Multiple sequence alignment - TraesCS2A01G447500

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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 TraesCS2A01G447500 chr2A 100.000 2795 0 0 1 2795 696314610 696317404 0.000000e+00 5162.0
1 TraesCS2A01G447500 chr2A 85.887 1821 189 42 835 2621 696825094 696826880 0.000000e+00 1877.0
2 TraesCS2A01G447500 chr2A 83.056 1204 158 19 999 2176 695999116 696000299 0.000000e+00 1051.0
3 TraesCS2A01G447500 chr2A 81.715 1143 142 35 999 2117 696040431 696041530 0.000000e+00 891.0
4 TraesCS2A01G447500 chr2A 83.966 817 80 30 999 1788 696219212 696220004 0.000000e+00 736.0
5 TraesCS2A01G447500 chr2A 78.710 310 55 7 1827 2133 696307908 696308209 2.460000e-46 196.0
6 TraesCS2A01G447500 chr2A 92.391 92 6 1 2621 2712 696826924 696827014 2.530000e-26 130.0
7 TraesCS2A01G447500 chr2A 93.976 83 4 1 2711 2792 696827272 696827354 1.180000e-24 124.0
8 TraesCS2A01G447500 chr2A 100.000 57 0 0 3071 3127 696317680 696317736 4.270000e-19 106.0
9 TraesCS2A01G447500 chr2A 94.643 56 3 0 3072 3127 696827643 696827698 1.540000e-13 87.9
10 TraesCS2A01G447500 chr2A 82.222 90 9 5 480 568 695998619 695998702 1.560000e-08 71.3
11 TraesCS2A01G447500 chr2B 89.306 2291 187 28 377 2622 663898120 663900397 0.000000e+00 2820.0
12 TraesCS2A01G447500 chr2B 80.741 1215 154 35 999 2176 663828972 663830143 0.000000e+00 874.0
13 TraesCS2A01G447500 chr2B 80.686 1196 149 39 999 2176 663838018 663839149 0.000000e+00 854.0
14 TraesCS2A01G447500 chr2B 88.612 281 16 11 5 278 663897747 663898018 8.360000e-86 327.0
15 TraesCS2A01G447500 chr2B 93.939 66 4 0 2225 2290 663180041 663179976 1.980000e-17 100.0
16 TraesCS2A01G447500 chr2D 89.857 2021 149 25 358 2342 556641750 556643750 0.000000e+00 2545.0
17 TraesCS2A01G447500 chr2D 88.986 799 65 13 999 1788 556365491 556366275 0.000000e+00 966.0
18 TraesCS2A01G447500 chr2D 80.865 1202 171 31 999 2176 556267229 556268395 0.000000e+00 891.0
19 TraesCS2A01G447500 chr2D 83.883 819 89 31 999 1788 556619139 556619943 0.000000e+00 741.0
20 TraesCS2A01G447500 chr2D 83.395 807 88 28 999 1782 556408039 556408822 0.000000e+00 706.0
21 TraesCS2A01G447500 chr2D 92.532 308 10 6 1 307 556641458 556641753 2.230000e-116 429.0
22 TraesCS2A01G447500 chr2D 90.244 287 22 4 2290 2572 556643797 556644081 1.370000e-98 370.0
23 TraesCS2A01G447500 chr2D 80.000 310 51 7 1827 2133 556619949 556620250 5.250000e-53 219.0
24 TraesCS2A01G447500 chr2D 88.690 168 15 2 2621 2786 556677959 556678124 5.290000e-48 202.0
25 TraesCS2A01G447500 chr2D 81.159 138 18 3 2229 2366 556351714 556351843 1.530000e-18 104.0
26 TraesCS2A01G447500 chr2D 77.703 148 16 11 430 567 556265730 556265870 1.200000e-09 75.0
27 TraesCS2A01G447500 chr2D 89.583 48 5 0 2575 2622 556677869 556677916 9.360000e-06 62.1
28 TraesCS2A01G447500 chr2D 94.737 38 2 0 3087 3124 556678130 556678167 3.370000e-05 60.2
29 TraesCS2A01G447500 chr1A 97.500 40 0 1 2753 2791 435052945 435052984 2.010000e-07 67.6
