Multiple sequence alignment - TraesCS3A01G228500

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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 TraesCS3A01G228500 chr3A 100.000 4064 0 0 1 4064 427214246 427210183 0.000000e+00 7505.0
1 TraesCS3A01G228500 chr3A 93.418 866 47 4 3200 4064 373330255 373329399 0.000000e+00 1275.0
2 TraesCS3A01G228500 chr3A 96.970 66 2 0 699 764 427213512 427213447 1.190000e-20 111.0
3 TraesCS3A01G228500 chr3A 96.970 66 2 0 735 800 427213548 427213483 1.190000e-20 111.0
4 TraesCS3A01G228500 chr3A 100.000 30 0 0 699 728 427213476 427213447 5.670000e-04 56.5
5 TraesCS3A01G228500 chr3A 100.000 30 0 0 771 800 427213548 427213519 5.670000e-04 56.5
6 TraesCS3A01G228500 chr3D 97.619 2814 66 1 876 3688 307941425 307938612 0.000000e+00 4824.0
7 TraesCS3A01G228500 chr3D 92.980 869 48 7 3200 4064 285115286 285114427 0.000000e+00 1254.0
8 TraesCS3A01G228500 chr3D 88.694 743 67 7 1 728 307942562 307941822 0.000000e+00 891.0
9 TraesCS3A01G228500 chr3D 96.677 331 11 0 3734 4064 307938613 307938283 5.940000e-153 551.0
10 TraesCS3A01G228500 chr3B 98.110 2593 48 1 849 3441 413802287 413804878 0.000000e+00 4516.0
11 TraesCS3A01G228500 chr3B 92.980 869 48 7 3200 4064 378138896 378139755 0.000000e+00 1254.0
12 TraesCS3A01G228500 chr3B 90.030 331 33 0 288 618 413764831 413765161 2.900000e-116 429.0
13 TraesCS3A01G228500 chr3B 95.294 255 12 0 3731 3985 413804925 413805179 4.890000e-109 405.0
14 TraesCS3A01G228500 chr3B 89.510 286 28 1 1 286 413708405 413708688 1.070000e-95 361.0
15 TraesCS3A01G228500 chr3B 93.827 81 4 1 761 840 413799882 413799962 1.980000e-23 121.0
16 TraesCS3A01G228500 chr7D 91.218 2209 182 4 988 3195 330439318 330437121 0.000000e+00 2994.0
17 TraesCS3A01G228500 chr7D 85.263 95 5 3 643 728 619011183 619011277 5.590000e-14 89.8
18 TraesCS3A01G228500 chr5B 82.609 644 109 2 1 641 546439750 546440393 2.120000e-157 566.0
19 TraesCS3A01G228500 chr5B 87.755 98 9 3 894 990 638464117 638464212 1.190000e-20 111.0
20 TraesCS3A01G228500 chr5A 86.127 173 16 7 822 990 635965483 635965315 3.230000e-41 180.0
21 TraesCS3A01G228500 chr5D 81.548 168 20 7 822 988 508629893 508629736 1.190000e-25 128.0
22 TraesCS3A01G228500 chr7B 83.178 107 8 3 632 728 713626336 713626442 5.590000e-14 89.8


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 TraesCS3A01G228500 chr3A 427210183 427214246 4063 True 1568.000000 7505 98.788000 1 4064 5 chr3A.!!$R2 4063
1 TraesCS3A01G228500 chr3A 373329399 373330255 856 True 1275.000000 1275 93.418000 3200 4064 1 chr3A.!!$R1 864
2 TraesCS3A01G228500 chr3D 307938283 307942562 4279 True 2088.666667 4824 94.330000 1 4064 3 chr3D.!!$R2 4063
