Multiple sequence alignment - TraesCS6D01G107300

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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 TraesCS6D01G107300 chr6D 100.000 3583 0 0 1 3583 71054297 71050715 0.000000e+00 6617.0
1 TraesCS6D01G107300 chr6D 79.167 96 12 5 2911 2998 131945932 131945837 3.860000e-05 60.2
2 TraesCS6D01G107300 chr6D 97.059 34 1 0 3297 3330 71050745 71050778 1.390000e-04 58.4
3 TraesCS6D01G107300 chr6D 97.059 34 1 0 3520 3553 71050968 71051001 1.390000e-04 58.4
4 TraesCS6D01G107300 chr6B 95.542 2759 89 14 249 2992 145576979 145574240 0.000000e+00 4383.0
5 TraesCS6D01G107300 chr6B 94.483 435 18 5 3150 3583 145573962 145573533 0.000000e+00 665.0
6 TraesCS6D01G107300 chr6B 96.774 155 3 1 2999 3151 145574153 145573999 1.280000e-64 257.0
7 TraesCS6D01G107300 chr6B 97.059 34 1 0 3297 3330 145573564 145573597 1.390000e-04 58.4
8 TraesCS6D01G107300 chr6B 96.875 32 1 0 3522 3553 145573787 145573818 2.000000e-03 54.7
9 TraesCS6D01G107300 chr2B 86.945 743 68 13 1 717 786503594 786504333 0.000000e+00 808.0
10 TraesCS6D01G107300 chr2B 86.461 746 71 11 1 717 786565873 786566617 0.000000e+00 791.0
11 TraesCS6D01G107300 chr2B 85.185 81 3 5 2920 2992 59218020 59217941 1.380000e-09 75.0
12 TraesCS6D01G107300 chr2B 82.051 78 11 2 2918 2992 668173466 668173389 2.990000e-06 63.9
13 TraesCS6D01G107300 chr1D 82.464 211 33 3 1025 1233 72501931 72501723 7.900000e-42 182.0
14 TraesCS6D01G107300 chr1D 77.647 255 49 7 1095 1345 71639735 71639485 8.010000e-32 148.0
15 TraesCS6D01G107300 chr1D 81.290 155 29 0 2260 2414 72434285 72434131 3.760000e-25 126.0
16 TraesCS6D01G107300 chr1A 82.464 211 33 3 1025 1233 71790101 71789893 7.900000e-42 182.0
17 TraesCS6D01G107300 chr1A 78.824 255 46 7 1095 1345 71724973 71724723 7.960000e-37 165.0
18 TraesCS6D01G107300 chr1B 81.081 222 38 3 1014 1233 113567839 113567620 1.320000e-39 174.0
19 TraesCS6D01G107300 chr1B 81.905 210 34 3 1026 1233 113818076 113817869 1.320000e-39 174.0
20 TraesCS6D01G107300 chr1B 79.741 232 39 7 1097 1324 112865988 112865761 1.030000e-35 161.0
21 TraesCS6D01G107300 chr1B 82.550 149 26 0 2266 2414 113212619 113212471 8.070000e-27 132.0
22 TraesCS6D01G107300 chr1B 82.550 149 26 0 2266 2414 113314980 113314832 8.070000e-27 132.0
23 TraesCS6D01G107300 chr1B 82.550 149 26 0 2266 2414 113497768 113497620 8.070000e-27 132.0
24 TraesCS6D01G107300 chr5B 79.216 255 45 7 1095 1345 626251032 626250782 1.710000e-38 171.0
25 TraesCS6D01G107300 chrUn 82.877 146 25 0 2260 2405 372933799 372933944 8.070000e-27 132.0
26 TraesCS6D01G107300 chr2A 82.759 87 8 4 2919 2998 84240805 84240719 1.780000e-08 71.3
