Multiple sequence alignment - TraesCS4A01G428700

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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 TraesCS4A01G428700 chr4A 100.000 3320 0 0 1 3320 699883052 699886371 0 6131
1 TraesCS4A01G428700 chr7A 89.559 3381 199 50 1 3318 30095604 30092315 0 4146
2 TraesCS4A01G428700 chr7D 89.153 3402 227 54 1 3320 29836634 29833293 0 4108


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 TraesCS4A01G428700 chr4A 699883052 699886371 3319 False 6131 6131 100.000 1 3320 1 chr4A.!!$F1 3319
1 TraesCS4A01G428700 chr7A 30092315 30095604 3289 True 4146 4146 89.559 1 3318 1 chr7A.!!$R1 3317
2 TraesCS4A01G428700 chr7D 29833293 29836634 3341 True 4108 4108 89.153 1 3320 1 chr7D.!!$R1 3319

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
943 1046 0.10412 GTTGTGGGGTTTCTGTTGCC 59.896 55.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2689 2795 0.035458 AAGCGGTCCTCAGGAACAAG 59.965 55.0 10.16 0.0 39.88 3.16 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
107 118 1.619363 CCCTCTTCCCATCCCACCA 60.619 63.158 0.00 0.00 0.00 4.17
114 125 2.538141 CCCATCCCACCACACCACT 61.538 63.158 0.00 0.00 0.00 4.00
352 396 2.572284 GGCACCGTCGCTAGAAGT 59.428 61.111 0.00 0.00 0.00 3.01
353 397 1.080025 GGCACCGTCGCTAGAAGTT 60.080 57.895 0.00 0.00 0.00 2.66
374 435 4.065281 GGTACAGCGCCCTCGTGT 62.065 66.667 2.29 3.69 38.14 4.49
419 480 1.610886 GCCTAGGAGTCGGTTTTGCTT 60.611 52.381 14.75 0.00 0.00 3.91
427 488 2.190841 CGGTTTTGCTTGGTCGGGT 61.191 57.895 0.00 0.00 0.00 5.28
431 492 3.835790 TTTGCTTGGTCGGGTCGGG 62.836 63.158 0.00 0.00 0.00 5.14
458 519 1.003718 GGGTTCCAGTTCCAGACCG 60.004 63.158 0.00 0.00 0.00 4.79
480 561 1.448069 GCCCCTCGATTCCTCCTTC 59.552 63.158 0.00 0.00 0.00 3.46
513 594 1.373497 GATGCCCGCGGATCTACAG 60.373 63.158 30.73 9.14 0.00 2.74
537 618 0.375454 CGCGTATTGATTTTCGGCCA 59.625 50.000 2.24 0.00 0.00 5.36
563 645 1.177401 GAGGAAATGGGGTGTTGCTC 58.823 55.000 0.00 0.00 35.46 4.26
635 717 4.362932 TGTCAAGTCTTAGCTCTGATCG 57.637 45.455 0.00 0.00 0.00 3.69
645 739 3.883830 AGCTCTGATCGATTTGTGAGT 57.116 42.857 0.00 0.00 0.00 3.41
646 740 3.519579 AGCTCTGATCGATTTGTGAGTG 58.480 45.455 0.00 0.00 0.00 3.51
647 741 3.056250 AGCTCTGATCGATTTGTGAGTGT 60.056 43.478 0.00 0.00 0.00 3.55
648 742 3.681897 GCTCTGATCGATTTGTGAGTGTT 59.318 43.478 0.00 0.00 0.00 3.32
