Multiple sequence alignment - TraesCS6A01G281300

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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 TraesCS6A01G281300 chr6A 100.000 2588 0 0 1 2588 511037367 511039954 0.000000e+00 4780.0
1 TraesCS6A01G281300 chr6A 88.222 433 50 1 1 432 523069591 523069159 1.370000e-142 516.0
2 TraesCS6A01G281300 chr6D 95.108 1574 49 7 973 2535 370041369 370042925 0.000000e+00 2455.0
3 TraesCS6A01G281300 chr6D 86.127 173 12 6 1850 2016 224751052 224751218 2.650000e-40 176.0
4 TraesCS6A01G281300 chr6B 95.785 1115 20 5 944 2047 555340928 555342026 0.000000e+00 1773.0
5 TraesCS6A01G281300 chr6B 87.316 544 40 11 444 985 555340413 555340929 1.710000e-166 595.0
6 TraesCS6A01G281300 chr6B 89.679 436 40 4 1 432 555339708 555340142 3.760000e-153 551.0
7 TraesCS6A01G281300 chr6B 88.808 411 43 2 1 410 680536545 680536953 3.840000e-138 501.0
8 TraesCS6A01G281300 chr6B 94.093 237 7 2 2302 2538 555342046 555342275 1.140000e-93 353.0
9 TraesCS6A01G281300 chr6B 87.903 124 11 3 481 602 680537228 680537349 2.680000e-30 143.0
10 TraesCS6A01G281300 chr6B 96.296 54 2 0 2535 2588 716477392 716477445 3.550000e-14 89.8
11 TraesCS6A01G281300 chr1B 89.401 434 44 2 1 432 544731290 544730857 1.750000e-151 545.0
12 TraesCS6A01G281300 chr1B 86.792 159 21 0 444 602 544730580 544730422 7.360000e-41 178.0
13 TraesCS6A01G281300 chr7A 89.171 434 42 4 1 432 197174918 197174488 1.050000e-148 536.0
14 TraesCS6A01G281300 chr7A 94.643 56 3 0 2533 2588 534783840 534783895 1.280000e-13 87.9
15 TraesCS6A01G281300 chr3D 89.598 423 43 1 7 429 61172589 61173010 1.050000e-148 536.0
16 TraesCS6A01G281300 chr3D 96.296 54 2 0 2535 2588 288825637 288825690 3.550000e-14 89.8
17 TraesCS6A01G281300 chr5D 88.657 432 46 2 1 432 450785346 450785774 8.210000e-145 523.0
18 TraesCS6A01G281300 chr5D 87.558 434 50 4 1 432 73830186 73829755 1.380000e-137 499.0
19 TraesCS6A01G281300 chr3B 88.564 411 43 4 1 411 96832647 96833053 1.790000e-136 496.0
20 TraesCS6A01G281300 chr3B 89.820 167 12 4 444 608 651601536 651601699 2.610000e-50 209.0
21 TraesCS6A01G281300 chr3B 84.571 175 16 6 1850 2016 332944680 332944509 2.060000e-36 163.0
22 TraesCS6A01G281300 chr2A 88.304 171 10 6 1854 2017 451810542 451810375 2.030000e-46 196.0
23 TraesCS6A01G281300 chr2D 86.857 175 13 5 1850 2017 342099803 342099632 1.220000e-43 187.0
24 TraesCS6A01G281300 chr2D 85.882 170 13 7 1855 2016 590154931 590154765 1.230000e-38 171.0
25 TraesCS6A01G281300 chr2B 86.857 175 13 5 1850 2017 407236346 407236175 1.220000e-43 187.0
