Multiple sequence alignment - TraesCS4B01G138400

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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 TraesCS4B01G138400 chr4B 100.000 3032 0 0 1 3032 182262011 182258980 0.000000e+00 5600.0
1 TraesCS4B01G138400 chr4B 99.195 621 5 0 1 621 182268877 182268257 0.000000e+00 1120.0
2 TraesCS4B01G138400 chr4A 89.114 2223 118 47 867 3032 450765743 450763588 0.000000e+00 2651.0
3 TraesCS4B01G138400 chr4A 90.066 151 10 2 690 840 450765874 450765729 1.110000e-44 191.0
4 TraesCS4B01G138400 chr4A 91.429 70 6 0 1452 1521 667005050 667005119 2.490000e-16 97.1
5 TraesCS4B01G138400 chr4D 91.140 1456 56 30 866 2274 119806439 119805010 0.000000e+00 1906.0
6 TraesCS4B01G138400 chr4D 94.363 816 37 2 2225 3032 119804902 119804088 0.000000e+00 1243.0
7 TraesCS4B01G138400 chr4D 95.402 87 4 0 758 844 119806506 119806420 4.080000e-29 139.0
8 TraesCS4B01G138400 chr5A 98.555 623 9 0 1 623 335385248 335385870 0.000000e+00 1101.0
9 TraesCS4B01G138400 chr5A 98.074 623 12 0 1 623 335391997 335392619 0.000000e+00 1085.0
10 TraesCS4B01G138400 chr5A 77.903 534 95 17 1035 1561 337941135 337941652 8.160000e-81 311.0
11 TraesCS4B01G138400 chr2B 98.395 623 10 0 1 623 513169034 513169656 0.000000e+00 1096.0
12 TraesCS4B01G138400 chr2B 98.234 623 11 0 1 623 513162231 513162853 0.000000e+00 1090.0
13 TraesCS4B01G138400 chr2B 90.278 72 6 1 1450 1521 699179954 699180024 3.220000e-15 93.5
14 TraesCS4B01G138400 chr1A 98.237 624 11 0 1 624 394313927 394314550 0.000000e+00 1092.0
15 TraesCS4B01G138400 chr7B 98.234 623 11 0 1 623 49152167 49151545 0.000000e+00 1090.0
16 TraesCS4B01G138400 chr7A 98.083 626 12 0 1 626 18845134 18844509 0.000000e+00 1090.0
17 TraesCS4B01G138400 chr7A 96.667 60 2 0 1450 1509 602227128 602227187 1.920000e-17 100.0
18 TraesCS4B01G138400 chr6A 98.074 623 12 0 1 623 2812875 2813497 0.000000e+00 1085.0
19 TraesCS4B01G138400 chr5D 83.180 327 52 3 1243 1567 254586676 254587001 2.290000e-76 296.0
20 TraesCS4B01G138400 chr5B 82.716 324 53 3 1246 1567 288178094 288177772 4.950000e-73 285.0
21 TraesCS4B01G138400 chr3A 93.056 72 5 0 1450 1521 625330514 625330585 4.130000e-19 106.0
22 TraesCS4B01G138400 chr2A 78.814 118 22 2 1450 1564 176671130 176671247 3.240000e-10 76.8


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 TraesCS4B01G138400 chr4B 182258980 182262011 3031 True 5600 5600 100.000 1 3032 1 chr4B.!!$R1 3031
1 TraesCS4B01G138400 chr4B 182268257 182268877 620 True 1120 1120 99.195 1 621 1 chr4B.!!$R2 620
2 TraesCS4B01G138400 chr4A 450763588 450765874 2286 True 1421 2651 89.590 690 3032 2 chr4A.!!$R1 2342
3 TraesCS4B01G138400 chr4D 119804088 119806506 2418 True 1096 1906 93.635 758 3032 3 chr4D.!!$R1 2274
4 TraesCS4B01G138400 chr5A 335385248 335385870 622 False 1101 1101 98.555 1 623 1 chr5A.!!$F1 622