649 743 4.201666 GCTCTGATCGATTTGTGAGTGTTC 60.202 45.833 0.00 0.00 0.00 3.18
650 744 4.245660 TCTGATCGATTTGTGAGTGTTCC 58.754 43.478 0.00 0.00 0.00 3.62
651 745 3.334691 TGATCGATTTGTGAGTGTTCCC 58.665 45.455 0.00 0.00 0.00 3.97
652 746 2.920724 TCGATTTGTGAGTGTTCCCA 57.079 45.000 0.00 0.00 0.00 4.37
653 747 2.766313 TCGATTTGTGAGTGTTCCCAG 58.234 47.619 0.00 0.00 0.00 4.45
654 748 2.367241 TCGATTTGTGAGTGTTCCCAGA 59.633 45.455 0.00 0.00 0.00 3.86
655 749 2.738846 CGATTTGTGAGTGTTCCCAGAG 59.261 50.000 0.00 0.00 0.00 3.35
656 750 3.744660 GATTTGTGAGTGTTCCCAGAGT 58.255 45.455 0.00 0.00 0.00 3.24
682 776 2.047274 TGTTCCAGTGCCGCTAGC 60.047 61.111 4.06 4.06 44.14 3.42
692 786 2.917198 GCCGCTAGCTAGTACCCCG 61.917 68.421 21.62 15.21 38.99 5.73
693 787 1.228063 CCGCTAGCTAGTACCCCGA 60.228 63.158 21.62 0.00 0.00 5.14
694 788 0.820891 CCGCTAGCTAGTACCCCGAA 60.821 60.000 21.62 0.00 0.00 4.30
695 789 1.027357 CGCTAGCTAGTACCCCGAAA 58.973 55.000 21.62 0.00 0.00 3.46
696 790 1.268948 CGCTAGCTAGTACCCCGAAAC 60.269 57.143 21.62 0.50 0.00 2.78
700 794 1.895131 AGCTAGTACCCCGAAACGAAA 59.105 47.619 0.00 0.00 0.00 3.46
701 795 1.995484 GCTAGTACCCCGAAACGAAAC 59.005 52.381 0.00 0.00 0.00 2.78
706 800 0.747644 ACCCCGAAACGAAACGGTTT 60.748 50.000 5.68 5.68 46.53 3.27
721 819 1.267532 CGGTTTTCGCGGATGAATCTG 60.268 52.381 6.13 0.00 36.26 2.90
752 850 7.277396 AGCAAGGTTTGAGTAGTTAGTTAACA 58.723 34.615 8.61 0.00 38.62 2.41
795 893 3.819564 AATCGGATTCAGATTCGGACA 57.180 42.857 6.26 0.00 34.91 4.02
838 936 9.883142 TTATTTCCATTTATTTGCTTTGGGTAG 57.117 29.630 0.00 0.00 0.00 3.18
881 983 4.835615 ACCAGCAATTATGTTTTGTACCCA 59.164 37.500 0.00 0.00 0.00 4.51
882 984 5.167845 CCAGCAATTATGTTTTGTACCCAC 58.832 41.667 0.00 0.00 0.00 4.61
885 987 4.170256 CAATTATGTTTTGTACCCACGGC 58.830 43.478 0.00 0.00 0.00 5.68
896 998 2.613506 CCCACGGCCGAAACAACTC 61.614 63.158 35.90 0.00 0.00 3.01
907 1009 4.347813 CCGAAACAACTCATCGTGTTTTT 58.652 39.130 3.53 0.00 35.02 1.94
910 1012 6.302313 CCGAAACAACTCATCGTGTTTTTATC 59.698 38.462 3.53 0.00 35.02 1.75
915 1017 7.077605 ACAACTCATCGTGTTTTTATCATGTG 58.922 34.615 0.00 0.00 0.00 3.21
924 1026 4.236935 GTTTTTATCATGTGTGTGCAGGG 58.763 43.478 0.00 0.00 0.00 4.45
943 1046 0.104120 GTTGTGGGGTTTCTGTTGCC 59.896 55.000 0.00 0.00 0.00 4.52