26 TraesCS6A01G281300 chr5B 87.578 161 19 1 446 606 65280174 65280015 4.400000e-43 185.0
27 TraesCS6A01G281300 chr1D 86.207 174 14 6 1850 2016 250738613 250738443 2.050000e-41 180.0
28 TraesCS6A01G281300 chr7B 88.652 141 16 0 468 608 497023296 497023436 3.420000e-39 172.0
29 TraesCS6A01G281300 chr3A 98.077 52 1 0 2537 2588 746884416 746884467 9.860000e-15 91.6
30 TraesCS6A01G281300 chr3A 94.737 57 2 1 2532 2588 576278504 576278449 1.280000e-13 87.9
31 TraesCS6A01G281300 chr5A 94.737 57 3 0 2532 2588 55038636 55038580 3.550000e-14 89.8
32 TraesCS6A01G281300 chr5A 91.935 62 4 1 2527 2588 491585564 491585504 4.590000e-13 86.1
33 TraesCS6A01G281300 chr5A 94.545 55 3 0 2534 2588 641061778 641061724 4.590000e-13 86.1
34 TraesCS6A01G281300 chr1A 96.296 54 2 0 2535 2588 266771275 266771328 3.550000e-14 89.8


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 TraesCS6A01G281300 chr6A 511037367 511039954 2587 False 4780.0 4780 100.00000 1 2588 1 chr6A.!!$F1 2587
1 TraesCS6A01G281300 chr6D 370041369 370042925 1556 False 2455.0 2455 95.10800 973 2535 1 chr6D.!!$F2 1562
2 TraesCS6A01G281300 chr6B 555339708 555342275 2567 False 818.0 1773 91.71825 1 2538 4 chr6B.!!$F2 2537
3 TraesCS6A01G281300 chr6B 680536545 680537349 804 False 322.0 501 88.35550 1 602 2 chr6B.!!$F3 601
4 TraesCS6A01G281300 chr1B 544730422 544731290 868 True 361.5 545 88.09650 1 602 2 chr1B.!!$R1 601

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
433 447 0.108615 CGGCTGAGTGAAGGACGATT 60.109 55.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2438 1.064825 AATCCCCGGTTCACTTGTCT 58.935 50.0 0.0 0.0 0.0 3.41 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
53 55 2.363306 ACAAGTCTGGCAAATGGTGA 57.637 45.000 0.00 0.00 0.00 4.02
55 57 4.032960 ACAAGTCTGGCAAATGGTGATA 57.967 40.909 0.00 0.00 0.00 2.15
87 93 3.251016 AGCATCCATAGAGCCTCTGTA 57.749 47.619 3.98 0.00 0.00 2.74
136 142 1.832167 GCGATCCTCTCCTGCTCCT 60.832 63.158 0.00 0.00 0.00 3.69
174 181 4.615682 GCATATCTGATGACAGGTCTCTCG 60.616 50.000 0.00 0.00 43.60 4.04
224 231 2.091499 ACATGACCCATGCCTGAATCAT 60.091 45.455 0.00 0.00 44.80 2.45
243 250 2.079170 TAGCTATCAGTGCTCCTGCT 57.921 50.000 0.00 0.00 41.25 4.24
248 255 2.574006 ATCAGTGCTCCTGCTTGAAA 57.426 45.000 0.00 0.00 41.25 2.69
254 261 2.819608 GTGCTCCTGCTTGAAATACCAA 59.180 45.455 0.00 0.00 40.48 3.67
262 269 4.406456 TGCTTGAAATACCAACCACATCT 58.594 39.130 0.00 0.00 0.00 2.90
350 357 2.102757 TCTAACGGCCTAACAACACACA 59.897 45.455 0.00 0.00 0.00 3.72
364 371 3.604875 ACACACATAACTTAGGGGACG 57.395 47.619 0.00 0.00 0.00 4.79
401 408 0.248296 GCATCAGAGACGAGGACGAC 60.248 60.000 0.00 0.00 42.66 4.34
