Multiple sequence alignment - TraesCS2A01G202200

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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 TraesCS2A01G202200 chr2A 100.000 3158 0 0 1 3158 176669596 176672753 0.000000e+00 5832.0
1 TraesCS2A01G202200 chr2D 94.213 2229 56 17 935 3158 163020506 163018346 0.000000e+00 3334.0
2 TraesCS2A01G202200 chr2B 94.292 1717 46 15 935 2627 224649058 224650746 0.000000e+00 2580.0
3 TraesCS2A01G202200 chr2B 95.926 540 13 5 2622 3158 224650940 224651473 0.000000e+00 867.0
4 TraesCS2A01G202200 chr4B 96.935 783 23 1 1 782 16678590 16679372 0.000000e+00 1312.0
5 TraesCS2A01G202200 chr4B 96.296 54 0 2 884 935 16679369 16679422 1.560000e-13 87.9
6 TraesCS2A01G202200 chr4B 78.814 118 22 2 1535 1652 182260562 182260448 3.380000e-10 76.8
7 TraesCS2A01G202200 chr5A 92.982 114 7 1 774 886 486728570 486728683 7.010000e-37 165.0
8 TraesCS2A01G202200 chr5A 93.636 110 7 0 777 886 706933967 706934076 7.010000e-37 165.0
9 TraesCS2A01G202200 chr7A 93.578 109 7 0 779 887 82179647 82179755 2.520000e-36 163.0
10 TraesCS2A01G202200 chr7A 86.992 123 8 7 2916 3031 669280532 669280411 7.110000e-27 132.0
11 TraesCS2A01G202200 chr4A 93.578 109 7 0 779 887 576584956 576584848 2.520000e-36 163.0
12 TraesCS2A01G202200 chr4A 92.035 113 9 0 775 887 59261922 59262034 3.260000e-35 159.0
13 TraesCS2A01G202200 chr4A 78.992 119 20 3 1535 1652 450765153 450765039 3.380000e-10 76.8
14 TraesCS2A01G202200 chr1D 92.857 112 8 0 776 887 100826382 100826493 2.520000e-36 163.0
15 TraesCS2A01G202200 chr1D 90.164 122 11 1 774 895 409496440 409496320 1.170000e-34 158.0
16 TraesCS2A01G202200 chr7D 92.793 111 8 0 777 887 21093604 21093714 9.060000e-36 161.0
17 TraesCS2A01G202200 chr7D 80.469 128 23 2 2916 3041 451927378 451927505 2.590000e-16 97.1
18 TraesCS2A01G202200 chr1A 92.035 113 9 0 777 889 427505497 427505609 3.260000e-35 159.0
19 TraesCS2A01G202200 chr5D 82.734 139 19 4 2916 3050 510126184 510126321 5.530000e-23 119.0
20 TraesCS2A01G202200 chr5D 82.171 129 17 4 2916 3041 281521346 281521471 4.310000e-19 106.0
21 TraesCS2A01G202200 chr4D 83.077 130 19 3 2916 3043 109244660 109244788 7.160000e-22 115.0
22 TraesCS2A01G202200 chr4D 78.151 119 21 3 1535 1652 119805859 119805745 1.570000e-08 71.3
23 TraesCS2A01G202200 chr3D 82.443 131 16 6 2916 3042 521340952 521341079 1.200000e-19 108.0
24 TraesCS2A01G202200 chr3D 80.620 129 22 2 2916 3042 30275455 30275582 2.590000e-16 97.1


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 TraesCS2A01G202200 chr2A 176669596 176672753 3157 False 5832.00 5832 100.0000 1 3158 1 chr2A.!!$F1 3157