27 TraesCS6D01G107300 chr7B 90.385 52 5 0 2350 2401 607929082 607929133 6.420000e-08 69.4
28 TraesCS6D01G107300 chr7B 80.000 105 9 7 2920 3014 296324243 296324345 2.310000e-07 67.6
29 TraesCS6D01G107300 chr7A 80.000 105 9 7 2920 3014 375877950 375878052 2.310000e-07 67.6
30 TraesCS6D01G107300 chr5A 93.182 44 3 0 2957 3000 567915949 567915906 8.300000e-07 65.8
31 TraesCS6D01G107300 chr5A 100.000 30 0 0 2916 2945 567915905 567915934 5.000000e-04 56.5
32 TraesCS6D01G107300 chr2D 81.818 88 7 6 2920 2999 114222990 114223076 8.300000e-07 65.8
33 TraesCS6D01G107300 chr3B 100.000 33 0 0 2957 2989 817823403 817823435 1.070000e-05 62.1
34 TraesCS6D01G107300 chr3B 97.143 35 0 1 2916 2950 8799693 8799726 1.390000e-04 58.4
35 TraesCS6D01G107300 chr3B 100.000 31 0 0 2916 2946 207304836 207304866 1.390000e-04 58.4
36 TraesCS6D01G107300 chr3B 92.500 40 2 1 2911 2950 455140527 455140565 5.000000e-04 56.5
37 TraesCS6D01G107300 chr6A 78.788 99 13 5 2911 3001 170907914 170907816 3.860000e-05 60.2
38 TraesCS6D01G107300 chr4B 94.737 38 1 1 2909 2945 37192989 37193026 1.390000e-04 58.4


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 TraesCS6D01G107300 chr6D 71050715 71054297 3582 True 6617.000000 6617 100.000000 1 3583 1 chr6D.!!$R1 3582
1 TraesCS6D01G107300 chr6B 145573533 145576979 3446 True 1768.333333 4383 95.599667 249 3583 3 chr6B.!!$R1 3334
2 TraesCS6D01G107300 chr2B 786503594 786504333 739 False 808.000000 808 86.945000 1 717 1 chr2B.!!$F1 716
3 TraesCS6D01G107300 chr2B 786565873 786566617 744 False 791.000000 791 86.461000 1 717 1 chr2B.!!$F2 716

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
491 511 0.250252 TCTGCAGCCGATGACAACAA 60.250 50.0 9.47 0.0 0.00 2.83 F
1419 1455 0.034089 TCCAGGAGCTCGACATCAGA 60.034 55.0 7.83 0.0 0.00 3.27 F
2339 2375 0.392998 ATTACGAAGGCTGTGGGCAG 60.393 55.0 0.00 0.0 45.23 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1854 0.034477 CCAGTTTAGGTGCCCGGATT 60.034 55.0 0.73 0.0 0.00 3.01 R
2527 2563 0.105778 TGACAAGTCATGGACACGCA 59.894 50.0 0.00 0.0 34.60 5.24 R
3219 3375 0.969917 AGCAACCAACTGCCACAACA 60.970 50.0 0.00 0.0 43.73 3.33 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
39 42 5.927465 AGAGATAGAGATAGAGAGGAGGGA 58.073 45.833 0.00 0.00 0.00 4.20
48 51 0.387565 GAGAGGAGGGAGATGAACGC 59.612 60.000 0.00 0.00 0.00 4.84
57 60 0.874390 GAGATGAACGCACCTTGCAA 59.126 50.000 0.00 0.00 45.36 4.08
66 69 1.213537 CACCTTGCAATGGCCTTCG 59.786 57.895 3.32 0.00 40.13 3.79
72 75 1.741770 GCAATGGCCTTCGTCGTCT 60.742 57.895 3.32 0.00 0.00 4.18
76 79 2.048127 GGCCTTCGTCGTCTGCTT 60.048 61.111 0.00 0.00 0.00 3.91
86 89 3.426568 GTCTGCTTCTGGTGCCGC 61.427 66.667 0.00 0.00 0.00 6.53
