Multiple sequence alignment - TraesCS2D01G463100

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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 TraesCS2D01G463100 chr2D 100.000 3641 0 0 1 3641 568946029 568942389 0.000000e+00 6724.0
1 TraesCS2D01G463100 chr2B 90.873 3276 160 73 393 3597 681544586 681541379 0.000000e+00 4265.0
2 TraesCS2D01G463100 chr2B 82.482 411 30 21 1 373 681545100 681544694 4.540000e-84 322.0
3 TraesCS2D01G463100 chr2A 91.830 2558 140 20 392 2920 708190540 708188023 0.000000e+00 3502.0
4 TraesCS2D01G463100 chr2A 84.125 674 40 33 2916 3544 708187963 708187312 1.130000e-164 590.0
5 TraesCS2D01G463100 chr2A 81.538 390 36 18 1 369 708191021 708190647 4.600000e-74 289.0
6 TraesCS2D01G463100 chr3B 100.000 29 0 0 1765 1793 736658554 736658582 2.000000e-03 54.7
7 TraesCS2D01G463100 chr3A 100.000 29 0 0 1765 1793 690957875 690957903 2.000000e-03 54.7


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 TraesCS2D01G463100 chr2D 568942389 568946029 3640 True 6724.000000 6724 100.0000 1 3641 1 chr2D.!!$R1 3640
1 TraesCS2D01G463100 chr2B 681541379 681545100 3721 True 2293.500000 4265 86.6775 1 3597 2 chr2B.!!$R1 3596
2 TraesCS2D01G463100 chr2A 708187312 708191021 3709 True 1460.333333 3502 85.8310 1 3544 3 chr2A.!!$R1 3543

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
238 268 0.390472 CCAGCTCCGGACTCTGTTTC 60.390 60.0 21.19 0.0 0.00 2.78 F
588 735 0.976641 ACTTGCGACCATCAAGAGGA 59.023 50.0 9.40 0.0 42.52 3.71 F
1430 1607 0.038159 AAGGCGTCCGAGAGTTCTTG 60.038 55.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1592 1.535896 TCAGTCAAGAACTCTCGGACG 59.464 52.381 6.08 0.0 35.45 4.79 R
2553 2730 0.895530 ATCTCGATGTGTTGGACCGT 59.104 50.000 0.00 0.0 0.00 4.83 R
3041 3293 0.250234 CAGCCCGTTTCTGGATGAGA 59.750 55.000 0.00 0.0 41.83 3.27 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
76 89 4.521062 CCGCCTCCTCTCGCCTTG 62.521 72.222 0.00 0.00 0.00 3.61
95 108 2.262915 CTCGTCCTCACCCACTGC 59.737 66.667 0.00 0.00 0.00 4.40
97 110 2.219325 CTCGTCCTCACCCACTGCTC 62.219 65.000 0.00 0.00 0.00 4.26
121 134 1.201736 GCCGTCGTCGTTGTTTATCAC 60.202 52.381 0.71 0.00 35.01 3.06
147 174 1.080839 GAGCCAGGCTCGATCGATC 60.081 63.158 26.09 14.83 45.85 3.69
148 175 1.800283 GAGCCAGGCTCGATCGATCA 61.800 60.000 26.09 11.08 45.85 2.92
215 245 1.409982 GCTCTCGCGCTGTCTTCTTC 61.410 60.000 5.56 0.00 0.00 2.87
230 260 1.219393 CTTCCTTCCAGCTCCGGAC 59.781 63.158 0.00 0.00 33.75 4.79
233 263 1.684049 CCTTCCAGCTCCGGACTCT 60.684 63.158 0.00 0.00 33.75 3.24
235 265 1.228894 TTCCAGCTCCGGACTCTGT 60.229 57.895 21.19 0.00 33.75 3.41
237 267 0.832135 TCCAGCTCCGGACTCTGTTT 60.832 55.000 21.19 0.00 0.00 2.83
238 268 0.390472 CCAGCTCCGGACTCTGTTTC 60.390 60.000 21.19 0.00 0.00 2.78
240 270 1.001406 CAGCTCCGGACTCTGTTTCTT 59.999 52.381 16.93 0.00 0.00 2.52
241 271 1.694696 AGCTCCGGACTCTGTTTCTTT 59.305 47.619 0.00 0.00 0.00 2.52
243 273 2.224314 GCTCCGGACTCTGTTTCTTTTG 59.776 50.000 0.00 0.00 0.00 2.44
244 274 2.808543 CTCCGGACTCTGTTTCTTTTGG 59.191 50.000 0.00 0.00 0.00 3.28
246 276 1.880027 CGGACTCTGTTTCTTTTGGGG 59.120 52.381 0.00 0.00 0.00 4.96
333 371 1.239347 GGCCGTCTTTGCTTCTTTCT 58.761 50.000 0.00 0.00 0.00 2.52
