Multiple sequence alignment - TraesCS2D01G053800

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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 TraesCS2D01G053800 chr2D 100.000 3264 0 0 1 3264 21143759 21140496 0.000000e+00 6028.0
1 TraesCS2D01G053800 chr7D 89.381 1940 124 33 720 2623 42809876 42811769 0.000000e+00 2366.0
2 TraesCS2D01G053800 chr7D 97.857 980 21 0 2285 3264 559065721 559066700 0.000000e+00 1694.0
3 TraesCS2D01G053800 chr7D 97.449 980 24 1 2285 3264 125901110 125900132 0.000000e+00 1670.0
4 TraesCS2D01G053800 chr7D 86.275 714 72 15 1 702 568456302 568457001 0.000000e+00 752.0
5 TraesCS2D01G053800 chr1D 98.265 980 17 0 2285 3264 380824711 380825690 0.000000e+00 1716.0
6 TraesCS2D01G053800 chr1D 97.449 980 25 0 2285 3264 323593437 323594416 0.000000e+00 1672.0
7 TraesCS2D01G053800 chr1D 87.722 790 51 14 771 1551 54465728 54466480 0.000000e+00 880.0
8 TraesCS2D01G053800 chr3B 97.454 982 23 2 2285 3264 104364493 104365474 0.000000e+00 1674.0
9 TraesCS2D01G053800 chr3B 83.486 1417 159 37 771 2159 710716215 710717584 0.000000e+00 1251.0
10 TraesCS2D01G053800 chr3B 84.352 409 39 11 312 711 807587078 807586686 8.550000e-101 377.0
11 TraesCS2D01G053800 chr3B 93.333 195 12 1 1621 1814 754019135 754018941 1.480000e-73 287.0
12 TraesCS2D01G053800 chr5D 97.449 980 25 0 2285 3264 557304601 557303622 0.000000e+00 1672.0
13 TraesCS2D01G053800 chr1A 97.041 980 29 0 2285 3264 154371934 154370955 0.000000e+00 1650.0
14 TraesCS2D01G053800 chr1A 83.189 577 29 35 771 1345 66845647 66845137 1.770000e-127 466.0
15 TraesCS2D01G053800 chr1A 100.000 28 0 0 1135 1162 66845117 66845090 6.000000e-03 52.8
16 TraesCS2D01G053800 chr7B 96.330 981 35 1 2285 3264 125734313 125735293 0.000000e+00 1611.0
17 TraesCS2D01G053800 chr7B 86.096 712 78 6 1 702 653340426 653341126 0.000000e+00 747.0
18 TraesCS2D01G053800 chr7B 94.118 306 17 1 1509 1814 396376413 396376717 6.380000e-127 464.0
19 TraesCS2D01G053800 chr7B 85.864 382 30 14 315 689 548747990 548747626 5.110000e-103 385.0
20 TraesCS2D01G053800 chr7B 91.282 195 16 1 1621 1814 634238992 634239186 6.940000e-67 265.0
21 TraesCS2D01G053800 chr2A 96.020 980 39 0 2285 3264 725179427 725180406 0.000000e+00 1594.0
22 TraesCS2D01G053800 chr2A 87.074 704 76 5 1 701 469874472 469875163 0.000000e+00 782.0
23 TraesCS2D01G053800 chr2A 83.042 572 31 32 771 1340 716817333 716817840 2.970000e-125 459.0
24 TraesCS2D01G053800 chr4D 85.543 1418 129 37 771 2159 435101794 435100424 0.000000e+00 1413.0