30 TraesCS2A01G447500 chr4D 95.000 40 1 1 2752 2791 3568002 3568040 9.360000e-06 62.1


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 TraesCS2A01G447500 chr2A 696314610 696317736 3126 False 2634.000000 5162 100.000000 1 3127 2 chr2A.!!$F5 3126
1 TraesCS2A01G447500 chr2A 696040431 696041530 1099 False 891.000000 891 81.715000 999 2117 1 chr2A.!!$F1 1118
2 TraesCS2A01G447500 chr2A 696219212 696220004 792 False 736.000000 736 83.966000 999 1788 1 chr2A.!!$F2 789
3 TraesCS2A01G447500 chr2A 695998619 696000299 1680 False 561.150000 1051 82.639000 480 2176 2 chr2A.!!$F4 1696
4 TraesCS2A01G447500 chr2A 696825094 696827698 2604 False 554.725000 1877 91.724250 835 3127 4 chr2A.!!$F6 2292
5 TraesCS2A01G447500 chr2B 663897747 663900397 2650 False 1573.500000 2820 88.959000 5 2622 2 chr2B.!!$F3 2617
6 TraesCS2A01G447500 chr2B 663828972 663830143 1171 False 874.000000 874 80.741000 999 2176 1 chr2B.!!$F1 1177
7 TraesCS2A01G447500 chr2B 663838018 663839149 1131 False 854.000000 854 80.686000 999 2176 1 chr2B.!!$F2 1177
8 TraesCS2A01G447500 chr2D 556641458 556644081 2623 False 1114.666667 2545 90.877667 1 2572 3 chr2D.!!$F6 2571
9 TraesCS2A01G447500 chr2D 556365491 556366275 784 False 966.000000 966 88.986000 999 1788 1 chr2D.!!$F2 789
10 TraesCS2A01G447500 chr2D 556408039 556408822 783 False 706.000000 706 83.395000 999 1782 1 chr2D.!!$F3 783
11 TraesCS2A01G447500 chr2D 556265730 556268395 2665 False 483.000000 891 79.284000 430 2176 2 chr2D.!!$F4 1746
12 TraesCS2A01G447500 chr2D 556619139 556620250 1111 False 480.000000 741 81.941500 999 2133 2 chr2D.!!$F5 1134

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
238 245 0.883833 CAAAGTCGCCAGCAGGATTT 59.116 50.0 0.00 0.00 36.89 2.17 F
1844 3036 0.318784 CGAACTATCTACAGCCGGGC 60.319 60.0 12.11 12.11 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 3184 0.033208 ATGTCAATCCCCGGTGCAAT 60.033 50.000 0.00 0.0 0.00 3.56 R
3083 4716 3.125829 TCGTGGATAGTAACACTCACGTC 59.874 47.826 14.64 0.0 41.62 4.34 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
56 57 9.770097 ACTGATGATATTGTAGGTGTTGATAAG 57.230 33.333 0.00 0.00 0.00 1.73
224 231 5.796424 ATCATTTGCTGAAACCTCAAAGT 57.204 34.783 0.00 0.00 37.44 2.66
238 245 0.883833 CAAAGTCGCCAGCAGGATTT 59.116 50.000 0.00 0.00 36.89 2.17
308 367 8.718102 ACGCAGACATGAGTTAAATTAATACT 57.282 30.769 0.00 0.00 35.79 2.12
309 368 8.818057 ACGCAGACATGAGTTAAATTAATACTC 58.182 33.333 0.00 9.14 35.79 2.59
310 369 9.035607 CGCAGACATGAGTTAAATTAATACTCT 57.964 33.333 14.85 1.69 39.18 3.24
324 383 9.790389 AAATTAATACTCTCTTCGTCACTAGTG 57.210 33.333 17.17 17.17 0.00 2.74
325 384 5.821516 AATACTCTCTTCGTCACTAGTGG 57.178 43.478 22.48 7.88 0.00 4.00
326 385 1.813786 ACTCTCTTCGTCACTAGTGGC 59.186 52.381 22.48 20.19 0.00 5.01
334 393 2.943843 GTCACTAGTGGCGAAAACAC 57.056 50.000 22.48 7.14 39.10 3.32
336 395 2.475487 GTCACTAGTGGCGAAAACACTC 59.525 50.000 22.48 0.00 45.50 3.51
337 396 2.364324 TCACTAGTGGCGAAAACACTCT 59.636 45.455 22.48 0.00 45.50 3.24