334 372 1.609072 GGCCGTCTTTGCTTCTTTCTT 59.391 47.619 0.00 0.00 0.00 2.52
335 373 2.812011 GGCCGTCTTTGCTTCTTTCTTA 59.188 45.455 0.00 0.00 0.00 2.10
373 415 1.546029 GGGGACAAGTTTTCATGGCTC 59.454 52.381 0.00 0.00 0.00 4.70
374 416 2.519013 GGGACAAGTTTTCATGGCTCT 58.481 47.619 0.00 0.00 0.00 4.09
375 417 2.893489 GGGACAAGTTTTCATGGCTCTT 59.107 45.455 0.00 0.00 0.00 2.85
376 418 3.305608 GGGACAAGTTTTCATGGCTCTTG 60.306 47.826 14.35 14.35 40.54 3.02
377 419 3.569701 GGACAAGTTTTCATGGCTCTTGA 59.430 43.478 19.31 0.00 38.82 3.02
378 420 4.320788 GGACAAGTTTTCATGGCTCTTGAG 60.321 45.833 19.31 0.00 38.82 3.02
389 476 2.108075 TGGCTCTTGAGTCCAAATCCAA 59.892 45.455 9.99 0.00 0.00 3.53
390 477 2.489722 GGCTCTTGAGTCCAAATCCAAC 59.510 50.000 0.00 0.00 0.00 3.77
397 535 8.477419 TCTTGAGTCCAAATCCAACTTATTTT 57.523 30.769 0.00 0.00 0.00 1.82
453 591 2.189594 TGCTCTGTGTCCAAATCCAG 57.810 50.000 0.00 0.00 0.00 3.86
477 615 1.135024 CATTTCCGAATGGGTTGGCTG 60.135 52.381 0.00 0.00 39.17 4.85
482 620 1.949525 CCGAATGGGTTGGCTGATTAG 59.050 52.381 0.00 0.00 0.00 1.73
488 626 6.576244 CGAATGGGTTGGCTGATTAGGATATA 60.576 42.308 0.00 0.00 0.00 0.86
489 627 6.915468 ATGGGTTGGCTGATTAGGATATAT 57.085 37.500 0.00 0.00 0.00 0.86
505 643 9.929180 TTAGGATATATTTCTGATCTTCAACGG 57.071 33.333 0.00 0.00 0.00 4.44
506 644 7.390027 AGGATATATTTCTGATCTTCAACGGG 58.610 38.462 0.00 0.00 0.00 5.28
538 684 1.599797 AGCGGTTGTGTTAGGTGCC 60.600 57.895 0.00 0.00 0.00 5.01
550 697 4.097286 GTGTTAGGTGCCTGTTTCTTTCAA 59.903 41.667 0.12 0.00 0.00 2.69
563 710 4.927267 TTCTTTCAAAGAGATAGGGCCA 57.073 40.909 6.18 0.00 39.03 5.36
564 711 4.927267 TCTTTCAAAGAGATAGGGCCAA 57.073 40.909 6.18 0.00 32.71 4.52
584 731 4.466828 CAAGTTTACTTGCGACCATCAAG 58.533 43.478 9.47 1.63 45.59 3.02
585 732 4.002906 AGTTTACTTGCGACCATCAAGA 57.997 40.909 9.40 0.00 42.52 3.02
587 734 2.672961 TACTTGCGACCATCAAGAGG 57.327 50.000 9.40 0.00 42.52 3.69
588 735 0.976641 ACTTGCGACCATCAAGAGGA 59.023 50.000 9.40 0.00 42.52 3.71
589 736 1.347707 ACTTGCGACCATCAAGAGGAA 59.652 47.619 9.40 0.00 42.52 3.36
590 737 2.026822 ACTTGCGACCATCAAGAGGAAT 60.027 45.455 9.40 0.00 42.52 3.01
591 738 2.028420 TGCGACCATCAAGAGGAATG 57.972 50.000 0.00 0.00 0.00 2.67
592 739 1.278985 TGCGACCATCAAGAGGAATGT 59.721 47.619 0.00 0.00 0.00 2.71
593 740 2.290260 TGCGACCATCAAGAGGAATGTT 60.290 45.455 0.00 0.00 0.00 2.71
594 741 2.749621 GCGACCATCAAGAGGAATGTTT 59.250 45.455 0.00 0.00 0.00 2.83
644 791 4.202274 GGAGGGATGGCTTCTCTACTAAAC 60.202 50.000 5.25 0.00 34.33 2.01
645 792 4.625963 AGGGATGGCTTCTCTACTAAACT 58.374 43.478 0.05 0.00 31.47 2.66
646 793 5.778542 AGGGATGGCTTCTCTACTAAACTA 58.221 41.667 0.05 0.00 31.47 2.24
647 794 6.203072 AGGGATGGCTTCTCTACTAAACTAA 58.797 40.000 0.05 0.00 31.47 2.24
648 795 6.672657 AGGGATGGCTTCTCTACTAAACTAAA 59.327 38.462 0.05 0.00 31.47 1.85
650 797 6.480651 GGATGGCTTCTCTACTAAACTAAAGC 59.519 42.308 0.07 0.00 37.50 3.51
654 801 7.297229 GCTTCTCTACTAAACTAAAGCCTTG 57.703 40.000 0.00 0.00 33.33 3.61
655 802 6.314152 GCTTCTCTACTAAACTAAAGCCTTGG 59.686 42.308 0.00 0.00 33.33 3.61
656 803 6.930068 TCTCTACTAAACTAAAGCCTTGGT 57.070 37.500 0.00 0.00 0.00 3.67
657 804 6.932947 TCTCTACTAAACTAAAGCCTTGGTC 58.067 40.000 0.00 0.00 0.00 4.02
