Multiple sequence alignment - TraesCS3A01G316200

Loading Multiple Alignment...

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 TraesCS3A01G316200 chr3A 100.000 6311 0 0 1 6311 556697117 556690807 0.000000e+00 11655
1 TraesCS3A01G316200 chr3A 99.201 626 5 0 5686 6311 265380810 265381435 0.000000e+00 1129
2 TraesCS3A01G316200 chr3A 85.208 480 61 8 11 486 728617849 728617376 9.510000e-133 484
3 TraesCS3A01G316200 chr3A 85.714 385 39 13 17 392 362905793 362905416 5.930000e-105 392
4 TraesCS3A01G316200 chr3A 81.225 506 73 14 11 501 728575925 728575427 7.670000e-104 388
5 TraesCS3A01G316200 chr3D 94.299 3701 143 24 11 3671 428967127 428970799 0.000000e+00 5603
6 TraesCS3A01G316200 chr3D 96.770 867 20 5 3668 4528 428971040 428971904 0.000000e+00 1439
7 TraesCS3A01G316200 chr3D 93.092 883 44 7 4807 5687 428972236 428973103 0.000000e+00 1277
8 TraesCS3A01G316200 chr3D 95.639 321 14 0 4441 4761 428971910 428972230 3.370000e-142 516
9 TraesCS3A01G316200 chr3B 95.160 3099 91 17 603 3671 561026018 561029087 0.000000e+00 4837
10 TraesCS3A01G316200 chr3B 94.009 1903 73 19 3764 5656 561029517 561031388 0.000000e+00 2844
11 TraesCS3A01G316200 chr3B 90.744 605 46 8 13 611 561024926 561025526 0.000000e+00 798
12 TraesCS3A01G316200 chr4B 99.361 626 4 0 5686 6311 248365038 248364413 0.000000e+00 1134
13 TraesCS3A01G316200 chr6A 99.201 626 5 0 5686 6311 180192944 180192319 0.000000e+00 1129
14 TraesCS3A01G316200 chr5B 99.201 626 5 0 5686 6311 336100241 336100866 0.000000e+00 1129
15 TraesCS3A01G316200 chr5B 99.201 626 5 0 5686 6311 695761923 695762548 0.000000e+00 1129
16 TraesCS3A01G316200 chr5B 98.892 632 5 2 5681 6311 598542267 598542897 0.000000e+00 1127
17 TraesCS3A01G316200 chr5B 98.736 633 7 1 5680 6311 461883218 461882586 0.000000e+00 1123
18 TraesCS3A01G316200 chr5A 99.201 626 5 0 5686 6311 149388534 149389159 0.000000e+00 1129
19 TraesCS3A01G316200 chr5A 82.970 505 65 12 10 505 123287368 123286876 2.700000e-118 436
20 TraesCS3A01G316200 chr7B 99.045 628 6 0 5684 6311 443843361 443843988 0.000000e+00 1127
21 TraesCS3A01G316200 chr7B 83.851 483 64 12 29 505 715282508 715282034 1.250000e-121 448
22 TraesCS3A01G316200 chr7B 84.541 414 50 11 22 429 64065200 64065605 1.270000e-106 398
23 TraesCS3A01G316200 chr5D 83.582 402 56 7 92 488 537172602 537172206 1.000000e-97 368