338 397 3.131396 CACTAGTGGCGAAAACACTCTT 58.869 45.455 15.49 0.00 45.50 2.85
339 398 4.038282 TCACTAGTGGCGAAAACACTCTTA 59.962 41.667 22.48 0.00 45.50 2.10
340 399 4.929808 CACTAGTGGCGAAAACACTCTTAT 59.070 41.667 15.49 0.00 45.50 1.73
341 400 6.071784 TCACTAGTGGCGAAAACACTCTTATA 60.072 38.462 22.48 0.00 45.50 0.98
342 401 6.757010 CACTAGTGGCGAAAACACTCTTATAT 59.243 38.462 15.49 0.00 45.50 0.86
343 402 6.757010 ACTAGTGGCGAAAACACTCTTATATG 59.243 38.462 0.00 0.00 45.50 1.78
344 403 5.488341 AGTGGCGAAAACACTCTTATATGT 58.512 37.500 0.00 0.00 45.50 2.29
345 404 5.938125 AGTGGCGAAAACACTCTTATATGTT 59.062 36.000 0.00 0.00 45.50 2.71
346 405 6.430000 AGTGGCGAAAACACTCTTATATGTTT 59.570 34.615 0.00 0.00 45.50 2.83
347 406 7.604927 AGTGGCGAAAACACTCTTATATGTTTA 59.395 33.333 3.01 0.00 45.50 2.01
348 407 7.903431 GTGGCGAAAACACTCTTATATGTTTAG 59.097 37.037 3.01 2.84 45.86 1.85
349 408 7.820386 TGGCGAAAACACTCTTATATGTTTAGA 59.180 33.333 3.01 0.00 45.86 2.10
350 409 8.114905 GGCGAAAACACTCTTATATGTTTAGAC 58.885 37.037 3.01 0.33 45.86 2.59
351 410 7.839837 GCGAAAACACTCTTATATGTTTAGACG 59.160 37.037 3.01 9.83 45.86 4.18
352 411 8.318876 CGAAAACACTCTTATATGTTTAGACGG 58.681 37.037 3.01 0.00 45.86 4.79
353 412 9.362539 GAAAACACTCTTATATGTTTAGACGGA 57.637 33.333 3.01 0.00 45.86 4.69
354 413 8.928270 AAACACTCTTATATGTTTAGACGGAG 57.072 34.615 0.67 0.00 45.01 4.63
355 414 7.040473 ACACTCTTATATGTTTAGACGGAGG 57.960 40.000 0.00 0.00 0.00 4.30
356 415 6.040616 ACACTCTTATATGTTTAGACGGAGGG 59.959 42.308 0.00 0.00 0.00 4.30
357 416 6.264744 CACTCTTATATGTTTAGACGGAGGGA 59.735 42.308 0.00 0.00 0.00 4.20
358 417 6.837568 ACTCTTATATGTTTAGACGGAGGGAA 59.162 38.462 0.00 0.00 0.00 3.97
359 418 7.509659 ACTCTTATATGTTTAGACGGAGGGAAT 59.490 37.037 0.00 0.00 0.00 3.01
360 419 8.945195 TCTTATATGTTTAGACGGAGGGAATA 57.055 34.615 0.00 0.00 0.00 1.75
378 447 3.769739 ATAGTGTTCTGCAGGTGACAA 57.230 42.857 15.13 0.00 0.00 3.18
383 452 1.331756 GTTCTGCAGGTGACAACACTG 59.668 52.381 15.13 0.00 45.32 3.66
390 459 1.172812 GGTGACAACACTGGGAAGGC 61.173 60.000 0.00 0.00 45.32 4.35
414 483 2.690497 CTCCTTTGACGATAGCTCCAGA 59.310 50.000 0.00 0.00 42.67 3.86
416 485 3.706594 TCCTTTGACGATAGCTCCAGATT 59.293 43.478 0.00 0.00 42.67 2.40
442 515 2.211250 TTCTACCGTGGCACTAGAGT 57.789 50.000 16.72 10.00 0.00 3.24
478 551 8.500773 CAAAATGAAGGAACTAGCGTACTTAAA 58.499 33.333 0.00 0.00 38.49 1.52
515 592 7.262772 TGAATTACAGGTGCTACACTACATAC 58.737 38.462 0.00 0.00 34.40 2.39
541 620 2.359531 CCTCGTAGACAGTCCATCTTCC 59.640 54.545 0.00 0.00 0.00 3.46
590 670 3.206150 TGCCGCTCTATCATTTTCCTTC 58.794 45.455 0.00 0.00 0.00 3.46
603 683 1.768684 TTCCTTCTTGCCTGCCTCGT 61.769 55.000 0.00 0.00 0.00 4.18
604 684 2.037136 CCTTCTTGCCTGCCTCGTG 61.037 63.158 0.00 0.00 0.00 4.35
605 685 1.004560 CTTCTTGCCTGCCTCGTGA 60.005 57.895 0.00 0.00 0.00 4.35
674 754 6.181190 CAGGAGGATATATCTGGTCTTACGA 58.819 44.000 12.42 0.00 0.00 3.43
698 778 3.432326 GCCAAATCTCCGGATCAACTACT 60.432 47.826 3.57 0.00 0.00 2.57
