Multiple sequence alignment - TraesCS3B01G061500

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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 TraesCS3B01G061500 chr3B 100.000 2453 0 0 1 2453 33335167 33332715 0.000000e+00 4530.0
1 TraesCS3B01G061500 chr3B 82.343 572 62 22 915 1455 33299187 33298624 6.180000e-126 460.0
2 TraesCS3B01G061500 chr3B 88.750 80 7 2 1373 1451 33340180 33340102 2.010000e-16 97.1
3 TraesCS3B01G061500 chr2A 95.530 962 41 1 1453 2414 714786990 714787949 0.000000e+00 1537.0
4 TraesCS3B01G061500 chr2A 78.502 307 42 16 1477 1768 17222639 17222342 1.940000e-41 180.0
5 TraesCS3B01G061500 chr1B 95.426 962 42 1 1453 2414 38594763 38595722 0.000000e+00 1531.0
6 TraesCS3B01G061500 chr1B 81.818 539 64 19 382 910 457010850 457010336 2.920000e-114 422.0
7 TraesCS3B01G061500 chr6B 94.628 968 41 4 1457 2416 713193780 713194744 0.000000e+00 1489.0
8 TraesCS3B01G061500 chr6B 96.387 858 31 0 1455 2312 142593123 142592266 0.000000e+00 1413.0
9 TraesCS3B01G061500 chr6B 96.364 550 20 0 1763 2312 142590127 142589578 0.000000e+00 905.0
10 TraesCS3B01G061500 chr6B 96.364 550 20 0 1763 2312 142591471 142590922 0.000000e+00 905.0
11 TraesCS3B01G061500 chr6B 83.798 932 116 20 3 910 331038424 331037504 0.000000e+00 852.0
12 TraesCS3B01G061500 chr5B 93.996 966 56 1 1450 2415 543744120 543745083 0.000000e+00 1461.0
13 TraesCS3B01G061500 chr5B 94.643 168 9 0 1488 1655 6217932 6218099 6.730000e-66 261.0
14 TraesCS3B01G061500 chr2B 86.557 915 86 18 3 912 250272977 250273859 0.000000e+00 974.0
15 TraesCS3B01G061500 chr2B 87.015 747 87 5 10 749 695779423 695780166 0.000000e+00 833.0
16 TraesCS3B01G061500 chr2B 87.183 671 80 3 3 670 26327292 26327959 0.000000e+00 758.0
17 TraesCS3B01G061500 chr2B 85.174 661 82 8 3 654 190056879 190057532 0.000000e+00 664.0
18 TraesCS3B01G061500 chr2B 82.488 651 84 20 271 911 742120147 742120777 5.970000e-151 544.0
19 TraesCS3B01G061500 chr4A 85.590 916 107 13 3 900 690667391 690668299 0.000000e+00 937.0
20 TraesCS3B01G061500 chr4A 93.909 591 25 4 1454 2036 644685199 644684612 0.000000e+00 881.0
21 TraesCS3B01G061500 chr4A 93.909 591 25 4 1454 2036 644733633 644733046 0.000000e+00 881.0
22 TraesCS3B01G061500 chr4A 91.055 559 30 7 1858 2416 712212728 712213266 0.000000e+00 737.0
23 TraesCS3B01G061500 chr4A 95.377 411 17 1 1455 1865 712210939 712211347 0.000000e+00 652.0
24 TraesCS3B01G061500 chr2D 87.500 784 77 9 1 779 14633662 14634429 0.000000e+00 885.0
25 TraesCS3B01G061500 chr2D 81.818 121 20 2 1299 1418 310268138 310268019 1.550000e-17 100.0
26 TraesCS3B01G061500 chr4B 83.804 920 131 13 3 912 619351211 619350300 0.000000e+00 857.0
27 TraesCS3B01G061500 chr4B 87.333 600 66 3 1821 2411 5924337 5923739 0.000000e+00 678.0