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 TraesCS3A01G316200 chr3A 556690807 556697117 6310 True 11655.000000 11655 100.000000 1 6311 1 chr3A.!!$R2 6310
1 TraesCS3A01G316200 chr3A 265380810 265381435 625 False 1129.000000 1129 99.201000 5686 6311 1 chr3A.!!$F1 625
2 TraesCS3A01G316200 chr3D 428967127 428973103 5976 False 2208.750000 5603 94.950000 11 5687 4 chr3D.!!$F1 5676
3 TraesCS3A01G316200 chr3B 561024926 561031388 6462 False 2826.333333 4837 93.304333 13 5656 3 chr3B.!!$F1 5643
4 TraesCS3A01G316200 chr4B 248364413 248365038 625 True 1134.000000 1134 99.361000 5686 6311 1 chr4B.!!$R1 625
5 TraesCS3A01G316200 chr6A 180192319 180192944 625 True 1129.000000 1129 99.201000 5686 6311 1 chr6A.!!$R1 625
6 TraesCS3A01G316200 chr5B 336100241 336100866 625 False 1129.000000 1129 99.201000 5686 6311 1 chr5B.!!$F1 625
7 TraesCS3A01G316200 chr5B 695761923 695762548 625 False 1129.000000 1129 99.201000 5686 6311 1 chr5B.!!$F3 625
8 TraesCS3A01G316200 chr5B 598542267 598542897 630 False 1127.000000 1127 98.892000 5681 6311 1 chr5B.!!$F2 630
9 TraesCS3A01G316200 chr5B 461882586 461883218 632 True 1123.000000 1123 98.736000 5680 6311 1 chr5B.!!$R1 631
10 TraesCS3A01G316200 chr5A 149388534 149389159 625 False 1129.000000 1129 99.201000 5686 6311 1 chr5A.!!$F1 625
11 TraesCS3A01G316200 chr7B 443843361 443843988 627 False 1127.000000 1127 99.045000 5684 6311 1 chr7B.!!$F2 627

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
54 55 0.306533 ACACGTTCAACATTGTCCGC 59.693 50.0 0.00 0.00 0.00 5.54 F
1717 2257 0.175073 GTTCGTGCCTAGAACCGGAT 59.825 55.0 9.46 0.00 41.38 4.18 F
1852 2399 0.250901 GTGGATTGTGGTGGCAGAGT 60.251 55.0 0.00 0.00 0.00 3.24 F
2768 3338 1.220529 GCCTTTGCTGCAGTTTTTCC 58.779 50.0 16.64 0.00 33.53 3.13 F
3968 4881 0.968405 TTTCTGGTTTCTGGCATGGC 59.032 50.0 13.29 13.29 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 2385 0.033601 AACCAACTCTGCCACCACAA 60.034 50.000 0.00 0.0 0.00 3.33 R
3393 3963 1.187567 ATGAACTTGGGGCAGGCAAC 61.188 55.000 0.00 0.0 0.00 4.17 R
3543 4113 1.485294 TTCCCAGCCTAGAAACGCCA 61.485 55.000 0.00 0.0 0.00 5.69 R
4395 5310 4.392921 ACTGGATGTGATCTTTCCGTAG 57.607 45.455 0.00 0.0 0.00 3.51 R
5506 6519 0.104120 TTGTGACACGGAGACACTGG 59.896 55.000 12.12 0.0 35.83 4.00 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
