Multiple sequence alignment - TraesCS3A01G095300

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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 TraesCS3A01G095300 chr3A 100.000 4369 0 0 1 4369 60667591 60663223 0.000000e+00 8069
1 TraesCS3A01G095300 chr3A 96.538 780 21 3 3580 4356 199767550 199768326 0.000000e+00 1286
2 TraesCS3A01G095300 chr3D 93.554 2932 144 31 627 3538 48445201 48442295 0.000000e+00 4325
3 TraesCS3A01G095300 chr3D 85.866 658 50 16 2 635 48445897 48445259 0.000000e+00 660
4 TraesCS3A01G095300 chr3B 94.624 2288 97 15 705 2990 76510653 76508390 0.000000e+00 3520
5 TraesCS3A01G095300 chr3B 87.440 629 49 12 2 623 76514803 76514198 0.000000e+00 697
6 TraesCS3A01G095300 chr3B 87.282 401 31 14 3179 3570 76506658 76506269 1.440000e-119 440
7 TraesCS3A01G095300 chr3B 94.624 93 5 0 634 726 76514028 76513936 1.270000e-30 145
8 TraesCS3A01G095300 chrUn 96.120 799 24 5 3574 4369 311219102 311218308 0.000000e+00 1297
9 TraesCS3A01G095300 chr4A 95.328 792 27 9 3581 4369 133830363 133831147 0.000000e+00 1249
10 TraesCS3A01G095300 chr4A 93.860 798 36 9 3577 4369 334526590 334527379 0.000000e+00 1190
11 TraesCS3A01G095300 chr1A 95.764 779 25 5 3584 4358 204365986 204365212 0.000000e+00 1249
12 TraesCS3A01G095300 chr1A 93.695 793 39 8 3581 4369 18303171 18303956 0.000000e+00 1177
13 TraesCS3A01G095300 chr2A 94.830 793 33 5 3580 4369 656546265 656545478 0.000000e+00 1230
14 TraesCS3A01G095300 chr6A 94.325 793 38 4 3580 4369 32877496 32878284 0.000000e+00 1208
15 TraesCS3A01G095300 chr5A 93.383 801 41 8 3576 4369 7677592 7678387 0.000000e+00 1175


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 TraesCS3A01G095300 chr3A 60663223 60667591 4368 True 8069.0 8069 100.0000 1 4369 1 chr3A.!!$R1 4368
1 TraesCS3A01G095300 chr3A 199767550 199768326 776 False 1286.0 1286 96.5380 3580 4356 1 chr3A.!!$F1 776
2 TraesCS3A01G095300 chr3D 48442295 48445897 3602 True 2492.5 4325 89.7100 2 3538 2 chr3D.!!$R1 3536
3 TraesCS3A01G095300 chr3B 76506269 76514803 8534 True 1200.5 3520 90.9925 2 3570 4 chr3B.!!$R1 3568
4 TraesCS3A01G095300 chrUn 311218308 311219102 794 True 1297.0 1297 96.1200 3574 4369 1 chrUn.!!$R1 795
5 TraesCS3A01G095300 chr4A 133830363 133831147 784 False 1249.0 1249 95.3280 3581 4369 1 chr4A.!!$F1 788
6 TraesCS3A01G095300 chr4A 334526590 334527379 789 False 1190.0 1190 93.8600 3577 4369 1 chr4A.!!$F2 792
7 TraesCS3A01G095300 chr1A 204365212 204365986 774 True 1249.0 1249 95.7640 3584 4358 1 chr1A.!!$R1 774
