Multiple sequence alignment - TraesCS1A01G404400

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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 TraesCS1A01G404400 chr1A 100.000 3621 0 0 1 3621 567989725 567986105 0.000000e+00 6687.0
1 TraesCS1A01G404400 chr1A 80.499 1364 244 17 1048 2405 570787943 570786596 0.000000e+00 1026.0
2 TraesCS1A01G404400 chr1A 77.665 1379 240 41 1057 2400 583991140 583989795 0.000000e+00 778.0
3 TraesCS1A01G404400 chr1A 84.566 784 89 18 3 764 34980029 34980802 0.000000e+00 749.0
4 TraesCS1A01G404400 chr1A 73.559 1388 296 55 1060 2402 570855849 570857210 7.080000e-127 464.0
5 TraesCS1A01G404400 chr1A 77.513 378 60 17 2203 2576 567479317 567478961 1.700000e-48 204.0
6 TraesCS1A01G404400 chr1D 91.422 2693 143 40 789 3452 473623829 473621196 0.000000e+00 3613.0
7 TraesCS1A01G404400 chr1D 85.332 784 97 14 1 766 249745852 249746635 0.000000e+00 795.0
8 TraesCS1A01G404400 chr1D 77.047 1490 274 38 1052 2510 486334232 486332780 0.000000e+00 795.0
9 TraesCS1A01G404400 chr1D 73.199 1388 301 50 1060 2402 475171805 475173166 1.540000e-118 436.0
10 TraesCS1A01G404400 chr1D 89.011 182 12 3 3448 3621 473621045 473620864 6.090000e-53 219.0
11 TraesCS1A01G404400 chr1D 77.368 380 62 16 2201 2576 473398967 473398608 1.700000e-48 204.0
12 TraesCS1A01G404400 chr1B 80.185 1625 256 38 1052 2658 660524258 660525834 0.000000e+00 1157.0
13 TraesCS1A01G404400 chr1B 92.330 678 46 3 1946 2617 658511317 658510640 0.000000e+00 959.0
14 TraesCS1A01G404400 chr1B 78.123 1353 271 21 1055 2400 660460034 660461368 0.000000e+00 835.0
15 TraesCS1A01G404400 chr1B 78.239 1374 235 42 1056 2398 677306241 677304901 0.000000e+00 822.0
16 TraesCS1A01G404400 chr1B 88.636 572 36 5 768 1310 658511888 658511317 0.000000e+00 669.0
17 TraesCS1A01G404400 chr1B 80.735 789 99 23 1400 2177 660786274 660787020 1.890000e-157 566.0
18 TraesCS1A01G404400 chr1B 73.035 1387 301 49 1060 2402 660453825 660455182 4.320000e-114 422.0
19 TraesCS1A01G404400 chr1B 77.895 380 60 15 2201 2576 658318661 658318302 7.870000e-52 215.0
20 TraesCS1A01G404400 chr1B 79.062 320 43 13 1060 1379 658403858 658404153 7.930000e-47 198.0
21 TraesCS1A01G404400 chr1B 74.747 396 80 13 1700 2089 542725778 542725397 3.740000e-35 159.0
22 TraesCS1A01G404400 chr1B 100.000 36 0 0 2544 2579 660896472 660896507 2.330000e-07 67.6
23 TraesCS1A01G404400 chr3D 83.565 791 98 22 1 766 49534018 49533235 0.000000e+00 712.0