28 TraesCS3B01G061500 chr7B 83.772 912 106 21 3 905 240330210 240329332 0.000000e+00 826.0
29 TraesCS3B01G061500 chr7B 82.837 839 114 21 21 848 628724053 628724872 0.000000e+00 725.0
30 TraesCS3B01G061500 chrUn 80.586 922 144 18 2 908 154951584 154950683 0.000000e+00 678.0
31 TraesCS3B01G061500 chrUn 80.586 922 144 18 2 908 155035641 155034740 0.000000e+00 678.0
32 TraesCS3B01G061500 chr3D 84.355 473 57 8 997 1453 20708381 20707910 4.810000e-122 448.0
33 TraesCS3B01G061500 chr3A 82.696 497 60 13 984 1455 28231418 28230923 3.770000e-113 418.0
34 TraesCS3B01G061500 chr3A 80.416 577 73 22 908 1447 28391420 28390847 1.060000e-108 403.0
35 TraesCS3B01G061500 chr3A 81.275 502 60 15 984 1453 28322792 28322293 2.300000e-100 375.0
36 TraesCS3B01G061500 chr3A 85.714 161 20 1 1298 1455 28371220 28371060 1.510000e-37 167.0
37 TraesCS3B01G061500 chr3A 78.788 231 44 5 1217 1446 28423744 28423518 1.520000e-32 150.0


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 TraesCS3B01G061500 chr3B 33332715 33335167 2452 True 4530.000000 4530 100.000000 1 2453 1 chr3B.!!$R2 2452
1 TraesCS3B01G061500 chr3B 33298624 33299187 563 True 460.000000 460 82.343000 915 1455 1 chr3B.!!$R1 540
2 TraesCS3B01G061500 chr2A 714786990 714787949 959 False 1537.000000 1537 95.530000 1453 2414 1 chr2A.!!$F1 961
3 TraesCS3B01G061500 chr1B 38594763 38595722 959 False 1531.000000 1531 95.426000 1453 2414 1 chr1B.!!$F1 961
4 TraesCS3B01G061500 chr1B 457010336 457010850 514 True 422.000000 422 81.818000 382 910 1 chr1B.!!$R1 528
5 TraesCS3B01G061500 chr6B 713193780 713194744 964 False 1489.000000 1489 94.628000 1457 2416 1 chr6B.!!$F1 959
6 TraesCS3B01G061500 chr6B 142589578 142593123 3545 True 1074.333333 1413 96.371667 1455 2312 3 chr6B.!!$R2 857
7 TraesCS3B01G061500 chr6B 331037504 331038424 920 True 852.000000 852 83.798000 3 910 1 chr6B.!!$R1 907
8 TraesCS3B01G061500 chr5B 543744120 543745083 963 False 1461.000000 1461 93.996000 1450 2415 1 chr5B.!!$F2 965
9 TraesCS3B01G061500 chr2B 250272977 250273859 882 False 974.000000 974 86.557000 3 912 1 chr2B.!!$F3 909
10 TraesCS3B01G061500 chr2B 695779423 695780166 743 False 833.000000 833 87.015000 10 749 1 chr2B.!!$F4 739
11 TraesCS3B01G061500 chr2B 26327292 26327959 667 False 758.000000 758 87.183000 3 670 1 chr2B.!!$F1 667
12 TraesCS3B01G061500 chr2B 190056879 190057532 653 False 664.000000 664 85.174000 3 654 1 chr2B.!!$F2 651
13 TraesCS3B01G061500 chr2B 742120147 742120777 630 False 544.000000 544 82.488000 271 911 1 chr2B.!!$F5 640
14 TraesCS3B01G061500 chr4A 690667391 690668299 908 False 937.000000 937 85.590000 3 900 1 chr4A.!!$F1 897
