Multiple sequence alignment - TraesCS1A01G041900

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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 TraesCS1A01G041900 chr1A 100.000 3908 0 0 1 3908 22792257 22788350 0.000000e+00 7217.0
1 TraesCS1A01G041900 chr1A 90.956 1957 138 15 968 2914 13228981 13230908 0.000000e+00 2597.0
2 TraesCS1A01G041900 chr1A 92.092 1821 112 11 1101 2915 13009792 13007998 0.000000e+00 2536.0
3 TraesCS1A01G041900 chr1A 93.299 1552 85 9 1382 2926 13212769 13214308 0.000000e+00 2272.0
4 TraesCS1A01G041900 chr1A 92.267 375 22 3 942 1312 13212371 13212742 3.460000e-145 525.0
5 TraesCS1A01G041900 chr1A 98.233 283 5 0 3032 3314 22779237 22778955 2.710000e-136 496.0
6 TraesCS1A01G041900 chr1A 82.267 344 56 4 948 1291 13266775 13267113 3.820000e-75 292.0
7 TraesCS1A01G041900 chr1A 82.162 185 19 8 1378 1558 13006113 13005939 3.150000e-31 147.0
8 TraesCS1A01G041900 chr1A 93.651 63 2 2 1438 1498 13005892 13005830 4.160000e-15 93.5
9 TraesCS1A01G041900 chr1A 100.000 28 0 0 956 983 13212354 13212381 7.000000e-03 52.8
10 TraesCS1A01G041900 chr1D 91.937 2158 117 33 912 3033 10843719 10845855 0.000000e+00 2968.0
11 TraesCS1A01G041900 chr1D 91.273 2097 132 25 947 3033 10764355 10762300 0.000000e+00 2811.0
12 TraesCS1A01G041900 chr1D 93.687 1283 77 3 1654 2932 10775143 10773861 0.000000e+00 1917.0
13 TraesCS1A01G041900 chr1D 88.231 1453 136 19 1609 3033 10836395 10837840 0.000000e+00 1703.0
14 TraesCS1A01G041900 chr1D 92.308 52 3 1 2982 3033 10762318 10762268 5.420000e-09 73.1
15 TraesCS1A01G041900 chr1B 90.754 2055 136 26 912 2932 16225766 16223732 0.000000e+00 2693.0
16 TraesCS1A01G041900 chr1B 91.909 1409 107 6 1523 2926 39732724 39734130 0.000000e+00 1964.0
17 TraesCS1A01G041900 chr1B 89.769 1388 117 16 1609 2975 23775548 23776931 0.000000e+00 1753.0
18 TraesCS1A01G041900 chr1B 95.142 597 10 2 3312 3908 39295546 39294969 0.000000e+00 924.0
19 TraesCS1A01G041900 chr1B 88.006 617 38 16 888 1490 39806041 39806635 0.000000e+00 697.0
20 TraesCS1A01G041900 chr1B 92.541 362 21 2 942 1300 23597394 23597752 7.490000e-142 514.0
21 TraesCS1A01G041900 chr1B 92.541 362 21 2 942 1300 23896170 23896528 7.490000e-142 514.0
22 TraesCS1A01G041900 chr1B 85.867 467 57 8 2449 2910 39738826 39739288 4.540000e-134 488.0
23 TraesCS1A01G041900 chr6A 99.452 730 4 0 1 730 617222141 617222870 0.000000e+00 1327.0
24 TraesCS1A01G041900 chr6A 98.903 729 8 0 1 729 616132024 616131296 0.000000e+00 1303.0
25 TraesCS1A01G041900 chr6A 98.233 283 5 0 3032 3314 573851631 573851913 2.710000e-136 496.0
26 TraesCS1A01G041900 chr2B 99.040 729 7 0 1 729 776223690 776222962 0.000000e+00 1308.0
27 TraesCS1A01G041900 chr2B 88.047 594 43 18 3317 3908 747755210 747755777 0.000000e+00 678.0