410 424 2.362120 GAGGACGACGAAGGGGGA 60.362 66.667 0.00 0.00 0.00 4.81
411 425 1.757340 GAGGACGACGAAGGGGGAT 60.757 63.158 0.00 0.00 0.00 3.85
414 428 1.141234 GACGACGAAGGGGGATCAC 59.859 63.158 0.00 0.00 0.00 3.06
433 447 0.108615 CGGCTGAGTGAAGGACGATT 60.109 55.000 0.00 0.00 0.00 3.34
434 448 1.646189 GGCTGAGTGAAGGACGATTC 58.354 55.000 0.00 0.00 0.00 2.52
441 455 0.320374 TGAAGGACGATTCGGCAGTT 59.680 50.000 14.90 6.35 36.10 3.16
442 456 1.270625 TGAAGGACGATTCGGCAGTTT 60.271 47.619 14.90 4.78 36.10 2.66
455 744 1.634702 GCAGTTTCTGACTCGCTAGG 58.365 55.000 0.66 0.00 36.10 3.02
458 747 3.677424 GCAGTTTCTGACTCGCTAGGAAT 60.677 47.826 0.66 0.00 36.10 3.01
476 765 3.372822 GGAATTGCCGATTCGACAGTTTA 59.627 43.478 7.83 0.00 44.21 2.01
478 767 4.536364 ATTGCCGATTCGACAGTTTATG 57.464 40.909 7.83 0.00 0.00 1.90
479 768 3.239587 TGCCGATTCGACAGTTTATGA 57.760 42.857 7.83 0.00 0.00 2.15
548 837 1.202114 CCACTATGTGCGCAACCAAAT 59.798 47.619 14.00 3.73 31.34 2.32
628 917 8.058847 TGCCCTAAGGTATGATTATTTGTTTCT 58.941 33.333 0.00 0.00 34.57 2.52
644 933 5.367945 TGTTTCTCCCTACACAACTTCTT 57.632 39.130 0.00 0.00 0.00 2.52
659 948 7.012421 ACACAACTTCTTCTCCTACATTTGTTC 59.988 37.037 0.00 0.00 0.00 3.18
679 968 3.023119 TCTCATGACAGCCTCTCTCTTC 58.977 50.000 0.00 0.00 0.00 2.87
702 991 1.529309 GGAGCCTCAACCCTCCATC 59.471 63.158 0.00 0.00 45.55 3.51
730 1019 4.086706 TGTTCCAGGTCCTTTTCTTCTC 57.913 45.455 0.00 0.00 0.00 2.87
738 1027 3.005897 GGTCCTTTTCTTCTCCCTTTTGC 59.994 47.826 0.00 0.00 0.00 3.68
756 1045 2.677003 CGGTGGTTGTCGCCATGAC 61.677 63.158 0.00 0.00 46.14 3.06
777 1066 2.482721 CGTTCAACCCTTACACACATCC 59.517 50.000 0.00 0.00 0.00 3.51
782 1071 4.141287 CAACCCTTACACACATCCTTTGA 58.859 43.478 0.00 0.00 0.00 2.69
785 1074 5.393866 ACCCTTACACACATCCTTTGATTT 58.606 37.500 0.00 0.00 0.00 2.17
788 1077 5.711976 CCTTACACACATCCTTTGATTTCCT 59.288 40.000 0.00 0.00 0.00 3.36
810 1099 0.188834 CCCCCTCTATCCCTCTTCGT 59.811 60.000 0.00 0.00 0.00 3.85
830 1119 3.120060 CGTCTTTCTCAATTGCCCTTCTG 60.120 47.826 0.00 0.00 0.00 3.02
834 1123 4.853924 TTCTCAATTGCCCTTCTGTTTC 57.146 40.909 0.00 0.00 0.00 2.78
842 1131 2.070028 GCCCTTCTGTTTCTTCTCGTC 58.930 52.381 0.00 0.00 0.00 4.20
877 1166 3.201290 AGTCATTGTCAGGCGAATGATC 58.799 45.455 0.00 0.00 39.97 2.92
887 1176 2.854772 CGAATGATCGCGTCGAAGA 58.145 52.632 10.15 0.00 42.96 2.87
888 1177 1.399572 CGAATGATCGCGTCGAAGAT 58.600 50.000 10.15 0.41 42.96 2.40
889 1178 1.781429 CGAATGATCGCGTCGAAGATT 59.219 47.619 10.15 7.22 42.96 2.40
890 1179 2.216488 CGAATGATCGCGTCGAAGATTT 59.784 45.455 10.15 0.00 42.96 2.17
