Multiple sequence alignment - TraesCS7A01G242900

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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 TraesCS7A01G242900 chr7A 100.000 5102 0 0 1 5102 218248197 218243096 0.000000e+00 9422.0
1 TraesCS7A01G242900 chr7A 80.872 826 155 2 2868 3690 218238184 218237359 0.000000e+00 647.0
2 TraesCS7A01G242900 chr7A 94.000 50 3 0 658 707 33483177 33483226 5.480000e-10 76.8
3 TraesCS7A01G242900 chr7D 95.487 2260 68 15 2036 4289 205749384 205747153 0.000000e+00 3578.0
4 TraesCS7A01G242900 chr7D 96.485 1337 37 3 714 2041 205766373 205765038 0.000000e+00 2200.0
5 TraesCS7A01G242900 chr7D 96.000 675 23 3 1 674 205767046 205766375 0.000000e+00 1094.0
6 TraesCS7A01G242900 chr7D 81.144 822 152 2 2868 3686 205738535 205737714 0.000000e+00 656.0
7 TraesCS7A01G242900 chr7D 88.333 60 3 4 662 718 635426665 635426607 9.170000e-08 69.4
8 TraesCS7A01G242900 chr7B 94.091 1980 80 13 2434 4393 196379270 196381232 0.000000e+00 2974.0
9 TraesCS7A01G242900 chr7B 97.504 1402 31 3 934 2332 196377875 196379275 0.000000e+00 2392.0
10 TraesCS7A01G242900 chr7B 95.672 647 21 6 1 645 196373984 196374625 0.000000e+00 1033.0
11 TraesCS7A01G242900 chr7B 81.356 826 151 2 2868 3690 196384265 196385090 0.000000e+00 669.0
12 TraesCS7A01G242900 chr7B 98.198 111 2 0 812 922 196375167 196375277 1.450000e-45 195.0
13 TraesCS7A01G242900 chr7B 95.000 60 1 2 734 793 196374701 196374758 5.440000e-15 93.5
14 TraesCS7A01G242900 chr7B 100.000 37 0 0 673 709 490679728 490679692 9.170000e-08 69.4
15 TraesCS7A01G242900 chr7B 89.286 56 4 2 665 718 516805205 516805150 9.170000e-08 69.4
16 TraesCS7A01G242900 chr7B 85.294 68 8 2 649 714 697558478 697558545 9.170000e-08 69.4
17 TraesCS7A01G242900 chr5A 97.743 709 14 1 4396 5102 544505844 544506552 0.000000e+00 1219.0
18 TraesCS7A01G242900 chr5A 93.927 708 41 2 4393 5098 23169199 23169906 0.000000e+00 1068.0
19 TraesCS7A01G242900 chr6A 97.595 707 15 2 4396 5102 1956439 1955735 0.000000e+00 1210.0
20 TraesCS7A01G242900 chr6A 95.056 708 34 1 4396 5102 34957092 34957799 0.000000e+00 1112.0
21 TraesCS7A01G242900 chr2A 94.476 706 37 2 4398 5102 637464265 637463561 0.000000e+00 1086.0
22 TraesCS7A01G242900 chr2A 94.184 705 39 2 4396 5098 249756148 249756852 0.000000e+00 1074.0
23 TraesCS7A01G242900 chr1B 94.310 703 39 1 4396 5098 551727237 551727938 0.000000e+00 1075.0
24 TraesCS7A01G242900 chr1B 93.927 708 41 2 4393 5098 95485197 95485904 0.000000e+00 1068.0
25 TraesCS7A01G242900 chr3B 93.689 713 43 2 4388 5098 501981090 501981802 0.000000e+00 1066.0
26 TraesCS7A01G242900 chr6B 80.255 942 174 9 2977 3911 670212895 670213831 0.000000e+00 699.0