25 TraesCS2D01G053800 chr4D 86.932 176 10 7 850 1024 435100423 435100260 5.560000e-43 185.0
26 TraesCS2D01G053800 chr5A 85.120 1418 135 35 771 2159 512719380 512720750 0.000000e+00 1380.0
27 TraesCS2D01G053800 chr5A 88.270 682 62 8 24 699 219062917 219062248 0.000000e+00 800.0
28 TraesCS2D01G053800 chr5A 87.518 705 70 10 1 699 193888512 193889204 0.000000e+00 798.0
29 TraesCS2D01G053800 chr5A 82.496 577 35 29 771 1345 567010593 567010081 2.310000e-121 446.0
30 TraesCS2D01G053800 chr5A 82.149 577 37 33 771 1345 247822928 247823440 5.000000e-118 435.0
31 TraesCS2D01G053800 chr7A 88.160 1174 90 23 726 1876 42497602 42498749 0.000000e+00 1352.0
32 TraesCS2D01G053800 chr7A 85.007 667 75 15 1 658 727856963 727857613 0.000000e+00 654.0
33 TraesCS2D01G053800 chr7A 87.971 557 61 4 1 552 702291455 702292010 0.000000e+00 652.0
34 TraesCS2D01G053800 chr7A 82.839 641 88 15 1979 2610 42498776 42499403 3.680000e-154 555.0
35 TraesCS2D01G053800 chr7A 84.380 589 33 28 760 1345 79797848 79798380 1.040000e-144 523.0
36 TraesCS2D01G053800 chr7A 82.609 575 34 32 773 1345 97557990 97557480 6.420000e-122 448.0
37 TraesCS2D01G053800 chr7A 86.262 313 28 9 771 1080 601863848 601863548 3.140000e-85 326.0
38 TraesCS2D01G053800 chr7A 93.333 120 8 0 1226 1345 293795335 293795454 9.310000e-41 178.0
39 TraesCS2D01G053800 chr4A 88.889 1026 81 23 1622 2623 650368734 650369750 0.000000e+00 1232.0
40 TraesCS2D01G053800 chr4A 90.314 733 31 9 720 1443 650367885 650368586 0.000000e+00 924.0
41 TraesCS2D01G053800 chr4A 83.189 577 31 33 771 1345 476163758 476164270 4.930000e-128 468.0
42 TraesCS2D01G053800 chr4A 87.089 395 35 5 312 702 622071438 622071820 1.800000e-117 433.0
43 TraesCS2D01G053800 chr4A 84.026 313 35 5 771 1080 418428695 418428395 1.480000e-73 287.0
44 TraesCS2D01G053800 chr4A 96.970 33 0 1 1131 1162 476164285 476164317 2.000000e-03 54.7
45 TraesCS2D01G053800 chrUn 87.042 710 73 4 1 702 93956412 93957110 0.000000e+00 784.0
46 TraesCS2D01G053800 chrUn 87.268 699 68 5 1 688 19722535 19723223 0.000000e+00 778.0
47 TraesCS2D01G053800 chr3A 86.835 714 75 11 1 711 718744039 718743342 0.000000e+00 780.0
48 TraesCS2D01G053800 chr3A 89.172 314 28 2 850 1162 401132503 401132811 1.420000e-103 387.0
49 TraesCS2D01G053800 chr3A 89.046 283 25 5 1879 2159 401132224 401132502 2.410000e-91 346.0
50 TraesCS2D01G053800 chr6D 90.595 521 39 4 187 702 100661947 100662462 0.000000e+00 682.0
51 TraesCS2D01G053800 chr2B 86.348 564 58 11 146 702 736899836 736899285 6.030000e-167 597.0
