Multiple sequence alignment - TraesCS6B01G360200

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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 TraesCS6B01G360200 chr6B 100.000 4756 0 0 1 4756 632183324 632178569 0.000000e+00 8783.0
1 TraesCS6B01G360200 chr6B 81.646 1482 216 32 1052 2513 562489893 562488448 0.000000e+00 1179.0
2 TraesCS6B01G360200 chr6D 93.151 4818 187 60 1 4756 419269731 419264995 0.000000e+00 6937.0
3 TraesCS6B01G360200 chr6D 82.451 1436 204 27 1052 2474 375689405 375688005 0.000000e+00 1212.0
4 TraesCS6B01G360200 chr6A 93.752 4065 149 33 734 4756 562688879 562684878 0.000000e+00 6002.0
5 TraesCS6B01G360200 chr6A 82.382 1436 205 26 1052 2474 517559763 517558363 0.000000e+00 1206.0
6 TraesCS6B01G360200 chr6A 85.212 683 48 26 1 663 562689526 562688877 0.000000e+00 652.0
7 TraesCS6B01G360200 chr2D 95.556 90 4 0 1510 1599 481595159 481595070 1.380000e-30 145.0
8 TraesCS6B01G360200 chr2D 100.000 28 0 0 2676 2703 275498 275525 9.000000e-03 52.8
9 TraesCS6B01G360200 chr2B 100.000 28 0 0 2676 2703 11077841 11077868 9.000000e-03 52.8
10 TraesCS6B01G360200 chr2A 100.000 28 0 0 2676 2703 260326 260299 9.000000e-03 52.8


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 TraesCS6B01G360200 chr6B 632178569 632183324 4755 True 8783 8783 100.000 1 4756 1 chr6B.!!$R2 4755
1 TraesCS6B01G360200 chr6B 562488448 562489893 1445 True 1179 1179 81.646 1052 2513 1 chr6B.!!$R1 1461
2 TraesCS6B01G360200 chr6D 419264995 419269731 4736 True 6937 6937 93.151 1 4756 1 chr6D.!!$R2 4755
3 TraesCS6B01G360200 chr6D 375688005 375689405 1400 True 1212 1212 82.451 1052 2474 1 chr6D.!!$R1 1422
4 TraesCS6B01G360200 chr6A 562684878 562689526 4648 True 3327 6002 89.482 1 4756 2 chr6A.!!$R2 4755
5 TraesCS6B01G360200 chr6A 517558363 517559763 1400 True 1206 1206 82.382 1052 2474 1 chr6A.!!$R1 1422

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
107 108 0.771127 AGCCCACAAGCAAGGTAAGA 59.229 50.000 0.00 0.00 34.23 2.10 F
605 630 0.829182 CTTGGAAAGTTGGGCTGGCT 60.829 55.000 0.00 0.00 39.70 4.75 F
713 741 0.960364 TCGCCATGCCTCTGGTTTTC 60.960 55.000 0.00 0.00 38.63 2.29 F
2414 2476 1.153823 CGTACCAGCTGGAGAACGG 60.154 63.158 39.19 21.69 38.94 4.44 F
2998 3076 0.464036 GCCAGGTCATATCGGTGTCA 59.536 55.000 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2019 2.680805 CGATAACCTGCACAACCTCCAT 60.681 50.000 0.00 0.00 0.00 3.41 R
2540 2614 0.039527 GCAATTCTTTTGGTCCGCGT 60.040 50.000 4.92 0.00 0.00 6.01 R
2616 2690 1.402968 CCAGTTGATCTTTCCATGGCG 59.597 52.381 6.96 0.00 0.00 5.69 R
3593 3688 0.251354 TCTGCTGGTTCATCTGCTCC 59.749 55.000 0.00 0.00 33.58 4.70 R
3963 4067 2.222729 GCTTAACGTGCGGTACTGAATG 60.223 50.000 5.68 2.49 0.00 2.67 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