1 TraesCS2A01G202200 chr2D 163018346 163020506 2160 True 3334.00 3334 94.2130 935 3158 1 chr2D.!!$R1 2223
2 TraesCS2A01G202200 chr2B 224649058 224651473 2415 False 1723.50 2580 95.1090 935 3158 2 chr2B.!!$F1 2223
3 TraesCS2A01G202200 chr4B 16678590 16679422 832 False 699.95 1312 96.6155 1 935 2 chr4B.!!$F1 934

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
742 743 0.171231 GTTCTCTTGATTTGGGGCGC 59.829 55.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2175 2198 0.462937 TTCCGGTGTCTGTGTTGGTG 60.463 55.0 0.0 0.0 0.0 4.17 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
43 44 5.434408 TGGAGTCTGATTGATGAGGAAATG 58.566 41.667 0.00 0.00 0.00 2.32
86 87 4.276183 GCAATTCATCTGATGCATGACTCT 59.724 41.667 2.46 0.00 38.63 3.24
170 171 4.096003 CGATCTGGTGGGCCCGTT 62.096 66.667 19.37 0.00 35.15 4.44
174 175 2.484287 ATCTGGTGGGCCCGTTGAAG 62.484 60.000 19.37 10.32 35.15 3.02
201 202 1.272781 CACGAGAGCGAGTTCCAATC 58.727 55.000 0.00 0.00 41.64 2.67
224 225 5.126869 TCACCTTTGAGCACTTTCAAATTCA 59.873 36.000 2.09 0.00 43.80 2.57
265 266 4.440829 GCCTTGATTCCGGGGCCA 62.441 66.667 4.39 0.00 38.77 5.36
275 276 4.082523 CGGGGCCATCGACAGTGT 62.083 66.667 4.39 0.00 0.00 3.55
289 290 1.990060 AGTGTGTATGGGCGGCTCT 60.990 57.895 9.56 0.00 0.00 4.09
319 320 3.809832 GCATAGCACGTGGACAGATAAAT 59.190 43.478 18.88 0.00 0.00 1.40
368 369 5.647658 GGTCATGTGAAGATTAATGTGGACA 59.352 40.000 0.00 0.00 0.00 4.02
427 428 3.373130 CAGCAATCTGTCGTGATGAACAT 59.627 43.478 0.00 0.00 32.93 2.71
444 445 2.888212 ACATGGCATGTACTTGGGTTT 58.112 42.857 30.56 2.56 42.78 3.27
479 480 0.776810 TCAAGGCCTTGTTCATCCCA 59.223 50.000 37.97 18.67 41.16 4.37
532 533 4.386711 CATTGGCTCTTGCTGATGATCTA 58.613 43.478 0.00 0.00 39.59 1.98
561 562 5.534654 TGAAAAAGGTTCACATAGGAACTGG 59.465 40.000 6.08 0.00 45.07 4.00
742 743 0.171231 GTTCTCTTGATTTGGGGCGC 59.829 55.000 0.00 0.00 0.00 6.53
781 783 5.106876 ACACCCCCAGTTTATGTATGTAC 57.893 43.478 0.00 0.00 0.00 2.90
782 784 4.786454 ACACCCCCAGTTTATGTATGTACT 59.214 41.667 0.00 0.00 0.00 2.73
783 785 5.104652 ACACCCCCAGTTTATGTATGTACTC 60.105 44.000 0.00 0.00 0.00 2.59
784 786 4.411212 ACCCCCAGTTTATGTATGTACTCC 59.589 45.833 0.00 0.00 0.00 3.85
785 787 4.202430 CCCCCAGTTTATGTATGTACTCCC 60.202 50.000 0.00 0.00 0.00 4.30
786 788 4.658901 CCCCAGTTTATGTATGTACTCCCT 59.341 45.833 0.00 0.00 0.00 4.20
787 789 5.221661 CCCCAGTTTATGTATGTACTCCCTC 60.222 48.000 0.00 0.00 0.00 4.30
788 790 5.221661 CCCAGTTTATGTATGTACTCCCTCC 60.222 48.000 0.00 0.00 0.00 4.30