27 TraesCS7A01G242900 chr6B 86.885 61 6 2 667 727 475270712 475270654 3.300000e-07 67.6
28 TraesCS7A01G242900 chr6D 79.872 939 180 8 2977 3911 445309058 445309991 0.000000e+00 678.0
29 TraesCS7A01G242900 chr6D 79.144 935 180 10 2977 3902 445263301 445264229 2.590000e-177 632.0
30 TraesCS7A01G242900 chrUn 78.648 932 178 18 2966 3892 79232535 79233450 2.630000e-167 599.0
31 TraesCS7A01G242900 chr5D 93.878 49 1 2 665 712 502881724 502881677 7.090000e-09 73.1
32 TraesCS7A01G242900 chr4B 93.750 48 3 0 665 712 638146271 638146318 7.090000e-09 73.1
33 TraesCS7A01G242900 chr1A 89.091 55 5 1 673 726 508630999 508630945 3.300000e-07 67.6


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 TraesCS7A01G242900 chr7A 218243096 218248197 5101 True 9422.000000 9422 100.000000 1 5102 1 chr7A.!!$R2 5101
1 TraesCS7A01G242900 chr7A 218237359 218238184 825 True 647.000000 647 80.872000 2868 3690 1 chr7A.!!$R1 822
2 TraesCS7A01G242900 chr7D 205747153 205749384 2231 True 3578.000000 3578 95.487000 2036 4289 1 chr7D.!!$R2 2253
3 TraesCS7A01G242900 chr7D 205765038 205767046 2008 True 1647.000000 2200 96.242500 1 2041 2 chr7D.!!$R4 2040
4 TraesCS7A01G242900 chr7D 205737714 205738535 821 True 656.000000 656 81.144000 2868 3686 1 chr7D.!!$R1 818
5 TraesCS7A01G242900 chr7B 196373984 196385090 11106 False 1226.083333 2974 93.636833 1 4393 6 chr7B.!!$F2 4392
6 TraesCS7A01G242900 chr5A 544505844 544506552 708 False 1219.000000 1219 97.743000 4396 5102 1 chr5A.!!$F2 706
7 TraesCS7A01G242900 chr5A 23169199 23169906 707 False 1068.000000 1068 93.927000 4393 5098 1 chr5A.!!$F1 705
8 TraesCS7A01G242900 chr6A 1955735 1956439 704 True 1210.000000 1210 97.595000 4396 5102 1 chr6A.!!$R1 706
9 TraesCS7A01G242900 chr6A 34957092 34957799 707 False 1112.000000 1112 95.056000 4396 5102 1 chr6A.!!$F1 706
10 TraesCS7A01G242900 chr2A 637463561 637464265 704 True 1086.000000 1086 94.476000 4398 5102 1 chr2A.!!$R1 704
11 TraesCS7A01G242900 chr2A 249756148 249756852 704 False 1074.000000 1074 94.184000 4396 5098 1 chr2A.!!$F1 702
12 TraesCS7A01G242900 chr1B 551727237 551727938 701 False 1075.000000 1075 94.310000 4396 5098 1 chr1B.!!$F2 702
13 TraesCS7A01G242900 chr1B 95485197 95485904 707 False 1068.000000 1068 93.927000 4393 5098 1 chr1B.!!$F1 705
14 TraesCS7A01G242900 chr3B 501981090 501981802 712 False 1066.000000 1066 93.689000 4388 5098 1 chr3B.!!$F1 710
15 TraesCS7A01G242900 chr6B 670212895 670213831 936 False 699.000000 699 80.255000 2977 3911 1 chr6B.!!$F1 934
16 TraesCS7A01G242900 chr6D 445309058 445309991 933 False 678.000000 678 79.872000 2977 3911 1 chr6D.!!$F2 934