944 1047 1.388065 TTGTGGGGTTTCTGTTGCCG 61.388 55.000 0.00 0.00 0.00 5.69
981 1084 2.191641 GCCACTGATCTCCAGGGC 59.808 66.667 0.00 0.00 45.00 5.19
1007 1110 4.343526 ACTTTATCGCTCACTCATGGAGAT 59.656 41.667 0.00 0.00 34.24 2.75
1023 1126 2.421424 GGAGATGGTTGATGCAGTTGAC 59.579 50.000 0.00 0.00 0.00 3.18
1044 1147 2.734606 CGGATACAAGTTTGCTGACGAA 59.265 45.455 0.00 0.00 0.00 3.85
1074 1177 2.159707 CGATGTCCGTGTTTGCTTTAGG 60.160 50.000 0.00 0.00 0.00 2.69
1075 1178 0.948678 TGTCCGTGTTTGCTTTAGGC 59.051 50.000 0.00 0.00 42.22 3.93
1171 1274 2.617274 GCGGACTTGCTGGGTCAAC 61.617 63.158 0.00 0.00 35.61 3.18
1172 1275 1.227823 CGGACTTGCTGGGTCAACA 60.228 57.895 0.00 0.00 35.61 3.33
1173 1276 0.817634 CGGACTTGCTGGGTCAACAA 60.818 55.000 0.00 0.00 35.61 2.83
1338 1444 3.491652 GGCGTTCTTCGAGCAGCC 61.492 66.667 4.26 4.26 42.86 4.85
1377 1483 0.320858 TCGTTGCCGAAACCTGCATA 60.321 50.000 0.00 0.00 40.86 3.14
1467 1573 3.060615 CCAGAAGCTGCTGCACCC 61.061 66.667 17.16 6.10 42.74 4.61
1473 1579 1.741327 AAGCTGCTGCACCCTTGTTG 61.741 55.000 18.42 0.00 42.74 3.33
1579 1685 3.118629 AGCTGCTCCTTTATTCGATGACA 60.119 43.478 0.00 0.00 0.00 3.58
1708 1814 3.498082 ACAAAACTGTTGTCAACGCTTC 58.502 40.909 11.03 0.00 0.00 3.86
1719 1825 0.242825 CAACGCTTCGGACTGGACTA 59.757 55.000 0.00 0.00 0.00 2.59
1823 1929 5.179555 GGATAACCACTGTCTTGACAAAGAC 59.820 44.000 10.90 10.90 46.85 3.01
1891 1997 1.116308 TGTTGTCTCGGTGGTTCAGA 58.884 50.000 0.00 0.00 0.00 3.27
1896 2002 0.313043 TCTCGGTGGTTCAGAACGAC 59.687 55.000 17.76 17.76 39.11 4.34
2109 2215 1.750399 GATGGATGCGGGCTTGTGT 60.750 57.895 0.00 0.00 0.00 3.72
2115 2221 0.322816 ATGCGGGCTTGTGTCAGAAT 60.323 50.000 0.00 0.00 0.00 2.40
2298 2404 1.489560 ATGGGGCGGTAGATAAGGGC 61.490 60.000 0.00 0.00 0.00 5.19
2299 2405 2.144738 GGGGCGGTAGATAAGGGCA 61.145 63.158 0.00 0.00 0.00 5.36
2387 2493 5.163693 CCGGTTATACCAACCAAATTCTCAC 60.164 44.000 6.95 0.00 38.47 3.51
2388 2494 5.413213 CGGTTATACCAACCAAATTCTCACA 59.587 40.000 6.95 0.00 38.47 3.58
2389 2495 6.403200 CGGTTATACCAACCAAATTCTCACAG 60.403 42.308 6.95 0.00 38.47 3.66
2390 2496 6.433093 GGTTATACCAACCAAATTCTCACAGT 59.567 38.462 1.30 0.00 38.42 3.55
2391 2497 7.361799 GGTTATACCAACCAAATTCTCACAGTC 60.362 40.741 1.30 0.00 38.42 3.51
2392 2498 3.897239 ACCAACCAAATTCTCACAGTCA 58.103 40.909 0.00 0.00 0.00 3.41
2393 2499 4.277476 ACCAACCAAATTCTCACAGTCAA 58.723 39.130 0.00 0.00 0.00 3.18