8 TraesCS3A01G095300 chr1A 18303171 18303956 785 False 1177.0 1177 93.6950 3581 4369 1 chr1A.!!$F1 788
9 TraesCS3A01G095300 chr2A 656545478 656546265 787 True 1230.0 1230 94.8300 3580 4369 1 chr2A.!!$R1 789
10 TraesCS3A01G095300 chr6A 32877496 32878284 788 False 1208.0 1208 94.3250 3580 4369 1 chr6A.!!$F1 789
11 TraesCS3A01G095300 chr5A 7677592 7678387 795 False 1175.0 1175 93.3830 3576 4369 1 chr5A.!!$F1 793

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
280 282 0.327924 AGGTGGTGCCATCGATTTGA 59.672 50.000 0.00 0.0 40.61 2.69 F
916 4405 0.445829 CTTGTGTGTGTGCGTTGTCA 59.554 50.000 0.00 0.0 0.00 3.58 F
2609 6101 1.002134 TAGCAGCAAGGGCCAAGAC 60.002 57.895 6.18 0.0 42.56 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 4896 1.679641 CCCCAATTTTACGGCCCGT 60.680 57.895 15.63 15.63 44.35 5.28 R
2811 6303 0.598158 TGTAACGTGTGACTTCCGGC 60.598 55.000 0.00 0.00 0.00 6.13 R
3840 8902 0.801067 GCGCATCGAGTTAAGTCGGT 60.801 55.000 27.64 21.04 40.49 4.69 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
17 18 4.753662 CCGTCGTCTCCCCCTCCA 62.754 72.222 0.00 0.00 0.00 3.86
98 99 2.358258 CCTCCTCCTCCCTCTCTCTAT 58.642 57.143 0.00 0.00 0.00 1.98
141 142 2.317149 GACCTGGATCTCCCTTGCCG 62.317 65.000 0.00 0.00 35.38 5.69
177 178 0.388006 CCGATTTGGTTTTCCGTGGC 60.388 55.000 0.00 0.00 44.36 5.01
213 215 1.406341 GGACGTCGATTTGGGGATTGA 60.406 52.381 9.92 0.00 0.00 2.57
219 221 4.061596 GTCGATTTGGGGATTGAGATCTC 58.938 47.826 16.21 16.21 32.66 2.75
229 231 2.279784 GAGATCTCCCCTTGCGCG 60.280 66.667 12.00 0.00 0.00 6.86
278 280 0.394352 GGAGGTGGTGCCATCGATTT 60.394 55.000 0.00 0.00 40.61 2.17
279 281 0.734889 GAGGTGGTGCCATCGATTTG 59.265 55.000 0.00 0.00 40.61 2.32
280 282 0.327924 AGGTGGTGCCATCGATTTGA 59.672 50.000 0.00 0.00 40.61 2.69
281 283 1.064463 AGGTGGTGCCATCGATTTGAT 60.064 47.619 0.00 0.00 40.61 2.57
282 284 1.750778 GGTGGTGCCATCGATTTGATT 59.249 47.619 0.00 0.00 34.13 2.57
361 381 4.200092 AGCCGGAATTTGGAGTTCTAATC 58.800 43.478 5.05 0.00 0.00 1.75
364 384 4.576463 CCGGAATTTGGAGTTCTAATCAGG 59.424 45.833 0.00 0.00 0.00 3.86
411 431 2.284190 GAGCTGATTTGGCTGTAGTCC 58.716 52.381 0.00 0.00 40.40 3.85
454 480 1.523032 GGTAGAATTGGGCGGTCGG 60.523 63.158 0.00 0.00 0.00 4.79
470 496 4.800993 GCGGTCGGATGATATAATCTCTTG 59.199 45.833 0.00 0.00 0.00 3.02
537 563 1.977594 ATCGTTTGAATCCCGCGTGC 61.978 55.000 4.92 0.00 0.00 5.34
553 579 2.351157 GCGTGCTTGAGCTGAGATTTTT 60.351 45.455 4.44 0.00 42.66 1.94
586 612 7.054124 AGAATGTATCGGTAACAATTCATGGT 58.946 34.615 8.78 0.00 0.00 3.55