3 TraesCS3A01G228500 chr3D 285114427 285115286 859 True 1254.000000 1254 92.980000 3200 4064 1 chr3D.!!$R1 864
4 TraesCS3A01G228500 chr3B 413799882 413805179 5297 False 1680.666667 4516 95.743667 761 3985 3 chr3B.!!$F4 3224
5 TraesCS3A01G228500 chr3B 378138896 378139755 859 False 1254.000000 1254 92.980000 3200 4064 1 chr3B.!!$F1 864
6 TraesCS3A01G228500 chr7D 330437121 330439318 2197 True 2994.000000 2994 91.218000 988 3195 1 chr7D.!!$R1 2207
7 TraesCS3A01G228500 chr5B 546439750 546440393 643 False 566.000000 566 82.609000 1 641 1 chr5B.!!$F1 640

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
35 36 0.104304 AGAACCACGACACCTGTGAC 59.896 55.0 3.94 0.0 39.73 3.67 F
709 718 0.107459 GAGAGGATGTTCACTGGGCC 60.107 60.0 0.00 0.0 0.00 5.80 F
749 758 0.188342 ACAAGTTCACTGGGGCCAAT 59.812 50.0 4.39 0.0 0.00 3.16 F
1635 3979 0.320697 GAAGGGGTAGTGACGCTGTT 59.679 55.0 0.00 0.0 38.54 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1124 3468 0.250513 GAGGAGTGATTTCGCCAGGT 59.749 55.000 0.0 0.00 0.00 4.00 R
2337 4682 0.407139 GCTGCCCATCCCTTCCATAT 59.593 55.000 0.0 0.00 0.00 1.78 R
2440 4785 4.769345 TTTTCCCATTCTTGCAAAAGGT 57.231 36.364 0.0 0.00 0.00 3.50 R
3217 5562 2.066262 TGATTTCGCAGTCGGAGAAAC 58.934 47.619 4.2 1.06 45.93 2.78 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
32 33 0.179056 CCAAGAACCACGACACCTGT 60.179 55.000 0.00 0.00 0.00 4.00
34 35 0.828022 AAGAACCACGACACCTGTGA 59.172 50.000 3.94 0.00 39.73 3.58
35 36 0.104304 AGAACCACGACACCTGTGAC 59.896 55.000 3.94 0.00 39.73 3.67
109 110 2.413371 GCGTCAAGAAATGCAAGACCTC 60.413 50.000 0.00 0.00 0.00 3.85
153 155 5.219841 GCGCAAAACAGATTATGAAAAGTCG 60.220 40.000 0.30 0.00 0.00 4.18
158 160 3.278574 CAGATTATGAAAAGTCGGGCCA 58.721 45.455 4.39 0.00 0.00 5.36
170 172 0.461339 TCGGGCCAATAAGAAGCGAC 60.461 55.000 4.39 0.00 0.00 5.19
177 179 0.988832 AATAAGAAGCGACCCCACCA 59.011 50.000 0.00 0.00 0.00 4.17
193 195 1.273327 CACCAGGAATTTCAGGTTGGC 59.727 52.381 0.00 0.00 30.44 4.52
211 213 1.893786 CGACCAGGTCTTCCTCAGG 59.106 63.158 17.95 0.00 43.07 3.86
217 219 2.637872 CCAGGTCTTCCTCAGGTTACAA 59.362 50.000 0.00 0.00 43.07 2.41
241 243 6.321717 ACCATACATTTAGACATTGTTTGCG 58.678 36.000 0.00 0.00 0.00 4.85
243 245 4.503741 ACATTTAGACATTGTTTGCGCT 57.496 36.364 9.73 0.00 0.00 5.92
246 248 1.448985 TAGACATTGTTTGCGCTCCC 58.551 50.000 9.73 0.00 0.00 4.30
326 328 0.248661 CGAGGTGACGTATGAGCTGG 60.249 60.000 0.00 0.00 0.00 4.85
359 363 3.572255 AGGATGCTCGATCTTTCTAGTCC 59.428 47.826 0.00 0.00 0.00 3.85
431 435 8.646004 CATCCTAATCTCTTCCATCACTTTCTA 58.354 37.037 0.00 0.00 0.00 2.10
435 439 9.829507 CTAATCTCTTCCATCACTTTCTAATGT 57.170 33.333 0.00 0.00 0.00 2.71
471 475 5.245531 TGTGGAGATATTGGACAAACACTC 58.754 41.667 0.00 0.00 0.00 3.51