24 TraesCS1A01G404400 chr3D 83.123 794 95 25 1 766 182343083 182343865 0.000000e+00 688.0
25 TraesCS1A01G404400 chr3D 83.420 772 91 20 1 754 42499104 42498352 0.000000e+00 682.0
26 TraesCS1A01G404400 chr3D 82.481 782 105 20 1 764 514006515 514007282 0.000000e+00 656.0
27 TraesCS1A01G404400 chr2D 83.565 791 98 24 3 767 630020280 630021064 0.000000e+00 712.0
28 TraesCS1A01G404400 chr2D 84.043 752 94 15 29 767 608381912 608381174 0.000000e+00 701.0
29 TraesCS1A01G404400 chr5D 83.120 782 97 25 4 764 525456439 525455672 0.000000e+00 680.0
30 TraesCS1A01G404400 chr5D 83.929 112 16 2 1964 2074 545917140 545917250 4.940000e-19 106.0
31 TraesCS1A01G404400 chr5D 79.130 115 24 0 1066 1180 81788561 81788447 3.000000e-11 80.5
32 TraesCS1A01G404400 chr7D 77.869 244 39 9 1053 1290 611082720 611082486 1.750000e-28 137.0
33 TraesCS1A01G404400 chr5B 90.196 102 10 0 3462 3563 646240795 646240694 2.270000e-27 134.0
34 TraesCS1A01G404400 chr7A 77.273 242 41 8 1053 1290 701038089 701037858 2.930000e-26 130.0
35 TraesCS1A01G404400 chr3A 75.449 167 37 4 2432 2596 35846475 35846639 1.080000e-10 78.7


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 TraesCS1A01G404400 chr1A 567986105 567989725 3620 True 6687 6687 100.0000 1 3621 1 chr1A.!!$R2 3620
1 TraesCS1A01G404400 chr1A 570786596 570787943 1347 True 1026 1026 80.4990 1048 2405 1 chr1A.!!$R3 1357
2 TraesCS1A01G404400 chr1A 583989795 583991140 1345 True 778 778 77.6650 1057 2400 1 chr1A.!!$R4 1343
3 TraesCS1A01G404400 chr1A 34980029 34980802 773 False 749 749 84.5660 3 764 1 chr1A.!!$F1 761
4 TraesCS1A01G404400 chr1A 570855849 570857210 1361 False 464 464 73.5590 1060 2402 1 chr1A.!!$F2 1342
5 TraesCS1A01G404400 chr1D 473620864 473623829 2965 True 1916 3613 90.2165 789 3621 2 chr1D.!!$R3 2832
6 TraesCS1A01G404400 chr1D 249745852 249746635 783 False 795 795 85.3320 1 766 1 chr1D.!!$F1 765
7 TraesCS1A01G404400 chr1D 486332780 486334232 1452 True 795 795 77.0470 1052 2510 1 chr1D.!!$R2 1458
8 TraesCS1A01G404400 chr1D 475171805 475173166 1361 False 436 436 73.1990 1060 2402 1 chr1D.!!$F2 1342
9 TraesCS1A01G404400 chr1B 660524258 660525834 1576 False 1157 1157 80.1850 1052 2658 1 chr1B.!!$F4 1606
10 TraesCS1A01G404400 chr1B 660460034 660461368 1334 False 835 835 78.1230 1055 2400 1 chr1B.!!$F3 1345
11 TraesCS1A01G404400 chr1B 677304901 677306241 1340 True 822 822 78.2390 1056 2398 1 chr1B.!!$R3 1342
12 TraesCS1A01G404400 chr1B 658510640 658511888 1248 True 814 959 90.4830 768 2617 2 chr1B.!!$R4 1849