54 55 0.306533 ACACGTTCAACATTGTCCGC 59.693 50.000 0.00 0.00 0.00 5.54
56 57 1.069296 CACGTTCAACATTGTCCGCAT 60.069 47.619 0.00 0.00 0.00 4.73
74 75 6.529829 GTCCGCATGCTTATTCAACATTTTTA 59.470 34.615 17.13 0.00 0.00 1.52
430 435 9.098355 TGAAGAGTGTTTTGTGTATAGATATGC 57.902 33.333 0.00 0.00 0.00 3.14
493 498 6.980397 AGCAAATAACAAGAACAGAAAACTGG 59.020 34.615 0.00 0.00 0.00 4.00
564 569 1.017387 CCCTGTGATCGCTTAAAGCC 58.983 55.000 7.94 0.00 38.18 4.35
709 1222 7.770897 GGAGGAAGTATGTTGATTCAGTACAAT 59.229 37.037 0.00 0.00 0.00 2.71
1154 1694 1.592400 CTGTACGAGGGCGACTTCCA 61.592 60.000 0.00 0.00 41.64 3.53
1364 1904 2.504244 CGTCGTCCTCCAGAACGC 60.504 66.667 0.00 0.00 0.00 4.84
1433 1973 0.391597 TTCGTGTCCCAGTTCCAGAC 59.608 55.000 0.00 0.00 0.00 3.51
1587 2127 6.183360 GGTTCGTGCATGGTAAATAAATGGTA 60.183 38.462 5.98 0.00 0.00 3.25
1637 2177 7.418597 CCTGGCAGTATAGTTTACTGAATGGTA 60.419 40.741 20.87 3.27 45.69 3.25
1638 2178 7.270047 TGGCAGTATAGTTTACTGAATGGTAC 58.730 38.462 20.87 4.87 45.69 3.34
1639 2179 7.125204 TGGCAGTATAGTTTACTGAATGGTACT 59.875 37.037 20.87 0.00 45.69 2.73
1717 2257 0.175073 GTTCGTGCCTAGAACCGGAT 59.825 55.000 9.46 0.00 41.38 4.18
1731 2271 4.348168 AGAACCGGATATTAATGCCAGTCT 59.652 41.667 9.46 0.58 0.00 3.24
1837 2384 9.687210 GTATTATTCGTGAGTTATGTATGTGGA 57.313 33.333 0.00 0.00 0.00 4.02
1839 2386 9.778741 ATTATTCGTGAGTTATGTATGTGGATT 57.221 29.630 0.00 0.00 0.00 3.01
1840 2387 6.902224 TTCGTGAGTTATGTATGTGGATTG 57.098 37.500 0.00 0.00 0.00 2.67
1841 2388 5.972935 TCGTGAGTTATGTATGTGGATTGT 58.027 37.500 0.00 0.00 0.00 2.71
1842 2389 5.810074 TCGTGAGTTATGTATGTGGATTGTG 59.190 40.000 0.00 0.00 0.00 3.33
1843 2390 5.006649 CGTGAGTTATGTATGTGGATTGTGG 59.993 44.000 0.00 0.00 0.00 4.17
1852 2399 0.250901 GTGGATTGTGGTGGCAGAGT 60.251 55.000 0.00 0.00 0.00 3.24
1870 2417 5.523552 GCAGAGTTGGTTTTTGCTTGTTAAT 59.476 36.000 0.00 0.00 0.00 1.40
1878 2425 6.096987 TGGTTTTTGCTTGTTAATGGTAGTCA 59.903 34.615 0.00 0.00 0.00 3.41
2095 2662 4.463070 TGGTTGGGTGTTTCTAAGGTTAC 58.537 43.478 0.00 0.00 0.00 2.50
2185 2752 3.149005 TGGAGTGTGTATGGGGTTTTC 57.851 47.619 0.00 0.00 0.00 2.29
2228 2795 4.280425 TGGAGAATTCGATGATCAGAGAGG 59.720 45.833 0.09 0.00 0.00 3.69
2246 2816 1.760480 GTCCTGGAGAGGGAGGAGC 60.760 68.421 0.00 0.00 39.12 4.70
2302 2872 2.116125 AAGCAGGGTGGGAGCAAC 59.884 61.111 0.00 0.00 0.00 4.17
