Multiple sequence alignment - TraesCS1A01G027800

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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 TraesCS1A01G027800 chr1A 100.000 3882 0 0 1 3882 13228021 13231902 0.000000e+00 7169.0
1 TraesCS1A01G027800 chr1A 94.283 2676 110 21 1001 3665 13212431 13215074 0.000000e+00 4054.0
2 TraesCS1A01G027800 chr1A 99.283 2092 15 0 1090 3181 13009797 13007706 0.000000e+00 3781.0
3 TraesCS1A01G027800 chr1A 90.734 1975 144 16 961 2906 22791290 22789326 0.000000e+00 2597.0
4 TraesCS1A01G027800 chr1A 94.805 308 13 3 3359 3665 13007700 13007395 9.760000e-131 477.0
5 TraesCS1A01G027800 chr1A 88.669 353 34 5 937 1285 13266763 13267113 3.580000e-115 425.0
6 TraesCS1A01G027800 chr1A 98.529 204 3 0 1090 1293 13272152 13272355 1.030000e-95 361.0
7 TraesCS1A01G027800 chr1A 78.835 515 69 33 1095 1585 22761950 22761452 1.050000e-80 311.0
8 TraesCS1A01G027800 chr1A 90.541 222 17 1 3663 3880 13258103 13258324 1.360000e-74 291.0
9 TraesCS1A01G027800 chr1A 90.090 222 18 1 3663 3880 13215240 13215461 6.350000e-73 285.0
10 TraesCS1A01G027800 chr1A 85.616 146 18 3 1386 1528 13006084 13005939 2.420000e-32 150.0
11 TraesCS1A01G027800 chr1B 91.082 2893 200 33 1021 3882 23597479 23600344 0.000000e+00 3860.0
12 TraesCS1A01G027800 chr1B 91.013 2893 200 35 1021 3882 23896255 23899118 0.000000e+00 3847.0
13 TraesCS1A01G027800 chr1B 91.431 2684 156 33 1027 3665 16225638 16222984 0.000000e+00 3615.0
14 TraesCS1A01G027800 chr1B 89.336 2063 181 27 1627 3665 39814791 39816838 0.000000e+00 2555.0
15 TraesCS1A01G027800 chr1B 93.062 1571 97 10 1493 3059 39732724 39734286 0.000000e+00 2287.0
16 TraesCS1A01G027800 chr1B 93.913 805 42 3 3085 3882 39734285 39735089 0.000000e+00 1208.0
17 TraesCS1A01G027800 chr1B 82.995 641 56 24 679 1293 39731818 39732431 7.390000e-147 531.0
18 TraesCS1A01G027800 chr1B 81.757 592 65 22 3086 3665 23776968 23777528 4.570000e-124 455.0
19 TraesCS1A01G027800 chr1B 90.625 224 16 3 3663 3882 16222798 16222576 3.790000e-75 292.0
20 TraesCS1A01G027800 chr1B 90.411 219 17 1 3668 3882 39817106 39817324 6.350000e-73 285.0
21 TraesCS1A01G027800 chr1B 89.640 222 18 2 3664 3880 39809202 39809423 1.060000e-70 278.0
22 TraesCS1A01G027800 chr1B 79.375 320 41 13 3 312 39731413 39731717 6.580000e-48 202.0
23 TraesCS1A01G027800 chr1B 89.032 155 15 2 498 651 56273925 56273772 1.420000e-44 191.0
24 TraesCS1A01G027800 chr1D 94.919 2047 91 6 1627 3665 10775142 10773101 0.000000e+00 3192.0
25 TraesCS1A01G027800 chr1D 94.987 1975 77 12 941 2906 10764362 10762401 0.000000e+00 3079.0
26 TraesCS1A01G027800 chr1D 90.312 1920 144 25 1001 2888 10843827 10845736 0.000000e+00 2477.0
27 TraesCS1A01G027800 chr1D 93.351 752 40 4 2920 3665 10762302 10761555 0.000000e+00 1103.0
28 TraesCS1A01G027800 chr1D 79.417 515 61 35 1095 1585 10930007 10930500 4.840000e-84 322.0
29 TraesCS1A01G027800 chr1D 92.523 214 12 1 3663 3872 10761367 10761154 1.750000e-78 303.0
30 TraesCS1A01G027800 chr1D 81.773 203 29 5 1389 1585 10836331 10836531 3.100000e-36 163.0