52 TraesCS2D01G053800 chr2B 92.810 306 18 2 1509 1814 588847721 588848022 1.070000e-119 440.0
53 TraesCS2D01G053800 chr6A 84.229 577 36 30 771 1345 357869932 357870455 8.080000e-141 510.0
54 TraesCS2D01G053800 chr6A 100.000 28 0 0 1135 1162 357870475 357870502 6.000000e-03 52.8
55 TraesCS2D01G053800 chr6B 93.137 306 19 2 1509 1814 35452824 35452521 6.420000e-122 448.0
56 TraesCS2D01G053800 chr5B 92.308 195 14 1 1621 1814 45134414 45134220 3.210000e-70 276.0
57 TraesCS2D01G053800 chr1B 91.597 119 9 1 975 1092 137217942 137217824 2.610000e-36 163.0


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 TraesCS2D01G053800 chr2D 21140496 21143759 3263 True 6028.00 6028 100.0000 1 3264 1 chr2D.!!$R1 3263
1 TraesCS2D01G053800 chr7D 42809876 42811769 1893 False 2366.00 2366 89.3810 720 2623 1 chr7D.!!$F1 1903
2 TraesCS2D01G053800 chr7D 559065721 559066700 979 False 1694.00 1694 97.8570 2285 3264 1 chr7D.!!$F2 979
3 TraesCS2D01G053800 chr7D 125900132 125901110 978 True 1670.00 1670 97.4490 2285 3264 1 chr7D.!!$R1 979
4 TraesCS2D01G053800 chr7D 568456302 568457001 699 False 752.00 752 86.2750 1 702 1 chr7D.!!$F3 701
5 TraesCS2D01G053800 chr1D 380824711 380825690 979 False 1716.00 1716 98.2650 2285 3264 1 chr1D.!!$F3 979
6 TraesCS2D01G053800 chr1D 323593437 323594416 979 False 1672.00 1672 97.4490 2285 3264 1 chr1D.!!$F2 979
7 TraesCS2D01G053800 chr1D 54465728 54466480 752 False 880.00 880 87.7220 771 1551 1 chr1D.!!$F1 780
8 TraesCS2D01G053800 chr3B 104364493 104365474 981 False 1674.00 1674 97.4540 2285 3264 1 chr3B.!!$F1 979
9 TraesCS2D01G053800 chr3B 710716215 710717584 1369 False 1251.00 1251 83.4860 771 2159 1 chr3B.!!$F2 1388
10 TraesCS2D01G053800 chr5D 557303622 557304601 979 True 1672.00 1672 97.4490 2285 3264 1 chr5D.!!$R1 979
11 TraesCS2D01G053800 chr1A 154370955 154371934 979 True 1650.00 1650 97.0410 2285 3264 1 chr1A.!!$R1 979
12 TraesCS2D01G053800 chr1A 66845090 66845647 557 True 259.40 466 91.5945 771 1345 2 chr1A.!!$R2 574
13 TraesCS2D01G053800 chr7B 125734313 125735293 980 False 1611.00 1611 96.3300 2285 3264 1 chr7B.!!$F1 979
14 TraesCS2D01G053800 chr7B 653340426 653341126 700 False 747.00 747 86.0960 1 702 1 chr7B.!!$F4 701
15 TraesCS2D01G053800 chr2A 725179427 725180406 979 False 1594.00 1594 96.0200 2285 3264 1 chr2A.!!$F3 979
16 TraesCS2D01G053800 chr2A 469874472 469875163 691 False 782.00 782 87.0740 1 701 1 chr2A.!!$F1 700