5 TraesCS4B01G138400 chr5A 335391997 335392619 622 False 1085 1085 98.074 1 623 1 chr5A.!!$F2 622
6 TraesCS4B01G138400 chr5A 337941135 337941652 517 False 311 311 77.903 1035 1561 1 chr5A.!!$F3 526
7 TraesCS4B01G138400 chr2B 513169034 513169656 622 False 1096 1096 98.395 1 623 1 chr2B.!!$F2 622
8 TraesCS4B01G138400 chr2B 513162231 513162853 622 False 1090 1090 98.234 1 623 1 chr2B.!!$F1 622
9 TraesCS4B01G138400 chr1A 394313927 394314550 623 False 1092 1092 98.237 1 624 1 chr1A.!!$F1 623
10 TraesCS4B01G138400 chr7B 49151545 49152167 622 True 1090 1090 98.234 1 623 1 chr7B.!!$R1 622
11 TraesCS4B01G138400 chr7A 18844509 18845134 625 True 1090 1090 98.083 1 626 1 chr7A.!!$R1 625
12 TraesCS4B01G138400 chr6A 2812875 2813497 622 False 1085 1085 98.074 1 623 1 chr6A.!!$F1 622

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
849 850 0.034186 ACATGCACCCACATACCCTG 60.034 55.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2166 2249 0.906775 TAACTCATTCCACGTCCCCC 59.093 55.0 0.0 0.0 0.0 5.4 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
260 261 1.569072 GTCTCTCCTCCTCCTCCTCTT 59.431 57.143 0.00 0.00 0.00 2.85
626 627 1.624312 TGCTACGTTCCCCAACACATA 59.376 47.619 0.00 0.00 32.14 2.29
627 628 2.277084 GCTACGTTCCCCAACACATAG 58.723 52.381 0.00 0.00 32.14 2.23
628 629 2.354403 GCTACGTTCCCCAACACATAGT 60.354 50.000 0.00 0.00 32.14 2.12
629 630 3.119029 GCTACGTTCCCCAACACATAGTA 60.119 47.826 0.00 0.00 32.14 1.82
630 631 3.604875 ACGTTCCCCAACACATAGTAG 57.395 47.619 0.00 0.00 32.14 2.57
631 632 2.901839 ACGTTCCCCAACACATAGTAGT 59.098 45.455 0.00 0.00 32.14 2.73
632 633 4.088634 ACGTTCCCCAACACATAGTAGTA 58.911 43.478 0.00 0.00 32.14 1.82
633 634 4.082026 ACGTTCCCCAACACATAGTAGTAC 60.082 45.833 0.00 0.00 32.14 2.73
634 635 4.159135 CGTTCCCCAACACATAGTAGTACT 59.841 45.833 8.14 8.14 32.14 2.73
635 636 5.658468 GTTCCCCAACACATAGTAGTACTC 58.342 45.833 5.96 0.00 32.14 2.59
636 637 4.284178 TCCCCAACACATAGTAGTACTCC 58.716 47.826 5.96 0.00 0.00 3.85
637 638 4.016851 TCCCCAACACATAGTAGTACTCCT 60.017 45.833 5.96 0.00 0.00 3.69
638 639 5.194334 TCCCCAACACATAGTAGTACTCCTA 59.806 44.000 5.96 0.00 0.00 2.94
639 640 6.075984 CCCCAACACATAGTAGTACTCCTAT 58.924 44.000 5.96 0.00 0.00 2.57
640 641 7.074109 TCCCCAACACATAGTAGTACTCCTATA 59.926 40.741 5.96 0.00 0.00 1.31
641 642 7.727186 CCCCAACACATAGTAGTACTCCTATAA 59.273 40.741 5.96 0.00 0.00 0.98
642 643 9.310449 CCCAACACATAGTAGTACTCCTATAAT 57.690 37.037 5.96 0.00 0.00 1.28
666 667 5.462034 AGTACGTACTACTAAGTTCTGCG 57.538 43.478 26.36 0.00 37.15 5.18
667 668 3.128465 ACGTACTACTAAGTTCTGCGC 57.872 47.619 0.00 0.00 37.15 6.09
668 669 2.099621 CGTACTACTAAGTTCTGCGCG 58.900 52.381 0.00 0.00 37.15 6.86
669 670 1.844962 GTACTACTAAGTTCTGCGCGC 59.155 52.381 27.26 27.26 37.15 6.86
670 671 0.797249 ACTACTAAGTTCTGCGCGCG 60.797 55.000 28.44 28.44 29.00 6.86