15 TraesCS3B01G061500 chr4A 644684612 644685199 587 True 881.000000 881 93.909000 1454 2036 1 chr4A.!!$R1 582
16 TraesCS3B01G061500 chr4A 644733046 644733633 587 True 881.000000 881 93.909000 1454 2036 1 chr4A.!!$R2 582
17 TraesCS3B01G061500 chr4A 712210939 712213266 2327 False 694.500000 737 93.216000 1455 2416 2 chr4A.!!$F2 961
18 TraesCS3B01G061500 chr2D 14633662 14634429 767 False 885.000000 885 87.500000 1 779 1 chr2D.!!$F1 778
19 TraesCS3B01G061500 chr4B 619350300 619351211 911 True 857.000000 857 83.804000 3 912 1 chr4B.!!$R2 909
20 TraesCS3B01G061500 chr4B 5923739 5924337 598 True 678.000000 678 87.333000 1821 2411 1 chr4B.!!$R1 590
21 TraesCS3B01G061500 chr7B 240329332 240330210 878 True 826.000000 826 83.772000 3 905 1 chr7B.!!$R1 902
22 TraesCS3B01G061500 chr7B 628724053 628724872 819 False 725.000000 725 82.837000 21 848 1 chr7B.!!$F1 827
23 TraesCS3B01G061500 chrUn 154950683 154951584 901 True 678.000000 678 80.586000 2 908 1 chrUn.!!$R1 906
24 TraesCS3B01G061500 chrUn 155034740 155035641 901 True 678.000000 678 80.586000 2 908 1 chrUn.!!$R2 906
25 TraesCS3B01G061500 chr3A 28390847 28391420 573 True 403.000000 403 80.416000 908 1447 1 chr3A.!!$R4 539

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
205 206 0.318360 CCACAACGTCTACTCGCACA 60.318 55.0 0.0 0.0 0.00 4.57 F
802 874 0.368907 CGCGCACGCTGTATTTTACT 59.631 50.0 13.7 0.0 39.32 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1113 1210 0.251916 TGTAGCCATTCCCGTTCCTG 59.748 55.0 0.0 0.0 0.0 3.86 R
2141 5380 0.800239 TCCCCTTCCTTCCTCTCCTT 59.200 55.0 0.0 0.0 0.0 3.36 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
19 20 4.309950 GCCGCCGGGGATTATCGT 62.310 66.667 21.95 0.00 38.47 3.73
92 93 3.822192 CGGCGATGTCCACCTCGA 61.822 66.667 0.00 0.00 36.35 4.04
141 142 4.000557 GCCCGCGCGTATGACATG 62.001 66.667 29.95 10.39 0.00 3.21
190 191 1.291184 CGCGCAGATGAACTTCCACA 61.291 55.000 8.75 0.00 0.00 4.17
199 200 4.281182 AGATGAACTTCCACAACGTCTACT 59.719 41.667 0.00 0.00 0.00 2.57
205 206 0.318360 CCACAACGTCTACTCGCACA 60.318 55.000 0.00 0.00 0.00 4.57
258 259 2.271800 CTGATAACAGAACAGGACCGC 58.728 52.381 0.00 0.00 46.03 5.68
294 295 0.694771 TGCAGTGCCTCCTTCTCATT 59.305 50.000 13.72 0.00 0.00 2.57
495 498 0.963225 TTCGGGACAGACGATGAACA 59.037 50.000 0.00 0.00 40.38 3.18
507 510 3.273434 ACGATGAACATTGGGATGACAG 58.727 45.455 6.93 0.00 36.73 3.51
511 514 4.097551 TGAACATTGGGATGACAGTTGA 57.902 40.909 0.00 0.00 36.73 3.18
513 516 3.507162 ACATTGGGATGACAGTTGACA 57.493 42.857 0.00 0.00 36.73 3.58
534 537 1.136305 CGATACCTCGGACAACACCAT 59.864 52.381 0.00 0.00 41.27 3.55
562 580 5.395879 GGATGATGATGATGATGAGGAGGAG 60.396 48.000 0.00 0.00 0.00 3.69
580 598 1.819903 GAGGACTGCGAGTAGGTTCTT 59.180 52.381 0.00 0.00 0.00 2.52