2394 2500 4.709397 ACCAACCAAATTCTCACAGTCAAA 59.291 37.500 0.00 0.00 0.00 2.69
2395 2501 5.186797 ACCAACCAAATTCTCACAGTCAAAA 59.813 36.000 0.00 0.00 0.00 2.44
2396 2502 6.105333 CCAACCAAATTCTCACAGTCAAAAA 58.895 36.000 0.00 0.00 0.00 1.94
2430 2536 4.097135 TCATTGTCGGATGTTGTTGTTGTT 59.903 37.500 0.00 0.00 0.00 2.83
2431 2537 3.412981 TGTCGGATGTTGTTGTTGTTG 57.587 42.857 0.00 0.00 0.00 3.33
2432 2538 2.750166 TGTCGGATGTTGTTGTTGTTGT 59.250 40.909 0.00 0.00 0.00 3.32
2433 2539 3.191581 TGTCGGATGTTGTTGTTGTTGTT 59.808 39.130 0.00 0.00 0.00 2.83
2434 2540 3.545873 GTCGGATGTTGTTGTTGTTGTTG 59.454 43.478 0.00 0.00 0.00 3.33
2435 2541 3.191581 TCGGATGTTGTTGTTGTTGTTGT 59.808 39.130 0.00 0.00 0.00 3.32
2498 2604 5.698545 AGTTCTTCTGCAGTATGTTCTTGTC 59.301 40.000 14.67 0.00 39.31 3.18
2500 2606 3.934457 TCTGCAGTATGTTCTTGTCGA 57.066 42.857 14.67 0.00 39.31 4.20
2511 2617 2.536761 TCTTGTCGAAAATCACCGGT 57.463 45.000 0.00 0.00 0.00 5.28
2515 2621 3.612472 TGTCGAAAATCACCGGTTTTC 57.388 42.857 16.88 16.88 40.45 2.29
2723 2829 1.233019 CGCTTAAGCATGGATCCTGG 58.767 55.000 26.29 6.07 42.21 4.45
2775 2881 4.079253 GTTCCATGGCCAAAAACTCTCTA 58.921 43.478 10.96 0.00 0.00 2.43
2776 2882 4.380843 TCCATGGCCAAAAACTCTCTAA 57.619 40.909 10.96 0.00 0.00 2.10
2807 2918 1.272092 TGATGGTTGCTTCTTCCAGGG 60.272 52.381 0.00 0.00 34.62 4.45
2818 2929 1.004277 TCTTCCAGGGTATGTTGCCAC 59.996 52.381 0.00 0.00 0.00 5.01
2897 3008 3.059461 GGACGTCTTACATTTTGCGACAA 60.059 43.478 16.46 0.00 0.00 3.18
2928 3039 4.451096 TGCCTCAAGATGTAAGACGTTTTC 59.549 41.667 0.00 0.00 0.00 2.29
2949 3061 5.817616 TCGACAAGAACGTCTTACATTTC 57.182 39.130 0.00 0.00 33.78 2.17
2964 3076 1.134367 CATTTCGCGACAGAGGGAGTA 59.866 52.381 9.15 0.00 34.56 2.59
3032 3144 4.524328 AGTCTTGGCAAGTTAATTCCCTTG 59.476 41.667 25.39 11.00 40.77 3.61
3070 3186 7.490840 TGGCAACATGATATTAACAATTCCTG 58.509 34.615 0.00 0.00 46.17 3.86
3129 3245 0.767998 TGTTCACCATGTGCCTACCA 59.232 50.000 0.00 0.00 32.98 3.25
3141 3257 5.622346 TGTGCCTACCAAATTTCCTTTTT 57.378 34.783 0.00 0.00 0.00 1.94
3172 3288 7.855904 CCTATATTCTTTGGTTATCACGTTTGC 59.144 37.037 0.00 0.00 0.00 3.68
3180 3296 0.109964 TATCACGTTTGCGCTTTGCC 60.110 50.000 9.73 0.00 45.60 4.52
3183 3299 1.067250 ACGTTTGCGCTTTGCCATT 59.933 47.368 9.73 0.00 45.60 3.16