2626 3196 7.390440 CCTCCACTTTGTACAAATAATGACTGA 59.610 37.037 20.83 11.16 0.00 3.41
2751 3321 4.947388 TCATGTTGTCTTATGGGTAAAGCC 59.053 41.667 0.00 0.00 0.00 4.35
2768 3338 1.220529 GCCTTTGCTGCAGTTTTTCC 58.779 50.000 16.64 0.00 33.53 3.13
2777 3347 2.266554 TGCAGTTTTTCCTTTTGTGCG 58.733 42.857 0.00 0.00 31.99 5.34
2840 3410 8.470002 AGTAAATTATTCTTGTTTCCCATGCTC 58.530 33.333 0.00 0.00 0.00 4.26
2879 3449 4.610605 TTTCGTGGGTTTCTGATGAGTA 57.389 40.909 0.00 0.00 0.00 2.59
3027 3597 7.741027 AAGATGAGAATATGTTGCTATGTGG 57.259 36.000 0.00 0.00 0.00 4.17
3221 3791 2.668457 GTCTCCGCAGTATGACTTTGTG 59.332 50.000 0.00 0.00 39.69 3.33
3335 3905 4.621769 AGCTGAAGGGTAAGTATGGTACT 58.378 43.478 0.00 0.00 41.73 2.73
3345 3915 6.766467 GGGTAAGTATGGTACTGAAATGGAAG 59.234 42.308 0.00 0.00 39.39 3.46
3366 3936 3.387374 AGAGATGCTTAGAGGTGATGGTG 59.613 47.826 0.00 0.00 0.00 4.17
3393 3963 5.967674 GCACATTATGATGAACTCTTTTCCG 59.032 40.000 4.20 0.00 36.73 4.30
3446 4016 5.511373 GCCTCCAGTTTTAAAAGAGCCATTT 60.511 40.000 0.00 0.00 0.00 2.32
3567 4137 3.195661 CGTTTCTAGGCTGGGAACATAC 58.804 50.000 20.39 8.44 41.51 2.39
3760 4574 7.812309 TCTCAGTTGTATTAATCAGTTCACG 57.188 36.000 0.00 0.00 0.00 4.35
3777 4690 8.627403 TCAGTTCACGGTTATATACTTAAGGAG 58.373 37.037 7.53 0.00 0.00 3.69
3967 4880 3.967332 ATTTTCTGGTTTCTGGCATGG 57.033 42.857 0.00 0.00 0.00 3.66
3968 4881 0.968405 TTTCTGGTTTCTGGCATGGC 59.032 50.000 13.29 13.29 0.00 4.40
3979 4892 1.819208 GGCATGGCGCATGTACTCA 60.819 57.895 10.83 0.00 43.10 3.41
4395 5310 2.774439 AAACTCATGCCGTTGACAAC 57.226 45.000 8.34 8.34 0.00 3.32
4568 5577 8.940768 TTAATATTTTTATCAACCTGCTTGGC 57.059 30.769 0.00 0.00 40.22 4.52
4580 5590 0.038343 TGCTTGGCGAAAAGGAATGC 60.038 50.000 0.00 0.00 0.00 3.56
4687 5697 5.931441 ATATAGGCTTGAAATTGAGCGTC 57.069 39.130 0.00 0.00 39.78 5.19
4862 5872 5.163963 CCTTTGTTTTGTCTGCTGTTGAAAC 60.164 40.000 9.59 9.59 0.00 2.78
4892 5902 4.442753 TGCAATGCAAGCATGATTCATCAT 60.443 37.500 5.01 0.00 41.08 2.45
4893 5903 4.150627 GCAATGCAAGCATGATTCATCATC 59.849 41.667 8.50 0.00 45.23 2.92
4894 5904 5.288804 CAATGCAAGCATGATTCATCATCA 58.711 37.500 8.50 0.00 45.23 3.07
4951 5961 8.946085 TGACTACTCCATGTGATTTGTTAAATC 58.054 33.333 7.21 7.21 45.86 2.17
5043 6053 6.671614 TTTTGACGCATATTTCGAAGGTAT 57.328 33.333 0.00 0.00 0.00 2.73
