Multiple sequence alignment - TraesCS6B01G172000

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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 TraesCS6B01G172000 chr6B 100.000 3798 0 0 1 3798 184726656 184722859 0.000000e+00 7014.0
1 TraesCS6B01G172000 chr6B 92.297 1467 96 3 1463 2926 184706520 184705068 0.000000e+00 2067.0
2 TraesCS6B01G172000 chr6B 92.135 1424 95 3 1506 2926 184701405 184699996 0.000000e+00 1993.0
3 TraesCS6B01G172000 chr6B 92.065 1424 96 4 1506 2926 184699004 184697595 0.000000e+00 1988.0
4 TraesCS6B01G172000 chr6B 91.713 1424 101 3 1506 2926 184704097 184702688 0.000000e+00 1960.0
5 TraesCS6B01G172000 chr6B 83.996 931 121 12 992 1899 185100015 185100940 0.000000e+00 869.0
6 TraesCS6B01G172000 chr6B 83.531 929 125 13 995 1899 185110525 185111449 0.000000e+00 843.0
7 TraesCS6B01G172000 chr6B 81.317 653 113 9 2173 2820 185112682 185113330 4.350000e-144 521.0
8 TraesCS6B01G172000 chr6B 83.627 568 61 17 3247 3798 184636765 184636214 4.380000e-139 505.0
9 TraesCS6B01G172000 chr6B 80.838 167 28 3 3036 3200 184682439 184682275 1.110000e-25 128.0
10 TraesCS6B01G172000 chr6B 92.000 50 4 0 3006 3055 184683330 184683281 1.890000e-08 71.3
11 TraesCS6B01G172000 chr6A 93.797 2386 105 19 729 3082 120130450 120128076 0.000000e+00 3546.0
12 TraesCS6B01G172000 chr6A 84.244 933 121 11 992 1899 121659029 121659960 0.000000e+00 885.0
13 TraesCS6B01G172000 chr6A 84.103 931 118 8 996 1899 121871004 121871931 0.000000e+00 872.0
14 TraesCS6B01G172000 chr6A 87.750 751 36 27 1 726 120131336 120130617 0.000000e+00 826.0
15 TraesCS6B01G172000 chr6A 83.553 760 79 22 3080 3798 120128046 120127292 0.000000e+00 669.0
16 TraesCS6B01G172000 chr6A 80.125 639 118 8 2187 2820 121872211 121872845 5.740000e-128 468.0
17 TraesCS6B01G172000 chr6D 92.547 2187 117 16 729 2908 100569040 100566893 0.000000e+00 3094.0
18 TraesCS6B01G172000 chr6D 85.054 930 113 13 992 1899 101202190 101203115 0.000000e+00 924.0
19 TraesCS6B01G172000 chr6D 85.109 920 119 5 995 1899 101212208 101213124 0.000000e+00 924.0
20 TraesCS6B01G172000 chr6D 81.916 929 137 13 997 1899 25440238 25439315 0.000000e+00 756.0
21 TraesCS6B01G172000 chr6D 81.595 652 116 4 2171 2820 101214328 101214977 1.550000e-148 536.0
22 TraesCS6B01G172000 chr6D 77.830 848 115 34 2946 3769 100566803 100566005 1.240000e-124 457.0
23 TraesCS6B01G172000 chr6D 96.970 264 6 2 1 264 100571304 100571043 3.480000e-120 442.0