17 TraesCS7A01G242900 chr6D 445263301 445264229 928 False 632.000000 632 79.144000 2977 3902 1 chr6D.!!$F1 925
18 TraesCS7A01G242900 chrUn 79232535 79233450 915 False 599.000000 599 78.648000 2966 3892 1 chrUn.!!$F1 926

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
690 692 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.0 0.00 0.0 0.00 2.74 F
1808 4800 0.872881 CGCAGCAGCAACAGCTTTTT 60.873 50.0 0.82 0.0 41.14 1.94 F
2517 5509 0.745845 AAGATGGCAGATGCGGACAC 60.746 55.0 0.00 0.0 43.26 3.67 F
4020 7024 0.108585 TCGCCAAGAAGGATATGCCC 59.891 55.0 0.00 0.0 41.22 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 5191 0.110373 GCAGTAAAACGTTCCAGGCG 60.110 55.000 0.00 0.00 0.00 5.52 R
2740 5734 1.893137 CTTCCAAAAGTTGTAGGGGGC 59.107 52.381 0.00 0.00 0.00 5.80 R
4075 7082 0.035056 GGGTACCTTGCTGACAGCAT 60.035 55.000 29.77 18.02 46.77 3.79 R
5051 10275 4.200092 GTCTGGTCCATCTTCCCAATAAC 58.800 47.826 0.00 0.00 0.00 1.89 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
224 226 2.828868 GCAGGCCATGGTCGGATA 59.171 61.111 21.42 0.00 0.00 2.59
225 227 1.598130 GCAGGCCATGGTCGGATAC 60.598 63.158 21.42 0.00 0.00 2.24
312 314 3.379372 CCATCCACCATTTTGTGAGCTAG 59.621 47.826 0.00 0.00 38.55 3.42
313 315 3.788227 TCCACCATTTTGTGAGCTAGT 57.212 42.857 0.00 0.00 38.55 2.57
315 317 4.575885 TCCACCATTTTGTGAGCTAGTAC 58.424 43.478 0.00 0.00 38.55 2.73
316 318 4.286032 TCCACCATTTTGTGAGCTAGTACT 59.714 41.667 0.00 0.00 38.55 2.73
317 319 5.482526 TCCACCATTTTGTGAGCTAGTACTA 59.517 40.000 1.89 1.89 38.55 1.82
318 320 5.581085 CCACCATTTTGTGAGCTAGTACTAC 59.419 44.000 0.00 0.00 38.55 2.73
327 329 2.288458 GAGCTAGTACTACGCCAGACAG 59.712 54.545 16.09 1.14 0.00 3.51
396 398 6.072230 CCAGCATCTATGAATTCTCTACTCGA 60.072 42.308 7.05 0.00 0.00 4.04
435 437 0.750182 GCCCCTAATTGCGGCTTGTA 60.750 55.000 0.00 0.00 39.70 2.41
608 610 5.261209 TGAATTGTGGGAGTTTTCTTGTG 57.739 39.130 0.00 0.00 0.00 3.33
679 681 9.508642 AAAATCTATAGCTTAATTGCTACTCCC 57.491 33.333 0.00 0.00 46.60 4.30
680 682 8.442660 AATCTATAGCTTAATTGCTACTCCCT 57.557 34.615 0.00 0.00 46.60 4.20
681 683 7.469537 TCTATAGCTTAATTGCTACTCCCTC 57.530 40.000 0.00 0.00 46.60 4.30
682 684 3.847671 AGCTTAATTGCTACTCCCTCC 57.152 47.619 0.00 0.00 42.10 4.30
683 685 2.103263 AGCTTAATTGCTACTCCCTCCG 59.897 50.000 0.00 0.00 42.10 4.63
684 686 2.158943 GCTTAATTGCTACTCCCTCCGT 60.159 50.000 0.00 0.00 0.00 4.69
685 687 3.718815 CTTAATTGCTACTCCCTCCGTC 58.281 50.000 0.00 0.00 0.00 4.79
686 688 0.831307 AATTGCTACTCCCTCCGTCC 59.169 55.000 0.00 0.00 0.00 4.79
687 689 1.049289 ATTGCTACTCCCTCCGTCCC 61.049 60.000 0.00 0.00 0.00 4.46
688 690 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