31 TraesCS1A01G027800 chr1D 88.750 80 9 0 1389 1468 10776416 10776337 8.880000e-17 99.0
32 TraesCS1A01G027800 chr5B 91.139 158 11 3 496 651 693967651 693967495 1.090000e-50 211.0
33 TraesCS1A01G027800 chr6B 89.308 159 14 2 495 651 652640545 652640702 3.060000e-46 196.0
34 TraesCS1A01G027800 chr6B 87.742 155 17 2 498 651 625804085 625803932 3.080000e-41 180.0
35 TraesCS1A01G027800 chr2D 87.805 164 17 3 490 651 305517729 305517891 5.120000e-44 189.0
36 TraesCS1A01G027800 chr2D 78.704 108 22 1 74 180 535569693 535569800 1.940000e-08 71.3
37 TraesCS1A01G027800 chr7B 87.500 160 18 2 493 651 711234323 711234165 2.380000e-42 183.0
38 TraesCS1A01G027800 chr7B 86.420 162 19 3 490 650 361477269 361477110 1.430000e-39 174.0
39 TraesCS1A01G027800 chr3D 87.821 156 17 2 497 651 561890760 561890914 8.570000e-42 182.0
40 TraesCS1A01G027800 chr2B 86.310 168 19 4 498 663 453265609 453265444 3.080000e-41 180.0


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 TraesCS1A01G027800 chr1A 13228021 13231902 3881 False 7169.000000 7169 100.000000 1 3882 1 chr1A.!!$F1 3881
1 TraesCS1A01G027800 chr1A 22789326 22791290 1964 True 2597.000000 2597 90.734000 961 2906 1 chr1A.!!$R2 1945
2 TraesCS1A01G027800 chr1A 13212431 13215461 3030 False 2169.500000 4054 92.186500 1001 3880 2 chr1A.!!$F5 2879
3 TraesCS1A01G027800 chr1A 13005939 13009797 3858 True 1469.333333 3781 93.234667 1090 3665 3 chr1A.!!$R3 2575
4 TraesCS1A01G027800 chr1B 23597479 23600344 2865 False 3860.000000 3860 91.082000 1021 3882 1 chr1B.!!$F1 2861
5 TraesCS1A01G027800 chr1B 23896255 23899118 2863 False 3847.000000 3847 91.013000 1021 3882 1 chr1B.!!$F3 2861
6 TraesCS1A01G027800 chr1B 16222576 16225638 3062 True 1953.500000 3615 91.028000 1027 3882 2 chr1B.!!$R2 2855
7 TraesCS1A01G027800 chr1B 39814791 39817324 2533 False 1420.000000 2555 89.873500 1627 3882 2 chr1B.!!$F6 2255
8 TraesCS1A01G027800 chr1B 39731413 39735089 3676 False 1057.000000 2287 87.336250 3 3882 4 chr1B.!!$F5 3879
9 TraesCS1A01G027800 chr1B 23776968 23777528 560 False 455.000000 455 81.757000 3086 3665 1 chr1B.!!$F2 579
10 TraesCS1A01G027800 chr1D 10843827 10845736 1909 False 2477.000000 2477 90.312000 1001 2888 1 chr1D.!!$F2 1887
11 TraesCS1A01G027800 chr1D 10773101 10776416 3315 True 1645.500000 3192 91.834500 1389 3665 2 chr1D.!!$R2 2276
12 TraesCS1A01G027800 chr1D 10761154 10764362 3208 True 1495.000000 3079 93.620333 941 3872 3 chr1D.!!$R1 2931

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
58 59 0.248990 GGTCAGCGCTGATGAGAGAG 60.249 60.0 39.91 11.45 42.18 3.20 F
854 869 0.249996 CTTTGCCTTGGCCCAACAAG 60.250 55.0 9.35 0.00 45.71 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1015 1046 0.612174 TCCTCCTCCGACTCCAACTG 60.612 60.0 0.0 0.0 0.0 3.16 R
2888 4297 7.730364 ACATCAGAACTAAGTTTACCAAGTG 57.270 36.0 0.0 0.0 0.0 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.904866 GGGTCAAAGTGCCACGCA 60.905 61.111 0.00 0.00 35.60 5.24
35 36 2.639286 GGTCAAAGTGCCACGCAG 59.361 61.111 0.00 0.00 40.08 5.18
