Multiple sequence alignment - TraesCS3B01G103600

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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 TraesCS3B01G103600 chr3B 100.000 4508 0 0 1 4508 70309779 70314286 0.000000e+00 8325.0
1 TraesCS3B01G103600 chr3B 100.000 316 0 0 427 742 70305002 70305317 6.500000e-163 584.0
2 TraesCS3B01G103600 chr3A 94.474 1900 82 3 744 2642 56768086 56769963 0.000000e+00 2905.0
3 TraesCS3B01G103600 chr3A 91.010 1891 108 20 2630 4508 56770483 56772323 0.000000e+00 2494.0
4 TraesCS3B01G103600 chr7A 82.975 2555 377 41 987 3504 16721553 16719020 0.000000e+00 2255.0
5 TraesCS3B01G103600 chr7A 79.968 2471 392 61 1107 3498 42456088 42453642 0.000000e+00 1725.0
6 TraesCS3B01G103600 chr7A 81.538 910 129 25 2505 3410 580655807 580654933 0.000000e+00 713.0
7 TraesCS3B01G103600 chr7A 81.250 112 18 1 1155 1263 580657218 580657107 2.230000e-13 87.9
8 TraesCS3B01G103600 chr4A 82.401 2557 384 35 987 3504 716935159 716937688 0.000000e+00 2169.0
9 TraesCS3B01G103600 chr4A 79.879 2470 387 65 1123 3504 650314283 650311836 0.000000e+00 1707.0
10 TraesCS3B01G103600 chr4A 96.475 766 3 1 1 742 551210029 551209264 0.000000e+00 1243.0
11 TraesCS3B01G103600 chr4A 96.354 768 2 4 1 742 590218339 590219106 0.000000e+00 1240.0
12 TraesCS3B01G103600 chr4A 96.229 769 5 1 1 745 601296591 601295823 0.000000e+00 1238.0
13 TraesCS3B01G103600 chr4A 96.214 766 3 3 1 742 540076059 540076822 0.000000e+00 1230.0
14 TraesCS3B01G103600 chr4A 86.597 1052 124 14 2457 3498 740178701 740179745 0.000000e+00 1146.0
15 TraesCS3B01G103600 chr4A 86.381 1050 127 14 2457 3498 739762109 739763150 0.000000e+00 1133.0
16 TraesCS3B01G103600 chr4A 98.973 292 3 0 451 742 601302829 601302538 1.440000e-144 523.0
17 TraesCS3B01G103600 chr4A 81.607 647 100 15 2858 3498 650291123 650290490 6.680000e-143 518.0
18 TraesCS3B01G103600 chr7D 81.278 1987 307 46 1552 3498 42801897 42799936 0.000000e+00 1548.0
19 TraesCS3B01G103600 chr7D 82.982 1140 171 12 987 2111 17399851 17398720 0.000000e+00 1009.0
20 TraesCS3B01G103600 chr7D 79.021 143 27 1 1124 1263 509697856 509697998 1.340000e-15 95.3
21 TraesCS3B01G103600 chr3D 90.645 1101 80 11 3414 4508 45018792 45019875 0.000000e+00 1441.0
22 TraesCS3B01G103600 chr2B 96.099 769 4 3 1 745 382238645 382237879 0.000000e+00 1230.0