107 110 1.685224 CCTAGTCCAAGGCTTGCCA 59.315 57.895 21.77 7.36 0.00 4.92
110 113 1.555075 CTAGTCCAAGGCTTGCCACTA 59.445 52.381 24.47 24.47 0.00 2.74
117 120 1.467920 AGGCTTGCCACTAATGCTTC 58.532 50.000 14.54 0.00 0.00 3.86
118 121 1.176527 GGCTTGCCACTAATGCTTCA 58.823 50.000 6.79 0.00 0.00 3.02
126 129 2.559440 CACTAATGCTTCAGAGGAGGC 58.441 52.381 0.00 0.00 45.65 4.70
131 134 1.153667 GCTTCAGAGGAGGCAGTCG 60.154 63.158 0.00 0.00 44.87 4.18
134 137 1.587043 TTCAGAGGAGGCAGTCGTCG 61.587 60.000 3.24 0.00 43.63 5.12
135 138 2.041115 CAGAGGAGGCAGTCGTCGA 61.041 63.158 0.00 0.00 43.63 4.20
157 160 1.065926 CACACTGCAGAATAGGAGGCA 60.066 52.381 23.35 0.00 34.66 4.75
185 188 2.203181 GCTCATGCTCCTCCTGCC 60.203 66.667 0.00 0.00 36.03 4.85
304 324 2.168728 GAGAGATTCACGGCTAGGGTTT 59.831 50.000 0.00 0.00 0.00 3.27
328 348 0.687757 CCAATCGGTCTCCCTCCTCA 60.688 60.000 0.00 0.00 0.00 3.86
335 355 1.062810 GGTCTCCCTCCTCACCATACT 60.063 57.143 0.00 0.00 0.00 2.12
340 360 0.824109 CCTCCTCACCATACTCGCAA 59.176 55.000 0.00 0.00 0.00 4.85
359 379 1.354101 ACCCAACCATCTACGGAACA 58.646 50.000 0.00 0.00 0.00 3.18
363 383 2.355716 CCAACCATCTACGGAACACCAT 60.356 50.000 0.00 0.00 0.00 3.55
387 407 1.077663 AGGGCCAACACATGAAATCCT 59.922 47.619 6.18 0.00 0.00 3.24
491 511 0.250252 TCTGCAGCCGATGACAACAA 60.250 50.000 9.47 0.00 0.00 2.83
496 516 1.675641 GCCGATGACAACAAGGGCT 60.676 57.895 0.00 0.00 41.76 5.19
498 518 0.321564 CCGATGACAACAAGGGCTCA 60.322 55.000 0.00 0.00 0.00 4.26
524 544 1.135094 CTGTGCCCCACCTCTCATAT 58.865 55.000 0.00 0.00 32.73 1.78
525 545 1.492176 CTGTGCCCCACCTCTCATATT 59.508 52.381 0.00 0.00 32.73 1.28
526 546 2.705658 CTGTGCCCCACCTCTCATATTA 59.294 50.000 0.00 0.00 32.73 0.98
539 559 5.006153 TCTCATATTAACACAGGACGGTG 57.994 43.478 1.05 1.05 44.35 4.94
554 575 0.926628 CGGTGGAACGCGTGAAAAAC 60.927 55.000 14.98 7.41 41.51 2.43
590 611 5.563592 TCATTGATTGTCACATCAACTCCT 58.436 37.500 10.62 0.00 39.29 3.69
623 650 3.493129 CAGTCCATCAAGAAAAACGACGA 59.507 43.478 0.00 0.00 0.00 4.20
625 652 2.473609 TCCATCAAGAAAAACGACGACG 59.526 45.455 5.58 5.58 45.75 5.12
628 655 2.801063 TCAAGAAAAACGACGACGAGT 58.199 42.857 15.32 0.00 42.66 4.18
725 758 8.161425 ACAATGGGATAGTACAAAGTACAAACT 58.839 33.333 9.68 0.00 37.65 2.66
780 814 2.862850 AGGTAAATCCTACCCGGACT 57.137 50.000 0.73 0.00 46.80 3.85
781 815 2.395619 AGGTAAATCCTACCCGGACTG 58.604 52.381 0.73 0.00 46.80 3.51
825 860 5.957771 ATCGGCCCATATATTATGTGAGT 57.042 39.130 0.00 0.00 0.00 3.41
833 868 7.362660 GCCCATATATTATGTGAGTCGTGTCTA 60.363 40.741 2.27 0.00 0.00 2.59
1074 1110 3.508840 GGCATTCCACGGAAGCGG 61.509 66.667 4.58 0.00 37.56 5.52