891 1180 3.656818 CGAATGATCGCGTCGAAGATTTC 60.657 47.826 10.15 2.61 42.96 2.17
892 1181 2.561733 TGATCGCGTCGAAGATTTCT 57.438 45.000 5.77 0.00 39.99 2.52
893 1182 3.685836 TGATCGCGTCGAAGATTTCTA 57.314 42.857 5.77 0.00 39.99 2.10
894 1183 4.224715 TGATCGCGTCGAAGATTTCTAT 57.775 40.909 5.77 0.00 39.99 1.98
895 1184 4.607955 TGATCGCGTCGAAGATTTCTATT 58.392 39.130 5.77 0.00 39.99 1.73
896 1185 5.041287 TGATCGCGTCGAAGATTTCTATTT 58.959 37.500 5.77 0.00 39.99 1.40
897 1186 5.518847 TGATCGCGTCGAAGATTTCTATTTT 59.481 36.000 5.77 0.00 39.99 1.82
898 1187 5.773239 TCGCGTCGAAGATTTCTATTTTT 57.227 34.783 5.77 0.00 40.67 1.94
955 1284 0.179116 TGCACGTGCTTTGTTTGCAT 60.179 45.000 37.59 0.00 42.69 3.96
961 1290 3.796178 ACGTGCTTTGTTTGCATTTGTAG 59.204 39.130 0.00 0.00 42.69 2.74
1105 1436 2.111878 GGACCCAGATGGCATCCG 59.888 66.667 23.33 13.79 37.83 4.18
1482 1813 2.126031 GTGGAGACGGCGAAGGAC 60.126 66.667 16.62 0.00 0.00 3.85
1588 1919 1.899814 AGATGGCCGTGTACTTCTGAA 59.100 47.619 0.00 0.00 0.00 3.02
1589 1920 2.501723 AGATGGCCGTGTACTTCTGAAT 59.498 45.455 0.00 0.00 0.00 2.57
1590 1921 2.851263 TGGCCGTGTACTTCTGAATT 57.149 45.000 0.00 0.00 0.00 2.17
1591 1922 2.695359 TGGCCGTGTACTTCTGAATTC 58.305 47.619 0.00 0.00 0.00 2.17
1592 1923 2.301870 TGGCCGTGTACTTCTGAATTCT 59.698 45.455 7.05 0.00 0.00 2.40
1593 1924 2.673368 GGCCGTGTACTTCTGAATTCTG 59.327 50.000 7.05 6.50 0.00 3.02
1594 1925 3.585862 GCCGTGTACTTCTGAATTCTGA 58.414 45.455 10.68 10.68 0.00 3.27
1788 2127 4.536065 CTGTTTCTGCTGCGTTCATAAAA 58.464 39.130 0.00 0.00 0.00 1.52
1875 2214 5.001232 TCCAAATATAGGCCAGTTAATCGC 58.999 41.667 5.01 0.00 0.00 4.58
2056 2401 9.674824 TCTTGAAAGTTACTACTAGTTCTTTCG 57.325 33.333 23.43 17.11 43.00 3.46
2072 2417 2.060326 TTCGGTCAGTAAAGCTGTCG 57.940 50.000 0.00 0.00 45.23 4.35
2092 2437 0.897621 GGCTAAGCTTTGCCAACCAT 59.102 50.000 36.80 0.00 46.27 3.55
2093 2438 2.099405 GGCTAAGCTTTGCCAACCATA 58.901 47.619 36.80 2.67 46.27 2.74
2145 2490 6.930164 AGAGCTGAATGAAGTTCTATGCATAG 59.070 38.462 25.13 25.13 36.14 2.23
2282 2627 9.060347 GCCTATTCAATCAAATTCTCTGTCATA 57.940 33.333 0.00 0.00 0.00 2.15
2292 2637 9.958180 TCAAATTCTCTGTCATAAAGGTAATCA 57.042 29.630 0.00 0.00 0.00 2.57
2308 2653 7.719871 AGGTAATCATGTCTAACAGTGTACT 57.280 36.000 0.00 0.00 0.00 2.73
2343 2688 2.180432 AGAACTTTTGGTACCGAGGC 57.820 50.000 7.57 2.73 0.00 4.70
2344 2689 1.697982 AGAACTTTTGGTACCGAGGCT 59.302 47.619 7.57 4.82 0.00 4.58
2345 2690 2.074576 GAACTTTTGGTACCGAGGCTC 58.925 52.381 7.57 3.87 0.00 4.70
2346 2691 1.349067 ACTTTTGGTACCGAGGCTCT 58.651 50.000 13.50 0.00 0.00 4.09