13 TraesCS1A01G404400 chr1B 660786274 660787020 746 False 566 566 80.7350 1400 2177 1 chr1B.!!$F5 777
14 TraesCS1A01G404400 chr1B 660453825 660455182 1357 False 422 422 73.0350 1060 2402 1 chr1B.!!$F2 1342
15 TraesCS1A01G404400 chr3D 49533235 49534018 783 True 712 712 83.5650 1 766 1 chr3D.!!$R2 765
16 TraesCS1A01G404400 chr3D 182343083 182343865 782 False 688 688 83.1230 1 766 1 chr3D.!!$F1 765
17 TraesCS1A01G404400 chr3D 42498352 42499104 752 True 682 682 83.4200 1 754 1 chr3D.!!$R1 753
18 TraesCS1A01G404400 chr3D 514006515 514007282 767 False 656 656 82.4810 1 764 1 chr3D.!!$F2 763
19 TraesCS1A01G404400 chr2D 630020280 630021064 784 False 712 712 83.5650 3 767 1 chr2D.!!$F1 764
20 TraesCS1A01G404400 chr2D 608381174 608381912 738 True 701 701 84.0430 29 767 1 chr2D.!!$R1 738
21 TraesCS1A01G404400 chr5D 525455672 525456439 767 True 680 680 83.1200 4 764 1 chr5D.!!$R2 760

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
292 308 0.032952 AGCAAAGCCGTTACTCGTGA 59.967 50.0 0.00 0.0 37.94 4.35 F
775 848 0.107654 AGTAGCTCCCACAAATCGGC 60.108 55.0 0.00 0.0 0.00 5.54 F
1563 1707 0.246086 CGGAGAGCTCTCTGCAAAGT 59.754 55.0 36.09 4.8 46.67 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 2029 1.065126 GTCCTGGCTGCTACCTGAAAT 60.065 52.381 0.0 0.0 0.00 2.17 R
2405 2624 0.867753 CATCTGTAGCTGCCGTCGTC 60.868 60.000 0.0 0.0 0.00 4.20 R
2875 3114 0.389948 CAGGTGCTCCCAGTAACGAC 60.390 60.000 0.0 0.0 34.66 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
181 189 1.947456 GGAAGCAAAACCGTGACTCTT 59.053 47.619 0.00 0.00 0.00 2.85
289 305 0.442699 GGAAGCAAAGCCGTTACTCG 59.557 55.000 0.00 0.00 39.52 4.18
290 306 1.145803 GAAGCAAAGCCGTTACTCGT 58.854 50.000 0.00 0.00 37.94 4.18
292 308 0.032952 AGCAAAGCCGTTACTCGTGA 59.967 50.000 0.00 0.00 37.94 4.35
293 309 0.863144 GCAAAGCCGTTACTCGTGAA 59.137 50.000 0.00 0.00 37.94 3.18
295 311 2.661979 GCAAAGCCGTTACTCGTGAAAG 60.662 50.000 0.00 0.00 37.94 2.62
403 435 5.600696 AGAAAAACCATGACTCGCAAAAAT 58.399 33.333 0.00 0.00 0.00 1.82
406 438 7.872483 AGAAAAACCATGACTCGCAAAAATAAT 59.128 29.630 0.00 0.00 0.00 1.28
445 481 4.442375 TTTTTCGTTTTCAAGAGGCACA 57.558 36.364 0.00 0.00 0.00 4.57
459 495 1.079543 GCACAGCCATGACTCTCGT 60.080 57.895 0.00 0.00 0.00 4.18
465 501 1.620819 AGCCATGACTCTCGTGAAAGT 59.379 47.619 0.00 0.00 35.46 2.66
504 540 5.542616 CGAAAGCAAAATCATGTCTCTCT 57.457 39.130 0.00 0.00 0.00 3.10
590 653 3.292492 AAGGAAGACCGGTGAAAAACT 57.708 42.857 14.63 0.00 41.83 2.66