24 TraesCS6B01G172000 chr6D 88.176 296 12 12 269 545 100570945 100570654 7.860000e-87 331.0
25 TraesCS6B01G172000 chr6D 94.891 137 7 0 592 728 100569351 100569215 8.260000e-52 215.0
26 TraesCS6B01G172000 chr6D 92.727 55 1 3 3195 3248 118400081 118400133 4.070000e-10 76.8
27 TraesCS6B01G172000 chr3A 84.211 114 14 2 3193 3306 136450462 136450571 1.440000e-19 108.0
28 TraesCS6B01G172000 chr5B 83.962 106 14 3 3690 3794 316362495 316362392 8.680000e-17 99.0
29 TraesCS6B01G172000 chr7B 84.706 85 13 0 3165 3249 690599724 690599808 6.760000e-13 86.1
30 TraesCS6B01G172000 chrUn 94.444 54 3 0 3195 3248 101814266 101814319 2.430000e-12 84.2
31 TraesCS6B01G172000 chr2A 92.857 56 4 0 3193 3248 388682244 388682189 8.740000e-12 82.4
32 TraesCS6B01G172000 chr5A 92.727 55 4 0 3193 3247 104156902 104156848 3.140000e-11 80.5
33 TraesCS6B01G172000 chr1D 91.379 58 5 0 3191 3248 365891404 365891461 3.140000e-11 80.5
34 TraesCS6B01G172000 chr2D 92.453 53 4 0 3196 3248 307859653 307859601 4.070000e-10 76.8
35 TraesCS6B01G172000 chr2B 91.071 56 5 0 3193 3248 359933309 359933364 4.070000e-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 TraesCS6B01G172000 chr6B 184722859 184726656 3797 True 7014.000000 7014 100.000000 1 3798 1 chr6B.!!$R2 3797
1 TraesCS6B01G172000 chr6B 184697595 184706520 8925 True 2002.000000 2067 92.052500 1463 2926 4 chr6B.!!$R4 1463
2 TraesCS6B01G172000 chr6B 185100015 185100940 925 False 869.000000 869 83.996000 992 1899 1 chr6B.!!$F1 907
3 TraesCS6B01G172000 chr6B 185110525 185113330 2805 False 682.000000 843 82.424000 995 2820 2 chr6B.!!$F2 1825
4 TraesCS6B01G172000 chr6B 184636214 184636765 551 True 505.000000 505 83.627000 3247 3798 1 chr6B.!!$R1 551
5 TraesCS6B01G172000 chr6A 120127292 120131336 4044 True 1680.333333 3546 88.366667 1 3798 3 chr6A.!!$R1 3797
6 TraesCS6B01G172000 chr6A 121659029 121659960 931 False 885.000000 885 84.244000 992 1899 1 chr6A.!!$F1 907
7 TraesCS6B01G172000 chr6A 121871004 121872845 1841 False 670.000000 872 82.114000 996 2820 2 chr6A.!!$F2 1824
8 TraesCS6B01G172000 chr6D 101202190 101203115 925 False 924.000000 924 85.054000 992 1899 1 chr6D.!!$F1 907
9 TraesCS6B01G172000 chr6D 100566005 100571304 5299 True 907.800000 3094 90.082800 1 3769 5 chr6D.!!$R2 3768
10 TraesCS6B01G172000 chr6D 25439315 25440238 923 True 756.000000 756 81.916000 997 1899 1 chr6D.!!$R1 902
11 TraesCS6B01G172000 chr6D 101212208 101214977 2769 False 730.000000 924 83.352000 995 2820 2 chr6D.!!$F3 1825

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