2347 2692 1.697982 ACTTTTGGTACCGAGGCTCTT 59.302 47.619 13.50 1.66 0.00 2.85
2348 2693 2.076863 CTTTTGGTACCGAGGCTCTTG 58.923 52.381 13.50 6.15 0.00 3.02
2349 2694 1.344065 TTTGGTACCGAGGCTCTTGA 58.656 50.000 13.50 0.00 0.00 3.02
2376 2721 9.712305 CTCTTGAGGTTTCACTTTTAGAGATTA 57.288 33.333 0.00 0.00 36.23 1.75
2422 2767 2.934887 TCAACATGCATCACCCTATGG 58.065 47.619 0.00 0.00 37.80 2.74
2538 2883 5.973565 GCATTTGCAGGAACATGATAAGTAC 59.026 40.000 0.00 0.00 41.59 2.73
2539 2884 6.183360 GCATTTGCAGGAACATGATAAGTACT 60.183 38.462 0.00 0.00 41.59 2.73
2540 2885 6.985188 TTTGCAGGAACATGATAAGTACTC 57.015 37.500 0.00 0.00 0.00 2.59
2541 2886 5.023533 TGCAGGAACATGATAAGTACTCC 57.976 43.478 0.00 0.00 0.00 3.85
2542 2887 4.141711 TGCAGGAACATGATAAGTACTCCC 60.142 45.833 0.00 0.00 0.00 4.30
2543 2888 4.101741 GCAGGAACATGATAAGTACTCCCT 59.898 45.833 0.00 0.00 0.00 4.20
2544 2889 5.740513 GCAGGAACATGATAAGTACTCCCTC 60.741 48.000 0.00 0.00 0.00 4.30
2545 2890 4.902448 AGGAACATGATAAGTACTCCCTCC 59.098 45.833 0.00 0.00 0.00 4.30
2546 2891 4.654262 GGAACATGATAAGTACTCCCTCCA 59.346 45.833 0.00 0.00 0.00 3.86
2547 2892 5.308237 GGAACATGATAAGTACTCCCTCCAT 59.692 44.000 0.00 0.00 0.00 3.41
2548 2893 6.183361 GGAACATGATAAGTACTCCCTCCATT 60.183 42.308 0.00 0.00 0.00 3.16
2549 2894 6.426646 ACATGATAAGTACTCCCTCCATTC 57.573 41.667 0.00 0.00 0.00 2.67
2550 2895 5.308237 ACATGATAAGTACTCCCTCCATTCC 59.692 44.000 0.00 0.00 0.00 3.01
2551 2896 4.890988 TGATAAGTACTCCCTCCATTCCA 58.109 43.478 0.00 0.00 0.00 3.53
2552 2897 5.285401 TGATAAGTACTCCCTCCATTCCAA 58.715 41.667 0.00 0.00 0.00 3.53
2553 2898 5.729229 TGATAAGTACTCCCTCCATTCCAAA 59.271 40.000 0.00 0.00 0.00 3.28
2554 2899 6.216662 TGATAAGTACTCCCTCCATTCCAAAA 59.783 38.462 0.00 0.00 0.00 2.44
2555 2900 5.536497 AAGTACTCCCTCCATTCCAAAAT 57.464 39.130 0.00 0.00 0.00 1.82
2556 2901 6.652205 AAGTACTCCCTCCATTCCAAAATA 57.348 37.500 0.00 0.00 0.00 1.40
2557 2902 6.848562 AGTACTCCCTCCATTCCAAAATAT 57.151 37.500 0.00 0.00 0.00 1.28
2558 2903 7.947782 AGTACTCCCTCCATTCCAAAATATA 57.052 36.000 0.00 0.00 0.00 0.86
2559 2904 7.978925 AGTACTCCCTCCATTCCAAAATATAG 58.021 38.462 0.00 0.00 0.00 1.31
2560 2905 6.848562 ACTCCCTCCATTCCAAAATATAGT 57.151 37.500 0.00 0.00 0.00 2.12
2561 2906 6.605119 ACTCCCTCCATTCCAAAATATAGTG 58.395 40.000 0.00 0.00 0.00 2.74
2562 2907 5.385198 TCCCTCCATTCCAAAATATAGTGC 58.615 41.667 0.00 0.00 0.00 4.40
2563 2908 4.216257 CCCTCCATTCCAAAATATAGTGCG 59.784 45.833 0.00 0.00 0.00 5.34
2564 2909 4.320494 CCTCCATTCCAAAATATAGTGCGC 60.320 45.833 0.00 0.00 0.00 6.09
2565 2910 3.568007 TCCATTCCAAAATATAGTGCGCC 59.432 43.478 4.18 0.00 0.00 6.53