23 TraesCS3B01G103600 chr6A 96.084 766 4 3 1 742 387982692 387983455 0.000000e+00 1225.0
24 TraesCS3B01G103600 chr6A 95.238 777 2 2 1 742 79279439 79278663 0.000000e+00 1197.0
25 TraesCS3B01G103600 chr6A 95.238 777 2 2 1 742 573852408 573851632 0.000000e+00 1197.0
26 TraesCS3B01G103600 chr6A 100.000 292 0 0 451 742 169516175 169516466 1.430000e-149 540.0
27 TraesCS3B01G103600 chr5B 96.084 766 5 2 1 742 22522066 22521302 0.000000e+00 1225.0
28 TraesCS3B01G103600 chr5B 94.783 115 6 0 4394 4508 67402643 67402757 3.580000e-41 180.0
29 TraesCS3B01G103600 chr1A 96.084 766 4 3 1 742 557474158 557474921 0.000000e+00 1225.0
30 TraesCS3B01G103600 chr1A 94.981 777 4 2 1 742 136941130 136940354 0.000000e+00 1186.0
31 TraesCS3B01G103600 chr4B 95.692 766 7 3 1 742 311355160 311354397 0.000000e+00 1208.0
32 TraesCS3B01G103600 chr6B 95.238 777 2 2 1 742 713735315 713734539 0.000000e+00 1197.0
33 TraesCS3B01G103600 chr2A 95.039 766 1 2 1 742 709853620 709852868 0.000000e+00 1170.0
34 TraesCS3B01G103600 chr7B 94.783 115 6 0 4394 4508 183942510 183942396 3.580000e-41 180.0
35 TraesCS3B01G103600 chr7B 82.143 112 17 1 1155 1263 538207946 538207835 4.800000e-15 93.5
36 TraesCS3B01G103600 chrUn 93.913 115 7 0 4394 4508 81709138 81709024 1.670000e-39 174.0
37 TraesCS3B01G103600 chrUn 93.913 115 7 0 4394 4508 433791318 433791432 1.670000e-39 174.0
38 TraesCS3B01G103600 chrUn 93.913 115 7 0 4394 4508 457177537 457177651 1.670000e-39 174.0
39 TraesCS3B01G103600 chrUn 93.913 115 7 0 4394 4508 464449023 464449137 1.670000e-39 174.0
40 TraesCS3B01G103600 chrUn 93.913 115 7 0 4394 4508 465368302 465368416 1.670000e-39 174.0


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 TraesCS3B01G103600 chr3B 70309779 70314286 4507 False 8325.00 8325 100.000 1 4508 1 chr3B.!!$F2 4507
1 TraesCS3B01G103600 chr3A 56768086 56772323 4237 False 2699.50 2905 92.742 744 4508 2 chr3A.!!$F1 3764
2 TraesCS3B01G103600 chr7A 16719020 16721553 2533 True 2255.00 2255 82.975 987 3504 1 chr7A.!!$R1 2517
3 TraesCS3B01G103600 chr7A 42453642 42456088 2446 True 1725.00 1725 79.968 1107 3498 1 chr7A.!!$R2 2391
4 TraesCS3B01G103600 chr7A 580654933 580657218 2285 True 400.45 713 81.394 1155 3410 2 chr7A.!!$R3 2255
5 TraesCS3B01G103600 chr4A 716935159 716937688 2529 False 2169.00 2169 82.401 987 3504 1 chr4A.!!$F3 2517