602 2003 0.026933 CGTCGTCTGATCTGGAGTCG 59.973 60.0 0.0 0.0 0.00 4.18 F
842 2421 0.035439 ACATCGGGAAACGCTTGGAT 60.035 50.0 0.0 0.0 43.86 3.41 F
1603 5566 0.336737 TGAGAGGAGGGAGGAGTTCC 59.663 60.0 0.0 0.0 46.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 5548 0.634465 AGGAACTCCTCCCTCCTCTC 59.366 60.0 0.00 0.0 44.77 3.20 R
2705 10451 0.541998 TCCACCATGTCGACCTCACT 60.542 55.0 14.12 0.0 0.00 3.41 R
3554 13033 0.238289 CACAAACGCCAGGTCACATC 59.762 55.0 0.00 0.0 0.00 3.06 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
67 71 6.778821 TGTAGACAAATGAGGATTCAGGAAA 58.221 36.000 0.00 0.00 36.61 3.13
70 74 7.020827 AGACAAATGAGGATTCAGGAAACTA 57.979 36.000 0.00 0.00 40.21 2.24
231 235 5.105716 TGGCTGTACAGATTAGAGAACTCAC 60.106 44.000 27.08 3.06 0.00 3.51
354 451 1.271707 GCTAGCTAGAGGATCGGGTCT 60.272 57.143 25.15 0.00 42.67 3.85
454 567 2.044946 GGCCAATGAGCTTCCCGT 60.045 61.111 0.00 0.00 0.00 5.28
470 583 3.676093 TCCCGTGCAAATTACATGTGTA 58.324 40.909 9.11 0.00 0.00 2.90
477 590 6.458070 CGTGCAAATTACATGTGTATGGATGA 60.458 38.462 9.11 0.00 38.66 2.92
480 593 7.975058 TGCAAATTACATGTGTATGGATGAAAG 59.025 33.333 9.11 0.00 38.66 2.62
481 594 7.436080 GCAAATTACATGTGTATGGATGAAAGG 59.564 37.037 9.11 0.00 38.66 3.11
483 596 4.860802 ACATGTGTATGGATGAAAGGGA 57.139 40.909 0.00 0.00 38.66 4.20
484 597 4.526970 ACATGTGTATGGATGAAAGGGAC 58.473 43.478 0.00 0.00 38.66 4.46
485 598 3.644966 TGTGTATGGATGAAAGGGACC 57.355 47.619 0.00 0.00 0.00 4.46
486 599 2.093181 TGTGTATGGATGAAAGGGACCG 60.093 50.000 0.00 0.00 0.00 4.79
487 600 2.169769 GTGTATGGATGAAAGGGACCGA 59.830 50.000 0.00 0.00 0.00 4.69
489 602 0.839946 ATGGATGAAAGGGACCGAGG 59.160 55.000 0.00 0.00 0.00 4.63
490 603 1.153147 GGATGAAAGGGACCGAGGC 60.153 63.158 0.00 0.00 0.00 4.70
492 605 1.956629 GATGAAAGGGACCGAGGCGA 61.957 60.000 0.00 0.00 0.00 5.54
493 606 1.550130 ATGAAAGGGACCGAGGCGAA 61.550 55.000 0.00 0.00 0.00 4.70
517 630 2.035783 GGACCACCCTTCCCTTGC 59.964 66.667 0.00 0.00 0.00 4.01
528 641 0.178938 TTCCCTTGCATGGAAAGGCA 60.179 50.000 19.85 0.00 42.52 4.75
533 646 1.252904 TTGCATGGAAAGGCAGCCTC 61.253 55.000 16.53 2.70 41.68 4.70
534 647 2.421399 GCATGGAAAGGCAGCCTCC 61.421 63.158 16.53 13.96 30.89 4.30
535 648 2.117156 CATGGAAAGGCAGCCTCCG 61.117 63.158 16.53 0.00 30.89 4.63
536 649 3.350031 ATGGAAAGGCAGCCTCCGG 62.350 63.158 16.53 0.00 30.89 5.14
537 650 4.035102 GGAAAGGCAGCCTCCGGT 62.035 66.667 16.53 0.00 30.89 5.28