494 498 1.577328 CCGCGGCTTGAACAAGATGT 61.577 55.000 14.67 0.00 40.79 3.06
537 541 2.222027 GCAAGACAACCAAGCTACACT 58.778 47.619 0.00 0.00 0.00 3.55
538 542 2.031682 GCAAGACAACCAAGCTACACTG 60.032 50.000 0.00 0.00 0.00 3.66
596 601 1.471119 CCTACTACTGCGACTTGGGA 58.529 55.000 0.00 0.00 0.00 4.37
617 622 4.142773 GGAACAAGTCGTGTGTGAAGAAAA 60.143 41.667 0.00 0.00 40.60 2.29
618 623 5.365403 AACAAGTCGTGTGTGAAGAAAAA 57.635 34.783 0.00 0.00 40.60 1.94
620 629 4.693566 ACAAGTCGTGTGTGAAGAAAAAGA 59.306 37.500 0.00 0.00 39.72 2.52
621 630 5.180492 ACAAGTCGTGTGTGAAGAAAAAGAA 59.820 36.000 0.00 0.00 39.72 2.52
641 650 0.321298 GGTGTTGGCGACCACACTAT 60.321 55.000 23.41 0.00 36.51 2.12
649 658 1.935933 CGACCACACTATACAAGGGC 58.064 55.000 0.00 0.00 28.14 5.19
652 661 2.500098 GACCACACTATACAAGGGCAGA 59.500 50.000 0.00 0.00 28.14 4.26
675 684 0.615850 AAGGAAGAGCTACACCAGGC 59.384 55.000 0.00 0.00 0.00 4.85
682 691 4.473520 CTACACCAGGCTGGCCCG 62.474 72.222 33.04 22.93 42.67 6.13
690 699 3.535962 GGCTGGCCCGAGAGAGAG 61.536 72.222 0.00 0.00 0.00 3.20
693 702 1.225983 CTGGCCCGAGAGAGAGAGA 59.774 63.158 0.00 0.00 0.00 3.10
694 703 0.819259 CTGGCCCGAGAGAGAGAGAG 60.819 65.000 0.00 0.00 0.00 3.20
696 705 1.529796 GCCCGAGAGAGAGAGAGGA 59.470 63.158 0.00 0.00 0.00 3.71
697 706 0.110486 GCCCGAGAGAGAGAGAGGAT 59.890 60.000 0.00 0.00 0.00 3.24
698 707 1.896220 CCCGAGAGAGAGAGAGGATG 58.104 60.000 0.00 0.00 0.00 3.51
699 708 1.142870 CCCGAGAGAGAGAGAGGATGT 59.857 57.143 0.00 0.00 0.00 3.06
700 709 2.422803 CCCGAGAGAGAGAGAGGATGTT 60.423 54.545 0.00 0.00 0.00 2.71
701 710 2.878406 CCGAGAGAGAGAGAGGATGTTC 59.122 54.545 0.00 0.00 0.00 3.18
702 711 3.540617 CGAGAGAGAGAGAGGATGTTCA 58.459 50.000 0.00 0.00 0.00 3.18
703 712 3.312421 CGAGAGAGAGAGAGGATGTTCAC 59.688 52.174 0.00 0.00 0.00 3.18
704 713 4.526970 GAGAGAGAGAGAGGATGTTCACT 58.473 47.826 0.00 0.00 0.00 3.41
705 714 4.272489 AGAGAGAGAGAGGATGTTCACTG 58.728 47.826 0.00 0.00 0.00 3.66
706 715 3.364549 AGAGAGAGAGGATGTTCACTGG 58.635 50.000 0.00 0.00 0.00 4.00
707 716 2.430332 GAGAGAGAGGATGTTCACTGGG 59.570 54.545 0.00 0.00 0.00 4.45
708 717 0.908198 AGAGAGGATGTTCACTGGGC 59.092 55.000 0.00 0.00 0.00 5.36
709 718 0.107459 GAGAGGATGTTCACTGGGCC 60.107 60.000 0.00 0.00 0.00 5.80
710 719 1.077429 GAGGATGTTCACTGGGCCC 60.077 63.158 17.59 17.59 0.00 5.80
711 720 1.852157 AGGATGTTCACTGGGCCCA 60.852 57.895 26.67 26.67 0.00 5.36
712 721 1.076549 GGATGTTCACTGGGCCCAA 59.923 57.895 28.29 10.56 0.00 4.12
713 722 0.324645 GGATGTTCACTGGGCCCAAT 60.325 55.000 28.29 15.00 0.00 3.16
714 723 0.819582 GATGTTCACTGGGCCCAATG 59.180 55.000 27.66 27.66 0.00 2.82
715 724 0.615544 ATGTTCACTGGGCCCAATGG 60.616 55.000 31.91 20.23 0.00 3.16
717 726 2.477893 TTCACTGGGCCCAATGGGT 61.478 57.895 31.91 20.56 46.51 4.51