671 672 2.067453 CTACTAAGTTCTGCGCGCGC 62.067 60.000 45.02 45.02 42.35 6.86
681 682 4.031044 GCGCGCGCACGTATAGTC 62.031 66.667 46.11 15.61 42.83 2.59
682 683 3.384399 CGCGCGCACGTATAGTCC 61.384 66.667 32.61 0.00 42.83 3.85
683 684 2.278336 GCGCGCACGTATAGTCCA 60.278 61.111 29.10 0.00 42.83 4.02
684 685 2.574222 GCGCGCACGTATAGTCCAC 61.574 63.158 29.10 0.00 42.83 4.02
685 686 2.283757 CGCGCACGTATAGTCCACG 61.284 63.158 8.75 0.00 44.80 4.94
697 698 5.398416 CGTATAGTCCACGTACATGTGAATG 59.602 44.000 9.11 3.36 42.55 2.67
712 713 1.876799 TGAATGTCGGTTGCGATTTGT 59.123 42.857 0.00 0.00 0.00 2.83
713 714 3.067833 TGAATGTCGGTTGCGATTTGTA 58.932 40.909 0.00 0.00 0.00 2.41
746 747 7.116662 GTGATTAAATCTGTTGCATTTGCTTGA 59.883 33.333 3.94 0.00 42.66 3.02
750 751 2.892215 TCTGTTGCATTTGCTTGATCCA 59.108 40.909 3.94 0.00 42.66 3.41
752 753 2.364647 TGTTGCATTTGCTTGATCCACA 59.635 40.909 3.94 0.00 42.66 4.17
753 754 2.728690 TGCATTTGCTTGATCCACAC 57.271 45.000 3.94 0.00 42.66 3.82
754 755 1.068402 TGCATTTGCTTGATCCACACG 60.068 47.619 3.94 0.00 42.66 4.49
755 756 1.068333 GCATTTGCTTGATCCACACGT 60.068 47.619 0.00 0.00 38.21 4.49
756 757 2.607771 GCATTTGCTTGATCCACACGTT 60.608 45.455 0.00 0.00 38.21 3.99
770 771 3.737266 CCACACGTTACGTACAAATGACT 59.263 43.478 10.89 0.00 38.32 3.41
845 846 5.580297 CCAATTTAAACATGCACCCACATAC 59.420 40.000 0.00 0.00 0.00 2.39
847 848 1.555967 AAACATGCACCCACATACCC 58.444 50.000 0.00 0.00 0.00 3.69
848 849 0.704076 AACATGCACCCACATACCCT 59.296 50.000 0.00 0.00 0.00 4.34
849 850 0.034186 ACATGCACCCACATACCCTG 60.034 55.000 0.00 0.00 0.00 4.45
850 851 0.034186 CATGCACCCACATACCCTGT 60.034 55.000 0.00 0.00 39.20 4.00
864 865 7.636150 ACATACCCTGTGTCCGTATATATAC 57.364 40.000 12.18 12.18 36.48 1.47
865 866 7.177184 ACATACCCTGTGTCCGTATATATACA 58.823 38.462 20.24 3.16 36.48 2.29
866 867 7.837689 ACATACCCTGTGTCCGTATATATACAT 59.162 37.037 20.24 1.96 36.48 2.29
867 868 8.692710 CATACCCTGTGTCCGTATATATACATT 58.307 37.037 20.24 0.00 32.87 2.71
868 869 7.549147 ACCCTGTGTCCGTATATATACATTT 57.451 36.000 20.24 0.00 32.87 2.32
869 870 8.654485 ACCCTGTGTCCGTATATATACATTTA 57.346 34.615 20.24 3.90 32.87 1.40
870 871 9.092338 ACCCTGTGTCCGTATATATACATTTAA 57.908 33.333 20.24 1.98 32.87 1.52
871 872 9.932207 CCCTGTGTCCGTATATATACATTTAAA 57.068 33.333 20.24 0.00 32.87 1.52
879 880 9.982291 CCGTATATATACATTTAAACATGCACC 57.018 33.333 20.24 0.00 32.87 5.01
880 881 9.982291 CGTATATATACATTTAAACATGCACCC 57.018 33.333 20.24 0.00 32.87 4.61
883 884 5.991933 ATACATTTAAACATGCACCCACA 57.008 34.783 0.00 0.00 0.00 4.17
884 885 4.888326 ACATTTAAACATGCACCCACAT 57.112 36.364 0.00 0.00 0.00 3.21
885 886 4.819769 ACATTTAAACATGCACCCACATC 58.180 39.130 0.00 0.00 0.00 3.06
886 887 3.951775 TTTAAACATGCACCCACATCC 57.048 42.857 0.00 0.00 0.00 3.51