789 791 5.509163 CCAGTTTATGTATGTACTCCCTCCG 60.509 48.000 0.00 0.00 0.00 4.63
790 792 5.068723 CAGTTTATGTATGTACTCCCTCCGT 59.931 44.000 0.00 0.00 0.00 4.69
791 793 5.659971 AGTTTATGTATGTACTCCCTCCGTT 59.340 40.000 0.00 0.00 0.00 4.44
792 794 5.779529 TTATGTATGTACTCCCTCCGTTC 57.220 43.478 0.00 0.00 0.00 3.95
793 795 3.377253 TGTATGTACTCCCTCCGTTCT 57.623 47.619 0.00 0.00 0.00 3.01
794 796 3.021695 TGTATGTACTCCCTCCGTTCTG 58.978 50.000 0.00 0.00 0.00 3.02
795 797 2.526888 ATGTACTCCCTCCGTTCTGA 57.473 50.000 0.00 0.00 0.00 3.27
796 798 2.297698 TGTACTCCCTCCGTTCTGAA 57.702 50.000 0.00 0.00 0.00 3.02
797 799 2.816411 TGTACTCCCTCCGTTCTGAAT 58.184 47.619 0.00 0.00 0.00 2.57
798 800 3.170717 TGTACTCCCTCCGTTCTGAATT 58.829 45.455 0.00 0.00 0.00 2.17
799 801 4.346730 TGTACTCCCTCCGTTCTGAATTA 58.653 43.478 0.00 0.00 0.00 1.40
800 802 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
801 803 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
802 804 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
803 805 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
804 806 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
805 807 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
806 808 3.612860 CCTCCGTTCTGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
807 809 2.991190 TCCGTTCTGAATTACTTGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
808 810 2.734606 CCGTTCTGAATTACTTGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
809 811 3.181530 CCGTTCTGAATTACTTGTCGCAG 60.182 47.826 0.00 0.00 0.00 5.18
810 812 3.181530 CGTTCTGAATTACTTGTCGCAGG 60.182 47.826 0.00 0.00 0.00 4.85
811 813 3.678056 TCTGAATTACTTGTCGCAGGT 57.322 42.857 0.00 0.91 0.00 4.00
812 814 4.794278 TCTGAATTACTTGTCGCAGGTA 57.206 40.909 0.00 0.00 0.00 3.08
813 815 5.339008 TCTGAATTACTTGTCGCAGGTAT 57.661 39.130 3.46 0.00 0.00 2.73
814 816 5.109210 TCTGAATTACTTGTCGCAGGTATG 58.891 41.667 3.46 0.00 0.00 2.39
815 817 5.079689 TGAATTACTTGTCGCAGGTATGA 57.920 39.130 3.46 0.00 0.00 2.15
816 818 5.483811 TGAATTACTTGTCGCAGGTATGAA 58.516 37.500 3.46 0.00 0.00 2.57
817 819 6.112734 TGAATTACTTGTCGCAGGTATGAAT 58.887 36.000 3.46 0.00 0.00 2.57
818 820 5.991328 ATTACTTGTCGCAGGTATGAATG 57.009 39.130 3.46 0.00 0.00 2.67
819 821 3.334583 ACTTGTCGCAGGTATGAATGT 57.665 42.857 0.00 0.00 0.00 2.71
820 822 4.465632 ACTTGTCGCAGGTATGAATGTA 57.534 40.909 0.00 0.00 0.00 2.29
821 823 5.023533 ACTTGTCGCAGGTATGAATGTAT 57.976 39.130 0.00 0.00 0.00 2.29
822 824 5.050490 ACTTGTCGCAGGTATGAATGTATC 58.950 41.667 0.00 0.00 0.00 2.24