28 TraesCS1A01G041900 chr2B 84.479 509 55 13 3308 3800 304258665 304258165 7.590000e-132 481.0
29 TraesCS1A01G041900 chr4A 98.774 734 9 0 1 734 726681584 726682317 0.000000e+00 1306.0
30 TraesCS1A01G041900 chr4A 98.641 736 9 1 1 736 36563641 36562907 0.000000e+00 1303.0
31 TraesCS1A01G041900 chr4A 90.050 603 47 11 3308 3908 198008321 198007730 0.000000e+00 769.0
32 TraesCS1A01G041900 chr4A 98.239 284 5 0 3031 3314 440929248 440928965 7.540000e-137 497.0
33 TraesCS1A01G041900 chr4A 98.233 283 5 0 3032 3314 440924007 440923725 2.710000e-136 496.0
34 TraesCS1A01G041900 chr3B 98.641 736 10 0 1 736 30404857 30405592 0.000000e+00 1304.0
35 TraesCS1A01G041900 chr3B 86.218 595 36 10 3321 3908 818230385 818230940 1.550000e-168 603.0
36 TraesCS1A01G041900 chr3B 85.835 593 46 18 3321 3908 818194637 818195196 2.600000e-166 595.0
37 TraesCS1A01G041900 chr7A 98.641 736 9 1 1 735 39016096 39015361 0.000000e+00 1303.0
38 TraesCS1A01G041900 chr6B 98.770 732 9 0 1 732 585916315 585915584 0.000000e+00 1303.0
39 TraesCS1A01G041900 chr5B 98.903 729 8 0 1 729 641128051 641128779 0.000000e+00 1303.0
40 TraesCS1A01G041900 chr5B 98.233 283 5 0 3032 3314 383547717 383547999 2.710000e-136 496.0
41 TraesCS1A01G041900 chr6D 87.479 591 54 13 3338 3908 98754554 98753964 0.000000e+00 664.0
42 TraesCS1A01G041900 chr2A 82.698 630 62 30 3311 3908 103208800 103209414 2.080000e-142 516.0
43 TraesCS1A01G041900 chr2A 83.252 615 47 28 3320 3908 240761844 240762428 7.490000e-142 514.0
44 TraesCS1A01G041900 chr4B 98.239 284 5 0 3031 3314 127095833 127096116 7.540000e-137 497.0
45 TraesCS1A01G041900 chr4B 98.233 283 5 0 3032 3314 127101077 127101359 2.710000e-136 496.0
46 TraesCS1A01G041900 chr7B 98.233 283 5 0 3032 3314 340646831 340646549 2.710000e-136 496.0
47 TraesCS1A01G041900 chr7B 97.909 287 5 1 3028 3314 340650958 340650673 2.710000e-136 496.0
48 TraesCS1A01G041900 chr3A 84.449 508 56 13 3308 3800 735327413 735326914 2.730000e-131 479.0
49 TraesCS1A01G041900 chr3A 80.449 624 67 34 3321 3908 459075655 459075051 3.610000e-115 425.0
50 TraesCS1A01G041900 chr2D 86.780 295 19 11 3630 3908 639858496 639858206 1.050000e-80 311.0


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 TraesCS1A01G041900 chr1A 22788350 22792257 3907 True 7217.000000 7217 100.000000 1 3908 1 chr1A.!!$R2 3907
1 TraesCS1A01G041900 chr1A 13228981 13230908 1927 False 2597.000000 2597 90.956000 968 2914 1 chr1A.!!$F1 1946
2 TraesCS1A01G041900 chr1A 13212354 13214308 1954 False 949.933333 2272 95.188667 942 2926 3 chr1A.!!$F3 1984
3 TraesCS1A01G041900 chr1A 13005830 13009792 3962 True 925.500000 2536 89.301667 1101 2915 3 chr1A.!!$R3 1814