721 801 3.165890 TCTTTGACTTACATCGTACGCG 58.834 45.455 11.24 3.53 39.92 6.01
777 1804 2.218603 GTTGGATAGTAATGGCCACGG 58.781 52.381 8.16 0.00 0.00 4.94
803 1830 4.678840 GCAGAATGGAAGGAAAATTCGCAT 60.679 41.667 0.00 0.00 35.83 4.73
898 1969 6.019479 GGAAGACAAGAAACATAGTCGCATAG 60.019 42.308 0.00 0.00 36.18 2.23
919 1993 2.615869 CTAGCTTGCTTCTGACCACTC 58.384 52.381 0.00 0.00 0.00 3.51
936 2018 3.274586 CCATCCATCACAGCGCCG 61.275 66.667 2.29 0.00 0.00 6.46
960 2042 1.194997 CCCGATCGACTCTAGCTTACG 59.805 57.143 18.66 0.00 0.00 3.18
991 2073 0.947180 TCGCCGTCGGGAAGAAAAAG 60.947 55.000 14.38 0.00 36.13 2.27
1316 2418 1.416401 CCAACTACTCCACACACCACT 59.584 52.381 0.00 0.00 0.00 4.00
1353 2498 1.375853 GCCGCCATGCACTGTCAATA 61.376 55.000 0.00 0.00 0.00 1.90
1571 2748 4.704833 CTGCCACCCGACCACCAG 62.705 72.222 0.00 0.00 0.00 4.00
1667 2853 1.078918 CATCGGCACTCTCAGGCAA 60.079 57.895 0.00 0.00 0.00 4.52
1734 2923 2.612221 GCAACTAACCTCGTAGCCAACT 60.612 50.000 0.00 0.00 0.00 3.16
1735 2924 3.660865 CAACTAACCTCGTAGCCAACTT 58.339 45.455 0.00 0.00 0.00 2.66
1736 2925 3.314541 ACTAACCTCGTAGCCAACTTG 57.685 47.619 0.00 0.00 0.00 3.16
1737 2926 2.895404 ACTAACCTCGTAGCCAACTTGA 59.105 45.455 0.00 0.00 0.00 3.02
1751 2940 3.369052 CCAACTTGATGGCTGCATCAAAT 60.369 43.478 20.08 12.75 46.84 2.32
1753 2942 2.829720 ACTTGATGGCTGCATCAAATGT 59.170 40.909 20.08 15.27 46.84 2.71
1754 2943 3.259876 ACTTGATGGCTGCATCAAATGTT 59.740 39.130 20.08 8.92 46.84 2.71
1756 2945 2.093921 TGATGGCTGCATCAAATGTTGG 60.094 45.455 0.50 0.00 38.50 3.77
1771 2960 1.032014 GTTGGGCTGAACTCAAGCAA 58.968 50.000 0.00 0.00 0.00 3.91
1788 2977 3.221771 AGCAACAGCATAGTTCCAAACA 58.778 40.909 0.00 0.00 0.00 2.83
1815 3007 3.366374 GCTCCAGGACAAGTTTAACATGC 60.366 47.826 0.00 0.00 0.00 4.06
1818 3010 3.568538 CAGGACAAGTTTAACATGCTGC 58.431 45.455 0.00 0.00 0.00 5.25
1823 3015 2.292828 AGTTTAACATGCTGCCTGGT 57.707 45.000 9.69 5.28 0.00 4.00
1824 3016 3.433306 AGTTTAACATGCTGCCTGGTA 57.567 42.857 9.69 4.24 0.00 3.25
1832 3024 1.191535 TGCTGCCTGGTACGAACTAT 58.808 50.000 0.00 0.00 0.00 2.12
1835 3027 2.621998 GCTGCCTGGTACGAACTATCTA 59.378 50.000 0.00 0.00 0.00 1.98
1844 3036 0.318784 CGAACTATCTACAGCCGGGC 60.319 60.000 12.11 12.11 0.00 6.13
1906 3098 4.711980 GCAGCAGCTGATCAATGC 57.288 55.556 27.39 19.94 40.29 3.56
1980 3175 1.929038 GCAACACTGCTGCATTCACAG 60.929 52.381 1.31 0.00 45.74 3.66
1999 3206 2.881266 CGCGTGATATTGCACCGGG 61.881 63.158 6.32 0.00 35.37 5.73
2001 3208 1.145156 CGTGATATTGCACCGGGGA 59.855 57.895 8.67 0.00 35.37 4.81
2117 3330 2.694109 GGAACTACTTGAGGACGGCTAT 59.306 50.000 0.00 0.00 0.00 2.97
2139 3352 9.095065 GCTATCGTCTATAGTTTCTTTTTCCAA 57.905 33.333 0.00 0.00 39.94 3.53
2168 3385 7.558161 AATAGATGTGTTGTGTATGATGGTG 57.442 36.000 0.00 0.00 0.00 4.17
2209 3428 2.277591 GCTTCATGCAACCAGGCCA 61.278 57.895 5.01 0.00 42.31 5.36
2247 3466 5.244851 GCAGTGTTAGATCCATCATAGAGGA 59.755 44.000 0.00 0.00 38.50 3.71
2291 3602 8.838365 ACATGCATTGATTTGTTTTTGTGTTAT 58.162 25.926 0.00 0.00 0.00 1.89