723 732 4.083155 GGCCCAATGGGTCTCCTA 57.917 61.111 21.02 0.00 45.53 2.94
724 733 1.532238 GGCCCAATGGGTCTCCTAC 59.468 63.158 21.02 0.27 45.53 3.18
725 734 1.279025 GGCCCAATGGGTCTCCTACA 61.279 60.000 21.02 0.00 45.53 2.74
726 735 0.846693 GCCCAATGGGTCTCCTACAT 59.153 55.000 21.02 0.00 46.51 2.29
727 736 1.477558 GCCCAATGGGTCTCCTACATG 60.478 57.143 21.02 0.00 46.51 3.21
728 737 1.477558 CCCAATGGGTCTCCTACATGC 60.478 57.143 10.91 0.00 38.25 4.06
729 738 1.477558 CCAATGGGTCTCCTACATGCC 60.478 57.143 0.00 0.00 0.00 4.40
730 739 1.212688 CAATGGGTCTCCTACATGCCA 59.787 52.381 0.00 0.00 0.00 4.92
731 740 0.839946 ATGGGTCTCCTACATGCCAC 59.160 55.000 0.00 0.00 0.00 5.01
732 741 0.546507 TGGGTCTCCTACATGCCACA 60.547 55.000 0.00 0.00 0.00 4.17
733 742 0.618458 GGGTCTCCTACATGCCACAA 59.382 55.000 0.00 0.00 0.00 3.33
734 743 1.407437 GGGTCTCCTACATGCCACAAG 60.407 57.143 0.00 0.00 0.00 3.16
735 744 1.279271 GGTCTCCTACATGCCACAAGT 59.721 52.381 0.00 0.00 0.00 3.16
736 745 2.290323 GGTCTCCTACATGCCACAAGTT 60.290 50.000 0.00 0.00 0.00 2.66
737 746 3.003480 GTCTCCTACATGCCACAAGTTC 58.997 50.000 0.00 0.00 0.00 3.01
738 747 2.637382 TCTCCTACATGCCACAAGTTCA 59.363 45.455 0.00 0.00 0.00 3.18
739 748 2.744202 CTCCTACATGCCACAAGTTCAC 59.256 50.000 0.00 0.00 0.00 3.18
740 749 2.371841 TCCTACATGCCACAAGTTCACT 59.628 45.455 0.00 0.00 0.00 3.41
741 750 2.485426 CCTACATGCCACAAGTTCACTG 59.515 50.000 0.00 0.00 0.00 3.66
742 751 1.321474 ACATGCCACAAGTTCACTGG 58.679 50.000 0.00 0.00 0.00 4.00
743 752 0.599558 CATGCCACAAGTTCACTGGG 59.400 55.000 0.00 0.00 0.00 4.45
744 753 0.540365 ATGCCACAAGTTCACTGGGG 60.540 55.000 0.00 0.00 0.00 4.96
745 754 2.564721 GCCACAAGTTCACTGGGGC 61.565 63.158 0.00 0.00 32.66 5.80
746 755 1.903404 CCACAAGTTCACTGGGGCC 60.903 63.158 0.00 0.00 0.00 5.80
747 756 1.152777 CACAAGTTCACTGGGGCCA 60.153 57.895 4.39 0.00 0.00 5.36
748 757 0.754957 CACAAGTTCACTGGGGCCAA 60.755 55.000 4.39 0.00 0.00 4.52
749 758 0.188342 ACAAGTTCACTGGGGCCAAT 59.812 50.000 4.39 0.00 0.00 3.16
750 759 0.604578 CAAGTTCACTGGGGCCAATG 59.395 55.000 4.39 0.00 0.00 2.82
751 760 0.542702 AAGTTCACTGGGGCCAATGG 60.543 55.000 4.39 0.00 0.00 3.16
752 761 1.984026 GTTCACTGGGGCCAATGGG 60.984 63.158 4.39 0.00 37.18 4.00
753 762 2.477893 TTCACTGGGGCCAATGGGT 61.478 57.895 4.39 0.00 36.17 4.51
754 763 2.362889 CACTGGGGCCAATGGGTC 60.363 66.667 4.39 0.00 38.40 4.46
755 764 2.535317 ACTGGGGCCAATGGGTCT 60.535 61.111 4.39 0.00 39.39 3.85
756 765 2.276740 CTGGGGCCAATGGGTCTC 59.723 66.667 4.39 0.00 40.87 3.36
757 766 3.346734 TGGGGCCAATGGGTCTCC 61.347 66.667 4.39 0.00 39.12 3.71
758 767 3.023735 GGGGCCAATGGGTCTCCT 61.024 66.667 4.39 0.00 39.39 3.69
759 768 1.696314 GGGGCCAATGGGTCTCCTA 60.696 63.158 4.39 0.00 39.39 2.94