823 825 4.937201 TGTCGCAGGTATGAATGTATCT 57.063 40.909 0.00 0.00 0.00 1.98
824 826 6.040504 ACTTGTCGCAGGTATGAATGTATCTA 59.959 38.462 0.00 0.00 0.00 1.98
825 827 6.013842 TGTCGCAGGTATGAATGTATCTAG 57.986 41.667 0.00 0.00 0.00 2.43
826 828 5.768164 TGTCGCAGGTATGAATGTATCTAGA 59.232 40.000 0.00 0.00 0.00 2.43
827 829 6.434340 TGTCGCAGGTATGAATGTATCTAGAT 59.566 38.462 10.73 10.73 0.00 1.98
828 830 6.749578 GTCGCAGGTATGAATGTATCTAGATG 59.250 42.308 15.79 0.00 0.00 2.90
829 831 6.434340 TCGCAGGTATGAATGTATCTAGATGT 59.566 38.462 15.79 0.00 0.00 3.06
830 832 7.610305 TCGCAGGTATGAATGTATCTAGATGTA 59.390 37.037 15.79 4.44 0.00 2.29
831 833 8.409371 CGCAGGTATGAATGTATCTAGATGTAT 58.591 37.037 15.79 6.61 0.00 2.29
862 864 9.813080 GTTTTAGATATATTCATTTCTGCGACC 57.187 33.333 0.00 0.00 0.00 4.79
863 865 9.554395 TTTTAGATATATTCATTTCTGCGACCA 57.446 29.630 0.00 0.00 0.00 4.02
864 866 8.763049 TTAGATATATTCATTTCTGCGACCAG 57.237 34.615 0.00 0.00 40.54 4.00
865 867 6.763355 AGATATATTCATTTCTGCGACCAGT 58.237 36.000 0.00 0.00 40.09 4.00
866 868 7.896811 AGATATATTCATTTCTGCGACCAGTA 58.103 34.615 0.00 0.00 40.09 2.74
867 869 8.367911 AGATATATTCATTTCTGCGACCAGTAA 58.632 33.333 0.00 0.00 40.09 2.24
868 870 9.155975 GATATATTCATTTCTGCGACCAGTAAT 57.844 33.333 0.00 0.00 38.95 1.89
869 871 7.807977 ATATTCATTTCTGCGACCAGTAATT 57.192 32.000 0.00 0.00 37.08 1.40
870 872 5.957842 TTCATTTCTGCGACCAGTAATTT 57.042 34.783 0.00 0.00 37.08 1.82
871 873 5.295431 TCATTTCTGCGACCAGTAATTTG 57.705 39.130 0.00 0.00 37.08 2.32
872 874 5.000591 TCATTTCTGCGACCAGTAATTTGA 58.999 37.500 0.00 0.00 37.08 2.69
873 875 5.471797 TCATTTCTGCGACCAGTAATTTGAA 59.528 36.000 0.00 0.00 37.08 2.69
874 876 5.759506 TTTCTGCGACCAGTAATTTGAAA 57.240 34.783 0.00 0.00 40.09 2.69
875 877 4.742438 TCTGCGACCAGTAATTTGAAAC 57.258 40.909 0.00 0.00 40.09 2.78
876 878 4.130857 TCTGCGACCAGTAATTTGAAACA 58.869 39.130 0.00 0.00 40.09 2.83
877 879 4.213270 TCTGCGACCAGTAATTTGAAACAG 59.787 41.667 0.00 0.00 40.09 3.16
878 880 4.130857 TGCGACCAGTAATTTGAAACAGA 58.869 39.130 0.00 0.00 0.00 3.41
879 881 4.759693 TGCGACCAGTAATTTGAAACAGAT 59.240 37.500 0.00 0.00 0.00 2.90
880 882 5.088739 GCGACCAGTAATTTGAAACAGATG 58.911 41.667 0.00 0.00 0.00 2.90
881 883 5.631026 CGACCAGTAATTTGAAACAGATGG 58.369 41.667 0.00 0.00 0.00 3.51
882 884 5.411361 CGACCAGTAATTTGAAACAGATGGA 59.589 40.000 7.72 0.00 0.00 3.41
883 885 6.402550 CGACCAGTAATTTGAAACAGATGGAG 60.403 42.308 7.72 0.22 0.00 3.86
884 886 6.306987 ACCAGTAATTTGAAACAGATGGAGT 58.693 36.000 7.72 0.00 0.00 3.85