6 TraesCS3B01G103600 chr4A 650311836 650314283 2447 True 1707.00 1707 79.879 1123 3504 1 chr4A.!!$R5 2381
7 TraesCS3B01G103600 chr4A 551209264 551210029 765 True 1243.00 1243 96.475 1 742 1 chr4A.!!$R1 741
8 TraesCS3B01G103600 chr4A 590218339 590219106 767 False 1240.00 1240 96.354 1 742 1 chr4A.!!$F2 741
9 TraesCS3B01G103600 chr4A 601295823 601296591 768 True 1238.00 1238 96.229 1 745 1 chr4A.!!$R2 744
10 TraesCS3B01G103600 chr4A 540076059 540076822 763 False 1230.00 1230 96.214 1 742 1 chr4A.!!$F1 741
11 TraesCS3B01G103600 chr4A 740178701 740179745 1044 False 1146.00 1146 86.597 2457 3498 1 chr4A.!!$F5 1041
12 TraesCS3B01G103600 chr4A 739762109 739763150 1041 False 1133.00 1133 86.381 2457 3498 1 chr4A.!!$F4 1041
13 TraesCS3B01G103600 chr4A 650290490 650291123 633 True 518.00 518 81.607 2858 3498 1 chr4A.!!$R4 640
14 TraesCS3B01G103600 chr7D 42799936 42801897 1961 True 1548.00 1548 81.278 1552 3498 1 chr7D.!!$R2 1946
15 TraesCS3B01G103600 chr7D 17398720 17399851 1131 True 1009.00 1009 82.982 987 2111 1 chr7D.!!$R1 1124
16 TraesCS3B01G103600 chr3D 45018792 45019875 1083 False 1441.00 1441 90.645 3414 4508 1 chr3D.!!$F1 1094
17 TraesCS3B01G103600 chr2B 382237879 382238645 766 True 1230.00 1230 96.099 1 745 1 chr2B.!!$R1 744
18 TraesCS3B01G103600 chr6A 387982692 387983455 763 False 1225.00 1225 96.084 1 742 1 chr6A.!!$F2 741
19 TraesCS3B01G103600 chr6A 79278663 79279439 776 True 1197.00 1197 95.238 1 742 1 chr6A.!!$R1 741
20 TraesCS3B01G103600 chr6A 573851632 573852408 776 True 1197.00 1197 95.238 1 742 1 chr6A.!!$R2 741
21 TraesCS3B01G103600 chr5B 22521302 22522066 764 True 1225.00 1225 96.084 1 742 1 chr5B.!!$R1 741
22 TraesCS3B01G103600 chr1A 557474158 557474921 763 False 1225.00 1225 96.084 1 742 1 chr1A.!!$F1 741
23 TraesCS3B01G103600 chr1A 136940354 136941130 776 True 1186.00 1186 94.981 1 742 1 chr1A.!!$R1 741
24 TraesCS3B01G103600 chr4B 311354397 311355160 763 True 1208.00 1208 95.692 1 742 1 chr4B.!!$R1 741
25 TraesCS3B01G103600 chr6B 713734539 713735315 776 True 1197.00 1197 95.238 1 742 1 chr6B.!!$R1 741
26 TraesCS3B01G103600 chr2A 709852868 709853620 752 True 1170.00 1170 95.039 1 742 1 chr2A.!!$R1 741

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
461 462 1.066358 GTGTACTAGGGTCCTTGTGGC 60.066 57.143 13.01 7.41 34.25 5.01 F
1464 1596 0.035725 TCGTGCTAAGAGACTCCGGA 60.036 55.000 2.93 2.93 0.00 5.14 F