625 651 4.141779 GGTCGTATAGTTGATTTGGGGTCT 60.142 45.833 0.00 0.00 0.00 3.85
629 731 7.224167 GTCGTATAGTTGATTTGGGGTCTTTAG 59.776 40.741 0.00 0.00 0.00 1.85
639 824 4.015872 TGGGGTCTTTAGTTTGTAGCAG 57.984 45.455 0.00 0.00 0.00 4.24
745 4234 4.549458 ACAGTGTTAAATGCTGACATTGC 58.451 39.130 8.56 0.00 45.90 3.56
762 4251 6.042437 TGACATTGCACCTAGATCTGTATCAT 59.958 38.462 5.18 0.00 34.28 2.45
812 4301 4.038642 TGGAAGGTAGTTTGAATGGTTTGC 59.961 41.667 0.00 0.00 0.00 3.68
908 4397 6.607689 TCTGAAAACTTAACTTGTGTGTGTG 58.392 36.000 0.00 0.00 0.00 3.82
909 4398 5.157781 TGAAAACTTAACTTGTGTGTGTGC 58.842 37.500 0.00 0.00 0.00 4.57
910 4399 3.398954 AACTTAACTTGTGTGTGTGCG 57.601 42.857 0.00 0.00 0.00 5.34
911 4400 2.352388 ACTTAACTTGTGTGTGTGCGT 58.648 42.857 0.00 0.00 0.00 5.24
916 4405 0.445829 CTTGTGTGTGTGCGTTGTCA 59.554 50.000 0.00 0.00 0.00 3.58
981 4470 4.014847 TGCGTTTGGAATCGATTCATTC 57.985 40.909 32.92 19.63 38.53 2.67
1054 4543 4.808042 ACATCCCCCAGAGAAAATTATGG 58.192 43.478 0.00 0.00 0.00 2.74
1056 4545 2.584965 TCCCCCAGAGAAAATTATGGCA 59.415 45.455 0.00 0.00 0.00 4.92
1070 4559 1.122019 ATGGCATACGAGTCCCCTCC 61.122 60.000 0.00 0.00 33.93 4.30
1374 4863 1.596477 GGATGATCACCAGAGCCGC 60.596 63.158 0.00 0.00 0.00 6.53
1407 4896 3.767673 AGTTTACCTTCCGCTCTGATGTA 59.232 43.478 0.00 0.00 0.00 2.29
1513 5002 3.843422 CTCCATCAGATAGAGACCCTGT 58.157 50.000 0.00 0.00 0.00 4.00
1785 5274 6.926272 AGGTGAGTAATATTTCAATCGCTCTC 59.074 38.462 0.00 0.00 0.00 3.20
1807 5296 5.573219 TCTGATGACATCCCATTCTTTTGT 58.427 37.500 12.90 0.00 0.00 2.83
1915 5404 4.039852 TCGTTGATAGTTAGCATGGGCATA 59.960 41.667 0.00 0.00 44.61 3.14
2225 5714 5.763876 AGGTTAGAATGGTACTTCTGCTT 57.236 39.130 7.46 0.00 36.21 3.91
2253 5743 5.831702 ATTTGATTGCTCATCTGGTCTTC 57.168 39.130 0.00 0.00 32.34 2.87
2285 5775 5.476599 TGTGTAGCTTTTGGCATAATGAAGT 59.523 36.000 0.00 0.00 44.79 3.01
2297 5787 6.884295 TGGCATAATGAAGTGCTAACTTAACT 59.116 34.615 0.00 0.00 46.84 2.24
2372 5862 2.101415 TCACAGAGGACTAATGGATGCG 59.899 50.000 0.00 0.00 0.00 4.73
2433 5924 7.054491 TGTGATGAATAGTCTAGCTAATGCA 57.946 36.000 0.00 0.00 42.74 3.96
2488 5979 9.885743 GCATTATTGTCAATTTCGTAAAATGAC 57.114 29.630 14.79 15.59 35.27 3.06
2494 5985 6.848800 TGTCAATTTCGTAAAATGACGTGAAG 59.151 34.615 16.55 0.00 43.39 3.02
2527 6018 5.125100 TCTCAAAACATTAAGCAGGCAAG 57.875 39.130 0.00 0.00 0.00 4.01
2574 6065 9.507329 TTGCTATGAGAGAAAAGAAAACAGTAT 57.493 29.630 0.00 0.00 0.00 2.12
2603 6094 1.674962 CTCAATTCTAGCAGCAAGGGC 59.325 52.381 0.00 0.00 41.61 5.19