58 59 0.248990 GGTCAGCGCTGATGAGAGAG 60.249 60.000 39.91 11.45 42.18 3.20
91 92 6.936279 TCTGAGATGGACGACTTAAAAAGAT 58.064 36.000 0.00 0.00 0.00 2.40
95 96 9.151471 TGAGATGGACGACTTAAAAAGATTTAG 57.849 33.333 0.00 0.00 32.80 1.85
98 99 7.662604 TGGACGACTTAAAAAGATTTAGGAC 57.337 36.000 0.00 0.00 33.58 3.85
102 103 6.653740 ACGACTTAAAAAGATTTAGGACCCAG 59.346 38.462 0.00 0.00 33.58 4.45
104 105 7.148457 CGACTTAAAAAGATTTAGGACCCAGAC 60.148 40.741 0.00 0.00 33.58 3.51
105 106 7.756614 ACTTAAAAAGATTTAGGACCCAGACT 58.243 34.615 0.00 0.00 33.58 3.24
123 124 6.366877 CCCAGACTTGCATTTTCAAAGTATTG 59.633 38.462 0.00 0.00 37.92 1.90
128 129 6.041979 ACTTGCATTTTCAAAGTATTGGGACT 59.958 34.615 0.00 0.00 37.15 3.85
132 133 6.294731 GCATTTTCAAAGTATTGGGACTCAGT 60.295 38.462 0.00 0.00 37.15 3.41
135 136 4.651778 TCAAAGTATTGGGACTCAGTTGG 58.348 43.478 0.00 0.00 37.15 3.77
141 142 1.909700 TGGGACTCAGTTGGCAATTC 58.090 50.000 1.92 0.00 0.00 2.17
142 143 1.144708 TGGGACTCAGTTGGCAATTCA 59.855 47.619 1.92 0.00 0.00 2.57
143 144 2.238521 GGGACTCAGTTGGCAATTCAA 58.761 47.619 1.92 0.00 0.00 2.69
144 145 2.029918 GGGACTCAGTTGGCAATTCAAC 60.030 50.000 1.92 2.55 45.22 3.18
161 162 2.997986 TCAACGAAAGAATTAGGACCGC 59.002 45.455 0.00 0.00 0.00 5.68
246 247 8.465273 AGGCAATTTTACTCTTTCAGTTAACT 57.535 30.769 1.12 1.12 36.43 2.24
306 312 6.938596 TGGGCTACCTCTTTAAGTTAAGTTTC 59.061 38.462 0.00 0.00 37.76 2.78
313 319 9.570468 ACCTCTTTAAGTTAAGTTTCTTTAGGG 57.430 33.333 0.00 0.00 0.00 3.53
314 320 9.011095 CCTCTTTAAGTTAAGTTTCTTTAGGGG 57.989 37.037 0.00 0.00 0.00 4.79
511 526 9.807921 TTGATAATTTAATACTCCCTCCATTCC 57.192 33.333 0.00 0.00 0.00 3.01
512 527 9.182642 TGATAATTTAATACTCCCTCCATTCCT 57.817 33.333 0.00 0.00 0.00 3.36
522 537 9.860393 ATACTCCCTCCATTCCTAAATATAAGT 57.140 33.333 0.00 0.00 0.00 2.24
523 538 7.978925 ACTCCCTCCATTCCTAAATATAAGTG 58.021 38.462 0.00 0.00 0.00 3.16
524 539 7.572861 ACTCCCTCCATTCCTAAATATAAGTGT 59.427 37.037 0.00 0.00 0.00 3.55
525 540 8.344939 TCCCTCCATTCCTAAATATAAGTGTT 57.655 34.615 0.00 0.00 0.00 3.32
526 541 8.787818 TCCCTCCATTCCTAAATATAAGTGTTT 58.212 33.333 0.00 0.00 0.00 2.83
527 542 9.421399 CCCTCCATTCCTAAATATAAGTGTTTT 57.579 33.333 0.00 0.00 0.00 2.43
543 558 6.467723 AGTGTTTTTAGAGATTGCACTACG 57.532 37.500 0.00 0.00 34.47 3.51
544 559 6.220930 AGTGTTTTTAGAGATTGCACTACGA 58.779 36.000 0.00 0.00 34.47 3.43
545 560 6.704493 AGTGTTTTTAGAGATTGCACTACGAA 59.296 34.615 0.00 0.00 34.47 3.85
546 561 6.790825 GTGTTTTTAGAGATTGCACTACGAAC 59.209 38.462 0.00 0.00 0.00 3.95
547 562 6.704493 TGTTTTTAGAGATTGCACTACGAACT 59.296 34.615 0.00 0.00 0.00 3.01
548 563 7.868922 TGTTTTTAGAGATTGCACTACGAACTA 59.131 33.333 0.00 0.00 0.00 2.24
549 564 7.807687 TTTTAGAGATTGCACTACGAACTAC 57.192 36.000 0.00 0.00 0.00 2.73
550 565 6.505044 TTAGAGATTGCACTACGAACTACA 57.495 37.500 0.00 0.00 0.00 2.74
551 566 5.584253 AGAGATTGCACTACGAACTACAT 57.416 39.130 0.00 0.00 0.00 2.29
552 567 6.694877 AGAGATTGCACTACGAACTACATA 57.305 37.500 0.00 0.00 0.00 2.29