885 887 7.458397 ACCAGTAATTTGAAACAGATGGAGTA 58.542 34.615 7.72 0.00 0.00 2.59
926 928 9.197306 AGTTGATTAAAGTTCAGTTTTTACCCT 57.803 29.630 0.00 0.00 0.00 4.34
1006 1009 1.384525 CACTCACCCCAAAACGTGAA 58.615 50.000 0.00 0.00 38.48 3.18
1070 1073 3.607370 GACTTCCCCCACCACTCGC 62.607 68.421 0.00 0.00 0.00 5.03
1137 1152 2.507324 GACTCAGGAAGACGCGCC 60.507 66.667 5.73 0.00 0.00 6.53
1198 1213 2.412112 GAGTACTACGCGGCCCAG 59.588 66.667 12.47 4.28 0.00 4.45
1339 1354 0.908910 TGTTCATGGTCCACGGCTAT 59.091 50.000 0.00 0.00 0.00 2.97
1462 1477 4.697756 TTGCAGGCCTTCGTCCCG 62.698 66.667 0.00 0.00 0.00 5.14
2123 2138 4.756642 CAGCAACTTCCTGACAAACATAGA 59.243 41.667 0.00 0.00 32.03 1.98
2124 2139 5.239306 CAGCAACTTCCTGACAAACATAGAA 59.761 40.000 0.00 0.00 32.03 2.10
2125 2140 6.006449 AGCAACTTCCTGACAAACATAGAAT 58.994 36.000 0.00 0.00 0.00 2.40
2126 2141 7.119699 CAGCAACTTCCTGACAAACATAGAATA 59.880 37.037 0.00 0.00 32.03 1.75
2127 2142 7.335422 AGCAACTTCCTGACAAACATAGAATAG 59.665 37.037 0.00 0.00 0.00 1.73
2128 2143 7.334421 GCAACTTCCTGACAAACATAGAATAGA 59.666 37.037 0.00 0.00 0.00 1.98
2129 2144 9.219603 CAACTTCCTGACAAACATAGAATAGAA 57.780 33.333 0.00 0.00 0.00 2.10
2130 2145 9.793259 AACTTCCTGACAAACATAGAATAGAAA 57.207 29.630 0.00 0.00 0.00 2.52
2131 2146 9.793259 ACTTCCTGACAAACATAGAATAGAAAA 57.207 29.630 0.00 0.00 0.00 2.29
2175 2198 4.913924 GCATTCTATTCGGATTGTGCAATC 59.086 41.667 14.59 14.59 44.82 2.67
2231 2254 4.576216 AATGTGCGACGATTATCTCTCT 57.424 40.909 0.00 0.00 0.00 3.10
2232 2255 5.690997 AATGTGCGACGATTATCTCTCTA 57.309 39.130 0.00 0.00 0.00 2.43
2386 2445 3.392228 AGCGTTGGATCTGCTGGA 58.608 55.556 0.00 0.00 37.62 3.86
2387 2446 1.220206 AGCGTTGGATCTGCTGGAG 59.780 57.895 0.00 0.00 37.62 3.86
2388 2447 2.467826 GCGTTGGATCTGCTGGAGC 61.468 63.158 0.00 0.00 42.50 4.70
2399 2458 4.473520 CTGGAGCCGGCGTTGGAT 62.474 66.667 23.20 0.68 0.00 3.41
2400 2459 4.467084 TGGAGCCGGCGTTGGATC 62.467 66.667 23.20 12.04 43.75 3.36
2401 2460 4.467084 GGAGCCGGCGTTGGATCA 62.467 66.667 23.20 0.00 46.29 2.92
2402 2461 2.892425 GAGCCGGCGTTGGATCAG 60.892 66.667 23.20 0.00 43.91 2.90
2880 3138 7.678947 AGTGCCTGTATTTGCATAGATATTC 57.321 36.000 0.00 0.00 40.07 1.75
3033 3294 3.621419 CCATGATGGCCTTTTCCCT 57.379 52.632 3.32 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.378339 GCATGCAATCAAATGCTCTACC 58.622 45.455 14.21 0.00 46.54 3.18
80 81 1.565759 CAAATCCCCCATCCAGAGTCA 59.434 52.381 0.00 0.00 0.00 3.41
86 87 1.500303 CTCCATCAAATCCCCCATCCA 59.500 52.381 0.00 0.00 0.00 3.41
170 171 1.403814 CTCTCGTGGATAGCCCTTCA 58.596 55.000 0.00 0.00 35.38 3.02