5063 6074 6.495526 AGGTATCCTAAGATCTGTAGCCTTTC 59.504 42.308 0.00 0.00 33.67 2.62
5086 6097 6.358178 TCTTTCCTCTGTCGATAGTCTACAT 58.642 40.000 9.16 0.00 37.40 2.29
5109 6120 2.618709 GTGTTTCCTTGGACACTTCCTG 59.381 50.000 7.37 0.00 43.31 3.86
5144 6155 2.368875 TGGTGCTTAGCCCTAGAATAGC 59.631 50.000 0.29 0.00 37.37 2.97
5150 6161 4.321675 GCTTAGCCCTAGAATAGCTGTCTC 60.322 50.000 5.11 0.00 37.37 3.36
5151 6162 3.611025 AGCCCTAGAATAGCTGTCTCT 57.389 47.619 5.11 2.66 37.37 3.10
5164 6175 8.606754 AATAGCTGTCTCTGTGATATCCATAT 57.393 34.615 0.00 0.00 0.00 1.78
5165 6176 9.706529 AATAGCTGTCTCTGTGATATCCATATA 57.293 33.333 0.00 0.00 0.00 0.86
5226 6237 0.247460 TGATGGGCGAGTTGAGTGAG 59.753 55.000 0.00 0.00 0.00 3.51
5275 6286 0.108945 GGGTGAAGAAGCTTGCATGC 60.109 55.000 16.37 16.37 0.00 4.06
5480 6493 3.584848 ACTGTTTCTGGGCTGTAGAATCT 59.415 43.478 0.00 0.00 34.42 2.40
5506 6519 5.924254 CACATCCAAATGGTTATGATGATGC 59.076 40.000 7.83 0.00 37.19 3.91
5561 6574 5.703978 ATGGTTGTGATGTTGATCGAAAA 57.296 34.783 0.00 0.00 0.00 2.29
5574 6587 6.806249 TGTTGATCGAAAAACATCTAAATGGC 59.194 34.615 11.11 0.00 37.19 4.40
5600 6615 8.458843 CGGTGATGTAAATCTAAAGAATGGTTT 58.541 33.333 0.00 0.00 0.00 3.27
5606 6621 8.296713 TGTAAATCTAAAGAATGGTTTCAGTGC 58.703 33.333 0.00 0.00 34.08 4.40
5607 6622 6.899393 AATCTAAAGAATGGTTTCAGTGCA 57.101 33.333 0.00 0.00 34.08 4.57
5626 6641 3.181492 TGCATGGTTTATATGGCGTTGTG 60.181 43.478 0.00 0.00 0.00 3.33
5645 6661 0.255890 GGCCTATGGATGTGGTGTGT 59.744 55.000 0.00 0.00 0.00 3.72
5660 6676 6.068010 TGTGGTGTGTTTTTCTCTATTCCAT 58.932 36.000 0.00 0.00 0.00 3.41
5680 6696 8.648698 TTCCATTGATATCTTTCTTTTGGACA 57.351 30.769 3.98 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.143073 GCGGACAATGTTGAACGTGTATAA 60.143 41.667 4.69 0.00 34.93 0.98
397 402 6.325919 ACACAAAACACTCTTCAAGAACAA 57.674 33.333 0.00 0.00 0.00 2.83
467 472 8.134895 CCAGTTTTCTGTTCTTGTTATTTGCTA 58.865 33.333 0.00 0.00 45.68 3.49
530 535 2.126031 GGGCGACGTCTTGAGTCC 60.126 66.667 14.70 4.93 35.33 3.85
564 569 4.218722 GGGTTGCCCGTATGTCTG 57.781 61.111 0.00 0.00 32.13 3.51
577 582 0.553819 TGGCTGGTTAACACAGGGTT 59.446 50.000 19.36 0.00 43.62 4.11
646 1151 6.546403 ACTCCGTATATTAGCTCTGTTCAGAA 59.454 38.462 0.00 0.00 0.00 3.02
648 1153 6.320494 ACTCCGTATATTAGCTCTGTTCAG 57.680 41.667 0.00 0.00 0.00 3.02