553 568 6.496571 AGAGATTGCACTACGAACTACATAC 58.503 40.000 0.00 0.00 0.00 2.39
554 569 6.095021 AGAGATTGCACTACGAACTACATACA 59.905 38.462 0.00 0.00 0.00 2.29
555 570 6.266323 AGATTGCACTACGAACTACATACAG 58.734 40.000 0.00 0.00 0.00 2.74
556 571 5.632244 TTGCACTACGAACTACATACAGA 57.368 39.130 0.00 0.00 0.00 3.41
557 572 5.830000 TGCACTACGAACTACATACAGAT 57.170 39.130 0.00 0.00 0.00 2.90
558 573 5.578776 TGCACTACGAACTACATACAGATG 58.421 41.667 0.00 0.00 39.16 2.90
560 575 6.316890 TGCACTACGAACTACATACAGATGTA 59.683 38.462 0.00 0.00 44.77 2.29
561 576 7.012989 TGCACTACGAACTACATACAGATGTAT 59.987 37.037 0.00 0.00 45.42 2.29
562 577 8.501580 GCACTACGAACTACATACAGATGTATA 58.498 37.037 5.21 0.00 45.42 1.47
603 618 9.429359 AGTGTAGATTCACTCATTCTTACTTTG 57.571 33.333 0.00 0.00 44.07 2.77
604 619 9.209175 GTGTAGATTCACTCATTCTTACTTTGT 57.791 33.333 0.00 0.00 35.68 2.83
608 623 9.950496 AGATTCACTCATTCTTACTTTGTATGT 57.050 29.630 0.00 0.00 0.00 2.29
612 627 9.856488 TCACTCATTCTTACTTTGTATGTAGTC 57.144 33.333 0.00 0.00 0.00 2.59
613 628 9.088512 CACTCATTCTTACTTTGTATGTAGTCC 57.911 37.037 0.00 0.00 0.00 3.85
614 629 9.036980 ACTCATTCTTACTTTGTATGTAGTCCT 57.963 33.333 0.00 0.00 0.00 3.85
619 634 9.524496 TTCTTACTTTGTATGTAGTCCTAGTGA 57.476 33.333 0.00 0.00 0.00 3.41
620 635 9.524496 TCTTACTTTGTATGTAGTCCTAGTGAA 57.476 33.333 0.00 0.00 0.00 3.18
624 639 9.036980 ACTTTGTATGTAGTCCTAGTGAAATCT 57.963 33.333 0.00 0.00 0.00 2.40
625 640 9.522804 CTTTGTATGTAGTCCTAGTGAAATCTC 57.477 37.037 0.00 0.00 0.00 2.75
626 641 8.824756 TTGTATGTAGTCCTAGTGAAATCTCT 57.175 34.615 0.00 0.00 0.00 3.10
627 642 8.824756 TGTATGTAGTCCTAGTGAAATCTCTT 57.175 34.615 0.00 0.00 0.00 2.85
628 643 9.256228 TGTATGTAGTCCTAGTGAAATCTCTTT 57.744 33.333 0.00 0.00 0.00 2.52
635 650 9.095700 AGTCCTAGTGAAATCTCTTTAAAGACT 57.904 33.333 13.99 10.56 0.00 3.24
636 651 9.713713 GTCCTAGTGAAATCTCTTTAAAGACTT 57.286 33.333 13.99 7.93 0.00 3.01
654 669 8.502105 AAAGACTTATATTTAGAAACGGGGTG 57.498 34.615 0.00 0.00 0.00 4.61
655 670 6.589135 AGACTTATATTTAGAAACGGGGTGG 58.411 40.000 0.00 0.00 0.00 4.61
660 675 4.645863 ATTTAGAAACGGGGTGGTAAGT 57.354 40.909 0.00 0.00 0.00 2.24
663 678 5.559148 TTAGAAACGGGGTGGTAAGTTAA 57.441 39.130 0.00 0.00 0.00 2.01
847 862 2.031012 GGTTGCTTTGCCTTGGCC 59.969 61.111 9.35 0.00 0.00 5.36
848 863 2.031012 GTTGCTTTGCCTTGGCCC 59.969 61.111 9.35 0.00 0.00 5.80
849 864 2.445464 TTGCTTTGCCTTGGCCCA 60.445 55.556 9.35 0.00 0.00 5.36
850 865 2.068821 TTGCTTTGCCTTGGCCCAA 61.069 52.632 9.35 0.00 0.00 4.12
851 866 2.031012 GCTTTGCCTTGGCCCAAC 59.969 61.111 9.35 0.00 0.00 3.77
852 867 2.806009 GCTTTGCCTTGGCCCAACA 61.806 57.895 9.35 0.00 0.00 3.33
853 868 1.828768 CTTTGCCTTGGCCCAACAA 59.171 52.632 9.35 0.00 0.00 2.83
854 869 0.249996 CTTTGCCTTGGCCCAACAAG 60.250 55.000 9.35 0.00 45.71 3.16
855 870 0.980231 TTTGCCTTGGCCCAACAAGT 60.980 50.000 9.35 0.00 44.89 3.16
864 879 2.518349 CCAACAAGTGGCACCGGT 60.518 61.111 15.27 0.00 41.72 5.28
865 880 1.228003 CCAACAAGTGGCACCGGTA 60.228 57.895 15.27 0.00 41.72 4.02