596 659 5.163632 GGAAGACCGGTGAAAAACTAAAACA 60.164 40.000 14.63 0.00 0.00 2.83
735 808 0.737715 GCTGATCGTTGCGAGGTTCT 60.738 55.000 6.34 0.00 39.91 3.01
759 832 4.095483 CGAAAGAGCCCTCGTTAACTAGTA 59.905 45.833 3.71 0.00 31.70 1.82
775 848 0.107654 AGTAGCTCCCACAAATCGGC 60.108 55.000 0.00 0.00 0.00 5.54
793 866 2.095161 CGGCGCCTGGTTAAATAAAACA 60.095 45.455 26.68 0.00 32.53 2.83
850 923 3.249189 GGGCTGACACCACTGGGA 61.249 66.667 0.00 0.00 38.05 4.37
869 942 1.067212 GACATGGTAAGGCGATCGTCT 59.933 52.381 18.23 18.23 0.00 4.18
948 1046 0.466555 CTCTCCCGAAGACGATCCCT 60.467 60.000 0.00 0.00 42.66 4.20
959 1057 2.178106 AGACGATCCCTGTCTATTCCCT 59.822 50.000 0.41 0.00 44.57 4.20
1014 1120 4.530857 GCCATGGAGGACGACCGG 62.531 72.222 18.40 0.00 41.22 5.28
1236 1351 4.485208 GAAAAGGACTCGCGCGCG 62.485 66.667 44.84 44.84 41.35 6.86
1318 1439 1.002274 ATGTTCCTCCCGGAGAGCT 59.998 57.895 16.69 0.00 41.74 4.09
1485 1621 2.457323 TTGCCGGTTCCCTGACCTT 61.457 57.895 1.90 0.00 37.56 3.50
1515 1657 1.078143 GAGCTTCCCGCACCTCAAT 60.078 57.895 0.00 0.00 42.61 2.57
1549 1693 1.786049 CGATGTCGGCATCTCGGAGA 61.786 60.000 26.18 10.62 46.96 3.71
1563 1707 0.246086 CGGAGAGCTCTCTGCAAAGT 59.754 55.000 36.09 4.80 46.67 2.66
1572 1716 2.922387 CTCTCTGCAAAGTGTGATCTCG 59.078 50.000 0.00 0.00 0.00 4.04
1879 2060 2.105477 CAGGTAGCAGCCAGGACAATAT 59.895 50.000 0.00 0.00 0.00 1.28
2092 2287 3.441572 GCTCCATGTCATTGTAAGTGCTT 59.558 43.478 0.00 0.00 0.00 3.91
2268 2487 0.468226 AAGTTTGACCCACTCGAGCA 59.532 50.000 13.61 0.00 0.00 4.26
2405 2624 4.702131 AGGAAATGGAAATCGGAGTTCTTG 59.298 41.667 16.60 0.00 0.00 3.02
2581 2815 1.909700 TGGCTGATCCCTTTGACAAC 58.090 50.000 0.00 0.00 0.00 3.32
2598 2832 0.321671 AACTCCTCGTGTGGATGTGG 59.678 55.000 0.00 0.00 35.30 4.17
2599 2833 0.832135 ACTCCTCGTGTGGATGTGGT 60.832 55.000 0.00 0.00 35.30 4.16
2617 2851 8.639761 GGATGTGGTAAGTGTGTTAGATATAGT 58.360 37.037 0.00 0.00 0.00 2.12
2647 2886 2.914777 GATGCTGGCGTCACCCTCTC 62.915 65.000 9.59 0.00 37.83 3.20
2648 2887 3.386237 GCTGGCGTCACCCTCTCT 61.386 66.667 0.00 0.00 37.83 3.10
2691 2930 1.349357 GGCTCCCTTGTTCTTCAGTCT 59.651 52.381 0.00 0.00 0.00 3.24
2692 2931 2.567615 GGCTCCCTTGTTCTTCAGTCTA 59.432 50.000 0.00 0.00 0.00 2.59
2693 2932 3.198853 GGCTCCCTTGTTCTTCAGTCTAT 59.801 47.826 0.00 0.00 0.00 1.98
2694 2933 4.406003 GGCTCCCTTGTTCTTCAGTCTATA 59.594 45.833 0.00 0.00 0.00 1.31
2739 2978 5.351465 TGCAAAATGGTCTTCTACTCGATTC 59.649 40.000 0.00 0.00 0.00 2.52