2609 6101 1.002134 TAGCAGCAAGGGCCAAGAC 60.002 57.895 6.18 0.00 42.56 3.01
2665 6157 6.295249 TGTGATTCACTTCATAACCAGTTGA 58.705 36.000 17.26 0.00 35.11 3.18
2781 6273 3.368531 GGATTCTGCCGAAGTACTTCAGT 60.369 47.826 29.95 11.16 39.46 3.41
2811 6303 4.240096 GGTCATTTGCTCAGTTCCATTTG 58.760 43.478 0.00 0.00 0.00 2.32
2894 6386 1.542108 GGATGGCAGGTACTCATCAGC 60.542 57.143 15.29 4.79 40.24 4.26
2900 6392 1.556911 CAGGTACTCATCAGCCACCTT 59.443 52.381 0.00 0.00 36.60 3.50
2959 6451 9.673454 TTTCAGCTAATGTATACATACACGTAG 57.327 33.333 18.56 15.66 45.11 3.51
3044 6671 4.351192 ACACGTTTGATTTTCACTTCTGC 58.649 39.130 0.00 0.00 0.00 4.26
3045 6672 4.096382 ACACGTTTGATTTTCACTTCTGCT 59.904 37.500 0.00 0.00 0.00 4.24
3046 6673 5.295787 ACACGTTTGATTTTCACTTCTGCTA 59.704 36.000 0.00 0.00 0.00 3.49
3048 6675 4.848299 CGTTTGATTTTCACTTCTGCTAGC 59.152 41.667 8.10 8.10 0.00 3.42
3049 6676 4.668576 TTGATTTTCACTTCTGCTAGCG 57.331 40.909 10.77 5.22 0.00 4.26
3052 6685 4.937620 TGATTTTCACTTCTGCTAGCGATT 59.062 37.500 10.77 0.00 0.00 3.34
3063 6696 8.893727 ACTTCTGCTAGCGATTGTTTAATATTT 58.106 29.630 10.77 0.00 0.00 1.40
3092 6725 5.865085 AGCTACAGAAAATTACACCAGTCA 58.135 37.500 0.00 0.00 0.00 3.41
3095 6728 6.204882 GCTACAGAAAATTACACCAGTCAGTT 59.795 38.462 0.00 0.00 0.00 3.16
3103 6736 7.404671 AATTACACCAGTCAGTTGAAAAACT 57.595 32.000 0.00 0.00 0.00 2.66
3104 6737 6.827586 TTACACCAGTCAGTTGAAAAACTT 57.172 33.333 0.00 0.00 0.00 2.66
3105 6738 5.059404 ACACCAGTCAGTTGAAAAACTTG 57.941 39.130 0.00 0.00 0.00 3.16
3132 6765 4.998033 AGTTCTTGTTACAGGCTAAAGCTC 59.002 41.667 1.39 0.00 41.70 4.09
3133 6766 3.939066 TCTTGTTACAGGCTAAAGCTCC 58.061 45.455 1.39 0.00 41.70 4.70
3140 6773 2.373502 ACAGGCTAAAGCTCCTTCAGTT 59.626 45.455 1.39 0.00 41.70 3.16
3141 6774 3.181439 ACAGGCTAAAGCTCCTTCAGTTT 60.181 43.478 1.39 0.00 41.70 2.66
3142 6775 4.041691 ACAGGCTAAAGCTCCTTCAGTTTA 59.958 41.667 1.39 0.00 41.70 2.01
3143 6776 4.633565 CAGGCTAAAGCTCCTTCAGTTTAG 59.366 45.833 1.39 0.00 41.70 1.85
3144 6777 4.287326 AGGCTAAAGCTCCTTCAGTTTAGT 59.713 41.667 1.39 0.00 41.70 2.24
3145 6778 5.004448 GGCTAAAGCTCCTTCAGTTTAGTT 58.996 41.667 1.39 0.00 41.70 2.24
3200 8248 1.565305 CAAGTCACCGCTAGCATCTC 58.435 55.000 16.45 0.77 0.00 2.75
3225 8273 6.074005 GCTCTTGTATTTGTTGAAACTCTCG 58.926 40.000 0.00 0.00 0.00 4.04
3226 8274 5.985781 TCTTGTATTTGTTGAAACTCTCGC 58.014 37.500 0.00 0.00 0.00 5.03
3227 8275 5.525745 TCTTGTATTTGTTGAAACTCTCGCA 59.474 36.000 0.00 0.00 0.00 5.10
3228 8276 5.090652 TGTATTTGTTGAAACTCTCGCAC 57.909 39.130 0.00 0.00 0.00 5.34