3199 3315 4.470334 GCCATTTGCATTAAGAGGGAAA 57.530 40.909 0.00 0.00 40.77 3.13
3201 3317 4.081476 GCCATTTGCATTAAGAGGGAAAGT 60.081 41.667 0.00 0.00 40.77 2.66
3202 3318 5.654497 CCATTTGCATTAAGAGGGAAAGTC 58.346 41.667 0.00 0.00 30.63 3.01
3203 3319 5.185635 CCATTTGCATTAAGAGGGAAAGTCA 59.814 40.000 0.00 0.00 30.63 3.41
3204 3320 6.127253 CCATTTGCATTAAGAGGGAAAGTCAT 60.127 38.462 0.00 0.00 30.63 3.06
3246 3362 3.197766 TGTACAGCTTAATGGAGGTGGAG 59.802 47.826 11.17 0.00 46.59 3.86
3262 3378 1.350019 TGGAGCATGCATCAGATAGGG 59.650 52.381 21.98 0.00 0.00 3.53
3281 3397 5.977489 AGGGTTGGAAATTTAGTTGCTAC 57.023 39.130 0.00 0.00 0.00 3.58
3306 3422 3.071479 TCATTGTCTTCACTAAACCGCC 58.929 45.455 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 103 1.497309 GGTGTGGTGGGATGGGAAGA 61.497 60.000 0.00 0.00 0.00 2.87
107 118 4.954118 TGGGGGCGAGAGTGGTGT 62.954 66.667 0.00 0.00 0.00 4.16
114 125 3.126703 TTGCAACTTGGGGGCGAGA 62.127 57.895 0.00 0.00 0.00 4.04
220 264 1.153349 CCTAAGGAAGCCGGCTGAC 60.153 63.158 33.60 25.59 0.00 3.51
427 488 4.726254 AACCCGTCCATCCCCCGA 62.726 66.667 0.00 0.00 0.00 5.14
438 499 1.752833 GTCTGGAACTGGAACCCGT 59.247 57.895 0.00 0.00 0.00 5.28
439 500 1.003718 GGTCTGGAACTGGAACCCG 60.004 63.158 0.00 0.00 0.00 5.28
513 594 2.298300 CGAAAATCAATACGCGGATGC 58.702 47.619 3.56 0.00 37.91 3.91
537 618 1.158007 ACCCCATTTCCTCACACCTT 58.842 50.000 0.00 0.00 0.00 3.50
576 658 2.348998 GACACACCTGCCTCTGGG 59.651 66.667 0.00 0.00 0.00 4.45
618 700 5.809562 CACAAATCGATCAGAGCTAAGACTT 59.190 40.000 0.00 0.00 0.00 3.01
619 701 5.126222 TCACAAATCGATCAGAGCTAAGACT 59.874 40.000 0.00 0.00 0.00 3.24
622 704 5.231779 CACTCACAAATCGATCAGAGCTAAG 59.768 44.000 0.00 0.00 0.00 2.18
635 717 3.744660 ACTCTGGGAACACTCACAAATC 58.255 45.455 0.00 0.00 33.48 2.17
665 759 1.254975 TAGCTAGCGGCACTGGAACA 61.255 55.000 9.55 0.00 44.79 3.18
678 772 2.292267 TCGTTTCGGGGTACTAGCTAG 58.708 52.381 19.44 19.44 0.00 3.42
682 776 2.253603 CGTTTCGTTTCGGGGTACTAG 58.746 52.381 0.00 0.00 0.00 2.57
700 794 0.725117 GATTCATCCGCGAAAACCGT 59.275 50.000 8.23 0.00 41.15 4.83
701 795 1.006832 AGATTCATCCGCGAAAACCG 58.993 50.000 8.23 0.00 42.21 4.44
706 800 4.024893 GCTTTATTCAGATTCATCCGCGAA 60.025 41.667 8.23 0.00 0.00 4.70
714 808 7.231317 ACTCAAACCTTGCTTTATTCAGATTCA 59.769 33.333 0.00 0.00 0.00 2.57
721 819 9.000486 ACTAACTACTCAAACCTTGCTTTATTC 58.000 33.333 0.00 0.00 0.00 1.75