107 108 0.771127 AGCCCACAAGCAAGGTAAGA 59.229 50.000 0.00 0.00 34.23 2.10
108 109 1.168714 GCCCACAAGCAAGGTAAGAG 58.831 55.000 0.00 0.00 0.00 2.85
109 110 1.826385 CCCACAAGCAAGGTAAGAGG 58.174 55.000 0.00 0.00 0.00 3.69
110 111 1.168714 CCACAAGCAAGGTAAGAGGC 58.831 55.000 0.00 0.00 0.00 4.70
111 112 1.271597 CCACAAGCAAGGTAAGAGGCT 60.272 52.381 0.00 0.00 38.45 4.58
115 116 3.245052 ACAAGCAAGGTAAGAGGCTGATT 60.245 43.478 0.00 0.00 36.58 2.57
245 251 5.223449 AGGTGATAGAAGAAACCAACGAA 57.777 39.130 0.00 0.00 35.01 3.85
278 284 2.899303 TGGTGAAGAGGAAAATCCCC 57.101 50.000 0.00 0.00 37.19 4.81
304 310 1.534729 GAGCTCTCTCTAGCCTAGCC 58.465 60.000 6.43 0.00 43.86 3.93
305 311 1.073923 GAGCTCTCTCTAGCCTAGCCT 59.926 57.143 6.43 0.00 43.86 4.58
306 312 2.304761 GAGCTCTCTCTAGCCTAGCCTA 59.695 54.545 6.43 0.00 43.86 3.93
307 313 2.305927 AGCTCTCTCTAGCCTAGCCTAG 59.694 54.545 1.17 1.17 43.86 3.02
308 314 2.711542 CTCTCTCTAGCCTAGCCTAGC 58.288 57.143 2.79 0.00 35.78 3.42
365 377 7.496346 TTCTTTCAGTGACATACCTCCTAAT 57.504 36.000 0.00 0.00 0.00 1.73
390 402 5.348724 CGTGCCGCTCTTTTGTGATATATAT 59.651 40.000 0.00 0.00 0.00 0.86
425 437 5.924825 GCTTTTCTTCATCTGCAGAACATTT 59.075 36.000 22.50 0.00 27.53 2.32
504 521 3.338818 TTCTGAGCAAGTTTTTCGCAG 57.661 42.857 0.00 0.00 0.00 5.18
574 599 5.870978 CAGAAAATGGGTCAAAATGGATCAC 59.129 40.000 0.00 0.00 0.00 3.06
605 630 0.829182 CTTGGAAAGTTGGGCTGGCT 60.829 55.000 0.00 0.00 39.70 4.75
660 688 2.699954 TCATTTGCCGAGTTCTTCCTC 58.300 47.619 0.00 0.00 0.00 3.71
661 689 1.740025 CATTTGCCGAGTTCTTCCTCC 59.260 52.381 0.00 0.00 0.00 4.30
662 690 1.056660 TTTGCCGAGTTCTTCCTCCT 58.943 50.000 0.00 0.00 0.00 3.69
663 691 1.056660 TTGCCGAGTTCTTCCTCCTT 58.943 50.000 0.00 0.00 0.00 3.36
664 692 1.056660 TGCCGAGTTCTTCCTCCTTT 58.943 50.000 0.00 0.00 0.00 3.11
691 719 1.782028 AAAGTTTGTCTCCGTGCCGC 61.782 55.000 0.00 0.00 0.00 6.53
692 720 3.723348 GTTTGTCTCCGTGCCGCC 61.723 66.667 0.00 0.00 0.00 6.13
693 721 4.243008 TTTGTCTCCGTGCCGCCA 62.243 61.111 0.00 0.00 0.00 5.69
695 723 3.950794 TTGTCTCCGTGCCGCCATC 62.951 63.158 0.00 0.00 0.00 3.51
706 734 4.923942 CGCCATCGCCATGCCTCT 62.924 66.667 0.00 0.00 0.00 3.69
707 735 3.285215 GCCATCGCCATGCCTCTG 61.285 66.667 0.00 0.00 0.00 3.35
708 736 2.593725 CCATCGCCATGCCTCTGG 60.594 66.667 0.00 0.00 39.45 3.86
709 737 2.191375 CATCGCCATGCCTCTGGT 59.809 61.111 0.00 0.00 38.63 4.00
713 741 0.960364 TCGCCATGCCTCTGGTTTTC 60.960 55.000 0.00 0.00 38.63 2.29
789 817 2.452064 CCAGTCAGGGTGGTGGTGT 61.452 63.158 0.00 0.00 0.00 4.16
904 933 1.519455 CTCCACGTCGGCATCTTCC 60.519 63.158 0.00 0.00 33.14 3.46
969 1004 4.803426 GCCTGACCGCTCAGACCG 62.803 72.222 9.37 0.00 46.32 4.79
970 1005 4.803426 CCTGACCGCTCAGACCGC 62.803 72.222 9.37 0.00 46.32 5.68