2343 3654 8.514330 TTTTGTCACTATAGTTGAAGGTTGTT 57.486 30.769 1.56 0.00 0.00 2.83
2351 3662 9.227777 ACTATAGTTGAAGGTTGTTAATTGGTC 57.772 33.333 0.00 0.00 0.00 4.02
2397 3712 6.819284 ACTTTCCATTGTCAATTCACATGTT 58.181 32.000 0.00 0.00 0.00 2.71
2446 3766 2.005451 GCCTCTACATCAAGTGCACAG 58.995 52.381 21.04 11.41 0.00 3.66
2514 3835 4.082571 GCAGACAACTCAAAATGCATAGGT 60.083 41.667 0.00 0.00 33.92 3.08
2549 3870 3.886505 ACAACGGTGTGGACAACATAAAT 59.113 39.130 4.62 0.00 41.97 1.40
2566 3887 9.577110 CAACATAAATGCTTCATCACAATTACT 57.423 29.630 0.00 0.00 0.00 2.24
2573 3894 4.034048 GCTTCATCACAATTACTACGGTGG 59.966 45.833 0.00 0.00 32.29 4.61
2582 3903 4.926140 ATTACTACGGTGGTTACTAGGC 57.074 45.455 1.49 0.00 0.00 3.93
2583 3904 2.220653 ACTACGGTGGTTACTAGGCA 57.779 50.000 0.00 0.00 0.00 4.75
2589 3910 0.037605 GTGGTTACTAGGCAGCACGT 60.038 55.000 9.26 0.00 32.14 4.49
2622 3943 3.821033 GCCTTAATGAAATAGCCGTGGAT 59.179 43.478 0.00 0.00 0.00 3.41
2624 3945 5.472137 GCCTTAATGAAATAGCCGTGGATTA 59.528 40.000 0.00 0.00 0.00 1.75
2699 4063 2.029838 ACACCAGCTCGATTTGGATC 57.970 50.000 18.99 0.00 37.89 3.36
2720 4343 9.219603 TGGATCGATCATGAAATATAGTTTTCC 57.780 33.333 25.93 4.98 35.23 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
224 231 1.277842 TCTAACAAATCCTGCTGGCGA 59.722 47.619 4.42 0.00 0.00 5.54
238 245 8.076910 AGACACTACTACTAGCTACTCTAACA 57.923 38.462 0.00 0.00 0.00 2.41
307 366 1.202087 CGCCACTAGTGACGAAGAGAG 60.202 57.143 25.11 5.73 38.76 3.20
308 367 0.803117 CGCCACTAGTGACGAAGAGA 59.197 55.000 25.11 0.00 38.76 3.10
309 368 0.803117 TCGCCACTAGTGACGAAGAG 59.197 55.000 28.61 11.84 42.18 2.85
310 369 2.936928 TCGCCACTAGTGACGAAGA 58.063 52.632 28.61 9.42 42.18 2.87
313 372 1.067364 TGTTTTCGCCACTAGTGACGA 59.933 47.619 27.35 27.35 43.35 4.20
314 373 1.191647 GTGTTTTCGCCACTAGTGACG 59.808 52.381 23.65 23.65 37.80 4.35
315 374 2.475487 GAGTGTTTTCGCCACTAGTGAC 59.525 50.000 24.68 12.19 43.00 3.67
316 375 2.364324 AGAGTGTTTTCGCCACTAGTGA 59.636 45.455 24.68 1.01 43.00 3.41
317 376 2.755650 AGAGTGTTTTCGCCACTAGTG 58.244 47.619 16.34 16.34 43.00 2.74
318 377 3.470645 AAGAGTGTTTTCGCCACTAGT 57.529 42.857 0.00 0.00 43.00 2.57
319 378 6.757010 ACATATAAGAGTGTTTTCGCCACTAG 59.243 38.462 0.00 0.00 43.00 2.57
320 379 6.636705 ACATATAAGAGTGTTTTCGCCACTA 58.363 36.000 0.00 0.00 43.00 2.74
321 380 5.488341 ACATATAAGAGTGTTTTCGCCACT 58.512 37.500 0.00 0.00 45.52 4.00
322 381 5.796350 ACATATAAGAGTGTTTTCGCCAC 57.204 39.130 0.00 0.00 0.00 5.01
323 382 6.811253 AAACATATAAGAGTGTTTTCGCCA 57.189 33.333 0.00 0.00 43.80 5.69
324 383 8.114905 GTCTAAACATATAAGAGTGTTTTCGCC 58.885 37.037 8.53 0.00 43.80 5.54
325 384 7.839837 CGTCTAAACATATAAGAGTGTTTTCGC 59.160 37.037 8.53 0.62 43.80 4.70
326 385 8.318876 CCGTCTAAACATATAAGAGTGTTTTCG 58.681 37.037 8.53 10.47 43.80 3.46
327 386 9.362539 TCCGTCTAAACATATAAGAGTGTTTTC 57.637 33.333 8.53 1.49 43.80 2.29
328 387 9.367444 CTCCGTCTAAACATATAAGAGTGTTTT 57.633 33.333 8.53 0.00 43.80 2.43