3229 8277 4.814234 TGTATTTGTTGAAACTCTCGCACT 59.186 37.500 0.00 0.00 0.00 4.40
3238 8286 5.936054 TGAAACTCTCGCACTACTAACTAC 58.064 41.667 0.00 0.00 0.00 2.73
3240 8288 2.351111 ACTCTCGCACTACTAACTACGC 59.649 50.000 0.00 0.00 0.00 4.42
3289 8337 4.074970 AGGTGCATCTTTGACCAAGTAAG 58.925 43.478 0.00 0.00 33.66 2.34
3320 8368 4.406972 CAGATGACCCAGAAGGAATACTCA 59.593 45.833 0.00 0.00 39.89 3.41
3329 8377 4.627467 CAGAAGGAATACTCACGGTTTCTG 59.373 45.833 0.00 0.00 35.78 3.02
3348 8396 1.717077 TGAAGACTGACTACCCTCCCT 59.283 52.381 0.00 0.00 0.00 4.20
3430 8486 2.484264 GGTTGTGCTCTGTCCATTGTAC 59.516 50.000 0.00 0.00 0.00 2.90
3434 8490 5.357742 TGTGCTCTGTCCATTGTACATAT 57.642 39.130 0.00 0.00 0.00 1.78
3435 8491 6.478512 TGTGCTCTGTCCATTGTACATATA 57.521 37.500 0.00 0.00 0.00 0.86
3436 8492 7.066307 TGTGCTCTGTCCATTGTACATATAT 57.934 36.000 0.00 0.00 0.00 0.86
3437 8493 7.154656 TGTGCTCTGTCCATTGTACATATATC 58.845 38.462 0.00 0.00 0.00 1.63
3438 8494 6.309009 GTGCTCTGTCCATTGTACATATATCG 59.691 42.308 0.00 0.00 0.00 2.92
3441 8497 4.827692 TGTCCATTGTACATATATCGCCC 58.172 43.478 0.00 0.00 0.00 6.13
3535 8596 1.087771 GCCCATTTTGCTGCAGATGC 61.088 55.000 20.43 3.09 42.50 3.91
3539 8600 1.066430 CATTTTGCTGCAGATGCCCTT 60.066 47.619 20.43 0.00 41.18 3.95
3540 8601 0.319083 TTTTGCTGCAGATGCCCTTG 59.681 50.000 20.43 0.00 41.18 3.61
3541 8602 0.828762 TTTGCTGCAGATGCCCTTGT 60.829 50.000 20.43 0.00 41.18 3.16
3542 8603 1.246056 TTGCTGCAGATGCCCTTGTC 61.246 55.000 20.43 0.00 41.18 3.18
3543 8604 2.413142 GCTGCAGATGCCCTTGTCC 61.413 63.158 20.43 0.00 41.18 4.02
3545 8606 2.825836 GCAGATGCCCTTGTCCCG 60.826 66.667 0.00 0.00 34.31 5.14
3546 8607 2.671070 CAGATGCCCTTGTCCCGT 59.329 61.111 0.00 0.00 0.00 5.28
3547 8608 1.450312 CAGATGCCCTTGTCCCGTC 60.450 63.158 0.00 0.00 0.00 4.79
3548 8609 2.124695 GATGCCCTTGTCCCGTCC 60.125 66.667 0.00 0.00 0.00 4.79
3551 8612 2.075355 ATGCCCTTGTCCCGTCCAAA 62.075 55.000 0.00 0.00 0.00 3.28
3563 8624 2.479656 CCCGTCCAAATTGCATTGTTTG 59.520 45.455 10.91 10.91 35.60 2.93
3570 8631 4.435693 CAAATTGCATTGTTTGTTCGACG 58.564 39.130 10.07 0.00 32.19 5.12
3571 8632 2.834574 TTGCATTGTTTGTTCGACGT 57.165 40.000 0.00 0.00 0.00 4.34
3572 8633 3.946308 TTGCATTGTTTGTTCGACGTA 57.054 38.095 0.00 0.00 0.00 3.57
3578 8639 5.447846 GCATTGTTTGTTCGACGTATGTATG 59.552 40.000 0.00 0.00 0.00 2.39
3582 8643 6.148264 TGTTTGTTCGACGTATGTATGTACA 58.852 36.000 0.00 0.00 40.98 2.90
3840 8902 8.387813 ACTTATGGTGTCCCTTATTCTAACAAA 58.612 33.333 0.00 0.00 0.00 2.83