4 TraesCS1A01G041900 chr1D 10843719 10845855 2136 False 2968.000000 2968 91.937000 912 3033 1 chr1D.!!$F2 2121
5 TraesCS1A01G041900 chr1D 10773861 10775143 1282 True 1917.000000 1917 93.687000 1654 2932 1 chr1D.!!$R1 1278
6 TraesCS1A01G041900 chr1D 10836395 10837840 1445 False 1703.000000 1703 88.231000 1609 3033 1 chr1D.!!$F1 1424
7 TraesCS1A01G041900 chr1D 10762268 10764355 2087 True 1442.050000 2811 91.790500 947 3033 2 chr1D.!!$R2 2086
8 TraesCS1A01G041900 chr1B 16223732 16225766 2034 True 2693.000000 2693 90.754000 912 2932 1 chr1B.!!$R1 2020
9 TraesCS1A01G041900 chr1B 39732724 39734130 1406 False 1964.000000 1964 91.909000 1523 2926 1 chr1B.!!$F4 1403
10 TraesCS1A01G041900 chr1B 23775548 23776931 1383 False 1753.000000 1753 89.769000 1609 2975 1 chr1B.!!$F2 1366
11 TraesCS1A01G041900 chr1B 39294969 39295546 577 True 924.000000 924 95.142000 3312 3908 1 chr1B.!!$R2 596
12 TraesCS1A01G041900 chr1B 39806041 39806635 594 False 697.000000 697 88.006000 888 1490 1 chr1B.!!$F6 602
13 TraesCS1A01G041900 chr6A 617222141 617222870 729 False 1327.000000 1327 99.452000 1 730 1 chr6A.!!$F2 729
14 TraesCS1A01G041900 chr6A 616131296 616132024 728 True 1303.000000 1303 98.903000 1 729 1 chr6A.!!$R1 728
15 TraesCS1A01G041900 chr2B 776222962 776223690 728 True 1308.000000 1308 99.040000 1 729 1 chr2B.!!$R2 728
16 TraesCS1A01G041900 chr2B 747755210 747755777 567 False 678.000000 678 88.047000 3317 3908 1 chr2B.!!$F1 591
17 TraesCS1A01G041900 chr2B 304258165 304258665 500 True 481.000000 481 84.479000 3308 3800 1 chr2B.!!$R1 492
18 TraesCS1A01G041900 chr4A 726681584 726682317 733 False 1306.000000 1306 98.774000 1 734 1 chr4A.!!$F1 733
19 TraesCS1A01G041900 chr4A 36562907 36563641 734 True 1303.000000 1303 98.641000 1 736 1 chr4A.!!$R1 735
20 TraesCS1A01G041900 chr4A 198007730 198008321 591 True 769.000000 769 90.050000 3308 3908 1 chr4A.!!$R2 600
21 TraesCS1A01G041900 chr3B 30404857 30405592 735 False 1304.000000 1304 98.641000 1 736 1 chr3B.!!$F1 735
22 TraesCS1A01G041900 chr3B 818230385 818230940 555 False 603.000000 603 86.218000 3321 3908 1 chr3B.!!$F3 587
23 TraesCS1A01G041900 chr3B 818194637 818195196 559 False 595.000000 595 85.835000 3321 3908 1 chr3B.!!$F2 587
24 TraesCS1A01G041900 chr7A 39015361 39016096 735 True 1303.000000 1303 98.641000 1 735 1 chr7A.!!$R1 734
25 TraesCS1A01G041900 chr6B 585915584 585916315 731 True 1303.000000 1303 98.770000 1 732 1 chr6B.!!$R1 731
26 TraesCS1A01G041900 chr5B 641128051 641128779 728 False 1303.000000 1303 98.903000 1 729 1 chr5B.!!$F2 728
27 TraesCS1A01G041900 chr6D 98753964 98754554 590 True 664.000000 664 87.479000 3338 3908 1 chr6D.!!$R1 570
28 TraesCS1A01G041900 chr2A 103208800 103209414 614 False 516.000000 516 82.698000 3311 3908 1 chr2A.!!$F1 597