652 1157 9.736414 TTTATCTACTCCGTATATTAGCTCTGT 57.264 33.333 0.00 0.00 0.00 3.41
681 1186 4.223032 ACTGAATCAACATACTTCCTCCGT 59.777 41.667 0.00 0.00 0.00 4.69
682 1187 4.759782 ACTGAATCAACATACTTCCTCCG 58.240 43.478 0.00 0.00 0.00 4.63
684 1189 8.723942 ATTGTACTGAATCAACATACTTCCTC 57.276 34.615 0.00 0.00 0.00 3.71
685 1190 9.520515 AAATTGTACTGAATCAACATACTTCCT 57.479 29.630 0.00 0.00 0.00 3.36
709 1222 3.805422 ACTGTCGCTGATTTCGTACAAAA 59.195 39.130 0.00 0.00 0.00 2.44
716 1229 4.259970 CCTGATTAACTGTCGCTGATTTCG 60.260 45.833 0.00 0.00 0.00 3.46
717 1230 4.870426 TCCTGATTAACTGTCGCTGATTTC 59.130 41.667 0.00 0.00 0.00 2.17
718 1231 4.832248 TCCTGATTAACTGTCGCTGATTT 58.168 39.130 0.00 0.00 0.00 2.17
719 1232 4.471904 TCCTGATTAACTGTCGCTGATT 57.528 40.909 0.00 0.00 0.00 2.57
720 1233 4.679373 ATCCTGATTAACTGTCGCTGAT 57.321 40.909 0.00 0.00 0.00 2.90
721 1234 4.183865 CAATCCTGATTAACTGTCGCTGA 58.816 43.478 0.00 0.00 0.00 4.26
722 1235 3.310774 CCAATCCTGATTAACTGTCGCTG 59.689 47.826 0.00 0.00 0.00 5.18
723 1236 3.197766 TCCAATCCTGATTAACTGTCGCT 59.802 43.478 0.00 0.00 0.00 4.93
724 1237 3.531538 TCCAATCCTGATTAACTGTCGC 58.468 45.455 0.00 0.00 0.00 5.19
1213 1753 2.684843 GGTCGTCGTCGCAGTAGGT 61.685 63.158 0.00 0.00 36.96 3.08
1364 1904 3.138798 GCAGCTGCATGGTGAGGG 61.139 66.667 33.36 0.00 46.27 4.30
1433 1973 1.369091 GGTGCGGTACTGGCAGAATG 61.369 60.000 23.66 8.86 41.83 2.67
1492 2032 2.432628 GACCTGGTCGAACCGCTG 60.433 66.667 11.71 0.00 42.58 5.18
1587 2127 4.524328 AGAAACTGAAATTCGCCAAAGGAT 59.476 37.500 0.00 0.00 32.04 3.24
1637 2177 5.831702 ACATCGAGAATAACGAACCTAGT 57.168 39.130 0.00 0.00 42.80 2.57
1638 2178 6.750501 TGAAACATCGAGAATAACGAACCTAG 59.249 38.462 0.00 0.00 42.80 3.02
1639 2179 6.623486 TGAAACATCGAGAATAACGAACCTA 58.377 36.000 0.00 0.00 42.80 3.08
1837 2384 0.185901 ACCAACTCTGCCACCACAAT 59.814 50.000 0.00 0.00 0.00 2.71
1838 2385 0.033601 AACCAACTCTGCCACCACAA 60.034 50.000 0.00 0.00 0.00 3.33
1839 2386 0.033601 AAACCAACTCTGCCACCACA 60.034 50.000 0.00 0.00 0.00 4.17
1840 2387 1.111277 AAAACCAACTCTGCCACCAC 58.889 50.000 0.00 0.00 0.00 4.16
1841 2388 1.480137 CAAAAACCAACTCTGCCACCA 59.520 47.619 0.00 0.00 0.00 4.17
1842 2389 1.806247 GCAAAAACCAACTCTGCCACC 60.806 52.381 0.00 0.00 0.00 4.61
1843 2390 1.136891 AGCAAAAACCAACTCTGCCAC 59.863 47.619 0.00 0.00 33.41 5.01