329 388 7.980099 CCTCCGTCTAAACATATAAGAGTGTTT 59.020 37.037 8.32 8.32 46.74 2.83
330 389 7.417570 CCCTCCGTCTAAACATATAAGAGTGTT 60.418 40.741 0.00 0.00 40.06 3.32
331 390 6.040616 CCCTCCGTCTAAACATATAAGAGTGT 59.959 42.308 0.00 0.00 0.00 3.55
332 391 6.264744 TCCCTCCGTCTAAACATATAAGAGTG 59.735 42.308 0.00 0.00 0.00 3.51
333 392 6.371278 TCCCTCCGTCTAAACATATAAGAGT 58.629 40.000 0.00 0.00 0.00 3.24
334 393 6.896021 TCCCTCCGTCTAAACATATAAGAG 57.104 41.667 0.00 0.00 0.00 2.85
335 394 7.850935 ATTCCCTCCGTCTAAACATATAAGA 57.149 36.000 0.00 0.00 0.00 2.10
336 395 8.804204 ACTATTCCCTCCGTCTAAACATATAAG 58.196 37.037 0.00 0.00 0.00 1.73
337 396 8.582437 CACTATTCCCTCCGTCTAAACATATAA 58.418 37.037 0.00 0.00 0.00 0.98
338 397 7.727186 ACACTATTCCCTCCGTCTAAACATATA 59.273 37.037 0.00 0.00 0.00 0.86
339 398 6.553852 ACACTATTCCCTCCGTCTAAACATAT 59.446 38.462 0.00 0.00 0.00 1.78
340 399 5.895534 ACACTATTCCCTCCGTCTAAACATA 59.104 40.000 0.00 0.00 0.00 2.29
341 400 4.715297 ACACTATTCCCTCCGTCTAAACAT 59.285 41.667 0.00 0.00 0.00 2.71
342 401 4.091549 ACACTATTCCCTCCGTCTAAACA 58.908 43.478 0.00 0.00 0.00 2.83
343 402 4.732672 ACACTATTCCCTCCGTCTAAAC 57.267 45.455 0.00 0.00 0.00 2.01
344 403 5.021458 AGAACACTATTCCCTCCGTCTAAA 58.979 41.667 0.00 0.00 0.00 1.85
345 404 4.401519 CAGAACACTATTCCCTCCGTCTAA 59.598 45.833 0.00 0.00 0.00 2.10
346 405 3.952323 CAGAACACTATTCCCTCCGTCTA 59.048 47.826 0.00 0.00 0.00 2.59
347 406 2.761208 CAGAACACTATTCCCTCCGTCT 59.239 50.000 0.00 0.00 0.00 4.18
348 407 2.738964 GCAGAACACTATTCCCTCCGTC 60.739 54.545 0.00 0.00 0.00 4.79
349 408 1.207329 GCAGAACACTATTCCCTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
350 409 1.207089 TGCAGAACACTATTCCCTCCG 59.793 52.381 0.00 0.00 0.00 4.63
351 410 2.420687 CCTGCAGAACACTATTCCCTCC 60.421 54.545 17.39 0.00 0.00 4.30
352 411 2.237392 ACCTGCAGAACACTATTCCCTC 59.763 50.000 17.39 0.00 0.00 4.30
353 412 2.026822 CACCTGCAGAACACTATTCCCT 60.027 50.000 17.39 0.00 0.00 4.20
354 413 2.027192 TCACCTGCAGAACACTATTCCC 60.027 50.000 17.39 0.00 0.00 3.97
355 414 3.003480 GTCACCTGCAGAACACTATTCC 58.997 50.000 17.39 0.00 0.00 3.01
356 415 3.664107 TGTCACCTGCAGAACACTATTC 58.336 45.455 17.39 0.00 0.00 1.75
357 416 3.769739 TGTCACCTGCAGAACACTATT 57.230 42.857 17.39 0.00 0.00 1.73
358 417 3.181455 TGTTGTCACCTGCAGAACACTAT 60.181 43.478 17.39 0.00 0.00 2.12
359 418 2.169561 TGTTGTCACCTGCAGAACACTA 59.830 45.455 17.39 2.14 0.00 2.74
360 419 1.065491 TGTTGTCACCTGCAGAACACT 60.065 47.619 17.39 0.00 0.00 3.55
378 447 1.920835 GGAGGAGCCTTCCCAGTGT 60.921 63.158 0.00 0.00 45.24 3.55
390 459 2.035321 GGAGCTATCGTCAAAGGAGGAG 59.965 54.545 0.00 0.00 40.87 3.69
414 483 3.315191 GTGCCACGGTAGAATGCAATAAT 59.685 43.478 0.00 0.00 33.11 1.28
416 485 2.093181 AGTGCCACGGTAGAATGCAATA 60.093 45.455 0.00 0.00 33.11 1.90
442 515 2.451273 TCCTTCATTTTGGGGTGGGTAA 59.549 45.455 0.00 0.00 0.00 2.85
515 592 2.092323 TGGACTGTCTACGAGGACATG 58.908 52.381 7.85 0.00 43.94 3.21
533 612 2.350522 GCTGCGGTATATGGAAGATGG 58.649 52.381 0.00 0.00 0.00 3.51