29 TraesCS1A01G041900 chr2A 240761844 240762428 584 False 514.000000 514 83.252000 3320 3908 1 chr2A.!!$F2 588
30 TraesCS1A01G041900 chr7B 340646549 340650958 4409 True 496.000000 496 98.071000 3028 3314 2 chr7B.!!$R1 286
31 TraesCS1A01G041900 chr3A 459075051 459075655 604 True 425.000000 425 80.449000 3321 3908 1 chr3A.!!$R1 587

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
877 878 2.243602 TCGCTAACGGACACCTTTTT 57.756 45.0 0.00 0.0 40.63 1.94 F
1119 1146 1.215679 AGGAGAAGGAGAGGTCCCGA 61.216 60.0 0.00 0.0 45.26 5.14 F
1876 1965 0.390860 ACTCTTTGCAGCGTCTGTCT 59.609 50.0 8.32 0.0 33.43 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 1950 0.319900 GGAGAGACAGACGCTGCAAA 60.320 55.000 0.0 0.0 36.84 3.68 R
2842 2963 0.533308 TTCCCAGCACCACACGTAAC 60.533 55.000 0.0 0.0 0.00 2.50 R
3520 4457 1.221840 GAGGAGCGCATGGGAGAAA 59.778 57.895 14.9 0.0 0.00 2.52 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
742 743 9.914131 GGATAATTAACCCATCTTAAAATCAGC 57.086 33.333 0.24 0.00 0.00 4.26
743 744 9.612620 GATAATTAACCCATCTTAAAATCAGCG 57.387 33.333 0.00 0.00 0.00 5.18
744 745 7.639113 AATTAACCCATCTTAAAATCAGCGA 57.361 32.000 0.00 0.00 0.00 4.93
745 746 7.639113 ATTAACCCATCTTAAAATCAGCGAA 57.361 32.000 0.00 0.00 0.00 4.70
746 747 5.567138 AACCCATCTTAAAATCAGCGAAG 57.433 39.130 0.00 0.00 0.00 3.79
747 748 4.843728 ACCCATCTTAAAATCAGCGAAGA 58.156 39.130 0.00 0.00 32.73 2.87
748 749 5.440610 ACCCATCTTAAAATCAGCGAAGAT 58.559 37.500 0.00 0.00 38.81 2.40
759 760 2.634815 AGCGAAGATGGAATGCTGAT 57.365 45.000 0.00 0.00 33.99 2.90
760 761 2.928334 AGCGAAGATGGAATGCTGATT 58.072 42.857 0.00 0.00 33.99 2.57
761 762 3.285484 AGCGAAGATGGAATGCTGATTT 58.715 40.909 0.00 0.00 33.99 2.17
762 763 3.314635 AGCGAAGATGGAATGCTGATTTC 59.685 43.478 0.00 0.00 33.99 2.17
763 764 3.065786 GCGAAGATGGAATGCTGATTTCA 59.934 43.478 0.00 0.00 31.23 2.69
764 765 4.439153 GCGAAGATGGAATGCTGATTTCAA 60.439 41.667 0.00 0.00 30.42 2.69
765 766 5.643664 CGAAGATGGAATGCTGATTTCAAA 58.356 37.500 0.00 0.00 30.42 2.69
766 767 6.094719 CGAAGATGGAATGCTGATTTCAAAA 58.905 36.000 0.00 0.00 30.42 2.44
767 768 6.755141 CGAAGATGGAATGCTGATTTCAAAAT 59.245 34.615 0.00 0.00 30.42 1.82
768 769 7.043590 CGAAGATGGAATGCTGATTTCAAAATC 60.044 37.037 8.25 8.25 43.91 2.17
871 872 5.520022 TTTTTCTTATCGCTAACGGACAC 57.480 39.130 0.00 0.00 40.63 3.67
872 873 2.857592 TCTTATCGCTAACGGACACC 57.142 50.000 0.00 0.00 40.63 4.16
873 874 2.372264 TCTTATCGCTAACGGACACCT 58.628 47.619 0.00 0.00 40.63 4.00
874 875 2.756760 TCTTATCGCTAACGGACACCTT 59.243 45.455 0.00 0.00 40.63 3.50
875 876 3.194116 TCTTATCGCTAACGGACACCTTT 59.806 43.478 0.00 0.00 40.63 3.11