174 175 2.136196 CTCGCTCTCGTGGATAGCCC 62.136 65.000 0.00 0.00 36.96 5.19
201 202 5.350633 TGAATTTGAAAGTGCTCAAAGGTG 58.649 37.500 5.28 0.00 45.80 4.00
224 225 6.684613 GCCAAGTCTGCCATGAATTATTCAAT 60.685 38.462 11.88 0.00 43.95 2.57
265 266 0.179111 CGCCCATACACACTGTCGAT 60.179 55.000 0.00 0.00 0.00 3.59
275 276 0.750850 GAAGTAGAGCCGCCCATACA 59.249 55.000 0.00 0.00 0.00 2.29
289 290 1.202256 CCACGTGCTATGCTCGAAGTA 60.202 52.381 10.91 0.00 46.28 2.24
319 320 2.614259 GATGGAGGAATCCAGCTCCTA 58.386 52.381 0.61 0.00 43.65 2.94
368 369 6.992664 ATCATTGTTCCTAGAGATAGCAGT 57.007 37.500 0.00 0.00 0.00 4.40
427 428 2.375174 AGAGAAACCCAAGTACATGCCA 59.625 45.455 0.00 0.00 0.00 4.92
444 445 2.945008 CCTTGAACAACAACTGCAGAGA 59.055 45.455 23.35 0.00 34.56 3.10
479 480 2.019984 GGCCATCGCTTCAAGAATCTT 58.980 47.619 0.00 0.00 34.44 2.40
561 562 5.470098 AGATTATTGATGGTCGCCATACAAC 59.530 40.000 10.74 1.13 45.26 3.32
619 620 9.491675 CTCATCTTCAGCTTTATATCATGAACT 57.508 33.333 0.00 0.00 0.00 3.01
620 621 9.486497 TCTCATCTTCAGCTTTATATCATGAAC 57.514 33.333 0.00 0.00 0.00 3.18
781 783 4.184629 CAAGTAATTCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
782 784 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
783 785 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
784 786 3.612860 CGACAAGTAATTCAGAACGGAGG 59.387 47.826 0.00 0.00 0.00 4.30
785 787 3.060895 GCGACAAGTAATTCAGAACGGAG 59.939 47.826 0.00 0.00 0.00 4.63
786 788 2.991190 GCGACAAGTAATTCAGAACGGA 59.009 45.455 0.00 0.00 0.00 4.69
787 789 2.734606 TGCGACAAGTAATTCAGAACGG 59.265 45.455 0.00 0.00 0.00 4.44
788 790 3.181530 CCTGCGACAAGTAATTCAGAACG 60.182 47.826 0.00 0.00 0.00 3.95
789 791 3.746492 ACCTGCGACAAGTAATTCAGAAC 59.254 43.478 0.00 0.00 0.00 3.01
790 792 4.002906 ACCTGCGACAAGTAATTCAGAA 57.997 40.909 0.00 0.00 0.00 3.02
791 793 3.678056 ACCTGCGACAAGTAATTCAGA 57.322 42.857 0.00 0.00 0.00 3.27
792 794 5.109210 TCATACCTGCGACAAGTAATTCAG 58.891 41.667 0.00 0.00 0.00 3.02
793 795 5.079689 TCATACCTGCGACAAGTAATTCA 57.920 39.130 0.00 0.00 0.00 2.57
794 796 6.037172 ACATTCATACCTGCGACAAGTAATTC 59.963 38.462 0.00 0.00 0.00 2.17
795 797 5.880332 ACATTCATACCTGCGACAAGTAATT 59.120 36.000 0.00 0.00 0.00 1.40
796 798 5.428253 ACATTCATACCTGCGACAAGTAAT 58.572 37.500 0.00 0.00 0.00 1.89
797 799 4.827692 ACATTCATACCTGCGACAAGTAA 58.172 39.130 0.00 0.00 0.00 2.24
798 800 4.465632 ACATTCATACCTGCGACAAGTA 57.534 40.909 0.00 0.00 0.00 2.24
799 801 3.334583 ACATTCATACCTGCGACAAGT 57.665 42.857 0.00 0.00 0.00 3.16