689 691 1.457831 GCTACTCCCTCCGTCCCAT 60.458 63.158 0.00 0.00 0.00 4.00
690 692 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.000 0.00 0.00 0.00 2.74
691 693 1.756690 GCTACTCCCTCCGTCCCATAA 60.757 57.143 0.00 0.00 0.00 1.90
692 694 2.890814 CTACTCCCTCCGTCCCATAAT 58.109 52.381 0.00 0.00 0.00 1.28
693 695 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
694 696 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
695 697 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
696 698 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
697 699 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
698 700 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
699 701 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
701 703 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
702 704 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
703 705 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
704 706 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
705 707 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
853 1256 3.615224 TTGGGTCGTTAGGTGGATTAC 57.385 47.619 0.00 0.00 0.00 1.89
1128 4120 3.326521 TGGTAACATCAGCATCCCCTAT 58.673 45.455 0.00 0.00 46.17 2.57
1134 4126 3.009916 ACATCAGCATCCCCTATCCATTC 59.990 47.826 0.00 0.00 0.00 2.67
1161 4153 2.492012 GAGCCTGATTGCTACCATGAG 58.508 52.381 0.00 0.00 42.95 2.90
1170 4162 3.951563 TGCTACCATGAGGGCTTTAAT 57.048 42.857 0.00 0.00 42.05 1.40
1187 4179 6.166982 GCTTTAATCTCACCTGTGACTACTT 58.833 40.000 0.00 0.00 35.46 2.24
1377 4369 2.823154 CAGAGAGAGAGGACCGTTCTTT 59.177 50.000 2.81 0.00 0.00 2.52
1386 4378 2.054140 GACCGTTCTTTGTTGCGCCA 62.054 55.000 4.18 0.00 0.00 5.69
1752 4744 2.306805 AGACTGGGTGATCAGCAATTCA 59.693 45.455 25.18 13.23 38.26 2.57
1808 4800 0.872881 CGCAGCAGCAACAGCTTTTT 60.873 50.000 0.82 0.00 41.14 1.94
1990 4982 6.969828 ACAACTTAAACTCAGTAGCTATGC 57.030 37.500 0.00 0.00 0.00 3.14
2199 5191 4.180057 TGCCATGGAATTTGCGAAAATAC 58.820 39.130 18.40 0.00 0.00 1.89
2209 5201 3.869866 CGAAAATACGCCTGGAACG 57.130 52.632 0.00 0.00 0.00 3.95
2416 5408 6.730960 TTGGTAACCGTTCACTGATTAATC 57.269 37.500 8.60 8.60 0.00 1.75
2417 5409 5.795972 TGGTAACCGTTCACTGATTAATCA 58.204 37.500 17.07 17.07 35.16 2.57
2484 5476 2.236146 ACATCGCTGGAATGTTACCTCA 59.764 45.455 0.00 0.00 0.00 3.86
2517 5509 0.745845 AAGATGGCAGATGCGGACAC 60.746 55.000 0.00 0.00 43.26 3.67
2679 5673 7.390027 ACCTATCATGGCTATTCACTAATGAC 58.610 38.462 0.00 0.00 33.38 3.06
2680 5674 7.236432 ACCTATCATGGCTATTCACTAATGACT 59.764 37.037 0.00 0.00 33.38 3.41
2681 5675 8.753133 CCTATCATGGCTATTCACTAATGACTA 58.247 37.037 0.00 0.00 33.38 2.59