2566 2911 3.569701 CCATTCCAAAATATAGTGCGCCT 59.430 43.478 4.18 3.99 0.00 5.52
2567 2912 4.539870 CATTCCAAAATATAGTGCGCCTG 58.460 43.478 4.18 0.00 0.00 4.85
2568 2913 1.946768 TCCAAAATATAGTGCGCCTGC 59.053 47.619 4.18 0.00 43.20 4.85
2578 2923 3.793144 GCGCCTGCACTTTCCGAG 61.793 66.667 0.00 0.00 42.15 4.63
2579 2924 3.121030 CGCCTGCACTTTCCGAGG 61.121 66.667 0.00 0.00 0.00 4.63
2580 2925 2.032681 GCCTGCACTTTCCGAGGT 59.967 61.111 0.00 0.00 0.00 3.85
2581 2926 2.035442 GCCTGCACTTTCCGAGGTC 61.035 63.158 0.00 0.00 0.00 3.85
2582 2927 1.376037 CCTGCACTTTCCGAGGTCC 60.376 63.158 0.00 0.00 0.00 4.46
2583 2928 1.371183 CTGCACTTTCCGAGGTCCA 59.629 57.895 0.00 0.00 0.00 4.02
2584 2929 0.250295 CTGCACTTTCCGAGGTCCAA 60.250 55.000 0.00 0.00 0.00 3.53
2585 2930 0.534203 TGCACTTTCCGAGGTCCAAC 60.534 55.000 0.00 0.00 0.00 3.77
2586 2931 0.250338 GCACTTTCCGAGGTCCAACT 60.250 55.000 0.00 0.00 0.00 3.16
2587 2932 1.814248 GCACTTTCCGAGGTCCAACTT 60.814 52.381 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.487325 TCAGACCTTCAGGACCAGGA 59.513 55.000 3.37 0.00 38.94 3.86
55 57 7.176340 GGCTCTATGGATGCTTAGAATGAAAAT 59.824 37.037 10.42 0.00 0.00 1.82
87 93 7.843490 AAACTACATATACAACTGCAACGAT 57.157 32.000 0.00 0.00 0.00 3.73
149 156 4.900652 AGAGACCTGTCATCAGATATGCTT 59.099 41.667 0.00 0.00 43.76 3.91
174 181 0.318784 AGAGAGTTGTTCGTCGTGCC 60.319 55.000 0.00 0.00 0.00 5.01
243 250 4.022416 GCACAGATGTGGTTGGTATTTCAA 60.022 41.667 14.44 0.00 45.72 2.69
248 255 1.003118 ACGCACAGATGTGGTTGGTAT 59.997 47.619 14.44 0.00 45.72 2.73
254 261 0.901827 TATGGACGCACAGATGTGGT 59.098 50.000 14.44 10.24 45.72 4.16
262 269 1.479323 GGACTAGGTTATGGACGCACA 59.521 52.381 0.00 0.00 0.00 4.57
309 316 5.422214 AGACAAGGTGTAGGATCGATTTT 57.578 39.130 0.00 0.00 0.00 1.82
350 357 0.397535 TCGCCCGTCCCCTAAGTTAT 60.398 55.000 0.00 0.00 0.00 1.89
364 371 2.469516 CCGGTAAGCAACATCGCCC 61.470 63.158 0.00 0.00 0.00 6.13
401 408 3.470888 AGCCGTGATCCCCCTTCG 61.471 66.667 0.00 0.00 0.00 3.79
410 424 0.247736 GTCCTTCACTCAGCCGTGAT 59.752 55.000 2.46 0.00 42.91 3.06
411 425 1.666011 GTCCTTCACTCAGCCGTGA 59.334 57.895 0.00 0.00 41.82 4.35
414 428 0.108615 AATCGTCCTTCACTCAGCCG 60.109 55.000 0.00 0.00 0.00 5.52
433 447 1.372997 GCGAGTCAGAAACTGCCGA 60.373 57.895 0.00 0.00 38.74 5.54
434 448 0.109272 TAGCGAGTCAGAAACTGCCG 60.109 55.000 0.00 0.00 38.74 5.69
441 455 2.418746 GGCAATTCCTAGCGAGTCAGAA 60.419 50.000 0.00 0.00 0.00 3.02
442 456 1.137086 GGCAATTCCTAGCGAGTCAGA 59.863 52.381 0.00 0.00 0.00 3.27
455 744 3.471495 AAACTGTCGAATCGGCAATTC 57.529 42.857 12.08 1.90 42.08 2.17