17 TraesCS2D01G053800 chr2A 716817333 716817840 507 False 459.00 459 83.0420 771 1340 1 chr2A.!!$F2 569
18 TraesCS2D01G053800 chr4D 435100260 435101794 1534 True 799.00 1413 86.2375 771 2159 2 chr4D.!!$R1 1388
19 TraesCS2D01G053800 chr5A 512719380 512720750 1370 False 1380.00 1380 85.1200 771 2159 1 chr5A.!!$F3 1388
20 TraesCS2D01G053800 chr5A 219062248 219062917 669 True 800.00 800 88.2700 24 699 1 chr5A.!!$R1 675
21 TraesCS2D01G053800 chr5A 193888512 193889204 692 False 798.00 798 87.5180 1 699 1 chr5A.!!$F1 698
22 TraesCS2D01G053800 chr5A 567010081 567010593 512 True 446.00 446 82.4960 771 1345 1 chr5A.!!$R2 574
23 TraesCS2D01G053800 chr5A 247822928 247823440 512 False 435.00 435 82.1490 771 1345 1 chr5A.!!$F2 574
24 TraesCS2D01G053800 chr7A 42497602 42499403 1801 False 953.50 1352 85.4995 726 2610 2 chr7A.!!$F5 1884
25 TraesCS2D01G053800 chr7A 727856963 727857613 650 False 654.00 654 85.0070 1 658 1 chr7A.!!$F4 657
26 TraesCS2D01G053800 chr7A 702291455 702292010 555 False 652.00 652 87.9710 1 552 1 chr7A.!!$F3 551
27 TraesCS2D01G053800 chr7A 79797848 79798380 532 False 523.00 523 84.3800 760 1345 1 chr7A.!!$F1 585
28 TraesCS2D01G053800 chr7A 97557480 97557990 510 True 448.00 448 82.6090 773 1345 1 chr7A.!!$R1 572
29 TraesCS2D01G053800 chr4A 650367885 650369750 1865 False 1078.00 1232 89.6015 720 2623 2 chr4A.!!$F3 1903
30 TraesCS2D01G053800 chr4A 476163758 476164317 559 False 261.35 468 90.0795 771 1345 2 chr4A.!!$F2 574
31 TraesCS2D01G053800 chrUn 93956412 93957110 698 False 784.00 784 87.0420 1 702 1 chrUn.!!$F2 701
32 TraesCS2D01G053800 chrUn 19722535 19723223 688 False 778.00 778 87.2680 1 688 1 chrUn.!!$F1 687
33 TraesCS2D01G053800 chr3A 718743342 718744039 697 True 780.00 780 86.8350 1 711 1 chr3A.!!$R1 710
34 TraesCS2D01G053800 chr3A 401132224 401132811 587 False 366.50 387 89.1090 850 2159 2 chr3A.!!$F1 1309
35 TraesCS2D01G053800 chr6D 100661947 100662462 515 False 682.00 682 90.5950 187 702 1 chr6D.!!$F1 515
36 TraesCS2D01G053800 chr2B 736899285 736899836 551 True 597.00 597 86.3480 146 702 1 chr2B.!!$R1 556
37 TraesCS2D01G053800 chr6A 357869932 357870502 570 False 281.40 510 92.1145 771 1345 2 chr6A.!!$F1 574

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
709 747 0.114168 CCCTCACCACCCCAATTGAA 59.886 55.0 7.12 0.0 0.0 2.69 F
1313 1390 0.908180 GGGACGAGAGGGGGAAGAAA 60.908 60.0 0.00 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2385 0.417437 TGGTTCATCTCCCTCCCAGA 59.583 55.0 0.0 0.0 0.0 3.86 R