673 820 3.641437 TGGTCTGCTTCAAATTTTCCG 57.359 42.857 0.00 0.00 0.00 4.30
692 839 1.808512 CGTATTATCTTGCCCGTGCCA 60.809 52.381 0.00 0.00 36.33 4.92
923 1091 8.385111 GTTTTGGATTCATCTATTGTTGCATTG 58.615 33.333 0.00 0.00 0.00 2.82
931 1099 5.503662 TCTATTGTTGCATTGCAGGTATG 57.496 39.130 11.76 2.88 40.61 2.39
934 1102 4.700268 TTGTTGCATTGCAGGTATGTAG 57.300 40.909 11.76 0.00 40.61 2.74
935 1103 3.684908 TGTTGCATTGCAGGTATGTAGT 58.315 40.909 11.76 0.00 40.61 2.73
941 1115 6.118852 TGCATTGCAGGTATGTAGTAATTCA 58.881 36.000 7.38 0.00 33.32 2.57
1056 1230 1.063616 CATGCTGTTGAAGGCGATGAG 59.936 52.381 0.00 0.00 0.00 2.90
1060 1234 1.207089 CTGTTGAAGGCGATGAGGGTA 59.793 52.381 0.00 0.00 0.00 3.69
1123 1297 7.605410 TCAAACAATTCTCCGTTCTTATACC 57.395 36.000 0.00 0.00 0.00 2.73
1133 1307 6.096564 TCTCCGTTCTTATACCCTTTCTTCTC 59.903 42.308 0.00 0.00 0.00 2.87
1149 1323 8.458843 CCTTTCTTCTCTTGTTGTTTCTTTGTA 58.541 33.333 0.00 0.00 0.00 2.41
1169 1343 5.965922 TGTATCAGGTGAACATAGTGTGAG 58.034 41.667 0.00 0.00 0.00 3.51
1268 1442 5.673514 TGGTTCCGTATTCAGGGTAATTAC 58.326 41.667 7.09 7.09 0.00 1.89
1430 1607 0.038159 AAGGCGTCCGAGAGTTCTTG 60.038 55.000 0.00 0.00 0.00 3.02
1487 1664 3.470567 CTCGTCACGCTTGTCGGC 61.471 66.667 9.67 0.00 43.86 5.54
1615 1792 2.066262 GCTGTTCGTCGATTCCTTCAA 58.934 47.619 0.00 0.00 0.00 2.69
1618 1795 2.415168 TGTTCGTCGATTCCTTCAATGC 59.585 45.455 0.00 0.00 0.00 3.56
1627 1804 4.271049 CGATTCCTTCAATGCTTGTCGTAT 59.729 41.667 0.00 0.00 0.00 3.06
1715 1892 0.671251 GTGTCAAAATTGCCGTGGGA 59.329 50.000 0.00 0.00 0.00 4.37
1811 1988 3.257393 CATTCTTCTCGACAAGGACCTG 58.743 50.000 0.00 0.00 0.00 4.00
1909 2086 3.384467 GGCACATTGTAAGCATAACCCAT 59.616 43.478 2.07 0.00 0.00 4.00
1924 2101 1.715931 ACCCATCCCCTGATTTGACAA 59.284 47.619 0.00 0.00 0.00 3.18
1925 2102 2.111613 ACCCATCCCCTGATTTGACAAA 59.888 45.455 2.48 2.48 0.00 2.83
1939 2116 9.903682 CTGATTTGACAAACTTCTTTCACATAT 57.096 29.630 1.94 0.00 0.00 1.78
1944 2121 9.944663 TTGACAAACTTCTTTCACATATTGTAC 57.055 29.630 0.00 0.00 30.58 2.90
1966 2143 9.692749 TGTACTTTCTGTTCTGACTAGTAATTG 57.307 33.333 0.00 0.00 0.00 2.32
1973 2150 5.932303 TGTTCTGACTAGTAATTGCACTTCC 59.068 40.000 0.00 0.00 0.00 3.46
2022 2199 1.751924 GCTATCCGAGGTCAAGTGACT 59.248 52.381 11.07 0.00 44.20 3.41
2067 2244 4.469469 TGGGGTTCTTCTCTTGGAAATT 57.531 40.909 0.00 0.00 33.07 1.82
2298 2475 4.672587 TCTACAGACATGGGCATTCTAC 57.327 45.455 0.00 0.00 0.00 2.59
2348 2525 0.454600 GCCGACATAGACGAAGACCA 59.545 55.000 0.00 0.00 0.00 4.02
2352 2529 2.032302 CGACATAGACGAAGACCAGGAG 59.968 54.545 0.00 0.00 0.00 3.69
2391 2568 1.523258 CCTGAAGATCGGCCTGCTG 60.523 63.158 0.00 0.00 0.00 4.41
2412 2589 2.112928 ACACAGGACGCAATGGCA 59.887 55.556 0.00 0.00 41.24 4.92
2532 2709 0.250640 AGCTCAAGGTCAGCACCAAG 60.251 55.000 0.00 0.00 46.68 3.61
2553 2730 4.680237 CACGGAGCGAACCAGGCA 62.680 66.667 0.00 0.00 0.00 4.75
2565 2742 2.203139 CAGGCACGGTCCAACACA 60.203 61.111 0.00 0.00 0.00 3.72
2625 2802 0.109919 CGTCGTCGGAGAATCACACA 60.110 55.000 0.00 0.00 39.69 3.72
2663 2840 0.378610 GCTGGACAGGAAATTAGCGC 59.621 55.000 0.00 0.00 0.00 5.92
2806 2988 1.132262 CCTGTCGTTTGCTTGTTGTGT 59.868 47.619 0.00 0.00 0.00 3.72
2807 2989 2.353269 CCTGTCGTTTGCTTGTTGTGTA 59.647 45.455 0.00 0.00 0.00 2.90