2685 3438 0.101399 ATAGCGAGCAGGAGTTCACG 59.899 55.000 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2446 2665 0.320683 TGATGTGCCAGAAGTCGGTG 60.321 55.0 0.0 0.0 0.00 4.94 R
3093 3849 0.180406 ACACATCCGCCTTGGTATCC 59.820 55.0 0.0 0.0 39.52 2.59 R
3843 4646 0.252330 TTACGAGGTGGGGTCATGGA 60.252 55.0 0.0 0.0 0.00 3.41 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
461 462 1.066358 GTGTACTAGGGTCCTTGTGGC 60.066 57.143 13.01 7.41 34.25 5.01
462 463 1.272807 GTACTAGGGTCCTTGTGGCA 58.727 55.000 13.01 0.00 34.25 4.92
463 464 1.207329 GTACTAGGGTCCTTGTGGCAG 59.793 57.143 13.01 0.00 34.25 4.85
742 815 2.737252 GCTCAGGTTGAAAGGTCTAACG 59.263 50.000 0.00 0.00 0.00 3.18
751 824 3.006537 TGAAAGGTCTAACGGAAGACTGG 59.993 47.826 16.13 0.00 44.42 4.00
759 832 1.949465 ACGGAAGACTGGTTGACAAC 58.051 50.000 9.97 9.97 0.00 3.32
784 857 2.173356 TGGAAATATCTGCACCTGGGAG 59.827 50.000 0.00 0.00 36.05 4.30
817 890 3.062774 GCAAAGAGAGGACTAAATCACGC 59.937 47.826 0.00 0.00 0.00 5.34
853 926 3.137544 TCCAACTAAAGGAAGCAAGACCA 59.862 43.478 0.00 0.00 30.71 4.02
1025 1099 2.281070 CACGAAGCTGTGGCCTGT 60.281 61.111 3.32 0.00 39.73 4.00
1041 1116 0.391528 CTGTGGTCATCATGTCGGCA 60.392 55.000 0.00 0.00 0.00 5.69
1056 1131 4.712425 GCACTGCCCAGCTTTGCG 62.712 66.667 0.00 0.00 30.37 4.85
1140 1221 2.125512 GCGCGGACCAATCTGACT 60.126 61.111 8.83 0.00 32.26 3.41
1149 1230 1.528824 CAATCTGACTGCGGGGGAT 59.471 57.895 0.00 0.00 0.00 3.85
1302 1419 2.115911 GTCGGTGGTGTGGTTTGCA 61.116 57.895 0.00 0.00 0.00 4.08
1368 1488 3.933722 CTCAGCATCCCGGCCGAT 61.934 66.667 30.73 10.80 0.00 4.18
1416 1548 2.763988 TAGAGCTGTGGAAGGCCCCA 62.764 60.000 0.00 0.00 0.00 4.96
1464 1596 0.035725 TCGTGCTAAGAGACTCCGGA 60.036 55.000 2.93 2.93 0.00 5.14
1534 1684 2.645567 CGACAGACACGCTCCTGT 59.354 61.111 4.20 4.20 45.37 4.00
1593 1767 0.389391 CGGACACAGAGTTCACCACT 59.611 55.000 0.00 0.00 39.07 4.00
1906 2104 3.476552 GAGAACACAACATCTTGGACCA 58.523 45.455 0.00 0.00 0.00 4.02
2013 2211 1.801178 GAGACCAAAGAACGGCTCAAG 59.199 52.381 0.00 0.00 31.18 3.02
2211 2415 2.512896 GAGGAGCAATGCCGGGAT 59.487 61.111 0.92 0.92 0.00 3.85
2337 2541 1.003118 ACAAAGGCGCTGATCAAGGTA 59.997 47.619 7.64 0.00 0.00 3.08
2392 2611 4.574674 AGAATGAGAAATGTACTGGCCA 57.425 40.909 4.71 4.71 0.00 5.36
2685 3438 0.101399 ATAGCGAGCAGGAGTTCACG 59.899 55.000 0.00 0.00 0.00 4.35