538 651 2.034221 GAAAGGCAGCCTCCGGTT 59.966 61.111 16.53 4.85 30.89 4.44
539 652 2.282462 AAAGGCAGCCTCCGGTTG 60.282 61.111 16.53 0.00 36.98 3.77
540 653 3.133365 AAAGGCAGCCTCCGGTTGT 62.133 57.895 16.53 0.00 36.29 3.32
541 654 3.850098 AAGGCAGCCTCCGGTTGTG 62.850 63.158 16.53 0.00 36.29 3.33
542 655 4.329545 GGCAGCCTCCGGTTGTGA 62.330 66.667 3.29 0.00 36.29 3.58
543 656 2.281484 GCAGCCTCCGGTTGTGAA 60.281 61.111 0.00 0.00 36.29 3.18
544 657 2.617274 GCAGCCTCCGGTTGTGAAC 61.617 63.158 0.00 0.00 36.29 3.18
552 665 3.763671 GGTTGTGAACCCAGCAGG 58.236 61.111 0.00 0.00 46.12 4.85
553 666 1.150536 GGTTGTGAACCCAGCAGGA 59.849 57.895 0.00 0.00 46.12 3.86
554 667 0.890996 GGTTGTGAACCCAGCAGGAG 60.891 60.000 0.00 0.00 46.12 3.69
555 668 0.108585 GTTGTGAACCCAGCAGGAGA 59.891 55.000 0.00 0.00 39.89 3.71
556 669 0.397941 TTGTGAACCCAGCAGGAGAG 59.602 55.000 0.00 0.00 39.89 3.20
557 670 1.376553 GTGAACCCAGCAGGAGAGC 60.377 63.158 0.00 0.00 39.89 4.09
558 671 2.270527 GAACCCAGCAGGAGAGCC 59.729 66.667 0.00 0.00 39.89 4.70
559 672 3.334054 AACCCAGCAGGAGAGCCC 61.334 66.667 0.00 0.00 39.89 5.19
562 675 4.154347 CCAGCAGGAGAGCCCGAC 62.154 72.222 0.00 0.00 40.87 4.79
563 676 4.154347 CAGCAGGAGAGCCCGACC 62.154 72.222 0.00 0.00 40.87 4.79
602 2003 0.026933 CGTCGTCTGATCTGGAGTCG 59.973 60.000 0.00 0.00 0.00 4.18
603 2004 0.378962 GTCGTCTGATCTGGAGTCGG 59.621 60.000 0.00 0.00 0.00 4.79
653 2054 1.927895 CATTCCTATCCTATCGCGCC 58.072 55.000 0.00 0.00 0.00 6.53
676 2077 0.453390 CAGAAAGATTGCGCCCTTCC 59.547 55.000 4.18 0.00 0.00 3.46
693 2094 2.275418 CCCCAAATCCCCTGACCG 59.725 66.667 0.00 0.00 0.00 4.79
703 2104 1.966451 CCCTGACCGTTGTTGAGGC 60.966 63.158 0.00 0.00 0.00 4.70
756 2334 4.383649 GCTGTGTCACTGCATACAAAATTG 59.616 41.667 25.00 0.00 41.83 2.32
757 2335 4.869215 TGTGTCACTGCATACAAAATTGG 58.131 39.130 4.27 0.00 0.00 3.16
758 2336 4.340666 TGTGTCACTGCATACAAAATTGGT 59.659 37.500 4.27 0.00 0.00 3.67
759 2337 5.163468 TGTGTCACTGCATACAAAATTGGTT 60.163 36.000 4.27 0.00 0.00 3.67
771 2350 2.278182 AATTGGTTACATGCCGGCGC 62.278 55.000 23.90 0.00 0.00 6.53
842 2421 0.035439 ACATCGGGAAACGCTTGGAT 60.035 50.000 0.00 0.00 43.86 3.41
879 2458 0.796312 CACACCGAAAGCTACGCAAT 59.204 50.000 7.56 0.00 0.00 3.56
880 2459 1.196808 CACACCGAAAGCTACGCAATT 59.803 47.619 7.56 0.00 0.00 2.32
987 2567 0.652592 GTCACACACACTCACACTGC 59.347 55.000 0.00 0.00 0.00 4.40
988 2568 0.461870 TCACACACACTCACACTGCC 60.462 55.000 0.00 0.00 0.00 4.85
991 2571 1.153168 ACACACTCACACTGCCCAC 60.153 57.895 0.00 0.00 0.00 4.61