779 789 0.599558 CATGCCACAAGTTCACTGGG 59.400 55.000 0.00 0.00 0.00 4.45
810 820 2.642311 TCTCCTACATGTTCAGCCCAAA 59.358 45.455 2.30 0.00 0.00 3.28
834 844 2.822399 CGTAGGTGAGGGCATCCC 59.178 66.667 0.00 0.00 45.90 3.85
850 860 4.315941 CCGGCTAAGGGATCGGGC 62.316 72.222 0.00 0.00 38.93 6.13
852 862 2.883828 CGGCTAAGGGATCGGGCAT 61.884 63.158 0.00 0.00 0.00 4.40
853 863 1.003233 GGCTAAGGGATCGGGCATC 60.003 63.158 0.00 0.00 0.00 3.91
975 3319 2.024846 AGATCGAAGAGGGAGAACCAGA 60.025 50.000 0.00 0.00 43.63 3.86
1056 3400 4.631740 TCCTCCACCACTCCCGCA 62.632 66.667 0.00 0.00 0.00 5.69
1124 3468 2.758089 GCTTCTACGCCTCCGTCGA 61.758 63.158 0.00 0.00 46.39 4.20
1281 3625 4.421479 CTCGTCGTTGCCTCCGCT 62.421 66.667 0.00 0.00 35.36 5.52
1635 3979 0.320697 GAAGGGGTAGTGACGCTGTT 59.679 55.000 0.00 0.00 38.54 3.16
1657 4001 4.081406 TGAGGTGTTTGATGAAATGGGAG 58.919 43.478 0.00 0.00 0.00 4.30
1804 4148 7.254556 CGAATATGATCACTTACAATGTGCTGT 60.255 37.037 0.00 0.00 35.58 4.40
1843 4187 2.336809 GCAGGATAGGCGAGACGG 59.663 66.667 0.00 0.00 0.00 4.79
1881 4225 5.473162 TGAAATGATGTCACGAAAGATGGTT 59.527 36.000 0.00 0.00 0.00 3.67
1998 4342 2.358195 GGGTGTGAAGATTGGGGCTTAT 60.358 50.000 0.00 0.00 0.00 1.73
2440 4785 7.054124 GGTCTCCTATGGTTCAATTGTCAATA 58.946 38.462 5.13 3.40 0.00 1.90
2845 5190 7.467811 GCATCAAACCTTCATCGAGAACATATT 60.468 37.037 0.00 0.00 31.61 1.28
3122 5467 2.731217 ACGTTGAATTTGTTGCTCAGC 58.269 42.857 0.00 0.00 0.00 4.26
3254 5599 3.996921 ATCATTAGCTGCCTATCCCAG 57.003 47.619 0.00 0.00 0.00 4.45
3372 5717 3.321111 ACTTTGTTAGCTGAGAACTCCGA 59.679 43.478 0.00 0.00 0.00 4.55
3419 5764 4.332828 AGGTAAAATCACCACCAGTAAGC 58.667 43.478 0.00 0.00 41.40 3.09
3421 5766 2.851263 AAATCACCACCAGTAAGCGA 57.149 45.000 0.00 0.00 0.00 4.93
3861 6208 7.102346 GCATTATATAGAGGTGTCTTCTGCAT 58.898 38.462 0.00 0.00 33.84 3.96
3904 6251 2.422127 AGAACTGGTGTTTTTGACCGTG 59.578 45.455 0.00 0.00 36.39 4.94
3915 6262 5.512082 TGTTTTTGACCGTGTTATTCAAACG 59.488 36.000 0.00 0.00 38.61 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.946221 GGAAGCAGTCACAGGTGTCG 60.946 60.000 0.00 0.00 0.00 4.35
32 33 0.250467 GCTTGGTCAGGAAGCAGTCA 60.250 55.000 0.00 0.00 44.43 3.41
34 35 4.809070 GCTTGGTCAGGAAGCAGT 57.191 55.556 0.00 0.00 44.43 4.40
95 96 3.758554 TGCCTTAAGAGGTCTTGCATTTC 59.241 43.478 3.36 0.00 45.44 2.17
136 138 3.279434 GGCCCGACTTTTCATAATCTGT 58.721 45.455 0.00 0.00 0.00 3.41
153 155 1.101635 GGGTCGCTTCTTATTGGCCC 61.102 60.000 0.00 0.00 0.00 5.80
158 160 0.988832 TGGTGGGGTCGCTTCTTATT 59.011 50.000 0.00 0.00 0.00 1.40
170 172 0.409484 ACCTGAAATTCCTGGTGGGG 59.591 55.000 6.91 0.00 37.06 4.96
177 179 1.534729 GTCGCCAACCTGAAATTCCT 58.465 50.000 0.00 0.00 0.00 3.36