2790 3543 1.879380 CTGGTTTTCGAGTTCATGCCA 59.121 47.619 0.00 0.00 0.00 4.92
3174 3952 2.203640 TGTCAGGAGCCGGTGTCT 60.204 61.111 1.90 0.00 0.00 3.41
3200 3981 1.768684 GACTTGCCACAGGGTGAGGA 61.769 60.000 0.00 0.00 35.23 3.71
3542 4335 1.683943 CATGTAAGCCCCTCCATGTG 58.316 55.000 0.00 0.00 32.08 3.21
3544 4337 1.207488 TGTAAGCCCCTCCATGTGCT 61.207 55.000 0.00 0.00 35.08 4.40
3546 4339 1.131638 TAAGCCCCTCCATGTGCTAG 58.868 55.000 0.00 0.00 32.82 3.42
3550 4343 1.496060 CCCCTCCATGTGCTAGTACA 58.504 55.000 16.34 16.34 34.63 2.90
3566 4359 8.762426 GTGCTAGTACAATACCTAATAAGTTGC 58.238 37.037 6.04 0.00 0.00 4.17
3582 4375 8.560576 AATAAGTTGCATTATATGTTTCACGC 57.439 30.769 0.00 0.00 0.00 5.34
3590 4383 9.051679 TGCATTATATGTTTCACGCTTAATACT 57.948 29.630 0.00 0.00 0.00 2.12
3615 4408 7.192852 AGTACAAGACAAGATGATCTCCAAT 57.807 36.000 0.00 0.00 0.00 3.16
3622 4415 8.043429 AGACAAGATGATCTCCAATAATTCCT 57.957 34.615 0.00 0.00 0.00 3.36
3659 4454 7.283329 AGTAACACTCCTTCAGAATTGTTCTT 58.717 34.615 0.00 0.00 38.11 2.52
3664 4459 8.816894 ACACTCCTTCAGAATTGTTCTTAGATA 58.183 33.333 0.00 0.00 38.11 1.98
3703 4505 6.380274 AGTCTAGTATGAAAATCCGACCAGAA 59.620 38.462 0.00 0.00 0.00 3.02
3713 4515 7.334421 TGAAAATCCGACCAGAATAGAGAAAAG 59.666 37.037 0.00 0.00 0.00 2.27
3720 4522 6.408206 CGACCAGAATAGAGAAAAGGGGTAAT 60.408 42.308 0.00 0.00 0.00 1.89
3737 4539 9.736819 AAGGGGTAATCAATAAATAATTCCCAA 57.263 29.630 0.00 0.00 30.04 4.12
3739 4541 9.374711 GGGGTAATCAATAAATAATTCCCAAGA 57.625 33.333 0.00 0.00 33.55 3.02
3797 4599 5.892119 CCACCCTATTGTAGTCTAGTCTGAA 59.108 44.000 0.00 0.00 0.00 3.02
3799 4601 7.070074 CCACCCTATTGTAGTCTAGTCTGAAAT 59.930 40.741 0.00 2.81 0.00 2.17
3802 4604 8.865090 CCCTATTGTAGTCTAGTCTGAAATCAT 58.135 37.037 0.00 0.00 0.00 2.45
3818 4620 6.051074 TGAAATCATGCGACTCAGAATGTAT 58.949 36.000 0.00 0.00 37.40 2.29
3833 4636 2.018542 TGTATCTGCACGGGCTAAAC 57.981 50.000 12.74 4.53 41.91 2.01
3843 4646 1.885163 CGGGCTAAACACTCCGGTCT 61.885 60.000 0.00 0.00 38.93 3.85
3861 4664 0.686441 CTCCATGACCCCACCTCGTA 60.686 60.000 0.00 0.00 0.00 3.43
3864 4667 0.611200 CATGACCCCACCTCGTAACA 59.389 55.000 0.00 0.00 0.00 2.41
3870 4673 0.682852 CCCACCTCGTAACAGGAACA 59.317 55.000 0.00 0.00 36.96 3.18
3881 4684 7.308348 CCTCGTAACAGGAACAAACAAATATGT 60.308 37.037 0.00 0.00 37.23 2.29