984 1019 3.905678 CCGCCTAGCTCGACCAGG 61.906 72.222 0.00 0.00 0.00 4.45
1940 1996 2.908015 GGCATCAGGCTCCGGTTA 59.092 61.111 0.00 0.00 44.01 2.85
2196 2252 2.267006 CTGCTCTCCATGGTGCGT 59.733 61.111 12.58 0.00 0.00 5.24
2414 2476 1.153823 CGTACCAGCTGGAGAACGG 60.154 63.158 39.19 21.69 38.94 4.44
2430 2504 2.116125 GGCTTGCCTGAGTGGGTT 59.884 61.111 4.11 0.00 36.00 4.11
2540 2614 3.827876 TCATTCTCCATCAAAAGCTGCAA 59.172 39.130 1.02 0.00 0.00 4.08
2554 2628 1.781025 CTGCAACGCGGACCAAAAGA 61.781 55.000 12.47 0.00 37.02 2.52
2616 2690 4.697352 AGCATATGTGTTGAGTTTCAGGTC 59.303 41.667 4.29 0.00 0.00 3.85
2710 2784 3.059352 AGATTGTGCAGGTTGGTACTC 57.941 47.619 0.00 0.00 0.00 2.59
2711 2785 2.371841 AGATTGTGCAGGTTGGTACTCA 59.628 45.455 0.00 0.00 0.00 3.41
2712 2786 1.961793 TTGTGCAGGTTGGTACTCAC 58.038 50.000 0.00 0.00 0.00 3.51
2713 2787 1.128200 TGTGCAGGTTGGTACTCACT 58.872 50.000 0.00 0.00 0.00 3.41
2714 2788 1.488812 TGTGCAGGTTGGTACTCACTT 59.511 47.619 0.00 0.00 0.00 3.16
2715 2789 2.701423 TGTGCAGGTTGGTACTCACTTA 59.299 45.455 0.00 0.00 0.00 2.24
2716 2790 3.244078 TGTGCAGGTTGGTACTCACTTAG 60.244 47.826 0.00 0.00 0.00 2.18
2717 2791 2.969950 TGCAGGTTGGTACTCACTTAGT 59.030 45.455 0.00 0.00 42.62 2.24
2718 2792 3.006537 TGCAGGTTGGTACTCACTTAGTC 59.993 47.826 0.00 0.00 39.80 2.59
2719 2793 3.834610 CAGGTTGGTACTCACTTAGTCG 58.165 50.000 0.00 0.00 39.80 4.18
2791 2869 5.238868 CGCCTCATTTCTTCAGATGATGAAT 59.761 40.000 10.79 1.74 46.71 2.57
2862 2940 0.537828 TTCCAGCTGCAGCAATCACA 60.538 50.000 38.24 15.55 45.16 3.58
2884 2962 1.659335 GTGCCGAAGAACGTCGTCA 60.659 57.895 0.00 0.16 39.43 4.35
2893 2971 0.529992 GAACGTCGTCATCCATCCCC 60.530 60.000 0.00 0.00 0.00 4.81
2926 3004 1.067250 GAGGATCCTGCTCGCAGAC 59.933 63.158 22.02 10.40 46.30 3.51
2947 3025 4.451150 GACGACATGAGCCGGGCA 62.451 66.667 23.09 0.60 0.00 5.36
2969 3047 1.671901 GACCCAGAAGCTCCTCGAGG 61.672 65.000 26.32 26.32 0.00 4.63
2998 3076 0.464036 GCCAGGTCATATCGGTGTCA 59.536 55.000 0.00 0.00 0.00 3.58
3005 3083 2.038659 TCATATCGGTGTCATCAGGCA 58.961 47.619 0.00 0.00 0.00 4.75
3163 3241 4.471726 GCCGTGACCGTCGACGAT 62.472 66.667 37.65 24.77 43.02 3.73
3190 3268 2.265739 GAGATGTGCCGCCACTCA 59.734 61.111 0.00 0.00 42.54 3.41
3276 3354 2.432146 TCCTTCGGAACTGATGATGGAG 59.568 50.000 0.00 0.00 32.76 3.86
3379 3460 6.881602 ACAAGAGGTAAATTGGCAAAAACAAA 59.118 30.769 3.01 0.00 0.00 2.83
3444 3528 3.988595 CGTAATTTGCGCAAATGCATTT 58.011 36.364 40.29 29.27 45.78 2.32
3445 3529 4.014685 CGTAATTTGCGCAAATGCATTTC 58.985 39.130 40.29 24.80 45.78 2.17
3446 3530 4.433936 CGTAATTTGCGCAAATGCATTTCA 60.434 37.500 40.29 20.57 45.78 2.69
3504 3589 1.376295 GAAGGGGCGCGGACTAAAA 60.376 57.895 8.83 0.00 0.00 1.52
3549 3642 2.277969 CAGTCACCAAGATAGCAGCAG 58.722 52.381 0.00 0.00 0.00 4.24