2283 2454 0.677288 TGAACGAATGGTGACCGAGT 59.323 50.0 0.0 0.0 0.0 4.18 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
190 194 3.505680 TGGATCAAATCTTTTGACACCCG 59.494 43.478 17.43 0.00 31.68 5.28
384 394 1.066215 TCTGATTGGTCCGTGGACATG 60.066 52.381 20.02 0.00 46.20 3.21
405 415 2.622629 CGCGGATCGTGCATGAAG 59.377 61.111 13.65 8.72 0.00 3.02
438 448 1.153706 CGCGGATCCAACGGTAGTT 60.154 57.895 13.41 0.00 42.15 2.24
552 583 1.231641 CAGATCCCCCGTCTCCTCT 59.768 63.158 0.00 0.00 0.00 3.69
564 595 2.043852 TCCTCTCTGTCTCGCCCC 60.044 66.667 0.00 0.00 0.00 5.80
618 653 4.592192 CAGATCCATCGCCGCCGT 62.592 66.667 0.00 0.00 35.54 5.68
630 668 3.382832 CGCCGTCACCTTCCTCCT 61.383 66.667 0.00 0.00 0.00 3.69
704 742 3.579302 CTGCCCTCACCACCCCAA 61.579 66.667 0.00 0.00 0.00 4.12
705 743 2.863484 TGCCCTCACCACCCCAAT 60.863 61.111 0.00 0.00 0.00 3.16
706 744 2.445155 GCCCTCACCACCCCAATT 59.555 61.111 0.00 0.00 0.00 2.32
707 745 1.984026 GCCCTCACCACCCCAATTG 60.984 63.158 0.00 0.00 0.00 2.32
708 746 1.773635 CCCTCACCACCCCAATTGA 59.226 57.895 7.12 0.00 0.00 2.57
709 747 0.114168 CCCTCACCACCCCAATTGAA 59.886 55.000 7.12 0.00 0.00 2.69
710 748 1.256812 CCTCACCACCCCAATTGAAC 58.743 55.000 7.12 0.00 0.00 3.18
711 749 1.203050 CCTCACCACCCCAATTGAACT 60.203 52.381 7.12 0.00 0.00 3.01
712 750 2.597455 CTCACCACCCCAATTGAACTT 58.403 47.619 7.12 0.00 0.00 2.66
713 751 3.499563 CCTCACCACCCCAATTGAACTTA 60.500 47.826 7.12 0.00 0.00 2.24
714 752 4.344104 CTCACCACCCCAATTGAACTTAT 58.656 43.478 7.12 0.00 0.00 1.73
715 753 4.340617 TCACCACCCCAATTGAACTTATC 58.659 43.478 7.12 0.00 0.00 1.75
716 754 4.085733 CACCACCCCAATTGAACTTATCA 58.914 43.478 7.12 0.00 35.85 2.15
750 788 4.602340 TCTAAATCAAGCCGGGAGATAC 57.398 45.455 2.18 0.00 0.00 2.24
757 795 1.146263 GCCGGGAGATACTGTTGGG 59.854 63.158 2.18 0.00 0.00 4.12
838 889 2.684192 AAATCCACCACCACCGCGAA 62.684 55.000 8.23 0.00 0.00 4.70
1211 1277 1.033746 CGCTGCAATCTGGGATGGTT 61.034 55.000 0.00 0.00 0.00 3.67
1217 1283 2.528564 CAATCTGGGATGGTTGGTTGT 58.471 47.619 0.00 0.00 0.00 3.32
1218 1284 2.220653 ATCTGGGATGGTTGGTTGTG 57.779 50.000 0.00 0.00 0.00 3.33
1249 1315 1.275856 CTGAGCTCCTTGTCTCTGCTT 59.724 52.381 12.15 0.00 33.83 3.91
1313 1390 0.908180 GGGACGAGAGGGGGAAGAAA 60.908 60.000 0.00 0.00 0.00 2.52
1341 1418 2.045926 CCGGGCTCAAGGACAAGG 60.046 66.667 0.00 0.00 0.00 3.61
1396 1478 1.069765 CGCCTCACGCCCAAGATAT 59.930 57.895 0.00 0.00 33.16 1.63
1459 1555 4.572985 TGCTTGATTCTGTTTTGTCAGG 57.427 40.909 0.00 0.00 36.25 3.86