2684 5678 8.837788 TCATGGCTATTCACTAATGACTAATG 57.162 34.615 0.00 0.00 33.38 1.90
2685 5679 8.650490 TCATGGCTATTCACTAATGACTAATGA 58.350 33.333 0.00 0.00 33.38 2.57
2736 5730 8.680903 CACTTCCACTCTGCTATTTATTTTGAT 58.319 33.333 0.00 0.00 0.00 2.57
3503 6500 7.372260 ACATACTTCTGGATGAGAGCTTAAT 57.628 36.000 0.00 0.00 30.18 1.40
3726 6730 2.371841 AGATAATGATGCCGGCCTTGTA 59.628 45.455 26.77 10.22 0.00 2.41
3915 6919 2.331194 CTTGAAAATTTGCGAGCCAGG 58.669 47.619 0.09 0.00 0.00 4.45
3932 6936 0.255318 AGGAAGAAGCCTGCTCCATG 59.745 55.000 0.00 0.00 36.76 3.66
3943 6947 3.965292 CTGCTCCATGTAATTCAGCAG 57.035 47.619 4.93 4.93 45.18 4.24
3960 6964 0.855349 CAGCAATGAGATACGACGGC 59.145 55.000 0.00 0.00 0.00 5.68
3984 6988 6.293081 GCGATCAGATTGTTGTGCAGTATAAT 60.293 38.462 0.00 0.00 0.00 1.28
4020 7024 0.108585 TCGCCAAGAAGGATATGCCC 59.891 55.000 0.00 0.00 41.22 5.36
4040 7044 1.463214 TTGAAGGGGGTGCTGAGGA 60.463 57.895 0.00 0.00 0.00 3.71
4056 7060 4.046938 TGAGGAATCGAGCAGACAATAC 57.953 45.455 0.00 0.00 0.00 1.89
4075 7082 7.861629 ACAATACACTATGGAAGAGGAAATCA 58.138 34.615 0.00 0.00 0.00 2.57
4103 7110 2.705658 CAGCAAGGTACCCCAGATGATA 59.294 50.000 8.74 0.00 29.10 2.15
4154 7161 5.673068 GCTCTGTTTGTATGACAATGAGCAG 60.673 44.000 22.80 15.47 45.03 4.24
4167 7174 7.052248 TGACAATGAGCAGATGTTCTTCATAT 58.948 34.615 0.00 0.00 36.83 1.78
4194 7201 3.114650 TCGAGGCATGCTCGAGAG 58.885 61.111 27.16 6.09 46.56 3.20
4217 7227 6.465948 AGAAAAATGTGCAAATATTCCTGCA 58.534 32.000 10.15 10.15 46.01 4.41
4261 7271 7.686938 CGAATTTGATAGTTTTTCTGTACCGAC 59.313 37.037 0.00 0.00 0.00 4.79
4262 7272 7.972832 ATTTGATAGTTTTTCTGTACCGACA 57.027 32.000 0.00 0.00 0.00 4.35
4279 7289 2.664916 GACAGTTTTGCGTGCATGAAT 58.335 42.857 10.93 0.00 0.00 2.57
4302 7312 6.783708 TTCCATTAGACCTGTGTTTTTGTT 57.216 33.333 0.00 0.00 0.00 2.83
4313 7323 8.057536 ACCTGTGTTTTTGTTTATGTCAGTTA 57.942 30.769 0.00 0.00 0.00 2.24
4322 7332 6.730960 TGTTTATGTCAGTTAAATCGGGTC 57.269 37.500 0.00 0.00 0.00 4.46
4329 7354 5.421056 TGTCAGTTAAATCGGGTCTCACTAT 59.579 40.000 0.00 0.00 0.00 2.12
4354 7379 2.979813 GTTTGTGCCAATGAAAGCGTAG 59.020 45.455 0.00 0.00 0.00 3.51
4358 7383 2.484264 GTGCCAATGAAAGCGTAGAGTT 59.516 45.455 0.00 0.00 0.00 3.01
4360 7385 3.058293 TGCCAATGAAAGCGTAGAGTTTG 60.058 43.478 0.00 0.00 0.00 2.93
4389 7414 4.996434 GCTGCGGGATGGCGCTAT 62.996 66.667 5.72 5.72 35.06 2.97
4393 7418 2.734723 CGGGATGGCGCTATCGTG 60.735 66.667 24.95 16.67 38.14 4.35
5003 10225 5.596836 TTCTGTGTTTCTTTTTGGCTGAT 57.403 34.783 0.00 0.00 0.00 2.90
5051 10275 3.936453 CCATCAAATCCTTGCCAACATTG 59.064 43.478 0.00 0.00 32.14 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