2822 3061 2.092968 CCCAGCCAGAATGTTGCTAGTA 60.093 50.000 0.00 0.00 31.73 1.82
2825 3064 4.036027 CCAGCCAGAATGTTGCTAGTATTG 59.964 45.833 0.00 0.00 31.73 1.90
2826 3065 4.637534 CAGCCAGAATGTTGCTAGTATTGT 59.362 41.667 0.00 0.00 31.73 2.71
2838 3077 6.785488 TGCTAGTATTGTGTCTTCTGTTTG 57.215 37.500 0.00 0.00 0.00 2.93
2842 3081 7.386848 GCTAGTATTGTGTCTTCTGTTTGGTTA 59.613 37.037 0.00 0.00 0.00 2.85
2849 3088 7.276658 TGTGTCTTCTGTTTGGTTAATACTCA 58.723 34.615 0.00 0.00 0.00 3.41
2874 3113 6.392625 TGTTTCTCTCCTATTCTATGTCGG 57.607 41.667 0.00 0.00 0.00 4.79
2875 3114 5.302059 TGTTTCTCTCCTATTCTATGTCGGG 59.698 44.000 0.00 0.00 0.00 5.14
2882 3121 4.516698 TCCTATTCTATGTCGGGTCGTTAC 59.483 45.833 0.00 0.00 0.00 2.50
2998 3237 9.774742 CCTTGTAACTTTTGTCTAGAAATATGC 57.225 33.333 0.00 0.00 0.00 3.14
3005 3244 9.155975 ACTTTTGTCTAGAAATATGCAGTACAG 57.844 33.333 0.00 0.00 0.00 2.74
3085 3326 7.840342 TTTGAAATTGCAACACACAAGTAAT 57.160 28.000 0.00 0.00 0.00 1.89
3106 3347 1.227943 GTGCAACCCTGTCTCTGCA 60.228 57.895 0.00 0.00 42.28 4.41
3140 3382 7.623089 GCAAGAATGTATCTTCTGTGTCAGAAC 60.623 40.741 7.92 1.32 45.42 3.01
3199 3441 6.475727 GCACTTGTCGCTACTTATTCTATTGA 59.524 38.462 0.00 0.00 0.00 2.57
3201 3443 7.488150 CACTTGTCGCTACTTATTCTATTGACA 59.512 37.037 0.00 0.00 32.53 3.58
3202 3444 8.198109 ACTTGTCGCTACTTATTCTATTGACAT 58.802 33.333 0.00 0.00 34.24 3.06
3313 3555 2.233186 TCCTGAGCTCATTCTGACACAG 59.767 50.000 18.63 0.75 0.00 3.66
3389 3632 1.896220 TGAGTTGAACTGTCCCATGC 58.104 50.000 0.90 0.00 0.00 4.06
3394 3637 0.184692 TGAACTGTCCCATGCCAACA 59.815 50.000 0.00 0.00 0.00 3.33
3397 3640 1.181098 ACTGTCCCATGCCAACAAGC 61.181 55.000 0.00 0.00 0.00 4.01
3398 3641 2.203972 CTGTCCCATGCCAACAAGCG 62.204 60.000 0.00 0.00 34.65 4.68
3420 3663 2.757314 CAGCTACTGTGAGTGAGGATGA 59.243 50.000 0.00 0.00 0.00 2.92
3494 3892 1.034838 ACGCTGTGGTTTTGCCTCAA 61.035 50.000 0.00 0.00 39.90 3.02
3515 3913 2.129607 GTGTTTGGCTGATGCACTTTG 58.870 47.619 0.00 0.00 41.91 2.77
3524 3922 4.229876 GCTGATGCACTTTGAGTTAAACC 58.770 43.478 0.00 0.00 39.41 3.27
3563 3966 6.418101 AGCTTCCTTGCTACTGATTATTCAA 58.582 36.000 0.00 0.00 42.10 2.69
3567 3970 9.512435 CTTCCTTGCTACTGATTATTCAATTTG 57.488 33.333 0.00 0.00 0.00 2.32
3587 3990 7.873739 ATTTGAGCTTACATTTTACAAGTGC 57.126 32.000 0.00 0.00 0.00 4.40
3593 3999 7.661040 AGCTTACATTTTACAAGTGCTCATTT 58.339 30.769 0.00 0.00 0.00 2.32
3599 4005 9.979578 ACATTTTACAAGTGCTCATTTCAAATA 57.020 25.926 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