1467 1563 1.068895 CTGTTTTGTCAGGCATTGGCA 59.931 47.619 13.20 0.00 43.71 4.92
1479 1575 3.951037 AGGCATTGGCATGTTACGAAATA 59.049 39.130 13.20 0.00 43.71 1.40
1495 1592 8.981647 GTTACGAAATACAAGTTTGTTCCTCTA 58.018 33.333 2.46 0.00 42.35 2.43
1507 1604 4.497473 TGTTCCTCTATTGCCAAAAACG 57.503 40.909 0.00 0.00 0.00 3.60
1565 1675 5.119125 GCTTTCACCCATTTTTCATCTTTCG 59.881 40.000 0.00 0.00 0.00 3.46
1566 1676 4.782019 TCACCCATTTTTCATCTTTCGG 57.218 40.909 0.00 0.00 0.00 4.30
1599 1719 6.049790 GGTCAGACCTTATTCAGTATTCACC 58.950 44.000 12.94 0.00 34.73 4.02
1604 1724 4.652421 ACCTTATTCAGTATTCACCGCCTA 59.348 41.667 0.00 0.00 0.00 3.93
1620 1743 5.747197 CACCGCCTACTATTTGTTACTACTG 59.253 44.000 0.00 0.00 0.00 2.74
1626 1749 7.687103 GCCTACTATTTGTTACTACTGCCATCT 60.687 40.741 0.00 0.00 0.00 2.90
1672 1795 4.638421 TCGACACCATGTTTCTTTGAACTT 59.362 37.500 0.00 0.00 0.00 2.66
1681 1804 6.645700 TGTTTCTTTGAACTTGTTTGCATC 57.354 33.333 0.00 0.00 0.00 3.91
1802 1954 3.067601 TGTGACAGTCGTTTGCTTCTCTA 59.932 43.478 0.00 0.00 0.00 2.43
1814 1966 6.538444 GTTTGCTTCTCTAGTTACATTCTGC 58.462 40.000 0.00 0.00 0.00 4.26
1815 1967 4.424626 TGCTTCTCTAGTTACATTCTGCG 58.575 43.478 0.00 0.00 0.00 5.18
1873 2028 9.803507 AGAATCATCATTTACATGTATGTGGAT 57.196 29.630 6.36 8.63 41.89 3.41
1922 2086 7.840342 ATTAGATGTGAACTTCTTGCTGTAG 57.160 36.000 4.40 0.00 33.24 2.74
1964 2130 2.033424 GCTGGAAACGCTTCAGTTTTCT 59.967 45.455 0.35 0.00 43.54 2.52
1965 2131 6.271284 AGCTGGAAACGCTTCAGTTTTCTG 62.271 45.833 0.35 3.65 43.54 3.02
1966 2132 2.223479 TGGAAACGCTTCAGTTTTCTGC 60.223 45.455 0.35 0.00 46.59 4.26
1976 2142 4.277515 TCAGTTTTCTGCATAGCTCAGT 57.722 40.909 0.00 0.00 46.59 3.41
1996 2162 5.897250 TCAGTGCCTATAGAGTGGACATTTA 59.103 40.000 0.00 0.00 0.00 1.40
2120 2291 8.364142 GTTCACCTCTGCAGATTCTTACTATAT 58.636 37.037 18.63 0.00 0.00 0.86
2146 2317 5.382616 GACAAACTAAAGGAGGAAAGGGAA 58.617 41.667 0.00 0.00 0.00 3.97
2163 2334 3.913163 AGGGAACAGAGAGAAGGAAATGT 59.087 43.478 0.00 0.00 0.00 2.71
2178 2349 7.723172 AGAAGGAAATGTTGAAGAAGAAGATGT 59.277 33.333 0.00 0.00 0.00 3.06
2214 2385 5.690464 ATAGCAGAAGAAGAAGATGGTGT 57.310 39.130 0.00 0.00 0.00 4.16
2283 2454 4.706842 AGCCCACTACTTCTTCTGAAAA 57.293 40.909 0.00 0.00 0.00 2.29
2316 2487 3.452755 TCGTTCAACTTCAGAGCTCAA 57.547 42.857 17.77 0.88 0.00 3.02
2681 2857 2.128771 TCCCAGTAAAGCAAGATGCC 57.871 50.000 0.00 0.00 46.52 4.40
2726 2902 8.806429 ATGATATTGGTGTACACTCAATTTGA 57.194 30.769 30.47 22.87 35.44 2.69
2834 3011 1.751544 GATGATGTGGCCTGCAGCA 60.752 57.895 18.13 18.13 46.50 4.41