800 802 5.292765 AGATACATTCATACCTGCGACAAG 58.707 41.667 0.00 0.00 0.00 3.16
801 803 5.276461 AGATACATTCATACCTGCGACAA 57.724 39.130 0.00 0.00 0.00 3.18
802 804 4.937201 AGATACATTCATACCTGCGACA 57.063 40.909 0.00 0.00 0.00 4.35
803 805 6.255596 TCTAGATACATTCATACCTGCGAC 57.744 41.667 0.00 0.00 0.00 5.19
804 806 6.434340 ACATCTAGATACATTCATACCTGCGA 59.566 38.462 4.54 0.00 0.00 5.10
805 807 6.625362 ACATCTAGATACATTCATACCTGCG 58.375 40.000 4.54 0.00 0.00 5.18
836 838 9.813080 GGTCGCAGAAATGAATATATCTAAAAC 57.187 33.333 0.00 0.00 39.69 2.43
837 839 9.554395 TGGTCGCAGAAATGAATATATCTAAAA 57.446 29.630 0.00 0.00 39.69 1.52
838 840 9.208022 CTGGTCGCAGAAATGAATATATCTAAA 57.792 33.333 0.00 0.00 39.69 1.85
839 841 8.367911 ACTGGTCGCAGAAATGAATATATCTAA 58.632 33.333 0.00 0.00 39.69 2.10
840 842 7.896811 ACTGGTCGCAGAAATGAATATATCTA 58.103 34.615 0.00 0.00 39.69 1.98
841 843 6.763355 ACTGGTCGCAGAAATGAATATATCT 58.237 36.000 0.00 0.00 39.69 1.98
842 844 8.534333 TTACTGGTCGCAGAAATGAATATATC 57.466 34.615 0.00 0.00 39.69 1.63
843 845 9.507329 AATTACTGGTCGCAGAAATGAATATAT 57.493 29.630 0.00 0.00 39.69 0.86
844 846 8.902540 AATTACTGGTCGCAGAAATGAATATA 57.097 30.769 0.00 0.00 39.69 0.86
845 847 7.807977 AATTACTGGTCGCAGAAATGAATAT 57.192 32.000 0.00 0.00 39.69 1.28
846 848 7.335673 TCAAATTACTGGTCGCAGAAATGAATA 59.664 33.333 0.00 0.00 39.69 1.75
847 849 6.150976 TCAAATTACTGGTCGCAGAAATGAAT 59.849 34.615 0.00 0.00 39.69 2.57
848 850 5.471797 TCAAATTACTGGTCGCAGAAATGAA 59.528 36.000 0.00 0.00 39.69 2.57
849 851 5.000591 TCAAATTACTGGTCGCAGAAATGA 58.999 37.500 0.00 0.00 39.69 2.57
850 852 5.295431 TCAAATTACTGGTCGCAGAAATG 57.705 39.130 0.00 0.00 39.69 2.32
851 853 5.957842 TTCAAATTACTGGTCGCAGAAAT 57.042 34.783 0.00 0.00 39.69 2.17
852 854 5.066634 TGTTTCAAATTACTGGTCGCAGAAA 59.933 36.000 0.00 0.00 39.69 2.52
853 855 4.576873 TGTTTCAAATTACTGGTCGCAGAA 59.423 37.500 0.00 0.00 39.69 3.02
854 856 4.130857 TGTTTCAAATTACTGGTCGCAGA 58.869 39.130 0.00 0.00 0.00 4.26
855 857 4.213270 TCTGTTTCAAATTACTGGTCGCAG 59.787 41.667 0.00 0.00 0.00 5.18
856 858 4.130857 TCTGTTTCAAATTACTGGTCGCA 58.869 39.130 0.00 0.00 0.00 5.10
857 859 4.742438 TCTGTTTCAAATTACTGGTCGC 57.258 40.909 0.00 0.00 0.00 5.19
858 860 5.411361 TCCATCTGTTTCAAATTACTGGTCG 59.589 40.000 0.00 0.00 0.00 4.79
859 861 6.431234 ACTCCATCTGTTTCAAATTACTGGTC 59.569 38.462 0.00 0.00 0.00 4.02
860 862 6.306987 ACTCCATCTGTTTCAAATTACTGGT 58.693 36.000 0.00 0.00 0.00 4.00
861 863 6.824305 ACTCCATCTGTTTCAAATTACTGG 57.176 37.500 0.00 0.00 0.00 4.00
862 864 7.607991 AGGTACTCCATCTGTTTCAAATTACTG 59.392 37.037 0.00 0.00 35.89 2.74