224 226 3.839432 GGCTTAGCTCCTCCGCGT 61.839 66.667 4.92 0.00 34.40 6.01
225 227 3.532155 AGGCTTAGCTCCTCCGCG 61.532 66.667 3.59 0.00 34.40 6.46
327 329 3.010420 GAGGTGGATGTTTACTTGAGCC 58.990 50.000 0.00 0.00 0.00 4.70
396 398 5.234752 GGGCAAAAATAACGGAACTTGATT 58.765 37.500 0.00 0.00 0.00 2.57
435 437 7.121907 AGCTATATCACACTCATCGATGTGTAT 59.878 37.037 27.34 20.61 44.43 2.29
598 600 6.454795 TCCTTTGGCAATATCACAAGAAAAC 58.545 36.000 0.00 0.00 0.00 2.43
608 610 2.554032 CCGGTCATCCTTTGGCAATATC 59.446 50.000 0.00 0.00 0.00 1.63
670 672 2.043248 GGGACGGAGGGAGTAGCA 60.043 66.667 0.00 0.00 0.00 3.49
674 676 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
675 677 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
676 678 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
678 680 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
679 681 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
680 682 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
708 710 9.490379 GGTTTGTCGACATTTTCCTATCTATAT 57.510 33.333 20.80 0.00 0.00 0.86
709 711 7.929785 GGGTTTGTCGACATTTTCCTATCTATA 59.070 37.037 20.80 0.00 0.00 1.31
710 712 6.766467 GGGTTTGTCGACATTTTCCTATCTAT 59.234 38.462 20.80 0.00 0.00 1.98
722 724 0.882927 CGTGTGGGGTTTGTCGACAT 60.883 55.000 20.80 0.00 0.00 3.06
723 725 1.521906 CGTGTGGGGTTTGTCGACA 60.522 57.895 15.76 15.76 0.00 4.35
725 727 2.109387 CCGTGTGGGGTTTGTCGA 59.891 61.111 0.00 0.00 0.00 4.20
853 1256 7.370383 ACTGGTACTGCTCAATTTTTGTATTG 58.630 34.615 0.00 0.00 36.95 1.90
1060 4052 2.231478 TCACCACTGCACTTAGTAGCTC 59.769 50.000 0.00 0.00 32.54 4.09
1161 4153 3.010420 GTCACAGGTGAGATTAAAGCCC 58.990 50.000 1.66 0.00 40.75 5.19
1170 4162 3.825014 GGTACAAGTAGTCACAGGTGAGA 59.175 47.826 1.66 0.00 40.75 3.27
1187 4179 1.420532 AAGTTTGGGAGGGCGGTACA 61.421 55.000 0.00 0.00 0.00 2.90
1263 4255 2.106477 TATTGGTGCTGTTGATGCGA 57.894 45.000 0.00 0.00 0.00 5.10
1377 4369 0.323302 TGTTCCTATCTGGCGCAACA 59.677 50.000 10.83 5.56 35.26 3.33
1808 4800 7.929245 TGTAGACATAGCTTGTGTAGTTTTGAA 59.071 33.333 0.00 0.00 39.18 2.69
2199 5191 0.110373 GCAGTAAAACGTTCCAGGCG 60.110 55.000 0.00 0.00 0.00 5.52
2209 5201 1.971695 AGGGCAGCGGCAGTAAAAC 60.972 57.895 11.88 0.00 43.71 2.43
2484 5476 5.033589 TGCCATCTTGACAAAAATGGTTT 57.966 34.783 21.65 0.00 40.66 3.27
2680 5674 8.716931 TGCCATTGCCAAATGACTAGTTCATTA 61.717 37.037 16.08 5.84 44.66 1.90
2681 5675 7.978793 TGCCATTGCCAAATGACTAGTTCATT 61.979 38.462 12.15 12.15 46.11 2.57
2682 5676 6.563798 TGCCATTGCCAAATGACTAGTTCAT 61.564 40.000 0.00 0.00 45.17 2.57
2683 5677 3.193267 GCCATTGCCAAATGACTAGTTCA 59.807 43.478 0.00 0.00 45.17 3.18