1299 1335 2.102252 CCTCTCCAAAATCCTCTCCGAG 59.898 54.545 0.00 0.00 0.00 4.63
1419 1455 0.034089 TCCAGGAGCTCGACATCAGA 60.034 55.000 7.83 0.00 0.00 3.27
1428 1464 2.786854 CTCGACATCAGATTCGTTCGT 58.213 47.619 12.04 0.00 36.60 3.85
1498 1534 3.723235 CTGGCATCCACCCTCGTCG 62.723 68.421 0.00 0.00 0.00 5.12
1534 1570 2.094338 GGCTGCAATTTCTCCAAAGAGG 60.094 50.000 0.50 0.00 40.83 3.69
1597 1633 2.144482 ACACTACGTTTCCTTGTCGG 57.856 50.000 0.00 0.00 0.00 4.79
1622 1658 2.158842 AGTTCCTACATGGCATGCTCTC 60.159 50.000 26.70 12.45 35.26 3.20
1791 1827 1.168714 GGTTGCTGCTACCTTCTTGG 58.831 55.000 23.12 0.00 42.93 3.61
1818 1854 1.483415 GGCGGTGGGACTATTCAGTTA 59.517 52.381 0.00 0.00 34.21 2.24
1944 1980 4.892655 TGCAGAATACATTTTTACGCTCG 58.107 39.130 0.00 0.00 0.00 5.03
1945 1981 4.201773 TGCAGAATACATTTTTACGCTCGG 60.202 41.667 0.00 0.00 0.00 4.63
1991 2027 4.400845 CGATCAGCTTGACAAACTTGATG 58.599 43.478 11.36 0.22 0.00 3.07
2029 2065 1.515020 CTCTCACTTCTGGCCCTCG 59.485 63.158 0.00 0.00 0.00 4.63
2122 2158 8.985315 ATTCATCCTTGCTATTCTCAACATAA 57.015 30.769 0.00 0.00 0.00 1.90
2166 2202 8.839310 ATCTAGTAGTTGATTGGCATGTAATC 57.161 34.615 14.26 14.26 35.59 1.75
2201 2237 1.952296 CCAGCTTTGACATATGCCTCC 59.048 52.381 1.58 0.00 0.00 4.30
2238 2274 5.235516 AGCTGCAGAAAAATTCAAAGATGG 58.764 37.500 20.43 0.00 0.00 3.51
2258 2294 3.824443 TGGATGTGAAAGACGTGTCTCTA 59.176 43.478 2.48 0.00 39.39 2.43
2264 2300 5.417894 TGTGAAAGACGTGTCTCTATATGGT 59.582 40.000 2.48 0.00 39.39 3.55
2285 2321 4.142138 GGTCCACTAGATTCAGTCGAATGT 60.142 45.833 13.18 0.00 42.06 2.71
2307 2343 3.593328 TCTTGGGACCCATCTCAAAGAAT 59.407 43.478 15.83 0.00 44.92 2.40
2335 2371 2.699954 ACTGAATTACGAAGGCTGTGG 58.300 47.619 0.00 0.00 0.00 4.17
2339 2375 0.392998 ATTACGAAGGCTGTGGGCAG 60.393 55.000 0.00 0.00 45.23 4.85
2527 2563 6.828785 GGTTTGGATGATGTCATTAACTACCT 59.171 38.462 0.00 0.00 36.57 3.08
2529 2565 5.368145 TGGATGATGTCATTAACTACCTGC 58.632 41.667 0.00 0.00 36.57 4.85
2532 2568 4.180817 TGATGTCATTAACTACCTGCGTG 58.819 43.478 0.00 0.00 0.00 5.34
2586 2622 5.376625 ACTGCTTGTTTTCTGAATGAGGTA 58.623 37.500 0.00 0.00 0.00 3.08
2594 2630 8.924511 TGTTTTCTGAATGAGGTAATTCTCTT 57.075 30.769 0.00 0.00 37.44 2.85
2673 2709 6.612306 GTTTTGTAGATGGAGTTAAAGCCTG 58.388 40.000 0.00 0.00 0.00 4.85
2696 2732 7.772292 CCTGAAGATCATATTGTCTTTTCCTCA 59.228 37.037 0.00 0.00 34.97 3.86
2706 2742 6.920569 TTGTCTTTTCCTCACTTTGTAGAC 57.079 37.500 0.00 0.00 33.25 2.59
2839 2875 9.483916 GGGTATGCCATACAAAAATAATTTACC 57.516 33.333 16.26 0.48 37.48 2.85
2877 2913 5.587844 ACATGATCAGGCTACACAATTCTTC 59.412 40.000 7.40 0.00 0.00 2.87