863 865 7.690256 AGGTACTCCATCTGTTTCAAATTACT 58.310 34.615 0.00 0.00 35.89 2.24
864 866 7.923414 AGGTACTCCATCTGTTTCAAATTAC 57.077 36.000 0.00 0.00 35.89 1.89
883 885 7.772332 AATCAACTGAAATCATACGAGGTAC 57.228 36.000 0.00 0.00 0.00 3.34
884 886 9.878667 TTTAATCAACTGAAATCATACGAGGTA 57.121 29.630 0.00 0.00 0.00 3.08
885 887 8.786826 TTTAATCAACTGAAATCATACGAGGT 57.213 30.769 0.00 0.00 0.00 3.85
930 932 0.320596 TGCCGTCGACCCGTATTTTT 60.321 50.000 10.58 0.00 0.00 1.94
931 933 1.015607 GTGCCGTCGACCCGTATTTT 61.016 55.000 10.58 0.00 0.00 1.82
932 934 1.446618 GTGCCGTCGACCCGTATTT 60.447 57.895 10.58 0.00 0.00 1.40
933 935 2.157305 TTGTGCCGTCGACCCGTATT 62.157 55.000 10.58 0.00 0.00 1.89
1006 1009 3.819877 GAGGCCGTTTCACCCACGT 62.820 63.158 0.00 0.00 35.81 4.49
1011 1014 3.647771 AGGGGAGGCCGTTTCACC 61.648 66.667 3.47 3.47 38.47 4.02
1041 1044 2.035442 GGGAAGTCGTTGCTGCCTC 61.035 63.158 0.00 0.00 34.50 4.70
1070 1073 4.410400 GAGGGGAACTGGTGCCGG 62.410 72.222 0.00 0.00 39.07 6.13
1339 1354 1.672030 CCAGCTGATGTCGTTGCCA 60.672 57.895 17.39 0.00 0.00 4.92
1462 1477 3.183776 GACGGCGACCTCGAGATCC 62.184 68.421 16.62 7.99 43.02 3.36
1717 1732 1.760875 GGGCACGATGGGGAGAGTA 60.761 63.158 0.00 0.00 0.00 2.59
2099 2114 2.722094 TGTTTGTCAGGAAGTTGCTGT 58.278 42.857 22.00 0.00 37.12 4.40
2126 2141 9.525409 CATTGTCTGTTTCTTTTGATCTTTTCT 57.475 29.630 0.00 0.00 0.00 2.52
2127 2142 8.271487 GCATTGTCTGTTTCTTTTGATCTTTTC 58.729 33.333 0.00 0.00 0.00 2.29
2128 2143 7.765360 TGCATTGTCTGTTTCTTTTGATCTTTT 59.235 29.630 0.00 0.00 0.00 2.27
2129 2144 7.267128 TGCATTGTCTGTTTCTTTTGATCTTT 58.733 30.769 0.00 0.00 0.00 2.52
2130 2145 6.808829 TGCATTGTCTGTTTCTTTTGATCTT 58.191 32.000 0.00 0.00 0.00 2.40
2131 2146 6.395426 TGCATTGTCTGTTTCTTTTGATCT 57.605 33.333 0.00 0.00 0.00 2.75
2132 2147 7.597743 AGAATGCATTGTCTGTTTCTTTTGATC 59.402 33.333 18.59 0.00 30.18 2.92
2133 2148 7.439381 AGAATGCATTGTCTGTTTCTTTTGAT 58.561 30.769 18.59 0.00 30.18 2.57
2146 2169 5.911280 CACAATCCGAATAGAATGCATTGTC 59.089 40.000 18.59 3.01 32.07 3.18
2175 2198 0.462937 TTCCGGTGTCTGTGTTGGTG 60.463 55.000 0.00 0.00 0.00 4.17
2476 2535 6.166984 TCACAGATTAAGGCTGGAGATAAG 57.833 41.667 11.47 0.00 37.69 1.73
2880 3138 7.024340 TCTTGAATGCTACGTACTAGTTAGG 57.976 40.000 0.00 0.00 0.00 2.69
2933 3192 3.522553 GGGTTCCTCAGTCAAACTATCG 58.477 50.000 0.00 0.00 0.00 2.92
3055 3317 4.558178 TGCTTTGTGCCATGTATGAAAAG 58.442 39.130 0.00 0.00 42.00 2.27
3084 3346 4.418013 TTGTGAACCATATTTGCTGTCG 57.582 40.909 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.