866 881 1.512156 CCAACAAGTGGCACCGGTAC 61.512 60.000 15.27 0.00 41.72 3.34
867 882 1.228033 AACAAGTGGCACCGGTACC 60.228 57.895 17.72 17.72 0.00 3.34
868 883 2.359478 CAAGTGGCACCGGTACCC 60.359 66.667 21.56 17.90 0.00 3.69
892 907 2.771943 TGATAAGTCACCTGGGCCTTAG 59.228 50.000 4.53 1.01 0.00 2.18
893 908 0.909623 TAAGTCACCTGGGCCTTAGC 59.090 55.000 4.53 0.00 38.76 3.09
938 953 7.031975 GCATAAGAATCAACAAAGAGGAAAGG 58.968 38.462 0.00 0.00 0.00 3.11
939 954 7.542025 CATAAGAATCAACAAAGAGGAAAGGG 58.458 38.462 0.00 0.00 0.00 3.95
1015 1046 1.067669 TCATCATGGCGTCTGTAGAGC 59.932 52.381 0.00 0.00 0.00 4.09
2319 3725 1.122019 ACTGGCCCATATCGAGGTCC 61.122 60.000 0.00 0.00 0.00 4.46
2888 4297 4.081087 TGGACTTTAGGCTGTAATCCTGTC 60.081 45.833 0.00 0.00 35.21 3.51
3149 4653 6.481976 TGTTAGACATGTATTAGGCGGAAATG 59.518 38.462 0.00 0.00 0.00 2.32
3153 4657 2.479837 TGTATTAGGCGGAAATGCGAG 58.520 47.619 0.00 0.00 35.06 5.03
3170 4677 3.226347 GCGAGCATTTGTCACTGTTAAC 58.774 45.455 0.00 0.00 0.00 2.01
3719 5513 4.851639 AGGATTTAGCACAATGAGAGGT 57.148 40.909 0.00 0.00 0.00 3.85
3813 5611 5.590259 ACTGTTGCTTGTAACACTCTTGATT 59.410 36.000 0.34 0.00 35.75 2.57
3851 5649 4.539870 CTGTTTTGAACGCATTGATGAGT 58.460 39.130 0.00 0.00 42.66 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.904866 TGCGTGGCACTTTGACCC 60.905 61.111 16.72 0.00 31.71 4.46
37 38 0.528033 CTCTCATCAGCGCTGACCAG 60.528 60.000 40.34 33.97 43.11 4.00
38 39 0.967380 TCTCTCATCAGCGCTGACCA 60.967 55.000 40.34 27.55 43.11 4.02
39 40 0.248990 CTCTCTCATCAGCGCTGACC 60.249 60.000 40.34 0.00 43.11 4.02
40 41 0.737804 TCTCTCTCATCAGCGCTGAC 59.262 55.000 40.34 0.00 43.11 3.51
42 43 2.512485 ATTCTCTCTCATCAGCGCTG 57.488 50.000 31.53 31.53 0.00 5.18
43 44 3.888323 TCTAATTCTCTCTCATCAGCGCT 59.112 43.478 2.64 2.64 0.00 5.92
44 45 4.235939 TCTAATTCTCTCTCATCAGCGC 57.764 45.455 0.00 0.00 0.00 5.92
45 46 6.583427 CAGATTCTAATTCTCTCTCATCAGCG 59.417 42.308 0.00 0.00 0.00 5.18
46 47 7.660112 TCAGATTCTAATTCTCTCTCATCAGC 58.340 38.462 0.00 0.00 0.00 4.26
47 48 9.070179 TCTCAGATTCTAATTCTCTCTCATCAG 57.930 37.037 0.00 0.00 0.00 2.90
58 59 6.744112 AGTCGTCCATCTCAGATTCTAATTC 58.256 40.000 0.00 0.00 0.00 2.17
91 92 3.806949 AATGCAAGTCTGGGTCCTAAA 57.193 42.857 0.00 0.00 0.00 1.85
95 96 2.238521 TGAAAATGCAAGTCTGGGTCC 58.761 47.619 0.00 0.00 0.00 4.46
98 99 4.326504 ACTTTGAAAATGCAAGTCTGGG 57.673 40.909 0.00 0.00 0.00 4.45
102 103 6.366061 GTCCCAATACTTTGAAAATGCAAGTC 59.634 38.462 0.00 0.00 34.60 3.01
104 105 6.458210 AGTCCCAATACTTTGAAAATGCAAG 58.542 36.000 0.00 0.00 34.60 4.01
105 106 6.041409 TGAGTCCCAATACTTTGAAAATGCAA 59.959 34.615 0.00 0.00 34.60 4.08
123 124 1.909700 TGAATTGCCAACTGAGTCCC 58.090 50.000 0.00 0.00 0.00 4.46
128 129 3.629855 TCTTTCGTTGAATTGCCAACTGA 59.370 39.130 8.02 5.10 43.02 3.41
132 133 6.015856 TCCTAATTCTTTCGTTGAATTGCCAA 60.016 34.615 16.77 0.00 42.12 4.52
135 136 5.800438 GGTCCTAATTCTTTCGTTGAATTGC 59.200 40.000 16.77 8.76 42.12 3.56
141 142 2.095372 GGCGGTCCTAATTCTTTCGTTG 59.905 50.000 0.00 0.00 0.00 4.10
142 143 2.027469 AGGCGGTCCTAATTCTTTCGTT 60.027 45.455 0.00 0.00 42.06 3.85