1852 2399 6.879400 ACTACCATTAACAAGCAAAAACCAA 58.121 32.000 0.00 0.00 0.00 3.67
1878 2425 9.558396 GTAGTATGTACTATCCACTGAACTAGT 57.442 37.037 3.44 0.00 40.55 2.57
2095 2662 4.396166 ACCCATCAAAATTCAAGCTAGACG 59.604 41.667 0.00 0.00 0.00 4.18
2185 2752 3.057315 CCACCAGTGCCTTCAAGTAATTG 60.057 47.826 0.00 0.00 0.00 2.32
2228 2795 1.760480 GCTCCTCCCTCTCCAGGAC 60.760 68.421 0.00 0.00 43.65 3.85
2246 2816 1.016130 ATCGTGAACTGCTCAAGCCG 61.016 55.000 0.00 0.00 41.18 5.52
2302 2872 0.606401 ACCCCAGCATCTTCAACACG 60.606 55.000 0.00 0.00 0.00 4.49
2626 3196 5.047377 GTCACATATGGGGAAACAACACAAT 60.047 40.000 4.82 0.00 0.00 2.71
2751 3321 4.392754 ACAAAAGGAAAAACTGCAGCAAAG 59.607 37.500 15.27 0.00 0.00 2.77
2777 3347 3.477899 AGACTAGCGTAAACACGGTAC 57.522 47.619 5.11 0.00 43.78 3.34
2941 3511 9.049523 GCATGATATCACTCATTAGAAGAACAA 57.950 33.333 7.78 0.00 33.59 2.83
2965 3535 4.793678 GCATGCTCCAAATTATTGATCGCA 60.794 41.667 11.37 0.00 38.94 5.10
3221 3791 3.940221 ACATCTGCTCATTCTTCTTCAGC 59.060 43.478 0.00 0.00 0.00 4.26
3323 3893 8.603898 TCTCTTCCATTTCAGTACCATACTTA 57.396 34.615 0.00 0.00 36.76 2.24
3335 3905 5.190528 ACCTCTAAGCATCTCTTCCATTTCA 59.809 40.000 0.00 0.00 36.25 2.69
3345 3915 3.386078 TCACCATCACCTCTAAGCATCTC 59.614 47.826 0.00 0.00 0.00 2.75
3366 3936 6.690194 AAAGAGTTCATCATAATGTGCCTC 57.310 37.500 0.00 0.00 34.32 4.70
3393 3963 1.187567 ATGAACTTGGGGCAGGCAAC 61.188 55.000 0.00 0.00 0.00 4.17
3543 4113 1.485294 TTCCCAGCCTAGAAACGCCA 61.485 55.000 0.00 0.00 0.00 5.69
3567 4137 8.671921 AGATGATAAACAAGCAAAGATACACTG 58.328 33.333 0.00 0.00 0.00 3.66
3691 4505 9.675464 TTCGTTTTTCTAATCCATGGTACTTAT 57.325 29.630 12.58 0.00 0.00 1.73
3701 4515 9.463902 TGGGTTTATATTCGTTTTTCTAATCCA 57.536 29.630 0.00 0.00 0.00 3.41
4066 4979 8.770438 AACAGAAGTGAAATTGCAAACTAAAA 57.230 26.923 1.71 0.00 0.00 1.52
4067 4980 9.862371 TTAACAGAAGTGAAATTGCAAACTAAA 57.138 25.926 1.71 0.00 0.00 1.85
4321 5236 9.930693 GTCCATATACAAGTTAGAATCCCTAAG 57.069 37.037 0.00 0.00 37.98 2.18
4395 5310 4.392921 ACTGGATGTGATCTTTCCGTAG 57.607 45.455 0.00 0.00 0.00 3.51
4568 5577 6.020360 GCTAGCAAAATAAGCATTCCTTTTCG 60.020 38.462 10.63 0.00 36.26 3.46
4580 5590 5.803020 ACTTCCGAAGCTAGCAAAATAAG 57.197 39.130 18.83 15.87 0.00 1.73
4832 5842 2.167487 GCAGACAAAACAAAGGTTCCCA 59.833 45.455 0.00 0.00 35.82 4.37
4862 5872 0.454789 TGCTTGCATTGCAACGATCG 60.455 50.000 19.77 14.88 43.99 3.69