217 219 6.321717 CGCAAACAATGTCTAAATGTATGGT 58.678 36.000 0.00 0.00 0.00 3.55
227 229 1.271108 TGGGAGCGCAAACAATGTCTA 60.271 47.619 11.47 0.00 0.00 2.59
234 236 4.577677 TGGCTGGGAGCGCAAACA 62.578 61.111 11.47 3.67 43.62 2.83
236 238 3.294493 GTTGGCTGGGAGCGCAAA 61.294 61.111 11.47 0.00 43.62 3.68
241 243 2.203480 TTGTGGTTGGCTGGGAGC 60.203 61.111 0.00 0.00 41.46 4.70
243 245 2.203480 GCTTGTGGTTGGCTGGGA 60.203 61.111 0.00 0.00 0.00 4.37
246 248 1.954528 CTGAGCTTGTGGTTGGCTG 59.045 57.895 0.00 0.00 36.37 4.85
289 291 3.618750 TTCACCCGTCGGACCACC 61.619 66.667 14.39 0.00 0.00 4.61
326 328 1.269517 CGAGCATCCTTCTGGTAGCTC 60.270 57.143 15.72 15.72 46.86 4.09
331 335 1.786937 AGATCGAGCATCCTTCTGGT 58.213 50.000 2.38 0.00 30.71 4.00
342 346 2.952978 TGGAGGACTAGAAAGATCGAGC 59.047 50.000 0.00 0.00 32.06 5.03
359 363 0.439985 CGAAGTTGCGACACATGGAG 59.560 55.000 6.90 0.00 0.00 3.86
411 415 8.954350 CAACATTAGAAAGTGATGGAAGAGATT 58.046 33.333 0.00 0.00 0.00 2.40
431 435 4.214310 TCCACAGGAACATTCACAACATT 58.786 39.130 0.00 0.00 0.00 2.71
435 439 3.855255 TCTCCACAGGAACATTCACAA 57.145 42.857 0.00 0.00 0.00 3.33
483 487 2.507484 CTTGCTCCCACATCTTGTTCA 58.493 47.619 0.00 0.00 0.00 3.18
494 498 1.304282 GAATCAGGCCTTGCTCCCA 59.696 57.895 0.00 0.00 0.00 4.37
552 556 1.467543 CGACGCGAAGATCTTCAAGGA 60.468 52.381 29.93 0.00 39.46 3.36
596 601 5.180492 TCTTTTTCTTCACACACGACTTGTT 59.820 36.000 0.00 0.00 35.67 2.83
608 613 4.112634 GCCAACACCTTCTTTTTCTTCAC 58.887 43.478 0.00 0.00 0.00 3.18
617 622 0.818040 GTGGTCGCCAACACCTTCTT 60.818 55.000 0.00 0.00 34.18 2.52
618 623 1.227853 GTGGTCGCCAACACCTTCT 60.228 57.895 0.00 0.00 34.18 2.85
620 629 1.822186 GTGTGGTCGCCAACACCTT 60.822 57.895 0.00 0.00 34.18 3.50
621 630 1.404479 TAGTGTGGTCGCCAACACCT 61.404 55.000 0.00 0.00 36.74 4.00
641 650 2.024176 TCCTTCTGTCTGCCCTTGTA 57.976 50.000 0.00 0.00 0.00 2.41
649 658 3.367910 GGTGTAGCTCTTCCTTCTGTCTG 60.368 52.174 0.00 0.00 0.00 3.51
652 661 2.564947 CTGGTGTAGCTCTTCCTTCTGT 59.435 50.000 0.00 0.00 0.00 3.41
675 684 0.819259 CTCTCTCTCTCTCGGGCCAG 60.819 65.000 4.39 0.00 0.00 4.85
682 691 4.336433 CAGTGAACATCCTCTCTCTCTCTC 59.664 50.000 0.00 0.00 0.00 3.20
690 699 0.107459 GGCCCAGTGAACATCCTCTC 60.107 60.000 0.00 0.00 0.00 3.20
693 702 1.434513 TTGGGCCCAGTGAACATCCT 61.435 55.000 26.87 0.00 0.00 3.24
694 703 0.324645 ATTGGGCCCAGTGAACATCC 60.325 55.000 26.87 0.00 0.00 3.51
696 705 0.615544 CCATTGGGCCCAGTGAACAT 60.616 55.000 40.78 22.36 36.00 2.71
697 706 1.228831 CCATTGGGCCCAGTGAACA 60.229 57.895 40.78 21.04 36.00 3.18
698 707 1.984026 CCCATTGGGCCCAGTGAAC 60.984 63.158 40.78 7.44 35.35 3.18
699 708 2.444696 CCCATTGGGCCCAGTGAA 59.555 61.111 40.78 22.22 35.35 3.18
709 718 1.477558 GGCATGTAGGAGACCCATTGG 60.478 57.143 0.00 0.00 37.80 3.16