143 144 1.553704 AGGCGGTCCTAATTCTTTCGT 59.446 47.619 0.00 0.00 42.06 3.85
144 145 2.311124 AGGCGGTCCTAATTCTTTCG 57.689 50.000 0.00 0.00 42.06 3.46
215 216 8.257306 ACTGAAAGAGTAAAATTGCCTCAAAAA 58.743 29.630 0.00 0.00 37.43 1.94
216 217 7.781056 ACTGAAAGAGTAAAATTGCCTCAAAA 58.219 30.769 0.00 0.00 37.43 2.44
217 218 7.346751 ACTGAAAGAGTAAAATTGCCTCAAA 57.653 32.000 0.00 0.00 37.43 2.69
218 219 6.959639 ACTGAAAGAGTAAAATTGCCTCAA 57.040 33.333 0.00 0.00 37.43 3.02
219 220 6.959639 AACTGAAAGAGTAAAATTGCCTCA 57.040 33.333 0.00 0.00 37.43 3.86
220 221 8.568794 AGTTAACTGAAAGAGTAAAATTGCCTC 58.431 33.333 7.48 0.00 37.43 4.70
221 222 8.465273 AGTTAACTGAAAGAGTAAAATTGCCT 57.535 30.769 7.48 0.00 37.43 4.75
222 223 9.529325 AAAGTTAACTGAAAGAGTAAAATTGCC 57.471 29.630 9.34 0.00 37.43 4.52
288 294 9.011095 CCCCTAAAGAAACTTAACTTAAAGAGG 57.989 37.037 0.00 0.00 0.00 3.69
332 338 6.270219 ACCTAAAGAGTTACCCCTCAAAAA 57.730 37.500 0.00 0.00 33.75 1.94
333 339 5.917545 ACCTAAAGAGTTACCCCTCAAAA 57.082 39.130 0.00 0.00 33.75 2.44
334 340 5.917545 AACCTAAAGAGTTACCCCTCAAA 57.082 39.130 0.00 0.00 33.75 2.69
335 341 5.486419 CCTAACCTAAAGAGTTACCCCTCAA 59.514 44.000 0.00 0.00 33.75 3.02
336 342 5.028131 CCTAACCTAAAGAGTTACCCCTCA 58.972 45.833 0.00 0.00 33.75 3.86
337 343 5.028802 ACCTAACCTAAAGAGTTACCCCTC 58.971 45.833 0.00 0.00 0.00 4.30
338 344 5.033867 ACCTAACCTAAAGAGTTACCCCT 57.966 43.478 0.00 0.00 0.00 4.79
339 345 5.768980 AACCTAACCTAAAGAGTTACCCC 57.231 43.478 0.00 0.00 0.00 4.95
497 512 9.101325 CACTTATATTTAGGAATGGAGGGAGTA 57.899 37.037 0.00 0.00 0.00 2.59
498 513 7.572861 ACACTTATATTTAGGAATGGAGGGAGT 59.427 37.037 0.00 0.00 0.00 3.85
499 514 7.978925 ACACTTATATTTAGGAATGGAGGGAG 58.021 38.462 0.00 0.00 0.00 4.30
500 515 7.947782 ACACTTATATTTAGGAATGGAGGGA 57.052 36.000 0.00 0.00 0.00 4.20
501 516 8.996651 AAACACTTATATTTAGGAATGGAGGG 57.003 34.615 0.00 0.00 0.00 4.30
517 532 8.656849 CGTAGTGCAATCTCTAAAAACACTTAT 58.343 33.333 0.00 0.00 37.93 1.73
518 533 7.868922 TCGTAGTGCAATCTCTAAAAACACTTA 59.131 33.333 0.00 0.00 37.93 2.24
519 534 6.704493 TCGTAGTGCAATCTCTAAAAACACTT 59.296 34.615 0.00 0.00 37.93 3.16
520 535 6.220930 TCGTAGTGCAATCTCTAAAAACACT 58.779 36.000 0.00 0.00 39.92 3.55
521 536 6.462073 TCGTAGTGCAATCTCTAAAAACAC 57.538 37.500 0.00 0.00 0.00 3.32
522 537 6.704493 AGTTCGTAGTGCAATCTCTAAAAACA 59.296 34.615 0.00 0.00 0.00 2.83
523 538 7.118422 AGTTCGTAGTGCAATCTCTAAAAAC 57.882 36.000 0.00 0.00 0.00 2.43
524 539 7.868922 TGTAGTTCGTAGTGCAATCTCTAAAAA 59.131 33.333 0.00 0.00 0.00 1.94
525 540 7.372714 TGTAGTTCGTAGTGCAATCTCTAAAA 58.627 34.615 0.00 0.00 0.00 1.52
526 541 6.916440 TGTAGTTCGTAGTGCAATCTCTAAA 58.084 36.000 0.00 0.00 0.00 1.85
527 542 6.505044 TGTAGTTCGTAGTGCAATCTCTAA 57.495 37.500 0.00 0.00 0.00 2.10
528 543 6.694877 ATGTAGTTCGTAGTGCAATCTCTA 57.305 37.500 0.00 0.00 0.00 2.43
529 544 5.584253 ATGTAGTTCGTAGTGCAATCTCT 57.416 39.130 0.00 0.00 0.00 3.10
530 545 6.263344 TGTATGTAGTTCGTAGTGCAATCTC 58.737 40.000 0.00 0.00 0.00 2.75