3081 3259 9.622004 GCGTTTTATCTGTAGAGTGCTATATTA 57.378 33.333 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.692115 ACACCAAAAGTTTCCCAAGATTT 57.308 34.783 0.00 0.00 0.00 2.17
87 91 3.258872 TGCAGTTGCCTCATAATTTGCTT 59.741 39.130 1.06 0.00 41.18 3.91
233 237 9.525409 TTGCAAAATTGGACCAAATAAAATTTG 57.475 25.926 11.82 14.96 32.36 2.32
237 241 7.630242 TGTTGCAAAATTGGACCAAATAAAA 57.370 28.000 11.82 0.00 0.00 1.52
340 350 8.377799 AGAATGCAGTATGATGTAATGACCATA 58.622 33.333 0.00 0.00 39.69 2.74
349 359 6.594744 ACCAATCAGAATGCAGTATGATGTA 58.405 36.000 23.27 0.00 38.34 2.29
352 362 5.068636 GGACCAATCAGAATGCAGTATGAT 58.931 41.667 17.81 17.81 38.34 2.45
405 415 3.558411 GCGAGCATCTGACGGTGC 61.558 66.667 0.00 0.00 41.57 5.01
438 448 1.133915 GTTGGTGTGGAAGGGTTGAGA 60.134 52.381 0.00 0.00 0.00 3.27
552 583 2.038813 TCCATGGGGCGAGACAGA 59.961 61.111 13.02 0.00 0.00 3.41
564 595 1.875514 CTCTCGCTCTCTCTCTCCATG 59.124 57.143 0.00 0.00 0.00 3.66
689 727 1.984026 CAATTGGGGTGGTGAGGGC 60.984 63.158 0.00 0.00 0.00 5.19
715 753 9.305925 GGCTTGATTTAGAATAATTTCCACTTG 57.694 33.333 0.00 0.00 31.84 3.16
716 754 8.190784 CGGCTTGATTTAGAATAATTTCCACTT 58.809 33.333 0.00 0.00 31.84 3.16
717 755 7.201821 CCGGCTTGATTTAGAATAATTTCCACT 60.202 37.037 0.00 0.00 31.84 4.00
718 756 6.918022 CCGGCTTGATTTAGAATAATTTCCAC 59.082 38.462 0.00 0.00 31.84 4.02
727 765 4.713792 ATCTCCCGGCTTGATTTAGAAT 57.286 40.909 0.00 0.00 0.00 2.40
730 768 4.202264 ACAGTATCTCCCGGCTTGATTTAG 60.202 45.833 0.00 0.00 0.00 1.85
757 795 3.370633 GGGAAGGGGATAGTGTTGAGAAC 60.371 52.174 0.00 0.00 0.00 3.01
838 889 1.898574 CGGGAACAACAAGCTGGCT 60.899 57.895 0.00 0.00 0.00 4.75
840 891 1.654220 CACGGGAACAACAAGCTGG 59.346 57.895 0.00 0.00 0.00 4.85
841 892 1.008538 GCACGGGAACAACAAGCTG 60.009 57.895 0.00 0.00 0.00 4.24
842 893 2.193536 GGCACGGGAACAACAAGCT 61.194 57.895 0.00 0.00 0.00 3.74
843 894 2.335011 GGCACGGGAACAACAAGC 59.665 61.111 0.00 0.00 0.00 4.01
1249 1315 1.832608 ACCTGCAGACACAGACCGA 60.833 57.895 17.39 0.00 40.25 4.69
1341 1418 0.747283 CAATCTGGCTCCTGACTGGC 60.747 60.000 0.00 0.00 35.26 4.85
1390 1472 5.067936 ACTCGTCTTCGATGAACCATATCTT 59.932 40.000 2.09 0.00 45.21 2.40
1396 1478 1.201647 GGACTCGTCTTCGATGAACCA 59.798 52.381 2.09 0.00 45.21 3.67
1459 1555 4.667262 TGTATTTCGTAACATGCCAATGC 58.333 39.130 0.00 0.00 37.29 3.56
1467 1563 8.161699 AGGAACAAACTTGTATTTCGTAACAT 57.838 30.769 0.00 0.00 41.31 2.71
1479 1575 4.469657 TGGCAATAGAGGAACAAACTTGT 58.530 39.130 0.00 0.00 44.72 3.16