710 719 1.212688 TGGCATGTAGGAGACCCATTG 59.787 52.381 0.00 0.00 33.88 2.82
711 720 1.212935 GTGGCATGTAGGAGACCCATT 59.787 52.381 0.00 0.00 33.88 3.16
712 721 0.839946 GTGGCATGTAGGAGACCCAT 59.160 55.000 0.00 0.00 33.88 4.00
713 722 0.546507 TGTGGCATGTAGGAGACCCA 60.547 55.000 0.00 0.00 33.88 4.51
714 723 0.618458 TTGTGGCATGTAGGAGACCC 59.382 55.000 0.00 0.00 0.00 4.46
715 724 1.279271 ACTTGTGGCATGTAGGAGACC 59.721 52.381 0.00 0.00 0.00 3.85
716 725 2.770164 ACTTGTGGCATGTAGGAGAC 57.230 50.000 0.00 0.00 0.00 3.36
717 726 2.637382 TGAACTTGTGGCATGTAGGAGA 59.363 45.455 0.00 0.00 0.00 3.71
718 727 2.744202 GTGAACTTGTGGCATGTAGGAG 59.256 50.000 0.00 0.00 0.00 3.69
719 728 2.371841 AGTGAACTTGTGGCATGTAGGA 59.628 45.455 0.00 0.00 0.00 2.94
720 729 2.485426 CAGTGAACTTGTGGCATGTAGG 59.515 50.000 0.00 0.00 0.00 3.18
721 730 2.485426 CCAGTGAACTTGTGGCATGTAG 59.515 50.000 0.00 0.00 0.00 2.74
722 731 2.503331 CCAGTGAACTTGTGGCATGTA 58.497 47.619 0.00 0.00 0.00 2.29
723 732 1.321474 CCAGTGAACTTGTGGCATGT 58.679 50.000 0.00 0.00 0.00 3.21
724 733 0.599558 CCCAGTGAACTTGTGGCATG 59.400 55.000 0.00 0.00 0.00 4.06
725 734 0.540365 CCCCAGTGAACTTGTGGCAT 60.540 55.000 0.00 0.00 0.00 4.40
726 735 1.152777 CCCCAGTGAACTTGTGGCA 60.153 57.895 0.00 0.00 0.00 4.92
727 736 2.564721 GCCCCAGTGAACTTGTGGC 61.565 63.158 0.00 0.00 0.00 5.01
728 737 1.903404 GGCCCCAGTGAACTTGTGG 60.903 63.158 0.00 0.00 0.00 4.17
729 738 0.754957 TTGGCCCCAGTGAACTTGTG 60.755 55.000 0.00 0.00 0.00 3.33
730 739 0.188342 ATTGGCCCCAGTGAACTTGT 59.812 50.000 0.00 0.00 0.00 3.16
731 740 0.604578 CATTGGCCCCAGTGAACTTG 59.395 55.000 0.00 0.00 36.00 3.16
732 741 0.542702 CCATTGGCCCCAGTGAACTT 60.543 55.000 10.96 0.00 36.00 2.66
733 742 1.077265 CCATTGGCCCCAGTGAACT 59.923 57.895 10.96 0.00 36.00 3.01
734 743 1.984026 CCCATTGGCCCCAGTGAAC 60.984 63.158 10.96 0.00 36.00 3.18
735 744 2.439553 GACCCATTGGCCCCAGTGAA 62.440 60.000 10.96 0.00 36.00 3.18
736 745 2.863484 ACCCATTGGCCCCAGTGA 60.863 61.111 10.96 0.00 36.00 3.41
737 746 2.362889 GACCCATTGGCCCCAGTG 60.363 66.667 0.00 3.07 34.11 3.66
738 747 2.535317 AGACCCATTGGCCCCAGT 60.535 61.111 0.00 0.00 33.59 4.00
739 748 2.276740 GAGACCCATTGGCCCCAG 59.723 66.667 0.00 0.00 33.59 4.45
740 749 2.500381 TAGGAGACCCATTGGCCCCA 62.500 60.000 0.00 0.00 33.59 4.96
741 750 1.696314 TAGGAGACCCATTGGCCCC 60.696 63.158 0.00 0.00 33.59 5.80
742 751 1.279025 TGTAGGAGACCCATTGGCCC 61.279 60.000 0.00 0.00 33.59 5.80
743 752 0.846693 ATGTAGGAGACCCATTGGCC 59.153 55.000 0.00 0.00 33.59 5.36
744 753 1.972872 CATGTAGGAGACCCATTGGC 58.027 55.000 0.00 0.00 33.59 4.52
745 754 1.477558 GGCATGTAGGAGACCCATTGG 60.478 57.143 0.00 0.00 37.80 3.16
746 755 1.212688 TGGCATGTAGGAGACCCATTG 59.787 52.381 0.00 0.00 33.88 2.82