876 877 2.467566 ATCGCTAACGGACACCTTTT 57.532 45.000 0.00 0.00 40.63 2.27
877 878 2.243602 TCGCTAACGGACACCTTTTT 57.756 45.000 0.00 0.00 40.63 1.94
1053 1080 2.674220 GGAGGAGGTGGAGGGCTTG 61.674 68.421 0.00 0.00 0.00 4.01
1119 1146 1.215679 AGGAGAAGGAGAGGTCCCGA 61.216 60.000 0.00 0.00 45.26 5.14
1159 1186 2.352032 CGGAAGCGGGAGGAGAACT 61.352 63.158 0.00 0.00 0.00 3.01
1164 1191 3.068691 CGGGAGGAGAACTGGCGA 61.069 66.667 0.00 0.00 0.00 5.54
1179 1207 2.103042 GCGAAGAAGCGAGGCACAT 61.103 57.895 0.00 0.00 0.00 3.21
1329 1361 3.077484 AGCCGGTGTAGTACTGTTCTA 57.923 47.619 5.39 0.00 33.60 2.10
1334 1366 5.290400 GCCGGTGTAGTACTGTTCTATTTTC 59.710 44.000 5.39 0.00 33.60 2.29
1371 1403 6.199342 GGTAGTAGAATTTTCTGATCGACAGC 59.801 42.308 3.07 0.00 45.38 4.40
1373 1405 4.935885 AGAATTTTCTGATCGACAGCAC 57.064 40.909 9.34 0.00 45.38 4.40
1404 1458 7.486232 GGGAACTGAATTAGTACGTTACAGTAC 59.514 40.741 0.00 8.60 45.31 2.73
1417 1474 5.048782 ACGTTACAGTACGATGTTTCACCTA 60.049 40.000 2.93 0.00 43.99 3.08
1418 1475 5.858049 CGTTACAGTACGATGTTTCACCTAA 59.142 40.000 0.00 0.00 43.99 2.69
1431 1488 9.178758 GATGTTTCACCTAAATAATCCTCTGTT 57.821 33.333 0.00 0.00 0.00 3.16
1433 1490 9.667107 TGTTTCACCTAAATAATCCTCTGTTAG 57.333 33.333 0.00 0.00 0.00 2.34
1527 1599 7.333423 TCCGTTTACTAGATTGGATTCAGTTTG 59.667 37.037 0.00 0.00 0.00 2.93
1763 1847 8.230486 AGTTAACTCGCAAGTCAAATAAGAATG 58.770 33.333 1.12 0.00 33.48 2.67
1876 1965 0.390860 ACTCTTTGCAGCGTCTGTCT 59.609 50.000 8.32 0.00 33.43 3.41
1947 2036 2.094286 AGACTCTGCAAACATCCTCTCG 60.094 50.000 0.00 0.00 0.00 4.04
1948 2037 1.895798 ACTCTGCAAACATCCTCTCGA 59.104 47.619 0.00 0.00 0.00 4.04
1972 2061 5.449553 TCAGCATAGTCTCCTCAGATGTAA 58.550 41.667 0.00 0.00 0.00 2.41
1983 2072 3.706594 CCTCAGATGTAAGCTTCCCAGTA 59.293 47.826 0.00 0.00 0.00 2.74
1989 2078 7.047891 CAGATGTAAGCTTCCCAGTAAATGTA 58.952 38.462 0.00 0.00 0.00 2.29
2010 2099 3.443045 GGCCGTGTCATTGCCAGG 61.443 66.667 9.95 0.00 44.70 4.45
2170 2270 9.959721 ACTGTTAATGTACATCTAAATGGAGTT 57.040 29.630 9.23 0.00 37.19 3.01
2447 2553 4.144297 GGTCTAATAAGCATTGATGGCCA 58.856 43.478 8.56 8.56 0.00 5.36
2455 2561 1.202336 GCATTGATGGCCAAGTACTGC 60.202 52.381 10.96 12.21 38.31 4.40
2676 2782 2.701951 TCATGATAGCACAGCAGATGGA 59.298 45.455 0.00 0.00 0.00 3.41
2842 2963 2.753452 ACTGCTGCAGATGAATTGGAAG 59.247 45.455 34.28 5.90 35.18 3.46
2878 2999 1.278127 GGAAGTTCGGATTCAGGGTCA 59.722 52.381 0.00 0.00 0.00 4.02
3226 3390 7.083858 CAGTCTAAGATGCTAGTCTAAGATGC 58.916 42.308 0.00 0.00 0.00 3.91
3246 3410 7.432869 AGATGCTAGTCTAAGATGCTAACTTG 58.567 38.462 0.00 0.00 0.00 3.16
3247 3411 5.907207 TGCTAGTCTAAGATGCTAACTTGG 58.093 41.667 0.00 0.00 0.00 3.61
3338 3503 8.208903 TCTTTACCTACTAATAAACCAGCCATC 58.791 37.037 0.00 0.00 0.00 3.51