458 747 3.369756 GTCATAAACTGTCGAATCGGCAA 59.630 43.478 12.08 0.00 42.08 4.52
476 765 2.729479 CCTCAGCCTGGCTCGTCAT 61.729 63.158 20.49 0.00 36.40 3.06
478 767 4.154347 CCCTCAGCCTGGCTCGTC 62.154 72.222 20.49 0.00 36.40 4.20
602 891 8.058847 AGAAACAAATAATCATACCTTAGGGCA 58.941 33.333 2.32 0.00 35.63 5.36
628 917 3.858135 AGGAGAAGAAGTTGTGTAGGGA 58.142 45.455 0.00 0.00 0.00 4.20
644 933 6.358974 TGTCATGAGAACAAATGTAGGAGA 57.641 37.500 0.00 0.00 0.00 3.71
659 948 2.101249 GGAAGAGAGAGGCTGTCATGAG 59.899 54.545 14.66 0.00 0.00 2.90
679 968 4.410400 GGGTTGAGGCTCCGGTGG 62.410 72.222 12.86 0.00 0.00 4.61
702 991 2.292828 AGGACCTGGAACAACAATGG 57.707 50.000 0.00 0.00 38.70 3.16
730 1019 1.362355 GACAACCACCGCAAAAGGG 59.638 57.895 0.00 0.00 35.02 3.95
753 1042 2.093606 TGTGTGTAAGGGTTGAACGTCA 60.094 45.455 0.00 0.00 0.00 4.35
756 1045 2.482721 GGATGTGTGTAAGGGTTGAACG 59.517 50.000 0.00 0.00 0.00 3.95
777 1066 2.849318 AGAGGGGGAGAGGAAATCAAAG 59.151 50.000 0.00 0.00 0.00 2.77
782 1071 2.157926 GGGATAGAGGGGGAGAGGAAAT 60.158 54.545 0.00 0.00 0.00 2.17
785 1074 0.026415 AGGGATAGAGGGGGAGAGGA 60.026 60.000 0.00 0.00 0.00 3.71
788 1077 1.790157 GAAGAGGGATAGAGGGGGAGA 59.210 57.143 0.00 0.00 0.00 3.71
810 1099 4.104383 ACAGAAGGGCAATTGAGAAAGA 57.896 40.909 10.34 0.00 0.00 2.52
830 1119 1.050767 CGACACGGACGAGAAGAAAC 58.949 55.000 0.00 0.00 0.00 2.78
834 1123 0.725118 GACACGACACGGACGAGAAG 60.725 60.000 0.00 0.00 34.70 2.85
842 1131 2.631418 ATGACTTAGACACGACACGG 57.369 50.000 0.00 0.00 0.00 4.94
898 1187 5.163457 CCCTGGTTCAAGCTTAGTTGAAAAA 60.163 40.000 0.00 0.00 45.65 1.94
899 1188 4.340950 CCCTGGTTCAAGCTTAGTTGAAAA 59.659 41.667 0.00 0.00 45.65 2.29
900 1189 3.888930 CCCTGGTTCAAGCTTAGTTGAAA 59.111 43.478 0.00 0.00 45.65 2.69
901 1190 3.486383 CCCTGGTTCAAGCTTAGTTGAA 58.514 45.455 0.00 0.00 42.79 2.69
902 1191 2.224769 CCCCTGGTTCAAGCTTAGTTGA 60.225 50.000 0.00 0.00 34.56 3.18
925 1214 2.245714 GCACGTGCAGGCTTAGAAGC 62.246 60.000 34.52 5.66 45.30 3.86
955 1284 4.332543 CCGATTTGCTATCAGTGCTACAAA 59.667 41.667 0.00 0.00 0.00 2.83
961 1290 1.016627 TGCCGATTTGCTATCAGTGC 58.983 50.000 0.00 0.00 0.00 4.40
1744 2083 1.135527 CCAAAGCCATACAGCCACATG 59.864 52.381 0.00 0.00 0.00 3.21
1788 2127 7.201732 CCAAGACAATATAGCACGGAATTTTCT 60.202 37.037 0.00 0.00 0.00 2.52
1875 2214 3.535561 AGCAATTAACTGACCGAGATGG 58.464 45.455 0.00 0.00 46.41 3.51
2092 2437 1.946984 ATCCCCGGTTCACTTGTCTA 58.053 50.000 0.00 0.00 0.00 2.59
2093 2438 1.064825 AATCCCCGGTTCACTTGTCT 58.935 50.000 0.00 0.00 0.00 3.41
2145 2490 8.876790 GGTGTTATGGTTTACAATCTACAGTAC 58.123 37.037 0.00 0.00 0.00 2.73