581 599 3.015327 GAGGACTGCGAGTAGGTTCTTA 58.985 50.000 0.00 0.00 0.00 2.10
639 664 7.916914 TTTTTATCTAGTTGCACCCTACTTC 57.083 36.000 0.00 0.00 0.00 3.01
788 857 2.266376 CTACTGGAGCTACACGCGCA 62.266 60.000 5.73 0.00 45.59 6.09
789 858 2.537792 TACTGGAGCTACACGCGCAC 62.538 60.000 5.73 0.00 45.59 5.34
802 874 0.368907 CGCGCACGCTGTATTTTACT 59.631 50.000 13.70 0.00 39.32 2.24
805 877 2.346244 GCGCACGCTGTATTTTACTACA 59.654 45.455 7.96 0.00 38.26 2.74
807 879 3.611113 CGCACGCTGTATTTTACTACAGT 59.389 43.478 11.62 0.00 46.75 3.55
833 905 4.063967 CCAGCACTGACCGCCGTA 62.064 66.667 0.00 0.00 0.00 4.02
866 938 2.050077 GGTGCGCTGAAAACTGGC 60.050 61.111 9.73 0.00 0.00 4.85
883 955 2.942879 CTTTTAGTGTGCCGCGCA 59.057 55.556 8.75 1.51 35.60 6.09
927 999 4.363990 AGCGTCCTCGGTGCACTG 62.364 66.667 20.12 20.12 46.08 3.66
936 1012 2.048023 CGGTGCACTGCCAATCCAT 61.048 57.895 17.98 0.00 0.00 3.41
941 1017 2.816087 GTGCACTGCCAATCCATATAGG 59.184 50.000 10.32 0.00 39.47 2.57
954 1030 7.319646 CAATCCATATAGGCTTGTCTAGTCTC 58.680 42.308 0.00 0.00 38.40 3.36
955 1031 6.207509 TCCATATAGGCTTGTCTAGTCTCT 57.792 41.667 0.00 0.00 38.40 3.10
973 1055 5.047377 AGTCTCTTGCCAACAAAGAAAACAA 60.047 36.000 0.00 0.00 34.74 2.83
974 1056 5.289434 GTCTCTTGCCAACAAAGAAAACAAG 59.711 40.000 0.00 0.00 34.74 3.16
975 1057 5.184864 TCTCTTGCCAACAAAGAAAACAAGA 59.815 36.000 0.00 0.00 39.59 3.02
987 1069 4.390264 AGAAAACAAGAAGAGGTAGCCAC 58.610 43.478 0.00 0.00 0.00 5.01
1025 1116 2.095053 GCTTCGAATTCAGCTCCTGTTC 59.905 50.000 9.86 0.00 32.87 3.18
1030 1121 1.841302 ATTCAGCTCCTGTTCCGGCA 61.841 55.000 0.00 0.00 32.61 5.69
1050 1141 1.687123 AGCCGCATAAAGGACGACTAT 59.313 47.619 0.00 0.00 0.00 2.12
1138 1235 1.377987 GGGAATGGCTACAACGGCA 60.378 57.895 0.00 0.00 43.95 5.69
1139 1236 1.654023 GGGAATGGCTACAACGGCAC 61.654 60.000 0.00 0.00 42.55 5.01
1140 1237 1.654023 GGAATGGCTACAACGGCACC 61.654 60.000 0.00 0.00 42.55 5.01
1141 1238 0.958382 GAATGGCTACAACGGCACCA 60.958 55.000 0.00 0.00 42.55 4.17
1161 1258 4.681978 GGACACAAGCCGGCGACT 62.682 66.667 23.20 6.88 0.00 4.18
1162 1259 2.260434 GACACAAGCCGGCGACTA 59.740 61.111 23.20 0.00 0.00 2.59
1163 1260 1.373748 GACACAAGCCGGCGACTAA 60.374 57.895 23.20 0.00 0.00 2.24
1185 1282 4.643387 GACCACCAGCCGGCTGTT 62.643 66.667 44.92 35.63 42.15 3.16
1188 1285 2.360350 CACCAGCCGGCTGTTGAT 60.360 61.111 44.92 28.95 38.51 2.57
1197 1294 2.825836 GCTGTTGATGAGGCGGGG 60.826 66.667 0.00 0.00 0.00 5.73
1215 1312 3.443045 CGCAAGGCCCACCATGAC 61.443 66.667 0.00 0.00 36.75 3.06
1264 1373 1.222387 GGTGGCCACGGCTATTACA 59.778 57.895 29.08 0.00 41.60 2.41
1265 1374 0.179029 GGTGGCCACGGCTATTACAT 60.179 55.000 29.08 0.00 41.60 2.29