3968 9030 2.749621 GTTCTGCTAACCAATGGTCAGG 59.250 50.000 16.47 7.17 33.12 3.86
3975 9037 6.905736 TGCTAACCAATGGTCAGGATAAATA 58.094 36.000 4.95 0.00 33.12 1.40
3976 9038 7.526041 TGCTAACCAATGGTCAGGATAAATAT 58.474 34.615 4.95 0.00 33.12 1.28
3977 9039 8.664992 TGCTAACCAATGGTCAGGATAAATATA 58.335 33.333 4.95 0.00 33.12 0.86
4007 9069 7.263100 AGAATATAATGCAACGCAAGATTCA 57.737 32.000 9.43 0.00 43.62 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.450115 GTGGAGGGGGAGACGACG 61.450 72.222 0.00 0.00 0.00 5.12
2 3 3.075641 GGTGGAGGGGGAGACGAC 61.076 72.222 0.00 0.00 0.00 4.34
3 4 4.393778 GGGTGGAGGGGGAGACGA 62.394 72.222 0.00 0.00 0.00 4.20
245 247 0.181350 ACCTCCCGATCAATCAAGCC 59.819 55.000 0.00 0.00 0.00 4.35
364 384 3.564027 CAACCGCTCCGATTCGCC 61.564 66.667 0.00 0.00 0.00 5.54
411 431 1.271054 GCTGCCCCACCTATGACTATG 60.271 57.143 0.00 0.00 0.00 2.23
500 526 5.613358 ACGATTTCAGGTTTCAATCTGTC 57.387 39.130 0.00 0.00 38.31 3.51
505 531 6.868339 GGATTCAAACGATTTCAGGTTTCAAT 59.132 34.615 0.00 0.00 34.33 2.57
514 540 1.129624 CGCGGGATTCAAACGATTTCA 59.870 47.619 0.00 0.00 0.00 2.69
537 563 8.950210 TCTAAATGGTAAAAATCTCAGCTCAAG 58.050 33.333 0.00 0.00 0.00 3.02
582 608 0.669077 GACGCGTATCCTCTCACCAT 59.331 55.000 13.97 0.00 0.00 3.55
586 612 1.434622 GACCGACGCGTATCCTCTCA 61.435 60.000 13.97 0.00 0.00 3.27
677 862 8.140112 ACAGTCTCATATTATCCTGGGATTAC 57.860 38.462 7.48 0.00 36.17 1.89
745 4234 8.722480 TCAAACAAATGATACAGATCTAGGTG 57.278 34.615 0.00 0.00 32.79 4.00
773 4262 6.347859 ACCTTCCAAACAAAAACAGTAACA 57.652 33.333 0.00 0.00 0.00 2.41
774 4263 7.541162 ACTACCTTCCAAACAAAAACAGTAAC 58.459 34.615 0.00 0.00 0.00 2.50
908 4397 1.329292 TGTAAGCAACAGTGACAACGC 59.671 47.619 0.00 0.00 33.01 4.84
909 4398 2.350192 TGTGTAAGCAACAGTGACAACG 59.650 45.455 0.00 0.00 39.29 4.10
910 4399 4.527564 GATGTGTAAGCAACAGTGACAAC 58.472 43.478 0.00 0.00 39.29 3.32
911 4400 3.247411 CGATGTGTAAGCAACAGTGACAA 59.753 43.478 0.00 0.00 39.29 3.18
916 4405 3.106242 TGTCGATGTGTAAGCAACAGT 57.894 42.857 0.00 0.00 39.29 3.55
954 4443 1.130373 TCGATTCCAAACGCAATGAGC 59.870 47.619 0.00 0.00 40.87 4.26
981 4470 2.665649 TATACAAGCCAGACACACCG 57.334 50.000 0.00 0.00 0.00 4.94
1070 4559 2.747460 CCGACAGTGGCCATGTGG 60.747 66.667 20.93 19.03 38.53 4.17
1374 4863 4.524053 GGAAGGTAAACTCCCCAATACAG 58.476 47.826 0.00 0.00 0.00 2.74
1407 4896 1.679641 CCCCAATTTTACGGCCCGT 60.680 57.895 15.63 15.63 44.35 5.28
1785 5274 5.416639 TCACAAAAGAATGGGATGTCATCAG 59.583 40.000 14.72 0.00 0.00 2.90
1900 5389 7.502060 AGATAGTTATATGCCCATGCTAACT 57.498 36.000 15.84 15.84 38.71 2.24