752 850 1.194781 AGTCGGCATTCAGACACCCT 61.195 55.000 0.00 0.00 39.67 4.34
795 893 7.001674 TGGAAATAAATAACATACTGCCCGAT 58.998 34.615 0.00 0.00 0.00 4.18
857 959 6.010850 TGGGTACAAAACATAATTGCTGGTA 58.989 36.000 0.00 0.00 0.00 3.25
865 967 2.756207 GGCCGTGGGTACAAAACATAAT 59.244 45.455 0.00 0.00 0.00 1.28
868 970 1.238625 CGGCCGTGGGTACAAAACAT 61.239 55.000 19.50 0.00 0.00 2.71
876 978 1.597578 GTTGTTTCGGCCGTGGGTA 60.598 57.895 27.15 1.01 0.00 3.69
881 983 1.289109 CGATGAGTTGTTTCGGCCGT 61.289 55.000 27.15 2.66 0.00 5.68
882 984 1.289109 ACGATGAGTTGTTTCGGCCG 61.289 55.000 22.12 22.12 37.20 6.13
885 987 3.602390 AAACACGATGAGTTGTTTCGG 57.398 42.857 0.00 0.00 37.20 4.30
896 998 5.059587 GCACACACATGATAAAAACACGATG 59.940 40.000 0.00 0.00 0.00 3.84
907 1009 2.224744 ACAACCCTGCACACACATGATA 60.225 45.455 0.00 0.00 0.00 2.15
910 1012 0.031043 CACAACCCTGCACACACATG 59.969 55.000 0.00 0.00 0.00 3.21
915 1017 2.912025 CCCCACAACCCTGCACAC 60.912 66.667 0.00 0.00 0.00 3.82
924 1026 0.104120 GGCAACAGAAACCCCACAAC 59.896 55.000 0.00 0.00 0.00 3.32
943 1046 2.353889 CAGCAATCTTCCACCTTCATCG 59.646 50.000 0.00 0.00 0.00 3.84
944 1047 2.098770 GCAGCAATCTTCCACCTTCATC 59.901 50.000 0.00 0.00 0.00 2.92
981 1084 5.532557 TCCATGAGTGAGCGATAAAGTATG 58.467 41.667 0.00 0.00 0.00 2.39
1007 1110 0.107643 TCCGTCAACTGCATCAACCA 59.892 50.000 0.00 0.00 0.00 3.67
1023 1126 2.333926 TCGTCAGCAAACTTGTATCCG 58.666 47.619 0.00 0.00 0.00 4.18
1044 1147 0.308068 CACGGACATCGCTCGTAGAT 59.692 55.000 0.00 0.00 43.89 1.98
1171 1274 1.135315 CAGAACGGGCATCGCTTTG 59.865 57.895 0.00 0.00 43.89 2.77
1172 1275 2.040544 CCAGAACGGGCATCGCTTT 61.041 57.895 0.00 0.00 43.89 3.51
1173 1276 2.436646 CCAGAACGGGCATCGCTT 60.437 61.111 0.00 0.00 43.89 4.68
1320 1426 3.843240 GCTGCTCGAAGAACGCCG 61.843 66.667 0.00 0.00 42.26 6.46
1338 1444 3.516615 GAACTCGGATTTGAGAGAGGTG 58.483 50.000 0.00 0.00 39.35 4.00
1404 1510 6.461577 AAAATCTCTTCCTCCTCCTTTTCT 57.538 37.500 0.00 0.00 0.00 2.52
1467 1573 0.875474 CTTGCAAACGGGCCAACAAG 60.875 55.000 4.39 5.50 0.00 3.16
1473 1579 4.056125 GGAGCTTGCAAACGGGCC 62.056 66.667 0.00 0.00 0.00 5.80
1506 1612 3.330267 AGCGGAGATGAAAACAGTCTTC 58.670 45.455 0.00 0.00 0.00 2.87
1540 1646 1.086634 GCTGAAGTCTCCATGGACGC 61.087 60.000 11.44 6.52 40.76 5.19