1284 1393 2.740826 GCCTACGCGCCTGACAAA 60.741 61.111 5.73 0.00 0.00 2.83
1329 1438 2.904866 TGGCACAACAAGGTCGGC 60.905 61.111 0.00 0.00 31.92 5.54
1384 1496 1.134189 TCCATCAGGCTTCTGCTGATG 60.134 52.381 17.96 17.96 44.60 3.07
1388 1500 4.386711 CATCAGGCTTCTGCTGATGATAA 58.613 43.478 19.40 0.00 45.99 1.75
1436 1548 3.056322 CACTACCCAACCACTACTACCAC 60.056 52.174 0.00 0.00 0.00 4.16
1442 1554 1.461559 ACCACTACTACCACTCTCGC 58.538 55.000 0.00 0.00 0.00 5.03
1469 1581 4.699522 GGTCAGGGTGGACACGGC 62.700 72.222 0.00 0.00 39.59 5.68
1712 1824 3.129462 TGAAGTTGAGGAGCGATACTGAG 59.871 47.826 0.00 0.00 0.00 3.35
1796 1916 0.032267 TGACGAACCGTGTGCATGTA 59.968 50.000 0.00 0.00 41.37 2.29
1832 1952 4.444720 CGTCTTGACTCAGTTTCAGGTTAC 59.555 45.833 0.00 0.00 0.00 2.50
1953 5186 3.288092 ACTCGTTCCTGGCTTTTCTTTT 58.712 40.909 0.00 0.00 0.00 2.27
1956 5189 3.115554 CGTTCCTGGCTTTTCTTTTGTG 58.884 45.455 0.00 0.00 0.00 3.33
2137 5376 1.595382 GCAAGAGGATACGGCGCAT 60.595 57.895 10.83 0.00 46.39 4.73
2141 5380 2.842462 AGGATACGGCGCATGGGA 60.842 61.111 14.90 0.00 46.39 4.37
2180 5419 3.721868 GGAACCTCGGGGACATGA 58.278 61.111 9.33 0.00 36.25 3.07
2189 5429 0.253044 CGGGGACATGATGGTTCACT 59.747 55.000 0.00 0.00 33.85 3.41
2258 5498 0.249573 GTGTTTTCTCGGTCCGACCA 60.250 55.000 17.87 0.00 38.47 4.02
2299 5539 0.974383 ACCGGACCGACATTTTCTCT 59.026 50.000 17.49 0.00 0.00 3.10
2322 5562 0.751277 CCAATATTGCAGCCCGGACA 60.751 55.000 10.11 0.00 0.00 4.02
2326 5566 1.549243 TATTGCAGCCCGGACAGACA 61.549 55.000 0.73 0.00 0.00 3.41
2416 5656 1.592400 CGTTCCGTCCAGCCTGAGTA 61.592 60.000 0.00 0.00 0.00 2.59
2417 5657 0.108756 GTTCCGTCCAGCCTGAGTAC 60.109 60.000 0.00 0.00 0.00 2.73
2418 5658 0.251653 TTCCGTCCAGCCTGAGTACT 60.252 55.000 0.00 0.00 0.00 2.73
2419 5659 0.622136 TCCGTCCAGCCTGAGTACTA 59.378 55.000 0.00 0.00 0.00 1.82
2420 5660 1.025812 CCGTCCAGCCTGAGTACTAG 58.974 60.000 0.00 0.00 0.00 2.57
2421 5661 1.025812 CGTCCAGCCTGAGTACTAGG 58.974 60.000 0.00 4.75 38.39 3.02
2422 5662 1.682394 CGTCCAGCCTGAGTACTAGGT 60.682 57.143 15.52 3.85 37.64 3.08
2423 5663 2.421107 CGTCCAGCCTGAGTACTAGGTA 60.421 54.545 15.52 0.00 37.64 3.08
2424 5664 2.950975 GTCCAGCCTGAGTACTAGGTAC 59.049 54.545 15.52 0.12 39.10 3.34
2441 5681 4.739587 GGTACTAAGGTAGCTCTGCTTT 57.260 45.455 0.00 0.00 41.57 3.51
2442 5682 5.087391 GGTACTAAGGTAGCTCTGCTTTT 57.913 43.478 0.00 0.00 41.57 2.27
2443 5683 5.110598 GGTACTAAGGTAGCTCTGCTTTTC 58.889 45.833 0.00 0.00 41.57 2.29
2444 5684 5.105269 GGTACTAAGGTAGCTCTGCTTTTCT 60.105 44.000 0.00 0.00 41.57 2.52
2445 5685 6.096564 GGTACTAAGGTAGCTCTGCTTTTCTA 59.903 42.308 0.00 0.00 41.57 2.10
2446 5686 5.968254 ACTAAGGTAGCTCTGCTTTTCTAC 58.032 41.667 0.00 0.00 40.44 2.59