2879 2915 5.423015 TGATCAGGCTACACAATTCTTCTC 58.577 41.667 0.00 0.00 0.00 2.87
2881 2917 5.489792 TCAGGCTACACAATTCTTCTCTT 57.510 39.130 0.00 0.00 0.00 2.85
2882 2918 6.605471 TCAGGCTACACAATTCTTCTCTTA 57.395 37.500 0.00 0.00 0.00 2.10
2918 2954 1.453155 AGGCATGGCTTGTTCGTTAG 58.547 50.000 17.44 0.00 0.00 2.34
2926 2962 2.233186 GGCTTGTTCGTTAGTACTCCCT 59.767 50.000 0.00 0.00 0.00 4.20
2992 3028 8.500753 AATGTCTTATATTTGTTTACAGCGGA 57.499 30.769 0.00 0.00 0.00 5.54
2993 3029 8.677148 ATGTCTTATATTTGTTTACAGCGGAT 57.323 30.769 0.00 0.00 0.00 4.18
2997 3033 9.037737 TCTTATATTTGTTTACAGCGGATGTAC 57.962 33.333 5.47 0.00 44.14 2.90
2998 3034 8.951787 TTATATTTGTTTACAGCGGATGTACT 57.048 30.769 5.47 0.00 44.14 2.73
3002 3038 7.675962 TTTGTTTACAGCGGATGTACTATTT 57.324 32.000 5.47 0.00 44.14 1.40
3003 3039 8.774890 TTTGTTTACAGCGGATGTACTATTTA 57.225 30.769 5.47 0.00 44.14 1.40
3004 3040 8.951787 TTGTTTACAGCGGATGTACTATTTAT 57.048 30.769 5.47 0.00 44.14 1.40
3030 3148 8.888579 TGCTATTACCTATTAGTCAGCTTTTC 57.111 34.615 0.00 0.00 0.00 2.29
3078 3196 7.895759 TGTTGAAATTAAAGGGAGAGAAATGG 58.104 34.615 0.00 0.00 0.00 3.16
3163 3319 8.579682 AGTTGTTTTACATCAGAAGATTTTGC 57.420 30.769 0.00 0.00 30.20 3.68
3176 3332 6.201615 CAGAAGATTTTGCTTTTTCCCAGTTC 59.798 38.462 0.00 0.00 0.00 3.01
3182 3338 5.612725 TTGCTTTTTCCCAGTTCTGAATT 57.387 34.783 1.00 0.00 0.00 2.17
3183 3339 5.612725 TGCTTTTTCCCAGTTCTGAATTT 57.387 34.783 1.00 0.00 0.00 1.82
3184 3340 6.723298 TGCTTTTTCCCAGTTCTGAATTTA 57.277 33.333 1.00 0.00 0.00 1.40
3219 3375 5.884232 TCAATATCTGCATGAAAGCAACTCT 59.116 36.000 0.00 0.00 45.13 3.24
3256 3412 5.469479 GTTGCTAACTTGCCATTTACACAT 58.531 37.500 0.00 0.00 0.00 3.21
3257 3413 5.720371 TGCTAACTTGCCATTTACACATT 57.280 34.783 0.00 0.00 0.00 2.71
3328 3484 9.330063 TCGATTGAAATCTAAAATCTATGCACT 57.670 29.630 0.00 0.00 33.24 4.40
3370 3526 1.243342 TTTCACTTCCCATGGCAGCG 61.243 55.000 6.09 0.00 0.00 5.18
3372 3528 2.045926 ACTTCCCATGGCAGCGAC 60.046 61.111 6.09 0.00 0.00 5.19
3415 3571 7.352522 TCAGGATAGGTTATGGAGGGTTAAATT 59.647 37.037 0.00 0.00 0.00 1.82
3444 3600 6.258230 TGCAATATTATATGGAAGCAGCAC 57.742 37.500 0.00 0.00 0.00 4.40
3445 3601 5.769162 TGCAATATTATATGGAAGCAGCACA 59.231 36.000 0.00 0.00 0.00 4.57
3446 3602 6.264970 TGCAATATTATATGGAAGCAGCACAA 59.735 34.615 0.00 0.00 0.00 3.33
3469 3625 2.702592 TAAATGTTAGCCGGACCCTG 57.297 50.000 5.05 0.00 0.00 4.45
3471 3627 1.575419 AATGTTAGCCGGACCCTGTA 58.425 50.000 5.05 0.00 0.00 2.74
3498 3654 7.116662 GCTGATTGCTTATTGTGTTTGATTTCA 59.883 33.333 0.00 0.00 38.95 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 51 1.213537 CGAAGGCCATTGCAAGGTG 59.786 57.895 10.60 1.41 40.13 4.00