4909 5919 0.855349 GTCAGTCACGTGCAGACTTG 59.145 55.000 20.12 11.13 43.47 3.16
4910 5920 0.747255 AGTCAGTCACGTGCAGACTT 59.253 50.000 22.60 12.84 43.47 3.01
4911 5921 1.267261 GTAGTCAGTCACGTGCAGACT 59.733 52.381 27.31 27.31 46.72 3.24
4912 5922 1.267261 AGTAGTCAGTCACGTGCAGAC 59.733 52.381 19.93 19.93 36.26 3.51
4913 5923 1.535896 GAGTAGTCAGTCACGTGCAGA 59.464 52.381 11.67 5.84 0.00 4.26
4914 5924 1.401670 GGAGTAGTCAGTCACGTGCAG 60.402 57.143 11.67 3.33 0.00 4.41
4915 5925 0.596577 GGAGTAGTCAGTCACGTGCA 59.403 55.000 11.67 0.00 0.00 4.57
4951 5961 4.892433 TGTTTCCTGCATTAACCAAATGG 58.108 39.130 0.00 0.00 44.45 3.16
5043 6053 6.127026 GGAAAGAAAGGCTACAGATCTTAGGA 60.127 42.308 0.00 0.00 30.56 2.94
5063 6074 6.627395 ATGTAGACTATCGACAGAGGAAAG 57.373 41.667 0.00 0.00 35.55 2.62
5086 6097 3.020984 GGAAGTGTCCAAGGAAACACAA 58.979 45.455 11.83 0.00 46.47 3.33
5109 6120 3.245518 AGCACCAAACAAAAGGAACAC 57.754 42.857 0.00 0.00 0.00 3.32
5118 6129 2.373836 TCTAGGGCTAAGCACCAAACAA 59.626 45.455 0.00 0.00 28.43 2.83
5391 6404 3.423571 AGCGTCGTTAATGAAGTCGTAG 58.576 45.455 11.50 0.00 0.00 3.51
5480 6493 7.255555 GCATCATCATAACCATTTGGATGTGTA 60.256 37.037 3.01 0.00 37.29 2.90
5506 6519 0.104120 TTGTGACACGGAGACACTGG 59.896 55.000 12.12 0.00 35.83 4.00
5536 6549 3.689161 TCGATCAACATCACAACCATTCC 59.311 43.478 0.00 0.00 0.00 3.01
5561 6574 3.620488 ACATCACCGCCATTTAGATGTT 58.380 40.909 0.00 0.00 44.86 2.71
5574 6587 7.553881 ACCATTCTTTAGATTTACATCACCG 57.446 36.000 0.00 0.00 0.00 4.94
5600 6615 2.877786 CGCCATATAAACCATGCACTGA 59.122 45.455 0.00 0.00 0.00 3.41
5606 6621 3.795150 GCCACAACGCCATATAAACCATG 60.795 47.826 0.00 0.00 0.00 3.66
5607 6622 2.360801 GCCACAACGCCATATAAACCAT 59.639 45.455 0.00 0.00 0.00 3.55
5626 6641 0.255890 ACACACCACATCCATAGGCC 59.744 55.000 0.00 0.00 0.00 5.19
5660 6676 6.434028 CAGGGTGTCCAAAAGAAAGATATCAA 59.566 38.462 5.32 0.00 34.83 2.57
5667 6683 3.023832 ACACAGGGTGTCCAAAAGAAAG 58.976 45.455 0.00 0.00 43.92 2.62
5672 6688 3.054287 TGTCTTACACAGGGTGTCCAAAA 60.054 43.478 5.13 0.00 43.92 2.44
5680 6696 6.264518 CCAAAACTTATTGTCTTACACAGGGT 59.735 38.462 0.00 0.00 35.97 4.34
6152 7168 4.218635 CAGTACTGAAGCTGAGTACAAGGA 59.781 45.833 26.59 1.09 45.61 3.36


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

AutoCloner maintained by Alex Coulton.