332 360 2.143594 GAGAGTCACGACCGTGCCTT 62.144 60.000 16.76 5.51 45.04 4.35
377 405 3.476552 TGCGAGTCATGGTTTTTCTTCT 58.523 40.909 0.00 0.00 0.00 2.85
382 410 7.961325 ATTATTTTTGCGAGTCATGGTTTTT 57.039 28.000 0.00 0.00 0.00 1.94
459 495 3.135994 GAGAGGCACGGTTTTACTTTCA 58.864 45.455 0.00 0.00 0.00 2.69
465 501 1.735198 CGCGAGAGGCACGGTTTTA 60.735 57.895 0.00 0.00 43.84 1.52
567 630 4.132336 GTTTTTCACCGGTCTTCCTTAGT 58.868 43.478 2.59 0.00 0.00 2.24
679 752 1.002257 AGCCATTCGCCACATGTCA 60.002 52.632 0.00 0.00 38.78 3.58
684 757 1.078918 CTCTCAGCCATTCGCCACA 60.079 57.895 0.00 0.00 38.78 4.17
732 805 0.966920 AACGAGGGCTCTTTCGAGAA 59.033 50.000 1.77 0.00 39.74 2.87
735 808 1.891150 AGTTAACGAGGGCTCTTTCGA 59.109 47.619 1.77 0.00 39.93 3.71
740 813 2.950975 GCTACTAGTTAACGAGGGCTCT 59.049 50.000 18.39 0.00 0.00 4.09
745 818 3.066481 GTGGGAGCTACTAGTTAACGAGG 59.934 52.174 18.39 7.20 0.00 4.63
759 832 2.436646 CGCCGATTTGTGGGAGCT 60.437 61.111 0.00 0.00 0.00 4.09
775 848 8.007152 GTGATTTTTGTTTTATTTAACCAGGCG 58.993 33.333 0.00 0.00 0.00 5.52
837 910 1.059584 ACCATGTCCCAGTGGTGTCA 61.060 55.000 8.74 4.58 46.55 3.58
850 923 1.067212 GAGACGATCGCCTTACCATGT 59.933 52.381 16.60 0.00 0.00 3.21
869 942 4.659172 CCAGCCCAGGCCAAACGA 62.659 66.667 5.01 0.00 43.17 3.85
901 997 3.682885 TAAACGGACGGCGAGCCA 61.683 61.111 16.62 0.00 35.37 4.75
902 998 3.184003 GTAAACGGACGGCGAGCC 61.184 66.667 16.62 13.92 0.00 4.70
948 1046 2.752154 GCCGAGGACTAGGGAATAGACA 60.752 54.545 0.00 0.00 35.30 3.41
959 1057 2.353610 GGGTTTCGGCCGAGGACTA 61.354 63.158 30.37 16.26 0.00 2.59
995 1097 3.083997 GGTCGTCCTCCATGGCCT 61.084 66.667 6.96 0.00 32.21 5.19
1141 1247 3.458163 CCAGCGGCGGGAGAGTAA 61.458 66.667 14.35 0.00 0.00 2.24
1290 1405 1.213926 GGGAGGAACATGAGCTGGATT 59.786 52.381 0.00 0.00 0.00 3.01
1515 1657 3.437049 CGACATCGTATAGGATGAGCTGA 59.563 47.826 31.89 0.00 45.27 4.26
1549 1693 2.302445 AGATCACACTTTGCAGAGAGCT 59.698 45.455 11.85 0.00 45.94 4.09
1563 1707 2.293318 AAGGCAGCCCGAGATCACA 61.293 57.895 8.22 0.00 35.76 3.58
1572 1716 1.747325 TTTGCAGAACAAGGCAGCCC 61.747 55.000 8.22 0.00 41.68 5.19
1761 1914 1.671979 TCACTCGTATAGTCACGGGG 58.328 55.000 0.20 0.00 46.80 5.73
1764 1917 3.542690 CCGAATCACTCGTATAGTCACG 58.457 50.000 0.00 0.00 46.65 4.35
1848 2023 3.198872 GGCTGCTACCTGAAATACTGTC 58.801 50.000 0.00 0.00 0.00 3.51
1854 2029 1.065126 GTCCTGGCTGCTACCTGAAAT 60.065 52.381 0.00 0.00 0.00 2.17
1879 2060 6.873605 CCTGAATATAGGTATGTTGAATGCGA 59.126 38.462 0.00 0.00 32.99 5.10