3913 4716 5.982356 TCAAAGGTTGATCAGTAGAGATGG 58.018 41.667 0.00 0.00 34.08 3.51
3921 4724 6.737720 TGATCAGTAGAGATGGCAAGTTAT 57.262 37.500 0.00 0.00 0.00 1.89
3926 4729 7.568349 TCAGTAGAGATGGCAAGTTATCAAAT 58.432 34.615 0.00 0.00 0.00 2.32
3934 4737 7.831193 AGATGGCAAGTTATCAAATCTGTAAGT 59.169 33.333 0.00 0.00 33.76 2.24
3962 4766 4.589374 ACAGTAGTGTAGCCTGAAGAACTT 59.411 41.667 0.00 0.00 34.05 2.66
3978 4782 5.810080 AGAACTTAAGAACAGCTACACCT 57.190 39.130 10.09 0.00 0.00 4.00
3985 4789 1.618837 GAACAGCTACACCTGGACTCA 59.381 52.381 0.00 0.00 37.16 3.41
3988 4792 1.066573 CAGCTACACCTGGACTCAAGG 60.067 57.143 0.00 0.00 0.00 3.61
3997 4801 0.696501 TGGACTCAAGGGCCCTAAAC 59.303 55.000 28.96 14.80 44.39 2.01
4093 4898 3.382227 TCCATAGCTTGCATCACAAATGG 59.618 43.478 0.00 0.00 42.16 3.16
4221 5026 7.065803 CCCAACTATGTGTTCGTAATGAATCTT 59.934 37.037 0.00 0.00 39.21 2.40
4264 5069 8.893563 ACCTCAAAATTTCCACCTAATTATCA 57.106 30.769 0.00 0.00 0.00 2.15
4315 5120 7.255942 CCCACAGGATAAAACAAAGACATCTTT 60.256 37.037 0.87 0.87 40.33 2.52
4321 5126 9.399403 GGATAAAACAAAGACATCTTTCTCAAC 57.601 33.333 3.84 0.00 43.72 3.18
4338 5143 5.642165 TCTCAACTTAGAGACTGGTTAGGT 58.358 41.667 0.00 0.00 39.62 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
742 815 3.477210 AGAGTTGTCAACCAGTCTTCC 57.523 47.619 12.17 0.00 0.00 3.46
751 824 6.072508 TGCAGATATTTCCAAGAGTTGTCAAC 60.073 38.462 7.68 7.68 0.00 3.18
759 832 3.881688 CCAGGTGCAGATATTTCCAAGAG 59.118 47.826 0.00 0.00 0.00 2.85
817 890 8.413229 TCCTTTAGTTGGATGACTTTTTCAAAG 58.587 33.333 0.00 0.00 37.92 2.77
894 968 6.872547 TCATCTTCTCTGTTCACTTCATCAAG 59.127 38.462 0.00 0.00 35.50 3.02
900 974 6.219473 TGTCTTCATCTTCTCTGTTCACTTC 58.781 40.000 0.00 0.00 0.00 3.01
1025 1099 0.391528 CAGTGCCGACATGATGACCA 60.392 55.000 0.00 0.00 0.00 4.02
1140 1221 2.070039 CCTCAAGGTATCCCCCGCA 61.070 63.158 0.00 0.00 0.00 5.69
1302 1419 1.678970 GCCCATGGAGGACGCTTTT 60.679 57.895 15.22 0.00 41.22 2.27
1416 1548 2.361610 CGCTTCATGCTGGGGGTT 60.362 61.111 0.00 0.00 40.11 4.11
1464 1596 2.257207 TCTCCGAGGAACTGGACATTT 58.743 47.619 0.00 0.00 41.55 2.32
1512 1662 1.215647 GAGCGTGTCTGTCGGGAAT 59.784 57.895 0.00 0.00 0.00 3.01
1549 1723 2.877708 GCTTGGAGAAGAGAAACCCCTG 60.878 54.545 0.00 0.00 0.00 4.45
1593 1767 4.329545 GCCAGGCTGAACCGACCA 62.330 66.667 17.94 0.00 46.52 4.02