1579 1685 2.936114 GCTCTTGAGCAGCAGTCTTGAT 60.936 50.000 16.71 0.00 36.82 2.57
1704 1810 2.292292 GAGATCTAGTCCAGTCCGAAGC 59.708 54.545 0.00 0.00 0.00 3.86
1708 1814 2.621055 CCAAGAGATCTAGTCCAGTCCG 59.379 54.545 0.00 0.00 0.00 4.79
1719 1825 2.548464 ACTCTGAGGCCAAGAGATCT 57.452 50.000 31.56 14.29 34.13 2.75
1823 1929 3.062763 ACAAACTCGTTCATCAGCTCAG 58.937 45.455 0.00 0.00 0.00 3.35
1891 1997 4.017808 AGACCTGAGCTATACTTGTCGTT 58.982 43.478 0.00 0.00 30.98 3.85
1896 2002 3.181471 CCCACAGACCTGAGCTATACTTG 60.181 52.174 3.76 0.00 0.00 3.16
2097 2203 0.323302 TATTCTGACACAAGCCCGCA 59.677 50.000 0.00 0.00 0.00 5.69
2109 2215 3.650070 ATTGCGCTCTCGATATTCTGA 57.350 42.857 9.73 0.00 38.10 3.27
2115 2221 3.258228 TGAAACAATTGCGCTCTCGATA 58.742 40.909 9.73 0.00 38.10 2.92
2235 2341 0.389296 TGCGGTAACACCACATCTCG 60.389 55.000 0.00 0.00 38.47 4.04
2287 2393 1.968704 GGGTTGCTGCCCTTATCTAC 58.031 55.000 8.62 0.00 45.22 2.59
2298 2404 2.119801 ACAAGCTGATAGGGTTGCTG 57.880 50.000 6.36 0.00 45.19 4.41
2299 2405 3.370953 CCTTACAAGCTGATAGGGTTGCT 60.371 47.826 6.36 0.00 45.19 3.91
2352 2458 6.225318 GTTGGTATAACCGGCTAATATCACA 58.775 40.000 0.00 0.00 42.58 3.58
2397 2503 7.710475 ACAACATCCGACAATGAGAAAATTTTT 59.290 29.630 4.63 0.00 0.00 1.94
2398 2504 7.209475 ACAACATCCGACAATGAGAAAATTTT 58.791 30.769 2.28 2.28 0.00 1.82
2399 2505 6.748132 ACAACATCCGACAATGAGAAAATTT 58.252 32.000 0.00 0.00 0.00 1.82
2400 2506 6.331369 ACAACATCCGACAATGAGAAAATT 57.669 33.333 0.00 0.00 0.00 1.82
2401 2507 5.964958 ACAACATCCGACAATGAGAAAAT 57.035 34.783 0.00 0.00 0.00 1.82
2402 2508 5.067153 ACAACAACATCCGACAATGAGAAAA 59.933 36.000 0.00 0.00 0.00 2.29
2403 2509 4.578516 ACAACAACATCCGACAATGAGAAA 59.421 37.500 0.00 0.00 0.00 2.52
2404 2510 4.133820 ACAACAACATCCGACAATGAGAA 58.866 39.130 0.00 0.00 0.00 2.87
2405 2511 3.738982 ACAACAACATCCGACAATGAGA 58.261 40.909 0.00 0.00 0.00 3.27
2406 2512 4.221342 CAACAACAACATCCGACAATGAG 58.779 43.478 0.00 0.00 0.00 2.90
2407 2513 3.629855 ACAACAACAACATCCGACAATGA 59.370 39.130 0.00 0.00 0.00 2.57
2408 2514 3.963665 ACAACAACAACATCCGACAATG 58.036 40.909 0.00 0.00 0.00 2.82
2430 2536 5.360999 TGATGGTTTTACAACATCCACAACA 59.639 36.000 0.00 0.00 34.15 3.33
2431 2537 5.689961 GTGATGGTTTTACAACATCCACAAC 59.310 40.000 0.00 0.00 34.15 3.32
2432 2538 5.221342 GGTGATGGTTTTACAACATCCACAA 60.221 40.000 0.00 0.00 34.15 3.33