3528 4465 1.990060 CCCCGAGCTCTTTCTCCCA 60.990 63.158 12.85 0.00 0.00 4.37
3642 4802 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
615 616 0.518636 CCGACTCGTTCCGTGAACTA 59.481 55.000 12.80 3.90 40.05 2.24
736 737 2.928334 AGCATTCCATCTTCGCTGATT 58.072 42.857 0.00 0.00 0.00 2.57
737 738 2.634815 AGCATTCCATCTTCGCTGAT 57.365 45.000 0.00 0.00 0.00 2.90
740 741 2.634815 ATCAGCATTCCATCTTCGCT 57.365 45.000 0.00 0.00 0.00 4.93
741 742 3.065786 TGAAATCAGCATTCCATCTTCGC 59.934 43.478 0.00 0.00 0.00 4.70
742 743 4.888038 TGAAATCAGCATTCCATCTTCG 57.112 40.909 0.00 0.00 0.00 3.79
743 744 8.128016 GATTTTGAAATCAGCATTCCATCTTC 57.872 34.615 10.71 0.00 43.29 2.87
849 850 4.389687 GGTGTCCGTTAGCGATAAGAAAAA 59.610 41.667 0.00 0.00 41.33 1.94
850 851 3.928375 GGTGTCCGTTAGCGATAAGAAAA 59.072 43.478 0.00 0.00 41.33 2.29
851 852 3.194116 AGGTGTCCGTTAGCGATAAGAAA 59.806 43.478 0.00 0.00 41.33 2.52
852 853 2.756760 AGGTGTCCGTTAGCGATAAGAA 59.243 45.455 0.00 0.00 41.33 2.52
853 854 2.372264 AGGTGTCCGTTAGCGATAAGA 58.628 47.619 0.00 0.00 41.33 2.10
854 855 2.865343 AGGTGTCCGTTAGCGATAAG 57.135 50.000 0.00 0.00 41.33 1.73
855 856 3.598019 AAAGGTGTCCGTTAGCGATAA 57.402 42.857 0.00 0.00 41.33 1.75
856 857 3.598019 AAAAGGTGTCCGTTAGCGATA 57.402 42.857 0.00 0.00 41.33 2.92
857 858 2.467566 AAAAGGTGTCCGTTAGCGAT 57.532 45.000 0.00 0.00 41.33 4.58
858 859 2.243602 AAAAAGGTGTCCGTTAGCGA 57.756 45.000 0.00 0.00 41.33 4.93
875 876 4.815846 GGTGTCCGTTAGTTCACCTAAAAA 59.184 41.667 6.02 0.00 44.57 1.94
876 877 4.379652 GGTGTCCGTTAGTTCACCTAAAA 58.620 43.478 6.02 0.00 44.57 1.52
877 878 3.993920 GGTGTCCGTTAGTTCACCTAAA 58.006 45.455 6.02 0.00 44.57 1.85
878 879 3.665745 GGTGTCCGTTAGTTCACCTAA 57.334 47.619 6.02 0.00 44.57 2.69
882 883 2.609737 CCTCAGGTGTCCGTTAGTTCAC 60.610 54.545 0.00 0.00 0.00 3.18
883 884 1.616865 CCTCAGGTGTCCGTTAGTTCA 59.383 52.381 0.00 0.00 0.00 3.18
884 885 1.067071 CCCTCAGGTGTCCGTTAGTTC 60.067 57.143 0.00 0.00 0.00 3.01
885 886 0.974383 CCCTCAGGTGTCCGTTAGTT 59.026 55.000 0.00 0.00 0.00 2.24
886 887 0.903454 CCCCTCAGGTGTCCGTTAGT 60.903 60.000 0.00 0.00 0.00 2.24
892 893 2.607750 TCAGCCCCTCAGGTGTCC 60.608 66.667 0.00 0.00 38.26 4.02
893 894 2.665603 GTCAGCCCCTCAGGTGTC 59.334 66.667 0.00 0.00 38.26 3.67
1053 1080 2.199236 CGGTCGTACAATAAAGGCTCC 58.801 52.381 0.00 0.00 0.00 4.70
1119 1146 0.705253 TCTTCTCCTCTTCCTCCCGT 59.295 55.000 0.00 0.00 0.00 5.28
1159 1186 4.002506 TGCCTCGCTTCTTCGCCA 62.003 61.111 0.00 0.00 0.00 5.69
1164 1191 0.610174 TCTCATGTGCCTCGCTTCTT 59.390 50.000 0.00 0.00 0.00 2.52
1179 1207 2.325661 TGGAGTCCATGACCTTCTCA 57.674 50.000 8.12 0.00 32.18 3.27
1230 1258 1.072806 AGGAAAAACCGGGTGTAGACC 59.927 52.381 6.32 0.00 44.74 3.85