1923 2121 0.840288 TCTTGCAGCCCCCTTCACTA 60.840 55.000 0.00 0.00 0.00 2.74
2211 2415 1.079819 GCAGTCGCTGAGGCAGTAA 60.080 57.895 10.46 0.00 38.60 2.24
2337 2541 1.978580 ACCTGAGAATTCCTTGTCCGT 59.021 47.619 0.65 0.00 0.00 4.69
2392 2611 1.474855 GCAAATGGCCACAACCTTGTT 60.475 47.619 8.16 0.00 39.91 2.83
2446 2665 0.320683 TGATGTGCCAGAAGTCGGTG 60.321 55.000 0.00 0.00 0.00 4.94
2447 2666 0.615331 ATGATGTGCCAGAAGTCGGT 59.385 50.000 0.00 0.00 0.00 4.69
2449 2668 2.609459 GGTAATGATGTGCCAGAAGTCG 59.391 50.000 0.00 0.00 0.00 4.18
2450 2669 3.873952 GAGGTAATGATGTGCCAGAAGTC 59.126 47.826 0.00 0.00 0.00 3.01
2451 2670 3.679917 CGAGGTAATGATGTGCCAGAAGT 60.680 47.826 0.00 0.00 0.00 3.01
2685 3438 1.202268 CCGATGGACTGTACCTCGTTC 60.202 57.143 15.05 0.00 32.80 3.95
2855 3611 4.545706 CGATGGCAAGGGCGGCTA 62.546 66.667 9.56 0.00 42.47 3.93
3087 3843 3.573491 GCCTTGGTATCCACGCGC 61.573 66.667 5.73 0.00 30.78 6.86
3093 3849 0.180406 ACACATCCGCCTTGGTATCC 59.820 55.000 0.00 0.00 39.52 2.59
3096 3852 1.206132 CTGTACACATCCGCCTTGGTA 59.794 52.381 0.00 0.00 39.52 3.25
3200 3981 1.063642 TGACCGTCTCATCATCCTCCT 60.064 52.381 0.00 0.00 0.00 3.69
3283 4067 3.059884 CAACAGTGTCTACGTCAGCATT 58.940 45.455 0.00 0.00 0.00 3.56
3294 4084 2.301296 CTCCATGTCCTCAACAGTGTCT 59.699 50.000 0.00 0.00 42.37 3.41
3441 4234 2.056906 AACAGTCTGGAGGGTGGTGC 62.057 60.000 4.53 0.00 0.00 5.01
3542 4335 8.882415 TGCAACTTATTAGGTATTGTACTAGC 57.118 34.615 0.00 0.00 0.00 3.42
3572 4365 8.991243 TTGTACTAGTATTAAGCGTGAAACAT 57.009 30.769 5.75 0.00 35.74 2.71
3574 4367 8.582096 GTCTTGTACTAGTATTAAGCGTGAAAC 58.418 37.037 18.12 10.57 0.00 2.78
3590 4383 7.718334 TTGGAGATCATCTTGTCTTGTACTA 57.282 36.000 0.00 0.00 0.00 1.82
3591 4384 6.611613 TTGGAGATCATCTTGTCTTGTACT 57.388 37.500 0.00 0.00 0.00 2.73
3592 4385 8.948631 TTATTGGAGATCATCTTGTCTTGTAC 57.051 34.615 0.00 0.00 0.00 2.90
3615 4408 4.623932 ACTCACTTGCACTCAGGAATTA 57.376 40.909 0.00 0.00 0.00 1.40
3682 4477 8.473358 TCTATTCTGGTCGGATTTTCATACTA 57.527 34.615 0.00 0.00 0.00 1.82
3686 4481 6.485830 TCTCTATTCTGGTCGGATTTTCAT 57.514 37.500 0.00 0.00 0.00 2.57
3713 4515 9.374711 TCTTGGGAATTATTTATTGATTACCCC 57.625 33.333 0.00 0.00 33.60 4.95
3753 4555 7.039270 GGGTGGATATTGGTTCATTTTTACAC 58.961 38.462 0.00 0.00 0.00 2.90
3765 4567 6.151049 AGACTACAATAGGGTGGATATTGGT 58.849 40.000 9.71 0.72 42.41 3.67