3591 3686 3.420893 TGGGACAAATAACAAGGAGCAG 58.579 45.455 0.00 0.00 31.92 4.24
3592 3687 2.755103 GGGACAAATAACAAGGAGCAGG 59.245 50.000 0.00 0.00 0.00 4.85
3593 3688 2.755103 GGACAAATAACAAGGAGCAGGG 59.245 50.000 0.00 0.00 0.00 4.45
3594 3689 2.755103 GACAAATAACAAGGAGCAGGGG 59.245 50.000 0.00 0.00 0.00 4.79
3595 3690 2.378547 ACAAATAACAAGGAGCAGGGGA 59.621 45.455 0.00 0.00 0.00 4.81
3596 3691 3.019564 CAAATAACAAGGAGCAGGGGAG 58.980 50.000 0.00 0.00 0.00 4.30
3597 3692 0.548510 ATAACAAGGAGCAGGGGAGC 59.451 55.000 0.00 0.00 0.00 4.70
3598 3693 0.840288 TAACAAGGAGCAGGGGAGCA 60.840 55.000 0.00 0.00 36.85 4.26
3721 3824 2.349249 GCTGCTTGCACGATCATATCAC 60.349 50.000 0.00 0.00 42.31 3.06
3751 3854 1.348696 TCCTCACTGAAGATGCTTGCA 59.651 47.619 0.00 0.00 0.00 4.08
3832 3935 7.637229 CAATCTGCACTATATTTGTTCTCTGG 58.363 38.462 0.00 0.00 0.00 3.86
3841 3945 3.769739 TTTGTTCTCTGGCTCTTGCTA 57.230 42.857 0.00 0.00 39.59 3.49
3852 3956 3.244526 TGGCTCTTGCTAGTCATCAACAA 60.245 43.478 0.00 0.00 39.59 2.83
3963 4067 2.109126 GCAGATCGTGGAACTGGGC 61.109 63.158 5.27 0.00 33.89 5.36
3972 4076 2.084546 GTGGAACTGGGCATTCAGTAC 58.915 52.381 6.96 5.00 46.17 2.73
4023 4129 5.296283 CACCATCAAGCAATGAAAACCAAAA 59.704 36.000 0.00 0.00 42.54 2.44
4032 4138 3.749665 TGAAAACCAAAAGATGCTGGG 57.250 42.857 0.00 0.00 37.00 4.45
4070 4176 1.069765 CAGGCCTAACATCGCGGAT 59.930 57.895 3.98 0.00 0.00 4.18
4131 4237 7.861372 GCATCTGAATCATTTTCATGGTCTAAG 59.139 37.037 0.00 0.00 0.00 2.18
4135 4241 9.605275 CTGAATCATTTTCATGGTCTAAGTCTA 57.395 33.333 0.00 0.00 0.00 2.59
4143 4250 6.546428 TCATGGTCTAAGTCTAAAGGAAGG 57.454 41.667 0.00 0.00 0.00 3.46
4249 4356 0.534877 ATGCCGGCGCTGATCATTAA 60.535 50.000 23.90 0.00 35.36 1.40
4250 4357 1.159713 TGCCGGCGCTGATCATTAAG 61.160 55.000 23.90 0.00 35.36 1.85
4251 4358 1.160329 GCCGGCGCTGATCATTAAGT 61.160 55.000 20.25 0.00 0.00 2.24
4252 4359 1.872237 GCCGGCGCTGATCATTAAGTA 60.872 52.381 20.25 0.00 0.00 2.24
4336 4472 0.320771 CTTGTACCTGCAGGAGCGTT 60.321 55.000 39.19 18.87 46.23 4.84
4342 4478 0.605319 CCTGCAGGAGCGTTGGTTAA 60.605 55.000 29.88 0.00 46.23 2.01
4344 4480 1.131126 CTGCAGGAGCGTTGGTTAATG 59.869 52.381 5.57 0.00 46.23 1.90
4364 4500 2.292016 TGGCAGTTGTGTTTGGATAACG 59.708 45.455 0.00 0.00 0.00 3.18
4382 4518 3.120321 ACGTGAGTGGATGCTAACAAA 57.880 42.857 0.00 0.00 46.97 2.83
4387 4523 4.518970 GTGAGTGGATGCTAACAAAGGAAA 59.481 41.667 0.00 0.00 0.00 3.13
4539 4676 5.466393 GGTGACAAAACAAATGGAATTCCTG 59.534 40.000 24.73 16.93 33.67 3.86
4551 4689 8.616076 CAAATGGAATTCCTGTAAGTATGACTC 58.384 37.037 24.73 0.00 33.67 3.36
4564 4702 7.922811 TGTAAGTATGACTCTGCAATGTAGATG 59.077 37.037 0.67 0.00 0.00 2.90
4584 4722 6.777782 AGATGTTCAGGAGAGATTTCAAGTT 58.222 36.000 0.00 0.00 0.00 2.66