541 620 1.071299 TGGCAGGCTGCGGTATATG 59.929 57.895 31.22 0.00 46.21 1.78
590 670 1.078918 TCATCACGAGGCAGGCAAG 60.079 57.895 0.00 0.00 0.00 4.01
603 683 0.610687 TGGGTGTACGCATGTCATCA 59.389 50.000 8.97 0.00 33.68 3.07
604 684 1.665679 CTTGGGTGTACGCATGTCATC 59.334 52.381 8.97 0.00 38.62 2.92
605 685 1.003118 ACTTGGGTGTACGCATGTCAT 59.997 47.619 8.97 0.00 41.14 3.06
674 754 0.918983 TTGATCCGGAGATTTGGCCT 59.081 50.000 11.34 0.00 30.90 5.19
698 778 4.409570 GCGTACGATGTAAGTCAAAGAGA 58.590 43.478 21.65 0.00 0.00 3.10
721 801 3.242316 CGGATACTCTAAACAAAAGGCGC 60.242 47.826 0.00 0.00 0.00 6.53
777 1804 3.881937 ATTTTCCTTCCATTCTGCTGC 57.118 42.857 0.00 0.00 0.00 5.25
843 1900 4.262079 GCTGCTGGTTTATATAGAGGTCGT 60.262 45.833 0.00 0.00 0.00 4.34
898 1969 1.082690 GTGGTCAGAAGCAAGCTAGC 58.917 55.000 6.62 6.62 34.02 3.42
919 1993 3.274586 CGGCGCTGTGATGGATGG 61.275 66.667 8.45 0.00 0.00 3.51
936 2018 1.858372 GCTAGAGTCGATCGGGCTCC 61.858 65.000 25.68 14.08 0.00 4.70
960 2042 4.200283 CGGCGACCTCCTCTGCTC 62.200 72.222 0.00 0.00 0.00 4.26
991 2073 1.747206 CGACCTCCCCATCACAAATCC 60.747 57.143 0.00 0.00 0.00 3.01
1031 2113 4.344865 GCCCCTTCTTGACGCCCA 62.345 66.667 0.00 0.00 0.00 5.36
1038 2120 2.359975 GTCCACGGCCCCTTCTTG 60.360 66.667 0.00 0.00 0.00 3.02
1242 2324 3.151710 CCGGCGTGGAGGGTGATA 61.152 66.667 6.01 0.00 42.00 2.15
1262 2344 0.961019 TAGGACGTACTTGTTGCCGT 59.039 50.000 5.12 0.00 36.04 5.68
1316 2418 1.671850 GGCTAAGCTGTTGTGCGAGTA 60.672 52.381 0.00 0.00 38.13 2.59
1353 2498 1.000274 GCAAAAGCCAACGGTGAAGAT 60.000 47.619 0.00 0.00 0.00 2.40
1488 2656 1.868997 GGATGTGCGTGTTCCAGTG 59.131 57.895 0.00 0.00 0.00 3.66
1651 2837 2.659016 CTTGCCTGAGAGTGCCGA 59.341 61.111 0.00 0.00 0.00 5.54
1656 2842 2.047465 CTGCGCTTGCCTGAGAGT 60.047 61.111 9.73 0.00 38.03 3.24
1736 2925 2.546778 CCAACATTTGATGCAGCCATC 58.453 47.619 0.00 0.00 46.46 3.51
1737 2926 1.208535 CCCAACATTTGATGCAGCCAT 59.791 47.619 0.00 0.00 0.00 4.40
1746 2935 2.942804 TGAGTTCAGCCCAACATTTGA 58.057 42.857 0.00 0.00 0.00 2.69
1751 2940 0.106769 TGCTTGAGTTCAGCCCAACA 60.107 50.000 0.00 0.00 0.00 3.33
1753 2942 1.032014 GTTGCTTGAGTTCAGCCCAA 58.968 50.000 0.00 0.00 0.00 4.12
1754 2943 0.106769 TGTTGCTTGAGTTCAGCCCA 60.107 50.000 0.00 0.00 0.00 5.36
1756 2945 0.039708 GCTGTTGCTTGAGTTCAGCC 60.040 55.000 0.00 0.00 43.55 4.85
1771 2960 4.012374 CAGGATGTTTGGAACTATGCTGT 58.988 43.478 12.16 0.00 35.64 4.40
1778 2967 1.425066 TGGAGCAGGATGTTTGGAACT 59.575 47.619 0.00 0.00 39.31 3.01
1803 2995 2.597455 ACCAGGCAGCATGTTAAACTT 58.403 42.857 6.27 0.00 39.31 2.66
1806 2998 2.080693 CGTACCAGGCAGCATGTTAAA 58.919 47.619 6.27 0.00 39.31 1.52
1808 3000 0.899019 TCGTACCAGGCAGCATGTTA 59.101 50.000 6.27 0.00 39.31 2.41
1815 3007 3.630769 TGTAGATAGTTCGTACCAGGCAG 59.369 47.826 0.00 0.00 0.00 4.85
1818 3010 3.004524 GGCTGTAGATAGTTCGTACCAGG 59.995 52.174 0.00 0.00 0.00 4.45
1823 3015 2.224606 CCCGGCTGTAGATAGTTCGTA 58.775 52.381 0.00 0.00 0.00 3.43