1329 1361 9.880157 TTCTACTACCAAGTATAAAGCGAAAAT 57.120 29.630 0.00 0.00 37.57 1.82
1345 1377 7.165460 TGTCGATCAGAAAATTCTACTACCA 57.835 36.000 0.00 0.00 35.34 3.25
1346 1378 6.199342 GCTGTCGATCAGAAAATTCTACTACC 59.801 42.308 16.09 0.00 46.27 3.18
1365 1397 0.108804 AGTTCCCATACGTGCTGTCG 60.109 55.000 0.00 0.00 0.00 4.35
1371 1403 5.457799 CGTACTAATTCAGTTCCCATACGTG 59.542 44.000 0.00 0.00 38.80 4.49
1373 1405 5.585390 ACGTACTAATTCAGTTCCCATACG 58.415 41.667 0.00 0.00 38.80 3.06
1404 1458 7.495934 ACAGAGGATTATTTAGGTGAAACATCG 59.504 37.037 0.00 0.00 39.98 3.84
1527 1599 6.861065 TCAGTGAGTTCCTGTTGTTAATTC 57.139 37.500 0.00 0.00 0.00 2.17
1651 1723 8.629158 AGTGATTTTTGCTGTTAAGTGATACAA 58.371 29.630 0.00 0.00 0.00 2.41
1666 1747 7.854534 ACTTTAGCAAAATCAGTGATTTTTGC 58.145 30.769 31.92 31.92 46.07 3.68
1690 1771 5.118510 CCATGCGAACCAAGTTAATTTCAAC 59.881 40.000 0.00 0.00 0.00 3.18
1779 1865 7.128109 TGTGTTCTTCCCATTTATATCCCACTA 59.872 37.037 0.00 0.00 0.00 2.74
1844 1932 7.167468 ACGCTGCAAAGAGTAAACAAAAATAAG 59.833 33.333 0.00 0.00 0.00 1.73
1858 1947 1.066914 GAGACAGACGCTGCAAAGAG 58.933 55.000 0.00 0.00 34.37 2.85
1861 1950 0.319900 GGAGAGACAGACGCTGCAAA 60.320 55.000 0.00 0.00 36.84 3.68
1876 1965 4.584743 ACTATCAGTGTATCGCATTGGAGA 59.415 41.667 0.00 0.00 35.77 3.71
1947 2036 4.523943 ACATCTGAGGAGACTATGCTGATC 59.476 45.833 0.00 0.00 44.43 2.92
1948 2037 4.482030 ACATCTGAGGAGACTATGCTGAT 58.518 43.478 0.00 0.00 44.43 2.90
1972 2061 5.316987 GCCATATACATTTACTGGGAAGCT 58.683 41.667 0.00 0.00 0.00 3.74
1983 2072 4.261572 GCAATGACACGGCCATATACATTT 60.262 41.667 2.24 0.00 0.00 2.32
1989 2078 2.719376 GGCAATGACACGGCCATAT 58.281 52.632 13.01 0.00 46.92 1.78
2010 2099 2.160417 GCACTTGTAGTCAATGCTGTCC 59.840 50.000 0.00 0.00 33.44 4.02
2170 2270 5.255687 TCGACAACCACCAGTACTAAGATA 58.744 41.667 0.00 0.00 0.00 1.98
2447 2553 5.955355 ACATCTTTCTCTCTAGGCAGTACTT 59.045 40.000 0.00 0.00 0.00 2.24
2455 2561 5.867903 ACCATGACATCTTTCTCTCTAGG 57.132 43.478 0.00 0.00 0.00 3.02
2676 2782 4.821805 CCACTTTCATCACTTGTAACCACT 59.178 41.667 0.00 0.00 0.00 4.00
2714 2820 5.125578 AGACAGATAGTAATGACACTTCGCA 59.874 40.000 0.00 0.00 0.00 5.10
2825 2931 4.393062 ACGTAACTTCCAATTCATCTGCAG 59.607 41.667 7.63 7.63 0.00 4.41
2842 2963 0.533308 TTCCCAGCACCACACGTAAC 60.533 55.000 0.00 0.00 0.00 2.50
3226 3390 7.341445 ACTCCAAGTTAGCATCTTAGACTAG 57.659 40.000 0.00 0.00 0.00 2.57
3338 3503 1.800315 CGACGTACCACCAGAAGCG 60.800 63.158 0.00 0.00 0.00 4.68
3360 3594 4.664150 AGGGACTTTTTCGCAAAATTGA 57.336 36.364 0.00 0.00 39.71 2.57
3520 4457 1.221840 GAGGAGCGCATGGGAGAAA 59.778 57.895 14.90 0.00 0.00 2.52
3642 4802 3.963374 TGGAGAGAGAGAGAGAGAGAGAG 59.037 52.174 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.