2122 5611 7.453126 GGATCCATAGAGGTAGAAGAATTCTGA 59.547 40.741 9.17 0.00 46.61 3.27
2253 5743 3.058639 GCCAAAAGCTACACAGAACTCTG 60.059 47.826 5.15 5.15 43.50 3.35
2297 5787 7.946381 TGGAGTACACCATATGCAAATTTTA 57.054 32.000 8.07 0.00 34.77 1.52
2462 5953 9.885743 GTCATTTTACGAAATTGACAATAATGC 57.114 29.630 19.17 0.37 44.77 3.56
2488 5979 7.381408 TGTTTTGAGATCACTACTTACTTCACG 59.619 37.037 0.00 0.00 0.00 4.35
2494 5985 9.974750 GCTTAATGTTTTGAGATCACTACTTAC 57.025 33.333 0.00 0.00 0.00 2.34
2527 6018 1.096386 AGCAATAGCAGAGCAGCAGC 61.096 55.000 0.00 0.00 45.49 5.25
2537 6028 6.350629 TCTCTCATAGCAATAGCAATAGCA 57.649 37.500 0.00 0.00 45.49 3.49
2538 6029 7.664082 TTTCTCTCATAGCAATAGCAATAGC 57.336 36.000 0.00 0.00 45.49 2.97
2539 6030 9.486497 TCTTTTCTCTCATAGCAATAGCAATAG 57.514 33.333 0.00 0.00 45.49 1.73
2540 6031 9.836864 TTCTTTTCTCTCATAGCAATAGCAATA 57.163 29.630 0.00 0.00 45.49 1.90
2541 6032 8.743085 TTCTTTTCTCTCATAGCAATAGCAAT 57.257 30.769 0.00 0.00 45.49 3.56
2542 6033 8.565896 TTTCTTTTCTCTCATAGCAATAGCAA 57.434 30.769 0.00 0.00 45.49 3.91
2574 6065 8.560355 TTGCTGCTAGAATTGAGTTTTGTATA 57.440 30.769 0.00 0.00 0.00 1.47
2575 6066 7.362401 CCTTGCTGCTAGAATTGAGTTTTGTAT 60.362 37.037 12.66 0.00 0.00 2.29
2576 6067 6.072508 CCTTGCTGCTAGAATTGAGTTTTGTA 60.073 38.462 12.66 0.00 0.00 2.41
2584 6075 1.683011 GGCCCTTGCTGCTAGAATTGA 60.683 52.381 12.66 0.00 37.74 2.57
2603 6094 7.447374 TGATAAGTAAAACATGTGGTCTTGG 57.553 36.000 0.00 0.00 0.00 3.61
2637 6129 6.205464 ACTGGTTATGAAGTGAATCACAAGTG 59.795 38.462 16.38 0.00 36.74 3.16
2665 6157 6.822667 TCTGAACATGCATACAAACTGATT 57.177 33.333 0.00 0.00 0.00 2.57
2781 6273 3.181451 ACTGAGCAAATGACCACTCTGAA 60.181 43.478 0.00 0.00 33.71 3.02
2811 6303 0.598158 TGTAACGTGTGACTTCCGGC 60.598 55.000 0.00 0.00 0.00 6.13
3016 6643 8.567948 AGAAGTGAAAATCAAACGTGTATTGAT 58.432 29.630 7.91 7.91 46.62 2.57
3065 6698 9.595823 GACTGGTGTAATTTTCTGTAGCTATAA 57.404 33.333 0.00 0.00 0.00 0.98
3066 6699 8.755028 TGACTGGTGTAATTTTCTGTAGCTATA 58.245 33.333 0.00 0.00 0.00 1.31
3067 6700 7.620880 TGACTGGTGTAATTTTCTGTAGCTAT 58.379 34.615 0.00 0.00 0.00 2.97
3103 6736 3.118038 AGCCTGTAACAAGAACTGTCCAA 60.118 43.478 0.00 0.00 37.23 3.53
3104 6737 2.438021 AGCCTGTAACAAGAACTGTCCA 59.562 45.455 0.00 0.00 37.23 4.02
3105 6738 3.127425 AGCCTGTAACAAGAACTGTCC 57.873 47.619 0.00 0.00 37.23 4.02
3132 6765 6.723131 GGCAACTACTAACTAAACTGAAGG 57.277 41.667 0.00 0.00 0.00 3.46
3169 6802 3.677424 GCGGTGACTTGCTAGAGAAGAAT 60.677 47.826 1.04 0.00 0.00 2.40