57 60 2.125512 GCAGACGACGAAGGCCAT 60.126 61.111 5.01 0.00 0.00 4.40
66 69 2.029844 GGCACCAGAAGCAGACGAC 61.030 63.158 0.00 0.00 0.00 4.34
107 110 2.170187 CTGCCTCCTCTGAAGCATTAGT 59.830 50.000 0.00 0.00 37.32 2.24
110 113 0.990374 ACTGCCTCCTCTGAAGCATT 59.010 50.000 0.00 0.00 37.32 3.56
117 120 1.987704 CTCGACGACTGCCTCCTCTG 61.988 65.000 0.00 0.00 0.00 3.35
118 121 1.747367 CTCGACGACTGCCTCCTCT 60.747 63.158 0.00 0.00 0.00 3.69
126 129 2.368105 GCAGTGTGCTCGACGACTG 61.368 63.158 8.77 8.77 40.96 3.51
127 130 2.049985 GCAGTGTGCTCGACGACT 60.050 61.111 0.00 0.00 40.96 4.18
129 132 2.050077 CTGCAGTGTGCTCGACGA 60.050 61.111 5.25 0.00 45.31 4.20
131 134 1.923204 CTATTCTGCAGTGTGCTCGAC 59.077 52.381 14.67 0.00 45.31 4.20
134 137 2.548875 CTCCTATTCTGCAGTGTGCTC 58.451 52.381 14.67 0.00 45.31 4.26
135 138 1.209019 CCTCCTATTCTGCAGTGTGCT 59.791 52.381 14.67 0.00 45.31 4.40
145 148 1.745264 GCGAGCTGCCTCCTATTCT 59.255 57.895 0.00 0.00 37.76 2.40
185 188 3.114616 CCTGACTGCCGACGCTTG 61.115 66.667 0.00 0.00 35.36 4.01
272 292 1.475441 GAATCTCTCCTTCACGCGCG 61.475 60.000 30.96 30.96 0.00 6.86
328 348 0.322187 GGTTGGGTTGCGAGTATGGT 60.322 55.000 0.00 0.00 0.00 3.55
335 355 0.390603 CGTAGATGGTTGGGTTGCGA 60.391 55.000 0.00 0.00 0.00 5.10
340 360 1.002773 GTGTTCCGTAGATGGTTGGGT 59.997 52.381 0.00 0.00 0.00 4.51
359 379 2.200930 TGTTGGCCCTTGCATGGT 59.799 55.556 16.81 0.00 40.13 3.55
363 383 0.758310 TTCATGTGTTGGCCCTTGCA 60.758 50.000 0.00 0.00 40.13 4.08
498 518 3.626924 GTGGGGCACAGACGGAGT 61.627 66.667 0.00 0.00 37.72 3.85
524 544 1.538634 CGTTCCACCGTCCTGTGTTAA 60.539 52.381 0.00 0.00 34.35 2.01
525 545 0.032403 CGTTCCACCGTCCTGTGTTA 59.968 55.000 0.00 0.00 34.35 2.41
526 546 1.227438 CGTTCCACCGTCCTGTGTT 60.227 57.895 0.00 0.00 34.35 3.32
554 575 5.813717 ACAATCAATGAATAGTGCATGTCG 58.186 37.500 0.00 0.00 0.00 4.35
557 578 6.557110 TGTGACAATCAATGAATAGTGCATG 58.443 36.000 0.00 0.00 0.00 4.06
558 579 6.762702 TGTGACAATCAATGAATAGTGCAT 57.237 33.333 0.00 0.00 0.00 3.96
590 611 0.468226 GATGGACTGGCCGTTGGATA 59.532 55.000 0.00 0.00 40.66 2.59
623 650 2.325583 TTGAGCTTCCAAACACTCGT 57.674 45.000 0.00 0.00 31.64 4.18
625 652 2.160417 CCGATTGAGCTTCCAAACACTC 59.840 50.000 0.00 0.00 0.00 3.51
628 655 2.151202 GTCCGATTGAGCTTCCAAACA 58.849 47.619 0.00 0.00 0.00 2.83
725 758 9.427821 TTTTGGGCCTATAATTGAGCTTATTAA 57.572 29.630 4.53 0.00 0.00 1.40
726 759 8.856103 GTTTTGGGCCTATAATTGAGCTTATTA 58.144 33.333 4.53 0.00 0.00 0.98
727 760 7.344352 TGTTTTGGGCCTATAATTGAGCTTATT 59.656 33.333 4.53 0.00 0.00 1.40
728 761 6.838612 TGTTTTGGGCCTATAATTGAGCTTAT 59.161 34.615 4.53 0.00 0.00 1.73
729 762 6.191315 TGTTTTGGGCCTATAATTGAGCTTA 58.809 36.000 4.53 0.00 0.00 3.09