909 910 7.513132 TCCATCTATAAATACGAACGTACTCG 58.487 38.462 9.19 8.05 44.50 4.18
910 911 7.384932 TCCATCTATAAATACGAACGTACTCGA 59.615 37.037 16.02 1.17 41.44 4.04
917 923 2.564771 ACGAACGTACTCGATCCCATA 58.435 47.619 16.02 0.00 41.44 2.74
942 948 4.522022 CCTCTCCTGCTTTCAGACAATTTT 59.478 41.667 0.00 0.00 42.95 1.82
952 958 6.304208 GCTTTCAGACAATTTTCGATCTTGAC 59.696 38.462 8.56 3.75 0.00 3.18
968 979 5.741388 TCTTGACAGTTTCTCTTCTTTGC 57.259 39.130 0.00 0.00 0.00 3.68
978 989 1.063912 CTCTTCTTTGCGCACACAACA 59.936 47.619 11.12 0.00 0.00 3.33
1115 1135 2.902343 GCTCCCCGCCAATGCTAC 60.902 66.667 0.00 0.00 34.43 3.58
1122 1142 1.674359 CCGCCAATGCTACACCAATA 58.326 50.000 0.00 0.00 34.43 1.90
1179 1202 1.338337 AGTGGATCGCTACCTTCATCG 59.662 52.381 0.00 0.00 0.00 3.84
1228 1267 6.316390 AGCTAGCACCATTAGTTACAACATTC 59.684 38.462 18.83 0.00 0.00 2.67
1229 1268 6.093495 GCTAGCACCATTAGTTACAACATTCA 59.907 38.462 10.63 0.00 0.00 2.57
1230 1269 7.201732 GCTAGCACCATTAGTTACAACATTCAT 60.202 37.037 10.63 0.00 0.00 2.57
2041 2098 3.251318 GACGACTGACGCCTCGTGT 62.251 63.158 0.00 0.00 43.06 4.49
2045 2102 2.661537 CTGACGCCTCGTGTGCAA 60.662 61.111 0.00 0.00 41.37 4.08
2080 2137 7.435068 TCCATAGGAACTTCTTTTCTTTTCG 57.565 36.000 0.00 0.00 41.75 3.46
2083 2140 7.803659 CCATAGGAACTTCTTTTCTTTTCGTTC 59.196 37.037 0.00 0.00 41.75 3.95
2124 2181 8.892723 TGACAGTGATCCATGAACATTAATTAC 58.107 33.333 0.00 0.00 0.00 1.89
2166 2249 4.519730 GGGCTACTACACTCTAGTACATGG 59.480 50.000 0.00 0.00 0.00 3.66
2168 2251 4.519730 GCTACTACACTCTAGTACATGGGG 59.480 50.000 0.00 0.00 0.00 4.96
2217 2305 3.257393 ACTCTAGTTTCTCAGCATTGCG 58.743 45.455 2.38 0.00 0.00 4.85
2219 2307 1.063174 CTAGTTTCTCAGCATTGCGCC 59.937 52.381 4.18 0.00 44.04 6.53
2221 2309 1.303561 TTTCTCAGCATTGCGCCCT 60.304 52.632 4.18 0.00 44.04 5.19
2266 2509 2.642311 TGGAGATCACCAAAGGCTACAA 59.358 45.455 9.69 0.00 36.96 2.41
2326 2572 2.333926 CAACATGCCACAAATCAGCTG 58.666 47.619 7.63 7.63 0.00 4.24
2364 2618 3.157087 AGACATAAACCAGCCAAACAGG 58.843 45.455 0.00 0.00 41.84 4.00
2368 2622 2.159179 AAACCAGCCAAACAGGAACT 57.841 45.000 0.00 0.00 41.22 3.01
2377 2631 3.181476 GCCAAACAGGAACTTGAATGTGT 60.181 43.478 0.00 0.00 41.22 3.72
2456 2710 1.755179 AATGAAGGAATGGCACCTCG 58.245 50.000 0.00 0.00 36.67 4.63
2458 2712 1.271856 TGAAGGAATGGCACCTCGTA 58.728 50.000 0.00 0.00 36.67 3.43
2490 2744 2.357569 GCTCCCCTCCATTTTCATCACT 60.358 50.000 0.00 0.00 0.00 3.41
2516 2770 2.743183 GCTACCTTCTACCATGCCAGTG 60.743 54.545 0.00 0.00 0.00 3.66
2692 2946 2.031120 CAGAAAGTTCCAGGTTGCCAA 58.969 47.619 0.00 0.00 0.00 4.52
2743 2997 4.351938 CTCGGCCACGACCAACGA 62.352 66.667 2.24 0.00 45.59 3.85
2744 2998 4.351938 TCGGCCACGACCAACGAG 62.352 66.667 2.24 0.00 45.59 4.18
2748 3002 4.351938 CCACGACCAACGAGCCGA 62.352 66.667 1.50 0.00 45.77 5.54
2749 3003 3.103911 CACGACCAACGAGCCGAC 61.104 66.667 1.50 0.00 45.77 4.79