4613 4751 3.553096 GGACAAGATGTCTACTATGGCGG 60.553 52.174 10.06 0.00 46.19 6.13
4619 4757 2.940158 TGTCTACTATGGCGGCTAGAA 58.060 47.619 11.43 0.00 0.00 2.10
4620 4758 2.885266 TGTCTACTATGGCGGCTAGAAG 59.115 50.000 11.43 4.76 0.00 2.85
4627 4765 0.465705 TGGCGGCTAGAAGATTCAGG 59.534 55.000 11.43 0.00 0.00 3.86
4628 4766 0.466124 GGCGGCTAGAAGATTCAGGT 59.534 55.000 0.00 0.00 0.00 4.00
4629 4767 1.576356 GCGGCTAGAAGATTCAGGTG 58.424 55.000 0.00 0.00 0.00 4.00
4630 4768 1.576356 CGGCTAGAAGATTCAGGTGC 58.424 55.000 0.00 0.00 0.00 5.01
4631 4769 1.137872 CGGCTAGAAGATTCAGGTGCT 59.862 52.381 0.00 0.00 0.00 4.40
4632 4770 2.801342 CGGCTAGAAGATTCAGGTGCTC 60.801 54.545 0.00 0.00 0.00 4.26
4633 4771 2.433970 GGCTAGAAGATTCAGGTGCTCT 59.566 50.000 0.00 0.00 0.00 4.09
4634 4772 3.118445 GGCTAGAAGATTCAGGTGCTCTT 60.118 47.826 0.00 0.00 32.09 2.85
4635 4773 4.100189 GGCTAGAAGATTCAGGTGCTCTTA 59.900 45.833 0.00 0.00 29.64 2.10
4636 4774 5.395768 GGCTAGAAGATTCAGGTGCTCTTAA 60.396 44.000 0.00 0.00 29.64 1.85
4637 4775 5.752955 GCTAGAAGATTCAGGTGCTCTTAAG 59.247 44.000 0.00 0.00 29.64 1.85
4638 4776 5.096443 AGAAGATTCAGGTGCTCTTAAGG 57.904 43.478 1.85 0.00 29.64 2.69
4639 4777 4.780021 AGAAGATTCAGGTGCTCTTAAGGA 59.220 41.667 1.85 0.00 29.64 3.36
4640 4778 5.249393 AGAAGATTCAGGTGCTCTTAAGGAA 59.751 40.000 1.85 0.00 29.64 3.36
4641 4779 5.707066 AGATTCAGGTGCTCTTAAGGAAT 57.293 39.130 1.85 1.87 0.00 3.01
4656 4794 7.050377 TCTTAAGGAATGTGCTCTAAGGAATG 58.950 38.462 1.85 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.028294 ACCAGTCTCTGATTGCAGTCAG 60.028 50.000 28.19 28.19 45.51 3.51
110 111 4.699257 ACCAAGAAGCTGAGCTAAAATCAG 59.301 41.667 7.68 0.00 45.71 2.90
111 112 4.655963 ACCAAGAAGCTGAGCTAAAATCA 58.344 39.130 7.68 0.00 38.25 2.57
115 116 4.760204 GGTAAACCAAGAAGCTGAGCTAAA 59.240 41.667 7.68 0.00 34.95 1.85
181 187 7.011482 GGTTGCGGCAAATAAGGATATAGATAG 59.989 40.741 18.23 0.00 0.00 2.08
195 201 1.846007 TATTCCTGGTTGCGGCAAAT 58.154 45.000 18.23 8.69 0.00 2.32
245 251 5.197224 TCTTCACCAATTTCTCCCATGAT 57.803 39.130 0.00 0.00 0.00 2.45
365 377 8.522016 GATATATATCACAAAAGAGCGGCACGA 61.522 40.741 16.41 0.00 43.15 4.35
390 402 7.414873 GCAGATGAAGAAAAGCATGTTCATAGA 60.415 37.037 6.89 0.00 33.71 1.98
425 437 0.667453 TGTTACACACAGGTACGCGA 59.333 50.000 15.93 0.00 0.00 5.87
519 540 4.974888 GCGTGTTAATTAACCGGACAAAAA 59.025 37.500 26.25 7.77 35.37 1.94
528 549 2.222953 CGGAGCTGCGTGTTAATTAACC 60.223 50.000 20.53 13.98 35.37 2.85
574 599 2.158460 ACTTTCCAAGTTCCCAGGAAGG 60.158 50.000 0.00 0.00 41.97 3.46
605 630 2.283604 TAGCCACGCACTCTCCCA 60.284 61.111 0.00 0.00 0.00 4.37
691 719 2.593725 CCAGAGGCATGGCGATGG 60.594 66.667 24.37 24.37 32.48 3.51
692 720 1.033746 AAACCAGAGGCATGGCGATG 61.034 55.000 14.30 15.62 44.80 3.84
693 721 0.323725 AAAACCAGAGGCATGGCGAT 60.324 50.000 14.30 3.33 44.80 4.58