780 814 3.124270 CGCATGTTAGGCACGCCA 61.124 61.111 11.35 0.00 38.92 5.69
781 815 4.536687 GCGCATGTTAGGCACGCC 62.537 66.667 0.30 0.00 43.58 5.68
825 860 1.379977 CTCCCTGGCCTAGACACGA 60.380 63.158 3.32 0.00 0.00 4.35
833 868 4.421554 TGCCTAGCTCCCTGGCCT 62.422 66.667 3.32 0.00 45.56 5.19
884 919 1.997874 AGACCTGGACAGATGGGCC 60.998 63.158 0.00 0.00 0.00 5.80
1074 1110 0.394565 AGCAGTTGTCACTCTGACCC 59.605 55.000 8.01 0.00 46.40 4.46
1386 1422 3.256960 TGGAGGTTGGTGAGGGCC 61.257 66.667 0.00 0.00 0.00 5.80
1419 1455 2.505557 GGCGACGGACGAACGAAT 60.506 61.111 16.13 0.00 45.77 3.34
1534 1570 0.865769 AAATTCGACAGTGGCACGAC 59.134 50.000 12.71 6.82 35.82 4.34
1597 1633 2.843701 CATGCCATGTAGGAACTCCTC 58.156 52.381 0.27 0.00 44.77 3.71
1622 1658 0.747283 CTCCAAGGCCTTGCAGCTAG 60.747 60.000 35.85 22.48 39.16 3.42
1818 1854 0.034477 CCAGTTTAGGTGCCCGGATT 60.034 55.000 0.73 0.00 0.00 3.01
1944 1980 2.301009 TCGTTCCCTAGAGAAAACACCC 59.699 50.000 0.00 0.00 0.00 4.61
1945 1981 3.672767 TCGTTCCCTAGAGAAAACACC 57.327 47.619 0.00 0.00 0.00 4.16
1991 2027 1.068954 GCTAAAGCCTTCACAGTGTGC 60.069 52.381 18.80 6.80 32.04 4.57
2029 2065 5.471456 AGGATGTCAAGAACAACATTCAGTC 59.529 40.000 0.00 0.00 42.37 3.51
2139 2175 6.932356 ACATGCCAATCAACTACTAGATTG 57.068 37.500 0.00 7.89 46.61 2.67
2148 2184 6.893583 AGACTAGATTACATGCCAATCAACT 58.106 36.000 18.06 10.68 35.30 3.16
2149 2185 7.928706 ACTAGACTAGATTACATGCCAATCAAC 59.071 37.037 16.55 9.24 35.30 3.18
2150 2186 8.023021 ACTAGACTAGATTACATGCCAATCAA 57.977 34.615 16.55 0.00 35.30 2.57
2166 2202 5.185249 TCAAAGCTGGTGGTAACTAGACTAG 59.815 44.000 8.00 8.00 37.06 2.57
2201 2237 4.564041 TCTGCAGCTAGAAACAGAAAGAG 58.436 43.478 9.47 0.00 36.27 2.85
2238 2274 6.638873 CCATATAGAGACACGTCTTTCACATC 59.361 42.308 0.38 0.00 40.61 3.06
2258 2294 5.386060 TCGACTGAATCTAGTGGACCATAT 58.614 41.667 0.00 0.00 31.66 1.78
2264 2300 4.950475 AGACATTCGACTGAATCTAGTGGA 59.050 41.667 10.04 0.00 42.94 4.02
2285 2321 2.631384 TCTTTGAGATGGGTCCCAAGA 58.369 47.619 16.55 9.28 36.95 3.02
2307 2343 4.873827 GCCTTCGTAATTCAGTATCACCAA 59.126 41.667 0.00 0.00 0.00 3.67
2335 2371 1.079612 GCAAAGCCAACATCCTGCC 60.080 57.895 0.00 0.00 0.00 4.85
2527 2563 0.105778 TGACAAGTCATGGACACGCA 59.894 50.000 0.00 0.00 34.60 5.24
2586 2622 8.051535 TGGATATGCTTCTTCTCAAAGAGAATT 58.948 33.333 9.64 0.00 45.84 2.17
2594 2630 8.529424 AAAATCATGGATATGCTTCTTCTCAA 57.471 30.769 0.00 0.00 34.21 3.02
2623 2659 1.691434 GTCCAAGGAATTGGCCACAAA 59.309 47.619 3.88 0.00 41.81 2.83
2624 2660 1.133199 AGTCCAAGGAATTGGCCACAA 60.133 47.619 3.88 0.00 41.81 3.33
2625 2661 0.482446 AGTCCAAGGAATTGGCCACA 59.518 50.000 3.88 0.00 41.81 4.17