3767 4569 8.423906 ACTAGACTACAATAGGGTGGATATTG 57.576 38.462 0.00 4.57 43.30 1.90
3776 4578 8.239038 TGATTTCAGACTAGACTACAATAGGG 57.761 38.462 0.00 0.00 0.00 3.53
3797 4599 5.851720 AGATACATTCTGAGTCGCATGATT 58.148 37.500 0.00 0.00 31.79 2.57
3799 4601 4.926140 AGATACATTCTGAGTCGCATGA 57.074 40.909 0.00 0.00 31.79 3.07
3818 4620 0.320421 GAGTGTTTAGCCCGTGCAGA 60.320 55.000 0.00 0.00 41.13 4.26
3843 4646 0.252330 TTACGAGGTGGGGTCATGGA 60.252 55.000 0.00 0.00 0.00 3.41
3861 4664 8.311109 GGGATTACATATTTGTTTGTTCCTGTT 58.689 33.333 0.00 0.00 37.28 3.16
3864 4667 8.664669 AAGGGATTACATATTTGTTTGTTCCT 57.335 30.769 0.00 0.00 37.28 3.36
3870 4673 9.942850 CCTTTGAAAGGGATTACATATTTGTTT 57.057 29.630 16.17 0.00 45.27 2.83
3903 4706 7.714377 CAGATTTGATAACTTGCCATCTCTACT 59.286 37.037 0.00 0.00 0.00 2.57
3905 4708 7.568349 ACAGATTTGATAACTTGCCATCTCTA 58.432 34.615 0.00 0.00 0.00 2.43
3921 4724 9.256477 CACTACTGTTACAACTTACAGATTTGA 57.744 33.333 9.03 0.00 43.45 2.69
3926 4729 7.365741 GCTACACTACTGTTACAACTTACAGA 58.634 38.462 9.03 0.00 43.45 3.41
3934 4737 5.537295 TCTTCAGGCTACACTACTGTTACAA 59.463 40.000 0.00 0.00 34.02 2.41
3962 4766 3.507411 AGTCCAGGTGTAGCTGTTCTTA 58.493 45.455 9.88 0.00 0.00 2.10
3978 4782 0.696501 GTTTAGGGCCCTTGAGTCCA 59.303 55.000 34.04 6.90 0.00 4.02
3985 4789 1.203137 GGTTCTTGGTTTAGGGCCCTT 60.203 52.381 34.04 14.81 0.00 3.95
3988 4792 1.893137 CTTGGTTCTTGGTTTAGGGCC 59.107 52.381 0.00 0.00 0.00 5.80
3997 4801 3.817709 TTTTTCCAGCTTGGTTCTTGG 57.182 42.857 0.00 0.00 39.03 3.61
4052 4857 5.534207 TGGATGTTGCATTTTTCTGAAGT 57.466 34.783 0.00 0.00 0.00 3.01
4055 4860 5.419788 AGCTATGGATGTTGCATTTTTCTGA 59.580 36.000 0.00 0.00 29.08 3.27
4056 4861 5.657474 AGCTATGGATGTTGCATTTTTCTG 58.343 37.500 0.00 0.00 29.08 3.02
4093 4898 2.032030 GCATGTCACATAATGGCGGTAC 60.032 50.000 0.00 0.00 34.72 3.34
4221 5026 2.771943 AGGTCCATCGAAGGCATTTAGA 59.228 45.455 0.65 0.00 0.00 2.10
4264 5069 8.567104 GGCAACCACTGAAATTCATTTTAATTT 58.433 29.630 0.00 0.00 40.79 1.82
4315 5120 5.642165 ACCTAACCAGTCTCTAAGTTGAGA 58.358 41.667 0.00 0.00 40.39 3.27
4321 5126 4.339814 CCAGCTACCTAACCAGTCTCTAAG 59.660 50.000 0.00 0.00 0.00 2.18
4323 5128 3.268856 ACCAGCTACCTAACCAGTCTCTA 59.731 47.826 0.00 0.00 0.00 2.43
4338 5143 1.724545 AACACCCACACTACCAGCTA 58.275 50.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.