2447 5687 5.717654 ACTAAGGTAGCTCTGCTTTTCTACT 59.282 40.000 0.00 0.00 40.44 2.57
2448 5688 4.729227 AGGTAGCTCTGCTTTTCTACTC 57.271 45.455 0.00 0.00 40.44 2.59
2449 5689 4.349365 AGGTAGCTCTGCTTTTCTACTCT 58.651 43.478 0.00 0.00 40.44 3.24
2450 5690 4.159506 AGGTAGCTCTGCTTTTCTACTCTG 59.840 45.833 0.00 0.00 40.44 3.35
2451 5691 4.081917 GGTAGCTCTGCTTTTCTACTCTGT 60.082 45.833 0.00 0.00 40.44 3.41
2452 5692 4.615588 AGCTCTGCTTTTCTACTCTGTT 57.384 40.909 0.00 0.00 33.89 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.830765 GCGGATGCCACGGTAGCA 62.831 66.667 3.25 3.25 45.94 3.49
81 82 2.675423 CCGAGGTCGAGGTGGACA 60.675 66.667 0.00 0.00 43.02 4.02
92 93 1.952635 GTTTCGAACGTGCCGAGGT 60.953 57.895 12.07 0.00 37.35 3.85
190 191 0.031585 TGCTTGTGCGAGTAGACGTT 59.968 50.000 0.00 0.00 43.34 3.99
225 226 0.106868 TTATCAGACGAGGCGGAGGA 60.107 55.000 0.00 0.00 0.00 3.71
249 250 4.988716 TGGTCCTCGCGGTCCTGT 62.989 66.667 6.13 0.00 39.04 4.00
280 281 1.078214 CGGCAATGAGAAGGAGGCA 60.078 57.895 0.00 0.00 0.00 4.75
284 285 0.826715 CTCCTCGGCAATGAGAAGGA 59.173 55.000 1.80 0.00 38.28 3.36
288 289 1.667154 CGTCCTCCTCGGCAATGAGA 61.667 60.000 1.80 0.00 38.28 3.27
337 338 2.188829 CGGCGATGTACTCCGGGTA 61.189 63.158 0.00 0.00 42.35 3.69
346 347 2.103538 GTTCTCGGCGGCGATGTA 59.896 61.111 34.71 19.77 0.00 2.29
495 498 2.038426 TCGTGTCAACTGTCATCCCAAT 59.962 45.455 0.00 0.00 0.00 3.16
534 537 4.159879 CCTCATCATCATCATCATCCTCGA 59.840 45.833 0.00 0.00 0.00 4.04
562 580 4.113354 CAATAAGAACCTACTCGCAGTCC 58.887 47.826 0.00 0.00 0.00 3.85
580 598 8.685427 TGCAACTAGATAAACTACGGTACAATA 58.315 33.333 0.00 0.00 0.00 1.90
581 599 7.490402 GTGCAACTAGATAAACTACGGTACAAT 59.510 37.037 0.00 0.00 0.00 2.71
638 663 9.379791 ACGATACATCACATAGATAGATAACGA 57.620 33.333 0.00 0.00 34.43 3.85
639 664 9.989869 AACGATACATCACATAGATAGATAACG 57.010 33.333 0.00 0.00 34.43 3.18
703 766 7.406031 ACTACGGTGAATATACATGGATAGG 57.594 40.000 3.54 0.00 0.00 2.57
718 781 1.991121 AACACTCTGGACTACGGTGA 58.009 50.000 0.00 0.00 0.00 4.02
821 893 1.301165 GTTTGGTACGGCGGTCAGT 60.301 57.895 13.24 0.00 0.00 3.41
825 897 2.031465 CTGGTTTGGTACGGCGGT 59.969 61.111 13.24 1.39 0.00 5.68
832 904 1.301623 CCCATCGCCTGGTTTGGTA 59.698 57.895 9.72 0.00 44.30 3.25
833 905 2.035626 CCCATCGCCTGGTTTGGT 59.964 61.111 9.72 0.00 44.30 3.67
851 923 0.459489 AAAAGCCAGTTTTCAGCGCA 59.541 45.000 11.47 0.00 32.54 6.09
866 938 0.109781 AATGCGCGGCACACTAAAAG 60.110 50.000 8.83 0.00 43.04 2.27
883 955 2.215451 ATCTCCAACAGCCGGCCAAT 62.215 55.000 26.15 5.69 0.00 3.16
888 960 1.817099 GAGCATCTCCAACAGCCGG 60.817 63.158 0.00 0.00 0.00 6.13
913 985 3.825160 TTGGCAGTGCACCGAGGAC 62.825 63.158 18.61 3.58 39.14 3.85
936 1012 4.585162 GGCAAGAGACTAGACAAGCCTATA 59.415 45.833 0.00 0.00 37.89 1.31