2750 3004 4.353437 ACGACCAACGAGCCGACC 62.353 66.667 1.50 0.00 45.77 4.79
2751 3005 4.052229 CGACCAACGAGCCGACCT 62.052 66.667 1.50 0.00 45.77 3.85
2752 3006 2.126031 GACCAACGAGCCGACCTC 60.126 66.667 1.50 0.00 37.22 3.85
2753 3007 3.644399 GACCAACGAGCCGACCTCC 62.644 68.421 1.50 0.00 37.27 4.30
2754 3008 4.796231 CCAACGAGCCGACCTCCG 62.796 72.222 1.50 0.00 37.27 4.63
2966 3244 6.806751 TGATAACTACCTATGTCTGCTTCAC 58.193 40.000 0.00 0.00 0.00 3.18
2994 3272 3.912528 AGCCAATTCAGCTCCCATCTATA 59.087 43.478 0.00 0.00 34.91 1.31
2997 3275 5.713861 GCCAATTCAGCTCCCATCTATATTT 59.286 40.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 3.550431 GCGGCCAGCCCTAGATGA 61.550 66.667 2.24 0.00 40.81 2.92
260 261 1.675310 CTTCGCCAAGCACCATGGA 60.675 57.895 21.47 0.00 40.56 3.41
640 641 8.119226 CGCAGAACTTAGTAGTACGTACTTATT 58.881 37.037 31.58 19.27 39.06 1.40
641 642 7.625553 CGCAGAACTTAGTAGTACGTACTTAT 58.374 38.462 31.58 21.94 39.06 1.73
642 643 6.455646 GCGCAGAACTTAGTAGTACGTACTTA 60.456 42.308 31.58 17.09 39.06 2.24
643 644 5.672321 GCGCAGAACTTAGTAGTACGTACTT 60.672 44.000 31.58 18.12 39.06 2.24
644 645 4.201763 GCGCAGAACTTAGTAGTACGTACT 60.202 45.833 29.62 29.62 44.69 2.73
645 646 4.025094 GCGCAGAACTTAGTAGTACGTAC 58.975 47.826 18.10 18.10 33.17 3.67
646 647 3.242091 CGCGCAGAACTTAGTAGTACGTA 60.242 47.826 8.75 0.00 33.17 3.57
647 648 2.475187 CGCGCAGAACTTAGTAGTACGT 60.475 50.000 8.75 0.00 33.17 3.57
648 649 2.099621 CGCGCAGAACTTAGTAGTACG 58.900 52.381 8.75 0.00 33.17 3.67
649 650 1.844962 GCGCGCAGAACTTAGTAGTAC 59.155 52.381 29.10 0.00 33.17 2.73
650 651 1.530441 CGCGCGCAGAACTTAGTAGTA 60.530 52.381 32.61 0.00 33.17 1.82
651 652 0.797249 CGCGCGCAGAACTTAGTAGT 60.797 55.000 32.61 0.00 35.68 2.73
652 653 1.910880 CGCGCGCAGAACTTAGTAG 59.089 57.895 32.61 5.79 0.00 2.57
653 654 2.156446 GCGCGCGCAGAACTTAGTA 61.156 57.895 46.11 0.00 41.49 1.82
654 655 3.479269 GCGCGCGCAGAACTTAGT 61.479 61.111 46.11 0.00 41.49 2.24
664 665 4.031044 GACTATACGTGCGCGCGC 62.031 66.667 45.02 45.02 42.83 6.86
665 666 3.384399 GGACTATACGTGCGCGCG 61.384 66.667 38.67 38.67 42.83 6.86
666 667 2.278336 TGGACTATACGTGCGCGC 60.278 61.111 27.26 27.26 42.83 6.86
667 668 3.597162 GTGGACTATACGTGCGCG 58.403 61.111 19.78 19.78 44.93 6.86
668 669 3.597162 CGTGGACTATACGTGCGC 58.403 61.111 0.00 0.00 40.59 6.09
672 673 9.228454 ACATTCACATGTACGTGGACTATACGT 62.228 40.741 19.05 8.27 42.24 3.57
673 674 4.541085 TCACATGTACGTGGACTATACG 57.459 45.455 19.05 0.00 46.31 3.06
674 675 6.270815 ACATTCACATGTACGTGGACTATAC 58.729 40.000 19.05 0.00 42.24 1.47
675 676 6.459670 ACATTCACATGTACGTGGACTATA 57.540 37.500 19.05 0.27 42.24 1.31
676 677 5.339008 ACATTCACATGTACGTGGACTAT 57.661 39.130 19.05 4.58 42.24 2.12
677 678 4.673320 CGACATTCACATGTACGTGGACTA 60.673 45.833 19.05 2.45 44.22 2.59