2156 2501 7.988599 GGTACTATGATGGTGTTATGGTTTACA 59.011 37.037 0.00 0.00 0.00 2.41
2275 2620 9.599866 TGTTAGACATGATTACCTTTATGACAG 57.400 33.333 0.00 0.00 0.00 3.51
2282 2627 8.594550 AGTACACTGTTAGACATGATTACCTTT 58.405 33.333 0.00 0.00 0.00 3.11
2308 2653 7.277539 CCAAAAGTTCTTTCAGCAACAATAACA 59.722 33.333 0.00 0.00 0.00 2.41
2311 2656 6.872920 ACCAAAAGTTCTTTCAGCAACAATA 58.127 32.000 0.00 0.00 0.00 1.90
2343 2688 4.954875 AGTGAAACCTCAAGAGTCAAGAG 58.045 43.478 5.19 5.19 37.80 2.85
2344 2689 5.359194 AAGTGAAACCTCAAGAGTCAAGA 57.641 39.130 0.00 0.00 37.80 3.02
2345 2690 6.442513 AAAAGTGAAACCTCAAGAGTCAAG 57.557 37.500 0.00 0.00 37.80 3.02
2346 2691 7.335627 TCTAAAAGTGAAACCTCAAGAGTCAA 58.664 34.615 0.00 0.00 37.80 3.18
2347 2692 6.884832 TCTAAAAGTGAAACCTCAAGAGTCA 58.115 36.000 0.00 0.00 37.80 3.41
2348 2693 7.210873 TCTCTAAAAGTGAAACCTCAAGAGTC 58.789 38.462 0.00 0.00 37.80 3.36
2349 2694 7.125792 TCTCTAAAAGTGAAACCTCAAGAGT 57.874 36.000 0.00 0.00 37.80 3.24
2422 2767 4.044426 GCACTCCACAAAATGTCTCAAAC 58.956 43.478 0.00 0.00 0.00 2.93
2538 2883 5.474876 GCACTATATTTTGGAATGGAGGGAG 59.525 44.000 0.00 0.00 0.00 4.30
2539 2884 5.385198 GCACTATATTTTGGAATGGAGGGA 58.615 41.667 0.00 0.00 0.00 4.20
2540 2885 4.216257 CGCACTATATTTTGGAATGGAGGG 59.784 45.833 0.00 0.00 0.00 4.30
2541 2886 4.320494 GCGCACTATATTTTGGAATGGAGG 60.320 45.833 0.30 0.00 0.00 4.30
2542 2887 4.320494 GGCGCACTATATTTTGGAATGGAG 60.320 45.833 10.83 0.00 0.00 3.86
2543 2888 3.568007 GGCGCACTATATTTTGGAATGGA 59.432 43.478 10.83 0.00 0.00 3.41
2544 2889 3.569701 AGGCGCACTATATTTTGGAATGG 59.430 43.478 10.83 0.00 0.00 3.16
2545 2890 4.539870 CAGGCGCACTATATTTTGGAATG 58.460 43.478 10.83 0.00 0.00 2.67
2546 2891 3.004734 GCAGGCGCACTATATTTTGGAAT 59.995 43.478 10.83 0.00 38.36 3.01
2547 2892 2.357637 GCAGGCGCACTATATTTTGGAA 59.642 45.455 10.83 0.00 38.36 3.53
2548 2893 1.946768 GCAGGCGCACTATATTTTGGA 59.053 47.619 10.83 0.00 38.36 3.53
2549 2894 1.675483 TGCAGGCGCACTATATTTTGG 59.325 47.619 10.83 0.00 45.36 3.28
2561 2906 3.793144 CTCGGAAAGTGCAGGCGC 61.793 66.667 0.00 0.00 39.24 6.53
2562 2907 3.121030 CCTCGGAAAGTGCAGGCG 61.121 66.667 0.00 0.00 0.00 5.52
2563 2908 2.032681 ACCTCGGAAAGTGCAGGC 59.967 61.111 0.00 0.00 0.00 4.85
2564 2909 1.376037 GGACCTCGGAAAGTGCAGG 60.376 63.158 0.00 0.00 0.00 4.85
2565 2910 0.250295 TTGGACCTCGGAAAGTGCAG 60.250 55.000 0.00 0.00 35.66 4.41
2566 2911 0.534203 GTTGGACCTCGGAAAGTGCA 60.534 55.000 0.00 0.00 32.02 4.57
2567 2912 0.250338 AGTTGGACCTCGGAAAGTGC 60.250 55.000 0.00 0.00 0.00 4.40
2568 2913 2.256117 AAGTTGGACCTCGGAAAGTG 57.744 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.