941 1017 2.739379 GTTGGCAAGAGACTAGACAAGC 59.261 50.000 0.00 0.00 0.00 4.01
954 1030 5.868801 TCTTCTTGTTTTCTTTGTTGGCAAG 59.131 36.000 0.00 0.00 35.82 4.01
955 1031 5.788450 TCTTCTTGTTTTCTTTGTTGGCAA 58.212 33.333 0.00 0.00 0.00 4.52
973 1055 1.203187 TGGTGAGTGGCTACCTCTTCT 60.203 52.381 0.00 0.00 37.84 2.85
974 1056 1.205893 CTGGTGAGTGGCTACCTCTTC 59.794 57.143 0.00 0.00 37.84 2.87
975 1057 1.270907 CTGGTGAGTGGCTACCTCTT 58.729 55.000 0.00 0.00 37.84 2.85
1011 1102 1.078143 GCCGGAACAGGAGCTGAAT 60.078 57.895 5.05 0.00 35.18 2.57
1030 1121 1.108776 TAGTCGTCCTTTATGCGGCT 58.891 50.000 0.00 0.00 43.25 5.52
1033 1124 1.792949 GCCATAGTCGTCCTTTATGCG 59.207 52.381 0.00 0.00 0.00 4.73
1091 1182 4.003788 CCCCTGTGCGTCTTCGGT 62.004 66.667 0.00 0.00 37.56 4.69
1095 1186 4.003788 CGGTCCCCTGTGCGTCTT 62.004 66.667 0.00 0.00 0.00 3.01
1103 1200 4.760047 CGTTCCTGCGGTCCCCTG 62.760 72.222 0.00 0.00 0.00 4.45
1113 1210 0.251916 TGTAGCCATTCCCGTTCCTG 59.748 55.000 0.00 0.00 0.00 3.86
1114 1211 0.988832 TTGTAGCCATTCCCGTTCCT 59.011 50.000 0.00 0.00 0.00 3.36
1121 1218 1.654023 GGTGCCGTTGTAGCCATTCC 61.654 60.000 0.00 0.00 0.00 3.01
1122 1219 0.958382 TGGTGCCGTTGTAGCCATTC 60.958 55.000 0.00 0.00 0.00 2.67
1123 1220 1.074072 TGGTGCCGTTGTAGCCATT 59.926 52.632 0.00 0.00 0.00 3.16
1124 1221 1.674322 GTGGTGCCGTTGTAGCCAT 60.674 57.895 0.00 0.00 0.00 4.40
1125 1222 2.281208 GTGGTGCCGTTGTAGCCA 60.281 61.111 0.00 0.00 0.00 4.75
1126 1223 3.053896 GGTGGTGCCGTTGTAGCC 61.054 66.667 0.00 0.00 0.00 3.93
1138 1235 4.619227 CGGCTTGTGTCCGGTGGT 62.619 66.667 0.00 0.00 42.99 4.16
1145 1242 1.373748 TTAGTCGCCGGCTTGTGTC 60.374 57.895 26.68 6.53 0.00 3.67
1146 1243 1.666872 GTTAGTCGCCGGCTTGTGT 60.667 57.895 26.68 6.88 0.00 3.72
1159 1256 0.893447 GGCTGGTGGTCGTAGTTAGT 59.107 55.000 0.00 0.00 0.00 2.24
1161 1258 1.597797 CCGGCTGGTGGTCGTAGTTA 61.598 60.000 2.29 0.00 42.07 2.24
1162 1259 2.654877 CGGCTGGTGGTCGTAGTT 59.345 61.111 0.00 0.00 38.36 2.24
1163 1260 3.379445 CCGGCTGGTGGTCGTAGT 61.379 66.667 2.29 0.00 42.07 2.73
1182 1279 4.776322 CGCCCCGCCTCATCAACA 62.776 66.667 0.00 0.00 0.00 3.33
1220 1317 3.423154 GGTGCTCCGCTTTCCACG 61.423 66.667 0.00 0.00 0.00 4.94
1222 1319 1.600636 CTTGGTGCTCCGCTTTCCA 60.601 57.895 0.00 0.00 36.30 3.53
1245 1354 1.222387 GTAATAGCCGTGGCCACCA 59.778 57.895 29.95 13.11 43.17 4.17
1278 1387 1.300620 CGTCTCGTGGGCTTTGTCA 60.301 57.895 0.00 0.00 0.00 3.58
1367 1476 4.505215 CCTTATCATCAGCAGAAGCCTGAT 60.505 45.833 0.00 0.00 43.02 2.90
1368 1477 3.181457 CCTTATCATCAGCAGAAGCCTGA 60.181 47.826 0.00 0.00 43.02 3.86
1375 1487 2.223900 CGTGCTCCTTATCATCAGCAGA 60.224 50.000 0.00 0.00 42.47 4.26
1378 1490 0.864455 GCGTGCTCCTTATCATCAGC 59.136 55.000 0.00 0.00 0.00 4.26