1585 5548 1.382522 CATGATCGGGGACAGGTTTG 58.617 55.000 0.00 0.00 0.00 2.93
1603 5566 0.336737 TGAGAGGAGGGAGGAGTTCC 59.663 60.000 0.00 0.00 46.00 3.62
1965 9051 3.047796 GCAAGCATGGCATATCTTTTCG 58.952 45.455 0.00 0.00 32.79 3.46
1989 9733 1.597663 CCACTTCCACGTGACTTTGAC 59.402 52.381 19.30 0.00 37.06 3.18
2081 9827 2.426381 GGTTCTAGTTCTAGGGTCCACG 59.574 54.545 6.96 0.00 0.00 4.94
2159 9905 6.146510 TGTTTACCTGTTCTATAAACTGCACG 59.853 38.462 7.41 0.00 38.85 5.34
2356 10102 5.392811 CGACCTAAAATACCTCAGACTCGTT 60.393 44.000 0.00 0.00 0.00 3.85
2434 10180 2.978156 TGGAGTCCTGCAAAATCCTT 57.022 45.000 11.33 0.00 0.00 3.36
2485 10231 1.240641 TTGTGAATGCGTGGGCGATT 61.241 50.000 0.00 0.00 44.10 3.34
2705 10451 4.697756 CGGCGGGGCTGAAGTCAA 62.698 66.667 0.00 0.00 37.02 3.18
2802 10548 6.017109 GTCCATGTATCGCCAGTTTGATTTAT 60.017 38.462 0.00 0.00 0.00 1.40
2854 10603 1.423395 CAGTCCTTTGTCTCTGACGC 58.577 55.000 0.00 0.00 34.95 5.19
2859 10608 1.269778 CCTTTGTCTCTGACGCTGTCA 60.270 52.381 10.24 10.24 40.50 3.58
2876 10625 4.033358 GCTGTCAAATGTCGAGACTTATGG 59.967 45.833 4.78 0.00 33.56 2.74
2890 10639 9.093970 TCGAGACTTATGGTGTAATGTTAATTG 57.906 33.333 0.00 0.00 0.00 2.32
2985 10790 8.682016 CAAAGTGTTAATTTTGTCGAATCACTC 58.318 33.333 0.00 0.00 33.46 3.51
3005 10810 9.822185 ATCACTCTTTATTTGCAAAGAAACTTT 57.178 25.926 24.08 10.72 42.43 2.66
3076 10913 3.192212 TCAATTGGCATAAATGTCACGCA 59.808 39.130 5.42 0.00 42.90 5.24
3078 10915 0.445829 TGGCATAAATGTCACGCACG 59.554 50.000 0.00 0.00 37.51 5.34
3107 10944 5.341993 CGCATGGTTATAAATTATGCAACCG 59.658 40.000 20.54 8.27 43.10 4.44
3110 10947 7.589395 CATGGTTATAAATTATGCAACCGCTA 58.411 34.615 11.12 0.00 41.27 4.26
3130 10967 7.041372 ACCGCTAATCCATATTAAATGTGACAC 60.041 37.037 0.00 0.00 0.00 3.67
3140 10977 9.636879 CATATTAAATGTGACACAAATGACCAA 57.363 29.630 13.23 1.06 0.00 3.67
3141 10978 9.859427 ATATTAAATGTGACACAAATGACCAAG 57.141 29.630 13.23 0.00 0.00 3.61
3145 10982 1.234821 GACACAAATGACCAAGCCGA 58.765 50.000 0.00 0.00 0.00 5.54
3148 10985 1.541147 CACAAATGACCAAGCCGACAT 59.459 47.619 0.00 0.00 0.00 3.06
3189 11026 6.470556 CGATAGCGATGAATAGTAGAACATGG 59.529 42.308 0.00 0.00 40.82 3.66
3194 11031 4.689612 TGAATAGTAGAACATGGGAGGC 57.310 45.455 0.00 0.00 0.00 4.70
3195 11032 3.391296 TGAATAGTAGAACATGGGAGGCC 59.609 47.826 0.00 0.00 0.00 5.19
3227 11064 2.482142 GCGAGGAAGAGTAGAACATGGG 60.482 54.545 0.00 0.00 0.00 4.00
3261 11553 0.253160 TGGGTCTTACCAGGCCTCAT 60.253 55.000 0.00 0.00 45.37 2.90