2808 2990 3.546020 CCTGTCGTTTGCTTGTTGTGTAG 60.546 47.826 0.00 0.00 0.00 2.74
2817 2999 3.738791 TGCTTGTTGTGTAGTACGATGTG 59.261 43.478 0.00 0.00 0.00 3.21
2849 3031 5.395546 GGAGATGGAGATGATCAAGATAGGC 60.396 48.000 0.00 0.00 0.00 3.93
2951 3203 2.707791 TGGATGGATCTCTAAAGGCCAG 59.292 50.000 5.01 0.00 33.04 4.85
3001 3253 6.127225 TGTTCTGAACAATTTGGAATGGACAA 60.127 34.615 20.14 0.00 38.72 3.18
3003 3255 6.514947 TCTGAACAATTTGGAATGGACAAAG 58.485 36.000 0.78 0.00 40.70 2.77
3008 3260 1.923356 TTGGAATGGACAAAGCCTCC 58.077 50.000 0.00 0.00 0.00 4.30
3024 3276 2.659428 CCTCCACCAAATTCATCTCCC 58.341 52.381 0.00 0.00 0.00 4.30
3026 3278 3.564133 CCTCCACCAAATTCATCTCCCAA 60.564 47.826 0.00 0.00 0.00 4.12
3027 3279 4.088634 CTCCACCAAATTCATCTCCCAAA 58.911 43.478 0.00 0.00 0.00 3.28
3028 3280 4.487804 TCCACCAAATTCATCTCCCAAAA 58.512 39.130 0.00 0.00 0.00 2.44
3030 3282 4.236935 CACCAAATTCATCTCCCAAAACG 58.763 43.478 0.00 0.00 0.00 3.60
3032 3284 3.056607 CCAAATTCATCTCCCAAAACGCT 60.057 43.478 0.00 0.00 0.00 5.07
3033 3285 4.157656 CCAAATTCATCTCCCAAAACGCTA 59.842 41.667 0.00 0.00 0.00 4.26
3034 3286 5.163519 CCAAATTCATCTCCCAAAACGCTAT 60.164 40.000 0.00 0.00 0.00 2.97
3035 3287 5.757850 AATTCATCTCCCAAAACGCTATC 57.242 39.130 0.00 0.00 0.00 2.08
3037 3289 4.487714 TCATCTCCCAAAACGCTATCTT 57.512 40.909 0.00 0.00 0.00 2.40
3038 3290 4.442706 TCATCTCCCAAAACGCTATCTTC 58.557 43.478 0.00 0.00 0.00 2.87
3039 3291 3.973206 TCTCCCAAAACGCTATCTTCA 57.027 42.857 0.00 0.00 0.00 3.02
3040 3292 4.280436 TCTCCCAAAACGCTATCTTCAA 57.720 40.909 0.00 0.00 0.00 2.69
3041 3293 4.843728 TCTCCCAAAACGCTATCTTCAAT 58.156 39.130 0.00 0.00 0.00 2.57
3042 3294 4.876107 TCTCCCAAAACGCTATCTTCAATC 59.124 41.667 0.00 0.00 0.00 2.67
3043 3295 4.843728 TCCCAAAACGCTATCTTCAATCT 58.156 39.130 0.00 0.00 0.00 2.40
3044 3296 4.876107 TCCCAAAACGCTATCTTCAATCTC 59.124 41.667 0.00 0.00 0.00 2.75
3045 3297 4.635765 CCCAAAACGCTATCTTCAATCTCA 59.364 41.667 0.00 0.00 0.00 3.27
3046 3298 5.297776 CCCAAAACGCTATCTTCAATCTCAT 59.702 40.000 0.00 0.00 0.00 2.90
3047 3299 6.425504 CCAAAACGCTATCTTCAATCTCATC 58.574 40.000 0.00 0.00 0.00 2.92
3048 3300 6.425504 CAAAACGCTATCTTCAATCTCATCC 58.574 40.000 0.00 0.00 0.00 3.51
3049 3301 4.944619 ACGCTATCTTCAATCTCATCCA 57.055 40.909 0.00 0.00 0.00 3.41
3124 3381 2.037121 TGTCGGCATCAAAGAGAACTGA 59.963 45.455 0.00 0.00 0.00 3.41
3178 3445 1.011451 GTCAAGCAGCTCCACGTCTC 61.011 60.000 0.00 0.00 0.00 3.36
3180 3447 3.923563 AAGCAGCTCCACGTCTCGC 62.924 63.158 0.00 0.00 0.00 5.03
3181 3448 4.427661 GCAGCTCCACGTCTCGCT 62.428 66.667 0.00 0.00 0.00 4.93
3182 3449 2.202544 CAGCTCCACGTCTCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
3183 3450 3.805307 AGCTCCACGTCTCGCTCG 61.805 66.667 0.00 0.00 0.00 5.03
3184 3451 4.838486 GCTCCACGTCTCGCTCGG 62.838 72.222 0.00 0.00 0.00 4.63
3332 3620 3.386932 ACATGTCAAACCATATGCCCT 57.613 42.857 0.00 0.00 0.00 5.19
3334 3622 1.473258 TGTCAAACCATATGCCCTGC 58.527 50.000 0.00 0.00 0.00 4.85
3338 3626 0.336048 AAACCATATGCCCTGCTGGT 59.664 50.000 9.00 0.00 43.74 4.00
3375 3667 4.539870 CCGTAGTCAACTCGTTAAAGTGA 58.460 43.478 0.00 0.00 0.00 3.41
3433 3735 1.008995 GAGAGACAGCGAGCGATCC 60.009 63.158 0.00 0.00 0.00 3.36