531 546 6.095021 TCTGTATGTAGTTCGTAGTGCAATCT 59.905 38.462 0.00 0.00 0.00 2.40
532 547 6.263344 TCTGTATGTAGTTCGTAGTGCAATC 58.737 40.000 0.00 0.00 0.00 2.67
533 548 6.203808 TCTGTATGTAGTTCGTAGTGCAAT 57.796 37.500 0.00 0.00 0.00 3.56
534 549 5.632244 TCTGTATGTAGTTCGTAGTGCAA 57.368 39.130 0.00 0.00 0.00 4.08
535 550 5.124936 ACATCTGTATGTAGTTCGTAGTGCA 59.875 40.000 0.00 0.00 44.66 4.57
536 551 5.579718 ACATCTGTATGTAGTTCGTAGTGC 58.420 41.667 0.00 0.00 44.66 4.40
578 593 9.209175 ACAAAGTAAGAATGAGTGAATCTACAC 57.791 33.333 0.00 0.00 40.60 2.90
582 597 9.950496 ACATACAAAGTAAGAATGAGTGAATCT 57.050 29.630 0.00 0.00 0.00 2.40
586 601 9.856488 GACTACATACAAAGTAAGAATGAGTGA 57.144 33.333 0.00 0.00 0.00 3.41
587 602 9.088512 GGACTACATACAAAGTAAGAATGAGTG 57.911 37.037 0.00 0.00 0.00 3.51
588 603 9.036980 AGGACTACATACAAAGTAAGAATGAGT 57.963 33.333 0.00 0.00 0.00 3.41
593 608 9.524496 TCACTAGGACTACATACAAAGTAAGAA 57.476 33.333 0.00 0.00 0.00 2.52
594 609 9.524496 TTCACTAGGACTACATACAAAGTAAGA 57.476 33.333 0.00 0.00 0.00 2.10
598 613 9.036980 AGATTTCACTAGGACTACATACAAAGT 57.963 33.333 0.00 0.00 0.00 2.66
599 614 9.522804 GAGATTTCACTAGGACTACATACAAAG 57.477 37.037 0.00 0.00 0.00 2.77
600 615 9.256228 AGAGATTTCACTAGGACTACATACAAA 57.744 33.333 0.00 0.00 0.00 2.83
601 616 8.824756 AGAGATTTCACTAGGACTACATACAA 57.175 34.615 0.00 0.00 0.00 2.41
602 617 8.824756 AAGAGATTTCACTAGGACTACATACA 57.175 34.615 0.00 0.00 0.00 2.29
609 624 9.095700 AGTCTTTAAAGAGATTTCACTAGGACT 57.904 33.333 18.22 4.86 35.32 3.85
610 625 9.713713 AAGTCTTTAAAGAGATTTCACTAGGAC 57.286 33.333 18.22 2.65 35.32 3.85
628 643 9.603921 CACCCCGTTTCTAAATATAAGTCTTTA 57.396 33.333 0.00 0.00 0.00 1.85
629 644 7.555195 CCACCCCGTTTCTAAATATAAGTCTTT 59.445 37.037 0.00 0.00 0.00 2.52
630 645 7.052248 CCACCCCGTTTCTAAATATAAGTCTT 58.948 38.462 0.00 0.00 0.00 3.01
631 646 6.157471 ACCACCCCGTTTCTAAATATAAGTCT 59.843 38.462 0.00 0.00 0.00 3.24
632 647 6.351711 ACCACCCCGTTTCTAAATATAAGTC 58.648 40.000 0.00 0.00 0.00 3.01
633 648 6.317663 ACCACCCCGTTTCTAAATATAAGT 57.682 37.500 0.00 0.00 0.00 2.24
634 649 7.989170 ACTTACCACCCCGTTTCTAAATATAAG 59.011 37.037 0.00 0.00 0.00 1.73
635 650 7.860584 ACTTACCACCCCGTTTCTAAATATAA 58.139 34.615 0.00 0.00 0.00 0.98
636 651 7.436320 ACTTACCACCCCGTTTCTAAATATA 57.564 36.000 0.00 0.00 0.00 0.86
637 652 6.317663 ACTTACCACCCCGTTTCTAAATAT 57.682 37.500 0.00 0.00 0.00 1.28
638 653 5.760484 ACTTACCACCCCGTTTCTAAATA 57.240 39.130 0.00 0.00 0.00 1.40
639 654 4.645863 ACTTACCACCCCGTTTCTAAAT 57.354 40.909 0.00 0.00 0.00 1.40
640 655 4.436113 AACTTACCACCCCGTTTCTAAA 57.564 40.909 0.00 0.00 0.00 1.85
641 656 5.071653 ACTTAACTTACCACCCCGTTTCTAA 59.928 40.000 0.00 0.00 0.00 2.10
642 657 4.592778 ACTTAACTTACCACCCCGTTTCTA 59.407 41.667 0.00 0.00 0.00 2.10
643 658 3.392285 ACTTAACTTACCACCCCGTTTCT 59.608 43.478 0.00 0.00 0.00 2.52
644 659 3.743521 ACTTAACTTACCACCCCGTTTC 58.256 45.455 0.00 0.00 0.00 2.78
645 660 3.862877 ACTTAACTTACCACCCCGTTT 57.137 42.857 0.00 0.00 0.00 3.60
646 661 3.862877 AACTTAACTTACCACCCCGTT 57.137 42.857 0.00 0.00 0.00 4.44