695 723 0.962356 AGAAAACCAGAGGCATGGCG 60.962 55.000 14.30 1.70 44.80 5.69
696 724 0.813821 GAGAAAACCAGAGGCATGGC 59.186 55.000 12.14 12.14 44.80 4.40
697 725 2.026449 AGAGAGAAAACCAGAGGCATGG 60.026 50.000 7.18 7.18 46.47 3.66
698 726 3.269178 GAGAGAGAAAACCAGAGGCATG 58.731 50.000 0.00 0.00 0.00 4.06
699 727 2.909006 TGAGAGAGAAAACCAGAGGCAT 59.091 45.455 0.00 0.00 0.00 4.40
700 728 2.301296 CTGAGAGAGAAAACCAGAGGCA 59.699 50.000 0.00 0.00 0.00 4.75
701 729 2.564947 TCTGAGAGAGAAAACCAGAGGC 59.435 50.000 0.00 0.00 31.15 4.70
702 730 4.454728 CTCTGAGAGAGAAAACCAGAGG 57.545 50.000 2.60 0.00 45.07 3.69
703 731 4.085733 TCCTCTGAGAGAGAAAACCAGAG 58.914 47.826 11.82 0.00 45.07 3.35
704 732 4.119556 TCCTCTGAGAGAGAAAACCAGA 57.880 45.455 11.82 0.00 45.07 3.86
705 733 4.819769 CTTCCTCTGAGAGAGAAAACCAG 58.180 47.826 11.82 0.00 45.07 4.00
706 734 3.007398 GCTTCCTCTGAGAGAGAAAACCA 59.993 47.826 11.82 0.00 45.07 3.67
707 735 3.595173 GCTTCCTCTGAGAGAGAAAACC 58.405 50.000 11.82 1.65 45.07 3.27
708 736 3.007398 TGGCTTCCTCTGAGAGAGAAAAC 59.993 47.826 11.82 8.61 45.07 2.43
709 737 3.242867 TGGCTTCCTCTGAGAGAGAAAA 58.757 45.455 11.82 0.00 45.07 2.29
713 741 1.202557 GCATGGCTTCCTCTGAGAGAG 60.203 57.143 11.82 2.18 41.96 3.20
878 907 1.098712 GCCGACGTGGAGAGAGAGAT 61.099 60.000 0.00 0.00 42.00 2.75
904 933 0.179166 CGTGCAATGATTTGGTCGGG 60.179 55.000 0.00 0.00 33.22 5.14
969 1004 2.058595 TTCCCTGGTCGAGCTAGGC 61.059 63.158 20.76 0.00 43.74 3.93
970 1005 1.677637 GGTTCCCTGGTCGAGCTAGG 61.678 65.000 16.64 18.55 44.58 3.02
984 1019 2.106683 CATTGCCTCGGTCGGTTCC 61.107 63.158 0.00 0.00 0.00 3.62
1625 1681 4.394712 GCACCAGGTGGAGGTCGG 62.395 72.222 21.77 0.00 37.23 4.79
1940 1996 3.386237 GGCCGCTCCACTCTCTGT 61.386 66.667 0.00 0.00 34.01 3.41
1963 2019 2.680805 CGATAACCTGCACAACCTCCAT 60.681 50.000 0.00 0.00 0.00 3.41
2145 2201 4.181010 ATCGGCCTTCGCATGCCT 62.181 61.111 13.15 0.00 45.71 4.75
2169 2225 1.005156 GGAGAGCAGGCCGATGATC 60.005 63.158 2.11 2.11 35.83 2.92
2196 2252 2.125552 CGCATGTCCTTCGCCTGA 60.126 61.111 0.00 0.00 0.00 3.86
2203 2259 4.028490 TTCGGGGCGCATGTCCTT 62.028 61.111 10.83 0.00 40.80 3.36
2414 2476 1.518903 GACAACCCACTCAGGCAAGC 61.519 60.000 0.00 0.00 35.39 4.01
2430 2504 3.785499 CTCGTCTCGTCGCCGACA 61.785 66.667 18.40 3.72 38.40 4.35
2540 2614 0.039527 GCAATTCTTTTGGTCCGCGT 60.040 50.000 4.92 0.00 0.00 6.01
2554 2628 2.350458 GCCACACCGGGATGCAATT 61.350 57.895 6.32 0.00 34.06 2.32
2616 2690 1.402968 CCAGTTGATCTTTCCATGGCG 59.597 52.381 6.96 0.00 0.00 5.69
2710 2784 4.380841 TGGTATACCAAGCGACTAAGTG 57.619 45.455 22.59 0.00 44.35 3.16
2862 2940 2.105528 ACGTTCTTCGGCACACGT 59.894 55.556 0.00 0.00 44.69 4.49
2884 2962 1.218704 CCATTGAAGTGGGGGATGGAT 59.781 52.381 0.00 0.00 39.66 3.41