678 679 3.585862 GACATTCACATGTACGTGGACT 58.414 45.455 19.05 5.52 44.22 3.85
679 680 2.344441 CGACATTCACATGTACGTGGAC 59.656 50.000 19.05 1.13 44.22 4.02
680 681 2.601804 CGACATTCACATGTACGTGGA 58.398 47.619 19.05 10.45 44.22 4.02
681 682 1.658596 CCGACATTCACATGTACGTGG 59.341 52.381 19.05 8.37 44.22 4.94
682 683 2.333926 ACCGACATTCACATGTACGTG 58.666 47.619 13.64 13.64 44.22 4.49
683 684 2.734606 CAACCGACATTCACATGTACGT 59.265 45.455 0.00 0.00 44.22 3.57
684 685 2.473868 GCAACCGACATTCACATGTACG 60.474 50.000 0.00 0.00 44.22 3.67
685 686 2.473868 CGCAACCGACATTCACATGTAC 60.474 50.000 0.00 0.00 44.22 2.90
686 687 1.729517 CGCAACCGACATTCACATGTA 59.270 47.619 0.00 0.00 44.22 2.29
688 689 0.795698 TCGCAACCGACATTCACATG 59.204 50.000 0.00 0.00 38.82 3.21
712 713 5.163933 GCAACAGATTTAATCACCGACGTTA 60.164 40.000 7.74 0.00 0.00 3.18
713 714 4.378046 GCAACAGATTTAATCACCGACGTT 60.378 41.667 7.74 0.00 0.00 3.99
746 747 4.386652 GTCATTTGTACGTAACGTGTGGAT 59.613 41.667 0.00 0.00 41.39 3.41
750 751 6.917477 TCTTTAGTCATTTGTACGTAACGTGT 59.083 34.615 0.00 0.00 41.39 4.49
752 753 7.928908 TTCTTTAGTCATTTGTACGTAACGT 57.071 32.000 0.00 0.00 44.35 3.99
753 754 7.469145 CGTTTCTTTAGTCATTTGTACGTAACG 59.531 37.037 0.00 0.00 0.00 3.18
754 755 7.264868 GCGTTTCTTTAGTCATTTGTACGTAAC 59.735 37.037 0.00 0.00 0.00 2.50
755 756 7.282916 GCGTTTCTTTAGTCATTTGTACGTAA 58.717 34.615 0.00 0.00 0.00 3.18
756 757 6.398830 CGCGTTTCTTTAGTCATTTGTACGTA 60.399 38.462 0.00 0.00 0.00 3.57
770 771 0.179210 GGATTGCGCGCGTTTCTTTA 60.179 50.000 32.35 2.27 0.00 1.85
845 846 9.932207 TTTAAATGTATATATACGGACACAGGG 57.068 33.333 16.29 0.00 36.06 4.45
853 854 9.982291 GGTGCATGTTTAAATGTATATATACGG 57.018 33.333 16.29 0.27 36.06 4.02
854 855 9.982291 GGGTGCATGTTTAAATGTATATATACG 57.018 33.333 16.29 1.72 36.06 3.06
857 858 9.360901 TGTGGGTGCATGTTTAAATGTATATAT 57.639 29.630 0.00 0.00 0.00 0.86
858 859 8.753497 TGTGGGTGCATGTTTAAATGTATATA 57.247 30.769 0.00 0.00 0.00 0.86
859 860 7.652524 TGTGGGTGCATGTTTAAATGTATAT 57.347 32.000 0.00 0.00 0.00 0.86
860 861 7.201866 GGATGTGGGTGCATGTTTAAATGTATA 60.202 37.037 0.00 0.00 0.00 1.47
861 862 5.991933 TGTGGGTGCATGTTTAAATGTAT 57.008 34.783 0.00 0.00 0.00 2.29
862 863 5.105554 GGATGTGGGTGCATGTTTAAATGTA 60.106 40.000 0.00 0.00 0.00 2.29
863 864 4.322650 GGATGTGGGTGCATGTTTAAATGT 60.323 41.667 0.00 0.00 0.00 2.71
864 865 4.183101 GGATGTGGGTGCATGTTTAAATG 58.817 43.478 0.00 0.00 0.00 2.32
865 866 3.837146 TGGATGTGGGTGCATGTTTAAAT 59.163 39.130 0.00 0.00 0.00 1.40
866 867 3.234353 TGGATGTGGGTGCATGTTTAAA 58.766 40.909 0.00 0.00 0.00 1.52
867 868 2.881734 TGGATGTGGGTGCATGTTTAA 58.118 42.857 0.00 0.00 0.00 1.52
868 869 2.593925 TGGATGTGGGTGCATGTTTA 57.406 45.000 0.00 0.00 0.00 2.01
869 870 1.826720 GATGGATGTGGGTGCATGTTT 59.173 47.619 0.00 0.00 29.73 2.83