647 662 3.862877 AAACTTAACTTACCACCCCGT 57.137 42.857 0.00 0.00 0.00 5.28
773 788 4.879545 ACTCCTACTTCTTGAACGCAAAAA 59.120 37.500 0.00 0.00 32.73 1.94
774 789 4.448210 ACTCCTACTTCTTGAACGCAAAA 58.552 39.130 0.00 0.00 32.73 2.44
775 790 4.067972 ACTCCTACTTCTTGAACGCAAA 57.932 40.909 0.00 0.00 32.73 3.68
776 791 3.746045 ACTCCTACTTCTTGAACGCAA 57.254 42.857 0.00 0.00 0.00 4.85
777 792 5.401531 AATACTCCTACTTCTTGAACGCA 57.598 39.130 0.00 0.00 0.00 5.24
778 793 7.823149 TTAAATACTCCTACTTCTTGAACGC 57.177 36.000 0.00 0.00 0.00 4.84
814 829 7.713073 GCAAAGCAACCTCTTTATCTCTATACT 59.287 37.037 0.00 0.00 34.76 2.12
820 835 4.013050 AGGCAAAGCAACCTCTTTATCTC 58.987 43.478 0.00 0.00 34.76 2.75
825 840 1.413812 CCAAGGCAAAGCAACCTCTTT 59.586 47.619 0.00 0.00 34.31 2.52
826 841 1.043022 CCAAGGCAAAGCAACCTCTT 58.957 50.000 0.00 0.00 34.31 2.85
827 842 1.466851 GCCAAGGCAAAGCAACCTCT 61.467 55.000 6.14 0.00 41.49 3.69
828 843 1.005748 GCCAAGGCAAAGCAACCTC 60.006 57.895 6.14 0.00 41.49 3.85
829 844 2.510551 GGCCAAGGCAAAGCAACCT 61.511 57.895 13.87 0.00 44.11 3.50
830 845 2.031012 GGCCAAGGCAAAGCAACC 59.969 61.111 13.87 0.00 44.11 3.77
848 863 1.512156 GGTACCGGTGCCACTTGTTG 61.512 60.000 34.01 0.00 35.28 3.33
849 864 1.228033 GGTACCGGTGCCACTTGTT 60.228 57.895 34.01 0.00 35.28 2.83
850 865 2.428622 GGTACCGGTGCCACTTGT 59.571 61.111 34.01 0.00 35.28 3.16
851 866 2.359478 GGGTACCGGTGCCACTTG 60.359 66.667 37.92 0.00 40.86 3.16
862 877 1.202498 GGTGACTTATCAGCGGGTACC 60.202 57.143 2.17 2.17 43.08 3.34
863 878 2.220479 GGTGACTTATCAGCGGGTAC 57.780 55.000 0.00 0.00 43.08 3.34
870 885 1.207791 AGGCCCAGGTGACTTATCAG 58.792 55.000 0.00 0.00 40.21 2.90
892 907 2.035626 TAGTGCTTTGGGCTGGGC 59.964 61.111 0.00 0.00 42.39 5.36
893 908 2.048603 GCTAGTGCTTTGGGCTGGG 61.049 63.158 0.00 0.00 42.39 4.45
908 923 6.317140 CCTCTTTGTTGATTCTTATGCTGCTA 59.683 38.462 0.00 0.00 0.00 3.49
939 954 2.877360 TAACATCGCCGCTGTCGACC 62.877 60.000 14.12 0.00 38.88 4.79
953 968 2.746472 GCCTCCGAGCAAATCCTAACAT 60.746 50.000 0.00 0.00 0.00 2.71
986 1017 3.144506 GACGCCATGATGAATGAATCCT 58.855 45.455 0.00 0.00 38.72 3.24
1015 1046 0.612174 TCCTCCTCCGACTCCAACTG 60.612 60.000 0.00 0.00 0.00 3.16
2888 4297 7.730364 ACATCAGAACTAAGTTTACCAAGTG 57.270 36.000 0.00 0.00 0.00 3.16
3044 4545 7.504924 TTGGTATAACAAGCCAGCATAATAC 57.495 36.000 0.00 0.00 33.41 1.89
3048 4549 7.093552 ACAAATTTGGTATAACAAGCCAGCATA 60.094 33.333 21.74 0.00 33.41 3.14
3049 4550 5.937975 AATTTGGTATAACAAGCCAGCAT 57.062 34.783 2.94 0.00 33.41 3.79
3050 4551 5.011533 ACAAATTTGGTATAACAAGCCAGCA 59.988 36.000 21.74 0.00 33.41 4.41
3149 4653 3.226347 GTTAACAGTGACAAATGCTCGC 58.774 45.455 0.00 0.00 0.00 5.03
3153 4657 3.002862 TGTCCGTTAACAGTGACAAATGC 59.997 43.478 16.03 0.00 34.98 3.56
3170 4677 8.712363 CACAGATAAATATGGTAGAAATGTCCG 58.288 37.037 0.00 0.00 0.00 4.79
3851 5649 1.210478 GGAGAAGCATGCCTCTTGGTA 59.790 52.381 19.61 0.00 35.27 3.25


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

AutoCloner maintained by Alex Coulton.