2893 2971 0.329261 TCCTCAGGCCATTGAAGTGG 59.671 55.000 5.01 0.00 42.35 4.00
2934 3012 3.321648 TCACTGCCCGGCTCATGT 61.322 61.111 11.61 1.69 0.00 3.21
2947 3025 1.254284 CGAGGAGCTTCTGGGTCACT 61.254 60.000 0.00 0.00 43.58 3.41
2969 3047 4.828925 GACCTGGCAGCCGAGCTC 62.829 72.222 9.56 2.73 36.40 4.09
3043 3121 0.693767 CCAGGAGGAGGAGCTGGAAT 60.694 60.000 0.00 0.00 37.37 3.01
3190 3268 0.765510 GGATCAGGCCGTTTATCCCT 59.234 55.000 14.38 0.00 33.21 4.20
3240 3318 0.972883 AAGGACTCTGTGGAGCTGAC 59.027 55.000 0.00 0.00 42.98 3.51
3399 3480 5.228635 GCGCAAAGTCATTGATATGAAACTG 59.771 40.000 0.30 0.00 42.23 3.16
3444 3528 8.525316 ACATTGCATGTTTTATTCTTCTGATGA 58.475 29.630 0.00 0.00 41.63 2.92
3445 3529 8.697846 ACATTGCATGTTTTATTCTTCTGATG 57.302 30.769 0.00 0.00 41.63 3.07
3504 3589 1.539827 GTGTATGCTGCCTTTTTCGGT 59.460 47.619 0.00 0.00 0.00 4.69
3549 3642 2.056481 GACTCATGCGCTTGGGATGC 62.056 60.000 28.02 13.46 43.55 3.91
3591 3686 1.452833 GCTGGTTCATCTGCTCCCC 60.453 63.158 0.00 0.00 0.00 4.81
3592 3687 0.747283 CTGCTGGTTCATCTGCTCCC 60.747 60.000 0.00 0.00 33.58 4.30
3593 3688 0.251354 TCTGCTGGTTCATCTGCTCC 59.749 55.000 0.00 0.00 33.58 4.70
3594 3689 2.105006 TTCTGCTGGTTCATCTGCTC 57.895 50.000 0.00 0.00 33.58 4.26
3595 3690 2.641305 GATTCTGCTGGTTCATCTGCT 58.359 47.619 0.00 0.00 33.58 4.24
3596 3691 1.674962 GGATTCTGCTGGTTCATCTGC 59.325 52.381 0.00 0.00 0.00 4.26
3597 3692 2.295885 GGGATTCTGCTGGTTCATCTG 58.704 52.381 0.00 0.00 0.00 2.90
3598 3693 1.213926 GGGGATTCTGCTGGTTCATCT 59.786 52.381 0.00 0.00 0.00 2.90
3721 3824 0.907486 TCAGTGAGGAAGCCAGATGG 59.093 55.000 0.00 0.00 38.53 3.51
3751 3854 4.814234 TGATCGTAAGTTGCAGTGAGTTTT 59.186 37.500 0.00 0.00 39.48 2.43
3785 3888 2.995258 CAACTTGTTGCAGTGCTGTTTT 59.005 40.909 17.60 0.00 0.00 2.43
3823 3926 2.232452 GACTAGCAAGAGCCAGAGAACA 59.768 50.000 0.00 0.00 43.56 3.18
3832 3935 5.149977 GTTTTGTTGATGACTAGCAAGAGC 58.850 41.667 0.00 0.00 42.56 4.09
3852 3956 9.194271 GCCAAATGCATTTTCATATTTTTGTTT 57.806 25.926 21.95 0.00 40.77 2.83
3899 4003 3.795623 ATGCCATTGATGTTCAGAAGC 57.204 42.857 0.00 0.00 0.00 3.86
3935 4039 3.006940 TCCACGATCTGCCATTAAACAC 58.993 45.455 0.00 0.00 0.00 3.32
3963 4067 2.222729 GCTTAACGTGCGGTACTGAATG 60.223 50.000 5.68 2.49 0.00 2.67
3972 4076 4.854291 TGAAATAATTTGCTTAACGTGCGG 59.146 37.500 0.00 0.00 0.00 5.69
4023 4129 3.327757 TCAACTGTAAGAACCCAGCATCT 59.672 43.478 0.00 0.00 37.43 2.90
4032 4138 5.175673 GCCTGCATTTTTCAACTGTAAGAAC 59.824 40.000 0.00 0.00 37.43 3.01
4070 4176 7.824704 TGTAAACTGTTTTGTAACGTCTGTA 57.175 32.000 11.48 0.00 37.06 2.74
4131 4237 5.533528 TGTTAGTTTTGCCCTTCCTTTAGAC 59.466 40.000 0.00 0.00 0.00 2.59
4135 4241 3.386726 GGTGTTAGTTTTGCCCTTCCTTT 59.613 43.478 0.00 0.00 0.00 3.11