3200 8248 5.990408 AGAGTTTCAACAAATACAAGAGCG 58.010 37.500 0.00 0.00 0.00 5.03
3225 8273 1.399791 AGTCGGCGTAGTTAGTAGTGC 59.600 52.381 6.85 0.00 0.00 4.40
3226 8274 3.754188 AAGTCGGCGTAGTTAGTAGTG 57.246 47.619 6.85 0.00 0.00 2.74
3227 8275 4.479619 CAAAAGTCGGCGTAGTTAGTAGT 58.520 43.478 6.85 0.00 0.00 2.73
3228 8276 3.302699 GCAAAAGTCGGCGTAGTTAGTAG 59.697 47.826 6.85 0.00 0.00 2.57
3229 8277 3.244976 GCAAAAGTCGGCGTAGTTAGTA 58.755 45.455 6.85 0.00 0.00 1.82
3238 8286 1.616872 GCAAATGGCAAAAGTCGGCG 61.617 55.000 0.00 0.00 43.97 6.46
3305 8353 3.611766 AACCGTGAGTATTCCTTCTGG 57.388 47.619 0.00 0.00 0.00 3.86
3320 8368 3.005578 GGTAGTCAGTCTTCAGAAACCGT 59.994 47.826 0.00 0.00 0.00 4.83
3329 8377 2.498078 CAAGGGAGGGTAGTCAGTCTTC 59.502 54.545 0.00 0.00 0.00 2.87
3348 8396 0.604073 TACGCGGTCAATGTCCTCAA 59.396 50.000 12.47 0.00 0.00 3.02
3379 8427 1.445410 TACATGTCGGTGCAGCGTC 60.445 57.895 34.29 29.47 0.00 5.19
3380 8428 1.736645 GTACATGTCGGTGCAGCGT 60.737 57.895 34.29 19.44 0.00 5.07
3381 8429 1.083806 ATGTACATGTCGGTGCAGCG 61.084 55.000 31.22 31.22 36.83 5.18
3384 8432 3.535280 ATGTATGTACATGTCGGTGCA 57.465 42.857 18.81 1.78 44.66 4.57
3507 8566 1.371932 CAAAATGGGCAGGCAAGCA 59.628 52.632 4.37 0.00 35.83 3.91
3510 8571 1.371932 CAGCAAAATGGGCAGGCAA 59.628 52.632 0.00 0.00 0.00 4.52
3535 8596 0.887933 CAATTTGGACGGGACAAGGG 59.112 55.000 0.00 0.00 0.00 3.95
3539 8600 1.271934 CAATGCAATTTGGACGGGACA 59.728 47.619 0.00 0.00 31.22 4.02
3540 8601 1.272212 ACAATGCAATTTGGACGGGAC 59.728 47.619 5.11 0.00 31.22 4.46
3541 8602 1.626686 ACAATGCAATTTGGACGGGA 58.373 45.000 5.11 0.00 31.22 5.14
3542 8603 2.453983 AACAATGCAATTTGGACGGG 57.546 45.000 5.11 0.00 31.22 5.28
3543 8604 3.129871 ACAAACAATGCAATTTGGACGG 58.870 40.909 19.58 4.81 39.61 4.79
3545 8606 4.505922 TCGAACAAACAATGCAATTTGGAC 59.494 37.500 19.58 13.65 39.61 4.02
3546 8607 4.505922 GTCGAACAAACAATGCAATTTGGA 59.494 37.500 19.58 0.00 39.61 3.53
3547 8608 4.605793 CGTCGAACAAACAATGCAATTTGG 60.606 41.667 19.58 7.62 39.61 3.28
3548 8609 4.026968 ACGTCGAACAAACAATGCAATTTG 60.027 37.500 15.90 15.90 40.83 2.32
3551 8612 3.347958 ACGTCGAACAAACAATGCAAT 57.652 38.095 0.00 0.00 0.00 3.56
3563 8624 4.794762 TGCTTGTACATACATACGTCGAAC 59.205 41.667 0.00 0.00 35.89 3.95
3633 8694 8.160106 GGGTCTTGATCCATTCTTATATTGAGT 58.840 37.037 0.00 0.00 0.00 3.41
3840 8902 0.801067 GCGCATCGAGTTAAGTCGGT 60.801 55.000 27.64 21.04 40.49 4.69


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

AutoCloner maintained by Alex Coulton.