870 871 1.006281 AGATGGATGTGGGTGCATGTT 59.994 47.619 0.00 0.00 29.73 2.71
871 872 0.627451 AGATGGATGTGGGTGCATGT 59.373 50.000 0.00 0.00 29.73 3.21
872 873 2.643995 TAGATGGATGTGGGTGCATG 57.356 50.000 0.00 0.00 29.73 4.06
873 874 4.999469 TTATAGATGGATGTGGGTGCAT 57.001 40.909 0.00 0.00 32.47 3.96
874 875 4.787135 TTTATAGATGGATGTGGGTGCA 57.213 40.909 0.00 0.00 0.00 4.57
875 876 5.351465 CGTATTTATAGATGGATGTGGGTGC 59.649 44.000 0.00 0.00 0.00 5.01
876 877 6.697395 TCGTATTTATAGATGGATGTGGGTG 58.303 40.000 0.00 0.00 0.00 4.61
877 878 6.928348 TCGTATTTATAGATGGATGTGGGT 57.072 37.500 0.00 0.00 0.00 4.51
878 879 6.310467 CGTTCGTATTTATAGATGGATGTGGG 59.690 42.308 0.00 0.00 0.00 4.61
879 880 6.866770 ACGTTCGTATTTATAGATGGATGTGG 59.133 38.462 0.00 0.00 0.00 4.17
880 881 7.869016 ACGTTCGTATTTATAGATGGATGTG 57.131 36.000 0.00 0.00 0.00 3.21
881 882 8.790718 AGTACGTTCGTATTTATAGATGGATGT 58.209 33.333 8.26 0.00 0.00 3.06
882 883 9.275231 GAGTACGTTCGTATTTATAGATGGATG 57.725 37.037 8.26 0.00 0.00 3.51
883 884 8.173775 CGAGTACGTTCGTATTTATAGATGGAT 58.826 37.037 8.26 0.00 35.91 3.41
884 885 7.384932 TCGAGTACGTTCGTATTTATAGATGGA 59.615 37.037 9.29 0.00 41.22 3.41
885 886 7.513132 TCGAGTACGTTCGTATTTATAGATGG 58.487 38.462 9.29 0.00 41.22 3.51
886 887 9.196948 GATCGAGTACGTTCGTATTTATAGATG 57.803 37.037 9.29 0.00 41.22 2.90
909 910 0.980423 GCAGGAGAGGGTATGGGATC 59.020 60.000 0.00 0.00 0.00 3.36
910 911 0.570218 AGCAGGAGAGGGTATGGGAT 59.430 55.000 0.00 0.00 0.00 3.85
917 923 0.980423 GTCTGAAAGCAGGAGAGGGT 59.020 55.000 0.00 0.00 42.53 4.34
942 948 5.713792 AGAAGAGAAACTGTCAAGATCGA 57.286 39.130 0.00 0.00 0.00 3.59
952 958 2.032054 TGTGCGCAAAGAAGAGAAACTG 59.968 45.455 14.00 0.00 0.00 3.16
968 979 0.179275 CGATCGACTTGTTGTGTGCG 60.179 55.000 10.26 0.00 0.00 5.34
998 1009 1.703438 GCTGCTGAGCTTGGTCATCG 61.703 60.000 5.83 0.00 42.52 3.84
1113 1133 1.910671 ACGAGGGCCTTTATTGGTGTA 59.089 47.619 7.89 0.00 0.00 2.90
1115 1135 1.065418 AGACGAGGGCCTTTATTGGTG 60.065 52.381 7.89 0.00 0.00 4.17
1122 1142 0.693049 ACATGAAGACGAGGGCCTTT 59.307 50.000 7.89 0.00 0.00 3.11
1160 1180 1.337071 TCGATGAAGGTAGCGATCCAC 59.663 52.381 0.00 0.00 33.09 4.02
1162 1182 2.600731 CATCGATGAAGGTAGCGATCC 58.399 52.381 21.02 0.00 44.87 3.36
1179 1202 7.064490 GCTTTAGCTAGATTAATCAGCTCCATC 59.936 40.741 29.48 19.68 39.84 3.51
1217 1256 7.110216 GCGTCGATCAATAATGAATGTTGTAAC 59.890 37.037 0.00 0.00 39.49 2.50
1218 1257 7.123190 GCGTCGATCAATAATGAATGTTGTAA 58.877 34.615 0.00 0.00 39.49 2.41
1220 1259 5.064579 TGCGTCGATCAATAATGAATGTTGT 59.935 36.000 0.00 0.00 39.49 3.32
1228 1267 3.476181 CTGCATGCGTCGATCAATAATG 58.524 45.455 14.09 0.00 0.00 1.90
1229 1268 2.481568 CCTGCATGCGTCGATCAATAAT 59.518 45.455 14.09 0.00 0.00 1.28
1230 1269 1.866601 CCTGCATGCGTCGATCAATAA 59.133 47.619 14.09 0.00 0.00 1.40
1329 1368 4.189188 CCGTGGCCCTCGTAGTCG 62.189 72.222 14.60 1.49 38.55 4.18