747 756 1.212935 GTGGCATGTAGGAGACCCATT 59.787 52.381 0.00 0.00 33.88 3.16
748 757 0.839946 GTGGCATGTAGGAGACCCAT 59.160 55.000 0.00 0.00 33.88 4.00
749 758 0.546507 TGTGGCATGTAGGAGACCCA 60.547 55.000 0.00 0.00 33.88 4.51
750 759 0.618458 TTGTGGCATGTAGGAGACCC 59.382 55.000 0.00 0.00 0.00 4.46
751 760 1.279271 ACTTGTGGCATGTAGGAGACC 59.721 52.381 0.00 0.00 0.00 3.85
752 761 2.770164 ACTTGTGGCATGTAGGAGAC 57.230 50.000 0.00 0.00 0.00 3.36
753 762 2.637382 TGAACTTGTGGCATGTAGGAGA 59.363 45.455 0.00 0.00 0.00 3.71
754 763 2.744202 GTGAACTTGTGGCATGTAGGAG 59.256 50.000 0.00 0.00 0.00 3.69
755 764 2.371841 AGTGAACTTGTGGCATGTAGGA 59.628 45.455 0.00 0.00 0.00 2.94
756 765 2.485426 CAGTGAACTTGTGGCATGTAGG 59.515 50.000 0.00 0.00 0.00 3.18
757 766 2.485426 CCAGTGAACTTGTGGCATGTAG 59.515 50.000 0.00 0.00 0.00 2.74
758 767 2.503331 CCAGTGAACTTGTGGCATGTA 58.497 47.619 0.00 0.00 0.00 2.29
759 768 1.321474 CCAGTGAACTTGTGGCATGT 58.679 50.000 0.00 0.00 0.00 3.21
810 820 1.623542 GCCCTCACCTACGGGTTCAT 61.624 60.000 0.00 0.00 44.73 2.57
834 844 2.788191 GATGCCCGATCCCTTAGCCG 62.788 65.000 0.00 0.00 0.00 5.52
1056 3400 2.034687 ATGAAACCTGCGCCAGCT 59.965 55.556 4.18 0.00 45.42 4.24
1111 3455 3.129502 CAGGTCGACGGAGGCGTA 61.130 66.667 9.92 0.00 0.00 4.42
1124 3468 0.250513 GAGGAGTGATTTCGCCAGGT 59.749 55.000 0.00 0.00 0.00 4.00
1217 3561 2.513259 GGGGGATGCGGGTCGAATA 61.513 63.158 0.00 0.00 0.00 1.75
1635 3979 4.081406 CTCCCATTTCATCAAACACCTCA 58.919 43.478 0.00 0.00 0.00 3.86
1843 4187 2.063266 CATTTCATGCAACACTGTGGC 58.937 47.619 13.09 7.39 32.23 5.01
1846 4190 4.278919 TGACATCATTTCATGCAACACTGT 59.721 37.500 0.00 0.00 0.00 3.55
1998 4342 9.515226 AGACCATTCAGCAAAATACTAAAAGTA 57.485 29.630 0.00 0.00 34.82 2.24
2337 4682 0.407139 GCTGCCCATCCCTTCCATAT 59.593 55.000 0.00 0.00 0.00 1.78
2415 4760 4.843728 TGACAATTGAACCATAGGAGACC 58.156 43.478 13.59 0.00 0.00 3.85
2440 4785 4.769345 TTTTCCCATTCTTGCAAAAGGT 57.231 36.364 0.00 0.00 0.00 3.50
2845 5190 4.263462 ACCCAATGCACTCAGAAGAATACA 60.263 41.667 0.00 0.00 0.00 2.29
3217 5562 2.066262 TGATTTCGCAGTCGGAGAAAC 58.934 47.619 4.20 1.06 45.93 2.78
3372 5717 3.379372 CCATTCGGAGCATTCACAATCTT 59.621 43.478 0.00 0.00 0.00 2.40
3753 6099 2.092753 TCTTGGCTTTCCTGGAGCATAG 60.093 50.000 9.78 6.32 41.89 2.23
3846 6193 2.027745 TCTCCAATGCAGAAGACACCTC 60.028 50.000 0.00 0.00 0.00 3.85
3861 6208 7.822161 TCTTTCAACTTCAAATGATCTCCAA 57.178 32.000 0.00 0.00 0.00 3.53
3904 6251 4.811557 AGCAGAGCCTATCGTTTGAATAAC 59.188 41.667 0.00 0.00 0.00 1.89
3958 6307 5.454062 TCCCAGAAAGAATGGTTCTCAAAA 58.546 37.500 0.00 0.00 39.61 2.44


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

AutoCloner maintained by Alex Coulton.