2684 5678 3.193267 TGCCATTGCCAAATGACTAGTTC 59.807 43.478 0.00 0.00 45.17 3.01
2685 5679 3.164268 TGCCATTGCCAAATGACTAGTT 58.836 40.909 0.00 0.00 45.17 2.24
2736 5730 3.076182 TCCAAAAGTTGTAGGGGGCAATA 59.924 43.478 0.00 0.00 0.00 1.90
2740 5734 1.893137 CTTCCAAAAGTTGTAGGGGGC 59.107 52.381 0.00 0.00 0.00 5.80
3503 6500 4.724399 TCCAAAATCTGACACCTTTGCTA 58.276 39.130 0.00 0.00 0.00 3.49
3726 6730 4.392047 TGAGTGATGAGACAAAATGTGCT 58.608 39.130 0.00 0.00 0.00 4.40
3915 6919 2.698855 TACATGGAGCAGGCTTCTTC 57.301 50.000 0.60 0.00 0.00 2.87
3932 6936 5.463392 TCGTATCTCATTGCTGCTGAATTAC 59.537 40.000 0.00 1.93 0.00 1.89
3943 6947 0.594028 TCGCCGTCGTATCTCATTGC 60.594 55.000 0.00 0.00 36.96 3.56
3960 6964 6.588348 TTATACTGCACAACAATCTGATCG 57.412 37.500 0.00 0.00 0.00 3.69
3984 6988 6.429692 TCTTGGCGAGTAAATCTTCAATTGAA 59.570 34.615 19.45 19.45 0.00 2.69
4020 7024 1.672356 CTCAGCACCCCCTTCAACG 60.672 63.158 0.00 0.00 0.00 4.10
4031 7035 0.174389 TCTGCTCGATTCCTCAGCAC 59.826 55.000 0.00 0.00 38.25 4.40
4035 7039 3.447229 TGTATTGTCTGCTCGATTCCTCA 59.553 43.478 0.00 0.00 0.00 3.86
4040 7044 5.069119 TCCATAGTGTATTGTCTGCTCGATT 59.931 40.000 0.00 0.00 0.00 3.34
4056 7060 5.238868 CAGCATGATTTCCTCTTCCATAGTG 59.761 44.000 0.00 0.00 39.69 2.74
4075 7082 0.035056 GGGTACCTTGCTGACAGCAT 60.035 55.000 29.77 18.02 46.77 3.79
4103 7110 2.634453 CCTTTGTTCAGGCCCAAAAGAT 59.366 45.455 0.00 0.00 30.75 2.40
4154 7161 5.725110 AGCGTGTCAATATGAAGAACATC 57.275 39.130 0.00 0.00 40.07 3.06
4167 7174 1.005037 ATGCCTCGAAGCGTGTCAA 60.005 52.632 0.00 0.00 34.65 3.18
4194 7201 6.724694 TGCAGGAATATTTGCACATTTTTC 57.275 33.333 10.15 0.00 44.72 2.29
4217 7227 6.500684 AATTCGTGACTTCAGCACAATAAT 57.499 33.333 0.00 0.00 36.06 1.28
4261 7271 2.409378 GGAATTCATGCACGCAAAACTG 59.591 45.455 7.93 0.00 0.00 3.16
4262 7272 2.035704 TGGAATTCATGCACGCAAAACT 59.964 40.909 7.93 0.00 0.00 2.66
4279 7289 6.783708 AACAAAAACACAGGTCTAATGGAA 57.216 33.333 0.00 0.00 0.00 3.53
4302 7312 6.070995 AGTGAGACCCGATTTAACTGACATAA 60.071 38.462 0.00 0.00 0.00 1.90
4313 7323 3.375699 ACTGGATAGTGAGACCCGATTT 58.624 45.455 0.00 0.00 35.34 2.17
4318 7328 3.600388 CACAAACTGGATAGTGAGACCC 58.400 50.000 0.00 0.00 37.19 4.46
4322 7332 3.057969 TGGCACAAACTGGATAGTGAG 57.942 47.619 0.00 0.00 37.19 3.51
4386 7411 3.546020 CGCTTGCATTTTACCCACGATAG 60.546 47.826 0.00 0.00 46.19 2.08
4389 7414 0.519519 CGCTTGCATTTTACCCACGA 59.480 50.000 0.00 0.00 0.00 4.35
4393 7418 1.516169 CCGCGCTTGCATTTTACCC 60.516 57.895 5.56 0.00 39.07 3.69
4785 8031 1.383523 GCGAGAAAAGGGCTAATGCT 58.616 50.000 0.00 0.00 39.59 3.79
5051 10275 4.200092 GTCTGGTCCATCTTCCCAATAAC 58.800 47.826 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.