3265 11557 2.043227 GTCTTACCAGGCCTCATAGCT 58.957 52.381 0.00 0.00 0.00 3.32
3309 12012 2.388310 GCGGAGGCTATTATTCCCTC 57.612 55.000 0.00 0.00 43.48 4.30
3316 12025 2.632537 GCTATTATTCCCTCCCTCCCA 58.367 52.381 0.00 0.00 0.00 4.37
3330 12039 2.225117 CCCTCCCAAAGTTTCACATCCT 60.225 50.000 0.00 0.00 0.00 3.24
3398 12874 1.227999 CGCGGCCGGTGATCATTTAT 61.228 55.000 29.38 0.00 0.00 1.40
3474 12952 7.156876 TGAATTTGCTTCGGTTTAGATGAAT 57.843 32.000 0.00 0.00 36.60 2.57
3476 12954 8.735315 TGAATTTGCTTCGGTTTAGATGAATAA 58.265 29.630 0.00 0.00 36.60 1.40
3548 13027 8.572855 AATTTCTTTGTTTTGGTTGAATTCCA 57.427 26.923 2.27 0.00 0.00 3.53
3554 13033 7.551035 TTGTTTTGGTTGAATTCCATTTGAG 57.449 32.000 2.27 0.00 34.75 3.02
3565 13044 3.354948 TCCATTTGAGATGTGACCTGG 57.645 47.619 0.00 0.00 0.00 4.45
3604 13083 4.411013 TGGATGACCGACTCTCATATCAT 58.589 43.478 0.00 0.00 39.42 2.45
3605 13084 4.460731 TGGATGACCGACTCTCATATCATC 59.539 45.833 0.00 0.00 41.02 2.92
3606 13085 4.438065 GGATGACCGACTCTCATATCATCG 60.438 50.000 0.00 0.00 42.11 3.84
3625 13104 4.739495 TGTCCAGACACCTTCCCA 57.261 55.556 0.00 0.00 36.21 4.37
3711 13191 8.573885 TGTATACTCCCTCGTTCACAAATATAG 58.426 37.037 4.17 0.00 0.00 1.31
3794 13275 6.208797 ACTCTAAGCGTGCCAATATACATCTA 59.791 38.462 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.954202 TCCTCATTTGTCTACATCGGTACT 59.046 41.667 0.00 0.00 0.00 2.73
454 567 7.401955 TTCATCCATACACATGTAATTTGCA 57.598 32.000 0.00 0.00 33.76 4.08
470 583 0.839946 CCTCGGTCCCTTTCATCCAT 59.160 55.000 0.00 0.00 0.00 3.41
477 590 0.179012 TTTTTCGCCTCGGTCCCTTT 60.179 50.000 0.00 0.00 0.00 3.11
493 606 0.468585 GGAAGGGTGGTCCGGTTTTT 60.469 55.000 0.00 0.00 41.52 1.94
499 612 2.351276 CAAGGGAAGGGTGGTCCG 59.649 66.667 0.00 0.00 41.52 4.79
501 614 0.967380 CATGCAAGGGAAGGGTGGTC 60.967 60.000 0.00 0.00 0.00 4.02
502 615 1.077265 CATGCAAGGGAAGGGTGGT 59.923 57.895 0.00 0.00 0.00 4.16
504 617 4.023137 CCATGCAAGGGAAGGGTG 57.977 61.111 0.00 0.00 43.46 4.61
517 630 2.117156 CGGAGGCTGCCTTTCCATG 61.117 63.158 24.26 5.13 31.76 3.66
536 649 0.108585 TCTCCTGCTGGGTTCACAAC 59.891 55.000 10.07 0.00 36.25 3.32
537 650 0.397941 CTCTCCTGCTGGGTTCACAA 59.602 55.000 10.07 0.00 36.25 3.33
538 651 2.061220 CTCTCCTGCTGGGTTCACA 58.939 57.895 10.07 0.00 36.25 3.58
539 652 1.376553 GCTCTCCTGCTGGGTTCAC 60.377 63.158 10.07 0.00 36.25 3.18
540 653 2.596851 GGCTCTCCTGCTGGGTTCA 61.597 63.158 10.07 0.00 36.25 3.18
541 654 2.270527 GGCTCTCCTGCTGGGTTC 59.729 66.667 10.07 0.00 36.25 3.62