2673 2709 8.729805 AGTGAGGAAAAGACAATATGATCTTC 57.270 34.615 0.00 0.00 34.01 2.87
2696 2732 7.097192 TCAAGCATTAATCTCGTCTACAAAGT 58.903 34.615 0.00 0.00 0.00 2.66
2706 2742 7.244166 AGACAATCTTCAAGCATTAATCTCG 57.756 36.000 0.00 0.00 0.00 4.04
2742 2778 7.396055 AGCAGCCATAATAAGTTTAGGTTTTGA 59.604 33.333 0.00 0.00 0.00 2.69
2763 2799 6.038050 AGAGTTTAGAATGCAAATAGAGCAGC 59.962 38.462 0.00 0.00 46.36 5.25
2795 2831 2.236395 ACCCTGTCGGAAATTACAGAGG 59.764 50.000 7.52 8.96 44.79 3.69
2839 2875 1.850377 TCATGTTGCAACTTTTGGCG 58.150 45.000 28.61 11.44 0.00 5.69
2881 2917 7.883311 GCCATGCCTAAGTAGGAAGATAAAATA 59.117 37.037 8.64 0.00 46.63 1.40
2882 2918 6.717084 GCCATGCCTAAGTAGGAAGATAAAAT 59.283 38.462 8.64 0.00 46.63 1.82
2969 3005 7.551262 ACATCCGCTGTAAACAAATATAAGACA 59.449 33.333 0.00 0.00 35.91 3.41
2981 3017 7.797123 GCAATAAATAGTACATCCGCTGTAAAC 59.203 37.037 0.00 0.00 41.93 2.01
3003 3039 9.853177 AAAAGCTGACTAATAGGTAATAGCAAT 57.147 29.630 0.00 0.00 32.64 3.56
3004 3040 9.326413 GAAAAGCTGACTAATAGGTAATAGCAA 57.674 33.333 0.00 0.00 32.64 3.91
3078 3196 9.846248 ATATGCACTGAACTAAAGATTTTGTTC 57.154 29.630 19.17 19.17 46.08 3.18
3163 3319 8.197439 ACTTGTAAATTCAGAACTGGGAAAAAG 58.803 33.333 1.93 2.03 0.00 2.27
3182 3338 6.463360 TGCAGATATTGACACTGACTTGTAA 58.537 36.000 0.00 0.00 34.07 2.41
3183 3339 6.036577 TGCAGATATTGACACTGACTTGTA 57.963 37.500 0.00 0.00 34.07 2.41
3184 3340 4.898320 TGCAGATATTGACACTGACTTGT 58.102 39.130 0.00 0.00 34.07 3.16
3198 3354 5.191426 ACAGAGTTGCTTTCATGCAGATAT 58.809 37.500 0.00 0.00 44.27 1.63
3199 3355 4.582869 ACAGAGTTGCTTTCATGCAGATA 58.417 39.130 0.00 0.00 44.27 1.98
3200 3356 3.418995 ACAGAGTTGCTTTCATGCAGAT 58.581 40.909 0.00 0.00 44.27 2.90
3219 3375 0.969917 AGCAACCAACTGCCACAACA 60.970 50.000 0.00 0.00 43.73 3.33
3328 3484 8.924511 AAAGGAGTTTCTAATTCATGAAGTCA 57.075 30.769 12.35 0.00 0.00 3.41
3370 3526 6.753180 TCCTGAATCTAGAACTATGCATGTC 58.247 40.000 10.16 4.09 0.00 3.06
3372 3528 7.980662 CCTATCCTGAATCTAGAACTATGCATG 59.019 40.741 10.16 1.82 0.00 4.06
3386 3542 4.846940 ACCCTCCATAACCTATCCTGAATC 59.153 45.833 0.00 0.00 0.00 2.52
3419 3575 7.147312 GTGCTGCTTCCATATAATATTGCAAA 58.853 34.615 1.71 0.00 0.00 3.68
3430 3586 8.042515 ACATTTATTTTTGTGCTGCTTCCATAT 58.957 29.630 0.00 0.00 0.00 1.78
3444 3600 5.105513 AGGGTCCGGCTAACATTTATTTTTG 60.106 40.000 0.00 0.00 0.00 2.44
3445 3601 5.020795 AGGGTCCGGCTAACATTTATTTTT 58.979 37.500 0.00 0.00 0.00 1.94
3446 3602 4.401202 CAGGGTCCGGCTAACATTTATTTT 59.599 41.667 0.00 0.00 0.00 1.82
3498 3654 5.014649 ACTGGAGAAAAGAGAAGCCCTTATT 59.985 40.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.