1384 1496 2.967615 GGCGGCGTGCTCCTTATC 60.968 66.667 9.37 0.00 45.43 1.75
1436 1548 2.356382 CTGACCTAGTACCTTGCGAGAG 59.644 54.545 1.22 0.00 0.00 3.20
1442 1554 1.831736 CCACCCTGACCTAGTACCTTG 59.168 57.143 0.00 0.00 0.00 3.61
1712 1824 4.152580 GTCGGTTTCAGAAGATTCAGTTCC 59.847 45.833 0.00 0.00 0.00 3.62
1832 1952 3.869065 TCCAACAACGGCCTAATCTAAG 58.131 45.455 0.00 0.00 0.00 2.18
1953 5186 4.460263 AGACATTACAACTGAAAGGCACA 58.540 39.130 0.00 0.00 39.30 4.57
1956 5189 5.452777 GTCAAGACATTACAACTGAAAGGC 58.547 41.667 0.00 0.00 39.30 4.35
2137 5376 1.555765 CCTTCCTTCCTCTCCTTCCCA 60.556 57.143 0.00 0.00 0.00 4.37
2141 5380 0.800239 TCCCCTTCCTTCCTCTCCTT 59.200 55.000 0.00 0.00 0.00 3.36
2180 5419 1.075482 CAGCCCCACAGTGAACCAT 59.925 57.895 0.62 0.00 0.00 3.55
2226 5466 1.711060 AAAACACAGTCACCGCCGTG 61.711 55.000 0.00 0.00 41.72 4.94
2258 5498 3.050275 GCTTTCACCGAGCCGCTT 61.050 61.111 0.00 0.00 34.06 4.68
2278 5518 0.974383 AGAAAATGTCGGTCCGGTCT 59.026 50.000 12.29 2.43 0.00 3.85
2299 5539 1.761667 GGGCTGCAATATTGGGCCA 60.762 57.895 23.67 0.00 44.04 5.36
2322 5562 2.490991 GACCGGTAGCAAAACTTGTCT 58.509 47.619 7.34 0.00 0.00 3.41
2326 5566 1.544759 CCAGGACCGGTAGCAAAACTT 60.545 52.381 7.34 0.00 0.00 2.66
2373 5613 2.046700 CTTTTGGGCCCGCTCGTA 60.047 61.111 19.37 0.00 0.00 3.43
2416 5656 4.166531 AGCAGAGCTACCTTAGTACCTAGT 59.833 45.833 0.00 0.00 36.99 2.57
2417 5657 4.721132 AGCAGAGCTACCTTAGTACCTAG 58.279 47.826 0.00 0.00 36.99 3.02
2418 5658 4.792513 AGCAGAGCTACCTTAGTACCTA 57.207 45.455 0.00 0.00 36.99 3.08
2419 5659 3.673543 AGCAGAGCTACCTTAGTACCT 57.326 47.619 0.00 0.00 36.99 3.08
2420 5660 4.739587 AAAGCAGAGCTACCTTAGTACC 57.260 45.455 0.00 0.00 38.25 3.34
2421 5661 5.968254 AGAAAAGCAGAGCTACCTTAGTAC 58.032 41.667 0.00 0.00 38.25 2.73
2422 5662 6.890814 AGTAGAAAAGCAGAGCTACCTTAGTA 59.109 38.462 0.00 0.00 38.25 1.82
2423 5663 5.717654 AGTAGAAAAGCAGAGCTACCTTAGT 59.282 40.000 0.00 0.00 38.25 2.24
2424 5664 6.096282 AGAGTAGAAAAGCAGAGCTACCTTAG 59.904 42.308 0.00 0.00 38.25 2.18
2425 5665 5.952947 AGAGTAGAAAAGCAGAGCTACCTTA 59.047 40.000 0.00 0.00 38.25 2.69
2426 5666 4.775253 AGAGTAGAAAAGCAGAGCTACCTT 59.225 41.667 0.00 0.00 38.25 3.50
2427 5667 4.159506 CAGAGTAGAAAAGCAGAGCTACCT 59.840 45.833 0.00 0.00 38.25 3.08
2428 5668 4.081917 ACAGAGTAGAAAAGCAGAGCTACC 60.082 45.833 0.00 0.00 38.25 3.18
2429 5669 5.066968 ACAGAGTAGAAAAGCAGAGCTAC 57.933 43.478 0.00 0.00 38.25 3.58
2430 5670 5.730296 AACAGAGTAGAAAAGCAGAGCTA 57.270 39.130 0.00 0.00 38.25 3.32
2431 5671 4.615588 AACAGAGTAGAAAAGCAGAGCT 57.384 40.909 0.00 0.00 42.56 4.09


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

AutoCloner maintained by Alex Coulton.