1944 2139 3.633525 AGCTGACAGCAAACATTTTCTGA 59.366 39.130 28.43 0.00 45.56 3.27
2085 2280 7.921786 TTTGTAGCAACAGATATAAGCACTT 57.078 32.000 0.00 0.00 36.83 3.16
2119 2321 5.658634 AGATCATAAGTCTGAACCACTGCTA 59.341 40.000 0.00 0.00 0.00 3.49
2177 2388 8.644318 AAATAAACGATATAGTGTCAGGTGAC 57.356 34.615 2.99 2.99 44.97 3.67
2268 2487 5.482878 AGATGGAGTTCAAGGCATTCAATTT 59.517 36.000 0.00 0.00 0.00 1.82
2405 2624 0.867753 CATCTGTAGCTGCCGTCGTC 60.868 60.000 0.00 0.00 0.00 4.20
2581 2815 1.182667 TACCACATCCACACGAGGAG 58.817 55.000 0.00 0.00 41.90 3.69
2617 2851 1.202114 CGCCAGCATCAAAAAGGCTAA 59.798 47.619 0.00 0.00 43.07 3.09
2632 2871 2.219325 GACAGAGAGGGTGACGCCAG 62.219 65.000 7.48 0.00 39.65 4.85
2647 2886 6.267817 CACATAATACCATTGCTTTGGACAG 58.732 40.000 11.80 0.23 39.25 3.51
2648 2887 5.126869 CCACATAATACCATTGCTTTGGACA 59.873 40.000 11.80 1.00 39.25 4.02
2691 2930 7.442364 GCAGAGCTTCACAAGAACCATTATATA 59.558 37.037 0.00 0.00 0.00 0.86
2692 2931 6.261826 GCAGAGCTTCACAAGAACCATTATAT 59.738 38.462 0.00 0.00 0.00 0.86
2693 2932 5.586243 GCAGAGCTTCACAAGAACCATTATA 59.414 40.000 0.00 0.00 0.00 0.98
2694 2933 4.397417 GCAGAGCTTCACAAGAACCATTAT 59.603 41.667 0.00 0.00 0.00 1.28
2708 2947 3.505293 AGAAGACCATTTTGCAGAGCTTC 59.495 43.478 0.00 0.00 0.00 3.86
2711 2950 4.006319 AGTAGAAGACCATTTTGCAGAGC 58.994 43.478 0.00 0.00 0.00 4.09
2739 2978 4.362279 AGTTACAAAGCACTGCATTGTTG 58.638 39.130 25.06 14.74 45.95 3.33
2803 3042 4.637534 ACAATACTAGCAACATTCTGGCTG 59.362 41.667 0.00 0.00 38.55 4.85
2804 3043 4.637534 CACAATACTAGCAACATTCTGGCT 59.362 41.667 0.00 0.00 41.51 4.75
2805 3044 4.396166 ACACAATACTAGCAACATTCTGGC 59.604 41.667 0.00 0.00 0.00 4.85
2806 3045 5.877012 AGACACAATACTAGCAACATTCTGG 59.123 40.000 0.00 0.00 0.00 3.86
2807 3046 6.974932 AGACACAATACTAGCAACATTCTG 57.025 37.500 0.00 0.00 0.00 3.02
2822 3061 8.691661 AGTATTAACCAAACAGAAGACACAAT 57.308 30.769 0.00 0.00 0.00 2.71
2825 3064 7.724305 TGAGTATTAACCAAACAGAAGACAC 57.276 36.000 0.00 0.00 0.00 3.67
2826 3065 8.783093 CAATGAGTATTAACCAAACAGAAGACA 58.217 33.333 0.00 0.00 0.00 3.41
2849 3088 7.437748 CCGACATAGAATAGGAGAGAAACAAT 58.562 38.462 0.00 0.00 0.00 2.71
2874 3113 1.079336 GGTGCTCCCAGTAACGACC 60.079 63.158 0.00 0.00 0.00 4.79
2875 3114 0.389948 CAGGTGCTCCCAGTAACGAC 60.390 60.000 0.00 0.00 34.66 4.34
2959 3198 9.849166 CAAAAGTTACAAGGTTTCTAGACAAAA 57.151 29.630 0.00 0.00 0.00 2.44
2960 3199 9.016438 ACAAAAGTTACAAGGTTTCTAGACAAA 57.984 29.630 0.00 0.00 0.00 2.83