542 655 3.334054 GGGCTCTCCTGCTGGGTT 61.334 66.667 10.07 0.00 36.25 4.11
545 658 4.154347 GTCGGGCTCTCCTGCTGG 62.154 72.222 2.58 2.58 38.67 4.85
546 659 4.154347 GGTCGGGCTCTCCTGCTG 62.154 72.222 0.00 0.00 38.67 4.41
560 673 4.265056 AGTGCACAACCGGGGGTC 62.265 66.667 21.04 0.00 33.12 4.46
561 674 4.265056 GAGTGCACAACCGGGGGT 62.265 66.667 21.04 0.00 37.65 4.95
564 677 4.619227 ACCGAGTGCACAACCGGG 62.619 66.667 33.00 22.45 43.13 5.73
602 2003 2.506438 CGTCTTCCTTCGCGTCCC 60.506 66.667 5.77 0.00 0.00 4.46
603 2004 2.506438 CCGTCTTCCTTCGCGTCC 60.506 66.667 5.77 0.00 0.00 4.79
653 2054 0.453390 GGGCGCAATCTTTCTGGAAG 59.547 55.000 10.83 0.00 36.67 3.46
676 2077 2.150014 AACGGTCAGGGGATTTGGGG 62.150 60.000 0.00 0.00 0.00 4.96
693 2094 3.657537 CGATTGACGCCTCAACAAC 57.342 52.632 0.00 0.00 39.28 3.32
703 2104 1.136252 CAGTCCTGTTTGCGATTGACG 60.136 52.381 0.00 0.00 45.66 4.35
842 2421 3.930838 CGTCACACACGCAGCTTA 58.069 55.556 0.00 0.00 42.87 3.09
884 2463 2.053811 CGACGCGCGTGAACAAAA 60.054 55.556 42.90 0.00 34.64 2.44
911 2490 2.543238 CGGGTTACTATCTTGAGCGGTC 60.543 54.545 7.89 7.89 0.00 4.79
968 2548 0.652592 GCAGTGTGAGTGTGTGTGAC 59.347 55.000 0.00 0.00 0.00 3.67
976 2556 2.256591 GCAGTGGGCAGTGTGAGTG 61.257 63.158 0.00 0.00 43.97 3.51
1557 3140 2.819154 CCGATCATGGTGCGCACA 60.819 61.111 38.60 25.68 0.00 4.57
1585 5548 0.634465 AGGAACTCCTCCCTCCTCTC 59.366 60.000 0.00 0.00 44.77 3.20
1603 5566 3.205395 CTCCTCGAGGACCTGCAG 58.795 66.667 30.49 15.61 39.78 4.41
1952 9038 4.965119 AGTGGAAACGAAAAGATATGCC 57.035 40.909 0.00 0.00 0.00 4.40
1965 9051 1.949465 AGTCACGTGGAAGTGGAAAC 58.051 50.000 17.00 2.73 42.10 2.78
1989 9733 4.860022 ACCATGGAAGGTAAATCTTGAGG 58.140 43.478 21.47 0.00 40.98 3.86
2153 9899 6.437928 ACAATAATAATACCAATGCGTGCAG 58.562 36.000 0.00 0.00 0.00 4.41
2159 9905 8.863872 AGGTCCTACAATAATAATACCAATGC 57.136 34.615 0.00 0.00 0.00 3.56
2434 10180 1.529226 CCTTTTGCACGTCATACCCA 58.471 50.000 0.00 0.00 0.00 4.51
2702 10448 1.000843 CACCATGTCGACCTCACTTGA 59.999 52.381 14.12 0.00 0.00 3.02
2705 10451 0.541998 TCCACCATGTCGACCTCACT 60.542 55.000 14.12 0.00 0.00 3.41
2755 10501 2.867624 ACGGAGTGTAGGTACAAGTCA 58.132 47.619 0.00 0.00 42.51 3.41
2802 10548 9.871238 GAGAATTTGTGACCTACTATTGAAGTA 57.129 33.333 0.00 0.00 39.80 2.24
2854 10603 5.062683 CACCATAAGTCTCGACATTTGACAG 59.937 44.000 4.78 0.00 33.56 3.51
2859 10608 7.103641 ACATTACACCATAAGTCTCGACATTT 58.896 34.615 0.00 0.00 0.00 2.32