1434 1473 1.210478 GGCAGCTGAGGAGATTGGTTA 59.790 52.381 20.43 0.00 0.00 2.85
1707 1746 1.209747 CCCTTGTAGCAGTAGGGGTTC 59.790 57.143 0.00 0.00 44.11 3.62
1775 1814 4.057428 GCACCTCGCTCTCCACGT 62.057 66.667 0.00 0.00 37.77 4.49
2041 2098 2.234896 ATGGATGATGGGTTGTTGCA 57.765 45.000 0.00 0.00 0.00 4.08
2045 2102 3.788142 AGTTCCTATGGATGATGGGTTGT 59.212 43.478 0.00 0.00 34.23 3.32
2080 2137 7.065443 TCACTGTCATCATGAATCAATCAGAAC 59.935 37.037 0.00 0.00 42.53 3.01
2083 2140 6.920569 TCACTGTCATCATGAATCAATCAG 57.079 37.500 0.00 5.92 42.53 2.90
2166 2249 0.906775 TAACTCATTCCACGTCCCCC 59.093 55.000 0.00 0.00 0.00 5.40
2168 2251 5.878669 AGTAAATTAACTCATTCCACGTCCC 59.121 40.000 0.00 0.00 0.00 4.46
2170 2253 7.360575 ACAGTAAATTAACTCATTCCACGTC 57.639 36.000 0.00 0.00 0.00 4.34
2266 2509 4.946160 TTGTTATTGAATCAGGGGAGGT 57.054 40.909 0.00 0.00 0.00 3.85
2326 2572 4.355543 TGTCTTGTTGCTTCTTGTTGTC 57.644 40.909 0.00 0.00 0.00 3.18
2364 2618 2.731217 AGCGCAAACACATTCAAGTTC 58.269 42.857 11.47 0.00 0.00 3.01
2368 2622 2.357323 TCTGAAGCGCAAACACATTCAA 59.643 40.909 11.47 0.00 30.10 2.69
2377 2631 4.456911 AGATGAGATTTTCTGAAGCGCAAA 59.543 37.500 11.47 0.00 0.00 3.68
2456 2710 2.488153 GAGGGGAGCATGTTTGTGTTAC 59.512 50.000 0.00 0.00 0.00 2.50
2458 2712 1.620822 GAGGGGAGCATGTTTGTGTT 58.379 50.000 0.00 0.00 0.00 3.32
2490 2744 3.433598 GGCATGGTAGAAGGTAGCATTGA 60.434 47.826 0.00 0.00 33.89 2.57
2516 2770 7.891183 AATTGGATGACGAACTATATGCTAC 57.109 36.000 0.00 0.00 0.00 3.58
2527 2781 8.094548 CCTGACCTATATTAATTGGATGACGAA 58.905 37.037 0.00 0.00 32.84 3.85
2576 2830 2.851824 CCTTGCGTGTGTTCTTGTTTTC 59.148 45.455 0.00 0.00 0.00 2.29
2606 2860 5.412640 CAATGCAAATCAGCTAAATGGACA 58.587 37.500 0.00 0.00 34.99 4.02
2607 2861 4.269363 GCAATGCAAATCAGCTAAATGGAC 59.731 41.667 0.00 0.00 34.99 4.02
2733 2987 4.353437 GGTCGGCTCGTTGGTCGT 62.353 66.667 0.00 0.00 40.80 4.34
2734 2988 3.966026 GAGGTCGGCTCGTTGGTCG 62.966 68.421 0.00 0.00 41.41 4.79
2735 2989 2.126031 GAGGTCGGCTCGTTGGTC 60.126 66.667 0.00 0.00 0.00 4.02
2736 2990 3.692406 GGAGGTCGGCTCGTTGGT 61.692 66.667 0.00 0.00 0.00 3.67
2737 2991 4.796231 CGGAGGTCGGCTCGTTGG 62.796 72.222 0.00 0.00 34.75 3.77
2747 3001 4.736896 GTGGTCGTGGCGGAGGTC 62.737 72.222 0.00 0.00 0.00 3.85
2755 3009 3.931247 TGGGTTCGGTGGTCGTGG 61.931 66.667 0.00 0.00 40.32 4.94
2756 3010 2.663852 GTGGGTTCGGTGGTCGTG 60.664 66.667 0.00 0.00 40.32 4.35
2820 3098 1.376609 CTGGAATGGGTGTTAGCGGC 61.377 60.000 0.00 0.00 0.00 6.53
2935 3213 9.360093 GCAGACATAGGTAGTTATCATTATGTC 57.640 37.037 12.23 12.23 43.61 3.06
2957 3235 1.376466 GGCTCCCTTGTGAAGCAGA 59.624 57.895 0.00 0.00 0.00 4.26
2966 3244 3.277962 AGCTGAATTGGCTCCCTTG 57.722 52.632 0.00 0.00 34.70 3.61


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

AutoCloner maintained by Alex Coulton.