3533 3840 1.603326 GAAACCACGGGCGAAGTAAAA 59.397 47.619 0.00 0.00 0.00 1.52
3555 3862 1.281656 GGTTGACAAAACCGAGCCG 59.718 57.895 0.00 0.00 0.00 5.52
3556 3863 1.161563 GGTTGACAAAACCGAGCCGA 61.162 55.000 0.00 0.00 0.00 5.54
3557 3864 0.658897 GTTGACAAAACCGAGCCGAA 59.341 50.000 0.00 0.00 0.00 4.30
3586 3893 3.317711 TCATCAAAAGCGAGGCAGAAAAA 59.682 39.130 0.00 0.00 0.00 1.94
3588 3895 4.320608 TCAAAAGCGAGGCAGAAAAATT 57.679 36.364 0.00 0.00 0.00 1.82
3589 3896 4.298332 TCAAAAGCGAGGCAGAAAAATTC 58.702 39.130 0.00 0.00 0.00 2.17
3611 3918 2.800881 AAAAAGCGAGGCAGAAAAGG 57.199 45.000 0.00 0.00 0.00 3.11
3612 3919 0.315251 AAAAGCGAGGCAGAAAAGGC 59.685 50.000 0.00 0.00 0.00 4.35
3620 3927 3.979497 CAGAAAAGGCCCCCGGGT 61.979 66.667 21.85 0.00 37.65 5.28
3621 3928 3.658422 AGAAAAGGCCCCCGGGTC 61.658 66.667 21.85 10.85 40.91 4.46
3622 3929 3.974293 GAAAAGGCCCCCGGGTCA 61.974 66.667 21.85 0.00 43.56 4.02
3623 3930 3.513566 AAAAGGCCCCCGGGTCAA 61.514 61.111 21.85 0.00 43.56 3.18
3624 3931 3.089419 AAAAGGCCCCCGGGTCAAA 62.089 57.895 21.85 0.00 43.56 2.69
3625 3932 3.820825 AAAGGCCCCCGGGTCAAAC 62.821 63.158 21.85 4.68 43.56 2.93
3628 3935 4.280019 GCCCCCGGGTCAAACTGT 62.280 66.667 21.85 0.00 37.65 3.55
3629 3936 2.518933 CCCCCGGGTCAAACTGTT 59.481 61.111 21.85 0.00 0.00 3.16
3630 3937 1.152631 CCCCCGGGTCAAACTGTTT 60.153 57.895 21.85 0.00 0.00 2.83
3631 3938 1.176619 CCCCCGGGTCAAACTGTTTC 61.177 60.000 21.85 0.00 0.00 2.78
3632 3939 1.512156 CCCCGGGTCAAACTGTTTCG 61.512 60.000 21.85 4.11 0.00 3.46
3633 3940 1.281656 CCGGGTCAAACTGTTTCGC 59.718 57.895 2.13 1.26 0.00 4.70
3634 3941 1.164041 CCGGGTCAAACTGTTTCGCT 61.164 55.000 2.13 0.00 0.00 4.93
3635 3942 0.041312 CGGGTCAAACTGTTTCGCTG 60.041 55.000 2.13 0.00 0.00 5.18
3636 3943 1.305201 GGGTCAAACTGTTTCGCTGA 58.695 50.000 2.13 0.00 0.00 4.26
3637 3944 1.002792 GGGTCAAACTGTTTCGCTGAC 60.003 52.381 12.44 12.44 36.50 3.51
3638 3945 1.668751 GGTCAAACTGTTTCGCTGACA 59.331 47.619 19.16 0.00 38.50 3.58
3639 3946 2.096819 GGTCAAACTGTTTCGCTGACAA 59.903 45.455 19.16 0.00 38.50 3.18
3640 3947 3.426963 GGTCAAACTGTTTCGCTGACAAA 60.427 43.478 19.16 0.00 38.50 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 89 2.997897 AGTGGGTGAGGACGAGGC 60.998 66.667 0.00 0.00 0.00 4.70
103 116 2.756686 GGTGATAAACAACGACGACG 57.243 50.000 5.58 5.58 45.75 5.12
204 234 1.447945 GCTGGAAGGAAGAAGACAGC 58.552 55.000 0.00 0.00 43.50 4.40
215 245 1.684049 AGAGTCCGGAGCTGGAAGG 60.684 63.158 3.06 0.00 40.44 3.46
230 260 5.291971 CATCAAACCCCAAAAGAAACAGAG 58.708 41.667 0.00 0.00 0.00 3.35
233 263 3.135530 CCCATCAAACCCCAAAAGAAACA 59.864 43.478 0.00 0.00 0.00 2.83
235 265 3.388913 ACCCATCAAACCCCAAAAGAAA 58.611 40.909 0.00 0.00 0.00 2.52
237 267 2.785357 ACCCATCAAACCCCAAAAGA 57.215 45.000 0.00 0.00 0.00 2.52
238 268 3.475575 CAAACCCATCAAACCCCAAAAG 58.524 45.455 0.00 0.00 0.00 2.27
240 270 1.771255 CCAAACCCATCAAACCCCAAA 59.229 47.619 0.00 0.00 0.00 3.28
241 271 1.344496 ACCAAACCCATCAAACCCCAA 60.344 47.619 0.00 0.00 0.00 4.12
243 273 1.346395 GAACCAAACCCATCAAACCCC 59.654 52.381 0.00 0.00 0.00 4.95
244 274 1.000394 CGAACCAAACCCATCAAACCC 60.000 52.381 0.00 0.00 0.00 4.11
246 276 1.684450 ACCGAACCAAACCCATCAAAC 59.316 47.619 0.00 0.00 0.00 2.93
333 371 3.965347 CCCGTTCTCCCCTAAAGATCTAA 59.035 47.826 0.00 0.00 0.00 2.10