1495 1592 4.817464 TGAGTACTGTACGTTTTTGGCAAT 59.183 37.500 11.97 0.00 0.00 3.56
1507 1604 4.498345 GGTGCAGCTAGATGAGTACTGTAC 60.498 50.000 13.26 9.93 41.44 2.90
1565 1675 3.983044 AAGGTCTGACCATGAACTACC 57.017 47.619 27.48 0.00 41.95 3.18
1566 1676 6.640518 TGAATAAGGTCTGACCATGAACTAC 58.359 40.000 27.48 11.58 41.95 2.73
1599 1719 4.743644 GGCAGTAGTAACAAATAGTAGGCG 59.256 45.833 0.00 0.00 0.00 5.52
1604 1724 7.148239 GCAAAGATGGCAGTAGTAACAAATAGT 60.148 37.037 0.00 0.00 0.00 2.12
1672 1795 2.549332 TCGAATGGCGATGCAAACA 58.451 47.368 0.00 0.00 45.59 2.83
1681 1804 0.861837 GAAGGCAGTATCGAATGGCG 59.138 55.000 13.87 0.00 45.91 5.69
1780 1931 2.159099 AGAGAAGCAAACGACTGTCACA 60.159 45.455 8.73 0.00 0.00 3.58
1802 1954 4.142687 GCAAATACACCGCAGAATGTAACT 60.143 41.667 0.00 0.00 39.31 2.24
1814 1966 3.896648 AACTGAACTGCAAATACACCG 57.103 42.857 0.00 0.00 0.00 4.94
1815 1967 5.240844 ACCTAAACTGAACTGCAAATACACC 59.759 40.000 0.00 0.00 0.00 4.16
1866 2021 9.793259 ATCGGAAAACATATAAGTTATCCACAT 57.207 29.630 0.00 0.00 0.00 3.21
1916 2080 2.167487 AGCTAGTTTCCAGCTCTACAGC 59.833 50.000 0.00 0.00 46.37 4.40
1951 2117 2.417933 AGCTATGCAGAAAACTGAAGCG 59.582 45.455 0.00 0.00 33.99 4.68
1964 2130 3.500343 TCTATAGGCACTGAGCTATGCA 58.500 45.455 16.45 0.00 43.93 3.96
1965 2131 3.509575 ACTCTATAGGCACTGAGCTATGC 59.490 47.826 8.27 8.27 44.79 3.14
1966 2132 4.082300 CCACTCTATAGGCACTGAGCTATG 60.082 50.000 0.00 0.00 44.79 2.23
1976 2142 7.933577 CAGATTTAAATGTCCACTCTATAGGCA 59.066 37.037 5.17 0.00 0.00 4.75
2034 2203 8.851541 AAATGTGAAAAATGCTCCATGTAATT 57.148 26.923 0.00 0.00 0.00 1.40
2120 2291 5.137551 CCTTTCCTCCTTTAGTTTGTCCAA 58.862 41.667 0.00 0.00 0.00 3.53
2146 2317 6.179906 TCTTCAACATTTCCTTCTCTCTGT 57.820 37.500 0.00 0.00 0.00 3.41
2163 2334 6.828273 TGAAACTTCCACATCTTCTTCTTCAA 59.172 34.615 0.00 0.00 0.00 2.69
2178 2349 7.423844 TCTTCTGCTATATCTGAAACTTCCA 57.576 36.000 0.00 0.00 0.00 3.53
2214 2385 0.417437 TGGTTCATCTCCCTCCCAGA 59.583 55.000 0.00 0.00 0.00 3.86
2283 2454 0.677288 TGAACGAATGGTGACCGAGT 59.323 50.000 0.00 0.00 0.00 4.18
2316 2487 2.544768 AGGGCAAGAACAGACCTGT 58.455 52.632 0.00 0.00 44.84 4.00
2517 2690 9.974980 TCTAATCCAGGTTTTGTTTTACAAATC 57.025 29.630 5.88 5.55 46.17 2.17
2804 2981 4.038282 GGCCACATCATCATATTTGAGCAA 59.962 41.667 0.00 0.00 34.73 3.91
2834 3011 2.356313 CAGCGTCGAAGCAGGTGT 60.356 61.111 24.95 0.81 40.15 4.16


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

AutoCloner maintained by Alex Coulton.