1824 3016 1.030457 CCCGGCTGTAGATAGTTCGT 58.970 55.000 0.00 0.00 0.00 3.85
1832 3024 1.455217 GAGGTAGCCCGGCTGTAGA 60.455 63.158 22.95 0.00 40.10 2.59
1835 3027 3.077556 CAGAGGTAGCCCGGCTGT 61.078 66.667 22.95 6.32 40.10 4.40
1844 3036 0.976641 TGGAGGTGTTGCAGAGGTAG 59.023 55.000 0.00 0.00 0.00 3.18
1906 3098 1.390565 ACTCGTTCCCGGAGACATAG 58.609 55.000 0.73 4.14 33.95 2.23
1925 3117 0.670162 GTTCAGCTGCTGCAAAGGAA 59.330 50.000 24.38 9.77 42.74 3.36
1977 3172 1.705337 GGTGCAATATCACGCGCTGT 61.705 55.000 5.73 1.79 38.67 4.40
1980 3175 2.053116 CGGTGCAATATCACGCGC 60.053 61.111 5.73 0.00 37.83 6.86
1984 3179 1.608590 CAATCCCCGGTGCAATATCAC 59.391 52.381 0.00 0.00 36.28 3.06
1989 3184 0.033208 ATGTCAATCCCCGGTGCAAT 60.033 50.000 0.00 0.00 0.00 3.56
1999 3206 1.750399 ACCGGCAGCATGTCAATCC 60.750 57.895 0.00 0.00 44.43 3.01
2001 3208 2.703798 GCACCGGCAGCATGTCAAT 61.704 57.895 14.06 0.00 44.43 2.57
2117 3330 9.496873 TCATTTGGAAAAAGAAACTATAGACGA 57.503 29.630 6.78 0.00 0.00 4.20
2134 3347 7.950512 ACACAACACATCTATTTCATTTGGAA 58.049 30.769 0.00 0.00 0.00 3.53
2165 3382 7.832503 AACGTTATAGGTTATGTACAACACC 57.167 36.000 15.93 15.93 0.00 4.16
2168 3385 7.967178 AGCAAACGTTATAGGTTATGTACAAC 58.033 34.615 0.00 0.00 0.00 3.32
2247 3466 9.570468 AATGCATGTTTTATCATCTCATCTACT 57.430 29.630 0.00 0.00 0.00 2.57
2308 3619 9.612620 CAACTATAGTGACAAAAACCAATTCTC 57.387 33.333 6.06 0.00 0.00 2.87
2312 3623 8.576442 CCTTCAACTATAGTGACAAAAACCAAT 58.424 33.333 6.06 0.00 0.00 3.16
2343 3654 7.611079 TCATGAGTCACATCAAATGACCAATTA 59.389 33.333 0.00 0.00 46.38 1.40
2416 3733 3.215151 TGATGTAGAGGCCGAGAGTAAG 58.785 50.000 0.00 0.00 0.00 2.34
2446 3766 4.152223 GGCAACATGTTAATTGTTTGGCTC 59.848 41.667 11.53 0.00 35.18 4.70
2514 3835 3.000041 CACCGTTGTGCAAGATAGCTAA 59.000 45.455 0.00 0.00 35.31 3.09
2544 3865 8.559536 CCGTAGTAATTGTGATGAAGCATTTAT 58.440 33.333 0.00 0.00 0.00 1.40
2549 3870 4.629634 CACCGTAGTAATTGTGATGAAGCA 59.370 41.667 0.00 0.00 0.00 3.91
2566 3887 0.819582 GCTGCCTAGTAACCACCGTA 59.180 55.000 0.00 0.00 0.00 4.02
2573 3894 0.037605 ACCACGTGCTGCCTAGTAAC 60.038 55.000 10.91 0.00 0.00 2.50
2582 3903 1.671054 CCCCACTAACCACGTGCTG 60.671 63.158 10.91 0.00 0.00 4.41
2583 3904 2.747686 CCCCACTAACCACGTGCT 59.252 61.111 10.91 1.35 0.00 4.40
2589 3910 2.280103 TCATTAAGGCCCCACTAACCA 58.720 47.619 0.00 0.00 0.00 3.67
2629 3993 8.519799 TGATCAAAGTAGAAAGGTTTGAGTTT 57.480 30.769 0.00 0.00 42.02 2.66
2664 4028 7.201644 CGAGCTGGTGTTATAGATGTCAAATTT 60.202 37.037 0.00 0.00 0.00 1.82
2669 4033 3.951680 TCGAGCTGGTGTTATAGATGTCA 59.048 43.478 0.00 0.00 0.00 3.58
2678 4042 3.531538 GATCCAAATCGAGCTGGTGTTA 58.468 45.455 13.67 0.00 34.11 2.41
3070 4694 5.388944 ACACTCACGTCGTCTCTATAAAAC 58.611 41.667 0.00 0.00 0.00 2.43
3083 4716 3.125829 TCGTGGATAGTAACACTCACGTC 59.874 47.826 14.64 0.00 41.62 4.34
3091 4724 7.766738 TCATAAAATTGCTCGTGGATAGTAACA 59.233 33.333 0.00 0.00 0.00 2.41
3095 4728 7.201732 CCTTTCATAAAATTGCTCGTGGATAGT 60.202 37.037 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.