2876 10625 9.571810 TTTCTGATGATGCAATTAACATTACAC 57.428 29.630 0.00 0.00 0.00 2.90
2890 10639 5.190992 TGCAATGGTATTTCTGATGATGC 57.809 39.130 0.00 0.00 0.00 3.91
2926 10700 9.733556 GTCATGGTGTTGGGATTTATGTATATA 57.266 33.333 0.00 0.00 0.00 0.86
2927 10701 7.390440 CGTCATGGTGTTGGGATTTATGTATAT 59.610 37.037 0.00 0.00 0.00 0.86
2932 10706 3.489059 GCGTCATGGTGTTGGGATTTATG 60.489 47.826 0.00 0.00 0.00 1.90
2936 10710 0.965363 GGCGTCATGGTGTTGGGATT 60.965 55.000 0.00 0.00 0.00 3.01
2939 10713 1.459455 TTTGGCGTCATGGTGTTGGG 61.459 55.000 0.00 0.00 0.00 4.12
2940 10714 0.318614 GTTTGGCGTCATGGTGTTGG 60.319 55.000 0.00 0.00 0.00 3.77
2941 10715 0.383590 TGTTTGGCGTCATGGTGTTG 59.616 50.000 0.00 0.00 0.00 3.33
3005 10810 6.186420 TCAAGGTGGCTGCAATATAGATAA 57.814 37.500 0.50 0.00 0.00 1.75
3078 10915 5.116983 GCATAATTTATAACCATGCGTGTGC 59.883 40.000 4.96 0.00 43.20 4.57
3084 10921 5.118510 GCGGTTGCATAATTTATAACCATGC 59.881 40.000 16.16 14.11 40.54 4.06
3130 10967 1.541147 ACATGTCGGCTTGGTCATTTG 59.459 47.619 7.87 0.00 0.00 2.32
3171 11008 5.241662 GCCTCCCATGTTCTACTATTCATC 58.758 45.833 0.00 0.00 0.00 2.92
3173 11010 3.391296 GGCCTCCCATGTTCTACTATTCA 59.609 47.826 0.00 0.00 0.00 2.57
3180 11017 2.742116 GGCGGCCTCCCATGTTCTA 61.742 63.158 12.87 0.00 0.00 2.10
3286 11989 2.338500 GGAATAATAGCCTCCGCTTCG 58.662 52.381 0.00 0.00 45.55 3.79
3302 12005 1.773541 AACTTTGGGAGGGAGGGAAT 58.226 50.000 0.00 0.00 0.00 3.01
3309 12012 2.171003 GGATGTGAAACTTTGGGAGGG 58.829 52.381 0.00 0.00 38.04 4.30
3316 12025 3.619979 CGAGCCCTAGGATGTGAAACTTT 60.620 47.826 11.48 0.00 38.04 2.66
3346 12069 1.219124 CCACGACATGGTCAGGAGG 59.781 63.158 0.00 0.00 44.46 4.30
3428 12904 9.621629 ATTCATTGCATTTTGACATATTTCCAT 57.378 25.926 0.00 0.00 0.00 3.41
3429 12905 9.451002 AATTCATTGCATTTTGACATATTTCCA 57.549 25.926 0.00 0.00 0.00 3.53
3474 12952 9.651913 GATGGCTTCCATTCAAACTTAAAATTA 57.348 29.630 0.00 0.00 45.26 1.40
3476 12954 7.105588 GGATGGCTTCCATTCAAACTTAAAAT 58.894 34.615 14.15 0.00 45.26 1.82
3492 12971 7.575365 CAAGTTTAAACAAATTGGATGGCTTC 58.425 34.615 20.06 0.00 0.00 3.86
3498 12977 8.674263 TTGATGCAAGTTTAAACAAATTGGAT 57.326 26.923 20.06 19.47 35.07 3.41
3548 13027 1.003580 ACGCCAGGTCACATCTCAAAT 59.996 47.619 0.00 0.00 0.00 2.32
3554 13033 0.238289 CACAAACGCCAGGTCACATC 59.762 55.000 0.00 0.00 0.00 3.06
3565 13044 0.387239 CCAAAGCTAGCCACAAACGC 60.387 55.000 12.13 0.00 0.00 4.84


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

AutoCloner maintained by Alex Coulton.