334 372 3.573695 CCCGTTCTCCCCTAAAGATCTA 58.426 50.000 0.00 0.00 0.00 1.98
335 373 2.399580 CCCGTTCTCCCCTAAAGATCT 58.600 52.381 0.00 0.00 0.00 2.75
373 415 8.524870 CAAAATAAGTTGGATTTGGACTCAAG 57.475 34.615 0.00 0.00 33.98 3.02
389 476 3.584834 GCGAATTGCACCCAAAATAAGT 58.415 40.909 0.00 0.00 45.45 2.24
429 567 2.727123 TTTGGACACAGAGCAAAGGA 57.273 45.000 0.00 0.00 0.00 3.36
453 591 2.417243 CCAACCCATTCGGAAATGAAGC 60.417 50.000 0.00 0.00 44.25 3.86
482 620 6.595716 CCCCGTTGAAGATCAGAAATATATCC 59.404 42.308 0.00 0.00 0.00 2.59
488 626 4.510167 ATCCCCGTTGAAGATCAGAAAT 57.490 40.909 0.00 0.00 0.00 2.17
489 627 4.301072 AATCCCCGTTGAAGATCAGAAA 57.699 40.909 0.00 0.00 0.00 2.52
538 684 5.124617 GGCCCTATCTCTTTGAAAGAAACAG 59.875 44.000 9.15 5.86 37.02 3.16
550 697 5.780958 AAGTAAACTTGGCCCTATCTCTT 57.219 39.130 0.00 0.00 34.38 2.85
563 710 4.385825 TCTTGATGGTCGCAAGTAAACTT 58.614 39.130 0.00 0.00 42.49 2.66
564 711 3.997021 CTCTTGATGGTCGCAAGTAAACT 59.003 43.478 0.00 0.00 42.49 2.66
574 721 4.002982 TGAAACATTCCTCTTGATGGTCG 58.997 43.478 0.00 0.00 0.00 4.79
590 737 9.761504 TGCTGATCATTTTAAAGAAATGAAACA 57.238 25.926 15.56 15.87 46.06 2.83
648 795 2.299326 ATTTGAAGCAGACCAAGGCT 57.701 45.000 0.00 0.00 43.46 4.58
650 797 4.309933 GGAAAATTTGAAGCAGACCAAGG 58.690 43.478 0.00 0.00 0.00 3.61
651 798 3.983344 CGGAAAATTTGAAGCAGACCAAG 59.017 43.478 0.00 0.00 0.00 3.61
652 799 3.383185 ACGGAAAATTTGAAGCAGACCAA 59.617 39.130 0.00 0.00 0.00 3.67
653 800 2.955660 ACGGAAAATTTGAAGCAGACCA 59.044 40.909 0.00 0.00 0.00 4.02
654 801 3.643159 ACGGAAAATTTGAAGCAGACC 57.357 42.857 0.00 0.00 0.00 3.85
655 802 8.398665 AGATAATACGGAAAATTTGAAGCAGAC 58.601 33.333 0.00 0.00 0.00 3.51
656 803 8.506168 AGATAATACGGAAAATTTGAAGCAGA 57.494 30.769 0.00 0.00 0.00 4.26
657 804 9.013490 CAAGATAATACGGAAAATTTGAAGCAG 57.987 33.333 0.00 0.00 0.00 4.24
673 820 1.961793 TGGCACGGGCAAGATAATAC 58.038 50.000 13.89 0.00 43.71 1.89
692 839 6.127140 GCCACTAGGTTATGATTATCCCGTAT 60.127 42.308 0.00 0.00 37.19 3.06
923 1091 9.360093 GTCAGATATGAATTACTACATACCTGC 57.640 37.037 0.00 0.00 39.27 4.85
931 1099 6.367422 GCAGGCTGTCAGATATGAATTACTAC 59.633 42.308 17.16 0.00 0.00 2.73
934 1102 5.303971 AGCAGGCTGTCAGATATGAATTAC 58.696 41.667 17.16 0.00 0.00 1.89
935 1103 5.557576 AGCAGGCTGTCAGATATGAATTA 57.442 39.130 17.16 0.00 0.00 1.40
941 1115 7.911130 ATATATGTAGCAGGCTGTCAGATAT 57.089 36.000 17.16 18.91 30.13 1.63
1123 1297 7.315890 ACAAAGAAACAACAAGAGAAGAAAGG 58.684 34.615 0.00 0.00 0.00 3.11
1133 1307 7.026631 TCACCTGATACAAAGAAACAACAAG 57.973 36.000 0.00 0.00 0.00 3.16
1149 1323 3.198635 CCCTCACACTATGTTCACCTGAT 59.801 47.826 0.00 0.00 0.00 2.90
1169 1343 4.812626 TCAACTCGTTGTAAGAAAAGACCC 59.187 41.667 9.38 0.00 41.16 4.46
1209 1383 1.691196 TCTTGTTTGCCCCACTGAAG 58.309 50.000 0.00 0.00 0.00 3.02
1415 1592 1.535896 TCAGTCAAGAACTCTCGGACG 59.464 52.381 6.08 0.00 35.45 4.79
1487 1664 1.673665 GGACCCTTCAGCACAGCAG 60.674 63.158 0.00 0.00 0.00 4.24
1615 1792 6.818644 AGAACATCTGTAAATACGACAAGCAT 59.181 34.615 0.00 0.00 0.00 3.79
1618 1795 6.090763 TGCAGAACATCTGTAAATACGACAAG 59.909 38.462 8.97 0.00 45.94 3.16
1627 1804 4.074259 AGCACATGCAGAACATCTGTAAA 58.926 39.130 6.64 0.00 45.94 2.01