2433 2539 4.279671 GGTGATGGTTTTACAACATCCACA 59.720 41.667 0.00 0.00 34.15 4.17
2434 2540 4.321675 GGGTGATGGTTTTACAACATCCAC 60.322 45.833 1.49 0.00 42.22 4.02
2435 2541 3.829601 GGGTGATGGTTTTACAACATCCA 59.170 43.478 1.49 0.00 42.22 3.41
2498 2604 5.796350 ATAGAGAAAACCGGTGATTTTCG 57.204 39.130 19.52 0.00 46.23 3.46
2610 2716 6.488683 CCTGGTTTACAATGTAACAAGGAAGA 59.511 38.462 17.07 0.00 44.82 2.87
2615 2721 8.842280 TCTTAACCTGGTTTACAATGTAACAAG 58.158 33.333 18.58 10.22 0.00 3.16
2618 2724 8.387190 ACTCTTAACCTGGTTTACAATGTAAC 57.613 34.615 18.58 1.81 0.00 2.50
2689 2795 0.035458 AAGCGGTCCTCAGGAACAAG 59.965 55.000 10.16 0.00 39.88 3.16
2723 2829 2.550830 TGCCAGAGAACAAAGTCCTC 57.449 50.000 0.00 0.00 0.00 3.71
2776 2882 4.612264 AGCAACCATCAAGCTCATTTTT 57.388 36.364 0.00 0.00 32.05 1.94
2781 2889 2.574006 AGAAGCAACCATCAAGCTCA 57.426 45.000 0.00 0.00 37.70 4.26
2785 2893 2.490903 CCTGGAAGAAGCAACCATCAAG 59.509 50.000 0.00 0.00 34.07 3.02
2818 2929 4.321230 GGAGTAAACAGGAGCAACCATTTG 60.321 45.833 2.96 0.00 42.04 2.32
2928 3039 4.615386 CGAAATGTAAGACGTTCTTGTCG 58.385 43.478 9.58 7.40 43.70 4.35
2929 3040 4.383679 GCGAAATGTAAGACGTTCTTGTC 58.616 43.478 9.58 4.96 37.29 3.18
2930 3041 3.121126 CGCGAAATGTAAGACGTTCTTGT 60.121 43.478 0.00 0.00 37.29 3.16
2931 3042 3.120616 TCGCGAAATGTAAGACGTTCTTG 59.879 43.478 6.20 0.00 37.29 3.02
2932 3043 3.120782 GTCGCGAAATGTAAGACGTTCTT 59.879 43.478 12.06 0.00 40.35 2.52
2949 3061 1.331138 CTTACTACTCCCTCTGTCGCG 59.669 57.143 0.00 0.00 0.00 5.87
2978 3090 3.490439 TCAGGACAGAAGCAACATCAA 57.510 42.857 0.00 0.00 0.00 2.57
3032 3144 4.460382 TCATGTTGCCAGATTTCCTTTCTC 59.540 41.667 0.00 0.00 0.00 2.87
3141 3257 9.542462 CGTGATAACCAAAGAATATAGGAAAGA 57.458 33.333 0.00 0.00 0.00 2.52
3166 3282 0.111178 CAAATGGCAAAGCGCAAACG 60.111 50.000 11.47 0.00 45.17 3.60
3180 3296 6.271488 TGACTTTCCCTCTTAATGCAAATG 57.729 37.500 0.00 0.00 0.00 2.32
3183 3299 6.721318 ACTATGACTTTCCCTCTTAATGCAA 58.279 36.000 0.00 0.00 0.00 4.08
3212 3328 8.408601 CCATTAAGCTGTACAAGAATGCTAAAT 58.591 33.333 6.95 0.00 33.28 1.40
3246 3362 1.884579 CCAACCCTATCTGATGCATGC 59.115 52.381 11.82 11.82 0.00 4.06
3262 3378 7.816640 TGATCTGTAGCAACTAAATTTCCAAC 58.183 34.615 0.00 0.00 0.00 3.77
3281 3397 5.446473 GCGGTTTAGTGAAGACAATGATCTG 60.446 44.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.