCG 60.476 50.000 0.00 0.00 46.54 4.94
3091 3325 2.747446 TCGAGGCTTTTGCTTATTCACC 59.253 45.455 0.00 0.00 46.54 4.02
3115 3349 1.000955 AGAAGACGACACGCCTTTCAT 59.999 47.619 0.00 0.00 28.41 2.57
3123 3357 0.249322 ACCCACAAGAAGACGACACG 60.249 55.000 0.00 0.00 0.00 4.49
3138 3372 0.471211 CTCCTTATCGGCCCTACCCA 60.471 60.000 0.00 0.00 33.26 4.51
3149 3383 9.003658 TGATTTCTCAACTTGTTTCTCCTTATC 57.996 33.333 0.00 0.00 0.00 1.75
3188 3422 0.693622 TTTGGGTACGCCATTGGAGA 59.306 50.000 13.81 0.00 36.17 3.71
3210 3444 3.248363 TCCGTGAACGTATAGTATGTCCG 59.752 47.826 1.75 0.00 37.74 4.79
3218 3452 3.752412 TCTGTGTCCGTGAACGTATAG 57.248 47.619 1.75 0.00 37.74 1.31
3221 3455 3.690628 TCATATCTGTGTCCGTGAACGTA 59.309 43.478 1.75 0.00 37.74 3.57
3226 3460 2.359214 GCTCTCATATCTGTGTCCGTGA 59.641 50.000 0.00 0.00 0.00 4.35
3235 3469 2.094286 GGATGTCCCGCTCTCATATCTG 60.094 54.545 0.00 0.00 0.00 2.90
3241 3475 1.596934 GTTGGATGTCCCGCTCTCA 59.403 57.895 0.00 0.00 37.93 3.27
3251 3485 1.440618 TGGTGTAGTGGGTTGGATGT 58.559 50.000 0.00 0.00 0.00 3.06
3255 3489 2.060050 TGTTTGGTGTAGTGGGTTGG 57.940 50.000 0.00 0.00 0.00 3.77
3262 3496 6.098409 CAGATAGGGTAGATGTTTGGTGTAGT 59.902 42.308 0.00 0.00 0.00 2.73
3265 3499 4.384208 GCAGATAGGGTAGATGTTTGGTGT 60.384 45.833 0.00 0.00 0.00 4.16
3266 3500 4.130118 GCAGATAGGGTAGATGTTTGGTG 58.870 47.826 0.00 0.00 0.00 4.17
3274 3508 1.509961 ACAGGGGCAGATAGGGTAGAT 59.490 52.381 0.00 0.00 0.00 1.98
3286 3520 1.770294 AGAAAACGAAAACAGGGGCA 58.230 45.000 0.00 0.00 0.00 5.36
3309 3543 4.896562 TGTACTTATTTTGAGTGACGCG 57.103 40.909 3.53 3.53 0.00 6.01
3447 3694 8.616076 CATTTAATGGAGAGGACTCAAACATAC 58.384 37.037 1.75 0.00 44.22 2.39
3452 3699 6.180472 GGTCATTTAATGGAGAGGACTCAAA 58.820 40.000 5.02 0.00 44.22 2.69
3454 3701 4.782691 TGGTCATTTAATGGAGAGGACTCA 59.217 41.667 5.02 0.00 44.22 3.41
3459 3706 6.567050 CATTTGTGGTCATTTAATGGAGAGG 58.433 40.000 5.02 0.00 0.00 3.69
3465 3712 6.091169 GGTTGAGCATTTGTGGTCATTTAATG 59.909 38.462 10.61 0.00 44.35 1.90
3466 3713 6.165577 GGTTGAGCATTTGTGGTCATTTAAT 58.834 36.000 10.61 0.00 44.35 1.40
3470 3717 2.964464 TGGTTGAGCATTTGTGGTCATT 59.036 40.909 10.61 0.00 44.35 2.57
3474 3721 2.363306 TCTGGTTGAGCATTTGTGGT 57.637 45.000 0.00 0.00 0.00 4.16
3534 3781 8.559536 TCTAGAATTTTATCCAAATGCATCGAC 58.440 33.333 0.00 0.00 35.09 4.20
3536 3783 9.173939 GTTCTAGAATTTTATCCAAATGCATCG 57.826 33.333 8.75 0.00 35.09 3.84
3556 3803 3.553511 AGCAAAATCGAGCGATGTTCTAG 59.446 43.478 6.11 0.00 34.70 2.43
3558 3805 2.349886 GAGCAAAATCGAGCGATGTTCT 59.650 45.455 6.11 6.76 34.70 3.01
3569 3816 4.691860 ATCCAACTTCAGAGCAAAATCG 57.308 40.909 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.