4143 4250 6.602009 AGGTTCATATAGGTGTTAGTTTTGCC 59.398 38.462 0.00 0.00 0.00 4.52
4249 4356 8.418597 TGAGTTACAAGACCTTATCAAGTACT 57.581 34.615 0.00 0.00 0.00 2.73
4250 4357 7.275999 GCTGAGTTACAAGACCTTATCAAGTAC 59.724 40.741 0.00 0.00 0.00 2.73
4251 4358 7.039293 TGCTGAGTTACAAGACCTTATCAAGTA 60.039 37.037 0.00 0.00 0.00 2.24
4252 4359 6.166982 GCTGAGTTACAAGACCTTATCAAGT 58.833 40.000 0.00 0.00 0.00 3.16
4336 4472 3.181471 CCAAACACAACTGCCATTAACCA 60.181 43.478 0.00 0.00 0.00 3.67
4342 4478 3.057596 CGTTATCCAAACACAACTGCCAT 60.058 43.478 0.00 0.00 0.00 4.40
4344 4480 2.292292 ACGTTATCCAAACACAACTGCC 59.708 45.455 0.00 0.00 0.00 4.85
4364 4500 3.674997 TCCTTTGTTAGCATCCACTCAC 58.325 45.455 0.00 0.00 0.00 3.51
4382 4518 4.487714 TTGCGTGAGATATCCTTTTCCT 57.512 40.909 0.00 0.00 0.00 3.36
4387 4523 8.398665 GTTAAGAATTTTGCGTGAGATATCCTT 58.601 33.333 0.00 0.00 0.00 3.36
4518 4655 7.926018 ACTTACAGGAATTCCATTTGTTTTGTC 59.074 33.333 26.22 0.00 38.89 3.18
4539 4676 7.923344 ACATCTACATTGCAGAGTCATACTTAC 59.077 37.037 0.00 0.00 0.00 2.34
4551 4689 4.763073 TCTCCTGAACATCTACATTGCAG 58.237 43.478 0.00 0.00 0.00 4.41
4564 4702 4.457257 CCCAACTTGAAATCTCTCCTGAAC 59.543 45.833 0.00 0.00 0.00 3.18
4613 4751 3.817709 AGAGCACCTGAATCTTCTAGC 57.182 47.619 0.00 0.00 0.00 3.42
4619 4757 5.045286 ACATTCCTTAAGAGCACCTGAATCT 60.045 40.000 3.36 0.00 0.00 2.40
4620 4758 5.065731 CACATTCCTTAAGAGCACCTGAATC 59.934 44.000 3.36 0.00 0.00 2.52
4627 4765 3.604582 AGAGCACATTCCTTAAGAGCAC 58.395 45.455 3.36 0.00 0.00 4.40
4628 4766 3.988976 AGAGCACATTCCTTAAGAGCA 57.011 42.857 3.36 0.00 0.00 4.26
4629 4767 4.813697 CCTTAGAGCACATTCCTTAAGAGC 59.186 45.833 3.36 0.00 0.00 4.09
4630 4768 6.227298 TCCTTAGAGCACATTCCTTAAGAG 57.773 41.667 3.36 0.00 0.00 2.85
4631 4769 6.620877 TTCCTTAGAGCACATTCCTTAAGA 57.379 37.500 3.36 0.00 0.00 2.10
4632 4770 6.825721 ACATTCCTTAGAGCACATTCCTTAAG 59.174 38.462 0.00 0.00 0.00 1.85
4633 4771 6.599244 CACATTCCTTAGAGCACATTCCTTAA 59.401 38.462 0.00 0.00 0.00 1.85
4634 4772 6.070251 TCACATTCCTTAGAGCACATTCCTTA 60.070 38.462 0.00 0.00 0.00 2.69
4635 4773 4.946157 CACATTCCTTAGAGCACATTCCTT 59.054 41.667 0.00 0.00 0.00 3.36
4636 4774 4.225942 TCACATTCCTTAGAGCACATTCCT 59.774 41.667 0.00 0.00 0.00 3.36
4637 4775 4.517285 TCACATTCCTTAGAGCACATTCC 58.483 43.478 0.00 0.00 0.00 3.01
4638 4776 6.317857 GTTTCACATTCCTTAGAGCACATTC 58.682 40.000 0.00 0.00 0.00 2.67
4639 4777 5.183904 GGTTTCACATTCCTTAGAGCACATT 59.816 40.000 0.00 0.00 0.00 2.71
4640 4778 4.702131 GGTTTCACATTCCTTAGAGCACAT 59.298 41.667 0.00 0.00 0.00 3.21
4641 4779 4.072131 GGTTTCACATTCCTTAGAGCACA 58.928 43.478 0.00 0.00 0.00 4.57
4712 4850 2.902486 AGATGCTGTCTGGACTTCTTGA 59.098 45.455 2.38 0.00 35.31 3.02


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

AutoCloner maintained by Alex Coulton.