2961 3200 8.570068 ACAAAAGTTACAAGGTTTCTAGACAA 57.430 30.769 0.00 0.00 0.00 3.18
2962 3201 8.044908 AGACAAAAGTTACAAGGTTTCTAGACA 58.955 33.333 0.00 0.00 0.00 3.41
2963 3202 8.434733 AGACAAAAGTTACAAGGTTTCTAGAC 57.565 34.615 0.00 0.00 0.00 2.59
2964 3203 9.760077 CTAGACAAAAGTTACAAGGTTTCTAGA 57.240 33.333 0.00 0.00 0.00 2.43
2965 3204 9.760077 TCTAGACAAAAGTTACAAGGTTTCTAG 57.240 33.333 0.00 0.00 0.00 2.43
2967 3206 9.457436 TTTCTAGACAAAAGTTACAAGGTTTCT 57.543 29.630 0.00 0.00 0.00 2.52
2972 3211 9.774742 GCATATTTCTAGACAAAAGTTACAAGG 57.225 33.333 0.00 0.00 0.00 3.61
2975 3214 9.502091 ACTGCATATTTCTAGACAAAAGTTACA 57.498 29.630 0.00 0.00 0.00 2.41
2978 3217 9.502091 TGTACTGCATATTTCTAGACAAAAGTT 57.498 29.630 0.00 0.00 0.00 2.66
2979 3218 9.155975 CTGTACTGCATATTTCTAGACAAAAGT 57.844 33.333 0.00 0.00 0.00 2.66
2980 3219 9.371136 TCTGTACTGCATATTTCTAGACAAAAG 57.629 33.333 0.00 0.00 0.00 2.27
2998 3237 7.965107 GCATCCAAAGAAATAAACTCTGTACTG 59.035 37.037 0.00 0.00 0.00 2.74
3013 3252 9.995003 AAGTTGTAATAAATTGCATCCAAAGAA 57.005 25.926 0.00 0.00 34.05 2.52
3041 3280 7.071069 TCAAATAGTGATCATACCTGCTGAT 57.929 36.000 0.00 0.00 36.07 2.90
3085 3326 1.339055 GCAGAGACAGGGTTGCACATA 60.339 52.381 0.00 0.00 36.59 2.29
3106 3347 7.831193 ACAGAAGATACATTCTTGCCTAAACAT 59.169 33.333 0.00 0.00 44.88 2.71
3231 3473 7.468084 GCACCTAAATGTACACAGAAGAAACAA 60.468 37.037 0.00 0.00 0.00 2.83
3358 3600 9.113838 GGACAGTTCAACTCATGTAAATATGAT 57.886 33.333 0.00 0.00 36.55 2.45
3362 3604 6.774673 TGGGACAGTTCAACTCATGTAAATA 58.225 36.000 0.00 0.00 0.00 1.40
3389 3632 1.230635 ACAGTAGCTGCGCTTGTTGG 61.231 55.000 9.73 0.00 40.44 3.77
3394 3637 0.668706 CACTCACAGTAGCTGCGCTT 60.669 55.000 9.73 0.00 40.44 4.68
3397 3640 0.457509 CCTCACTCACAGTAGCTGCG 60.458 60.000 0.00 0.00 34.37 5.18
3398 3641 0.891373 TCCTCACTCACAGTAGCTGC 59.109 55.000 0.00 0.00 34.37 5.25
3420 3663 3.619487 GCCTGCTCTCAGAGTTCAGAAAT 60.619 47.826 17.62 0.00 42.95 2.17
3494 3892 1.696063 AAGTGCATCAGCCAAACACT 58.304 45.000 0.00 0.00 43.14 3.55
3515 3913 7.148557 GCTCTGAGTACTCATTTGGTTTAACTC 60.149 40.741 25.35 0.00 39.13 3.01
3524 3922 5.083533 AGGAAGCTCTGAGTACTCATTTG 57.916 43.478 25.35 17.88 39.13 2.32
3563 3966 7.661040 AGCACTTGTAAAATGTAAGCTCAAAT 58.339 30.769 0.00 0.00 0.00 2.32
3567 3970 6.241207 TGAGCACTTGTAAAATGTAAGCTC 57.759 37.500 0.00 0.00 44.45 4.09


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

AutoCloner maintained by Alex Coulton.