1715 1892 2.594592 GCAAGTCCACGGGCAACT 60.595 61.111 0.00 0.00 0.00 3.16
1811 1988 4.929211 CCAAAATCAGAAATTTTCGGGGTC 59.071 41.667 9.01 0.00 34.02 4.46
1909 2086 4.453480 AGAAGTTTGTCAAATCAGGGGA 57.547 40.909 0.40 0.00 0.00 4.81
1925 2102 9.561069 ACAGAAAGTACAATATGTGAAAGAAGT 57.439 29.630 0.00 0.00 0.00 3.01
1944 2121 7.386299 AGTGCAATTACTAGTCAGAACAGAAAG 59.614 37.037 0.00 0.00 0.00 2.62
1973 2150 3.198635 TGGAGCCAAGTATCCTCTGAAAG 59.801 47.826 0.00 0.00 36.50 2.62
1995 2172 4.835615 ACTTGACCTCGGATAGCATATTCT 59.164 41.667 0.00 0.00 0.00 2.40
2067 2244 2.549992 GGTGTTACATCTGCCACTGACA 60.550 50.000 0.00 0.00 0.00 3.58
2140 2317 8.531530 GTCAATAAACGCTATTTGCAAATAAGG 58.468 33.333 27.26 23.11 43.06 2.69
2262 2439 3.141398 CTGTAGAAAAGGTGCAGCAGAA 58.859 45.455 19.63 0.00 0.00 3.02
2272 2449 3.071874 TGCCCATGTCTGTAGAAAAGG 57.928 47.619 0.00 0.00 0.00 3.11
2298 2475 1.398739 TCTTCTAGACGCTCTTGCTCG 59.601 52.381 0.00 0.00 36.97 5.03
2348 2525 1.470996 GCATGCCTCCTCGATCTCCT 61.471 60.000 6.36 0.00 0.00 3.69
2352 2529 2.356793 CGGCATGCCTCCTCGATC 60.357 66.667 33.07 4.92 0.00 3.69
2391 2568 1.081906 CATTGCGTCCTGTGTGCAC 60.082 57.895 10.75 10.75 38.55 4.57
2553 2730 0.895530 ATCTCGATGTGTTGGACCGT 59.104 50.000 0.00 0.00 0.00 4.83
2641 2818 2.293170 GCTAATTTCCTGTCCAGCTCC 58.707 52.381 0.00 0.00 0.00 4.70
2645 2822 1.017387 GGCGCTAATTTCCTGTCCAG 58.983 55.000 7.64 0.00 0.00 3.86
2663 2840 3.122278 ACGACAATGTACAAATCGAACGG 59.878 43.478 24.81 4.91 36.64 4.44
2765 2947 1.390525 GCCCCATTAACCCAACCCT 59.609 57.895 0.00 0.00 0.00 4.34
2806 2988 7.121315 CCATCTCCAGATATTCACATCGTACTA 59.879 40.741 0.00 0.00 32.63 1.82
2807 2989 6.071672 CCATCTCCAGATATTCACATCGTACT 60.072 42.308 0.00 0.00 32.63 2.73
2808 2990 6.071896 TCCATCTCCAGATATTCACATCGTAC 60.072 42.308 0.00 0.00 32.63 3.67
2817 2999 7.421087 TGATCATCTCCATCTCCAGATATTC 57.579 40.000 0.00 0.00 32.63 1.75
2849 3031 6.036470 TGTGAATCGTACTATCTTGCAAGAG 58.964 40.000 31.14 21.75 38.66 2.85
2860 3042 5.836821 AGCAAGAGATGTGAATCGTACTA 57.163 39.130 0.00 0.00 0.00 1.82
2861 3043 4.727507 AGCAAGAGATGTGAATCGTACT 57.272 40.909 0.00 0.00 0.00 2.73
2862 3044 5.120830 ACAAAGCAAGAGATGTGAATCGTAC 59.879 40.000 0.00 0.00 0.00 3.67
2951 3203 1.005156 GCCTCCTCGAGATCATGCC 60.005 63.158 15.71 0.00 0.00 4.40
3001 3253 3.359950 GAGATGAATTTGGTGGAGGCTT 58.640 45.455 0.00 0.00 0.00 4.35
3003 3255 2.027385 GGAGATGAATTTGGTGGAGGC 58.973 52.381 0.00 0.00 0.00 4.70
3008 3260 4.236935 CGTTTTGGGAGATGAATTTGGTG 58.763 43.478 0.00 0.00 0.00 4.17
3024 3276 6.037500 TGGATGAGATTGAAGATAGCGTTTTG 59.962 38.462 0.00 0.00 0.00 2.44
3026 3278 5.674525 TGGATGAGATTGAAGATAGCGTTT 58.325 37.500 0.00 0.00 0.00 3.60
3027 3279 5.069648 TCTGGATGAGATTGAAGATAGCGTT 59.930 40.000 0.00 0.00 0.00 4.84
3028 3280 4.586421 TCTGGATGAGATTGAAGATAGCGT 59.414 41.667 0.00 0.00 0.00 5.07
3030 3282 6.073873 CGTTTCTGGATGAGATTGAAGATAGC 60.074 42.308 0.00 0.00 0.00 2.97
3032 3284 6.283694 CCGTTTCTGGATGAGATTGAAGATA 58.716 40.000 0.00 0.00 0.00 1.98
3033 3285 5.121811 CCGTTTCTGGATGAGATTGAAGAT 58.878 41.667 0.00 0.00 0.00 2.40
3034 3286 4.507710 CCGTTTCTGGATGAGATTGAAGA 58.492 43.478 0.00 0.00 0.00 2.87
3035 3287 3.624861 CCCGTTTCTGGATGAGATTGAAG 59.375 47.826 0.00 0.00 0.00 3.02
3037 3289 2.680805 GCCCGTTTCTGGATGAGATTGA 60.681 50.000 0.00 0.00 0.00 2.57
3038 3290 1.672881 GCCCGTTTCTGGATGAGATTG 59.327 52.381 0.00 0.00 0.00 2.67
3039 3291 1.561542 AGCCCGTTTCTGGATGAGATT 59.438 47.619 0.00 0.00 0.00 2.40
3040 3292 1.134280 CAGCCCGTTTCTGGATGAGAT 60.134 52.381 0.00 0.00 41.83 2.75
3041 3293 0.250234 CAGCCCGTTTCTGGATGAGA 59.750 55.000 0.00 0.00 41.83 3.27
3042 3294 1.372087 GCAGCCCGTTTCTGGATGAG 61.372 60.000 0.00 0.00 41.83 2.90
3043 3295 1.377202 GCAGCCCGTTTCTGGATGA 60.377 57.895 0.00 0.00 41.83 2.92
3044 3296 2.753966 CGCAGCCCGTTTCTGGATG 61.754 63.158 0.00 0.00 42.18 3.51
3045 3297 2.436646 CGCAGCCCGTTTCTGGAT 60.437 61.111 0.00 0.00 32.41 3.41
3046 3298 4.697756 CCGCAGCCCGTTTCTGGA 62.698 66.667 0.00 0.00 34.38 3.86
3048 3300 2.966309 GAACCGCAGCCCGTTTCTG 61.966 63.158 0.00 0.00 35.73 3.02
3049 3301 2.668550 GAACCGCAGCCCGTTTCT 60.669 61.111 0.00 0.00 35.73 2.52
3102 3359 2.414481 CAGTTCTCTTTGATGCCGACAG 59.586 50.000 0.00 0.00 0.00 3.51
3114 3371 1.040646 TGCACGGAGTCAGTTCTCTT 58.959 50.000 0.00 0.00 41.61 2.85
3332 3620 1.891919 GCCGTTCAACAGACCAGCA 60.892 57.895 0.00 0.00 0.00 4.41
3334 3622 0.951040 GGAGCCGTTCAACAGACCAG 60.951 60.000 0.00 0.00 0.00 4.00
3338 3626 2.342279 CGGGAGCCGTTCAACAGA 59.658 61.111 0.00 0.00 42.73 3.41
3357 3649 5.067413 TGTCTCTCACTTTAACGAGTTGACT 59.933 40.000 0.00 0.00 36.17 3.41
3375 3667 1.369839 TTCGATCGCTCGCTGTCTCT 61.370 55.000 11.09 0.00 44.65 3.10
3433 3735 2.358582 TCACTGACTTGTGCATTGGTTG 59.641 45.455 0.00 0.00 37.81 3.77
3513 3820 1.228533 TTTACTTCGCCCGTGGTTTC 58.771 50.000 0.00 0.00 0.00 2.78
3554 3861 5.208624 TCGCTTTTGATGATTCTTCTTCG 57.791 39.130 1.76 0.00 0.00 3.79
3555 3862 5.567552 CCTCGCTTTTGATGATTCTTCTTC 58.432 41.667 1.76 0.00 0.00 2.87
3556 3863 4.142513 GCCTCGCTTTTGATGATTCTTCTT 60.143 41.667 1.76 0.00 0.00 2.52
3557 3864 3.376546 GCCTCGCTTTTGATGATTCTTCT 59.623 43.478 1.76 0.00 0.00 2.85
3596 3903 2.360475 GGCCTTTTCTGCCTCGCT 60.360 61.111 0.00 0.00 45.70 4.93
3603 3910 3.938637 GACCCGGGGGCCTTTTCTG 62.939 68.421 27.92 0.00 39.32 3.02
3604 3911 3.658422 GACCCGGGGGCCTTTTCT 61.658 66.667 27.92 0.00 39.32 2.52
3605 3912 3.516949 TTGACCCGGGGGCCTTTTC 62.517 63.158 27.92 12.06 39.32 2.29
3606 3913 3.089419 TTTGACCCGGGGGCCTTTT 62.089 57.895 27.92 0.00 39.32 2.27
3607 3914 3.513566 TTTGACCCGGGGGCCTTT 61.514 61.111 27.92 0.68 39.32 3.11
3608 3915 4.295199 GTTTGACCCGGGGGCCTT 62.295 66.667 27.92 1.66 39.32 4.35
3611 3918 3.802852 AACAGTTTGACCCGGGGGC 62.803 63.158 27.92 16.71 39.32 5.80
3612 3919 1.152631 AAACAGTTTGACCCGGGGG 60.153 57.895 27.92 5.70 42.03 5.40
3613 3920 1.512156 CGAAACAGTTTGACCCGGGG 61.512 60.000 27.92 12.73 0.00 5.73
3614 3921 1.946267 CGAAACAGTTTGACCCGGG 59.054 57.895 22.25 22.25 0.00 5.73
3615 3922 1.164041 AGCGAAACAGTTTGACCCGG 61.164 55.000 2.34 0.00 0.00 5.73
3616 3923 0.041312 CAGCGAAACAGTTTGACCCG 60.041 55.000 2.34 1.81 0.00 5.28
3617 3924 1.002792 GTCAGCGAAACAGTTTGACCC 60.003 52.381 2.34 0.00 33.74 4.46
3618 3925 1.668751 TGTCAGCGAAACAGTTTGACC 59.331 47.619 2.34 0.00 37.85 4.02
3619 3926 3.398954 TTGTCAGCGAAACAGTTTGAC 57.601 42.857 2.34 6.10 38.82 3.18


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

AutoCloner maintained by Alex Coulton.